high performance computing on graphics processing units: hgpu.org

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines […]

Neural development represents not only an exciting and complex field of study, with ongoing progress, but it also became the epicentre of neuroscience and developmental biology, as it strives to describe the underlying cellular and molecular mechanisms by which the central nervous system emerges during the various levels of embryonic development phases. The nervous system […]

A tri-hybrid port of General Electric’s in-house, 3D, Computational Fluid Dynamics (CFD) code TACOMA is created utilizing MPI, OpenMP, and OpenACC technologies. This new port targets improved performance on NVidia Kepler accelerator GPUs, such as those installed in the world’s second largest supercomputer, Titan, the Department of Energy’s 27 petaFLOP Cray XK7 located at Oak […]

This tutorial will demonstrate how to use features in NAMD and VMD to harness the computational power of graphics processing units (GPUs) to accelerate simulation, visualization and analysis. You will learn how to drastically improve the efficiency of your computational work, achieving large speedups over CPU only methods. You will explore ways of investigating large […]

The graphic processing unit (GPU) gets strong computing ability with relatively low energy and money consumption, it has been widely used in the field of large-scale simulation and computation. Among which the CPU-GPU heterogeneous collaborative computing model has become an effective ways to solve the simulation performance of large-scale artificial society. But there are lots […]

Motivated by computational capacity and power efficiency, techniques for integrating graphics processing units (GPUs) into real-time systems have become an active area of research. While much of this work has focused on single-GPU systems, multiple GPUs may be used for further benefits. Similar to CPUs in multiprocessor systems, GPUs in multi-GPU systems may be managed […]

Traditional ways of increasing computer performance has been increasing speed and bit size. Although this kept us going for more than half of a century, methodology has hit a major road block due to power consumption and heat dissipation. The remedy found for this problem has been creating multiple cores/heterogeneous computing systems on a single […]

There is an abundance of computing power sitting in computer labs waiting to be harnessed. Previous research in this area has shown promising results networking clusters of workstations together in order to solve bigger problems faster at a fraction of the cost for supercomputer time. There are, of course, challenges to using these sorts of […]

As the era of Moore’s Law and increasing CPU clock rates nears its stopping point the focus of chip and hardware design has shifted to increasing the number of computation cores present on the chip. This increase can be most clearly seen in the rise of Graphic Processing Units (GPU) where hundreds or thousands of […]

BLAST, short for Basic Local Alignment Search Tool, is a fundamental algorithm in the life sciences that compares biological sequences. However, with the advent of next-generation sequencing (NGS) and increase in sequence read-lengths, whether at the outset or downstream from NGS, the exponential growth of sequence databases is arguably outstripping our ability to analyze the […]

Large-scale simulation can provide a wide range of information needed to develop and validate theoretical models for multiphase flow in porous medium systems. In this paper, we consider a coupled solution in which a multiphase flow simulator is coupled to an analysis approach used to extract the interfacial geometries as the flow evolves. This has […]

The proverb above describes the essence of this paper and the motivation behind the development of our Interactive Parallelization Tool (IPT) that can transform serial applications into multiple parallel variants. The end-users of the IPT are required to develop an understanding about the basic concepts involved in parallel programming (viz. concurrency, data distribution and data […]