SCI Publications

2007


P.A. Koshevoy, T. Tasdizen, R.T. Whitaker. “Automatic Assembly of TEM Mosaics and Mosaic Stacks Using Phase Correlation,” SCI Institute Technical Report, No. UUSCI-2007-004, University of Utah, 2007.


L. Krishnan, J.B. Hoying, H. Ngyuen, H. Song, J.A. Weiss. “Interaction of Angiogenic Microvessels with the Extracellular Matrix,” In American Journal of Physiology: Heart and Circulation Physiology, Vol. 293, No. 6, pp. H3650--H36588. 2007.


D. Laney, P.-T. Bremer, A. Mascarenhas, P. Miller, V. Pascucci. “Understanding the Structure of the Turbulent Mixing Layer in Hydrodynamic Instabilities,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 1, pp. 1053--1060. January, 2007.


S. Lew, C. Wolters, A. Anwander, S. Makeig, R.S. MacLeod. “Low Resolution Conductivity Estimation to Improve Source Localization,” In New Frontiers in Biomagnetism. Proceedings of the 15th International Conference on Biomagnetism, Vancouver, BC, Canada, August 21-25, 2006., International Congress Series, Vol. 1300, pp. 149--152. June, 2007.


G.-S. Li, X. Tricoche, C.D. Hansen. “Visualizing Unsteady Flows on Surfaces Using Spherical Parameterization,” SCI Institute Technical Report, No. UUSCI-2007-013, University of Utah, 2007.


Y. Livnat, S.G. Parker, C.R. Johnson. “Fast Isosurface Extraction Methods for Large Image Data Sets,” In Handbook of Medical Imaging: Processing and Analysis, 2nd Edition, Ch. 44, Edited by Isaac Bankman, Academic Press, 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