Publications and presentations citing W&M HPC resources, 2000-2004

2004
  • W. Al-Saidi, H. Krakauer, and S. Zhang. Quantum Monte Carlo Study of Ground State Properties of Transition Metal Oxides. Fundamental Physics of Ferroelectrics 2004, Williamsburg, VA, February 2004.
  • K. J. Barker. Runtime support for load balancing of parallel adaptive and irregular applications. Ph.D. dissertation, Department of Computer Science, College of William and Mary, Williamsburg, VA, May 2004.
  • K. Barker, A. Chernikov, N. Chrisochoides, and K. Pingali. A load balancing framework for adaptive and asynchronous applications. IEEE Transactions on Parallel and Distributed Computing, Vol. 15, No. 2, February 2004, pp. 183-192.
  • A. Chernikov and N. Chrisochoides. Practical and efficient point insertion scheduling method for parallel guaranteed quality Delaunay refinement. 18th Annual ACM International Conference on Supercomputing, Saint-Malo, France, June 26–July 1, 2004, pp. 48–57.
  • A. Chernikov and N. Chrisochoides. Scheduling Point Insertion for Parallel Delaunay Meshing. Poster presentation, 13th International Meshing Roundtable, Williamsburg VA, September 2004.
  • A. Chernikov and N. Chrisochoides. Parallel Guaranteed Quality Planar Delaunay Mesh Generation by Concurrent Point Insertion. 14th Annual Fall Workshop on Computational Geometry, Massachusetts Institute of Technology, Cambridge, MA, Nov. 19-20, 2004.
  • N. Chrisochoides, A. Chernikov, A. Kot, and A. Fedorov. Parallel mesh generation: Web-services and COTS software. International Conference on Spectral and High Order Methods (ICOSAHOM 2004), Minisymposium ICO-MS17 Curvilinear Meshing and High Order Surface Representation, Brown University, Providence, Rhode Island, June 21-25, 2004.
  • A. Fedorov and N. Chrisochoides. Location management in object-based distributed computing. Cluster 2004, San Diego, California, September 20-23, 2004.
  • A. Fedorov and N. Chrisochoides. Communication support for dynamic load balancing of irregular adaptive applications. 3rd Workshop on Compile and Runtime Techniques for Parallel Computing (2004 International Conference on Parallel Processing), Montreal, Quebec, August 15–18, 2004.
  • A. Fedorov and N. Chrisochoides. Location management in distributed computing. SIAM Parallel Processing 2004, San Francisco, California, February 25–27, 2004.
  • J. A. Hayes. A framework for implementing bioinformatics knowledge-exploration systems. Masters thesis, Department of Applied Science, College of William and Mary, Williamsburg, VA, 2004.
  • D. I. Malyarenko, H. Chen, A. L. Wilkerson, E. R. Tracy, W. E. Cooke, D. M. Manos, M. Sasinowski, and O. J. Semmes. Ga+ TOF-SIMS lineshape analysis for resolution enhancement of MALDI MS spectra of a peptide mixture. Applied Surface Science, Vol. 231-232, June 15, 2004, pp.357-361.
  • D. I. Malyarenko, W. E. Cooke, E. R. Tracy, and D. M. Manos. Signal conditioning and filtering of SELDI mass spectrometry time series. Invited presentation, Interface 2004: 36th Symposium on the Interface: Computational Biology and Bioinformatics, Baltimore, MD, May 26-29, 2004.
  • B. Mazzag, C. Tiganelli, and G. D. Smith. Analysis of the effect of residual Ca2+ on the stochastic gating of Ca2+-regulated Ca2+ channel models. Poster presentation, Biophysical Society Annual Meeting, Program No. 579, Baltimore, MD, February 2004.
  • J. M. Squyres. A component architecture for the Message Passing Interface (MPI): the systems services interface (SSI) of LAM/MPI. Ph.D. dissertation, Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, April 2004.
  • M. Zangrilli and B. Lowekamp. Using passive traces of application traffic in a network monitoring system. Proceedings of the 13th IEEE International Symposium on High Performance Distributed Computing, Honolulu, June 4-6, 2004, pp. 77-86.
  • J. Zhang, V. D. Nguyen, and G. D. Smith. Direct calculation of puff statistics from stochastic automata network models of instantaneously-coupled intracellular Ca2+ channels. Poster presentation, Biophysical Society Annual Meeting, Program No. 578, Baltimore, MD, February 2004.
2003
  • K. J. Barker and N. P. Chrisochoides. An evaluation of a framework for the dynamic load balancing of highly adaptive and irregular parallel applications. Proceedings ACM/IEEE SC2003, Phoenix, Arizona, November 15-21, 2003, CD-ROM.
  • A. Chernikov and N. Chrisochoides. Automatic domain decomposition for parallel 2D constrained Delaunay mesh generation. 4th Symposium on Trends in Unstructured Mesh Generation, Albuquerque, NM, July 27-31, 2003.
  • N. Chrisochoides, A. Fedorov, B. B. Lowekamp, M. Zangrilli, and C. Lee. A case study of optimistic computing on the Grid: parallel mesh generation. Proceedings of 2003 International Parallel and Distributed Processing Symposium (IPDPS'03), Nice, France, April 22-26, 2003, p. 204b.
  • A. Fedorov. Location management in a mobile object runtime environment. Masters thesis, Department of Computer Science, College of William and Mary, Williamsburg, VA, 2003.
  • A. Fedorov and N. Chrisochoides. Clam: light communication layer for asynchronous mobile computations. Poster presentation, LACSI 2003: 4th Symposium of the Los Alamos Computer Science Institute, Santa Fe, NM, October 27-29, 2003.
  • M. Huertas, J. R. Groff, and G. D. Smith. The effect of feedback inhibition in network simulations of retinogeniculate transmission. Poster presentation, Society for Neuroscience Annual Meeting, Program No. 68.12, New Orleans, LA, November 8-12, 2003.
  • L. Linardakis. A parallel two dimensional Delaunay decoupling method. Masters thesis, Department of Computer Science, College of William and Mary, Williamsburg, VA, December 2003.
  • D. Malyarenko, M. Sasinowski, H. Chen, D. Manos, M. Trosset, W. Cooke, E. Tracy. Preprocessing and statistical analysis of mass spectrometry proteomics data. In Final Report: NIH SBIR Phase I: 1-R43-CA101479-01 (INCOGEN, EVMS, W&M), April 1 - October 1, 2003.
  • D. Malyarenko, E. Tracy, D. Manos, M. Trosset, M. Sasinowski. PCA-LDA classification of mass spectra for prostate cancer data set. In CTRF Annual Report (11/01/02-10/31/03), Bringing the Future of Bioinformatics to Virginia (INCOGEN, W&M, VBI), Virginia Center for Innovative Technology, October 2003.
  • J. R. McCombs, R. T. Mills, and A. Stathopoulos. Dynamic load balancing of an iterative eigensolver on networks of heterogeneous clusters. Proceedings of 2003 International Parallel and Distributed Processing Symposium (IPDPS'03), Nice, France, April 22-26, 2003.
  • J. R. McCombs and A. Stathopoulos. Parallel, multigrain iterative solvers for hiding network latencies on MPPs and networks of clusters. Parallel Computing, Vol. 29, No. 9, September 2003, pp. 1237-1259.
  • M. Zangrilli and B. Lowekamp. Comparing passive network monitoring of grid application traffic with active probes. Proceedings of the 4th International Workshop on Grid Computing (GRID '03), Phoenix, Arizona, November 17, 2003, pp. 84-91.
2002
  • E. C. Allman. The ground state of Hubbard-like models. Ph.D. dissertation, Department of Physics, College of William and Mary, Williamsburg, VA, 2002.
  • S. Chen, L. Xiao, and X. Zhang. Adaptive and virtual reconfiguration for dynamic job scheduling in clusters. Proceedings of the 22nd International Conference on Distributed Computing Systems (ICDCS 2002), Vienna, Austria, July 2-5, 2002, pp.35-42.
  • X. Chen and X. Zhang. Popularity-based PPM: an effective web prefetching technique for high accuracy and low storage. Proceedings of the 2002 International Conference on Parallel Processing, Vancouver, British Columbia, Aug. 17-21, 2002.
  • J. R. McCombs and A. Stathopoulos. Multigrain parallelism for eigenvalue computatons on networks of clusters. Proceedings of the Eleventh IEEE International Symposium on High Performance Distributed Computing, Edinburgh, Scotland, July 24-26, 2002, pp.143-149.
  • D. Nave, N. Chrisochoides, and L. P. Chew. Guaranteed-quality parallel Delaunay refinement for restricted polyhedral domains. Proceedings of the 18th Annual Symposium on Computational Geometry, Barcelona, Spain, June 5-7, 2002.
  • G. D. Smith. An extended DeYoung-Keizer-like IP3R receptor model that accounts for domain Ca2+-mediated inactivation. In Recent Research Developments in Biophysical Chemistry, Vol. II, C. A. Condat and A. Baruzzi, eds., Research Signpost, June 2002.
  • G. D. Smith and S. M. Sherman. Detectability of excitatory vs. inhibitory drive in a thalamocortical relay neuron model.' Journal of Neuroscience,'' 22(23), Dec. 1, 2002, pp. 10242-10250.
  • A. Stathopoulos and K. Wu. A block orthogonalization procedure with constant synchronization requirements. SIAM Journal on Scientific Computing, Vol. 23, No. 6 (2002), pp. 2165-2182..
  • L. Xiao, X. Zhang, and Z. Xu. A reliable and scalable peer-to-peer Web document sharing system. Proceedings of 2002 International Parallel and Distributed Processing Symposium (IPDPS 2002), Fort Lauderdale, Florida, April 15-19, 2002.
  • L. Xiao, S. Chen, and X. Zhang. Dynamic cluster resource allocations for jobs with known and unknown memory demands. IEEE Transactions on Parallel and Distributed Systems, Vol. 13, No. 3, March 2002, pp. 223-240.
2001
  • S. Chen, L. Xiao, and X. Zhang. Dynamic load sharing with unknown memory demands in clusters. Proceedings of the 21st International Conference on Distributed Computing Systems (ICDCS'2001), Phoenix, Arizona, April 16-19, 2001, pp. 109-118.
  • G. Ciardo, A. Riska, E. Smirni. EquiLoad: a load balancing policy for clustered web servers. Performance Evaluation, Vol. 46(2-3), Oct. 2001, pp. 101-124.
  • R. T. Mills, A. Stathopoulos, and E. Smirni. Algorithmic modifications to the Jacobi-Davidson parallel eigensolver to dynamically balance external CPU and memory load. Proceedings of the International Conference on Supercomputing 2001, Sorrento, Italy, June 18-22, 2001, pp. 454-463.
  • W. J. Seufzer. Application of the genetic algorithm to an ecological simulation. Ph.D. dissertation, Virginia Institute of Marine Science, College of William and Mary, Williamsburg, VA, July 2001.
  • A. Stathopoulos. Improving performance of eigen-methods on parallel, shared resource platforms. Invited talk, Computer Science Department, University of Ioannina, Greece, June 2001.
  • A. Stathopoulos and J. R. McCombs. Multigrain hybrid parallel algorithms for eigenvalue calculations. 5th IMACS Conference on Iterative Methods in Scientific Computing, Heraklion, Crete, May 2001.
2000
  • L. Xiao, X. Zhang, and S. A. Kubricht. Improving memory performance of sorting algorithms. ACM Journal on Experimental Algorithmics, Vol. 5, No. 3, 2000, pp. 1-23.
  • Z. Zhang, Z. Zhu, and X. Zhang. A permutation-based page interleaving scheme to reduce row-buffer conflicts and exploit data locality. Proceedings of the 33rd Annual International Symposium on Microarchitecture (Micro-33), Dec. 2000, pp. 32-41.