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DOE OSTI2024

Iterative methods in GPU-resident linear solvers for nonlinear constrained optimization

Linear solvers are major computational bottlenecks in a wide range of decision support and optimization computations. The challenges become even more pronounced on heterogeneous hardware, where traditional sparse numerical linear algebra methods are often inefficient. For example, methods for solving ill-conditioned linear systems have relied on conditional branching, which degrades performance on hardware accelerators such as graphical processing units (GPUs). To improve the efficiency of solving ill-conditioned systems, our computational strategy separates computations that are efficient on GPUs from those that need to run on traditional central processing units (CPUs). Our strategy maximizes the reuse of expensive CPU computations. Iterative methods, which thus far have not been broadly used for ill-conditioned linear systems, play an important role in our approach. In particular, we extend ideas from Arioli et al., (2007) to implement iterative refinement using inexact LU factors and flexible generalized minimal residual (FGMRES), with the aim of efficient performance on GPUs. In conclusion, we focus on solutions that are effective within broader application contexts, and discuss how early performance tests could be improved to be more predictive of the performance in a realistic environment.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

SPH modeling of biomass granular flow: Theoretical implementation and experimental validation

The commercialization of biomass-derived energy is impeded by flowability challenges arising from the feeding and handling of granular biomass materials in full-scale biorefineries. To overcome these obstacles, a robust and accurate model to simulate the flow of granular biomass is indispensable. However, conventional mesh-based numerical codes are limited by inherent mesh distortion in simulating large deformation that commonly occurs in granular biomass handling. Here, in this study, we propose a graphics processing unit (GPU)-accelerated meshless Smoothed Particle Hydrodynamics (SPH) code to model the flow of granular biomass materials. A modified void ratio-based mass conversation, a hybrid particle-to-particle/surface frictional boundary treatment, and a hypoplastic constitutive model are implemented. Four numerical examples, an elastic block sliding on inclined planes, sand column collapse, Angle of Repose, and axial compression tests for pine chips, were simulated using the developed SPH code. The results demonstrate good agreement between numerical predictions and analytical and experimental data for all four examples, validating the SPH code and increasing confidence that it can be applied to simulate more complex granular biomass handling processes, such as hopper feeding or auger conveyance.

09 BIOMASS FUELS↗

DOE OSTI2024

A High-Performance Discrete-Element Framework for Simulating Flow and Jamming of Moisture Bearing Biomass Feedstocks

We developed and verified a high-performance open-source discrete element method (DEM) solver with simultaneously-supported feedstock-specific interaction models, including bonded-sphere, liquid bridge, cohesion, and non-linear contact models. Our solver uses parallel data structures on hybrid central and graphics processing unit (CPU/GPU) architectures, with favorable strong scaling performance observed for large problem sizes comprised of (100 M particles), and 4X single-node GPU speedup. The particles for corn stover feedstock were conceptualized and calibrated based on experimental measurements and results. Sensitivity analyses demonstrate that the mass flow rate from a wedge hopper is governed primarily by moisture content, friction coefficient, and cohesion energy density. The model is used to reproduce experimentally observed hopper jamming results, highlighting that the experimental no-flow trends can only be achieved by using non-spherical particles, liquid bridge and cohesion models, highlighting the importance of using concurrent feedstock specialized models for the effective representation of biomass material handling problems.

bioenergy↗

DOE OSTI2021

Uncertainty quantification for Multiphase-CFD simulations of bubbly flows: a machine learning-based Bayesian approach supported by high-resolution experiments

In this paper, we developed a machine learning-based Bayesian approach to inversely quantify and reduce the uncertainties of multiphase computational fluid dynamics (MCFD) simulations for bubbly flows. The proposed approach is supported by high-resolution two-phase flow measurements, including those by double-sensor conductivity probes, high-speed imaging, and particle image velocimetry. Local distributions of key physical quantities of interest (QoIs), including the void fraction and phasic velocities, are obtained to support the Bayesian inference. In the process, the epistemic uncertainties of the closure relations are inversely quantified while the aleatory uncertainties from stochastic fluctuations of the system are evaluated based on experimental uncertainty analysis. The combined uncertainties are then propagated through the MCFD solver to obtain uncertainties of the QoIs, based on which probability-boxes are constructed for validation. The proposed approach relies on three machine learning methods: feedforward neural networks and principal component analysis for surrogate modeling, and Gaussian processes for model form uncertainty modeling. The whole process is implemented within the framework of an open-source deep learning library PyTorch with graphics processing unit (GPU) acceleration, thus ensuring the efficiency of the computation. The results demonstrate that with the support of high-resolution data, the uncertainties of MCFD simulations can be significantly reduced. The proposed approach has the potential for other applications that involve numerical models with empirical parameters.

42 ENGINEERING↗

DOE OSTI2021

Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

The rapid increase in computing power, especially with the integration of graphics processing units, has dramatically increased the capabilities of molecular dynamics simulations. To date, these capabilities extend from running very long simulations (tens to hundreds of microseconds) to thousands of short simulations. However, the expansive data generated in these simulations must be made interpretable not only by the investigator who performs them but also by others as well. Here, we demonstrate how integrating learning techniques, such as artificial intelligence, machine learning, and neural networks, into analysis pipelines can reveal the kinetics of Alzheimer's disease (AD) protein aggregation. Finally, we review select AD targets, describe current simulation methods, and introduce learning concepts and their application in AD, highlighting limitations and potential solutions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

I ntera C hem : Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics

InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree–Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Finally, best practices for the maintenance and distribution of GAMESS are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Speeding Up Hartree–Fock in JuliaChem with Density Fitting

In this work, the density fitting (DF) approximation is added to the restricted Hartree–Fock (RHF) implementation in the JuliaChem computational chemistry code. Utilizing a DF algorithm that uses symmetry and integral screening, a significant reduction in time to compute the Fock matrix is achieved. The symmetry and screening DF-RHF techniques were adapted to be performed on graphics processing units (GPUs), which are well suited to perform the matrix multiplications that comprise the bulk of the Fock build time in DF-RHF. The JuliaChem DF-RHF GPU algorithm employs a novel approach that automatically switches between two DF-RHF algorithms depending on the number of basis functions in the calculation. The JuliaChem GPU DF-RHF implementation demonstrates up to 2× speedup for Fock build times compared to the existing best-in-class GPU DF-RHF implementation by operating directly on screened intermediate matrices. Due to the high portability of the Julia language code, the JuliaChem CPU and GPU DF-RHF implementations could be benchmarked on a variety of CPU and GPU architectures from multiple hardware vendors.

Hayes, John J. [Ames Laboratory, and Iowa State Un↗

DOE OSTI2023

Simulating the Excited-State Dynamics of Polaritons with Ab Initio Multiple Spawning

Over the past decade, there has been a growth of interest in polaritonic chemistry, where the formation of hybrid light–matter states (polaritons) can alter the course of photochemical reactions. These hybrid states are created by strong coupling between molecules and photons in resonant optical cavities and can even occur in the absence of light when the molecule is strongly coupled with the electromagnetic fluctuations of the vacuum field. Here, we present a first-principles model to simulate nonadiabatic dynamics of such polaritonic states inside optical cavities by leveraging graphical processing units (GPUs). Our first implementation of this model is specialized for a single molecule coupled to a single-photon mode confined inside the optical cavity but with any number of excited states computed using complete active space configuration interaction (CASCI) and a Jaynes–Cummings-type Hamiltonian. Using this model, we have simulated the excited-state dynamics of a single salicylideneaniline (SA) molecule strongly coupled to a cavity photon with the ab initio multiple spawning (AIMS) method. We demonstrate how the branching ratios of the photodeactivation pathways for this molecule can be manipulated by coupling to the cavity. We also show how one can stop the photoreaction from happening inside of an optical cavity. Finally, we also investigate cavity-based control of the ordering of two excited states (one optically bright and the other optically dark) inside a cavity for a set of molecules, where the dark and bright states are close in energy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

COLUMBUS─An Efficient and General Program Package for Ground and Excited State Computations Including Spin–Orbit Couplings and Dynamics

The COLUMBUS program system provides the tools for performing high-level multireference (MR) computations, including the multireference configuration interaction (MRCI) method and its multireference averaged quadratic coupled cluster (MR-AQCC) extension, allowing computations on a wide range of fascinating atomic and molecular systems, including the treatment of open-shells and complicated excited state phenomena. The inclusion of spin−orbit coupling (SOC) directly within the MRCI step enables the description of systems containing heavy elements, such as lanthanides and actinides, whose properties are strongly influenced by SOC. Analytic energy gradients and nonadiabatic couplings at the correlated MRCI level provide the foundation for a variety of dynamics studies, giving insight into ultrafast photochemistry. New and ongoing method developments in COLUMBUS include the computation of spin densities, improved descriptions of ionic states, enhancements to the AQCC method, and the porting of COLUMBUS to graphical processing units (GPUs). New external interfaces enable an enhanced description of electronic resonances and molecules in strong laser fields. This work highlights these new developments while providing a detailed account of the diverse applications of COLUMBUS in recent years.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Implementation of McMurchie–Davidson Algorithm for Gaussian AO Integrals Suited for SIMD Processors

We report an implementation of the McMurchie− Davidson evaluation scheme for 1- and 2-particle Gaussian AO integrals designed for processors with Single Instruction Multiple Data (SIMD) instruction sets. Like in our recent MD implementation for graphical processing units (GPUs) [Asadchev, A.; Valeev, E. F.. J. Chem. Phys. 2024, 160, 244109.], variable-sized batches of shellsets of integrals are evaluated at a time. By optimizing for the floating point instruction throughput rather than minimizing the number of operations, this approach achieves up to 50% of the theoretical hardware peak FP64 performance for many common SIMD-equipped platforms (AVX2, AVX512, NEON), which translates to speedups of up to 30 over the state-of-the-art one-shellset-at-a-time implementation of Obara−Saika-type schemes in Libint for a variety of primitive and contracted integrals. As with our previous work, we rely on the standard C++ programming language such as the std::simd standard library feature to be included in the 2026 ISO C++ standard without any explicit code generation to keep the code base small and portable. The implementation is part of the open source LibintX library freely available at https://github.com/ValeevGroup/libintx.

Basis sets↗

DOE OSTI2025

A GPU‐Based Ocean Dynamical Core for Routine Mesoscale‐Resolving Climate Simulations

Abstract We describe an ocean hydrostatic dynamical core implemented in Oceananigans optimized for Graphical Processing Unit (GPU) architectures. On 64 A100 GPUs, equivalent to 16 computational nodes in current state‐of‐the‐art supercomputers, our dynamical core can simulate a decade of near‐global ocean dynamics per wall‐clock day at an 8‐km horizontal resolution; a resolution adequate to resolve the ocean's mesoscale eddy field. Such efficiency, achieved with relatively modest hardware resources, suggests that climate simulations on GPUs can incorporate fully eddy‐resolving ocean models. This removes a major source of systematic bias in current IPCC coupled model projections, the parameterization of ocean eddies, and represents a major advance in climate modeling. We discuss the computational strategies, focusing on GPU‐specific optimization and numerical implementation details that enable such high performance.

Silvestri, Simone [Massachusetts Institute of Tech↗

DOE OSTI2025

ERF: Energy Research and Forecasting Model

High performance computing (HPC) architectures have undergone rapid development in recent years. As a result, established software suites face an ever increasing challenge to remain performant on and portable across modern systems. Many of the widely adopted atmospheric modeling codes cannot fully (or in some cases, at all) leverage the acceleration provided by General-Purpose Graphics Processing Units, leaving users of those codes constrained to increasingly limited HPC resources. Energy Research and Forecasting (ERF) is a regional atmospheric modeling code that leverages the latest HPC architectures, whether composed of only Central Processing Units (CPUs) or incorporating GPUs. ERF contains many of the standard discretizations and basic features needed to model general atmospheric dynamics. The modular design of ERF provides a flexible platform for exploring different physics parameterizations and numerical strategies. ERF is built on a state-of-the-art, well-supported, software framework (AMReX) that provides a performance portable interface and ensures ERF's long-term sustainability on next generation computing systems. This paper details the numerical methodology of ERF, presents results for a series of verification/validation cases, and documents ERF's performance on current HPC systems. The roughly 5× speed up of ERF (using GPUs) over Weather Research and Forecasting (CPUs only) for a 3D squall line test case highlights the significance of leveraging GPU acceleration.

17 WIND ENERGY↗

DOE OSTI2025

JAX-CanVeg: A Differentiable Land Surface Model

Land surface models consider the exchange of water, energy, and carbon along the soil-canopy-atmosphere continuum, which is challenging to model due to their complex interdependency and associated challenges in representing and parameterizing them. Differentiable modeling provides a new opportunity to capture these complex interactions by seamlessly hybridizing process-based models with deep neural networks (DNNs), benefiting both worlds, that is, the physical interpretation of process-based models and the learning power of DNNs. Here, we developed a differentiable land model, JAX-CanVeg. The new model builds on the legacy CanVeg by incorporating advanced functionalities through JAX in the graphic processing unit support, automatic differentiation, and integration with DNNs. We demonstrated JAX-CanVeg's hybrid modeling capability by applying the model at four flux tower sites with varying aridity. To this end, we developed a hybrid version of the Ball-Berry equation that emulates the water stress impact on stomatal closure to explore the capability of the hybrid model in (a) improving the simulations of latent heat fluxes (LE) and net ecosystem exchange (NEE), (b) improving the optimization trade-off when learning observations of both LE and NEE, and (c) benefiting a multi-layer canopy model setup. Our results show that the proposed hybrid model improved the simulations of LE and NEE at all sites, with an improved optimization trade-off over the process-based model. Additionally, the multi-layer canopy set benefited hybrid modeling at some sites. Anchored in differentiable modeling, our study provides a new avenue for modeling land-atmosphere interactions by leveraging the benefits of both data-driven learning and process-based modeling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Adaptive Grid Redistribution for a 1D Model of Turbulence and Clouds

In global atmospheric models, resolving stratocumulus (Sc) in the vertical is computationally expensive. However, Sc appear only under special meteorological conditions. Therefore, there is motivation to refine the vertical grid levels adaptively. In order to facilitate the possibility of parallelization on graphical processing units, our grid adaptation method prescribes the number of vertical levels a priori. Then grid levels are relocated toward altitude ranges in need of refinement. Because the method relocates existing grid levels, rather than adding extra levels, there is a risk of creating regions with overly coarse grid spacing, that is, voids in the grid mesh. To prevent such voids from forming, a simple method is developed to impose a maximum grid spacing. To decide where to place enhanced resolution, the authors develop an empirical mesh refinement criterion. It refines grid spacing near the ground, near strong temperature gradients, and within clouds. Our grid adaptation method is implemented in a single-column model and evaluated on four test cases: decaying stratocumulus, developing shallow cumulus, a quasi-stationary stratocumulus deck, and the diurnal cycle of a dry boundary layer. In the stratocumulus cases, mesh refinement leads to improvements in both the time evolution of fields and their time averages. The other two cases show smaller differences.

Carstensen, Steffen [Univ. of Wisconsin, Milwaukee↗

DOE OSTI2024

All-optical image denoising using a diffractive visual processor

Abstract Image denoising, one of the essential inverse problems, targets to remove noise/artifacts from input images. In general, digital image denoising algorithms, executed on computers, present latency due to several iterations implemented in, e.g., graphics processing units (GPUs). While deep learning-enabled methods can operate non-iteratively, they also introduce latency and impose a significant computational burden, leading to increased power consumption. Here, we introduce an analog diffractive image denoiser to all-optically and non-iteratively clean various forms of noise and artifacts from input images – implemented at the speed of light propagation within a thin diffractive visual processor that axially spans <250 × λ, where λ is the wavelength of light. This all-optical image denoiser comprises passive transmissive layers optimized using deep learning to physically scatter the optical modes that represent various noise features, causing them to miss the output image Field-of-View (FoV) while retaining the object features of interest. Our results show that these diffractive denoisers can efficiently remove salt and pepper noise and image rendering-related spatial artifacts from input phase or intensity images while achieving an output power efficiency of ~30–40%. We experimentally demonstrated the effectiveness of this analog denoiser architecture using a 3D-printed diffractive visual processor operating at the terahertz spectrum. Owing to their speed, power-efficiency, and minimal computational overhead, all-optical diffractive denoisers can be transformative for various image display and projection systems, including, e.g., holographic displays.

36 MATERIALS SCIENCE↗