Harold E. Trease

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.

Morphometric Comparison of Clavicle Outlines from 3D Bone Scans and 2D Chest Radiographs: A Shortlisting Tool to Assist Radiographic Identification of Human Skeletons†

This paper describes a computerized clavicle identification system primarily designed to resolve the identities of unaccounted‐for U.S. soldiers who fought in the Korean War. Elliptical Fourier analysis is used to quantify the clavicle outline shape from skeletons and postero‐anterior antemortem chest radiographs to rank individuals in terms of metric distance. Similar to leading fingerprint identification systems, shortlists of the top matching candidates are extracted for subsequent human visual assessment. Two independent tests of the computerized system using 17 field‐recovered skeletons and 409 chest radiographs demonstrate that true‐positive matches are captured within the top 5% of the sample 75% of the time. These results are outstanding given the eroded state of some field‐recovered skeletons and the faintness of the 1950s photofluorographs. These methods enhance the capability to resolve several hundred cold cases for which little circumstantial information exists and current DNA and dental record technologies cannot be applied.

Toward interoperable mesh, geometry and field components for PDE simulation development

Mesh-based PDE simulation codes are becoming increasingly sophisticated and rely on advanced meshing and discretization tools. Unfortunately, it is still difficult to interchange or interoperate tools developed by different communities to experiment with various technologies or to develop new capabilities. To address these difficulties, we have developed component interfaces designed to support the information flow of mesh-based PDE simulations. We describe this information flow and discuss typical roles and services provided by the geometry, mesh, and field components of the simulation. Based on this delineation for the roles of each component, we give a high-level description of the abstract data model and set of interfaces developed by the Department of Energy’s Interoperable Tools for Advanced Petascale Simulation (ITAPS) center. These common interfaces are critical to our interoperability goal, and we give examples of several services based upon these interfaces including mesh adaptation and mesh improvement.

Potential Technology for Studying Dosimetry and Response to Airborne Chemical and Biological Pollutants

Advances in computational, and imaging techniques have enabled the rapid development of three-dimensional (3-D) models of biological systems in unprecedented detail. Using these advances, 3-D models of the lungs and nasal passages of the rat and human are being developed to ultimately improve predictions of airborne pollutant dosimetry. Techniques for imaging the respiratory tract by magnetic resonance imaging (MRI) were developed to improve the speed and accuracy of geometric data collection for mesh reconstruction. The MRI resolution is comparable to that obtained by manual measurements but at much greater speed and accuracy. Newly developed software (NWGrid) was utilized to translate imaging data from MR into 3-D mesh structures. Together, these approaches significantly reduced the time to develop a 3-D model. This more robust airway structure will ultimately facilitate modeling gas or vapor exchange between the respiratory tract and vasculature as well as enable linkages of dosimetry with cell response models. The 3-D, finite volume, viscoelastic mesh structures form the geometric basis for computational fluid dynamics modeling of inhalation, exhalation and the delivery of individual particles (or concentrations of gas or vapors) to discrete regions of the respiratory tract. The ability of these 3-D models to resolve dosimetry at such a high level of detail will require new techniques to measure regional airflows and particulate deposition for model validation.

Interoperable mesh and geometry tools for advanced petascale simulations

SciDAC applications have a demonstrated need for advanced software tools to manage the complexities associated with sophisticated geometry, mesh, and field manipulation tasks, particularly as computer architectures move toward the petascale. The Center for Interoperable Technologies for Advanced Petascale Simulations (ITAPS) will deliver interoperable and interchangeable mesh, geometry, and field manipulation services that are of direct use to SciDAC applications. The premise of our technology development goal is to provide such services as libraries that can be used with minimal intrusion into application codes. To develop these technologies, we focus on defining a common data model and data-structure neutral interfaces that unify a number of different services such as mesh generation and improvement, front tracking, adaptive mesh refinement, shape optimization, and solution transfer operations. We highlight the use of several ITAPS services in SciDAC applications.

The TSTT Mesh Interface

PDE-based numerical simulation applications commonly use basic software infrastructure to manage mesh, geometry, and discretization data. The commonality of this infrastructure implies the software is theoretically amenable to re-use. However, the traditional reliance on library-based implementations of these functionalities hampers experimentation with different software instances that provide similar functionality. This is especially true for meshing and geometry libraries where applications often directly access the underlying data structures, which can be quite different from implementation to implementation. Thus, using different libraries interchangeably or interoperably for this functionality has proven difficult at best and has hampered the wide spread use of advanced meshing and geometry tools developed by the research community. To address these issues, the Terascale Simulation Tools and Technologies center is working to develop standard interfaces to enable the creation of interoperable and interchangeable simulation tools. In this paper, we focus on a languageand data-structure-independent interface supporting query and modification of mesh data conforming to a general abstract data model. We describe the model and interface, and provide programming “best practices” recommendations based on early experience implementing and using the interface.

Generalized Quasicontinuum Approach to Atomistic-Continuum Modeling of Complex Oxides

A formalism of the Quasicontinuum (QC) method suitable for atomistic-continuum modeling of oxide crystals is presented. Multiple interacting quasicontinua, one per sublattice, which overlap in the physical crystal space are used to model the oxide crystals. The method is implemented with the shell model for atomic interactions in ionic crystals, along with the Wolfs method for treating the long-range forces. Results are presented for the structural relaxation of strained and unstrained Fe2O3

Unstructured data analysis of streaming video using parallel, high-throughput algorithms

crystal under periodic boundary conditions.