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DOE OSTI2020

MPI Session: External Network Transport Implementation (V.1.0)

The MPI Sessions extensions to the MPI standard have been accepted by the MPI Forum and will be included in the upcoming MPI 4 version of the standard. MPI Sessions has the potential to address several limitations of MPI’s current specification: MPI cannot be initialized within an MPI process from different application components without a priori knowledge or coordination; MPI cannot be initialized more than once; and, MPI cannot be reinitialized after MPI finalization. MPI Sessions also offers the possibility for more flexible ways for individual components of an application to express the capabilities they require from MPI at a finer granularity than is presently possible. A prototype of MPI Sessions, based on the Open MPI implementation of the MPI standard, was developed to facilitate acceptance of the Sessions proposal by the Forum. The initial implementation had some limitations, one of the more significant ones being that it was limited in its ability to fully exploit modern network APIs such as OFI libfabric and OpenUCX and underlying network hardware. This report presents enhancements to the prototype implementation of MPI Sessions that removes this restriction for the networks to be used in the next generation of DOE exa–scale systems. Open MPI was used as the implementation vehicle, but results here are also relevant to other middleware stacks.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Demonstration and performance testing of extreme-resolution simulations with static meshes on Summit (CPU & GPU) for a parked-turbine configuration and an actuator-line (mid-fidelity model) wind farm configuration (ECP-Q4 FY2020 Milestone Report)

17 WIND ENERGY↗

DOE OSTI2019

Nalu-Wind and OpenFAST: A high-fidelity modeling and simulation environment for wind energy. Milestone ECP-Q2-FY19

The goal of the ExaWind project is to enable predictive simulations of wind farms comprised of many megawatt-scale turbines situated in complex terrain. Predictive simulations will require computational fluid dynamics (CFD) simulations for which the mesh resolves the geometry of the turbines and captures the rotation and large deflections of blades. Whereas such simulations for a single turbine are arguably petascale class, multi-turbine wind farm simulations will require exascale-class resources. The primary physics codes in the ExaWind project are Nalu-Wind, which is an unstructured-grid solver for the acoustically incompressible Navier-Stokes equations, and OpenFAST, which is a whole-turbine simulation code. The Nalu-Wind model consists of the mass-continuity Poisson-type equation for pressure and a momentum equation for the velocity. For such modeling approaches, simulation times are dominated by linear-system setup and solution for the continuity and momentum systems. For the ExaWind challenge problem, the moving meshes greatly affect overall solver costs as reinitialization of matrices and recomputation of preconditioners is required at every time step. This milestone represents the culmination of several parallel development activities towards the goal of establishing a full-physics simulation capability for modeling wind turbines operating in turbulent atmospheric inflow conditions. The demonstration simulation performed in this milestone is the first step towards the "ground truth" simulation and includes the following components: neutral atmospheric boundary layer inflow conditions generated using a precursor simulation, a hybrid RANS/LES simulation of the wall-resolved turbine geometry, hybridization of the turbulence equations using a blending function approach to transition from the atmospheric scales to the blade boundary layer scales near the turbine, fluid-structure interaction (FSI) that accounts for the complete set of blade deformations (bending, twisting and pitch motion, yaw and tower displacements) by coupling to a comprehensive turbine dynamics code (OpenFAST). The use of overset mesh methodology for the simulations in this milestone presents a significant deviation from the previous efforts where a sliding mesh approach was employed to model the rotation of the turbine blades. The choice of overset meshes was motivated by the need to handle arbitrarily large deformations of the blade and to allow for blade pitching in the presence of a controller and the ease of mesh generation compared to the sliding mesh approach. FSI and the new timestep algorithm used in the simulations were developed in partnership with the A2e High-Fidelity Modeling project. The individual physics components were verified and validated (V%V) through extensive code-to-code comparisons and with experiments where possible. The detailed V&V efforts provide confidence in the final simulation where these physics models were combined together even though no detailed experimental data is available to perform validation of the final configuration. Taken together, this milestone successfully demonstrated the most advanced simulation to date that has been performed with Nalu-Wind.

17 WIND ENERGY↗

DOE OSTI2019

High-order methods for wind turbine simulations and moving to next-generation platforms

The goal of the ExaWind project is to enable predictive simulations of wind farms comprised of many megawatt-scale turbines situated in complex terrain. Predictive simulations will require computational fluid dynamics (CFD) simulations for which the mesh resolves the geometry of the turbines and captures the rotation and large deflections of blades. Whereas such simulations for a single turbine are arguably petascale class, multi-turbine wind farm simulations will require exascale-class resources. The primary physics codes in the ExaWind project are Nalu-Wind, which is an unstructured-grid solver for the acoustically incompressible Navier-Stokes equations, and OpenFAST, which is a whole-turbine simulation code. The Nalu-Wind model consists of the mass-continuity Poisson-type equation for pressure and a momentum equation for the velocity. For such modeling approaches, simulation times are dominated by linear-system setup and solution for the continuity and momentum systems. For the ExaWind challenge problem, the moving meshes greatly affect overall solver costs as reinitialization of matrices and recomputation of preconditioners is required at every time step. This milestone represents an effort to increase the fidelity of Nalu-Wind at a fixed resolution through the implementation of a tensor-product based, matrix-free high order scheme. High order finite element methods have increased local work per datum communicated and have the potential to provide significantly more accurate solutions at a fixed number of degrees of freedom. Previous to this milestone, Nalu-Wind had an arbitrary order Control Volume Finite Element Method discretization as a solver option, but it required too much memory and was too slow to be of practical use. The work in this milestone addresses these issues by first implementing an implicit, high order solver that only partially assembles the global system. This reduces the memory footprint of the high-order scheme by orders of magnitude for higher polynomial orders. Second, a faster, tensor-product based method for evaluating the action of the left-hand side was implemented. This reduces the amount of computational work required by the scheme and dramatically enhanced the time-to-solution on example problems. Finally, this milestone is an evaluation of the value of high order methods in the wind application space. With the enhancements to memory and computational cost, accuracy vs. time-to-solution was evaluated for several resolutions on an under-resolved Taylor Green vortex test case. Results show that the high order scheme is cost-competitive with the production low-order schemes in Nalu-Wind, being moderately more expensive than the production edge-based vertex centered finite volume scheme. The evaluation of accuracy on the test case shows a potential benefit to high order at the highest resolution while not deteriorating accuracy on the lowest tested resolution. More work is needed to show value in the wind application, but positive strides have been made.

17 WIND ENERGY↗

DOE OSTI2021

Qubit-efficient entanglement spectroscopy using qubit resets

One strategy to fit larger problems on NISQ devices is to exploit a tradeoff between circuit width and circuit depth. Unfortunately, this tradeoff still limits the size of tractable problems since the increased depth is often not realizable before noise dominates. Here, we develop qubit-efficient quantum algorithms for entanglement spectroscopy which avoid this tradeoff. In particular, we develop algorithms for computing the trace of the n -th power of the density operator of a quantum system, T r ( ρ n ) , (related to the Rényi entropy of order n ) that use fewer qubits than any previous efficient algorithm while achieving similar performance in the presence of noise, thus enabling spectroscopy of larger quantum systems on NISQ devices. Our algorithms, which require a number of qubits independent of n , are variants of previous algorithms with width proportional to n , an asymptotic difference. The crucial ingredient in these new algorithms is the ability to measure and reinitialize subsets of qubits in the course of the computation, allowing us to reuse qubits and increase the circuit depth without suffering the usual noisy consequences. We also introduce the notion of effective circuit depth as a generalization of standard circuit depth suitable for circuits with qubit resets. This tool helps explain the noise-resilience of our qubit-efficient algorithms and should aid in designing future algorithms. We perform numerical simulations to compare our algorithms to the original variants and show they perform similarly when subjected to noise. Additionally, we experimentally implement one of our qubit-efficient algorithms on the Honeywell System Model H0, estimating T r ( ρ n ) for larger n than possible with previous algorithms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Biomass burning aerosol radiative effects in the Southeast Atlantic depend strongly on meteorological forcing method

Biomass burning aerosols (BBAs) from African fires may strongly impact Earth’s radiation budget in the southeast Atlantic (SEA), but the sign and magnitude of the overall radiative effect (RE) remain uncertain. Aerosol–climate models are needed to separately quantify direct, indirect, and semi-direct REs. Here, we evaluate improved simulations with the UK Met Office's Unified Model and explore REs resulting from various methods used to match observed meteorology (nudging or running forecasts reinitialized at different frequencies). REs are calculated as differences in radiative fluxes between simulations with and without smoke emissions and with and without aerosol absorption. All model setups agree on net warming for the SEA dominated by the direct effect. Simulated smoke, clouds, and the direct effect agree better with observations than previous studies using the same model, though biases in aerosol extinction and liquid water path remain. Changes in cloud droplet number concentration due to BBA self-lofting influence how cleanly we can separate cloud effects into semi-direct and indirect effects. Total RE, which remains unaffected, ranges from +3.0 to +7.9 W m −2 . The 4.9 W m −2 spread arises mainly from simulated semi-direct effects. Forecasts three days long or less probably do not allow time for plausible differences in boundary layer properties due to semi-direct effects to accumulate. Free running simulations with and without smoke accumulate differences in meteorology that are likely spurious “butterfly effects”. We recommend future research quantifying BBA REs over weeks to months to use meteorological forcing techniques that allow aerosol absorption to affect the boundary layer.

Giuffrida, Eric [Carnegie Mellon University, Pitts↗

DOE OSTI2026

Aerosol-deep convection interaction based on joint cell-thermal tracking in Large Eddy Simulations during the TRACER campaign

In cumulus clouds, aerosol concentrations control cloud droplet concentrations, modifying cloud radiative properties, precipitation processes, and cloud electrification. However, mechanisms of aerosol-deep convection interactions are not well understood due to complex cloud dynamics and microphysics. We investigate the interaction of aerosols with isolated deep convection using Large Eddy Simulations of two cases during the TRacking Aerosol Convection interactions ExpeRiment (TRACER) near Houston, Texas, using a joint cell-thermal tracking algorithm. Cumulus thermals are droplet generators, since supersaturation and droplet nucleation coincide with thermal centers, where the strongest updrafts occur. Primary ice crystal formation does not take place inside thermals, but at layers where previous thermals detrained moisture. As subsequent thermals containing supercooled droplets penetrate these layers, hail and graupel form at or near these thermals. Higher aerosol concentrations result in higher droplet concentrations that suppress drizzle, delay warm rain processes, and transport more moisture aloft. This increases snow and ice amount, as well as graupel and hail, leading to more lightning. Polluted thermals initiate at slightly higher altitudes, and are slightly larger and faster, suggesting a weak invigoration. We also find more thermals per cell, but fewer isolated cells, since convection is more aggregated and intense, especially near the end of the 24 h simulation. Non-linear mesoscale feedback likely triggered by temperature and moisture responses to aerosol-thermal interactions causes the aggregation. Time-lagged aerosol-reinitialization experiments show that the mesoscale response is the predominant forcing for the invigoration. These changes happen within one day, on a smaller scale than previously suggested.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1972

Recursive filter initialization.

Description of an initialization technique which partially accounts for the interrelation between the true-state vector errors when recursive filtering is applied in space navigation systems. The technique reduces the undesirable transient effects of the first few measurements and inhibits filter divergence when the interval between measurements is inordinately large. The key feature of this technique is the inclusion of the effect of a number of pseudo-measurements of certain orbital parameters into the initial covariance matrix. The pseudo-measurement technique has been shown to be useful when reinitialization of the error covariance matrix is required to prevent filter divergence.

Battin, R. H.↗

NASA NTRS1972

Space shuttle guidance, navigation and control equation document no. 19: Prelaunch alignment and platform compensation

The prelaunch-alignment program which aligns the stable platform to some desired orientation with respect to the local navigation reference frame is discussed. The alignment progresses in three distinct phases: coarse aligning, leveling, and gyrocompassing. While the program is in the leveling or gyrocompassing phase, a new launch azimuth may be specified without reinitiating the program. At liftoff, control is passed to a navigation monitor/control program. A description of the stable-platform-compensation program is included. The programs and equations given are similar to those used for Apollo.

Gallagher, J. L.↗

NASA NTRS1974

Investigation of pilot's role and display requirements in automatic landings

Two experimental capabilities were developed on the PDP-12 computers. The first of these was an experimental monitor to perform experiments in the psychophysics of visual target motion prediction, discrimination, etc., and exercises the (limited) graphical capabilities of the PDP-12. The original monitor was modified to include the capability of handling more than 64 stimuli without reinitializing the program. The second experimental monitor was programmed and was used to investigate pilot decisions in low visibility approaches. The details of this experimental capability, which has great potential for exploring decisions and behavior, are described in detail.

Curry, R. E.↗

NASA NTRS1985

Variational mesoscale satellite data assimilation and initialization

The problems of mesoscale satellite data assimilation were examined. Assimilation of satellite data to improve the forecasts made by mesoscale forecast models was undertaken. Assimilation of high resolution satellite derived temperature data into a mesoscale model with horizontal resolution of 50 to 60 km is reported. Unlike global assimilation, in which a small portion of the forecast model domain is subject to data insertion at virtually every time step, the mesoscale assimilation virtually all of the forecast model domain is subject to data insertion at one time step. The mesoscale problem lends itself naturally to intermittent data assimilation and the forecast model is reinitialized whenever a new satellite pass covers its domain with data. The satellite data assimilation as an initialization problem are discussed.

Sasaki, Y. K.↗

NASA NTRS1986

Design requirements and development of an airborne descent path definition algorithm for time navigation

The design requirements for a 4D path definition algorithm are described. These requirements were developed for the NASA ATOPS as an extension of the Local Flow Management/Profile Descent algorithm. They specify the processing flow, functional and data architectures, and system input requirements, and recommended the addition of a broad path revision (reinitialization) function capability. The document also summarizes algorithm design enhancements and the implementation status of the algorithm on an in-house PDP-11/70 computer. Finally, the requirements for the pilot-computer interfaces, the lateral path processor, and guidance and steering function are described.

Izumi, K. H.↗

NASA NTRS1986

Numerical studies of the margin of vortices with decaying cores

The merging of vortices to a single one is a canonical incompressible viscous flow problem. The merging process begins when the core sizes or the vortices are comparable to their distances and ends when the contour lines of constant vorticity lines are circularized around one center. Approximate solutions to this problem are constructed by adapting the asymptotic solutions for distinct vortices. For the early stage of merging, the next-order terms in the asymptotic solutions are added to the leading term. For the later stage of merging, the vorticity distribution is reinitialized by vortices with overlapping core structures guided by the 'rule of merging' and the velocity of the 'vortex centers' are then defined by a minimum principle. To show the accuracy of the approximate solution, it is compared with the finite-difference solution.

Liu, G. C.↗

NASA NTRS1988

Fatigue crack closure behavior at high stress ratios

Fatigue crack delay behavior at high stress ratio caused by single peak overloads was investigated in two thicknesses of 7475-T731 aluminum alloy. Closure measurements indicated no closure occurred before or throughout the overload plastic zones following the overload. This was further substantiated by comparing the specimen compliance following the overload with the compliance of a low R ratio test when the crack was fully open. Scanning electron microscope studies revealed that crack tunneling and possibly reinitiation of the crack occurred, most likely a result of crack-tip blunting. The number of delay cycles was greater for the thinner mixed mode stress state specimen than for the thicker plane strain stress state specimen, which is similar to low R ratio test results and may be due to a larger plastic zone for the mixed mode cased.

Turner, C. Christopher↗

NASA NTRS1989

Summary of 1987 and 1988 manatee aerial surveys at Kennedy Space Center

Aerial surveys of manatees conducted since 1977 at Kennedy Space Center (KSC) have provided a very useful and cost effective monitoring tool in the assessment of abundance and distribution of manatees in the northern Banana River. Data collected in the mid 1980's as part of the KSC Environmental Monitoring Program indicated that the numbers of manatees utilizing the northern Banana River had increased dramatically from earlier years and that the animals appeared to have changed their distribution patterns within the area as well (Provancha and Provancha 1988). United States Fish and Wildlife Service (USFWS) and Florida Department of Natural Resources (FLDNR) conducted bimonthly aerial surveys in 1986 for the entire Florida east coast. Their data clearly show that the Banana River has the highest concentration of manatees during the non-winter months when compared to all other segments of the east coast surveys (B. Wiegle/FLDNR, unpublished data). They further show that, in spring, an average of 71 percent of the manatees in Brevard county were located in the Banana River. During that period 85 percent of the animals were north of the NASA Causeway (State Road (SR) 402) in the KSC security zone. These data indicate the importance of the KSC waters to the Florida east coast manatee population. We reinitiated KSC surveys in 1987 to document distributions and numbers of manatees during the spring influx. Aerial censuses were continued throughout the year in 1988 and this report provides a summary of our findings for the two years.

Provancha, Jane A.↗

NASA NTRS1991

On the optimal use of fictitious time in variation of parameters methods with application to BG14

The optimal way to use fictitious time in variation of parameter methods is presented. Setting fictitious time to zero at the end of each step is shown to cure the instability associated with some types of problems. Only some parameters are reinitialized, thereby retaining redundant information.

Gottlieb, Robert G.↗

NASA NTRS1993

Estimate fusion for lunar rendezvous

The new derivation presented for an algorithm that fuses two Kalman filter outputs clearly demonstrates the combination of estimates to be capable of 'optimally' minimizing the trace of the fused covariance matrix. The method also furnishes an estimate whose error ellipses are contained within the intersection of the error ellipses from each filter. The 'reinitialized Kalman filter' obtained by these means is applied to the problem of lunar rendezvous.

Carpenter, J. R.↗