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DOE OSTI2024

MDLoader: A Hybrid Model-Driven Data Loader for Distributed Graph Neural Network Training

Scalable data management is essential for processing large scientific dataset on HPC platforms for distributed deep learning. In-memory distributed storage is preferred for its speed, enabling rapid, random, and frequent data access required by stochastic optimizers. Processes use one-sided or collective communication to fetch remote data, with optimal performance depending on (i) dataset characteristics, (ii) training scale, and (iii) interconnection network. Empirical analysis shows collective communication excels with larger mini-batch sizes and/or fewer processes, whereas one-sided communication outperforms at larger scales. We propose MDLoader, a hybrid in-memory data loader for distributed graph neural network training. MDLoader features a model-driven performance estimator that dynamically selects between one-sided and collective communication at the beginning of training using Tree of Parzen Estimators (TPE). Evaluations on NERSC Perlmutter and OLCF Summit show MDLoader outperforms single-backend loaders by up to 2.83 × and predicts the suitable communication method with 96.3% (Perlmutter) and 94.3% (Summit) success rate.

Bae, Jonghyun↗

DOE OSTI2024

An Experimental Setup for Mechanical Vibration Analysis Using VLC

This study explores the potential applications across various domains, including earthquake detection and warning systems, where the system’s sensitivity to ground vibrations can contribute to early seismic event detection. Additionally, the study paves the way of developing applications of VLC/T in mechanical vibration and stability analysis of engines and platforms, offering insights into structural integrity and performance optimization. These multifaceted applications underscore the adaptability and potential of VLC/T systems in diverse fields, heralding advancements in sensing, communication, and security technologies. To achieve this, in this study, Peak to Average Power Ratio (PAPR) is proposed to represent the impact of mechanical shocks and vibrations generated by several weights dropped onto the platform with which the receiver is fixed. Even though non-contact measurement methodology is preferred for various reasons, the proposed measurement campaign obtains the data in contact form; however, the system and signal model proposed in this study could easily be extended into non-contact form. Considering the fact that the proposed measurement campaign employs off-the-shelf products, it is cost-effective and very scalable.

Yilmaz, Ahmet Mucahit↗

DOE OSTI2020

PredCom: A Predictive Approach to Collecting Approximated Communication Traces

Communication traces collected from MPI applications are an important source of information for performance optimization as they can help analysts determine communication patterns and identify inefficiencies. However, their collection, especially at scale, is time consuming, since it usually requires running the complete target application on a large number of nodes. In this work, we present PredCom, a tool-chain to generate a predictive communication proxy based on information gathered from a few small scale runs, which allows us to extract approximate communication traces with an accuracy high enough for most analysis goals. For this, we combine LLVM passes on the original source code (to capture static program structure) with parameter prediction (to capture dynamic and scaling behavior). This approach drastically reduces the time needed for collecting the communication traces, even for traces on large numbers of MPI processes. Here, we demonstrate that PredCom generates communication traces of various applications up to 1612x faster with an accuracy loss of 0.11 on average compared to the original large-scale traces, and we show that the generated traces can be used to optimize process placement.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Memory-Aware External Facelist Calculation: A Data-Parallel Atomic Hash Counting Approach

Unstructured volumetric meshes serve as fundamental data representations in various scientific simulations and analyses. They play a crucial role in representing complex computational domains and are essential for important numerical techniques, such as finite element analysis. Whenever such a mesh is read from a file, streamed in-situ, or generated by algorithms, scientific visualization libraries rely on calculating the external surface of a geometry, named “external facelist”, to produce a polygonal mesh for rendering. Consequently, external facelist calculation has become one of the most widely used algorithms in the scientific visualization domain, necessitating optimal performance. In this paper, we explore relevant work on external facelist calculation algorithms in two common visualization libraries, VTK and Viskores, assess their performance and memory constraints, and introduce a novel memory-aware external facelist calculation algorithm employing an atomic hash counting approach. This algorithm fully leverages Viskores' data-parallel primitive operations, facilitating its execution across diverse many-core architectures. Our algorithm features the lowest memory footprint on the GPU and the second-lowest on the CPU among all evaluated methods, and it also delivers the fastest performance on both CPU and GPU. It has been made available under an open-source license in the VTK and Viskores visualization systems.

Tsalikis, Spiros [Kitware] (ORCID:0000000151137195↗

DOE OSTI2021

Integrating continuous hypermutation with high–throughput screening for optimization of cis,cis –muconic acid production in yeast

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Strangers in a foreign land: ‘Yeastizing’ plant enzymes

Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Using Machine Learning Tools to Predict Compressor Stall

Clean energy has become an increasingly important consideration in today’s power systems. As the push for clean energy continues, many coal-fired power plants are being decommissioned in favor of renewable power sources such as wind and solar. However, the intermittent nature of renewables means that dynamic load following traditional power systems is crucial to grid stability. With high flexibility and fast response at a wide range of operating conditions, gas turbine systems are poised to become the main load following component in the power grid. Yet, rapid changes in load can lead to fluid flow instabilities in gas turbine power systems. These instabilities often lead to compressor surge and stall, which are some of the most critical problems facing the safe and efficient operation of compressors in turbomachinery today. Although the topic of compressor surge and stall has been extensively researched, no methods for early prediction have been proven effective. This study explores the utilization of machine learning tools to predict compressor stall. The long short-term memory (LSTM) model, a form of recurrent neural network (RNN), was trained using real compressor stall datasets from a 100 kW recuperated gas turbine power system designed for hybrid configuration. Two variations of the LSTM model, classification and regression, were tested to determine optimal performance. The regression scheme was determined to be the most accurate approach, and a tool for predicting compressor stall was developed using this configuration. Overall, results show that the tool is capable of predicting stalls 5–20 ms before they occur. With a high-speed controller capable of 5 ms time-steps, mitigating action could be taken to prevent compressor stall before it occurs.

42 ENGINEERING↗

DOE OSTI2020

Control-Oriented Modeling of Lithium-Ion Batteries

Battery management systems (BMSs), which monitor and optimize performance while ensuring safety, require control-oriented models, i.e., models tailored to the design and implementation of estimation and control algorithms. Physics-based electrochemical models describe detailed battery phenomena, but are too computationally intensive for use in estimation and control applications. Single particle models (SPMs), which retain some of the physics of electrochemical models, are often used for control-oriented battery modeling since they are computationally efficient; however, they are only valid over very low frequency ranges and C-rates. Empirical equivalent circuit models (ECMs) are also used for control-oriented battery modeling since they are computationally efficient and can describe battery behavior over wide frequency ranges; however, they provide no physical understanding of the battery and, therefore, have limited applicability. Further, fractional order terms (e.g., Warburg impedances) are often employed, making the models unwieldy for use in the time domain. This work provides a control-oriented battery model that combines the benefits of SPM and ECM models, while overcoming their limitations. The proposed model incorporates some of the battery physics found in electrochemical models, can easily be used in both the time and frequency domains, and describes battery behavior over its entire frequency range. A linearized single particle model, which incorporates key electrochemical parameters, is used for modeling battery physics at very low frequencies. For low frequencies, integer-order linear systems are used to approximate diffusion physics described by Warburg impedances, and high frequency behavior is modeled by the double layer capacitance effect. The proposed battery model is more computationally efficient than full electrochemical models since it does not require the solution of PDEs, is accurate for a wider frequency range than the SPM considered in this paper, and does not suffer from the unwieldiness and limited applicability of empirical ECMs. Finally, the model is validated in the time and frequency domains via a comparison to pseudo-two-dimensional (P2D) model simulations and experimental data.

25 ENERGY STORAGE↗

DOE OSTI2021

Multidimensional Numerical Modeling of Combustion Dynamics in a Non-Premixed Rotating Detonation Engine With Adaptive Mesh Refinement

In the present work, a novel computational fluid dynamics (CFD) methodology was developed to simulate full-scale non-premixed rotating detonation engines (RDEs). A unique feature of the modeling approach was the incorporation of adaptive mesh refinement (AMR) to achieve a good trade-off between model accuracy and computational expense. Here, unsteady Reynolds-averaged Navier–Stokes (RANS) simulations were performed for an Air Force Research Laboratory (AFRL) non-premixed RDE configuration with hydrogen as fuel and air as the oxidizer. The finite-rate chemistry model, along with a ten-species detailed kinetic mechanism, was employed to describe the H 2 -Air combustion chemistry. Three distinct operating conditions were simulated, corresponding to the same global equivalence ratio of unity but different fuel/air mass flowrates. For all conditions, the capability of the model to capture essential detonation wave dynamics was assessed. An exhaustive verification and validation study was performed against experimental data in terms of a number of waves, wave frequency, wave height, reactant fill height, oblique shock angle, axial pressure distribution in the channel, and fuel/air plenum pressure. The CFD model was demonstrated to accurately predict the sensitivity of these wave characteristics to the operating conditions, both qualitatively and quantitatively. A comprehensive heat release analysis was also conducted to quantify detonative versus deflagrative burning for the three simulated cases. The present CFD model offers a potential capability to perform rapid design space exploration and/or performance optimization studies for realistic full-scale RDE configurations.

42 ENGINEERING↗

DOE OSTI2023

Melt-grown semi-insulating Mn:β-Ga 2 O 3 single crystals exhibiting unique visible absorptions and luminescence

In this study, several acceptor dopants have been explored in β-Ga 2 O 3 to produce semi-insulating substrates and epitaxial films. Fe and Mg make up the majority of research thus far; however, other transition metals provide potential alternatives for optimized performance. β-Ga 2 O 3 bulk single crystals were grown by the Czochralski and vertical gradient freeze methods with a nominal dopant concentration of 0.25 at. % Mn. Ultraviolet-visible-near infrared spectroscopy and photoluminescence revealed polarization- and orientation-dependent optical absorptions (pleochroism) coupled with an orange luminescence. All samples were electrically insulating, on the order of 10 9 –10 11 ohm cm at room temperature, indicative of acceptor doping. Actual dopant concentrations of the intentionally doped transition metal and background impurities were determined via glow discharge mass spectrometry, indicating the macroscale segregation behavior. High-temperature resistivity measurements indicated an experimental acceptor level of 1.7 ± 0.2 eV. Hydrogenation of samples resulted in an increase in the orange luminescence and O–H stretching modes observable in the infrared spectrum. Density functional theory calculations were performed to determine the likely site-occupancy and acceptor level of Mn in the bandgap.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Sixteen multiple-amplifier sensing charge-coupled devices and characterization techniques targeting the next generation of astronomical instruments

We present a candidate sensor for future spectroscopic applications, such as a Stage-5 Spectroscopic Survey Experiment or the Habitable Worlds Observatory. This type of charge-coupled device (CCD) sensor features multiple in-line amplifiers at its output stage allowing multiple measurements of the same charge packet, either in each amplifier or in the different amplifiers. Recently, the operation of an eight-amplifier sensor has been experimentally demonstrated, and we present the operation of a 16-amplifier sensor. This new sensor enables a noise level of ∼1 erms− with a single sample per amplifier. In addition, it is shown that sub-electron noise can be achieved using multiple samples per amplifier. In addition to demonstrating the performance of the 16-amplifier sensor, we aim to create a framework for future analysis and performance optimization of this type of detectors. New models and techniques are presented to characterize specific parameters, which are absent in conventional CCDs and Skipper CCDs: charge transfer between amplifiers and independent and common noise in the amplifiers and their processing.

16 multiple-amplifer sensing CCD (MAS-CCD)↗

DOE OSTI2022

Hamiltonian engineering of spin-orbit–coupled fermions in a Wannier-Stark optical lattice clock

Engineering a Hamiltonian system with tunable interactions provides opportunities to optimize performance for quantum sensing and explore emerging phenomena of many-body systems. An optical lattice clock based on partially delocalized Wannier-Stark states in a gravity-tilted shallow lattice supports superior quantum coherence and adjustable interactions via spin-orbit coupling, thus presenting a powerful spin model realization. The relative strength of the on-site and off-site interactions can be tuned to achieve a zero density shift at a “magic” lattice depth. This mechanism, together with a large number of atoms, enables the demonstration of the most stable atomic clock while minimizing a key systematic uncertainty related to atomic density. Interactions can also be maximized by driving off-site Wannier-Stark transitions, realizing a ferromagnetic to paramagnetic dynamical phase transition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Quantum Noise Mitigation: Introducing the Robust Quantum Circuit Scheduler for Enhanced Fidelity and Throughput

Undoubtedly, quantum computing offers valuable acceleration for solving intricate problems. One of the primary hurdles lies in executing large-scale quantum applications on backend machines. Qubit noise, among other factors, dramatically influences the execution process. Implementing effective scheduling techniques for quantum circuits is crucial for practical quantum computing and preventing excessive waiting times. The quantum realm is distinct from classical computing in terms of optimization, performance, utilization, and waiting periods. Consequently, the parameters and components of quantum circuit scheduling diverge from those of classical computing. This paper presents Quantum Noise Mitigation: Introducing the Robust Quantum Circuit Scheduler for Enhanced Fidelity and Throughput, a straightforward yet effective scheduling framework and policy that enhances noise resilience, throughput, and the fidelity of quantum circuits. Drawing inspiration from classical methods, our scheduling approach incorporates additional constraints tailored for quantum logic. The outcome demonstrates a substantial improvement in fidelity and resource management, which is vital for real-world quantum applications.

Baheri, Betis↗

DOE OSTI2022

Finite Element Modeling of Electrochemical Polishing of Niobium in Hydrofluoric-Sulfuric Acid Electrolyte

Niobium (Nb) used in superconducting radio-frequency cavities requires smooth surface to achieve optimal performance. In this work, a finite element model that coupled electrochemistry, heat transfer, and fluid dynamics was developed to investigate the electrochemical polishing mechanisms of Nb, using experimentally measured polarization results of coupon samples as validations. The current and potential distribution, oxide growth kinetics of Nb in a complex cavity geometry was investigated as a function of temperature and coolant flow. A low temperature coolant with intermediate flow rate was found to reduce surface current and ensure oxide uniformity. These results could shed light on the design of future particle accelerators.

SRF accelerator cavity↗

DOE OSTI2024

Ultrasonic Nondestructive Diagnosis of Cylindrical Batteries Under Various Charging Rates

Lithium-ion batteries have been used increasingly as electrochemical energy storage systems for electronic devices and vehicles. It is important to accurately estimate the state of charge (SoC) of a battery management system to control the battery operation to optimize performance, lifetime, and safety. The current work experimentally leverages ultrasonic diagnostic technology to investigate the SoC of lithium-ion batteries during the charge/discharge processes. A cylindrical-type nickel-cobalt-aluminum (NCA)–based 2500mAh 20A (INR18650-25R) battery was used for ultrasonic measurements with various charge/discharge rates of C/10.4, C/5.2, and C/1.3 at constant currents. The ultrasonic signals were analyzed for extracting wave velocity and wave attenuation. For all the testing rates, wave velocity increased in the charge process and decreased in the discharge process. Further, velocity profiles corresponding to lower rates of C/10.4 and C/5.2 exhibited primary peaks at the maximum SoCs, whereas the absolute wave velocity of C/1.3 rate showed primary peaks that occurred slightly after the SoC peak, indicating a delayed maximum Young's modulus. The wave attenuation computed for the C/10.4 rate had local maxima in the charge and discharge processes and depicted negative correlations with SoC, ranging from 0% to 18%, and positive correlations with SoC from 18% to 85%. On the other hand, the wave attenuation curves of the C/1.3 rate showed no local peaks and had negative correlations with SoC, ranging from 0% to 28%, and positive correlations with SoC ranging from 28% to 53%.

25 ENERGY STORAGE↗

DOE OSTI2021

Devastator Parallel Discrete Event Simulation Runtime (Devastator) v1.0

The Devastator runtime is a modern C++ implementation of optimistic parallel discrete event simulation methods. Devastator allows simulation application code to productively specify their component and event functionality with C++14 constructs. It utilizes GASNet-EX for distributed memory communication and includes parallel performance optimizations such as light-weight thread message queues and asynchronous GVT. Furthermore, it supports efficient event broadcasts and pause-rewind-resume functionality to support periodic load balancing and outer loop optimization algorithms.

Chan, Cy↗

DOE OSTI2025

OpenARC

OpenARC is an open-sourced, very High-Level Intermediate Representation (HLIR)-based, extensible compiler framework, where various performance optimizations, traceability mechanisms, fault tolerance techniques, etc., can be built for better debuggability/performance/resilience on the complex accelerator computing. OpenARC is the first OpenACC compiler supporting Altera FPGAs, in addition to NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis.

Lee, Seyong [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2025

Vedizar Fingerprinter

SAND2025-03289O Vedizar Fingerprinter simplifies the process of identifying devices on a network by analyzing traffic data. It uses a unique library to recognize different devices, making it easier for users to understand what is happening on their networks. This software is ideal for IT and operational technology environments, helping organizations monitor their networks effectively. By saving results in a database, it allows for easy access and review of device information. Users can enhance their network security and optimize performance without needing specialized hardware or technical expertise. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Jacobellis, John [Sandia National Lab. (SNL-CA), L↗