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At least 685 records · Page 38

Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, an open-source mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or protein data bank ID and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Efficient Storage-Driven Machine Learning Model for Performance in the Era of Multimodal Scientific Data

Scientific workflows are increasingly relying on machine learning (ML), simulation, and hybrid techniques to predict, understand, and optimize the behavior of complex experiments. High-performance computing has greatly improved researchers’ ability to acquire diverse data modalities in these workflows. Recent studies suggest that the performance of machine learning models can be improved by integrating data from various sources. Unfortunately, these workloads pose unprecedent pressure on the network storage to meet the demands associated with accessing these multimodal data. To mitigate the impact of intensive IO, we propose a solution that utilizes a multi-tier High-Performance Computing (HPC) distributed storage and data processing framework, placing computation where the data resides for better performance. By adopting this project, the scientific community will gain new opportunities to explore multimodal storage-driven possibilities, integrating multiple scientific data sources with advanced streaming frameworks. Additionally, our framework effectively utilizes computing resources and bridges the gaps identified by HPC experts. Our proposed approach tackles scalability and persistence challenges by leveraging native persistency, which has posed difficulties in traditional approaches. Furthermore, we seek to enhance fault-tolerance and load-balance of computations by leveraging real-time streaming in diverse scientific computing environments, thereby propelling advanced scientific computing research into the next generation.

97 MATHEMATICS AND COMPUTING↗

Real-time High-resolution X-Ray Computed Tomography

Computed Tomography (CT) serves as a key imaging technology that relies on computationally intensive filtering and back-projection algorithms for 3D image reconstruction. While conventional high-resolution image reconstruction (> 2K3) solutions provide quick results, they typically treat reconstruction as an offline workload to be performed remotely on large-scale HPC systems. The growing demand for post-construction AI-driven analytics and the need for real-time adjustments call for high-resolution reconstruction solutions that are feasible on local computing resources, i.e. a multi-GPU server at most. In this paper, we propose a novel approach that utilizes Tensor Cores to optimize image reconstruction without sacrificing precision. We also introduce a framework designed to enable real-time execution of end-to-end distributed image reconstruction in a multi-GPU environment. Evaluations conducted on a single Nvidia A100 and H100 GPU show performance improvements of 1.91 × and 2.15 × compared to highly optimized production libraries. Furthermore, our framework, when deployed on 8-card Nvidia A100 GPU system, demonstrates the ability to reconstruct real-world datasets into 20483 volumes (32 GB) in slightly more than one minute and 40963 volumes (256 GB) in 7 minutes.

Wu, Du↗

tomoCAM : fast model-based iterative reconstruction via GPU acceleration and non-uniform fast Fourier transforms

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM , is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter -based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Using Signal Clustering Similarity for Detecting CAN Masquerade Attacks

The computer code assumes that time series representing the physical signals of the vehicle have been extracted from the CAN bus. The main input of the computer code is the multivariate time series representation of the signals in the CAN bus. The computer code cluster these time series using agglomerative hierarchical clustering from benign and attack datasets. Based on this, it generates probability distributions from the similarity of the obtained clusters based in each scenario---benign and attack---using the CluSim method (https://github.com/Hoosier-Clusters/clusim). Finally, it compares how a new data collection compares with the previous distribution to provide and probability score for an intrusion.

Moriano, Pablo↗

Diaspora: Resilience-Enabling Services for Real-Time Distributed Workflows

The need for real-time processing to enable automated decision making and experimental steering has driven a shift from high-performance computing workflows on a centralized system to a distributed approach that integrates remote data sources, edge devices, and diverse compute facilities. Under this paradigm, data can be processed close to the source where it is generated, thus reducing latency and bandwidth usage. System resilience is thus a key challenge, requiring distributed workflows to survive component failures and to meet stringent quality-of-service requirements, which results in the need to mitigate anomalies such as congestion and low availability of resources. To address these challenges, we propose Diaspora, a unified resilience framework that is inspired by event-driven communication patterns used in public clouds. Specifically, we propose an event fabric that extends across sites, facilities, and computations to provide timely, reliable, and accurate information about data, application, and resource status. On top of the event fabric, we build resilience-enabling services that combine QoS-aware data streaming, resilient data views, resilient compute and data resources, and anomaly detection and prediction, all of which collectively enhance workflow resilience for these scientific cases.

Rao, Nageswara↗

Towards modelling AR Sco: generalized particle dynamics and strong radiation-reaction regimes

Numerical simulations of relativistic plasmas have become more feasible, popular, and crucial for various astrophysical sources with the availability of computational resources. The necessity for high-accuracy particle dynamics is especially highlighted in pulsar modelling due to the extreme associated electromagnetic fields and particle Lorentz factors. Including the radiation-reaction force in the particle dynamics adds even more complexity to the problem, but is crucial for such extreme astrophysical sources. We have also realized the need for such modelling concerning magnetic mirroring and particle injection models proposed for AR Sco, the first white dwarf pulsar. This paper demonstrates the benefits of using higher-order explicit numerical integrators with adaptive time-step methods to solve the full particle dynamics with radiation-reaction forces included. We show that for standard test scenarios, namely various combinations of uniform E- and B-fields and a static dipole B-field, the schemes we use are equivalent to and in extreme field cases outperform standard symplectic integrators in accuracy. We show that the higher-order schemes have massive computational time improvements due to the adaptive time-steps we implement, especially in non-uniform field scenarios and included radiation reaction where the particle gyro-radius rapidly changes. When balancing accuracy and computational time, we identified the adaptive Dormand–Prince eighth-order scheme to be ideal for our use cases. The schemes we use maintain accuracy and stability in describing the particle dynamics and we indicate how a charged particle enters radiation-reaction equilibrium and conforms to the analytical Aristotelian Electrodynamics expectations.

79 ASTRONOMY AND ASTROPHYSICS↗

Computing the Paschen curve for argon with speed-limited particle-in-cell simulation

Upon inclusion of collisions, the speed-limited particle-in-cell (SLPIC) simulation method successfully computed the Paschen curve for argon. The 1D3V simulations modeled an electron cascade across an argon-filled capacitor, including electron-neutral ionization, electron-neutral elastic collisions, electron-neutral excitation, and ion-induced secondary electron emission. In electrical breakdown, the timescale difference between ion and electron motion makes traditional PIC methods computationally slow. To decrease this timescale difference and speed up computation, here we used SLPIC, a time-domain algorithm that limits the speed of the fastest electrons in the simulation. The SLPIC algorithm facilitates a straightforward, fully kinetic treatment of dynamics and collisions. SLPIC was as accurate as PIC, but ran up to 200 times faster. SLPIC accurately computed the Paschen curve for argon over three orders of magnitude in pressure.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Automatic Detection of Defects in High-Reliability Components

Disastrous consequences can result from defects in manufactured parts—particularly the high consequence parts developed at Sandia. Identifying flaws in as-built parts can be done with nondestructive means, such as X-ray Computed Tomography (CT). However, due to artifacts and complex imagery, the task of analyzing the CT images falls to humans. Human analysis is inherently unreproducible, unscalable, and can easily miss subtle flaws. We hypothesized that deep learning methods could improve defect identification, increase the number of parts that can effectively be analyzed, and do it in a reproducible manner. We pursued two methods: 1) generating a defect-free version of a scan and looking for differences (PandaNet), and 2) using pre-trained models to develop a statistical model of normality (Feature-based Anomaly Detection System: FADS). Both PandaNet and FADS provide good results, are scalable, and can identify anomalies in imagery. In particular, FADS enables zero-shot (training-free) identification of defects for minimal computational cost and expert time. It significantly outperforms prior approaches in computational cost while achieving comparable results. FADS’ core concept has also shown utility beyond anomaly detection by providing feature extraction for downstream tasks.

47 OTHER INSTRUMENTATION↗

Asynchronous GPU-based DEM solver embedded in commercial CFD software with polyhedral mesh support

A novel graphical processing unit-based discrete element method solver is introduced to improve stability, performance, and provide seamless integration into commercial or open-source computational fluid dynamics software. A key innovation is eliminating a need for network communication between solvers, which was previously required for cross-platform coupling. This is accomplished by a direct coupling method that employs dynamic-linked libraries. Furthermore, the solver optimizes memory usage by streamlining the particle-cell search algorithm by eliminating the cells' searching grid. This ensures the solver is compatible with a wide range of mesh types, providing high geometric flexibility. The approach simplifies the simulation process by directly incorporating computational fluid dynamics mesh information into the discrete element method solver. The performance analysis indicates about sixteen times boost in computational speed compared to benchmark central processing unit-based solvers. Finally, the solver's compatibility with polyhedral meshes, a vital advantage for complex geometries, is tested against a referenced study regarding the simulation of an immersed-tube fluidized bed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The Role of Nuclear Data Sensitivities in Prompt α-Eigenvalue Predictions of Delayed Critical Benchmarks

Alpha (α) eigenvalues, which describe the logarithmic time derivative of the neutron population in a multiplying system, are integral to time-dependent behavior and diagnostic applications. However, uncertainties in the evaluated nuclear data can significantly impact the accuracy of transport simulations for such quantities. This work explores the use of machine learning models to predict two key outputs, α-eigenvalues and keff bias, using input features derived from α-eigenvalue sensitivities to nuclear data. The criticality safety benchmark models used in this study come from the International Handbook of Evaluated Criticality Safety Benchmark Experiments. Three models, random forest, XGBoost, and NGBoost, are trained on both energy-resolved and energy-summed α sensitivities. For the α-eigenvalue bias prediction, NGBoost achieved the highest R 2 (0.9476) using energy-resolved features, while XGBoost performed best using summed sensitivities. In contrast, when predicting the keff bias, all the models showed moderate predictive capability (best R 2 ≈ 0.72), as the mapping from the static α-sensitivities to the static keff bias was less direct. SHAP (SHapley Additive exPlanations) analysis was used to interpret the model predictions. Across both prediction tasks, the features associated with neutron capture [H-1 (n, γ)], uranium scattering reactions (such as 235 U elastic/inelastic), and actinide capture/fission reactions (such as 239 Pu and 234 U) were consistently identified as the most impactful. This highlights the key role of specific nuclear reactions and energy ranges in shaping both time-dependent and steady-state criticality behavior. These results demonstrated that α-sensitivities, despite being computed for time-dependent metrics, can provide valuable insights for predicting both α-eigenvalues and the keff bias. Moreover, machine learning models offer a promising pathway for uncovering important nuclear data dependencies and guiding future data evaluation efforts.

Nuclear data↗

Addressing deep array effects and impacts to wake steering with the cumulative-curl wake model

Abstract. Wind farm design and analysis heavily rely on computationally efficient engineering models that are evaluated many times to find an optimal solution. A recent article compared the state-of-the-art Gauss-curl hybrid (GCH) model to historical data of three offshore wind farms. Two points of model discrepancy were identified therein: poor wake predictions for turbines experiencing a lot of wakes and wake interactions between two turbines over long distances. The present article addresses those two concerns and presents the cumulative-curl (CC) model. Comparison of the CC model to high-fidelity simulation data and historical data of three offshore wind farms confirms the improved accuracy of the CC model over the GCH model in situations with large wake losses and wake recovery over large inter-turbine distances. Additionally, the CC model performs comparably to the GCH model for single- and fewer-turbine wake interactions, which were already accurately modeled. Lastly, the CC model has been implemented in a vectorized form, greatly reducing the computation time for many wind conditions. The CC model now enables reliable simulation studies for both small and large offshore wind farms at a low computational cost, thereby making it an ideal candidate for wake-steering optimization and layout optimization.

17 WIND ENERGY↗

H-AMR: A New GPU-accelerated GRMHD Code for Exascale Computing with 3D Adaptive Mesh Refinement and Local Adaptive Time Stepping

General relativistic magnetohydrodynamic (GRMHD) simulations have revolutionized our understanding of black hole accretion. Here, we present a GPU-accelerated GRMHD code H-AMR with multifaceted optimizations that, collectively, accelerate computation by 2–5 orders of magnitude for a wide range of applications. First, it introduces a spherical grid with 3D adaptive mesh refinement that operates in each of the three dimensions independently. This allows us to circumvent the Courant condition near the polar singularity, which otherwise cripples high-resolution computational performance. Second, we demonstrate that local adaptive time stepping on a logarithmic spherical-polar grid accelerates computation by a factor of ≲10 compared to traditional hierarchical time-stepping approaches. Jointly, these unique features lead to an effective speed of ~10 9 zone cycles per second per node on 5400 NVIDIA V100 GPUs (i.e., 900 nodes of the OLCF Summit supercomputer). We illustrate H-AMR's computational performance by presenting the first GRMHD simulation of a tilted thin accretion disk threaded by a toroidal magnetic field around a rapidly spinning black hole. With an effective resolution of 13,440 × 4608 × 8092 cells and a total of ≲22 billion cells and ~0.65 × 10 8 time steps, it is among the largest astrophysical simulations ever performed. We find that frame dragging by the black hole tears up the disk into two independently precessing subdisks. The innermost subdisk rotation axis intermittently aligns with the black hole spin, demonstrating for the first time that such long-sought alignment is possible in the absence of large-scale poloidal magnetic fields.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling the U.S. Western Electric Interconnection to Understand the Consequences of Hydrometeorological Extremes and Options for Risk Mitigation

Electricity grid operators around the world face a dual challenge; withstanding increasingly severe weather and the longer term impacts of climate change, while simultaneously decarbonizing. Extreme weather events such as heat waves and droughts are rising in both severity and frequency, which is threatening the reliability of electricity grids through increased demand, generation capacity losses, and equipment failures. Consequently, incorporating hydrometeorological stressors into computational power systems analysis is becoming an even more critical tool in long term planning and short term operations. However, there is a general lack of open-source customizable grid simulation software capable of exhaustively stress testing the grid under hydrometeorological uncertainty, and/or examining potential risk mitigation pathways. A related, persistent challenge for power system modelers is striking an appropriate balance between model fidelity (e.g. spatial scale and time resolution) and computational tractability (wall clock run-time). In this study, we are proposing a solution to this problem with open-source software that allows users to seamlessly customize the scale and track the accuracy of grid operations models. Our approach allows users to search over numerous model parameters (network topology, mathematical formulation, economic hurdle rates, and transmission line scaling) to identify model instantiations that accommodate experimental design. Further, we use this approach to demonstrate the importance of including extreme weather events in model validation and model selection. Focusing on the occurrence of heatwaves and droughts in the U.S. Western Interconnection, we examine role of extreme events in balancing tradeoffs between model fidelity and run-time at the model design stage.

Economics↗

Multi-element flow-driven spectral chaos (ME-FSC) method for uncertainty quantification of dynamical systems

The flow-driven spectral chaos (FSC) is a recently developed method for tracking and quantifying uncertainties in the long-time response of stochastic dynamical systems using the spectral approach. The method uses a novel concept called enriched stochastic flow maps as a means to construct an evolving finite-dimensional random function space that is both accurate and computationally efficient in time. In this paper, we present a multi-element version of the FSC method (the ME-FSC method for short) to tackle (mainly) those dynamical systems that are inherently discontinuous over the probability space. In ME-FSC, the random domain is partitioned into several elements, and then the problem is solved separately on each random element using the FSC method. Subsequently, results are aggregated to compute the probability moments of interest using the law of total probability. To demonstrate the effectiveness of the ME-FSC method in dealing with discontinuities and long-time integration of stochastic dynamical systems, four representative numerical examples are presented in this paper, including the Van-der-Pol oscillator problem and the Kraichnan-Orszag three-mode problem. Results show that the ME-FSC method is capable of solving problems that have strong nonlinear dependencies over the probability space, both reliably and at low computational cost.

97 MATHEMATICS AND COMPUTING↗

A Stochastic Reduced-Order Model for Statistical Microstructure Descriptors Evolution

Integrated computational materials engineering (ICME) models have been a crucial building block for modern materials development, relieving heavy reliance on experiments and significantly accelerating the materials design process. However, ICME models are also computationally expensive, particularly with respect to time integration for dynamics, which hinders the ability to study statistical ensembles and thermodynamic properties of large systems for long time scales. To alleviate the computational bottleneck, we propose to model the evolution of statistical microstructure descriptors as a continuous-time stochastic process using a non-linear Langevin equation, where the probability density function (PDF) of the statistical microstructure descriptors, which are also the quantities of interests (QoIs), is modeled by the Fokker–Planck equation. In this work, we discuss how to calibrate the drift and diffusion terms of the Fokker–Planck equation from the theoretical and computational perspectives. The calibrated Fokker–Planck equation can be used as a stochastic reduced-order model to simulate the microstructure evolution of statistical microstructure descriptors PDF. Considering statistical microstructure descriptors in the microstructure evolution as QoIs, we demonstrate our proposed methodology in three integrated computational materials engineering (ICME) models: kinetic Monte Carlo, phase field, and molecular dynamics simulations.

97 MATHEMATICS AND COMPUTING↗

Surrogate Model for Distribution Networks Influenced by Weather

Here, we propose a method for generating reduced representations of time series and for constructing low dimensional surrogate models for time dependent calculations of power and voltage in distribution networks. We employ Fourier polynomials. The surrogate model strategy is aimed at reducing the computational cost of time dependent simulations, albeit, at the expense of fidelity. The reduced representation is achieved by identifying a small and most consequential subset of degrees of freedom. In power and voltage distribution networks dynamics that are heavily influenced by strong cyclic weather events, e.g., the hourly, diurnal and seasonal cycles, the weather/climate time series spectrum exposes these most energetic components. Once the degrees of freedom are identified their amplitudes are optimized using training data. The key challenge in using spectral methods in power network surrogates is addressing the computation of quotients. For this we propose a numerically-stable deconvolution strategy.

Weather events↗

Parallelized real-time physics codes for plasma control on DIII-D

A real-time safe multi-threading library was developed on the DIII-D plasma control system to optimize the real-time TORBEAM and real-time STRIDE physics codes. These physics codes are crucial for future fusion power plant operation as they provide information about electron cyclotron wave propagation and heating as well as inform about ideal plasma stability limits. The real-time TORBEAM code executed consistently in under 20 ms while the real-time STRIDE code computes in 100 ms. The multi-threading library developed in this work can be applied to other real-time physics-based codes that will be crucial for the next generation of fusion devices.

DIII-D↗