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At least 163 records · Page 9

First principles reaction discovery: from the Schrodinger equation to experimental prediction for methane pyrolysis

Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of the methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

Effect of image resolution on automated classification of chest X-rays

Deep learning (DL) models have received much attention lately for their ability to achieve expert-level performance on the accurate automated analysis of chest X-rays (CXRs). Recently available public CXR datasets include high resolution images, but state-of-the-art models are trained on reduced size images due to limitations on graphics processing unit memory and training time. As computing hardware continues to advance, it has become feasible to train deep convolutional neural networks on high-resolution images without sacrificing detail by downscaling. This study examines the effect of increased resolution on CXR classification performance. We used the publicly available MIMIC-CXR-JPG dataset, comprising 377,110 high resolution CXR images for this study. We applied image downscaling from native resolution to 2048 × 2048 pixels, 1024 × 1024 pixels, 512 × 512 pixels, and 256 × 256 pixels and then we used the DenseNet121 and EfficientNet-B4 DL models to evaluate clinical task performance using these four downscaled image resolutions. We find that while some clinical findings are more reliably labeled using high resolutions, many other findings are actually labeled better using downscaled inputs. We qualitatively verify that tasks requiring a large receptive field are better suited to downscaled low resolution input images, by inspecting effective receptive fields and class activation maps of trained models. Lastly, we show that stacking an ensemble across resolutions outperforms each individual learner at all input resolutions while providing interpretable scale weights, indicating that diverse information is extracted across resolutions.

47 OTHER INSTRUMENTATION↗

Celeritas Midterm SciDAC Report

Celeritas is a new Monte Carlo (MC) code that helps satisfy the increasing demand for high energy physics (HEP) detector simulation, using Graphics Processing Unit (GPU) hardware on high performance computing (HPC) systems to model Large Hadron Collider (LHC) experiments and beyond. This report details the project’s progress midway through its SciDAC funding period, highlighting the first complete implementation of standard electromagnetic (EM) physics on GPUs, initial results for performance and scalability on Leadership Computing Facilities (LCFs), and preliminary integration into the CMS and ATLAS experiments. By integrating HEP domain knowledge with expertise in MC transport, Celeritas has catalyzed a shift in the HEP community’s perception of GPU platforms as the future for HPC simulations.

97 MATHEMATICS AND COMPUTING↗

Efficient Anomaly Detection Driven By Different Machine Learning Architectures And Models

The rapid growth and ubiquitous adoption of the internet and cyber-physical systems (CPS) have fundamentally transformed modern communication, work, and human-system interactions. While networks now form the backbone of critical digital ecosystems, enabling seamless data transmission across diverse, interconnected systems, this increased connectivity also expands the attack surface, making real-time detection of network intrusions and anomalies a pressing challenge. Detecting unusual activities within network infrastructure requires advanced data traffic analysis to differentiate between legitimate and malicious interactions. Traditional approaches to network anomaly detectionâ??such as rule-based and signature-based systemsâ??often depend on predefined patterns to identify known anomalies, limiting their effectiveness against emerging, stealthy, or previously unseen threats. These conventional methods suffer from high false alarm rates and fail to adapt to the ever-evolving nature of network traffic, particularly in large-scale, decentralized environments where data volume, velocity, and variety are constantly increasing. This dissertation presents artificial intelligence (AI)-driven approaches to anomaly detection that leverage graphics processing unit (GPU)-enabled high-performance computing (HPC) platforms for processing massive network traffic data and monitoring the components of cyber-physical systems (CPS) for potentially hazardous conditions. The research advances several key contributions: (1) Designing efficient machine learning techniques for CPS condition monitoring and anomaly detection; (2) enabling federated learning (FL) frameworks that enable distributed detection while preserving data privacy and system resilience; (3) exploring graph-based methodologies combining graph neural networks (GNN) and graph machine learning (ML) approaches for the Internet of Things (IoT) and automotive network security, and (4) performing distributed edge computing optimizations that integrate FL with scalable technologies for reduced communication overhead. Through extensive experiments, these methodologies demonstrate that complex anomaly detection and condition monitoring tasks can be achieved while balancing computational efficiency and detection accuracy through fine-grained network information processing. The frameworks developed in this research establish a robust foundation for network anomaly detection, providing scalable, adaptive, and privacy-preserving solutions for safeguarding CPS and IoT networks in an increasingly interconnected digital landscape. The practical implications of these research findings are significant, as they can inform the development of next-generation network security systems and contribute to the protection of critical infrastructure against sophisticated cyber attacks.

Marfo, William↗

On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

The predominance of Kohn–Sham density functional theory (KS-DFT) for the theoretical treatment of large experimentally relevant systems in molecular chemistry and materials science relies primarily on the existence of efficient software implementations which are capable of leveraging the latest advances in modern high-performance computing (HPC). With recent trends in HPC leading toward increasing reliance on heterogeneous accelerator-based architectures such as graphics processing units (GPU), existing code bases must embrace these architectural advances to maintain the high levels of performance that have come to be expected for these methods. In this work, we purpose a three-level parallelism scheme for the distributed numerical integration of the exchange-correlation (XC) potential in the Gaussian basis set discretization of the Kohn–Sham equations on large computing clusters consisting of multiple GPUs per compute node. In addition, we purpose and demonstrate the efficacy of the use of batched kernels, including batched level-3 BLAS operations, in achieving high levels of performance on the GPU. We demonstrate the performance and scalability of the implementation of the purposed method in the NWChemEx software package by comparing to the existing scalable CPU XC integration in NWChem.

97 MATHEMATICS AND COMPUTING↗

Toward Large-Scale Image Segmentation on Summit

Semantic segmentation of images is an important computer vision task that emerges in a variety of application domains such as medical imaging, robotic vision and autonomous vehicles to name a few. While these domain-specific image analysis tasks involve relatively small image sizes (~ 10 2 × 10 2 ), there are many applications that need to train machine learning models on image data with extents that are orders of magnitude larger (~10 4 × 10 4 ). Training deep neural network (DNN) models on large extent images is extremely memory-intensive and often exceeds the memory limitations of a single graphical processing unit, a hardware accelerator of choice for computer vision workloads. Here, an efficient, sample parallel approach to train U-Net models on large extent image data sets is presented. Its advantages and limitations are analyzed and near-linear strong-scaling speedup demonstrated on 256 nodes (1536 GPUs) of the Summit supercomputer. Using a single node of the Summit supercomputer, an early evaluation of a recently released model parallel framework called GPipe is demonstrated to deliver ~ 2X speedup in executing a U-Net model with an order of magnitude larger number of trainable parameters than reported before. Performance bottlenecks for pipelined training of U-Net models are identified and mitigation strategies to improve the speedups are discussed. Together, these results open up the possibility of combining both approaches into a unified scalable pipelined and data parallel algorithm to efficiently train U-Net models with very large receptive fields on data sets of ultra-large extent images.

Seal, Sudip↗

GPU-resident sparse direct linear solvers for alternating current optimal power flow analysis

Integrating renewable resources within the transmission grid at a wide scale poses significant challenges for economic dispatch as it requires analysis with more optimization parameters, constraints, and sources of uncertainty. This motivates the investigation of more efficient computational methods, especially those for solving the underlying linear systems, which typically take more than half of the overall computation time. In this paper, we present our work on sparse linear solvers that take advantage of hardware accelerators, such as graphical processing units (GPUs), and improve the overall performance when used within economic dispatch computations. We treat the problems as sparse, which allows for faster execution but also makes the implementation of numerical methods more challenging. We present the first GPU-native sparse direct solver that can execute on both AMD and NVIDIA GPUs. We demonstrate significant performance improvements when using high-performance linear solvers within alternating current optimal power flow (ACOPF) analysis. Furthermore, we demonstrate the feasibility of getting significant performance improvements by executing the entire computation on GPU-based hardware. Finally, we identify outstanding research issues and opportunities for even better utilization of heterogeneous systems, including those equipped with GPUs.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Kernel fusion in atomistic spin dynamics simulations on Nvidia GPUs using tensor core

In atomistic spin dynamics simulations, the time cost of constructing the space- and time-displaced pair correlation function in real space increases quadratically as the number of spins N, leading to significant computational effort. The GEMM subroutine can be adopted to accelerate the calculation of the dynamical spin-spin correlation function, but the computational cost of simulating large spin systems (>40000 spins) on CPUs remains expensive. In this work, we perform the simulation on the graphics processing unit (GPU), a hardware solution widely used as an accelerator for scientific computing and deep learning. Here we show that GPUs can accelerate the simulation up to 25-fold compared to multi-core CPUs when using the GEMM subroutine on both. To hide memory latency, we fuse the element-wise operation into the GEMM kernel using CUTLASS that can improve the performance by 26% ~ 33% compared to implementation based on cuBLAS. Furthermore, we perform the on-the-fly calculation in the epilogue of the GEMM subroutine to avoid saving intermediate results on global memory, which makes the large-scale atomistic spin dynamics simulation feasible and affordable.

97 MATHEMATICS AND COMPUTING↗

Stabilized bases for high-order, interpolation semi-Lagrangian, element-based tracer transport

In a computational fluid model of the atmosphere, the advective transport of trace species, or tracers, can be computationally expensive. For efficiency, models often use semi-Lagrangian advection methods. High-order interpolation semi-Lagrangian (ISL) methods, in particular, can be extremely efficient, if the problem of property preservation specific to them can be addressed. Atmosphere models often use geometrically and logically nonuniform grids for efficiency and, as a result, element-based discretizations. Such grids and discretizations make stability a particular problem for ISL methods. Generally, high-order, element-based ISL methods that use the natural polynomial interpolant associated with a nodal finite-element discretization are unstable. Here, we derive new bases having order of accuracy up to nine, with positive nodal weights, that stabilize the element-based ISL method. We use these bases to construct the linear advection operator in the property-preserving Interpolation Semi-Lagrangian Element-based Transport (Islet) method. Then we discuss key software implementation details. Finally, we show performance results for the Energy Exascale Earth System Model's atmosphere dynamical core, comparing the original and new transport methods. These simulations used up to 27,600 Graphical Processing Units (GPU) on the Oak Ridge Leadership Computing Facility's Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

Apparatus and method for providing workload distribution of threads among multiple compute units

In some examples, thermal aware optimization logic determines a characteristic (e.g., a workload or type) of a wavefront (e.g., multiple threads). For example, the characteristic indicates whether the wavefront is compute intensive, memory intensive, mixed, and/or another type of wavefront. The thermal aware optimization logic determines temperature information for one or more compute units (CUs) in one or more processing cores. The temperature information includes predictive thermal information indicating expected temperatures corresponding to the one or more CUs and historical thermal information indicating current or past thermal temperatures of at least a portion of a graphics processing unit (GPU). The logic selects the one or more compute units to process the plurality of threads based on the determined characteristic and the temperature information. The logic provides instructions to the selected subset of the plurality of CUs to execute the wavefront.

Rao, Karthik↗

Apparatus and method for providing workload distribution of threads among multiple compute units

In some examples, thermal aware optimization logic determines a characteristic (e.g., a workload or type) of a wavefront (e.g., multiple threads). For example, the characteristic indicates whether the wavefront is compute intensive, memory intensive, mixed, and/or another type of wavefront. The thermal aware optimization logic determines temperature information for one or more compute units (CUs) in one or more processing cores. The temperature information includes predictive thermal information indicating expected temperatures corresponding to the one or more CUs and historical thermal information indicating current or past thermal temperatures of at least a portion of a graphics processing unit (GPU). The logic selects the one or more compute units to process the plurality of threads based on the determined characteristic and the temperature information. The logic provides instructions to the selected subset of the plurality of CUs to execute the wavefront.

Rao, Karthik↗

Collective mode Brownian dynamics: A method for fast relaxation of statistical ensembles

Sampling equilibrium configurations of correlated systems of particles with long relaxation times (e.g., polymeric solutions) using conventional molecular dynamics and Monte Carlo methods can be challenging. This is especially true for systems with complicated, extended bond network topologies and other interactions that make the use and design of specialized relaxation protocols infeasible. We introduce a method based on Brownian dynamics simulations that can reduce the computational time it takes to reach equilibrium and draw decorrelated samples. Importantly, the method is completely agnostic to the particle configuration and the specifics of interparticle forces. In particular, we develop a mobility matrix that excites non-local, collective motion of N particles and can be computed efficiently in $\mathcal{O}(N)$ time. Particle motion in this scheme is computed by integrating the overdamped Langevin equation with an Euler–Maruyama scheme, in which Brownian displacements are drawn efficiently using a low-rank representation of the mobility matrix in position and wave space. We demonstrate the efficacy of the method with various examples from the realm of soft condensed matter and release a massively parallel implementation of the code as a plugin for the open-source package HOOMD-blue [J. A. Anderson et al., J. Comput. Phys. 227, 5342 (2008) and J. Glaser et al., Comput. Phys. Commun. 192, 97 (2015)] which runs on graphics processing units

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Developing a Decision Support Engine to Enable Irrigation Modernization - Poster

Irrigation systems in the United States are some of the oldest continually utilized infrastructure in existence today, with some systems exceeding 100 years in age. They are operated to meet farming demands but are managed through a balance of varying influence: policies limiting water usage, stakeholder interests, and environmental impacts. Irrigation modernization is defined as a set of activities that update and improve existing irrigation systems, including, but not limited to improving water quantity, development of distributed energy resources for surrounding communities, ecosystem services, and improved agricultural yields. Modernizing an existing irrigation system can enable stakeholders to combat changing environmental and population demands but is difficult because the complexity involved in determining the potential benefits and consequences of irrigation modernization is high. We are combining a large amount of various geospatial, tabular, and temporal data with subject matter expertise into a decision support engine that will enable stakeholders to determine the benefits and consequences of irrigation modernization in their irrigation systems. A web-based GIS will allow the user to construct the modifications out of a palette of modernization options, which will be sent to the analytics engine for computations, and back to the web client for a graphical display and comparison of relevant metrics. Our development process involves four phases: 1) identify mechanisms of modernization, 2) identify data requirements, data streams, first principles and applicable algorithms necessary to quantify modernization mechanisms, 3) create ‘modules’ for each modernization mechanism, these modules will form the decision support engine, each capable of performing independently but can also inform other modules when needed, 4) Merge the decision support engine with a user interface, capable of ingesting user inputs and returning insights into the impacts of a modernization project as they relate to economic, environmental, monetary, and energy generation. Once complete, it is our intention that this tool will be fundamental in irrigation modernization projects, providing a strong analytical basis from which stakeholders can quickly make informed decisions regarding project development.

13 HYDRO ENERGY↗

Subspace recursive Fermi-operator expansion strategies for large-scale DFT eigenvalue problems on HPC architectures

Quantum mechanical calculations for material modeling using Kohn–Sham density functional theory (DFT) involve the solution of a nonlinear eigenvalue problem for N smallest eigenvector-eigenvalue pairs, with N proportional to the number of electrons in the material system. Here, these calculations are computationally demanding and have asymptotic cubic scaling complexity with the number of electrons. Large-scale matrix eigenvalue problems arising from the discretization of the Kohn–Sham DFT equations employing a systematically convergent basis traditionally rely on iterative orthogonal projection methods, which are shown to be computationally efficient and scalable on massively parallel computing architectures. However, as the size of the material system increases, these methods are known to incur dominant computational costs through the Rayleigh–Ritz projection step of the discretized Kohn–Sham Hamiltonian matrix and the subsequent subspace diagonalization of the projected matrix. This work explores the potential of polynomial expansion approaches based on recursive Fermi-operator expansion as an alternative to the subspace diagonalization of the projected Hamiltonian matrix to reduce the computational cost. Subsequently, we perform a detailed comparison of various recursive polynomial expansion approaches to the traditional approach of explicit diagonalization on both multi-node central processing unit and graphics processing unit architectures and assess their relative performance in terms of accuracy, computational efficiency, scaling behavior, and energy efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics

TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Here, electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Polariton spectra under the collective coupling regime. II. 2D non-linear spectra

In our previous work [Mondal et al., J. Chem. Phys. 162, 014114 (2025)], we developed several efficient computational approaches to simulate exciton–polariton dynamics described by the Holstein–Tavis–Cummings (HTC) Hamiltonian under the collective coupling regime. Here, we incorporated these strategies into the previously developed Lindblad-partially linearized density matrix (⁠$\mathscr{L}$-PLDM) approach for simulating 2D electronic spectroscopy (2DES) of exciton–polariton under the collective coupling regime. In particular, we apply the efficient quantum dynamics propagation scheme developed in Paper I to both the forward and the backward propagations in the PLDM and develop an efficient importance sampling scheme and graphics processing unit vectorization scheme that allow us to reduce the computational costs from $\mathscr{O}$($\mathscr{K}$ 2 )$\mathscr{O}$(T 3 ) to $\mathscr{O}$($\mathscr{K}$)$\mathscr{O}$(T 0 ) for the 2DES simulation, where $\mathscr{K}$ is the number of states and T is the number of time steps of propagation. As a result, we further simulated the 2DES for an HTC Hamiltonian under the collective coupling regime and analyzed the signal from both rephasing and non-rephasing contributions of the ground state bleaching, excited state emission, and stimulated emission pathways.

2D non-linear spectra↗

The critical importance of software for HEP

Particle physics has an ambitious and broad global experimental programme for the coming decades. Large investments in building new facilities are already underway or under consideration. Scaling the present processing power and data storage needs by the foreseen increase in data rates in the next decade for HL-LHC is not sustainable within the current budgets. As a result, a more efficient usage of computing resources is required in order to realise the physics potential of future experiments. Software and computing are an integral part of experimental design, trigger and data acquisition, simulation, reconstruction, and analysis, as well as related theoretical predictions. A significant investment in computing and software is therefore critical. Advances in software and computing, including artificial intelligence (AI) and machine learning (ML), will be key for solving these challenges. Making better use of new processing hardware such as graphical processing units (GPUs) or ARM chips is a growing trend. This forms part of a computing solution that makes efficient use of facilities and contributes to the reduction of the environmental footprint of HEP computing. The HEP community already provided a roadmap for software and computing for the last EPPSU, and this paper updates that, with a focus on the most resource critical parts of our data processing chain.

97 MATHEMATICS AND COMPUTING↗