high performance computing on graphics processing units: hgpu.org

Current methods for tuberculosis nucleic acid detection require amplification and labeling before detection is possible. We propose here a method for direct detection using Tethered Particle Motion: gold nanoparticles are tethered to a glass substrate by single-stranded DNA molecules consisting of the complementary sequence to the target. Detection takes place by observing a change in […]

Multifactor dimensionality reduction (MDR) method has been widely applied to detect gene-gene interactions that are well recognized as playing an important role in understanding complex traits, such as disease susceptibility. However, because of an exhaustive analysis of MDR, the current MDR software has some limitations to be extended to the genome-wide association studies (GWAS) with […]

A parallelization of the low-frequency multilevel fast multipole algorithm (MLFMA) for graphics processing units (GPUs) is presented. The implementation exhibits speedups between 10 and 30 compared to a serial CPU implementation of the algorithm. The error of the MLFMA on the GPU is controllable down to machine precision. Under the typical method-of-moments (MoM) error requirement […]

In this paper, we describe our experiment developing an implementation of the Linpack benchmark for TianHe-1, a petascale CPU/GPU supercomputer system, the largest GPU-accelerated system ever attempted before. An adaptive optimization framework is presented to balance the workload distribution across the GPUs and CPUs with the negligible runtime overhead, resulting in the better performance than […]

SAR processing can be applied to ice sounder data to improve along-track resolution and clutter suppression. This paper presents a time-domain back-projection technique for SAR focusing of ice sounder data. With this technique, variations in flight track and ice surface slope can be accurately accommodated at the expense of computation time. The back-projection algorithm can […]

We present an interface to the graphics processing unit (GPU) from MATLAB, and four algorithms from numerical linear algebra available through this interface; matrix-matrix multiplication, Gauss-Jordan elimination, PLU factorization, and tridiagonal Gaussian elimination. In addition to being a high level abstraction to the GPU, the interface offers background processing, enabling computations to be executed on […]

The shader in the GPU increases flexibility and enables customizations of vertex and fragment processing, and it also provides the programmer with various special effects essential in development of realistic 3D virtual scene. Compared to a CPU based simulation of the ocean water, the shader-based simulation in this paper reduces the complexity of the model […]

Protein structure prediction (PSP) is the process of searching for the min energy of the protein. While many algorithms have being put forward to predict the structure of protein, the complicated computation make the time cost of the algorithms are significantly expensive. CUDA, the newly developing technology, makes us use Graphic Processing Unit (GPU) that […]

GPU platforms are becoming increasingly attractive for implementing accelerators because they feature a larger number of cores with improved programmability. In this paper, we describe our implementation of a state-of-the-art academic multi-level analytical placer mPL on Nvidia’s massively parallel GT200 series platforms. We detail our efforts on performance tuning and optimizations. When compared to software […]

The Coarse-Grained Monte Carlo (CGMC) method is a multi-scale stochastic mathematical and simulation framework for spatially distributed systems. CGMC simulations are important tools for studying phenomena such as catalysis, crystal growth, surface diffusion, phase transitions on single crystals, and cell membrane receptor dynamics. In parallel CGMC, the tau-leap method is used for parallel simulations that […]

We present a real-time reverse radiosity method for compensating indirect scattering effects that occur with immersive and semi-immersive projection displays. It computes a numerical solution directly on the GPU and is implemented with pixel shading and multi-pass rendering which together realizes a Jacobi solver for sparse matrix linear equation systems. Our method is validated and […]

Illustrative visualization of complex vasculature has been one of the indispensable components in medical education and training. In this paper, we propose a rendering pipeline which incorporates various perception-aware techniques for informative vascular illustration. Chromostereopsis rendering, isophote-based line hatching, and enhanced silhouette drawing have been integrated seamlessly through multiple shader passes. With advanced GPU acceleration […]