Search NASA⌕ Search

SEARCH · Search NASA

Results for “Cluster Computing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

GENIE(++): A Multi-Block Structured Grid System

The computer code GENIE++ is a continuously evolving grid system containing a multitude of proven geometry/grid techniques. The generation process in GENIE++ is based on an earlier version. The process uses several techniques either separately or in combination to quickly and economically generate sculptured geometry descriptions and grids for arbitrary geometries. The computational mesh is formed by using an appropriate algebraic method. Grid clustering is accomplished with either exponential or hyperbolic tangent routines which allow the user to specify a desired point distribution. Grid smoothing can be accomplished by using an elliptic solver with proper forcing functions. B-spline and Non-Uniform Rational B-splines (NURBS) algorithms are used for surface definition and redistribution. The built in sculptured geometry definition with desired distribution of points, automatic Bezier curve/surface generation for interior boundaries/surfaces, and surface redistribution is based on NURBS. Weighted Lagrance/Hermite transfinite interpolation methods, interactive geometry/grid manipulation modules, and on-line graphical visualization of the generation process are salient features of this system which result in a significant time savings for a given geometry/grid application.

Williams, Tonya↗
NASA NTRS1996

Parallel NPARC: Implementation and Performance

Version 3 of the NPARC Navier-Stokes code includes support for large-grain (block level) parallelism using explicit message passing between a heterogeneous collection of computers. This capability has the potential for significant performance gains, depending upon the block data distribution. The parallel implementation uses a master/worker arrangement of processes. The master process assigns blocks to workers, controls worker actions, and provides remote file access for the workers. The processes communicate via explicit message passing using an interface library which provides portability to a number of message passing libraries, such as PVM (Parallel Virtual Machine). A Bourne shell script is used to simplify the task of selecting hosts, starting processes, retrieving remote files, and terminating a computation. This script also provides a simple form of fault tolerance. An analysis of the computational performance of NPARC is presented, using data sets from an F/A-18 inlet study and a Rocket Based Combined Cycle Engine analysis. Parallel speedup and overall computational efficiency were obtained for various NPARC run parameters on a cluster of IBM RS6000 workstations. The data show that although NPARC performance compares favorably with the estimated potential parallelism, typical data sets used with previous versions of NPARC will often need to be reblocked for optimum parallel performance. In one of the cases studied, reblocking increased peak parallel speedup from 3.2 to 11.8.

Townsend, S. E.↗
NASA NTRS1998

Parallel Implicit Algorithms for CFD

The main goal of this project was efficient distributed parallel and workstation cluster implementations of Newton-Krylov-Schwarz (NKS) solvers for implicit Computational Fluid Dynamics (CFD.) "Newton" refers to a quadratically convergent nonlinear iteration using gradient information based on the true residual, "Krylov" to an inner linear iteration that accesses the Jacobian matrix only through highly parallelizable sparse matrix-vector products, and "Schwarz" to a domain decomposition form of preconditioning the inner Krylov iterations with primarily neighbor-only exchange of data between the processors. Prior experience has established that Newton-Krylov methods are competitive solvers in the CFD context and that Krylov-Schwarz methods port well to distributed memory computers. The combination of the techniques into Newton-Krylov-Schwarz was implemented on 2D and 3D unstructured Euler codes on the parallel testbeds that used to be at LaRC and on several other parallel computers operated by other agencies or made available by the vendors. Early implementations were made directly in Massively Parallel Integration (MPI) with parallel solvers we adapted from legacy NASA codes and enhanced for full NKS functionality. Later implementations were made in the framework of the PETSC library from Argonne National Laboratory, which now includes pseudo-transient continuation Newton-Krylov-Schwarz solver capability (as a result of demands we made upon PETSC during our early porting experiences). A secondary project pursued with funding from this contract was parallel implicit solvers in acoustics, specifically in the Helmholtz formulation. A 2D acoustic inverse problem has been solved in parallel within the PETSC framework.

Keyes, David E.↗
NASA NTRS2016

Phase-Retrieval Uncertainty Estimation and Algorithm Comparison for the JWST-ISIM Test Campaign

Phase retrieval, the process of determining the exitpupil wavefront of an optical instrument from image-plane intensity measurements, is the baseline methodology for characterizing the wavefront for the suite of science instruments (SIs) in the Integrated Science Instrument Module (ISIM) for the James Webb Space Telescope (JWST). JWST is a large, infrared space telescope with a 6.5-meter diameter primary mirror. JWST is currently NASA's flagship mission and will be the premier space observatory of the next decade. ISIM contains four optical benches with nine unique instruments, including redundancies. ISIM was characterized at the Goddard Space Flight Center (GSFC) in Greenbelt, MD in a series of cryogenic vacuum tests using a telescope simulator. During these tests, phase-retrieval algorithms were used to characterize the instruments. The objective of this paper is to describe the Monte-Carlo simulations that were used to establish uncertainties (i.e., error bars) for the wavefronts of the various instruments in ISIM. Multiple retrieval algorithms were used in the analysis of ISIM phase-retrieval focus-sweep data, including an iterativetransform algorithm and a nonlinear optimization algorithm. These algorithms emphasize the recovery of numerous optical parameters, including low-order wavefront composition described by Zernike polynomial terms and high-order wavefront described by a point-by-point map, location of instrument best focus, focal ratio, exit-pupil amplitude, the morphology of any extended object, and optical jitter. The secondary objective of this paper is to report on the relative accuracies of these algorithms for the ISIM instrument tests, and a comparison of their computational complexity and their performance on central and graphical processing unit clusters. From a phase-retrieval perspective, the ISIM test campaign includes a variety of source illumination bandwidths, various image-plane sampling criteria above and below the Nyquist- Shannon critical sampling value, various extended object sizes, and several other impactful effects.

Design Analysis↗
DOE OSTI2020

Scalable Heterogeneous Execution of a Coupled-Cluster Model with Perturbative Triples

The CCSD(T) coupled-cluster model with perturbative triples is considered a gold standard for computational modeling of the correlated behavior of electrons in molecular systems. A fundamental constraint is the relatively small global-memory capacity in GPUs compared to the main-memory capacity on host nodes, necessitating relatively smaller tile sizes for high-dimensional tensor contractions in NWChem's GPU-accelerated implementation of the CCSD(T) method. A coordinated redesign is described to address this limitation and associated data movement overheads, including a novel fused GPU kernel for a set of tensor contractions, along with inter-node communication optimization and data caching. The new implementation of GPU-accelerated CCSD(T) improves overall performance by 3.4x. Finally, we discuss the trade-offs in using this fused algorithm on current and future supercomputing platforms.

Kim, Jinsung↗
DOE OSTI2016

Atomistic clustering-ordering and high-strain deformation of an Al 0.1 CrCoFeNi high-entropy alloy

Here, computational investigations of structural, chemical, and deformation behavior in high-entropy alloys (HEAs), which possess notable mechanical strength, have been limited due to the absence of applicable force fields. To extend investigations, we propose a set of intermolecular potential parameters for a quinary Al-Cr-Co-Fe-Ni alloy, using the available ternary Embedded Atom Method and Lennard-Jones potential in classical molecular-dynamics simulations. The simulation results are validated by a comparison to first-principles Korringa-Kohn-Rostoker (KKR) - Coherent Potential Approximation (CPA) [KKR-CPA] calculations for the HEA structural properties (lattice constants and bulk moduli), relative stability, pair probabilities, and high-temperature short-range ordering. The simulation (MD)-derived properties are in quantitative agreement with KKR-CPA calculations (first-principles) and experiments. We study Al x CrCoFeNi for Al ranging from 0 ≤ x ≤2 mole fractions, and find that the HEA shows large chemical clustering over a wide temperature range for x < 0.5. At various temperatures high-strain compression promotes atomistic rearrangements in Al 0.1 CrCoFeNi, resulting in a clustering-to-ordering transition that is absent for tensile loading. Large fluctuations under stress, and at higher temperatures, are attributed to the thermo-plastic instability in Al 0.1 CrCoFeNi.

36 MATERIALS SCIENCE↗
NASA NTRS2011

Software Testing and Verification in Climate Model Development

Over the past 30 years most climate models have grown from relatively simple representations of a few atmospheric processes to a complex multi-disciplinary system. Computer infrastructure over that period has gone from punch card mainframes to modem parallel clusters. Model implementations have become complex, brittle, and increasingly difficult to extend and maintain. Existing verification processes for model implementations rely almost exclusively upon some combination of detailed analysis of output from full climate simulations and system-level regression tests. In additional to being quite costly in terms of developer time and computing resources, these testing methodologies are limited in terms of the types of defects that can be detected, isolated and diagnosed. Mitigating these weaknesses of coarse-grained testing with finer-grained "unit" tests has been perceived as cumbersome and counter-productive. In the commercial software sector, recent advances in tools and methodology have led to a renaissance for systematic fine-grained testing. We discuss the availability of analogous tools for scientific software and examine benefits that similar testing methodologies could bring to climate modeling software. We describe the unique challenges faced when testing complex numerical algorithms and suggest techniques to minimize and/or eliminate the difficulties.

Clune, Thomas L.↗
DOE OSTI2023

Organo‐Functionalized Lacunary Double Cubane‐Type Oxometallates: Synthesis, Structure, and Properties of [(M II Cl) 2 (V IV O) 2 {((HOCH 2 CH 2 )(H)N(CH 2 CH 2 O))(HN(CH 2 CH 2 O) 2 )} 2 ] (M=Co, Zn)

Abstract Organofunctionalized tetranuclear clusters [(M II Cl) 2 (V IV O) 2 {((HOCH 2 CH 2 )(H)N(CH 2 CH 2 O))(HN(CH 2 CH 2 O) 2 )} 2 ] (1, M=Co,2: M=Zn) containing an unprecedented oxometallacyclic {M 2 V 2 Cl 2 N 4 O 8 } (M=Co, Zn) framework have been prepared by solvothermal reactions. The new oxo‐alkoxide compounds were fully characterized by spectroscopic methods, magnetic susceptibility measurement, DFT and ab initio computational methods, and complete single‐crystal X‐ray diffraction structure analysis. The isostructural clusters are formed of edge‐sharing octahedral {VO 5 N} and trigonal bipyramidal {MO 3 NCl} units. Diethanolamine ligates the bimetallic lacunary double cubane core of1and2in an unusual two‐mode fashion, unobserved previously. In the crystalline state, the clusters of1and2are joined by hydrogen bonds to form a three‐dimensional network structure. Magnetic susceptibility data indicate weakly antiferromagnetic interactions between the vanadium centers [J iso (V IV −V IV )=−5.4(1); −3.9(2) cm −1 ], and inequivalent antiferromagnetic interactions between the cobalt and vanadium centers [J iso (V IV −Co II )=−12.6 and −7.5 cm −1 ] contained in1.

Chemistry↗
DOE OSTI2021

Data–Driven Velocity Model Evaluation Using K–Means Clustering

In this work, we develop a data-driven clustering method to evaluate a velocity model using surface wave velocity dispersion. This is done by first computing theoretical dispersion curves for 1-D velocity profiles of all the grid locations and then splitting the resulting dispersion curves into a certain number of groups via the K-means clustering. The observed dispersion curves are also clustered following the same procedure and the velocity model is assessed by comparing the spatial patterns obtained for the observed and synthetic data sets. The method is applied to evaluate two community velocity models in southern California, CVM-S4.26 and CVM-H15.1, using phase velocity maps derived for 3–16 s Rayleigh waves. We found a good correlation in the spatial distribution of clusters between the result of CVM-S4.26 and that of the observed data, suggesting that the CVM-S4.26 fits the observed dispersion maps better than the CVM-H15.1 in terms of features extracted from the clustering analysis.

58 GEOSCIENCES↗
DOE OSTI2015

The temperature and size distribution of large water clusters from a non-equilibrium model

A hybrid Lagrangian-Eulerian approach is used to examine the properties of water clusters formed in neon-water vapor mixtures expanding through microscale conical nozzles. Experimental size distributions were reliably determined by the sodium doping technique in a molecular beam machine. The comparison of computed size distributions and experimental data shows satisfactory agreement, especially for (H{sub 2}O){sub n} clusters with n larger than 50. Thus validated simulations provide size selected cluster temperature profiles in and outside the nozzle. This information is used for an in-depth analysis of the crystallization and water cluster aggregation dynamics of recently reported supersonic jet expansion experiments.

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

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronic structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li + /PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Correlations from Ion Pairing and the Nernst-Einstein Equation

In this work, we present a new approximation to ionic conductivity well suited to dynamical atomic-scale simulations, based on the Nernst-Einstein equation. In our approximation, ionic aggregates constitute the elementary charge carriers, and are considered as noninteracting species. This approach conveniently captures the dominant effect of ion-ion correlations on conductivity, short range interactions in the form of clustering. In addition to providing better estimates to the conductivity at a lower computational cost than exact approaches, this new method allows us to understand the physical mechanisms driving ion conduction in concentrated electrolytes. As an example, we consider Li + conduction in poly(ethylene oxide), a standard solid-state polymer electrolyte. Using our newly developed approach, we are able to reproduce recent experimental results reporting negative cation transference numbers at high salt concentrations, and to confirm that this effect can be caused by a large population of negatively charged clusters involving cations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Nonlinear effects of dark energy clustering beyond the acoustic scales

We extend the resummation method of Anselmi and Pietroni (2012) to compute the total density power spectrum in models of quintessence characterized by a vanishing speed of sound. For standard ΛCDM cosmologies, this resummation scheme allows predictions with an accuracy at the few percent level beyond the range of scales where acoustic oscillations are present, therefore comparable to other, common numerical tools. In addition, our theoretical approach indicates an approximate but valuable and simple relation between the power spectra for standard quintessence models and models where scalar field perturbations appear at all scales. This, in turn, provides an educated guess for the prediction of nonlinear growth in models with generic speed of sound, particularly valuable since no numerical results are yet available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Comparative I/O workload characterization of two leadership class storage clusters. In: PDSW '15 Proceedings of the 10th Parallel Data Storage Workshop

The Oak Ridge Leadership Computing Facility (OLCF) is a leader in large-scale parallel file system development, design, deployment and continuous operation. For the last decade, the OLCF has designed and deployed two large center-wide parallel file systems. The first instantiation, Spider 1, served the Jaguar supercomputer and its predecessor, Spider 2, now serves the Titan supercomputer, among many other OLCF computational resources. The OLCF has been rigorously collecting file and storage system statistics from these Spider systems since their transition to production state. In this paper we present the collected I/O workload statistics from the Spider 2 system and compare it to the Spider 1 data. Our analysis show that the Spider 2 workload is more more write-heavy I/O compared to Spider 1 (75% vs. 60%, respectively). The data also show the OLCF storage policies such as periodic purges are effectively managing the capacity resource of Spider 2. Furthermore, due to improvements in tdm_multipath and ib_srp software, we are utilizing the Spider 2 system bandwidth and latency resources more effectively. The Spider 2 bandwidth usage statistics shows that our system is working within the design specifications. However, it is also evident that our scientific applications can be more effectively served by a burst buffer storage layer. All the data has been collected by monitoring tools developed for the Spider ecosystem. We believe the observed data set and insights will help us better design the next-generation Spider file and storage system. It will also be helpful to the larger community for building more effective large-scale file and storage systems.

Gunasekaran, Raghul↗
NASA NTRS1985

H2O/Ni(100) and NH3/Ni(100) - A computational approach

The adsorption of NH3 and H2O on the Ni(100) is treated using a cluster model. The adsorption is found to have only a small effect on the HXH angle. Rotation about the principal ligand axis requires virtually no energy. Ligand tilts of 15 deg are found to require small amounts of energy, leading to the suggestion that the ESDIAD signal is a result of excited tilting modes, not a change in the HXH angle. For H2O additional bending modes are considered and all are found to be quite flat in energy.

Bauschlicher, C. W., Jr.↗
DOE OSTI2019

Quantum chemistry as a benchmark for near-term quantum computers

We present a quantum chemistry benchmark for noisy intermediate-scale quantum computers that leverages the variational quantum eigensolver, active-space reduction, a reduced unitary coupled cluster ansatz, and reduced density purification as error mitigation. We demonstrate this benchmark using 4 of the available qubits on the 20-qubit IBM Tokyo and 16-qubit Rigetti Aspen processors via the simulation of alkali metal hydrides (NaH, KH, RbH), with accuracy of the computed ground state energy serving as the primary benchmark metric. We further parameterize this benchmark suite on the trial circuit type, the level of symmetry reduction, and error mitigation strategies. Our results demonstrate the characteristically high noise level present in near-term superconducting hardware, but provide a relevant baseline for future improvement of the underlying hardware, and a means for comparison across near-term hardware types. We also demonstrate how to reduce the noise in post processing with specific error mitigation techniques. Particularly, the adaptation of McWeeny purification of noisy density matrices dramatically improves accuracy of quantum computations, which, along with adjustable active space, significantly extends the range of accessible molecular systems. We demonstrate that for specific benchmark settings and a selected range of problems, the accuracy metric can reach chemical accuracy when computing over the cloud on certain quantum computers.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1993

A distributed version of the NASA Engine Performance Program

Distributed NEPP, a version of the NASA Engine Performance Program, uses the original NEPP code but executes it in a distributed computer environment. Multiple workstations connected by a network increase the program's speed and, more importantly, the complexity of the cases it can handle in a reasonable time. Distributed NEPP uses the public domain software package, called Parallel Virtual Machine, allowing it to execute on clusters of machines containing many different architectures. It includes the capability to link with other computers, allowing them to process NEPP jobs in parallel. This paper discusses the design issues and granularity considerations that entered into programming Distributed NEPP and presents the results of timing runs.

Cours, Jeffrey T.↗