Towards a Mini-App for Smoothed Particle Hydrodynamics at Exascale

The smoothed particle hydrodynamics (SPH) technique is a purely Lagrangian method, used in numerical simulations of fluids in astrophysics and computational fluid dynamics, among many other fields. SPH simulations with detailed physics represent computationally-demanding calculations. The parallelization of SPH codes is not trivial due to the absence of a structured grid. Additionally, the performance of the SPH codes can be, in general, adversely impacted by several factors, such as multiple time-stepping, long-range interactions, and/or boundary conditions. This work presents insights into the current performance and functionalities of three SPH codes: SPHYNX, ChaNGa, and SPH-flow. These codes are the starting point of an interdisciplinary co-design project, SPH-EXA, for the development of an Exascale-ready SPH mini-app. To gain such insights, a rotating square patch test was implemented as a common test simulation for the three SPH codes and analyzed on two modern HPC systems. Furthermore, to stress the differences with the codes stemming from the astrophysics community (SPHYNX and ChaNGa), an additional test case, the Evrard collapse, has also been carried out. This work extrapolates the common basic SPH features in the three codes for the purpose of consolidating them into a pure-SPH, Exascale-ready, optimized, mini-app. Moreover, the outcome of this serves as direct feedback to the parent codes, to improve their performance and overall scalability.Comment: 18 pages, 4 figures, 5 tables, 2018 IEEE International Conference on Cluster Computing proceedings for WRAp1

SPH-EXA: Enhancing the Scalability of SPH codes Via an Exascale-Ready SPH Mini-App

Numerical simulations of fluids in astrophysics and computational fluid dynamics (CFD) are among the most computationally-demanding calculations, in terms of sustained floating-point operations per second, or FLOP/s. It is expected that these numerical simulations will significantly benefit from the future Exascale computing infrastructures, that will perform 10^18 FLOP/s. The performance of the SPH codes is, in general, adversely impacted by several factors, such as multiple time-stepping, long-range interactions, and/or boundary conditions. In this work an extensive study of three SPH implementations SPHYNX, ChaNGa, and XXX is performed, to gain insights and to expose any limitations and characteristics of the codes. These codes are the starting point of an interdisciplinary co-design project, SPH-EXA, for the development of an Exascale-ready SPH mini-app. We implemented a rotating square patch as a joint test simulation for the three SPH codes and analyzed their performance on a modern HPC system, Piz Daint. The performance profiling and scalability analysis conducted on the three parent codes allowed to expose their performance issues, such as load imbalance, both in MPI and OpenMP. Two-level load balancing has been successfully applied to SPHYNX to overcome its load imbalance. The performance analysis shapes and drives the design of the SPH-EXA mini-app towards the use of efficient parallelization methods, fault-tolerance mechanisms, and load balancing approaches.Comment: arXiv admin note: substantial text overlap with arXiv:1809.0801

Contribution to the search for binaries among Am stars - VII. Orbital elements of seven new spectroscopic binaries, implications on tidal effects

International audienceWe present the results of a radial-velocity study of seven Am stars (HD 3970, 35035, 93946, 151746, 153286, 204751 and 224002) observed at the Observatoire de Haute-Provence (OHP) and the Cambridge Observatories with CORAVEL instruments. We find that these systems are single-lined spectroscopic binaries whose orbital elements are determined for the first time. Among this sample, HD 35035 and 153286 have long periods, with P = 2.8 and 9.5yr, respectively, which is rather unusual for Am stars. Four systems have orbits with large eccentricities (with e >= 0.4). Physical parameters are inferred from this study for the primaries of those systems. We then investigate the influence of tidal interaction, which has already led to the synchronism of the primaries and/or to the circularization of the orbits of some systems belonging to this sample. We extend this study to the list of 33 objects studied in this series of papers and derive values of the critical fractional radii r = R/a for circularization and synchronization of Am-type binaries. We find that the stars with r >~ 0.15 are orbiting on circular orbits and that synchronism is likely for all components with r >~ 0.20

Repeated games for eikonal equations, integral curvature flows and non-linear parabolic integro-differential equations

The main purpose of this paper is to approximate several non-local evolution equations by zero-sum repeated games in the spirit of the previous works of Kohn and the second author (2006 and 2009): general fully non-linear parabolic integro-differential equations on the one hand, and the integral curvature flow of an interface (Imbert, 2008) on the other hand. In order to do so, we start by constructing such a game for eikonal equations whose speed has a non-constant sign. This provides a (discrete) deterministic control interpretation of these evolution equations. In all our games, two players choose positions successively, and their final payoff is determined by their positions and additional parameters of choice. Because of the non-locality of the problems approximated, by contrast with local problems, their choices have to "collect" information far from their current position. For integral curvature flows, players choose hypersurfaces in the whole space and positions on these hypersurfaces. For parabolic integro-differential equations, players choose smooth functions on the whole space

Characterizing Metabolic Alterations in Palbociclib-Resistant ER+ Breast Cancer

Characterizing Metabolic Alterations in Palbociclib-Resistant ER+ Breast Cancer Jessica Shunnarah1, Susan M. Dougherty2, Yoannis Imbert-Fernandez3 1ULBB Program, 2Department of Medicine, University of Louisville Abstract Diverse mechanisms of resistance to inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) have been described including cell cycle alterations and metabolic changes. Palbociclib was the first CDK4/6inhibitor approved against estrogen receptor positive (ER+) breast cancer however, the development of resistance has limited its success. This study investigates the changes in the expression of key metabolic enzymes using an in vivo model of palbociclib resistance. Palbociclib-resistant patient derive xenografts (PDXs) were generated by treating NSG mice that had ER+ breast cancer was implanted into the mammary fat pat of NSG mice with palbociclib until the tumors grew in the presence of the drug.. At endpoint, the tumors were harvested, flash frozen, and pulverized for western blot analysis. Our analysis shows the up regulation in some of the metabolic enzymes. We have concluded that resistance to palbociclib ER+ breast cancer increases the expression of Glutaminase (GLS1) in the presence and absence of palbociclib. Palbociclib treatment also leads to an increase 6-phosphofructo-2 kinase/fructose-2,6-biphosphotase-3 (PFKFB3) and Glucose-6-phosphate dehydrogenase (G6PDH) and transketolase in both palbociclib-sensitive and palbociclib-resistant PDX models. Keywords: Palbociclib, estrogen receptor positive, patient derive xenograft, glutaminase, 6-phosphofructo-2 kinase/fructo, glucose-6-phosphate dehydrogenas

Orbital and physical parameters of eclipsing binaries from the ASAS catalogue -- I. A sample of systems with components' masses between 1 and 2 M⊙_\odot

We derive the absolute physical and orbital parameters for a sample of 18 detached eclipsing binaries from the \emph{All Sky Automated Survey} (ASAS) database based on the available photometry and our own radial velocity measurements. The radial velocities (RVs) are computed using spectra we collected with the 3.9-m Anglo-Australian Telescope and its \emph{University College London Echelle Spectrograph} and the 1.9-m SAAO Radcliffe telescope and its \emph{Grating Instrument for Radiation Analysis with a Fibre Fed Echelle}. In order to obtain as precise RVs as possible, most of the systems were observed with an iodine cell available at the AAT/UCLES and/or analyzed using the two-dimensional cross-correlation technique (TODCOR). The RVs were measured with TODCOR using synthetic template spectra as references. However, for two objects we used our own approach to the tomographic disentangling of the binary spectra to provide observed template spectra for the RV measurements and to improve the RV precision even more. For one of these binaries, AI Phe, we were able to the obtain an orbital solution with an RV $rms$ of 62 and 24 m s$^{-1}$ for the primary and secondary respectively. For this system, the precision in $M \sin^3{i}$ is 0.08%. For the analysis, we used the photometry available in the ASAS database. We combined the RV and light curves using PHOEBE and JKTEBOP codes to obtain the absolute physical parameters of the systems. Having precise RVs we were able to reach $\sim$0.2 % precision (or better) in masses in several cases but in radii, due to the limited precision of the ASAS photometry, we were able to reach a precision of only 1% in one case and 3-5 % in a few more cases. For the majority of our objects, the orbital and physical analysis is presented for the first time.Comment: 16 pages, 2 figures, 6 tables in the main text, 1 table in appendix, to appear in MNRA

On the Numerical Approximations of an Optimal Correction Problem

The numerical solution of an optimal correction problem for a damped random linear oscillator is studied. A numerical algorithm for the discretized system of the associated dynamic programming equation is given. To initiate the computation, we adopt a numerical scheme derived from the deterministic version of the problem. Next, a correction-type algorithm based on a discrete maximum principle is introduced to ensure the convergence of the iteration procedure