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

On the smoothness of nonlinear system identification

We shed new light on the \textit{smoothness} of optimization problems arising in prediction error parameter estimation of linear and nonlinear systems. We show that for regions of the parameter space where the model is not contractive, the Lipschitz constant and $\beta$-smoothness of the objective function might blow up exponentially with the simulation length, making it hard to numerically find minima within those regions or, even, to escape from them. In addition to providing theoretical understanding of this problem, this paper also proposes the use of multiple shooting as a viable solution. The proposed method minimizes the error between a prediction model and the observed values. Rather than running the prediction model over the entire dataset, multiple shooting splits the data into smaller subsets and runs the prediction model over each subset, making the simulation length a design parameter and making it possible to solve problems that would be infeasible using a standard approach. The equivalence to the original problem is obtained by including constraints in the optimization. The new method is illustrated by estimating the parameters of nonlinear systems with chaotic or unstable behavior, as well as neural networks. We also present a comparative analysis of the proposed method with multi-step-ahead prediction error minimization

Process length variation in cysts of a dinoflagellate, Lingulodinium machaerophorum, in surface sediments: Investigating its potential as salinity proxy

“Many authors have contributed to writing this paper. Those listed in the metadata are: the main/contact author, the first listed author and Brunel University author(s). For a full list of the authors, please see the PDF version.”A biometrical analysis of the dinoflagellate cyst Lingulodinium machaerophorum (Deflandre and Cookson 1955) Wall, 1967 in 144 globally distributed surface sediment samples revealed that the average process length is related to summer salinity and temperature at a water depth of 30 m by the equation (salinity/temperature) = (0.078*average process length + 0.534) with R² = 0.69. This relationship can be used to reconstruct palaeosalinities, albeit with caution. The particular ecological window can be associated with known distributions of the corresponding motile stage Lingulodinium polyedrum (Stein) Dodge, 1989. Confocal laser microscopy showed that the average process length is positively related to the average distance between process bases (R²=0.78), and negatively related to the number of processes (R²=0.65). These results document the existence of two end members in cyst formation: one with many short, densely distributed processes and one with a few, long, widely spaced processes, which can be respectively related to low and high salinity/temperature ratios. Obstruction during formation of the cysts causes anomalous distributions of the processes. From a biological perspective, processes function to facilitate sinking of the cysts through clustering

Magnon Heat Conductivity and Mean Free Paths in Two-Leg Spin Ladders: A Model-Independent Determination

The magnon thermal conductivity $\kappa_{\mathrm{mag}}$ of the spin ladders in $\rm Sr_{14}Cu_{24-x}Zn_xO_{41}$ has been investigated at low doping levels $x=0$, 0.125, 0.25, 0.5 and 0.75. The Zn-impurities generate nonmagnetic defects which define an upper limit for $l_{\mathrm{mag}}$ and therefore allow a clear-cut relation between $l_{\mathrm{mag}}$ and $\kappa_{\mathrm{mag}}$ to be established independently of any model. Over a large temperature range we observe a progressive suppression of $\kappa_{\mathrm{mag}}$ with increasing Zn-content and find in particular that with respect to pure $\rm Sr_{14}Cu_{24}O_{41}$ $\kappa_{\mathrm{mag}}$ is strongly suppressed even in the case of tiny impurity densities where $l_{\mathrm{mag}}\lesssim 374$~{\AA}. This shows unambiguously that large $l_{\mathrm{mag}}\approx 3000$~{\AA} which have been reported for $\rm Sr_{14}Cu_{24}O_{41}$ and $\rm La_{5}Ca_9Cu_{24}O_{41}$ on basis of a kinetic model are in the correct order of magnitude

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

Dynamical analysis of the cluster pair: A3407 + A3408

We carried out a dynamical study of the galaxy cluster pair A3407 \& A3408 based on a spectroscopic survey obtained with the 4 meter Blanco telescope at the CTIO, plus 6dF data, and ROSAT All-Sky-Survey. The sample consists of 122 member galaxies brighter than $m_R=20$. Our main goal is to probe the galaxy dynamics in this field and verify if the sample constitutes a single galaxy system or corresponds to an ongoing merging process. Statistical tests were applied to clusters members showing that both the composite system A3407 + A3408 as well as each individual cluster have Gaussian velocity distribution. A velocity gradient of $\sim 847\pm 114$ $\rm km\;s^{-1}$ was identified around the principal axis of the projected distribution of galaxies, indicating that the global field may be rotating. Applying the KMM algorithm to the distribution of galaxies we found that the solution with two clusters is better than the single unit solution at the 99\% c.l. This is consistent with the X-ray distribution around this field, which shows no common X-ray halo involving A3407 and A3408. We also estimated virial masses and applied a two-body model to probe the dynamics of the pair. The more likely scenario is that in which the pair is gravitationally bound and probably experiences a collapse phase, with the cluster cores crossing in less than $\sim$1 $h^{-1}$ Gyr, a pre-merger scenario. The complex X-ray morphology, the gas temperature, and some signs of galaxy evolution in A3408 suggests a post-merger scenario, with cores having crossed each other $\sim 1.65 h^{-1}$Gyr ago, as an alternative solution.Comment: 17 pages, 12 figures, submitted to MNRAS, accepted 2016 May 9. Received 2016 May 9; in original form 2016 April 1

Influence of temperature fluctuations on plasma turbulence investigations with Langmuir probes

The reliability of Langmuir probe measurements for plasma-turbulence investigations is studied on GEMR gyro-fluid simulations and compared with results from conditionally sampled I-V characteristics as well as self-emitting probe measurements in the near scrape-off layer of the tokamak ASDEX Upgrade. In this region, simulation and experiment consistently show coherent in-phase fluctuations in density, plasma potential and also in electron temperature. Ion-saturation current measurements turn out to reproduce density fluctuations quite well. Fluctuations in the floating potential, however, are strongly influenced by temperature fluctuations and, hence, are strongly distorted compared to the actual plasma potential. These results suggest that interpreting floating as plasma-potential fluctuations while disregarding temperature effects is not justified near the separatrix of hot fusion plasmas. Here, floating potential measurements lead to corrupted results on the ExB dynamics of turbulent structures in the context of, e.g., turbulent particle and momentum transport or instability identification on the basis of density-potential phase relations