high performance computing on graphics processing units: hgpu.org

Discovery of motifs that are repeated in groups of biological sequences is a major task in bioinformatics. Iterative methods such as expectation maximization (EM) are used as a common approach to find such patterns. However, corresponding algorithms are highly compute-intensive due to the small size and degenerate nature of biological motifs. Runtime requirements are likely […]

Recently there has been a lot of interest in graph-based analysis. One of the most important aspects of graph-based analysis is to measure similarity between nodes in a graph. SimRank is a simple and influential measure of this kind, based on a solid graph theoretical model. However, existing methods on SimRank computation suffer from two […]

High Performance Computing (HPC) or scientific codes are being executed across a wide variety of computing platforms from embedded processors to massively parallel GPUs. We present a comparison of the Basic Linear Algebra Subroutines (BLAS) using double-precision floating point on an FPGA, CPU and GPU. On the CPU and GPU, we utilize standard libraries on […]

Skinning of skeletally deformable models is extensively used for real-time animation of characters, creatures and similar objects. The standard solution, linear blend skinning, has some serious drawbacks that require artist intervention. Therefore, a number of alternatives have been proposed in recent years. All of them successfully combat some of the artifacts, but none challenge the […]

We present a viewpoint-based approach for the quick fusion of multiple stereo depth maps. Our method selects depth estimates for each pixel that minimize violations of visibility constraints and thus remove errors and inconsistencies from the depth maps to produce a consistent surface. We advocate a two-stage process in which the first stage generates potentially […]

In this paper we present a hybrid technique for correcting distortions that appear when projecting images onto geometrically complex, colored and textured surfaces. It analyzes the optical flow that results from perspective distortions during motions of the observer and tries to use this information for computing the correct image warping. If this fails due to […]

We describe a sort-last parallel volume rendering system based on single pass volume raycasting performed in the fragment shader unit. The architecture is aimed for displaying data sets that utilize the total distributed texture memory at interactive framerates. We use non-uniform texture bricks that are constructed and distributed by means of a kd-tree to employ […]

We introduce a GPU-friendly technique that efficiently exploits the highly structured nature of urban environments to ensure rendering quality and interactive performance of city exploration tasks. Central to our approach is a novel discrete representation, called BlockMap, for the efficient encoding and rendering of a small set of textured buildings far from the viewer. A […]

We present a framework for real-time animation of explosions that runs completely on the GPU. The simulation allows for arbitrary internal boundaries and is governed by a combustion process, a Stable Fluid solver, which includes thermal expansion, and turbulence modeling. The simulation results are visualised by two particle systems rendered using animated textures. The results […]

By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and sparse linear algebra algorithms can be significantly enhanced while maintaining the 64-bit accuracy of the resulting solution. The approach presented here can apply not only to conventional processors but also to exotic technologies such as Field Programmable Gate […]

We present a pre-processing strategy including imaging, segmentation, and model reconstruction that is well suited for previously published GPU-accelerated techniques for surgical simulation. In particular we describe these modeling steps as a prerequisite for our virtual open heart surgery simulator. A short description including relevant references is presented for each of the steps.

The high-throughput needs in electron tomography and in single particle analysis have driven the parallel implementation of several reconstruction algorithms and software packages on computing clusters. Here, we report on the implementation of popular reconstruction algorithms as weighted backprojection, simultaneous iterative reconstruction technique (SIRT) and simultaneous algebraic reconstruction technique (SART) on common graphics processors (GPUs). […]