Publications

Doerfler, D.W. (2008). MPI Task Placement on Multicores [Presentation]. https://www.osti.gov/biblio/1712886

Pedretti, K. (2008). TLBs DRAMs and Other Scary Things [Presentation]. https://www.osti.gov/biblio/1712887

Brightwell, R.B. (2008). Application and Operating System Software Challenges in the Multi-core Era [Presentation]. https://www.osti.gov/biblio/1712888

Heroux, M.A. (2008). Application Performance Assessment and Modeling [Conference]. https://www.osti.gov/biblio/1145945

Thompson, A.P. (2008). LAMMPS: Molecular Dynamics Simulation of Dynamic Materials Response [Presentation]. https://www.osti.gov/biblio/1712870

Ferreira, K.B., Brightwell, R.B., & Brightwell, R.B. (2008). Characterizing Application Sensitivity to OS Interference Using Kernel-Level Noise Injection [Conference]. https://www.osti.gov/biblio/1145507

Brightwell, R.B. (2008). A Prototype Implementation of MPI for SMARTMAP [Conference]. https://www.osti.gov/biblio/1145530

Brightwell, R.B. (2008). Lightweight Kernel Support for Direct Shared Memory Access on a Multi-Core Processor [Conference]. https://www.osti.gov/biblio/1145620

Moreland, K. (2008). Large Scale Visualization with ParaView (SC08 Tutorial Proposal) [Presentation]. https://www.osti.gov/biblio/1710336

Pedretti, K. (2008). Quad-core Catamount and R&D in Multi-core Lightweight Kernels [Conference]. https://www.osti.gov/biblio/1145512

Debenedictis, E. (2008). How to Reach Zettaflops [Conference]. https://www.osti.gov/biblio/1145796

Phipps, E.T. (2008). Enabling Predictive Simulation Through Embedded Sensitivity Analysis and Uncertainty Quantification [Presentation]. https://www.osti.gov/biblio/1710337

Boman, E.G. (2008). Combinatorial Algorithms Enabling Computational Science [Presentation]. https://www.osti.gov/biblio/1712562

Hu, J.J. (2008). A Current Overview of the Trilinos Project [Conference]. https://www.osti.gov/biblio/1145483

Berry, J. (2008). Informatics Architectures [Presentation]. https://www.osti.gov/biblio/1712563

Wylie, B.N. (2008). A Unified Scalable Visualization Architecture [Presentation]. https://www.osti.gov/biblio/1712565

Phelps, S., Heroux, M.A., Wen, Z., & Wen, Z. (2008). BEC: An Enhanced PGAS Parallel Programming Model [Conference]. https://www.osti.gov/biblio/1145566

Moreland, K. (2008). Ultravis quarterly report - 2008/04 [Presentation]. https://www.osti.gov/biblio/1712567

Smith, B., Spencer, F.W., & Spencer, F.W. (2008). Model-Assisted Probability of Detection Validation of Eddy Current Inspection for Cracks in Lap Splice Fastener Holes [Conference]. https://www.osti.gov/biblio/1145551

Smith, B., Spencer, F.W., & Spencer, F.W. (2008). Model-Assisted Probability of Detection Validation of Eddy Current Inspection for Cracks in Lap Splice Fastener Holes [Conference]. https://www.osti.gov/biblio/1145479

Wilson, A.T. (2008). An Ever-Growing Avalanche: Large Data and Visualization [Presentation]. https://www.osti.gov/biblio/1712591

Debenedictis, E. (2008). Issues in the Future of Computing [Presentation]. https://www.osti.gov/biblio/1710271

Vaughan, C.T., Doerfler, D.W., Leland, R.W., & Leland, R.W. (2008). Investigating the balance between capacity and capability workloads across large scale computing platforms [Conference]. https://www.osti.gov/biblio/1145679

Levenhagen, M., Hemmert, K.S., Brightwell, R.B., & Brightwell, R.B. (2008). High Message Rate NIC-Based Atomics: Design and Performance Considerations [Conference]. https://www.osti.gov/biblio/1145790

Moreland, K. (2008). DOECGF 2008 ParaView Update [Presentation]. https://www.osti.gov/biblio/1710279

Moreland, K. (2008). Vis Tutorial Proposal: Advanced ParaView Visualization [Presentation]. https://www.osti.gov/biblio/1710280

Joo, J., Plimpton, S.J., Faulon, J.-L., & Faulon, J.-L. (2008). Noise-induced oscillatory shuttling of NF-kappaB in a two compartment IKK-NF-kappaB-IkappaB-A20 signaling model. PLOS Computational Biology. https://www.osti.gov/biblio/1145660

Joo, J., Plimpton, S.J., Faulon, J.-L., & Faulon, J.-L. (2008). Statistical ensemble approach to modeling NF-kappaB signaling. Journal of Theoretical Biology. https://www.osti.gov/biblio/1145746

Riesen, R. (2008). Simulating a Cluster on a Cluster [Conference]. https://www.osti.gov/biblio/1145513

Heroux, M.A., Wen, Z., & Wen, Z. (2008). The BEC Programming Model [Conference]. https://www.osti.gov/biblio/1145814

Voth, T.E., Strickland, J., & Strickland, J. (2008). Unstructured Mesh CFD Research [Presentation]. https://www.osti.gov/biblio/1710286

Berry, J. (2008). Cray XMT Brings New Energy to High-Performance Computing. SciDAC Review. https://www.osti.gov/biblio/1145568

Berry, J. (2008). Graph Analysis with High-Performance Computing [Presentation]. https://www.osti.gov/biblio/1712586

Stewart, J. (2008). UQ methods in DAKOTA employed by NuGET team to achieve critical QMU milestone [Presentation]. https://www.osti.gov/biblio/1710295

Caskey, S.A., Gaudioso, J.M., Salerno, R.M., & Salerno, R.M. (2008). Biosecurity Risk Assessment Methodology Overview [Presentation]. https://www.osti.gov/biblio/1710296

Rutherford, B., Romero, V., Hoekstra, R.J., Castro, J.P., & Castro, J.P. (2008). Uncertainty Quantification for the Simple Prototype Analysis [Presentation]. https://www.osti.gov/biblio/1712592

Oberkampf, W.L., Trucano, T.G., & Trucano, T.G. (2008). Verification and validation benchmarks [Conference]. Nuclear Engineering and Design. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=39149123528&origin=inward

Hendrickson, B.A., Berry, J.W., & Berry, J.W. (2008). Graph analysis with high-performance computing. Computing in Science and Engineering, 10(2), pp. 14-19. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=39749119225&origin=inward

Oliner, A.J., Stearley, J., & Stearley, J. (2008). Alert Detection in System Logs [Conference]. https://www.osti.gov/biblio/1146400

Wills, A.E. (2008). Functional Development at a National Lab [Conference]. https://www.osti.gov/biblio/1146280

Womble, D.E., Morgan, H.S., Doerfler, D.W., Giunta, A.A., & Giunta, A.A. (2008). Informatics : the rest of the story [Conference]. https://www.osti.gov/biblio/943933

Carpenter, J.H., Desjarlais, M.P., Wills, A.E., & Wills, A.E. (2008). A New Wide-Range Equation of State for Tungsten [Conference]. https://www.osti.gov/biblio/1146035

Salinger, A.G., Frischknecht, A.L., & Frischknecht, A.L. (2008). Tramonto: Software for Nanostructured Fluids in Materials and Biology [Presentation]. https://www.osti.gov/biblio/1712931

Edwards, H.C. (2008). A Programming Model for Hybrid Parallelism with Consistent Numerical Results [Conference]. https://www.osti.gov/biblio/1146264

Wills, A.E. (2008). Accurate and fast DFT calculations with the AM05 functional [Conference]. https://www.osti.gov/biblio/1146379

Moreland, K. (2008). Multi Core Processing [Presentation]. https://www.osti.gov/biblio/1713119

Heroux, M.A. (2008). Challenges in Programming Next-generation Parallel Computer Systems [Conference]. https://www.osti.gov/biblio/1146046

Chevalier, C. (2008). Parallel Sparse Matrix Ordering [Presentation]. https://www.osti.gov/biblio/1713120

Dunlavy, D.M., Basilico, J.D., Verzi, S.J., Bauer, T.L., & Bauer, T.L. (2008). Yucca Mountain licensing support network archive assistant. https://doi.org/10.2172/932885

Robinson, A.C., Kaye, R.J., Lamppa, D.C., Lemke, R.W., Garasi, C.J., & Garasi, C.J. (2008). Establishing high-fidelity M&S capabilities as a means of experiment prediction and guidance for EM launch applications [Conference]. https://www.osti.gov/biblio/952828

Riesen, R., Brightwell, R.B., Ferreira, K.B., & Ferreira, K.B. (2008). Designing and Implementing Lightweight Kernels for Capability Computing. Concurrency and Computation: Practice and Experience. https://www.osti.gov/biblio/1141189

Wylie, B.N. (2008). TLP Mockup [Conference]. https://www.osti.gov/biblio/1146184

Barrett, B. (2008). Challenges in Building Scalable HPC Networks [Presentation]. https://www.osti.gov/biblio/1713122

Lin, P.T., Shadid, J.N., Hoekstra, R.J., Hennigan, G., & Hennigan, G. (2008). Parallel Block-Oriented Preconditioners for FEM Modeling of Semiconductor Devices [Conference]. https://www.osti.gov/biblio/1145977

Bartlett, R. (2008). Analytic Sensitivities in Large-scale Production Applications via Automatic Differentiation with Sacado [Conference]. https://www.osti.gov/biblio/1146307

Hoekstra, R.J., Thornquist, H., Day, D.M., Boman, E.G., & Boman, E.G. (2008). Partitioning and Preconditioning for Circuit Simulation [Conference]. https://www.osti.gov/biblio/1146153

Bartlett, R. (2008). Overview of the Vertical Integration of Trilinos Solver Algorithms in a Production Application Code [Conference]. https://www.osti.gov/biblio/1145581

Pawlowski, R., Shadid, J.N., Phipps, E.T., Bartlett, R., & Bartlett, R. (2008). Analysis Tools for Large-scale Simulation with Application to Magnetohydrodynamics Physics [Conference]. https://www.osti.gov/biblio/1145798

Huff, T.B., Turgeon, J., Baldonado, E., Stubblefield, W.A., Kennedy, B.C., Saba, A.W., & Saba, A.W. (2008). Sustaining knowledge in the neutron generator community and benchmarking study. https://doi.org/10.2172/933224

Hart, W.E. (2008). Statistical Challenges for Global Optimization Experiments [Conference]. https://www.osti.gov/biblio/1145493

Berry, J. (2008). The MultiThreaded Graph Library [Presentation]. https://www.osti.gov/biblio/1713125

Shadid, J.N. (2008). Robust Scalable Accurate and Efficient Computational Formulation and Solution Methods for Transport/Reaction and Extended MHD Simulations [Presentation]. https://www.osti.gov/biblio/1712438

Dunlavy, D.M., Kolda, T.G., Kegelmeyer, W.P., & Kegelmeyer, W.P. (2008). Tensor Decompositions for Analyzing Multi-link Graphs [Conference]. https://www.osti.gov/biblio/1145612

Hjalmarson, H.P., Hartman, F., Wills, A.E., Crozier, P., & Crozier, P. (2008). The Physics of Intense High Energy Ionizing Radiation Effects on Insulators and Semiconductors [Presentation]. https://www.osti.gov/biblio/1712613

Morrow, J.D., Bader, B., Chew, P.A., Speed, A., & Speed, A. (2008). Automated Analysis for Understanding Large Text Corpora: Analyzing text to understand individuals and groups [Conference]. https://www.osti.gov/biblio/1145531

Gaudioso, J.M. (2008). Biosafety and Biosecurity--A Growing Concern [Conference]. https://www.osti.gov/biblio/1145442

Vaughan, C.T. (2008). Preliminary Results with AMD Quadcore Processors [Conference]. https://www.osti.gov/biblio/1145617

Collins, M.J. (2008). An Upper Bound for Set Systems with the Identifiable Parent Property [Conference]. https://www.osti.gov/biblio/1145521

Shadid, J.N. (2008). Progress on the Development on Fully-implicit Fully-coupled Unstructured FE Solution Methods for Resistive MHD Simulations [Presentation]. https://www.osti.gov/biblio/1712631

Bartlett, R. (2008). Invasive Sensitivities and Optimization: From Research to Applications [Presentation]. https://www.osti.gov/biblio/1713023

Joo, J., Plimpton, S.J., Faulon, J.-L., & Faulon, J.-L. (2008). NF-kB Shuttling Patterns in Single Cells [Conference]. https://www.osti.gov/biblio/1146353

Crozier, P., Plimpton, S.J., Thompson, A.P., & Thompson, A.P. (2008). A brief survey of the LAMMPS MD code: intro case studies and future development [Presentation]. https://www.osti.gov/biblio/1712928

Hart, W.E., Riesen, L., Berry, J., Heaphy, R.T., Phillips, C.A., & Phillips, C.A. (2008). Nightly Software Testing in Acro with EXACT and FAST [Presentation]. https://www.osti.gov/biblio/1712959

Romero, L. (2008). Horizontally Spinning levitrons- A new configuration for spin stabilized magnetic levitation [Presentation]. https://www.osti.gov/biblio/1712973

Doerfler, D.W. (2008). Application Performance On Multicores [Presentation]. https://www.osti.gov/biblio/1712894

Heroux, M.A., Edwards, H.C., Williams, A.B., & Williams, A.B. (2008). Application Performance on Multicore Architectures: Mantevo Project Some Results & Predictions [Presentation]. https://www.osti.gov/biblio/1712895

Gaudioso, J.M. (2008). Building a Solid Foundation for Laboratory Biosafety and Biosecurity [Conference]. https://www.osti.gov/biblio/1145979

Doerfler, D.W., Vaughan, C.T., & Vaughan, C.T. (2008). A Preliminary Evaluation of Quad-Core Processors for Sandia Applications [Conference]. https://www.osti.gov/biblio/1145921

Brightwell, R.B., Pedretti, K., Ferreira, K.B., & Ferreira, K.B. (2008). Instrumentation and Analysis of MPI Queue Times on the SeaStar High-Performance Network [Conference]. https://www.osti.gov/biblio/1145976

Lucero, J.L. (2008). The Challenges of Implementing a Modeling Tool in the Intelligence Community [Conference]. https://www.osti.gov/biblio/1145969

Boman, E.G. (2008). Hypergraph-based Unyssetric Nested Dissection Ordering for Sparse LU Factorization. SIAM Journal on Scientific Computing. https://www.osti.gov/biblio/1146284

Thompson, A.P. (2008). Reactive Molecular Dynamics Simulations of Shocked PETN [Conference]. https://www.osti.gov/biblio/1146129

Leung, V.J. (2008). Parallel job scheduling policies to improve fairness : a case study. https://doi.org/10.2172/929521

Debenedictis, E. (2008). Computing in the Next 20 Years: Talk Driven by a Findings Digest of Frontiers of Extreme Computing 2007 Zettaflops Workshop [Conference]. https://www.osti.gov/biblio/1146230

Romero, L. (2008). Dissipation-induced heteroclinic orbits in tippe tops. Proposed for publication in SIAM Review.. https://www.osti.gov/biblio/949032

Robinson, A.C., Brunner, T.A., Carroll, S., Richarddrake, ., Garasi, C.J., Gardiner, T., Haill, T., Hanshaw, H., Hensinger, D., Labreche, D., Lemke, R., Love, E., Luchini, C., Mosso, S., Niederhaus, J., Ober, C.C., Petney, S., Rider, W., Scovazzi, G., … Voth, T. (2008). ALEGRA: An arbitrary Lagrangian-Eulerian multimaterial, multiphysics code [Conference]. 46th AIAA Aerospace Sciences Meeting and Exhibit. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=74949106632&origin=inward

Knupp, P., Bond, R.B., & Bond, R.B. (2008). Impact of Coding Mistakes on Numerical Error and Uncertainty in Solutions to PDEs [Conference]. https://www.osti.gov/biblio/1146096

Wylie, B.N. (2008). Integration of Information and Volume Visualization for Analysis of Cell Lineage and Gene Expression during Embryogenesis [Conference]. https://www.osti.gov/biblio/1146245

Gaudioso, J.M. (2008). Survey of Bioscience Research Practices in Asia: Questionnaire and Responses [Presentation]. https://www.osti.gov/biblio/1713089

Parks, M.L., Plimpton, S.J., Lehoucq, R.B., Silling, S.A., & Silling, S.A. (2008). Peridynamics with LAMMPS : a user guide. https://doi.org/10.2172/959309

Moreland, K. (2008). Ultravis Team Meeting Progress 2008-02 [Presentation]. https://www.osti.gov/biblio/1713099

Hart, W.E., Berry, J., Boman, E.G., Carr, R.D., Riesen, L., Phillips, C.A., Watson, J., & Watson, J. (2008). Sandia/EPA TEVA-SPOT Water Security Team Chosen as Finalist for 2008 Edelman Award Competition [Presentation]. https://www.osti.gov/biblio/1713101

Debenedictis, E. (2008). Frontiers of Extreme Computing 2007 [Conference]. https://www.osti.gov/biblio/1146320

Banks, J.W., Shadid, J.N., & Shadid, J.N. (2008). An FCT Method for High-Speed Flows on Structured Overlapping Meshes Part II: A Comparison with a High-Resolution Godunov Method. Journal of Computational Physics. https://www.osti.gov/biblio/1146200

Banks, J.W., Shadid, J.N., & Shadid, J.N. (2008). An FCT Method for High-Speed Flows on Structured Overlapping Meshes Part I: Algorithm Description. Journal of Computational Physics. https://www.osti.gov/biblio/1146347

Heroux, M.A., Wen, Z., & Wen, Z. (2008). The BEC parallel programming environment and initial applications [Conference]. https://www.osti.gov/biblio/942208

Wills, A.E. (2008). The AM05 functional: Important formulas and background information for implementing AM05 into DFT codes [Presentation]. https://www.osti.gov/biblio/1713006

Adams, S.S., Hendrickson, S.M., Dornburg, C.C., Davidson, G.S., & Davidson, G.S. (2008). The Effectiveness of Electronic Brainstorming in an Industrial Setting [Conference]. https://www.osti.gov/biblio/1146277

Lehoucq, R.B. (2008). PSEUDO-TRANSIENT CONTINUATION FOR NONLINEAR TRANSIENT ELASTICITY. International Journal of Numerical Methods in Engineering. https://www.osti.gov/biblio/1146152

Berry, J., Carr, R.D., Hart, W.E., Leung, V.J., Phillips, C.A., Watson, J., & Watson, J. (2008). Designing Contamination Warning System for Municipal Water Networks Using Imperfect Sensors. Journal of Water Resources Planning and Management. https://www.osti.gov/biblio/1146387