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

Action minimizing orbits in the n-body problem with simple choreography constraint

In 1999 Chenciner and Montgomery found a remarkably simple choreographic motion for the planar 3-body problem (see \cite{CM}). In this solution 3 equal masses travel on a eight shaped planar curve; this orbit is obtained minimizing the action integral on the set of simple planar choreographies with some special symmetry constraints. In this work our aim is to study the problem of $n$ masses moving in \RR^d under an attractive force generated by a potential of the kind $1/r^\alpha$, $\alpha >0$, with the only constraint to be a simple choreography: if $q_1(t),...,q_n(t)$ are the $n$ orbits then we impose the existence of x \in H^1_{2 \pi}(\RR,\RR^d) such that q_i(t)=x(t+(i-1) \tau), i=1,...,n, t \in \RR, where $\tau = 2\pi / n$. In this setting, we first prove that for every d,n \in \NN and $\alpha>0$, the lagrangian action attains its absolute minimum on the planar circle. Next we deal with the problem in a rotating frame and we show a reacher phenomenology: indeed while for some values of the angular velocity minimizers are still circles, for others the minima of the action are not anymore rigid motions.Comment: 24 pages; 4 figures; submitted to Nonlinearit

A global glacial ocean state estimate constrained by upper-ocean temperature proxies

Author Posting. © American Meteorological Society, 2018. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 31 (2018): 8059-8079, doi:10.1175/JCLI-D-17-0769.1.We use the method of least squares with Lagrange multipliers to fit an ocean general circulation model to the Multiproxy Approach for the Reconstruction of the Glacial Ocean Surface (MARGO) estimate of near sea surface temperature (NSST) at the Last Glacial Maximum (LGM; circa 23–19 thousand years ago). Compared to a modern simulation, the resulting global, last-glacial ocean state estimate, which fits the MARGO data within uncertainties in a free-running coupled ocean–sea ice simulation, has global-mean NSSTs that are 2°C lower and greater sea ice extent in all seasons in both the Northern and Southern Hemispheres. Increased brine rejection by sea ice formation in the Southern Ocean contributes to a stronger abyssal stratification set principally by salinity, qualitatively consistent with pore fluid measurements. The upper cell of the glacial Atlantic overturning circulation is deeper and stronger. Dye release experiments show similar distributions of Southern Ocean source waters in the glacial and modern western Atlantic, suggesting that LGM NSST data do not require a major reorganization of abyssal water masses. Outstanding challenges in reconstructing LGM ocean conditions include reducing effects from model biases and finding computationally efficient ways to incorporate abyssal tracers in global circulation inversions. Progress will be aided by the development of coupled ocean–atmosphere–ice inverse models, by improving high-latitude model processes that connect the upper and abyssal oceans, and by the collection of additional paleoclimate observations.DEA was supported by a NSF Graduate Research Fellowship and NSF Grant OCE-1060735. OM acknowledges support from the NSF. GF was supported by NASA Award 1553749 and Simons Foundation Award 549931

Depth of interaction and bias voltage depenence of the spectral response in a pixellated CdTe detector operating in time-over-threshold mode subjected to monochromatic X-rays

High stopping power is one of the most important figures of merit for X-ray detectors. CdTe is a promising material but suffers from: material defects, non-ideal charge transport and long range X-ray fluorescence. Those factors reduce the image quality and deteriorate spectral information. In this project we used a monochromatic pencil beam collimated through a 20μm pinhole to measure the detector spectral response in dependance on the depth of interaction. The sensor was a 1mm thick CdTe detector with a pixel pitch of 110μm, bump bonded to a Timepix readout chip operating in Time-Over-Threshold mode. The measurements were carried out at the Extreme Conditions beamline I15 of the Diamond Light Source. The beam was entering the sensor at an angle of \texttildelow20 degrees to the surface and then passed through \texttildelow25 pixels before leaving through the bottom of the sensor. The photon energy was tuned to 77keV giving a variation in the beam intensity of about three orders of magnitude along the beam path. Spectra in Time-over-Threshold (ToT) mode were recorded showing each individual interaction. The bias voltage was varied between -30V and -300V to investigate how the electric field affected the spectral information. For this setup it is worth noticing the large impact of fluorescence. At -300V the photo peak and escape peak are of similar height. For high bias voltages the spectra remains clear throughout the whole depth but for lower voltages as -50V, only the bottom part of the sensor carries spectral information. This is an effect of the low hole mobility and the longer range the electrons have to travel in a low field

Un nouveau poisson intéressant l'industrie de la conserve des côtes d'Afrique : Le Paracubiceps Ledanoisi (BELLOC)

Un poisson peu connu de la Côte Occidentale d'Afrique, le Paracubiceps Ledanoisi (Belloc) a été expérimenté en vue d'une mise en conserve. Les essais techniques ont été satisfaisants et ne nécessitent plus qu'une mise au point. Il semble par ailleurs que les stocks de ce poisson soient suffisamment importants pour en permettre une exploitation commerciale. Le but à atteindre est l'obtention d'une conserve de bonne qualité mais d'un prix de revient suffisamment bas pour pouvoir être vendue dans les pays africains dont la possibilité d'absorption est très grande en ce domain

Distribution and origin of natural gas leakage in the Colorado Basin, offshore Argentina 2 Margin, South America: seismic interpretation and 3D basin modelling

The detailed analysis of a dense 2D seismic reflection dataset and data from 8 exploration wells, allowed us to identify, map out and characterize possible indications of past and present-day hydrocarbon leakage (i.e. gas chimneys, gas pockets, and seafloor mounds and pockmarks) on the continental shelf and slope of the Colorado Basin, offshore Argentina, where Permian, Jurassic and Early Cretaceous source rocks are potentially present and may be currently mature. Identified gas leakage features, developed both in the syn-rift and post-rift successions, were also analysed in relation to the structural the stratigraphic elements of the basin. A family of seabed pockmarks, located close to an array of submarine channels, was identified on the distal slope of the basin. These pockmarks are overlying a series of sub-vertical to vertical seismic chimneys in the subsurface. A calibrated basin-wide 3D petroleum system model comprising generation and migration of hydrocarbons was carried out and compared with the observations from the seismic analysis. Preliminary results from this model indicate that although synrift and early Cretaceous source rock (SR) intervals may be depleted in the central areas of the basin, an active kitchen from the Aptian SR may be present below the slope areas. Hydrocarbon migration pathways predicted by the 3D model (Hybrid method) coincide with the interpreted seismic chimneys underlying the observed seabed slope pockmarks. Hence, our results indicate that thermogenic gas may be currently generated in the distal slope of the basin from mature early post-rift source rocks within the Early Cretaceous (Aptian) sequences and migrates vertically, due to seal failure, through the stratigraphic column. This migrating thermogenic gas is feeding the seafloor pockmarks identified in the distal slope of the basin, although up-dip lateral migration along stratigraphic layers to the more proximal slope areas cannot be ruled out. The present work represents the first published study integrating detailed seismic analysis and 3D basin modelling linking observed gas-leakage indicators and associated seepage pathways, to their relative abundance, distribution and feeding systems offshore Argentina’s continental margin