Large-scale linear system solver using secondary storage: Self-energy in hybrid nanostructures

We present a Fortran library which can be used to solve large-scale dense linear systems, Ax=b. The library is based on the LU decomposition included in the parallel linear algebra library PLAPACK and on its out-of-core extension POOCLAPACK. The library is complemented with a code which calculates the self-polarization charges and self-energy potential of axially symmetric nanostructures, following an induced charge computation method. Illustrative calculations are provided for hybrid semiconductor–quasi-metal zero-dimensional nanostructures. In these systems, the numerical integration of the self-polarization equations requires using a very fine mesh. This translates into very large and dense linear systems, which we solve for ranks up to 3×¹⁰⁵. It is shown that the self-energy potential on the semiconductor–metal interface has important effects on the electronic wavefunction.

Program summary

Program title: HDSS (Huge Dense System Solver)Catalogue identifier: AEHU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 98 889No. of bytes in distributed program, including test data, etc.: 1 009 622Distribution format: tar.gzProgramming language: Fortran 90, CComputer: Parallel architectures: multiprocessors, computer clustersOperating system: Linux/UnixHas the code been vectorized or parallelized?: Yes. 4 processors used in the sample tests; tested from 1 to 288 processorsRAM: 2 GB for the sample tests; tested for up to 80 GBClassification: 7.3External routines: MPI, BLAS, PLAPACK, POOCLAPACK. PLAPACK and POOCLAPACK are included in the distribution file.Nature of problem: Huge scale dense systems of linear equations, Ax=B, beyond standard LAPACK capabilities. Application to calculations of self-energy potential in dielectrically mismatched semiconductor quantum dots.Solution method: The linear systems are solved by means of parallelized routines based on the LU factorization, using efficient secondary storage algorithms when the available main memory is insufficient. The self-energy solver relies on an induced charge computation method. The differential equation is discretized to yield linear systems of equations, which we then solve by calling the HDSS library.Restrictions: Simple precision. For the self-energy solver, axially symmetric systems must be considered.Running time: About 32 minutes to solve a system with approximately 100 000 equations and more than 6000 right-hand side vectors using a four-node commodity cluster with a total of 32 Intel cores.     

Frequency domain regularization of d-dimensional structure tensor-based directional fields

The present work is intended to address two of the major difficulties that can be found when tackling the estimation of the local orientation of the data in a scene, a task which is usually accomplished by means of the computation of the structure tensor-based directional field. On one hand, the orientation information only exists in the non-homogeneous regions of the dataset, while it is zero in the areas where the gradient (i.e. the first-order intensity variation) remains constant. Due to this lack of information, there are many cases in which the overall shape of the represented objects cannot be precisely inferred from the directional field. On the other hand, the orientation estimation is highly dependent on the particular choice of the averaging window used for its computation (since a collection of neighboring gradient vectors is needed to obtain a dominant orientation), typically resulting in vector fields which vary from very irregular (thus yielding a noisy estimation) to very uniform (but at the expense of a loss of angular resolution). The proposed solution to both drawbacks is the regularization of the directional field; this process extends smoothly the previously computed vectors to the whole dataset while preserving the angular information of relevant structures. With this purpose, the paper introduces a suitable mathematical framework and deals with the d-dimensional variational formulation which is derived from it. The proposed formulation is finally translated into the frequency domain in order to obtain an increase of insight on the regularization problem, which can be understood as a low-pass filtering of the directional field. The frequency domain point of view also allows for an efficient implementation of the resulting iterative algorithm. Simulation experiments involving datasets of different dimensionality prove the validity of the theoretical approach.     

Acoustic scattering solver based on single level FMM for multi-GPU systems

In this paper, we present a heterogeneous parallel solver of a high frequency single level Fast Multipole Method (FMM) for the Helmholtz equation applied to acoustic scattering. The developed solution uses multiple GPUs to tackle the compute bound steps of the FMM (aggregation, disaggregation, and near interactions) while the CPU handles a memory bound step (translation) using OpenMP. The proposed solver performance is measured on a workstation with two GPUs (NVIDIA GTX 480) and is compared with that of a distributed memory solver run on a cluster of 32 nodes (HP BL465c) with an Infiniband network. Some energy efficiency results are also presented in this work.     

A collaborative platform for cognitive decision making in the Knowledge Society

Two key aspects of the Knowledge Society are the interconnection between the actors involved in the decision making processes and the importance of the human factor, particularly the citizen’s continuous learning and education. This paper presents a new module devoted to knowledge extraction and diffusion that has been incorporated into a previously developed decision making tool concerning the Internet and related with the multicriteria selection of a discrete number of alternatives (PRIOR-Web). Quantitative and qualitative procedures using data and text mining methods have been employed in the extraction of knowledge. Graphical visualisation tools have been incorporated in the diffusion stage of the methodological approach suggested when dealing with decision making in the Knowledge Society. The resulting collaborative platform is being used as the methodological support for the cognitive democracy known as e-cognocracy.     

A probabilistic integrated object recognition and tracking framework

This paper describes a probabilistic integrated object recognition and tracking framework called PIORT, together with two specific methods derived from it, which are evaluated experimentally in several test video sequences. The first step in the proposed framework is a static recognition module that provides class probabilities for each pixel of the image from a set of local features. These probabilities are updated dynamically and supplied to a tracking decision module capable of handling full and partial occlusions. The two specific methods presented use RGB color features and differ in the classifier implemented: one is a Bayesian method based on maximum likelihood and the other one is based on a neural network. The experimental results obtained have shown that, on one hand, the neural net based approach performs similarly and sometimes better than the Bayesian approach when they are integrated within the tracking framework. And on the other hand, our PIORT methods have achieved better results when compared to other published tracking methods in video sequences taken with a moving camera and including full and partial occlusions of the tracked object.     

IDR/UPM facilities for liquid bridge experimentation on Earth under microgravity conditions

Besides space laboratories for in-orbit experimentation, Earth based facilities for laboratory experimentation are of paramount importance for the enhancement on liquid bridge knowledge. In spite of the constraints imposed by simulated microgravity (which force to work either with very small size liquid bridges or by using the Plateau tank technique, amongst other techniques), the availability and accessibility of Earth facilities can circumvent in many cases the drawbacks associated with simulated microgravity conditions. To support theoretical and in orbit experimental studies on liquid bridges under reduced gravity conditions, several ground facilities were developed at IDR. In the following these ground facilities are briefly described, and main results obtained by using them are cited.     

Sex, Age, and Training Modulate Spatial Memory in the Rhesus Monkey (Macaca mulatta).

The authors tested 90 rhesus monkeys (Macaca mulatta) on a task of spatial memory, the spatial Delayed Recognition Span Test. The results showed that performance declined significantly with age, males had greater scores than females, and the rate of apparent decline with age was greater in males than in females. Both working and reference memory declined with age, but only working memory showed sex differences. The authors compared these data with that of 22 monkeys who were trained on a simpler version of the task before formal testing. Training had no effect on males but dramatically improved working memory in young females. The results confirm a male advantage in spatial working memory at a young age and confirm a greater decline with age in males than in females. It is important to note that prior training completely reverses the deficits of young females. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Sequential Compatibility Effects and Cognitive Control: Does Conflict Really Matter?

Although it is widely accepted that control mechanisms are necessary for human behavior to be adapted, very little is known about how such mechanisms are recruited. A suggestion to fill the gap was put forward by M. M. Botvinick, T. S. Braver, C. S. Carter, D. M. Barch, and J. D. Cohen (2001), who proposed the conflict-loop theory. This theory has been successful in accounting for the reduction of compatibility effects after an incompatible trial: The level of conflict being, on average, higher during an incompatible trial, more control occurs after such a trial. The authors have tested this prediction by sorting the trials on the basis of amount of conflict (quantified by the electromyographic activity) they presented. A reduction of the compatibility effect was observed after incompatible trials, but it was independent of the level of conflict on previous trials, suggesting that the conflict does not trigger changes in executive control. Consequences for the conflict monitoring model are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A Narrowing-based Instantiation Rule for Rewriting-based Fold/Unfold Transformations

In this paper we show how to transfer some developments done in the field of functionallogic programming (FLP) to a pure functional setting (FP). More exactly, we propose a complete fold/unfold based transformation system for optimizing lazy functional programs. Our main contribution is the definition of a safe instantiation rule which is used to enable effective unfolding steps based on rewriting. Since instantiation has been traditionally considered problematic in FP, we take advantage of previous experiences in the more general setting of FLP where instantiation is naturally embedded into an unfolding rule based on narrowing. Inspired by the so called needed narrowing strategy, our instantiation rule inherits the best properties of this refinement of narrowing. Our proposal optimizes previous approaches (that require more transformation effort) defined in the specialized literature of pure FP by anticipating bindings on unifiers used to instantiate a given program rule and by generating redexes at different positions on instantiated rules in order to enable subsequent unfolding steps. As a consequence, our correct/complete technique avoids redundant rules and preserves the natural structure of programs.