Publications
K. Yoshii, K. Iskra, H. Naik, P. Beckman, and P. C. Broekema, "Performance and Scalability Evaluation of ``Big Memory" on Blue Gene Linux," Preprint ANL/MCS-P1690-1109, November 2009. [pdf]
[more info]
J. M. Wozniak and M. Wilde, "Case Studies in Storage Access by Loosely Coupled Petascale Applications," Preprint ANL/MCS-P1691-1109, November 2009. [pdf]
[more info]
J. A. Insley, T. Leggett, and M. E. Papka, "Using Dynamic Accounts to Enable Access to Advanced Resources through Science Gateways," Preprint ANL/MCS-P1682-1009, October 2009. [pdf]
[more info]
M. Min and T. Lee, "A Spectral-Element Discontinuous Galerkin Lattice Boltzmann Method for Incompressible Flows," Preprint ANL/MCS-P1688-1009, October 2009. [pdf]
[more info]
E. M. Constantinescu, V. M. Zavala, M. Rocklin, S. Lee, and M. Anitescu, "A Computational Framework for Uncertainty Quantification and Stochastic Optimization in Unit Commitment with Wind Power Generation," Preprint ANL/MCS-P1681-1009, October 2009. [pdf]
[more info]
V. M. Zavala, E. M. Constantinescu, and M. Anitescu, "Economic Impacts of Advanced Weather Forecasting in Energy System Operations," Preprint ANL/MCS-P1687-1009, October 2009. [pdf]
[more info]
S. Narayan, J. A. Chandy, S. Lang, P. Carns, and R. Ross, "Uncovering Errors: The Cost of Detecting Silent Data Corruption," Preprint ANL/MCS-P1689-1009, October 2009.
[more info]
E. M Constantinescu, V. M. Zavala, M. Rocklin, S. Lee, and M. Anitescu, "Unit Commitment with Wind Power Generation: Integrating Wind Forecast Uncertainty and Stochastic Programming," Technical Memorandum ANL/MCS-TM-309, September 2009. [pdf]
[more info]
A. Lyons, "Acyclic and Star Colorings of Cographs," Preprint ANL/MCS-P1675-0909, September 2009. [pdf]
[more info]
R. E. Grant, A. Afsahi, and P. Balaji, "Evaluation of ConnectX Virtual Protocol Interconnect for Data Centers," Preprint ANL/MCS-P1672-0909, September 2009. [pdf]
[more info]
C. S. Henry, M. DeJongh, A. A. Best, P. M. Frybarger, and R. L. Stevens, "High-Throughput Generation and Optimization of Genome-Scale Metabolic Models," Preprint ANL/MCS-P1673-0909, September 2009. [pdf]
[more info]
M. Wilde, Z. Zhang, B. Clifford, M. Hategan, S. Kenny, K. Iskra, P. Beckman, I. Foster, I. Raicu, and A. Espinosa, "Parallel Scripting for Applications at the Petascale and Beyond," Preprint ANL/MCS-P1676-0909, September 2009. [pdf]
[more info]
J. Chen and I. Safro, "A Measure of the Connection Strengths between Graph Vertices with Applications," Preprint ANL/MCS-P1677-0909, September 2009. [pdf]
[more info]
Z. Xie and J. M. Bowman, "Permutationally Invariant Polynomial Basis for Molecular Energy Surface Fitting via Monomial Symmetrization," Preprint ANL/MCS-P1674-0909, September 2009. [pdf]
[more info]
P. Balaji, H. Naik, and N. Desai, "Understanding Network Saturation Behavior on Large-Scale Blue Gene/P Systems," Preprint ANL/MCS-P1671-0909, September 2009. [pdf]
[more info]
P. Carns, R. Latham, R. Ross, K. Iskra, S. Lang, and K. Riley, "24/7 Characterization of Petascale I/O Workloads," Preprint ANL/MCS-P1660-0809, August 2009. [pdf]
[more info]
Z. Hou, M. Wilde, X. Zhou, I. Foster, and J. Tie, "ADEM: An Automation Tool for Application Software Deployment and Management on OSG," Preprint ANL/MCS-P1659-0809, August 2009. [pdf]
[more info]
C. M. Patrick, R. Garg, S. W. Son, and M. Kandemir, "Improving I/O Performance Using Soft-QoS-Based Dynamic Storage Cache Partitioning," Preprint ANL/MCS-P1661-0809, August 2009. [pdf]
[more info]
J. Shin, M. W. Hall, J. Chame, C. Chen, and P. D. Hovland, "Autotuning and Specialization: Speeding up Matrix Multiply for Small Matrices with Compiler Technology," Preprint ANL/MCS-P1664-0809, August 2009. [pdf]
[more info]
J. Wilkening, A. Wilke, N. Desai, and F. Meyer, "Using Clouds for Metagenomics: A Case Study," Preprint ANL/MCS-P1665-0809, August 2009. [pdf]
[more info]
S. W. Son, M. Kandemir, Y. Zhang, and R. Garg, "Topology-Aware I/O Caching for Shared Storage Systems," Preprint ANL/MCS-P1668-0809, August 2009. [pdf]
[more info]
V. Bui, B. Norris, and L. C. McInnes, "An Automated Component-Based Performance Experiment Environment," Preprint ANL/MCS-P1666-0809, August 2009. [pdf]
[more info]
B. Smith and H. Zhang, "Sparse Triangular Solve Revisited: Data Layout Crucial to Better Performance," Preprint ANL/MCS-P1658-0809, August 2009. [pdf]
[more info]
S. Lang, R. Latham, D. Kimpe, and R. Ross, "Interfaces for Coordinated Access in the File System," Preprint ANL/MCS-P1662-0809, August 2009. [pdf]
[more info]
L. Li, T. L. Dahlgren, L. C. McInnes, and B. Norris, "Interface Contract Enforcement for Improvement of Computational Quality of Service (CQoS) for Scientific Components," Preprint ANL/MCS-P1663-0809, August 2009. [pdf]
[more info]
T. Peterka, R. B. Ross, H.-W. Shen, K.-L. Ma, W. Kendall, and H. Yu, "Parallel Visualization on Leadership Computing Resources," Preprint ANL/MCS-P1656-0709, July 2009. [pdf]
[more info]
C. S. Henry, F. Xia, and R. Stevens, "Application of High-Performance Computing to the Reconstruction, Analysis, and Optimization of Genome-Scale Metabolic Models," Preprint ANL/MCS-P1647-0709, July 2009. [pdf]
[more info]
S. Lang, P. Carns, R. Latham, R. Ross, K. Harms, and W. Allcock, "I/O Performance Challenges at Leadership Scale," Preprint ANL/MCS-P1648-0709, July 2009. [pdf]
[more info]
B. Sotomayor, R. S. Montero, I. M. Llorente, and I. Foster, "An Open Source Solution for Virtual Infrastructure Management in Private and Hybrid Clouds," Preprint ANL/MCS-P1649-0709, July 2009. [pdf]
[more info]
A. Choudhary, W.-K. Liao, K. Gao, A. Nisar, R. Ross, R. Thakur, and R. Latham, "Scalable I/O and Analytics," Preprint ANL/MCS-P1651-0709, July 2009. [pdf]
[more info]
M. Wilde, I. Raicu, A. Espinosa, Z. Zhang, B. Clifford, M. Hategan, S. Kenny, K. Iskra, P. Beckman, and I. Foster, "Extreme-Scale Scripting: Opportunities for Large Task-Parallel Applications on Petascale Computers," Preprint ANL/MCS-P1652-0709, July 2009. [pdf]
[more info]
A. Singh, P. Balaji, and W. Feng, "GePSeA: A General-Purpose Software Acceleration Framework for Lightweight Task Offloading," Preprint ANL/MCS-P1653-0709, July 2009. [pdf]
[more info]
M. Hereld, R. Hudson, J. Norris, M. E. Papka, and T. Uram, "Enabling Scientific Teamwork," Preprint ANL/MCS-P1654-0709, July 2009. [pdf]
[more info]
M. Hall, J. Chame, C. Chen, J. Shin, and G. Rudy, "Transformation Recipes for Code Generation and Auto-Tuning," Preprint ANL/MCS-P1657-0709, July 2009. [pdf]
[more info]
R. Ross, R. Latham, W. Gropp, E. Lusk, and R. Thakur, "Processing MPI Datatypes Outside MPI," Preprint ANL/MCS-P1635-0609, June 2009. [pdf]
[more info]
D. Giannakis, R. Rosner, and P. F. Fischer, "Instabilities in Free-Surface Hartmann Flow at Low Magnetic Prandtl Numbers," Preprint ANL/MCS-P1637-0609, June 2009. [pdf]
[more info]
V. M. Zavala and M. Anitescu, "On-Line Nonlinear Programming as a Generalized Equation," Preprint ANL/MCS-P1641-0609, June 2009. [pdf]
[more info]
G. Hocky, M. Wilde, J. DeBartolo, M. Hategan, I. Foster, T. R. Sosnick, K. F. Freed, "Toward Petascale ab initio Protein Folding through Parallel Scripting," Preprint ANL/MCS-P1645-0609, June 2009. [pdf]
[more info]
O. Hernandez, B. Chapman, V. Bui, and R. Kufrin, "Open-Source Software Support for the OpenMP Runtime API for Profiling," Preprint ANL/MCS-P1646-0609, June 2009. [pdf]
[more info]
D. Giannakis, P. F. Fischer, and R. Rosner, "A Spectral Galerkin Method for the Coupled Orr-Sommerfeld and Induction Equations for Free-Surface MHD," J. of Computational Physics, vol. 228, 2009, pp. 1188-1233. Also Preprint ANL/MCS-P1639-0609, June 2009. [pdf]
[more info]
T. J. Tautges and A. Caceres, "Scalable Parallel Solution Coupling for Multi-Physics Reactor Simulation," Preprint ANL/MCS-P1636-0609, June 2009. [pdf]
[more info]
V. M. Zavala, "Stability Analysis of an Approximate Scheme for Moving Horizon Estimation," Preprint ANL/MCS-P1644-0609, June 2009. [pdf]
[more info]
T. Peterka, H. Yu, R. Ross, K.-L. Ma, and R. Latham, "End-to-End Study of Parallel Volume Rendering on the IBM Blue Gene/P," Preprint ANL/MCS-P1642-0609, June 2009. [pdf]
[more info]
P. Balaji, D. Buntinas, D. Goodell, W. Gropp, S. Kumar, E. Lusk, R. Thakur, and J. L. Traff, "MPI on a Million Processors," Preprint ANL/MCS-P1621-0509, May 2009. [pdf]
[more info]
H. Zhu, D. Goodell, W. Gropp, and R. Thakur, "Hierarchical Collectives in MPICH2," Preprint ANL/MCS-P1622-0509, May 2009. [pdf]
[more info]
P. Balaji, D. Buntinas, D. Goodell, W. Gropp, and R. Thakur, "Fine-Grained Multithreading Support for Hybrid Threaded MPI Programming," Preprint ANL/MCS-P1623-0509, May 2009. [pdf]
[more info]
T. Peterka, D. Goodell, R. Ross, H.-W. Shen, and R. Thakur, "Configurable Algorithm for Parallel Image-Compositing Applications," Preprint ANL/MCS-P1624-0509, May 2009. [pdf]
[more info]
G. Garzoglio, I. Aldermhini, M. Altunay, R. Ananthakrishnan, J. Bester, K. Chadwick, V. Ciaschini, Y. Demchenko, A. Ferraro, A. Forti, D. Groep, T. D. Hesselroth, J. Hover, O. Koeroo, C. La Joie, T. Levshina, Z. Miller, J. Packard, H. Sagehaug, I. Sfiligoi, N. Sharma, S. Timm, F. Siebenlist, V. Venturi, and J. Weigand, "XACML Profile and Implementation for Authorization Interoperability between OSG and EGEE," Preprint ANL/MCS-P1626-0509, May 2009. [pdf]
[more info]
F. Siebenlist, R. Ananthakrishnan, D. E. Bernholdt, L. Cinquini, I. T. Foster, D. E. Middleton, N. Miller, and D. N. Williams, "Earth System Grid Authentication Infrastructure: Integrating Local Authentication, OpenID and PKI," Preprint ANL/MCS-P1627-0509, May 2009. [pdf]
[more info]
E. Lusk, "Slouching Towards Exascale," Preprint ANL/MCS-P1628-0509, May 2009. [pdf]
[more info]
J. G. Blas, F. Isaila, J. Carretero, R. Latham, and R. Ross, "Multiple-Level MPI File Write-Back and Prefetching for Blue Gene Systems," Preprint ANL/MCS-P1632-0509, May 2009. [pdf]
[more info]
D. Buntinas, B. Goglin, D. Goodell, G. Mercier, and S. Moreaud, "Cache-Efficient, Intranode, Large-Message MPI Communication with MPICH2-Nemesis," Preprint ANL/MCS-P1620-0509, May 2009. [pdf]
[more info]
S. Leyffer, J. Linderoth, J. Luedtke, A. Miller, and T. Munson, "Applications and Algorithms for Mixed Integer Nonlinear Programming," Preprint ANL/MCS-P1630-0509, May 2009. [pdf]
[more info]
B. R. de Supinski, S. Alam, D. H. Bailey, L. Carrington, C. Daley, A. Dubey, T. Gamblin, D. Gunter, P. D. Hovland, H. Jagode, K. Karananic, G. Marin, J. Mellor-Crummey, S. Moore, B. Norris, L. Oliker, C. Olschanowsky, P. C. Roth, M. Schulz, S. Shende, A. Snavely, W. Spear, M. Tikir, J. Vetter, P. Worley, and N. Wright, "Modeling the Office of Science Ten Year Facilities Plan: The PERI Architecture Tiger Team," Preprint ANL/MCS-P1631-0509, May 2009. [pdf]
[more info]
I. Raicu, I. T. Foster, Y. Zhao, P. Little, C. M. Moretti, A. Chaudhary, and D. Thain, "The Quest for Scalable Support of Data-Intensive Workloads in Distributed Systems," Preprint ANL/MCS-P1596-0409, April 2009. [pdf]
[more info]
G. Santhanaraman, P. Balaji, K. Gopalakrishnan, R. Thakur, W. Gropp, and D. K. Panda, "Natively Supporting True One-Sided Communication in MPI on Multi-Core Systems with InfiniBand," Preprint ANL/MCS-P1598-0409, April 2009. [pdf]
[more info]
E. M. Constantinescu and A. Sandu, "Achieving Very High Order for Implicit Explicit Time Stepping: Extrapolation Methods," Technical Memorandum ANL/MCS-TM-306, April 2009. [pdf]
[more info]
W. Feng, P. Balaji, and A. Singh, "Network Interface Cards as First-Class Citizens," Preprint ANL/MCS-P1599-0409, April 2009. [pdf]
[more info]
L. Liming, J.-P. Navarro, E. Blau, J. Brechin, C. Catlett, M. Dahan, D. Diehl, R. Dooley, M. Dwyer, K. Ericson, I. Foster, E. Hanna, D. L. Hart, C. Jordan, R. Light, S. Martin, J. McGee, L. Pearlman, J. Reilly, T. Scavo, M. Shapiro, S. Smallen, W. Smith, and N. Wilkins-Diehr, "TeraGrid's Integrated Information Service," Preprint ANL/MCS-P1607-0409, April 2009. [pdf]
[more info]
P. Balaji, A. Chan, R. Thakur, W. Gropp, and E. Lusk, "Toward Message Passing for a Million Processes: Characterizing MPI on a Massive Scale Blue Gene/P," Preprint ANL/MCS-P1616-0409, April 2009. [pdf]
[more info]
J. Bresnahan, M. Link, R. Kettimuthu, and I. Foster, "UDT as an Alternative Transport Protocol for GridFTP," Preprint ANL/MCS-P1614A-0409, April 2009. [pdf]
[more info]
G. Hocky, M. Wilde, J. DeBartolo, M. Hategan, I. Foster, T. R. Sosnick, K. F. Freed, "Towards Petascale ab initio Protein Folding Through Parallel Scripting," Preprint ANL/MCS-P1612-0409, April 2009. [pdf]
[more info]
P. Lai, P. Balaji, R. Thakur, and D. K. Panda, "ProOnE: A General-Purpose Protocol Onload Engine for Multi- and Many-Core Architectures," Preprint ANL/MCS-P1617-0409, April 2009. [pdf]
[more info]
M. Min and P. F. Fischer, "Spectral-Element Discontinuous Galerkin (SEDG) Simulations with a Moving Window Algorithm for Wakefield Calculations," Preprint ANL/MCS-P1615-0409, April 2009. [pdf]
[more info]
A. Lyons, "Acyclic and Star Colorings of Joins of Graphs and an Algorithm for Cographs," Proc. 8th Cologne_Twente Workshop on Graphs and Combinatorial Optimization, 2009, pp. 199-202. Also Preprint ANL/MCS-P1610-0409, April 2009. [pdf]
[more info]
D. Kaushik, M. Smith, A. Wollaber, B. Smith, A. Siegel, and W. S. Yang, "Enabling High Fidelity Neutron Transport Simulations on Petascle Architectures," Preprint ANL/MCS-P1608-0409, April 2009. [pdf]
[more info]
J. W. Larson, "Information-Theoretic Strategies for Quantifying Variability and Model-Reality Comparison in the Climate System," Preprint ANL/MCS-P1609-0409, April 2009. [pdf]
[more info]
F. Meyer, R. Overbeek, and A. Rodriguez, "FIGfams: Yet Another Set of Protein Families," Preprint ANL/MCS-P1613A-0409, April 2009. [pdf]
[more info]
E. M. Constantinescu and A. Sandu, "Extrapolated Implicit-Explicit Time Stepping.," Preprint ANL/MCS-P1612A-0409, April 2009. [pdf]
[more info]
H. Naik, R. Gupta, and P. Beckman, "Analyzing Checkpointing Trends for Applications on the IBM Blue Gene/P System," Preprint ANL/MCS-P1590-0309, March 2009. [pdf]
[more info]
R. Gupta, P. Beckman, B. H. Park, E. Lusk, P. Hargrove, A. Geist, D. K. Panda, A. Lumsdaine, and J. Dongarra, "CIFTS: A Coordinated Infrastructure for Fault-Tolerant Systems," Preprint ANL/MCS-P1591-0309, March 2009. [pdf]
[more info]
V. M. Zavala, E. M. Constantinescu, T. Krause, and M. Anitescu, "On-Line Economic Optimization of Energy Systems Using Weather Forecast Information," Preprint ANL/MCS-P1588-0309, March 2009. [pdf]
[more info]
K. Yoshii, K. Iskra, P. C. Broekema, H. Naik, and P. Beckman, "Characterizing the Performance of Big Memory on Blue Gene Linux," Preprint ANL/MCS-P1589-0309, March 2009. [pdf]
[more info]
M. Altunay, S. Leyffer, J. T. Linderoth, Z. Xie, "Optimal Security Response to Attacks on Open Science Grids," Preprint ANL/MCS-P1593-0309, March 2009. [pdf]
[more info]
N. Ali, P. Carns, K. Iskra, D. Kimpe, S. Lang, R. Latham, R. Ross, L. Ward, and P. Sadayappan, "Scalable I/O Forwarding Framework for High-Performance Computing Systems," Preprint ANL/MCS-P1594-0309, March 2009. [pdf]
[more info]
J. Utke and U. Naumann, "Combinatorial Problems in Open/AD," Preprint ANL/MCS-P1595-0309, March 2009. [pdf]
[more info]
A. Tasora and M. Anitescu, "A Convex Complementarity Approach for Simulating Large Granular Flows," Preprint ANL/MCS-P1592-0309, March 2009. [pdf]
[more info]
B. Norris, A. Hartono, E. Jessup, and J. Siek, "Generating Empirically Optimized Composed Matrix Kernels from MATLAB Prototypes," Preprint ANL/MCS-P1581-0209, February 2009. [pdf]
[more info]
L. Li, J. P. K enny, M.-S. Wu, K. Huck, A. Gaenko, M. S. Gordon, C. L. Janssen, L. C. McInnes, H. M. Netzloff, B. Norris, T. L. Windus, "Adaptive Application Composition in Quantum Chemistry," Preprint ANL/MCS-P1575-0209, February 2009. [pdf]
[more info]
M. M. Strout, N. Osheim, D. Rostron, P. D. Hovland, and A. Pothen, "Evaluation of Hierarchical Mesh Reorderings," Preprint ANL/MCS-P1578-0209, February 2009. [pdf]
[more info]
C. S. Henry, J. F. Zinner, M. P. Cohoon, and R. L. Stevens, "iBsu1101: An Improved Genome-Scale MetabolicModel of B. subtilis Based on SEED Annotations," Preprint ANL/MCS-P1579-0209, February 2009. [pdf]
[more info]
I. Safro, P. Hovland, J. Shin, and M. Strout, "Improving Random Walk Performance," Preprint ANL/MCS-P1585-0209, February 2009. [pdf]
[more info]
J. Larson, "Graphical Notation for Diagramming Coupled Systems," Preprint ANL/MCS-P1581-0209, February 2009. [pdf]
[more info]
V. M. Zavala, E. M. Constantinescu, T. Krause, and M. Anitescu, "Weather Forecast-Based Optimization of Integrated Energy Systems," Technical Memorandum ANL/MCS-TM-305, February 2009. [pdf]
[more info]
O. Roderick and I. Safro, "Polynomial Interpolation for Predicting Decisions and Recovering Missing Data," Preprint ANL/MCS-P1586-0209, February 2009. [pdf]
[more info]
J. Bresnahan, M. Link, R. Kettimuthu, and I. Foster, "GridFTP Multilinking," Preprint ANL/MCS-P1582-0209, February 2009. [pdf]
[more info]
E. M. Constantinescu and A. Sandu, "Optimal Explicit Strong-Stability-Preserving General Linear Methods," Preprint ANL/MCS-P1584-0209, February 2009. [pdf]
[more info]
N. Desai, D. Buntinas, D. Buettner, P. Balaji, A. Chan, "Improving Resource Availability by Relaxing Network Allocation Constraints on the Blue Gene/P," Preprint ANL/MCS-P1587-0209, February 2009. [pdf]
[more info]
X. Shi and R. Stevens, "A Bayesian Approach to High-Throughput Biological Model Generation," Preprint ANL/MCS-P1567-0109, January 2009. [pdf]
[more info]
V. M. Zavala, M. Anitescu, and T. Krause, "On the Optimal On-Line Management of Photovoltaic-Hydrogen Hybrid Energy Systems," Preprint ANL/MCS-P1569-0109, January 2009. [pdf]
[more info]
T. Peterka, R. Ross, H. Yu, K.-L. Ma, R. Kooima, and J. Girado, "Autostereoscopic Display of Large-Scale Scientific Visualization," Preprint ANL/MCS-P1566-0109, January 2009. [pdf]
[more info]
T. J. Tautges, "Canonical Numbering Systems for Finite-Element Codes," Preprint ANL/MCS-P1573-0109, January 2009. [pdf]
[more info]
P. Carns, S. Lang, R. Ross, M. Vilayannur, J. Kunkel, andT. Ludwig, "Small-File Access in Parallel File Systems," Preprint ANL/MCS-P1571-0109, January 2009. [pdf]
[more info]
E. Constantinescu and A. Sandu, "Explicit Time Stepping Methods with High Stage Order and Monotonicity Properties," Preprint ANL/MCS-P1576-0109, January 2009. [pdf]
[more info]
E. Constantinescu and A. Sandu, "Optimal Explicit Strong-Stability-Preserving General Linear Methods: Complete Results," Technical Memorandum ANL/MCS-TM-304, January 2009. [pdf]
[more info]
R. Thakur and W. Gropp, "Test Suite for Evaluating Performance of Multithreaded MPI Communication," Preprint ANL/MCS-P1570-0109, January 2009. [pdf]
[more info]
M. Hereld, R. Stevens, T. Sterling, and G. R. Gao, "Structured Hints: Extracting and Abstracting Domain Expertise," Technical Memorandum ANL/MCS-TM-303, January 2009. [pdf]
[more info]
S. Leyffer, "A Complementarity Constraint Formulation of Convex Multiobjective Optimization Problems," Preprint ANL/MCS-P1290-0905, September 2005. [pdf]
[more info]
T. Bae, A. K. Banger, A. Wallace, E. M. Glass, F. Aslund, O. Schneewind, D. M. Missiakas, "Staphylococcus Aureus Virulence Genes Identified by Bursa Aurealis Mutagenesis and Nematode Killing," Preprint ANL/MCS-P1165-0604, June 2004. [pdf]
[more info]
