Performance Models for Data Transfers: A Case Study with Molecular Chemistry Kernels

With increasing complexity of hardwares, systems with different memory nodes are ubiquitous in High Performance Computing (HPC). It is paramount to develop strategies to overlap the data transfers between memory nodes with computations in order to exploit the full potential of these systems. In this article, we consider the problem of deciding the order of data transfers between two memory nodes for a set of independent tasks with the objective to minimize the makespan. We prove that with limited memory capacity, obtaining the optimal order of data transfers is a NP-complete problem. We propose several heuristics for this problem and provide details about their favorable situations. We present an analysis of our heuristics on traces, obtained by running 2 molecular chemistry kernels, namely, Hartree-Fock (HF) and Coupled Cluster Single Double (CCSD) on 10 nodes of an HPC system. Our results show that some of our heuristics achieve significant overlap for moderate memory capacities and are very close to the lower bound of makespan

Effect of the curvature and the {\beta} parameter on the nonlinear dynamics of a drift tearing magnetic island

We present numerical simulation studies of 2D reduced MHD equations investigating the impact of the electronic \beta parameter and of curvature effects on the nonlinear evolution of drift tearing islands. We observe a bifurcation phenomenon that leads to an amplification of the pressure energy, the generation of E \times B poloidal flow and a nonlinear diamagnetic drift that affects the rotation of the magnetic island. These dynamical modifications arise due to quasilinear effects that generate a zonal flow at the onset point of the bifurcation. Our simulations show that the transition point is influenced by the \beta parameter such that the pressure gradient through a curvature effect strongly stabilizes the transition. Regarding the modified rotation of the island, a model for the frequency is derived in order to study its origin and the effect of the \beta parameter. It appears that after the transition, an E \times B poloidal flow as well as a nonlinear diamagnetic drift are generated due to an amplification of the stresses by pressure effects

Large-Eddy Simulations of Fluid and Magnetohydrodynamic Turbulence Using Renormalized Parameters

In this paper a procedure for large-eddy simulation (LES) has been devised for fluid and magnetohydrodynamic turbulence in Fourier space using the renormalized parameters. The parameters calculated using field theory have been taken from recent papers by Verma [Phys. Rev. E, 2001; Phys. Plasmas, 2001]. We have carried out LES on $64^3$ grid. These results match quite well with direct numerical simulations of $128^3$. We show that proper choice of parameter is necessary in LES.Comment: 12 pages, 4 figures: Proper figures inserte

Self-gravitating Brownian particles in two dimensions: the case of N=2 particles

We study the motion of N=2 overdamped Brownian particles in gravitational interaction in a space of dimension d=2. This is equivalent to the simplified motion of two biological entities interacting via chemotaxis when time delay and degradation of the chemical are ignored. This problem also bears some similarities with the stochastic motion of two point vortices in viscous hydrodynamics [Agullo & Verga, Phys. Rev. E, 63, 056304 (2001)]. We analytically obtain the density probability of finding the particles at a distance r from each other at time t. We also determine the probability that the particles have coalesced and formed a Dirac peak at time t (i.e. the probability that the reduced particle has reached r=0 at time t). Finally, we investigate the variance of the distribution and discuss the proper form of the virial theorem for this system. The reduced particle has a normal diffusion behaviour for small times with a gravity-modified diffusion coefficient =r_0^2+(4k_B/\xi\mu)(T-T_*)t, where k_BT_{*}=Gm_1m_2/2 is a critical temperature, and an anomalous diffusion for large times ~t^(1-T_*/T). As a by-product, our solution also describes the growth of the Dirac peak (condensate) that forms in the post-collapse regime of the Smoluchowski-Poisson system (or Keller-Segel model) for T<T_c=GMm/(4k_B). We find that the saturation of the mass of the condensate to the total mass is algebraic in an infinite domain and exponential in a bounded domain.Comment: Revised version (20/5/2010) accepted for publication in EPJ

Quercetin prevents progression of disease in elastase/LPS-exposed mice by negatively regulating MMP expression

Abstract Background Chronic obstructive pulmonary disease (COPD) is characterized by chronic bronchitis, emphysema and irreversible airflow limitation. These changes are thought to be due to oxidative stress and an imbalance of proteases and antiproteases. Quercetin, a plant flavonoid, is a potent antioxidant and anti-inflammatory agent. We hypothesized that quercetin reduces lung inflammation and improves lung function in elastase/lipopolysaccharide (LPS)-exposed mice which show typical features of COPD, including airways inflammation, goblet cell metaplasia, and emphysema. Methods Mice treated with elastase and LPS once a week for 4 weeks were subsequently administered 0.5 mg of quercetin dihydrate or 50% propylene glycol (vehicle) by gavage for 10 days. Lungs were examined for elastance, oxidative stress, inflammation, and matrix metalloproteinase (MMP) activity. Effects of quercetin on MMP transcription and activity were examined in LPS-exposed murine macrophages. Results Quercetin-treated, elastase/LPS-exposed mice showed improved elastic recoil and decreased alveolar chord length compared to vehicle-treated controls. Quercetin-treated mice showed decreased levels of thiobarbituric acid reactive substances, a measure of lipid peroxidation caused by oxidative stress. Quercetin also reduced lung inflammation, goblet cell metaplasia, and mRNA expression of pro-inflammatory cytokines and muc5AC. Quercetin treatment decreased the expression and activity of MMP9 and MMP12 in vivo and in vitro, while increasing expression of the histone deacetylase Sirt-1 and suppressing MMP promoter H4 acetylation. Finally, co-treatment with the Sirt-1 inhibitor sirtinol blocked the effects of quercetin on the lung phenotype. Conclusions Quercetin prevents progression of emphysema in elastase/LPS-treated mice by reducing oxidative stress, lung inflammation and expression of MMP9 and MMP12.http://deepblue.lib.umich.edu/bitstream/2027.42/78260/1/1465-9921-11-131.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78260/2/1465-9921-11-131.pdfPeer Reviewe

Loop Quantum Cosmology: A Status Report

The goal of this article is to provide an overview of the current state of the art in loop quantum cosmology for three sets of audiences: young researchers interested in entering this area; the quantum gravity community in general; and, cosmologists who wish to apply loop quantum cosmology to probe modifications in the standard paradigm of the early universe. An effort has been made to streamline the material so that, as described at the end of section I, each of these communities can read only the sections they are most interested in, without a loss of continuity.Comment: 138 pages, 15 figures. Invited Topical Review, To appear in Classical and Quantum Gravity. Typos corrected, clarifications and references adde