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At least 235 records · Page 13

A Concept for Run-Time Support of the Chapel Language

A document presents a concept for run-time implementation of other concepts embodied in the Chapel programming language. (Now undergoing development, Chapel is intended to become a standard language for parallel computing that would surpass older such languages in both computational performance in the efficiency with which pre-existing code can be reused and new code written.) The aforementioned other concepts are those of distributions, domains, allocations, and access, as defined in a separate document called "A Semantic Framework for Domains and Distributions in Chapel" and linked to a language specification defined in another separate document called "Chapel Specification 0.3." The concept presented in the instant report is recognition that a data domain that was invented for Chapel offers a novel approach to distributing and processing data in a massively parallel environment. The concept is offered as a starting point for development of working descriptions of functions and data structures that would be necessary to implement interfaces to a compiler for transforming the aforementioned other concepts from their representations in Chapel source code to their run-time implementations.

James, Mark↗

Parallel rendering

This article provides a broad introduction to the subject of parallel rendering, encompassing both hardware and software systems. The focus is on the underlying concepts and the issues which arise in the design of parallel rendering algorithms and systems. We examine the different types of parallelism and how they can be applied in rendering applications. Concepts from parallel computing, such as data decomposition, task granularity, scalability, and load balancing, are considered in relation to the rendering problem. We also explore concepts from computer graphics, such as coherence and projection, which have a significant impact on the structure of parallel rendering algorithms. Our survey covers a number of practical considerations as well, including the choice of architectural platform, communication and memory requirements, and the problem of image assembly and display. We illustrate the discussion with numerous examples from the parallel rendering literature, representing most of the principal rendering methods currently used in computer graphics.

Crockett, Thomas W.↗

A massively-parallel, unstructured overset method for mesh connectivity

Here we present a method that dynamically and efficiently performs connectivity calculations between many O(10 5 ) moving, unstructured overset meshes in parallel. In order to connect overset meshes, elements exterior to the solution domain must be removed from the simulation. In regions with many overlapping meshes, elements must be selectively removed to reduce redundancy while maintaining a solution over the entire domain. Around masked regions interpolation partner pairing is required between meshes to provide boundary conditions. For general unstructured meshes, these steps involve challenging computational geometry calculations which must be efficient and automatic. For many moving meshes each step must be massively parallelized and scalable to large numbers of computational cores. To establish communication patterns a parallelized master/slave algorithm is used which minimizes global communication and storage. To remove elements a parallel ‘Forest Fire’ flood-fill algorithm is used to set a masking variable. For interpolation partner pairing, and other necessary searches, k-dimensional tree data structures (k-d trees) are extensively used. Often in a calculation, the connectivity between overset meshes remains largely the same between time steps. The temporal coherence of the various objects in the connectivity calculation is directly used to only update necessary information with time, resulting in substantial cost savings. Details of the different algorithms are presented. Resulting connectivity and timings are shown for complex geometries. Parallel scaling is demonstrated for 100,000 spherical particles within a channel up to 492,000 processors.

97 MATHEMATICS AND COMPUTING↗

Portable Data-Parallel Surface Reconstruction on a Uniform Rectilinear Grid

With the increasing heterogeneity and on-node parallelism of high-performance computing hardware, a major challenge is to develop portable and efficient algorithms and software. In this work, we present our implementation of a portable code to perform surface reconstruction using NVIDIA's Thrust library. Surface reconstruction is a technique commonly used in volume tracking methods for simulations of multimaterial flow with interfaces. Here, we have designed a 3D mesh data structure that is easily mapped to the 1D vectors used by Thrust and at the same time is simple to use and uses familiar data structure terminology (such as cells, faces, vertices, and edges). With this new data structure in place, we have implemented a piecewise linear interface reconstruction algorithm in 3 dimensions that effectively exploits the symmetry present in a uniform rectilinear computational cell. Finally, we report performance results, which show that a single implementation of these algorithms can be compiled to multiple backends (specifically, multi-core CPUs, NVIDIA GPUs, and Intel Xeon Phi processors), making efficient use of the available parallelism on each. We also compare performance of our implementation to a legacy FORTRAN implementation in Message Passing Interface (MPI) and show performance parity on single and multi-core CPU and achieved good parallel speed-ups on GPU. In conclusion, our research demonstrates the advantage of performance portability of the underlying data-parallel programming model.

97 MATHEMATICS AND COMPUTING↗

NavP: Structured and Multithreaded Distributed Parallel Programming

This slide presentation reviews some of the issues around distributed parallel programming. It compares and contrast two methods of programming: Single Program Multiple Data (SPMD) with the Navigational Programming (NAVP). It then reviews the distributed sequential computing (DSC) method and the methodology of NavP. Case studies are presented. It also reviews the work that is being done to enable the NavP system.

parallel programming↗

Pervasive shifts in forest dynamics in a changing world

Forest dynamics arise from the interplay of environmental drivers and disturbances with the demographic processes of recruitment, growth, and mortality, subsequently driving biomass and species composition. However, forest disturbances and subsequent recovery are shifting with global changes in climate and land use, altering these dynamics. Changes in environmental drivers, land use, and disturbance regimes are forcing forests toward younger, shorter stands. Rising carbon dioxide, acclimation, adaptation, and migration can influence these impacts. Recent developments in Earth system models support increasingly realistic simulations of vegetation dynamics. In parallel, emerging remote sensing datasets promise qualitatively new and more abundant data on the underlying processes and consequences for vegetation structure. In combination, these advances hold promise for improving the scientific understanding of changes in vegetation demographics and disturbances.

54 ENVIRONMENTAL SCIENCES↗

Concurrent file operations in a high performance FORTRAN

Distributed memory multiprocessor systems can provide the computing power necessary for large scale scientific applications. A critical performance issue for a number of these applications is the efficient transfer of data to secondary storage. Recently several research groups have proposed FORTRAN language extensions for exploiting the data parallelism of such scientific codes on distributed memory architectures. However, few of these high performance FORTRAN's provide appropriate constructs for controlling the use of the parallel I/O capabilities of modern multiprocessing machines. In this paper, we propose constructs to specify I/O operations for distributed data structures in the context of Vienna Fortran. These operations can be used by the programmer to provide information which can help the compiler and runtime environment make the most efficient use of the I/O subsystem.

Brezany, Peter↗

Adapting high-level language programs for parallel processing using data flow

EASY-FLOW, a very high-level data flow language, is introduced for the purpose of adapting programs written in a conventional high-level language to a parallel environment. The level of parallelism provided is of the large-grained variety in which parallel activities take place between subprograms or processes. A program written in EASY-FLOW is a set of subprogram calls as units, structured by iteration, branching, and distribution constructs. A data flow graph may be deduced from an EASY-FLOW program.

Standley, Hilda M.↗

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of orientation-dependent deformation mechanisms in additively manufactured Zr using in-situ micromechanical testing: Twinning and orientation gradient

Here, orientation-dependent plasticity in zirconium (Zr)-alloy, which is produced through ultrasonic additive manufacturing (UAM) with subsequent hot-isostatic pressing (HIP), was analyzed by recording electron backscattered diffraction (EBSD) data during in-situ micromechanical testing. Three (0001) plane orientations of a hexagonal close-packed (HCP) structure were analyzed parallel to (1) the rolling direction [X||tensile direction (TD)], (2) the build direction [Z], and (3) the transverse direction [Y]. The analysis revealed that the grains with ~<0001>||TD show twin-dominant plasticity with three variants from {10 $\overline{1}$ 2}<$\overline{1}$ 011>; minor slipping with ($10\overline{1}$ 1)[$\overline{2}$ 113], and ($11\overline{2}$ 2)[$\overline{1} \overline{1}$ 23] pyramidal slip has also been observed. However, grains with orientation ~<0001>⊥TD are mainly sensitive to dislocations assisted plasticity-leading to orientation gradients formation. Furthermore, the neck formation was identified as originating from higher populated micro-crack locations and their association with localized plasticity at defect points in the UAM material. These results demonstrate that minimization of impurities to enable grain growth across prior foil interfaces makes HIP an effective methodology for producing Zr plate, with deformation characteristics expected for conventionally manufactured Zr.

36 MATERIALS SCIENCE↗

Practical procedures for sensor quality assessment

Sensors are increasingly deployed for process monitoring and control. These produce on-line measurements at a high frequency, in parallel with low-frequency laboratory measurements. Compared to laboratory practices, sensor data quality assessment and control practices are far less structured at most utilities. This leads to inaccurate sensor data with unknown uncertainty factors.This chapter shows how to establish standard operating procedures (SOPs) to support sensor data quality assessment and control and subsequent maintenance actions by producing relevant sensor metadata. Furthermore, SOPs are provided for the most commonly used wastewater quality sensors, inspired by utility and academic best practices. This chapter builds on definitions provided in Chapter 3 and provides additional definitions specifically related to sensors maintenance. Chapter 6 complements the methods in this chapter, which are based on reference measurements, with data-analytical techniques.

Alferes, Janelcy↗

Level-set Modeling Simulations of Chemical Vapor Infiltration for Ceramic Matrix Composites Manufacturing

Silicon-carbide (SiC) reinforced ceramic matrix composites (CMCs) are a key enabling technology to reduce fuel consumption and emissions of gas turbine engines. In one manufacturing approach, chemical vapor infiltration (CVI) is limited to only coating SiC fibers. The preform is then fabricated using a lay-up of basic plys or 2-D woven sheets composed of the precoated fibers. At the other extreme, CVI is used to completely densify a 3-D woven preform shaped almost like the gas turbine component itself. The latter approach is more suitable for highly engineered components which sit directly in the gas path of the engine, for example, a high pressure turbine blade. In this case, the geometry is necessarily complex for aerodynamic, stress, and lifing (multi-physics) requirements. Presently, optimizing the CVI-dominated manufacturing approach is largely by trial-and-error. In this work, a first-principles modeling of CVI is performed to realize optimization of SiC/SiC CMC manufacturing. The modeling is based on a level-set framework to describe the interface between the vapor and solid phases. A finite-difference numerical scheme using an immersed boundary method is developed for fixed, structured meshes. Massively parallel direct numerical simulations (DNS) of CVI through fiber-woven geometries are performed using one-step chemistry, and over a range of Thiele moduli. Illustrative applications of the resulting large DNS data sets are given, including the development of fiber-weave specific infiltration models and structure functions for mean-field (porous media) Computational Fluid Dynamics (CFD) simulations of CVI.

36 MATERIALS SCIENCE↗

Dataset of simulated vibrational density of states and X-ray diffraction profiles of mechanically deformed and disordered atomic structures in Gold, Iron, Magnesium, and Silicon

This dataset is comprised of a library of atomistic structure files and corresponding X-ray diffraction (XRD) profiles and vibrational density of states (VDoS) profiles for bulk single crystal silicon (Si), gold (Au), magnesium (Mg), and iron (Fe) with and without disorder introduced into the atomic structure and with and without mechanical loading. Included with the atomistic structure files are descriptor files that measure the stress state, phase fractions, and dislocation content of the microstructures. All data was generated via molecular dynamics or molecular statics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. This dataset can inform the understanding of how local or global changes to a materials microstructure can alter their spectroscopic and diffraction behavior across a variety of initial structure types (cubic diamond, face-centered cubic (FCC), hexagonal close-packed (HCP), and body-centered cubic (BCC) for Si, Au, Mg, and Fe, respectively) and overlapping changes to the microstructure (i.e., both disorder insertion and mechanical loading).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Structure of the November 12, 1978, quasi-parallel interplanetary shock

The jump in plasma parameters exhibited by the intense interplanetary shock event of Nov. 12, 1978 is analyzed using ISEE 1, 2 and 3 data. Magnetic and electric field measurements indicated that the shock magnetic field profile was similar to the earth bow shock profile. Data on the electron and proton densities, temperatures, bulk velocities and alpha particles showed a steady electron temperature increase across the shock on a 12 earth radii scale. The upstream and downstream flow parameters are found to be within 10 percent of Rankin-Hugoniot jump conditions. The shock moved at 614 km/sec and had three dissipative scales, one a few Larmor radii determined by the magnetic field jump, a second 10 earth radii correlated with the electron equilibrium and the other 30 earth radii connected to the energetic proton foreshock.

Kennel, C. F.↗

A strategy for reducing turnaround time in design optimization using a distributed computer system

There is a need to explore methods for reducing lengthly computer turnaround or clock time associated with engineering design problems. Different strategies can be employed to reduce this turnaround time. One strategy is to run validated analysis software on a network of existing smaller computers so that portions of the computation can be done in parallel. This paper focuses on the implementation of this method using two types of problems. The first type is a traditional structural design optimization problem, which is characterized by a simple data flow and a complicated analysis. The second type of problem uses an existing computer program designed to study multilevel optimization techniques. This problem is characterized by complicated data flow and a simple analysis. The paper shows that distributed computing can be a viable means for reducing computational turnaround time for engineering design problems that lend themselves to decomposition. Parallel computing can be accomplished with a minimal cost in terms of hardware and software.

Young, Katherine C.↗

Efficient, Parallel At-scale Correlation Analysis for Atom Probe Tomography on Hybrid Architectures

Atom probe tomography (APT) is a material probing technique that has undergone dramatic improvements in its capability to map individual atoms within a material sample resulting in data files with hundreds of millions of atoms. Understanding the nano-structural features hidden in these massive amounts of atomic data is a crucial analysis task for materials scientists. However, fast analysis capabilities for large APT workloads remains a critical bottleneck. In this paper, we present the design, implementation and detailed performance evaluations of a parallel software capable of efficiently performing extremely time-consuming correlation analyses of massive high density APT data. Starting with shared memory implementations to motivate our design choices, we extend the implementation to hybrid architectures keeping realistic APT workloads in mind. Detailed performance analyses of three different parallel implementations of the software are supported by empirical results on a Cray XC30 and a Cray XC40 architecture. Its usefulness is demonstrated by reducing the turnaround time of an end-to-end APT correlation analysis on 100 millions atoms by three orders of magnitude using 2048 MPI ranks on 1024 nodes (24 cores per node) of a Cray XC30. The software reported here equips material scientists for the first time with a high-speed scalable capability for efficient and timely analyses of massive APT data.

Lu, Hao↗

Response of the Dielectric Parameters of (110)SrTiO{sub 3} Films to the Formation of Ferroelectric Domains in Their Volume

Three-layer SrRuO{sub 3}/SrTiO{sub 3}/SrRuO{sub 3} heterostructures were grown by laser evaporation on (110)LaAlO{sub 3} substrates. Photolithography and ion etching are used to form plane-parallel film capacitors, in which a layer of strontium titanate is placed between two film electrodes of strontium ruthenate. Data on the structure and orientation of the intermediate SrTiO{sub 3} layer in the grown heterostructures were obtained. The variation of the dielectric constant and dielectric loss of the SrTiO{sub 3} intermediate layer upon varying the temperature and intensity of an external electric field was studied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electrical Capacitance Volume Tomography with High-Contrast Dielectrics

The Electrical Capacitance Volume Tomography (ECVT) system has been designed to complement the tools created to sense the presence of water in nonconductive spacecraft materials, by helping to not only find the approximate location of moisture but also its quantity and depth. The ECVT system has been created for use with a new image reconstruction algorithm capable of imaging high-contrast dielectric distributions. Rather than relying solely on mutual capacitance readings as is done in traditional electrical capacitance tomography applications, this method reconstructs high-resolution images using only the self-capacitance measurements. The image reconstruction method assumes that the material under inspection consists of a binary dielectric distribution, with either a high relative dielectric value representing the water or a low dielectric value for the background material. By constraining the unknown dielectric material to one of two values, the inverse math problem that must be solved to generate the image is no longer ill-determined. The image resolution becomes limited only by the accuracy and resolution of the measurement circuitry. Images were reconstructed using this method with both synthetic and real data acquired using an aluminum structure inserted at different positions within the sensing region. The cuboid geometry of the system has two parallel planes of 16 conductors arranged in a 4 4 pattern. The electrode geometry consists of parallel planes of copper conductors, connected through custom-built switch electronics, to a commercially available capacitance to digital converter. The figure shows two 4 4 arrays of electrodes milled from square sections of copper-clad circuit-board material and mounted on two pieces of glass-filled plastic backing, which were cut to approximately square shapes, 10 cm on a side. Each electrode is placed on 2.0-cm centers. The parallel arrays were mounted with the electrode arrays approximately 3 cm apart. The open ends were surrounded by a metal guard to reduce the sensitivity of the electrodes to outside interference and to help maintain the spacing between the arrays. Other uses for this innovation potentially include quantifying the amount of commodity remaining in the fuel and oxidizer tanks while on-orbit without having to fire spacecraft engines. Another orbit application is moisture sensing in plant-growth experiments because microgravity causes moisture in soil to distribute itself in unusual ways. At the moment, the hardware and image reconstruction technique may only be of interest to people involved in nondestructive evaluation. The reconstructed image takes almost a full week to reproduce with existing computer power. However, because computer power and speeds follows Moore s Law, execution times are likely to become acceptable within the next five to eight years. The code was written in Mathematica for dedicated use with the ECVT system. In its present form, it is not suitable to be used directly as a consumer product. However, the code could be likely improved by rewriting it in a compiled language such as C or Fortran.

Nurge, Mark↗