Posts
Nov, 1
GPGPU: general purpose computation on graphics hardware
The graphics processor (GPU) on today’s commodity video cards has evolved into an extremely powerful and flexible processor. The latest graphics architectures provide tremendous memory bandwidth and computational horsepower, with fully programmable vertex and pixel processing units that support vector operations up to full IEEE floating point precision. High level languages have emerged for graphics […]
Nov, 1
A GPU accelerated storage system
Massively multicore processors, like, for example, Graphics Processing Units (GPUs), provide, at a comparable price, a one order of magnitude higher peak performance than traditional CPUs. This drop in the cost of computation, as any order-of-magnitude drop in the cost per unit of performance for a class of system components, triggers the opportunity to redesign […]
Nov, 1
OpenVIDIA: parallel GPU computer vision
Graphics and vision are approximate inverses of each other: ordinarily Graphics Processing Units (GPUs) are used to convert "numbers into pictures" (i.e. computer graphics). In this paper, we propose using GPUs in approximately the reverse way: to assist in "converting pictures into numbers" (i.e. computer vision). The OpenVIDIA project uses single or multiple graphics cards […]
Nov, 1
GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment
Molecular Biologists frequently compute multiple sequence alignments (MSAs) to identify similar regions in protein families. However, aligning hundreds of sequences by popular MSA tools such as ClustalW requires several hours on sequential computers. Due to the rapid growth of biological sequence databases biologists have to compute MSAs in a far shorter time. In this paper […]
Nov, 1
GPU Simulation and Rendering of Volumetric Effects for Computer Games and Virtual Environments
Abstract As simulation and rendering capabilities continue to increase, volumetric effects like smoke, fire or explosions will be frequently encountered in computer games and virtual environments. In this paper, we present techniques for the visual simulation and rendering of such effects that keep up with the demands for frame rates imposed by such environments. This […]
Nov, 1
Fast parallel Particle-To-Grid interpolation for plasma PIC simulations on the GPU
Particle-In-Cell (PIC) methods have been widely used for plasma physics simulations in the past three decades. To ensure an acceptable level of statistical accuracy relatively large numbers of particles are needed. State-of-the-art Graphics Processing Units (GPUs), with their high memory bandwidth, hundreds of SPMD processors, and half-a-teraflop performance potential, offer a viable alternative to distributed […]
Nov, 1
GPU Accelerated Smith-Waterman
We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. […]
Nov, 1
CUDA-Lite: Reducing GPU programming complexity
Abstract. The computer industry has transitioned into multi-core and many-core parallel systems. The CUDA programming environment from NVIDIA is an attempt to make programming many-core GPUs more accessible to programmers. However, there are still many burdens placed upon the programmer to maximize performance when using CUDA. One such burden is dealing with the complex memory […]
Nov, 1
Program optimization space pruning for a multithreaded gpu
Program optimization for highly-parallel systems has historically been considered an art, with experts doing much of the performance tuning by hand. With the introduction of inexpensive, single-chip, massively parallel platforms, more developers will be creating highly-parallel applications for these platforms, who lack the substantial experience and knowledge needed to maximize their performance. This creates a […]
Nov, 1
Interactive, GPU-Based Level Sets for 3D Segmentation
While level sets have demonstrated a great potential for 3D medical image segmentation, their usefulness has been limited by two problems. First, 3D level sets are relatively slow to compute. Second, their formulation usually entails several free parameters which can be very difficult to correctly tune for specific applications. This paper presents a tool for […]
Nov, 1
High-throughput sequence alignment using Graphics Processing Units
BACKGROUND:The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for […]
