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

A Study of the Methods Used by a Selected Group of Directors of Nursing Service in the Planning of Rotation and Assignments for Staff Nurses

The problem was to study the methods used by a selected group of directors of nursing service when planning rotation and assignments for their staff nurse group. The data were gathered by means of a questionnaire, so constructed that it was possible to (l) identify present day methods of rotation and assignment; (2) determine problems encountered in the process, and (3) elicit from the participants their recommendations for alleviating these problems. The increasing emphasis on personnel administration as a valuable tool of management prompted the desire to explore this area. The analysis of the data indicated that the majority of directors of nursing service participating in this study encountered problems when planning staff nurse rotation and assignments. Problems were more pronounced in rotation practices rather than assignment practices. Turnover and job dissatisfaction was ascribed to rotation more frequently than to assignment. Some of the participants seemed to believe problems in this area were inevitable. Recommendations offered by the directors of nursing service for alleviating the problems included good human relations, active staff education, sound personnel policies, attractive remuneration for evening and night duty, group planning for policy making and problem solving and an understanding of the individual personal preferences and domestic responsibilities of the nurse. Because of the present impetus toward meeting the individual\u27s social, psychological and emotional needs, it is apparent that there is a need for further study in this area. Where the nurse works and when she works will have much to do with her gaining satisfaction from her work situation. Soliciting the head nurse’s opinion concerning present day assignment and rotation practices is recommended in order to gain further insight into this problem. Also, a survey of the staff nurse\u27s reaction to this aspect of nursing service administration should prove Worthwhile

Metastatic melanoma: An unusual presentation

In this report we describe a case of a malignant cutaneous melanoma metastasizing to the pleural surface and peritoneal cavity 5 years after surgical resection of the primary lesion. Malignant cutaneous melanoma is a very aggressive cancer able to metastasize anywhere in the body. Pleural secondary lesions represent a rare event described only in a small number of patients and the association with peritoneal localizations may suggest an uncommon pattern of spread that we discuss. Free full text available at www.tumorionline.it

Oxidation Alters the Architecture of the Phenylalanyl-tRNA Synthetase Editing Domain to Confer Hyperaccuracy

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not being directly implicated in PheRS activity. Here, we solve a 3.6 Å cryo-electron microscopy structure of oxidized S. Typhimurium PheRS. We find that oxidation results in widespread structural rearrangements in the β-subunit editing domain and enlargement of its editing domain. Oxidization also enlarges the phenylalanyl-adenylate binding pocket but to a lesser extent. Together, these changes likely explain why oxidation leads to hyperaccurate editing and decreased misincorporation of tyrosine. Taken together, these results help increase our understanding of the survival of S. Typhimurium during human infection