Publications
J. Larson, R. Jacob, and E. Ong, "The Model Coupling Toolkit: A New Fortran90 Toolkit for Building Multiphysics Parallel Coupled Models," Inter. J. High Perform. Comput. Appl., vol. 19, no. 3, 2004, pp. 277-292. Also Preprint ANL/MCS-P1208-1204, December 2004. [pdf]
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R. Kettimuthu, V. Subramani, S. Srinivasan, T. Gopalsamy, D. K. Panda, and P. Sadayappan, "Selective Preemption Strategies for Parallel Job Scheduling," Preprint ANL/MCS-P1209-1204, December 2004. [pdf]
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S. Leyffer, G. Lopez-Calva, and J. Nocedal, "Interior Methods for Mathematical Programs with Complementarity Constraints," Preprint ANL/MCS-P1211-1204, December 2004. [pdf]
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P. F. Fischer, G. K. Leaf, and J. M. Restrepo, "Influence of Wall Proximity on the Lift and Drag of a Particle in an Oscillatory Flow," Preprint ANL/MCS-P1212-1204, December 2004. [pdf]
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A. Majumder and R. Stevens, "Perceptual Photometric Seamlessness in Projection-Based Tiled Displays," ACM Transactions on Graphics, vol. 24, no. 1, ACM, 2004, pp. 118-139. Also Preprint ANL/MCS-P1205-1104, November 2004. [pdf]
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P. H. Beckman, "Building the TeraGrid," Preprint ANL/MCS-P1206-1104, November 2004. [pdf]
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E. D. Frank and R. L. Stevens, "Process Modeling for High-Throughput Biology," Technical Memorandum ANL/MCS-TM-276, October 2004. [pdf]
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J. M. Schopf and S. J. Newhouse, "State of Grid Users: 25 Conversations with UK eScience Groups," Technical Memorandum ANL/MCS-TM-278, October 2004. [pdf]
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S. Son, B. Allcock, and M. Livny, "CODO: Firewall Traversal by Cooperative On-Demand Opening," Preprint ANL/MCS-P1200-1004, October 2004. [pdf]
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K. Keahey, M. E. Papka, Q. Peng, D. Schissel, G. Abla, T. Araki, J. Burruss, E. Feibush, P. Lane, S. Klasky, T. Leggett, D. McCune, L. Randerson, "Grid Support for Collaborative Control Room in Fusion Science," Preprint ANL/MCS-P1201-1004, October 2004. [pdf]
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M. S. Min, T. W. Lee, P. F. Fischer, and S.K. Gray, "Fourier Spectral Simulations and Gegenbauer Reconstructions for Electromagnetic Waves in the Presence of a Metal Nanoparticle," Preprint ANL/MCS-P1202-1004, October 2004. [pdf]
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K. Amin, G. von Laszewski, A. R. Mikler, "Toward an Architecture for Ad Hoc Grids," Preprint ANL/MCS-P1204-1004, October 2004. [pdf]
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E. D. Frank and R. L. Stevens, "Process Modeling for High-Throughput Biology," Preprint ANL/MCS-TM-276, October 2004. [pdf]
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U. Naumann and J. Utke, "Optimality-Preserving Elimination of Linearities in Jacobian Accumulation," Preprint ANL/MCS-P1194-0904, September 2004. [pdf]
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J. Utke, "Flattening Basic Blocks," Preprint ANL/MCS-P1196-0904, September 2004. [pdf]
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G.-X. Yu, E. Marland, N. T. Karonis, and N. Maltsev, "A Knowledge-Based Voting Algorithm for Automated Protein Functional Annotation," Preprint ANL/MCS-P1197-0904, September 2004. [pdf]
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N. Maltsev, E. M. Glass, G. Ovchinnikova, and Z. Gu, "Molecular Mechanisms Involved in Robustness of Yeast Central Metabolism Against Null Mutations," Preprint ANL/MCS-P1198-0904, September 2004. [pdf]
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G.-X. Yu, E. M. Glass, N. T. Karonis, N. Maltsev, "A Knowledge-Based Voting Algorithm for Automated Protein Functional Annotation," Preprint ANL/MCS-P1199-0904, September 2004.
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Y. K. Kuan, P. F. Fischer, F. Loth, "Surface Reconstruction of In Vivo Geometry Base on Medical Images using Multilevel Radial Basis Functions," Preprint ANL/MCS-P1210-0904, September 2004. [pdf]
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Y. Zhao, M. Wilde, I. Foster, J. Voeckler, T. Jordan, E. Quigg, and J. Dobson, "Grid Middleware Services for Virtual Data Discovery, Composition, and Integration," Preprint ANL/MCS-P1195-0904, September 2004. [pdf]
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R. Padmanabhan, W. McCune, "Tarski Theorems on Self-Dual Equational Bases for Groups," Preprint ANL/MCS-P1092-0903, August 2004. [pdf]
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B. Addis and S. Leyffer, "A Trust-Region Algorithm for Global Optimization," Preprint ANL/MCS-P1190-0804, August 2004. [pdf]
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Y. Chen, B. F. Hobbs, S. Leyffer, and T. S. Munson, "Leader-Follower Equilibria for Electric Power and NOx Allowances Markets," Preprint ANL/MCS-P1191-0804, August 2004. [pdf]
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R. Padmanabhan, W. McCune, R. Veroff, "Levi's Commutator Theorems for Cancellative Semigroups," Semigroup Forum, vol. 71, 2004, pp. 152-157. Also Preprint ANL/MCS-P1192-0804, August 2004. [pdf]
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W. D. Gropp, "Issues in Accurate and Reliable Use of Parallel Computing in Numerical Programs," Preprint ANL/MCS-P1193-0804, August 2004. [pdf]
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iachin, M. Krishnan, J. A. Kohl, J. W. Larson, S. Lefantzi, J. Nieplocha, B. Norris, S. G. Parker, J. Ray, and S. Zhou, "Parallel PDE-Based Simulations Using the Common Component Architecture," Preprint ANL/MCS-P1179-0704, July 2004. [pdf]
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G. G. Maisuradze, A. Kawano, D. L. Thompson, A. F. Wagner, and M. Minkoff, "Interpolating Moving Least-Squares Methods for Fitting Potential Energy Surfaces: Analysis of an Application to a Six-Dimensional System," Preprint ANL/MCS-P1187-0704, July 2004. [pdf]
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Y. Guo, A. Kawano, D. L. Thompson, A. F. Wagner, and M. Minkoff, "Interpolating Moving Least-Squares Methods for Fitting Potential Energy Surfaces: Applications to Classical Dynamics Calculations," Preprint ANL/MCS-P1188-0704, July 2004. [pdf]
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T. Araki, "Autonomic WWW Server Management with Distributed Resources," Preprint ANL/MCS-P1185-0704, July 2004. [pdf]
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W. E. Allcock, I. Foster, R. Madduri, "Reliable Data Transport: A Critical Service for the Grid," Preprint ANL/MCS-P1166-0604, June 2004. [pdf]
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M. M. Strout and P. D. Hovland, "Metrics and Models for Reordering Transformations," Preprint ANL/MCS-P1167-0604, June 2004. [pdf]
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R. Kettimuthu and W. Allcock, "Improved Selective Acknowledgment Scheme for TCP," Preprint ANL/MCS-P1168-0604, June 2004. [pdf]
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R. Overbeek, T. Disz, and R. Stevens, "A Peer-to-Peer Environment for Annotation of Genomes: The SEED," Preprint ANL/MCS-P1169-0604, June 2004. [pdf]
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W. van Drongelen, H. C. Lee, M. Hereld, D. Jones, M. Cohoon, F. Elsen, M. E. Papka, and R. L. Stevens,, "Simulation of Neocortical Epileptiform Activity Using Parallel Computing," Neurocomputing, vol. 58, 2004, pp. 1203-1209. Also Preprint ANL/MCS-P1170-0604, June 2004. [pdf]
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W. van Drongelen, H. C. Lee, M. Hereld, Z. Chen, F. P. Elsen, and R. L. Stevens, "Emergent Epileptiform Activity in Neural Networks with Weak Excitatory Synapses," IEEE Trans. Neural Syst. Rehab. Eng., vol. 13, no. 2, IEEE Engineering in Medicine and Biology Society, 2004, pp. 236-241. Also Preprint ANL/MCS-P1171-0604, June 2004. [pdf]
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W. van Drongelen, H. C. Lee, H. Koch, F. Elsen, M. S. Carroll, M. Hereld, R. L. Stevens,, "Interaction between Cellular Voltage-Sensitive Conductance and Network Parameters in a Model of the Neocortex Can Generate Epileptiform Bursting," Proc. IEEE 26th Annual International Conference of Engineering in Medicine and Biology Society, vol. 2, no. 1, 2004, pp. 4003-4005. Also Preprint ANL/MCS-P1172-0604, June 2004. [pdf]
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C. E. Frouzakis, A. G. Tomboulides, P. Papas, P. F. Fischer, R. M. Rais, P. A. Monkewitz, and K. Boulouchos, , "Three-Dimensional Numerical Simulations of Cellular Jet Diffusion Flames," Proc. 30th International Symposium on Combustion, Chicago, July 25-30, 2004, . Also Preprint ANL/MCS-P1173-0604, June 2004. [pdf]
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S. J. Benson, L. McInnes, J. J. More', and J. Sarich, "Scalable Algorithms in Optimization: Computational Experiments," Preprint ANL/.MCS-P1175-0604, June 2004. [pdf]
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J. Lee, X. Ma, R. Ross, R. Thakur, M. Winslett,, "RFS: Efficient and Flexible Remote File Access for MPI-IO," Preprint ANl/MCS-P1176-0604, June 2004. [pdf]
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W. Yu, D. Buntinas, and D. K. Panda, "Scalable and High Performance NIC-Based All-to-All Broadcast Over Myrinet/GM," Preprint ANL/MCS-P1177-0604, June 2004. [pdf]
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W. Gropp, R. Ross, and N. Miller, "Providing Efficient I/O Redundancy in MPI Environments," Preprint ANL/MCS-P1178-0604, June 2004. [pdf]
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R. Latham, R. Ross, and R. Thakur, "The Impact of File Systems on MPI-IO Scalability," Preprint ANL/MCS-P1182-0604, June 2004. [pdf]
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G. Almasi, C. Archer, J. G. Castanos, J. Gunnels, C. C. Erway, P. Heidelberger, X. Martorell, J. E. Moreira, K. Pinnow, J. Ratterman, B. Steinmacher-burow, W. Gropp, B. Toonen, "The Design and Implementation of Message Passing Services for the BlueGene/L Supercomputer," Preprint ANL/MCS-P1183-0604, June 2004. [pdf]
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J. N. Lyness, "A Prototype Four-Dimensional Galerkin-Type Integral," RIMS, vol. 41, no. 4, 2004, pp. 843-851. Also Preprint ANL/MCS-P1186-0604, June 2004. [pdf]
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T. Bae, A. K. Banger, A. Wallace, E. M. Glass, F. Aslund, O. Schneewind, D. M. Missiakas, "Staphylococcus Aureus Virulence Genes Identified by Bursa Aurealis Mutagenesis and Nematode Killing," Preprint ANL/MCS-P1165-0604, June 2004. [pdf]
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E. D. Dolan, J. J. More', and T. S. Munson,, "Optimality Measures for Performance Profiles," SIAM J. Optimization, vol. 16, no. 3, Society for Industrial and Applied Mathematics, 2004, pp. 891-909. Also Argonne Report ANL/MCS-P1155-0504, May 2004. [pdf]
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R. Thakur, W. Gropp, and B. Toonen, "Minimizing Synchronization Overhead in the Implementation of MPI One-Sided Communication," Preprint ANL/MCS-P1158-0504, May 2004. [pdf]
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L. F. Diachin, P. Knupp, T. Munson, and S. Shontz, "A Comparison of Inexact Newton and Coordinate Descent Mesh Optimization Techniques," Preprint ANL/MCS-P1159-0504, May 2004. [pdf]
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N. Desai, R. Bradshaw, A. Lusk, and E. Lusk, "MPI Cluster System Software," Recent Advances in Parallel Virtual Machine and Message Passing Interface, vol. 3241, Springer Berlin / Heidelberg, 2004, pp. 277-286. Also Preprint ANL/MCS-P1160-0504, May 2004. [pdf]
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M. Anitescu, "Optimization-Based Simulation of Nonsmooth Rigid Multibody Dynamics," Preprint ANL/MCS-P1161-0504, May 2004. [pdf]
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F. A. Potra, M. Anitescu, B. Gavrea, and J. Trinkle, "A Linearly Implicit Trapezoidal Method for Integrating Stiff Multibody Dynamics with Contact, Joints, and Friction," Preprint ANL/MCS-P1162-0504, May 2004. [pdf]
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U. Naumann, J. Utke, and A. Lyons, "Control Flow Reversal for Adjoint Code Generation," Preprint ANL/MCS-P1163-0504, May 2004. [pdf]
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W. Jiang, J. Liu, H.-W. Jin, D. K. Panda, D. Buntinas, R. Thakur, W. Gropp, "Efficient Implementation of MPI-2 Passive One-Sided Communication on InfiniBand Clusters," Preprint ANL/MCS-P1164-0504, May 2004. [pdf]
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W. Ligon and R. Ross, "Parallel I/O and the Parallel Virtual File System," Beowulf Cluster Computing with Linux, second edition, 2004, pp. 593. Also Preprint ANL/MCS-P1174-0504, May 2004. [pdf]
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J. Utke, "OpenAD: Algorithm Implementation User Guide," Technical Memorandum ANL/MCS-TM-274, April 2004. [pdf]
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M. Anitescu, "Global Convergence of an Eleastic Mode Approach for a Class of Mathematical Programs with Complementarity Constraints," Preprint ANL/MCS-P1143-0404, April 2004. [pdf]
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M. R. Paul, K-H. Chiam, M. C. Cross, and P. F. Fischer , "Rayleigh-Benard Convection in Large-Aspect-Ratio Domains," Preprint ANL/MCS-P1144-0404, April 2004. [pdf]
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U. Naumann, J. Utke, A. Lyons, and M. Fagan, "Control Flow Reversal for Adjoint Code Generation," Preprint ANL/MCS-P1145-0404, April 2004. [pdf]
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L. Wos, "Milestones for Automated Reasoning," Preprint ANL/MCS-P1146-0404, April 2004. [pdf]
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M. Hereld, R. L. Stevens, W. van Drongelen, H. C. Lee, "Developing a Petascale Neural Simulation," Preprint ANL/MCS-P1147-0404, April 2004. [pdf]
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J. P. Kenny, S .J. Benson, Y. Alexeev, J. Sarich, C. L. Janssen, L. C. McInnes, M. Krishnan, J. Nieplocha, E. Jurruss, C. Fahlstrom, T. L. Windus, "Component-Based Integration of Chemistry and Optimization Software," J. Comput. Chem, vol. 25, no. 14, 2004, pp. 1717-1725. Also Preprint ANL/MCS-P1148-0404, April 2004. [pdf]
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N. Desai, R. Bradshaw, and E. Lusk, "Component-Based Cluster Systems Software Architecture: A Case Study," Preprint ANL/MCS-P1149-0404, April 2004. [pdf]
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N. T. Karonis, M. E. Papka, J. Binns, J. Bresnahan, J. M. Link, "Effective Use of Dedicated Wide-Area Networks for High-Performance Distributed Computing," Preprint ANL/MCS-P1151-0404, April 2004. [pdf]
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C. H. Bischof, P. D. Hovland, and B. Norris, "On the Implementation of Automatic Differentiation Tools," Preprint ANL/MCS-P1152-0404, April 2004. [pdf]
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S. L. Lee and P. D. Hovland, "Derivative Techniques for Forward Sensitivity Analysis in Time-Dependent Problems," Preprint ANL/MCS-P1153-0404, April 2004. [pdf]
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W. Gropp and E. Lusk, "Fault Tolerance in MPI Programs," Preprint ANL/MCS-P1154-0404, April 2004. [pdf]
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J. Peng, M. Anitescu, and S. Akella, "Optimal Control of Multiple Robot Systems with Friction using MPCC," Preprint ANL/MCS-P1157-0404, April 2004. [pdf]
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A.-V. Demiguel, M. P. Freidlander, F. J. Nogales, and S. Scholtes, "An Interior-Point Method for MPECs Based on Strictly Feasible Relaxations," SIAM J. Optimization, vol. 16, no. 2, 2004, pp. 587-609. Also Preprint ANL/MCS-P1150-0404, April 2004. [pdf]
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G. von Laszewski, G. W. Pieper, and P. Wagstrom, "Gestalt of the Grid," Performance Evaluation and Characterization of Parallel and Distributed Computing Tools, 2004, . Also Argonne Report ANL/MCS-P1156-0504, April 2004. [pdf]
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B. Norris, J. Ray, R. Armstrong, L. C. McInnes, D. E. Bernholt, W. R. Elwasif, A. D. Malony, S. Shende, "Computational Quality of Service for Scientific Components," Preprint ANL/MCS-P1131-0304, March 2004. [pdf]
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D.P. Schissel, K.Keahey, T.Araki, J.R. Burruss, E.Feibush, S.M.Flanagan, T. W. Fredian, M. J. Greenwald, S. A. Klasky, T. Leggett, K. Li, D. C. McCune, P. Lane, M. E. Papka, Q. Peng, L. Randerson, A.Sanderson, J.Stillerman, M. R. Thompson, G. Wallace, "The National Fusion Collaboratory Project: Applying Grid Technology for Magnetic Fusion Research," 2004, . Also Preprint ANL/MCS-P1133-0304, March 2004. [pdf]
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T. Munson, "An Averaging Method for Nash Games with Shared Decision Variables," Preprint ANL/MCS-P1134-0304, March 2004. [pdf]
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T. Munson, "Mesh Shape-Quality Optimization Using the Inverse Mean-Ratio Metric," Preprint ANL/MCS-P1136-0304, March 2004. [pdf]
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A. Kawano, Y. Guo, D. L. Thompson, A. F. Wagner, M. Minkoff, "Improving the Accuracy of Interpolated Potential Energy Surfaces by Using an Analytical Zeroth-Order Potential Function," Journal of Chemical Physics, vol. 120, no. 14, 2004, pp. 6414-6422. Also Preprint ANL/MCS-P1137-0304, March 2004. [pdf]
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K. Keahey, M. E. Papka, Q. Peng, D. Schissel, G. Abla, T. Araki, J. Burruss, S. Feibush, P. Lane, S. Klasky, T. Leggett, D. McCune, and L. Randerson, "Grids for Experimental Science: The Virtual Control Room," 2004, . Also Preprint ANL/MCS-P1139-0304, March 2004. [pdf]
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R. Thakur, R. Rabenseifner, and W. Gropp, "Optimization of Collective Communication Operations in MPICH," Preprint ANL/MCS-P1140-0304, March 2004. [pdf]
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K. Keahey, K. Doering, and I. Foster, "From Sandbox to Playground: Dynamic Virtual Environments in the Grid," Preprint ANL/MCS-P1141-0304, March 2004. [pdf]
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J. Wu, P. Wyckoff, D. Panda, and R. Ross, "Unifier: Unifying Cache Management and Communication Buffer Management for PVFS over InfiniBand," 2004, . Also Preprint ANL/MCS-P1122-0204, February 2004. [pdf]
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P. M. Dickens and J. W. Larson, "Classifiers for the Causes of Data Loss Using Packet-Loss Signatures," Preprint ANL/MCS-P1123-0204, February 2004. [pdf]
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G. von Laszewski, J. Gawor, P. Plaszczak, M. Hategan, K. Amin, R. Madduri, S. Gose, S. Shankar, "An Overview of Grid File Transfer Patterns and Their Implementation in the Java CoG Kit," J. Neural Parallel and Scientific Computations, vol. 12, no. 3, Dynamic Publisher, Atlanta, GA, 2004, pp. 329-352. Also Preprint ANL/MCS-P1126-1203, February 2004. [pdf]
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R. Al-Ali, G. von Laszewski, K. Amin, M. Hategan, O. Rana, D. Walker, N. Zaluzec, "QoS Support for High-Performance Scientific Grid Applications," Preprint ANL/MCS-P1129-0204, February 2004. [pdf]
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W. Allcock, J. Bresnahan, R. Kettimuthu, J. Link, "The Globus eXtensible Input/Output System (XIO): A Protocol Independent IO System for the Grid," Preprint ANL/MCS-P1130-0204, February 2004. [pdf]
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V. Welch, I. Foster, C. Kesselman, O. Mulmo, L. Pearlman, S. Tuecke, J. Gawor, S. Meder, F. Siebenlist, "X.509 Proxy Certificates for Dynamic Delegation," Preprint ANL/MCS-P1132-0204, February 2004. [pdf]
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E. D. Dolan, J. J. More', and T. S. Munson, "Benchmarking Optimization Software with COPS 3.0," Technical Memorandum ANL/MCS-TM-273, February 2004. [pdf]
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A. Zagaris, H. G. Kaper, and T. J. Kaper, "Fast and Slow Dynamics for the Computational Singular Perturbation Method," SIAM J. Multiscale Model. Simul., vol. 2, no. 4, Siam, 2004, pp. 613-638. Also Preprint ANL/MCS-P1114-0104, January 2004. [pdf]
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X. Zhang and J. M. Schopf, "Performance Analysis of the Globus Toolkit Monitoring and Discovery Service," Preprint ANL/MCS-P1115-0104, January 2004. [pdf]
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M. Grimsditch, L. Giovannini, F. Montoncello, F. Nizzoli, G. K. Leaf, H. G. Kaper, "Normal Modes in Ferromagnetic Nanoparticles: A Dynamical Matrix Approach," Preprint ANL/MCS-P1116-0104, January 2004. [pdf]
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H. Gao, I. R. Judson, T. Uram, T. L. Disz, M. E. Papka, R. L. Stevens, "Capability Matching of Data Streams with Network Services," Preprint ANL/MCS-P1118-0104, January 2004. [pdf]
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W. Jiang, J. Liu, H.-W. Jin, D. K. Panda, W. Gropp, and R. Thakur, "High Performance MPI-2 One-Sided Communication over InfiniBand," Preprint ANL/MCS-P1119-0104, January 2004. [pdf]
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W. Yu, D. Buntinas, R. L. Graham, and D. K. Panda, "Efficient and Scalable Barrier over Quadrics and Myrinet with a New NIC-based Collective Message Passing Protocol," Preprint ANL/MCS-P1121-0204, January 2004. [pdf]
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