high performance computing on graphics processing units: hgpu.org

A comparative analysis of high-performance implementations of two state of the art index structures that are of particular interest in the field of bioinformatics applications to accelerate the alignment of DNA sequences is presented. The two indexes are based on suffix trees and suffix arrays and were implemented in two different platforms: a quad-core CPU […]

Image segmentation is the task of splitting a digital image into one or more regions of interest. It is a fundamental problem in computer vision and many different methods, each with their own advantages and disadvantages, exist for the task. Image segmentation is a particularly difficult task for several reasons. Firstly, the ambiguous nature of […]

Particle in cell (PIC) algorithm is a widely used method in plasma physics to study the trajectories of charged particles under electromagnetic fields. The PIC algorithm is computationally intensive and its time requirements are proportional to the number of charged particles involved in the simulation. The focus of the paper is to parallelize the PIC […]

Molecular docking is an important problem of bioinformatics aiming at the prediction of binding poses of molecules. Auto Dock is a popular, open-source docking software applying a computationally expensive but parallelizable algorithm. This paper introduces an FPGA-based and a GPU-based implementation of Auto Dock and shows how the original algorithm can be effectively accelerated on […]

The tensor eigenproblem has many important applications, generating both mathematical and application-specific interest in the properties of tensor eigenpairs and methods for computing them. A tensor is an m-way array, generalizing the concept of a matrix (a 2-way array). Kolda and Mayo have recently introduced a generalization of the matrix power method for computing real-valued […]

The increasing computing requirements for GPUs (Graphics Processing Units) have favoured the design and marketing of commodity devices that nowadays can also be used to accelerate general purpose computing. Therefore, future high performance clusters intended for HPC (High Performance Computing) will likely include such devices. However, high-end GPU-based accelerators used in HPC feature a considerable […]

Field Programmable Gate Arrays (FPGAs) are now considered to be one of the preferred computing platforms for high performance computing applications, such as Monte Carlo simulations, due to their large computational power and low power consumption. Unlike other state-of-the-art computing platforms, such as General Purpose Processors (GPPs) and General Purpose Graphics Processing Units (GPGPU), FPGAs […]

Increasing chip power density has brought application specific accelerator architectures to the forefront as an energy and area efficient solution. While GPGPU systems take advantage of specialized hardware to perform computationally intensive tasks faster than chip multiprocessor (CMP) systems, accelerators are hardware units that are designed to execute a specific application efficiently. Real-time ultrasound imaging […]

Transrectal Electric Impedance Tomography (TREIT) has been proposed jointly with ultrasound (US) imaging of the prostate to enhance the standard clinical imaging. Reconstructing TREIT images involves a solution of an inverse problem. The reconstruction is based on two steps: solving and updating an estimate of the dielectric property distribution through solution of an inverse problem. […]

General purpose GPU (GPGPU) computing has produced the fastest running supercomputers in the world. For continued sustainable progress, GPU computing at scale also need to address two open issues: a) how increase applications mean time between failures (MTBF) as we increase supercomputer’s component counts, and b) how to minimize unnecessary energy consumption. Since energy consumption […]

Heterogeneous multicores are envisioned to be a promising design paradigm to combat today’s challenges of power, memory, and reliability walls that are impeding chip design using deep submicron technology. Future multicores are expected to integrate multiple different cores, including GPGPUs, custom accelerators and configurable cores. In this paper, we introduce an important dimension-technology-using which heterogeneity […]

We have developed GSNP, a software package with GPU acceleration, for single-nucleotide polymorphism detection on DNA sequences generated from second-generation sequencing equipment. Compared with SOAPsnp, a popular, high-performance CPU-based SNP detection tool, GSNP has several distinguishing features: First, we design a sparse data representation format to reduce memory access as well as branch divergence. Second, […]