Data-Intensive Computing Initiative (DICI)
Select Publications
Journal Articles
Anderson DN, WK Hensley, DS Barnett, DK Fagan, JI McIntyre, and JC Hayes. 2006. "A probabilistic derivation of gamma-ray attenuation and application: Bayesian mass estimation with a low count spectrum." Nuclear Instruments and Methods in Physics Research. Section A, Accelerators, Spectrometers, Detectors and Associated Equipment 569(3):894-899.
Beecroft J, D Addison, D Hewson, M McLaren, D Roweth, F Petrini, and J Nieplocha. 2006. "QsNetII : Defining High-Performance Network Design." In IEEE Micro 25(4):34-47, July/August 2005.
Chin SH. 2007. "Data-Intensive Computing Paving Way for Advances in Biology." SciDAC Review (Accepted).
Farber R. 2007. "Buy Your Next Supercomputer at Costco." Scientific Computing 24(5):13+.
Farber R. 2007. "Data Management, the Victorian era child of the 21st century." Scientific Computing 24(4):12+.
Farber R. 2007. "Finding the Insight to Balance Science-driven Computation and Experiment for Innovation." Innovation: America's Journal of Technology Commercialization 5(24):24+.
Farber R. 2007. "HPC balance and common sense." Scientific Computing 24(3):12+.
Farber R. 2007. "Power and Cooling — The HPC Brick Wall." Scientific Computing 24(6):16+.
Farber R. 2007. "The Cure for HPC Neurosis: Multiple, Virtual Personalities!" Scientific Computing 24(7):16+.
Frachtenberg E, D Feitelson, F Petrini, and J Fernandez. 2006. "Adaptive Parallel Job Scheduling with Flexible CoScheduling." IEEE Transactions on Parallel and Distributed Systems 16(11).
Hachigian DJ. 2007. "Data-Intensive Computing Laying the Foundation for Biological Breakthroughs." DOE Pulse.
Huang Z, RT Guttromson, J Nieplocha, and RG Pratt. 2007. "Transforming Power Grid Operations via High-Performance Computing." Scientific Computing 24(5).
Manke KL. 2006. "Comin' Atcha!" Innovation: America's Journal of Technology Commercialization 4(5):14-16.
Nieplocha J, A Marquez, F Petrini, and D Chavarría-Miranda. 2007. "Unconventional Architectures Address Challenges in High-Throughput Sciences." SciDAC Review. Fall 2007. [Accepted]
Palmer BJ, SM Kathmann, M Krishnan, V Tipparaju, and J Nieplocha. 2007. "The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free Energy States." Journal of Chemical Theory and Computation 3(2):P583-592.
Petrini F, A Moody, J Fernandez, E Frachtenberg, and DK Panda. 2006. "NIC-based Reduction Algorithms for Large-scale Clusters." International Journal of High Performance Computing and Networking (IJHPCN) 4(3/4).
Petrini F, J Nieplocha, and V Tipparaju. 2006. "SFT: Scalable Fault Tolerance." ACM SIGOPS Operating Systems Review 40(2).
Pettigrew MF, and H Resat. 2007. "Multinomial Tau-Leaping Method for Stochastic Kinetic Simulations." Journal of Chemical Physics 126(8):Art. No. 084101.
Sanfilippo AP, C Posse, B Gopalan, RM Riensche, N Beagley, BL Baddeley, SC Tratz, and ML Gregory. 2007. "Combining Hierarchical and Associative Gene Ontology Relations with Textual Evidence in Estimating Gene and Gene Product Similarity." IEEE Transactions on NanoBioscience 6(1):51-59. doi:10.1109/TNB.2007.891886
Scarpazza DP, O Villa, and F Petrini. 2007. "Programming the Cell Processor." Dr. Dobb's Journal 31(4):26,28-30.
Schuchardt KL, TD Gibson, EG Stephan, and G Chin. 2006. Applying Content Management to Automated Provenance Store." Concurrency and Computation: Practice and Experience.
Shah A, CS Oehmen, JK Harper, and BM Webb-Robertson. 2007. "Integrating Subcellular Location for Improving Machine Learning Models of Remote Homology Detection in Eukaryotic Organisms." Computational Biology and Chemistry 31(2):138-142.
Shah A, M Singhal, KR Klicker, EG Stephan, HS Wiley, and KM Waters. 2007. "Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager." Bioinformatics 23(7):906-909.
Tartakovsky AM, P Meakin, TD Scheibe, and RM Eichler West. 2007. "Simulations of reactive transport and precipitation with smoothed particle hydrodynamics." Journal of Computational Physics 222(2):654-672.
Tartakovsky AM, and P Meakin. 2006. "Pore-scale modeling of immiscible and miscible fluid flows using smoothed particle hydrodynamics." Advances in Water Resources 29(10):1464-1478.
Webb-Robertson BM, M Singhal, ES Peterson, KR Klicker, CS Oehmen, JN Adkins, and SL Havre. 2007. "PQuad - A Visual Analysis Platform for Proteomic Data Exploration of Microbial Organism." Bioinformatics.
Wong PC, HP Foote, G Chin, JR, PS Mackey, and KA Perrine. 2006. "Graph Signatures for Visual Analytics." IEEE Transactions on Visualization and Computer Graphics 12(6):1399-1413.
Wong PC, SJ Rose, G Chin, Jr, D Frincke, RA May, II, C Posse, AP Sanfilippo, and JJ Thomas. 2006. "Walking the Path-A New Journey to Explore and Discover through Visual Analytics." Information Visualization 5(4):237-249. doi:10.1057/palgrave.ivs.9500133
Conference Papers
Babar MA, and I Gorton. 2007. "A Tool for Managing Software Architecture Knowledge." In Second Workshop on Sharing and Reusing architectural Knowledge - Architecture, rationale, and Design Intent (SHARK/ADI 2007), at 29th IEEE Int. Conf. on Software Engineering (ICSE 2007), May, 20-26, 2007, Minneapolis, Minnesota.
Babar MA, and I Gorton. 2007. "Architecture Knowledge Management: Challenges, Approaches, and Tools." In Proceedings of the 29th IEEE International Conference on Software Engineering, pp. 170-17, May, 20-26, 2007, Minneapolis, Minnesota.
Bui NB, L Zhu, I Gorton, and Y Liu. 2007. "Benchmark Generation using Domain Specific Modeling." In Proceedings of the 2007 IEEE Australian Software Engineering Conference, pp. 169-180. Melbourne, Victoria, Australia.
Cannon WR, and BM Webb-Robertson. 2007. "Computational Proteomics: High-throughput Analysis for Systems Biology." In Biocomputing 2007. Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3 - 7 January 2007, ed. RB Altman, AK Dunker, L Hunter, T Murray & TE Klein, pp. 403-408. World Scientific Publishing Company, Singapore, Singapore.
Chavarria-Miranda D, and A Marquez. 2007. "Assessing the Potential of Hybrid HPC Systems for Scientific Applications." In Proceedings of the 2007 ACM International Conference on Computing Frontiers. ACM Press, New York.
Chavarria-Miranda D, J Nieplocha, and V Tipparaju. 2006. "Topology-aware Tile Mapping for Clusters of SMPs." In Proceedings of the 2006 ACM International Conference on Computing Frontiers. ACM, Ischia, Italy.
Garcia PE, J Fernandez, F Petrini, and JM Garcia. 2006. "Cluster Computing with QsNetII." In Euro PVM/MPI 2005, Sorrento, Italy, September 2005.
Garcia PE, J Fernandez-Peinador, F Petrini, and JM Garcia. 2006. "Assessing MPI Performance on QsNetII." In Euro PVM/MPI 2005, Sorrento, Italy, September 2005.
Gorton I, D Chavarría-Miranda, M Krishnan, and J Nieplocha. 2007. "A High-Performance Event Service for HPC Applications." In Third International Workshop on Software Engineering for High Performance Computing Applications. IEEE Computer Society, Wash DC, DC.
Gorton I, Y Liu, and N Trivedi. 2006. "An Extensible, Lightweight Architecture for Adaptive J2EE Applications ." In SEM '06. Proceedings of the 6th international workshop on Software engineering and middleware. Foundations of Software Engineering, pp. 47-54. ACM Press, New York, NY.
Jiang S, K Davis, F Petrini, X Ding, and X Zhang. 2006. "COCA: A Locality- Aware Cooperative Cache Management Protocol to Improve Network File System Performance." In Proceedings of the 26th International Conference on Distributed Computing Systems, pp.42-42, Lisboa, Portugal, July 2006.
Kot A, V Tipparaju, J Nieplocha, MT Bruggencate, and N Chrisochoides. 2007. "Evaluation of Remote Memory Access Communication on the Cray XT3. " In Workshop on communication architecture for clusteres. Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International 26-30 March 2007 pp. 1-7, Long Beach, California.
Krishnan M and J Nieplocha. 2006. "Memory Efficient Parallel Matrix Multiplication Operation for Irregular Problems. " In 20th IEEE International Parallel & Distributed Processing Symposium. ACM SIGMICRO Computing Frontiers, Ischia, Italy.
Krishnan M, SJ Bohn, WE Cowley, VL Crow, and J Nieplocha. 2007. "Scalable Visual Analytics of Massive Textual Datasets." In IEEE International Parallel & Distributed Processing Symposium. IEEE Computer Society, Long Beach , CA.
Liu Y, and I Gorton. 2007. "Implementing Adaptive Performance Management in Server Applications." In Software Engineering for Adaptive and Self-Managing Systems (SEAMS 2007).
Liu Y, I Gorton, and V Le. 2007. "A Configurable Event Correlation Architecture for Adaptive J2EE Applications. " In 2007 IEEE Australian Software Engineering Conference.
Liu Y, L Zhu, and I Gorton. 2007. "Performance Assessment for e-Government Services: An Experience Report. " In The 10th International ACM SIGSOFT Symposium on Component-Based Software Engineering.
Nieplocha J, A Marquez, J Feo, D Chavarría-Miranda, G Chin, Jr, C Scherrer, and N Beagley. 2007. "Evaluating the Potential of Multithreaded Platforms for Irregular Scientific Computations. " In Proceedings of the 4th International Conference on Computing Frontiers, Ischia, Italy, May 07 - 09, 2007, pp. 47-58. ACM Press, New York.
Nieplocha J, V Tipparaju, and M Krishnan. 2006. "Optimizing Strided Remote Memory Access Operations on the Quadrics QsNetII Network Interconnect. " In Proceedings of the Eighth International Conference on High-Performance Computing in Asia-Pacific Region, 2005, pp. 28-35. Institute of Electrical and Electronics Engineers, Inc.,Piscataway, New Jersey.
Oehmen C and J Nieplocha. 2006. "ScalaBLAST: A Scalable Implementation of BLAST for High-Performance Data-Intensive Bioinformatics Analysis." IEEE Transactions on Parallel and Distributed Systems. [In Press]
Sanfilippo AP, B Baddeley, C Posse, and PD Whitney. 2007. "A Layered Dempster-Shafer Approach to Scenario Construction and Analysis." In IEEE International Conference on Intelligence and Security Informatics 2007 (ISI 2007). IEEE , Los Alamitos, CA.
Scarpazza DP, O Villa, and F Petrini. 2007. "Peak-Performance DFA-based String Matching on the Cell Processor. " In IPDPS07 Workshop on System Tools. Institute of Electrical and Electronics Engineers, Inc., Piscataway, New Jersey.
Scarpazza DP, O Villa, F Petrini, and J Fernandez-Peinador. 2007. "Challenges in Mapping Graph Exploration Algorithms on Advanced Multi-core Processors." In International Parallel and Distributed Processing Symposium 2007. Institute of Electrical and Electronics Engineers, Inc., Piscataway, New Jersey.
Scarpazza DP, P Mullaney, O Villa, F Petrini, V Tipparaju, and J Nieplocha. 2007. "Transparent System-level Migration of PGAs Applications using Xen on Infiniband. " In IEEE Cluster 2007. (Accepted).
Scherrer C, N Beagley, J Nieplocha, A Marquez, J Feo, and D Chavarría-Miranda. 2007. "Probability Convergence in a Multithreaded Counting Application. " In Workshop on Multithreaded Architectures and Applications, pp. 1-5. IPDPS 2007. IEEE.
Schuchardt K. 2006. "Towards a Provenance Architecture." Presented by K Schuchardt (Invited Speaker) at the Kepler Provenance Working Meeting, San Diego, California on January 19, 2006.
Stephan EG, TJ Critchlow, AL Corrigan, ES Peterson, RD Lins Neto, TA Soares, and T Straatsma. 2007. "Effectively Managing Large-Scale Scientific Simulation Data." In The 24th International Conference on Data Engineering. PNNL-SA-56017, Pacific Northwest National Laboratory, Richland, Washington (submitted).
Thurman DA, JP Almquist, I Gorton, AS Wynne, and J Chatterton. 2007. "SIFT - A Component-Based Integration Architecture for Enterprise Analytics." In ICCBSS '07. Sixth International IEEE Conference on Commercial-off-the-Shelf (COTS)-Based Software Systems, 26 February - 2 March 2007. Banff, Alberta, Canada, pp. 82-92. Institute of Electrical and Electronics Engineers, Piscataway, NJ. doi:10.1109/ICCBSS.2007.35
Trease LL, HE Trease, and J Fowler. 2007. "Quantitative 3D Imaging, Segmentation and Feature Extraction of the Respiratory System in Small Mammals for Computational Biophysics Simulations." In The Eighth IASTED International Conference on Signal and Image Processing, SIP 2006, pp. 335-340. Acta Press, Anaheim, CA.
Zhu L, and I Gorton. 2007. "UML Profiles for Design Decisions and Non-Functional Requirements. " In 2nd International Workshop on Sharing and Reusing architectural Knowledge - Architecture, Rationale, and Design Intent (SHARK/ADI'07: ICSE Workshops 2007).
Zhu L, J Liu, NB Bui, I Gorton, 2007. "Revel8or: Model Driven Capacity Planning Tool Suite" in Proceedings of the 29th International Conference on Software Engineering (ICSE 2007), Minneapolis, Minnesota.
Zhu L, M Staples, and I Gorton, "An Infrastructure for Indexing and Organizing Best Practices," in Realizing Evidence-Based Software Engineering (REBSE2) workshop at ICSE 07, 2007.