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Reference | Publication | Mathematics and Computer Science Division

MCS 2012 Publications

R. Kettimuthu, Lacinski, L., Link, M., Pickett, K., Tuecke, S., and Foster, I. T., “Instant GridFTP”, in 9th Workshop on High Performance Grid and Cloud Computing, 2012.

S. J. Kim, Son, S. W., Kandemir, M., Liao, W. - K., Thakur, R., and Choudhary, A., “Dynamic Tracing of Parallel I/O Activity in HPC Applications”, 2012.

J. Dinan, Goodell, D., Gropp, W. D., Thakur, R., and Balaji, P., “Efficient Multithreaded Context ID Allocation in MPI*”, in EuroMPI'12, 2012.

J. Brown, Knepley, M. G., May, D. A., McInnes, L. Curfman, and Smith, B. F., “Composable LInear Solvers for Multiphysics”, in 11th International Symposium on Parallel and Distributed Computing, Munich, Germany, 2012.

T. Peterkaand Ross, R. B., “Versatile Communication Algorithms for Data Analysis”, in EuroMPI'12, 2012.

H. Cole-Mullen, Lyons, A., and Utke, J., “Storing Versus Recomputation on Multiple DAGs”, in Recent Advances in Algorithmic Differentiation, Lecture Notes in Computational Science and Engineering, vol. 87, New York: Springer, 2012, pp. 197-207.

S. M. Aithal, “A Comparative Study of NOx Computation Methods Coupled to Quasi-Dimensional Models in SI Engines.”, in ICEF2012, Vancouver, BC, Canada, 2012.

D. Ozog, Hammond, J. R., Dinan, J., Balaji, P., Shende, S., and Malony, A. D., “Inspector-Executor Load Balancing Algorithms for Block-Sparse Tensor Contractions”, in ICS '13, 2012.

P. H. Carns, Harms, K., Kimpe, D., Wozniak, J. M., Ross, R. B., Ward, L., Curry, M., Klundt, R., Danielson, G., Karakoyunlu, C., Chandy, J. A., Settlemyer, B., and Gropp, W. D., “A Case for Optimistic Coordination in HPC Storage Systems”, in SC2012, Salt Lake City, UT, 2012.

B. Adams, Insepov, Z., and Norem, J., “Simulations of Fast X-Ray Detectors Based on Multichannel Plates”, in International Parallel and Distributed Processing Symposium (IPDPS 2012)), New Orleans, LA, 2012.

D. Kimpe, Mohror, K., Moody, A., Van Essen, B., Gokhale, M., Ross, R. B., and de Supinski, B. R., “Integrated In-System Storage Architecture for High Performance Computing”, in ROSS '12, 2012.

T. Peterka, Kwan, J., Pope, A., Finkel, H., Heitmann, K., Habib, S., Wang, J., and Zagaris, G., “Meshing the Universe: Integrating Analysis in Cosmological Simulations”, in SC Ultrascale Visualization Workshop, 2012.

J. A. Reed, Utke, J., and Abdel-khalik, H. S., “Combining Automatic Differentiation Methods for High Dimensional Nonlinear Models”, in Recent Advances in Algorithmic Differentiation: Lecture Notes in Computational Science and Engineering, vol. 87, Springer, 2012, pp. 23-33.

J. Chen, “On Use of Discrete Laplace Operator for Preconditioning Kernel Matrices”, SIAM Journal on Scientific Computing, vol. 35, no. 2, pp. A577-A602, 2012.

F. X. Giraldo, Kelly, J. F., and Constantinescu, E. M., “Implicit-Explicit Formulations of a Three-Dimensional Nonhydrostatic Unified Model of the Atmosphere (NUMA)”, SIAM Journal on Scientific Computing, vol. 35, no. 5, pp. B1162-B1194, 2012.

D. E. Keyes, McInnes, L. Curfman, Woodward, C., Gropp, W. D., Myra, E., and Pernice, M., “Multiphysics Simulations: Challenges and Opportunities”, 2012.

T. Heyn, Anitescu, M., Tasora, A., and Negrut, D., “Using Krylov Subspace and Spectral Methods for Solving Complementarit Problems in Many-Body Contact Dynamics Simulation”, International Journal for Numerical Methods in Engineering, 2012.

A. Gainaru, Cappello, F., Snir, M., and Kramer, W., “Fault Prediction Under the Mircroscope: A Closer Look into HPC Systems”, in SC'12, 2012.

S. Abhyankarand Flueck, A. J., “Real-Time Power System Dynamics Simulation Using a Parallel Block-Jacobi Preconditioned Newton-GMRES Scheme”, in 2nd International Workshop on High Performance Computing, Networking, and Analytics for the Power Grid , Salt Lake City, UT, 2012.

J. Chenand Burer, S., “Globally Solving Nonconvex Quadratic Programming Problems via Completely Positive Programming”, Mathematical Programming Computation, vol. 4, no. 1, 2012.

R. Jainand Tautges, T. J., “RGG: Reactor Geometry (and mesh) Generator”, in 2012 International Congress on the Advances in Nuclear Power Plants, 2012.

L. Wos, “The Legacy of a Great Researcher”, in Automated Reasoning and Mathematics: Essays in Memory of William McCune, Springer-Verlag, 2012.

M. S. Min, Fu, J., and Mametjanov, A., “Hybrid Programming and Performance for Beam Propagation Modeling”, in 11th International Computatioal Accelerator Physics Conference (ICAP 2012), Rostock-Warnemunde, Germany, 2012.

S. Xiao, Balaji, P., Zhu, Q., Thakur, R., Coghlan, S. M., Lin, H., Wen, G., Hong, J., and Feng, W., “VOCL: An Optimized Environment for Transparent Virtualization of Graphics Processing Units”, in 1st Innovative Parallel Computing, San Jose, CA, 2012.

I. T. Foster, Kettimuthu, R., Martin, S., Tuecke, S., Milroy, D., Palen, B., Hauser, T., and Braden, J., “Campus Bridging Made Easy via Globus Services”, in XSEDE '12, Chicago, IL, 2012.

N. A. Best, Elliott, J., and Foster, I. T., “Synthesis of a Complete Land Use/Land Cover Data Set for Conterminous United States”, 2012.

J. M. Wozniak, Wilde, M., and Katz, D. S., “JETS: Language and System Support for Many-Parallel-Task Workflows”, J. Grid Computing, 2012.

J. J. More'and Wild, S. M., “Estimating Derivatives of Noisy Simulations”, ACM Transactions on Mathematical Software (TOMS), vol. 38, no. 3, 2012.

J. Elliott, Franklin, M., Foster, I. T., Judd, K., and Munson, T. S., “Propagation of Data Error and Parametric Sensitivity in Computable General Equilibrium Model Forecasts”, Computational Economics, vol. 39, 2012.

A. Lyons, Safro, I., and Utke, J., “Randomized Heuristics for Exploiting Jacobian Scarcity”, Optimization Methods & Software, vol. 27, no. 2, 2012.

J. Elliott, Foster, I. T., Kortum, S., Jush, G. K., Munson, T. S., and Weisbach, D., “Unilateral Carbon Taxes, Border Tax Adjustments and Carbon Leakage”, University of Chicago Institute for Law and Economics, Chicago, IL, 2012.

S. T. Choiand Saunders, M. A., “Algorithm & Documentation: MINRES-QLP for Singular Symmetric and Hermitian Linear Equations and Least-Squares Problems”, ACM Transactions on Mathematical Software (TOMS), 2012.

A. Wilke, Harrison, T., Wilkening, J., Field, D., Glass, E. M., Kyrpides, N., Mavrommatis, K., and Meyer, F., “The M5nr: A Novel Non-Redundant Database Containing Protein Sequences and Annotations from Multiple Sources and Associated Tools”, BMC Bioinformatics, vol. 13, no. 1, 2012.

Z. Insepov, Rest, J., Yacout, A. M., Ye, B., Yun, D., Kuksin, A. Y., Norman, G. E., Stegailov, V. V., and Yanilkin, A. V., “Atomistic and Kinetic Simulations of Radiation Damage in Molybdenum”, in Materiasl Research Society (MRS) Proceedings, vol. 1444, 2012.

A. Kannanand Wild, S. M., “Benefits of Deeper Analysis in Simulation-Based Groundwater Optimization Problems”, in Computational Methods in Water Resources (CMW 2012), University of Illinois at Urbana-Champaign, 2012.

Z. Zhang, Katz, D. S., Wozniak, J. M., Espinosa, A., and Foster, I. T., “Design and Analysis of Data Management in Scalable Parallel Scripting”, in SC'12, Salt Lake City, UT, 2012.

J. Jenkins, Balaji, P., Dinan, J., Samatova, N. F., and Thakur, R., “Enabling Fast, Noncontiguous GPU Data Movement in Hybrid MPI+GPU Environments”, in CLUSTER '12, Beijing, China, 2012.

S. Mohanty, Jain, R., Majumdar, S., Tautges, T. J., and Srinivasan, M., “Coupled Field-Structural Analysis of HTGR Fuel Brick Using Abaqus”, in ICAPP '12, Chicago. IL, 2012.

N. Goldberg, Leyffer, S., and Munson, T. S., “A New Perspective on Convex Relations of Sparse SVM”, 2012.

J. Leigh, Johnson, A., Renambot, L., Vishwanath, V., Peterka, T., and Schwarz, N., “Visualization of Large-Scale Distributed Data”, in Data Intensive Distributed Computing, 2012.

E. M. Glassand Meyer, F., “Analysis of Metagenomics Data”, Bioinformatics for High Throughput Sequencing, 2012.

K. Yoshii, Iskra, K., Gupta, R., Beckman, P. H., Vishwanath, V., Yu, C., and Coghlan, S. M., “Evaluating Power Monitoring Capabilities on IBM Blue Gene/P and Blue Gene/Q”, in CLUSTER '12, Beijing, China, 2012.

J. Fu, Min, M. S., Latham, R., and Carothers, C. D., “I/O Threads to Reduce Checkpoint Blocking for an Electromagnetics Solver on Blue Gene/P and Cray XK6”, in ROSS '12, Venice, Italy, 2012.

C. Sigovan, Muelder, C., Ma, K., Cope, J., Iskra, K., and Ross, R. B., “A Visual Network Analysis Method for Large Scale Parallel I/O Systems”, in International Parallel and Distributed Processing Symposium (IPDPS 2013), 2012.

D. Kimpe, Carns, P. H., Harms, K., Wozniak, J. M., Lang, S., and Ross, R. B., “AESOP: Expressing Concurrency in High-Performance System Software”, in Networking, Architecture and Storage (NAS), 2012.

D. Goodell, Kim, S. J., Latham, R., Kandemir, M., and Ross, R. B., “An Evolutionary Path to Object Storage Access”, in SCC '12, Salt Lake City, UT, 2012.

G. C. Fox, von Laszewski, G., Diaz, J., Keahey, K., Fortes, J., Figueiredo, R., Smallen, S., Smith, W., and Grimshaw, A., “FutureGrid: A Reconfigurable Testbed for Cloud, HPC and Grid Computing”, in Contemporary High Performance Computing: From Petascale toward Exascale, Chapman & Hall, 2012.

P. Belotti, Kirches, C., Leyffer, S., Linderoth, J. T., Luedtke, J., and Mahajan, A., “Mixed-Integer Nonlinear Optimization”, 2012.

L. Zamboni, Cherchi, A., and Carril, A. F., “Characterization of Heat Waves: An Example for La Plata Basin”, 2012.

J. Chen, McInnes, L. Curfman, and Zhang, H., “Analysis and Practical Use of Flexible Bicgstab”, 2012.

J. J. More'and Wild, S. M., “Do You Trust Derivatives or Differences?*”, Journal of Computational Physics, vol. 273, pp. 268-277, 2012.

V. M. Zavala, “Clustering-Based Interior-Point Strategies for Stochastic Programs”, 2012.

R. L. Jacob, Krishna, J., Xu, X., Mickelson, S. A., Tautges, T. J., Wilde, M., Latham, R., Foster, I. T., Ross, R. B., Hereld, M., Larson, J. W., Bochev, P., Peterson, K., Taylor, M., Schuchardt, K., Yin, J., Middleton, D. E., Haley, M., Brown, D., Brownrigg, R., Huang, W., Shea, D., Vertenstein, M., Ma, K., and Xie, J., “Bringing Task and Data Parallelism to Analysis of Climate Model Output”, in Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW) , 2012.

J. Chen, Hovland, P. D., Munson, T. S., and Utke, J., “An Integer Programming Approach to Optimal Derivative Accumulation”, in Recent Advances in Algorithmic Differentiation, Lecture Notes in Computational Science and Engineering, 2012.

S. T. Choi, “Minimal Residual Methods for Complex Symmetric, Skew Symmetric, and Skew Hermitian Systems”, 2012.

C. Teng, Min, M., and Wang, J., “Pseudospectral and Runge-Kutta-Nystrom Methods for Second-Order Wave Equations: Stable and Accurate Boundary Treatments”, 2012.

D. Pugmire, Peterka, T., and Garth, C., “Parallel Integral Curves”, 2012.

M. L. Stein, Chen, J., and Anitescu, M., “Difference Filter Preconditioning for Large Covariance Matrices”, SIAM Journal on Matrix Analysis and Applications, vol. 33, no. 1, pp. 52-72, 2012.

M. Anitescu, Chen, J., and Wang, L., “A Matrix-Free Approach for Solving the Parametric Gaussian Process Maximum Likelihood Problem”, SIAM Journal on Scientific Computing, vol. 34, no. 1, pp. A240-A262, 2012.

J. Chen, Wang, L., and Anitescu, M., “A Fast Summation Tree Code for Matern Kernel”, SIAM Journal on Scientific Computing, vol. 36, no. 1, pp. A289-A309, 2012.

“ExM: High Level Dataflow Programming for Extreme-Scale Systems”, in 4th USENIX Workshop on Hot Topics in Parallelism , 4th USENIX Workshop on Hot Topics in Parallelism , 2012.

B. F. Smith, McInnes, L. Curfman, Constantinescu, E. M., Adams, M. L., Balay, S., Brown, J., Knepley, M. G., and Zhang, H., “PETSc's Software Strategy for the Design Space of Composable Extreme-Scale Solvers”, in DOE Exascale Research Conference, Portland, OR, 2012.

P. Balaji, Buntinas, D., and Kimpe, D., “Fault Tolerance Techniques for Scalable Computing”, 2012.

J. W. Larson, “Visualizing Climate Variability with Time-Dependent Probability Density Functions, Detecting it with Information Theory”, Procedia Computer Science, vol. 9, pp. 917-926, 2012.

N. Liu, Cope, J., Carns, P. H., Carothers, C. D., Ross, R. B., Grider, G., Crume, A., and Maltzahn, C., “On the Role of Burst Buffers in Leadership-Class Storage Systems”, in Proceedings of MSST/SNAPI 2012, Pacific Grove, CA, 2012.

J. Akerley, Greiner, M., Obabko, A. V., and Fischer, P. F., “Flow Destabilization and Heat Transfer Augmentation in an Array of Grooved Passages with Developing Flow”, 2012.

J. M. Wozniak, Armstrong, T. G., Maheshwari, K., Lusk, E. L., Katz, D. S., Wilde, M., and Foster, I. T., “Turbine: A Distributed-Memory Dataflow Engine for Extreme-Scale Many-Task Applications”, in Proceedings SWEET 2012, Scottsdale, AZ, 2012.

A. Mahajan, Leyffer, S., and Kirches, C., “Solving Mixed-Integer Nonlinear Programs by QP-Diving”, 2012.

V. M. Zavala, “Real-Time Resolution of Conflicting Objectives in Building Energy Management: An Utopia-Tracking Approach”, presented at the 03/2012, 2012.

L. Curfman McInnes, Smith, B. F., Zhang, H., and R. Mills, T., “Hierarchical and Nested Krylov Methods for Extreme-Scale Computing”, 2012.

K. A. Pruitt, Leyffer, S., Newman, A. M., and Braun, R. J., “Optimal Design and Dispatch of Distributed Generation Systems”, 2012.

C. Choudary, Godwin, J., Holewinski, J., Karthik, D., Lowell, D., Mametjanov, A., Norris, B., Sabin, G., and Sadayappan, P., “Stencil-Aware GPU Optimization of Iterative Solvers*”, 2012.

A. Gutfraind, Meyers, L. A., and Safro, I., “Multiscale Network Generation”, 2012.

Z. Insepovand Miller, R. J., “Activation of Nanoflows for Fuel Cells”, 2012.

T. Nelson, Belter, G., Siek, J. G., Jessup, E., and Norris, B., “Reliable Generation of High-Performance Matrix Algebra”, 2012.

J. Dinan, Balaji, P., Hammond, J. R., Krishnamoorthy, S., and Tipparaju, V., “Supporting the Global Arrays PGAS Model Using MPI One-Sided Communication”, in Proc. 26th Intl. Parallel and Distributed Processing Symp. (IPDPS), Shanghai, China, 2012.

A. N. Adhikari, Peng, J., Wilde, M., Xu, J., Freed, K. F., and Sosnick, T. R., “Modeling Large Regions in Proteins: Applications to Loops, Termini and Folding”, Protein Science, vol. 21, no. 1, pp. 107-121, 2012.

N. Liu, Carothers, C. D., Cope, J., Carns, P. H., and Ross, R. B., “Model and Simulation of Exascale Communication Networks”, Journal of Simulation, 2012.

T. O. Delmont, Prestat, E., Keegan, K. P., Faubladier, M., Robe, P., Clark, I. M., Pelletier, E., Hirsch, P. R., Meyer, F., Gilbert, J. A., Le Paslier, D., Simonet, P., and Vogel, T. M., “Structure, Fluctuation and Magnitude of a Natural Grassland Soil Metagenome”, ISME Journal, 2012.

I. Safro, Sanders, P., and Schulz, C., “Advanced Coarsening Schemes for Graph Partitioning”, in Experimental Algorithms, Lecture Notes in Computer Science, Bordeaux, France, 2012.

L. Zamboni, Cherchi, A., Barreiro, M., and Kurcharski, F., “Dynamic of the Impact of ENSO Flavors on Precipitation over La Plata Basin”, 2012.

E. Gawlik, Munson, T. S., Sarich, J., and Wild, S. M., “The TAO Linearly-Constrained Augmented Lagrangian Method for PDE-Constrained Optimization”, 2012.

T. S. Munson, Sarich, J., Wild, S. M., Benson, S. J., and McInnes, L. Curfman, “TAO 2.0 Users Manual”, 2012.

N. Goldberg, Leyffer, S., and Safro, I., “Optimal Response to Epidemics and Cyber Attacks in Networks”, 2012.

O. Roderick, Anitescu, M., and Wang, Z., “Reduced Order Approximations in Uncertainty Analysis of Nuclear Engineering Applications”, 2012.

K. Iskra, Yoshii, K., Gupta, R., and Beckman, P. H., “Advanced Virtual Memory for Exascale”, 2012.

J. M. Wozniak, Armstrong, T. G., Wilde, M., Katz, D. S., Lusk, E. L., and Foster, I. T., “Scalable Data Flow Programming for Many-Task Applications”, 2012.

T. J. Tautges, Kraftcheck, J. A., Bertram, N., Sachdeva, V., and Magerlein, J., “Mesh Interface Resolution and Ghost Exchange in a Parallel Mesh Representation”, in Workshop on Large-Scale Parallel Processing, Shanghai, China, 2012.

Z. Insepov, Starikov, S. V., Yun, D., and Yacout, A. M., “Multiscale Simulation Models of Xe Bubble Formation in Irradiated Mo”, 2012.

Z. Insepov, Kuksin, A. Y., Rest, J., Starikov, S. V., Yanilkin, A. V., Yacout, A. M., Ye, B., and Yun, D., “Simulation of Ion Irradiation of Nuclear Materials and Comparison with Experiment”, 2012.

T. Peterka, Kwan, J., Pope, A., Finkel, H., Heitmann, K., and Habib, S., “Meshing the Universe: Identifying Voids in Cosmological Simulations Through in Situ Parallel Voronoi Tessellation”, 2012.

M. McCourt, Rognlien, T. D., McInnes, L. Curfman, and Zhang, H., “Improving Parallel Scalability for Edge Plasma Transport Simulations with Neutral Gas Species”, 2012.

K. Iskra, Yoshii, K., Gupta, R., and Beckman, P. H., “Power Management for Exascale”, 2012.

A. Mametjanov, Norris, B., Zeng, X., Drewniak, B. A., Utke, J., Anitescu, M., and Hovland, P. D., “Applying Automatic Differentiation to the Community Land Model”, in 6th International Conference on Automatic Differentiation (AD2012), Fort Collins, CO, 2012.

S. H. K. Narayanan, Norris, B., Hovland, P. D., and Gebremedhin, A. H., “Implementation of Partial Separability in a Source-to-Source Transformation AD Tool”, in 6th International Conference on Automatic Differentiation (AD2012), Fort Collins, CO, 2012.

L. Hascoetand Utke, J., “Handling Pointers and Dynamic Memory”, 2012.

J. Chenand Li, L., “Parallelizing the Conjugate Gradient Algorithm for Multilevel Toeplitz Systems”, in Int. Conf. on Computational Science (ICCS 2013) , Barcelona, Spain, 2012.

J. A. Insley, Paliath, U., and Gupta, A., “Turbulent Mixing Noise from Jet Exhaust Nozzles”, in High Performance Computing Networking, Storage, and Analysis Companion, Seattle, Washington, 2012.

Y. Peng, Knight, C., Blood, P., Crosby, L., and Voth, G. A., “Extending Parallel Scalability of LAMMPS and Multiscale Reactive Molecular Simulations”, 2012.

A. Mametjanov, Lowell, D., Ma, C., and Norris, B., “Autotuning Stencil-Based Computations on GPUs”, 2012.

D. Kim, Larson, J. W., and Chiu, K., “Dynamic Load Balancing for Malleable Model Coupling”, in International Conference on Computational Science (ICCS 2012) , 2012.

M. Anitescu, Roderick, O., and Utke, J., “Derivative-Based Uncertainty Quantification: Automatic Differentiation Tools for SAS”, 2012.

Z. Insepovand Norem, J., “Can Surface Cracks and Unipolar Arcs Explain Breakdown and Gradient Limits?”, 2012.

N. Goldberg, Kim, Y., Leyffer, S., and Veselka, T., “Adaptively Refined Dynamic Program for Linear Spline Regression”, 2012.

O. Roderickand Anitescu, M., “Intrusive Uncertainty Quantification for NeK5000: Development of Intrusive Uncertainty Quantification for High-Dimensional, High-Fidelity Codes”, 2012.

L. Grinberg, Insley, J. A., Fedosov, D. A., Morozov, V., Papka, M. E., and Karniadakis, G., “Tightly Coupled Atomistic-Continum Simulations of Brain Blood Flow on Petaflop Supercomputers”, Computer Science Engineering, vol. 14, no. 6, pp. 58-67, 2012.

B. Dudson, Farley, S., and McInnes, L. Curfman, “Improved Nonlinear Solvers in BOUT++”, 2012.

D. P. Kouri, Heinkenschloos, M., Ridzal, D., and Waanders, B. G. Van Blo, “A Trust-Region Algorithm with Adaptive Stochastic Collocation for PDE Optimization Under Uncertainty”, 2012.

V. M. Zavalaand Anitescu, M., “Scalable Nonlinear Programming via Exact Differentiable Penalty Functions and Trust-Region Newton Methods”, 2012.

P. H. Carns, Harms, K., Latham, R., and Ross, R. B., “Performance Analysis of Darshan 2.2.3 on the Cray XE6 Platform”, 2012.

A. R. Siegel, Smith, K., Romano, P. K., Forget, B., and Felker, K. G., “Multi-Core Performance Studies of a Monte Carlo Neutron Transport Code”, 2012.

D. - H. Kim, Larson, J. W., and Chiu, K., “Malleable Model Coupling with Prediction”, in Proceedings of the The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID 2012), Ottawa, Canada, 2012.

M. Schwanen, Duggleby, A., and Fischer, P. F., “Orthogonal Decompostition Analysis and Optimization of Turbine Vane Endwall Horseshoe Vortex Dynamics and Heat Transfer”, 2012.