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At least 91 records · Page 5

Exploiting parallel computing with limited program changes using a network of microcomputers

Network computing and multiprocessor computers are two discernible trends in parallel processing. The computational behavior of an iterative distributed process in which some subtasks are completed later than others because of an imbalance in computational requirements is of significant interest. The effects of asynchronus processing was studied. A small existing program was converted to perform finite element analysis by distributing substructure analysis over a network of four Apple IIe microcomputers connected to a shared disk, simulating a parallel computer. The substructure analysis uses an iterative, fully stressed, structural resizing procedure. A framework of beams divided into three substructures is used as the finite element model. The effects of asynchronous processing on the convergence of the design variables are determined by not resizing particular substructures on various iterations.

Rogers, J. L., Jr.↗

A Methodology for the Design and Verification of Globally Asynchronous/Locally Synchronous Architectures

Recent advanced in model-checking have made it practical to formally verify the correctness of many complex synchronous systems (i.e., systems driven by a single clock). However, many computer systems are implemented by asynchronously composing several synchronous components, where each component has its own clock and these clocks are not synchronized. Formal verification of such Globally Asynchronous/Locally Synchronous (GA/LS) architectures is a much more difficult task. In this report, we describe a methodology for developing and reasoning about such systems. This approach allows a developer to start from an ideal system specification and refine it along two axes. Along one axis, the system can be refined one component at a time towards an implementation. Along the other axis, the behavior of the system can be relaxed to produce a more cost effective but still acceptable solution. We illustrate this process by applying it to the synchronization logic of a Dual Fight Guidance System, evolving the system from an ideal case in which the components do not fail and communicate synchronously to one in which the components can fail and communicate asynchronously. For each step, we show how the system requirements have to change if the system is to be implemented and prove that each implementation meets the revised system requirements through modelchecking.

Miller, Steven P.↗

Investigation of periodically driven systems by x-ray absorption spectroscopy using asynchronous data collection mode

Here, we report the development, testing, and demonstration of a setup for modulation excitation spectroscopy experiments at the Inner Shell Spectroscopy beamline of National Synchrotron Light Source - II. A computer algorithm and dedicated software were developed for asynchronous data processing and analysis. We demonstrate the reconstruction of X-ray absorption spectra for different time points within the modulation pulse using a model system. This setup and the software are intended for a broad range of functional materials which exhibit structural and/or electronic responses to the external stimulation, such as catalysts, energy and battery materials, and electromechanical devices.

36 MATERIALS SCIENCE↗

Accelerating DCA++ (Dynamical Cluster Approximation) Scientific Application on the Summit supercomputer

Optimizing scientific applications on today’s accelerator-based high performance computing systems can be challenging, especially when multiple GPUs and CPUs with heterogeneous memories and persistent non-volatile memories are present. An example is Summit, an accelerator-based system at the Oak Ridge Leadership Computing Facility (OLCF) that is rated as the world’s fastest supercomputer to-date. New strategies are thus needed to expose the parallelism in legacy applications, while being amenable to efficient mapping to the underlying architecture.In this paper we discuss our experiences and strategies to port a scientific application, DCA++, to Summit. DCA++ is a highperformance research application that solves quantum manybody problems with a cutting edge quantum cluster algorithm, the dynamical cluster approximation.Our strategies aim to synergize the strengths of the different programming models in the code. These include: (a) streamlining the interactions between the CPU threads and the GPUs, (b) implementing computing kernels on the GPUs and decreasing CPU-GPU memory transfers, (c) allowing asynchronous GPU communications, and (d) increasing compute intensity by combining linear algebraic operations.Full-scale production runs using all 4600 Summit nodes attained a peak performance of 73.5 PFLOPS with a mixed precision implementation.We observed a perfect strong and weak scaling for the quantum Monte Carlo solver in DCA++, while encountering about 2× input/output (I/O) and MPI communication overhead on the time-to-solution for the full machine run. Our hardware agnostic optimizations are designed to alleviate the communication and I/O challenges observed, while improving the compute intensity and obtaining optimal performance on a complex, hybrid architecture like Summit.

Balduzzi, Giovanni↗

A Parallel Particle Swarm Optimization Algorithm Accelerated by Asynchronous Evaluations

A parallel Particle Swarm Optimization (PSO) algorithm is presented. Particle swarm optimization is a fairly recent addition to the family of non-gradient based, probabilistic search algorithms that is based on a simplified social model and is closely tied to swarming theory. Although PSO algorithms present several attractive properties to the designer, they are plagued by high computational cost as measured by elapsed time. One approach to reduce the elapsed time is to make use of coarse-grained parallelization to evaluate the design points. Previous parallel PSO algorithms were mostly implemented in a synchronous manner, where all design points within a design iteration are evaluated before the next iteration is started. This approach leads to poor parallel speedup in cases where a heterogeneous parallel environment is used and/or where the analysis time depends on the design point being analyzed. This paper introduces an asynchronous parallel PSO algorithm that greatly improves the parallel e ciency. The asynchronous algorithm is benchmarked on a cluster assembled of Apple Macintosh G5 desktop computers, using the multi-disciplinary optimization of a typical transport aircraft wing as an example.

Venter, Gerhard↗

Integrating a ponderomotive guiding center algorithm into a quasi-static particle-in-cell code based on azimuthal mode decomposition

High fidelity modeling of plasma based acceleration (PBA) requires the use of three dimensional, fully nonlinear, and kinetic descriptions based on the particle-in-cell (PIC) method. In PBA an intense particle beam or laser (driver) propagates through a tenuous plasma whereby it excites a plasma wave wake. Three-dimensional PIC algorithms based on the quasi-static approximation (QSA) have been successfully applied to efficiently model the interaction between relativistic charged particle beams and plasma. In a QSA PIC algorithm, the plasma response to a charged particle beam or laser driver is calculated based on forces from the driver and self-consistent forces from the QSA form of Maxwell's equations. These fields are then used to advance the charged particle beam or laser forward by a large time step. Since the time step is not limited by the regular Courant-Friedrichs-Lewy (CFL) condition that constrains a standard 3D fully electromagnetic PIC code, a 3D QSA PIC code can achieve orders of magnitude speedup in performance. Recently, a new hybrid QSA PIC algorithm that combines another speedup technique known as an azimuthal Fourier decomposition has been proposed and implemented. This hybrid algorithm decomposes the electromagnetic fields, charge and current density into azimuthal harmonics and only the Fourier coefficients need to be updated, which can reduce the algorithmic complexity of a 3D code to that of a 2D code. Modeling the laser-plasma interaction in a full 3D electromagnetic PIC algorithm is very computationally expensive due the enormous disparity of physical scales to be resolved. In the QSA the laser is modeled using the ponderomotive guiding center (PGC) approach. We describe how to implement a PGC algorithm compatible for the QSA PIC algorithms based on the azimuthal mode expansion. Here this algorithm permits time steps orders of magnitude larger than the cell size and it can be asynchronously parallelized. Details on how this is implemented into the QSA PIC code that utilizes an azimuthal mode expansion, QPAD, are also described. Benchmarks and comparisons between a fully 3D explicit PIC code (OSIRIS), as well as a few examples related to laser wakefield acceleration, are presented.

97 MATHEMATICS AND COMPUTING↗

pnnl/arena

CFA ARENA is a novel programming model with the support of a runtime targeting asynchronous data-centric execution paradigm in a distributed system. All the machine nodes in ARENA are connected by a ring network to bring the specialized computation to the data rather than the reverse to minimize data movement. The programming interfaces are implemented using C++

Tan, Cheng↗

DSMC analysis in a heterogeneous parallel computing environment

A methodology for implementing parallel DSMC codes in a heterogeneous computing environment is described. The methodology involves the use of a common message-passing software library together with recently developed software that handles the actual interprocessor communications in a standard manner across a variety of computing platforms. Benchmark tests using a simple DSMC model problem were performed on an Intel iPSC/860, a Cray-YMP and a group of Sun workstations. The approach was found to give speedups that scaled linearly with problem size on all the computing platforms tested. This methodology was then incorporated into a production-type DSMC code to allow the simulation of problems that would not otherwise have been practical. The application of this production code to simulations of hypersonic shear flows and shock-lip interactions under near-continuum conditions is described. Synchronous and asynchronous models for implementing parallelism into DSMC simulations are also described and both models are shown to produce the same steady-state result.

Wilmoth, R. G.↗

An active learning high-throughput microstructure calibration framework for solving inverse structure–process problems in materials informatics

Determining a process–structure–property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials design are often considered in the context of process–property linkage by bypassing the materials structure, or in the context of structure–property linkage as in microstructure-sensitive design problems. However, there is a lack of research effort in studying materials design problems in the context of process–structure linkage, which has a great implication in reverse engineering. In this paper, given a target microstructure, we propose an active learning high-throughput microstructure calibration framework to derive a set of processing parameters, which can produce an optimal microstructure that is statistically equivalent to the target microstructure. The proposed framework is formulated as a noisy multi-objective optimization problem, where each objective function measures a deterministic or statistical difference of the same microstructure descriptor between a candidate microstructure and a target microstructure. Furthermore, to significantly reduce the physical waiting wall-time, we enable the high-throughput feature of the microstructure calibration framework by adopting an asynchronously parallel Bayesian optimization to exploit high-performance computing resources. Case studies in additive manufacturing and grain growth are used to demonstrate the applicability of the proposed framework, where kinetic Monte Carlo (kMC) simulation is used as a forward predictive model, such that for a given target microstructure, the target processing parameters that produced this microstructure are successfully recovered.

36 MATERIALS SCIENCE↗

Extending the Roofline Model for Asynchronous Many-Task Runtimes

New architectural trends and extreme scale parallelism challenge the efficient mapping of applications to large scale and emerging systems. Fine-grained Asynchronous Manytask Runtimes (AMR) offer a unique flexibility to hide the varying latencies of contentious operations, and facilitate the effective exploitation of abundant resources. By decomposing work into smaller asynchronous chunks, the impact of unpredictable operations can be mitigated through a tighter overlapping of tasks. Unfortunately, the cost of this decomposition comes at a potentially steep price in the form of runtime overhead which can at times rival the cost of the computation itself. This leads to the question, how large should a task be? A common practice for application developers is to experimentally determine the granularity of a task after a code has been parallelized. Instead, we propose a new methodology based on an extended Roofline model to provide practical upper bounds on the throughput performance of an application. First, we extend the Roofline model to support not only latency hiding analysis, but also a multidimensional amortized analysis. By combining this new methodology with a serial application and an AMR implementation, we can predict the worst case runtime overhead attribution of individual runtime features prior to the development of parallel code. Thus, this runtimecentric methodology can provide a vehicle for application/runtime codesign by providing a comprehensive bottleneck analysis based on existing runtime features.

Suetterlein, Joshua D.↗

Comparison of High-Fidelity Computational Tools for Wing Design of a Distributed Electric Propulsion Aircraft

A variety of tools, from fundamental to high order, have been used to better understand applications of distributed electric propulsion to aid the wing and propulsion system design of the Leading Edge Asynchronous Propulsion Technology (LEAPTech) project and the X-57 Maxwell airplane. Three high-fidelity, Navier-Stokes computational fluid dynamics codes used during the project with results presented here are FUN3D, STAR-CCM+, and OVERFLOW. These codes employ various turbulence models to predict fully turbulent and transitional flow. Results from these codes are compared for two distributed electric propulsion configurations: the wing tested at NASA Armstrong on the Hybrid-Electric Integrated Systems Testbed truck, and the wing designed for the X-57 Maxwell airplane. Results from these computational tools for the high-lift wing tested on the Hybrid-Electric Integrated Systems Testbed truck and the X-57 high-lift wing presented compare reasonably well. The goal of the X-57 wing and distributed electric propulsion system design achieving or exceeding the required 𝐶 (sub L) = 3.95 for stall speed was confirmed with all of the computational codes.

Deere, Karen A.↗

Specification and verification of gate-level VHDL models of synchronous and asynchronous circuits

We present a mathematical definition of hardware description language (HDL) that admits a semantics-preserving translation to a subset of VHDL. Our HDL includes the basic VHDL propagation delay mechanisms and gate-level circuit descriptions. We also develop formal procedures for deriving and verifying concise behavioral specifications of combinational and sequential devices. The HDL and the specification procedures have been formally encoded in the computational logic of Boyer and Moore, which provides a LISP implementation as well as a facility for mechanical proof-checking. As an application, we design, specify, and verify a circuit that achieves asynchronous communication by means of the biphase mark protocol.

Russinoff, David M.↗

Self-organized Segregation on the Grid

We consider an agent-based model with exponentially distributed waiting times in which two types of agents interact locally over a graph, and based on this interaction and on the value of a common intolerance threshold τ, decide whether to change their types. This is equivalent to a zero-temperature ising model with Glauber dynamics, an asynchronous cellular automaton with extended Moore neighborhoods, or a Schelling model of self-organized segregation in an open system, and has applications in the analysis of social and biological networks, and spin glasses systems. Some rigorous results were recently obtained in the theoretical computer science literature, and this work provides several extensions. We enlarge the intolerance interval leading to the expected formation of large segregated regions of agents of a single type from the known size ϵ>0 to size ≈0.134. Namely, we show that for 0.433<τ<1/2 (and by symmetry 1/2<τ<0.567), the expected size of the largest segregated region containing an arbitrary agent is exponential in the size of the neighborhood. We further extend the interval leading to expected large segregated regions to size ≈0.312 considering “almost segregated” regions, namely regions where the ratio of the number of agents of one type and the number of agents of the other type vanishes quickly as the size of the neighborhood grows. In this case, we show that for 0.344<τ≤0.433 (and by symmetry for 0.567≤τ<0.656) the expected size of the largest almost segregated region containing an arbitrary agent is exponential in the size of the neighborhood. This behavior is reminiscent of supercritical percolation, where small clusters of empty sites can be observed within any sufficiently large region of the occupied percolation cluster. The exponential bounds that we provide also imply that complete segregation, where agents of a single type cover the whole grid, does not occur with high probability for p=1/2 and the range of intolerance considered.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Performance evaluation of automated manufacturing systems using generalized stochastic Petri Nets

The main objective of this research is to develop a generic modeling methodology with a flexible and modular framework to aid in the design and performance evaluation of integrated manufacturing systems using a unified model. After a thorough examination of the available modeling methods, the Petri Net approach was adopted. The concurrent and asynchronous nature of manufacturing systems are easily captured by Petri Net models. Three basic modules were developed: machine, buffer, and Decision Making Unit. The machine and buffer modules are used for modeling transfer lines and production networks. The Decision Making Unit models the functions of a computer node in a complex Decision Making Unit Architecture. The underlying model is a Generalized Stochastic Petri Net (GSPN) that can be used for performance evaluation and structural analysis. GSPN's were chosen because they help manage the complexity of modeling large manufacturing systems. There is no need to enumerate all the possible states of the Markov Chain since they are automatically generated from the GSPN model.

Al-Jaar, Robert Y.↗

Symbolic Computation of Strongly Connected Components Using Saturation

Finding strongly connected components (SCCs) in the state-space of discrete-state models is a critical task in formal verification of LTL and fair CTL properties, but the potentially huge number of reachable states and SCCs constitutes a formidable challenge. This paper is concerned with computing the sets of states in SCCs or terminal SCCs of asynchronous systems. Because of its advantages in many applications, we employ saturation on two previously proposed approaches: the Xie-Beerel algorithm and transitive closure. First, saturation speeds up state-space exploration when computing each SCC in the Xie-Beerel algorithm. Then, our main contribution is a novel algorithm to compute the transitive closure using saturation. Experimental results indicate that our improved algorithms achieve a clear speedup over previous algorithms in some cases. With the help of the new transitive closure computation algorithm, up to 10(exp 150) SCCs can be explored within a few seconds.

Zhao, Yang↗

Physics-Dynamics Coupling in Weather, Climate, and Earth System Models: Challenges and Recent Progress

Geophysical models of the atmosphere and ocean invariably involve parameterizations. These represent two distinct areas: a) Subgrid processes which the model cannot (yet) resolve, due to its discrete resolution, and b) sources in the equation, due to radiation for example. Hence coupling between these physics parameterizations and the resolved fluid dynamics and also between the dynamics of the different fluids in the system (air and water) is necessary. This coupling is an important aspect of geophysical models. However, often model development is strictly segregated into either physics or dynamics. Hence, this area has many more unanswered questions than in-depth understanding. Furthermore, recent developments in the design of dynamical cores (significant increase of resolution, move to non-hydrostatic equation sets etc), extended process physics (prognostic micro physics, 3D turbulence, non-vertical radiation etc) and predicted future changes of the computational infrastructure (Exascale with its need for task parallelism, data locality and asynchronous time stepping for example) is adding even more complexity and new questions.

Gross, Markus↗

On the Suitability of MPI as a PGAS Runtime

Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI models for designing scalable applications. At the same time, MPI remains a ubiquitous communication subsystem due to its standardization, high performance, and availability on leading platforms. In this paper, we explore the suitability of using MPI as a scalable PGAS communication subsystem. We focus on the Remote Memory Access (RMA) communication in PGAS models which typically includes {\em get, put,} and {\em atomic memory operations}. We perform an in-depth exploration of design alternatives based on MPI. These alternatives include using a semantically-matching interface such as MPI-RMA, as well as not-so-intuitive interfaces such as MPI two-sided with a combination of multi-threading and dynamic process management. With an in-depth exploration of these alternatives and their shortcomings, we propose a novel design which is facilitated by the data-centric view in PGAS models. This design leverages a combination of highly tuned MPI two-sided semantics and an automatic, user-transparent split of MPI communicators to provide asynchronous progress. We implement the asynchronous progress ranks approach and other approaches within the Communication Runtime for Exascale which is a communication subsystem for Global Arrays. Our performance evaluation spans pure communication benchmarks, graph community detection and sparse matrix-vector multiplication kernels, and a computational chemistry application. The utility of our proposed PR-based approach is demonstrated by a 2.17x speed-up on 1008 processors over the other MPI-based designs.

Computational modeling↗