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At least 1,117 records · Page 62

A performance spectrum for parallel computational frameworks that solve PDEs

Summary Important computational physics problems are often large‐scale in nature, and it is highly desirable to have robust and high performing computational frameworks that can quickly address these problems. However, it is no trivial task to determine whether a computational framework is performing efficiently or is scalable. The aim of this paper is to present various strategies for better understanding the performance of any parallel computational frameworks for solving PDEs. Important performance issues that negatively impact time‐to‐solution are discussed, and we propose a performance spectrum analysis that can enhance one's understanding of critical aforementioned performance issues. As proof of concept, we examine commonly used finite element simulation packages and software and apply the performance spectrum to quickly analyze the performance and scalability across various hardware platforms, software implementations, and numerical discretizations. It is shown that the proposed performance spectrum is a versatile performance model that is not only extendable to more complex PDEs such as hydrostatic ice sheet flow equations but also useful for understanding hardware performance in a massively parallel computing environment. Potential applications and future extensions of this work are also discussed.

Chang, J.↗

Design Rules for Metal‐Organic Framework Stability in High‐Pressure Hydrogen Environments

Abstract Stability of metal‐organic frameworks (MOFs) under hydrogen is of particular importance for a diverse range of applications, including catalysis, gas separations, and hydrogen storage. Hydrogen in gaseous form is known to be a strong reducing agent and can potentially react with the secondary building units of a MOF and decompose the porous framework structure. Moreover, rapid pressure swings expected in vehicular hydrogen storage could create significant mechanical stresses within MOF crystals that cause partial or complete pore collapse. In this work, we examined the stability of a structurally representative suite of MOFs by testing them under both static (70 MPa) and dynamic hydrogen exposure (0.5 to 10 MPa, 1000 pressure cycles) at room temperature. We aim to provide stability information for development of near room‐temperature hydrogen storage media based on MOFs and suggest framework design rules to avoid materials unstable for hydrogen storage under relevant technical conditions.

Wang, Timothy C.↗

Assessment of wildland fire impacts on watershed annual water yield: Analytical framework and case studies in the United States

More than 50% of water supplies in the conterminous United States originate on forestland or rangeland and are potentially under increasing stress as a result of larger and more severe wildfires. Little is known, however, about the long-term impacts of fire on annual water yield and the role of climate variability within this context. We here propose a framework for evaluating wildland fire impacts on streamflow that combines double-mass analysis with new methods (change point analysis, climate elasticity modeling, and process-based modeling) to distinguish between multiyear fire and climate impacts. The framework captures a wide range of fire types, watersheds characteristics, and climate conditions using streamflow data, as opposed to other approaches requiring paired watersheds. The process is illustrated with three case studies. A watershed in Arizona experienced a +266% increase in annual water yield in the 5 years after a wildfire, where +219% was attributed to wildfire and +24% to precipitation trends. In contrast, a California watershed had a lower (–64%) post-fire net water yield, comprised of enhanced flow (+38%) attributed to wildfire offset (–102%) by lower precipitation in the post-fire period. Changes in streamflow within a watershed in South Carolina had no apparent link to periods of prescribed burning but matched a very wet winter and reports of storm damage. As a result, the presented framework is unique in its ability to detect and quantify fire or other disturbances, even if the date or nature of the disturbance event is uncertain, and regardless of precipitation trends.

54 ENVIRONMENTAL SCIENCES↗

A framework for predicting impacts on ecosystem services from (sub)organismal responses to chemicals

Protection of ecosystem services is increasingly emphasized as a risk-assessment goal, but there are wide gaps between current ecological risk-assessment endpoints and potential effects on services provided by ecosystems. The authors present a framework that links common ecotoxicological endpoints to chemical impacts on populations and communities and the ecosystem services that they provide. This framework builds on considerable advances in mechanistic effects models designed to span multiple levels of biological organization and account for various types of biological interactions and feedbacks. For illustration, the authors introduce 2 case studies that employ well-developed and validated mechanistic effects models: the inSTREAM individual-based model for fish populations and the AQUATOX ecosystem model. They also show how dynamic energy budget theory can provide a common currency for interpreting organism-level toxicity. Lastly, they suggest that a framework based on mechanistic models that predict impacts on ecosystem services resulting from chemical exposure, combined with economic valuation, can provide a useful approach for informing environmental management.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer‐based monolithic column with incorporated chiral metal–organic framework for enantioseparation of methyl phenyl sulfoxide using nano‐liquid chromatography

A new approach to the preparation of enantioselective porous polymer monolithic columns with incorporated chiral metal–organic framework for nano‐liquid chromatography has been developed. While no enantioseparation was achieved with monolithic poly(4‐vinylpyridine‐co‐ethylene dimethacrylate) column, excellent separations of both enantiomers of (±)‐methyl phenyl sulfoxide were achieved with its counterpart prepared after admixing metal–organic framework [Zn 2 (benzene dicarboxylate)(l‐lactic acid)(dmf)], which is synthesized from zinc nitrate, l ‐lactic acid, and benzene dicarboxylic acid in the polymerization mixture. These novel monolithic columns combined selectivity of the chiral framework with the excellent hydrodynamic properties of polymer monoliths, may provide a great impact on future studies in the field of chiral analysis by liquid chromatography.

Wang, Xin↗

Decoding Antenna Behavior in Metal—Organic Frameworks

Metal–organic frameworks (MOFs) define a solid-state platform for developing artificial photosystems. Efficient anisotropic exciton migrations in these frameworks entail “antenna behavior” that can power up the distal interior reaction centers (RC), driving charge separation between donor-acceptor pairs. Reminiscent of the natural light-harvesting complex, such processes can achieve high quantum yield by exploiting the vast interior surface of the porous crystallites. It is important to understand the optimum positioning of the RC site relative to the anisotropic exciton migration path within these frameworks. The efficiency of such antenna behavior is probed here through Stern–Volmer (SV) type analysis with a series of node-anchored redox quenchers, ferrocene-carboxylate, ferrocene acetate, and dinitrobenzoate. Decoding various intrinsic processes, this work constructs a revised SV formalism in solid assembly that hosts ultrafast anisotropic exciton migration to account for the intrinsic exciton hopping rate from the extrinsic electron transfer rate, and the dimension of effective quenching. In conclusion, this transformative understanding can be applied to other relevant solid-state assemblies.

Saha, Bapan [Southern Illinois University, Carbond↗

Jay : A software framework for prototyping and evaluating offloading applications in hybrid edge clouds

Abstract We present Jay , a software framework for offloading applications in hybrid edge clouds. Jay provides an API, services, and tools that enable mobile application developers to implement, instrument, and evaluate offloading applications using configurable cloud topologies, offloading strategies, and job types. We start by presenting Jay 's job model and the concrete architecture of the framework. We then present the programming API with several examples of customization. Then, we turn to the description of the internal implementation of Jay instances and their components. Finally, we describe the Jay Workbench, a tool that allows the setup, execution, and reproduction of experiments with networks of hosts with different resource capabilities organized with specific topologies. The complete source code for the framework and workbench is provided in a GitHub repository.

Silva, Joaquim↗

BeamDyn: a high-fidelity wind turbine blade solver in the FAST modular framework

Here, this paper presents a numerical implementation of the geometrically exact beam theory based on the Legendre-spectral-finite-element (LSFE) method. The displacement-based geometrically exact beam theory is presented, and the special treatment of three-dimensional rotation parameters is reviewed. An LSFE is a high-order finite element with nodes located at the Gauss-Legendre-Lobatto points. These elements can be an order of magnitude more computationally efficient than low-order finite elements for a given accuracy level. The new module, BeamDyn, is implemented in the FAST modularization framework for dynamic simulation of highly flexible composite-material wind turbine blades within the FAST aeroelastic engineering model. The framework allows for fully interactive simulations of turbine blades in operating conditions. Numerical examples are provided to validate BeamDyn and examine the LSFE performance as well as the coupling algorithm in the FAST modularization framework. BeamDyn can also be used as a stand-alone high-fidelity beam tool.

17 WIND ENERGY↗

Framework for assessing land‐management effects on at‐risk species: Example of SE USA wood pellet production and gopher tortoise ( Gopherus polyphemus )

Abstract Land‐management choices made for economic and societal gains intrinsically influence landscapes and species that are dependent upon them. We propose a simple analysis framework to examine critical intersections between land‐management choices and the life‐history conditions of selected species of concern, thereby facilitating the identification of mitigation practices that can reduce negative impacts on species at risk. We test the proposed framework through application to gopher tortoise ( Gopherus polyphemus ), a keystone species that is the focus of conservation efforts across the southeastern region of United States of America, where wood pellets are being produced for bioenergy. Production of these wood pellets for export to Europe and Asia has drastically increased in the past decade, raising concerns about potential harm to biodiversity since many species in the forests sourcing pellet production were already at risk prior to the development of this new commodity. Identifying the mechanisms of potential impacts of wood pellet production on species of concern is essential to establishing meaningful management recommendations that can enhance conservation efforts while supporting sustainable bioenergy. By considering the intersections between life‐history conditions of gopher tortoise and forest‐management practices related to woody biomass extraction for pellet production, we identify several mechanisms by which the wood‐pellet industry might affect this species of concern, both positively and negatively. We then identify mitigation practices that can help offset the potential impacts of logging, thinning, and dead wood removal on gopher tortoise. Our analysis framework may be transferable to other species of concern and land‐management practices across diverse landscapes. This article is categorized under: Bioenergy > Economics and Policy Bioenergy > Climate and Environment

54 ENVIRONMENTAL SCIENCES↗

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework

Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.

59 BASIC BIOLOGICAL SCIENCES↗

An Event Detection Framework for Virtual Observation System: Anomaly Identification for an ACME Land Simulation

Based on previous work on in-situ data transfer infrastructure and compiler-based software analysis, we have designed a virtual observation system for real time computer simulations. This paper presents an event detection framework for a virtual observation system. By using signal processing and detection approaches to the memory-based data streams, this framework can be reconfigured to capture high-frequency events and low-frequency events. These approaches used in the framework can dramatically reduce the data transfer needed for in-situ data analysis (between distributed computing nodes or between the CPU/GPU nodes). In the paper, we also use a terrestrial ecosystem system simulation within the Earth System Model to demonstrate the practical values of this effort.

Yao, Cindy↗

Interplay of the CGC and TMD frameworks to all orders in kinematic twist

A framework for an improved TMD (iTMD) factorization scheme at small x, involving off-shell perturbative subamplitudes, was recently developed as an interpolation between the TMD k t $\ll$ Q regime and the BFKL k t ~ Q regime. Here, we observe the relation between CGC and iTMD amplitudes. We first show how the dipolesize expansion of CGC amplitudes resembles the twist expansion of a TMD amplitude. Then, by isolating kinematic twists, we prove that iTMD amplitudes are obtained with infinite kinematic twist accuracy by simply getting rid of all genuine twist contributions in a CGC amplitude. Lastly, we compare the amplitudes obtained via a proper kinematic twist expansion to those obtained via a more standard dilute expansion to show the relation between the iTMD framework and the dilute low x framework. This allows to reinterpret the dilute expansion as a Wandzura-Wilczek approximation in the large k t regime

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Developing a Consistent Travel-Time Framework for Comparing Three-Dimensional Velocity Models for Seismic Location Accuracy

Abstract Location algorithms have historically relied on simple, one-dimensional (1D) velocity models for fast seismic event locations. 1D models are generally used as travel-time lookup tables, one for each seismic phase, with travel-times pre-calculated for event distance and depth. These travel-time lookup tables are extremely fast to use and this fast computational speed makes them the preferred type of velocity model for operational needs. Higher-dimensional (i.e., three-dimensional—3D) seismic velocity models are becoming readily available and provide more accurate event locations over 1D models. The computational requirements of these 3D models tend to make their operational use prohibitive. Additionally, comparing location accuracy for 3D seismic velocity models tends to be problematic, as each model is determined using different ray-tracing algorithms. Attempting to use a different algorithm than the one used to develop a model usually results in poor travel-time prediction. We demonstrate and test a framework to create first-P and first-S 3D travel-time correction surfaces using an open-source framework ( PCalc + GeoTess , https://www.sandia.gov/salsa3d/software/geotess ) that easily stores 3D travel-time and uncertainty data. This framework produces fast travel-time and uncertainty predictions and overcomes the ray-tracing algorithm hurdle because the lookup tables can be generated using the exact ray-tracing algorithm that is preferred for a model.

3D velocity models↗

ViennaX: a parallel plugin execution framework for scientific computing

We present the free open source plugin execution framework ViennaX for modularizing and parallelizing scientific simulations. In general, functionality is abstracted by the notion of a task, which is implemented as a plugin. The plugin system facilitates the utilization of both, already available functionality as well as new implementations. Each task can define arbitrary data dependencies which are used by ViennaX to build a task graph. The framework supports the execution of this dependence graph based on the message passing interface in either a serial or a parallel fashion. The applied modular approach allows for defining highly flexible simulations, as plugins can be easily exchanged. The framework's general design as well as implementation details are discussed. Applications based on the Mandelbrot set and the solution of a partial differential equation are investigated, and performance results are shown.

Weinbub, Josef↗

A framework for detection and attribution of regional precipitation change: Application to the United States historical record

Abstract Despite the emerging influence of anthropogenic climate change on the global water cycle, at regional scales the combination of observational uncertainty, large internal variability, and modeling uncertainty undermine robust statements regarding the human influence on precipitation. Here, we use output from global climate models in a perfect-data sense to develop a framework for conducting regional detection and attribution (D&A) for precipitation, starting with the contiguous United States (CONUS) where observational uncertainty is lower than in other regions. Our unified approach can simultaneously detect systematic trends in mean and extreme precipitation, attribute trends to anthropogenic forcings, compute the effects of forcings as a function of time, and map the effects of individual forcings. Model output is used to conduct a set of tests that yield a parsimonious representation for characterizing seasonal precipitation over the CONUS for the historical record (1900 to present day), which ensures our D&A is insensitive to structural uncertainty. Our framework is developed using synthetic data in a Pearl-causal perspective wherein causality can be identified using intervention-based simulations. While the hypothesis-based framework and accompanying generalized D&A formula we develop should be widely applicable, we include a strong caution that the hypothesis-guided simplification of the formula for the historical climatic record of CONUS as described in this paper will likely fail to hold in other geographic regions and under future warming.

54 ENVIRONMENTAL SCIENCES↗

A General Framework for Monitoring Image Acquisition Workflow in the Radiology Environment: Timeliness for Acute Stroke CT Imaging

Many facets of an image acquisition workflow leave a digital footprint, making workflow analysis amenable to an informatics-based solution. This paper describes a detailed framework for analyzing workflow and uses acute stroke response timeliness in CT as a practical demonstration. We review methods for accessing the digital footprints resulting from common technologist/device interactions. This overview lays a foundation for obtaining data for workflow analysis. We demonstrate the method by analyzing CT imaging efficiency in the setting of acute stroke. We successfully used digital footprints of CT technologists to analyze their workflow. We presented an overview of other digital footprints including but not limited to contrast administration, patient positioning, billing, reformat creation, and scheduling. A framework for analyzing image acquisition workflow was presented. This framework is transferable to any modality, as the key steps of image acquisition, image reconstruction, image post processing, and image transfer to PACS are common to any imaging modality in diagnostic radiology.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A smeared crack modeling framework accommodating multi-directional fracture at finite strains

A generic smeared crack modeling framework predicated on the deformation gradient decomposition (DGD) approach is proposed for use in dynamic fracture problems at finite strains, accommodating failure along multiple mutually orthogonal fracture planes embedded within an independently defined bulk material model. Within this constitutive framework, the traction equilibrium conditions imposed at each failure surface are used to determine the associated crack displacements stored as internal state variables. In general, the enforcement of interfacial equilibrium entails the implicit solution of a non-linear system of equations within the constitutive update procedure. However, if inertial effects arising due to the relative motion of the fractured material are incorporated within the model, the traction equilibrium conditions are shown to give rise to corresponding dynamic equations of motion governing the time-evolution of the crack opening displacements. For dynamic problems, an explicit time-integration procedure is devised to efficiently update the material state, subject to a set of internal frictionless contact constraints to prevent material inversion. Finally, the efficacy of the proposed modeling framework is investigated through several benchmark dynamic fracture problems run within the explicit finite element code DYNA3D.

42 ENGINEERING↗

Panda: A Compiler Framework for Concurrent CPU $+$ GPU Execution of 3D Stencil Computations on GPU-accelerated Supercomputers

We present a new compiler framework for truly heterogeneous 3D stencil computation on GPU clusters. Our framework consists of a simple directive-based programming model and a tightly integrated source-to-source compiler. Annotated with a small number of directives, sequential stencil C codes can be automatically parallelized for large-scale GPU clusters. The most distinctive feature of the compiler is its capability to generate hybrid MPI$+$ CUDA$+$ OpenMP code that uses concurrent CPU$+$ GPU computing to unleash the full potential of powerful GPU clusters. The auto-generated hybrid codes hide the overhead of various data motion by overlapping them with computation. Test results on the Titan supercomputer and the Wilkes cluster show that auto-translated codes can achieve about 90 % of the performance of highly optimized handwritten codes, for both a simple stencil benchmark and a real-world application in cardiac modeling. The user-friendliness and performance of our domain-specific compiler framework allow harnessing the full power of GPU-accelerated supercomputing without painstaking coding effort.

97 MATHEMATICS AND COMPUTING↗