BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations

Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study 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 single acceleration (or homogeneous) platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform, incorporating three distinct acceleration technologies, a Dataflow Engine, a Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different instances of a state-of-the-art neuron model, modeling 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 circumstances that can drastically change application workload characteristics. Main results: The synthetic approach of three HPC technologies demonstrated that BrainFrame is better able to cope with the modeling diversity encountered. Our performance analysis shows clearly that the model directly affect performance and all three technologies are required to cope with all the model use cases.Comment: 16 pages, 18 figures, 5 table

A Practical Hardware Implementation of Systemic Computation

It is widely accepted that natural computation, such as brain computation, is far superior to typical computational approaches addressing tasks such as learning and parallel processing. As conventional silicon-based technologies are about to reach their physical limits, researchers have drawn inspiration from nature to found new computational paradigms. Such a newly-conceived paradigm is Systemic Computation (SC). SC is a bio-inspired model of computation. It incorporates natural characteristics and defines a massively parallel non-von Neumann computer architecture that can model natural systems efficiently. This thesis investigates the viability and utility of a Systemic Computation hardware implementation, since prior software-based approaches have proved inadequate in terms of performance and flexibility. This is achieved by addressing three main research challenges regarding the level of support for the natural properties of SC, the design of its implied architecture and methods to make the implementation practical and efficient. Various hardware-based approaches to Natural Computation are reviewed and their compatibility and suitability, with respect to the SC paradigm, is investigated. FPGAs are identified as the most appropriate implementation platform through critical evaluation and the first prototype Hardware Architecture of Systemic computation (HAoS) is presented. HAoS is a novel custom digital design, which takes advantage of the inbuilt parallelism of an FPGA and the highly efficient matching capability of a Ternary Content Addressable Memory. It provides basic processing capabilities in order to minimize time-demanding data transfers, while the optional use of a CPU provides high-level processing support. It is optimized and extended to a practical hardware platform accompanied by a software framework to provide an efficient SC programming solution. The suggested platform is evaluated using three bio-inspired models and analysis shows that it satisfies the research challenges and provides an effective solution in terms of efficiency versus flexibility trade-off

Heterogeneous architecture to process swarm optimization algorithms

Desde años recientes, el paralelismo hace parte de la arquitectura de las computadoras personales al incluir unidades de co-procesamiento como las unidades de procesamiento gráfico, para conformar así una arquitectura heterogénea. Este artículo presenta la implementación de algoritmos de enjambres sobre esta arquitectura para resolver problemas de optimización de funciones, destacando su estructura inherentemente paralela y sus propiedades de control distribuido. En estos algoritmos se paralelizan los individuos de la población y las dimensiones del problema gracias a la granuralidad del sistema de procesamiento, que además proporciona una baja latencia de comunicaciones entre los individuos debido al procesamiento embebido. Para evaluar las potencialidades de los algoritmos de enjambres sobre la plataforma heterogénea, son implementados dos de ellos: el algoritmo de enjambre de partículas y el algoritmo de enjambre de bacterias. Se utiliza la aceleración como métrica para contrastar los algoritmos en la arquitectura heterogénea compuesta por una GPU NVIDIA GTX480 y una unidad de procesamiento secuencial, donde el algoritmo de enjambre de partículas obtiene una aceleración de hasta 36,82x y el algoritmo de enjambre de bacterias logra una aceleración de hasta 9,26x. Además, se evalúa el efecto al incrementar el tamaño en las poblaciones donde la aceleración es significativamente diferenciable pero con riesgos en la calidad de las soluciones.Since few years ago, the parallel processing has been embedded in personal computers by including co-processing units as the graphics processing units resulting in a heterogeneous platform. This paper presents the implementation of swarm algorithms on this platform to solve several functions from optimization problems, where they highlight their inherent parallel processing and distributed control features. In the swarm algorithms, each individual and dimension problem are parallelized by the granularity of the processing system which also offer low communication latency between individuals through the embedded processing. To evaluate the potential of swarm algorithms on graphics processing units we have implemented two of them: the particle swarm optimization algorithm and the bacterial foraging optimization algorithm. The algorithms’ performance is measured using the acceleration where they are contrasted between a typical sequential processing platform and the NVIDIA GeForce GTX480 heterogeneous platform; the results show that the particle swarm algorithm obtained up to 36.82x and the bacterial foraging swarm algorithm obtained up to 9.26x. Finally, the effect to increase the size of the population is evaluated where we show both the dispersion and the quality of the solutions are decreased despite of high acceleration performance since the initial distribution of the individuals can converge to local optimal solution

Exploring and interrogating astrophysical data in virtual reality

Scientists across all disciplines increasingly rely on machine learning algorithms to analyse and sort datasets of ever increasing volume and complexity. Although trends and outliers are easily extracted, careful and close inspection will still be necessary to explore and disentangle detailed behaviour, as well as identify systematics and false positives. We must therefore incorporate new technologies to facilitate scientific analysis and exploration. Astrophysical data is inherently multi-parameter, with the spatial-kinematic dimensions at the core of observations and simulations. The arrival of mainstream virtual-reality (VR) headsets and increased GPU power, as well as the availability of versatile development tools for video games, has enabled scientists to deploy such technology to effectively interrogate and interact with complex data. In this paper we present development and results from custom-built interactive VR tools, called the iDaVIE suite, that are informed and driven by research on galaxy evolution, cosmic large-scale structure, galaxy–galaxy interactions, and gas/kinematics of nearby galaxies in survey and targeted observations. In the new era of Big Data ushered in by major facilities such as the SKA and LSST that render past analysis and refinement methods highly constrained, we believe that a paradigm shift to new software, technology and methods that exploit the power of visual perception, will play an increasingly important role in bridging the gap between statistical metrics and new discovery. We have released a beta version of the iDaVIE software system that is free and open to the community