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

The partition function of the two-matrix model as an isomonodromic tau-function

We consider the Itzykson-Zuber-Eynard-Mehta two-matrix model and prove that the partition function is an isomonodromic tau function in a sense that generalizes Jimbo-Miwa-Ueno's. In order to achieve the generalization we need to define a notion of tau-function for isomonodromic systems where the ad-regularity of the leading coefficient is not a necessary requirement.Comment: 22 pages, 1 figur

Kinetics of thorium and particle cycling along the U.S. GEOTRACES North Atlantic Transect

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 125 (2017): 106-128, doi:10.1016/j.dsr.2017.05.003.The high particle reactivity of thorium has resulted in its widespread use in tracing processes impacting marine particles and their chemical constituents. The use of thorium isotopes as tracers of particle dynamics, however, largely relies on our understanding of how the element scavenges onto particles. Here, we estimate apparent rate constants of Th adsorption (k1), Th desorption (k−1), bulk particle degradation (β-1), and bulk particle sinking speed (w) along the water column at 11 open-ocean stations occupied during the GEOTRACES North Atlantic Section (GA03). First, we provide evidence that the budgets of Th isotopes and particles at these stations appear to be generally dominated by radioactive production and decay sorption reactions, particle degradation, and particle sinking. Rate parameters are then estimated by fitting a Th and particle cycling model to data of dissolved and particulate 228,230,234Th, 228Ra, particle concentrations, and 234,238U estimates based on salinity, using a nonlinear programming technique. We find that the adsorption rate constant (k1) generally decreases with depth across the section: broadly, the time scale 1/k1 averages 1.0 yr in the upper 1000 m and (1.4–1.5) yr below. A positive relationship between k1 and particle concentration (P) is found, i.e., , k1 ∝ Pb where b ≥ 1, consistent with the notion that k1 increases with the number of surface sites available for adsorption. The rate constant ratio, K = k1/(k-1 + β-1), which measures the collective influence of rate parameters on Th scavenging, averages 0.2 for most stations and most depths. We clarify the conditions under which K/P is equivalent to the distribution coefficient, KD, test that the conditions are met at the stations, and find that decreases with P, in line with a particle concentration effect (dKD/dP < 0). In contrast to the influence of colloids as envisioned by the Brownian pumping hypothesis, we provide evidence that the particle concentration effect arises from the joint effect of P on the rate constants for thorium attachment to, and detachment from, particles.We acknowledge the U.S. National Science Foundation for providing funding for this study (grant OCE-1232578) and for U.S. GEOTRACES North Atlantic section ship time, sampling, and data analysis. The U.S. NSF also supported the generation of 230Th data (OCE-0927064 to LDEO, OCE-O092860 to WHOI, and OCE-0927754 to UMN) and 228,234Th data (OCE-0925158 to WHOI)

Cell-Associated HIV-1 RNA in Blood as Indicator of Virus Load in Lymph Nodes

We have developed sensitive assays for viremia and cell-associated human immunodeficiency virus type 1 (HIV-1) RNA and DNA to assess the predictive value of virological parameters determined in blood for virus load in lymph nodes (LNs). Eighteen patients were included; 13 received stavudine/didanosine/hydroxyurea and 5 stavudine/didanosine, and all had viremia 3 months. At the time of LN biopsy (median, 10 months), the median viremia was 2.09 log copies/mL (range, <0.70-3.34). Cell-associated HIV-1 RNA and DNA were detectable in blood and LNs of all patients. The median cell-associated RNA and DNA were 2.16 log copies/106 cells and 2.60 log copies/106 cells in blood versus 4.31 log RNA copies/106 cells and 3.26 log DNA copies/106 cells in LNs. Regression analysis shows that, in treated patients with sustained low viremia, cell-associated RNA and DNA in blood are better predictors of virus load in LNs than viremi

Topological expansion of beta-ensemble model and quantum algebraic geometry in the sectorwise approach

We solve the loop equations of the $\beta$-ensemble model analogously to the solution found for the Hermitian matrices $\beta=1$. For \beta=1$, the solution was expressed using the algebraic spectral curve of equation$y^2=U(x)$. For arbitrary$\beta$, the spectral curve converts into a Schr\"odinger equation$((\hbar\partial)^2-U(x))\psi(x)=0$with$\hbar\propto (\sqrt\beta-1/\sqrt\beta)/N$. This paper is similar to the sister paper~I, in particular, all the main ingredients specific for the algebraic solution of the problem remain the same, but here we present the second approach to finding a solution of loop equations using sectorwise definition of resolvents. Being technically more involved, it allows defining consistently the B-cycle structure of the obtained quantum algebraic curve (a D-module of the form$y^2-U(x)$, where$[y,x]=\hbar$) and to construct explicitly the correlation functions and the corresponding symplectic invariants$F_h$, or the terms of the free energy, in 1/N^2$-expansion at arbitrary $\hbar$. The set of "flat" coordinates comprises the potential times $t_k$ and the occupation numbers \widetilde{\epsilon}_\alpha$. We define and investigate the properties of the A- and B-cycles, forms of 1st, 2nd and 3rd kind, and the Riemann bilinear identities. We use these identities to find explicitly the singular part of$\mathcal F_0$that depends exclusively on$\widetilde{\epsilon}_\alpha$.Comment: 58 pages, 7 figure

Double scaling limits of random matrices and minimal (2m,1) models: the merging of two cuts in a degenerate case

In this article, we show that the double scaling limit correlation functions of a random matrix model when two cuts merge with degeneracy $2m$ (i.e. when $y\sim x^{2m}$ for arbitrary values of the integer $m$) are the same as the determinantal formulae defined by conformal $(2m,1)$ models. Our approach follows the one developed by Berg\`{e}re and Eynard in \cite{BergereEynard} and uses a Lax pair representation of the conformal $(2m,1)$ models (giving Painlev\'e II integrable hierarchy) as suggested by Bleher and Eynard in \cite{BleherEynard}. In particular we define Baker-Akhiezer functions associated to the Lax pair to construct a kernel which is then used to compute determinantal formulae giving the correlation functions of the double scaling limit of a matrix model near the merging of two cuts.Comment: 37 pages, 4 figures. Presentation improved, typos corrected. Published in Journal Of Statistical Mechanic

Dynamical percolation on general trees

H\"aggstr\"om, Peres, and Steif (1997) have introduced a dynamical version of percolation on a graph $G$. When $G$ is a tree they derived a necessary and sufficient condition for percolation to exist at some time $t$. In the case that $G$ is a spherically symmetric tree, H\"aggstr\"om, Peres, and Steif (1997) derived a necessary and sufficient condition for percolation to exist at some time $t$ in a given target set $D$. The main result of the present paper is a necessary and sufficient condition for the existence of percolation, at some time $t\in D$, in the case that the underlying tree is not necessary spherically symmetric. This answers a question of Yuval Peres (personal communication). We present also a formula for the Hausdorff dimension of the set of exceptional times of percolation.Comment: 24 pages; to appear in Probability Theory and Related Field

Large deviations of the maximal eigenvalue of random matrices

We present detailed computations of the 'at least finite' terms (three dominant orders) of the free energy in a one-cut matrix model with a hard edge a, in beta-ensembles, with any polynomial potential. beta is a positive number, so not restricted to the standard values beta = 1 (hermitian matrices), beta = 1/2 (symmetric matrices), beta = 2 (quaternionic self-dual matrices). This model allows to study the statistic of the maximum eigenvalue of random matrices. We compute the large deviation function to the left of the expected maximum. We specialize our results to the gaussian beta-ensembles and check them numerically. Our method is based on general results and procedures already developed in the literature to solve the Pastur equations (also called "loop equations"). It allows to compute the left tail of the analog of Tracy-Widom laws for any beta, including the constant term.Comment: 62 pages, 4 figures, pdflatex ; v2 bibliography corrected ; v3 typos corrected and preprint added ; v4 few more numbers adde