Research and Publications that make use of PETSc

Nano-simulations

@INPROCEEDINGS{
asc2013,
author = "S. Abhyankar and B. F. Smith and E. Constantinescu",
title = "Evaluation of overlapping restricted additive Schwarz preconditioning for parallel solution of very large power flow problems",
booktitle = "HiPCNA-PG’13",
year = 2013
}
@INPROCEEDINGS{as2013,
author = "S. Abhyankar and B. F. Smith",
title = "{PETSc:} An Advanced Math and Computing Framework for Rapidly Developing Parallel Smart Grid Applications",
booktitle = "Proceedings of the IEEE PES General Meeting",
year = 2013
}
@techreport{tspaper,
title = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library},
author = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and Barry F. Smith},
type = {Preprint},
number = {ANL/MCS-P5061-0114},
institution = {ANL},
month = {January},
year = {2014}
}
@TechReport{bb2008,
author = "Tomasz Blachowicz and Bartlomiej Baron",
title = "A graphical extension for the Windows version of the Parallel Finite Element Micromagnetics Package (MagParExt)",
url = "http://arxiv.org/abs/0807.2655",
year = 2008
}

@Article{jacvgv2008,
author = "R. Y. Jaafar and A Asenjo and O Chubykalo-Fesenko and M Vazquez and E M Gonzalez and J L Vicent",
title = "Field induced vortex dynamics in magnetic Ni nanotriangles",
journal = "Nanotechnology",
volume = 19,
year = 2008,
url = "http://dx.doi.org/10.1088/0957-4484/19/28/285717"
}

@Article{yjdwh2008,
author = "Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He",
title = "Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy",
journal = "Journal of the Magnetics Society of Japan",
volume = 32,
year = 2008,
pages = "50-53",
url = "http://www.jstage.jst.go.jp/article/msjmag/32/2_1/32_50/_article"
}


@Article{mtrtrsa2008,
author = "D. Makarov and S. Tibus and C. T. Rettner and T. Thomson and B. D. Terris and T. Schrefl and M. Albrecht",
title = "Magnetic strip patterns induced by focused ion beam irradiation",
journal = "J. Appl. Phys.",
volume = 103,
year = 2008,
url = "http://dx.doi.org/10.1063/1.2894587"
}

@INPROCEEDINGS{tmrttsa2008,
author = "S. Tibus and D. Makarov and C. T. Rettner and T. Thomson and B. D. Terris and T. Schrefl and M. Albrecht",
title = "Patterning of magnetic films by focused ion beam irradiation",
booktitle = "Intermag 2008 paper no. CM-05, submitted to IEEE Trans. Magn.",
year = 2008
}

@article{yjdbh2007,
author = "Lin Yuan and Jianju Jiang and Yongjiang di and Shaowei Bie and Huahui He",
title = "Micromagnetic simulation of the magnetic dispersion angle and effective damping factor for the single-phase soft magnetic films",
journal = "J. Magn. Magn. Mater.",
Volume = 320,
Number = 7,
pages = "1393-1397",
url = "http://dx.doi.org/10.1016/j.jmmm.2007.11.025"
}

@article{lxky2007,
author = "DENG Lian-wen and HUANG Xiao-zhong and ZH0U Ke-sheng and YANG",
title = "Micromagnetic simulation and experimental study on microwave permeability of nano-magnetic films",
journal = "Transactions of Nonferrous Metals Society of China",
year = 2007,
pages = "756-759",
url = "http://www.ysxbcn.com/icnfm2007/part2B/s0756.pdf"
}

@article{yjdwh2008a,
author = "Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He",
title = "Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy",
journal = "Journal of the Magnetics Society of Japan",
Volume = 32,
year = 2008,
pages = "50-53",
url = "http://dx.doi.org/10.3379/msjmag.32.50"
}

@article{lylw2007,
author = "Ching-Ming Lee and L. X. Ye and J. M. Lee and Te-Ho Wu",
title = "Micromagnetic study of magnetization reversal in patterned DyFeCo thin films",
journal = "Phys. Stat. Sol.",
volume = 204,
Number = 12,
pages = "4049-4052",
year = 2007,
url = "http://dx.doi.org/10.1002/pssa.200777359"
}

@INPROCEEDINGS{sg2007,
author = "Simon Greaves",
title = "Micromagnetic Simulations of Magnetic Recording Media",
booktitle = "High Performance Computing on Vector Systems 2007",
url = "http://dx.doi.org/10.1007/978-3-540-74384-2_17"
}

@article{bsc2007,
author = "Nadjib Benatmane and Werner Scholz and T.W. Clinton",
title = "Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings",
journal = "IEEE Trans. Magn.",
volume = 43,
year = 2007,
pages = "2884-2886",
url = "http://dx.doi.org/10.1109/TMAG.2007.892867"
}

@article{ffbf,
author = "T. Fischbacher and M. Franchin and G. Bordignon and H. Fangohr",
title = "A Systematic Approach to Multiphysics Extensions of Finite-Element-Based Micromagnetic Simulations: Nmag.",
journal = "IEEE Trans. Magn. Volume",
Volume = 43,
pages = "2896-2898",
url = "http://dx.doi.org/10.1109/TMAG.2007.893843"
}

@inbook{dfssfs2006,
author = "R. Dittrich and J. Fidler and D. Suess and W. Schol and H. Forster, T. Schrefl",
chapter = "Computational Aspects of Micromagnetics",
title = "The Science of Hysteresis",
editor = " G. Bertotti and I. Mayergoyz",
url = "http://books.elsevier.com/us/elsevier/us/subindex.asp?maintarget=&isbn=0124808743"No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}

@inbook{fss,
author = "J. Fidler and T. Schrefl and W. Scholz",
chapter = "Computational Micromagnetics",
title = "Handbook of Theoretical and Computational Nanotechnology",
editor = "M. Rieth and W. Schommers",
url = "http://www.amazon.com/gp/product/158883042X"No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}

@inbook{shbsef,
author = "Thomas Schrefl and Gino Hrkac and Simon Bance and Dieter Suess and Otmar Ertl and Josef Fidler",
chapter = "Numerical Methods in Micromagnetics (Finite Element Method)",
title = "Handbook of Magnetism and Advanced Magnetic Materials",
editor = "Helmut Kronmueller and Stuart Parkin",
url = "http://dx.doi.org/10.1002/9780470022184.hmm203"No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}

@inbook{sfs,
author = "D. Suess and J. Fidler and T. Schrefl",
chapter = "Micromagnetic Simulation of magnetic materials",
title = "Handbook of Magnetic Materials",
editor = "K. H. J. Buschow",
url = "http://www.amazon.com/gp/product/0444518509"No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}

@article{fsxzs,
author = "J. Fernandez-de-Castro and Xiao Shen and Jianhua Xue and Yuming Zhou and S. Sharma",
title = "Writer Flux Closure and Transition Degradation Mechanism in Perpendicular Recording.",
journal = "IEEE Trans. Magn. Volume",
volume = 43,
pages = "2175-2177",
url = "http://dx.doi.org/10.1109/TMAG.2007.893122"
}

@article{sb2006,
author = "W. Scholz and S. Batra",
title = "Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads",
journal = "IEEE Trans. Magn.",
volume = 42,
year = 2006,
pages = "2264--2266",
url = "http://magnet.atp.tuwien.ac.at/scholz/projects/papers/ieee/scholz_2006_42_2264.pdf"
}

@article{bsr2006,
author = "S. Batra and W. Scholz and T. Roscamp",
title = "Effect of thermal fluctuation field on the noise performance of a perpendicular recording system",
journal = "J. Appl. Phys.",
volume = 99,
year = 2006,
url = "http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf"
}

@inproceedings{japios2006,
author = "F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. Subramanian",
title = "Micromagnetic simulations of the dependence of domain wall width with grain size in systems with cubic and uniaxial anisotropy.",
booktitle = "Intermag 2006 Conference"
}

@article{kbmb2006,
author = "A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain",
title = "A Micromagnetic Study of the Effect of Spatial Variations in Damping in Perpendicular Recording Heads",
journal = "IEEE Trans. Magn.",
volume = 42,
year = 2006,
pages = "2428--2430",
url = "http://dx.doi.org/10.1109/TMAG.2006.879430"
}

@article{cclcw2006,
author = "C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu",
title = "Control of Domain Wall Motion in Permalloy Ring",
journal = "IEEE Trans. Magn.",
volume = 42,
year = 2006,
pages = "2960--2962",
url = "http://dx.doi.org/10.1109/TMAG.2006.878414"
}

@article{bfmfzczg2007,
author = "Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot",
title = "Micromagnetic modelling of ferromagnetic cones",
journal = "J. Magn. Magn. Mater.",
Volume = 312,
year = 2007,
Pages = "234-238",
url = "http://eprints.soton.ac.uk/45900/"
}

@PhdThesis{rb2005,
author = "Richard Boardman",
title = "Computer simulation studies of magnetic nanostructures",
school = "Computational Engineering and Design Group, School of Engineering Sciences, University of Southampton, United Kingdom",
year = 2005,
url = "http://www.soton.ac.uk/~rpb/thesis.pdf"No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}

@inproceedings{cwwy2006,
author = "I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu",
title = "MPI Performance Analysis Tools on Blue Gene/L",
booktitle = "ACM/IEEE SC 2006 Conference (SC'06)",
year = 2006,
url = "http://sc06.supercomputing.org/schedule/pdf/pap159.pdf"
}

@inproceedings{ch2006,
author = "I.-H. Chung and J.K. Hollingsworth",
title = "A Case Study Using Automatic Performance Tuning for Large-Scale Scientific Programs",
booktitle = "High Performance Distributed Computing, 2006 15th IEEE International Symposium",
pages = "45--56",
url = "http://dx.doi.org/10.1109/HPDC.2006.1652135"
}

@article{lkpl2005,
author = "C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee",
title = "Multibit MRAM using a pair of memory cells",
journal = "IEEE Trans. Magn.",
volume = 41,
year = 2005,
pages = "2670-2672",
url = "http://dx.doi.org/10.1109/TMAG.2005.855288"
}

@article{gscn2005,
author = "K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad",
title = "Vortex state oscillations in soft magnetic cylindrical dots",
journal = "Phys. Rev. B",
volume = 71,
year = 2005,
url = "http://dx.doi.org/10.1103/PhysRevB.71.144407"
}

@PhdThesis{mda,
author = "Massimiliano d'Aquino",
title = "Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles",
school = " Universita di Napoli Federico II.",
url = "http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf"No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}

@techreport{ssdfssf2003,
author = "T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. Stehno and J. Fidler",
title = "Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films",
url = "http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html"
}

@inproceedings{sb2006a,
author = "W. Scholz and S. Batra",
title = "Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads",
booktitle = "Intermag 2006 Conference, San Diego, CA, paper no. EF-03"
}

@article{scholz-batra1,
author = {W. Scholz and S. Batra},
title = "Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular Recording",
journal = {IEEE Trans. Magn.},
note = {submitted},
year = 2005
}

@article{scholz-batra2,
author = {W. Scholz and S. Batra},
title = "Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording",
journal = {IEEE Trans. Magn.},
volume = 41,
year = 2005,
pages = {702-706}
}
@article{daquino-scholz1,
author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler},
title = "Micromagnetic Analysis of Fast Precessional Switching",
journal = {J. Magn. Magn. Mater.},
volume = {290-291},
year = 2005,
pages = {510-513}
}
@article{aq-scholz-fid,
author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler},
title = "Numerical and analytical study of fast precessional switching",
journal = {J. Appl. Phys.},
volume = 95,
year = 2004,
pages = {7055-7057}
}
@inproceedings{gar-tabik-gar,
author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones},
title = "Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and Scatterers",
booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP'04)},
year = 2004,
pages = {80--}
}
@inproceedings{aq-scholz-mia,
author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano},
title = "Analysis of fast precessional switching in magnetic thin films",
booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)},
year = 2004,
pages = {257-260}
}
@article{scholz-fid-seus,
author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. Dittrich and V. Tsiantos},
title = "Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy Axes",
journal = {J. Magn. Magn. Mater.},
year = 2004,
pages = {1524-1525}
}
@article{boardman-zimmerman,
author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and Peter de Groot},
title = "Micromagnetic simulation studies of ferromagnetic part-spheres",
journal = {Journal of Applied Physics},
year = 2005
}
@article{lim-kim-park,
author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee},
title = "High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell",
journal = {IEEE Trans. Magn.},
note = {submitted}
}
@article{scholz-suess2,
author = {W. Scholz and D. Suess and T. Schrefl and and J. Fidler},
title = "Micromagnetic simulation of magnetization reversal in small particles with surface anisotropy",
journal = {J. Appl. Phys.},
volume = 95,
year = 2004,
pages = {6807-6809}
}
@article{scholz-schrefl1,
author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. Tsiantos},
title = "Micromagnetic simulation of the pinning and depinning process in permanent magnets",
journal = {IEEE Trans. Magn.},
volume = 39,
year = 2003,
pages = {2920-2922}
}
@article{scholz-guslienko,
author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. W. Chantrell and J. Fidler},
title = "Transition from single-domain to vortex state in soft magnetic cylindrical nanodots",
journal = {J. Magn. Magn. Mater.},
volume = 266,
year = 2003,
pages = {155-163}
}
@article{scholz1,
author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. Forster and V. Tsiantos},
title = "Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures",
journal = "Comp. Mat. Sci",
year = 2003,
pages = "366--383",
volume = 28,
url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}
}
@phdthesis{scholz2,
author = {W. Scholz},
title = "Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures",
school = {Vienna University of Technology, Vienna, Austria},
year = 2003No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@article{scholz3,
author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. Forster and J. Fidler},
title = "Implementation of a high performance parallel finite element micromagnetics package",
journal = {J. Magn. Magn. Mater.},
year = 2004,
url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}
}

@InBook{zhanggladwell1,
AUTHOR = "W. Zhang and I. Gladwell",
chapter = "Performance of MOL for Surface Motion Driven by a Laplacian of Curvature",
editor = "Z. Chen and R.E. Ewing and Z.-C. Shi",
YEAR = "2000",
TITLE = "Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in Physics, vol. 552",
publisher = "Springer",
pages = "4190-"No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@article{wolf1,
author = "A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov",
title = "Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline thin films",
journal = "Phil. Mag. A",
year = "2003",
Lab = {ANL}
}
@article{wolf2,
author = "A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter",
title = "Mesoscopic simulation of two dimensional grain growth with anisotropic grain-boundary properties",
journal = "Computational Materials Science",
year = "2001",
volume = "23",
pages = "15--32",
Lab = {ANL}
}
@article{wolf3,
author = "D. Moldovan and S. R. Phillpot and A. J. Haslan",
title = "Role of grain rotation in grain growth by mesoscale simulation",
journal = "Phil. Mag. A",
year = "2002",
volume = "82",
pages = "1271--1297",
Lab = {ANL}
}

@article{saut,
author = { Olivier Saut},
title = "Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal",
journal = "SIAM Journal on Scientific Computing",
year = 2004,
note = "submitted",
url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}
}

Biology -- Medical

@article{
Ataseven,
author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er},
title = {Parallel implementation of the accelerated BEM approach for EMSI of the human brain},
journal = {Medical and Biological Engineering and Computing},
month = {February},
year = {2008},
note = {doi 10.1007/s11517-008-0316-0}
}
@article{dennis-eberhart-03,
author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons},
pages = "832-840",
volume = 125,
number = 6,
title = "Finite-element simulation of cooling of realistic 3-D human head and neck",
journal = "J Biomech Eng",
year = 2003,
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}
}
@conference{gu7174parallel,
title = {{A parallel reduced-space sequential-quadratic programming algorithm for frequency-domain small animal optical tomography}},
author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.},
booktitle = {Proc. of SPIE Vol},
volume = {7174},
number = {717406},
pages = {1}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@article{barchanski2005using,
title = {{Using domain decomposition techniques for the calculation of low-frequency electric current densities in high-resolution 3D human anatomy models}},
author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, T.},
journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering},
volume = {24},
number = {2},
pages = {458--467},
issn = {0332-1649},
year = {2005},
publisher = {Emerald Group Publishing Limited}
}
@article{MotrescuRienen05,
author = {V. C. Motrescu and U. van Rienen},
pages = "227--231",
volume = 3,
title = "Computation of currents induced by ELF electric fields in anisotropic human tissues using the Finite Integration Technique",
journal = "Advances in Radio Science",
year = 2005,
url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}
}
@article{MotrescuRienen04,
author = {V. C. Motrescu and U. van Rienen},
pages = "309--313",
volume = 2,
title = "Computation of electrostatic fields in anisotropic human tissues using the Finite Integration Technique (FIT)",
journal = "Advances in Radio Science",
year = 2004,
url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}
}
@InProceedings{dbl2,
author = "Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo",
title = "Computational arterial flow modeling using a parallel {Navier-Stokes} solver",
booktitle = "ECCOMAS2000",
year = "2000",
url = "http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html"
}
@Unpublished{cell,
title = {Parallel Simulation Engines for Whole-Cell Models},
author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin Weber},
note = {Poster at Second International Conference on Systems Biology (ICSB) 2001},
url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf},
institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen},
year = 2001No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@article{barker2010two,
title = {Two-level Newton and hybrid Schwarz preconditioners for fluid-structure interaction},
author = {Barker, A.T. and Cai, X.C.},
journal = {SIAM Journal on Scientific Computing},
volume = {32},
number = {4},
pages = {2395--2417},
year = {2010},
publisher = {Society for Industrial and Applied Mathematics}
}
@article{barker2010scalable,
title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction with application to blood flow modeling},
author = {Barker, A.T. and Cai, X.C.},
journal = {Journal of Computational Physics},
volume = {229},
number = {3},
pages = {642--659},
year = {2010},
publisher = {Elsevier}
}
@article{barker2009nks,
title = {NKS for fully coupled fluid-structure interaction with application},
author = {Barker, A.T. and Cai, X.C.},
journal = {Domain Decomposition Methods in Science and Engineering XVIII},
pages = {275--282},
year = {2009},
publisher = {Springer}
}


Treating fractures of the hip and spine is a major medical cost. Understanding bone mechanical properties and how they may lead to fractures is thus an important medical research activity. PETSc and Prometheus have been used for extremely large scale finite element simulation of the solid mechanics of a portion of a human spine by a team of doctors and computational scientists. This computation was a winner of a Gordon Bell Special Prize at SC2004 and ran scalably with over 4000 processors.

@article{arbenz2008scalable,
title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element analysis of human bone structures},
author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.},
journal = {International Journal for Numerical Methods in Engineering},
volume = {73},
number = {7},
pages = {927--947},
year = {2008},
publisher = {Wiley Online Library}
}
@inproceedings{Adams-04,
Author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.},
Booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing},
Title = {Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom},
Note = {Gordon Bell Award},
Year = {2004}
}
@InProceedings{Adams-03b,
author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.},
title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP},
booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing},
year = {2003}
}
@inproceedings{oghattas2002,
author = "Volkan Akcelik and George Biros and Omar Ghattas",
title = "Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation",
booktitle = "Procceedings of SC2002",
url = "http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf",
note = "Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed by time-dependent PDEs, and scalability results for an inverse wave propagation problem of determining the material field of an acoustic medium. Using the algorithm, they solved a synthetic inverse wave propagation problem though a pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 processors.",
year = "2002"
}

Arrhythmias are disorders of the regular rhythmic beating of the heart; they are the cause of the majority of sudden cardiac deaths. The heart beat is controlled by electrical signals moving through the heart. PETSc has been used by several research groups to simulate the electronic behavior of the heart in an attempt to more fully understand the developments of arrhthmias.

@inproceedings{
oghattas2000,
author = "J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. Walkington",
title = "A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic Interfaces",
booktitle = "Procceedings of SC2000",
url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf",
note = "Blood flow modeling at the microscale including effects on individual blood cells, for designing heart assist pumps, etc.",
year = "2000"
}
@InBook{cfps2006,
author = {P. Colli Franzone and L. F. Pavarino and G. Savare},
editor = {A. Quarteroni et al.},
title = {Complex Systems in Biomedicine},
chapter = {Computational Electrocardiology: mathematical and numerical modeling},
publisher = {Springer-Verlag},
pages = {187--241},
year = {2006}No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@Inproceedings{cfpst2007,
author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi},
title = {Determining recovery times from transmembrane action potentials and unipolar electrograms in normal heart tissue},
booktitle = {FIMH07},
publisher = {Springer-Verlag},
volume = {4466},
pages = {139--149},
year = {2007}
}
@article{seemann2010framework,
title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain Equations Using PETSc}},
author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and D{\\"o}ssel, O.},
journal = {Progress in Industrial Mathematics at ECMI 2008},
pages = {363--369},
year = {2010},
publisher = {Springer}
}
@INPROCEEDINGS{pft2005,
AUTHOR = "Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi",
TITLE = "Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with Intramural Heterogeneity",
BOOKTITLE = "Functional Imaging and modeling of the Heart (FIMH05)",
PAGES = "267--277",
EDITORS = "A. Frangi et al.",
PUBLISHER = "Springer, Lecture Notes in Computer Science (LNCS), v. 3504",
YEAR = "2005"
}
@article{bgcp2005,
author = "Boyce E. Griffith and Charles S. Peskin",
title = "On the order of accuracy of the immersed boundary method: Higher order convergence rates for sufficiently smooth problems",
journal = "Journal of Computational Physics",
year = "2005",
volume = "208",
pages = "75--105"
}
@article{griffith2007adaptive,
title = {An adaptive, formally second order accurate version of the immersed boundary method},
author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.},
journal = {Journal of Computational Physics},
volume = {223},
number = {1},
pages = {10--49},
year = {2007},
publisher = {Elsevier}
}
@phdthesis{Griffith05,
author = {Boyce Griffith},
title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and parallel version of the immersed boundary method},
school = {New York University},
year = 2005No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@phdthesis{Murillo,
author = {Maria S. Murillo},
title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial Differential Equations with an Application in Computational Biology},
school = {University of Colorado at Boulder},
year = 2002No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@article{spv2004,
author = "Rodrigo Weber Dos Santos and G. Plank and S. Bauer",
title = "Parallel multigrid preconditioner for the cardiac bidomain model",
journal = "IEEE Trans. Biomed. Eng",
year = "2004",
volume = "51",
pages = "1960--1968"
}
@article{vphl2003,
author = "E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon",
title = " Computational Tools for Modeling Electrical Activity in Cardiac Tissue",
journal = "J. Electrocardiol.",
year = "2003",
volume = "36",
pages = "69--74"
}
@INPROCEEDINGS{spbv2003,
AUTHOR = "Rodrigo Weber Dos Santos and G. Plank and S. Bauer and and E.J. Vigmond",
TITLE = "Preconditioning Techniques for the Bidomain Equations",
BOOKTITLE = "Proceedings of the 15th International Conference on Domain Decomposition Methods",
PAGES = "571--580",
PUBLISHER = "Springer, Lecture Notes in Computational Science and Engineering (LNCSE).",
NOTE = "",
URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
YEAR = "2003"
}
@article{franz-pavir-04,
author = "P. Colli Franzone and L.~F. Pavarino",
title = "A parallel solver for reaction-diffusion systems in computational electrocardiology",
journal = "Mathematical Models and Methods in Applied Sciences",
year = "2004",
volume = "14",
number = 6,
pages = "883--912"
}
@article{franz-pavir-05,
author = "P. Colli Franzone and L.~F. Pavarino and B. Taccardi",
title = "Simulating patterns of excitation, repolarization and action potential durationwith cardiac Bidomain and Monodomain models",
journal = "Mathematical Biosciences",
year = "2005",
volume = "197",
number = 1,
pages = "35--66"
}
@article{franz-pavir-06,
author = "P. Colli Franzone and L.~F. Pavarino and B. Taccardi",
title = "Effects of transmural electrical heterogeneities and electrotonic interactions on the dispersion of cardiac repolarization and action potential duration: a simulation study",
journal = "Mathematical Biosciences",
year = "2006",
volume = "204",
number = 1,
pages = "132--165"
}
@INPROCEEDINGS{colli-franz-sim,
AUTHOR = "P. Colli-Franzone and L.F. Pavarino and B. Taccardi",
TITLE = "MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS",
BOOKTITLE = "MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X Mediterranean Conference on Medical and Biological Engineering",
URL = "http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf",
YEAR = "2004"
}
@INPROCEEDINGS{pf2003,
AUTHOR = "Luca F. Pavarino and Piero Colli Franzone",
TITLE = "Parallel Solution of Cardiac Reaction-Diffusion Models",
BOOKTITLE = "Proceedings of the 15th International Conference on Domain Decomposition Methods",
PAGES = "669--776",
PUBLISHER = "Springer, Lecture Notes in Computational Science and Engineering (LNCSE).",
NOTE = "",
URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
YEAR = "2003"
}
@article{maria-is04,
author = "Maria Murillo and Xiao-Chuan Cai",
title = "A fully implicit parallel algorithm for simulating the non-linear electrical activity of the heart",
journal = "Numerical Linear Algebra with Applications",
year = "2004",
volume = "11",
pages = "261 - 277",
url = "http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT"
}
@article{murli2007monitoring,
title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical Imaging in a Grid computing PSE}},
author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. and Lapegna, M.},
journal = {Grid-Based Problem Solving Environments},
pages = {421--432},
year = {2007},
publisher = {Springer}
}
@article{Carracciuolo:2006:TPC,
author = {Carracciuolo, L. and D'Amore, L. and Murli, A.},
title = {Towards a parallel component for imaging in PETSc programming environment: a case study in 3-D echocardiography},
journal = {Parallel Comput.},
volume = {32},
issue = {1},
month = {January},
year = {2006},
issn = {0167-8191},
pages = {67--83},
numpages = {17},
url = {http://dx.doi.org/10.1016/j.parco.2005.09.001},
doi = {http://dx.doi.org/10.1016/j.parco.2005.09.001},
acmid = {1141218},
publisher = {Elsevier Science Publishers B. V.},
address = {Amsterdam, The Netherlands, The Netherlands},
keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel component},
}
@article{damore2011integration,
title = {Integration of emerging computer technologies for an efficient image sequences analysis},
journal = "Integrated Computer-Aided Engineering ",
volume = "18",
number = "4",
pages = "365 - 378",
year = "2011",
note = "",
issn = "1875-8835",
doi = "http://dx.doi.org/10.3233/ICA-2011-0382",
url = "http://iospress.metapress.com/content/KM614806M50TKVP7",
author = "L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli",
keywords = "Image sequence ",
keywords = "pipe and filters ",
keywords = "parallel computing ",
keywords = "multicore processors "
}
@InProceedings{eth_biwi_00721,
author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and and G. Székely},
title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using a Schur Complement Preconditioner},
booktitle = {Euro-Par 2009 Parallel Processing},
year = {2009},
month = {August},
pages = {747-759},
volume = {5704},
editor = {H. Sips and D. Epema and and H.-X. Lin},
series = {Lecture Notes in Computer Science},
publisher = {Springer},
keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, parallel Krylov solver}
}

@article{
ganser2004deformable,
title = {A deformable digital brain atlas system according to Talairach and Tournoux},
author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.},
journal = {Medical Image Analysis},
volume = {8},
number = {1},
pages = {3--22},
year = {2004},
publisher = {Elsevier}
}
@Unpublished{TACCsurgery,
title = "TACC supercomputer performs laser cancer surgery on canine",
url = "http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser",
note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in Austin performed laser surgery on a dog in Houston without the intervention of a surgeon. The treatment was developed collaboratively by computational experts from the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, leading technologists from the M.D. Anderson Cancer Center in Houston, and cyberinfrastructure specialists and systems from TACC. Using precise lasers, state-of-the-art thermal imaging technology, and advanced computational methods, dynamic, data-driven treatments are being pursued as a minimally invasive alternative to the standard treatment of cancer.} No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@article{ffhbresso2008,
author = "Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. Tinsley Oden",
title = "Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment",
journal = "Engineering with Computers",
note = "Special issue on Computational Bioengineering",
year = "2008",
url = "http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf"
}
@techreport{dobbhbbbdeffghkkps2008,
Author = "K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon and S. Prudhomme and R. J. Stafford",
TITLE = "Computational Infrastructure for the Real-Time Patient-Specific Treatment of Cancer",
year = 2008,
INSTITUTION = "University of Texas at Austin",
URL = "http://www.tacc.utexas.edu/research/users/features/cancer.pdf"
}
@article{ogdb2004,
author = "A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber",
title = "Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging",
journal = "Physics in Medicine and Biology",
year = "2004",
volume = "49",
pages = "2955--2947"
}
@INPROCEEDINGS{majumdar11,
AUTHOR = "A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. Baldridge and P. Krysl",
TITLE = "A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery",
BOOKTITLE = "ICCS 2005",
PAGES = "672--679",
editor = "V.S. Sunderam et al.",
YEAR = "2005"
}
@CONFERENCE{sermesant-etal:03,
AUTHOR = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and Ayache, H.},
TITLE = {A parallel implementation of non-rigid registration using a volumetric biomechanical model},
BOOKTITLE = {Second International Workshop on Biomedical Image Registration {WBIR'03}},
ADDRESS = {Philadelphia, PA, USA},
PUBLISHER = {Springer-Verlag},
EDITOR = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.},
SERIES = {Lecture Notes in Computer Science},
VOLUME = {2717},
PAGES = {398-407},
DATE = {june 23-24},
YEAR = {2003},
url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@CONFERENCE{sermesant-etal:04,
AUTHOR = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. Wolfson and M. Shenton and H. Handels and R. Kikinis},
TITLE = {A Novel Nonrigid Registration Algorithm And Applications},
BOOKTITLE = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001},
ADDRESS = {Philadelphia, PA, USA},
PUBLISHER = {Springer-Verlag},
EDITOR = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.},
SERIES = {Lecture Notes in Computer Science},
VOLUME = {2208},
PAGES = {923},
YEAR = {2003},
url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@article{warfield-haker-talos-05,
author = "Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis",
title = "Capturing intraoperative deformations: research experience at Brigham and Women's hospital",
journal = "Medical Image Analysis",
url = "http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf",
year = "2005"
}
@article{brain3,
author = "Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis",
title = "Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of Deformation during Image Guided Neurosurgery",
journal = "Computing and Visualization in Science",
url = "http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf",
year = "2002"
}
@article{brain2,
author = "Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron Kikinis and Simon K. Warfield",
title = "Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite Element Biomechanical Model",
journal = "IEEE Transactions on Medical Imaging",
url = "http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf",
year = "2001"
}
@inproceedings{brain1,
author = "Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and Ferenc A. Jolesz and Ron Kikinis",
title = "Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image Guided Neurosurgery",
booktitle = "Proceedings of SC2000",
url = "http://www.sc2000.org/techpapr/papers/pap.pap230.pdf",
year = 2000
}
@article{Vanne06,
author = "V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and M. Lassas and M. Kalke",
title = "Parallelized Bayesian inversion for three-dimensional dental X-ray imaging",
journal = "IEEE Transactions on Medical Imaging",
volume = "25",
number = "2",
month = "February",
year = "2006",
pages = "218--228"
}

Fusion

@article{
facets-scidac08,
title = "First Results from Core-Edge Parallel Composition in the {FACETS} Project",
author = "J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. Stotler and A. Pigarov",
journal = "J. Phys.: Conf. Ser.",
volume = 125,
year = 2008,
pages = "012040",
url = "http://www.iop.org/EJ/abstract/1742-6596/125/1/012040"
}
@article{facets-scidac09,
title = "Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project",
author = "J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar and A. Pigarov and H. Zhang",
journal = "J. Phys.: Conf. Ser.",
volume = 180,
year = 2009,
pages = "012056",
url = "http://iopscience.iop.org/1742-6596/180/1/012056"
}
@inProceedings{facets-scidac10,
title = "Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the {FACETS} Code",
author = "A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. Pigarov and H. Zhang",
booktitle = "Proceedings of SciDAC 2010 Conference",
year = 2010,
url = "http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf"
}
@inproceedings{facets-fec2010,
title = "Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using the {FACETS} Framework",
author = "J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang",
booktitle = "Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, Republic of Korea",
year = 2010
}
@inproceedings{facets-epdp2010,
title = "{FACETS}: A Framework for Parallel Coupling of Fusion Components",
author = "J. Cary and A. Hakim and M. Miah and S. Kruger and A. Pletzer and S. Shasharina and S. Vadlamani and A. Pankin and R. Cohen and T. Epperly and T. Rognlien and R. Groebner and S. Balay and L. McInnes and H. Zhang",
booktitle = "Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing), Pisa, Italy",
year = 2010
}
@article{CarlssonCary09,
author = {Johan Carlsson, John R. Cary},
title = {The hypersecant Jacobian approximation for quasi-Newton solves of sparse nonlinear systems},
journal = {arXiv},
year = {2009},
note = {http://arxiv.org/abs/0905.1054},
url = {http://arxiv.org/pdf/0905.1054v1}
}
@InProceedings{oshahjs2006,
author = {F. Ogando and A. Signell and J.A. Heikkinen and M. Aspn\"as and S. Henriksson and S.J. Janhunen and T.P. Kiviniemi},
title = "Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of application",
booktitle = "33rd EPS Conference on Plasma Phys.",
year = "2006",
url = "http://epsppd.epfl.ch/Roma/pdf/P4_153.pdf",
note = "European fusion code"
}
@article{Zhu2006,
author = "P. Zhu and A. Bhattacharjee and K. Germaschewski",
title = "Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities",
journal = "Phys. Rev. Lett.",
volume = "96",
number = "065001",
year = "2006",
note = "doi:10.1103/PhysRevLett.96.065001"
}
@InProceedings{ppc2005,
author = "B. Philip and M. Pernice and L.Chacon",
title = "Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh Refinement",
booktitle = "Proceedings of the 16th International Conference on Domain Decomposition methods",
year = "2005",
Lab = {LANL}
}
@article{PP2005,
author = "M. Pernice and B. Philip",
title = "Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh Refinement",
year = "2005",
journal = "SIAM J. of Sci. Comput.",
Lab = {LANL}
}
@article{GT2004,
author = "A. H. Glasser and X. Z. Tang",
title = "The SEL macroscopic modeling code",
year = "2004",
journal = "Computer Physics Communications",
pages = "237--243",
volume = "164",
Lab = {LANL}
}
@article{NL2006,
author = "Y. Nishimura and Z.Lin",
title = "A finite element mesh in a tokamak edge geometry",
year = "2006",
journal = "Contributions to Plasma Physics",
volume = 22,
Lab = {PPPL}
}
@article{NLLE2004,
author = "Y. Nishimura and Z.Lin and J.Lewandowski and S.Ethier",
title = "A finite element Poisson solver for gyrokinetic particle simulations in a global field aligned mesh",
year = "2006",
journal = "J. Comput. Phys.",
volume = 214,
pages = "657",
Lab = {PPPL}
}
@InProceedings{lnlle2004,
author = "J.L.V Lewandowski and Y.Nishimura and W.W.Lee and Z.Lin and S. Ethier",
title = "Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons",
booktitle = "Sherwood Fusion Theory Conference, Missoula, MT",
year = "2004",
url = "http://www.sherwoodtheory.org/sherwood04/program/1e15.pdf",
Lab = {PPPL}
}
@InProceedings{NLCLEW2004,
author = "Y. Nishimura and Z.Lin and L.Chen and J.Lewandowski and S.Ethier and W. Wang",
title = "Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron model",
booktitle = "Sherwood Fusion Theory Conference, Missoula, MT",
year = "2004",
url = "http://www.sherwoodtheory.org/sherwood04/program/1C32.pdf",
Lab = {PPPL}
}
@Article{tb1,
author = "X.~Z.~Tang and A.~H.~Boozer",
title = "Numerical studies of a steady state axisymmetric co-axial helicity injection plasma",
journal = "Physics of Plasmas",
year = "2004",
pages = "171--185",
volume = "11",
Lab = {LANL}
}
@Unpublished{nlcw,
title = {Inclusion of electromagnetic effects into gyrokinetic particle simulations},
author = {Y. Nishimura and Z.Lin and L.Chen and W. Wang},
note = {American Physical Society 45th Annual Meeting Division of Plasma Physics, Albuquerque, New Mexico, October 2003},
year = "2003"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@techreport{tang2001,
Author = "X. Z. Tang and G. Y. Fu and S. C. Jardin and L. L. Lowe and W. Park and H. R. Strauss",
TITLE = "Resistive Magnetohydrodynamics Simulation of Fusion Plasmas",
year = 2001,
INSTITUTION = "Princeton Plasma Physics Laboratory",
number = "PPPL-3532",
URL = "http://www.pppl.gov/pub_report/2001/PPPL-3532.pdf",
note = "Presented at 10th Society for Industrial and Applied Mathematics (SIAM) Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 12-14, 2001.",
Lab = {PPPL}
}

Geosciences

@article{
ScheltingaMyersPietrzak10,
author = {Terwisscha van Scheltinga, ArjenD. and Myers, PaulG. and Pietrzak, JulieD.},
title = {A finite element sea ice model of the Canadian Arctic Archipelago},
journal = {Ocean Dynamics},
volume = {60},
number = {6},
pages = {1539-1558},
year = {2010},
issn = {1616-7341},
doi = {10.1007/s10236-010-0356-5},
url = {http://dx.doi.org/10.1007/s10236-010-0356-5},
publisher = {Springer-Verlag},
keywords = {Ocean modelling; Unstructured meshes; Sea ice; Arctic Ocean; Canadian Arctic Archipelago; Freshwater flux},
language = {English}
}
@inbook{DeStefanoAndreasiSecchi13,
author = {M. De Stefano and F. Golfré Andreasi and A. Secchi},
title = {Towards preconditioned nonlinear conjugate gradients for generic geophysical inversions},
booktitle = {SEG Technical Program Expanded Abstracts 2013},
chapter = {626},
pages = {3226--3230},
doi = {10.1190/segam2013-0244.1},
URL = {http://library.seg.org/doi/abs/10.1190/segam2013-0244.1},
eprint = {http://library.seg.org/doi/pdf/10.1190/segam2013-0244.1}No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@article{PourhietHuetMayLabrousseJolivet12,
author = {L. Le Pourhiet and B. Huet and D. A. May and L. Labrousse and L. Jolivet},
title = {Kinematic interpretation of the 3D shapes of metamorphic core complexes},
journal = {Geochem. Geophys. Geosyst.},
volume = {13},
pages = {Q09002},
year = {2012},
doi = {doi:10.1029/2012GC004271}
}
@article{LechmannMayKausSchmalholz11,
author = {S. M. Lechmann and D. A. May and B. J. P. Kaus and S. M. Schmalholz},
title = {Comparing thin-sheet models with 3-D multilayer models for continental collision},
journal = {Geophysical Journal International},
volume = {187},
year = {10–-33},
year = {2011},
doi = {doi: 10.1111/j.1365-246X.2011.05164.x}
}
@article{stefano:R69,
author = {Michele De Stefano and Federico Golfr\'{e} Andreasi and Simone Re and Massimo Virgilio and Fred F. Snyder},
collaboration = {},
title = {Multiple-domain, simultaneous joint inversion of geophysical data with application to subsalt imaging},
publisher = {SEG},
year = {2011},
journal = {Geophysics},
volume = {76},
number = {3},
pages = {R69-R80},
keywords = {geophysical image processing; inverse problems; seismology},
url = {http://dx.doi.org/10.1190/1.3554652},
doi = {10.1190/1.3554652}
}
@article{stefano:806,
author = {Michele De Stefano},
collaboration = {},
title = {Simultaneous joint inversion for susceptibility and velocity},
publisher = {SEG},
year = {2011},
journal = {SEG Technical Program Expanded Abstracts},
volume = {30},
number = {1},
pages = {806-810},
keywords = {3D; imaging; inversion; magnetics; multiparameter},
url = {http://dx.doi.org/10.1190/1.3628198},
doi = {10.1190/1.3628198}
}
@article{MayKnepley2011,
author = {Dave A. May and Matthew G. Knepley},
title = {Optimal, scalable forward models for computing gravity anomalies},
journal = {Geophysical Journal International},
volume = {187},
number = {1},
pages = {161--177},
url = {http://arxiv.org/abs/1107.5951},
note = {\url{http://arxiv.org/abs/1107.5951}},
year = {2011}
}
@inproceedings{BourdinKnepleyMaurini2010,
author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini},
title = {Numerical Simulation of Reservoir Stimulation - A Variational Approach},
booktitle = {Proceedings of the 37th Stanford Geothermal Workshop},
url = {http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf},
note = {\url{http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf}},
address = {Stanford, CA},
year = {2010}
}
@inproceedings{BourdinKnepleyMaurini2010b,
author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini},
title = {Secondary Thermal Cracks in {EGS}: a Variational Approach},
booktitle = {Proceedings of the 34th Annual Meeting of the Geothermal Resources Council},
url = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf},
note = {\url{https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}},
address = {Sacramento, CA},
year = {2010}
}
@article{chen2007full,
title = {Full 3D tomography for the crustal structure of the Los Angeles region},
author = {Chen, P. and Zhao, L. and Jordan, T.H.},
journal = {Bulletin of the Seismological Society of America},
volume = {97},
number = {4},
pages = {1094},
year = {2007},
publisher = {Seismol Soc America}
}
@article {brown2010ens, author = {Brown, Jed}, affiliation = {Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, Zürich, Switzerland}, title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}}, journal = {Journal of Scientific Computing}, publisher = {Springer Netherlands}, issn = {0885-7474}, keyword = {Mathematics and Statistics}, pages = {48-63}, volume = {45}, issue = {1}, url = {http://dx.doi.org/10.1007/s10915-010-9396-8}, doi = {10.1007/s10915-010-9396-8}, year = {2010} }
@phdthesis{brown2011,
title = {Computational methods for ice flow simulation},
author = {Jed Brown},
school = {ETH Z{\"u}rich},
year = 2011No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@article{brown2013tmeice,
title = {Achieving textbook multigrid efficiency for hydrostatic ice flow},
author = {Jed Brown and Barry F. Smith and Aron Ahmadia},
journal = {SIAM Journal on Scientific Computing},
volume = 35,
number = 2,
year = {2013},
pages = {359--375},
doi = {10.1137/110834512},
note = {Also preprint ANL/MCS-P743-1298}
}
@inproceedings{brown2013quasinewton,
author = {Jed Brown and Peter Brune},
title = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type methods},
year = {2013},
booktitle = {International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering},
pages = {2554--2565},
}
@misc{spiegelman-siampp10,
title = "Block Preconditioners and Advanced Software for Multiphysics Problems in Solid Earth Geodynamics",
author = "Marc Spiegelman",
note = "presentation at the 2010 SIAM Conference on Parallel Processing for Scientific Computing",
year = 2010
}
@Article{Schauer2011a,
author = "Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. Quintana-Ort\'{\i}",
title = "Large scale simulation of wave propagation in soils interacting with structures using {FEM} and {SBFEM}",
journal = "Journal of Computational Acoustics",
volume = "19",
number = "1",
pages = "75--93",
year = "2011",
doi = "http://dx.doi.org/10.1142/S0218396X11004316"
}
@misc{bsa2010,
author = {J. Brown and B. Smith and A. Ahmadia},
title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow},
note = {submitted to SIAM Journal on Scientific Computing},
year = {2012},
}

@Article{weatherley12,
author = {S. Weatherley and R.F. Katz},
title = {Melting and channelized magmatic flow in chemically heterogeneous, upwelling mantle},
journal = {Geochem.\ Geophys.\ Geosys.},
year = 2012,
volume = 13,
number = 1,
pages = {Q0AC18},
doi = {10.1029/2011GC003989},
}

@Article{katz12,
author = {R.F. Katz and S. Weatherley},
title = {Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges},
journal = {Earth\ Planet.\ Sci.\ Lett.},
year = 2012,
doi = {10.1016/j.epsl.2012.04.042},
volume = {335-336},
pages = {226-237}
}

@Article{katz10b,
author = {R.F. Katz},
title = {Porosity-driven convection and asymmetry beneath mid-ocean ridges},
journal = {Geochem.\ Geophys.\ Geosys.},
volume = {10},
number = {Q0AC07},
year = {2010},
doi = {10.1029/2010GC003282},
}

@Article{england10,
author = {P.C. England and R.F. Katz},
title = {Melting above the anhydrous solidus controls the location of volcanic arcs},
journal = {Nature},
year = {2010},
volume = {467},
pages = {700--703},
doi = {10.1038/nature09417},
}

@Article{weatherley10,
author = {S. Weatherley and R.F. Katz},
title = {Plate-Driven Mantle Dynamics and Global Patterns of Mid-Ocean Ridge Bathymetry},
journal = {Geochem.\ Geophys.\ Geosys.},
year = {2010},
volume = {11},
number = {10},
doi = {10.1029/2010GC003192},
}
@Article{katz10,
author = {R.F. Katz and M.G. Worster},
title = {The stability of ice-sheet grounding lines},
journal = {Proc.~Roy.~Soc.~A},
year = {2010},
volume = {466},
pages = {1597--1620},
doi = {10.1098/rspa.2009.0434},
url = {http://www.earth.ox.ac.uk/~richardk/publications/Katz_Worster_PRSA10.pdf}
}
@article{kyrkesmith2013stress,
title = {Stress balances of ice streams in a vertically integrated, higher-order formulation},
author = {Kyrke-Smith, T.M. and Katz, R.F. and Fowler, A.C.},
journal = {Journal of Glaciology},
volume = {59},
number = {215},
pages = {449--466},
year = {2013},
doi = {10.3189/2013JoG12J140}
}
@Article{takei2013anisotropy1,
author = {Takei Y. and R.F. Katz},
title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. Governing equations and linearised analysis}},
journal = {J.\ Fluid\ Mech.},
year = 2013,
volume = 734,
pages = {424-455},
doi = {10.1017/jfm.2013.482}
}
@Article{katz2013anisotropy2,
author = {Katz R.F. and Y. Takei},
title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. Numerical solutions of the full equations}},
journal = {J.\ Fluid\ Mech.},
year = 2013,
volume = 734,
pages = {456-485},
doi = {10.1017/jfm.2013.483}
}
@Article{kyrke-smith2014subglacial,
author = {Kyrke-Smith, T.M. and R.F. Katz and A.C. Fowler},
title = {Subglacial hydrology and the formation of ice streams},
journal = {Proc.\ Roy.\ Soc.\ A},
year = {2014},
volume = {470},
number = {2161},
doi = {10.1098/rspa.2013.0494}
}
@article{bueler2009shallow,
title = {{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled ice sheet model}},
author = {Bueler, E. and Brown, J.},
journal = {Journal of Geophysical Research-Earth Surface},
volume = {114},
number = {F3},
pages = {F03008},
year = {2009},
publisher = {American Geophysical Union}
}
@article{bueler2007est,
title = {{Exact solutions to the thermomechanically coupled shallow ice approximation: effective tools for verification}},
author = {Bueler, E. and Brown, J. and Lingle, C.},
journal = {J. Glaciol},
volume = {53},
pages = {499--516},
year = {2007}
}
@article{bueler2007fcv,
title = {{Fast computation of a viscoelastic deformable Earth model for ice-sheet simulations}},
author = {Bueler, E. and Lingle, C.S. and Brown, J.},
journal = {Ann. Glaciol},
volume = {46},
pages = {97--105},
year = {2007}
}
@article {bueler2005iso, author = {E. Bueler and C. S. Lingle and J. A. Kallen-Brown and D. N. Covey and L. N. Bowman}, title = {Exact solutions and numerical verification for isothermal ice sheets}, journal = {J. Glaciol.}, volume = {51}, number = {173}, pages = {291--306}, year = {2005}, }
@article{chao2008programming,
title = {{Programming on Numerical Simulation of Tsunami with PETSc and FEPG}},
author = {Chao-fan, Z. and Yao-lin, S.},
journal = {Earthquake},
year = {2008}
}
%Aagaard, B., Williams, C., Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), EarthScope National Meeting, Austin, Texas, May 17–20.
%Aagaard, B., Williams, C., and Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), Southern California Earthquake Center Annual Meeting, Palm Springs, California, September 11–14.
%Aagaard, B., Williams, C., and Knepley, M. (2012). PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation (abstract), Seismological Society of America Annual Meeting, San Diego, California, April 17-19.
@article{AagaardKnepleyWilliams13,
title = {A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element Models of Quasi-static and Dynamic Crustal Deformation},
author = {Brad T. Aagaard and Matthew G. Knepley and Charles A. Williams},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {118},
number = {6},
pages = {3059--3079},
issn = {2169-9356},
url = {http://dx.doi.org/10.1002/jgrb.50217},
note = {\url{http://dx.doi.org/10.1002/jgrb.50217}},
doi = {10.1002/jgrb.50217},
keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics},
year = {2013}
}

@inproceedings{AagaardKnepleyWilliams11,
author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley},
title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
note = {Fall Meeting Supplemental, Abstract DI14A-08},
year = {2011}
}
@inproceedings{Knepley10,
author = {Matthew G. {Knepley}},
title = {Acceleration of low order finite element computation with {GPUs} (Invited)},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
note = {Fall Meeting Supplemental, Abstract IN44A-01},
year = {2010}
}

@inproceedings{MayKnepleyGurnis09,
author = {Dave A. May and Matthew G. Knepley and Michael Gurnis},
title = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
note = {Fall Meeting Supplemental, Abstract P31A-A1241},
year = {2009}
}
@inproceedings{YuenKnepleyErlebacherWright09,
author = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright},
title = {The Coming Role of {GPU} in Computational Geodynamics},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
note = {Fall Meeting Supplemental, Abstract DI22A-05},
year = {2009}
}
@inproceedings{AagaardKnepleyWilliams08,
author = {Brad Aagaard and Charles A. Williams and Matthew G. Knepley},
title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
volume = {89},
number = {53},
note = {Fall Meeting Supplemental, Abstract T41A-1925},
year = {2007}
}
@inproceedings{AagaardKnepleyWilliams07,
author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley},
title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
volume = {88},
number = {52},
note = {Fall Meeting Supplemental, Abstract T21B-1798},
year = {2007}
}
@inproceedings{AagaardKnepleyWilliams05,
author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley},
title = {Development of software for studying earthquakes across multiple spatial and temporal scales by coupling quasi-static and dynamic simulations},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
volume = {86},
number = {52},
note = {Fall Meeting Supplemental, Abstract S53A-1072},
year = {2005}
}
@inproceedings{WilliamsGableHagerMeadeAagaardKnepley08,
author = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and Brad Aagaard and Matthew G. Knepley},
title = {Modeling of Multiple Earthquake Cycles in Southern California Using the {SCEC} Community Fault Model},
booktitle = {Proceedings of Geosciences '08},
address = {Wellington, NZ},
month = {November},
year = {2008}
}
@techreport{Zhang07,
title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for Tsunamis},
author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi},
type = {Preprint},
number = {ANL/MCS-P1459-0907},
institution = {ANL},
month = {September},
year = {2007}
}
@Article{katz08b,
author = {Richard F. Katz},
title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic focusing at mid-ocean ridges},
journal = {J. Petrology},
year = {2008},
volume = {49},
pages = {2099--2121},
doi = {10.1093/petrology/egn058}
}
@article{hgrhkjvv2008,
title = "On preconditioning for a parallel solution of the Richards equation",
author = "Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena",
journal = "Computers and Geosciences",
volume = "34",
pages = "1958--1963",
year = "2008",
}
@article{MayMoresi2008,
title = "Preconditioned iterative methods for {Stokes} flow problems arising in computational geodynamics",
journal = "Physics of the Earth and Planetary Interiors",
volume = "171",
number = "1-4",
pages = "33--47",
year = "2008",
note = "{R}ecent Advances in Computational Geodynamics: Theory, Numerics and Applications",
issn = "0031-9201",
doi = "DOI: 10.1016/j.pepi.2008.07.036",
url = "http://dx.doi.org/10.1016/j.pepi.2008.07.036",
author = "Dave A. May and Louis Moresi",
keywords = "Stokes flow",
keywords = "Krylov",
keywords = "Preconditioner",
keywords = "Schur complement",
keywords = "BFBt"
}
@Article{katz08a,
author = {R.F. Katz and M.G. Worster},
title = {Simulation of directional solidification, thermochemical convection, and chimney formation in a {H}ele-{S}haw cell},
journal = {J. Comp. Phys.},
volume = {227},
pages = {9823-9840},
year = {2008},
doi = {10.1016/j.jcp.2008.06.039}
}
@Article{aabg2007,
author = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas},
title = {Full waveform inversion for seismic velocity and anelastic losses in heterogeneous structures},
journal = {Bulletin of Seismological Society of America},
year = {2007},
volume = {97},
pages = {1990--2008}
}
@Article{katz2006,
author = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman},
title = {The dynamics of melt and shear localization in partially molten aggregates},
journal = {Nature},
year = {2006},
volume = {442},
pages = {676--679},
month = {August},
day = {10},
url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}
}
@InProceedings{mqrs2003,
author = "Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl",
year = "2003",
title = "Parallel Preconditioning for Sedimentary Basin Simulations",
booktitle = "Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, Sozopol, Bulgaria, June 4-8, 2003"
}
@InProceedings{lichtner1,
author = "Chuan Lu and Peter C. Lichtner",
year = "2005",
title = "{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in Geologic Media",
booktitle = "Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL",
Lab = {LANL}
}
@Article{smw2003,
author = {R. Scheichl and R. Masson and J. Wendebourg},
title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations},
journal = {Computational Geosciences},
year = {2003},
volume = {7},
pages = {295--318},
url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}
}
@Article{kees-miller-03,
author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley},
title = {Versatile multilevel Schwarz preconditioners for multiphase flow},
journal = {Computational Geosciences},
year = {2003},
volume = {7},
pages = {91--114}
}
@Article{bk2003,
author = {JN Buur and T Kuehnel},
title = {Improving depth imaging by automated model updating},
journal = {The Leading Edge},
year = {2003},
volume = {22},
pages = {310-318}
}

Simulation of the earth's mantle and crust is valuable to understanding earthquakes, volcanos, etc. PETSc has been used for a variety of these simulations.

@InProceedings{appelbe1,
author = "B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi",
year = "2003",
title = "Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and computational methodology",
page = "781",
booktitle = "Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference Proceedings",
publisher = "Springer-Verlag",
URL = "http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf"
}
@InProceedings{gd1,
Author = "Guillaume Dumont and Michel Kern",
TITLE = "Parallelization of a 3D Seismic Migration Code with PETSc",
year = 1999,
booktitle = "Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing"
}
               

Figures from the work of Richard Katz @PhdThesis{KatzThesis,
author = {R.F. Katz},
title = {The deep roots of volcanoes: models of magma dynamics with applications to subduction zones},
school = {Columbia University},
year = {2005},
url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@incollection{KnepleyKatzSmith06,
author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry},
affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL USA},
title = {Developing a Geodynamics Simulator with {PETSc}},
booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers},
series = {Lecture Notes in Computational Science and Engineering},
editor = {Bruaset, Are Magnus and Tveito, Aslak},
publisher = {Springer Berlin Heidelberg},
isbn = {978-3-540-31619-0},
keyword = {Mathematics and Statistics},
pages = {413-438},
volume = {51},
url = {http://dx.doi.org/10.1007/3-540-31619-1_12},
note = {10.1007/3-540-31619-1\_12},
year = {2006}
}
@Article{Katz04,
author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte},
title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in the global mid-ocean ridge system},
journal = {Geophys.\ Res.\ Letts.},
year = {2004},
volume = {31},
pages = {L15605},
}
@Article{Katz07,
author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and Ethan Coon},
title = {Numerical simulation of geodynamic processes with the {Portable Extensible Toolkit for Scientific Computation}},
journal = {Phys. Earth Planet. In.},
volume = {163},
pages = {52--68},
year = {2007}
}
@article{williams2006development,
title = {{Development of a package for modeling stress in the lithosphere}},
author = {Williams, CA},
journal = {Eos Trans. AGU},
volume = {87},
pages = {36},
year = {2006}
}
@Article{GoversWortel05,
author = {R. Govers and M.J.R. Wortel},
title = {Lithosphere tearing at STEP faults: response to edges of subduction zones},
journal = {Earth and Planetary Science Letters},
volume = {236/1-2},
pages = {505-523},
year = {2005},
}
@InProceedings{snark2,
author = "B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi",
year = "2002",
title = "Towards Rapid Geoscience Model Development - The {Snark} Project",
booktitle = "Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop"
}
@Article{snark1,
author = "Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang Tan and Feng Wang",
title = "Snark - A Reusable Framwork for Geoscience Computational Models",
journal = "Submitted to Pure and Applied Geosciences"
}
@InProceedings{earthquake2003,
author = "Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and Tiankai Tu",
year = "2003",
title = "High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers",
booktitle = "Proceedings of SC2003",
note = "A winner of the Gordon Bell Prize for special achievement at SC2003"
}
@inproceedings{Stefano12,
author = {Michele De Stefano},
title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data},
booktitle = {PIERS Proceedings},
month = {August},
address = {Moscow, RUSSIA},
pages = {491--495},
year = {2012}
}
%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY=


@article{khatiwala07,
author = "Khatiwala, S.",
title = "A computational framework for simulation of biogeochemical tracers in the ocean",
journal = "Glob. Biogeochem. Cycles",
volume = "21",
doi = "doi:10.1029/2007GB002923",
year = 2007,
url = " http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf"
}
@Article{dks2004,
author = "Sergey Danilov, Gennady Kivman and Jens Schroeter",
journal = "Ocean Modelling",
year = "2004",
volume = "6(2)",
pages = "125-150",
title = "A finite-element Ocean Model: Principles and Evaluation",
url = "http://www.sciencedirect.com/science?_ob=IssueURL&_tockey=%23TOC%236214%232004%23999939997%231%23FLA%23Volume_6,_Issue_2,_Pages_101-190_(2004)&_auth=y&view=c&_acct=C000007278&_version=1&_urlVersion=0&_userid=97338&md5=c3a50a31c599d8d38c8ce1f29117f267"
}
@Article{danilov1,
author = {S. Danilov and G. Kivman and J. Schroter},
year = 2004,
title = {Evaluation of an eddy-permitting finite-element ocean model in the North Atlantic},
journal = {Ocean Modelling}
}
@Article{nerger1,
author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter},
year = 2004,
title = {Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to a Finite Element Model of the North Atlantic},
journal = {Journal of marine systems},
}
@conference{rakowsky2003self,
title = {{A self-adaptive finite element model of the atmosphere}},
author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.},
booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002},
pages = {279},
isbn = {981238376X},
year = {2003},
organization = {World Scientific Pub Co}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@Article{lauter3,
author = {M. Lauter},
year = 2004,
title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell},
journal = {Berichte zur Polar- und Meeresforschung},
}
@Article{lauter2,
author = {M. Lauter and D. Handorf and K. Dethloff},
year = 2004,
title = {Unsteady analytical solutions of the spherical shallow water equations},
journal = {Journal of computational physics}
}
@PhdThesis{lauter1,
author = {M. Lauter},
year = 2004,
title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell},
institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@Article{frickenhaus1,
author = {S. Frickenhaus and W. Hiller and M. Best},
year = 2005,
title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of parallel numerical atmosphere and ocean models},
journal = {Ocean Modelling},
volume = {10},
pages = {185--191}
}
@article{0266-5611-24-3-034015,
author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak},
title = {A Newton-CG method for large-scale three-dimensional elasticfull-waveform seismic inversion},
journal = {Inverse Problems},
volume = {24},
number = {3},
pages = {034015 (26pp)},
url = {http://stacks.iop.org/0266-5611/24/034015},
year = {2008},
abstract = {We present a nonlinear optimization method for large-scale3D elastic full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear iterations with inner conjugate gradient linear iterations, globalized by an Armijo backtracking line search, solved on a sequence of finer grids and higher frequencies to remain in the vicinity of the global optimum, inexactly terminated to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total variation operator to capture sharp interfaces, finely discretized by finite elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, implemented in matrix-free fashion with adjoint-based computation of reduced gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime waveform storage, and partitioned spatially across processors to parallelize the solutions of the forward and adjoint wave equations and the evaluation of gradient-like information. Several numerical examples demonstrate the grid independence of linear and nonlinear iterations, the effectiveness of the preconditioner, the ability to solve inverse problems with up to 17 million inversion parameters on up to 2048 processors, the effectiveness of multiscale continuation in keeping iterates in the basin of attraction of the global minimum, and the ability to fit the observational data while reconstructing the model with reasonable resolution and capturing sharp interfaces.}
}

Environmental -- Subsurface Flow


Modeling surface flow of water is valuable for both flood control and agricultural and environmental reasons. For example, regenerating the Florida Everglades requires extensive understanding of the surface water characteristics over thousands of square miles. PETSc has been used for a variety of these simulations.

@article{
mills2009modeling,
title = {Modeling subsurface reactive flows using leadership-class computing},
author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and Mahinthakumar, G.K. and Smith, B.F.},
journal = {Journal of Physics: Conference Series},
volume = {180},
pages = {012062},
year = {2009},
publisher = {IOP Publishing}
}
@conference{mills2007simulating,
title = {{Simulating subsurface flow and transport on ultrascale computers using PFLOTRAN}},
author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.},
booktitle = {Journal of Physics: Conference Series},
volume = {78},
pages = {012051},
year = {2007},
organization = {IOP Publishing}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@inproceedings{mills2009,
title = {Modeling subsurface reactive flows using leadership-class computing},
author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and Mahinthakmuar, G. and Smith, B.},
booktitle = {Journal of Physics: Conference Series},
volume = {180},
pages = {102062},
year = {2009},
organization = {IOP Publishing}
}
@Unpublished{stomp,
title = "STOMP (Subsurface Transport Over Multiple Phases) webpage",
url = "http://stomp.pnl.gov/"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@INPROCEEDINGS{htfc2003,
AUTHOR = "L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings",
TITLE = "Methods and Experiences For Parallelizing Flood Models",
YEAR = "2003",
BOOKTITLE = "Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th European PVM/MPI User's Group Meeting",
NOTE = "Springer Lecture Notes in Computer Science, Volume 2840",
URL = "http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1"
}
@inproceedings{hulchy-tran-astalos-fmsip,
AUTHOR = "L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and D.Froehlich",
TITLE = "Flood Modeling System and Its Parallelization",
YEAR = "2002",
BOOKTITLE = "Proceedings of the International Conference on Parallel Computing in Electrical Engineering",
URL = "http://portal.acm.org/citation.cfm?id=824476.825951"
}
@inproceedings{gy1,
AUTHOR = "J. P. Gwo and G. T. Yeh",
TITLE = "High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive Transport at Watershed Scale",
YEAR = "2004",
BOOKTITLE = "The International Conference on Computational Methods",
URL = "http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf"
}
@conference{cheng2009efficient,
title = {{An efficient parallel method for large-scale groundwater flow equation based on PETSc}},
author = {Cheng, T. and Ji, X. and Wang, Q.},
booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth Conference on},
pages = {190--193},
organization = {IEEE}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@Unpublished{sfrsm,
title = "The South Florida Regional Simulation Model and Hydrologic Simulation Engine",
url = "http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf",
note = "Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for its linear solves" No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}

@inproceedings{Bart_Omar:SC05,
AUTHOR = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders},
TITLE = {Dynamic data driven inversion for terascale simulations: real-time indentification of airborne contaminants},
BOOKTITLE = {Proceedings of SC2005},
ORGANIZATION = {IEEE/ACM},
ADDRESS = {Seattle, WA},
YEAR = {2005},
MONTH = {November},
url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf",
Lab = "SNL"
}
@InProceedings{anton-krassimir-lscc,
Author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev},
TITLE = "Comparison of Two Local Refinement Methods for Large Scale Air Pollution Simulations",
booktitle = "Large-Scale Scientific Computing: 4th International Conference, LSSC 2003",
volume = "2907",
year = 2003,
publisher = "Springer-Verlag",
url = "http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1"
}
@INPROCEEDINGS{aa2001,
AUTHOR = "Anton Antonov",
TITLE = "Object-Oriented Framework for Large Scale Air Pollution Modeling",
YEAR = "2001",
BOOKTITLE = "Large-Scale Scientific Computing : Third International Conference, LSSC 2001, Sozopol, Bulgaria",
NOTE = "Springer Lecture Notes in Computer Science, Volume 2179",
URL = "http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1"
}

@Article{grassley-simmons-kercher-00,
author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher},
year = 2000,
title = {Mineralogical heterogeneity in fractured, porous media and its representation in reactive transport models},
journal = {Applied Geochemistry},
volume = {17},
pages = {699--708},
Lab = {LLNL}
}
@Article{glassey-nitao-03,
author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson and Carl I. Steefel and James R. Kercher},
year = 2003,
title = {The impact of climate change on vadose zone pore waters and its implication for long-term monitoring},
journal = {Computers and Geosciences},
volume = {29},
pages = {399-411},
Lab = {LLNL}
}
@Article{steefel-depaolo-lichtner-05,
author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner},
year = 2005,
title = {Reactive transport modeling: An essential tool and a new research approach for the Earth sciences},
journal = {Earth and Planetary Science Letters},
Lab = {LLNL,LANL}
}

Sample strong scaling for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) @Article{
km2004,
author = "A. Keese and H. G. Matthies",
journal = "Computers and Structures",
year = "2005",
volume = "83",
pages = "1033--1047",
title = "Hierarchical parallelisation for the solution of stochastic finite element equations",
url = "http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V28-4FPDPWM-1&_user=1722207&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000053990&_version=1&_urlVersion=0&_userid=1722207&md5=89d48cd6fd5e80989372246d8dda400f"
}
@Unpublished{hvl2002,
title = {Numerical Modeling of NAPL Source Zone Treatment},
author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner},
note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.},
url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf},
year = "2002",
Lab = {LANL}No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@phdthesis{hammond2003,
author = {Glenn E. Hammond},
title = "Innovative Methods for Solving Multicomponent Biogeochemical Groundwater Transport on Supercomputers",
school = {University of Illinois at Urbana-Champaign},
year = 2003,
url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@Unpublished{uk,
title = "Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large Scale Environmental Flows and Transport Processes",
url = "http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html",
note = "EPA funded work to simulate turbulent dispersion of toxic chemicals around buildings and in Green Bay. Used PETSc for its linear solvers",
year = 1999No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@inproceedings{hammond2002,
Author = "Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner",
TITLE = "Modeling Multicomponent Reactive Transport on Parallel Computers Using {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners",
year = 2002,
URL = "http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf",
booktitle = "Proceedings of the XIV International Conference on Computational Methods in Water Resources, Delft, The Netherlands.",
Lab = {LANL}
}
@techreport{steefel1,
Author = "C. I. Steefel",
TITLE = "Software for modeling multicomponent, multidimensional reactive transport",
year = 2001,
INSTITUTION = "Lawrence Livermore National Laboratory",
number = "UCRL-MA-143182",
Lab = {LLNL}
}
@ARTICLE{steefel2,
author = {C. I. Steefel and A. C. Lasaga},
title = "A coupled model for transport of multiple chemical-species and kinetic precipitation dissolution reactions with application to reactive flow in single-phase hydrothermal systems",
journal = {Americal Journal of Science},
year = 1994,
pages = {529-592},
volume = 294,
number = 5
}
@techreport{steefel3,
Author = "C. I. Steefel and S. B. Yabusaki",
TITLE = "OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: User's manual and programmer's guide",
year = 1996,
INSTITUTION = "Pacific Northwest National Laboratory",
number = "PNNL-11166",
Lab = {PNNL}
}
@ARTICLE{2005hvl,
author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner},
title = "Application of {J}acobian-free {N}ewton-{K}rylov with physics-based preconditioning to biogeochemical transport",
journal = {Advances in Water Resources},
year = 2005,
pages = {359--376},
volume = 28,
url = { http://www.sciencedirect.com/science?_ob=IssueURL&_tockey=%23TOC%235953%232005%23999719995%23576651%23FLA%23Volume_28,_Issue_4,_Pages_315-427_(April_2005)&_auth=y&view=c&_acct=C000059129&_version=1&_urlVersion=0&_userid=2914253&md5=0d485527443c6192356cc508e1621002},
Lab = {LANL}
}
@article{wang-zabar-05,
author = "J Wang and N Zabaras",
journal = "Int. J. Heat and Mass Transfer",
title = "A Markov random field model of contamination source identification in porous media flow",
year = 2005
}
@InBook{kp1,
author = "Jong G. Kim and Hyoung W. Park",
chapter = "Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous Media",
url = "http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1",
title = "Lecture Notes in Computer Science",
publisher = "Springer-Verlag",
volume = 3044,
year = 2004No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@ARTICLE{2001AGUSM...H32A06K,
author = {{Kim}, J.~G. and {Kim}, J.},
title = {Parallel Implementation of Finite Element Groundwater Flow Model},
journal = {AGU Spring Meeting Abstracts},
year = 2001,
pages = {32-+},
}
@ARTICLE{lzb2005,
author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap},
title = "CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA",
journal = {Journal of Hydraulic Engineering},
year = 2005,
volume = 131,
number = 4,
pages = {247--258}
}
@ARTICLE{Rao2005,
author = {Prasada Rao},
title = "A parallel RMA2 model for simulating large-scale free surface flows",
journal = {Environmental Modelling and Software},
year = 2005,
pages = {47--53},
}
@INPROCEEDINGS{pr1,
AUTHOR = "Prasada Rao",
TITLE = "An Efficient Scalable Finite Element Model for Simulating Large Scale Hydrodynamic Flows",
YEAR = "2003",
BOOKTITLE = "Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics Conference",
URL = "http://www.ce.washington.edu/em03/proceedings/papers/477.pdf"
}
@INPROCEEDINGS{lichtner2004,
AUTHOR = "Peter C. Lichtner and Andrew Wolfsberg",
TITLE = "Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand Challenge Supercomputing Problem",
YEAR = "2004",
BOOKTITLE = "MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport Modeling of Inorganic Contaminants, Radionuclides and Nutrients",
note = "Also Los Alamos National Laboratory report: LA-UR-04-1826",
Lab = {LANL}
}

@Article{aba01:petsc-app,
author = {Jason Abate and Peng Wang and Kamy Sepehrnoori},
title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s},
journal = "Int. J. High Performance Computing Applications",
year = 2001,
volume = 15,
number = 1,
pages = {13--21},
month = {Spring},
}
@PhdThesis{tjb200,
author = {Thomas James Byer},
title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface Facilities},
school = {Stanford},
year = 2000No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@InProceedings{puchyr2006,
author = {Peter J. Puchyr},
title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a Win32 Cluster},
booktitle = {Proceedings of the Canadian International Petroleum Conference},
note = {Paper number CIPC2006-207},
year = {2006}
}
@InProceedings{texas98,
author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith and G. A. Pope},
title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir Simulation},
booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation Symposium},
note = "also available as Argonne preprint ANL/MCS-P743-1298",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf",
year = {1998}
}

CFD

@article{
Carracciuolo20111382,
title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows in high performance computing environment},
journal = "Journal of Non-Newtonian Fluid Mechanics ",
volume = "166",
number = {23--24},
pages = {1382--1395},
year = "2011",
issn = "0377-0257",
doi = "http://dx.doi.org/10.1016/j.jnnfm.2011.08.014",
url = "http://www.sciencedirect.com/science/article/pii/S0377025711002163",
author = "L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. Maffettone and A. Murli",
keywords = "Parallel computations",
keywords = "Viscoelastic flows",
keywords = "DEVSS-G",
keywords = "\{PETSc\}",
keywords = "Finite element method",
keywords = "High performance computing "
}
@article{BungartzGatzhammerLiebMehlNeckel11,
author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, Miriam and Neckel, Tobias},
title = {Towards multi-phase flow simulations in the PDE framework Peano},
journal = {Computational Mechanics},
volume = {48},
number = {3},
pages = {365-376},
year = {2011},
issn = {0178-7675},
doi = {10.1007/s00466-011-0626-1},
url = {http://dx.doi.org/10.1007/s00466-011-0626-1},
publisher = {Springer-Verlag},
keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; Thermohydraulics; Two-phase flow},
language = {English}
}

@article{bpr:cfl,
author = "H.~M. B{\"u}cker and B. Pollul and A. Rasch",
title = "{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler Equations}",
journal = "International Journal for Numerical Methods in Fluids",
year = 2009,
volume = 59,
number = 1,
pages = "1--18",
doi = "10.1002/fld.1798",
}
@inbook{Bonfiglioli_Campobasso_Carpentieri_2010,
author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B},
title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently preconditioned newton-krylov solver},
publisher = {Curran Associates},
year = {2010},
url = {http://www.proceedings.com/05932.html}No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}

@article{Bonfiglioli_rans_2005,
author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, Bernardo},
title = {RANS simulations of a junction flow},
journal = {International Journal of Computational Fluid Dynamics},
volume = {19},
number = {2},
pages = {179-189},
year = {2005},
URL = {http://www.tandfonline.com/doi/abs/10.1080/10618560410001729126}
}

@incollection {Bonfiglioli__Carpentieri_rans_2008, author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza Italy}, title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS Equations Using Fluctuation Splitting Schemes}, booktitle = {Numerical Mathematics and Advanced Applications}, editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, publisher = {Springer Berlin Heidelberg}, isbn = {978-3-540-69777-0}, pages = {151-158}, url = {http://dx.doi.org/10.1007/978-3-540-69777-0_17}, year = {2008} }

@incollection {Bonfiglioli__Carpentieri_ens_2007, author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, Italy}, title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} Problems on Unstructured Grids}, booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, series = {Lecture Notes in Computer Science}, editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, publisher = {Springer Berlin / Heidelberg}, isbn = {978-3-540-75754-2}, pages = {676-685}, volume = {4699}, url = {http://dx.doi.org/10.1007/978-3-540-75755-9_83}, year = {2007} }

@article{TerrelScottKnepleyKirby08,
author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby},
title = {Automated {FEM} Discretizations for the {Stokes} Equation},
journal = {BIT},
volume = {48},
number = {2},
year = {2008}
}

@Article{MartaMaderMartinsWeideAlonso07,
Author = "A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. J. Alonso",
TITLE = "A methodology for the development of discrete adjoint solvers using automatic differentiation tools",
Journal = "Computational Fluid Dyanmics",
volume = 21,
pages = "307--327",
year = 2007
}
@techreport{avb2008,
Author = "V.R. Ambati and J.J.W. van der Vegt and O. Bokhove",
TITLE = "Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface Waves",
year = 2008,
INSTITUTION = "University of Twente, the Netherlands",
url = "http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf"
}
@InProceedings{bdsm2005,
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title = {a parallel coupled algorithm for collocated grids and its application to Large Eddy Simulation of a turbulent wake},
school = {University of Zaragoza (Spain)},
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@TechReport{af2007,
title = "Preconditioning based on a partially implicit implementation of Momentum Interpolation for coupled solvers",
institution = "Fluid Mechanics Group of the University of Zaragoza (Spain)",
year = "2007",
author = "A. Cubero and N. Fueyo"
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author = {Richard Dwight},
title = {Robust Mesh Deformation using the Linear Elasticity Equations},
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author = {Richard Dwight and Joel Brezillon},
title = {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based Optimization},
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@PhdThesis{Dwight2006a,
author = {Richard Dwight},
title = {Efficiency Improvements of {RANS}-Based Analysis and Optimization using Implicit and Adjoint Methods on Unstructured Grids},
school = {School of Mathematics, University of Manchester},
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Author = {George Biros and Lexing Ying and Denis Zorin},
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title = "Multidimensional Residual Distribution Schemes for the Pseudo-Compressible {Euler} and {Navier-Stokes} equations on Unstructured Meshes",
institution = "Universita della Basilicata via della Tecnica 3",
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journal = "Journal of Hydraulic Research",
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Author = {R. V. Wilson and P. M. Carrica and F. Stern},
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Author = {P. M. Carrica and R. V. Wilson and F. Stern},
TITLE = "Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem",
journal = "Computers and Fluids",
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year = 2005
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Author = {M. T. Jozkowski},
TITLE = "Application of Algebraic Multigrid Methods to the Solution of Stratified Flows About Submerged Bodies",
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year = 2005
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AUTHOR = "A.Bonfiglioli",
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AUTHOR = "L. A. Barba",
TITLE = "Computing high-Reynolds number vortical flows: a highly accurate method with a fully meshless formulation",
YEAR = "2004",
BOOKTITLE = "International Conference on Parallel CFD, Grand Canary, May 2004",
note = "Submitted"
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AUTHOR = "L. A. Barba and A. Leonard",
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YEAR = "2004",
BOOKTITLE = "Proceedings of ICTAM meeting in Warsaw, August 2004",
note = "Submitted"
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author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi},
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author = {Matthew Knepley and Denis Vanderstraeten},
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AUTHOR = "W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application",
BOOKTITLE = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing},
EDITOR = "",
PUBLISHER = "",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z",
YEAR = "1999",
note = {Winner of Gordon Bell Special Prize at SC 99}
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author = {Artur Cristea and Victor Sofonea},
title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems},
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author = {Artur Cristea and Victor Sofonea},
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author = {Artur Cristea and Victor Sofonea},
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AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}",
BOOKTITLE = "Proceedings of the First MIT Conference on Computational Fluid and Solid Mechanics",
EDITOR = "",
LOCATION = "Cambridge, MA",
YEAR = "2001",
month = jun,
url = "http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf"
}
@INPROCEEDINGS{gkks00,
AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} Code",
BOOKTITLE = "Proceedings of the 7th International Conference on High Performance Computing (HiPC '2000)",
EDITOR = "",
LOCATION = "Bangalore, India",
YEAR = "2000",
pages = "395--404",
url = "http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf"
}
@INPROCEEDINGS{gkks-sc00,
AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application",
BOOKTITLE = "Proceedings of SC2000",
EDITOR = "",
PUBLISHER = "IEEE Computer Society",
YEAR = "2000",
URL = "http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf"
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@INPROCEEDINGS{knepleysamehsarin99,
AUTHOR = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin},
TITLE = {Design of Large Scale Parallel Simulations},
BOOKTITLE = {Proceedings of Parallel CFD'99},
EDITORS = {A. {Ecer et al.}},
PUBLISHER = {Elsevier},
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AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "Towards Realistic Performance Bounds for Implicit {CFD} codes",
BOOKTITLE = "Proceedings of Parallel CFD'99",
EDITORS = {A. {Ecer et al.}},
PUBLISHER = "Elsevier",
YEAR = "1999"
}
@INPROCEEDINGS{KKS97,
AUTHOR = "D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "On the Interaction of Architecture and Algorithm in the Domain-Based Parallelization of an Unstructured Grid Incompressible Flow Code",
BOOKTITLE = "Proceedings of the 10th International Conference on Domain Decomposition Methods",
EDITOR = "J. Mandel et al.",
PAGES = "311--319",
PUBLISHER = "Wiley",
NOTE = "",
YEAR = "1997"
}
@INPROCEEDINGS{KKS99,
AUTHOR = "D. K. Kaushik and D. E. Keyes and B. F. Smith",
TITLE = "{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and Incompressible Flows on Unstructured Grids",
BOOKTITLE = "Proceedings of the 11th International Conference on Domain Decomposition Methods",
EDITORS = "C.-H. {Lai et al.}",
PUBLISHER = "Domain Decomposition Press, Bergen",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z",
YEAR = "1999"
}
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AUTHOR = "D. E. Keyes and D. K. Kaushik and B. F. Smith",
TITLE = "Perspectives for {CFD} on Petaflops Systems",
BOOKTITLE = "CFD Review 1998",
EDITOR = "M. Hafez and K. Oshima",
PUBLISHER = "World Scientific, Singapore",
PAGES = "1079--1096",
NOTE = "",
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AUTHOR = "P. D. Hovland and L. C. McInnes",
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year = 2000,
journal = "Parallel Computing",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z",
note = "special issue of Parallel Computing on ``Parallel Computing in Aerospace''"
}

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author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley},
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booktitle = {Proceedings of ParCFD2008},
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Wave propagation and the Helmholtz equation

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publisher = {SIAM},
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note = {Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5}
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@InProceedings{Toselli-wave-98,
author = {Andrea Toselli},
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year = 1998,
publisher = {SIAM},
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@InProceedings{mcinnes-wave-98,
author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes},
title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods},
booktitle = {Mathematical and Numerical Aspects of Wave Propagation},
editor = {John A. DeSanto},
year = 1998,
publisher = {SIAM},
address = {Philadelphia},
pages = {623--625},
note = {Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5}
}
@InProceedings{mska98,
author = "L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi",
title = "Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the Parallel Computation of {H}elmholtz Problems",
booktitle = "Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods",
editor = "J. Mandel et al.",
publisher = "AMS",
pages = "349--357",
year = 1998
}
@InProceedings{ccew98,
author = "X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund",
title = "Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation",
booktitle = "Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods",
editor = "J. Mandel et al.",
publisher = "AMS",
pages = "437-445",
year = 1998
}
@InProceedings{ra98a,
author = "R. Susan-Resiga and H. M. Atassi",
title = "Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic Problems",
booktitle = "Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference",
publisher = "AIAA",
pages = "86-96",
note = "AIAA paper 98-2218",
year = 1998
}
@InProceedings{ar98c,
author = "H. M. Atassi and R. Susan-Resiga",
title = "Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: General Formulation",
booktitle = "Proceedings of the ASME Noise Control and Acoustics Division",
publisher = "ASME",
note = "NCA-25",
pages = "375-379",
year = 1998
}
@InProceedings{ra98b,
author = "R. Susan-Resiga and H. M. Atassi",
title = "Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: Numerical Implementation and Applications",
booktitle = "Proceedings of the ASME Noise Control and Acoustics Division",
publisher = "ASME",
note = "NCA-25",
pages = "381 -388",
year = 1998
}
@InProceedings{cai-dd10-98,
author = "Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. Widlund",
title = "Overlapping {S}chwarz methods for solving {H}elmholtz's Equation",
booktitle = "Domain Decomposition Methods 10",
editors = "Jan Mandel and Charbel Farhat and Xiao-Chuan Cai",
series = "Contemporary Mathematics",
volume = "218",
publisher = "American Mathematical Society",
address = "Providence, Rhode Island",
year = "1998",
pages = "437--445",
}
@inproceedings{alghamdi2011petclaw,
title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython},
booktitle = {Proceedings of SpringSim 2011},
publisher = {ACM},
author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and Kyle T. Mandli and Lisandro Dalcin},
year = {2011}
}
@article{pyclaw2012,
author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew Emmett},
title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems},
journal = {SIAM Journal on Scientific Computing},
volume = {34},
number = {4},
pages = {C210--C231},
note = {\url{http://arxiv.org/abs/1111.6583}},
year = {2012}
}

Optimization

@PhdThesis{
Prudencio1,
author = {Ernesto Prudencio},
Title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software for Optimization Problems Constrained by Partial Differential Equations},
school = {University of Colorado, Boulder},
year = 2005,No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@Article{Prudencio2,
author = "Ernesto Prudencio and X. C. Cai",
title = "Parallel multilevel restricted {Schwarz} preconditioners with pollution removing for {PDE}-constrained optimization",
journal = "SIAM J. Sci. Comp.",
note = "Submitted with revisions"
}
@Article{Prudencio3,
author = "Ernesto Prudencio and R. Byrd and X. C. Cai",
title = "Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for {PDE}-constrained Optimization Problems",
journal = "SIAM J. Sci. Comp.",
Volume = "27",
pages = "1305--1328",
year = "2006"
}
@inproceedings{Prudencio4,
title = "Domain decomposition methods for {PDE}-constrained optimization problems",
author = "Ernesto Prudencio and R. Byrd and X. C. Cai",
booktitle = "VECPAR 2004",
editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma},
publisher = "Springer",
year = "2004",
pages = "569--582"
}
@Article{belhamadia-fortin-pcp,
author = "Youssef Belhamadia and Andre Fortin and Eric Chamberland",
title = "Three-dimensional anisotropic mesh adaptation for phase change problems",
journal = "Journal of Computational Physics",
Volume = "201",
pages = "753-770",
year = "2004",
url = "http://portal.acm.org/citation.cfm?id=1055817.1055834#references"
}
@Article{biros00,
author = "George Biros and Omar Ghattas",
title = "A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization",
journal = "SIAG-Opt Views and News",
Volume = "11",
number = "2",
year = "2000",
month = "august",
url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf"
}
@article{bmm01,
Author = "Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}",
journal = "ACM Transactions on Mathematical Software",
TITLE = "A case study in the performance and scalability of optimization algorithms",
year = 2001,
volume = 27,
number = 3,
pages = "361--376",
}
@inproceedings{oghattas1999,
author = "George Biros and Omar Ghattas",
title = "Parallel preconditioners for {KKT} systems arising in optimal control of viscous incompressible flows",
booktitle = "Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999",
url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf",
year = 1999
}
@inproceedings{hkms00,
title = "Using Automatic Differentiation for Second-order Matrix-free Methods in PDE-constrained Optimization",
author = "P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono",
url = "http://www.icase.edu/\~{ }keyes/papers/ad2000.ps",
booktitle = "Automatic Differentiation of Algorithms: From Simulation to Optimization",
editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent Hasco\"{e}t and Uwe Naumann},
publisher = "Springer",
year = "2002"
}
% old version: replace with biros2005pln1
@techreport{bg011,
author = "George Biros and Omar Ghattas",
title = "Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part I: The Krylov-Schur Solver",
institution = "Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University",
year = "2001",
url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf"
}
% old version: replace with biros2005pln2
@techreport{bg012,
author = "George Biros and Omar Ghattas",
title = "Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to Optimal Control of Steady Viscous Flows",
institution = "Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University",
year = "2001",
url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf"
}

Fast Algorithms

@inproceedings{
ly2003,
author = "Lexing Ying and G. Biros and D. Zorin and H. Langston",
title = "A New Parallel Kernel-independent Fast Multipole Method",
booktitle = "Proceedings of the ACM/IEEE conference on Supercomputing 2003",
YEAR = "2003",
note = "Winner of the Best Student Paper at SC2003"
}
@article{YokotaBarbaKnepley10,
author = {Rio Yokota and L A Barba and Matthew G Knepley},
title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {199},
number = {25-28},
pages = {1793--1804},
url = {http://arxiv.org/abs/0909.5413v1},
note = {\url{http://arxiv.org/abs/0909.5413v1}},
year = {2010}
}
@article{CruzKnepleyBarba10,
author = {Felipe A Cruz and Matthew G Knepley and L A Barba},
title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library},
journal = {International Journal of Numerical Methods in Engineering},
volume = {85},
number = {4},
pages = {403--428},
url = {http://arxiv.org/abs/0905.2637},
note = {\url{http://arxiv.org/abs/0905.2637}},
year = {2010}
}

Other Application Areas

@inproceedings{
YanRhodes11,
author = {Yan, Baoqiang and Rhodes, Philip J.},
title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets},
booktitle = {Proceedings of the 2011 International Conference on Parallel Processing},
series = {ICPP '11},
pages = {355--364},
year = {2011},
isbn = {978-0-7695-4510-3},
numpages = {10},
url = {http://dx.doi.org/10.1109/ICPP.2011.70},
doi = {10.1109/ICPP.2011.70},
acmid = {2066965},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning},
}
@Article{Hakansson2013MDStochasticLiouville,
author = "Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and Stulz, Eugen",
title = "Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville equation study",
journal = "Phys. Chem. Chem. Phys.",
year = "2013",
volume = "15",
issue = "26",
pages = "10930-10941",
publisher = "The Royal Society of Chemistry",
doi = "10.1039/C3CP50788B",
url = "http://dx.doi.org/10.1039/C3CP50788B",
}
@Article{Hakansson2011StochasticLiouville,
author = "Hakansson, Par and Nair, Prasanth B.",
title = "Implicit numerical schemes for the stochastic Liouville equation in Langevin form",
journal = "Phys. Chem. Chem. Phys.",
year = "2011",
volume = "13",
issue = "20",
pages = "9578-9589",
publisher = "The Royal Society of Chemistry",
doi = "10.1039/C1CP20400A",
url = "http://dx.doi.org/10.1039/C1CP20400A",
}
@INPROCEEDINGS{wang:lee:scidac2011,
author = "Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman McInnes and Todd Munson and Barry Smith",
title = "A Differential Variational Inequality Approach for the Simulation of Heterogeneous Materials",
booktitle = "Proceedings of SciDAC 2011 Conference",
year = 2011
}

@article{BourdinLarsenRichardson2011,
author = {Blaise Bourdin and Christopher Larsen and Casey Richardson},
title = {A time-discrete model for dynamic fracture based on crack regularization},
journal = {International Journal of Fracture},
volume = {168},
issue = {2},
pages = {133--143},
doi = {10.1007/s10704-010-9562-x},
url = {http://dx.doi.org/10.1007/s10704-010-9562-x},
year = {2011}
}

@book{BourdinFrancfortMarigo,
author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo},
title = {The Variational Approach to Fracture},
publisher = {Springer},
year = {2008}
}

@article{BourdinFrancfortMarigo2008,
author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo},
title = {The Variational Approach to Fracture},
journal = {J. Elasticity},
volume = {91},
issue = {1},
pages = {1--148},
url = {http://dx.doi.org/10.1007/s10659-007-9107-3},
year = {2008}
}

@article{lahtinen2008spectrum,
title = {Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model},
author = {Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, J.K.},
journal = {Annals of Physics},
volume = {323},
number = {9},
pages = {2286--2310},
year = {2008},
publisher = {Elsevier}
}
@inproceedings{roark2004discriminative,
title = {Discriminative language modeling with conditional random fields and the perceptron algorithm},
author = {Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.},
booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics},
pages = {47},
year = {2004},
organization = {Association for Computational Linguistics}
}
@article{roark2007discriminative,
title = {Discriminative n-gram language modeling},
author = {Roark, B. and Saraclar, M. and Collins, M.},
journal = {Computer Speech \& Language},
volume = {21},
number = {2},
pages = {373--392},
year = {2007},
publisher = {Elsevier}
}
@conference{garcia2011parallel,
title = {{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D nanodevice simulators}},
author = {Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and Aldegunde, M.},
booktitle = {Electron Devices (CDE), 2011 Spanish Conference on},
pages = {1--4},
organization = {IEEE}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@conference{wesley2006parallel,
title = {{A parallel artificial neural network implementation}},
author = {Wesley-Smith, I.},
booktitle = {Proceedings of The National Conference On Undergraduate Research (NCUR)},
year = {2006}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@article{hcsw1,
author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu},
title = {Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions},
journal = {Computer Physics Communications},
volumne = 181,
year = 2010,
pages = {1529--1537}
}
@article{hh1,
author = {C.-Y. Huang and F.-N. Hwang},
title = {Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for bifurcation analysis of incompressible sudden expansion flows},
journal = {Applied Numerical Mathematics},
Volume = 60,
year = 2010,
pages = {738--751}
}
@article{hwhw1,
author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. Wang},
title = {A parallel additive Schwarz preconditioned Jacobi-Davidson algorithm for polynomial eigenvalue problems in quantum dot simulation},
journal = {Journal of Computational Physics},
Volume = 229,
year = 2010,
pages = {2932--2947}
}
@article{wei2011parallel,
title = {{A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with Application in Quantum Dot Simulation}},
author = {Wei, Z.H. and Hwang, F.N. and Huang, T.M. and Wang, W.},
journal = {Domain Decomposition Methods in Science and Engineering XIX},
pages = {157--164},
year = {2011},
publisher = {Springer}
}
@article{flores2007sequential,
title = {{Sequential and parallel resolution of the two-group transient neutron diffusion equation using second-degree iterative methods}},
author = {Flores-S{\'a}nchez, O. and Vidal, V. and Garc{\'\i}a, V. and Flores-S{\'a}nchez, P.},
journal = {High Performance Computing for Computational Science-VECPAR 2006},
pages = {426--438},
year = {2007},
publisher = {Springer}
}
@inproceedings{GordonBell09,
author = {Dinesh Kaushik and Michael Smith and Allan Wollaber and Barry Smith and Andrew Siegel and Won Sik Yang},
title = {Enabling High Fidelity Neutron Transport Simulations on Petascale Architectures},
booktitle = {ACM/IEEE Proceedings of SC2009: High Performance Networking and Computing},
note = {{SC'09 Gordon Bell} Prize Finalist},
year = {2009}
}

@article{KnepleyKarpeevDavidovitsEisenbergGillespie10,
author = {Matthew G. Knepley and Dmitry A. Karpeev and Seth Davidovits and Robert~S. Eisenberg and Dirk Gillespie},
title = {An Efficient Algorithm for Classical Density Functional Theory in Three Dimensions: Ionic Solutions},
journal = {Journal of Physical Chemistry},
volume = {132},
number = {12},
pages = {124101--124111},
url = {http://arxiv.org/abs/0910.1531},
note = {\url{http://arxiv.org/abs/0910.1531}},
year = {2010}
}
@article{KnepleyKarpeevEisenbergGillespie09,
author = {{Knepley}, M.~G. and {Karpeev}, D.~A. and {Eisenberg}, R.~S. and {Gillespie}, D.},
title = {{Energetics of Calcium Selectivity: A Three-Dimensional Classical Density Functional Theory Approach}},
journal = {Biophysical Journal},
month = {feb},
volume = {96},
pages = {661},
doi = {10.1016/j.bpj.2008.12.3494},
year = {2009}
}
@Article{scx2008,
author = "SUWITO AND XIAO-CHUAN CAI AND YUNPING XI",
title = "PARALLEL FINITE ELEMENT METHOD FOR COUPLED CHLORIDE MOISTURE DIFFUSION IN CONCRETE",
journal = "INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING",
Volume = "3",
number = "4",
year = "2006",
url = "http://www.math.ualberta.ca/ijnam/Volume-3-2006/No-4-06/2006-04-06.pdf"
}
@TechReport{kdgs2008,
year = 2008,
school = "Centro Internacional de Methodos Numericos en Ingenieria, Argentina",
title = "High Performance Simulations of Electrokinetic Flow and Transport in Microfluidic Chips",
author = "Pablo A. Klera and Lisandro D. Dalcin and Fabio A. Guarnieria and Mario A. Stortia",
url = "http://www.cimec.org.ar/ojs/index.php/cmm/article/view/1383"
}
@article {springerlink:10.1007/s10915-011-9551-x, author = {Schauer, Marco and Roman, Jose and Quintana-Ortí, Enrique and Langer, Sabine}, affiliation = {Institut für Angewandte Mechanik, Technische Universität Carolo-Wilhelmina zu Braunschweig, Spielmannstraße 11, 38106 Braunschweig, Germany}, title = {Parallel Computation of 3-D Soil-Structure Interaction in Time Domain with a Coupled FEM/SBFEM Approach}, journal = {Journal of Scientific Computing}, publisher = {Springer Netherlands}, issn = {0885-7474}, keyword = {Mathematics and Statistics}, pages = {1-22}, url = {http://dx.doi.org/10.1007/s10915-011-9551-x}, note = {10.1007/s10915-011-9551-x} }
@techreport{jj2007,
author = "Boris Jeremic and Guanzhou Jie",
title = "Parallel Finite Element Computations for Soil-Foundation-Structure Interaction Problems Report",
institution = "UCD CompGeoMech 02--2007",
year = "2007",
url = "http://sokocalo.engr.ucdavis.edu/~jeremic/wwwpublications/CV-R23.pdf"
}
@Unpublished{Kuiper08,
title = "Fast 3D frequency-dependent Radiative Transfer for Magneto-Hydrodynamics",
author = "Rolf Kuiper",
institution = "Max-Planck-Institute for Astronomy",
url = "http://www.mpia.de/~kuiper/MAKEMAKE.html",
year = 2008No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@inproceedings{srksyp2008,
author = {M. A. Smith and C. Rabiti and D. Kaushik and B. Smith and W. S. Yang and G. Palmiotti},
title = {Fast reactor core simulations using the {UNIC} code},
booktitle = {Proceedings of the International Conference on the Physics of Reactors, Nuclear Power: A Sustainable Resource},
year = {2008}
}
@INPROCEEDINGS{psrlkssl2007,
AUTHOR = {G. Palmiotti and M. A. Smith and C. Rabiti and M. Leclere and D. Kaushik and A. Siegel and B. Smith and E. E. Lewis},
TITLE = "{UNIC}: Ultimate Neutronic Investigation Code",
BOOKTITLE = "Joint International Topical Meeting on Mathematics and Computation and Supercomputing in Nuclear Applications",
YEAR = "2007"
}
@INPROCEEDINGS{sprkssl2007,
AUTHOR = {M. A. Smith and G. Palmiotti and C. Rabiti and D. Kaushik and A. Siegel and B. Smith and E. E. Lewis},
TITLE = "{PNFE} Component of the {UNIC} Code",
BOOKTITLE = "Joint International Topical Meeting on Mathematics and Computation and Supercomputing in Nuclear Applications",
YEAR = "2007"
}
@inproceedings{dc-oop-03,
AUTHOR = "H. Digonnet and T. Coupez",
TITLE = "Object-oriented programming for fast-and-easy development of parallel applications in forming processes simulation",
BOOKTITLE = "Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics",
YEAR = "2003"
}
@INPROCEEDINGS{dc-cfm-03,
AUTHOR = "H. Digonnet and T. Coupez",
TITLE = "Calcul parallele en mise en forme des materiaux",
BOOKTITLE = "XVIeme Congres Francais de Mecanique",
YEAR = "2003"
}
@INPROCEEDINGS{dsc-pcsev-04,
AUTHOR = "H. Digonnet and L. Silva and T. Coupez",
TITLE = "Parallel computation for solving efficiently viscoelastic fluid flow problems",
BOOKTITLE = "Proceedings of ECCOMAS 2004",
YEAR = "2004"
}
@INPROCEEDINGS{dsc-pca3fs-04,
AUTHOR = "H. Digonnet and L. Silva and T. Coupez",
TITLE = "Parallel computation applied to 3D FE simulation of polymer injection molding",
BOOKTITLE = "Proceedings of WCCM VI",
YEAR = "2004"
}
@INPROCEEDINGS{dbcs-cpaac-05,
AUTHOR = "H. Digonnet and O. Basset and T. Coupez and L. Silva",
TITLE = "Calcul parallele appliqu aux coulements de fluides complexe",
BOOKTITLE = "Proceedings of Eme Congres Francais de Mecanique",
YEAR = "2005"
}

@article{sz2010,
author = "B. Smith and H. Zhang",
title = "Sparse Triangular Solves for {ILU} Revisited: Data Layout Crucial to Better Performance",
journal = "International Journal of High Performance Computing Applications",
volume = 25,
number = 4,
pages = "386--391",
year = 2011
}

@article{zssz2006,
author = "H. Zhang and B. Smith and M. Sternberg and P. Zapol",
title = "{SIPs}: Shift-and-Invert Parallel Spectral Transformations",
journal = "TOMS",
url = "http://math.nist.gov/toms/Current.html#v33n2",
Volumne = "33",
number = 2,
year = 2007
}
@article{gs2006,
author = "Fang Jin and Nivedita R. Gupta and Kathleen J. Stebe",
title = "The detachment of a viscous drop in a viscous solution in the presence of a soluble surfactant",
journal = "Phys. Fluids",
volume = 18,
year = 2006,
url = "http://scitation.aip.org/dbt/dbt.jsp?KEY=PHFLE6&Volume=LASTVOL&Issue=LASTISS"
}
@article{jmemsci,
author = "Bo Zhou and Adam Powell",
title = "Phase Field Simulations of Liquid-Liquid Demixing During Immersion Precipitation of Polymeric Membranes in 2D and 3D",
journal = "J. Membrane Sci.",
volume = 268,
number = 2,
pages = "150--164",
year = 2006,
month = jan,
day = 15,
url = "http://dx.doi.org/10.1016/j.memsci.2005.05.030"
}
@INPROCEEDINGS{vbde2002,
AUTHOR = "Anke Veser and Wolfgang Breitung and Sergey Dorofeev and Alexander Efimenko",
TITLE = "Flame Acceleration Distance in Obstacle-Laden Tubes",
BOOKTITLE = "Proceedings of the NINTH INTERNATIONAL CONFERENCE ON NUMERICAL COMBUSTION",
url = "http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf",
YEAR = "2002"
}
@INPROCEEDINGS{wid2005,
AUTHOR = "Alexander I. Bobenko and Peter Schrader",
TITLE = "Discrete Willmore Flow",
BOOKTITLE = "Eurographics Symposium on Geometry Processing",
url = "http://www.math.tu-berlin.de/\~{ }bobenko/Papers/Willmore.pdf",
YEAR = "2005",
editor = "M. Desbrun and H. Pottmann"
}
@article{stj2003,
author = "A. Scascighini and A. Troxler and R. Jeltsch",
journal = "International Journal for Numerical Methods in Fluids",
volume = 41,
issue = 4,
title = "A numerical method for inverse design based on the inverse Euler equations",
year = 2003,
pages = "339--355",
url = "http://www3.interscience.wiley.com/cgi-bin/abstract/102521480/ABSTRACT"
}
@PhdThesis{AS2001,
author = {ANDREA SCASCIGHINI},
title = {A Numerical Method for the Design of Internal Flow Configurations Based on the Inverse Euler Equations},
school = {SWISS FEDERAL INSTITUTE OF TECHNOLOGY, ZURICH},
year = {2001},
url = {http://www.sam.math.ethz.ch/\~{ }andrea/}No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@article{hb2005,
author = "E. McKay Hyde and Oscar P. Bruno",
journal = "Journal of Computational Physics",
volume = 202,
title = "A fast, higher-order solver for scattering by penetrable bodies in three dimensions",
year = 2005,
pages = "236--261",
url = "http://www.acm.caltech.edu/\~{ }bruno/hyde_bruno_3d_jcp.pdf"
}
@mastersThesis{d2002,
author = {Matthew F Dixon},
title = {PARALLEL SOLUTION OF HIGH ORDER FINITE DIFFERENCE SCHEMES FOR PRICING MULTI-DIMENSIONAL AMERICAN OPTIONS},
school = {READING UNIVERSITY},
year = {2002},
url = {http://www.ma.ic.ac.uk/\~{ }mdixion/papers/MScThesis.pdf.gz}No htmlformatsMastersthesis found for entry mastersthesis No fieldlistMastersthesis found for entry mastersthesis
}
@techreport{gzb,
author = "David Gleich and Leonid Zhukov and Pavel Berkhin",
title = "Fast Parallel PageRank: A Linear System Approach",
institution = "Stanford University",
year = "2004",
url = "http://www.gg.caltech.edu/\~{ }zhukov/papers/ParallelPageRank-paper.pdf"
}
@PhdThesis{yergeau-99,
author = {Daniel W. Yergeau},
title = {A DIAL-AN-OPERATOR APPROACH TO SIMULATION OF IMPURITY DIFFUSION IN SEMICONDUCTORS},
school = {Stanford},
year = {1999},
url = {http://www-tcad.stanford.edu/tcad/pubs/theses/yergeau.pdf}No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@inproceedings{rathkopf-miller-00,
AUTHOR = "J.A. Rathkopf and D.S. Miller and J.M. Owen and L.M. Stuart and M.R. Zika and P.G. Eltgroth and N.K. Madsen and K.P. McCandless and P.F. Nowak and M.K. Nemanic and N.A. Gentile and N.D. Keen and T.S. Palmer",
TITLE = "{KULL}: {LLNL}'s {ASCI} Inertial Confinement Fusion Simulation Code",
YEAR = "2000",
BOOKTITLE = "Physor 2000 American Nuclear Society Topical Meeting on Advances in Reactor Physics and Mathematics and Computation into the Next Millennium",
url = "http://www.llnl.gov/tid/lof/documents/pdf/237860.pdf",
Lab = "LLNL"
}
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author = "A. Bonfiglioli and P. De Palma and G. Pascazio and M. Napolitano",
journal = "Journal of Turbomachinery",
volume = 127,
title = "An Implicit Fluctuation Splitting Scheme for Turbomachinery Flows",
year = 2005,
pages = "395-401"
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@INPROCEEDINGS{fettig-sobh-05,
AUTHOR = "John Fettig and Nahil Sobh and Dmitriy V. Melnikov and Jean-Pierre Leburton",
TITLE = "High Performance Algorithms for Scalable Spin-Qubit Circuits with Quantum Dots",
YEAR = "2005",
BOOKTITLE = "Proceedings of the 5th International Conference on Linux Clusters",
url = "http://www.linuxclustersinstitute.org/Linux-HPC-Revolution/Archive/PDF05/28-Fettig_J.pdf"
}
@techreport{melnikov-matagne-05,
Author = "Dmitriy V. Melnikov and Philippe Matagne and Jean-Pierre Leburton and D.G. Austing and G. Yu and S. Tarucha and John Fettig and Nahil Sobh",
TITLE = "Spin configurations in circular and rectangular vertical quantum dots in a magnetic field: Three-dimensional self-consistent simulation",
year = 2005,
Number = "Arxiv preprint cond-mat/0506585",
URL = "http://arxiv.org/pdf/cond-mat/0506585"
}
@INPROCEEDINGS{richard-smedley-03,
AUTHOR = "Richard P. Smedley-Stevenson",
TITLE = "PARALLEL THERMAL RADIATION TRANSPORT IN TWO DIMENSIONS",
YEAR = "2003",
BOOKTITLE = "18th International Conference on Transport Theory (18 ICTT)",
url = "http://www.iprj.uerj.br/\~{ }ricardob/Evento_Cientifico_html/poster03j.pdf"
}
@article{guan-godoy-ravaioli-03,
author = "D. Guan and A. Godoy and U. Ravaioli and F. Gamiz",
journal = "Journal of Computational Electronics",
volume = 2,
title = "Comparison Between Non-Equilibrium Green's Function and Monte Carlo Simulations for Transport in a Silicon Quantum Wire Structure",
year = 2003,
pages = "335--339"
}
@article{OvtchinnikovCai04,
author = "S. Ovtchinnikov and X.-C. Cai",
journal = "Numer. Lin. Alg. Applics",
volume = 11,
title = "One-level Newton-Krylov-Schwarz algorithm for unsteady nonlinear radiation diffusion problem",
year = 2004,
pages = "867--881"
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title = "Floating Solids: Combining Phase Field and Fluid-Structure Interactions",
author = "Adam Powell and David Dussault",
journal = "Appl. Numer. Anal. Comp. Math.",
volume = 2,
number = 1,
year = 2005,
pages = "157--166"
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@Article{dhh2005,
author = {G. Deli\'ege and F. Henrotte and K. Hameyer},
title = {Accuracy analysis of the thrust force in 2D-3D finite element models},
journal = {International Journal for Computation and Mathematics in Electrical and Electronic Engineering (COMPEL)},
year = {2005},
}
@Article{dhh2004,
author = {G. Deli\'ege and F. Henrotte and W. Deprez and K. Hameyer},
title = {Finite element modelling of ion convection by electrostatic forces},
journal = {IEE Proceedings Science, Measurement and Technology},
year = {2004},
volume = {151},
number = {6},
}

@Article{Adams-07b,
author = {Adams M.F.},
title = {Algebraic Multigrid Techniques for Strongly Indefinite Linear Systems from Direct Frequency Response Analysis in Solid Mechanics},
journal = {Computional Mechanics},
year = {2007},
volume = {39},
number = {4},
pages = {497-507}
}

@INPROCEEDINGS{wc2004,
AUTHOR = "A. Wheelock and D. Cooke",
TITLE = "Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three Dimensions",
YEAR = "2004",
BOOKTITLE = "40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit",
URL = "http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282"
}
@INPROCEEDINGS{allard-gouranton-ipts2002,
AUTHOR = "Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin",
TITLE = "Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster",
YEAR = "2002",
BOOKTITLE = "Immersive Projection Technology Symposium",
URL = "http://www-id.imag.fr/\~{ }allardj/files/ipts2002.pdf"
}
@article{icc,
author = {D Ioan and G Ciuprina and C Ciobotaru},
title = {Hybrid and concurrent algorithms for nonlinear magnetic field problems},
journal = {IEEE Transactions on Magnetics},
year = 2000,
url = {http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/20/19005/00877735.pdf}
}
@INPROCEEDINGS{hs1,
AUTHOR = "Brian J. Henz and Dale R. Shires",
TITLE = "Development and Performance Analysis of a Parallel Finite Element Application Implemented in an Object-Oriented Programming Framework",
YEAR = "2003",
BOOKTITLE = "PDPTA 2003",
PAGES = "1286-1292",
NOTE = "Resin Transfer Modeling"
}
@techreport{b2000,
Author = "Rickard Bergstrom",
TITLE = "Least-Squares Finite Element Methods for Electromagnetic Applications",
year = 2000,
INSTITUTION = "Chalmers",
number = "2000-05",
URL = "http://www.phi.chalmers.se/pub/preprints/ps/phiprint-2000-05.ps"
}
@article{fs2004,
author = {Petri Fast and Michael J. Shelley},
title = {A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele Shaw Flow},
journal = {Journal of Computational Physics},
year = 2004,
volume = {195},
url = {http://www.math.nyu.edu/faculty/shelley/papers/FS2004.pdf},
pages = {117-142}
}
@mastersthesis{wallach,
author = "Hanna Wallach",
title = "Efficient Training of Conditional Random Fields",
school = "University of Edinburgh",
year = "2002",
url = "http://scholar.google.com/url?sa=U&q=http://www.hcrc.ed.ac.uk/\~{ }osborne/msc-projects/wallach.ps.gz"No htmlformatsMastersthesis found for entry mastersthesis No fieldlistMastersthesis found for entry mastersthesis
}
@article{something,
author = {T Rylander and A Bondeson},
title = {Stability of explicit-implicit hybrid time-stepping schemes for Maxwells equations},
journal = {Journal of Computational Physics},
year = 2002,
volume = {179},
pages = {426-438}
}
@techreport{uf1,
Author = "Uwe Fabricius",
TITLE = "Comparison of two implementations of AMG-preconditioned CG considering an electrostatic problem",
year = 2004,
INSTITUTION = "Friedrich Alexander Universitat Erlangen Nurnberg Germany",
URL = "http://www10.informatik.uni-erlangen.de/de/Publications/TechnicalReports/TechRep04-1.pdf",
number = "04-1"
}
@INBOOK{sg1,
author = "Natalia Seoane and A.J.Garca-Loureiro",
chapter = "Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity Equation",
url = "http://www.springerlink.com/app/home/contribution.asp?wasp=h0xlulyhugck3y2gnt2l&referrer=parent&backto=issue,79,112;journal,212,1787;linkingpublicationresults,1:105633,1",
title = "Lecture Notes in Computer Science",
publisher = "Springer-Verlag",
volume = 3037,
year = 2004No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
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@article{NikYilmazGiviSheikhiPope10,
author = {M. B. Nik and S. L. Yilmaz and P. Givi and M. R. H. Sheikhi and S. B. Pope},
title = {Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function},
journal = {AIAA Journal},
volume = {48},
number = {7},
pages = {1513--1522},
year = {2010}
}
@article{NikYilmazSheikhiGivi10,
author = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi},
title = {Grid Resolution Effects on VSFMDF/LES},
journal = {Flow, Turbulence and Combustion},
doi = {10.1007/s10494-010-9272-5},
year = {2010}
}
@phdthesis{Abhyankar2011thesis,
author = {Shrirang Abhyankar},
title = {Development of an implicitly coupled electromechanical and electromagnetic transients simulator for power systems},
school = {Illinois Institute of Technology},
year = 2011No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@InProceedings{AbhyankarHiPCNA11-1,
author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck},
title = {Using {PETSc} to Develop Scalable Applications for Next-Generation Power Grid},
year = 2011,
booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid},
url = "http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf",
publisher = {ACM}
}
@InProceedings{AbhyankarHiPCNA11-2,
author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and H. Flueck},
title = {Development of a parallel three-phase transient stability simulator for power systems},
year = 2011,
booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid},
publisher = {ACM}
}
@InProceedings{AbhyankarPESGeneral2012,
author = {Shrirang Abhyankar and A. Flueck},
title = {An implicitly-coupled solution approach for combined electromechanical and electromagnetic transients simulation},
year = 2012,
booktitle = {Proceedings of the IEEE PES General Meeting},
publisher = {IEEE}
}
@article{IdemaLahayeVuikSluis2012,
author = {Reijer Idema and Domenico Lahaye and Cornelis Vuik and Lou van der Sluis},
title = {Scalable Newton-Krylov solver for very large Power Flow problems},
journal = {IEEE Transactions on Power Systems},
year = 2012,
volume = 27,
pages = {390-396}
}


Material failure, for example, cracking of steel beams resulting in bridge collapse and corrosion, is a little understood phenomena. Thus simulations are important for prediction and prevention. PETSc has been used in a variety of studies of material failure.

@InProceedings{gray2,
Author = "Yuan He and Joshua Gray and Richard Braatz and Richard Alkire",
TITLE = "Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel",
year = 2004,
booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}
}
@InProceedings{gray1,
Author = "J. Gray and and C. Homescu and L. Petzold and Richard Alkire",
TITLE = "Algorithms and Computing Architectures for Solving Differential-Algebraic Equation Systems Typically Encountered in Models of Corrosion Pit Initiation",
year = 2003,
booktitle = "Abstracts of the Electrochemical Society 204th meeting"
}
@INPROCEEDINGS{crack2,
AUTHOR = "Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. Wawrzynek",
TITLE = "A multiscale modeling approach to crack initiation in metallic polycrystals",
BOOKTITLE = "44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference",
url = "http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=TRD&recid=A0325099AH",
YEAR = "2003"
}
@techreport{hdams1,
Author = "Gerd Heber and Andrew J. Dolgert and Maxirn Alt and Karen A. Mazurkiewicz and Lynd Stringer",
TITLE = "Fracture Mechanics on the Intel Itanium Architecture",
year = 2001,
INSTITUTION = "Intel Corporation",
URL = "http://cedar.intel.com/media/pdf/scs/cptconitanium.pdf"
}
@inproceedings{ihwi,
Author = "E. Iesulauro and G. Heber and P. A. Wawrzynek and A. R. Ingraffea",
TITLE = "Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation",
booktitle = "International Conference ON Computational Engineering and Sciences",
year = 2002,
URL = "http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf"
}
@INPROCEEDINGS{crack,
AUTHOR = "Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis and Paul A. Wawrzynek",
TITLE = "Parallel FEM Simulation of Crack Propagation",
BOOKTITLE = "Proceedings of Irregular 2000",
url = "http://www.cs.cornell.edu/stodghil/papers/irregular00.ps",
YEAR = "2000"
}
@InProceedings{Beaudoin98,
author = {A. J. Beaudoin},
title = {Use of Polycrystal Plasticity Theory in Assessing Material Performance},
booktitle = {Simulation of materials processing: Theory, methods, and applications - Proceedings of the Sixth International Conference, NUMIFORM'98},
editor = {J. Hu\'etink and F. P. T. Baaijens},
OPTvolume = {},
OPTnumber = {},
OPTseries = {},
year = 1998,
OPTorganization = {},
publisher = {A. A. Balkema Publishers},
address = {Rotterdam, Netherlands},
month = JUN,
OPTpages = {},
}

@techreport{defordheld1,
Author = "JF DeFord and BL Held",
TITLE = "RF3P-A New Parallel Driven Frequency Electromagnetic Solver",
year = 2002,
INSTITUTION = "Simulation Technology and Applied Research",
URL = "http://www.staarinc.com/support/papers/aces2002.pdf",
NOTE = "Discusses their parallel commercial solver that uses PETSc"
}
@PhdThesis{Sande2003,
author = {Hans Vande Sande},
title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic Quasi-Static Electromagnetic Systems},
school = {Katholieke Universiteit Leuven, Belgium},
year = 2003No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@article{sdchh2004,
author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer},
title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System Tolerance},
journal = {IEEE Transactions on Magnetics},
year = 2004,
volume = {40},
pages = {1306--1309}
}
@Article{Holst-Lindblom-etal:2004,
author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. Scheel and Lawrence E. Kidder},
title = {Optimal constraint projection for hyperbolic evolution systems},
journal = {Phys. Rev. D},
year = 2004,
volume = 70,
pages = 084017
}
@Article{marm2005,
author = {Matthew Anderson and Richard A. Matzner},
title = {Extended Lifetime in Computational Evolution of Isolated Black Holes},
journal = {Foundations of Physics},
volume = 35,
pages = {1572--9516},
year = 2005
}
@Article{Cook-Pfeiffer:2004,
author = {Cook, Gregory B. and Pfeiffer, Harald P.},
title = {Excision boundary conditions for black hole initial data},
journal = {Phys. Rev. D},
volume = 70,
pages = {104016--24},
year = 2004
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@Article{Pfeiffer-Kidder-etal:2005,
author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre Shoemaker},
title = {Initial data for {E}instein's equations with superposed gravitational waves},
journal = {Phys. Rev. D},
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volume = {71},
pages = {024020}
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@Article{Pfeiffer-Kidder-etal:2003,
author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, Saul A.},
title = {A multidomain spectral method for solving elliptic equations},
journal = "CPC",
year = 2003,
volume = {152},
pages = {253--273},
note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. For a related online version, see arXiv:gr-qc/0202096}
}
@Article{Pfeiffer-Cook-Teukolsky:2002,
author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.},
title = {Comparing initial-data sets for binary black hole},
journal = "PRD",
year = {2002},
volume = {66},
pages = {024047},
note = {for a related online version, seearXiv:gr-qc/0203085}
}
@PhdThesis{Pfeiffer:2003,
author = {Pfeiffer, Harald P.},
title = {Initial Data for Black Hole Evolutions},
school = {Cornell University},
year = 2003No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@techreport{h1,
Author = "Erik Schnetter",
TITLE = "A fast apparent horizon algorithm",
year = 2002,
Number = "Arxiv preprint gr-qc/0206003",
URL = "http://arxiv.org/pdf/gr-qc/0206003"
}
@article{h2,
Author = "Erik Schnetter",
TITLE = "Finding apparent horizons and other 2-surfaces of constant expansion",
year = 2003,
journal = "Class. Quantum Grav.",
pages = "4719-4737",
volume = 20,
URL = "http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf"
}

@article{Adams-03a,
Author = {Adams, M.~F.},
Journal = {Numerical Linear Algebra with Applications},
Number = {2-3},
Pages = {141-153},
Title = {Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics},
Volume = {11},
Year = {2004}
}
@Article{vandesande1,
author = "H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer",
journal = "IEEE TRANSACTIONS ON MAGNETICS",
year = "2003",
volume = "39",
pages = "1709--1712",
title = "Solving Nonlinear Magnetic Problems Using Newton Trust Region Methods"
}
@InProceedings{vbde1,
author = "Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith",
year = "2002",
title = "Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the Uintah PSE",
booktitle = "In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 2002",
pages = "49-55",
url = "http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf",
note = "Extended abstract"
}
@Unpublished{ep1,
title = "An Inherently-Parallel Method for Solving Discretized Diffusion Equations",
author = "Bradley R. Eccleston and Todd S. Palmer",
institution = "Department of Nuclear Engineering, Oregon State University",
url = "http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf",
note = "Funded under the ASCI Level III: Computational Transport Issues for Large-Scale Parallel Simulations",
year = 1999No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@inproceedings{teo2007scalable,
title = {A scalable modular convex solver for regularized risk minimization},
author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.},
booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining},
pages = {727--736},
year = {2007},
organization = {ACM}
}
@InProceedings{rm02,
author = "Robert Malouf",
year = "2002",
title = "A comparison of algorithms for maximum entropy Parameter estimation",
booktitle = "In Proceedings of the Sixth Conference on Natural Language Learning (CoNLL-2002)",
pages = "49-55",
url = "http://bulba.sdsu.edu/malouf/papers/conll02.pdf"
}
@Unpublished{hrv02,
title = "Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}",
author = "V. Hernandex and J. E. Roman and V. Vidal",
note = "Submitted to CMMSE",No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Article{tmh2001,
author = "Manfred Gilli and Evis Kellezi and Giorgio Pauletto",
journal = "Journal of Economic Dynamics and Control",
year = "2002",
volume = "26",
pages = "1499-1515",
title = "Solving finite difference schemes arising in trivariate option pricing"
}
@INPROCEEDINGS{a2,
AUTHOR = "C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes",
TITLE = "Comparison of three algorithms for nonlinear metal cutting problems",
BOOKTITLE = "Proceedings of the 11th International Conference on Domain Decomposition Methods",
EDITOR = "C.-H. Lai et al.",
PUBLISHER = "Domain Decomposition Press, Bergen",
url = "http://www.ddm.org/DD11/Palansuriya.ps.gz",
YEAR = "1999"
}
@Unpublished{mmmdcmaa-web-page,
title = "{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and {A}coustics {W}eb Page",
url = "http://www.cs.odu.edu/\~{ }keyes/nsf",
author = "David E. Keyes",
Institution = "Old Dominion University",No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@conference{liu2010parallelization,
title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}},
author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.},
booktitle = {International Symposium on Parallel and Distributed Processing with Applications},
pages = {528--535},
year = {2010},
organization = {IEEE}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@Unpublished{oil-reservoir-sim-web-page,
title = "{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation",
url = "http://www.pe.utexas.edu/CPGE/new_generation",
institution = "University of Texas at Austin and Argonne National Laboratory",
key = "University of Texas at Austin and Argonne National Laboratory",No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Article{tmh2001b,
author = "V. Thiagarajan and K. Milfeld and KT. Milfeld",
journal = "IEEE TRANSACTIONS ON MAGNETICS ",
year = "2001",
volume = "37",
pages = "143--146",
title = "Adapting EMAP3D to parallel processing"
}
@Article{Harbury98,
author = "HK Harbury and W Porod",
journal = "VLSI Design",
year = "1998",
volume = "6",
pages = "47--51",
title = "Parallel computation for electronic waves in quantum corrals"
}
@Article{Bludszuwei98,
author = "Mark Bludszuweit",
journal = "Journal of Lightwave Technology",
year = "1998",
volume = "16",
number = "7",
pages = "1336--42",
title = "Mixed Finite Element Beam Propagation Method"
}
@Article{s1,
author = "J. L. Friedman and N. Stergioulas",
journal = "Astrophysics Journal",
year = "1998",
volume = "492",
number = "301",
pages = "",
title = ""
}
@Article{s1a,
author = "S. M. Morsink and N. Stergioulas and S. Blattnig",
journal = "Astrophysics Journal",
year = "1999",
volume = "510",
number = "854",
pages = "",
title = ""
}
@phdthesis{s2,
Author = "N. Stergioulas",
TITLE = "Ph. D. thesis",
year = 1996,
INSTITUTION = "University of Wisconsin-Milwaukee",No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@inproceedings{coral1,
AUTHOR = "L. Kettunen and K. Forsman and D. Levine and W. Gropp",
TITLE = "Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and Parallel Computing Environment",
BOOKTITLE = "Proceedings of the Miami TEAM Workshop",
LOCATION = "Florida International University, Department of Electrical Engineering and Computing Science",
MONTH = Nov,
YEAR = 1993
}
@inproceedings{coral2,
AUTHOR = "L. Kettunen and K. Forsman and D. Levine and W. Gropp",
TITLE = "Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation",
BOOKTITLE = "Proceedings of Aix-les-Bains TEAM Workshop",
MONTH = Dec,
YEAR = 1994
}
@inproceedings{coral3,
AUTHOR = "L. Kettunen and K. Forsman and D. Levine and W. Gropp",
TITLE = "Computational Electromagnetics and Parallel Dense Matrix Computations",
BOOKTITLE = "Proceedings of the SIAM Parallel Processing for Scientific Computing Conference",
LOCATION = "Florida International University, Department of Electrical Engineering and Computing Science",
YEAR = 1995
}
@InProceedings{mijalkovic,
author = {Slobodan Mijalkovi\'{c}},
title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor Process Simulation},
booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held Gent, Belgium, September 27--30, 1999.},
editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels},
OPTvolume = {14},
OPTseries = {Lecture Notes in Computational Science and Engineering},
year = 2000,
publisher = {Springer},
address = {Berlin},
OPTpages = {179--184},
}
@Article{Bludszuwei98a,
author = "Mark Bludszuweit",
journal = "Journal of Lightwave Technology",
year = "1998",
volume = "16",
number = "7",
pages = "1336--42",
title = "Mixed Finite Element Beam Propagation Method"
}
@Article{gilli-pauletto-1998,
author = "Manfred Gilli and Giorgio Pauletto",
title = "Parallel {K}rylov Methods for Econometric Model Simulation",
journal = "Computational Economics",
year = "2000",
volume = "16",
pages = "173--186"
}

Software Packages that use or interface to PETSc

@article{Logg07,
author = {Logg, Anders},
title = {Automating the Finite Element Method},
journal = {Archives of Computational Methods in Engineering},
volume = {14},
number = {2},
pages = {93-138},
year = {2007},
doi = {10.1007/s11831-007-9003-9},
url = {http://dx.doi.org/10.1007/s11831-007-9003-9},
publisher = {Kluwer Academic Publishers},
issn = {1134-3060},
language = {English}
}
@article{JezequelCouturierDenis12,
author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe},
title = {Solving large sparse linear systems in a grid environment: the GREMLINS code versus the PETSc library},
journal = {The Journal of Supercomputing},
volume = {59},
number = {3},
pages = {1517-1532},
year = {2012},
issn = {0920-8542},
doi = {10.1007/s11227-011-0563-y},
url = {http://dx.doi.org/10.1007/s11227-011-0563-y},
publisher = {Springer US},
keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; Sparse linear solver},
language = {English}
}

@Unpublished{feap-web-page,
title = {FEAP: A Finite Element Analysis Program},
url = {http://www.ce.berkeley.edu/projects/feap/},
author = {FEAP Team},
note = {Uses PETSc linear solvers - iterative and direct}No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}

@Unpublished{parpre-web-page,
title = "{ParPre} {W}eb {P}age",
url = "http://www.cs.utk.edu/\~{ }eijkhout/parpre.html",
Institution = "University of Tennessee",
author = "Victor Eijkhout",
note = "This is no longer supported. A set of preconditioners built on PETSc"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{pism,
title = "PISM: a Parallel Ice Sheet Model",
author = "The PISM Team",
note = "We have developed a numerical model of ice sheets called PISM (a Parallel Ice Sheet Model). The thickness, temperature, velocity and age of the ice are all simulated, as is the deformation of the earth underneath the ice. New techniques for fast ice dynamics, earth deformation, and verification have are included.",
url = "http://www.pism-docs.org/"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{oofem,
title = "OOFEM - an object oriented finite element package",
author = "Borek Patzak",
url = "http://www.oofem.org"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{dks2openfvm,
title = "OpenFVM - a finite volume based general purpose CFD solver",
author = "Open source development",
url = "http://openfvm.sourceforge.net/"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{sundar-2008w,
title = "DENDRO: a parallel geometric multigrid library for trilinear finite elements on octree meshes",
author = "H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros",
institution = "University of Pennsylvania",
url = "http://www.seas.upenn.edu/~csela/dendro/html/index.html"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{khatiwala07-software,
title = "A computational framework for simulation of biogeochemical tracers in the ocean",
author = "Khatiwala, S.",
institution = "Columbia University",
url = "http://www.ldeo.columbia.edu/\~{ }spk"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@INBOOK{JiaoLiMa99,
author = "Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma",
chapter = "SIFFEA:Scalable Integrated Framework for Finite Element Analysis",
url = "http://portal.acm.org/citation.cfm?id=646895.709725",
title = "Lecture Notes in Computer Science",
publisher = "Springer-Verlag",
volume = 1732,
year = 1999No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@Article{crow1,
author = {C. S. Crow IV},
title = "DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations",
journal = "Hopkins Undergraduate Research Journal",
year = 2003,
url = "http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf"
}
@Unpublished{petsc-python,
title = "PETSc for Python",
author = "L. Dalcin and R. Paz and M. Storti",
institution = "International Center for Computer Methods in Engineering",
url = "http://www.cimec.org.ar/python",
note = "Provides Python bindings for PETSc via SWIG"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{cfdship,
title = "{CFDShip-Iowa}",
author = "Pablo M. Carrica and Robert V. Wilson and Fred Stern",
institution = "University of Iowa",
url = "http://www.iihr.uiowa.edu/\~{ }cfdship/",
note = "CFDShip-Iowa is a multiblock free surface flow solver that uses overset structured grids, designed for ship applications"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{bvw,
title = "Multiflow",
author = "Berend van Wachem",
institution = "Mechanical Engineering - Chalmers University of Technology",
url = "http://www.tfd.chalmers.se/\~{ }berend/page3.html",
note = "MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase flows."No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{dks2,
title = "FENA - A Finite Element Model for the North Atlantic",
author = "Jens Schroeter",
institution = "Alfred-Wegener-Institute for Polar and Marine Research",
url = "http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@techreport{piwonski2010idea,
title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in {3-D}},
author = {Piwonski, J. and Slawig, T.},
year = {2010},
institution = {Christian-Albrechts-Universit\"at zu Kiel},
url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}
}
@Unpublished{metos3d-web,
title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D},
author = {Piwonski, J. and Slawig, T.},
institution = {Christian-Albrechts-Universit\"at zu Kiel},
url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{magpar,
author = "W. Scholz",
title = "Magpar: Parallel Micromagnetics Code",
Institution = "Vienna University of Technology",
url = "http://magnet.atp.tuwien.ac.at/scholz/magpar/"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Misc{libMesh:sourceforge,
author = {},
title = {{libMesh}:a C++ framework for the numerical simulation of partial differential equations on serial and parallel platforms},
note = {[Online]},
URL = {http://libmesh.sourceforge.net}
}
@misc{moose-web-page,
title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})},
author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek Gaston and John Peterson and Jason Miller},
institution = {Idaho National Laboratory},
howpublished = {\url{http://mooseframework.org}}
}
@article{gaston2009moose,
title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear equations},
author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.},
journal = {Nuclear Engineering and Design},
volume = {239},
number = {10},
pages = {1768--1778},
year = {2009},
publisher = {Elsevier}
}
@article{tonks2012object,
title = {An object-oriented finite element framework for multiphysics phase field simulations},
author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.},
journal = {Computational Materials Science},
volume = {51},
number = {1},
pages = {20--29},
year = {2012},
publisher = {Elsevier}
}
@Misc{PyLithManual,
author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif Strand and Charles Williams},
title = {{PyLith} User Manual Version 1.6.1},
year = {2011},
url = {http://geodynamics.org/cig/software/pylith/pylith_manual-1.6.2.pdf}
}
@Misc{pylith-web-page,
author = {Brad Aagaard and Matthew G. Knepley and Charles Williams},
title = {{PyLith}},
year = {2012},
url = {http://geodynamics.org/cig/software/pylith/},
howpublished = {\url{http://geodynamics.org/cig/software/pylith/}}
}
@Misc{GaleManual,
author = {Walter Landry and Luke Hodkinson and Susan Kientz},
title = {Gale User Manual Version 2.0.0},
year = {2011},
url = {http://geodynamics.org/cig/software/gale/gale.pdf}
}
@Unpublished{underworld,
author = "Louis Moresi",
title = "{UnderWorld}: A Geodynamics Modelling Code",
Institution = "Monash University",
url = "http://www.mcc.monash.edu/twiki/view/Codes"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@article{moresi2007computational,
title = {Computational approaches to studying non-linear dynamics of the crust and mantle},
author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and M{\"u}hlhaus, H.B.},
journal = {Physics of the Earth and Planetary Interiors},
volume = {163},
number = {1-4},
pages = {69--82},
year = {2007},
publisher = {Elsevier}
}
@article{pitt2009chaste,
title = {Chaste: a test-driven approach to software development for biological modelling},
author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. and Walter, A. and others},
journal = {Computer Physics Communications},
volume = {180},
number = {12},
pages = {2452--2471},
year = {2009},
publisher = {Elsevier}
}
@misc{fenicsproject,
title = {{The FEniCS project}},
author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.},
note = {A continually updated technical report. \url{http://fenicsproject.org}},
url = {http://fenicsproject.org},
year = {2011}
}
@Unpublished{Snark,
title = "Snark: A suite of software for geoscientific applications and a philosophy of scientific software development",
Institution = "Victorian Partnership for Advanced Computing",
url = "http://vpac.org/Snark"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Misc{imoose:sourceforge,
author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok},
title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}},
note = {[Online]},
URL = {http://imoose.sourceforge.net}
}
@Unpublished{FoSSI,
author = "Stephan Frickenhaus",
title = "FoSSI: Family of Simplified Solver Interfaces, offers scalable access to MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector codes",
Institution = "AWI-Bremerhaven, Germanny",
url = "http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{fun3dweb,
author = "Dinesh Kaushik",
title = "PETSC-FUN3D Benchmark Page",
Institution = "ODU/ANL",
url = "http://www.mcs.anl.gov/petsc-fun3d",
note = "CFD Benchmark of some solvers in PETSc"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{scirun,
author = "SCIRun Development Team",
title = "SCIRun",
Institution = "University of Utah",
url = "http://www.sci.utah.edu/stories/2001/jul_scirun120.html",
note = "SCIRun now uses PETSc linear solvers"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@misc{prometheus,
author = "Mark F. Adams",
title = "Prometheus - A scalable unstructured finite element solver",
Institution = "Berkeley",
howpublished = "\url{http://www.cs.berkeley.edu/~madams/prometheus}",
url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}
}
@Unpublished{Illuminator,
author = "Adam C. Powell, IV",
title = "Illuminator Distributed Visualization Library",
url = "http://lyre.mit.edu/\~{ }powell/Illuminator.html"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@unpublished{rheoplast,
title = "RheoPlast Phase Field Multi-Physics Code",
author = "Adam Powell and David Dussault and Bo Zhou",
url = "http://lyre.mit.edu/\~{ }powell/rheoplast.html"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Misc{tao-web-page,
title = "{Toolkit for Advanced Optimization (TAO)} {W}eb Page",
author = "Todd Munson and Jason Sarich and Stefan Wild and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}",
Institution = "Mathematics and Computer Science Division, Argonne National Laboratory",
howpublished = {\url{http://www.mcs.anl.gov/tao}}
}
@TechReport{tao-user-ref,
title = "{Toolkit for Advanced Optimization (TAO) Users Manual}",
author = "Todd Munson and Jason Sarich and Stefan Wild and Steve Benson and Lois Curfman McInnes",
Institution = "Argonne National Laboratory",
Year = 2014,
Number = "ANL/MCS-TM-322 - Revision 3.5",
url = "http://www.mcs.anl.gov/tao",
}
@Unpublished{MEFpp-web-page,
title = "{MEF++} {W}eb {P}age",
url = "http://www.giref.ulaval.ca/ressources/projets/mefpp.html",
Institution = "Groupe Interdisiplinaire de Recherche en Elements Finis",
author = "Eric Chamberland",
note = "A finite element code for fluid dynamics, solid mechanics, thermal and multiphysics"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{tipetsc-web-page,
title = "Ti-PETSc - an interface to PETSc from Titanium",
Institution = "Berkeley",
url = "http://www.nersc.gov/\~{ }yunhe/cs267/final/paper.pdf"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@misc{multiphase-web-page,
Author = "Q. Zou",
title = "Multiphase flow with {PETSc}",
Institution = "LANL",
howpublished = "\url{http://cnls-www.lanl.gov/~qzou}",
url = {http://cnls-www.lanl.gov/\~{ }qzou},
Lab = {LANL}
}
@misc{electromag-web-page,
title = "{EMSolve Web} page",
Institution = "LLNL",
howpublished = "http://www.llnl.gov/casc/emsolve",
url = {http://www.Llnl.gov/casc/emsolve},
author = "Daniel {White et al.}",
Lab = {LLNL}
}
@Unpublished{fe-software-web-page,
Institution = "Kuleuven",
title = "Finite element software",
url = "http://www.esat.kuleuven.ac.be/elen/research/software-development"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Misc{petsc-web-page,
author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune and Kris Buschelman and Victor Eijkhout and William~D. Gropp and Dinesh Kaushik and Matthew~G. Knepley and Lois Curfman McInnes and Karl Rupp and Barry~F. Smith and Hong Zhang},
title = {{PETS}c {W}eb page},
url = {http://www.mcs.anl.gov/petsc},
howpublished = {\url{http://www.mcs.anl.gov/petsc}},
year = {2014}
}
@Unpublished{petsc-debian-package,
author = "Adam C. Powell, IV",
title = "Debian package for PETSc",
url = "http://lyre.mit.edu/\~{ }powell/petsc.html"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{cactus,
title = "Cactus Website",
url = "http://www.cactuscode.org/",
note = "Provides two interface to the PETSc solvers"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Unpublished{PETSc-FEM,
author = "Mario Storti and Norberto Nigro",
title = "PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program",
Institution = "Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)",
url = "http://www.cimec.org.ar/petscfem"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@misc{fidap,
title = "FIDAP 8.5",
howpublished = "\url{http://www.fluent.com}",
url = {http://www.fluent.com},
note = "Fluent's commercial finite element fluid code uses PETSc for parallel linear solves.",
key = "FIDAP 8.5"
}
@Unpublished{slepc,
author = "Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and Vicente Hern\'andez and Vicent Vidal",
title = "{SLEPc} Homepage",
url = "http://www.grycap.upv.es/slepc/",
note = "Scalable Library for Eigenvalue Problem Computations"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@techreport{slepc-users-manual,
author = "Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and Vicente Hern\'andez and Vicent Vidal",
title = "{SLEPc} Users Manual",
number = "DISC-II/24/02",
url = "http://www.grycap.upv.es/slepc/",
note = "Scalable Library for Eigenvalue Problem Computations"
}
@misc{OpenFOAM,
title = "OpenFOAM",
howpublished = "\url{http://www.openfoam.com}",
url = {http://www.openfoam.com},
note = "OpenFOAM is a free, open source CFD software package. It allows PETSc linear algebra and solvers to be used underneath.",
key = "OpenFOAM 2.2.1"
}
@misc{deal.II,
title = "deal.II",
howpublished = "\url{http://www.dealii.org}",
url = {http://www.dealii.org},
note = "deal.II is a C++ library targeting adaptive finite elements and error estimation. It allows PETSc linear algebra and solvers to be used underneath.",
key = "deal.II 5.0"
}
@article{bangerth2007deal,
title = {{deal.II---A general-purpose object-oriented finite element library}},
author = {Bangerth, W. and Hartmann, R. and Kanschat, G.},
journal = {ACM Transactions on Mathematical Software (TOMS)},
volume = {33},
number = {4},
pages = {24--es},
issn = {0098-3500},
year = {2007},
publisher = {ACM}
}
@misc{globalarrays,
author = "Jarek {Nieplocha et al.}",
title = "Global Arrays",
Institution = "Pacific Northwest National Laboratories",
howpublished = "\url{http://www.emsl.pnl.gov/docs/global}",
url = {http://www.emsl.pnl.gov/docs/global},
note = "Global arrays can use PETSc linear solvers",
Lab = {PNNL}
}

Software Engineering

@TechReport{
ass2012,
author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens},
title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}},
institution = {Argonne National Laboratory},
type = "Preprint",
year = 2012,
number = "ANL/MCS-P2011-0112"
}

@techreport{ClearyKnepley99,
author = {Andrew Cleary and Matthew G. Knepley},
title = {Solvers as Operators},
institution = {Lawrence Livermore National Laboratory},
type = {Technical Report},
number = {UCRL-ID-135342},
year = {1999}
}

@techreport{smcabbkz2012,
author = "Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang",
title = "{PETSc's} Software Strategy for the Design Space of Composable Extreme-Scale Solvers",
institution = "Argonne National Laboratory",
type = "Preprint",
note = "{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR",
year = 2012,
number = "ANL/MCS-P2059-0312"
}

@inproceedings{mhwpmhs2009,
author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin and G. E. Hammond and B. Smith},
title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing Toolkit {MPI} at Scale},
booktitle = {Cray Users Group Conference},
year = {2009}
}
@inproceedings{msmhls2010,
author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. Lichtner and B. F. Smith},
title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} {BlueGene} Architectures},
booktitle = {Proceedings of SciDAC 2010 Annual Meeting},
year = {2010}
}
@incollection{msk2013,
author = {Victor Minden and Barry F. Smith and Matthew G. Knepley},
title = {Preliminary Implementation of {PETSc} Using {GPUs}},
booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
series = {Lecture Notes in Earth System Sciences},
editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
url = {http://dx.doi.org/10.1007/978-3-642-16405-7_7},
publisher = {Springer Berlin Heidelberg},
pages = {131--140},
year = {2013},
isbn = {978-3-642-16404-0},
}
@incollection{KnepleyYuen13,
author = {Matthew G. Knepley and David A. Yuen},
title = {Why Scientists and Engineers need {GPU}s today},
booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
series = {Lecture Notes in Earth System Sciences},
editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
doi = {10.1007/978-3-642-16405-7_1},
url = {http://dx.doi.org/10.1007/978-3-642-16405-7_1},
publisher = {Springer Berlin Heidelberg},
pages = {131--140},
year = {2013},
isbn = {978-3-642-16404-0},
}
@incollection{KarpeevKnepleyBrune13,
author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune},
title = {Accurate Evaluation of Local Averages on {GPGPUs}},
booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
series = {Lecture Notes in Earth System Sciences},
editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
doi = {10.1007/978-3-642-16405-7_30},
url = {http://dx.doi.org/10.1007/978-3-642-16405-7_30},
publisher = {Springer Berlin Heidelberg},
pages = {487--501},
year = {2013},
isbn = {978-3-642-16404-0},
}
@incollection{ZhengEtAl13,
title = {{GPU} Implementation of Multigrid Solver for Stokes Equation with Strongly Variable Viscosity},
author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
series = {Lecture Notes in Earth System Sciences},
editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
doi = {10.1007/978-3-642-16405-7_21},
url = {http://dx.doi.org/10.1007/978-3-642-16405-7_21},
publisher = {Springer Berlin Heidelberg},
pages = {321--333},
year = {2013},
isbn = {978-3-642-16404-0},
}
@article{ZhengEtAl13b,
title = {Implementation of a multigrid solver on {GPU} for Stokes equations with strongly variable viscosity based on Matlab and CUDA},
author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
journal = {IJHPCA},
url = {http://hpc.sagepub.com/content/early/2013/03/03/1094342013478640.abstract},
note = {\url{http://hpc.sagepub.com/content/early/2013/03/03/1094342013478640.abstract}},
year = {2013}
}
@inbook{s2011,
author = "B. Smith",
chapter = "PETSc, the Portable, Extensible Toolkit for Scientific computing",
title = "Encyclopedia of Parallel Computing",
bookeditor = "D. Padua",
publisher = "Springer",
year = "2011"No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@article{AcostaMejia06,
author = {Carlos D. Acosta and Carlos E. Mej\'ia},
title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc},
journal = {Lecturas Matem\'aticas},
volume = {27},
year = {2006},
pages = {213--224}
}


@InProceedings{QuenetteMoresiSunterAppelbe07,
author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe},
title = {Explaining StGermain: An aspect oriented environment for building extensible computational mechanics modeling software},
booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007},
publisher = {IEEE},
pages = {1--8},
yerar = {2007},
}
@Article{dfm1,
title = "Vectorized sparse matrix multiply for compressed row storage format",
author = "E. F. D'Azevedo and M. R. Fahey and R. T. Mills",
journal = "Lecture Notes in Computer Science",
year = "2005",
pages = "99--106",
volume = "3514",
lab = "ORNL"
}
@InProceedings{LaniQuintinoKimpeDeconinckVandewallePoedts05,
author = "Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan Vandewalle and Stefaan Poedts",
title = "The COOLFluiD Framework: Design Solutions for High Performance Object Oriented Scientific Computing Software",
booktitle = "Computational Science ICCS 2005: 5th International Conference",
year = "2005",
note = "Lecture Notes in Computer Science",
volume = "3514",
publisher = "Springer-Verlag GmbH"
}
@InProceedings{dalcin-paz-storti,
author = "L. Dalcin and R. Paz and M. Storti",
title = "Desarrollo de Aplicaciones Paralelas en Python",
booktitle = "Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). Bariloche, Argentina",
year = "2004"
}
@Article{mpi-python,
author = "L. Dalcin and R. Paz and M. Storti",
title = "MPI for Python",
journal = "Journal of Parallel and Distributed Computing",
year = "2005"
}
@Unpublished{hrv02a,
title = "{SLEPc}: Scalable Library for Eigenvalue Problem Computations",
author = "V. Hernandex and J. E. Roman and V. Vidal",
note = "Submited to VecPar 2002",
year = 2002No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@article{knyazev2007block,
title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and {PETSc}},
author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.},
journal = {SIAM Journal on Scientific Computing},
volume = {29},
pages = {2224-2239},
url = {http://dx.doi.org/10.1137/060661624},
year = {2007}
}

@mastersthesis{aarrestad-master,
author = "Asbjorn Hoiland Aarrestad",
title = "Time Dependent Solution of the Schrodinger Equation for Parallel Computers",
school = "University of Bergen",
month = "August",
year = "2003",
url = "http://www.parallab.uib.no/projects/molecul/matrix/",
note = {Implemented Runge-Kutta methods using PETSc}No htmlformatsMastersthesis found for entry mastersthesis No fieldlistMastersthesis found for entry mastersthesis
}
@phdthesis{kaushik-phd,
author = "D. K. Kaushik",
title = "Performance Modeling and Prediction for the Scalable Solution of Partial Differential Equations on Unstructured Grids",
school = "Old Dominion University",
month = "December",
year = "2002",
url = "http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps"No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@techreport{rb1,
AUTHOR = "Rickard Bergstrom",
TITLE = "Object Oriented Implementation of a General Finite Element Code",
NUMBER = "2002-13",
INSTITUTION = "Chalmers Finite Element Center, Chalmers University of Technology",
YEAR = 2002,
url = "http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf",
note = "Discribes a finite element software package that uses PETSc for its solvers"
}
@InProceedings{dbl1,
author = "Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew",
title = "A Parallel General Purpose Finite Element System",
booktitle = "IX SIAM Conference on Parallel Processing for Scientific Computing",
publisher = "SIAM",
year = "1999",
url = "http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz",
note = "Describes software that uses PETSc for its parallel linear solves"
}
@Article{p1,
title = "Parallel Components for PDEs and Optimization: Some Issues and Experiences",
author = "B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes and B. Smith",
journal = "Parallel Computing",
year = "2002",
pages = "1811--1831",
volume = "28 (12)"
}
@Article{Automatic-AD,
AUTHOR = "Paul Hovland and Boyana Norris and Barry Smith",
TITLE = "Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}",
YEAR = 2005,
journal = "Future Generation Computer Systems",
volume = 21,
number = 8,
pages = "1426--1438"
}
@techreport{remote-math,
author = "Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry Smith",
title = "Remote Access to Mathematical Software",
number = "ANL/MCS-P889-0601",
institution = "Mathematics and Computer Science Division, Argonne National Laboratory",
month = "June",
year = "2001",
url = "http://icm.mcs.kent.edu/research/iamc01proceedings.html"
}
@INPROCEEDINGS{gropp98,
AUTHOR = "William D. Gropp",
TITLE = "Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why",
PUBLISHER = "SIAM",
BOOKTITLE = "Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing",
year = 1999,
pages = "21-29"
}
@INPROCEEDINGS{knepleysarin99,
author = {Matthew Knepley and Vivek Sarin},
title = {Algorithm Development for Large Scale Computing},
publisher = {SIAM},
booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing},
note = {\url{http://books.google.com/books?id=2Da5OcnjPSgC&lpg=PA58&ots=TJCK64BUeg&dq=Bill%20Gropp%20Science%20Engineering%20Object%20Oriented&pg=PA138#v=onepage&q&f=false}},
year = {1999}
}
@INBOOK{bgms00,
author = "S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith",
chapter = "Software for the Scalable Solution of {PDEs}",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z",
title = "CRPC Handbook of Parallel Computing",
editor = "J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon and A. White",
publisher = "Morgan Kaufmann Publishers",
year = 2002No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@INPROCEEDINGS{hovland_norris_smith98,
AUTHOR = "Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith",
TITLE = "Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific Computations",
PUBLISHER = "SIAM",
BOOKTITLE = "Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z",
note = "also available as Argonne preprint ANL/MCS-P731-1098",
year = 1999,
pages = "129-137"
}
@InProceedings{efficient,
author = "Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
title = "Efficient Management of Parallelism in Object Oriented Numerical Software Libraries",
booktitle = "Modern Software Tools in Scientific Computing",
editor = "E. Arge and A. M. Bruaset and H. P. Langtangen",
publisher = "Birkhauser Press",
pages = "163--202",
year = 1997,
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z"
}
@TechReport{petsc-user-ref,
author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune and Kris Buschelman and Victor Eijkhout and William~D. Gropp and Dinesh Kaushik and Matthew~G. Knepley and Lois Curfman McInnes and Karl Rupp and Barry~F. Smith and Hong Zhang},
title = {{PETS}c Users Manual},
institution = {Argonne National Laboratory},
year = 2014,
number = {ANL-95/11 - Revision 3.5},
url = {http://www.mcs.anl.gov/petsc}
}
@TechReport{petsc-developers,
author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune and Kris Buschelman and Victor Eijkhout and William~D. Gropp and Dinesh Kaushik and Matthew~G. Knepley and Lois Curfman McInnes and Karl Rupp and Barry~F. Smith and Hong Zhang},
title = {{PETS}c Developers Manual},
institution = {Argonne National Laboratory},
year = 2011,
url = {http://www.mcs.anl.gov/petsc}
}
@Unpublished{alice-memory-snooper,
author = {Ibrahima Ba and Barry~F. Smith},
title = {The {ALICE} Memory Snooper},
year = 1999No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@TechReport{petsc-user-ref-polish,
Author = "Marcin Bojko and Piotr Krzyzanowski",
Title = "Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc",
Institution = "Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski",
Year = 1998,
note = "An introduction to PETSc in Polish"
}
@inproceedings{abghmn00,
title = "Integrating Automatic Differentiation with Object-Oriented Toolkits for High-Performance Scientific Computing",
author = "J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. Norris",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z",
booktitle = "Automatic Differentiation of Algorithms: From Simulation to Optimization",
editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent Hasco\"{e}t and Uwe Naumann},
publisher = "Springer",
year = "2002"
}
@Unpublished{petsc-mpi-paper,
Author = "Lois Curfman McInnes and Barry F. Smith",
Title = "{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software Libraries",
Note = "Proceedings of the MPI Developers Conference, Notre Dame, IN",
Month = Jun,
Year = "1995"No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@INPROCEEDINGS{miss-paper,
AUTHOR = "William D. Gropp and Barry F. Smith",
TITLE = "Scalable, Extensible, and Portable Numerical Libraries",
PUBLISHER = "IEEE",
YEAR = "1994",
BOOKTITLE = "Proceedings of the Scalable Parallel Libraries Conference",
ADDRESS = "Mississippi State University",
pages = "87--93",
keyword = "numerical libraries, scientific computing, parallel computing"
}
@INPROCEEDINGS{snes-paper,
AUTHOR = "William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
TITLE = "Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained Minimization Problems",
PUBLISHER = "IEEE",
YEAR = "1995",
BOOKTITLE = "Proceedings of the Scalable Parallel Libraries Conference",
ADDRESS = "Mississippi State University",
pages = "60-67",
keyword = "nonlinear equations, optimization, superconductivity, parallel computing"
}
@article{dsneutral,
author = {Barry F. Smith and William D. Gropp},
title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of Sparse Linear Systems},
journal = {Scientific Programming},
volume = {5},
pages = {329--336},
key = {GroppSmith96 ! KSP design},
year = {1996}
}
@inproceedings{bgms98,
author = "Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
title = "A Microkernel Design for Component-based Parallel Numerical Software Systems",
booktitle = "Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing",
publisher = "SIAM",
pages = "58-67",
note = "also available as Argonne preprint ANL/MCS-P727-0998",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z",
year = "1998"
}
@Article{hkm98,
author = "M. E. Hayder and D. E. Keyes and P. Mehrotra",
title = "A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal {PDE} Computation",
journal = "Advances in Engineering Software",
volume = 29,
pages = "415-424",
year = 1998
}
@techreport{pdpta99,
AUTHOR = "L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. Smith",
TITLE = "Infrastructure and Interfaces for Large-Scale Numerical Software",
note = "to appear in the Proceedings of the 1999 International Conference on Parallel and Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las Vegas, Nevada",
institution = "Mathematics and Computer Science Division, Argonne National Laboratory",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z",
number = "ANL/MCS-P751-0599",
year = 1999
}
@inproceedings{bbh:com,
author = "C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland",
title = "{On Combining Computational Differentiation and Toolkits for Parallel Scientific Computing}",
booktitle = "Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International Euro-Par Conference, Munich, Germany, August/September 2000",
year = 2000,
editor = "A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller",
volume = "1900",
series = "Lecture Notes in Computer Science",
pages = "86--94",
address = "Berlin",
publisher = "Springer",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z"
}

@inproceedings{overture00,
author = "K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith",
title = " {PETSc and Overture}: Lessons Learned Developing an Interface between Components",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z",
booktitle = "Proceedings of the International Federation for Information Processing Working Conference on Software Architectures for Scientific Computing, Kluwer",
year = "2000",
pages = "57--68"
}
@techreport{smith97,
title = "An Interface for Efficient Vector Scatters and Gathers on Parallel Machines",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z",
number = "ANL/MCS-P701",
author = "Barry F. Smith",
Institution = "Mathematics and Computer Science Division, Argonne National Laboratory"
}
@Article{smith98,
author = "Barry Smith",
title = "The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction",
journal = "SIGNUM Newsletter",
year = "1998",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z"
}
@techreport{AD-PETSC-TM,
title = "Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of {PETSc}",
author = "Christian Bischof and Paul Hovland and Po-Ting Wu",
year = 1997,
type = "Technical Memorandum",
institution = "ANL",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z",
number = "ANL/MCS-TM-233"
}

Algorithm design and analysis

@article{
bassi2014agglomeration,
title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh free},
author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro},
journal = {Mathematical Models and Methods in Applied Sciences},
volume = {24},
number = {08},
pages = {1495--1539},
year = {2014},
publisher = {World Scientific}
}
@ARTICLE{JhuraniDemkowicz12,
author = {{Jhurani}, C. and {Demkowicz}, L.},
title = "{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. Part II: Algorithms for the Moore-Penrose pseudoinverse}",
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = 213,
pages = {418-426},
year = 2012,
month = mar,
doi = {10.1016/j.cma.2011.06.003},
adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}
}
@article{YangCai11,
author = {Yang, Haijian and Cai, Xiao-Chuan},
title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear Complementarity Problems},
journal = {J. Sci. Comput.},
issue_date = {May 2011},
volume = {47},
number = {2},
month = may,
pages = {258--280},
year = {2011},
issn = {0885-7474},
numpages = {23},
url = {http://dx.doi.org/10.1007/s10915-010-9436-4},
doi = {10.1007/s10915-010-9436-4},
acmid = {1971246},
publisher = {Plenum Press},
address = {New York, NY, USA},
keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz preconditioners, Semismooth Newton, Two-level methods},
}
@article{Rheinbach09,
author = {Rheinbach, Oliver},
title = {Parallel Iterative Substructuring in Structural Mechanics},
journal = {Archives of Computational Methods in Engineering},
volume = {16},
number = {4},
pages = {425-463},
year = {2009},
issn = {1134-3060},
doi = {10.1007/s11831-009-9035-4},
url = {http://dx.doi.org/10.1007/s11831-009-9035-4},
publisher = {Springer Netherlands},
language = {English}
}
@Article{KnepleyTerrel2013,
author = {Matthew G. Knepley and Andy R. Terrel},
title = {Finite Element Integration on {GPUs}},
journal = {{ACM} Transactions on Mathematical Software},
volume = {39},
number = {2},
accepted = {17 April 2012},
year = {2013},
abstract = {We present a novel finite element integration method for low order elements on GPUs. We achieve more than 100GF for element integration on first order discretizations of both the Laplacian and Elasticity operators on an NVIDIA GTX285, which has a nominal single precision peak flop rate of 1 TF/s and bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.},
url = {http://arxiv.org/abs/1103.0066},
note = {\url{http://arxiv.org/abs/1103.0066}}
}
@Misc{KnepleyRuppTerrel2014,
author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel},
title = {Finite Element Integration with Quadrature on Accelerators},
year = {2014}
}
@techreport{pbmkbsxt2012,
title = "Composing Scalable Nonlinear Algebraic Solvers",
author = "Peter Brune and Mathew Knepley and Barry Smith and Xuemin Tu",
year = 2013,
type = "Preprint",
number = "ANL/MCS-P2010-0112",
institution = "Argonne National Laboratory"
}

@article{mszm2014,
title = "Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing",
author = "Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills",
number = {40},
pages = {17--31},
year = {2014},
journal = "Parallel Computing",
url = "http://dx.doi.org/10.1016/j.parco.2013.10.001"
}

@techreport{mszm2012,
title = "Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing",
author = "Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills",
year = 2012,
number = "ANL/MCS-P2097-0512",
institution = "Argonne National Laboratory"
}


@inproceedings{bkmms2012,
author = {J. Brown and M. G. Knepley and D. A. May and L. C. McInnes and B. F. Smith},
title = {Composable Linear Solvers for Multiphysics},
booktitle = {Proceeedings of the 11th International Symposium on Parallel and Distributed Computing (ISPDC 2012)},
year = {2012},
url = {http://doi.ieeecomputersociety.org/10.1109/ISPDC.2012.16},
publisher = {IEEE Computer Society},
pages = {55--62},
}

@article{BourdinBucurOudet2009,
author = {Blaise Bourdin and D. Bucur and E. Oudet},
title = {Optimal Partitions for Eigenvalues},
journal = {SIAM J. Sci. Comput.},
volume = {31},
number = {6},
pages = {4100--4114},
year = {2009}
}

@inbook{KimnBourdin2007,
author = {J.-H. Kimn and Blaise Bourdin},
title = {Numerical implementation of overlapping balancing domain decomposition methods on unstructured meshes},
editor = {O. B. Widlund and D. E. Keyes},
booktitle = {Domain Decomposition Methods in Science and Engineering XVI},
series = {Lecture Notes in Computational Science and Engineering},
number = {55},
publisher = {Springer-Verlag},
pages = {309--315},
url = "http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf",
year = {2007}No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@Article{bjm2005,
author = {AH Baker and ER Jessup and T Manteuffel},
title = {A Technique for Accelerating the Convergence of Restarted GMRES},
journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS},
year = {2005}
}
@unpublished{Sundar-2008a,
author = {R.S. Sampath and G. Biros},
title = {A parallel geometric multigrid method for finite elements on octree meshes},
URL = {http://www.seas.upenn.edu/\~{ }rahulss}No htmlformatsUnpublished found for entry unpublished No fieldlistUnpublished found for entry unpublished
}
@Article{Sundar-2008,
author = {H. Sundar and R.S. Sampath and G. Biros},
title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel},
journal = {SIAM Journal on Scientific Computing},
year = {2008},
URL = {http://www.seas.upenn.edu/\~{ }rahulss}
}
@InProceedings{Sundar-2007,
author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros},
title = {Low-constant parallel algorithms for finite element simulations using linear octrees},
booktitle = {SC'07: ACM/IEEE Conference on Supercomputing},
year = {2007},
URL = {http://www.seas.upenn.edu/\~{ }rahulss}
}
@InProceedings{Adams-98a,
author = {Adams, Mark ~F.},
title = {A Parallel Maximal Independent Set Algorithm},
booktitle = {Proceedings 5th copper mountain conference on iterative methods},
year = {1998}
}
@article{akcelik2005ddd,
title = {{Dynamic data-driven inversion for terascale simulations: real-time identification of airborne contaminants}},
author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and van Bloemen Waanders, B.},
journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing},
year = {2005},
publisher = {IEEE Computer Society Washington, DC, USA}
}
@InBook{Akcelik-2006,
author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van Bloemen Waanders},
bookeditor = {M. Heroux and P. Raghaven and H. Simon},
title = {Frontiers of Parallel Computing},
chapter = {Parallel algorithms for {PDE}-constrained optimization},
publisher = {SIAM},
year = {2006}No htmlformatsInbook found for entry inbook No fieldlistInbook found for entry inbook
}
@Article{dt,
author = "Matthew F. Dixon and C. J. Kenneth Tan",
title = "Using Distributed Computers to Deterministically Approximate Higher Dimensional Convection Diffusion Equations",
journal = "The Journal of Supercomputing",
year = "2004",
pages = "235--253",
volume = 28,
url = "http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1"
}
@phdthesis{hwang2004,
author = {Feng-Nan Hwang},
title = "Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in Computational Fluid Dynamics",
school = {University of Colorado at Boulder},
year = 2004No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@phdthesis{baker,
author = {{A. H.} Baker},
title = "On improving the performance of the linear solver restarted {GMRES}",
school = {University of Colorado at Boulder},
year = 2003No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@techreport{KlawonnRheinbach601,
author = "Axel Klawonn and Oliver Rheinbach",
title = {A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional Linear Elasticity Using a Transformation of Basis},
institution = {Universit\"at Duisburg-Essen},
year = 2005,
type = "Technical Report",
number = "SM-E-601"
}
@techreport{KlawonnRheinbach609,
author = "Axel Klawonn and Oliver Rheinbach",
title = {Inexact FETI-DP Methods},
institution = {Universit\"at Duisburg-Essen},
year = 2005,
type = "Technical Report",
number = "SM-E-609"
}
@techreport{KlawonnRheinbach607,
author = "Axel Klawonn and Oliver Rheinbach",
title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems},
institution = {Universit\"at Duisburg-Essen},
year = 2005,
type = "Technical Report",
number = "SM-E-607"
}
@Article{kul-natraj-pbp,
author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung},
title = {Performance of a parallel mixed finite element implementation for fourth order clamped anisotropic plate bending problems in distributed memory environments},
journal = {Applied Mathematics and Computation},
volume = {155},
year = {2004},
number = 3,
pages = {753--777}
}


@ARTICLE{Bramkamp2006UEJ,
author = "F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch",
title = "Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method",
journal = "Computers \& Fluids",
volume = "35",
number = "10",
pages = "1063--1073",
doi = "10.1016/j.compfluid.2005.10.003 <http://dx.doi.org/10.1016/j.compfluid.2005.10.003>",
abstract = "In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the derivation of the analytic flux Jacobian can become quite complicated depending on the complexity of the numerical flux calculation. Practically, the derivation of the exact Jacobian by hand is an unrealistic option because of the enormous man-hour investment needed. In this work, automatic differentiation is used to evaluate the exact Jacobian of upwind schemes implemented in the flow solver QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically approximated by first-order forward differences. For a two-dimensional airfoil under three different flight conditions (quasi-incompressible flow, compressible subsonic flow, and transonic flow), we show that the robustness and performance of the present finite volume scheme is significantly improved by using exact Jacobians.",
year = "2006",
}

@Article{shahbazi1,
author = {Khosro Shahbazi},
title = {An explicit expression for the penalty parameter of the interior penalty method},
journal = {Journal of Computational Physics},
volume = {205},
year = {2005},
pages = {401--407}
}
@techreport{kk,
title = "A Parallel Lanczos Algorithm for Eigensystem Calculation",
author = "Hans-Peter Kersken and Uwe Kuster",
year = 1999,
institution = "University of Stuttgart",
url = "http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf",
number = "310"
}
@Article{miha-mija,
author = {M. D. Mihajlovi and S. Mijalkovi},
title = {A component decomposition preconditioning for 3D stress analysis problems},
journal = {Numerical Linear Algebra with Applications},
volume = {9},
year = {2002},
pages = {567--583},
url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}
}
@Article{bjm,
author = "M Benzi and W Joubert and G Mateescu",
journal = "Electronic Transactions on Numerical Analysis",
year = "1999",
volume = "8",
pages = "88--114",
title = "Numerical experiments with parallel orderings for {ILU} preconditioners",
url = "http://scholar.google.com/url?sa=U&q=http://emis.bibl.cwi.nl/journals/ETNA/vol.8.1999/pp88-114.dir/pp88-114.ps"
}
@phdthesis{hyde,
author = {EMK Hyde},
title = "Fast, High-Order Methods for Scattering by Inhomogeneous Media",
school = {Caltech},
year = 2003,
url = "http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf"No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@Article{km2003,
author = "A. Keese and H. G. Matthies",
journal = "Proceedings in Applied Mathematics and Mechanics",
year = "2003",
volume = "2",
pages = "485--486",
title = "Parallel Solution of Stochastic PDEs",
url = "http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT"
}
@Article{whszss,
author = "Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld and Otmar Scherzer and H. Siegfried Stiehl",
journal = "Real Time Imaging",
year = "2001",
volume = "7",
pages = "31--45",
title = "Fast parallel algorithms for a broad class of nonlinear variational diffusion approaches",
url = "http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz"
}
@techreport{baker1,
title = "An Efficient Block Variant of GMRES",
author = "A. H. Baker and J. M. Dennis and E. R. Jessup",
year = 2003,
type = "Technical Report",
institution = "University of Colorado, Boulder",
url = "http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf",
number = "CU-CS-957-03"
}
@INPROCEEDINGS{mc2003,
AUTHOR = "Leszek Marcinkowski and Xiao-Chuan Cai",
TITLE = "Parallel Performance of Some Two-Level {ASPIN} Algorithms",
BOOKTITLE = "Proceedings of the 15th International Conference on Domain Decomposition Methods",
PAGES = "639--646",
PUBLISHER = "Springer, Lecture Notes in Computational Science and Engineering (LNCSE).",
NOTE = "",
URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
YEAR = "2003"
}
@INPROCEEDINGS{kt2003,
AUTHOR = "Deepak V. Kulkarni and Daniel A. Tortorelli",
TITLE = "A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems",
BOOKTITLE = "Proceedings of the 15th International Conference on Domain Decomposition Methods",
PAGES = "615--622",
PUBLISHER = "Springer, Lecture Notes in Computational Science and Engineering (LNCSE).",
NOTE = "",
URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
YEAR = "2003"
}
@INPROCEEDINGS{krw2003,
AUTHOR = "Axel Klawonn and Oliver Rheinbach and Olof B. Widlund",
TITLE = "Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 3D",
BOOKTITLE = "Proceedings of the 15th International Conference on Domain Decomposition Methods",
PAGES = "361--368",
PUBLISHER = "Springer, Lecture Notes in Computational Science and Engineering (LNCSE).",
NOTE = "",
URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
YEAR = "2003"
}
@INPROCEEDINGS{hc2003,
AUTHOR = "Feng-Nan Hwang and Xiao-Chuan Cai",
TITLE = "Improving Robustness and Parallel Scalability of {Newton's} Method Through Nonlinear Preconditioning",
BOOKTITLE = "Proceedings of the 15th International Conference on Domain Decomposition Methods",
PAGES = "201--208",
PUBLISHER = "Springer, Lecture Notes in Computational Science and Engineering (LNCSE).",
NOTE = "",
URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
YEAR = "2003"
}
@INPROCEEDINGS{g2003,
AUTHOR = "P. Goldfeld",
TITLE = "Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and (Generalized) {Stokes} and Parallel Implementation",
BOOKTITLE = "Proceedings of the 14th International Conference on Domain Decomposition Methods",
PAGES = "209--216",
EDITOR = "I. Herrera and D. Keyes and O. Widlund and R. Yates",
PUBLISHER = "National Autonomous University of Mexico (UNAM)",
NOTE = "",
URL = "http://www.ddm.org/DD14",
YEAR = "2003"
}
@INPROCEEDINGS{dhv2003,
AUTHOR = "Zdenek Dostal and David Horak and Oldrich Vlach",
TITLE = "Toward scalable FETI algorithm for variational inequalities with applications to composites",
BOOKTITLE = "Proceedings of the 14th International Conference on Domain Decomposition Methods",
PAGES = "395--401",
EDITOR = "I. Herrera and D. Keyes and O. Widlund and R. Yates",
PUBLISHER = "National Autonomous University of Mexico (UNAM)",
NOTE = "",
URL = "http://www.ddm.org/DD14",
YEAR = "2003"
}
@INPROCEEDINGS{dhsv2002,
AUTHOR = "Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak",
TITLE = "Scalabilities of FETI for variational inequalities and contact shape optimization",
BOOKTITLE = "Proceedings of the 13th International Conference on Domain Decomposition Methods",
PAGES = "359--367",
EDITOR = "N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov",
PUBLISHER = "CIMNE, Barcelona, Spain",
NOTE = "",
URL = "http://www.ddm.org/DD13",
YEAR = "2002"
}
@INPROCEEDINGS{cky2002,
AUTHOR = "Xiao-Chuan Cai and David E. Keyes and David P. Young",
TITLE = "A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked Duct Flows",
BOOKTITLE = "Proceedings of the 13th International Conference on Domain Decomposition Methods",
PAGES = "343--350",
EDITOR = "N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov",
PUBLISHER = "CIMNE, Barcelona, Spain",
NOTE = "",
URL = "http://www.ddm.org/DD13",
YEAR = "2002"
}
@CONFERENCE{li-etal:03,
AUTHOR = {Li, Z. and Lanteri S. and Saad, Y.},
TITLE = {Multiplicative-additive preconditioning combination for general sparse linear systems},
BOOKTITLE = {2003 International Conference on Preconditioning Techniques for Large Sparse Matrix Problems in Scientific and Industrial Applications},
ADDRESS = {Napa, California, USA},
DATE = {october 27-29},
YEAR = {2003}No htmlformatsConference found for entry conference No fieldlistConference found for entry conference
}
@article{bashir2008hessian,
title = {Hessian-based model reduction for large-scale systems with initial-condition inputs},
author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, J.},
journal = {International journal for numerical methods in engineering},
volume = {73},
number = {6},
pages = {844--868},
year = {2008},
publisher = {Wiley Online Library}
}
@article{bashir2007hessian,
title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems},
author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, K.},
journal = {Computational Science--ICCS 2007},
pages = {1010--1017},
year = {2007},
publisher = {Springer}
}
@article{akcelik2011fast,
title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear inverse problems based on low-rank partial {H}essian approximations},
author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Wilcox, L.},
journal = {SIAM Journal on Scientific Computing},
volume = {33},
number = {1},
year = {2011},
}
@inproceedings{ff2003,
author = "Abul K. M. Fahimuddin and Heike Fassbender",
title = "Model Reduction for Large Scale Applications in Microsystem Technology",
booktitle = "Proceedings of the 2004 SIAM Parallel Processing Conference",
YEAR = "2003"
}
@inproceedings{d2b2004,
author = "Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost",
title = "Parallel Computation of a Fully Implicit Finite Volume Method Using Different Ordering Strategies",
booktitle = "Proceedings of AIAA Conference, Reno, Nevada",
YEAR = "2004"
}
@inproceedings{d2v2005,
author = "Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili",
title = "A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid Flow Equations",
booktitle = "The 13th Annual Conference on Computational Fluid Dynamics",
YEAR = "2005"
}
@inproceedings{dvs2006,
author = "Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider",
title = "The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit Mixed Convection Equations",
booktitle = " The 44th AIAA Aerospace Sciences Meeting and Exhibit",
YEAR = "2006"
}
@Article{dsv2006,
author = "Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili",
title = "Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid Flow Equations",
journal = "Computational Fluid Dynamics",
year = "2006",
volume = 15,
number = 1
}
@Article{Lahaye03,
author = "Lahaye, D. and Vandewalle, S. and Hameyer, K.",
title = "An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems",
journal = "J. Comput. Appl. Math.",
year = "2004",
pages = "267--275",
volume = 168
}
@techreport{brmn,
title = "Faster {PDE}-based Simulations Using Robust Composite Linear Solvers",
author = "S. Bhowmick and P. Raghavan and L. McInnes and B. Norris",
year = 2002,
type = "Technical Report",
institution = {ANL},
number = "ANL/MCS-P993-0902",
note = "To appear in Future Generation Computer Systems"
}
@inproceedings{mnbr,
author = "L. McInnes and B. Norris and S. Bhowmick and P. Raghavan",
title = "Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} Algorithms",
booktitle = "Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics",
YEAR = "2003",
}
@inproceedings{bmnr,
author = "S. Bhowmick and L. McInnes and B. Norris and P. Raghavan",
title = "The Role of Multi-Method Linear Solvers in {PDE}-based Simulations",
booktitle = "Proceedings of the 2003 International Conference on Computational Science and its Applications, Lecture notes in Computer Science 2677",
editor = "V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer",
pages = "828--839",
YEAR = "2003",
}
@Article{ph03,
author = "M. Pernice and R. D. Hornung",
title = "Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids",
journal = "Computing and Visualization in Science",
year = "2003",
Lab = {LANL}
}

@article{Adams-02,
Author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S},
Journal = {J. Comp. Phys.},
Number = {2},
Pages = {593-610},
Title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel},
Volume = {188},
Year = {2003}
}
@inproceedings{adams2001distributed,
title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid smoothers},
author = {Adams, M.F.},
booktitle = {Supercomputing, ACM/IEEE 2001 Conference},
pages = {14--14},
year = {2001},
organization = {IEEE}
}
@PhdThesis{Els01,
author = {Ulrich Elsner},
title = {Static and Dynamic Graph Partitioning. A comparative study of existing algorithms},
school = {Technical University Chemnitz},
year = 2002,
publisher = {Logos Verlag, Berlin},
ISBN = {3-89722-923-4},
annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare different graph partitioning algorithms} No htmlformatsPhdthesis found for entry phdthesis No fieldlistPhdthesis found for entry phdthesis
}
@techreport{ckk02,
title = "Pseudo-Transient Continuation and Differential-Algebraic Equations",
author = "Todd S. Coffey and C. T. Kelley and David E. Keyes",
year = 2002,
type = "Technical Report",
institution = {ODU},
url = "http://www.math.odu.edu/\~{ }keyes",
note = "Submitted to the special issue of the SIAM Journal of Scientific Computing dedicated to papers from the 2002 Copper Mountain Conference on Iterative Methods"
}
@Article{gpw2002,
title = "Balancing Neumann-Neumann Preconditioners for Mixed Approximations of Heterogeneous Problems in Linear Elasticity",
author = "Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund",
year = 2003,
pages = "283--324",
volume = 95,
url = "http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf",
journal = "Numerische Mathematik"
}
@Article{dh1,
title = "Scalability and FETI based algorithm for large discretized variational inequalities",
author = "Z Dostal and D Horak",
year = 2003,
pages = "347--357",
volume = 61,
url = "http://portal.acm.org/citation.cfm?id=770222.770239",
journal = "Mathematics and Computers in Simulation"
}
@inproceedings{dhsv1,
author = "Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak",
url = "http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf",
title = "36 Scalabilities of FETI for Variational Inequalities and Contact Shape Optimization",
booktitle = "Proceedings of the 13th International Conference on Domain Decomposition Methods",
editor = " N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. Kuznetsov"
}
@Article{Lahaye02,
author = "Domenico Lahaye and S. Vandewalle and K. Hameyer",
title = "An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems",
journal = "IEEEMAGN",
year = "2002",
volume = "38",
number = "2",
pages = "413-416"
}
@article{ckm01,
author = "X.-C. Cai and D. E. Keyes and L. Marcinkowski",
url = "http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps",
title = "Nonlinear additive {Schwarz} preconditioners and applications in computational fluid dynamics",
journal = "International Journal of Numerical Methods in Fluid Mechanics",
year = 2002,
volume = 40,
pages = "1463--1470"
}
@inproceedings{cky01,
author = "X.-C. Cai and D. E. Keyes and D. P. Young",
url = "http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps",
title = "A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked duct flow",
booktitle = "Proceedings of the 13th International Conference on Domain Decomposition Methods",
editor = " N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. Kuznetsov",
year = 2002
}
@article{ck02,
author = "X.-C. Cai and D. E. Keyes",
url = "http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps",
title = "Nonlinearly preconditioned inexact {Newton} algorithms",
journal = "SIAM J. Sci. Comput.",
year = "2002",
pages = "183--200",
volume = "24"
}
@article{c04,
author = "Feng-Nan Hwang and X.-C. Cai",
url = "http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf",
title = "A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm for incompressible {Navier-Stokes} equations",
journal = "Journal of Computational Physics",
year = 2005,
volume = 204,
pages = "666--691"
}
@article{hc06,
author = "Feng-Nan Hwang and X.-C. Cai",
url = "http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf",
title = "A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} Algorithms",
journal = "Computer Methods in Applied Mechanics and Engineering",
year = 2006,
volume = 196,
pages = "1603--1611"
}
@InProceedings{Adams-01,
author = {Mark F. Adams},
title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid Smoothers},
booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing},
address = {Denver, Colorado},
month = {November},
year = {2001}
}
@BOOK{1dl,
AUTHOR = "Domenico Lahaye",
TITLE = "Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field Computations",
YEAR = "2001",
PUBLISHER = "Katholieke Universiteit Leuven",
NOTES = "Thesis"
}

@article{Adams-00,
Author = {Adams, M.~F.},
Journal = {International Journal for Numerical Methods in Engineering},
Number = {8},
Pages = {1241-1262},
Title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large Deformation Elasticity and Plasticity},
Volume = {48},
Year = {2000}
}
@article{adams2002evaluation,
Author = {Adams, M.~F.},
Journal = {International Journal for Numerical Methods in Engineering},
Number = {1},
Pages = {519-534},
Title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element Problems in Solid Mechanics},
Volume = {55},
Year = {2002}
}
@Article{Lahaye00,
author = "Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.",
title = "Algebraic Multigrid for Complex Symmetric Systems",
journal = "IEEEMAGN",
year = "2000",
volume = "36",
number = "4",
pages = "1535--1538",
}

@InProceedings{Adams-99c,
author = {Mark F. Adams and J. Demmel},
title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured Finite Element Problems},
booktitle = {Proceedings of SC99: High Performance Networking and Computing},
address = {Portland, Oregon},
month = {November},
year = {1999}
}
@Article{chan95,
author = "T. Chan and B. Smith and J. Zou",
title = "Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse Grids",
journal = "Numer. Math.",
year = "1995",
volume = "73",
pages = "149--167"
}
@TechReport{Adams-CSD-98-993,
pages = "11",
year = "1998",
type = "Technical Report",
number = "CSD-98-993",
institution = "University of California, Berkeley",
title = "A Parallel Maximal Independent Set Algorithm",
bibdate = "March 11, 1998",
author = "Mark F. Adams and James Demmel",
abstract = "The parallel construction of maximal independent sets is a useful building block for many algorithms in the computational sciences, including graph coloring and multigrid coarse grid creation on unstructured meshes. We present an efficient asynchronous maximal independent set algorithm for use on parallel computers, for ``well partitioned'' graphs, that arise from finite element (FE) models. For appropriately partitioned bounded degree graphs, it is shown that the running time of our algorithm under the P-RAM computational model is of $O(1)$, which is an improvement over the previous best P-RAM complexity for this class of graphs. We present numerical experiments on an IBM SP, that confirm our P-RAM complexity model is indicative of the performance one can expect with practical partitions on graphs from FE problems.",
month = mar # " 11,",
}
@TechReport{k676,
year = "1994",
type = "Technical Report",
number = "TR1994-676",
institution = "New York University",
title = "An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty Term",
author = "Axel Klawonn",
url = "http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf"
}
@BOOK{ak1,
AUTHOR = "Axel Klawonn",
TITLE = "Preconditioners for Indefinite Problems",
YEAR = "1995",
PUBLISHER = "Westfalishen Wilhelms-Universitat Munster",
url = "http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf",
NOTES = "Thesis"
}

@TechReport{KnepleyKarpeev05,
pages = {41},
year = {2005},
type = {Technical Report},
number = {ANL/MCS-P1295-1005},
institution = {Argonne National Laboratory},
title = {Flexible Representation of Computational Meshes},
author = {Matthew G. Knepley and Dmitry A. Karpeev},
abstract = "",
url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf},
note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}},
month = {October}
}

@TechReport{KnepleyKarpeev07A,
pages = "14",
year = "2007",
type = "Technical Report",
number = "ANL/MCS-P1455-0907",
institution = "Argonne National Laboratory",
title = "Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution",
author = "Matthew G. Knepley and Dmitry A. Karpeev",
abstract = "",
url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf",
note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}},
month = "February"
}

@article{KnepleyKarpeev09,
author = {Matthew G. Knepley and Dmitry A. Karpeev},
title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution},
journal = {Scientific Programming},
volume = {17},
number = {3},
pages = {215--230},
year = {2009},
doi = {10.3233/SPR-2009-0249},
url = {http://arxiv.org/abs/0908.4427},
note = {\url{http://arxiv.org/abs/0908.4427}}
}
@article {biezuner2012computing, author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of Sublinear Supersolutions}, journal = {Journal of Scientific Computing}, publisher = {Springer Netherlands}, issn = {0885-7474}, keyword = {Mathematics and Statistics}, pages = {180--201}, volume = 52, issue = 1, year = 2012, url = {http://dx.doi.org/10.1007/s10915-011-9540-0}, doi = {10.1007/s10915-011-9540-0} }

Books

@article{
verleyeuser,
title = {{User friendly permeability predicting software for technical textiles}},
author = {Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and Roose, D.},
journal = {status: published},
issn = {1560-6074},
publisher = {Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}
}
@BOOK{pacheco,
AUTHOR = "Peter Pacheco",
TITLE = "Parallel Programming with MPI",
YEAR = "1997",
PUBLISHER = "Morgan-Kaufmann",
note = "Devotes a couple of sections to PETSc"
}
@BOOK{1sbg,
AUTHOR = "Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp",
TITLE = "Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial Differential Equations",
YEAR = "1996",
PUBLISHER = "Cambridge University Press",
url = "http://www.mcs.anl.gov/~bsmith/ddbook.html"
}


@misc{petsc-fem:homepage,
title = "{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program",
author = "M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and G. Rodriguez and G. Filippini",
howpublished = "\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}"
}
@misc{petsc4py-web-page,
author = {Lisandro Dalcin},
title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries},
howpublished = {\url{http://code.google.com/p/petsc4py/}},
note = {http://code.google.com/p/petsc4py/}
}

@article{libMeshPaper06,
author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey},
title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening Simulations}},
journal = {Engineering with Computers},
volume = {22},
number = {3--4},
pages = {237--254},
year = {2006},
note = {\url{http://dx.doi.org/10.1007/s00366-006-0049-3}}
}

@misc{sisiphus:homepage,
title = "{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, High-Resolution, Unstructured Simulations",
author = "T. {Tautges et al.}",
howpublished = "\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}"
}

@misc{pflotran:homepage,
title = "{PFLOTRAN} project",
author = "P. {Lichtner et al.}",
howpublished = "\url{http://ees.lanl.gov/pflotran/}"
}

@misc{pism:homepage,
title = "{PISM}: A Parallel Ice Sheet Model",
author = "E. {Bueler et al.}",
howpublished = "\url{http://pism-docs.org}"
}
@misc{dohp:homepage,
title = "Dohp: Dual order $hp$-finite elements",
author = "J. Brown",
howpublished = "\url{http://dohp.org}"
}

@article{McCourtRognlienEtAl12,
title = "Improving parallel scalability for edge plasma transport simulations with neutral gas species",
author = "M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang",
journal = "Computational Science and Discovery",
year = "2012",
volume = "5",
number = "014012",
doi = "10.1088/1749-4699/5/1/014012",
note = "Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 2011)"
}

@misc{petclaw-github,
title = {Pet{C}law Software},
author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia},
year = {2011},
howpublished = {\url{https://github.com/pyclaw/pyclaw}}
}
@misc{pyclaw-web-page,
author = {Kyle T. Mandli and David I. Ketcheson and others},
title = {{PyClaw} software},
howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}},
url = {http://clawpack.github.io/doc/pyclaw/},
year = {2012}
}
@article{ketcheson2011highorder,
title = {High-order wave propagation algorithms for general hyperbolic systems},
author = {Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.},
year = {2011},
note = {submitted}
}

@article{biros2005pln1,
title = {{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained optimization. Part I: The {Krylov-Schur} solver}},
author = {Biros, G. and Ghattas, O.},
journal = {SIAM Journal on Scientific Computing},
volume = {27},
number = {2},
pages = {687--713},
year = {2005},
publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}
}
@article{biros2005pln2,
title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained optimization. Part {II}: The {Lagrange Newton} solver, and its application to optimal control of steady viscous flows},
author = {Biros, G. and Ghattas, O.},
journal = {SIAM Journal on Scientific Computing},
volume = {27},
number = {2},
pages = {714--739},
year = {2005},
publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}
}
@misc{issm:homepage,
title = {{I}ce {S}heet {S}ystem {M}odel},
author = {Eric Larour and Mathieu Morlighem and Helene Seroussi},
year = {2010},
note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}
}
@article{morlighem2010spatial,
title = {Spatial patterns of basal drag inferred using control methods from a full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est {A}ntarctica},
author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and Aubry, D.},
journal = {Geophysical Research Letters},
volume = {37},
number = {14},
pages = {L14502},
year = {2010},
publisher = {American Geophysical Union}
}
@article{Jardin2012plasmas,
title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics of tokamak plasmas},
author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen},
journal = {Computational Science \& Discovery},
volume = {5},
number = {1},
url = "http://stacks.iop.org/1749-4699/5/014002",
year = {2012},
}

@techreport{cmz2012,
title = "Analysis and Practical Use of Flexible {BiCGStab}",
author = "Jie Chen and Lois Curfman McInnes and Hong Zhang",
year = 2012,
type = "Preprint",
note = "submitted to {SIAM Journal on Scientific Computing}",
number = "ANL/MCS-P3039-0912",
institution = "Argonne National Laboratory"
}

@article{KnepleyBrownRuppSmith13,
author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.},
title = {Achieving High Performance with Unified Residual Evaluation},
journal = {ArXiv e-prints},
eprint = {1309.1204},
archivePrefix = "arXiv",
primaryClass = "cs.MS",
keywords = {Computer Science - Mathematical Software, Computer Science - Computational Engineering, Finance, and Science},
year = 2013,
month = sep,
adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@book{FEniCSBook,
title = {Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
editor = {Anders Logg, Kent-Andre Mardal, Garth Wells},
publisher = {Springer},
isbn = {978-3-642-23098-1},
year = {2012}
}

@ARTICLE{DemidovAhnertRuppGottschling12,
author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.},
title = "{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1212.6326},
primaryClass = "cs.MS",
keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Computational Physics},
year = 2012,
month = dec,
adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@INPROCEEDINGS{ViennaCL,
author = {Rupp, K. and Rudolf, F. and Weinbub, J.},
title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}},
booktitle = {Intl.~Workshop on GPUs and Scientific Applications},
year = {2010},
pages = {51-56},
}
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