Asynchronous In Situ Processing with Gromacs: Taking Advantage of GPUs

International audienceNumerical simulations using supercomputers are producing an ever growing amount of data. Efficient production and analysis of these data are the key to future discoveries. The in situ paradigm is emerging as a promising solution to avoid the I/O bottleneck encountered in the file system for both the simulation and the analytics by treating the data as soon as they are produced in memory. Various strategies and implementations have been proposed in the last years to support in situ treatments with a low impact on the simulation performance. Yet, little efforts have been made when it comes to perform in situ analytics with hybrid simulations supporting accelerators like GPUs. In this article, we propose a study of the in situ strategies with Gromacs, a molecular dynamic simulation code supporting multi-GPUs, as our application target. We specifically focus on the computational resources usage of the machine by the simulation and the in situ analytics. We finally extend the usual in situ placement strategies to the case of in situ analytics running on a GPU and study their impact on both Gromacs performance and the resource usage of the machine. We show in particular that running in situ analytics on the GPU can be a more efficient solution than on the CPU especially when the CPU is the bottleneck of the simulation

Toward a first-principles integrated simulation of tokamak edge plasmas

Performance of the ITER is anticipated to be highly sensitive to the edge plasma condition. The edge pedestal in ITER needs to be predicted from an integrated simulation of the necessary first-principles, multi-scale physics codes. The mission of the SciDAC Fusion Simulation Project (FSP) Prototype Center for Plasma Edge Simulation (CPES) is to deliver such a code integration framework by (1) building new kinetic codes XGC0 and XGC1, which can simulate the edge pedestal buildup; (2) using and improving the existing MHD codes ELITE, M3D-OMP, M3D-MPP and NIMROD, for study of large-scale edge instabilities called Edge Localized Modes (ELMs); and (3) integrating the codes into a framework using cutting-edge computer science technology. Collaborative effort among physics, computer science, and applied mathematics within CPES has created the first working version of the End-to-end Framework for Fusion Integrated Simulation (EFFIS), which can be used to study the pedestal-ELM cycles

Fetal gender is not associated with either gestational diabetes mellitus or placental weight: A cohort study

Aim. - This study assessed whether male fetal gender increases the risk of maternal gestational diabetes mellitus (GDM) and investigated the association with placental weight. Methods. - The study included 20,149 women without pregestational diabetes who delivered singletons at our hospital between January 2002 and December 2010. There was universal screening for GDM, and all placentas were weighed at delivery. Results. - GDM (affecting 14.2% of women) was not associated with fetal gender (male fetuses in women without and with GDM: 51.8% vs. 51.7%, respectively; P = 0.957), and remained likewise after logistic -regression analysis of risk factors for GDM (OR: 1.007, 95% CI: 0.930-1.091; P=0.858). Placental weights were 600 +/- 126 g, 596 +/- 123 g, 584 +/- 118 g and 587 +/- 181 gin women with GDM/female, GDM/male, no GDM/female and no GDM/male fetuses, respectively (GDM effect: P=0.017; gender effect: P=0.41; GDM* gender effect: P=0.16). Conclusion. - The present results suggest that fetal gender is not associated with GDM and, while placental weights were higher in cases of GDM, there were still no gender effects. (C) 2016 Elsevier Masson SAS. All rights reserved

Propaganda, survival, and living to tell the truth : an analysis of North Korean refugee memoirs

Recent international events have heightened global interest in the North Korean regime’s engagement with the world; however, information about North Korea remains largely nebulous, due to the continuing secrecy of the regime. This study provides a rich understating of North Korean refugee identity and gives voice to individuals who have experienced the oppressive conditions of North Korea, their often dangerous escapes via multiple countries, and nonlinear or frequently difficult times of readjustment. It takes as its focus the role and impact of deception in different stages of North Korean refugee life before, during, and after escape. Specifically, we examine how North Korean refugee memoirists discuss the topics of truthfulness and deception in their own words. Using thematic analysis, we discovered three primary themes, including discovering and dealing with propaganda, deceiving as a means of survival, and finding the truth and living to tell it. Lastly, we end with a call to action aimed at empowering survivor voices, utilizing information to create change in North Korea, and offering future directions for scholars, practitioners, and human rights advocates