high performance computing on graphics processing units: hgpu.org

BACKGROUND: Three-dimensional (3D) reconstruction in electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a […]

BACKGROUND: Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level […]

Financial derivatives are financial instruments whose payoff is linked to some fundamental financial assets or indices. They are essential tools for speculation and risk-management. This paper focuses on the pricing of a common type of derivatives: convertible bonds (CBs), which incorporate the features of both bonds and stocks. Chambers and Lu propose a popular two-factor […]

The main goal of this project was to explore the possibility of applying CUDA to the Point Based Color Bleeding global illumination algorithm. This project tackled the creation of surfels, the storage of surfels in an octree, representation of an octree in CUDA, and the transversal of an octree in CUDA. Future work will include […]

Massively parallel desktop computing capabilities now well within the reach of individual academics modify the environment for posterior simulation in fundamental and potentially quite advantageous ways. But to fully exploit these benefits algorithms that conform to parallel computing environments are needed. Sequential Monte Carlo comes very close to this ideal whereas other approaches like Markov […]

Image segmentation is a computationally expensive task that continuously presents performance challenges due to the increasing volume of available high resolution remote sensing images. Nowadays, Graphics Processing Units (GPUs) are emerging as an attractive computing platform for general purpose computations due to their extremely high floating-point processing performance and their comparatively low cost. In the […]

Efficient stencil operations are essential in explicit schemes for evolutionary PDEs. In particular, for conservation and balance laws, the solution will in many cases have non-constant values only in a portion of the grid. We present novel methods that through simple observation of the stencil and the distribution of conserved quantities, reduce both the memory […]

In heterogeneous systems that include CPUs and GPUs, the data transfers between these components play a critical role in determining the performance of applications. Software pipelining is a common approach to mitigate the overheads of those transfers. In this paper we investigate advanced software-pipelining optimizations for the double-precision general matrix multiplication (DGEMM) algorithm running on […]

GPUs have become part of most commodity systems. Nonetheless, they are often underutilized when not executing graphics-intensive or special-purpose numerical computations, which are rare in consumer workloads. Emerging architectures, such as integrated CPU/GPU combinations, may create an opportunity to utilize these otherwise unused cycles for offloading traditional systems tasks. Garbage collection appears to be a […]

Graphics processing units have now been used for scientific calculations for over a decade, going from early proof-of-concepts to industrial use today. The inherent reason is that graphics processors are far more powerful than CPUs when it comes to both floating point operations and memory bandwidth, illustrated by the fact that three of the top […]

The term software performance engineering (SPE) is a systematic and quantitative approach for constructing software systems to meet the performance objectives such as response time, throughput, scalability and resource utilization. Optimization is major concern in achieving performance parameters. Optimization is performed during run-time, or in the design phase. This paper proposes the coding practices in […]

We focus on the following computational chemistry problem: Given a subset of the exact distances between atoms, reconstruct the three-dimensional position of each atom in the given molecule. The distance matrix is generally sparse. This problem is both important and challenging. Our contribution is a novel combination of two known techniques (parallel breadth-first search and […]