high performance computing on graphics processing units: hgpu.org

This paper presents a new GPU-based algorithm to compute ambient occlusion. We first examine how ambient occlusion is related to the physically founded rendering equation. The correspondence is made by introducing a fuzzy membership function that defines what “near occlusions” mean. Then we develop a method to calculate ambient occlusion in real-time without any pre-computation. […]

A parallel implementation of the split-step Fourier method utilizing the general purpose parallel computing architecture for graphics processing units CUDA is presented. Results of the GPU-implementation are compared to a conventional CPU-based approach regarding computation time and accuracy. We developed a novel implementation with a significantly higher accuracy than the CUDA intrinsic FFT in single […]

The exact evaluation of the disconnected diagram contributions to the flavor-singlet pseudoscalar meson mass, the nucleon sigma term and the nucleon electromagnetic form factors, is carried out utilizing GPGPU technology with the NVIDIA CUDA platform. The disconnected loops are also computed using stochastic methods with several noise reduction techniques. Various dilution schemes as well as […]

In this paper we cast the problem of tomography in the realm of computer graphics. By using PBRT (physically based rendering toolkit) we create a scripting environment that simplifies the programming of tomography algorithms such as maximum-likelihood expectation maximization (ML-EM) or simultaneous algebraic reconstruction technique (SART, a deviant of ART). This allows the rapid development […]

Graphics Processing Units (GPUs) have recently emerged as a new platform for high performance, general-purpose computing. Because current GPUs employ deep multithreading to hide latency, they only have small, per-core caches to capture reuse and eliminate unnecessary off-chip accesses. This paper shows that for general-purpose workloads, the ability to copy cache lines between private caches […]

The most pervasive compute operation carried out in almost all bioinformatics applications is pairwise sequence homology detection (or sequence alignment). Due to exponentially growing sequence databases, computing this operation at a large-scale is becoming expensive. An effective approach to speed up this operation is to integrate a very high number of processing elements in a […]

Real-time H.264 encoding of high-definition (HD) video (up to 1080p) is a challenge workload to most existing programmable processors. Instead, the novel programmable parallel processors such as stream processor, Graphic processor unit (GPU) and DSP offer a different and very promising technology for these demands. Thus, parallel computing for H.264 encoding on these processors is […]

We present a fast GPU-based algorithm to approximate the swept volume (SV) boundary of arbitrary polygon soup models. Despite the extensive research on calculating the volume swept by an object along a trajectory, the efficient algorithms described have imposed constraints on both the trajectories and geometric models. By proposing a general algorithm that handles flat […]

As video cards become faster and more programmable, physical simulations implemented on graphics processors become possible. This paper examines different programmable stages of the nVidia graphics processor (GPLI), and their use to simulate electrical activation of cells in a tissue sample using a cellular automaton model. Comparable tissue simulation programs were written to run on […]

Many recent research efforts have been devoted to the use of commodity hardware for solving computationally-intensive scientific problems. Among such problems, hyperspectral imaging has created new processing challenges in the remote sensing community. Hyperspectral sensors are now capable of collecting hundreds of images, corresponding to different wavelength channels, for the same area on the surface […]

Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This paper shows how the EpiSimdemics interaction-based simulation system can be applied to the general contagion diffusion problem. Two specific problems, computational epidemiology and human immune system modeling, are given as examples. We then show how the graphics processing unit (GPU) […]

The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie’s Stochastic Simulation Algorithm (SSA) is a standard algorithm to simulate well-stirred biochemical systems, butthe computational burden makes this algorithm slow to compute for many realistic problems. Recent programmability improvements allow […]