Ebook: High Performance Computing for Computational Science - VECPAR 2012: 10th International Conference, Kope, Japan, July 17-20, 2012, Revised Selected Papers

This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on High Performance Computing for Computational Science, VECPAR 2012, held in Kope, Japan, in July 2012. The 28 papers presented together with 7 invited talks were carefully selected during two rounds of reviewing and revision. The papers are organized in topical sections on CPU computing, applications, finite element method from various viewpoints, cloud and visualization performance, method and tools for advanced scientific computing, algorithms and data analysis, parallel iterative solvers on multicore architectures.

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This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on High Performance Computing for Computational Science, VECPAR 2012, held in Kope, Japan, in July 2012. The 28 papers presented together with 7 invited talks were carefully selected during two rounds of reviewing and revision. The papers are organized in topical sections on CPU computing, applications, finite element method from various viewpoints, cloud and visualization performance, method and tools for advanced scientific computing, algorithms and data analysis, parallel iterative solvers on multicore architectures.

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This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on High Performance Computing for Computational Science, VECPAR 2012, held in Kope, Japan, in July 2012. The 28 papers presented together with 7 invited talks were carefully selected during two rounds of reviewing and revision. The papers are organized in topical sections on CPU computing, applications, finite element method from various viewpoints, cloud and visualization performance, method and tools for advanced scientific computing, algorithms and data analysis, parallel iterative solvers on multicore architectures.
Content:
Front Matter....Pages -
Barriers to Exascale Computing....Pages 1-3
Toward a Theory of Algorithm-Architecture Co-design....Pages 4-8
Visualization of Strong Ground Motion from the 2011 Off Tohoku, Japan (Mw=9.0) Earthquake Obtained from Dense Nation-Wide Seismic Network and Large-Scale Parallel FDM Simulation....Pages 9-16
Grand Challenge in Life Science on K Computer....Pages 17-22
HPC/PF - High Performance Computing Platform: An Environment That Accelerates Large-Scale Simulations....Pages 23-27
Programming the LU Factorization for a Multicore System with Accelerators....Pages 28-35
Efficient Two-Level Preconditioned Conjugate Gradient Method on the GPU....Pages 36-49
Parallelization of the QR Decomposition with Column Pivoting Using Column Cyclic Distribution on Multicore and GPU Processors....Pages 50-58
A High Performance SYMV Kernel on a Fermi-core GPU....Pages 59-71
Optimizing Memory-Bound SYMV Kernel on GPU Hardware Accelerators....Pages 72-79
Numerical Simulation of Long-Term Fate of CO2 Stored in Deep Reservoir Rocks on Massively Parallel Vector Supercomputer....Pages 80-92
High Performance Simulation of Complicated Fluid Flow in 3D Fractured Porous Media with Permeable Material Matrix Using LBM....Pages 93-104
Parallel Scalability Enhancements of Seismic Response and Evacuation Simulations of Integrated Earthquake Simulator....Pages 105-117
QMC=Chem: A Quantum Monte Carlo Program for Large-Scale Simulations in Chemistry at the Petascale Level and beyond....Pages 118-127
Optimizing Sparse Matrix Assembly in Finite Element Solvers with One-Sided Communication....Pages 128-139
Implementation and Evaluation of 3D Finite Element Method Application for CUDA....Pages 140-148
Evaluation of Two Parallel Finite Element Implementations of the Time-Dependent Advection Diffusion Problem: GPU versus Cluster Considering Time and Energy Consumption....Pages 149-162
A Service-Oriented Architecture for Scientific Computing on Cloud Infrastructures....Pages 163-176
Interactive Volume Rendering Based on Ray-Casting for Multi-core Architectures....Pages 177-186
Automatic Generation of the HPC Challenge’s Global FFT Benchmark for BlueGene/P....Pages 187-200
Matrix Multiplication on Multidimensional Torus Networks....Pages 201-215
High Performance CPU Kernels for Multiphase Compressible Flows....Pages 216-225
Efficient Algorithm for Linear Systems Arising in Solutions of Eigenproblems and Its Application to Electronic-Structure Calculations....Pages 226-235
Control Formats for Unsymmetric and Symmetric Sparse Matrix–Vector Multiplications on OpenMP Implementations....Pages 236-248
Sparsification on Parallel Spectral Clustering....Pages 249-260
An Experimental Study of Global and Local Search Algorithms in Empirical Performance Tuning....Pages 261-269
A Multi GPU Read Alignment Algorithm with Model-Based Performance Optimization....Pages 270-277
OpenMP/MPI Hybrid Parallel ILU(k) Preconditioner for FEM Based on Extended Hierarchical Interface Decomposition for Multi-core Clusters....Pages 278-291
Parallel Smoother Based on Block Red-Black Ordering for Multigrid Poisson Solver....Pages 292-299
Software Transactional Memory, OpenMP and Pthread Implementations of the Conjugate Gradients Method – A Preliminary Evaluation....Pages 300-313
A Smart Tuning Strategy for Restart Frequency of GMRES(m) with Hierarchical Cache Sizes....Pages 314-328
Adaptive Off-Line Tuning for Optimized Composition of Components for Heterogeneous Many-Core Systems....Pages 329-345
A Domain-Specific Compiler for Linear Algebra Operations....Pages 346-361
Designing Linear Algebra Algorithms by Transformation: Mechanizing the Expert Developer....Pages 362-378
Accelerating the Reorthogonalization of Singular Vectors with a Multi-core Processor....Pages 379-390
Auto-tuning the Matrix Powers Kernel with SEJITS....Pages 391-403
Auto-tuning of Numerical Programs by Block Multi-color Ordering Code Generation and Job-Level Parallel Execution....Pages 404-419
Automatic Parameter Optimization for Edit Distance Algorithm on GPU....Pages 420-434
Automatic Tuning of Parallel Multigrid Solvers Using OpenMP/MPI Hybrid Parallel Programming Models....Pages 435-450
A Predictive Performance Model for Stencil Codes on Multicore CPUs....Pages 451-466
Back Matter....Pages -

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This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on High Performance Computing for Computational Science, VECPAR 2012, held in Kope, Japan, in July 2012. The 28 papers presented together with 7 invited talks were carefully selected during two rounds of reviewing and revision. The papers are organized in topical sections on CPU computing, applications, finite element method from various viewpoints, cloud and visualization performance, method and tools for advanced scientific computing, algorithms and data analysis, parallel iterative solvers on multicore architectures.
Content:
Front Matter....Pages -
Barriers to Exascale Computing....Pages 1-3
Toward a Theory of Algorithm-Architecture Co-design....Pages 4-8
Visualization of Strong Ground Motion from the 2011 Off Tohoku, Japan (Mw=9.0) Earthquake Obtained from Dense Nation-Wide Seismic Network and Large-Scale Parallel FDM Simulation....Pages 9-16
Grand Challenge in Life Science on K Computer....Pages 17-22
HPC/PF - High Performance Computing Platform: An Environment That Accelerates Large-Scale Simulations....Pages 23-27
Programming the LU Factorization for a Multicore System with Accelerators....Pages 28-35
Efficient Two-Level Preconditioned Conjugate Gradient Method on the GPU....Pages 36-49
Parallelization of the QR Decomposition with Column Pivoting Using Column Cyclic Distribution on Multicore and GPU Processors....Pages 50-58
A High Performance SYMV Kernel on a Fermi-core GPU....Pages 59-71
Optimizing Memory-Bound SYMV Kernel on GPU Hardware Accelerators....Pages 72-79
Numerical Simulation of Long-Term Fate of CO2 Stored in Deep Reservoir Rocks on Massively Parallel Vector Supercomputer....Pages 80-92
High Performance Simulation of Complicated Fluid Flow in 3D Fractured Porous Media with Permeable Material Matrix Using LBM....Pages 93-104
Parallel Scalability Enhancements of Seismic Response and Evacuation Simulations of Integrated Earthquake Simulator....Pages 105-117
QMC=Chem: A Quantum Monte Carlo Program for Large-Scale Simulations in Chemistry at the Petascale Level and beyond....Pages 118-127
Optimizing Sparse Matrix Assembly in Finite Element Solvers with One-Sided Communication....Pages 128-139
Implementation and Evaluation of 3D Finite Element Method Application for CUDA....Pages 140-148
Evaluation of Two Parallel Finite Element Implementations of the Time-Dependent Advection Diffusion Problem: GPU versus Cluster Considering Time and Energy Consumption....Pages 149-162
A Service-Oriented Architecture for Scientific Computing on Cloud Infrastructures....Pages 163-176
Interactive Volume Rendering Based on Ray-Casting for Multi-core Architectures....Pages 177-186
Automatic Generation of the HPC Challenge’s Global FFT Benchmark for BlueGene/P....Pages 187-200
Matrix Multiplication on Multidimensional Torus Networks....Pages 201-215
High Performance CPU Kernels for Multiphase Compressible Flows....Pages 216-225
Efficient Algorithm for Linear Systems Arising in Solutions of Eigenproblems and Its Application to Electronic-Structure Calculations....Pages 226-235
Control Formats for Unsymmetric and Symmetric Sparse Matrix–Vector Multiplications on OpenMP Implementations....Pages 236-248
Sparsification on Parallel Spectral Clustering....Pages 249-260
An Experimental Study of Global and Local Search Algorithms in Empirical Performance Tuning....Pages 261-269
A Multi GPU Read Alignment Algorithm with Model-Based Performance Optimization....Pages 270-277
OpenMP/MPI Hybrid Parallel ILU(k) Preconditioner for FEM Based on Extended Hierarchical Interface Decomposition for Multi-core Clusters....Pages 278-291
Parallel Smoother Based on Block Red-Black Ordering for Multigrid Poisson Solver....Pages 292-299
Software Transactional Memory, OpenMP and Pthread Implementations of the Conjugate Gradients Method – A Preliminary Evaluation....Pages 300-313
A Smart Tuning Strategy for Restart Frequency of GMRES(m) with Hierarchical Cache Sizes....Pages 314-328
Adaptive Off-Line Tuning for Optimized Composition of Components for Heterogeneous Many-Core Systems....Pages 329-345
A Domain-Specific Compiler for Linear Algebra Operations....Pages 346-361
Designing Linear Algebra Algorithms by Transformation: Mechanizing the Expert Developer....Pages 362-378
Accelerating the Reorthogonalization of Singular Vectors with a Multi-core Processor....Pages 379-390
Auto-tuning the Matrix Powers Kernel with SEJITS....Pages 391-403
Auto-tuning of Numerical Programs by Block Multi-color Ordering Code Generation and Job-Level Parallel Execution....Pages 404-419
Automatic Parameter Optimization for Edit Distance Algorithm on GPU....Pages 420-434
Automatic Tuning of Parallel Multigrid Solvers Using OpenMP/MPI Hybrid Parallel Programming Models....Pages 435-450
A Predictive Performance Model for Stencil Codes on Multicore CPUs....Pages 451-466
Back Matter....Pages -
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