Lawrence Berkeley National Lab

DST Recent Publications List


2016

  • Miller DC, Agarwal DA, Bhattacharyya D, Boverhof J, Cheah Y-W, Chen Y, Eslick JC, Leek J, Ma J, Mahapatra P, Ng B, Sahinidis N, Tong C, and Zitney SE. Innovative computational tools and models for the design, optimization and control of carbon capture processes. In 26th European Symposium on Computer Aided Process Engineering – ESCAPE 26, pages 2391–2396, June 2016.
  • Jonathan Ganz, Matt Bishop, and Sean Peisert. Security Analysis of Scantegrity, an Electronic Voting System. Technical report, UC Davis Technical Report, 2016.
  • Alberto Gonzalez, Jason Leigh, Sean Peisert, Brian Tierney, Andrew Lee, and Jennifer M. Schopf. NetSage: Open Privacy-Aware Network Measurement, Analysis, And Visualization Service. In Proceedings of TNC16 Networking Conference, Prague, Czech Republic, June 2016.
  • Mahdi Jamei, Emma Stewart, Sean Peisert, Anna Scaglione, Chuck McParland, Ciaran Roberts, and Alex McEachern. Micro Synchrophasor-Based Intrusion Detection in Automated Distribution Systems: Towards Critical Infrastructure Security. IEEE Internet Computing, 20(5), Sept./Oct. 2016.
  • Sean Peisert, William K. Barnett, Eli Dart, James Cuff, Robert L. Grossman, Edward Balas, Ari Berman, Anurag Shankar, and Brian Tierney. The Medical Science DMZ. Journal of the American Medical Informatics Association (JAMIA), May 2, 2016. (doi:10.1093/jamia/ocw032)

2015

2014

  • Alexy Agranovsky, David Camp, Christoph Garth, E. Wes Bethel, Kenneth I. Joy, and Hank Childs. Improved Post Hoc Flow Analysis Via Lagrangian Representations. In Proceedings of the IEEE Symposium on Large Data Visualization and Analysis (LDAV), pages 67–75, Paris, France, November 2014. LBNL-6731E, bf Best paper award.
  • David H. Bailey, Stephanie Ger, Marcos López de Prado, Alexander Sim, and Kesheng Wu. Statistical overfitting and backtest performance. http://ssrn.com/abstract=2507040, 2014. To appear in "Risk-Based and Factor Investing", Quantitative Finance Elsevier, 2015.
  • Javier Rojas Balderrama, Matthieu Simonin, Lavanya Ramakrishnan, Valerie Hendrix, Christine Morin, Deborah Agarwal, and Cédric Tedeschi. Combining workflow templates with a shared space-based execution model. In Proceedings of the 9th Workshop on Workflows in Support of Large-Scale Science, pages 50–58. IEEE Press, 2014.
  • DD Baldocchi, D Agarwal, D Papale, and MS Torn. Update on fluxnet and the role of flux networks in biogeosciences. AGU Fall Meeting Abstracts, 1:05, 2014.
  • Kenes Beketayev, Damir Yeliussizov, Dmitriy Morozov, Gunther H. Weber, and Bernd Hamann. Measuring the distance between merge trees. In Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, editors, Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, Mathematics and Visualization, pages 151–166. Springer-Verlag, 2014. LBNL-6629E.
  • Spyros Blanas, Kesheng Wu, Surendra Byna, Bin Dong, and Arie Shoshani. Parallel data analysis directly on scientific file formats. In SIGMOD'14, pages 385–396, 2014. (doi:10.1145/2588555.2612185)
  • Tiancheng Chang, Sisi Duan, Hein Meling, and Sean Peisert. P2S: A Fault-Tolerant Publish/Subscribe Infrastructure. In Proceedings of the 8th ACM International Conference on Distributed Event Based Systems (DEBS), pages 189–197, May 26–29, 2014.
  • Ryan Chard, Saba Sehrish, Alex Rodriguez, Ravi Madduri, Thomas D Uram, Marc Paterno, Katrin Heitmann, Shreyas Cholia, Jim Kowalkowski, and Salman Habib. Pdacs: a portal for data analysis services for cosmological simulations. In Proceedings of the 9th Gateway Computing Environments Workshop, pages 30–33. IEEE Press, 2014.
  • Hank Childs, Scott Biersdorff, David Poliakoff, David Camp, and Allen D. Malony. Particle Advection Performance Over Varied Architectures and Workloads. In 21th Annual International Conference on High Performance Computing, HiPC 2014, Goa, India, December 2014. LBNL-6730E.
  • Hsuan-Te Chiu, Jerry Chou, Venkat Vishwanath, Surendra Byna, and Kesheng Wu. Simplifying index file structure to improve I/O performance of parallel indexing. In The 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2014), 2014.
  • Shreyas Cholia and Terence Sun. The newt platform: an extensible plugin framework for creating restful hpc apis. In Proceedings of the 9th Gateway Computing Environments Workshop, pages 17–20. IEEE Press, 2014.
  • Robert Cowles, Craig Jackson, Von Welch, and Shreyas Cholia. A model for identity management in future scientific collaboratories. International Symposium on Grids and Clouds (ISGC), 2014.
  • Elif Dede, Zacharia Fadika, Madhusudhan Govindaraju, and Lavanya Ramakrishnan. Benchmarking MapReduce Implementations Under Different Application Scenarios. 2014.
  • Elif Dede, Zacharia Fadika, Madhusudhan Govindaraju, and Lavanya Ramakrishnan. MARIANE: Using MApReduce In HPC Environments. 2014.
  • Elif Dede, Bedri Sendir, Pinar Kuzlu, Madhusudhan Govindaraju, and Lavanya Ramakrishnan. A Processing Pipeline for Cassandra Datasets Based on Hadoop Streaming. In IEEE International Congress on Big Data, 2014.
  • Bin Dong, S. Byna, and Kesheng Wu. Parallel query evaluation as a scientific data service. In Cluster Computing (CLUSTER), 2014 IEEE International Conference on, pages 194–202, September 2014. (doi:10.1109/CLUSTER.2014.6968765)
  • Sisi Duan, Karl Levitt, Hein Meling, Sean Peisert, and Haibin Zhang. Byzantine Fault Tolerance from Intrusion Detection. In Proceedings of the 33rd IEEE International Symposium on Reliable Distributed Systems (SRDS), pages 253–264, Nara, Japan, Oct. 6–9, 2014.
  • Sisi Duan, Hein Meling, Sean Peisert, and Haibin Zhang. BChain: Byzantine Replication with High Throughput and Embedded Reconfiguration. In Proceedings of the 18th International Conference on Principles of Distributed Systems (OPODIS), Cortina, Italy, Dec. 15–19, 2014.
  • VL Freedman, D Agarwal, K Bensema, S Finsterle, CW Gable, EH Keating, H Krishnan, C Lansing, W Moeglein, GSH Pau, et al. Akuna: An open source user environment for managing subsurface simulation workflows. AGU Fall Meeting Abstracts, 1:04, 2014.
  • Richard Gerber, William Allcock, Chris Beggio, Stuart Campbell, Andrew Cherry, Shreyas Cholia, Eli Dart, Clay England, Tim Fahey, Fernanda Foertter, et al. Doe high performance computing operational review (hpcor): Enabling data-driven scientific discovery at hpc facilities. Technical report, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US), 2014.
  • Angela Harris, John Gamon, Gilberto Pastorello, and Christopher Wong. Retrieval of the photochemical reflectance index for assessing xanthophyll cycle activity: a comparison of near-surface optical sensors. Biogeosciences Discussions, 11(8):11903–11942, 2014. (doi:10.5194/bgd-11-11903-2014)
  • William Harvey, In-Hee Park, Oliver Ruebel, Valerio Pascucci, Peer-Timo Bremer, Chenglong Li, and Yusu Wang. A collaborative visual analytics suite for protein folding research. Journal of Molecular Graphics and Modelling, 53:59–71, 2014.
  • Tonglin Hawk, Ioan Raicu, and Lavanya Ramakrishnan. Scalable State Management for Scientific Applications in the Cloud. In IEEE International Congress on Big Data, 2014.
  • Mark Howison and E.Wes Bethel. GPU-Accelerated Denoising of 3D Magnetic Resonance Images. Journal of Real-Time Image Processing, pages 1–12, June 2014. LBNL-6707E. (doi:10.1007/s11554-014-0436-8)
  • SS Hubbard, D Agarwal, JF Banfield, HR Beller, E Brodie, P Long, PS Nico, CI Steefel, TK Tokunaga, and KH Williams. Genome-to-watershed predictive understanding of terrestrial environments. AGU Fall Meeting Abstracts, 1:0020, 2014.
  • Georgia Koutsandria, Vishak Muthukumar, Masood Parvania, Sean Peisert, Chuck McParland, and Anna Scaglione. A Hybrid Network IDS for Protective Digital Relays in the Power Transmission Grid. In Proceedings of the 5th IEEE International Conference on Smart Grid Communications (SmartGridComm), pages 908–913, Venice, Italy, Nov. 3–6, 2014.
  • Jialin Liu, S. Byna, Bin Dong, Kesheng Wu, and Yong Chen. Model-driven data layout selection for improving read performance. In Parallel Distributed Processing Symposium Workshops (IPDPSW), 2014 IEEE International, pages 1708–1716, May 2014. (doi:10.1109/IPDPSW.2014.190)
  • Qing Liu, Jeremy Logan, Yuan Tian, Hasan Abbasi, Norbert Podhorszki, Jong Youl Choi, Scott Klasky, Roselyne Tchoua, Jay Lofstead, Ron Oldfield, Manish Parashar, Nagiza Samatova, Karsten Schwan, Arie Shoshani, Matthew Wolf, Kesheng Wu, and Weikuan Yu. Hello ADIOS: the challenges and lessons of developing leadership class I/O frameworks. Concurrency and Computation: Practice and Experience, 26:1453–1473, 2014. (doi:10.1002/cpe.3125)
  • Philip E LONG, Susan S HUBBARD, Jillian F BANFIELD, Harry R BELLER, Eoin L BRODIE, Peter S NICO, Carl I STEEFEL, Tetsu K TOKUNAGA, Kenneth H WILLIAMS, and Deborah A AGARWAL. Predictive understanding of subsurface biogeochemical functioning: Using genomes to inform watershed-scale models. 2014 GSA Annual Meeting in Vancouver, British Columbia, 2014.
  • Chuck McParland, Sean Peisert, and Anna Scaglione. Monitoring Security of Networked Control Systems: It's the Physics. IEEE Security & Privacy, 12(6):32–39, 2014.
  • O Menzer, G Pastorello, S Metzger, C Poindexter, D Agarwal, and D Papale. Mapping ameriflux footprints: Towards knowing the flux source area across a network of towers. AGU Fall Meeting Abstracts, 1:0155, 2014.
  • David C. Miller, Madhava Syamlal, David Mebane, Curt Storlie, Debangsu Bhattacharyya, Nikolaos V. Sahinidis, Deb Agarwal, Charles Tong, Stephen E. Zitney, Avik Sarkar, Xin Sun, Sankaran Sundaresan, Emily Ryan, Dave Engel, and Crystal Dale. Carbon capture simulation initiative: A case study in multiscale modeling and new challenges. 5, 2014.
  • Masood Parvania, Georgia Koutsandria, Vishak Muthukumar, Sean Peisert, Chuck McParland, and Anna Scaglione. Hybrid Control Network Intrusion Detection Systems for Automated Power Distribution Systems. In Proceedings of the 1st International Workshop on Trustworthiness of Smart Grids (ToSG), Atlanta, GA, June 23, 2014.
  • G Pastorello, B Faybishenko, C Poindexter, O Menzer, D Agarwal, D Papale, and DD Baldocchi. Evaluation of growing season milestones, using eddy covariance time-series of net ecosystem exchange. AGU Fall Meeting Abstracts, 1:0207, 2014.
  • G Pastorello, C Poindexter, D Agarwal, D Papale, C van Ingen, and MS Torn. An overview of ameriflux data products and methods for data acquisition, processing, and publication. AGU Fall Meeting Abstracts, 1:0158, 2014.
  • G Pastorello, C Poindexter, C van Ingen, D Papale, and D Agarwal. The many facets of integrating data and metadata for research networks: experience from the ameriflux network. AGU Fall Meeting Abstracts, 1:05, 2014.
  • Gilberto Pastorello, Deb Agarwal, Taghrid Samak, Dario Papale, Carlo Trotta, Alessio Ribeca, Cristina Poindexter, Boris Faybishenko, Dan Gunter, Rachel Hollowgrass, and Eleonora Canfora. Observational data patterns for time series data quality assessment. In Proceedings of the 10th IEEE International Conference on e-Science, Guaruja, Brazil, October 2014.
  • Sean Peisert and Jonathan Margulies. Closing the gap on securing energy sector control systems [guest editors' introduction]. Security & Privacy, IEEE, 12(6):13–14, 2014.
  • Sean Peisert, Jonathan Margulies, Eric Byres, Paul Dorey, Dale Peterson, and Zach Tudor. Control systems security from the front lines. Security & Privacy, IEEE, 12(6):55–58, 2014.
  • Sean Peisert, Jonathan Margulies, David M Nicol, Himanshu Khurana, and Chris Sawall. Designed-in security for cyber-physical systems. Security & Privacy, IEEE, 12(5):9–12, 2014.
  • Lavanya Ramakrishnan, Sarah Poon, Val Hendrix, Dan Gunter, Gilberto Pastorello, and Deb Agarwal. Experiences with user-centered design for the tigres workflow api. In Proceedings of the 10th IEEE International Conference on e-Science, Guaruja, Brazil, October 2014.
  • Oliver Rubel, Cameron G.R. Geddes, Min Chen, Estelle Cormier-Michel, and E. Wes Bethel. Feature-Based Analysis of Plasma-Based Particle Acceleration Data. IEEE Transactions on Visualization and Computer Graphics, 20(2):196–210, February 2014. (doi:10.1109/TVCG.2013.107)
  • F. Rusu, P. Nugent, and K. Wu. Implementing the palomar transient factory real-time detection pipeline in GLADE: Results and observations. In Databases in Networked Information Systems, volume 8381 of Lecture Notes in Computer Science, pages 53–66, 2014. http://link.springer.com/chapter/10.1007/978-3-319-05693-7_4.
  • Jung Heon Song, Marcos López de Prado, Horst D. Simon, and Kesheng Wu. Exploring irregular time series through non-uniform fast fourier transform. In Proceedings of the 7th Workshop on High Performance Computational Finance, WHPCF '14, pages 37–44, Piscataway, NJ, USA, 2014. IEEE Press. (doi:10.1109/WHPCF.2014.8)
  • Jung Heon Song, Kesheng Wu, and Horst D Simon. Parameter Analysis of the VPIN (Volume synchronized Probability of Informed Trading) Metric. 2014.
  • D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.
  • Gunther H. Weber and Helwig Hauser. Interactive visual exploration and analysis. In Charles D. Hansen, Min Chen, Chris R. Johnson, Arie E. Kaufman, and Hans Hagen, editors, Scientific Visualization: Uncertainty, Multifield, Bio-Medical and Scalable Visualization, Mathematics and Visualization, pages 161–174. Springer-Verlag, 2014. LBNL-6655E.
  • Gunther H. Weber, Hans Johansen, Daniel T. Graves, and Terry J. Ligocki. Simulating urban environments for energy analysis. In Proceedings Visualization in Environmental Sciences (EnvirVis), 2014. LBNL-6652E.
  • L. Wu, K. Wu, A. Sim, M. Churchill, J. Y. Choi, A. Stathopoulos, CS Chang, and S. Klasky. High-performance outlier detection algorithm for finding blob-filaments in plasma. In 5th International Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC'14), 2014.

2013

  • Deb Agarwal, Sam Pullman, Jessica Voytek, Gilberto Z. Pastorello, Dario Papale, Sebastien Biraud, Wai yin S. Chan, Susan S. Hubbard, and Margaret S. Torn. Enabling mobile data and metadata collection and submission in support of ameriflux and ngee data collection and access. San Francisco, CA, December 2013. Suppl., AbstractIN33B-1536.
  • E Wes Bethel, Prabhat Prabhat, Suren Byna, Oliver Rübel, K John Wu, and Michael Wehner. Why high performance visual data analytics is both relevant and difficult. In IS&T/SPIE Electronic Imaging, pages 86540B–86540B–10. International Society for Optics and Photonics, 2013. (doi:10.1117/12.2010980)
  • You-Wei Cheah, Richard Canon, Beth Plale, and Lavanya Ramakrishnan. Milieu: Provenance Collection and Query Framework for High Performance Computing Systems. In IEEE Big Data Congress [Acceptance rate:30%], 2013.
  • Jong Y. Choi, Kesheng Wu, Jacky C. Wu, Alex Sim, Qing G. Liu, Matthew Wolf, CS Chang, and Scott Klasky. ICEE: Wide-area in transit data processing framework for near real-time scientific applications. In PDAC workshop, SC13, 2013. http://sc13.supercomputing.org/sites/default/files/WorkshopsArchive/pdfs/wp148s1.pdf.
  • Elif Dede, Madhusudhan Govindaraju, Daniel Gunter, Richard Canon, and Lavanya Ramakrishnan. Semi-Structured Data Analysis using MongoDB and MapReduce: A Performance Evaluation. In Proceedings of the 4th international workshop on Scientific cloud computing, 2013.
  • Massimo Di Pierro, James Hetrick, Shreyas Cholia, James Simone, and Carleton DeTar. The new “gauge connection” at nersc. 2013.
  • B. Dong, S. Byna, and K. Wu. SDS: a framework for scientific data services. In Proceedings of the 8th Parallel Data Storage Workshop, 2013. http://www.pdsw.org/pdsw13/papers/p27-pdsw13-dong.pdf.
  • Bin Dong, S. Byna, and Kesheng Wu. Expediting scientific data analysis with reorganization of data. In Cluster Computing (CLUSTER), 2013 IEEE International Conference on, pages 1–8, September 2013. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6702675. (doi:10.1109/CLUSTER.2013.6702675)
  • Boris Faybishenko, Deb Agarwal, Dennis Baldocchi, Catharine van Ingen, Sebastien Biraud, Gilberto Pastorello, and Dario Papale. Intercomparison of the ameriflux in situ measurements across multiple biomes as an alternative to climatic classification. In American Geophysical Union, Fall Meeting 2013, San Francisco, CA, December 2013. Abstract B21C-04.
  • Eugen Feller, Lavanya Ramakrishnan, and Christine Morin. On the Performance and Energy Efficiency of Hadoop Deployment Models. In The IEEE International Conference on Big Data 2013 (IEEE BigData 2013), Oct 2013.
  • John Gamon, Fred Huemmrich, Craig Emmerton, Elyn Humphreys, Peter Lafleur, Gilberto Pastorello, Adrian Rocha, Gus Shaver, Vincent St.Louis, Mario Tenuta, Donnette Thayer, and Scott Williamson. Observing dynamic arctic surface optical properties with an optical sensor network. In American Geophysical Union, Fall Meeting 2013, San Francisco, CA, December 2013. Abstract B41G-03.
  • W. Gu, J. Choi, M. Gu, H. D. Simon, and K. Wu. Fast change point detection for electricity market analysis. In 2013 IEEE International Conference on Big Data, pages 50–57, 2013. (doi:10.1109/BigData.2013.6691733)
  • Dan Gunter, Lavanya Ramakrishnan, Sarah Poon, Gilberto Pastorello, Val Hendrix, and Deb Agarwal. Experiences with user-centered design for the tigres workflow api (poster). In Proceedings of the 9th IEEE International Conference on e-Science, Beijing, China, October 2013.
  • Valerie Hendrix, Lavanya Ramakrishnan, Youngryel Ryu, Catharine van Ingen, Keith R. Jackson, and Deborah Agarwal. CAMP: Community access MODIS pipeline. Future Generation Computer Systems, 2013.
  • Anubhav Jain, Shyue Ping Ong, Geoffroy Hautier, Wei Chen, William Davidson Richards, Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, et al. Commentary: The materials project: A materials genome approach to accelerating materials innovation. APL Materials, 1(1):011002, 2013.
  • Kuan-Wu Lin, Surendra Byna, Jerry Chou, and Kesheng Wu. Optimizing FastQuery performance on Lustre file system. In Proceedings of the 25th International Conference on Scientific and Statistical Database Management, page 29. ACM, 2013.
  • E. Masanet, A. Shehabi, L. Ramakrishnan, J. Liang, X. Ma, B. Walker, V. Hendrix, and P Mantha. The energy efficiency potential of cloud-based software: A u.s.case study. Technical Report 6298E, Lawrence Berkeley National Lab, Berkeley, June 2013.
  • Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier, Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent L Chevrier, Kristin A Persson, and Gerbrand Ceder. Python materials genomics (pymatgen): A robust, open-source python library for materials analysis. Computational Materials Science, 68:314–319, 2013.
  • Gilberto Pastorello, John Gamon, and Deb Agarwal. Comparison of broadband optical sensor responses for proxy ndvi measurements. In American Geophysical Union, Fall Meeting 2013, San Francisco, CA, December 2013. Abstract B51M-07.
  • Sean Peisert and Matt Bishop. Dynamic, Flexible, and Optimistic Access Control. Technical Report CSE-2013-76, University of California at Davis, March 2013.
  • Sean Peisert, Ed Talbot, and Tom Kroeger. Principles of Authentication. In Proceedings of the 2013 New Security Paradigms Workshop (NSPW) (to appear), Banff, Canada, Sept. 9-12 2013.
  • Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Susan Coghlan, Shane Canon, Anping Liu, Devarshi Ghoshal, Krishna Muriki, and Nicholas J. Wright. On the Road to Exascale Computing: Contemporary Architectures in High Performance Computing, chapter Magellan - A Testbed to Explore Cloud Computing for Science. Chapman & Hall/CRC Press, 2013.
  • Alex Romosan, Arie Shoshani, Kesheng Wu, Victor Markowitz, and Kostas Mavrommatis. Accelerating gene context analysis using bitmaps. In Proceedings of the 25th International Conference on Scientific and Statistical Database Management, page 26. ACM, 2013. (doi:10.1145/2484838.2484856)
  • Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E Wes Bethel, Trent R Northen, and Benjamin P Bowen. Openmsi: a high-performance web-based platform for mass spectrometry imaging. Analytical chemistry, 85(21):10354–10361, 2013.
  • Sean Whalen, Sean Peisert, and Matt Bishop. Multiclass Classification of Distributed Memory Parallel Computations. Pattern Recognition Letters (PRL), 34(3):322–329, February 2013.
  • Kesheng Wu, Wes Bethel, Ming Gu, David Leinweber, and Oliver Rübel. A big data approach to analyzing market volatility. Algorithmic Finance, 2(3):241–267, 2013. (doi:10.3233/AF-13030)
  • Kesheng Wu, Wes Bethel, Ming Gu, David Leinweber, and Oliver Rübel. Testing VPIN on big data. Available at SSRN 2318259, 2013. http://ssrn.com/abstract=2318259.

2012

  • Deb Agarwal, Arthur Wiedmer, Boris Faybishenko, Tad Whiteside, James Hunt, Gary Kushner, Alex Romosan, and Shoshani Arie. A methodology for management of heterogeneous site characterization and modeling data. In Proceedings XIX International Conference on Water Resources (CMWR), Urbana-Champaign, IL, June 2012.
  • E. W. Bethel, Surendra Byna, Jerry Chou, Estelle Cormier-Michel, Cameron G. R. Geddes, Mark Howison, Fuyu Li, Prabhat, Ji Qiang, Oliver Rübel, Rob D. Ryne, Michael Wehner, and Kesheng Wu. Big data analysis and visualization: What do LINACS and tropical storms have in common? In 11th International Computational Accelerator Physics Conference, ICAP 2012, Germany, August 2012. LBNL-5766E.
  • E. Wes Bethel, David Leinweber, Oliver Rübel, and Kesheng Wu. Federal market information technology in the post-flash crash era: Roles for supercomputing. The Journal of Trading, 7(2):9–25, 2012. (doi:10.3905/jot.2012.7.2.009)
  • EW Bethel, S. Byna, J. Chou, E. Cormier-Michel, CGR Geddes, M. Howison, F. Li, J. Q. Prabhat, O. Rübel, RD Ryne, et al. Big data analaysis and visualization: What do LINACS and tropical storms have in common? In 11th International Computational Accelerator Physics Conference, ICAP 2012, 2012.
  • Surendra Byna, Jerry Chou, Oliver Rübel, Prabhat, Homa Karimabadi, William S. Daughton, Vadim Roytershteyn, E. Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Andrew Uselton, and Kesheng Wu. Parallel I/O, Analysis, and Visualization of a Trillion Particle Simulation. In Proceedings of SuperComputing 2012, November 2012.
  • Lizzie Coles-Kemp, Carrie Gates, Dieter Gollmann, Sean Peisert, Christian W Probst, Lizzie Coles-Kemp, Carrie Gates, Dieter Gollmann, Sean Peisert, and Christian Probst. Organizational processes for supporting sustainable security (dagstuhl seminar 12501). Dagstuhl Reports, 2(12):37–48, 2012.
  • Elif Dede, Zacharia Fadika, Jessica Hartog, Modhusudhan Govindaraju, Lavanya Ramakrishnan, Daniel Gunter, and Richard Shane Canon. Marissa: Mapreduce implementation for streaming science applications. In eScience, 2012.
  • Adel El-Atawy and Taghrid Samak. End-to-end verification of qos policies. In 2012 IEEE Network Operations and Management Symposium, Maui, HI, USA, April 16-20, 2012, pages 426–434, 2012.
  • Zacharia Fadika, Madhusudhan Govindaraju, Shane Canon, and Lavanya Ramakrishnan. Evaluating hadoop for data-intensive scientific operations. IEEE Cloud Computing, 2012.
  • Devarshi Ghoshal and Lavanya Ramakrishnan. Frieda: Flexible robust intelligent elastic data management in cloud environments. In The Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012) Best Paper Award, 2012.
  • Daniel Gunter, Shreyas Cholia, Anubhav Jain, Michael Kocher, Kristin Persson, Lavanya Ramakrishnan, Shyue Ping Ong, and Gerbrand Ceder. Community accessible datastore of high-throughput calculations: Experiences from the materials project. In 5th workshop on Many-Task Computing on Grids and Supercomputers (MTAGS), 2012.
  • Val Hendrix, Doug Benjamin, and Yushu Yao. Scientific Cluster Deployment and Recovery - Using puppet to simplify cluster management. Journal of Physics: Conference Series, 396, December 2012. (doi:10.1088/1742-6596/396/4/042027)
  • Anubhav Jain, Geoffroy Hautier, Shyue Ping Ong, Charles Moore, Byoungwoo Kang, Hailong Chen, Xiaohua Ma, Jae Chul Kim, Michael Kocher, Dan Gunter, et al. Materials project: A public materials database and its application to lithium ion battery cathode design. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 243. AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, 2012.
  • Ezra Kissel, Ahemd El-Hassany, Guilherme Fernandes, Martin Swany, Dan Gunter, Taghrid Samak, and Jennifer Schopf. Scalable integrated performance analysis of multi-gigabit networks. In 5th Workshop on Distributed Autonomous Network Management System (DANMS), co-located with NOMS 2012, 2012.
  • Ezra Kissel, Ahmed El-Hassany, Guilherme Fernandes, Martin Swany, Dan Gunter, Taghrid Samak, and Jennifer M. Schopf. Scalable Integrated Performance Analysis of Multi-Gigabit Networks. In Fifth International Workshop on Distributed Autonomous Network Management Systems 2012 (DANMS'12). IEEE/IFIP Network Operations and Management Symposium, April 2012.
  • Xiao Li, Zhifang Wang, Vishak Muthukumar, Anna Scaglione, Chuck McParland, and Sean Peisert. Networked Loads in the Distribution Grid. In Proceedings of the 2012 APSIPA Annual Summit and Conference, Hollywood, CA, Dec. 3–6 2012.
  • G. F. Lofstead, Q. Liu, J. Logan, Y. Tian, H. Abbasi, N. Podhorszki, J. Y. Choi, S. Klasky, R. Tchoua, R. A. Oldfield, et al. Hello ADIOS: The challenges and lessons of developing leadership class I/O frameworks. Technical report, Sandia National Laboratories, 2012.
  • Benson Ma, Arie Shoshani, Alex Sim, Kesheng Wu, Yong-Ik Byun, Jaegyoon Hahm, and Min-Su Shin. Efficient attribute-based data access in astronomy analysis. In The 2nd International Workshop on Network-Aware Data Management Workshop (NDM2012), pages 562–571. IEEE, 2012. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6495862.
  • Fernando Harald Barreiro Megino, Doug Benjamin, Kaushik De, Ian Gable, Val Hendrix, Sergey Panitkin, Michael Paterson, Asoka De Silva, Daniel van der Ster, Ryan Taylor, Roberto A. Vitillo, and Rod Walker. Exploiting Virtualization and Cloud Computing in ATLAS. Journal of Physics: Conference Series, 396, December 2012. (doi:10.1088/1742-6596/396/3/032011)
  • Dario Papale, Deborah Agarwal, Dennis Baldocchi, Robert Cook, Joshua B. Fisher, and Catharine van_Ingen. Database maintenance, data sharing policy, collaboration. In Marc Aubinet, Timo Vesala, and Dario Papale, editors, Eddy Covariance, pages 399–424. Springer, 2012. (doi:10.1007/978-94-007-2351-1_16)
  • Sean Peisert, Ed Talbot, and Matt Bishop. Turtles All The Way Down: A Clean-Slate, Ground-Up, First-Principles Approach to Secure Systems. In Proceedings of the 2012 New Security Paradigms Workshop (NSPW), pages 15–26, Bertinoro, Italy, September 19–21, 2012.
  • E. Pourabbas, A. Shoshani, and K. Wu. Minimizing index size by reordering rows and columns. In SSDBM, pages 467–484. Springer Berlin/Heidelberg, 2012.
  • Prabhat, Oilver Rübel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, and E. W. Bethel. TECA: A parallel toolkit for extreme climate analysis. In Third Workshop on Data Mining in Earth System Science (DMESS 2012) at the International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, June 2012. (doi:10.1016/j.procs.2012.04.093)
  • Lavanya Ramakrishnan, Richard Shane Canon, Krishna Muriki, Iwona Sakrejda, and Nicholas J. Wright. Evaluating interconnect and virtualization performance for high performance computing. In Special Issue of ACM Performance Evaluation Review, volume 40(2), 2012.
  • O. Rübel, S. Byna, K. Wu, F. Li, M. Wehner, W. Bethel, et al. TECA: A parallel toolkit for extreme climate analysis. Procedia Computer Science, 9:866–876, 2012. (doi:10.1016/j.procs.2012.04.093)
  • Taghrid Samak, Dan Gunter, Monte Goode, Ewa Deelman, Gideon Juve, Fabio Silva, and Karan Vahi. Failure analysis of distributed scientific workflows executing in the cloud. In 8th International Conference on Network and Service Management, CNSM 2012, Las Vegas, USA, October 22-26, 2012, 2012.
  • Taghrid Samak, Dan Gunter, and Valerie Hendrix. Scalable analysis of network measurements with hadoop and pig. In 5th Workshop on Distributed Autonomous Network Management System (DANMS), co-located with NOMS 2012, 2012.
  • Taghrid Samak, Dan Gunter, and Zhong Wang. Prediction of Protein Solubility in E. Coli. In eScience, 2012.
  • Allen R. Sanderson, Brad Whitlock, Oliver Rübel, Hank Childs, Gunther H. Weber, Prabhat, and Kesheng Wu. A system for query based analysis and visualization. In Third International Eurovis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, June 2012. LBNL-5507E.
  • Karen Schuchardt, Deb Agarwal, Stefan Finsterle, Carl Gable, Ian Gorto, Luke Gosink, and etal. Akuna - integrated toolsets supporting advanced subsurface flow and transport simulations for environmental management. In to appear in XIX International Conference on Water Resources (CMWR), Urbana-Champaign, IL, June 2012.
  • Karan Vahi, Ian Harvey, Taghrid Samak, Dan Gunter, Kieran Evans, David Rogers, Ian Taylor, Monte Goode, Fabio Silva, Eddie Al-Shakarchi, Gaurang Mehta, Andrew Jones, and Ewa Deelman. A General Approach to Real-time Workflow Monitoring. In The Seventh Workshop on Workflows in Support of Large-Scale Science (WORKS12), in conjunction with SC 2012, Salt Lake City, November 10-16 2012, Salt Lake City, USA, November 2012.
  • Sean Whalen, Sophie Engle, Sean Peisert, and Matt Bishop. Network-Theoretic Classification of Parallel Computation Patterns. International Journal of High Performance Computing Applications (IJHPCA), 26(2):159–169, May 2012.
  • Ichitaro Yamazaki and Kesheng Wu. A communication-avoiding thick-restart lanczos method on a distributed-memory system. In Euro-Par 2011: Parallel Processing Workshops, volume 7155 of Lecture Notes in Computer Science, pages 345–354, 2012. http://www.springerlink.com/content/22u4q771v53062t7/. (doi:10.1007/978-3-642-29737-3_39)

2011

  • Deb Agarwal, You-Wei Cheah, Dan Fay, Jonathan Fay, Dean Guo, Tony Hey, Marty Humphrey, Keith Jackson, Jie Li, Christophe Poulain, Youngryel Ryu, and Catharine van_Ingen. Data-intensive science: The terapixel and modisazure projects. International Journal of High Performance Computing Applications, 25(3):304–316, 2011. (doi:10.1177/1094342011414746)
  • E. W. Bethel, D. Leinweber, O. Rübel, and K. Wu. Federal market information technology in the post flash crash era: Roles for supercomputing. In WHPCF, pages 23–30, New York, NY, USA, 2011. ACM. (doi:10.1145/2088256.2088267)
  • Suren Byna, Prabhat, Michael F. Wehner, and Kesheng Wu. Detecting atmospheric rivers in large climate datasets. In PDAC-11, 2011. (doi:10.1145/2110205.2110208)
  • J. Chou, K. Wu, O. Rübel, M. Howison, J. Qiang, Prabhat, B. Austin, E. W. Bethel, R. D. Ryne, and A. Shoshani. Parallel index and query for large scale data analysis. In SC11, 2011. (doi:10.1145/2063384.2063424)
  • Jerry Chou, Kesheng Wu, and Prabhat. FastQuery: A general indexing and querying system for scientific data. In SSDBM, pages 573–574, 2011. (doi:10.1007/978-3-642-22351-8_42)
  • Jerry Chou, Kesheng Wu, and Prabhat. FastQuery: A parallel indexing system for scientific data. In IASDS. IEEE, 2011. (doi:10.1109/CLUSTER.2011.86)
  • Miller DC, Syamlal M, Meza JC, Brown DL, Fox MM, Khaleel M, Cottrell RK, Kress JD, Sun X, Sundaresan S, Sahinidis N, Zitney SE, Agarwal DA, Tong C, Lin G, Letellier BC, Engel D, Calafiura P, Richards GA, and Shinn JH. Overview of the us does carbon capture simulation initiative for accelerating the commercialization of ccs technology. In 36th International Technical Conference on Clean Coal & Fuel Systems, Clearwater, Florida, June 2011.
  • Miller DC, Syamlal M, Meza JC, Brown DL, Fox MM, Khaleel M, Cottrell RK, Kress JD, Sun X, Sundaresan S, Sahinidis N, Zitney SE, Agarwal DA, Tong C, Lin G, Letellier BC, Engel D, Calafiura P, Richards GA, and Shinn JH. The us department of energys carbon capture simulation initiative. In 10th Annual Conference on Carbon Capture & Sequestration, May 2011.
  • Elif Dede, Lavanya Ramakrishnan, Dan Gunter, and Madhusudhan Govindaraju. Riding the Elephant: Managing Ensembles with Hadoop. In The 4th Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS). IEEE, November 2011.
  • Massimo Di Pierro, James Hetrick, Shreyas Cholia, and David Skinner. Making qcd lattice data accessible and organized through advanced web interfaces. arXiv preprint arXiv:1112.2193, 2011.
  • Zacharia Fadika, Elif Dede, Madhusudhan Govindaraju, and Lavanya Ramakrishnan. Benchmarking mapreduce implementations for application usage scenarios. Grid 2011: 12th IEEE/ACM International Conference on Grid Computing, 0:1–8, 2011. (doi:http://grid2011.mnm-team.org/?page_id=138)
  • Zacharia Fadika, Elif Dede, Madhusudhan Govindaraju, and Lavanya Ramakrishnan. Mariane: Mapreduce implementation adapted for hpc environments. Grid 2011: 12th IEEE/ACM International Conference on Grid Computing, 0:1–8, 2011. (doi:http://grid2011.mnm-team.org/?page_id=138)
  • Devarshi Ghoshal, Richard Shane Canon, and Lavanya Ramakrishnan. I/o performance of virtualized cloud environments. In The Second International Workshop on Data Intensive Computing in the Clouds (DataCloud-SC11), 2011.
  • Dan Gunter, Ewa Deelman, Taghrid Samak, Christopher X. Brooks, Monte Goode, Gideon Juve, Gaurang Mehta, Priscilla Moraes, Fabio Silva, D. Martin Swany, and Karan Vahi. Online workflow management and performance analysis with stampede. In 7th International Conference on Network and Service Management, CNSM 2011, Paris, France, October 24-28, 2011, pages 1–10, 2011.
  • Dan Gunter, Taghrid Samak, Ewa Deelman, Christopher H. Brooks, Monte Goode, Gideon Juve, Gaurang Mehta, Priscilla Moraes, Fabio Silva, Martin Swany, and Karan Vahi. Online Workflow Management and Performance Analysis with STAMPEDE. 7th International Conference on Network and Service Management (CNSM 2011), 2011.
  • Keith R. Jackson, Krishna Muriki, Lavanya Ramakrishnan, Karl J. Runge, and Rollin C. Thomas. Performance and cost analysis of the supernova factory on the amazon aws cloud. Sci. Program., 19:107–119, April 2011.
  • Jinoh Kim, Hasan Abbasi, Luis Chacón, Ciprian Docan, Scott Klasky, Qing Liu, Norbert Podhorszki, Arie Shoshani, and Kesheng Wu. Parallel in situ indexing for data-intensive computing. In LDAV, pages 65–72. IEEE, 2011. (doi:10.1109/LDAV.2011.6092319)
  • Ezra Kissel, Dan Gunter, Taghrid Samak, Ahmed El-Hassany, Guilherme Fernandes, and Martin Swany. An Instrumentation and Measurement Framework for End-to-End Performance Analysis. Technical Report 2011/04, University of Delaware, 2011.
  • Kamesh Madduri and Kesheng Wu. Massive-scale RDF processing using compressed bitmap indexes. In SSDBM, pages 470–479. Springer, 2011. (doi:10.1007/978-3-642-22351-8_30)
  • David C. Miller, Deborah A. Agarwal, Xin Sun, and Charles Tong. iCCSI and the role of advanced computing in accelerating the commercial deployment of carbon capture systems. In Proceedings of the SciDAC 2011 Conference, Denver, CO, July 2011.
  • Massimiliano Pala, Shreyas Cholia, Scott A Rea, and Sean W Smith. Federated pki authentication in computing grids: Past, present, and future. Cloud, Grid and High Performance Computing: Emerging Applications, pages 165–179, 2011.
  • Prabhat, S. Byna, C. Paciorek, G. Weber, K. Wu, T. Yopes, M. Wehner, W. Collins, G. Ostrouchov, R. Strelitz, and E. W. Bethel. Pattern detection and extreme value analysis on large climate data. DOE/BER Climate and Earth System Modeling PI Meeting, September 2011.
  • Prabhat, S. Byna, C. Paciorek, G. Weber, K. Wu, T. Yopes, M. F. Wehner, G. Ostrouchov, D. Pugmire, R. Strelitz, W. Collins, and E. W. Bethel. Pattern detection and extreme value analysis on large climate data. AGU Fall Meeting Abstracts, December 2011. http://adsabs.harvard.edu/abs/2011AGUFMIN41C..03P.
  • Prabhat, Quincey Koziol, Karen Schuchardt, E. Wes Bethel, Jerry Chuo, Mark Howison, Mike McGreevy, Bruce Palmer, Oliver Ruebel, and Kesheng Wu. ExaHDF5: An I/O platform for exascale data models, analysis and performance. In SciDAC 2011, 2011. http://www.mcs.anl.gov/uploads/cels/papers/scidac11/final/Prabhat.pdf.
  • L. Ramakrishnan, P. T. Zbiegel, S. Campbell, R. Bradshaw, R.S. Canon, S. Coghlan, I. Sakrejda, N. Desai, T. Declerck, and A. Liu. Magellan: Experiences from a science cloud. In proceedings of the 2nd international workshop on Scientific cloud computing,ScienceCloud'11, pages 49–58, San Jose, CA, June 2011. ACM.
  • Lavanya Ramakrishnan, Richard Shane Canon, Krishna Muriki, Iwona Sakrejda, and Nicholas J. Wright. Evaluating interconnect and virtualization performance for high performance computing. In Proceedings of 2nd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems (PMBS11), 2011.
  • Lavanya Ramakrishnan, Jeffrey Chase, Dennis Gannon, Daniel Nurmi, and Rich Wolski. Deadline-sensitive workflow orchestration without explicit rescource control. J. Parallel Distributed Computing, 71(3):343–353, March 2011. (doi:10.1016/j.jpdc.2010.11.010)
  • R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, C. G. R. Geddes, W. Leemans, X. Li, Prabhat, J. Qiang, O. Rübel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon, and N. Yampolsky. High performance computing in accelerator science: Past successes, future challenges. ASCR/BES Workshop on Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery, October 2011.
  • Taghrid Samak, Dan Gunter, Ewa Deelman, Gideon Juve, Gaurang Mehta, Fabio Silva, and Karan Vahi. Online Fault and Anomaly Detection for Large-Scale Scientific Workflows. In 13th IEEE International Conference on High Performance Computing and Communications (HPCC-2011), Banff, Alberta, Canada, September 2011. IEEE, IEEE Computer Society.
  • Taghrid Samak, Dan Gunter, Monte Goode, Ewa Deelman, Gaurang Mehta, Fabio Silva, and Karan Vahi. Failure Prediction and Localization in Large Scientific Workflows. In The Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS11), Seattle, WA, USA, November 2011.
  • Taghrid Samak, Daniel Gunter, Monte Goode, Ewa Deelman, Gideon Juve, and Fabio Silva. Using Machine Learning Techniques for Online Failure Prediction in Large Scientific Workflows. 2011.
  • Sean Whalen, Sean Peisert, and Matt Bishop. Network-Theoretic Classification of Parallel Computation Patterns. In Proceedings of the First International Workshop on Characterizing Applications for Heterogeneous Exascale Systems (CACHES), Tucson, AZ, June 4, 2011.
  • Kesheng Wu, Surendra Byna, Doron Rotem, and Arie Shoshani. Scientific data services – A high-performance I/O system with array semantics. In HPCDB. IEEE, 2011. Preprint as LBNL-5309E. (doi:10.11v45/2125636.2125640)
  • Kesheng Wu, Rishi R Sinha, Chad Jones, Stephane Ethier, Scott Klasky, Kwan-Liu Ma, Arie Shoshani, and Marianne Winslett. Finding regions of interest on toroidal meshes. Computational Science & Discovery, 4(1):015003, 2011. (doi:10.1088/1749-4699/4/1/015003)
  • Weikuan Yu, Kesheng Wu, Wei-Shinn Ku, Cong Xu, and Juan Gao. BMF: Bitmapped mass fingerprinting for fast protein identification. In CLUSTER, 2011. (doi:10.1109/CLUSTER.2011.11)