GPU Solutions to Multi-scale Problems in Science and Engineering

1. Why Do Scientists and Engineers Need GPU’s Today?
Matthew G. Knepley, David A. Yuen

2. Happenings at the GPU Conference
Xian-yu Lang, Long Wang, David A. Yuen

3. Efficiency, Energy Efficiency and Programming of Accelerated HPC Servers: Highlights of PRACE Studies
Lennart Johnsson

4. GRAPE and GRAPE-DR
Junichiro Makino

5. Parray: A Unifying Array Representation for Heterogeneous Parallelism
Yifeng Chen, Xiang Cui, Hong Mei

6. Practical Random Linear Network Coding on GPUs
Xiaowen Chu, Kaiyong Zhao

7. Preliminary Implementation of PETSc Using GPUs
Victor Minden, Barry Smith, Matthew G. Knepley

8. Multi-scale Continuum-Particle Simulation on CPU–GPU Hybrid Supercomputer
Wei Ge, Ji Xu, Qingang Xiong, Xiaowei Wang, Feiguo Chen, Limin Wang, Chaofeng Hou, Ming Xu, Jinghai Li

9. GPU Best Practices for HPC Applications at Industry Scale
Peng Wang, Stan Posey

10. Simulation of 1D Condensing Flows with CESE Method on GPU Cluster
Wei Ran, Wan Cheng, Fenghua Qin, Xisheng Luo

11. Two-Way Coupled Sprays and Liquid Surface: A GPU-Based Multi-Scale Fluid Animation Method
Guijuan Zhang, Gaojin Wen, Shengzhong Feng

12. High Performance Implementation of Binomial Option Pricing Using CUDA
Yechen Gui, Shenzhong Feng, Gaojin Wen, Guijuan Zhang, Yanyi Wan, Tao Liu

13. Research of Acceleration MS-Alignment Identifying Post-Translational Modifications on GPU
Zhai Yantang, Tu Qiang, Lang Xianyu, Lu Zhonghua, Chi Xuebin

14. GPU Tuning for First-Principle Electronic Structure Simulations
Yue Wu, Weile Jia, Lin-Wang Wang, Weiguo Gao, Long Wang, Xuebin Chi

15. Nucleation and Reaction of Dislocations in Some Metals and Intermetallic Compound TiAl
D. S. Xu, H. Wang, R. Yang

16. Large-Scale Numerical Weather Prediction on GPU Supercomputer
Takayuki Aoki, Takashi Shimokawabe

17. Targeting Atmospheric Simulation Algorithms for Large, Distributed-Memory, GPU-Accelerated Computers
Matthew R. Norman

18. Investigation of Solving 3D Navier–Stokes Equations with Hybrid Spectral Scheme Using GPU
Ying Xu, Lei Xu, D. D. Zhang, J. F. Yao

19. Correlation of Reservoir and Earthquake by Multi Temporal-Spatial Scale Flow Driven Pore-Network Crack Model in Parallel CPU and GPU Platform
B. J. Zhu, C. Liu, Y. L. Shi, D. A. Yuen

20. A Full GPU Simulation of Evolving Fracture Networks in a Heterogeneous Poro-Elasto-Plastic Medium with Effective-Stress-Dependent Permeability
Boris Galvan, Stephen Miller

21. GPU Implementation of Multigrid Solver for Stokes Equation with Strongly Variable Viscosity
Liang Zheng, Taras Gerya, Matthew Knepley, David A. Yuen, Huai Zhang, Yaolin Shi

22. High Rayleigh Number Mantle Convection on GPU
David A. Sanchez, Christopher Gonzalez, David A. Yuen, Grady B. Wright, Gregory A. Barnett

23. High-Order Discontinuous Galerkin Methods by GPU Metaprogramming
Andreas Klöckner, Timothy Warburton, Jan S. Hesthaven

24. Accelerating Large-Scale Simulation of Seismic Wave Propagation by Multi-GPUs and Three-Dimensional Domain Decomposition
Taro Okamoto, Hiroshi Takenaka, Takeshi Nakamura, Takayuki Aoki

25. Support Operator Rupture Dynamics on GPU
Shenyi Song, Yichen Zhou, Tingxing Dong, David A. Yuen

26. A Geometric Multigrid Solver on GPU Clusters
Harald Koestler, Daniel Ritter, Christian Feichtinger

27. Accelerating 2-Dimensional CFD on Multi-GPU Supercomputer
Sen Li, Xinliang Li, Long Wang, Zhonghua Lu, Xuebin Chi

28. Efficient Rendering of Order Independent Transparency on the GPUs
Fang Liu

29. Performance Evaluation of Fast Fourier Transform Application on Heterogeneous Platforms
Xiaojun Li, Yang Gao, Xinyu Ma, Ying Liu

30. Accurate Evaluation of Local Averages on GPGPUs
Dmitry A. Karpeev, Matthew G. Knepley, Peter R. Brune

31. Accelerating Swarm Intelligence Algorithms with GPU-Computing
Robin M. Weiss

32. Asynchronous Parallel Logic Simulation on Modern Graphics Processors
Yangdong Deng, Yuhao Zhu, Wang Bo

33. Implementations of Main Algorithms for Generalized Symmetric Eigenproblem on GPU Accelerator
Yonghua Zhao, Fang Liu, Yangang Wang, Xuebin Chi

34. Using Mixed Precision Algorithm for LINPACK Benchmark on AMD GPU
Xianyi Zhang, Yunquan Zhang, Lei Wang

35. Parallel Lattice Boltzmann Method on CUDA Architecture
Weibing Feng, Wu Zhang, Bing He, Kai Wang

36. Iterative Deblurring of Large 3D Datasets from Cryomicrotome Imaging Using an Array of GPUs
Thomas Geenen, Pepijn Horssen, Jos A.E. Spaan, Maria Siebes, Jeroen P.H.M. Wijngaard

37. WebViz: A Web-Based Collaborative Interactive Visualization System for Large-Scale Data Sets
Yichen Zhou, Robin M. Weiss, Elizabeth McArthur, David Sanchez, Xiang Yao, Dave Yuen, Mike R. Knox, W. Walter Czech

38. Interactive Visualization Tool for Planning Cancer Treatment
R. Wcisło, W. Dzwinel, P. Gosztyla, D. A. Yuen, W. Czech

39. High Throughput Heterogeneous Computing and Interactive Visualization on a Desktop Supercomputer
S. Zhang, R. Weiss, S. Wang, G. A. Barnett, D. A. Yuen

40. Applications of Microtomography to Multiscale System Dynamics: Visualisation, Characterisation and High Performance Computation
Jie Liu, Klaus Regenauer-Lieb, Chris Hines, Shuxia Zhang, Paul Bourke, Florian Fusseis, David A. Yuen

41. Three-Dimensional Reconstruction of Electron Tomography Using Graphic Processing Units (GPUs)
Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu

Keywords: Computer Science, Numeric Computing, Geophysics/Geodesy, Continuum Mechanics and Mechanics of Materials, Physical Chemistry