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PubMed2005

Building the TeraGrid.

On 1 October 2004, the most ambitious high-performance Grid project in the United States-the TeraGrid-became fully operational. Resources at nine sites--the San Diego Supercomputer Center, the California Institute of Technology, the National Center for Supercomputing Applications, the University of Chicago/Argonne National Laboratory, Pittsburgh Supercomputing Center, Texas Advanced Computing Center, Purdue University, Indiana University and Oak Ridge National Laboratory-were joined via an ultra-fast optical network, unified policies and security procedures and a sophisticated distributed computing software environment. Funded by the National Science Foundation, the TeraGrid enables scientists and engineers to combine distributed, multiple data sources with computation at any of the sites or link massively parallel computer simulations to extreme-resolution visualizations at remote sites. A single shared utility lets multiple resources be easily leveraged and provides improved access to advanced computational capabilities. One of the demonstrations of this new model for using distributed resources, Teragyroid, linked the infrastructure of the TeraGrid with computing resources in the United Kingdom via a transatlantic data fibre link. Once connected, the software framework of the RealityGrid project was used to successfully explore lattice-Boltzmann simulations involving lattices of over one billion sites.

Computer Security↗
PubMed2005

Towards performance control on the Grid.

Advances in computational Grid technologies are enabling the development of simulations of complex biological and physical systems. Such simulations can be assembled from separate components--separately deployable computation units of well-defined functionality. Such an assemblage can represent an application composed of interacting simulations or might comprise multiple instances of a simulation executing together, each running with different simulation parameters. However, such assemblages need the ability to cope with heterogeneous and dynamically changing execution environments, particularly where such changes can affect performance. This paper describes the design and implementation of a prototype performance control system (PerCo), which is capable of monitoring the progress of simulations and redeploying them so as to optimize performance. The ability to control performance by redeployment is demonstrated using an assemblage of lattice Boltzmann simulations running with and without control policies. The cost of using PerCo is evaluated and it is shown that PerCo is able to reduce overall execution time.

Benchmarking↗
PubMed2005

WEDS: a Web services-based environment for distributed simulation.

Web services have the potential to radically enhance the ability of researchers to make use of distributed computing resources, but jargon and a plethora of standards make their use almost impossible for the scientist without prior experience of the necessary technologies. A powerful and simple WSRF-based middleware scheme is presented, designed to let scientists remotely deploy single or multiple instances of a pre-existing code across multiple resources, and giving steering, visualization and workflow functionality with only simple modifications to program code. It is hoped that the development and implementation of such a toolkit will be relevant not only to the problem of deploying workstation-class codes in real time, but also the move towards more tractable alternatives to the Globus toolkit for deployment of processes in a high-performance computing environment.

Computer Simulation↗
PubMed2005

A practical toolkit for computational steering.

Computational steering refers to the real-time interaction of a scientist with their running simulation code. Despite the many benefits associated with computational steering, its uptake to date has been limited. In this paper we discuss the reasons for this and how the computational steering library and associated tools developed as part of the RealityGrid project aim to tackle them. We describe the functionality of the steering library and the use of Grid services in constructing a generic, dynamic architecture for discovering, steering and connecting visualization software to running simulations. The use of on-line visualization for providing feedback to the scientist is described, including the ways in which it may be enhanced through tools such as Chromium and Access Grid. Finally, we illustrate the flexibility of our approach by describing the functionality that has been added to various simulation codes as part of the RealityGrid project.

Computer Graphics↗
PubMed2005

Steering UNICORE applications with VISIT.

The UNICORE (UNiform Interface to COmputing REsources) software provides a Grid infrastructure together with a computing portal for engineers and scientists to access supercomputer centres from anywhere on the Internet. While UNICORE is primarily designed for the submission and control of batch jobs, it is also feasible to establish an on-line connection between an application and the UNICORE user-client. This opens up the possibility of performing on-line visualization and computational steering of applications under UNICORE control while maintaining the security provided by this system. This contribution describes the design of a steering extension to UNICORE based on the steering toolkit VISIT (VISualization Interface Toolkit). VISIT is a lightweight library that supports bidirectional data exchange between visualizations and parallel applications. As an example application, a parallel simulation of a laser-plasma interaction that can be steered by an AVS/Express application is presented.

Computer Graphics↗
PubMed2005

Improving scientists' interaction with complex computational-visualization environments based on a distributed grid infrastructure.

The grid has the potential to transform collaborative scientific investigations through the use of closely coupled computational and visualization resources, which may be geographically distributed, in order to harness greater power than is available at a single site. Scientific applications to benefit from the grid include visualization, computational science, environmental modelling and medical imaging. Unfortunately, the diversity, scale and location of the required resources can present a dilemma for the scientific worker because of the complexity of the underlying technology. As the scale of the scientific problem under investigation increases so does the nature of the scientist's interaction with the supporting infrastructure. The increased distribution of people and resources within a grid-based environment can make resource sharing and collaborative interaction a critical factor to their success. Unless the technological barriers affecting user accessibility are reduced, there is a danger that the only scientists to benefit will be those with reasonably high levels of computer literacy. This paper examines a number of important human factors of user interaction with the grid and expresses this in the context of the science undertaken by RealityGrid, a project funded by the UK e-Science programme. Critical user interaction issues will also be highlighted by comparing grid computational steering with supervisory control systems for local and remote access to the scientific environment. Finally, implications for future grid developers will be discussed with a particular emphasis on how to improve the scientists' access to what will be an increasingly important resource.

Computer Graphics↗
PubMed2005

A grid-enabled lightweight computational steering client: a .NET PDA implementation.

The grid has been developed to support large-scale computer simulations in a diverse range of scientific and engineering fields. Consequently, the increasing availability of powerful distributed computing resources is changing how scientists undertake large-scale modelling/simulation. Instead of being limited to local computing resources, scientists are now able to make use of supercomputing facilities around the world. These grid resources comprise specialized distributed three-dimensional visualization environments through to massive computational systems. The scientist usually accesses these resources from reasonably high-end desktop computers. Even though most modern desktop computers are provided with reasonably powerful three-dimensional graphical hardware, not all scientific applications require high-end three-dimensional visualization because the data of interest is essentially numerical or two-dimensional graphical data. For these applications, a much simpler two-dimensional graphical displays can be used. Since large jobs can take many hours to complete the scientist needs access to a technology that will allow them to still monitor and control their job while away from their desks. This paper describes an effective method of monitoring and controlling a set of chained computer simulations by means of a lightweight steering client based on a small personal digital assistant (PDA). The concept of using a PDA to steer a series of computational jobs across a supercomputing resource may seem strange at first but when scientists realize they can use these devices to connect to their computation wherever there is a wireless network (or cellular phone network) the concept becomes very compelling. Apart from providing a much needed easy-to-use interface, the PDA-based steering client has the benefit of freeing the scientist from the desktop. It is during this monitoring stage that the hand-held PDA client is of particular value as it gives the application scientist greater freedom to leave his or her desk but still communicate with their simulation, with the proviso that they remain within the range of a wireless network.

Computer Graphics↗
PubMed2005

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids.

During the last 2.5 years, the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational Grids. Since smoothly working production Grids are not yet available, we have been able to substantially influence the direction of software and Grid deployment within the project. In this paper, we review our results from large-scale three-dimensional lattice Boltzmann simulations performed over the last 2.5 years. We describe how the proactive use of computational steering, and advanced job migration and visualization techniques enabled us to do our scientific work more efficiently. The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organization of liquid cubic mesophases.

Computer Graphics↗
PubMed2005

Physical and computational scaling issues in lattice Boltzmann simulations of binary fluid mixtures.

We describe some scaling issues that arise when using lattice Boltzmann (LB) methods to simulate binary fluid mixtures--both in the presence and absence of colloidal particles. Two types of scaling problem arise: physical and computational. Physical scaling concerns how to relate simulation parameters to those of the real world. To do this effectively requires careful physics, because (in common with other methods) LB cannot fully resolve the hierarchy of length, energy and time-scales that arise in typical flows of complex fluids. Care is needed in deciding what physics to resolve and what to leave unresolved, particularly when colloidal particles are present in one or both of two fluid phases. This influences steering of simulation parameters such as fluid viscosity and interfacial tension. When the physics is anisotropic (for example, in systems under shear) careful adaptation of the geometry of the simulation box may be needed; an example of this, relating to our study of the effect of colloidal particles on the Rayleigh-Plateau instability of a fluid cylinder, is described. The second and closely related set of scaling issues are computational in nature: how do you scale-up simulations to very large lattice sizes? The problem is acute for systems undergoing shear flow. Here one requires a set of blockwise co-moving frames to the fluid, each connected to the next by a Lees-Edwards like boundary condition. These matching planes lead to small numerical errors whose cumulative effects can become severe; strategies for minimizing such effects are discussed.

Complex Mixtures↗
PubMed2005

Vortex core identification in viscous hydrodynamics.

We describe a software package designed for the investigation of topological fluid dynamics with a novel algorithm for locating and tracking vortex cores. The package is equipped with modules for generating desired vortex knots and links and evolving them according to the Navier-Stokes equations, while tracking and visualizing them. The package is parallelized using a message passing interface for a multiprocessor environment and makes use of a computational steering library for dynamic user intervention.

Algorithms↗
PubMed2005

Grid computing and biomolecular simulation.

Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

Biopolymers↗
PubMed1990

Direct solution of continuous densities given the Fourier magnitudes.

In order to apply direct methods routinely to macromolecular crystals it will be necessary to generate a non-atomic theory which is applicable to continuous densities. Reformulation of the 'phase problem' in terms of deconvoluting an autocorrelation function or Patterson synthesis reduces the problem from a theoretically intractable transcendental problem to a system of simultaneous quadratic equations. These quadratic equations may, in principle, always be solved by conjugate direction search techniques. The phase problem is shown to be a class P problem, admitting a deterministic solution in polynomial time. Two algorithms are presented with running times proportional to N2points and Npoints log Npoints per step. These algorithms are a pixel-by-pixel search and a conjugate gradients search. When the data are exact and complete the Fourier magnitudes are readily inverted by them to find the image. An example with real data, from a 15mer of DNA, is also shown.

DNA↗
PubMed1998

Ensembles of radial basis function networks for spectroscopic detection of cervical precancer.

The mortality related to cervical cancer can be substantially reduced through early detection and treatment. However, current detection techniques, such as Pap smear and colposcopy, fail to achieve a concurrently high sensitivity and specificity. In vivo fluorescence spectroscopy is a technique which quickly, noninvasively and quantitatively probes the biochemical and morphological changes that occur in precancerous tissue. A multivariate statistical algorithm was used to extract clinically useful information from tissue spectra acquired from 361 cervical sites from 95 patients at 337-, 380-, and 460-nm excitation wavelengths. The multivariate statistical analysis was also employed to reduce the number of fluorescence excitation-emission wavelength pairs required to discriminate healthy tissue samples from precancerous tissue samples. The use of connectionist methods such as multilayered perceptrons, radial basis function (RBF) networks, and ensembles of such networks was investigated. RBF ensemble algorithms based on fluorescence spectra potentially provide automated and near real-time implementation of precancer detection in the hands of nonexperts. The results are more reliable, direct, and accurate than those achieved by either human experts or multivariate statistical algorithms.

Algorithms↗
PubMed2001

Fast EM-like methods for maximum "a posteriori" estimates in emission tomography.

The maximum-likelihood (ML) approach in emission tomography provides images with superior noise characteristics compared to conventional filtered backprojection (FBP) algorithms. The expectation-maximization (EM) algorithm is an iterative algorithm for maximizing the Poisson likelihood in emission computed tomography that became very popular for solving the ML problem because of its attractive theoretical and practical properties. Recently, (Browne and DePierro, 1996 and Hudson and Larkin, 1994) block sequential versions of the EM algorithm that take advantage of the scanner's geometry have been proposed in order to accelerate its convergence. In Hudson and Larkin, 1994, the ordered subsets EM (OS-EM) method was applied to the ML problem and a modification (OS-GP) to the maximum a posteriori (MAP) regularized approach without showing convergence. In Browne and DePierro, 1996, we presented a relaxed version of OS-EM (RAMLA) that converges to an ML solution. In this paper, we present an extension of RAMLA for MAP reconstruction. We show that, if the sequence generated by this method converges, then it must converge to the true MAP solution. Experimental evidence of this convergence is also shown. To illustrate this behavior we apply the algorithm to positron emission tomography simulated data comparing its performance to OS-GP.

Algorithms↗
PubMed2001

Likelihood maximization for list-mode emission tomographic image reconstruction.

The maximum a posteriori (MAP) Bayesian iterative algorithm using priors that are gamma distributed, due to Lange, Bahn and Little, is extended to include parameter choices that fall outside the gamma distribution model. Special cases of the resulting iterative method include the expectation maximization maximum likelihood (EMML) method based on the Poisson model in emission tomography, as well as algorithms obtained by Parra and Barrett and by Huesman et al. that converge to maximum likelihood and maximum conditional likelihood estimates of radionuclide intensities for list-mode emission tomography. The approach taken here is optimization-theoretic and does not rely on the usual expectation maximization (EM) formalism. Block-iterative variants of the algorithms are presented. A self-contained, elementary proof of convergence of the algorithm is included.

Algorithms↗
PubMed2004

Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.

Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 10(6)-fold slower finite difference Poisson-Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent-accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pK(a)s of >200 ionizable groups from 15 proteins.

Algorithms↗
PubMed1991

Cardiac electrophysiological experiments in numero, Part II: Models of electrophysiological processes.

This article is the second part of a three article series reviewing computer simulation models of the heart, in particular of cardiac electrophysiology. The previous section of the review discussed the methodological principles of the construction and application of computer models. This article overviews the development of mathematical and computer modeling studies applied to cardiology. The models are classified according to the physiological processes that were simulated; this article distinguishes models oriented to cardiac mechanics, hemodynamics, and electrophysiology. The electrophysiology models are discussed in more detail and the review classifies them into four main categories: models of cellular processes, models of tissue behavior, models of the ventricular electric field, and models of macroconduction disturbances. In each category, the historical development of the models and their key achievements are described.

Animals↗