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At least 1,117 records · Page 62

Studying performance portability of LAMMPS across diverse GPU-based platforms

The molecular dynamics simulation software, LAMMPS, utilizes the Kokkos acceleration library to port computation to a diverse set of architectures including those based on GPU accelerators. In addition to Kokkos, LAMMPS contains a vast code base that leverages the CUDA application programming interface using library functions such as cuFFT, CUDA's fast-fourier transform (FFT) library, and, more recently, also support for AMD's Heterogeneous Interface for Portability (HIP) that is rapidly growing. While preparing LAMMPS tests for the AMD GPU-based test system precursors to Frontier, we investigated several strategies for accelerating LAMMPS on AMD GPUs, using the AMD Instinct MI100 and MI250X. In this work, we integrated the HIP FFT library, hipFFT, into the particle-particle particle-mesh (PPPM) long-range solver, which allowed the porting of PPPM calculations to the GPUs. Kokkos behavior on the MI100 and MI250X was also investigated through the package kokkos command of LAMMPS, targeting communication, memory usage, and particle grid decomposition. The Tersoff, Reax, Lennard-Jones (LJ), EAM, Granular, and PPPM potentials were investigated in this effort, and results from these experiments are provided. In conclusion, the selected potentials were run on Spock (AMD Instinct MI100), Crusher (AMD Instinct MI250X), AFW HPC11 (NVIDIA A100) and Summit (NVIDIA V100), for comparison. Operational roofline models were constructed and analyzed for the Tersoff, Reax, and Lennard–Jones potentials on Crusher and Summit.

97 MATHEMATICS AND COMPUTING↗

h5bench: A unified benchmark suite for evaluating HDF5 I/O performance on pre‐exascale platforms

Summary Parallel I/O is a critical technique for moving data between compute and storage subsystems of supercomputers. With massive amounts of data produced or consumed by compute nodes, high‐performant parallel I/O is essential. I/O benchmarks play an important role in this process; however, there is a scarcity of I/O benchmarks representative of current workloads on HPC systems. Toward creating representative I/O kernels from real‐world applications, we have created h5bench , a set of I/O kernels that exercise hierarchical data format version 5 (HDF5) I/O on parallel file systems in numerous dimensions. Our focus on HDF5 is due to the parallel I/O library's heavy usage in various scientific applications running on supercomputing systems. The various tests benchmarked in the h5bench suite include I/O operations (read and write), data locality (arrays of basic data types and arrays of structures), array dimensionality (one‐dimensional arrays, two‐dimensional meshes, three‐dimensional cubes), I/O modes (synchronous and asynchronous). In this paper, we present the observed performance of h5bench executed along several of these dimensions on existing supercomputers (Cori and Summit) and pre‐exascale platforms (Perlmutter, Theta, and Polaris). h5bench measurements can be used to identify performance bottlenecks and their root causes and evaluate I/O optimizations. As the I/O patterns of h5bench are diverse and capture the I/O behaviors of various HPC applications, this study will be helpful to the broader supercomputing and I/O community.

97 MATHEMATICS AND COMPUTING↗

Tailored Solvation and Interface Structures by Tetrahydrofuran-Derived Electrolyte Facilitates Ultralow Temperature Lithium Metal Battery Operations

Ineffectiveness of Li-ion batteries (LIBs) in cold climates hinders electronics to work in various conditions including frigid environments, despite high demands. Given that intrinsic properties of LIB materials cause this problem, optimized cell chemistries ultimately are required for low-temperature usage. In this study, Li-metal batteries (LMBs) composed of a Li-metal anode (LMA) stabilized by a localized high-concentration electrolyte (LHCE) are found to significantly enhance low-temperature performance. The LHCE allows the LMA to have compact and regular deposition and excellent plating/stripping efficiency at sub-zero temperatures. The LHCE produces an inorganic-rich solid-electrolyte interphase with larger amounts of Li 2 O/LiF interfaces, dominance of ion aggregates in Li + solvation, and enhanced Li + transport, which can greatly improve the LMA stability. LMB full cells based on LiNi 0.8 Co 0.1 Mn 0.1 O 2 cathodes with the tailored electrolyte show high retentions of 75 and 64 % at -20 and -40 °C, respectively. Furthermore, the LMB configuration retains its charge-discharge capability even at -60 °C.

25 ENERGY STORAGE↗

Efficient Fast Fractionation of Biomass Using a Diol-Based Deep Eutectic Solvent for Facilitating Enzymatic Hydrolysis and Obtaining High-Quality Lignin

Current DES pretreatment is often performed under relatively severe conditions with high temperature, long time, and high DES usage. This work studied a short-time diol DES (deep eutectic solvent) pretreatment under mild conditions to fractionate the bamboo, facilitate enzymatic hydrolysis, and obtain high-quality lignin. At an optimized condition of 130 °C for only 10 min, lignin and xylan removal reached 61.34% and 84.15 %, with residual glucan showing a ~90% enzymatic hydrolysis yield. Equally important, the dissolved lignin could be readily recovered with 97.51% yield, exhibiting 96.65 % β-O-4 preservation. The fractionation and lignin protection mechanisms were unveiled by XRD, FTIR, cellulose-DP, 2D HSQC NMR, 31 P NMR and GPC analysis. Finally, this study highlighted that short-time fractionation of bamboo can be achieved by a diol-based DES which is an ideal strategy to upgrade the lignocellulose biomass for high enzymatic hydrolysis yields and high-quality lignin stream.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Community‐based observing for social–ecological science: lessons from the Arctic

Environmental monitoring and observation by members of local communities have become increasingly common in the US and Canada over the past several decades. During the same period, social–ecological systems ( SES ) science has been developed to explain and predict human and environmental interactions, but empirical methods to generate matched social and ecological datasets are uncommon. Community‐based observing ( CBO ) methodologies were developed in the Arctic to allow for production of environmental data in a social context and are also well suited to provide empirical data for SES science. Community‐based observing networks and systems ( CBONS ) and community observer forums ( COF ) are methodologies developed from collaborations between community members, researchers, and government agencies. Here, we describe CBONS and COF methodologies, provide examples of their usage, and suggest ways in which they can benefit empirical SES science. We conclude by outlining efforts to expand the use of CBO to new knowledge and geographic domains.

Griffith, David L.↗

A convection-permitting dynamically downscaled dataset over the Midwestern United States

Climate change is expected to have far-reaching effects at both the global and regional scale, but local effects are difficult to determine from coarse-resolution climate studies. Dynamical downscaling can provide insight into future climate projections on local scales. Here, we present a new dynamically downscaled dataset for Indiana and the surrounding regions. Output from the Community Earth System Model (CESM) version 1 is downscaled using the Weather Research and Forecasting model (WRF). Simulations are run with a 24-hr reinitialization strategy and a 12-hr spin-up window. WRF output is bias corrected to the National Centers for Environmental Protection/National Center for Atmospheric Research 40-year Reanalysis project (NCEP) using a modified quantile mapping method. Bias-corrected 2-m air temperature and accumulated precipitation are the initial focus, with additional variables planned for future releases. Regional climate change signals agree well with larger global studies, and local fine-scaled features are visible in the resulting dataset, such as urban heat islands, frontal passages, and orographic temperature gradients. This high-resolution climate dataset could be used for down-stream applications focused on impacts across the domain, such as urban planning, energy usage, water resources, agriculture and public health.

54 ENVIRONMENTAL SCIENCES↗

Costs of immune responses are related to host body size and lifespan

A central assumption in ecological immunology is that immune responses are costly, with costs manifesting directly (e.g., increases in metabolic rate and increased amino acid usage) or as tradeoffs with other life processes (e.g., reduced growth and reproductive success). Across taxa, host longevity, timing of maturity, and reproductive effort affect the organization of immune systems. It is reasonable, therefore, to expect that these and related factors should also affect immune activation costs. Specifically, species that spread their breeding efforts over a long lifetime should experience lower immune costs than those that mature and breed quickly and die comparatively early. Likewise, body mass should affect immune costs, as body size affects the extent to which hosts are exposed to parasites as well as how hosts can combat infections (via its effects on metabolic rates and other factors). Here in this paper, we used phylogenetic meta-regression to reveal that, in general, animals incur costs of immune activation, but small species that are relatively long-lived incur the largest costs. These patterns probably arise because of the relative need for defense when infection risk is comparatively high and fitness can only be realized over a comparatively long period. However, given the diversity of species considered here and the overall modest effects of body mass and life history on immune costs, much more research is necessary before generalizations are appropriate.

59 BASIC BIOLOGICAL SCIENCES↗

Beyond cancer treatment – a review of total lymphoid irradiation for heart and lung transplant recipients

Immunosuppressive drugs used in the management of heart and lung transplants have a large monetary and quality of life cost due to their side effects. Total lymphoid irradiation (TLI) is one method of minimising the need for or replacing post-operative immunosuppressive drugs. A literature review was conducted on electronic databases using defined search terms. The aim was to establish the indications for the use of TLI, its advantages and disadvantages and the weaknesses associated with the methods used in related research. Eight articles were located that focused on TLI usage in combating organ rejection. These studies identified that the use of TLI resulted in a reduction in early rejection. One study reported a drop in rejection episodes from 0.46 to 0.14 episodes per patient per month once the TLI was complete. While the short-term prognosis is excellent, the long-term outlook is less positive with an increased risk of organ rejection and myelodysplasia 3.5 years post-TLI. This review reminds us that radiation therapy (RT) is not exclusively indicated for cancer treatment. While TLI cannot replace immunosuppressive drug therapy, it can offer a treatment option for people that cannot tolerate immunosuppressive drugs, or when conventional anti-rejection treatment is no longer viable. Reported long-term complications suggest that TLI should be used with caution. However, this modality should not be overlooked in cases of chronic rejection. Further research is required to establish the efficacy of RT in the treatment of transplant patients who are unsuitable for drug-based anti-rejection therapies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

MacroSheds: A synthesis of long-term biogeochemical, hydroclimatic, and geospatial data from small watershed ecosystem studies

The US Federal Government supports hundreds of watershed monitoring efforts from which solute fluxes can be calculated. Although instrumentation and methods vary between studies, the data collected and their motivating questions are remarkably similar. Nevertheless, little effort toward their compilation has previously been made. The MacroSheds project has developed a future-friendly system for harmonizing daily time series of streamflow, precipitation, and solute chemistry from 169+ watersheds, and supplementing each with watershed attributes. Here, we describe the breadth of MacroSheds data, and detail the steps involved in rendering each data product. We provide recommendations for usage and discuss when other datasets might be more suitable. The MacroSheds dataset is an unprecedented resource for watershed science, and for hydrology, as a small-watershed supplement to existing collections of streamflow predictors, like CAMELS and GAGES-II. The MacroSheds platform includes a web dashboard for visualization and an R package for data access and analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Polyolefin Innovations Toward Circularity and Sustainable Alternatives

The unprecedented growth and socioeconomic impacts of polyolefins clearly outline a major success story in the world of polymer science. Polyolefins revolutionizes industries such as health care, construction, and food packaging. Despite the benefits of polyolefins, there is a rising concern for the environment due to high production volume (i.e., fossil fuel consumption), often short usage time, and problems related to waste management and accumulation in the natural environment. Creating a circular economy for polyolefins through effective recycling technologies has the potential to decrease the environmental impact of these materials. This perspective discusses polyolefins and their impact, existing and emerging recycling/upcycling solutions, and recycle-by-design alternatives that are challenging the status quo.

circular economy↗

A New Estimator to Correct for Bias from Tag Rate Expansion on Natural-Origin Fish Attributes in Mixed-Stock Analysis Using Parentage-Based Tagging

Abstract In fisheries where hatchery- and natural-origin conspecifics occur as mixed stocks, it is often important to estimate both the natural-origin proportion of the mixture and the composition of attributes within the natural-origin portion (e.g., genetic stock, sex, and age-class). These estimates are facilitated by parentage-based tagging, which allows large numbers of hatchery fish to be efficiently tagged and later identified. When tag rates are less than 100%, the untagged fish in the mixture include both untagged hatchery fish and natural-origin fish. Unbiased estimation of the abundance and attribute composition of the natural-origin portion requires an estimator that accounts for tag rates. Two estimators are described: one “accounting-style” estimator similar to previously described approaches and one maximum likelihood method. These estimators were evaluated and compared using simulations mimicking estimation of the composition of fish migrating past a dam. The two estimators performed similarly at reducing bias when tag rates were high, but the maximum likelihood method had smaller mean square error when tag rates were low. We provide an R package to allow usage of this estimator in a wide variety of fisheries applications.

Delomas, Thomas A. (ORCID:000000015154759X)↗

Passage and survival of juvenile salmonid smolts through dams in the Columbia and Snake Rivers, 2010-2018

Minimizing the mortality and migration time of juvenile salmon (smolts) passing dams is a longstanding objective in the pursuit of salmon recovery in the Columbia River Basin. We compiled and analyzed 40 juvenile salmonid acoustic-tag studies that were performed at seven of the eight hydroelectric projects in the Federal Columbia River Power System between 2010–2018. We found the utilization of non-turbine routes decreased monotonically moving downstream from the Snake River to the mainstem Columbia River and that route usage and associated mortality differed substantially between the dams in the two rivers. Spillways were the predominant passage route at mainstem Columbia River dams, whereas passage through surface weirs and juvenile bypass systems was more common and generally provided higher survival at Snake River dams. Stocks exhibited variable passage behaviors and mortalities, with the estimated probability of an individual passing through all eight dams in the system and never using a turbine route at 0.31, 0.47, and 0.60 for subyearling Chinook Salmon, yearling Chinook Salmon, and steelhead, respectively. Although subyearling Chinook Salmon were generally more likely to pass through a turbine route, they also experienced less turbine-associated mortality than other stocks, especially steelhead. Notably, the proportion of smolts passing through the spillway relative to the amount of water released was lowest at Bonneville Dam, the largest and lowermost dam in the system. Bonneville Dam also stood out as having the highest proportion of smolts passing through turbines, but the lowest rate of turbine-associated mortality.

Skalski, J R.↗

Limited‐memory adaptive snapshot selection for proper orthogonal decomposition

Summary Reduced order models are useful for accelerating simulations in many‐query contexts, such as optimization, uncertainty quantification, and sensitivity analysis. However, offline training of reduced order models (ROMs) can have prohibitively expensive memory and floating‐point operation costs in high‐performance computing applications, where memory per core is limited. To overcome this limitation for proper orthogonal decomposition, we propose a novel adaptive selection method for snapshots in time that limits offline training costs by selecting snapshots according an error control mechanism similar to that found in adaptive time‐stepping ordinary differential equation solvers. The error estimator used in this work is related to theory bounding the approximation error in time of proper orthogonal decomposition‐based ROMs, and memory usage is minimized by computing the singular value decomposition using a single‐pass incremental algorithm. Results for a viscous Burgers' test problem demonstrate convergence in the limit as the algorithm error tolerances go to zero; in this limit, the full‐order model is recovered to within discretization error. A parallel version of the resulting method can be used on supercomputers to generate proper orthogonal decomposition‐based ROMs, or as a subroutine within hyperreduction algorithms that require taking snapshots in time, or within greedy algorithms for sampling parameter space. Copyright © 2016 John Wiley & Sons, Ltd.

Oxberry, Geoffrey M.↗

Peridynamic bond-associated correspondence model: Stability and convergence properties

The correspondence approach is a powerful technique that permits the usage of standard constitutive models from local theory within a peridynamic formulation. However, the conventional correspondence formulation suffers from material instability, i.e. zero-energy modes, that must be controlled for it to be applied in practice. The recently-introduced correspondence reformulation based on the use of a bond-associated deformation gradient can inherently remove the material instability. In this paper, we characterize some important properties, i.e. balance of linear momentum, balance of angular momentum and material stability, of the bond-associated correspondence model. The convergence behavior is also examined. Here, the accuracy of this approach is further demonstrated by comparing model predictions against local reference solutions and results from the conventional correspondence model with penalty stabilization for both two-dimensional and three-dimensional problems.

42 ENGINEERING↗

Round-robin weathering test of various polymeric back-sheets for PV modules with different ultraviolet irradiation and sample temperatures

Durability assessment of materials exposed to natural weathering with expected service lifetimes of more than 20 years requires accelerated testing of the UV stability, especially for polymeric materials. Fraunhofer ISE organized an interlaboratory comparison for testing different back-sheets in various test laboratories using different UV sources. The five participating test laboratories used three different types of UV sources. The interaction of the UV radiation with the polymers used in PV modules is main subject of this round-robin. Laminates were produced by using solar glass and a suitable EVA encapsulant combined with 10 different back-sheets. The simultaneous usage of different optical filters allowed to investigate roughly the spectral sensitivity and the intensity impact. The degradation was followed by spectral reflectance and transmittance measurements and calculation of the yellowness index as degradation indicator. Clear differences in the degradation behavior of the different products were found.

14 SOLAR ENERGY↗

Manning condensation in ion exchange membranes: A review on ion partitioning and diffusion models

Here, the rational design of ion exchange membranes (IEMs) is becoming more pertinent as their usage becomes broader and as their staple applications (i.e., electrodialysis, flow batteries, and fuel cells) improve in commercial viability. Such efforts would be catalyzed by an improved fundamental understanding of ion transport in IEMs. This review discusses recent progress in modeling ion partitioning and diffusion in IEMs in an effort to relate IEM performance metrics to fundamental membrane properties over which researchers and membrane manufacturers possess direct and sometimes precise control. Central focus is given to the Donnan-Manning model for ion partitioning and the Manning-Meares model for ion diffusion in IEMs. These two frameworks, which are derived from Manning's counter-ion condensation theory for polyelectrolyte solutions, have been widely used within the IEM literature since their recent introduction. To explore this topic, the mathematical derivation of both models is revisited, followed by a survey of experimental and computational discussions of counter-ion condensation in IEMs. Alternative models which fulfill similar roles in predicting IEM transport properties are compared. This review concludes by highlighting the uniquely favorable positions of the Donnan-Manning and Manning-Meares models and discussing their prospects as leading predictors of IEM partitioning and diffusive properties.

25 ENERGY STORAGE↗

Energetics Applications for the Oil and Gas Industry

Here, early motivation and use of energetic materials in the Western World by Alfred Nobel was intended to facilitate mining, construction, and demolition activities. The motivation for the work was the recognized need for a safer energetic material as an alternate to unstabilized nitroglycerine. The invention of dynamite by Nobel was widely adopted in the civilian world and brought a fortune to Nobel, resulting in the formation of the annual Nobel Prize awards, recognizing significant achievements across many fields of endeavour. Nonetheless, further development of energetics was primarily motivated by and funded for military purposes, rather than civilian usage. And indeed much investment has been given to the development and characterization of military energetics and their application. An example application is the precision shaped charge, primarily developed as a means of focusing energy in a narrow metallic jet for deep penetration of heavy armor. However, the largest costumer today and for many years for shaped charges is not the military, but rather the oil and gas industry, which has adapted the military technology for perforation of oil and gas wells. While there are similar aspects to desired penetration capabilities in both applications, there are enough differences to warrant energetics R & D focused on oil and gas industry needs.

02 PETROLEUM↗

The Role of Pentaerythritol Tetranitrate (PETN) Aging in Determining Detonator Firing Characteristics

Pentaerythritol tetranitrate (PETN) is one of the most commonly used explosives for both military and mining applications. PETN is used in EBW (exploding bridge wire) and EFI (exploding foil initiator) detonator devices. Due the widespread usage of PETN, studies focusing on how the explosive changes with age, primarily its function in detonators has received particular interest. Aging studies have identified several factors that affect PETN detonator function over time, most notably the specific surface area of the explosive powder. Though small-scale studies have been performed on specific detonator systems with isolated batches of material, what is missing is a large statistically-significant study focusing on PETN aging characteristics - such as powder coarsening - and their influence on detonator performance. Herein we report the first large statistically viable PETN aging study focusing on four batches of PETN powder from the same stock of PETN using two stabilizers, polysaccharide and TriPEON. PETN was aged both as a free-flowing powder as well as in modified EBW RP-2 detonators, for one month at 75 °C. The PETN powder has been analyzed chemically using Fisher specific surface area analysis, SEM imaging and light scattering particle size analysis. Additionally the detonators were tested for performance through voltage-sweep threshold testing and function time measurements. Findings from the study indicate that aging at 75 °C for one month significantly changes the specific surface area and particle size of unstabilized PETN, leading to increases in detonator function time, but not detonator threshold values. Powders stabilized with TriPEON displayed less significant increases in function time, while powder stabilized with polysaccharide exhibited no aging effects, despite the high temperature aging.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗