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At least 1,153 records · Page 64

PETSc/TAO developments for GPU-based early exascale systems

The Portable Extensible Toolkit for Scientific Computation (PETSc) library provides scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization via the Toolkit for Advanced Optimization (TAO). PETSc is used in dozens of scientific fields and is an important building block for many simulation codes. During the U.S. Department of Energy’s Exascale Computing Project, the PETSc team has made substantial efforts to enable efficient utilization of the massive fine-grain parallelism present within exascale compute nodes and to enable performance portability across exascale architectures. We recap some of the challenges that designers of numerical libraries face in such an endeavor, and then discuss the many developments we have made, which include the addition of new GPU backends, features supporting efficient on-device matrix assembly, better support for asynchronicity and GPU kernel concurrency, and new communication infrastructure. In conclusion, we evaluate the performance of these developments on some pre-exascale systems as well as the early exascale systems Frontier and Aurora, using compute kernel, communication layer, solver, and mini-application benchmark studies, and then close with a few observations drawn from our experiences on the tension between portable performance and other goals of numerical libraries.

Exascale Computing Project (ECP)↗

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Determining Mating Type and Ploidy in Rhodotorula toruloides and its Effect on Growth on Sugars from Lignocellulosic Biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33–9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032–0.131 (g/g) and lipid contents were 13.5–53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

Conversion↗

TRISO Particle Isolation and Graphite Removal Using SRNL Vapor Digestion Technology

Tri-structural isotropic fueled reactors are planned to come online in the next decade, but there is not currently a widely agreed upon disposition pathway for this new fuel stream. For long term used nuclear fuel storage, there would be a significant benefit if the waste volume could be reduced or mitigated. Most of the volume from used TRISO fuel contains graphite. SRNL currently has an active patent which describes one pathway to digest the graphite. One benefit in the utilization of this pathway is that multiple cylindrical pieces can be stacked end-to-end in a reaction tube, then nitric acid and water vapor can be flowed through the tube, and the weight change of the individual cores can provide both a reaction profile and overall oxidant use efficiency. The reaction of nitric acid and graphite passes through a series of intermediate products – NO 2 , NO, and N 2 O – from reaction and decomposition to eventually form N2. The data shows that NO2 grows in with increasing temperature between 500-600°C and then decreases by way of either reaction with graphite or decomposition. Nitric oxide, a reaction and thermal decomposition product of NO 2 , exhibits a consistent decline as a function of temperature, which is consistent with the literature. Similarly, the concentrations of N 2 O and N 2 increase as a function of temperature as their reactions with graphite become more favorable.

Advanced Reactors↗

Multivariate regression modelling for gender prediction using volatile organic compounds from hand odor profiles via HS-SPME-GC-MS

The efficacy of using human volatile organic compounds (VOCs) as a form of forensic evidence has been well demonstrated with canines for crime scene response, suspect identification, and location checking. Although the use of human scent evidence in the field is well established, the laboratory evaluation of human VOC profiles has been limited. This study used Headspace-Solid Phase Microextraction-Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS) to analyze human hand odor samples collected from 60 individuals (30 Females and 30 Males). The human volatiles collected from the palm surfaces of each subject were interpreted for classification and prediction of gender. The volatile organic compound (VOC) signatures from subjects’ hand odor profiles were evaluated with supervised dimensional reduction techniques: Partial Least Squares-Discriminant Analysis (PLS-DA), Orthogonal-Projections to Latent Structures Discriminant Analysis (OPLS-DA), and Linear Discriminant Analysis (LDA). The PLS-DA 2D model demonstrated clustering amongst male and female subjects. The addition of a third component to the PLS-DA model revealed clustering and minimal separation of male and female subjects in the 3D PLS-DA model. The OPLS-DA model displayed discrimination and clustering amongst gender groups with leave one out cross validation (LOOCV) and 95% confidence regions surrounding clustered groups without overlap. The LDA had a 96.67% accuracy rate for female and male subjects. The culminating knowledge establishes a working model for the prediction of donor class characteristics using human scent hand odor profiles.

59 BASIC BIOLOGICAL SCIENCES↗

Semi-Analytical Hierarchical Bayesian Inference of Nonlinear Model Structure in Stochastic Dynamics: Applied to Compartmental Models of Infectious Diseases

A Bayesian computational framework for parsimonious inference in stochastic nonlinear dynamical systems is presented. This framework enables the concurrent estimation of system states, time-varying parameters, time-invariant parameters, and the optimal sparsity structure of the model parameters. Because differential equation-based models are often simplified mechanistic or phenomenological representations, robust inference from noisy measurement data requires explicit treatment of model error and uncertainty. Model error and time-varying parameters can be represented as random processes, enabling inference while making minimal assumptions about the underlying sources of discrepancy and variability. Adopting stochastic differential equation representations affords the model significant flexibility, but can also render it susceptible to overfitting during statistical inversion, where the inferred model may track noise rather than the underlying signal. To alleviate the effects of overfitting and to enable the discovery of the optimal sparse representation of the time-invariant parameters, a Bayesian sparse learning algorithm is embedded within the framework. This sparse learning framework adopts an approximate hierarchical Bayesian setting defined by a series of semi-analytical expressions. The model structure inference framework is validated using a stochastic compartmental model for tracking and forecasting active cases of an infectious disease. Compartmental models describe population-level infectious disease dynamics through interactions among population fractions grouped by disease state. Mathematically, such models consist of a system of coupled ordinary differential equations. This example adopts an expressive compartmental model that includes multiple possible interactions between disease states, motivated by early uncertainty surrounding COVID-19 reinfection dynamics and their implications for long-term epidemic forecasting. The sparse learning exercise permits the inference of a priori unknown epidemiological dynamics from simulated public health data, discovering the nested compartmental model that optimizes the trade-off between average data-fit and model complexity. It is shown that inducing sparsity among the model parameters eliminates redundant interactions between compartments, equivalently revealing the optimal coupling structure between differential equations.

97 MATHEMATICS AND COMPUTING↗

Watermarks in stream processing systems: semantics and comparative analysis of Apache Flink and Google cloud dataflow

Streaming data processing is an exercise in taming disorder: from oftentimes huge torrents of information, we hope to extract powerful and timely analyses. But when dealing with streaming data, the unbounded and temporally disordered nature of real-world streams introduces a critical challenge: how does one reason about the completeness of a stream that never ends? In this paper, we present a comprehensive definition and analysis of watermarks, a key tool for reasoning about temporal completeness in infinite streams.First, we describe what watermarks are and why they are important, highlighting how they address a suite of stream processing needs that are poorly served by eventually-consistent approaches:• Computing a single correct answer, as in notifications.• Reasoning about a lack of data, as in dip detection.• Performing non-incremental processing over temporal subsets of an infinite stream, as in statistical anomaly detection with cubic spline models.• Safely and punctually garbage collecting obsolete inputs and intermediate state.• Surfacing a reliable signal of overall pipeline health.Second, we describe, evaluate, and compare the semantically equivalent, but starkly different, watermark implementations in two modern stream processing engines: Apache Flink and Google Cloud Dataflow.

Akidau, Tyler↗

Transport and Retention of Particulate Organic Matter in Sand: Lab Experiments and Modelling

Flow-through reactor (FTR) experiments were conducted at three different downward vertical flow rates to study the transport and retention of particulate organic matter (Chlorella powder) in riverbed sediments. This data package includes data files (.csv) regarding effluent collected from the FTRs during the experiments (time, duration, volume of each sample collection; concentration of nonreactive bromide tracer; concentration of suspended Chlorella determined by absorbance measurements) and sediment (sand) slices collected from the FTRs after the experiments (mass of Chlorella retained in 1 cm depth intervals determined by loss-on-ignition method). More detailed descriptions of data are provided in the data dictionary, and detailed methods are available in the associated MSc thesis listed in ‘Related References.’ The data dictionary and file level meta data (FLMD) are included in the data package as both .csv and .xlsx files. This data package also includes timelapse videos (.mp4) of the experiments, and modelling scripts associated with the experiments. The modelling scripts are included as MATLAB ‘live scripts’ (.mlx, which can be run using MATLAB), and are also included as .pdf and .html files with output plots included (which can be viewed without a MATLAB license and installation). The data files and modelling scripts are organized into a .zip folder for each of the three FTR experiments (three flow rates).

54 ENVIRONMENTAL SCIENCES↗

Validation and Recalibration of the Solubility Models in Support of the Heater Test in Salt Formations

The US Department of Energy Office of Nuclear Energy is conducting a brine availability heater test to characterize the thermal, mechanical, hydrological and chemical response of salt at elevated temperatures. In the heater test, brines will be collected and analyzed for chemical compositions. In order to support the geochemical modeling of chemical evolutions of the brines during the heater test, we are recalibrating and validating the solubility models for the mineral constituents in salt formations up to 100°C, based on the solubility data in multiple component systems as well as simple systems from literature. In this work, we systematically compare the model-predicted values based on the various solubility models related to the constituents of salt formations, with the experimental data. As halite is the dominant constituent in salt formations, we first test the halite solubility model in the Na-Mg-Cl dominated brines. We find the existing halite solubility model systematically over-predict the solubility of halite. We recalibrate the halite model, which can reproduce halite solubilities in Na-Mg-Cl dominated brines well. As gypsum/anhydrite in salt formations controls the sulfate concentrations in associated brines, we test the gypsum solubility model in NaCl solutions up to 5.87 mol•kg –1 from 25 ° C to 50 ° C. The testing shows that the current gypsum solubility model reproduces the experimental data well when NaCl concentrations are less than 1 mol•kg –1 . However, at NaCl concentrations higher than 1, the model systematically overpredicts the solubility of gypsum. In the Na + —Cl – —SO 4 2– —CO 3 2– system, the validation tests up to 100 ° C demonstrate that the model excellently reproduces the experimental data for the solution compositions equilibrated with one single phase such as halite (NaCl) or thenardite (Na 2 SO 4 ), with deviations equal to, or less than, 1.5 %. The model is much less ideal in reproducing the compositions in equilibrium with the assemblages of halite + thenardite, and of halite + thermonatrite (Na 2 CO 3 •H 2 O), with deviations up to 31 %. The high deviations from the experimental data for the multiple assemblages in this system at elevated temperatures may be attributed to the facts that the database has the Pitzer interaction parameters for Cl – —CO 3 2– and SO 4 2– —CO 3 2– only at 25 ° C. Finally, in the Na + —Ca 2+ —SO 4 2– —HCO 3 – system, the validation tests also demonstrate that the model reproduces the equilibrium compositions for one single phase such as gypsum better than the assemblages of more than one phase.

36 MATERIALS SCIENCE↗

Navigating the complexities of solvent and binder selection for solution processing of sulfide solid-state electrolytes

We introduce a paradigm of solvent and binder selection for solution-processing Li 6 PS 5 Cl solid-state electrolyte particles based on Hansen solubility parameters. Treatment of the Li 6 PS 5 Cl in selected solvents results in particle morphological change, but crystallographic structure remains intact. Although solution processing reduced the Li 6 PS 5 Cl ionic conductivity, it promotes interfacial stability by alleviating reduction of the solid electrolyte in contact with Li metal. In conclusion, these findings have the potential to enhance the stability, structural integrity, and performance of sulfide solid-state electrolytes in practical applications.

25 ENERGY STORAGE↗

Bioinspired synthesis of thermally stable and mechanically strong nanocomposite coatings

Abstract An innovative biomimetic method has been developed to synthesize layered nanocomposite coatings using silica and sugar-derived carbon to mimic the formation of a natural seashell structure. The layered nanocomposites are fabricated through alternate coatings of condensed silica and sugar. Sugar-derived carbon is a cost-effective material as well as environmentally friendly. Pyrolysis of sugar will form polycyclic aromatic carbon sheets, i.e., carbon black. The resulting final nanocomposite coatings can survive temperatures of more than 1150 °C and potentially up to 1650 °C. These coatings have strong mechanical properties, with hardness of more than 11 GPa and elastic modulus of 120 GPa, which are 80% greater than those of pure silica. The layered coatings have many applications, such as shielding in the form of mechanical barriers, body armor, and space debris shields. Graphical abstract

36 MATERIALS SCIENCE↗

Wildfires identification: Semantic segmentation using support vector machine classifier

This paper deals with wildfire identification in the Alaska regions as a semantic segmentation task using support vector machine classifiers. Instead of colour information represented by means of BGR channels, we proceed with a normalized reflectance over 152 days so that such time series is assigned to each pixel. We compare models associated with $\mathcal{l}1$-loss and $\mathcal{l}2$-loss functions and stopping criteria based on a projected gradient and duality gap in the presented benchmarks.

Pecha, Marek↗

Hydroxylpyromorphite, a mineral important to lead remediation: Modern description and characterization

Abstract Hydroxylpyromorphite, Pb5(PO4)3(OH), has been documented in the literature as a synthetic and naturally occurring phase for some time but has not previously been formally described as a mineral. It is fully described here for the first time using crystals collected underground in the Copps mine, Gogebic County, Michigan. Hydroxylpyromorphite occurs as aggregates of randomly oriented hexagonal prisms, primarily between about 20–35 μm in length and 6–10 μm in diameter. The mineral is colorless and translucent with vitreous luster and white streak. The Mohs hardness is ~3½–4; the tenacity is brittle, the fracture is irregular, and indistinct cleavage was observed on {001}. Electron microprobe analyses provided the empirical formula Pb4.97(PO4)3(OH0.69F0.33Cl0.06)Σ1.08. The calculated density using the measured composition is 7.32 g/cm3. Powder X-ray diffraction data for the type material is compared to data previously reported for hydroxylpyromorphite from the talc mine at Rabenwald, Austria, and from Whytes Cleuch, Wanlockhead, Scotland. Hydroxylpyromorphite is hexagonal, P63/m, at 100 K, a = 9.7872(14), c = 7.3070(10) Å, V = 606.16(19) Å3, and Z = 2. The structure [R1 = 0.0181 for 494 F>4σ(F) reflections] reveals that hydroxylpyromorphite adopts a column anion arrangement distinct from other members of the apatite supergroup due to the presence of fluorine and steric constraints imposed by stereoactive lone-pair electrons of Pb2+ cations. The F– anion sites are displaced slightly from hydroxyl oxygen anions, which allows for stronger hydrogen-bonding interactions that may in turn stabilize the observed column-anion arrangement and overall structure. Our modern characterization of hydroxylpyromorphite provides deeper understanding to a mineral useful for remediation of lead-contaminated water.

Geochemistry & Geophysics↗

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗

Round 3 Update of Stress Testing Results for Organic Light-Emitting Diode Panels and Luminaires

Organic light-emitting diode (OLED) sources are a potential solid-state lighting technology for use in indoor lighting applications. Some of the advantages offered by OLEDs include thin profiles, low glare, diffuse lighting, and unique form factors. The U.S. Department of Energy (DOE) has released six technical reports focused on OLED technologies to provide information and analysis to the lighting industry. These reports include the evaluation of two different field deployment sites, a market analysis, a tear-down analysis, and two independent assessments of the performance of select commercially available OLED products. This report builds on earlier DOE efforts with OLED technology by updating information about previously benchmarked commercial OLED products. Specifically, this report provides updated findings about the robustness and reliability of commercial OLED products.

42 ENGINEERING↗

Impacts of High Variable Renewable Energy Futures on Electric-Sector Decision Making: Demand-Side Effects

Previous work by the Berkeley Lab describes how high shares of variable renewable energy (VRE) such as wind and solar power could change wholesale electricity price dynamics. These include the timing of when electricity is cheap or expensive, locational differences in the cost of electricity, and the degree of regularity or predictability in those costs. Many decentralized decision-makers on the demand-side may not yet have considered the implications of these possible future changes. In this report, we evaluate the sensitivity of a set of demand-side decisions to different levels of VRE penetration ranging from a low of 5-20% to a high of 40-50%. The analysis builds on hourly wholesale energy and capacity prices in different VRE scenarios for four wholesale markets in the United States for the year 2030 (CAISO, ERCOT, NYISO, and SPP). The principal question for this exploration is whether private and public electric-sector decisions that are made based on assumptions reflecting low VRE levels still achieve their intended objective in a high VRE scenario with 40-50% wind and solar? This scoping report evaluates the impacts of changing patterns of peak system needs on the benefits of demand reductions by examining the altered value of different energy efficiency (EE) measures. Similarly, we investigate new opportunities for large energy consumers that may arise from periods with very low wholesale electricity prices. We calculate the value of new process investments (e.g., hydrogen production and other generalized electro-commodities), showcase the varying value of new product storage investments (such as reservoir extensions at a desalination plant), and estimate the benefits of increased process flexibility that uses electricity as a process-input in addition to traditional fossil fuels (e.g., district energy systems). Finally, many decentralized decision-makers and end-use customers are not directly exposed to wholesale electricity prices but instead receive price signals from their retail electricity rates. As wind and solar shares increase, we compare the economic efficiency of flat retail rates relative to more dynamic time-of-use tariffs with and without critical peak-pricing events.

14 SOLAR ENERGY↗