251 research outputs found
A Spiking Neural P System Simulator Based on CUDA
In this paper we present a Spiking Neural P system (SNP
system) simulator based on graphics processing units (GPUs). In particular
we implement the simulator using NVIDIA CUDA enabled GPUs.
The massively parallel architecture of current GPUs is very suitable for
the maximally parallel computations of SNP systems. We simulate a
wider variety of SNP systems, after presenting a previous work on SNP
system matrix representation which led to their simulation in GPUs, and
the simulation algorithm included here. Finally, we compare and present
the performance speedups of the CPU-GPU based simulator over the
CPU only simulator.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420
Simulating FRSN P Systems with Real Numbers in P-Lingua on sequential and CUDA platforms
Fuzzy Reasoning Spiking Neural P systems (FRSN P systems,
for short) is a variant of Spiking Neural P systems incorporating
fuzzy logic elements that make it suitable to model fuzzy diagnosis knowledge
and reasoning required for fault diagnosis applications. In this sense,
several FRSN P system variants have been proposed, dealing with real
numbers, trapezoidal numbers, weights, etc. The model incorporating
real numbers was the first introduced [13], presenting promising applications
in the field of fault diagnosis of electrical systems. For this variant,
a matrix-based algorithm was provided which, when executed on parallel
computing platforms, fully exploits the model maximally parallel
capacities. In this paper we introduce a P-Lingua framework extension
to parse and simulate FRSN P systems with real numbers. Two simulators,
implementing a variant of the original matrix-based simulation
algorithm, are provided: a sequential one (written in Java), intended to
run on traditional CPUs, and a parallel one, intended to run on CUDAenabled
devices.Ministerio de Economía y Competitividad TIN2012-3743
Simulating Spiking Neural P systems without delays using GPUs
We present in this paper our work regarding simulating a type of P system
known as a spiking neural P system (SNP system) using graphics processing units
(GPUs). GPUs, because of their architectural optimization for parallel
computations, are well-suited for highly parallelizable problems. Due to the
advent of general purpose GPU computing in recent years, GPUs are not limited
to graphics and video processing alone, but include computationally intensive
scientific and mathematical applications as well. Moreover P systems, including
SNP systems, are inherently and maximally parallel computing models whose
inspirations are taken from the functioning and dynamics of a living cell. In
particular, SNP systems try to give a modest but formal representation of a
special type of cell known as the neuron and their interactions with one
another. The nature of SNP systems allowed their representation as matrices,
which is a crucial step in simulating them on highly parallel devices such as
GPUs. The highly parallel nature of SNP systems necessitate the use of hardware
intended for parallel computations. The simulation algorithms, design
considerations, and implementation are presented. Finally, simulation results,
observations, and analyses using an SNP system that generates all numbers in
- {1} are discussed, as well as recommendations for future work.Comment: 19 pages in total, 4 figures, listings/algorithms, submitted at the
9th Brainstorming Week in Membrane Computing, University of Seville, Spai
An Improved GPU Simulator For Spiking Neural P Systems
Spiking Neural P (SNP) systems, variants of Psystems (under Membrane and Natural computing), are computing models that acquire abstraction and inspiration from the way neurons 'compute' or process information. Similar to other P system variants, SNP systems are Turing complete models that by nature compute non-deterministically and in a maximally parallel manner. P systems usually trade (often exponential) space for (polynomial to constant) time. Due to this nature, P system variants are currently limited to parallel simulations, and several variants have already been simulated in parallel devices. In this paper we present an improved SNP system simulator based on graphics processing units (GPUs). Among other reasons, current GPUs are architectured for massively parallel computations, thus making GPUs very suitable for SNP system simulation. The computing model, hardware/software considerations, and simulation algorithm are presented, as well as the comparisons of the CPU only and CPU-GPU based simulators.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420
GeNN: a code generation framework for accelerated brain simulations
Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ.
GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials,
Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/
Recommended from our members
Efficient spiking neural network model of pattern motion selectivity in visual cortex
Simulating large-scale models of biological motion perception is challenging, due to the required memory to store the network structure and the computational power needed to quickly solve the neuronal dynamics. A low-cost yet high-performance approach to simulating large-scale neural network models in real-time is to leverage the parallel processing capability of graphics processing units (GPUs). Based on this approach, we present a two-stage model of visual area MT that we believe to be the first large-scale spiking network to demonstrate pattern direction selectivity. In this model, component-direction- selective (CDS) cells in MT linearly combine inputs from V1 cells that have spatiotemporal receptive fields according to the motion energy model of Simoncelli and Heeger. Pattern-direction-selective (PDS) cells in MT are constructed by pooling over MT CDS cells with a wide range of preferred directions. Responses of our model neurons are comparable to electrophysiological results for grating and plaid stimuli as well as speed tuning. The behavioral response of the network in a motion discrimination task is in agreement with psychophysical data. Moreover, our implementation outperforms a previous implementation of the motion energy model by orders of magnitude in terms of computational speed and memory usage. The full network, which comprises 153,216 neurons and approximately 40 million synapses, processes 20 frames per second of a 40∈×∈40 input video in real-time using a single off-the-shelf GPU. To promote the use of this algorithm among neuroscientists and computer vision researchers, the source code for the simulator, the network, and analysis scripts are publicly available. © 2014 Springer Science+Business Media New York
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
CuSNP: Spiking Neural P Systems Simulators in CUDA
Spiking neural P systems (in short, SN P systems) are models
of computation inspired by biological neurons. CuSNP is a project involving
sequential (CPU) and parallel (GPU) simulators for SN P systems. In this
work, we report the following results: a P-Lingua le parser is included, for
ease of use when performing simulations; extension of the matrix representation
of SN P systems to include delay; comparison and analysis of our simulators
by simulating two types (bitonic and generalized) of parallel sorting networks;
extension of supported types of regular expressions in SN P systems. Our GPU
simulator is better suited for generalized sorting as compared to bitonic sorting
networks, and the GPU simulators run up to 50 faster than our CPU simulator.
Finally, we discuss our experiments and provide directions for further work
Improving Simulations of Spiking Neural P Systems in NVIDIA CUDA GPUs: CuSNP
Spiking neural P systems (in short, SN P systems) are parallel models of
computations inspired by the spiking ( ring) of biological neurons. In SN P systems, neurons
function as spike processors and are placed on nodes of a directed graph. Synapses,
the connections between neurons, are represented by arcs or directed endges in the graph.
Not only do SN P systems have parallel semantics (i.e. neurons operate in parallel), but
their structure as directed graphs allow them to be represented as vectors or matrices.
Such representations allow the use of linear algebra operations for simulating the
evolution of the system con gurations, i.e. computations. In this work, we continue the
implementations of SN P systems with delays, i.e. a delay is associated with the sending
of a spike from a neuron to its neighbouring neurons. Our implementation is based on
a modi ed representation of SN P systems as vectors and matrices for SN P systems
without delays. We us massively parallel processors known as graphics processing units
(in short, GPUs) from NVIDIA. For experimental validation, we use SN P systems implementing
generalized sorting networks. We report a speedup, i.e. the ratio between the
running time of the sequential over the parallel simulator, of up to approximately 51
times for a 512-size input to the sorting network
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