David E. Bernholdt's research while affiliated with Oak Ridge National Laboratory and other places

Publications (176)

Article
We present a data-driven strategy for effective construction of a surrogate model in high-dimensional parameter space for the ion energy-angle distribution (IEAD) output of hPIC simulations of plasma-surface interactions. The methodology is based on a bin-by-bin least-squares fitting of the IEAD in the parameter space. The fitting is performed in a...
Article
Full-text available
Fission gas release within uranium dioxide nuclear fuel occurs as gas atoms diffuse through grains and arrive at grain boundary (GB) bubbles; these GB bubbles grow and interconnect with grain edge bubbles; and grain edge tunnels grow and connect to free surfaces. In this study, a hybrid multi-scale/multi-physics simulation approach is presented to...
Article
Full-text available
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven me...
Preprint
Full-text available
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principledriven met...
Presentation
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Presentation on the current status of the SOLLVE OMPVV test suite, next directions for the project, and a short guide on using the test suite.
Conference Paper
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Software engineering (SWE) for modeling, simulation, and data analytics for computational science and engineering (CSE) is challenging, with ever-more sophisticated, higher fidelity simulation of ever-larger, more complex problems involving larger data volumes, more domains, and more researchers. Targeting both commodity and custom high-end compute...
Article
Full-text available
The OpenMP language features have been evolving to meet the rapid development in hardware platforms. This journal focuses on evaluating implementations of OpenMP 4.5 target offload features in compilers such as Clang, XL and GCC that are an integral part of the software harness on supercomputers and clusters. We use Summit (Top supercomputer in the...
Article
Resiliency is and will be a critical factor in determining scientific productivity on current and exascale supercomputers, and beyond. Applications oblivious to and incapable of handling transient soft and hard errors could waste supercomputing resources or, worse, yield misleading scientific insights. We introduce a novel application‐driven silent...
Preprint
Full-text available
This paper presents a method for solving the supervised learning problem in which the output is highly nonlinear and discontinuous. It is proposed to solve this problem in three stages: (i) cluster the pairs of input-output data points, resulting in a label for each point; (ii) classify the data, where the corresponding label is the output; and fin...
Preprint
Full-text available
This paper presents a method for solving the supervised learning problem in which the output is highly nonlinear and discontinuous. It is proposed to solve this problem in three stages: (i) cluster the pairs of input-output data points, resulting in a label for each point; (ii) classify the data, where the corresponding label is the output; and fin...
Article
Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, s...
Article
In the paper 'Continuum-scale modeling of helium bubble bursting under plasma-exposed tungsten surfaces (2018 Nucl. Fusion 58 126034)', equation (1) is wrong, it should be: (Formula Presented). where the last term is subtracted instead of added. This error was missed during the proofreading process.
Preprint
Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, s...
Article
We present a comparison between a continuum-scale drift-diffusion-reaction cluster dynamics prediction of helium retention in low-energy helium plasma exposed tungsten and experimental measurements, in a temperature regime that did not produce tungsten fuzz. Our cluster dynamics model, Xolotl, has been successfully benchmarked to high helium implan...
Article
Full-text available
The Exascale Computing Project (ECP) is currently the primary effort in the United States focused on developing “exascale” levels of computing capabilities, including hardware, software, and applications. In order to obtain a more thorough understanding of how the software projects under the ECP are using, and planning to use the Message Passing In...
Conference Paper
The OpenMP language features have been evolving to meet the rapid development in hardware platforms. DOE applications tend to push the bleeding edge of features ratified in the OpenMP specification and tend to expose the rough edges of the features' implementations. The software harness on DOE supercomputers such as Titan and (upcoming) Summit incl...
Article
In this work, the surface response of a tungsten plasma-facing component was simulated by a cluster-dynamics code, Xolotl, with a focus on quantifying the impact of uncertainty in one of the input parameters to Xolotl, namely, the incident helium flux. The simulated conditions involve a tungsten surface exposed to 100 eV helium ion implantations wi...
Chapter
OpenMP has been widely adopted for shared memory systems for over a decade. With the heterogeneity trend in architectures rapidly growing, the programming model needed to evolve such that applications could not only be ported to traditional CPUs but also to accelerators often acting as discrete or integrated devices to CPUs. To that end, OpenMP sta...
Article
Full-text available
We consider using regression to fit a theory-based log-linear ansatz, as well as higher order approximations, for the thermal energy confinement of a Tokamak as a function of device features. We use general linear models based on total order polynomials, as well as deep neural networks. The results indicate that the theory-based model fits the data...
Article
Full-text available
We consider using regression to fit a theory-based log-linear ansatz, as well as higher order approximations, for the thermal energy confinement of a Tokamak as a function of device features. We use general linear models based on total order polynomials, as well as deep neural networks. The results indicate that the theory-based model fits the data...
Article
We present a hierarchical multiscale modeling study of implanted helium (He) segregation near grain boundaries (GBs) of tungsten. We extend our spatially dependent cluster dynamics model to two spatial dimensions in order to take into account the biased drift of mobile He clusters toward the GBs observed in atomic-scale simulations. We are able to...
Article
We present ?programmer-guided reliability? (PGR) as a systematic conceptual approach to address the expected rise in soft errors in coming extreme-scale systems at the application level. The approach involves instrumentation of the application with code to detect data corruption errors. The location and nature of these error detectors are at the di...
Conference Paper
In the world of high-performance computing, fault tolerance and application resilience are becoming some of the primary concerns because of increasing hardware failures and memory corruptions. While the research community has been investigating various options, from system-level solutions to application-level solutions, standards such as the Messag...
Conference Paper
Full-text available
The economics of software tools have proven challenging to understand for users and stakeholders in CSE. In the past, many funding agencies have supported academic and governmental research that produced high-value (but not necessarily high-quality) software as a byproduct of the proposed research, not as a direct aim of the proposal or line item i...
Conference Paper
Full-text available
Current HPC system software lacks support for emerging application deployment scenarios that combine one or more simulations with in situ analytics, sometimes called multi-component or multi-enclave applications. This paper presents an initial design study, implementation, and evaluation of mechanisms supporting composite multi-enclave applications...
Conference Paper
The multicore generation of scientific high performance computing has provided a platform for the realization of Exascale computing, and has also underscored the need for new paradigms in coding parallel applications. The current standard for writing parallel applications requires programmers to use languages designed for sequential execution. Thes...
Conference Paper
This paper describes our vision for Hobbes, an operating system and runtime (OS/R) framework for extreme-scale systems. The Hobbes design explicitly supports application composition, which is emerging as a key approach for applications to address scalability and power concerns anticipated with coming extreme-scale architectures. We make use of virt...
Conference Paper
Programming with communication libraries such as the Message Passing Interface (MPI) obscures the high-level intent of the communication in an application and makes static communication analysis difficult to do. Compilers are unaware of communication libraries' specifics, leading to the exclusion of communication patterns from any automated analysi...
Conference Paper
The increasing availability of large scale computing capabilities has accelerated the development of high-fidelity coupled simulations. Such simulations typically involve the integration of models that implement various aspects of the complex phenomena under investigation. Coupled simulations are playing an integral role in fields such as climate m...
Conference Paper
The increasing availability of large scale computing capabilities has accellerated the development of high-fidelity coupled simulations. Such simulations typically involve the integration of models that implement various aspects of the complex phenomena under investigation. Coupled simulations are playing an integral role in fields such as climate...
Article
Full-text available
The goal of the COMPOSE-HPC project is to 'democratize' tools for automatic transformation of program source code so that it becomes tractable for the developers of scientific applications to create and use their own transformations reliably and safely. This paper describes our approach to this challenge, the creation of the KNOT tool chain, which...
Article
Full-text available
This paper discusses on-going work with the Integrated Plasma Simulator (IPS), a framework for coupled multiphysics simulations of plasmas, to allow simulations to run through the loss of nodes on which the simulation is executing.While many different techniques are available to improve the fault tolerance of computational science applications on h...
Article
Full-text available
Parareal is a novel algorithm that allows the solution of time-dependent systems of differential or partial differential equations (PDE) to be parallelized in the temporal domain. Parareal-based implementations of PDE problems can take advantage of this parallelism to significantly reduce the time to solution for a simulation (though at an increase...
Conference Paper
Many modern scientific applications, which are designed to utilize high performance parallel computers, occupy hundreds of thousands of computational cores running for days or even weeks. Since many scientists compete for resources, most supercomputing centers practice strict scheduling policies and perform meticulous accounting on their usage. Thu...
Conference Paper
Full-text available
This paper discusses the Integrated Plasma Simulator (IPS), a framework for coupled multiphysics simulation of fusion plasmas, in the context of many-task computing. The IPS supports multiple levels of parallelism: individual computational tasks can be parallel, components can launch multiple tasks concurrently, tasks from multiple components can b...
Article
We present the design and implementation of a component-based simulation framework for the execution of coupled time-dependent plasma modeling codes. The Integrated Plasma Simulator (IPS) provides a flexible lightweight component model that streamlines the integration of stand alone codes into coupled simulations. Standalone codes are adapted to th...
Article
As computing capabilities have increased, the coupling of computational models has become an increasingly viable and therefore important way of improving the physical fidelity of simulations. Applications currently using some form of multicode or multi-component coupling include climate modeling, rocket simulations, and chemistry. In recent years,...
Article
Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to...
Article
Full-text available
Abtract: The Integrated Plasma Simulator (IPS) provides a framework within which some of the most advanced, massively-parallel fusion modeling codes can be interoperated to provide a detailed picture of the multi-physics processes involved in fusion experiments. The presentation will cover four topics: 1) recent improvements to the IPS, 2) applicat...
Article
Full-text available
This paper discusses a program synthesis system to facil-itate the generation of high-performance parallel programs for a class of computations encountered in quantum chem-istry and physics. These computations are expressible as a set of tensor contractions and arise in electronic structure modeling. An overview is provided of the synthesis system...
Article
Climate scientists face a wide variety of practical problems, but there is an overarching need to efficiently access and manipulate climate model data. Increasingly, for example, researchers must assemble and analyze large datasets that are archived in different formats on disparate platforms, and extract portions of datasets to compute statistical...
Article
In the component approach, components are said to inter-act through well-defined interfaces. Conventionally, these interfaces are based on method signatures which define the syntax, if not the semantics of the interface. However in many cases, this does not encompass all of the interactions a component has with its peers. In the Integrated Plasma S...
Conference Paper
In this paper, we discuss the recent ESG's development and implementation efforts concerning its authentication infrastructure. ESG's requirements are to make the user's logon-experience as easy as possible, and to facilitate the integration of the security services and the Grid components for both the developers and system administrators. To meet...
Article
Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to...
Article
Full-text available
Interface contract enforcement is intended to help scientists gain confidence in software built from third-party components. Unfamiliar components present increased risk of incorrect or unanticipated usage patterns and unexpected component behavior. Executable interface contracts can address these issues but may incur unacceptable overhead. Researc...
Article
The international climate community is expected to generate hundreds of petabytes of simulation data within the next five to seven years. This data must be accessed and analyzed by thousands of analysts worldwide in order to provide accurate and timely estimates of the likely impact of climate change on physical, biological, and human systems. Clim...
Article
Full-text available
As computers scale up dramatically to tens and hundreds of thousands of cores, develop deeper computational and memory hierarchies, and increased heterogeneity, developers of scientific software are increasingly challenged to express complex parallel simulations effectively and efficiently. In this paper, we explore the three languages developed un...
Article
Full-text available
The broad scientific objectives of the SWIM (Simulation of Wave Interaction with MHD) project are twofold: (1) improve our understanding of interactions that both radio frequency (RF) wave and particle sources have on extended-MHD phenomena, and to substantially improve our capability for predicting and optimizing the performance of burning plasmas...
Conference Paper
Full-text available
As high-end computer systems present users with rapidly increasing numbers of processors, possibly also incorporating attached co-processors, programmers are increasingly challenged to express the necessary levels of concurrency with the dominant parallel programming model, Fortran+MPI+OpenMP (or minor variations). In this paper, we examine the lan...
Conference Paper
Full-text available
The recent advances in high performance computing, storage and networking technologies have enabled fundamental changes in current climate research. While sharing datasets and results is already common practice in climate modeling, direct sharing of the analysis and visualization process is also becoming feasible. We report our efforts to develop a...
Article
The grid environment contains a large and growing number of widely distributed sites with heterogeneous resources. It is a great challenge to dynamically manage and account for usage data of grid resources, such as computational, network, and storage resources. A distributed Resource Usage Data management and Accounting (RUDA) system is designed to...
Article
Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this paper, we propose an instrumentation framework for message-passing systems to characterize the degree of overlap of communication with computation in the exe...
Article
Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this report, we describe an instrumentation framework developed for message-passing systems to characterize the degree of overlap of communication with computatio...
Article
Full-text available
Understanding the earth's climate system and how it might be changing is a preeminent scientific challenge. Global climate models are used to simulate past, present, and future climates, and experiments are executed continuously on an array of distributed supercomputers. The resulting data archive, spread over several sites, currently contains upwa...