## Posts

Oct, 28

### An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

The Smith Waterman algorithm for sequence alignment is one of the main tools of bioinformatics. It is used for sequence similarity searches and alignment of similar sequences. The high end Graphical Processing Unit (GPU), used for processing graphics on desktop computers, deliver computational capabilities exceeding those of CPUs by an order of magnitude. Recently these […]

Oct, 28

### Acceleration technique for volume rendering using 2D texture based ray plane casting on GPU

In this paper, we present a very fast new GPU-based algorithm for volume rendering using the ray plane casting technique. It consists of preprocessing and main processing. In preprocessing, we reduce the waste of memory and produce the texture data which can be efficiently traversed concurrently in main processing by converting the volume data into […]

Oct, 28

### An efficient, model-based CPU-GPU heterogeneous FFT library

General-purpose computing on graphics processing units (GPGPU) is becoming popular in HPC because of its high peak performance. However, in spite of the potential performance improvements as well as recent promising results in scientific computing applications, its real performance is not necessarily higher than that of the current high-performance CPUs, especially with recent trends towards […]

Oct, 28

### Visualization and GPU-accelerated simulation of medical ultrasound from CT images

We present a fast GPU-based method for simulation of ultrasound images from volumetric CT scans and their visualization. The method uses a ray-based model of the ultrasound to generate view-dependent ultrasonic effects such as occlusions, large-scale reflections and attenuation combined with speckle patterns derived from pre-processing the CT image using a wave-based model of ultrasound […]

Oct, 28

### GPU Ray Marching for Real-Time Rendering of Participating Media

This paper presents a GPU based ray marching algorithm for real-time rendering of participating media. We fire a ray at each pixel being shaded on the cube surface, and then we find an intersection between the ray and inner-volume recorded by a 3D texture, using both linear and binary searches. At this intersection, the ray […]

Oct, 28

### Fast Simulations of Gravitational Many-body Problem on RV770 GPU

The gravitational many-body problem is a problem concerning the movement of bodies, which are interacting through gravity. However, solving the gravitational many-body problem with a CPU takes a lot of time due to O(N^2) computational complexity. In this paper, we show how to speed-up the gravitational many-body problem by using GPU. After extensive optimizations, the […]

Oct, 28

### Jump flooding in GPU with applications to Voronoi diagram and distance transform

This paper studies jump flooding as an algorithmic paradigm in the general purpose computation with GPU. As an example application of jump flooding, the paper discusses a constant time algorithm on GPU to compute an approximation to the Voronoi diagram of a given set of seeds in a 2D grid. The errors due to the […]

Oct, 28

### String Matching on a Multicore GPU Using CUDA

Graphics processing units (GPUs) have evolved over the past few years from dedicated graphics rendering devices to powerful parallel processors, outperforming traditional central processing units (CPUs) in many areas of scientific computing. The use of GPUs as processing elements was very limited until recently, when the concept of general-purpose computing on graphics processing units (GPGPU) […]

Oct, 28

### Pseudo-random number generators for Monte Carlo simulations on Graphics Processing Units

Basic uniform pseudo-random number generators are implemented on ATI Graphics Processing Units (GPU). The performance results of the realized generators (multiplicative linear congruential (GGL), XOR-shift (XOR128), RANECU, RANMAR, RANLUX and Mersenne Twister (MT19937)) on CPU and GPU are discussed. The obtained speed-up factor is hundreds of times in comparison with CPU. RANLUX generator is found […]

Oct, 28

### Compute Pairwise Manhattan Distance and Pearson Correlation Coefficient of Data Points with GPU

Graphics processing units (GPUs) are powerful computational devices tailored towards the needs of the 3-D gaming industry for high-performance, real-time graphics engines. Nvidia Corporation released a new generation of GPUs designed for general-purpose computing in 2006, and it released a GPU programming language called CUDA in 2007. The DNA microarray technology is a high throughput […]

Oct, 28

### Motion Compensation and Reconstruction of H.264/AVC Video Bitstreams using the GPU

Most modern computers are equipped with powerful yet cost-effective graphics processing units (GPUs) to accelerate graphics operations. Although programmable shaders on these GPUs were designed for the creation of 3-D rendering effects, they can also be used as generic processing units for vector data. This paper proposes a hardware Tenderer capable of executing motion compensation, […]

Oct, 28

### GPU-based object-order ray-casting for large datasets

We propose a GPU-based object-order ray-casting algorithm for the rendering of large volumetric datasets, such as the Visible Human CT datasets. A volumetric dataset is decomposed into small sub-volumes, which are then organized using a min-max octree structure. The small sub-volumes are stored in the leaf nodes of the min-max octree, which are also called […]