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At least 163 records · Page 9

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗

Parallel Navier-Stokes computations on shared and distributed memory architectures

We study a high order finite difference scheme to solve the time accurate flow field of a jet using the compressible Navier-Stokes equations. As part of our ongoing efforts, we have implemented our numerical model on three parallel computing platforms to study the computational, communication, and scalability characteristics. The platforms chosen for this study are a cluster of workstations connected through fast networks (the LACE experimental testbed at NASA Lewis), a shared memory multiprocessor (the Cray YMP), and a distributed memory multiprocessor (the IBM SPI). Our focus in this study is on the LACE testbed. We present some results for the Cray YMP and the IBM SP1 mainly for comparison purposes. On the LACE testbed, we study: (1) the communication characteristics of Ethernet, FDDI, and the ALLNODE networks and (2) the overheads induced by the PVM message passing library used for parallelizing the application. We demonstrate that clustering of workstations is effective and has the potential to be computationally competitive with supercomputers at a fraction of the cost.

Hayder, M. Ehtesham↗

Gilgamesh: A Multithreaded Processor-In-Memory Architecture for Petaflops Computing

Processor-in-Memory (PIM) architectures avoid the von Neumann bottleneck in conventional machines by integrating high-density DRAM and CMOS logic on the same chip. Parallel systems based on this new technology are expected to provide higher scalability, adaptability, robustness, fault tolerance and lower power consumption than current MPPs or commodity clusters. In this paper we describe the design of Gilgamesh, a PIM-based massively parallel architecture, and elements of its execution model. Gilgamesh extends existing PIM capabilities by incorporating advanced mechanisms for virtualizing tasks and data and providing adaptive resource management for load balancing and latency tolerance. The Gilgamesh execution model is based on macroservers, a middleware layer which supports object-based runtime management of data and threads allowing explicit and dynamic control of locality and load balancing. The paper concludes with a discussion of related research activities and an outlook to future work.

management locality load balance↗

Statistical Analysis of NAS Parallel Benchmarks and LINPACK Results

In the last three years extensive performance data have been reported for parallel machines both based on the NAS Parallel Benchmarks, and on LINPACK. In this study we have used the reported benchmark results and performed a number of statistical experiments using factor, cluster, and regression analyses. In addition to the performance results of LINPACK and the eight NAS parallel benchmarks, we have also included peak performance of the machine, and the LINPACK n and n(sub 1/2) values. Some of the results and observations can be summarized as follows: 1) All benchmarks are strongly correlated with peak performance. 2) LINPACK and EP have each a unique signature. 3) The remaining NPB can grouped into three groups as follows: (CG and IS), (LU and SP), and (MG, FT, and BT). Hence three (or four with EP) benchmarks are sufficient to characterize the overall NPB performance. Our poster presentation will follow a standard poster format, and will present the data of our statistical analysis in detail.

Meuer, Hans-Werner↗

High order parallel numerical schemes for solving incompressible flows

The use of parallel computers for numerically solving flow fields has gained much importance in recent years. This paper introduces a new high order numerical scheme for computational fluid dynamics (CFD) specifically designed for parallel computational environments. A distributed MIMD system gives the flexibility of treating different elements of the governing equations with totally different numerical schemes in different regions of the flow field. The parallel decomposition of the governing operator to be solved is the primary parallel split. The primary parallel split was studied using a hypercube like architecture having clusters of shared memory processors at each node. The approach is demonstrated using examples of simple steady state incompressible flows. Future studies should investigate the secondary split because, depending on the numerical scheme that each of the processors applies and the nature of the flow in the specific subdomain, it may be possible for a processor to seek better, or higher order, schemes for its particular subcase.

Lin, Avi↗

Ensuring correct rollback recovery in distributed shared memory systems

Distributed shared memory (DSM) implemented on a cluster of workstations is an increasingly attractive platform for executing parallel scientific applications. Checkpointing and rollback techniques can be used in such a system to allow the computation to progress in spite of the temporary failure of one or more processing nodes. This paper presents the design of an independent checkpointing method for DSM that takes advantage of DSM's specific properties to reduce error-free and rollback overhead. The scheme reduces the dependencies that need to be considered for correct rollback to those resulting from transfers of pages. Furthermore, in-transit messages can be recovered without the use of logging. We extend the scheme to a DSM implementation using lazy release consistency, where the frequency of dependencies is further reduced.

Janssens, Bob↗

Parallel Implementation of the Discontinuous Galerkin Method

This paper describes a parallel implementation of the discontinuous Galerkin method. Discontinuous Galerkin is a spatially compact method that retains its accuracy and robustness on non-smooth unstructured grids and is well suited for time dependent simulations. Several parallelization approaches are studied and evaluated. The most natural and symmetric of the approaches has been implemented in all object-oriented code used to simulate aeroacoustic scattering. The parallel implementation is MPI-based and has been tested on various parallel platforms such as the SGI Origin, IBM SP2, and clusters of SGI and Sun workstations. The scalability results presented for the SGI Origin show slightly superlinear speedup on a fixed-size problem due to cache effects.

Baggag, Abdalkader↗

The Hydrogen Abstraction from A Diamond(111) Surface in A Uniform Electric Field

Bond breaking in a strong electric field is shown to arise from a crossing of the ionic and covalent asymptotes. The specific example of hydrogen abstraction from a diamond(111) surface is studied using a cluster model. The addition of nearby atoms in both the parallel and perpendicular direction to the electric field are found to have an effect. It is also shown that the barrier is not only related to the position of the ionic and covalent asymptotes.

Ricca, Alessandra↗

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↗

The Evolution of the Galaxy Rest-Frame Ultraviolet Luminosity Function Over the First Two Billion Years

We present a robust measurement and analysis of the rest-frame ultraviolet (UV) luminosity function at z = 4 to 8. We use deep Hubble Space Telescope imaging over the CANDELS/GOODS fields, the Hubble Ultra Deep Field and the Hubble Frontier Field deep parallel observations near the Abell 2744 and MACS J0416.1- 2403 clusters. The combination of these surveys provides an effective volume of 0.6-1.2 ×10(exp 6) Mpc(exp 3) over this epoch, allowing us to perform a robust search for bright (M(sub UV) less than −21) and faint (M(sub UV) = −18) galaxies. We select galaxies using a well-tested photometric redshift technique with careful screening of contaminants, finding a sample of 7446 galaxies at 3.5 less than z less than 8.5, with more than 1000 galaxies at z of approximately 6 - 8. We measure both a stepwise luminosity function for galaxies in our redshift samples, as well as a Schechter function, using a Markov Chain Monte Carlo analysis to measure robust uncertainties. At the faint end our UV luminosity functions agree with previous studies, yet we find a higher abundance of UV-bright galaxies at z of greater than or equal to 6. Our bestfit value of the characteristic magnitude M* is consistent with −21 at z of greater than or equal to 5, different than that inferred based on previous trends at lower redshift. At z = 8, a single power-law provides an equally good fit to the UV luminosity function, while at z = 6 and 7, an exponential cutoff at the bright-end is moderately preferred. We compare our luminosity functions to semi-analytical models, and find that the lack of evolution in M* is consistent with models where the impact of dust attenuation on the bright-end of the luminosity function decreases at higher redshift, though a decreasing impact of feedback may also be possible. We measure the evolution of the cosmic star-formation rate (SFR) density by integrating our observed luminosity functions to M(sub UV) = −17, correcting for dust attenuation, and find that the SFR density declines proportionally to (1 + z)((exp −4.3)(+/-)(0.5)) at z greater than 4, consistent with observations at z greater than or equal to 9. Our observed luminosity functions are consistent with a reionization history that starts at redshift of approximately greater than 10, completes at z greater than 6, and reaches a midpoint (x(sub HII) = 0.5) at 6.7 less than z less than 9.4. Finally, using a constant cumulative number density selection and an empirically derived rising star-formation history, our observations predict that the abundance of bright z = 9 galaxies is likely higher than previous constraints, though consistent with recent estimates of bright z similar to 10 galaxies.

Galaxy↗

Motions in Prominence Barbs Observed on the Solar Limb

We analyze and discuss an example of prominence barbs observed on the limb on 2016 January 7 by the Hinode/Solar Optical Telescope in Ca II and H alpha, the Interface Region Imaging Spectrograph, with slit jaw images and Mg II spectral data, and the Solar Dynamics Observatory's Atmospheric Imaging Assembly. In the recent literature there has been a debate concerning whether these features, sometimes referred to as "tornadoes," are rotating. Our data analysis provides no evidence for systematic rotation in the barbs. We do find line-of-sight motions in the barbs that vary with location and time. We also discuss observations of features moving along the barbs. These moving features are elongated parallel to the solar limb and tend to come in clusters of features moving along the same or similar paths in the plane of the sky during a period of 10 minutes to an hour, moving toward or away from the limb. The motion may have a component along the line of sight as well. The spectral data indicate that the features are Doppler shifted. We discuss possible explanations for these features.

Kucera, T. A.↗

NETRA: A parallel architecture for integrated vision systems. 1: Architecture and organization

Computer vision is regarded as one of the most complex and computationally intensive problems. An integrated vision system (IVS) is considered to be a system that uses vision algorithms from all levels of processing for a high level application (such as object recognition). A model of computation is presented for parallel processing for an IVS. Using the model, desired features and capabilities of a parallel architecture suitable for IVSs are derived. Then a multiprocessor architecture (called NETRA) is presented. This architecture is highly flexible without the use of complex interconnection schemes. The topology of NETRA is recursively defined and hence is easily scalable from small to large systems. Homogeneity of NETRA permits fault tolerance and graceful degradation under faults. It is a recursively defined tree-type hierarchical architecture where each of the leaf nodes consists of a cluster of processors connected with a programmable crossbar with selective broadcast capability to provide for desired flexibility. A qualitative evaluation of NETRA is presented. Then general schemes are described to map parallel algorithms onto NETRA. Algorithms are classified according to their communication requirements for parallel processing. An extensive analysis of inter-cluster communication strategies in NETRA is presented, and parameters affecting performance of parallel algorithms when mapped on NETRA are discussed. Finally, a methodology to evaluate performance of algorithms on NETRA is described.

Choudhary, Alok N.↗

Measuring the Hubble constant and our Virgo-infall velocity independently

A sample of spiral galaxies with B(sub T) less than 14.5 located in two local volumes, one in the direction of, but behind, the Virgo Cluster (behind-Virgo volume (BV)) and the other in the opposite direction (anti-Virgo volume (AV)), were used via a Tully-Fisher (TF) relation to derive the following two parameters: H(sub AB), the mean Hubble ratio between AV and BV, and delta v(sub parallel), the peculiar velocity of the Local Group in the direction of the Virgo Cluster (VC) with respect to a uniformly expanding reference system defined by our AV and BV sub-samples. The two sampled volumes, separated by a velocity interval of 5600 km/s, form an antipodal pair. This particular geometry not only allows us to derive the two parameters independently but also reduces the dynamical effect of the Local Supercluster on H(sub AB) without increasing the Malmquist bias. By limiting our sample to spiral galaxies having large velocity widths W(sub R), we effectively reduce the TF scatter and Malmquist bias in our sample. The TF zero point and dispersion were then determined by further correcting for the small residual Malmquist bias. An additional sample of fainter galaxies was used to test for a non-Gaussian tail to the TF disperison. We found no evidence for such a tail and formally give an upper limit of about 18% for the fractional contribution of an unseen tail. The average intrinsic TF dispersion for the dominant Gaussian component is sigma(sub TF)(sup 0) approximately 0.33 mag for W(sub R) approximately equal to or greater than 180 km/s. Our numerical results are delta v(sub parallel) approximately equals 414 +/- 82 km/s and H(sub AB) approximately equals (84.0 +/- 2.4)(1 + epsilon) km/s Mpc, where (1 + epsilon) accounts for any systematic error between the calibrators and the sample galaxies. Various dynamical models were tested to explore the effect on H(sub AB) of the uncertainties in the local velocity field. Constrained by our observed delta v(sub parallel) as well as other observational quantities, we found that the rms deviation from unity of H(sub AB)/H(sub 0) (where H(sub 0) is the Hubble constant for each model) is 5%, making H(sub AB) a good indicator for H(sub 0). Taking this variation as an additional error, our formal estimate for the Hubble constant is H(sub 0) approximately equals (84 +/- 5)(1 + epsilon) km/s Mpc.

Lu, Nanyao Y.↗

Parallel computational fluid dynamics - Implementations and results

The present volume on parallel CFD discusses implementations on parallel machines, numerical algorithms for parallel CFD, and performance evaluation and computer science issues. Attention is given to a parallel algorithm for compressible flows through rotor-stator combinations, a massively parallel Euler solver for unstructured grids, a fast scheme to analyze 3D disk airflow on a parallel computer, and a block implicit multigrid solution of the Euler equations. Topics addressed include a 3D ADI algorithm on distributed memory multiprocessors, clustered element-by-element computations for fluid flow, hypercube FFT and the Fourier pseudospectral method, and an investigation of parallel iterative algorithms for CFD. Also discussed are fluid dynamics using interface methods on parallel processors, sorting for particle flow simulation on the connection machine, a large grain mapping method, and efforts toward a Teraflops capability for CFD.

Simon, Horst D.↗

Impact of Magnetic Draping, Convection, and Field Line Tying on Magnetopause Reconnection Under Northward IMF

We simulate a northward IMF cusp reconnection event at the magnetopause using the OpenGGCM resistive MHD code. The ACE input data, solar wind parameters, and dipole tilt belong to a 2002 reconnection event observed by IMAGE and Cluster. Based on a fully three-dimensional skeleton separators, nulls, and parallel electric fields, we show magnetic draping, convection, ionospheric field line tying play a role in producing a series of locally reconnecting nulls with flux ropes. The flux ropes in the cusp along the global separator line of symmetry. In 2D projection, the flux ropes the appearance of a tearing mode with a series of 'x's' and 'o's' but bearing a kind of 'guide field' that exists only within the magnetopause. The reconnecting field lines in the string of ropes involve IMF and both open and closed Earth magnetic field lines. The observed magnetic geometry reproduces the findings of a superposed epoch impact parameter study derived from the Cluster magnetometer data for the same event. The observed geometry has repercussions for spacecraft observations of cusp reconnection and for the imposed boundary conditions reconnection simulations.

Wendel, Deirdre E.↗

Parallel architectures for iterative methods on adaptive, block structured grids

A parallel computer architecture well suited to the solution of partial differential equations in complicated geometries is proposed. Algorithms for partial differential equations contain a great deal of parallelism. But this parallelism can be difficult to exploit, particularly on complex problems. One approach to extraction of this parallelism is the use of special purpose architectures tuned to a given problem class. The architecture proposed here is tuned to boundary value problems on complex domains. An adaptive elliptic algorithm which maps effectively onto the proposed architecture is considered in detail. Two levels of parallelism are exploited by the proposed architecture. First, by making use of the freedom one has in grid generation, one can construct grids which are locally regular, permitting a one to one mapping of grids to systolic style processor arrays, at least over small regions. All local parallelism can be extracted by this approach. Second, though there may be a regular global structure to the grids constructed, there will be parallelism at this level. One approach to finding and exploiting this parallelism is to use an architecture having a number of processor clusters connected by a switching network. The use of such a network creates a highly flexible architecture which automatically configures to the problem being solved.

Gannon, D.↗

Experimental studies of the properties of 'simulated' upstream turbulence using a statistical multipoint method

In this report we present a different approach to the multipoint measurement of magnetic fields and plasma. This is called the multi-spacecraft ensemble technique (MET), essentially free of process restrictions, such as linearity and stationarity. We comprehensively discuss the other conditions and limitations intrinsic to this statistical method. We also show the results of the application of the ensemble method to the synthetic data obtained from a hybrid simulation in the region upstream of a quasi-parallel shock. The important implications of the above approach for the CLUSTER mission are discussed.

Orlowski, D. S.↗

Observations of parallel ion energization in the equatorial region

In this paper an example of bounce-phase-clustered ions such as earlier reported by Mellwain (1976), Quinn (1978) and Quinn and Mellwain (1979) is examined in detail. The cluster has small pitch angle, but investigation of the energy time dispersion properties of the cluster reveals that it was formed at the equator. The acceleration region extended over about 2.4 earth radii along the field direction. It is suggested that the ion cluster is set up by acceleration during a transient convection surge, and the properties of such a process are discussed.

Quinn, J. M.↗