high performance computing on graphics processing units: hgpu.org

The Simplex algorithm is a well known method to solve linear programming (LP) problems. In this paper, we propose a parallel implementation of the Simplex on a CPU-GPU systems via CUDA. Double precision implementation is used in order to improve the quality of solutions. Computational tests have been carried out on randomly generated instances for […]

Voronoi diagram(VD) is a fundamental data structure in computational geometry. With the rapid development of programmable graphics programmable units, utilizing GPU to construct VD has been an optimal strategy. Considering the bridles of state-of-art algorithms, a seed flooding algorithm(SFA) is presented to achieve both robustness and high performance. The experimental results shows that SFA can […]

Numerical calculations with finite-difference time-domain (FDTD) on metallic nanostructures in a broad optical spectrum require an accurate approximation of the permittivity of dispersive materials. Here, we present the algorithms behind B-CALM (Belgium-California Light Machine), an open-source 3D-FDTD solver operating on Graphical Processing Units (GPU’s) with multi-pole dispersion models. Our modified architecture shows a reduction in […]

Tissue Doppler imaging is a routinely used diagnostic tool for assessing myocardial function in real time. The required signal processing is computationally intensive, including modified auto-correlation, scan conversion, image mapping. Parallel algorithms and implementations based on GPU platform are proposed in this paper to increase the computation efficiency. The experimental signal data is acquired from […]

Direct volume rendering has become a popular method for visualizing volumetric datasets. Even though computers are continually getting faster, it remains a challenge to incorporate sophisticated illumination models into direct volume rendering while maintaining interactive frame rates. In this paper, we present a novel approach for advanced illumination in direct volume rendering based on GPU […]

Accelerating applications with GPUs has recently garnered a lot of interest from the scientific computing community. While tools for optimizing individual kernels are readily available, there is a lack of support for the specific needs of the HPC area. Most importantly, integration with existing parallel programming models (MPI and threading) and scalability to the full […]

A comparative analysis of high-performance implementations of two state of the art index structures that are of particular interest in the field of bioinformatics applications to accelerate the alignment of DNA sequences is presented. The two indexes are based on suffix trees and suffix arrays and were implemented in two different platforms: a quad-core CPU […]

Image segmentation is the task of splitting a digital image into one or more regions of interest. It is a fundamental problem in computer vision and many different methods, each with their own advantages and disadvantages, exist for the task. Image segmentation is a particularly difficult task for several reasons. Firstly, the ambiguous nature of […]

Particle in cell (PIC) algorithm is a widely used method in plasma physics to study the trajectories of charged particles under electromagnetic fields. The PIC algorithm is computationally intensive and its time requirements are proportional to the number of charged particles involved in the simulation. The focus of the paper is to parallelize the PIC […]

Molecular docking is an important problem of bioinformatics aiming at the prediction of binding poses of molecules. Auto Dock is a popular, open-source docking software applying a computationally expensive but parallelizable algorithm. This paper introduces an FPGA-based and a GPU-based implementation of Auto Dock and shows how the original algorithm can be effectively accelerated on […]

The tensor eigenproblem has many important applications, generating both mathematical and application-specific interest in the properties of tensor eigenpairs and methods for computing them. A tensor is an m-way array, generalizing the concept of a matrix (a 2-way array). Kolda and Mayo have recently introduced a generalization of the matrix power method for computing real-valued […]

The increasing computing requirements for GPUs (Graphics Processing Units) have favoured the design and marketing of commodity devices that nowadays can also be used to accelerate general purpose computing. Therefore, future high performance clusters intended for HPC (High Performance Computing) will likely include such devices. However, high-end GPU-based accelerators used in HPC feature a considerable […]