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DOE OSTI2013

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2001

Design of Unstructured Adaptive (UA) NAS Parallel Benchmark Featuring Irregular, Dynamic Memory Accesses

We describe the design of a new method for the measurement of the performance of modern computer systems when solving scientific problems featuring irregular, dynamic memory accesses. The method involves the solution of a stylized heat transfer problem on an unstructured, adaptive grid. A Spectral Element Method (SEM) with an adaptive, nonconforming mesh is selected to discretize the transport equation. The relatively high order of the SEM lowers the fraction of wall clock time spent on inter-processor communication, which eases the load balancing task and allows us to concentrate on the memory accesses. The benchmark is designed to be three-dimensional. Parallelization and load balance issues of a reference implementation will be described in detail in future reports.

Feng, Hui-Yu↗

DOE OSTI2024

Investigating Cu-Site Doped Cu–Sb–S Nanoparticles Using Photoelectron and Electron Paramagnetic Resonance Spectroscopy

Tetrahedrite (Cu 12 Sb 4 S 13 ) and famatinite (Cu 3 SbS 4 ) are good candidates for green energy applications because they possess promising thermoelectric and photovoltaic properties as well as contain earth-abundant and nontoxic constituents. Herein, X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and electron paramagnetic resonance spectroscopy (EPR) methods examined inherent electronic properties and interatomic magnetic interactions of Cu-site doped tetrahedrite and famatinite nanomaterials. An energy-efficient modified polyol method was utilized for the synthesis of tetrahedrite and famatinite nanoparticles doped on the Cu-site with Zn, Fe, Ni, Mn, and Co. This is the first parallel study of tetrahedrite and famatinite nanomaterials with XPS, UPS, and EPR methods alongside a systematic analysis of dopant-dependent effects on the electronic structure and magnetic interactions for each material. XPS showed that the Cu and Sb species in tetrahedrite and famatinite possess different oxidation states, while UPS characterization reveals larger dopant-dependent shifts in the work function for tetrahedrite nanoparticles (4.21 to 4.79 eV) than for famatinite nanoparticles (4.57 to 4.77 eV). Finally, all famatinite nanoparticles display an EPR signal, indicating trace amounts of paramagnetic Cu(II) present below the detection limit of XPS. For tetrahedrite, EPR signatures were observed only for the Zn-doped and Mn-doped nanoparticles, suggesting signal broadening from Cu–Cu spin exchange or spin–lattice relaxation. This study demonstrates the complementary nature of XPS and EPR techniques for studying the oxidation states of metals in solid-state nanomaterials. Comparing the electronic and magnetic properties of tetrahedrite and famatinite while studying the impact of dopant incorporation will guide future endeavors in designing sustainable, high-performance materials for renewable energy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1972

A study of optical scattering methods in laboratory plasma diagnosis

Electron velocity distributions are deduced along axes parallel and perpendicular to the magnetic field in a pulsed, linear Penning discharge in hydrogen by means of a laser Thomson scattering experiment. Results obtained are numerical averages of many individual measurements made at specific space-time points in the plasma evolution. Because of the high resolution in k-space and the relatively low maximum electron density 2 x 10 to the 13th power/cu cm, special techniques were required to obtain measurable scattering signals. These techniques are discussed and experimental results are presented.

Phipps, C. R., Jr.↗

NASA NTRS1989

Parallel solution of pentadiagonal systems using generalized odd-even elimination

A method for the solution of pentadiagonal systems of linear equations is presented. The method is a generalization of ordinary odd-even elimination used for tridiagonal systems. Using n processors, an n x n pentadiagonal system can be solved using the new method (generalized odd-even elimination) in time proportional to log(2) n.

Levit, Creon↗

NASA NTRS1996

High-Performance Parallel Analysis of Coupled Problems for Aircraft Propulsion

This research program dealt with the application of high-performance computing methods to the numerical simulation of complete jet engines. The program was initiated in January 1993 by applying two-dimensional parallel aeroelastic codes to the interior gas flow problem of a bypass jet engine. The fluid mesh generation, domain decomposition and solution capabilities were successfully tested. Attention was then focused on methodology for the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion driven by these structural displacements. The latter is treated by a ALE technique that models the fluid mesh motion as that of a fictitious mechanical network laid along the edges of near-field fluid elements. New partitioned analysis procedures to treat this coupled three-component problem were developed during 1994 and 1995. These procedures involved delayed corrections and subcycling, and have been successfully tested on several massively parallel computers, including the iPSC-860, Paragon XP/S and the IBM SP2. For the global steady-state axisymmetric analysis of a complete engine we have decided to use the NASA-sponsored ENG10 program, which uses a regular FV-multiblock-grid discretization in conjunction with circumferential averaging to include effects of blade forces, loss, combustor heat addition, blockage, bleeds and convective mixing. A load-balancing preprocessor tor parallel versions of ENG10 was developed. During 1995 and 1996 we developed the capability tor the first full 3D aeroelastic simulation of a multirow engine stage. This capability was tested on the IBM SP2 parallel supercomputer at NASA Ames. Benchmark results were presented at the 1196 Computational Aeroscience meeting.

Felippa, C. A.↗

NASA NTRS1999

Emission of Sound From Turbulence Convected by a Parallel Mean Flow in the Presence of a Confining Duct

An approximate method for calculating the noise generated by a turbulent flow within a semi-infinite duct of arbitrary cross section is developed. It is based on a previously derived high-frequency solution to Lilley's equation, which describes the sound propagation in transversely-sheared mean flow. The source term is simplified by assuming the turbulence to be axisymmetric about the mean flow direction. Numerical results are presented for the special case of a ring source in a circular duct with an axisymmetric mean flow. They show that the internally generated noise is suppressed at sufficiently large upstream angles in a hard walled duct, and that acoustic liners can significantly reduce the sound radiated in both the upstream and downstream regions, depending upon the source location and Mach number of the flow.

Goldstein, Marvin E.↗

NASA NTRS1999

Emission of Sound from Turbulence Convected by a Parallel Mean Flow in the Presence of a Confining Duct

An approximate method for calculating the noise generated by a turbulent flow within a semi-infinite duct of arbitrary cross section is developed. It is based on a previously derived high-frequency solution to Lilley's equation, which describes the sound propagation in a transversely-sheared mean flow. The source term is simplified by assuming the turbulence to be axisymmetric about the mean flow direction. Numerical results are presented for the special case of a ring source in a circular duct with an axisymmetric mean flow. They show that the internally generated noise is suppressed at sufficiently large upstream angles in a hard walled duct, and that acoustic liners can significantly reduce the sound radiated in both the upstream and downstream regions, depending upon the source location and Mach number of the flow.

Goldstein, Marvin E.↗

DOE OSTI2026

Integral Kernel Methods for Nonlinear Parabolic-Elliptic Systems

Nonlinear parabolic-elliptic systems arise in many physical, biological, and chemical phenomena such as chemotaxis, ion transport, self-gravitating particles, and Brownian vortices. Existing methods struggle with the strong coupling and high nonlinearity and nonlocality of some of these systems, especially the ill-conditioned, convection-dominated problems. To overcome numerical difficulties, current approaches rely on initial guesses, preconditioning, or iterative techniques with no convergence guarantees. They might suffer from poor scalability, large memory usage, and difficulty to parallelize. Inspired by the connection of parabolic-elliptic systems to stochastic processes, we introduce a novel meshless, monolithic, and fully explicit method that naturally encapsulates the elliptic and parabolic operators into a single step which updates each node deterministically with global information. By being fully quadrature-based, it avoids solving systems of discretized equations and does not utilize initial guesses or preconditioning, while requiring little memory and being easy to parallelize. We first derive the method in an integral kernel formulation with quadratic complexity in the number of integration nodes and then leverage kernel-independent fast multipole methods (FMM) to present a scalable algorithm with linear complexity. We provide numerical examples for the Poisson-Nernst-Planck equations in one, two, and three dimensions, together with the derivation of the integral kernel for each case. Furthermore, the examples demonstrate the fast convergence and scalability of the FMM-accelerated algorithm, as well as its suitability for convection-dominated problems, making it competitive against traditional PDE solvers.

PDE systems↗

DOE OSTI2015

A parallel multi-domain solution methodology applied to nonlinear thermal transport problems in nuclear fuel pins

This paper describes an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors is described. Details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstrating the achieved efficiency of the algorithm are presented. Furthermore, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1999

I/O Parallelization for the Goddard Earth Observing System Data Assimilation System (GEOS DAS)

The National Aeronautics and Space Administration (NASA) Data Assimilation Office (DAO) at the Goddard Space Flight Center (GSFC) has developed the GEOS DAS, a data assimilation system that provides production support for NASA missions and will support NASA's Earth Observing System (EOS) in the coming years. The DAO's support of the EOS project along with the requirement of producing long-term reanalysis datasets with an unvarying system levy a large I/O burden on the future system. The DAO has been involved in prototyping parallel implementations of the GEOS DAS for a number of years and is now converting the production version from shared-memory parallelism to distributed-memory parallelism using the portable Message-Passing Interface (MPI). If the MPI-based GEOS DAS is to meet these production requirements, we must make I/O from the parallel system efficient. We have designed a scheme that allows efficient I/O processing while retaining portability, reducing the need for post-processing, and producing data formats that are required by our users, both internal and external. The first phase of the GEOS DAS Parallel I/O System (GPIOS) will expand upon the common method of gathering global data to a Single PE for output. Instead of using a PE also tasked with primary computation, a number of PEs will be dedicated to I/O and its related tasks. This allows the data transformations and formatting required prior to output to take place asynchronously with respect to the GEOS DAS assimilation cycle, improving performance and generating output data sets in a format convenient for our users. I/O PEs can be added as needed to handle larger data volumes or to meet user file specifications. We will show I/O performance results from a prototype MPI GCM integrated with GPIOS. Phase two of GPIOS development will examine ways of integrating new software technologies to further improve performance and build scalability into the system. The maturing of MPI-IO implementations and other supporting libraries such as parallel HDF should provide performance gains while retaining portability.

Lucchesi, R.↗

DOE OSTI2015

Fully coupled simulation of cosmic reionization. I. numerical methods and tests

Here, we describe an extension of the Enzo code to enable fully coupled radiation hydrodynamical simulation of inhomogeneous reionization in large similar to(100 Mpc)(3) cosmological volumes with thousands to millions of point sources. We solve all dynamical, radiative transfer, thermal, and ionization processes self-consistently on the same mesh, as opposed to a postprocessing approach which coarse-grains the radiative transfer. But, we employ a simple subgrid model for star formation which we calibrate to observations. The numerical method presented is a modification of an earlier method presented in Reynolds et al. differing principally in the operator splitting algorithm we use to advance the system of equations. Radiation transport is done in the gray flux-limited diffusion (FLD) approximation, which is solved by implicit time integration split off from the gas energy and ionization equations, which are solved separately. This results in a faster and more robust scheme for cosmological applications compared to the earlier method. The FLD equation is solved using the hypre optimally scalable geometric multigrid solver from LLNL. By treating the ionizing radiation as a grid field as opposed to rays, our method is scalable with respect to the number of ionizing sources, limited only by the parallel scaling properties of the radiation solver. We test the speed and accuracy of our approach on a number of standard verification and validation tests. We show by direct comparison with Enzo's adaptive ray tracing method Moray that the well-known inability of FLD to cast a shadow behind opaque clouds has a minor effect on the evolution of ionized volume and mass fractions in a reionization simulation validation test. Finally, we illustrate an application of our method to the problem of inhomogeneous reionization in a 80 Mpc comoving box resolved with 3200(3) Eulerian grid cells and dark matter particles.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1991

Dynamic analysis and control of lightweight manipulators with flexible parallel link mechanisms

The flexible parallel link mechanism is designed for increased rigidity to sustain the buckling when it carries a heavy payload. Compared to a one link flexible manipulator, a two link flexible manipulator, especially the flexible parallel mechanism, has more complicated characteristics in dynamics and control. The objective of this research is the theoretical analysis and the experimental verification of dynamics and control of a two link flexible manipulator with a flexible parallel link mechanism. Nonlinear equations of motion of the lightweight manipulator are derived by the Lagrangian method in symbolic form to better understand the structure of the dynamic model. A manipulator with a flexible parallel link mechanism is a constrained dynamic system whose equations are sensitive to numerical integration error. This constrained system is solved using singular value decomposition of the constraint Jacobian matrix. The discrepancies between the analytical model and the experiment are explained using a simplified and a detailed finite element model. The step response of the analytical model and the TREETOPS model match each other well. The nonlinear dynamics is studied using a sinusoidal excitation. The actuator dynamic effect on a flexible robot was investigated. The effects are explained by the root loci and the Bode plot theoretically and experimentally. For the base performance for the advanced control scheme, a simple decoupled feedback scheme is applied.

Lee, Jeh Won↗

NASA NTRS1988

TRAPEDS: Producing traces for multicomputers via execution-driven simulation

Trace-driven simulation is an important aid in performance analysis of computer systems. Capturing address traces for these simulations is a difficult problem for single processors and particularly for multicomputers. Even when existing trace methods can be used on multicomputers, the amount of collected data typically grows with the number of processors, so I/O and trace storage costs increase. A new technique is presented which modifies the executable code to dynamically collect the address trace from the user code and analyzes this trace during the execution of the program. This method helps resolve the I/O and storage problems and facilitates parallel analysis of the address trace. If a trace stored on disk is desired, the generated trace information can also be written to files during execution, with a resultant drop in program execution speed. An initial implementation on the Intel iPSC/2 hypercube multicomputer is detailed, and sample simulation results are presented. The effect of this trace collection method on execution time is illustrated.

Stunkel, Craig B.↗

NASA NTRS1989

TRAPEDS - Producing traces for multicomputers via execution driven simulation

Stunkel, Craig B.↗

NASA NTRS1995

Preliminary large-eddy simulations of flow around a NACA 4412 airfoil using unstructured grids

Large-eddy simulation (LES) has matured to the point where application to complex flows is desirable. The extension to higher Reynolds numbers leads to an impractical number of grid points with existing structured-grid methods. Furthermore, most real world flows are rather difficult to represent geometrically with structured grids. Unstructured-grid methods offer a release from both of these constraints. However, just as it took many years for structured-grid methods to be well understood and reliable tools for LES, unstructured-grid methods must be carefully studied before we can expect them to attain their full potential. In the past two years, important building blocks have been put into place making possible a careful study of LES on unstructured grids. The first building block was an efficient mesh generator which allowed the placement of points according to smooth variation of physical length scales. This variation of length scales is in all three directions independently, which allows a large reduction in points when compared to structured-grid methods, which can only vary length scales in one direction at a time. The second building block was the development of a dynamic model appropriate for unstructured grids. The principle obstacle was the development of an unstructured-grid filtering operator. In the past year, some of the new filters developed by Jansen have been implemented into a highly parallelized finite element code based on the Galerkin/least-squares finite element method. We have chosen the NACA 4412 airfoil at maximum lift as the first simulation for a variety of reasons. First, it is a problem of significant interest since it would be the first LES of an aircraft component. Second, this flow has been the subject of three experimental studies. The third reason for considering this flow is the variety of flow features which provide an important test of the dynamic model. Only the dynamic model can be expected to perform satisfactorily in this variety of situations: from the laminar regions where it must not modify the flow at all to the turbulent boundary layers and wake where it must represent a wide variety of subgrid-scale structures. The flow configuration we have chosen is that of Wadcock (1987) at Reynolds number based on chord Re(sub c) = u(sub infinity)c/v = 1.64 x 10(exp 6), Mach number M = 0.2, and 12 deg angle of attack.

Jansen, Kenneth↗

NASA NTRS1983

A lifting surface theory in rotational flow

The partial differential equation for small disturbance steady rotational flow in three dimensions is solved through an integral equation approach. The solution is obtained by using the method of weighted residuals. Specific applications are directed to wings in nonuniform subsonic parallel streams with velocity varying in vertical and spanwise directions and to airfoils in nonuniform freestream. Comparison with limited known results indicates that the present method is reasonably accurate. Numerical results for the lifting pressure of airfoil, lift, induced drag, and pitching moments of airfoil, lift, induced drag, and pitching moments of elliptic, rectangular, and delta wings in a jet, wake, or monotonic sheared stream are presented. It is shown that, in addition to the effect of local dynamic pressures, a positive velocity gradient tends to enhance the lift.

Shiau, M. J.↗

NASA NTRS1994

Microwave radiative transfer through horizontally inhomogeneous precipitating clouds

Recent advances in cloud microphysical models have led to realistic three-dimensional distributions of cloud constituents. Radiative transfer schemes can make use of this detailed knowledge in order to study the effects of horizontal as well as vertical inhomogeneities within clouds. This study looks specifically at the differences between three-dimensional radiative transfer results and those obtained by plane parallel, independent pixel approximations in the microwave spectrum. A three-dimensional discrete ordinates method as well as a backward Monte Carlo method are used to calculate realistic radiances emerging from the cloud. Analyses between these models and independent pixel approximations reveal that plane parallel approximations introduce two distinct types of errors. The first error is physical in nature and is related to the fact that plane parallel approximations do not allow energy to leak out of dense areas into surrouding areas. In general, it was found that these errors are quite small for emission-dominated frequencies (37 GHz and lower) and that physical errors are highly pronounced only at scattering frequencies (85 GHz) where large deviations and biases up to 8 K averaged over the entire cloud were found. The second error is more geometric in nature and is related to the fact that plane parallel approximations cannot accommodate physical boundaries in the horizontal dimension for off-nadir viewing angles. The geometric errors were comparable in magnitude for all frequencies. Their magnitude, however, depends on a number of factors including the scheme used to deal with the edge, the nature of the surface, and the viewing angle.

Roberti, Laura↗