Partitioning strategy for efficient nonlinear finite element dynamic analysis on multiprocessor computers

A computational procedure is presented for the nonlinear dynamic analysis of unsymmetric structures on vector multiprocessor systems. The procedure is based on a novel hierarchical partitioning strategy in which the response of the unsymmetric and antisymmetric response vectors (modes), each obtained by using only a fraction of the degrees of freedom of the original finite element model. The three key elements of the procedure which result in high degree of concurrency throughout the solution process are: (1) mixed (or primitive variable) formulation with independent shape functions for the different fields; (2) operator splitting or restructuring of the discrete equations at each time step to delineate the symmetric and antisymmetric vectors constituting the response; and (3) two level iterative process for generating the response of the structure. An assessment is made of the effectiveness of the procedure on the CRAY X-MP/4 computers

Dynamical aspects of mean field plane rotators and the Kuramoto model

The Kuramoto model has been introduced in order to describe synchronization phenomena observed in groups of cells, individuals, circuits, etc... We look at the Kuramoto model with white noise forces: in mathematical terms it is a set of N oscillators, each driven by an independent Brownian motion with a constant drift, that is each oscillator has its own frequency, which, in general, changes from one oscillator to another (these frequencies are usually taken to be random and they may be viewed as a quenched disorder). The interactions between oscillators are of long range type (mean field). We review some results on the Kuramoto model from a statistical mechanics standpoint: we give in particular necessary and sufficient conditions for reversibility and we point out a formal analogy, in the N to infinity limit, with local mean field models with conservative dynamics (an analogy that is exploited to identify in particular a Lyapunov functional in the reversible set-up). We then focus on the reversible Kuramoto model with sinusoidal interactions in the N to infinity limit and analyze the stability of the non-trivial stationary profiles arising when the interaction parameter K is larger than its critical value K_c. We provide an analysis of the linear operator describing the time evolution in a neighborhood of the synchronized profile: we exhibit a Hilbert space in which this operator has a self-adjoint extension and we establish, as our main result, a spectral gap inequality for every K>K_c.Comment: 18 pages, 1 figur

A spatial model of autocatalytic reactions

Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive protocells, and they could have provided the ideal environment for pre-biotic reactions to occur. In this paper, we investigate the stochastic dynamics of a set of autocatalytic reactions, within a spatially bounded domain, so as to mimic a primordial cell. The discreteness of the constituents of the autocatalytic reactions gives rise to large sustained oscillations, even when the number of constituents is quite large. These oscillations are spatio-temporal in nature, unlike those found in previous studies, which consisted only of temporal oscillations. We speculate that these oscillations may have a role in seeding membrane instabilities which lead to vesicle division. In this way synchronization could be achieved between protocell growth and the reproduction rate of the constituents (the protogenetic material) in simple protocells.Comment: Submitted to Phys. Rev.

Synchronicity From Synchronized Chaos

The synchronization of loosely coupled chaotic oscillators, a phenomenon investigated intensively for the last two decades, may realize the philosophical notion of synchronicity. Effectively unpredictable chaotic systems, coupled through only a few variables, commonly exhibit a predictable relationship that can be highly intermittent. We argue that the phenomenon closely resembles the notion of meaningful synchronicity put forward by Jung and Pauli if one identifies "meaningfulness" with internal synchronization, since the latter seems necessary for synchronizability with an external system. Jungian synchronization of mind and matter is realized if mind is analogized to a computer model, synchronizing with a sporadically observed system as in meteorological data assimilation. Internal synchronization provides a recipe for combining different models of the same objective process, a configuration that may also describe the functioning of conscious brains. In contrast to Pauli's view, recent developments suggest a materialist picture of semi-autonomous mind, existing alongside the observed world, with both exhibiting a synchronistic order. Basic physical synchronicity is manifest in the non-local quantum connections implied by Bell's theorem. The quantum world resides on a generalized synchronization "manifold", a view that provides a bridge between nonlocal realist interpretations and local realist interpretations that constrain observer choice .Comment: 1) clarification regarding the connection with philosophical synchronicity in Section 2 and in the concluding section 2) reference to Maldacena-Susskind "ER=EPR" relation in discussion of role of wormholes in entanglement and nonlocality 3) length reduction and stylistic changes throughou

Parallel Implementation of the PHOENIX Generalized Stellar Atmosphere Program. II: Wavelength Parallelization

We describe an important addition to the parallel implementation of our generalized NLTE stellar atmosphere and radiative transfer computer program PHOENIX. In a previous paper in this series we described data and task parallel algorithms we have developed for radiative transfer, spectral line opacity, and NLTE opacity and rate calculations. These algorithms divided the work spatially or by spectral lines, that is distributing the radial zones, individual spectral lines, or characteristic rays among different processors and employ, in addition task parallelism for logically independent functions (such as atomic and molecular line opacities). For finite, monotonic velocity fields, the radiative transfer equation is an initial value problem in wavelength, and hence each wavelength point depends upon the previous one. However, for sophisticated NLTE models of both static and moving atmospheres needed to accurately describe, e.g., novae and supernovae, the number of wavelength points is very large (200,000--300,000) and hence parallelization over wavelength can lead both to considerable speedup in calculation time and the ability to make use of the aggregate memory available on massively parallel supercomputers. Here, we describe an implementation of a pipelined design for the wavelength parallelization of PHOENIX, where the necessary data from the processor working on a previous wavelength point is sent to the processor working on the succeeding wavelength point as soon as it is known. Our implementation uses a MIMD design based on a relatively small number of standard MPI library calls and is fully portable between serial and parallel computers.Comment: AAS-TeX, 15 pages, full text with figures available at ftp://calvin.physast.uga.edu/pub/preprints/Wavelength-Parallel.ps.gz ApJ, in pres

Paraiso : An Automated Tuning Framework for Explicit Solvers of Partial Differential Equations

We propose Paraiso, a domain specific language embedded in functional programming language Haskell, for automated tuning of explicit solvers of partial differential equations (PDEs) on GPUs as well as multicore CPUs. In Paraiso, one can describe PDE solving algorithms succinctly using tensor equations notation. Hydrodynamic properties, interpolation methods and other building blocks are described in abstract, modular, re-usable and combinable forms, which lets us generate versatile solvers from little set of Paraiso source codes. We demonstrate Paraiso by implementing a compressive hydrodynamics solver. A single source code less than 500 lines can be used to generate solvers of arbitrary dimensions, for both multicore CPUs and GPUs. We demonstrate both manual annotation based tuning and evolutionary computing based automated tuning of the program.Comment: 52 pages, 14 figures, accepted for publications in Computational Science and Discover

A compiler approach to scalable concurrent program design

The programmer's most powerful tool for controlling complexity in program design is abstraction. We seek to use abstraction in the design of concurrent programs, so as to separate design decisions concerned with decomposition, communication, synchronization, mapping, granularity, and load balancing. This paper describes programming and compiler techniques intended to facilitate this design strategy. The programming techniques are based on a core programming notation with two important properties: the ability to separate concurrent programming concerns, and extensibility with reusable programmer-defined abstractions. The compiler techniques are based on a simple transformation system together with a set of compilation transformations and portable run-time support. The transformation system allows programmer-defined abstractions to be defined as source-to-source transformations that convert abstractions into the core notation. The same transformation system is used to apply compilation transformations that incrementally transform the core notation toward an abstract concurrent machine. This machine can be implemented on a variety of concurrent architectures using simple run-time support. The transformation, compilation, and run-time system techniques have been implemented and are incorporated in a public-domain program development toolkit. This toolkit operates on a wide variety of networked workstations, multicomputers, and shared-memory multiprocessors. It includes a program transformer, concurrent compiler, syntax checker, debugger, performance analyzer, and execution animator. A variety of substantial applications have been developed using the toolkit, in areas such as climate modeling and fluid dynamics

A Solution for the Generalized Synchronization of a Class of Chaotic Systems Based on Output Feedback

A solution to the output-feedback generalized synchronization problem for two chaotic systems, namely, the master and the slave, is presented. The solution assumes that the slave is controlled by a single input, and the states of each system are partially known. To this end, both systems are expressed in their corresponding observable generalized canonical form, through their differential primitive element. The nonavailable state variables of both systems are recovered using a suitable Luenberger observer. The convergence analysis was carried out using the linear control approach in conjunction with the Lyapunov method. Convincing numerical simulations are presented to assess the effectiveness of the obtained solution

CMOS design of chaotic oscillators using state variables: a monolithic Chua's circuit

This paper presents design considerations for monolithic implementation of piecewise-linear (PWL) dynamic systems in CMOS technology. Starting from a review of available CMOS circuit primitives and their respective merits and drawbacks, the paper proposes a synthesis approach for PWL dynamic systems, based on state-variable methods, and identifies the associated analog operators. The GmC approach, combining quasi-linear VCCS's, PWL VCCS's, and capacitors is then explored regarding the implementation of these operators. CMOS basic building blocks for the realization of the quasi-linear VCCS's and PWL VCCS's are presented and applied to design a Chua's circuit IC. The influence of GmC parasitics on the performance of dynamic PWL systems is illustrated through this example. Measured chaotic attractors from a Chua's circuit prototype are given. The prototype has been fabricated in a 2.4- mu m double-poly n-well CMOS technology, and occupies 0.35 mm/sup 2/, with a power consumption of 1.6 mW for a +or-2.5-V symmetric supply. Measurements show bifurcation toward a double-scroll Chua's attractor by changing a bias current