high performance computing on graphics processing units: hgpu.org

Abstract There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular […]

The recent interest in GPGPU, (General-Purpose computation on Graphics Processing Unit), has stimulated improvements in the programmability of the GPU. Although the utilization of new languages like OpenCL and CUDA facilitate GPU programming, different challenges have to be overcome to optimize the results of a direct implementation. Specifically, a straightforward implementation of the Monte Carlo […]

We propose a single chain slip-spring model, which is based on the slip-spring model by Likhtman [A. E. Likhtman, Macromolecules, 38, 6128 (2005)], for fast rheology simulations of entangled polymers on a GPU. We modify the original slip-spring model slightly for efficient calculations on a GPU. Our model is designed to satisfy the detailed balance […]

Integrated circuit (IC) design automation has traditionally followed a hierarchical approach. Modern IC design flow is divided into sequentially-addressed design and optimization layers; each successively finer in design detail and data granularity while increasing in computational complexity. Eventual agreement across the design layers signals design closure. Obtaining design closure is a continual problem, as lack […]

Molecular dynamics is a widely used simulation technique to investigate material properties and structural changes under external forces. The availability of more powerful clusters and algorithms continues to increase the spatial and temporal extents of the simulation domain. This poses a particular challenge for the visualization of the underlying processes which might consist of millions […]

AMD’s first Fusion Accelerated Processor Unit (APU) codenamed "Zacate" combines a pair of x86 CPUs cores codenamed "Bobcat", 1MB L2 Cache, Client Northbridge (CNB), with a DirectX" 11 Radeon HD5000 graphics/multimedia controller on a single die. The CNB provides an interface to a sin gle 64b DDR3 memory channel, which can operate at up to […]

Recent advances in highly parallel, multithreaded, manycore Graphics Processing Units (GPUs) have been enabling massive parallel implementations of many applications in bioinformatics. In this paper, we describe a parallel implementation of genome-wide association studies (GWAS) using Compute Unified Device Architecture (CUDA). Using a single NVIDIA GTX 280 graphics card, we achieve speedups of about 15 […]

A reconfigurable processor tailored for accelerating Phylogenetic Inference is proposed. In this paper, a programmable and scalable architectural platform instantiates an array of coarse grained light weight processing elements and allows arbitrary partitioning and scheduling schemes and capable of solving complete Maximum Likelihood algorithm and deal with arbitrarily large sequences. The key difference of the […]

We present an efficient method for volume rendering by ray casting on the CPU. We employ coherent packet traversal of an implicit bounding volume hierarchy, heuristically pruned using preintegrated transfer functions, to exploit empty or homogeneous space. We also detail SIMD optimizations for volumetric integration, trilinear interpolation, and gradient lighting. The resulting system performs well […]

Face detection is an important aspect for biometrics, video surveillance and human computer interaction. We present a multi-GPU implementation of the Viola-Jones face detection algorithm that meets the performance of the fastest known FPGA implementation. The GPU design offers far lower development costs, but the FPGA implementation consumes less power. We discuss the performance programming […]

This paper presents a novel Graphics Processing Unit (GPU)-based system for pedestrian detection with stereo vision in real images on mobile robot. The process of obtaining a dense disparity map on a GPU for real-time applications and the edge property of the scene to extract a region of interest (ROI) is designed. After extracting the […]

Sequence alignment is one of the most fundamental and important operation in bioinformatics. Through sequence alignment, we can find the sequence’s information of function, structure and evolution. BLAST is one of the most popular algorithms in the field of sequence alignment. In this paper, we have designed a GPU-based parallel BLAST algorithm and implemented it […]