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At least 127 records · Page 7

Lustre Unveiled: Evolution, Design, Advancements, and Current Trends

The Lustre filesystem serves as a vital element in high-performance parallel storage, meeting the rising demands of scientific, research, and enterprise environments. Widely deployed across HPC environments, ranging from small-scale applications in AI/ML, to domains like oil and gas, drug discovery, and meteorology, and manufacturing, Lustre addresses the universal challenge of efficiently accessing vast and ever-increasing volumes of data. Lustre is the filesystem of choice on six out of the top 10 fastest supercomputers in the world today, over 65% of the top 100, and also for over 60% of the top 500. Despite its widespread popularity, there is a lack of a complete and up-to-date reference, covering Lustre’s evolution, design, and various advancements made over the years. In this journal, we aim to fill this gap by providing a comprehensive journey of Lustre, including its history with significant contributions to HPC, detailed architecture and design elements, exploration of advancements added through its evolution, and future directions. Additionally, we present a comparison of Lustre with other prominent storage technologies of the era. To illustrate the current state of Lustre, we analyze several filesystem trends, including utilization, performance, and usage patterns on Orion, the Lustre filesystem on the first exascale supercomputer Frontier. We hope that this journal serves as a comprehensive educational reference for the current and future generations interested in HPC filesystem storage aspects.

97 MATHEMATICS AND COMPUTING↗

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. In this work, we hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. Results: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. Conclusion: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales.

59 BASIC BIOLOGICAL SCIENCES↗

VAST: the Void Analysis Software Toolkit

Voids are expansive regions in the universe containing significantly fewer galaxies than surrounding galaxy clusters and filaments. They are a fundamental feature of the cosmic web and provide important information about galaxy physics and cosmology. For example, correlations between voids and luminous tracers of large-scale structure improve constraints on the expansion of the universe as compared to using tracers alone, and numerous studies have shown that the void environment influences the evolution of galaxies. However, what constitutes a void is vague and formulating a concrete definition to use in a void-finding algorithm is not trivial. As a result, several different algorithms exist to identify these cosmic underdensities. Our Void Analysis Software Toolkit, or VAST, provides Python 3 implementations of two such algorithms: VoidFinder and V 2 . This consolidation of two popular void-finding algorithms allows the user to, for example, easily compare the results of their analysis using different void definitions.

97 MATHEMATICS AND COMPUTING↗

Analysis of hydrogen infrastructure for the feasibility, economics, and sustainability of a fuel cell powered data center

Data centers used for internet data services, cloud computing, and/or data storage consume vast amounts of electricity and are increasing rapidly in capacity. Consequently, their power consumption has raised concerns about energy sustainability and environmental impacts. Large-scale, on-site renewable energy could help reduce data centers’ carbon footprint; however, wind and solar power alone cannot provide an uninterrupted power supply to computer servers due to their natural variability. Instead, reliable power integration can be achieved by using fuel cells powered by hydrogen from sustainable resources (e.g., wind and solar energy). Establishing a hydrogen infrastructure will be critical for realizing these benefits and establishing fuel cells as a viable power source for data centers. Here, to facilitate the development of novel carbon-free fuel cell data enters, this paper presents renewable power integrated with hydrogen infrastructures in four scenarios to provide reliable hydrogen supply from production to storage. Various paths were analyzed toward a hydrogen supply infrastructure by determining the proper component sizes and calculating the cost of meeting the server load. We used a microgrid modeling software, Hybrid Optimization of Multiple Energy Resources (HOMER), and studied the feasibility of fuel cell powered data centers employing renewable hydrogen. The modeling results show various renewable integration configurations to meet reliable and sustainable power requirement under four scenarios for a carbon-free data center.

08 HYDROGEN↗

Unraveling the functional dark matter through global metagenomics

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

54 ENVIRONMENTAL SCIENCES↗

Carbon flux estimates are sensitive to data source: a comparison of field and lab temperature sensitivity data

Abstract A large literature exists on mechanisms driving soil production of the greenhouse gases CO 2 and CH 4 . Although it is common knowledge that measurements obtained through field studies vs. laboratory incubations can diverge because of the vastly different conditions of these environments, few studies have systematically examined these patterns. These data are used to parameterize and benchmark ecosystem- to global-scale models, which are then susceptible to the biases of the source data. Here, we examine how greenhouse gas measurements may be influenced by whether the measurement/incubation was conducted in the field vs. laboratory, focusing on CO 2 and CH 4 measurements. We use Q 10 of greenhouse gas flux (temperature sensitivity) for our analyses because this metric is commonly used in biological and Earth system sciences and is an important parameter in many modeling frameworks. We predicted that laboratory measurements would be less variable, but also less representative of true field conditions. However, there was greater variability in the Q 10 values calculated from lab-based measurements of CO 2 fluxes, because lab experiments explore extremes rarely seen in situ , and reflect the physical and chemical disturbances occurring during sampling, transport, and incubation. Overall, respiration Q 10 values were significantly greater in laboratory incubations (mean = 4.19) than field measurements (mean = 3.05), with strong influences of incubation temperature and climate region/biome. However, this was in part because field measurements typically represent total respiration (Rs), whereas lab incubations typically represent heterotrophic respiration (Rh), making direct comparisons difficult to interpret. Focusing only on Rh-derived Q 10 , these values showed almost identical distributions across laboratory ( n = 1110) and field ( n = 581) experiments, providing strong support for using the former as an experimental proxy for the latter, although we caution that geographic biases in the extant data make this conclusion tentative. Due to a smaller sample size of CH 4 Q 10 data, we were unable to perform a comparable robust analysis, but we expect similar interactions with soil temperature, moisture, and environmental/climatic variables. Our results here suggest the need for more concerted efforts to document and standardize these data, including sample and site metadata.

54 ENVIRONMENTAL SCIENCES↗

Machine learning enabling high-throughput and remote operations at large-scale user facilities

Imaging, scattering, and spectroscopy are fundamental in understanding and discovering new functional materials. Contemporary innovations in automation and experimental techniques have led to these measurements being performed much faster and with higher resolution, thus producing vast amounts of data for analysis. These innovations are particularly pronounced at user facilities and synchrotron light sources. Machine learning (ML) methods are regularly developed to process and interpret large datasets in real-time with measurements. However, there remain conceptual barriers to entry for the facility general user community, whom often lack expertise in ML, and technical barriers for deploying ML models. Herein, we demonstrate a variety of archetypal ML models for on-the-fly analysis at multiple beamlines at the National Synchrotron Light Source II (NSLS-II). We describe these examples instructively, with a focus on integrating the models into existing experimental workflows, such that the reader can easily include their own ML techniques into experiments at NSLS-II or facilities with a common infrastructure. The framework presented here shows how with little effort, diverse ML models operate in conjunction with feedback loops via integration into the existing Bluesky Suite for experimental orchestration and data management.

36 MATERIALS SCIENCE↗

Turbulence theories and statistical closure approaches

When discussing research in physics and in science more generally, it is common to ascribe equal importance to the three components of the scientific trinity: theoretical, experimental, and computational studies. This review will explore the future of modern turbulence theory by tracing its history, which began in earnest with Kolmogorov’s 1941 analysis of turbulence cascade and inertial range [A.N. Kolmogorov, Dokl. Akad. Nauk SSSR, 30, 299, (1941); 32, 19, (1941)]. The 80th Anniversary of Kolmogorov’s landmark study is a welcome opportunity to survey the achievements and evaluate the future of the theoretical approach of turbulence research. Over the years, turbulence theories have been critically important in laying the foundation of our understanding of the nature of turbulent flows. In particular, the Direct Interaction Approximation (DIA) [R.H. Kraichnan, J. Fluid Mech., 5, 497 (1959)] and its subsequent development, known as the statistical closure approach, can be identified as perhaps the most profound single advancement. The remarkable success of the statistical closure has furnished a platform to study such essential concepts as the energy transfer process and interacting scales, and the roles of the straining and sweeping motions. More recently, the quasi-Lagrangian formulation of V. L’vov & I. Procaccia and Kraichnan’s solvable passive scalar model provided powerful ways to explore another fundamental aspect of turbulent flows, the phenomena of intermittency, and the associated anomalous scaling exponents. In the meantime, the theory of fluid equilibria has been developed to describe the large-scale structures that can emerge from turbulent cascades of two-dimensional and geophysical flows at a later time. And yet, despite all these successes, analytical treatments suffer from mathematical complexities. As a result, the utility of theoretical approaches has been limited to relatively idealized flows. On the other hand, in recent decades, computational abilities and experimental facilities have reached an unprecedented scale. Looking beyond the horizon, the imminent deployment of exascale supercomputers will generate complete datasets of the entire flow field of key benchmark flows, allowing researchers to extract additional measurements concerning fully developed, complex turbulent flow fields far beyond those available from the statistical closure theories. Some other developments that could potentially influence the future course of turbulence theories include the advancement of machine learning, artificial intelligence, and data science; likely disruptions arising from the advent of quantum computation; and the increasingly prominent role of turbulence research in providing more accurate climate scientific data. Finally, turbulence theorists can leverage these developments by asking the right questions and developing advanced, sophisticated frameworks that will be able to predict and correlate vast amounts of data from the other two components of the trinity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Adaptive pruning-based optimization of parameterized quantum circuits

Abstract Variational hybrid quantum–classical algorithms are powerful tools to maximize the use of noisy intermediate-scale quantum devices. While past studies have developed powerful and expressive ansatze, their near-term applications have been limited by the difficulty of optimizing in the vast parameter space. In this work, we propose a heuristic optimization strategy for such ansatze used in variational quantum algorithms, which we call ‘parameter-efficient circuit training (PECT)’. Instead of optimizing all of the ansatz parameters at once, PECT launches a sequence of variational algorithms, in which each iteration of the algorithm activates and optimizes a subset of the total parameter set. To update the parameter subset between iterations, we adapt the Dynamic Sparse Reparameterization scheme which was originally proposed for training deep convolutional neural networks. We demonstrate PECT for the Variational Quantum Eigensolver, in which we benchmark unitary coupled-cluster ansatze including UCCSD and k -UpCCGSD, as well as the Low-Depth Circuit Ansatz (LDCA), to estimate ground state energies of molecular systems. We additionally use a layerwise variant of PECT to optimize a hardware-efficient circuit for the Sycamore processor to estimate the ground state energy densities of the one-dimensional Fermi-Hubbard model. From our numerical data, we find that PECT can enable optimizations of certain ansatze that were previously difficult to converge and more generally can improve the performance of variational algorithms by reducing the optimization runtime and/or the depth of circuits that encode the solution candidate(s).

Physics↗

The Random Ray Method Versus Multigroup Monte Carlo: The Method of Characteristics in OpenMC and SCONE

The Random Ray Method (TRRM) is a recently developed approach to solving neutral particle transport problems based on the Method of Characteristics. While the method previously has been implemented only in closed-source or limited-functionality codes, this work describes its implementation in two open-source Monte Carlo codes: OpenMC and SCONE. The random ray implementations required small modifications to the existing Multigroup Monte Carlo (MGMC) solvers, offering a rare venue for redundant, fine-grained, "apples-to-apples" speed and accuracy comparisons between transport methods. To this end, TRRM and MGMC solvers are evaluated against each other using each code's native capabilities on reactor eigenvalue problems with different degrees of energy discretization. On the C5G7 benchmark (featuring only seven energy groups), TRRM achieves a maximum pin power error comparable to or lower than that of MGMC for a given run time. On a problem with 69 energy groups, MGMC is found to scale more efficiently, obtaining a lower pin power error for a given run time. However, the defining difference between the two transport methods is found to be their vastly different uncertainty distributions. Specifically, TRRM is found to maintain similar levels of accuracy and uncertainty throughout the simulation domain whereas MGMC can exhibit orders-of-magnitude greater errors in areas of the problem that feature low neutron flux. For instance, TRRM provided an up to 373 times speed advantage compared with MGMC for computing the flux in low-flux regions in the moderator surrounding the C5G7 core.

42 ENGINEERING↗

Combinatorial Evaluation of Physical Feature Engineering, Classical Machine Learning, and Deep Learning Models for Synchrophasor Data at Scale

A major objective of the project was to train and evaluate the effectiveness of multiple event and anomaly detection, identification and classification deep temporal learning models for processing of real-time phasor measurement unit (PMU) data streams. A vast dataset, consisting of two years of phasor measurements from all three U.S. Interconnections, was curated and released by the Department of Energy (DOE) through Pacific Northwest National Laboratory (PNNL). The dataset also included an event log that provided event times and types (e.g. generator trips, line trips, planned service events, transformer operations, etc.). Our analysis of this dataset addressed six (6) of the eleven (11) research priorities identified in Funding Opportunity Announcement (FOA) DE-FOA-0001861 “Big Data Analysis of Synchrophasor Data” (FOA 1861). Rather than being limited to pre-determined specific algorithms, this project relied on the uniquely structured, highly performant underlying time series database capabilities of the PredictiveGrid platform to assess the vast dataset utilizing a wide variety of algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Ocean Energy for Ocean Worlds

Energy systems generating power from ocean waves, currents, tides, and thermal and salinity gradients are being developed to power oceanographic instrumentation and autonomous vehicles in Earth’s oceans. Exploration missions enabled or extended with in-situ energy harvesting on Earth may be similar to those on extra-terrestrial ocean worlds including mapping, biogeochemical sampling, acoustic monitoring, search for building blocks of life, and physical oceanographic characterization. With the addition of ocean energy available at the point of observation, data can be collected on larger spatial and temporal scales, enabling more comprehensive missions on other worlds. Power resource characteristics (e.g. current speed, variability) will similarly need to be assessed. Earth and extra-terrestrial ocean missions share vast technical challenges including high expense, need for advanced autonomy, ability to survive in the harshest environments, and limited communications or opportunities for intervention. Marine energy systems may be the only option for in-situ generation in certain scenarios (e.g., under a thick layer of ice) or advantageous over onboard energy storage options that may interfere with the natural environment (e.g., radioisotope thermoelectric generators). This work provides an overview of existing marine energy technology pertaining to ocean observations, highlights emerging research and development and new funding and program initiatives, explores similarities in mission requirements between terrestrial and extra-terrestrial applications, and suggests innovation pathways towards enabling high-value ocean world exploration powered by ocean energy.

Cavagnaro, Robert J.↗

Low-cost, high-efficiency III-V photovoltaics enabled by remote epitaxy through graphene (Final Technical Report)

One of the most important outcomes of this project was that the team developed a method to directly grow graphene layer in wafer-scale on III-V substrates. Conventionally, graphene had to be transferred for remote epitaxy, which has imposed significant challenges in scalability, film quality, and substrate recycling, due to the transfer-related issues. The newly developed method of directly forming 2D layers by Metal-Organic Chemical Vapor Deposition (MOCVD) has realized wafer-scale, defect-free graphene formation for remote epitaxy, which has huge implications not only for solar cells but also in expanding the scalability and the possibility for heterointegration with dissimilar material platforms. Another important outcome was on better understanding of remote epitaxy mechanism. The growth of III-V on graphene is vastly different from directly growing films on III-V substrates, because the surface energy of graphene is very small, meaning that the nucleation density on graphene will be much lower than exposed III-V surfaces. Also, the graphene and the interface properties critically affect remote interaction through graphene. With this obtained knowledge regarding III-V remote epitaxy, we were able to achieve wafer-scale single-crystalline remote epitaxy, 100% exfoliation of the remote epitaxial films, as well as multiple times of GaAs wafer reusability demonstration. The general rule of thumbs found during this project will be a stepping stone for the growth and fabrication of various high-performance devices by remote epitaxy. Lastly, because remote epitaxy and 2DLT offer a pathway to isolate single-crystal membranes from the host wafers, the wafer-scale remote epitaxy processes developed in this project could open up pathways for new functionality and multi-functionality by heterointegration of remote epitaxially formed membranes.

14 SOLAR ENERGY↗

DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman’s path integral formalism of quantum mechanics. Here, the flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

36 MATERIALS SCIENCE↗

Cooperative Research and Development Agreement between National Energy Technology Laboratory and Princeton University (Abstract)

The National Energy Technology Laboratory (NETL) and Princeton University will collaborate in the development of microwave-plasma technology to convert methane into hydrogen and valuable solid carbon materials. The effort will combine NETL’s vast resources for microwave-enhanced process development, characterization, and design with Princeton University’s extensive expertise in the study of non-equilibrium plasmas employing supersonic nozzles. Lab-scale experiments will be conducted for different conditions to convert and compare their respective performance in hydrogen production. Computational modeling will be performed to verify results from experimental studies conducted in both labs.

08 HYDROGEN↗

The Significance of Aggregation Methods in Functional Group Modeling

The growth of forests and the feedbacks between forests and environmental changes are central issues in the planetary carbon cycle, global climate change, and basic plant ecology. A challenge to understanding both growth and feedbacks from local to global scales is that many critical metabolic processes vary among species. An innovation in solving this challenge is the recognition that species can be lumped into “functional groups” based on metabolic similarity, and these functional groups can then be studied in computational models that simulate ecosystem function. Despite the vast resources devoted to functional group studies and the progress made by them, an important logical and biological question has not been formally addressed, “How do the groupings alter the results of modeling studies?” To what extent do modeling results depend on the choices made in aggregating taxa into functional groups. Here, we consider the effects of using different aggregation strategies in simulating the carbon dynamics of a deciduous forest. Understanding the impacts that aggregation strategy has on efforts to simulate regional-to-global-scale forest dynamics offers insights into both ecosystem regulation and model function and addresses this central problem in the study of carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

Micro–macro finite element modeling method for rub response in abradable coating materials

Gas turbine engines experience “rub” when the rotating blades come in contact with a static abradable coating. This results in extreme strain rates and dynamics inside a high-temperature/high-pressure environment. Current rub models are phenomenological and do not reflect the underlying microstructures, thus limiting their prediction accuracy. In this work, a microstructure-informed, reduced order modeling framework is introduced for simulating abradable coating “rub" behavior. This framework comprises a microscale model constructed based on digitized abradable microstructure and explicitly simulates the mechanical behavior of each constituent phases and their interactions. After calibration and validation with experiment data, the calibrated microscale model is used to generate data across a vast range of applied strain rates and temperature with various load paths. Then, the virtually generated data are used to fit the macroscopic-reduced order model, which enables fast component scale rub simulation without compromising the integrity of the complex material behavior. In conclusion, the proposed effort will address the technical challenge of predicting abradable material behavior during rub through the application of multiscale modeling from microstructure to engines behavior, effectively reducing the development costs and time of new abradable material for better “rub” properties.

36 MATERIALS SCIENCE↗

An Internal Digital Image Correlation Technique for High-Strain Rate Dynamic Experiments

Full-field, quantitative visualization techniques, such as digital image correlation (DIC), have unlocked vast opportunities for experimental mechanics. However, DIC has traditionally been a surface measurement technique, and has not been extended to perform measurements on the interior of specimens for dynamic, full-scale laboratory experiments. This limitation restricts the scope of physics which can be investigated through DIC measurements, especially in the context of heterogeneous materials. The focus of this study is to develop a method for performing internal DIC measurements in dynamic experiments. The aim is to demonstrate its feasibility and accuracy across a range of stresses (up to 650 MPa), strain rates (10 3 - 10 6 s -1 ), and high-strain rate loading conditions (e.g., ramped and shock wave loading). Internal DIC is developed based on the concept of applying a speckle pattern at an inner-plane of a transparent specimen. The high-speed imaging configuration is coupled to the traditional dynamic experimental setups, and is focused on the internal speckle pattern. During the experiment, while the sample deforms dynamically, in-plane, two-dimensional deformations are measured via correlation of the internal speckle pattern. In this study, the viability and accuracy of the internal DIC technique is demonstrated for split-Hopkinson (Kolsky) pressure bar (SHPB) and plate impact experiments. The internal DIC experimental technique is successfully demonstrated in both the SHPB and plate impact experiments. In the SHPB setting, the accuracy of the technique is excellent throughout the deformation regime, with measurement noise of approximately 0.2% strain. In the case of plate impact experiments, the technique performs well, with error and measurement noise of 1% strain. The internal DIC technique has been developed and demonstrated to work well for full-scale dynamic high-strain rate and shock laboratory experiments, and the accuracy is quantified. Here, the technique can aid in investigating the physics and mechanics of the dynamic behavior of materials, including local deformation fields around dynamically loaded material heterogeneities.

36 MATERIALS SCIENCE↗