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NERSC Staff Publications & Presentations

Prabhat

2013

E. Wes Bethel, Prabhat, Suren Byna, Oliver R\ ubel, K. John Wu, Michael Wehner, “Why High Performance Visual Data Anaytics is Both Relevant and Difficult”, Visualization and Data Analysis, IS\&T/SPIE Electronic Imaging 2013, San Francisco, CA, USA, 2013,

Babak Behzad, Joseph Huchette, Huong Luu, Suren Byna, Yushu Yao, Prabhat, “A Framework for Auto-tuning HDF5 Applications”, HPDC, 2013,

Suren Byna, Andrew Uselton, Prabhat, David Knaak, Helen He, “Trillion Particles, 120,000 cores, and 350 TBs: Lessons Learned from a Hero I/O Run on Hopper”, Cray User Group Meeting, 2013,

Wei-Chen Chen, George Ostrouchov, Dave Pugmire, Prabhat, Michael Wehner, “Exploring multivariate relationships in Large Spatial Data with Parallel Model-Based Clustering and Scalable Graphics”, Technometrics, 2013,

Daithi Stone, Chris Paciorek, Prabhat, Pardeep Pall, Michael Wehner, “Inferring the anthropogenic contribution to local temperature extremes”, PNAS, 2013, 110 (7),

Dean N. Williams, Timo Bremer, Charles Doutriaux, John Patchett, Galen Shipman, Blake Haugen, Ross Miller, Brian Smith, Chad Steed, E. Wes Bethel, Hank Childs, Harinarayan Krishnan, Prabhat, Michael Wehner, Claudio T. Silva, Emanuele Santos, David Koop, Tommy Ellqvist, Huy T. Vo, Jorge Poco, Berk Geveci, Aashish Chaudhary, Andrew Bauer, Alexander Pletzer, Dave Kindig, Gerald L. Potter, Thomas P. Maxwell, “The Ultra-scale Visualization Climate Data Analysis Tools: Data Analysis and Visualization for Geoscience Data”, IEEE Special Issue: Cutting-Edge Research in Visualization, 2013,

Prabhat, William D. Collins, Michael Wehner, “Extreme-Scale Climate Analytics”, Google Regional PhD Summit, 2013,

Prabhat, William D. Collins, Michael Wehner, Suren Byna, Chris Paciorek, “Big Data Challenges in Climate Science”, Berkeley Atmospheric Science Symposium, 2013,

Prabhat, Pattern Detection for Large Climate Datasets, Climate 2013, 2013,

Prabhat, Data Formats, Data Models and Parallel I/O, CRD Division Review, 2013,

2012

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 1, 2012, LBNL 5767E

Erin LeDell, Prabhat, Dmitry Yu Zubarev, Brian Austin, Jr. William A. Lester, “Classification of Nodal Pockets in Many-Electron Wave Functions via Machine Learning”, Journal of Mathematical Chemistry, January 1, 2012, 50:2043,

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

Allen R. Sanderson, Brad Whitlock, Oliver R\ ubel, Hank Childs, Gunther H. Weber, Prabhat, Kesheng Wu, “A System for Query Based Analysis and Visualization”, Third International EuroVis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, 2012, 25--29, LBNL 5507E

Surendra Byna, Jerry Chou, Oliver R\ ubel, Prabhat, Homa Karimabadi, William S. Daughton, Vadim Roytershteyn, E. Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Andrew Uselton, Kesheng Wu, “Parallel I/O, analysis, and visualization of a trillion particle simulation”, SC 12, Los Alamitos, CA, USA, IEEE Computer Society Press, 2012, 59:1--59:1,

Michael Wehner, Surendra Byna, Prabhat, Thomas Yopes, John Wu, “Atmospheric Rivers in the CMIP3/5 Historical and Projection Simulations”, World Climate Research Programme (WCRP) Workshop on CMIP5 Model Analysis, 2012,

E. Wes Bethel, Surendra Byna, Jerry Chou, Estelle Cormier-Michel, Cameron G. R. Geddes, Mark Howison, Fuyu Li, Prabhat, Ji Qiang, Oliver R\ ubel, Robert D. Ryne, Michael Wehner, Kesheng Wu, “Big Data Analysis and Visualization: What Do LINACS and Tropical Storms Have In Common?”, 11th International Computational Accelerator Physics Conference, ICAP 2012, Rostock-Warnem\ unde, Germany, 2012,

Babak Behzad, Joseph Huchette, Huong Luu, Suren Byna, Yushu Yao, Prabhat, “Auto-Tuning of Parallel I/O Parameters for HDF5 Applications”, SC, 2012,

Surendra Byna, Jerry Chou, Oliver R\ ubel, Prabhat, Homa Karimabadi, William S. Daughton, Vadim Roytershteyn, E. Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Andrew Uselton, Kesheng Wu, “Parallel Data, Analysis, and Visualization of a Trillion Particles”, XLDB, 2012,

E. Wes Bethel, Rob Ross, Wei-Ken Liao, Prabhat, Karen Schuchardt, Peer-Timo Bremer, Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, John Patchett, Han-Wei Shen, David Pugmire, Dean Williams, “Recent Advances in Visual Data Exploration and Analysis of Climate Data”, SciDAC 3 Principal Investigator Meeting, 2012,

Oliver Ruebel, Cameron Geddes, Min Chen, Estelle Cormier, Ji Qiang, Rob Ryne, Jean-Luc Vey, David Grote, Jerry Chou, Kesheng Wu, Mark Howison, Prabhat, Brian Austin, Arie Shoshani, E. Wes Bethel, “Scalable Data Management, Analysis and Visualization of Particle Accelerator Simulation Data”, SciDAC 3 Principal Investigator Meeting, 2012,

Prabhat, Suren Byna, Kesheng Wu, Jerry Chou, Mark Howison, Joey Huchette, Wes Bethel, Quincey Koziol, Mohammad Chaarawi, Ruth Aydt, Babak Behzad, Huong Luu, Karen Schuchardt, Bruce Palmer, “Updates from the ExaHDF5 project: Trillion particle run, Auto-Tuning and the Virtual Object Layer”, DOE Exascale Research Conference, 2012,

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, J\ org Meyer, Prabhat, Oliver R\ ubel, Daniela Ushizima, Gunther Weber, “Towards Exascale: High Performance Visualization and Analytics -- Project Status Report”, 2012,

Oliver Rubel, Wes Bethel, Prabhat, Kesheng Wu, “Query Driven Visualization and Analysis”, High Performance Visualization: Enabling Extreme-Scale Scientific Insight, (CRC Press: 2012)

Prabhat, 13TB, 80,000 cores and TECA: The search for extreme events in climate datasets, American Geophysical Union Meeting, 2012,

Mehmet Balman, Eric Pouyoul, Yushu Yao, Loring E. Wes Bethel, Prabhat, John Shalf, Alex Sim, Brian L. Tierney, “Experiences with 100G Network Applications”, Proceedings of the 5th International Workshop on Data Intensive and Distributed Computing (DIDC 2012), Delft, Netherlands, 2012,

Prabhat, Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, E. Wes Bethel, “TECA: A Parallel Toolkit for Extreme Climate Analysis”, Third Worskhop on Data Mining in Earth System Science (DMESS 2012) at the International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, 2012,

Michael F. Wehner, Prabhat, Surendra Byna, Fuyu Li, Erin LeDell, Thomas Yopes, Gunther Weber, Wes Bethel, and William D. Collins, TECA, 13TB, 80,000 Processors: Or: Characterizing Extreme Weather in a Changing Climate, Second Workshop on Understanding Climate Change from Data, 2012,

Michael Wehner, Kevin Reed, Prabhat, Surendra Byna, William D. Collins, Fuyu Liand Travis O Brien, Julio Bacmeister, Andrew Gettelman, High Resolution CAM5.1 Simulations, 14th International Specialist Meeting on the Next Generation Models of Climate and Sustainability for Advanced High Performance Computing Facilities, 2012,

Wei-Chen Chen, George Ostrouchov, David Pugmire, Prabhat, Michael Wehner, Model Based Clustering Analysis of Large Climate Simulation Datasets, Joint Statistical Meeting, 2012,

2011

R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, G. R. Geddes, W. Leemans, Prabhat X. Li, J. Qiang, R\ ubel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon, 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, 2011,

Michael Philpott, Prabhat, Yoshiyuki Kawazoe, “Magnetism and Bonding in Graphene Nanodots with H modified Edge and Apex”, J. Chem Physics, 2011, 135,

Richard Martin, Prabhat, David Donofrio, Maciek Haranczyk, “Accelerating Analysis of void spaces in porous materials on multicore and GPU platforms”, International Journal of High Performance Computing Applications, 2011,

Surendra Byna, Prabhat, Michael F. Wehner, Kesheng John Wu, “Detecting atmospheric rivers in large climate datasets”, PDAC 11, New York, NY, USA, ACM, 2011, 7--14,

Wei Zhuo, Prabhat, Chris Paciorek, Cari Kaufman, “Distributed Kriging Analysis for Large Spatial Data”, ICDM 11, 2011,

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, 2011,

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

Prabhat, “ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance”, DOE/ASCR Exascale kickoff meeting, 2011,

Jerry Chou, Kesheng Wu, Prabhat, “FastQuery: A Parallel Indexing System for Scientific Data”, CLUSTER 11, Washington, DC, USA, IEEE Computer Society, 2011, 455--464,

Jerry Chou, Kesheng Wu, Prabhat, “FastQuery: A general Index and Query system for scientific data”, Scientific and Statistical Database Management Conference, 2011,

Richard Martin, Prabhat, Maciek Haranczyk, James Sethian, “PDE-based analysis of void space of porous materials on multicore CPUs”, Manycore and Accelerator-based High-performance Scientific Computing, 2011,

Richard Martin, Thomas Willems, Chris Rycroft, Prabhat, Michael Kazi, Maciek Haranczyk, “High Throughput structure analysis and descriptor generation for crystalline porous materialsi”, International Conference on Chemical Structures, 2011,

Prabhat, Scientific Visualization 101, LBL Open House, 2011,

Prabhat, Pattern Detection and Extreme Value Analysis for Climate Data, American Geophysical Union Meeting, 2011,

Prabhat, Visualization and Analysis of Global Cloud Resolving Models, Geophysical Fluid Dynamics Lab, 2011,

2010

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, Kesheng Wu, “Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-Dimensional Scientific Data”, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010,

      

H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. Weber, E. W. Bethel, “Extreme Scaling of Production Visualization Software on Diverse Architectures”, Computer Graphics and Applications, May 2010, 30 (3):22 - 31,

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rübel, Gunther Weber, Bernard Hamann, Peter Messmer, and Hans Hagen, “Automated Detection and Analysis of Particle Beams in Laser-Plasma Accelerator Simulations”, In-Tech, ( 2010) Pages: 367 - 389

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, January 1, 2010,

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), 2010, 429:329–334,

Prabhat, Scientific Visualization, LBL Open House, 2010,

Tina Zhuo, Prabhat, Chris Paciorek, Cari Kaufman, “Distributed Likelihoods Computation for Large Spatial Data”, SuperComputing, 2010,

Prabhat, Visualization and Analysis of Climate data, LBL Earth Sciences Division Seminar, 2010,

2009

Oliver R\ ubel, Cameron G. R. Geddes, Estelle Cormier-Michel Kesheng Wu, Prabhat, Gunther H. Weber, Daniela M. Ushizima, Peter Messmer, Hans Hagen, Bernd Hamann, Wes Bethel, “Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data”, IOP Computational Science \& Discovery, ( 2009)

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. Kr\ uger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. R\ ubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu., “Occam s Razor and Petascale Visual Data Analysis”, Journal of Physics Conference Series, Proceedings of SciDAC 2009, 2009, 180:012084,

2008

Oliver R\ ubel, Prabhat, Kesheng Wu, Hank Childs, Jeremy Meredith, Cameron G. R. Geddes, Estelle Cormier-Michel, Sean Ahern, Gunther H. weber, Peter Messmer, Hans Hagen, Bernd Hamann, E. Wes Bethel, “High Performance Multivariate Visual Data Exploration for Extemely Large Data”, SuperComputing 2008 (SC08), Austin, Texas, USA, 2008,

1969

Maciej Haranczyk, Richard Martin, Prabhat, James Sethian, “Computational Approaches for the High-Throughput Analysis of Porous materials for Energy related applications”, SciDAC 2011, 1969,

Prabhat, Dmitry Zubarev, W.A. Lester, “Statistical Exploration of Electronic Structure of Molecules from Quantum Monte Carlo Simulations”, 1969,

Jerry Chou, Kesheng Wu, Prabhat, “Design of FastQuery: how to generalize Indexing and Querying systems for scientific data”, 1969,

Matthew Andrews

2011

J. Hick, M. Andrews, Leveraging the Business Value of Tape, FujiFilm Executive IT Summit 2011, June 9, 2011,

Describes how tape is used in the HPSS Archive and HPSS Backup systems at NERSC.  Includes some examples of our organizations tape policies, our roadmap to Exascale and an example of tape in the Exascale Era, our observed tape reliability, and an overview of our locally developed Parallel Incremental Backup System (PIBS) which performs backups of our NGF file system.

2010

Neal Master, Matthew Andrews, Jason Hick, Shane Canon, Nicholas J. Wright, “Performance Analysis of Commodity and Enterprise Class Flash Devices”, Petascale Data Storage Workshop (PDSW), November 2010,

Katie Antypas

2013

Zhengji Zhao, Katie Antypas, Nicholas J Wright, “Effects of Hyper-Threading on the NERSC workload on Edison”, 2013 Cray User Group Meeting, May 9, 2013,

Katie Antypas, Best Practices for Reading and Writing Data on HPC Systems, NUG Meeting 2013, February 14, 2013,

Katie Antypas, NERSC-8 Project, NUG Meeting, February 12, 2013,

NERSC-8 Project Overview

2012

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, “Shared Library Performance on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, “Cray Cluster Compatibility Mode on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, Germany., May 1, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, Cray Cluster Compatibility Mode on Hopper, A talk in the Cray User Group meeting, April 29-May-3, 2012, Stuttgart, German., May 1, 2012,

Yun (Helen) He and Katie Antypas, “Running Large Jobs on a Cray XE6 System”, Cray User Group 2012 Meeting, Stuttgart, Germany, April 30, 2012,

A.C. Uselton, K.B. Antypas, D. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, CUG Proceedings, Edinburgh, Scotland, March 1, 2012,

2011

K. Antypas, Parallel I/O From a User's Perspective, HPC Advisory Council, December 6, 2011,

Zhengji Zhao, Mike Davis, Katie Antypas, Rei Lee and Tina Butler, Shared Library Performance on Hopper, Oct. 26, 2011, Cray Quarterly Meeting at St Paul, MN, October 26, 2011,

Yun (Helen) He and Katie Antypas, Mysterious Error Messages on Hopper, NERSC/Cray Quarterly Meeting, July 25, 2011,

K. Antypas, Y. He, “Transitioning Users from the Franklin XT4 System to the Hopper XE6 System”, Cray User Group 2011 Procceedings, Fairbanks, Alaska, May 2011,

The Hopper XE6 system, NERSC’s first peta-flop system with over 153,000 cores has increased the computing hours available to the Department of Energy’s Office of Science users by more than a factor of 4. As NERSC users transition from the Franklin XT4 system with 4 cores per node to the Hopper XE6 system with 24 cores per node, they have had to adapt to a lower amount of memory per core and on- node I/O performance which does not scale up linearly with the number of cores per node. This paper will discuss Hopper’s usage during the “early user period” and examine the practical implications of running on a system with 24 cores per node, exploring advanced aprun and memory affinity options for typical NERSC applications as well as strategies to improve I/O performance.

K. Antypas, The Hopper XE6 System: Delivering High End Computing to the Nation’s Science and Research Community, Cray Quarterly Review, April 1, 2011,

A. Dubey, K. Antypas, C. Daley, “Parallel algorithms for moving Lagrangian data on block structured Eulerian meshes”, Parallel Computing, 2011, 37:101--113,

2010

K. Antypas, Introduction to Parallel I/O, ASTROSIM 2010 Workshop, July 19, 2010,

A. Uselton, K. Antypas, D. M. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, Proceedings of the 2010 Cray User Group Meeting, Edinburgh, Scotland, Edinburgh, Scotland, May 24, 2010,

2009

K. Antypas, NERSC: Delivering High End Scientific Computing to the Nation's Research Community, November 5, 2009,

A. Dubey, K. Antypas, M.K. Ganapathy, L.B. Reid, K.M. Riley, D. Sheeler, A. Siegel, K. Weide, “Extensible Component Based Architecture for FLASH: A Massively Parallel, Multiphysics Simulation Code”, Parallel Computing, July 1, 2009, 35 (10-1:512-522,

K. Antypas and A. Uselton, “MPI-I/O on Franklin XT4 System at NERSC”, CUG Proceedings, Atlanta, CA, May 28, 2009,

2008

H. Shan, K. Antypas, J.Shalf., “Characterizing and Predicting the I/O Performance of HPC Applications Using a Parameterized Synthetic Benchmark.”, Supercomputing, Reno, NV, November 17, 2008,

Antypas, K., Shalf, J., Wasserman, H., “NERSC‐6 Workload Analysis and Benchmark Selection Process”, LBNL Technical Report, August 13, 2008, LBNL 1014E

Science drivers for NERSC-6

R. Fisher, S. Abarzhi, K. Antypas, S. M. Asida, A. C. Calder, F. Cattaneo, P. Constantin, A. Dubey, I. Foster, J. B. Gallagher, M. K. Ganapathy, C.C. Glendenin, L. Kadano, D.Q. Lamb, S. Needham, M. Papka, T. Plewa, L.B. Reid, P. Rich, K. Riley, and D. Sheeler., “Tera-scale Turbulence Computation on BG/L Using the FLASH3 Code”, IBM Journal of Research and Development., March 1, 2008, Vol 52 (:127-136,

K. Antypas, J. Shalf, H. Wasserman, “NERSC-6 Workload Analysis and Benchmark Selection Process”, January 1, 2008,

John Shalf, Honzhang Shan, Katie Antypas, I/O Requirements for HPC Applications, talk, January 1, 2008,

J. Shalf, K. Antypas, H.J. Wasserman, Recent Workload Characterization Activities at NERSC, Santa Fe Workshop, January 1, 2008,

2006

A. C. Calder, N. T. Taylor, K. Antypas, and D. Sheeler, “A Case Study of Verifying and Validating an Astrophysical Simulation Code”, Astronomical Society of the Pacific, March 26, 2006, 119,

K.B. Antypas, A. C. Calder, A. Dubey, J. B. Gallagher, J. Joshi, D. Q. Lamb, T. Linde, E. Lusk, O. E. B. Messer, A. Mignone, H. Pan, M. Papka, F. Peng, T. Plewa, P. M. Ricker, K. Riley, D. Sheeler, A. Siegel, N. Taylor, J. W. Truran, N. Vladimirova, G. Weirs, D. Yu, Z. Zhang., “FLASH: Applications and Future.”, Parallel Computational Fluid Dynamics 2005: Theory and Applications, edited by A. Deane, G. Brenner, A. Ecer, D. R. Emerson, j. McDonough, J. Periaux, N. Satofuka, D. Tromeur-Dervout., January 1, 2006, 325,

Brian Austin

2013

Hongzhang Shan, Brian Austin, Wibe De Jong, Leonid Oliker, Nicholas Wright, Edoardo Apra, “Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms”, SC'13, November 11, 2013,

Brian Austin, Matthew Cordery, Harvey Wasserman, Nicholas J. Wright, “Performance Measurements of the NERSC Cray Cascade System”, 2013 Cray User Group Meeting, May 9, 2013,

Brian Austin, NERSC, “Characterization of the Cray Aries Network”, May 6, 2013,

2012

Hongzhang Shan, Brian Austin, Nicholas Wright, Erich Strohmaier, John Shalf, Katherine Yelick, “Accelerating Applications at Scale Using One-Sided Communication”, The 6th Conference on Partitioned Global Address Programming Models, Santa Barbara, CA, October 10, 2012,

M. Reinsch, B. Austin, J. Corlett, L. Doolittle, P. Emma, G. Penn, D. Prosnitz, J. Qiang, A. Sessler, M. Venturini, J. Wurtele, “Machine Parameter Studies for and FEL Facility using STAFF”, Proceedings of IPAC2012, New Orleans, Louisiana, USA, May 20, 2012, 1768,

D.Y. Zubarev, B.M. Austin, W.A. Lester Jr, “Practical Aspects of Quantum Monte Carlo for the Electronic Structure of Molecules”, Practical Aspects of Computational Chemistry I: An Overview of the Last Two Decades and Current Trends, January 1, 2012, 255,

D.Y. Zubarev, B.M. Austin, W.A. Lester Jr, “Quantum Monte Carlo for the x-ray absorption spectrum of pyrrole at the nitrogen K-edge”, The Journal of chemical physics, January 1, 2012, 136:144301,

Erin LeDell, Prabhat, Dmitry Yu Zubarev, Brian Austin, Jr. William A. Lester, “Classification of Nodal Pockets in Many-Electron Wave Functions via Machine Learning”, Journal of Mathematical Chemistry, January 1, 2012, 50:2043,

Oliver Ruebel, Cameron Geddes, Min Chen, Estelle Cormier, Ji Qiang, Rob Ryne, Jean-Luc Vey, David Grote, Jerry Chou, Kesheng Wu, Mark Howison, Prabhat, Brian Austin, Arie Shoshani, E. Wes Bethel, “Scalable Data Management, Analysis and Visualization of Particle Accelerator Simulation Data”, SciDAC 3 Principal Investigator Meeting, 2012,

2011

J.N. Corlett, B. Austin, K.M. Baptiste, J.M. Byrd, P. Denes, R. Donahue, L. Doolittle, R.W. Falcone, D. Filippetto, S. Fournier, D. Li, H.A. Padmore, C. Papadopoulos, C. Pappas, G. Penn, M. Placidi, S. Prestemon, D. Prosnitz, J. Qiang, A. Ratti, M. Reinsch, F. Sannibale, R. Schlueter, R.W. Schoenlein, J.W. Staples, T. Vecchione, M. Venturini, R. Wells, R. Wilcox, J. Wurtele, A. Charman, E. Kur, A.A. Zholents, “A Next Generation Light Source Facility at LBNL”, PAC 11 Conference Proceedings, January 1, 2011,

Brian Austin, Ji Qiang, Jonathan Wurtele, Alice Koniges, “Influences of architecture and threading on the MPI communication strategies in an accelerator simulation code.”, SciDAC 2011, Denver, CO, 2011,

Jerry Chou, Mark Howison, Brian Austin, Kesheng Wu, Ji Qiang E. Wes Bethel, Arie Shoshani, Oliver R\ ubel, Prabhat, Rob D. Ryne, “Parallel Index and Query for Large Scale Data Analysis”, SC 11, Seattle, WA, USA, January 1, 2011, 30:1--30:1,

B.M. Austin, D.Y. Zubarev, WA Lester, “Quantum Monte Carlo and Related Approaches.”, Chemical Reviews, January 1, 2011,

Matthias Reinsch, Brian Austin, John Corlett, Lawrence Doolittle, Gregory Penn, Donald Prosnitz, Ji Qiang, Andrew Sessler, Marco Menturini, Jonathan Wurtele, “System Trade Analysis for an FEL Facility”, Free Electron Laser Conference FEL 2011, Shanghai, China, January 1, 2011,

2010

Jinhua Wang, Dominik Domin, Brian Austin, Dmitry Yu, Jarrod McClean, Michael Frenklach, Tian Cui, Jr. Lester, “A Diffusion Monte Carlo Study of the O-H Bond Dissociation of Phenol”, J. Phys. Chem. A, January 1, 2010, 114:9832,

William A. Lester Brian Austin, “Fixed-Node Correlation Function Diffusion Monte Carlo: an approach to Fermi excited states”, Bulletin of the American Physical Society, January 1, 2010,

Naoto Umezawa, Brian Austin, “Self-interaction-free nonlocal correlation energy functional associated with a Jastrow function”, Bulletin of the American Physical Society, January 1, 2010, 55,

2009

Naoto Umezawa, Brian Austin, Jr William A. Lester, Effective one-body potential fitted for many-body interactions associated with a Jastrow function: application to the quantum Monte Carlo calculations, Bulletin of the American Physical Society, January 1, 2009,

2006

B. Austin, A. Aspuru-Guzik, R. Salomon-Ferrer, Jr. W.A. Lester, “Linear-Scaling Evaluation of the Local Energy in Quantum Monte Carlo”, Advances in Quantum Monte Carlo, American Chemical Society, January 1, 2006,

Alex Sodt, Greg J. O. Beran, Yousung Jung, Brian Austin, Martin Head-Gordon, “A Fast Implementation of Perfect Pairing and Imperfect Pairing Using the Resolution of the Identity Approximation”, Journal of Chemical Theory and Computation, January 1, 2006, 2:300-305,

2005

Gregory J. O. Beran, Brian Austin, Alex Sodt, Martin Head-Gordon, “Unrestricted Perfect Pairing: The Simplest Wave-Function-Based Model Chemistry beyond Mean Field”, The Journal of Physical Chemistry A, January 1, 2005, 109:9183,

A. Aspuru--Guzik, R. Salom\ on--Ferrer, B. Austin, R. Perusqu\ \ia--Flores, M.A. Griffin, R.A. Oliva, D. Skinner, D. Domin, W.A. Lester Jr, “Zori 1.0: A parallel quantum Monte Carlo electronic structure package”, Journal of Computational Chemistry, January 1, 2005, 26:856--862,

A. Aspuru-Guzik, R. Salomon-Ferrer, B. Austin, Jr. Lester, “A sparse algorithm for the evaluation of the local energy in quantum Monte Carlo”, J. Comp. Chem., January 1, 2005, 26:708,

Clayton L. Bagwell, Jr.

2013

Clayton Bagwell, How to Submit a 2014 ERCAP Request, September 16, 2013,

Video presentation and accompanying PowerPoint slides on "How to Submit a 2014 ERCAP Request".

2012

Clayton Bagwell, How to Submit an ERCAP Request, September 6, 2012,

David Bailey

2009

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, “Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, 2009 J. Phys.: Conf. Ser. 180 012079, July 1, 2009,

Juan Meza, Scott Campbell, David Bailey, Mathematical and Statistical Opportunities in Cyber Security, arXiv preprint arXiv:0904.1616, 2009,

2008

Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, David Bailey,, “Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, An award winning paper (ACM Gordon Bell Prize for algorithm innovation in SC08), Proceedings of the 2008 ACM/IEEE conference on Supercomputing, Article No. 65 (2008)., November 20, 2008,

Sam Williams, Kaushik Datta, Jonathan Carter, Leonid Oliker, John Shalf, Katherine Yelick, David Bailey, “PERI - Auto-tuning Memory Intensive Kernels for Multicore”, SciDAC: Scientific Discovery Through Advanced Computing, Journal of Physics: Conference Series, January 1, 2008,

2007

John Shalf, Shoaib Kamil, David Bailey, Erich Strohmaier, Power Efficiency and the Top500, talk, January 1, 2007,

2006

John Shalf, David Bailey, Top500 Power Efficiency, talk, January 1, 2006,

Nicholas Balthaser

2014

Nicholas Balthaser, Lisa Gerhardt, NERSC Archival Storage: Best Practices, Joint Facilities User Forum on Data-Intensive Computing, June 18, 2014,

Nick Balthaser, NERSC; Lisa Gerhardt, NERSC, Introduction to NERSC Archival Storage: HPSS, February 3, 2014,

2013

N. Balthaser, GlobusOnline/HPSS Live Demo, HUF 2013, November 5, 2013,

Live demonstration using the GlobusOnline data transfer software to store files to the NERSC archive for 2013 HPSS Users Forum meeting.

N. Balthaser, LBNL/NERSC Site Report: HPSS in Production, HUF 2013, November 5, 2013,

Overview of HPSS infrastructure and practices at LBNL/NERSC for 2013 HPSS Users Forum meeting.

N. Balthaser, W. Hurlbert, T10KC Technology in Production, May 9, 2013,

Report to 2012  Large Tape User Group meeting regarding our production statistics and experiences using the Oracle T10000C tape drive.

2012

N. Balthaser, J. Hick, W. Hurlbert, StorageTek Tape Analytics: Pre-Release Evaluation at LBNL, LTUG 2012, April 25, 2012,

A report to the Large Tape Users Group (LTUG) annual conference on a pre-release evaluation of the new software product, StorageTek Tape Analytics (STA).  We provide a user's perspective on what we found useful, some suggestions for improvement, and some key new features that would enhance the product.

2011

N. Balthaser, D. Hazen, “HSI Best Practices for NERSC Users”, May 2, 2011, LBNL 4745E

 

In this paper we explain how to obtain and install HSI, create a NERSC authentication token, and transfer data to and from the system. Additionally we describe methods to optimize data transfers and avoid common pitfalls that can degrade data transfers and storage system performance.

 

Jeffrey Broughton

2014

Jeff Broughton, NERSC, NERSC Update for NUG2014, February 6, 2014,

Tina Butler

2012

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, “Shared Library Performance on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

2011

Zhengji Zhao, Mike Davis, Katie Antypas, Rei Lee and Tina Butler, Shared Library Performance on Hopper, Oct. 26, 2011, Cray Quarterly Meeting at St Paul, MN, October 26, 2011,

David Camp

2013

David Camp, Hari Krishnan, David Pugmire, Christoph Garth, Ian Johnson, E. Wes Bethel, Kenneth I. Joy, 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,

2012

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 31, 2012) Pages: 357-371

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 31, 2012)

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 1, 2012,

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 1, 2012, LBNL 5767E

2011

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 1, 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, October 1, 2011,

Scott Campbell

2012

Scott Campbell, Jason Lee, “Prototyping a 100G Monitoring System”, 20th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2012), February 12, 2012,

The finalization of the 100 Gbps Ethernet Specification has been a tremendous increase in these rates arriving into data centers creating the need to perform security monitoring at 100 Gbps no longer simply an academic exercise. We show that by leveraging the ‘heavy tail flow effect’ on the IDS infrastructure, it is possible to perform security analysis at such speeds within the HPC environment. Additionally, we examine the nature of current traffic characteristics, how to scale an IDS infrastructure to 100Gbps.

2011

Scott Campbell, Jason Lee, “Intrusion Detection at 100G”, The International Conference for High Performance Computing, Networking, Storage, and Analysis, November 14, 2011,

Driven by the growing data transfer needs of the scientific community and the standardization of the 100 Gbps Ethernet Specification, 100 Gbps is now becoming a reality for many HPC sites. This tenfold increase in bandwidth creates a number of significant technical challenges. We show that by using the heavy tail flow effect as a filter, it should be possible to perform active IDS analysis at this traffic rate using a cluster of commodity systems driven by a dedicated load balancing mechanism. Additionally, we examine the nature of current network traffic characteristics applying them to 100Gpbs speeds

Lavanya Ramakrishnan, Piotr T. Zbiegel, Scott Campbell, Rick Bradshaw, Richard Shane Canon, Susan Coghlan, Iwona Sakrejda, Narayan Desai, Tina Declerck, Anping Liu, “Magellan: Experiences from a Science Cloud”, Proceedings of the 2nd International Workshop on Scientific Cloud Computing, ACM ScienceCloud '11, Boulder, Colorado, and New York, NY, 2011, 49 - 58,

Scott Campbell, Steve Chan and Jason Lee, “Detection of Fast Flux Service Networks”, Australasian Information Security Conference 2011, January 17, 2011,

Fast Flux Service Networks (FFSN) utilize high availability server techniques for malware distribution. FFSNs are similar to commercial content distribution networks (CDN), such as Akamai, in terms of size, scope, and business model, serving as an outsourced content delivery service for clients.  Using an analysis of DNS traffic, we derive a sequential hypothesis testing algorithm based entirely on traffic characteristics and dynamic white listing to provide real time detection of FFDNs in live traffic.  We improve on existing work, providing faster and more accurate detection of FFSNs. We also identify a category of hosts not addressed in previous detectors - Open Content Distribution Networks (OCDN) that share many of the characteristics of FFSNs

Scott Campbell, “Local System Security via SSHD Instrumentation”, USENIX LISA, January 1, 2011,

2009

Scott Campbell, Defense against the cyber dark arts, netWorker, Pages: 40--ff 2009,

Juan Meza, Scott Campbell, David Bailey, Mathematical and Statistical Opportunities in Cyber Security, arXiv preprint arXiv:0904.1616, 2009,

Scott Campbell, The Last Word-Defense Against the Cyber Dark Arts-Don t expect white or black hats or orderly distinction between legal and illegal intent in an attacker s motivation., netWorker: The Craft of Network Computing, Pages: 39 2009,

2006

E. Wes Bethel, Scott Campbell, Eli Dart, Jason Lee, Steven A. Smith, Kurt Stockinger, Brian Tierney, Kesheng Wu, “Interactive Analysis of Large Network Data Collections Using Query-Driven Visualization”, DOE Report, September 26, 2006, LBNL 59166

Realizing operational analytics solutions where large and complex data must be analyzed in a time-critical fashion entails integrating many different types of technology. Considering the extreme scale of contemporary datasets, one significant challenge is to reduce the duty cycle in the analytics discourse process. This paper focuses on an interdisciplinary combination of scientific data management and visualization/analysistechnologies targeted at reducing the duty cycle in hypothesis testing and knowledge discovery. We present an application of such a combination in the problem domain of network traffic dataanalysis. Our performance experiment results, including both serial and parallel scalability tests, show that the combination can dramatically decrease the analytics duty cycle for this particular application. The combination is effectively applied to the analysis of network traffic data to detect slow and distributed scans, which is a difficult-to-detect form of cyberattack. Our approach is sufficiently general to be applied to a diverse set of data understanding problems as well as used in conjunction with a diverse set of analysis and visualization tools

Stephen Q Lau, Scott Campbell, William T Kramer, Brian L Tierney, Computing protection in open HPC environments, Proceedings of the 2006 ACM/IEEE conference on Supercomputing, Pages: 207 2006,

Kurt Stockinger, E Bethel, Scott Campbell, Eli Dart, Kesheng Wu, Detecting distributed scans using high-performance query-driven visualization, Proceedings of the 2006 ACM/IEEE conference on Supercomputing, Pages: 82 2006,

E Wes Bethel, Scott Campbell, Eli Dart, Kurt Stockinger, Kesheng Wu, Accelerating network traffic analytics using query-driven visualization, Visual Analytics Science And Technology, 2006 IEEE Symposium On, Pages: 115--122 2006,

Scott Campbell, How to think about security failures, Communications of the ACM, Pages: 37--39 2006,

Richard Shane Canon

2014

S. Parete-Koon, B. Caldwell, S. Canon, E. Dart, J. Hick, J. Hill, C. Layton, D. Pelfrey, G. Shipman, D. Skinner, J. Wells, J. Zurawski, “HPC's Pivot to Data”, Conference, May 5, 2014,

 

Computer centers such as NERSC and OLCF have traditionally focused on delivering computational capability that enables breakthrough innovation in a wide range of science domains. Accessing that computational power has required services and tools to move the data from input and output to computation and storage. A pivot to data is occurring in HPC. Data transfer tools and services that were previously peripheral are becoming integral to scientific workflows.  Emerging requirements from high-bandwidth detectors, highthroughput screening techniques, highly concurrent simulations, increased focus on uncertainty quantification, and an emerging open-data policy posture toward published research are among the data-drivers shaping the networks, file systems, databases, and overall HPC environment. In this paper we explain the pivot to data in HPC through user requirements and the changing resources provided by HPC with particular focus on data movement. For WAN data transfers we present the results of a study of network performance between centers

 

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

2013

Jay Srinivasan, Richard Shane Canon, “Evaluation of A Flash Storage Filesystem on the Cray XE-6”, CUG 2013, May 2013,

Flash storage and other solid-state storage technolo-gies are increasingly being considered as a way to address the growing gap between computation and I/O. Flash storage has a number of benefits such as good random read performance and lower power consumption. However, it has a number of challenges too, such as high cost and high-overhead for write operations. There are a number of ways Flash can be integrated into HPC systems. This paper will discuss some of the approaches and show early results for a Flash file system mounted on a Cray XE-6 using high-performance PCI-e based cards. We also discuss some of the gaps and challenges in integrating flash intoHPC systems and potential mitigations as well as new solid state storage technologies and their likely role in the future

David Skinner and Shane Canon, NERSC and High Throughput Computing, February 12, 2013,

You-Wei Cheah, Richard Canon, Plale, Lavanya Ramakrishnan, “Milieu: Lightweight and Configurable Big Data Provenance for Science”, BigData Congress, 2013, 46-53,

2012

Elif Dede, Fadika, Hartog, Govindaraju, Ramakrishnan, Gunter, Shane Richard Canon, “MARISSA: MApReduce Implementation for Streaming Science Applications”, eScience, October 8, 2012, 1-8,

Zacharia Fadika, Madhusudhan Govindaraju, Shane Richard Canon, Lavanya Ramakrishnan, “Evaluating Hadoop for Data-Intensive Scientific Operations”, IEEE Cloud 2012, June 24, 2012,

Emerging sensor networks, more capable instruments, and ever increasing simulation scales are generating data at a rate that exceeds our ability to effectively manage, curate, analyze, and share it. Data-intensive computing is expected to revolutionize the next-generation software stack. Hadoop, an open source implementation of the MapReduce model provides a way for large data volumes to be seamlessly processed through use of large commodity computers. The inherent parallelization, synchronization and fault-tolerance the model offers, makes it ideal for highly-parallel data-intensive applications. MapReduce and Hadoop have traditionally been used for web data processing and only recently been used for scientific applications. There is a limited understanding on the performance characteristics that scientific data intensive applications can obtain from MapReduce and Hadoop. Thus, it is important to evaluate Hadoop specifically for data-intensive scientific operations -- filter, merge and reorder-- to understand its various design considerations and performance trade-offs. In this paper, we evaluate Hadoop for these data operations in the context of High Performance Computing (HPC) environments to understand the impact of the file system, network and programming modes on performance.

Jay Srinivasan, Richard Shane Canon, Lavanya Ramakrishnan, “My Cray can do that? Supporting Diverse Workloads on the Cray XE-6”, CUG 2012, May 2012,

The Cray XE architecture has been optimized to support tightly coupled MPI applications, but there is an in- creasing need to run more diverse workloads in the scientific and technical computing domains. These needs are being driven by trends such as the increasing need to process “Big Data”. In the scientific arena, this is exemplified by the need to analyze data from instruments ranging from sequencers, telescopes, and X-ray light sources. These workloads are typically throughput oriented and often involve complex task dependencies. Can platforms like the Cray XE line play a role here? In this paper, we will describe tools we have developed to support high-throughput workloads and data intensive applications on NERSC’s Hopper system. These tools include a custom task farmer framework, tools to create virtual private clusters on the Cray, and using Cray’s Cluster Compatibility Mode (CCM) to support more diverse workloads. In addition, we will describe our experience with running Hadoop, a popular open-source implementation of MapReduce, on Cray systems. We will present our experiences with this work including successes and challenges. Finally, we will discuss future directions and how the Cray platforms could be further enhanced to support these class of workloads.

Richard Shane Canon, Magellan Project: Clouds for Science?, Coalition for Academic Scientific Computation, February 29, 2012,

This presentation gives a brief overview of the Magellan Project and some of its findings.

2011

Katherine Yelick, Susan Coghlan, Brent Draney, Richard Shane Canon, Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Anping Liu, Scott Campbell, Piotr T. Zbiegiel, Tina Declerck, Paul Rich, “The Magellan Report on Cloud Computing for Science”, U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), December 2011,

Ghoshal, Devarshi and Canon, Richard Shane and Ramakrishnan, Lavanya, “Understanding I/O Performance of Virtualized Cloud Environments”, The Second International Workshop on Data Intensive Computing in the Clouds (DataCloud-SC11), 2011,

We compare the I/O performance using IOR benchmarks on two cloud computing platforms - Amazon and the Magellan cloud testbed.

Richard Shane Canon, Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities, Metagenomics Informatics Challenges Workshop, October 12, 2011,

Lavanya Ramakrishnan & Shane Canon, NERSC, Hadoop and Pig Overview, October 2011,

The MapReduce programming model and its open source implementation Hadoop is gaining traction in the scientific community for addressing the needs of data focused scientific applications. The requirements of these scientific applications are significantly different from the web 2.0 applications that have  traditionally used Hadoop. The tutorial  will provide an overview of Hadoop technologies, discuss some use cases of Hadoop for science and present the programming challenges with using Hadoop for legacy applications. Participants will access the Hadoop system at NERSC for the hands-on component of the tutorial.

Lavanya Ramakrishnan, Richard Shane Canon, Krishna Muriki, Iwona Sakrejda, and Nicholas J. Wright., “Evaluating Interconnect and Virtualization Performance for High Performance Computing”, Proceedings of 2nd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems (PMBS11), 2011,

In this paper we detail benchmarking results that characterize the virtualization overhead and its impact on performance. We also examine the performance of various interconnect technologies with a view to understanding the performance impacts of various choices. Our results show that virtualization can have a significant impact upon performance, with at least a 60% performance penalty. We also show that less capable interconnect technologies can have a significant impact upon performance of typical HPC applications. We also evaluate the performance of the Amazon Cluster compute instance and show that it performs approximately equivalently to a 10G Ethernet cluster at low core counts.

Lavanya Ramakrishnan, Piotr T. Zbiegel, Scott Campbell, Rick Bradshaw, Richard Shane Canon, Susan Coghlan, Iwona Sakrejda, Narayan Desai, Tina Declerck, Anping Liu, “Magellan: Experiences from a Science Cloud”, Proceedings of the 2nd International Workshop on Scientific Cloud Computing, ACM ScienceCloud '11, Boulder, Colorado, and New York, NY, 2011, 49 - 58,

Shane Canon, Debunking Some Common Misconceptions of Science in the Cloud, ScienceCloud 2011, June 29, 2011,

This presentation addressed five common misconceptions of cloud computing including: clouds are simple to use and don’t require system administrators; my job will run immediately in the cloud; clouds are more efficient; clouds allow you to ride Moore’s Law without additional investment; commercial Clouds are much cheaper than operating your own system.

2010

Neal Master, Matthew Andrews, Jason Hick, Shane Canon, Nicholas J. Wright, “Performance Analysis of Commodity and Enterprise Class Flash Devices”, Petascale Data Storage Workshop (PDSW), November 2010,

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

Lavanya Ramakrishnan, R. Jackson, Canon, Cholia, John Shalf, “Defining future platform requirements for e-Science clouds”, SoCC, New York, NY, USA, 2010, 101-106,

Kesheng Wu, Kamesh Madduri, Shane Canon, “Multi-Level Bitmap Indexes for Flash Memory Storage”, IDEAS '10: Proceedings of the Fourteenth International Database Engineering and Applications Symposium, Montreal, QC, Canada, 2010,

2009

Richard Shane Canon, Cosmic Computing: Supporting the Science of the Planck Space Based Telescope, LISA 2009, November 5, 2009,

The scientific community is creating data at an ever-increasing rate. Large-scale experimental devices such as high-energy collider facilities and advanced telescopes generate petabytes of data a year. These immense data streams stretch the limits of the storage systems and of their administrators. The Planck project, a space-based telescope designed to study the Cosmic Microwave Background, is a case in point. Launched in May 2009, the Planck satellite will generate a data stream requiring a network of storage and computational resources to store and analyze the data. This talk will present an overview of the Planck project, including the motivation and mission, the collaboration, and the terrestrial resources supporting it. It will describe the data flow and network of computer resources in detail and will discuss how the various systems are managed. Finally, it will highlight some of the present and future challenges in managing a large-scale data system.

Nick Cardo

2014

Yun (Helen) He and Nick Cardo, Babbage: the MIC Testbed System at NERSC, NERSC Brown Bag, Oakland, CA, April 3, 2014,

2009

James M. Craw, Nicholas P. Cardo, Yun (Helen) He, and Janet M. Lebens, “Post-Mortem of the NERSC Franklin XT Upgrade to CLE 2.1”, Cray User Group Meeting 2009, Atlanta, GA, May 2009,

This paper will discuss the lessons learned of the events leading up to the production deployment of CLE 2.1 and the post install issues experienced in upgrading NERSC's XT4 system called Franklin.

 

James M. Craw, Nicholas P. Cardo, Yun (Helen) He, and Janet M. Lebens, Post-Mortem of the NERSC Franklin XT Upgrade to CLE 2.1, Cray User Group Meeting, May 2009,

2008

Yun (Helen) He, William T.C. Kramer, Jonathan Carter, and Nicholas Cardo, Franklin: User Experiences, CUG User Group Meeting 2008, May 5, 2008,

Yun (Helen) He, William T.C. Kramer, Jonathan Carter, and Nicholas Cardo, “Franklin: User Experiences”, Cray User Group Meetin 2008, May 4, 2008, LBNL 2014E

The newest workhorse of the National Energy Research Scientific Computing Center is a Cray XT4 with 9,736 dual core nodes. This paper summarizes Franklin user experiences from friendly early user period to production period. Selected successful user stories along with top issues affecting user experiences are presented.

 

2003

D. Skinner, N. Cardo, “An Analysis of Node Asymmetries on seaborg. nersc. gov”, January 1, 2003,

Jonathan Carter

2011

Samuel Williams, Oliker, Carter, John Shalf, “Extracting ultra-scale Lattice Boltzmann performance via hierarchical and distributed auto-tuning”, SC, November 1, 2011, 55,

2010

S. Ethier, M. Adams, J. Carter, L. Oliker, “Petascale Parallelization of the Gyrokinetic Toroidal Code”, VECPAR: High Performance Computing for Computational Science, June 2010,

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick, “Auto-Tuning Stencil Computations on Diverse Multicore Architectures”, Scientific Computing with Multicore and Accelerators, edited by Jakub Kurzak, David A. Bader, Jack Dongarra, 2010,

2008

K. Datta, M. Murphy, V. Volkov, S. Williams, J. Carter, L. Oliker, D. Patterson, J. Shalf, K. Yelick, “Stencil computation optimization and auto-tuning on state-of-the-art multicore architectures”, Proceedings of the 2008 ACM/IEEE Conference on High Performance Computing and Networking ("Supercomputing", SC08), November 15, 2008,

Yun (Helen) He, William T.C. Kramer, Jonathan Carter, and Nicholas Cardo, Franklin: User Experiences, CUG User Group Meeting 2008, May 5, 2008,

Yun (Helen) He, William T.C. Kramer, Jonathan Carter, and Nicholas Cardo, “Franklin: User Experiences”, Cray User Group Meetin 2008, May 4, 2008, LBNL 2014E

The newest workhorse of the National Energy Research Scientific Computing Center is a Cray XT4 with 9,736 dual core nodes. This paper summarizes Franklin user experiences from friendly early user period to production period. Selected successful user stories along with top issues affecting user experiences are presented.

 

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, “Scientific Application Performance On Leading Scalar and Vector Supercomputering Platforms”, IJHPCA, January 1, 2008, 22:5-20,

2007

Jonathan Carter, Yun (Helen) He, John Shalf, Hongzhang Shan, Erich Strohmaier, and Harvey Wasserman, “The Performance Effect of Multi-Core on Scientific Applications”, Cray User Group 2007, May 2007, LBNL 62662

The historical trend of increasing single CPU performance has given way to roadmap of increasing core count. The challenge of effectively utilizing these multi- core chips is just starting to be explored by vendors and application developers alike. In this study, we present some performance measurements of several complete scientific applications on single and dual core Cray XT3 and XT4 systems with a view to characterizing the effects of switching to multi-core chips. We consider effects within a node by using applications run at low concurrencies, and also effects on node- interconnect interaction using higher concurrency results. Finally, we construct a simple performance model based on the principle on-chip shared resource—memory bandwidth—and use this to predict the performance of the forthcoming quad-core system.

 

Jonathan Carter, Helen He*, John Shalf, Erich Strohmaier, Hongzhang Shan, and Harvey Wasserman, The Performance Effect of Multi-Core on Scientific Applications, Cray User Group 2007, May 2007,

J. Levesque, J. Larkin, M. Foster, J. Glenski, G. Geissler, S. Whalen, B. Waldecker, J. Carter, D. Skinner, H. He, H. Wasserman, J. Shalf, H. Shan, “Understanding and mitigating multicore performance issues on the AMD opteron architecture”, March 1, 2007, LBNL 62500

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3and XT4systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

 

Leonid Oliker, Andrew Canning, Johnathan Carter, Costin Iancu, Mike Lijewski, Shoaib Kamil, John Shalf, Hongzhang Shan, Erich Strohmaier, Stephane Ethier, Tom Goodale, “Scientific Application Performance on Candidate PetaScale Platforms”, IPDPS, January 1, 2007, 1-12,

2006

Jonathan Carter, Tony Drummond, Parry Husbands, Paul Hargrove, Bill Kramer, Osni Marques, Esmond Ng, Lenny Oliker, John Shalf, David Skinner, Kathy Yelick, “Software Roadmap to Plug and Play Petaflop/s”, Lawrence Berkeley National Laboratory Technical Report, #59999, July 31, 2006,

Jonathan Carter, Leonid Oliker, John Shalf, “Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems”, VECPAR, January 1, 2006, 490-503,

L. Oliker, S. Kamil, A. Canning, J. Carter, C. Iancu, J. Shalf, H. Shan, D. Skinner, E. Strohmaier, T. Goodale, “Application Scalability and Communication Signatures on Leading Supercomputing Platforms”, January 1, 2006,

2005

Horst D. Simon, William T. C. Kramer, David H. Bailey, Michael J. Banda, E. Wes Bethel, Jonathon T. Carter, James M. Craw, William J. Fortney, John A. Hules, Nancy L. Meyer, Juan C. Meza, Esmond G. Ng, Lynn E. Rippe, William C. Saphir, Francesca Verdier, Howard A. Walter, Katherine A. Yelick, “Science-Driven Computing: NERSC’s Plan for 2006–2010”, LBNL Technical Report 57582, 2005,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stephane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Performance evaluation of the SX-6 vector architecture for scientific computations”, Concurrency - Practice and Experience, January 1, 2005, 17:69-93,

2004

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, “Scientific Computations on Modern Parallel Vector Systems”, SC, January 1, 2004, 10,

2003

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stepahane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations”, SC, January 1, 2003, 38,

Steve Chan

2011

Scott Campbell, Steve Chan and Jason Lee, “Detection of Fast Flux Service Networks”, Australasian Information Security Conference 2011, January 17, 2011,

Fast Flux Service Networks (FFSN) utilize high availability server techniques for malware distribution. FFSNs are similar to commercial content distribution networks (CDN), such as Akamai, in terms of size, scope, and business model, serving as an outsourced content delivery service for clients.  Using an analysis of DNS traffic, we derive a sequential hypothesis testing algorithm based entirely on traffic characteristics and dynamic white listing to provide real time detection of FFDNs in live traffic.  We improve on existing work, providing faster and more accurate detection of FFSNs. We also identify a category of hosts not addressed in previous detectors - Open Content Distribution Networks (OCDN) that share many of the characteristics of FFSNs

Henry R. Childs

2013

David Camp, Hari Krishnan, David Pugmire, Christoph Garth, Ian Johnson, E. Wes Bethel, Kenneth I. Joy, 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,

Gunther H. Weber, Hank Childs, Jeremy S. Meredith, “Recent Advances in VisIt: Parallel Crack-free Isosurface Extraction”, Numerical Modeling of Space Plasma Flows: Astronum-2012 (Astronomical Society of the Pacific Conference Series), 2013,

2010

David Camp, Christoph Garth, Hank Childs, David Pugmire, Kenneth Joy, “Streamline Integration using MPI-Hybrid Parallelism on Large Multi-Core Architecture”, IEEE Transactions on Visualization and Computer Graphics, December 7, 2010,

 

M. Howison, E. W. Bethel, H. Childs, “Hybrid Parallelism for Volume Rendering on Large, Multi-Core Systems”, Journal of Physics: Conference Series, Proceedings of SciDAC 2010, Chattanooga TN, July 2010,

 

T. Fogal, H. Childs, S. Shankar, J. Kruger, R. D. Bergeron, P. Hatcher, “Large Data Visualization on Distributed Memory Multi-GPU Clusters”, High Performance Graphics 2010, Saarbruken, Germany, Saarbruken, Germany, June 2010,

 

J. Meredith, H. Childs, “Visualization and Analysis-Oriented Reconstruction of Material Interfaces”, Eurographics/IEEE Symposium on Visualization (EuroVis), Bordeaux, France, June 2010,

 

 



 

 

 

Mark Howison, E. Wes Bethel, and Hank Childs, “MPI-Hybrid Parallelism for Volume Rendering on Large, Multi-Core Systems”, Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (EGPGV’10),, Norrköping, Sweden, May 2, 2010,

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, Kesheng Wu, “Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-Dimensional Scientific Data”, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010,

      

H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. Weber, E. W. Bethel, “Extreme Scaling of Production Visualization Software on Diverse Architectures”, Computer Graphics and Applications, May 2010, 30 (3):22 - 31,

M. Isenberg, P. Lindstrom, H. Childs, “Parallel and Streaming Generation of Ghost Data for Structured Grids”, Computer Graphics and Applications May/June 2010, May 2010, 30 (3):50 - 62,

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), 2010, 429:329–334,

Shreyas Cholia

2014

Fox W., Correa J., Cholia S., Skinner D., Ophus C., “NCEM Hub, A Science Gateway for Electron Microscopy in Materials Science”, LBNL Tech Report on NCEMhub, May 1, 2014,

Electron microscopy (EM) instrumentation is making a detector-driven transition to Big Data. High capability cameras bring new resolving power but also an exponentially increasing demand for bandwidth and data analysis. In practical terms this means that users of advanced microscopes find it increasingly challenging to take data with them and instead need an integrated data processing pipeline. in 2013 NERSC and NCEM staff embarked on a pilot to prototype data services that provide such a pipeline. This tech report details the NCEM Hub pilot as it concluded in May 2014.

Shreyas Cholia, NERSC, Web Portal Opportunities at NERSC, February 3, 2014,

Shreyas Cholia, NERSC, Data Transfer at NERSC, February 3, 2014,

2013

Massimo Di Pierro, James Hetrick, Shreyas Cholia, James Simone, and Carleton DeTar., “The new “Gauge Connection” at NERSC”, 21st International Lattice Data Grid Workshop, December 2013,

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, Benjamin P. Bowen, “OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging”, Analytical Chemistry, 2013, 85 (21), pp 10354–10361, October 2, 2013,

Anubhav Jain, Shyue Ping Ong, Geoffroy Hautier, Wei Chen, William Davidson Richards, Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, Kristin A. Persson, “The Materials Project: A materials genome approach to accelerating materials innovation”, APL Mat. 1, 011002 (2013); http://dx.doi.org/10.1063/1.4812323, July 2013,

Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier, Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent L. Chevrier, Kristin A. Persson, Gerbrand Ceder, “Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis”, Computational Materials Science, Volume 68, February 2013, Pages 314-319, ISSN 0927-0256, 10.1016/j.commatsci.2012.10.028., February 1, 2013,

2012

Dan Gunter, Shreyas Cholia, Anubhav Jain, Michael Kocher, Kristin Persson, Lavanya Ramakrishnan, Shyue Ping Ong, Gerbrand Ceder, “Community Accessible Datastore of High-Throughput Calculations: Experiences from the Materials Project”, 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS) 2012, November 12, 2012,

2011

M. Di Pierro, J. Hetrick, S. Cholia, D. Skinner, “Making QCD Lattice Data Accessible and Organized through Advanced Web Interfaces”, Arxiv preprint arXiv:1112.2193, December 1, 2011, abs/1112,

2010

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

Lavanya Ramakrishnan, R. Jackson, Canon, Cholia, John Shalf, “Defining future platform requirements for e-Science clouds”, SoCC, New York, NY, USA, 2010, 101-106,

S. Cholia, D. Skinner, J. Boverhof, “NEWT: A RESTful service for building High Performance Computing web applications”, Gateway Computing Environments Workshop (GCE), 2010, January 1, 2010, 1--11,

2009

Shreyas Cholia, Hwa-Chun Wendy Lin, “Integrating Grid Services into the Cray XT4 Environment”, Cray Users Group 2009, May 4, 2009,

2008

Massimiliano Pala, Shreyas Cholia, Scott A Rea, Sean W Smith, “Extending PKI Interoperability in Computational Grids”, 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid CCGRID p. 645-650, IJGHPC 1(2): 45-55 (2009), May 30, 2008,

Shreyas Cholia, R. Jefferson Porter, “Publication and Protection of Sensitive Site Information in a Grid Infrastructure”, 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (CCGRID) p. 639-644, IJGHPC 1(2): 56-73 (2009), May 30, 2008,

Matthew Cordery

2013

M. J. Cordery, B. Austin, H. J. Wasserman, C. S. Daley, N. J. Wright, S. D. Hammond, D. Doerfler, “Analysis of Cray XC30 Performance using Trinity-NERSC-8 benchmarks and comparison with Cray XE6 and IBM BG/Q”, SC'13, November 11, 2013,

Brian Austin, Matthew Cordery, Harvey Wasserman, Nicholas J. Wright, “Performance Measurements of the NERSC Cray Cascade System”, 2013 Cray User Group Meeting, May 9, 2013,

1997

Cordery, M.J., G. F. Davies, and I.H. Campbell, “Genesis of flood basalts from eclogite-bearing mantle plumes”, 1997,

1993

Cordery, M.J., J. Phipps Morgan, “Convection and melting at mid-ocean ridges”, Journal of Geophysical Research, 1993,

1992

Cordery, M.J. and J. Phipps Morgan, “Melting and mantle flow at a mid-cean spreading center”, Earth and Planetary Science Letters, 1992,

1989

Von Herzen, R.P., M.J. Cordery, R.S. Detrick, and C. Fang, “Heat flow and the thermal origin of hotspot swells”, Journal of Geophysical Research, 1989,

Joaquin Correa

2014

Wen-Ting Tsai, Ahmed Hassan, Purbasha Sarkar, Joaquin Correa, Zoltan Metlagel, Danielle M. Jorgens, Manfred Auer, “From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data”, August 13, 2014,

The bottleneck for cellular 3D electron microscopy is feature extraction (segmentation) in highly complex 3D density maps. We have developed a set of criteria, which provides guidance regarding which segmentation approach (manual, semi-automated, or automated) is best suited for different data types, thus providing a starting point for effective segmentation.

Correa, J., Skinner D., Auer M., “Integrated tools for next generation bioimaging”, Conference in Medical Image Understanding and Analysis (MIUA) | Royal Holloway, Egham, July 9, 2014,

Correa, J., OME Workshop (ybd), OME Users Meeting | Institut Pasteur, Paris, June 5, 2014,

Correa, J., “Enabling Science from Big Image Data using Cross Cutting Infrastructure”, International Conference on Big Data Science and Computing | Stanford University, May 27, 2014,

Fox W., Correa J., Cholia S., Skinner D., Ophus C., “NCEM Hub, A Science Gateway for Electron Microscopy in Materials Science”, LBNL Tech Report on NCEMhub, May 1, 2014,

Electron microscopy (EM) instrumentation is making a detector-driven transition to Big Data. High capability cameras bring new resolving power but also an exponentially increasing demand for bandwidth and data analysis. In practical terms this means that users of advanced microscopes find it increasingly challenging to take data with them and instead need an integrated data processing pipeline. in 2013 NERSC and NCEM staff embarked on a pilot to prototype data services that provide such a pipeline. This tech report details the NCEM Hub pilot as it concluded in May 2014.

Joaquin Correa, Scalable web-based computational bioimaging solutions at NERSC, CryoEM meeting - SLAC National Accelerator Laboratory | Stanford University, April 17, 2014,

Joaquin Correa, David Skinner, “BIG DATA BIOIMAGING: Advances in Analysis, Integration, and Dissemination”, Keystone Symposia on Molecular and Cellular Biology, March 24, 2014,

A fundamental problem currently for the biological community is to adapt computational solutions known broadly in data-centric science toward the specific challenges of data scaling in bioimaging. In this work we target software solutions fit for these tasks which leverages success in large scale data-centric science outside of bioimaging.

2013

Joaquin Correa, Integrated Tools for NGBI--Lessons Learned and Successful Cases, LBNL Integrated Bioimaging Initiative, September 4, 2013,

 

NextGen Bioimaging (NGBI) requires a reliable and flexible solution for multi-modal, high-throughput and high-performance image processing and analysis. In order to solve this challenge, we have developed an OMERO-based modular and flexible platform that integrates a suite of general-purpose processing software, a set of custom-tailored algorithms, specific bio-imaging applications and NERSC's high performance computing resources and its science gateways.
This under-development platform provides a shared scalable one-stop-shop web-service for producers and consumers of models built on imaging data to refine pixel data into actionable knowledge resources.

 

2012

Michael Joo, Roseann Csencsits, Adam Barnebey, Andrew Tauscher, Ahmed Hassan, Danielle Jorgens, Marcin Zemla, Romy Chartaborky, Gareth Butland, Jennifer He, David Stahl, Nicholas Elliot, Matthew Fields, Manfred Auer, Steven M. Yannone, “Microbial Metal Reduction: Metal Reduction & Structures in Microbes”, ENIGMA: Ecosystems and Networks Integrated with Genes and Molecular Assemblies, 2012,

Jonathan P. Remis, Bernhar Knierim, Monica Lin, Amita Gorur, Mitalee Desai, Manfred Auer, W.J. Costerton, J. Berleman, Trent Northen, D. Wei, B. Van Leer, “Microbial Communities: A Tale of Social Bacteria and Nature's Solution to Biomass Recalcitrance”, 2012,

Jonathan P. Remis, Berhnhard Knierim, Amita Gorur, Ambrose Leung, Danielle M. Jorgens, Mitalee Desai, Monica Lin, David A. Ball, Roseann Csencsits, Jan Liphardt, Bill Consterton, Ken Downing, Phil Hugenholtz, Manfred Auer, “Microbial Communities: The Social Side of Bacteria from Macromolecules to Community Organization”, PCAP - Protein Complex Analysis Project, 2012,

Purbasha Sarkar, Patanjali Varanasi, Lan Sun, Elene Bosneaga, Lina Prak, Bernhard Knierim, Marcin Zemla, Michael Joo, David Larson, Roseann Csencsits, Bahram Parvin, Kenneth H. Downing, Manfred Auer, “BioFuels 2.0: Plant cell walls - Towards rational cell wall engineering”, EBI (Energy BioSciences Institute) and JBEI (Joint BioEnergy Institute), 2012,

James M. Craw

2009

James M. Craw, Nicholas P. Cardo, Yun (Helen) He, and Janet M. Lebens, “Post-Mortem of the NERSC Franklin XT Upgrade to CLE 2.1”, Cray User Group Meeting 2009, Atlanta, GA, May 2009,

This paper will discuss the lessons learned of the events leading up to the production deployment of CLE 2.1 and the post install issues experienced in upgrading NERSC's XT4 system called Franklin.

 

James M. Craw, Nicholas P. Cardo, Yun (Helen) He, and Janet M. Lebens, Post-Mortem of the NERSC Franklin XT Upgrade to CLE 2.1, Cray User Group Meeting, May 2009,

2001

William T. C. Kramer, Wes Bethel, James Craw, Brent Draney, William Fortney, Brent Gorda, William Harris, Nancy Meyer, Esmond Ng, Francesca Verdier, Howard Walter, Tammy Welcome, “NERSC Strategic Implementation Plan 2002-2006”, ”, LBNL Technical Report 5465 Vol. 2, 2001,

Christopher S. Daley

2013

M. J. Cordery, B. Austin, H. J. Wasserman, C. S. Daley, N. J. Wright, S. D. Hammond, D. Doerfler, “Analysis of Cray XC30 Performance using Trinity-NERSC-8 benchmarks and comparison with Cray XE6 and IBM BG/Q”, SC'13, November 11, 2013,

C. Daley, Preparing for Mira: experience with FLASH multiphysics simulations, Mira Community Conference, 2013,

2012

A. Dubey, A. Calder, C. Daley, C., R. Fisher, Jordan, D.Q. Lamb, L.B. Reid, D.M. Townsley, K. Weide, “Pragmatic Optimizations for Best Scientific Utilization of Large Supercomputers”, International Journal of High Performance Computing Applications, 2012,

A. Dubey, C. Daley, J. ZuHone, P. M. Ricker, K. Weide, C. Graziani, “Imposing a Lagrangian Particle Framework on an Eulerian Hydrodynamics Infrastructure in FLASH”, The Astrophysical Journal Supplements, 2012, 201:27,

C. Daley, J. Bachan, S. Couch, A. Dubey, M., B. Gallagher, D. Lee, K. Weide, “Adding shared memory parallelism to FLASH for many-core architectures”, TACC-Intel Highly Parallel Computing Symposium, 2012,

C. Daley, M. Vanella, K. Weide, A. Dubey, E. Balaras, “Optimization of Multigrid Based Elliptic Solver for Large Scale Simulations the FLASH Code”, Concurrency and Computation: Practice and Experience, 2012, 24:2346--2361,

R. Latham, C. Daley, W.K. Liao, K. Gao, R. Ross, A. Dubey, A. Choudhary, “A case study for scientific I/O: improving the FLASH astrophysics code”, Computational Science and Discovery, 2012, 5:015001,

2011

D. Lee, G. Xia, C. Daley, A. Dubey, S., C. Graziani, D.Q. Lamb, K. Weide, “Progress in development of HEDP capabilities in FLASH's Unsplit Staggered Mesh MHD solver”, Astrophysics and Space Science, 2011, 336:157-162,

V. Vishwanath, M. Hereld, M. E. Papka, R. Hudson, G. Jordan, C. Daley, “In Situ Data Analytics and I/O Acceleration of FLASH simulations on leadership-class systems with GLEAN”, SciDAC, Journal of Physics: Conference Series, 2011,

A. Dubey, K. Antypas, C. Daley, “Parallel algorithms for moving Lagrangian data on block structured Eulerian meshes”, Parallel Computing, 2011, 37:101--113,

2010

A. Dubey, C. Daley, K. Weide, “Challenges of Computing with FLASH on Largest HPC Platforms”, AIP Conference Proceedings, 2010, 1281:1773,

2009

B. R. de Supinski, S. Alam, D. H. Bailey, L., C. Daley, A. Dubey, T., D. Gunter, P. D. Hovland, H., K. Karavanic, G. Marin, J., S. Moore, B. Norris, L., C. Olschanowsky, P. C. Roth, M., S. Shende, A. Snavely, Spear, M. Tikir, J. Vetter, P. Worley, N. Wright, “Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team”, Journal of Physics: Conference Series, 2009, 180:012039,

Tina M. Declerck

2013

Richard A. Gerber, Tina Declerck. Zhengji Zhao, Edison Update, February 12, 2013,

Overview and update on the installation and configuration of Edison, NERSC's new Cray XC30 supercomputer.

2011

Lavanya Ramakrishnan, Piotr T. Zbiegel, Scott Campbell, Rick Bradshaw, Richard Shane Canon, Susan Coghlan, Iwona Sakrejda, Narayan Desai, Tina Declerck, Anping Liu, “Magellan: Experiences from a Science Cloud”, Proceedings of the 2nd International Workshop on Scientific Cloud Computing, ACM ScienceCloud '11, Boulder, Colorado, and New York, NY, 2011, 49 - 58,

Jack Deslippe

2014

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

Jack Deslippe, NERSC, Preparing Applications for Future NERSC Architectures, February 6, 2014,

2013

Jack Deslippe, Building Applications on Edison, October 10, 2013,

Jack Deslippe, Georgy Samsonidze, Manish Jain, Marvin L Cohen, Steven G Louie, “Coulomb-hole summations and energies for GW calculations with limited number of empty orbitals: a modified static remainder approach”, Physical Review B (arXiv preprint arXiv:1208.0266), 2013,

Jack Deslippe, Zhengji Zhao, “Comparing Compiler and Library Performance in Material Science Applications on Edison”, Paper. Proceedings of the Cray User Group 2013, 2013,

2012

Megan Bowling, Zhengji Zhao and Jack Deslippe, “The Effects of Compiler Optimizations on Materials Science and Chemistry Applications at NERSC”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Megan Bowling, Zhengji Zhao and Jack Deslippe, The Effects of Compiler Optimizations on Materials Science and Chemistry Applications at NERSC, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Jack Deslippe, Georgy Samsonidze, David Strubbe, Manish Jain, Marvin L. Cohen, Steven G. Louie, “BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials”, Comput. Phys. Comm., 2012,

Johannes Lischner, Jack Deslippe, Manish Jain, Steven G Louie, “First-Principles Calculations of Quasiparticle Excitations of Open-Shell Condensed Matter Systems”, Physical Review Letters, 2012, 109:36406,

Kaihui Liu, Jack Deslippe, Fajun Xiao, Rodrigo B Capaz, Xiaoping Hong, Shaul Aloni, Alex Zettl, Wenlong Wang, Xuedong Bai, Steven G Louie, others, “An atlas of carbon nanotube optical transitions”, Nature Nanotechnology, 2012, 7:325--329,

2011

Georgy Samsonidze, Manish Jain, Jack Deslippe, Marvin L Cohen, Steven G Louie, “Simple Approximate Physical Orbitals for GW Quasiparticle Calculations”, Physical Review Letters, 2011, 107:186404,

David A Siegel, Cheol-Hwan Park, Choongyu Hwang, Jack Deslippe, Alexei V Fedorov, Steven G Louie, Alessandra Lanzara, “Many-body interactions in quasi-freestanding graphene”, Proceedings of the National Academy of Sciences, 2011, 108:11365--113,

Jack Deslippe, Manish Jain, Georgy Samsonidze, Marvin Cohen, Steven Louie, The sc-COHSEX+ GW and the static off-diagonal GW approaches to quasiparticle wavefunctions and energies, Bulletin of the American Physical Society, 2011,

2010

Jack Deslippe, Cheol-Hwan Park, Manish Jain, Steven Louie, First-principles Calculations of the Quasiparticle and Optical Excitations in Metallic Carbon Nanostructures, Bulletin of the American Physical Society, 2010,

2009

Li Yang, Jack Deslippe, Cheol-Hwan Park, Marvin L Cohen, Steven G Louie, “Excitonic effects on the optical response of graphene and bilayer graphene”, Physical review letters, 2009, 103:186802,

Jack Deslippe, Mario Dipoppa, David Prendergast, Marcus VO Moutinho, Rodrigo B Capaz, Steven G Louie, “Electron-Hole Interaction in Carbon Nanotubes: Novel Screening and Exciton Excitation Spectra”, Nano Lett, 2009, 9:1330--1334,

Jack Deslippe, David Prendergast, Steven Louie, Nonlinear Optical Properties of Carbon Nanotubes from First Principles, Bulletin of the American Physical Society, 2009,

2008

Jack Deslippe, Steven G Louie, “Excitons and many-electron effects in the optical response of carbon nanotubes and other one-dimensional nanostructures”, Proceedings of SPIE, the International Society for Optical Engineering, 2008, 68920U--1,

Jack Deslippe, Mario Dipoppa, David Prendergast, Rodrigo Capaz, Steven Louie, Effective One-Dimensional Electron-Hole Interaction in Single-Walled Carbon Nanotubes, Bulletin of the American Physical Society, 2008,

2007

Jack Deslippe, Catalin D Spataru, David Prendergast, Steven G Louie, “Bound excitons in metallic single-walled carbon nanotubes”, Nano letters, 2007, 7:1626--1630,

Feng Wang, David J Cho, Brian Kessler, Jack Deslippe, P James Schuck, Steven G Louie, Alex Zettl, Tony F Heinz, Y Ron Shen, “Observation of excitons in one-dimensional metallic single-walled carbon nanotubes”, Physical review letters, 2007, 99:227401,

Jack Deslippe, David Prendergast, Steven Louie, Electron Self-Energy Corrections to Quasiparticle Excitations in Graphene and Large Diameter Single-Walled Carbon Nanotubes, Bulletin of the American Physical Society, 2007,

2006

Jack Deslippe, Catalin Spataru, Steven Louie, Bound excitons and optical absorption spectra of (10, 10) metallic single-walled carbon nanotubes, Bulletin of the American Physical Society, 2006,

2004

Jack Deslippe, R Tedstrom, Murray S Daw, D Chrzan, T Neeraj, M Mills, “Dynamic scaling in a simple one-dimensional model of dislocation activity”, Philosophical Magazine, 2004, 84:2445--2454,

2003

Jianjun Dong, Jack Deslippe, Otto F Sankey, Emmanuel Soignard, Paul F McMillan, “Theoretical study of the ternary spinel nitride system Si\_ $\$3$\$ N\_ $\$4$\$-Ge\_ $\$3$\$ N\_ $\$4$\$”, Physical Review B, 2003, 67:094104,

Deslippe Jack, Jianjun Dong, First principles calculations of thermodynamical properties of cage-like silicon clathrate materials, APS Meeting Abstracts, Pages: 25002 2003,

David Donofrio

2011

Jens Krueger, Donofrio, Shalf, Mohiyuddin, Williams, Oliker, Franz-Josef Pfreund, “Hardware/software co-design for energy-efficient seismic modeling”, SC, November 1, 2011, 73,

Keren Bergman, Hendry, Hargrove, Shalf, Jacob, Scott Hemmert, Rodrigues, David Resnick, “Let there be light!: the future of memory systems is photonics and 3D stacking”, MSPC, January 1, 2011, 43-48,

John Shalf, Donofrio, Rowen, Oliker, Michael F. Wehner, Green Flash: Climate Machine (LBNL), Encyclopedia of Parallel Computing, Pages: 809-819 January 1, 2011,

2009

David Donofrio, Oliker, Shalf, F. Wehner, Rowen, Krueger, Kamil, Marghoob Mohiyuddin, “Energy-Efficient Computing for Extreme-Scale Science”, IEEE Computer, January 1, 2009, 42:62-71,

Sudip Dosanjh

2014

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

2013

Richard A. Barrett, Shekhar Borkar, Sudip S. Dosanjh, Simon D. Hammond, Michael A. Heroux, X. Sharon Hu, Justin Luitjens, Steven G. Parker, John Shalf, Li Tang, “On the Role of Co-design in High Performance Computing”, Transition of HPC Towards Exascale Computing, E.H. D'Hollander et. al (Eds.), IOS Press, 2013, ( November 1, 2013)

Rolf Riesen, Sudip Dosanjh, Larry Kaplan, “The ExaChallenge Symposium”, IBM Research Paper, August 26, 2013,

S. Dosanjh, R. Barrett, D. Doerfler, S. Hammond, K. Hemmert, M. Heroux, P. Lin, K. Pedretti, A. Rodrigues, T. Trucano, J.Juitjens, “Exascale Design Space Exploration and Co-Design”, Future Generation Computer Systems, special issue on Extreme Scale Parallel Architectures and Systems, in press, available online, May 2, 2013,

2012

R. Barrett, S. Dosanjh, et al., “Towards Codesign in High Performance Computing Systems”, IEEE/ACM International Conference on Computer-Aided Design (ICCAD), San Jose, CA, November 5, 2012,

2011

R. Sevens, A. White, S. Dosanjh, et al., “Scientific Grand Challenges: Architectures and Technology for Extreme-Scale Computing Report”, 2011,

D. Doerfler, S. Dosanjh, J. Morrison, M. Vigil, “Production Petascale Computing”, Cray Users Group Meeting, Fairbanks, Alaska, 2011,

J. Ang, R. Brightwell, S. Dosanjh, et al., “Exascale Computing and the Role of Co-Design”, ( 2011)

J. Dongarra et al., “The International Exascale Software Project Roadmap”, International Journal of High Performance Computing Applications, 25:1, 2011,

2010

R. Leland and S. Dosanjh, “Computing at Exascale: A Value Proposition”, Sandia National Laboratories Report, November 16, 2010,

S. Hu, R. Murphy, S. Dosanjh, K. Olukoton, S. Poole, “Hardware/Software Co- Design for High Performance Computing”, Proceedings of CODES+ISSS’10, October 24, 2010,

A. Rodrigues, S. Dosanjh, S. Hemmert, “Co-Design for High Performance Computing”, Proceedings of the International Conference on Numerical Analysis and Applied Mathematics, Rhodes, Greece, September 18, 2010,

J. Ang, D. Doerfler, S. Dosanjh, K. Koch, J. Morrison, M. Vigil, “The Alliance for Computing at the Extreme Scale”, Proceedings of the Cray Users Group Meeting, Edinburgh, Scotland, May 24, 2010,

K. Alvin, B. Barrett, R. Brightwell, S. Dosanjh, A. Geist, S. Hemmert, M. Heroux, D. Kothe, R. Murphy, J. Nichols, R. Oldfield, A. Rodrigues, J. Vetter, “On the Path to Exascale”, International Journal of Distributed Systems and Technologies, 1(2):1– 22, May 22, 2010,

J. Tomkins, R. Brightwell, W. Camp, S. Dosanjh et al., “The Red Storm Architecture and Early Experiences with Multi-Core Processors”, International Journal of Distributed Systems and Technologies, Vol. 1, Issue 2, pp. 74-93, April 19, 2010,

John Shalf, S. Dosanjh, John Morrison, “Exascale Computing Technology Challenges”, VECPAR, edited by J.M.L.M. Palma et al. , (Springer-Verlag: 2010) Pages: 1-25

High Performance Computing architectures are expected to change dramatically in the next decade as power and cooling constraints limit increases in microprocessor clock speeds. Consequently computer companies are dramatically increasing on-chip parallelism to improve performance. The traditional doubling of clock speeds every 18-24 months is being replaced by a doubling of cores or other parallelism mechanisms. During the next decade the amount of parallelism on a single microprocessor will rival the number of nodes in early massively parallel supercomputers that were built in the 1980s. Applications and algorithms will need to change and adapt as node architectures evolve. In particular, they will need to manage locality to achieve performance. A key element of the strategy as we move forward is the co-design of applications, architectures and programming environments. There is an unprecedented opportunity for application and algorithm developers to influence the direction of future architectures so that they meet DOE mission needs. This article will describe the technology challenges on the road to exascale, their underlying causes, and their effect on the future of HPC system design.

2009

A. Geist, S. Dosanjh, “IESP Exascale Challenge: Co-Design of Architectures and Algorithms”, International Journal of High Performance Computing, Vol. 23, No. 4, pp. 401–402, September 18, 2009,

Brent R. Draney

2013

Brent Draney, NERSC's New Building Update, February 12, 2013,

2011

Katherine Yelick, Susan Coghlan, Brent Draney, Richard Shane Canon, Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Anping Liu, Scott Campbell, Piotr T. Zbiegiel, Tina Declerck, Paul Rich, “The Magellan Report on Cloud Computing for Science”, U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), December 2011,

2009

W. Allcock, R. Carlson, S. Cotter, E. Dart, V. Dattoria, B. Draney, R. Gerber, M. Helm, J. Hick, S. Hicks, S. Klasky, M. Livny, B. Maccabe, C. Morgan, S. Morss, L. Nowell, D. Petravick, J. Rogers, Y. Sekine, A. Sim, B. Tierney, S. Turnbull, D. Williams, L. Winkler, F. Wuerthwein, “ASCR Science Network Requirements”, Workshop, April 15, 2009,

ESnet publishes reports from Network and Science Requirement Workshops on a regular basis.  This report was the product of a two-day workshop in Washington DC that addresses science requirements impacting operations of networking for 2009.

2001

William T. C. Kramer, Wes Bethel, James Craw, Brent Draney, William Fortney, Brent Gorda, William Harris, Nancy Meyer, Esmond Ng, Francesca Verdier, Howard Walter, Tammy Welcome, “NERSC Strategic Implementation Plan 2002-2006”, ”, LBNL Technical Report 5465 Vol. 2, 2001,

Kirsten Fagnan

2014

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

Kjiersten Fagnan, NERSC, Running Jobs at NERSC: NUG 2014, February 3, 2014,

Richard A. Gerber

2014

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Fusion Energy Sciences: Target 2017”, May 1, 2014,

Richard A. Gerber, Support for Astronomy and Astrophysics at NERSC, April 3, 2014,

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

Richard A. Gerber, Zhengji Zhao, Woo-Sun Yang, Debugging and Optimization Tools, Presented at UC Berkeley CS267 class, February 2014, February 19, 2014,

Richard A. Gerber, NERSC, NERSC 2013 User Survey Results, February 6, 2014,

Richard A. Gerber, NERSC, NERSC Requirement Reviews for NUG 2014, February 6, 2014,

Kim Cupps, et al., “High Performance Computing Operations Review Report”, January 6, 2014,

2013

Richard A. Gerber, Communicating with NERSC Communities, November 20, 2013,

Richard A Gerber, Zhengji Zhao, NERSC Job Data, November 20, 2013,

Richard A. Gerber, “NERSC’s Edison Delivers High-Impact Science Results From Day One”, November 2013,

NERSC’s Edison Delivers High-Impact Science Results From Day One, SC13 display poster.

Richard A. Gerber, “Bringing Better Materials to Market in Half the Time”, November 2013,

Bringing Better Materials to Market in Half the Time, SC13 poster

Richard Gerber (Berkeley Lab), Ken Bloom (U. Nebraska-Lincoln), “Report of the Snowmass 2013 Computing Frontier Working Group on Distributed Computing and Facility Infrastructures”, to be included in proceedings of Community Summer Study ("Snowmass") 2013, November 11, 2013,

A. Koniges, R. Gerber, D. Skinner, Y. Yao, Y. He, D. Grote, J-L Vay, H. Kaiser, and T. Sterling, “Plasma Physics Simulations on Next Generation Platforms”, 55th Annual Meeting of the APS Division of Plasma Physics, Volume 58, Number 16, November 11, 2013,

The current high-performance computing revolution provides opportunity for major increases in computational power over the next several years, if it can be harnessed. This transition from simply increasing the single-processor and network performance to a different architectural paradigms forces application programmers to rethink the basic models of parallel programming from both the language and problem division standpoints. One of the major computing facilities available to researchers in fusion energy is the National Energy Research Scientific Computing Center. As the mission computing center for DOE, Office of Science, NERSC is tasked with helping users to overcome the challenges of this revolution both through the use of new parallel constructs and languages and also by enabling a broader user community to take advantage of multi-core performance. We discuss the programming model challenges facing researchers in fusion and plasma physics in for a variety of simulations ranging from particle-in-cell to fluid-gyrokinetic and MHD models.

Richard Gerber and Harvey Wasserman, eds., “Large Scale Computing and Storage Requirements for High Energy Physics - Target 2017”, November 8, 2013,

Richard Gerber, NUG Webinar for November 2013, November 7, 2013,

Richard Gerber, Edison Overview (Focus on hardware relevant for performance), October 10, 2013,

Richard Gerber, Data-Driven Science at NERSC, August 8, 2013,

Richard Gerber, High-Performance Parallel I/O, August 6, 2013,

Richard Gerber, NERSC/Berkeley Lab and Ken Bloom, University of Nebraska-Lincoln, Snowmass Computing Frontier I2: Distributed Computing and Facility Infrastructures, July 31, 2013,

Richard Gerber, Dirac Science Highlights 2013, June 25, 2013,

Richard Gerber, Introduction to High Performance Computing, June 10, 2013,

Introduction to High Performance Computing presented to Berkeley Lab Computing Sciences summer interns.

Richard Gerber, Harvey Wasserman, “High Performance Computing and Storage Requirements for Biological and Environmental Research Target 2017”, June 6, 2013, LBNL LBNL-6256E

Richard A. Gerber, HIgh Performance Computing and Big Data (for High Energy Physics theory), April 2, 2013,

Richard A. Gerber, Fusion Energy Sciences Requirements Review Overview and Goals, March 19, 2013,

Richard Gerber, NUG March 2013 Webinar, March 7, 2013,

NERSC User Group Teleconference and Webinar Slides for March 7, 2013

Richard A. Gerber, Debugging and Optimization Tools, February 19, 2013,

Debugging and Optimization Tools, presented for UC Berkeley CS267 "Applications of Parallel Computers" class, Feb. 19, 2013.

Richard Gerber, Trends, Discovery, & Innovation at NUG User Day 2013, February 19, 2013,

Richard A. Gerber, Tina Declerck. Zhengji Zhao, Edison Update, February 12, 2013,

Overview and update on the installation and configuration of Edison, NERSC's new Cray XC30 supercomputer.

Richard A. Gerber, Harvey Wasserman, NERSC Requirements Reviews, February 12, 2013,

An update on the NERSC Requirements Reviews at NUG 2013. Richard Gerber and Harvey Wasserman, NERSC>

Richard Gerber, Requirements Reviews Update, February 12, 2013,

Richard A. Gerber, Getting Started at NERSC, January 17, 2013,

Getting Started at NERSC Webinar, January 17, 2013, Richard Gerber, NERSC User Services

Richard Gerber, Kathy Yelick, Lawrence Berkeley National Laboratory, “Data Requirements from NERSC Requirements Reviews”, January 9, 2013,

2012

Richard A. Gerber, Job Analytics, November 8, 2012,

Richard A. Gerber, Batch Strategies of Maximizing Throughput and Allocation, NERSC Users Group Monthly Webinar, October 2012, October 4, 2012,

Richard A. Gerber, Uses for High Performance Computing, June 12, 2012,

Who uses High Peformance Computing and what do they do with it? Presented for LBNL Summer Interns, June 12, 2012.

Richard A. Gerber, Introduction to High Performance Computers, June 12, 2012,

Introduction for High Performance Computers. Presented to LBNL Summer Interns, June 12, 2012.

Richard A. Gerber, Challenges in HPC, June 12, 2012,

Challenges in High Performance Computing. Presented to LBNL Summer Interns, June 12, 2012.

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Nuclear Physics”, Workshop, March 26, 2012, LBNL LBNL-5355E

Report of the user requirements workshop for lattice gauge theory and nuclear physics computation at NERSC that took place May 26, 2011

Debugging and Optimization Tools, Presented to UC Berkeley CS 267 Class, Applications of Parallel Computer, February 16, 2012,

User Requirements Gathered for the NERSC7 Procurement, February 3, 2012,

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Advanced Computational Science Research”, Workshop, January 2012, LBNL LBNL-5249E

2011

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Fusion Energy Sciences”, Workshop, December 2011,

HPC I/O in Scaling  to  Petascale  and  Beyond:  Performance  Analysis  and  Optimization  of  Applications, SC11, November 13, 2011,

Richard A. Gerber, Introduction to HPC Systems, NERSC New User Training, September 13, 2011,

Richard A. Gerber, Experiences with Tools at NERSC, Programming weather, climate, and earth-­‐system models on heterogeneous mul-­‐core platorms, NCAR, Boulder, CO, September 7, 2011,

NERSC Overview for Environmental Energy Technologies, Berkeley Lab, Environmental Energy Technologies Division, Berkeley, CA, June 2011,

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Basic Energy Sciences”, Workshop, June 10, 2011, LBNL LBNL-4809E

Getting Started at NERSC, NERSC Training Webinar Berkeley Lab OSF, Oakland, CA, June 7, 2011,

NERSC Overview for the Joint Genome Institute, DOE Joint Genome Institute, Walnut Creek, CA, May 2, 2011,

Richard Gerber, Computers - BSA Merit Badge, March 2011,

Richard Gerber, Debugging and Optimization Tools, Presented to CS267 class at UC-Berkeley, February 11, 2011,

2010

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for High Energy Physics”, Workshop, November 15, 2010,

Richard A. Gerber, Large Scale Computing and Storage Requirements for High Energy Physics, NUG 2010, Cray Quarterly, NERSC OSF, Oakland, CA, October 28, 2010,

Richard A. Gerber, Introduction to Computing at NERSC, October 20, 2010,

Submitting and Running Jobs on the Cray XT5, Joint XT Workshop, Berkeley, CA, February 1, 2010,

2009

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Biological and Environmental Research”, Workshop, October 19, 2009, LBNL LBNL-2710E

Computing and Storage Requirements for Biological and Environmental Researchj, NUG 2009, Boulder, CO, October 7, 2009,

W. Allcock, R. Carlson, S. Cotter, E. Dart, V. Dattoria, B. Draney, R. Gerber, M. Helm, J. Hick, S. Hicks, S. Klasky, M. Livny, B. Maccabe, C. Morgan, S. Morss, L. Nowell, D. Petravick, J. Rogers, Y. Sekine, A. Sim, B. Tierney, S. Turnbull, D. Williams, L. Winkler, F. Wuerthwein, “ASCR Science Network Requirements”, Workshop, April 15, 2009,

ESnet publishes reports from Network and Science Requirement Workshops on a regular basis.  This report was the product of a two-day workshop in Washington DC that addresses science requirements impacting operations of networking for 2009.

Richard A. Gerber, Breakthrough Science at NERSC, Cray Technical Workshop, Isle of Pines, SC, February 25, 2009,

2008

Richard A. Gerber, Franklin File Systems and I/O, NERSC Users Group, Oakland, CA, October 2, 2008,

Richard Gerber, “Franklin Interactive Node Responsiveness”, June 9, 2008,

Richard A. Gerber, Performance Monitoring on NERSC’s POWER 5 System, May 22, 2008,

2007

Richard A. Gerber, Running Jobs on Franklin, September 19, 2007,

Richard A. Gerber, Application and System Memory Use, Configuration, and Problems on Bassi, July 17, 2007,

2006

Richard A. Gerber, Bassi - NERSC's New IBM POWER 5, NUG 2006, Princeton, NJ, June 13, 2006,

Richard A. Gerber, Experiences Configuring, Validating, and Monitoring Bassi, NUG 2006, Princeton, NJ, June 13, 2006,

2000

Nathan C. Hearn, Susan A. Lamb, Robert A. Gruendl (Univ. of Ill.), Richard A. Gerber (NERSC/Berkeley Lab), “The Colliding Galaxy System Arp 119: Numerical Models and Infrared Observations”, Astronomical Society of the Pacific Conference Series, January 17, 2000, 215:46H,

1999

Lamb, S. A.; Hearn, N. C.; Gerber, R. A., “Velocity Fields in Impacted Gaseous Galactic Discs: A Numerical Survey using N-body/SPH Simulations”, Bulletin of the American Astronomical Society, May 17, 1999, 31:829,

1997

Lamb, S. A.; Gerber, R. A.; Rudnick, G. H.; Dewing, M., “Starbursts in Collisionally Produced Ring Galaxies: Comparisons Between Numerical Models and Observed Systems”, Revista Mexicana de Astronomia y Astrofisica Serie de Conferencias, May 3, 1997, 6:151,

1996

Richard A. Gerber, “Global Effects of Softening n-Body Galaxies”, Astrophysical Journal, August 1, 1996, 466:724-731,

Smith, B.F.; Gerber, R.A.; Steiman-Cameron, T.Y.; Miller, R.H., “The Response of Disks to Oscillatory Modes in Galaxies”, Bulletin of the American Astronomical Society, June 17, 1996, 28:1189,

Rudnick, G. H.; Lamb, S. A.; Gerber, R. A.; Dewing, M., “A Comparison between Numerical Models of Collisionally Produced Ring Galaxies and Observed Systems”, Bulletin of the American Astronomical Society, May 13, 1996, 28:826,

Gerber, R.A. & Lamb, S.A., “A Stellar and Gas Dynamical Numerical Model of Ring Galaxies”, Monthly Notices of the Royal Astronomical Society, January 8, 1996, 278:345,

1995

Gerber, R. A.; Smith, B. F.; Steiman-Cameron, T. Y., “The Response of Disks to Oscillatory Modes in Galaxies”, Bulletin of the American Astronomical Society, December 11, 1995, 27:1353,

Gerber, Richard A, “Some Consequences of Using Gravitational Softening to Model N-body Galaxies”, Bulletin of the American Astronomical Society, June 12, 1995, 27:1201,

1994

Lamb, S. A.; Gerber, R. A.; Balsara, D. S., “Off-Center Collisions Involving Rotating Disk Galaxies: 3-D Numerical Simulations”, Bulletin of the American Astronomical Society, December 12, 1994, 26:1430,

Richard A. Gerber and Susan A. Lamb, “A Model for Collisionally Induced Disturbed Structure in Disk Galaxies”, Astrophysical Journal, August 20, 1994, 431:604-616,

Susan A. Lamb, NORDITA and Neils Bohr Institute; Richard A. Gerber University of Illinois at Urbana-Champaign; and Dinshaw Balsara, Johns Hopkins University, “Galactic Scale Gas Flows in Colliding Galaxies: a-Dimensional, N-bodyjHydrodynamics Experiments”, Astrophysics and Space Science, May 1994, 216:337-346,

Gerber, Richard A., “Some Consequences of Using Gravitational Softening to Model N-body Galaxies”, Bulletin of the American Astronomical Society, March 1994, 27:885,

1993

Stellar and gas dynamics of interacting ring galaxies, Richard A. Gerber, Ph.D., October 1, 1993,

Susan A. Lamb, Richard A. Gerber, Dinshaw S. Balsara, “Galaxies in Collision: The Formation of Rings and Arcs”, Astron. Ges., Abstr. Ser, June 1, 1993, 8:56,

Stellar and Gas Dynamics of Interacting Ring Galaxies: Front Material, Richard A. Gerber, May 1993,

Stellar and Gas Dynamics of Interacting Ring Galaxies: Chapter 1 - Introduction, Richard A. Gerber, May 1993,

1992

Richard A. Gerber, Susan A. Lamb, and Dinshaw Balsara, “A Model of Ring Galaxies: Arp 147-Like Systems”, Astrophysical Journal, November 1, 1992, 399:L51-L54,

Gerber, R. A.; Lamb, S. A., “Models for Collisionally Induced Disturbed Structure in Disk Galaxies”, Bulletin of the American Astronomical Society, May 18, 1992, 24:811,

1991

Gerber, R. A.; Lamb, S. A.; Balsara, D. S., “A Model for Ring Galaxies: Arp 147-Like Systems”, Bulletin of the American Astronomical Society, September 17, 1991, 23:1391G,

R.A. Gerber, S.A. Lamb (Univ. of Ill.), and D.S. Balsara (JHU), “Ring Formation in Off-Axis Collisions of Galaxies”, Bulletin of the American Astronomical Society, March 11, 1991, BAAS 23:953G,

1990

Gerber, Richard A.; Balsara, Dinshaw S.; Lamb, Susan A, “Dynamical experiments on models of colliding disk galaxies”, NASA, Marshall Space Flight Center, Paired and Interacting Galaxies: International Astronomical Union Colloquium, November 12, 1990, 124:737-742,

R.A. Gerber, S.A. Lamb (Univ. of Illinois at Urbana-Champaign), D.S. Balsara (Johns Hopkins Univ.), “Combined Hydrodynamical and N-Body Studies of Colliding Galaxies: The Formation of Ring Galaxies”, 177th Meeting of the American Astronomical Society, July 9, 1990, 22:1243G,

Gerber, R. A. and Lamb, S. A. and Miller, R. H., and Smith, B. F., “Models of colliding galaxies: kinetic energy and density enhancement”, Dynamics and Interactions of Galaxies, Proceedings, Springer, Berlin (Germany, F.R.), June 4, 1990, 223,

Gerber. R. A.; Lamb, S. A.; Miller, R. H.; Smith, B. F., “Potential Sites for Star Formation in Colliding Galaxies”, Astrophysics and Space Science Library, Workshop of the Advanced School of Astronomy, February 12, 1990, 160:366G,

Lamb, S. A.; Miller, R. H.; Gerber, R. A.; Smith, B. F., “Models of Colliding Galaxies: Kinetic Energy and Density Enhancements”, Astrophysics and Space Science Library, Kona Symposium of Millimetre and Submillimetre Astronomy, January 8, 1990, 158:235L,

1989

R. A. Gerber, D. S. Balsara, and S. A. Lamb (Univ. of Ill.), “Potential Sites of Star Formation in Interacting Galaxies: Numerical Experiments”, Bulletin of the American Astronomical Society, September 11, 1989, 21:1163G,

1988

S.A Lamb, R.A. Gerber (U. Illinois), R.H. Miller (U. Chicago), B.F. Smith (NASA/Ames), “Models of Colliding Galaxies: Kinetic Energy and Density Enhancements”, 173rd Meeting of the American Astronomical Society, September 10, 1988,

Lisa Gerhardt

2014

Nicholas Balthaser, Lisa Gerhardt, NERSC Archival Storage: Best Practices, Joint Facilities User Forum on Data-Intensive Computing, June 18, 2014,

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

IceCube Collaboration: M. G. Aartsen et al, “Energy Reconstruction Methods in the IceCube Neutrino Telescope”, Journal of Instrumentation 9 P03009, March 2014,

Nick Balthaser, NERSC; Lisa Gerhardt, NERSC, Introduction to NERSC Archival Storage: HPSS, February 3, 2014,

IceCube Collaboration: M. G. Aartsen et al, “Improvement in Fast Particle Track Reconstruction with Robust Statistics”, Nuclear Instruments and Methods A736 143-149, February 2014,

2013

IceCube Collaboration: M. G. Aartsen et al, “Search for Time-Independent Neutrino Emission from Astrophysical Sources with 3 yr of IceCube Data”, Astrophysical Journal 779 132, December 2013,

IceCube Collaboration: M. G. Aartsen et al, “Probing the Origin of Cosmic Rays with Extremely High Energy Neutrinos Using the IceCube Observatory”, Physical Review D88 112008, December 2013,

IceCube Collaboration: M. G. Aartsen et al, “An IceCube Search for Dark Matter Annihilation in Nearby Galaxies and Galaxy Clusters”, Physical Review D88 122001, December 2013,

IceCube Collaboration: M. G. Aartsen et al, “Evidence for High-Energy Extraterrestrial Neutrinos at the IceCube Detector”, Science 342 1242856, November 2013,

IceCube Collaboration: M. G. Aartsen et al, “South Pole Glacial Climate Reconstruction from Multi-Borehole Laser Particulate Stratigraphy”, Journal of Glaciology 59 1117-1128, October 2013,

IceCube Collaboration: M. G. Aartsen et al, “Measurement of the Cosmic Ray Energy Spectrum with IceTop-73”, Physical Review D88 042004, August 28, 2013,

IceCube Collaboration: R. Abbasi et al, “Measurement of Atmospheric Neutrino Oscillations with IceCube”, Physical Review Letters 111 081801, August 2013,

IceCube Collaboration: R. Abbasi et al, “First Observation of PeV-energy Neutrinos with IceCube”, Physical Review Letters 111 021103, July 2013,

IceCube Collaboration: M. G. Aartsen et al., “Measurement of South Pole Ice Transparency with the IceCube LED Calibration System”, Nuclear Instruments and Methods A711 73-89, May 2013,

Annette M. Greiner

2013

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, Benjamin P. Bowen, “OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging”, Analytical Chemistry, 2013, 85 (21), pp 10354–10361, October 2, 2013,

Damian Hazen

2012

Damian Hazen, Jason Hick, “MIR Performance Analysis”, June 12, 2012, LBNL LBNL-5896E

 

We provide analysis of Oracle StorageTek T10000 Generation B (T10KB) Media Information Record (MIR) Per- formance Data gathered over the course of a year from our production High Performance Storage System (HPSS). The analysis shows information in the MIR may be used to improve tape subsystem operations. Most notably, we found the MIR information to be helpful in determining whether the drive or tape was most suspect given a read or write error, and for helping identify which tapes should not be reused given their history of read or write errors. We also explored using the MIR Assisted Search to order file retrieval requests. We found that MIR Assisted Search may be used to reduce the time needed to retrieve collections of files from a tape volume. 

 

2011

N. Balthaser, D. Hazen, “HSI Best Practices for NERSC Users”, May 2, 2011, LBNL 4745E

 

In this paper we explain how to obtain and install HSI, create a NERSC authentication token, and transfer data to and from the system. Additionally we describe methods to optimize data transfers and avoid common pitfalls that can degrade data transfers and storage system performance.

 

D. Hazen, J. Hick, W. Hurlbert, M. Welcome, Media Information Record (MIR) Analysis, LTUG 2011, April 19, 2011,

Presentation of Storage Systems Group findings from a year-long effort to collect and analyze Media Information Record (MIR) statistics from our in-production Oracle enterprise tape drives at NERSC.  We provide information on the data collected, and some highlights from our analysis. The presentation is primarily intended to declare that the information in the MIR is important to users or customers to better operating and managing their tape environments.

2010

D. Hazen, J. Hick, HPSS v8 Metadata Conversion, HPSS 8.1 Pre-Design Meeting, April 7, 2010,

Provided information about the HPSS metadata conversion software to other developers of HPSS.  Input was important to establishing a design for the version 8 HPSS metadata conversions.

Yun Helen He

2014

Yun (Helen) He and Nick Cardo, Babbage: the MIC Testbed System at NERSC, NERSC Brown Bag, Oakland, CA, April 3, 2014,

Yun (Helen) He, Performance Analysis Tools and Cray Reveal, NERSC User Group Meeting, Oakland, CA, February 3, 2014,

2013

A. Koniges, R. Gerber, D. Skinner, Y. Yao, Y. He, D. Grote, J-L Vay, H. Kaiser, and T. Sterling, “Plasma Physics Simulations on Next Generation Platforms”, 55th Annual Meeting of the APS Division of Plasma Physics, Volume 58, Number 16, November 11, 2013,

The current high-performance computing revolution provides opportunity for major increases in computational power over the next several years, if it can be harnessed. This transition from simply increasing the single-processor and network performance to a different architectural paradigms forces application programmers to rethink the basic models of parallel programming from both the language and problem division standpoints. One of the major computing facilities available to researchers in fusion energy is the National Energy Research Scientific Computing Center. As the mission computing center for DOE, Office of Science, NERSC is tasked with helping users to overcome the challenges of this revolution both through the use of new parallel constructs and languages and also by enabling a broader user community to take advantage of multi-core performance. We discuss the programming model challenges facing researchers in fusion and plasma physics in for a variety of simulations ranging from particle-in-cell to fluid-gyrokinetic and MHD models.

Yun (Helen) He, Adding OpenMP to Your Code Using Cray Reveal, NERSC Performance on Edison Training Event, Oakland, CA, October 10, 2013,

Yun (Helen) He, Using the Cray perftools-lite Performance Measurement Tool, NERSC Performance on Edison Training Event, Oakland, CA, October 10, 2013,

“Programming Environments, Applications, and Documentation SIG”, Cray User Group 2013, May 6, 2013,

Yun (Helen) He, Programming Environments, Applications, and Documentation SIG, Cray User Group 2013, Napa Valley, CA., May 6, 2013,

Yun (Helen) He, Hybrid MPI/OpenMP Programming, NERSC User Group Meeting 2012, Oakland, CA, February 15, 2013,

Suren Byna, Andrew Uselton, Prabhat, David Knaak, Helen He, “Trillion Particles, 120,000 cores, and 350 TBs: Lessons Learned from a Hero I/O Run on Hopper”, Cray User Group Meeting, 2013,

2012

Zhengji Zhao, Yun (Helen) He and Katie Antypas, “Cray Cluster Compatibility Mode on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, Germany., May 1, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, Cray Cluster Compatibility Mode on Hopper, A talk in the Cray User Group meeting, April 29-May-3, 2012, Stuttgart, German., May 1, 2012,

Yun (Helen) He and Katie Antypas, “Running Large Jobs on a Cray XE6 System”, Cray User Group 2012 Meeting, Stuttgart, Germany, April 30, 2012,

Yun (Helen) He, Programming Environments, Applications, and Documentation SIG, Cray User Group 2012, April 30, 2012,

Zhengji Zhao and Helen He, Using Cray Cluster Compatibility Mode on Hopper, A talk NERSC User Group meeting, Feb 2, 2012, Oakland, CA, February 2, 2012,

Yun (Helen) He and Woo-Sun Yang, Using Hybrid MPI/OpenMP, UPC, and CAF at NERSC, NERSC User Group Meeting 2012, Oakland, CA, February 2, 2012,

2011

Zhengji Zhao and Helen He, Cray Cluster Compatibility Mode on Hopper, A Brown Bag Lunch talk at NERSC, Dec. 8, 2011, Oakland, CA, December 8, 2011,

Helen He, Huge Page Related Issues with N6 Benchmarks on Hopper, NERSC/Cray Quarterly Meeting, October 26, 2011,

Yun (Helen) He and Katie Antypas, Mysterious Error Messages on Hopper, NERSC/Cray Quarterly Meeting, July 25, 2011,

K. Antypas, Y. He, “Transitioning Users from the Franklin XT4 System to the Hopper XE6 System”, Cray User Group 2011 Procceedings, Fairbanks, Alaska, May 2011,

The Hopper XE6 system, NERSC’s first peta-flop system with over 153,000 cores has increased the computing hours available to the Department of Energy’s Office of Science users by more than a factor of 4. As NERSC users transition from the Franklin XT4 system with 4 cores per node to the Hopper XE6 system with 24 cores per node, they have had to adapt to a lower amount of memory per core and on- node I/O performance which does not scale up linearly with the number of cores per node. This paper will discuss Hopper’s usage during the “early user period” and examine the practical implications of running on a system with 24 cores per node, exploring advanced aprun and memory affinity options for typical NERSC applications as well as strategies to improve I/O performance.

P. M. Stewart, Y. He, “Benchmark Performance of Different Compilers on a Cray XE6”, Fairbanks, AK, CUG Proceedings, May 23, 2011,

There are four different supported compilers on NERSC's recently acquired XE6, Hopper. Our users often request guidance from us in determining which compiler is best for a particular application. In this paper, we will describe the comparative performance of different compilers on several MPI benchmarks with different characteristics. For each compiler and benchmark, we will establish the best set of optimization arguments to the compiler.

Yun (Helen) He, Programming Environments, Applications, and Documentation SIG, Cray User Group Meeting 2011, Fairbanks, AK, May 23, 2011,

Michael Stewart, Yun (Helen) He*, Benchmark Performance of Different Compilers on a Cray XE6, Cray User Group 2011, May 2011,

Katie Antypas, Yun (Helen) He*, Transitioning Users from the Franklin XT4 System to the Hopper XE6 System, Cray User Group 2011, Fairbanks, AK, May 2011,

Yun (Helen) He, Introduction to OpenMP, Using the Cray XE6 Workshop, NERSC., February 7, 2011,

2010

Yun (Helen) He, Introduction to OpenMP, NERSC User Group 2010 Meeting, Oakland, CA, October 18, 2010,

Wendy Hwa-Chun Lin, Yun (Helen) He, and Woo-Sun Yang, “Franklin Job Completion Analysis”, Cray User Group 2010 Proceedings, Edinburgh, UK, May 2010,

The NERSC Cray XT4 machine Franklin has been in production for 3000+ users since October 2007, where about 1800 jobs run each day. There has been an on-going effort to better understand how well these jobs run, whether failed jobs are due to application errors or system issues, and to further reduce system related job failures. In this paper, we talk about the progress we made in tracking job completion status, in identifying job failure root cause, and in expediting resolution of job failures, such as hung jobs, that are caused by system issues. In addition, we present some Cray software design enhancements we requested to help us track application progress and identify errors.

 

Yun (Helen) He, User Services SIG (Special Interest Group), Cray User Group Meeting 2010, Edinburgh, UK, May 24, 2010,

Yun (Helen) He, Wendy Hwa-Chun Lin, and Woo-Sun Yang, Franklin Job Completion Analysis, Cray User Group Meeting 2010, May 2010,

2009

Yun (Helen) He, “User and Performance Impacts from Franklin Upgrades”, Cray User Group Meeting 2009, Atlanta, GA, May 2009, LBNL 2013E

The NERSC flagship computer Cray XT4 system "Franklin" has gone through three major upgrades: quad core upgrade, CLE 2.1 upgrade, and IO upgrade, during the past year.  In this paper, we will discuss the various aspects of the user impacts such as user access, user environment, and user issues etc from these upgrades. The performance impacts on the kernel benchmarks and selected application benchmarks will also be presented.

Yun (Helen) He, User and Performance Impacts from Franklin Upgrades, Cray User Group Meeting 2009, May 4, 2009,

James M. Craw, Nicholas P. Cardo, Yun (Helen) He, and Janet M. Lebens, “Post-Mortem of the NERSC Franklin XT Upgrade to CLE 2.1”, Cray User Group Meeting 2009, Atlanta, GA, May 2009,

This paper will discuss the lessons learned of the events leading up to the production deployment of CLE 2.1 and the post install issues experienced in upgrading NERSC's XT4 system called Franklin.

 

James M. Craw, Nicholas P. Cardo, Yun (Helen) He, and Janet M. Lebens, Post-Mortem of the NERSC Franklin XT Upgrade to CLE 2.1, Cray User Group Meeting, May 2009,

Helen He, Job Completion on Franklin, NERSC/Cray Quarterly Meeting, April 2009,

Helen He, CrayPort Desired Features, NERSC/Cray Quarterly Meeting, April 2009,

2008

Yun (Helen) He, Franklin Quad Core Update/Differences, NERSC User Group Meeting 2008, October 2008,

Yun (Helen) He, William T.C. Kramer, Jonathan Carter, and Nicholas Cardo, Franklin: User Experiences, CUG User Group Meeting 2008, May 5, 2008,

Yun (Helen) He, William T.C. Kramer, Jonathan Carter, and Nicholas Cardo, “Franklin: User Experiences”, Cray User Group Meetin 2008, May 4, 2008, LBNL 2014E

The newest workhorse of the National Energy Research Scientific Computing Center is a Cray XT4 with 9,736 dual core nodes. This paper summarizes Franklin user experiences from friendly early user period to production period. Selected successful user stories along with top issues affecting user experiences are presented.

 

2007

Yun (Helen) He, “Franklin Early User Report”, December 2007,

Helen He, Franklin Overview, NERSC User Group Meeting 2007, September 2007,

Jonathan Carter, Yun (Helen) He, John Shalf, Hongzhang Shan, Erich Strohmaier, and Harvey Wasserman, “The Performance Effect of Multi-Core on Scientific Applications”, Cray User Group 2007, May 2007, LBNL 62662

The historical trend of increasing single CPU performance has given way to roadmap of increasing core count. The challenge of effectively utilizing these multi- core chips is just starting to be explored by vendors and application developers alike. In this study, we present some performance measurements of several complete scientific applications on single and dual core Cray XT3 and XT4 systems with a view to characterizing the effects of switching to multi-core chips. We consider effects within a node by using applications run at low concurrencies, and also effects on node- interconnect interaction using higher concurrency results. Finally, we construct a simple performance model based on the principle on-chip shared resource—memory bandwidth—and use this to predict the performance of the forthcoming quad-core system.

 

Jonathan Carter, Helen He*, John Shalf, Erich Strohmaier, Hongzhang Shan, and Harvey Wasserman, The Performance Effect of Multi-Core on Scientific Applications, Cray User Group 2007, May 2007,

J. Levesque, J. Larkin, M. Foster, J. Glenski, G. Geissler, S. Whalen, B. Waldecker, J. Carter, D. Skinner, H. He, H. Wasserman, J. Shalf, H. Shan, “Understanding and mitigating multicore performance issues on the AMD opteron architecture”, March 1, 2007, LBNL 62500

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3and XT4systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

 

2006

Y. He, C. Ding, M. Vertenstein, N. Norton, B. Kauffman, A. Craig, and J. Wolfe, “Concurrent Single-Executable CCSM with MPH Library”, U.S. Department of Energy Climate Change Prediction Program (CCPP) Science Team Meeting, April 2006,

C. Covey, I. Fung, Y. He, F. Hoffman, and J. John, “Diagnosis and Intercomparison of Climate Models with Interactive Biochemistry”, U.S. Department of Energy Climate Change Prediction Program (CCPP) Science Team Meeting, April 2006,

F. Hoffman, I. Fung, J. John, J. Randerson, P. Thornton, J. Foley, N. Mahowald, K. Lindsay, M. Vertenstein, C. Covey, Y. He, W. Post, D. Erickson, and the CCSM Biogeochemistry Working Group., “Terrestrial Biogeochemistry Intercomparison Experiments”, U.S. Department of Energy Climate Change Prediction Program (CCPP) Science Team Meeting, April 2006,

Yun He and Chris Ding, MPH: a Library for Coupling Multi-Component Models on Distributed Memory Architectures and its Applications, The 8th International Workshop on Next Generation Climate Models for Advanced High Performance Computing Facilities, February 23, 2006,

Yu-Heng Tseng, Chris Ding, Yun He*, Efficient parallel I/O with ZioLib in Community Atmosphere Model (CAM), The 8th International Workshop on Next Generation Climate Models for Advanced High Performance Computing Facilities, February 2006,

Yun He, Status of Single-Executable CCSM Development, CCSM Software Engineering Working Group Meeting, January 25, 2006,

2005

Y. He and C. H.Q. Ding, “Automatic Multi-Instance Simulations of an Existing Climate Program”, Berkeley Atmospheric Sciences Center, Fifth Annual Symposium, October 14, 2005,

Yun He, Chris H.Q. Ding, “Coupling Multi-Component Models with MPH on Distributed Memory Computer Architectures”, International Journal of High Performance Computing Applications, August 2005, Vol.19,:329-340,

 

A growing trend in developing large and complex applications on today’s Teraflop scale computers is to integrate stand-alone and/or semi-independent program components into a comprehensive simulation package. One example is the Community Climate System Model which consists of atmosphere, ocean, land-surface and sea-ice components. Each component is semi-independent and has been developed at a different institution. We study how this multi-component, multi-executable application can run effectively on distributed memory architectures. For the first time, we clearly identify five effective execution modes and develop the MPH library to support application development utilizing these modes. MPH performs component-name registration, resource allocation and initial component handshaking in a flexible way.

 

A.P. Craig, R.L. Jacob, B. Kauffman, T. Bettge, J. Larson, E. Ong, C. Ding, and Y. He, “CPL6: The New Extensible, High-Performance Parallel Coupler for the Community Climate System Model”, International Journal of High Performance Computing Applications, August 2005, Vol.19,:309-327,

Coupled climate models are large, multiphysics applications designed to simulate the Earth's climate and predict the response of the climate to any changes in forcing or boundarey conditions. The Community Climate System Model (CCSM) is a widely used state-of-art climate model that has released several versions to the climate community over the past ten years. Like many climate models, CCSM employs a coupler, a functional unit that coordinates the exchange of data between parts of the climate system such as the atmosphere and ocean. This paper describes the new coupler, cpl6, contained in the latest version of CCSM, CCSM3. Cpl6 introduces distributed-memory parallelism to the coupler, a class library for important coupler functions, and a standarized interface for component models. Cpl6 is implemented entirely in Fortran90 and uses the Model Coupling Toolkit as the base for most of its classes. Cpl6 gives improved performance over previous versions and scales well on multiple platforms.

Yun He, Status of Single-Executable CCSM Development, CCSM Software Engineering Working Group Meeting, March 15, 2005,

H.S. Cooley, W.J. Riley, M.S. Torn, and Y. He, “Impact of Agricultural Practice on Regional Climate in a Coupled Land Surface Mesoscale Model”, Journal of Geophysical Research-Atmospheres, February 2005, Vol.110,,

We applied a coupled climate (MM5) and land-surface (LSM1) model to examine the effects of early and late winter wheat harvest on regional climate in the Department of Energy Atmospheric Radiation Measurement (ARM) Climate Research Facility in the Southern Great Plains, where winter wheat accounts for 20% of the land area.

2004

Yun He, Status of Single-Executable CCSM Development, Climate Change Prediction Program (CCPP) Meeting, October 2004,

Yun He, MPH: a Library for Coupling Multi-Component Models on Distributed Memory Architectures and its Applications, Scientific Computing Seminar, Lawrence Berkeley National Laboratory, October 2004,

Chris Ding, Yun He, “Integrating Program Component Executables on Distributed Memory Architectures via MPH”, Proceedings of International Parallel and Distributed Processing Symposium, April 2004,

Yun He and Chris H.Q. Ding, “MPI and OpenMP Paradigms on Cluster of SMP Architectures: The Vacancy Tracking Algorithm for Multi-dimensional Array Transposition”, Journal of Parallel and Distributed Computing Practice, 2004, Issue 5,,

We evaluate remapping multi-dimensional arrays on cluster of SMP architectures under OpenMP, MPI, and hybrid paradigms. Traditional method of multi-dimensional array transpose needs an auxiliary array of the same size and a copy back stage. We recently developed an in-place method using vacancy tracking cycles. The vacancy tracking algorithm outperforms the traditional 2-array method as demonstrated by extensive comparisons. Performance of multi-threaded parallelism using OpenMP are first tested with different scheduling methods and different number of threads. Both methods are then parallelized using several parallel paradigms. At node level, pure OpenMP outperforms pure MPI by a factor of 2.76 for vacancy tracking method. Across entire cluster of SMP nodes, by carefully choosing thread numbers, the hybrid MPI/OpenMP implementation outperforms pure MPI by a factor of 3.79 for traditional method and 4.44 for vacancy tracking method, demonstrating the validity of the parallel paradigm of mixing MPI with OpenMP.

 

2003

Yun He and Chris Ding, “MPH: a Library for Coupling Multi-Component Models on Distributed Memory Architectures”, SuperComputing 2003, November 2003,

W.J. Riley, H.S. Cooley, Y. He, and M.S. Torn, “Coupling MM5 with ISOLSM: Development, Testing, and Applications”, Thirteenth PSU/NCAR Mesoscale Modeling System Users' Workshop, June 10, 2003, LBNL 53018

W.J. Riley, H.S. Cooley, Y. He*, and M.S. Torn, Coupling MM5 with ISOLSM: Development, Testing, and Applications, Thirteenth PSU/NCAR Mesoscale Modeling System Users' Workshop, NCAR, June 2003,

Y. He and C. H.Q. Ding, “An Evaluation of MPI and OpenMP Paradigms for Multi-Dimensional Data Remapping”, Lecture Notes in Computer Science, Vol 2716., edited by M.J. Voss, ( June 2003) Pages: 195-210

Y. He and C. Ding, “Multi-Program Multi Program-Components Handshaking (MPH) Utility Version 4 User's Manual”, May 2003, LBNL 50778

Helen He, Hybrid MPI and OpenMP Programming on the SP, NERSC User Group (NUG) Meeting, Argonne National Lab, May 2003,

Helen He, Hybrid OpenMP and MPI Programming on the SP: Successes, Failures, and Results, NERSC User Training 2003, Lawrence Berkeley National Laboratory, March 2003,

2002

Yun He, Chris H.Q. Ding, “MPI and OpenMP paradigms on cluster of SMP architectures: the vacancy tracking algorithm for multi-dimensional array transposition”, Proceedings of the 2002 ACM/IEEE conference on Supercomputing, November 2002,

Yun He, Chris H.Q. Ding, MPI and OpenMP Paradigms on Cluster of SMP Architectures: the Vacancy Tracking Algorithm for Multi-Dimensional Array Transpose, SuperComputing 2002, November 2002,

Chris Ding and Yun He, “Climate Modeling: Coupling Component Models by MPH for Distributed Multi-Component Environment”, Proceedings of the Tenth Workshop on the Use of High Performance Computing in Meteorology, World Scientific Publishing Company, Incorporated, November 2002, 219-234,

C. H.Q. Ding and Y. He*, Effective Methods in Reducing Communication Overheads in Solving PDE Problems on Distributed-Memory Computer Architectures, Grace Hopper Celebration of Women in Computing 2002, October 2002,

Yun He, Chris H.Q. Ding, MPI and OpenMP Paradigms on Cluster of SMP Architectures: the Vacancy Tracking Algorithm for Multi-Dimensional Array Transpose, WOMPAT 2002: Workshop on OpenMP Applications and Tools, University of Alaska, August 2002,

2001

C. H.Q. Ding and Y. He, “A Ghost Cell Expansion Method for Reducing Communications in Solving PDE Problems”, Proceedings of SuperComputing 2001 Conference, November 2001, LBNL 47929

C. H.Q. Ding and Y. He, “MPH: a Library for Distributed Multi-Component Environment”, May 2001, LBNL 47930

Y. He and C. H.Q. Ding, “Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications”, Journal of Supercomputing, vol.18, March 2001, 18:259-277,

2000

Y. He and C. H.Q. Ding, “Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications”, Proceedings of the Ninth Workshop on the Use of High Performance Computing in Meteorology: Developments in Teracomputing, November 2000, 296-317,

Y. He, C. H.Q. Ding, Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications, the Ninth Workshop on the Use of High Performance Computing in Meteorology: Developments in Teracomputing, European Centre for Medium-Range Weather Forecasts, 2000,

Yun He, Ti-Petsc: Integrating Titanium with PETSc, Invited talk at A Workshop on the ACTS Toolkit: How can ACTS work for you? Lawrence Berkeley National Laboratory, September 2000,

Yun He, Computational Ocean Modeling, Invited talk, Computer Science Graduate Fellow (CSGF) Workshop, Lawrence Berkeley National Laboratory, July 2000,

Y. He, C. H.Q. Ding, Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications, International Conference on Supercomputing (ICS'00), May 2000,

X.-H. Yan, Y. He, R. D. Susanto, and W. T. Liu, “Multisensor Studies on El Nino-Southern Oscillations and Variabilities in Equatorial Pacific”, J. of Adv. Marine Sciences and Tech. Society, 4(2), 2000, 4(2):289-301,

1999

C. H.Q. Ding and Y. He, “Data Organization and I/O in a Parallel Ocean Circulation Model”, Proceedings of Supercomputing 1999 Conference, November 1999, LBNL 43384

Yun He, Computational Aspects of Modular Ocean Model Development, invited talk at Jet Propulsion Laboratory, April 1, 1999,

1998

Yun He, Correlation Analyses of Scatterometer Wind, Altimeter Sea Level and SST Data for the Tropical Pacific Ocean, American Geophysical Union, 1998 Spring Meeting, May 1998,

1997

Y. He, X.-H. Yan, and W. T. Liu, “Surface Heat Fluxes in the Western Equatorial Pacific Ocean Estimated by an Inverse Mixed Layer Model and by Bulk Parameterization”, Journal of Physical Oceanography, Vol.27, No.11, November 1997, Vol.27, :2477-2487,

Yun He, El Nino 1997, 1997 Coast Day, College of Marine Studies, University of Delaware, October 1, 1997,

X.-H. Yan, Y. He, W. T. Liu, Q. Zheng, and C.-R. Ho, “Centroid Motion of the Western Pacific Warm Pool in the Recent Three El Nino Events,”, Journal of Physical Oceanography, Vol.27, No.5, May 1997, Vol.27, :837-845,

1996

Yun He, Estimation of Surface Net Heat Flux in the Western Tropical Pacific Using TOPEX/Poseidon Altimeter Data, American Geophysical Union, 1996 Spring Meeting, May 1, 1996,

Jason Hick

2014

J. Hick, Scalability Challenges in Large-Scale Tape Environments, IEEE Mass Storage Systems & Technologies 2014, June 4, 2014,

Provides an overview of NERSC storage systems and focuses on challenges we experience with HPSS at NERSC and with the tape industry.

S. Parete-Koon, B. Caldwell, S. Canon, E. Dart, J. Hick, J. Hill, C. Layton, D. Pelfrey, G. Shipman, D. Skinner, J. Wells, J. Zurawski, “HPC's Pivot to Data”, Conference, May 5, 2014,

 

Computer centers such as NERSC and OLCF have traditionally focused on delivering computational capability that enables breakthrough innovation in a wide range of science domains. Accessing that computational power has required services and tools to move the data from input and output to computation and storage. A pivot to data is occurring in HPC. Data transfer tools and services that were previously peripheral are becoming integral to scientific workflows.  Emerging requirements from high-bandwidth detectors, highthroughput screening techniques, highly concurrent simulations, increased focus on uncertainty quantification, and an emerging open-data policy posture toward published research are among the data-drivers shaping the networks, file systems, databases, and overall HPC environment. In this paper we explain the pivot to data in HPC through user requirements and the changing resources provided by HPC with particular focus on data movement. For WAN data transfers we present the results of a study of network performance between centers

 

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

Jason Hick, NERSC, Storage Systems: 2014 and beyond, February 6, 2014,

2013

J. Hick, A Storage Outlook for Energy Sciences: Data Intensive, Throughput and Exascale Computing, FujiFilm Executive IT Summit 2013, October 24, 2013,

Provides an overview of the computational and storage systems at NERSC.  Discusses the major types of computation scientists conduct at the facility, the challenges and opportunities the storage systems will face in the near future, and the role of tape technology at the Center.

J. Hick, Storage at a Distance, Open Fabrics Alliance User Day 2013, April 19, 2013,

Presentation to generate discussion on current state-of-the-practice for the topic of storage at a distance and synergy with Open Fabrics Alliance users.

J. Hick, GPFS at NERSC/LBNL, SPXXL Winter 2013, January 7, 2013,

A report to SPXXL conference participants on state of the NERSC Global File System architecture, achievements and directions.

2012

Z. Liu, M. Veeraraghavan, Z. Yan, C. Tracyy, J. Tiez, I. Fosterz, J. Dennisx, J. Hick, Y. Lik and W. Yang, “On using virtual circuits for GridFTP transfers”, Conference, November 12, 2012,

The goal of this work is to characterize scientific data transfers and to determine the suitability of dynamic virtual circuit service for these transfers instead of the currently used IP-routed service. Specifically, logs collected by servers executing a commonly used scientific data transfer application, GridFTP, are obtained from three US super-computing/scientific research centers, NERSC, SLAC, and NCAR, and analyzed. Dynamic virtual circuit (VC) service, a relatively new offering from providers such as ESnet and Internet2, allows for the selection of a path on which a rate-guaranteed connection is established prior to data transfer. Given VC setup overhead, the first analysis of the GridFTP transfer logs characterizes the duration of sessions, where a session consists of multiple back-to-back transfers executed in batch mode between the same two GridFTP servers. Of the NCAR-NICS sessions analyzed, 56% of all sessions (90% of all transfers) would have been long enough to be served with dynamic VC service. An analysis of transfer logs across four paths, NCAR-NICS, SLAC-BNL, NERSC-ORNL and NERSC-ANL, shows significant throughput variance, where NICS, BNL, ORNL, and ANL are other US national laboratories. For example, on the NERSC-ORNL path, the inter-quartile range was 695 Mbps, with a maximum value of 3.64 Gbps and a minimum value of 758 Mbps. An analysis of the impact of various factors that are potential causes of this variance is also presented.

Damian Hazen, Jason Hick, “MIR Performance Analysis”, June 12, 2012, LBNL LBNL-5896E

 

We provide analysis of Oracle StorageTek T10000 Generation B (T10KB) Media Information Record (MIR) Per- formance Data gathered over the course of a year from our production High Performance Storage System (HPSS). The analysis shows information in the MIR may be used to improve tape subsystem operations. Most notably, we found the MIR information to be helpful in determining whether the drive or tape was most suspect given a read or write error, and for helping identify which tapes should not be reused given their history of read or write errors. We also explored using the MIR Assisted Search to order file retrieval requests. We found that MIR Assisted Search may be used to reduce the time needed to retrieve collections of files from a tape volume. 

 

N. Balthaser, J. Hick, W. Hurlbert, StorageTek Tape Analytics: Pre-Release Evaluation at LBNL, LTUG 2012, April 25, 2012,

A report to the Large Tape Users Group (LTUG) annual conference on a pre-release evaluation of the new software product, StorageTek Tape Analytics (STA).  We provide a user's perspective on what we found useful, some suggestions for improvement, and some key new features that would enhance the product.

“NERSC Exceeds Reliability Standards With Tape-Based Active Archive”, Active Archive Alliance Case Study, February 10, 2012,

J. Hick, NERSC Site Update (NGF), SPXXL Winter 2012, January 10, 2012,

Update to NERSC Global File (NGF) System, based on IBM's GPFS, to the SPXXL User Group community.  Includes an overview of NERSC, the file systems that comprise NGF, some of our experiences with GPFS, and recommendations for improving scalability.

2011

M. Cary, J. Hick, A. Powers, HPC Archive Solutions Made Simple, Half-day Tutorial at Super Computing (SC11), November 13, 2011,

Half-day tutorial at SC11 where attendees were provided detailed information about HPC archival storage systems for general education.  The tutorial was the first SC tutorial to cover the topic of archival storage and helped sites to understand the characteristics of these systems, the terminology for archives, and how to plan, size and manage these systems.

J. Hick, Digital Archiving and Preservation in Government Departments and Agencies, Oracle Open World 2011, October 6, 2011,

Attendees of this invited talk at Oracle Open World 2011 heard about the NERSC Storage Systems Group and the HPSS Archive and Backup systems we manage.  Includes information on why we use disk and tape to store data, and an introduction to the Large Tape Users Group (LTUG).

J. Hick, J. Hules, A. Uselton, “DOE HPC Best Practices Workshop: File Systems and Archives”, Workshop, September 27, 2011,

The Department of Energy has identified the design, implementation, and usability of file systems and archives as key issues for current and future HPC systems. This workshop addresses current best practices for the procurement, operation, and usability of file systems and archives. Furthermore, the workshop addresses whether system challenges can be met by evolving current practices.

J. Hick, The NERSC Global Filesystem (NGF), Computing in Atmospheric Sciences 2011 (CAS2K11), September 13, 2011,

Provides the Computing in Atmospheric Sciences 2011 conference attendees an overview and configuration details of the NERSC Global Filesystem (NGF).  Includes a few lessons learned and future directions for NGF.

J. Hick, M. Andrews, Leveraging the Business Value of Tape, FujiFilm Executive IT Summit 2011, June 9, 2011,

Describes how tape is used in the HPSS Archive and HPSS Backup systems at NERSC.  Includes some examples of our organizations tape policies, our roadmap to Exascale and an example of tape in the Exascale Era, our observed tape reliability, and an overview of our locally developed Parallel Incremental Backup System (PIBS) which performs backups of our NGF file system.

J. Hick, Storage Supporting DOE Science, Preservation and Archiving Special Interest Group (PASIG) 2011, May 12, 2011,

Provided attendees of the Preservation and Archiving Special Interest Group conference attendees with an overview of NERSC, the Storage Systems Group, and the HPSS Archives and NGF File Systems we support.  Includes some information on a large tape data migration and our observations on the reliability of tape at NERSC.

D. Hazen, J. Hick, W. Hurlbert, M. Welcome, Media Information Record (MIR) Analysis, LTUG 2011, April 19, 2011,

Presentation of Storage Systems Group findings from a year-long effort to collect and analyze Media Information Record (MIR) statistics from our in-production Oracle enterprise tape drives at NERSC.  We provide information on the data collected, and some highlights from our analysis. The presentation is primarily intended to declare that the information in the MIR is important to users or customers to better operating and managing their tape environments.

J. Hick, I/O Requirements for Exascale, Open Fabrics Alliance 2011, April 4, 2011,

This talk provides an overview of the DOE Exascale effort, high level IO requirements, and an example of exascale era tape storage.

2010

Neal Master, Matthew Andrews, Jason Hick, Shane Canon, Nicholas J. Wright, “Performance Analysis of Commodity and Enterprise Class Flash Devices”, Petascale Data Storage Workshop (PDSW), November 2010,

“Re-thinking data strategies is critical to keeping up”, J. Hick, HPC Source Magazine, June 1, 2010,

D. Hazen, J. Hick, HPSS v8 Metadata Conversion, HPSS 8.1 Pre-Design Meeting, April 7, 2010,

Provided information about the HPSS metadata conversion software to other developers of HPSS.  Input was important to establishing a design for the version 8 HPSS metadata conversions.

Sim A., Gunter D., Natarajan V., Shoshani A., Williams D., Long J., Hick J., Lee J., Dart E., “Efficient Bulk Data Replication for the Earth System Grid”, Data Driven E-science: Use Cases and Successful Applications of Distributed Computing Infrastructures (Isgc 2010), Springer-Verlag New York Inc, 2010, 435,

D. Cook, J. Hick, J. Minton, H. Newman, T. Preston, G. Rich, C. Scott, J. Shoopman, J. Noe, J. O'Connell, G. Shipman, D. Watson, V. White, “HPSS in the Extreme Scale Era: Report to DOE Office of Science on HPSS in 2018–2022”, Lawrence Berkeley National Laboratory technical report LBNL-3877E, 2010, LBNL 3877E

Kettimuthu Raj, Sim Alex, Gunter Dan, Allcock Bill, Bremer Peer T., Bresnahan John, Cherry Andrew, Childers Lisa, Dart Eli, Foster Ian, Harms Kevin, Hick Jason, Lee Jason, Link Michael, Long Jeff, Miller Keith, Natarajan Vijaya, Pascucci Valerio, Raffenetti Ken, Ressman David, Williams Dean, Wilson Loren, Winkler Linda, “Lessons Learned from Moving Earth System Grid Data Sets over a 20 Gbps Wide-Area Network”, Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing HPDC 10, New York NY USA, 2010, 316--319,

A. Sim, D. Gunter, V. Natarajan, A. Shoshani, D. Williams, J. Long, J. Hick, J. Lee, E. Dart, “Efficient Bulk Data Replication for the Earth System Grid”, International Symposium on Grid Computing, 2010,

2009

A. Shoshani, D. Rotem, Scientific Data Management: Challenges, Technology, and Deployment, Book, (December 16, 2009)

This book provides a comprehensive understanding of the latest techniques for managing data during scientific exploration processes, from data generation to data analysis.

J. Hick, Sun StorageTek Tape Hardware Migration Experiences, LTUG 2009, April 24, 2009,

Talk addresses specific experiences and lessons learned in migrating our entire HPSS archive from StorageTek 9310 Powderhorns using 9840A, 9940B, and T10KA tape drives to StorageTek SL8500 Libraries using 9840D and T10KB tape drives.

W. Allcock, R. Carlson, S. Cotter, E. Dart, V. Dattoria, B. Draney, R. Gerber, M. Helm, J. Hick, S. Hicks, S. Klasky, M. Livny, B. Maccabe, C. Morgan, S. Morss, L. Nowell, D. Petravick, J. Rogers, Y. Sekine, A. Sim, B. Tierney, S. Turnbull, D. Williams, L. Winkler, F. Wuerthwein, “ASCR Science Network Requirements”, Workshop, April 15, 2009,

ESnet publishes reports from Network and Science Requirement Workshops on a regular basis.  This report was the product of a two-day workshop in Washington DC that addresses science requirements impacting operations of networking for 2009.

2008

A. Mokhtarani, W. Kramer, J. Hick, “Reliability Results of NERSC Systems”, Web site, August 28, 2008,

In order to address the needs of future scientific applications for storing and accessing large amounts of data in
an efficient way, one needs to understand the limitations of current technologies and how they may cause system
instability or unavailability. A number of factors can impact system availability ranging from facility-wide
power outage to a single point of failure such as network switches or global file systems. In addition, individual
component failure in a system can degrade the performance of that system. This paper focuses on analyzing both
of these factors and their impacts on the computational and storage systems at NERSC. Component failure data
presented in this report primarily focuses on disk drive in on of the computational system and tape drive failure
in HPSS. NERSC collected available component failure data and system-wide outages for its computational and
storage systems over a six-year period and made them available to the HPC community through the Petascale
Data Storage Institute.

Eric L. Hjort

2012

Eric Hjort, Larry Pezzaglia, Iwona Sakrejda, PDSF at NERSC: Site Report, A talk at the HEPiX Spring 2012 Workshop, Prague, Czech Republic, April 24, 2012,

PDSF is a commodity Linux cluster at NERSC which has been in continuous operation since 1996. This talk will provide a status update on the PDSF system and summarize recent changes at NERSC. Highlighted PDSF changes include the conversion to xCAT-managed netboot node images, the ongoing deployment of Scientific Linux 6, and the introduction of XRootD for STAR.

Wayne E. Hurlbert

2013

N. Balthaser, W. Hurlbert, T10KC Technology in Production, May 9, 2013,

Report to 2012  Large Tape User Group meeting regarding our production statistics and experiences using the Oracle T10000C tape drive.

2012

N. Balthaser, J. Hick, W. Hurlbert, StorageTek Tape Analytics: Pre-Release Evaluation at LBNL, LTUG 2012, April 25, 2012,

A report to the Large Tape Users Group (LTUG) annual conference on a pre-release evaluation of the new software product, StorageTek Tape Analytics (STA).  We provide a user's perspective on what we found useful, some suggestions for improvement, and some key new features that would enhance the product.

2011

J. Hick, J. Hules, A. Uselton, “DOE HPC Best Practices Workshop: File Systems and Archives”, Workshop, September 27, 2011,

The Department of Energy has identified the design, implementation, and usability of file systems and archives as key issues for current and future HPC systems. This workshop addresses current best practices for the procurement, operation, and usability of file systems and archives. Furthermore, the workshop addresses whether system challenges can be met by evolving current practices.

D. Hazen, J. Hick, W. Hurlbert, M. Welcome, Media Information Record (MIR) Analysis, LTUG 2011, April 19, 2011,

Presentation of Storage Systems Group findings from a year-long effort to collect and analyze Media Information Record (MIR) statistics from our in-production Oracle enterprise tape drives at NERSC.  We provide information on the data collected, and some highlights from our analysis. The presentation is primarily intended to declare that the information in the MIR is important to users or customers to better operating and managing their tape environments.

Keith Jackson

2010

Keith Jackson, Lavanya Ramakrishnan, Karl Runge, and Rollin Thomas, “Seeking Supernovae in the Clouds: A Performance Study”, ScienceCloud 2010, the 1st Workshop on Scientific Cloud Computing, Chicago, Illinois, June 2010,

Lavanya Ramakrishnan, R. Jackson, Canon, Cholia, John Shalf, “Defining future platform requirements for e-Science clouds”, SoCC, New York, NY, USA, 2010, 101-106,

Doug Jacobsen

2014

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

Yushu Yao, NERSC; Douglas Jacobsen, NERSC, Connecting to NERSC, NUG 2014, February 3, 2014,

Jihan Kim

2012

Allison Dzubak, Li-Chiang Lin, Jihan Kim, Joseph Swisher, Roberta Poloni, Sergei Maximoff, Berend Smit, Laura Gagliardi, “Ab initio Carbon Capture in Open-Site Metal Organic Frameworks”, Nature Chemistry, 2012,

Jihan Kim, Richard Martin, Oliver Ruebel, Maciej Haranczyk, Berend Smit, “High-throughput Characterization of Porous Materials Using Graphics Processing Units”, Journal of Chemical Theory and Computation, 2012,

Jihan Kim, Li-Chiang Lin, Richard Martin, Joseph Swisher, Maciej Haranczyk, Berend Smit, “Large Scale Computational Screening of Zeolites for Ethene/Ethane Separation”, Langmuir, 2012,

Richard Martin, Thomas Willems, Li-Chiang Lin, Jihan Kim, Joseph Swisher, Berend Smit, Maciej Harancyzk, “Similarity-driven Discovery of Porous Materials for Adsorption-based Separations”, In Preparation, 2012,

Li-Chiang Lin, Adam Berger, Richard Martin, Jihan Kim (co-first author), Joseph Swisher, Kuldeep Jariwala, Chris Rycroft, Abhoyjit Brown, Michael Deem, Maciej Haranczyk, Berend Smit, “In Silico Screening of Carbon Capture Materials”, Nature Materials, 2012,

Jihan Kim, Berend Smit, “Efficient Monte Carlo Simulations of Gas Molecules Inside Porous Materials”, Journal of Chemical Theory and Computation, 2012,

J. Kim, A. Koniges, R.L. Martin, J. Swisher, M. Haranczyk, B. Smit, Computational Screening of Novel Carbon Capture Materials, 2012 GTC GPU Conference, 2012,

2011

Jihan Kim, Alice Koniges, Richard Martin, Maciej Harancyzk, Joseph Swisher, Berend Smit, “GPU Computational Screening of Carbon Capture Materials - Paper”, Proceedings of the 2011 SciDAC Conference, 2011,

Jihan Kim, Jocelyn Rodgers, Manuel Athenes, Berend Smit, “Molecular Monte Carlo Simulations Using Graphics Processing Units: To Waste Recycle or Not?”, Journal of Chemical Theory and Computation, 2011,

J. Kim, A. Koniges, R.L Martin, M. Haranczyk, J. Swisher, B. Smit, “GPU Computational Screening of Carbon Capture Materials”, 2011 SciDAC Conference, Denver, CO, 2011,

2010

J. Kim, A. Koniges, B. Smit, M. Head-Gordon, “Calculation of RI-MP2 Gradient using Fermi GPUs”, Molecular Quantum Mechanics 2010, May 2010,

Alice Koniges, Robert Preissl, Jihan Kim, D Eder, A Fisher, N Masters, V Mlaker, S Ethier, W Wang, M Head-Gordon, N Wichmann, “Application acceleration on current and future Cray platforms,”, BEST PAPER, Proc. Cray User Group Meeting, Edinburgh, Scotland, May 2010,

Alice Evelyn Koniges

2014

J.N. Brooks, A. Hassanein, A. Koniges, P.S. Krstic, T.D. Rognlien, T. Sizyuk, V. Sizyuk, and D. P. Stotler, “Scientific and Computational Challenges in Coupled Plasma Edge/Plasma-Material Interactions for Fusion Tokamaks”, Contrib. Plasma Phys. 54, No. 4-6, 329 – 340, 2014,

Alice Koniges, APPS on HPX, US Department of Energy, Exascale Software Stack, PI Meeting, Boston MA, May 27-28, 2014,

Alice Koniges, Multimaterial Multiphysics Modeling of Complex Experimental Configurations, LBNL Center for Beam Physics Seminar Series, February 14, 2014,

Alice Koniges, Nathan Masters, Aaron Fisher, David Eder, Wangyi Liu, Robert Anderson, David Benson,
and Andrea Bertozzi,
“Multi-Matierial ALE with AMR for Modeling Hot Plasmas and Cold Fragmenting Materials”, Invited for special issue of Plasma Science and Technology (in review), 2014,

A.C. Fisher, D.S. Bailey, T.B. Kaiser, D.C. Eder, B.T.N. Gunney, N.D.
Masters, A.E. Koniges, R.W. Anderson,
“An AMR Capable Finite Element Diffusion Solver for ALE Hydrocodes”, Invited for special issue of Plasma Science and Technology (in review), 2014,

Alice Koniges, Wangyi Liu, Steven Lidia, Thomas Schenkel, John Barnard, Alex Friedman, David Eder, Aaron Fisher, and Nathan Masters, “Advanced Target Effects Modeling for Ion Accelerators and other High-Energy-Density Experiments”, The Eighth International Conference on Inertial Fusion Sciences and Application (in review), 2014,

JJ Barnard, RM More, M Terry, A Friedman, E Henestroza, A Koniges, JW Kwan, A Ng, PA Ni, W Liu, BG Logan, E Startsev, A Yuen, “NDCX-II target experiments and simulations”, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment Volume 733, January 2014,

2013

Pavan Balaji, Alice Koniges, Robert Harrison, Tim Mattson, Nick Wright, David Bernholdt, Application Grand Challenges in the Heterogeneous Accelerator Era, SC13 Birds of a Feather: Invited Panelist, November 21, 2013,

Accelerators have gained prominence as the next disruptive technology with a potential to provide a non-incremental jump in performance. However, the number of applications that have actually moved to accelerators is still limited because of many reasons, arguably the biggest of which is the gap in understanding between accelerator and application developers. This BoF is an application oriented session that aims to bring the two camps of application developers and accelerator developers head-to-head.

Tim Mattson, Alice Koniges, Simon McIntosh-Smith, OpenCL: A Hands-On Introduction, SC13 Tutorial, November 18, 2013,

OpenCL is an open standard for programming heterogeneous parallel computers composed of CPUs, GPUs and other processors. OpenCL consists of a framework to manipulate the host CPU and one or more compute devices (CPUs, GPUs or accelerators), and a C-based programming language for writing programs for the compute devices. Using OpenCL, a programmer can write parallel programs that harness all of the resources of a heterogeneous computer. In this hands-on tutorial, we will introduce OpenCL. For ease of learning we will focus on the easier to use C++ API, but attendees will also gain an understanding of OpenCLs C API. The format will be a 50/50 split between lectures and exercises. Students will use their own laptops (Windows, Linux or OS/X) and log into a remote server running an OpenCL platform on a range of different processors. Alternatively, students can load OpenCL onto their own laptops prior to the course (Intel, AMD and NVIDIA provide OpenCL SDKs. Apple laptops with X-code include OpenCL by default). By the end of the course, attendees will be able to write and optimize OpenCL programs, and will have a collection of example codes to help with future OpenCL program development.

Alice Koniges, Wangyi Liu, John Barnard, Alex Friedman, Grant Logan, David Eder, Aaron Fisher, Nathan Masters, and Andrea Bertozzi, “Modeling warm dense matter experiments using the 3D ALE-AMR code and the move toward exascale computing”, EPJ Web of Conferences 59, 09006, 2013,

D. Eder, D. Bailey, F. Chambers, I. Darnell, P. Di Nicola, S. Dixit, A. Fisher, G.Gururangan, D. Kalantar, A. Koniges, W. Liu, M. Marinak, N. Masters, V. Mlaker, R. Prasad, S. Sepke, P. Whitman, “Observations and modeling of debris and shrapnel impacts on optics and diagnostics at the National Ignition Facility”, EPJ Web of Conferences 59, 08010, 2013,

A. Koniges, R. Gerber, D. Skinner, Y. Yao, Y. He, D. Grote, J-L Vay, H. Kaiser, and T. Sterling, “Plasma Physics Simulations on Next Generation Platforms”, 55th Annual Meeting of the APS Division of Plasma Physics, Volume 58, Number 16, November 11, 2013,

The current high-performance computing revolution provides opportunity for major increases in computational power over the next several years, if it can be harnessed. This transition from simply increasing the single-processor and network performance to a different architectural paradigms forces application programmers to rethink the basic models of parallel programming from both the language and problem division standpoints. One of the major computing facilities available to researchers in fusion energy is the National Energy Research Scientific Computing Center. As the mission computing center for DOE, Office of Science, NERSC is tasked with helping users to overcome the challenges of this revolution both through the use of new parallel constructs and languages and also by enabling a broader user community to take advantage of multi-core performance. We discuss the programming model challenges facing researchers in fusion and plasma physics in for a variety of simulations ranging from particle-in-cell to fluid-gyrokinetic and MHD models.

Alice Koniges, “The Petascale Initiative in Computational Science and Engineering”, Final Report, October 31, 2013,

D.C. Eder, A.C. Fisher, A.E. Koniges and N.D. Masters, “Modelling debris and shrapnel generation in inertial confinement fusion experiments”, Nuclear Fusion 53 113037, 2013,

Modelling and mitigation of damage are crucial for safe and economical operation of high-power laser facilities. Experiments at the National Ignition Facility use a variety of targets with a range of laser energies spanning more than two orders of magnitude (~14 kJ to ~1.9 MJ). Low-energy inertial confinement fusion experiments are used to study early-time x-ray load symmetry on the capsule, shock timing, and other physics issues. For these experiments, a significant portion of the target is not completely vaporized and late-time (hundreds of ns) simulations are required to study the generation of debris and shrapnel from these targets. Damage to optics and diagnostics from shrapnel is a major concern for low-energy experiments. We provide the first full-target simulations of entire cryogenic targets, including the Al thermal mechanical package and Si cooling rings. We use a 3D multi-physics multi-material hydrodynamics code, ALE-AMR, for these late-time simulations. The mass, velocity, and spatial distribution of shrapnel are calculated for three experiments with laser energies ranging from 14 to 250 kJ. We calculate damage risk to optics and diagnostics for these three experiments. For the lowest energy re-emit experiment, we provide a detailed analysis of the effects of shrapnel impacts on optics and diagnostics and compare with observations of damage sites.

Jean-Luc Vay, Cameron G. R. Geddes, Alice Koniges, Alex Friedman, David P. Grote, David L. Bruhwiler, John P. Verboncoeur, “White Paper on DOE-HEP Accelerator Modeling Science Activities”, originally presented at the US Department of Energy workshop: Community Summer Study, October 1, 2013,

A. Koniges, W. Lui, Y. He, D. Eder, A. Fisher, N. Masters, and R. W. Anderson, Multi-Material Plasma Modeling on HPC Platforms, Invited: 23rd International Conference on Numerical Simulation of Plasmas Beijing, China, September 13, 2013,

A. Koniges, W. Lui, S. Lidia, T. Schenkel, J. Barnard, A. Friedman, D. Eder, A. Fisher, and N. Masters, Advanced Target Effects Modeling for Ion Accelerators and other High-Energy-Density Experiments, 8th International Conference on Inertial Fusion Sciences and Applications, Nara, Japan, September 10, 2013,

Alice Koniges, Jean-Luc Vay, Alex Friedman, Hartmut Kaiser, and Thomas Sterling, Invited Talk: Consideration of Asynchronous Algorithms for Particle-Grid Simulations, DOE Workshop on Applied Mathematics Research for Exascale Computing, Washington DC, August 21-22,, 2013,

Alice Koniges, Jean-Luc Vay, Alex Friedman,Hartmut Kaiser, and Thomas Sterling, “Position Paper: Consideration of Asynchronous Algorithms for Particle-Grid Simulations”, 2013,

A. Friedman, R. H. Cohen, D. P. Grote, W. M. Sharp, I. D. Kaganovich, A. E. Koniges, W. Liu, “Heavy Ion Beams and Interactions with Plasmas and Targets (HEDLP and IFE)”, NERSC FES Requirements Workshop: Heavy Ion Fusion and Non-Neutral Plasmas, March 2013,

Alice Koniges, Praveen Narayanan, Robert Preissl, Xuefei Yuan, Proxy Design and Optimization in Fusion and Accelerator Physics, SIAM Conference on Computational Science and Engineering, February 25, 2013,

David E. Keyes, Lois Curfman McInnes, Carol Woodward, William Gropp, Eric Myra, Michael Pernice,
John Bell, Jed Brown, Alain Clo, Jeffrey Connors, Emil Constantinescu, Don Estep, Kate Evans,
Charbel Farhat, Ammar Hakim, Glenn Hammond, Glen Hansen, Judith Hill, Tobin Isaac, Xiaomin Jiao, Kirk Jordan,
Dinesh Kaushik, Efthimios Kaxiras, Alice Koniges, et al.,
“Multiphysics Simulations Challenges and Opportunities”, International Journal of High Performance Computing Applications, February 2013, 27:4--83,

J. Barnard, R. M. More, P. A. Ni, A. Friedman, E. Henestroza, I. Kaganovich, A. Koniges, J. W. Kwan, W. Liu, A. Ng,
B.G. Logan, E. Startsev, M. Terry, A. Yuen,
NDCX-II Experimental Plans and Target Simulations, West Coast High Energy Density Science Cooperative Meeting Berkeley and Palo Alto, California, January 2013,

Xuefei Yuan, Xiaoye S Li, Ichitaro Yamazaki, Stephen C Jardin, Alice E Koniges, David E Keyes, “Application of PDSLin to the magnetic reconnection problem”, Computational Science & Discovery, 2013, 6:014002,

2012

Alice Koniges, Katherine Yelick, Rolf Rabenseifner, Reinhold Bader, David Eder, Filip Blagojevic, Robert Preissl, Paul Hargrove, Introduction to PGAS (UPC and CAF) and Hybrid for Multicore Programming, SC12 Full Day Tutorial, November 2012,

Michael A. Heroux, Alice E. Koniges, David F. Richards, Richard F. Barrett, Thomas Brunner, Using Application Proxies for Co-design of Future HPC Computer Systems and Applications, SC12 Full Day Tutorial, November 2012,

Wangyi Liu, John Barnard, Alice Koniges, David Eder, Nathan Masters, Aaron Fisher, Alex Friedman, “A numerical scheme for including surface tension effects in hydrodynamic simulation: a full Korteweg type model without parasitic flows”, APS DPP 2012, 2012,

Thomas Ludwig, Costas Bekas, Alice Koniges, Kengo Nakajima, “Topic 15: High Performance and Scientific Applications”, Euro-Par 2012 Parallel Processing, Springer, 2012, Lecture:779--780,

Alice Koniges, Opportunities and Challenges for Domain-Specific Languages in Fusion Applications, ASCR Exascale PI Meeting, October 2012,

Alice Koniges, Mike Heroux, Using Applicaton Proxies for Co-design of Future HPC Computer Systems and Applicatons, Dagstuhl Co-design Workshop, May 22, 2012,

J. Kim, A. Koniges, R.L. Martin, J. Swisher, M. Haranczyk, B. Smit, Computational Screening of Novel Carbon Capture Materials, 2012 GTC GPU Conference, 2012,

Gabriele Jost, Alice Koniges, “Hardware Trends and Implications for Programming Models”, Handbook of Research on Computational Science and Engineering: Theory and Practice, ( 2012) Pages: 1-21

2011

Jihan Kim, Alice Koniges, Richard Martin, Maciej Harancyzk, Joseph Swisher, Berend Smit, “GPU Computational Screening of Carbon Capture Materials - Paper”, Proceedings of the 2011 SciDAC Conference, 2011,

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Alice Koniges, David Eder, “Modeling droplet breakup effects with applications in the warm dense matter NDCX experiment”, APS DPP, 2011,

Cherri M. Pancake, Debra Goldfarb, Alice Koniges, Candy Culhane, The View, HPC Edition, SC11 Panel, November 2011,

This panel will be a take-off on ABC's popular morning talk program. A lively format will be used to cover a number of controversial topics in the development and application of HPC. Four women from the HPC world will serve as "co-hosts," discussing topics with international experts associated with specific topics, such as Jean-Yves Berthou (European Exascale Software Initiative), Dave Turek (IBM), Ryan Waite (Microsoft), and Matt Fetes (venture capitalist). The goal is to air a variety of viewpoints in a lively and entertaining way. The panel will raise thought-provoking questions such as why the HPC community has such a hard time converging on standards, whether co-design is really affordable at HPC scales, why efficiency isn't our goal rather than scalability, whether exascale investments can really pay off, and why high-level languages haven't had real impact in HPC. Interactive polling will be used to involve the audience in charting a course for HPC's future - so be sure to bring your laptop or smartphone.

Robert Preissl, Nathan Wichmann, Bill Long, John Shalf, Stephane Ethier, Alice Koniges, “Multithreaded global address space communication techniques for gyrokinetic fusion applications on ultra-scale platforms”, Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, 78,

Sean Farley, Ben Dudson, Praveen Narayanan, Lois Curfman McInnes, Maxim Umansky, Xuexiao Xu, Satish Balay, John Cary, Alice Koniges, Carol Woodward, Hong Zhang, “BOUT++: Performance Characterization and Recent Advances in Design”, International Conference on Numerical Simulations of Plasmas, Long Beach, New Jersey, 2011, 2011,

David Eder, David Bailey, Andrea Bertozzi, Aaron Fisher, Alice Koniges, Wangyi Liu, Nathan Masters, Marty Marniak, Late-Time Numerical Simulations of High-Energy-Density (HED) Targets, Twenty Second International Conference on Numerical Simulations of Plasmas, September 7, 2011,

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Velemir Mlaker,
Alice Koniges, David Eder,
“Modeling droplet breakup effects in warm dense matter experiments with diffuse interface methods in the ALE-AMR code”, Proceedings of the 2011 SciDAC Conference, August 4, 2011,

Alice Koniges, Multiphysics Simulations: Challenges and Opportunities -- Insertion Paths, Panel - Institute for Computing in Science, Workshop, August 2011,

Saman Amarasinghe, Mary Hall, Richard Lethin, Keshav Pingali, Dan Quinlan, Vivek Sarkar, John Shalf, Robert Lucas, Katherine Yelick, Pavan Balaji, Pedro C. Diniz, Alice Koniges, Marc Snir, Sonia R. Sachs, “Exascale Programming Challenges”, 2011,

Alice Koniges, Challenges and Application Gems on the Path to Exascale, http://science.energy.gov/ascr/research/computer-science/programming-challenges-workshop/, July 2011,

J. Kim, A. Koniges, R.L Martin, M. Haranczyk, J. Swisher, B. Smit, “GPU Computational Screening of Carbon Capture Materials”, 2011 SciDAC Conference, Denver, CO, 2011,

W. M. Sharp, A. Friedman, D. P. Grote, J. J. Barnard, R. H. Cohen, M. A. Dorf, S. M. Lund, L. J. Perkins, M. R. Terry, B. G. Logan, F. M. Bieniosek, A. Faltens, E. Henestroza, J.-Y. Jung, J. W. Kwan, , A. E. Koniges, E. P. Lee, S. M. Lidia, P. A. Ni, L. L. Reginato, P. K. Roy, P. A. Seidl, J. H. Takakuwa, J.-L. Vay, W. L. Waldron, R. C. Davidson, E. P. Gilson, I. D. Kaganovich, H. Qin, E. Startsev, I. Haber, R. A. Kishek, “Inertial Fusion Driven By Intense Heavy-Ion Beams”, Proceedings of 2011 Particle Accelerator Conference, New York, NY, USA, March 2011, 1386-1393,

CH Still, A Arsenlis, RB Bond, MJ Steinkamp, S Swaminarayan, DE Womble, AE Koniges, JR Harrison, JH Chen, “NNSA ASC Exascale Environment Planning, Applications Working Group, Report February 2011”, 2011,

Brian Austin, Ji Qiang, Jonathan Wurtele, Alice Koniges, “Influences of architecture and threading on the MPI communication strategies in an accelerator simulation code.”, SciDAC 2011, Denver, CO, 2011,

Wangyi Liu, John Bernard, Alex Friedman, Nathan Masters, Aaron Fisher, Velemir Mlaker, Alice Koniges, David Eder, “Modeling droplet breakup effects in warm dense matter experiments with diffuse interface methods in ALE-AMR code”, SciDAC conference, 2011,

Praveen Narayanan, Alice Koniges, Leonid Oliker, Robert Preissl, Samuel Williams, Nicholas J Wright, Maxim Umansky, Xueqiao Xu, Benjamin Dudson, Stephane Ethier, Weixing Wang, Jeff Candy, John R. Cary, “Performance Characterization for Fusion Co-design Applications”, Proceedings of CUG, 2011,

2010

J. Kim, A. Koniges, B. Smit, M. Head-Gordon, “Calculation of RI-MP2 Gradient using Fermi GPUs”, Molecular Quantum Mechanics 2010, May 2010,

Alice Koniges, Robert Preissl, Jihan Kim, D Eder, A Fisher, N Masters, V Mlaker, S Ethier, W Wang, M Head-Gordon, N Wichmann, “Application acceleration on current and future Cray platforms,”, BEST PAPER, Proc. Cray User Group Meeting, Edinburgh, Scotland, May 2010,

Alice Koniges, Robert Preissl, Stephan Ethier, John Shalf, What’s Ahead for Fusion Computing?, International Sherwood Fusion Theory Conference, April 2010,

Hongzhang Shan, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J Wright, “Analyzing the effect of different programming models upon performance and memory usage on cray xt5 platforms”, CUG2010, Edinburgh, Scotland, 2010,

AE Koniges, ND Masters, AC Fisher, RW Anderson, DC Eder, TB Kaiser, DS Bailey, B Gunney, P Wang, B Brown, K Fisher, F Hansen, BR Maddox, DJ Benson, M Meyers, A Geille, “ALE-AMR: A new 3D multi-physics code for modeling laser/target effects”, Journal of Physics: Conference Series, 2010, 244:032019,

 

D. C. Eder, R. W. Anderson, D. S. Bailey, P. Bell, D. J. Benson, A. L. Bertozzi, W. Bittle, D, Bradley, C. G. Brown, T. J. Clancy, H. Chen, J. M. Chevalier, P. Combis, L. Dauffy, C. S. Debonnel, M. J. Eckart, A. C. Fisher, A. Geille, V. Y. Glebov, J. Holder, J. P. Jadaud, O. Jones, T. B. Kaiser, D. Kalantar, H. Khater, J. Kimbrough, A. E. Koniges, O. L. Landen, B. J. MacGowan, N. D. Masters, A. MacPhee, B. R. Maddox, M. Meyers, S. Osher, R. Prasad, D. Raffestin, J. Raimbourg, V. Rekow, C. Sangster, P. Song, C. Stoeckl, M. L. Stowell, J. M. Teran, A. Throop, R. Tommasini, J. Vierne, D. White, P. Whitman, “Assessment and Mitigation of Radiation, EMP, Debris and Shrapnel Impacts at Mega-Joule Class Laser Facilities”, J. Physics, Conference Series, 2010, 244:0320018,

N. Masters, T.B. Kaiser, R.W. Anderson, D.C. Eder, A.C. Fisher, A.E. Koniges, “Laser Ray Tracing in a Parallel Arbitrary Lagrangian Eulerian Adaptive Mesh Refinement Hydrocode”, J. Physics, Conf. Ser. 244: 032022, 2010,

AC Fisher, DS Bailey, TB Kaiser, BTN Gunney, ND Masters, AE Koniges, DC Eder, RW Anderson, “Modeling heat conduction and radiation transport with the diffusion equation in NIF ALE-AMR”, Journal of Physics: Conference Series, 2010, 244:022075,

Hongzhang Shan, Filip Blagojevic, Seung-Jai Min, Paul Hargrove, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J Wright, “A programming model performance study using the NAS parallel benchmarks”, Scientific Programming, 2010, 18:153--167,

Robert Preissl, Alice Koniges, Stephan Ethier, Weixing Wang, Nathan Wichmann, “Overlapping communication with computation using OpenMP tasks on the GTS magnetic fusion code”, Scientific Programming, 2010, 18:139--151,

Gabriele Jost, Alice Koniges, “Special Issue: Exploring languages for expressing medium to massive on-chip parallelism”, Scientific Programming, 2010, 18:125--126,

2009

MA Meyers, H Jarmakani, BY Cao, CT Wei, B Kad, BA Remington, EM Bringa, B Maddox, D Kalantar, D Eder, A Koniges, “Laser compression and fragmentation of metals”, DYMAT 2009-9th International Conference on the Mechanical and Physical Behaviour of Materials under Dynamic Loading, 2009, 2:999--1006,

D C Eder, A E Koniges, N D Masters, A C Fisher, R W Anderson, K R Gaunt and D J Benson, Fragmentation and penetration visualization from the multi-physics ALE-AMR code, SciDAC 2009 J. Phys.: Conf. Ser. 180 013001, June 15, 2009,

 

On Monday, June 15, 2009, the SciDAC 2009 conference sponsored an Electronic Visualization and Poster Night. Scientists involved in DOE Office of Science research, such as SciDAC, INCITE, and core-funded programs, were encouraged to submit an image or animation to be shown at this event. A DVD of those images and animations is attached to the inside back cover of this proceedings book. 

 

A. E. Koniges, N. D. Masters, A. C. Fisher, R. W. Anderson, D. C. Eder, D. Benson, T. B. Kaiser, B. T. Gunney, P. Wang, B. R. Maddox, J. F. Hansen, D. H. Kalantar, P. Dixit, H. Jarmakani, M. A. Meyers, “A Predictive Model of Fragmentation using Adaptive Mesh Refinement and a Hierarchical Material Model”, LLNL-TR-411072, March 5, 2009,

Alice Koniges,D. Eder,O. Landen,R. Anderson,A. Fisher,B. Gunney,N. Masters,B. Maddox,F. Hansen,B. Brown,K. Fisher,T. Kaiser,A. Geille,J-P. Jadaud,J-M. Chevalier,D. Raffestin,D. Benson,M. Meyers,H. Jarmakani,B. Blue5, “Target Design and Debris Modeling with NIF ALE-AMR”, NIF Design Review, 2009,

2008

Tim Frazier, Alice Koniges, The National Ignition Facility Data Requirements, SC08 BOF: Computing with Massive and Persistent Data, 2008,

Subhash Saini, Robert Ciotti, Brian TN Gunney, Thomas E Spelce, Alice Koniges, Don Dossa, Panagiotis Adamidis, Rolf Rabenseifner, Sunil R Tiyyagura, Matthias Mueller, “Performance evaluation of supercomputers using hpcc and imb benchmarks”, Journal of Computer and System Sciences, 2008, 74:965--982,

DC Eder, AE Koniges, OL Landen, ND Masters, AC Fisher, OS Jones, TI Suratwala, LJ Suter, “Debris and shrapnel mitigation procedure for NIF experiments”, Journal of Physics: Conference Series, 2008, 112:032023,

AC Fisher, ND Masters, P Dixit, DJ Benson, AE Koniges, RW Anderson, BTN Gunney, P Wang, R Becker, “Hierarchical material models for fragmentation modeling in NIF-ALE-AMR”, Journal of Physics: Conference Series, 2008, 112:022027,

ND Masters, RW Anderson, NS Elliott, AC Fisher, BT Gunney, AE Koniges, “Interface reconstruction in two-and three-dimensional arbitrary Lagrangian-Eulerian adaptive mesh refinement simulations”, Journal of Physics: Conference Series, 2008, 112:022017,

AE Koniges, C. Debonnel, J. Andrew, D. Eder, D. Kalantar, N. Masters, A. Fisher, R. Anderson, B. Gunney, B. Brown, K. Sain, F. Bonneau, J-L. Bourgade, J-M .Chevalier, P. Combis, A. Geille, J-P. Jadaud, R. Maroni, D. Raffestin, J-L. Ulmer, J. Vierne, M. Tobin, M. Meyers, H. Jarmakani, “Experiments for the validation of debris and shrapnel calculations”, Journal of Physics: Conference Series, 2008, 112:032072,

Alice E Koniges, Brian TN Gunney, Robert W Anderson, Aaron C Fisher, Nathan D Masters, “Development Strategies for Modern Predictive Simulation Codes”, Advances in Parallel Computing, 2008, 15:697--704,

Harinarayan Krishnan

2013

David Camp, Hari Krishnan, David Pugmire, Christoph Garth, Ian Johnson, E. Wes Bethel, Kenneth I. Joy, 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,

Dean N. Williams, Timo Bremer, Charles Doutriaux, John Patchett, Galen Shipman, Blake Haugen, Ross Miller, Brian Smith, Chad Steed, E. Wes Bethel, Hank Childs, Harinarayan Krishnan, Prabhat, Michael Wehner, Claudio T. Silva, Emanuele Santos, David Koop, Tommy Ellqvist, Huy T. Vo, Jorge Poco, Berk Geveci, Aashish Chaudhary, Andrew Bauer, Alexander Pletzer, Dave Kindig, Gerald L. Potter, Thomas P. Maxwell, “The Ultra-scale Visualization Climate Data Analysis Tools: Data Analysis and Visualization for Geoscience Data”, IEEE Special Issue: Cutting-Edge Research in Visualization, 2013,

2012

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, J\ org Meyer, Prabhat, Oliver R\ ubel, Daniela Ushizima, Gunther Weber, “Towards Exascale: High Performance Visualization and Analytics -- Project Status Report”, 2012,

Jason Lee

2013

Daya Bay Collaboration: F.P. An, A.B. Balantekin, H.R. Band, W. Beriguete, et. al, “Spectral measurement of electron antineutrino oscillation amplitude and frequency at Daya Bay”, Phys. Rev. Letter, October 24, 2013,


A measurement of the energy dependence of antineutrino disappearance at the Daya Bay Reactor Neutrino Experiment is reported. Electron antineutrinos from six GW reactors were detected with six detectors deployed in two near (effective baselines 512 m and 561 m) and one far (1579 m) underground experimental halls. Using 217 days of data, 41589 (203809 and 92912) antineutrino candidates were detected in the far hall (near halls). An improved measurement of the oscillation amplitude and the first direct measurement of the mass-squared difference is obtained using the observed rates and energy spectra in a three-neutrino framework. 

This value obtained is consistent with measured by muon neutrino disappearance, supporting the three-flavor oscillation model.

Full Author List:

F.P. An, A.B. Balantekin, H.R. Band, W. Beriguete, M. Bishai, S. Blyth, R.L. Brown, I. Butorov, G.F. Cao, J. Cao, R. Carr, Y.L. Chan, J.F. Chang, Y. Chang, C. Chasman, H.S. Chen, H.Y. Chen, S.J. Chen, S.M. Chen, X.C. Chen, X.H. Chen, Y. Chen, Y.X. Chen, Y.P. Cheng, J.J. Cherwinka, M.C. Chu, J.P. Cummings, J. de Arcos, Z.Y. Deng, Y.Y. Ding, M. Diwan, E. Draeger, X.F. Du, D.A. Dwyer, W.R. Edwards, S.R. Ely, J.Y. Fu, L.Q. Ge, R. Gill, M. Gonchar, G.H. Gong, H. Gong, Y.A. Gornushkin, W.Q. Gu, M.Y. Guan, X.H. Guo, R.W. Hackenburg, R.L. Hahn, G.H. Han, S. Hans,M. He, K.M. Heeger, Y.K. Heng, P. Hinrichs, J. Hor, Y.B. Hsiung, B.Z. Hu, L.J. Hu, L.M. Hu, T. Hu, W. Hu, E.C. Huang, H.X. Huang, H.Z. Huang, X.T. Huang, P. Huber, G. Hussain, Z. Isvan, D.E. Jaffe, P. Jaffke, S. Jetter, X.L. Ji, X.P. Ji, H.J. Jiang, J.B. Jiao, R.A. Johnson, L. Kang, S.H. Kettell, M. Kramer, K.K. Kwan, M.W. Kwok, T. Kwok, W.C. Lai, W.H. Lai, K. Lau, L. Lebanowski, J. Lee, R.T. Lei, R. Leitner,A. Leung, J.K.C. Leung, C.A. Lewis, D.J. Li, F. Li, G.S. Li, Q.J. Li, W.D. Li, X.N. Li, X.Q. Li, Y.F. Li, Z.B. Li, H. Liang, C.J. Lin, G.L. Lin, S.K. Lin, Y.C. Lin, J.J. Ling, J.M. Link, L. Littenberg, B. Littlejohn,D.W. Liu, H. Liu, J.C. Liu, J.L. Liu, S.S. Liu, Y.B. Liu, C. Lu, H.Q. Lu, K.B. Luk, Q.M. Ma, X.B. Ma, X.Y. Ma, Y.Q. Ma, K.T. McDonald, M.C. McFarlane, R.D. McKeown, Y. Meng, I. Mitchell, Y. Nakajima, J. Napolitano, D. Naumov, E. Naumova, I. Nemchenok, H.Y. Ngai, W.K. Ngai, Z. Ning, J.P. Ochoa-Ricoux, A. Olshevski, S. Patton, V. Pec, J.C. Peng, L.E. Piilonen, L. Pinsky, C.S.J. Pun, F.Z. Qi, M. Qi, X. Qian, N. Raper, B. Ren, J. Ren, R. Rosero, B. Roskovec, X.C. Ruan, B.B. Shao, H. Steiner, G.X. Sun, J.L. Sun, Y.H. Tam, H.K. Tanaka, X. Tang, H. Themann, S. Trentalange, O. Tsai, K.V. Tsang, R.H.M. Tsang, C.E. Tull, Y.C. Tung, B. Viren, V. Vorobel, C.H. Wang, L.S. Wang, L.Y. Wang, L.Z. Wang, M. Wang, N.Y. Wang, R.G. Wang, W. Wang, W.W. Wang, Y.F. Wang, Z. Wang, Z. Wang, Z.M. Wang, D.M. Webber, H.Y. Wei, Y.D. Wei, L.J. Wen, K. Whisnant, C.G. White, L. Whitehead, T.S. Wise, H.L.H. Wong, S.C.F. Wong, E. Worcester, Q. Wu, D.M. Xia, J.K. Xia, X. Xia, Z.Z. Xing, J. Xu, J.L. Xu, J.Y. Xu, Y. Xu, T. Xue, J. Yan, C.G. Yang, L. Yang, M.S. Yang, M. Ye, M.F. Yeh, Y.S. Yeh, B.L. Young, G.Y. Yu, J.Y. Yu, Z.Y. Yu, S.L. Zang, L. Zhan, C. Zhang, F.H. Zhang, J.W. Zhang, Q.M. Zhang, S.H. Zhang, Y.C. Zhang, Y.H. Zhang, Y.M. Zhang, Y.X. Zhang, Z.J. Zhang, Z.P. Zhang, Z.Y. Zhang, J. Zhao, Q.W. Zhao, Y.B. Zhao, L. Zheng, W.L. Zhong, L. Zhou, Z.Y. Zhou, H.L. Zhuang, J.H. Zou


2012

Daya Bay Collaboration, F. P. An, Q. An, J. Z. Bai et al., “Improved Measurement of Electron Antineutrino Disappearance at Daya Bay”, October 23, 2012,

ABSTRACT: We report an improved measurement of the neutrino mixing angle $\theta_{13}$ from the Daya Bay Reactor Neutrino Experiment. We exclude a zero value for $\sin^22\theta_{13}$ with a significance of 7.7 standard deviations. Electron antineutrinos from six reactors of 2.9 GW$_{\rm th}$ were detected in six antineutrino detectors deployed in two near (flux-weighted baselines of 470 m and 576 m) and one far (1648 m) underground experimental halls. Using 139 days of data, 28909 (205308) electron antineutrino candidates were detected at the far hall (near halls). The ratio of the observed to the expected number of antineutrinos assuming no oscillations at the far hall is $0.944\pm 0.007({\rm stat.}) \pm 0.003({\rm syst.})$. An analysis of the relative rates in six detectors finds $\sin^22\theta_{13}=0.089\pm 0.010({\rm stat.})\pm0.005({\rm syst.})$ in a three-neutrino framework.

Full Author List:

F. P. An, Q. An, J. Z. Bai, A. B. Balantekin, H. R. Band, W. Beriguete, M. Bishai, S. Blyth, R. L. Brown, G. F. Cao, J. Cao, R. Carr, W. T. Chan, J. F. Chang, Y. Chang, C. Chasman, H. S. Chen, H. Y. Chen, S. J. Chen, S. M. Chen, X. C. Chen, X. H. Chen, X. S. Chen, Y. Chen, Y. X. Chen, J. J. Cherwinka, M. C. Chu, J. P. Cummings, Z. Y. Deng, Y. Y. Ding, M. V. Diwan, E. Draeger, X. F. Du, D. Dwyer, W. R. Edwards, S. R. Ely, S. D. Fang, J. Y. Fu, Z. W. Fu, L. Q. Ge, R. L. Gill, M. Gonchar, G. H. Gong, H. Gong, Y. A. Gornushkin, W. Q. Gu, M. Y. Guan, X. H. Guo, R. W. Hackenburg, R. L. Hahn, S. Hans, H. F. Hao, M. He, Q. He, K. M. Heeger, Y. K. Heng, P. Hinrichs, Y. K. Hor, Y. B. Hsiung, B. Z. Hu, T. Hu, H. X. Huang, H. Z. Huang, X. T. Huang, P. Huber, V. Issakov, Z. Isvan, D. E. Jaffe, S. Jetter, X. L. Ji, X. P. Ji, H. J. Jiang, J. B. Jiao, R. A. Johnson, L. Kang, S. H. Kettell, M. Kramer, K. K. Kwan, M. W. Kwok, T. Kwok, C. Y. Lai, W. C. Lai, W. H. Lai, K. Lau, L. Lebanowski, J. Lee, R. T. Lei, R. Leitner, J. K. C. Leung, K. Y. Leung, C. A. Lewis, F. Li, G. S. Li, Q. J. Li, W. D. Li, X. B. Li, X. N. Li, X. Q. Li, Y. Li, Z. B. Li, H. Liang, C. J. Lin, G. L. Lin, S. K. Lin, Y. C. Lin, J. J. Ling, J. M. Link, L. Littenberg, B. R. Littlejohn, D. W. Liu, J. C. Liu, J. L. Liu, Y. B. Liu, C. Lu, H. Q. Lu, A. Luk, K. B. Luk, Q. M. Ma, X. B. Ma, X. Y. Ma, Y. Q. Ma, K. T. McDonald, M. C. McFarlane, R. D. McKeown, Y. Meng, D. Mohapatra, Y. Nakajima, J. Napolitano, D. Naumov, I. Nemchenok, H. Y. Ngai, W. K. Ngai, Y. B. Nie, Z. Ning, J. P. Ochoa-Ricoux, A. Olshevski, S. Patton, V. Pec, J. C. Peng, L. E. Piilonen, L. Pinsky, C. S. J. Pun, F. Z. Qi, M. Qi, X. Qian, N. Raper, J. Ren, R. Rosero, B. Roskovec, X. C. Ruan, B. B. Shao, K. Shih, H. Steiner, G. X. Sun, J. L. Sun, N. Tagg, Y. H. Tam, H. K. Tanaka, X. Tang, H. Themann, Y. Torun, S. Trentalange, O. Tsai, K. V. Tsang, R. H. M. Tsang, C. E. Tull, Y. C. Tung, B. Viren, V. Vorobel, C. H. Wang, L. S. Wang, L. Y. Wang, L. Z. Wang, M. Wang, N. Y. Wang, R. G. Wang, W. Wang, X. Wang, Y. F. Wang, Z. Wang, Z. M. Wang, D. M. Webber, H. Y. Wei, Y. D. Wei, L. J. Wen, K. Whisnant, C. G. White, L. Whitehead, Y. Williamson, T. Wise, H. L. H. Wong, E. T. Worcester, F. F. Wu, Q. Wu, J. B. Xi, D. M. Xia, Z. Z. Xing, J. Xu, J. L. Xu, Y. Xu, T. Xue, C. G. Yang, L. Yang, M. Ye, M. Yeh, Y. S. Yeh, B. L. Young, Z. Y. Yu, L. Zhan, C. Zhang, F. H. Zhang, J. W. Zhang, Q. M. Zhang, S. H. Zhang, Y. C. Zhang, Y. H. Zhang, Y. X. Zhang, Z. J. Zhang, Z. P. Zhang, Z. Y. Zhang, J. Zhao, Q. W. Zhao, Y. B. Zhao, L. Zheng, W. L. Zhong, L. Zhou, Z. Y. Zhou, H. L. Zhuang, J. H. Zou

F. P. An, J. Z. Bai, A. B. Balantekin, et al., “Observation of electron-antineutrino disappearance at Daya Bay”, March 8, 2012,

The Daya Bay Reactor Neutrino Experiment has measured a non-zero value for the neutrino mixing angle θ13 with a significance of 5.2 standard deviations. Antineutrinos from six 2.9 GWth reactors were detected in six antineutrino detectors deployed in two near (flux-weighted baseline 470 m and 576 m) and one far (1648 m) underground experimental halls. With 55 days of data, 10416 (80376) electron antineutrino candidates were detected at the far hall (near halls). The ratio of the observed to expected number of antineutrinos at the far hall is  R=0.940 ±0.011( stat) ± 0.004( syst). A rate-only analysis finds sin2 2 θ13 - 0.092 ± 0.016( stat}) ± 0.005(syst) in a three-neutrino framework.

Full Author list: F. P. An, J. Z. Bai, A. B. Balantekin, H. R. Band, D. Beavis, W. Beriguete, M. Bishai, S. Blyth, R. L. Brown, G. F. Cao, J. Cao, R. Carr, W. T. Chan, J. F. Chang, Y. Chang, C. Chasman, H. S. Chen, H. Y. Chen, S. J. Chen, S. M. Chen, X. C. Chen, X. H. Chen, X. S. Chen, Y. Chen, Y. X. Chen, J. J. Cherwinka, M. C. Chu, J. P. Cummings, Z. Y. Deng, Y. Y. Ding, M. V. Diwan, L. Dong, E. Draeger, X. F. Du, D. A. Dwyer, W. R. Edwards, S. R. Ely, S. D. Fang, J. Y. Fu, Z. W. Fu, L. Q. Ge, V. Ghazikhanian, R. L. Gill, J. Goett, M. Gonchar, G. H. Gong, H. Gong, Y. A. Gornushkin, L. S. Greenler, W. Q. Gu, M. Y. Guan, X. H. Guo, R. W. Hackenburg, R. L. Hahn, S. Hans, M. He, Q. He, W. S. He, K. M. Heeger, Y. K. Heng, P. Hinrichs, T. H. Ho, Y. K. Hor, Y. B. Hsiung, B. Z. Hu, T. Hu, T. Hu, H. X. Huang, H. Z. Huang, P. W. Huang, X. Huang, X. T. Huang, P. Huber, Z. Isvan, D. E. Jaffe, S. Jetter, X. L. Ji, X. P. Ji, H. J. Jiang, W. Q. Jiang, J. B. Jiao, R. A. Johnson, L. Kang, S. H. Kettell, M. Kramer, K. K. Kwan, M. W. Kwok, T. Kwok, C. Y. Lai, W. C. Lai, W. H. Lai, K. Lau, L. Lebanowski, J. Lee, M. K. P. Lee, R. Leitner, J. K. C. Leung, K. Y. Leung, C. A. Lewis, B. Li, F. Li, G. S. Li, J. Li, Q. J. Li, S. F. Li, W. D. Li, X. B. Li, X. N. Li, X. Q. Li, Y. Li, Z. B. Li, H. Liang, J. Liang, C. J. Lin, G. L. Lin, S. K. Lin, S. X. Lin, Y. C. Lin, J. J. Ling, J. M. Link, L. Littenberg, B. R. Littlejohn, B. J. Liu, C. Liu, D. W. Liu, H. Liu, J. C. Liu, J. L. Liu, S. Liu, X. Liu, Y. B. Liu, C. Lu, H. Q. Lu, A. Luk, K. B. Luk, T. Luo, X. L. Luo, L. H. Ma, Q. M. Ma, X. B. Ma, X. Y. Ma, Y. Q. Ma, B. Mayes, K. T. McDonald, M. C. McFarlane, R. D. McKeown, Y. Meng, D. Mohapatra, J. E. Morgan, Y. Nakajima, J. Napolitano, D. Naumov, I. Nemchenok, C. Newsom, H. Y. Ngai, W. K. Ngai, Y. B. Nie, Z. Ning, J. P. Ochoa-Ricoux, A. Olshevski, A. Pagac, S. Patton, C. Pearson, V. Pec, J. C. Peng, L. E. Piilonen, L. Pinsky, C. S. J. Pun, F. Z. Qi, M. Qi, X. Qian, N. Raper, R. Rosero, B. Roskovec, X. C. Ruan, B. Seilhan, B. B. Shao, K. Shih, H. Steiner, P. Stoler, G. X. Sun, J. L. Sun, Y. H. Tam, H. K. Tanaka, X. Tang, H. Themann, Y. Torun, S. Trentalange, O. Tsai, K. V. Tsang, R. H. M. Tsang, C. Tull, B. Viren, S. Virostek, V. Vorobel, C. H. Wang, L. S. Wang, L. Y. Wang, L. Z. Wang, M. Wang, N. Y. Wang, R. G. Wang, T. Wang, W. Wang, X. Wang, X. Wang, Y. F. Wang, Z.Wang, Z.Wang, Z. M.Wang, D. M.Webber, Y. D.Wei, L. J.Wen, D. L.Wenman, K. Whisnant, C. G. White, L. Whitehead, C. A. Whitten Jr., J. Wilhelmi, T. Wise, H. C. Wong, H. L. H. Wong, J. Wong, E. T. Worcester, F. F. Wu, Q. Wu, D. M. Xia, S. T. Xiang, Q. Xiao, Z. Z. Xing, G. Xu, J. Xu, J. Xu, J. L. Xu, W. Xu, Y. Xu, T. Xue, C. G. Yang, L. Yang, M. Ye, M. Yeh, Y. S. Yeh, K. Yip, B. L. Young, Z. Y. Yu, L. Zhan, C. Zhang, F. H. Zhang, J. W. Zhang, Q. M. Zhang, K. Zhang, Q. X. Zhang, S. H. Zhang, Y. C. Zhang, Y. H. Zhang, Y. X. Zhang, Z. J. Zhang, Z. P. Zhang, Z. Y. Zhang, J. Zhao, Q. W. Zhao, Y. B. Zhao, L. Zheng, W. L. Zhong, L. Zhou, Z. Y. Zhou, H. L. Zhuang, J. H. Zou

Scott Campbell, Jason Lee, “Prototyping a 100G Monitoring System”, 20th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2012), February 12, 2012,

The finalization of the 100 Gbps Ethernet Specification has been a tremendous increase in these rates arriving into data centers creating the need to perform security monitoring at 100 Gbps no longer simply an academic exercise. We show that by leveraging the ‘heavy tail flow effect’ on the IDS infrastructure, it is possible to perform security analysis at such speeds within the HPC environment. Additionally, we examine the nature of current traffic characteristics, how to scale an IDS infrastructure to 100Gbps.

2011

Scott Campbell, Jason Lee, “Intrusion Detection at 100G”, The International Conference for High Performance Computing, Networking, Storage, and Analysis, November 14, 2011,

Driven by the growing data transfer needs of the scientific community and the standardization of the 100 Gbps Ethernet Specification, 100 Gbps is now becoming a reality for many HPC sites. This tenfold increase in bandwidth creates a number of significant technical challenges. We show that by using the heavy tail flow effect as a filter, it should be possible to perform active IDS analysis at this traffic rate using a cluster of commodity systems driven by a dedicated load balancing mechanism. Additionally, we examine the nature of current network traffic characteristics applying them to 100Gpbs speeds

Scott Campbell, Steve Chan and Jason Lee, “Detection of Fast Flux Service Networks”, Australasian Information Security Conference 2011, January 17, 2011,

Fast Flux Service Networks (FFSN) utilize high availability server techniques for malware distribution. FFSNs are similar to commercial content distribution networks (CDN), such as Akamai, in terms of size, scope, and business model, serving as an outsourced content delivery service for clients.  Using an analysis of DNS traffic, we derive a sequential hypothesis testing algorithm based entirely on traffic characteristics and dynamic white listing to provide real time detection of FFDNs in live traffic.  We improve on existing work, providing faster and more accurate detection of FFSNs. We also identify a category of hosts not addressed in previous detectors - Open Content Distribution Networks (OCDN) that share many of the characteristics of FFSNs

2010

Sim A., Gunter D., Natarajan V., Shoshani A., Williams D., Long J., Hick J., Lee J., Dart E., “Efficient Bulk Data Replication for the Earth System Grid”, Data Driven E-science: Use Cases and Successful Applications of Distributed Computing Infrastructures (Isgc 2010), Springer-Verlag New York Inc, 2010, 435,

Kettimuthu Raj, Sim Alex, Gunter Dan, Allcock Bill, Bremer Peer T., Bresnahan John, Cherry Andrew, Childers Lisa, Dart Eli, Foster Ian, Harms Kevin, Hick Jason, Lee Jason, Link Michael, Long Jeff, Miller Keith, Natarajan Vijaya, Pascucci Valerio, Raffenetti Ken, Ressman David, Williams Dean, Wilson Loren, Winkler Linda, “Lessons Learned from Moving Earth System Grid Data Sets over a 20 Gbps Wide-Area Network”, Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing HPDC 10, New York NY USA, 2010, 316--319,

A. Sim, D. Gunter, V. Natarajan, A. Shoshani, D. Williams, J. Long, J. Hick, J. Lee, E. Dart, “Efficient Bulk Data Replication for the Earth System Grid”, International Symposium on Grid Computing, 2010,

2007

Chin Guok, Jason R Lee, Karlo Berket, “Improving the Bulk Data Transfer Experience”, Management of IP Networks and Services Special Issue, January 1, 2007,

Scientific computations and collaborations increasingly rely on the network to provide high-speed data transfer, dissemination of results, access to instruments, support for computational steering, etc. The Energy Sciences Network is establishing a science data network that is logically separate from the production IP core network. One of the requirements of the science data network is the ability to provide user driven bandwidth allocation. In a shared network environment, some reservations may not be granted due to the lack of available bandwidth on any single path.  In many cases, the available bandwidth across multiple paths would be sufficient to grant the reservation.  In this paper we investigate how to utilize the available bandwidth across multiple paths in the case of bulk data transfer.

Matthias Vallentin, Robin Sommer, Jason Lee, Craig Leres, Vern Paxson, Brian Tierney,, “The NIDS Cluster: Scalable, Stateful Network Intrusion Detection on Commodity Hardware”, Proceedings of the Symposium on Recent Advances in Intrusion Detection, Queensland, Australia,, January 1, 2007,

2006

E. Wes Bethel, Scott Campbell, Eli Dart, Jason Lee, Steven A. Smith, Kurt Stockinger, Brian Tierney, Kesheng Wu, “Interactive Analysis of Large Network Data Collections Using Query-Driven Visualization”, DOE Report, September 26, 2006, LBNL 59166

Realizing operational analytics solutions where large and complex data must be analyzed in a time-critical fashion entails integrating many different types of technology. Considering the extreme scale of contemporary datasets, one significant challenge is to reduce the duty cycle in the analytics discourse process. This paper focuses on an interdisciplinary combination of scientific data management and visualization/analysistechnologies targeted at reducing the duty cycle in hypothesis testing and knowledge discovery. We present an application of such a combination in the problem domain of network traffic dataanalysis. Our performance experiment results, including both serial and parallel scalability tests, show that the combination can dramatically decrease the analytics duty cycle for this particular application. The combination is effectively applied to the analysis of network traffic data to detect slow and distributed scans, which is a difficult-to-detect form of cyberattack. Our approach is sufficiently general to be applied to a diverse set of data understanding problems as well as used in conjunction with a diverse set of analysis and visualization tools

C. Guok, D. Robertson, M. Thompson, J. Lee, B. Tierney and William Johnston, “Intra and Interdomain Circuit Provisioning Using the OSCARS Reservation System”, GridNETS 2006, January 1, 2006, LBNL 60373

Ruoming Pang, Mark Allman, Vern Paxson, Jason Lee, “The Devil and Packet Trace Anonymization”, ACM Computer Communication Review, January 1, 2006, LBNL 57630

2005

Ruoming Pang, Mark Allman, Mike Bennett, Jason Lee, Vern Paxson, Brian Tierney, “A First Look at Modern Enterprise Traffic”, ACM SIGCOMM/USENIX Internet Measurement Conference, October 1, 2005,

Daniel K. Gunter, Keith R. Jackson, David E. Konerding, Jason R. Lee, Brian L. Tierney, “Essential Grid Workflow Monitoring Elements”, The 2005 International Conference on Grid Computing and Applications, January 1, 2005, LBNL 57428

Antony Antony, Johan Blom, Cees de Laat, Jason Lee, “Exploring practical limitations of TCP over TransAtlantic networks”, the DataTAG Project, special issue, Future Generation Computer Systems, volume 21 issue 4 (2005), January 1, 2005,

2004

Wim Sjouw, Antony Antony, Johan Blom, Cees de Laat and Jason Lee, “TCP Behaviour On Transatlantic Lambda's”, Grid Computing: First European Across Grids Conference, Santiago de Compostela, Spain, February 1, 2004,

Ian Foster, et al., “The Grid2003 Production Grid: Principles and Practice”, HPDC 2004, January 1, 2004,

2003

Antony Antony, Johan Blom, Cees de Laat, Jason Lee, Wim Sjouw,, “Microscopic Examination of TCP Flows Over Transatlantic Links”, iGrid2002 special issue, Future Generation Computer Systems, volume 19 issue 6, January 1, 2003,

2002

J. Lee, D. Gunter, M. Stoufer, B. Tierney, “Monitoring Data Archives for Grid Environments”, Proceeding of IEEE Supercomputing 2002 Conference, November 1, 2002, LBNL 50216

D. Gunter, B. Tierney, K. Jackson, J. Lee, M. Stoufer, “Dynamic Monitoring of High-Performance Distributed Applications”, Proceedings of the 11th IEEE Symposium on High Performance Distributed Computing, June 1, 2002, LBNL 49698

2001

B. Allcock, Foster, I., Nefedova, V., Chervenak, A., Deelman, E., Kesselman, C., Sim, A., Shoshani, A., Lee, J., Drach, B., Williams, D, “High-Performance Remote Access to Climate Simulation Data: A Challenge Problem for Data Grid Technologies”, Proceeding of the IEEE Supercomputing 2001 Conference, November 1, 2001,

J. Lee, D. Gunter, B. Tierney, W. Allock, J. Bester, J.Bresnahan, S. Tecke, “Applied Techniques for High Bandwidth Data Transfers across Wide Area Networks”, CHEP01 Beijing China, September 1, 2001, LBNL 46269

B. Tierney, D. Gunter, J. Lee, M. Stoufer, “Enabling Network-Aware Applications”, Proceedings of the 10th IEEE Symposium on High Performance Distributed Computing, August 1, 2001, LBNL 47611

D. Agarwal, B. Tierney, D. Gunter, J. Lee, and W. Johnston, “Network Aware High-Performance Distributed Applications”, Proceedings of the Workshop on New Visions for Large-Scale Networks: Research and Applications, March 1, 2001, LBNL 47518

2000

W. Bethel, Tierney, B., Lee, J., Gunter, D., Lau, S., “Using High-Speed WANs and Network Data Caches to Enable Remote and Distributed Visualization”, Proceeding of the IEEE Supercomputing 2000 Conference, November 1, 2000, LBNL 45365

Tierney, B., W. Johnston, J. Lee,, “A Cache-based Data Intensive Distributed Computing Architecture for Grid Applications”, CERN School of Computing, September 1, 2000,

D. Gunter, B. Tierney, B. Crowley, M. Holding, J. Lee, “NetLogger: A Toolkit for Distributed System Performance Analysis”, Proceedings of the IEEE Mascots 2000 Conference, August 1, 2000, LBNL 46269

1998

W. Johnston, J. Guojun, C. Larsen, J. Lee, G. Hoo, M. Thompson, B. Tierney (LBNL) and J. Terdiman (Kaiser Permanente Division of Research), “Real-Time Generation and Cataloguing of Large Data-Objects in Widely Distributed Environments”, International Journal of Digital Libraries, special issue on "Digital Libraries in Medicine,", May 1, 1998,

1996

Johnston, W., B. Tierney, J. Lee, G. Hoo, and M. Thompson, “Distributed Large Data-Object Environments: End-to-End Performance Analysis of High Speed Distributed Storage Systems in Wide Area ATM Networks”, Fifth NASA Goddard Space Flight Center Conference on Mass Storage Systems and Technologies, University of Maryland, College Park, MD, September 1, 1996, LBNL 39064

1995

Tierney, B., W. Johnston, G. Hoo, J. Lee, “Demonstrations of a Remote Distributed Parallel Storage Server (DPSS)”, Supercomputing 1995, November 1, 1995, LBNL 38001

Design and Implementation of a Image Server System, Jason R. Lee, October 1995,

Tierney, B., W. Johnston, G. Hoo, J. Lee, “Performance Analysis in High-Speed Wide Area ATM Networks: Top-to-bottom end-to-end Monitoring”, MAGIC Symposium, Minneapolis MN, August 1995, August 1, 1995,

Johnston, W. E., B. L. Tierney, H. M. Herzog, G. Hoo, G. Jin, J. R. Lee, “Distributed Parallel Data Storage Systems: A Scalable Approach to High Speed Image Servers”, ACM-Multimedia, 1995, LBNL LBL-35408

1994

Tierney, B., W. Johnston, H. Herzog, G. Hoo, G. Jin, and J. Lee, “The Image Server System: A Scalable, Software Approach to High-Speed Distributed Storage,”, ARPA Networking PI Meeting, Santa Fe, NM, October 1, 1994, LBNL 36218

Tierney, B., W. Johnston, L.T. Chen, H. Herzog, G. Hoo, and J. Lee, “The Image Server System: A High-Speed Parallel Distributed Data Server”, July 1, 1994, LBNL 36002

Johnston, W., B. Tierney, H. Herzog, G. Hoo, G.Jin, J. Lee, “Time and MAGIC: Precision Network Timing in the MAGIC Testbed”, MAGIC Technical Symposium, Lawrence Kansas, July, 1994, June 1, 1994,

Johnston, W. E., B. L. Tierney, H. M. Herzog, G. Hoo, G. Jin, J. R. Lee, “Using High Speed Networks to Enable Distributed Parallel Image Server Systems”, SuperComputing 1994, January 1, 1994,

Johnston, W. E., B. L. Tierney, H. M. Herzog, G. Hoo, G. Jin, J. R. Lee, “System Issues in Implementing High Speed Distributed Parallel Storage Systems”, Usenix 1994, 1994,

Tierney, B., W. Johnston, Hanan Herzog, G. Hoo, G. Jin, and J. Lee, “The Image Server System: An Example of a Gigabit Network Testbed Application”, Gigabit Jamboree, Washington DC, January 1, 1994, LBNL LBL-36318

1969

Brian L. Tierney, Tom Dunigan, Jason R. Lee, Dan Gunter, Martin Stoufer, “Improving Distributed Application Performance Using TCP Instrumentation”, December 31, 1969, LBNL 52590

Rei Chi Lee

2012

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, “Shared Library Performance on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

2011

Zhengji Zhao, Mike Davis, Katie Antypas, Rei Lee and Tina Butler, Shared Library Performance on Hopper, Oct. 26, 2011, Cray Quarterly Meeting at St Paul, MN, October 26, 2011,

WangYi Liu

2013

Alice Koniges, Wangyi Liu, John Barnard, Alex Friedman, Grant Logan, David Eder, Aaron Fisher, Nathan Masters, and Andrea Bertozzi, “Modeling warm dense matter experiments using the 3D ALE-AMR code and the move toward exascale computing”, EPJ Web of Conferences 59, 09006, 2013,

D. Eder, D. Bailey, F. Chambers, I. Darnell, P. Di Nicola, S. Dixit, A. Fisher, G.Gururangan, D. Kalantar, A. Koniges, W. Liu, M. Marinak, N. Masters, V. Mlaker, R. Prasad, S. Sepke, P. Whitman, “Observations and modeling of debris and shrapnel impacts on optics and diagnostics at the National Ignition Facility”, EPJ Web of Conferences 59, 08010, 2013,

A. Friedman, R. H. Cohen, D. P. Grote, W. M. Sharp, I. D. Kaganovich, A. E. Koniges, W. Liu, “Heavy Ion Beams and Interactions with Plasmas and Targets (HEDLP and IFE)”, NERSC FES Requirements Workshop: Heavy Ion Fusion and Non-Neutral Plasmas, March 2013,

J. Barnard, R. M. More, P. A. Ni, A. Friedman, E. Henestroza, I. Kaganovich, A. Koniges, J. W. Kwan, W. Liu, A. Ng,
B.G. Logan, E. Startsev, M. Terry, A. Yuen,
NDCX-II Experimental Plans and Target Simulations, West Coast High Energy Density Science Cooperative Meeting Berkeley and Palo Alto, California, January 2013,

2012

Wangyi Liu, John Barnard, Alice Koniges, David Eder, Nathan Masters, Aaron Fisher, Alex Friedman, “A numerical scheme for including surface tension effects in hydrodynamic simulation: a full Korteweg type model without parasitic flows”, APS DPP 2012, 2012,

Wangyi Liu, Andrea Bertozzi, and Theodore Kolokolnikov, “Diffuse interface surface tension models in an expanding flow”, Comm. Math. Sci., 2012, 10(1):387-418,

2011

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Alice Koniges, David Eder, “Modeling droplet breakup effects with applications in the warm dense matter NDCX experiment”, APS DPP, 2011,

David Eder, David Bailey, Andrea Bertozzi, Aaron Fisher, Alice Koniges, Wangyi Liu, Nathan Masters, Marty Marniak, Late-Time Numerical Simulations of High-Energy-Density (HED) Targets, Twenty Second International Conference on Numerical Simulations of Plasmas, September 7, 2011,

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Velemir Mlaker,
Alice Koniges, David Eder,
“Modeling droplet breakup effects in warm dense matter experiments with diffuse interface methods in the ALE-AMR code”, Proceedings of the 2011 SciDAC Conference, August 4, 2011,

Wangyi Liu, John Bernard, Alex Friedman, Nathan Masters, Aaron Fisher, Velemir Mlaker, Alice Koniges, David Eder, “Modeling droplet breakup effects in warm dense matter experiments with diffuse interface methods in ALE-AMR code”, SciDAC conference, 2011,

2010

Wangyi Liu, Martin B. Short, Yasser E. Taima, and Andrea L. Bertozzi, “Multiscale Collaborative Searching Through Swarming”, Proceedings of the 7th International Conference on Informatics in Control, Automation, and Robotics (ICINCO), June 2010,

Filipe Maia

2010

Filipe Maia, Chao Yang, Stefano Marchesini, “Compressive Auto-Indexing in Femtosecond Nanocrystallography”, Lawrence Berkeley National Laboratory technical report, 2010, LBNL 4008E

   

Filipe Maia, Alastair MacDowell, Stefano Marchesini, Howard A. Padmore, Dula Y. Parkinson, Jack Pien, Andre Schirotzek, Chao Yang, “Compressive Phase Contrast Tomography”, SPIE Optics and Photonics, San Diego, CA, 2010,

    

Krishna Muriki

2010

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

Praveen Narayanan

2013

Alice Koniges, Praveen Narayanan, Robert Preissl, Xuefei Yuan, Proxy Design and Optimization in Fusion and Accelerator Physics, SIAM Conference on Computational Science and Engineering, February 25, 2013,

2011

Sean Farley, Ben Dudson, Praveen Narayanan, Lois Curfman McInnes, Maxim Umansky, Xuexiao Xu, Satish Balay, John Cary, Alice Koniges, Carol Woodward, Hong Zhang, “BOUT++: Performance Characterization and Recent Advances in Design”, International Conference on Numerical Simulations of Plasmas, Long Beach, New Jersey, 2011, 2011,

Praveen Narayanan, Alice Koniges, Leonid Oliker, Robert Preissl, Samuel Williams, Nicholas J Wright, Maxim Umansky, Xueqiao Xu, Benjamin Dudson, Stephane Ethier, Weixing Wang, Jeff Candy, John R. Cary, “Performance Characterization for Fusion Co-design Applications”, Proceedings of CUG, 2011,

Trever Christian Nightingale

2013

Trever Nightingale, Introduction to Google Chromebooks, LBL Tech Day Lightning Talk, October 10, 2013,

Introduction to Google Chromebooks.  The good parts reviewers often leave out.

2011

T. Nightingale, No Cost ZFS On Low Cost Hardware, NERSC High Performance Computing Seminar, June 14, 2011,

Today's data generation rates and terabyte hard drives have led to a new breed of commodity servers that have very large filesystems. This talk looks at the implications and describes the decision to deploy ZFS under FreeBSD on NERSC servers. Included will be a look at pertinent ZFS features, configuration decisions adopted, experiences with ZFS so far, and how we are using the features ZFS brings with it to gain some new functionality that was not possible with previous filesystems.

Peter E. Nugent

2013

S. Hachinger, P. A. Mazzali, M. Sullivan, R. S., K. Maguire, A. Gal-Yam, D. A. Howell, P. E., E. Baron, J. Cooke, I. Arcavi, D., B. Dilday, P. A. James, M. M. Kasliwal, S. R., E. O. Ofek, R. R. Laher, J. Parrent, J. Surace, O. Yaron, E. S. Walker, “The UV/optical spectra of the Type Ia supernova SN 2010jn: a bright supernova with outer layers rich in iron-group elements”, Monthly Notices of the RAS, 2013, 429:2228-2248,

 Radiative transfer studies of Type Ia supernovae (SNe Ia) hold the promise of constraining both the density profile of the SN ejecta and its stratification by element abundance which, in turn, may discriminate between different explosion mechanisms and progenitor classes. Here we analyse the Type Ia SN 2010jn (PTF10ygu) in detail, presenting and evaluating near-ultraviolet (near-UV) spectra from the Hubble Space Telescope and ground-based optical spectra and light curves. SN 2010jn was discovered by the Palomar Transient Factory (PTF) 15 d before maximum light, allowing us to secure a time series of four near-UV spectra at epochs from -10.5 to +4.8 d relative to B-band maximum. The photospheric near-UV spectra are excellent diagnostics of the iron-group abundances in the outer layers of the ejecta, particularly those at very early times. Using the method of `Abundance Tomography' we derive iron-group abundances in SN 2010jn with a precision better than in any previously studied SN Ia. Optimum fits to the data can be obtained if burned material is present even at high velocities, including significant mass fractions of iron-group elements. This is consistent with the slow decline rate (or high `stretch') of the light curve of SN 2010jn, and consistent with the results of delayed-detonation models. Early-phase UV spectra and detailed time-dependent series of further SNe Ia offer a promising probe of the nature of the SN Ia mechanism.

 

 

2012

Joshua S. Bloom, Daniel Kasen, Ken J. Shen, Peter E. Nugent, Nathaniel R. Butler, Melissa L. Graham, D. Andrew Howell, Ulrich Kolb, Stefan Holmes, Carole A. Haswell, Vadim Burwitz, Juan Rodriguez, and Mark Sullivan, “SN 2010jp (PTF10aaxi): a jet in a Type II supernova”, Monthly Notices of the Royal Astronomical Society, February 2012, 2181,

We present photometry and spectroscopy of the peculiar Type II supernova (SN) SN 2010jp, also named PTF10aaxi. The light curve exhibits a linear decline with a relatively low peak absolute magnitude of only −15.9 (unfiltered), and a low radioactive decay luminosity at late times, which suggests a low synthesized nickel mass of M (56 Ni) ≲ 0.003  M. Spectra of SN 2010jp display an unprecedented triple-peaked Hα line profile, showing (1) a narrow (full width at half-maximum >rsim800 km s−1) central component that suggests shock interaction with dense circumstellar material (CSM); (2) high-velocity blue and red emission features centred at −12 600 and +15 400 km s−1, respectively; and (3) very broad wings extending from −22 000 to +25 000 km s−1. These features persist over multiple epochs during the ∼100 d after explosion. We propose that this line profile indicates a bipolar jet-driven explosion, with the central component produced by normal SN ejecta and CSM interaction at mid and low latitudes, while the high-velocity bumps and broad-line wings arise in a non-relativistic bipolar jet. Two variations of the jet interpretation seem plausible: (1) a fast jet mixes 56Ni to high velocities in polar zones of the H-rich envelope; or (2) the reverse shock in the jet produces blue and red bumps in Balmer lines when a jet interacts with dense CSM. Jet-driven Type II SNe are predicted for collapsars resulting from a wide range of initial masses above 25 M, especially at subsolar metallicity. This seems consistent with the SN host environment, which is either an extremely low-luminosity dwarf galaxy or the very remote parts of an interacting pair of star-forming galaxies. It also seems consistent with the apparently low 56Ni mass that may accompany black hole formation. We speculate that the jet survives to produce observable signatures because the star’s H envelope was very low mass, having been mostly stripped away by the previous eruptive mass-loss indicated by the Type IIn features in the spectrum. http://dx.doi.org/10.1111/j.1365-2966.2011.20104.x

Joshua S. Bloom, Daniel Kasen, Ken J. Shen, Peter E. Nugent, Nathaniel R. Butler, Melissa L. Graham, D. Andrew Howell, Ulrich Kolb, Stefan Holmes, Carole A. Haswell, Vadim Burwitz, Juan Rodriguez, and Mark Sullivan, “A Compact Degenerate Primary-star Progenitor of SN 2011fe”, Astrophysical Journal, January 2012, 744:L17,

While a white dwarf (WD) is, from a theoretical perspective, the most plausible primary star of a Type Ia supernova (SN Ia), many other candidates have not been formally ruled out. Shock energy deposited in the envelope of any exploding primary contributes to the early SN brightness and, since this radiation energy is degraded by expansion after the explosion, the diffusive luminosity depends on the initial primary radius. We present a new non-detection limit of the nearby SN Ia 2011fe, obtained at a time that appears to be just 4 hr after explosion, allowing us to directly constrain the initial primary radius (Rp ). Coupled with the non-detection of a quiescent X-ray counterpart and the inferred synthesized 56Ni mass, we show that Rp lsim0.02 R  (a factor of five smaller than previously inferred), that the average density of the primary must be ρ p > 104 g cm–3, and that the effective temperature must be less than a few × 105 K. This rules out hydrogen-burning main-sequence stars and giants. Constructing the helium-burning and carbon-burning main sequences, we find that such objects are also excluded. By process of elimination, we find that only degeneracy-supported compact objects—WDs and neutron stars—are viable as the primary star of SN 2011fe. With few caveats, we also restrict the companion (secondary) star radius to R c lsim 0.1 R , excluding Roche-lobe overflowing red giant and main-sequence companions to high significance.

http://dx.doi.org/10.1088/2041-8205/744/2/L17

2011

Thomas, R. C.; Aldering, G.; Antilogus, P.; Aragon, C.; Bailey, S.; Baltay, C.; Bongard, S.; Buton, C.; Canto, A.; Childress, M.; Chotard, N.; Copin, Y.; Fakhouri, H. K.; Gangler, E.; Hsiao, E. Y.; Kerschhaggl, M.; Kowalski, M.; Loken, S.; Nugent, P.; Paech, K.; Pain, R.; Pecontal, E.; Pereira, R.; Perlmutter, S.; Rabinowitz, D.; Rigault, M.; Rubin, D.; Runge, K.; Scalzo, R.; Smadja, G.; Tao, C.; Weaver, B. A.; Wu, C.; (The Nearby Supernova Factory); Brown, P. J.; Milne, P. A., “Type Ia Supernova Carbon Footprints”, Astrophysical Journal, December 2011, 743:27,

We present convincing evidence of unburned carbon at photospheric velocities in new observations of five Type Ia supernovae (SNe Ia) obtained by the Nearby Supernova Factory. These SNe are identified by examining 346 spectra from 124 SNe obtained before +2.5 days relative to maximum. Detections are based on the presence of relatively strong C II λ6580 absorption "notches" in multiple spectra of each SN, aided by automated fitting with the SYNAPPS code. Four of the five SNe in question are otherwise spectroscopically unremarkable, with ions and ejection velocities typical of SNe Ia, but spectra of the fifth exhibit high-velocity (v > 20, 000 km s–1) Si II and Ca II features. On the other hand, the light curve properties are preferentially grouped, strongly suggesting a connection between carbon-positivity and broadband light curve/color behavior: three of the five have relatively narrow light curves but also blue colors and a fourth may be a dust-reddened member of this family. Accounting for signal to noise and phase, we estimate that 22+10 – 6% of SNe Ia exhibit spectroscopic C II signatures as late as –5 days with respect to maximum. We place these new objects in the context of previously recognized carbon-positive SNe Ia and consider reasonable scenarios seeking to explain a physical connection between light curve properties and the presence of photospheric carbon. We also examine the detailed evolution of the detected carbon signatures and the surrounding wavelength regions to shed light on the distribution of carbon in the ejecta. Our ability to reconstruct the C II λ6580 feature in detail under the assumption of purely spherical symmetry casts doubt on a "carbon blobs" hypothesis, but does not rule out all asymmetric models. A low volume filling factor for carbon, combined with line-of-sight effects, seems unlikely to explain the scarcity of detected carbon in SNe Ia by itself. http://dx.doi.org/10.1088/0004-637X/743/1/27


Li, Weidong; Bloom, Joshua S.; Podsiadlowski, Philipp; Miller, Adam A.; Cenko, S. Bradley; Jha, Saurabh W.; Sullivan, Mark; Howell, D. Andrew; Nugent, Peter E.; Butler, Nathaniel R.; Ofek, Eran O.; Kasliwal, Mansi M.; Richards, Joseph W.; Stockton, Alan; Shih, Hsin-Yi; Bildsten, Lars; Shara, Michael M.; Bibby, Joanne; Filippenko, Alexei V.; Ganeshalingam, Mohan; Silverman, Jeffrey M.; Kulkarni, S. R.; Law, Nicholas M.; Poznanski, Dovi; Quimby, Robert M.; McCully, Curtis; Patel, Brandon; Maguire, Kate; Shen, Ken J., “Exclusion of a luminous red giant as a companion star to the progenitor of supernova SN 2011fe”, Nature, December 2011, 480:348-350,

Type Ia supernovae are thought to result from a thermonuclear explosion of an accreting white dwarf in a binary system1, 2, but little is known of the precise nature of the companion star and the physical properties of the progenitor system. There are two classes of models1, 3: double-degenerate (involving two white dwarfs in a close binary system2, 4) and single-degenerate models5, 6. In the latter, the primary white dwarf accretes material from a secondary companion until conditions are such that carbon ignites, at a mass of 1.38 times the mass of the Sun. The type Ia supernova SN 2011fe was recently detected in a nearby galaxy7. Here we report an analysis of archival images of the location of SN 2011fe. The luminosity of the progenitor system (especially the companion star) is 10–100 times fainter than previous limits on other type Ia supernova progenitor systems8, 9, 10, allowing us to rule out luminous red giants and almost all helium stars as the mass-donating companion to the exploding white dwarf.

Nugent, Peter E.; Sullivan, Mark; Cenko, S. Bradley; Thomas, Rollin C.; Kasen, Daniel; Howell, D. Andrew; Bersier, David; Bloom, Joshua S.; Kulkarni, S. R.; Kandrashoff, Michael T.; Filippenko, Alexei V.; Silverman, Jeffrey M.; Marcy, Geoffrey W.; Howard, Andrew W.; Isaacson, Howard T.; Maguire, Kate; Suzuki, Nao; Tarlton, James E.; Pan, Yen-Chen; Bildsten, Lars; Fulton, Benjamin J.; Parrent, Jerod T.; Sand, David; Podsiadlowski, Philipp; Bianco, Federica B.; Dilday, Benjamin; Graham, Melissa L.; Lyman, Joe; James, Phil; Kasliwal, Mansi M.; Law, Nicholas M.; Quimby, Robert M.; Hook, Isobel M.; Walker, Emma S.; Mazzali, Paolo; Pian, Elena; Ofek, Eran O.; Gal-Yam, Avishay; Poznanski, Dovi, “Supernova SN 2011fe from an exploding carbon-oxygen white dwarf star”, Nature, December 2011, 480:344-347,

Type Ia supernovae have been used empirically as `standard candles' to demonstrate the acceleration of the expansion of the Universe even though fundamental details, such as the nature of their progenitor systems and how the stars explode, remain a mystery. There is consensus that a white dwarf star explodes after accreting matter in a binary system, but the secondary body could be anything from a main-sequence star to a red giant, or even another white dwarf. This uncertainty stems from the fact that no recent type Ia supernova has been discovered close enough to Earth to detect the stars before explosion. Here we report early observations of supernova SN 2011fe in the galaxy M101 at a distance from Earth of 6.4 megaparsecs. We find that the exploding star was probably a carbon-oxygen white dwarf, and from the lack of an early shock we conclude that the companion was probably a main-sequence star. Early spectroscopy shows high-velocity oxygen that slows rapidly, on a timescale of hours, and extensive mixing of newly synthesized intermediate-mass elements in the outermost layers of the supernova. A companion paper uses pre-explosion images to rule out luminous red giants and most helium stars as companions to the progenitor. http://dx.doi.org/10.1038/nature10644

Iair Arcavi, Avishay Gal-Yam, Ofer Yaron, Assaf Sternberg, Itay Rabinak, Eli Waxman, Mansi M. Kasliwal, Robert M. Quimby, Eran O. Ofek, Assaf Horesh, Shrinivas R. Kulkarni, Alexei V. Filippenko, Jeffrey M. Silverman, S. Bradley Cenko, Weidong Li, Joshua S. Bloom, Mark Sullivan, Peter E. Nugent, Dovi Poznanski, Evgeny Gorbikov, Benjamin J. Fulton, D. Andrew Howell, David Bersier, Amedee Riou, Stephane Lamotte-Bailey, Thomas Griga, Judith G. Cohen, Stephan Hachinger, David Polishook, Dong Xu, Sagi Ben-Ami, Ilan Manulis, Emma S. Walker, Kate Maguire, Yen-Chen Pan, Thomas Matheson, Paolo A. Mazzali, Elena Pian, Derek B. Fox, Neil Gehrels, Nicholas Law, Philip James, Jonathan M. Marchant, Robert J. Smith, Chris J. Mottram, Robert M. Barnsley, Michael T. Kandrashoff and Kelsey I. Clubb, “SN 2011dh: Discovery of a Type IIb Supernova from a Compact Progenitor in the Nearby Galaxy M51”, Astrophysical Journal, December 2011, 742:L18,

On 2011 May 31 UT a supernova (SN) exploded in the nearby galaxy M51 (the Whirlpool Galaxy). We discovered this event using small telescopes equipped with CCD cameras and also detected it with the Palomar Transient Factory survey, rapidly confirming it to be a Type II SN. Here, we present multi-color ultraviolet through infrared photometry which is used to calculate the bolometric luminosity and a series of spectra. Our early-time observations indicate that SN 2011dh resulted from the explosion of a relatively compact progenitor star. Rapid shock-breakout cooling leads to relatively low temperatures in early-time spectra, compared to explosions of red supergiant stars, as well as a rapid early light curve decline. Optical spectra of SN 2011dh are dominated by H lines out to day 10 after explosion, after which He i lines develop. This SN is likely a member of the cIIb (compact IIb) class, with progenitor radius larger than that of SN 2008ax and smaller than the eIIb (extended IIb) SN 1993J progenitor. Our data imply that the object identified in pre-explosion Hubble Space Telescope images at the SN location is possibly a companion to the progenitor or a blended source, and not the progenitor star itself, as its radius (~1013 cm) would be highly inconsistent with constraints from our post-explosion spectra. http://dx.doi.org/10.1088/2041-8205/742/2/L18

Corsi, A.; Ofek, E. O.; Frail, D. A.; Poznanski, D.; Arcavi, I.; Gal-Yam, A.; Kulkarni, S. R.; Hurley, K.; Mazzali, P. A.; Howell, D. A.; Kasliwal, M. M.; Green, Y.; Murray, D.; Sullivan, M.; Xu, D.; Ben-ami, S.; Bloom, J. S.; Cenko, S. B.; Law, N. M.; Nugent, P.; Quimby, R. M.; Pal'shin, V.; Cummings, J.; Connaughton, V.; Yamaoka, K.; Rau, A.; Boynton, W.; Mitrofanov, I.; Goldsten, J., “PTF 10bzf (SN 2010ah): A Broad-line Ic Supernova Discovered by the Palomar Transient Factory”, Astrophysical Journal, November 2011, 741:76,

We present the discovery and follow-up observations of a broad-line Type Ic supernova (SN), PTF 10bzf (SN 2010ah), detected by the Palomar Transient Factory (PTF) on 2010 February 23. The SN distance is cong218 Mpc, greater than GRB 980425/SN 1998bw and GRB 060218/SN 2006aj, but smaller than the other SNe firmly associated with gamma-ray bursts (GRBs). We conducted a multi-wavelength follow-up campaign with Palomar 48 inch, Palomar 60 inch, Gemini-N, Keck, Wise, Swift, the Allen Telescope Array, Combined Array for Research in Millimeter-wave Astronomy, Westerbork Synthesis Radio Telescope, and Expanded Very Large Array. Here we compare the properties of PTF 10bzf with those of SN 1998bw and other broad-line SNe. The optical luminosity and spectral properties of PTF 10bzf suggest that this SN is intermediate, in kinetic energy and amount of 56Ni, between non-GRB-associated SNe like 2002ap or 1997ef, and GRB-associated SNe like 1998bw. No X-ray or radio counterpart to PTF 10bzf was detected. X-ray upper limits allow us to exclude the presence of an underlying X-ray afterglow as luminous as that of other SN-associated GRBs such as GRB 030329 or GRB 031203. Early-time radio upper limits do not show evidence for mildly relativistic ejecta. Late-time radio upper limits rule out the presence of an underlying off-axis GRB, with energy and wind density similar to the SN-associated GRB 030329 and GRB 031203. Finally, by performing a search for a GRB in the time window and at the position of PTF 10bzf, we find that no GRB in the interplanetary network catalog could be associated with this SN. http://dx.doi.org/10.1088/0004-637X/741/2/76

Agüeros, Marcel A.; Covey, Kevin R.; Lemonias, Jenna J.; Law, Nicholas M.; Kraus, Adam; Batalha, Natasha; Bloom, Joshua S.; Cenko, S. Bradley; Kasliwal, Mansi M.; Kulkarni, Shrinivas R.; Nugent, Peter E.; Ofek, Eran O.; Poznanski, Dovi; Quimby, Robert M., “The Factory and the Beehive. I. Rotation Periods for Low-mass Stars in Praesepe”, Astrophysical Journal, October 2011, 740:110,

Stellar rotation periods measured from single-age populations are critical for investigating how stellar angular momentum content evolves over time, how that evolution depends on mass, and how rotation influences the stellar dynamo and the magnetically heated chromosphere and corona. We report rotation periods for 40 late-K to mid-M star members of the nearby, rich, intermediate-age (~600 Myr) open cluster Praesepe. These rotation periods were derived from ~200 observations taken by the Palomar Transient Factory of four cluster fields from 2010 February to May. Our measurements indicate that Praesepe's mass-period relation transitions from a well-defined singular relation to a more scattered distribution of both fast and slow rotators at ~0.6 M sun. The location of this transition is broadly consistent with expectations based on observations of younger clusters and the assumption that stellar spin-down is the dominant mechanism influencing angular momentum evolution at 600 Myr. However, a comparison to data recently published for the Hyades, assumed to be coeval to Praesepe, indicates that the divergence from a singular mass-period relation occurs at different characteristic masses, strengthening the finding that Praesepe is the younger of the two clusters. We also use previously published relations describing the evolution of rotation periods as a function of color and mass to evolve the sample of Praesepe periods in time. Comparing the resulting predictions to periods measured in M35 and NGC 2516 (~150 Myr) and for kinematically selected young and old field star populations suggests that stellar spin-down may progress more slowly than described by these relations. http://dx.doi.org/10.1088/0004-637X/740/2/110

Cano, Z.; Bersier, D.; Guidorzi, C.; Kobayashi, S.; Levan, A. J.; Tanvir, N. R.; Wiersema, K.; D'Avanzo, P.; Fruchter, A. S.; Garnavich, P.; Gomboc, A.; Gorosabel, J.; Kasen, D.; Kopač, D.; Margutti, R.; Mazzali, P. A.; Melandri, A.; Mundell, C. G.; Nugent, P. E.; Pian, E.; Smith, R. J.; Steele, I.; Wijers, R. A. M. J.; Woosley, S. E., “XRF 100316D/SN 2010bh and the Nature of Gamma-Ray Burst Supernovae”, Astrophysical Journal, October 2011, 740:41,

We present ground-based and Hubble Space Telescope optical and infrared observations of Swift XRF 100316D/SN 2010bh. It is seen that the optical light curves of SN 2010bh evolve at a faster rate than the archetype gamma-ray burst supernova (GRB-SN) 1998bw, but at a similar rate to SN 2006aj, an SN that was spectroscopically linked with XRF 060218, and at a similar rate to the non-GRB associated Type Ic SN 1994I. We estimate the rest-frame extinction of this event from our optical data to be E(B - V) = 0.18 ± 0.08 mag. We find the V-band absolute magnitude of SN 2010bh to be MV = -18.62 ± 0.08, which is the faintest peak V-band magnitude observed to date for spectroscopically confirmed GRB-SNe. When we investigate the origin of the flux at t - t 0 = 0.598 days, it is shown that the light is not synchrotron in origin, but is likely coming from the SN shock breakout. We then use our optical and infrared data to create a quasi-bolometric light curve of SN 2010bh, which we model with a simple analytical formula. The results of our modeling imply that SN 2010bh synthesized a nickel mass of M Ni ≈ 0.1 M sun, ejected M ej ≈ 2.2 M sun, and has an explosion energy of E k ≈ 1.4 × 1052erg. Thus, while SN 2010bh is an energetic explosion, the amount of nickel created during the explosion is much less than that of SN 1998bw and only marginally more than SN 1994I. Finally, for a sample of 22 GRB-SNe we check for a correlation between the stretch factors and luminosity factors in the R band and conclude that no statistically significant correlation exists.

Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program 11709. http://dx.doi.org/10.1088/0004-637X/740/1/41

 

Levitan, David; Fulton, Benjamin J.; Groot, Paul J.; Kulkarni, Shrinivas R.; Ofek, Eran O.; Prince, Thomas A.; Shporer, Avi; Bloom, Joshua S.; Cenko, S. Bradley; Kasliwal, Mansi M.; Law, Nicholas M.; Nugent, Peter E.; Poznanski, Dovi; Quimby, Robert M.; Horesh, Assaf; Sesar, Branimir; Sternberg, Assaf, “PTF1 J071912.13+485834.0: An Outbursting AM CVn System Discovered by a Synoptic Survey”, Astrophysical Journal, October 2011, 739:68,

We present extensive photometric and spectroscopic observations of PTF1 J071912.13+485834.0, an outbursting AM CVn system discovered by the Palomar Transient Factory (PTF). AM CVn systems are stellar binaries with some of the smallest separations known and orbital periods ranging from 5 to 65 minutes. They are believed to be composed of a white dwarf accretor and a (semi-)degenerate He-rich donor and are considered to be the helium equivalents of cataclysmic variables (CVs). We have spectroscopically and photometrically identified an orbital period of 26.77 ± 0.02 minutes for PTF1 J071912.13+485834.0 and found a super-outburst recurrence time of greater than 65 days along with the presence of "normal" outbursts—rarely seen in AM CVn systems but well known in super-outbursting CVs. We present a long-term light curve over two super-cycles as well as high-cadence photometry of both outburst and quiescent stages, both of which show clear variability. We also compare both the outburst and quiescent spectra of PTF1 J071912.13+485834.0 to other known AM CVn systems, and use the quiescent phase-resolved spectroscopy to determine the origin of the photometric variability. Finally, we draw parallels between the different subclasses of SU UMa-type CVs and outbursting AM CVn systems. We conclude by predicting that the PTF may more than double the number of outbursting AM CVn systems known, which would greatly increase our understanding of AM CVn systems. http://dx.doi.org/10.1088/0004-637X/739/2/68

Krisciunas, Kevin; Li, Weidong; Matheson, Thomas; Howell, D. Andrew; Stritzinger, Maximilian; Aldering, Greg; Berlind, Perry L.; Calkins, M.; Challis, Peter; Chornock, Ryan; Conley, Alexander; Filippenko, Alexei V.; Ganeshalingam, Mohan; Germany, Lisa; González, Sergio; Gooding, Samuel D.; Hsiao, Eric; Kasen, Daniel; Kirshner, Robert P.; Howie Marion, G. H.; Muena, Cesar; Nugent, Peter E.; Phelps, M.; Phillips, Mark M.; Qiu, Yulei; Quimby, Robert; Rines, K.; Silverman, Jeffrey M.; Suntzeff, Nicholas B.; Thomas, Rollin C.; Wang, Lifan, “The Most Slowly Declining Type Ia Supernova 2001ay”, Astrophysical Journal, September 2011, 142:74,

We present optical and near-infrared photometry, as well as ground-based optical spectra and Hubble Space Telescope ultraviolet spectra, of the Type Ia supernova (SN) 2001ay. At maximum light the Si II and Mg II lines indicated expansion velocities of 14,000 km s–1, while Si III and S II showed velocities of 9000 km s–1. There is also evidence for some unburned carbon at 12,000 km s–1. SN 2001ay exhibited a decline-rate parameter of Δm 15(B) = 0.68 ± 0.05 mag; this and the B-band photometry at t gsim +25 day past maximum make it the most slowly declining Type Ia SN yet discovered. Three of the four super-Chandrasekhar-mass candidates have decline rates almost as slow as this. After correction for Galactic and host-galaxy extinction, SN 2001ay had MB = –19.19 and MV = –19.17 mag at maximum light; thus, it was not overluminous in optical bands. In near-infrared bands it was overluminous only at the 2σ level at most. For a rise time of 18 days (explosion to bolometric maximum) the implied 56Ni yield was (0.58 ± 0.15)/α M , with α = L max/E Ni probably in the range 1.0-1.2. The 56Ni yield is comparable to that of many Type Ia SNe. The "normal" 56Ni yield and the typical peak optical brightness suggest that the very broad optical light curve is explained by the trapping of γ rays in the inner regions. http://dx.doi.org/10.1088/0004-6256/142/3/74

Gal-Yam, Avishay; Kasliwal, Mansi M.; Arcavi, Iair; Green, Yoav; Yaron, Ofer; Ben-Ami, Sagi; Xu, Dong; Sternberg, Assaf; Quimby, Robert M.; Kulkarni, Shrinivas R.; Ofek, Eran O.; Walters, Richard; Nugent, Peter E.; Poznanski, Dovi; Bloom, Joshua S.; Cenko, S. Bradley; Filippenko, Alexei V.; Li, Weidong; Silverman, Jeffrey M.; Walker, Emma S.; Sullivan, Mark; Maguire, K.; Howell, D. Andrew; Mazzali, Paolo A.; Frail, Dale A.; Bersier, David; James, Phil A.; Akerlof, C. W.; Yuan, Fang; Law, Nicholas; Fox, Derek B.; Gehrels, Neil, “Real-time Detection and Rapid Multiwavelength Follow-up Observations of a Highly Subluminous Type II-P Supernova from the Palomar Transient Factory Survey”, Astrophysical Journal, August 2011, 736:159,

The Palomar Transient Factory (PTF) is an optical wide-field variability survey carried out using a camera with a 7.8 deg2 field of view mounted on the 48 inch Oschin Schmidt telescope at Palomar Observatory. One of the key goals of this survey is to conduct high-cadence monitoring of the sky in order to detect optical transient sources shortly after they occur. Here, we describe the real-time capabilities of the PTF and our related rapid multiwavelength follow-up programs, extending from the radio to the γ-ray bands. We present as a case study observations of the optical transient PTF10vdl (SN 2010id), revealed to be a very young core-collapse (Type II-P) supernova having a remarkably low luminosity. Our results demonstrate that the PTF now provides for optical transients the real-time discovery and rapid-response follow-up capabilities previously reserved only for high-energy transients like gamma-ray bursts. http://dx.doi.org/10.1088/0004-637X/736/2/159

van Eyken, Julian C.; Ciardi, David R.; Rebull, Luisa M.; Stauffer, John R.; Akeson, Rachel L.; Beichman, Charles A.; Boden, Andrew F.; von Braun, Kaspar; Gelino, Dawn M.; Hoard, D. W.; Howell, Steve B.; Kane, Stephen R.; Plavchan, Peter; Ramírez, Solange V.; Bloom, Joshua S.; Cenko, S. Bradley; Kasliwal, Mansi M.; Kulkarni, Shrinivas R.; Law, Nicholas M.; Nugent, Peter E.; Ofek, Eran O.; Poznanski, Dovi; Quimby, Robert M.; Grillmair, Carl J.; Laher, Russ; Levitan, David; Mattingly, Sean; Surace, Jason A., “The Palomar Transient Factory Orion Project: Eclipsing Binaries and Young Stellar Objects”, Astrophysical Journal, August 2011, 142:60,

The Palomar Transient Factory (PTF) Orion project is one of the experiments within the broader PTF survey, a systematic automated exploration of the sky for optical transients. Taking advantage of the wide (3fdg5 × 2fdg3) field of view available using the PTF camera installed at the Palomar 48 inch telescope, 40 nights were dedicated in 2009 December to 2010 January to perform continuous high-cadence differential photometry on a single field containing the young (7-10 Myr) 25 Ori association. Little is known empirically about the formation of planets at these young ages, and the primary motivation for the project is to search for planets around young stars in this region. The unique data set also provides for much ancillary science. In this first paper, we describe the survey and the data reduction pipeline, and present some initial results from an inspection of the most clearly varying stars relating to two of the ancillary science objectives: detection of eclipsing binaries and young stellar objects. We find 82 new eclipsing binary systems, 9 of which are good candidate 25 Ori or Orion OB1a association members. Of these, two are potential young W UMa type systems. We report on the possible low-mass (M-dwarf primary) eclipsing systems in the sample, which include six of the candidate young systems. Forty-five of the binary systems are close (mainly contact) systems, and one of these shows an orbital period among the shortest known for W UMa binaries, at 0.2156509 ± 0.0000071 days, with flat-bottomed primary eclipses, and a derived distance that appears consistent with membership in the general Orion association. One of the candidate young systems presents an unusual light curve, perhaps representing a semi-detached binary system with an inflated low-mass primary or a star with a warped disk, and may represent an additional young Orion member. Finally, we identify 14 probable new classical T-Tauri stars in our data, along with one previously known (CVSO 35) and one previously reported as a candidate weak-line T-Tauri star (SDSS J052700.12+010136.8). http://dx.doi.org/10.1088/0004-6256/142/2/60

Levan, A. J.; Tanvir, N. R.; Cenko, S. B.; Perley, D. A.; Wiersema, K.; Bloom, J. S.; Fruchter, A. S.; Postigo, A. de Ugarte; O'Brien, P. T.; Butler, N.; van der Horst, A. J.; Leloudas, G.; Morgan, A. N.; Misra, K.; Bower, G. C.; Farihi, J.; Tunnicliffe, R. L.; Modjaz, M.; Silverman, J. M.; Hjorth, J.; Thöne, C.; Cucchiara, A.; Cerón, J. M. Castro; Castro-Tirado, A. J.; Arnold, J. A.; Bremer, M.; Brodie, J. P.; Carroll, T.; Cooper, M. C.; Curran, P. A.; Cutri, R. M.; Ehle, J.; Forbes, D.; Fynbo, J.; Gorosabel, J.; Graham, J.; Hoffman, D. I.; Guziy, S.; Jakobsson, P.; Kamble, A.; Kerr, T.; Kasliwal, M. M.; Kouveliotou, C.; Kocevski, D.; Law, N. M.; Nugent, P. E.; Ofek, E. O.; Poznanski, D.; Quimby, R. M.; Rol, E.; Romanowsky, A. J.; Sánchez-Ramírez, R.; Schulze, S.; Singh, N.; van Spaandonk, L.; Starling, R. L. C.; Strom, R. G.; Tello, J. C.; Vaduvescu, O.; Wheatley, P. J.; Wijers, R. A. M. J.; Winters, J. M.; Xu, D., “An Extremely Luminous Panchromatic Outburst from the Nucleus of a Distant Galaxy”, Science, July 2011, 333:199-,

Variable x-ray and γ-ray emission is characteristic of the most extreme physical processes in the universe. We present multiwavelength observations of a unique γ-ray-selected transient detected by the Swift satellite, accompanied by bright emission across the electromagnetic spectrum, and whose properties are unlike any previously observed source. We pinpoint the event to the center of a small, star-forming galaxy at redshift z = 0.3534. Its high-energy emission has lasted much longer than any γ-ray burst, whereas its peak luminosity was ˜100 times higher than bright active galactic nuclei. The association of the outburst with the center of its host galaxy suggests that this phenomenon has its origin in a rare mechanism involving the massive black hole in the nucleus of that galaxy. http://dx.doi.org/10.1126/science.1207143

Kleiser, Io K. W.; Poznanski, Dovi; Kasen, Daniel; Young, Timothy R.; Chornock, Ryan; Filippenko, Alexei V.; Challis, Peter; Ganeshalingam, Mohan; Kirshner, Robert P.; Li, Weidong; Matheson, Thomas; Nugent, Peter E.; Silverman, Jeffrey M., “Peculiar Type II supernovae from blue supergiants”, Monthly Notices of the Royal Astronomical Society, July 2011, 415:372-382,

The vast majority of Type II supernovae (SNeII) are produced by red supergiants, but SN 1987A revealed that blue supergiants (BSGs) can produce members of this class as well, albeit with some peculiar properties. This best-studied event revolutionized our understanding of SNe and linking it to the bulk of Type II events is essential. We present here the optical photometry and spectroscopy gathered for SN 2000cb, which is clearly not a standard SNII and yet is not a SN 1987A analogue. The light curve of SN 2000cb is reminiscent of that of SN 1987A in shape, with a slow rise to a late optical peak, but on substantially different time-scales. Spectroscopically, SN 2000cb resembles a normal SNII, but with ejecta velocities that far exceed those measured for SN 1987A or normal SNeII, above 18 000 km s−1 for Hα at early times. The red colours, high velocities, late photometric peak and our modelling of this object all point towards a scenario involving the high-energy explosion of a small-radius star, most likely a BSG, producing 0.1 M of 56Ni. Adding a similar object to the sample, SN 2005ci, we derive a rate of ∼2 per cent of the core-collapse rate for this loosely defined class of BSG explosions. http://dx.doi.org/10.1111/j.1365-2966.2011.18708.x

Quimby, R. M.; Kulkarni, S. R.; Kasliwal, M. M.; Gal-Yam, A.; Arcavi, I.; Sullivan, M.; Nugent, P.; Thomas, R.; Howell, D. A.; Nakar, E.; Bildsten, L.; Theissen, C.; Law, N. M.; Dekany, R.; Rahmer, G.; Hale, D.; Smith, R.; Ofek, E. O.; Zolkower, J.; Velur, V.; Walters, R.; Henning, J.; Bui, K.; McKenna, D.; Poznanski, D.; Cenko, S. B.; Levitan, D., “Hydrogen-poor superluminous stellar explosions”, Nature, June 2011, 474:487-489,

Supernovae are stellar explosions driven by gravitational or thermonuclear energy that is observed as electromagnetic radiation emitted over weeks or more. In all known supernovae, this radiation comes from internal energy deposited in the outflowing ejecta by one or more of the following processes: radioactive decay of freshly synthesized elements (typically 56Ni), the explosion shock in the envelope of a supergiant star, and interaction between the debris and slowly moving, hydrogen-rich circumstellar material. Here we report observations of a class of luminous supernovae whose properties cannot be explained by any of these processes. The class includes four new supernovae that we have discovered and two previously unexplained events (SN 2005ap and SCP 06F6) that we can now identify as members of the same class. These supernovae are all about ten times brighter than most type Ia supernova, do not show any trace of hydrogen, emit significant ultraviolet flux for extended periods of time and have late-time decay rates that are inconsistent with radioactivity. Our data require that the observed radiation be emitted by hydrogen-free material distributed over a large radius (~1015 centimetres) and expanding at high speeds (>104 kilometres per second). These long-lived, ultraviolet-luminous events can be observed out to redshifts z>4.

Cano, Z.; Bersier, D.; Guidorzi, C.; Margutti, R.; Svensson, K. M.; Kobayashi, S.; Melandri, A.; Wiersema, K.; Pozanenko, A.; van der Horst, A. J.; Pooley, G. G.; Fernandez-Soto, A.; Castro-Tirado, A. J.; Postigo, A. De Ugarte; Im, M.; Kamble, A. P.; Sahu, D.; Alonso-Lorite, J.; Anupama, G.; Bibby, J. L.; Burgdorf, M. J.; Clay, N.; Curran, P. A.; Fatkhullin, T. A.; Fruchter, A. S.; Garnavich, P.; Gomboc, A.; Gorosabel, J.; Graham, J. F.; Gurugubelli, U.; Haislip, J.; Huang, K.; Huxor, A.; Ibrahimov, M.; Jeon, Y.; Jeon, Y.-B.; Ivarsen, K.; Kasen, D.; Klunko, E.; Kouveliotou, C.; Lacluyze, A.; Levan, A. J.; Loznikov, V.; Mazzali, P. A.; Moskvitin, A. S.; Mottram, C.; Mundell, C. G.; Nugent, P. E.; Nysewander, M.; O'Brien, P. T.; Park, W.-K.; Peris, V.; Pian, E.; Reichart, D.; Rhoads, J. E.; Rol, E.; Rumyantsev, V.; Scowcroft, V.; Shakhovskoy, D.; Small, E.; Smith, R. J.; Sokolov, V. V.; Starling, R. L. C.; Steele, I.; Strom, R. G.; Tanvir, N. R.; Tsapras, Y.; Urata, Y.; Vaduvescu, O.; Volnova, A.; Volvach, A.; Wijers, R. A. M. J.; Woosley, S. E.; Young, D. R., “A tale of two GRB-SNe at a common redshift of z0.54”, Monthly Notices of the Royal Astronomical Society, May 2011, 413:669-685,

We present ground-based and Hubble Space Telescope optical observations of the optical transients (OTs) of long-duration Gamma Ray Bursts (GRBs) 060729 and 090618, both at a redshift of z= 0.54. For GRB 060729, bumps are seen in the optical light curves (LCs), and the late-time broad-band spectral energy distributions (SEDs) of the OT resemble those of local Type Ic supernovae (SNe). For GRB 090618, the dense sampling of our optical observations has allowed us to detect well-defined bumps in the optical LCs, as well as a change in colour, that are indicative of light coming from a core-collapse SN. The accompanying SNe for both events are individually compared with SN1998bw, a known GRB supernova, and SN1994I, a typical Type Ic supernova without a known GRB counterpart, and in both cases the brightness and temporal evolution more closely resemble SN1998bw. We also exploit our extensive optical and radio data for GRB 090618, as well as the publicly available Swift-XRT data, and discuss the properties of the afterglow at early times. In the context of a simple jet-like model, the afterglow of GRB 090618 is best explained by the presence of a jet-break at t-to > 0.5 d. We then compare the rest-frame, peak V-band absolute magnitudes of all of the GRB and X-Ray Flash (XRF)-associated SNe with a large sample of local Type Ibc SNe, concluding that, when host extinction is considered, the peak magnitudes of the GRB/XRF-SNe cannot be distinguished from the peak magnitudes of non-GRB/XRF SNe.

Childress, M.; Aldering, G.; Aragon, C.; Antilogus, P.; Bailey, S.; Baltay, C.; Bongard, S.; Buton, C.; Canto, A.; Chotard, N.; Copin, Y.; Fakhouri, H. K.; Gangler, E.; Kerschhaggl, M.; Kowalski, M.; Hsiao, E. Y.; Loken, S.; Nugent, P.; Paech, K.; Pain, R.; Pecontal, E.; Pereira, R.; Perlmutter, S.; Rabinowitz, D.; Runge, K.; Scalzo, R.; Thomas, R. C.; Smadja, G.; Tao, C.; Weaver, B. A.; Wu, C., “Keck Observations of the Young Metal-poor Host Galaxy of the Super-Chandrasekhar-mass Type Ia Supernova SN 2007if”, Astrophysical Journal, May 2011, 733:3,

We present Keck LRIS spectroscopy and g-band photometry of the metal-poor, low-luminosity host galaxy of the super-Chandrasekhar-mass Type Ia supernova SN 2007if. Deep imaging of the host reveals its apparent magnitude to be mg = 23.15 ± 0.06, which at the spectroscopically measured redshift of z helio = 0.07450 ± 0.00015 corresponds to an absolute magnitude of Mg = -14.45 ± 0.06. Galaxy g - r color constrains the mass-to-light ratio, giving a host stellar mass estimate of log(M */M sun) = 7.32 ± 0.17. Balmer absorption in the stellar continuum, along with the strength of the 4000 Å break, constrains the age of the dominant starburst in the galaxy to be t burst = 123+165-77 Myr, corresponding to a main-sequence turnoff mass of M/M sun = 4.6+2.6-1.4. Using the R 23 method of calculating metallicity from the fluxes of strong emission lines, we determine the host oxygen abundance to be 12 + log(O/H)KK04 = 8.01 ± 0.09, significantly lower than any previously reported spectroscopically measured Type Ia supernova host galaxy metallicity. Our data show that SN 2007if is very likely to have originated from a young, metal-poor progenitor. http://dx.doi.org/10.1088/0004-637X/733/1/3

Barth, Aaron J.; Nguyen, My L.; Malkan, Matthew A.; Filippenko, Alexei V.; Li, Weidong; Gorjian, Varoujan; Joner, Michael D.; Bennert, Vardha Nicola; Botyanszki, Janos; Cenko, S. Bradley; Childress, Michael; Choi, Jieun; Comerford, Julia M.; Cucciara, Antonino; da Silva, Robert; Duchêne, Gaspard; Fumagalli, Michele; Ganeshalingam, Mohan; Gates, Elinor L.; Gerke, Brian F.; Griffith, Christopher V.; Harris, Chelsea; Hintz, Eric G.; Hsiao, Eric; Kandrashoff, Michael T.; Keel, William C.; Kirkman, David; Kleiser, Io K. W.; Laney, C. David; Lee, Jeffrey; Lopez, Liliana; Lowe, Thomas B.; Moody, J. Ward; Morton, Alekzandir; Nierenberg, A. M.; Nugent, Peter; Pancoast, Anna; Rex, Jacob; Rich, R. Michael; Silverman, Jeffrey M.; Smith, Graeme H.; Sonnenfeld, Alessandro; Suzuki, Nao; Tytler, David; Walsh, Jonelle L.; Woo, Jong-Hak; Yang, Yizhe; Zeisse, Carl, “Broad-line Reverberation in the Kepler-field Seyfert Galaxy Zw 229-015”, Astrophysical Journal, May 2011, 732:121,

The Seyfert 1 galaxy Zw 229-015 is among the brightest active galaxies being monitored by the Kepler mission. In order to determine the black hole mass in Zw 229-015 from Hβ reverberation mapping, we have carried out nightly observations with the Kast Spectrograph at the Lick 3 m telescope during the dark runs from 2010 June through December, obtaining 54 spectroscopic observations in total. We have also obtained nightly V-band imaging with the Katzman Automatic Imaging Telescope at Lick Observatory and with the 0.9 m telescope at the Brigham Young University West Mountain Observatory over the same period. We detect strong variability in the source, which exhibited more than a factor of two change in broad Hβ flux. From cross-correlation measurements, we find that the Hβ light curve has a rest-frame lag of 3.86+0.69-0.90 days with respect to the V-band continuum variations. We also measure reverberation lags for Hα and Hγ and find an upper limit to the Hδ lag. Combining the Hβ lag measurement with a broad Hβ width of σline = 1590 ± 47 km s-1 measured from the rms variability spectrum, we obtain a virial estimate of M BH = 1.00+0.19-0.24 × 107 M sun for the black hole in Zw 229-015. As a Kepler target, Zw 229-015 will eventually have one of the highest-quality optical light curves ever measured for any active galaxy, and the black hole mass determined from reverberation mapping will serve as a benchmark for testing relationships between black hole mass and continuum variability characteristics in active galactic nuclei.

Sullivan, M.; Kasliwal, M. M.; Nugent, P. E.; Howell, D. A.; Thomas, R. C.; Ofek, E. O.; Arcavi, I.; Blake, S.; Cooke, J.; Gal-Yam, A.; Hook, I. M.; Mazzali, P.; Podsiadlowski, P.; Quimby, R.; Bildsten, L.; Bloom, J. S.; Cenko, S. B.; Kulkarni, S. R.; Law, N.; Poznanski, D., “The Subluminous and Peculiar Type Ia Supernova PTF 09dav”, Astrophysical Journal, May 2011, 732:118,

PTF 09dav is a peculiar subluminous Type Ia supernova (SN) discovered by the Palomar Transient Factory (PTF). Spectroscopically, it appears superficially similar to the class of subluminous SN1991bg-like SNe, but it has several unusual features which make it stand out from this population. Its peak luminosity is fainter than any previously discovered SN1991bg-like SN Ia (MB ~ -15.5), but without the unusually red optical colors expected if the faint luminosity were due to extinction. The photospheric optical spectra have very unusual strong lines of Sc II and Mg I, with possible Sr II, together with stronger than average Ti II and low velocities of ~6000 km s-1. The host galaxy of PTF09dav is ambiguous. The SN lies either on the extreme outskirts (~41 kpc) of a spiral galaxy or in an very faint (MR >= -12.8) dwarf galaxy, unlike other 1991bg-like SNe which are invariably associated with massive, old stellar populations. PTF 09dav is also an outlier on the light-curve-width-luminosity and color-luminosity relations derived for other subluminous SNe Ia. The inferred 56Ni mass is small (0.019 ± 0.003 M sun), as is the estimated ejecta mass of 0.36 M sun. Taken together, these properties make PTF 09dav a remarkable event. We discuss various physical models that could explain PTF 09dav. Helium shell detonation or deflagration on the surface of a CO white dwarf can explain some of the features of PTF 09dav, including the presence of Sc and the low photospheric velocities, but the observed Si and Mg are not predicted to be very abundant in these models. We conclude that no single model is currently capable of explaining all of the observed signatures of PTF 09dav. http://dx.doi.org/10.1088/0004-637X/732/2/118

Chotard, N.; Gangler, E.; Aldering, G.; Antilogus, P.; Aragon, C.; Bailey, S.; Baltay, C.; Bongard, S.; Buton, C.; Canto, A.; Childress, M.; Copin, Y.; Fakhouri, H. K.; Hsiao, E. Y.; Kerschhaggl, M.; Kowalski, M.; Loken, S.; Nugent, P.; Paech, K.; Pain, R.; Pecontal, E.; Pereira, R.; Perlmutter, S.; Rabinowitz, D.; Runge, K.; Scalzo, R.; Smadja, G.; Tao, C.; Thomas, R. C.; Weaver, B. A.; Wu, C.; Nearby Supernova Factory, “The reddening law of type Ia supernovae: separating intrinsic variability from dust using equivalent widths”, Astronomy & Astrophysics, May 2011, 529:L4,

We employ 76 type Ia supernovae (SNe Ia) with optical spectrophotometry within 2.5 days of B-band maximum light obtained by the Nearby Supernova Factory to derive the impact of Si and Ca features on the supernovae intrinsic luminosity and determine a dust reddening law. We use the equivalent width of Si ii λ4131 in place of the light curve stretch to account for first-order intrinsic luminosity variability. The resulting empirical spectral reddening law exhibits strong features that are associated with Ca ii and Si ii λ6355. After applying a correction based on the Ca ii H&K equivalent width we find a reddening law consistent with a Cardelli extinction law. Using the same input data, we compare this result to synthetic rest-frame UBVRI-like photometry to mimic literature observations. After corrections for signatures correlated with Si ii λ4131 and Ca ii H&K equivalent widths and introducing an empirical correlation between colors, we determine the dust component in each band. We find a value of the total-to-selective extinction ratio, RV = 2.8 ± 0.3. This agrees with the Milky Way value, in contrast to the low RVvalues found in most previous analyses. This result suggests that the long-standing controversy in interpreting SN Ia colors and their compatibility with a classical extinction law, which is critical to their use as cosmological probes, can be explained by the treatment of the dispersion in colors, and by the variability of features apparent in SN Ia spectra. http://dx.doi.org/1 0.1051/0004-6361/201116723

 

Miller, Adam A.; Hillenbrand, Lynne A.; Covey, Kevin R.; Poznanski, Dovi; Silverman, Jeffrey M.; Kleiser, Io K. W.; Rojas-Ayala, Bárbara; Muirhead, Philip S.; Cenko, S. Bradley; Bloom, Joshua S.; Kasliwal, Mansi M.; Filippenko, Alexei V.; Law, Nicholas M.; Ofek, Eran O.; Dekany, Richard G.; Rahmer, Gustavo; Hale, David; Smith, Roger; Quimby, Robert M.; Nugent, Peter; Jacobsen, Janet; Zolkower, Jeff; Velur, Viswa; Walters, Richard; Henning, John; Bui, Khanh; McKenna, Dan; Kulkarni, Shrinivas R.; Klein, Christopher R.; Kandrashoff, Michael; Morton, Alekzandir, “Evidence for an FU Orionis-like Outburst from a Classical T Tauri Star”, Astrophysical Journal, April 1, 2011, 730:80,

We present pre- and post-outburst observations of the new FU Orionis-like young stellar object PTF 10qpf (also known as LkHα 188-G4 and HBC 722). Prior to this outburst, LkHα 188-G4 was classified as a classical T Tauri star (CTTS) on the basis of its optical emission-line spectrum superposed on a K8-type photosphere and its photometric variability. The mid-infrared spectral index of LkHα 188-G4 indicates a Class II-type object. LkHα 188-G4 exhibited a steady rise by ~1 mag over ~11 months starting in August 2009, before a subsequent more abrupt rise of >3 mag on a timescale of ~2 months. Observations taken during the eruption exhibit the defining characteristics of FU Orionis variables: (1) an increase in brightness by gsim4 mag, (2) a bright optical/near-infrared reflection nebula appeared, (3) optical spectra are consistent with a G supergiant and dominated by absorption lines, the only exception being Hα which is characterized by a P Cygni profile, (4) near-infrared spectra resemble those of late K-M giants/supergiants with enhanced absorption seen in the molecular bands of CO and H2O, and (5) outflow signatures in H and He are seen in the form of blueshifted absorption profiles. LkHα 188-G4 is the first member of the FU Orionis-like class with a well-sampled optical to mid-infrared spectral energy distribution in the pre-outburst phase. The association of the PTF 10qpf outburst with the previously identified CTTS LkHα 188-G4 (HBC 722) provides strong evidence that FU Orionis-like eruptions represent periods of enhanced disk accretion and outflow, likely triggered by instabilities in the disk. The early identification of PTF 10qpf as an FU Orionis-like variable will enable detailed photometric and spectroscopic observations during its post-outburst evolution for comparison with other known outbursting objects. http://dx.doi.org/10.1088/0004-637X/730/2/80

K.~R Poznanski Bloom Rebull Law Rahmer Nugent Walters Kulkarni Covey, “PTF10nvg: An Outbursting Class I Protostar in the Pelican/North American Nebula”, \aj, January 1, 2011, 141:40,

Maguire, K.; Sullivan, M.; Thomas, R. C.; Nugent, P.; Howell, D. A.; Gal-Yam, A.; Arcavi, I.; Ben-Ami, S.; Blake, S.; Botyanszki, J.; Buton, C.; Cooke, J.; Ellis, R. S.; Hook, I. M.; Kasliwal, M. M.; Pan, Y.-C.; Pereira, R.; Podsiadlowski, P.; Sternberg, A.; Suzuki, N.; Xu, D.; Yaron, O.; Bloom, J. S.; Cenko, S. B.; Kulkarni, S. R.; Law, N.; Ofek, E. O.; Poznanski, D.; Quimby, R. M., “PTF10ops - a subluminous, normal-width light curve Type Ia supernova in the middle of nowhere”, Monthly Notices of the Royal Astronomical Society, January 1, 2011, 418:747-758,

A.~M Nugent Quimby Hook Gal-Yam Jacobsen Walters Smith, Galaxy Zoo Supernovae, \mnras, Pages: 1309-1319 January 1, 2011,

2010

D. a Filippenko Li Poznanski, An Unusually Fast-Evolving Supernova, Science, Pages: 58- 2010,

I. a Ofek Cenko Poznanski J\ onsson Rahmer Velur McKenna Arcavi, Core-collapse Supernovae from the Palomar Transient Factory: Indications for a Different Population in Dwarf Galaxies, \apj, Pages: 777-784 2010,

R. Amanullah, C. Lidman, D. Rubin, G. Aldering, P. Astier, K. Barbary, M. S. Burns, A. Conley, K. S. Dawson, S. E. Deustua, M. Doi, S. Fabbro, L. Faccioli, H. K. Fakhouri, G. Folatelli, A. S. Fruchter, H. Furusawa, G. Garavini, G. Goldhaber, A. Goobar, D. E. Groom, I. Hook, D. A. Howell, N. Kashikawa, A. G. Kim, R. A. Knop, M. Kowalski, E. Linder, J. Meyers, T. Morokuma, S. Nobili, J. Nordin, P. Nugent, L. Östman, R. Pain, N. Panagia, S. Perlmutter, J. Raux, P. Ruiz-Lapuente, A. L. Spadafora, M. Strovink, N. Suzuki, L. Wang, W. M. Wood-Vasey, N. Yasuda, “Spectra and Hubble Space Telescope Light Curves of Six Type Ia Supernovae at 0.511 < z < 1.12 and the Union2 Compilation”, Supernova Cosmology Project, Astrophysical Journal, January 2010, 716 (1):712-738,

N. a Silverman Marcy Yelda Smith, Discovery of Precursor Luminous Blue Variable Outbursts in Two Recent Optical Transients: The Fitfully Variable Missing Links UGC 2773-OT and SN 2009ip, \aj, Pages: 1451-1467 2010,

B.~D Quataert Nugent Metzger, Electromagnetic counterparts of compact object mergers powered by the radioactive decay of r-process nuclei, \mnras, Pages: 2650-2662 2010,

S.~B Morgan Castro-Tirado de Ugarte Postigo Kulkarni Starr Cenko, Unveiling the Origin of Grb 090709A: Lack of Periodicity in a Reddened Cosmological Long-Duration Gamma-Ray Burst, \aj, Pages: 224-234 2010,

R.~A Bailey Childress Gal-Yam Loken Pereira Rau Tao Scalzo, Nearby Supernova Factory Observations of SN 2007if: First Total Mass Measurement of a Super-Chandrasekhar-Mass Progenitor, \apj, Pages: 1073-1094 2010,

S. a Nugent Darbha, Nickel-rich outflows produced by the accretion-induced collapse of white dwarfs: light curves and spectra, \mnras, Pages: 846-854 2010,

E.~O Cenko Nugent Forster Law Shen Hale Walters Ofek, Supernova PTF 09UJ: A Possible Shock Breakout from a Dense Circumstellar Wind, \apj, Pages: 1396-1401 January 1, 2010,

Kasliwal, Kulkarni, Gal-Yam, Yaron, Quimby, Ofek, Nugent, Poznanski, Jacobsen, Sternberg, Arcavi, Howell, Sullivan, Rich, Burke, Brimacombe, Milisavljevic, Fesen, Bildsten, Shen, Cenko, Bloom, Hsiao, Law, Gehrels, Immler, Dekany, Rahmer, Hale, Smith, Zolkower, Velur, Walters, Henning, Bui, McKenna, “Rapidly Decaying Supernova 2010X: A Candidate Ia Explosion”, Astrophysical Journal Letters, 2010, 723 (1):L98-L102,

Kozłowski, Kochanek, Stern, Prieto, Stanek, Thompson, Assef, Drake, Szczygieł, Woźniak, Nugent, Ashby, Beshore, Brown, Dey, Griffith, Harrison, Jannuzi, Larson, Madsen, Pilecki, Pojmański, Skowron, Vestrand, Wren, “SDWFS-MT-1: A Self-obscured Luminous Supernova at z ~= 0.2”, Astrophysical Journal, 2010, 722 (2):1624-1632,

D. a Poznanski, Type II-P Supernovae as Standard Candles: The SDSS-II Sample Revisited, \apj, Pages: 956-959 2010,

A.~A Bloom Ganeshalingam Smith Miller, SN 2008iy: an unusual Type IIn Supernova with an enduring 400-d rise time, \mnras, Pages: 305-317 2010,

2009

S. a Baltay Chotard Nugent Perlmutter Runge Tao Bailey, Using spectral flux ratios to standardize SN Ia luminosities, \aap, Pages: L17-L20 January 1, 2009,

M. a Nugent Sullivan, The Mean Type Ia Supernova Spectrum Over the Past Nine Gigayears, \apjl, Pages: L76-L80 January 1, 2009,

2008

P. a Nugent, Optimizing Type Ia supernova follow-up in future dark energy surveys, Journal of Physics Conference Series, Pages: 012011 January 1, 2008,

2006

A. a Tanvir Dell Antonio Castro Cer\ on Antonelli Fynbo Nugent Thorsett Levan, Infrared and Optical Observations of GRB 030115 and its Extremely Red Host Galaxy: Implications for Dark Bursts, \apj, Pages: 471-482 January 1, 2006,

P. a Leonard Conley Pain Nugent, “Toward a Cosmological Hubble Diagram for Type II-P Supernovae”, \apj, January 1, 2006, 645:841-850,

Leonid Oliker

2013

Hongzhang Shan, Brian Austin, Wibe De Jong, Leonid Oliker, Nicholas Wright, Edoardo Apra, “Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms”, SC'13, November 11, 2013,

2011

Robert Preissl, Nathan Wichmann, Bill Long, John Shalf, Stephane Ethier, Alice Koniges, “Multithreaded global address space communication techniques for gyrokinetic fusion applications on ultra-scale platforms”, Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, 78,

Kamesh Madduri, Z. Ibrahim, Williams, Im, Ethier, Shalf, Leonid Oliker, “Gyrokinetic toroidal simulations on leading multi- and manycore HPC systems”, SC, November 1, 2011, 23,

Samuel Williams, Oliker, Carter, John Shalf, “Extracting ultra-scale Lattice Boltzmann performance via hierarchical and distributed auto-tuning”, SC, November 1, 2011, 55,

Jens Krueger, Donofrio, Shalf, Mohiyuddin, Williams, Oliker, Franz-Josef Pfreund, “Hardware/software co-design for energy-efficient seismic modeling”, SC, November 1, 2011, 73,

J. Dongarra, P. Beckman, T. Moore, P. Aerts, G. Aloisio, J.C. Andre, D. Barkai, J.Y. Berthou, T. Boku, B. Braunschweig, others, “The international exascale software project roadmap”, International Journal of High Performance Computing Applications, January 2011, 25:3--60,

2010

Jack Dongarra, John Shalf, David Skinner, Kathy Yelick, “International Exascale Software Project (IESP) Roadmap, version 1.1”, October 18, 2010,

Gilbert Hendry, Johnnie Chan, Shoaib Kamil, Lenny Oliker, John Shalf, Luca P. Carloni, and Keren Bergman, “Silicon Nanophotonic Network-On-Chip Using TDM Arbitration”, IEEE Symposium on High Performance Interconnects (HOTI) 5.1, August 2010,

S. Ethier, M. Adams, J. Carter, L. Oliker, “Petascale Parallelization of the Gyrokinetic Toroidal Code”, VECPAR: High Performance Computing for Computational Science, June 2010,

A. Chandramowlishwaran, S. Williams, L. Oliker, I. Lashuk, G. Biros, R. Vuduc, “Optimizing and Tuning the Fast Multipole Method for State-of-the-Art Multicore Architectures”, Proceedings of 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS), April 2010,

 

Shoaib Kamil, Chan, Oliker, Shalf, Samuel Williams, “An auto-tuning framework for parallel multicore stencil computations”, IPDPS, January 1, 2010, 1-12,

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick, “Auto-Tuning Stencil Computations on Diverse Multicore Architectures”, Scientific Computing with Multicore and Accelerators, edited by Jakub Kurzak, David A. Bader, Jack Dongarra, 2010,

Shoaib Kamil, Oliker, Pinar, John Shalf, “Communication Requirements and Interconnect Optimization for High-End Scientific Applications”, IEEE Trans. Parallel Distrib. Syst., 2010, 21:188-202,

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, “Parallel I/O performance: From events to ensembles”, IPDPS, Atlanta, Georgia, 2010, 1-11,

2009

David Donofrio, Oliker, Shalf, F. Wehner, Rowen, Krueger, Kamil, Marghoob Mohiyuddin, “Energy-Efficient Computing for Extreme-Scale Science”, IEEE Computer, January 1, 2009, 42:62-71,

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms”, Journal of Parallel and Distributed Computing, January 1, 2009, 69:762-777,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, “Optimization of sparse matrix-vector multiplication on emerging multicore platforms”, Parallel Computing, January 1, 2009, 35:178--194,

Kaushik Datta, Kamil, Williams, Oliker, Shalf, Katherine A. Yelick, “Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors”, SIAM Review, January 1, 2009, 51:129-159,

2008

K. Datta, M. Murphy, V. Volkov, S. Williams, J. Carter, L. Oliker, D. Patterson, J. Shalf, K. Yelick, “Stencil computation optimization and auto-tuning on state-of-the-art multicore architectures”, Proceedings of the 2008 ACM/IEEE Conference on High Performance Computing and Networking ("Supercomputing", SC08), November 15, 2008,

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Lattice Boltzmann simulation optimization on leading multicore platforms”, International Parallel and Distributed Processing Symposium (IPDPS), April 14, 2008, 1-14,

M. Wehner, L. Oliker, J. Shalf, Ultra-Efficient Exascale Scientific Computing, talk, January 1, 2008,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, “Scientific Application Performance On Leading Scalar and Vector Supercomputering Platforms”, IJHPCA, January 1, 2008, 22:5-20,

Michael F. Wehner, Oliker, John Shalf, “Towards Ultra-High Resolution Models of Climate and Weather”, IJHPCA, January 1, 2008, 22:149-165,

2007

Leonid Oliker, Andrew Canning, Johnathan Carter, Costin Iancu, Mike Lijewski, Shoaib Kamil, John Shalf, Hongzhang Shan, Erich Strohmaier, Stephane Ethier, Tom Goodale, “Scientific Application Performance on Candidate PetaScale Platforms”, IPDPS, January 1, 2007, 1-12,

Julian Borrill, Leonid Oliker, John Shalf, Hongzhang Shan, “Investigation of leading HPC I/O performance using a scientific-application derived benchmark”, SC, January 1, 2007, 10,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms, International Conference for High-Performance Computing, Networking, Storage, and Analysis, January 1, 2007,

Shoaib Kamil, Ali Pinar, Dan Gunter, Mike Lijewski, Leonid Oliker, John Shalf, “Reconfigurable hybrid interconnection for static and dynamic scientific applications”, Conf. Computing Frontiers, January 1, 2007, 183-194,

John Shalf, Shoaib Kamil, David Skinner, Leonid Oliker, Interconnect Requirements for HPC Applications, talk, January 1, 2007,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “Scientific computing kernels on the Cell processor”, International Journal of Parallel Programming, January 1, 2007, 35:263--298,

2006

Jonathan Carter, Tony Drummond, Parry Husbands, Paul Hargrove, Bill Kramer, Osni Marques, Esmond Ng, Lenny Oliker, John Shalf, David Skinner, Kathy Yelick, “Software Roadmap to Plug and Play Petaflop/s”, Lawrence Berkeley National Laboratory Technical Report, #59999, July 31, 2006,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “The potential of the cell processor for scientific computing”, Proceedings of the 3rd conference on Computing frontiers, January 1, 2006, 9--20,

Jonathan Carter, Leonid Oliker, John Shalf, “Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems”, VECPAR, January 1, 2006, 490-503,

L. Oliker, S. Kamil, A. Canning, J. Carter, C. Iancu, J. Shalf, H. Shan, D. Skinner, E. Strohmaier, T. Goodale, “Application Scalability and Communication Signatures on Leading Supercomputing Platforms”, January 1, 2006,

S. Kamil, K. Datta, S. Williams, L. Oliker, J. Shalf, K. Yelick, “Implicit and explicit optimizations for stencil computations”, Proceedings of the 2006 workshop on Memory system performance and correctness, January 1, 2006, 51--60,

2005

John Shalf, Kamil, Oliker, David Skinner, “Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect”, SC, January 1, 2005, 17,

Horst Simon, William Kramer, William Saphir, John Shalf, David Bailey, Leonid Oliker, Michael Banda, C. William McCurdy, John Hules, Andrew Canning, Marc Day, Philip Colella, David Serafini, Michael Wehner, Peter Nugent, “Science-Driven System Architecture: A New Process for Leadership Class Computing”, Journal of the Earth Simulator, January 1, 2005, 2,

S. Kamil, J. Shalf, L. Oliker, D. Skinner, “Understanding ultra-scale application communication requirements”, Workload Characterization Symposium, 2005. Proceedings of the IEEE International, January 1, 2005, 178--187,

Shoaib Kamil,Parry Husbands, Leonid Oliker, John Shalf, Katherine A. Yelick, “Impact of modern memory subsystems on cache optimizations for stencil computations”, Memory System Performance, January 1, 2005, 36-43,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stephane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Performance evaluation of the SX-6 vector architecture for scientific computations”, Concurrency - Practice and Experience, January 1, 2005, 17:69-93,

2004

Gorden Griem, Oliker, Shalf, Katherine A. Yelick, “Identifying Performance Bottlenecks on Modern Microarchitectures Using an Adaptable Probe”, IPDPS, January 1, 2004,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, “Scientific Computations on Modern Parallel Vector Systems”, SC, January 1, 2004, 10,

2003

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stepahane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations”, SC, January 1, 2003, 38,

Larry Pezzaglia

2013

Larry Pezzaglia, “Supporting Multiple Workloads, Batch Systems, and Computing Environments on a Single Linux Cluster”, Cray User Group 2013, May 9, 2013,

2012

Larry Pezzaglia, CHOS in Production: Supporting Multiple Linux Environments on PDSF at NERSC, A talk at the HEPiX Spring 2012 Workshop, Prague, Czech Republic, April 25, 2012,

The CHOS[1] software package combines a Linux kernel module, a PAM module, and batch system integration to provide a mechanism for concurrently supporting multiple Linux environments on a single Linux system. This presentation gives an introduction to CHOS and details how NERSC has deployed this utility on the PDSF HPC system to meet the complex, and often conflicting, software environment requirements of multiple applications. The CHOS utility has been in continuous use on PDSF for over 8 years, and has proven to be a robust and simple approach to ensure optimal software environments for HENP workloads.

[1] CHOS was written by Shane Canon of NERSC, and the code is available on GitHub. The CHOS technology is explained in detail in this paper.

Eric Hjort, Larry Pezzaglia, Iwona Sakrejda, PDSF at NERSC: Site Report, A talk at the HEPiX Spring 2012 Workshop, Prague, Czech Republic, April 24, 2012,

PDSF is a commodity Linux cluster at NERSC which has been in continuous operation since 1996. This talk will provide a status update on the PDSF system and summarize recent changes at NERSC. Highlighted PDSF changes include the conversion to xCAT-managed netboot node images, the ongoing deployment of Scientific Linux 6, and the introduction of XRootD for STAR.

Jefferson R. Porter

2008

Shreyas Cholia, R. Jefferson Porter, “Publication and Protection of Sensitive Site Information in a Grid Infrastructure”, 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (CCGRID) p. 639-644, IJGHPC 1(2): 56-73 (2009), May 30, 2008,

Robert Preissl

2013

Alice Koniges, Praveen Narayanan, Robert Preissl, Xuefei Yuan, Proxy Design and Optimization in Fusion and Accelerator Physics, SIAM Conference on Computational Science and Engineering, February 25, 2013,

2012

Alice Koniges, Katherine Yelick, Rolf Rabenseifner, Reinhold Bader, David Eder, Filip Blagojevic, Robert Preissl, Paul Hargrove, Introduction to PGAS (UPC and CAF) and Hybrid for Multicore Programming, SC12 Full Day Tutorial, November 2012,

2011

Praveen Narayanan, Alice Koniges, Leonid Oliker, Robert Preissl, Samuel Williams, Nicholas J Wright, Maxim Umansky, Xueqiao Xu, Benjamin Dudson, Stephane Ethier, Weixing Wang, Jeff Candy, John R. Cary, “Performance Characterization for Fusion Co-design Applications”, Proceedings of CUG, 2011,

2010

Robert Preissl, Bronis R. de Supinski, Martin Schulz, Daniel J. Quinlan, Dieter Kranzlmüller, Thomas Panas, “Exploitation of Dynamic Communication Patterns through Static Analysis”, Proc. International Conference on Parallel Processing (ICPP), September 13, 2010,

Alice Koniges, Robert Preissl, Jihan Kim, D Eder, A Fisher, N Masters, V Mlaker, S Ethier, W Wang, M Head-Gordon, N Wichmann, “Application acceleration on current and future Cray platforms,”, BEST PAPER, Proc. Cray User Group Meeting, Edinburgh, Scotland, May 2010,

Alice Koniges, Robert Preissl, Stephan Ethier, John Shalf, What’s Ahead for Fusion Computing?, International Sherwood Fusion Theory Conference, April 2010,

Robert Preissl, Alice Koniges, Stephan Ethier, Weixing Wang, Nathan Wichmann, “Overlapping communication with computation using OpenMP tasks on the GTS magnetic fusion code”, Scientific Programming, 2010, 18:139--151,

Lavanya Ramakrishnan

2013

You-Wei Cheah, Richard Canon, Plale, Lavanya Ramakrishnan, “Milieu: Lightweight and Configurable Big Data Provenance for Science”, BigData Congress, 2013, 46-53,

2012

Dan Gunter, Shreyas Cholia, Anubhav Jain, Michael Kocher, Kristin Persson, Lavanya Ramakrishnan, Shyue Ping Ong, Gerbrand Ceder, “Community Accessible Datastore of High-Throughput Calculations: Experiences from the Materials Project”, 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS) 2012, November 12, 2012,

Elif Dede, Fadika, Hartog, Govindaraju, Ramakrishnan, Gunter, Shane Richard Canon, “MARISSA: MApReduce Implementation for Streaming Science Applications”, eScience, October 8, 2012, 1-8,

Zacharia Fadika, Madhusudhan Govindaraju, Shane Richard Canon, Lavanya Ramakrishnan, “Evaluating Hadoop for Data-Intensive Scientific Operations”, IEEE Cloud 2012, June 24, 2012,

Emerging sensor networks, more capable instruments, and ever increasing simulation scales are generating data at a rate that exceeds our ability to effectively manage, curate, analyze, and share it. Data-intensive computing is expected to revolutionize the next-generation software stack. Hadoop, an open source implementation of the MapReduce model provides a way for large data volumes to be seamlessly processed through use of large commodity computers. The inherent parallelization, synchronization and fault-tolerance the model offers, makes it ideal for highly-parallel data-intensive applications. MapReduce and Hadoop have traditionally been used for web data processing and only recently been used for scientific applications. There is a limited understanding on the performance characteristics that scientific data intensive applications can obtain from MapReduce and Hadoop. Thus, it is important to evaluate Hadoop specifically for data-intensive scientific operations -- filter, merge and reorder-- to understand its various design considerations and performance trade-offs. In this paper, we evaluate Hadoop for these data operations in the context of High Performance Computing (HPC) environments to understand the impact of the file system, network and programming modes on performance.

Jay Srinivasan, Richard Shane Canon, Lavanya Ramakrishnan, “My Cray can do that? Supporting Diverse Workloads on the Cray XE-6”, CUG 2012, May 2012,

The Cray XE architecture has been optimized to support tightly coupled MPI applications, but there is an in- creasing need to run more diverse workloads in the scientific and technical computing domains. These needs are being driven by trends such as the increasing need to process “Big Data”. In the scientific arena, this is exemplified by the need to analyze data from instruments ranging from sequencers, telescopes, and X-ray light sources. These workloads are typically throughput oriented and often involve complex task dependencies. Can platforms like the Cray XE line play a role here? In this paper, we will describe tools we have developed to support high-throughput workloads and data intensive applications on NERSC’s Hopper system. These tools include a custom task farmer framework, tools to create virtual private clusters on the Cray, and using Cray’s Cluster Compatibility Mode (CCM) to support more diverse workloads. In addition, we will describe our experience with running Hadoop, a popular open-source implementation of MapReduce, on Cray systems. We will present our experiences with this work including successes and challenges. Finally, we will discuss future directions and how the Cray platforms could be further enhanced to support these class of workloads.

Lavanya Ramakrishnan, Richard Canon, Muriki, Sakrejda, Nicholas J. Wright, “Evaluating Interconnect and Virtualization Performance forHigh Performance Computing”, SIGMETRICS Performance Evaluation Review, 2012, 40:55-60,

2011

Katherine Yelick, Susan Coghlan, Brent Draney, Richard Shane Canon, Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Anping Liu, Scott Campbell, Piotr T. Zbiegiel, Tina Declerck, Paul Rich, “The Magellan Report on Cloud Computing for Science”, U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), December 2011,

Ghoshal, Devarshi and Canon, Richard Shane and Ramakrishnan, Lavanya, “Understanding I/O Performance of Virtualized Cloud Environments”, The Second International Workshop on Data Intensive Computing in the Clouds (DataCloud-SC11), 2011,

We compare the I/O performance using IOR benchmarks on two cloud computing platforms - Amazon and the Magellan cloud testbed.

Lavanya Ramakrishnan & Shane Canon, NERSC, Hadoop and Pig Overview, October 2011,

The MapReduce programming model and its open source implementation Hadoop is gaining traction in the scientific community for addressing the needs of data focused scientific applications. The requirements of these scientific applications are significantly different from the web 2.0 applications that have  traditionally used Hadoop. The tutorial  will provide an overview of Hadoop technologies, discuss some use cases of Hadoop for science and present the programming challenges with using Hadoop for legacy applications. Participants will access the Hadoop system at NERSC for the hands-on component of the tutorial.

Lavanya Ramakrishnan, Richard Shane Canon, Krishna Muriki, Iwona Sakrejda, and Nicholas J. Wright., “Evaluating Interconnect and Virtualization Performance for High Performance Computing”, Proceedings of 2nd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems (PMBS11), 2011,

In this paper we detail benchmarking results that characterize the virtualization overhead and its impact on performance. We also examine the performance of various interconnect technologies with a view to understanding the performance impacts of various choices. Our results show that virtualization can have a significant impact upon performance, with at least a 60% performance penalty. We also show that less capable interconnect technologies can have a significant impact upon performance of typical HPC applications. We also evaluate the performance of the Amazon Cluster compute instance and show that it performs approximately equivalently to a 10G Ethernet cluster at low core counts.

Lavanya Ramakrishnan, Piotr T. Zbiegel, Scott Campbell, Rick Bradshaw, Richard Shane Canon, Susan Coghlan, Iwona Sakrejda, Narayan Desai, Tina Declerck, Anping Liu, “Magellan: Experiences from a Science Cloud”, Proceedings of the 2nd International Workshop on Scientific Cloud Computing, ACM ScienceCloud '11, Boulder, Colorado, and New York, NY, 2011, 49 - 58,

2010

Keith Jackson, Lavanya Ramakrishnan, Karl Runge, and Rollin Thomas, “Seeking Supernovae in the Clouds: A Performance Study”, ScienceCloud 2010, the 1st Workshop on Scientific Cloud Computing, Chicago, Illinois, June 2010,

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

Lavanya Ramakrishnan, R. Jackson, Canon, Cholia, John Shalf, “Defining future platform requirements for e-Science clouds”, SoCC, New York, NY, USA, 2010, 101-106,

Oliver Ruebel

2013

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, Benjamin P. Bowen, “OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging”, Analytical Chemistry, 2013, 85 (21), pp 10354–10361, October 2, 2013,

2012

Oliver Rübel, Soile V. E. Keränen, Mark D. Biggin, David W. Knowles, H. Weber, Hans Hagen, Bernd Hamann, E. Wes Bethel, “Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data”, Mathematical Methods for Visualization in Medicine and Life Sciences II, (Springer-Verlag: 2012) Pages: 267--286, LBNL 4891E

Allen R. Sanderson, Brad Whitlock, Oliver R\ ubel, Hank Childs, Gunther H. Weber, Prabhat, Kesheng Wu, “A System for Query Based Analysis and Visualization”, Third International EuroVis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, 2012, 25--29, LBNL 5507E

E. Wes Bethel, Surendra Byna, Jerry Chou, Estelle Cormier-Michel, Cameron G. R. Geddes, Mark Howison, Fuyu Li, Prabhat, Ji Qiang, Oliver R\ ubel, Robert D. Ryne, Michael Wehner, Kesheng Wu, “Big Data Analysis and Visualization: What Do LINACS and Tropical Storms Have In Common?”, 11th International Computational Accelerator Physics Conference, ICAP 2012, Rostock-Warnem\ unde, Germany, 2012,

E. Wes Bethel, Rob Ross, Wei-Ken Liao, Prabhat, Karen Schuchardt, Peer-Timo Bremer, Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, John Patchett, Han-Wei Shen, David Pugmire, Dean Williams, “Recent Advances in Visual Data Exploration and Analysis of Climate Data”, SciDAC 3 Principal Investigator Meeting, 2012,

Oliver Ruebel, Cameron Geddes, Min Chen, Estelle Cormier, Ji Qiang, Rob Ryne, Jean-Luc Vey, David Grote, Jerry Chou, Kesheng Wu, Mark Howison, Prabhat, Brian Austin, Arie Shoshani, E. Wes Bethel, “Scalable Data Management, Analysis and Visualization of Particle Accelerator Simulation Data”, SciDAC 3 Principal Investigator Meeting, 2012,

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, J\ org Meyer, Prabhat, Oliver R\ ubel, Daniela Ushizima, Gunther Weber, “Towards Exascale: High Performance Visualization and Analytics -- Project Status Report”, 2012,

Oliver Rubel, Wes Bethel, Prabhat, Kesheng Wu, “Query Driven Visualization and Analysis”, High Performance Visualization: Enabling Extreme-Scale Scientific Insight, (CRC Press: 2012)

Prabhat, Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, E. Wes Bethel, “TECA: A Parallel Toolkit for Extreme Climate Analysis”, Third Worskhop on Data Mining in Earth System Science (DMESS 2012) at the International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, 2012,

2011

R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, G. R. Geddes, W. Leemans, Prabhat X. Li, J. Qiang, R\ ubel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon, 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, 2011,

Prabhat, “ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance”, DOE/ASCR Exascale kickoff meeting, 2011,

2010

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, Kesheng Wu, “Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-Dimensional Scientific Data”, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010,

      

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rübel, Gunther Weber, Bernard Hamann, Peter Messmer, and Hans Hagen, “Automated Detection and Analysis of Particle Beams in Laser-Plasma Accelerator Simulations”, In-Tech, ( 2010) Pages: 367 - 389

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, B. Hamann, “Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data”, IEEE Transactions on Computational Biology and Bioinformatics, Jan/Mar 2010, January 2010, 7 (1):64-79,

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), 2010, 429:329–334,

2009

Oliver R\ ubel, Cameron G. R. Geddes, Estelle Cormier-Michel Kesheng Wu, Prabhat, Gunther H. Weber, Daniela M. Ushizima, Peter Messmer, Hans Hagen, Bernd Hamann, Wes Bethel, “Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data”, IOP Computational Science \& Discovery, ( 2009)

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. Kr\ uger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. R\ ubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu., “Occam s Razor and Petascale Visual Data Analysis”, Journal of Physics Conference Series, Proceedings of SciDAC 2009, 2009, 180:012084,

2008

Oliver R\ ubel, Prabhat, Kesheng Wu, Hank Childs, Jeremy Meredith, Cameron G. R. Geddes, Estelle Cormier-Michel, Sean Ahern, Gunther H. weber, Peter Messmer, Hans Hagen, Bernd Hamann, E. Wes Bethel, “High Performance Multivariate Visual Data Exploration for Extemely Large Data”, SuperComputing 2008 (SC08), Austin, Texas, USA, 2008,

Iwona Sakrejda

2012

Eric Hjort, Larry Pezzaglia, Iwona Sakrejda, PDSF at NERSC: Site Report, A talk at the HEPiX Spring 2012 Workshop, Prague, Czech Republic, April 24, 2012,

PDSF is a commodity Linux cluster at NERSC which has been in continuous operation since 1996. This talk will provide a status update on the PDSF system and summarize recent changes at NERSC. Highlighted PDSF changes include the conversion to xCAT-managed netboot node images, the ongoing deployment of Scientific Linux 6, and the introduction of XRootD for STAR.

Lavanya Ramakrishnan, Richard Canon, Muriki, Sakrejda, Nicholas J. Wright, “Evaluating Interconnect and Virtualization Performance forHigh Performance Computing”, SIGMETRICS Performance Evaluation Review, 2012, 40:55-60,

2011

Katherine Yelick, Susan Coghlan, Brent Draney, Richard Shane Canon, Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Anping Liu, Scott Campbell, Piotr T. Zbiegiel, Tina Declerck, Paul Rich, “The Magellan Report on Cloud Computing for Science”, U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), December 2011,

Lavanya Ramakrishnan, Richard Shane Canon, Krishna Muriki, Iwona Sakrejda, and Nicholas J. Wright., “Evaluating Interconnect and Virtualization Performance for High Performance Computing”, Proceedings of 2nd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems (PMBS11), 2011,

In this paper we detail benchmarking results that characterize the virtualization overhead and its impact on performance. We also examine the performance of various interconnect technologies with a view to understanding the performance impacts of various choices. Our results show that virtualization can have a significant impact upon performance, with at least a 60% performance penalty. We also show that less capable interconnect technologies can have a significant impact upon performance of typical HPC applications. We also evaluate the performance of the Amazon Cluster compute instance and show that it performs approximately equivalently to a 10G Ethernet cluster at low core counts.

Lavanya Ramakrishnan, Piotr T. Zbiegel, Scott Campbell, Rick Bradshaw, Richard Shane Canon, Susan Coghlan, Iwona Sakrejda, Narayan Desai, Tina Declerck, Anping Liu, “Magellan: Experiences from a Science Cloud”, Proceedings of the 2nd International Workshop on Scientific Cloud Computing, ACM ScienceCloud '11, Boulder, Colorado, and New York, NY, 2011, 49 - 58,

1997

I. Sakrejda, others, “Global features of heavy ion collisions from the NA36”, January 1, 1997,

John Shalf

2012

Hongzhang Shan, Brian Austin, Nicholas Wright, Erich Strohmaier, John Shalf, Katherine Yelick, “Accelerating Applications at Scale Using One-Sided Communication”, The 6th Conference on Partitioned Global Address Programming Models, Santa Barbara, CA, October 10, 2012,

Mehmet Balman, Eric Pouyoul, Yushu Yao, Loring E. Wes Bethel, Prabhat, John Shalf, Alex Sim, Brian L. Tierney, “Experiences with 100G Network Applications”, Proceedings of the 5th International Workshop on Data Intensive and Distributed Computing (DIDC 2012), Delft, Netherlands, 2012,

Hongzhang Shan, J. Wright, Shalf, A. Yelick, Wagner, Nathan Wichmann, “A preliminary evaluation of the hardware acceleration of Cray Gemini interconnect for PGAS languages and comparison with MPI”, SIGMETRICS Performance Evaluation Review, 2012, 40:92-98,

2011

Robert Preissl, Nathan Wichmann, Bill Long, John Shalf, Stephane Ethier, Alice Koniges, “Multithreaded global address space communication techniques for gyrokinetic fusion applications on ultra-scale platforms”, Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, 78,

Kamesh Madduri, Z. Ibrahim, Williams, Im, Ethier, Shalf, Leonid Oliker, “Gyrokinetic toroidal simulations on leading multi- and manycore HPC systems”, SC, November 1, 2011, 23,

Samuel Williams, Oliker, Carter, John Shalf, “Extracting ultra-scale Lattice Boltzmann performance via hierarchical and distributed auto-tuning”, SC, November 1, 2011, 55,

Jens Krueger, Donofrio, Shalf, Mohiyuddin, Williams, Oliker, Franz-Josef Pfreund, “Hardware/software co-design for energy-efficient seismic modeling”, SC, November 1, 2011, 73,

Saman Amarasinghe, Mary Hall, Richard Lethin, Keshav Pingali, Dan Quinlan, Vivek Sarkar, John Shalf, Robert Lucas, Katherine Yelick, Pavan Balaji, Pedro C. Diniz, Alice Koniges, Marc Snir, Sonia R. Sachs, “Exascale Programming Challenges”, 2011,

J. Dongarra, P. Beckman, T. Moore, P. Aerts, G. Aloisio, J.C. Andre, D. Barkai, J.Y. Berthou, T. Boku, B. Braunschweig, others, “The international exascale software project roadmap”, International Journal of High Performance Computing Applications, January 2011, 25:3--60,

Keren Bergman, Hendry, Hargrove, Shalf, Jacob, Scott Hemmert, Rodrigues, David Resnick, “Let there be light!: the future of memory systems is photonics and 3D stacking”, MSPC, January 1, 2011, 43-48,

John Shalf, Donofrio, Rowen, Oliker, Michael F. Wehner, Green Flash: Climate Machine (LBNL), Encyclopedia of Parallel Computing, Pages: 809-819 January 1, 2011,

John Shalf, Quinlan, Curtis Janssen, “Rethinking Hardware-Software Codesign for Exascale Systems”, IEEE Computer, January 1, 2011, 44:22-30,

2010

Jack Dongarra, John Shalf, David Skinner, Kathy Yelick, “International Exascale Software Project (IESP) Roadmap, version 1.1”, October 18, 2010,

Gilbert Hendry, Johnnie Chan, Shoaib Kamil, Lenny Oliker, John Shalf, Luca P. Carloni, and Keren Bergman, “Silicon Nanophotonic Network-On-Chip Using TDM Arbitration”, IEEE Symposium on High Performance Interconnects (HOTI) 5.1, August 2010,

J. A. Colmenares, S. Bird, H. Cook, P. Pearce, D. Zhu, J. Shalf, K. Asanovic, J. Kubiatowicz, “Resource Management in the Tessellation Manycore OS”, Proceedings of the Second USENIX Workshop on Hot Topics in Parallelism (HotPar'10), Berkeley, California, June 2010,

Alice Koniges, Robert Preissl, Stephan Ethier, John Shalf, What’s Ahead for Fusion Computing?, International Sherwood Fusion Theory Conference, April 2010,

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

John Shalf, S. Dosanjh, John Morrison, “Exascale Computing Technology Challenges”, VECPAR, edited by J.M.L.M. Palma et al. , (Springer-Verlag: 2010) Pages: 1-25

High Performance Computing architectures are expected to change dramatically in the next decade as power and cooling constraints limit increases in microprocessor clock speeds. Consequently computer companies are dramatically increasing on-chip parallelism to improve performance. The traditional doubling of clock speeds every 18-24 months is being replaced by a doubling of cores or other parallelism mechanisms. During the next decade the amount of parallelism on a single microprocessor will rival the number of nodes in early massively parallel supercomputers that were built in the 1980s. Applications and algorithms will need to change and adapt as node architectures evolve. In particular, they will need to manage locality to achieve performance. A key element of the strategy as we move forward is the co-design of applications, architectures and programming environments. There is an unprecedented opportunity for application and algorithm developers to influence the direction of future architectures so that they meet DOE mission needs. This article will describe the technology challenges on the road to exascale, their underlying causes, and their effect on the future of HPC system design.

Shoaib Kamil, Chan, Oliker, Shalf, Samuel Williams, “An auto-tuning framework for parallel multicore stencil computations”, IPDPS, January 1, 2010, 1-12,

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick, “Auto-Tuning Stencil Computations on Diverse Multicore Architectures”, Scientific Computing with Multicore and Accelerators, edited by Jakub Kurzak, David A. Bader, Jack Dongarra, 2010,

Shoaib Kamil, Oliker, Pinar, John Shalf, “Communication Requirements and Interconnect Optimization for High-End Scientific Applications”, IEEE Trans. Parallel Distrib. Syst., 2010, 21:188-202,

Lavanya Ramakrishnan, R. Jackson, Canon, Cholia, John Shalf, “Defining future platform requirements for e-Science clouds”, SoCC, New York, NY, USA, 2010, 101-106,

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, “Parallel I/O performance: From events to ensembles”, IPDPS, Atlanta, Georgia, 2010, 1-11,

2009

John Shalf, Harvey Wasserman, Breakthrough Computing in Petascale Applications and Petascale System Examples at NERSC, HPC User Forum, April 10, 2009,

Gilbert Hendry, Kamil, Biberman, Chan, G. Lee, Mohiyuddin, Jain, Bergman, P. Carloni, Kubiatowicz, Oliker, John Shalf, “Analysis of photonic networks for a chip multiprocessor using scientific applications”, NOCS, January 1, 2009, 104-113,

G. Hendry, S.A. Kamil, A. Biberman, J. Chan, B.G. Lee, M Mohiyuddin, A. Jain, K. Bergman, L.P. Carloni, J. Kubiatocics, L. Oliker, J. Shalf, Analysis of Photonic Networks for Chip Multiprocessor Using Scientific Applications, NOCS2009, January 1, 2009,

Joseph Gebis, Oliker, Shalf, Williams, Katherine A. Yelick, “Improving Memory Subsystem Performance Using ViVA: Virtual Vector Architecture”, ARCS, January 1, 2009, 146-158,

Kamesh Madduri, Williams, Ethier, Oliker, Shalf, Strohmaier, Katherine A. Yelick, “Memory-efficient optimization of Gyrokinetic particle-to-grid interpolation for multicore processors”, SC, January 1, 2009,

Marghoob Mohiyuddin, Murphy, Oliker, Shalf, Wawrzynek, Samuel Williams, “A design methodology for domain-optimized power-efficient supercomputing”, SC, January 1, 2009,

John Shalf, Jason Hick, Storage Technology Fundamentals, Scientific Data Management: Challenges, Technology, and Deployment, January 1, 2009,

Julian Borrill, Oliker, Shalf, Shan, Andrew Uselton, “HPC global file system performance analysis using a scientific-application derived benchmark”, Parallel Computing, January 1, 2009, 35:358-373,

S. Amarasinghe, D. Campbell, W. Carlson, A. Chien, W. Dally, E. Elnohazy, M. Hall, R. Harrison, W. Harrod, K. Hill, J. Hiller, S. Karp, C. Koelbel, D. Koester, P. Kogge, J. Levesque, D. Reed, V. Sarkar, R. Schreiber, M. Richards, A. Scarpelli, J. Shalf, A. Snavely, T. Sterling, “ExaScale Software Study: Software Challenges in Extreme Scale Systems”, DARPA IPTO, January 1, 2009,

John Shalf, Thomas Sterling, “Operating Systems For Exascale Computing”, January 1, 2009,

John Shalf, Erik Schnetter, Gabrielle Allen, Edward Seidel, Cactus and the Role of Frameworks in Complex Multiphysics HPC Applications, talk, January 1, 2009,

John Shalf, Auto-Tuning: The Big Questions (Panel), talk, January 1, 2009,

John Shalf, David Donofrio, Green Flash: Extreme Scale Computing on a Petascale Budget, talk, January 1, 2009,

John Shalf, Challenges of Energy Efficient Scientific Computing, talk, January 1, 2009,

John Shalf, Harvey Wasserman, Breakthrough Computing in Petascale Applications and Petascale System Examples at NERSC, talk, January 1, 2009,

John Shalf, Satoshi Matsuoka, IESP Power Efficiency Research Priorities, talk, January 1, 2009,

Brian van Straalen, Shalf, J. Ligocki, Keen, Woo-Sun Yang, “Scalability challenges for massively parallel AMR applications”, IPDPS, January 1, 2009, 1-12,

David Donofrio, Oliker, Shalf, F. Wehner, Rowen, Krueger, Kamil, Marghoob Mohiyuddin, “Energy-Efficient Computing for Extreme-Scale Science”, IEEE Computer, January 1, 2009, 42:62-71,

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms”, Journal of Parallel and Distributed Computing, January 1, 2009, 69:762-777,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, “Optimization of sparse matrix-vector multiplication on emerging multicore platforms”, Parallel Computing, January 1, 2009, 35:178--194,

Kaushik Datta, Kamil, Williams, Oliker, Shalf, Katherine A. Yelick, “Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors”, SIAM Review, January 1, 2009, 51:129-159,

2008

H. Shan, K. Antypas, J.Shalf., “Characterizing and Predicting the I/O Performance of HPC Applications Using a Parameterized Synthetic Benchmark.”, Supercomputing, Reno, NV, November 17, 2008,

K. Datta, M. Murphy, V. Volkov, S. Williams, J. Carter, L. Oliker, D. Patterson, J. Shalf, K. Yelick, “Stencil computation optimization and auto-tuning on state-of-the-art multicore architectures”, Proceedings of the 2008 ACM/IEEE Conference on High Performance Computing and Networking ("Supercomputing", SC08), November 15, 2008,

Antypas, K., Shalf, J., Wasserman, H., “NERSC‐6 Workload Analysis and Benchmark Selection Process”, LBNL Technical Report, August 13, 2008, LBNL 1014E

Science drivers for NERSC-6

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Lattice Boltzmann simulation optimization on leading multicore platforms”, International Parallel and Distributed Processing Symposium (IPDPS), April 14, 2008, 1-14,

Sam Williams, Jonathan Carter, Leonid Oliker, John Shalf, Katherine Yelick, Lattice Boltzmann Simulation Optimization on Leading Multicore Architectures, January 1, 2008,

Shoaib Kamil, Shalf, Erich Strohmaier, “Power efficiency in high performance computing”, IPDPS, January 1, 2008, 1-8,

Hongzhang Shan, Antypas, John Shalf, “Characterizing and predicting the I/O performance of HPC applications using a parameterized synthetic benchmark”, SC, January 1, 2008, 42,

Sam Williams, Kaushik Datta, Jonathan Carter, Leonid Oliker, John Shalf, Katherine Yelick, David Bailey, “PERI - Auto-tuning Memory Intensive Kernels for Multicore”, SciDAC: Scientific Discovery Through Advanced Computing, Journal of Physics: Conference Series, January 1, 2008,

Shantenu Jha, Hartmut Kaiser, Andre Merzky, John Shalf, SAGA - The Simple API for Grid Applications - Motivation, Design, and Implementation, Encyclopedia of Grid Technologies and Applications, January 1, 2008,

Gabrielle Allen (LSU/CCT), Gene Allen (MSC Inc.), Kenneth Alvin (SNL), Matt Drahzal (IBM), David Fisher (DoD-Mod), Robert Graybill (USC/ISI), Bob Lucas (USC/ISI), Tim Mattson (Intel), Hal Morgan (SNL), Erik Schnetter (LSU/CCT), Brian Schott (USC/ISI), Edward Seidel (LSU/CCT), John Shalf (LBNL/NERSC), Shawn Shamsian (MSC Inc.), David Skinner (LBNL/NERSC), Siu Tong (Engeneous), “Frameworks for Multiphysics Simulation : HPC Application Software Consortium Summit Concept Paper”, January 1, 2008,

K. Antypas, J. Shalf, H. Wasserman, “NERSC-6 Workload Analysis and Benchmark Selection Process”, January 1, 2008,

John Shalf, Honzhang Shan, Katie Antypas, I/O Requirements for HPC Applications, talk, January 1, 2008,

John Shalf, NERSC User IO Cases, talk, January 1, 2008,

J. Shalf, K. Antypas, H.J. Wasserman, Recent Workload Characterization Activities at NERSC, Santa Fe Workshop, January 1, 2008,

John Shalf, Neuroinformatics Congress: Future Hardware Challenges for Scientific Computing, talk, January 1, 2008,

M. Wehner, L. Oliker, J. Shalf, Ultra-Efficient Exascale Scientific Computing, talk, January 1, 2008,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, “Scientific Application Performance On Leading Scalar and Vector Supercomputering Platforms”, IJHPCA, January 1, 2008, 22:5-20,

Michael F. Wehner, Oliker, John Shalf, “Towards Ultra-High Resolution Models of Climate and Weather”, IJHPCA, January 1, 2008, 22:149-165,

2007

Jonathan Carter, Yun (Helen) He, John Shalf, Hongzhang Shan, Erich Strohmaier, and Harvey Wasserman, “The Performance Effect of Multi-Core on Scientific Applications”, Cray User Group 2007, May 2007, LBNL 62662

The historical trend of increasing single CPU performance has given way to roadmap of increasing core count. The challenge of effectively utilizing these multi- core chips is just starting to be explored by vendors and application developers alike. In this study, we present some performance measurements of several complete scientific applications on single and dual core Cray XT3 and XT4 systems with a view to characterizing the effects of switching to multi-core chips. We consider effects within a node by using applications run at low concurrencies, and also effects on node- interconnect interaction using higher concurrency results. Finally, we construct a simple performance model based on the principle on-chip shared resource—memory bandwidth—and use this to predict the performance of the forthcoming quad-core system.

 

Jonathan Carter, Helen He*, John Shalf, Erich Strohmaier, Hongzhang Shan, and Harvey Wasserman, The Performance Effect of Multi-Core on Scientific Applications, Cray User Group 2007, May 2007,

J. Levesque, J. Larkin, M. Foster, J. Glenski, G. Geissler, S. Whalen, B. Waldecker, J. Carter, D. Skinner, H. He, H. Wasserman, J. Shalf, H. Shan, “Understanding and mitigating multicore performance issues on the AMD opteron architecture”, March 1, 2007, LBNL 62500

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3and XT4systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

 

Leonid Oliker, Andrew Canning, Johnathan Carter, Costin Iancu, Mike Lijewski, Shoaib Kamil, John Shalf, Hongzhang Shan, Erich Strohmaier, Stephane Ethier, Tom Goodale, “Scientific Application Performance on Candidate PetaScale Platforms”, IPDPS, January 1, 2007, 1-12,

Hongzhang Shan, John Shalf, Using IOR to Analyze the I/O performance for HPC Platforms, CUG.org, January 1, 2007,

Julian Borrill, Leonid Oliker, John Shalf, Hongzhang Shan, “Investigation of leading HPC I/O performance using a scientific-application derived benchmark”, SC, January 1, 2007, 10,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms, International Conference for High-Performance Computing, Networking, Storage, and Analysis, January 1, 2007,

Shoaib Kamil, Ali Pinar, Dan Gunter, Mike Lijewski, Leonid Oliker, John Shalf, “Reconfigurable hybrid interconnection for static and dynamic scientific applications”, Conf. Computing Frontiers, January 1, 2007, 183-194,

L. Oliker, J. Shalf, J. Carter, A. Canning, S. Kamil, M. Lijewski, S. Ethier, Performance Characteristics of Potential Petascale Scientific Applications, Petascale Computing: Algorithms and Applications, January 1, 2007,

John Shalf, “The New Landscape of Parallel Computer Architecture”, Journal of Physics: Conference Series, IOP Electronics Journals, January 1, 2007,

Shoaib Kamil, John Shalf, “Measuring Power Efficiency of NERSC s Newest Flagship Machine”, January 1, 2007,

John Shalf, Landscape of Computing Architecture: Introduction to the Berkeley View, talk, January 1, 2007,

John Shalf, About Memory Bandwidth and Multicore, talk, January 1, 2007,

John Shalf, The Landscape of Parallel Computing Architecture, talk, January 1, 2007,

John Shalf, Overturning the Conventional Wisdom for the Multicore Era: Everything You Know is Wrong, talk, January 1, 2007,

John Shalf, Honzhang Shan, User Perspective on HPC I/O Requirements, talk, January 1, 2007,

John Shalf, NERSC Workload Analysis, talk, January 1, 2007,

John Shalf, NERSC Power Efficiency Analysis, talk, January 1, 2007,

John Shalf, Memory Subsystem Performance and QuadCore Predictions, talk, January 1, 2007,

John Shalf, Shoaib Kamil, David Skinner, Leonid Oliker, Interconnect Requirements for HPC Applications, talk, January 1, 2007,

John Shalf, Shoaib Kamil, David Bailey, Erich Strohmaier, Power Efficiency and the Top500, talk, January 1, 2007,

John Shalf, Power, Cooling, and Energy Consumption for the Petascale and Beyond, talk, January 1, 2007,

John Shalf, Petascale Computing Application Challenges, talk, January 1, 2007,

Shoaib Kamil, John Shalf, Power Efficiency Metrics for the Top500, talk, January 1, 2007,

Erik Schnetter, Ott, Allen, Diener, Goodale, Radke, Seidel, John Shalf, “Cactus Framework: Black Holes to Gamma Ray Bursts”, CoRR, January 1, 2007, abs/0707,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “Scientific computing kernels on the Cell processor”, International Journal of Parallel Programming, January 1, 2007, 35:263--298,

2006

Jonathan Carter, Tony Drummond, Parry Husbands, Paul Hargrove, Bill Kramer, Osni Marques, Esmond Ng, Lenny Oliker, John Shalf, David Skinner, Kathy Yelick, “Software Roadmap to Plug and Play Petaflop/s”, Lawrence Berkeley National Laboratory Technical Report, #59999, July 31, 2006,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “The potential of the cell processor for scientific computing”, Proceedings of the 3rd conference on Computing frontiers, January 1, 2006, 9--20,

Jonathan Carter, Leonid Oliker, John Shalf, “Performance Evaluation of Scientific Applications on Modern Parallel Vector Systems”, VECPAR, January 1, 2006, 490-503,

Tom Goodale, Shantenu Jha, Hartmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic, Hrabri, John Shalf, “SAGA: A Simple API for Grid Applications -- High-Level Application Programming on the Grid”, Computational Methods in Science and Technology, January 1, 2006, 12,

Hongzhang Shan, John Shalf, “Analysis of Parallel IO on Modern HPC Platforms”, January 1, 2006,

John Shalf, David Bailey, Top500 Power Efficiency, talk, January 1, 2006,

L. Oliker, S. Kamil, A. Canning, J. Carter, C. Iancu, J. Shalf, H. Shan, D. Skinner, E. Strohmaier, T. Goodale, “Application Scalability and Communication Signatures on Leading Supercomputing Platforms”, January 1, 2006,

S. Kamil, K. Datta, S. Williams, L. Oliker, J. Shalf, K. Yelick, “Implicit and explicit optimizations for stencil computations”, Proceedings of the 2006 workshop on Memory system performance and correctness, January 1, 2006, 51--60,

Luke J. Gosink, John Shalf, Kurt Stockinger, John Wu, Wes Bethel, “HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets using Fast Bitmap Indices”, SSDBM, January 1, 2006, 149-158,

2005

Kurt Stockinger, Shalf, Wu, E. Wes Bethel, “Query-Driven Visualization of Large Data Sets”, IEEE Visualization, January 1, 2005, 22,

John Shalf, Kamil, Oliker, David Skinner, “Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect”, SC, January 1, 2005, 17,

Horst Simon, William Kramer, William Saphir, John Shalf, David Bailey, Leonid Oliker, Michael Banda, C. William McCurdy, John Hules, Andrew Canning, Marc Day, Philip Colella, David Serafini, Michael Wehner, Peter Nugent, “Science-Driven System Architecture: A New Process for Leadership Class Computing”, Journal of the Earth Simulator, January 1, 2005, 2,

John Shalf, John Bell, Andrew Canning, Lin-Wang Wang, Juan Meza, Rob Ryne, Ji Qiang, Kathy Yelick, “Berkeley Petascale Applications”, January 1, 2005,

S. Kamil, J. Shalf, L. Oliker, D. Skinner, “Understanding ultra-scale application communication requirements”, Workload Characterization Symposium, 2005. Proceedings of the IEEE International, January 1, 2005, 178--187,

Shoaib Kamil,Parry Husbands, Leonid Oliker, John Shalf, Katherine A. Yelick, “Impact of modern memory subsystems on cache optimizations for stencil computations”, Memory System Performance, January 1, 2005, 36-43,

Kurt Stockinger, John Shalf, Wes Bethel, Kesheng Wu, “DEX: Increasing the Capability of Scientific Data Analysis by Using Efficient Bitmap Indices to Accelerate Scientific Visualization”, SSDBM, January 1, 2005, 35-44,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stephane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Performance evaluation of the SX-6 vector architecture for scientific computations”, Concurrency - Practice and Experience, January 1, 2005, 17:69-93,

Ruxandra Bondarescu, Allen, Daues, Kelley, Russell, Seidel, Shalf, Malcolm Tobias, “The Astrophysics Simulation Collaboratory Portal: a framework for effective distributed research”, Future Generation Comp. Syst., January 1, 2005, 21:259-270,

2004

Gorden Griem, Oliker, Shalf, Katherine A. Yelick, “Identifying Performance Bottlenecks on Modern Microarchitectures Using an Adaptable Probe”, IPDPS, January 1, 2004,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, Stephane Ethier, “Scientific Computations on Modern Parallel Vector Systems”, SC, January 1, 2004, 10,

2003

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stepahane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations”, SC, January 1, 2003, 38,

T. J. Jankun-Kelly, Kreylos, Ma, Hamann, I. Joy, Shalf, E. Wes Bethel, “Deploying Web-Based Visual Exploration Tools on the Grid”, IEEE Computer Graphics and Applications, January 1, 2003, 23:40-50,

Gunther H. Weber, Oliver Kreylos, John Shalf, Wes Bethel, Bernd Hamann, Gerik Scheuermann, “Parallel Cell Projection Rendering of Adaptive Mesh Refinement Data”, IEEE Symposium on Parallel and Large-Data Visualization and Graphics, January 1, 2003, 51-60,

E. Wes Bethel, Mark Abram, John Shalf, Frank, Jim P. Ahrens, Steve Parker, Nagiza F. Samatova, Mark Miller, “Interoperability of Visualization Software and Data Models is NOT an Achievable Goal”, IEEE Visualization, January 1, 2003, 607-610,

E. Wes Bethel, John Shalf, “Grid-Distributed Visualizations Using Connectionless Protocols”, IEEE Computer Graphics and Applications, January 1, 2003, 23:51-59,

John Shalf, E. Wes Bethel, “The Grid and Future Visualization System Architectures”, IEEE Computer Graphics and Applications, January 1, 2003, 23:6-9,

Gabrielle Allen, Goodale, Radke, Russell, Seidel, Davis, Dolkas, D. Doulamis, Kielmann, Merzky, Nabrzyski, Pukacki, Shalf, Ian J. Taylor, “Enabling Applications on the Grid: A Gridlab Overview”, IJHPCA, January 1, 2003, 17:449-466,

2002

Gabrielle Allen, Angulo, Goodale, Kielmann, Merzky, Nabrzyski, Pukacki, Russell, Radke, Seidel, Shalf, Ian J. Taylor, “GridLab: Enabling Applications on the Grid”, GRID, January 1, 2002, 39-45,

Tom Goodale, Allen, Lanfermann, Mass\ o, Radke, Seidel, John Shalf, “The Cactus Framework and Toolkit: Design and Applications”, VECPAR, January 1, 2002, 197-227,

Michael Russell, Allen, Daues, T. Foster, Seidel, Novotny, Shalf, Gregor von Laszewski, “The Astrophysics Simulation Collaboratory: A Science Portal Enabling Community Software Development”, Cluster Computing, January 1, 2002, 5:297-304,

Gregor von Laszewski, Russell, T. Foster, Shalf, Allen, Daues, Novotny, Edward Seidel, “Community software development with the Astrophysics Simulation Collaboratory”, Concurrency and Computation: Practice and Experience, January 1, 2002, 14:1289-1301,

2001

Michael Russell, Gabrielle Allen, Greg Daues, Ian T. Foster, Ed Seidel, Jason Novotny, John Shalf, Gregor von Laszewski, “The Astrophysics Simulation Collaboratory Portal: A Science Portal Enabling Community Software Development”, HPDC, January 1, 2001, 207-215,

Gunther H. Weber, Kreylos, J. Ligocki, Shalf, Hagen, Hamann, I. Joy, Kwan-Liu Ma, “High-quality Volume Rendering of Adaptive Mesh Refinement Data”, VMV, January 1, 2001, 121-128,

Gabrielle Allen, Benger, Dramlitsch, Goodale, Hege, Lanfermann, Merzky, Radke, Seidel, John Shalf, “Cactus Tools for Grid Applications”, Cluster Computing, January 1, 2001, 4:179-188,

Gabrielle Allen, Angulo, T. Foster, Lanfermann, Liu, Radke, Seidel, John Shalf, “The Cactus Worm: Experiments with Dynamic Resource Discovery and Allocation in a Grid Environment”, IJHPCA, January 1, 2001, 15:345-358,

2000

Gabrielle Allen, Benger, Goodale, Hege, Lanfermann, Merzky, Radke, Seidel, John Shalf, “The Cactus Code: A Problem Solving Environment for the Grid”, HPDC, January 1, 2000, 253-,

1999

Werner Benger, T. Foster, Novotny, Seidel, Shalf, Smith, Paul Walker, “Numerical Relativity in a Distributed Environment”, PPSC, January 1, 1999,

Gabrielle Allen, Tom Goodale, Gerd Lanfermann, Thomas Radke, Ed Seidel, Werner Benger, Hans Christian Hege, Andre Merzky, Juan Masso, John Shalf, “Solving Einstein's Equations on Supercomputers”, IEEE Computer, January 1, 1999, 32:52-58,

Michael L. Norman, John Shalf, Stuart Levy, Greg Daues, “Diving Deep: Data-Management and Visualization Strategies for Adaptive Mesh Refinement Simulations”, Computing in Science and Engineering, January 1, 1999, 1:36-47,

1996

M. L. Norman, P. Beckman, G. L. Bryan, J. Dubinski, D. Gannon, L. Hernquist, K. Keahey, J. P. Ostriker, J. Shalf, J. Welling, and S. Yang, “Galaxies Collide on the I-WAY: An Example of Heterogeneous Wide-Area Collaborative Supercomputing”, The International Journal of Supercomputer Applications and High Performance Computing, January 1, 1996, 10:132-144,

Hongzhang Shan

2013

Hongzhang Shan, Brian Austin, Wibe De Jong, Leonid Oliker, Nicholas Wright, Edoardo Apra, “Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms”, SC'13, November 11, 2013,

2012

Hongzhang Shan, Brian Austin, Nicholas Wright, Erich Strohmaier, John Shalf, Katherine Yelick, “Accelerating Applications at Scale Using One-Sided Communication”, The 6th Conference on Partitioned Global Address Programming Models, Santa Barbara, CA, October 10, 2012,

Hongzhang Shan, J. Wright, Shalf, A. Yelick, Wagner, Nathan Wichmann, “A preliminary evaluation of the hardware acceleration of Cray Gemini interconnect for PGAS languages and comparison with MPI”, SIGMETRICS Performance Evaluation Review, 2012, 40:92-98,

2010

Hongzhang Shan, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J Wright, “Analyzing the effect of different programming models upon performance and memory usage on cray xt5 platforms”, CUG2010, Edinburgh, Scotland, 2010,

2009

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, “Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, 2009 J. Phys.: Conf. Ser. 180 012079, July 1, 2009,

2008

Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, David Bailey,, “Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, An award winning paper (ACM Gordon Bell Prize for algorithm innovation in SC08), Proceedings of the 2008 ACM/IEEE conference on Supercomputing, Article No. 65 (2008)., November 20, 2008,

H. Shan, K. Antypas, J.Shalf., “Characterizing and Predicting the I/O Performance of HPC Applications Using a Parameterized Synthetic Benchmark.”, Supercomputing, Reno, NV, November 17, 2008,

John Shalf, Honzhang Shan, Katie Antypas, I/O Requirements for HPC Applications, talk, January 1, 2008,

2007

Jonathan Carter, Yun (Helen) He, John Shalf, Hongzhang Shan, Erich Strohmaier, and Harvey Wasserman, “The Performance Effect of Multi-Core on Scientific Applications”, Cray User Group 2007, May 2007, LBNL 62662

The historical trend of increasing single CPU performance has given way to roadmap of increasing core count. The challenge of effectively utilizing these multi- core chips is just starting to be explored by vendors and application developers alike. In this study, we present some performance measurements of several complete scientific applications on single and dual core Cray XT3 and XT4 systems with a view to characterizing the effects of switching to multi-core chips. We consider effects within a node by using applications run at low concurrencies, and also effects on node- interconnect interaction using higher concurrency results. Finally, we construct a simple performance model based on the principle on-chip shared resource—memory bandwidth—and use this to predict the performance of the forthcoming quad-core system.

 

Jonathan Carter, Helen He*, John Shalf, Erich Strohmaier, Hongzhang Shan, and Harvey Wasserman, The Performance Effect of Multi-Core on Scientific Applications, Cray User Group 2007, May 2007,

J. Levesque, J. Larkin, M. Foster, J. Glenski, G. Geissler, S. Whalen, B. Waldecker, J. Carter, D. Skinner, H. He, H. Wasserman, J. Shalf, H. Shan, “Understanding and mitigating multicore performance issues on the AMD opteron architecture”, March 1, 2007, LBNL 62500

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3and XT4systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

 

Hongzhang Shan, John Shalf, Using IOR to Analyze the I/O performance for HPC Platforms, CUG.org, January 1, 2007,

Julian Borrill, Leonid Oliker, John Shalf, Hongzhang Shan, “Investigation of leading HPC I/O performance using a scientific-application derived benchmark”, SC, January 1, 2007, 10,

John Shalf, Honzhang Shan, User Perspective on HPC I/O Requirements, talk, January 1, 2007,

2006

Hongzhang Shan, John Shalf, “Analysis of Parallel IO on Modern HPC Platforms”, January 1, 2006,

L. Oliker, S. Kamil, A. Canning, J. Carter, C. Iancu, J. Shalf, H. Shan, D. Skinner, E. Strohmaier, T. Goodale, “Application Scalability and Communication Signatures on Leading Supercomputing Platforms”, January 1, 2006,

Hemant Shukla

2011

Hemant Shukla, Hsi-Schive, Tak-Pong Woo, Tzihong Chiueh, “Multi-science applications with single codebase - GAMER - for massively parallel architectures”, SC, January 1, 2011, 37,

2009

S. K. Sirothia, G. Swarup, H. Shukla, Observations at 325 MHz of the WMAP Cold Spot, Astronomical Society of the Pacific Conference Series, Pages: 51 January 1, 2009,

2007

E. Young, H. Shukla, A. Bonissent, A. Kim, SNAP Collaboration, SNAP Spectrum Simulation: Spectra and Analysis, Bulletin of the American Astronomical Society, Pages: #132.26 January 1, 2007,

2006

Brown, M.G. and Bebek, C. and Bernstein, G. and Bonissent, A. and Carithers, B. and Cole, D. and Figer, D. and Gerdes, D. and Gladney, L. and Lorenzon, W. and Kim, A. and Kushner, G. and Kuznetsova, N. and Lampton, M. and Levi, M. and Linder, E. and McKee, S. and Miquel, R. and Mostek, N. and Mufson, S. and Perlmutter, S. and Schubnell, M. and Seshadri, S. and Shukla, H. and Smith, R. and Stebbins, A. and Stoughton, C. and Tarle, G.,, “Development of NIR detectors and science-driven requirements for SNAP”, Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, January 1, 2006, 6265,

2004

H. Shukla, M.S. Yun, NZ Scoville, “Dense, Ionized, and Neutral Gas Surrounding Sagittarius A*”, The Astrophysical Journal, January 1, 2004, 616:231,

2002

H. Bushouse, B. Simon, H. Shukla, E. Wyckoff, “A Python-Based IRAF Regression Testing System”, Astronomical Society of the Pacific Conference Series, January 1, 2002, 281:129,

2001

H. Shukla, A. Sivaramakrishnan, M. Troy, R.~G. Dekany, Using Past Data in Adaptive Optics Wavefront Reconstruction, Bulletin of the American Astronomical Society, Pages: #145.03 January 1, 2001,

2000

A. Sivaramakrishnan, B. Simon, S. Holfeltz, H. Shukla, M. Sosey, The new NICMOS Exposure Time Calculator: Software and Installation, NICMOS ISR-00-005, 15 pages, Pages: 5 January 1, 2000,

1999

K. B. Marvel, H. Shukla, G. Rhee, Radio sources in 14 Abell clusters (Marvel+, 1999), VizieR Online Data Catalog, Pages: 147 January 1, 1999,

K.B. Marvel, H. Shukla, G. Rhee, “A VLA Search for Head-Tail Radio Sources in Abell Clusters”, The Astrophysical Journal Supplement Series, January 1, 1999, 120:147,

H. Shukla, S. Scott, S. Weaver, “Remote Observing With Java”, Astronomical Data Analysis Software and Systems VIII, January 1, 1999, 172:95,

1996

H. Shukla, R.E. Stoner, “Correlation of Ultraviolet and Radio Flux in Three Active Galactic Nuclei”, The Astrophysical Journal Supplement Series, January 1, 1996, 106:41,

S. D. Ryder, R.~J. Buta, H. Toledo, H. Shukla, L. Staveley-Smith, W. Walsh, Neutral Hydrogen in the Ringed Barred Galaxies NGC 1433 and NGC 6300, The Astrophysical Journal, Pages: 665 January 1, 1996,

H. Shukla, S. D. Ryder, “Radio Continuum Emission in the Resonance-Ring Galaxies NGC 1433 and NGC 6300”, Astronomical Society of the Pacific Conference Series, January 1, 1996, 91:250,

David E. Skinner

2014

S. Parete-Koon, B. Caldwell, S. Canon, E. Dart, J. Hick, J. Hill, C. Layton, D. Pelfrey, G. Shipman, D. Skinner, J. Wells, J. Zurawski, “HPC's Pivot to Data”, Conference, May 5, 2014,

 

Computer centers such as NERSC and OLCF have traditionally focused on delivering computational capability that enables breakthrough innovation in a wide range of science domains. Accessing that computational power has required services and tools to move the data from input and output to computation and storage. A pivot to data is occurring in HPC. Data transfer tools and services that were previously peripheral are becoming integral to scientific workflows.  Emerging requirements from high-bandwidth detectors, highthroughput screening techniques, highly concurrent simulations, increased focus on uncertainty quantification, and an emerging open-data policy posture toward published research are among the data-drivers shaping the networks, file systems, databases, and overall HPC environment. In this paper we explain the pivot to data in HPC through user requirements and the changing resources provided by HPC with particular focus on data movement. For WAN data transfers we present the results of a study of network performance between centers

 

Fox W., Correa J., Cholia S., Skinner D., Ophus C., “NCEM Hub, A Science Gateway for Electron Microscopy in Materials Science”, LBNL Tech Report on NCEMhub, May 1, 2014,

Electron microscopy (EM) instrumentation is making a detector-driven transition to Big Data. High capability cameras bring new resolving power but also an exponentially increasing demand for bandwidth and data analysis. In practical terms this means that users of advanced microscopes find it increasingly challenging to take data with them and instead need an integrated data processing pipeline. in 2013 NERSC and NCEM staff embarked on a pilot to prototype data services that provide such a pipeline. This tech report details the NCEM Hub pilot as it concluded in May 2014.

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

Joaquin Correa, David Skinner, “BIG DATA BIOIMAGING: Advances in Analysis, Integration, and Dissemination”, Keystone Symposia on Molecular and Cellular Biology, March 24, 2014,

A fundamental problem currently for the biological community is to adapt computational solutions known broadly in data-centric science toward the specific challenges of data scaling in bioimaging. In this work we target software solutions fit for these tasks which leverages success in large scale data-centric science outside of bioimaging.

2013

A. Koniges, R. Gerber, D. Skinner, Y. Yao, Y. He, D. Grote, J-L Vay, H. Kaiser, and T. Sterling, “Plasma Physics Simulations on Next Generation Platforms”, 55th Annual Meeting of the APS Division of Plasma Physics, Volume 58, Number 16, November 11, 2013,

The current high-performance computing revolution provides opportunity for major increases in computational power over the next several years, if it can be harnessed. This transition from simply increasing the single-processor and network performance to a different architectural paradigms forces application programmers to rethink the basic models of parallel programming from both the language and problem division standpoints. One of the major computing facilities available to researchers in fusion energy is the National Energy Research Scientific Computing Center. As the mission computing center for DOE, Office of Science, NERSC is tasked with helping users to overcome the challenges of this revolution both through the use of new parallel constructs and languages and also by enabling a broader user community to take advantage of multi-core performance. We discuss the programming model challenges facing researchers in fusion and plasma physics in for a variety of simulations ranging from particle-in-cell to fluid-gyrokinetic and MHD models.

Anubhav Jain, Shyue Ping Ong, Geoffroy Hautier, Wei Chen, William Davidson Richards, Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, Kristin A. Persson, “The Materials Project: A materials genome approach to accelerating materials innovation”, APL Mat. 1, 011002 (2013); http://dx.doi.org/10.1063/1.4812323, July 2013,

David Skinner and Shane Canon, NERSC and High Throughput Computing, February 12, 2013,

2012

Tools for Performance Debugging HPC Applications, February 16, 2012,

2011

M. Di Pierro, J. Hetrick, S. Cholia, D. Skinner, “Making QCD Lattice Data Accessible and Organized through Advanced Web Interfaces”, Arxiv preprint arXiv:1112.2193, December 1, 2011, abs/1112,

J. Dongarra, P. Beckman, T. Moore, P. Aerts, G. Aloisio, J.C. Andre, D. Barkai, J.Y. Berthou, T. Boku, B. Braunschweig, others, “The international exascale software project roadmap”, International Journal of High Performance Computing Applications, January 2011, 25:3--60,

K. Furlinger, N.J. Wright, D. Skinner, “Comprehensive Performance Monitoring for GPU Cluster Systems”, Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on, 2011, 1377--1386,

2010

Jack Dongarra, John Shalf, David Skinner, Kathy Yelick, “International Exascale Software Project (IESP) Roadmap, version 1.1”, October 18, 2010,

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, “Parallel I/O performance: From events to ensembles”, IPDPS, Atlanta, Georgia, 2010, 1-11,

S. Cholia, D. Skinner, J. Boverhof, “NEWT: A RESTful service for building High Performance Computing web applications”, Gateway Computing Environments Workshop (GCE), 2010, January 1, 2010, 1--11,

Karl F\ urlinger, J. Wright, David Skinner, “Effective Performance Measurement at Petascale Using IPM”, ICPADS, January 1, 2010, 373-380,

K. Fuerlinger, N.J. Wright, D. Skinner, “Performance analysis and workload characterization with ipm”, Tools for High Performance Computing 2009, January 1, 2010, 31--38,

K. Fuerlinger, N.J. Wright, D. Skinner, C. Klausecker, D. Kranzlmueller, “Effective Holistic Performance Measurement at Petascale Using IPM”, Competence in High Performance Computing 2010, January 1, 2010, 15--26,

2009

K. F\ urlinger, D. Skinner, “Performance profiling for OpenMP tasks”, Evolving OpenMP in an Age of Extreme Parallelism, January 1, 2009, 132--139,

W. Kramer, D. Skinner, “Consistent Application Performance at the Exascale”, International Journal of High Performance Computing Applications, January 1, 2009, 23:392,

W. Kramer, D. Skinner, “An Exascale Approach to Software and Hardware Design”, International Journal of High Performance Computing Applications, January 1, 2009, 23:389,

D. Skinner, A. Choudary, “On the Importance of End-to-End Application Performance Monitoring and Workload Analysis at the Exascale”, International Journal of High Performance Computing Applications, January 1, 2009, 23:357--360,

2008

Gabrielle Allen (LSU/CCT), Gene Allen (MSC Inc.), Kenneth Alvin (SNL), Matt Drahzal (IBM), David Fisher (DoD-Mod), Robert Graybill (USC/ISI), Bob Lucas (USC/ISI), Tim Mattson (Intel), Hal Morgan (SNL), Erik Schnetter (LSU/CCT), Brian Schott (USC/ISI), Edward Seidel (LSU/CCT), John Shalf (LBNL/NERSC), Shawn Shamsian (MSC Inc.), David Skinner (LBNL/NERSC), Siu Tong (Engeneous), “Frameworks for Multiphysics Simulation : HPC Application Software Consortium Summit Concept Paper”, January 1, 2008,

2007

J. Levesque, J. Larkin, M. Foster, J. Glenski, G. Geissler, S. Whalen, B. Waldecker, J. Carter, D. Skinner, H. He, H. Wasserman, J. Shalf, H. Shan, “Understanding and mitigating multicore performance issues on the AMD opteron architecture”, March 1, 2007, LBNL 62500

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3and XT4systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

 

John Shalf, Shoaib Kamil, David Skinner, Leonid Oliker, Interconnect Requirements for HPC Applications, talk, January 1, 2007,

W.T.C. Kramer, H. Walter, G. New, T. Engle, R. Pennington, B. Comes, B. Bland, B. Tomlison, J. Kasdorf, D. Skinner, others, “Report of the workshop on petascale systems integration for large scale facilities”, January 1, 2007,

2006

Jonathan Carter, Tony Drummond, Parry Husbands, Paul Hargrove, Bill Kramer, Osni Marques, Esmond Ng, Lenny Oliker, John Shalf, David Skinner, Kathy Yelick, “Software Roadmap to Plug and Play Petaflop/s”, Lawrence Berkeley National Laboratory Technical Report, #59999, July 31, 2006,

H. Wang, D.E. Skinner, M. Thoss, “Calculation of reactive flux correlation functions for systems in a condensed phase environment: A multilayer multiconfiguration time-dependent Hartree approach”, The Journal of chemical physics, January 1, 2006, 125:174502,

L. Oliker, S. Kamil, A. Canning, J. Carter, C. Iancu, J. Shalf, H. Shan, D. Skinner, E. Strohmaier, T. Goodale, “Application Scalability and Communication Signatures on Leading Supercomputing Platforms”, January 1, 2006,

2005

John Shalf, Kamil, Oliker, David Skinner, “Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect”, SC, January 1, 2005, 17,

A. Aspuru--Guzik, R. Salom\ on--Ferrer, B. Austin, R. Perusqu\ \ia--Flores, M.A. Griffin, R.A. Oliva, D. Skinner, D. Domin, W.A. Lester Jr, “Zori 1.0: A parallel quantum Monte Carlo electronic structure package”, Journal of Computational Chemistry, January 1, 2005, 26:856--862,

J. Borrill, J. Carter, L. Oliker, D. Skinner, R. Biswas, “Integrated performance monitoring of a cosmology application on leading HEC platforms”, Parallel Processing, 2005. ICPP 2005. International Conference on, January 1, 2005, 119--128,

D. Skinner, “Performance monitoring of parallel scientific applications”, January 1, 2005,

S. Kamil, J. Shalf, L. Oliker, D. Skinner, “Understanding ultra-scale application communication requirements”, Workload Characterization Symposium, 2005. Proceedings of the IEEE International, January 1, 2005, 178--187,

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stephane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Performance evaluation of the SX-6 vector architecture for scientific computations”, Concurrency - Practice and Experience, January 1, 2005, 17:69-93,

2004

D. Skinner, “Scaling up parallel scientific applications on the IBM SP”, January 1, 2004,

2003

Leonid Oliker, Andrew Canning, Jonathan Carter, John Shalf, David Skinner, Stepahane Ethier, Rupak Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, “Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations”, SC, January 1, 2003, 38,

D. Skinner, N. Cardo, “An Analysis of Node Asymmetries on seaborg. nersc. gov”, January 1, 2003,

1999

D.E. Skinner, W.H. Miller, “Application of the semiclassical initial value representation and its linearized approximation to inelastic scattering”, Chemical physics letters, January 1, 1999, 300:20--26,

1998

D.E. Skinner, T.C. Germann, W.H. Miller, “Quantum Mechanical Rate Constants for O+ OH⇌ H+ O2 for Total Angular Momentum J> 0”, The Journal of Physical Chemistry A, January 1, 1998, 102:3828--3834,

1995

D.E. Skinner, D.P. Colombo Jr, J.J. Cavaleri, R.M. Bowman, “Femtosecond investigation of electron trapping in semiconductor nanoclusters”, The Journal of Physical Chemistry, January 1, 1995, 99:7853--7856,

Jay Srinivasan

2014

Jay Srinivasan, Computational Systems Group Update for NUG 2014, February 6, 2014,

2013

Jay Srinivasan, Richard Shane Canon, “Evaluation of A Flash Storage Filesystem on the Cray XE-6”, CUG 2013, May 2013,

Flash storage and other solid-state storage technolo-gies are increasingly being considered as a way to address the growing gap between computation and I/O. Flash storage has a number of benefits such as good random read performance and lower power consumption. However, it has a number of challenges too, such as high cost and high-overhead for write operations. There are a number of ways Flash can be integrated into HPC systems. This paper will discuss some of the approaches and show early results for a Flash file system mounted on a Cray XE-6 using high-performance PCI-e based cards. We also discuss some of the gaps and challenges in integrating flash intoHPC systems and potential mitigations as well as new solid state storage technologies and their likely role in the future

2012

Jay Srinivasan, Richard Shane Canon, Lavanya Ramakrishnan, “My Cray can do that? Supporting Diverse Workloads on the Cray XE-6”, CUG 2012, May 2012,

The Cray XE architecture has been optimized to support tightly coupled MPI applications, but there is an in- creasing need to run more diverse workloads in the scientific and technical computing domains. These needs are being driven by trends such as the increasing need to process “Big Data”. In the scientific arena, this is exemplified by the need to analyze data from instruments ranging from sequencers, telescopes, and X-ray light sources. These workloads are typically throughput oriented and often involve complex task dependencies. Can platforms like the Cray XE line play a role here? In this paper, we will describe tools we have developed to support high-throughput workloads and data intensive applications on NERSC’s Hopper system. These tools include a custom task farmer framework, tools to create virtual private clusters on the Cray, and using Cray’s Cluster Compatibility Mode (CCM) to support more diverse workloads. In addition, we will describe our experience with running Hadoop, a popular open-source implementation of MapReduce, on Cray systems. We will present our experiences with this work including successes and challenges. Finally, we will discuss future directions and how the Cray platforms could be further enhanced to support these class of workloads.

Michael Stewart

2011

P. M. Stewart, Y. He, “Benchmark Performance of Different Compilers on a Cray XE6”, Fairbanks, AK, CUG Proceedings, May 23, 2011,

There are four different supported compilers on NERSC's recently acquired XE6, Hopper. Our users often request guidance from us in determining which compiler is best for a particular application. In this paper, we will describe the comparative performance of different compilers on several MPI benchmarks with different characteristics. For each compiler and benchmark, we will establish the best set of optimization arguments to the compiler.

David P. Turner

2014

David Turner, NERSC, Accounts and Allocations, February 3, 2014,

David Turner, NERSC, NERSC Computing Environment, February 3, 2014,

David Turner, NERSC, NERSC File Systems and How to Use Them, February 3, 2014,

Andrew Uselton

2013

Suren Byna, Andrew Uselton, Prabhat, David Knaak, Helen He, “Trillion Particles, 120,000 cores, and 350 TBs: Lessons Learned from a Hero I/O Run on Hopper”, Cray User Group Meeting, 2013,

2012

A.C. Uselton, K.B. Antypas, D. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, CUG Proceedings, Edinburgh, Scotland, March 1, 2012,

Surendra Byna, Jerry Chou, Oliver R\ ubel, Prabhat, Homa Karimabadi, William S. Daughton, Vadim Roytershteyn, E. Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Andrew Uselton, Kesheng Wu, “Parallel I/O, analysis, and visualization of a trillion particle simulation”, SC 12, Los Alamitos, CA, USA, IEEE Computer Society Press, 2012, 59:1--59:1,

2011

J. Hick, J. Hules, A. Uselton, “DOE HPC Best Practices Workshop: File Systems and Archives”, Workshop, September 27, 2011,

The Department of Energy has identified the design, implementation, and usability of file systems and archives as key issues for current and future HPC systems. This workshop addresses current best practices for the procurement, operation, and usability of file systems and archives. Furthermore, the workshop addresses whether system challenges can be met by evolving current practices.

2010

A. Uselton, K. Antypas, D. M. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, Proceedings of the 2010 Cray User Group Meeting, Edinburgh, Scotland, Edinburgh, Scotland, May 24, 2010,

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, “Parallel I/O performance: From events to ensembles”, IPDPS, Atlanta, Georgia, 2010, 1-11,

2009

K. Antypas and A. Uselton, “MPI-I/O on Franklin XT4 System at NERSC”, CUG Proceedings, Atlanta, CA, May 28, 2009,

Daniela Mayumi Ushizima

2012

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 (Proceedings IEEE Vis 2012), 2012, 18:2041--2050, LBNL 5964E

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, J\ org Meyer, Prabhat, Oliver R\ ubel, Daniela Ushizima, Gunther Weber, “Towards Exascale: High Performance Visualization and Analytics -- Project Status Report”, 2012,

2010

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 UCSF Medical Sciences, September 2010,

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, September 2010,

 

 

A. Uselton, K. Antypas, D. M. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, Proceedings of the 2010 Cray User Group Meeting, Edinburgh, Scotland, Edinburgh, Scotland, May 24, 2010,

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, Kesheng Wu, “Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-Dimensional Scientific Data”, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010,

      

D. M. Ushizima and F. Medeiros, “Retinopathy Diagnosis from Ocular Fundus Image Analysis”, Modeling and Analysis of Biomedical Image, SIAM Conference on Imaging Science (IS10), Chicago, IL, April 12, 2010,

D. M. Ushizima, J. Cuadros, “Ocular Fundus for Retinopathy Characterization”, Bay Area Vision Meeting, Berkeley, CA, February 5, 2010,

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rübel, Gunther Weber, Bernard Hamann, Peter Messmer, and Hans Hagen, “Automated Detection and Analysis of Particle Beams in Laser-Plasma Accelerator Simulations”, In-Tech, ( 2010) Pages: 367 - 389

2009

Oliver R\ ubel, Cameron G. R. Geddes, Estelle Cormier-Michel Kesheng Wu, Prabhat, Gunther H. Weber, Daniela M. Ushizima, Peter Messmer, Hans Hagen, Bernd Hamann, Wes Bethel, “Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data”, IOP Computational Science \& Discovery, ( 2009)

Francesca Verdier

2013

Francesca Verdier, NERSC Accomplishments and Plans, February 12, 2013,

2005

Horst D. Simon, William T. C. Kramer, David H. Bailey, Michael J. Banda, E. Wes Bethel, Jonathon T. Carter, James M. Craw, William J. Fortney, John A. Hules, Nancy L. Meyer, Juan C. Meza, Esmond G. Ng, Lynn E. Rippe, William C. Saphir, Francesca Verdier, Howard A. Walter, Katherine A. Yelick, “Science-Driven Computing: NERSC’s Plan for 2006–2010”, LBNL Technical Report 57582, 2005,

2001

William T. C. Kramer, Wes Bethel, James Craw, Brent Draney, William Fortney, Brent Gorda, William Harris, Nancy Meyer, Esmond Ng, Francesca Verdier, Howard Walter, Tammy Welcome, “NERSC Strategic Implementation Plan 2002-2006”, ”, LBNL Technical Report 5465 Vol. 2, 2001,

1999

William T. C. Kramer, Francesca Verdier, Keith Fitzgerald, James Craw, Tammy Welcome, “High Performance Computing Facilities for the Next Millennium”, LBNL Technical Report 44700, 1999,

1992

Francesca Verdier, “UNIX at the Cornell Theory Center”, Cornell Theory Center Forefronts, July 4, 1992,

1988

Francesca Verdier, Shahin Kahn, “Programming for Parallelism on the FPSBUS”, Cornell Theory Center Technical Report CTC88TR14, 1988,

1987

Francesca Verdier, “Vectorization Gives You Free Cycles!”, Cornell Theory Center Forefronts, March 7, 1987,

Howard Walter

2005

Horst D. Simon, William T. C. Kramer, David H. Bailey, Michael J. Banda, E. Wes Bethel, Jonathon T. Carter, James M. Craw, William J. Fortney, John A. Hules, Nancy L. Meyer, Juan C. Meza, Esmond G. Ng, Lynn E. Rippe, William C. Saphir, Francesca Verdier, Howard A. Walter, Katherine A. Yelick, “Science-Driven Computing: NERSC’s Plan for 2006–2010”, LBNL Technical Report 57582, 2005,

2001

William T. C. Kramer, Wes Bethel, James Craw, Brent Draney, William Fortney, Brent Gorda, William Harris, Nancy Meyer, Esmond Ng, Francesca Verdier, Howard Walter, Tammy Welcome, “NERSC Strategic Implementation Plan 2002-2006”, ”, LBNL Technical Report 5465 Vol. 2, 2001,

Harvey J. Wasserman

2014

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Fusion Energy Sciences: Target 2017”, May 1, 2014,

Harvey Wasserman, NERSC, New User Training: Introduction to NERSC, NUG 2014: NERSC Users' Group Meeting, February 3, 2014,

2013

M. J. Cordery, B. Austin, H. J. Wasserman, C. S. Daley, N. J. Wright, S. D. Hammond, D. Doerfler, “Analysis of Cray XC30 Performance using Trinity-NERSC-8 benchmarks and comparison with Cray XE6 and IBM BG/Q”, SC'13, November 11, 2013,

Richard Gerber and Harvey Wasserman, eds., “Large Scale Computing and Storage Requirements for High Energy Physics - Target 2017”, November 8, 2013,

Richard Gerber, Harvey Wasserman, “High Performance Computing and Storage Requirements for Biological and Environmental Research Target 2017”, June 6, 2013, LBNL LBNL-6256E

Brian Austin, Matthew Cordery, Harvey Wasserman, Nicholas J. Wright, “Performance Measurements of the NERSC Cray Cascade System”, 2013 Cray User Group Meeting, May 9, 2013,

Richard A. Gerber, Harvey Wasserman, NERSC Requirements Reviews, February 12, 2013,

An update on the NERSC Requirements Reviews at NUG 2013. Richard Gerber and Harvey Wasserman, NERSC>

2012

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Nuclear Physics”, Workshop, March 26, 2012, LBNL LBNL-5355E

Report of the user requirements workshop for lattice gauge theory and nuclear physics computation at NERSC that took place May 26, 2011

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Advanced Computational Science Research”, Workshop, January 2012, LBNL LBNL-5249E

2011

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Fusion Energy Sciences”, Workshop, December 2011,

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Basic Energy Sciences”, Workshop, June 10, 2011, LBNL LBNL-4809E

2010

Leonid Oliker, Jonathan Carter, V. Beckner, J. Bell, H. J. Wasserman, M. Adams, S. Ethier, and E. Schnetter, “Large-Scale Numerical Simulations on High-End Computational Platforms”, Chapman & Hall/CRC Computational Science, edited by David H. Bailey, Robert F. Lucas, Samuel Williams, (Chapman & Hall/CRC Computational Science: November 23, 2010)

ISBN 9781439815694

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for High Energy Physics”, Workshop, November 15, 2010,

Harvey Wasserman, Simulation Science at NERSC, Cray Technical Workshop Japan, September 7, 2010,

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

2009

Richard A. Gerber, Harvey J. Wasserman, “Large Scale Computing and Storage Requirements for Biological and Environmental Research”, Workshop, October 19, 2009, LBNL LBNL-2710E

Harvey Wasserman, Extreme Scale Data Intensive Computing at NERSC, Los Alamos Computer Science Symposium, Workshop on Performance Analysis of Extreme-Scale Systems and Applications, October 14, 2009,

John Shalf, Harvey Wasserman, Breakthrough Computing in Petascale Applications and Petascale System Examples at NERSC, HPC User Forum, April 10, 2009,

2008

Harvey Wasserman, Future Scientific Computing Challenges at NERSC, University of Southampton, September 30, 2008,

Harvey Wasserman, Breakthrough Science at NERSC, Cray Technical Workshop, Europ, September 24, 2008,

Antypas, K., Shalf, J., Wasserman, H., “NERSC‐6 Workload Analysis and Benchmark Selection Process”, LBNL Technical Report, August 13, 2008, LBNL 1014E

Science drivers for NERSC-6

K. Antypas, J. Shalf, H. Wasserman, “NERSC-6 Workload Analysis and Benchmark Selection Process”, January 1, 2008,

J. Shalf, K. Antypas, H.J. Wasserman, Recent Workload Characterization Activities at NERSC, Santa Fe Workshop, January 1, 2008,

2007

Jonathan Carter, Yun (Helen) He, John Shalf, Hongzhang Shan, Erich Strohmaier, and Harvey Wasserman, “The Performance Effect of Multi-Core on Scientific Applications”, Cray User Group 2007, May 2007, LBNL 62662

The historical trend of increasing single CPU performance has given way to roadmap of increasing core count. The challenge of effectively utilizing these multi- core chips is just starting to be explored by vendors and application developers alike. In this study, we present some performance measurements of several complete scientific applications on single and dual core Cray XT3 and XT4 systems with a view to characterizing the effects of switching to multi-core chips. We consider effects within a node by using applications run at low concurrencies, and also effects on node- interconnect interaction using higher concurrency results. Finally, we construct a simple performance model based on the principle on-chip shared resource—memory bandwidth—and use this to predict the performance of the forthcoming quad-core system.

 

Jonathan Carter, Helen He*, John Shalf, Erich Strohmaier, Hongzhang Shan, and Harvey Wasserman, The Performance Effect of Multi-Core on Scientific Applications, Cray User Group 2007, May 2007,

J. Levesque, J. Larkin, M. Foster, J. Glenski, G. Geissler, S. Whalen, B. Waldecker, J. Carter, D. Skinner, H. He, H. Wasserman, J. Shalf, H. Shan, “Understanding and mitigating multicore performance issues on the AMD opteron architecture”, March 1, 2007, LBNL 62500

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3and XT4systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

 

Gunther Weber

2014

Kenes Beketayev, Damir Yeliussizov, Dmitriy Morozov, Gunther H. Weber, Bernd Hamann, “Measuring the Distance Between Merge Trees”, Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, (Springer-Verlag: 2014)

Dmitriy Morozov, Gunther H. Weber, “Distributed Contour Trees”, Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, (Springer-Verlag: 2014)

Gunther H. Weber, Helwig Hauser, “Interactive Visual Exploration and Analysis”, Scientific Visualization: Uncertainty, Multifield, Bio-Medical and Scalable Visualization, (Springer-Verlag: 2014)

2013

Patrick Oesterling, Christian Heine, Gunther H. Weber, Scheuermann, “Visualizing nD Point Clouds as Topological Landscape Profiles to Guide Data Analysis”, IEEE Transactions on Visualization and Computer Graphics, 2013, 19(3):514-526, LBNL 5694E

Dmitriy Morozov, Gunther H. Weber, “Distributed Merge Trees”, Proceedings of the 18th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 13), New York, NY, USA, ACM, 2013, 93--102, LBNL 6137E

Gunther H. Weber, Hank Childs, Jeremy S. Meredith, “Recent Advances in VisIt: Parallel Crack-free Isosurface Extraction”, Numerical Modeling of Space Plasma Flows: Astronum-2012 (Astronomical Society of the Pacific Conference Series), 2013,

2012

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 31, 2012) Pages: 357-371

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 1, 2012, LBNL 5767E

Gunther H. Weber, Peer-Timo Bremer, Valerio Pascucci, “Topological Cacti: Visualizing Contour-based Statistics”, Topological Methods in Data Analysis and Visualization II: Theory, Algorithms, and Applications, (Springer-Verlag: January 1, 2012) Pages: 63--76, LBNL 5018E

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 (Proceedings IEEE Vis 2012), 2012, 18:2041--2050, LBNL 5964E

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

Oliver Rübel, Soile V. E. Keränen, Mark D. Biggin, David W. Knowles, H. Weber, Hans Hagen, Bernd Hamann, E. Wes Bethel, “Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data”, Mathematical Methods for Visualization in Medicine and Life Sciences II, (Springer-Verlag: 2012) Pages: 267--286, LBNL 4891E

Kenes Beketayev, Gunther H. Weber, Dmitriy Morozov, Aidos Abzhanov, Bernd Hamann, “Geometry-Preserving Topological Landscapes”, Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, ACM, 2012, 155--160, LBNL 6082E

Dogan Demir, Kenes Beketayev, Gunther H. Weber, Peer-Timo Bremer, Valerio Pascucci, Bernd Hamann, “Topology Exploration with Hierarchical Landscapes”, Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, ACM, 2012, 147--154, LBNL 6083E

Allen R. Sanderson, Brad Whitlock, Oliver R\ ubel, Hank Childs, Gunther H. Weber, Prabhat, Kesheng Wu, “A System for Query Based Analysis and Visualization”, Third International EuroVis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, 2012, 25--29, LBNL 5507E

Gunther H. Weber, Peer-Timo Bremer, “In-situ Analysis: Challenges and Opportunities”, 2012, LBNL 5692E

Gunther H. Weber, Kenes Beketayev, Peer-Timo Bremer, Hamann, Maciej Haranczyk, Mario Hlawitschka, Pascucci, “Comprehensible Presentation of Topological Information”, 2012, LBNL 5693E

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, J\ org Meyer, Prabhat, Oliver R\ ubel, Daniela Ushizima, Gunther Weber, “Towards Exascale: High Performance Visualization and Analytics -- Project Status Report”, 2012,

2011

Kenes Beketayev, Gunther H. Weber, Maciej Haranczyk, Bremer, Mario Hlawitschka, Bernd Hamann, “Visualization of Topology of Transformation Pathways in Complex Systems”, Computer Graphics Forum (Special Issue, Proceedings Symposium on Visualization), January 2011, 663--672, LBNL 5242E

Gunther H. Weber, Peer-Timo Bremer, Attila Gyulassy and, “Topology-based Feature Definition and Analysis”, Numerical Modeling of Space Plasma Flows---ASTRONUM-2010, Astronomical Society of the Pacific, January 1, 2011, 444:292--297,

E. Deines, G.H. Weber, C. Garth, B. Van Straalen, S. Borovikov, D.F. Martin, K. Joy, “On the Computation of Integral Curves in Adaptive Mesh Refinement Vector Fields”, Proceedings of Dagstuhl Seminar on Scientific Visualization 2009, January 1, 2011,

Peer-Timo Bremer, Gunther H. Weber, Julien Tierny, Pascucci, Marcus S. Day, John B. Bell, “Interactive Exploration and Analysis of Large Scale Turbulent Combustion Topology-based Data Segmentation”, IEEE Transactions on Visualization and Computer Graphics, 2011, 17:1307-1324,

Gunther H. Weber, Peer-Timo Bremer, Marcus S. Day, John B. Bell Valerio Pascucci, “Feature Tracking Using Reeb Graphs”, Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, (Springer-Verlag: 2011) Pages: 241--253, LBNL 4226E

Brian MacCarthy, Hamish Carr, Gunther H. Weber, “Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering”, 2011, LBNL LBNL-5019E

2010

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, October 2010,

 

 

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, Kesheng Wu, “Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-Dimensional Scientific Data”, Proceedings of International Conference on Computational Science, ICCS 2010, May 2010,

      

H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. Weber, E. W. Bethel, “Extreme Scaling of Production Visualization Software on Diverse Architectures”, Computer Graphics and Applications, May 2010, 30 (3):22 - 31,

Peer-Timo Bremer, Gunther H. Weber, Valerio Pascucci, Marcus S. Day, John B. Bell, “Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames”, IEEE Transactions on Visualization and Computer Graphics, 2010, 16:248--260,

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rübel, Gunther Weber, Bernard Hamann, Peter Messmer, and Hans Hagen, “Automated Detection and Analysis of Particle Beams in Laser-Plasma Accelerator Simulations”, In-Tech, ( 2010) Pages: 367 - 389

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, B. Hamann, “Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data”, IEEE Transactions on Computational Biology and Bioinformatics, Jan/Mar 2010, January 2010, 7 (1):64-79,

Min-Yu Huang, Gunther H. Weber, Xiao-Yong Li, Mark D. Biggin, Bernd Hamann, “Quantitative Visualization of ChIP-chip Data by Using Linked Views”, IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2010), Workshop on Integrative Data Analysis in Systems Biology (IDASB), 2010, 195–200,

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), 2010, 429:329–334,

2003

Gunther H. Weber, Oliver Kreylos, John Shalf, Wes Bethel, Bernd Hamann, Gerik Scheuermann, “Parallel Cell Projection Rendering of Adaptive Mesh Refinement Data”, IEEE Symposium on Parallel and Large-Data Visualization and Graphics, January 1, 2003, 51-60,

2001

Gunther H. Weber, Kreylos, J. Ligocki, Shalf, Hagen, Hamann, I. Joy, Kwan-Liu Ma, “High-quality Volume Rendering of Adaptive Mesh Refinement Data”, VMV, January 1, 2001, 121-128,

Mike L. Welcome

2011

D. Hazen, J. Hick, W. Hurlbert, M. Welcome, Media Information Record (MIR) Analysis, LTUG 2011, April 19, 2011,

Presentation of Storage Systems Group findings from a year-long effort to collect and analyze Media Information Record (MIR) statistics from our in-production Oracle enterprise tape drives at NERSC.  We provide information on the data collected, and some highlights from our analysis. The presentation is primarily intended to declare that the information in the MIR is important to users or customers to better operating and managing their tape environments.

Nicholas Wright

2014

Sudip Dosanjh, Shane Canon, Jack Deslippe, Kjiersten Fagnan, Richard Gerber, Lisa Gerhardt, Jason Hick, Douglas Jacobsen, David Skinner, Nicholas J. Wright, “Extreme Data Science at the National Energy Research Scientific Computing (NERSC) Center”, Proceedings of International Conference on Parallel Programming – ParCo 2013, ( March 26, 2014)

2013

M. J. Cordery, B. Austin, H. J. Wasserman, C. S. Daley, N. J. Wright, S. D. Hammond, D. Doerfler, “Analysis of Cray XC30 Performance using Trinity-NERSC-8 benchmarks and comparison with Cray XE6 and IBM BG/Q”, SC'13, November 11, 2013,

Hongzhang Shan, Brian Austin, Wibe De Jong, Leonid Oliker, Nicholas Wright, Edoardo Apra, “Performance Tuning of Fock Matrix and Two-Electron Integral Calculations for NWChem on Leading HPC Platforms”, SC'13, November 11, 2013,

Zhengji Zhao, Katie Antypas, Nicholas J Wright, “Effects of Hyper-Threading on the NERSC workload on Edison”, 2013 Cray User Group Meeting, May 9, 2013,

Brian Austin, Matthew Cordery, Harvey Wasserman, Nicholas J. Wright, “Performance Measurements of the NERSC Cray Cascade System”, 2013 Cray User Group Meeting, May 9, 2013,

Nick Wright, NERSC Initiative: Preparing Applications for Exascale, February 12, 2013,

Andrew Uselton, Nicholas J. Wright, “A file system utilization metric for I/O characterization”, 2013 Cray User Group Conference, Napa, CA, 2013,

2012

Hongzhang Shan, Brian Austin, Nicholas Wright, Erich Strohmaier, John Shalf, Katherine Yelick, “Accelerating Applications at Scale Using One-Sided Communication”, The 6th Conference on Partitioned Global Address Programming Models, Santa Barbara, CA, October 10, 2012,

Hongzhang Shan, J. Wright, Shalf, A. Yelick, Wagner, Nathan Wichmann, “A preliminary evaluation of the hardware acceleration of Cray Gemini interconnect for PGAS languages and comparison with MPI”, SIGMETRICS Performance Evaluation Review, 2012, 40:92-98,

Lavanya Ramakrishnan, Richard Canon, Muriki, Sakrejda, Nicholas J. Wright, “Evaluating Interconnect and Virtualization Performance forHigh Performance Computing”, SIGMETRICS Performance Evaluation Review, 2012, 40:55-60,

2011

Lavanya Ramakrishnan, Richard Shane Canon, Krishna Muriki, Iwona Sakrejda, and Nicholas J. Wright., “Evaluating Interconnect and Virtualization Performance for High Performance Computing”, Proceedings of 2nd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems (PMBS11), 2011,

In this paper we detail benchmarking results that characterize the virtualization overhead and its impact on performance. We also examine the performance of various interconnect technologies with a view to understanding the performance impacts of various choices. Our results show that virtualization can have a significant impact upon performance, with at least a 60% performance penalty. We also show that less capable interconnect technologies can have a significant impact upon performance of typical HPC applications. We also evaluate the performance of the Amazon Cluster compute instance and show that it performs approximately equivalently to a 10G Ethernet cluster at low core counts.

Zhengji Zhao and Nick Wright, “Performance of Density Functional Theory codes on Cray XE6”, A paper presented in the Cray User Group meeting, May 23-26, 2011, Fairbanks, Alaska., May 24, 2011,

Zhengji Zhao and Nick Wright, Performance of Density Functional Theory codes on Cray XE6, A talk in Cray User Group meeting 2011, May 23-26, 2011, Fairbanks, Alaska., May 23, 2011,

K. Furlinger, N.J. Wright, D. Skinner, “Comprehensive Performance Monitoring for GPU Cluster Systems”, Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on, 2011, 1377--1386,

Praveen Narayanan, Alice Koniges, Leonid Oliker, Robert Preissl, Samuel Williams, Nicholas J Wright, Maxim Umansky, Xueqiao Xu, Benjamin Dudson, Stephane Ethier, Weixing Wang, Jeff Candy, John R. Cary, “Performance Characterization for Fusion Co-design Applications”, Proceedings of CUG, 2011,

2010

Neal Master, Matthew Andrews, Jason Hick, Shane Canon, Nicholas J. Wright, “Performance Analysis of Commodity and Enterprise Class Flash Devices”, Petascale Data Storage Workshop (PDSW), November 2010,

Hongzhang Shan, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J Wright, “Analyzing the effect of different programming models upon performance and memory usage on cray xt5 platforms”, CUG2010, Edinburgh, Scotland, 2010,

Keith R. Jackson, Ramakrishnan, Muriki, Canon, Cholia, Shalf, J. Wasserman, Nicholas J. Wright, “Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud”, CloudCom, Bloomington, Indiana, January 1, 2010, 159-168,

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, “Parallel I/O performance: From events to ensembles”, IPDPS, Atlanta, Georgia, 2010, 1-11,

Karl F\ urlinger, J. Wright, David Skinner, “Effective Performance Measurement at Petascale Using IPM”, ICPADS, January 1, 2010, 373-380,

K. Fuerlinger, N.J. Wright, D. Skinner, “Performance analysis and workload characterization with ipm”, Tools for High Performance Computing 2009, January 1, 2010, 31--38,

K. Fuerlinger, N.J. Wright, D. Skinner, C. Klausecker, D. Kranzlmueller, “Effective Holistic Performance Measurement at Petascale Using IPM”, Competence in High Performance Computing 2010, January 1, 2010, 15--26,

2009

B. R. de Supinski, S. Alam, D. H. Bailey, L., C. Daley, A. Dubey, T., D. Gunter, P. D. Hovland, H., K. Karavanic, G. Marin, J., S. Moore, B. Norris, L., C. Olschanowsky, P. C. Roth, M., S. Shende, A. Snavely, Spear, M. Tikir, J. Vetter, P. Worley, N. Wright, “Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team”, Journal of Physics: Conference Series, 2009, 180:012039,

N.J. Wright, S. Smallen, C.M. Olschanowsky, J. Hayes, A. Snavely, “Measuring and Understanding Variation in Benchmark Performance”, DoD High Performance Computing Modernization Program Users Group Conference (HPCMP-UGC), 2009, 2009, 438 -443,

2008

Wayne Pfeiffer, Nicholas J. Wright, “Modeling and predicting application performance on parallel computers using HPC challenge benchmarks”, IPDPS, 2008, 1-12,

2007

John Michalakes, Hacker, Loft, O. McCracken, Snavely, J. Wright, E. Spelce, C. Gorda, Robert Walkup, “WRF nature run”, SC, 2007, 59,

Woo-Sun Yang

2014

Richard A. Gerber, Zhengji Zhao, Woo-Sun Yang, Debugging and Optimization Tools, Presented at UC Berkeley CS267 class, February 2014, February 19, 2014,

Woo-Sun Yang, Debugging Tools, February 3, 2014,

2013

Woo-Sun Yang, Debugging and Performance Analysis Tools at NERSC, BOUT++ 2013 Workshop, September 3, 2013,

2010

Wendy Hwa-Chun Lin, Yun (Helen) He, and Woo-Sun Yang, “Franklin Job Completion Analysis”, Cray User Group 2010 Proceedings, Edinburgh, UK, May 2010,

The NERSC Cray XT4 machine Franklin has been in production for 3000+ users since October 2007, where about 1800 jobs run each day. There has been an on-going effort to better understand how well these jobs run, whether failed jobs are due to application errors or system issues, and to further reduce system related job failures. In this paper, we talk about the progress we made in tracking job completion status, in identifying job failure root cause, and in expediting resolution of job failures, such as hung jobs, that are caused by system issues. In addition, we present some Cray software design enhancements we requested to help us track application progress and identify errors.

 

Yun (Helen) He, Wendy Hwa-Chun Lin, and Woo-Sun Yang, Franklin Job Completion Analysis, Cray User Group Meeting 2010, May 2010,

Yushu Yao

2014

Yushu Yao, NERSC; Douglas Jacobsen, NERSC, Connecting to NERSC, NUG 2014, February 3, 2014,

2013

A. Koniges, R. Gerber, D. Skinner, Y. Yao, Y. He, D. Grote, J-L Vay, H. Kaiser, and T. Sterling, “Plasma Physics Simulations on Next Generation Platforms”, 55th Annual Meeting of the APS Division of Plasma Physics, Volume 58, Number 16, November 11, 2013,

The current high-performance computing revolution provides opportunity for major increases in computational power over the next several years, if it can be harnessed. This transition from simply increasing the single-processor and network performance to a different architectural paradigms forces application programmers to rethink the basic models of parallel programming from both the language and problem division standpoints. One of the major computing facilities available to researchers in fusion energy is the National Energy Research Scientific Computing Center. As the mission computing center for DOE, Office of Science, NERSC is tasked with helping users to overcome the challenges of this revolution both through the use of new parallel constructs and languages and also by enabling a broader user community to take advantage of multi-core performance. We discuss the programming model challenges facing researchers in fusion and plasma physics in for a variety of simulations ranging from particle-in-cell to fluid-gyrokinetic and MHD models.

Yushu Yao, NERSC Parallel Database Evaluation, February 12, 2013,

2012

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, “Shared Library Performance on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Babak Behzad, Joseph Huchette, Huong Luu, Suren Byna, Yushu Yao, Prabhat, “Auto-Tuning of Parallel I/O Parameters for HDF5 Applications”, SC, 2012,

Surendra Byna, Jerry Chou, Oliver R\ ubel, Prabhat, Homa Karimabadi, William S. Daughton, Vadim Roytershteyn, E. Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Andrew Uselton, Kesheng Wu, “Parallel Data, Analysis, and Visualization of a Trillion Particles”, XLDB, 2012,

Mehmet Balman, Eric Pouyoul, Yushu Yao, Loring E. Wes Bethel, Prabhat, John Shalf, Alex Sim, Brian L. Tierney, “Experiences with 100G Network Applications”, Proceedings of the 5th International Workshop on Data Intensive and Distributed Computing (DIDC 2012), Delft, Netherlands, 2012,

Katherine A. Yelick

2013

Richard Gerber, Kathy Yelick, Lawrence Berkeley National Laboratory, “Data Requirements from NERSC Requirements Reviews”, January 9, 2013,

2012

Alice Koniges, Katherine Yelick, Rolf Rabenseifner, Reinhold Bader, David Eder, Filip Blagojevic, Robert Preissl, Paul Hargrove, Introduction to PGAS (UPC and CAF) and Hybrid for Multicore Programming, SC12 Full Day Tutorial, November 2012,

Hongzhang Shan, Brian Austin, Nicholas Wright, Erich Strohmaier, John Shalf, Katherine Yelick, “Accelerating Applications at Scale Using One-Sided Communication”, The 6th Conference on Partitioned Global Address Programming Models, Santa Barbara, CA, October 10, 2012,

NERSC Accomplishments and Plans, February 3, 2012,

Hongzhang Shan, J. Wright, Shalf, A. Yelick, Wagner, Nathan Wichmann, “A preliminary evaluation of the hardware acceleration of Cray Gemini interconnect for PGAS languages and comparison with MPI”, SIGMETRICS Performance Evaluation Review, 2012, 40:92-98,

2011

Katherine Yelick, Susan Coghlan, Brent Draney, Richard Shane Canon, Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Anping Liu, Scott Campbell, Piotr T. Zbiegiel, Tina Declerck, Paul Rich, “The Magellan Report on Cloud Computing for Science”, U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), December 2011,

Saman Amarasinghe, Mary Hall, Richard Lethin, Keshav Pingali, Dan Quinlan, Vivek Sarkar, John Shalf, Robert Lucas, Katherine Yelick, Pavan Balaji, Pedro C. Diniz, Alice Koniges, Marc Snir, Sonia R. Sachs, “Exascale Programming Challenges”, 2011,

J. Dongarra, P. Beckman, T. Moore, P. Aerts, G. Aloisio, J.C. Andre, D. Barkai, J.Y. Berthou, T. Boku, B. Braunschweig, others, “The international exascale software project roadmap”, International Journal of High Performance Computing Applications, January 2011, 25:3--60,

2010

Jack Dongarra, John Shalf, David Skinner, Kathy Yelick, “International Exascale Software Project (IESP) Roadmap, version 1.1”, October 18, 2010,

K. Datta, S. Williams, V. Volkov, J. Carter, L. Oliker, J. Shalf, K. Yelick, “Auto-Tuning Stencil Computations on Diverse Multicore Architectures”, Scientific Computing with Multicore and Accelerators, edited by Jakub Kurzak, David A. Bader, Jack Dongarra, 2010,

2009

Joseph Gebis, Oliker, Shalf, Williams, Katherine A. Yelick, “Improving Memory Subsystem Performance Using ViVA: Virtual Vector Architecture”, ARCS, January 1, 2009, 146-158,

Kamesh Madduri, Williams, Ethier, Oliker, Shalf, Strohmaier, Katherine A. Yelick, “Memory-efficient optimization of Gyrokinetic particle-to-grid interpolation for multicore processors”, SC, January 1, 2009,

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms”, Journal of Parallel and Distributed Computing, January 1, 2009, 69:762-777,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, “Optimization of sparse matrix-vector multiplication on emerging multicore platforms”, Parallel Computing, January 1, 2009, 35:178--194,

2008

K. Datta, M. Murphy, V. Volkov, S. Williams, J. Carter, L. Oliker, D. Patterson, J. Shalf, K. Yelick, “Stencil computation optimization and auto-tuning on state-of-the-art multicore architectures”, Proceedings of the 2008 ACM/IEEE Conference on High Performance Computing and Networking ("Supercomputing", SC08), November 15, 2008,

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Lattice Boltzmann simulation optimization on leading multicore platforms”, International Parallel and Distributed Processing Symposium (IPDPS), April 14, 2008, 1-14,

Sam Williams, Jonathan Carter, Leonid Oliker, John Shalf, Katherine Yelick, Lattice Boltzmann Simulation Optimization on Leading Multicore Architectures, January 1, 2008,

Sam Williams, Kaushik Datta, Jonathan Carter, Leonid Oliker, John Shalf, Katherine Yelick, David Bailey, “PERI - Auto-tuning Memory Intensive Kernels for Multicore”, SciDAC: Scientific Discovery Through Advanced Computing, Journal of Physics: Conference Series, January 1, 2008,

2007

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms, International Conference for High-Performance Computing, Networking, Storage, and Analysis, January 1, 2007,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “Scientific computing kernels on the Cell processor”, International Journal of Parallel Programming, January 1, 2007, 35:263--298,

2006

Jonathan Carter, Tony Drummond, Parry Husbands, Paul Hargrove, Bill Kramer, Osni Marques, Esmond Ng, Lenny Oliker, John Shalf, David Skinner, Kathy Yelick, “Software Roadmap to Plug and Play Petaflop/s”, Lawrence Berkeley National Laboratory Technical Report, #59999, July 31, 2006,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “The potential of the cell processor for scientific computing”, Proceedings of the 3rd conference on Computing frontiers, January 1, 2006, 9--20,

S. Kamil, K. Datta, S. Williams, L. Oliker, J. Shalf, K. Yelick, “Implicit and explicit optimizations for stencil computations”, Proceedings of the 2006 workshop on Memory system performance and correctness, January 1, 2006, 51--60,

2005

John Shalf, John Bell, Andrew Canning, Lin-Wang Wang, Juan Meza, Rob Ryne, Ji Qiang, Kathy Yelick, “Berkeley Petascale Applications”, January 1, 2005,

Horst D. Simon, William T. C. Kramer, David H. Bailey, Michael J. Banda, E. Wes Bethel, Jonathon T. Carter, James M. Craw, William J. Fortney, John A. Hules, Nancy L. Meyer, Juan C. Meza, Esmond G. Ng, Lynn E. Rippe, William C. Saphir, Francesca Verdier, Howard A. Walter, Katherine A. Yelick, “Science-Driven Computing: NERSC’s Plan for 2006–2010”, LBNL Technical Report 57582, 2005,

Tarek El-Ghazawi, William Carlson, Thomas Sterling, Katherine Yelick, UPC: Distributed Shared-Memory Programming, January 1, 2005,

Shoaib Kamil,Parry Husbands, Leonid Oliker, John Shalf, Katherine A. Yelick, “Impact of modern memory subsystems on cache optimizations for stencil computations”, Memory System Performance, January 1, 2005, 36-43,

R. Vuduc, J.W. Demmel, K.A. Yelick, “OSKI: A library of automatically tuned sparse matrix kernels”, Journal of Physics: Conference Series, January 1, 2005, 16:521,

2004

Al Trivelpiece, Rupak Biswas, Jack Dongarra, Peter Paul, Katherine Yelick, Assessment of High-End Computing Research and Development in Japan, Available from http://www.wtec.org/reports.htm, January 1, 2004,

Xuefei Yuan

2013

Alice Koniges, Praveen Narayanan, Robert Preissl, Xuefei Yuan, Proxy Design and Optimization in Fusion and Accelerator Physics, SIAM Conference on Computational Science and Engineering, February 25, 2013,

Xuefei Yuan, Xiaoye S Li, Ichitaro Yamazaki, Stephen C Jardin, Alice E Koniges, David E Keyes, “Application of PDSLin to the magnetic reconnection problem”, Computational Science & Discovery, 2013, 6:014002,

Zhengji Zhao

2014

Richard A. Gerber, Zhengji Zhao, Woo-Sun Yang, Debugging and Optimization Tools, Presented at UC Berkeley CS267 class, February 2014, February 19, 2014,

Zhengji Zhao, NERSC, Best Practices for Best Performance on Edison, February 6, 2014,

Zhengji Zhao, NERSC, Available Software at NERSC, February 3, 2014,

2013

Richard A Gerber, Zhengji Zhao, NERSC Job Data, November 20, 2013,

Zhengji Zhao, Katie Antypas, Nicholas J Wright, “Effects of Hyper-Threading on the NERSC workload on Edison”, 2013 Cray User Group Meeting, May 9, 2013,

Richard A. Gerber, Tina Declerck. Zhengji Zhao, Edison Update, February 12, 2013,

Overview and update on the installation and configuration of Edison, NERSC's new Cray XC30 supercomputer.

Jack Deslippe, Zhengji Zhao, “Comparing Compiler and Library Performance in Material Science Applications on Edison”, Paper. Proceedings of the Cray User Group 2013, 2013,

2012

Megan Bowling, Zhengji Zhao and Jack Deslippe, “The Effects of Compiler Optimizations on Materials Science and Chemistry Applications at NERSC”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, “Shared Library Performance on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Megan Bowling, Zhengji Zhao and Jack Deslippe, The Effects of Compiler Optimizations on Materials Science and Chemistry Applications at NERSC, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, “Cray Cluster Compatibility Mode on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, Germany., May 1, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, Cray Cluster Compatibility Mode on Hopper, A talk in the Cray User Group meeting, April 29-May-3, 2012, Stuttgart, German., May 1, 2012,

Zhengji Zhao and Helen He, Using Cray Cluster Compatibility Mode on Hopper, A talk NERSC User Group meeting, Feb 2, 2012, Oakland, CA, February 2, 2012,

2011

Zhengji Zhao and Helen He, Cray Cluster Compatibility Mode on Hopper, A Brown Bag Lunch talk at NERSC, Dec. 8, 2011, Oakland, CA, December 8, 2011,

Zhengji Zhao, Mike Davis, Katie Antypas, Rei Lee and Tina Butler, Shared Library Performance on Hopper, Oct. 26, 2011, Cray Quarterly Meeting at St Paul, MN, October 26, 2011,

Zhengji Zhao and Nick Wright, “Performance of Density Functional Theory codes on Cray XE6”, A paper presented in the Cray User Group meeting, May 23-26, 2011, Fairbanks, Alaska., May 24, 2011,

Zhengji Zhao and Nick Wright, Performance of Density Functional Theory codes on Cray XE6, A talk in Cray User Group meeting 2011, May 23-26, 2011, Fairbanks, Alaska., May 23, 2011,

Zhengji Zhao, Introduction to Materials Science and Chemistry Applications at NERSC, NERSC User Training, April 5, 2011, Oakland, CA, April 5, 2011,

Zhengji Zhao, Tips to Compile Materials Science and Chemistry Codes at NERSC, NERSC User Training, April 5, 2011, Oakland, CA., April 5, 2011,

Rob Cunningham, Zhengji Zhao, Compiling Code on the XE6, A talk at NERSC Cray XE6 user training, Feb 7-8, 2011, Oakland, CA., February 7, 2011,

2010

David H. Bailey, Lin-Wang Wang, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, and Byounghak Lee, “Tuning an Electronic Structure Code”, a book chapter in Performance Tuning of Scientific Applications, edited by David H. Bailey, Robert F. Lucas, Samuel W. Williams (2010)., ( November 23, 2010)

Zhengji Zhao, Overview NERSC Facilities and Usage, A talk at Workshop on Leadership-class Machines, Petascale Applications, and Performance Strategies, July 19–22, 2010, Snowbird, Utah, July 21, 2010,

Zhengji Zhao, Node mapping and the parallel performance of the LS3DF code on BG/P, An invited talk at ScicomP 16, May10-14, 2010,San Francesco, CA., May 10, 2010,

2009

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, “Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, 2009 J. Phys.: Conf. Ser. 180 012079, July 1, 2009,

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, An invited poster presentation in SciDac meeting, June 14-18, 2009, San Diego, CA., June 14, 2009,

Zhengji Zhao, and Lin-Wang Wang, The application of the LS3DF method to CdSe/CdS core/shell structures, A talk at Cray User Group meeting, May 4-7, 2009, Atlanta, GA., May 5, 2009,

Zhengji Zhao, and Lin-Wang Wang, “The application of the LS3DF method to CdSe/CdS core/shell structures”, A paper presented in the Cray User Group meeting, May 4-7, 2009, Atlanta, GA, May 4, 2009,

Lin-Wang Wang, Byounghak Lee, Zhengji Zhao, Hongzhang Shan, Juan Meza, Erich Strohmaier, David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, An invited talk at Cray Technical Workshop North America, February 24-25, 2009, Charleston, SC., February 24, 2009,

2008

Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, David Bailey,, “Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, An award winning paper (ACM Gordon Bell Prize for algorithm innovation in SC08), Proceedings of the 2008 ACM/IEEE conference on Supercomputing, Article No. 65 (2008)., November 20, 2008,

Lin-Wang Wang, Byounghak Lee, Zhengji Zhao, Hongzhang Shan, Juan Meza, Erich Strohmaier and David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, A talk in SC08, Nov 20, 2008, Austin, Texas., November 20, 2008,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, “A divide and conquer linear scaling three dimensional fragment method for large scale electronic structure calculations”, J. Phys.: Condens. Matter 20 (2008) 294203., June 24, 2008,

Maho Nakata, Bastiaan J. Braams, Katsuki Fujisawa, Mituhiro Fukuda, Jerome K. Percus, Makoto Yamashita, and Zhengji Zhao, “Variational calculation of second-order reduced density matrices by strong N-representability conditions and an accurate semidefinite programming solver”, J. Chem. Phys., 128, 1, (2008), April 29, 2008,

Lin-Wang Wang, Zhengji Zhao, and Juan Meza, “Linear-scaling three-dimensional fragment method for large-scale electronic structure calculations”, Phys. Rev. B 77, 165113 (2008), April 10, 2008,

2007

Zhengji Zhao, Lin-Wang Wang and Juan Meza, A New O(N) Method for Petascale Nanoscience Simulations, the ACM Best poster (SC07) at International Conferences for High Performance Computing, Networking, Storage and Analysis,Nov. 10-16, 2007, Reno, CA., November 10, 2007,

Zhengji Zhao, Third Party Software, A talk at NERSC User Meeting, Sept. 17, 2007, Oakland, CA., September 17, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, The linear scaling 3-dimensional fragment method for petascale nanoscience simulations, A poster presented in STANFORD 50: State of the Art & Future Directions of Computational Mathematics & Numerical Computing, March 29-31, 2007, Palo Alto, California., May 29, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, A Linear Scaling 3-Dimensional Fragment Method for Petascale Nanoscience Simulations, A poster presented in Office of Advanced Scientific Computing Research (OSCAR) 2007 Applied Mathematics PI Meeting, May 22 - 24, 2007, Livermore, CA., May 22, 2007,

Bastiaan Braams, Jerry Percus and Zhengji Zhao, “The T1 and T2 representability conditions”, Reduced-Density-Matrix Mechanics -- with applications to many-electron atoms and molecules, A book edited by David Mazziotti, John Wiley Advances in Chemical Physics Series (2007)., ( March 27, 2007)

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling NanoScience Simulations for Petascale Computing, A talk presented in APS March 5-9, 2007, Denver, Colorado., March 5, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling 3D Fragment Method for Petascale Nanoscience Simulations, A poster presented in SIAM Computational Science and Engineering (CSE), Feb 19-23, 2007, Costa Mesa, California., February 19, 2007,