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DOE OSTI2025

CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets

Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind, and perform chemistry. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) can access the intrinsic heterogeneity of these complexes and are therefore key tools for understanding their function. However, 3D reconstruction of the collected imaging data presents a challenging computational problem, especially without any starting information, a setting termed ab initio reconstruction. Here, in this study, we introduce cryoDRGN-AI, a method leveraging an expressive neural representation and combining an exhaustive search strategy with gradient-based optimization to process challenging heterogeneous datasets. Using cryoDRGN-AI, we reveal new conformational states in large datasets, reconstruct previously unresolved motions from unfiltered datasets, and demonstrate ab initio reconstruction of biomolecular complexes from in situ data. With this expressive and scalable model for structure determination, we hope to unlock the full potential of cryo-EM and cryo-ET as a high-throughput tool for structural biology and discovery.

Levy, Axel [Stanford Univ., CA (United States); SL↗

DOE OSTI2020

A Survey of Constrained Gaussian Process: Approaches and Implementation Challenges

Gaussian process regression is a popular Bayesian framework for surrogate modeling of expensive data sources. As part of a larger effort in scientific machine learning, many recent works have incorporated physical constraints or other a priori information within Gaussian process regression to supplement limited data and regularize the behavior of the model. We provide an overview and survey of several classes of Gaussian process constraints, including positivity or bound constraints, monotonicity and convexity constraints, differential equation constraints provided by linear PDEs, and boundary condition constraints. We compare the strategies behind each approach as well as the differences in implementation, concluding with a discussion of the computational challenges introduced by constraints.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Toward shell model interactions with credible uncertainties

Background: The nuclear shell model is a powerful framework for predicting nuclear structure observables, but relies on interaction matrix elements fit to experimental data as its inputs. Extending the shell model's applicability, particularly toward dripline nuclei, requires efficient fitting methods and credible uncertainty quantification. Traditional approaches face computational challenges and may underestimate uncertainties. Purpose: We develop and test a framework combining eigenvector continuation and Markov chain Monte Carlo to efficiently fit shell model interaction matrix elements and quantify their uncertainties. Methods: Eigenvector continuation is used to emulate shell model calculations, reducing computational costs. The emulator enables Markov chain Monte Carlo sampling to optimize interaction matrix elements and rigorously assess parametric uncertainties. Here, the framework is benchmarked using the USDB interaction in the 𝑠⁢𝑑 shell. Results: The emulator reproduces the USDB interaction with negligible error, validating its use in shell model fitting applications. However, we find that to obtain credible predictive intervals, the model defect of the shell model itself, rather than experimental or emulator error, must be taken into account in order to obtain credible uncertainties. Conclusions: The proposed framework provides an efficient and rigorous approach for fitting shell model interactions and quantifying uncertainties. Further, the normality assumption used in the past appears sufficient to describe the distribution of interaction matrix elements. However, it is crucial to account for model correlations to avoid underestimating uncertainties.

Nuclear forces↗

DOE OSTI2022

Enhancing scalability of a matrix-free eigensolver for studying many-body localization

We propose several techniques to enhance the parallel scalability of a matrix-free eigensolver designed for studying many-body localization (MBL) of quantum spin chain models with nearest-neighbor interactions and on-site disorder. This type of problem is computationally challenging because the dimension of the associated Hamiltonian matrix grows exponentially with respect to the number of spins L, and we need to average over different realizations of the random disorder to obtain relevant statistical behavior. For each disorder realization, we need to compute eigenvalues from different regions of the spectrum and their corresponding eigenvectors. In previous work, the interior eigenstates for a single eigenvalue problem are computed via the shift-and-invert Lanczos algorithm. Due to the extremely high memory footprint of the LU factorizations, this technique is not well suited for large L’s. For example, we need thousands of compute nodes on modern high performance computing infrastructures to go beyond L = 24. The matrix-free approach does not suffer from this memory bottleneck, however, its scalability is limited by a computation and communication load imbalance. To reduce this imbalance and to significantly enhance the scalability of the matrix-free eigensolver, we reorder the matrix and leverage the consistent space runtime, CSPACER. We also show its efficiency in managing irregular communication patterns at scale compared to optimized MPI non-blocking two-sided and one-sided RMA implementation variants. This effort enables us to study MBL for spin chains with a larger number of spins. The efficiency and effectiveness of the proposed algorithm is demonstrated by computing eigenstates on a massively parallel many-core high performance computer.

METIS↗

DOE OSTI2020

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory's (ORNL's) Leadership Computing Facility (OLCF) continues to surpass its operational target goals: supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high performance computing (HPC) needs; and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2019 was a big year as OLCF staff ran five world-class resources (the leadershipclass computers Titan and Summit, the large analysis cluster called Eos, and the massive parallel filesystems called Atlas and Alpine)) and also began power and cooling upgrades for a 2021 exascale system called Frontier. While continuing exceptional operation of Titan, Eos, and Rhea, the OLCF released the Summit supercomputer for production on January 1, 2019. Summit debuted as the most capable and efficient system in its class and has been recognized as the most powerful system in the world for its performance on both the high performance linpack (HPL) and conjugate gradient (HPCG) benchmark applications since June 2018 according to TOP500. Summit represents the culmination of a multiyear effort between the OLCF, IBM, NVIDIA, and Mellanox to deliver a system that is unmatched for modeling, simulation, data analysis, and learning. To hit the ground running with science-ready applications on day one, application teams worked closely with the OLCF through the Center for Accelerated Application Readiness (CAAR) program for years in advance of the Summit deployment. CY 2019 was filled with outstanding results and accomplishments: a very high rating from users on overall satisfaction for the sixth year in a row; a tremendous amount of core-hours delivered to researchers from two leadership-class systems; and success in delivering on the allocation split of roughly 60%, 30%, and 10% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director's Discretionary (DD) programs, respectively (see Operational Performance section). These accomplishments, coupled with the high utilization rates (overall and capability usage), represent the fulfillment of the promise of both leadership-class machines: efficient facilitation of leadership-class computational applications. Table ES.1 presents a summary of the 2019 OLCF metric targets and the associated results. More information can be found in the Operational Performance section for each OLCF resource. The scientific accomplishments of OLCF users are a strong indication of long-term operational success, with publications this year in such notable journals and publications as Nature, Nature Physics, Nature Plants, Physical Review X, Journal of the American Physical Society, Cell, Nano Letters, and Trends in Biotechnology. Crucial domain-specific discoveries facilitated by resources at the OLCF are described in the High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility (OAR) Strategic Results section. For example, researchers used Summit to pinpoint and understand the production of proteins from genetic information, including mutations and the functional expression of disease (Section 8.2).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Phase field model of fluid-driven fracture in elastic media: Immersed-fracture formulation and validation with analytical solutions

Propagation of fluid-driven fractures plays an important role in natural and engineering processes, including transport of magma in the lithosphere, geologic sequestration of carbon dioxide, and oil and gas recovery from low-permeability formations, among many others. The simulation of fracture propagation poses a computational challenge as a result of the complex physics of fracture and the need to capture disparate length scales. Phase field models represent fractures as a diffuse interface and enjoy the advantage that fracture nucleation, propagation, branching, or twisting can be simulated without ad hoc computational strategies like remeshing or local enrichment of the solution space. Here we propose a new quasi-static phase field formulation for modeling fluid-driven fracturing in elastic media at small strains. The approach fully couples the fluid flow in the fracture (described via the Reynolds lubrication approximation) and the deformation of the surrounding medium. The flow is solved on a lower dimensionality mesh immersed in the elastic medium. This approach leads to accurate coupling of both physics. We assessed the performance of the model extensively by comparing results for the evolution of fracture length, aperture, and fracture fluid pressure against analytical solutions under different fracture propagation regimes. Thus, the excellent performance of the numerical model in all regimes builds confidence in the applicability of phase field approaches to simulate fluid-driven fracture.

58 GEOSCIENCES↗

DOE OSTI2016

Emergent properties of nuclei from ab initio coupled-cluster calculations

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO${}_{{\rm{sat}}}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the ${J}^{\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$ states in ${}^{\mathrm{17,23,25}}$O, and—contrary to naive shell-model expectations—the level ordering of the ${J}^{\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$ states in ${}^{\mathrm{53,55,61}}$Ca.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

A Fast Time-Stepping Strategy for Dynamical Systems Equipped with a Surrogate Model

Simulation of complex dynamical systems arising in many applications is computationally challenging due to their size and complexity. Model order reduction, machine learning, and other types of surrogate modeling techniques offer cheaper and simpler ways to describe the dynamics of these systems but are inexact and introduce additional approximation errors. In order to overcome the computational difficulties of the full complex models, on one hand, and the limitations of surrogate models, on the other, this work proposes a new accelerated time-stepping strategy that combines information from both. This approach is based on the multirate infinitesimal general-structure additive Runge--Kutta framework. The inexpensive surrogate model is integrated with a small time step to guide the solution trajectory, and the full model is treated with a large time step to occasionally correct for the surrogate model error and ensure convergence. Here, we provide a theoretical error analysis, and several numerical experiments, to show that this approach can be significantly more efficient than using only the full or only the surrogate model for the integration.

Surrogate models↗

DOE OSTI2020

Deep learning for NLTE spectral opacities

Computer simulations of high energy density science experiments are computationally challenging, consisting of multiple physics calculations including radiation transport, hydrodynamics, atomic physics, nuclear reactions, laser–plasma interactions, and more. To simulate inertial confinement fusion (ICF) experiments at high fidelity, each of these physics calculations should be as detailed as possible. However, this quickly becomes too computationally expensive even for modern supercomputers, and thus many simplifying assumptions are made to reduce the required computational time. Much of the research has focused on acceleration techniques for the various packages in multiphysics codes. In this work, we explore a novel method for accelerating physics packages via machine learning. The non-local thermodynamic equilibrium (NLTE) package is one of the most expensive calculations in the simulations of indirect drive inertial confinement fusion, taking several tens of percent of the total wall clock time. We explore the use of machine learning to accelerate this package, by essentially replacing the physics calculation with a deep neural network that has been trained to emulate the physics code. Overall, we demonstrate the feasibility of this approach on a simple problem and perform a side-by-side comparison of the physics calculation and the neural network inline in an ICF Hohlraum simulation. We show that the neural network achieves a 10× speed up in NLTE computational time while achieving good agreement with the physics code for several quantities of interest.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Tuning and Verification of an Internal Flooding Model for Dynamic PRA

In probabilistic risk assessment (PRA), the likelihoods and consequences of basic events are combined to determine possible system level outcomes and the likelihood of each outcome given an initial event. Both the consequences and likelihoods of basic events may be informed by the use of mathematical models or experimental data regarding the phenomena of interest. In either case, the impact of uncertainties on the results need to be evaluated. If a model is used to predict the evolution of an initiating event, uncertainty quantification can be computationally challenging for complex phenomena with many epistemic (e.g., model) uncertainties. In this work, a reduced order model is introduced for the flooding analysis of a multi-room building at a nuclear power plant under uncertainties which can require long run times using high fidelity computer models. The reduced order model focuses on macro-level transfer of water between rooms and tracks the water level within each room. In order to verify the model's fidelity, its results for the phenomena involved in a scenario of interest are compared to those of a computational fluid dynamics (CFD) code, which are taken to represent reality. This work does not focus on the overall fidelity of the flooding model, as the goal of the project for which it was developed is to develop a methodology rather than to analyze a particular case. The focus instead is on the tunability and verifiability of the reduced order model for relevant physical measures. In analyzing a particular case, the model may be required to incorporate more realistic description of phenomena; however, the procedure described in this work may be used to verify its performance as well. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Assessing boundary condition and parametric uncertainty in numerical-weather-prediction-modeled, long-term offshore wind speed through machine learning and analog ensemble

To accurately plan and manage wind power plants, not only does the time-varying wind resource at the site of interest need to be assessed but also the uncertainty connected to this estimate. Numerical weather prediction (NWP) models at the mesoscale represent a valuable way to characterize the wind resource offshore, given the challenges connected with measuring hub-height wind speed. The boundary condition and parametric uncertainty associated with modeled wind speed is often estimated by running a model ensemble. However, creating an NWP ensemble of long-term wind resource data over a large region represents a computational challenge. Here, we propose two approaches to temporally extrapolate wind speed boundary condition and parametric uncertainty using a more convenient setup in which a mesoscale ensemble is run over a short-term period (1 year), and only a single model covers the desired long-term period (20 year). We quantify hub-height wind speed boundary condition and parametric uncertainty from the short-term model ensemble as its normalized across-ensemble standard deviation. Then, we develop and apply a gradient-boosting model and an analog ensemble approach to temporally extrapolate such uncertainty to the full 20-year period, for which only a single model run is available. As a test case, we consider offshore wind resource characterization in the California Outer Continental Shelf. Both of the proposed approaches provide accurate estimates of the long-term wind speed boundary condition and parametric uncertainty across the region (R 2 >0.75), with the gradient-boosting model slightly outperforming the analog ensemble in terms of bias and centered root-mean-square error. At the three offshore wind energy lease areas in the region, we find a long-term median hourly uncertainty between 10 % and 14 % of the mean hub-height wind speed values. Finally, we assess the physical variability in the uncertainty estimates. In general, we find that the wind speed uncertainty increases closer to land. Also, neutral conditions have smaller uncertainty than the stable and unstable cases, and the modeled wind speed in winter has less boundary condition and parametric sensitivity than summer.

17 WIND ENERGY↗

DOE OSTI2025

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗

DOE OSTI2022

HiPACE++: A portable, 3D quasi-static particle-in-cell code

Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static, three-dimensional particle-in-cell code HiPACE++. By decomposing all the computation of a 3D domain in successive 2D transverse operations and choosing appropriate memory management, HiPACE++ demonstrates orders-of-magnitude speedups on modern scientific GPUs over CPU-only implementations. The 2D transverse operations are performed on a single GPU, avoiding time-consuming communications. The longitudinal parallelization is done through temporal domain decomposition, enabling near-optimal strong scaling from 1 to 512 GPUs. HiPACE++ is a modular, open-source code enabling efficient modeling of plasma accelerators from laptops to state-of-the-art supercomputers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Final Technical Report: Integrated Distribution-Transmission Analysis for Very High Penetration Solar PV

Transmission and distribution simulations have historically been conducted separately, echoing their division in grid operations and planning while avoiding inherent computational challenges. Today, however, rapid growth in distributed energy resources (DERs)--including distributed generation from solar photovoltaics (DGPV)--requires understanding the unprecedented interactions between distribution and transmission. To capture these interactions, especially for high-penetration DGPV scenarios, this research project developed a first-of-its-kind, high performance computer (HPC) based, integrated transmission-distribution tool, the Integrated Grid Modeling System (IGMS). The tool was then used in initial explorations of system-wide operational interactions of high-penetration DGPV.

14 SOLAR ENERGY↗

DOE OSTI2023

Rolling Horizon Based Temporal Decomposition for the Offline Pickup and Delivery Problem with Time Windows

The offline pickup and delivery problem with time windows (PDPTW) is a classical combinatorial optimization problem in the transportation community, which has proven to be very challenging computationally. Due to the complexity of the problem, practical problem instances can be solved only via heuristics, which trade-off solution quality for computational tractability. Among the various heuristics, a common strategy is problem decomposition, that is, the reduction of a large-scale problem into a collection of smaller sub-problems, with spatial and temporal decompositions being two natural approaches. While spatial decomposition has been successful in certain settings, effective temporal decomposition has been challenging due to the difficulty of stitching together the sub-problem solutions across the decomposition boundaries. In this work, we introduce a novel temporal decomposition scheme for solving a class of PDPTWs that have narrow time windows, for which it is able to provide both fast and high-quality solutions. We utilize techniques that have been popularized recently in the context of online dial-a-ride problems along with the general idea of rolling horizon optimization. To the best of our knowledge, this is the first attempt to solve offline PDPTWs using such an approach. To show the performance and scalability of our framework, we use the optimization of paratransit services as a motivating example. Due to the lack of benchmark solvers similar to ours (i.e., temporal decomposition with an online solver), we compare our results with an offline heuristic algorithm using Google OR-Tools. In smaller problem instances (with an average of 129 requests per instance), the baseline approach is as competitive as our framework. However, in larger problem instances (approximately 2,500 requests per instance), our framework is more scalable and can provide good solutions to problem instances of varying degrees of difficulty, while the baseline algorithm often fails to find a feasible solution within comparable compute times.

Kim, Youngseo↗

DOE OSTI2024

Optimizing Desalination Operations for Energy Flexibility

Despite the value of energy optimization in desalination processes, modeling dynamic operations for monthly billing periods has remained a computational challenge. This work proposes a framework for energy flexibility optimization, which includes new modeling features for independent operation of parallel skids, start-up delays associated with chemical stabilization, the consideration of industrial energy tariff structures, and inclusion of hourly electrical carbon intensities. This is done using a modular and computationally efficient formulation that guarantees a globally optimal solution with standard optimization solvers. In this study, the approach is demonstrated in two distinct case studies: a seawater desalination plant in Santa Barbara, CA, and an indirect potable reuse facility in San Jose, CA. Trends predicted from the model are validated against operational facility measurements from a demand response shutdown event. Preliminary results show that optimizing energy flexibility can result in 18.51% monthly cost savings over energy efficiency-optimized operation. The value extracted from a facility-wide shutdown during peak electricity price hours is hampered by start-up delays in post-treatment chemical stabilization. In cases in which a facility does not have much excess capacity, using a flow equalization tank or operating over a wide recovery range may be cost-effective.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Efficient Neural Network Approaches for Conditional Optimal Transport with Applications in Bayesian Inference

In this work, we present two neural network approaches that approximate the solutions of static and dynamic conditional optimal transport (COT) problems. Both approaches enable conditional sampling and conditional density estimation, which are core tasks in Bayesian inference—particularly in the simulation-based (“likelihood-free”) setting. Our methods represent the target conditional distribution as a transformation of a tractable reference distribution. Obtaining such a transformation, chosen here to be an approximation of the COT map, is computationally challenging even in moderate dimensions. To improve scalability, our numerical algorithms use neural networks to parameterize candidate maps and further exploit the structure of the COT problem. Our static approach approximates the map as the gradient of a partially input convex neural network. It uses a novel numerical implementation to increase computational efficiency compared to state-of-the-art alternatives. Our dynamic approach approximates the conditional optimal transport via the flow map of a regularized neural ODE; compared to the static approach, it is slower to train but offers more modeling choices and can lead to faster sampling. We demonstrate both algorithms numerically, comparing them with competing state-of-the-art approaches, using benchmark datasets and simulation-based Bayesian inverse problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Reconstruction of Charged Particle Tracks in Realistic Detector Geometry Using a Vectorized and Parallelized Kalman Filter Algorithm

One of the most computationally challenging problems expected for the High-Luminosity Large Hadron Collider (HL-LHC) is finding and fitting particle tracks during event reconstruction. Algorithms used at the LHC today rely on Kalman filtering, which builds physical trajectories incrementally while incorporating material e ects and error estimation. Recognizing the need for faster computational throughput, we have adapted Kalman-filterbased methods for highly parallel, many-core SIMD and SIMT architectures that are now prevalent in high-performance hardware. Previously we observed significant parallel speedups, with physics performance comparable to CMS standard tracking, on Intel Xeon, Intel Xeon Phi, and (to a limited extent) NVIDIA GPUs. While early tests were based on artificial events occurring inside an idealized barrel detector, we showed subsequently that our mkFit software builds tracks successfully from complex simulated events (including detector pileup) occurring inside a geometrically accurate representation of the CMS-2017 tracker. Here, we report on advances in both the computational and physics performance of mkFit, as well as progress toward integration with CMS production software. Recently we have improved the overall eciency of the algorithm by preserving short track candidates at a relatively early stage rather than attempting to extend them over many layers. Moreover, mkFit formerly produced an excess of duplicate tracks; these are now explicitly removed in an additional processing step. We demonstrate that with these enhancements, mkFit becomes a suitable choice for the first iteration of CMS tracking, and eventually for later iterations as well. We plan to test this capability in the CMS High Level Trigger during Run 3 of the LHC, with an ultimate goal of using it in both the CMS HLT and oine reconstruction for the HL-LHC CMS tracker.

Cerati, Giuseppe↗