The Art of High Performance Computing for Computational Science, Vol. 2

1. Front Matter

   Pages i-ix

   PDF

2. Supercomputers and Application Performance

   • Kazuo Minami

   Pages 1-9

3. Performance Optimization of Applications

   • Kazuo Minami

   Pages 11-39

4. Case Studies of Performance Optimization of Applications

   • Kazuo Minami, Kiyoshi Kumahata

   Pages 41-88

5. O(N) Methods

   • Taisuke Ozaki

   Pages 89-115

6. Acceleration of Classical Molecular Dynamics Simulations

   • Y. Andoh, N. Yoshii, J. Jung, Y. Sugita

   Pages 117-157

7. Large-Scale Quantum Chemical Calculation

   • Kazuya Ishimura, Masato Kobayashi

   Pages 159-201

8. Back Matter

   Pages 203-206

   PDF

This book presents advanced and practical techniques for performance optimization for highly parallel processing. Featuring various parallelization techniques in material science, it is a valuable resource for anyone developing software codes for computational sciences such as physics, chemistry, biology, earth sciences, space science, weather, disaster prevention and manufacturing, as well as for anyone using those software codes.

Chapter 1 outlines supercomputers and includes a brief explanation of the history of hardware. Chapter 2 presents procedures for performance evaluation, while Chapter 3 describes the set of tuned applications in materials science, nanoscience and nanotechnology, earth science and engineering on the K computer. Introducing the order-N method, based on density functional theory (DFT) calculation, Chapter 4 explains how to extend the applicability of DFT to large-scale systems by reducing the computational complexity. Chapter 5 discusses acceleration and parallelization in classical molecular dynamics simulations, and lastly, Chapter 6 explains techniques for large-scale quantum chemical calculations, including the order-N method.

This is the second of the two volumes that grew out of a series of lectures in the K computer project in Japan. The first volume addresses more basic techniques, and this second volume focuses on advanced and concrete techniques.

• High Parallelization
• Performance Optimization
• High Performance Computing
• Supercomputer
• K Computer
• Order-N Method
• Density Functional Theory
• Material Science
• Molecular Dynamics Simulation
• Large-scale Quantum Chemical Calculation

• Osaka University, Toyonaka, Japan

  Masaaki Geshi

Masaaki Geshi is an Associate Professor at the Institute for NanoScience Design at Osaka University. He received a Ph.D. in science from Kanazawa University in 2000. His research interests include materials design, from first-principles calculations to the synthesis process for new materials, and high-pressure physics.

Policies and ethics