high performance computing on graphics processing units: hgpu.org

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 […]

Multigrid algorithms are among the fastest iterative methods known today for solving large linear and some non-linear systems of equations. Greatly optimized for serial operation, they still have a great potential for parallelism not fully realized. In this work, we present a novel multigrid algorithm designed to work entirely inside many-core architectures like the graphics […]

This paper presents a novel PRT-based method that uses precomputed visibility cuts for interactive relighting with all-frequency environment maps and arbitrary dynamic BRDFs. Our method is inspired by the recent Lightcuts approach [24] and we parameterize distant environment lighting onto uniformly distributed sample points over the sphere. Using a binary tree structure of the points, […]

We propose a hybrid particle and texture based approach for the visualization of time-dependent vector fields. The underlying space-time framework builds a dense vector field representation in a two-step process: 1) particle-based forward integration of trajectories in spacetime for temporal coherence, and 2) texture-based convolution along another set of paths through the spacetime for spatially […]

This paper presents a pipeline for high quality volume rendering of adaptive mesh refinement (AMR) datasets. We introduce a new method allowing high quality visualization of hexahedral cells in this context; this method avoids artifacts like discontinuities in the isosurfaces. To achieve this, we choose the number and placement of sampling points over the cast […]