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At least 973 records · Page 54

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations. To make advancements in all the aforementioned scientific areas, many technical aspects need to be more thoroughly studied and deeply understood in parallel discrete event simulation (PDES). The unique dynamics inherent in a discrete event modeling approach, by their very nature, intersect and influence the entire stack of the computing system, including (a) the unique nature of the instruction sets exercised in PDES workloads without a predominance of high-precision floating point operations, (b) virtual time-constrained multi-threaded execution of many logical processes per processor, (c) extremely variable and difficult to predict network traffic characteristics, (d) interfaces and inter-dependencies with machine learning and artificial intelligence codes at higher software layers, and (e) highly challenging load balancing needs, especially in effectively accounting for accelerated/extremely heterogeneous computing in current and future high-performance computing systems. Efficient and accurate parallel execution of PDES workloads is also dominated by challenges in dealing with their asynchronous concurrency fundamentally present at the model level. Conservative synchronization, optimistic/speculative synchronization, and their hybrid schemes open new questions in fundamental computer science with respect to reversibility of computation and prediction (lookahead) of behaviors inherent within model codes. On the implementation front, there are relatively few scalable, general-purpose parallel discrete event simulators in the world, and even fewer have been studied on emerging hardware platforms. To enable scientific advances using PDES, the research needs in computer science must also be pursued and met in the intersection of the algorithmic and hardware-aware aspects of scalable PDES engines. This report is aimed at capturing a computer science-oriented view of this important area of research in PDES, presenting a sample of important applications with their inherent discrete event technology elements. Needs are outlined in core areas of parallel discrete event research as well as cross-cutting directions in computer science research that positively impact scientific advancements across several important application areas. A selection of priority research opportunities in advanced computing for PDES is identified to serve as reference for key research topics and their order of importance for scientific advancements.

97 MATHEMATICS AND COMPUTING↗

Radiological Scouting, Monitoring and Inspection Using Drones

Human populations and natural ecosystems are bound to be exposed to ionizing radiation from the deposition of artificial radionuclides resulting from nuclear accidents, nuclear devices or radiological dispersive devices (“dirty bombs”). On the other hand, Naturally Occurring Radioactive Material industries such as phosphate production or uranium mining, contribute to the on site storage of residuals with enhanced concentrations of natural radionuclides. Therefore, in the context of the European agreements concerning nuclear energy, namely the European Atomic Energy Community Treaty, monitoring is an essential feature of the environmental radiological surveillance. In this work, we obtain 3D maps from outdoor scenarios, and complete such maps with measured radiation levels and with its radionuclide signature. In such scenarios, we face challenges such as unknown and rough terrain, limited number of sampled locations and the need for different sensors and therefore different tasks. We propose a radiological solution for scouting, monitoring and inspecting an area of interest, using a fleet of drones and a controlling ground station. First, we scout an area with a Light Detection and Ranging sensor onboard a drone to accurately 3D-map the area. Then, we monitor that area with a Geiger–Müller Counter at a low-vertical distance from the ground to produce a radiological (heat)map that is overlaid on the 3D map of the scenario. Next, we identify the hotspots of radiation, and inspect them in detail using a drone by landing on them, to reveal its radionuclide signature using a Cadmium–Zinc–Telluride detector. We present the algorithms used to implement such tasks both at the ground station and on the drones. The three mission phases were validated using actual experiments in three different outdoor scenarios. We conclude that drones can not only perform the mission efficiently, but in general they are faster and as reliable as personnel on the ground.

Pinto, Luís Ramos (ORCID:0000000319975484)↗

Data-Driven Compositional Optimization in Misspecified Regimes

With a manifold growth in the scale and intricacy of systems, the challenges of parametric misspecification become pronounced. These concerns are further exacerbated in compositional settings, which emerge in problems complicated by modeling risk and robustness. In “Data-Driven Compositional Optimization in Misspecified Regimes,” the authors consider the resolution of compositional stochastic optimization problems, plagued by parametric misspecification. In considering settings where such misspecification may be resolved via a parallel learning process, the authors develop schemes that can contend with diverse forms of risk, dynamics, and nonconvexity. They provide asymptotic and rate guarantees for unaccelerated and accelerated schemes for convex, strongly convex, and nonconvex problems in a two-level regime with extensions to the multilevel setting. Surprisingly, the nonasymptotic rate guarantees show no degradation from the rate statements obtained in a correctly specified regime and the schemes achieve optimal (or near-optimal) sample complexities for general T-level strongly convex and nonconvex compositional problems.

Business & Economics↗

Complex paths around the sign problem

The Monte Carlo evaluation of path integrals is one of a few general purpose methods to approach strongly coupled systems. It is used in all branches of physics, from QCD and nuclear physics to the correlated electron systems. However, many systems of great importance (dense matter inside neutron stars, the repulsive Hubbard model away from half filling, and dynamical and nonequilibrium observables) are not amenable to the Monte Carlo method as it currently stands due to the so-called sign problem. Here, a new set of ideas recently developed to tackle the sign problem based on the complexification of field space and the Picard-Lefshetz theory accompanying it is reviewed. The mathematical ideas underpinning this approach, as well as the algorithms developed thus far, are described together with nontrivial examples where the method has already been proved successful. Directions of future work, including the burgeoning use of machine learning techniques, are delineated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Enriched immersed finite element and isogeometric analysis: algorithms and data structures

Immersed finite element methods provide a convenient analysis framework for problems involving geometrically complex domains, such as those found in topology optimization and microstructures for engineered materials. However, their implementation remains a major challenge due to, among other things, the need to apply nontrivial stabilization schemes and generate custom quadrature rules. This article introduces the robust and computationally efficient algorithms and data structures comprising an immersed finite element preprocessing framework. The input to the preprocessor consists of a background mesh and one or more geometries defined on its domain. The output is structured into groups of elements with custom quadrature rules formatted such that common finite element assembly routines may be used without or with only minimal modifications. The key to the preprocessing framework is the construction of material topology information, concurrently with the generation of a quadrature rule, which is then used to perform enrichment and generate stabilization rules. While the algorithmic framework applies to a wide range of immersed finite element methods using different types of meshes, integration, and stabilization schemes, the preprocessor is presented within the context of the extended isogeometric analysis. This method utilizes a structured B-spline mesh, a generalized Heaviside enrichment strategy considering the material layout within individual basis functions’ supports, and face-oriented ghost stabilization. Using a set of examples, the effectiveness of the enrichment and stabilization strategies is demonstrated alongside the preprocessor’s robustness in geometric edge cases. Additionally, the performance and parallel scalability of the implementation are evaluated.

Computer implementation↗

SPLENDAQ: A Detector-Agnostic Data Acquisition System for Small-Scale Physics Experiments

Many scientific applications from rare-event searches to condensed matter system characterization to high-rate nuclear experiments require time-domain triggering on a raw stream of data, where the triggering is generally threshold-based or randomly acquired. When carrying out detector R &D, there is a need for a general data acquisition (DAQ) system to quickly and efficiently process such data. In the SPLENDOR collaboration, we are developing the Python-based SPLENDAQ package for this exact purpose—it offers two main features for offline analysis of continuous data: a threshold triggering algorithm based on the time-domain optimal filter formalism and an algorithm for randomly choosing nonoverlapping segments for noise measurements. Further, combined with the commercially available Moku platform, developed by Liquid Instruments, we have a full pipeline of event building off raw data with minimal setup. Here, we review the underlying principles of this detector-agnostic DAQ package and give concrete examples of its utility in various applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

LeptonInjector and LeptonWeighter: A neutrino event generator and weighter for neutrino observatories

In this work, we present a high-energy neutrino event generator, called LeptonInjector, alongside an event weighter, called LeptonWeighter. Both are designed for large-volume Cherenkov neutrino telescopes such as IceCube. The neutrino event generator allows for quick and flexible simulation of neutrino events within and around the detector volume, and implements the leading Standard Model neutrino interaction processes relevant for neutrino observatories: neutrino-nucleon deep-inelastic scattering and neutrino-electron annihilation. In this paper, we discuss the event generation algorithm, the weighting algorithm, and the main functions of the publicly available code, with examples. Program summary: Program Titles: LeptonInjector and LeptonWeighter CPC Library link to program files: https://doi.org/10.17632/662gkpjfd9.1 Developer's repository links: https://github.com/icecube/LeptonInjector and https://github.com/icecube/LeptonWeighter Licensing provisions: GNU Lesser General Public License, version 3. Programming Language: C++11 External Routines: • Boost • HDF5 • nuflux (https://github.com/icecube/nuflux) • nuSQuIDS (https://github.com/arguelles/nuSQuIDS) • Photospline (https://github.com/icecube/photospline) • SuiteSparse (https://github.com/DrTimothyAldenDavis/SuiteSparse) Nature of problem: LeptonInjector: Generate neutrino interaction events of all possible topologies and energies throughout and around a detector volume. LeptonWeighter: Reweight Monte Carlo events, generated by a set of LeptonInjector Generators, to any desired physical neutrino flux or cross section. Solution method: LeptonInjector: Projected ranges of generated leptons and the extent of the detector, in terms of column depth, are used to inject events in and around the detector volume. Event kinematics follow distributions provided in cross section files. LeptonWeighter: Event generation probabilities are calculated for each Generator, which are then combined into a generation weight and used to calculate an overall event weight.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Comparison of multiobjective optimization methods for the $\mathrm{LCLS-II}$ photoinjector

Particle accelerators are among some of the largest science experiments in the world and can consist of thousands of components with a wide variety of input ranges. These systems can easily become unwieldy optimization problems during design and operations studies. Starting in the early 2000s, searching for better beam dynamics configurations became synonymous with heuristic optimization methods in the accelerator physics community. Genetic algorithms and particle swarm optimization are currently the most widely used. These algorithms can take thousands of simulation evaluations to find optimal solutions for one machine prototype. For large facilities such as the Linac Coherent Light Source (LCLS) and others, this equates to a limited exploration of many possible design configurations. In this paper, the LCLS-II photoinjector is optimized with three optimization algorithms. All optimizations were started from both a uniform random and Latin hypercube sample. In all cases, the optimizations started from Latin hypercube samples outperformed optimizations started from uniform samples. All three algorithms were able to optimize the photoinjector, with the model-based methods approximating the Pareto front in fewer simulation evaluations. This work, in combination with previous optimization observations, indicates objective penalties have a strong impact on the efficiency of such methods. In general, we recommend heuristic methods for initial optimizations and model-based methods when information about the objective space is available.

43 PARTICLE ACCELERATORS↗

Maximum bound principle preserving integrating factor Runge–Kutta methods for semilinear parabolic equations

A large class of semilinear parabolic equations satisfy the maximum bound principle (MBP) in the sense that the time-dependent solution preserves for any time a uniform pointwise bound imposed by its initial and boundary conditions. Here, the MBP plays a crucial role in understanding the physical meaning and the well-posedness of the mathematical model. Investigation on numerical algorithms with preservation of the MBP has attracted increasingly attentions in recent years, especially for the temporal discretizations, since the violation of MBP may lead to nonphysical solutions or even blow-ups of the algorithms. In this paper, we study high-order MBP-preserving time integration schemes by means of the integrating factor Runge-Kutta (IFRK) method. Beginning with the space-discrete system of semilinear parabolic equations, we present the IFRK method in general form and derive the sufficient conditions for the method to preserve the MBP. In particular, we show that the classic four-stage, fourth-order IFRK scheme is MBP preserving for some typical semilinear systems although not strong stability preserving, which can be instantly applied to the Allen-Cahn type of equations. To our best knowledge, this is the first time to present a fourth-order linear numerical method preserving the MBP. In addition, convergence of these numerical schemes is proved theoretically and verified numerically, as well as their efficiency by simulations of 2D and 3D long-time evolutional behaviors. Numerical experiments are also carried out for a model which is not a typical gradient flow as the Allen-Cahn type of equations.

97 MATHEMATICS AND COMPUTING↗

Maximizing efficiency of dataset compression for machine learning potentials with information theory

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

36 MATERIALS SCIENCE↗

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways

Abstract Motivation Estimating causal queries, such as changes in protein abundance in response to a perturbation, is a fundamental task in the analysis of biomolecular pathways. The estimation requires experimental measurements on the pathway components. However, in practice many pathway components are left unobserved (latent) because they are either unknown, or difficult to measure. Latent variable models (LVMs) are well-suited for such estimation. Unfortunately, LVM-based estimation of causal queries can be inaccurate when parameters of the latent variables are not uniquely identified, or when the number of latent variables is misspecified. This has limited the use of LVMs for causal inference in biomolecular pathways. Results In this article, we propose a general and practical approach for LVM-based estimation of causal queries. We prove that, despite the challenges above, LVM-based estimators of causal queries are accurate if the queries are identifiable according to Pearl’s do-calculus and describe an algorithm for its estimation. We illustrate the breadth and the practical utility of this approach for estimating causal queries in four synthetic and two experimental case studies, where structures of biomolecular pathways challenge the existing methods for causal query estimation. Availability and implementation The code and the data documenting all the case studies are available at https://github.com/srtaheri/LVMwithDoCalculus. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Survey of Gravitationally lensed objects in HSC Imaging (SuGOHI). VIII. New galaxy-scale lenses from the HSC SSP

Abstract We conduct a search for galaxy-scale strong gravitational lens systems in Data Release 4 of the Hyper Suprime-Cam Subaru Strategic Program (HSC SSP), consisting of data taken up to the S21A semester. We select 103191 luminous red galaxies from the Baryon Oscillation Spectroscopic Survey (BOSS) sample that have deep multiband imaging from the HSC SSP and use the YattaLens algorithm to identify lens candidates with blue arc-like features automatically. The candidates are visually inspected and graded based on their likelihood of being a lens. We find eight definite lenses, 28 probable lenses, and 138 possible lenses. The new lens candidates generally have lens redshifts in the range 0.3 ≲ zL ≲ 0.9, a key intermediate redshift range to study the evolution of galaxy structure. Follow-up spectroscopy will confirm these new lenses and measure source redshifts to enable detailed lens modeling.

Astronomy & Astrophysics↗

Unified architecture for quantum lookup tables

Quantum access to arbitrary classical data encoded in unitary black-box oracles underlies interesting data-intensive quantum algorithms, such as machine learning or electronic structure simulation. The feasibility of these applications depends crucially on gate-efficient implementations of these oracles, which are commonly some reversible versions of the Boolean circuit for a classical lookup table. Here, we present a general parametrized architecture for quantum circuits implementing a lookup table that encompasses all prior work in realizing a continuum of optimal trade-offs between qubits, non-Clifford gates, and error resilience, up to logarithmic factors. Our architecture assumes only local 2D connectivity, yet recovers results, with the appropriate parameters, polylogarithmic error scaling. We also identify regimes, such as simultaneous sublinear scaling, in all parameters. These results enable tailoring implementations of the commonly used lookup table primitive to any given quantum device with constrained resources.

quantum circuits↗

A Heterogeneous System for Eagle Detection, Deterrent, and Wildlife Collision Detection for Wind Turbines (Final Technical Report)

This report summarizes the design, implementation, and test of an integrated system for automated detection and deterrence of eagles, with included wind turbine blade strike detection and imaging functionality. A machine learning approach was used in conjunction with a 360° camera system for automated detection and classification of golden eagles. This was developed using footage obtained from trained golden eagles and other raptors, in collaboration with wildlife biologists and professional bird handlers. Oregon State University developed a visual deterrent system, which uses inflatable anthropomorphic sculptures with random, kinetic motion to deter eagles, and conducted limited field testing on live eagles; the deterrent can be triggered by the visual detection of eagles using the vision system. Finally, a multi-sensor module was developed that is mounted at the turbine blade root. This module measures vibration and other motions to detect blade strikes, and an integrated on-blade camera captures an image of any impacting objects. Long-term, this blade strike detection system is intended to support an automatic monitoring and certification system for the eagle detection and deterent system. Independent field testing of each system component is described. Testing of the integrated system on an operational wind turbine was conducted across three separate field tests. This includes multi-day fields tests on a General Electric 1.5MW wind turbine at the National Renewable Energy Laboratory (NREL) National Wind Technology Center (NWTC) in Boulder, CO in October 2018 and July 2019; installation procedures, test procedures, and a summary of collected data are presented. A third multi-day on-turbine field test is also presented, which was performed using a General Electric 1.5MW wind turbine at the North American Wind Research and Training Center (NAWRTC) at Mesalands Community College, Tucumcari, NM in April 2019. Across these field tests, the vision system was demonstrated using unmanned aerial vehicles (UAV), and the eagle classification algorithm was not tested; the visual deterrent system was demonstrated, including automatic, remote deployment following surrogate visual detections; and, multi-sensor on-blade data was recorded across multiple wind turbine operational conditions and through more than 100 surrogate blade strikes using soft projectiles, including the successful demonstration of automatic image capture of striking objects. This data set was also used for offline development and validation of enhanced collision detection algorithms. As summarized in this report, the development and field validation of an integrated detection, deterrent, and blade collision detection system represents a critical proof of concept for future technology development of related detection and deterrent technologies, where both deterrent as well as collision detection recording devices are needed for future siting, monitoring, and operation of wind turbine installations, both onshore and offshore.

17 WIND ENERGY↗

Breaking the mold: Overcoming the time constraints of molecular dynamics on general-purpose hardware

The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of accuracy, atom count (spatial scale), and duration (temporal scale). Since the mid-2000s, computer platforms have, however, failed to provide strong scaling for MD, as scale-out central processing unit (CPU) and graphics processing unit (GPU) platforms that provide substantial increases to spatial scale do not lead to proportional increases in temporal scale. Important scientific problems therefore remained inaccessible to direct simulation, prompting the development of increasingly sophisticated algorithms that present significant complexity, accuracy, and efficiency challenges. While bespoke MD-only hardware solutions have provided a path to longer timescales for specific physical systems, their impact on the broader community has been mitigated by their limited adaptability to new methods and potentials. In this work, we show that a novel computing architecture, the Cerebras wafer scale engine, completely alters the scaling path by delivering unprecedentedly high simulation rates up to 1.144 M steps/s for 200 000 atoms whose interactions are described by an embedded atom method potential. This enables direct simulations of the evolution of materials using general-purpose programmable hardware over millisecond timescales, dramatically increasing the space of direct MD simulations that can be carried out. In this paper, we provide an overview of advances in MD over the last 60 years and present our recent result in the context of historical MD performance trends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A conservative phase-space moving-grid strategy for a 1D-2V Vlasov–Fokker–Planck Solver

In this work, we develop a conservative configuration- and velocity-space (i.e., phase-space) moving-grid strategy for the Vlasov–Fokker–Planck (VFP) equation in a planar geometry. The velocity-space grid is normalized and shifted in terms of the thermal speed and the bulk-fluid velocity, respectively. The configuration-space grid is moved according to a mesh-motion-partial-differential equation (MMPDE), which equidistributes a monitor function that is inversely proportional to the gradient-length scales of the macroscopic plasma quantities. The resulting inertial terms in the transformed VFP equations are discretized to ensure the discrete conservation of mass, momentum, and energy. To satisfy the discrete conservation theorems in the presence of phase-space mesh motion, we employ the method of discrete nonlinear constraints – explored in previous studies – but the underlying symmetries are determined in a much more efficient manner than before. The conservative grid-adaptivity strategy provides an efficient scheme that resolves important physical structures in the phase-space while controlling the computational complexity at all times. We demonstrate the favorable features of the proposed algorithm through a set of test cases of increasing complexity. The problems test independent components of the algorithms, as well as the integrated capability on settings relevant to inertial confinement fusion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An Extension of the Athena++ Code Framework for Radiation-magnetohydrodynamics in General Relativity Using a Finite-solid-angle Discretization

We extend the general-relativistic magnetohydrodynamics (GRMHD) capabilities of Athena++ to incorporate radiation. The intensity field in each finite-volume cell is discretized in angle, with explicit transport in both space and angle properly accounting for the effects of gravity on null geodesics, and with matter and radiation coupled in a locally implicit fashion. Here we describe the numerical procedure in detail, verifying its correctness with a suite of tests. Motivated in particular by black hole accretion in the high-accretion-rate, thin-disk regime, we demonstrate the application of the method to this problem. With excellent scaling on flagship computing clusters, the port of the algorithm to the GPU-enabled AthenaK code now allows the simulation of many previously intractable radiation-GRMHD systems.

79 ASTRONOMY AND ASTROPHYSICS↗

Bayesian projection pursuit regression

In projection pursuit regression (PPR), a univariate response variable is approximated by the sum of $M$ “ridge functions,” which are flexible functions of one-dimensional projections of a multivariate input variable. Traditionally, optimization routines are used to choose the projection directions and ridge functions via a sequential algorithm, and $M$ is typically chosen via cross-validation. Here, we introduce a novel Bayesian version of PPR, which has the benefit of accurate uncertainty quantification. To infer appropriate projection directions and ridge functions, we apply novel adaptations of methods used for the single ridge function case ($M$=1), called the Bayesian Single Index Model; and use a Reversible Jump Markov chain Monte Carlo algorithm to infer the number of ridge functions $M$. We evaluate the predictive ability of our model in 20 simulated scenarios and for 23 real datasets, in a bake-off against an array of state-of-the-art regression methods. Finally, we generalize this methodology and demonstrate the ability to accurately model multivariate response variables. Its effective performance indicates that Bayesian Projection Pursuit Regression is a valuable addition to the existing regression toolbox.

97 MATHEMATICS AND COMPUTING↗