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At least 325 records · Page 18

Experiences with Cray multi-tasking

The issues involved in modifying an existing code for multitasking is explored. They include Cray extensions to FORTRAN, an examination of the application code under study, designing workable modifications, specific code modifications to the VAX and Cray versions, performance, and efficiency results. The finished product is a faster, fully synchronous, parallel version of the original program. A production program is partitioned by hand to run on two CPUs. Loop splitting multitasks three key subroutines. Simply dividing subroutine data and control structure down the middle of a subroutine is not safe. Simple division produces results that are inconsistent with uniprocessor runs. The safest way to partition the code is to transfer one block of loops at a time and check the results of each on a test case. Other issues include debugging and performance. Task startup and maintenance (e.g., synchronization) are potentially expensive.

Miya, E. N.↗

Characterization of robotics parallel algorithms and mapping onto a reconfigurable SIMD machine

The kinematics, dynamics, Jacobian, and their corresponding inverse computations are six essential problems in the control of robot manipulators. Efficient parallel algorithms for these computations are discussed and analyzed. Their characteristics are identified and a scheme on the mapping of these algorithms to a reconfigurable parallel architecture is presented. Based on the characteristics including type of parallelism, degree of parallelism, uniformity of the operations, fundamental operations, data dependencies, and communication requirement, it is shown that most of the algorithms for robotic computations possess highly regular properties and some common structures, especially the linear recursive structure. Moreover, they are well-suited to be implemented on a single-instruction-stream multiple-data-stream (SIMD) computer with reconfigurable interconnection network. The model of a reconfigurable dual network SIMD machine with internal direct feedback is introduced. A systematic procedure internal direct feedback is introduced. A systematic procedure to map these computations to the proposed machine is presented. A new scheduling problem for SIMD machines is investigated and a heuristic algorithm, called neighborhood scheduling, that reorders the processing sequence of subtasks to reduce the communication time is described. Mapping results of a benchmark algorithm are illustrated and discussed.

Lee, C. S. G.↗

Analysis of a Memory Device Failure

The recent failure of a vintage memory device presented a unique challenge to failure analysts. Normally device layouts, fabrication parameters and other technical information were available to assist the analyst in the analysis. However, this device was out of production for many years and the manufacturer was no longer in business, so the information was not available. To further complicate this analysis, the package leads were all but removed making additional electrical testing difficult. Under these conditions, new and innovative methods were used to analyze the failure. The external visual exam, radiography, PIND, and leak testing were performed with nominal results. Since electrical testing was precluded by the short lead lengths, the device was delidded to expose the internal structures for microscopic examination. No failure mechanism was identified. The available electrical data suggested an ESD or low level EOS type mechanism which left no visible surface damage. Due to parallel electrical paths, electrical probing on the chip failed to locate the failure site. Two non-destructive Scanning Electron Microscopy techniques, CIVA (Charge Induced Voltage Alteration) and EBIC (Electron Beam Induced Current), and a liquid crystal decoration technique which detects localized heating were employed to aid in the analysis. CIVA and EBIC isolated two faults in the input circuitry, and the liquid crystal technique further localized two hot spots in regions on two input gates. Removal of the glassivation and metallization revealed multiple failure sites located in the gate oxide of two input transistors suggesting machine (testing) induced damage.

Nicolas, David P.↗

Probing the nature of dark matter with accreted globular cluster streams

ABSTRACT The steepness of the central density profiles of dark matter (DM) in low-mass galaxy haloes (e.g. dwarf galaxies) is a powerful probe of the nature of DM. We propose a novel scheme to probe the inner profiles of galaxy subhaloes using stellar streams. We show that the present-day morphological and dynamical properties of accreted globular cluster (GC) streams – those produced from tidal stripping of GCs that initially evolved within satellite galaxies and later merged with the Milky Way (MW) – are sensitive to the central DM density profile and mass of their parent satellites. GCs that accrete within cuspy cold dark matter (CDM) subhaloes produce streams that are physically wider and dynamically hotter than streams that accrete inside cored subhaloes. A first comparison of MW streams ‘GD-1’ and ‘Jhelum’ (likely of accreted GC origin) with our simulations indicates a preference for cored subhaloes. If these results hold up in future data, the implication is that either the DM cusps were erased by baryonic feedback, or their subhaloes naturally possessed cored density profiles implying particle physics models beyond CDM. Moreover, accreted GC streams are highly structured and exhibit complex morphological features (e.g. parallel structures and ‘spurs’). This implies that the accretion scenario can naturally explain the recently observed peculiarities in some of the MW streams. We also propose a novel mechanism for forming ‘gaps’ in stellar streams when the remnant of the parent subhalo (which hosted the GC) later passes through the GC stream. This encounter can last a longer time (and have more of an impact) than the random encounters with DM subhaloes previously considered, because the GC stream and its parent subhalo are on similar orbits with small relative velocities. Current and future surveys of the MW halo will uncover numerous faint stellar streams and provide the data needed to substantiate our preliminary tests with this new probe of DM.

(Galaxy:) globular clusters: individual↗

The Severe Weather Outbreak of 10 November 2002: Lightning and Radar Analysis of Storms in the Deep South

On the afternoon and evening of 10 November 2002, the Midwest and Deep South were struck by a major outbreak of severe storms that produced some 80 tornadoes. In terms of number of tornadoes, this was the largest outbreak in the United States since November 1992. Some 32 of the tornadoes occurred in Tennessee, Mississippi, Alabama and Georgia, including several long-track killers. We use the North Alabama Lightning Mapping Array (LMA) and other data sources to perform a comprehensive analysis of the structure and evolution of the outbreak. Most of the Southern tornadoes occurred in isolated, fast-moving supercell storms that formed in warm, moist air ahead of a major cold front. Storms tended to form in lines parallel to storm cell motion, resulting in many communities being hit multiple times by severe storms that evening. Supercells in Tennessee produced numerous strong tornadoes with short to medium-length track paths, while the supercells further south produced several very long-track tornadoes. Radar data indicate that the Tennessee storms tended to split frequently, apparently limiting their ability to sustain long-lived tornadoes, while storms further south split at most one time. The differences between these storms appear to be related to the presence of stronger jetstream winds in Tennessee relative to those present in Mississippi, Alabama and Georgia. LMA-derived flash rates associated with most of the supercell storm cores were about 1-2 flashes per second. Rapid increases in lightning rates (or "jumps") occurred prior to tornado touchdown in many instances. Lightning "holes" (lightning-free regions associated with the echo-free vault) occurred in two of the Tennessee supercells. The complexity of the relationship between lightning and storm severity is revealed by the behavior of one Alabama supercell, which produced a peak flash rate of nearly 14 flashes per second, well after the end of its long-track tornado, while interacting and ultimately merging with a daughter supercell on its southwest flank. Close examination of this powerful storm indicates that its prodigious flash rate was the result of strong flash activity over an unusually large area, rather than a concentrated core of extremely high flash rate activity.

Buechler, D. E.↗

Highly parallel structured adaptive mesh refinement using parallel language-based approaches

Adaptive mesh refinement (AMR) calculations carried out on structured meshes play an exceedingly important role in several areas of science and engineering. A strategy for using Fortran 90 in an object-oriented fashion is presented. This permits AMR applications to be expressed in terms of familiar abstractions that are natural to the process of solving AMR hierarchies. The OpenMP features that are useful for parallel processing of AMR hierarchies in a load balanced fashion on multiprocessors is described.

computational↗

Integrating remote sensing techniques at Cuprite, Nevada: AVIRIS, Thematic Mapper, and field spectroscopy

The Cuprite mining district in southwestern Nevada has become a test site for remote sensing studies with numerous airborne scanners and ground sensor data sets collected over the past fifteen years. Structurally, the Cuprite region can be divided into two areas with slightly different alteration and mineralogy. These zones lie on either side of a postulated low-angle structural discontinuity that strikes nearly parallel to US Route 95. Hydrothermal alternation at Cuprite was classified into three major zones: silicified, opalized, and argillized. These alteration types form a bulls-eye pattern east of the highway and are more linear on the west side of the highway making a striking contrast from the air and the imagery. Cuprite is therefore an ideal location for remote sensing research as it exhibits easily identified hydrothermal zoning, is relatively devoid of vegetation, and contains a distinctive spectrally diagnostic mineral suite including the ammonium feldspar buddingtonite, several types of alunite, different jarosites, illite, kaolinite, smectite, dickite, and opal. This present study brings a new dimension to these previous remote sensing and ground data sets compiled for Cuprite. The development of a higher resolution field spectrometer now provides the capability to combine extensive in-situ mineralogical data with a new geologic field survey and detailed Airborne Visible/Infrared Imaging Spectrometers (AVIRIS) images. The various data collection methods and the refinement of the integrated techniques are discussed.

Hill, Bradley↗

Using SpF to Achieve Petascale for Legacy Pseudospectral Applications

Pseudospectral (PS) methods possess a number of characteristics (e.g., efficiency, accuracy, natural boundary conditions) that are extremely desirable for dynamo models. Unfortunately, dynamo models based upon PS methods face a number of daunting challenges, which include exposing additional parallelism, leveraging hardware accelerators, exploiting hybrid parallelism, and improving the scalability of global memory transposes. Although these issues are a concern for most models, solutions for PS methods tend to require far more pervasive changes to underlying data and control structures. Further, improvements in performance in one model are difficult to transfer to other models, resulting in significant duplication of effort across the research community. We have developed an extensible software framework for pseudospectral methods called SpF that is intended to enable extreme scalability and optimal performance. Highlevel abstractions provided by SpF unburden applications of the responsibility of managing domain decomposition and load balance while reducing the changes in code required to adapt to new computing architectures. The key design concept in SpF is that each phase of the numerical calculation is partitioned into disjoint numerical kernels that can be performed entirely inprocessor. The granularity of domain decomposition provided by SpF is only constrained by the datalocality requirements of these kernels. SpF builds on top of optimized vendor libraries for common numerical operations such as transforms, matrix solvers, etc., but can also be configured to use open source alternatives for portability. SpF includes several alternative schemes for global data redistribution and is expected to serve as an ideal testbed for further research into optimal approaches for different network architectures. In this presentation, we will describe our experience in porting legacy pseudospectral models, MoSST and DYNAMO, to use SpF as well as present preliminary performance results provided by the improved scalability.

DYNAMO↗

SpF: Enabling Petascale Performance for Pseudospectral Dynamo Models

Pseudospectral (PS) methods possess a number of characteristics (e.g., efficiency, accuracy, natural boundary conditions) that are extremely desirable for dynamo models. Unfortunately, dynamo models based upon PS methods face a number of daunting challenges, which include exposing additional parallelism, leveraging hardware accelerators, exploiting hybrid parallelism, and improving the scalability of global memory transposes. Although these issues are a concern for most models, solutions for PS methods tend to require far more pervasive changes to underlying data and control structures. Further, improvements in performance in one model are difficult to transfer to other models, resulting in significant duplication of effort across the research community.We have developed an extensible software framework for pseudospectral methods called SpF that is intended to enable extreme scalability and optimal performance. High-level abstractions provided by SpF unburden applications of the responsibility of managing domain decomposition and load balance while reducing the changes in code required to adapt to new computing architectures. The key design concept in SpF is that each phase of the numerical calculation is partitioned into disjoint numerical kernels that can be performed entirely in-processor. The granularity of domain-decomposition provided by SpF is only constrained by the data-locality requirements of these kernels. SpF builds on top of optimized vendor libraries for common numerical operations such as transforms, matrix solvers, etc., but can also be configured to use open source alternatives for portability. SpF includes several alternative schemes for global data redistribution and is expected to serve as an ideal testbed for further research into optimal approaches for different network architectures.In this presentation, we will describe the basic architecture of SpF as well as preliminary performance data and experience with adapting legacy dynamo codes. We will conclude with a discussion of planned extensions to SpF that will provide pseudospectral applications with additional flexibility with regard to time integration, linear solvers, and discretization in the radial direction.

Pseudospectral (PS)↗

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oblique, parallel, and quasi-parallel morphology of collisionless shocks

The question as to whether nonperpendicular, oblique shocks are disguised in the bow shock system by its infinite radius-of-curvature is addressed in light of the most recent data, which indicate that the quasi-perpendicular/quasi-parallel division is not merely real, but intrinsic. An attempt is presently made to summarize observational results on nonperpendicular shocks with the express intention of understanding the shock as an interactive structure that is dependent on the geometry of shock propagation. A foundation for the reconciliation of some rather complex or apparently contradictory quasi-parallel features is suggested.

Greenstadt, Eugene W.↗

Mesoscale modeling and semi-analytical approach for the microstructure-aware effective thermal conductivity of porous polygranular materials

Here we established a comprehensive modeling approach for investigating the microstructure-aware effective thermal conductivity ($κ_{eff}$) for porous microstructures containing solid particles and gaseous pores. Our approach combines the mesoscale computational modeling framework and the semi-analytical method, allowing for efficient prediction of $κ_{eff}$ for realistic porous microstructures, while considering complicated microstructural thermal conduction pathways effectively in the prediction. We used the diffuse-interface mesoscale computational model to generate extensive simulated $κ_{eff}$ data for realistic digital representations of microstructures with wide ranges of porosity ($f_p$), thermal conductivity of the gas phase ($κ_g$), and thermal conductivity of the solid phase ($κ_s$). From the simulated data, we identified two property variation regimes for $κ_{eff}$: (1) a slow $κ_{eff}$ increase for $κ_s ~ κ_g$; and (2) a faster $κ_{eff}$ increase for $κ_s \gg κ_g$. To capture the key features of the relationship between the microstructure and $κ_{eff}$, we derived a semi-analytical model by introducing structure and intensification factors. The two new factors incorporate the calibrated effective contribution of the solid volume with $κ_s$ and additional interfacial effects into the prediction of $κ_{eff}$, respectively, allowing for consideration of parallel, serial, and interfacial conduction mechanisms effectively. Using the selected simulation data, we quantified key model parameters within the semi-analytical model and verified that the parameterized model exhibits excellent agreement with simulated $κ_{eff}$ for the entire range of the parameter space.

36 MATERIALS SCIENCE↗

An asynchronous parallel high-throughput model calibration framework for crystal plasticity finite element constitutive models

Crystal plasticity finite element model (CPFEM) is a powerful numerical simulation in the integrated computational materials engineering toolboxes that relates microstructures to homogenized materials properties and establishes the structure–property linkages in computational materials science. However, to establish the predictive capability, one needs to calibrate the underlying constitutive model, verify the solution and validate the model prediction against experimental data. Bayesian optimization (BO) has stood out as a gradient-free efficient global optimization algorithm that is capable of calibrating constitutive models for CPFEM. Here in this paper, we apply a recently developed asynchronous parallel constrained BO algorithm to calibrate phenomenological constitutive models for stainless steel 304 L, Tantalum, and Cantor high-entropy alloy.

304L stainless steel↗

Portable Parallel Algorithms and Frameworks for Exascale Graph Analytics

Graphs (or networks) are a tool used to model the interactions among various entities. Efficiently processing large graphs has recently attracted significant attention due to the applications of graphs in various domains, such as biology, chemistry, and cyber-security. Analyzing the structure and properties of these graphs is an important component of many scientific computing pipelines. With the explosion in the volume of data, graphs have become very large and can contain hundreds of billions of vertices and trillions of edges. Therefore, it is crucial to develop high-performance methods to enable graph analysis to be done quickly and energy-efficiently. Furthermore, these solutions should be highly parallel in order to take advantage of modern parallel machines. However, designing efficient solutions is not enough. With the wide variety of computing environments available, each with different programmability and performance characteristics, it is necessary to develop solutions that are portable in terms of both performance (i.e., provide theoretical guarantees) and programmability (i.e., provide high level abstractions).

97 MATHEMATICS AND COMPUTING↗

Parallelization and Performance Portability in Hydrodynamics Codes

With the eve of Exascale computing, performance and portability are at the forefront of all scientific codes. Adding more cores and more energy to a system is no longer a sustainable way to achieve performance, and extra effort must now be made to improve performance in all areas of code and code development. Using hydrodynamic codes as a basis, this work explores numerous techniques to achieve performance in different ways. Adaptive mesh refinement (AMR) is a necessary technique to improve memory optimization in mesh-based simulations. However it is invasive and conventionally difficult to integrate into existing applications, so we present a new branch of AMR to create a smooth transition to these optimizations, which not only improves performance, but also greatly reduces developer effort. We introduce the concept of this improvement as Phantom-Cell AMR, and assess theoretically the improvements, as well as present an application of its use. Other work included involves and investigation into an efficient data structure that ensures optimal memory layout for cache performance, with a target of making codes performant and portable across all architectures. All of the work targets both performance and portability, not just on CPU hardware, but specifically across GPU architectures. Parallel performance is key to all of the methods presented, but the research makes a great effort to improve the portability of all applications to prepare for current high performance computing systems and those on the horizon.

97 MATHEMATICS AND COMPUTING↗

OpenMP in VASP: Threading and SIMD

Abstract The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process‐level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread‐ and data‐level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data‐level parallelism through OpenMP SIMD constructs together with a generic high‐level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI‐only version as well as a 2× increased performance of collective operations using the multiple‐endpoint MPI feature. The high‐level vector coding scheme applied to VASP's general gradient approximation routine gives up 9× performance gain on AVX512 platforms with the Intel compiler.

Wende, Florian↗

Data Mining and Visualization of High-Dimensional ICME Data for Additive Manufacturing

Integrated computational materials engineering (ICME) methods combining CALPHAD with process-based simulations can produce rich, high-dimensional data for alloy and process design. In ICME methods for metallurgical applications, the visualization and interpretation of such high-dimensional data has previously been through heat maps represented in 2 or 3 dimensions. While such an approach is ideal when one variable is varied at a time, in the case of high-dimensional data with multiple variables varied simultaneously, as is the case in additive manufacturing, interpreting the trends through two- or three-dimensional heat maps becomes challenging. Here, we propose a strategy of mixed visual data mining and quantitative analysis for high-dimensional metallurgical and process data using high-throughput thermodynamic calculations. Two case studies show the application of the proposed approach. The first case study investigated the effects of feedstock chemistry on the δ ferrite formation in 316L stainless steel powders used for binder jet additive manufacturing. The second case study linked Scheil–Gulliver calculations to a process model for dissimilar joining of aluminum alloys 5356 and 6111 during laser hot-wire additive manufacturing. Both cases contained thousands of calculated data points, showcasing the utility of visual data analysis through parallel coordinate plotting, Pearson correlation coefficient matrices, and scatter matrices compared to traditional process maps. These visualization techniques can be extended to many additive manufacturing problems to capture process–structure–property relationships for additively manufactured components.

36 MATERIALS SCIENCE↗

Flow physics

A discussion is presented on the coupling of computational analysis and experiment. It is believed that this coupling is critical in developing new aerodynamic insights. Additionally, new methods for analyzing and interpreting data are discussed. These methods need to be developed in small-scale research studies and then applied to large-scale technology programs. The specific objectives of this program are threefold: (1) provide definitive data sets for the assessment of numerical simulations to the Navier-Stokes equations; (2) incorporate advanced instrumentation to measure the spatial and temporal structure of fluid flows; and (3) develop true parallelism between computational and experimental research using the 'scientific workstation' concept. The discussion is presented in viewgraph form.

Davis, Sanford↗