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Cloud workload prediction based on workflow execution time discrepancies

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arXiv 2018年

作者： Kecskemeti, Gabor Nemeth, Zsolt Kertesz, Attila Ranjan, Rajiv Department of Computer Science Liverpool John Moores University Laboratory of Parallel and Distributed Systems MTA SZTAKI Software Engineering Department University of Szeged School of Computing Newcastle University

Infrastructure as a service clouds hide the complexity of maintaining the physical infrastructure with a slight disadvantage: they also hide their internal working details. Should users need knowledge about these details e.g., to increase the reliability or performance of their applications, they would need solutions to detect behavioural changes in the underlying system. Existing runtime solutions for such purposes offer limited capabilities as they are mostly restricted to revealing weekly or yearly behavioural periodicity in the infrastructure. This article proposes a technique for predicting generic background workload by means of simulations that are capable of providing additional knowledge of the underlying private cloud systems in order to support activities like cloud orchestration or workflow enactment. Our technique uses long-running scientific workflows and their behaviour discrepancies and tries to replicate these in a simulated cloud with known (trace-based) workloads. We argue that the better we can mimic the current discrepancies the better we can tell expected workloads in the near future on the real life cloud. We evaluated the proposed prediction approach with a biochemical application on both real and simulated cloud infrastructures. The proposed algorithm has shown to produce significantly (∼20%) better workload predictions for the future of simulated clouds than random workload selection. Copyright © 2018, The Authors. All rights reserved.

关键词： Infrastructure as a service (IaaS)

Large margin multi-modal multi-task feature extraction for image classification

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arXiv 2019年

作者： Luo, Yong Wen, Yonggang Tao, Dacheng Gui, Jie Xu, Chao School of Electronics Engineering and Computer Science Peking University Beijing China Division of Networks and Distributed Systems School of Computer Engineering Nanyang Technological University Singapore Centre for Quantum Computation & Intelligent Systems Faculty of Engineering & Information Technology University of Technology Sydney Sydney Australia Centre for Quantum Computation & Intelligent Systems Faculty of Engineering and Information Technology University of Technology Sydney 81 Broadway Street UltimoNSW2007 Australia Hefei Institute of Intelligent Machines Chinese Academy of Sciences Hefei230031 China Center for Research on Intelligent Perception and Computing National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing100190 China

The features used in many image analysis-based applications are frequently of very high dimension. Feature extraction offers several advantages in high-dimensional cases, and many recent studies have used multi-task feature extraction approaches, which often outperform single-task feature extraction approaches. However, most of these methods are limited in that they only consider data represented by a single type of feature, even though features usually represent images from multiple modalities. We therefore propose a novel large margin multi-modal multi-task feature extraction (LM3FE) framework for handling multi-modal features for image classification. In particular, LM3FE simultaneously learns the feature extraction matrix for each modality and the modality combination coefficients. In this way, LM3FE not only handles correlated and noisy features, but also utilizes the complementarity of different modalities to further help reduce feature redundancy in each modality. The large margin principle employed also helps to extract strongly predictive features so that they are more suitable for prediction (e.g., classification). An alternating algorithm is developed for problem optimization and each sub-problem can be efficiently solved. Experiments on two challenging real-world image datasets demonstrate the effectiveness and superiority of the proposed method. Copyright © 2019, The Authors. All rights reserved.

关键词： Feature extraction

Roadmap on Electronic Structure Codes in the Exascale Era

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arXiv 2022年

作者： Gavini, Vikram Baroni, Stefano Blum, Volker Bowler, David R. Buccheri, Alexander Chelikowsky, James R. Das, Sambit Dawson, William Delugas, Pietro Dogan, Mehmet Draxl, Claudia Galli, Giulia Genovese, Luigi Giannozzi, Paolo Giantomassi, Matteo Gonze, Xavier Govoni, Marco Gulans, Andris Gygi, François Herbert, John M. Kokott, Sebastian Kühne, Thomas D. Liou, Kai-Hsin Miyazaki, Tsuyoshi Motamarri, Phani Nakata, Ayako Pask, John E. Plessl, Christian Ratcliff, Laura E. Richard, Ryan M. Rossi, Mariana Schade, Robert Scheffler, Matthias Schütt, Ole Suryanarayana, Phanish Torrent, Marc Truflandier, Lionel Windus, Theresa L. Xu, Qimen Yu, Victor W.-Z. Perez, Danny Department of Mechanical Engineering University of Michigan Ann ArborMI48109 United States SISSA ISAS Trieste Trieste34136 Italy IOM-CNR Trieste Trieste34136 Italy Duke University DurhamNC27708 United States London Centre for Nanotechnology LondonWC1H 0AH United Kingdom WPI-MANA National Institute for Materials Science Ibaraki305-0044 Japan Humboldt-Universität zu Berlin Berlin10117 Germany McKetta Department of Chemical Engineering University of Texas at Austin AustinTX78712 United States Center for Computational Materials Oden Institute University of Texas at Austin AustinTX78712 United States Department of Physics University of Texas at Austin AustinTX78712 United States RIKEN Center for Computational Science Hyogo Kobe650-0047 Japan Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States Materials Science Division Argonne National Laboratory LemontIL60439 United States Université Grenoble Alpes MEM L_Sim GrenobleF-38000 France University of Udine Udine33100 Italy IMCN Université catholique de Louvain Louvain-la-neuve Belgium University of Latvia RīgaLV-1586 Latvia University of California DavisCA95616 United States Department of Chemistry & Biochemistry The Ohio State University ColumbusOH43210 United States Berlin14195 Germany Dynamics of Condensed Matter Center for Sustainable Systems Design Chair of Theoretical Chemistry Paderborn University D-33098 Germany Paderborn Center for Parallel Computing Paderborn University D-33098 Germany Department of Computational and Data Sciences Indian Institute of Science Karnataka Bengaluru560012 India Lawrence Livermore National Laboratory LivermoreCA94550 United States Department of Computer Science Paderborn University D-33098 Germany Centre for Computational Chemistry School of Chemistry University of Bristol BristolBS8 1TS United Kingdom Ames National Laboratory AmesIA50011 United States Iowa State University AmesIA50

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing. Copyright © 2022, The Authors. All rights reserved.

关键词： Electronic structure

Cribriform pattern detection in prostate histopathological images using deep learning models

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arXiv 2019年

作者： Singh, Malay Kalaw, Emarene Mationg Jie, Wang Al-Shabi, Mundher Wong, Chin Fong Giron, Danilo Medina Chong, Kian-Tai Tan, Maxine Zeng, Zeng Lee, Hwee Kuan Unit Institute of Molecular and Cell Biology Singapore Imaging Informatics Division Bioinformatics Institute Singapore Department of Computer Science School of Computing National University of Singapore Singapore UQ Centre for Clinical Research University of Queensland Brisbane Australia Distributed Analytics Lab Institute for Infocomm Research Singapore School of Engineering Monash University Malaysia Selangor Darul Ehsan Malaysia Department of Pathology Tan Tock Seng Hospital Singapore PanAsia Surgery Pte Ltd Mount Elizabeth Novena Hospital Singapore Surgi-TEN Specialists Pte Ltd Farrer Park Hospital Singapore Singapore Singapore Eye Research Institute Singapore

Architecture, size, and shape of glands are most important patterns used by pathologists for assessment of cancer malignancy in prostate histopathological tissue slides. Varying structures of glands along with cumbersome manual observations may result in subjective and inconsistent assessment. Cribriform gland with irregular border is an important feature in Gleason pattern 4. We propose using deep neural networks for cribriform pattern classification in prostate histopathological images. 163708 Hematoxylin and Eosin (H&E) stained images were extracted from histopathologic tissue slides of 19 patients with prostate cancer and annotated for cribriform patterns. Our automated image classification system analyses the H&E images to classify them as either 'Cribriform' or 'Non-cribriform'. Our system uses various deep learning approaches and hand-crafted image pixel intensity-based features. We present our results for cribriform pattern detection across various parameters and configuration allowed by our system. The combination of fine-tuned deep learning models outperformed the state-of-art nuclei feature based methods. Our image classification system achieved the testing accuracy of 85.93 ± 7.54 (cross-validated) and 88.04 ± 5.63 (additional unseen test set) across three folds. In this paper, we present an annotated cribriform dataset along with analysis of deep learning models and hand-crafted features for cribriform pattern detection in prostate histopathological images. Copyright © 2019, The Authors. All rights reserved.

关键词： Urology

CP2K: An electronic structure and molecular dynamics software package quickstep: Efficient and accurate electronic structure calculations

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arXiv 2020年

作者： Kühne, Thomas D. Iannuzzi, Marcella Ben, Mauro Del Rybkin, Vladimir V. Seewald, Patrick Stein, Frederick Laino, Teodoro Khaliullin, Rustam Z. Schütt, Ole Schiffmann, Florian Golze, Dorothea Wilhelm, Jan Chulkov, Sergey Bani-Hashemian, Mohammad Hossein Weber, Valéry Borštnik, Urban Taillefumier, Mathieu Jakobovits, Alice Shoshana Lazzaro, Alfio Pabst, Hans Müller, Tiziano Schade, Robert Guidon, Manuel Andermatt, Samuel Holmberg, Nico Schenter, Gregory K. Hehn, Anna Bussy, Augustin Belleflamme, Fabian Tabacchi, Gloria Glöß, Andreas Lass, Michael Bethune, Iain Mundy, Christopher J. Plessl, Christian Watkins, Matt VandeVondele, Joost Krack, Matthias Hutter, Jürg Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry Paderborn University Warburger Str. 100 PaderbornD-33098 Germany Department of Chemistry University of Zurich Winterthurerstrasse 190 ZürichCH-8057 Switzerland Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States IBM Research - Zurich Säumerstrasse 4 RüschlikonCH-8803 Switzerland Department of Chemistry McGill University CH-801 Sherbrooke St. West MontrealQCH3A 0B8 Canada Department of Materials ETH Zürich ZürichCH-8092 Switzerland Centre of Policy Studies Victoria University Melbourne Australia Department of Applied Physics Aalto University Otakaari 1 EspooFI-02150 Finland Institute of Theoretical Physics University of Regensburg Universitätsstraße 31 RegensburgD-93053 Germany School of Mathematics and Physics University of Lincoln Brayford Pool Lincoln United Kingdom Integrated Systems Laboratory ETH Zürich ZürichCH-8092 Switzerland Scientific IT Services ETH Zürich Zürich Switzerland ETH Zürich HPE Switzerland GmbH Basel Switzerland Intel Extreme Computing Software and Systems Zürich Switzerland Department of Computer Science and Paderborn Center for Parallel Computing Paderborn University Warburger Str. 100 PaderbornD-33098 Germany Department of Chemistry and Materials Science Aalto University P.O. Box 16100 Aalto00076 Finland Physical Science Division Pacific Northwest National Laboratory P. O. Box 999 RichlandWA99352 United States Department of Science and High Technology University of Insubria INSTM via Valleggio 9 ComoI-22100 Italy BASF SE Carl-Bosch-Straße 38 Ludwigshafen am RheinD-67056 Germany Hartree Centre Science and Technology Facilities Council United Kingdom Laboratory for Scientific Computing and Modelling Paul Scherrer Institute Villigen PSICH-5232 Switzerland

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension. Copyright © 2020, The Authors. All rights reserved.

关键词： Electronic structure

Detailed and clock-driven simulation for HPC interconnection network

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Frontiers of computer science 2016年第5期10卷 797-811页

作者： Wenhao ZHOU Juan CHEN Chen CUI Qian WANG Dezun DONG Yuhua TANG State Key Laboratory of High Performance Computing School of Computer National University of Defense Technology Changsha 410073 China Science and Technology on Parallel and Distributed Processing Laboratory National University of Defense Technology Changsha 410073 China

Performance and energy consumption of high performance computing （HPC） interconnection networks have a great significance in the whole supercomputer, and building up HPC interconnection network simulation plat- form is very important for the research on HPC software and hardware technologies. To effectively evaluate the per- formance and energy consumption of HPC interconnection networks, this article designs and implements a detailed and clock-driven HPC interconnection network simulation plat- form, called HPC-NetSim. HPC-NetSim uses application- driven workloads and inherits the characteristics of the de- tailed and flexible cycle-accurate network simulator. Besides, it offers a large set of configurable network parameters in terms of topology and routing, and supports router＇s on/off states. We compare the simulated execution time with the real execution time of Tianhe-2 subsystem and the mean error is only 2.7%. In addition, we simulate the network behaviors with different network structures and low-power modes. The results are also consistent with the theoretical analyses.

关键词： high performance computing clock-driven sim-ulation interconnection network BookSim

An environment for sustainable research software in Germany and beyond: Current state, open challenges, and call for action

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arXiv 2020年

作者： Anzt, Hartwig Bach, Felix Druskat, Stephan Löffler, Frank Loewe, Axel Renard, Bernhard Y. Seemann, Gunnar Struck, Alexander Achhammer, Elke Aggarwal, Piush Appel, Franziska Bader, Michael Brusch, Lutz Busse, Christian Chourdakis, Gerasimos Dabrowski, Piotr W. Ebert, Peter Flemisch, Bernd Friedl, Sven Fritzsch, Bernadette Funk, Maximilian D. Gast, Volker Goth, Florian Grad, Jean-Noël Hermann, Sibylle Hohmann, Florian Janosch, Stephan Kutra, Dominik Linxweiler, Jan Muth, Thilo Peters-Kottig, Wolfgang Rack, Fabian Raters, Fabian H.C. Rave, Stephan Reina, Guido Reißig, Malte Ropinski, Timo Schaarschmidt, Joerg Seibold, Heidi Thiele, Jan P. Uekerman, Benjamin Unger, Stefan Weeber, Rudolf Germany Innovative Computing Lab University of Tennessee KnoxvilleTN United States Department of English Studies Friedrich Schiller University Jena Germany Germany Department of Computer Science Humboldt-Universität zu Berlin Germany Heinz Nixdorf Chair for Distributed Information Systems Friedrich Schiller University Jena Germany Michael Stifel Center Jena Germany Center for Computation and Technology Louisiana State University Baton Rouge United States Germany Robert Koch Institute Berlin Germany Hasso Plattner Institute Faculty of Digital Engineering University of Potsdam Germany Institute for Experimental Cardiovascular Medicine University Heart Centre Freiburg Bad Krozingen Germany Faculty of Medicine University of Freiburg Freiburg Germany Matters of Activity. Image Space Material. Cluster of Excellence at Humboldt-Universität zu Berlin Germany Technische Universität München Germany Language Technology Lab Universität Duisburg-Essen Germany Germany Department of Informatics Technical University of Munich Germany Technische Universität Dresden Germany Deutsches Krebsforschungszentrum Heidelberg Germany Scientific Computing in Computer Science Technical University Munich Germany School of Computing Communication and Business Hochschule für Technik und Wirtschaft Berlin Germany Center for Bioinformatics Saar Saarland Informatics Campus Germany Institute for Modelling Hydraulic and Environmental Systems University of Stuttgart Germany Berlin Institute of Health Germany Scientific Computing Alfred Wegener Institute Helmholtz Center for Polar and Marine Research Bremerhaven Germany Max-Planck-Gesellschaft e.V. Institut für Theoretische Physik und Astrophysik Universität Würzburg Germany Institut für Computerphysik University of Stuttgart Germany University Library University of Stuttgart Germany Universität Bremen Germany Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany European Molecular Biology Laboratory Heidelb

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. Copyright © 2020, The Authors. All rights reserved.

关键词： Software design

Direct method-green's theory: From PDE to BIE in the geometric transformation

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Direct method-green's theory: From PDE to BIE in the geometr...

2016 International Conference on Wavelet Analysis and Pattern Recognition, ICWAPR 2016

作者： Yang, Li-Na Li, Tao-Shen Tang, Yuan Yan Xu, Jia Pan, Jian-Jia Luo, Hui-Wu Zheng, Xian-Wei School of Computer Electronics and Information Guangxi University Nanning530004 China Department of Computer and Information Science Faculty of Science and Technology University of Macau China Guangxi Colleges Universities Key Laboratory of Parallel and Distributed Computing Nanning530004 China

ISBN: (纸本)9781509035885

In this research, we apply the Green's theory for converting the partial differential equation to the boundary integral equation for geometric transformation. Green's theory is designed specifically for integral equation. It is efficient in detecting the singularity point to the geometric transformation that has been verified. Experimental results show that the Green's theory has good performance. © 2016 IEEE.

关键词： Partial differential equations

Algorithms for multidimensional frontier visualization based on optimization methods using distributed computations 8

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Algorithms for multidimensional frontier visualization based...

8th International Conference on Optimization and Applications, OPTIMA 2017

作者： Afanasiev, Alexander P. Krivonozhko, Vladimir E. Lychev, Andrey V. Sukhoroslov, Oleg V. Centre for Distributed Computing Institute for Information Transmission Problems Russian Academy of Sciences Nakhimovsky Prospekt 36-1 Moscow117218 Russia National University of Science and Technology MISiS Leninskiy Prospekt 4 Moscow119049 Russia Lomonosov Moscow State University GSP-1 Vorobievy Gory Moscow119991 Russia National Research University Higher School of Economics Myasnitskaya str. 20 Moscow101000 Russia Federal Research Center Computer Science and Control Russian Academy of Sciences Vavilov st. 44-2 Moscow119333 Russia

In data envelopment analysis, methods for constructing sections of the frontier have been recently proposed to visualize the production possibility set. The aim of this paper is to develop, prove and test the methods for the visualization of production possibility sets using distributed computations. In this article a general scheme of the algorithm for constructing sections (visualization) of production possibility set is proposed. An algorithm for constructing a generalized production function is described in detail. Also, the possibilities of implementing certain schemes in a distributed computing environment are considered. © Copyright by the paper's authors.

关键词： Visualization