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Reference | Publication | Mathematics and Computer Science Division

MCS 2013 Publications

“MPI on Millions of Cores”, 2013.

P. Brune, Knepley, M. G., Smith, B. F., and Tu, X., “Composing Scalable Nonlinear Algebraic Solvers”, 2013.

M. McCourt, Smith, B. F., and Zhang, H., “Efficient Sparse Matrix-Matrix Products Using Colorings”, 2013.

F. Cappello, Di, S., Robert, Y., Vivien, F., Kondo, D., and Wang, C. - L., “Optimization of Cloud Task Processing with Checkpoint-Restart Mechanism”, in IEEE/ACM SC13, Denver, CO, 2013.

C. Reano, Mayo, R., Quintana-Orti, E. S., Silla, F., Duato, J., and Pena, A. J., “Influence of infiniband FDR on the performance of remote GPU virtualization.”, in IEEE Cluster 2013, Indianapolis, IN, 2013.

Z. Zhang, Katz, D. S., Armstrong, T. G., Wozniak, J. M., and Foster, I. T., “Parallelizing the Execution of Sequential Scripts”, in Super Computing (SC13), Denver, CO, 2013.

W. D. Groppand Snir, M., “Programming for Exascale Computers”, 2013.

J. Chen, Li, T. L. H., and Anitescu, M., “A Parallel Linear Solver for Multilevel Toeplitz Systems with Possibly Several Right-Hand Sides”, 2013.

S. Castruccio, McInerney, D. J., Stein, M. L., Liu, F., Jacob, R. L., and Moyer, E. J., “Statistical Emulation of Climate Model Projections Based on Precomputed GCM Runs”, 2013.

A. Vishnu, Song, S., Marquez, A., Barker, K., Kerbyson, D., Cameron, K., and Balaji, P., “Designing Energy Efficient Communication Runtime Systems: A View From PGAS Models”, 2013.

A. Wilke, Bischof, J., Harrison, T., Brettin, T., D'Souza, M., Gerlach, W., Matthews, H., Paczian, T., Wilkening, J., Glass, E. M., Desai, N. L., and Meyer, F., “A RESTful API for Accessing Microbial Community Data for MG-RAST”, 2013.

R. L. Jacob, Krishna, J., Xu, X., Tautges, T. J., Grindeanu, I., Latham, R., Peterson, K., Bochev, P., Haley, M., Brown, D., Brownrigg, R., Shea, D., Huang, W., and Middleton, D. E., “ParNCL and ParGAL: Data Parallel Tools for Post-Processing of Large-Scale Earth Science Data”, in International Conference on Computational Science (ICCS 2013), Barcelona, Spain, 2013, vol. 18, pp. 1245–1254.

A. R. Siegel, Smith, K., Felker, K. G., Romano, P. K., Forget, B., and Beckman, P. H., “Improved Cache Performance in Monte Carlo Transport Calculations Using Energy Banding”, Computer Physics Communications, vol. 185, pp. 1195-1199, 2013.

A. Callejo, Narayanan, S. H. K., J. de Jalon, G., and Norris, B., “Performance of Automatic Differentiation Tools in The Dynamic Simulation of Multibody Systems Based on a Semi-Recursive Penalty Formulation”, Computer Methods in Applied Mechanics and Engineering, 2013.

S. S. Patel, Min, M. S., Uga, K. C., and Lee, T., “A Spectral-Element Discontinuous Galerkin Lattice Boltzmann Method for Simulating Natural Convection Heat Transfer in a Horizontal Concentric Annulus”, Computers and Fluids, vol. 95, 2013.

J. Chen, Wang, J., and Anitescu, M., “A Parallel Tree Code for Computing Matrix-Vector Products with the Matern Kernel”, 2013.

M. Anitescu, Chen, J., and Stein, M. L., “An Inversion-Free Estimating Equation Approach for Gaussian Process Models”, 2013.

P. Balaprakash, Tiwari, A., and Wild, S. M., “Multi-Objective Optimization of HPC Kernels for Performance, Power, and Energy”, in 4th International Workshop on Performance Modeling, Benchmarking, and Simulation of HPC Systems (PMBS12), 2013.

J. Soumagne, Kimpe, D., Zounmevo, J. A., and Chaarawi, M., “Mercury: Enabling Remote Procedure Call for High-Performance Computing”, in Cluster 2013, Indianapolis, IN, 2013.

B. Nicolaeand Cappello, F., “Al-Ckpt: Leveraging Memory Access Patterns for Adaptive Asynchronous Incremental Checkpointing”, in HPDC'13, New York City, 2013.

P. Balajiand Kimpe, D., “On the Reproducibility of MPI Reduction Operations”, in High Performance computing and Communications (HPCC 2013), Zhangjiajie, China, 2013.

R. Jainand Tautges, T. J., “PostBL: Post-Mesh Boundary Layer Mesh Generation Tool”, in 22nd International Meshing Roundtable, Orlando, FL, 2013.

X. Zhao, Balaji, P., Gropp, W. D., and Thakur, R., “Optimization Strategies for MPI-Interoperable Active Messages”, in 13th IEEE International Conference on Scalable Computing and Communication, Chengdu, China, 2013.

J. Jenkins, Dinan, J., Balaji, P., Peterka, T., Samatova, N. F., and Thakur, R., “Processing MPI Derived Datatypes on Noncontiguous GPU-Resident Data”, IEEE Transactions on Parallel and Distributed Systems, 2013.

T. Hoefler, Dinan, J., Buntinas, D., Balaji, P., Barrett, B., Brightwell, R., Gropp, W. D., Kale, V., and Thakur, R., “MPI + MPI: A New Hybrid Approach to Parallel Programming with MPI Plus Shared Memory”, Computing, vol. 95, pp. 1121-1136, 2013.

E. M. Constantinescuand Anitescu, M., “Physics-Based Covariance Models for Gaussian Processes with Multiple Outputs”, International Journal for Uncertainty Quantification, vol. 3, no. 1, 2013.

J. M. Salazar, Diwekar, U., Constantinescu, E. M., and Zavala, V. M., “Stochastic Optimization Approach to Water Management in Cooling-Constrained Power Plants”, Applied Energy, vol. 112, pp. 12-22, 2013.

E. M. Constantinescuand Sandu, A., “Extrapolated Multirate Methods for Differential Equations with Multiple Time Scales”, Journal on Scientific Computing, vol. 56, no. 1, pp. 28-44, 2013.

X. Zeng, Drewniak, B. A., and Constantinescu, E. M., “Calibration of the Crop Model in the Community Land Model”, Geoscientific Model Development, vol. 6, pp. 379-398, 2013.

S. Leyfferand Kirches, C., “TACO - A Toolkit for AMPL Control Optimization”, Mathematical Programming Computation, pp. 1-39, 2013.

J. R. Trammand Siegel, A. R., “Memory Bottlenecks and Memory Contention in Multi-Core Monte Carlo Transport Codes”, in Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo, Paris, 2013.

S. Wallace, Vishwanath, V., Coghlan, S. M., Tramm, J. R., Lan, Z., and Papka, M. E., “Application Power Profiling on IBM Blue Gene/Q”, in Cluster Computing (CLUSTER), 2013 IEEE International Conference, Indianapolis, IN, 2013.

A. Tasoraand Anitescu, M., “A Complementarity-Based Rolling Friction Model for Rigid Contacts”, Meccanica, vol. 48, no. 7, pp. 1643-1659, 2013.

M. L. Stein, Chen, J., and Anitescu, M., “Stochastic Approximation of Score Functions for Gaussian Processes”, Annals of Applied Statistics, vol. 7, no. 2, pp. 1162-1191, 2013.

P. K. Romano, Siegel, A. R., Forget, B., and Smith, K., “Data Decomposition of Monte Carlo Particle Transport Simulations via Tally Servers”, Journal of Computational Physics, vol. 252, pp. 20-36, 2013.

S. Bogner, Bulgac, A., Carlson, J., Engel, J., Fann, G., Furnstahl, R. J., Gandolfi, S., Hagen, G., Horoi, M., Johnson, C., Kortelainen, M., Lusk, E. L., Maris, P., Nam, H., Navratil, P., Nazarewicz, W., Ng, E., Nobre, G. P. A., Ormand, E., Papenbrock, T., Pei, J., Pieper, S. C., Quaglioni, S., Roche, K. J., Sarich, J., Schunck, N., Sosonkina, M., Terasaki, J., Thompson, I., Vary, J. P., and Wild, S. M., “Computational Nuclear Quantum Many-Body Problem: The UNEDF Project”, Computer Physics Communications, vol. 184, no. 10, pp. 2235-2250, 2013.

V. M. Zavala, “Inference of Building Occupancy Signals Using Moving Horizon Estimation and Fourier Regularization”, Journal of Process Control, 2013.

M. Lubin, Hall, J. A. Julian, Petra, C. G., and Anitescu, M., “Parallel Distributed-Memory Simplex for Large-Scale Stochastic LP Problems”, Computational Optimization and Applications, vol. 55, no. 3, pp. 571-596, 2013.

S. Devoidand Desai, N. L., “Poncho: Enabling Smart Administration of Full Private Clouds”, in 27th Large Installation System Administraction Conference, Washington, D.C., 2013.

K. Maheshwari, Rodriguez, A., Kelly, D., Madduri, R., Wozniak, J. M., Wilde, M., and Foster, I. T., “Enabling Multi-task computation on Galaxy-based Gateways using Swift”, in Science Gateway Institute Workshop, IEEE Cluster 2013, Indianpolis, IN, 2013.

M. Otten, Brown, J., and Smith, B. F., “Scientific Application Web Server (SAWs) Users Manual”, 2013.

Y. He, Min, M., and Nicholls, D., “A Spectral Element Method with Transparent Boundary Condition for Periodic Layered Media Scattering”, Journal of Computational Physics, 2013.

Y. He, Min, M., and Nicholls, D., “A Spectral Element Method with Transparent Boundary Condition for Periodic Layered Media Scattering”, Journal of Computational Physics, 2013.

A. Moawad, Halbach, S., Pagerit, S., Rousseau, A., Balaprakash, P., and Wild, S. M., “Novel Process to Use Vehicle Simulations Directly as Inputs to DOT's Cafe Modeling System”, ANL/ESD-13/13, 2013.

M. Snir, Wisniewski, R. W., Abraham, J. A., Adve, S. V., Bagchi, S., Balaji, P., Belak, J., Bose, P., Cappello, F., Carlson, B., Chien, A. A., Coteus, P., Debardeleben, N. A., Diniz, P., Engelmann, C., Erez, M., Fazzari, S., Geist, A., Gupta, R., Johnson, F., Krishnamoorthy, S., Leyffer, S., Liberty, D., Mitra, S., Munson, T. S., Schreiber, R., Stearley, J., and Hensbergen, E. V., “Addressing Failures in Exascale Computing”, 2013.

C. L. Phillips, “A Learning Heuristic for Space Mapping and Searching Self-Organizing Systems Using Adaptive Mesh Refinement”, 2013.

G. Pieperand McInness, L. Curfman, “The remarkable career of a pioneering computational scientist”, SIAM News, 2013.

T. G. Armstrong, Wozniak, J. M., Wilde, M., and Foster, I. T., “Compiler optimization for data-driven task parallelism on distributed memory systems”, in 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Orlando, FL, 2013.

K. G. Felker, Siegel, A. R., Smith, K., Romano, P. K., and Forget, B., “The Energy Band Memory Server Algorithm for Parallel Monte Carlo Transport Calculations”, in Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo, Paris, France, 2013.

L. A. Bautist Gomezand Cappello, F., “Detecting Silent Data Corruption through Data Dynamic Monitoring for Scientific Applications”, in 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Orlando, FL, 2013.

L. A. Bautist Gomezand Cappello, F., “Detecting Silent Data Corruption through Data Dynamic Monitoring for Scientific Applications”, in 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Orlando, FL, 2013.

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 2013 International Conference on Parallel Processing, Lyon, France, 2013.

A. M. Aji, Balaji, P., Dinan, J., Feng, W., and Thakur, R., “Synchronization and Ordering Semantics in Hybrid MPI+GPU Programming”, in The Third International Workshop on Accelerators and Hybrid Exascale System, IEEE International Parallel and Distributed Processing Symposium, Boston, MA, 2013.

P. Lama, Li, Y., Aji, A. M., Balaji, P., Dinan, J., Xiao, S., Zhang, Y., Feng, W., Thakur, R., and Zhou, X., “pVOCL: Power-Aware Dynamic Placement and Migration in Virtualized GPU Environments”, in 33rd International Conference on Distributed Computing Systems, Philadephia, PA, 2013.

A. M. Aji, Panwar, L. S., Ji, F., Chabbi, M., Murthy, K., Balaji, P., Bisset, K. R., Dinan, J., Feng, W., Mellor-Crummey, J., Ma, X., and Thakur, R., “On The Efficacy of GPU-Integrated MPI for Scientific Applications”, in The 22nd Internation ACM Symposium on High Performance Parallel and Distributed Computing (HPDC), New York, NY, 2013.

“Online Performance Projection for Clusters with Heterogeneous GPUs”, in 19th IEEE International Conference on Parallel and Distributed Systems, Seoul, KOR, 2013.

“Online Performance Projection for Clusters with Heterogeneous GPUs”, in 19th IEEE International Conference on Parallel and Distributed Systems, Seoul, KOR, 2013.

A. Vishnu, Krishnan, M., and Balaji, P., “Dynamic Time-Variant Connection Management for PGAS Models on InfiniBand”, in The Third International Workshop on Accelerators and Hybrid Exascale System, IEEE International Parallel and Distributed Processing Symposium, Boston, MA, 2013.

A. Vishnu, Krishnan, M., and Balaji, P., “Dynamic Time-Variant Connection Management for PGAS Models on InfiniBand”, in The Third International Workshop on Accelerators and Hybrid Exascale System, IEEE International Parallel and Distributed Processing Symposium, Boston, MA, 2013.

V. M. Zavala, “A Stochastic Optimal Control Model for Natural Gas Network Operations”, 2013.

J. Larsonand Wild, S. M., “Non-Intrusive Termination of Noisy Optimization”, Optimization Methods and Software, vol. 28, no. 5, pp. 993-1011, 2013.

P. Balaprakash, Tiwari, A., and Wild, S. M., “Multi-Objective of HPC Kernels for Performance, Power, and Energy”, 2013.

P. Balaprakash, Alexeev, Y., Mickelson, S. A., Leyffer, S., Jacob, R. L., and Craig, A. P., “Machine Learning based Load-Balancing for the CESM Climate Modeling Package”, in IEEE Transactions on Parallel and Distributed Systems, Denver, CO, 2013.

S. Di, Wang, C. - L., and Cappello, F., “Adaptive Algorithm for Minimizing Cloud Task Length with Prediction Errors”, IEEE Transactions on Cloud Computing, vol. 2, 2013.

M. S. Bouguerra, Gainaru, A., and Cappello, F., “Failure Prediction: What To Do with Unpredicted Failures?”, 2013.

K. Rupp, Tillet, P., Smith, B. F., Grasser, T., and Jungel, A., “A Note on the GPU Acceleratoin of Eigenvalue Computations”, in ICNAAM 11th International Conference of Numerical Analysis and Applied Mathematics, Rhodes, Greece, 2013.

T. L. Disz, Edirisinghe, J. N., Faria, J. P., Hausmann, A., Henry, C. S., Olson, R., Overbeek, R. A., Pusch, G. D., Shukla, M., Vonstein, V., and Wattam, A. R., “Developing a Protocol for Annotating Sets of Closely-related Genomes: Example Genus Brucella”, 3 Biotech, 2013.

J. Bischof, Harrison, T., Paczian, T., Glass, E. M., Wilke, A., and Meyer, F., “Metazen – Metadata Capture for Metagenomes”, BMC Bioinformatics, 2013.

K. Maheshwari, Jung, E., Meng, J., Vishwanath, V., and Kettimuthu, R., “Model-Driven Multisite Workflow Scheduling Based on Task-Resource Adaptation”, IEEE Cluster 2013. Indianapolis, IN, 2013.

F. Isaila, Garcia, J., Carretero, J., Ross, R. B., and Kimpe, D., “Making the Case for Reforming the I/O Software Stack of Extreme-Scale Systems”, EASC 2013. Edinburgh, Scotland, 2013.

E. Jungand Kettimuthu, R., “An Overview of Parallelism Exploitation and Cross-Layer Optimization for Big Data Transfers”, 2013.

M. Kortelainen, McDonnell, J., Nazarewicz, W., Olsen, E., Reinhard, P. G., Sarich, J., Schunck, N., Wild, S. M., Davesne, D., Erler, J., and Pastore, A., “Nuclear Energy Density Optimization: Shell Structure”, Physical Review C, vol. 89, p. 054314, 2013.

S. Wang, Ward, J., Leyffer, S., Wild, S. M., Jacobsen, C., and Vogt, S., “Unsupervised Cell Identification on Multidimensional X-ray Fluorescence Datasets”, Journal of Synchrotron Radiation, vol. 21, no. 3, pp. 568-579, 2013.

S. M. Wildand Shoemaker, C., “Global Convergence of Radial Basis Function Trust-Region Algorithms for Derivative-Free Optimization”, SIAM Review, vol. 55, no. 2, pp. 349-371, 2013.

A. Ekstrom, Baardsen, G., Forssen, C., Hagen, G., Hjorth-Jensen, M., Jansen, G. R., Machleidt, R., Nazarewicz, W., Papenbrock, T., Sarich, J., and Wild, S. M., “Optimized Chiral Nucleon-Nucleon Interaction at Next-to-Next-to-Leading Order”, Phys. Rev. Lett., vol. 110, 2013.

S. M. Wild, Gramacy, R. B., and Taddy, M. A., “Variable Selection and Sensitivity Analysis via Dynamic Trees with an Application to Computer Code Performance Tuning”, The Annals of Applied Statistics, vol. 7, no. 1, pp. 51-80, 2013.

A. Mametjanov, Min, M., Norris, B., and Hovland, P. D., “Accelerating Performance of NekCEM with MPI and CUDA”, Super Computing (SC13). Denver, CO, 2013.

J. Dinan, Balaji, P., Buntinas, D., Goodell, D., Gropp, W. D., and Thakur, R., “An Implementation and Evaluation of the MPI 3.0 One-Sided Communication Interface”, 2013.

S. Valcke, Balaji, P., Craig, A. P., DeLuca, C., Dunlap, R., Ford, R. W., Jacob, R. L., Larson, J. W., O'Kuinghttons, R., and Riley, G. D., “Coupling Technologies for Earth System Modeling”, 2013.

J. Xu, Zhufu, X., Zhao, R., Li, C., Qi, X., Yang, L., and Min, M., “Comparisons of Different Electromagnetic Solvers for Accelerator Simulations”, 2013.

T. Hoefler, Dinan, J., Thakur, R., Barrett, B., Balaji, P., Gropp, W. D., and Underwood, K., “Remote Memory Access Programming in MPI-3”, ACM Transactions on Parallel Computing, 2013.

R. K. K. Aziz, Devoid, S., Disz, T. L., Edwards, R. A., Gerdes, S. Y., Henry, C. S., Olsen, G. J., Olson, R., Overbeek, R. A., Parrello, B., Pusch, G. D., Stevens, R. L., Vonstein, V., and Xia, F., “SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models”, 2013.

J. P. Faria, Overbeek, R. A., Xia, F., Rocha, M., and Henry, C. S., “Genome-Scale Bacterial Transcriptional Regulatory Networks: Reconstruction and Integrated Analysis with Metabolic Models”, 2013.

J. M. Wozniak, Armstrong, T. G., Wilde, M., Katz, D. S., Lusk, E. L., and Foster, I. T., “Swift/T: Scalabale Data Flow Programming for Many-Task Applications”, 2013.

W. D. Pointer, Bradley, K., Fischer, P. F., Smith, M., Tautges, T. J., Ferencz, R., Martineau, R., Jain, R., Obabko, A. V., and Obabko, A. V., “Developing a Comprehensive Software Suite for Advanced Reactor Performance and Safety Analysis”, 2013.

J. Xu, Zhufu, X., Zhao, R., Sun, J., Li, C., Yang, L., and Min, M., “Performance Evaluation for Electromagnetic Solvers with Interpolatory and Hierarchical Ne ́de ́lec Vector Bases”, 2013.

M. Lubin, Martin, K., Petra, C. G., and Sandikci, B., “On Parallelizing Dual Decomposition in Stochastic Integer Programming”, Operations Research Letters, vol. 41, no. 3, 2013.

J. Jenkins, Dinan, J., Balaji, P., Peterka, T., Samatova, N. F., and Thakur, R., “MPI Derived Datatypes Processing on Noncontiguous GPU-Resident Data”, 2013.

S. M. Aithal, “Analysis of the Current Signature in a Constant-Volume Combustion Chamber”, Combustion Science and Technology, vol. 185, no. 2, 2013.

D. P. Kouri, “A Multilevel Stochastic Collocation Algorithm for Optimization of PDES with Uncertain Coefficients”, in SIAM Conference on Computational Science & Engineering, 2013.

P. Balaprakash, Buntinas, D., Chan, A., Guha, A., Gupta, R., Narayanan, S. H. K., Chien, A. A., Hovland, P. D., and Norris, B., “Exascale Workload Characterization and Architecture Implications”, in 21st High Performance Computing Synposium, San Diego, 2013.

A. Cherchi, Carril, A. F., Zamboni, L., and Menendez, C., “LPB Hydro-Climate Variability as Simulated by GCM Experiments: Role of Remote SST Forcing”, Climate Dynamics, 2013.

J. Elliott, Glotter, M., Best, N. A., Boote, K., Jones, J. P., Hatfield, J., Rosenzweig, C., Smith, L. A., and Foster, I. T., “Predicting Agricultural Impacts of Large-Scale Drought: 2012 and The Case for Better Modeling”, University of Chicago Center for Robust Decisionmaking on Climate & Energy Policy, RDCEP Working Paper No. 13-01, 2013.

S. Li, Hoefler, T., and Snir, M., “NUMA-Aware Shared-Memory Collective Communication for MPI”, in HPDC'13, New York, 2013.

A. Tasora, Anitescu, M., Negrini, S., and Negrut, D., “A Compliant Visco-Plastic Particle Contact Model Based on Differential Variational Inequalities”, International Journal of Non-Linear Mechanics, vol. 53, 2013.

L. Wolfand Pieper, G. W., “Biology at the Exascale”, SciDAC Rev. , vol. 16, no. Spec. ed., pp. 32 - 39, 2013.

K. Hatz, Leyffer, S., Schloder, J. P., and Bock, H. G., “Regularizing Bilevel Nonlinear Programs by Lifting”, SIAM Journal on Optimization, 2013.

J. Dinan, Balaji, P., Goodell, D., Miller, D., Snir, M., and Thakur, R., “Enabling MPI Interoperability Through Flexible Communication Endpoints”, in EuroMPI 2013, Madrid, Spain, 2013.

A. J. Pena, Carvalho, R. G. Correa, Dinan, J., Balaji, P., Thakur, R., and Gropp, W. D., “Analysis of Topology-Dependent MPI Performance on Gemini Networks”, in EuroMPI 2013, Madrid, Spain, 2013.

P. H. Carns, Yao, Y., Harms, K., Latham, R., Ross, R. B., and Antypas, K., “Production I/O Characterization on the Cray XE6”, in CUG2013, Napa Valley, CA, 2013.

A. V. Obabko, Fischer, P. F., Tautges, T. J., Goloviznin, V. M., Zaytsev, M. A., Chudanov, V. V., Pervichkno, V. A., Aksenova, A. E., and Karabasov, S., “Large Eddy Simulation of Thermo-Hydraulic Mixing in a T-Junction”, in Nuclear Reactor Thermal Hydraulics and Other Applications , 2013.

O. Roderickand Anitescu, M., “Use of Multi-Fidelity Training Data in Uncertainty Analysis of Nuclear Engineering Applications”, in American Nuclear Society 2013; Atlanta, Georgia, 2013.

J. Brownand Brune, P., “Low-Rank Quasi-Newton Updates for Robust Jacobian Lagging in Newton Methods”, 2013.

M. V. Stoitsov, Schunck, N., Kortelainen, M., Michel, N., Nam, H., Olsen, E., Sarich, J., and Wild, S. M., “Axially Deformed Solution of the Skyrme-Hartree-Fock-Bogolyubov Equations Using the Transformed Harmonic Oscillator Basis (II) HFBTHO v2.00c: A New Version of the Program”, Computer Physics Communications, vol. 184, no. 6, 2013.

T. G. Armstrong, Wozniak, J. M., Wilde, M., and Foster, I. T., “Compiler Optimization for Distributed Dynamic Data Flow Programs”, 2013.

J. Brown, Knepley, M. G., and Smith, B. F., “Run-Time Extensibility: Anything Less is Unsustainable”, in SC 13, Denver, CO, 2013.

T. J. Tautges, Fischer, P. F., Grindeanu, I., Jain, R., Mahajan, A., Obabko, A. V., Smith, M. A., Merzari, E., and Ferencz, R., “SHARP Assembly-Scale Multiphysics Demonstration Simulations”, ANL/MCS-NE-13-9, 2013.

B. Behzad, Byna, S., Koziol, Q., Luu, H. V. T., Prabhat, A., Huchette, J., Aydt, R., and Snir, M., “Taming Parallel I/O Complexity with Auto-Tuning”, in SC2013, 2013.

E. Jung, Kettimuthu, R., and Vishwanath, V., “Toward Optimizing Disk-to-Disk Transfer on 100G Networks”, 2013.

A. Gainaru, Cappello, F., Snir, M., and Kramer, W., “Failure Prediction for HPC Systems and Applications: Current Situation and Open Issues”, International Journal of High Performance Computing Applications, vol. 27, no. 3, p. 2730282, 2013.

Z. Zhou, Lan, Z., Tang, W., and Desai, N. L., “Reducing Energy Costs for IBM Blue Gene/P via Power-Aware Job Scheduling”, in Job Scheduling Strategies for Parallel Processors Workshop (JSSPP 2013), Boston, MA, 2013.

J. Brown, Smith, B. F., and Ahmadia, A., “Achieving Textbook Multigrid Efficiency for Hydrostatic Ice Sheet Flow”, SIAM Journal Sci. Comput., vol. 35, no. 2, pp. 8359-8375, 2013.

P. Balaprakash, Rupp, K., Mametjanov, A., Gramacy, R. B., Hovland, P. D., and Wild, S. M., “Empirical Performance Modeling of GPU Kernels Using Active Learning”, in International Conference on Parallel Computing - ParCo2013 , Munich, Germany , 2013.

P. Balaprakash, Wild, S. M., and Hovland, P. D., “Performance Modeling for Exascale Autotuning: An Integrated Approach”. 2013.

S. Diand Cappello, F., “GloudSim: Google Trace based Cloud Simulator with Virtual Machines”, 2013.

M. G. Knepley, Brown, J., Rupp, K., and Smith, B. F., “Achieving High Performance with Unified Residual Evaluation”, 2013.

M. G. Knepley, Brown, J., McInnes, L. Curfman, and Smith, B. F., “Accurately Citing Software and Algorithms used in Publications”, in WSSSPE Workshop at SC13, Denver, CO, 2013.

S. Abhyankar, Smith, B. F., and Constantinescu, E. M., “Evaluation of Overlapping Restricted Additive Schwarz Preconditioning for Parallel Solution of Very Large Power Flow Problems”, in The International Conference for High Performance Computing, Network, Storage and Analysis (SC 2013) , Denver, CO, 2013.

J. M. Wozniak, Armstrong, T. G., Krieder, S. J., Maheshwari, K., Wilde, M., and Foster, I. T., “Mega Python: Scalable Interlanguage Scripting for Scientific Computing”, in SC 13, Denver, CO, 2013.

M. Snir, Wisniewski, R. W., Abraham, J. A., Adve, S. V., Bagchi, S., Balaji, P., Belak, J., Bose, P., Cappello, F., Carlson, B., Chien, A. A., Coteus, P., Debardeleben, N. A., Diniz, P., Engelmann, C., Erez, M., Fazzari, S., Geist, A., Gupta, R., Johnson, F., Krishnamoorthy, S., Leyffer, S., Liberty, D., Mitra, S., Munson, T. S., Schreiber, R., Stearley, J., and Hensbergen, E. V., “Addressing Failures in Exascale Computing*”, International Journal of High Performance Computing, 2013.

J. Zhang, Behzad, B., and Snir, M., “Design of A Multithreaded Barnes-Hut Algorithm for Multicore Clusters”, 2013.

M. Miller, Diachin, L. F., Balay, S., McInnes, L. Curfman, and Smith, B. F., “Package Management and Practices Essential for Interoperability: Lessons Learned and Strategies Developed for FASTMath”, in SC 13, Denver, CO, 2013.

A. Wilke, Glass, E. M., Bartels, D., Bischof, J., Braithwaite, D., D'Souza, M., Gerlach, W., Harrison, T., Keegan, K. P., Matthews, H., Kottmann, R., Paczian, T., Tang, W., Trimble, W. L., Yilmaz, P., Wilkening, J., Desai, N. L., and Meyer, F., “A Metagenomics Portal for a Democratized Sequencing World”, Methods enzymol., vol. 531, pp. 487-523, 2013.

J. M. Wozniak, Peterka, T., Armstrong, T. G., Dinan, J., Lusk, E. L., Wilde, M., and Foster, I. T., “Dataflow Coordination of Data-Parallel Tasks via MPI 3.0”, in EuroMPI'13, 2013.

X. Zhao, Balaji, P., Gropp, W. D., and Thakur, R., “MPI-Interoperable Generalized Active Messages”, in 19th IEEE International Conference on Parallel and Distributed Systems, Seoul, KOR, 2013.

F. Cappello, Bouteiller, A., Herault, T., and Robert, Y., “Multi-Criteria Checkpointing Strategies: Optimizing Response-Time Versus Resource Utilization”, in Europar 2013, Aachen, 2013.

B. Nicolaeand Cappello, F., “BlobCR: Virtual Disk Based Checkpoint-Restart for HPC Applications on IaaS Clouds”, Parallel and Distributed Computing, vol. 73, no. 5, pp. 698–711, 2013.

P. Balaprakash, Wild, S. M., and Hovland, P. D., “An Experimental Study of Global and Local Search Algorithms in Empirical Performance Tuning”, in 10th International Meeting on High-Performance Computing for Computational Science (VECPAR 2012), Kobe, Japan, 2013.

F. Cappello, Ropars, T., Martsinkevich, R. V., Guermouche, A., and Schiper, A., “SPBC: Leveraging the Characteristics of MPI HPC Applications for Scalable Checkpointing”, in Super Computing (SC13), Denver, CO, 2013.

Z. Zhang, Katz, D. S., Wilde, M., Wozniak, J. M., and Foster, I. T., “MTC Envelope: Defining the Capability of Large Scale Computers in the Context of Parallel Scripting Applications”, in HPDC'13, 2013.

S. Abhyankarand Flueck, A. J., “Parallel-in-Space-and-Time Scheme for Implicitly Coupled Electromechanical and Electromagnetic Transients Simulation”, in International Conference on Power Systems Transients, Vancouver, BC, Canada, 2013.

J. M. Wozniak, Armstrong, T. G., Wilde, M., Katz, D. S., Lusk, E. L., and Foster, I. T., “A Model for Tracing and Debugging Large-Scale Task-Parallel Programs with MPE”, in Workshop on Leveraging Abstractions and Semantics in High-performance Computing, 2013.

S. M. Aithaland Wild, S. M., “Development of a Fast, Robust Numerical Tool for The Design, Optimization and Control of IC Engines”, in SAE 11th International Conference on Engines & Vehicles, Capri, Italy, 2013.

L. A. Bautist Gomezand Cappello, F., “Improving Floating Point Compression through Binary Masks”, in IEEE BigData 2013, Santa Barbara, California, 2013.

W. Tang, Wilkening, J., Desai, N. L., Gerlach, W., Wilke, A., and Meyer, F., “A Scalable Data Analysis Platform for Metagenomics”, in The Proceedings of the 2013 IEEE International Conference on Big Data, Santa Clara, CA, 2013.

A. Wilke, Glass, E. M., Bischof, J., Braithwaite, D., D'Souza, M., Gerlach, W., Harrison, T., Keegan, K. P., Matthews, H., Paczian, T., Tang, W., Trimble, W. L., Wilkening, J., Desai, N. L., and Meyer, F., “MG-RAST A Technical Report and Manual for Version 3.3.6”, ANL/MCS-TM-333, 2013.

K. Rupp, Tillet, P., Smith, B. F., Grasser, T., and Jungel, A., “A Note on the GPU Acceleratoin of Eigenvalue Computations”, in ICNAAM 11th International Conference of Numerical Analysis and Applied Mathematics, Rhodes, Greece, 2013.

J. Walker, Merzari, E., Obabko, A. V., Fischer, P. F., and Siegel, A. R., “Accurate Prediction of the Wall Shear Stress in Rod Bundles with the Spectral Element Method at High Reynolds Numbers”, International Journal of Heat and Fluid Flow , 2013.

P. Balaprakash, Gramacy, R. B., and Wild, S. M., “Active-Learning-Based Surrogate Models for Empirical Performance Tuning”, in IEEE Cluster 2013, Indianapolis, IN, 2013.

G. Antoniu, Bigot, J., Blanchet, C., Bouge, L., Briant, F., Cappello, F., Costan, A., Desprez, F., Fedak, G., Gault, S., Keahey, K., Nicolae, B., Perez, C., Simonet, A., Suter, F., Tang, B., and Terreux, R., “Scalable Data Management for Map-Reduce-based Data-Intensive Applications: A View for Cloud and Hybrid Infrastructures”, International Journal of Cloud Computing, vol. 2, no. 2/3, pp. 150-170, 2013.