Parallel structurally-symmetric sparse matrix-vector products on multi-core processors

We consider the problem of developing an efficient multi-threaded implementation of the matrix-vector multiplication algorithm for sparse matrices with structural symmetry. Matrices are stored using the compressed sparse row-column format (CSRC), designed for profiting from the symmetric non-zero pattern observed in global finite element matrices. Unlike classical compressed storage formats, performing the sparse matrix-vector product using the CSRC requires thread-safe access to the destination vector. To avoid race conditions, we have implemented two partitioning strategies. In the first one, each thread allocates an array for storing its contributions, which are later combined in an accumulation step. We analyze how to perform this accumulation in four different ways. The second strategy employs a coloring algorithm for grouping rows that can be concurrently processed by threads. Our results indicate that, although incurring an increase in the working set size, the former approach leads to the best performance improvements for most matrices.Comment: 17 pages, 17 figures, reviewed related work section, fixed typo

Sustainable management of miombo woodlands in the Northern part of Mozambique (Niassa National Reserve - NNR).

Poster presented at Commiting Science to Global Development. Lisbon (Portugal). 29-30 Sep 2009

Confining potential in a color dielectric medium with parallel domain walls

We study quark confinement in a system of two parallel domain walls interpolating different color dielectric media. We use the phenomenological approach in which the confinement of quarks appears considering the QCD vacuum as a color dielectric medium. We explore this phenomenon in QCD_2, where the confinement of the color flux between the domain walls manifests, in a scenario where two 0-branes (representing external quark and antiquark) are connected by a QCD string. We obtain solutions of the equations of motion via first-order differential equations. We find a new color confining potential that increases monotonically with the distance between the domain walls.Comment: RevTex4, 5 pages, 1 figure; version to appear in Int. J. Mod. Phys.

Mutual information in random Boolean models of regulatory networks

The amount of mutual information contained in time series of two elements gives a measure of how well their activities are coordinated. In a large, complex network of interacting elements, such as a genetic regulatory network within a cell, the average of the mutual information over all pairs is a global measure of how well the system can coordinate its internal dynamics. We study this average pairwise mutual information in random Boolean networks (RBNs) as a function of the distribution of Boolean rules implemented at each element, assuming that the links in the network are randomly placed. Efficient numerical methods for calculating show that as the number of network nodes N approaches infinity, the quantity N exhibits a discontinuity at parameter values corresponding to critical RBNs. For finite systems it peaks near the critical value, but slightly in the disordered regime for typical parameter variations. The source of high values of N is the indirect correlations between pairs of elements from different long chains with a common starting point. The contribution from pairs that are directly linked approaches zero for critical networks and peaks deep in the disordered regime.Comment: 11 pages, 6 figures; Minor revisions for clarity and figure format, one reference adde

The Apparent Fractal Conjecture: Scaling Features in Standard Cosmologies

This paper presents an analysis of the smoothness problem in cosmology by focussing on the ambiguities originated in the simplifying hypotheses aimed at observationally verifying if the large-scale distribution of galaxies is homogeneous, and conjecturing that this distribution should follow a fractal pattern in perturbed standard cosmologies. This is due to a geometrical effect, appearing when certain types of average densities are calculated along the past light cone. The paper starts reviewing the argument concerning the possibility that the galaxy distribution follows such a scaling pattern, and the premises behind the assumption that the spatial homogeneity of standard cosmology can be observable. Next, it is argued that to discuss observable homogeneity one needs to make a clear distinction between local and average relativistic densities, and showing how the different distance definitions strongly affect them, leading the various average densities to display asymptotically opposite behaviours. Then the paper revisits Ribeiro's (1995: astro-ph/9910145) results, showing that in a fully relativistic treatment some observational average densities of the flat Friedmann model are not well defined at z ~ 0.1, implying that at this range average densities behave in a fundamentally different manner as compared to the linearity of the Hubble law, well valid for z < 1. This conclusion brings into question the widespread assumption that relativistic corrections can always be neglected at low z. It is also shown how some key features of fractal cosmologies can be found in the Friedmann models. In view of those findings, it is suggested that the so-called contradiction between the cosmological principle, and the galaxy distribution forming an unlimited fractal structure, may not exist.Comment: 30 pages, 2 figures, LaTeX. This paper is a follow-up to gr-qc/9909093. Accepted for publication in "General Relativity and Gravitation