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At least 559 records · Page 31

Mapping unstructured grid computations to massively parallel computers

Investigated here is this mapping problem: assign the tasks of a parallel program to the processors of a parallel computer such that the execution time is minimized. First, a taxonomy of objective functions and heuristics used to solve the mapping problem is presented. Next, we develop a highly parallel heuristic mapping algorithm, called Cyclic Pairwise Exchange (CPE), and discuss its place in the taxonomy. CPE uses local pairwise exchanges of processor assignments to iteratively improve an initial mapping. A variety of initial mapping schemes are tested and recursive spectral bipartitioning (RSB) followed by CPE is shown to result in the best mappings. For the test cases studied here, problems arising in computational fluid dynamics and structural mechanics on unstructured triangular and tetrahedral meshes, RSB and CPE outperform methods based on simulated annealing. Much less time is required to do the mapping and the results obtained are better. Compared with random and naive mappings, RSB and CPE reduce the communication time two fold for the test problems used. Finally, we use CPE in two applications on a CM-2. The first application is a data parallel mesh-vertex upwind finite volume scheme for solving the Euler equations on 2-D triangular unstructured meshes. CPE is used to map grid points to processors. The performance of this code is compared with a similar code on a Cray-YMP and an Intel iPSC/860. The second application is parallel sparse matrix-vector multiplication used in the iterative solution of large sparse linear systems of equations. We map rows of the matrix to processors and use an inner-product based matrix-vector multiplication. We demonstrate that this method is an order of magnitude faster than methods based on scan operations for our test cases.

Hammond, Steven Warren↗

Multiscale Mathematics for Biomass Conversion to Renewable Hydrogen

Our two key accomplishments in the first three years were towards the development of, (1) a mathematically rigorous and at the same time computationally flexible framework for parallelization of Kinetic Monte Carlo methods, and its implementation on GPUs, and (2) spatial multilevel coarse-graining methods for Monte Carlo sampling and molecular simulation. A common underlying theme in both these lines of our work is the development of numerical methods which are at the same time both computationally efficient and reliable, the latter in the sense that they provide controlled-error approximations for coarse observables of the simulated molecular systems. Finally, our key accomplishment in the last year of the grant is that we started developing (3) pathwise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of nonequilibrium extended (high-dimensional) systems. We discuss these three research directions in some detail below, along with the related publications.

97 MATHEMATICS AND COMPUTING↗

Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

Rose, Geoffrey K.↗

Parametric binary dissection

Binary dissection is widely used to partition non-uniform domains over parallel computers. This algorithm does not consider the perimeter, surface area, or aspect ratio of the regions being generated and can yield decompositions that have poor communication to computation ratio. Parametric Binary Dissection (PBD) is a new algorithm in which each cut is chosen to minimize load + lambda x(shape). In a 2 (or 3) dimensional problem, load is the amount of computation to be performed in a subregion and shape could refer to the perimeter (respectively surface) of that subregion. Shape is a measure of communication overhead and the parameter permits us to trade off load imbalance against communication overhead. When A is zero, the algorithm reduces to plain binary dissection. This algorithm can be used to partition graphs embedded in 2 or 3-d. Load is the number of nodes in a subregion, shape the number of edges that leave that subregion, and lambda the ratio of time to communicate over an edge to the time to compute at a node. An algorithm is presented that finds the depth d parametric dissection of an embedded graph with n vertices and e edges in O(max(n log n, de)) time, which is an improvement over the O(dn log n) time of plain binary dissection. Parallel versions of this algorithm are also presented; the best of these requires O((n/p) log(sup 3)p) time on a p processor hypercube, assuming graphs of bounded degree. How PBD is applied to 3-d unstructured meshes and yields partitions that are better than those obtained by plain dissection is described. Its application to the color image quantization problem is also discussed, in which samples in a high-resolution color space are mapped onto a lower resolution space in a way that minimizes the color error.

Bokhari, Shahid H.↗

Galerkin/Runge-Kutta discretizations for parabolic equations with time dependent coefficients

A new class of fully discrete Galerkin/Runge-Kutta methods is constructed and analyzed for linear parabolic initial boundary value problems with time dependent coefficients. Unlike any classical counterpart, this class offers arbitrarily high order convergence while significantly avoiding what has been called order reduction. In support of this claim, error estimates are proved, and computational results are presented. Additionally, since the time stepping equations involve coefficient matrices changing at each time step, a preconditioned iterative technique is used to solve the linear systems only approximately. Nevertheless, the resulting algorithm is shown to preserve the original convergence rate while using only the order of work required by the base scheme applied to a linear parabolic problem with time independent coefficients. Furthermore, it is noted that special Runge-Kutta methods allow computations to be performed in parallel so that the final execution time can be reduced to that of a low order method.

Keeling, Stephen L.↗

Galerkin/Runge-Kutta discretizations for parabolic equations with time-dependent coefficients

A new class of fully discrete Galerkin/Runge-Kutta methods is constructed and analyzed for linear parabolic initial boundary value problems with time dependent coefficients. Unlike any classical counterpart, this class offers arbitrarily high order convergence while significantly avoiding what has been called order reduction. In support of this claim, error estimates are proved, and computational results are presented. Additionally, since the time stepping equations involve coefficient matrices changing at each time step, a preconditioned iterative technique is used to solve the linear systems only approximately. Nevertheless, the resulting algorithm is shown to preserve the original convergence rate while using only the order of work required by the base scheme applied to a linear parabolic problem with time independent coefficients. Furthermore, it is noted that special Runge-Kutta methods allow computations to be performed in parallel so that the final execution time can be reduced to that of a low order method.

Keeling, Stephen L.↗

Do optimization methods in deep learning applications matter?

With advances in deep learning, exponential data growth and increasing model complexity, developing efficient optimization methods are attracting much research attention. Several implementations favor the use of Conjugate Gradient (CG) and Stochastic Gradient Descent (SGD) as being practical and elegant solutions to achieve quick convergence, however, these optimization processes also present many limitations in learning across deep learning applications. Recent research is exploring higher-order optimization functions as better approaches, but these present very complex computational challenges for practical use. Comparing first and higher-order optimization functions, in this paper, our experiments reveal that Levemberg-Marquardt (LM) significantly supersedes optimal convergence but suffers from very large processing time increasing the training complexity of both, classification and reinforcement learning problems. Our experiments compare off-the-shelf optimization functions(CG, SGD, LM and L-BFGS) in standard CIFAR, MNIST, CartPole and FlappyBird experiments.The paper presents arguments on which optimization functions to use and further, which functions would benefit from parallelization efforts to improve pretraining time and learning rate convergence.

Ozyildirim, Buse Melis↗

Ignition Delay Times and CO Composition during Ethanol Combustion in Miniature Shock Tube

Ignition delay times and composition of CO were measured simultaneously in a miniature high repetition rate shock tube (HRRST) using chemiluminescence and tunable diode laser absorption spectroscopy. Mixtures of 1% ethanol with oxygen and balance argon were tested with equivalence ratios 0.5, 1, and 1.2, over pressure range of 1.6 to 1.8 bar, and temperature range of 1180 to 1400K. Ignition delay times in this range were compared with those in larger shock tubes using several different techniques. One method included using the Livengood-Wu integral (and improved estimates from measured pressure trace). Another method involved direct modeling of conditions in the miniature shock tube using the measured pressure trace. CO composition was measured in parallel with the ignition delay time experiments. Comparison was made with mechanisms in the literature. Experiments were also performed doping CO into the Ar bath gas and conducting two-line CO measurements using TDLAS before ignition. With proper calibration, this measurement is sensitive to temperature.

Sutar, Ashish↗

Accelerated molecular dynamics simulations of dislocation climb in nickel

We report the mechanical behavior of materials operating under high temperatures is strongly influenced by creep mechanisms such as dislocation climb, which is controlled by the diffusion of vacancies. However, atomistic simulations of these mechanisms have traditionally been impractical due to the long time scales required. To overcome these time scale challenges, we use Parallel Trajectory Splicing (ParSplice), an accelerated molecular dynamics method, to simulate dislocation climb in nickel. We focus on modeling the activity of a vacancy near a jog on an edge dislocation in order to observe vacancy pipe diffusion and vacancy absorption at the jog. From rigorously constructed trajectories encompassing more than 2000 vacancy absorption events over a simulation time of more than 4μs at 900 K, a comprehensive sampling of available atomistic mechanisms is collated and analyzed further with molecular statics calculations. We estimate average rates for pipe diffusion and vacancy absorption into the jog using data from the dynamic and static calculations, finding very good agreement. Our results strongly suggest that the dominant mechanism for vacancy absorption by jogs is via biased diffusion to the dislocation core followed by fast pipe diffusion to the jog.

36 MATERIALS SCIENCE↗

Virtual machine-based simulation platform for mobile ad-hoc network-based cyber infrastructure

In modeling and simulating complex systems such as mobile ad-hoc networks (MANETs) in de-fense communications, it is a major challenge to reconcile multiple important considerations: the rapidity of unavoidable changes to the software (network layers and applications), the difficulty of modeling the critical, implementation-dependent behavioral effects, the need to sustain larger scale scenarios, and the desire for faster simulations. Here we present our approach in success-fully reconciling them using a virtual time-synchronized virtual machine(VM)-based parallel ex-ecution framework that accurately lifts both the devices as well as the network communications to a virtual time plane while retaining full fidelity. At the core of our framework is a scheduling engine that operates at the level of a hypervisor scheduler, offering a unique ability to execute multi-core guest nodes over multi-core host nodes in an accurate, virtual time-synchronized manner. In contrast to other related approaches that suffer from either speed or accuracy issues, our framework provides MANET node-wise scalability, high fidelity of software behaviors, and time-ordering accuracy. The design and development of this framework is presented, and an ac-tual implementation based on the widely used Xen hypervisor system is described. Benchmarks with synthetic and actual applications are used to identify the benefits of our approach. The time inaccuracy of traditional emulation methods is demonstrated, in comparison with the accurate execution of our framework verified by theoretically correct results expected from analytical models of the same scenarios. In the largest high fidelity tests, we are able to perform virtual time-synchronized simulation of 64-node VM-based full-stack, actual software behaviors of MANETs containing a mix of static and mobile (unmanned airborne vehicle) nodes, hosted on a 32-core host, with full fidelity of unmodified ad-hoc routing protocols, unmodified application executables, and user-controllable physical layer effects including inter-device wireless signal strength, reachability, and connectivity.

97 MATHEMATICS AND COMPUTING↗

Parametric Study of a YAV-8B Harrier in Ground Effect using Time-Dependent Navier-Stokes Computations

A process is described which enables the generation of 35 time-dependent viscous solutions for a YAV-8B Harrier in ground effect in one week. Overset grids are used to model the complex geometry of the Harrier aircraft and the interaction of its jets with the ground plane and low-speed ambient flow. The time required to complete this parametric study is drastically reduced through the use of process automation, modern computational platforms, and parallel computing. Moreover, a dual-time-stepping algorithm is described which improves solution robustness. Unsteady flow visualization and a frequency domain analysis are also used to identify and correlated key flow structures with the time variation of lift.

Pandya, Shishir↗

An S N Algorithm for Modern Architectures

LANL discrete ordinates transport packages are required to perform large, computationally intensive time-dependent calculations on massively parallel architectures, where even a single such calculation may need many months to complete. While KBA methods scale out well to very large numbers of compute nodes, we are limited by practical constraints on the number of such nodes we can actually apply to any given calculation. Instead, we describe a modified KBA algorithm that allows realization of the reductions in solution time offered by both the current, and future, architectural changes within a compute node.

97 MATHEMATICS AND COMPUTING↗

High-resolution turbulent simulations using the Connection Machine-2

The spectral method provides an efficient algorithm for solving the 3D incompressible Navier-Stokes equations in periodic boundaries. Most people, so far, have used vectorized machines, such as the CRAY-2, to implement fast Fourier transformations and time integrations in the spectral calculations. In this paper, new results are presented using the spectral calculations on the Connection Machine-2 with a parallel algorithm. The large memory of the Connection Machine-2 and the parallel algorithm allows, of the first time, to implement a 512-cubed mesh resolution for high Reynolds number flows. The computational speed of the present code is about 30 percent faster than the fastest CRAY-2 simulations with four processors. Parallel machines, such as the Connection Machine-2, will possibly provide new computational power for understanding the intermittency and cascade mechanism in fluid turbulence.

Chen, Shiyi↗

Planning in time - Windows and durations for activities and goals

The present general purpose automated planner/scheduler generates parallel plans aimed at the achievement of goals having imposed time constraints, with both durations and start time windows being specifiable for sets of goal conditions. Deterministic durations of such parallel plan activities as actions, events triggered by circumstances, inferences, and scheduled events entirely outside the actor's control, are explicitly modeled and may be any computable function of the activity variables. The final plan network resembles a PERT chart. Examples are given from the traditional 'blocksworld', and from a realistic 'Spaceworld' in which an autonomous spacecraft photographs objects in deep space and transmits the information to earth.

Vere, S. A.↗

The Mega Mesospheric Parachute

The current understanding and modeling of the upper reaches of the atmosphere is incomplete. Upper atmospheric interactions with the lower atmosphere, effects of ionizing radiation, high altitude cloud phenomena, and the dynamical interaction with the magnetosphere require greater definition. The scientific objective of obtaining a greater understanding of the upper atmosphere can be achieved by designing, implementing, testing, and utilizing a facility that provides long period in-situ measurements of the mesosphere. Current direct sub-sonic measurements of the upper atmosphere are hampered by the approximately one minute sub-sonic observation window of a ballistic sounding rocket regardless of the launch angle. In-situ measurements at greater than transonic speeds impart energy into the molecular atmospheric system and distort the true atmospheric chemistry. A long duration, sub-sonic capability will significantly enhance our ability to observe and measure: (1) mesospheric lightning phenomena (sprites and blue jets) (2) composition, structure and stratification of noctilucent clouds (3) physics of seasonal radar echoes, gravity wave phenomena (4) chemistry of mesospheric gaseous ratio mixing (5) mesospheric interaction of ionizing radiation (6) dynamic electric and magnetic fields This new facility will also provide local field measurements which complement those that can be obtained through external measurements from satellite and ground-based platforms. The 400 foot (approximately 130 meter) diameter lightweight mega-mesospheric parachute system, deployed with a sounding rocket, is proposed herein as a method to increase sub-sonic mesospheric measurement time periods by more than an order of magnitude. The report outlines a multi-year evolving science instrumentation suite in parallel with the development of the mega meso-chute facility. The developmental issues surrounding the meso-chute are chiefly materials selection (thermal and structural) and deployment mechanism physics. Three mission cases were conceived and developed to include cost and schedules estimates. Each scenario has increasing scientific utility with paralleling launch weight, parachute hang-time, deployment altitude, and parachute size: (1) Case #1: $8.4M@24 months, 6kg payload, 20 min., 50km alt., 80 m. dia. (2) Case #2: $10.4M@24 months, 6kg payload, 20 min., 60km alt, 130m. dia. (3) Case #3: $13.6M@36 months, 30kg payload, 30 min., 90km alt., 200m. dia. The initial breakout cost for the parachute system is approximately $2M@24 months. This report identifies that although the challenges of the mega-meso-chute may be difficult, they can be surmounted and valuable results can be achieved.

Kloesel, Kurt J.↗