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At least 595 records · Page 33

Early experiences evaluating the HPE/Cray ecosystem for AMD GPUs

Summary The Oak Ridge Leadership Computing Facility (OLCF) has a long history of supporting and promoting GPU‐accelerated computing starting with the deployment of the Titan supercomputer in 2021 and continuing with the Summit supercomputer which has a theoretical peak performance of approximately 200 petaflops. Because the majority of Summit's computational power comes from its 27,972 GPUs, users must port their applications to one of the supported programming models in order to make efficient use of the system. To prepare the transition to Frontier, the OLCF's exascale supercomputer, users will need to adapt to an entirely new ecosystem which will include new hardware and software technologies. First, users will need to familiarize themselves with the AMD Radeon GPU architecture. Furthermore, users who have been previously relying on CUDA will need to transition to the Heterogeneous‐Computing Interface for Portability (HIP) or one of the other supported programming models (e.g., OpenMP, OpenACC). In this work, we describe our initial experiences and lessons learned in porting three applications or proxy apps currently running on Summit to the HPE/Cray ecosystem to leverage the compute power from AMD GPUs: minisweep, GenASiS, and Sparkler. Each one is representative of current production workloads utilized at the OLCF, different programming languages, and different programming models.

Melesse Vergara, Verónica G.↗

Biocatalytic Carboxylic Acid Reduction and Transamination in Cell‐Free Lysates at High Substrate Loading

Chemoselective reduction of stable carboxylic acids to reactive aldehydes is of interest across many industries. While carboxylic acid reductases (CARs) are promising biocatalysts for this chemistry, poor chemoselectivity and low yield are commonly obtained when using less expensive crude lysate preparations and prerequisite ATP and NADPH regeneration systems. Here, in this work, we developed a highly chemoselective multienzyme cascade featuring a CAR and an ω-transaminase (TA) in crude lysate format, with conversion of the dicarboxylic acid terephthalic acid (TPA) into the diamine para -xylylenediamine (pXDA) as the model chemistry. We improved chemoselectivity for pXDA using engineered aldehyde-stabilizing Escherichia coli strains, though desired product yields remained modest. We next found that CAR activity was limited at high substrate loadings and overcame this bottleneck by modulating the ratio of polyphosphate (polyP 6 ) to Mg 2+ , enabling volumetric scaling and increased substrate loading up to 50 mM TPA. We then showcased the portability of this platform across substrates, resulting in the synthesis of four other high-value amines from carboxylate precursors. The combination of high carboxyl group turnover, up to 93.5 mM under the tested conditions, and the simplicity of crude enzyme preparation is a promising platform for sustainable functional group interconversion.

60 APPLIED LIFE SCIENCES↗

In Situ/Operando (Soft) X-ray Spectroscopy Study of Beyond Lithium-ion Batteries

The lightweight, rechargeable lithium-ion battery is one of the dominant energy storage devices globally in portable electronics due to its high energy density, no memory effect, wide operating voltage, lightweight, and good charge efficiency. However, due to safety concerns, the depletion of lithium reserves, and the corresponding increase of cost, an alternative battery system becomes more and more desirable. To develop alternative battery systems with low cost and high material abundance, for example, sodium, magnesium, zinc, and calcium, it is important to understand the chemical and electronic structure of materials. Additionally, soft X-ray spectroscopy, for example, X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy (XES), and resonant inelastic soft X-ray scattering (RIXS), is an element-specific technique with sensitivity to the local chemical environment and structural order of the element of interest. Modern soft X-ray systems enable operando experiments that can be applied to amorphous and crystalline samples, making it a powerful tool for studying the electronic and structural changes in electrode and electrolyte species. In this article, the application of in situ/operando (soft) X-ray spectroscopy in beyond lithium-ion batteries is reviewed to demonstrate how such spectroscopic characterizations could facilitate the interpretation of interfacial phenomena under in situ/operando condition and subsequent development of the beyond lithium-ion batteries.

(soft) X-ray spectroscopy↗

Systems Theory Principles and Complex Systems Engineering Concepts for Protection and Resilience in Critical Infrastructure: Lessons from the Nuclear Sector

Part of the Presidential Policy Directive 21 (PPD-21) (PPD 2013) mandate includes evaluating safety, security, and safeguards (or nonproliferation) mechanisms traditionally implemented within the nuclear reactors, materials, and waste sector of critical infrastructure—including a complex, dynamic set of risks and threats within an all-hazards approach. In response, research out of Sandia National Laboratories (Sandia) explores the ability of systems theory principles (hierarchy and emergence) and complex systems engineering concepts (multidomain interdependence) to better understand and address these risks and threats. Herein, this Sandia research explores the safety, safeguards, and security risks of three different nuclear sector-related activities—spent nuclear fuel transportation, small modular reactors, and portable nuclear power reactors—to investigate the complex and dynamic risk related to the PPD-21-mandated all-hazards approach. This research showed that a systems-theoretic approach can better identify inter-dependencies, conflicts, gaps, and leverage points across traditional safety, security, and safeguards hazard mitigation strategies in the nuclear reactors, materials, and waste sector. Resulting from this, mitigation strategies from applying systems theoretic principles and complex systems engineering concepts can be (1) designed to better capture interdependencies, (2) implemented to better align with real-world operational uncertainties, and (3) evaluated as a systems-level whole to better identify, characterize, and manage PPD-21's all hazards strategies.

42 ENGINEERING↗

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Abstract Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far‐reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1–4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant‐based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid‐response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non‐invasive imaging, sensors, and plug‐and‐play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence‐assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.

59 BASIC BIOLOGICAL SCIENCES↗

Injection Locking of Gigahertz‐Frequency Surface Acoustic Wave Phononic Crystal Oscillator

Low-noise gigahertz (GHz) frequency sources are essential for applications in signal processing, sensing, and telecommunications. Surface acoustic wave (SAW) resonator-based oscillators offer compact form factors and low-phase noise due to their short mechanical wavelengths and high-quality (Q) factors. However, their small footprint makes them vulnerable to environmental variation, resulting in their poor long-term frequency stability. Injection locking is widely used to suppress frequency drift of lasers and oscillators by synchronizing to an ultra-stable reference. Here, injection locking of a 1-GHz SAW phononic-crystal oscillator is demonstrated, achieving 40-dB phase noise reduction at low offset frequencies and unperturbed low noise at large offset frequencies. Compared to a free-running SAW oscillator, which typically exhibits frequency drifts of several hundred hertz over minutes, the injection-locked oscillator reduces the frequency deviation to below 0.35 Hz. The locking range and oscillator dynamics is also investigated in the injection pulling region. The demonstrated injection-locked SAW oscillator could find applications in high-performance portable telecommunications and sensing systems.

injection locking↗

3D LiMn 2 O 4 nThin Film Deposited by ALD: A Road toward High-Capacity Electrode for 3D Li-Ion Microbatteries

Miniaturized electronics suffer from a lack of energy autonomy. In that context, the fabrication of lithium-ion solid-state microbatteries with high performance is mandatory for powering the next generation of portable electronic devices. Here, the fabrication of a thin film positive electrode for 3D Li-ion microbatteries made by the atomic layer deposition (ALD) method and in situ lithiation step is demonstrated. The 3D electrodes based on spinel LiMn 2 O 4 films operate at high working potential (4.1 V vs Li/Li + ) and are capable of delivering a remarkable surface capacity (approximate to 180 mu Ah cm -2 ) at low C-rate while maintaining more than 40 mu Ah cm -2 at C/2 (time constant = 2 h). Both the thickness of the electrode material and the 3D gain of the template are carefully tuned to maximize the electrode performance. Further, advanced characterization techniques such as transmission electron and X-ray transmission microscopies are proposed as perfect tools to study the conformality of the deposited films and the interfaces between each layer: no interdiffusion or segregation are observed. This work represents a major issue towards the fabrication of 3D-lithiated electrode by ALD-without any prelithiation step by electrochemical technique-making it an attractive solution for the fabrication of 3D Li-ion solid-state microbatteries with semiconductor processing methods.

3D Li-ion micro-batteries↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sparse Matrix-Based HPC Tomography

Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster frame rates, larger fields of view or higher resolution, so high performance solutions are currently widely used for analysis. Tomographic instruments can vary significantly from one to another, including the hardware employed for reconstruction: from single CPU workstations to large scale hybrid CPU/GPU supercomputers. Furthermore, flexibility on the software interfaces and reconstruction engines are also highly valued to allow for easy development and prototyping. This paper presents a novel software framework for tomographic analysis that tackles all aforementioned requirements. The proposed solution capitalizes on the increased performance of sparse matrix-vector multiplication and exploits multi-CPU and GPU reconstruction over MPI. Furthermore, the solution is implemented in Python and relies on CuPy for fast GPU operators and CUDA kernel integration, and on SciPy for CPU sparse matrix computation. As opposed to previous tomography solutions that are tailor-made for specific use cases or hardware, the proposed software is designed to provide flexible, portable and high-performance operators that can be used for continuous integration at different production environments, but also for prototyping new experimental settings or for algorithmic development. The experimental results demonstrate how our implementation can even outperform state-of-the-art software packages used at advanced X-ray sources worldwide.

97 MATHEMATICS AND COMPUTING↗

The Kokkos OpenMPTarget Backend: Implementation and Lessons Learned

As the supercomputing landscape diversifies, solutions such as Kokkos to write vendor agnostic applications and libraries have risen in popularity. Kokkos provides a programming model designed for performance portability, which allows developers to write a single source implementation that can run efficiently on various architectures. At its heart, Kokkos maps parallel algorithms to architecture and vendor specific backends written in lower level programming models such as CUDA and HIP. Another approach to writing vendor agnostic parallel code is using OpenMP’s directives based approach, which lets developers annotate code to express parallelism. It is implemented at the compiler level and is supported by all major high performance computing vendors, as well as the primary Open Source toolchains GNU and LLVM. Since its inception, Kokkos has used OpenMP to parallelize on CPU architectures. In this paper, we explore leveraging OpenMP for a GPU backend and discuss the challenges we encountered when mapping the Kokkos APIs and semantics to OpenMP target constructs. As an exemplar workload we chose a simple conjugate gradient solver for sparse matrices. We find that performance on NVIDIA and AMD GPUs varies widely based on details of the implementation strategy and the chosen compiler. Furthermore, the performance of the OpenMP implementations decreases with increasing complexity of the investigated algorithms.

Gayatri, Rahulkumar↗

A Segregated Approach for Modeling the Electrochemistry in the 3-D Microstructure of Li-Ion Batteries and Its Acceleration Using Block Preconditioners

Abstract Battery performance is strongly correlated with electrode microstructure. Electrode materials for lithium-ion batteries have complex microstructure geometries that require millions of degrees of freedom to solve the electrochemical system at the microstructure scale. A fast-iterative solver with an appropriate preconditioner is then required to simulate large representative volume in a reasonable time. In this work, a finite element electrochemical model is developed to resolve the concentration and potential within the electrode active materials and the electrolyte domains at the microstructure scale, with an emphasis on numerical stability and scaling performances. The block Gauss-Seidel (BGS) numerical method is implemented because the system of equations within the electrodes is coupled only through the nonlinear Butler–Volmer equation, which governs the electrochemical reaction at the interface between the domains. The best solution strategy found in this work consists of splitting the system into two blocks—one for the concentration and one for the potential field—and then performing block generalized minimal residual preconditioned with algebraic multigrid, using the FEniCS and the Portable, Extensible Toolkit for Scientific Computation libraries. Significant improvements in terms of time to solution (six times faster) and memory usage (halving) are achieved compared with the MUltifrontal Massively Parallel sparse direct Solver. Additionally, BGS experiences decent strong parallel scaling within the electrode domains. Last, the system of equations is modified to specifically address numerical instability induced by electrolyte depletion, which is particularly valuable for simulating fast-charge scenarios relevant for automotive application.

25 ENERGY STORAGE↗

Small scale electron linear accelerators for industrial applications

Linear accelerators (linacs), producing electron or X-ray radiation in the MeV range, are critical tools for industrial irradiation, medical device sterilization, food pasteurization, non-destructive testing, security, medical, and many other applications. Many of these applications require compact and flexible radiation sources. In this paper, we present new technologies for small-scale electron linear accelerators and examples of their practical implementations. Furthermore, these developments include low energy accelerators with self-shielding options and form factors, ranging from cabinet-size to hand-portable generators; medium-energy accelerators for novel radiotherapy and security applications; and high-energy 10 MeV linacs capable of reaching 20–35 kW beam power for emerging industrial and phytosanitary applications

43 PARTICLE ACCELERATORS↗

Metal concentration and leaf spatial distribution assessed by synchrotron µXRF in Brazilian nickel hyperaccumulators

Background and Aims: The limited number of known hyperaccumulator species in tropical regions, including Brazil, has hampered the development of nickel (Ni) agromining. In addition, the mechanisms underlying metal accumulation and distribution in these species remain poorly understood, despite their pivotal role in identifying species with economic potential. Furthermore, this study assessed the accumulation potential and foliar spatial distribution of metals in three Brazilian hyperaccumulator species (Pfaffia sarcophylla, Justicia lanstyakii, and Lippia lupulina) growing in one of the world’s largest mafic–ultramafic complexes. Methods Concentrations of Ni and other metals in leaves were determined using portable X-ray fluorescence (pXRF) and inductively coupled plasma optical emission spectroscopy (ICP-OES). Synchrotron-based X-ray microfluorescence (SR-µXRF) was employed to map the spatial distribution of metals across intact leaves. Results: The results revealed leaf Ni concentrations ranging from 320 to 1,950 mg kg⁻ 1 in P. sarcophylla, 1,640 to 6,810 mg kg⁻ 1 in L. lupulina, and 1,990 to 4,900 mg kg⁻ 1 in J. lanstyakii. Nickel, Mn, and Co exhibited similar distribution patterns, concentrating mainly in the leaf margins and veins across all species, while Ca, K, and Mg co-localization suggests regulatory mechanisms for adaptation. Conclusion: Although these plants exhibited Ni hyperaccumulation, our findings suggest limited commercial potential for agromining. Further research on genetic variability and nutrient assimilation, particularly in P. sarcophylla, is recommended to elucidate the mechanisms underlying Ni accumulation and intraspecific variability.

36 MATERIALS SCIENCE↗

Platinum and Palladium Monolayer Electrocatalysts for Formic Acid Oxidation

The direct formic acid fuel cell holds great promise as a next generation portable power source. In this paper we report an experimental study on Pt and Pd monolayer (Pt* and Pd*) atop the close-packed facet of transition metal substrates (denoted Pt*/M or Pd*/M, where M = Pt, Pd, Ir, Au, Rh and Ru) model catalysts for formic acid oxidation (FAO) and demonstrate a promotional effect on Pt*/Au(111) and Pd*/Pt(111) surfaces. Contrary to findings on monometallic surfaces, in situ infrared reflection adsorption spectroscopy collected during formic acid oxidation at potentials anodic of 375 mV reveal that the poisoning reaction intermediate CO is not formed on the monolayer surfaces, suggesting a promotion of the direct mechanisms of FAO at the expense of the indirect mechanism through CO. Our density functional theory calculations on model surfaces with 1:1 stoichiometry for overlayer to support metal atoms for the thermochemistry of the elementary steps defined by adsorbed CO, OH, COOH, and HCOO on the (111) facet of Pt, PtML/Au, Pd, and PdML/Pt largely attribute the promotional effect observed for the monolayer catalysts to easier removal of CO brought about by easier activation of water, relative to the monometallic catalysts. This synergy between experiments and theory brings us closer to a fundamental understanding of FAO electrocatalysts under reaction conditions, paving the way to achieving more active electrocatalysts possibly with less Pt or Pd; a pre-requisite for the mass commercialization of this technology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Catalysis Process Development for Hydrogen Storage/Generation with LOHCs

The hydrogen as green energy carrier is an envisioned future. Hydrogen storage is a key enabling technology for the advancement of hydrogen and fuel cell technologies in applications including stationary power, portable power, and transportation. Hydrogen has the highest energy per mass of any fuel; however, its low ambient temperature density results in a low energy per unit volume, therefore requiring the development of advanced storage methods that have potential for higher energy density.

08 HYDROGEN↗

Using yttrium as an indicator to estimate total rare earth element concentration: a case study of anthracite-associated clays from northeastern Pennsylvania

Abstract This study demonstrated using yttrium (Y) as an indicator to estimate the total rare earth element and Y contents (REY) in coal-associated samples and to facilitate selection of samples with high REY assays in a fast and inexpensive manner. More than 10 anthracite-associated samples were collected from each of three Pennsylvanian sites (sites B, J and C) based on Thorium gamma ray logging suggesting high REY content. Several samples from each site were analyzed by ICP-MS to determine the rare earth distribution patterns and to establish the site-specific linear equations of Y and REY. The Y contents of the remaining samples were measured by a portable X-ray fluorescence analyzer, and the REY values were estimated based on the site-specific linear equation developed earlier. R-squared values above 0.70 were obtained for all the estimation equations from all three sites on both a whole sample basis and an ash basis. Previously, ash content has been widely used as an indicator of high REY content. This may not be applicable for a specific site. Site B in this study is an example where ash contents could not be statistically correlated with REY, so using Y for estimation is more applicable. The demonstrated sample screening process is suitable for samples from sites that share more similar distribution patterns (either MREY or LREY or HREY) as well as for samples from sites that share multiple distribution patterns (LREY/MREY/HREY) depending on the desirable accuracy. The demonstrated process lowers the analytical cost from $70 to 80 dollars per sample to $10–15 per sample while significantly reducing the processing time and acid consumption for ICP digestion. This is particularly true when a relatively large sample size is involved, for example, 100 samples from one site analyzed by ICP-MS/OES.

Yang, Xiaojing↗

Machine learning for arbitrary single-qubit rotations on an embedded device

Here, in this study, we present a technique for using machine learning (ML) for single-qubit gate synthesis on field-programmable logic for a superconducting transmon-based quantum computer based on simulated studies. Our approach is multi-stage. We first “bootstrap” a model based on simulation with access to the full state vector for measuring gate fidelity. We next present an algorithm, named adapted randomized benchmarking (ARB), for fine-tuning the gate on hardware based on measurements of the devices. We also present techniques for deploying the model on programmable devices with care to reduce the required resources. While the techniques here are applied to a transmon-based computer, many of them are portable to other architectures.

97 MATHEMATICS AND COMPUTING↗

Progress of Nanotechnology for Lithium-Sulfur Batteries

Lithium-Sulfur (Li-S) battery has been proposed and investigated since the 1960s as an effective energy storage device via reversible electrochemical reactions. As the fast development and commercialization of Li-ion battery (LIB) technology kept moving forward, no breakthroughs have been attained to solve critical technical issues facing Li-S batteries during the following decades. In the year 2000s, Li-S batteries reattracted significant interests in the research field owing to their low-cost advantages, high theoretical specific energy of 2600 Wh kg -1 , which is at least 3 times higher than the current LIB technology. The low-cost and high abundance of sulfur (i.e., the cathode active material), make Li-S batteries more appealing than LIBs given the fact that the latter use critical materials such as cobalt and nickel in the manufacturing of the cathodes. Moreover, the high-energy and low-cost features make the Li-S battery a promising energy storage technology in practical applications such as portable devices, electric vehicles, and grid storage when coupled with the harvesting of solar or wind renewable energies. For example, since 2007, SION Power Corporation (Tucson, USA) and Oxis Energy (UK) made progress towards the commercialization of Li-S batteries with products showing specific energies over 350 Wh kg -1 for powering electric vehicles. To be on a par with the current LIB technology, the ultimate goal of achieving 500 Wh kg -1 for Li-S battery will make it more competitive for widespread commercialization.

Li, Mengya↗