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DOE OSTI2022

The SODA Approach: Leveraging High-Level Synthesis for Hardware/Software Co-design and Hardware Specialization: Invited

Novel "converged" applications combine phases of scientific simulation with data analysis and machine learning. Each computational phase can benefit from specialized accelerators. However, algorithms evolve so quickly that mapping them on existing accelerators is suboptimal or even impossible. This paper presents the SODA (Software Defined Accelerators) framework, a modular, multi-level, open-source, no-human-in-the-loop, hardware synthesizer that enables end-to-end generation of specialized accelerators. SODA is composed of SODA-Opt, a high-level frontend developed in MLIR that interfaces with domain-specific programming frameworks and allows performing system level design, and Bambu, a state-of-the-art high-level synthesis engine that can target different device technologies. The framework implements design space exploration as compiler optimization passes. We show how the modular, yet tight, integration of the high-level optimizer and lower-level HLS tools enables the generation of accelerators optimized for the computational patterns of converged applications. We then discuss some of the research opportunities that such a framework allows, including system-level design, profile driven optimization, and supporting new optimization metrics.

Bohm Agostini, Nicolas↗

DOE OSTI2022

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Abstract Background The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. Results Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae , Candidatus Thioglobaceae , Metamycoplasmataceae , unclassified Pseudomonadales , Rhodobacteraceae , unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae . Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae . Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae , may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae , which lack such capacity. Conclusion This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae , Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

PORFLOW Implementation of Special Waste from Models for Slit and Engineered Trenches in the E-Area Low Level Waste Facility Performance Assessment

The implementation of special waste forms (SWFs) in the deterministic PORFLOW Slit Trench (ST) and Engineered Trench (ET) models to be used in the next revision of the E-Area Low Level Waste Facility’s (ELLWFs) Performance Assessment (PA) is outlined in this report. Four SWF implementation methods will be used: effective K d , delayed release, solubility-controlled/diffusion-controlled release, and complex SWF model updates. In addition, the implementation of models that address the presence of tall used equipment storage boxes in ST08-10 is considered a special waste form and will be described.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Soil Sample Plan in Support of the Site 300 Explosives Waste Treatment Facility Ecological Risk Assessment Pursuant to the Hazardous Waste Facility Permit, Part V, Special Condition #14 a-f. August 2020

The Department of Toxic Substances Control issued the Final Hazardous Waste Facility Permit to Lawrence Livermore National Laboratory, Site 300 in 2017. As part of the continual process to ensure waste treatment emissions are not impacting ecological receptors, LLNL analyzed soil samples in the vicinity of the Explosive Waste Treatment Facility (EWTF) Burn Units (i.e., Burn Cage and Burn Pan) and the Detonation Pad. Soil samples were analyzed by EPA Solid Waste 846 Methods for furans, explosives, metals, and semivolatile compounds. In all samples, furans, explosives, and semi-volatile organic compounds were not detected. Metals were detected at concentrations below background levels. This soil sample plan will sample the same four downwind areas of the Burn Units and the same downwind areas of the Detonation, as well as including four new sample locations. The four new locations will be located to the northeast and southwest of the Burn Units and Detonation (as shown in Figure 3). The constituents to be analyzed are in Tables 2 and 3. Perchlorate was not identified as a constituent of concern in the 2007 Soil Sampling Plan. However, for this plan, all soil samples will be analyzed for perchlorate. After completion of the sampling event, a soil sample report will be submitted to DTSC in accordance with requirements specified in the Hazardous Waste Facility Permit, Part V, Special Conditions 16 a-f. This proposed soil sampling plan will be fully implemented no later than one year after receiving DTSC approval, in accordance with the Hazardous Waste Facility Permit, Part V, Special Condition 15.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Soil Sample Workplan in Support of the Site 300 Explosives Waste Treatment Facility Ecological Risk Assessment Pursuant to the Hazardous Waste Facility Permit (Part V, Special Condition #14 a-f)

The Department of Toxic Substances Control issued the Final Hazardous Waste Facility Permit to Lawrence Livermore National Laboratory, Site 300 in 2017. As part of the continual process to ensure waste treatment emissions are not impacting ecological receptors, LLNL analyzed soil samples in the vicinity of the Explosive Waste Treatment Facility (EWTF) Burn Units (i.e., Burn Cage and Burn Pan) and the Detonation Pad. Soil samples were analyzed by EPA Solid Waste 846 Methods for furans, explosives, metals, and semi-volatile compounds. In all samples, furans, explosives, and semi-volatile organic compounds were not detected. Metals were detected at concentrations below background levels. This soil sample plan will sample the same four downwind areas of the Burn Units and the same downwind areas of the Detonation, as well as including four new sample locations. The four new locations will be located to the northeast and southwest of the Burn Units and Detonation (as shown in Figure 3). The constituents to be analyzed are in Tables 7 and 8. Perchlorate was not identified as a constituent of concern in the 2007 Soil Sampling Plan. However, for this plan, all soil samples will be analyzed for perchlorate. Nitrate and all CAM17 metals have been added to the sampling plan to comply with DTSC comments received in correspondence dated June 4, 2021. After completion of the sampling event, a soil sample report will be submitted to DTSC in accordance with requirements specified in the Hazardous Waste Facility Permit, Part V, Special Conditions 16 a-f. This proposed soil sampling plan will be fully implemented no later than one year after receiving DTSC approval, in accordance with the Hazardous Waste Facility Permit, Part V, Special Condition 15.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2022

Traditional Forensic Examinations on Bulk Special Nuclear Material

The Federal Bureau of Investigation (FBI) Laboratory at Quantico, Virginia is responsible for the forensic examination of radiological evidence and evidence contaminated with radioactive materials. Due to these unique hazards and the necessary specialized safety protocols, the FBI has developed a network of Partner Laboratories (PLs) across the United States of America to support conventional forensic examinations of radiological evidence and evidence contaminated with radioactive materials. In support of this, the FBI Laboratory has established the Hazardous Evidence Analysis Team (HEAT), a group of qualified forensic examiners, scientists, technicians, and photographers who can deploy to laboratories outside of the FBI Laboratory at Quantico, VA to perform conventional forensics on evidence containing/contaminated with hazardous materials. One of the FBI’s PLs, the United States Department of Energy’s Los Alamos National Laboratory (LANL), in Los Alamos, New Mexico, has unique facilities, personnel, and procedures to secure, safely handle, and process significant quantities of special nuclear material (SNM). While LANL’s procedures for working with SNM are well established, working with SNM under evidentiary controls is not. Close cooperation between LANL and FBI HEAT is required due to FBI policies on evidence handling, as well as the challenges associated with the exploitation and preservation of conventional forensics (fingerprints, trace evidence, and photography) on SNM evidence.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2021

Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Special Issue: 10th Anniversary of Atmosphere: Climatology and Meteorology

During the last decade, the number of open access science journals has increased, and these have become an avenue for publishing quality science in a relatively fast and economical way. The Multidisciplinary Digital Publishing Institute (MDPI) journal Atmosphere published its first volume in 2010, and recently celebrated 10 years with the publication of this special commemorative issue. Atmosphere is a peer reviewed, open access journal described as cross disciplinary. Furthermore, the journal attracts authorship from across the globe. During the first few years, the regular issue of Atmosphere was a quarterly publication, but, by 2019, was issued each month. Furthermore, the journal publishes research articles and notes, communications, review articles, and case studies, as well as timely Special Issues.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

A Unified Perspective on Poincaré and Galilei Relativity: I. Special Relativity

A semantic adjustment to what physicists mean by the terms ‘special relativity’ and ‘general relativity’ is suggested, which prompts a conceptual shift to a more unified perspective on physics governed by the Poincaré group and physics governed by the Galilei group. After exploring the limits of a unified perspective available in the setting of 4-dimensional spacetime, a particular central extension of the Poincaré group—analogous to the Bargmann group that is a central extension of the Galilei group—is presented that deepens a unified perspective on Poincaré and Galilei physics in a 5-dimensional spacetime setting. The immediate focus of this paper is classical physics on affine 4-dimensional and 5-dimensional spacetimes (‘special relativity’ as redefined here), including the electrodynamics that gave rise to Poincaré physics in the first place, but the results here may suggest the existence of a ‘Galilei general relativity’ more extensive than generally known, to be pursued in the sequel.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Entity—Hardware-agnostic Particle-in-cell Code for Plasma Astrophysics. I. Curvilinear Special Relativistic Module

Entity is a new-generation, fully open-source particle-in-cell (PIC) code developed to overcome key limitations in astrophysical plasma modeling, particularly the extreme separation of scales and the performance challenges associated with evolving, GPU-centric computing infrastructures. It achieves hardware-agnostic performance portability across various GPU and CPU architectures using the Kokkos library. Crucially, Entity maintains a high standard for usability, clarity, and customizability, offering a robust and easy-to-use framework for developing new algorithms and grid geometries, which allows extensive control without requiring edits to the core source code. This paper details the core general-coordinate special relativistic module. Entity is the first PIC code designed to solve the Vlasov–Maxwell system in general coordinates, enabling a coordinate-agnostic framework that provides the foundational structure for straightforward extension to arbitrary coordinate geometries. The core methodology achieves numerical stability by solving particle equations of motion in the global orthonormal Cartesian basis, despite using generalized coordinates like Cartesian, axisymmetric spherical, and quasi-spherical grids. Charge conservation is ensured via a specialized current deposition technique using conformal currents. The code exhibits robust scalability and performance portability on major GPU platforms (AMD MI250X, NVIDIA A100, and Intel Max Series), with the 3D particle pusher and the current deposition operating efficiently at about 2 ns per particle per time step. Functionality is validated through a comprehensive suite of standard Cartesian plasma tests and the accurate modeling of relativistic magnetospheres in curvilinear axisymmetric geometries.

Hakobyan, Hayk [Flatiron Institute, New York, NY (↗

NASA NTRS1961

Structural and High-Temperature Tensile Properties of Special Pitch-Coke Graphites

The room-temperature structural properties and the tensile properties up to 5000 F (275O C) were determined for ten grades of specially prepared petroleum-coke coal-tar-pitch graphites which were graphitized at 5430 F (3000 C). One impregnation with coal-tar pitch increased the bulk density from 1.41 to 1.57 g/cm3 and the maximum strength at 4500 F (2500 C) from 4000 to 5700 psi. None of the processing parameters studied had a marked effect on the closed porosity or the X-ray structure or the per cent graphitization. The coarse-particle filler resulted in the lowest coefficient of thermal expansion and the fine-particle filler in the highest coefficient. A marked improvement in uniformity of tensile strength was observed. A standard-deviation analysis gave a one-sigma value of approximately 150 psi for one of these special grades and values of 340-420 psi for three commercial grades.

GRAPHITE↗

NASA NTRS1964

Codes with special correlation.

Uniform binary codes with special correlation including transorthogonality and simplex code, Hadamard matrices and difference sets uniform binary codes with special correlation including transorthogonality and simplex code, Hadamard matrices and difference sets

AUTOCORRELATION↗

NASA NTRS1975

S-192 analysis: Conventional and special data processing techniques

The author has identified the following significant results. Multispectral scanner data gathered over test sites in southeast Michigan were analyzed. This analysis showed the data to be somewhat deficient especially in terms of the limited signal range in most SDOs and also in regard to SDO-SDO misregistration. Further analysis showed that the scan line straightening algorithm increased the misregistration of the data. Data were processed using the conic format. The effects of such misregistration on classification accuracy was analyzed via simulation and found to be significant. Results of employing conventional as well as special, unresolved object, processing techniques were disappointing due, at least in part, to the limited signal range and noise content of the data. Application of a second class of special processing techniques, signature extension techniques, yielded better results. Two of the more basic signature extension techniques seemed to be useful in spite of the difficulties.

Nalepka, R. F.↗

NASA NTRS1977

Symbolic Laplace transforms of special functions

A MACSYMA implementation of the Laplace transform for special functions is described. The generalized hypergeometric functions are used as a basis for the representation of approximately fifty special functions. Only a relatively small number of formulas that generally involve generalized hypergeometric functions are utilized for the integration stage. A sample of actual examples and their timing is provided.

Avgoustis, Y.↗

NASA NTRS1978

Specialized computer architectures for computational aerodynamics

In recent years, computational fluid dynamics has made significant progress in modelling aerodynamic phenomena. Currently, one of the major barriers to future development lies in the compute-intensive nature of the numerical formulations and the relative high cost of performing these computations on commercially available general purpose computers, a cost high with respect to dollar expenditure and/or elapsed time. Today's computing technology will support a program designed to create specialized computing facilities to be dedicated to the important problems of computational aerodynamics. One of the still unresolved questions is the organization of the computing components in such a facility. The characteristics of fluid dynamic problems which will have significant impact on the choice of computer architecture for a specialized facility are reviewed.

Stevenson, D. K.↗

NASA NTRS1978

A Special Purpose Architecture for Finite Element Analysis

The analysis of aerospace structures by the finite element method consumes considerable computer time. The cost of this resource and the designer's desire to have rapid feedback concerning such questions as the effect of a change in loading of the structure or in a parameter of some structural material led to the design of a special purpose parallel computing system for finite element analysis. As a special purpose computer, the architecture of this finite element computer is closely tied to computational aspects of the particular problem. Various aspects of an MIMD array of microprocessors are related to the requirements of the class of finite element analysis problems which it is intended to solve.

Jordan, H. F.↗

NASA NTRS1979

Problems in processing multizonal video information at specialized complexes

Architectural requirements of a minicomputer-based specialized complex for automated digital analysis of multizonal video data are examined. The logic structure of multizonal video data and the complex mathematical provision required for the analysis of such data are described. The composition of the specialized complex, its operating system, and the required set of peripheral devices are discussed. It is noted that although much of the analysis can be automated, the operator-computer dialog mode is essential for certain stages of the analysis.

Shamis, V. A.↗

NASA NTRS1981

Special activity utilization of GDSCC antennas during 1980

In addition to direct spacecraft project support, the GDSCC antennas also support special activities. These activities can be categorized as advanced system program, crustal dynamics program, and radio astronomy program activities. The goals of these types of activities that received tracking support at Goldstone are discussed. All Goldstone stations (DSSs 11, 12, 13, and 14) provided a total of 2814.5 tracking hours to special activities during the period January through December 1980.

Jackson, E. B.↗