high performance computing on graphics processing units: hgpu.org

Many bioinformatics studies require the analysis of RNA or DNA structures. More specifically, extensive work is done to elaborate efficient algorithms able to predict the 2-D folding structures of RNA or DNA sequences. However, the high computational complexity of the algorithms, combined with the rapid increase of genomic data, triggers the need of faster methods. […]

Algebraic Dynamic Programming (ADP) is a framework to encode a broad range of optimization problems, including common bioinformatics problems like RNA folding or pairwise sequence alignment. The ADP compiler translates such ADP programs into C. As all the ADP problems have similar data dependencies in the dynamic programming tables, a generic parallelization is possible. We […]

In this paper, the attractive features of evolutionary algorithm and Markov Chain Monte Carlo are combined into a new Differential Evolutionary Markov Chain Monte Carlo (DE-MCMC) method for multi-objective optimization problems with continuous variables. The DE-MCMC evolves a population of Markov chains through differential evolution (DE) toward a diversified set of solutions at the Pareto […]

As the most accurate model for simulating light propagation in heterogeneous tissues, Monte Carlo (MC) method has been widely used in the field of optical molecular imaging. However, MC method is time-consuming due to the calculations of a large number of photons propagation in tissues. The structural complexity of the heterogeneous tissues further increases the […]

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 […]