Bruce J. Palmer

Advances, Applications and Performance of the Global Arrays Shared Memory Programming Toolkit

This paper describes capabilities, evolution, performance, and applications of the Global Arrays (GA) toolkit. GA was created to provide application programmers with an inteface that allows them to distribute data while maintaining the type of global index space and programming syntax similar to that available when programming on a single processor. The goal of GA is to free the programmer from the low level management of communication and allow them to deal with their problems at the level at which they were originally formulated. At the same time, compatibility of GA with MPI enables the programmer to take advatage of the existing MPI software/libraries when available and appropriate. The variety of applications that have been implemented using Global Arrays attests to the attractiveness of using higher level abstractions to write parallel code.

The ion pairing and hydration structure of Ni2+ in supercritical water at 425 °C determined by x-ray absorption fine structure and molecular dynamics studies

The ion pairing structure of Ni(Br)2 solutions (0.2 and 0.4 molal) under supercritical conditions was determined using x-ray absorption fine structure (XAFS) spectroscopy. These first measurements of the average bulk structure show that approximately one Br− counterion is associated with each Ni2+. The Ni2+-to-Br− distance of 2.40 A is very accurately determined and the strength of this interaction, as indicated by the Debye–Waller factor (σ2=0.009 A2), shows that the bromine anion is very tightly bound to the nickel cation under these supercritical conditions. In addition to the onset of ion pairing interactions, there is also a dramatic transition in the hydration structure. Results show a loss of about 50% of the waters in the first shell upon going from ambient to a hydrothermal condition of 425 °C and 690 bar. Finally, we use molecular dynamics simulations with refined intermolecular potentials to directly calculate XAFS spectra that are shown to quantitatively reproduce the experimental results for ...

Alternative Hamiltonian for molecular dynamics simulations in the grand canonical ensemble

An alternative to the Hamiltonian of Cagin and Pettitt for performing molecular dynamics simulations in the grand canonical ensemble is presented and used as the basis for a new algorithm. The algorithm is tested on the ideal gas and the truncated and shifted Lennard‐Jones fluid. Simulations are used to calculate the vapor–liquid coexistence points for the Lennard‐Jones system and are found to be in agreement with previous calculations using Gibbs ensemble calculations and with the Nicolas equation of state. Simulations are also performed on the Lennard‐Jones solid.

An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.g., plume to aquifer scales and years to centuries). While the multiscale nature of hydrogeologic problems is widely recognized, technological limitations in computation and characterization restrict most practical modeling efforts to fairly coarse representations of heterogeneous properties and processes. For some modern problems, the necessary level of simplification is such that model parameters may lose physical meaning and model predictive ability is questionable for any conditions other than those to which the model was calibrated. Recently, there has been broad interest across a wide range of scientific and engineering disciplines in simulation approaches that more rigorously account for the multiscale nature of systems of interest. In this article, we review a number of such approaches and propose a classification scheme for defining different types of multiscale simulation methods and those classes of problems to which they are most applicable. Our classification scheme is presented in terms of a flowchart (Multiscale Analysis Platform), and defines several different motifs of multiscale simulation. Within each motif, the member methods are reviewed and example applications are discussed. We focus attention on hybrid multiscale methods, in which two or more models with different physics described at fundamentally different scales are directly coupled within a single simulation. Very recently these methods have begun to be applied to groundwater flow and transport simulations, and we discuss these applications in the context of our classification scheme. As computational and characterization capabilities continue to improve, we envision that hybrid multiscale modeling will become more common and also a viable alternative to conventional single-scale models in the near future.

Molecular dynamics implementation of the Gibbs ensemble calculation

A molecular dynamics version of the Gibbs ensemble calculation is proposed. This calculation is based on an extended Hamiltonian formalism that treats the temperature, volume, and the coupling of a single particle to the rest of the system as continuous dynamical degrees of freedom with their own equations of motion. Calculations on the truncated and shifted Lennard‐Jones fluid are presented and compared to the Gibbs ensemble Monte Carlo results of Smit. Quantitative agreement is found between the molecular dynamics and Monte Carlo calculations.

A Component-Based Framework for Smoothed Particle Hydrodynamics Simulations of Reactive Fluid Flow in Porous Media

The development of a framework to support smoothed particle hydrodynamics (SPH) simulations of fluid flow and transport in porous media is described. The framework is built using the Common Component Architecture (CCA) toolkit and it supports SPH simulations using a variety of different SPH models and setup formats. The SPH simulation code is decomposed into independent components that represent self-contained units of functionality. Different physics models can be developed within the framework by re-implementing key components but no modification of other components is required. A model for defining components and developing abstract interfaces that support a high degree of modularity and minimal dependencies between components is discussed in detail.

A Redundant Communication Approach to Scalable Fault Tolerance in PGAS Programming Models

Recent trends in high-performance computing point toward increasingly large machines with millions of processing, storage, and networking elements. Unfortunately, the reliability of these machines is inversely proportional to their size, resulting in a system-wide mean time between failures (MTBF), ranging from a few days to a few hours. As such, for long-running applications, the ability to efficiently recover from frequent failures is essential. Traditional forms of fault tolerance, such as checkpoint/restart, suffer from performance issues related to limited I/O and memory bandwidth. In this paper, we present a fault-tolerance mechanism that reduces the cost of failure recovery by maintaining shadow data structures and performing redundant remote memory accesses. Results from a computational chemistry application running at scale show that our techniques provide applications with a high degree of fault tolerance and low (2%-4%) overhead for 2048 processors.

The extensible computational chemistry environment: a problem solving environment for high performance theoretical chemistry

The Extensible Computational Chemistry Environment (Ecce) is a suite of distributed applications that are integrated as a comprehensive problem solving environment for computational chemistry. Ecce provides scientists with an easily used graphical user interface to the tasks of setting up complex molecular modeling calculations, distributed use of high performance computers, and scientific visualization and analysis. Ecces flexible, standards-based architecture is an extensible framework that represents a significant milestone in production systems, both in the field of computational chemistry and problem solving environment research. Its base problem solving architecture components and concepts are applicable to problem solving environments beyond the computational chemistry domain.

Overview of the global arrays parallel software development toolkit

The Global Arrays (GA) toolkit provides a global address space programming model to MPI applications. GA library allows programmers to distribute data while maintaining the type of global index space and programming syntax similar to what is available when programming on a single processor. The goal of GA is to free the programmers from the low level management of communication and allow them to deal with their problems at the level at which they were originally formulated. The compatibility of GA with MPI makes it possible to use distributed and global views of the data in the same application. The variety of applications that have been implemented using Global Arrays attests to the attractiveness of using higher level abstractions to write parallel code. The tutorial will provide an overview of GA toolkit, its applications, and compare GA to related programming models such as UPC, Co-Array Fortran, and X10.

Constant pressure–constant temperature simulations of liquid water and carbon dioxide

Rigid and flexible models of liquid water and carbon dioxide are simulated using Andersen–Nose constant pressure–constant temperature molecular dynamics. Both equilibrium and dynamical properties are investigated and compared with constant energy simulations of the same models. The results of the constant pressure–constant temperature simulations are in very close agreement with the constant energy simulations, even for dynamical quantities.