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Publications

2017

Stone, D. A., H. Krishnan, R. Lance, S. Sippel, and M. F. Wehner, "The First and Second Hackathons of the International CLIVAR C20C+ Detection and Attribution Project", CLIVAR Exchanges, 2017,

Timmermans, B., D. Stone, M. Wehner, and H. Krishnan, "Impact of tropical cyclones on modeled wind-wave climate", Geophysical Research Letters, 2017, 44:1393-1401, doi: 10.1002/2016GL071681

E. Wes Bethel, In Situ Processing Overview and Relevance to the HPC Community, SIAM Conference on Computational Science and Engineering, MS74: In Situ Methods and Infrastructures: Faster Insight Through Smarter Computing, 2017,

Angélil, O., D. Stone, M. Wehner, C. J. Paciorek, H. Krishnan, W. Collins, "An independent assessment of anthropogenic attribution statements for recent extreme temperature and rainfall events", Journal of Climate, 2017, 30:5-16, doi: 10.1175/JCLI-D-16-0077.1

2016

M. Wehner, D. Stone, H. Krishnan, K. AchutaRao, F. Castillo, "The deadly combination of heat and humidity in India and Pakistan in summer 201", Bulletin of the American Meteorological Society, 2016, 97:S81-S86, doi: 10.1175/BAMS-D-16-0145.2

Utkarsh Ayachit, Andrew Bauer, Earl P. N. Duque, Greg Eisenhauer, Nicola Ferrier, Junmin Gu, Kenneth E. Jansen, Burlen Loring, Zarija Lukić, Suresh Menon, Dmitriy Morozov, Patrick O'Leary, Reetesh Ranjan, Michel Rasquin, Christopher P. Stone, Venkat Vishwanath, Gunther H. Weber, Brad Whitlock, Matthew Wolf, K. John Wu, E. Wes Bethel, "Performance analysis, design considerations, and applications of extreme-scale in situ infrastructures", Supercomputing, 2016, 79,

Utkarsh Ayachit, Andrew Bauer, Earl P. N. Duque, Greg Eisenhauer, Nicola Ferrier, Junmin Gu, Kenneth Jansen, Burlen Loring, Zarija Luki\ c, Suresh Menon, Dmitriy Morozov, Patrick O Leary, Michel Rasquin, Christopher P. Stone, Venkat Vishwanath, Gunther H. Weber, Brad Whitlock, Matthew Wolf, K. John Wu, E. Wes Bethel, "Performance Analysis, Design Considerations, and Applications of Extreme-scale In Situ Infrastructures", ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis (SC16), Salt Lake City, UT, USA, 2016, doi: 10.1109/SC.2016.78

Andrew C. Bauer, Kenneth E. Jansen, E. Wes Bethel, Utkarsh Ayachit, Michel Rasquin, Benjamin Matthews, Steve Jordan, "In Situ Analysis and Visualization at Scale with PHASTA and ParaView Catalyst on Mira and Theta", SC16 Scientific Visualization Showcase, 2016,

Utkarsh Ayachit, Brad Whitlock, Matthew Wolf, Burlen Loring, Berk Geveci, David Lonie, E. Wes Bethel, "The SENSEI Generic In Situ Interface", Proceedings of In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization (ISAV 2016), Salt Lake City, UT, USA, 2016,

E. Wes Bethel, Martin Greenwald, Kerstin Kleese van Dam, Manish Parashar, Stefan M. Wild, H. Steven Wiley, "Management, Analysis, and Visualization of Experimental and Observational Data -- The Convergence of Data and Computing", Proceedings of the 2016 IEEE 12th International Conference on eScience, Baltimore, MD, USA, 2016,

Hoa Nguyen, D\ aith\ i Stone, E. Wes Bethel, "Statistical Projections for Multi-dimensional Visual Data Exploration", 6th IEEE Symposium on Large Data Analysis and Visualization, 2016,

moderator E. Wes Bethel (organizer, Hank Childs, Ken Moreland, Dave Pugmire, Matt Larsen, Matthieu Dorier, In Situ Efforts and Challenges in Large Data Analysis and Visualization, IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2016,

Talita Perciano, Daniela Ushizima, E. Wes Bethel, Yariv Mizrahi, James Sethian, "Reduced-complexity Image Segmentation Under Parallel Markov Random Field Formulation Using Graph Partitioning", IEEE International Conference on Image Processing (ICIP), Phoenix, AZ, USA, 2016,

Sugeerth Murugesan, Kristofer Bouchard, Jesse A. Brown, Bernd Hamann, William W. Seeley, Andrew Trujillo, Gunther H. Weber, "Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity", IEEE Transactions on Computational Biology and Bioinformatics, 2016, LBNL 1005732, doi: 10.1109/TCBB.2016.2564970

Patrick Oesterling, Christian Heine, Gunther H. Weber, Dmitriy Morozov, Gerik Scheuermann, Computing and Visualizing Time-Varying Merge Trees for High-Dimensional Data, Mathematics and Visualization, 2016,

Md. Mostofa Ali Patwary, Nadathur Rajagopalan Satish, Narayanan Sundaram, Jialin Liu, Peter Sadowski, Evan Racah, Suren Byna, Craig Tull, Wahid Bhimji, Prabhat, and Pradeep Dubey,, "PANDA: Extreme Scale Parallel K-Nearest Neighbor on Distributed Architectures", 30th IEEE International Parallel & Distributed Processing Symposium (IPDPS) 2016, Chicago, May 23, 2016,

Wahid Bhimji, Debbie Bard, Melissa Romanus, David Paul, Andrey Ovsyannikov, Brian Friesen, Matt Bryson, Joaquin Correa, Glenn K. Lockwood, Vakho Tsulaia, Suren Byna, Steve Farrell, Doga Gursoy, Chris Daley, Vince Beckner, Brian Van Straalen, Nicholas Wright, Katie Antypas, Prabhat,, "Accelerating Science with the NERSC Burst Buffer Early User Program", Cray User Group (CUG) 2016, May 10, 2016,

2015

Stone, D., H. Shiogama, P. Wolski, O. Angélil, S. Cholias, N. Christidis, A. Dittus, C. Folland, A. King, J. Kinter, H. Krishnan, S.-K. Min, M. Wehner, "The C20C+ Detection and Attribution Project", Fall Meeting of the American Geophysical Union, 2015,

Soyoung Jeon, Prabhat, Suren Byna, Junmin Gu, William Collins, and Michael Wehner,, "Characterization of extreme precipitation within atmospheric river events over California", Advances in Statistical Climatology, Meteorology and Oceanography (ASCMO), November 21, 2015, 1:45-57, doi: 10.5194/ascmo-1-45-2015

Md. Mostofa Ali Patwary, Suren Byna, Nadathur Rajagopalan Satish, Narayanan Sundaram, Zarija Lukic, Vadim Roytershteyn, Michael J. Anderson, Yushu Yao, Mr Prabhat, and Pradeep Dubey, "BD-CATS: Big Data Clustering at Trillion Particle Scale", Supercomputing 2015 (SC15), Supercomputing 2015 (SC15), November 17, 2015,

Babak Behzad, Suren Byna, Prabhat and Marc Snir, "Pattern-driven Parallel I/O Tuning", 10th Parallel Data Storage Workshop (PDSW) 2015, held in conjunction with SC15, 10th Parallel Data Storage Workshop (PDSW) 2015, to be held in conjunction with SC15, November 16, 2015,

Shane Snyder, Philip Carns, Robert Latham, Misbah Mubarak, Chris Carothers, Babak Behzad, Huong Vu Thanh Luu, Suren Byna, and Prabhat, "Techniques for Modeling Large-scale HPC I/O Workloads", the 6th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS15), in conjunction with SC15, the 6th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performa, November 15, 2015,

Babak Behzad, Suren Byna, Stefan Wild, Prabhat and Marc Snir, "Dynamic Model-driven Parallel I/O Performance Tuning", IEEE Cluster 2015, 2015,

H. Luu, M. Winslett, W. Gropp, R. Ross, P. Carns, K. Harms, Prabhat, S. Byna, Y. Yao,, "A Multi-platform Study of I/O Behavior on Petascale Supercomputers", The 24th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC) 2015, 2015,

Wehner, M., Prabhat, K. A. Reed, D. Stone, W. D. Collins, and J. Bacmeister, "Resolution dependence of future tropical cyclone projections of CAM5.1 in the US CLIVAR Hurricane Working Group idealized configurations", Journal of Climate, 2015, 28:3905-3925, doi: 10.1175/JCLI-D-14-00311.1

2014

Soyoung Jeon, Christopher Paciorek, Prabhat, Surendra Byna, William Collins, Michael Wehner, "Uncertainty Quantification for Characterizing Spatial Tail Dependence under Statistical Framework", AGU, Fall Meeting 2014, 2014,

Babak Behzad, Surendra Byna, Stefan M. Wild, Mr. Prabhat, Marc Snir, "Improving Parallel I/O Autotuning with Performance Modeling", ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC 2014), New York, NY, USA, ACM, 2014, 253--256, doi: 10.1145/2600212.2600708

Gunther H. Weber, Hans Johansen, Daniel T. Graves, Terry J. Ligocki, "Simulating Urban Environments for Energy Analysis", Proceedings Visualization in Environmental Sciences (EnvirVis), 2014, LBNL 6652E,

Dáithí Stone, Michael Wehner, Shreyas Cholia, Harinarayan Krishnan, Piotr Wolski, Mark Tadross, Chris Folland, Nikos Christidis, Hideo Shiogama, "The C20C+ Detection and Attribution Project", Integrated Climate Modeling Principal Investigator Meeting 2014, 2014,

M Scot Breitenfeld, Kalyana Chadalavada, Robert Sisneros, Surendra Byna, Quincey Koziol, Neil Fortner, Prabhat, Venkat Vishwanath, "Recent Progress in Tuning Performance of Large-scale I/O with Parallel HDF5", The 9th Parallel Data Storage Workshop (PDSW) held in conjunction with SC14, 2014,

Gunther H. Weber, Helwig Hauser, "Interactive Visual Exploration and Analysis", Mathematics and Visualization, (Springer-Verlag: 2014) Pages: 161--174, LBNL 6655E,

Patrick Oesterling, Christian Heine, Gunther H. Weber, Gerik Scheuermann, "A Topology-Based Approach to Visualize the Thematic Composition of Document Collections", Theory and Applications of Natural Language Processing, (Springer International Publishing: 2014) Pages: 63-85 doi: 10.1007/978-3-319-12655-5_4

Kenes Beketayev, Damir Yeliussizov, Dmitriy Morozov, Gunther H. Weber, Bernd Hamann, "Measuring the Distance Between Merge Trees", Mathematics and Visualization, (Springer-Verlag: 2014) Pages: 151--166

Dmitriy Morozov, Gunther H. Weber, "Distributed Contour Trees", Mathematics and Visualization, (Springer-Verlag: 2014) Pages: 89-102

2013

Babak Behzad, Huong Vu Thanh Luu, Joseph Huchette, Surendra Byna, Prabhat, Ruth Aydt, Quincey Koziol, and Marc Snir, "Taming parallel I/O complexity with auto-tuning", In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '13), 2013,

David Camp, Hari Krishnan, David Pugmire, Christoph Garth, Ian Johnson, E. Wes Bethel, Kenneth I. Joy, and Hank Childs., "GPU Acceleration of Particle Advection Workloads in a Parallel, Distributed Memory Setting", Proceedings of Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), May 5, 2013,

Hank Childs, Berk Geveci, William J. Schroeder, Jeremy S. Meredith, Kenneth Moreland, Christopher Sewell, Torsten Kuhlen, E.Wes Bethel, "Research Challenges for Visualization Software", IEEE Computer, May 1, 2013, 46:34-43, LBNL 6239E,

Patrick Oesterling, Christian Heine, Gunther H. Weber, Gerik Scheuermann, "Visualizing global structure of nD point clouds as topological 1D height to enable supervised local data analysis", IEEE Transactions on Visualization and Computer Graphics, 2013, 19:514-526, LBNL 5694E,

E. Wes Bethel, Prabhat, Suren Byna, Oliver Rübel, K. John Wu, and Michael Wehner, "Why High Performance Visual Data Analytics is both Relevant and Difficult", Proceedings of Visualization and Data Analysis 2013, IS&T/SPIE Electronic Imaging 2013, San Francisco, CA, USA, SPIE, February 2013, LBNL LBNL-6063E,

Kesheng Wu, Wes Bethel, Ming Gu, David, Oliver R\ ubel, "A Big Data Approach to Analyzing Market Volatility", Algorithmic Finance, 2013, 2:241--267, LBNL LBNL-6382E, doi: 10.3233/AF-13030

Understanding the microstructure of the financial market requires the processing of a vast amount of data related to individual trades, and sometimes even multiple levels of quotes. Analyzing such a large volume of data requires tremendous computing power that is not easily available to financial academics and regulators. Fortunately, public funded High Performance Computing (HPC) power is widely available at the National Laboratories in the US. In this paper we demonstrate that the HPC resource and the techniques for data-intensive sciences can be used to greatly accelerate the computation of an early warning indicator called Volume-synchronized Probability of Informed trading (VPIN). The test data used in this study contains five and a half year's worth of trading data for about 100 most liquid futures contracts, includes about 3 billion trades, and takes 140GB as text files. By using (1) a more efficient file format for storing the trading records, (2) more effective data structures and algorithms, and (3) parallelizing the computations, we are able to explore 16,000 different ways of computing VPIN in less than 20 hours on a 32-core IBM DataPlex machine. Our test demonstrates that a modest computer is sufficient to monitor a vast number of trading activities in real-time -- an ability that could be valuable to regulators.

Our test results also confirm that VPIN is a strong predictor of liquidity-induced volatility. With appropriate parameter choices, the false positive rates are about 7% averaged over all the futures contracts in the test data set. More specifically, when VPIN values rise above a threshold (CDF > 0.99), the volatility in the subsequent time windows is higher than the average in 93% of the cases.

Kesheng Wu, Wes Bethel, Ming Gu, David, Oliver R\ ubel, Testing VPIN on Big Data, Available at SSRN 2318259, 2013,

2012

Cyrus Harrison, Paul Navratil, Maysam Mossalem, Ming Jiang, Hank Childs, "Efficient Dynamic Derived Field Generation on Many-Core Architectures Using Python", Workshop on Python for High Performance and Scientific Computing (PyHPC 2012), held in conjunction with the ACM/IEEE Conference on SuperComputing (SC12), November 2012, 11-20,

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", SuperComputing 2012 (SC12), Salt Lake City, Utah, November 2012,

E. Wes Bethel and Mark Howison, "Multi-core and Many-core Shared-memory Parallel Raycasting Volume Rendering Optimization and Tuning", International Journal of High Performance Computing Applications, 2012, LBNL 5362E,

Hank Childs, Eric Brugger, Brad Whitlock, Jeremy Meredith, Sean Ahern, David Pugmire, Kathleen Biagas, Mark Miller, Cyrus Harrison, Gunther H. Weber, Hari Krishnan, Thomas Fogal, Allen Sanderson, Christoph Garth, E. Wes Bethel, David Camp, Oliver Rubel, Marc Durant, Jean M. Favre, Paul Navratil, "VisIt: An End-User Tool For Visualizing and Analyzing Very Large Data", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 357--372

Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel, "Visualization at Extreme Scale Concurrency", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 291--306

Hank Childs, "Parallel Visualization Frameworks", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 9--24

Hank Childs, Kwan-Liu Ma, Hongfeng Yu, Brad Whitlock, Jeremy Meredith, Jean Favre, Scott Klasky, Norbert Podhorszki, Karsten Schwan, Matthew Wolf, Manish Parashar, Fan Zhang, "In Situ Processing", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 171--198

E. Wes Bethel, David Camp, Hank Childs, Christoph Garth, Mark Howison, Kenneth I. Joy, David Pugmire, "Hybrid Parallelism", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 261--290

E. Wes Bethel, Hank Childs, Charles Hansen (editors), High Performance Visualization---Enabling Extreme-Scale Scientific Insight, Chapman & Hall, CRC Computational Science, (CRC Press/Francis--Taylor Group: October 2012)

Gunther H. Weber, Hank Childs, Jeremy S. Meredith, "Efficient Parallel Extraction of Crack-free Isosurfaces from Adaptive Mesh Refinement (AMR) Data", Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), October 2012, 31--38, LBNL 5799E,

Paul Navratil, Bill Barth, Hank Childs, "Virtual Rheoscopic Fluids for Dense, Large-Scale Fluid Flow Visualizations", Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), October 2012, 79--84,

David Camp, Hank Childs, Christoph Garth, David Pugmire, Kenneth I. Joy, "Parallel Stream Surface Computation for Large Data Sets", Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), October 2012, 39--47, LBNL 5776E,

Tamay M. Ozgokmen, Andrew C. Poje, Paul F. Fischer, Hank Childs, Harinarayan Krishnan, Christoph Garth, Angelique C. Haza, Edward Ryan, "On multi-scale dispersion under the influence of surface mixed layer instabilities", Ocean Modelling, October 2012, 56:16-30,

Oliver Rübel, Cameron, G. R. Geddes, Min Chen, Estelle Cormier-Michel, and E. Wes Bethel, "Query-driven Analysis of Plasma-based Particel Acceleration Data", Poster Abstracts of IEEE VisWeek, October 2012,

Kelly P. Gaither, Hank Childs, Karl Schulz, Cyrus Harrison, Bill Barth, Diego Donzis, P.K. Yeung, "Using Visualization and Data Analysis to Understand Critical Structures in Massive Time Varying Turbulent Flow Simulations", IEEE Computer Graphics and Applications, July 2012, 32:34-45, LBNL 5911E,

Mehmet Balman, Eric Pouyoul, Yushu Yao, E. Wes Bethel, Burlen Loring, Prabhat, John Shalf, Alex Sim, and Brian L. Tierney, "Experiences with 100G Network Applications", In Proceedings of the Fifth international Workshop on Data-intensive Distributed Computing, in conjunction with ACM High Performance Distributing Computing (HPDC) Conference, 2012, Delft, Netherlands, June 2012, LBNL 5603E, doi: 10.1145/2286996.2287004

100Gbps networking has finally arrived, and many research and educational in- stitutions have begun to deploy 100Gbps routers and services. ESnet and Internet2 worked together to make 100Gbps networks available to researchers at the Super- computing 2011 conference in Seattle Washington. In this paper, we describe two of the first applications to take advantage of this network. We demonstrate a visu- alization application that enables remotely located scientists to gain insights from large datasets. We also demonstrate climate data movement and analysis over the 100Gbps network. We describe a number of application design issues and host tuning strategies necessary for enabling applications to scale to 100Gbps rates. 

Prabhat, Oliver Rübel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner and E. Wes Bethel, "TECA: A Parallel Toolkit for Extreme Climate Analysis", Procedia Computer Science, Proceedings of the International Conference on Computational Science, ICCS 2012, Presented at Third Worskhop on Data Mining in Earth System Science (DMESS 2012), Omaha, Nebraska, June 2012, 9:866–876, LBNL 5352E, doi: 10.1016/j.procs.2012.04.093

We present TECA, a parallel toolkit for detecting extreme events in large climate datasets. Modern climate datasets expose parallelism across a number of dimensions: spatial locations, timesteps and ensemble members. We design TECA to exploit these modes of parallelism and demonstrate a prototype implementation for detecting and tracking three classes of extreme events: tropical cyclones, extra-tropical cyclones and atmospheric rivers. We process a modern TB-sized CAM5 simulation dataset with TECA, and demonstrate good runtime performance for the three case studies.

Hank Childs, Torsten Kuhlen, Fabio Marton (editors), Proceedings of the EuroGraphics Symposium on Parallel Graphics and Visualization (EGPGV), EuroGraphics Association, (EuroGraphics Association: May 2012)

Paul Navratil, Donald Fussell, Calvin Lin, Hank Childs, "Dynamic Scheduling for Large-Scale Distributed-Memory Ray Tracing", Proceedings of EuroGraphics Symposium on Parallel Graphics and Visualization (EGPGV), May 2012, 61-70, LBNL 5930E,

Gunther H. Weber, Kenes Beketayev, Peer-Timo Bremer, Bernd Hamann, Maciej Haranczyk, Mario Hlawitschka, Valerio Pascucci, "Comprehensible Presentation of Topological Information", Status report for DOE Exascale Research Conference, April 2012, LBNL 5693E,

Gunther H. Weber, Dmitriy Morozov, Kenes Beketayev, John Bell, Peer-Timo Bremer, Marc Day, Bernd Hamann, Christian Heine, Maciej Haranczyk, Mario Hlawitschka, Valerio Pascucci, Patrick Oesterling, Gerik Scheuermann, "Topology-based Visualization and Analysis of High-dimensional Data and Time-varying Data at the Extreme Scale", DOE Exascale Research Conference, April 2012,

Gunther H. Weber, Peer-Timo Bremer, "In-situ Analysis: Challenges and Opportunities", Position paper for DOE Exascale Research Conference, April 2012, LBNL 5692E,

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, Joerg Meyer, Prabhat, Oliver Ruebel, Daniela Ushizima, Gunther Weber, "Towards Exascale: High Performance Visualization and Analytics – Project Status Report. Technical Report", DOE Exascale Research Conference, April 2012,

Jihan Kim, Richard L. Martin, Oliver Rübel, Maciej Haranczyk & Berend Smit, "High-throughput Characterization of Porous Materials Using Graphics Processing Units", Journal of Chemical Theory and Computation, March 16, 2012, 8:1684–1693, LBNL 5409E, doi: 10.1021/ct200787v

We have developed a high-throughput graphics processing unit (GPU) code that can characterize a large database of crystalline porous materials. In our algorithm, the GPU is utilized to accelerate energy grid calculations, where the grid values represent interactions (i.e., Lennard-Jones + Coulomb potentials) between gas molecules (i.e., CH4 and CO2) and materials’ framework atoms. Using a parallel flood fill central processing unit (CPU) algorithm, inaccessible regions inside the framework structures are identified and blocked, based on their energy profiles. Finally, we compute the Henry coefficients and heats of adsorption through statistical Widom insertion Monte Carlo moves in the domain restricted to the accessible space. The code offers significant speedup over a single core CPU code and allows us to characterize a set of porous materials at least an order of magnitude larger than those considered in earlier studies. For structures selected from such a prescreening algorithm, full adsorption isotherms can be calculated by conducting multiple Grand Canonical Monte Carlo (GCMC) simulations concurrently within the GPU.

Soile V.E. Keränen, Oliver Rübel, David W. Knowles and Mark D. Biggin, "Computational modeling of cis-regulatory modules from 3D exprression data in Drosophila blastoderm atlas", Drosophila Genetics, March 2012,

Ushizima, D.M., Weber, G., Morozov, D., Bethel, W., Sethian, J.A., "Algorithms for Microstructure Description applied to Microtomography", Carbon Cycle 2.0 Symposium, February 10, 2012,

Richard L. Martin, Prabhat, David D. Donofrio, James A. Sethian & Maciej Haranczyk, "Accelerating Analysis of void spaces in porous materials on multicore and GPU platforms", International Journal of High Performance Computing Applications, February 5, 2012, 26:347-357,

Developing computational tools that enable discovery of new materials for energy-related applications is a challenge. Crystalline porous materials are a promising class of materials that can be used for oil refinement, hydrogen or methane storage as well as carbon dioxide capture. Selecting optimal materials for these important applications requires analysis and screening of millions of potential candidates. Recently, we proposed an automatic approach based on the Fast Marching Method (FMM) for performing analysis of void space inside materials, a critical step preceding expensive molecular dynamics simulations. This breakthrough enables unsupervised, high-throughput characterization of large material databases. The algorithm has three steps: (1) calculation of the cost-grid which represents the structure and encodes the occupiable positions within the void space; (2) using FMM to segment out patches of the void space in the grid of (1), and find how they are connected to form either periodic channels or inaccessible pockets; and (3) generating blocking spheres that encapsulate the discovered inaccessible pockets and are used in proceeding molecular simulations. In this work, we expand upon our original approach through (A) replacement of the FMM-based approach with a more computationally efficient flood fill algorithm; and (B) parallelization of all steps in the algorithm, including a GPU implementation of the most computationally expensive step, the cost-grid generation. We report the acceleration achievable in each step and in the complete application, and discuss the implications for high-throughput material screening.

Samuel Gerber, Oliver Rübel, Peer-Timo Bremer, Valerio Pascucci and Ross T. Whitaker, "Morse-Smale Regression", Journal of Computational and Graphical Statistics, January 2012, doi: 10.1080/10618600.2012.657132

  • Download File: MSR.pdf (pdf: 292 KB)

E. Wes Bethel, "Exploration of Optimization Options for Increasing Performance of a GPU Implementation of a Three-dimensional Bilateral Filter", 2012, LBNL 5406E,

Daniela M. Ushizima, Dmitriy Morozov, Gunther H. Weber, Andrea G.C. Bianchi, James A. Sethian, E. Wes Bethel, "Augmented Topological Descriptors of Pore Networks for Material Science", IEEE Transactions on Visualization and Computer Graphics (Proc. IEEE Vis 2012), 2012, 18:2041-2050, LBNL 5964E,

E. W. Bethel and D. Leinweber and O. Rubel and K. Wu, "Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing", The Journal of Trading, 2012, 7:9-24, LBNL 5263E, doi: 10.3905/jot.2012.7.2.009

O. R\ ubel, S. Byna, K. Wu, F. Li, M., W. Bethel, others, "TECA: A Parallel Toolkit for Extreme Climate", Procedia Computer Science, Elsevier, 2012, 9:866--876, doi: 10.1016/j.procs.2012.04.093

O. Rübel, S.V.E. Keränen, M.D. Biggin, D.W. Knowles, G.H. Weber, H. Hagen, B. Hamann, and E.W. Bethel, "Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data", Mathematics and Visualization, Visualization in Medicine and Life Sciences II, Progress and New Challenges, edited by L. Linsen and B. Hamann and H. Hagen and H.-C. Hege, (Springer Verlag: 2012) Pages: 267-285, LBNL 4891E,

Mark Howison, E. Wes Bethel, Hank Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi- and Many-core Systems", IEEE Transactions on Visualization and Computer Graphics, January 2012, 18:17-29, LBNL 4370E,

E. W. Bethel, Surendra Byna, Jerry Chou, Cormier-Michel, Cameron G. R. Geddes, Howison, Fuyu Li, Prabhat, Ji Qiang, R\ ubel, Rob D. Ryne, Michael Wehner, Wu, "Big Data Analysis and Visualization: What Do LINACS Tropical Storms Have In Common?", 11th International Computational Accelerator Physics ICAP 2012, Germany, 2012,

Allen R. Sanderson, Brad Whitlock, Oliver, Hank Childs, Gunther H. Weber, , Kesheng Wu, "A System for Query Based Analysis and Visualization", Third International Eurovis Workshop on Visual EuroVA 2012, Vienna, Austria, January 2012, LBNL 5507E,

EW Bethel, S. Byna, J. Chou, E., CGR Geddes, M. Howison, F. Li J. Q. Prabhat, O. R\ ubel, RD Ryne and, Big Data Analaysis and Visualization: What Do LINACS Tropical Storms Have In Common?, 11th International Computational Accelerator Physics ICAP 2012, 2012,

2011

Tina Zhuo, Prabhat, Chris Paciorek and Cari Kaufman, "Distributed Kriging Analysis for Large Spatial Data", Proceedings of IEEE ICDM Workshop on Knowledge Discovery from Climate Data, Vancuover, Canada, December 2011,

Suren Byna, Prabhat, Michael F. Wehner and Kesheng Wu, "Detecting Atmospheric Rivers in Large Climate Datasets", Proceedings of the 2nd International Workshop on Petascale Data Analytics: Challenges, and Opportunities (PDAC-11/ Supercomputing11/ ACM/IEEE), November 14, 2011, Seattle, Washington, 2011, doi: 10.1145/2110205.2110208

Extreme precipitation events on the western coast of North America are often traced to an unusual weather phenomenon known as atmospheric rivers. Although these storms may provide a significant fraction of the total water to the highly managed western US hydrological system, the resulting intense weather poses severe risks to the human and natural infrastructure through severe flooding and wind damage. To aid the understanding of this phenomenon, we have developed an efficient detection algorithm suitable for analyzing large amounts of data. In addition to detecting actual events in the recent observed historical record, this detection algorithm can be applied to global climate model output providing a new model validation methodology. Comparing the statistical behavior of simulated atmospheric river events in models to observations will enhance confidence in projections of future extreme storms. Our detection algorithm is based on a thresholding condition on the total column integrated water vapor established by Ralph et al. (2004) followed by a connected component labeling procedure to group the mesh points into connected regions in space. We develop an efficient parallel implementation of the algorithm and demonstrate good weak and strong scaling. We process a 30-year simulation output on 10,000 cores in under 3 seconds.

Uselton, A., Ushizima, D.M., "I/O Workload Analysis with Server-side Data Collection", Supercomputing (SC), November 13, 2011,

Huang, M.-Y., Mackey, L., Keraenen, S.V.E., Weber, G.H., Jordan, M.I., Knowles, D.W., Biggin, M.D. and Hamann, B., "Visually Relating Gene Expression and in vivo DNA Binding Data", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine 2011 (IEEE BIBM 2011), Los Alamitos, California, IEEE Computer Society Press, November 2011, 586-589, LBNL 5423E,

E. Wes Bethel, David Leinweber, Oliver Rübel, Kesheng Wu, "Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing", Workshop on High Performance Computational Finance at SC11, Seattle, WA, USA, November 2011, LBNL 5263E,

David Camp, Christoph Garth, Hank Childs, Dave Pugmire, Kenneth I. Joy, "Streamline Integration Using MPI-Hybrid Parallelism on a Large Multicore Architecture", IEEE Transactions on Visualization and Computer Graphics, November 2011, 17:1702-1713, LBNL 4563E, doi: http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.259

Jerry Chou, Kesheng Wu, Oliver Rübel, Mark Howison, Ji Qiang, Prabhat, Brian Austin, E. Wes Bethel, Rob D. Ryne, and Arie Shoshani, "Parallel Index and Query for Large Scale Data Analysis", In Proceedings of Supercomputing 2011, Seattle, WA, USA, 2011, 1-11, LBNL 5317E, doi: 10.1145/2063384.2063424

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", Workshop on Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery, October 2011,

David Camp, Hank Childs, Amit Chourasia, Christoph Garth, Kenneth Joy, "Evaluating the Benefits of An Extended Memory Hierarchy for Parallel Streamline Algorithms", Proceedings IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) 2011, Providence, RI, USA, IEEE Press, October 2011, 57-64, LBNL 5503E,

Prabhat, Suren Byna. Chris Paciorek, Gunther Weber, Kesheng Wu, Thomas Yopes, Michael Wehner, William Collins, George Ostrouchov, Richard Strelitz, E. Wes Bethel, "Pattern Detection and Extreme Value Analysis on Large Climate Data", DOE/BER Climate and Earth System Modeling PI Meeting, September 2011,

Michael Philpott, Prabhat and Yoshiyuki Kawazoe, "Magnetism and Bonding in Graphene Nanodots with H modified Interior, Edge and Apex", J. Chem Physics, August 2011,

Ushizima, D.M., Parkinson, D., Nico, P., Ajo-Franklin, J., Macdowell, A., Kocar, B., Bethel E.W, Sethian J.A., "Statistical segmentation and porosity quantification of 3D x-ray microtomography", XXXIV Applications of Digital Image Processing: Proceeding of SPIE 2011, San Diego, CA, USA, August 2011,

Christopher Paciorek, Michael Wehner, and Prabhat, "Computationally-efficient Spatial Analysis of Precipitation Extremes Using Local Likelihood", Statistical and Applied Mathematical Sciences Institute Uncertainty Quantification program, Climate Modeling Opening Workshop, August 2011,

Ushizima, D.M., Weber, G.H., Ajo-Franklin, J., Kim, Y., Macdowell, A., Morozov, D., Nico, P., Parkinson, D., Trebotich, D., Wan, J., and Bethel E.W., "Analysis and visualization for multiscale control of geologic CO2", Journal of Physics: Conference Series, Proceedings of SciDAC 2011, July 2011, LBNL Denver, CO, USA,

Richard L. Martin, Thomas F. Willems, Chris H. Rycroft, Prabhat, Michael Kazi and Maciej Haranczyk, "High-throughput structure analysis and descriptor generation for crystalline porous materials", International Conference on Chemical Structures (Noordwijkerhout, Netherlands), June 5, 2011,

Weber, G.H., Bremer, P.T., Gyulassy A., and Pascucci, "Topology-based Feature Definition and Analysis", Numerical Modeling of Space Plasma Flows, San Diego, CA, USA, Astronomical Society of the Pacific, June 2011, 444:292-297, LBNL 5020E,

Beketayev, K., Weber, G.H., Haranczyk, M., Bremer, P.-T., Hlawitschka, M., and Hamann, B., "Topology-based Visualization of Transformation Pathways in Complex Chemical Systems", Computer Graphics Forum (Special Issue, Proc. Eurographics / IEEE Symposium on Visualization), June 2011, 663-672, LBNL 5242E,

C. Harrison, H. Childs, and K. P. Gaither, "Data-Parallel Mesh Connected Components Labeling and Analysis", Proceedings of EuroGraphics Symposium on Parallel Graphics and Visualization, April 2011, 131-140, LBNL 5944E, doi: 10.2312/EGPGV/EGPGV11/131-140

Richard L. Martin, Maciej Haranczyk, Prabhat and James A. Sethian, "PDE-based analysis of void space of porous materials on multicore CPUs", Manycore and Accelerator-based High-performance Scientific Computing 2011 (Berkeley, CA), January 24, 2011,

Maciej Haranczyk, Richard L. Martin, Prabhat, James A. Sethian & E. Wes Bethel, "Computational Approaches for the High-Throughput Analysis of Porous materials for Energy related applications", Scientific Discovery through Advanced Computing 2011, 2011,

MacCarthy, B., Carr, H., Weber, G.H., "Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering", 2011, LBNL 5019E,

Weber, G.H., Bremer, P.-T. and Pascucci, V., "Topological Cacti: Visualizing Contour-based Statistics", Topological Methods in Data Analysis and Visualization II, (Springer Verlag: 2011) Pages: 63-76, LBNL 5018E,

Deines E., Weber, G.H., Garth, C., Van Straalen, B. Borovikov, S., Martin, D.F., and Joy, K.I., "On the computation of integral curves in adaptive mesh refinement vector fields", Proceedings of Dagstuhl Seminar on Scientific Visualization 2009, Schloss Dagstuhl, 2011, 2:73-91, LBNL 4972E,

  • Download File: 7.pdf (pdf: 799 KB)

Bremer, P.-T., Weber, G.H., Tierny, J., Pascucci, V., Day, M.S., and Bell, J.B., "Interactive Exploration and Analysis of Large Scale Turbulent Combustion Using Topology-based Data Segmentatio", IEEE Transactions on Visualization and Computer Graphics, 2011, 17(9):1307-1324, LBNL 5921E, doi: 10.1109/TVCG.2010.253

G.H. Weber, P.-T. Bremer, M.S. Day, J.B. Bell, and V. Pascucci, "Feature tracking using Reeb graphs", Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, edited by V. Pascucci, X. Tricoche, H. Hagen, and J. Tierny,, (Springer Verlag: 2011) Pages: 241-253, LBNL 4226E,

Prabhat, Quincey Koziol, Karen Schuchardt, E. Wes Bethel, Jerry Chuo, Mark Howison, Mike McGreevy, Bruce Palmer, Oliver Ruebel and John Wu, "ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance", Scientific Discovery Through Advanced Computing 2011, 2011,

Jerry Chuo, John Wu, Prabhat, "FastQuery: A Parallel Indexing System for Scientific Data", Workshop on Interfaces and Abstractions for Scientific Data Storage, IEEE Cluster, 2011,

Prabhat, Dmitry Zubarev and W. A. Lester, "Statistical Exploration of Electronic Structure of Molecules from Quantum Monte Carlo Simulations", 2011, LBNL 4564E,

Luke J. Gosink, Christoph Garth, John C. Anderson, E. Wes Bethel, and Kenneth I. Joy, "An Application of Multivariate Statistical Analysis for Query-Driven Visualization", IEEE Transactions on Visualization and Computer Graphics, 2011, 11:264-275, LBNL 3536E, doi: 10.1109/TVCG.2010.80

J. Chou, K. Wu, O. R\ ubel, M. Howison, Qiang, Prabhat, B. Austin, E. W. Bethel, D. Ryne, A. Shoshani, "Parallel Index and Query for Large Scale Data", SC11, 2011, doi: 10.1145/2063384.2063424

Jerry Chuo, John Wu, Prabhat, "Design of FastQuery: how to generalize Indexing and Querying systems for scientific data", 2011,

E. Wes Bethel, John van Rosendale, Dale Southard, Kelly Gaither, Hank Childs, Eric Brugger, Sean Ahern, "Visualization at Supercomputing Centers: The Tale of Little Big Iron and the Three Skinny Guys", IEEE Computer Graphics and Applications, January 2011, 31:90-95, LBNL 4180E,

H. Childs, S. Ahern, J. Meredith, M. Miller, and K. I. Joy, "Comparative Visualization Using Cross-Mesh Field Evaluations and Derived Quantities", Scientific Visualization: Interactions, Features, Metaphors, Dagstuhl, Germany, Dagstuhl Follow-Ups, January 2011, 2:59-72, LBNL 5943E, doi: 10.4230/DFU.Vol2.SciViz.2011.59

Jerry Chuo, John Wu, Prabhat, "FastQuery: a general Index and Query system for scientific data", Scientific and Statistical Database Management Conference 2011, 2011,

2010

Min-Yu Huang, Gunther H. Weber, Xiao-Yong Li, Mark D. Biggin, and Bernd Hamann, "Quantitative Visualization of ChIP-chip Data by Using Linked Views", Proceedings IEEE International Conference on Bioinformatics and Biomedicine 2010 (IEEE BIBM 2010) Workshops, Workshop on Integrative Data Analysis in Systems Biology (IDASB), Los Alamitos, California, IEEE Computer Society Press, December 8, 2010, 195-200, LBNL 4491E,

O. Rübel, Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-energy Physics, Schriftenreihe Informatik, (Der Dekan (hrsg), Fachbereich Informatik, Technische Universität Kaiserslautert: December 2010) LBNL 3155E,

Patrick Oesterling, Gerik Scheuermann, Sven Teresniak, Gerhard Heyer, Steffen Koch, Thomas Ertl, Gunther H. Weber, "Two-stage Framework for a Topology-Based Projection and Visualization of Classified Document Collections", Proceedings IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST), Salt Lake City, Utah, USA, October 2010, LBNL 4074E,

Mark Howison, Andreas Adelmann, E. Wes Bethel, Achim Gsell, Benedikt Oswald, Prabhat, "H5hut: A High-Performance I/O Library for Particle-Based Simulations", Proceedings of 2010 Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS10), Heraklion, Crete, Greece, September 2010, LBNL 4021E,

D. M. Ushizima, F. N. S. Medeiros, J. Cuadros, C. I. O. Martins, "Vessel Network Detection Using Contour Evolution and Color Components", Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Buenos Aires, Argentina, PubMed-MedLine, September 2010, 3129-3132,

C. Rycroft, D. M. Ushizima, R. Saye, C. M. Ghajar, J. A. Sethian, "Building a physical cell simulation and comparing with confocal microscopy", Bay Area Physical Sciences - Oncology Center (NCI) Meeting 2010, UCSF Medical Sciences, September 2010,

Mark Howison, Quincey Koziol, David Knaak, John Mainzer, John Shalf, "Tuning HDF5 for Lustre File Systems", Proceedings of 2010 Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS10), Heraklion, Crete, Greece, September 2010, LBNL 4803E,

M. Howison, E. W. Bethel, and H. Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems", Journal of Physics: Conference Series, Proceedings of SciDAC 2010, Chattanooga, TN, USA, July 2010, LBNL 4024E,

T.Fogal, H. Childs, S. Shankar, J. Kruger, R.D. Bergeron, and P. Hatcher, "Large Data Visualization on Distributed Memory Multi-GPU Clusters", High Performance Graphics 2010, June 2010, 57-66, LBNL 4571E,

J. Meredith and H. Childs, "Visualization and Analysis-Oriented Reconstruction of Material Interfaces", Computer Graphics Forum (Proceedings of Eurographics/IEEE-VGTC Symposium on Visualization 2010 (EuroVis 2010)), June 2010, 1241-1250, LBNL 4567E,

M. Howison, E. W. Bethel, and H. Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems", Proceedings of Astronum 2010, San Diego, CA, USA, June 2010, LBNL 4024E,

Oliver Rübel, Sean Ahern, E. Wes Bethel, Mark. D Biggin, Hank Childs, Estelle Cormier-Michel, Angela DePace, Michael B. Eisen, Charless C. Fowlkes, Cameron G. R. Geddes, Hans Hagen, Bernd Hamann, Min-Yu Huang, Soile V. E. Keränen, David W. Knowles, Cris L. Luengo Hendriks, Jitendra Malik, Jeremy Meredith, Peter Messmer, Prabhat, Daniela Ushizima, Gunther H. Weber, and Kesheng Wu, "Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-dimensional Scientific Data", Procedia Computer Science, Proceedings of International Conference on Computational Science, ICCS 2010, June 2010, LBNL 3669E,

Martin Isenburg, Peter Lindstrom, and Hank Childs, "Parallel and Streaming Generation of Ghost Data for Structured Grids", IEEE Computer Graphics and Applications, May 2010, 30:32-44, doi: 10.1109/MCG.2010.26

Mark Howison, E. Wes Bethel, Hank Childs, "MPI-hybrid Parallelism for Volume Rendering on Large, Multi-core Systems", In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), Norköping, Sweden, May 2010, LBNL 3297E,

A.Uselton, K.Antypas, D.M.Ushizima, J.Sukharev, "File System Monitoring as a Window Into User I/O Requirements", CUG-2010, May 2010,

D. M. Ushizima, F. Medeiros, "Retinopathy diagnosis from ocular fundus image analysis, Modeling and Analysis of Biomedical Image", SIAM Conference on Imaging Science (IS10), Chicago, Il, April 2010,

O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. Luengo Hendriks, S. V. E. Keränen, M. Eisen, D. Knowles, J. Malik, H. Hagen and B. Hamann, "Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data", IEEE Transactions on Computational Biology and Bioinformatics, March 2010, 7:64-79, LBNL 382E,

D. M. Ushizima and J. Cuadros, "Ocular fundus for retinopathy characterization", Bay Area Vision Meeting, February 5, 2010,

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rubel, Gunther Weber, Bernard Hamann, Peter Messmer, Hans Hagen, "Automated detection and analysis of particle beams in laser-plasma accelerator simulations", Machine Learning, edited by Yagang Zhang, (In-Teh: February 2010) Pages: 367-389, LBNL 3845E,

Gladeston C. Leite, Daniela M. Ushizima, Fátima N. S. Medeiros, Gilson G. De Lima, "Wavelet Analysis for Wind Fields Estimation", Sensors, 2010, 10:5994--6016, doi: 10.3390/s100605994

Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel, "Extreme Scaling of Production Visualization Software on Diverse Architectures", IEEE Computer Graphics and Applications, January 2010, 30:22--31, LBNL 3403E,

E. Wes Bethel, "Using wesBench to Study the Rendering Performance of Graphics Processing Units", 2010, LBNL 3025E,

E. A. Carvalho, D. M. Ushizima, F. N. S. Medeiros, C. I. O. Martins, R. C. P. Marques, I. N. S. Oliveira, "SAR imagery segmentation by statistical region growing and hierarchical merging", Digital Signal Processing, 2010, 20:1365-1378, doi: 10.1016/j.dsp.2009.10.014

G. H. Weber, S. Ahern, E.W. Bethel, S. Borovikov, H.R. Childs, E. Deines, C. Garth, H. Hagen, B. Hamann, K.I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. Rübel, B. Van Straalen and K. Wu, "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization", Numerical Modeling of Space Plasma Flows: Astronum-2009 (Astronomical Society of the Pacific Conference Series, 3185E, 2010, 429:329-334,

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, "Parallel I/O performance: From events to ensembles", International Parallel & Distributed Processing Symposium (IPDPS), 2010, 1-11,

P.-T. Bremer, G.H. Weber, V. Pascucci, M.S. Day and John B. Bell, "Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames", IEEE Transactions on Visualization and Computer Graphics, 2010, 16:248-260, LBNL 2276E, doi: 10.1109/TVCG.2009.69

2009

Luke J. Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy, "Data Parallel Bin-Based Indexing for Answering Queries on Multi-core Architectures", SSDBM 2009, 2009, 110-129,

 

 

E. Wes Bethel, Hank Childs, Ajith Mascarenhas, Valerio Pascucci, and Prabhat, "Scientific Data Management Challenges in High Performance Visual Data Analysis", Scientific Data Management: Challenges, Existing Technology, and Deployment, edited by Arie Shoshani and Doron Rotem, (Chapman & Hall CRC Press: December 2009) LBNL 1449E,

P.-T. Bremer, G.H. Weber, J. Tierny, V. Pascucci, M.S. Day and J.B. Bell, "A Topological Framework for the Interactive Exploration of Large Scale Turbulent Combustion", Proceedings of the 5th IEEE International Conference on e-Science, Oxford, UK, December 2009, 247-254, LBNL 3183E, doi: 10.1109/e-Science.2009.42

D. Pugmire, H. Childs, C. Garth, S. Ahern, G.H. Weber, "Scalable computation of streamlines on very large datasets", Proc. Supercomputing, Portland, OR, USA, November 2009, LBNL 3264E,

O. Rübel, C.G.R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G.H. Weber, D.M. Ushizima, P. Messmer, H. Hagen, B. Hamann, and E.W. Bethel, "Automatic Beam Path Analysis of laser Wakefield Particle Acceleration Data", IOP Computational Science & Discovery, November 2009, 2, LBNL 2734E,

E. W. Bethel, C. Johnson, S. Ahern, J. Bell, P.-T. Bremer, H. Childs, E. Cormier-Michel, M. Day, E. Deines, T. Fogal, C. Garth, C. G. R. Geddes, H. Hagen, B. Hamann, C. Hansen, J. Jacobsen, K. Joy, J. Kruger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. Rubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu, "Occam's Razor and Petascale Visual Data Analysis", SciDAC 2009, J. of Physics: Conference Series, San Diego, California, July 2009, LBNL 2210E,

N. Shah, N., S. E. Dillard, G.H. Weber, B. Hamann, "Volume visualization of multiple alignment of large genomic DNA", Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration, edited by Torsten Moller and Bernd Hamann and Robert Russell, (Springer-Verlag: July 2009) Pages: 325-342, LBNL 63126,

Luke Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy, "Data Parallel Bin-based Indexing for Answering Queries on Multi-core Architecture", Proceedings of the 21st International Conference on Scientific and Statistical Database Management (SSDBM), June 2009, 5566:110-129, LBNL 2211E,

E. Wes Bethel, Oliver Rübel, Prabhat, Kesheng Wu, Gunther H. Weber, Valerio Pascucci, Hank Childs, Ajith Mascarenhas, Jeremy Meredith, and Sean Ahern, "Modern Scientific Visualization is More than Just Pretty Pictures", Numerical Modeling of Space Plasma Flows: Astronum-2008 (Astronomical Society of the Pacific Conference Series, St. Thomas, USVI, June 2009, 301-317, LBNL 1450E,

Mark Howison and Carlo Sequin, "CAD Tools for Creating Space-filling 3D Escher Tiles", Computer-Aided Design and Applications, Reno, NV, USA, June 2009, 6:737-748, LBNL 2467E,

Shoaib Kamil, Cy Chan, Samuel Williams, Leonid Oliker, John Shalf, Mark Howison, E. Wes Bethel, Prabhat, "A Generalized Framework for Auto-tuning Stencil Computations", BEST PAPER AWARD - Cray User Group Conference (CUG), Atlanta, GA, May 4, 2009, LBNL 2078E,

Best Paper Award

M. Hlawitschka, G.H. Weber, A. Anwander, O.T. Carmichael, B. Hamann and G. Scheuermann, "Interactive Volume Rendering of Diffusion Tensor Data", Visualization and Processing of Tensor Fields: Advances and Perspectives, (Springer-Verlag: April 2009) Pages: 161-176, LBNL 2286E,

S. E. Dillard, V. Natarjan, G. H. Weber, V. Pascucci and B. Hamann, "Topology-guided Tessellation of Quadratic Elements", International Journal of Computational Geometry & Applications (IJCGA), April 2009, 19:195-211, LBNL 63771,

E. Wes Bethel, "High Performance, Three-Dimensional Bilateral Filtering", 2009, LBNL 1601E,

G. H. Weber, O. Rübel, M.-Y. Huang, A. H. DePace, C. C. Fowlkes, S. V. E. Keränen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles, J. Malik, M. D. Biggin and B. Hamann, "Visual exploration of three-dimensional gene expression using physical views and linked abstract views", IEEE Transactions on Computational Biology and Bioinformatics, 2009, 6:296-309, LBNL 63776, doi: 10.1109/TCBB.2007.70249

"Smashing the Trillion Zone Barrier", H. Childs, Scientific Computing, 2009,

C. Garth, E. Deines, K. Joy, E. W. Bethel, H. Childs, G. Weber, S. Ahern, D. Pugmire, A. Sanderson, C. Johnson, Twists and Turns: Vector Field Visual Data Analysis for Petascale Computational Science, SciDAC Review, Pages: 10-21, 2009,

K Wu et al., "FastBit: Interactively Searching Massive Data", SciDAC 2009, 2009, LBNL 2164E, doi: 10.1088/1742-6596/180/1/012053

C. I. O. Martins, D. M. Ushizima, F. N. S. Medeiros, F. N. Bezerra, R. C. P. Marques, N. D. A. Mascarenhas, "Iterative Self-dual Reconstruction on Radar Image Recovery", Proc. of IEEE Workshop on Applications of Computer Vision, Snowbird, Utah, 2009, 37-42, LBNL 3846E,

C. G. R. Geddes, E Cormier-Michel, E. H. Esarey, C. B. Schroeder, J.-L. Vay, W. P. Leemans, D. L.. Bruhwiler, J. R. Cary, B. Cowan, M. Durant, P. Hamill, P. Messmer, P. Mullowney, C. Nieter, K. Paul, S. Shasharina, S. Veitzer, G. Weber, O. Rübel, D. Ushizima, Prabhat, E. W.Bethel, K. Wu, Large Fields for Smaller Facility Sources, SciDAC Review, Pages: 13-21, 2009,

Regis C. P. Marques, Fatima N. S. Medeiros, Daniela M. Ushizima, "Target Dectection on SAR Images Using Level Set Methods", IEEE Transactions on Systems, Man and Cybernetics, 2009, 39:214-222, LBNL 958E, doi: 10.1109/TSMCC.2008.2006685

2008

O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "High Performance Multivariate Visual Data Exploration for Extemely Large Data", Supercomputing (SC), Austin, Texas, USA, November 2008, LBNL 716E,

O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data", IEEE Visualization 2008, October 2008,

B. Paul, S. Ahern, E. W. Bethel, E. Brugger, R. Cook, J. Daniel, K. Lewis, J. Owen, and D. Southard, "Chromium Renderserver: Scalable and Open Remote Rendering Infrastructure", IEEE Transactions on Visualization and Computer Graphics, May 2008, 14:627-639, LBNL 63693,

C. C. Fowlkes, C. L. Luengo Hendriks, S. V. E. Keränen, G. H. Weber, O. Rübel, M.-Y. Huang, S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, J. Malik, "A Quantitative Spatio-temporal Atlas of Gene Expression in the Drosophila Blastoderm", Cell, April 18, 2008, 133:364-374,

G.H. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E.W. Bethel, "Visualization of Scalar Adaptive Mesh Refinement Data", Numerical Modeling of Space Plasma Flows: Astronum-2007 (Astronomical Society of the Pacific Conference Series), April 2008, 385:309-320, LBNL 220E,

J. Chen, I. Yoon and E. W. Bethel, "Interactive, Internet Delivery of Visualization via Structured, Prerendered Multiresolution Imagery.", IEEE Transactions on Visualization and Computer Graphics, March 2008, 14:302-312, LBNL 62252,

C.I.O. Martins, R.M.S. Veras, G.L.B. Ramalho, F.N.S. Medeiros, D. M. Ushizima, "Automatic Microaneurysm Detection and Characterization Through Digital Color Fundus Images", Brazilian Artificial Intelligence Community Conference, Tenth Brazilian Symposium on Neural Networks, Proceedings of IEEE SBRN'2008, 2008,

Daniela Ushizima, Oliver Rübel, Prabhat, Gunther Weber, E. Wes Bethel, Cecilia Aragon, Cameron Geddes, Estelle Cormier-Michel, Bernd Hamann, Peter Messmer, Hans Hagen, "Automated Analysis for Detecting Beams in Laser Wakefield Simulations", 2008 Seventh International Conference on Machine Learning and Applications, Proceedings of IEEE ICMLA'08, 2008, 382-387, LBNL 960E,

Luke J. Gosink, John C. Anderson, E. Wes Bethel, Kenneth I. Joy, "Query-Driven Visualization of Time-Varying Adaptive Mesh Refinement Data", IEEE Transactions on Visualization and Computer Graphics, 2008, 14:1715-1722, LBNL 803E,

Luke J. Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy, "Bin-Hash Indexing: A Parallel Method for Fast Query Processing", 2008, LBNL 729E,

M.-Y. Huang, O. Rübel, G.H. Weber, C.L. Luengo Hendriks, M.D. Biggin, H. Hagen, B. Hamann, "Segmenting Gene Expression Patterns of Early-stage Drosophila Embryos.", Mathematical Methods for Visualization in Medicine and Life Sciences, edited by L. Linsen, H. Hagen, B. Hamann, (Springer-Verlag: January 2008) Pages: 313--327, LBNL 62450,

E. Wes Bethel, Chris Johnson, Charles Hansen, Claudio Silva, Steven Parker, Allen Sanderson, Lee Myers, Martin Cole, Xavier Tricoche, Sean Ahern, George Ostrouchov, Dave Pugmire, Jamison Daniel, Jeremy Meredith, Valerio Pascucci, Hank Childs, Peer-Timo Bremer, Ajith Mascarenhas, Ken Joy, Bernd Hamann, Christoph Garth, Cecilia Aragon, Gunther Weber, and Prabhat, Seeing the Unseeable, SciDAC Review, Pages: 24-33, 2008,

O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, S. V. E. Keränen, C. C. Fowlkes, C. L. Luengo Hendriks, A. H. DePace, L. Simirenko, M. B. Eisen, M. D. Biggin, H. Hagen, J. Malik, D. W. Knowles and B. Hamann, "PointCloudXplore 2: Visual Exploration of 3D Gene Expression", Visualization of Large and Unstructured Data Sets, edited by C. Garth, H. Hagen, M. Hering-Bertram, (Gesellschaft fuer Informatik (GI): 2008) LBNL 249E,

William T.C. Kramer, John M. Shalf, E. Wes Bethel, D. Agarwal, Michael Banda, John Hules, Juan C. Meza, Leonid Oliker, Horst Simon, David Skinner, Francesca Verdier, Howard Walter, Michael Wehner, and Katherine Yelick, "HPC in 2016: A View Point from NERSC", Proceedings of the Cray User Group Conference, Helsinki, Finland, 2008,

2006

K. Wu, K. Stockinger, A. Shoshani, Wes, "FastBit--Helps Finding the Proverbial Needle in a", 2006, LBNL LBNL-PUB/963,

Luke Gosink, John Shalf, Kurt Stockinger, Wu, Wes Bethel, "HDF5-FastQuery: Accelerating Complex Queries on Datasets using Fast Bitmap Indices", SSDBM 2006, Vienna, Austria, July 2006, IEEE Computer Society Press., 2006, 149--158,

2005

E. Wes Bethel, Scott Campbell, Eli Dart, Lee, Steven A. Smith, Kurt Stockinger, Tierney, Kesheng Wu, "Interactive Analysis of Large Network Data Collections Query-Driven Visualization", 2005,

Kurt Stockinger, John Shalf, Wes Bethel, Wu, "Query-Driven Visualization of Large Data Sets", IEEE Visualization 2005, Minneapolis, MN, October 2005, 2005, 22, doi: 10.1109/VIS.2005.84

2001

Gunther H. Weber, Oliver Kreylos, Terry J. Ligocki, Jonh Shalf, Hans Hagen, Bernd Hamann, Ken I. Joy, Kwan-Liu Ma, High-quality Volume Rendering of Adaptive Mesh Refinement Data, VMV, Pages: 121-128 2001,