NERSC Staff Publications

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,

S. Hachinger, P. A. Mazzali, M. Sullivan, R. S. Ellis, K. Maguire, A. Gal-Yam, D. A. Howell, P. E. Nugent, E. Baron, J. Cooke, I. Arcavi, D. Bersier, B. Dilday, P. A. James, M. M. Kasliwal, S. R. Kulkarni, 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 Royal Astronomical Society, 2013, 490,

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”, Accepted 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

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,

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

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

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

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

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

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

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

The Daya Bay Reactor Neutrino Experiment has measured a non-zero value for the neutrino mixing angle θ₁₃ with a significance of 5.2 standard deviations. Antineutrinos from six 2.9 GW_th 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

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

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,

K. F\ urlinger, N.J. Wright, D. Skinner, C. Klausecker, D. Kranzlm\ uller, “Effective Holistic Performance Measurement at Petascale Using IPM”, Competence in High Performance Computing 2010, January 1, 2012, 15--26,

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”, accepted, Journal of Mathematical Chemistry, January 1, 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, “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 (R_p ). Coupled with the non-detection of a quiescent X-ray counterpart and the inferred synthesized ⁵⁶Ni mass, we show that R_p lsim 0.02 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

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

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,

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 system^{1, 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 models^{1, 3}: double-degenerate (involving two white dwarfs in a close binary system^{2, 4}) and single-degenerate models^{5, 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 systems^{8, 9, 10}, allowing us to rule out luminous red giants and almost all helium stars as the mass-donating companion to the exploding white dwarf.

Nugent, Peter E.; Sullivan, Mark; Cenko, S. Bradley; Thomas, Rollin C.; Kasen, Daniel; Howell, D. Andrew; Bersier, David; Bloom, Joshua S.; Kulkarni, S. R.; Kandrashoff, Michael T.; Filippenko, Alexei V.; Silverman, Jeffrey M.; Marcy, Geoffrey W.; Howard, Andrew W.; Isaacson, Howard T.; Maguire, Kate; Suzuki, Nao; Tarlton, James E.; Pan, Yen-Chen; Bildsten, Lars; Fulton, Benjamin J.; Parrent, Jerod T.; Sand, David; Podsiadlowski, Philipp; Bianco, Federica B.; Dilday, Benjamin; Graham, Melissa L.; Lyman, Joe; James, Phil; Kasliwal, Mansi M.; Law, Nicholas M.; Quimby, Robert M.; Hook, Isobel M.; Walker, Emma S.; Mazzali, Paolo; Pian, Elena; Ofek, Eran O.; Gal-Yam, Avishay; Poznanski, Dovi, “Supernova SN 2011fe from an exploding carbon-oxygen white dwarf star”, Nature, December 2011, 480:344-347,

Type Ia supernovae have been used empirically as `standard candles' to demonstrate the acceleration of the expansion of the Universe even though fundamental details, such as the nature of their progenitor systems and how the stars explode, remain a mystery. There is consensus that a white dwarf star explodes after accreting matter in a binary system, but the secondary body could be anything from a main-sequence star to a red giant, or even another white dwarf. This uncertainty stems from the fact that no recent type Ia supernova has been discovered close enough to Earth to detect the stars before explosion. Here we report early observations of supernova SN 2011fe in the galaxy M101 at a distance from Earth of 6.4 megaparsecs. We find that the exploding star was probably a carbon-oxygen white dwarf, and from the lack of an early shock we conclude that the companion was probably a main-sequence star. Early spectroscopy shows high-velocity oxygen that slows rapidly, on a timescale of hours, and extensive mixing of newly synthesized intermediate-mass elements in the outermost layers of the supernova. A companion paper uses pre-explosion images to rule out luminous red giants and most helium stars as companions to the progenitor. http://dx.doi.org/10.1038/nature10644

Iair Arcavi, Avishay Gal-Yam, Ofer Yaron, Assaf Sternberg, Itay Rabinak, Eli Waxman, Mansi M. Kasliwal, Robert M. Quimby, Eran O. Ofek, Assaf Horesh, Shrinivas R. Kulkarni, Alexei V. Filippenko, Jeffrey M. Silverman, S. Bradley Cenko, Weidong Li, Joshua S. Bloom, Mark Sullivan, Peter E. Nugent, Dovi Poznanski, Evgeny Gorbikov, Benjamin J. Fulton, D. Andrew Howell, David Bersier, Amedee Riou, Stephane Lamotte-Bailey, Thomas Griga, Judith G. Cohen, Stephan Hachinger, David Polishook, Dong Xu, Sagi Ben-Ami, Ilan Manulis, Emma S. Walker, Kate Maguire, Yen-Chen Pan, Thomas Matheson, Paolo A. Mazzali, Elena Pian, Derek B. Fox, Neil Gehrels, Nicholas Law, Philip James, Jonathan M. Marchant, Robert J. Smith, Chris J. Mottram, Robert M. Barnsley, Michael T. Kandrashoff and Kelsey I. Clubb, “SN 2011dh: Discovery of a Type IIb Supernova from a Compact Progenitor in the Nearby Galaxy M51”, Astrophysical Journal, December 2011, 742:L18,

On 2011 May 31 UT a supernova (SN) exploded in the nearby galaxy M51 (the Whirlpool Galaxy). We discovered this event using small telescopes equipped with CCD cameras and also detected it with the Palomar Transient Factory survey, rapidly confirming it to be a Type II SN. Here, we present multi-color ultraviolet through infrared photometry which is used to calculate the bolometric luminosity and a series of spectra. Our early-time observations indicate that SN 2011dh resulted from the explosion of a relatively compact progenitor star. Rapid shock-breakout cooling leads to relatively low temperatures in early-time spectra, compared to explosions of red supergiant stars, as well as a rapid early light curve decline. Optical spectra of SN 2011dh are dominated by H lines out to day 10 after explosion, after which He i lines develop. This SN is likely a member of the cIIb (compact IIb) class, with progenitor radius larger than that of SN 2008ax and smaller than the eIIb (extended IIb) SN 1993J progenitor. Our data imply that the object identified in pre-explosion Hubble Space Telescope images at the SN location is possibly a companion to the progenitor or a blended source, and not the progenitor star itself, as its radius (~1013 cm) would be highly inconsistent with constraints from our post-explosion spectra. http://dx.doi.org/10.1088/2041-8205/742/2/L18

Corsi, A.; Ofek, E. O.; Frail, D. A.; Poznanski, D.; Arcavi, I.; Gal-Yam, A.; Kulkarni, S. R.; Hurley, K.; Mazzali, P. A.; Howell, D. A.; Kasliwal, M. M.; Green, Y.; Murray, D.; Sullivan, M.; Xu, D.; Ben-ami, S.; Bloom, J. S.; Cenko, S. B.; Law, N. M.; Nugent, P.; Quimby, R. M.; Pal'shin, V.; Cummings, J.; Connaughton, V.; Yamaoka, K.; Rau, A.; Boynton, W.; Mitrofanov, I.; Goldsten, J., “PTF 10bzf (SN 2010ah): A Broad-line Ic Supernova Discovered by the Palomar Transient Factory”, Astrophysical Journal, November 2011, 741:76,

We present the discovery and follow-up observations of a broad-line Type Ic supernova (SN), PTF 10bzf (SN 2010ah), detected by the Palomar Transient Factory (PTF) on 2010 February 23. The SN distance is cong 218 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,

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 M_V = -18.62 ± 0.08, which is the faintest peak V-band magnitude observed to date for spectroscopically confirmed GRB-SNe. When we investigate the origin of the flux at t - t ₀ = 0.598 days, it is shown that the light is not synchrotron in origin, but is likely coming from the SN shock breakout. We then use our optical and infrared data to create a quasi-bolometric light curve of SN 2010bh, which we model with a simple analytical formula. The results of our modeling imply that SN 2010bh synthesized a nickel mass of M _Ni ≈ 0.1 M _sun, ejected M _ej ≈ 2.2 M _sun, and has an explosion energy of E _k ≈ 1.4 × 10⁵²erg. Thus, while SN 2010bh is an energetic explosion, the amount of nickel created during the explosion is much less than that of SN 1998bw and only marginally more than SN 1994I. Finally, for a sample of 22 GRB-SNe we check for a correlation between the stretch factors and luminosity factors in the R band and conclude that no statistically significant correlation exists.

Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program 11709. http://dx.doi.org/10.1088/0004-637X/740/1/41

Levitan, David; Fulton, Benjamin J.; Groot, Paul J.; Kulkarni, Shrinivas R.; Ofek, Eran O.; Prince, Thomas A.; Shporer, Avi; Bloom, Joshua S.; Cenko, S. Bradley; Kasliwal, Mansi M.; Law, Nicholas M.; Nugent, Peter E.; Poznanski, Dovi; Quimby, Robert M.; Horesh, Assaf; Sesar, Branimir; Sternberg, Assaf, “PTF1 J071912.13+485834.0: An Outbursting AM CVn System Discovered by a Synoptic Survey”, Astrophysical Journal, October 2011, 739:68,

We present extensive photometric and spectroscopic observations of PTF1 J071912.13+485834.0, an outbursting AM CVn system discovered by the Palomar Transient Factory (PTF). AM CVn systems are stellar binaries with some of the smallest separations known and orbital periods ranging from 5 to 65 minutes. They are believed to be composed of a white dwarf accretor and a (semi-)degenerate He-rich donor and are considered to be the helium equivalents of cataclysmic variables (CVs). We have spectroscopically and photometrically identified an orbital period of 26.77 ± 0.02 minutes for PTF1 J071912.13+485834.0 and found a super-outburst recurrence time of greater than 65 days along with the presence of "normal" outbursts—rarely seen in AM CVn systems but well known in super-outbursting CVs. We present a long-term light curve over two super-cycles as well as high-cadence photometry of both outburst and quiescent stages, both of which show clear variability. We also compare both the outburst and quiescent spectra of PTF1 J071912.13+485834.0 to other known AM CVn systems, and use the quiescent phase-resolved spectroscopy to determine the origin of the photometric variability. Finally, we draw parallels between the different subclasses of SU UMa-type CVs and outbursting AM CVn systems. We conclude by predicting that the PTF may more than double the number of outbursting AM CVn systems known, which would greatly increase our understanding of AM CVn systems. http://dx.doi.org/10.1088/0004-637X/739/2/68

Krisciunas, Kevin; Li, Weidong; Matheson, Thomas; Howell, D. Andrew; Stritzinger, Maximilian; Aldering, Greg; Berlind, Perry L.; Calkins, M.; Challis, Peter; Chornock, Ryan; Conley, Alexander; Filippenko, Alexei V.; Ganeshalingam, Mohan; Germany, Lisa; González, Sergio; Gooding, Samuel D.; Hsiao, Eric; Kasen, Daniel; Kirshner, Robert P.; Howie Marion, G. H.; Muena, Cesar; Nugent, Peter E.; Phelps, M.; Phillips, Mark M.; Qiu, Yulei; Quimby, Robert; Rines, K.; Silverman, Jeffrey M.; Suntzeff, Nicholas B.; Thomas, Rollin C.; Wang, Lifan, “The Most Slowly Declining Type Ia Supernova 2001ay”, Astrophysical Journal, September 2011, 142:74,

We present optical and near-infrared photometry, as well as ground-based optical spectra and Hubble Space Telescope ultraviolet spectra, of the Type Ia supernova (SN) 2001ay. At maximum light the Si II and Mg II lines indicated expansion velocities of 14,000 km s^–1, while Si III and S II showed velocities of 9000 km s^–1. There is also evidence for some unburned carbon at 12,000 km s^–1. SN 2001ay exhibited a decline-rate parameter of Δm ₁₅(B) = 0.68 ± 0.05 mag; this and the B-band photometry at t gsim +25 day past maximum make it the most slowly declining Type Ia SN yet discovered. Three of the four super-Chandrasekhar-mass candidates have decline rates almost as slow as this. After correction for Galactic and host-galaxy extinction, SN 2001ay had M_B = –19.19 and M_V = –19.17 mag at maximum light; thus, it was not overluminous in optical bands. In near-infrared bands it was overluminous only at the 2σ level at most. For a rise time of 18 days (explosion to bolometric maximum) the implied ⁵⁶Ni yield was (0.58 ± 0.15)/α M _☉, with α = L _max/E _Ni probably in the range 1.0-1.2. The ⁵⁶Ni yield is comparable to that of many Type Ia SNe. The "normal" ⁵⁶Ni yield and the typical peak optical brightness suggest that the very broad optical light curve is explained by the trapping of γ rays in the inner regions. http://dx.doi.org/10.1088/0004-6256/142/3/74

Gal-Yam, Avishay; Kasliwal, Mansi M.; Arcavi, Iair; Green, Yoav; Yaron, Ofer; Ben-Ami, Sagi; Xu, Dong; Sternberg, Assaf; Quimby, Robert M.; Kulkarni, Shrinivas R.; Ofek, Eran O.; Walters, Richard; Nugent, Peter E.; Poznanski, Dovi; Bloom, Joshua S.; Cenko, S. Bradley; Filippenko, Alexei V.; Li, Weidong; Silverman, Jeffrey M.; Walker, Emma S.; Sullivan, Mark; Maguire, K.; Howell, D. Andrew; Mazzali, Paolo A.; Frail, Dale A.; Bersier, David; James, Phil A.; Akerlof, C. W.; Yuan, Fang; Law, Nicholas; Fox, Derek B.; Gehrels, Neil, “Real-time Detection and Rapid Multiwavelength Follow-up Observations of a Highly Subluminous Type II-P Supernova from the Palomar Transient Factory Survey”, Astrophysical Journal, August 2011, 736:159,

The Palomar Transient Factory (PTF) is an optical wide-field variability survey carried out using a camera with a 7.8 deg² field of view mounted on the 48 inch Oschin Schmidt telescope at Palomar Observatory. One of the key goals of this survey is to conduct high-cadence monitoring of the sky in order to detect optical transient sources shortly after they occur. Here, we describe the real-time capabilities of the PTF and our related rapid multiwavelength follow-up programs, extending from the radio to the γ-ray bands. We present as a case study observations of the optical transient PTF10vdl (SN 2010id), revealed to be a very young core-collapse (Type II-P) supernova having a remarkably low luminosity. Our results demonstrate that the PTF now provides for optical transients the real-time discovery and rapid-response follow-up capabilities previously reserved only for high-energy transients like gamma-ray bursts. http://dx.doi.org/10.1088/0004-637X/736/2/159

van Eyken, Julian C.; Ciardi, David R.; Rebull, Luisa M.; Stauffer, John R.; Akeson, Rachel L.; Beichman, Charles A.; Boden, Andrew F.; von Braun, Kaspar; Gelino, Dawn M.; Hoard, D. W.; Howell, Steve B.; Kane, Stephen R.; Plavchan, Peter; Ramírez, Solange V.; Bloom, Joshua S.; Cenko, S. Bradley; Kasliwal, Mansi M.; Kulkarni, Shrinivas R.; Law, Nicholas M.; Nugent, Peter E.; Ofek, Eran O.; Poznanski, Dovi; Quimby, Robert M.; Grillmair, Carl J.; Laher, Russ; Levitan, David; Mattingly, Sean; Surace, Jason A., “The Palomar Transient Factory Orion Project: Eclipsing Binaries and Young Stellar Objects”, Astrophysical Journal, August 2011, 142:60,

The Palomar Transient Factory (PTF) Orion project is one of the experiments within the broader PTF survey, a systematic automated exploration of the sky for optical transients. Taking advantage of the wide (3 fdg 5 × 2 fdg 3) field of view available using the PTF camera installed at the Palomar 48 inch telescope, 40 nights were dedicated in 2009 December to 2010 January to perform continuous high-cadence differential photometry on a single field containing the young (7-10 Myr) 25 Ori association. Little is known empirically about the formation of planets at these young ages, and the primary motivation for the project is to search for planets around young stars in this region. The unique data set also provides for much ancillary science. In this first paper, we describe the survey and the data reduction pipeline, and present some initial results from an inspection of the most clearly varying stars relating to two of the ancillary science objectives: detection of eclipsing binaries and young stellar objects. We find 82 new eclipsing binary systems, 9 of which are good candidate 25 Ori or Orion OB1a association members. Of these, two are potential young W UMa type systems. We report on the possible low-mass (M-dwarf primary) eclipsing systems in the sample, which include six of the candidate young systems. Forty-five of the binary systems are close (mainly contact) systems, and one of these shows an orbital period among the shortest known for W UMa binaries, at 0.2156509 ± 0.0000071 days, with flat-bottomed primary eclipses, and a derived distance that appears consistent with membership in the general Orion association. One of the candidate young systems presents an unusual light curve, perhaps representing a semi-detached binary system with an inflated low-mass primary or a star with a warped disk, and may represent an additional young Orion member. Finally, we identify 14 probable new classical T-Tauri stars in our data, along with one previously known (CVSO 35) and one previously reported as a candidate weak-line T-Tauri star (SDSS J052700.12+010136.8). http://dx.doi.org/10.1088/0004-6256/142/2/60

Levan, A. J.; Tanvir, N. R.; Cenko, S. B.; Perley, D. A.; Wiersema, K.; Bloom, J. S.; Fruchter, A. S.; Postigo, A. de Ugarte; O'Brien, P. T.; Butler, N.; van der Horst, A. J.; Leloudas, G.; Morgan, A. N.; Misra, K.; Bower, G. C.; Farihi, J.; Tunnicliffe, R. L.; Modjaz, M.; Silverman, J. M.; Hjorth, J.; Thöne, C.; Cucchiara, A.; Cerón, J. M. Castro; Castro-Tirado, A. J.; Arnold, J. A.; Bremer, M.; Brodie, J. P.; Carroll, T.; Cooper, M. C.; Curran, P. A.; Cutri, R. M.; Ehle, J.; Forbes, D.; Fynbo, J.; Gorosabel, J.; Graham, J.; Hoffman, D. I.; Guziy, S.; Jakobsson, P.; Kamble, A.; Kerr, T.; Kasliwal, M. M.; Kouveliotou, C.; Kocevski, D.; Law, N. M.; Nugent, P. E.; Ofek, E. O.; Poznanski, D.; Quimby, R. M.; Rol, E.; Romanowsky, A. J.; Sánchez-Ramírez, R.; Schulze, S.; Singh, N.; van Spaandonk, L.; Starling, R. L. C.; Strom, R. G.; Tello, J. C.; Vaduvescu, O.; Wheatley, P. J.; Wijers, R. A. M. J.; Winters, J. M.; Xu, D., “An Extremely Luminous Panchromatic Outburst from the Nucleus of a Distant Galaxy”, Science, July 2011, 333:199-,

Variable x-ray and γ-ray emission is characteristic of the most extreme physical processes in the universe. We present multiwavelength observations of a unique γ-ray-selected transient detected by the Swift satellite, accompanied by bright emission across the electromagnetic spectrum, and whose properties are unlike any previously observed source. We pinpoint the event to the center of a small, star-forming galaxy at redshift z = 0.3534. Its high-energy emission has lasted much longer than any γ-ray burst, whereas its peak luminosity was ˜100 times higher than bright active galactic nuclei. The association of the outburst with the center of its host galaxy suggests that this phenomenon has its origin in a rare mechanism involving the massive black hole in the nucleus of that galaxy. http://dx.doi.org/10.1126/science.1207143

Kleiser, Io K. W.; Poznanski, Dovi; Kasen, Daniel; Young, Timothy R.; Chornock, Ryan; Filippenko, Alexei V.; Challis, Peter; Ganeshalingam, Mohan; Kirshner, Robert P.; Li, Weidong; Matheson, Thomas; Nugent, Peter E.; Silverman, Jeffrey M., “Peculiar Type II supernovae from blue supergiants”, Monthly Notices of the Royal Astronomical Society, July 2011, 415:372-382,

The vast majority of Type II supernovae (SNeII) are produced by red supergiants, but SN 1987A revealed that blue supergiants (BSGs) can produce members of this class as well, albeit with some peculiar properties. This best-studied event revolutionized our understanding of SNe and linking it to the bulk of Type II events is essential. We present here the optical photometry and spectroscopy gathered for SN 2000cb, which is clearly not a standard SNII and yet is not a SN 1987A analogue. The light curve of SN 2000cb is reminiscent of that of SN 1987A in shape, with a slow rise to a late optical peak, but on substantially different time-scales. Spectroscopically, SN 2000cb resembles a normal SNII, but with ejecta velocities that far exceed those measured for SN 1987A or normal SNeII, above 18 000 km s⁻¹ for Hα at early times. The red colours, high velocities, late photometric peak and our modelling of this object all point towards a scenario involving the high-energy explosion of a small-radius star, most likely a BSG, producing 0.1 M_⊙ of ⁵⁶Ni. Adding a similar object to the sample, SN 2005ci, we derive a rate of ∼2 per cent of the core-collapse rate for this loosely defined class of BSG explosions. http://dx.doi.org/10.1111/j.1365-2966.2011.18708.x

Quimby, R. M.; Kulkarni, S. R.; Kasliwal, M. M.; Gal-Yam, A.; Arcavi, I.; Sullivan, M.; Nugent, P.; Thomas, R.; Howell, D. A.; Nakar, E.; Bildsten, L.; Theissen, C.; Law, N. M.; Dekany, R.; Rahmer, G.; Hale, D.; Smith, R.; Ofek, E. O.; Zolkower, J.; Velur, V.; Walters, R.; Henning, J.; Bui, K.; McKenna, D.; Poznanski, D.; Cenko, S. B.; Levitan, D., “Hydrogen-poor superluminous stellar explosions”, Nature, June 2011, 474:487-489,

Supernovae are stellar explosions driven by gravitational or thermonuclear energy that is observed as electromagnetic radiation emitted over weeks or more. In all known supernovae, this radiation comes from internal energy deposited in the outflowing ejecta by one or more of the following processes: radioactive decay of freshly synthesized elements (typically ⁵⁶Ni), the explosion shock in the envelope of a supergiant star, and interaction between the debris and slowly moving, hydrogen-rich circumstellar material. Here we report observations of a class of luminous supernovae whose properties cannot be explained by any of these processes. The class includes four new supernovae that we have discovered and two previously unexplained events (SN 2005ap and SCP 06F6) that we can now identify as members of the same class. These supernovae are all about ten times brighter than most type Ia supernova, do not show any trace of hydrogen, emit significant ultraviolet flux for extended periods of time and have late-time decay rates that are inconsistent with radioactivity. Our data require that the observed radiation be emitted by hydrogen-free material distributed over a large radius (~10¹⁵ centimetres) and expanding at high speeds (>10⁴ kilometres per second). These long-lived, ultraviolet-luminous events can be observed out to redshifts z>4.

Cano, Z.; Bersier, D.; Guidorzi, C.; Margutti, R.; Svensson, K. M.; Kobayashi, S.; Melandri, A.; Wiersema, K.; Pozanenko, A.; van der Horst, A. J.; Pooley, G. G.; Fernandez-Soto, A.; Castro-Tirado, A. J.; Postigo, A. De Ugarte; Im, M.; Kamble, A. P.; Sahu, D.; Alonso-Lorite, J.; Anupama, G.; Bibby, J. L.; Burgdorf, M. J.; Clay, N.; Curran, P. A.; Fatkhullin, T. A.; Fruchter, A. S.; Garnavich, P.; Gomboc, A.; Gorosabel, J.; Graham, J. F.; Gurugubelli, U.; Haislip, J.; Huang, K.; Huxor, A.; Ibrahimov, M.; Jeon, Y.; Jeon, Y.-B.; Ivarsen, K.; Kasen, D.; Klunko, E.; Kouveliotou, C.; Lacluyze, A.; Levan, A. J.; Loznikov, V.; Mazzali, P. A.; Moskvitin, A. S.; Mottram, C.; Mundell, C. G.; Nugent, P. E.; Nysewander, M.; O'Brien, P. T.; Park, W.-K.; Peris, V.; Pian, E.; Reichart, D.; Rhoads, J. E.; Rol, E.; Rumyantsev, V.; Scowcroft, V.; Shakhovskoy, D.; Small, E.; Smith, R. J.; Sokolov, V. V.; Starling, R. L. C.; Steele, I.; Strom, R. G.; Tanvir, N. R.; Tsapras, Y.; Urata, Y.; Vaduvescu, O.; Volnova, A.; Volvach, A.; Wijers, R. A. M. J.; Woosley, S. E.; Young, D. R., “A tale of two GRB-SNe at a common redshift of z0.54”, Monthly Notices of the Royal Astronomical Society, May 2011, 413:669-685,

We present ground-based and Hubble Space Telescope optical observations of the optical transients (OTs) of long-duration Gamma Ray Bursts (GRBs) 060729 and 090618, both at a redshift of z= 0.54. For GRB 060729, bumps are seen in the optical light curves (LCs), and the late-time broad-band spectral energy distributions (SEDs) of the OT resemble those of local Type Ic supernovae (SNe). For GRB 090618, the dense sampling of our optical observations has allowed us to detect well-defined bumps in the optical LCs, as well as a change in colour, that are indicative of light coming from a core-collapse SN. The accompanying SNe for both events are individually compared with SN1998bw, a known GRB supernova, and SN1994I, a typical Type Ic supernova without a known GRB counterpart, and in both cases the brightness and temporal evolution more closely resemble SN1998bw. We also exploit our extensive optical and radio data for GRB 090618, as well as the publicly available Swift-XRT data, and discuss the properties of the afterglow at early times. In the context of a simple jet-like model, the afterglow of GRB 090618 is best explained by the presence of a jet-break at t-t_o > 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 m_g = 23.15 ± 0.06, which at the spectroscopically measured redshift of z _helio = 0.07450 ± 0.00015 corresponds to an absolute magnitude of M_g = -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 σ_line = 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 (M_B ~ -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 (M_R >= -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, R_V = 2.8 ± 0.3. This agrees with the Milky Way value, in contrast to the low R_Vvalues found in most previous analyses. This result suggests that the long-standing controversy in interpreting SN Ia colors and their compatibility with a classical extinction law, which is critical to their use as cosmological probes, can be explained by the treatment of the dispersion in colors, and by the variability of features apparent in SN Ia spectra. http://dx.doi.org/1 0.1051/0004-6361/201116723

Miller, Adam A.; Hillenbrand, Lynne A.; Covey, Kevin R.; Poznanski, Dovi; Silverman, Jeffrey M.; Kleiser, Io K. W.; Rojas-Ayala, Bárbara; Muirhead, Philip S.; Cenko, S. Bradley; Bloom, Joshua S.; Kasliwal, Mansi M.; Filippenko, Alexei V.; Law, Nicholas M.; Ofek, Eran O.; Dekany, Richard G.; Rahmer, Gustavo; Hale, David; Smith, Roger; Quimby, Robert M.; Nugent, Peter; Jacobsen, Janet; Zolkower, Jeff; Velur, Viswa; Walters, Richard; Henning, John; Bui, Khanh; McKenna, Dan; Kulkarni, Shrinivas R.; Klein, Christopher R.; Kandrashoff, Michael; Morton, Alekzandir, “Evidence for an FU Orionis-like Outburst from a Classical T Tauri Star”, Astrophysical Journal, April 1, 2011, 730:80,

We present pre- and post-outburst observations of the new FU Orionis-like young stellar object PTF 10qpf (also known as LkHα 188-G4 and HBC 722). Prior to this outburst, LkHα 188-G4 was classified as a classical T Tauri star (CTTS) on the basis of its optical emission-line spectrum superposed on a K8-type photosphere and its photometric variability. The mid-infrared spectral index of LkHα 188-G4 indicates a Class II-type object. LkHα 188-G4 exhibited a steady rise by ~1 mag over ~11 months starting in August 2009, before a subsequent more abrupt rise of >3 mag on a timescale of ~2 months. Observations taken during the eruption exhibit the defining characteristics of FU Orionis variables: (1) an increase in brightness by gsim4 mag, (2) a bright optical/near-infrared reflection nebula appeared, (3) optical spectra are consistent with a G supergiant and dominated by absorption lines, the only exception being Hα which is characterized by a P Cygni profile, (4) near-infrared spectra resemble those of late K-M giants/supergiants with enhanced absorption seen in the molecular bands of CO and H₂O, and (5) outflow signatures in H and He are seen in the form of blueshifted absorption profiles. LkHα 188-G4 is the first member of the FU Orionis-like class with a well-sampled optical to mid-infrared spectral energy distribution in the pre-outburst phase. The association of the PTF 10qpf outburst with the previously identified CTTS LkHα 188-G4 (HBC 722) provides strong evidence that FU Orionis-like eruptions represent periods of enhanced disk accretion and outflow, likely triggered by instabilities in the disk. The early identification of PTF 10qpf as an FU Orionis-like variable will enable detailed photometric and spectroscopic observations during its post-outburst evolution for comparison with other known outbursting objects. http://dx.doi.org/10.1088/0004-637X/730/2/80

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

A. Dubey, K. B. Antypas, C. Daley, “Parallel Algorithms for Moving Lagrangian Data on Block Structured Eulerian Meshes”, Parallel Computing, 2011, 37 (2):101 - 113,

K.~R Poznanski Bloom Rebull Law Rahmer Nugent Walters Kulkarni Covey, “PTF10nvg: An Outbursting Class I Protostar in the Pelican/North American Nebula”, \aj, January 1, 2011, 141:40,

Maguire, K.; Sullivan, M.; Thomas, R. C.; Nugent, P.; Howell, D. A.; Gal-Yam, A.; Arcavi, I.; Ben-Ami, S.; Blake, S.; Botyanszki, J.; Buton, C.; Cooke, J.; Ellis, R. S.; Hook, I. M.; Kasliwal, M. M.; Pan, Y.-C.; Pereira, R.; Podsiadlowski, P.; Sternberg, A.; Suzuki, N.; Xu, D.; Yaron, O.; Bloom, J. S.; Cenko, S. B.; Kulkarni, S. R.; Law, N.; Ofek, E. O.; Poznanski, D.; Quimby, R. M., “PTF10ops - a subluminous, normal-width light curve Type Ia supernova in the middle of nowhere”, Monthly Notices of the Royal Astronomical Society, January 1, 2011, 418:747-758,

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,

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,

John Shalf, Quinlan, Curtis Janssen, “Rethinking Hardware-Software Codesign for Exascale Systems”, IEEE Computer, January 1, 2011, 44:22-30,

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

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

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

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,

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,

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

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,

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,

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

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,

D. C. Eder, et al, “Assessment and Mitigation of Radiation, EMP, Debris and Shrapnel Impacts at Mega-Joule Class Laser Facilities”, J. Physics, Conference, 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,

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

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,

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,

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,

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,

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,

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,

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,

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,

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,

Supinski Bronis R., Alam Sadaf, Bailey David H., Carrington Laura, Daley Chris, Dubey Anshu, Gamblin Todd, Gunter Dan, Hovland Paul D., Jagode Heike, Karavanic Karen, Marin Gabriel, Mellor-Crummey John, Moore Shirley, Norris Boyana, Oliker Leonid, Olschanowsky Catherine, Roth Philip C., Schulz Martin, Shende Sameer, Snavely Allan, Spear Wyatt, Tikir Mustafa, Vetter Jeff, Worley Pat, Wright Nicholas, “Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team”, Journal of Physics: Conference Series, 2009, 180:012039+,

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,

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,

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 ---> 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,

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

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms”, Journal of Parallel and Distributed Computing, January 1, 2009, 69:762-777,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, “Optimization of sparse matrix-vector multiplication on emerging multicore platforms”, Parallel Computing, January 1, 2009, 35:178--194,

Kaushik Datta, Kamil, Williams, Oliker, Shalf, Katherine A. Yelick, “Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors”, SIAM Review, January 1, 2009, 51:129-159,

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,

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,

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,

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,

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,

Maho Nakata, Bastiaan J. Braams, Katsuki Fujisawa, Mituhiro Fukuda, Jerome K. Percus, Makoto Yamashita, and Zhengji Zhao, “Variational calculation of second-order reduced density matrices by strong N-representability conditions and an accurate semidefinite programming solver”, J. Chem. Phys., 128, 1, (2008), April 29, 2008,

Lin-Wang Wang, Zhengji Zhao, and Juan Meza, “Linear-scaling three-dimensional fragment method for large-scale electronic structure calculations”, Phys. Rev. B 77, 165113 (2008), April 10, 2008,

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

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

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B.I. Abelev, others, “System-size independence of directed flow at the Heavy-Ion Collider”, Phys.Rev.Lett., January 1, 2008, 101:252301,

B.I. Abelev, others, “Charge Independent(CI) and Charge Dependent(CD) as a function of Centrality formed from Delta imum Delta eta Charged Pair Correlations in Minimum”, Phys.Rev.C, January 1, 2008,

B.I. Abelev, others, “Charmed hadron production at low transverse momentum in collisions at RHIC”, January 1, 2008,

B.I. Abelev, others, “Centrality dependence of charged hadron and strange”, Phys.Rev., January 1, 2008, C77:054901,

B.I. Abelev, others, “Forward Neutral Pion Transverse Single Spin Asymmetries”, Phys.Rev.Lett., January 1, 2008, 101:222001,

B.I. Abelev, others, “Spin alignment measurements of the K*0(892) and phi vector mesons in heavy ion collisions at”, Phys.Rev., January 1, 2008, C77:061902,

B.I. Abelev, others, “Hadronic resonance production in d+Au collisions at”, Phys.Rev., January 1, 2008, C78:044906,

B.I. Abelev, others, “rho0 photoproduction in ultraperipheral relativistic ion collisions at s(NN)**(1/2)”, Phys.Rev., January 1, 2008, C77:034910,

B.I. Abelev, others, “Longitudinal double-spin asymmetry for inclusive jet”, Phys.Rev.Lett., January 1, 2008, 100:232003,

B.I. Abelev, others, “Enhanced strange baryon production in Au + Au collisions”, Phys.Rev., January 1, 2008, C77:044908,

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

Michael F. Wehner, Oliker, John Shalf, “Towards Ultra-High Resolution Models of Climate and Weather”, IJHPCA, January 1, 2008, 22:149-165,

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

Download File: LBNL-62500.pdf (pdf: 2.4 MB)

Over the past 15 years, microprocessor performance has doubled approximately every 18 months through increased clock rates and processing efficiency. In the past few years, clock frequency growth has stalled, and microprocessor manufacturers such as AMD have moved towards doubling the number of cores every 18 months in order to maintain historical growth rates in chip performance. This document investigates the ramifications of multicore processor technology on the new Cray XT4 systems based on AMD processor technology. We begin by walking through the AMD single-core and dual-core and upcoming quad-core processor architectures. This is followed by a discussion of methods for collecting performance counter data to understand code performance on the Cray XT3 and XT4 systems. We then use the performance counter data to analyze the impact of multicore processors on the performance of microbenchmarks such as STREAM, application kernels such as the NAS Parallel Benchmarks, and full application codes that comprise the NERSC-5 SSP benchmark suite. We explore compiler options and software optimization techniques that can mitigate the memory bandwidth contention that can reduce computing efficiency on multicore processors. The last section provides a case study of applying the dual-core optimizations to the NAS Parallel Benchmarks to dramatically improve their performance.1

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

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

John Shalf, “The New Landscape of Parallel Computer Architecture”, Journal of Physics: Conference Series, IOP Electronics Journals, January 1, 2007,

W.T.C. Kramer, H. Walter, G. New, T. Engle, R. Pennington, B. Comes, B. Bland, B. Tomlison, J. Kasdorf, D. Skinner, others, “Report of the workshop on petascale systems integration for large scale facilities”, January 1, 2007,

B.I. Abelev, others, “Forward Lambda production and nuclear stopping power in”, Phys.Rev., January 1, 2007, C76:064904,

B.I. Abelev, others, “Measurement of transverse single-spin asymmetries for production in proton-proton collisions at s**(1/2)”, Phys.Rev.Lett., January 1, 2007, 99:142003,

B.I. Abelev, others, “Global polarization measurement in Au+Au collisions”, Phys.Rev., January 1, 2007, C76:024915,

B.I. Abelev, others, “Energy dependence of pi+-, p and anti-p transverse”, Phys.Lett., January 1, 2007, B655:104-113,

B.I. Abelev, others, “Partonic flow and phi-meson production in Au + Au”, Phys.Rev.Lett., January 1, 2007, 99:112301,

B.I. Abelev, others, “Charged particle distributions and nuclear modification”, Phys.Lett.B, January 1, 2007,

B.I. Abelev, others, “Erratum: Transverse momentum and centrality dependence high-\pt\ non-photonic electron suppression in Au+Au”, Phys.Rev.Lett., January 1, 2007, 98:192301,

J. Adams, others, “Delta phi Delta eta Correlations in Central Au+Au”, Phys.Rev., January 1, 2007, C75:034901,

J. Adams, others, “Scaling Properties of Hyperon Production in Au+Au”, Phys.Rev.Lett., January 1, 2007, 98:062301,

J. Adams, others, “The Energy dependence of $p_t$ angular correlations from mean-p($t$) fluctuation scale dependence in ion collisions at the SPS and RHIC”, J.Phys.G, January 1, 2007, G34:451-466,

B.I. Abelev, others, “Strangelet search at RHIC”, Phys.Rev., January 1, 2007, C76:011901,

John Adams, others, “Transverse momentum correlations and minijet dissipation Au-Au collisions at s(NN)**(1/2)-GeV”, J.Phys.G, January 1, 2007, G34:799-816,

Erik Schnetter, Ott, Allen, Diener, Goodale, Radke, Seidel, John Shalf, “Cactus Framework: Black Holes to Gamma Ray Bursts”, CoRR, January 1, 2007, abs/0707,

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “Scientific computing kernels on the Cell processor”, International Journal of Parallel Programming, January 1, 2007, 35:263--298,

M.Fukuda, B.J.B.Braams, M.Nakata, M.L.Overton, J.K.Percus, M.Yamashita, and Z. Zhao, “Large-scale semi-definite programs in electronic structure calculations”, Mathematical Programming, series B 109, 553-580, Springer Berlin / Heidelberg, (2006)., January 1, 2007,

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

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

M. Nakata, B. J. Braams, M. Fukuda, J. K. Percus, M. Yamashita, and Z. Zhao, “Simple Hamiltonians which exhibit drastic failures by variational determination of the 2-RDM with some well known N-representability conditions”, J. Chem. Phys., 125, 244109 (2006), December 27, 2006,

Zhengji Zhao , Lin-Wang Wang, and Fengmin Wu, “Wavefunction localizations in bulged CdSe nanowires”, J. of Comp. and Theo. Nano., pp.247-251, vol.4, no. 2, (2007)., July 2, 2006,

Zhengji Zhao , Juan Meza, and Michel Van Hove, “Using Pattern Search Methods for Surface Structure Determination”, J. Phys.: Condens. Matter 18, 8693-8706 (2006), June 9, 2006,

Zhao, Zhengji, Wang, Lin-Wang and Meza, Juan, “Motif based Hessian matrix for ab initio geometry optimization of nanostructures”, Phys. Rev. B 73, 193309 (2006), May 17, 2006,

P. a Leonard Conley Pain Nugent, “Toward a Cosmological Hubble Diagram for Type II-P Supernovae”, \apj, January 1, 2006, 645:841-850,

Y. Shao, L. F. Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. T. Brown, A. T.B. Gilbert, L. V. Slipchenko, S. V. Levchenko, D. P O Neill, “Advances in methods and algorithms in a modern quantum chemistry program package”, Phys. Chem. Chem. Phys., January 1, 2006, 8:3172-3191,

Tom Goodale, Shantenu Jha, Hartmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic, Hrabri, John Shalf, “SAGA: A Simple API for Grid Applications -- High-Level Application Programming on the Grid”, Computational Methods in Science and Technology, January 1, 2006, 12,

H. Wang, D.E. Skinner, M. Thoss, “Calculation of reactive flux correlation functions for systems in a condensed phase environment: A multilayer multiconfiguration time-dependent Hartree approach”, The Journal of chemical physics, January 1, 2006, 125:174502,

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

J. Adams, others, “The Multiplicity dependence of inclusive $p_t$ spectra”, Phys.Rev., January 1, 2006, D74:032006,

J. Adams, others, “Direct observation of dijets in central Au+Au collisions”, Phys.Rev.Lett., January 1, 2006, 97:162301,

J. Adams, others, “Forward neutral pion production in p+p and d+Au”, Phys.Rev.Lett., January 1, 2006, 97:152302,

John Adams, others, “Measurements of identified particles at intermediate momentum in the STAR experiment from Au + Au”, Phys.Rev.C, January 1, 2006,

J. Adams, others, “Identified hadron spectra at large transverse momentum”, Phys.Lett., January 1, 2006, B637:161-169,

J. Adams, others, “Multiplicity and pseudorapidity distributions of charged and photons at forward pseudorapidity in Au + Au”, Phys.Rev., January 1, 2006, C73:034906,

J. Adams, others, “Proton - lambda correlations in central Au+Au collisions”, Phys.Rev., January 1, 2006, C74:064906,

J. Adams, others, “Directed flow in Au+Au collisions at s(NN)**(1/2)”, Phys.Rev., January 1, 2006, C73:034903,

John Adams, others, “Transverse-momentum p(t) correlations on (eta, phi) from”, J.Phys.G, January 1, 2006, G32:L37-L48,

John Adams, others, “Minijet deformation and charge-independent angular on momentum subspace (eta, phi) in Au-Au”, Phys.Rev., January 1, 2006, C73:064907,

John Adams, others, “Hadronization geometry and charge-dependent number on axial momentum space in Au-Au”, Phys.Lett., January 1, 2006, B634:347-355,

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

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

Download File: mph_hpca.pdf (pdf: 142 KB)

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

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

Download File: cpl6hpca.pdf (pdf: 325 KB)

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

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

Download File: MM5LSMJGR.pdf (pdf: 1.3 MB)

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

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

Horst Simon, William Kramer, William Saphir, John Shalf, David Bailey, Leonid Oliker, Michael Banda, C. William McCurdy, John Hules, Andrew Canning, Marc Day, Philip Colella, David Serafini, Michael Wehner, Peter Nugent, “Science-Driven System Architecture: A New Process for Leadership Class Computing”, Journal of the Earth Simulator, January 1, 2005, 2,

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

D. Skinner, “Performance monitoring of parallel scientific applications”, January 1, 2005,

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

C.A. Gagliardi, others, “Recent high-p(T) results from STAR”, Eur.Phys.J., January 1, 2005, C43:263-270,

A.A.P. Suaide, others, “Charm production in the STAR experiment at RHIC”, Eur.Phys.J., January 1, 2005, C43:193-200,

M. Calderon de la Barca Sanchez, others, “Open charm production from d + Au collisions in STAR”, Eur.Phys.J., January 1, 2005, C43:187-192,

J. Adams, others, “Incident energy dependence of pt correlations at RHIC”, Phys.Rev., January 1, 2005, C72:044902,

J. Adams, others, “Multi-strange baryon elliptic flow in Au + Au collisions”, Phys.Rev.Lett., January 1, 2005, 95:122301,

J. Adams, others, “Multiplicity and pseudorapidity distributions of photons”, Phys.Rev.Lett., January 1, 2005, 95:062301,

J. Adams, others, “Distributions of charged hadrons associated with high momentum particles in pp and Au + Au collisions”, Phys.Rev.Lett., January 1, 2005, 95:152301,

John Adams, others, “Experimental and theoretical challenges in the search the quark gluon plasma: The STAR Collaboration s assessment of the evidence from RHIC collisions”, Nucl.Phys., January 1, 2005, A757:102-183,

J. Adams, others, “K(892)* resonance production in Au+Au and p+p collisions”, Phys.Rev., January 1, 2005, C71:064902,

J. Adams, others, “Pion interferometry in Au+Au collisions at S(NN)**(1/2)”, Phys.Rev., January 1, 2005, C71:044906,

J. Adams, others, “Azimuthal anisotropy in Au+Au collisions at s(NN)**(1/2)”, Phys.Rev., January 1, 2005, C72:014904,

J. Adams, others, “Open charm yields in d + Au collisions at s(NN)**(1/2)”, Phys.Rev.Lett., January 1, 2005, 94:062301,

J. Adams, others, “Transverse-momentum dependent modification of dynamic”, Phys.Rev., January 1, 2005, C71:031901,

John Adams, others, “phi meson production in Au + Au and p+p collisions at”, Phys.Lett., January 1, 2005, B612:181-189,

John Adams, others, “Pion, kaon, proton and anti-proton transverse momentum from p + p and d + Au collisions at”, Phys.Lett., January 1, 2005, B616:8-16,

J. Adams, others, “Event by event <p(t)> fluctuations in Au - Au”, Phys.Rev., January 1, 2005, C71:064906,

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

Ruxandra Bondarescu, Allen, Daues, Kelley, Russell, Seidel, Shalf, Malcolm Tobias, “The Astrophysics Simulation Collaboratory Portal: a framework for effective distributed research”, Future Generation Comp. Syst., January 1, 2005, 21:259-270,

J. Demmel, J. Dongarra, V. Eijkhout, E. Fuentes, A. Petitet, R. Vuduc, R.C. Whaley, K. Yelick, “Self-adapting linear algebra algorithms and software”, Proceedings of the IEEE, January 1, 2005, 93:293--312,

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

Zhengji Zhao , Bastiaan J. Braams, Mituhiro Fukuda, Michael L. Overton and Jerome K. Percus, “The Reduced Density Matrix Method for Electronic Structure Calculations and the Role of Three-Index Representability Conditions”, J. Chem. Phys. 120, 2095 (2004), February 1, 2004,

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

Download File: hybridPDCP.pdf (pdf: 123 KB)

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

H. Shukla, M.S. Yun, NZ Scoville, “Dense, Ionized, and Neutral Gas Surrounding Sagittarius A*”, The Astrophysical Journal, January 1, 2004, 616:231,

D. Skinner, “Scaling up parallel scientific applications on the IBM SP”, January 1, 2004,

J. Adams, others, “Pseudorapidity asymmetry and centrality dependence of hadron spectra in d + Au collisions at”, Phys.Rev., January 1, 2004, C70:064907,

R. Sturrock, others, “A step towards a computing grid for the LHC experiments: data challenge 1”, Nucl.Instrum.Methods, January 1, 2004,

J. Adams, others, “Azimuthal anisotropy and correlations at large momenta in p+p and Au+Au collisions at”, Phys.Rev.Lett., January 1, 2004, 93:252301,

J. Adams, others, “Measurements of transverse energy distributions in Au +”, Phys.Rev., January 1, 2004, C70:054907,

J. Adams, others, “Centrality and pseudorapidity dependence of charged production at intermediate $p_T$ in Au + Au”, Phys.Rev., January 1, 2004, C70:044901,

J. Adams, others, “Production of e+ e- pairs accompanied by nuclear in ultra-peripheral heavy ion collision”, Phys.Rev., January 1, 2004, C70:031902,

H. Caines, others, “An update from STAR - using strangeness to probe heavy ion collisions”, J.Phys.G, January 1, 2004, G30:S61-S73,

J. Adams, others, “Photon and neutral pion production in Au + Au collisions”, Phys.Rev., January 1, 2004, C70:044902,

J. Adams, others, “Azimuthally sensitive HBT in Au + Au collisions at”, Phys.Rev.Lett., January 1, 2004, 93:012301,

J. Adams, others, “Cross-sections and transverse single spin asymmetries in neutral pion production from proton collisions at”, Phys.Rev.Lett., January 1, 2004, 92:171801,

J. Adams, others, “Azimuthal anisotropy at RHIC: The First and fourth”, Phys.Rev.Lett., January 1, 2004, 92:062301,

J. Adams, others, “Identified particle distributions in pp and Au+Au”, Phys.Rev.Lett., January 1, 2004, 92:112301,

J. Adams, others, “Multistrange baryon production in Au-Au collisions at”, Phys.Rev.Lett., January 1, 2004, 92:182301,

J. Adams, others, “Rho0 production and possible modification in Au+Au and”, Phys.Rev.Lett., January 1, 2004, 92:092301,

J. Adams, others, “Rapidity and centrality dependence of proton and production from Au-197 + Au-197 collisions at”, Phys.Rev., January 1, 2004, C70:041901,

John Adams, others, “Particle type dependence of azimuthal anisotropy and modification of particle production in Au + Au”, Phys.Rev.Lett., January 1, 2004, 92:052302,

C. Adler, others, “Kaon production and kaon to pion ratio in Au+Au”, Phys.Lett., January 1, 2004, B595:143-150,

E.J. Im, K. Yelick, R. Vuduc, “Sparsity: Optimization framework for sparse matrix kernels”, International Journal of High Performance Computing Applications, January 1, 2004, 18:135--158,

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

T. J. Jankun-Kelly, Kreylos, Ma, Hamann, I. Joy, Shalf, E. Wes Bethel, “Deploying Web-Based Visual Exploration Tools on the Grid”, IEEE Computer Graphics and Applications, January 1, 2003, 23:40-50,

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

J. Adams, others, “Pion kaon correlations in Au+Au collisions at s(NN)**1/2”, Phys.Rev.Lett., January 1, 2003, 91:262302,

J. Adams, others, “Multiplicity fluctuations in Au+Au collisions at”, Phys.Rev., January 1, 2003, C68:044905,

J. Adams, others, “Three pion HBT correlations in relativistic heavy ion from the STAR experiment”, Phys.Rev.Lett., January 1, 2003, 91:262301,

J. Adams, others, “Evidence from d + Au measurements for final state of high p(T) hadrons in Au+Au collisions at”, Phys.Rev.Lett., January 1, 2003, 91:072304,

J. Adams, others, “Transverse momentum and collision energy dependence of p(T) hadron suppression in Au+Au collisions at energies”, Phys.Rev.Lett., January 1, 2003, 91:172302,

M. Anderson, J. Berkovitz, W. Betts, R., F. Bieser, others, “The Star time projection chamber: A Unique tool for high multiplicity events at RHIC”, Nucl.Instrum.Meth., January 1, 2003, A499:659-678,

J. Adams, others, “Narrowing of the balance function with centrality in au”, Phys.Rev.Lett., January 1, 2003, 90:172301,

K.H. Ackermann, others, “STAR detector overview”, Nucl.Instrum.Meth., January 1, 2003, A499:624-632,

John Adams, others, “Strange anti-particle to particle ratios at mid-rapidity”, Phys.Lett., January 1, 2003, B567:167-174,

C. Adler, others, “Disappearance of back-to-back high $p_T$ hadron in central Au+Au collisions at”, Phys.Rev.Lett., January 1, 2003, 90:082302,

C. Adler, others, “Azimuthal anisotropy and correlations in the hard regime at RHIC”, Phys.Rev.Lett., January 1, 2003, 90:032301,

E. Wes Bethel, John Shalf, “Grid-Distributed Visualizations Using Connectionless Protocols”, IEEE Computer Graphics and Applications, January 1, 2003, 23:51-59,

John Shalf, E. Wes Bethel, “The Grid and Future Visualization System Architectures”, IEEE Computer Graphics and Applications, January 1, 2003, 23:6-9,

Gabrielle Allen, Goodale, Radke, Russell, Seidel, Davis, Dolkas, D. Doulamis, Kielmann, Merzky, Nabrzyski, Pukacki, Shalf, Ian J. Taylor, “Enabling Applications on the Grid: A Gridlab Overview”, IJHPCA, January 1, 2003, 17:449-466,

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

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

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

R. Bellwied, M.J. Bennett, V. Bernardo, H., W. Christie, others, “Distributed drift chamber design for rare particle in relativistic heavy ion collisions”, Nucl.Instrum.Meth., January 1, 2002, A485:371-384,

L.S. Barnby, others, “Strangeness in Au + Au collisions at s(NN)**(1/2) observed with the STAR detector”, J.Phys.G, January 1, 2002, G28:1535-1542,

C. Adler, others, “Centrality dependence of high $p_T$ hadron suppression”, Phys.Rev.Lett., January 1, 2002, 89:202301,

C. Adler, others, “Coherent rho0 production in ultraperipheral heavy ion”, Phys.Rev.Lett., January 1, 2002, 89:272302,

C. Adler, others, “Elliptic flow from two and four particle correlations in”, Phys.Rev., January 1, 2002, C66:034904,

C. Adler, others, “K*(892)0 production in relativistic heavy ion collisions”, Phys.Rev., January 1, 2002, C66:061901,

C. Adler, others, “Azimuthal anisotropy of K0(S) and Lambda + anti-Lambda at mid-rapidity from Au + Au collisions at”, Phys.Rev.Lett., January 1, 2002, 89:132301,

C. Adler, others, “Midrapidity phi production in Au + Au collisions at s N”, Phys.Rev., January 1, 2002, C65:041901,

C. Adler, others, “Midrapidity Lambda and anti-Lambda production in Au + Au”, Phys.Rev.Lett., January 1, 2002, 89:092301,

C. Adler, others, “Results from the STAR experiment”, Nucl.Phys., January 1, 2002, A698:64-77,

Michael Russell, Allen, Daues, T. Foster, Seidel, Novotny, Shalf, Gregor von Laszewski, “The Astrophysics Simulation Collaboratory: A Science Portal Enabling Community Software Development”, Cluster Computing, January 1, 2002, 5:297-304,

Gregor von Laszewski, Russell, T. Foster, Shalf, Allen, Daues, Novotny, Edward Seidel, “Community software development with the Astrophysics Simulation Collaboratory”, Concurrency and Computation: Practice and Experience, January 1, 2002, 14:1289-1301,

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

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

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

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

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

Download File: HPAJSC.pdf (pdf: 236 KB)

C. Adler, others, “Measurement of inclusive anti-protons from Au+Au”, Phys.Rev.Lett., January 1, 2001, 87:262302,

C. Adler, others, “Anti-deuteron and anti-He-3 production in s(NN)**(1/2) Au+Au collisions”, Phys.Rev.Lett., January 1, 2001, 87:262301,

C. Adler, others, “Pion interferometry of s(NN)**(1/2) 130-GeV Au+Au at RHIC”, Phys.Rev.Lett., January 1, 2001, 87:082301,

C. Adler, others, “Identified particle elliptic flow in Au + Au collisions”, Phys.Rev.Lett., January 1, 2001, 87:182301,

C. Adler, others, “Multiplicity distribution and spectra of negatively”, Phys.Rev.Lett., January 1, 2001, 87:112303,

C. Adler, others, “Midrapidity anti-proton to proton ratio from Au + Au”, Phys.Rev.Lett., January 1, 2001, 86:4778,

E. Andersen, others, “Measurement of negative particle multiplicity in S - Pb at 200-GeV/c per nucleon with the NA36 TPC”, Phys.Lett., January 1, 2001, B516:249-256,

K.H. Ackermann, others, “Elliptic flow in Au + Au collisions at (S(NN))**(1/2) GeV”, Phys.Rev.Lett., January 1, 2001, 86:402-407,

Gabrielle Allen, Benger, Dramlitsch, Goodale, Hege, Lanfermann, Merzky, Radke, Seidel, John Shalf, “Cactus Tools for Grid Applications”, Cluster Computing, January 1, 2001, 4:179-188,

Gabrielle Allen, Angulo, T. Foster, Lanfermann, Liu, Radke, Seidel, John Shalf, “The Cactus Worm: Experiments with Dynamic Resource Discovery and Allocation in a Grid Environment”, IJHPCA, January 1, 2001, 15:345-358,

E.J. Im, K. Yelick, “Optimizing sparse matrix computations for register reuse in SPARSITY”, Computational Science—ICCS 2001, January 1, 2001, 127--136,

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

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

J. Lin, others, “Hardware controls for the STAR experiment at RHIC”, IEEE Trans.Nucl.Sci., January 1, 2000, 47:210-213,

E.J. Im, K.A. Yelick, “Optimizing the performance of sparse matrix-vector multiplication”, January 1, 2000,

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

Download File: ElNinomst.pdf (pdf: 152 KB)

D.E. Skinner, W.H. Miller, “Application of the semiclassical initial value representation and its linearized approximation to inelastic scattering”, Chemical physics letters, January 1, 1999, 300:20--26,

K.B. Marvel, H. Shukla, G. Rhee, “A VLA Search for Head-Tail Radio Sources in Abell Clusters”, The Astrophysical Journal Supplement Series, January 1, 1999, 120:147,

D. Reichhold, F. Bieser, M. Bordua, G. Cherney, J. Chrin, others, “Development of the hardware controls system for the STAR”, Conf.Proc., January 1, 1999, C991004:385-387,

K.H. Ackermann, others, “The STAR time projection chamber”, Nucl.Phys., January 1, 1999, A661:681-685,

B. Monreal, S.A. Bass, M. Bleicher, S. Greiner Esumi, others, “Deuterons and space momentum correlations in high-energy collisions”, Phys.Rev., January 1, 1999, C60:031901,

Gabrielle Allen, Tom Goodale, Gerd Lanfermann, Thomas Radke, Ed Seidel, Werner Benger, Hans Christian Hege, Andre Merzky, Juan Masso, John Shalf, “Solving Einstein's Equations on Supercomputers”, IEEE Computer, January 1, 1999, 32:52-58,

Michael L. Norman, John Shalf, Stuart Levy, Greg Daues, “Diving Deep: Data-Management and Visualization Strategies for Adaptive Mesh Refinement Simulations”, Computing in Science and Engineering, January 1, 1999, 1:36-47,

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

D.E. Skinner, T.C. Germann, W.H. Miller, “Quantum Mechanical Rate Constants for O+ OH⇌ H+ O2 for Total Angular Momentum J> 0”, The Journal of Physical Chemistry A, January 1, 1998, 102:3828--3834,

H. Wieman, D.L. Adams, N. Added, Agakishiev, S.A. Akimenko, others, “Recent developments on the STAR detector system at”, Nucl.Phys., January 1, 1998, A638:559-564,

H. Appelshauser, others, “Spectator nucleons in Pb + Pb collisions at 158-A-GeV”, Eur.Phys.J., January 1, 1998, A2:383-390,

K. Yelick, L. Semenzato, G. Pike, C. Miyamoto, B. Liblit, A. Krishnamurthy, P. Hilfinger, S. Graham, D. Gay, P. Colella, others, “Titanium: A high-performance Java dialect”, Concurrency Practice and Experience, January 1, 1998, 10:825--836,

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

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

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

I. Sakrejda, others, “Global features of heavy ion collisions from the NA36”, January 1, 1997,

H. Wieman, others, “STAR TPC at RHIC”, IEEE Trans.Nucl.Sci., January 1, 1997, 44:671-678,

T. Yates, others, “Lambda and anti-lambda reconstruction in central Pb + Pb using a time projection chamber”, J.Phys.G, January 1, 1997, G23:1889-1893,

V. Friese, others, “Phi production in 158-GeV/u Pb + Pb collisions”, J.Phys.G, January 1, 1997, G23:1837-1843,

C. Bormann, others, “Kaon, Lambda and anti-lambda production in Pb + Pb at 158-GeV per nucleon”, J.Phys.G, January 1, 1997, G23:1817-1825,

G. Odyniec, others, “Xi (Omega) production in Pb + Pb collisions at”, J.Phys.G, January 1, 1997, G23:1827-1835,

W. Betts, F. Bieser, R. Bossingham, M. Cherney Botlo, others, “Results from the STAR TPC system test”, IEEE Trans.Nucl.Sci., January 1, 1997, 44:592-597,

D. Patterson, T. Anderson, N. Cardwell, R. Fromm, K. Keeton, C. Kozyrakis, R. Thomas, K. Yelick, “A case for intelligent RAM”, Micro, IEEE, January 1, 1997, 17:34--44,

C.E. Kozyrakis, S. Perissakis, D. Patterson, T. Anderson, K. Asanovic, N. Cardwell, R. Fromm, J. Golbus, B. Gribstad, K. Keeton, others, “Scalable processors in the billion-transistor era: IRAM”, Computer, January 1, 1997, 30:75--78,

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

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

Download File: 1996ApJ...466..724G2.pdf (pdf: 1.3 MB)

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

Download File: 1996MNRAS.278..345G2.pdf (pdf: 3 MB)

H. Shukla, R.E. Stoner, “Correlation of Ultraviolet and Radio Flux in Three Active Galactic Nuclei”, The Astrophysical Journal Supplement Series, January 1, 1996, 106:41,

I.M. Sakrejda, “Strangeness production at RHIC energies as seen by the detector”, Heavy Ion Phys., January 1, 1996, 4:117-121,

M. L. Norman, P. Beckman, G. L. Bryan, J. Dubinski, D. Gannon, L. Hernquist, K. Keahey, J. P. Ostriker, J. Shalf, J. Welling, and S. Yang, “Galaxies Collide on the I-WAY: An Example of Heterogeneous Wide-Area Collaborative Supercomputing”, The International Journal of Supercomputer Applications and High Performance Computing, January 1, 1996, 10:132-144,

D.E. Skinner, D.P. Colombo Jr, J.J. Cavaleri, R.M. Bowman, “Femtosecond investigation of electron trapping in semiconductor nanoclusters”, The Journal of Physical Chemistry, January 1, 1995, 99:7853--7856,

D. Philip Colombo, K.A. Roussel, J. Saeh, D.E. Skinner, J.J. Cavaleri, R.M. Bowman, others, “Femtosecond study of the intensity dependence of electron-hole dynamics in TiO2 nanoclusters”, Chemical physics letters, January 1, 1995, 232:207--214,

J.J. Cavaleri, D.E. Skinner, D.P. Colombo Jr, R.M. Bowman, “Femtosecond study of the size-dependent charge carrier dynamics in ZnO nanocluster solutions”, The Journal of chemical physics, January 1, 1995, 103:5378,

E.G. Judd, others, “Recent results from the NA36 experiment”, Nucl.Phys., January 1, 1995, A590:291C-306C,

P. Alvarez de Lara, others, “Study of very peripheral S Pb and S-S interactions at per nucleon”, Phys.Lett., January 1, 1995, B351:418-423,

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

Download File: 1994ApJ431604G.pdf (pdf: 793 KB)

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

Download File: lambgalactic-scale-gas-flows-in-colliding-galaxies.pdf (pdf: 629 KB)

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

E. Andersen, others, “Strangeness production in 200-GeV/c/A sulphur lead from the NA36 experiment”, January 1, 1994,

E. Andersen, others, “Doubly strange particle production in high-energy hadron and nucleus nucleus collisions”, January 1, 1994,

E. Andersen, others, “NA36 strangeness production: Multistrange baryons”, January 1, 1994,

E. Andersen, others, “Production of Lambda, Anti-lambda, and Xi-, Anti-xi+ in S + Pb collisions at 200-GeV/c per nucleon”, Phys.Lett., January 1, 1994, B327:433-438,

E. Andersen, others, “Strangeness production in p + Pb reactions at”, Nucl.Phys., January 1, 1994, A566:487C-490C,

E. Andersen, R. Blaes, Michael G. Cherney, B. de Cruz, C. Fernandez, others, “Results from the NA36 experiment on the production of”, Nucl.Phys., January 1, 1994, A566:217C-224C,

E. Andersen, others, “Multiplicity dependence of strangeness production in S + collisions at 200-GeV/c per nucleon”, Phys.Lett., January 1, 1993, B316:603-607,

E. Andersen, others, “Multiply strange baryon and anti-baryon production in S Pb collisions at 200-Gev/c per nucleon”, Phys.Lett.B, January 1, 1993,

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

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

Download File: 1992ApJ399L51G.pdf (pdf: 2.3 MB)

E. Andersen, P.D. Barnes, R. Blaes, H. Brom Braun, others, “Target dependence of central rapidity Lambda production sulfur-nucleus collisions at 200 GeV/c per nucleon”, Phys.Rev., January 1, 1992, C46:727-735,

Michael G. Cherney, E. Andersen, P. Barnes, R., B. de la Cruz, others, “Enhanced strangeness production at mid-rapidity”, January 1, 1992, 1177-1178,

R. Zybert, others, “Strangeness production in S-32 + Pb collisions at Results from the NA-36 experiment”, January 1, 1992,

Iwona Sakrejda, “Strangeness production in S + Pb and p + Pb collisions 200-GeV/c per nucleon”, January 1, 1992,

B. de la Cruz, others, “p(T) distributions and temperature determination from peripheral S Pb interactions at 200-A-GeV/c”, January 1, 1992,

M.E. Beddo, others, “STAR: Conceptual design report for the Solenoidal at RHIC”, January 1, 1992,

E. Andersen, others, “Strangeness production at mid-rapidity in S + Pb at 200-GeV/c per nucleon.”, Phys.Lett., January 1, 1992, B294:127-130,

E. Andersen, P.D. Barnes, R. Blaes, H. Brom Braun, others, “A High speed Fastbus VME data acquisition system for the NA36 experiment”, Nucl.Instrum.Meth., January 1, 1992, A320:300-304,

E. Andersen, others, “Results from CERN experiment NA36 on strangeness”, Nucl.Phys., January 1, 1992, A544:309-320,

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

E. Andersen, P.D. Barnes, B. Castano, Michael G., M. Cohler, others, “Determination of the primary vertex position in the NA36”, Nucl.Instrum.Meth., January 1, 1991, A301:69-75,

K. Kadija, others, “Update to the RHIC Letter of Intent for an experiment on and jet production at mid-rapidity”, January 1, 1991,

Michael G. Cherney, others, “HIGH SPEED READOUT FOR A TIME PROJECTION CHAMBER IN THE DATA ACQUISITION SYSTEM”, Nucl.Instrum.Meth., January 1, 1989, A283:796-798,

C. Garabatos, others, “A TPC IN THE CONTEXT OF HEAVY ION COLLISIONS”, Nucl.Instrum.Meth., January 1, 1989, A283:553-556,

John M. Nelson, others, “MEASUREMENT OF S AND PROTON COLLISIONS AT 200-A/GEV/C A TIME PROJECTION CHAMBER”, Nucl.Phys., January 1, 1989, A498:515C-522C,

E. Andersen, others, “A MEASUREMENT OF CROSS-SECTIONS FOR S-32 INTERACTIONS Al, Fe, Cu, Ag AND Pb AT 200-GeV/c PER NUCLEON”, Phys.Lett., January 1, 1989, B220:328,

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

P. Yepes, others, “NA36: Cross-sections and strange particle production status”, January 1, 1988,

C.R. Gruhn, others, “The NA36 TPC and experience with relativistic sulphur collisions at the CERN SPS.”, January 1, 1988,

P.D. Barnes, others, “A MEASUREMENT OF CROSS-SECTIONS FOR O-16 Al AND O-16 Pb AT 60-GeV/c AND 200-GeV/c per NUCLEON”, Phys.Lett., January 1, 1988, B206:146,

G.E. Diebold, P.D. Barnes, R. Blaes, Braun, B. Castano, others, “The NA36 time projection chamber: An Interim report on a designed for a relativistic heavy ion experiment”, January 1, 1987,

Walter M. Geist, P.D. Barnes, R. Blaes, H., B. Castano, others, “FIRST RESULTS FROM NA36”, January 1, 1987,

P. Yepes, others, “NA36 SETUP AND FIRST RESULTS FROM THE S-32 ION BEAMS”, January 1, 1987,

C. Garabatos, others, “THE NA36 TIME PROJECTION CHAMBER. FIRST OPERATION AND”, January 1, 1987,

I. Sakrejda, “ANALYSIS OF THE REACTION PI- P ---> PI+ PI- N AT HIGH”, January 1, 1986,

K. Rybicki, I. Sakrejda, J. Turnau, “OBSERVATION OF THE SCALAR MESON AT 1260-MeV IN THE pi- p ---> pi+ pi- n AT 17.2-GeV/c”, Acta Phys.Polon., January 1, 1986, B17:317,

K. Rybicki, I. Sakrejda, “INDICATION FOR A BROAD J(PC) 2++ MESON AT 840-MEV IN THE REACTION PI- P ---> PI+ PI- N AT HIGH”, Z.Phys., January 1, 1985, C28:65-74,

Ilona Sakrejda, “ANALYSIS OF THE REACTION PI- P ---> PI+ PI- N AT HIGH MOMENTUM TRANSFER”, January 1, 1984,

I. Sakrejda, J. Turnau, “PROPERTIES OF THE REGGE EXCHANGE AMPLITUDES WITH THE A1 NUMBERS”, Acta Phys.Polon., January 1, 1981, B12:305-316,

December 31, 1969,

Download File: SR.pdf (pdf: 329 KB)

JH Chen, R. Sankaran, ER Hawkes, JH Sutherland, D. Skinner, “2005 Joule Software Effectiveness Study of S3D Applied to the INCITE Goal”, December 31, 1969,

I. Sakrejda, “Analysis of the reaction pi-p --> pi+pi-n at high transfer”, December 31, 1969,

Jihan Kim, Berend Smit, “Efficient Monte Carlo Simulations of Gas Molecules Inside Porous Materials”, Journal of Chemical Theory and Computation, December 31, 1969,

J. Dongarra, et al., “The International Exascale Software Project Roadmap”, International Journal of High Performance Computing Applications, 1969,

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

December 31, 1969,

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

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,

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,

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

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,

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,

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,

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,

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, German., May 1, 2012,

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

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

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.

Kenes Beketayev, Gunther H. Weber, Dmitriy Morozov, Aidos Abzhanov, Bernd Hamann, “Geometry-Preserving Topological Landscapes”, Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, ACM, 2012, 155--160, LBNL 6082E

Dogan Demir, Kenes Beketayev, Gunther H. Weber, Peer-Timo Bremer, Valerio Pascucci, Bernd Hamann, “Topology Exploration with Hierarchical Landscapes”, Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, ACM, 2012, 147--154, LBNL 6083E

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

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,

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,

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,

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

Robert Preissl, Wichmann, Long, Shalf, Ethier, Alice E. Koniges, “Multithreaded global address space communication techniques for gyrokinetic fusion applications on ultra-scale platforms”, SC, November 1, 2011, 15,

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

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

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

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,

Download File: ioperformance.pdf (pdf: 174 KB)

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

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,

Download File: pmbs11.pdf (pdf: 441 KB)

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.

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,

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,

Download File: P1871.pdf (pdf: 318 KB)

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,

Download File: CUG2011Hopperpaper.pdf (pdf: 1.5 MB)

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,

Download File: CUG2011CompilerPaper.pdf (pdf: 518 KB)

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.

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

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,

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,

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,

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

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

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,

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,

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,

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

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

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

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

Richard Martin, 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,

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,

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,

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,

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

Download File: IESP-roadmap-1.1.pdf (pdf: 2.4 MB)

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,

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,

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,

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,

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,

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”, ScienceCloud 2010, the 1st Workshop on Scientific Cloud Computing, Chicago, Illinois, June 2010,

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

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,

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,

H. Shan, H. Jin, K. Fuerlinger, A. Koniges, N. J. Wright, “Analyzing the Effect of Different Programming Models Upon Performance and Memory Usage on Cray XT5 Platforms”, Proceedings of the 2010 Cray User Group, Edinburgh, Scotland, May 24, 2010,

Download File: Cug2010Shan.pdf (pdf: 288 KB)

Alice Koniges, Robert Preissl, Jihan Kim, David Eder, Aaron Fisher, Nathan Masters, Velimir Mlaker, Stephane Ethier, Weixing Wang, Martin Head-Gordon, and Nathan Wichmann, “Application Acceleration on Current and Future Cray Platforms”, Proceedings of the 2010 Cray User Group Meeting, Edinburgh, Scotland, May 24, 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,

Download File: cug2010JobComp.pdf (pdf: 429 KB)

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.

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,

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,

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,

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, Seattle, Washington, April 2010,

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

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

A. E. Koniges, N. D. Masters, A. C. Fisher, R. W. Anderson, D. C. Eder, T. B. Kaiser, D. S. Bailey, B. Gunney, P. Wang, B. Brown, K. Fisher, F. Hansen, B. R. Maddox, D. J. Benson, M. Meyers, A. Geille, “ALE-AMR: A New 3D Multi-Physics Code for Modeling Laser/Target Effects”, Proceedings of the Sixth International Conference on Inertial Fusion Sciences and Applications, Journal of Physics: Conference Series, 2010, 244 (3):032019,

Shoaib Kamil, Chan, Oliker, Shalf, Samuel Williams, “An auto-tuning framework for parallel multicore stencil computations”, IPDPS, January 1, 2010, 1-12,

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, New York, NY, USA, 2010, 101-106,

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,

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,

N. Masters, D. C. Eder, T. B. Kaiser, A. E. Koniges, A. Fisher, “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,

A. Fisher, D. S. Bailey, T. B. Kaiser, B. T. N. Gunney, N. D. Masters, A. E. Koniges, D. C. Eder, and R. W. Anderson, “Modeling Heat Conduction and Radiation Transport with the Diffusion Equation in NIF ALE-AMR”, J. Physics, Conf. Ser. 244: 022075, 2010,

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,

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

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

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,

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

Download File: CUG2009FranklinUpgradesfinal.pdf (pdf: 145 KB)

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.

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,

Download File: CLE2.1Post-Mortem2009.pdf (pdf: 233 KB)

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.

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,

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,

Brian van Straalen, Shalf, J. Ligocki, Keen, Woo-Sun Yang, “Scalability challenges for massively parallel AMR applications”, IPDPS, January 1, 2009, 1-12,

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,

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

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

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

Download File: sc08final2.pdf (pdf: 598 KB)

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

Download File: CUG2008FranklinUserExperiencesfinal.pdf (pdf: 253 KB)

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

Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, “Lattice Boltzmann simulation optimization on leading multicore platforms”, International Parallel and Distributed Processing Symposium (IPDPS), April 14, 2008, 1-14,

Download File: LBMHDipdps08final.pdf (pdf: 560 KB)

Shoaib Kamil, Shalf, Erich Strohmaier, “Power efficiency in high performance computing”, IPDPS, January 1, 2008, 1-8,

Hongzhang Shan, Antypas, John Shalf, “Characterizing and predicting the I/O performance of HPC applications using a parameterized synthetic benchmark”, SC, January 1, 2008, 42,

Wayne Pfeiffer, Nicholas J. Wright, “Modeling and predicting application performance on parallel computers using HPC challenge benchmarks”, IPDPS, 2008, 1-12,

“22nd IEEE International Symposium on Parallel and Distributed IPDPS 2008, Miami, Florida USA, April 14-18, 2008”, IPDPS, IEEE, January 1, 2008,

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

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

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

Download File: CUG2007slides2.pdf (pdf: 465 KB)

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

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

Julian Borrill, Leonid Oliker, John Shalf, Hongzhang Shan, “Investigation of leading HPC I/O performance using a scientific-application derived benchmark”, SC, January 1, 2007, 10,

Shoaib Kamil, Ali Pinar, Dan Gunter, Mike Lijewski, Leonid Oliker, John Shalf, “Reconfigurable hybrid interconnection for static and dynamic scientific applications”, Conf. Computing Frontiers, January 1, 2007, 183-194,

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

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

S. Williams, J. Shalf, L. Oliker, S. Kamil, P. Husbands, K. Yelick, “The potential of the cell processor for scientific computing”, Proceedings of the 3rd conference on Computing frontiers, January 1, 2006, 9--20,

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

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

Brown, M.G. and Bebek, C. and Bernstein, G. and Bonissent, A. and Carithers, B. and Cole, D. and Figer, D. and Gerdes, D. and Gladney, L. and Lorenzon, W. and Kim, A. and Kushner, G. and Kuznetsova, N. and Lampton, M. and Levi, M. and Linder, E. and McKee, S. and Miquel, R. and Mostek, N. and Mufson, S. and Perlmutter, S. and Schubnell, M. and Seshadri, S. and Shukla, H. and Smith, R. and Stebbins, A. and Stoughton, C. and Tarle, G.,, “Development of NIR detectors and science-driven requirements for SNAP”, Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, January 1, 2006, 6265,

S. Kamil, K. Datta, S. Williams, L. Oliker, J. Shalf, K. Yelick, “Implicit and explicit optimizations for stencil computations”, Proceedings of the 2006 workshop on Memory system performance and correctness, January 1, 2006, 51--60,

Luke J. Gosink, John Shalf, Kurt Stockinger, John Wu, Wes Bethel, “HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets using Fast Bitmap Indices”, SSDBM, January 1, 2006, 149-158,

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

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

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

Kurt Stockinger, Shalf, Wu, E. Wes Bethel, “Query-Driven Visualization of Large Data Sets”, IEEE Visualization, January 1, 2005, 22,

John Shalf, Kamil, Oliker, David Skinner, “Analyzing Ultra-Scale Application Communication Requirements for a Reconfigurable Hybrid Interconnect”, SC, January 1, 2005, 17,

J. Borrill, J. Carter, L. Oliker, D. Skinner, R. Biswas, “Integrated performance monitoring of a cosmology application on leading HEC platforms”, Parallel Processing, 2005. ICPP 2005. International Conference on, January 1, 2005, 119--128,

S. Kamil, J. Shalf, L. Oliker, D. Skinner, “Understanding ultra-scale application communication requirements”, Workload Characterization Symposium, 2005. Proceedings of the IEEE International, January 1, 2005, 178--187,

Shoaib Kamil,Parry Husbands, Leonid Oliker, John Shalf, Katherine A. Yelick, “Impact of modern memory subsystems on cache optimizations for stencil computations”, Memory System Performance, January 1, 2005, 36-43,

Kurt Stockinger, John Shalf, Wes Bethel, Kesheng Wu, “DEX: Increasing the Capability of Scientific Data Analysis by Using Efficient Bitmap Indices to Accelerate Scientific Visualization”, SSDBM, January 1, 2005, 35-44,

R. Vuduc, J.W. Demmel, K.A. Yelick, “OSKI: A library of automatically tuned sparse matrix kernels”, Journal of Physics: Conference Series, January 1, 2005, 16:521,

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

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

Download File: mph_ipdps.pdf (pdf: 71 KB)

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

Gorden Griem, Oliker, Shalf, Katherine A. Yelick, “Identifying Performance Bottlenecks on Modern Microarchitectures Using an Adaptable Probe”, IPDPS, January 1, 2004,

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

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

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

Download File: MM5workshop.pdf (pdf: 655 KB)

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

Gunther H. Weber, Oliver Kreylos, John Shalf, Wes Bethel, Bernd Hamann, Gerik Scheuermann, “Parallel Cell Projection Rendering of Adaptive Mesh Refinement Data”, IEEE Symposium on Parallel and Large-Data Visualization and Graphics, January 1, 2003, 51-60,

E. Wes Bethel, Mark Abram, John Shalf, Frank, Jim P. Ahrens, Steve Parker, Nagiza F. Samatova, Mark Miller, “Interoperability of Visualization Software and Data Models is NOT an Achievable Goal”, IEEE Visualization, January 1, 2003, 607-610,

P. Husbands, C. Iancu, K. Yelick, “A performance analysis of the Berkeley UPC compiler”, Proceedings of the 17th annual international conference on Supercomputing, January 1, 2003, 63--73,

C. Bell, D. Bonachea, Y. Cote, J. Duell, P. Hargrove, P. Husbands, C. Iancu, M. Welcome, K. Yelick, “An evaluation of current high-performance networks”, Parallel and Distributed Processing Symposium, 2003. Proceedings. International, January 1, 2003, 10--pp,

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

Download File: mixedsc02.pdf (pdf: 2.6 MB)

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

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

Chris H.Q. Ding and Yun He, “Effective Methods in Reducing Communication Overheads in Solving PDE Problems on Distributed-Memory Computer Architectures”, Proceedings of Grace Hopper Celebration of Women in Computing 2002, October 2002,

Download File: heatghc02.pdf (pdf: 12 MB)

H. Bushouse, B. Simon, H. Shukla, E. Wyckoff, “A Python-Based IRAF Regression Testing System”, Astronomical Society of the Pacific Conference Series, January 1, 2002, 281:129,

Gabrielle Allen, Angulo, Goodale, Kielmann, Merzky, Nabrzyski, Pukacki, Russell, Radke, Seidel, Shalf, Ian J. Taylor, “GridLab: Enabling Applications on the Grid”, GRID, January 1, 2002, 39-45,

Tom Goodale, Allen, Lanfermann, Mass\ o, Radke, Seidel, John Shalf, “The Cactus Framework and Toolkit: Design and Applications”, VECPAR, January 1, 2002, 197-227,

R. Vuduc, J.W. Demmel, K.A. Yelick, S. Kamil, R. Nishtala, B. Lee, “Performance optimizations and bounds for sparse matrix-vector multiply”, Supercomputing, ACM/IEEE 2002 Conference, January 1, 2002, 26--26,

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

Download File: heatsc01.pdf (pdf: 353 KB)

Michael Russell, Gabrielle Allen, Greg Daues, Ian T. Foster, Ed Seidel, Jason Novotny, John Shalf, Gregor von Laszewski, “The Astrophysics Simulation Collaboratory Portal: A Science Portal Enabling Community Software Development”, HPDC, January 1, 2001, 207-215,

Gunther H. Weber, Kreylos, J. Ligocki, Shalf, Hagen, Hamann, I. Joy, Kwan-Liu Ma, “High-quality Volume Rendering of Adaptive Mesh Refinement Data”, VMV, January 1, 2001, 121-128,

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

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

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

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

Gabrielle Allen, Benger, Goodale, Hege, Lanfermann, Merzky, Radke, Seidel, John Shalf, “The Cactus Code: A Problem Solving Environment for the Grid”, HPDC, January 1, 2000, 253-,

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

Download File: momsc99.pdf (pdf: 82 KB)

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

Eun-Jin Im, Katherine Yelick, “Optimizing Sparse Matrix Vector Multiplication on SMPs”, Ninth SIAM Conference on Parallel Processing for Scientific Computing, San Antonio, TX, January 1, 1999,

H. Shukla, S. Scott, S. Weaver, “Remote Observing With Java”, Astronomical Data Analysis Software and Systems VIII, January 1, 1999, 172:95,

Werner Benger, T. Foster, Novotny, Seidel, Shalf, Smith, Paul Walker, “Numerical Relativity in a Distributed Environment”, PPSC, January 1, 1999,

R.H. Arpaci-Dusseau, E. Anderson, N. Treuhaft, D.E. Culler, J.M. Hellerstein, D. Patterson, K. Yelick, “Cluster I/O with River: Making the fast case common”, Proceedings of the sixth workshop on I/O in parallel and distributed systems, January 1, 1999, 10--22,

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

Download File: 1997RMxAC6151L.pdf (pdf: 496 KB)

R. Fromm, S. Perissakis, N. Cardwell, C. Kozyrakis, B. McGaughy, D. Patterson, T. Anderson, K. Yelick, “The energy efficiency of IRAM architectures”, Computer Architecture, 1997. Conference Proceedings. The 24th Annual International Symposium on, January 1, 1997, 327--337,

D. Patterson, T. Anderson, N. Cardwell, R. Fromm, K. Keeton, C. Kozyrakis, R. Thomas, K. Yelick, “Intelligent RAM (IRAM): Chips that remember and compute”, Solid-State Circuits Conference, 1997. Digest of Technical Papers. 43rd ISSCC., 1997 IEEE International, January 1, 1997, 224--225,

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

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

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

H. Shukla, S. D. Ryder, “Radio Continuum Emission in the Resonance-Ring Galaxies NGC 1433 and NGC 6300”, Astronomical Society of the Pacific Conference Series, January 1, 1996, 91:250,

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

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

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

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

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

R.H. Arpaci, D.E. Culler, A. Krishnamurthy, S.G. Steinberg, K. Yelick, “Empirical evaluation of the CRAY-T3D: A compiler perspective”, ACM SIGARCH Computer Architecture News, January 1, 1995, 23:320--331,

S. Chakrabarti, J. Demmel, K. Yelick, “Modeling the benefits of mixed data and task parallelism”, Proceedings of the seventh annual ACM symposium on Parallel algorithms and architectures, January 1, 1995, 74--83,

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

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

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

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

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

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

Download File: 1993AGAb856L.pdf (pdf: 279 KB)

D.E. Culler, A. Dusseau, S.C. Goldstein, A. Krishnamurthy, S. Lumetta, T. Von Eicken, K. Yelick, “Parallel programming in Split-C”, Supercomputing 93. Proceedings, January 1, 1993, 262--273,

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

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

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

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

Download File: 1990NASCP3098737G.pdf (pdf: 1.1 MB)

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

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

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

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

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

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

“GPU Computational Screening of Carbon Capture Materials”, SciDAC 2011, December 31, 1969,

December 31, 1969,

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.

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)

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

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

Oliver Rübel, Soile V. E. Keränen, Mark D. Biggin, David W. Knowles, H. Weber, Hans Hagen, Bernd Hamann, E. Wes Bethel, “Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data”, Mathematical Methods for Visualization in Medicine and Life Sciences II, (Springer-Verlag: 2012) Pages: 267--286, LBNL 4891E

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

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

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

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)

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

Download File: ShalfVecpar2010.pdf (pdf: 1.1 MB)

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.

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

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)

Bastiaan Braams, Jerry Percus and Zhengji Zhao, “The T1 and T2 representability conditions”, Reduced-Density-Matrix Mechanics -- with applications to many-electron atoms and molecules, A book edited by David Mazziotti, John Wiley Advances in Chemical Physics Series (2007)., ( March 27, 2007)

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

Richard A. Gerber, FES Review Overview and Goals, March 19, 2013,

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

Download File: NUG-Teleconference-Mar-2.pdf (pdf: 2.9 MB)

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

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

Download File: HPCTools-Gerber.pdf (pdf: 6.7 MB)

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

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

Download File: Edison-Update.pdf (pdf: 15 MB)

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,

Download File: Requirement-Reviews.pdf (pdf: 5 MB)

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

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

Download File: NewUser-January-2013.pdf (pdf: 8.6 MB)

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

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

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

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

Download File: NUG-Teleconference-Nov.pdf (pdf: 3.5 MB)

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

Download File: NUG-Batch-noanims2.pdf (pdf: 2.7 MB)

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

Download File: HPCOverview-June-12-2012.pdf (pdf: 19 MB)

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

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

Download File: Gerber-HPC-june-12-2012.pdf (pdf: 15 MB)

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

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

Download File: ChallengesInHPC-June-2012.pdf (pdf: 8.7 MB)

Challenges in High Performance Computing. Presented to LBNL Summer Interns, June 12, 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 talk in the Cray User Group meeting, April 29-May-3, 2012, Stuttgart, German., May 1, 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,

Download File: chos.pdf (pdf: 796 KB)

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,

Download File: pdsfsitereport.pdf (pdf: 1.6 MB)

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.

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,

Download File: HPCTools-Gerber.pdf (pdf: 6.7 MB)

Tools for Performance Debugging HPC Applications, February 16, 2012,

Download File: HPCAppPerf2012CS267.pdf (pdf: 5.1 MB)

NERSC Accomplishments and Plans, February 3, 2012,

Download File: NERSC-Overview-NUG12.pdf (pdf: 12 MB)

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

Download File: Gerber-User-Req.pdf (pdf: 6.7 MB)

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,

K. Antypas, Best Practices for Reading and Writing Data on HPC Systems, February 1, 2012,

Download File: Readingand-WritingDataNUGFeb2012.ppt (ppt: 5.1 MB)

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

Download File: SPXXL2012NERSCupdate.pdf (pdf: 1.8 MB)

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.

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

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

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

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

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,

Download File: HPCAdvisoryCouncilIOTalkDec2011.pptx (pptx: 10 MB)

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

Download File: SC11-IO.pdf (pdf: 8.4 MB)

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

Download File: SC11ArchiveTutorialFinal.pdf (pdf: 2.9 MB)

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.

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,

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

Download File: NERSCOpenWorld2011.pdf (pdf: 3.2 MB)

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.

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

Download File: HickNERSCNGF.pdf (pdf: 1.6 MB)

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,

Download File: IntroHPCSystems-NewUser.pdf (pdf: 14 MB)

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

Download File: HPCToolsExperiences.pdf (pdf: 2.6 MB)

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

K. Antypas, NERSC: National Energy Research Scientific Computing Center, July 18, 2011,

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,

Download File: eetd.pdf (pdf: 12 MB)

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.

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

Download File: Fuji2011BusinessValueOfTape.pdf (pdf: 5.1 MB)

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,

Download File: NewUser-June-2011.pdf (pdf: 16 MB)

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,

Download File: CUG2011CompilerSlides.pdf (pdf: 5.8 MB)

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,

Download File: CUG2011Hopperslides.pdf (pdf: 13 MB)

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

Download File: PASIGLBNLStorage.pdf (pdf: 6.6 MB)

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,

Download File: Gerber-JGI.pdf (pdf: 12 MB)

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

Download File: NERSCMIRAnalysis2011.pdf (pdf: 5.6 MB)

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,

Download File: OFANERSCExascaleIO.pdf (pdf: 6.6 MB)

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

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

N. Balthaser, Introduction to Archival Storage at NERSC, March 8, 2011,

Presentation explaining how to get started using the NERSC archival storage system

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

Download File: Computers-BSA.pdf (pdf: 2.2 MB)

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

Download File: HPCTools-CS267.pdf (pdf: 4.7 MB)

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,

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,

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,

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

Download File: HEP-NUG-WS-forcray.pdf (pdf: 16 MB)

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

Download File: NERSC-Intro-NUG.pdf (pdf: 21 MB)

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

Download File: ASTROSIMParallelIO2010.pdf (pdf: 45 MB)

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

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

Download File: CUG2010Job.pdf (pdf: 735 KB)

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,

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.

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

Download File: RunningJobs-JointXT.pdf (pdf: 1.5 MB)

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,

Prabhat, Scientific Visualization, LBL Open House, 2010,

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

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,

Download File: EducauseNov2009antypas.pdf (pdf: 17 MB)

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

Download File: GerberR-NUG-09-BERRep.pdf (pdf: 3.1 MB)

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, An invited poster presentation in SciDac meeting, June 14-18, 2009, San Diego, CA., June 14, 2009,

Zhengji Zhao, and Lin-Wang Wang, The application of the LS3DF method to CdSe/CdS core/shell structures, A talk at Cray User Group meeting, May 4-7, 2009, Atlanta, GA., May 5, 2009,

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

Download File: CUG2009FranklinUpgradesslidesfinal.pdf (pdf: 227 KB)

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,

Download File: CLE2.1Post-MortemPresentation.pdf (pdf: 1.2 MB)

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,

Download File: LTUG09HardwareLessonsLearned.pdf (pdf: 1.2 MB)

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.

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

Download File: BreakthroughScienceNERSC-CTW.pdf (pdf: 7.3 MB)

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,

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,

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

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,

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

Download File: Franklin-IO-NUG.pdf (pdf: 427 KB)

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

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

Download File: CUG2008slidesFranklinUserExperiencesfinal.pdf (pdf: 731 KB)

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

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

Zhengji Zhao, Lin-Wang Wang and Juan Meza, A New O(N) Method for Petascale Nanoscience Simulations, the ACM Best poster (SC07) at International Conferences for High Performance Computing, Networking, Storage and Analysis,Nov. 10-16, 2007, Reno, CA., November 10, 2007,

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

Download File: Franklin-IO-NUG2.pdf (pdf: 427 KB)

Zhengji Zhao, Third Party Software, A talk at NERSC User Meeting, Sept. 17, 2007, Oakland, CA., September 17, 2007,

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

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, The linear scaling 3-dimensional fragment method for petascale nanoscience simulations, A poster presented in STANFORD 50: State of the Art & Future Directions of Computational Mathematics & Numerical Computing, March 29-31, 2007, Palo Alto, California., May 29, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, A Linear Scaling 3-Dimensional Fragment Method for Petascale Nanoscience Simulations, A poster presented in Office of Advanced Scientific Computing Research (OSCAR) 2007 Applied Mathematics PI Meeting, May 22 - 24, 2007, Livermore, CA., May 22, 2007,

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

Download File: CUG2007slides.pdf (pdf: 465 KB)

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling NanoScience Simulations for Petascale Computing, A talk presented in APS March 5-9, 2007, Denver, Colorado., March 5, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling 3D Fragment Method for Petascale Nanoscience Simulations, A poster presented in SIAM Computational Science and Engineering (CSE), Feb 19-23, 2007, Costa Mesa, California., February 19, 2007,

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

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling NanoScience Simulations for Petascale Computing,, An invited talk in the HPC for Nano-science and Technology workshop, International Conference for High Performance Computing, Nov. 11-17, 2006, Tampa, FL., November 17, 2006,

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

Download File: BassiintroNUG06.pdf (pdf: 14 MB)

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

Download File: BassiExperiences-NUG-2006.pdf (pdf: 1.6 MB)

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

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

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

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

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

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

Download File: ccsmse.ppt (ppt: 189 KB)

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

Download File: mph_101504.pdf (pdf: 1.7 MB)

Helen He, Hybrid OpenMP and MPI Programming and Tuning, 2004 NERSC User Group (NUG) Meeting, June 1, 2004,

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

Download File: MM5yhe.pdf (pdf: 878 KB)

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

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

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

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

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

Download File: ghc2002.pdf (pdf: 2.3 MB)

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

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

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

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

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

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

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

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

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

Download File: Data-Requirements-from-NERSC-v5.pdf (pdf: 214 KB)

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

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

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

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

Download File: NERSC-ASCR-WorkshopReport.pdf (pdf: 1.4 MB)

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

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,

Download File: MagellanFinalReport.pdf (pdf: 10 MB)

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

Download File: NERSC-FES-WorkshopReport.pdf (pdf: 1.8 MB)

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

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

Download File: 5BPWS-report.pdf (pdf: 11 MB)

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.

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

Download File: NERSC-BES-WorkshopReport.pdf (pdf: 14 MB)

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

Download File: HSIBestPractices-Balthaser-Hazen-2011-06-09.pdf (pdf: 245 KB)

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.

Brian MacCarthy, Hamish Carr, Gunther H. Weber, “Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering”, 2011, LBNL LBNL-5019E

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,

Download File: NERSC-HEP-WorkshopReport.pdf (pdf: 8.6 MB)

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

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

Download File: NERSC-BER-WorkshopReport.pdf (pdf: 1.7 MB)

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,

Download File: ASCR-Net-Req-Workshop-2009-Final-Report.pdf (pdf: 4.5 MB)

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.

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,

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

Download File: LBNL-934480.pdf (pdf: 1.2 MB)

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

Download File: NERSCWorkload.pdf (pdf: 5 MB)

Science drivers for NERSC-6

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

Download File: Franklin-Interactive-Response.pdf (pdf: 338 KB)

Gabrielle Allen (LSU/CCT), Gene Allen (MSC Inc.), Kenneth Alvin (SNL), Matt Drahzal (IBM), David Fisher (DoD-Mod), Robert Graybill (USC/ISI), Bob Lucas (USC/ISI), Tim Mattson (Intel), Hal Morgan (SNL), Erik Schnetter (LSU/CCT), Brian Schott (USC/ISI), Edward Seidel (LSU/CCT), John Shalf (LBNL/NERSC), Shawn Shamsian (MSC Inc.), David Skinner (LBNL/NERSC), Siu Tong (Engeneous), “Frameworks for Multiphysics Simulation : HPC Application Software Consortium Summit Concept Paper”, January 1, 2008,

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

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

Shoaib Kamil, John Shalf, “Measuring Power Efficiency of NERSC s Newest Flagship Machine”, January 1, 2007,

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

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

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

Hongzhang Shan, John Shalf, “Analysis of Parallel IO on Modern HPC Platforms”, January 1, 2006,

Lin-Wang Wang, “A Survey of Codes and Algorithms used in NERSC Chemical Science Allocations”, January 1, 2006,

Lin-Wang Wang, “A Brief Comparison Between Grid-Based Real-Space Algorithms and Spectral Algorithms for Electronic Structure Calculations”, January 1, 2006,

Lin-Wang Wang, Zhengji Zhao, Juan Meza, “Petascale Calculations of Electronic Structures of Nanostructures with Hundreds of Thousands of Processors”, January 1, 2006,

Lin-Wang Wang, Zhengji Zhao, Juan Meza, “Linear Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations”, January 1, 2006,

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

K. Asanovic, R. Bodik, B.C. Catanzaro, J.J. Gebis, P. Husbands, K. Keutzer, D.A. Patterson, W.L. Plishker, J. Shalf, S.W. Williams, others, “The landscape of parallel computing research: A view from berkeley”, January 1, 2006,

John Shalf, John Bell, Andrew Canning, Lin-Wang Wang, Juan Meza, Rob Ryne, Ji Qiang, Kathy Yelick, “Berkeley Petascale Applications”, January 1, 2005,

Lin-Wang Wang, “A Survey of Codes and Algorithms used in NERSC Materials Science Allocations”, January 1, 2005,

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

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

Download File: mph4manual.pdf (pdf: 218 KB)

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

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

William T. C. Kramer, Francesca Verdier, Keith Fitzgerald, James Craw, Tammy Welcome, “High Performance Computing Facilities for the Next Millennium”, LBNL Technical Report 44700, 1999,

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

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

Francesca Verdier, “UNIX at the Cornell Theory Center”, Cornell Theory Center Forefronts, July 4, 1992,

Francesca Verdier, Shahin Kahn, “Programming for Parallelism on the FPSBUS”, Cornell Theory Center Technical Report CTC88TR14, 1988,

Francesca Verdier, “Vectorization Gives You Free Cycles!”, Cornell Theory Center Forefronts, March 7, 1987,

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

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

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

Enhancing the quantum Monte Carlo method for electronic properties of large molecules and excited states, Brian Austin, January 1, 2009,

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

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

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

Download File: ThesisPreamble.pdf (pdf: 1013 KB)

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

Download File: Thesis-Chapter1.pdf (pdf: 3.1 MB)

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

Download File: AAA-Case-Study-NERSC-FINAL2-6-12.pdf (pdf: 426 KB)

“Lawrence Berkeley National Laboratory Meets Exponential Data Storage Increases to Support Scientific Research”, Web Site, August 11, 2011,

“NERSC: Proving Tape as Cost-Effective and Reliable Primary Data Storage”, M. Peters, Web site, December 1, 2010,

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

Download File: SC08HPC1Big-Picture.pdf (pdf: 93 KB)

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

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,

Download File: poster2012.pdf (pdf: 818 KB)

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,

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,

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,

Download File: poster.pdf (pdf: 941 KB)

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 ALE-AMR code”, SciDAC conference, 2011,

Download File: poster2.pdf (pdf: 903 KB)

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, 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,

R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, G. R. Geddes, W. Leemans, Prabhat X. Li, J. Qiang, R\ ubel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon, N. Yampolsky, “High Performance Computing in Accelerator Science: Past Successes, Future Challenges”, ASCR/BES Workshop on Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery, 2011,

Prabhat, 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,

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,

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,

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

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

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

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

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

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

December 31, 1969,

Mark Howison, E. Wes Bethel, GPU-accelerated Denoising of 3D Magnetic Resonance Images, Journal of Real Time Image Processing, 2013,

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,

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

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,

R.~C Thomas, SYNAPPS: Data-Driven Analysis for Supernova Spectroscopy, \pasp, Pages: 237-248 January 1, 2011,

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,

J.~D Ofek Seibert Foster Schiminovich Lee Szalay Neill, The Extreme Hosts of Extreme Supernovae, \apj, Pages: 15 January 1, 2011,

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,

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

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

I. a Ofek Cenko Poznanski J\ onsson Rahmer Velur McKenna Arcavi, Core-collapse Supernovae from the Palomar Transient Factory: Indications for a Different Population in Dwarf Galaxies, \apj, Pages: 777-784 2010,

N. a Silverman Marcy Yelda Smith, Discovery of Precursor Luminous Blue Variable Outbursts in Two Recent Optical Transients: The Fitfully Variable Missing Links UGC 2773-OT and SN 2009ip, \aj, Pages: 1451-1467 2010,

B.~D Quataert Nugent Metzger, Electromagnetic counterparts of compact object mergers powered by the radioactive decay of r-process nuclei, \mnras, Pages: 2650-2662 2010,

S.~B Morgan Castro-Tirado de Ugarte Postigo Kulkarni Starr Cenko, Unveiling the Origin of Grb 090709A: Lack of Periodicity in a Reddened Cosmological Long-Duration Gamma-Ray Burst, \aj, Pages: 224-234 2010,

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,

R.~A Bailey Childress Gal-Yam Loken Pereira Rau Tao Scalzo, Nearby Supernova Factory Observations of SN 2007if: First Total Mass Measurement of a Super-Chandrasekhar-Mass Progenitor, \apj, Pages: 1073-1094 2010,

S. a Nugent Darbha, Nickel-rich outflows produced by the accretion-induced collapse of white dwarfs: light curves and spectra, \mnras, Pages: 846-854 2010,

E.~O Cenko Nugent Forster Law Shen Hale Walters Ofek, Supernova PTF 09UJ: A Possible Shock Breakout from a Dense Circumstellar Wind, \apj, Pages: 1396-1401 January 1, 2010,

D. a Poznanski, Type II-P Supernovae as Standard Candles: The SDSS-II Sample Revisited, \apj, Pages: 956-959 2010,

A.~A Bloom Ganeshalingam Smith Miller, SN 2008iy: an unusual Type IIn Supernova with an enduring 400-d rise time, \mnras, Pages: 305-317 2010,

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. 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,

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,

John Shalf, Jason Hick, Storage Technology Fundamentals, Scientific Data Management: Challenges, Technology, and Deployment, 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,

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,

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,

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,

Kowalski M. a Amadon Blanc Covarrubias Ellis Farris Gates Goobar Hook Lidman Miller Newberg Perdereau Prasad Rubenstein Schaefer Soderberg Strovink Walton Supernova Cosmology Project, Improved Cosmological Constraints from New Old and Combined Supernova Data Sets, \apj, Pages: 749-778 January 1, 2008,

P. a Nugent, Optimizing Type Ia supernova follow-up in future dark energy surveys, Journal of Physics Conference Series, Pages: 012011 January 1, 2008,

J.~S Rischard Bloom, Towards a real-time transient classification engine, Astronomische Nachrichten, Pages: 284 January 1, 2008,

R.~S Gal-Yam Basa Guy Perrett Ellis, Verifying the Cosmological Utility of Type Ia Supernovae: Implications of a Dispersion in the Ultraviolet Spectra, \apj, Pages: 51-69 January 1, 2008,

M. a Amadon Blanc Covarrubias Ellis Farris Gates Goobar Hook Lidman Miller Newberg Perdereau Prasad Rubenstein Schaefer Soderberg Strovink Walton Supernova Cosmology Project Kowalski, Improved Cosmological Constraints from New, Old, and Combined Supernova Data Sets, \apj, Pages: 749-778 January 1, 2008,

Sam Williams, Jonathan Carter, Leonid Oliker, John Shalf, Katherine Yelick, Lattice Boltzmann Simulation Optimization on Leading Multicore Architectures, January 1, 2008,

Shantenu Jha, Hartmut Kaiser, Andre Merzky, John Shalf, SAGA - The Simple API for Grid Applications - Motivation, Design, and Implementation, Encyclopedia of Grid Technologies and Applications, January 1, 2008,

Harvey Wasserman, NERSC Workload Analysis and Benchmark Approach, talk, January 1, 2008,

Harvey Wasserman, Breakthrough Science at NERSC, talk, January 1, 2008,

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

John Shalf, NERSC User IO Cases, talk, January 1, 2008,

Harvey Wasserman, Future Scientific Computing Challenges at NERSC, talk, January 1, 2008,

John Shalf, Neuroinformatics Congress: Future Hardware Challenges for Scientific Computing, talk, January 1, 2008,

M. Wehner, L. Oliker, J. Shalf, Ultra-Efficient Exascale Scientific Computing, talk, January 1, 2008,

Cy Chan, Generalized Multicore Autotuning for Stencil-based PDE Solvers, talk, January 1, 2008,

Brent Draney, Scott Campbell, Howard Walter, NERSC Cyber Security Challenges That Require DOE Development and Support, 2008,

Jagadish H. V., Chapman Adriane, Elkiss Aaron, Jayapandian Magesh, Li Yunyao, Nandi Arnab, Yu Cong, Making database systems usable, SIGMOD 07: Proceedings of the 2007 ACM SIGMOD international conference on Management of data, Pages: 13--24 January 1, 2007,

G. a Amanullah Bronder Doi Goldhaber Howell Kuznetsova Morokuma Perlmutter Ruiz-Lapuente Smith Walton Garavini, Quantitative comparison between type Ia supernova spectra at low and high redshifts: a case study, \aap, Pages: 411-424 January 1, 2007,

S.~E Kasen R\ opke Woosley, Type Ia supernovae, Journal of Physics Conference Series, Pages: 012081 January 1, 2007,

D. a Kasen, The light curves and spectra of supernova explosions: multi-dimensional time-dependent Monte Carlo radiative transfer calculations, Journal of Physics Conference Series, Pages: 012037 January 1, 2007,

E.~Y Pritchet Phillips Hsiao, K-Corrections and Spectral Templates of Type Ia Supernovae, \apj, Pages: 1187-1200 January 1, 2007,

R.~C Bailey Buton Gilles Pain Perlmutter Runge Weaver Thomas, Nearby Supernova Factory Observations of SN 2006D: On Sporadic Carbon Signatures in Early Type Ia Supernova Spectra, \apjl, Pages: L53-L56 January 1, 2007,

Hongzhang Shan, John Shalf, Using IOR to Analyze the I/O performance for HPC Platforms, CUG.org, January 1, 2007,

S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms, International Conference for High-Performance Computing, Networking, Storage, and Analysis, January 1, 2007,

L. Oliker, J. Shalf, J. Carter, A. Canning, S. Kamil, M. Lijewski, S. Ethier, Performance Characteristics of Potential Petascale Scientific Applications, Petascale Computing: Algorithms and Applications, January 1, 2007,

Harvey Wasserman, NERSC XT3/XT4 Benchmarking, talk, January 1, 2007,

John Shalf, Landscape of Computing Architecture: Introduction to the Berkeley View, talk, January 1, 2007,

John Shalf, About Memory Bandwidth and Multicore, talk, January 1, 2007,

John Shalf, The Landscape of Parallel Computing Architecture, talk, January 1, 2007,

John Shalf, Overturning the Conventional Wisdom for the Multicore Era: Everything You Know is Wrong, talk, January 1, 2007,

John Shalf, Honzhang Shan, User Perspective on HPC I/O Requirements, talk, January 1, 2007,

John Shalf, NERSC Workload Analysis, talk, January 1, 2007,

John Shalf, NERSC Power Efficiency Analysis, talk, January 1, 2007,

John Shalf, Memory Subsystem Performance and QuadCore Predictions, talk, January 1, 2007,

John Shalf, Shoaib Kamil, David Skinner, Leonid Oliker, Interconnect Requirements for HPC Applications, talk, January 1, 2007,

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

John Shalf, Power, Cooling, and Energy Consumption for the Petascale and Beyond, talk, January 1, 2007,

John Shalf, Petascale Computing Application Challenges, talk, January 1, 2007,

Shoaib Kamil, John Shalf, Power Efficiency Metrics for the Top500, talk, January 1, 2007,

E. Young, H. Shukla, A. Bonissent, A. Kim, SNAP Collaboration, SNAP Spectrum Simulation: Spectra and Analysis, Bulletin of the American Astronomical Society, Pages: #132.26 January 1, 2007,

Kasen D. a, Time-dependent Monte Carlo Radiative Transfer Calculations for Three-dimensional Supernova Spectra Light Curves and Polarization, \apj, Pages: 366-380 January 1, 2006,

G. a Bauer Gangler Lee P\ econtal Rabinowitz Thomas Aldering, Nearby Supernova Factory Observations of SN 2005gj: Another Type Ia Supernova in a Massive Circumstellar Envelope, \apj, Pages: 510-527 January 1, 2006,

D.~A Conley Guy Hook Perrett Howell, The type Ia supernova SNLS-03D3bb from a super-Chandrasekhar-mass white dwarf star, \nat, Pages: 308-311 January 1, 2006,

A. a Tanvir Dell Antonio Castro Cer\ on Antonelli Fynbo Nugent Thorsett Levan, Infrared and Optical Observations of GRB 030115 and its Extremely Red Host Galaxy: Implications for Dark Bursts, \apj, Pages: 471-482 January 1, 2006,

Conley A. a Amanullah Garavini Hook Kowalski Nugent Spadafora Thomas, Measurement of $\Omega$$_m$ $\Omega$$_Î›$ from a Blind Analysis of Type Ia Supernovae with CMAGIC: Using Color Information to Verify the Acceleration of the Universe, \apj, Pages: 1-20 January 1, 2006,

Fruchter A.~S Vreeswijk Burud Conselice Garnavich Gull Levay Petro Sahu Woosley, Long $\gamma$-ray bursts and core-collapse supernovae have different environments, \nat, Pages: 463-468 January 1, 2006,

M. a Astier Carlberg Guy Pain Regnault Baumont Perlmutter Sullivan, Photometric Selection of High-Redshift Type Ia Supernova Candidates, \aj, Pages: 960-972 January 1, 2006,

D. a Kasen, Time-dependent Monte Carlo Radiative Transfer Calculations for Three-dimensional Supernova Spectra, Light Curves, and Polarization, \apj, Pages: 366-380 January 1, 2006,

A. a Amanullah Garavini Hook Kowalski Nugent Spadafora Thomas Conley, Measurement of $\Omega$$_m$, $\Omega$$_Î›$ from a Blind Analysis of Type Ia Supernovae with CMAGIC: Using Color Information to Verify the Acceleration of the Universe, \apj, Pages: 1-20 January 1, 2006,

A.~S Vreeswijk Burud Conselice Garnavich Gull Levay Petro Sahu Woosley Fruchter, Long $\gamma$-ray bursts and core-collapse supernovae have different environments, \nat, Pages: 463-468 January 1, 2006,

A. a Amanullah Garavini Hook Kowalski Nugent Spadafora Thomas Conley, Measurement of $\Omega$$_m$, $\Omega$$_Î›$ from a Blind Analysis of Type Ia Supernovae with CMAGIC: Using Color Information to Verify the Acceleration of the Universe, \apj, Pages: 1-20 January 1, 2006,

A.~S Vreeswijk Burud Conselice Garnavich Gull Levay Petro Sahu Woosley Fruchter, Long $\gamma$-ray bursts and core-collapse supernovae have different environments, \nat, Pages: 463-468 January 1, 2006,

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

A. a Amanullah Garavini Hook Kowalski Nugent Spadafora Thomas Conley, Measurement of $\Omega$$_m$, $\Omega$$_Î›$ from a Blind Analysis of Type Ia Supernovae with CMAGIC: Using Color Information to Verify the Acceleration of the Universe, \apj, Pages: 1-20 January 1, 2006,

A.~S Vreeswijk Burud Conselice Garnavich Gull Levay Petro Sahu Woosley Fruchter, Long $\gamma$-ray bursts and core-collapse supernovae have different environments, \nat, Pages: 463-468 January 1, 2006,

Scott Campbell, Brian L Tierney, William TC Kramer Lawrence Berkeley National Laboratory National Energy Research Scientific Computing Center kramer@ nersc. gov, 2006,

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

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

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

E Bethel, Scott Campbell, Eli Dart, John Shalf, Kurt Stockinger, Kesheng Wu, High Performance Visualization Using Query-Driven Visualization and Analytics, 2006,

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

I.~M Burns Fabbro Gibbons Kim Nobili Perlmutter Schaefer Stanishev Wang Hook, Spectra of High-Redshift Type Ia Supernovae and a Comparison with Their Low-Redshift Counterparts, \aj, Pages: 2788-2803 January 1, 2005,

J.~P Hjorth Sahu Tanvir Castro Cer\ on Holland Nugent Watson Fynbo, On the Afterglow and Host Galaxy of GRB 021004: A Comprehensive Study with the Hubble Space Telescope, \apj, Pages: 317-327 January 1, 2005,

G. a Astier Dahl\ en Fadeyev Gates Goobar Hook Knop Lidman Mouchet Nugent Quimby Ruiz-Lapuente Smith Walton Garavini, Spectroscopic Observations and Analysis of the Unusual Type Ia SN 1999ac, \aj, Pages: 2278-2292 January 1, 2005,

Nobili S. a Lidman Astier Ellis Gibbons Howell Pain Regnault Schahmaneche Thomas, Restframe I-band Hubble diagram for type Ia supernovae up to redshift z \tilde 0.5, \aap, Pages: 789-804 January 1, 2005,

J. a Levan Castro Cer\ on Burud Gorosabel, A possible bright blue supernova in the afterglow of GRB 020305, \aap, Pages: 411-418 January 1, 2005,

R.~J Riess Foley, A Definitive Measurement of Time Dilation in the Spectral Evolution of the Moderate-Redshift Type Ia Supernova 1997ex, \apjl, Pages: L11-L14 January 1, 2005,

A. a Branch Castro Cer\ on Golenetskii Hjorth Ulanov Levan, GRB 020410: A Gamma-Ray Burst Afterglow Discovered by Its Supernova Light, \apj, Pages: 880-888 January 1, 2005,

C. a Nobili Astier Deustua Fadeyev Groom Knop Motohara Prasad Ruiz-Lapuente Schahmaneche Stanishev Yasuda Lidman, Spectroscopic confirmation of high-redshift supernovae with the ESO VLT., \aap, Pages: 843-851 January 1, 2005,

S. a Lidman Astier Ellis Gibbons Howell Pain Regnault Schahmaneche Thomas Nobili, Restframe I-band Hubble diagram for type Ia supernovae up to redshift z \tilde 0.5, \aap, Pages: 789-804 January 1, 2005,

Tarek El-Ghazawi, William Carlson, Thomas Sterling, Katherine Yelick, UPC: Distributed Shared-Memory Programming, January 1, 2005,

P.N. Hilfinger, D.O. Bonachea, K. Datta, D. Gay, S.L. Graham, B.R. Liblit, G. Pike, J.Z. Su, K.A. Yelick, Titanium Language Reference Manual, version 2.19, January 1, 2005,

S. a Lidman Astier Ellis Gibbons Howell Pain Regnault Schahmaneche Thomas Nobili, Restframe I-band Hubble diagram for type Ia supernovae up to redshift z \tilde 0.5, \aap, Pages: 789-804 January 1, 2005,

Kurt Stockinger, Kesheng Wu, Scott Campbell, Stephen Lau, Mike Fisk, Eugene Gavrilov, Alex Kent, Christopher E Davis, Rick Olinger, Rob Young, others, Network Traffic Analysis With Query Driven Visualization SC 2005 HPC Analytics Results, Proceedings of the 2005 ACM/IEEE conference on Supercomputing, Pages: 72 2005,

W.~M Loken Wang Pain Castera P\ econtal Wood-Vasey, The Nearby Supernova Factory, \nar, Pages: 637-640 January 1, 2004,

E. a Baron, Type IIP Supernovae as Cosmological Probes: A Spectral-fitting Expanding Atmosphere Model Distance to SN 1999em, \apjl, Pages: L91-L94 January 1, 2004,

D. a Ellis Kneib Stern, Discovery of a Transient U-Band Dropout in a Lyman Break Survey: A Tidally Disrupted Star at z3.3?, \apj, Pages: 690-697 January 1, 2004,

D. a Kasen, Could There Be a Hole in Type Ia Supernovae?, \apj, Pages: 876-887 January 1, 2004,

G. a Aldering Balland Dahl\ en Fan Goldhaber Hardin Kent Lidman Mour\~ao Perdereau Raux Ruiz-Lapuente Schahmaneche Stanishev Supernova Cosmology Project Garavini, Spectroscopic Observations and Analysis of the Peculiar SN 1999aa, \aj, Pages: 387-404 January 1, 2004,

Krisciunas K. a Persson Clocchiatti Gonzalez Nugent Stritzinger Williams, Optical and Infrared Photometry of the Nearby Type Ia Supernovae 1999ee 2000bh 2000ca and 2001ba, \aj, Pages: 1664-1681 January 1, 2004,

J. a Bacon Kim Aldering Barrelet Bester Bower Commins Ealet Fruchter Goldhaber Harvey Johnston Kushner Levi Malina Morgan Musser Palaio Prieto Rusin Smith Szymkowiak Tomasch Walder Rhodes, Weak lensing from space I: instrumentation and survey strategy, Astroparticle Physics, Pages: 377-389 January 1, 2004,

K. a Persson Clocchiatti Gonzalez Nugent Stritzinger Williams Krisciunas, Optical and Infrared Photometry of the Nearby Type Ia Supernovae 1999ee, 2000bh, 2000ca, and 2001ba, \aj, Pages: 1664-1681 January 1, 2004,

Al Trivelpiece, Rupak Biswas, Jack Dongarra, Peter Paul, Katherine Yelick, Assessment of High-End Computing Research and Development in Japan, Available from http://www.wtec.org/reports.htm, January 1, 2004,

M. Yun, Dense Ionized Gas in the Nuclear Starburst Region of Arp 220, Astronomical Society of the Pacific Conference Series, Pages: 27 January 1, 2004,

Knop R.~A Blanc Doi Fruchter Gibbons Hardin Lee Nugent Perlmutter Ruiz-Lapuente Schahmaneche Stanishev Wood-Vasey, New Constraints on $\Omega$$_M$ $\Omega$$_Î›$ and w from an Independent Set of 11 High-Redshift Supernovae Observed with the Hubble Space Telescope, \apj, Pages: 102-137 January 1, 2003,

D. a Wheeler Hauschildt Kasen, Analysis of the Flux and Polarization Spectra of the Type Ia Supernova SN 2001el: Exploring the Geometry of the High-Velocity Ejecta, \apj, Pages: 788-808 January 1, 2003,

L. a Wheeler Fransson Wang, Spectropolarimetry of SN 2001el in NGC 1448: Asphericity of a Normal Type Ia Supernova, \apj, Pages: 1110-1128 January 1, 2003,

S. a Nobili, The intrinsic colour dispersion in Type Ia supernovae, \aap, Pages: 901-912 January 1, 2003,

M. a Astier Deustua Fruchter Goobar Howell Lidman Nugent Perlmutter Ruiz-Lapuente Spadafora Yasuda Sullivan, The Hubble diagram of type Ia supernovae as a function of host galaxy morphology, \mnras, Pages: 1057-1075 January 1, 2003,

E. a Turatto Baron, Determination of Primordial Metallicity and Mixing in the Type II-P Supernova 1993W, \apj, Pages: 1199-1210 January 1, 2003,

R.~A Blanc Doi Fruchter Gibbons Hardin Lee Nugent Perlmutter Ruiz-Lapuente Schahmaneche Stanishev Wood-Vasey Knop, New Constraints on $\Omega$$_M$, $\Omega$$_Î›$, and w from an Independent Set of 11 High-Redshift Supernovae Observed with the Hubble Space Telescope, \apj, Pages: 102-137 January 1, 2003,

L.-G Phillips Perlmutter Krisciunas Candia Bowers Galaz Groom McCarthy Quimby Szentgyorgyi York Strolger, The Type Ia Supernova 1999aw: A Probable 1999aa-like Event in a Low-Luminosity Host Galaxy, \aj, Pages: 2905-2919 January 1, 2002,

A. a Nugent Goobar, Cosmological parameters from lensed supernovae, \aap, Pages: 25-32 January 1, 2002,

Ben\ \itez N. a Chornock, The Magnification of SN 1997ff the Farthest Known Supernova, \apjl, Pages: L1-L4 January 1, 2002,

R. a Aldering Goldhaber Hook Kim McMahon Perlmutter Schaefer Pain, The Distant Type Ia Supernova Rate, \apj, Pages: 120-132 January 1, 2002,

P. a Nugent, K-Corrections and Extinction Corrections for Type Ia Supernovae, \pasp, Pages: 803-819 January 1, 2002,

R.~C Nugent Pun Mitchell, Detailed Spectroscopic Analysis of SN 1987A: The Distance to the Large Magellanic Cloud Using the Spectral-fitting Expanding Atmosphere Method, \apj, Pages: 293-305 January 1, 2002,

N. a Chornock Ben\ \itez, The Magnification of SN 1997ff, the Farthest Known Supernova, \apjl, Pages: L1-L4 January 1, 2002,

A.~G Schmidt Budav\ ari Filippenko Shapley Stern Riess, The Farthest Known Supernova: Support for an Accelerating Universe and a Glimpse of the Epoch of Deceleration, \apj, Pages: 49-71 January 1, 2001,

G. a Astier Fabbro Irwin McMahon Pennypacker Schaefer Goldhaber, Timescale Stretch Parameterization of Type Ia Supernova B-Band Light Curves, \apj, Pages: 359-368 January 1, 2001,

S. a Podariu, Cosmological Model Parameter Determination from Satellite-acquired Supernova Apparent Magnitude versus Redshift Data, \apj, Pages: 39-46 January 1, 2001,

H. Shukla, A. Sivaramakrishnan, M. Troy, R.~G. Dekany, Using Past Data in Adaptive Optics Wavefront Reconstruction, Bulletin of the American Astronomical Society, Pages: #145.03 January 1, 2001,

M. a Madau Sullivan, A strategy for finding gravitationally lensed distant supernovae, \mnras, Pages: 549-556 January 1, 2000,

G. a Aldering, The Rise Times of High- and Low-Redshift Type IA Supernovae Are Consistent, \aj, Pages: 2110-2117 January 1, 2000,

E.~J Nugent Lentz, Metallicity Effects in Non-LTE Model Atmospheres of Type IA Supernovae, \apj, Pages: 966-976 January 1, 2000,

A. a Knop Fabbro Kim Pennypacker Irwin Walton Matheson Couch Goobar, The Acceleration of the Universe: Measurements of Cosmological Parameters from Type la Supernovae, Physica Scripta Volume T, Pages: 47 January 1, 2000,

A. Sivaramakrishnan, B. Simon, S. Holfeltz, H. Shukla, M. Sosey, The new NICMOS Exposure Time Calculator: Software and Installation, NICMOS ISR-00-005, 15 pages, Pages: 5 January 1, 2000,

R.~L Gilliland, High-Redshift Supernovae in the Hubble Deep Field, \apj, Pages: 30-49 January 1, 1999,

S. a Knop Fabbro Kim Pain Ellis Walton Matheson Couch Perlmutter, Measurements of Omega and Lambda from 42 High-Redshift Supernovae, \apj, Pages: 565-586 January 1, 1999,

K. B. Marvel, H. Shukla, G. Rhee, Radio sources in 14 Abell clusters (Marvel+, 1999), VizieR Online Data Catalog, Pages: 147 January 1, 1999,

W.W. Carlson, J.M. Draper, D.E. Culler, K. Yelick, E. Brooks, K. Warren, Introduction to UPC and language specification, January 1, 1999,

A.~G Kirshner Riess, Snapshot Distances to Type IA Supernovae: All in One Night s Work, \apj, Pages: 935 January 1, 1998,

S. a Deustua Goldhaber Kim McMahon Pennypacker Walton Perlmutter, Erratum: Discovery of a supernova explosion at half the age of the Universe, \nat, Pages: 311 January 1, 1998,

S. a Deustua Goldhaber Kim Nugent Ruiz-Lapuente Perlmutter, Discovery of a supernova explosion at half the age of the universe, \nat, Pages: 51 January 1, 1998,

Abiteboul Serge, Quass Dallan, Mchugh Jason, Widom Jennifer, Wiener Janet, The Lorel Query Language for Semistructured Data, International Journal on Digital Libraries, Pages: 68--88 January 1, 1997,

P.~E Nugent, Non-Local Thermodynamic Equilibrium Spectrum Synthesis of Type IA Supernovae, January 1, 1997,

P. a Hauschildt Nugent, Synthetic Spectra of Hydrodynamic Models of Type IA Supernovae, \apj, Pages: 812 January 1, 1997,

A. a Fisher, Evidence for a High-velocity Carbon-rich Layer in the Type IA SN 1990N, \apjl, Pages: L89 January 1, 1997,

Branch D. a, The Hubble constant supernova light curves and spectra and radiation transport, Physics of Plasmas, Pages: 2016-2022 January 1, 1997,

D. a Branch, The Hubble constant, supernova light curves and spectra, and radiation transport, Physics of Plasmas, Pages: 2016-2022 January 1, 1997,

Tsatalos Odysseas G., Solomon Marvin H., Ioannidis Yannis E., The GMAP: a versatile tool for physical data independence, VLDB Journal, Pages: 367--378 January 1, 1996,

E. a Baron, Non-local thermodynamic equilibrium effects in modelling of supernovae near maximum light., \mnras, Pages: 297-315 January 1, 1996,

D. a Branch, On van den Bergh s Method for Measuring the Hubble Constant from Type IA Supernovae, \apjl, Pages: L7 January 1, 1996,

S. D. Ryder, R.~J. Buta, H. Toledo, H. Shukla, L. Staveley-Smith, W. Walsh, Neutral Hydrogen in the Ringed Barred Galaxies NGC 1433 and NGC 6300, The Astrophysical Journal, Pages: 665 January 1, 1996,

Jain Manoj, Mendhekar Anurag, Van Gucht Dirk, A Uniform Data Model for Relational Data and Meta-Data Query Processing, In Proceedings of the Seventh International Conference on Management of Data, Pages: 146--165 January 1, 1995,

P. a Hauschildt Nugent, Evidence for a Spectroscopic Sequence among Type 1a Supernovae, \apjl, Pages: L147 January 1, 1995,

Nugent P. a Vaughan, Erratum: Low Hubble Constant from the Physics of Type Ia Supernovae [Phys. Rev. Lett. 75 394 (1995)], Physical Review Letters, Pages: 1874 January 1, 1995,

P. a Vaughan Nugent, Low Hubble Constant from the Physics of Type Ia Supernovae, Physical Review Letters, Pages: 394-397 January 1, 1995,

P. a Nugent, Spectrum synthesis of the Type IA supernovae SN 1992A and SN 1981B, \apjl, Pages: L33-L36 January 1, 1995,

P. a Vaughan Nugent, Erratum: Low Hubble Constant from the Physics of Type Ia Supernovae [Phys. Rev. Lett. 75, 394 (1995)], Physical Review Letters, Pages: 1874 January 1, 1995,

D. a Nugent Branch, The distance to the type IA supernova 1972E and its parent galaxy NGC 5253: A prediction, \apjl, Pages: L87-L90 January 1, 1994,

D. a Branch, On the relative frequencies of spectroscopically normal and peculiar type IA supernovae, \aj, Pages: 2383-2391 January 1, 1993,

NERSC Staff Publications & Presentations

Journal Article

2013

Jack Deslippe, Georgy Samsonidze, Manish Jain, Marvin L Cohen, Steven G Louie, “Coulomb-hole summations and energies for GW calculations with limited number of empty orbitals: a modified static remainder approach”, Accepted 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

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),

2012

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

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

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

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

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

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

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

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

K. F\ urlinger, N.J. Wright, D. Skinner, C. Klausecker, D. Kranzlm\ uller, “Effective Holistic Performance Measurement at Petascale Using IPM”, Competence in High Performance Computing 2010, January 1, 2012, 15--26,

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”, accepted, Journal of Mathematical Chemistry, January 1, 2012,

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

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

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

2011

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,

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,

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,

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

A. Dubey, K. B. Antypas, C. Daley, “Parallel Algorithms for Moving Lagrangian Data on Block Structured Eulerian Meshes”, Parallel Computing, 2011, 37 (2):101 - 113,

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. 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,

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,

John Shalf, Quinlan, Curtis Janssen, “Rethinking Hardware-Software Codesign for Exascale Systems”, IEEE Computer, January 1, 2011, 44:22-30,

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

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

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

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,

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,

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

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,

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,

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

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,

D. C. Eder, et al, “Assessment and Mitigation of Radiation, EMP, Debris and Shrapnel Impacts at Mega-Joule Class Laser Facilities”, J. Physics, Conference, 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,

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

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,

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,

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,

B.I. Abelev, others, “Observation of Two-source Interference in the Reaction Au Au ---> Au Au rho0”, Phys.Rev.Lett., January 1, 2009, 102:112301,