SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

An internationally recognized leader in visualization, scientific computing, and image analysis

SCI Publications

2007


J. Luitjens, M. Berzins, T.C. Henderson. “Parallel Space Filling Curve Generation Through Sorting,” In Journal of Concurrency and Computation, Vol. 19, No. 10, pp. 1387--1402. 2007.


J. Luitjens, B. Worthen, M. Berzins, T.C. Henderson. “Scalable Parallel AMR for the Uintah Multiphysics Code,” In Petascale Computing Algorithms and Applications, Edited by D. Bader, Chapman and Hall/CRC, 2007.


J. Luitjens, M. Berzins, T. Henderson. “Parallel space-filling curve generation through sorting,” In Concurrency and Computation: Practice and Experience, Vol. 19, No. 10, pp. 1387--1402. July, 2007.
DOI: 10.1002/cpe.1179

ABSTRACT

In this paper we consider the scalability of parallel space-filling curve generation as implemented through parallel sorting algorithms. Multiple sorting algorithms are studied and results show that space-filling curves can be generated quickly in parallel on thousands of processors. In addition, performance models are presented that are consistent with measured performance and offer insight into performance on still larger numbers of processors. At large numbers of processors, the scalability of adaptive mesh refined codes depends on the individual components of the adaptive solver. One such component is the dynamic load balancer. In adaptive mesh refined codes, the mesh is constantly changing resulting in load imbalance among the processors requiring a load-balancing phase. The load balancing may occur often, requiring the load balancer to perform quickly. One common method for dynamic load balancing is to use space-filling curves. Space-filling curves, in particular the Hilbert curve, generate good partitions quickly in serial. However, at tens and hundreds of thousands of processors serial generation of space-filling curves will hinder scalability. In order to avoid this issue we have developed a method that generates space-filling curves quickly in parallel by reducing the generation to integer sorting.


T.J. Lujan, M.S. Dalton, B.M. Thompson, B.J. Ellis, J.A. Weiss. “Effect of ACL Deficiency on MCL Strains and Joint Kinematics,” In Journal of Biomechanical Engineering, Vol. 129, No. 3, pp. 386--392. 2007.


T.J. Lujan, C.J. Underwood, H.B. Henninger, B.M. Thompson, J.A. Weiss. “Effect of Dermatan Sulfate Glycosaminoglycans on the Quasi-Static Material Properties of the Human Medial Collateral Ligament,” In Journal of Orthopaedic Research, Vol. 25, No. 7, pp. 894--903. 2007.


M. Malik, Y. Birnbaum, R.S. MacLeod, V. Shusterman. “Markers of impaired repolarization,” In Journal of Electrocardiology, Vol. 40, No. 1, pp. S54--S57. January, 2007.


M.D. Meyer, B. Nelson, R.M. Kirby, R.T. Whitaker. “Particle Systems for Efficient and Accurate Finite Element Visualization,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 5, pp. 1015--1026. 2007.


M.D. Meyer, R.M. Kirby, R.T. Whitaker. “Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, IEEE, pp. 1704--1711. Nov, 2007.


D. Nain, M. Styner, M. Niethammer, J.J. Levitt, M.E. Shenton, G. Gerig, A. Bobick, A. Tannenbaum. “Statistical Shape Analysis of Brain Structures Using Spherical Wavelets,” In Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2007), IEEE Press, pp. 209--212. 2007.


O. Nemitz, T. Tasdizen, M. Rumpf, R.T. Whitaker. “Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data,” In Journal of Mathematical Imaging and Vision, Vol. 7, No. 3, pp. 217--229. 2007.
DOI: 10.1007/s10851-006-0645-2


E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. “Unconditionally Stable Discretizations of the Immersed Boundary Equations,” In Journal of Computational Physics, Vol. 222, No. 2, pp. 702--719. 2007.


E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. “Unconditionally Stable Discretizations of the Immersed Boundary Equations,” In Journal of Computational Physics, Vol. 222, No. 2, pp. 702--719. March, 2007.


T. Ochotta, C.E. Scheidegger, J. Schreiner, Y. Lima, R.M. Kirby, C.T. Silva. “A Unified Projection Operator for Moving Least Squares Surfaces,” SCI Institute Technical Report, No. UUSCI-2007-006, University of Utah, 2007.


L. Omberg, G.H. Golub, O. Alter. “A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data From Different Studies,” In Proceedings of the National Academy of Sciences, Vol. 104, No. 47, Proceedings of the National Academy of Sciences, pp. 18371–-18376. November, 2007.
DOI: 10.1073/pnas.0709146104


R. Palmer, G. Gopalakrishnan, R.M. Kirby. “Semantics Driven Dynamic Partial-Order Reduction of MPI-based Parallel Programs,” In Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD), London, UK, Note: Awarded Best Paper, 2007.


S.G. Parker, S. Boulos, J. Bigler, A. Robison. “RTSL: a Ray Tracing Shading Language,” In In 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing, pp. 149--160. 2007.


S.G. Parker, R. Armstrong, D. Bernholdt, T. Dahlgren, T. Epperly, J. Kenny, M. Krishnan, G. Kumfert, J. Larson, L.C. McInnes, J. Nieplocha, J. Ray, S. Shasharina. “Enabling Advanced Scientific Computing Software,” In CTWatch Quarterly, Vol. 3, No. 4, 2007.


V. Pascucci, G. Scorzelli, P.-T. Bremer, A. Mascarenhas. “Robust On-line Computation of Reeb Graphs: Simplicity and Speed,” In ACM Transactions on Graphics: ACM SIGGRAPH 2007 Papers, ACM Press, New York, NY, USA pp. 1057--1066. 2007.


S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Palmer, R. Thakur, W. Gropp. “Practical Model Checking Method for Verifying Correctness of MPI Programs,” In Recent Advances in Parallel Virtual Machine and Message Passing Interface - Proceedings of EuroPVM-MPI 2007, Paris, France, Vol. 4757/2007, pp. 344--353. 2007.


N.S. Phatak, Q. Sun, S.-E. Kim, D.L. Parker, R.K. Sanders, A.I. Veress, B.J. Ellis, J.A. Weiss. “Noninvasive Determination of Ligament Strain with Deformable Image Registration,” In Annals of Biomedical Engineering, Vol. 35, No. 7, pp. 1175--1187. February, 2007.