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At least 829 records · Page 46

Position Paper - pFLogger: The Parallel Fortran Logging framework for HPC Applications

In the context of high performance computing (HPC), software investments in support of text-based diagnostics, which monitor a running application, are typically limited compared to those for other types of IO. Examples of such diagnostics include reiteration of configuration parameters, progress indicators, simple metrics (e.g., mass conservation, convergence of solvers, etc.), and timers. To some degree, this difference in priority is justifiable as other forms of output are the primary products of a scientific model and, due to their large data volume, much more likely to be a significant performance concern. In contrast, text-based diagnostic content is generally not shared beyond the individual or group running an application and is most often used to troubleshoot when something goes wrong. We suggest that a more systematic approach enabled by a logging facility (or logger) similar to those routinely used by many communities would provide significant value to complex scientific applications. In the context of high-performance computing, an appropriate logger would provide specialized support for distributed and shared-memory parallelism and have low performance overhead. In this paper, we present our prototype implementation of pFlogger a parallel Fortran-based logging framework, and assess its suitability for use in a complex scientific application.

Fortran↗

POSITION PAPER - pFLogger: The Parallel Fortran Logging Framework for HPC Applications

In the context of high performance computing (HPC), software investments in support of text-based diagnostics, which monitor a running application, are typically limited compared to those for other types of IO. Examples of such diagnostics include reiteration of configuration parameters, progress indicators, simple metrics (e.g., mass conservation, convergence of solvers, etc.), and timers. To some degree, this difference in priority is justifiable as other forms of output are the primary products of a scientific model and, due to their large data volume, much more likely to be a significant performance concern. In contrast, text-based diagnostic content is generally not shared beyond the individual or group running an application and is most often used to troubleshoot when something goes wrong. We suggest that a more systematic approach enabled by a logging facility (or 'logger') similar to those routinely used by many communities would provide significant value to complex scientific applications. In the context of high-performance computing, an appropriate logger would provide specialized support for distributed and shared-memory parallelism and have low performance overhead. In this paper, we present our prototype implementation of pFlogger - a parallel Fortran-based logging framework, and assess its suitability for use in a complex scientific application.

Clune, Thomas L.↗

pFlogger: The Parallel Fortran Logging Utility

In the context of high performance computing (HPC), software investments in support of text-based diagnostics, which monitor a running application, are typically limited compared to those for other types of IO. Examples of such diagnostics include reiteration of configuration parameters, progress indicators, simple metrics (e.g., mass conservation, convergence of solvers, etc.), and timers. To some degree, this difference in priority is justifiable as other forms of output are the primary products of a scientific model and, due to their large data volume, much more likely to be a significant performance concern. In contrast, text-based diagnostic content is generally not shared beyond the individual or group running an application and is most often used to troubleshoot when something goes wrong. We suggest that a more systematic approach enabled by a logging facility (or 'logger)' similar to those routinely used by many communities would provide significant value to complex scientific applications. In the context of high-performance computing, an appropriate logger would provide specialized support for distributed and shared-memory parallelism and have low performance overhead. In this paper, we present our prototype implementation of pFlogger - a parallel Fortran-based logging framework, and assess its suitability for use in a complex scientific application.

Clune, Tom↗

Study of Advanced Occupant Models to Quantify Injury Risk for eVTOL Vehicles

Urban transportation is currently evolving from traditional ground-based vehicles (cars, taxis, and buses) to include air-based electric vertical take-off and landing (eVTOL) vehicles which can be utilized for on-demand transportation, cargo transport, and emergency services. These new eVTOL vehicles are designed to be small, lightweight, and able to operate autonomously without user intervention. Safety is a big part of eventual eVTOL adoption, however gaps in the consideration of safety features exist. Anthropomorphic test devices (ATDs) are used in aerospace crashworthiness standards to quantify occupant injury risk and develop improved safety designs for emergency landing situations, but the ATDs currently used in aircraft certification requirements were developed many decades ago. Developments have occurred over the years involving ATD technology, which includes a host of newer and more biofidelic ATDs such as the Test Device for Human Occupant Restraint (THOR). Increased computing power has also allowed for detailed computational human body models (HBMs) to be created, such as the Global Human Body Model Consortium (GHBMC). This study aims to assess the capability of both HBMs and new ATD designs to identify injury mechanisms within eVTOL relevant emergency landing conditions. Finite element (FE) analysis was used to expand upon full-scale and seat level impact testing conducted by researchers at the National Aeronautics and Space Administration (NASA) to look at effects of occupant model configurations on prediction of injury. The GHBMC HBM and THOR ATD models were simulated in the seat level test conditions to characterize differences between these advanced assessment tools and traditional ATDs in the isolated seat loading environment. Results identified key differences in the responses from each of the models utilized and compared their impact response in head, neck, and spinal injury metrics. The THOR model identified potential risks for head injuries due to head impacts on the seat, however it predicted lower spinal loads than the other occupant surrogates. The GHBMC showed distinctly different biomechanical responses compared to the ATD. The GHBMC model is much more deformable than the ATDs and it exhibited higher distribution of forces and increased sensitivity to the duration of acceleration pulses. Both models incorporated into this study identified key mechanisms for injury that should be considered for passenger safety in the development of these novel aircraft. In addition, this study demonstrated the value of FE modeling for running a variety of complex human surrogates to identify potential injury mechanisms for consideration in regulation and development of new aircraft. Continued research in this field to improve validation these models will only lead to safer aircraft and more comprehensive safety measures.

Crashworthiness↗

Study of Advanced Occupant Models to Quantify Injury Risk for eVTOL Vehicles

Urban transportation is currently evolving from traditional ground-based vehicles (cars, taxis, and buses) to include air-based electric vertical take-off and landing (eVTOL) vehicles which can be utilized for on-demand transportation, cargo transport, and emergency services. These new eVTOL vehicles are designed to be small, lightweight, and able to operate autonomously without user intervention. Safety is a big part of eventual eVTOL adoption, however gaps in the consideration of safety features exist. Anthropomorphic test devices (ATDs) are used in aerospace crashworthiness standards to quantify occupant injury risk and develop improved safety designs for emergency landing situations, but the ATDs currently used in aircraft certification requirements were developed many decades ago. Developments have occurred over the years involving ATD technology, which includes a host of newer and more biofidelic ATDs such as the Test Device for Human Occupant Restraint (THOR). Increased computing power has also allowed for detailed computational human body models (HBMs) to be created, such as the Global Human Body Model Consortium (GHBMC). This study aims to assess the capability of both HBMs and new ATD designs to identify injury mechanisms within eVTOL relevant emergency landing conditions. Finite element (FE) analysis was used to expand upon full-scale and seat level impact testing conducted by researchers at the National Aeronautics and Space Administration (NASA) to look at effects of occupant model configurations on prediction of injury. The GHBMC HBM and THOR ATD models were simulated in the seat level test conditions to characterize differences between these advanced assessment tools and traditional ATDs in the isolated seat loading environment. Results identified key differences in the responses from each of the models utilized and compared their impact response in head, neck, and spinal injury metrics. The THOR model identified potential risks for head injuries due to head impacts on the seat, however it predicted lower spinal loads than the other occupant surrogates. The GHBMC showed distinctly different biomechanical responses compared to the ATD. The GHBMC model is much more deformable than the ATDs and it exhibited higher distribution of forces and increased sensitivity to the duration of acceleration pulses. Both models incorporated into this study identified key mechanisms for injury that should be considered for passenger safety in the development of these novel aircraft. In addition, this study demonstrated the value of FE modeling for running a variety of complex human surrogates to identify potential injury mechanisms for consideration in regulation and development of new aircraft. Continued research in this field to improve validation these models will only lead to safer aircraft and more comprehensive safety measures.

Crashworthiness↗

Tuning the Legacy Survey of Space and Time (LSST) Observing Strategy for Solar System Science

Abstract The Vera C. Rubin Observatory is expected to start the Legacy Survey of Space and Time (LSST) in early to mid-2025. This multiband wide-field synoptic survey will transform our view of the solar system, with the discovery and monitoring of over five million small bodies. The final survey strategy chosen for LSST has direct implications on the discoverability and characterization of solar system minor planets and passing interstellar objects. Creating an inventory of the solar system is one of the four main LSST science drivers. The LSST observing cadence is a complex optimization problem that must balance the priorities and needs of all the key LSST science areas. To design the best LSST survey strategy, a series of operation simulations using the Rubin Observatory scheduler have been generated to explore the various options for tuning observing parameters and prioritizations. We explore the impact of the various simulated LSST observing strategies on studying the solar system’s small body reservoirs. We examine what are the best observing scenarios and review what are the important considerations for maximizing LSST solar system science. In general, most of the LSST cadence simulations produce ±5% or less variations in our chosen key metrics, but a subset of the simulations significantly hinder science returns with much larger losses in the discovery and light-curve metrics.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluating the factors influencing accuracy, interpretability, and reproducibility in the use of machine learning classifiers in biology to enable standardization

The complexity and variability of biological data has promoted the increased use of machine learning methods to understand processes and predict outcomes. These same features complicate reliable, reproducible, interpretable, and responsible use of such methods, resulting in questionable relevance of the derived. outcomes. Here we systematically explore challenges associated with applying machine learning to predict and understand biological processes using a well- characterized in vitro experimental system. We evaluated factors that vary while applying machine learning classifers: (1) type of biochemical signature (transcripts vs. proteins), (2) data curation methods (pre- and post-processing), and (3) choice of machine learning classifier. Using accuracy, generalizability, interpretability, and reproducibility as metrics, we found that the above factors significantly mod- ulate outcomes even within a simple model system. Our results caution against the unregulated use of machine learning methods in the biological sciences, and strongly advocate the need for data standards and validation tool-kits for such studies.

59 BASIC BIOLOGICAL SCIENCES↗

When ancient numerical demons meet physics-informed machine learning: adjoint-based gradients for implicit differentiable modeling

Recent advances in differentiable modeling, a genre of physics-informed machine learning that trains neural networks (NNs) together with process-based equations, have shown promise in enhancing hydrological models' accuracy, interpretability, and knowledge-discovery potential. Current differentiable models are efficient for NN-based parameter regionalization, but the simple explicit numerical schemes paired with sequential calculations (operator splitting) can incur numerical errors whose impacts on models' representation power and learned parameters are not clear. Implicit schemes, however, cannot rely on automatic differentiation to calculate gradients due to potential issues of gradient vanishing and memory demand. Here we propose a “discretize-then-optimize” adjoint method to enable differentiable implicit numerical schemes for the first time for large-scale hydrological modeling. The adjoint model demonstrates comprehensively improved performance, with Kling–Gupta efficiency coefficients, peak-flow and low-flow metrics, and evapotranspiration that moderately surpass the already-competitive explicit model. Therefore, the previous sequential-calculation approach had a detrimental impact on the model's ability to represent hydrological dynamics. Furthermore, with a structural update that describes capillary rise, the adjoint model can better describe baseflow in arid regions and also produce low flows that outperform even pure machine learning methods such as long short-term memory networks. The adjoint model rectified some parameter distortions but did not alter spatial parameter distributions, demonstrating the robustness of regionalized parameterization. Despite higher computational expenses and modest improvements, the adjoint model's success removes the barrier for complex implicit schemes to enrich differentiable modeling in hydrology.

58 GEOSCIENCES↗

Advances in Hyperspectral Image Classification Methods for Vegetation and Agricultural Cropland Studies

Hyperspectral data are becoming more widely available via sensors on airborne and unmanned aerial vehicle (UAV) platforms, as well as proximal platforms. While space-based hyperspectral data continue to be limited in availability, multiple spaceborne Earth-observing missions on traditional platforms are scheduled for launch, and companies are experimenting with small satellites for constellations to observe the Earth, as well as for planetary missions. Land cover mapping via classification is one of the most important applications of hyperspectral remote sensing and will increase in significance as time series of imagery are more readily available. However, while the narrow bands of hyperspectral data provide new opportunities for chemistry-based modeling and mapping, challenges remain. Hyperspectral data are high dimensional, and many bands are highly correlated or irrelevant for a given classification problem. For supervised classification methods, the quantity of training data is typically limited relative to the dimension of the input space. The resulting Hughes phenomenon, often referred to as the curse of dimensionality, increases potential for unstable parameter estimates, overfitting, and poor generalization of classifiers. This is particularly problematic for parametric approaches such as Gaussian maximum likelihood–based classifiers that have been the backbone of pixel-based multispectral classification methods. This issue has motivated investigation of alternatives, including regularization of the class covariance matrices, ensembles of weak classifiers, development of feature selection and extraction methods, adoption of nonparametric classifiers, and exploration of methods to exploit unlabeled samples via semi-supervised and active learning. Data sets are also quite large, motivating computationally efficient algorithms and implementations. This chapter provides an overview of the recent advances in classification methods for mapping vegetation using hyperspectral data. Three data sets that are used in the hyperspectral classification literature (e.g., Botswana Hyperion satellite data and AVIRIS airborne data over both Kennedy Space Center and Indian Pines) are described in Section 3.2 and used to illustrate methods described in the chapter. An additional high-resolution hyperspectral data set acquired by a SpecTIR sensor on an airborne platform over the Indian Pines area is included to exemplify the use of new deep learning approaches, and a multiplatform example of airborne hyperspectral data is provided to demonstrate transfer learning in hyperspectral image classification. Classical approaches for supervised and unsupervised feature selection and extraction are reviewed in Section 3.3. In particular, nonlinearities exhibited in hyperspectral imagery have motivated development of nonlinear feature extraction methods in manifold learning, which are outlined in Section 3.3.1.4. Spatial context is also important in classification of both natural vegetation with complex textural patterns and large agricultural fields with significant local variability within fields. Approaches to exploit spatial features at both the pixel level (e.g., co-occurrence–based texture and extended morphological attribute profiles [EMAPs]) and integration of segmentation approaches (e.g., HSeg) are discussed in this context in Section 3.3.2. Recently, classification methods that leverage nonparametric methods originating in the machine learning community have grown in popularity. An overview of both widely used and newly emerging approaches, including support vector machines (SVMs), Gaussian mixture models, and deep learning based on convolutional neural networks is provided in Section 3.4. Strategies to exploit unlabeled samples, including active learning and metric learning, which combine feature extraction and augmentation of the pool of training samples in an active learning framework, are outlined in Section 3.5. Integration of image segmentation with classification to accommodate spatial coherence typically observed in vegetation is also explored, including as an integrated active learning system. Exploitation of multisensor strategies for augmenting the pool of training samples is investigated via a transfer learning framework in Section 3.5.1.2. Finally, we look to the future, considering opportunities soon to be provided by new paradigms, as hyperspectral sensing is becoming common at multiple scales from ground-based and airborne autonomous vehicles to manned aircraft and space-based platforms.

Pasolli, Edoardo↗

Cost-constrained adaptive simulations of transient spray combustion in a gas turbine combustor

Predictive high-fidelity simulations of turbulent spray combustion must capture the combined effects of complex chemistry, multiphase evaporating flow and spray-flame interactions to achieve physical accuracy. Finite-rate chemistry (FRC) combined with a realistic chemical mechanism is a combustion model well-suited for this purpose, but has a high computational cost due to the large number and stiffness of transported chemical species. In contrast, flamelet-based models achieve lower cost by transporting a small number of quantities of reduced stiffness, but assumptions regarding local flame topology, boundary conditions and inter-phase coupling limit their physical accuracy. Recently, the Pareto-efficient combustion (PEC) framework was developed to dynamically assign combustion models based on local cost and accuracy metrics in gas-phase reacting flows. In this work, we extend this PEC framework to spray combustion through the rigorous analysis of the multiphase coupling terms in the governing equations. The derivation shows that spray evaporation causes errors in the prediction of species mass fractions for flamelet-based models due to the sensitivity of the local thermo-chemical state to changes in composition caused by fuel vaporization across combustion regimes present in practical spray combustion devices. Sub-model assignment is formulated as a multiple-choice knapsack problem, where computational cost is directly controlled through the fraction of the domain assigned to the FRC sub-model. The extended PEC formulation is applied to the simulation of a realistic rich-quench-lean gas turbine combustor at steady-state conditions, as well as transient operation resulting in lean blow-out (LBO). Analysis of transient simulations during LBO demonstrates the extended PEC formulation’s capacity to dynamically adapt to changing conditions within the combustor. Transient combustor dynamics are shown to approach convergence with limited increases in computational cost, while retaining substantial computational cost reduction compared to monolithic FRC simulations. Through PEC simulations with increasing fractions of the domain assigned to FRC, monolithic flamelet simulations are shown to over-predict flame stability during LBO. Finally, the extended PEC formulation is thus shown to overcome deficiencies of monolithic models by controlling modeling error for multiphase combustion modeling.

33 ADVANCED PROPULSION SYSTEMS↗

Information Content of Aerosol Retrievals in the Sunglint Region

We exploit quantitative metrics to investigate the information content in retrievals of atmospheric aerosol parameters (with a focus on single-scattering albedo), contained in multi-angle and multi-spectral measurements with sufficient dynamical range in the sunglint region. The simulations are performed for two classes of maritime aerosols with optical and microphysical properties compiled from measurements of the Aerosol Robotic Network. The information content is assessed using the inverse formalism and is compared to that deriving from observations not affected by sunglint. We find that there indeed is additional information in measurements containing sunglint, not just for single-scattering albedo, but also for aerosol optical thickness and the complex refractive index of the fine aerosol size mode, although the amount of additional information varies with aerosol type.

aerosols↗

Dense 3D-Reconstruction from Monocular Image Sequences for Computationally Constrained UAS

The ability to find safe landing sites over complex 3D terrain is an essential safety feature for fully autonomous small unmanned aerial systems (UAS), which requires on-board perception for 3D reconstruction and terrain analysis if the overflown terrain is unknown. This is a challenge for UAS that are limited in size, weight and computational power, such as small rotorcrafts executing autonomous missions on Earth, or in planetary applications such as the Mars Helicopter. For such a computationally constraint system, we propose a structure from motion approach that uses inputs from a single downward facing camera to produce dense point clouds of the overflown terrain in real time. In contrast to existing approaches, our method uses metric pose information from a visual-inertial odometry algorithm as camera pose priors, which allows deploying a fast pose refinement step to align camera frames such that a conventional stereo algorithm can be used for dense 3D reconstruction. We validate the performance of our approach with extensive evaluations in simulation, and demonstrate the feasibility with data from UAS flights.

Brockers, Roland↗

Uncertainty Estimates for Fitting Zernike Polynomials to Discrete Data

Zernike polynomials are a widely used metric in modern optical analysis. They conveniently represent surfaces as a series of weighted terms corresponding to various optical aberrations. Ideally, each term is independent of others in the series, but Zernike polynomials lose this property when working with sets of discrete data. This gives rise to uncertainty in each polynomial’s actual contribution and affects metrology and simulation estimates of their relative weights. Several factors influencing these estimates are the number and arrangement of sample locations, the method for calculating the weights, and the total number of Zernike terms used in the calculation. Discussed is the uncertainty associated with linear regression using random sampling. Other topics reviewed are complex Zernike polynomials and vector spaces of functions.

Zernike Polynomials↗

C3 generic workstation: Performance metrics and applications

The large number of integrated dependent measures available on a command, control, and communications (C3) generic workstation under development are described. In this system, embedded communications tasks will manipulate workload to assess the effects of performance-enhancing drugs (sleep aids and decongestants), work/rest cycles, biocybernetics, and decision support systems on performance. Task performance accuracy and latency will be event coded for correlation with other measures of voice stress and physiological functioning. Sessions will be videotaped to score non-verbal communications. Physiological recordings include spectral analysis of EEG, ECG, vagal tone, and EOG. Subjective measurements include SWAT, fatigue, POMS and specialized self-report scales. The system will be used primarily to evaluate the effects on performance of drugs, work/rest cycles, and biocybernetic concepts. Performance assessment algorithms will also be developed, including those used with small teams. This system provides a tool for integrating and synchronizing behavioral and psychophysiological measures in a complex decision-making environment.

Eddy, Douglas R.↗

Neural embedding: learning the embedding of the manifold of physics data

In this paper, we present a method of embedding physics data manifolds with metric structure into lower dimensional spaces with simpler metrics, such as Euclidean and Hyperbolic spaces. We then demonstrate that it can be a powerful step in the data analysis pipeline for many applications. Using progressively more realistic simulated collisions at the Large Hadron Collider, we show that this embedding approach learns the underlying latent structure. With the notion of volume in Euclidean spaces, we provide for the first time a viable solution to quantifying the true search capability of model agnostic search algorithms in collider physics (i.e. anomaly detection). Finally, we discuss how the ideas presented in this paper can be employed to solve many practical challenges that require the extraction of physically meaningful representations from information in complex high dimensional datasets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Characterizing the acceleration time of laser-driven ion acceleration with data-informed neural networks

Peak ion energy is an important figure-of-merit in short-pulse, laser-driven ion acceleration and is dependent on an associated acceleration time. Standard metrics for these quantities depend on analytical results such as the self-similar fluid model or empirical models based on relatively small experimental and simulation datasets. In this work we attempt to use a data-informed neural network (NN) as a surrogate model for a large ensemble of PIC simulations to investigate an effective acceleration time. We explore the application of a stacked convolutional and recurrent NN architecture for improved regression by incorporating the time dependencies of the data into the training process. Of particular note is how pretraining a network on lower fidelity data, e.g. 1D analytical results, greatly improves the network's ability to learn more complex, higher fidelity data. Finally, the dependency of the acceleration time on various laser and plasma parameters is explored.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The Effect of Updraft Entrainment on Convective Cell Deepening in Realistic Large-Eddy Simulations

Entrainment of surrounding cooler and drier air into convective updrafts is one of the key processes that influence deep convection initiation and growth. Numerous studies have investigated the effect of entrainment on isolated convective cloud growth in idealized simulations, but the importance of this effect in realistic conditions with many interacting convective clouds remains uncertain. We examine the impact of entrainment on the depth reached by convective clouds in realistic large-eddy simulations (LES) over central Argentina during the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign. Cloudy updrafts and their associated properties are assigned to convective cells tracked with radar reflectivity signatures. Several thousand convective cells are tracked over two high convective available potential energy (CAPE) and two low CAPE cases that support cells of varying depths and intensities. Entrainment is calculated explicitly as the fluxes of air into the outer surface of each cloudy updraft. Single-predictor logistic regression models are used to determine the relative importance of updraft, near-updraft, and preconvective initiation atmospheric conditions in predicting whether convective cells become deep. We then build a multiple-predictor regression model pairing important updraft and meteorological metrics with fractional entrainment rate. The probability of cells transitioning to deep convection is most sensitive to ambient 600-hPa relative humidity (42% of total metric contribution to cloud depth predictability), followed by low-level CAPE (28%), cloud-base updraft width (19%), and fractional entrainment (11%). Thus, the initial width of the updraft along with potential buoyancy and its dilution through the midtroposphere collectively determine whether deep convection will result from shallower clouds.

54 ENVIRONMENTAL SCIENCES↗

Critical Assessment of Metagenome Interpretation: the second round of challenges

Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

54 ENVIRONMENTAL SCIENCES↗