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At least 451 records · Page 25

Software Defined Architectures for Portability and Performance

The Software Defined Architectures for Portability and Performance (SODAPOP) project developed a co-design framework to partition and map converged applications on specialized heterogeneous architectures. We started from key domain applications that combine scientific simulation with data analytics and machine learning as drivers to integrate our framework. The framework includes high-level compilers that interfaces with high-level programming frameworks, domain-specific optimization passes, and hardware-oriented optimizations. The framework leverages hardware generators to enable specialization and facilitate exploration of custom system designs.

97 MATHEMATICS AND COMPUTING↗

Studies of whistler propagation along a plasma density gradient that is parallel to the magnetic field

Low frequency plasma wave generation in space is important for both scientific and practical applications. One of the most promising techniques for doing this is to directly inject whistler waves into the space environment from an antenna onboard one or more satellites. This technique has been discussed for years, but there are still open questions about the best way to generate plasma waves. So far, most theoretical [Kondrat92], lab based [Pribyl2010, Stenzel2016] and space-based experiments [DSX] have focused on studying the generation of whistler waves from an electric dipole antenna. However, a dipole antenna is very inefficient because it puts a lot of energy in waves that are not effective for most applications. Theoretical [Kondrat92] and lab experimental [Stenzel2016] results indicate that a loop antenna is much more efficient at generating whistler waves than a dipole antenna. A satellite experiment will need to be developed to demonstrate that whistler waves can be generated from a loop antenna in the space environment. The challenge is that to efficiently transmit whistler modes in the natural plasma environment of space, the loop antenna will have to be very large. For example, at L=2 (one earth radius away from the surface of the earth) a loop antenna would need a radius on the order of ~200 m to radiate efficiently, as shown in fig. 1, left. The antenna size and complexity would require a prohibitively large and expensive satellite mission. Our proposed innovation is to exploit the fact that the characteristic wavelength of whistler waves decreases in more dense plasma, which reduces the size needed for an antenna to radiate efficiently. Fortunately, a technique already exists for enhancing the local plasma density in space, called a plasma contactor [Kovaleski2001]. A plasma contactor can be used to create a local environment where the plasma density is enhanced around the satellite, which in turn reduces the size of an antenna that is needed to radiate efficiently (Fig. 1, right).

42 ENGINEERING↗

A standards perspective on genomic data reusability and reproducibility

Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi’Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series “A Year of Data Reuse” in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting Water Cycle Characteristics from Percolation Theory and Observational Data

The fate of water and water-soluble toxic wastes in the subsurface is of high importance for many scientific and practical applications. Although solute transport is proportional to water flow rates, theoretical and experimental studies show that heavy-tailed (power-law) solute transport distribution can cause chemical transport retardation, prolonging clean-up time-scales greatly. However, no consensus exists as to the physical basis of such transport laws. In percolation theory, the scaling behavior of such transport rarely relates to specific medium characteristics, but strongly to the dimensionality of the connectivity of the flow paths (for example, two- or three-dimensional, as in fractured-porous media or heterogeneous sediments), as well as to the saturation characteristics (i.e., wetting, drying, and entrapped air). In accordance with the proposed relevance of percolation models of solute transport to environmental clean-up, these predictions also prove relevant to transport-limited chemical weathering and soil formation, where the heavy-tailed distributions slow chemical weathering over time. The predictions of percolation theory have been tested in laboratory and field experiments on reactive solute transport, chemical weathering, and soil formation and found accurate. Recently, this theoretical framework has also been applied to the water partitioning at the Earth’s surface between evapotranspiration, ET, and run-off, Q, known as the water balance. A well-known phenomenological model by Budyko addressed the relationship between the ratio of the actual evapotranspiration (ET) and precipitation, ET/P, versus the aridity index, ET 0 /P, with P being the precipitation and ET 0 being the potential evapotranspiration. Existing work was able to predict the global fractions of P represented by Q and ET through an optimization of plant productivity, in which downward water fluxes affect soil depth, and upward fluxes plant growth. In the present work, based likewise on the concepts of percolation theory, we extend Budyko’s model, and address the partitioning of run-off Q into its surface and subsurface components, as well as the contribution of interception to ET. Using various published data sources on the magnitudes of interception and information regarding the partitioning of Q, we address the variability in ET resulting from these processes. The global success of this prediction demonstrated here provides additional support for the universal applicability of percolation theory for solute transport as well as guidance in predicting the component of subsurface run-off, important for predicting natural flow rates through contaminated aquifers.

54 ENVIRONMENTAL SCIENCES↗

An Ultra-Compact X-ray Regenerative Amplifier Free-Electron Laser

There is a growing interest in designing and building compact X-ray Free Electron Lasers (FELs) for scientific and industry applications. In this paper, we report an X-ray Regenerative Amplifier FEL (XRAFEL) design based on a proposed Ultra Compact X-ray FEL configuration. Our results show that an XRAFEL can dramatically enhance the temporal coherence and increase the spectral brightness of the radiation in the hard X-ray regime without increasing the footprint of the FEL configuration. The proposed compact, fully coherent, and high-flux hard X-ray source holds promise as a valuable candidate for a wide range of high-impact applications in both academia and industry.

Singleton, Madison↗

Exploring the High-Pressure Phases of Carbon through X-ray Diffraction of Dynamic Compression Experiments on Sandia’s Z Pulsed Power Facility

The carbon phase diagram is rich with polymorphs which possess very different physical and optical properties ideal for different scientific and engineering applications. An understanding of the dynamically driven phase transitions in carbon is particularly important for applications in inertial confinement fusion, as well as planetary and meteorite impact histories. Experiments on the Z Pulsed Power Facility at Sandia National Laboratories generate dynamically compressed high-pressure states of matter with exceptional uniformity, duration, and size that are ideal for investigations of fundamental material properties. X-ray diffraction (XRD) is an important material physics measurement because it enables direct observation of the strain and compression of the crystal lattice, and it enables the detection and identification of phase transitions. Several unique challenges of dynamic compression experiments on Z prevent using XRD systems typically utilized at other dynamic compression facilities, so novel XRD diagnostics have been designed and implemented. We performed experiments on Z to shock compress carbon (pyrolytic graphite) samples to pressures of 150–320 GPa. The Z-Beamlet Laser generated Mn-Heα (6.2 keV) X-rays to probe the shock-compressed carbon sample, and the new XRD diagnostics measured changes in the diffraction pattern as the carbon transformed into its high-pressure phases. Quantitative analysis of the dynamic XRD patterns in combination with continuum velocimetry information constrained the stability fields and melting of high-pressure carbon polymorphs.

36 MATERIALS SCIENCE↗

A Comprehensive Review of Latent Space Dynamics Identification Algorithms for Intrusive and Non-Intrusive Reduced-Order-Modeling

Numerical solvers of partial differential equations (PDEs) have been widely employed for simulating physical systems. However, the computational cost remains a major bottleneck in various scientific and engineering applications, which has motivated the development of reduced-order models (ROMs). Recently, machine-learning-based ROMs have gained significant popularity and are promising for addressing some limitations of traditional ROM methods, especially for advection dominated systems. In this chapter, we focus on a particular framework known as Latent Space Dynamics Identification (LaSDI), which transforms the high-fidelity data, governed by a PDE, to simpler and low-dimensional latent-space data, governed by ordinary differential equations (ODEs). These ODEs can be learned and subsequently interpolated to make ROM predictions. Each building block of LaSDI can be easily modulated depending on the application, which makes the LaSDI framework highly flexible. In particular, we present strategies to enforce the laws of thermodynamics into LaSDI models (tLaSDI), enhance robustness in the presence of noise through the weak form (WLaSDI), select high-fidelity training data efficiently through active learning (gLaSDI, GPLaSDI), and quantify the ROM prediction uncertainty through Gaussian processes (GPLaSDI). We demonstrate the performance of different LaSDI approaches on Burgers equation, a non-linear heat conduction problem, and a plasma physics problem, showing that LaSDI algorithms can achieve relative errors of less than a few percent and up to thousands of times speed-ups.

Computational Engineering, Finance, and Science (c↗

Discrete global grid system-based flow routing datasets in the Amazon and Yukon basins

Abstract. Discrete global grid systems (DGGS) are emerging spatial data structures widely used to organize geospatial datasets across scales. While DGGS have found applications in various scientific disciplines, including atmospheric science and ecology, their integration into physically based hydrological models and Earth system models (ESMs) has been hindered by the lack of flow routing datasets based on DGGS. In response to this gap, this study pioneers the development of new flow routing datasets using icosahedral Snyder equal-area (ISEA) DGGS and a novel mesh-independent flow direction model. We present flow routing datasets for two large basins, the tropical Amazon River basin and the Arctic Yukon River basin. These datasets (1) facilitate the adoption of DGGS for hydrological models and (2) provide flow routing inputs for evaluation of DGGS-based flow routing in the Amazon and Yukon river basins. The data are available at https://doi.org/10.5281/zenodo.8377765 (Liao, 2023).

54 ENVIRONMENTAL SCIENCES↗

On Performance Prediction of Big Data Transfer in High-performance Networks

Big data generated by large-scale scientific and industrial applications need to be transferred between different geographical locations for remote storage, processing, and analysis. High-speed dedicated connections provisioned in High-performance Networks (HPNs) are increasingly utilized to carry out such big data transfer. HPN management highly relies on an important capability of performance (mainly throughput) prediction to reserve sufficient bandwidth and meanwhile avoid over-provisioning that may result in unnecessary resource waste. This capability is critical to improving the resource (mainly bandwidth) utilization of dedicated connections and meeting various user requests for data transfer. Conventional methods conduct performance prediction by fitting prior observed transfer history with predefined loss functions, without considering unobservable latent factors such as competing loads on end hosts. Such latent factors also have a significant impact on the application-level data transfer performance, which may result in an inaccurate prediction model. In this paper, we first investigate the impact of latent factors and propose a clustering-based method to eliminate their negative impact on performance prediction. We then develop a robust machine learning-based performance predictor by: i) incorporating the proposed latent factor elimination method into data preprocessing, and ii) adopting a customized domain guided loss function. Extensive experimental results show that our predictor achieves significantly higher prediction accuracy than several other state-of-the-art methods.

Liu, Wuji↗

Optical encoder devices and systems

Devices, systems and methods for encoding information using optical components are described. Information associated with a first optical signal (e.g., an optical pump) is encoded onto the phase of a second optical signal (e.g., an optical probe) using cross phase modulation (XPM) in a non-linear optical medium. The optical signals are multiplexed together into the nonlinear optical medium. The probe experiences a modified index of refraction as it propagates through the medium and thus accumulates a phase change proportional to the intensity of the pump. The disclosed devices can be incorporated into larger components and systems for various applications such as scientific diagnostics, radar, remote sensing, wireless communications, and quantum computing that can benefit from encoding and generation of low noise, high resolution signals. Examples of the encoded information includes intrinsic noise from the optical source, or others signals of interest, such as electrical, optical, X-ray, or high-energy particle signals.

Buckley, Brandon Walter↗

Optical encoder devices and systems

Devices, systems and methods for encoding information using optical components are described. Information associated with a first optical signal (e.g., an optical pump) is encoded onto the phase of a second optical signal (e.g., an optical probe) using cross phase modulation (XPM) in a non-linear optical medium. The optical signals are multiplexed together into the nonlinear optical medium. The probe experiences a modified index of refraction as it propagates through the medium and thus accumulates a phase change proportional to the intensity of the pump. The disclosed devices can be incorporated into larger components and systems for various applications such as scientific diagnostics, radar, remote sensing, wireless communications, and quantum computing that can benefit from encoding and generation of low noise, high resolution signals. Examples of the encoded information includes intrinsic noise from the optical source, or others signals of interest, such as electrical, optical, X-ray, or high-energy particle signals.

Buckley, Brandon Walter↗

Deep Learning with Physics Priors as Generalized Regularizers

In various scientific and engineering applications, there is typically an approximate model of the underlying complex system, even though it contains both aleatoric and epistemic uncertainties. In this paper, we present a principled method to incorporate these approximate models as physics priors in modeling, to prevent overfitting and enhancing the generalization capabilities of the trained models. Utilizing the structural risk minimization (SRM) inductive principle pioneered by Vapnik, this approach structures the physics priors into generalized regularizers. The experimental results demonstrate that our method achieves up to two orders of magnitude of improvement in testing accuracy.

Liu, Frank↗

FTK: A Simplicial Spacetime Meshing Framework for Robust and Scalable Feature Tracking

In this work, we present the Feature Tracking Kit (FTK), a framework that simplifies, scales, and delivers various feature-tracking algorithms for scientific data. The key of FTK is our simplicial spacetime meshing scheme that generalizes both regular and unstructured spatial meshes to spacetime while tessellating spacetime mesh elements into simplices. The benefits of using simplicial spacetime meshes include (1) reducing ambiguity cases for feature extraction and tracking, (2) simplifying the handling of degeneracies using symbolic perturbations, and (3) enabling scalable and parallel processing. The use of simplicial spacetime meshing simplifies and improves the implementation of several feature-tracking algorithms for critical points, quantum vortices, and isosurfaces. As a software framework, FTK provides end users with VTK/ParaView filters, Python bindings, a command line interface, and programming interfaces for feature-tracking applications. We demonstrate use cases as well as scalability studies through both synthetic data and scientific applications including tokamak, fluid dynamics, and superconductivity simulations. We also conduct end-to-end performance studies on the Summit supercomputer. FTK is open sourced under the MIT license: https://github.com/hguo/ftk.

97 MATHEMATICS AND COMPUTING↗

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations. To make advancements in all the aforementioned scientific areas, many technical aspects need to be more thoroughly studied and deeply understood in parallel discrete event simulation (PDES). The unique dynamics inherent in a discrete event modeling approach, by their very nature, intersect and influence the entire stack of the computing system, including (a) the unique nature of the instruction sets exercised in PDES workloads without a predominance of high-precision floating point operations, (b) virtual time-constrained multi-threaded execution of many logical processes per processor, (c) extremely variable and difficult to predict network traffic characteristics, (d) interfaces and inter-dependencies with machine learning and artificial intelligence codes at higher software layers, and (e) highly challenging load balancing needs, especially in effectively accounting for accelerated/extremely heterogeneous computing in current and future high-performance computing systems. Efficient and accurate parallel execution of PDES workloads is also dominated by challenges in dealing with their asynchronous concurrency fundamentally present at the model level. Conservative synchronization, optimistic/speculative synchronization, and their hybrid schemes open new questions in fundamental computer science with respect to reversibility of computation and prediction (lookahead) of behaviors inherent within model codes. On the implementation front, there are relatively few scalable, general-purpose parallel discrete event simulators in the world, and even fewer have been studied on emerging hardware platforms. To enable scientific advances using PDES, the research needs in computer science must also be pursued and met in the intersection of the algorithmic and hardware-aware aspects of scalable PDES engines. This report is aimed at capturing a computer science-oriented view of this important area of research in PDES, presenting a sample of important applications with their inherent discrete event technology elements. Needs are outlined in core areas of parallel discrete event research as well as cross-cutting directions in computer science research that positively impact scientific advancements across several important application areas. A selection of priority research opportunities in advanced computing for PDES is identified to serve as reference for key research topics and their order of importance for scientific advancements.

97 MATHEMATICS AND COMPUTING↗

Development of an immersion fiber optic Raman probe for real-time analysis of molten materials

This study presents an advancement in high-temperature Raman spectroscopy, specifically for analyzing molten materials. It introduces an approach by integrating a fiber-optic Raman probe with a copper block protection system designed to endure extreme thermal conditions. The copper block features an open port designed to accommodate an external telescope with a 3 cm focal length, enabling Raman spectra collection in challenging high-temperature environments. A built-in gas channel ensures a continuous flow of argon gas to prevent flux intrusion. The robust copper block acts as a reliable shield, safeguarding the fiber-optic Raman probe within molten materials. This enhancement maintains the probe's integrity and significantly improves its resilience, making it ideal for rigorous investigations of molten substances. This advancement is particularly relevant in metallurgy, where flux materials impact production quality and efficiency. The ability to acquire Raman signals under elevated thermal conditions offers opportunities for studying molecular dynamics, compositional changes, and chemical interactions within molten substances. This introduced direct immersion probing technique has implications, benefiting both scientific and industrial fields. It holds promise for advancing research and exploration in various contexts, from fundamental scientific inquiries to practical applications in metallurgical processes, where flux materials are critical for optimizing production quality and efficiency. Furthermore, this approach enhances the capabilities of high-temperature Raman spectroscopy, making it a valuable tool for investigating molten materials and their properties in diverse settings.

Argon↗

Orchestration of materials science workflows for heterogeneous resources at large scale

In the era of big data, materials science workflows need to handle large-scale data distribution, storage, and computation. Any of these areas can become a performance bottleneck. We present a framework for analyzing internal material structures (e.g., cracks) to mitigate these bottlenecks. We demonstrate the effectiveness of our framework for a workflow performing synchrotron X-ray computed tomography reconstruction and segmentation of a silica-based structure. Our framework provides a cloud-based, cutting-edge solution to challenges such as growing intermediate and output data and heavy resource demands during image reconstruction and segmentation. Specifically, our framework efficiently manages data storage, scaling up compute resources on the cloud. The multi-layer software structure of our framework includes three layers. A top layer uses Jupyter notebooks and serves as the user interface. A middle layer uses Ansible for resource deployment and managing the execution environment. A low layer is dedicated to resource management and provides resource management and job scheduling on heterogeneous nodes (i.e., GPU and CPU). At the core of this layer, Kubernetes supports resource management, and Dask enables large-scale job scheduling for heterogeneous resources. The broader impact of our work is four-fold: through our framework, we hide the complexity of the cloud’s software stack to the user who otherwise is required to have expertise in cloud technologies; we manage job scheduling efficiently and in a scalable manner; we enable resource elasticity and workflow orchestration at a large scale; and we facilitate moving the study of nonporous structures, which has wide applications in engineering and scientific fields, to the cloud. While we demonstrate the capability of our framework for a specific materials science application, it can be adapted for other applications and domains because of its modular, multi-layer architecture.

97 MATHEMATICS AND COMPUTING↗

The Future of Computing: Integrating Scientific Computation on Neuromorphic Systems

Neuromorphic computing is known for its integration of algorithms and hardware elements that are inspired by the brain. Conventionally, this nontraditional method of computing is used for many neural or learning inspired applications. Unfortunately, this has resulted in the field of neuromorphic computing being relatively narrow in scope. In this paper we discuss two research areas actively trying to widen the impact of neuromorphic systems. The first is Fugu, a high-level programming interface designed to bridge the gap between general computer scientists and those who specialize in neuromorphic areas. The second aims to map classical scientific computing problems onto these frameworks through the example of random walks. This elucidates a class of scientific applications that are conducive to neuromorphic algorithms.

97 MATHEMATICS AND COMPUTING↗