high performance computing on graphics processing units: hgpu.org

Graphical processing units are now being used with dramatic effect to accelerate quantum chemistry applications. The authors give a brief introduction to electronic structure methods and describe their efforts to accelerate a correlated quantum chemistry code. They propose and analyze two new tools for accelerating matrix-multiplications where single-precision accuracy is insuffcient.

Multi-core processors are no longer the future of computing-they are the present day reality. A typical mass-produced CPU features multiple processor cores, while a GPU (Graphics Processing Unit) may have hundreds or even thousands of cores. With the rise of multi-core architectures has come the need to teach advanced programmers a new and essential skill: […]

During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent-solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed-ups up to a factor of 54 (single-precision GPU vs. […]

To explore progressively larger biomolecular systems, methods to model explicit solvent cheaply are required. In this work, the use of Graphics Processing Units, found in commodity video cards, for solving the constraints, calculating the non-bonded forces and generating the pair list in the case of the fully constrained three site SPC water model is investigated. […]

The advent of powerful cosmological surveys demands a new generation of high-precision, large-volume, and high dynamic range simulations of structure formation in the Universe. Key aims of these simulations are understanding why the expansion of the Universe is accelerating and what dark matter is made of. The availability of Roadrunner, the world’s first petaflop platform, […]

Modern graphics cards, commonly used in desktop computers, have evolved beyond a simple interface between processor and display to incorporate sophisticated calculation engines that can be applied to general purpose computing. The Monte Carlo algorithm for modelling photon transport in turbid media has been implemented on an NVIDIA 8800GT graphics card using the CUDA toolkit. […]

The wide diversity of computer architectures today requires a new approach to software development. OpenMM is an abstraction layer for molecular mechanics simulations, allowing a single program to run efficiently on a variety of hardware platforms.

In a previous article [Brown et al., J Chem Theory Comput 2009, 4, 1620], we described a quadrature-based formulation of the Kohn-Sham Coulomb problem that allows for efficient parallelization over thousands of small processor cores. Here, we present the analytic gradients of this modified Kohn-Sham scheme, and describe the parallel implementation of the gradients on […]

Holographic optical tweezers allow the three-dimensional, dynamic, multipoint manipulation of micron sized objects using laser light. Exploiting the massive parallel architecture of modern GPUs we can generate highly optimized holograms at video frame-rate allowing the precise interactive micro-manipulation of complex structures.

As we enter the era of billion transistor chips, computer architects face significant challenges in effectively harnessing the large amount of computational potential available in modern CMOS technology. Chip designers have been moving away from maximizing single-thread performance via exponential scaling of clock frequencies toward chip multiprocessors (CMPs) in order to better manage trade-offs among […]

We have previously suggested a minimally invasive approach to include hardware accelerators into an existing large-scale parallel finite element PDE solver toolkit, and implemented it into our software FEAST. Our concept has the important advantage that applications built on top of FEAST benefit from the acceleration immediately, without changes to application code. In this paper […]

The main contribution of this thesis is to demonstrate that graphics processors (GPUs) as representatives of emerging many-core architectures are very well-suited for the fast and accurate solution of large sparse linear systems of equations, using parallel multigrid methods on heterogeneous compute clusters. Such systems arise for instance in the discretisation of (elliptic) partial differential […]