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High-Performance Computing Infrastructure for South East Europe's Research Communities

Results of the HP-SEE User Forum 2012

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  • © 2014

Overview

Editors:
  1. Mihnea Dulea

    1. Physics and Nuclear Engineering, Horia Hulubei National Institute, Magurele, Romania

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  2. Aneta Karaivanova

    1. Bulgarian Academy of Sciences (IICT-BAS), Institute of Information and Communication Technologies, Sofia, Bulgaria

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  3. Anastasis Oulas

    1. Hellenic Centre for Marine Research (IMBBC-HCMR), Institute of Marine Biology, Biotechnology and Aquacultures, Heraklion, Crete, Greece

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  4. Ioannis Liabotis

    1. GRNET S.A. Greek Research & Technology Network, Athens, Greece

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  5. Danica Stojiljkovic

    1. University of Belgrade (IPB-UOB) Institute of Physics Belgrade, Belgrade, Serbia

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  6. Ognjen Prnjat

    1. GRNET S.A. Greek Research & Technology Network, Athens, Greece

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  • Recent advances in high-performance computing and network operations for computational physics, computational chemistry and life sciences
  • Post-proceedings of HP-SEE User Forum 2012, held in Belgrade, Serbia on October 17-19, 2012
  • Written by leading experts in the field

Part of the book series: Modeling and Optimization in Science and Technologies (MOST, volume 2)

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Table of contents (20 chapters)

  1. Front Matter

    Pages 1-9
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  2. Simulation of Electron Transport Using HPC Infrastructure in South-Eastern Europe

    • Emanouil Atanassov, Todor Gurov, Aneta Karaivanova
    Pages 1-13

  3. Density Waves in Dipolar Bose-Einstein Condensates by Means of Symbolic Computations

    • Alexandru I. Nicolin, Ionel Rata
    Pages 15-21

  4. Using Parallel Computing to Calculate Static Interquark Potential in LQCD

    • Dafina Xhako, Rudina Zeqirllari, Artan Boriçi
    Pages 23-30

  5. Modelling of Disaster Spreading Dynamics

    • Igor Stanković, Milan Žeželj, Jelena Smiljanić, Aleksandar Belić
    Pages 31-42

  6. Determination of Zone of Flow Instability in a Gas Flow Past a Square Particle in a Narrow Microchannel

    • Kiril Shterev, Stefan Stefanov
    Pages 43-50

  7. Quenched Hadron Spectroscopy Using FermiQCD

    • Rudina Zeqirllari, Dafina Xhako, Artan Boriçi
    Pages 51-58

  8. Self-Avoiding Hamiltonian Walks Counting in Parallel Processing Mode

    • Igor Ševo, Sreten Lekić, Mihajlo Savić
    Pages 59-66

  9. Conformational Analysis and HF ab initio Geometry Optimization of Kyotorphine and Its Sulfo-Analogues Norsulfoarginine-Tyrosine and Tyrosine-Norsulfoarginine

    • Nicolay I. Dodoff, Tatyana A. Dzimbova, Tamara I. Pajpanova
    Pages 67-74

  10. Dynamics of Uninhibited and Covalently Inhibited Cysteine Protease on Non-physiological pH

    • Branko J. Drakulić, Marija Gavrović-Jankulović
    Pages 75-82

  11. Mechanisms of Polarization

    • Aggelos Avramopoulos, Heribert Reis, Manthos G. Papadopoulos
    Pages 83-92

  12. Some Aspects of the Comparative Study of Semi-empirical Combustion Models on FLUENT and OpenFOAM Codes

    • Sreten Lekić, Mihajlo Savić, Petar Gvero
    Pages 93-98

  13. Development of a Hybrid Statistical Physics – Quantum Mechanical Methodology for Computer Simulations of Condensed Phases and Its Implementation on High-Performance Computing Systems

    • Ljupčo Pejov, Dragan Sahpaski, Emilija Kohls, Anastas Mishev
    Pages 99-108

  14. Solvatochromic Effect for the Denaturation and Mutation Processes in DNA: Computational Study

    • Jumber Kereselidze, Marine Kvaraia, Zurab Pachulia, George Mikuchadze
    Pages 109-115

  15. Dynamic Features of Complex Systems: A Molecular Simulation Study

    • Armen Poghosyan, Levon Arsenyan, Hrachya Astsatryan
    Pages 117-121

  16. Using Adaptive Mesh Refinement Strategy for Numerical Solving of Gas Dynamics Problems on Multicore Computers

    • Boris Rybakin, Peter Bogatencov, Grigore Secrieru, Nicolai Iluha
    Pages 123-130

  17. Number Theory Algorithms on GPU Clusters

    • Emanouil Atanassov, Dobromir Georgiev, Nikolai Manev
    Pages 131-138

  18. Advanced Vulnerability Assessment Tool for Distributed Systems

    • Sandor Acs, Miklos Kozlovszky, Peter Kotcauer
    Pages 139-146

  19. Performance and Scalability Evaluation of Short Fragment Sequence Alignment Applications

    • Gergely Windisch, Miklos Kozlovszky, Ákos Balaskó
    Pages 147-154

  20. Implementation and Benchmarking of New FFT Libraries in Quantum ESPRESSO

    • Dušan Stanković, Petar Jovanović, Aleksandar Jović, Vladimir Slavnić, Dušan Vudragović, Antun Balaž
    Pages 155-162
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Keywords

About this book

This book is a collection of carefully reviewed papers presented during the HP-SEE User Forum, the meeting of the High-Performance Computing Infrastructure for South East Europe’s (HP-SEE) Research Communities, held in October 17-19, 2012, in Belgrade, Serbia. HP-SEE aims at supporting and integrating regional HPC infrastructures; implementing solutions for HPC in the region; and making HPC resources available to research communities in SEE, region, which are working in a number of scientific fields with specific needs for massively parallel execution on powerful computing resources. HP-SEE brings together research communities and HPC operators from 14 different countries and enables them to share HPC facilities, software, tools, data and research results, thus fostering collaboration and strengthening the regional and national human network; the project specifically supports research groups in the areas of computational physics, computational chemistry and the life sciences. The contributions presented in this book are organized in four main sections: computational physics; computational chemistry; the life sciences; and scientific computing and HPC operations.

 

Editors and Affiliations

  • Physics and Nuclear Engineering, Horia Hulubei National Institute, Magurele, Romania

    Mihnea Dulea

  • Bulgarian Academy of Sciences (IICT-BAS), Institute of Information and Communication Technologies, Sofia, Bulgaria

    Aneta Karaivanova

  • Hellenic Centre for Marine Research (IMBBC-HCMR), Institute of Marine Biology, Biotechnology and Aquacultures, Heraklion, Crete, Greece

    Anastasis Oulas

  • GRNET S.A. Greek Research & Technology Network, Athens, Greece

    Ioannis Liabotis, Ognjen Prnjat

  • University of Belgrade (IPB-UOB) Institute of Physics Belgrade, Belgrade, Serbia

    Danica Stojiljkovic

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