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At least 865 records · Page 48

The 'Biologically-Inspired Computing' Column

The field of Biology changed dramatically in 1953, with the determination by Francis Crick and James Dewey Watson of the double helix structure of DNA. This discovery changed Biology for ever, allowing the sequencing of the human genome, and the emergence of a "new Biology" focused on DNA, genes, proteins, data, and search. Computational Biology and Bioinformatics heavily rely on computing to facilitate research into life and development. Simultaneously, an understanding of the biology of living organisms indicates a parallel with computing systems: molecules in living cells interact, grow, and transform according to the "program" dictated by DNA. Moreover, paradigms of Computing are emerging based on modelling and developing computer-based systems exploiting ideas that are observed in nature. This includes building into computer systems self-management and self-governance mechanisms that are inspired by the human body's autonomic nervous system, modelling evolutionary systems analogous to colonies of ants or other insects, and developing highly-efficient and highly-complex distributed systems from large numbers of (often quite simple) largely homogeneous components to reflect the behaviour of flocks of birds, swarms of bees, herds of animals, or schools of fish. This new field of "Biologically-Inspired Computing", often known in other incarnations by other names, such as: Autonomic Computing, Pervasive Computing, Organic Computing, Biomimetics, and Artificial Life, amongst others, is poised at the intersection of Computer Science, Engineering, Mathematics, and the Life Sciences. Successes have been reported in the fields of drug discovery, data communications, computer animation, control and command, exploration systems for space, undersea, and harsh environments, to name but a few, and augur much promise for future progress.

Hinchey, Mike↗

Operational experience and R&D results using the Google Cloud for High-Energy Physics in the ATLAS experiment

The ATLAS experiment at CERN relies on a Worldwide Distributed Computing Grid infrastructure to support its physics program at the Large Hadron Collider. ATLAS has integrated cloud computing resources to complement its Grid infrastructure and conducted an R&D program on Google Cloud Platform. These initiatives leverage key features of commercial cloud providers: lightweight configuration and operation, elasticity and availability of diverse infrastructures. Here this paper examines the seamless integration of cloud computing services as a conventional Grid site within the ATLAS workflow management and data management systems, while also offering new setups for interactive, parallel analysis. It underscores pivotal results that enhance the on-site computing model and outlines several R&D projects that have benefited from large-scale, elastic resource provisioning models. Furthermore, this study discusses the impact of cloud-enabled R&D projects in three domains: accelerators and AI/ML, ARM CPUs and columnar data analysis techniques.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Parallel Load Balancing for Adaptive Unstructured Meshes

Mesh adaption is a powerful tool for efficient unstructured-grid computations but causes load imbalance among processors on a parallel machine. We describe a novel method to dynamically balance the processor workloads with a global view. Mesh question, repartitioning, processor assignment, and remapping are critical components of the framework that must be accomplished rapidly and efficiently so as not to cause a significant overhead to the numerical simulation. A data redistribution model will also be presented that predicts the remapping cost. This model is required to determine whether the gain from a balanced workload distribution offsets the cost of data movement. Results presented will demonstrate that this is an effective dynamic load balancing strategy which remains viable on a large number of processors.

Biswas, Rupak↗

Orbit-modulated transport and sources in time-dependent plasmas

The orbit-modulation framework for steady-state ion-orbit boundary fluxes is reformulated to apply to time-dependent plasmas. The new formulation can quantify the extent to which orbit fluxes are affected by the time dependence of the distribution function, and may be applied both to time-dependent physical scenarios and to computationally expensive simulations that are unable to reach a true steady state. As the system tends to a time-independent state, the orbit-loss fluxes approach their steady-state values, which are determined entirely by upstream transport (turbulent and collisional) and upstream sources and sinks. This result holds for the fluxes of any moments that are expressible in terms of the invariants that determine the orbits, including parallel toroidal angular momentum.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

MEUMAPPS (Microstructure Evolution Using Massively Parallel Phase-field Simulations)

The software “MEUMAPPS” is a h high-performance computing code used to simulate microstructure evolution associated with diffusional solid-state transformations in structural alloys. Understanding microstructure evolution during thermo-mechanical processing of structural alloys is the first step towards designing and processing alloys for specific applications by meeting property requirements demanded by the application. In this instance, the code is an important component in predicting processing-structure linkages during additive manufacturing of structural alloys as a function of processing parameters and alloy composition used in an additive manufacturing process. The code provides a detailed three-dimensional distribution of different types of phases / constituents and their morphologies, as well as the compositions of these phases that make up the microstructure. The microstructure is simulated by solving the governing partial differential equations using a Fourier Spectral Method.

Radhakrishnan, Balasubram↗

Evolution of the SLATE linear algebra library

SLATE (Software for Linear Algebra Targeting Exascale) is a distributed, dense linear algebra library targeting both CPU-only and GPU-accelerated systems, developed over the course of the Exascale Computing Project (ECP). While it began with several documents setting out its initial design, significant design changes occurred throughout its development. In some cases, these were anticipated: an early version used a simple consistency flag that was later replaced with a full-featured consistency protocol. In other cases, performance limitations and software and hardware changes prompted a redesign. Sequential communication tasks were parallelized; host-to-host MPI calls were replaced with GPU device-to-device MPI calls; more advanced algorithms such as Communication Avoiding LU and the Random Butterfly Transform (RBT) were introduced. Early choices that turned out to be cumbersome, error prone, or inflexible have been replaced with simpler, more intuitive, or more flexible designs. Applications have been a driving force, prompting a lighter weight queue class, nonuniform tile sizes, and more flexible MPI process grids. Of paramount importance has been building a portable library that works across several different GPU architectures – AMD, Intel, and NVIDIA – while keeping a clean and maintainable codebase. Here we explore the evolving design choices and their effects, both in terms of performance and software sustainability.

Gates, Mark↗

Flexible language constructs for large parallel programs

The goal of the research described is to develop flexible language constructs for writing large data parallel numerical programs for distributed memory (MIMD) multiprocessors. Previously, several models have been developed to support synchronization and communication. Models for global synchronization include SIMD (Single Instruction Multiple Data), SPMD (Single Program Multiple Data), and sequential programs annotated with data distribution statements. The two primary models for communication include implicit communication based on shared memory and explicit communication based on messages. None of these models by themselves seem sufficient to permit the natural and efficient expression of the variety of algorithms that occur in large scientific computations. An overview of a new language that combines many of these programming models in a clean manner is given. This is done in a modular fashion such that different models can be combined to support large programs. Within a module, the selection of a model depends on the algorithm and its efficiency requirements. An overview of the language and discussion of some of the critical implementation details is given.

Rosing, Matthew↗

Additive Manufactured Composite Phase-Change Material for Thermal Energy Storage Applications

Phase-change materials play a critical role in industrial energy storage applications to drive efficiency improvements, thermal energy management, and carbon emissions reductions. Recently, it has been shown that rapid solidification of alloys with metastable immiscibility in the liquid phase has the potential to form unique microstructures in which a low-melting phase is uniformly distributed in a high-melting matrix. This feature can be exploited using additive manufacturing to produce components with complex geometries containing such unique phase-change microstructures. Phase-field simulations utilizing high-performance computing were used to provide a detailed description of the evolution of the active phase during service in terms of their morphology and composition in different polycrystalline matrix grain morphologies that are typically produced during additive manufacturing. Phase field simulations were performed using, MEUMAPPS-SL (Microstructure Evolution Using Massively Parallel Phase-field Simulations – Solid Liquid) code that was developed in-house by the Oak Ridge National Laboratory. The simulations utilized the capabilities of the Kestrel supercomputer at the National Renewable Energy Laboratory. The simulation results were compared with experimental results generated at Siemens Energy, Inc. The results indicate that the kinetics of liquid spreading along grain boundaries is largely determined by the mobility of the triple line along the intersection of the grain boundary liquid and the grain boundary plane.

25 ENERGY STORAGE↗

Maximum likelihood estimation for distributed parameter models of flexible spacecraft

A distributed-parameter model of the NASA Solar Array Flight Experiment spacecraft structure is constructed on the basis of measurement data and analyzed to generate a priori estimates of modal frequencies and mode shapes. A Newton-Raphson maximum-likelihood algorithm is applied to determine the unknown parameters, using a truncated model for the estimation and the full model for the computation of the higher modes. Numerical results are presented in a series of graphs and briefly discussed, and the significant improvement in computation speed obtained by parallel implementation of the method on a supercomputer is noted.

Taylor, L. W., Jr.↗

Computational heat transfer analysis for oscillatory channel flows

An accurate finite-difference scheme has been utilized to investigate oscillatory, laminar and incompressible flow between two-parallel-plates and in circular tubes. The two-parallel-plates simulate the regenerator of a free-piston Stirling engine (foil type regenerator) and the channel wall was included in the analysis (conjugate heat transfer problem). The circular tubes simulate the cooler and heater of the engine with an isothermal wall. The study conducted covered a wide range for the maximum Reynolds number (from 75 to 60,000), Valensi number (from 2.5 to 700), and relative amplitude of fluid displacement (0.714 and 1.34). The computational results indicate a complex nature of the heat flux distribution with time and axial location in the channel. At the channel mid-plane we observed two thermal cycles (out of phase with the flow) per each flow cycle. At this axial location the wall heat flux mean value, amplitude and phase shift with the flow are dependent upon the maximum Reynolds number, Valensi number and relative amplitude of fluid displacement. At other axial locations, the wall heat flux distribution is more complex.

Ibrahim, Mounir↗

Experimental and Computational Analysis of a Rotating Detonation Combustor

Rotating detonation combustor (RDC) research has progressed along parallel experimental and computational paths with limited opportunities for validation. Validation is a crucial step to ensure RDC simulations provide an accurate representation of the physical phenomena, and thus, can be used with confidence for design optimization in different applications. In this study, data from a quasi-two-dimensional computational fluid dynamic simulation in an annular RDC are compared with experimental measurements including particle image velocimetry at 100 kHz. Results show good agreement between measured and simulated dynamic pressures, Chapman-Jouguet speeds, and static pressure distributions. Velocity measurements at the annulus exit show good temporal and quantitative agreement with simulations including spikes from the passing shock.

Detonation↗

Heating and acceleration of ions with Kappa distribution functions by low‐frequency Alfvén wave

Abstract Heating and acceleration of ions with Kappa distribution functions (with parameter ) in low‐beta plasmas, by a low‐frequency Alfvén wave, is investigated using test‐particle simulations, yielding interesting new results. As long as the Alfvén wave amplitude is sufficiently large, the computed net heating energy of ions becomes independent of the wave frequency and amplitude, always approaching the same value of . The eventual energy of ions is dictated only by the initial ion energy and the ratio of the magnetic field energy density to the plasma density. The heating effect of the Kappa ions increases with . During the heating process, the ions are picked up by the Alfvén wave and pitch angle scattered, forming a quasi‐isotropic spherical shell velocity distribution. The Kappa ions are accelerated in the parallel direction, reaching a bulk flow speed roughly equal to the local Alfvén speed. Higher ‐value in the initial Kappa distribution leads to faster saturation. The above results may explain certain features of the ion heating and acceleration in the solar wind and corona.

Li, Kehua↗

Integrating PGAS and MPI-based Graph Analysis

This project demonstrates that Chapel programs can interface with MPI-based libraries written in C++ without storing multiple copies of shared data. Chapel is a language for productive parallel computing using global address spaces (PGAS). We identified two approaches to interface Chapel code with the MPI-based Grafiki and Trilinos libraries. The first uses a single Chapel executable to call a C function that interacts with the C++ libraries. The second uses the mmap function to allow separate executables to read and write to the same block of memory on a node. We also encapsulated the second approach in Docker/Singularity containers to maximize ease of use. Comparisons of the two approaches using shared and distributed memory installations of Chapel show that both approaches provide similar scalability and performance.

97 MATHEMATICS AND COMPUTING↗

Checkpoint-based forward recovery using lookahead execution and rollback validation in parallel and distributed systems

This thesis studies a forward recovery strategy using checkpointing and optimistic execution in parallel and distributed systems. The approach uses replicated tasks executing on different processors for forwared recovery and checkpoint comparison for error detection. To reduce overall redundancy, this approach employs a lower static redundancy in the common error-free situation to detect error than the standard N Module Redundancy scheme (NMR) does to mask off errors. For the rare occurrence of an error, this approach uses some extra redundancy for recovery. To reduce the run-time recovery overhead, look-ahead processes are used to advance computation speculatively and a rollback process is used to produce a diagnosis for correct look-ahead processes without rollback of the whole system. Both analytical and experimental evaluation have shown that this strategy can provide a nearly error-free execution time even under faults with a lower average redundancy than NMR.

Long, Junsheng↗

Productive Programming of Distributed Systems with the SHAD C++ Library

High-performance computing (HPC) is often perceived as a matter of making large-scale systems (e.g., clusters) run as fast as possible, regardless the required programming effort. However, the idea of "bringing HPC to the masses" has recently emerged. Inspired by this vision, we have designed SHAD, the Scalable High-performance Algorithms and Data-structures library. SHAD is open source software, written in C++, for C++ developers. Unlike other HPC libraries for distributed systems, which rely on SPMD models, SHAD adopts a shared-memory programming abstraction, to make C++ programmers feel at home. Underneath, SHAD manages tasking and data-movements, moving the computation where data resides and taking advantage of asynchrony to tolerate network latency. At the bottom of his stack, SHAD can interface with multiple runtime systems: this not only improves developer’s productivity, by hiding the complexity of such software and of the underlying hardware, but also greatly enhance code portability. Thanks to its abstraction layers, SHAD can indeed target different systems, ranging from laptops to HPC clusters, without any need for modifying the user-level code. We have prototyped and open-sourced the implementation of (a subset of) the C++ standard library (STL) targeting multi-node HPC clusters. Our work allows plain STL-based C++ code to scale on HPC systems, with no need for rewriting the code to exploit the complex hardware. SHAD is available under Apache v2 License at https://github.com/pnnl/SHAD. In this paper we overview the design of the SHAD library, depicting its main components: runtime systems abstractions for tasking; parallel and distributed data-structures; STL-compliant interfaces and algorithms.

Castellana, Vito G.↗

Satellite Image Mosaic Engine

A computer program automatically builds large, full-resolution mosaics of multispectral images of Earth landmasses from images acquired by Landsat 7, complete with matching of colors and blending between adjacent scenes. While the code has been used extensively for Landsat, it could also be used for other data sources. A single mosaic of as many as 8,000 scenes, represented by more than 5 terabytes of data and the largest set produced in this work, demonstrated what the code could do to provide global coverage. The program first statistically analyzes input images to determine areas of coverage and data-value distributions. It then transforms the input images from their original universal transverse Mercator coordinates to other geographical coordinates, with scaling. It applies a first-order polynomial brightness correction to each band in each scene. It uses a data-mask image for selecting data and blending of input scenes. Under control by a user, the program can be made to operate on small parts of the output image space, with check-point and restart capabilities. The program runs on SGI IRIX computers. It is capable of parallel processing using shared-memory code, large memories, and tens of central processing units. It can retrieve input data and store output data at locations remote from the processors on which it is executed.

Plesea, Lucian↗

Independent pixel and Monte Carlo estimates of stratocumulus albedo

Monte Carlo radiative transfer methods are employed here to estimate the plane-parallel albedo bias for marine stratocumulus clouds. This is the bias in estimates of the mesoscale-average albedo, which arises from the assumption that cloud liquid water is uniformly distributed. The authors compare such estimates with those based on a more realistic distribution generated from a fractal model of marine stratocumulus clouds belonging to the class of 'bounded cascade' models. In this model the cloud top and base are fixed, so that all variations in cloud shape are ignored. The model generates random variations in liquid water along a single horizontal direction, forming fractal cloud streets while conserving the total liquid water in the cloud field. The model reproduces the mean, variance, and skewness of the vertically integrated cloud liquid water, as well as its observed wavenumber spectrum, which is approximately a power law. The Monte Carlo method keeps track of the three-dimensional paths solar photons take through the cloud field, using a vectorized implementation of a direct technique. The simplifications in the cloud field studied here allow the computations to be accelerated. The Monte Carlo results are compared to those of the independent pixel approximation, which neglects net horizontal photon transport. Differences between the Monte Carlo and independent pixel estimates of the mesoscale-average albedo are on the order of 1% for conservative scattering, while the plane-parallel bias itself is an order of magnitude larger. As cloud absorption increases, the independent pixel approximation agrees even more closely with the Monte Carlo estimates. This result holds for a wide range of sun angles and aspect ratios. Thus, horizontal photon transport can be safely neglected in estimates of the area-average flux for such cloud models. This result relies on the rapid falloff of the wavenumber spectrum of stratocumulus, which ensures that the smaller-scale variability, where the radiative transfer is more three-dimensional, contributes less to the plane-parallel albedo bias than the larger scales, which are more variable. The lack of significant three-dimensional effects also relies on the assumption of a relatively simple geometry. Even with these assumptions, the independent pixel approximation is accurate only for fluxes averaged over large horizontal areas, many photon mean free paths in diameter, and not for local radiance values, which depend strongly on the interaction between neighboring cloud elements.

Cahalan, Robert F.↗

2-D Modeling of Nanoscale MOSFETs: Non-Equilibrium Green's Function Approach

We have developed physical approximations and computer code capable of realistically simulating 2-D nanoscale transistors, using the non-equilibrium Green's function (NEGF) method. This is the most accurate full quantum model yet applied to 2-D device simulation. Open boundary conditions and oxide tunneling are treated on an equal footing. Electrons in the ellipsoids of the conduction band are treated within the anisotropic effective mass approximation. Electron-electron interaction is treated within Hartree approximation by solving NEGF and Poisson equations self-consistently. For the calculations presented here, parallelization is performed by distributing the solution of NEGF equations to various processors, energy wise. We present simulation of the "benchmark" MIT 25nm and 90nm MOSFETs and compare our results to those from the drift-diffusion simulator and the quantum-corrected results available. In the 25nm MOSFET, the channel length is less than ten times the electron wavelength, and the electron scattering time is comparable to its transit time. Our main results are: (1) Simulated drain subthreshold current characteristics are shown, where the potential profiles are calculated self-consistently by the corresponding simulation methods. The current predicted by our quantum simulation has smaller subthreshold slope of the Vg dependence which results in higher threshold voltage. (2) When gate oxide thickness is less than 2 nm, gate oxide leakage is a primary factor which determines off-current of a MOSFET (3) Using our 2-D NEGF simulator, we found several ways to drastically decrease oxide leakage current without compromising drive current. (4) Quantum mechanically calculated electron density is much smaller than the background doping density in the poly silicon gate region near oxide interface. This creates an additional effective gate voltage. Different ways to. include this effect approximately will be discussed.

Svizhenko, Alexei↗