High performance computing of fiber scattering simulation

ACM International Conference Proceeding Series

Volumn 2015-February, Issue , 2015, Pages 90-98

  Yu, Leiming ^a   Zhang, Yan ^a   Gong, Xiang ^a   Roy, Nilay ^b   Makowski, Lee ^b   Kaeli, David ^a  

^a Northeastern University ^*  (United States)

^b NORTHEASTERN UNIVERSITY   (United States)

Author keywords

Cluster; Fiber scattering simulation; GPU

Indexed keywords

CELLULOSE; COMPUTER GRAPHICS; COMPUTER GRAPHICS EQUIPMENT; ENERGY RESOURCES; FORWARD SCATTERING; PROGRAM PROCESSORS; X RAY SCATTERING;

CLUSTER; HIGH PERFORMANCE COMPUTING; MOLECULAR SCATTERING; OPTIMIZATION APPROACH; SCATTERING SIMULATIONS; STRUCTURAL INFORMATION; STRUCTURAL PARAMETER; WORK-LOAD DISTRIBUTION;

GRAPHICS PROCESSING UNIT;

EID: 84938823095     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2716282.2716285     Document Type: Conference Paper

References (35)

1. CUDA C Programming Guide. NVIDIA Corporation, Feb, 2014.
2. Ashwin M Aji, Lokendra S Panwar, Feng Ji, Milind Chabbi, Karthik Murthy, Pavan Balaji, Keith R Bisset, James Dinan, Wuchun Feng, John MellorCrummey, et al. On the efficacy of gpu-integrated mpi for scientific applications. In Proceedings of the 22nd international symposium on High-performance parallel and distributed computing, pages 191-202. ACM, 2013.
3. Axel Arnold, Olaf Lenz, Stefan Kesselheim, Rudolf Weeber, Florian Fahrenberger, Dominic Roehm, Peter Košovan, and Christian Holm. Espresso 3.1: Molecular dynamics software for coarse-grained models. In Meshfree methods for partial differential equations VI, pages 1-23. Springer, 2013.
4. Andreas Athanasopoulos, Anastasios Dimou, Vasileios Mezaris, and Ioannis Kompatsiaris. Gpu acceleration for support vector machines. In Procs. 12th Inter. Workshop on Image Analysis for Multimedia Interactive Services (WIAMIS 2011), Delft, Netherlands, 2011.
5. Jeffrey DiMarco and Michela Taufer. Performance impact of dynamic parallelism on different clustering algorithms. In SPIE Defense, Security, and Sensing, pages 87520E-87520E. International Society for Optics and Photonics, 2013.
6. Wu-chun Feng, Yong Cao, Debprakash Patnaik, and Naren Ramakrishnan. Temporal data mining for neuroscience. GPU Computing Gems Emerald Edition, page 211, 2011.
7. OTTO Glatter. A new method for the evaluation of small-angle scattering data. Journal of Applied Crystallography, 10(5):415-421, 1977.
8. OTTO Glatter. The interpretation of real-space information from small-angle scattering experiments. Journal of Applied Crystallography, 12(2):166-175, 1979.
9. Richard V Greene and Biosciences Center Director. National renewable energy laboratory. 2013.
10. Robert D Hagan. Multi-GPU Load Balancing for Simulation and Rendering. PhD thesis, Virginia Polytechnic Institute and State University, 2011.
11. Hideyo Inouye, Paul E Fraser, and Daniel A Kirschner. Structure of beta-crystallite assemblies formed by alzheimer beta-amyloid protein analogues: analysis by x-ray diffraction. Biophysical journal, 64(2):502-519, 1993.
12. Hideyo Inouye, Yan Zhang, Lin Yang, Nagarajan Venugopalan, Robert F Fischetti, S Charlotte Gleber, Stefan Vogt, W Fowle, Bryan Makowski, Melvin Tucker, et al. Multiscale deconstruction of molecular architecture in corn stover. Scientific reports, 4, 2014.
13. Andrew Kerr, Gregory Diamos, and Sudhakar Yalamanchili. Modeling gpu-cpu workloads and systems. In Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units, pages 31-42. ACM, 2010.
14. Dimitri Komatitsch, Gordon Erlebacher, Dominik Göddeke, and David Michéa. High-order finite-element seismic wave propagation modeling with mpi on a large gpu cluster. Journal of Computational Physics, 229(20):7692-7714, 2010.
15. Jiliang Liu, Hideyo Inouye, Nagarajan Venugopalan, Robert F Fischetti, S Charlotte Gleber, Stefan Vogt, Joanne C Cusumano, Jeong Im Kim, Clint Chapple, and Lee Makowski. Tissue specific specialization of the nanoscale architecture of arabidopsis. Journal of structural biology, 184(2):103-114, 2013.
16. Weiguo Liu, Bertil Schmidt, Gerrit Voss, and Wolfgang Muller-Wittig. Streaming algorithms for biological sequence alignment on gpus. Parallel and Distributed Systems, IEEE Transactions on, 18(9):1270-1281, 2007.
17. Massachusetts Green High Performance Computing Center. http://www.northeastern.edu/rc.
18. William Shu Lai Mok and Michael Jerry Antal Jr. Uncatalyzed solvolysis of whole biomass hemicellulose by hot compressed liquid water. Industrial & Engineering Chemistry Research, 31(4):1157-1161, 1992.
19. Yoshiharu Nishiyama, Paul Langan, and Henri Chanzy. Crystal structure and hydrogen-bonding system in cellulose Iβ from synchrotron x-ray and neutron fiber diffraction. Journal of the American Chemical Society, 124(31):9074-9082, 2002.
20. Yoshiharu Nishiyama, Junji Sugiyama, Henri Chanzy, and Paul Langan. Crystal structure and hydrogen bonding system in cellulose Iα from synchrotron x-ray and neutron fiber diffraction. Journal of the American Chemical Society, 125(47):14300-14306, 2003.
21. NVIDIA. Nvidia's Next Generation CUDATM Compute Architecture, KeplerTM GK110, 2012.
22. NVIDIA. Profiler, Compute Visual, August 2014.
23. CUDA NVidia. Occupancy calculator, 2009.
24. DK Panda. Mvapich2: A high performance mpi library for nvidia gpu clusters with infiniband. GTC2013,(March 20, 2013), 2013.
25. Fanny Nina Paravecino and David Kaeli. Accelerated connected component labeling using cuda framework. In Computer Vision and Graphics, pages 502-509. Springer, 2014.
26. Dino Quintero, Luis Carlos Cruz, Ricardo Machado Picone, Dusan Smolej, Daniel de Souza Casali, Gheorghe Tudor, Joanna Wong, et al. IBM Platform Computing Solutions Reference Architectures and Best Practices. IBM Redbooks, 2014.
27. Martin Schweiger. Gpu-accelerated finite element method for modelling light transport in diffuse optical tomography. Journal of Biomedical Imaging, 2011:10, 2011.
28. John A Stratton, Nasser Anssari, Christopher Rodrigues, I-Jui Sung, Nady Obeid, Liwen Chang, Geng Daniel Liu, and Wen-mei Hwu. Optimization and architecture effects on gpu computing workload performance. In Innovative Parallel Computing (InPar), 2012, pages 1-10. IEEE, 2012.
29. Top500. List of top 500 supercomputers. http://www.top500.org/lists/2014/06/, 2014.
30. Stanley Tzeng, Anjul Patney, and John D Owens. Task management for irregular-parallel workloads on the gpu. In Proceedings of the Conference on High Performance Graphics, pages 29-37. Eurographics Association, 2010.
31. Yash Ukidave, Amir Kavyan Ziabari, Perhaad Mistry, Gunar Schirner, and David Kaeli. Analyzing power efficiency of optimization techniques and algorithm design methods for applications on heterogeneous platforms. International Journal of High Performance Computing Applications, page 1094342014526907, 2014.
32. Hao Wang, Sreeram Potluri, Miao Luo, Ashish Kumar Singh, Xiangyong Ouyang, Sayantan Sur, and Dhabaleswar K Panda. Optimized non-contiguous mpi datatype communication for gpu clusters: Design, implementation and evaluation with mvapich2. In Cluster Computing (CLUSTER), 2011 IEEE International Conference on, pages 308-316. IEEE, 2011.
33. Nathan Whitehead and Alex Fit-Florea. Precision & performance: Floating point and ieee 754 compliance for nvidia gpus. rn (A+ B), 21:1-1874919424, 2011.
34. Yan Zhang, Leiming Yu, David Kaeli, and Lee Makowski. Fast simulation of x-ray diffraction patterns from cellulose fibrils using gpus. In Northeast Bioengineering Conference (NEBEC), 2014 40th Annual, pages 1-2. IEEE, 2014.
35. Kaiyong Zhao and Xiaowen Chu. G-blastn: accelerating nucleotide alignment by graphics processors. Bioinformatics, page btu047, 2014.