High-Performance Computing Infrastructure for South East Europe's Research Communities: Results of the HP-SEE User Forum 2012 (Modeling and Optimization in Science and Technologies Book 2)

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. High-Performance Computing Infrastructure for South East Europe’s Research Communities Preface 5 Organization 7 Contents 9 Simulation of Electron Transport Using HPCInfrastructure in South-Eastern Europe 11 1 Introduction 11 2 The Quantum Kinetic Integral Equation 13 3 Monte Carlo Approach 15 4 Parallel Implementation and Numerical Results 18 5 Conclusions and Future Work 21 References 22 Density Waves in Dipolar Bose-Einstein Condensates by Means of Symbolic Computations 24 1 Introduction 24 2 Variational Treatment 25 3 Roton-Maxon Structures 26 4 Conclusions 29 References 29 Using Parallel Computing to Calculate Static Interquark Potential in LQCD 31 1 Introduction 31 2 Materials and Methods 32 2.1 The Static Quark-Antiquark Potential 32 2.2 FermiQCD and BG – HPC Cluster 33 3 Preliminary Physics Results 35 3.1 Quark-Antiquark Potential from Planar and Volume Wilson Loops 35 4 Conclusions 37 References 37 Modelling of Disaster Spreading Dynamics 39 1 Introduction 39 2 Percolation Probability Density 41 3 Fire Spreading on Percolating Networks 44 4 Cascade Failures 46 5 Conclusion 49 References 49 Determination of Zone of Flow Instability in a Gas Flow Past a Square Particle in a Narrow Microchannel 51 1 Introduction 51 2 Continuum Model Equations 53 3 Problem Formulation, Results and Discussion 54 4 Conclusions 57 References 57 Quenched Hadron Spectroscopy Using FermiQCD 59 1 Introduction 59 1.1 Introduction to Lattice QCD 59 1.2 Introduction to FermiQCD 60 2 Materials and Methods 61 3 Results and Discussions 62 4 Conclusions 65 References 66 Self-Avoiding Hamiltonian Walks Counting in Parallel Processing Mode 67 1 Introduction 67 2 Hamiltonian Walks on Sierpinski Gasket Fractals 68 3 Hamiltonian Walks on Given-Mandelbrot Fractals 70 4 Implementation and Parallelization 71 4.1 Parallelization and Scalability 73 5 Summary and Conclusion 74 References 74 Conformational Analysis and HF ab initio Geometry Optimization of Kyotorphine and Its Sulfo-Analogues Norsulfoarginine-Tyrosine and Tyrosine-Norsulfoarginine 75 1 Introduction 75 2 Computational 76 3 Results and Discussion 76 References 82 Dynamics of Uninhibited and Covalently Inhibited Cysteine Protease on Non-physiological pH 83 1 Introduction 83 2 Results and Discussion 85 3 Conclusions 88 4 Experimental 89 References 90 Mechanisms of Polarization 91 1 Introduction 91 2 Methods 91 3 Results and Discussion 92 3.1 Squaraines 92 3.2 Lithiated Derivatives 93 3.3 Noble Gas Derivatives 95 References 98 Some Aspects of the Comparative Study of Semi-empirical Combustion Models on FLUENT and OpenFOAM Codes 101 1 Introduction 101 2 Combustion Mechanisms 102 2.1 Theory – Species Transport Equations 102 3 Combustion Simulation Results 103 4 Scalability Testing 103 4.1 Execution Times 104 4.2 Scalability Analysis 105 5 Summary and Conclusion 106 References 106 Development of a Hybrid Statistical Physics – Quantum Mechanical Methodology for Computer Simulations of Condensed Phases and Its Implementation on High-Performance Computing Systems 107 1 Introduction 108 2 Computational Details and Algorithms 109 3 Results and Discussion 111 4 Conclusions and Directions for Future work 116 References 116 Solvatochromic Effect for the Denaturation and Mutation Processes in DNA: Computational Study 117 1 Introduction 117 2 Methods 118 3 Implementation on the HPC Infrastructure 118 4 Results and Discussion 119 5 Conclusion 122 References 122 Dynamic Features of Complex Systems: A Molecular Simulation Study 124 1 Introduction 124 2 Construction and Simulation Data 125 3 Results and Discussions 125 4 Conclusion 127 References 127 Using Adaptive Mesh Refinement Strategy for Numerical Solving of Gas Dynamics Problems on Multicore Computers 129 1 Introduction 129 2 Methods 130 2.1 Formulation of the Problem 130 2.2 AMR Method 131 2.3 Calculation Algorithm 132 3 Results 133 3.1 AMR PAR 64-Bit Application 133 3.2 Adopting AMR PAR Application to the Regional HPCResources 134 4 Discussion and Conclusions 135 4.1 Future Work 135 References 136 Number Theory Algorithms on GPU Clusters 137 1 Introduction 137 2 Preliminaries 138 3 Implementation Details and Computational Experiments 139 3.1 Description of the Implementation and Experiments 139 3.2 Computational Resources Used 142 3.3 Obtained Results 142 4 Conclusion and Future Work 143 References 144 Advanced Vulnerability Assessment Tool for Distributed Systems 145 1 Introduction 145 1.1 Large Scientific Computing Resources 145 1.2 Motivation 146 1.3 Vulnerability Trends 146 2 Related Work 146 3 Design and Implementation 148 3.1 Architecture 148 3.2 Introducing gLite Based Resources 149 4 Investigating the Results of the Test Scans 150 4.1 SEE-GRID VO 150 4.2 HP-SEE Supercomputing Infrastructure 150 5 Conclusion and Future Work 151 References 152 Performance and Scalability Evaluation of Short Fragment Sequence Alignment Applications 153 1 Introduction 153 2 HP-SEE’s Bioinformatics eScience Gateway 154 2.1 Disease Gene Mapper 154 2.2 Deep Aligner 154 3 Performance Analysis 155 3.1 Job 1 155 3.2 Job 2 155 3.3 Job 3 156 4 Performance Measurement Results 156 4.1 Runtime Benchmark 156 4.2 DB Fragment Numbers 157 4.3 Real World Performance 158 5 Conclusion 160 6 Future Work 160 References 160 Implementation and Benchmarking of New FFT Libraries in Quantum ESPRESSO 161 1 Introduction 161 2 Quantum ESPRESSO Code Structure and AppliedModifications 162 2.1 Enabling FFTE Library in Quantum ESPRESSO 162 2.2 Enabling FFTW3 Threading in Quantum ESPRESSO 163 3 PerformanceTests 164 3.1 FFTE Performance 164 3.2 FFTW3 Threaded Performance 165 4 Conclusions 168 References 168 An Analysis of FFTW and FFTE Performance 169 1 Introduction 169 2 FFT Libraries and Methods 170 2.1 FFTW 170 2.2 FFTE 170 3 Benchmarking of FFT Libraries Using Developed In-HouseCodes 171 4 FFT Benchmark Codes Results and Interpretation 171 4.1 CURIE Results 172 4.2 JUGENE Results 174 5 Conclusions and Recommendations 176 References 176 Author Index 177 Front Matter....Pages 1-9 Simulation of Electron Transport Using HPC Infrastructure in South-Eastern Europe....Pages 1-13 Density Waves in Dipolar Bose-Einstein Condensates by Means of Symbolic Computations....Pages 15-21 Using Parallel Computing to Calculate Static Interquark Potential in LQCD....Pages 23-30 Modelling of Disaster Spreading Dynamics....Pages 31-42 Determination of Zone of Flow Instability in a Gas Flow Past a Square Particle in a Narrow Microchannel....Pages 43-50 Quenched Hadron Spectroscopy Using FermiQCD....Pages 51-58 Self-Avoiding Hamiltonian Walks Counting in Parallel Processing Mode....Pages 59-66 Conformational Analysis and HF ab initio Geometry Optimization of Kyotorphine and Its Sulfo-Analogues Norsulfoarginine-Tyrosine and Tyrosine-Norsulfoarginine....Pages 67-74 Dynamics of Uninhibited and Covalently Inhibited Cysteine Protease on Non-physiological pH....Pages 75-82 Mechanisms of Polarization....Pages 83-92 Some Aspects of the Comparative Study of Semi-empirical Combustion Models on FLUENT and OpenFOAM Codes....Pages 93-98 Development of a Hybrid Statistical Physics – Quantum Mechanical Methodology for Computer Simulations of Condensed Phases and Its Implementation on High-Performance Computing Systems....Pages 99-108 Solvatochromic Effect for the Denaturation and Mutation Processes in DNA: Computational Study....Pages 109-115 Dynamic Features of Complex Systems: A Molecular Simulation Study....Pages 117-121 Using Adaptive Mesh Refinement Strategy for Numerical Solving of Gas Dynamics Problems on Multicore Computers....Pages 123-130 Number Theory Algorithms on GPU Clusters....Pages 131-138 Advanced Vulnerability Assessment Tool for Distributed Systems....Pages 139-146 Performance and Scalability Evaluation of Short Fragment Sequence Alignment Applications....Pages 147-154 Implementation and Benchmarking of New FFT Libraries in Quantum ESPRESSO....Pages 155-162 An Analysis of FFTW and FFTE Performance....Pages 163-170 Back Matter....Pages 171-171