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End-To-End Solution for Integrated Workload and Data Management using GlideinWMS and Globus Online

Journal of Physics: Conference Series 2012年第3期396卷

作者： Parag Mhashilkar Zachary Miller Rajkumar Kettimuthu Gabriele Garzoglio Burt Holzman Cathrin Weiss Xi Duan Lukasz Lacinski Scientific Computing Division Fermi National Accelerator Laboratory Batavia. IL 60563 USA Department of Computer Sciences University of Wisconsin-Madison Madison WI 53706 USA Mathematics and Computer Science Division Argonne National Laboratory Argonne IL 60637 USA Computation Institute The University of Chicago and Argonne National Laboratory Chicago IL 60637 USA IIT College of Science and Letters Illinois Institute of Technology Chicago IL 60616 USA

Grid computing has enabled scientific communities to effectively share computing resources distributed over many independent sites. Several such communities, or Virtual Organizations (VO), in the Open science Grid and the European Grid Infrastructure use the GlideinWMS system to run complex application work-flows. GlideinWMS is a pilot-based workload management system (WMS) that creates an on-demand, dynamically-sized overlay Condor batch system on Grid resources. While the WMS addresses the management of compute resources, however, data management in the Grid is still the responsibility of the VO. In general, large VOs have resources to develop complex custom solutions, while small VOs would rather push this responsibility to the infrastructure. The latter requires a tight integration of the WMS and the data management layers, an approach still not common in modern Grids. In this paper we describe a solution developed to address this shortcoming in the context of Center for Enabling Distributed Peta-scale science (CEDPS) by integrating GlideinWMS with Globus Online (GO). Globus Online is a fast, reliable file transfer service that makes it easy for any user to move data. The solution eliminates the need for the users to provide custom data transfer solutions in the application by making this functionality part of the GlideinWMS infrastructure. To achieve this, GlideinWMS uses the file transfer plug-in architecture of Condor. The paper describes the system architecture and how this solution can be extended to support data transfer services other than Globus Online when used with Condor or GlideinWMS.

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Crystalline phase discriminating neutron tomography using advanced reconstruction methods

arXiv

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arXiv 2021年

作者： Ametova, Evelina Burca, Genoveva Chilingaryan, Suren Fardell, Gemma Jørgensen, Jakob S. Papoutsellis, Evangelos Pasca, Edoardo Warr, Ryan Turner, Martin Lionheart, William R.B. Withers, Philip J. Henry Royce Institute Department of Materials The University of Manchester M13 9PL United Kingdom Laboratory for Application of Synchrotron Radiation Karlsruhe Institute of Technology Germany ISIS Pulsed Neutron and Muon Source STFC UKRI Rutherford Appleton Laboratory United Kingdom Department of Mathematics The University of Manchester M13 9PL United Kingdom Institute for Data Processing and Electronics Karlsruhe Institute of Technology Germany Scientific Computing Department STFC UKRI Rutherford Appleton Laboratory United Kingdom Department of Applied Mathematics and Computer Science Technical University of Denmark Denmark Research IT Services The University of Manchester M13 9PL United Kingdom

Time-of-flight neutron imaging offers complementary attenuation contrast to X-ray computed tomography (CT), coupled with the ability to extract additional information from the variation in attenuation as a function of neutron energy (time of flight) at every point (voxel) in the image. In particular Bragg edge positions provide crystallographic information and therefore enable the identification of crystalline phases directly. Here we demonstrate Bragg edge tomography with high spatial and spectral resolution. We propose a new iterative tomographic reconstruction method with a tailored regularisation term to achieve high quality reconstruction from low-count data, where conventional filtered back-projection (FBP) fails. The regularisation acts in a separated mode for spatial and spectral dimensions and favours characteristic piece-wise constant and piecewise smooth behaviour in the respective dimensions. The proposed method is compared against FBP and a state-of-the-art regulariser for multi-channel tomography on a multi-material phantom. The proposed new regulariser which accommodates specific image properties outperforms both conventional and state-of-the-art methods and therefore facilitates Bragg edge fitting at the voxel level. The proposed method requires significantly shorter exposure to retrieve features of interest. This in turn facilitates more efficient usage of expensive neutron beamline time and enables the full utilisation of state-of-the-art high resolution detectors. © 2021, CC BY.

关键词： Iterative methods

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Cognitive virtual microscopy: a cognition-driven visual explorer for histopathology – the MICO ANR TecSan 2010 initiative

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BMC Proceedings 2011年第1期5卷 1-1页

作者： Daniel Racoceanu Nicolas Loménie Ludovic Roux French National Center for Scientific Research – IPAL UMI CNRS Singapore 138632 Republic of Singapore Department of Computer Science School of Computing National University of Singapore Singapore 117417 Republic of Singapore University Paris Descartes 75270 Paris Cedex 06 France University Joseph Fourier 38041 Grenoble Cedex 9 France

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IoT Based Smart Agriculture Monitoring, Automation and Intrusion Detection System

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Journal of Physics: Conference Series 2021年第1期1962卷

作者： Ahmad Faisol Suhaimi Naimah Yaakob Sawsan Ali Saad Khairul Azami Sidek Mohamed Elobaid Elshaikh Alaa K.Y. Dafhalla Ong Bi Lynn Mahathir Almashor Faculty of Electronic Engineering technology Universiti Malaysia Perlis (UniMAP) Perlis Malaysia Advanced Computing Centre of Excellence (CoE) Universiti malaysia Perlis (UniMAP) Perlis Malaysia Department of Computer Engineering College of Computer Science and Engineering University of Ha'il Kingdom of Saudi Arabia Department of Electrical and Computer Engineering Kulliyyah of Engineering International Islamic University Malaysia (IIUM) Selangor Malaysia Data61 Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia

Manual irrigation is still widely used in agricultural field using traditional drip and can watering. However, traditional irrigation systems are inefficient and inexact, leading to either insufficient or excessive watering. Moreover, it is difficult for farmers to predict suitable quantities at the appropriate time. Manual monitoring of the crop field may also lead to human error and is potentially risky for rural areas. Farmers may also not be aware of intrusions if they are not on location. Therefore, this project is designed to develop a smart monitoring and automated irrigation system to provide not only efficient water consumption based on specific conditions, but also enables real-time monitoring of the environment. Furthermore, this system prevents damage to plants and reduces the likelihood of plant theft. This system uses NodeMCU ESP32 as a microcontroller that collects environmental data such as humidity, temperature, soil moisture levels from sensors. The NodeMCU is integrated with a relay and RTC module to irrigate plants at specific times and is also equipped with a passive infrared sensor to detect intruders near the crop-field. Upon detection, an ESP32 camera is used to automatically capture the current conditions and farmers will be subsequently notified. Warnings are also sent to farmers upon detection of unwanted circumstances such as extreme temperature, which could prevent instances of open burning. The utility of the developed prototype is evident in the way it automatically irrigates the crop field without human intervention. Farmers may monitor and manually control the irrigation process using an attached Android application. Additionally, they may manually activate a buzzer warn off any potential malicious actors.

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Selection of Spatiotemporal Features in Breast MRI to Differentiate between Malignant and Benign Small Lesions Using computer-Aided Diagnosis

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Advances in Artificial Neural Systems 2012年第1期2012卷

作者： F. Steinbruecker A. Meyer-Baese C. Plant T. Schlossbauer U. Meyer-Baese Department of Computer Science Technical University of Munich 8574 Garching Germanytum.de Department of Scientific Computing Florida State University Tallahassee FL 32306-4120 USAfsu.edu Institute for Clinical Radiology University of Munich 81377 Munich Germanyuni-muenchen.de Department of Electrical and Computer Engineering FAMU/FSU College of Engineering Tallahassee FL 32310-6046 USAfsu.edu

Automated detection and diagnosis of small lesions in breast MRI represents a challenge for the traditional computer-aided diagnosis (CAD) systems. The goal of the present research was to compare and determine the optimal feature sets describing the morphology and the enhancement kinetic features for a set of small lesions and to determine their diagnostic performance. For each of the small lesions, we extracted morphological and dynamical features describing both global and local shape, and kinetics behavior. In this paper, we compare the performance of each extracted feature set for the differential diagnosis of enhancing lesions in breast MRI. Based on several simulation results, we determined the optimal feature number and tested different classification techniques. The results suggest that the computerized analysis system based on spatiotemporal features has the potential to increase the diagnostic accuracy of MRI mammography for small lesions and can be used as a basis for computer-aided diagnosis of breast cancer with MR mammography.

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Foundational Competencies and Responsibilities of a Research Software Engineer

arXiv

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arXiv 2023年

作者： Goth, Florian Alves, Renato Braun, Matthias Castro, Leyla Jael Chourdakis, Gerasimos Christ, Simon Cohen, Jeremy Druskat, Stephan Erxleben, Fredo Grad, Jean-Noël Hagdorn, Magnus Hodges, Toby Juckeland, Guido Kempf, Dominic Lamprecht, Anna-Lena Linxweiler, Jan Löffler, Frank Martone, Michele Schwarzmeier, Moritz Seibold, Heidi Thiele, Jan Philipp Waldow, Harald von Wittke, Samantha Institute for Theoretical Physics and Astrophysics University of Würzburg Germany European Molecular Biology Laboratory Heidelberg Germany Cluster of Excellence IntCDC University of Stuttgart Germany ZB MED Information Centre for Life Sciences Cologne Germany School of Computation Information and Technology Technical University of Munich Garching Germany Institute for Parallel and Distributed Systems University of Stuttgart Stuttgart Germany Leibniz University Hannover Department of Cell Biology and Biophysics Computational Biology Germany Imperial College London London United Kingdom Institute for Software Technology Berlin Germany Humboldt-Universität zu Berlin Department of Computer Science Berlin Germany Helmholtz-Zentrum Dresden-Rossendorf Germany Institute for Computational Physics University of Stuttgart Germany Geschäftsbereich IT Charité Universitätsmedizin Berlin Germany The Carpentries United States Heidelberg University Scientific Software Center Germany Institute of Computer Science University of Potsdam Germany Technische Universität Braunschweig Germany Michael Stifel Center Jena Friedrich Schiller University Jena Germany Leibniz Supercomputing Centre Garching Germany Mathematical Modeling and Analysis TU Darmstadt Germany IGDORE Munich Germany Weierstrass Institute Berlin Germany Leibniz University Hannover Institute of Applied Mathematics Scientific Computing Hannover Germany Johann Heinrich von Thünen Institute Centre for Information Management Germany

The term Research Software Engineer, or RSE, emerged a little over 10 years ago as a way to represent individuals working in the research community but focusing on software development. The term has been widely adopted and there are a number of high-level definitions of what an RSE is. However, the roles of RSEs vary depending on the institutional context they work in. At one end of the spectrum, RSE roles may look similar to a traditional research role. At the other extreme, they resemble that of a software engineer in industry. Most RSE roles inhabit the space between these two extremes. Therefore, providing a straightforward, comprehensive definition of what an RSE does and what experience, skills and competencies are required to become one is challenging. In this community paper we define the broad notion of what an RSE is, explore the different types of work they undertake, and define a list of foundational competencies as well as values that outline the general profile of an RSE. Further research and training can build upon this foundation of skills and focus on various aspects in greater detail. We expect that graduates and practitioners will have a larger and more diverse set of skills than outlined here. On this basis, we elaborate on the progression of these skills along different dimensions. We look at specific types of RSE roles, propose recommendations for organisations, and give examples of future specialisations. An appendix details how existing curricula fit into this framework. © 2023, CC BY.

关键词： computer aided software engineering

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An assessment of some preconditioning techniques in shell problems

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International Journal for Numerical Methods in Biomedical Engineering 1999年第10期14卷

作者： Michele Benzi Reijo Kouhia Miroslav Tůma Scientific Computing Group CIC-19 Los Alamos National Laboratory Los Alamos NM 87545 U.S.A. Laboratory of Structural Mechanics Helsinki University of Technology P.O. Box 2100 02015 HUT Finland Institute of Computer Science Czech Academy of Sciences 182 07 Prague 8 Czech Republic

Preconditioned Krylov subspace methods have proved to be efficient in solving large, sparse linear systems in many areas of scientific computing. The success of these methods in many cases is due to the existence of good preconditioning techniques. In problems of structural mechanics, like the analysis of heat transfer and deformation of solid bodies, iterative solution of the linear equation system can result in a significant reduction of computing time. Also many preconditioning techniques can be applied to these problems, thus facilitating the choice of an optimal preconditioning on the particular computer architecture available. However, in the analysis of thin shells the situation is not so transparent. It is well known that the stiffness matrices generated by the FE discretization of thin shells are very ill-conditioned. Thus, many preconditioning techniques fail to converge or they converge too slowly to be competitive with direct solvers. In this study, the performance of some general preconditioning techniques on shell problems is examined. © 1998 John Wiley & Sons, Ltd.

关键词： preconditioning conjugate gradient finite elements shells

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Searching for gravitational wave bursts from cosmic string cusps with the Parkes Pulsar Timing Array

arXiv

引用

arXiv 2020年

作者： Yonemaru, N. Kuroyanagi, S. Hobbs, George Takahashi, K. Zhu, X.-J. Coles, W.A. Dai, S. Howard, E. Manchester, R. Reardon, D. Russell, C. Shannon, R. Thyagarajan, N. Spiewak, R. Wang, J.-B. Kumamoto University Graduate School of Science and Technology Kumamoto860-8555 Japan CSIRO Astronomy and Space Science PO Box 76 EppingNSW1710 Australia Nagoya University Graduate School of Science Nagoya464-8601 Japan Instituto de Física Teórica UAM-CSIC Universidad Autonóma de Madrid Cantoblanco Madrid28049 Spain International Research Organization for Advanced Science and Technology Kumamoto University Kumamoto860-8555 Japan School of Physics and Astronomy Monash University VIC3800 Australia OzGrav: Australian Research Council Centre of Excellence for Gravitational Wave Discovery Electrical and Computer Engineering University of California at San Diego San diegoCA United States Department of Physics and Astronomy Macquarie University Sydney2109 Australia Centre for Quantum Dynamics Griffith University BrisbaneQLD4111 Australia Centre for Astrophysics and Supercomputing Swinburne University of Technology P.O. Box 218 HawthornVIC3122 Australia CSIRO Scientific Computing Services Australian Technology Park Locked Bag 9013 AlexandriaNSW1435 Australia National Radio Astronomy Observatory 1003 Lopezville Rd SocorroNM87801 United States Xinjiang Astronomical Observatory Chinese Academy of Science 150 Science 1-Street UrumqiXinjiang830011 China Key Laboratory of Radio Astronomy Chinese Academy of Science 150 Science 1-Street UrumqiXinjiang830011 China

Cosmic strings are potential gravitational wave (GW) sources that can be probed by pulsar timing arrays (PTAs). In this work we develop a detection algorithm for a GW burst from a cusp on a cosmic string, and apply it to Parkes PTA data. We find four events with a false alarm probability less than 1%. However further investigation shows that all of these are likely to be spurious. As there are no convincing detections we place upper limits on the GW amplitude for different event durations. From these bounds we place limits on the cosmic string tension of G μ∼ 10−5, and highlight that this bound is independent from those obtained using other techniques. We discuss the physical implications of our results and the prospect of probing cosmic strings in the era of Square Kilometre Array (SKA). © 2020, CC BY.

关键词： Pulsars

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Keep Your Friends Close and Your Colleagues Nearby: The Hidden Ties That Improve STEM Education

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Change 2019年第1期51卷 42页

作者： Mestre, Jose P. Herman, Geoffrey L. Tomkin, Jonathan H. West, Matthew Jose P. Mestre (mestre@illinois.edu). A theoretical nuclear physicist by training Mestre’s research focuses on the learning of physics contributing in areas such as the acquisition and use of knowledge by experts and novices transfer of learning problem solving and instructional design. He has offered Congressional testimony on The Science of Learning has published numerous articles and books and is a Fellow of the American Physical Society.http://***/0000-0003-2110-1954 Geoffrey L. Herman (glherman@illinois.edu). Herman has a Ph.D. in Electrical and Computer Engineering and is a Teaching Assistant Professor in Computer Science and a Research Assistant Professor in the Department of Curriculum & Instruction at the University of Illinois. His research focuses on how students learn engineering and computing concepts and studying processes for creating systemic instructional change in college settings. Previously he was a postdoctoral researcher in Engineering Education at Purdue University.http://***/0000-0002-9501-2295 Jonathan H. Tomkin (tomkin@illinois.edu). Tomkin is a mathematically based geoscientist with two research focus areas: first he uses models and large data sets to determine how climates glaciers tectonics and landscapes interact. Second he explores how new technological and organizational approaches can improve STEM education. He produced the first geoscience MOOC is the editor of an open-source textbook and has published widely in both geoscience and STEM education. Matthew West (mwest@illinois.edu). Matthew West is an Associate Professor of Mechanical Science and Engineering at the University of Illinois with research interests in scientific computing that include time integration of deterministic and stochastic systems distributed computation and particle methods for simulation and estimation. In education he researches computer-based assessment and the development of innovative teaching cultures. Professor West is a University of Illinois Distinguished Teacher-Scholar and Colleg

A science department on the campus of the University of Illinois has received numerous national awards for excellence in undergraduate teaching. The secret to their success? For nearly two decades, they have collaboratively used evidence-based instructional practices (EBIP) in their introductory level courses. Despite these successes and efforts to spread their EBIP, no other departments followed this department's lead. Then, suddenly six years ago, many instructors from other departments began adopting EBIP in their classrooms. This article asks what was the catalyst for this change? Why had previous attempts at institutional change failed? The authors answer these questions by analyzing their efforts to transform the teaching practices in large-enrollment science and engineering introductory courses on their campus.

关键词： STEM Education Evidence Based Practice Teaching Methods Undergraduate Study College Faculty Educational Change Communities of Practice Mentors School CultureIllinois

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IDEAS: Immersive dome experiences for accelerating science

arXiv

引用

arXiv 2019年

作者： Faherty, Jacqueline K. SubbaRao, Mark Wyatt, Ryan Ynnerman, Anders deGrasse Tyson, Neil Geller, Aaron Weber, Maria Rosenfield, Philip Stoeckle, Gabriel Weiskopf, Daniel Magnor, Marcus Williams, Peter K.G. Abbott, Brian Marchetti, Lucia Jarrrett, Thomas Fay, Jonathan Peek, Joshua Graur, Or Durrell, Patrick Homeier, Derek Preston, Heather Müller, Thomas Vos, Johanna M. Brown, David Godfrey, Paige Giorla Rice, Emily Gagliuffi, Daniella Bardalez Bock, Alexander American Museum of Natural History Hayden Planetarium Adler Planetarium International Planetarium Society California Academy of Sciences Linköping University Adler Planetarium University of Chicago AAS WorldWide Telescope Instituto de Astronomiá UNAM Natural History Museum Vienna Austria Visualization Research Center University of Stuttgart Computer Graphics Lab TU Braunschweig Center for Astrophysics | Harvard & Smithsonian American Astronomical Society American Museum of Natural History Hayden Planetarium University of Cape Town Iziko Planetarium & Digital Dome Space Telescope Science Institute Johns Hopkins University Youngstown State University Ward Beecher Planetarium Förderkreis Planetarium Göttingen Germany Calusa Nature Center & Planetarium Haus der Astronomie MPIA Microsoft Research Slooh CUNY Macaulay Honors College Scientific Computing and Imaging Institute University of Utah

Astrophysics lies at the crossroads of big datasets (such as the Large Synoptic Survey Telescope and Gaia), open source software to visualize and interpret high dimensional datasets (such as Glue, WorldWide Telescope, and OpenSpace), and uniquely skilled software engineers who bridge data science and research fields. At the same time, more than 4,000 planetariums across the globe immerse millions of visitors in scientific data. We have identified the potential for critical synergy across data, software, hardware, locations, and content that-if prioritized over the next decade-will drive discovery in astronomical research. Planetariums can and should be used for the advancement of scientific research. Current facilities such as the Hayden Planetarium in New York City, Adler Planetarium in Chicago, Morrison Planetarium in San Francisco, the Iziko Planetarium & Digital Dome Research Consortium in Cape Town, and Visualization Center C in Norrköping are already developing software which ingests catalogs of astronomical and multi-disciplinary data critical for exploration research primarily for the purpose of creating scientific storylines for the general public. We propose a transformative model whereby scientists become the audience and explorers in planetariums, utilizing software for their own investigative purposes. In this manner, research benefits from the authentic and unique experience of data immersion contained in an environment bathed in context and equipped for collaboration. Consequently, in this white paper we argue that over the next decade the research astronomy community should partner with planetariums to create visualization-based research opportunities for the field. Realizing this vision will require new investments in software and human capital. Copyright © 2019, The Authors. All rights reserved.

关键词： Planetariums

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