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At least 289 records · Page 16

SolCalc: A Suite for the Calculation and the Display of Magnetic Fields Generated by Solenoid Systems

SolCalc is a software suite that computes and displays magnetic fields generated by a three dimensional (3D) solenoid system. Examples of such systems are the Mu2e magnet system and Helical Solenoids for muon cooling systems. SolCalc was originally coded in Matlab, and later upgraded to a compiled version (called MEX) to improve solving speed. Matlab was chosen because its graphical capabilities represent an attractive feature over other computer languages. Solenoid geometries can be created using any text editor or spread sheets and can be displayed dynamically in 3D. Fields are computed from any given list of coordinates. The field distribution on the surfaces of the coils can be displayed as well. SolCalc was benchmarked against a well-known commercial software for speed and accuracy and the results compared favorably.

43 PARTICLE ACCELERATORS↗

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↗

An immersed interface method for microstructure-scale electrochemical battery models: numerical formulation and performance portable implementation

We present the numerical formulation, verification, and performance portable implementation of an immersed interface method for microstructure scale electrochemical modeling of batteries. The innovation in this approach is the resolution of chemical species and electrostatic potential discontinuities at active interfaces without the use of interface conforming unstructured grids. A unified formulation on Cartesian grids for all domains (electrodes and electrolyte) is used with interfacial flux conditions applied using volume fraction or “color” function gradients. We have developed one dimensional and two dimensional test cases with analytic solutions for electrochemical modeling using which we verified the consistency and accuracy of our scheme. Our solver is also validated against solutions from a macroscale model and an unstructured multi-subdomain solver for a full lithium ion cell. We then demonstrated the utility of our solver on an image-based complex battery electrode microstructure at high charging rate. Our technique also exhibits good scalability on distributed memory architectures using central processing units (CPU), with problem sizes up to 1.8 billion degrees of freedom and with 5400 ranks. Initial performance studies of our open-source performance portable solver showed about 70 times speed up using a graphics processing unit (GPU) compared to single compute core for a problem with 4 million cells.

25 ENERGY STORAGE↗

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↗

The order of three lowest-energy states of the six-electron harmonium at small force constant

The order of low-energy states of six-electron harmonium is uncertain in the case of strong correlation, which is not a desired situation for the model system being considered for future testing of approximate methods of quantum chemistry. The computational study of these states has been carried out at the frequency parameter ω = 0.01, using the variational method with the basis of symmetry-projected, explicitly correlated Gaussian (ECG) lobe functions. It has revealed that the six-electron harmonium at this confinement strength is an octahedral Wigner molecule, whose order of states is different than in the strong confinement regime and does not agree with the earlier predictions. The results obtained for ω = 0.5 and 10 are consistent with the findings based on the Hund’s rules for the s{sup 2}p{sup 4} electron configuration. Substantial part of the computations has been carried out on the graphical processing units and the efficiency of these devices in calculation of the integrals over ECG functions has been compared with traditional processors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rasterization with Data-Parallel Primitives

Parallel rasterization can suffer from race conditions during fragment generation, which is traditionally addressed by using specialized hardware accessible via vendor graphics APIs. Unfortunately, graphics APIs are increasingly problematic on high-performance computers, either because they are not provided or because of concerns about dependencies with in situ visualization. In response, we present a hardware-agnostic rasterization algorithm that handles race conditions using only data-parallel primitives (DPPs), enabling efficient rendering on HPC systems without graphics API dependencies and aligning with recent efforts to deliver visualization software with DPPs. Our evaluation consists of three phases: (1) evaluating portability across different CPU and GPU architectures, (2) evaluating competitiveness with a community standard, and (3) evaluating performance across varying workloads and available parallelism. The supporting experiments run on both AMD and NVIDIA GPUs, considering data sets as large as 460 million triangles and 160 million pixels. While performance generally falls short of graphics API baselines, it achieves interactive frame rates on most workloads. As a result, we conclude our approach is a viable solution for rasterization on high-performance computers since our approach is portably performant across different architectures without the need for specialized vendor support.

Buckley, Makani [University of Oregon] (ORCID:0009↗

A GPU-based 2D shallow water quality model

In this paper, a 2D shallow water flow solver integrated with a water quality model is presented. The interaction between the main water quality constituents included is based on the Water Quality Analysis Simulation Program. Efficiency is achieved by computing with a combination of a Central Processing Unit (CPU) and a Graphics Processing Unit (GPU) device. This technique is intended to provide robust and accurate simulations with high computation speedups with respect to a single-core CPU in real events. The proposed numerical model is evaluated in cases that include the transport and reaction of water quality components over irregular bed topography and dry–wet fronts, verifying that the numerical solution in these situations conserves the required properties (C-property and positivity). The model can operate in any steady or unsteady form allowing an efficient assessment of the environmental impact of water flows. The field data from an unsteady river reach test case are used to show that the model is capable of predicting the measured temporal distribution of dissolved oxygen and water temperature, proving the robustness and computational efficiency of the model, even in the presence of noisy signals such as wind speed.

54 ENVIRONMENTAL SCIENCES↗

Multi-GPU implementation of a VMAT treatment plan optimization algorithm

Purpose: Volumetric modulated arc therapy (VMAT) optimization is a computationally challenging problem due to its large data size, high degrees of freedom, and many hardware constraints. High-performance graphics processing units (GPUs) have been used to speed up the computations. However, GPU’s relatively small memory size cannot handle cases with a large dose-deposition coefficient (DDC) matrix in cases of, e.g., those with a large target size, multiple targets, multiple arcs, and/or small beamlet size. The main purpose of this paper is to report an implementation of a column-generation-based VMAT algorithm, previously developed in the authors’ group, on a multi-GPU platform to solve the memory limitation problem. While the column-generation-based VMAT algorithm has been previously developed, the GPU implementation details have not been reported. Hence, another purpose is to present detailed techniques employed for GPU implementation. The authors also would like to utilize this particular problem as an example problem to study the feasibility of using a multi-GPU platform to solve large-scale problems in medical physics. Methods: The column-generation approach generates VMAT apertures sequentially by solving a pricing problem (PP) and a master problem (MP) iteratively. In the authors’ method, the sparse DDC matrix is first stored on a CPU in coordinate list format (COO). On the GPU side, this matrix is split into four submatrices according to beam angles, which are stored on four GPUs in compressed sparse row format. Computation of beamlet price, the first step in PP, is accomplished using multi-GPUs. A fast inter-GPU data transfer scheme is accomplished using peer-to-peer access. The remaining steps of PP and MP problems are implemented on CPU or a single GPU due to their modest problem scale and computational loads. Barzilai and Borwein algorithm with a subspace step scheme is adopted here to solve the MP problem. A head and neck (H and N) cancer case is then used to validate the authors’ method. The authors also compare their multi-GPU implementation with three different single GPU implementation strategies, i.e., truncating DDC matrix (S1), repeatedly transferring DDC matrix between CPU and GPU (S2), and porting computations involving DDC matrix to CPU (S3), in terms of both plan quality and computational efficiency. Two more H and N patient cases and three prostate cases are used to demonstrate the advantages of the authors’ method. Results: The authors’ multi-GPU implementation can finish the optimization process within ∼1 min for the H and N patient case. S1 leads to an inferior plan quality although its total time was 10 s shorter than the multi-GPU implementation due to the reduced matrix size. S2 and S3 yield the same plan quality as the multi-GPU implementation but take ∼4 and ∼6 min, respectively. High computational efficiency was consistently achieved for the other five patient cases tested, with VMAT plans of clinically acceptable quality obtained within 23–46 s. Conversely, to obtain clinically comparable or acceptable plans for all six of these VMAT cases that the authors have tested in this paper, the optimization time needed in a commercial TPS system on CPU was found to be in an order of several minutes. Conclusions: The results demonstrate that the multi-GPU implementation of the authors’ column-generation-based VMAT optimization can handle the large-scale VMAT optimization problem efficiently without sacrificing plan quality. The authors’ study may serve as an example to shed some light on other large-scale medical physics problems that require multi-GPU techniques.

60 APPLIED LIFE SCIENCES↗

Experimental determination of radiated internal wave power without pressure field data

We present a method to determine, using only velocity field data, the time-averaged energy flux (J) and total radiated power P for two-dimensional internal gravity waves. Both (J) and P are determined from expressions involving only a scalar function, the stream function ψ. We test the method using data from a direct numerical simulation for tidal flow of a stratified fluid past a knife edge. The results for the radiated internal wave power given by the stream function method agree to within 0.5% with results obtained using pressure and velocity data from the numerical simulation. The results for the radiated power computed from the stream function agree well with power computed from the velocity and pressure if the starting point for the stream function computation is on a solid boundary, but if a boundary point is not available, care must be taken to choose an appropriate starting point. We also test the stream function method by applying it to laboratory data for tidal flow past a knife edge, and the results are found to agree with the direct numerical simulation. The supplementary material includes a Matlab code with a graphical user interface that can be used to compute the energy flux and power from two-dimensional velocity field data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Non-Traditional Supercomputing

The High-Performance Computing of today is much different than the supercomputing resources a few decades ago. The supercomputers of the past were huge complexes of hundreds of interconnected computers that had large teams of specialists to keep them running. Today, while supercomputers like Summit (the world's most powerful supercomputer as of June 2018, installed at Oak Ridge National Laboratory) are still in high demand for extremely fast computational power (over 200,000 trillion calculations per second, or 200 petaflops), researchers at Sandia now have access to non-traditional computing resources in the way of very powerful graphics processing units (GPUs). These GPU systems have enabled an entirely new avenue of exploration for Sandia, allowing researchers to further tackle problems in energy, advanced materials, artificial intelligence, and nuclear weapons. Many teams at Sandia utilize these GPU clusters to build models through the use of machine learning. These models are faster representations of their code-driven counterparts and can often be leveraged from the exascale computing resources of traditionally larger systems with huge boosts in performance. We highlight two resources for these smaller systems: the team that builds the hardware, and the team that researches and builds the machine learning algorithms.

97 MATHEMATICS AND COMPUTING↗

A parallel and performance portable implementation of a full-field crystal plasticity model

We have developed a parallel implementation of an Elasto-Viscoplastic Fast Fourier Transform-based (EVPFFT) micromechanical solver to enable computationally efficient crystal plasticity modeling for polycrystalline materials. Our primary focus lies in achieving performance portability, allowing a single EVPFFT implementation to run optimally on various homogeneous architectures, including multi-core Central Processing Units (CPUs), as well as on heterogeneous computer architectures comprising multi-core CPUs and Graphics Processing Units (GPUs) from different vendors. To accomplish this goal, we have leveraged MATAR, a C++ software library that simplifies the creation and utilization of multidimensional dense or sparse matrix and array data structures. These data structures are designed to be portable across diverse architectures through the use of Kokkos, a performance-portable library. Additionally, we have employed the Message Passing Interface (MPI) to efficiently distribute the computational workload among processors. The heFFTe (Highly Efficient FFT for Exascale) library is used to facilitate the performance portability of the fast Fourier transforms (FFTs) computation. The computational performance of EVPFFT is evaluated and presented in terms of parallel scalability and simulation runtime on different high-performance computing (HPC) architectures. As a result, the utility of the developed framework to efficiently simulate the micro-mechanical fields in polycrystalline microstructures in engineering applications is discussed.

36 MATERIALS SCIENCE↗

Next-Generation Marine Energy Software Needs Assessment

Over the past decade the marine energy industry has continued to grow and evolve, with new concepts and technologies constantly being pursued. Additionally, the field of computing is vastly different today than it was five or ten years ago. By utilizing advanced software and hardware architectures, like graphics processing units as well as parallelization and high-performance computing resources, software can produce higher quality outputs and a higher volume of outputs. These software and hardware resources can enable the marine energy community to exploit computational advancements from other research fields, which can include machine learning, differentiable programming, and controls co-design. Better integration of existing software and development of potential new software is necessary to take advantage of trends in modern computing and respond to the current and future needs of the marine energy community. In order to better understand the existing marine energy software landscape and industry needs, DOE's Water Power Technologies Office (WPTO) tasked Sandia National Laboratories and the National Renewable Energy Laboratory to update the needs assessment by identifying existing software gaps and software needs, and assisting WPTO in planning the next wave of marine energy software development. The proposed effort involved cataloguing and analyzing the available data on existing software related to marine energy. The marine energy software landscape has vastly changed in the last ten years. There are now nearly 230 different software packages utilized by the marine energy sector, compared to a decade ago when the Cardinal Engineering survey identified approximately 40 software packages. In 2012, the marine energy software landscape was captured in two tables, whereas the current marine energy software landscape required development of a software database to collect and categorize software.

16 TIDAL AND WAVE POWER↗

Experiences Detecting Defective Hardware in Exascale Supercomputers

In May 2022, the newest supercomputer to top the TOP 500 list was Frontier at Oak Ridge National Laboratory, demonstrating the capability of computing more than 1.1 quintillion (1018) floating-point calculations every second. Driving this ground-breaking rate of computing is Frontier’s more than 37,000 graphics processing units (GPUs) and 9,408 central processing units (CPUs). In total, Frontier contains more than 60 million parts. At this scale, the smallest margin of error may generate hundreds of hardware errors across the system. These errors are capable of directly hindering world-class science performed on Frontier if not found. In this work, we describe and evaluate two strategies for finding hardware-level faults in Frontier’s 9,408 compute nodes. There are two strategies developed: the first uses the Slurm scheduler to scavenge available compute time to run the node screen, the second builds upon the lessons learned in the first strategy and enforces a weekly screen of each node. Using June 2023 as a case study, we find that the first scheduling strategy consumed more than ten times the resources as the second scheduling strategy, but successfully detected five hardware defects in Frontier. We summarize the lessons learned while developing and running a node screen on the world’s first exascale supercomputer.

Hagerty, Nick↗

SimELIT: A Novel GUI-Based Comprehensive Ion Trajectory Simulation Software for Mass Spectrometry

Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, in this work, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations–(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N 2 ) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.

97 MATHEMATICS AND COMPUTING↗

Design of a graphical user interface for few-shot machine learning classification of electron microscopy data

The recent growth in data generation by modern electron microscopes requires rapid, scalable, and flexible approaches to image segmentation and analysis. Few-shot machine learning, which can richly classify images from a handful of user-provided examples, is a promising route to high-throughput analysis. However, current command-line implementations of such approaches can be slow and unintuitive to use, lacking the real-time feedback necessary to perform effective classification. Here we report on the development of a Python-based graphical user interface that enables end users to easily conduct and visualize the output of few-shot learning models. This interface is portable and can be hosted locally or on the web, providing the opportunity to reproducibly conduct, share, and crowd-source few-shot analyses.

97 MATHEMATICS AND COMPUTING↗

Multi-node and Multi-core Performance Studies of a Monte Carlo code RMC

Over the past 15 years the architecture of high-performance computing systems has become increasingly heterogeneous with individual computing cores being subdivided into nodes and even auxiliary co-processing units such as graphics processing units or the Intel many integrated core co-processors. In fact, future computer platforms is moving toward a larger number of nodes and cores with lower memory available per node. Today, several production Monte Carlo codes use some types of hybrid parallelism strategy that makes use of shared-memory parallelism within a computing node and message-passing parallelism between nodes, which enables the codes to utilize available computing resources as much as possible, both among and within computing nodes on a cluster. The so-called hybrid parallelization is also possible with Reactor Monte Carlo Code RMC by activating both MPI and OpenMP parallel algorithms together. On HPC' which typically consists of several or several-ten thousand nodes equipping 16-32 computing intra-cores per node, simulation of RMC can be carried out in the hybrid parallelization with the MPI inter-node parallelization and the OpenMP intra-node parallelization. RMC has adopted a hybrid message-passing and shared-memory approach to parallelism, which enables the code to utilize available computing resources, both among and within computing nodes on a cluster. Shared-memory parallelism is especially valuable for large-model simulations because it enables multiple compute cores within a node to share common model information such as the geometry description, material, cross section and tally data, thus reducing the memory usage per processor. The calculation on the Tianhe-2 supercomputer took 6144 cores, resulting in a rate of 173,314,000 neutrons/minute for BEAVRS benchmark. While pin-wise full core H-M benchmark burnup calculations with millions of depletion regions was selected using MPI/OpenMP parallelism, the speed of 6,144 cores reach 1,843,200 burnable regions per minute. Keeping up with the continuing trend for increases in the number of computing resources within modern HPC systems is a significant challenge for teams that develop and maintain high-performance MC radiation transport solvers. order to address this challenge, RMC has adopted a hybrid message-passing and shared-memory approach to parallelism, which enables the code to utilize available computing resources, both among and within computing nodes on a cluster. Shared-memory parallelism is especially valuable for large-model simulations because it enables multiple compute cores within a node to share common model information such as the geometry description, material and composition definitions, and cross section data, thus reducing the memory usage per processor. The parallel performance has been studied by using two complex and representative benchmarks, H-M and BEAVRS benchmark. All simulations were run on Intel Xeon E5-2692 12 core, 2.2 GHz processors at MilkyWay-2 Super Computer with up to 12,288 available computing cores. While employing MPI parallelism, excellent parallel efficiency is achieved even above 12,000 processors and RMC reaches the parallel efficiency of 96% on 12,288 cores for the pin-by-pin computation of the BEAVRS benchmark. While BEAVRS criticality benchmark was selected using MPI/OpenMP parallelism, the speed of 6,144 cores reach 173,314,000 particles per minute. While pin-wise full core H-M benchmark burnup calculations with millions of depletion regions was selected using MPI/OpenMP parallelism, the speed of 6,144 cores reach 1,843,200 burnable regions per minute. Results from these studies demonstrate that RMC, using the hybrid parallel model described in this paper, is able to handle pin-wise full core burnup calculations with millions of depletion regions and scales well through thousands of processors. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Many-body perturbation theory with hybrid density functional theory starting points accelerated by adaptively compressed exchange

We report on the use of the adaptively compressed exchange (ACE) operator to accelerate many-body perturbation theory (MBPT) calculations, including G 0 W 0 and the Bethe–Salpeter equation (BSE), for hybrid density functional theory starting points. We show that by approximating the exact exchange operator with the low-rank ACE operator, substantial computational savings can be achieved with systematically controllable errors in the quasiparticle energies computed with full-frequency G 0 W 0 and the optical absorption spectra and vertical excitation energies computed by solving the BSE within density matrix perturbation theory. Our implementation makes use of the ACE-accelerated electronic Hamiltonian to carry out both G 0 W 0 and BSE without explicitly computing empty states. We show the robustness of the approach and present the computational gains obtained on both the central processing unit and graphics processing unit nodes. In conclusion, our work will facilitate the exploration and evaluation of fine-tuned hybrid starting points aimed at enhancing the accuracy of MBPT calculations without involving computationally demanding self-consistency in Hedin’s equations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Discrete Hankel Transform Approach to Nuclear Data Processing for Fusion Applications

This study introduces advancements to the numerical solutions employed in the processing of nuclear data for fusion applications. It leverages the convolution theorem and Fourier transform techniques to enhance computational efficiency and broaden applicability. Building upon a previously reported discrete Hankel transform approach for Doppler broadening, this work refines the solution of convolution integrals central to these applications. The methodology provides a general and unified framework for evaluating any convolution operation, regardless of whether the underlying problem involves temperature effects in nuclear reactions. The applicability to the nuclear data processing for fusion is demonstrated by deriving the convolution integrals for some of the fusion-related quantities. As before, the convolution operation utilizes a Gaussian-based kernel; however, the discrete Hankel transform of order $𝛼$ = $\frac{1}{2}$ is now applied to the forward Fourier transform of the nonkernel argument, rather than the inverse Fourier transform. This modification eliminates the need for the integration of the nonkernel, cross section–based function, which is a step that posed challenges for certain pointwise cross-section representations. It also removes the requirement for cross-section linearization. Optimized for graphics processing unit architectures, the approach significantly improves computational performance. These advancements are currently under evaluation as the foundation for the next-generation thermonuclear data file processing codes being developed at Lawrence Livermore National Laboratory.

Nuclear science and engineering↗