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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs

Detecting sequence homology between protein sequences is a fundamental problem in computational molecular biology, with a pervasive application in nearly all analyses that aim to structurally and functionally characterize protein molecules. While detecting the homology between two protein sequences is relatively inexpensive, detecting pairwise homology for a large number of protein sequences can become computationally prohibitive for modern inputs, often requiring millions of CPU hours. Yet, there is currently no robust support to parallelize this kernel. In this paper, we identify the key characteristics that make this problemparticularly hard to parallelize, and then propose a new parallel algorithm that is suited for detecting homology on large data sets using distributed memory parallel computers. Our method, called pGraph, is a novel hybrid between the hierarchical multiple-master/worker model and producer-consumer model, and is designed to break the irregularities imposed by alignment computation and work generation. Experimental results show that pGraph achieves linear scaling on a 2,048 processor distributed memory cluster for a wide range of inputs ranging from as small as 20,000 sequences to 2,560,000 sequences. In addition to demonstrating strong scaling, we present an extensive report on the performance of the various system components and related parametric studies.

Environmental Molecular Sciences Laboratory↗
NASA NTRS1998

Trace-Driven Debugging of Message Passing Programs

In this paper we report on features added to a parallel debugger to simplify the debugging of parallel message passing programs. These features include replay, setting consistent breakpoints based on interprocess event causality, a parallel undo operation, and communication supervision. These features all use trace information collected during the execution of the program being debugged. We used a number of different instrumentation techniques to collect traces. We also implemented trace displays using two different trace visualization systems. The implementation was tested on an SGI Power Challenge cluster and a network of SGI workstations.

Frumkin, Michael↗
NASA NTRS1978

Effect of grazing flow on the acoustic impedance of Helmholtz resonators consisting of single and clustered orifices

A semiempirical fluid mechanical model is presented which predicts impedance of a Helmholtz resonator consisting of a single cavity-backed orifice as a function of grazing flow speed, boundary-layer thickness, incident sound amplitude and frequency, and resonator geometry. The incident and cavity sound fields are connected in terms of an orifice discharge coefficient. The effect of multiple orifices was studied experimentally. Interaction between orifices is important only for orifices aligned parallel to the grazing flow. Resistance was virtually independent of both orifice relative spacing and number. Reactance was found to be quite dependent upon orifice spacing but insensitive to the number of orifices.

Hersh, A. S.↗
DOE OSTI2016

Solar wind compressible turbulence near proton scales: Cluster observations

The solar wind compressible turbulence attracts more attention recently due to its possible role in plasma heating. Using the plasma density and magnetic field measured simultaneously by the Cluster C1 probe, we statistically investigate the wave characteristics of the proton-scale compressible turbulence. In most cases, the density and magnetic field strength fluctuations almost show no positive correlation, suggesting the absence of fast mode waves. Moreover, the magnetic compressibility C{sub b} as measured by the level of magnetic fluctuations parallel to the background field, is enhanced continuously around proton scales and is consistent with kinetic Alfvén wave (KAW) prediction. Interestingly, kinetic slow mode waves (KSW) are identified in a few cases through large values of C{sub b} and plasma compressibility C{sub p}, together with the the anti-correlation between n and B. We suggest that both KAW and KSW can account for the compressible fluctuations energy, while their relative proportions under certain plasma condition require further studies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1984

Design, fabrication and testing of a multibeam forming network

A concept for a multiple beam forming network to route signals from eight input ports to twenty-one output ports so as to form eight independent seven-element cluster radiators was designed, fabricated, and tested. The operating frequency band is 2.226 to 2.254 GHz and the maximum power to any input port is two watts. The network consists of eight seven-way power dividers connected to twenty-one seven-way power combiners. The network utilizes barline circuits between parallel ground planes for the power distribution and collection. Interconnections are made with short rigid co-axial lines built into the network. The concept, general design procedures, mechanical configuration, and electrical performance are described. It appears that the network is quite satisfactory for demonstrating practical feasibility of the technical concept.

Source record↗
NASA NTRS1996

The " Swarm of Ants vs. Herd of Elephants" Debated Revisited: Performance Measurements of PVM-Overflow Across a Wide Spectrum of Architectures

The Gorden Bell Prizes given out at Supercomputing every year includes at least two catergories: performance (highest GFLOP count) and price-performance (GFLOP/million $$) for real applications. In the past five years, the winners of the price-performance categories all came from networks of work-stations. This reflects three important facts: 1. supercomputers are still too expensive for the masses; 2. achieving high performance for real applications takes real work; and, most importantly; 3. it is possible to obtain acceptable performance for certain real applications on network of work stations. With the continued advance of network technology as well as increased performance of "desktop" workstation, the "Swarm of Ants vs. Herd of Elephants" debate, which began with vector multiprocessors (VPPs) against SIMD type multiprocessors (e.g. CM2), is now recast as VPPs against Symetric Multiprocessors (SMPs, e.g. SGI PowerChallenge). This paper reports on performance studies we performed solving a large scale (2-million grid pt.s) CFD problem involving a Boeing 747 based on a parallel version of OVERFLOW that utilizes message passing on PVM. A performance monitoring tool developed under NASA HPCC, called AIMS, was used to instrument and analyze the the performance data thus obtained. We plan to compare its performance data obtained across a wide spectrum of architectures including: the Cray C90, IBM/SP2, SGI/Power Challenge Cluster, to a group of workstations connected over a simple network. The metrics of comparison includes speed-up, price-performance, throughput, and turn-around time. We also plan to present a plan of attack for various issues that will make the execution of Grand Challenge Applications across the Global Information Infrastructure a reality.

Yan, Jerry C.↗
NASA NTRS2008

Modeling Kicks from the Merger of Generic Black-hole Binaries

Recent numerical relativistic results demonstrate that the merger of comparable-mass spinning black holes has a maximum "recoil kick" of up to approx. 4000 km/s. However the scaling of these recoil velocities with mass ratio is poorly understood. We present new runs showing that the maximum possible kick parallel to the orbital axis does not scale as approx. eta(sup 2) (where eta is the symmetric mass ratio), as previously proposed, but is more consistent with approx. eta(sup 3). We discuss the effect of this dependence on galactic ejection scenarios and retention of intermediate-mass black holes in globular clusters. S

Baker, John G.↗
DOE OSTI2019

Approximate Green’s Function Coupled Cluster A Method Employing Effective Dimension Reduction

The Green’s function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structures of molecular structures and periodic systems, especially when electrons are strongly correlated. However, in order for the GFCC method to become an approach that can be routinely used in the electronic structure calculations, more robust linear algebraic techniques and approximations need to be employed to reduce its extremely high computational overhead. In our recent studies, we showed that the GFCC equation can be numerically solved by seeking solutions of multiple linear systems in the frequency regime of interest, which can be easily distributed in a massively parallel environment, and broaden the avenue for more state-of-the-art numerical linear algebraic tools associated with multiple linear systems to be kicked in to this field. In the present pursuit of this practice, we show a successful application of model order reduction (MOR) techniques in the GFCC framework. Briefly speaking, for a frequency regime of interest that requires a high resolution of spectral function, instead of solving GFCC linear equation in the original dimension for every single frequency point, an easily-solvable linear system model with reduced dimension can be built upon projecting the original GFCC linear system into a subspace, from which the interpolation and extrapolation can give a reasonable approximation to the results of the original GFCC linear equations. Here, we show that the subspace can be properly constructed in an iterative manner from the auxiliary vectors of the GFCC linear equations at some select frequencies inside the frequency regime. During the iterations, the quality of the subspace, as well as the linear system model, can be systematically improved. The approach is tested in this work in terms of the efficiency and accuracy of computing spectral functions for some typical molecular systems including carbon monoxide, 1,3-butadiene, benzene, and adenine molecules. As a byproduct, the high quality linear system model is also found to be able to provide high quality initial guess for the existing linear solver to improve the convergence performance.

Peng, Bo↗
DOE OSTI2025

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Real-space pseudopotential method for computing the vibrational Stark effect

The vibrational Stark shift is an important effect in determining the electrostatic environment for molecular or condensed matter systems. However, accurate ab initio calculations of the vibrational Stark effect are a technically demanding challenge. In this paper, we make use of density functional theory constructed on a real-space grid to expedite the computation of this effect. Our format is especially advantageous for the investigation of small molecules in finite fields as cluster boundary conditions eliminate spurious supercell interactions and allow for charged systems, while convergence is controlled by a single parameter, the grid spacing. The Stark tuning rate is highly sensitive to the interaction between anharmonicity in a vibrational mode and the applied field. To ensure this subtle interaction is fully captured, we apply three parallel approaches: a direct finite field, a perturbative method, and a molecular dynamics method. Finally, we illustrate this method by applying it to several small molecules containing C–O and C–N bonds and show that a consistent result can be obtained.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Roadmap on photonic, electronic and atomic collision physics: I. Light–matter interaction

We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. In Roadmap I, we focus on the light–matter interaction. In this area, studies of ultrafast electronic and molecular dynamics have been rapidly growing, with the advent of new light sources such as attosecond lasers and x-ray free electron lasers. In parallel, experiments with established synchrotron radiation sources and femtosecond lasers using cutting-edge detection schemes are revealing new scientific insights that have never been exploited. Relevant theories are also being rapidly developed. Target samples for photon-impact experiments are expanding from atoms and small molecules to complex systems such as biomolecules, fullerene, clusters and solids. This Roadmap aims to look back along the road, explaining the development of these fields, and look forward, collecting contributions from twenty leading groups from the field.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2002

Scaling NASA Applications to 1024 CPUs on Origin 3K

The long and highly successful joint SGI-NASA research effort in ever larger SSI systems was to a large degree the result of the successful development of the MLP scalable parallel programming paradigm developed at ARC: 1) MLP scaling in real production codes justified ever larger systems at NAS; 2) MLP scaling on 256p Origin 2000 gave SGl impetus to productize 256p; 3) MLP scaling on 512 gave SGI courage to build 1024p O3K; and 4) History of MLP success resulted in IBM Star Cluster based MLP effort.

Taft, Jim↗
DOE OSTI2011

Using the Global Arrays Toolkit to Reimplement NumPy for Distributed Computation

Global Arrays (GA) is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared memory programming interface to manipulate distributed defense arrays. Using a combination of GA and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Scalability studies will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Global Arrays↗
DOE OSTI2019

High resolution ENDOR spectroscopy combined with quantum chemical calculations reveals the structure of the nitrogenase Janus intermediate E4(4H)

We have shown that the key state in N2 reduction to two NH3 by the enzyme nitrogenase is the E4(4H), ‘Janus’ intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed the catalytic multi-metallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of structure - the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of ‘anchor’ Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties of the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed by DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a pulsed-ENDOR protocol (‘PESTRE’) to obtain absolute hyperfine-interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its ‘anchoring’ Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result: the freeze-trapped, lowest-energy Janus intermediate structure is E4(4H)(a).

Hoeke, Veronica↗
DOE OSTI2015

Chemical accuracy from quantum Monte Carlo for the benzene dimer

We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

PWR internal flow modeling with fuel assemblies details

This study is an example of a massive parallel computing of the coolant flow in a nuclear reactor. It resolves the flow velocities in each assembly on pin level and predicts the flow distribution in complex geometries such as the lower and upper reactor plenums. The size of the developed model (1.035 billion cells) required the runs to be executed on the NCCS clusters (www.nccs.gov). STAR-CCM+ code (www.ed-adapco.com) was installed on two clusters: JAGUARXT5 and FROST, both of which were capable of executing this model. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2015

Aberration‐Corrected Transmission Electron Microscopy and In Situ XAFS Structural Characterization of Pt/γ‐Al 2 O 3 Nanoparticles

Abstract Aberration‐corrected (AC) STEM, AC TEM and in situ X‐ray absorption fine structure spectroscopy (XAFS) were used to characterize the Pt clusters present on a 0.35 wt % Pt on γ‐alumina support after reduction in hydrogen at 700 °C. STEM high‐angle annular dark field imaging shows that cluster formation takes place at temperatures up to approximately 350 °C, and this is followed by gradual growth in cluster size for heat treatments in hydrogen up to 700 °C. The STEM data show that after 700 °C reduction the Pt clusters are present in a narrow size distribution centered at 0.88 nm, and using a method involving a redistribution of the Pt atoms using a high electron dosage in the STEM, it is shown that the clusters are present in two‐dimensional morphology. This conclusion is verified using intensity line scans. The in situ extended X‐ray absorption fine structure data are in good agreement with these observations. High‐resolution AC–TEM, which uses a broad coherent electron beam, and can thus offer advantages relative to STEM for structure determination of fine clusters, supported by image simulations of through‐focus series, were used to analyze the structures of Pt particles. The structures determined by using AC–TEM are consistent with STEM and EXAFS data in having a flat two‐dimensional morphology. Comparison of AC–STEM and AC TEM data for the same 700 °C reduced sample suggests that parallel‐beam TEM mode of imaging may be advantageous because of the less pronounced beam‐induced structural rearrangements that occur when imaging with a fine STEM probe.

Sinkler, Wharton↗
DOE OSTI2019

Counting Kmers for Biological Sequences at Large Scale

Counting the abundance of all the distinct kmers in biological sequence data is a fundamental step in bioinformatics. These applications include de novo genome assembly, error correction, etc. With the development of sequencing technology, the sequence data in a single project can reach Petabyte-scale or Terabyte-scale nucleotides. Counting demand for the abundance of these sequencing data is beyond the memory and computing capacity of single computing node, and how to process it efficiently is a challenge on a high-performance computing cluster. As such, we propose SWAPCounter, a highly scalable distributed approach for kmer counting. This approach is embedded with an MPI streaming I/O module for loading huge data set at high speed, and a counting bloom filter module for both memory and communication efficiency. By overlapping all the counting steps, SWAPCounter achieves high scalability with high parallel efficiency. In this work, the experimental results indicate that SWAPCounter has competitive performance with two other tools on shared memory environment, KMC 2 , and MSPKmerCounter. Moreover, SWAPCounter also shows the highest scalability under strong scaling experiments. In our experiment on Cetus supercomputer, SWAPCounter scales to 32,768 cores with 79% parallel efficiency (using 2048 cores as baseline) when processing 4 TB sequence data of 1000 Genomes. The source code of SWAPCounter is publicly available at https://github.com/mengjintao/SWAPCounter.

59 BASIC BIOLOGICAL SCIENCES↗