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At least 1,009 records · Page 56

Tail queues: A multi-threaded matching architecture

As we approach exascale, computational parallelism will have to drastically increase in order to meet throughput targets. Many–core architectures have exacerbated this problem by trading reduced clock speeds, core complexity, and computation throughput for increasing parallelism. This presents two major challenges for communication libraries such as MPI: the library must leverage the performance advantages of thread level parallelism and avoid the scalability problems associated with increasing the number of processes to that scale. Hybrid programming models, such as MPI+X, have been proposed to address these challenges. MPI THREAD MULTIPLE is MPI's thread safe mode. While there has been work to optimize it, it largely remains non–performant in most implementations. While current applications avoid MPI multithreading due to performance concerns, it is expected to be utilized in future applications. One of the major synchronous data structures required by MPI is the matching engine. In this paper, we present a parallel matching algorithm that can improve MPI matching for multithreaded applications. We then perform a feasibility study to demonstrate the performance benefit of the technique.

97 MATHEMATICS AND COMPUTING↗

Emergence of the polydeterminant in QCD

A generalization of the determinant appears in particle physics in effective Lagrangian interaction terms that model the chiral anomaly in quantum chromodynamics (Giacosa et al. in Phys Rev D 97(9):091901, 2018, Phys Rev D 109(7):L071502, 2024), in particular in connection to mesons. This polydeterminant function, known in the mathematical literature as a mixed discriminant, associates N distinct N x N complex matrices into a complex number and reduces to the usual determinant when all matrices are taken as equal. Here, we explore the main properties of the polydeterminant applied to (quantum) fields by using a formalism and a language close to high-energy physics approaches. We discuss its use as a tool to write down novel chiral anomalous Lagrangian terms and present an explicit illustrative model for mesons. Finally, the extension of the polydeterminant as a function of tensors is shown.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

CHARM-SYCL: New Unified Programming Environment for Multiple Accelerator Types

Addressing performance portability across diverse accelerator architectures has emerged as a major challenge in the development of application and programming systems for high-performance computing environments. Although recent programming systems that focus on performance portability have significantly improved productivity in an effort to meet this challenge, the problem becomes notably more complex when compute nodes are equipped with multiple accelerator types—each with unique performance attributes, optimal data layout, and binary formats. To navigate the intricacies of multi-accelerator programming, we propose CHARM-SYCL as an extension of our CHARM multi-accelerator execution environment [27]. This environment will combine our SYCL-based performance-portability programming front end with a back end for extremely heterogeneous architectures as implemented with the IRIS runtime from Oak Ridge National Laboratory. Our preliminary evaluation indicates potential productivity boost and reasonable performance compared to vendor-specific programming system and runtimes.

Fujita, Norihisa↗

Final Report of the Project "From the finite element method to the virtual element method"

The Finite Element Method (FEM) is a powerful numerical tool that is being used in a large number of engineering applications. The FEM is constructed on triangular/tetrahedral and quadrilateral/hexahedral meshes. Extending the FEM to general polygonal/polyhedral meshes in straightforward way turns out to be extremely difficult and leads to very complex and computationally expensive schemes. The reason for this failure is that the construction of the basis functions on elements with a very general shape is a non-trivial and complex task. In this project we developed a new family of numerical methods, dubbed the Virtual Element Method (VEM) for the numerical approximation of partial differential equations (PDE) of elliptic type suitable to polygonal and polyhedral unstructured meshes. We successfully formulated, implemented and tested these methods and studied both theoretically and numerically their stability, robustness and accuracy for diffusion problems, convection-reaction-diffusion problems, the Stokes equations and the biharmonic equations.

97 MATHEMATICS AND COMPUTING↗

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling

The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.

58 GEOSCIENCES↗

Fast All-Sky Radiation Model for Solar Applications (FARMS): A Brief Overview of Mechanisms, Performance, and Applications: Preprint

Solar radiation can be computed using radiative transfer models, such as the Rapid Radiation Transfer Model (RRTM) and its general circulation model applications, and used for various energy applications. Due to the complexity of computing radiation fields in aerosol and cloudy atmospheres, simulating solar radiation can be extremely time-consuming, but many approximations--e.g., the two-stream approach and the delta-M truncation scheme--can be utilized. To provide a new fast option for computing solar radiation, we developed the Fast All-sky Radiation Model for Solar applications (FARMS) by parameterizing the simulated diffuse horizontal irradiance and direct normal irradiance for cloudy conditions from the RRTM runs using a 16-stream discrete ordinates radiative transfer method. The solar irradiance at the surface was simulated by combining the cloud irradiance parameterizations with a fast clear-sky model, REST2. To understand the accuracy and efficiency of the newly developed fast model, we analyzed FARMS runs using cloud optical and microphysical properties retrieved using GOES data from 2009-2012. The global horizontal irradiance for cloudy conditions was simulated using FARMS and RRTM for global circulation modeling with a two-stream approximation and compared to measurements taken from the U.S. Department of Energy's Atmospheric Radiation Measurement Climate Research Facility Southern Great Plains site. Our results indicate that the accuracy of FARMS is comparable to or better than the two-stream approach; however, FARMS is approximately 400 times more efficient because it does not explicitly solve the radiative transfer equation for each individual cloud condition. Radiative transfer model runs are computationally expensive, but this model is promising for broad applications in solar resource assessment and forecasting. It is currently being used in the National Solar Radiation Database, which is publicly available from the National Renewable Energy Laboratory at http://nsrdb.nrel.gov.

14 SOLAR ENERGY↗

Collective I/O Tuning Using Analytical and Machine-Learning Models

The ever larger demand of scientific applications for computation and data is currently driving a continuous increase in scale of parallel computers. The inherent complexity of scaling up a computing systems in terms of both hardware and software stack exposes an increasing number of factors impacting the performance and complicating the process of optimization. In particular, the optimization of parallel I/O has become increasingly challenging due to increasing storage hierarchy and well known performance variability of shared storage systems. This paper focuses on model-based autotuning of the two-phase collective I/O algorithm from a popular MPI distribution on the Blue Gene/Q architecture. We propose a novel hybrid model, constructed as a composition of analytical models for communication and storage operations and black-box models for the performance of the individual operations. We perform an in-depth study of the complexity involved in performance modeling including architecture, software stack and noise. In particular we address this challenges of modeling the performance of shared storage systems by building a benchmark that helps synthesizing factors such as topology, file caching, and noise. The experimental results show that the hybrid approach produces significantly better results than state-of-the-art machine learning approaches and shows a higher robustness to noise, at the cost of a higher modeling complexity

I/O performance modeling↗

Application of a numerical differencing analyzer computer program to a Modular Integrated Utility System

This paper describes the application of a numerical differencing analyzer computer program to the thermal analyzation of a MIUS model. The MIUS model which was evaluated is one which would be required to support a 648-unit Garden Apartment Complex. This computer program was capable of predicting the thermal performance of this MIUS from the impressed electrical, heating, and cooling loads.

Brandli, A. E.↗

Computational Thermodynamic Study to Predict Complex Phase Equilibria in the Nickel-Base Superalloy Rene N6

A previous study by Ritzert et al. on the formation and prediction of topologically closed packed (TCP) phases in the nickel-base superalloy Rene' N6 is re-examined with computational thermodynamics. The experimental data on phase distribution in forty-four alloys with a composition within the patent limits of the nickel-base superalloy Rene' N6 provide a good basis for comparison to and validation of a commercial nickel superalloy database used with ThermoCalc. Volume fraction of the phases and partitioning of the elements are determined for the forty-four alloys in this dataset. The baseline heat treatment of 400 h at 1366 K was used. This composition set is particularly interesting since small composition differences lead to dramatic changes in phase composition. In general the calculated values follow the experimental trends. However, the calculations indicated no TCP phase formation when the experimental measurements gave a volume percent of TCP phase less than 2 percent. When TCP phases were predicted, the calculations under-predict the volume percent of TCP phases by a factor of 2 to 8. The calculated compositions of the gamma and gamma' phases show fair agreement with the measurements. However, the calculated compositions of the P Phase do not agree with those measured. This may be due to inaccuracies in the model parameters for P phase and/or issues with the microprobe analyses of these phases. In addition, phase fraction diagrams and sigma and P phase solvus temperatures are calculated for each of the alloys. These calculations indicate that P phase is the primary TCP phase formed for the alloys considered here at 1366 K. Finally, a series of isopleths are calculated for each of the seven alloying elements. These show the effect of each alloying element on creating TCP phases.

Copland, Evan H.↗

Complex Oxides for Brain–Inspired Computing: A Review

The fields of brain-inspired computing, robotics, and, more broadly, artificial intelligence (AI) seek to implement knowledge gleaned from the natural world into human-designed electronics and machines. In this review, the opportunities presented by complex oxides, a class of electronic ceramic materials whose properties can be elegantly tuned by doping, electron interactions, and a variety of external stimuli near room temperature, are discussed. The review begins with a discussion of natural intelligence at the elementary level in the nervous system, followed by collective intelligence and learning at the animal colony level mediated by social interactions. An important aspect highlighted is the vast spatial and temporal scales involved in learning and memory. The focus then turns to collective phenomena, such as metal-to-insulator transitions (MITs), ferroelectricity, and related examples, to highlight recent demonstrations of artificial neurons, synapses, and circuits and their learning. First-principles theoretical treatments of the electronic structure, and in situ synchrotron spectroscopy of operating devices are then discussed. The implementation of the experimental characteristics into neural networks and algorithm design is then revewed. Finally, outstanding materials challenges that require a microscopic understanding of the physical mechanisms, which will be essential for advancing the frontiers of neuromorphic computing, are highlighted.

36 MATERIALS SCIENCE↗

Biomimetic, Soft-Material Synapse for Neuromorphic Computing: from Device to Network

Neuromorphic computing refers to a variety of brain-inspired computers, devices, and models inspired by the interconnectivity, performance, and energy efficiency of the human brain. Unlike the ubiquitous von Neumann computer architectures with complex processor cores and sequential computation, biological neurons and synapses operate by storing and processing information simultaneously with the capacity of flexible adaptation resulting in massive computational capability with much less power consumption. The search for a synaptic material which can closely imitate bio-synapse has led to an alamethicin-doped, synthetic biomembrane which can emulate key synaptic functions due to generic memristive property enabling learning and computation. This two-terminal, biomolecular memristor, in contrast to its solid-state counterparts, features similar structure, switching mechanism, and ionic transport modality as biological synapses while consuming considerably lower power. In this paper, we outline a methodology for using this biomolecular synapse to build neural networks capable of solving real-world problems. The physical mechanism underlying its volatile memristance is explored followed by the development of a model of this device for circuit simulation. We outline a circuit design technique to integrate this synapse with solid-state neuron circuit for hardware implementation. Based on these results, we develop a high level simulation framework and use a training scheme called Evolutionary Optimization for Neuromorphic System (EONS) to generate networks for solving two problems, namely iris dataset classification and EEG classification task. The small network size and comparable to state-of-the-art accuracy of these preliminary networks show its potential to enhance synaptic functionality in next generation neuromorphic hardware.

Sakib hasan, Md↗

Space station data management system assessment methodology

A computer-aided modeling tool and methodology was developed and is currently being used to assess candidate designs for the Space Station Data Management System (DMS). The DMS will be a complex distributed computer system including processors, storage devices, local area networks, and software that will support all processing functions on board the Space Station. The methodology produces assessments of the performance, reliability, cost, and physical attributes of the candidate designs. This paper describes the architecture and design of the modeling tool and presents the modeling methodology.

Jones, W. R.↗

Accelerating Scientific Simulations with Bi-Fidelity Weighted Transfer Learning

High-fidelity modeling is an essential design tool for many engineering applications. However, for complex systems, computational cost can be a limiting factor. Analyzing parameter sensitivity, uncertainty quantification, and design optimization require many model evaluations. Surrogate models are often used to develop the relationship between model parameters and quantities of interest. However, in the case of complex systems, surrogate models require several degrees of freedom and, thus, a large number of data points to determine the correct dependencies. For many applications, this may be prohibitively expensive. The reduction of computational requirements can be achieved by leveraging low-fidelity models. Low-fidelity models represent the system at a coarser resolution with the advantage of computational efficiency. Therefore, a bi-fidelity modeling paradigm, which augments the accuracy of a low-fidelity model in a computationally efficient manner by invoking limited runs of a high-fidelity model, can be leveraged to sufficiently balance the accuracy and computational requirements. In this work, a bi-fidelity weighted transfer learning method using neural networks was applied to a computational fluid dynamics heat transfer modeling problem. The transfer learning advantage was investigated as a function of hyperparameters. Our main finding is that the use of a bi-fidelity modeling paradigm achieves accuracy close to that of a high-fidelity Gaussian process model while significantly reducing computational cost. The bi-fidelity model achieves comparable performance with 90 high-fidelity samples-that is, 60% less than the samples needed to achieve similar accuracy without the use of bi-fidelity modeling,

Borowiec, Katarzyna↗

Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery

Passive permeation of cellular membranes is a key feature of many therapeutics. The relevance of passive permeability spans all biological systems as they all employ biomembranes for compartmentalization. A variety of computational techniques are currently utilized and under active development to facilitate the characterization of passive permeability. These methods include lipophilicity relations, molecular dynamics simulations, and machine learning, which vary in accuracy, complexity, and computational cost. This review briefly introduces the underlying theories, such as the prominent inhomogeneous solubility diffusion model, and covers a number of recent applications. Various machine-learning applications, which have demonstrated good potential for high-volume, data-driven permeability predictions, are also discussed. Due to the confluence of novel computational methods and next-generation exascale computers, we anticipate an exciting future for computationally driven permeability predictions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Higher order turbulence closure models

Theoretical models are developed and numerical studies conducted on various types of flows including both elliptic and parabolic. The purpose of this study is to find better higher order closure models for the computations of complex flows. This report summarizes three new achievements: (1) completion of the Reynolds-stress closure by developing a new pressure-strain correlation; (2) development of a parabolic code to compute jets and wakes; and, (3) application to a flow through a 180 deg turnaround duct by adopting a boundary fitted coordinate system. In the above mentioned models near-wall models are developed for pressure-strain correlation and third-moment, and incorporated into the transport equations. This addition improved the results considerably and is recommended for future computations. A new parabolic code to solve shear flows without coordinate tranformations is developed and incorporated in this study. This code uses the structure of the finite volume method to solve the governing equations implicitly. The code was validated with the experimental results available in the literature.

Amano, Ryoichi S.↗

Computer program for calculation of complex chemical equilibrium compositions and applications. Part 1: Analysis

This report presents the latest in a number of versions of chemical equilibrium and applications programs developed at the NASA Lewis Research Center over more than 40 years. These programs have changed over the years to include additional features and improved calculation techniques and to take advantage of constantly improving computer capabilities. The minimization-of-free-energy approach to chemical equilibrium calculations has been used in all versions of the program since 1967. The two principal purposes of this report are presented in two parts. The first purpose, which is accomplished here in part 1, is to present in detail a number of topics of general interest in complex equilibrium calculations. These topics include mathematical analyses and techniques for obtaining chemical equilibrium; formulas for obtaining thermodynamic and transport mixture properties and thermodynamic derivatives; criteria for inclusion of condensed phases; calculations at a triple point; inclusion of ionized species; and various applications, such as constant-pressure or constant-volume combustion, rocket performance based on either a finite- or infinite-chamber-area model, shock wave calculations, and Chapman-Jouguet detonations. The second purpose of this report, to facilitate the use of the computer code, is accomplished in part 2, entitled 'Users Manual and Program Description'. Various aspects of the computer code are discussed, and a number of examples are given to illustrate its versatility.

Gordon, Sanford↗

An Objective and Efficient Method for Assessing the Impact of Reduced-Precision Calculations On Solution Correctness

Recent studies have shown that reducing the precision of floating-point calculations in an atmospheric model can improve the models' computational performance without affecting model fidelity, but code changes are needed to accommodate lower precision, and a small number of calculations might need to retain higher precision to prevent undue round-off error. For complex and computationally expensive systems like the Energy Exascale Earth System Model (E3SM), a method is needed to objectively assess the quality of the lower-precision simulations and to quickly identify problematic code pieces This paper demonstrates that solution correctness can be evaluated through a simple and quantitative error metric based on time step convergence. The proposed test method can unambiguously detect the accumulation of precision error and objectively assess its impact on solution accuracy. Since fast physical processes are known to affect key features of the multi-year mean climate in an atmospheric model, we show that the convergence test applied to short simulations can provide useful information about the impact of reduced precision on a model’s long-term behavior. In contrast, the traditional way of climate model evaluation requires multi-year simulations and involves inspecting many physical quantities for statistical significance in the presence of natural variability. The simplicity, computational efficiency, and objectivity of the proposed method makes it very attractive for high-resolution model development. The method is also expected to be applicable to other models that numerically solve time evolution equations.

97 MATHEMATICS AND COMPUTING↗

Suppression of Composition g -modes in Chemically Equilibrating Warm Neutron Stars

We investigate the impact of chemical equilibration and the resulting bulk viscosity on nonradial oscillation modes of warm neutron stars at temperatures up to T ≈ 5 MeV, relevant for protoneutron stars and neutron star postmerger remnants. In this regime, the relaxation rate of weak interactions becomes comparable to the characteristic frequencies of composition g-modes in the core, resulting in resonant damping. To capture this effect, we introduce the dynamical sound speed, a complex, frequency-dependent generalization of the adiabatic sound speed that encodes both the restoring force and the dissipative effects of bulk compression. Using realistic weak reaction rates and three representative equations of state, we compute the complex frequencies of composition g-modes with finite-temperature profiles. We find that bulk viscous damping becomes increasingly significant with temperature and can completely suppress composition g-modes. In contrast, the f-mode remains largely unaffected by bulk viscosity due to its nearly divergence-free character. Our results highlight the sensitivity of g-mode behavior to thermal structure, weak reaction rates, and the equation of state, and establish the dynamical sound speed as a valuable descriptor characterizing oscillation properties in dissipative neutron star matter.

Neutron stars↗