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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Roadmap on electronic structure codes in the exascale era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Near real-time streaming analysis of big fusion data

Experiments on fusion plasmas produce high-dimensional data time series with ever-increasing magnitude and velocity, but turn-around times for analysis of this data have not kept up. For example, many data analysis tasks are often performed in a manual, ad-hoc manner some time after an experiment. In this article, we introduce the Delta framework that facilitates near real-time streaming analysis of big and fast fusion data. By streaming measurement data from fusion experiments to a high-performance compute center, Delta allows computationally expensive data analysis tasks to be performed in between plasma pulses. This article describes the modular and expandable software architecture of Delta and presents performance benchmarks of individual components as well as of an example workflow. Focusing on a streaming analysis workflow where electron cyclotron emission imaging (ECEi) data is measured at KSTAR on the National Energy Research Scientific Computing Center's (NERSC's) supercomputer we routinely observe data transfer rates of about 4 Gigabit per second. In NERSC, a demanding turbulence analysis workflow effectively utilizes multiple nodes and graphical processing units and executes them in under 5 min. We further discuss how Delta uses modern database systems and container orchestration services to provide web-based real-time data visualization. For the case of ECEi data we demonstrate how data visualizations can be augmented with outputs from machine learning models. Here, by providing session leaders and physics operators, results of higher-order data analysis using live visualizations may make more informed decisions on how to configure the machine for the next shot.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Spin-glass dynamics in the presence of a magnetic field: exploration of microscopic properties

The synergy between experiment, theory, and simulations enables a microscopic analysis of spin-glass dynamics in a magnetic field in the vicinity of and below the spin-glass transition temperature T g . The spin-glass correlation length, ξ(t, t w ; T), is analysed both in experiments and in simulations in terms of the waiting time t w after the spin glass has been cooled down to a stabilised measuring temperature T < T g and of the time t after the magnetic field is changed. This correlation length is extracted experimentally for a CuMn 6 at. % single crystal, as well as for simulations on the Janus II special-purpose supercomputer, the latter with time and length scales comparable to experiment. The non-linear magnetic susceptibility is reported from experiment and simulations, using ξ(t, t w ; T) as the scaling variable. Previous experiments are reanalysed, and disagreements about the nature of the Zeeman energy are resolved. The growth of the spin-glass magnetisation in zero-field magnetisation experiments, M ZFC (t, t w ; T), is measured from simulations, verifying the scaling relationships in the dynamical or non-equilibrium regime. Lastly, our preliminary search for the de Almeida–Thouless line in D = 3 is discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

ExaWind: A multifidelity modeling and simulation environment for wind energy

We introduce the open-source ExaWind modeling and simulation environment for wind energy. The primary physics codes of ExaWind are Nalu-Wind and OpenFAST. Nalu-Wind is a wind-focused computational fluid dynamics (CFD) code that is coupled to the whole-turbine simulation code OpenFAST. The ExaWind environment was created under U.S. Department of Energy funding to achieve the highest-fidelity simulations of wind turbines and wind farms to date, with the goal of enabling disruptive changes to turbine and plant design and operation. Innovation will be gleaned through better understanding of the complex flow dynamics in wind farms, including wake evolution and the impact of wakes on downstream turbines and turbulent flow from complex terrain. High-fidelity predictive simulations employ hybrid turbulence models, geometry/boundary-layer-resolving CFD meshes, atmospheric turbulence, nonlinear structural dynamics, and fluid-structure interaction. While there is an emphasis on very high-fidelity simulations (e.g., blade resolved with full fluid-structure coupling), the ExaWind environment supports lower-fidelity modeling capabilities including actuator-line and -disk methods. Important in the development of ExaWind codes is that the codes scale well on today's largest petascale supercomputers and on the next-generation platforms that will enable exascale computing.

17 WIND ENERGY↗
DOE OSTI2022

Organizing Large Data Sets for Efficient Analyses on HPC Systems

Upcoming exascale applications could introduce significant data management challenges due to their large sizes, dynamic work distribution, and involvement of accelerators such as graphical processing units, GPUs. In this work, we explore the performance of reading and writing operations involving one such scientific application on two different supercomputers. Our tests showed that the Adaptable Input and Output System, ADIOS, was able to achieve speeds over 1TB/s, a significant fraction of the peak I/O performance on Summit. We also demonstrated the querying functionality in ADIOS could effectively support common selective data analysis operations, such as conditional histograms. In tests, this query mechanism was able to reduce the execution time by a factor of five. More importantly, ADIOS data management framework allows us to achieve these performance improvements with only a minimal amount of coding effort.

Gu, Junmin↗
DOE OSTI2021

Simulations of future particle accelerators: issues and mitigations

The ever increasing demands placed upon machine performance have resulted in the need for more comprehensive particle accelerator modeling. Computer simulations are key to the success of particle accelerators. Many aspects of particle accelerators rely on computer modeling at some point, sometimes requiring complex simulation tools and massively parallel supercomputing. Examples include the modeling of beams at extreme intensities and densities (toward the quantum degeneracy limit), and with ultra-fine control (down to the level of individual particles). In the future, adaptively tuned models might also be relied upon to provide beam measurements beyond the resolution of existing diagnostics. Much time and effort has been put into creating accelerator software tools, some of which are highly successful. However, there are also shortcomings such as the general inability of existing software to be easily modified to meet changing simulation needs. In this paper possible mitigating strategies are discussed for issues faced by the accelerator community as it endeavors to produce better and more comprehensive modeling tools. This includes lack of coordination between code developers, lack of standards to make codes portable and/or reusable, lack of documentation, among others.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Scaling neural simulations in STACS

Abstract As modern neuroscience tools acquire more details about the brain, the need to move towards biological-scale neural simulations continues to grow. However, effective simulations at scale remain a challenge. Beyond just the tooling required to enable parallel execution, there is also the unique structure of the synaptic interconnectivity, which is globally sparse but has relatively high connection density and non-local interactions per neuron. There are also various practicalities to consider in high performance computing applications, such as the need for serializing neural networks to support potentially long-running simulations that require checkpoint-restart. Although acceleration on neuromorphic hardware is also a possibility, development in this space can be difficult as hardware support tends to vary between platforms and software support for larger scale models also tends to be limited. In this paper, we focus our attention on Simulation Tool for Asynchronous Cortical Streams (STACS), a spiking neural network simulator that leverages the Charm++ parallel programming framework, with the goal of supporting biological-scale simulations as well as interoperability between platforms. Central to these goals is the implementation of scalable data structures suitable for efficiently distributing a network across parallel partitions. Here, we discuss a straightforward extension of a parallel data format with a history of use in graph partitioners, which also serves as a portable intermediate representation for different neuromorphic backends. We perform scaling studies on the Summit supercomputer, examining the capabilities of STACS in terms of network build and storage, partitioning, and execution. We highlight how a suitably partitioned, spatially dependent synaptic structure introduces a communication workload well-suited to the multicast communication supported by Charm++. We evaluate the strong and weak scaling behavior for networks on the order of millions of neurons and billions of synapses, and show that STACS achieves competitive levels of parallel efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs

Genome-wide association studies (GWAS) at biobank scale are computationally intensive, especially for admixed populations requiring robust statistical models. SAIGE is a widely used method for generalized linear mixed-model GWAS but is limited by its CPU-based implementation, making phenome-wide association studies impractical for many research groups. We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. Applied to 2068 phenotypes from 635 969 participants in the Million Veteran Program, including diverse and admixed populations, SAIGE-GPU achieved a 5-fold speedup in mixed model fitting on supercomputing infrastructure and cloud platforms. We further optimized the variant association testing step through multi-core and multi-trait parallelization. Deployed on Google Cloud Platform and Azure, the method provided substantial cost and time savings. Source code and binaries are available for download at https://github.com/saigegit/SAIGE/tree/SAIGE-GPU-1.3.3. A code snapshot is archived at Zenodo for reproducibility (DOI: [10.5281/zenodo.17642591]). SAIGE-GPU is available in a containerized format for use across HPC and cloud environments and is implemented in R/C++ and runs on Linux systems.

Rodriguez, Alex [Argonne National Laboratory (ANL)↗
DOE OSTI2024

Towards Autonomous Experiments by Connecting High Performance Microscopy with High Performance Computing

The digitization of controls, data, and analysis in microscopy is bringing the idea of autonomous microscopes closer to reality than ever before. Automated transmission electron microscopy (TEM) is already fairly routine for some experiments the only require simple repetitive tasks such as imaging biological macromolecules for single particle cryoEM [1], tilt series for electron tomography [2], and movies for crystallography [3]. The vast majority of TEM experiments are conducted completely by human operators who choose the regions of interest, optimize experimental parameters, and make decisions about data quality visually during an experiment. The field is still a long way from having completely autonomous TEMs that can adapt to sample difficulties and tune experimental parameters based on data quality and desired experimental outcomes. Part of the issue is the lack of capability for feeding information learned from on-line, live data analysis back into the on-going experiment [4]. Furthermore, this presentation will discuss current capabilities for large scale data reduction and analysis using high performance computing (i.e. supercomputing) and progress towards developing a true feed-back loop that places data analysis and theory in the experimental loop.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The ABACUS cosmological N -body code

We present abacus, a fast and accurate cosmological N-body code based on a new method for calculating the gravitational potential from a static multipole mesh. The method analytically separates the near- and far-field forces, reducing the former to direct 1/r 2 summation and the latter to a discrete convolution over multipoles. The method achieves 70 million particle updates per second per node of the Summit supercomputer, while maintaining a median fractional force error of 10 -5 . We express the simulation time-step as an event-driven ‘pipeline’, incorporating asynchronous events such as completion of co-processor work, input/output, and network communication. abacus has been used to produce the largest suite of N-body simulations to date, the abacussummit suite of 60 trillion particles, incorporating on-the-fly halo finding. abacus enables the production of mock catalogues of the volume and resolution required by the coming generation of cosmological surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

ABACUSSUMMIT : a massive set of high-accuracy, high-resolution N -body simulations

We present the public data release of the AbacusSummit cosmological N-body simulation suite, produced with the Abacus N-body code on the Summit supercomputer of the Oak Ridge Leadership Computing Facility. Abacus achieves $\mathcal {O}(10^{-5})$ median fractional force error at superlative speeds, calculating 70M particle updates per second per node at early times, and 45M particle updates per second per node at late times. The simulation suite totals roughly 60 trillion particles, the core of which is a set of 139 simulations with particle mass $2\times 10^{9}\, h^{-1}\, \mathrm{M}_\odot$ in box size $2\, h^{-1}\, \mathrm{Gpc}$. The suite spans 97 cosmological models, including Planck 2018, previous flagship simulation cosmologies, and a linear derivative and cosmic emulator grid. A subsuite of 1883 boxes of size $500\, h^{-1}\, \mathrm{Mpc}$ is available for covariance estimation. AbacusSummit data products span 33 epochs from z = 8 to 0.1 and include light cones, full particle snapshots, halo catalogues, and particle subsets sampled consistently across redshift. AbacusSummit is the largest high-accuracy cosmological N-body data set produced to date.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Random circuit block-encoded matrix and a proposal of quantum LINPACK benchmark

The LINPACK benchmark reports the performance of a computer for solving a system of linear equations with dense random matrices. Although this task was not designed with a real application directly in mind, the LINPACK benchmark has been used to define the list of TOP500 supercomputers since the debut of the list in 1993. We propose that a similar benchmark, called the quantum LINPACK benchmark, could be used to measure the whole machine performance of quantum computers. The success of the quantum LINPACK benchmark should be viewed as the minimal requirement for a quantum computer to perform a useful task of solving linear algebra problems, such as linear systems of equations. We propose an input model called the Random Circuit Block-Encoded Matrix (RACBEM), which is a proper generalization of a dense random matrix in the quantum setting. The RACBEM model is efficient to be implemented on a quantum computer and can be designed to optimally adapt to any given quantum architecture, with relying on a black-box quantum compiler. Besides solving linear systems, the RACBEM model can be used to perform a variety of linear algebra tasks relevant to many physical applications, such as computing spectral measures, time series generated by a Hamiltonian simulation, and thermal averages of the energy. We implement these linear algebra operations on IBM Q quantum devices as well as quantum virtual machines, and demonstrate their performance in solving scientific computing problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Simulating lossy Gaussian boson sampling with matrix-product operators

Gaussian boson sampling, a computational model that is widely believed to admit quantum supremacy, has already been experimentally demonstrated and is claimed to surpass the classical simulation capabilities of even the most powerful supercomputers today. However, whether the current approach limited by photon loss and noise in such experiments prescribes a scalable path to quantum advantage is an open question. Here, to understand the effect of photon loss on the scalability of Gaussian boson sampling, we analytically derive the asymptotic operator entanglement entropy scaling, which relates to the simulation complexity. As a result, we observe that efficient tensor network simulations are likely possible under the N out ∝ √N scaling of the number of surviving photons N out in the number of input photons N. We numerically verify this result using a tensor network algorithm with U⁡(1) symmetry, and we overcome previous challenges due to the large local Hilbert-space dimensions in Gaussian boson sampling with hardware acceleration. Additionally, we observe that increasing the photon number through larger squeezing does not increase the entanglement entropy significantly. Finally, we numerically find the bond dimension necessary for fixed accuracy simulations, providing more direct evidence for the complexity of tensor networks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Fully self-consistent finite-temperature $GW$ in Gaussian Bloch orbitals for solids

In this work, we present algorithmic and implementation details for the fully self-consistent finite-temperature $GW$ method in Gaussian Bloch orbitals for solids. Our implementation is based on the finite-temperature Green's function formalism in which all equations are solved on the imaginary axis, without resorting to analytical continuation during the self-consistency. No quasiparticle approximation is employed and all matrix elements of the self-energy are explicitly evaluated. The method is tested by evaluating the band gaps of selected semiconductors and insulators. We show agreement with other, differently formulated, finite-temperature sc ⁢$GW$ implementations when finite-size corrections and basis-set errors are taken into account. By migrating computationally intensive calculations to graphics processing units, we obtain scalable results on large supercomputers with nearly optimal performance. Our work demonstrates the applicability of Gaussian orbital based sc⁢ $GW$ for ab initio correlated material simulations and provides a sound starting point for embedding methods built on top of $GW$.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Entanglement rearrangement in self-consistent nuclear structure calculations

Background: Entanglement plays a central role in a diverse array of increasingly important research areas, including quantum computation, simulation, measurement, sensing, and communication. Extensive suites of investigations have been performed to better understand entanglement in atomic and molecular quantum many-body systems, while the exploration of entanglement in the structure of nuclei and their reactions is presently in its infancy. Purpose: The goal of this work is to begin investigating the entanglement properties of nuclei from first-principles nuclear many-body calculations. We attempt to identify common features and emergent structures of entanglement that could ultimately lead to new and natural many-body schemes. With an eye toward quantum accelerators in future hybrid-supercomputers, criteria for partitioning nuclear many-body calculations into quantum and classical components may provide advantages in future large-scale computations. Along the way we look for explanations of the relative success of phenomenological models such as the nuclear shell model, and for better ways to match to low-energy nuclear effective field theories and lattice QCD calculations to nuclear many-body techniques that are based upon entanglement. Method: We explore the entanglement between single-particle states in 4 He and 6 He. The patterns of entanglement emerging from different single-particle bases are compared, and possible links with the convergence of observables are explored, in particular, ground-state energies. The nuclear wave functions are obtained by performing active-space no-core configuration-interaction calculations using a two-body nucleon-nucleon interaction derived from chiral effective field theory. Entanglement measures within single-particle bases exhibiting different degrees of complexity are determined, in particular, harmonic oscillator (HO), Hartree-Fock (HF), natural (NAT) and variational natural (VNAT) bases. Specifically, single-orbital entanglement entropy, two-orbital mutual information, and negativity are studied. Results: The entanglement structures in 4 He and 6 He are found to be more localized within NAT and VNAT bases than within a HO basis for the optimal HO parameters we have worked with. In particular a core-valence structure clearly emerges from the full no-core calculation of 6 He. Here, the two-nucleon mutual information shows that the VNAT basis, which typically exhibits good convergence properties, effectively decouples the active and inactive spaces. Conclusions: Measures of one- and two-nucleon entanglement are found to be useful in analyzing the structure of nuclear wave functions, in particular the efficacy of basis states, and may provide useful metrics toward developing more efficient schemes for ab initio computations of the structure and reactions of nuclei, and quantum many-body systems more generally.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Interpretable AI forecasting for numerical relativity waveforms of quasicircular, spinning, nonprecessing binary black hole mergers

We present a deep-learning artificial intelligence model (AI) that is capable of learning and forecasting the late-inspiral, merger and ringdown of numerical relativity waveforms that describe quasicircular, spinning, nonprecessing binary black hole mergers. We used the NRHybSur3dq8 surrogate model to produce train, validation and test sets of ℓ = |m| = 2 waveforms that cover the parameter space of binary black hole mergers with mass ratios q ≤ 8 and individual spins |s$^{z}_ {(1,2)}$| ≤ 0.8. These waveforms cover the time range t ∊ [-5000 M, 130 M], where t = 0M marks the merger event, defined as the maximum value of the waveform amplitude. We harnessed the ThetaGPU supercomputer at the Argonne Leadership Computing Facility to train our AI model using a training set of 1.5 million waveforms. We used 16 NVIDIA DGX A100 nodes, each consisting of 8 NVIDIA A100 Tensor Core GPUs and 2 AMD Rome CPUs, to fully train our model within 3.5 h. Our findings show that artificial intelligence can accurately forecast the dynamical evolution of numerical relativity waveforms in the time range t ∊ [-100 M, 130 M]. Sampling a test set of 190,000 waveforms, we find that the average overlap between target and predicted waveforms is ≳99% over the entire parameter space under consideration. We also combined scientific visualization and accelerated computing to identify what components of our model take in knowledge from the early and late-time waveform evolution to accurately forecast the latter part of numerical relativity waveforms. This work aims to accelerate the creation of scalable, computationally efficient and interpretable artificial intelligence models for gravitational wave astrophysics

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here, in this work, we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Quantifying Memory in Spin Glasses

Rejuvenation and memory, long considered the distinguishing features of spin glasses, have recently been proven to result from the growth of multiple length scales. This insight, enabled by simulations on the Janus II supercomputer, has opened the door to a quantitative analysis. We combine numerical simulations with comparable experiments to introduce two coefficients that quantify memory. A third coefficient has been recently presented by Freedberg et al. Here, we show that these coefficients are physically equivalent by studying their temperature and waiting-time dependence.

36 MATERIALS SCIENCE↗