high performance computing on graphics processing units: hgpu.org

The first part of this paper surveys co-processor approaches for commodity based clusters in general, not only with respect to raw performance, but also in view of their system integration and power consumption. We then extend previous work on a small GPU cluster by exploring the heterogeneous hardware approach for a large-scale system with up […]

High performance computing in heterogeneous environments is a dynamically developing area. A number of highly efficient heterogeneous parallel algorithms have been designed over last decade. At the same time, scientific software based on the algorithms is very much under par. The paper analyses main issues encountered by scientific programmers during implementation of heterogeneous parallel algorithms […]

Breadth-first search (BFS) has wide applications in electronic design automation (EDA) as well as in other fields. Researchers have tried to accelerate BFS on the GPU, but the two published works are both asymptotically slower than the fastest CPU implementation. In this paper, we present a new GPU implementation of BFS that uses a hierarchical […]

Aberrant intracellular signaling plays an important role in many diseases. The causal structure of signal transduction networks can be modeled as Bayesian Networks (BNs), and computationally learned from experimental data. However, learning the structure of Bayesian Networks (BNs) is an NP-hard problem that, even with fast heuristics, is too time consuming for large, clinically important […]

BACKGROUND: Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent advent of programming for graphical processing units (GPU) opens up the possibility of developing more integrative, detailed and predictive biological models while […]

We present a simulation and visualization system for a critical application-analysis of the thermal fluid dynamics inside a pressurized water reactor of a nuclear power plant when cold water is injected into the reactor vessel. We employ a hybrid thermal lattice Boltzmann method (HTLBM), which has the advantages of ease of parallelization and ease of […]

Recent advances in scanning technology provide high resolution EM (Electron Microscopy) datasets that allow neuroscientists to reconstruct complex neural connections in a nervous system. However, due to the enormous size and complexity of the resulting data, segmentation and visualization of neural processes in EM data is usually a difficult and very time-consuming task. In this […]

PURPOSE: We present a system which supports deformable image registration guided by a haptic device. METHODS: The haptic device is tied to a block matching method where a set of uniformly distributed control points determine the block positions. Each control point constitutes a particle in a mass spring grid which limits the space of allowed […]

Surface reconstruction (Bloomenthal and Wyvill, Introduction to Implicit Surfaces, 1997) is a fundamental work in Computer Aided Design (CAD) and Computer Graphics (CG). In this paper, motivated by the physical polar field model (Yuxu Lin Chun Chen in Proceedings of the 3rd Pacific-Rim Symposium on Image and Video Technology, 1997), we propose a novel implicit […]

Traditional approaches for rendering segmented volumetric data sets usually deliver unsatisfactory results, such as insufficient frame rate, low image quality, and intermixing artifacts. In this paper, we introduce a novel “color encoding” technique, based on graphics processing unit (GPU) accelerated raycasting and post-color attenuated classification, to address this problem. The result is an algorithm that […]

General Purpose computing over Graphical Processing Units (GPGPUs) is a huge shift of paradigm in parallel computing that promises a dramatic increase in performance. But GPGPUs also bring an unprecedented level of complexity in algorithmic design and software development. In this paper we describe the challenges and design choices involved in parallelizing a hybrid of […]

The availability of low cost powerful parallel graphics cards has stimulated the port of Genetic Programming (GP) on Graphics Processing Units (GPUs). Our work focuses on the possibilities offered by Nvidia G80 GPUs when programmed in the CUDA language. In a first work we have showed that this setup allows to develop fine grain parallelization […]