Publications
J. Shin, P. Malusare, and P. D. Hovland, "Design and Implementation of a Context-Sensitive, Flow-Sensitive Activity Analysis Algorithm for Automatic Differentiation," Preprint ANL/MCS-P1465-1207, December 2007. [pdf]
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S. Park, "Comparison of the Serial and Parallel Algorithms of Generalized Ensemble Simulations: An Analytical Approach," Preprint ANL/MCS-P1473-1207, December 2007. [pdf]
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H. S. Abdel-Khalik, P. D. Hovland, A. Lyons, T. E. Stover, and J. Utke, "A Low Rank Approach to Automatic Differentiation," Preprint ANL/MCS-P1467-1207, December 2007. [pdf]
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I. Charpentier, C. Dal Cappello, and J. Utke, "Efficient Higher-Order Derivatives of the Hypergeometric Function," Preprint ANL/MCS-P1468-1207, December 2007. [pdf]
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A. Lyons and J. Utke, "On the Practical Exploitation of Scarsity," Preprint ANL/MCS-P1469-1207, December 2007. [pdf]
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L. Hascoet, J. Utke, and U. Naumann, "Cheaper Adjoints by Reversing Address Computations," Preprint ANL/MCS-P1470-1207, December 2007. [pdf]
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J. J. More' and S. M. Wild, "Benchmarking Derivative-Free Optimization Algorithms," Preprint ANL/MCS-P1471-1207, December 2007. [pdf]
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M. Islam, P. Balaji, G. Sabin, and P. Sadayappan, "Analyzing and Minimizing the Impact of Opportunity Cost in QoS-aware Job Scheduling," Preprint ANL/MCS-P1605-1207, December 2007. [pdf]
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M. Islam, P. Balaji, G. Sabin, and P. Sadayappan, "Analyzing and Minimizing the Impact of Opportunity Cost in QoS-aware Job Scheduling," Preprint ANL/MCS-P1605-1207, December 2007. [pdf]
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Z. Insepov, M. Terasawa, and K. Takayama, "Surface Erosion and Modification by Highly Charged Ions," Preprint ANL/MCS-P1484-1007, October 2007. [pdf]
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J. N. Brooks and J. P. Allain, "Particle Deposition and Optical Response of ITER Motional Stark Effect Diagnostic First Mirrors," Preprint ANL/MCS-P1460-1007, October 2007. [pdf]
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M. Min, P. F. Fischer, and Y.-C. Chae, "Wake Fields in TESLA Accelerating Structures: Spectral Element Discontinuous Galerkin (SEDG) Simulations," Preprint ANL/MCS-P1462-1007, October 2007. [pdf]
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A. Chan, W. Gropp, and E. Lusk, "An Efficient Format for Nearly Constant-Time Access to Arbitrary Time Intervals in Large Trace Files," Preprint ANL/MCS-P1464-0907, September 2007. [pdf]
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J. Bresnahan, M. Link, G. Khanna, Z. Imani, R. Kettimuthu, and I. Foster, "Globus GridFTP: What's New in 2007," Preprint ANL/MCS-P1458-0907, September 2007. [pdf]
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C. Zhang, M. G. Knepley, D. A. Yuen, and Y. Shi, "Two New Approaches in Solving the Nonlinear Shallow Water Equations for Tsunamis," Preprint ANL/MCS-P1459-0907, September 2007. [pdf]
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M. G. Knepley and D. A. Karpeev, "Mesh Algorithms for PDE with Sieve I: Mesh Distribution," Preprint ANL/MCS-P1455-0907, September 2007. [pdf]
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C. Rabiti, M. A. Smith, W. Yang, G. Palmiotti, A. Caceres, A. Siegel, T. J. Tautges, J. Lottes, P. Fischer, and D. Kaushik, "Status Report on SHARP Coupling Framework," Argonne Report ANL-AFCI-215, September 2007. [pdf]
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W. D. Gropp, D. K. Kaushik, M. Minkoff, and B. F. Smith, "Improving the Performance of Tensor Matrix Vector Multiplication in Quantum Chemistry Codes," Technical Memorandum ANL/MCS-TM-297, September 2007. [pdf]
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S. Leyffer and T. Munson, "A Globally Convergent Filter Method for MPECs," Preprint ANL/MCS-P1457-0907, September 2007. [pdf]
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R. Thakur and W. Gropp, "Test Suite for Evaluating Performance of MPI Implementations That Support MPI_THREAD_MULTIPLE," Preprint ANL/MCS-P1418-0507, September 2007. [pdf]
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D. R. Dechow, B. Norris, and J. Amundson, "The Common Component Architecture for Particle Accelerator Simulations," Preprint ANL/MCS-P1449-0807, August 2007. [pdf]
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J. N. Lyness, "Numerical Evaluation of a Fixed-Amplitude Variable-Phase Integral," Preprint ANL/MCS-P1450-0807, August 2007. [pdf]
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K. Iskra, J. W. Romein, K. Yoshii, and P. Beckman, "ZOID: I/O-Forwarding Infrastructure for Petascale Architectures," Proc. 13th ACM SIGPLAN Principles and Practice of Parallel Programming, Salt Lake City, 2007, pp. 153-162. Also Preprint ANL/MCS-P1453-0807, August 2007. [pdf]
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A. A. Rodriguez, T. Bompada, M. Syed, P. K. Shah, and N. Maltsev, "Evolutionary Analysis of Enzymes Using Chisel," Preprint ANL/MCS-P1454-0807, August 2007. [pdf]
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P. Balaji, W. Feng, J. Archuleta, H. Lin, R. Kettimuthu, R. Thakur, and X. Ma, "ParaMEDIC: Parallel Metadata Environment for Distributed I/O and Computing," Preprint ANL/MCS-P1452-0807, August 2007. [pdf]
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S. Park, "Weights and Acceptance Ratios in Generalized Ensemble Simulations," Preprint ANL/MCS-P1451-0807, August 2007. [pdf]
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J. J. Moré, T. S. Munson, and J. Sarich, "Optimization in SciDAC Applications," Preprint ANL/MCS-P1437-0707, July 2007. [pdf]
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T. Peterka, R. L. Kooima, D. J. Sandin, A. Johnson, J. Leigh, and T. A. DeFanti, "Advances in the Dynallax Solid-State Dynamic Parallax Barrier Autostereoscopic Visualization Display System," Preprint ANL/MCS-P1438-0707, July 2007. [pdf]
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S. Pervez, G. Gopalakrishnan, R. M. Kirby, R. Palmer, R. Thakur, and W. Gropp, "Practical Model-Checking Mehtod for Verifying Correctness of MPI Programs," Preprint ANL/MCS-P1440-0707, July 2007. [pdf]
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J. Bresnahan, R. Kettimuthu, M. Link, and I. Foster, "Harnessing Multicore Processors for High-Speed Secure Transfer," Preprint ANL/MCS-P1442-0707, July 2007. [pdf]
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J. M. Dennis, R. Jacob, M. Vertenstein, T. Craig, and R. Loy, "Toward an Ultra-High Resolution Community Climate System Model for the BlueGene Platform," Preprint ANL/MCS-P1446-0707, July 2007. [pdf]
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N. Desai, E. Lusk, A. Cherry, and T. Voran, "The Computer as Software Component: A Mechanism for Developing and Testing Resource Management Software," Preprint ANL/MCS-P1447-0707, July 2007. [pdf]
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P. Balaji, W. Feng, S. Bhagvat, D. K. Panda, R. Thakur, and W. Gropp, "Analyzing the Impact of Supporting Out-of-Order Communication on In-order Performance with iWARP," IEEE/ACM International Conference for High Performance Computing, Networking, Storage and Analysis (SC), Reno, Nevada, 2007, . Also Preprint ANL/MCS-P1448-0707, July 2007. [pdf]
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A. Baranovski, S. Bharathi, J. Bresnahan, A. Chervenak, I. Foster, D. Fraser, T. Freeman, D. Gunter, K. Jackson, K. Keahey, C. Kesselman, D. E. Konerding, N. Leroy, M. Link, M. Livny, N. Miller, R. Miller, G. Oleynik, L. Pearlman, J. M. Schopf, R. Schuler, and B. Tierney, "Enabling Distributed Petascale Science," Preprint ANL/MCS-P1445-0707, July 2007. [pdf]
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L. Yang, C. Liu, J. M. Schopf, and I. Foster, "Anomaly Detection and Diagnosis in Grid Environments," Preprint ANL/MCS-P1444-0707, July 2007. [pdf]
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K. Keahey, T. Freeman, J. Lauret, and D. Olson, "Virtual Workspaces for Scientific Applications," Preprint ANL/MCS-P1443-0707, July 2007. [pdf]
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J. L. Träff, W. Gropp, and R. Thakur, "Self-Consistent MPI Performance Requirements," Preprint ANL/MCS-P1439-0707, July 2007. [pdf]
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H. G. Kaper, S. Wang, and M. Yari, "Formation and Persistence of Spatiotemporal Turing Patterns," Preprint ANL/MCS-P1427-0607, June 2007. [pdf]
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R. Thakur and W. Gropp, "Open Issues in MPI Implementation," Preprint ANL/MCS-P1426-0607, June 2007. [pdf]
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L. C. McInnes, T. Dahlgren, J. Nieplocha, D. Bernholdt, B. Allan, R. Armstrong, D. Chavarria, W. Elwasif, I. Gorton, J. Kenny, M. Krishan, A. Malony, B. Norris, J. Ray, and S. Shende, "Research Initiatives for Plug-and-Play Scientific Computing," Preprint ANL/MCS-P1428-0607, June 2007. [pdf]
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I. Konkashbaev, P. Fischer, A. Hassanein, and N. V. Mokhov, "Enhancement of Heat Removal Using Concave Liquid Metal Targets for High-Power Accelerators," Preprint ANL/MCS-P1429-0607, June 2007. [pdf]
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W. Elwasif, B. Norris, B. Allan, and R. Armstrong, "Bocca: A Development Environment for HPC Components," Preprint ANL/MCS-P1430-0607, June 2007. [pdf]
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G. Narayanaswamy, P. Balaji, and W. Feng, "An Analysis of 10-Gigabit Ethernet Protocol Stacks in Multicore Environments," Preprint ANL/MCS-P1432-0607, June 2007. [pdf]
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S. Pervez, G. Gopalakrishnan, R. M. Kirby, R. Thakur, and W. Gropp, "Formal Methods Applied to HPC Software Design: A Case Study of Locking Based on MPI One-Sided Communication," Preprint ANL/MCS-P1433-0607, June 2007. [pdf]
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K. Abhishek, S. Leyffer, and J. T. Linderoth, "Modeling without Categorical Variables: A Mixed-Integer Nonlinear Program for the Optimization of Thermal Insulation," Preprint ANL/MCS-P1434-0607, June 2007. [pdf]
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M. Min, P. F. Fischer, and Y.-C. Chae, "Spectral Element Discontinuous Galerkin Simulations for Wake Potential Calculations: NEKCEM," Preprint ANL/MCS-P1435-0607, June 2007. [pdf]
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M. Min, Y.-H. Chin, P. F. Fischer, Y.-C. Chae, and K.-J. Kim, "Fourier Spectral Simulations for Wake Fields in Conducting Cavities," Preprint ANL/MCS-P1436-0607, June 2007. [pdf]
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J. Shin, "SIMD Programming by Expansion," Preprint ANL/MCS-P1425-0607, June 2007. [pdf]
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Y. Zhao, M. Hategan, B. Clifford, I. Foster, G. von Laszewski, V. Nefedova, I. Raicu, T. Stef-Praun, and M. Wilde, "Swift: Fast, Reliable, Loosely Coupled Parallel Computation," Preprint ANL/MCS-P1416-0507, May 2007. [pdf]
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R. Latham, W. Gropp, R. Ross, and R. Thakur, "Extending the MPI-2 Generlaized Request Interface," Preprint ANL/MCS-P1417-0507, May 2007. [pdf]
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W. D. Gropp and R. Thakur, "Revealing the Performance of MPI RMA Implementations," Preprint ANL/MCS-P1419-0507, May 2007. [pdf]
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J. P. Allain, M. Nieto, M. R. Hendricks, P. Plotkin, S. S. Harilal, and A. Hassanein, "IMPACT: A Facility for Studying the Interaction of Low-Energy Intense Charged Particle Beams with Dynamic Heterogeneous Surfaces," Preprint ANL/MCS-P1420-0507, May 2007. [pdf]
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P. Balaji, S. Bhagvat, D. K. Panda, R. Thakur, and W. Gropp, "Advanced Flow-control Mechanisms for the Sockets Direct Protocol over InfiniBand," Preprint ANL/MCS-P1422-0507, May 2007. [pdf]
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Z. Insepov, "Surface Erosion and Modification by Energetic Ions," Preprint ANL/MCS-P1423-0507, May 2007. [pdf]
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M. Anitescu and A. Tasora, "An Iterative Approach for Cone Complementarity Problems for Nonsmooth Dynamics," Preprint ANL/MCS-P1413-0507, May 2007. [pdf]
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D. Buntinas, G. Mercier and W. Gropp, "Design and Evaluation of Nemesis, a Scalable, Low-Latency, Message-Passing Communication Subsystem," Preprint ANL/MCS-P1307-1105, May 2007. [pdf]
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J. P. Allain, M. Nieto, M. Hendricks, S. S. Harilal, and A. Hassanein, "Debris and Radiation-Induced Damage Effects on EUV Nanolithography Source Collector Mirror Optics Performance," Preprint ANL/MCS-P1406-0407, April 2007. [pdf]
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B. Clifford, I. Foster, J.-S. Voeckler, M. Wilde, and Y. Zhao, "Tracking Provenance in a Virtual Data Grid," Concurrency and Computation: Practice and Experience, vol. 20, no. 5, 2007, pp. 565-575. Also Preprint ANL/MCS-P1407-0407, April 2007. [pdf]
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S. S. Varghese, S. H. Frankel, and P. F. Fischer, "Modeling Transition to Turbulence in Eccentric Stenotic Flows," Preprint ANL/MCS-P1408-0407, April 2007. [pdf]
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Z. Insepov, A. Hassanein, J. Norem, and D. R. Swenson, "Advanced Surface Polishing using Gas Cluster Ion Beams," Preprint ANL/MCS-P1409-0407, April 2007. [pdf]
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F. Loth, P. F. Fischer, and H. S. Bassiouny, "Blood Flow in End-to-Side Anastomoses," Preprint ANL/MCS-P1410-0407, April 2007. [pdf]
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J. Shin, "Introducing Control Flow into Vectorized Code," Preprint ANL/MCS-P1411-0407, April 2007. [pdf]
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J. W. Larson and B. Norris, "Component Specification for Parallel Coupling Infrastructure," Preprint ANL/MCS-P1412-0407, April 2007. [pdf]
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M. Hereld, R. L. Stevens, W. van Drongelen, and H. C. Lee, "Framework for Interactive Million-Neuron Simulation," Journal of Clinical Neurophysiology, vol. 24, no. 2, 2007, pp. 189-196. Also Preprint ANL/MCS-P1360-0706, April 2007. [pdf]
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P. Balaji, D. Buntinas, S. Balay, B. Smith, R. Thakur and W. Gropp , "Nonuniformly Communicating Noncontiguous Data: A Case Study with PETSc and MPI," Preprint ANL/MCS-P1380-1006, March 2007. [pdf]
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Z. Insepov. T. Bazhirov, G. Norman, and V. Stegailov, "Computer Simulation of Bubble Formation," Preprint ANL/MCS-P1398-0307, March 2007. [pdf]
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J. P. Allain, M. Nieto, M. Hendricks, A. Hassanein, C. Tarrio, S. Grantham, and V. Bakshi, "Energetic and Thermal Sn Interactgions and their Effect on EUVL Source Collector Mirror Lifetime at High Temperatures," Preprint ANL/MCS-P1400-0307, March 2007. [pdf]
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Z. Insepov, A. Hassanein, T. T. Bazhirov, G. E. Norman, and V. V. Stegailov, "Molecular Dynamics Simulations of Bubble Formation and Cavitation in Liquid Metals," Preprint ANL/MCS-P1402-0307, March 2007. [pdf]
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D. Sulakhe, A. Rodriguez, M. Wilde, I. Foster, and N. Maltsev, "Interoperability of GADU in Using Heterogeneous Grid Resources for Bioinformatics Applications," Preprint ANL/MCS-P1403-0307, March 2007. [pdf]
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J. N. Lyness and S. Joe, "Determination of the Rank of an Integration Lattice," Preprint ANL/MCS-P1404-0307, March 2007. [pdf]
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P. Fischer, J. Lottes, A. Siegel, and G. Palmiotti, "Large Eddy Simulation of Wire-Wrapped Fuel Pins: Hydrodynamics of a Single Pin," Preprint ANL/MCS-P1405-0307, March 2007. [pdf]
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J. P. Bardhan, M. D. Altman, J. K. White, and B. Tidor, "Efficient Optimization of Electrostatic Interactions between Biomolecules," Preprint ANL/MCS-P1399-0307, March 2007. [pdf]
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M. Anitescu, G. Palmiotti, and W.-S. Yang, "Stochastic Finite-Element Approximation of the Parametric Dependence of Eigenvalue Problem Solution," Preprint ANL/MCS-P1397-0307, March 2007. [pdf]
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D. Buntinas, G. Mercier, and W. Gropp, "Implementation and Evaluation of Shared-Memory Communication and Synchronization Operations in MPICH2 using the Nemesis Communication Subsystem," Parallel Computing, vol. 33, no. 9, 2007, pp. 634-644, March 2007. [pdf]
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R. Fletcher, S. Leyffer, and P. Toint, "A Brief History of Filter Methods," SIAG/OPT Views-and-News, vol. 18, no. 1, SIAM, 2007, pp. 2-12. Also Preprint ANL/MCS-P1372-0906, March 2007. [pdf]
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S. Oster, S. Langella, S. Hastings, D. Ervin, R. Madduri, J. Phillips, T. Kurc, F. Siebenlist, P. Covitz, K. Shanbhag, I. Foster, and J. Saltz, "caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research," Preprint ANL/MCS-P1466-0207, February 2007. [pdf]
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J. Bresnahan, M. Link, R. Kettimuthu, D. Fraser, and I. Foster, "GridFTP Pipelining," Preprint ANL/MCS-P1393-0207, February 2007.
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E. T. Ong, J. W. Larson, B. Norris, R. L. Jacob, M. Tobis, and M. Steder, "Multilingual Interfaces for Parallel Coupling in Multiphysics and Multiscale Systems," Preprint ANL/MCS-P1395-0207, February 2007. [pdf]
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M. R. Paul, M. I. Einarsson, P. F. Fischer, and M. C. Cross, "Extensive Chaos in Rayleigh-Benard Convection," Preprint ANL/MCS-P1396-0207, February 2007. [pdf]
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J. W. Larson, "Ten Organising Principles for Coupling in Multiphysics and Multiscale Models," ANZIAM, vol. 48, 2007, pp. C1090-C1111. Also Preprint ANL/MCS-P1414-0207, February 2007. [pdf]
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M. Tobis, M. Steder, R. L. Jacob, R. T. Pierrehumbert, J. W. Larson, and E. T. Ong, "PyMCT and PyCPL: Refactoring the Community Climate System Model," Preprint ANL/MCS-P1415-0207, February 2007. [pdf]
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N. Desai, E. Lusk, and R. Bradshaw, "A Composition Environment for MPI Programs," Preprint ANL/MCS-P1391-0207, February 2007. [pdf]
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P. Beckman, K. Iskra, K. Yoshii, S. Coghlan, and A. Nataraj, "Benchmarking the Effects of Operating System Interference on Extreme-Scale Parallel Machines," Preprint ANL/MCS-P1390-0107, January 2007. [pdf]
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J. Jung and A. Hassanein, "Three-Phase CFD Analytical Modeling of Blood Flow," Preprint ANL/MCS-P1386-0107, January 2007. [pdf]
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R. Latham, R. Ross, and R. Thakur, "Implementing MPI-IO Atomic Mode and Shared File Pointers Using MPI One-sided Communication," Preprint ANL/MCS-P1388-0107, January 2007. [pdf]
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C. Falzone, A. Chan, E. Lusk, and W. Gropp, "A Portable Method for Finding User Errors in the Usage of MPI Collective Operations," Preprint ANL/MCS-P1389-0107, January 2007. [pdf]
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B. Norris, A. Hartono, and W. Gropp, "Annotations for Productivity and Performance Portability," Preprint ANL/MCS-P1392-0107, January 2007. [pdf]
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D. Karpeev, I. S. Aranson, L. S. Tsimring, and H. G. Kaper, "Interactions of Semiflexible Filaments and Molecular Motors," Phys. Rev. E, vol. 76, 2006, pp. 051905. Also Preprint ANL/MCS-P1381-1206, December 2006. [pdf]
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R. Fletcher, S. Leyffer, and P. Toint, "A Brief History of Filter Methods," SIAG/OPT Views-and-News, vol. 18, no. 1, 2006, pp. 2-12. Also Preprint ANL/MCS-P1372-0906, September 2006. [pdf]
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M. Hereld, R. L. Stevens, W. van Drongelen, H. C. Lee, "Framework for Interactive Million-Neuron Simulation," Journal of Clinical Neurophysiology, vol. 24, no. 2, 2006, pp. 189-196. Also Preprint ANL/MCS-P1360-0706, July 2006. [pdf]
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