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At least 1,333 records · Page 74

Exploring the use of I/O nodes for computation in a MIMD multiprocessor

As parallel systems move into the production scientific-computing world, the emphasis will be on cost-effective solutions that provide high throughput for a mix of applications. Cost effective solutions demand that a system make effective use of all of its resources. Many MIMD multiprocessors today, however, distinguish between 'compute' and 'I/O' nodes, the latter having attached disks and being dedicated to running the file-system server. This static division of responsibilities simplifies system management but does not necessarily lead to the best performance in workloads that need a different balance of computation and I/O. Of course, computational processes sharing a node with a file-system service may receive less CPU time, network bandwidth, and memory bandwidth than they would on a computation-only node. In this paper we begin to examine this issue experimentally. We found that high performance I/O does not necessarily require substantial CPU time, leaving plenty of time for application computation. There were some complex file-system requests, however, which left little CPU time available to the application. (The impact on network and memory bandwidth still needs to be determined.) For applications (or users) that cannot tolerate an occasional interruption, we recommend that they continue to use only compute nodes. For tolerant applications needing more cycles than those provided by the compute nodes, we recommend that they take full advantage of both compute and I/O nodes for computation, and that operating systems should make this possible.

Kotz, David↗

Alkali Metal Ions Dictate the Structure and Reactivity of an Iron(II) Imido Complex

The presence of redox innocent metal ions has been proposed to modulate the reactivity of metal ligand multiple bonds; however, insight from structure/function relationships is limited. Here, alkali metal reduction of the Fe(III) imido complex [Ph 2 B( t BuIm) 2 Fe=NDipp] (1) provides the series of structurally characterized Fe(II) imido complexes [Ph 2 B( t BuIm) 2 Fe=NDippLi(THF) 2 ] (2), [Ph 2 B( t BuIm) 2 Fe=NDippNa(THF) 3 ] (3), and [Ph 2 B( t BuIm) 2 Fe=NDippK] 2 (4), in which the alkali metal cations coordinate the imido ligand. Structural investigations demonstrate that the alkali metal ions modestly lengthen the Fe=N bond distance from that in the charge separated complex [Ph 2 B( t BuIm) 2 Fe=NDipp][K(18-C-6)THF 2 ] (5), with the longest bond observed for the smallest alkali metal ion. In contrast to 5, the imido ligands in 2–4 can be protonated and alkylated to afford Fe(II) amido complexes. Combined experimental and computational studies reveal that the alkali metal polarizes the Fe=N bond, and the basicity of imido ligand increases according to 5 < 4 ≈ 3 < 2. The basicity of the imido ligands influences the relative rates of reaction with 1,4-cyclohexadiene, specifically by gating access to complex 5, which is the species that is active for HAT. All complexes 2–4 react with benzophenone form metastable Fe(II) intermediates that subsequently eliminate the metathesis product Ph 2 C=NDipp, with relative rates dependent on the alkali metal ion. By contrast, the same reaction with 5 does not lead to the formation of Ph 2 C=NDipp. Furthermore, these results demonstrate that the coordination of alkali metal ions dictate both the structure and reactivity of the imido ligand and moreover can direct the reactivity of reaction intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Graph-based quantum response theory and shadow Born–Oppenheimer molecular dynamics

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born–Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. Further, the proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗

Improving Schrödinger Equation Implementations with Gray Code for Adiabatic Quantum Computers

We reformulate the continuous-space Schrödinger equation in terms of spin Hamiltonians. For the kinetic energy operator, the critical concept facilitating the reduction in model complexity is the idea of position encoding. A binary encoding of position produces a spin-1/2 Heisenberg-like model and yields exponential improvement in space complexity when compared to classical computing. Encoding with a binary reflected Gray code (BRGC), and a Hamming-distance-2 Gray code (H2GC) reduces the model complexity down to the 𝑋⁢𝑍 and transverse Ising model, respectively. For 𝐴 qubits BRGC yields 2 𝐴 positions and is reduced to its 2-local form with O⁡(𝐴) ancillary qubits. H2GC yields 2 𝐴/2+1 positions with O⁡(𝐴 2 ) three-local penalty terms. We also identify the bijective mapping between diagonal unitaries and the Walsh series, producing the mapping of any real potential to a series of 𝑘 -local Ising models through the fast Walsh transform. Finally, in a finite volume, we provide some numerical evidence to support the claim that the total time needed for adiabatic evolution is protected by the infrared cutoff of the system. As a result, initial state preparation from a free-field wave function to an interacting system is expected to exhibit polynomial time complexity with volume and constant scaling with respect to lattice discretization for all encodings. For H2GC, if the evolution starts with the transverse Hamiltonian due to hardware restrictions, then penalties are dynamically introduced such that the low-lying spectrum reproduces the energy levels of the Laplacian. The adiabatic evolution of the penalty Hamiltonian is therefore sensitive to the ultraviolet scale. It is expected to exhibit polynomial time complexity with lattice discretization, or exponential time complexity with respect to the number of qubits given a fixed volume.

97 MATHEMATICS AND COMPUTING↗

Design consideration in constructing high performance embedded Knowledge-Based Systems (KBS)

As the hardware trends for artificial intelligence (AI) involve more and more complexity, the process of optimizing the computer system design for a particular problem will also increase in complexity. Space applications of knowledge based systems (KBS) will often require an ability to perform both numerically intensive vector computations and real time symbolic computations. Although parallel machines can theoretically achieve the speeds necessary for most of these problems, if the application itself is not highly parallel, the machine's power cannot be utilized. A scheme is presented which will provide the computer systems engineer with a tool for analyzing machines with various configurations of array, symbolic, scaler, and multiprocessors. High speed networks and interconnections make customized, distributed, intelligent systems feasible for the application of AI in space. The method presented can be used to optimize such AI system configurations and to make comparisons between existing computer systems. It is an open question whether or not, for a given mission requirement, a suitable computer system design can be constructed for any amount of money.

Dalton, Shelly D.↗

Preparing angular momentum eigenstates using engineered quantum walks

Coupled angular-momentum eigenstates are widely used in atomic and nuclear physics calculations and are building blocks for spin networks and the Schur transform. To combine two angular momenta J 1 and J 2 , forming eigenstates of their total angular momentum J=J 1 +J 2 , we develop a quantum-walk scheme that does not require inputting O(j 3 ) nonzero Clebsch–Gordan (CG) coefficients classically. In fact, our scheme may be regarded as a unitary method for computing CG coefficients on quantum computers with a typical complexity of O⁡(j) and a worst-case complexity of O⁡(j 3 ). Equivalently, our scheme provides decompositions of the dense CG unitary into sparser unitary operations. Our scheme prepares angular-momentum eigenstates using a sequence of Hamiltonians to move an initial state deterministically to desired final states, which are usually highly entangled states in the computational basis. In contrast with usual quantum walks, whose Hamiltonians are prescribed, we engineer the Hamiltonians in su⁡(2)×su⁡(2), which are inspired by, but different from, Hamiltonians that govern magnetic resonances and dipole interactions. To achieve a deterministic preparation of both ket and bra states, we use projection and destructive interference to double pinch the quantum walks, such that each step is a unit-probability population transfer within a two-level system. We test our state preparation scheme on classical computers, reproducing tables of CG coefficients. Finally, we also implement small test problems on current quantum hardware.

97 MATHEMATICS AND COMPUTING↗

Managing Complexity in Multidisciplinary Visualization

As high performance computing technology progresses, computational simulations are becoming more advanced in their capabilities. In the computational aerosciences domain, single discipline steady-state simulations computed on a single grid are far from the state-of-the-art. In their place are complex, time-dependent multidisciplinary simulations that attempt to model a given geometry more realistically. The product of these multidisciplinary simulations is a massive amount of data stored in different formats, grid topologies, units of measure, etc., as a result of the differences in the simulated physical domains. In addition to the challenges posed by setting up and performing the simulation, additional challenges exist in analyzing computational results. Visualization plays an important role in the advancement of multidisciplinary simulations. To date, visualization has been used to aid in the interpretation of large amounts of simulation data. Because the human visual system is effective in digesting a large amount of information presented graphically, visualization has helped simulation scientists to understand complex simulation results. As these simulations become even more complex, integrating several different physical domains, visualization will be critical to digest the massive amount of information. Another important role for visualization is to provide a common communication medium from which the domain scientists can use to develop, debug, and analyze their work. Multidisciplinary analyses are the next step in simulation technology, not only in computational aerosciences, but in many other areas such as global climate modeling. Visualization researchers must understand and work towards the challenges posed by multidisciplinary simulation scenarios. This paper addresses some of these challenges, describing technologies that must be investigated to create a useful visualization analysis tool for domain scientists.

Miceli, Kristina D.↗

Insights into Constraining Rate Coefficients in Fuel Oxidation Mechanisms Using Genetic Algorithm Optimization

Accurate fuel oxidation mechanisms can enable predictive capabilities that aid in advancing combustion technologies. High-level computational kinetics can yield reasonable rate coefficients with uncertainties, in some cases, below a factor of 2. Computed rate coefficients can be constrained further by optimizing against experimental data. Here, we explore the application of genetic algorithm (GA) optimization to constrain computed rate coefficients in complex fuel oxidation mechanisms in conjunction with temperature-dependent species mole fractions from jet-stirred reactor (JSR) measurements. Cyclohexane is a model candidate for understanding the reactivity of cyclic fuels. In this work, we optimize the rate coefficients of the most recent literature cyclohexane mechanism, which incorporates theoretically computed rate coefficients for the reaction networks stemming from the first and second O 2 addition pathways, against the experimental results of two separate literature JSR studies. Optimization consistency is evaluated by carrying out three GA optimizations: fitting to the temperature-dependent species mole fractions in each JSR experiment separately and simultaneously fitting the species mole fractions in both experiments. Local sensitivity analyses are used to identify five influential low-temperature oxidation reactions for optimization. Although the three optimizations do not yield identical rate coefficients, the direction of change in all five rate coefficients is consistent among the three optimizations. Performance of the models from the three optimizations is assessed against literature ignition delay times with differences in the level of agreement observed among the different optimizations. In conclusion, comparisons are made with our recent optimization work of a cyclopentane oxidation master-equation model against time-resolved species concentrations, and insights and improvements of the strategy for constraining rate coefficients using GA optimization are discussed.

33 ADVANCED PROPULSION SYSTEMS↗

Comparison of free vortex wake and blade element momentum results against large-eddy simulation results for highly flexible turbines under challenging inflow conditions

Abstract. Throughout wind energy development, there has been a push to increase wind turbine size due to the substantial economic benefits. However, increasing turbine size presents several challenges, both physically and computationally. Modeling large, highly flexible wind turbines requires highly accurate models to capture the complicated aeroelastic response due to large deflections and nonstraight blade geometries. Additionally, the development of floating offshore wind turbines requires modeling techniques that can predict large rotor and tower motion. Free vortex wake methods model such complex physics while remaining computationally tractable to perform key simulations necessary during the turbine design process. Recently, a free vortex wake model – cOnvecting LAgrangian Filaments (OLAF) – was added to the National Renewable Energy Laboratory's engineering tool OpenFAST to allow for the aerodynamic modeling of highly flexible turbines along with the aero-hydro-servo-elastic response capabilities of OpenFAST. In this work, free vortex wake and low-fidelity blade element momentum (BEM) results are compared to high-fidelity actuator-line computational fluid dynamics simulation results via the Simulator fOr Wind Farm Applications (SOWFA) method for a highly flexible downwind turbine for varying yaw misalignment, shear exponent, and turbulence intensity conditions. Through these comparisons, it was found that for all considered quantities of interest, SOWFA, OLAF, and BEM results compare well for steady inflow conditions with no yaw misalignment. For OLAF results, this strong agreement with the SOWFA results was consistent for all yaw misalignment values. The BEM results, however, deviated significantly more from the SOWFA results with increasing absolute yaw misalignment. Differences between OLAF and BEM results were dominated by the yaw misalignment angle, with varying shear exponent and turbulence intensity leading to more subtle differences. Overall, OLAF results were more consistent than BEM results when compared to SOWFA results under challenging inflow conditions.

17 WIND ENERGY↗

Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these 'grand challenge' applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data. In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small form factor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed for the Log Structured File System. Finally, we will construct a protototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a Cornerstone of any coherent program in high performance computing and communications.

Katz, Randy H.↗

Large Hyperfine Coupling Arising from Pseudo- 2 S Ground States in a Series of Lutetium(II) Metallocene Complexes

The synthesis of molecules with strong coupling between electronic and nuclear spins represents an important challenge in molecular quantum information science. Here, we report the synthesis and characterization of the divalent lutetium metallocene complexes Lu(Cp Me 5 )(Cp iPr 5 ) (Cp Me 5 = pentamethylcyclopentadienyl; Cp iPr 5 = pentaisopropylcyclopentadienyl), Lu(Cp iPr 4 Et ) 2 (Cp iPr 4 Et = ethyltetraisopropylcyclopentadienyl), and Lu(Cp iPr 4 ) 2 (Cp iPr 4 = tetraisopropylcyclopentadienyl). The molecular structures of these complexes, as determined through singlecrystal X-ray diffraction, feature a common bent sandwich geometry, with average Cp–Lu–Cp angles ranging from 159.9° to 152.6°. Analysis of continuous-wave electron paramagnetic resonance (EPR) spectra for the complexes reveals nearly isotropic g tensors with only a slight deviation from that of a free electron. Moreover, an extremely large splitting of the eight-line spectra indicates the presence of strong hyperfine coupling, and simulations provide isotropic hyperfine coupling constants of A iso = 4.38, 4.30, and 4.17 GHz across the series, where the value of A iso is found to decrease as the Cp–Lu–Cp angle becomes more acute. Notably, these values are the largest yet observed for any lanthanide complex. Moreover, EPR and computational analysis show that the large values of A iso stem from large s-orbital character up to 41.2% in the corresponding singly occupied molecular orbitals. To our knowledge, this degree of s-character in a molecular orbital is the largest yet reported for an open-shell isolable complex. These results outline a general strategy toward the isolation of paramagnetic molecules with strong hyperfine coupling and highly isotropic doublet electronic ground states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Performance measures for control computers

As real-time systems become more complex, the problem of controlling them safely becomes more difficult. When computers are in control of time-critical systems such as aircraft, nuclear reactors, and life-support systems, they must meet stringent performance requirements. However, these requirements cannot be properly stated without appropriate performance measures. Such measures are reviewed and analyzed in this paper.

Krishna, C. M.↗

Direct numerical simulations of turbulent reacting flows with shock waves and stiff chemistry using many-core/GPU acceleration

Compressible reacting flows may display sharp spatial variation related to shocks, contact discontinuities or reactive zones embedded within relatively smooth regions. The presence of such phenomena emphasizes the relevance of shock-capturing schemes such as the weighted essentially non-oscillatory (WENO) scheme as an essential ingredient of the numerical solver. However, these schemes are complex and have more computational cost than the simple high-order compact or non-compact schemes. In this paper, we present the implementation of a seventh-order, minimally-dissipative mapped WENO (WENO7M) scheme in a newly developed direct numerical simulation (DNS) code called KAUST Adaptive Reactive Flows Solver (KARFS). In order to make efficient use of the computer resources and reduce the solution time, without compromising the resolution requirement, the WENO routines are accelerated via graphics processing unit (GPU) computation. The performance characteristics and scalability of the code are studied using different grid sizes and block decomposition. Furthermore, the performance portability of KARFS is demonstrated on a variety of architectures including NVIDIA Tesla P100 GPUs and NVIDIA Kepler K20X GPUs. In addition, the capability and potential of the newly implemented WENO7M scheme in KARFS to perform DNS of compressible flows is also demonstrated with model problems involving shocks, isotropic turbulence, detonations and flame propagation into a stratified mixture with complex chemical kinetics.

97 MATHEMATICS AND COMPUTING↗

hPIC2: A hardware-accelerated, hybrid particle-in-cell code for dynamic plasma-material interactions

The exascale era of high performance computing promises to bring the field of computational plasma physics ever closer to the goal of accurate multiscale modeling. Such computers will rely on hardware acceleration to offload work to dedicated components, notably general-purpose graphics processing units (GPUs). However, devices from different manufacturers require software to be written with different parallel programming models, greatly increasing the code maintenance burden of applications designed to perform on more than one such device. hPIC2 is a hybrid plasma simulation code developed with the Kokkos performance portability framework to target the architectures that will drive exascale computing for the foreseeable future. As a hybrid simulation code, hPIC2 investigates the simultaneous use of various plasma models on the same domain, at the same time. hPIC2 also optionally couples to RustBCA, which accurately models ion-material interactions using the binary collision approximation (BCA) method. In conclusion, hPIC2 therefore achieves scalable performance on a variety of computing architectures when simulating complex and diverse plasmas, particularly near plasma-material interfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Digital filter synthesis computer program

Digital filter synthesis computer program expresses any continuous function of a complex variable in approximate form as a computational algorithm or difference equation. Once the difference equation has been developed, digital filtering can be performed by the program on any input data list.

Moyer, R. A.↗

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa

Abstract The intrinsic tenase (Xase) complex, formed by factors (f) VIIIa and fIXa, forms on activated platelet surfaces and catalyzes the activation of factor X to Xa, stimulating thrombin production in the blood coagulation cascade. The structural organization of the membrane-bound Xase complex remains largely unknown, hindering our understanding of the structural underpinnings that guide Xase complex assembly. Here, we aimed to characterize the Xase complex bound to a lipid nanodisc with biolayer interferometry (BLI), Michaelis–Menten kinetics, and small-angle X-ray scattering (SAXS). Using immobilized lipid nanodiscs, we measured binding rates and nanomolar affinities for fVIIIa, fIXa, and the Xase complex. Enzyme kinetic measurements demonstrated the assembly of an active enzyme complex in the presence of lipid nanodiscs. An ab initio molecular envelope of the nanodisc-bound Xase complex allowed us to computationally model fVIIIa and fIXa docked onto a flexible lipid membrane and identify protein–protein interactions. Our results highlight multiple points of contact between fVIIIa and fIXa, including a novel interaction with fIXa at the fVIIIa A1–A3 domain interface. Lastly, we identified hemophilia A/B-related mutations with varying severities at the fVIIIa/fIXa interface that may regulate Xase complex assembly. Together, our results support the use of SAXS as an emergent tool to investigate the membrane-bound Xase complex and illustrate how mutations at the fVIIIa/fIXa dimer interface may disrupt or stabilize the activated enzyme complex.

Hematology↗

Unstructured CFD and Noise Prediction Methods for Propulsion Airframe Aeroacoustics

Using unstructured mesh CFD methods for Propulsion Airframe Aeroacoustics (PAA) analysis has the distinct advantage of precise and fast computational mesh generation for complex propulsion and airframe integration arrangements that include engine inlet, exhaust nozzles, pylon, wing, flaps, and flap deployment mechanical parts. However, accurate solution values of shear layer velocity, temperature and turbulence are extremely important for evaluating the usually small noise differentials of potential applications to commercial transport aircraft propulsion integration. This paper describes a set of calibration computations for an isolated separate flow bypass ratio five engine nozzle model and the same nozzle system with a pylon. These configurations have measured data along with prior CFD solutions and noise predictions using a proven structured mesh method, which can be used for comparison to the unstructured mesh solutions obtained in this investigation. This numerical investigation utilized the TetrUSS system that includes a Navier-Stokes solver, the associated unstructured mesh generation tools, post-processing utilities, plus some recently added enhancements to the system. New features necessary for this study include the addition of two equation turbulence models to the USM3D code, an h-refinement utility to enhance mesh density in the shear mixing region, and a flow adaptive mesh redistribution method. In addition, a computational procedure was developed to optimize both solution accuracy and mesh economy. Noise predictions were completed using an unstructured mesh version of the JeT3D code.

Pao, S. Paul↗