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At least 919 records · Page 51

Super-Resolution for Renewable Energy Resource Data with Wind from Reanalysis Data and Application to Ukraine

With a potentially increasing share of the electricity grid relying on wind to provide generating capacity and energy, there is an expanding global need for historically accurate, spatiotemporally continuous, high-resolution wind data. Conventional downscaling methods for generating these data based on numerical weather prediction have a high computational burden and require extensive tuning for historical accuracy. In this work, we present a novel deep learning-based spatiotemporal downscaling method using generative adversarial networks (GANs) for generating historically accurate high-resolution wind resource data from the European Centre for Medium-Range Weather Forecasting Reanalysis version 5 data (ERA5). In contrast to previous approaches, which used coarsened high-resolution data as low-resolution training data, we use true low-resolution simulation outputs. We show that by training a GAN model with ERA5 as the low-resolution input and Wind Integration National Dataset Toolkit (WTK) data as the high-resolution target, we achieved results comparable in historical accuracy and spatiotemporal variability to conventional dynamical downscaling. This GAN-based downscaling method additionally reduces computational costs over dynamical downscaling by two orders of magnitude. We applied this approach to downscale 30 km, hourly ERA5 data to 2 km, 5 min wind data for January 2000 through December 2023 at multiple hub heights over Ukraine, Moldova, and part of Romania. With WTK coverage limited to North America from 2007–2013, this is a significant spatiotemporal generalization. The geographic extent centered on Ukraine was motivated by stakeholders and energy-planning needs to rebuild the Ukrainian power grid in a decentralized manner. This 24-year data record is the first member of the super-resolution for renewable energy resource data with wind from the reanalysis data dataset (Sup3rWind).

17 WIND ENERGY↗

One-sweep moment-based semi-implicit-explicit integration for gray thermal radiation transport

Thermal radiation transport (TRT) is a time dependent, high dimensional partial integro-differential equation. In practical applications such as inertial confinement fusion, TRT is coupled to other physics such as hydrodynamics, plasmas, etc., and the timescales one is interested in capturing are often much slower than the radiation timescale. As a result, TRT is treated implicitly, and due to its stiffness and high dimensionality, is often a dominant computational cost in multiphysics simulations. Here we develop a new approach for implicit-explicit (IMEX) integration of gray TRT in the deterministic SN setting, which requires only one sweep per stage, with the simplest first-order method requiring only one sweep per time step. The partitioning of equations is done via a moment-based high-order low-order formulation of TRT, where the streaming operator and first two moments are used to capture the asymptotic stiff regimes of the streaming limit and diffusion limit. Absorption-reemission is treated explicitly, and although stiff, is sufficiently damped by the implicit solve that we achieve stable accurate time integration without incorporating the coupling of the high order and low order equations implicitly. Due to nonlinear coupling of the high-order and low-order equations through temperature-dependent opacities, to facilitate IMEX partitioning and higher-order methods, we use a semi-implicit integration approach amenable to nonlinear partitions. In conclusion, results are demonstrated on thick Marshak and crooked pipe benchmark problems, demonstrating orders of magnitude improvement in accuracy and wallclock compared with the standard first-order implicit integration typically used.

97 MATHEMATICS AND COMPUTING↗

An Overset Grid Motion Driver for Resolving Entry Vehicle CFD Simulations with Large Changes in Wake Orientation

Time-accurate computational fluid dynamics (CFD) simulations using overset meshes can enable reduced computational cost compared to a rigid, monolithic mesh for blunt-body atmospheric entry vehicles. If the vehicle has a significant change in attitude, the high-density region of the overset mesh designed for resolving the subsonic wake can be kept in position as the wake orientation changes relative to the body. Current simulations generally keep the wake mesh fixed in attitude while the body rotates, assuming the wake orientation remains relatively constant. However, changes in the relative velocity over a long-duration simulation or effects of the body geometry can invalidate this assumption. This work presents a method for calculating the desired mesh orientation to resolve a blunt body wake using the atmosphere-relative velocity of the vehicle. A motion driver using these calculations is implemented in a CFD-in-the-loop flight model bridging the FUN3D flow solver and POST2 trajectory propagator. Overset meshing is performed using the Yoga extension for FUN3D. Results are presented for simulations with both overset and monolithic meshes under large changes in relative velocity (and therefore wake orientation). The results demonstrate that the motion driver successfully orients an overset wake mesh to capture the subsonic wake with sufficient resolution despite variable body rotation and body-relative freestream velocity.

Computational Fluid Dynamics↗

An Overset Grid Motion Driver for Resolving Entry Vehicle CFD Simulations with Large Changes in Wake Orientation

Time-accurate computational fluid dynamics (CFD) simulations using overset meshes can enable reduced computational cost compared to a rigid, monolithic mesh for blunt-body atmospheric entry vehicles. If the vehicle has a significant change in attitude, the high-density region of the overset mesh designed for resolving the subsonic wake can be kept in position as the wake orientation changes relative to the body. Current simulations generally keep the wake mesh fixed in attitude while the body rotates, assuming the wake orientation remains relatively constant. However, changes in the relative velocity over a long-duration simulation or effects of the body geometry can invalidate this assumption. This work presents a method for calculating the desired mesh orientation to resolve a blunt body wake using the atmosphere-relative velocity of the vehicle. A motion driver using these calculations is implemented in a CFD-in-the-loop flight model bridging the FUN3D flow solver and POST2 trajectory propagator. Overset meshing is performed using the Yoga extension for FUN3D. Results are presented for simulations with both overset and monolithic meshes under large changes in relative velocity (and therefore wake orientation). The results demonstrate that the motion driver successfully orients an overset wake mesh to capture the subsonic wake with sufficient resolution despite variable body rotation and body-relative freestream velocity.

CFD↗

Challenging Common Assumptions of Thick-Wall Chamber Dynamics in Inertial Fusion Systems Using MOOSE-based Multiphysics Simulations

As an increasing number of companies look toward commercial Inertial Fusion Energy (IFE) designs, there is a pressing need to understand the physics of thick-wall chamber gas dynamics. The thick liquid wall approach implements a renewable wall to mitigate the fusion target emissions, thereby reducing the radiation damage rate and significantly extending the lifetime of chamber structures, leading to increased plant availability and reduced waste streams in comparison to dry wall chamber designs. It is necessary, however, to assess the critical performance and safety aspects of these systems. For example, it is crucial to predict (1) where the mass ablated from the liquid walls will vent, which determines the placement of condensing surfaces; (2) debris propagation up the beam lines, which provides essential information for design and protection requirements; (3) peak pressures and impulse on chamber walls, which affect chamber structural design; and (4) momentum transfer to the liquid jets, which constrains the shape and positioning of the jets. In turn, the chamber design and its liquid walls affect shielding requirements, material activation, and tritium fuel cycle. Currently available simulation tools, however, are unable to accurately capture key thick-wall chamber dynamics. Significant assumptions are often made to simplify the system and reduce computational cost and modeling capability needs, but the impact of these assumptions on simulation predictions has not been evaluated. For example, no three-dimensional simulations can be found in the open literature to evaluate gas venting and momentum transfer to the jets with simulations using two-dimensional domains to represent complex three-dimensional geometries. Moreover, limited studies have been dedicated to jet breakup due to both turbulence and neutron heating, and no studies have been found that evaluate how jet breakup can impact shock-jet interaction. Furthermore, effects of radiative heat transfer have rarely been included for the hydrodynamic phase of shock propagation, and integration of proper equations of state in shock dynamics codes has been mostly exploratory. In this study, we use the flexible, high-fidelity Multiphysics Object-Oriented Simulation Environment (MOOSE) to model these complex phenomena and inform design and safety studies. Capabilities to model thick-wall chamber gas dynamics are being developed, and the impact of the assumptions listed above (i.e., two-dimensional vs three-dimensional, absence of jet breakout, no radiative heat transfer, and ideal gas behavior) are being quantified.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Efficient Reliability Analysis using Generalized Multifidelity Modeling and Explainable Active Learning

To assess the reliability of critical technologies like nuclear plants and infrastructure systems and improve the robustness of design, engineers have to quantify the uncertainties surrounding the system behavior accurately. However, the complexity of the problem can make standard reliability analysis algorithms prohibitively expensive, primarily due to the high computational cost of estimating the system response at each iteration. This cost can be greatly reduced by using multi-fidelity modeling and machine learning to build a surrogate model to replace the expensive response function. We propose a general and robust method for building surrogates from multiple Low Fidelity (LF) models coupled with machine learning to retain accuracy. Our framework first constructs “Corrected Low Fidelity models” (CLFs) by coupling a High Fidelity (HF) model inferred Gaussian Process correction term with each of the LF models. It then uses the correction terms to assign model probabilities to each of these CLFs in an explainable way before using them to assemble the final surrogate. No assumptions are made about the type of the LF models or their correlation with the HF model. The proposed surrogate modeling framework is used within the subset simulation algorithm (a variance-reduced MCMC-based reliability analysis algorithm) for enhanced efficiency. Additionally, an active learning step is added to the algorithm to adaptively decide when the surrogate is not sufficiently accurate, at which point the HF model is called and used to refine the surrogate. Through a frame buckling example, our method is shown to be highly efficient at reducing the expensive HF model calls while accurately estimating the failure probability.

97 MATHEMATICS AND COMPUTING↗

Connectivity-informed drainage network generation using deep convolution generative adversarial networks

Abstract Stochastic network modeling is often limited by high computational costs to generate a large number of networks enough for meaningful statistical evaluation. In this study, Deep Convolutional Generative Adversarial Networks (DCGANs) were applied to quickly reproduce drainage networks from the already generated network samples without repetitive long modeling of the stochastic network model, Gibb’s model. In particular, we developed a novel connectivity-informed method that converts the drainage network images to the directional information of flow on each node of the drainage network, and then transforms it into multiple binary layers where the connectivity constraints between nodes in the drainage network are stored. DCGANs trained with three different types of training samples were compared; (1) original drainage network images, (2) their corresponding directional information only, and (3) the connectivity-informed directional information. A comparison of generated images demonstrated that the novel connectivity-informed method outperformed the other two methods by training DCGANs more effectively and better reproducing accurate drainage networks due to its compact representation of the network complexity and connectivity. This work highlights that DCGANs can be applicable for high contrast images common in earth and material sciences where the network, fractures, and other high contrast features are important.

42 ENGINEERING↗

Semi-Annual Report for Horizontal Compact High Temperature Gas Reactor (HC-HTGR) Development during Performance Period April 2023 – September 2023

Horizontal Compact High Temperature Gas Reactor (HC-HTGR) is being designed by a multi-disciplinary team of nuclear, mechanical, and structural engineers under the support of a DOE-NE Advanced Reactor Demonstration Program’s Advanced Reactor Concepts-20 (ARC-20) award. The objective of this ARC-20 project is to deliver a conceptual design for the proposed HC-HTGR in 3 years and support its commercialization as a safe, low-cost HTGR. Argonne National Laboratory (Argonne) is responsible for the design and analysis of the reactor cavity cooling system (RCCS) as a safety system for passive decay heat removal of the reactor concept. Additionally, Argonne is providing analysis of the primary coolant system to ensure temperatures within the core remain below safety margins during steady-state and potential accident scenarios. This fourth semi-annual report summarized the progress made at Argonne on the two tasks during the second half of FY23. As a part of the RCCS design task, recent efforts have been made to complete a conceptual design of the RCCS for the HC-HTGR, including the design update of the water panel and system configuration favorable in point of view of fabrication and system operation. Design calculations were conducted under various heat load conditions to validate the system design. Transient simulations using RELAP5-3D were conducted to investigate system dynamics under transients of interest and to evaluate the system performance in the design condition. The results demonstrated the overall system feasibility that the RCCS design maintains structures temperatures lower than maximum allowable temperature with sufficient system inventory without any active heat sink. In the primary system thermal hydraulics task, the preliminary analysis was performed for a long term pressurized conduction cooldown (PCC) transient. This analysis used a combination of a fully resolved and coarse homogenized mesh to predict the temperature distribution for the steady-state initial condition and the PCC transient. The steady-state initial condition was determined using a fully resolved full core model with 3D solid to 1D fluid coupling. The fully resolved mesh was also used to model the first 20 seconds of the PCC. The temperature difference between fuel pins and the graphite matrix becomes minimal and the dominant heat transfer shifts to a larger scale radially towards the RCCS. After 20 seconds, a homogenized coarse mesh is used, greatly reducing the computational costs of the model. These results demonstrate that the core is designed to passively remove enough decay heat in a protected loss of primary coolant flow to prevent an unsafe rise of core temperatures.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Challenging Common Assumptions of Thick-Wall Chamber Dynamics in Inertial Fusion Systems using MOOSE

As an increasing number of companies look toward commercial Inertial Fusion Energy (IFE) designs, there is a pressing need to understand the physics of thick-wall chamber gas dynamics. The thick liquid wall approach implements a renewable wall to mitigate the fusion target emissions, thereby reducing the radiation damage rate and significantly extending the lifetime of chamber structures, leading to increased plant availability and reduced waste streams in comparison to dry wall chamber designs. It is necessary, however, to assess the critical performance and safety aspects of these systems. For example, it is crucial to predict (1) where the mass ablated from the liquid walls will vent, which determines the placement of condensing surfaces; (2) debris propagation up the beam lines, which provides essential information for design and protection requirements; (3) peak pressures and impulse on chamber walls, which affect chamber structural design; and (4) momentum transfer to the liquid jets, which constrains the shape and positioning of the jets. In turn, the chamber design and its liquid walls affect shielding requirements, material activation, and tritium fuel cycle. Currently available simulation tools, however, are unable to accurately capture key thick-wall chamber dynamics. Significant assumptions are often made to simplify the system and reduce computational cost and modeling capability needs, but the impact of these assumptions on simulation predictions has not been evaluated. For example, no three-dimensional simulations can be found in the open literature to evaluate gas venting and momentum transfer to the jets with simulations using two-dimensional domains to represent complex three-dimensional geometries. Moreover, limited studies have been dedicated to jet breakup due to both turbulence and neutron heating, and no studies have been found that evaluate how jet breakup can impact shock-jet interaction. Furthermore, effects of radiative heat transfer have rarely been included for the hydrodynamic phase of shock propagation, and integration of proper equations of state in shock dynamics codes has been mostly exploratory. In this study, we use the flexible, high-fidelity Multiphysics Object-Oriented Simulation Environment (MOOSE) to model these complex phenomena and inform design and safety studies. Capabilities to model thick-wall chamber gas dynamics are being developed, and the impact of the assumptions listed above (i.e., two-dimensional vs three-dimensional, absence of jet breakout, no radiative heat transfer, and ideal gas behavior) are being quantified.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A lumped particle direct simulation Monte-Carlo method combined with the collisional-radiative model for simulations of non-equilibrium laser-induced plasma plumes

Collisional plasma plumes induced by laser irradiation of material targets exhibit large variations in local density as well as ionization and excitation states, making purely hydrodynamic or kinetic simulations inaccurate or infeasible. To address this challenge and capture non-equilibrium effects in laser-induced plasma plumes at arbitrary degrees of ionization, we develop a hybrid computational approach that combines the kinetic direct simulation Monte Carlo (DSMC) method with a collisional-radiative model (CRM). This ℓDSMC-CRM approach utilizes a lumped particle method to represent minor fractions of excited ions in particle-based simulations and a special coarse-graining technique for atomic spectra and photoionization rates, ensuring numerical convergence at reduced computational cost. The hybrid approach is applied to simulate spatially homogeneous relaxation as well as one- and two-dimensional expansions of plasma plumes induced by irradiation of a copper target by a nanosecond laser pulse in a vacuum or background gas. The comparison with an equilibrium model, where local Saha-Boltzmann equilibrium is enforced, shows that the non-equilibrium effects play a dominant role. The equilibrium model can fail to predict the flow structure and strongly underestimate the degree of absorption of laser radiation by the plume. The ℓDSMC-CRM approach is validated against experimental data demonstrating reasonable agreement with the experimental electron density and temperature, while the equilibrium model is found to dramatically underestimate electron density and temperature. The flexibility of the ℓDSMC-CRM approach allows for its seamless integration into existing DSMC frameworks, making it a valuable tool for high-fidelity plasma modeling in laser-material interactions, laser-based manufacturing, and beyond.

97 MATHEMATICS AND COMPUTING↗

Multilevel Convergence Analysis of Multigrid-Reduction-in-Time

This study presents a multilevel convergence framework for multigrid-reduction-in-time (MGRIT) as a generalization of previous two-grid estimates. The framework provides a priori upper bounds on the convergence of MGRIT V- and F-cycles, with different relaxation schemes, by deriving the respective residual and error propagation operators. The residual and error operators are functions of the time-stepping operator, analyzed directly and bounded in the norm, both numerically and analytically. We present various upper bounds of different computational cost and varying sharpness. These upper bounds are complemented by proposing analytic formulae for the approximate convergence factor of V-cycle algorithms that take the number of fine grid time points, the temporal coarsening factors, and the eigenvalues of the time-stepping operator as parameters. The paper concludes with supporting numerical investigations of parabolic (anisotropic diffusion) and hyperbolic (wave equation) model problems. We assess the sharpness of the bounds and the quality of the approximate convergence factors. Observations from these numerical investigations demonstrate the value of the proposed multilevel convergence framework for estimating MGRIT convergence a priori and for the design of a convergent algorithm. We further highlight that observations in the literature are captured by the theory, including that two-level Parareal and multilevel MGRIT with F-relaxation do not yield scalable algorithms and the benefit of a stronger relaxation scheme. An important observation is that with increasing numbers of levels MGRIT convergence deteriorates for the hyperbolic model problem, while constant convergence factors can be achieved for the diffusion equation. The theory also indicates that L-stable Runge--Kutta schemes are more amendable to multilevel parallel-in-time integration with MGRIT than A-stable Runge--Kutta schemes.

97 MATHEMATICS AND COMPUTING↗

An in-silico NMR laboratory for nuclear magnetic shieldings computed via finite fields: Exploring nucleus-specific renormalizations of MP2 and MP3

Here we developed and implemented a method-independent, fully numerical, finite difference approach to calculating nuclear magnetic resonance shieldings, using gauge-including atomic orbitals. The resulting capability can be used to explore non-standard methods, given only the energy as a function of finite-applied magnetic fields and nuclear spins. For example, standard second-order Møller-Plesset theory (MP2) has well-known efficacy for 1H and 13C shieldings and known limitations for other nuclei such as 15N and 17O. It is, therefore, interesting to seek methods that offer good accuracy for 15N and 17O shieldings without greatly increased compute costs, as well as exploring whether such methods can further improve 1H and 13C shieldings. Using a small molecule test set of 28 species, we assessed two alternatives: κ regularized MP2 (κ-MP2), which provides energy-dependent damping of large amplitudes, and MP2.X, which includes a variable fraction, X, of third-order correlation (MP3). The aug-cc-pVTZ basis was used, and coupled cluster with singles and doubles and perturbative triples [CCSD(T)] results were taken as reference values. Our κ-MP2 results reveal significant improvements over MP2 for 13C and 15N, with the optimal κ value being element-specific. κ-MP2 with κ = 2 offers a 30% rms error reduction over MP2. For 15N, κ-MP2 with κ = 1.1 provides a 90% error reduction vs MP2 and a 60% error reduction vs CCSD. On the other hand, MP2.X with a scaling factor of 0.6 outperformed CCSD for all heavy nuclei. These results can be understood as providing renormalization of doubles amplitudes to partially account for neglected triple and higher substitutions and offer promising opportunities for future applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometry-aware framework for deep energy method: An application to structural mechanics with hyperelastic materials

Here, in this work, we introduce a novel physics-informed framework named the Geometry-Aware Deep Energy Method (GADEM) for solving structural mechanics problems on different geometries. As the weak form of the physical system equation (or the energy-based approach) has demonstrated clear advantages compared to the strong form for solving solid mechanics problems, GADEM employs the weak form and aims to infer the solution on multiple shapes of geometries. Integrating a geometry-aware framework into an energy-based method results in an effective physics-informed deep learning model in terms of accuracy and computational cost. Different ways to represent the geometric information and to encode the geometric latent vectors are investigated in this work. We introduce a loss function of GADEM which is minimized based on the potential energy of all considered geometries. An adaptive learning method is also employed for the sampling of collocation points to enhance the performance of GADEM. We present some applications of GADEM to solve solid mechanics problems, including a loading simulation of a toy tire involving contact mechanics and large deformation hyperelasticity. The numerical results of this work demonstrate the remarkable capability of GADEM to infer the solution on various and new shapes of geometries using only one trained model.

97 MATHEMATICS AND COMPUTING↗

Accelerating computational fluid dynamics simulation of post-combustion carbon capture modeling with MeshGraphNets

Packed columns are commonly used in post-combustion processes to capture CO 2 emissions by providing enhanced contact area between a CO 2 -laden gas and CO 2 -absorbing solvent. To study and optimize solvent-based post-combustion carbon capture systems (CCSs), computational fluid dynamics (CFD) can be used to model the liquid–gas countercurrent flow hydrodynamics in these columns and derive key determinants of CO 2 -capture efficiency. However, the large design space of these systems hinders the application of CFD for design optimization due to its high computational cost. In contrast, data-driven modeling approaches can produce fast surrogates to study large-scale physics problems. We build our surrogates using MeshGraphNets (MGN), a graph neural network framework that efficiently learns and produces mesh-based simulations. We apply MGN to a random packed column modeled with over 160K graph nodes and a design space consisting of three key input parameters: solvent surface tension, inlet velocity, and contact angle. Our models can adapt to a wide range of these parameters and accurately predict the complex interactions within the system at rates over 1700 times faster than CFD, affirming its practicality in downstream design optimization tasks. This underscores the robustness and versatility of MGN in modeling complex fluid dynamics for large-scale CCS analyses.

97 MATHEMATICS AND COMPUTING↗

An investigation of the multi-mode Richtmyer-Meshkov instability at a gas/HE interface using Pagosa

Here, in this work, we present a hydrocode Pagosa and explore the Richtmyer-Meshkov Instability (RMI) at an air/high explosive (HE) interface for the first time that is important but has not received much attention yet in the high explosive safety field. Thus, the presented Pagosa can be expected to predict the whole deflagration-to-detonation transition (DDT) process in future. In Pagosa, spatial discretization is implemented on cubic staggered grids by computing different variables at the vertex and the cell center, respectively, a special operator-splitting technique is employed to reduce the computational cost, and an artificial viscosity is added to handle the discontinuous shock waves in our simulations. To quantitatively evaluate the capability of Pagosa to solve these kinds of instabilities, the single mode Rayleigh-Taylor instability (RTI) and the multimode RMI at an air/SF 6 interface are first performed, respectively. The Pagosa results are compared with the related numerical solutions in the existing references and the experimental result. Moreover, a theoretical derivation of growth of RTI is also provided based on our numerical method. Subsequently, we explore the multi-mode RMI at an air/HE interface as well as the effects of several factors using Pagosa. Numerical results show that Pagosa is a powerful toolset to generate the right structures and the amplitude of RTI and RMI at an air/SF 6 interface. The solid HE can be penetrated by a strong shock wave and forms RMI deformations. The RMI at an air/HE interface behaves very different than at an air/SF 6 interface, periodic, decreased oscillation is observed due to material character, and is very sensitive to the initial simulation settings, that is, a tiny change in physical quantities will lead to a remarkable RMI structure, which is also observed in a shock bubble interaction. The findings in this work are significant, and will present a new insight for the high explosive field.

97 MATHEMATICS AND COMPUTING↗

Conditioned quantum-assisted deep generative surrogate for particle-calorimeter interactions

Particle collisions at accelerators like the Large Hadron Collider (LHC), recorded by experiments such as ATLAS and CMS, enable precise standard model measurements and searches for new phenomena. Simulating these collisions significantly influences experiment design and analysis but incurs immense computational costs, projected at millions of CPU-years annually during the high luminosity LHC (HL-LHC) phase. Currently, simulating a single event with Geant4 consumes around 1000 CPU seconds, with calorimeter simulations especially demanding. To address this, we propose a conditioned quantum-assisted generative model, integrating a conditioned variational autoencoder (VAE) and a conditioned restricted Boltzmann machine (RBM). Our RBM architecture is tailored for D-Wave’s Pegasus-structured advantage quantum annealer for sampling, leveraging the flux bias for conditioning. This approach combines classical RBMs as universal approximators for discrete distributions with quantum annealing’s speed and scalability. We also introduce an adaptive method for efficiently estimating effective inverse temperature, and validate our framework on Dataset 2 of CaloChallenge.

97 MATHEMATICS AND COMPUTING↗

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗

Active operator learning with predictive uncertainty quantification for partial differential equations

With the increased prevalence of neural operators being used to provide rapid solutions to partial differential equations (PDEs), understanding the accuracy of model predictions and the associated error levels is necessary for deploying reliable surrogate models in scientific applications. Existing uncertainty quantification (UQ) frameworks employ ensembles or Bayesian methods, which can incur substantial computational costs during both training and inference. Here, we propose a lightweight predictive UQ method tailored for Deep operator networks (DeepONets) that also generalizes to other operator networks. Numerical experiments on linear and nonlinear PDEs demonstrate that the framework’s uncertainty estimates are unbiased and provide accurate out-of-distribution uncertainty predictions with a sufficiently large training dataset. Our framework provides fast inference and uncertainty estimates that can efficiently drive outer-loop analyses that would be prohibitively expensive with conventional solvers. We demonstrate how predictive uncertainties can be used in the context of Bayesian optimization and active learning problems to yield improvements in accuracy and data-efficiency for outer-loop optimization procedures. In the active learning setup, we extend the framework to Fourier Neural Operators (FNO) and describe a generalized method for other operator networks. To enable real-time deployment, we introduce an inference strategy based on precomputed trunk outputs and a sparse placement matrix, reducing evaluation time by more than a factor of five. Our method provides a practical route to uncertainty-aware operator learning in time-sensitive settings.

97 MATHEMATICS AND COMPUTING↗