NERSCPowering Scientific Discovery for 50 Years

Publications & Presentations - Archive

2016

Daya Bay Collaboration, F.P. An et al., "Improved Measurement of the Reactor Antineutrino Flux and Spectrum at Daya Bay", Chinese Physics C, 2017, 41(1): 13002-013002, December 26, 2016,

A new measurement of the reactor antineutrino flux and energy spectrum by the Daya Bay reactor neutrino experiment is reported. The antineutrinos were generated by six 2.9 GWth nuclear reactors and detected by eight antineutrino detectors deployed in two near (560 m and 600 m flux-weighted baselines) and one far (1640 m flux-weighted baseline) underground experimental halls. With 621 days of data, more than 1.2 million inverse beta decay (IBD) candidates were detected. The IBD yield in the eight detectors was measured, and the ratio of measured to predicted flux was found to be 0:946±0:020 (0:992±0:021) for the Huber+Mueller (ILL+Vogel) model. A 2.9σ deviation was found in the measured IBD positron energy spectrum compared to the predictions. In particular, an excess of events in the region of 4-6 MeV was found in the measured spectrum, with a local significance of 4.4σ. A reactor antineutrino spectrum weighted by the IBD cross section is extracted for model-independent predictions.

Adam P. Arkin et al, The DOE Systems Biology Knowledgebase (KBase), Biorxiv, December 22, 2016, doi: 10.1101/096354

Evan Racah, Seyoon Ko, Peter Sadowski, Wahid Bhimji, Craig Tull, Sang-Yun Oh, Pierre Baldi, Prabhat, "Revealing Fundamental Physics from the Daya Bay Neutrino Experiment using Deep Neural Networks", ICMLA, 2016,

A. Ovsyannikov, Performance Advantages of Using a Burst Buffer for Scientific Workflows, Bay Area Scientific Computing Day (BASCD 2016), December 3, 2016,

Yun (Helen) He, CESM MG2/HOMME, NESAP Hackathon Meeting at NERSC, Berkeley, CA., November 29, 2016,

C. Yang, S. Yazar, G. Gooden, and A. Hewitt, "Data-Driven Workflows on Crays with Hybrid Scheduling: A Case Study of Celera on Magnus", Supercomputing Conference (SC'16), November 2016,

Debbie Bard, Wahid Bhimji, David Paul, Glenn K Lockwood, Nicholas J Wright, Katie Antypas, Prabhat Prabhat, Steve Farrell, Andrey Ovsyannikov, Melissa Romanus, others, "Experiences with the Burst Buffer at NERSC", Supercomputing Conference, November 16, 2016, LBNL LBNL-1007120,

Richard A Gerber, IXPUG Birds of a Feather Welcome, Birds of a Feather @ SC16, November 16, 2016,

A. Ovsyannikov, Case study: Chombo-Crunch and VisIt for carbon sequestration, Supercomputing Conference, Birds of a Feather: "Burst Buffers: Early Experiences and Outlook", November 15, 2016,

Tiffany A. Connors, Ritu Arora, "A Scalable Approach for Topic Modeling with R", Supercomputing Conference (SC) 2016, November 15, 2016,

Andrey Ovsyannikov, Melissa Romanus, Brian Van Straalen, Gunther H Weber, David Trebotich, "Scientific workflows at datawarp-speed: Accelerated data-intensive science using nersc's burst buffer", 2016 1st Joint International Workshop on Parallel Data Storage and data Intensive Scalable Computing Systems (PDSW-DISCS), Salt Lake City, UT, USA, IEEE, November 14, 2016, 1--6, LBNL LBNL-1006680, doi: 10.1109/PDSW-DISCS.2016.005

Tim Mattson, Alice Koniges, Clay Breshears, Programming Irregular Applications with OpenMP: A Hands-On Introduction, SC16 Tutorial, November 14, 2016,

Hongzhang Shan, Samuel Williams, Yili Zheng, Weiqun Zhang, Bei Wang, Stephane Ethier, Zhengji Zhao, "Experiences of Applying One-Sided Communication to Nearest-Neighbor Communication", http://conferences.computer.org/paw/2016/, Salt Lake City, Utah, November 14, 2016,

C.S. Daley, D. Ghoshal, G.K. Lockwood, S. Dosanjh, L. Ramakrishnan, N.J. Wright, "Performance Characterization of Scientific Workflows for the Optimal Use of Burst Buffers", Workflows in Support of Large-Scale Science (WORKS-2016), CEUR-WS.org, 2016, 1800:69-73,

Deborah Bard, Burst Buffers: Early Experiences and Outlook, Supercomputing 2016, November 14, 2016,

The long-awaited Burst Buffer technology is now being deployed on major supercomputing systems, including new machines at NERSC, LANL, ANL, and KAUST. In this BOF, we discuss early experience with Burst Buffers from both a systems and a user’s perspective, including challenges faced and perspectives for future development. Short presentations from early adopters will be followed by general discussion with the audience. We hope that this BOF will attract interest and participation from end-users and software/hardware developers. 

See www.burstbuffer.org for presentations. 

T. Barnes, B. Cook, J. Deslippe, D. Doerfler, B. Friesen, Y.H. He, T. Kurth, T. Koskela, M. Lobet, T. Malas, L. Oliker, A. Ovsyannikov, A. Sarje, J.-L. Vay, H. Vincenti, S. Williams, P. Carrier, N. Wichmann, M. Wagner, P. Kent, C. Kerr, J. Dennis, "Evaluating and Optimizing the NERSC Workload on Knights Landing", PMBS 2016: 7th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems. Supercomputing Conference, Salt Lake City, UT, USA, IEEE, November 13, 2016, LBNL LBNL-1006681, doi: 10.1109/PMBS.2016.010

Shane Snyder, Philip Carns, Kevin Harms, Robert Ross, Glenn K. Lockwood, Nicholas J. Wright, "Modular HPC I/O characterization with Darshan", Proceedings of the 5th Workshop on Extreme-Scale Programming Tools (ESPT'16), Salt Lake City, UT, November 13, 2016, 9-17, doi: 10.1109/ESPT.2016.9

Contemporary high-performance computing (HPC) applications encompass a broad range of distinct I/O strategies and are often executed on a number of different compute platforms in their lifetime. These large-scale HPC platforms employ increasingly complex I/O subsystems to provide a suitable level of I/O performance to applications. Tuning I/O workloads for such a system is nontrivial, and the results generally are not portable to other HPC systems. I/O profiling tools can help to address this challenge, but most existing tools only instrument specific components within the I/O subsystem that provide a limited perspective on I/O performance. The increasing diversity of scientific applications and computing platforms calls for greater flexibility and scope in I/O characterization.

In this work, we consider how the I/O profiling tool Darshan can be improved to allow for more flexible, comprehensive instru- mentation of current and future HPC I/O workloads.We evaluate the performance and scalability of our design to ensure that it is lightweight enough for full-time deployment on production HPC systems. We also present two case studies illustrating how a more comprehensive instrumentation of application I/O workloads can enable insights into I/O behavior that were not previously possible. Our results indicate that Darshan’s modu- lar instrumentation methods can provide valuable feedback to both users and system administrators, while imposing negligible overheads on user applications.

Richard A. Gerber, Success Through Community, Closing Remarks at Intel HPC Developer Conference 2016, November 13, 2016,

Ritu Arora, Trung Nguyen Ba, Tiffany A. Connors, "Pecos: A scalable solution for analyzing and managing qualitative data", DataCloud '16 Proceedings of the 7th International Workshop on Data-Intensive Computing in the Cloud, November 13, 2016,

R Gerber, J Deslippe, D Doerfler, Many Cores for the Masses: Lessons Learned from Application Readiness Efforts at NERSC for the Knights Landing based Cori System, Intel HPC Developers Conference, November 12, 2016,

Carleton DeTar, Douglas Doerfler, Steven Gottlieb, Ashish Jha, Dhiraj Kalamkar, Ruizi Li, Doug Toussaint, "MILC staggered conjugate gradient performance on Intel KNL", 34th International Symposium on Lattice Field Theory (Lattice 2016), Southampton, UK, November 3, 2016,

Taylor Groves, "Characterizing and Improving Power and Performance in HPC Networks (Doctoral Showcase)", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, November 1, 2016,

Robert J. Harrison, Gregory Beylkin, Florian A. Bischoff, Justus A. Calvin, George I. Fann, Jacob Fosso-Tande, Diego Galindo, Jeff R. Hammond, Rebecca Hartman-Baker, Judith C. Hill, Jun Jia, Jakob S. Kottmann, M-J. Yvonne Ou, Laura E. Ratcliff, Matthew G. Reuter, Adam C. Richie-Halford, Nichols A. Romero, Hideo Sekino, William A. Shelton, Bryan E. Sundahl, W. Scott Thornton, Edward F. Valeev, Álvaro Vázquez-Mayagoitia, Nicholas Vence, Yukina Yokoi, "MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation", SIAM Journal on Scientific Computing, October 27, 2016, 38:S123-S142,

This Letter reports an improved search for light sterile neutrino mixing in the electron antineutrino disappearance channel with the full configuration of the Daya Bay Reactor Neutrino Experiment. With an additional 404 days of data collected in eight antineutrino detectors, this search benefits from 3.6 times the statistics available to the previous publication, as well as from improvements in energy calibration and background reduction. A relative comparison of the rate and energy spectrum of reactor antineutrinos in the three experimental halls yields no evidence of sterile neutrino mixing in the 2×104|Δm241|0.3eV2 mass range. The resulting limits on sin22θ14 are improved by approx imately a factor of 2 over previous results and constitute the most stringent constraints to date in the |Δm241|0.2eV2 region.

Daya Bay and MINOS Collaborations, P. Adamson et al., "Limits on Active to Sterile Neutrino Oscillations from Disappearance Searches in the MINOS, Daya Bay, and Bugey-3 Experiments", Physical Review Letters, October 7, 2016,

Searches for a light sterile neutrino have been performed independently by the MINOS and the Daya Bay experiments using the muon (anti)neutrino and electron antineutrino disappearance channels, respectively. In this Letter, results from both experiments are combined with those from the Bugey-3 reactor neutrino experiment to constrain oscillations into light sterile neutrinos. The three experiments are sensitive to complementary regions of parameter space, enabling the combined analysis to probe regions allowed by the Liquid Scintillator Neutrino Detector (LSND) and MiniBooNE experiments in a minimally extended four-neutrino flavor framework. Stringent limits on sin22θμe are set over 6 orders of magnitude in the sterile mass-squared splitting Δm241. The sterile-neutrino mixing phase space allowed by the LSND and MiniBooNE experiments is excluded for Δm241<0.8eV2 at 95%CLs.

Douglas Doerfler, Jack Deslippe, Samuel Williams, Leonid Oliker, Brandon Cook, Thorsten Kurth, Mathieu Lobet, Tareq M. Malas, Jean-Luc Vay, Henri Vincenti, "Applying the Roofline Performance Model to the Intel Xeon Phi Knights Landing Processor", High Performance Computing. ISC High Performance 2016. Lecture Notes in Computer Science, Volume 9945, October 6, 2016, doi: 10.1007/978-3-319-46079-6_24

Brandon Cook, Pieter Maris, Meiyue Shao, Nathan Wichmann, Marcus Wagner, John O'Neill, Thanh Phung, Gaurav Bansal, "High Performance Optimizations for Nuclear Physics Code MFDn on KNL", ISC Workshops, October 6, 2016, doi: 10.1007/978-3-319-46079-6_26

Zhaoyi Meng, Alice Koniges, Yun (Helen) He, Samuel Williams, Thorsten Kurth, Brandon Cook, Jack Deslippe, Andrea L. Bertozzi, OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms, IWOMP 2016, October 6, 2016,

Thorsten Kurth, Balint Joo, Dhiraj Kalamkar, Karthikeyan Vaidyanathan, Aaron Walden, "Optimizing Wilson-Dirac operator and linear solvers for Intel KNL", Springer Lecture Notes in Computer Science, October 6, 2016,

Tareq Malas, Thorsten Kurth, Jack Deslippe, "Optimization of the sparse matrix-vector products of an IDR Krylov iterative solver in EMGeo for the Intel KNL manycore processor", Springer Lecture Notes in Computer Science, October 6, 2016,

Jack, Deslippe, Felipe H. da Jornada, Derek Vigil-Fowler, Taylor Barnes, Nathan Wichmann, Karthik Raman, Ruchira Sasanka, Steven G. Louie, "Optimizing Excited-State Electronic-Structure Codes for Intel Knights Landing: A Case Study on the BerkeleyGW Software.", Springer Lecture Notes in Computer Science (ISC 2016), Springer International Publishing, October 6, 2016, 402,

Alice Koniges, Brandon Cook, Jack Deslippe, Thorston Kurth, Hongzhang Shan, MPI usage at NERSC: Present and Future, EuroMPI 2016, September 26, 2016,

Alice Koniges, Brandon Cook, Jack Deslippe, Thorston Kurth, Hongzhang Shan, "MPI usage at NERSC: Present and Future", EuroMPI 2016, Edinburgh, Scotland, UK, September 26, 2016,

Alice Koniges, Brandon Cook, Jack Deslippe, Thorston Kurth, Hongzhang Shan, "MPI usage at NERSC: Present and Future", EuroMPI 2016, September 26, 2016,

Richard A Gerber, Using NERSC for Research in High Energy Physics Theory, Particle Physics Generators @ Fermilab, September 22, 2016,

Yun (Helen) He, Process and Thread Affinity with MPI/OpenMP on KNL, Intel Xeon Phi User Group (IXPUG) 2016 Annual US Meeting, September 22, 2016,

IXPUG2016 event web page: https://www.ixpug.org/events/ixpug-2016

Andrey Ovsyannikov, Enabling high-performance simulation of subsurface flows with Chombo-Crunch on Intel Xeon Phi, 2016 IXPUG US Annual Meeting, September 21, 2016,

Zhaoyi Meng, Alice Koniges, Yun (Helen) He, Samuel Williams, Thorsten Kurth, Brandon Cook, Jack Deslippe, Andrea L. Bertozzi, "OpenMP Parallelization and Optimization of Graph-Based Machine Learning Algorithms", Lecture Notes in Computer Science, Springer, 2016, 9903:17-31, doi: 10.1007/978-3-319-45550-1_2

Richard A Gerber, Application Readiness for KNL at NERSC, IXPUG 2016 Conference, September 20, 2016,

Richard A Gerber, IXPUG 2016 Welcome, IXPUG 2016 Conference, September 19, 2016,

Yun (Helen) He, NERSC Early KNL Experiences, NCAR Multi-core 6 Workshop, Boulder, CO., September 13, 2016,

Multi-Core Workshop event web page: https://www2.cisl.ucar.edu/events/workshops/multicore-workshop/2016/2016-agenda

Richard A Gerber, September 2016 NERSC Update, September 7, 2016,

Robert Leland, Mahesh Rajan, Michael A. Heroux, Douglas W. Doerfler, "Performance, Efficiency, and Effectiveness of Supercomputers", Sandia National Laboratories, Sandia Report SAND2016-3730, September 2016,

Lisa Gerhardt, Jeff Porter, Nick Balthaser, Lessons Learned from Running an HPSS Globus Endpoint, 2016 HPSS User Forum, September 1, 2016,

The NERSC division of LBNL has been running HPSS in production since 1998. The archive is quite popular with roughly 100TB IO every day from the ~6000 scientists that use the NERSC facility. We maintain a Globus-HPSS endpoint that transfers over 1PB / month of data into and out of HPSS. Getting Globus and HPSS to mesh well can be challenging. This talk gives an overview of some of the lessons learned.

Matthew GF Dosanjh, Taylor Groves, Ryan E Grant, Ron Brightwell, Patrick G Bridges, "RMA-MT: a benchmark suite for assessing MPI multi-threaded RMA performance", Cluster, Cloud and Grid Computing (CCGrid), 2016 16th IEEE/ACM International Symposium on, IEEE, September 1, 2016, 550--559,

Friesen, B., Almgren, A., Lukić, Z., Weber, G., Morozov, D., Day, M., "In situ and in-transit analysis of cosmological simulations", Computational Astrophysics and Cosmology, edited by Simon Portegies Zwart, August 26, 2016, 3:1-18, LBNL LBNL-1006104, doi: 10.1186/s40668-016-0017-2

Modern cosmological simulations have reached the trillion-element scale, rendering data storage and subsequent analysis formidable tasks. To address this circumstance, we present a new MPI-parallel approach for analysis of simulation data while the simulation runs, as an alternative to the traditional workflow consisting of periodically saving large data sets to disk for subsequent `offline' analysis. We demonstrate this approach in the compressible gasdynamics/N-body code Nyx, a hybrid MPI+OpenMP code based on the BoxLib framework, used for large-scale cosmological simulations. We have enabled on-the-fly workflows in two different ways: one is a straightforward approach consisting of all MPI processes periodically halting the main simulation and analyzing each component of data that they own ('in situ'). The other consists of partitioning processes into disjoint MPI groups, with one performing the simulation and periodically sending data to the other 'sidecar' group, which post-processes it while the simulation continues ('in-transit'). The two groups execute their tasks asynchronously, stopping only to synchronize when a new set of simulation data needs to be analyzed. For both the in situ and in-transit approaches, we experiment with two different analysis suites with distinct performance behavior: one which finds dark matter halos in the simulation using merge trees to calculate the mass contained within iso-density contours, and another which calculates probability distribution functions and power spectra of various fields in the simulation. Both are common analysis tasks for cosmology, and both result in summary statistics significantly smaller than the original data set. We study the behavior of each type of analysis in each workflow in order to determine the optimal configuration for the different data analysis algorithms.

Andrey Ovsyannikov, Science with the Burst Buffer, NERSC Data Day, August 22, 2016,

Amy Nicholson, Evan Berkowitz, Chia Cheng Chang, Kate Clark, Balint Joo, Thorsten Kurth, Enrico Rinaldi, Brian Tiburzi, Pavlos Varnas, Andre Walker-Loud, "Neutrinoless double beta decay from Lattice QCD", PoSLAT, August 16, 2016,

Daya Bay Collaboration, F.P. An et al., "Study of the wave packet treatment of neutrino oscillation at Daya Bay,", The European Physical Journal C, August 11, 2016,

The disappearance of reactor ν¯e observed by the Daya Bay experiment is examined in the framework of a model in which the neutrino is described by a wave packet with a relative intrinsic momentum dispersion σrel. Three pairs of nuclear reactors and eight antineutrino detectors, each with good energy resolution, distributed among three experimental halls, supply a high-statistics sample of ν¯e acquired at nine different baselines. This provides a unique platform to test the effects which arise from the wave packet treatment of neutrino oscillation. The modified survival probability formula was used to fit Daya Bay data, providing the first experimental limits: 2.381017<σrel<0.23. Treating the dimensions of the reactor cores and detectors as constraints, the limits are improved: 1014σrel<0.23, and an upper limit of σrel<0.20 is obtained. All limits correspond to a 95\% C.L. Furthermore, the effect due to the wave packet nature of neutrino oscillation is found to be insignificant for reactor antineutrinos detected by the Daya Bay experiment thus ensuring an unbiased measurement of the oscillation parameters sin22θ13 and Δm232 within the plane wave model.

Jeremy Kemp, Alice Koniges, Yun (Helen) He, and Barbara Chapman, "Advanced Programming Model Constructs Using Tasking on the Latest NERSC (Knights Landing) Hardware", CS Summer Student Poster Session, August 4, 2016,

Ahana Roy Choudhury, Yun (Helen) He, and Alice Koniges, "Advanced OpenMP Constructs, Tuning, and Tools at NERSC", CS Summer Student Poster Session, August 4, 2016,

Nigel Tan, Mathieu Lobet, Alice Koniges, Henri Vicenti, Dong Li, Jean-Luc Vay, "Improving Cache Performance in PICSAR’s Maxwell’s Equations Solver through Field Tiling", SC Summer Student Poster Session, August 4, 2016,

MeiYue Shao, Lin Lin, Chao Yang, Fang Liu, Felipe H. Da Jornada, Jack Deslippe, Steven G. Louie, "Low rank approximation in G0W0 calculations.", Science China Mathematics, August 1, 2016,

Dilworth Y. Parkinson, Keith Beattie, Xian Chen, Joaquin Correa, Eli Dart, Benedikt J. Daurer, Jack R. Deslippe, Alexander Hexemer, Harinarayan Krishnan, Alastair A. MacDowell, Filipe R. N. C. Maia, Stefano Marchesini, Howard A. Padmore, Simon J. Patton, Talita Perciano, James A. Sethian, David Shapiro, Rune Stromsness, Nobumichi Tamura, Brian L. Tierney, Craig E. Tull, Daniela Ushizima, "Real-time data-intensive computing.", AIP Conference Proceedings, July 2016, 1741,

Debbie Bard, Using Containers and HPC to Solve the Mysteries of the Universe, DockerCon 2016, June 27, 2016,

Container technology is being used to answer some of the biggest questions in science today - what is the Universe made of? How has it evolved over time? Scientists use vast quantities of data to study these questions, and analyzing this data requires Big Data solutions on high performance computing resources. In this talk we discuss why containers are being deployed on the Cori supercomputer at NERSC (the National Energy Research Scientific Computing center) to answer fundamental scientific questions. We will give examples of the use of Docker in simulating complex physical processes and analyzing experimental data in fields as diverse as particle physics, cosmology, astronomy, genomics and material science. We will demonstrate how container technology is being used to facilitate access to scientific computing resources by scientists from around the globe. Finally, we will discuss how container technology has the potential to revolutionize scientific publishing, and could solve the problem of scientific reproducibility.

Richard A Gerber, Application Performance on Intel Xeon Phi - Being Prepared for KNL and Beyond, ISC 2016 Workshop Introduction, June 23, 2016,

R Li, C DeTar, D Doerfler, S Gottlieb, A Jha, D Kalamakar, D Toussaint, Porting the MIMD Lattice Computation (MILC) Code to the Intel Xeon Phi Knights Landing Processor, ISC High Performance 2016 International Workshops: Application Performance on Intel Xeon Phi – Being Prepared for KNL & Beyond, June 23, 2016,

Richard A Gerber, Cori: Enabling World-Changing Science, Intel Collaboration Hub @ ISC 2016, June 22, 2016,

Gerber, Richard A., et al., "Application Performance on Intel Xeon Phi–Being Prepared for KNL and Beyond", High Performance Computing: ISC High Performance 2016 International Workshops, ExaComm, E-MuCoCoS, HPC-IODC, IXPUG, IWOPH, P3MA, VHPC, Frankfurt, Germany, June 19–23, 2016, Revised Selected Papers. Vol. 9945. Springer, 2016., June 19, 2016,

Gerber, Richard A., et al. "Application Performance on Intel Xeon Phi–Being Prepared for KNL and Beyond." High Performance Computing: ISC High Performance 2016 International Workshops, ExaComm, E-MuCoCoS, HPC-IODC, IXPUG, IWOPH, P3MA, VHPC, Frankfurt, Germany, June 19–23, 2016, Revised Selected Papers. Vol. 9945. Springer, 2016.

Richard A Gerber, NERSC Allocations 2016-17, June 14, 2016,

Yun (Helen) He, Running Jobs on Cori with SLURM, Cori Phase 1 Training, Berkeley, CA, June 14, 2016,

Taylor Groves, Improving Power and Performance in HPC Networks, AMD Research - Austin, June 10, 2016,

Richard A Gerber, High Performance Computing and NERSC for High School Students, June 6, 2016,

Shane Canon, Doug Jacobsen, "Shifter: Containers for HPC", Cray User Group, London, England, May 13, 2016,

Container-based computed is rapidly changing the way software is developed, tested, and deployed. This paper builds on previously presented work on a prototype framework for running containers on HPC platforms. We will present a detailed overview of the design and implementation of Shifter, which in partnership with Cray has extended on the early prototype concepts and is now in production at NERSC. Shifter enables end users to execute containers using images constructed from various methods including the popular Docker-based ecosystem. We will discuss some of the improvements over the initial prototype including an improved image manager, integration with SLURM, integration with the burst buffer, and user controllable volume mounts. In addition, we will discuss lessons learned, performance results, and real-world use cases of Shifter in action. We will also discuss the potential role of containers in scientific and technical computing including how they complement the scientific process. We will conclude with a discussion about the future directions of Shifter.

Michael Ringenburg, Shuxia Zhang, Kristyn
Maschhoff, Bill Sparks, Evan Racah, Prabhat,
"Characterizing the Performance of Analytics Workloads on the Cray XC40", Cray User Group, May 13, 2016,

Jialin Liu, Evan Racah, Quincey Koziol, Richard Shane Canon,
Alex Gittens, Lisa Gerhardt, Suren Byna, Mike F. Ringenburg, Prabhat,
"H5Spark: Bridging the I/O Gap between Spark and Scientific Data Formats on HPC Systems", Cray User Group, May 13, 2016,

Tina Declerck, Katie Antypas, Deborah Bard, Wahid Bhimji, Shane Canon, Shreyas Cholia, Helen (Yun) He, Douglas Jacobsen, Prabhat, Nicholas J. Wright, "Cori - A System to Support Data-Intensive Computing", Cray User Group Meeting 2016, London, England, May 2016,

Tina Declerck, Katie Antypas, Deborah Bard, Wahid Bhimji, Shane Canon, Shreyas Cholia, Helen (Yun) He, Douglas Jacobsen, Prabhat, Nicholas J. Wright, Cori - A System to Support Data-Intensive Computing, Cray User Group Meeting 2016, London, England, May 12, 2016,

Douglas M. Jacobsen, James F. Botts, and Yun (Helen) He, "SLURM. Our Way.", Cray User Group Meeting 2016, London, England, May 2016,

Douglas M. Jacobsen, James F. Botts, and Yun (Helen) He, SLURM. Our Way., Cray User Group Meeting 2016. London, England., May 12, 2016,

Colin A. MacLean, "Maintaining Large Software Stacks in a Cray Ecosystem with Gentoo Portage", Cray User Group, London, England, 2016,

Wahid Bhimji, Debbie Bard, Melissa Romanus, David Paul, Andrey Ovsyannikov, Brian Friesen, Matt Bryson, Joaquin Correa, Glenn K Lockwood, Vakho Tsulaia, others, "Accelerating science with the NERSC burst buffer early user program", Cray User Group, May 11, 2016, LBNL LBNL-1005736,

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 700 different projects spanning a wide variety of scientific computing applications. The use-cases of the Burst Buffer at NERSC are therefore also considerable and diverse. We describe here performance measurements and lessons learned from the Burst Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its capability to enable new scientific advancements. To the best of our knowledge this is the first time a Burst Buffer has been stressed at scale by diverse, real user workloads and therefore these lessons will be of considerable benefit to shaping the developing use of Burst Buffers at HPC centers.

Zhengji Zhao, and Martijn Marsman, "Estimating the Performance Impact of the MCDRAM on KNL Using Dual-Socket Ivy Bridge nodes on Cray XC30", https://cug.org/, London, UK, May 11, 2016,

Ashley Barker, Chris Fusion, Richard Gerber, Yun (Helen) He, Frank Indiviglio, Best Practices for Managing HPC User Documentation and Communication, Cray User Group Meeting 2016, London, England, May 10, 2016,

K.S. Hemmert, M. Rajan, R. Hoekstra, M.W. Glass, S.D. Hammond, S. Dawson, M. Vigil, D. Grunau, J. Lujan, D. Morton, H. Nam, P. Peltz Jr., A. Torrez, C. Wright, "Trinity: Architecture and Early Experience", Proceedings of the Cray Users Group Conference, London, UK, May 2016,

Annette Greiner, Evan Racah, Shane Canon, Jialin Liu, Yunjie Liu, Debbie Bard, Lisa Gerhardt, Rollin Thomas, Shreyas Cholia, Jeff Porter, Wahid Bhimji, Quincey Koziol, Prabhat, "Data-Intensive Supercomputing for Science", Berkeley Institute for Data Science (BIDS) Data Science Faire, May 3, 2016,

Review of current DAS activities for a non-NERSC audience.

Debbie Bard, Accelerating Science with the NERSC Burst Buffer Early User Program, Salishan Conference on High-Speed Computing, April 28, 2016,

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 750 different projects spanning a wide variety of scientific applications, including climate modeling, combustion, fusion, astrophysics, computational biology, and many more. The potential applications of the Burst Buffer at NERSC are therefore also considerable and diverse.

I will discuss the Burst Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its different capabilities to enable new scientific advancements. I will present details of the program, in-depth performance results and lessons-learnt from highlighted projects.

F. P. An, et al. (Daya Bay Collaboration), "New measurement of θ13 via neutron capture on hydrogen at Daya Bay", Phys. Rev. D 93, 072011, April 21, 2016, doi: 10.1103/PhysRevD.93.072011

Andrey Ovsyannikov, Chombo-Crunch and VisIt for Carbon Sequestration and In-Transit Data Analysis Using Burst Buffers, DOE Centers of Excellence Performance Portability Meeting, April 21, 2016,

Mostofa Patwary, Nadathur Satish, Narayanan Sundaram, Jialin Liu, Peter Sadowski, Evan Racah, Suren Byna, Craig Tull, Wahid Bhimji, Prabhat, Pradeep Dubey, "PANDA: Extreme Scale Parallel K-Nearest Neighbor on Distributed Architectures", IPDPS 2016, April 5, 2016,

Taylor Groves, Ryan Grant, Dorian Arnold, "Network-induced Memory Contention.", Salishan Conference on High Speed Computing, Gleneden Beach, OR,, April 1, 2016,

Salman Habib, Robert Roser (HEP Leads), Richard Gerber, Katie Antypas, Katherine Riley, Tim Williams, Jack Wells, Tjerk Straatsma (ASCR Leads), A. Almgren, J. Amundson, S. Bailey, D. Bard, K. Bloom, B. Bockelman, A. Borgland, J. Borrill, R. Boughezal, R. Brower, B. Cowan, H. Finkel, N. Frontiere, S. Fuess, L. Ge, N. Gnedin, S. Gottlieb, O. Gutsche, T. Han, K. Heitmann, S. Hoeche, K. Ko, O. Kononenko, T. LeCompte, Z. Li, Z. Lukic, W. Mori, P. Nugent, C.-K. Ng, G. Oleynik, B. O'Shea, N. Padmanabhan, D. Petravick, F.J. Petriello, J. Power, J. Qiang, L. Reina, T.J. Rizzo, R. Ryne, M. Schram, P. Spentzouris, D. Toussaint, J.-L. Vay, B. Viren, F. Wurthwein, L. Xiao, "ASCR/HEP Exascale Requirements Review Report", arXiv:1603.09303 [physics.comp-ph], March 31, 2016,

Clayton Bagwell, Richard Gerber, NUG 2016 Business Meeting: Allocations, NUG Business Meeting presentation, March 24, 2016,

NUG (NERSC Users Group) Business meeting: Allocations

Rebecca J. Hartman-Baker, Past, Present, and Future Parallel Programming Paradigms, March 24, 2016,

Yun (Helen) He, Wahid Bhimji, Cori: User Update, NERSC User Group Meeting, March 24, 2016,

HBM Tools and Applications in VASP, http://www.nersc.gov/users/NUG/annual-meetings/nug-2016/, March 23, 2016,

Yun (Helen) He, Advanced OpenMP and CESM Case Study, NERSC User Group Annual Meeting 2016, Berkeley, CA, March 23, 2016,

Clayton Bagwell, NUG 2016 New User Training - Accounts & Allocations, NUG New User Training presentation, March 21, 2016,

NUG (NERSC Users Group) New User Training; Accounts and Allocations

Yun (Helen) He, Submitting and Running Jobs, NERSC User Group Meeting 2016, Berkeley, CA, March 21, 2016,

Michael A. Purvis, Alexander Schafgans, Daniel J. W. Brown, Igor Fomenkov, Rob Rafac, Josh Brown, Yezheng Tao, Slava Rokitski, Mathew Abraham, Mike Vargas, Spencer Rich, Ted Taylor, David Brandt, Alberto Pirati, Aaron Fisher, Howard Scott, Alice Koniges, David Eder, Scott Wilks, Anthony Link, Steven Langer, "Advancements in predictive plasma formation modeling", Proc. SPIE 9776, Extreme Ultraviolet (EUV) Lithography VII, 97760K (March 18, 2016); doi:10.1117/12.2221991, March 18, 2016,

This modeling is performed to advance the rate of learning about optimal EUV generation for laser produced plasmas and to provide insights where experimental results are not currently available. The goal is to identify key physical processes necessary for an accurate and predictive model capable of simulating a wide range of conditions. This modeling will help to drive source performance scaling in support of the EUV Lithography roadmap. The model simulates pre-pulse laser interaction with the tin droplet and follows the droplet expansion into the main pulse target zone. Next, the interaction of the expanded droplet with the main laser pulse is simulated. We demonstrate the predictive nature of the code and provide comparison with experimental results. ALE-AMR and other codes are used for the modeling.

Clayton Bagwell, Richard Gerber, NERSC Brown Bag: Allocations, NERSC Brown Bag presentation, March 17, 2016,

Brown Bag presentation to NERSC staff on how Allocations work and the new scavenger queues.

Yun (Helen) He, Climate Applications Support at NERSC, NERSC Climate PIs Telecon, March 16, 2016,

Jesse Livezey, Gopala Anumanchipalli, Brian Cheung, Prabhat, Michael DeWeese, Edward Chang, Kristofer Bouchard, "Deep networks reveal the structure of motor control in sensorimotor cortex during speech production", CoSyne 2016, March 1, 2016,

Richard A Gerber, Application Preparedness for Next Generation Computational Systems and Integration with Data-Intensive Workflows, February 26, 2016,

Richard A. Gerber, NERSC Science and Strategic Results, February 16, 2016,

SV Venkatakrishnan, K Aditya Mohan, Keith Beattie, Joaquin Correa, Eli Dart, Jack R Deslippe, Alexander Hexemer, Harinarayan Krishnan, Alastair A MacDowell, Stefano Marchesini, Simon J Patton, Talita Perciano, James A Sethian, Rune Stromsness, Brian L Tierney, Craig E Tull, Daniela Ushizima, Dilworth Y Parkinson, "Making Advanced Scientific Algorithms and Big Scientific Data Management More Accessible", Electronic Imaging, February 14, 2016, 2016 Is.:1,

Daya Bay Collaboration: F.P. An, A.B. Balantekin, H.R. Band, W. Beriguete, et. al,, "Measurement of the Reactor Antineutrino Flux and Spectrum at Daya Bay", Journal, February 11, 2016, doi: 10.1016/j.nuclphysbps.2015.09.298

Yun (Helen) He, Cori: User Services Report, NERSC/Cray Quarterly Meeting, February 10, 2016,

Smith, M., Sullivan, M., D'Andrea, C. B., Castander, F. J., Casas, R., Prajs, S., Papadopoulos, A., Nichol, R. C., Karpenka, N. V., Bernard, S. R., Brown, P., Cartier, R., Cooke, J., Curtin, C., Davis, T. M., Finley, D. A., Foley, R. J., Gal-Yam, A., Goldstein, D. A., González-Gaitán, S., Gupta, R. R., Howell, D. A., Inserra, C., Kessler, R., Lidman, C., Marriner, J., Nugent, P., Pritchard, T. A., Sako, M., Smartt, S., Smith, R. C., Spinka, H., Thomas, R. C., Wolf, R. C., Zenteno, A., Abbott, T. M. C., Benoit-Lévy, A., Bertin, E., Brooks, D., Buckley-Geer, E., Carnero Rosell, A., Carrasco Kind, M., Carretero, J., Crocce, M., Cunha, C. E., da Costa, L. N., Desai, S., Diehl, H. T., Doel, P., Estrada, J., Evrard, A. E., Flaugher, B., Fosalba, P., Frieman, J., Gerdes, D. W., Gruen, D., Gruendl, R. A., James, D. J., Kuehn, K., Kuropatkin, N., Lahav, O., Li, T. S., Marshall, J. L., Martini, P., Miller, C. J., Miquel, R., Nord, B., Ogando, R., Plazas, A. A., Reil, K., Romer, A. K., Roodman, A., Rykoff, E. S., Sanchez, E., Scarpine, V., Schubnell, M., Sevilla-Noarbe, I., Soares-Santos, M., Sobreira, F., Suchyta, E., Swanson, M. E. C., Tarle, G., Walker, A. R., Wester, W., "DES14X3taz: A Type I Superluminous Supernova Showing a Luminous, Rapidly Cooling Initial Pre-peak Bump", The Astrophysical Journal Letters, 2016, doi: 10.3847/2041-8205/818/1/L8

We present DES14X3taz, a new hydrogen-poor superluminous supernova (SLSN-I) discovered by the Dark Energy Survey (DES) supernova program, with additional photometric data provided by the Survey Using DECam for Superluminous Supernovae. Spectra obtained using Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy on the Gran Telescopio CANARIAS show DES14X3taz is an SLSN-I at z = 0.608. Multi-color photometry reveals a double-peaked light curve: a blue and relatively bright initial peak that fades rapidly prior to the slower rise of the main light curve. Our multi-color photometry allows us, for the first time, to show that the initial peak cools from 22,000 to 8000 K over 15 rest-frame days, and is faster and brighter than any published core-collapse supernova, reaching 30% of the bolometric luminosity of the main peak. No physical 56Ni-powered model can fit this initial peak. We show that a shock-cooling model followed by a magnetar driving the second phase of the light curve can adequately explain the entire light curve of DES14X3taz. Models involving the shock-cooling of extended circumstellar material at a distance of ≃400 {\text{}}{R}⊙ are preferred over the cooling of shock-heated surface layers of a stellar envelope. We compare DES14X3taz to the few double-peaked SLSN-I events in the literature. Although the rise times and characteristics of these initial peaks differ, there exists the tantalizing possibility that they can be explained by one physical interpretation.

Alex Gittens, Jey Kottalam, Jiyan Yang, Michael F Ringenburg, Jatin Chhugani, Evan Racah, Mohitdeep Singh, Yushu Yao, Curt Fischer, Oliver Ruebel, Benjamin Bowen, Norman Lewis, Michael W Mahoney, Venkat Krishnamurthy, Prabhat, "A multi-platform evaluation of the randomized CX low-rank matrix factorization in Spark", The 5th International Workshop on Parallel and Distributed Computing for Large Scale Machine Learning and Big Data Analytics, IPDPS, February 1, 2016,

Grace X. Y. Zheng, Billy T. Lau, Michael Schnall-Levin, Mirna Jarosz, John M. Bell, Christopher M. Hindson, Sofia Kyriazopoulou-Panagiotopoulou, Donald A. Masquelier, Landon Merrill, Jessica M. Terry, Patrice A. Mudivarti, Paul W. Wyatt, Rajiv Bharadwaj, Anthony J. Makarewicz, Yuan Li, Phillip Belgrader, Andrew D. Price, Adam J. Lowe, Patrick Marks, Gerard M. Vurens, Paul Hardenbol, Luz Montesclaros, Melissa Luo, Lawrence Greenfield, Alexander Wong, David E. Birch, Steven W. Short, Keith P. Bjornson, Pranav Patel, Erik S. Hopmans, Christina Wood, Sukhvinder Kaur, Glenn K. Lockwood, David Stafford, Joshua P. Delaney, Indira Wu, Heather S. Ordonez, Susan M. Grimes, Stephanie Greer, Josephine Y. Lee, Kamila Belhocine, Kristina M. Giorda, William H. Heaton, Geoffrey P. McDermott, Zachary W. Bent, Francesca Meschi, Nikola O. Kondov, Ryan Wilson, Jorge A. Bernate, Shawn Gauby, Alex Kindwall, Clara Bermejo, Adrian N. Fehr, Adrian Chan, Serge Saxonov, Kevin D. Ness, Benjamin J. Hindson, Hanlee P. Ji, "Haplotyping germline and cancer genomes with high-throughput linked-read sequencing", Nature Biotechnology, February 1, 2016, 31:303-311, doi: 10.1038/nbt.3432

Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.

Parrent, J. T., Howell, D. A., Fesen, R. A., Parker, S., Bianco, F. B., Dilday, B., Sand, D., Valenti, S., Vinkó, J., Berlind, P., Challis, P., Milisavljevic, D., Sanders, N., Marion, G. H., Wheeler, J. C., Brown, P., Calkins, M. L., Friesen, B., Kirshner, R., Pritchard, T., Quimby, R., Roming, P., "Comparative analysis of SN 2012dn optical spectra: days -14 to +114", Monthly Notices of the Royal Astronomical Society, January 29, 2016, 457:3702-3723, doi: 10.1093/mnras/stw239

SN 2012dn is a super-Chandrasekhar mass candidate in a purportedly normal spiral (SAcd) galaxy, and poses a challenge for theories of type Ia supernova diversity. Here we utilize the fast and highly parametrized spectrum synthesis tool, SYNAPPS, to estimate relative expansion velocities of species inferred from optical spectra obtained with six facilities. As with previous studies of normal SN Ia, we find that both unburned carbon and intermediate-mass elements are spatially coincident within the ejecta near and below 14 000 km s−1. Although the upper limit on SN 2012dn's peak luminosity is comparable to some of the most luminous normal SN Ia, we find a progenitor mass exceeding ∼1.6 M is not strongly favoured by leading merger models since these models do not accurately predict spectroscopic observations of SN 2012dn and more normal events. In addition, a comparison of light curves and host-galaxy masses for a sample of literature and Palomar Transient Factory SN Ia reveals a diverse distribution of SN Ia subtypes where carbon-rich material remains unburned in some instances. Such events include SN 1991T, 1997br, and 1999aa where trace signatures of C III at optical wavelengths are presumably detected.

Yun (Helen) He, Cori and Edison Queues, NERSC User Group (NUG) Telecon, January 21, 2016,

Alex Gittens, Nick Cavanaugh, Karthik Kashinath, Travis O’Brien, Prabhat, Michael Mahoney, "Large-scale Parallelized EOF Computation on the CSFR Ocean Temperature Field", American Meteorological Society 2015, January 12, 2016,

Daya Bay Collaboration, "The Detector System of The Daya Bay Reactor Neutrino Experiment", edited by Daya Bay Collaboration (F P. An et al.), January 8, 2016, doi: 10.1016/j.nima.2015.11.144

T. Malas, J. Hornich, G. Hager, H. Ltaief, C. Pflaum, D. Keyes, "Optimization of an electromagnetics code with multi-core wavefront diamond blocking and multi-dimensional intra-tile parallelization", International Parallel and Distributed Processing Symposium, 2016,

Taylor Groves, Ryan E Grant, Scott Hemmer, Simon Hammond, Michael Levenhagen, Dorian C Arnold, "(SAI) Stalled, Active and Idle: Characterizing Power and Performance of Large-Scale Dragonfly Networks", Cluster Computing (CLUSTER), 2016 IEEE International Conference on, January 1, 2016, 50--59,

Taylor Groves, Ryan E Grant, Dorian Arnold, "NiMC: Characterizing and eliminating network-induced memory contention", Parallel and Distributed Processing Symposium, 2016 IEEE International, January 1, 2016, 253--262,

Meiyue Shao, H Felipe, Chao Yang, Jack Deslippe, Steven G Louie, "Structure preserving parallel algorithms for solving the Bethe–Salpeter eigenvalue problem", Linear Algebra and its Applications, January 1, 2016, 488:148,

Johannes Blaschke, Maurice Maurer, Karthik Menon, Andreas Zoettl, Holger Stark, "Phase separation and coexistence of hydrodynamically interacting microswimmers", Soft Matter, 2016, 12:9821-9831, doi: 10.1039/C6SM02042A

Ang, JA, Cook, J, Domino, SP, Glass, MW, Hammond, SD, Hemmert, KS, Heroux, Hoekstra, RJ, Laros III, JH, Lin, PT, Nam, H, Neely, R, Rodrigues, AF, Trott, CR, "Exascale Co-design Progress and Accomplishments.", "Advances in Parallel Computing series," Fox, G, Getov, V, Grandinetti, L, Joubert, G, Sterling, T (Eds.), Convergence of Big Data and High-Performance Computing, IOS Press, Amsterdam, New York, Tokyo, SAND2017-8788B, ( 2016)

Abhinav Thota, Robert Henschel, Stephen Simms, White Paper: Lustre WAN over 100Gbps, 2016,

2015

Brian Austin, Hardware Trends and Challenges the for Computational Chemistry, Pacifichem, December 18, 2015,

Uma Tumuluri, Meijun Li, Brandon Cook, Bobby Sumpter, Sheng Dai, Zili Wu, "Surface Structure Dependence of SO2 Interaction with Ceria Nanocrystals with Well-defined Surface Facets", The Journal of Physical Chemistry C, 2015,

Andy Miller, Albert Wu, Jeff Regier, Ryan Adams, Jon McAuliffe, Dustin Lang, David Schlegel, Prabhat, "A stochastic process model of quasar spectral energy distribution", NIPS 2015, December 15, 2015,

Jesse Livezey, Gopala Anumanchipalli, Brian Cheung, Prabhat, Fritz Sommer, Michael DeWeese, Kris Bouchard, Edward Chang, "Classifying spoken syllables from human sensorimotor cortex with deep networks", NIPS 2015 Workshop, December 15, 2015,

Jeff Regier, Jon McAuliffe, Prabhat, "A deep generative model for astronomical images of galaxies", NIPS 2015 Workshop, December 15, 2015,

Jasper Snoek, Oren Rippel, Kevin Swersky, Ryan Kiros, Nadathur Satish, Narayanan Sundaram, Md. Mostofa Ali Patwary, Prabhat, Ryan Adams, "Scalable Bayesian Optimization using Deep Neural Networks", Deep Learning Symposium at NIPS 2015, December 15, 2015,

Tiffany Connors, Apan Qasem, "Power-performance analysis of metaheuristic search algorithms on the GPU", 2015 Sixth International Green and Sustainable Computing Conference (IGSC), December 14, 2015,

Andrey Ovsyannikov, Brian Van Straalen, Daniel Graves, David Trebotich, "Porting Chombo-Crunch to next-generation architecture", Bay Area Scientific Computing Day, December 11, 2015,

Richard A. Gerber, Katie Antypas, Sudip Dosanjh, Jack Deslippe, Nick Wright, Jay Srinivasan, Systems Roadmap and Plans for Supporting Extreme Data Science, December 10, 2015,

Michael Wehner, Kevin Reed, Prabhat, Daithi Stone, "Inconsistencies in future changes in tropical cyclone statistics between CMIP5-class models and state of the art high resolution atmospheric models", American Geophysical Union Meeting 2015, December 9, 2015,

Prabhat, Daithi Stone, Xiaolan Wang, Michael Wehner, William D. Collins, "Detection and Attribution of Extra-Tropical Cyclone activity in CMIP-5", American Geophysical Union Meeting 2015, December 8, 2015,

Prabhat, Yunjie Liu, Evan Racah, Joaquin Correa, Amir Khosrowshahi, David Lavers, Kenneth Kunkel, Michael Wehner, William D. Collins, "Deep Learning for Climate Pattern Detection", American Geophysical Union Meeting 2015, December 8, 2015,

Yunjie Liu, Karthik Kashinath, Prabhat, Travis O’Brien, "Systematic Characterization of Cyclogenesis in High Resolution Climate Model Simulations", American Geophysical Union Meeting 2015, December 8, 2015,

"Deep Learning for Science", Prabhat, Kris Bouchard, Wahid Bhimji, Evan Racah, NERSC Science Highlight, December 8, 2015,

Alice Koniges, Research on the Path to Exascale at NERSC, Sustainable Research Pathways Workshop, December 8, 2015,

Yun (Helen) He, NERSC Systems Update, NERSC Climate PIs Telecon, December 4, 2015,

Yun (Helen) He, NERSC Climate Applications, NERSC Climate PIs Telecon, December 4, 2015,

Baron, E., Hoeflich, P., Friesen, B., Sullivan, M., Hsiao, E., Ellis, R. S., Gal-Yam, A., Howell, D. A., Nugent, P. E., Dominguez, I., Krisciunas, K., Phillips, M. M., Suntzeff, N., Wang, L., and Thomas, R. C., "Spectral models for early time SN 2011fe observations", Monthly Notices of the Royal Astronomical Society, 2015, 454:2549, doi: 10.1093/mnras/stv1951

We use observed UV through near-IR spectra to examine whether SN 2011fe can be understood in the framework of Branch-normal Type Ia supernovae (SNe Ia) and to examine its individual peculiarities. As a benchmark, we use a delayed-detonation model with a progenitor metallicity of Z/20. We study the sensitivity of features to variations in progenitor metallicity, the outer density profile, and the distribution of radioactive nickel. The effect of metallicity variations in the progenitor have a relatively small effect on the synthetic spectra. We also find that the abundance stratification of SN 2011fe resembles closely that of a delayed-detonation model with a transition density that has been fit to other Branch-normal SNe Ia. At early times, the model photosphere is formed in material with velocities that are too high, indicating that the photosphere recedes too slowly or that SN 2011fe has a lower specific energy in the outer ≈0.1 M than does the model. We discuss several explanations for the discrepancies. Finally, we examine variations in both the spectral energy distribution and in the colours due to variations in the progenitor metallicity, which suggests that colours are only weak indicators for the progenitor metallicity, in the particular explosion model that we have studied. We do find that the flux in the U band is significantly higher at maximum light in the solar metallicity model than in the lower metallicity model and the lower metallicity model much better matches the observed spectrum.

This research investigates thermal conductivity properties of Cu/Zr alloys combined with diamond particles to form a composite that possess superior thermal conductivity. This article describes the use of a theoretical calculation and finite element analysis to compare to previously published experimental observations. Both theoretical calculations and finite element analysis indicate that experimental results cannot be explained solely by an improved interface between the matrix and diamond particles, as originally suggested. This study shows that the experimental results, theoretical calculations, and finite element analysis are in agreement when the thermal conductivity of the matrix is adjusted to compensate for the amount of zirconium lost to the interface. This finding can be used to predict the thermal conductivity of a composite material composed of a Cu/Zr matrix with diamond particles.

C. J. Yang, C. Harris, S. Young, and G. Morahan, "Adapting Genome-Wide Association Workflows for HPC Processing at Pawsey", Supercomputing Conference (SC'15), November 2015,

C.S. Daley, L. Ramakrishnan, S. Dosanjh, N.J. Wright, "Analyses of Scientific Workflows for Effective Use of Future Architectures", The 6th International Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC-15), 2015,

Tim Mattson, Alice Koniges, Simon McIntosh-Smith, Portable Programs for Heterogeneous Computing: A Hands-On Introduction, Tutorial, SC15, November 16, 2015,

Jia-An Yan, Mack A Dela Cruz, Brandon Cook, Kalman Varga, "Structural, electronic and vibrational properties of few-layer 2H-and 1T-TaSe2", Scientific Reports, 2015,

"Modeling the Impact of Thread Configuration on Power and Performance of GPUs", Supercomputing Conference (SC) 2015, November 16, 2015,

Prabhat, BD-CATS: Big Data Clustering at Trillion Particle Scale, Intel HPC Developers Conference, November 15, 2015,

Hartmut Kaiser, Steven Brandt, Alice Koniges, Thomas Heller, Sameer Shende, Bryce Lelbach, Massivley Parallel Task-Based Programming with HPX, Tutorial, SC15, November 15, 2015,

Luther Martin, and Zhengji Zhao, Optimization Strategies for Materials Science Applications on Cori: An Intel Knights Landing, Many Integrated Core Architecture, ACM Student Research Competition in SC15, (Luther Martin won a Silver Medal), http://sc15.supercomputing.org/, November 15, 2015,

C. Yang, Programming for Bioinformatics on the Supercomputer Magnus at Pawsey, 11th GeneMappers Conference, November 2015,

Colin A. MacLean, Neil C. Hong, James Prendergast, "hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets", Mol Biol Evol., November 2015, 32(11):3027-9, doi: 10.1093/molbev/msv172

"Big Science Problems, Big Data Solutions", Prabhat, O'Reilly Media article, November 10, 2015,

Prabhat, Top 10 Problems in Scientific Big Data Analytics, Invited talk at AMPLab, UC Berkeley, November 10, 2015,

"Tackling a Trillion", Prabhat, Suren Byna, Mostofa Patwary, ASCR Discovery Research Highlight, November 10, 2015,

Yun (Helen) He, SLURM Resource Manager is Coming to NERSC, NERSC User Group (NUG) Telecon, November 6, 2015,

Amy Nicholson, Evan Berkowitz, Enrico Rinaldi, Pavlos Vranas, Thorsten Kurth, Balint Joo, Mark Strother, Andre Walker-Loud, "Two-nucleon scattering in multiple partial waves", Conference, PoSLAT, November 6, 2015,

Thorsten Kurth, Evan Berkowitz, Enrico Rinaldi, Pavlos Vranas, Amy Nicholson, Mark Strother, Andre Walker-Loud, "Nuclear Parity Violation from Lattice QCD", Conference, PoSLAT, November 6, 2015,

Mostafa Patwary, Suren Byna, Nadathur Satish, Narayanan Sundaram, Zarija Lukic, Vadim Roytershteyn, Yushu Yao, Prabhat, Pradeep Dubey, "BD-CATS: Big Data Clustering at Trillion Particle Scale", SC 2015, November 3, 2015,

Shane Snyder, Phil Carns, Rob Latham, Rob Ross, Misbah Mubarak, Christopher Carothers, Babak Behzad, Huong Luu, Suren Byna, Prabhat, "Techniques for Modeling Large Scale HPC I/O workloads", SC PMBS workshop 2015, November 3, 2015,

Babak Behzad, Suren Byna, Prabhat, Marc Snir, "Pattern Driven Parallel I/O Tuning", SC 2015 PDSW Workshop, November 3, 2015,

Sean Mackesey, Prabhat, Gyorgi Buzsaki, Amir Khosrowshahi, Fritz Sommer, "A high performance computing web service for local field potential analysis", SfN Neuroscience 2015, November 3, 2015,

Alice Koniges, Jayashree Ajay Candadai, Hartmut Kaiser, Kevin Huck, Jeremy Kemp, Thomas Heller, Matthew Anderson, Andrew Lumsdaine, Adrian Serio, Michael Wolf, Bryce Adelstein Lelbach, Ron Brightwell, Thomas Sterling, "HPX Applications and Performance Adaptation", SC15, 2015,

Soyoung Jeon, Prabhat, Suren Byna, Bill Collins, Michael Wehner, "Characterization of Extreme Precipitation within Atmospheric River Events over California", Journal of Advances in Statistical Climatology, Meteorology and Oceanography, November 1, 2015,

Patrick Huck, Dan Gunter, Shreyas Cholia, Donald Winston, AT N'Diaye, Kristin Persson, "User applications driven by the community contribution framework MPContribs in the Materials Project", Concurrency and Computation: Practice and Experience, 2015,

Annette Greiner, Trent Northen, Suzanne Kosina, Richard Baran, Benjamin Bowen, Stefan Jenkins, Tami Swenson, "Seeing the Web of Microbes", Visualization in Data Science (VDS) at IEEE Vis 2015, October 26, 2015,

Michiel J van Setten, Fabio Caruso, Sahar Sharifzadeh, Xinguo Ren, Matthias Scheffler, Fang Liu, Johannes Lischner, Lin Lin, Jack R Deslippe, Steven G Louie, Chao Yang, Florian Weigend, Jeffrey B Neaton, Ferdinand Evers, Patrick Rinke, "GW 100: Benchmarking G 0 W 0 for molecular systems", Journal of chemical theory and computation, October 22, 2015, 11:5665,

Prabhat, Scientific Big Data: Challenges and Opportunities, Invited Talk at IIT Mumbai, October 20, 2015,

Yun (Helen) He, CCE/8.4.0 Beta Feedback from NERSC Users, NERSC/Cray Quarterly Meeting, October 20, 2015,

Prabhat, Scientific Big Data: Challenges and Opportunities, Invited Talk at UC Berkeley, Department of Statistics, October 15, 2015,

Prabhat, Scientific Big Data: Challenges and Opportunities, Invited Talk at Oxford University, October 10, 2015,

Kris Bouchard, Jesse Livezey, Alex Bujan, Prabhat, Sharmodeep Bhattacharyya, Fritz Sommer, Peter Denes, Eddie Chang, "Scalable Analytic Methods for Data Driven Discovery in Neuroscience", MSRI workshop on Neural Computation, October 8, 2015,

Yun (Helen) He, Nested OpenMP, NERSC User Group (NUG) Telecon, October 8, 2015,

Prabhat, Kris Bouchard, Annette Greiner, Oliver Ruebel, Peter Denes, Alex Bujan, Sean Mackesey, Jesse Livezey, Jeff Teeters, Fritz Sommer, Eddie Chang, "Supporting Experimental Neuroscience @ NERSC", MSRI workshop on Neural Computation, October 7, 2015,

Richard Grotjahn, Robert Black, Ruby Leung, Michael F. Wehner, Mathew Barlow, Mike Bosilovich, Sasha Gershunov, William Gutowski, John Gyakum, Richard W. Katz, Arun Kumar, Yun-Young Lee, Young-Kwon Lim, Christopher J. Paciorek, Prabhat, "North American Extreme Temperature Events and Related Large Scale Meteorological Patterns: Statistical Tools, Dynamics, Modeling, and Trends", Journal of Climate 2015, October 1, 2015,

Jiyan Yang, Jey Kottalam, Mohit Singh, Oliver Ruebel, Curt Fischer, Ben Bowen, Michael Mahoney, Prabhat, "Implementing Randomized Matrix Algorithms on Spark", XLDB 2015, October 1, 2015,

Babak Behzad, Suren Byna, Stefan Wild, Prabhat, Marc Snir, "Dynamic Model-driven Parallel I/O Performance Tuning", IEEE CLUSTER 2015, October 1, 2015,

Yun (Helen) He, Alice Koniges, Richard Gerber, Katie Antypas, Using OpenMP at NERSC, OpenMPCon 2015, invited talk, September 30, 2015,

D Doerfler, Understanding Application Data Movement Characteristics using Intel’s VTune Amplifier and Software Development Emulator Tools, Intel Xeon Phi Users Group (IXPUG) 2015, Annual Meeting, September 30, 2015,

Alice Koniges, Tim Mattson, Yun (Helen) He, Richard Gerber, Enabling Application Portability across HPC Platforms: An Application Perspective, OpenMPCon 2015, invited talk, September 29, 2015,

Kristopher A. Standish, Tristan M. Carland, Glenn K. Lockwood, Wayne Pfeiffer, Mahidhar Tatineni, C Chris Huang, Sarah Lamberth, Yauheniya Cherkas, Carrie Brodmerkel, Ed Jaeger, Lance Smith, Gunaretnam Rajagopal, Mark E. Curran, Nicholas J. Schork, "Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies", BMC Bioinformatics, September 2015, 16, doi: 10.1186/s12859-015-0736-4

Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads associated with NGS technologies requires care and sophistication in order to draw compelling inferences about phenotypic consequences of variation in human genomes. It has been shown that different approaches to variant calling from NGS data can lead to different conclusions. Ensuring appropriate accuracy and quality in variant calling can come at a computational cost.

We describe our experience implementing and evaluating a group-based approach to calling variants on large numbers of whole human genomes. We explore the influence of many factors that may impact the accuracy and efficiency of group-based variant calling, including group size, the biogeographical backgrounds of the individuals who have been sequenced, and the computing environment used. We make efficient use of the Gordon supercomputer cluster at the San Diego Supercomputer Center by incorporating job-packing and parallelization considerations into our workflow while calling variants on 437 whole human genomes generated as part of large association study.

We ultimately find that our workflow resulted in high-quality variant calls in a computationally efficient manner. We argue that studies like ours should motivate further investigations combining hardware-oriented advances in computing systems with algorithmic developments to tackle emerging ‘big data’ problems in biomedical research brought on by the expansion of NGS technologies.

Yun (Helen) He, Lessons Learned from Selected NESAP Applications, NCAR Multi-Core 5 Workshop 2015, September 16, 2015,

F. P. An et al. (Daya Bay Collaboration), "New Measurement of Antineutrino Oscillation with the Full Detector Configuration at Daya Bay", Phys. Rev. Lett. 115, 111802, September 11, 2015, Vol. 115, doi: http://dx.doi.org/10.1103/PhysRevLett.115.111802

We report a new measurement of electron antineutrino disappearance using the fully constructed Daya Bay Reactor Neutrino Experiment. The final two of eight antineutrino detectors were installed in the summer of 2012. Including the 404 days of data collected from October 2012 to November 2013 resulted in a total exposure of 6.9 x 10^5 GW,ton a day, a 3.6 times increase over our previous results. Improvements in energy calibration limited variations between detectors to 0.2%. Removal of six radioactive calibration sources reduced the background by a factor of 2 for the detectors in the experimental hall furthest from the reactors. Direct prediction of the antineutrino signal in the far detectors based on the measurements in the near detectors explicitly minimized the dependence of the measurement on models of reactor antineutrino emission.

"Celeste: A New Model for Cataloging the Universe", Prabhat, Jeff Regier, Jon McAuliffe, Ryan Adams, David Schlegel, NERSC Science Highlight, September 9, 2015,

Zhengji Zhao, Scott French, Jack Deslippe, Mathias Jacquelin, Brian Friesen, and Helen He, Application Readiness for NERSC Cori, Berkeley Lab CS Strategic Review 2015, September 9, 2015,

A, Bhagatwala, R. Sankaran, S. Kokjohn, J.H. Chen, "Numerical investigation of spontaneous flame propagation under RCCI conditions", Combustion and Flame, 2015,

Goldstein, D. A., D'Andrea, C. B., Fischer, J. A., Foley, R. J., Gupta, R. R., Kessler, R., Kim, A. G., Nichol, R. C., Nugent, P. E., Papadopoulos, A., Sako, M., Smith, M., Sullivan, M., Thomas, R. C., Wester, W., Wolf, R. C., Abdalla, F. B., Banerji, M., Benoit-Levy, A., Bertin, E., Brooks, D., Carnero Rosell, A., Castander, F. J., da Costa, L. N., Covarrubias, R., DePoy, D. L., Desai, S., Diehl, H. T., Doel, P., Eifler, T. F., Fausti Neto, A., Finley, D. A., Flaugher, B., Fosalba, P., Frieman, J., Gerdes, D., Gruen, D., Gruendl, R. A., James, D., Kuehn, K., Kuropatkin, N., Lahav, O., Li, T. S., Maia, M. A. G., Makler, M., March, M., Marshall, J. L., Martini, P., Merritt, K. W., Miquel, R., Nord, B., Ogando, R., Plazas, A. A., Romer, A. K., Roodman, A., Sanchez, E., Scarpine, V., Schubnell, M., Sevilla-Noarbe, I., Smith, R. C., Soares-Santos, M., Sobreira, F., Suchyta, E., Swanson, M. E. C., Tarle, G., Thaler, J., and Walker, A. R., "Automated Transient Identification in the Dark Energy Survey", The Astronomical Journal, 2015, 150:82, doi: 10.1088/0004-6256/150/3/82

We describe an algorithm for identifying point-source transients and moving objects on reference-subtracted optical images containing artifacts of processing and instrumentation. The algorithm makes use of the supervised machine learning technique known as Random Forest. We present results from its use in the Dark Energy Survey Supernova program (DES-SN), where it was trained using a sample of 898,963 signal and background events generated by the transient detection pipeline. After reprocessing the data collected during the first DES-SN observing season (2013 September through 2014 February) using the algorithm, the number of transient candidates eligible for human scanning decreased by a factor of 13.4, while only 1.0% of the artificial Type Ia supernovae (SNe) injected into search images to monitor survey efficiency were lost, most of which were very faint events. Here we characterize the algorithm’s performance in detail, and we discuss how it can inform pipeline design decisions for future time-domain imaging surveys, such as the Large Synoptic Survey Telescope and the Zwicky Transient Facility. An implementation of the algorithm and the training data used in this paper are available at at http://portal.nersc.gov/project/dessn/autoscan.

Jialin Liu, Yu Zhuang, Yong Chen, "Hierarchical Collective I/O Scheduling for High-Performance Computing", Big Data Research, September 1, 2015,

Jialin Liu, Yong Chen, Surendra Byna, "Collective Computing for Scientific Big Data Analysis", 44th International Conference on Parallel Processing Workshops (ICPPW), September 1, 2015,

Prabhat, Surendra Byna, Venkatram Vishwanath, Eli Dart, Michael Wehner, William D. Collins, "TECA: Petascale Pattern Recognition for Climate Science", CAIP 2015, August 25, 2015,

Clayton L. Bagwell, Jr., How to Submit a 2016 ERCAP Request, August 21, 2015,

Daya Bay Collaboration: F.P. An, A.B. Balantekin, H.R. Band, W. Beriguete, et. al, "The Muon System of the Daya Bay Reactor Antineutrino Experiment", Nuclear Instruments and Methods in Physics, August 20, 2015, Volume 7, doi: http://dx.doi.org/10.1016/j.nima.2014.09.070

The Daya Bay experiment consists of functionally identical antineutrino detectors immersed in pools of ultrapure water in three well-separated underground experimental halls near two nuclear reactor complexes. These pools serve both as shields against natural, low-energy radiation and as water Cherenkov detectors that efficiently detect cosmogenic muons using arrays of photomultiplier tubes. Each pool is covered by a plane of resistive plate chambers as an additional means of detecting muons. The design, construction, operation, and performance of these muon detectors are described.

Babak Behzad, Suren Byna, Stefan Wild, Prabhat and Marc Snir, "Dynamic Model-driven Parallel I/O Performance Tuning", IEEE Cluster 2015, August 1, 2015,

Paul T. Lin, Michael A. Heroux, Richard F. Barrett, Alan B. Williams, "Assessing a mini-application as a performance proxy for a finite element method engineering application", Concurrency and Computation: Practice and Experience, July 30, 2015, 27:5374–5389, doi: 10.1002/cpe.3587

Glenn K. Lockwood, Rick Wagner, Mahidhar Tatineni, "Storage utilization in the long tail of science", Proceedings of the 2015 XSEDE Conference, July 26, 2015, doi: 10.1145/2792745.2792777

 

The increasing expansion of computations in non-traditional domain sciences has resulted in an increasing demand for research cyberinfrastructure that is suitable for small- and mid-scale job sizes. The computational aspects of these emerging communities are coming into focus and being addressed through the deployment of several new XSEDE resources that feature easy on-ramps, customizable software environments through virtualization, and interconnects optimized for jobs that only use hundreds or thousands of cores; however, the data storage requirements for these emerging communities remains much less well characterized.

To this end, we examined the distribution of file sizes on two of the Lustre file systems within the Data Oasis storage system at the San Diego Supercomputer Center (SDSC). We found that there is a very strong preference for small files among SDSC's users, with 90% of all files being less than 2 MB in size. Furthermore, 50% of all file system capacity is consumed by files under 2 GB in size, and these distributions are consistent on both scratch and projects storage file systems. Because parallel file systems like Lustre and GPFS are optimized for parallel IO to large, widestripe files, these findings suggest that parallel file systems may not be the most suitable storage solutions when designing cyberinfrastructure to meet the needs of emerging communities.

 

Yun (Helen) He and CESM MG2 Team, NESAP CESM MG2 Update, NERSC/Cray Quarterly Meeting, July 22, 2015,

Yun (Helen) He and XGC1 Team., NESAP XGC1 Dungeon Update, NERSC/Cray Quarterly Meeting, July 22, 2015,

"‘Data Deluge’ Pushes Mass Spec Imaging to New Heights", Prabhat, Ben Bowen, Oliver Ruebel, Michael Mahoney, NERSC Science Highlight, July 15, 2015,

R. Jefferson Porter, RNC Computing, DOE NP Office Heavy-Ion Program Review, July 13, 2015,

Jasper Snoek, Oren Rippel, Kevin Swersky, Ryan Kiros, Nadathur Satish, Narayanan Sundaram, Md. Mostofa Ali Patwary, Prabhat, Ryan Adams, "Scalable Bayesian Optimization using Deep Neural Networks", ICML 2015, July 7, 2015,

Jialin Liu, Yong Chen, "Segmented In-Advance Computing for Fast Scientific Discovery", Transactions on Cloud Computing, 2015,

A. Bhagatwala, Z. Luo, H. Shen, J.A. Sutton, T. Lu, J.H. Chen, "Numerical and experimental investigation of turbulent DME jet flames", Proceedings of the Combustion Institute, 2015,

A. Krisman, E.R. Hawkes, M. Talei, A. Bhagatwala, J.H. Chen, "Polybrachial structures in dimethyl ether edge-flames at NTC conditions", Proceedings of the Combustion Institute, 2015,

The fabrication, testing and modeling of thermal annealed pyrolytic graphite (TPG) encapsulated heat spreaders was explored for potential use in the cooling of microelectronic devices. The 60 mm diameter, 5 mm thick heat spreaders were created using field-assisted sintering technology (FAST). The TPG encapsulated heat spreaders were compared to their simple aluminum and copper versions through both experimental measurements and numerical calculations. The results show that TPG encapsulated heat spreaders yield lower and more uniform surface temperatures when exposed to identical heating conditions. Heat spreaders such as these should be considered for cooling the next generation of high power density microelectronic devices.

J.-L. Vay, E. Esarey, A. Koniges, J. Barnard, A. Friedman, D. Grote, Predictive Community Computational Tools for Virtual Plasma Science Experiments, Frontiers of Plasma Science Workshops - Town Hall, June 30, 2015,

J. Park, M. Smelyanskiy, K. Vaidyanathan, A. Heinecke, D Kalamkar, M Patwary, V. Pirogov, P. Dubey, X. Liu, C. Rosales, C. Mazauric, C. Daley, "Optimizations in a high-performance conjugate gradient benchmark for IA-based multi- and many-core processors", International Journal of High Performance Computing Applications, 2015, doi: 10.1177/1094342015593157

Brian Austin, Eric Roman, Xiaoye Sherry Li, "Resilient Matrix Multiplication of Hierarchical Semi-Separable Matrices", Proceedings of the 5th Workshop on Fault Tolerance for HPC at eXtreme Scale, Portland, OR, June 15, 2015,

Huong Luu, Marianne Winslett, William Gropp, Kevin Harms, Phil Carns, Robert Ross, Yushu Yao, Suren Byna, Prabhat, "A Multi-platform Study of I/O Behavior on Petascale Supercomputers", HPDC 2015, June 9, 2015,

Zhengji Zhao, Using VASP at NERSC, NERSC User Training, Oakland, CA, June 5, 2015,

Alice Koniges, Shreyas Cholia, Prabhat, Yushu Yao, "Data and Workflow Solutions for Fusion using NERSC", DOE FES/ASCR Workshop on Integrated Simulations for Magnetic Fusion Energy Sciences, June 2, 2015,

N.J. Wright, S. S. Dosanjh, A. K. Andrews, K. Antypas, B. Draney, R.S Canon, S. Cholia, C.S. Daley, K. M. Fagnan, R.A. Gerber, L. Gerhardt, L. Pezzaglia, Prabhat, K.H. Schafer, J. Srinivasan, "Cori: A Pre-Exascale Computer for Big Data and HPC Applications", Big Data and High Performance Computing 26 (2015): 82., ( June 2015) doi: 10.3233/978-1-61499-583-8-82

Extreme data science is becoming increasingly important at the U.S. Department of Energy's National Energy Research Scientific Computing Center (NERSC). Many petabytes of data are transferred from experimental facilities to NERSC each year. Applications of importance include high-energy physics, materials science, genomics, and climate modeling, with an increasing emphasis on large-scale simulations and data analysis. In response to the emerging data-intensive workloads of its users, NERSC made a number of critical design choices to enhance the usability of its pre-exascale supercomputer, Cori, which is scheduled to be delivered in 2016. These data enhancements include a data partition, a layer of NVRAM for accelerating I/O, user defined images and a customizable gateway for accelerating connections to remote experimental facilities.

Scott French, Yili Zheng, Barbara Romanowicz, Katherine Yelick, "Parallel Hessian Assembly for Seismic Waveform Inversion Using Global Updates", IEEE International Parallel & Distributed Processing Symposium (IPDPS) 2015, May 25, 2015, doi: 10.1109/IPDPS.2015.58

Brandon Cook, Arthur Russakoff, Kálmán Varga, "Coverage dependent work function of graphene on a Cu (111) substrate with intercalated alkali metals", Applied Physics Letters, 2015,

J. Hick, Future Directions and How SPXXL Can Help, SPXXL Summer 2015, May 21, 2015,

Discussion of how NERSC may look in 2020, some challenges to getting there, and a proposal for how the SPXXL user group can help.

J. Hick, R. Lee, R. Cheema, K. Fagnan, GPFS for Life Sciences at NERSC, GPFS User Group Meeting, May 20, 2015,

A report showing both high and low-level changes made to our life sciences workloads to support them on GPFS file systems.

Doug Jacobsen, Shane Canon, Contain This, Unleashing Docker for HPC, NERSC Webcast, May 15, 2015,

Evan Racah, Silvia Crivelli, Yushu Yao, "Machine Learning with Spark: Exploring MLlib Random Forests Performance on Edison", BIDS Data Science Faire, May 15, 2015,

Clayton Bagwell, Allocating Fixed Hours to Users Instead of Repo Percentage in NIM, 2015 NUG (NERSC Users Group) Presentation, May 14, 2015,

Michael Wehner, Prabhat, Kevin A. Reed, Daithi Stone, William D. Collins, Julio Bacmeister, "Resolution dependence of future tropical cyclone projections of CAM5.1 in the US CLIVAR Hurricane Working Group idealized configurations", J. Climate special issue on CliVAR 2015, May 5, 2015,

Richard Gerber, Harvey Wasserman, "Large Scale Production Computing and Storage Requirements for Advanced Scientific Computing Research: Target 2017", April 28, 2015,

Prabhat, Scientific Big Data: Challenges and Opportunities, Invited Talk at Brown University, April 28, 2015,

Suren Byna, Brian Austin, "Evaluation of Parallel I/O Performance and Energy with Frequency Scaling on Cray XC30", Cray User Group Meeting, April 2015,

Doug Jacobsen, Shane Canon, "Contain This, Unleashing Docker for HPC", Cray User Group 2015, April 23, 2015,

Doug Jacobsen, "procmon: Real-time process monitoring on the Cray XC-30", Cray User Group 2015, April 21, 2015,

C. Yang, Managing Bioinformatics Software Stack on Magnus, Pawsey Supercomputing Centre Bioinformatics Expo, April 2015,

Alice Koniges, Research Careers in Government Laboratories, Latinos in the Mathematical Sciences Conference, invited talk, April 8, 2015,

Zhengji Zhao, Intel Tools for Optimizations, A talk given at Cray Quarterly Business Review Meeting, St. Paul, MN, April 8, 2015,

Fang Liu, Lin Lin, Derek Vigil-Fowler, Johannes Lischner, Alexander F. Kemper, Sahar Sharifzadeh, Felipe Homrich da Jornada, Jack Deslippe, Chao Yang, Jeffrey B. Neaton, Steven G. Louie, "Numerical integration for ab initio many-electron self energy calculations within the GW approximation.", Journal of Computational Physics, April 1, 2015,

Jack Deslippe, Brian Austin, Chris Daley, Woo-Sun Yang, "Lessons learned from optimizing science kernels for Intel's "Knights-Corner" architecture", CISE, April 1, 2015,

Mahesh Rajan, Doug Doerfler, Mike Tupek, Si Hammond, "An Investigation of Compiler Vectorization on Current and Next-generation Intel Processors using Benchmarks and Sandia’s SIERRA Applications", Cray User Group (CUG) 2015, April 2015,

Jiyan Yang, Oliver Ruebel, Prabhat, Michael Mahoney, Ben Bowen, "Identifying important ions and positions in mass spectroscopy imaging data using CUR matrix decompositions", Analytical Chemistry, March 31, 2015,

"BigNeuron", Prabhat, Kris Bouchard, Shreyas Cholia, Annette Greiner, NERSC Science Highlight, March 31, 2015,

Yushu Yao, SciDB @ NERSC, March 23, 2015,

Yun (Helen) He, OpenMP Basics and MPI/OpenMP Scaling, Tutorial presented to LBNL Computational Research Division postdocs, March 23, 2015,

Brian Austin, Alex Druinsky, Xiaoye Sherry Li, Osni, A. Marques, Eric Roman, Incorporating Error Detection and Recovery Into Hierarchically Semi-Separable Matrix Operations, SIAM CSE 15, March 17, 2015,

Kim, A. G., Padmanabhan, N., Aldering, G., Allen, S. W., Baltay, C., Cahn, R. N., D'Andrea, C. B., Dalal, N., Dawson, K. S., Denney, K. D., Eisenstein, D. J., Finley, D. A., Freedman, W. L., Ho, S., Holz, D. E., Kasen, D., Kent, S. M., Kessler, R., Kuhlmann, S., Linder, E. V., Martini, P., Nugent, P. E., Perlmutter, S., Peterson, B. M., Riess, A. G., Rubin, D., Sako, M., Suntzeff, N. V., Suzuki, N., Thomas, R. C., Wood-Vasey, W. M., and Woosley, S. E., "Distance probes of dark energy", Astroparticle Physics, 2015, 63:2, doi: 10.1016/j.astropartphys.2014.05.007

This document presents the results from the Distances subgroup of the Cosmic Frontier Community Planning Study (Snowmass 2013). We summarize the current state of the field as well as future prospects and challenges. In addition to the established probes using Type Ia supernovae and baryon acoustic oscillations, we also consider prospective methods based on clusters, active galactic nuclei, gravitational wave sirens and strong lensing time delays.

Richard Gerber, NERSC Science 2014, February 24, 2015,

Katie Antypas, The Cori System, February 24, 2015,

R. Jefferson Porter, ALICE USA T2 Operations, ALICE Tier-1 / Tier-2 Workshop, February 24, 2015,

Prabhat, Data and Analytics Strategy, February 23, 2015,

Richard A. Gerber, Performance and Debugging Tools for HPC, February 17, 2015,

Guest lecture in UC Berkeley CS 267 - Applications of Parallel Computers

M. G. Aartsen et al., "Flavor Ratio of Astrophysical Neutrinos above 35 TeV in IceCube", Physical Review Letters, February 11, 2015, doi: 10.1103/PhysRevLett.114.171102

Alice Koniges, Nathan Masters, Aaron Fisher, David Eder, Wangyi Liu, Robert Anderson, David Benson,
and Andrea Bertozzi,
"Multi-Material ALE with AMR for Modeling Hot Plasmas and Cold Fragmenting Materials", Plasma Science and Technology 17, No. 2, 117-128, 2015, doi: 10.1088/1009-0630/17/2/05

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", Plasma Science and Technology 17, No. 2, 109-116, 2015, doi: 10.1088/1009-0630/17/2/04

Shyue Ping Ong, Shreyas Cholia, Anubhav Jain, Miriam Brafman, Dan Gunter, Gerbrand Ceder, Kristin A Persson, "The Materials Application Programming Interface (API): A simple, flexible and efficient API for materials data based on REpresentational State Transfer (REST) principles", Computational Materials Science, February 1, 2015, doi: 10.1016/j.commatsci.2014.10.037

Saunders, C., Aldering, G., Antilogus, P., Aragon, C., Bailey, S., Baltay, C., Bongard, S., Buton, C., Canto, A., Cellier-Holzem, F., Childress, M., Chotard, N., Copin, Y., Fakhouri, H. K., Feindt, U., Gangler, E., Guy, J., Kerschhaggl, M., Kim, A. G., Kowalski, M., Nordin, J., 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., Thomas, R. C., Weaver, B. A., and Wu, C., "Type Ia Supernova Distance Modulus Bias and Dispersion from K-correction Errors: A Direct Measurement Using Light Curve Fits to Observed Spectral Time Series", The Astrophysical Journal, 2015, 800:57, doi: 10.1088/0004-637X/800/1/57

We estimate systematic errors due to K-corrections in standard photometric analyses of high-redshift Type Ia supernovae. Errors due to K-correction occur when the spectral template model underlying the light curve fitter poorly represents the actual supernova spectral energy distribution, meaning that the distance modulus cannot be recovered accurately. In order to quantify this effect, synthetic photometry is performed on artificially redshifted spectrophotometric data from 119 low-redshift supernovae from the Nearby Supernova Factory, and the resulting light curves are fit with a conventional light curve fitter. We measure the variation in the standardized magnitude that would be fit for a given supernova if located at a range of redshifts and observed with various filter sets corresponding to current and future supernova surveys. We find significant variation in the measurements of the same supernovae placed at different redshifts regardless of filters used, which causes dispersion greater than ~0.05 mag for measurements of photometry using the Sloan-like filters and a bias that corresponds to a 0.03 shift in w when applied to an outside data set. To test the result of a shift in supernova population or environment at higher redshifts, we repeat our calculations with the addition of a reweighting of the supernovae as a function of redshift and find that this strongly affects the results and would have repercussions for cosmology. We discuss possible methods to reduce the contribution of the K-correction bias and uncertainty.

Richard Gerber, Harvey Wasserman, "Large Scale Computing and Storage Requirements for Nuclear Physics - Target 2017", January 28, 2015,

Zhengji Zhao, A Burst Buffer Use Case, Cray Quarterly Business Review Meeting, Oakland, CA, January 28, 2015,

Chris Paciorek, Benjamin Lipschitz, Tina Zhuo, Cari Kaufman, Prabhat, Rollin Thomas, Parallelized Gaussian Processes in R, Joint Statistical Meeting 2014, January 21, 2015,

Thorsten Kurth, Andrew Pochinsky, Abhinav Sarje, Sergey Syritsyn, Andre Walker-Loud, "High-Performance I/O: HDF5 for Lattice QCD", Conference, PoSLAT, January 18, 2015,

Prabhat, Deep Learning for Big Data, DOE ASCR Workshop on Machine Learning, January 9, 2015,

Massimiliano Albanese, Michael Berry, David Brown, Scott Campbell, Stephen Crago, George Cybenko, Jon DeLapp, Christopher L. DeMarco, Jeff Draper, Manuel Egele, Stephan Eidenbenz, Tina Eliassi-Rad, Vergle Gipson, Ryan Goodfellow, Paul Hovland, Sushil Jajodia, Cliff Joslyn, Alex Kent, Sandy Landsberg, Larry Lanes, Carolyn Lauzon, Steven Lee, Sven Leyffer, Robert Lucas, David Manz, Celeste Matarazzo, Jackson R. Mayo, Anita Nikolich, Masood Parvania, Garrett Payer, Sean Peisert, Ali Pinar, Thomas Potok, Stacy Prowell, Eric Roman, David Sarmanian, Dylan Schmorrow, Chris Strasburg, V.S. Subrahmanian, Vipin Swarup, Brian Tierney, Von Welch, "ASCR Cybersecurity for Scientific Computing Integrity", DOE Workshop Report, January 7, 2015,

At the request of the U.S. Department of Energy’s (DOE) Advanced Scientific Computing Research (ASCR) program, a workshop was held January 7–9, 2015, in Rockville, Md., to examine computer security research gaps and approaches for assuring scientific computing integrity specific to the mission of the DOE Office of Science. Issues included research computation and simulation that takes place on ASCR computing facilities and networks, as well as network-connected scientific instruments, such as those run by other DOE Office of Science programs. Workshop participants included researchers and operational staff from DOE national laboratories, as well as academic researchers and industry experts. Participants were selected based on the prior submission of abstracts relating to the topic. Additional input came from previous DOE workshop reports [DOE08,BB09] relating to security. Several observers from DOE and the National Science Foundation also attended.

Michael Berry, Tom Potok, Prasanna Balaprakash, Hank Hoffman, Raju Vatsavi, Prabhat, "Machine Learning and Understanding for Intelligent Extreme Scale Scientific Computing and Discovery", DOE ASCR Workshop Report, January 7, 2015,

Richard F. Barrett, Paul Crozier, Douglas W. Doerfler, Michael A. Heroux, Paul Lin, Heidi K. Thornquist, Timothy G. Trucano, Courtenay T. Vaughan, "Assessing the Role of Mini-Applications in Predicting Key Performance Characteristics of Scientific and Engineering Applications", Journal of Parallel and Distributed Computing, Volume 75, Pages 107-122, January 2015,

T. Maier, D. Benjamin, W. Bhimji, Elmsheuser, P. van Gemmeren, D. Malon, N. Krumnack, "ATLAS I/O performance optimization in as-deployed environments", J. Phys. Conf. Ser., 2015, 664:042033, doi: 10.1088/1742-6596/664/4/042033 ,

Michela Massimi, Wahid Bhimji, "Computer simulations and experiments: The case of the Higgs boson", Stud. Hist. Philos. Mod. Phys., 2015, 51:71-81, doi: 10.1016/j.shpsb.2015.06.003

Georges Aad, others (ATLAS and CMS Collaborations), "Combined Measurement of the Higgs Boson Mass in pp collisions at sqrt{s}=7 and 8 TeV with the ATLAS and CMS Experiments", Phys. Rev. Lett., 2015, 114:191803, doi: 10.1103/PhysRevLett.114.191803

Georges Aad, others (ATLAS Collaboration), "Identification of Boosted, Hadronically Decaying W and Comparisons with ATLAS Data Taken at sqrt(s) = 8 TeV", Submitted to Eur. Phys. J. C, 2015,

T. Malas, G. Hager, H. Ltaief, H. Stengel, G. Wellein, D. Keyes, "Multicore-Optimized Wavefront Diamond Blocking for Optimizing Stencil Updates", SIAM Journal on Scientific Computing, 2015, 37:C439-C464, doi: 10.1137/140991133

T. Malas, G. Hager, H. Ltaief, D. Keyes, Advanced tiling techniques for memory-starved streaming numerical kernels, 2015,

T. Malas, G. Hager, H. Ltaief, D. Keyes, Multi-dimensional intra-tile parallelization for memory-starved stencil computations, arXiv preprint arXiv:1510.04995, 2015,

T. M. Malas, Tiling and Asynchronous Communication Optimizations for Stencil Computations, 2015,

A. Ovsyannikov, D. Kim, A. Mani, P. Moin, "Numerical study of turbulent two-phase Couette flow", Pages: 41-52 January 1, 2015,

Taylor Groves, Samuel K Gutierrez, Dorian Arnold, "A LogP Extension for Modeling Tree Aggregation Networks", Cluster Computing (CLUSTER), 2015 IEEE International Conference on, 2015, 666--673,

Taylor Groves, Ryan Grant, "Power Aware, Dynamic Provisioning of HPC Networks", Sandia National Labs report, 2015,

Richard F. Barrett, Paul S. Crozier, Douglas W. Doerfler, Michael A. Heroux, Paul T. Lin, Heidi K. Thornquist, Timothy G. Trucano, Courtenay T. Vaughan, "Assessing the role of mini-applications in predicting key performance characteristics of scientific and engineering applications", Journal of Parallel and Distributed Computing, January 1, 2015, 75:107-122, doi: 10.1016/j.jpdc.2014.09.006

Stephen Lien Harrell, Hai Ah Nam, Ver\ onica G. Vergara Larrea, Kurt Keville, Dan Kamalic, "Student Cluster Competition: A Multi-Disciplinary Undergraduate HPC Educational Tool", EduHPC 15, New York, NY, USA, Association for Computing Machinery, 2015, doi: 10.1145/2831425.2831428

Matthew R. Link, Stephen C. Simms, Craig A. Stewart, Robert Henschel, Benjamin Fulton, Use of IU parallel computing resources and high performance file systems - July 2013 to Dec 2014, 2015,

Harold E.B. Dennis, Adam S. Ward, Tyler Balson, Yuwei Li, Robert Henschel, Shawn Slavin, Stephen Simms, Holger Brunst, "High Performance Computing Enabled Simulation of the Food-Water-Energy System: Simulation of Intensively Managed Landscapes", PEARC17, New York, NY, USA, Association for Computing Machinery, 2015, 1--10, doi: 10.1145/3093338.3093381

Chris Harris, Patrick O Leary, Michael Grauer, Aashish Chaudhary, Chris Kotfila, Robert O Bara, "Dynamic Provisioning and Execution of HPC Workflows Using Python", 2016 6th Workshop on Python for High-Performance and Scientific Computing (PyHPC), 2015, 1-8, doi: 10.1109/PyHPC.2016.005

Marcus D. Hanwell, Wibe A. de Jong, Christopher J. Harris, "Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application", Journal of Cheminformatics, 2015, 9:55, doi: 10.1186/s13321-017-0241-z

Patrick O Leary, Mark Christon, Sebastien Jourdain, Chris Harris, Markus Berndt, Andrew Bauer, "HPCCloud: A Cloud/Web-Based Simulation Environment", 2015 IEEE 7th International Conference on Cloud Computing Technology and Science (CloudCom), 2015, 25-33, doi: 10.1109/CloudCom.2015.33

2014

Glenn K. Lockwood, Stephen H. Garofalini, "Proton dynamics at the water-silica interface via dissociative molecular dynamics", Journal of Physical Chemistry C, December 26, 2014, 118:29750-2975, doi: 10.1021/jp507640y

A robust and accurate dissociative potential that reproduces the structural and dynamic properties of bulk and nanoconfined water, and proton transport similar to ab initio calculations in bulk water, is used for reactive molecular dynamics simulations of the proton dynamics at the silica/water interface. The simulations are used to evaluate the lifetimes of protonated sites at the interfaces of water with planar amorphous silica surfaces and cylindrical pores in amorphous silica with different densities of water confined in the pores. In addition to lifetimes, the donor/acceptor sites are evaluated and discussed in terms of local atomistic structure. The results of the lifetimes of the protonated sites, including H3O+, SiOH, SiOH2+, and Si–(OH+)–Si sites, are considered. The lifetime of the hydronium ion, H3O+, is considerably shorter near the interface than in bulk water, as are the lifetimes of the other protonated sites. The results indicate the beneficial effect of the amorphous silica surface in enhancing proton transport in wet silica as seen in electrochemical studies and provide the specific molecular mechanisms.

"A Standard for Neuroscience Data", Oliver Ruebel, Kris Bouchard, Prabhat, NERSC Science Highlight, December 16, 2014,

Jeffrey Regier, Brenton Partridge, Jon McAuliffe, Ryan Adams, Matt Hoffman, Dustin Lang, David Schlegel, Prabhat, "Celeste: Scalable variational inference for a generative model of astronomical images", NIPS 2014 Workshop on Advances in Variational Inference, December 9, 2014,

Soyoung Jeon, Chris Paciorek, Prabhat, Suren Byna, William Collins, Michael Wehner, "Uncertainty Quantification for characterizing spatial tail dependence under statistical framework", American Geophysical Union Meeting 2014, December 9, 2014,

Michael Wehner, Prabhat, Fuyu Li, William Collins, "The effect of horizontal resolution of the simulation of precipitation extremes in the Community Atmospheric Model version 5.1", American Geophysical Union Meeting 2014, December 9, 2014,

Michael F. Wehner, Kevin Reed, Fuyu Li, Prabhat, Julio Bacmeister, Cheng-Ta Chen, Surenda Byna, Chris Paciorek, Peter Gleckler, Ken Sperber, William D. Collins, Andrew Gettelman, Kesheng Wu, Christiane Jablonowski, Chris Algieri, "The effect of horizontal resolution on AMIP simulation quality in the Community Atmospheric Model, CAM5.1", JAMES, December 9, 2014,

J.L. Vay, T. Drummond, A. Koniges, B. Loring, C. Mitchell, J. Qiang, O. Ruebel, R. Ryne, H. Vincent, D. P. Grote, A. Hübl, Advanced Modeling of Particle Accelerators, NERSC Exascale Science Application Program Meeting, December 4, 2014,

V. Sabelnikov, A. Ovsyannikov, M. Gorokhovski, "Modified level set equation and its numerical assessment", Journal of Computational Physics, December 1, 2014, 278:1-30, doi: 10.1016/j.jcp.2014.08.018

Shreyas Cholia, Terence Sun, "The NEWT platform: an extensible plugin framework for creating ReSTful HPC APIs", Gateway Computing Environments Workshop (GCE), 2014 9th, November 21, 2014, doi: 10.1109/GCE.2014.14

Ryan Chard, Saba Sehrish, Alex Rodriguez, Ravi Madduri, Thomas D Uram, Marc Paterno, Katrin Heitmann, Shreyas Cholia, Jim Kowalkowski, Salman Habib, "PDACS: a portal for data analysis services for cosmological simulations", Gateway Computing Environments Workshop (GCE), 2014 9th, November 21, 2014, doi: 10.1109/GCE.2014.7

Jean-Luc Vay, Leroy Anthony Drummond, Alice Koniges, Brendan Godfrey, Irving Haber, "Scalable Arbitrary-Order Pseudo-Spectral Electromagnetic Solver", SC14, November 17, 2014,

Jean-Luc Vay, Leroy Anthony Drummond, Alice Koniges, Brendan Godfrey, Irving Haber, "Scalable Arbitrary-Order Pseudo-Spectral Electromagnetic Solver", SC14, November 17, 2014,

Tim Mattson, Alice Koniges, Simon McIntosh-Smith, OpenCL: A Hands-on Introduction, SC14 Tutorial, November 17, 2014,

Yu Jung Lo, Samuel Williams, Brian Van Straalen, Terry J. Ligocki,Matthew J. Cordery, Nicholas J. Wright, Mary W. Hall, Leonid Oliker, "Roofline Model Toolkit: A Practical Tool for Architectural and Program Analysis", SC'14, November 16, 2014,

Jack Deslippe, Abdelilah Essiari, Simon J. Patton, Taghrid Samak, Craig E. Tull, Alexander Hexemer, Dinesh Kumar, Dilworth Parkinson, Polite Stewart., "Workflow management for real-time analysis of lightsource experiments", Proceedings of the 9th Workshop on Workflows in Support of Large-Scale Science (SC14), November 16, 2014, 31-40,

Alice Koniges, Enabling Physics Insight with Multidimensional Computer Simulations, SC14 Broader Engagement Program, November 16, 2014,

Richard A. Gerber, Exascale Computing, Big Data, and World-Class Science at NERSC, November 13, 2014,

Talk given at San Jose State University Physics Department colloquium on Nov. 13, 2014.

Richard A. Gerber et al., "High Performance Computing Operational Review: Enabling Data-Driven Scientific Discovery at DOE HPC Facilities", November 7, 2014,

Douglas Doerfler, First Experiences with 64-bit ARM Moonshot, HP-CAST 23, November 2014,

Alex Druinsky, Brian Austin, Xiaoye Sherry Li, Osni Marques, Eric Roman, Samuel Williams, "A Roofline Performance Analysis of an Algebraic Multigrid PDE Solver", SC14, November 2014,

Brian Austin, Nicholas Wright, "Measurement and interpretation of microbenchmark and application energy use on the Cray XC30", Proceedings of the 2nd International Workshop on Energy Efficient Supercomputing, November 2014,

Thorsten Kurth, Noriyoshi Ishii, Takumi Doi, Sinya Aoki, Tetsuo Hatsuda, "Phase shifts in I=2 ππ-scattering from two lattice approaches", Conference, November 2014,

Yun (Helen) He, Explore MPI/OpenMP Scaling on NERSC Systems, NERSC OpenMP and Vectorization Training, October 28, 2014,

Zhengji Zhao, Cori and NERSC Exascale Application Program (NESAP), NWChem Developers Workshop at Seattle, WA, October 28, 2014,

Quincey Koziol, Ruth Aydt, Russ Rew, Mark Howison, Mark Miller, Prabhat, "HDF5", Book Chapter in High Performance Parallel I/O, Prabhat, Quincey editors, CRC Press., ( October 23, 2014)

Suren Byna, Prabhat, Homa Karimabadi, Bill Daughton, "Parallel I/O for a Trillion Particle Plasma Physics Simulation", Book Chapter in Prabhat, Quincey Koziol, editors, High Performance Parallel I/O, CRC Press/Francis-Taylor Group. 2014, ( October 23, 2014)

Mark Howison, Suren Byna, Prabhat, "Iota", Book Chapter in Prabhat, Quincey Koziol, editors, High Performance Parallel I/O, CRC Press/Francis-Taylor Group. 2014, ( October 23, 2014)

Alice Koniges, Invited Career Seminar, UC Berkeley: Women in Mathematics, October 21, 2014,

K. Antypas, B.A Austin, T.L. Butler, R.A. Gerber, C.L Whitney, N.J. Wright, W. Yang, Z Zhao, "NERSC Workload Analysis on Hopper", Report, October 17, 2014, LBNL 6804E,

M. Scot Breitenfeld, Kalyana Chadalavada, Robert Sisneros, Suren Byna, Quincey Koziol, Neil Fortner, Prabhat, Venkat Vishwanath, "Tuning Performance of Large scale I/O with Parallel HDF5", SC’14 PDSW Workshop, October 15, 2014,

Richard A. Gerber, Harvey J. Wasserman, "Large Scale Computing and Storage Requirements for Basic Energy Sciences: Target 2017", October 10, 2014,

Zhengji Zhao, Automatic Library Tracking Database at NERSC, ALTD Review Meeting at NERSC, Oakland CA, October 8, 2014,

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", High Performance Computing Systems. Performance Modeling, Benchmarking and Simulation (PMBS 2013). Lecture Notes in Computer Science, Volume 8551, October 1, 2014,

Douglas Doerfler, Dr. Tom Bradicich, An Evaluation of 64-bit ARM for use in High-Performance Modeling and Simulation Architecture, ARM TechCon 2014, October 2014,

Manish Jain, Jack Deslippe, Georgy Samsonidze, M.L. Cohen, J.R. Chelikowsky, S.G. Louie, "Improved quasiparticle wavefunctions and mean field for G0W0 calculations: Diagonalization of the static-COHSEX operator", Physical Review B, September 26, 2014,

Richard A. Gerber et al., "DOE High Performance Computing Operational Review: Enabling Data-Driven Discovery at DOE High Performance Computing Facilities", September 19, 2014,

Richard A. Gerber et al., "DOE High Performance Computing Operational Review (HPCOR): Enabling Data-Driven Scientific Discovery at DOE HPC Facilities", September 17, 2014,

Johannes Lischner, Sahar Sharifzadeh, Jack Deslippe, J. Neaton, and S. G. Louie, "Effects of Self-consistency and Plasmon-pole Models on GW Calculations for Closed-shell Molecules", Physical Review B, September 17, 2014,

Huaiyu Yuan, Scott French, Paul Cupillard, Barbara Romanowicz, "Lithospheric expression of geological units in central and eastern North America from full waveform tomography", Earth and Planetary Science Letters, 2014, 402:176, doi: 10.1016/j.epsl.2013.11.057

Justin Blair, Richard S. Canon, Jack Deslippe, Abdelilah Essiari, Alexander Hexemer, Alastair A. MacDowell, Dilworth Y. Parkinson, Simon J. Patton, Lavanya Ramakrishnan, Nobumichi Tamura, Brian L. Tierney, Craig E. Tull, "High performance data management and analysis for tomography", Proc. SPIE 9212, Developments in X-Ray Tomography IX, September 12, 2014,

Clayton Bagwell, Allison Andrews, Automated Provisioning and Management of NGF via NIM, September 10, 2014,

Friesen, B., Baron, E., Wisniewski, J. P., Parrent, J. T., Thomas, R. C., Miller, Timothy R., and Marion, G. H., "Near-infrared Line Identification in Type Ia Supernovae during the Transitional Phase", The Astrophysical Journal, 2014, 792:120, doi: 10.1088/0004-637X/792/2/120

We present near-infrared synthetic spectra of a delayed-detonation hydrodynamical model and compare them to observed spectra of four normal Type Ia supernovae ranging from day +56.5 to day +85. This is the epoch during which supernovae are believed to be undergoing the transition from the photospheric phase, where spectra are characterized by line scattering above an optically thick photosphere, to the nebular phase, where spectra consist of optically thin emission from forbidden lines. We find that most spectral features in the near-infrared can be accounted for by permitted lines of Fe II and Co II. In addition, we find that [Ni II] fits the emission feature near 1.98 μm, suggesting that a substantial mass of 58Ni exists near the center of the ejecta in these objects, arising from nuclear burning at high density.

Shahzeb Siddiqui, "Automatic Performance Tuning of Parallel and Accelerated Seismic Imaging Kernels", EAGE Workshop on High Performance Computing for Upstream, European Association of Geoscientists & Engineer, September 1, 2014, doi: https://doi.org/10.3997/2214-4609.20141941

Scott French, Barbara Romanowicz, "Whole-mantle radially anisotropic shear velocity structure from spectral-element waveform tomography", Geophysical Journal International, 2014, doi: 10.1093/gji/ggu334

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, doi: 10.3791/51673

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.

Mahesh Rajan, Douglas W. Doerfler, Richard Frederick Barrett, Joel O. Stevenson, Anthony Michael Agelastos, Ryan Phillip Shaw, Harold Edward Meyer, "Experiences with Sandia National Laboratories HPC applications and MPI Performance", MVAPICH Users Group Meeting, August 2014,

Rebecca J. Hartman-Baker, Daniel J. Grimwood, Valerie Maxville, "Evaluating Parallel Programming Tools to Support Code Development for Accelerators", Procedia Computer Science, 2014, 2076-2079,

Zhengji Zhao, Quality and Testing of PE releases, Cray Quarterly Business Meeting, Oakland CA, July 30, 2014,

Daya Bay Collaboration: F.P. An, A.B. Balantekin, H.R. Band, W. Beriguete, et. al, "Search for a Light Sterile Neutrino at Daya Bay", Phys. Rev. Letter, July 27, 2014,

A search for light sterile neutrino mixing was performed with the first 217 days of data from the Daya Bay Reactor Antineutrino Experiment. The experiment's unique configuration of multiple baselines from six 2.9~GWth nuclear reactors to six antineutrino detectors deployed in two near (effective baselines 512~m and 561~m) and one far (1579~m) underground experimental halls makes it possible to test for oscillations to a fourth (sterile) neutrino in the 10−3 eV2<|Δm241|<0.3 eV2 range. The relative spectral distortion due to electron antineutrino disappearance was found to be consistent with that of the three-flavor oscillation model. The derived limits on sin22θ14 cover the 10−3 eV2≲|Δm241|≲0.1 eV2 region, which was largely unexplored

Rusen Oktem, Prabhat, James Lee, Aaron Thomas, Paquita Zuidema, David Romps, "Stereo Photogrammetry of oceanic clouds", Journal of Atmospheric and Oceanic Technology, July 24, 2014,

Scott Campbell, "Open Science, Open Security", 9th International Workshop on Security and High Performance Computing Systems, July 22, 2014,

 

We propose that to address the growing problems with complexity and data volumes in HPC security wee need to refactor how we look at data by creating tools that not only select data, but analyze and represent it in a manner well suited for intuitive analysis. We propose a set of rules describing what this means, and provide a number of production quality tools that represent our current best effort in implementing these ideas.

 

Dong Ju Choi, Glenn K. Lockwood, Robert S. Sinkovits, Mahidhar Tatineni, "Performance of applications using dual-rail InfiniBand 3D torus network on the Gordon supercomputer", Proceedings of the 2014 XSEDE Conference, July 13, 2014, doi: 10.1145/2616498.2616541

Multi-rail InfiniBand networks provide options to improve bandwidth, increase reliability, and lower latency for multi-core nodes. The Gordon supercomputer at SDSC, with its dual-rail InfiniBand 3-D torus network, is used to evaluate the performance impact of using multiple rails. The study was performed using the OSU micro-benchmarks, the P3FFT application kernel, and scientific applications LAMMPS and AMBER. The micro-benchmarks confirmed the bandwidth and latency performance benefits. At the application level, performance improvements depended on the communication level and profile.

Glenn K. Lockwood, Mahidhar Tatineni, Rick Wagner, "SR-IOV: Performance benefits for virtualized interconnects", Proceedings of the 2014 XSEDE Conference, July 13, 2014, doi: 10.1145/2616498.2616537

The demand for virtualization within high-performance computing is rapidly growing as new communities, driven by both new application stacks and new computing modalities, continue to grow and expand. While virtualization has traditionally come with significant penalties in I/O performance that have precluded its use in mainstream large-scale computing environments, new standards such as Single Root I/O Virtualization (SR-IOV) are emerging that promise to diminish the performance gap and make high-performance virtualization possible. To this end, we have evaluated SR-IOV in the context of both virtualized InfiniBand and virtualized 10 gigabit Ethernet (GbE) using micro-benchmarks and real-world applications. We compare the performance of these interconnects on non-virtualized environments, Amazon's SR-IOV-enabled C3 instances, and our own SR-IOV-enabled InfiniBand cluster and show that SR-IOV significantly reduces the performance losses caused by virtualization. InfiniBand demonstrates less than 2% loss of bandwidth and less than 10% increase in latency when virtualized with SR-IOV. Ethernet also benefits, although less dramatically, when SR-IOV is enabled on Amazon's cloud.

Jeff A. Tracey, James K. Sheppard, Glenn K. Lockwood, Amit Chourasia, Mahidhar Tatineni, Robert N. Fisher, Robert S. Sinkovits, "Efficient 3D movement-based kernel density estimator and application to wildlife ecology", Proceedings of the 2014 XSEDE Conference, San Diego, CA, July 13, 2014, doi: 10.1145/2616498.2616541

We describe an efficient implementation of a 3D movement- based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.

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,

A. Bhagatwala, J.H. Chen, T. Lu, "Direct numerical simulations of HCCI/SACI with ethanol", Combustion and Flame, 2014,

Daya Bay Collaboration: F.P. An, A.B. Balantekin, H.R. Band, W. Beriguete, et. al, "Independent Measurement of Theta13 via Neutron Capture on Hydrogen at Daya Bay", Phys. Rev. Letter, June 25, 2014,

A new measurement of the θ13 mixing angle has been obtained at the Daya Bay Reactor Neutrino Experiment via the detection of inverse beta decays tagged by neutron capture on hydrogen. The antineutrino events for hydrogen capture are distinct from those for gadolinium capture with largely different systematic uncertainties, allowing a determination independent of the gadolinium-capture result and an improvement on the precision of θ13 measurement. With a 217-day antineutrino data set obtained with six antineutrino detectors and from six 2.9 GWth reactors, the rate deficit observed at the far hall is interpreted as sin22θ13=0.083±0.018 in the three-flavor oscillation model. When combined with the gadolinium-capture result from Daya Bay, we obtain sin22θ13=0.089±0.008 as the final result for the six-antineutrino-detector configuration of the Daya Bay experiment.

Alice Koniges, David Eder, Aaron Fisher, Wangyi Lui, Nathan Masters, John Barnard, "Multi-Physics Plasma Modeling for a Range of Applications on HPC Platforms", 41st EPS Conference on Plasma Physics, June 23, 2014,

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

C. J. Yang, Q. Guo, D. Huang, and S. Nordholm, "Exploiting Cyclic Prefix for Joint Detection, Decoding and Channel Estimation in OFDM via EM Algorithm and Message Passing", IEEE International Conference on Communications (ICC'14), pp. 4674-4679, June 2014,

Alice Koniges, Applications on HPX: a new runtime for exascale / Summary of recent DOE Exascale Meetings, NERSC Brown Bag, June 13, 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, doi: 10.1002/ctpp.201410014

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

D. Khotyanovsky, A. Kudryavtsev, A. Ovsyannikov, "A comparative study of accuracy of shock capturing schemes for simulation of shock/acoustic wave interactions", International Journal of Aeroacoustics, June 1, 2014, 13:261-274, doi: 10.1260/1475-472X.13.3-4.261

Michael Kagan, Glenn K. Lockwood, Stephen H. Garofalini, "Reactive simulations of the activation barrier to dissolution of amorphous silica in water", Physical Chemistry Chemical Physics, May 28, 2014, 16:9294-9301, doi: 10.1039/c4cp00030g

Molecular dynamics simulations employing reactive potentials were used to determine the activation barriers to the dissolution of the amorphous SiO2 surface in the presence of a 2 nm overlayer of water. The potential of mean force calculations of the reactions of water molecules with 15 different starting Q4 sites (Qi is the Si site with i bridging oxygen neighbors) to eventually form the dissolved Q0 site were used to obtain the barriers. Activation barriers for each step in the dissolution process, from the Q4 to Q3 to Q2 to Q1 to Q0 were obtained. Relaxation runs between each reaction step enabled redistribution of the water above the surface in response to the new Qi site configuration. The rate-limiting step observed in the simulations was in both the Q32 reaction (a Q3 site changing to a Q2 site) and the Q21 reaction, each with an average barrier of ∼14.1 kcal mol(-1). However, the barrier for the overall reaction from the Q4 site to a Q0 site, averaged over the maximum barrier for each of the 15 samples, was 15.1 kcal mol(-1). This result is within the lower end of the experimental data, which varies from 14-24 kcal mol(-1), while ab initio calculations using small cluster models obtain values that vary from 18-39 kcal mol(-1). Constraints between the oxygen bridges from the Si site and the connecting silica structure, the presence of pre-reaction strained siloxane bonds, and the location of the reacting Si site within slight concave surface contours all affected the overall activation barriers.

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,

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

Larry Pezzaglia, Cluster Consolidation at NERSC, A talk at the HEPiX Spring 2014 Workshop, Annecy-le-Vieux, France, May 22, 2014,

In 2012, NERSC began deployment of "Mendel", a 500+ node, Infiniband-attached, Linux "meta-cluster" which transparently expands NERSC production clusters and services in a scalable and maintainable fashion. The success of the software automation infrastructure behind the Mendel multi-clustering model encouraged investigation into even more aggressive consolidation efforts.

This talk will detail one such effort: under the constraints of a 24x7, disruption-sensitive environment, NERSC staff merged a 400-node legacy production cluster, consisting of multiple hardware generations and ad-hoc software configurations, into Mendel's automation infrastructure. By leveraging the hierarchical management features of the xCAT software package in combination with other open-source and in-house tools, such as Cfengine and CHOS, NERSC abstracted the unique characteristics of both clusters away below a unified management interface. Consequently, both cluster components are now managed as a single, albeit complex, integrated system.

Additionally, this talk will provide an update on the PDSF system at NERSC, including improvements to trending data collection and ongoing CHOS development.

 

Kin Fai Mak, Felipe H. da Jornada, Keliang He, Jack Deslippe, Nicholas Petrone, James Hone, Jie Shan, Steven G. Louie, and Tony F. Heinz, "Tuning Many-Body Interactions in Graphene: The Effects of Doping on Excitons and Carrier Lifetimes", Physical Review Letters, May 20, 2014, 112:207401,

A Dubey, K Antypas, AC Calder, C Daley, B Fryxell, JB Gallagher, DQ Lamb, D Lee, K Olson, LB Reid, P Rich, PM Ricker, KM Riley, R Rosner, A Siegel, NT Taylor, K Weide, FX Timmes, N Vladimirova, J ZuHone, "Evolution of FLASH, a multi-physics scientific simulation code for high-performance computing", The International Journal of High Performance Computing Applications, May 2014, 28:225--237, doi: 10.1177/1094342013505656

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

 

S. Parete-Koon, B. Caldwell, S. Canon, E. Dart, J. Hick, J. Hill, C. Layton, D. Pelfrey, G. Shipman, D. Skinner, H. Nam, J. Wells, J. Zurawski, "HPC’s Pivot to Data", Proceedings of the Cray Users Group Conference, Lugano, Switzerland, May 2014,

Zhengji Zhao, Doug Petesch, David Knaak, and Tina Declerck, "I/O Performance on Cray XC30", Cray User Group Meeting, May 4, 2014,

Zhengji Zhao, Doug Petesch, David Knaak, and Tina Declerck, I/O Performance on Cray XC30, Cray User Group Meeting, May 4-8, 2014, Lugano, Switzerland, May 4, 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.

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

We present a sample of normal Type Ia supernovae (SNe Ia) from the Nearby Supernova Factory data set with spectrophotometry at sufficiently late phases to estimate the ejected mass using the bolometric light curve. We measure 56Ni masses from the peak bolometric luminosity, then compare the luminosity in the 56Co-decay tail to the expected rate of radioactive energy release from ejecta of a given mass. We infer the ejected mass in a Bayesian context using a semi-analytic model of the ejecta, incorporating constraints from contemporary numerical models as priors on the density structure and distribution of 56Ni throughout the ejecta. We find a strong correlation between ejected mass and light-curve decline rate, and consequently 56Ni mass, with ejected masses in our data ranging from 0.9 to 1.4 M. Most fast-declining (SALT2 x1 < -1) normal SNe Ia have significantly sub-Chandrasekhar ejected masses in our fiducial analysis.

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

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

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

Douglas Doerfler, The Role of Advanced Technology Systems in the ASC Platform Strategy, Salishan Conference on High-Speed Computing, April 2014,

Douglas Doerfler, Trinity: Next-Generation Supercomputer for the ASC Program, HPC User Forum, April 1, 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, "Search for a Diffuse Flux of Astrophysical Muon Neutrinos with the IceCube 59-string Configuration", Physical Review D89 062007, March 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.

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

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

Parrent, J. T., Friesen, B., Parthasarathy, M., "A Review of Type Ia Supernova Spectra", Astrophysics and Space Science, 2014, 351:1-52, doi: 10.1007/s10509-014-1830-1

SN 2011fe was the nearest and best-observed type Ia supernova in a generation, and brought previous incomplete datasets into sharp contrast with the detailed new data. In retrospect, documenting spectroscopic behaviors of type Ia supernovae has been more often limited by sparse and incomplete temporal sampling than by consequences of signal-to-noise ratios, telluric features, or small sample sizes. As a result, type Ia supernovae have been primarily studied insofar as parameters discretized by relative epochs and incomplete temporal snapshots near maximum light. Here we discuss a necessary next step toward consistently modeling and directly measuring spectroscopic observables of type Ia supernova spectra. In addition, we analyze current spectroscopic data in the parameter space defined by empirical metrics, which will be relevant even after progenitors are observed and detailed models are refined.

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

M. G. Aartsen et al., "Search for non-relativistic Magnetic Monopoles with IceCube", European Physics Journal, February 14, 2014, doi: 10.1140/epjc/s10052-014-2938-8

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

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

Jay Srinivasan, Computational Systems Group Update for NUG 2014, February 6, 2014,

Zhengji Zhao, NERSC, Best Practices for Best Performance on Edison, February 6, 2014,

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

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

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

Michael Bailey, Scott Campbell, Michael Corn, Deborah A. Frincke, Ardoth Hassler, Craig Jackson, James A. Marsteller, Rodney J. Petersen, Mark Servilla, Von Welch, "Report of the 2013 NSF Cybersecurity Summit for Cyberinfrastructure and Large Facilities Designing Cybersecurity Programs in Support of Science", February 5, 2014,

Harvey Wasserman, NERSC, New User Training: Introduction to NERSC, NUG 2014: NERSC Users' Group Meeting, February 3, 2014,

David Turner, NERSC, Accounts and Allocations, February 3, 2014,

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

David Turner, NERSC, NERSC Computing Environment, February 3, 2014,

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

David Turner, NERSC, NERSC File Systems and How to Use Them, February 3, 2014,

Zhengji Zhao, NERSC, Available Software at NERSC, February 3, 2014,

Woo-Sun Yang, Debugging Tools, February 3, 2014,

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

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

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

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

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,

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

S.S. Dosanjh, R.F. Barrett, D.W. Doerfler, S.D. Hammond, K.S. Hemmert, M.A. Heroux, P.T. Lin, K.T. Pedretti, A.F. Rodrigues, T.G. Trucano, J.P. Juitjens, "Exascale Design Space Exploration and Co-Design", Future Generation Computer Systems, Volume 30, Pages 46-58, January 2014,

J. Aasi, J. Abadie, B. P. Abbott, R. Abbott, T., M. R. Abernathy, T. Accadia, F. Acernese, C. Adams, T. Adams, et al., First Searches for Optical Counterparts to Gravitational-wave Candidate Events, Astrophysical Journal Supplement, Pages: 7 2014, doi: 10.1088/0067-0049/211/1/7

A. Goobar, J. Johansson, R. Amanullah, Y. Cao, D. A., M. M. Kasliwal, R. Ferretti, P. E., C. Harris, A. Gal-Yam, E. O. Ofek, S. P., M. Dennefeld, S. Valenti, I., D. P. K. Banerjee, V. Venkataraman, V., N. M. Ashok, S. B. Cenko, R. F. Diaz, C., A. Horesh, D. A. Howell, S. R. Kulkarni, S., T. Petrushevska, D. Sand, J., V. Stanishev, J. S. Bloom, J. Surace, T. J. Dupuy, M. C. Liu, The Rise of SN 2014J in the Nearby Galaxy M82, Astrophysical Journal Letters, Pages: L12 2014, doi: 10.1088/2041-8205/784/1/L12

Y.-C. Pan, M. Sullivan, K. Maguire, I. M. Hook, P. E., D. A. Howell, I. Arcavi, J. Botyanszki, S. B., J. DeRose, H. K. Fakhouri, A. Gal-Yam, E., S. R. Kulkarni, R. R. Laher, C. Lidman, J. Nordin, E. S. Walker, D. Xu, The host galaxies of Type Ia supernovae discovered by the Palomar Transient Factory, Monthly Notices of the RAS, Pages: 1391-1416 2014, doi: 10.1093/mnras/stt2287

A. Corsi, E. O. Ofek, A. Gal-Yam, D. A. Frail, S. R., D. B. Fox, M. M. Kasliwal, M., A. Horesh, J. Carpenter, K. Maguire, I., S. B. Cenko, Y. Cao, K. Mooley, Y.-C., B. Sesar, A. Sternberg, D. Xu, D., P. James, J. S. Bloom, P. E. Nugent, A Multi-wavelength Investigation of the Radio-loud Supernova PTF11qcj and its Circumstellar Environment, Astrophysical Journal, Pages: 42 2014, doi: 10.1088/0004-637X/782/1/42

E. O. Ofek, A. Zoglauer, S. E. Boggs, N. M. Barri\ ere, S. P., C. L. Fryer, F. A. Harrison, S. B., S. R. Kulkarni, A. Gal-Yam, I. Arcavi, E., J. S. Bloom, F. Christensen, W. W. Craig, W., A. V. Filippenko, B. Grefenstette, C. J., R. Laher, K. Madsen, E. Nakar, P. E., D. Stern, M. Sullivan, J. Surace, W. W. Zhang, SN 2010jl: Optical to Hard X-Ray Observations Reveal an Explosion Embedded in a Ten Solar Mass Cocoon, Astrophysical Journal, Pages: 42 2014, doi: 10.1088/0004-637X/781/1/42

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)

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,

Elif Dede, Zacharia Fadika, Madhusudhan Govindaraju, Lavanya Ramakrishnan, "Benchmarking MapReduce Implementations Under Different Application Scenarios", Future Generation Computer Systems, 2014,

Elif Dede, Zacharia Fadika, Madhusudhan Govindaraju, Lavanya Ramakrishnan, "MARIANE: Using MApReduce In HPC Environments", Future Generation Computer Systems, 2014,

Elif Dede, Bedri Sendir, Pinar Kuzlu, Madhusudhan Govindaraju, Lavanya Ramakrishnan, "A Processing Pipeline for Cassandra Datasets Based on Hadoop Streaming", IEEE International Congress on Big Data, 2014,

Tonglin Hawk, Ioan Raicu, Lavanya Ramakrishnan, "Scalable State Management for Scientific Applications in the Cloud", IEEE International Congress on Big Data, 2014,

Lavanya Ramakrishnan, Sarah Poon, Gilberto Z. Pastorello, Daniel Gunter, Valerie Hendrix, Deborah Agarwal, "Scientist-Centered Design for eScience:A Tigres Case Study", IEEE eScience, 2014,

T. Malas, G. Hager, H. Ltaief, D. Keyes, Towards energy efficiency and maximum computational intensity for stencil algorithms using wavefront diamond temporal blocking, arXiv preprint arXiv:1410.5561, 2014,

T. Malas, G. Hager, H. Ltaief, H. Stengel, G. Wellein, D. Keyes, Optimizing Stencil Computations: Multicore-optimized wavefront diamond blocking on Shared and Distributed Memory Systems, 2014,

Taylor Groves, Kurt B Ferreira, "BALANCING POWER AND TIME OF MPI OPERATIONS", CCR, 2014,

Paul Lin, Matthew Bettencourt, Stefan Domino, Travis Fisher, Mark Hoemmen, Jonathan Hu, Eric Phipps, Andrey Prokopenko, Siva Rajamanickam, Christopher Siefert, Stephen Kennon, "Towards extreme-scale simulations for low Mach fluids with second-generation Trilinos", Parallel Processing Letters, January 1, 2014, 24:1-20, doi: 10.1142/S0129626414420055

Borbala Hunyadi, Daan Camps, Laurent Sorber, Wim Van Paesschen, Maarten De Vos, Sabine Van Huffel, Lieven De Lathauwer, "Block term decomposition for modelling epileptic seizures", EURASIP Journal on Advances in Signal Processing, 2014, 2014, doi: 10.1186/1687-6180-2014-139

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,

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,

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,

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.

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

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

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.

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

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,

Kevin Gott, Anil Kulkarni, Jogender Singh, "A Comparison of Continuum, DSMC and Free Molecular Modeling Techniques for Physical Vapor Deposition", 2013 ASME International Mechanical Engineering Congress and Exposition, 2013, IMECE201, doi: 10.1115/IMECE2013-66433

Advanced Physical Vapor Deposition (PVD) techniques are available that produce thin-film coatings with adaptive nano-structure and nano-chemistry. However, such components are manufactured through trial-and-error methods or in repeated small increments due to a lack of adequate knowledge of the underlying physics. Successful computational modeling of PVD technologies would allow coatings to be designed before fabrication, substantially improving manufacturing potential and efficiency.

Previous PVD modeling efforts have utilized three different physical models depending on the expected manufacturing pressure: continuum mechanics for high pressure flows, Direct Simulation Monte Carlo (DSMC) modeling for intermediate pressure flows or free-molecular (FM) dynamics for low pressure flows. However, preliminary calculations of the evaporation process have shown that a multi-physics fluidic solver that includes all three models may be required to accurately simulate PVD coating processes. This is due to the high vacuum and intermolecular forces present in vapor metals which cause a dense continuum region to form immediately after evaporation and expands to a rarefied region before depositing on the target surface.

This paper seeks to understand the effect flow regime selection has on the predicted deposition profile of PVD processes. The model is based on experiments performed at the Electron-Beam PVD (EB-PVD) laboratory at the Applied Research Lab at Penn State. CFD, DSMC and FM models are separately used to simulate a coating process and the deposition profiles are compared. The mass deposition rates and overall flow fields of each model are compared to determine if the underlying physics significantly alter the predicted coating profile. Conclusions are drawn on the appropriate selection of fluid physics for future PVD simulations.

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,

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,

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,

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.

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) doi: 10.3233/978-1-61499-324-7-141

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

C. J. Yang, Q. Guo, D. Huang, and S. Nordholm, "Enhanced Data Detection in OFDM Systems using Factor Graph", IEEE International Conference on Wireless Communications and Signal Processing (WCSP'13), pp. 1-5, October 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.

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


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, doi: 10.1088/0029-5515/53/11/113037

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.

P. Mohapatra, A Dubey, C. Daley, M. Vanella, and E. Balaras, "Parallel Algorithms for Using Lagrangian Markers in Immersed Boundary Method with Adaptive Mesh Refinement in FLASH", Computer Architecture and High Performance Computing (SBAC-PAD), October 2013, doi: 10.1109/SBAC-PAD.2013.27

Stephan Dürr, Zoltán Fodor, Christian Hoelbling, Stefan Krieg, Thorsten Kurth, Laurent Lellouch, Thomas Lippert, Rehan Malak, Thibaut Métivet, Antonin Portelli, Alfonso Sastre, Kálmán Szabó, "Lattice QCD at the physical point meets SU(2) chiral perturbation theory", Journal, October 14, 2013,

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

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

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,

Zhengji Zhao, Process and Thread Affinity with OpenMP, NERSC User Training on Edison Performance, Oakland, CA, October 10, 2013,

Babak Behzad, Huong Luu, Joey Huchette, Suren Byna, Prabhat, Ruth Aydt, Quincey Koziol, Marc Snir, "Taming Parallel I/O Complexity with Auto-Tuning", SuperComputing 2013, October 9, 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, doi: 10.1021/ac402540a

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,

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,

S. Bogner,A. Bulgac, J. Carlson, J. Engel, G. Fann, R.J. Furnstahl, S. Gandolfi, G. Hagen, M. Horoi, C. Johnson, M. Kortelainen, E. Lusk, P. Maris, H. Nam, P. Navratil, W. Nazarewicz, E. Ng, G.P.A. Nobre, E. Ormand, T. Papenbrock, J. Pei, S.C. Pieper, S. Quaglioni, K.J. Roche, J. Sarich, N. Schunck, M. Sosonkina, J. Terasaki, I. Thompson, J.P. Vary, S.M. Wild, "Computational nuclear quantum many-body problem: The UNEDF project", CPC 184 2235-2250 (2013), October 1, 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".

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,

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.

 

Woo-Sun Yang, Debugging and Performance Analysis Tools at NERSC, BOUT++ 2013 Workshop, September 3, 2013,

A. Dubey, K. Weide, D. Lee, J. Bachan, C. Daley, S. Olofin, N. Taylor, P. M. Rich, and L. B. Reid, "Ongoing verification of a multiphysics community code: FLASH", Software: Practice and Experience, September 2013, doi: 10.1002/spe.2220

Michael A. Heroux, Richard Frederick Barrett, James Michael Willenbring, Daniel W Barnette, David Beckingsale, James F Belak, Mike Boulton, Paul Crozier, Douglas W. Doerfler, Harold C. Edwards, Wayne Gaudin, Timothy C Germann, Simon David Hammond, Andy Herdman, Stephen Jarvis, Paul Lin, Justin Luitjens, Andrew Mallinson, Simon McIntosh-Smith, Susan M Mniszewski, Jamaludin Mohd-Yusof, David F Richards, Christopher Sewell, Sriram Swaminarayan, Heidi K. Thornquist, Christian Robert Trott, Courtenay T. Vaughan, Alan B. Williams, R&D 100 Award, Mantevo Suite 1.0, R&D Magazine, August 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,

Rolf Riesen, Sudip Dosanjh, Larry Kaplan, "The ExaChallenge Symposium", IBM Research Paper, August 26, 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,

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

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, doi: 10.1063/1.4812323

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, July 2013, doi: 10.1177/1094342012464404

Zhengji Zhao, Edison Phase I Early User Science Results, A brown bag talk at NERSC, Oakland CA; Cray Quarterly Business Review Meeting, St. Paul, MN, July 22, 2013,

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

H. Nam and D.J. Dean, "Re-entrance in nuclei: competitive phenomena", J. Phys.: Conf. Ser. 445 012029 (2013), July 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.

Sz. Borsanyi, S. Dürr, Z. Fodor, J. Frison, C. Hoelbling, S.D. Katz, S. Krieg, Th. Kurth, L. Lellouch, Th. Lippert, A. Portelli, A. Ramos, A. Sastre, K. Szabo, "Isospin splittings in the light baryon octet from lattice QCD and QED", Journal, June 10, 2013,

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

C. J. Yang, Q. Guo, D. Huang, and S. Nordholm, "A Factor Graph Approach to Exploiting Cyclic Prefix for Equalization in OFDM systems", IEEE Transactions on Communications, vol. 61, no. 12, pp. 4972-4983, June 2013,

Chris Paciorek, Benjamin Lipschitz, Tina Zhuo, Cari Kaufman, Prabhat, Rollin Thomas, "Parallelized Gaussian Processes in R", Journal of Statistical Software, May 23, 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,

T. Kurth, N. Ishii, T. Doi, S. Aoki, T. Hatsuda, "Phase shifts in I=2ππ-scattering from two lattice approaches", Journal, May 20, 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.

Larry Pezzaglia, "Supporting Multiple Workloads, Batch Systems, and Computing Environments on a Single Linux Cluster", Cray User Group 2013, May 9, 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,

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

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

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

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.

Scott French, Vedran Lekic, Barbara Romanowicz, "Waveform Tomography Reveals Channeled Flow at the Base of the Oceanic Asthenosphere", Science, 2013, 342:227, doi: 10.1126/science.1241514

C. J. Yang, Q. Guo, D. Huang, and S. Nordholm, "Exploiting Cyclic Prefix in Turbo FDE Systems using Factor Graph", IEEE Wireless Communications and Networking Conference (WCNC'13), pp. 2536-2541, April 2013,

Glenn K. Lockwood, Stephen H. Garofalini, "Lifetimes of excess protons in water using a dissociative water potential", Journal of Physical Chemistry B, April 8, 2013, 117:4089-4097, doi: 10.1021/jp310300x

Molecular dynamics simulations using a dissociative water potential were applied to study transport of excess protons in water and determine the applicability of this potential to describe such behavior. While originally developed for gas-phase molecules and bulk liquid water, the potential is transferrable to nanoconfinement and interface scenarios. Applied here, it shows proton behavior consistent with ab initio calculations and empirical models specifically designed to describe proton transport. Both Eigen and Zundel complexes are observed in the simulations showing the Eigen–Zundel–Eigen-type mechanism. In addition to reproducing the short-time rattling of the excess proton between the two oxygens of Zundel complexes, a picosecond-scale lifetime was also found. These longer-lived H3O+ ions are caused by the rapid conversion of the local solvation structure around the transferring proton from a Zundel-like form to an Eigen-like form following the transfer, effectively severing the path along which the proton can rattle. The migration of H+ over long times (>100 ps) deviates from the conventional short-time multiexponentially decaying lifetime autocorrelation model and follows the t–3/2 power-law behavior. The potential function employed here matches many of the features of proton transport observed in ab initio molecular dynamics simulations as well as the highly developed empirical valence bond models, yet is computationally very efficient, enabling longer time and larger systems to be studied.

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

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

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,

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

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

Francesca Verdier, NERSC Accomplishments and Plans, February 12, 2013,

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

NERSC-8 Project Overview

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

Nick Wright, NERSC Initiative: Preparing Applications for Exascale, February 12, 2013,

Yushu Yao, NERSC Parallel Database Evaluation, February 12, 2013,

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

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

David Skinner and Shane Canon, NERSC and High Throughput Computing, February 12, 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, doi: http://dx.doi.org/10.1016/j.commatsci.2012.10.028

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,

M. V. Stoitsov, N. Schunck, M. Kortelainen, N. Michel, H. Nam, E. Olsen, J. Sarich, S. Wild, "Axially deformed solution of the Skyrme-Hartree-Fock-Bogolyubov equations using the transformed harmonic oscillator basis (II)", HFBTHO v2.00c: a new version of the program, arXiv:1210.1825 [nucl-th], 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,

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.

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, doi: 10.1093/mnras/sts492

 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.

 

 

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,

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, doi: 10.1109/TVCG.2012.120

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,

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, Best Paper Award., 2013,

Mark Howison, E. Wes Bethel, GPU-accelerated Denoising of 3D Magnetic Resonance Images, Journal of Real Time Image Processing, 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,

P. A. Mazzali S. Hachinger, The UV/optical spectra of the Type Ia supernova SN 2010jn: a supernova with outer layers rich in iron-group elements, Monthly Notices of the Royal Astronomical Society, Pages: 490 2013, doi: 10.1093/mnras/sts492

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,

A. Horesh, C. Stockdale, D. B. Fox, D. A. Frail, J., S. R. Kulkarni, E. O. Ofek, A., M. M. Kasliwal, I. Arcavi, R. Quimby, S. B., P. E. Nugent, J. S. Bloom, N. M. Law, D., E. Gorbikov, D. Polishook, O. Yaron, S., K. W. Weiler, F. Bauer, S. D. Van Dyk, S., N. Panagia, D. Pooley, N. Kassim, An early and comprehensive millimetre and centimetre wave and X-ray study of SN 2011dh: a non-equipartition blast wave expanding into a massive stellar wind, Monthly Notices of the RAS, Pages: 1258-1267 2013, doi: 10.1093/mnras/stt1645

J. M. Silverman, J. Vinko, M. M. Kasliwal, O. D., Y. Cao, J. Johansson, D. A. Perley, D., J. C. Wheeler, R. Amanullah, I. Arcavi, J. S., A. Gal-Yam, A. Goobar, S. R. Kulkarni, R., W. H. Lee, G. H. Marion, P. E. Nugent, I. Shivvers, SN 2000cx and SN 2013bh: extremely rare, nearly twin Type Ia supernovae, Monthly Notices of the RAS, Pages: 1225-1237 2013, doi: 10.1093/mnras/stt1647

K. Maguire, M. Sullivan, F. Patat, A. Gal-Yam, I. M., S. Dhawan, D. A. Howell, P. Mazzali, P. E., Y.-C. Pan, P. Podsiadlowski, J. D., A. Sternberg, S. Valenti, C. Baltay, D., N. Blagorodnova, T.-W. Chen, N. Ellman, U., F. F\ orster, M. Fraser, S. Gonz\ alez-Gait\ an, M. L., C. Guti\ errez, S. Hachinger, E., C. Inserra, C. Knapic, R. R. Laher, G., S. Margheim, R. McKinnon, M. Molinaro, N., E. O. Ofek, D. Rabinowitz, A. Rest, D., R. Smareglia, S. J. Smartt, F. Taddia, E. S. Walker, N. A. Walton, D. R. Young, A statistical analysis of circumstellar material in Type Ia supernovae, Monthly Notices of the RAS, Pages: 222-240 2013, doi: 10.1093/mnras/stt1586

W. Zheng, J. M. Silverman, A. V. Filippenko, D., P. E. Nugent, M. Graham, X. Wang, S., F. Ciabattari, P. L. Kelly, O. D. Fox, I., K. I. Clubb, S. B. Cenko, D. Balam, D. A., E. Hsiao, W. Li, G. H. Marion, D., J. Vinko, J. C. Wheeler, J. Zhang, The Very Young Type Ia Supernova 2013dy: Discovery, and Strong Carbon Absorption in Early-time Spectra, Astrophysical Journal Letters, Pages: L15 2013, doi: 10.1088/2041-8205/778/1/L15

L. P. Singer, S. B. Cenko, M. M. Kasliwal, D. A., E. O. Ofek, D. A. Brown, P. E. Nugent, S. R., A. Corsi, D. A. Frail, E. Bellm, J., I. Arcavi, T. Barlow, J. S. Bloom, Y., N. Gehrels, A. Horesh, F. J. Masci, J., A. Rau, J. A. Surace, O. Yaron, Discovery and Redshift of an Optical Afterglow in 71 deg$^2$: iPTF13bxl and GRB 130702A, Astrophysical Journal Letters, Pages: L34 2013, doi: 10.1088/2041-8205/776/2/L34

Y. Cao, M. M. Kasliwal, I. Arcavi, A. Horesh, P., S. Valenti, S. B. Cenko, S. R. Kulkarni, A., E. Gorbikov, E. O. Ofek, D. Sand, O., M. Graham, J. M. Silverman, J. C. Wheeler, G. H., E. S. Walker, P. Mazzali, D. A. Howell, K. L., A. K. H. Kong, J. S. Bloom, P. E. Nugent, J., F. Masci, J. Carpenter, N. Degenaar, C. R. Gelino, Discovery, Progenitor and Early Evolution of a Stripped Envelope Supernova iPTF13bvn, Astrophysical Journal Letters, Pages: L7 2013, doi: 10.1088/2041-8205/775/1/L7

J. M. Silverman, P. E. Nugent, A. Gal-Yam, M., D. A. Howell, A. V. Filippenko, Y.-C. Pan, S. B. Cenko, I. M. Hook, Late-time Spectral Observations of the Strongly Interacting Type Ia Supernova PTF11kx, Astrophysical Journal, Pages: 125 2013, doi: 10.1088/0004-637X/772/2/125

S. Taubenberger, M. Kromer, S. Hachinger, P. A., S. Benetti, P. E. Nugent, R. A. Scalzo, R., V. Stanishev, J. Spyromilio, F. Bufano, S. A. Sim, B. Leibundgut, W. Hillebrandt, Super-Chandrasekhar Type Ia Supernovae at nebular epochs, Monthly Notices of the RAS, Pages: 3117-3130 2013, doi: 10.1093/mnras/stt668

J. M. Silverman, P. E. Nugent, A. Gal-Yam, M., D. A. Howell, A. V. Filippenko, I., S. Ben-Ami, J. S. Bloom, S. B. Cenko, Y., R. Chornock, K. I. Clubb, A. L. Coil, R. J., M. L. Graham, C. V. Griffith, A., M. M. Kasliwal, S. R. Kulkarni, D. C., W. Li, T. Matheson, A. A. Miller, M., E. O. Ofek, Y.-C. Pan, D. A. Perley, D., R. M. Quimby, T. N. Steele, A. Sternberg, D. Xu, O. Yaron, Type Ia Supernovae Strongly Interacting with Their Circumstellar Medium, Astrophysical Journal Supplement, Pages: 3 2013, doi: 10.1088/0067-0049/207/1/3

C. Baltay, D. Rabinowitz, E. Hadjiyska, E. S. Walker, P., P. Coppi, N. Ellman, U. Feindt, R. McKinnon, B. Horowitz, A. Effron, The La Silla-QUEST Low Redshift Supernova Survey, Publications of the ASP, Pages: 683-694 2013, doi: 10.1086/671198

E. Terziev, N. M. Law, I. Arcavi, C. Baranec, J. S., K. Bui, M. P. Burse, P. Chorida, H. K., R. G. Dekany, A. L. Kraus, S. R. Kulkarni, P., E. O. Ofek, S. Punnadi, A. N. Ramaprakash, R. Riddle, M. Sullivan, S. P. Tendulkar, Millions of Multiples: Detecting and Characterizing Close-separation Binary Systems in Synoptic Sky Surveys, Astrophysical Journal Supplement, Pages: 18 2013, doi: 10.1088/0067-0049/206/2/18

S. B. Cenko, S. R. Kulkarni, A. Horesh, A. Corsi, D. B., J. Carpenter, D. A. Frail, P. E. Nugent, D. A., D. Gruber, A. Gal-Yam, P. J. Groot, G., E. O. Ofek, A. Rau, C. L. MacLeod, A. A., J. S. Bloom, A. V. Filippenko, M. M., N. M. Law, A. N. Morgan, D. Polishook, D., R. M. Quimby, B. Sesar, K. J. Shen, J. M. Silverman, A. Sternberg, Discovery of a Cosmological, Relativistic Outburst via its Rapidly Fading Optical Emission, Astrophysical Journal, Pages: 130 2013, doi: 10.1088/0004-637X/769/2/130

R. L. Barone-Nugent, C. Lidman, J. S. B. Wyithe, J., D. A. Howell, I. M. Hook, M. Sullivan, P. E., I. Arcavi, S. B. Cenko, J. Cooke, A., E. Y. Hsiao, M. M. Kasliwal, K. Maguire, E. Ofek, D. Poznanski, D. Xu, Erratum: Near-infrared observations of type Ia supernovae: The best known standard candle for cosmology, Monthly Notices of the RAS, Pages: L90 2013, doi: 10.1093/mnrasl/slt038

D. Levitan, T. Kupfer, P. J. Groot, S. R. Kulkarni, T. A., G. V. Simonian, I. Arcavi, J. S. Bloom, R., P. E. Nugent, E. O. Ofek, B. Sesar, J. Surace, Five new outbursting AM CVn systems discovered by the Palomar Transient Factory, Monthly Notices of the RAS, Pages: 996-1007 2013, doi: 10.1093/mnras/sts672

S. Tang, Y. Cao, L. Bildsten, P. Nugent, E., S. R. Kulkarni, R. Laher, D. Levitan, F., E. O. Ofek, T. A. Prince, B. Sesar, J. Surace, R Coronae Borealis Stars in M31 from the Palomar Transient Factory, Astrophysical Journal Letters, Pages: L23 2013, doi: 10.1088/2041-8205/767/2/L23

E. Y. Hsiao, G. H. Marion, M. M. Phillips, C. R., C. Winge, N. Morrell, C. Contreras, W. L., M. Kromer, E. E. E. Gall, C. L., P. H\ oflich, M. Im, Y. Jeon, R. P., P. E. Nugent, S. E. Persson, G., M. Roth, V. Stanishev, M. Stritzinger, N. B. Suntzeff, The Earliest Near-infrared Time-series Spectroscopy of a Type Ia Supernova, Astrophysical Journal, Pages: 72 2013, doi: 10.1088/0004-637X/766/2/72

E. O. Ofek, M. Sullivan, S. B. Cenko, M. M. Kasliwal, A., S. R. Kulkarni, I. Arcavi, L. Bildsten, J. S., A. Horesh, D. A. Howell, A. V. Filippenko, R., D. Murray, E. Nakar, P. E. Nugent, J. M., N. J. Shaviv, J. Surace, O. Yaron, An outburst from a massive star 40days before a supernova explosion, Nature, Pages: 65-67 2013, doi: 10.1038/nature11877

P. W. Nugent, J. A. Shaw, S. Piazzolla, Infrared Cloud Imager Development for Atmospheric Optical Communication Characterization, and Measurements at the JPL Table Mountain Facility, Interplanetary Network Progress Report, Pages: C1 2013,

E. O. Ofek, D. Fox, S. B. Cenko, M. Sullivan, O., D. A. Frail, A. Horesh, A. Corsi, R. M., N. Gehrels, S. R. Kulkarni, A., P. E. Nugent, O. Yaron, A. V. Filippenko, M. M., L. Bildsten, J. S. Bloom, D., I. Arcavi, R. R. Laher, D. Levitan, B. Sesar, J. Surace, X-Ray Emission from Supernovae in Dense Circumstellar Matter Environments: A Search for Collisionless Shocks, Astrophysical Journal, Pages: 42 2013, doi: 10.1088/0004-637X/763/1/42

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

Andrew Uselton, Nicholas J. Wright, "A file system utilization metric for I/O characterization", 2013 Cray User Group Conference, Napa, CA, 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,

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,

Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Susan Coghlan, Shane Canon, Anping Liu, Devarshi Ghoshal, Krishna Muriki, Nicholas J. Wright, "Magellan - A Testbed to Explore Cloud Computing for Science", On the Road to Exascale Computing: Contemporary Architectures in High Performance Computing, (Chapman & Hall/CRC Press: 2013)

Valerie Hendrix, Lavanya Ramakrishnan, Youngryel Ryu, Catharine van Ingen, Keith R. Jackson, Deborah Agarwal, "CAMP: Community access MODIS pipeline", Future Generation Computer Systems, 2013,

Eugen Feller, Lavanya Ramakrishnan, Christine Morin, "On the Performance and Energy Efficiency of Hadoop Deployment Models", The IEEE International Conference on Big Data 2013 (IEEE BigData 2013), Santa Clara, U.S.A, 2013,

Elif Dede, Madhusudhan Govindaraju, Daniel Gunter, Richard Canon, Lavanya Ramakrishnan, "Semi-Structured Data Analysis using MongoDB and MapReduce: A Performance Evaluation", Proceedings of the 4th international workshop on Scientific cloud computing, 2013,

You-Wei Cheah, Richard Canon, Beth Plale, Lavanya Ramakrishnan, "Milieu: Lightweight and Configurable Big Data Provenance for Science", IEEE Big Data Congress, 2013,

E. Masanet, A. Shehabi, L. Ramakrishnan, J. Liang, X. Ma, B. Walker, V. Hendrix, P Mantha, "The Energy Efficiency Potential of Cloud-Based Software: A U.S.Case Study", 2013, LBNL 6298E,

Lavanya Ramakrishnan, Adam Scovel, Iwona Sakrejda, Susan Coghlan, Shane Canon, Anping Liu, Devarshi Ghoshal, Krishna Muriki and Nicholas J. Wright, "CAMP", On the Road to Exascale Computing: Contemporary Architectures in High Performance Computing, (Chapman & Hall/CRC Press: January 1, 2013)

Tareq Malas, Aron J. Ahmadia, Jed Brown, John A. Gunnels, David E. Keyes, "Optimizing the performance of streaming numerical kernels on the IBM Blue Gene/P PowerPC 450 processor", International Journal of High Performance Computing Applications, 2013, 27:193-209, doi: 10.1177/1094342012444795

Taylor Groves, Dorian Arnold, Yihua He, "In-network, Push-based Network Resource Monitoring: Scalable, Responsive Network Management", Proceedings of the Third International Workshop on Network-Aware Data Management, 2013, 8,

Joshua D Goehner, Taylor L Groves, Dorian C Arnold, Dong H Ahn, Gregory L Lee, "An Optimal Algorithm for Extreme Scale Job Launching", Trust, Security and Privacy in Computing and Communications (TrustCom), 2013 12th IEEE International Conference on, 2013, 1115--1122,

Klaus Roeller, Johannes Blaschke, Stephan Herminghaus, Juergen Vollmer, "Arrest of the flow of wet granular matter", Journal of Fluid Mechanics, 2013, 738:407--422, doi: 10.1017/jfm.2013.587

Johannes Blaschke, Juergen Vollmer, "Granular Brownian motors: Role of gas anisotropy and inelasticity", Phys. Rev. E, 2013, 87:040201, doi: 10.1103/PhysRevE.87.040201

Hai Ah Nam, Jason Hill, Suzanne Parete-Koon, "The Practical Obstacles of Data Transfer: Why Researchers Still Love Scp", NDM 13, New York, NY, USA, Association for Computing Machinery, 2013, doi: 10.1145/2534695.2534703

Matthew R. Link, David Y. Hancock, Kurt Seiffert, Stephen Simms, Scott Michael, Craig A. Stewart, Usage of Indiana University computation and data cyberinfrastructure in FY 2011/2012 and assessment of future needs, 2013,

Mike J. Floyd, Kurt Seiffert, Craig A. Stewart, George Turner, Dennis Cromwell, Dave Hancock, Kristy Kallback-Rose, Matthew R. Link, Steve Simms, Troy Williams, Storage Briefing: Trends and IU, 2013,

Michael Kluge, Stephen Simms, Thomas William, Robert Henschel, Andy Georgi, Christian Meyer, Matthias S. Mueller, Craig A. Stewart, Wolfgang Wünsch, Wolfgang E. Nagel, "Performance and quality of service of data and video movement over a 100 Gbps testbed", Future Generation Computer Systems, 2013, 29:230--240, doi: 10.1016/j.future.2012.05.028

A Dubey, K Antypas, A Calder, B Fryxell, D Lamb, P Ricker, L Reid, K Riley, R Rosner, A Siegel, F Timmes, N Vladimirova, K Weide, "The Software Development Process of FLASH, a Multiphysics Simulation Code", 2013, 1--8,

2012

D. Duke, H. Carr, A. Knoll, N. Schunck, H. Nam, A. Staszczak,, "Visualizing Nuclear Scission Through a Multifield Extension of Topological Analysis", IEEE Trans. Visualization and Computer Graphics, vol. 18, no. 12, pp. 2033-2040, Dec. 2012, December 1, 2012,

Glenn K. Lockwood, Stephen H. Garofalini, "Reactions between water and vitreous silica during irradiation", Journal of Nuclear Materials, November 30, 2012, 430:239-245, doi: 10.1016/j.jnucmat.2012.07.004

Molecular dynamics simulations were conducted to determine the response of a vitreous silica surface in contact with water to radiation damage. The defects caused by radiation damage create channels that promote high H+ mobility and result in significantly higher concentration and deeper penetration of H+ in the silica subsurface. These subsurface H+ hop between acidic sites such as SiOH2+ and Si–(OH)–Si until subsequent radiation ruptures siloxane bridges and forms subsurface non-bridging oxygens (NBOs); existing excess H+ readily bonds to these NBO sites to form SiOH. The high temperature caused by irradiation also promotes the diffusion of molecular H2O into the subsurface, and although H2O does not penetrate as far as H+, it readily reacts with ruptured bridges to form 2SiOH. These SiOH sites are thermally stable and inhibit the reformation of bridges that would otherwise occur in the absence of water. In addition to this reduction of self-healing, the presence of water during the self-irradiation of silica may cause an increase in the glass’s proton conductivity.

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,

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,

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.

Richard F. Barrett, Simon D. Hammond, Courtenay T. Vaughan, Doug W. Doerfler, Michael A. Heroux, Justin P. Luitjens, Duncan Roweth, "Navigating An Evolutionary Fast Path to Exascale", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS12), November 2012,

Mahesh Rajan, Douglas W. Doerfler, Paul T. Lin, Simon D. Hammond, Richard F. Barrett, Courtney T. Vaughan, "Unprecedented Scalability and Performance of the New NNSA Tri-Lab Linux Capacity Cluster 2", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS12), November 2012,

Richard Barrett, Paul Crozier, Doug Doerfler, Simon Hammond, Mike Heroux, Paul Lin, Tim Trucano, Courtenay Vaughan, Alan Williams, "Assessing the Predictive Capabilities of Mini-applications", The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC12), November 2012,

Robert Henschel, Stephen Simms, David Hancock, Scott Michael, Tom Johnson, Nathan Heald, Thomas William, Donald Berry, Matt Allen, Richard Knepper, Matthew Davy, Matthew Link, Craig A. Stewart, "Demonstrating lustre over a 100Gbps wide area network of 3,500km", SC '12, Washington, DC, USA, IEEE Computer Society Press, 2012, 1--8, doi: 10.1109/SC.2012.43

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

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,

Friesen, B., Baron, E., Branch, D., Chen, B., Parrent, J., Thomas, R. C., "Supernova Resonance-scattering Line Profiles in the Absence of a Photosphere", The Astrophysical Journal Supplements Series, 2012, 203:1, doi: 10.1088/0067-0049/203/1/12

In supernova (SN) spectroscopy relatively little attention has been given to the properties of optically thick spectral lines in epochs following the photosphere's recession. Most treatments and analyses of post-photospheric optical spectra of SNe assume that forbidden-line emission comprises most if not all spectral features. However, evidence exists that suggests that some spectra exhibit line profiles formed via optically thick resonance-scattering even months or years after the SN explosion. To explore this possibility, we present a geometrical approach to SN spectrum formation based on the "Elementary Supernova" model, wherein we investigate the characteristics of resonance-scattering in optically thick lines while replacing the photosphere with a transparent central core emitting non-blackbody continuum radiation, akin to the optical continuum provided by decaying 56Co formed during the explosion. We develop the mathematical framework necessary for solving the radiative transfer equation under these conditions and calculate spectra for both isolated and blended lines. Our comparisons with analogous results from the Elementary Supernova code SYNOW reveal several marked differences in line formation. Most notably, resonance lines in these conditions form P Cygni-like profiles, but the emission peaks and absorption troughs shift redward and blueward, respectively, from the line's rest wavelength by a significant amount, despite the spherically symmetric distribution of the line optical depth in the ejecta. These properties and others that we find in this work could lead to misidentification of lines or misattribution of properties of line-forming material at post-photospheric times in SN optical spectra.

A. Ovsyannikov, V. Sabelnikov, M. Gorokhovski, "A new level set equation and its numerical assessments", Proceedings of the Summer Program, Center for Turbulence Research, Stanford University, November 1, 2012, 315-324,

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)

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,

Daya Bay Collaboration, F. P. An, Q. An, J. Z. Bai et al., "Improved Measurement of Electron Antineutrino Disappearance at Daya Bay", Phys. Rev. Letter, October 23, 2012, doi: 10/2012; DOI:10.1088/1674-1137/37/1/011001

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

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,

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

Brandon Cook, William R French, Kálmán Varga, "Electron transport properties of carbon nanotube–graphene contacts", Applied Physics Letters, 2012,

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

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,

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

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

V. Sabelnikov, A. Ovsyannikov, M. Gorokhovski, "Modified level set equation for gas-liquid interface and its numerical solution", ICLASS 2012, 12th Triennial International Conference on Liquid, Heidelberg, Germany, September 2, 2012,

V. Sabelnikov, A. Ovsyannikov, M. Gorokhovski, "Modified level set equation for gas-liquid interface and its numerical solution", ECCOMAS 2012 - European Congress on Computational Methods in Applied Sciences and Engineering, Vienna, Austria, September 1, 2012,

A. Bhagatwala, S.K. Lele, "Interaction of a converging spherical shock wave with isotropic turbulence", Physics of Fluids, 2012,

Zhengji Zhao, Megan Bowling, and Jack Deslippe, Using Cray Compilers at NERSC - Usability and Performance, Cray Quarterly Business Review Meeting, Oakland, CA, July 25, 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,

K Kallback-Rose, D Antolovic, R Ping, K Seiffert, C Stewart, T Miller, "Conducting K-12 Outreach to Evoke Early Interest in IT, Science, and Advanced Technology", ACM, July 16, 2012,

This is a preprint of a paper presented at XSEDE '12: The 1st Conference of the Extreme Science and Engineering Discovery Environment, Chicago, Illinois.

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,

D. A. Pigg, G. Hagen, H. Nam, T. Papenbrock, "Time-dependent coupled-cluster method for atomic nuclei", Phys. Rev. C 86, 014308 (2012), July 2012,

Zhengji Zhao, Introduction to Materials Science and Chemistry Applications at NERSC, NERSC User Training Event, Oakland CA, June 26, 2012,

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.

Scott Michael, Liang Zhen, Robert Henschel, Stephen Simms, Eric Barton, Matthew Link, "A study of lustre networking over a 100 gigabit wide area network with 50 milliseconds of latency", DIDC '12, New York, NY, USA, Association for Computing Machinery, 2012, 43--52, doi: 10.1145/2286996.2287005

Jihan Kim, Berend Smit, "Efficient Monte Carlo Simulations of Gas Molecules Inside Porous Materials", Journal of Chemical Theory and Computation, 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, doi: 10.1088/0067-0049/201/2/27

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

Who uses High Performance 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.

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. 

 

Parrent, J. T., Howell, D. A., Friesen, B., Thomas, R. C., Fesen, R. A., Milisavljevic, D., Bianco, F. B., Dilday, B., Nugent, P., Baron, E., Arcavi, I., Ben-Ami, S., Bersier, D., Bildsten, L., Bloom, J., Cao, Y., Cenko, S. B., Filippenko, A. V., Gal-Yam, A., Kasliwal, M. M., Konidaris, N., Kulkarni, S. R., Law, N. M., Levitan, D., Maguire, K., Mazzali, P. A., Ofek, E. O., Pan, Y., Polishook, D., Poznanski, D., Quimby, R. M., Silverman, J. M., Sternberg, A., Sullivan, M., Walker, E. S., Xu, Dong, Buton, C., Pereira, R., "Analysis of the Early-time Optical Spectra of SN 2011fe in M101", The Astrophysical Journal Letters, 2012, 752, doi: 10.1088/2041-8205/752/2/L26

The nearby Type Ia supernova (SN Ia) SN 2011fe in M101 (cz = 241 km s–1) provides a unique opportunity to study the early evolution of a "normal" SN Ia, its compositional structure, and its elusive progenitor system. We present 18 high signal-to-noise spectra of SN 2011fe during its first month beginning 1.2 days post-explosion and with an average cadence of 1.8 days. This gives a clear picture of how various line-forming species are distributed within the outer layers of the ejecta, including that of unburned material (C+O). We follow the evolution of C II absorption features until they diminish near maximum light, showing overlapping regions of burned and unburned material between ejection velocities of 10,000 and 16,000 km s–1. This supports the notion that incomplete burning, in addition to progenitor scenarios, is a relevant source of spectroscopic diversity among SNe Ia. The observed evolution of the highly Doppler-shifted O I λ7774 absorption features detected within 5 days post-explosion indicates the presence of O I with expansion velocities from 11,500 to 21,000 km s–1. The fact that some O I is present above C II suggests that SN 2011fe may have had an appreciable amount of unburned oxygen within the outer layers of the ejecta.

Paul T. Lin, "Improving multigrid performance for unstructured mesh drift-diffusion simulations on 147,000 cores", International Journal for Numerical Methods in Engineering, May 30, 2012, 91:971-989, doi: 10.1002/nme.4315

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

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,

Zhengji Zhao, Application and Development Software, A talk given at the N7 design review meeting, Oakland, CA, May 10, 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,

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.

H. Nam, M. Stoitsov, W. Nazarewicz, A. Bulgac, G. Hagen, M. Kortelainen, P. Maris, J. C. Pei, K. J. Roche, N. Schunck, I. Thompson, J. P. Vary, S. M. Wild
J.,
"UNEDF: Advanced Scientific Computing Collaboration Transforms the Low-Energy Nuclear Many-Body Problem", Phys.: Conf. Ser. 402 012033, 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,

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.

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.

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,

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,

Mahesh Rajan, Courtenay T. Vaughan, Doug W. Doerfler, Richard F. Barrett, Kevin T. Pedretti, Karl S. Hemmert, "Application-driven Analysis of Two Generations of Capability Computing Platforms: Purple and Cielo", Computation and Concurrency: Practice and Experience, Volume 24, Issue 18, March 2012,

Gemmill, Jill, et al, "Security at the Cyberborder, Workshop Report", March 28, 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

F. P. An, J. Z. Bai, A. B. Balantekin, et al., "Observation of electron-antineutrino disappearance at Daya Bay", Phys. Rev. Letter, 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

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,

Szabolcs Borsanyi, Stephan Durr, Zoltan Fodor, Christian Hoelbling, Sandor D. Katz, Stefan Krieg, Thorsten Kurth, Laurent Lellouch, Thomas Lippert, Craig McNeile, Kalman K. Szabo, "High-precision scale setting in lattice QCD", Journal, March 1, 2012,

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.

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

Tools for Performance Debugging HPC Applications, February 16, 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.

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

NERSC Accomplishments and Plans, February 3, 2012,

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

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

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

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.

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,

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,

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,

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

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

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,

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, doi: 10.1109/TVCG.2012.200

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, doi: 10.1145/2425296.2425324

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, doi: 10.1145/2425296.2425323

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, doi: 10.2312/PE/EuroVAST/EuroVA12/025-029

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,

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

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,

Oliver R\ ubel, Cameron G.R. Geddes, Min Chen, Estelle Cormier-Michel, E. Wes Bethel, Feature-based Analysis of Plasma-based Particle Acceleration Data, IEEE Transactions on Visualization and Computer Graphics (TVCG), 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,

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,

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,

Kevin Reed Michael Wehner, Christiane Jablonowski, Towards Projecting Changes in Tropical Cyclones with High Resolution CAM5.1, CESM Workshop, 2012,

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

Xuefei Yuan, Jin Chen, Xiaoye Li, Ichitaro Yamazaki, Stephen Jardin, Alice Koniges, David Keyes, "Scalability improvement of M3D-C1 via the block Jacobi preconditioner using PDSLin", Bulletin of the American Physical Society, 2012,

Alice Koniges, Xuefei Yuan, Wangyi Liu, Praveen Narayanan, Robert Preissl, Stephane Ethier, Weixang Wang, Stephen Jardin, Jeff Candy, Enabling Fusion Codes for Upcoming Exascale Platforms, Bulletin of the American Physical Society, 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 doi: 10.4018/978-1-61350-116-0.ch001

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, doi: 10.1002/cpe.2821

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, doi: 10.1088/1749-4699/5/1/015002

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,

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,

8th IEEE International Conference on E-Science, e-Science 2012, Chicago, IL, USA, October 8-12, 2012, e-Science, 2012,

Gunther H. Weber, Hank Childs, Jeremy S. Meredith, Efficient Parallel Extraction of Crack-free Isosurfaces from Adaptive Mesh Refinement (AMR) Data, Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), Pages: 31--38 2012, doi: 10.1109/LDAV.2012.6378973

Antonin Portelli, Stephan Durr, Zoltan Fodor, Julien Frison, Christian Hoelbling, Sandor D. Katz, Stefan Krieg, Thorsten Kurth, Laurent Lellouch, Thomas Lippert Alberto Ramos, Kalman K. Szabo, "Systematic errors in partially-quenched QCD plus QED lattice simulations", Conference, PoSLAT, January 2012,

Johannes Blaschke, Tobias Lapp, Bjoern Hof, Juergen Vollmer, "Breath Figures: Nucleation, Growth, Coalescence, and the Size Distribution of Droplets", Phys. Rev. Lett., 2012, 109:068701, doi: 10.1103/PhysRevLett.109.068701

Jonathan Bolte, Julie Wernert, Kurt Seiffert, Stephen C. Simms, Matthew R. Link, Marlon Pierce, Suresh Marru, David Y. Hancock, Therese Miller, Craig A. Stewart, Indiana University Pervasive Technology Institute – Research Technologies: XSEDE Service Provider and XSEDE subcontract report (PY1: 1 July 2011 to 30 June 2012), 2012,

Robert Henschel, Stephen C. Simms, David Y. Hancock, Scott Michael, Tom Johnson, Nathan Heald, Thomas William, Donald Berry, Matt Allen, Richard Knepper, Matthew Davy, Matthew R. Link, Craig A. Stewart, Technical Report: Report on Lustre use across an experimental 100Gb network spanning 2,175 mi, 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,

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


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,

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

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,

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

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

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

Ying Ma, Glenn K. Lockwood, Stephen H. Garofalini, "Development of a transferable variable charge potential for the study of energy conversion materials FeF2 and FeF3", Journal of Physical Chemistry C, November 18, 2011, 115:24198-2420, doi: 10.1021/jp207181s

A variable charge potential is developed that is suitable for the simulations of energy conversion materials FeF2 and FeF3. Molecular dynamics simulations using this potential show that the calculated structural and elastic properties of both FeF2 and FeF3 are in good agreement with experimental data. Such a transferability of this potential rests in the fact that the difference in the bond characteristic between FeF2 and FeF3 is properly accounted for by the variable charge approach. The calculated equilibrium charges are also in excellent agreement with first-principles Bader charges. Surface energies obtained by the variable charge method are closer to the first-principles data than are fixed charge models, indicating the importance of variable charge method for the simulations of the surface. A significant decrease in atomic charges is observed only for the outermost one or two layers, which is also observed in the first-principles calculations.

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,

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

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

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.

Christopher R Iacovella, William R French, Brandon Cook, Paul RC Kent, Peter T Cummings, "Role of polytetrahedral structures in the elongation and rupture of gold nanowires", ACS Nano, 2011,

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

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,

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, doi: 10.1007/s10509-011-0654-5

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.

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,

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

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

G. Hagen and H. Nam, "Computational aspects of nuclear coupled-cluster theory", Proceedings of the Yukawa International Seminar 2011 (YKIS2011) and Long-Term Workshop on Dynamics and Correlations in Exotic Nuclei (DCEN2011), October 2011,

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).

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.

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

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,

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.

Vedran Lekic, Scott French, Barbara Romanowicz, "Lithospheric Thinning Beneath Rifted Regions of Southern California", Science, 2011, 334:783, doi: 10.1126/science.1208898

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.

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 platforms, NCAR, Boulder, CO, September 7, 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,

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,

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

Kevin Pedretti, Ron Brightwell, Doug Doerfler, K. Scott Hemmert, James H. Laros, III, "The Impact of Injection Bandwidth Performance on Application Scalability", EuroMPI 2011. Lecture Notes in Computer Science, Volume 6960, September 2011,

S. Durr, Z. Fodor, T. Hemmert, C. Hoelbling, J. Frison, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, A. Portelli, A. Ramos, A. Schafer, K.K. Szabo, "Sigma term and strangeness content of octet baryons", Journal, September 1, 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,

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

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

S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, C. McNeile, A. Portelli, K.K. Szabo, "Kaon bag parameter B(K) at the physical mass point", Conference, PosLAT, August 2011,

G. Bali, S. Collins, S. Durr, Z. Fodor, R. Horsley, C. Hoelbling, S.D. Katz, I. Kanamori, S. Krieg, T. Kurth L. Lellouch, T. Lippert, C. McNeile, Y. Nakamura, D. Pleiter, P. Perez-Rubio, P. Rakow, A. Schafer, G.Schierholz K.K. Szabo, F. Winter, J. Zanotti, "Spectra of heavy-light and heavy-heavy mesons containing charm quarks, including higher spin states for Nf=2+1", Conference, PoSLAT, 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, ASCR Programming Challenges Workshop, July 2011,

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

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,

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,

M. Stoitsov, H. Nam, W. Nazarewicz, A. Bulgac, G. Hagen, M. Kortelainen, J. C. Pei, K. J. Roche, N. Schunck, I. Thompson, J.P. Vary, S. M. Wild, "UNEDF: Advanced Scientific Computing Transforms the Low-Energy Nuclear Many-Body Problem", Proceedings for SciDAC 2011, Denver, CO, July 2011,

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

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.

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

Kevin Gott, Anil Kulkarni, Jogender Singh, "Construction and Application of Unified Flow Solver for use with Physical Vapor Deposition (PVD) Modeling", 6th OpenFOAM Workshop, June 13, 2011,

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

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.

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

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.

Douglas W. Doerfler, ASC Salutes, National Nuclear Security Administration Advanced Simulation & Computing Program Office, June 2011,

S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, C. McNeile, A. Portelli, K.K. Szabo, "Precision computation of the kaon bag parameter", Journal, June 1, 2011,

Katie Antypas, Tina Butler, Jonathan Carter, "The Hopper System: How the Largest XE6 in the World went from Requirements to Reality", Cray User Group Proceedings, May 31, 2011,

Rebecca J. Hartman-Baker, Hai Ah Nam, "Optimizing Nuclear Physics Codes on the XT5", Proceedings of CUG 2011, 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,

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.

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,

"Programming Environment, Applications, and Documentation" SIG Group, CUG 2011 Special Interest Group, Fairbanks, AK., May 23, 2011,

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,

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

Courtenay T. Vaughan, Mahesh Rajan, Douglas W. Doerfler, Richard F. Barrett, Kevin Pedretti, "Investigating the Impact of the Cielo Cray XE6 Architecture on Scientific Application Codes", IPDPS 2011 International Workshop on Large-Scale Parallel Processing (LSPP'11), May 2011,

Brandon Cook, Peter Dignard, Kálmán Varga, "Calculation of electron transport in multiterminal systems using complex absorbing potentials", Physical Review B, May 16, 2011,

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.

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

 

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

 

Douglas Doerfler, Mahesh Rajan, Cindy Nuss, Cornell Wright, Tom Spelce, "Application-Driven Acceptance of Cielo, an XE6 Petascale Capability Platform", Cray User Group (CUG) 2011, May 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.

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,

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.

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

Manuel Vigil, Douglas Doerfler, Sudip Dosanjh, John Morrison, 2010 Defense Programs Award of Excellence for Significant Contributions to the Stockpile Stewardship Program, Successful Deployment of Cielo Petascale Supercomputer, National Nuclear Security Administration, April 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,

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

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

A. Bhagatwala, S.K. Lele, "Interaction of a Taylor blast wave with isotropic turbulence", Physics of Fluids, 2011,

Kevin Gott, Anil Kulkarni, Jogender Singh, Multi-Regime Computational Flow Modeling of Vapor Transport Mechanism of Physical Vapor Deposition (PVD) Coating Manufacturing Processes, Penn State College of Engineering Research Symposium (CERS) 2011, 2011,

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

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

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

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,

P. Maris, J.P. Vary, P. Navratil, W.E. Ormand, H. Nam, D.J. Dean, "Origin of the anomalous long lifetime of 14C", Phys. Rev. Lett. 105, 202502, 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

Starling R.~L Sakamoto Rowlinson Malesani O Brien Vergani Cano Evans Gehrels van der Horst Kamble Kaper Stamatikos, Discovery of the nearby long soft GRB 100316D with an associated supernova, \mnras, Pages: 2792-2803 January 1, 2011,

Thomas, R. C., Nugent, P. E., and Meza, J. C., "SYNAPPS: Data-Driven Analysis for Supernova Spectroscopy", Publications of the Astronomical Society of the Pacific, January 1, 2011, 123:237-248, doi: 10.1086/658673

J. a Howell Cenko Law Cooke, Hubble Space Telescope Studies of Nearby Type Ia Supernovae: The Mean Maximum Light Ultraviolet Spectrum and its Dispersion, \apjl, Pages: L35 January 1, 2011,

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,

J.~D Ofek Seibert Foster Schiminovich Lee Szalay Neill, The Extreme Hosts of Extreme Supernovae, \apj, Pages: 15 January 1, 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,

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,

R.~L Sakamoto Rowlinson Malesani O Brien Vergani Cano Evans Gehrels van der Horst Kamble Kaper Stamatikos Starling, Discovery of the nearby long, soft GRB 100316D with an associated supernova, \mnras, Pages: 2792-2803 January 1, 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,

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,

"25th IEEE International Symposium on Parallel and Distributed IPDPS 2011, Anchorage, Alaska, USA, 16-20 May 2011 - Workshop Proceedings", IPDPS Workshops, IEEE, January 1, 2011,

"Conference on High Performance Computing Networking, Storage Analysis, SC 2011, Seattle, WA, USA, November 12-18, 2011", SC, ACM, January 1, 2011,

Adamczyk, others, "Directed Flow of Identified Particles in Au + Au", January 1, 2011,

G. Agakishiev, others, "Measurement of the $W \to e \nu$ and $Z/\gamma^* \to Production Cross Sections at Mid-rapidity in", January 1, 2011,

G. Agakishiev, others, "Anomalous centrality evolution of two-particle angular from Au-Au collisions at $\sqrts_\rm NN$", January 1, 2011,

H. Agakishiev, others, "Evolution of the differential transverse momentum function with centrality in Au+Au collisions", Phys.Lett., January 1, 2011, B704:467-473,

H. Agakishiev, others, "Observation of the antimatter helium-4 nucleus", Nature, January 1, 2011, 473:353,

H. Agakishiev, others, "High $p_T$ non-photonic electron production in $p+p$", Phys.Rev., January 1, 2011, D83:052006,

H. Agakishiev, others, "Studies of di-jet survival and surface emission bias in collisions via angular correlations with respect to leading hadrons", Phys.Rev., January 1, 2011, C83:061901,

M.M. Aggarwal, others, "Strange and Multi-strange Particle Production in Au+Au", Phys.Rev., January 1, 2011, C83:024901,

M.M. Aggarwal, others, "Measurement of the parity-violating longitudinal asymmetry for $W^\pm$ boson production in", Phys.Rev.Lett., January 1, 2011, 106:062002,

M.M. Aggarwal, others, "Scaling properties at freeze-out in relativistic heavy collisions", Phys.Rev., January 1, 2011, C83:034910,

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,

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,

Robert Preissl, Wichmann, Long, Shalf, Ethier, Alice E. Koniges, "Multithreaded global address space communication techniques for gyrokinetic fusion applications on ultra-scale platforms", SC, 2011, 15,

Kamesh Madduri, Z. Ibrahim, Williams, Im, Ethier, Shalf, Leonid Oliker, "Gyrokinetic toroidal simulations on leading multi- and manycore HPC systems", SC, January 1, 2011, 23,

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

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

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,

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, doi: http://doi.acm.org/10.1145/2063384.2063424

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,

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

M. a Aragon Buton Copin Kowalski Pain Rabinowitz Tao Kerschhaggl, Cosmology with the Nearby Supernova Factory, Progress in Particle and Nuclear Physics, Pages: 335-339 January 1, 2011,

A.~M Nugent Quimby Hook Gal-Yam Jacobsen Walters Smith, Galaxy Zoo Supernovae, \mnras, Pages: 1309-1319 January 1, 2011,

M.~M Quimby Gal-Yam Howell Miller Poznanski Neill Gehrels Dekany Zolkower Bui Kasliwal, PTF 10fqs: A Luminous Red Nova in the Spiral Galaxy Messier 99, \apj, Pages: 134 January 1, 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,

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,

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,

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,

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, doi: 10.1109/TVCG.2010.80

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 5019E,

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, doi: 10.1177/1094342011431591

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, doi: 10.1145/2110205.2110208

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, doi: 10.1109/CLUSTER.2011.86

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,

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,

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Alice Koniges, David Eder, Modeling droplet breakup effects with diffuse interface methods in ALE-AMR code with application in modeling NDCX-II experiments, Bulletin of the American Physical Society, 2011,

D Eder, D Bailey, F Chamgers, I Darnell, PD Nicola, S Dixit, A Fisher, G Gururangan, D Kalantar, A Koniges, others, Observations and Modeling of Debris and Shrapnel Impacts on Optics and Diagnostics at the National Ignition Facility, 2011,

Jack Deslippe, S.G. Louie, "Ab initio Theories of the Structural, Electronic, and Optical Properties of Semiconductors: Bulk Systems to Nanostructures.", Comprehensive Semiconductor Science and Technology., (Elsevier: 2011) Pages: 42-76

T. M. Malas, Optimizing the performance of streaming numerical kernels on the IBM Blue Gene/P PowerPC 450, 2011,

Khaled Z. Ibrahim, S. Hofmeyr, Eric Roman, "Optimized Pre-Copy Live Migration for Memory Intensive Applications", The International Conference for High Performance Computing, Networking, Storage, and Analysis, 2011,

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,

 

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)

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

D.J. Dean, K. Langanke, H. Nam, and W. Nazarewicz, Reentrance Phenomenon in Heated Rotating Nuclei in the Shell Model Monte Carlo Approach, Phys. Rev. Lett. 105, 212504 (2010), "Reentrance Phenomenon in Heated Rotating Nuclei in the Shell Model Monte Carlo Approach", Phys. Rev. Lett. 105, 212504, November 2010,

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

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

Richard F Barrett, Courtenay T Vaughan, Mahesh Rajan, Douglas W Doerfler, "From Red Storm to Cielo: Performance Analysis of ASC Simulation Programs Across an Evolution of Multicore Architectures", The ACM/IEEE Conference on High Performance Networking and Computing (SC10), November 2010,

S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth,L. Lellouch, T. Lippert, K.K. Szabo, G. Vulvert, "Lattice QCD at the physical point: Simulation and analysis details", Journal, November 2010,

S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert,K.K. Szabo, G. Vulvert, "Lattice QCD at the physical point: light quark masses", Journal, November 2010,

A. Ramos, S. Durr, Z. Fodor, J. Frison, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, A. Portelli, K.K. Szabo, "Decayconstantsandsigmatermsfromthela ce", Conference, PoSICHEP, November 2010,

A. Portelli, S. Durr, Z. Fodor, J. Frison, C. Holbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, K.K. Szabo, A. Ramos, "Electromagnetic corrections to light hadron masses", Conference, November 2010,

J. Frison, S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, A. Portelli, A. Ramos, K.K. Szabo, "Rho decay width from the lattice", Conference, PoSLAT, November 2010,

J. Frison, S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, A. Portelli, A. Ramos, K.K. Szabo, "Scaling study for 2 HEX smeared fermions: hadron and quark masses", Conference, PoSLAT, November 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,

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,

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

Jack Dongarra, John Shalf, David Skinner, Kathy Yelick, "International Exascale Software Project (IESP) Roadmap, version 1.1", October 18, 2010,

Yun (Helen) He, Introduction to OpenMP, NERSC User Group 2010 Meeting, Oakland, CA, October 18, 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, LBNL 4074E,

 

 

 

David Abt, Karen Fischer, Scott French, Heather Ford, Huaiyu Yuan, Barbara Romanowicz, "North American lithospheric discontinuity structure imaged by Ps and Sp receiver functions", Journal of Geophysical Research, 2010, 115, doi: 10.1029/2009JB006914

A. Dubey, C. Daley, K. Weide, "Challenges of Computing with FLASH on Largest HPC Platforms", AIP Conference Proceedings, 2010, 1281:1773, doi: http://dx.doi.org/10.1063/1.3498219

Paul T. Lin, John N. Shadid, "Towards large-scale multi-socket, multicore parallel simulations: Performance of an MPI-only semiconductor device simulator", Journal of Computational Physics, September 20, 2010, 229:6804-6818, doi: 10.1016/j.jcp.2010.05.023

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,

Mahesh Rajan, Douglas Doerfler, "HPC application performance and scaling: understanding trends and future challenges with application benchmarks on past, present and future Tri-Lab computing systems", 8th International Conference of Numerical Analysis and Applied Mathematics, September 17, 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,

Harvey Wasserman, Simulation Science at NERSC, Cray Technical Workshop Japan, September 7, 2010,

Paul T. Lin, John N. Shadid, Raymond S. Tuminaro, Marzio Sala, Gary L. Hennigan, Roger P. Pawlowski, "A parallel fully coupled algebraic multilevel preconditioner applied to multiphysics PDE applications: drift-diffusion, flow/transport/reaction, resistive MHD", International Journal for Numerical Methods in Fluids, September 3, 2010, 64:1148-1179, doi: 10.1002/fld.2402

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,

 

 

S. Durr, Z. Fodor, J. Frison, T. Hemmert, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, A. Portelli, A. Ramos, A. Schafer, K.K. Szabo, "Sigma term and strangeness content of the nucleon", Conference, PoSLAT, September 2010,

Joshua Walgenbach, Stephen C. Simms, Kit Westneat, Justin P. Miller, "Enabling Lustre WAN for production use on the TeraGrid: a lightweight UID mapping scheme", TG '10, New York, NY, USA, Association for Computing Machinery, 2010, 1--6, doi: 10.1145/1838574.1838593

Scott Michael, Stephen Simms, W. B. Breckenridge, Roger Smith, Matthew Link, "A compelling case for a centralized filesystem on the TeraGrid: enhancing an astrophysical workflow with the data capacitor WAN as a test case", TG '10, New York, NY, USA, Association for Computing Machinery, 2010, 1--7, doi: 10.1145/1838574.1838587

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,

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,

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

 

Keith Jackson, Lavanya Ramakrishnan, Karl Runge, and Rollin Thomas, "Seeking Supernovae in the Clouds: A Performance Study", HPDC '10: Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, ACM, June 2010, 421–429, doi: 10.1145/1851476.1851538

Best Paper, ScienceCloud 2010

Today, our picture of the Universe radically differs from that of just over a decade ago. We now know that the Universe is not only expanding as Hubble discovered in 1929, but that the rate of expansion is accelerating, propelled by mysterious new physics dubbed "Dark Energy." This revolutionary discovery was made by comparing the brightness of nearby Type Ia supernovae (which exploded in the past billion years) to that of much more distant ones (from up to seven billion years ago). The reliability of this comparison hinges upon a very detailed understanding of the physics of the nearby events. As part of its effort to further this understanding, the Nearby Supernova Factory (SNfactory) relies upon a complex pipeline of serial processes that execute various image processing algorithms in parallel on ~10TBs of data.

This pipeline has traditionally been run on a local cluster. Cloud computing offers many features that make it an attractive alternative. The ability to completely control the software environment in a Cloud is appealing when dealing with a community developed science pipeline with many unique library and platform requirements. In this context we study the feasibility of porting the SNfactory pipeline to the Amazon Web Services environment. Specifically we: describe the tool set we developed to manage a virtual cluster on Amazon EC2, explore the various design options available for application data placement, and offer detailed performance results and lessons learned from each of the above design options.

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,

 

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

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

 

 



 

 

 

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

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,

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,

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,

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

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,

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,

Courtenay Vaughan, Douglas Doerfler, "Analyzing Multicore Characteristics for a Suite of Applications on an XT5 System", Cray User Group (CUG) 2010, May 2010,

J. Tomkins, R. Brightwell, W. Camp, S. Dosanjh, S. Kelly, P. Lin, C. Vaughan, J. Levesque, V. Tipparaju, "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, doi: 10.4018/jdst.2010040105

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. 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.

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,

 

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

Mahesh Rajan, Douglas Doerfler, Courtenay T. Vaughan, Marcus Epperson, Jeff Ogden, "Application Performance on the Tri-Lab Linux Capacity Cluster - TLCC", International Journal of Distributed Systems and Technologies, Volume 1, Issue 2, April 2010,

Scott French, Linda Warren, Karen Fischer, Geoffrey Abers, Wilfried Strauch, J. Marino Protti, Victor Gonzalez, "Constraints on upper plate deformation in the Nicaraguan subduction zone from earthquake relocation and directivity analysis", Geochemistry, Geophysics, Geosystems, 2010, 11, doi: 10.1029/2009GC002841

Fernando Fuentes, Houssain Kettani, George Ostrouchov, Mario Stoitsov, Hai Ah Nam, "Exploration of High-Dimensional Nuclei Data", ICCSN, pp.521-524, 2010 Second International Conference on Communication Software and Networks, February 2010,

E. Johnsen, J. Larsson, A. Bhagatwala, W.H. Cabot, P. Moin, B.J. Olson, P. Rawat, S.K. Shankar,
B. Sjogreen, H. Yee, X. Zhong, S.K. Lele,
"Assessment of high resolution methods for numerical simulations of compressible turbulence with shock waves", Journal of Computational Physics, 2010,

Glenn K. Lockwood, Stephen H. Garofalini, "Effect of moisture on the self-healing of vitreous silica under irradiation", Journal of Nuclear Materials, February 16, 2010, 400:73-78, doi: 10.1016/j.jnucmat.2010.02.012

Although it is widely understood that water interacts extensively with vitreous silicates, atomistic simulations of the response of these materials to ballistic radiation, such as neutron or ion radiation, have excluded moisture. In this study, molecular dynamics simulations were used to simulate the collision cascades and defect formation that would result from such irradiation of silica in the presence of moisture. Using an interatomic potential that allows for the dissociation of water, it was found that the reaction between molecular water or pre-dissociated water (as OH− and H+) and the ruptured Si–O–Si bonds that result from the collision cascade inhibits a significant amount of the structural recovery that was previously observed in atomistic simulations of irradiation in perfectly dry silica. The presence of moisture not only resulted in a greater accumulation of non-bridging oxygen defects, but reduced the local density of the silica and altered the distribution of ring sizes. The results imply that an initial presence of moisture in the silica during irradiation could increase the propensity for further ingress of moisture via the low density pathways and increased defect concentration.

D. M. Ushizima, J. Cuadros, "Ocular Fundus for Retinopathy Characterization", Bay Area Vision Meeting, Berkeley, CA, February 5, 2010,

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

Kevin Gott, Anil Kulkarni, Jogender Singh, "The Effect of Flow Regime Selection on Physical Vapor Deposition Flow Modeling", Penn State Graduate Student Exhibition, 2010,

Kevin Gott, Anil Kulkarni, Jogender Singh, "A New Near-Saturated Equation of State for Titanium Vapor for use in Models Simulating Physical Vapor Deposition (PVD) Processes", 20th National and 9th International ISHMT-ASME Heat and Mass Transfer Conference, 2010,

Standard physical vapor deposition models are analyzed to determine if any of the basic assumptions fail to accurately describe the flow field. Interestingly, the most basic assumption of ideal gas behavior appears to incorrectly convey the physics of PVD fabrication. Even though at first glance the ideal gas approximation seems to be a reasonable assumption given the low pressure/high temperature condition of the flow, recent research into the thermodynamic properties of titanium vapor indicates a very different behavior. Calculation of compressibility factors required to fit the thermodynamic data to other common equations of state such as Van der Waals, Dieterici, Berthelot, and Redlich-Kwong equations of state also showed unexpected behavior. Therefore, a new equation of state is suggested in this paper to more accurately describe titanium vapor and other similar vaporized metals near their saturated state. Properties calculated from this equation of state match the available thermodynamic data well.

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, January 1, 2010, 159-168,

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,

 

John Shalf, S. Dosanjh, John Morrison, "Exascale Computing Technology Challenges", VECPAR, ( 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,

D. a Filippenko Li Poznanski, An Unusually Fast-Evolving Supernova, Science, Pages: 58- 2010,

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, doi: 10.1109/TVCG.2009.69

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,

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,

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

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,

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

   

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,

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,

    

Lavanya Ramakrishnan, R. Jackson, Canon, Cholia, John Shalf, "Defining future platform requirements for e-Science clouds", SoCC, 2010, 101-106,

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,

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,

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,

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,

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,

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,

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,

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,

Logothetis Dionysios, Olston Christopher, Reed Benjamin, Webb Kevin C., Yocum Ken, Stateful bulk processing for incremental analytics, SoCC 10, Pages: 51--62 January 1, 2010,

Stonebraker Michael, SQL databases v. NoSQL databases, Commun. ACM, Pages: 10--11 January 1, 2010,

Leavitt Neal, Will NoSQL Databases Live Up to Their Promise?, Computer, Pages: 12--14 January 1, 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,

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,

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,

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

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,

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. 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,

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,

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,

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,

M.~M Yaron Poznanski Howell Brimacombe Bildsten Hsiao Dekany Zolkower Bui Kasliwal, Rapidly Decaying Supernova 2010X: A Candidate .Ia Explosion, \apjl, Pages: L98-L102 January 1, 2010,

S. a Prieto Assef Wo\ zniak Beshore Harrison Pilecki Vestrand Koz\lowski, SDWFS-MT-1: A Self-obscured Luminous Supernova at z \~ 0.2, \apj, Pages: 1624-1632 January 1, 2010,

R. a Astier Dawson Faccioli Fruchter Goldhaber Howell Kowalski Nobili Pain Ruiz-Lapuente Suzuki Supernova Cosmology Project Amanullah, Spectra and Hubble Space Telescope Light Curves of Six Type Ia Supernovae at 0.511 \lt z \lt 1.12 and the Union2 Compilation, \apj, Pages: 712-738 January 1, 2010,

S. a Prieto Assef Wo\ zniak Beshore Harrison Pilecki Vestrand Koz\lowski, SDWFS-MT-1: A Self-obscured Luminous Supernova at z \~ 0.2, \apj, Pages: 1624-1632 January 1, 2010,

R. a Astier Dawson Faccioli Fruchter Goldhaber Howell Kowalski Nobili Pain Ruiz-Lapuente Suzuki Supernova Cosmology Project Amanullah, Spectra and Hubble Space Telescope Light Curves of Six Type Ia Supernovae at 0.511 \lt z \lt 1.12 and the Union2 Compilation, \apj, Pages: 712-738 January 1, 2010,

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,

"Cloud Computing, Second International Conference, CloudCom November 30 - December 3, 2010, Indianapolis, Indiana, USA, Proceedings", CloudCom, IEEE, January 1, 2010,

Karl F\ urlinger, J. Wright, David Skinner, "Effective Performance Measurement at Petascale Using IPM", ICPADS, January 1, 2010, 373-380,

"IEEE 16th International Conference on Parallel and Distributed Systems, ICPADS 2010, 8-10 Dec. 2010, Shanghai, China", ICPADS, IEEE, January 1, 2010,

"24th IEEE International Symposium on Parallel and Distributed IPDPS 2010, Atlanta, Georgia, USA, 19-23 April 2010 - Conference Proceedings", IPDPS, IEEE, January 1, 2010,

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,

H. Agakishiev, others, "Measurements of Dihadron Correlations Relative to the", January 1, 2010,

M.M. Aggarwal, others, "An Experimental Exploration of the QCD Phase Diagram: Search for the Critical Point and the Onset of", January 1, 2010,

M.M. Aggarwal, others, "Measurement of the Bottom contribution to non-photonic", Phys.Rev.Lett., January 1, 2010, 105:202301,

M.M. Aggarwal, others, "Balance Functions from Au$+$Au, $d+$Au, and $p+p$", Phys.Rev., January 1, 2010, C82:024905,

M.M. Aggarwal, others, "Higher Moments of Net-proton Multiplicity Distributions RHIC", Phys.Rev.Lett., January 1, 2010, 105:022302,

M.M. Aggarwal, others, "Azimuthal di-hadron correlations in d+Au and Au+Au", Phys.Rev., January 1, 2010, C82:024912,

B.I. Abelev, M.M. Aggarwal, Z. Ahammed, A.V., I. Alekseev, others, "Longitudinal scaling property of the charge balance in Au + Au collisions at 200 GeV", Phys.Lett., January 1, 2010, B690:239-244,

B.I. Abelev, others, "Charged and strange hadron elliptic flow in Cu+Cu", Phys.Rev., January 1, 2010, C81:044902,

B.I. Abelev, others, "$\Upsilon$ cross section in $p+p$ collisions at", Phys.Rev., January 1, 2010, D82:012004,

B.I. Abelev, others, "Three-particle coincidence of the long range correlation in high energy nucleus-nucleus", Phys.Rev.Lett., January 1, 2010, 105:022301,

B.I. Abelev, others, "Inclusive pi^0, eta, and direct photon production at transverse momentum in p+p and d+Au collisions at", Phys.Rev., January 1, 2010, C81:064904,

B.I. Abelev, others, "Studying Parton Energy Loss in Heavy-Ion Collisions via and Charged-Particle Azimuthal", Phys.Rev., January 1, 2010, C82:034909,

B.I. Abelev, others, "Observation of pi+ pi- pi+ pi- Photoproduction in Heavy Ion Collisions at STAR", Phys.Rev., January 1, 2010, C81:044901,

B.I. Abelev, others, "Spectra of identified high-$p_T$ $\pi^\pm$ and", Phys.Rev., January 1, 2010, C81:054907,

B.I. Abelev, others, "Identified particle production, azimuthal anisotropy, interferometry measurements in Au+Au collisions at", Phys.Rev., January 1, 2010, C81:024911,

B.I. Abelev, others, "Observation of charge-dependent azimuthal correlations possible local strong parity violation in heavy ion", Phys.Rev., January 1, 2010, C81:054908,

B.I. Abelev, others, "Center of mass energy and system-size dependence of production at forward rapidity at RHIC", Nucl.Phys., January 1, 2010, A832:134-147,

B.I. Abelev, others, "System size dependence of associated yields in jets", Phys.Lett., January 1, 2010, B683:123-128,

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,

S. a Prieto Assef Wo\ zniak Beshore Harrison Pilecki Vestrand Koz\lowski, SDWFS-MT-1: A Self-obscured Luminous Supernova at z \~ 0.2, \apj, Pages: 1624-1632 January 1, 2010,

R. a Astier Dawson Faccioli Fruchter Goldhaber Howell Kowalski Nobili Pain Ruiz-Lapuente Suzuki Supernova Cosmology Project Amanullah, Spectra and Hubble Space Telescope Light Curves of Six Type Ia Supernovae at 0.511 \lt z \lt 1.12 and the Union2 Compilation, \apj, Pages: 712-738 January 1, 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,

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

Prabhat, Scientific Visualization, LBL Open House, 2010,

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

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, doi: 10.3233/SPR-2010-0311

DC Eder, RW Anderson, DS Bailey, P Bell, DJ Benson, AL Bertozzi, W Bittle, D Bradley, CG Brown, TJ Clancy, others, Assessment and mitigation of radiation, EMP, debris \& shrapnel impacts at megajoule-class laser facilities, Journal of Physics: Conference Series, Pages: 032018 2010,

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

S. Durr, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, A. Ramos, K.K. Szabo, "The ratio FK/Fpi in QCD", Journal, January 2010,

A. Kudryavstev, A. Ovsyannikov, "Numerical investigation of the interaction of acoustic disturbances with a shock wave", TsAGI Science Journal, January 1, 2010, 41:47-57, doi: 10.1615/TsAGISciJ.v41.i1.50

Craig A. Stewart, Stephen Simms, Beth Plale, Matthew Link, David Y. Hancock, Geoffrey C. Fox, What is cyberinfrastructure, SIGUCCS 10, Pages: 37--44 2010, doi: 10.1145/1878335.1878347

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.

W. Joubert, D. Kothe, H. Nam, "Preparing for Exascale: ORNL Leadership Computing Facility Application Requirements and Strategy", https://www.olcf.ornl.gov/olcf-media/center-reports/, December 2009,

Kevin Gott, Anil Kulkarni, Jogender Singh, "A Combined Rarefied and Continuum Flow Regime Model for Physical Vapor Deposition (PVD) Manufacturing Processes", Proceedings of the ASME International Mechanical Engineering Congress and Exposition 2009, 2009, 15-21,

Several modifications to physical vapor deposition (PVD) models are proposed to address the deficiencies in current theoretical studies. Simple calculations show that the flow regime of PVD fabrications will most likely vary from a continuum flow to a rarefied flow in the vacuum chamber as the vapor cloud expands toward the substrate. The flow regime for an evaporated ideal gas is calculated and then an improved equation of state is constructed and analyzed that more accurately describes vaporized metals. The result, combined with experimental observations, suggests PVD fabrication is best represented by a multi-regime flow. Then, a CFD analysis is summarized that further validates the multi-regime analysis hypothesis. Finally, a methodology for constructing and implementing the results of a theoretical multi-regime PVD model is presented.

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.

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

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

Paul T. Lin, John N. Shadid, Marzio Sala, Raymond S. Tuminaro, Gary L. Hennigan, Robert J. Hoekstra, "Performance of a parallel algebraic multilevel preconditioner for stabilized finite element semiconductor device modeling", Journal of Computational Physics, September 20, 2009, 228:6250-6267, doi: 10.1016/j.jcp.2009.05.024

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,

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,

A D Barrett, K N Gott, J M Barrett, D J Barrett, D T Rusk, "Sensitivity of host-seeking nymphal lone star ticks (Acari: Ixodidae) to immersion in heated water", Journal of Medical Entomology, 2009, 46(5):1240-1243, doi: 10.1603/033.046.0537

Host-seeking nymphal Amblyomma americanum (L.) (Acari: Ixodidae) were placed into heated water, and their survival or their torpidity was recorded as a function of exposure time. Exposures were determined that either kill the nymphs or affect their mobility. All nymphs died when exposed for a minute or more to a temperature > 51 degrees C. Nearly all nymphs remained motionless for a period of time when exposed for 3 min to a temperature > 44 degrees C.

Glenn K. Lockwood, Stephen H. Garofalini, "Bridging oxygen as a site for proton adsorption on the vitreous silica surface", Journal of Chemical Physics, August 21, 2009, 131:074703, doi: 10.1063/1.3205946

Molecular dynamics computer simulations were used to study the protonation of bridging oxygen (Si-O-Si) sites present on the vitreous silica surface in contact with water using a dissociative water potential. In contrast to first-principles calculations based on unconstrained molecular analogs, such as H7Si2O7+ molecules, the very limited flexibility of neighboring SiO4 tetrahedra when embedded in a solid surface means that there is a relatively minor geometric response to proton adsorption, requiring sites predisposed to adsorption. Simulation results indicate that protonation of bridging oxygen occurs at predisposed sites with bridging angles in the 125°-135° range, well below the bulk silica mean of approximately 150°, consistent with various ab initio calculations, and that a small fraction of such sites are present in all ring sizes. The energy differences between dry and protonated bridges at various angles observed in the simulations coincide completely with quantum calculations over the entire range of bridging angles encountered in the vitreous silica surface. Those sites with bridging angles near 130° support adsorbed protons more stably, resulting in the proton remaining adsorbed for longer periods of time. Vitreous silica has the necessary distribution of angular strain over all ring sizes to allow protons to adsorb onto bridging oxygen at the surface, forming acidic surface groups that serve as ideal intermediate steps in proton transfer near the surface. In addition to hydronium formation and water-assisted proton transfer in the liquid, protons can rapidly move across the water-silica interface via strained bridges that are predisposed to transient proton adsorption. Thus, an excess proton at any given location on a silica surface can move by either water-assisted or strained bridge-assisted diffusion depending on the local environment. The result of this would be net migration that is faster than it would be if only one mechanism is possible. These simulation results indicate the importance of performing large size and time scale simulations of the structurally heterogeneous vitreous silica exposed to water to describe proton transport at the interface between water and the silica surface.

A. Bhagatwala, S.K. Lele, "A modified artificial viscosity approach for compressible turbulence simulations", Journal of Computational Physics, 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,

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,

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. 

 

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,

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

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

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,

H. Nam, D. J. Dean, J.P. Vary, and P. Maris, "Computing Atomic Nuclei on the Cray XT5", Proceedings of the Cray Users Group Conference, Atlanta, GA, May 2009,

Mahesh Rajan, Douglas W Doerfler, Courtenay T Vaughan, "Red Storm/Cray XT4: A Superior Architecture for Scalability", Cray User Group (CUG) 2009, 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,

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.

John Shalf, Harvey Wasserman, Breakthrough Computing in Petascale Applications and Petascale System Examples at NERSC, HPC User Forum, April 10, 2009,

Scott French, Karen Fischer, Ellen Syracuse, Michael Wysession, "Crustal structure beneath the Florida-to-Edmonton broadband seismometer array", Geophysical Research Letters, 2009, 35, doi: 10.1029/2008GL036331

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, doi: 10.2172/950085

Brian J. Martin, Andrew J. Leiker, James H. Laros, III, Douglas W. Doerfler, "Performance Analysis of the SiCortex SC092", The 10th LCI International Conference on High-Performance Clustered Computing, March 2009,

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

Douglas W. Doerfler, Analyzing the Application Performance Impact of Using High-Speed Inter-Socket Communication Networks, Workshop on The Influence of I/O on Microprocessor Architecture (IOM-2009), February 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,

Law N.~M Quimby Bloom Brown Djorgovski Fox Helou Laher Poznanski Shara Velur, The Palomar Transient Factory: System Overview Performance and First Results, \pasp, Pages: 1395-1408 January 1, 2009,

A. a Ciardi Grillmair Ofek Bildsten Helfand Sullivan Rau, Exploring the Optical Transient Sky with the Palomar Transient Factory, \pasp, Pages: 1334-1351 January 1, 2009,

A. a Kulkarni Filippenko Waldman Drake Miller Arcavi Gal-Yam, Supernova 2007bi as a pair-instability explosion, \nat, Pages: 624-627 January 1, 2009,

J.~D Ganeshalingam Li Patat Butler Herczeg Simon, Variable Sodium Absorption in a Low-extinction Type Ia Supernova, \apj, Pages: 1157-1170 January 1, 2009,

S. a Barbary Faccioli Goobar Knop Pain Spadafora Nobili, Constraining Dust and Color Variations of High-z SNe Using NICMOS on the Hubble Space Telescope, \apj, Pages: 1415-1427 January 1, 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,

D. a Amanullah Dawson Goobar Nobili Ruiz-Lapuente Suzuki Rubin, Looking Beyond Lambda with the Union Supernova Compilation, \apj, Pages: 391-403 January 1, 2009,

D. a Ganeshalingam Foley Cenko Modjaz Wong Poznanski, Improved Standardization of Type II-P Supernovae: Application to an Expanded Sample, \apj, Pages: 1067-1079 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,

K. a Amanullah Fadeyev Goobar Konishi Morokuma Schlegel Takanashi Barbary, Discovery of an Unusual Optical Transient with the Hubble Space Telescope, \apj, Pages: 1358-1362 January 1, 2009,

N.~M Quimby Bloom Brown Djorgovski Fox Helou Laher Poznanski Shara Velur Law, The Palomar Transient Factory: System Overview, Performance, and First Results, \pasp, Pages: 1395-1408 January 1, 2009,

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,

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,

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,

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,

B.I. Abelev, others, "Longitudinal double-spin asymmetry and cross section for neutral pion production at midrapidity in", Phys.Rev., January 1, 2009, D80:111108,

B.I. Abelev, others, "Longitudinal Spin Transfer to Lambda and anti-Lambda in Polarized Proton-Proton Collisions at s**(1/2)", Phys.Rev., January 1, 2009, D80:111102,

B.I. Abelev, others, "Azimuthal Charged-Particle Correlations and Possible Strong Parity Violation", Phys.Rev.Lett., January 1, 2009, 103:251601,

B.I. Abelev, others, "Yields and elliptic flow of d(anti-d) and", January 1, 2009,

B.I. Abelev, others, "Long range rapidity correlations and jet production in energy nuclear collisions", Phys.Rev., January 1, 2009, C80:064912,

B.I. Abelev, others, "Neutral Pion Production in Au+Au Collisions at", Phys.Rev., January 1, 2009, C80:044905,

B.I. Abelev, others, "Growth of Long Range Forward-Backward Multiplicity with Centrality in Au+Au Collisions at", Phys.Rev.Lett., January 1, 2009, 103:172301,

B.I. Abelev, others, "J/psi production at high transverse momentum in p+p and", Phys.Rev., January 1, 2009, C80:041902,

B.I. Abelev, others, "Pion Interferometry in Au+Au and Cu+Cu Collisions at", Phys.Rev., January 1, 2009, C80:024905,

B.I. Abelev, others, "K/pi Fluctuations at Relativistic Energies", Phys.Rev.Lett., January 1, 2009, 103:092301,

B.I. Abelev, others, "Measurement of D* Mesons in Jets from p+p Collisions at", Phys.Rev., January 1, 2009, D79:112006,

B.I. Abelev, others, "Observation of Two-source Interference in the Reaction Au Au ---&gt; Au Au rho0", Phys.Rev.Lett., January 1, 2009, 102:112301,

B.I. Abelev, others, "Energy and system size dependence of phi meson in Cu+Cu and Au+Au collisions", Phys.Lett., January 1, 2009, B673:183-191,

B.I. Abelev, others, "Measurements of phi meson production in relativistic collisions at RHIC", Phys.Rev., January 1, 2009, C79:064903,

B.I. Abelev, others, "Systematic Measurements of Identified Particle Spectra $p p, d^+$ Au and Au+Au Collisions from STAR", Phys.Rev., January 1, 2009, C79:034909,

B.I. Abelev, others, "Beam-Energy and System-Size Dependence of Dynamical Net Fluctuations", Phys.Rev., January 1, 2009, C79:024906,

B.I. Abelev, others, "Indications of Conical Emission of Charged Hadrons at", Phys.Rev.Lett., January 1, 2009, 102:052302,

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,

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", J. Parallel Distrib. Comput., January 1, 2009, 69:762-777,

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,

K. Asanovic, R. Bodik, J. Demmel, T. Keaveny, K. Keutzer, J. Kubiatowicz, N. Morgan, D. Patterson, K. Sen, J. Wawrzynek, others, "A view of the parallel computing landscape", Communications of the ACM, January 1, 2009, 52:56--67,

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,

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,

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,

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)

K. Wu, S. Ahern, E. W. Bethel, J. Chen, Childs, E. Cormier-Michel, C. G. R. Geddes J. Gu, H. Hagen, B. Hamann, W. Koegler J. Laurent, J. Meredith, P. Messmer, Otoo, V. Perevoztchikov, A. Poskanzer, , O. R\ ubel, A. Shoshani, A. Sim, K. Stockinger, G. Weber, W.-M. Zhang, FastBit: Interactively Searching Massive Data, Journal of Physics Conference Series, Proceedings of SciDAC 2009, Pages: 012053 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,

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,

Taylor Groves, Jeff Knockel, Eric Schulte, "BFS vs CFS scheduler comparison", 2009,

Xiao Chen, Jian Shen, Taylor Groves, Wu Jie, "Probability Delegation Forwarding in Delay Tolerant Networks", Computer Communications and Networks, 2009. ICCCN 2009. Proceedings of 18th Internatonal Conference on, IEEE, January 1, 2009,

Paul Martinsen, Johannes Blaschke, Rainer Kuennemeyer, Robert Jordan, "Accelerating Monte Carlo simulations with an NVIDIA graphics processor", Comput Phys Commun, 2009, 180:1983--1989, doi: 10.1016/j.cpc.2009.05.013

A Dubey, K Antypas, MK Ganapathy, LB Reid, K Riley, D Sheeler, A Siegel, K Weide, "Extensible component-based architecture for FLASH, a massively parallel, multiphysics simulation code", Parallel Computing, 2009, 35:512--522, doi: 10.1016/j.parco.2009.08.001

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,

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,

Sarah S. Poon, Rollin C. Thomas, Cecilia R. Aragon, Brian Lee, "Context-linked virtual assistants for distributed teams: an astrophysics case study", CSCW '08: Proceedings of the 2008 ACM conference on Computer supported cooperative work, ACM, November 8, 2008, 361–370, doi: 10.1145/1460563.1460623

Best Paper Honorable Mention, CSCW'08

There is a growing need for distributed teams to analyze complex and dynamic data streams and make critical decisions under time pressure. Via a case study, we discuss potential guidelines for the design of software tools to facilitate such collaborative decision-making. We introduce the term context-linked to characterize systems where both task and context information are included in a shared space. We describe a novel, lightweight, context-linked event notification/virtual assistant system developed to aid a cross-cultural, geographically distributed team of astrophysicists to remotely maneuver a custom-built instrument under challenging operational conditions, where critical decisions must be made in as little as 45 seconds. The system has been in use since 2005 by a major international astrophysics collaboration. We describe the design and implementation of the event notification system and then present a case study, based on event log analysis and user interviews, of its effectiveness in substantially improving user performance during time-critical science tasks. Finally, we discuss the implications of context linking for supporting common ground in distributed teams.

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

S. Durr, Z. Fodor, J. Frison, C. Hoelbling, R. Hoffmann,S.D. Katz, S. Krieg, T. Kurth, L. Lellouch, T. Lippert, K.K. Szabo, G. Vulvert, "Ab-Initio Determination of Light Hadron Masses", Journal, November 2008,

Glenn K. Lockwood, Shenghong Zhang, Stephen H. Garofalini, "Anisotropic dissolution of α-alumina (0001) and (1120) surfaces into adjoining silicates", Journal of the American Ceramic Society, October 24, 2008, 91:3536-3541, doi: 10.1111/j.1551-2916.2008.02715.x

The dissolutions of the (0001) and (1120) orientations of α-Al2O3 into calcium silicate, aluminosilicate, and calcium aluminosilicate melts were modeled using molecular dynamics simulations. In all cases, it was found that the (1120) surface of the crystal destabilizes and melts at a lower temperature than does the (0001) surface. This anisotropy in dissolution counters the anisotropy in grain growth, in which the outward growth of the (1120) surface occurs more rapidly than that on the (0001) surface, causing platelets. However, anisotropic dissolution occurred only at a certain temperature range, above which dissolution behavior was isotropic. The presence of calcium in the contacting silicate melt plays an important role in this anisotropic dissolution, similar to its role in anisotropic grain growth observed previously. However, anisotropic dissolution also occurs in the silicate melts not containing calcium, indicating the importance of the different surface energies. In combination with previous simulations of anisotropic grain growth in alumina, these simulations reveal a complex kinetic competition between preferential adsorption and growth versus preferential dissolution of the (1120) orientation in comparison with the (0001) orientation as a function of temperature and local composition. This, in turn, indicates potential processing variations in which to design morphology in alumina.

Stephen C. Simms, Craig A. Stewart, Scott D. McCaulay, "Cyberinfrastructure resources for U.S. Scholarship: the TeraGrid", SIGUCCS '08, Pages: 341--344 2008, doi: 10.1145/1449956.1450057

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

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

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.

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

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,

Richard Gerber, "Franklin Interactive Node Responsiveness", June 9, 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,

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