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Reference | Publication | Mathematics and Computer Science Division

MCS 2010 - 2000 Publications

2010

D. Ron, Safro, I., and Brandt, A., “A Fast Multigrid Algorithm for Energy Minimization under Planar Density Constraints”, SIAM Multiscale Modeling and Simulations, vol. 8, no. 5, pp. 1599-1620, 2010.

C. S. Henry, Overbeek, R. A., and Stevens, R. L., “Building the Blueprint of Life”, Biotechnology Journal, vol. 5, no. 7, 2010.

T. Peterka, Kendall, W., Goodell, D., Nouanesengsy, B., Shen, H. - W., Huang, J., Moreland, K., Thakur, R., and Ross, R. B., “Performance of Communication Patterns for Extreme-Scale Analysis and Visualization”, in SciDAC 2010, Chattanooga, TN, 2010.

J. M. Wozniak, Son, S. W., and Ross, R. B., “Distributed Object Storage Rebuild Analysis via Simulation with GOBS”, in Dependable Systems and Networks Workshops (DSN-W), Chicago, IL, 2010.

A. Alessandri, Baglietto, M., Battistelli, G., and Zavala, V. M., “Advances in Moving Horizon Estimation for Nonlinear Systems”, in Conference on Decision and Control (CDC) 2010, 2010.

T. Hoefler, Gropp, W. D., Thakur, R., and Traff, J. L., “Toward Performance Models of MPI Implementations for Understanding Application Scaling Issues”, in EuroMPI'10, 2010.

V. M. Zavala, Botterud, A., and Constantinescu, E. M., “Computational and Economic Limitations of Dispatch Operations in the Next-Generation Power Grid”, in Innovative Technologies for an Efficient and Reliable Electricity Supply (CITRES), Waltham, MA, 2010.

R. T. Mills, Sripathi, V., Mahinthakumar, G., Hammond, G. E., Lichtner, P. C., and Smith, B. F., “Engineering PFLOTRAN for Scalable Performance on Cray XT and IBM BlueGene Architectures”, in SciDAC 2010, 2010.

W. Wu, Uram, T. D., Wilde, M., Hereld, M., and Papka, M. E., “Accelerating Science Gateway Development with Web 2.0 and Swift”, in TG '10 , 2010.

V. M. Zavala, Wang, J., Leyffer, S., Constantinescu, E. M., Anitescu, M., and Conzelmann, G., “Proactive Energy Management for Next-Generation Building Systems”, in Fourth National Conference of IBPSA-USA, New York, 2010.

H. Subramoni, Lai, P., Kettimuthu, R., and Panda, D. K., “High Performance Data Transfer in Grid Environment Using GridFTP over InfiniBand”, in Cluster, Cloud and Grid Computing (CCGrid), Melbourne, Australia, 2010.

E. M. Constantinescuand Sandu, A., “Optimal Explicit Strong-Stability-Preserving General Linear Methods”, SIAM J. Sci. Comput., vol. 32, no. 5, pp. 3130-3150, 2010.

S. Leyffer, “Experiments with MINLP Branching Techniques”, in European Workship on Mixed Integer Nonlinear Programming, 2010.

V. M. Zavalaand Anitescu, M., “Achieving Higher Frequencies in Large-Scale Nonlinear Model Predictive Control”, in Conference on Decision and Control (CDC) 2010, 2010.

K. Ohta, Kimpe, D., Cope, J., Iskra, K., Ross, R. B., and Ishikawa, Y., “Optimization Techniques at the I/O Forwarding Layer”, in Cluster 2010, Heraklion, Greece, 2010.

J. W. Larson, “Can We Define Climate Using Information Theory?”, in Earth Environment Science 11, 2010.

V. Minden, Smith, B. F., and Knepley, M. G., “Preliminary Implementation of PETSc Using GPUs”, in 2010 International Wokshop of GPU Solutions in Multiscale Problems in Science and Engineering, 2010.

R. A. Overbeek, Aziz, R. K. K., Bartels, D., Disz, T. L., Edwards, R. A., Gerdes, S. Y., Henry, C. S., Olsen, G. J., Olson, R., Osterman, A. L., Paczian, T., Parrello, B., Pusch, G. D., Rodriguez, A., Stevens, R. L., Vassieva, O., Vonstein, V., Wilke, A., and Zagnitko, O. P., “Programmatic Access to the SEED Data Via the Network”, 2010.

V. Vishwanath, Hereld, M., Iskra, K., Kimpe, D., Morozov, V., Papka, M. E., Ross, R. B., and Yoshii, K., “Accelerating I/O Forwarding in IBM Blue Gene/P Systems”, in SC 10, New Orleans, Louisiana, 2010.

C. Ollivier-Gooch, Diachin, L. F., Shephard, M. S., Tautges, T. J., Kraftcheck, J. A., Leung, V., Luo, X., and Miller, M., “An Interoperable, Data-Structure-Neutral Component for Mesh Query and Manipulation”, ACM Trans. Math. Soft., vol. 37, no. 3, p. article 29, 2010.

J. A. Gilbert, Meyer, F., Antonopoulos, D. A., Balaji, P., C. Brown, T., Brown, C. T., Desai, N. L., Eisen, J. A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, A., Shade, A., and Stevens, R. L., “The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project”, Stand. Genomics Sci., vol. 3, no. 3, p. 6, 2010.

M. Kandemir, Muralidhara, S. P., Karakot, M., and Son, S. W., “Computation Mapping for Multi-Level Storage Cache Hierarchies”, in ACM HPDC 2010, Chicago, Illinois, 2010.

T. G. Armstrong, Zhang, Z., Katz, D. S., Wilde, M., and Foster, I. T., “Scheduling Many-Task Workloads on Supercomputers: Dealing with Trailing Tasks”, in 3rd IEEE Workshop on Many-Task compouting on Grids and Supercomputers (MTAGS10), 2010.

S. Peckham, Hutton, E., and Norris, B., “A Component-Based Approach to Integrated Modeling in the Geosciences: The Design of CSDMS”, Computers and Geoscience: Modeling for Environmental Change, 2010.

S. J. Kim, Zhang, Y., Son, S. W., Prabhakar, R., Kandemir, M., Patrick, C., Liao, W. - K., and Choudhary, A., “Automated Tracing of I/O Stack”, in EuroMPI'10, 2010.

D. A. Antonopoulos, Glass, E. M., and Meyer, F., “Analyzing Metagenomic Data: Inferring Microbial Community Function with MG-RAST”, in Metagenomics and Its Applications in Agriculture, Biomedicine and Environmental Studies, Agricultural Research Service, 2010, pp. 47-60.

Z. Insepov, Rest, J., Hofman, G. L., Yacout, A. M., Kuksin, A. Y., Norman, G. E., Starikov, S. V., Stegailov, V. V., and Yanilkin, A. V., “A New Multiscale Approach to Nuclear Fuel Simulations: Atomistic Validation of the Kinetic Method”, Trans. Am. Nucl. Soc., vol. 102, 2010.

J. Elliott, Foster, I. T., Judd, K., Moyer, E., and Munson, T. S., “CIM-EARTH: Community Integrated Model of Economic and Resource Trajectories for Humankind”, 2010.

R. Latham, “The Parallel-netCDF I/O Library”, 2010.

J. Cope, Iskra, K., Kimpe, D., and Ross, R. B., “Bridging HPC and Grid File I/O with IOFSL”, in Applied Parallel and Scientific Computing (PARA 2010), 2010.

T. Hoefler, Rabenseifner, R., Ritzdorf, H., de Supinski, B. R., Thakur, R., and Traff, J. L., “The Scalable Process Topology Interface of MPI 2.2”, Concurrency and Computation: Practice and Experience, vol. 23, no. 4, pp. 293-310, 2010.

F. Youand Leyffer, S., “Oil Spill Response Planning with MINLP”, SIAG/OPT Views-and-News, vol. 21, no. 2, pp. 1-7, 2010.

M. S. Minand Lee, T., “A Spectral-Element Discontinuous Galerkin Lattice Boltzmann Method for Incompressible Flows”, J. Comput. Phys., vol. 230, pp. 245-259, 2010.

J. A. Gilbert, Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J., Ley, R., Fierer, N., Field, D., Kyrpides, N., Glockner, F. - O., Klenk, H. - P., Wommack, K. E., Glass, E. M., Docherty, K., Gallery, R., Stevens, R. L., and Knight, R., “The Earth Microbiome Project”, in 1st EMP meeting on sample selection and acquisition, 2010.

B. Kreaseck, Strout, M. M., and Hovland, P. D., “Depth Analysis of MPI Programs”, 2010.

W. Wu, Uram, T. D., Wilde, M., Hereld, M., and Papka, M. E., “A Web 2.0-Based Scientific Application Framework”, in International Conference on Web Services (ICWS), 2010.

T. J. Tautgesand Jain, R., “Creating Geometry and Mesh Models for Nuclear Reactor Core Geometries Using a Lattice Hierarchy-Based Approach”, in Proc. 19th International Meshing Roundtable, Chattanooga, TN, 2010.

V. M. Zavalaand Kannan, A., “A Game-Theoretical Dynamic Model for Electricity Markets”, 2010.

“ADIC2: Development of a Component Source Transformation System for Differentiating C and C++”, ICCS, vol. 1, no. 1, pp. 1838-1847, 2010.

J. Fu, Min, M. S., Latham, R., and Carothers, C. D., “Parallel I/O Performance for Application-Level Checkpointing on the Blue Gene/P System”, in CLUSTER '11, 2010, pp. 465-473.

R. Kettimuthu, Sim, A., Gunter, D., Allcock, W. E., Bremer, P., Bresnahan, J., Cherry, A., Childers, L., Dart, E., Foster, I. T., Harms, K., Hick, J., Lee, J., Link, M., Long, J., Miller, K., Natarajan, V., Pascucci, V., Raffenetti, K., Ressman, D., Williams, D., Wilson, L., and Winkler, L., “Lessons Learned from Moving Earth System Grid Data Sets Over a 20 Gbps Wide-Area Network”, ACM HPDC , 2010.

M. Hereld, Insley, J. A., Olson, E., Papka, M. E., Uram, T. D., and Vishwanath, V., “Modeling Resource-Coupled Computations”, 2009 Ultrascale Visualization Workshop . Portland, OR , 2010.

L. Wolfand Pieper, G. W., “Biology and Medical Research at the Exascale”, SciDAC Review, vol. 16, no. special issue , pp. 32-39, 2010.

J. Foster, Bunge, J., Gilbert, J. A., and Moore, J., “Measuring the Microbiome: Perspective on Advances in Exploring Microbial Life”, Briefings in Bioinformatics, 2010.

Z. Insepov, Ivanov, V., Elam, J., and Adams, B., “Charge Relaxation and Gain Depletion for Candidate Secondary Electron Emission Materials”, in Proc. 2010 IEEE Nuclear Science Symposium Record, Knoxville, Tenn., 2010.

F. You, Pinto, J. M., Capon, E., Grossmann, I. E., Arora, N., and Megan, L., “Optimal Distribution-Inventory Planning of Industrial Gases: I. Fast Computational Strategies for Large-Scale Problems”, Ind. Eng. Chem. Res., vol. 50, no. 5, pp. 2910-2927, 2010.

B. Eisenberg, “Crowded Charges in Ion Channels”, in Advances in Chemical Physics, vol. 148, Wiley, 2010.

W. Liu, Tieman, B., Kettimuthu, R., and Foster, I. T., “Moving Huge Scientific Datasets Over the Internet”, Concurrency and Computation: Practice & Experience, vol. 23, no. 18, pp. 2402-2420, 2010.

J. Dinan, Balaji, P., Lusk, E. L., Sadayappan, P., and Thakur, R., “Hybrid Parallel Programming with MPI and Unified Parallel C”, in 7th ACM International Conference on Computing Frontiers, Bertinoro, Italy, 2010.

Y. Li, Anitescu, M., Roderick, O., and Hickernell, F., “Orthogonal Bases for Polynomial Regression with Derivative Information in Uncertainty Quantification”, 2010.

R. Kottmann, Wilke, A., Meyer, F., and Glockner, F. - O., “Bioinformatic Resources for Marine Microbial Genomics”, 2010.

L. M. R. Gadelha, Jr., Clifford, B., Mattoso, M., Wilde, M., and Foster, I. T., “Provenance Management in Swift with Implementation Details”, 2010.

P. Balaprakash, Wild, S. M., and Hovland, P. D., “Can Search Algorithms Save Large-Scale Automatic Performance Tuning?”, in Proceedings ICCS 2011 in Procedia Computer Science, Tsukuba, Japan, 2010.

W. Liu, Kettimuthu, R., Li, B., and Foster, I. T., “An Adaptive Strategy for Scheduling Data-Intensive Applications in Grid Environments”, in Proc. IEEE 17th International Conf. on Telecommunications, Doha, 2010.

J. Xu, Mustapha, B., and Min, M. S., “Efficient Numerical and Parallel Methods for Beam Dynamics Simulations”, 2010.

R. Ranjan, Pantano, C., and Fischer, P. F., “Direct Simulation of Turbulent Swept Flow Over a Wire in a Channel”, Journal of Fluid Mechanics, vol. 651, pp. 165-209, 2010.

P. H. Carns, Ross, R. B., and Lang, S., “Object Storage Semantics for Replicated Concurrent-Writer File Systems”, in 2010 Workshop on Inerfaces and Architectures for Scientific Data Storage, Heraklion, Crete, Greece, 2010.

M. Anitescuand Tasora, A., “An Iterative Approach for Cone Complementarity Problems for Nonsmooth Dynamics”, Comput. Optimization Appl., vol. 47, no. 2, pp. 207-235, 2010.

S. V. Starikov, Insepov, Z., and Rest, J., “Radiation Defects by Xe Ion Implantation and Self-Interstitial Clusters Evolution in Molybdenum”, Physical Review B, 2010.

F. Youand Leyffer, S., “Mixed-Integer Dynamic Optimization for Oil-Spill Response Planning with Integration of a Dynamic Oil Weathering Model”, AIChE J., vol. 57, no. 12, pp. 3555-3564, 2010.

R. Kettimuthu, Schuler, R., Keator, D., Feller, M., Wei, D., Link, M., Liming, L., Ames, J., Chervenak, A. L., Foster, I. T., and Kesselman, C., “A Data Management Framework for Distributed Biomedical Research Environments”, in Proc. 6th IEEE International Conf. on e-Science Workshops, Brisbane, QLD, 2010.

M. J. Hole, Wilson, H. R., Abeysuriya, R., and Larson, J. W., “Ideal MHD Stability of a Spherical Tokamak Power Plant and a Component Test Facility”, Plasma Physic. Control. Fusion, vol. 52, no. 12, 2010.

J. M. Wozniak, Jacobs, B., Latham, R., Lang, S., Son, S. W., and Ross, R. B., “C-MPI: A DHT Implementation for Grid and HPC Environments”, presented at the 04/2010, 2010.

Z. Insepov, Norem, J., and Veitzer, S., “Ion Solid Interaction and Surface Modification at rf Breakdown in High-Gradient Linacs”, presented at the 08/2010, 2010.

D. Kimpe, Goodell, D., and Ross, R. B., “MPI Datatype Marshalling: A Case Study in Datatype Equivalence”, in 17th EuroMPI conference, Stuttgart, Germany, 2010.

S. W. Son, Lang, S., Carns, P. H., Ross, R. B., Thakur, R., Ozisikyilmaz, B., Kumar, P., Liao, W. - K., and Choudhary, A., “Enabling Active Storage on Parallel I/O Software Stacks”, in Proceedings of 26th IEEE Conference on Mass Storage Systems and Technologies, Incline Village, NV, USA, 2010.

D. Ron, Safro, I., and Brandt, A., “Relaxation-Based Coarsening and Multiscale Graph Organization”, Multiscale Modeling Simulation, vol. 9, no. 1, pp. 407-423, 2010.

J. P. Faria, Rocha, M., Stevens, R. L., and Henry, C. S., “Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models”, in Advances in Bioinformatics, 2010.

D. Buntinas, Malozemoff, A., and Utke, J., “Efficient Generated Libraries for Asynchronous Derivative Computation”, in Procedia Computer Science, Proc. ICCS 2010, Amsterdam, Netherlands, 2010.

Z. Insepov, Ivanov, V., and Frisch, H., “Comparison of Candidate Secondary Electron Emission Materials”, Nuclear Instruments and Methods in Physics Research Section B, vol. 268, no. 20, pp. 3315-3320, 2010.

D. Goodell, Balaji, P., Buntinas, D., Dozsa, G., Gropp, W. D., Kumar, S., de Supinski, B. R., and Thakur, R., “Minimizing MPI Resource Contention in Multithreaded Multicore Environments”, in Proc. IEEE International Conf. on Cluster Computing, Heraklion, Greece, 2010.

W. Kendall, Peterka, T., Huang, J., Shen, H. - W., and Ross, R. B., “Accelerating and Benchmarking Radix-k Image Compositing at Large Scale”, in Proc. EGPGV, Norrkoping, Sweden, 2010.

J. L. McClean, Bader, D. C., Bryan, F. O., Maltrud, M. E., Dennis, J. M., Mirin, A. A., Jones, P. W., Vertenstein, M., Ivanova, D. P., Kim, Y. Y., Boyle, J. S., Jacob, R. L., Norton, N., Craig, A. P., and Worley, P. H., “A Prototype Two-Decade Fully-Coupled Fine-Resolution CCSM Simulation”, Ocean Modelling, vol. 39, no. 1, pp. 10-30, 2010.

P. Balaji, Feng, W., Lin, H., Archuleta, J., Matsuoka, S., Warren, A., Setubal, J., Lusk, E. L., Thakur, R., Foster, I. T., Katz, D. S., Jha, S., Shinpaugh, K., Coghlan, S. M., and Reed, D., “Global-Scale Distributed I/O with ParaMEDIC”, Concurrency and Computat.: Prac. Exper., vol. 22, no. 16, pp. 2266-2281, 2010.

J. Krishna, Balaji, P., Lusk, E. L., Thakur, R., and Tiller, F., “Implementing MPI on Windows: Comparison with Common Approaches on Unix”, in 17th EuroMPI Conference, Lecture Notes in Computer Science, Springer, Stuttgart, Germany, 2010, 2010.

G. Dozsa, Kumar, S., Balaji, P., Buntinas, D., Goodell, D., Gropp, W. D., Ratterman, J., and Thakur, R., “Enabling Concurrent Multithreaded MPI Communication on Multicore Petascale Systems”, in 17th EuroMPI conference, Stuttgart, Germany, 2010.

M. Alexe, Roderick, O., Utke, J., Anitescu, M., Fanning, T., and Hovland, P. D., “Using Automatic Differentiation in Sensitivity Analysis of Nuclear Simulation Models”, Trans. American Nuc. Soc., vol. 102, pp. 235-237, 2010.

G. D. Hartand Anitescu, M., “An O(m+n) Measure of Penetration Depth between Convex Polyhedral Bodies for Rigid Multibody Dynamics”, 2010.

S. Moreaud, Goglin, B., Namyst, R., and Goodell, D., “Optimizing MPI Communication within Large Multicore Nodes with Kernel Assistance”, in Proc. Parallel & Distributed Processing, Workshops and PhD Forum, 2010.

A. Alessandri, Baglietto, M., Battistelli, G., and Zavala, V. M., “Computationally Efficient, Approximate Moving Horizon State Estimation for Nonlinear Systems”, in Proc. 8th IFAC Symposium on Nonlinear Control Systems, Bologna, Italy, 2010.

P. Balaji, Buntinas, D., Goodell, D., Gropp, W. D., and Thakur, R., “Fine-Grained Multithreading Support for Hybrid Threaded MPI Programming”, Int. J. High Perform. Comput.Appl., vol. 24, no. 1, pp. 49-57, 2010.

V. M. Zavalaand Anitescu, M., “Real-Time Optimization as a Generalized Equation”, SIAM J. Control Optim., vol. 48, pp. 5444-5454, 2010.

A. Tasoraand Anitescu, M., “A Convex Complementarity Approach for Simulating Large Granular Flows”, J. Comput. Nonlinear Dynam., vol. 5, no. 3, p. 031004 (10 pages), 2010.

B. A. Lockwoodand Anitescu, M., “Gradient-Enhanced Universal Kriging for Uncertainty Propagation”, 2010.

M. Altunay, Leyffer, S., Linderoth, J. T., and Xie, Z., “Optimal Response to Attacks on Open Science Grids”, Computer Networks, vol. 55, no. 1, pp. 61-73, 2010.

A. Mahajan, “Presolving Mixed Integer Linear Programs”, 2010.

E. M. Constantinescu, Zavala, V. M., Rocklin, M., Lee, S., and Anitescu, M., “A Computational Framework for Uncertainty Quantification and Stochastic Optimization in Unit Commitment with Wind Power Generation”, IEEE Transactions on Power Systems, vol. 26, no. 1, pp. 431-441, 2010.

Z. Insepov, Norem, J., and Veitzer, S., “Atomistic Mechanisms of rf Breakdown in High-Gradient Linacs”, Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, vol. 268, no. 6, pp. 642-650, 2010.

P. Marshall, Keahey, K., and Freeman, T., “Elastic Site - Using Clouds to Elastically Extend Site Resources”, in 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing, Melbourne, VIC, Australia, 2010.

J. DeBartolo, Hocky, G., Wilde, M., Xu, J., Freed, K. F., and Sosnick, T. R., “Protein Structure Prediction Enhanced with Evolutionary Diversity: SPEED”, Protein Science, vol. 19, no. 3, pp. 520-534, 2010.

A. S. Warlaumont, Lee, H. C., Benayoun, M., Stevens, R. L., and Hereld, M., “Systematic Comparison of the Behaviors Produced by Computational Models of Epileptic Neocortex”, J. CLinical Neurophysicology, vol. 27, no. 6, pp. 479-483, 2010.

P. H. Beckman, Foster, I. T., Wilde, M., and Raicu, I., “Scalable Parallel Scripting for Scientific Computing”, SciDAC Review, vol. 17, pp. 38-53, 2010.

E. M. Constantinescuand Sandu, A., “Extrapolated Implicit-Explicit Time Stepping”, SIAM J. Sci. Comput., vol. 31, no. 6, pp. 4452-4477, 2010.

P. Balaji, Chan, A., Gropp, W. D., Thakur, R., and Lusk, E. L., “The Importance of Non-Data-Communication Overheads in MPI”, International Journal of High Performance Computing Applications, vol. 24, no. 1, pp. 5-15, 2010.

E. L. Lusk, Pieper, S. C., and Butler, R. M., “More Scalability, Less Pain: A Simple Programming Model and Its Implementation for Extreme Computing”, SciDAC Review, vol. 17, pp. 30-37, 2010.

2009

S. Narayan, Chandy, J. A., Lang, S., Carns, P. H., and Ross, R. B., “Uncovering Errors: The Cost of Detecting Silent Data Corruption”, presented at the 10/2009, 2009.

J. M. Wozniakand Wilde, M., “Case Studies in Storage Access by Loosely Coupled Petascale Applications”, in Proceedings of the 4th Annual Workshop on Petascale Data Storage, Portland, Oregon, USA, 2009.

V. M. Zavala, Constantinescu, E. M., and Anitescu, M., “Economic Impacts of Advanced Weather Forecasting in Energy System Operations”, presented at the 10/2009, 2009.

J. A. Insley, Leggett, T., and Papka, M. E., “Using Dynamic Accounts to Enable Access to Advanced Resources through Science Gateways”, in Proceedings of the 5th Grid Computing Environments Workshop, Portland, Oregon, USA, 2009.

P. Balaji, Naik, H., and Desai, N. L., “Understanding Network Saturation Behavior on Large-Scale Blue Gene/P Systems”, in Proceedings of the 2009 15th International Conference on Parallel and Distributed Systems, 2009.

Z. Xieand Bowman, J. M., “Permutationally Invariant Polynomial Basis for Molecular Energy Surface Fitting via Monomial Symmetrization”, Journal of Chemical Theory and Computation, vol. 6, no. 1, pp. 26-34, 2009.

M. Wilde, Zhang, Z., Clifford, B., Hategan, M., Kenny, S., Iskra, K., Beckman, P. H., Foster, I. T., Raicu, I., and Espinosa, A., “Parallel scripting for applications at the petascale and beyond”, Computer, vol. 42, no. 11, pp. 50-60, 2009.

W. Wu, Uram, T. D., and Papka, M. E., “Web 2.0 Based Social Informatics Data Grid”, in Proceedings of the 5th Grid Computing Environments Workshop, Portland, Oregon, USA, 2009.

J. Shin, Hall, M. W., Chame, J., Chen, C., Fischer, P. F., and Hovland, P. D., “Speeding Up Nek5000 with Autotuning and Specialization”, in Proceedings of the 24th ACM International Conference on Supercomputing, Tsukuba, Ibaraki, Japan, 2009.

O. Roderickand Safro, I., “Learning of Highly-Filtered Data Manifold Using Spectral Methods”, presented at the 02/2009, 2009.

M. Alexe, Roderick, O., Utke, J., Anitescu, M., Hovland, P. D., and Fanning, T., “Automatic Differentiation of Codes in Nuclear Engineering Applications”, 2009.

S. Nam, Deshpande, S., Vishwanath, V., Jeong, B., Renambot, L., and Leigh, J., “Multi-Application Inter-Tile Synchronization on Ultra-High-Resolution Display Walls”, in Proceedings of the first annual ACM SIGMM conference on Multimedia systems, Phoenix, Arizona, USA, 2009.

S. H. K. Narayanan, Norris, B., and Hovland, P. D., “Generating Performance Bounds from Source Code”, presented at the 10/2009, 2009.

J. Chenand Safro, I., “Algebraic Distance on Graphs”, 2009.

E. M. Glass, Wilkening, J., Wilke, A., Antonopoulos, D. A., and Meyer, F., “Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes”, 2009.

F. Meyer, Overbeek, R. A., and Rodriguez, A., “FIGfams: Yet Another Set of Protein Families”, Nucleic Acids Research, vol. 37, no. 20, pp. 6643-6654, 2009.

S. W. Son, Kandemir, M., Zhang, Y., and Garg, R., “Topology-Aware I/O Caching for Shared Storage Systems”, presented at the 08/2009, 2009.

T. Peterka, Yu, H., Ross, R. B., Ma, K. - L., and Latham, R., “End-to-End Study of Parallel Volume Rendering on the IBM Blue Gene/P”, in Proceedings of the 2009 International Conference on Parallel Processing, 2009.

A. Lyons, “Acyclic and Star Colorings of Joins of Graphs and an Algorithm for Cographs”, in Proc. 8th Cologne_Twente Workshop on Graphs and Combinatorial Optimization, 2009.

J. Wilkening, Wilke, A., Desai, N. L., and Meyer, F., “Using Clouds for Metagenomics: A Case Study”, in IEEE Cluster 2009, New Orleans, Louisiana, USA, 2009.

J. Shin, Hall, M. W., Chame, J., Chen, C., and Hovland, P. D., “Autotuning and Specialization: Speeding up Matrix Multiply for Small Matrices with Compiler Technology”, in In The Fourth International Workshop on Automatic Performance Tuning, 2009.

C. M. Patrick, Garg, R., Son, S. W., and Kandemir, M., “Improving I/O Performance Using Soft-QoS-Based Dynamic Storage Cache Partitioning”, in IEEE Cluster 2009, New Orleans, Louisiana, USA, 2009.

Z. Hou, Wilde, M., Zhou, X., Foster, I. T., and Tie, J., “ADEM: An Automation Tool for Application Software Deployment and Management on OSG”, presented at the 08/2009, 2009.

V. Thi Bui, Norris, B., and McInnes, L. Curfman, “An Automated Component-Based Performance Experiment Environment”, in Proceedings of the 2009 Workshop on Component-Based High Performance Computing, Portland, Oregon, USA, 2009.

R. E. Grant, Afsahi, A., and Balaji, P., “Evaluation of ConnectX Virtual Protocol Interconnect for Data Centers”, in Proceedings of the 2009 15th International Conference on Parallel and Distributed Systems, 2009.

A. Lyons, “Acyclic and Star Colorings of Cographs”, 2009.

E. M. Constantinescu, Zavala, V. M., Rocklin, M., Lee, S., and Anitescu, M., “Unit Commitment with Wind Power Generation: Integrating Wind Forecast Uncertainty and Stochastic Programming”, 2009.

J. W. Larson, “Information-Theoretic Strategies for Quantifying Variability and Model-Reality Comparison in the Climate System”, presented at the 04/2009, 2009.

S. Lang, Latham, R., Kimpe, D., and Ross, R. B., “Interfaces for Coordinated Access in the File System”, presented at the 08/2009, 2009.

B. F. Smithand Zhang, H., “Sparse Triangular Solve Revisited: Data Layout Crucial to Better Performance”, 2009.

M. Hereld, Hudson, R., Norris, J., Papka, M. E., and Uram, T. D., “Enabling Scientific Teamwork”, in Journal of Physics: Conference Series, 2009.

J. Larssonand Lele, S. K., “Direct Numerical Simulation of Canonical Shock/Turbulence Interaction”, Physics of Fluids, vol. 21, no. 12, p. 126101, 2009.

F. Isaila, J. Blas, G., and Carretero, J., “Latency Hiding File I/O for Blue Gene Systems”, in 2009 Nineth IEEE International Symposium on Cluster Computing and the Grid, Shanghai, 2009.

E. M. Constantinescuand Sandu, A., “Optimal Explicit Strong-Stability-Preserving General Linear Methods: Complete Results”, 2009.

Y. Hong, Peterka, T., and Shen, H. W., “Histogram-Based I/O Optimization for Visualizing Large-Scale Data”, in SuperComputing 2009 (SC 2009) , Portland, OR, 2009.

W. Guan, Gray, A., and Leyffer, S., “Mixed-Integer Support Vector Machine”, in 2nd NIPS Workshop on Optimization for Machine Learning (OPT 2009) , Sutcliffe, England , 2009.

J. Chenand Safro, I., “A Measure of the Connection Strengths between Graph Vertices with Applications”, in Workshop on Algorithm Engineering & Experiments (ALENEX 2010) , Austin, TX , 2009.

R. Gupta, Beckman, P. H., Park, B. H., Lusk, E. L., Hargrove, P., Geist, A., Panda, D. K., Lumsdaine, A., and Dongarra, J., “CIFTS: A Coordinated Infrastructure for Fault-Tolerant Systems”, in 38th International Conference on Parallel Processing, Vienna, Austria, 2009.

D. Buettner, Desai, N. L., Lan, Z., and Tang, W., “Fault-Aware Utility-Based Job Scheduling on BlueGene/P Systems”, in 2009 IEEE Conference on Cluster Computing (Cluster 2009), New Orleans, LA, 2009.

L. Liming, Navarro, J. P., Blau, E., Brechin, J., Catlett, C., Dahan, M., Diehl, D., Dooley, R., Dwyer, M., Ericson, K., Foster, I. T., Hanna, E., Hart, D. L., Jordan, C., Light, R., Martin, S., McGee, J., Pearlman, L., Reilly, J., Scavo, T., Shapiro, M., Smallen, S., Smith, W., and Wilkins-Diehr, N., “TeraGrid's Integrated Information Service”, in Proceedings of the 5th Grid Computing Environments Workshop, Portland, Oregon, USA, 2009.

T. Peterka, Ross, R. B., Yu, H., Ma, K. - L., Kooima, R. L., and Girado, J., “Autostereoscopic Display of Large-Scale Scientific Visualization”, in Proceedings of SPIE, San Jose, CA, USA, 2009.

L. Li, Kenny, J. P., Wu, M. - S., Huck, K. A., Gaenko, A., Gordon, M. S., Janssen, C. L., McInnes, L. Curfman, Netzloff, H. M., Norris, B., and Windus, T. L., “Adaptive Application Composition in Quantum Chemistry”, in Proceedings of the 5th International Conference on the Quality of Software Architectures: Architectures for Adaptive Software Systems, East Stroudsburg, PA, USA, 2009.

F. E. Angly, Willner, D., Prieto-Davo, A., Edwards, R. A., Schmieder, R., Vega-Thurber, R., Antonopoulos, D. A., Barott, K., Cottrell, M. T., Desnues, C., Dinsdale, E. A., Furlan, M., Haynes, M., Henn, M. R., Hu, Y., Kirchman, D. L., McDole, T., McPherson, J. D., Meyer, F., Miller, R. M., Mundt, E., Naviaux, R. K., Rodriguez-Mueller, B., Stevens, R. L., Wegley, L., Zhang, L., Zhu, B., and Rohwer, F., “The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes”, PLoS Comput Biol., vol. 5, no. 12, 2009.

L. Li, Dahlgren, T., McInnes, L. Curfman, and Norris, B., “Interface Contract Enforcement for Improvement of Computational Quality of Service (CQoS) for Scientific Components”, in Proceedings of the 2009 Workshop on Component-Based High Performance Computing, Portland, Oregon, USA, 2009.

J. Dwyer, Lee, H., Martell, A., Stevens, R. L., Hereld, M., and van Drongelen, W., “Oscillation in a Network Model of Neocortex”, Neurocomputing, vol. 73, no. 7, pp. 1051-1056, 2009.

P. Balaji, Buntinas, D., Goodell, D., Gropp, W. D., Krishna, J., Lusk, E. L., and Thakur, R., “PMI: A Scalable Parallel Process-Management Interface for Extreme-Scale Systems”, in 17th EuroMPI Conference, Lecture Notes in Computer Science, Springer, Stuttgart, Germany, 2010, 2009.

B. R. de Supinski, Alam, S., Bailey, D. H., Carrington, L., Daley, C., Dubey, A., Gamblin, T., Gunter, D., Hovland, P. D., Jagode, H., Karananic, K., Marin, G., Mellor-Crummey, J., Moore, S., Norris, B., Oliker, L., Olschanowsky, C., Roth, P. C., Schulz, M., Shende, S., Snavely, A., Spear, W., Tikir, M., Vetter, J. S., Worley, P. H., and Wright, N., “Modeling the Office of Science Ten Year Facilities Plan: The PERI Architecture Tiger Team”, in Journal of Physics: Conference Series, 2009.

M. W. Hall, Chame, J., Chen, C., Shin, J., and Rudy, G., “Loop Transformation Recipes for Code Generation and Auto-Tuning”, Languages and Compilers for Parallel Computing, vol. 5898, 2009.

V. M. Zavala, Anitescu, M., and Krause, T., “On the Optimal On-Line Management of Photovoltaic-Hydrogen Hybrid Energy Systems”, Computer Aided Chemical Engineering, vol. 27, no. 10, pp. 1725-1736, 2009.

D. A. Hanson, Kryukov, Y., Leyffer, S., and Munson, T. S., “Optimal Control Model of Technology Transition”, International Journal of Global Energy Issues, vol. 33, no. 3/4, pp. 154-175, 2009.

D. S. Katz, Daly, J., Debardeleben, N. A., Elnozahy, M., Kramer, B., Lathrop, L., Nystrom, N., Milfeld, K., Sanielevici, S., Cott, S., and Votta, L., “2009 Fault Tolerance for Extreme-Scale Computing Workshop, Albuquerque, NM - March 19-20, 2009”, 2009.

P. H. Carns, Latham, R., Ross, R. B., Iskra, K., Lang, S., and Riley, K., “24/7 Characterization of Petascale I/O Workloads”, in Proceedings of the First Workshop on Interfaces and Abstractions for Scientific Data Storage, New Orleans, LA, USA, 2009.

C. Stacey, Trefonides, M., Kendall, T., and Finley, B., “The Water Fountain vs. the Fire Hose: An Examination and Comparison of Two Large Enterprise Mail Service Migrations”, presented at the 08/2009, 2009.

O. Roderickand Safro, I., “Polynomial Interpolation for Predicting Decisions and Recovering Missing Data”, presented at the 02/2009, 2009.

K. Yoshii, Iskra, K., Broekema, P. C., Naik, H., and Beckman, P. H., “Characterizing the Performance of Big Memory on Blue Gene Linux”, in Proceedings of the 2009 International Conference on Parallel Processing Workshops, 2009.

M. Hereld, Stevens, R. L., Sterling, T., and Gao, G. R., “Structured Hints: Extracting and Abstracting Domain Expertise”, 2009.

V. M. Zavala, Constantinescu, E. M., Krause, T., and Anitescu, M., “Weather Forecast-Based Optimization of Integrated Energy Systems”, 2009.

T. Peterka, Ross, R. B., Shen, H. - W., Ma, K. - L., Kendall, W., and Yu, H., “Parallel Visualization on Leadership Computing Resources”, in Journal of Physics: Conference Series, 2009.

V. M. Zavala, Constantinescu, E. M., Krause, T., and Anitescu, M., “On-Line Economic Optimization of Energy Systems Using Weather Forecast Information”, J. Process Control, vol. 19, no. 10, pp. 1725-1736, 2009.

J. W. Larson, “Graphical Notation for Diagramming Coupled Systems”, in Computational Science � ICCS 2009, 2009.

I. Safro, Hovland, P. D., Shin, J., and Strout, M. M., “Improving Random Walk Performance”, presented at the 02/2009, 2009.

J. Bresnahan, Link, M., Kettimuthu, R., and Foster, I. T., “GridFTP Multilinking”, presented at the 02/2009, 2009.

X. Zeng, Anitescu, M., Pereira, C., and Regalbuto, M., “A Framework for Chemical Plant Safety Assessment under Uncertainty”, Studies Inform. Control, vol. 18, no. 1, pp. 7-20, 2009.

M. Rocklinand Constantinescu, E. M., “Adjoint Sensitivity Analysis for Wind Power Generation”, 2009.

A. Tasoraand Anitescu, M., “A Matrix-Free Cone Complementarity Approach for Solving Large-Scale, Nonsmooth, Ridig Body Dynamics”, 2009.

J. Elliott, Foster, I. T., Judd, K., Moyer, E., and Munson, T. S., “CIM-EARTH: Framework and Case Study”, B.E. Journal of Economic Analysis & Policy, vol. 10, no. 2, 2009.

H. Fang, Leyffer, S., and Munson, T. S., “A Pivoting Algorithm for Linear Programming with Linear Complementarity Constraints”, Optimization Methods Software, 2009.

N. L. Desai, Buntinas, D., Buettner, D., Balaji, P., and Chan, A., “Improving Resource Availability by Relaxing Network Allocation Constraints on the Blue Gene/P”, in 2009 International Conference on Parallel Processing, Vienna, Austria, 2009.

C. S. Henry, Zinner, J. F., Cohoon, M. P., and Stevens, R. L., “iBsu1103: An Improved Genome-Scale MetabolicModel of B. subtilis Based on SEED Annotations”, 2009.

X. Shiand Stevens, R. L., “A Bayesian Approach to High-Throughput Biological Model Generation”, in Bioinformatics and Computational Biology, 2009.

S. Leyffer, “A Complementarity Constraint Formulation of Convex Multiobjective Optimization Problems”, INFORMS J. on Computing, vol. 21, no. 2, pp. 257-267, 2009.

T. J. Tautges, “Canonical Numbering Systems for Finite-Element Codes”, 2009.

B. Norris, Hartono, A., Jessup, E., and Siek, J. G., “Generating Empirically Optimized Composed Matrix Kernels from MATLAB Prototypes”, in Proceedings of the 9th International Conference on Computational Science: Part I, Baton Rouge, LA, USA, 2009.

E. M. Constantinescuand Sandu, A., “Explicit Time Stepping Methods with High Stage Order and Monotonicity Properties”, presented at the 01/2009, 2009.

H. Naik, Gupta, R., and Beckman, P. H., “Analyzing Checkpointing Trends for Applications on the IBM Blue Gene/P System”, in Proceedings of the 2009 International Conference on Parallel Processing Workshops, 2009.

D. Giannakis, Fischer, P. F., and Rosner, R., “A Spectral Galerkin Method for the Coupled Orr-Sommerfeld and Induction Equations for Free-Surface MHD”, J. of Computational Physics, vol. 228, pp. 1188-1233, 2009.

D. Buntinas, Goglin, B., Goodell, D., Mercier, G., and Moreaud, S., “Cache-Efficient, Intranode, Large-Message MPI Communication with MPICH2-Nemesis”, in Proceedings of the 2009 International Conference on Parallel Processing, 2009.

P. Lai, Balaji, P., Thakur, R., and Panda, D. K., “ProOnE: A General-Purpose Protocol Onload Engine for Multi- and Many-Core Architectures”, in Computer Science - Research and Development, 2009.

G. J. Blas, Isaila, F., Carretero, J., Latham, R., and Ross, R. B., “Multiple-Level MPI File Write-Back and Prefetching for Blue Gene Systems”, in Recent Advances in Parallel Virtual Machine and Message Passing Interface, Espoo, Finland, 2009.

G. Hocky, Wilde, M., DeBartolo, J., Hategan, M., Foster, I. T., Sosnick, T. R., and Freed, K. F., “Towards Petascale ab initio Protein Folding Through Parallel Scripting”, presented at the 04/2009, 2009.

E. L. Lusk, “Slouching Towards Exascale”, International Journal of High Performance Computing, vol. 23, no. 4, pp. 337-339, 2009.

F. Siebenlist, Ananthakrishnan, R., Bernholdt, D. E., Cinquini, L., Foster, I. T., Middleton, D. E., Miller, N., and Williams, D. N., “Earth System Grid Authentication Infrastructure: Integrating Local Authentication, OpenID and PKI”, presented at the 05/2009, 2009.

S. Leyffer, Linderoth, J. T., Luedtke, J., Miller, A., and Munson, T. S., “Applications and Algorithms for Mixed Integer Nonlinear Programming”, in Journal of Physics: Conference Series, 2009.

V. M. Zavala, “Stability Analysis of an Approximate Scheme for Moving Horizon Estimation”, Comput. Chem. Eng., vol. 34, no. 10, pp. 1662-1670, 2009.

A. Singh, Balaji, P., and Feng, W., “GePSeA: A General-Purpose Software Acceleration Framework for Lightweight Task Offloading”, in Proceedings of the 2009 International Conference on Parallel Processing, 2009.

M. Wilde, Raicu, I., Espinosa, A., Zhang, Z., Clifford, B., Hategan, M., Kenny, S., Iskra, K., Beckman, P. H., and Foster, I. T., “Extreme-Scale Scripting: Opportunities for Large Task-Parallel Applications on Petascale Computers”, in Journal of Physics: Conference Series, 2009.

A. Choudhary, Liao, W. - K., Gao, K., Nisar, A., Ross, R. B., Thakur, R., and Latham, R., “Scalable I/O and Analytics”, in Journal of Physics: Conference Series, 2009.

B. Sotomayor, Montero, R. S., Llorente, I. M., and Foster, I. T., “An Open Source Solution for Virtual Infrastructure Management in Private and Hybrid Clouds”, 2009.

S. Lang, Carns, P. H., Latham, R., Ross, R. B., Harms, K., and Allcock, W. E., “I/O Performance Challenges at Leadership Scale”, in Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, Portland, Oregon, 2009.

C. S. Henry, Xia, F., and Stevens, R. L., “Application of High-Performance Computing to the Reconstruction, Analysis, and Optimization of Genome-Scale Metabolic Models”, in Journal of Physics: Conference Series, 2009.

M. S. Minand Fischer, P. F., “Spectral-Element Discontinuous Galerkin (SEDG) Simulations with a Moving Window Algorithm for Wakefield Calculations”, presented at the 04/2009, 2009.

G. Garzoglio, Aldermhini, I., Altunay, M., Ananthakrishnan, R., Bester, J., Chadwick, K., Ciaschini, V., Demchenko, Y., Ferraro, A., Forti, A., Groep, D., Hesselroth, T. D., Hover, J., Koeroo, O., La Joie, C., Levshina, T., Miller, Z., Packard, J., Sagehaug, H., Sfiligoi, I., Sharma, N., Timm, S., Siebenlist, F., Venturi, V., and Weigand, J., “XACML Profile and Implementation for Authorization Interoperability between OSG and EGEE”, in Journal of Physics: Conference Series, 2009.

I. Raicu, Foster, I. T., Zhao, Y., Little, P., Moretti, C. M., Choudhary, A., and Thain, D., “The Quest for Scalable Support of Data-Intensive Workloads in Distributed Systems”, in Proceedings of the 18th ACM international symposium on High performance distributed computing, Garching, Germany, 2009.

N. Ali, Carns, P. H., Iskra, K., Kimpe, D., Lang, S., Latham, R., Ross, R. B., Ward, L., and Sadayappan, P., “Scalable I/O Forwarding Framework for High-Performance Computing Systems”, in Name: Proceedings of the 2009 IEEE International Conference on Cluster Computing, New Orleans, LA, USA, 2009.

M. M. Strout, Osheim, N., Rostron, D., Hovland, P. D., and Pothen, A., “Evaluation of Hierarchical Mesh Reorderings”, in Computational Science, ICCS 2009, 2009.

S. M. Wildand Shoemaker, C., “Global Convergence of Radial Basis Function Trust Region Derivative-Free Algorithms”, 2009.

B. F. Smith, “PETSc - The Portable, Extensible Toolkit for Scientific Computation”, 2009.

W. Liu, Kettimuthu, R., Tieman, B., Madduri, R., Li, B., and Foster, I. T., “GridFTP GUI: An Easy and Efficient Way to Transfer Data in Grid”, presented at the 07/2009, 2009.

A. Guerra, Newman, A. M., and Leyffer, S., “Concrete Structure Design Using Mixed-Integer Nonlinear Programming with Complementarity Constraints”, 2009.

G. Santhanaraman, Balaji, P., Gopalakrishnan, K., Thakur, R., Gropp, W. D., and Panda, D. K., “Natively Supporting True One-Sided Communication in MPI on Multi-Core Systems with InfiniBand”, in Proceedings of the 2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2009.

T. Peterka, Goodell, D., Ross, R. B., Shen, H. - W., and Thakur, R., “A Configurable Algorithm for Parallel Image-Compositing Applications”, in Proceedings of the Conference on High Performance Computing, Networking, Storage, and Analysis, Portland, Oregon, USA, 2009.

H. Zhu, Goodell, D., Gropp, W. D., and Thakur, R., “Hierarchical Collectives in MPICH2”, in Recent Advances in Parallel Virtual Machine and Message Passing Interface, Espoo, Finland, 2009.

J. Bresnahan, Link, M., Kettimuthu, R., and Foster, I. T., “UDT as an Alternative Transport Protocol for GridFTP”, presented at the 04/2009, 2009.

J. Utkeand Naumann, U., “Combinatorial Problems in Open/AD”, presented at the 03/2009, 2009.

P. Balaji, Chan, A., Thakur, R., Gropp, W. D., and Lusk, E. L., “Toward Message Passing for a Million Processes: Characterizing MPI on a Massive Scale Blue Gene/P”, in Computer Science - Research and Development, 2009.

W. Feng, Balaji, P., and Singh, A., “Network Interface Cards as First-Class Citizens”, presented at the 04/2009, 2009.

E. M. Constantinescuand Sandu, A., “Achieving Very High Order for Implicit Explicit Time Stepping: Extrapolation Methods”, 2009.

2008

E. A. Dinsdale, Edwards, R. A., Hall, D., Angly, F. E., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., McDaniel, L., Moran, M. A., Nelson, K. E., Nilsson, C., Olson, R., Paul, J., Brito, B. R., Ruan, Y., Swan, B. K., Stevens, R. L., Valentine, D. L., Thurber, R. V., Wegley, L., White, B. A., and Rohwer, F., “Functional Metagenomic Profiling of Nine Biomes”, Nature., vol. 452, no. 7187, pp. 629-632, 2008.

T. Scogland, Balaji, P., Feng, W., and Narayanaswamy, G., “Asymmetric Interactions in Symmettric Multi-core Systems: Analysis, Enhancements, and Evaluation”, presented at the 11/2008, 2008.

Z. Insepov, Norem, J., Hassanein, A., and Wu, A. T., “Advanced Surface Polishing for Accelerator Technology using Ion Beams”, presented at the 08/2008, 2008.

S. F. Siegel, Siegel, A. R., and Rabiti, C., “UNIC Code: Algorithmic Specification of the Method of Long Characteristics”, ANL/MCS-TM-301, 2008.

A. Tasoraand Anitescu, M., “A Fast NCP Solver for Large Rigid-Body Problems with Contacts, Friction, and Joint”, 2008.

D. N. Williams, Ananthakrishnan, R., Bernholdt, D. E., Bharathi, S., Brown, D., Chen, M., Chervenak, A. L., Cinquini, L., Drach, R., Foster, I. T., Fox, P., Fraser, D., Hankin, S., Jones, P., Kesselman, C., Middleton, D. E., Schwidder, J., Schweitzer, R., Schuler, R., Shoshani, A., Siebenlist, F., Sim, A., Strand, W. G., and Wilhelmi, N., “The Earth System Grid: Enabling Access to Multi-model Climate Simulation Data”, 2008.

P. Balaji, Feng, W., and Lin, H., “Semantics-based Distributed I/O with the ParaMEDIC Framework”, in High Performance Distributed Computing 2008 (HPDC 2008), Boston, MA, 2008.

F. Meyer, Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., Wilkening, J., and Edwards, R. A., “The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes”, BMC Bioinformatics, vol. 9, p. 386, 2008.

D. K. Kaushik, Smith, M., Wollaber, A., Smith, B. F., Siegel, A. R., and Yang, W. - S., “Enabling High Fidelity Neutron Transport Simulations on Petascle Architectures”, in Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, Portland, Oregon, 2008.

T. J. Tautges, Knoop, S. E., and Rickmeyer, T. J., “Local Topological Modification of Hexahedral Meshes. Part I: A Set of Dual-Based Operations”, in Centre d'ete Mathematiue de Recherche Avancee en Calcul Scientifique (CEMRACS'07) , Luminy, France , 2008.

L. Childers, Liming, L., and Foster, I. T., “Perspectives on Distributed Computing: Thirty People, Four User Types, and the Distributed Computing User Experience”, ANL/MCS/CI-31 , 2008.

D. N. Williams, Ananthakrishnan, R., Bernholdt, D. E., Bharathi, S., Brown, D., Chen, M., Chervenak, A. L., Cinquini, L., Drach, R., Foster, I. T., Fox, P., Hankin, S., Henson, V. E., Jones, P., Middleton, D. E., Schwidder, J., Schweitzer, R., Schuler, R., Shoshani, A., Siebenlist, F., Sim, A., Strand, W. G., Wilhelmi, N., and Su, M., “Data Management and Analysis for the Earth System Grid”, in Scientific Discovery through Advanced Computing (SciDAC 2008) , Seattle, WA, 2008.

P. F. Fischer, Lottes, J. W., Pointer, D., and Siegel, A. R., “Petascale Algorithms for Reactor Hydrodynamics”, in Journal of Physics: Conference Series, 2008, vol. 125.

P. Balaji, Feng, W., Archuleta, J., Lin, H., Kettimuthu, R., Thakur, R., and Ma, X., “Semantics-based Distributed I/O for mpiBLAST”, in High Performance Distributed Computing 2008 (HPDC 2008) , Boston, MA, 2008.

R. K. K. Aziz, Bartels, D., Best, A. A., DeJongh, M., Disz, T. L., Edwards, R. A., Formsma, K., Gerdes, S. Y., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R. L., Vassieva, O., Vonstein, V., Wilke, A., and Zagnitko, O. P., “The RAST Server: Rapid Annotations Using Subsystems Technology”, BMC Genomics , vol. 9, no. Feb. 8. 2008, p. 75 , 2008.

D. Buntinas, Bosilca, G., Graham, R. L., Vallee, G., and Watson, G. R., “A Scalable Tools Communication Infrastructure”, in 6th Annual Symposium on OSCAR and HPC Cluster Systems (OSCAR 2008) , Quebec, Canada , 2008.

M. Vilayannur, Lang, S., Ross, R. B., Klundt, R., and Ward, L., “Extending the POSIX I/O Interface: A Parallel File System Perspective”, ANL/MCS-TM-302, 2008.

B. Clifford, Foster, I. T., Voeckler, J., Wilde, M., and Zhao, Y., “Tracking Provenance in a Virtual Data Grid”, Concurrency and Computation: Practice and Experience, vol. 20, no. 5, pp. 565-575, 2008.

J. N. Lynessand Lottes, J. W., “Asymptotic Expansions for Oscillatory Integrals Using Inverse Functions”, BIT, vol. 49, no. 2, pp. 397-417, 2008.

R. Thakurand Gropp, W. D., “Test Suite for Evaluating Performance of Multithreaded MPI Communication”, Parallel Computing, vol. 35, no. 12, pp. 608-617, 2008.

J. Utke, Hascoet, L., Hill, C., Hovland, P. D., and Naumann, U., “Toward Adjoinable MPI”, presented at the 08/2008, 2008.

R. B. Ross, Latham, R., Gropp, W. D., Lusk, E. L., and Thakur, R., “Processing MPI Datatypes Outside MPI”, in 16th EuroPVM/MPI Users, Lecture Notes in Computer Science, Springer, Espoo, Finland, 2009, 2008.

E. L. Luskand Chan, A., “Early Experiments with the OpenMP/MPI Hybrid Programming Model”, in International Workshop on OpenMP (IWOMP 2008), Lecture Notes on Computer Science, Springer, West Lafayette, IN, 2008, 2008.

K. Iskra, Romein, J. W., Yoshii, K., and Beckman, P. H., “ZOID: I/O-Forwarding Infrastructure for Petascale Architectures”, in Proc. 13th ACM SIGPLAN Principles and Practice of Parallel Programming, Salt Lake City, 2008.

E. T. Ong, Larson, J. W., Norris, B., Tobis, M., Steder, M., and Jacob, R. L., “A Multilingual Programming Model for Coupled Systems”, IJMCE, DOI: 10.1615/IntJMultCompEng.v6.i1.40, vol. 6, no. 1, pp. 39-51, 2008.

P. Balaji, Chan, A., Gropp, W. D., Thakur, R., and Lusk, E. L., “Non-Data-Communication Overheads in MPI: Analysis on Blue Gene/P”, in 15th EuroPVM/MPI Users, Dublin, Ireland, Best Paper Award, 2008.

P. Balaji, Feng, W., Lin, H., Archuleta, J., Matsuoka, S., Warren, A., Setubal, J., Lusk, E. L., Thakur, R., Foster, I. T., Katz, D. S., Jha, S., Shinpaugh, K., Coghlan, S. M., and Reed, D., “Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer”, in International Supercomputing Conference, Outstanding Paper Award, Dresden, Germany, 2008.

N. L. Desai, Bradshaw, R., and Lusk, E. L., “Disparity: Scalable Anomaly Detection for Clusters”, in 37th International Conference on Parallel Processing - Workshops, Portland, OR, 2008.

K. Schmitt, Anitescu, M., and Negrut, D., “Efficient Sampling for Spatial Uncertainty Quantification in Multibody System Dynamics Applications”, Int. J. Numer. Meth. Engng, vol. 80, no. 5, pp. 537-564, 2008.

P. H. Carns, Lang, S., Ross, R. B., Vilayannur, M., Kunkel, J., and Ludwig, T., “Small-File Access in Parallel File Systems”, in Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing, 2008.

B. I. Gavrea, Anitescu, M., and Potra, F. A., “Convergence of a Class of Semi-implicit Time-stepping Schemes for Nonsmooth Rigid Multibody Dynamics”, SIAM J. on Optimization, vol. 19, no. 2, pp. 969-1001, 2008.

D. Negrut, Anitescu, M., El-Azab, A., and Zapol, P., “Quasicontinuum-like Reduction of DFT Calculations of Nanostructures”, J. Nanosci. Nanotechnol., vol. 8, pp. 3729-3740, 2008.

M. Kumar, Chaube, V., Balaji, P., Feng, W., and Jin, H. - W., “Making a Case for Proactive Flow Control in Optical Circuit-Switched Networks”, presented at the 12/2008, 2008.

F. Siebenlist, Ananthakrishnan, R., Bernholdt, D. E., Cinquini, L., Foster, I. T., Middleton, D. E., Miller, N., and Williams, D. N., “Enhancing the Earth System Grid Security Infrastructure through Single Sign-On and Autoprovisioning”, in Proceedings of the 5th Grid Computing Environments Workshop, Portland, Oregon, USA, 2008.

L. Li, Norris, B., Johansson, H., McInnes, L. Curfman, and Ray, J., “Component Infrastructure for Managing Performance Data and Runtime Adaptation of Parallel Applications”, in PARA 2008, Trondheim, Norway, 2008.

R. Gupta, Naik, H., and Beckman, P. H., “Understanding Checkpointing Overheads on Massive-Scale Systems: Analysis of the IBM Blue Gene/P System”, International Journal of High Performance Computing Applications, 2008.

J. C. Silverstein, Walsh, C., Dech, F., Olson, E., Papka, M. E., Parsad, N., and Stevens, R. L., “Multi-Parallel Open Technology to Enable Collaborative Volume Visualization”, in MMCR16, Long Beach, CA, USA, 2008.

T. J. Tautgesand Caceres, A., “Scalable Parallel Solution Coupling for Multi-Physics Reactor Simulation”, in Journal of Physics: Conference Series, 2008.

H. Lin, Balaji, P., Poole, R., Sosa, C., Ma, X., and Feng, W., “Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture”, presented at the 11/2008, 2008.

P. Balaji, Buntinas, D., Goodell, D., Gropp, W. D., Kumar, S., Lusk, E. L., Thakur, R., and Traff, J. L., “MPI on a Million Processors”, in 16th EuroPVM/MPI Users, Lecture Notes in Computer Science, Springer, Espoo, Finland, 2009, 2008.

Q. Li, Ferris, M. C., and Munson, T. S., “Linear Algebra Enhancements to the PATH Solver”, 2008.

D. Giannakis, Rosner, R., and Fischer, P. F., “Instabilities in Free-Surface Hartmann Flow at Low Magnetic Prandtl Numbers”, Journal of Fluid Mechanics, vol. 636, pp. 217-277, 2008.

O. Hernandez, Chapman, B., Bui, V. Thi, and Kufrin, R., “Open-Source Software Support for the OpenMP Runtime API for Profiling”, in Proceedings of the 2009 International Conference on Parallel Processing Workshops, 2008.

2007

P. F. Fischer, Lottes, J. W., Siegel, A. R., and Palmiotti, G., “Large Eddy Simulation of Wire-Wrapped Fuel Pins: Hydrodynamics of a Single Pin”, 2007.

S. Park, “Weights and Acceptance Ratios in Generalized Ensemble Simulations”, 2007.

D. Buntinas, Mercier, G., and Gropp, W. D., “Implementation and Evaluation of Shared-Memory Communication and Synchronization Operations in MPICH2 using the Nemesis Communication Subsystem”, 2007.

Z. Insepov, Bazhirov, T., Norman, G. E., and Stegailov, V. V., “Computer Simulation of Bubble Formation”, in Joint International Topical Meeting on Mathematics & Computations and Supercomputing in Nuclear Applications (M&C + SNA 2007) , Monterey, CA, 2007.

L. Wosand Fitelson, B., “The Automation of Sound Reasoning and Successful Proof Finding”, in Companion to Philosophical Logic, Oxford, UK: Blackwell Publishing Ltd., 2007.

D. A. Karpeev, Aranson, I. S., Tsimring, L. S., and Kaper, H. G., “Interactions of Semiflexible Filaments and Molecular Motors”, Phys. Rev. E , vol. 76, no. (Pt. 1) , p. 051905 , 2007.

W. D. Groppand Thakur, R., “Revealing the Performance of MPI RMA Implementations”, 2007.

R. Thakurand Gropp, W. D., “Test Suite for Evaluating Performance of MPI Implementations that Support MPI THREAD MULTIPLE”, in EuroPVM/MPI 2007 , Paris, France , 2007, vol. 35 , pp. 608-617 .

Z. Insepov, “New Nanopumping Effects with Carbon Nanotubes”, 2007.

H. G. Kaper, Wang, S., and Yari, M., “Formation and Persistence of Spatiotemporal Turing Patterns”, 2007.

M. R. Paul, Einarsson, M. I., Fischer, P. F., and Cross, M. C., “Extensive Chaos in Rayleigh-Benard Convection”, 2007.

“Modeling without Categorical Variables: A Mixed-Integer Nonlinear Program for the Optimization of Thermal Insulation”, 2007.

J. Jungand Hassanein, A., “Three-Phase CFD Analytical Modeling of Blood Flow”, 2007.

R. Latham, Gropp, W. D., Ross, R. B., and Thakur, R., “Extending the MPI-2 Generalized Request Interface”, 2007.

B. Norris, Hartono, A., and Gropp, W. D., Annotations for Productivity and Performance Portability. 2007.

J. Bresnahan, Link, M., Kettimuthu, R., Fraser, D., and Foster, I. T., “GridFTP Pipelining”, in TeraGrid '07 , Madison, WI , 2007.

W. R. Elwasif, Norris, B., Allan, B. A., and Armstrong, R., “Bocca: A Development Environment for HPC Components”, in Joint HPC-GECO/CompFrame'07 Workshop , Montreal, Canada, 2007.

I. Konkashbaev, Fischer, P. F., Hassanein, A., and Mokhov, N. V., “Enhancement of Heat Removal Using Concave Liquid Metal Targets for High-Power Accelerators”, in Particle Accelerator Conference (PAC07) , Albuquerque, NM , 2007.

R. Thakurand Gropp, W. D., “Open Issues in MPI Implementation”, in 12th Asia-Pacific Computer Systems Architecture Conference (ACSAC 2007) , Seoul, Korea , 2007.

T. Peterka, Kooima, R. L., Sandin, D. J., Johnson, A., Leigh, J., and DeFanti, T. A., “Advances in the Dynallax Solid-State Dynamic Parallax Barrier Autostereoscopic Visualization Display System”, IEEE Trans. Vis. Comput. Graphics , vol. 14 , no. 13 , pp. 487-499 , 2007.

A. Rodriguez, Bompada, T., Shah, P. K., and Maltsev, N., “Evolutionary Analysis of Enzymes Using Chisel”, Bioinform. , vol. 23 , pp. 2961-2968 , 2007.

J. N. Lyness, “Numerical Evaluation of a Fixed-Amplitude Variable-Phase Integral”, Numerical Algorithms , vol. 49, pp. 235-249 , 2007.

C. Rabiti, Smith, M. A., Palmiotti, G., Caceres, A., Siegel, A. R., Tautges, T. J., Lottes, J. W., Fischer, P. F., and Kaushik, D., “Status Report on SHARP Coupling Framework”, ANL-AFCI-215, 2007.

G. Narayanaswamy, Balaji, P., and Feng, W., “An Analysis of 10-Gigabit Ethernet Protocol Stacks in Multicore Environments”, in 15th Annual IEEE Symposium on High-Performance Interconnects , Palo Alto, CA , 2007.

M. S. Min, Fischer, P. F., and Chae, Y., “Particle Accelerator Conference (PAC07) ”, in Particle Accelerator Conference (PAC07) , Albuquerque, NM , 2007.

J. P. Bardhan, Altman, J. P., White, M. D., and Tidor, B., “Efficient Optimization of Electrostatic Interactions between Biomolecules”, in 46th IEEE Conference on Decision and Control , New Orleans, LA , 2007.

J. N. Lynessand Joe, S., “Determination of the Rank of an Integration Lattice”, BIT , vol. 48, no. 1 , pp. 79-93 , 2007.

J. W. Larsonand Norris, B., “Component Specification for Parallel Coupling Infrastructure”, in International Conference on Computational Science and Its Application (ICCSA 2007) , Malaysia , 2007.

J. Shin, “Introducing Control Flow into Vectorized Code”, in 16th International Conference on Parallel Architectures and Compilation Techniques PACT-2007 , Brasov, Romania, 2007.

F. Loth, Fischer, P. F., and Bassiouny, H. S., “Blood Flow in End-to-Side Anastomoses”, Annu. Rev. Fluid Mech. , vol. 40, no. 2008 , pp. 367-393 , 2007.

Z. Insepov, Hassanein, A., Norem, J., and Swenson, D. R., “Advanced Surface Polishing using Gas Cluster Ion Beams”, Nucl. Instrum. Methods Phys. Res. B , vol. 261 , no. 1-2, pp. 664-668 , 2007.

J. P. Allain, Nieto, M., Hendricks, M., Harilal, S. S., and Hassanein, A., “Debris and Radiation-Induced Damage Effects on EUV Nanolithography Source Collector Mirror Optics Performance”, in Society of Photo-Optical Instrumentation Engineers - Europe Optics and Optoelectronics , Prague, Czech Republic , 2007.

Z. Insepov, “Surface Erosion and Modification by Energetic Ions”, in 18th International Conference on Ion-Surface Interactions (ISI-2007) , Zvenigorod, Russia , 2007.

P. Balaji, Bhagvat, S., Panda, D. K., Thakur, R., and Gropp, W. D., “Advanced Flow-Control Mechanisms for the Sockets Direct Protocol Over InfiniBand”, in 2007 International Conference on Parallel Processing ICPP 2007 , XiAn, China , 2007.

“IMPACT: A Facility for Studying the Interaction of Low-Energy Intense Charged Particle Beams with Dynamic Heterogeneous Surfaces”, Rev. Sci. Instrum. , vol. 78 , p. 113105 , 2007.

J. Shin, “SIMD Programming by Expansion”, in 40th Annual IEEE/ACM International Symposium on Microarchitecture (MICRO 40) , Chicago, IL , 2007.

L. Curfman McInnes, Dahlgren, T., Nieplocha, J., Bernholdt, D. E., Allan, B. A., Armstrong, R., Chavarria, D., Elwasif, W. R., Gorton, I., Kenney, J., Krishan, M., Malony, A. D., Norris, B., Ray, J., and Shende, S., “Research Initiatives for Plug-and-Play Scientific Computing”, in Scientific Discovery through Advanced Computing (SciDAC 2007) , Boston, MA , 2007.

S. Pervez, Gopalakrishnan, G., Kirby, G., Thakur, R., and Gropp, W. D., “Formal Methods Applied to HPC Software Design: A Case Study of Locking Based on MPI One-Sided Communication”. 2007.

M. S. Min, Chin, Y. H., Fischer, P. F., Chae, Y., Chul, Y., and Kim, K. J., “Fourier Spectral Simulations for Wake Fields in Conducting Cavities”, in Particle Accelerator Conference (PAC07) , Albuquerque, NM, 2007.

Y. Zhao, Hategan, M., Clifford, B., Foster, I. T., von Laszewski, G., Nefedova, V., Raicu, I., Stef-Praun, I., and Wilde, M., “Swift: Fast, Reliable, Loosely Coupled Parallel Computation”, in IEEE 2007 International Conference on Web Services (ICWS) , Salt Lake City, UT, 2007.

Z. Insepov, Hassanein, A., Bazhirov, T., Norman, T. T., and Stegailov, V. V., “Molecular Dynamics Simulations of Bubble Formation and Cavitation in Liquid Metals”, in 17th ANS Topical Meeting on the Technology of Fusion Energy , Albuquerque, NM, 2007.

D. Sulakhe, Rodriguez, A., Wilde, M., Foster, I. T., and Maltsev, N., “Interoperability of GADU in Using Heterogeneous Grid Resources for Bioinformatics Applications”, IEEE Trans. Inf. Technol. Biomed. , vol. 12 , no. 2 , pp. 241-246, 2007.

S. Oster, Langella, S., Hastings, S., Ervin, S., Madduri, R., Phillips, R., Kurc, T., Siebenlist, F., Covitz, P., Shanbhag, K., Foster, I. T., and Saltz, J., “caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research”, J. Am. Inform. Assoc. , vol. 15 , no. 2, pp. 138-149 , 2007.

J. Bresnahan, Kettimuthu, R., Link, M., and Foster, I. T., “Harnessing Multicore Processors for High-Speed Secure Transfer”, 26th Annual IEEE Conference on Computer Communications (IEEE INFOCOM 2007) . Anchorage, AK , 2007.

S. Pervez, Gopalakrishnan, G., Kirby, R. M., Palmer, R., Thakur, R., and Gropp, W. D., “Practical Model-Checking Mehtod for Verifying Correctness of MPI Programs”. 2007.

E. T. Ong, Larson, J. W., Norris, B., Jacob, R. L., Tobis, M., and Steder, M., “Multilingual Interfaces for Parallel Coupling in Multiphysics and Multiscale Systems”, in International Conference on Computational Science (ICCS 2007) , Beijing, China, 2007.

A. Lyonsand Utke, J., “On the Practical Exploitation of Scarsity”, in 5th International Conference on Automatic Differentiation (AD 2008) , Bonn, Germany , 2007, vol. 64 , pp. 103-114 .

J. J. More', Munson, T. S., and Sarich, J., “Optimization in SciDAC Applications”, in Scientific Discovery through Advanced Computing (SciDAC 2007) , Boston, MA , 2007, vol. 78 , p. 012052 .

M. S. Min, Fischer, P. F., and Chae, Y., “Wake Fields in TESLA Accelerating Structures: Spectral Element Discontinuous Galerkin (SEDG) Simulations”, in 13th International Workshop on RF Superconductivity (SRF 2007) , Beijing, China , 2007.

L. Yang, Liu, C., Schopf, J. M., and Foster, I. T., “Anomaly Detection and Diagnosis in Grid Environments”, in International Conference for High Performance Computing, Networking, Storage, and Analysis (SC07) , Reno, NV, 2007.

J. Bresnahan, Link, M., Khanna, G., Imani, Z., Kettimuthu, R., and Foster, I. T., “Globus GridFTP: What’s New in 2007”, in GridNets 2007 1st International Conference on Networks for Grid Applications , Lyon, France , 2007.

J. Shin, Malusare, P., and Hovland, P. D., “Design and Implementation of a Context-Sensitive, Flow-Sensitive Activity Analysis Algorithm for Automatic Differentiation”, in 5th International Conference on Automatic Differentiation (AD 2008) , Bonn, Germany, 2007, vol. 64 , pp. 115-125.

P. Balaji, Feng, W., Archuleta, J., Lin, H., Kettimuthu, R., and Thakur, R., “ParaMEDIC: Parallel Metadata Environment for Distributed I/O and Computing”, in 13th ACM SIGPLAN Principles and Practice of Parallel Programming (PPoPP 2008) , Salt Lake City, UT , 2007.

M. Tobis, Steder, M., Jacob, R. L., Pierrehumbert, R. T., Larson, J. W., and Ong, E. T., “PyMCT and PyCPL: Refactoring the Community Climate System Model”. 2007.

J. P. Allain, Nieto, M., Hendricks, M., Hassanein, A., Grantham, S., and Bakshi, V., “Energetic and Thermal Sn Interactions and their Effect on EUVL Source Collector Mirror Lifetime at High Temperatures”, in 17th ANS Topical Meeting on the Technology of Fusion Energy , Albuquerque, NM, 2007.

S. Alam, Barrett, R., Bast, M., Fahey, M. R., Kuehn, J., McCurdy, C., Rogers, J., Roth, P. C., Vetter, J. S., Worley, P. H., and Yu, W., “Early Evaluation of IBM BlueGene/P”, presented at the 12/2007, 2007.

H. S. Abdel-khalik, Hovland, P. D., Lyons, A., Stover, T. E., and Utke, J., “A Low Rank Approach to Automatic Differentiation”, in 5th International Conference on Automatic Differentiation (AD 2008), Bonn, Germany , 2007, vol. 64 , pp. 55-65 .

J. L. Traff, Gropp, W. D., and Thakur, R., “Self-Consistent MPI Performance Requirements”, in EuroPVM/MPI 2007 , Paris, France, 2007, vol. 4757 , pp. 36-45 .

D. Dechow, Norris, B., and Amundson, J. F., “The Common Component Architecture for Particle Accelerator Simulations”, in OOPSLA 2007 , Montreal, Canada , 2007, pp. 111-120 .

I. Charpentier, Dal Cappello, C., and Utke, J., “Efficient Higher-Order Derivatives of the Hypergeometric Function”, in 5th International Conference on Automatic Differentiation (AD 2008) , Bonn, Germany, 2007, vol. 64, pp. 127-137 .

K. Keahey, Freeman, T., Lauret, J., and Olson, D., “Virtual Workspaces for Scientific Applications”, in Scientific Discovery through Advanced Computing (SciDAC 2007) , Boston, MA, 2007, vol. 78, p. 012038 .

C. Zhang, Knepley, M. G., Yuen, D. A., and Shi, Y., “Two New Approaches in Solving the Nonlinear Shallow Water Equations for Tsunamis”, Phys. Earth Planet. Inter. , 2007.

C. Chevalierand Safro, I., “Comparison of Coarsening Schemes for Multilevel Graph Partitioning”, presented at the 12/2007, 2007.

M. Hereld, Stevens, R. L., van Drongelen, W., and Lee, H. C., “Framework for Interactive Million-Neuron Simulation”, Journal of Clinical Neurophysiology, vol. 24, no. 2, pp. 189-196, 2007.

M. Anitescu, Palmiotti, G., and Yang, W. - S., “Stochastic Finite-Element Approximation of the Parametric Dependence of Eigenvalue Problem Solution”, in Proc. 2007 Mathematics, Computation and Supercomputing in Nuclear Applicati, Monterey, CA, 2007.

I. Alderman, Altunay, M., Ananthakrishnan, R., Bester, J., Chadwick, K., Ciaschini, V., Demchenko, Y., Ferraro, A., Forti, A., Garzoglio, G., Groep, D., Hesselroth, T. D., Hover, J., Koeroo, O., La Joie, C., Levshina, T., Miller, Z., Packard, J., Sagehaug, H., Sergeev, V., Sfiligoi, I., Sharma, N., Siebenlist, F., Venturi, V., and Weigand, J., “Definition and Implementation of a SAML-XACML Profile for Authorization Interoperability across Grid Middleware Implementations in OSG and EGEE”, Journal of Grid Computing, vol. 7, no. 3, pp. 297-307, 2007.

A. Hartono, Norris, B., and Sadayappan, P., “Annotation-Based Empirical Performance Tuning Using Orio”, presented at the 12/2007, 2007.

A. T. Wu, Swenson, D. R., Kneisel, P., Wu, G., Insepov, Z., Saunders, J., Manus, R., Golden, B., Castagnola, S., Sommer, W., Harms, E., Khabiboulline, T., Murayi, W., and Edwards, H., “Investigation of Surface Treatments of Niobium Flat Samples and SRF Cavities by Gas Cluster Ion Beam Technique for Particle Accelerators”, 2007.

D. R. Swenson, Wu, A. T., Degenkolb, E., and Insepov, Z., “Gas Cluster Ion Beam Surface Treatments for Reducing Field Emission and Breakdown of Electrodes and SRF Cavities”, Nuclear Instruments and Methods in Physics Research B, vol. 261, pp. 630-633, 2007.

K. Abhishek, Leyffer, S., and Linderoth, J. T., “FilMINT: An Outer-Approximation-Based Solver for Nonlinear Mixed Integer Programs”, 2007.

E. M. Constantinescu, “On the Order of General Linear Methods”, 2007.

T. Peterka, Ross, R. B., Yu, H., Ma, K. - L., Kendall, W., and Huang, J., “Assessing and Improving Large Scale Parallel Volume Rendering on the IBM Blue Gene/P”, presented at the 12/2007, 2007.

A. Tasora, Negrut, D., and Anitescu, M., “Large-Scale Parallel Multibody Dynamics with Frictional Contact on the Graphical Processing Unit”, Proceedings of the Institution of Mechanical Engineers, Part K: Journal of Multi-body Dynamics, vol. 222, no. 4, pp. 315-326, 2007.

R. Kettimuthu, Wantao, L., Siebenlist, F., and Foster, I. T., “Communicating Security Assertions over the GridFTP Control Channel”, presented at the 12/2007, 2007.

H. G. Kaper, Wang, S., and Yari, M., “Dynamical Transitions of Turing Patterns”, 2007.

K. Schmitt, Madsen, J., Anitescu, M., and Negrut, D., “A Gaussian Process-Based Approach for Handling Uncertainty in Vehicle Dynamics Simulation”, in ASME Conference Proceedings, ASME 2008 International Mechanical Engineering Congress and Exposition, 2007.

R. Fletcher, Leyffer, S., and Toint, P., “A Brief History of Filter Methods”, SIAG/OPT Views-and-News, vol. 18, no. 1, pp. 2-12, 2007.

P. Balaji, Bhagvat, S., Thakur, R., and Panda, D. K., “Sockets Direct Protocol for Hybrid Network Stacks: A Case Study with iWARP over 10G Ethernet.”, presented at the 12/2007, 2007.

X. Shiand Stevens, R. L., “SWARM: A Scientific Workflow for Supporting Bayesian Approaches to Improve Metabolic Models”, presented at the 12/2007, 2007.

M. Anitescuand Birge, J. R., “Convergence of Stochastic Average Approximation for Stochastic Optimization Problems with Mixed Expectation and Per-Scenario Constraints”, 2007.

D. W. Cranstonand Hovland, P. D., “Colorings for Efficient Derivative Computation on Grids with Periodic Boundaries”, 2007.

J. N. Brooksand Allain, J. P., “Particle Deposition and Optical Response of ITER Motional Stark Effect Diagnostic First Mirrors”, Nucl. Fusion, vol. 48, p. 045003 (9 pp.), 2007.

A. Tasora, Negrut, D., and Anitescu, M., “A GPU-Based Implementation of a Core Convex Complementarity Approach for Simulating Rigid Body Dynamics with Frictional Contact”, presented at the 12/2007, 2007.

N. L. Desai, Bradshaw, R., Lueninghoener, C., Cherry, A., Coghlan, S. M., and Scullin, W., “Petascale System Management Experiences”, in Proceedings of the 22nd Large Installation System Administration Conference, San Diego, CA, 2007.

I. Raicu, Zhang, Z., Wilde, M., Foster, I. T., Beckman, P. H., Iskra, K., and Clifford, B., “Toward Loosely Coupled Programming on Petascale Systems”, in Proceedings of the 2008 ACM/IEEE conference on Supercomputing, Austin, Texas, 2007.

M. Hereld, Papka, M. E., and Uram, T. D., “Collaboration as a Second Thought”, presented at the 12/2007, 2007.

Z. Insepov, Terasawa, M., and Takayama, K., “Surface Erosion and Modification by Highly Charged Ions”, 2007.

S. Vakkalanka, DeLisi, M., Gopalakrishnan, G., Kirby, R. M., Thakur, R., and Gropp, W. D., “Implementing Efficient Dynamic Formal Verification Methods for MPI Programs”, presented at the 12/2007, 2007.

S. Sharma, Vakkalanka, S., Gopalakrishnan, G., Kirby, R. M., Thakur, R., and Gropp, W. D., “A Formal Approach to Detect Functionally Irrelevant Barriers in MPI Programs”, presented at the 12/2007, 2007.

F. Meyer, Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Stevens, R. L., Wilke, A., Wilkening, J., and Edwards, R. A., “The Metagenomics RAST Server - A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes”, 2007.

G. Narayanaswamy, Balaji, P., and Feng, W., “Impact of Network Sharing in Multi-core Architectures”, presented at the 12/2007, 2007.

T. Peterka, Ross, R. B., Yu, H., Ma, K. - L., and Kooima, R. L., “Coupling Massively Parallel Volume Rendering with Autostereoscopic 3D Display Environments”, presented at the 12/2007, 2007.

J. L. Traff, Ripke, A., Siebert, C., Balaji, P., Thakur, R., and Gropp, W. D., “A Simple, Pipelined Algorithm for Large, Irregular All-Gather Problems”, presented at the 12/2007, 2007.

P. Balaji, Buntinas, D., Goodell, D., Gropp, W. D., and Thakur, R., “Toward Efficient Support for Multithreaded MPI Communication”, presented at the 12/2007, 2007.

W. D. Gropp, Kimpe, D., Ross, R. B., Thakur, R., and Traff, J. L., “Self-Consistent MPI-IO Performance Requirements and Expectations”, presented at the 12/2007, 2007.

N. L. Desai, Lusk, E. L., Cherry, A., and Voran, T., “The Computer as Software Component: A Mechanism for Developing and Testing Resource Management Software”, in Cluster Computing 2007, Austin, TX, 2007.

J. M. Dennis, Jacob, R. L., Vertenstein, M., Craig, T., and Loy, R., “Toward an Ultra-High Resolution Community Climate System Model for the BlueGene Platform”, in Journal of Physics: Conference Series, 2007.

J. W. Larson, “Ten Organising Principles for Coupling in Multiphysics and Multiscale Models”, ANZIAM, vol. 48, pp. C1090-C1111, 2007.

P. F. Fischer, Leaf, G. K., and Restrepo, J. M., “Influence of Torque on the Lift and Drag of a Particle in an Oscillatory Flow”, 2007.

J. P. Bardhan, “Interpreting the Coulomb-Field Approximation for Generalized-Born Electrostatics Using Boundary-Integral Equation Theory.”, J. Chem. Phys., 2007.

A. Chan, Balaji, P., Gropp, W. D., and Thakur, R., “Communication Analysis of Parallel 3D FFT for Flat Cartesian Meshes on Large Blue Gene Systems”, presented at the 12/2007, 2007.

D. K. Kaushik, Gropp, W. D., Minkoff, M., and Smith, B. F., “Improving the performance of tensor matrix vector multiplication in cumulative reaction probability based quantum chemistry codes”, in Proceedings of the 15th international conference on High performance computing, Bangalore, India, 2007.

K. A. Huck, Hernandez, O., Bui, V. Thi, Chandrasekaran, S., Chapman, B., Malony, A. D., McInnes, L. Curfman, and Norris, B., “Capturing Performance Knowledge for Automated Analysis”, presented at the 12/2007, 2007.

S. Park, Lau, A. Y., and Roux, B., “Computing Conformational Free Energy by Deactivated Morphing”, 2007.

J. P. Bardhan, “Numerical Solution of Boundary Integral Equations for Molecular Electrostatics”, 2007.

J. R. Cary, Chandy, J. A., Cohen, R. H., Krasheninnikov, S., McCune, D. C., Estep, D. J., Larson, J. W., Malony, A. D., Pankin, A., Worley, P. H., Carlsson, J. A., Hakim, A. H., Hamill, P., Kruger, S., Miah, M., Muzsala, S., Pletzer, A., Shasharina, S., Wade-Stein, D., Wang, N., Balay, S., McInnes, L. Curfman, Zhang, H., Casper, T., Diachin, L. F., Epperly, T., Indireshkumar, T. D., Stotler, D., and Pigarov, A. Yu, “First Results from Core-Edge Parallel Composition in the FACETS Project”, presented at the 12/2007, 2007.

P. Spentzouris, Cary, J. R., McInnes, L. Curfman, Mori, W., Ng, C., Ng, E., and Ryne, R., “Community Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies”, presented at the 12/2007, 2007.

P. Gu, Wang, J., and Ross, R. B., “Bridging the Gap Between Parallel File Systems and Local File Systems: A Case Study with PVFS”, presented at the 12/2007, 2007.

J. F. Amundson, Dechow, D., McInnes, L. Curfman, Norris, B., Spentzouris, P., and Stoltz, P., “Multiscale, Multiphysics Beam Dynamics Framework Design and Applications”, presented at the 12/2007, 2007.

A. Baranovski, Beattie, K., Bharathi, S., Boverhof, J., Bresnahan, J., Chervenak, A. L., Foster, I. T., Freeman, T., Gunter, D., Keahey, K., Kesselman, C., Kettimuthu, R., Leroy, N., Link, M., Livny, M., Madduri, R., Oleynik, G., Pearlman, L., Schuler, R., and Tierney, B., “Enabling Petascale Science: Data Management, Troubleshooting and Scalable Science Services”, presented at the 12/2007, 2007.

N. L. Desai, Lusk, E. L., Buettner, D., Cherry, A., and Voran, T., “Simulating Failures on Large-Scale Systems”, in 37th International Conference on Parallel Processing - Workshops, IEEE, 2007.

M. Hereld, Olson, E., Papka, M. E., and Uram, T. D., “Streaming Visualization for Collaborative Environments”, Journal of Physics: Conference Series, vol. 125, no. 1, 2007.

R. A. Edwards, “The Smallest Cells Pose the Biggest Problems: High Performance Computing and the Analysis of Metagenome Sequence Data”, presented at the 12/2007, 2007.

P. Balaji, Feng, W., Bhagvat, S., Panda, D. K., Thakur, R., and Gropp, W. D., “Analyzing the Impact of Supporting Out-of-Order Communication on In-order Performance with iWARP”, in IEEE/ACM International Conference for High Performance Computing, Networking, Storage and Analysis (SC), Reno, Nevada, 2007.

A. Chan, Gropp, W. D., and Lusk, E. L., “An Efficient Format for Nearly Constant-Time Access to Arbitrary Time Intervals in Large Trace Files”, Sci. Programming , vol. 16 , no. 2-3 , pp. 155-165, 2007.

R. Kettimuthu, Wantao, L., Link, J. M., and Bresnahan, J., “A GridFTP Transport Driver for Globus XIO”, presented at the 12/2007, 2007.

V. Thi Bui, Norris, B., Huck, K. A., McInnes, L. Curfman, Li, L., Hernandez, O., and Chapman, B., “A Component Infrastructure for Performance and Power Modeling of Parallel Scientific Applications”, presented at the 12/2007, 2007.

W. M. Washington, Drake, J. B., Buja, L., Anderson, D., Bader, D. C., Dickinson, R., Erickson, D., Gent, P., Ghan, S., Jones, P., and Jacob, R. L., “The Use of the Climate-Science Computational End Station (CCES) Development and Grand Challenge Team for the Next IPCC Assessment: An Operational Plan”, presented at the 12/2007, 2007.

T. Dahlgren, Bernholdt, D. E., and McInnes, L. Curfman, “Gaining Confidence in Scientific Applications through Executable Interface Contracts”, presented at the 12/2007, 2007.

G. R. Gao, Sterling, T., Stevens, R. L., Hereld, M., and Zhu, W., “ParalleX: A Study of a New Parallel Computation Model”, in IEEE International Parallel and Distributed Processing Symposium, Rhodes Island, Greece, 2007.

J. J. More'and Wild, S. M., “Benchmarking Derivative-Free Optimization Algorithms”, SIAM J. Optimization , vol. 20 , no. 1 , pp. 172-191 , 2007.

L. Hascoet, Utke, J., and Naumann, U., “Cheaper Adjoints by Reversing Address Computations”, Sci. Programming , vol. 16, pp. 81-92 , 2007.

S. Park, “Comparison of the Serial and Parallel Algorithms of Generalized Ensemble Simulations: An Analytical Approach”, Phys. Rev. E , vol. 77, p. 016709 (Pt. 2) , 2007.

R. T. Fisher, Kadanoff, L., Lamb, D. Q., Dubey, A., Plewa, T., Calder, A. C., Cattaneo, F., Constantin, P., Foster, I. T., Papka, M. E., Abarzhi, S. I., Asida, S. M., Rich, P. M., Glendenin, C. C., Antypas, K., Sheeler, D. J., Reid, L. B., Gallagher, B., and Needham, S. G., “Terascale Turbulence Computation on BG/L Using the FLASH3 Code”, IBM Journal of Research and Development, vol. 52, no. 1, pp. 127 - 136, 2007.

L. K. McNeil, Reich, C., Aziz, R. K. K., Bartels, D., Cohoon, M. P., Disz, T. L., Edwards, R. A., Gerdes, S. Y., Hwang, K., Kubal, M., Margaryan, G. R., Meyer, F., Mihalo, W., Olsen, G. J., Olson, R., Osterman, A. L., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Rodinov, D. A., Shi, X., Vassieva, O., Vonstein, V., Zagnitko, O. P., Xia, F., Zinner, J. F., Overbeek, R. A., and Stevens, R. L., “The National Microbial Pathogen Database Resource (NMPDR): A Genomics Platform Based on Subsystem Annotation”, Nucleic Acids Res, vol. 35, pp. 347-353, 2007.

C. G. Petra, Gavrea, B. I., Anitescu, M., and Potra, F. A., “A Computational Study of the Use of an Optimization-Based Method for Simulating Large Multibody Systems”, 2007.

J. C. Silverstein, Walsh, C., Dech, F., Olson, E., Papka, M. E., Parsad, N., and Stevens, R. L., “Immersive Virtual Anatomy course Using a Cluster of Volume Visualization Machines and Passive Stereo”, in Medicine Meets Virtual Reality 15 (MMVR15) Conference,, Long Beach, CA, 2007.

T. Freemanand Keahey, K., “Flying Low: Simple Leases with Workspace Pilot”, presented at the 12/2007, 2007.

T. Leeand Leaf, G. K., “Eulerian Description of High-Order Bounce-Back Scheme for Lattice Boltzmann Equation with Curved Boundary”, 2007.

R. B. Ross, Peterka, T., Shen, H. - W., Hong, Y., Ma, K. - L., Yu, H., and Moreland, K., “Visualization and Parallel I/O at Extreme Scale”, presented at the 12/2007, 2007.

M. Anitescuand Park, S., “Short Communication: A Linear Programming Approach for the Least-Squares Protein Morphing Problem”, 2007.

N. L. Desai, Balaji, P., Sadayappan, P., and Islam, M., “Are Nonblocking Networks Really Needed for High-End-Computing Workloads?”, presented at the 12/2007, 2007.

K. Keaheyand Freeman, T., “Contextualization: Providing One-Click Virtual Clusters”, presented at the 12/2007, 2007.

J. Chame, Chen, C., Dongarra, J., Hall, M. W., Hollingsworth, J. K., Hovland, P. D., Moore, S., Seymour, K., Shin, J., Tiwari, A., Williams, S., You, H., and Bailey, D. H., “PERI Auto-Tuning”, presented at the 12/2007, 2007.

A. Bhateleand Kale, L., “Benefits of Topology Aware Mapping for Mesh Interconnects”, 2007.

S. Leyfferand Munson, T. S., “A Globally Convergent Filter Method for MPECs”, 2007.

M. Islam, Balaji, P., Sabin, G., and Sadayappan, P., “Analyzing and Minimizing the Impact of Opportunity Cost in QoS-aware Job Scheduling”, in Proceedings of the 2007 International Conference on Parallel Processing, Xi, 2007.

W. D. Gropp, Kaushik, D. K., Minkoff, M., and Smith, B. F., “Improving the Performance of Tensor Matrix Vector Multiplication in Quantum Chemistry Codes”, 2007.

E. G. Boman, Bozdag, D., Catalyurek, U. V., Devine, K. D., Gebremedhin, A. H., Hovland, P. D., and Pothen, A., “Combinatorial Algorithms for Computational Science and Engineering”, presented at the 12/2007, 2007.

B. Sotomayor, Keahey, K., and Foster, I. T., “Combining Batch Execution and Leasing Using Virtual Machines”, presented at the 12/2007, 2007.

2006

B. Q. Deng, Allain, J. P., Luo, Z. M., Peng, L. L., and Yan, J. C., “Near-Surface Bipartition Model for the Study of Material Response of Plasma-Facing Surfaces Exposed to Energetic Charged Particles”, 2006.

C. Gotbrath, Barrett, B., Gropp, W. D., Lusk, E. L., and Squyres, J., “An Interface to Support the Identification of Dynamic MPI 2 Processes for Scalable Parallel Debugging”, in 13th EuroPVM/MPI Users, Bonn, Germany, 2006, 2006.

J. M. Schopf, Raicu, I., Pearlman, L., Miller, N., Kesselman, C., Foster, I. T., and D'Souza, M., “Monitoring and Discovery in a Web Services Framework: Functionality and Performance of Globus Toolkit MDS4”, 2006.

J. M. Schopf, Pearlman, L., Miller, N., Kesselman, C., Foster, I. T., and D'Souza, M., “Monitoring the Grid with the Globus Toolkit MDS4”, 2006.

B. Q. Deng, Allain, J. P., and Peng, L. L., “Effects of a Liquid Lithium Curtain as the Frist Wall in the Fuson Experimental Breeder (FEB-E) Reactor Plasma”, 2006.

E. M. Glassand D'Souza, M., “Pathos and PathoGene Databases - Support for Biodefense and Emerging Infectious Disease Research”, 2006.

T. Leeand Fischer, P. F., “Eliminating Parasitic Currents in the Lattice Boltzmann Equation Method for Nonideal Gases”, 2006.

M. M. Stroutand Hovland, P. D., “Linearity Analysis for Automatic Differentiation”, 2006.

J. Shinand Hovland, P. D., “Comparison of Two Activity Analyses for Automatic Differentiation: Context-Sensitive Flow-Insensitive vs. Context-Insensitive Flow-Sensitive”, 2006.

D. Sulakheand D'Souza, M., “GNARE - A Grid-Based Server for the Analysis of User Submitted Genomes”, 2006.

W. D. Groppand Lumsdaine, A., “Parallel Tools and Environments: A Survey”, 2006.

S. Dong, Insley, J. A., Karonis, N. T., Papka, M. E., Binns, J., and Karniadakis, G., “Simulating and Visualizing the Human Arterial System on the TeraGrid”, Future Generation Computing System, vol. 22, no. 8, pp. 1011-1017, 2006.

J. P. Allain, Nieto, M., Hassanein, A., Titov, V., Plotkin, P., Hendricks, M., Hinson, E., Chrobak, C., van der Velden, M. H. L., and Rice, B., “Effect of Charged-Particle Bombardment on Collector Mirror Reflectivity in EUV Lithography Devices”, 2006.

W. van Drongelen, Loch, H., Elsen, F. P., Lee, H. C., Mrejeru, A., Doren, E., Marcuccilli, C. J., Hereld, M., Stevens, R. L., and Ramirez, J. - M., “The Role of Persistent Sodium Current in Bursting Activity of Mouse Neocortical Networks in Vitro”, J Neurophysiol, vol. 96, no. 5, pp. 2564-2577, 2006.

B. Norris, Bhowmick, S., Kaushik, D. K., and McInnes, L. Curfman, “Middleware for Dynamic Adaptation of Component Applications”, 2006.

L. Curfman McInnes, Ray, J., Armstrong, R., Dahlgren, T., Malony, A. D., Norris, B., Shende, S., Kenny, J. P., and Steensland, J., “Computational Quality of Service for Scientific CCA Applications: Composition, Substitution, and Reconfiguration”, 2006.

S. Y. Gerdes, Edwards, R. A., Kubal, M., Fonstein, M., Stevens, R. L., and Osterman, A. L., “Essential Genes on Metabolic Maps”, Curr Opin Biotechnol, vol. 17, no. 5, pp. 448-456, 2006.

J. N. Brooks, Allain, J. P., and Rognlien, T. D., “Erosion/ Redecomposition Analysis of the ITER First Wall with Convective and Non-convective Plasma Transport”, 2006.

P. F. Fischer, Loth, F., Lee, S. - W., Smith, D., Tufo, H. M., and Bassiouny, H. S., “Parallel Simulation of High Reynolds Number Vascular Flows”, 2006.

C. Falzone, Chan, A., Lusk, E. L., and Gropp, W. D., “A Portable Method for Finding User Errors in the Usage of MPI Collective Operations”, International Journal of High Performance Computing Applications, vol. 21, no. 2, pp. 155-165, 2006.

T. Freeman, Keahey, K., Sotomayor, B., Zhang, X., Foster, I. T., and Scheftner, D., “Virtual Clusters for Grid Communities”, 2006.

P. H. Beckman, Iskra, K., Yoshii, K., and Coghlan, S. M., “Operating System Issues for Petascale Systems”, ACM, 2006.

M. Yan, Leaf, G. K., Kaper, H. G., Novosad, V., Vavassori, P., Camley, R. E., and Grimsditch, M., “Stripe Domains, Dynamic Modes, and Magnetic Phase Transitions”, 2006.

P. F. Fischer, Loth, F., Lee, S. E., Lee, S. - W., Smith, D. S., and Bassiouny, H. S., “Simulation of High Reynolds Number Vascular Flows”, 2006.

M. Nieto, Allain, J. P., Titov, V., Hendricks, M. R., Hassanein, A., Rokusek, D., Chrobak, C., Tarrio, C., Barad, Y., Grantham, S., Lucatorto, T., and Rice, B., “Effect of Xenon Bombardment on Ruthenium-Coated Grazing Incidence Collector Mirror Lifetime for EUV Lithography”, presented at the 04/2006, 2006.

S. Langella, Oster, S., Hastings, S., Siebenlist, F., Kurc, T., and Saltz, J., “Dorian: Grid Service Infrastructure for Identity Management and Federation”, 2006.

J. A. Insley, Papka, M. E., Dong, S., Karniadakis, G., and Karonis, N. T., “Runtime Visualization of the Human Arterial Tree”, IEEE Educational Activities Departm, Baltimore, MD, 2006.

I. Constandache, Olmedilla, D., Siebenlist, F., and Nejdl, W., “Policy-driven Negotiation for Authorization in the Grid”, 2006.

P. H. Beckman, Iskra, K., Yoshii, K., and Coghlan, S. M., “The Influence of Operating Systems on the Performance of Collective Operations at Extreme Scale”, 2006.

R. Latham, Ross, R. B., and Thakur, R., “Can MPI Be Used for Persistent Parallel Services?”, 2006.

S. Pervez, Gopalakrishnan, G., Kirby, R. M., Thakur, R., and Gropp, W. D., “Formal Verification of Programs That Use MPI One-Sided Communication”, 2006.

B. Lang, Foster, I. T., Siebenlist, F., Ananthakrishnan, R., and Freeman, T., “A Multipolicy Authorization Framework for Grid Security”, IEEE Computer Society, 2006.

D. Sulakhe, Rodriguez, A., Wilde, M., Foster, I. T., and Maltsev, N., “Using Multiple Grid Resources for Bioinformatics Applications in GADU”, 2006.

S. Leyffer, “Complementarity Constraints as Nonlinear Equations: Theory and Numerical Experience”, 2006.

I. R. Judson, Lefvert, S., Olson, E., and Uram, T. D., “Virtual Venue Management Users Manual: Access Grid Toolkit Documentation, Version 2.3”, 2006.

M. Hereld, Papka, M. E., Binns, J., and Stevens, R. L., “CupHolder: A Multi-Person Interactive High-Resolution Workstation”, presented at the 02/2006, 2006.

J. Binns, DiCarlo, J., Insley, J. A., Leggett, T., Lueninghoener, C., Navarro, J. P., and Papka, M. E., “Enabling Community Access to TeraGrid Visualization Resources, Concurrency and Computation: Practice and Experience”, Concurr. Comput.-Pract. Exp., vol. 19, no. 6, pp. 783 - 794, 2006.

R. J. Aiken, “The Grand Challenge of Managing the Petascale Facility”, 2006.

V. Sizyuk, Hassanein, A., Morozov, V., and Sizyuk, T., “Heights Integrated Model as Instrument for Simulation of Hydrodynamic, Radiation Transport, and Heat Conduction Phenomena of Laser-Produced Plasma in EUV Applications”, presented at the 02/2006, 2006.

P. D. Hovland, Norris, B., Utke, J., and Strout, M. M., “Term Graphs for Imperative Programming Languages”, 2006.

B. Kreaseck, Ramos, L., Easterday, S., Strout, M. M., and Hovland, P. D., “Hybrid Static/Dynamic Activity Analysis”, 2006.

K. Keahey, Foster, I. T., Freeman, T., Rana, A., Sotomayor, B., and Wurthwein, F., “Division of Labor: Tools for Growth and Scalability of Grids”, 2006.

K. Keahey, Chase, J., and Foster, I. T., “Virtual Playgrounds: Managing Virtual Resources in the Grid”, 2006.

I. T. Foster, Keahey, K., Kesselman, C., Laure, E., M. Martin, L. S., Rynge, M., and Singh, G., “Embedding Community-Specific Resource Managers in General-Purpose Grid Infrastructure”, 2006.

I. R. Judson, Olson, E., Price, S. D., and Uram, T. D., “Web Services Toolkit Interoperability”, 2006.

M. Yan, Leaf, G. K., Kaper, H. G., Novosad, V., Vavassori, P., Camley, R. E., and Grimsditch, M., “Dynamic Origin of Stripe Domains in Cobalt Bars”, 2006.

J. Bresnahan, Kettimuthu, R., and Foster, I. T., “XIOPerf: A Tool for Evaluating Network Protocols”, 2006.

W. D. Groppand Thakur, R., “Issues in Developing a Thread-Safe MPI Implementation”, 2006.

W. D. Groppand Thakur, R., “Thread Safety in an MPI Implementation: Requirements and Analysis”, 2006.

S. Bhowmickand Hovland, P. D., “A Polynomial Time Algorithm for the Detection of Axial Symmetry in Directed Acyclic Graphs”, 2006.

M. D'Souza, “Sentra: A Database of Signal Transduction Proteins for Comparative Genome Analysis”, Nucleic Acids Research, vol. 35, pp. D271-73, 2006.

S. Pervez, Gopalakrishnan, G., Kirby, R. M., Thakur, R., and Gropp, W. D., “A Case Study in Using Formal Methods to Verify Programs That Use MPI One-Sided Communication”, 2006.

P. Balaji, Buntinas, D., Balay, S., Smith, B. F., Thakur, R., and Gropp, W. D., “Nonuniformly Communicating Noncontiguous Data: A Case Study with PETSc and MPI”, 2006.

Y. Zhao, Wilde, M., and Foster, I. T., “Applying the Virtual Data Provenance Model”, 2006.

M. Yan, Leaf, G. K., Kaper, H. G., Novosad, V., Vavassori, P., Camley, R. E., and Grimsditch, M., “Formation of Stripe Domains in Cobalt Bars via Magnetic Soft Mode Instability”, 2006.

S. Byna, Sun, X. - H., Thakur, R., and Gropp, W. D., “Automatic Memory Optimizations for Improving MPI Derived Datatype Performance”, 2006.

R. E. Camley, Leaf, G. K., Kaper, H. G., Yan, M., and Grimsditch, M., “Phase Transitions and Reversal Mechanisms in Nanosized Magnetic Bars: The Influence of Bulk and Localized Spin Wave Modes”, 2006.

G. von Laszewski, DiCarlo, J., and Allcock, W. E., “A Portal for Visualizing Grid Usage”, 2006.

W. van Drongelen, Lee, H. C., Stevens, R. L., and Hereld, M., “Propagation of Seizurelike Activity in a Model of Neocortex”, 2006.

Z. Insepov, Hassanein, A., and Swenson, D. R., “Computer Simulation of Surface Modification with Ion Beams”, 2006.

B. Lang, Foster, I. T., Siebenlist, F., Ananthakrishnan, R., and Freeman, T., “Attribute Based Access Control for Grid Comptuing”, 2006.

N. L. Desai, Bradshaw, R., Hagedorn, J., and Lueninghoener, C., “Directing Change Using Bcfg2,”, 2006.

V. Nefedova, Jacob, R. L., Foster, I. T., Liu, Z., Liu, Y., Deelman, E., Mehta, G., Su, M. - H., and Vahi, K., “Automating Climate Science: Large Ensemble Simulations on the TeraGrid with the GriPhyN Virtual Data System”, 2006.

J. P. Allain, Coventry, M. D., and Ruzic, D. N., “Kinematic and Thermodynamic Effects on Liquid Lithium Sputtering”, 2006.

T. Leeand Fischer, P. F., “A Lattice Boltzmann Equation Method without Parasitic Currents and Its Application in Droplet Coalescence”, 2006.

2005

M. Anitescuand Layton, W. J., “Sensitivities in Large Eddy Simulation and Improved Estimates of Turbulent Flow Functionals”, Society for Industrial and Applied Mathematics, 2005.

E. M. Gertzand Griffin, J. D., “Support Vector Machine Classifiers for Large Data Sets”, 2005.

M. Beeson, Veroff, R., and Wos, L., “Double-Negation Elimination in Some Propositional Logics”, Studia Logica, vol. 80, no. 2, pp. 195-234, 2005.

G. X. Yu, Glass, E. M., Karonis, N. T., and Maltsev, N., “A Knowledge-Based Voting Algorithm for Automated Protein Functional Annotation”, Wiley-Liss, Inc., 2005.

L. Wos, “The Flowering of Automated Reasoning”, in A Portrait to a Scientist: Logic, AI and Politics, A Festschrift in Honor of J. H. Siekmann, Springer, 2005.

J. Binns, Dech, F., Papka, M. E., Silverstein, J. C., and Stevens, R. L., “Developing a Distributed Collaborative Radiological Visualization Application”, in From Grid to Healthgrid: Proceedings of Healthgrid 2005, 2005.

M. Hereldand Stevens, R. L., “Large Neural Simulations on Large Parallel Computers”, in International Journal of Bioelectromagnetism, 2005.

K. Aminand von Laszewski, G., “Quality Assured Ad Hoc Grids”, 2005.

S. Leyfferand Munson, T. S., “Solving Multi-Leader-Follower Games”, 2005.

L. Wosand Spinks, M., “The Arrival of Automated Reasoning”, 2005.

H. G. Kaperand Tipei, S., “DISSCO: A Unified Approach to Sound Synthesis and Composition”, 2005.

S. J. Bensonand Ye, Y., “DSDP5: Software for Semidefinite Programming”, 2005.

P. F. Fischerand Tzanos, C., “Filtered Simulations of Turbulence in a Reactor Rod Bundle Flow”, 2005.

J. N. Lynessand Sorevik, T., “Five-Dimensional K-Optimal Lattice Rules”, 2005.

D. Sulakhe, Rodriguez, A., and D'Souza, M., “GNARE: An Environment for Grid-Based High-Throughput Genome Analysis”, IEEE, 2005.

M. G. Knepleyand Karpeev, D. A., “Flexible Representation of Computational Meshes”, 2005.

J. C. Silverstein, Dech, F., Binns, J., Jones, D., Papka, M. E., and Stevens, R. L., “Distributed Collaborative Radiological Visualization using Access Grid”, Medicine Meets Virtual Reality 13: The Magical Next Becomes the Medical Now, vol. 111, pp. 477-481, 2005.

J. M. Schopfand D'Souza, M., “Monitoring and Discovery in a Web Services Framework: Functionality and Performance of the Globus Toolkit's MDS4”, 2005.

W. van Drongelen, Lee, H. C., Koch, H., Hereld, M., Elsen, F. P., Chen, Z., and Stevens, R. L., “Emergent Epileptiform Activity in Neural Networks with Weak Excitatory Synapses”, in IEEE Trans Neural Syst Rehabil Eng., 2005.

W. E. Allcock, Bresnahan, J., Kettimuthu, R., Link, M., Dumitrescu, C. L., Raicu, I., and Foster, I. T., “The Globus Striped GridFTP Framework and Server”, 2005.

S. Bhowmick, Kaushik, D. K., McInnes, L. Curfman, Norris, B., and Raghavan, P., “Parallel Adaptive Solvers in Compressible PETSc-FUN3D Simulations”, 2005.

N. L. Desai, Bradshaw, R., Matott, S., Bittner, S., Coghlan, S. M., Evard, R., Lueninghoener, C., Leggett, T., Navarro, J. P., Rackow, E., Stacey, C., and Stacey, T., “A Case Study in Configuration Management Tool Deployment”, 2005.

L. Meyer, Annis, J., Wilde, M., Mattoso, M., and Foster, I. T., “Planning Spatial Workflows to Optimize Grid Performance”, 2005.

M. Hereldand Stevens, R. L., “Pixel-Aligned Warping for Multiprojector Tiled Displays”, in IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05), 2005.

R. L. Grossman, Sabala, M., Alimohideen, J., Anand, A., Chaves, J., Dillenburg, J., Eick, S., Leigh, J., Nelson, P., Papka, M. E., Rorem, D., Stevens, R. L., Vejcik, S., Wilkinson, L., and Zhang, P., “Real Time Change Detection and Alerts from Highway Traffic Data”, in Proceedings of the 2005 ACM/IEEE conference on Supercomputing, Seattle, WA, 2005.

D. Buntinas, Mercier, G., and Gropp, W. D., “Data Transfers Between Processes in an SMP System: Performance Study and Application to MPI”, in Proceedings of the 2006 International Conference on Parallel Processing (IC, Columbus, OH, 2005.

K. Amin, von Laszewski, G., Hategan, M., Al-Ali, R., Rana, O. F., and Walker, D., “An Abstraction Model for a Grid Execution Framework”, 2005.

G. von Laszewski, “The Grid-Idea and Its Evolution”, 2005.

C. S. Verma, Fischer, P. F., Lee, S. E., and Loth, F., “An All-Hex Meshing Strategy for Bifurcation Geometries in Vascular Flow Simulation”, 2005.

M. M. Strout, Mellor-Crummey, J., and Hovland, P. D., “Representation-Independent Program Analysis”, 2005.

T. S. Munson, “Optimizing the Quality of Mesh Elements”, presented at the 06/2005, 2005.

Y. Zhao, Wilde, M., Foster, I. T., Voeckler, J., Dobson, J., Jordan, T., and Quigg, E., “Virtual Data Grid Middleware Services for Data-Intensive Science”, presented at the 06/2005, 2005.

R. B. Ross, Thakur, R., and Choudhary, A., “Achievements and Challenges for I/O in Computational Science”, 2005.

H. Zhang, Smith, B. F., Sternberg, M., and Zapol, P., “SIPs: Shift-and-Invert Parallel Spectral Transformations”, ACM, 2005.

P. D. Hovland, Norris, B., Strout, M. M., Bhowmick, S., and Utke, J., “Sensitivity Analysis and Design Optimization through Automatic Differentiation”, 2005.

P. F. Fischer, “Anistropic Diffusion in a Toroidal Geometry”, 2005.

N. L. Desai, Lusk, E. L., and Bradshaw, R., “MPISH2: Unix Integration for MPI Programs”, in 12th EuroPVM/MPI Users, Sorrento, Italy, 2005.

R. Latham, Ross, R. B., Thakur, R., and Toonen, B., “Implementing MPI-IO Shared File Pointers without File System Support”, 2005.

C. Falzone, Chan, A., Lusk, E. L., and Gropp, W. D., “Collective Error Detection for MPI Collective Operations”, in 12th EuroPVM/MPI Users, Sorrento, Italy, 2005, 2005.

W. E. Allcock, Chervenak, A. L., Foster, I. T., Kesselman, C., and Livny, M., “Data Grid Tools: Enabling Science on Big Distributed Data”, 2005.

B. Norris, “Software Architecture Issues in Scientific Component Development”, 2005.

S. Leyffer, “The Return of the Active Set Method”, 2005.

D. Negrut, Rampalli, R., Ottarsson, G., and Sajdak, A., “On the use of the HHT Method in the Context of Index 3 Differential Algebraic Equations of Multibody Dynamics”, 2005.

I. T. Foster, “Service-Oriented Science”, 2005.

M. Anitescu, “Mathematical Programs with Equilibrium Constraints and Applications to Control”, 2005.

Z. Insepov, Wolf, D., and Hassanein, A., “Nanopumping Using Carbon Nanotubes”, Nano Letters, vol. 6, no. 9, pp. 1893-1895, 2005.

W. McCune, Padmanabhan, R., Rose, M. A., and Veroff, R., “Automated Discovery of Single Axioms for Ortholattices”, Algebra Universalis, vol. 52, no. 4, pp. 541-549, 2005.

E. L. Lusk, Desai, N. L., Bradshaw, R., Lusk, A., and Butler, R. M., “An Interoperability Approach to System Software, Tools, and Libraries for Clusters”, International Journal of High Performance Computing Applications, vol. 20, no. 3, pp. 401-407, 2005.

D. Buntinas, Mercier, G., and Gropp, W. D., “Design and Evaluation of Nemesis, a Scalable, Low-Latency, Message-Passing Communication Subsystem”, IEEE Computer Society, Singapore, Singapore, 2005.

N. L. Desai, Lusk, A., Bradshaw, R., and Lusk, E. L., “MPISH: A Parallel Shell for MPI Programs”, in 19th IEEE International Parallel and Distributed Processing Symposium, Denver, CO, 2005.

R. L. Jacob, Larson, J. W., and Ong, E. T., “MxN Communication and Parallel Interpolation in CCSM3 Using the Model Coupling Toolkit”, 2005.

H. Lee, Hereld, M., Stevens, R. L., and van Drongelen, W., “Epileptiform Activity Patterns in Coupled Neuronal Networks”, 2005.

J. Utke, Naumann, U., Fagan, M., Tallent, N., Strout, M. M., Heimbach, P., Hill, C., and Wunsch, C., “OpenAD/F: A Modular, Open-Source Tool for Automatic Differentiation of Fortran Codes”, 2005.

K. Keahey, Foster, I. T., Freeman, T., Zhang, X., and Galron, D., “Virtual Workspaces in the Grid”, 2005.

R. Thakur, Gropp, W. D., and Toonen, B., “Optimizing the Synchronization Operations in MPI One-Sided Communication”, 2005.

M. S. Min, “Disctoninuous Galerkin Method Based on Quadrilateral Mesh for Maxwell's Equations”, 2005.

L. Yang, Schopf, J. M., and Foster, I. T., “Improving Parallel Data Transfer Times Using Predicted Variances in Shared Networks”, 2005.

R. B. Ross, Latham, R., Gropp, W. D., Thakur, R., and Toonen, B., “Implementing MPI-IO Atomic Mode Without File System Support”, 2005.

T. L. Disz, Kubal, M., Olson, R., Overbeek, R. A., and Stevens, R. L., “Challenges in Large Scale Distributed Computing: Bioinformatics”, 2005.

L. F. Diachin, Knupp, P., Munson, T. S., and Shontz, S., “A Comparison of Two Optimization Methods for Mesh Quality Improvement”, 2005.

M. Anitescu, Tseng, P., and Wright, S. J., “Elastic-Mode Algorithms for Mathematical Programs with Equilibrium Constraints: Global Convergence and Stationarity Properties”, 2005.

D. Rosenberg, Fournier, A., Fischer, P. F., and Pouquet, N., “Geophysical-Astrophysical Spectral-Element Adaptive Refinement (GASpAR): Object-oriented h-adaptive code for geophysical fluid dynamics simulation”, 2005.

D. Negrut, Anitescu, M., Munson, T. S., and Zapol, P., “Simulating Nanoscale Processes in Solids using DFT and the Quasicontinuum Method”, 2005.

L. Yang, Schopf, J. M., Dumitrescu, C. L., and Foster, I. T., “Statistical Data Reduction for Efficient Application Performance Monitoring”, 2005.

W. D. Groppand Thakur, R., “An Evaluation of Implementation Options for MPI One-Sided Communication”, 2005.

G. von Laszewskiand Hategan, M., “Workflow Concepts of the Java CoG Kit”, J. of Grid Comput., vol. 3, no. 3, pp. 239-258, 2005.

U. Naumannand Utke, J., “Source Templates for the Automatic Generation of Adjoint Code through Static Call Graph Reversal”, 2005.

D. E. Stewartand Anitescu, M., “Optimal Control of Systems with Discontinuous Differential Equations”, 2005.

N. Maltsev, Glass, E. M., Sulakhe, D., Rodriguez, A., Syed, M. H., Bompada, T., Zhang, Y., and D'Souza, M., “PUMA2 - Grid-Based High-Throughput Analysis of Genomes and Metabolic Pathway”, 2005.

T. S. Munsonand Hovland, P. D., “The FeasNewt Benchmark”, 2005.

G. von Laszewskiand Kodeboyina, D., “A Repository Service for Grid Workflow Components”, 2005.

D. Buntinasand Gropp, W. D., “Understanding the Requirements Imposed by Programming Model Middleware on a Common Communication Subsystem”, in Designing a Common Communication Subsystem, vol. 3666, Springer Berlin / Heidelberg, 2005, pp. 156-166.

J. G. Kim, Hunke, E. C., and Lipscomb, W. H., “A Sensitivity Analysis and Parameter Tuning Scheme for Global Sea Ice Modeling”, 2005.

L. Curfman McInnes, Norris, B., and Veljkovic, I., “Computational Quality of Service in Parallel CFD”, 2005.

W. E. Allcock, “Programming with the Globus Toolkit GridFTP Client Library”, 2005.

K. Amin, von Laszewski, G., Sosonkin, M., Mikler, A. R., and Hategan, M., “Ad Hoc Grid Security Infrastructure”, 2005.

R. Padmanabhan, McCune, W., and Veroff, R., “Lattice Laws Forcing Distributivity Under Unique Complementation”, 2005.

I. T. Foster, Nefedova, V., Liming, L., Ananthakrishnan, R., Madduri, R., Pearlman, L., Mulmo, O., and Ahsant, M., “Streamlining Grid Operations: Definition and Deployment of a Portal-based User Registration Service”, 2005.

S. J. Benson, “Parallel Semidefinite Programming and Combinatorial Optimization”, 2005.

M. Yan, Leaf, G. K., Kaper, H. G., Camley, R. E., and Grimsditch, M., “Spin Wave Modes in a Cobalt Square Vortex”, 2005.

X. Zhang, Freschl, J. L., and Schopf, J. M., “Scalability Analysis of Three Monitoring and Information Systems: MDS2, R-GMA, and Hawkeye”, 2005.

M. Anitescu, Negrut, D., Zapol, P., and El-Azab, A., “A Note on the Regularity of Reduced Models Obtained by Quasi-continuum-like Approaches”, 2005.

J. Lee, Ross, R. B., Atchley, S., Beck, M., and Thakur, R., “MPI-IO/L: Efficient Remote I/O for MPI-IO via Logistical Networking”, 2005.

S. S. Varghese, Frankel, S. H., and Fischer, P. F., “Direct Numerical Simulation of Stenotic Flows. Part 1. Steady Flow”, 2005.

S. S. Varghese, Frankel, S. H., and Fischer, P. F., “Direct Numerical Simulation of Stenotic Flows. Part 2. Pulsatile Flow”, 2005.

D. Buntinasand Gropp, W. D., “Designing a Common Communication Subsystem”, 2005.

2004

W. D. Gropp, Ross, R. B., and Miller, N., “Providing Efficient I/O Redundancy in MPI Environments”, 2004.

W. Yu, Buntinas, D., and Panda, D. K., “Scalable and High Performance NIC-Based All-to-All Broadcast Over Myrinet/GM”, 2004.

J. Lee, Ma, X., Ross, R. B., Thakur, R., and Winslett, M., “RFS: Efficient and Flexible Remote File Access for MPI-IO”, 2004.

S. J. Benson, McInnes, L. Curfman, More', J. J., and Sarich, J., “Scalable Algorithms in Optimization: Computational Experiments”, 2004.

B. A. Allan, Diachin, L. F., Benson, S. J., Armstrong, R., Bernholdt, D. E., Dahlgren, T., Krishnan, M., Kohl, J. A., Larson, J. W., Lefantzi, S., McInnes, L. Curfman, Nieplocha, J., Norris, B., Parker, S. G., Ray, J., and Zhou, S., “Parallel PDE-Based Simulations Using the Common Component Architecture”, 2004.

G. G. Maisuradze, Kawano, A., Thompson, D. L., Wagner, A. F., and Minkoff, M., “Interpolating Moving Least-Squares Methods for Fitting Potential Energy Surfaces: Analysis of an Application to a Six-Dimensional System”, 2004.

J. N. Lyness, “A Prototype Four-Dimensional Galerkin-Type Integral”, 2004.

G. Almasi, Archer, C., Castanos, J. G., Gunnels, J., Erway, C. C., Heidelberger, P., Martorell, X., Moreira, J. E., Pinnow, K., Ratterman, J., Steinmacher-burow, B., Gropp, W. D., and Toonen, B., “The Design and Implementation of Message Passing Services for the BlueGene/L Supercomputer”, 2004.

R. Latham, Ross, R. B., and Thakur, R., “The Impact of File Systems on MPI-IO Scalability”, 2004.

W. B. Ligon, IIIand Ross, R. B., “Parallel I/O and the Parallel Virtual File System”, 2004.

C. E. Frouzakis, Tomboulides, A. G., Papas, P., Fischer, P. F., Rais, R. M., Monkewitz, P. A., and Boulouchos, K., “Three-Dimensional Numerical Simulations of Cellular Jet Diffusion Flames”, 2004.

W. Jiang, Liu, J., Jin, H. - W., Panda, D. K., Buntinas, D., Thakur, R., and Gropp, W. D., “Efficient Implementation of MPI-2 Passive One-Sided Communication on InfiniBand Clusters”, 2004.

M. Anitescu, “Optimization-Based Simulation of Nonsmooth Rigid Multibody Dynamics”, 2004.

N. L. Desai, Bradshaw, R., Lusk, A., and Lusk, E. L., “MPI Cluster System Software”, Springer, 2004.

W. E. Allcock, Foster, I. T., and Madduri, R., “Reliable Data Transport: A Critical Service for the Grid”, 2004.

R. A. Overbeek, Disz, T. L., and Stevens, R. L., “A Peer-to-Peer Environment for Annotation of Genomes: The SEED”, 2004.

R. Kettimuthuand Allcock, W. E., “Improved Selective Acknowledgment Scheme for TCP”, 2004.

M. M. Stroutand Hovland, P. D., “Metrics and Models for Reordering Transformations”, 2004.

L. F. Diachin, Knupp, P., Munson, T. S., and Shontz, S., “A Comparison of Inexact Newton and Coordinate Descent Mesh Optimization Techniques”, 2004.

Y. Guo, Kawano, A., Thompson, D. L., Wagner, A. F., and Minkoff, M., “Interpolating Moving Least-Squares Methods for Fitting Potential Energy Surfaces: Applications to Classical Dynamics Calculations”, 2004.

W. E. Allcock, Bresnahan, J., Kettimuthu, R., and Link, J. M., “The Globus eXtensible Input/Output System (XIO): A Protocol Independent IO System for the Grid”, 2004.

D. P. Schissel, Keahey, K., Araki, T., Burruss, J. R., Feibush, E., Flanagan, S. M., Fredian, T. W., Greenwald, M. J., Klasky, S. A., Leggett, T., Li, K., McCune, D. C., Lane, P., Papka, M. E., Peng, Q., Randerson, L., Sanderson, A., Stillerman, J., Thompson, M. R., and Wallace, G., “The National Fusion Collaboratory Project: Applying Grid Technology for Magnetic Fusion Research”, 2004.

K. Keahey, Papka, M. E., Peng, Q., Schissel, D. P., Abla, G., Araki, T., Burruss, J. R., Feibush, E., Lane, P., Klasky, S. A., Leggett, T., McCune, D. C., and Randerson, L., “Grid Support for Collaborative Control Room in Fusion Science”, 2004.

J. W. Larson, Jacob, R. L., and Ong, E. T., “The Model Coupling Toolkit: A New Fortran90 Toolkit for Building Multiphysics Parallel Coupled Models”, 2004.

S. W. Son, Allcock, W. E., and Livny, M., “CODO: Firewall Traversal by Cooperative On-Demand Opening”, 2004.

J. P. Kenny, Benson, S. J., Alexeev, Y., Sarich, J., Janssen, C. L., McInnes, L. Curfman, Krishnan, M., Nieplocha, J., Jurruss, E., Fahlstrom, C., and Windus, T. L., “Component-Based Integration of Chemistry and Optimization Software”, 2004.

K. Keahey, Papka, M. E., Peng, Q., Schissel, D. P., Abla, G., Araki, T., Burruss, J. R., Feibush, S., Lane, P., Klasky, S. A., Leggett, T., McCune, D. C., and Randerson, L., “Grids for Experimental Science: The Virtual Control Room”, 2004.

F. A. Potra, Anitescu, M., Gavrea, B. I., and Trinkle, J., “A Linearly Implicit Trapezoidal Method for Integrating Stiff Multibody Dynamics with Contact, Joints, and Friction”, 2004.

W. van Drongelen, Lee, H. C., Hereld, M., Jones, D., Cohoon, M. P., Elsen, F. P., Papka, M. E., and Stevens, R. L., “Simulation of Neocortical Epileptiform Activity Using Parallel Computing”, 2004.

U. Naumannand Utke, J., “Optimality-Preserving Elimination of Linearities in Jacobian Accumulation”, 2004.

R. Padmanabhan, McCune, W., and Veroff, R., “Levi's Commutator Theorems for Cancellative Semigroups”, 2004.

Y. Chen, Hobbs, B. F., Leyffer, S., and Munson, T. S., “Leader-Follower Equilibria for Electric Power and NOx Allowances Markets”, 2004.

B. Addisand Leyffer, S., “A Trust-Region Algorithm for Global Optimization”, 2004.

J. Utke, “Flattening Basic Blocks”, 2004.

W. van Drongelen, Lee, H. C., Koch, H., Elsen, F. P., Carroll, M. S., Hereld, M., and Stevens, R. L., “Interaction between Cellular Voltage-Sensitive Conductance and Network Parameters in a Model of the Neocortex Can Generate Epileptiform Bursting”, 2004.

R. A. Overbeek, Stevens, R. L., and Disz, T. L., “The SEED: A Peer to Peer Environment for Genome Annotation”, Communications of the ACM, vol. 47, no. 11, pp. 46 - 51, 2004.

A. Majumderand Stevens, R. L., “Color Nonuniformity in Projection Based Displays: Analysis and Solutions”, in IEEE Transactions on Visualization and Computer Graphics, 2004.

W. Xingfu, Taylor, V. E., Geisler, J., and Stevens, R. L., “Isocoupling: Reusing Kernel Coupling Values to Predict the Performance of Parallel Applications”, in Proceedings International Parallel and Distributed Processing Symposium (IPDPS) 2004, Sante Fe, New Mexico, 2004.

W. D. Gropp, “Issues in Accurate and Reliable Use of Parallel Computing in Numerical Programs”, 2004.

T. Araki, “Autonomic WWW Server Management with Distributed Resources”, 2004.

T. Bae, Banger, A. K., Wallace, A., Glass, E. M., Aslund, F., Schneewind, O., and Missiakas, D. M., “Staphylococcus Aureus Virulence Genes Identified by Bursa Aurealis Mutagenesis and Nematode Killing”, 2004.

G. von Laszewski, Pieper, G. W., and Wagstrom, P., “Gestalt of the Grid”, 2004.

A. - V. Demiguel, Freidlander, M. P., Nogales, F. J., and Scholtes, S., “An Interior-Point Method for MPECs Based on Strictly Feasible Relaxations”, 2004.

X. Zhangand Schopf, J. M., “Performance Analysis of the Globus Toolkit Monitoring and Discovery Service”, 2004.

E. D. Frankand Stevens, R. L., “Process Modeling for High-Throughput Biology”, 2004.

E. D. Dolan, More', J. J., and Munson, T. S., “Benchmarking Optimization Software with COPS 3.0”, 2004.

K. Amin, von Laszewski, G., and Mikler, A. R., “Toward an Architecture for Ad Hoc Grids”, 2004.

Y. Zhao, Wilde, M., Foster, I. T., Voeckler, J., Jordan, T., Quigg, E., and Dobson, J., “Grid Middleware Services for Virtual Data Discovery, Composition, and Integration”, 2004.

G. von Laszewski, Gawor, J., Plaszczak, P., Hategan, M., Amin, K., Madduri, R., Gose, S., and Shankar, S., “An Overview of Grid File Transfer Patterns and Their Implementation in the Java CoG Kit”, Dynamic Publisher, Atlanta, GA, 2004.

J. Wu, Wyckoff, P., Panda, D. K., and Ross, R. B., “Unifier: Unifying Cache Management and Communication Buffer Management for PVFS over InfiniBand”, 2004.

W. Yu, Buntinas, D., Graham, R. L., and Panda, D. K., “Efficient and Scalable Barrier over Quadrics and Myrinet with a New NIC-based Collective Message Passing Protocol”, 2004.

W. Jiang, Liu, J., Jin, H. - W., Panda, D. K., Gropp, W. D., and Thakur, R., “High Performance MPI-2 One-Sided Communication over InfiniBand”, 2004.

H. Gao, Judson, I. R., Uram, T. D., Disz, T. L., Papka, M. E., and Stevens, R. L., “Capability Matching of Data Streams with Network Services”, IEEE Computer Society, Chicago, IL, USA, 2004.

M. Grimsditch, Giovannini, L., Montoncello, F., Nizzoli, F., Leaf, G. K., and Kaper, H. G., “Normal Modes in Ferromagnetic Nanoparticles: A Dynamical Matrix Approach”, 2004.

A. Zagaris, Kaper, H. G., and Kaper, T. J., “Fast and Slow Dynamics for the Computational Singular Perturbation Method”, SIAM J. Multiscale Model. Simul., vol. 2, no. 4, pp. 613-638, 2004.

R. Padmanabhanand McCune, W., “Tarski Theorems on Self-Dual Equational Bases for Groups”, 2004.

R. Al-Ali, von Laszewski, G., Amin, K., Hategan, M., Rana, O. F., Walker, D., and Zaluzec, N. J., “QoS Support for High-Performance Scientific Grid Applications”, 2004.

B. Norris, Ray, J., Armstrong, R., McInnes, L. Curfman, Bernholdt, D. E., Elwasif, W. R., Malony, A. D., and Shende, S., “Computational Quality of Service for Scientific Components”, 2004.

P. F. Fischer, Leaf, G. K., and Restrepo, J. M., “Influence of Wall Proximity on the Lift and Drag of a Particle in an Oscillatory Flow”, 2004.

S. Leyffer, Lopez-Calva, G., and Nocedal, J., “Interior Methods for Mathematical Programs with Complementarity Constraints”, 2004.

Y. K. Kuan, Fischer, P. F., and Loth, F., “Surface Reconstruction of In Vivo Geometry Base on Medical Images using Multilevel Radial Basis Functions”, 2004.

R. Kettimuthu, Subramani, V., Srinivasan, S., Gopalsamy, T., Panda, D. K., and Sadayappan, P., “Selective Preemption Strategies for Parallel Job Scheduling”, 2004.

P. H. Beckman, “Building the TeraGrid”, 2004.

M. S. Min, Lee, T. W., Fischer, P. F., and Gray, S. K., “Fourier Spectral Simulations and Gegenbauer Reconstructions for Electromagnetic Waves in the Presence of a Metal Nanoparticle”, 2004.

N. Maltsev, Glass, E. M., Ovchinnikova, G., and Gu, Z., “Molecular Mechanisms Involved in Robustness of Yeast Central Metabolism Against Null Mutations”, 2004.

V. Welch, Foster, I. T., Kesselman, C., Mulmo, O., Pearlman, L., Tuecke, S., Gawor, J., Meder, S., and Siebenlist, F., “X.509 Proxy Certificates for Dynamic Delegation”, 2004.

J. Utke, “OpenAD: Algorithm Implementation User Guide”, 2004.

R. Thakur, Gropp, W. D., and Toonen, B., “Minimizing Synchronization Overhead in the Implementation of MPI One-Sided Communication”, 2004.

N. T. Karonis, Papka, M. E., Binns, J., Bresnahan, J., and Link, J. M., “Effective Use of Dedicated Wide-Area Networks for High-Performance Distributed Computing”, 2004.

N. L. Desai, Bradshaw, R., and Lusk, E. L., “Component-Based Cluster Systems Software Architecture: A Case Study”, in 6th International IEEE Conference on Cluster Computing, San Diego, San Diego, CA, 2004.

L. Wos, “Milestones for Automated Reasoning”, 2004.

C. H. Bischof, Hovland, P. D., and Norris, B., “On the Implementation of Automatic Differentiation Tools”, 2004.

J. Peng, Anitescu, M., and Akella, S., “Optimal Control of Multiple Robot Systems with Friction using MPCC”, 2004.

E. D. Dolan, More', J. J., and Munson, T. S., “Optimality Measures for Performance Profiles”, Society for Industrial and Applied Mathematics, 2004.

W. D. Groppand Lusk, E. L., “Fault Tolerance in MPI Programs”, International Journal of High Performance Computing Applications, vol. 18, no. 3, pp. 363-372, 2004.

S. L. Leeand Hovland, P. D., “Derivative Techniques for Forward Sensitivity Analysis in Time-Dependent Problems”, 2004.

M. R. Paul, Chiam, K. - H., Cross, M. C., and Fischer, P. F., “Rayleigh-Benard Convection in Large-Aspect-Ratio Domains”, 2004.

M. Anitescu, “Global Convergence of an Eleastic Mode Approach for a Class of Mathematical Programs with Complementarity Constraints”, 2004.

T. S. Munson, “An Averaging Method for Nash Games with Shared Decision Variables”, 2004.

J. M. Schopfand Newhouse, S., “State of Grid Users: 25 Conversations with UK eScience Groups”, 2004.

P. M. Dickensand Larson, J. W., “Classifiers for the Causes of Data Loss Using Packet-Loss Signatures”, 2004.

T. S. Munson, “Mesh Shape-Quality Optimization Using the Inverse Mean-Ratio Metric”, 2004.

K. Keahey, Doering, K., and Foster, I. T., “From Sandbox to Playground: Dynamic Virtual Environments in the Grid”, 2004.

R. Thakur, Rabenseifner, R., and Gropp, W. D., “Optimization of Collective Communication Operations in MPICH”, 2004.

A. Kawano, Guo, Y., Thompson, D. L., Wagner, A. F., and Minkoff, M., “Improving the Accuracy of Interpolated Potential Energy Surfaces by Using an Analytical Zeroth-Order Potential Function”, Journal of Chemical Physics, vol. 120, no. 14, pp. 6414-6422, 2004.

A. Majumderand Stevens, R. L., “Perceptual Photometric Seamlessness in Projection-Based Tiled Displays”, ACM Transactions on Graphics, vol. 24, no. 1, pp. 118-139, 2004.

2003

A. Ching, Choudhary, A., Coloma, K., Liao, W. - K., Ross, R. B., and Gropp, W. D., “Noncontiguous I/O Accesses Through MPI-IO”, 2003.

G. G. Maisuradze, Thompson, D. L., Wagner, A. F., and Minkoff, M., “Interpolating Moving Least Squares Methods for Fitting Potential Energy Surfaces: Detailed Analysis of One-Dimensional Applications”, 2003.

I. T. Fosterand Foster, I. T., “A Peer-to-Peer Approach to Resource Location in Grid Environments”, Kluwer Academic, 2003.

I. T. Foster, “Computation Scheduling and Data Replication Algorithms for Data Grids”, Kluwer Academic, 2003.

J. M. Schopfand Yang, L., “Using Predicted Variance for Conservative Scheduling on Shared Resources”, Kluwer Academic, 2003.

B. - D. Leeand Schopf, J. M., “Run-Time Prediction of Parallel Applications on Shared Environment”, 2003.

K. Keahey, Ripeanu, M., and Koering, K., “Dynamic Creation and Management of Runtime Environments in the Grid”, 2003.

M. R. Thompson, Essiari, A., Keahey, K., Welch, V., Lang, S., and Liu, B., “Fine-Grained Authorization for Job and Resource Management Using Akenti and the Globus Toolkit”, 2003.

K. Keahey, Welch, V., Lang, S., Liu, B., and Meder, S., “Fine-Grained Authorization for Job Execution in the Grid: Design and Implementation”, 2003.

M. Anitescu, Layton, W. J., and Pahlevani, F., “Unconditional Stability for Numerical Scheme Combining Implicit Timestepping for Local Effects and Explicit Timestepping for Nonlocal Effects”, 2003.

S. Leyffer, “The Penalty Interior-Point Method Fails to Converge”, 2003.

N. L. Desai, Lusk, A., Bradshaw, R., and Evard, R., “BCFG: A Configuration Management Tool for Heterogeneous Environments”, presented at the 09/2003, 2003.

B. Nitzberg, Schopf, J. M., and Jones, J. P., “PBS Pro: Grid Computing and Scheduling Attributes”, Kluwer Academic, 2003.

J. J. Evans, Hood, C. S., and Gropp, W. D., “Exploring the Relationship Between Parallel Application Run-Time Variability and Network Performance in Clusters”, 2003.

L. Yang, Schopf, J. M., and Foster, I. T., “Conservative Scheduling: Using Predicted Variance to Improve Scheduling Decisions in Dynamic Environments”, 2003.

R. B. Ross, Miller, N., and Gropp, W. D., “Implementing Fast and Reusable Datatype Processing”, 2003.

U. Naumann, “Statement-Level Optimality of Tangent-Linear and Adjoint Models”, 2003.

M. Hereld, Stevens, R. L., van Drongelen, W., and Lee, H. C., “Developing a Petascale Neural Simulation”, 2003.

U. Naumann, Utke, J., Lyons, A., and Fagan, M., “Control Flow Reversal for Adjoint Code Generation”, IEEE Computer Society, 2003.

M. Hereld, “Local Methods for Measuring Tiled Display Alignment”, 2003.

K. Czajkowski, Foster, I. T., Kesselman, C., and Tuecke, S., “Grid Service Level Agreements”, Kluwer Academic, 2003.

H. Dail, Sievert, O., Berman, F., Casanova, H., YarKhan, A., Vadhiyar, S., Dongarra, J., Liu, C., Yang, L., Angulo, D., and Foster, I. T., “Scheduling in the Grid Application Development Software Project”, Kluwer Academic, 2003.

J. M. Schopf, “Ten Actions When Grid Scheduling”, 2003.

I. T. Fosterand Kesselman, C., “The Grid in a Nutshell”, Kluwer Academic, 2003.

Y. Zhou, “Eigenvalue Computation from the Optimization Perspective: On Jacobi-Davidson, IIGD, RQI, and Newton Updates”, 2003.

U. Naumannand Utke, J., “Reduction of Edge Labeled DAGs through Constant Folding”, 2003.

G. von Laszewski, Amin, K., Hategan, M., Zaluzec, N. J., Hampton, S., and Rossi, A., “GridAnt: A Client-Controllable Grid Workflow System”, 2003.

W. McCune, “OTTER 3.3 Reference Manual”, 2003.

W. E. Allcock, Bresnahan, J., Bunn, J., Hedge, S., Insley, J. A., Kettimuthu, R., Newman, H., Ravot, S., Rimovsky, T., Steenberg, C., and Winkler, L., “Grid-Enables Particle Physics Event Analysis: Experiences Using a 10 Gb, High-Latency Network for a High-Energy Physics Application”, 2003.

X. Zhang, Freschl, J. L., and Schopf, J. M., “A Performance Study of Monitoring and Information Services for Distribution Systems”, 2003.

G. von Laszewski, Alunkal, B. K., and Veljkovic, I., “Toward Reputable Grids”, 2003.

S. Anand, Yoginath, S., von Laszewski, G., Alunkal, B. K., and Sun, X. - H., “Flow-based Multistage Co-allocation Service”, 2003.

B. K. Alunkal, Veljkovic, I., von Laszewski, G., and Amin, K., “Reputation-Based Grid Resource Selection”, 2003.

M. Hereld, Judson, I. R., and Stevens, R. L., “DottyToto: A Measurement Engine for Aligning Multiprojector Display Systems”, in Projection displays IX, Santa Clara, CA, 2003.

W. McCune, Padmanabhan, R., Rose, M. A., and Veroff, R., “Short Equational Bases for Ortholattices”, 2003.

S. Langand Meder, S., “Security and Credential Management on the Grid”, 2003.

U. Naumannand Riehme, J., “A Differentiation-Enabled Fortran 95 Compiler”, 2003.

S. J. Benson, Krishnan, M., McInnes, L. Curfman, Nieplocha, J., and Sarich, J., “Using the GA and TAO Toolkits for Solving Large-Scale Optimization Problems on Parallel Computers”, 2003.

J. - S. Pangand Leyffer, S., “On the Global Minimization of the Value-at-Risk”, 2003.

G. von Laszewski, Alunkal, B. K., Gawor, J., Madduri, R., Plaszczak, P., and Sun, X. - H., “A File Transfer Component for Grids”, 2003.

T. Ozgokmen, Fischer, P. F., Duan, J., and Iliescu, T., “Three-Dimensional Turbulent Bottom Density Currents from a High-Order Nonhydrostatic Spectral Element Model”, 2003.

K. Amin, von Laszewski, G., and Mikler, A. R., “Grid Computing for the Masses: An Overview”, 2003.

L. Randerson, Burruss, J. R., Feibush, E., Flanagan, S. M., Keahey, K., Ludescher, C., McCune, D. C., Peng, Q., Schissel, D. P., and Thompson, M. R., “Building Application Services on the Grid: The National Fusion Collaboratory”, 2003.

J. Liu, Jiang, W., Wyckoff, P., Panda, D. K., Ashton, D., Buntinas, D., Gropp, W. D., and Toonen, B., “Design and Implementation of MPICH2 over InfiniBand with RDMA Support”, 2003.

K. Amin, Hategan, M., von Laszewski, G., and Zaluzec, N. J., “Abstracting the Grid”, 2003.

G. D. Hartand Anitescu, M., “A Hard-Constraint Time-Stepping Approach for Rigid Multibody Dynamics with Joints, Contact, and Friction”, 2003.

P. J. Moon, Sandi, G., Kizilel, R., and Stevens, D., “Computational Simulation of Lithium Ion Transport through Polymer Nanocomposite Membranes”, 2003.

P. W. Arzberger, Farazdel, A., Konagaya, A., Ang, L., Shimojo, S., and Stevens, R. L., “Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that Will Drive Future Science”, New Generation Computing, vol. 22, no. 2, pp. 97-110, 2003.

A. A. Dunca, “Optimal Design of Fluid Flow Using Subproblems Reduced by Large Eddy Simulation”, 2003.

P. J. Moon, Sandi, G., Stevens, D., and Kizilel, R., “Computational Modeling of Ionic Transport in Continuous and Batch Electrodialysis”, 2003.

R. Al-Ali, Amin, K., von Laszewski, G., Rana, O. F., and Walker, D., “An OGSA-Based Quality of Service Framework”, 2003.

J. No, Thakur, R., and Choudhary, A., “High-Performance Scientific Data Management System”, 2003.

U. Naumann, “Optimal Accumulation of Jacobian Matrices by Elimination Methods on the Dual Computational Graph”, Springer-Verlag, 2003.

K. Keaheyand Motawi, K., “The Taming of the Grid: Virtual Application Services”, 2003.

U. Naumannand Walther, A., “An Introduction to Using Software Tools for Automatic Differentiation”, 2003.

R. M. Butler, Desai, N. L., Lusk, A., and Lusk, E. L., “The Process Management Component of a Scalable Systems Software Environment”, in 5th IEEE International Conference on Cluster Computing, Pittsburgh, PA, 2003.

S. Leyffer, “Mathematical Programs with Complementarity Constraints”, 2003.

V. Welch, Siebenlist, F., Foster, I. T., Bresnahan, J., Czajkowski, K., Gawor, J., Kesselman, C., Meder, S., Pearlman, L., and Tuecke, S., “Security for Grid Services”, 2003.

M. Anitescu, Miller, A., and Hart, G. D., “Constraint Stabilization for Time-Stepping Approaches for Rigid Multibody Dynamics with Joints, Contact, and Friction”, 2003.

U. Naumannand Heimbach, P., “Coupling Tangent-Linear and Adjoint Models”, 2003.

J. J. Evans, Baik, S., Hood, C. S., and Gropp, W. D., “Toward Understanding Soft Faults in High Performance Cluster Networks”, 2003.

G. von Laszewski, Gawor, J., Krishnan, S., and Jackson, K., “Commodity Grid Kits - Middleware for Building Grid Computing Environments”, 2003.

M. Cohen, Naumann, U., and Riehme, J., “Towards Differentiation-Enabled Fortran 95 Compiler Technology”, ACM, 2003.

A. Albrecht, Gottschling, P., and Naumann, U., “Markowitz-Type Heuristics for Computing Jacobian Matrices Efficiently”, Springer LNCS, 2003.

W. McCune, Padmanabhan, R., Rose, M. A., and Veroff, R., “Short Equational Bases for Ortholattices: Proofs and Countermodels”, 2003.

W. McCune, “Mace4 Reference Manual and Guide”, 2003.

O. S. Matlin, McCune, W., and Lusk, E. L., “Methods to Model-Check Parallel Systems Software”, 2003.

M. Hereld, Judson, I. R., and Stevens, R. L., “Application Performance Evaluation of the HTMT Architecture”, 2003.

R. Evard, Beckman, P. H., Bittner, S., Bradshaw, R., Coghlan, S. M., Desai, N. L., Finley, B., Rackow, E., and Navarro, J. P., “The Production Cluster Construction Checklist”, 2003.

S. J. Benson, McInnes, L. Curfman, and More', J. J., “TAO Users Manual”, 2003.

R. L. Stevens, Papka, M. E., and Disz, T. L., “Prototyping the Workspaces of the Future”, IEEE Internet Computing, vol. 7, no. 4, pp. 51 - 58, 2003.

S. Bhowmick, McInnes, L. Curfman, Norris, B., and Raghavan, P., “The Role of Multimethod Linear Solvers in PDE-Based Simulations”, 2003.

K. Keahey, Araki, T., and Lane, P., “Agreement-Based Interactions for Experimental Science”, 2003.

S. J. Bensonand Munson, T. S., “Flexible Complementarity Solvers for Large-Scale Applications”, 2003.

K. Keahey, Welch, V., Lang, S., Liu, B., and Meder, S., “Fine-Grain Authorization Policies in the GRID: Design and Implementation”, 2003.

J. W. Lottesand Fischer, P. F., “Hybrid Multigrid/Schwarz Algorithms for the Spectral Element Method”, 2003.

A. Zagaris, Kaper, H. G., and Kaper, T. J., “Analysis of the Computational Singular Perturbation Reduction Method for Chemical Kinetics”, 2003.

M. Grimsditch, Leaf, G. K., Kaper, H. G., Karpeev, D. A., and Camley, R. E., “Normal Modes of Spin Excitations in Magnetic Nano-Particles”, 2003.

J. Li, Liao, W. - K., Choudhary, A., Ross, R. B., Thakur, R., Gropp, W. D., and Latham, R., “Parallel netCDF: A Scientific High-Performance I/O Interface”, 2003.

L. Pearlman, Kesselman, C., Welch, V., Foster, I. T., and Tuecke, S., “The Community Authorization Service: Status and Future”, 2003.

J. N. Lyness, “Notes on Lattice Rules”, Journal of Complexity, vol. 19, pp. 321-331, 2003.

J. N. Lynessand Sorevik, T., “Four-Dimensional Lattice Rules Generated by Skew-Circulant Matrices”, Math. Comput., vol. 73, no. 245, pp. 279-295, 2003.

S. Newhouse, MacLaren, J., and Keahey, K., “Trading Grid Services within the UK e-Science Grid”, Kluwer Academic Publishers, 2003.

R. L. Stevens, Papka, M. E., and Disz, T. L., “The Access Grid: Prototyping - Workspaces of the Future”, 2003.

O. F. Rana, Shaikhali, A., and von Laszewski, G., “Creating and Managing Grid Services”, 2003.

M. R. Paul, Chiam, K. - H., Cross, M. C., Fischer, P. F., and Greenside, H. S., “Pattern Formation and Dynamics in Rayleigh-Benard Convection: Numerical Simulations of Experimentally Realistic Geomtries”, 2003.

M. Anitescu, “A Fixed Time-Step Approach for Multibody Dynamics with Contact and Friction”, 2003.

S. Vazhkudaiand Schopf, J. M., “Using Regression Techniques to Predict Large Data Transfers”, 2003.

U. Naumannand Gottschling, P., “Simulated Annealing for Optimal Pivot Selection in Jacobian Accumulation”, 2003.

N. T. Karonis, Papka, M. E., Binns, J., Bresnahan, J., Insley, J. A., Jones, D., and Link, J. M., “High-Resolution Remote Rendering of Large Datasets in a Collaborative Environment”, 2003.

A. Rodriguez, Sulakhe, D., Marland, E., Nefedova, V., Yu, G. X., and Maltsev, N., “GADU - Genome Analysis and Database Update Pipeline”, 2003.

P. D. Hovland, Keahey, K., McInnes, L. Curfman, Norris, B., Freitag, L., and Raghavan, P., “A Quality-of-Service Architecture for High-Performance Numerical Components”, 2003.

A. Grimshawand Tuecke, S., “Grid Services Extend Web Services”, 2003.

S. Byna, Gropp, W. D., Sun, X. - H., and Thakur, R., “Improving the Performance of MPI Derived Datatypes by Optimizing Memory-Access Cost”, 2003.

I. Lee, Raghavan, P., and Fischer, P. F., “An O(n log n) Solution Algorithm for Spectral Element Methods”, 2003.

O. S. Matlinand McCune, W., “Encapsulation for Practical Simplification Procedures”, 2003.

R. Thakurand Gropp, W. D., “Improving the Performance of Collective Operations in MPICH”, 2003.

L. Freitagand Loy, R., “Theoretical Cost Comparison of Remote Visualization Strategies”, 2003.

2002

J. N. Lynessand Monegato, G., “Asymptotic Expansions for Two-Dimensional Hypersingular Integrals”, 2002.

M. Vilayannur, Ross, R. B., Carns, P. H., Thakur, R., Sivasubramaniam, A., and Kandemir, M., “Improving the Performance of the POSIX I/O Interface to PVFS”, 2002.

K. Amin, Nijsure, S., and von Laszewski, G., “Open Collaborative Grid Service Architecture (OCGSA)”, 2002.

J. M. Restrepoand Leaf, G. K., “Noise Effects on Wave-Generated Transport Induced by Ideal Waves”, 2002.

R. Thakurand Gropp, W. D., “Improving the Performance of MPI Collective Communication on Switched Networks”, 2002.

M. P. Freidlanderand Saunders, M. A., “A Globally Convergent Linearly Constrained Lagrangian Method for Nonlinear Optimization”, 2002.

M. Dvorak, Taylor, J. A., and Mickelson, S. A., “Designing a Flexible Grid Enabled Scientific Modeling Interface”, 2002.

S. A. Mickelson, Taylor, J. A., and Dvorak, M., “Simplifying the Task of Generating Climate Simulations and Visualizations”, 2002.

I. R. Judson, “Access Grid Node Minimum Requirements”, 2002.

C. J. Anderson, Arritt, R. W., Takle, E. S., Pan, Z., Gutowski, Jr., W. J., Otieno, F. O., da Silva, R., Caya, D., Chen, S. - C., Christensen, J. H., Gaertner, M. A., Gallardo, C., Giorgi, F., Hong, S. - Y., Jones, C., Juang, H. - M. H., Katzfey, J. J., Lapenta, W. M., Laprise, R., Larson, J. W., Liston, G. E., McGregor, J. L., Pielke, Sr., R. A., Roads, J. O., and Taylor, J. A., “Hydrological Processes in Regional Climate Model Simulations of the Central United States Flood of June-July 1993”, 2002.

L. Pearlman, Welch, V., Foster, I. T., Kesselman, C., and Tuecke, S., “A Community Authorization Service for Group Collaboration”, 2002.

G. X. Yuand Marland, E., “Establishment of a Knowledge Base for Function Annotations in High-Throughput Sequence Analysis”, 2002.

S. Bhowmick, Raghavan, P., McInnes, L. Curfman, and Norris, B., “Faster PDE-Based Simulations Using Robust Composite Linear Solvers”, 2002.

A. Majumderand Stevens, R. L., “LAM: Luminance Attenuation Map for Photometric Uniformity in Projection Based Displays”, ACM, Hong Kong, China, 2002.

K. Keaheyand Welch, V., “Fine-Grain Authorization for Resource Management in the Grid Environment”, 2002.

B. Nitzbergand Schopf, M. M., “Current Activities in the Scheduling and Resource Management Area of the Global Grid Forum”, 2002.

A. Majumderand Stevens, R. L., “Color Non-Uniformity in Projection Based Displays: Analysis and Solutions”, 2002.

I. T. Foster, Siebenlist, F., Tuecke, S., and Welch, V., “Security and Certification Issues in Grid Computing”, 2002.

C. Liu, Yang, L., Foster, I. T., and Angulo, D., “Design and Evaluation of a Resource Selection Framework for Grid Applications”, 2002.

L. Curfman McInnes, Norris, B., Bhowmick, S., and Raghavan, P., “Adaptive Sparse Linear Solvers for Implicit CFD using Newton-Krylov Algorithms”, 2002.

L. Yang, Foster, I. T., and Schopf, J. M., “Homeostatic and Tendency-based CPU Load Predictions”, 2002.

M. Anitescuand Hart, G. D., “Solving Nonconvex Problems of Multibody Dynamics with Contact and Small Friction by Successive Convex Relaxation”, 2002.

E. D. Dolan, Fourer, R., Goux, J. - P., and Munson, T. S., “Kestrel: A Callable Interface to the NEOS Server”, 2002.

P. D. Hovland, Norris, B., and Smith, B. F., “Making Automatic Differentiation Truly Automatic: Coupling PETSc with ADIC”, 2002.

M. Anitescuand Hart, G. D., “A Constraint-Stabilized Time-Stepping Approach for Rigid Multibody Dynamics with Joints, Contact and Friction”, 2002.

K. Keahey, Fredian, T. W., Peng, Q., Schissel, D. P., Thompson, M. R., Foster, I. T., Greenwald, M. J., and McCune, D. C., “Computational Grids in Action: The National Fusion Collaboratory”, 2002.

P. D. Hovlandand Norris, B., “Users' Guide to ADIC 1.1”, 2002.

R. Madduri, Hood, C. S., and Allcock, W. E., “Reliable File Transfer in Grid Environments”, 2002.

Z. Ernst, Fitelson, B., Harris, K., and Wos, L., “Shortest Axiomatizations of Implicational S4 and S5”, 2002.

E. T. Ong, Larson, J. W., and Jacob, R. L., “A Real Application of the Model Coupling Toolkit”, 2002.

G. von Laszewski, Blau, E., Gletzinger, M., Gawor, J., Lane, P., Martin, S., and Russell, M., “Software, Component, and Service Deployment in Computational Grids”, 2002.

S. Vazhkudai, Schopf, J. M., and Foster, I. T., “Predicting the Performance of Wide Area Data Transfers”, 2002.

U. Naumann, “Reducing the Memory Requirement in Reverse Mode Automatic Differentiation by Solving TBR Flow Equations”, 2002.

L. Wos, “A Spectrum of Applications of Automated Reasoning”, 2002.

B. Norris, Balay, S., Benson, S. J., Freitag, L., Hovland, P. D., McInnes, L. Curfman, and Smith, B. F., “Parallel Components for PDEs and Optimization: Some Issues and Experiences”, 2002.

N. Maltsev, Marland, E., Yu, G. X., Bhatnagar, S., and Lusk, E. L., “Sentra, A Database of Signal Transduction Proteins”, Nucleic Acids Research, vol. 30, no. 1, pp. 349-350, 2002.

T. Iliescuand Fischer, P. F., “Large Eddy Simulation of Turbulent Channel Flows by the Rational LES Model”, 2002.

I. T. Foster, “The Grid: A New Infrastructure for 21st Century Science”, 2002.

L. Hascoet, Naumann, U., and Pascual, V., “TBR Analysis in Reverse-Mode Automatic Differentiation”, 2002.

U. Naumann, S. Tadjouddine, F. M., and Phyce, J., “A Standard Interface for Elimination Sequences in Automatic Differentiation”, 2002.

E. D. Dolan, Fourer, R., More', J. J., and Munson, T. S., “The NEOS Server for Optimization: Version 4 and Beyond”, 2002.

G. von Laszewski, “Grid Computing: Enabling a Vision for Collaborative Research”, 2002.

U. Naumann, “On Optimal Jacobian Accumulation for Single Expression use Programs”, 2002.

N. T. Karonis, Toonen, B., and Foster, I. T., “MPICH-G2: A Grid-Enabled Implementation of the Message Passing Interface”, 2002.

L. Freitag, “Creating Interoperable Meshing and Discretization Software: Teh Terascale Simulation Tools and Technology Center”, 2002.

N. T. Karonis, de Supinski, B. R., Foster, I. T., Gropp, W. D., Lusk, E. L., and Lacour, S., “A Multilevel Approach to Topology-Aware Collective Operations in Computational Grids”, 2002.

L. Freitag, Knupp, P., Munson, T. S., and Shontz, S., “A Comparison of Optimization Software for Mesh Shape-Quality Improvement Problems”, 2002.

G. von Laszewski, Foster, I. T., Gawor, J., Schreiber, A., and Pena, C. J., “InforGram: A Grid Service that Supports Both Infomation Queries and Job Execution”, 2002.

W. E. Allcock, Bester, J., Bresnahan, J., Foster, I. T., Gawor, J., Insley, J. A., Link, J. M., and Papka, M. E., “GridMapper: A Tool for Visualizing the Behavior of Large-Scale Distributed Systems”, 2002.

P. D. Hovland, Naumann, U., and Norris, B., “An XML-Based Platform for Semantic Transformation of Numerical Programs”, 2002.

S. Vazhkudaiand Schopf, J. M., “Predicting Sporadic Grid Data Transfers”, 2002.

L. Freitag, Leurent, T., Knupp, P., and Melander, D., “MESQUITE Design: Issues in the Development of a Mesh Quality Improvement Toolkit”, 2002.

I. T. Foster, Voeckler, J., Wilde, M., and Zhao, Y., “Chimera: A Virtual Data System for Representing, Querying, and Automating Data Derivation”, 2002.

M. Anitescuand Hart, G. D., “A Fixed-Point Iteration Approach for Multibody Dynamics with Contact and Small Friction”, 2002.

T. Iliescuand Fischer, P. F., “Backscatter in the Rational LES Model”, 2002.

P. M. Dickensand Gropp, W. D., “An Evaluation of a User-Level Data Transfer Mechanism for High-Performance Networks”, 2002.

G. von Laszewski, Russell, M., Foster, I. T., Shalf, J., Allen, G., Daues, G., Novotny, J., and Seidel, E., “Community Software Development with the Astrophysics Simulation Collaboratory”, 2002.

G. von Laszewski, Ruscic, B., Wagstrom, P., Krishnan, S., Amin, K., Nijsure, S., Bittner, S., Pinzon, R., Hewson, J. C., Morton, M. L., Minkoff, M., and Wagner, A. F., “A Grid Service-Based Active Thermochemical Table Framework”, 2002.

L. Wos, Ulrich, D., and Fitelson, B., “Vanquishing the XCB Question: The Methodological Discovery of the Last Shortest Axiom for the Equivalential Calculus”, 2002.

J. Annis, Zhao, Y., Voeckler, J., Wilde, M., Kent, S., and Foster, I. T., “Applying Chimera Virtual Data Concepts to Cluster Finding in the Sloan Sky Survey”, 2002.

M. R. Paul, Cross, M. C., and Fischer, P. F., “Rayleigh-Benard Convection with a Radial Ramp in Plate Separation”, 2002.

S. Vazhkudaiand Schopf, J. M., “Using Disk Throughput Data in Predictions of End-to-End Grid Data Transfers”, 2002.

S. Krishnan, Wagstrom, P., and von Laszewski, G., “GSFL: A Workflow Framework for Grid Services”, 2002.

J. N. Lynessand Joe, S., “The Number of Lattice Rules of Specified Upper Class and Rank”, 2002.

A. Ching, Choudhary, A., Liao, W. - K., Ross, R. B., and Gropp, W. D., “Noncontiguous I/O through PVFS”, 2002.

M. W. Knop, Dinda, P. A., and Schopf, J. M., “Windows Performance Monitoring and Data Reduction using WatchTower”, 2002.

L. Wosand Thiele, T., “Hilbert's New Problem”, 2002.

J. J. More', “Computing Mountain Passes and Transition States”, 2002.

W. D. Gropp, “Building Library Components That Can Use Any MPI Implementation”, 2002.

W. McCune, Padmanabhan, R., and Veroff, R., “Yet Another Single Law for Lattices”, 2002.

W. D. Groppand Lusk, E. L., “Goals Guiding Design: PVM and MPI”, in 4th IEEE International Conference on Cluster Computing, San Diego, CA, 2002.

J. P. Navarro, Evard, R., Nurmi, D., and Desai, N. L., “Scalable Cluster Administration - Chiba City I Approach and Lessons Learned”, 2002.

R. Evard, Desai, N. L., Navarro, J. P., and Nurmi, D., “Clusters as Large-Scale Development Facilities”, 2002.

L. Wos, Ulrich, D., and Fitelson, B., “XCB, the Last of the Shortest Single Axioms for the Classical Equivalential Calculus”, 2002.

M. Russell, Allen, G., Daues, G., Foster, I. T., Seidel, E., Novotny, J., Shalf, J., and von Laszewski, G., “The Astrophysics Simulation Collaboratory: A Science Portal Enabling Community Software Development”, 2002.

L. Wos, Veroff, R., and Pieper, G. W., “Logical Basis for the Automation of Reasoning: Case Studies”, 2002.

2001

R. Thieleand Wos, L., “Hilbert's Twenty-Fourth Problem”, 2001.

M. A. Roseand Wilkinson, K., “Application of Model Search to Lattice Theory”, 2001.

W. McCune, “Single Axioms: With and Without Computers”, 2001.

I. T. Foster, “Grid Technologies and Applications: Architecture and Achievements”, 2001.

W. D. Gropp, “Learning from the Success of MPI”, 2001.

G. Allen, Angulo, D., Foster, I. T., Lanfermann, G., Liu, C., Radke, T., Seidel, E., and Shalf, J., “The Cactus Worm: Experiments with Dynamic Resource Discovery and Allocation in a Grid Environment”, 2001.

P. F. Fischer, Kruse, G. W., and Loth, F., “Spectral Element Methods for Transitional Flows”, 2001.

H. G. Kaperand Kaper, T. J., “Asymptotic Analysis of Two Reduction Methods for Systems of Chemical Reactions”, 2001.

L. Wos, “The Strategy of Cramming”, 2001.

S. Vazhkudaiand von Laszewski, G., “A Greedy Grid - The Grid Economic Engine Directive”, 2001.

R. B. Ross, Nurmi, D., Cheng, A., and Zingale, M., “A Case Study in Application I/O on Linux Clusters”, 2001.

A. Schreiber, “The Integrated Simulation Environment TENT”, 2001.

E. M. Gertzand Wright, S. J., “Object-Oriented Software for Quadratic Programming”, 2001.

P. F. Fischerand Iliescu, T., “A 3D Channel Flow Simulation at RE[sub \tau] = 180 Using a Rational LES Model”, 2001.

S. Verma, Gawor, J., von Laszewski, G., and Parashar, M., “A CORBA Commodity Grid Kit”, 2001.

G. von Laszewski, Foster, I. T., Thiruvathukal, G. K., and Toonen, B., “A Computational Framework for Telemedicine”, 2001.

L. C. Berselli, Galdi, G. P., Iliescu, T., and Layton, W. J., “Mathematical Analysis for the Rational Large Eddy Simulation Model”, 2001.

J. W. Larson, Jacob, R. L., Foster, I. T., and Guo, J., “The Model Coupling Toolkit”, 2001.

L. Freitagand Plassman, P. E., “Untangling Mapped Quadrilateral Meshes with Concave Boundaries”, 2001.

R. B. Rossand Ligon, III, W. B., “Server-Side Scheduling in Cluster Parallel I/O Systems”, Sterling, 2001.

Z. Ernst, Fitelson, B., Harris, K., and Wos, L., “A Concise Axiomatization of RM{sub ->}”, 2001.

O. S. Matlin, Lusk, E. L., and McCune, W., “SPINning Parallel Systems Software”, in 9th International SPIN Workshop, Lecture Notes in Computer Science, Springer, Grenoble, France, 2002, 2001.

X. Wu, Taylor, V. E., Li, X., Geisler, J., Lan, Z., Stevens, R. L., Hereld, M., and Judson, I. R., “Design and Development of Prophesy Performance Database for distributed Scientific Applications”, in 10th SIAM Conference on Parallel Processing for Scientific Computing, 2001.

P. D. Chaand de Pillis, L. G., “Model Updating by Adding Known Masses”, International Journal for Numerical Methods in Engineering, vol. 50, no. 11, pp. 2547-2571, 2001.

E. D. Dolan, Hovland, P. D., More', J. J., Norris, J., and Smith, B. F., “Remote Access to Mathematical Software”, 2001.

Y. Wang, De Carlo, F., Mancini, D. C., McNulty, I., Tieman, B., Bresnahan, J., Foster, I. T., Insley, J. A., Lane, P., and von Laszewski, G., “A High-Throughput X-Ray Microtomography System at the Advanced Photon Source”, 2001.

E. T. Ong, Lusk, E. L., and Gropp, W. D., “Scalable Unix Commands for Parallel Processors: A High-Performance Implementation”, 8th EuroPVM/MPI Users, vol. 2131, pp. 410-418, 2001.

E. M. Gertz, Gill, P. E., and Muetherig, J., “Users Guide for SnadiOpt: A Package Adding Automatic Differentiation to Snopt”, 2001.

E. M. Gertzand Wright, S. J., “OOQP User Guide”, 2001.

R. L. Jacob, Schafer, C., Foster, I. T., Robis, M., and Anderson, J., “Computational Design and Performance of the Fast Ocean Atmosphere Model, Version One”, 2001.

J. S. Jiang, Kaper, H. G., and Leaf, G. K., “Numerical Simulations at Magnetic Reversal in Layered Spring Magnets”, 2001.

I. R. Judson, “The [mu]Mural: A Six-Projector Tiled Display”, 2001.

W. McCune, “MACE 2.0 Reference Manual and Guide”, 2001.

J. A. Taylorand Larson, J. W., “Resolution Dependence in Modeling Extreme Weather Events”, 2001.

E. D. Dolanand Munson, T. S., “The Kestrel Interface to the NEOS Server”, 2001.

E. D. Dolan, “NEOS Server 4.0 Administrative Guide”, 2001.

S. J. Wright, “Effects of Finite-Precision Arithmetic on Interior-Point Methods for Nonlinear Programming”, 2001.

J. T. Linderothand Wright, S. J., “Decomposition Algorithms for Stochastic Programming on a Computational Grid”, 2001.

L. R. Leung, Michalakes, J. G., and Bian, X., “Parallelization of a Subgrid Orographic Precipitation Scheme in an MM5-based Regional Climate Model”, 2001.

R. Shepard, Wagner, A. F., Tilson, J. L., and Minkoff, M., “The Subspace Projected Approximate Matrix (SPAM) Modification of the Davidson Method”, 2001.

M. Garbey, Kaper, H. G., and Romanyukha, N., “A Fast Solver for Systems of Reaction-Diffusion Equations”, 2001.

T. Colin, Galusinski, C., and Kaper, H. G., “Waves in Ferromagnetic Media”, 2001.

T. Iliescu, John, V., and Layton, W. J., “Convergence of Finite Element Approximations of Large Eddy Motion”, 2001.

M. R. Paul, Cross, M. C., Fischer, P. F., and Greenside, H. S., “Power Law Behavior of Power Spectra in Low Prandtl Number Rayleigh-Benard convection”, 2001.

M. Anitescuand Potra, F. A., “A Time-Stepping Method for Stiff Multibody Dynamics with Contact and Friction”, 2001.

E. M. Gertz, “A Quasi-Newton Trust-Region Method”, 2001.

S. J. Bensonand Ye, Y., “DSDP3: Dual Scaling Algorithm for General Positive Semidefinite Programming”, 2001.

E. D. Dolanand More', J. J., “Benchmarking Optimization Software with Performance Profiles”, 2001.

J. S. Jiang, Kaper, H. G., and Leaf, G. K., “Hysteresis in Layered Spring Magnets”, 2001.

J. G. Michalakes, Chen, S., Dudhia, J., Hart, L., Klemp, J., Middlecoff, J., and Skamarock, W., “Development of a Next-Generation Regional Weather Research and Forecast Model”, 2001.

S. Vazhkudai, Tuecke, S., and Foster, I. T., “Replica Selection in the Globus Data Grid,”, 2001.

I. T. Foster, Kesselman, C., and Tuecke, S., “The Anatomy of the Grid - Enabling Scalable Virtual Organizations”, 2001.

W. E. Allcock, Bester, J., Bresnahan, J., Chervenak, A. L., Foster, I. T., Kesselman, C., Meder, S., Nefedova, V., Quesnel, D., and Tuecke, S., “Secure, Efficient Data Transport and Replica Management for High-Performance Data-Intensive Computing”, 2001.

R. M. Butler, Gropp, W. D., and Lusk, E. L., “Components and Interfaces of a Process Management System for Parallel Programs”, Parallel Computing, vol. 27, pp. 1417-1429, 2001.

2000

G. von Laszewski, Foster, I. T., Gawor, J., and Lane, P., “A Java Commodity Grid Kit”, 2000.

R. M. Butler, Engert, D., Foster, I. T., Kesselman, C., Tuecke, S., Volmer, J., and Welch, V., “A National-Scale Authentication Infrastructure”, 2000.

P. M. Dickensand Thakur, R., “On Implementing High-Performance Collective I/O”, 2000.

W. D. Gropp, Kaushik, D. K., Keyes, D. E., and Smith, B. F., “Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance CFD”, 2000.

P. M. Dickensand Thakur, R., “An Evaluation of Java's I/O Capabilities for High-Performance Computing”, 2000.

W. McCune, Veroff, R., Fitelson, B., Harris, K., Feist, A., and Wos, L., “Short Single Axioms for Boolean Algebra”, 2000.

W. McCune, “The Robbins Equation”, 2000.

H. M. Becker, Buschelman, K. R., and Hovland, P. D., “A Matrix-Matrix Multiplication Approach to the Automatic Differentiation and Parallelization of Straight-Line Codes”, VDE Verlag, 2000.

M. C. Ferrisand Munson, T. S., “Semismooth Support Vector Machines”, 2000.

J. J. More', “Automatic Differentiation Tools in Optimization Software”, 2000.

K. R. Buschelman, Gropp, W. D., McInnes, L. Curfman, and Smith, B. F., “PETSc and Overture: Lessons Learned Developing an Interface between Components”, Kluwer Academic, 2000.

T. Iliescu, “Genuinely Nonlinear Models for Convection-Dominated Problems”, 2000.

B. Norrisand Hovland, P. D., “A Distributed Application Server for Automatic Differentiation”, 2000.

P. D. Hovland, Keyes, D. E., McInnes, L. Curfman, and Samyono, W., “Using Automatic Differentiation for Second-Order Matrix-free Methods in PDE-constrained Optimization”, 2000.

W. D. Gropp, Kaushik, D. K., Keyes, D. E., and Smith, B. F., “Performance Modeling and Tuning of an Unstructured Mesh CFD Application”, 2000.

J. N. Lynessand Cools, R., “Notes on a Search for Optimal Lattice Rules”, 2000.

B. Fitelsonand Wos, L., “Axiomatic Proofs through Automated Reasoning”, 2000.

W. D. Gropp, “Runtime Checking of Datatype Signatures in MPI”, 2000.

L. Wos, “Appendix (to P825): Conjectures Concerning Proof, Design, and Verification”, 2000.

S. Balay, Gropp, W. D., McInnes, L. Curfman, and Smith, B. F., “Software for the Scalable Solution of PDEs”, 2000.

W. D. Gropp, Kaushik, D. K., Keyes, D. E., and Smith, B. F., “Understanding the Parallel Scalability of an Implicit Unstructured Mesh CFD Code”, 2000.

I. T. Fosterand Kesselman, C., “Computational Grids”, Springer-Verlag, 2000.

A. Roy, Foster, I. T., Gropp, W. D., Karonis, N. T., Sander, V., and Toonen, B., “MPICH-GQ: Quality-of-Service for Message Passing Programs”, 2000.

R. Thakurand Gropp, W. D., “Parallel I/O”, 2000.

B. Fitelsonand Wos, L., “Finding Missing Proofs with Automated Reasoning”, 2000.

H. G. Kaperand Nordborg, H., “The Frozen-Field Approximation and the Ginzburg-Landau Equations of Superconductivity”, 2000.

S. J. Bensonand Ye, Y., “Approximating Maximum Stable Set and Minimum Graph Coloring Problems with the Positive Semidefinite Relaxation”, 2000.

F. A. Potraand Wright, S. J., “Interior-Point Methods”, 2000.

R. Rosner, Calder, A. C., Dursi, J., Fryxell, B., Lamb, D. Q., Niemeyer, J. C., Olson, K., Ricker, P., Timmes, F. X., Truran, J. W., Tufo, H. M., Young, Y. - N., Zingale, M., Lusk, E. L., and Stevens, R. L., “Flash Code: Studying Astrophysical Thermonuclear Flashes”, Computing in Science and Engineering, vol. 2, no. 2, pp. 33-41, 2000.

D. Bonachea, Dickens, P. M., and Thakur, R., “High-Performance File I/O in Java: Existing Approaches and Bulk I/O Extensions”, 2000.

C. H. Bischofand Becker, H. M., “Computing Derivatives of Computer Programs”, 2000.

S. J. Wright, “Constraint Identification and Algorithm Stabilization for Degenerate Nonlinear Programs”, 2000.

M. Anitescu, “On Solving Mathematical Programs with Complementarity Constraints as Nonlinear Programs”, 2000.

A. C. Calder, Curtis, B. C., Dursi, J., Fryxell, B., Henry, G., MacNeice, P., Olson, K., Ricker, P., Rosner, R., Timmes, F. X., Tufo, H. M., Truran, J. W., and Zingale, M., “High-Performance Reactive Fluid Flow Simulations Using Adaptive Mesh Refinement on Thousands of Processors”, 2000.

G. von Laszewski, Insley, J. A., Foster, I. T., Bresnahan, J., Kesselman, C., Su, M. - H., Thiebaux, M., Rivers, M. L., Wang, S., Tieman, B., and McNulty, I., “Real-Time Analysis, Visualization, and Steering of Microtomography Experiments at Photon Sources”, 2000.

J. A. Taylorand Orr, J. C., “The Natural Latitudinal Distribution of Atmospheric CO2”, 2000.

L. Freitagand Loy, R., “Comparison of Remote Visualization Strategies for Interactive Exploration of Large Data Sets”, 2000.

A. Choudhary, Kandemir, M., No, J., Memik, G., Shen, X., Liao, W. - K., Nagesh, H., More, S., Taylor, V. E., Thakur, R., and Stevens, R. L., “Data Management for Large-Scale Scientific Computations in High Performance Distributed Systems”, Cluster Computing, vol. 3, no. 1, pp. 45 - 60, 2000.

J. No, Thakur, R., Kaushik, D. K., Freitag, L., and Choudhary, A., “A Scientific Data Management System for Irregular Applications”, 2000.

J. Bresnahan, Insley, J. A., and Papka, M. E., “Interacting with Scientific Visualizations: User-Interface Tools within Spatially Immersive Displays”, 2000.

W. D. Gropp, Kaushik, D. K., Keyes, D. E., and Smith, B. F., “High Performance Parallel Implicit CFD”, 2000.

L. Wosand Fitelson, B., “Automating the Search for Answers to Open Questions”, 2000.

J. - P. Goux, Linderoth, J. T., and Yoder, M., “Metacomputing and the Master-Worker Paradigm”, 2000.

J. A. Taylor, “Global Environmental Management: A Historical Perspective”, 2000.

J. A. Taylor, “Workshop Report - Bridging the Climate Information Gap”, 2000.

W. McCune, “Single Axioms for Boolean Algebra”, 2000.

M. M. Marino, “Relativistic Pseudopotentional Incorporating Core/Valence Polarization and Nonlocal Effects”, 2000.

E. D. Dolanand More', J. J., “Benchmarking Optimization Software with COPS”, 2000.

G. von Laszewski, Gawor, J., Lane, P., Rehn, N., and Russell, M., “Features of the Java Commodity Grid Kit”, Concurrency Computat.: Pract. Exper., vol. 14, no. 13, pp. 1045-1055, 2000.

R. Veroffand McCune, W., “A Short Sheffer Axiom for Boolean Algebra”, 2000.

N. T. Karonis, de Supinski, B. R., Foster, I. T., Gropp, W. D., Lusk, E. L., and Bresnahan, J., “Exploiting Hierarchy in Parallel Computer Networks to Optimize Collective Operation Performance”, in 14th International Parallel and Distributed Processing Symposium, IEEE Electronic Library, Cancun, Mexico, 2000.

P. B. Albee, Stockman, G. C., and Smucker, A. J. M., “Extraction of Pores from Microtomographic Reconstructions of Intact Soil Aggregates”, 2000.

W. D. Gropp, Keyes, D. E., McInnes, L. Curfman, and Tidriri, M. D., “Globalized Newton-Krylov-Schwarz Algorithms and Software for Parallel Implicit CFD”, 2000.

W. McCuneand Shumsky, O., “System Description: IVY”, 2000.

H. G. Kaperand Nordborg, H., “The Ginzburg-Landau Equations of Superconductivity in the Limit of Weak Coupling Near the Upper Critical Field”, 2000.

B. Fitelsonand Wos, L., “Missing Proofs Found”, 2000.

L. Wos, “Conquering the Meredith Single Axiom”, 2000.

L. Wos, “A Milestone Reached and a Secret Revealed”, 2000.

R. M. Butler, Gropp, W. D., and Lusk, E. L., “A Scalable Process-Management Environment for Parallel Programs”, in 7th EuroPVM/MPI Users, Balatonfured, Hungary, 2000.

L. Freitagand Knupp, P., “Tetrahedral Mesh Improvement via Optimization of the Element Condition Number”, 2000.

E. G. de Pillisand de Pillis, L. G., “The Long-Term Impmact of University Budget Cuts: A Mathematical Model”, 2000.

G. von Laszewski, Shudo, K., and Muraoka, Y., “Grid-based Asynchronous Migration of Execution Context in Java Virtual Machines”, 2000.

M. Hereld, Judson, I. R., and Stevens, R. L., “Introduction to Building Projection-based Tiled Display Systems”, 2000.

L. Childers, Disz, T. L., Olson, R., Papka, M. E., Stevens, R. L., and Udeshi, T., “Access Grid: Immersive Group-to-Group Collaborative Visualization”, 2000.

J. Abate, Benson, S. J., Grignon, L., Hovland, P. D., McInnes, L. Curfman, and Norris, B., “Integrating Automatic Differentiation with Object-Oriented Toolkits for High-Performance Scientific Computing”, 2000.

J. G. Kimand Hovland, P. D., “Sensitivity Analysis and Parameter Tuning of a Sea-Ice Model”, 2000.

S. L. Leeand Hovland, P. D., “Sensitivity Analysis Using Parallel ODE Solvers and Automatic Differentiation inC: SensPVODE and ADIC”, 2000.

L. Freitagand Loy, R., “Using Desktop Graphics Workstations for Interactive Remote Exploration of Large Data Sets”, 2000.

T. Canfield, Chien, T., Domanus, H., Tentner, A., Tzanos, C., Valentin, R., and Weber, D., “A Coupled Newton-Krylov Solver for Improved CHAD Cache Utilization and Performance”, 2000.

E. A. Yildirimand Wright, S. J., “Warm-start Strategies in Interior-Point Methods for Linear Programming”, 2000.

J. No, Thakur, R., and Choudhary, A., “Integrating Parallel File I/O and Database Support for High-Performance Scientific Data Management”, 2000.

C. H. Bischof, Becker, H. M., and Hovland, P. D., “On Combining Computational Differentiation and Toolkits for Parallel Scientific Computing”, 2000.

P. D. Hovlandand McInnes, L. Curfman, “Parallel Simulation of Compressible Flow Using Automatic Differentiation and PETSc”, 2000.

T. Udeshi, Hudson, R., and Papka, M. E., “Seamless Multiresolution Isosurfaces Using Wavelets”, 2000.

S. J. Wright, “On Reduced Convex QP Formulations of Monotone LCP Problems”, 2000.

I. T. Foster, Roy, A., and Sander, V., “A Quality of Service Architecture that Combines Resource Reservation and Application Adaptation”, 2000.

L. G. de Pillisand de Pillis, E. G., “A Mathematical Framework for Understanding Continuum Effects of Budget Fluctuations on a University”, 2000.

L. G. de Pillisand Radunskaya, A., “A Mathematical Tumor Model with Immune Resistance and Drug Therapy: an Optimal Control Approach”, 2000.

P. H. Carns, Ligon, III, W. B., Ross, R. B., and Thakur, R., “PVFS: A Parallel File System for Linux Clusters”, 2000.

G. von Laszewski, Su, M. - H., Foster, I. T., and Kesselman, C., “Quasi Real-Time Microtomography Experiments at Photon Sources”, 2000.

M. Anitescu, “Nonlinear Programs with Unbounded Lagrange Multiplier Sets”, 2000.