1423

Posts

Nov, 6

Automatic fitting of spiking neuron models to electrophysiological recordings

Spiking models can accurately predict the spike trains produced by cortical neurons in response to somatically injected currents. Since the specific characteristics of the model depend on the neuron, a computational method is required to fit models to electrophysiological recordings. The fitting procedure can be very time consuming both in terms of computer simulations and […]
Nov, 6

Optimization of linked list prefix computations on multithreaded GPUs using CUDA

We present a number of optimization techniques to compute prefix sums on linked lists and implement them on multithreaded GPUs using CUDA. Prefix computations on linked structures involve in general highly irregular fine grain memory accesses that are typical of many computations on linked lists, trees, and graphs. While the current generation of GPUs provides […]
Nov, 6

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

PMID: 20199097 Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of […]
Nov, 6

A GPU implementation for LBG and SOM training

Vector quantization (VQ) is an effective technique applicable in a wide range of areas, such as image compression and pattern recognition. The most time-consuming procedure of VQ is codebook training, and two of the frequently used training algorithms are LBG and self-organizing map (SOM). Nowadays, desktop computers are usually equipped with programmable graphics processing units […]
Nov, 6

A matrix approach to tomographic reconstruction and its implementation on GPUs

Electron tomography allows elucidation of the molecular architecture of complex biological specimens. Weighted backprojection (WBP) is the standard reconstruction method in the field. In this work, three-dimensional reconstruction with WBP is addressed from a matrix perspective by formulating the problem as a set of sparse matrix-vector products, with the matrix being constant and shared by […]
Nov, 6

Exploring the multiple-GPU design space

Graphics Processing Units (GPUs) have been growing in popularity due to their impressive processing capabilities, and with general purpose programming languages such as NVIDIA’s CUDA interface, are becoming the platform of choice in the scientific computing community. Previous studies that used GPUs focused on obtaining significant performance gains from execution on a single GPU. These […]
Nov, 6

GPU Computing for Atmospheric Modeling

Much success has been achieved using GPUs to accelerate existing applications that are highly data parallel, or that are dominated by small, intense computational kernels. What are the prospects for porting existing large scientific models that do not fit this mold? We take an expensive routine from the CAM atmosphere model, and port it to […]
Nov, 6

A Practical Quicksort Algorithm for Graphics Processors

In this paper we present GPU-Quicksort, an efficient Quicksort algorithm suitable for highly parallel multi-core graphics processors. Quicksort has previously been considered as an inefficient sorting solution for graphics processors, but we show that GPU-Quicksort often performs better than the fastest known sorting implementations for graphics processors, such as radix and bitonic sort. Quicksort can […]
Nov, 6

StoreGPU: exploiting graphics processing units to accelerate distributed storage systems

Today Graphics Processing Units (GPUs) are a largely underexploited resource on existing desktops and a possible cost-effective enhancement to high-performance systems. To date, most applications that exploit GPUs are specialized scientific applications. Little attention has been paid to harnessing these highly-parallel devices to support more generic functionality at the operating system or middleware level. This […]
Nov, 6

Programming model for a heterogeneous x86 platform

The client computing platform is moving towards a heterogeneous architecture consisting of a combination of cores focused on scalar performance, and a set of throughput-oriented cores. The throughput oriented cores (e.g. a GPU) may be connected over both coherent and non-coherent interconnects, and have different ISAs. This paper describes a programming model for such heterogeneous […]
Nov, 6

Maintaining constant frame rates in 3D texture-based volume rendering

3D texture-based volume rendering is a popular way of realizing direct volume visualization on graphics hardware. However, the slice-oriented texture memory layout of many current CPUs may lead to a strongly view-dependent performance, which reduces the fields of application of volume rendering. In this short technical note, we propose a slight modification of texture-based volume […]
Nov, 6

Accelerating Dust Temperature Calculations with Graphics Processing Units

When calculating the infrared spectral energy distributions (SEDs) of galaxies in radiation-transfer models, the calculation of dust grain temperatures is generally the most time-consuming part of the calculation. Because of its highly parallel nature, this calculation is perfectly suited for massively parallel general-purpose Graphics Processing Units (GPUs). This paper presents an implementation of the calculation […]
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