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% petsc_uses = {KSP, SNES, TS, TAO},
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% There are some additional historical comments below which may be of interest,
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@Misc{ semver-webpage,
author = {{Semantic Versioning 2.0.0}},
note = {\url{https://semver.org}}
}
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title = {{OpenBLAS}},
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@Misc{ openacc-website,
title = {{OpenACC}},
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@Misc{ bueler2020petsc,
title = {{PETSc} for Partial Differential Equations: Numerical Solutions in {C} and {P}ython},
author = {Bueler, Ed},
year = {2020},
publisher = {SIAM},
petsc_uses = {KSP}
}
@TechReport{ petscforgpuexascale,
title = {Toward Performance-Portable {PETSc} for {GPU}-based Exascale Systems},
author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener
and Matthew Knepley and Scott E. Kruger and Hannah~Morgan and Todd Munson and Karl
Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang},
institution = {Argonne National Laboratory},
number = {ANL/MCS-P9401-1020},
note = {\url{https://arxiv.org/abs/2011.00715}},
year = {2020},
petsc_uses = {KSP}
}
@Article{ mills2021,
title = {Toward performance-portable {PETS}c for {GPU}-based exascale systems},
journal = {Parallel Computing},
volume = {108},
pages = {102831},
year = {2021},
issn = {0167-8191},
doi = {https://doi.org/10.1016/j.parco.2021.102831},
url = {https://www.sciencedirect.com/science/article/pii/S016781912100079X},
author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener
and Matthew Knepley and Scott E. Kruger and Hannah Morgan and Todd Munson and Karl
Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang}
}
@Article{ mills2024,
title = {{PETSc/TAO} Developments for Early Exascale Systems},
author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and
Jacob Faibussowitsch and Tobin Isaac and Matthew G. Knepley and Todd Munson and
Hansul Suh and Stefano Zampini and Hong Zhang and Junchao Zhang},
journal = {International Journal of High Performance Computing Applications},
url = {http://arxiv.org/abs/2401.05868},
doi = {https://doi.org/10.1177/10943420241303710},
year = {2024}
}
@Article{ rupp:2016:pis:2988256.2907944,
author = {Karl Rupp and Josef Weinbub and Ansgar J\"{u}ngel and Tibor Grasser},
title = {Pipelined Iterative Solvers with Kernel Fusion for Graphics Processing Units},
journal = {ACM Trans. Math. Softw.},
issue_date = {September 2016},
volume = {43},
number = {2},
month = aug,
year = {2016},
issn = {0098-3500},
pages = {11:1--11:27},
articleno = {11},
numpages = {27},
doi = {10.1145/2907944},
acmid = {2907944},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {BiCGStab method, CUDA, GMRES method, GPU, Iterative solvers, OpenCL, conjugate
gradient method},
petsc_uses = {KSP}
}
@Article{ dalcin2011parallel,
title = {Parallel distributed computing using python},
author = {Dalcin, Lisandro D and Paz, Rodrigo R and Kler, Pablo A and Cosimo, Alejandro},
journal = {Advances in Water Resources},
volume = {34},
number = {9},
pages = {1124--1139},
year = {2011},
publisher = {Elsevier},
petsc_uses = {KSP}
}
@Article{ mendezpongaortiz2018,
title = {Diffusive molecular dynamics simulations of lithiation of silicon nanopillars},
author = {JP Mendez and M Ponga and M Ortiz},
journal = {Journal of the Mechanics and Physics of Solids},
year = {2018},
petsc_uses = {KSP}
}
@TechReport{ morgan2020evaluation,
title = {Evaluation of {PETS}c on a Heterogeneous Architecture, the {OLCF} {S}ummit
System: Part 1: Vector Node Performance},
author = {Morgan, Hannah Mairs and Mills, Richard Tran and Smith, Barry},
year = {2020},
institution = {Argonne National Laboratory},
url = {https://publications.anl.gov/anlpubs/2020/04/159190.pdf},
petsc_uses = {KSP}
}
@TechReport{ pdeconstrainedspectraladjoints,
title = {PDE constrained optimization, error estimation and control with spectral elements
using PETSc and TAO},
author = {Oana Marin and Emil Constantinescu and Barry Smith},
type = {Preprint},
number = {ANL/MCS-P9031-1117},
institution = {ANL},
month = nov,
year = {2017},
petsc_uses = {KSP}
}
@InProceedings{ asc2013,
author = {S. Abhyankar and B. F. Smith and E. Constantinescu},
title = {Evaluation of overlapping restricted additive {S}chwarz preconditioning for
parallel solution of very large power flow problems},
booktitle = {HiPCNA-PG’13},
year = {2013},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = jan,
year = {2014},
petsc_uses = {KSP}
}
@TechReport{ abhyankaretal2018,
author = {Shrirang Abhyankar and Jed Brown and Emil M. Constantinescu and Debojyoti Ghosh
and Barry F. Smith and Hong Zhang},
title = {{PETSc/TS}: {A} Modern Scalable {ODE/DAE} Solver Library},
journal = {arXiv e-preprints},
eprint = {1806.01437},
archiveprefix = {arXiv},
year = {2018},
petsc_uses = {KSP}
}
@Article{ zhang2021cams,
title = {Optimal checkpointing for adjoint multistage time-stepping schemes},
author = {Hong Zhang and Emil M. Constantinescu},
journal = {arXiv e-preprints},
eprint = {2202.11890},
archiveprefix = {arXiv},
year = {2022},
petsc_uses = {KSP}
}
@InProceedings{ zhangconstantinescu2021b,
title = {Revolve-based adjoint checkpointing for multistage time integration},
author = {Hong Zhang and Emil M. Constantinescu},
booktitle = {Proceedings of the International Conference on Computational Science (ICCS)},
month = jun,
year = {2021},
petsc_uses = {KSP}
}
@Article{ zhang2022tsadjoint,
author = {Zhang, Hong and Constantinescu, Emil M. and Smith, Barry F.},
title = {{PETSc TSAdjoint: A Discrete Adjoint ODE Solver for First-Order and Second-Order
Sensitivity Analysis}},
journal = {SIAM Journal on Scientific Computing},
volume = {44},
number = {1},
pages = {C1-C24},
year = {2022},
doi = {10.1137/21M140078X},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1088/0957-4484/19/28/285717},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1063/1.2894587},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1016/j.jmmm.2007.11.025},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.3379/msjmag.32.50},
petsc_uses = {KSP}
}
@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},
doi = {10.1002/pssa.200777359},
petsc_uses = {KSP}
}
@InProceedings{ sg2007,
author = {Simon Greaves},
title = {Micromagnetic Simulations of Magnetic Recording Media},
booktitle = {High Performance Computing on Vector Systems 2007},
doi = {10.1007/978-3-540-74384-2_17},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/TMAG.2007.892867},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/TMAG.2007.893843},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1002/9780470022184.hmm203},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/TMAG.2007.893122},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/TMAG.2006.879430},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/TMAG.2006.878414},
petsc_uses = {KSP}
}
@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/},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/HPDC.2006.1652135},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/TMAG.2005.855288},
petsc_uses = {KSP}
}
@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},
doi = {10.1103/PhysRevB.71.144407},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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--},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ scholz-suess2,
author = {W. Scholz and D. Suess and T. Schrefl 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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@PhDThesis{ scholz2,
author = {W. Scholz},
title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures},
school = {Vienna University of Technology, Vienna, Austria},
year = {2003},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
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@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-},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
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@Article{ saut,
author = { Olivier Saut},
title = {Bidimensional Study of the {M}axwell-{B}loch 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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Biology -- Medical
% LiteralHTML:
@InBook{ khanallorenziayachepennec2016,
title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model
of Brain Deformation in {Alzheimer's} Disease},
booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing},
author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec},
editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol
Miller},
pages = {167--176},
isbn = {978-3-319-28329-6},
doi = {10.1007/978-3-319-28329-6_15},
publisher = {Springer International Publishing},
year = {2016},
petsc_uses = {KSP}
}
@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 = feb,
year = {2008},
doi = {10.1007/s11517-008-0316-0},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2001},
petsc_uses = {KSP}
}
@Article{ barker2010two,
title = {Two-level {N}ewton and hybrid {S}chwarz 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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ mirams2013,
author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan
and Yi Cui and Gary R Mirams},
title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data
to predict {QT} interval changes in the rabbit ventricular wedge},
journal = {Journal of pharmacological and toxicological methods},
volume = {68},
number = {1},
pages = {88--96},
year = {2013},
doi = {10.1016/j.vascn.2013.04.004},
petsc_uses = {KSP}
}
% LiteralHTML:
|
% LiteralHTML: 
% LiteralHTML: 
% LiteralHTML:
% LiteralHTML:Treating fractures of the hip and spine is a major medical cost.
% LiteralHTML:Understanding bone mechanical properties and how they may lead to
% LiteralHTML:fractures is thus an important medical research activity. PETSc and
% LiteralHTML:Prometheus have been used for extremely large scale finite element
% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a
% LiteralHTML:team of doctors and computational scientists. This computation was
% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably
% LiteralHTML:with over 4000 processors.
% LiteralHTML:
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML:
|
% LiteralHTML: 
% LiteralHTML: 
% LiteralHTML:
% LiteralHTML:
% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the
% LiteralHTML: heart; they are the cause of the majority of sudden cardiac
% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving
% LiteralHTML: through the heart. PETSc has been used by several research groups to
% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more
% LiteralHTML: fully understand the developments of arrhthmias.
% LiteralHTML:
@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 {L}agrangian 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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2005},
petsc_uses = {KSP}
}
@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 = {2002},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InProceedings{ spbv2003,
author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer 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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = jan,
year = {2006},
issn = {0167-8191},
pages = {67--83},
numpages = {17},
doi = {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},
petsc_uses = {KSP}
}
@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 = {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, pipe and filters, parallel computing, multicore processors},
petsc_uses = {KSP}
}
@InProceedings{ eth_biwi_00721,
author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and G.
Székely},
title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using
a {S}chur Complement Preconditioner},
booktitle = {Euro-Par 2009 Parallel Processing},
year = {2009},
month = aug,
pages = {747-759},
volume = {5704},
editor = {H. Sips and D. Epema 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},
petsc_uses = {KSP}
}
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@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},
petsc_uses = {KSP}
}
@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.},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 {B}righam and {W}omen's
hospital},
journal = {Medical Image Analysis},
url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf},
year = {2005},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 {B}ayesian inversion for three-dimensional dental {X}-ray imaging},
journal = {IEEE Transactions on Medical Imaging},
volume = {25},
number = {2},
month = feb,
year = {2006},
pages = {218--228},
petsc_uses = {KSP}
}
@InProceedings{ knepleybardhan2015,
title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics},
author = {Matthew G. Knepley and Jaydeep P. Bardhan},
booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \&
Exposition},
volume = {9},
pages = {V009T12A04},
doi = {10.1115/IMECE2015-53579},
year = {2015},
petsc_uses = {KSP}
}
@InProceedings{ bardhanknepley2015,
title = {Multiscale models and approximation algorithms for protein electrostatics},
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII},
volume = {61},
pages = {163--174},
url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf},
doi = {10.2495/BEM380131},
publisher = {WIT Press},
year = {2015},
petsc_uses = {KSP}
}
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@InProceedings{ adamsbrennanknepleywang2022,
title = {{Landau} collision operator in the {CUDA} programming model applied to thermal
quench plasmas},
author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang},
booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference
(IPDPS '22)},
doi = {10.1109/IPDPS53621.2022.00020},
year = {2022},
petsc_uses = {DMPlex}
}
@Misc{ adamsknepleybrennan2021,
title = {Runaway Electron Generation with High-Performance, Structure Preserving
Discretization of {F}okker--{P}lank--{L}andau},
author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan},
year = {2021},
petsc_uses = {KSP}
}
@Article{ adamshirvijokiknepleybrownisaacmills2017,
title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging
Architectures},
author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin
Isaac and Richard Mills},
journal = {SIAM Journal on Scientific Computing},
volume = {39},
number = {6},
pages = {C452--C465},
doi = {10.1137/17M1118828},
eprint = {1702.08880},
year = {2017},
petsc_uses = {KSP}
}
@Article{ pusztayknepleyadams2022,
title = {Conservative Projection Between {FEM} and Particle Bases},
author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams},
journal = {SIAM Journal on Scientific Computing},
volume = {44},
number = {4},
pages = {C310--C319},
doi = {10.1137/21M145407},
year = {2022}
}
@Article{ hirvijoki2017,
author = {Eero Hirvijoki and Mark F. Adams},
title = {Conservative discretization of the {Landau} collision integral},
journal = {Physics of Plasmas},
volume = {24},
number = {3},
pages = {032121},
doi = {10.1063/1.4979122},
year = {2017},
petsc_uses = {KSP}
}
@Article{ mollenadamsknepleyhagerchang2021,
title = {Implementation of higher-order velocity mapping between marker particles and grid
in the particle-in-cell code {XGC}},
author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C.
S. Chang},
journal = {Journal of Plasma Physics},
volume = {87},
number = {2},
pages = {905870229},
eprint = {2012.11764},
doi = {10.1017/S0022377821000441},
year = {2021},
petsc_uses = {KSP}
}
@Article{ lsmh2014,
author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander},
title = {Comparison of particle trajectories and collision operators for collisional
transport in nonaxisymmetric plasmas},
journal = { Physics of Plasmas},
volume = {21},
year = {2014},
petsc_uses = {KSP}
}
@Article{ lpcep2014,
author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai},
title = {Radially global delta-f computation of neoclassical phenomena in a tokamak
pedestal},
journal = {Plasma Physics and Controlled Fusion},
volume = {56},
year = {2014},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ carlssoncary09,
author = {Johan Carlsson, John R. Cary},
title = {The hypersecant {J}acobian approximation for quasi-{N}ewton solves of sparse
nonlinear systems},
journal = {arXiv},
year = {2009},
note = {http://arxiv.org/abs/0905.1054},
url = {http://arxiv.org/pdf/0905.1054v1},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ zhu2006,
author = {P. Zhu and A. Bhattacharjee and K. Germaschewski},
title = {Intermediate nonlinear evolution of the {P}arker instability: Formation of
convection-induced discontinuities and absence of finite-time singularities},
journal = {Phys. Rev. Lett.},
volume = {96},
number = {065001},
year = {2006},
doi = {10.1103/PhysRevLett.96.065001},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ nlle2004,
author = {Y. Nishimura and Z.Lin and J.Lewandowski and S.Ethier},
title = {A finite element {P}oisson solver for gyrokinetic particle simulations in a global
field aligned mesh},
year = {2006},
journal = {J. Comput. Phys.},
volume = {214},
pages = {657},
lab = {PPPL},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
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@Article{ valerathomasgarciacastillo2019,
author = {Manuel Valera and Mary P. Thomas and Mariangel Garcia and Jose E. Castillo},
title = {Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear
Coastal Ocean Model},
journal = {Journal of Marine Science and Engineering},
volume = {7},
number = {6},
article-number= {185},
url = {https://www.mdpi.com/2077-1312/7/6/185},
issn = {2077-1312},
doi = {10.3390/jmse7060185},
year = {2019},
petsc_uses = {KSP}
}
@Article{ furuichimat2015,
title = {Implicit solution of the material transport in Stokes flow simulation: Toward
thermal convection simulation surrounded by free surface},
author = {Mikito Furuichi and Dave A May},
journal = {Computer Physics Communications},
volume = {192},
pages = {1--11},
year = {2015},
petsc_uses = {KSP}
}
@Article{ sharplesmoresivelicjadamecmay2016,
title = {Simulating faults and plate boundaries with a transversely isotropic plasticity
model},
author = {Wendy Sharples and Louis N Moresi and Mirko Velic and Margarete A Jadamec and
Dave A May},
journal = {Physics of the Earth and Planetary Interiors},
volume = {252},
pages = {77--90},
year = {2016},
petsc_uses = {KSP}
}
@Article{ spiegelmanmaywilson2016,
title = {On the solvability of incompressible {S}tokes with viscoplastic rheologies in
geodynamics},
author = {Marc Spiegelman and Dave A May and Cian R Wilson},
journal = {Geochemistry, Geophysics, Geosystems},
volume = {17},
number = {6},
pages = {2213--2238},
year = {2016},
petsc_uses = {KSP}
}
@Article{ buiteretal2016,
title = {Benchmarking numerical models of brittle thrust wedges},
author = {Susanne JH Buiter and Guido Schreurs and Markus Albertz and Taras V Gerya and
Boris Kaus and Walter Landry and Laetitia {Le Pourhiet} and Yury Mishin and David
L Egholm and Michele Cooke and Bertrand Maillot and Cedric Thieulot and Tony Crook
and Dave May and Pauline Souloumiac and Christopher Beaumont},
journal = {Journal of structural geology},
volume = {92},
pages = {140--177},
year = {2016},
petsc_uses = {KSP}
}
@Article{ afanasievboehmdrielkrischerrietmannmayknepleyfichtner2019,
title = {Modular and flexible spectral-element waveform modelling in two and three
dimensions},
author = {Michael Afanasiev and Christian Boehm and Martin van Driel and Lion Krischer and
Max Rietmann and Dave A. May and Matthew G. Knepley and Andreas Fichtner},
journal = {Geophysical Journal International},
volume = {216},
number = {3},
pages = {1675--1692},
doi = {10.1093/gji/ggy469},
year = {2019},
petsc_uses = {KSP}
}
@Article{ haplaknepleyafanasievboehmdrielkrischerfichtner2020,
title = {Fully Parallel Mesh {I/O} using {PETSc} {DMPlex} with an Application to Waveform
Modeling},
author = {Vaclav Hapla and Matthew G. Knepley and Michael Afanasiev and Christian Boehm and
Martin van Driel and Lion Krischer and Andreas Fichtner},
journal = {SIAM Journal on Scientific Computing},
volume = {43},
number = {2},
pages = {C127--C153},
eprint = {http://arxiv.org/abs/2004.08729},
doi = {10.1137/20M1332748},
year = {2021},
petsc_uses = {KSP}
}
@Article{ parsani2021,
title = {High-order accurate entropy-stable discontinuous collocated {G}alerkin methods with
the summation-by-parts property for compressible {CFD} frameworks: Scalable {SSDC}
algorithms and flow solver},
author = {Matteo Parsani and Radouan Boukharfane and Irving Reyna Nolasco and David C. {Del
Rey Fernández} and Stefano Zampini and Bilel Hadri and Lisandro Dalcin},
journal = {Journal of Computational Physics},
volume = {424},
pages = {109844},
issn = {0021-9991},
doi = {https://doi.org/10.1016/j.jcp.2020.109844},
url = {http://www.sciencedirect.com/science/article/pii/S0021999120306185},
year = {2021},
petsc_uses = {KSP}
}
@Article{ ambartsumyanbouakaramthanhghattaskeyesstadlerturkiyyahzampini2020,
title = {Hierarchical matrix approximations of {Hessians} arising in inverse problems
governed by {PDEs}},
author = {I. Ambartsumyan and W. Bouakaram and Than Bui-Thanh and Omar Ghattas and David
Keyes and Georg Stadler and George Turkiyyah and Stefano Zampini},
journal = {SIAM Journal of Scientific Computing},
volume = {42},
number = {5},
pages = {A3397--A3426},
year = {2020}
}
@Article{ zampinibouakaramturkiyyahkniokeyes2022,
title = {H2Opus: a distributed memory {multi-GPU} software for non-local operators},
author = {Stefano Zampini and W. Bouakaram and George Turkiyyah and O. Knio and David E.
Keyes},
journal = {Advances on Computational Mathematics},
note = {In press},
year = {2022}
}
@Article{ dassizampiniscacchi2022,
title = {Robust and scalable adaptive {BDDC} preconditioners for virtual element
discretizations of elliptic equations in mixed form},
author = {F. Dassi and Stefano Zampini and S. Scacchi},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {391},
pages = {114620},
year = {2022}
}
@Article{ youngoppenheimdimant2017,
author = {Matthew A. Young and Meers M. Oppenheim and Yakov S. Dimant},
title = {Hybrid simulations of coupled {F}arley-{B}uneman/gradient drift instabilities in the
equatorial E region ionosphere},
journal = {Journal of Geophysical Research: Space Physics},
volume = {122},
number = {5},
issn = {2169-9402},
doi = {10.1002/2017JA024161},
pages = {5768--5781},
year = {2017},
petsc_uses = {KSP}
}
@Article{ rioussetpatylillisfillingimenglandwithershale2013,
title = {Three-dimensional multifluid modeling of atmospheric electrodynamics in {M}ars'
dynamo region},
author = {Jeremy A Riousset and Carol S Paty and Robert J Lillis and Matthew O Fillingim
and Scott L England and Paul G Withers and John P M Hale},
journal = {Journal of Geophysical Research: Space Physics},
volume = {118},
number = {6},
pages = {3647--3659},
year = {2013},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
@Article{ chien2016representation,
title = {Representation of topography by partial steps using the immersed boundary method
in a vector vorticity equation model (VVM)},
author = {Chien, Mu-Hua and Wu, Chien-Ming},
journal = {Journal of Advances in Modeling Earth Systems},
year = {2016},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
@Article{ berger2015parallel,
title = {Parallel preconditioners for monolithic solution of shear bands},
author = {Berger-Vergiat, Luc and McAuliffe, Colin and Waisman, Haim},
journal = {Journal of Computational Physics},
year = {2015},
publisher = {Elsevier},
petsc_uses = {KSP}
}
@Article{ may2015496,
title = {A scalable, matrix-free multigrid preconditioner for finite element
discretizations of heterogeneous {S}tokes flow },
journal = {Computer Methods in Applied Mechanics and Engineering },
volume = {290},
number = {0},
pages = {496--523},
year = {2015},
issn = {0045-7825},
doi = {10.1016/j.cma.2015.03.014},
author = {D.A. May and J. Brown and L. {Le Pourhiet}},
petsc_uses = {KSP}
}
@Article{ isaacknepley2017,
title = {Support for Non-conformal Meshes in {PETSc}'s {DMPlex} Interface},
author = {Tobin Isaac and Matthew G. Knepley},
journal = {ArXiv e-prints},
eprint = {1508.02470},
year = {2017},
note = {\url{http://arxiv.org/abs/1508.02470}},
petsc_uses = {DMPlex}
}
@Article{ knepleylangegorman2017,
title = {Unstructured Overlapping Mesh Distribution in Parallel},
author = {Matthew G. Knepley and Michael Lange and Gerard J. Gorman},
journal = {ArXiv e-prints},
eprint = {1506.06194},
year = {2017},
note = {\url{http://arxiv.org/abs/1506.06194}},
petsc_uses = {DMPlex}
}
@Article{ langemitchellknepleygorman2015,
title = {Efficient mesh management in {Firedrake} using {PETSc-DMPlex}},
author = {Michael Lange and Lawrence Mitchell and Matthew G. Knepley and Gerard J. Gorman},
journal = {SIAM Journal on Scientific Computing},
volume = {38},
number = {5},
pages = {S143--S155},
eprint = {http://arxiv.org/abs/1506.07749},
doi = {10.1137/15M1026092},
year = {2016},
petsc_uses = {DMPlex}
}
@InProceedings{ langeknepleygorman2015,
title = {Flexible, Scalable Mesh and Data Management using {PETSc DMPlex}},
author = {Michael Lange and Matthew G. Knepley and Gerard J. Gorman},
booktitle = {Proceedings of the Exascale Applications and Software Conference},
month = apr,
url = {http://www.easc2015.ed.ac.uk/sites/default/files/attachments/EASC15Proceedings.pdf},
year = {2015},
petsc_uses = {DMPlex}
}
@InProceedings{ wallworkknepleybarralpiggott2022,
title = {Parallel Metric-Based Mesh Adaptation in {PETSc} using {ParMmg}},
author = {Joseph G. Wallwork and Matthew G. Knepley and Nicolas Barral and Matthew D.
Piggott},
booktitle = {SIAM International Meshing Roundtable Workshop 2022},
editor = {Trevor Robinson},
month = jan,
address = {Seattle, WA},
pages = {1--5},
url = {http://imr.sandia.gov/papers/imr31/2026_imr31RJ_Wallwork.pdf},
year = {2022},
petsc_uses = {DMPlex}
}
@InProceedings{ timalsinaknepley2023,
title = {Tetrahedralization of a Hexahedral Mesh},
author = {Aman Timalsina and Matthew G. Knepley},
booktitle = {SIAM International Meshing Roundtable Workshop 2023},
year = {2023},
petsc_uses = {DMPlex}
}
@Article{ farrellknepleywechsungmitchell2020,
title = {{PCPATCH}: software for the topological construction of multigrid relaxation
methods},
author = {Patrick E Farrell and Matthew G Knepley and Lawrence Mitchell and Florian
Wechsung},
journal = {ACM Transaction on Mathematical Software},
eprint = {http://arxiv.org/abs/1912.08516},
volume = {47},
number = {3},
pages = {1--22},
issn = {0098-3500},
doi = {10.1145/3445791},
publisher = {Association for Computing Machinery},
issue_date = {September 2021},
year = {2021},
petsc_uses = {KSP,DMPlex}
}
@Article{ laakmann2022augmented,
title = {An augmented Lagrangian preconditioner for the magnetohydrodynamics equations at high Reynolds and coupling numbers},
author = {Fabian Laakmann and Patrick E Farrell and Lawrence Mitchell},
journal = {SIAM Journal on Scientific Computing},
volume = {44},
number = {4},
pages = {B1018--B1044},
year = {2022}
}
@Article{ papadopoulosfarrellsurowiec2021,
title = {Computing multiple solutions of topology optimization problems},
author = {Papadopoulos, Ioannis PA and Farrell, Patrick E and Surowiec, Thomas M},
journal = {SIAM Journal on Scientific Computing},
volume = {43},
number = {3},
pages = {A1555--A1582},
year = {2021}
}
@Article{ jiangzhanghuschneiderzorinpanozzo2021,
title = {Bijective and coarse high-order tetrahedral meshes},
author = {Jiang, Zhongshi and Zhang, Ziyi and Hu, Yixin and Schneider, Teseo and Zorin, Denis and Panozzo, Daniele},
journal = {ACM Transactions on Graphics (TOG)},
volume = {40},
number = {4},
pages = {1--16},
year = {2021}
}
@Article{ abumaclachlanfarrell2023,
title = {Monolithic multigrid for implicit {Runge--Kutta} discretizations of incompressible fluid flow},
author = {Abu-Labdeh, Razan and MacLachlan, Scott and Farrell, Patrick E},
journal = {Journal of Computational Physics},
volume = {478},
pages = {111961},
year = {2023}
}
@Article{ farrellkirbymarchena2021,
title = {{Irksome}: Automating {Runge--Kutta} time-stepping for finite element methods},
author = {Farrell, Patrick E and Kirby, Robert C and Marchena-Menendez, Jorge},
journal = {ACM Transactions on Mathematical Software (TOMS)},
volume = {47},
number = {4},
pages = {1--26},
year = {2021}
}
@Article{ farrellgazca2020,
title = {An augmented Lagrangian preconditioner for implicitly constituted non-Newtonian incompressible flow},
author = {Farrell, Patrick E and Gazca-Orozco, Pablo Alexei},
journal = {SIAM Journal on Scientific Computing},
volume = {42},
number = {6},
pages = {B1329--B1349},
year = {2020}
}
@Article{ farrellmitchellscottwechsung2022,
title = {Robust multigrid methods for nearly incompressible elasticity using macro elements},
author = {Farrell, Patrick E and Mitchell, Lawrence and Scott, L Ridgway and Wechsung, Florian},
journal = {IMA Journal of Numerical Analysis},
volume = {42},
number = {4},
pages = {3306--3329},
year = {2022}
}
@Article{ shihstadlerwechsung2022,
title = {Robust multigrid techniques for augmented Lagrangian preconditioning of incompressible Stokes equations with extreme viscosity variations},
author = {Shih, Yu-hsuan and Stadler, Georg and Wechsung, Florian},
journal = {SIAM Journal on Scientific Computing},
volume = {45},
number = {3},
pages = {S27--S53},
year = {2022}
}
@Article{ adlerhehumaclachlanohm2022,
title = {Monolithic multigrid for a reduced-quadrature discretization of poroelasticity},
author = {Adler, James H and He, Yunhui and Hu, Xiaozhe and MacLachlan, Scott and Ohm, Peter},
journal = {SIAM Journal on Scientific Computing},
volume = {45},
number = {3},
pages = {S54--S81},
year = {2022}
}
@Article{ xiafarrellwechsung2021,
title = {Augmented Lagrangian preconditioners for the Oseen--Frank model of nematic and cholesteric liquid crystals},
author = {Xia, Jingmin and Farrell, Patrick E and Wechsung, Florian},
journal = {BIT Numerical Mathematics},
volume = {61},
pages = {607--644},
year = {2021}
}
@Article{ budisahukuchtamardalzikatanov2023,
title = {Algebraic multigrid methods for metric-perturbed coupled problems},
author = {Budisa, Ana and Hu, Xiaozhe and Kuchta, Miroslav and Mardal, Kent-Andre and Zikatanov, Ludmil Tomov},
journal = {arXiv preprint arXiv:2305.06073},
year = {2023}
}
@Article{ laakmannhufarrell2023,
title = {Structure-preserving and helicity-conserving finite element approximations and preconditioning for the Hall MHD equations},
author = {Laakmann, Fabian and Hu, Kaibo and Farrell, Patrick E},
journal = {Journal of Computational Physics},
volume = {492},
pages = {112410},
year = {2023}
}
@Article{ hongkrauskuchtalymberymardalrognes2022,
title = {Robust approximation of generalized Biot-Brinkman problems},
author = {Hong, Qingguo and Kraus, Johannes and Kuchta, Miroslav and Lymbery, Maria and Mardal, Kent-Andr{\'e} and Rognes, Marie E},
journal = {Journal of Scientific Computing},
volume = {93},
number = {3},
pages = {77},
year = {2022}
}
@Article{ boonkuchtamardalruiz2021,
title = {Robust preconditioners for perturbed saddle-point problems and conservative discretizations of {Biot's} equations utilizing total pressure},
author = {Boon, Wietse M and Kuchta, Miroslav and Mardal, Kent-Andre and Ruiz-Baier, Ricardo},
journal = {SIAM Journal on Scientific Computing},
volume = {43},
number = {4},
pages = {B961--B983},
year = {2021}
}
@Article{ papadopoulosfarrell2023,
title = {Preconditioners for computing multiple solutions in three-dimensional fluid topology optimization},
author = {Papadopoulos, Ioannis PA and Farrell, Patrick E},
journal = {SIAM Journal on Scientific Computing},
volume = {45},
number = {6},
pages = {B853--B883},
year = {2023}
}
@Article{ farrellhamdanmaclachlan2022,
title = {A new mixed finite-element method for H2 elliptic problems},
author = {Farrell, Patrick E and Hamdan, Abdalaziz and MacLachlan, Scott P},
journal = {Computers \& Mathematics with Applications},
volume = {128},
pages = {300--319},
year = {2022}
}
@Article{ harpertuminaro2023,
title = {Compression and Reduced Representation Techniques for Patch-Based Relaxation},
author = {Harper, Graham and Tuminaro, Ray},
journal = {arXiv preprint arXiv:2306.10025},
year = {2023}
}
@Article{ kirbykernell2021,
title = {Preconditioning mixed finite elements for tide models},
author = {Kirby, Robert C and Kernell, Tate},
journal = {Computers \& Mathematics with Applications},
volume = {82},
pages = {212--227},
year = {2021}
}
@Book{ xia2023,
title = {Computing and Analysing Energy Minimisation Problems in Liquid Crystals: Implementation Using Firedrake},
author = {Xia, Jingmin},
year = {2023},
publisher = {World Scientific}
}
@PhDThesis{ leveque2022,
title = {Preconditioned iterative methods for optimal control problems with time-dependent PDEs as constraints},
author = {Leveque, Santolo},
school = {The University of Edinburgh},
year = {2022}
}
@PhDThesis{ brubeck2022,
title = {Optimal-complexity and robust multigrid methods for high-order FEM},
author = {Pablo D. Brubeck},
school = {Oxford University},
year = {2022}
}
@Misc{ firedrakeproject,
title = {{The {F}iredrake project}},
author = {David A Ham and Firedrake Team},
url = {http://firedrakeproject.org},
year = {2022},
petsc_uses = {KSP}
}
@Article{ rathgeberhammitchelllangeluporinimcraeberceamarkallkelly2016,
title = {Firedrake: automating the finite element method by composing abstractions},
author = {Florian Rathgeber and David A Ham and Lawrence Mitchell and Michael Lange and
Fabio Luporini and Andrew TT McRae and Gheorghe-Teodor Bercea and Graham R Markall
and Paul HJ Kelly},
journal = {ACM Transactions on Mathematical Software (TOMS)},
volume = {43},
number = {3},
pages = {24},
year = {2016},
petsc_uses = {KSP}
}
@Article{ mitchellmuller2016,
title = {High level implementation of geometric multigrid solvers for finite element
problems: Applications in atmospheric modelling},
author = {Lawrence Mitchell and Eike Hermann M{\"u}ller},
journal = {Journal of Computational Physics},
volume = {327},
pages = {1--18},
year = {2016},
petsc_uses = {KSP}
}
@Article{ mcraeberceamitchellhamcotter2016,
title = {Automated generation and symbolic manipulation of tensor product finite
elements},
author = {Andrew TT McRae and Gheorghe-Teodor Bercea and Lawrence Mitchell and David A Ham
and Colin J Cotter},
journal = {SIAM Journal on Scientific Computing},
volume = {38},
number = {5},
pages = {S25--S47},
year = {2016},
petsc_uses = {KSP}
}
@Article{ berceamcraehammitchellrathgebernardiluporinikelly2016,
title = {A structure-exploiting numbering algorithm for finite elements on extruded
meshes, and its performance evaluation in {Firedrake}},
author = {Gheorghe-Teodor Bercea and Andrew TT McRae and David A Ham and Lawrence Mitchell
and Florian Rathgeber and L. Nardi and Fabio Luporini and Paul HJ Kelly},
journal = {Geoscientific Model Development},
volume = {9},
number = {10},
pages = {3803--3815},
doi = {10.5194/gmd-9-3803-2016},
year = {2016},
petsc_uses = {KSP}
}
@InProceedings{ markallrathgebermitchellloriantbertollihamkelly2013,
author = {Graham R. Markall and Florian Rathgeber and Lawrence Mitchell and Nicolas Loriant
and Carlo Bertolli and David A. Ham and Paul HJ Kelly},
editor = {Julian Martin Kunkel and Thomas Ludwig and Hans Werner Meuer},
title = {Performance-Portable Finite Element Assembly Using {PyOP2} and {FEniCS}},
booktitle = {Proceedings of 28th International Supercomputing Conference, ISC 2013},
publisher = {Springer Berlin Heidelberg},
pages = {279--289},
isbn = {978-3-642-38750-0},
doi = {10.1007/978-3-642-38750-0_21},
year = {2013},
petsc_uses = {KSP}
}
@Article{ kirbymitchell2017,
title = {Solver composition across the {PDE}/linear algebra barrier},
author = {Robert C Kirby and Lawrence Mitchell},
journal = {arXiv preprint arXiv:1706.01346},
year = {2017},
petsc_uses = {KSP}
}
@Article{ saibaba2012application,
title = {Application of hierarchical matrices to linear inverse problems in
geostatistics},
author = {Saibaba, Arvind Krishna and Ambikasaran, Sivaram and Yue Li, J and Kitanidis,
Peter K and Darve, Eric F},
journal = {Oil and Gas Science and Technology-Revue de l'IFP-Institut Francais du Petrole},
volume = {67},
number = {5},
pages = {857},
year = {2012},
petsc_uses = {KSP}
}
@Article{ collignonkausmayfernandez14,
author = {Collignon, M. and Kaus, B. and May, D.A. and Fern\'andez, N.},
title = {Influences of surface processes on fold growth during {3-D} detachment folding},
journal = {Geochem Geophy Geosy},
year = {2014},
petsc_uses = {KSP}
}
@Article{ fernandezkaus14,
author = {Fern\'andez, N. and Kaus, B.},
title = {Fold interaction and wavelength selection in {3D} models of multilayer detachment
folding},
journal = {Tectonophysics},
year = {2014},
petsc_uses = {KSP}
}
@Article{ baumannkauspopov14,
author = {Baumann, T. and Kaus, B. J. P. and Popov, A.},
title = {Constraining effective rheology through parallel joint geodynamic inversion},
journal = {Tectonophysics},
year = {2014},
petsc_uses = {KSP}
}
@Article{ lechmannschmalholzhetenyimaykaus14,
author = {Lechmann, S. M. and Schmalholz, S. M. and Hetenyi, G. and May, D. A. and Kaus, B.
J. P.},
title = {Quantifying the impact of mechanical layering and underthrusting on the dynamics
of the modern {India-Asia} collisional system with {3-D} numerical models},
journal = { Journal of Geophysical Research - Solid Earth},
year = {2014},
petsc_uses = {KSP}
}
@InBook{ fernandezkaus14b,
author = {Fern\'andez N. and Kaus B.J.P.},
title = {Analytical and numerical investigation of {3D} multilayer detachment},
booktitle = {Mathematics of Planet Earth},
editor = {Pardo-Ig\'uzquiza E. and Guardiola-Albert C. and Heredia J. and Moreno-Merino L.
and Dur\'an J.J. and Vargas-Guzman J.A.},
publisher = {Springer},
year = {2014},
petsc_uses = {KSP}
}
@Article{ hossein-hsueh-etal-2014a,
author = {Hossein, M.Z. and Hsueh, C.-J. and Bourdin, B. and Bhattacharya, K.},
journal = {J. Mech. Phys. Solids},
pages = {320--348},
title = {Effective toughness of heterogeneous media},
volume = {71},
year = {2014},
petsc_uses = {KSP}
}
@Unpublished{ leon-baldelli-bourdin-2014a,
author = {Le\'{o}n Baldelli, A.A. and Bourdin, B.},
month = aug,
note = {Submitted.},
title = {On the asymptotic derivation of Winkler-type energies from {3D} elasticity},
year = {2014},
petsc_uses = {KSP}
}
@Article{ leon-baldelli-babadjian-etal-2013a,
author = {Leòn-Baldelli, A. A. and Babadjian, J.-F. and Bourdin, B. and Henao, D. and
Maurini, C.},
journal = {J. Mech. Phys. Solids},
pages = {15-32},
title = {A Variational Model For Fracture And Delamination Of Thin Films},
volume = {70},
year = {2014},
petsc_uses = {KSP}
}
@Article{ mesgarnejad-bourdin-etal-2014a,
author = {Mesgarnejad, A. and Bourdin, B. and Khonsari, M. M.},
journal = {Comp. Methods Appl. Mech. Engng.},
title = {Validation simulations for the variational approach to fracture},
volume = {Submitted},
year = {2014},
petsc_uses = {KSP}
}
@InProceedings{ bourdin-chukwudozie-etal-2013a,
author = {Bourdin, B. and Chukwudozie, C. and Yoshioka, K.},
booktitle = {Proceedings of the 38th Workshop on Geothermal Reservoir Engineering Stanford
University, Stanford, CA},
title = {A Variational Approach To The Modeling And Numerical Simulation Of Hydraulic
Fracturing Under In-Situ Stresses},
year = {2013},
petsc_uses = {KSP}
}
@Article{ maurini-bourdin-etal-2012a,
author = {Maurini, C. and Bourdin, B. and Gauthier, G. and Lazarus, V.},
journal = {Int. J. Fracture},
number = {1-2},
pages = {75-91},
title = {Crack patterns obtained by unidirectional drying of a colloidal suspension in a
capillary tube: experiments and numerical simulations using a two-dimensional
variational approach},
volume = {184},
year = {2013},
petsc_uses = {KSP}
}
@Article{ mesgarnejad-bourdin-etal-2013a,
author = {Mesgarnejad, A. and Bourdin, B. and Khonsari, M.M.},
journal = {J. Mech. Phys Solids},
number = {11},
pages = {2360--2379},
title = {A variational approach to the fracture of brittle thin films under out of plane
loading},
volume = {61},
year = {2013},
petsc_uses = {KSP}
}
@InProceedings{ bourdin-chukwudozie-etal-2012a,
author = {Bourdin, B. and Chukwudozie, C. and Yoshioka, K.},
booktitle = {Proceedings of the 2012 SPE Annual Technical Conference and Exhibition},
title = {A Variational Approach to the Numerical Simulation of Hydraulic Fracturing},
volume = {SPE 159154},
year = {2012},
petsc_uses = {KSP}
}
@Article{ millerdawsonfarthinghouhuangkeeskelleylangtangen13,
author = {Cass T. Miller and Clint N. Dawson and Matthew W. Farthing and Thomas Y. Hou and
Jingfang Huang and Christopher E. Kees and C.T. Kelley and Hans Petter
Langtangen},
title = {Numerical simulation of water resources problems: Models, methods, and trends},
journal = {Advances in Water Resources},
volume = {51},
number = {0},
pages = {405--437},
year = {2013},
note = {35th Year Anniversary Issue},
issn = {0309-1708},
doi = {10.1016/j.advwatres.2012.05.008},
petsc_uses = {KSP}
}
@Article{ scheltingamyerspietrzak10,
author = {Terwisscha van Scheltinga, ArjenD. and Myers, PaulG. and Pietrzak, JulieD.},
title = {A finite element sea ice model of the {C}anadian Arctic Archipelago},
journal = {Ocean Dynamics},
volume = {60},
number = {6},
pages = {1539-1558},
year = {2010},
issn = {1616-7341},
doi = {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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {10.1029/2012GC004271},
petsc_uses = {KSP}
}
@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},
pages = {10--33},
year = {2011},
doi = {10.1111/j.1365-246X.2011.05164.x},
petsc_uses = {KSP}
}
@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},
doi = {10.1190/1.3554652},
petsc_uses = {KSP}
}
@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},
doi = {10.1190/1.3628198},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf},
note = {\url{https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}},
address = {Stanford, CA},
year = {2010},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/s10915-010-9396-8},
year = {2010},
petsc_uses = {KSP}
}
@PhDThesis{ brown2011,
title = {Computational methods for ice flow simulation},
author = {Jed Brown},
school = {ETH Z{\"u}rich},
year = {2011},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {10.1142/S0218396X11004316},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ kellerkatz2016,
title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere},
author = {Tobias Keller and Richard F. Katz},
journal = {Journal of Petrology},
doi = {10.1093/petrology/egw030},
url = {http://petrology.oxfordjournals.org/content/early/2016/07/15/petrology.egw030.abstract},
eprint = {http://petrology.oxfordjournals.org/content/early/2016/07/15/petrology.egw030.full.pdf+html},
year = {2016},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ spiegelmanwilsonvankeken2013,
author = {{Spiegelman}, M.~W. and {Wilson}, C.~R. and {Van Keken}, P.~E. },
title = {{TerraFERMA: The Transparent Finite Element Rapid Model Assembler for
multi-physics problems in the solid Earth sciences}},
journal = {AGU Fall Meeting Abstracts},
keywords = {0560 COMPUTATIONAL GEOPHYSICS Numerical solutions, 1902 INFORMATICS Community
modeling frameworks, 1906 INFORMATICS Computational models, algorithms},
year = {2013},
month = dec,
pages = {A2208},
adsurl = {http://adsabs.harvard.edu/abs/2013AGUFMDI31A2208S},
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
petsc_uses = {KSP}
}
@Article{ bueler2009shallow,
title = {{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled
ice sheet model}},
author = {Ed Bueler and Jed Brown},
journal = {Journal of Geophysical Research-Earth Surface},
volume = {114},
number = {F3},
pages = {F03008},
year = {2009},
publisher = {American Geophysical Union},
petsc_uses = {KSP}
}
@Article{ bueler2007est,
title = {{Exact solutions to the thermomechanically coupled shallow ice approximation:
effective tools for verification}},
author = {Ed Bueler and Jed Brown and Craig Lingle},
journal = {J. Glaciol},
volume = {53},
pages = {499--516},
year = {2007},
petsc_uses = {KSP}
}
@Article{ bueler2007fcv,
title = {{Fast computation of a viscoelastic deformable Earth model for ice-sheet
simulations}},
author = {Ed Bueler and Craig S. Lingle and Jed Brown},
journal = {Ann. Glaciol},
volume = {46},
pages = {97--105},
year = {2007},
petsc_uses = {KSP}
}
@Article{ bueler2005iso,
author = {Ed Bueler and Craig S. Lingle and Jed A. Kallen-Brown and David N. Covey and
Latrice N. Bowman},
title = {Exact solutions and numerical verification for isothermal ice sheets},
journal = {J. Glaciol.},
volume = {51},
number = {173},
pages = {291--306},
year = {2005},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ marti2014,
author = {Marti, P. and Schaeffer, N. and Hollerbach, R. and Cébron, D. and Nore, C. and
Luddens, F. and Guermond, J.-L. and Aubert, J. and Takehiro, S. and Sasaki, Y. and
Hayashi, Y.-Y. and Simitev, R. and Busse, F. and Vantieghem, S. and Jackson, A.},
title = {Full sphere hydrodynamic and dynamo benchmarks},
journal = {Geophysical Journal International},
year = {2014},
doi = {10.1093/gji/ggt518},
url = {http://gji.oxfordjournals.org/content/early/2014/01/26/gji.ggt518.abstract},
petsc_uses = {KSP}
}
@InProceedings{ ganfulukyangxueyang2013,
author = {Gan, Lin and Fu, Haohuan and Luk, Wayne and Yang, Chao and Xue, Wei and Yang,
Guangwen},
title = {Global Atmospheric Simulation on a Reconfigurable Platform},
booktitle = {Proceedings of the 2013 IEEE 21st Annual International Symposium on
Field-Programmable Custom Computing Machines},
series = {FCCM '13},
pages = {230--},
year = {2013},
isbn = {978-0-7695-4969-9},
doi = {10.1109/FCCM.2013.26},
acmid = {2495688},
publisher = {IEEE Computer Society},
petsc_uses = {KSP}
}
@InProceedings{ ganfuchaolukxuemencerhuangyang2014,
author = {Lin Gan and Haohuan Fu and Chao Yang and Luk, W. and Wei Xue and Mencer, O. and
Xiaomeng Huang and Guangwen Yang},
booktitle = {Field Programmable Logic and Applications (FPL), 2014 24th International
Conference on},
title = {A highly-efficient and green data flow engine for solving {E}uler atmospheric
equations},
year = {2014},
month = sep,
pages = {1-6},
doi = {10.1109/FPL.2014.6927462},
petsc_uses = {KSP}
}
%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},
doi = {10.1002/jgrb.50217},
keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics},
year = {2013},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InProceedings{ knepley10b,
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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 {S}outhern {C}alifornia Using the {SCEC}
Community Fault Model},
booktitle = {Proceedings of Geosciences '08},
address = {Wellington, NZ},
month = nov,
year = {2008},
petsc_uses = {KSP}
}
@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 = sep,
year = {2007},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ hgrhkjvv2008,
title = {On preconditioning for a parallel solution of the {R}ichards 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},
petsc_uses = {KSP}
}
@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 = {10.1016/j.pepi.2008.07.036},
author = {Dave A. May and Louis Moresi},
keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt},
petsc_uses = {KSP}
}
@Article{ kausmuhlhausmay2010,
title = {A stabilization algorithm for geodynamic numerical simulations with a free
surface},
author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May},
journal = {Physics of the Earth and Planetary Interiors},
volume = {181},
number = {1},
pages = {12--20},
year = {2010},
petsc_uses = {KSP}
}
@Article{ duretzmaygeryatackley2011,
title = {Discretization errors and free surface stabilization in the finite difference and
marker-in-cell method for applied geodynamics: A numerical study},
author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley},
journal = {Geochemistry, Geophysics, Geosystems},
volume = {12},
number = {7},
year = {2011},
petsc_uses = {KSP}
}
@Article{ furuichimaytackley2011,
title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a
{Schur} complement approach with mixed precision arithmetic},
author = {Mikito Furuichi and Dave A May and Paul J Tackley},
journal = {Journal of Computational Physics},
volume = {230},
number = {24},
pages = {8835--8851},
year = {2011},
petsc_uses = {KSP}
}
@Article{ kellermaykaus2013,
title = {Numerical modelling of magma dynamics coupled to tectonic deformation of
lithosphere and crust},
author = {Tobias Keller and Dave A May and Boris JP Kaus},
journal = {Geophysical Journal International},
volume = {195},
number = {3},
pages = {1406--1442},
year = {2013},
petsc_uses = {KSP}
}
@Article{ schellartfreemanstegmanmoresimay2007,
title = {Evolution and diversity of subduction zones controlled by slab width},
author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A
May},
journal = {Nature},
volume = {446},
number = {7133},
pages = {308--311},
year = {2007},
petsc_uses = {KSP}
}
@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012,
title = {A comparison of numerical surface topography calculations in geodynamic
modelling: an evaluation of the sticky air method},
author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter
and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley},
journal = {Geophysical Journal International},
volume = {189},
number = {1},
pages = {38--54},
year = {2012},
petsc_uses = {KSP}
}
@Article{ stegmanfreemanschellartmoresimay2006,
title = {Influence of trench width on subduction hinge retreat rates in {3-D} models of slab
rollback},
author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A
May},
journal = {Geochemistry, Geophysics, Geosystems},
volume = {7},
number = {3},
year = {2006},
petsc_uses = {KSP}
}
@InProceedings{ may2014ptatin,
title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics},
author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}},
booktitle = {Proceedings of {SC14}: The {International Conference for High Performance
Computing, Networking, Storage and Analysis}},
organization = {ACM},
pages = {274--284},
year = {2014},
doi = {10.1109/SC.2014.28},
petsc_uses = {KSP}
}
@Article{ maybrownpourhiet2015,
title = {A scalable, matrix-free multigrid preconditioner for finite element
discretizations of heterogeneous {Stokes} flow},
author = {David A May and Jed Brown and Laetitia {Le Pourhiet}},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {290},
pages = {496--523},
year = {2015},
doi = {10.1016/j.cma.2015.03.014},
petsc_uses = {KSP}
}
@Article{ duretzmayyamato2016,
title = {A free surface capturing discretization for the staggered grid finite difference
scheme},
author = {Thibault Duretz and Dave A May and Philippe Yamato},
journal = {Geophysical Journal International},
volume = {204},
number = {3},
pages = {1518--1530},
year = {2016},
petsc_uses = {KSP}
}
@Article{ rhebergenwellskatzwathen2014,
author = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen},
title = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics},
journal = {SIAM J. Sci. Comput.},
volume = {36},
pages = {A1960--A1977},
year = {2014},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = aug,
day = {10},
url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ hammondlichtnermills2014,
title = {Evaluating the Performance of Parallel Subsurface Simulators: An Illustrative
Example with {PFLOTRAN}},
author = {Glenn E. Hammond and Peter C. Lichtner and Richard Tran Mills},
journal = {Water Resources Research},
volume = {50},
number = {1},
pages = {208--228},
doi = {10.1002/2012WR013483},
year = {2014},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ frederickbuffett2016,
title = {Submarine groundwater discharge as a possible formation mechanism for
permafrost-associated gas hydrate on the circum-Arctic continental shelf},
author = {Jennifer M. Frederick and Bruce A. Buffett},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {121},
number = {3},
pages = {1383--1404},
issn = {2169-9356},
doi = {10.1002/2015JB012627},
year = {2016},
petsc_uses = {KSP}
}
% LiteralHTML:
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% LiteralHTML:
% LiteralHTML:Simulation of the earth's mantle and crust is valuable to
% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a
% LiteralHTML:variety of these simulations.
% LiteralHTML:
% LiteralHTML:
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
@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},
petsc_uses = {KSP}
}
% LiteralHTML: 
% LiteralHTML: 
% LiteralHTML:
% LiteralHTML: 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},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/3-540-31619-1_12},
year = {2006},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InProceedings{ stefano12,
author = {Michele De Stefano},
title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data},
booktitle = {PIERS Proceedings},
month = aug,
address = {Moscow, RUSSIA},
pages = {491--495},
year = {2012},
petsc_uses = {KSP}
}
%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY=
% LiteralHTML:
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% LiteralHTML: 
@Article{ khatiwala07,
author = {Khatiwala, S.},
title = {A computational framework for simulation of biogeochemical tracers in the ocean},
journal = {Glob. Biogeochem. Cycles},
volume = {21},
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},
petsc_uses = {KSP}
}
@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 {N}orth
{A}tlantic},
journal = {Ocean Modelling},
petsc_uses = {KSP}
}
@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 {K}alman Filter and the {SEIK} Filter applied to
a Finite Element Model of the {N}orth {A}tlantic},
journal = {Journal of marine systems},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ lauter3,
author = {M. Lauter},
year = {2004},
title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven
AtmosphArenmodell},
journal = {Berichte zur Polar- und Meeresforschung},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@PhDThesis{ lauter1,
author = {M. Lauter},
year = {2004},
title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven
AtmosphArenmodell},
institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ 0266-5611-24-3-034015,
author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak},
title = {A {N}ewton-{CG} method for large-scale three-dimensional elastic full-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-scale 3D 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.},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Environmental -- Subsurface Flow
% LiteralHTML:
% LiteralHTML:
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% LiteralHTML:
% LiteralHTML:Modeling surface flow of water is valuable for both flood control and
% LiteralHTML:agricultural and environmental reasons. For example, regenerating the
% LiteralHTML:Florida Everglades requires extensive understanding of the surface water
% LiteralHTML:characteristics over thousands of square miles. PETSc has been used
% LiteralHTML:for a variety of these simulations.
% LiteralHTML:
% LiteralHTML:
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ guo2013parallel,
title = {A parallel, fully coupled, fully implicit solution to reactive transport in
porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method
},
journal = {Advances in Water Resources },
volume = {53},
number = {0},
pages = {101 - 108},
year = {2013},
note = {},
issn = {0309-1708},
doi = {10.1016/j.advwatres.2012.10.010},
author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David
Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita},
keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block
preconditioner},
petsc_uses = {KSP}
}
@Unpublished{ stomp,
title = {STOMP (Subsurface Transport Over Multiple Phases) webpage},
url = {http://stomp.pnl.gov/},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
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@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 = nov,
url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf},
lab = {SNL},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
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@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
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% LiteralHTML: 
% LiteralHTML:
% LiteralHTML: Sample strong scaling for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL)
@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018,
title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing
Strategies for Large-Scale Numerical Simulations},
author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody
J. Permann and Andrew E. Slaughter and Richard C. Martineau},
booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for
Large-Scale Systems (scalA)},
pages = {65-72},
doi = {10.1109/ScalA.2018.00012},
month = nov,
year = {2018},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {1999},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2004},
petsc_uses = {KSP}
}
@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-+},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
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@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},
petsc_uses = {KSP}
}
@PhDThesis{ tjb200,
author = {Thomas James Byer},
title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface
Facilities},
school = {Stanford},
year = {2000},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: CFD
% LiteralHTML:
@Article{ farrellmitchellscottwechsung2021,
title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the
stationary incompressible {Navier-Stokes} equations},
author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian
Wechsung},
journal = {The SMAI journal of computational mathematics},
volume = {7},
pages = {75--96},
year = {2021},
petsc_uses = {KSP}
}
@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021,
title = {Monolithic Multigrid Methods for Magnetohydrodynamics},
author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott
P MacLachlan and Ray S Tuminaro},
journal = {SIAM Journal on Scientific Computing},
number = {0},
pages = {S70--S91},
year = {2021},
petsc_uses = {KSP}
}
@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021,
title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible
hyperelasticity},
author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo
Oyar\'ua and Ricardo Ruiz-Baier},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {374},
pages = {113562},
issn = {0045-7825},
doi = {https://doi.org/10.1016/j.cma.2020.113562},
url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477},
year = {2021},
petsc_uses = {KSP}
}
@Article{ farrellmitchellwechsung2018,
title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible
{Navier-Stokes} equations at high {Reynolds} number},
author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung},
journal = {SIAM Journal on Scientific Computing},
volume = {41},
number = {5},
eprint = {1810.03315},
pages = {A3073-A3096},
year = {2019},
petsc_uses = {KSP}
}
@Article{ hevuikklaij2017,
title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations
discretized by a finite volume method},
author = {Xin He and Cornelis Vuik and Christiaan Klaij},
journal = {Journal of Numerical Mathematics},
volume = {25},
number = {2},
pages = {89--105},
year = {2017},
petsc_uses = {KSP}
}
@InProceedings{ zou2015newton,
title = {Newton--Krylov methods in applications of two-phase flow problems with phase
appearance/disappearance},
author = {Zou, L and Zhao, H and Zhang, H},
booktitle = {ANS 2015 Annual Meeting, June},
volume = {7},
number = {11},
year = {2015},
petsc_uses = {KSP}
}
@Article{ guermond2009nonlinear,
title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a
Fourier/finite element technique and an interior penalty method},
author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline},
journal = {Journal of computational physics},
volume = {228},
number = {8},
pages = {2739--2757},
year = {2009},
publisher = {Elsevier},
petsc_uses = {KSP}
}
@Article{ erzincanlisahin2015,
title = {The numerical simulation of the wing kinematics effects on near wake topology and
aerodynamic performance in hovering {D}rosophila flight},
author = {Belkis Erzincanli and Mehmet Sahin},
journal = {Computers \& Fluids},
volume = {122},
pages = {90--110},
year = {2015},
publisher = {Elsevier},
petsc_uses = {KSP}
}
@Article{ ekensahin2015,
title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid
structure interaction problems},
author = {Ali Eken and Mehmet Sahin},
journal = {International Journal for Numerical Methods in Fluids},
year = {2015},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
@Article{ hwangsucai2015,
title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method
for transonic full potential equation},
author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai},
journal = {Computers \& Fluids},
volume = {110},
number = {30},
pages = {96--107},
year = {2015},
doi = {10.1016/j.compfluid.2014.04.005},
petsc_uses = {KSP}
}
@Article{ yanghwangcai2016,
title = {Nonlinear Preconditioning Techniques for Full-Space {L}agrange--{N}ewton Solution of
{PDE}-Constrained Optimization Problems},
author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai},
journal = {SIAM Journal on Scientific Computing},
volume = {38},
number = {5},
pages = {A2756--A2778},
year = {2016},
petsc_uses = {KSP}
}
@Article{ khanaidun2011,
author = {Irfan Khan and Cyrus K. Aidun},
title = {Direct numerical simulation of saturated deformable porous media using parallel
hybrid Lattice-{B}oltzmann and finite element method},
journal = {Int. J. Numer. Meth. Eng.},
volume = {86},
pages = {1379--1395},
year = {2011},
petsc_uses = {KSP}
}
@Article{ khanaidun2014,
author = {Irfan Khan and Cyrus K. Aidun},
title = {Modeling the deformation of saturate porous media using direct numerical
simulation},
journal = {Int. J. Multiphase Flow},
doi = {10.1016/j.ijmultiphaseflow.2014.12.003},
year = {2014},
petsc_uses = {KSP}
}
@Article{ mofidi2014simulations,
author = {A. Mofidi and P. M. Carrica},
title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder
and Propeller},
journal = {Computers and Fluids},
pages = {191--203},
year = {2014},
petsc_uses = {KSP}
}
@Article{ paik2014fluidstructure,
author = {K. Paik and P. M. Carrica},
title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free
Surface in a Rolling Tank},
journal = {Ocean Engineering},
pages = {201--212},
year = {2014},
petsc_uses = {KSP}
}
@Article{ castro2013bubble,
author = {A. M. Castro and P. M. Carrica},
title = {Bubble size distribution prediction for large-scale ship flows: {Model}
evaluation and numerical issues},
journal = {International Journal of Multiphase Flow 57},
pages = {131--150},
year = {2013},
petsc_uses = {KSP}
}
@Article{ carrica2013turn,
author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern},
title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with
Dynamic Overset Grids},
journal = {Journal of Marine Science and Technology},
pages = {166--181},
year = {2013},
petsc_uses = {KSP}
}
@Article{ castro2013eulerian,
author = {A. M. Castro and P. M. Carrica},
title = {Eulerian polydispersed modeling of bubbly flows around ships with application to
{Athena} {R}/V,},
journal = {International Shipbuilding Progress},
pages = {403--433},
year = {2013},
petsc_uses = {KSP}
}
@Article{ chase2013overset,
author = {N. Chase and T. Michael and P. M. Carrica},
title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and
{Maneuvering} {Conditions}},
journal = {International Shipbuilding Progress},
pages = {171--205},
year = {2013},
petsc_uses = {KSP}
}
@Article{ sadathosseini2013wu,
author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F.
Stern},
title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and
Free Surge Conditions in Short and Long Head Waves},
journal = {Ocean Engineering},
volume = {59},
pages = {240--273},
year = {2013},
petsc_uses = {KSP}
}
@Article{ chase2013cfd,
author = {N. Chase and P. M. Carrica},
title = {{CFD} Simulations of a Submarine Propeller and Application to Self-Propulsion of a
Submarine},
journal = {Ocean Engineering},
pages = {68--80},
year = {2013},
petsc_uses = {KSP}
}
@Article{ carrica2012cfd,
author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern},
title = {{CFD} Analysis of Broaching for a Model Surface Combatant with Explicit Simulation
of Moving Rudders and Rotating Propellers},
journal = {Computers and Fluids 53},
pages = {117--132},
year = {2012},
petsc_uses = {KSP}
}
@Article{ sakamoto2012urans,
author = {N. Sakamoto and P. M. Carrica and F. Stern},
title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1:
Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives},
publisher = {Journal of Marine Science and Technology},
pages = {422--445},
year = {2012},
petsc_uses = {KSP}
}
@Article{ sakamoto2012uransb,
author = {N. Sakamoto and P. M. Carrica and F. Stern},
title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2:
Analysis and Validation of Local Flow Characteristics},
journal = {Journal of Marine Science and Technology},
pages = {446--468},
year = {2012},
petsc_uses = {KSP}
}
@Article{ li2012dynamic,
author = {Y. Li and T. Xing and K. Paik and P. M. Carrica},
title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics},
journal = {Renewable Energy},
pages = {285--298},
year = {2012},
petsc_uses = {KSP}
}
@Article{ huang2012a,
author = {J. Huang and P. M. Carrica and F. Stern},
title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind},
journal = {International Journal for Numerical Methods in Fluids},
pages = {160--180},
year = {2012},
petsc_uses = {KSP}
}
@Article{ huang2012b,
author = {J. Huang and P. M. Carrica and F. Stern},
title = {A geometry-based level set method for curvilinear overset grids with application
to ship hydrodynamics},
journal = {International Journal for Numerical Methods in Fluids},
pages = {494--521},
year = {2012},
petsc_uses = {KSP}
}
@Article{ carrica2011computations,
author = {P. M. Carrica and H. Fu and F. Stern},
title = {Computations of self-propulsion free to sink and trim and of motions in head
waves of the {KRISO} {Container} {Ship} ({KCS}) model},
journal = {Applied Ocean Research},
pages = {309--320},
year = {2011},
petsc_uses = {KSP}
}
@Article{ bhushan2011scalability,
author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern},
title = {Scalability and Validation Study for Large Scale Surface Combatant Computations
Using {CFDShip}-Iowa},
journal = {International Journal of High Performance Computing Applications},
pages = {466--487},
year = {2011},
petsc_uses = {KSP}
}
@Article{ castro2011full,
author = {A. M. Castro and P. M. Carrica and F. Stern},
title = {Full scale self-propulsion computations using discretized propeller for the
{KRISO} container ship {KCS}},
journal = {Computers and Fluids},
pages = {35--47},
year = {2011},
petsc_uses = {KSP}
}
@Article{ kandasamy2011multifidelity,
author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and
D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal},
title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing {C}atamaran
for Low Wake},
journal = {Journal of Marine Science and Technology},
pages = {143--156},
year = {2011},
petsc_uses = {KSP}
}
@Article{ kandasamy2011cfd,
author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and
D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal},
title = {{CFD} Validation Studies for a High-speed Foil-assisted Semi-planing {C}atamaran},
journal = {Journal of Marine Science and Technology},
pages = {157--167},
year = {2011},
petsc_uses = {KSP}
}
@Article{ sadathosseini2011cfd,
author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto
and S. Yamamura and A. Mastuda},
title = {{CFD} System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding,
Periodic Motion and Broaching},
journal = {Ocean Engineering},
pages = {88--110},
year = {2011},
petsc_uses = {KSP}
}
@Article{ mosaviraad2010development,
author = {M. Mosaviraad and P. M. Carrica and F. Stern},
title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO}
with Comparison to Regular Wave and Transient Wave Group Procedures Using
{URANS}},
journal = {Ocean Engineering},
pages = {653--666},
year = {2010},
petsc_uses = {KSP}
}
@Article{ carrica2010largescale,
author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F.
Stern},
title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and
Heave Problems for a Surface Combatant},
journal = {Computers and Fluids},
pages = {1095--1111},
year = {2010},
petsc_uses = {KSP}
}
@Article{ carrica2010selfpropulsion,
author = {P. M. Carrica and A. M. Castro and F. Stern},
title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller
with Dynamic Overset Grids},
journal = {Journal of Marine Science and Technology},
pages = {316--330},
year = {2010},
petsc_uses = {KSP}
}
@Article{ ismail2010evaluation,
author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern},
title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional
Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker},
journal = {International Journal of Numerical Methods in Fluids},
pages = {850--886},
year = {2010},
petsc_uses = {KSP}
}
@Article{ kandasamy2010integral,
author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern},
title = {Integral Force/Moment Waterjet Model for {CFD} Simulations},
journal = {Journal of Fluids Engineering},
pages = {101103},
year = {2010},
petsc_uses = {KSP}
}
@Article{ kirk:2014de,
author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A},
title = {{Modeling hypersonic entry with the fully-implicit {N}avier--{S}tokes (FIN-S)
stabilized finite element flow solver}},
journal = {Computers {\&} Fluids},
year = {2014},
volume = {92},
number = {0},
pages = {281--292},
month = mar,
petsc_uses = {KSP}
}
@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 = {10.1016/j.jnnfm.2011.08.014},
author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L.
Maffettone and A. Murli},
keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element
method, High performance computing},
petsc_uses = {KSP}
}
@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},
publisher = {Springer-Verlag},
keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics;
Thermohydraulics; Two-phase flow},
language = {English},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1080/10618560410001729126},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/978-3-540-69777-0_17},
year = {2008},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/978-3-540-75755-9_83},
year = {2007},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@TechReport{ avb2008,
author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove},
title = {Variational Space-time (Dis)continuous {G}alerkin Method for Linear Free Surface
Waves},
year = {2008},
institution = {University of Twente, the Netherlands},
url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf},
petsc_uses = {KSP}
}
@InProceedings{ bdsm2005,
author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal},
title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids},
booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit},
year = {2005},
url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf},
petsc_uses = {KSP}
}
@InProceedings{ ms2006,
author = {S. Muller and Y. Stiriba},
title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR
STEADY COMPRESSIBLE FLOWS},
booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006},
year = {2006},
url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf},
petsc_uses = {KSP}
}
@Article{ araujoteixeiracunhagroth08,
author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth},
title = {Parallel three-dimensional simulation of the injection molding process},
journal = {International Journal for Numerical Methods in Fluids},
year = {2008},
url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0},
petsc_uses = {KSP}
}
@PhDThesis{ a2008,
author = {A. Cubero},
title = {a parallel coupled algorithm for collocated grids and its application to Large
Eddy Simulation of a turbulent wake},
school = {University of Zaragoza (Spain)},
year = {2008},
petsc_uses = {KSP}
}
@Article{ afa2007,
author = {A. Cubero and N. Fueyo},
title = {A Compact Momentum Interpolation Method for unsteady flows and relaxation},
journal = {Numerical Heat Transfer, part B-Fundamentals},
volume = {56},
number = {6},
pages = {507--529},
year = {2007},
url = {http://www.informaworld.com/smpp/content~content=a782025305~db=all~order=page},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InCollection{ dwight2004,
author = {Richard Dwight},
title = {Robust Mesh Deformation using the Linear Elasticity Equations},
booktitle = {Computational Fluid Dynamics 2006},
editor = {H. Deconinck and E. Dick},
publisher = {Springer},
year = {2006},
url = {http://www.maths.man.ac.uk/\~{
}rdwight/pub/rdwight-ICCFD4-LinElastDeformation-2006.pdf},
petsc_uses = {KSP}
}
@InProceedings{ dwight2006,
author = {Richard Dwight and Joel Brezillon},
title = {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based
Optimization},
booktitle = {Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV.
AIAA-2006-0690},
year = {2006},
url = {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-AIAAReno-ApproxAdjoint.pdf},
petsc_uses = {KSP}
}
@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},
year = {2006},
url = {http://www.maths.man.ac.uk/\~{
}rdwight/pub/rdwight-PhDThesis-ImplicitAndAdjoint.pdf},
petsc_uses = {KSP}
}
@InProceedings{ lhdfrh,
author = {M. Lauter and D. Handorf and K. Dethloff and S. Frickenhaus and N. Rakowsky and
W. Hiller},
title = {An adaptive Lagrange-Galerkin shallow-water model on the sphere},
booktitle = {Workshop Proceedings Current Development in Shallow Water Models on the Sphere
March, 10-14, 2003, Munich University of Technology, German},
year = {2003},
petsc_uses = {KSP}
}
@InProceedings{ brios-ying-2002,
author = {George Biros and Lexing Ying and Denis Zorin},
title = {The Embedded Boundary Integral Method (EBI) for the Incompressible
{Navier-Stokes} equations},
booktitle = {IABEM 2002, International Association for Boundary Element Methods, UT Austin},
year = {2002},
petsc_uses = {KSP}
}
@InProceedings{ mohsen-straatman-ins,
author = {S.A. Mohsen Karimian and Anthony G. Straatman},
title = {Benchmarking of a {3D}, unstructured, finite volume code for incompressible
{Navier-Stokes} equation on a cluster of distributed-memory computers},
booktitle = {Proceedings of the 19th International Symposium on High Performance Computing
Systems and Applications},
pages = {11--16},
year = {2005},
url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046},
petsc_uses = {KSP}
}
@TechReport{ bonglioli-icnmfd98,
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},
year = {1996},
author = {A. Bonglioli},
url = {http://www.unibas.it/utenti/bonfiglioli/icnmfd98.ps.gz},
petsc_uses = {KSP}
}
@Article{ deng-piquet-ctf,
author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"},
title = {A new fully coupled method for computing turbulent flows},
journal = {Computers and Fluids},
volume = {30},
pages = {445--472},
year = {2001},
petsc_uses = {KSP}
}
@InProceedings{ knepleysarinsameh99b,
title = {Multilevel Preconditioning for Parallel {CFD}},
author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh},
booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix
Problems In Industrial Applications},
address = {Minneapolis, MN},
year = {1999},
petsc_uses = {KSP}
}
@InProceedings{ garbey1,
author = {M. Garbey and B. Hadri and W. Shyy.},
title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer
Problems on the Grid},
booktitle = {Aerospace Sciences Meeting and Exhibit},
note = {Paper No. 2005-1386},
year = {2005},
petsc_uses = {KSP}
}
@Article{ carrica2007unsteady,
title = {An unsteady single-phase level set method for viscous free surface flows},
author = {Carrica, PM and Wilson, RV and Stern, F.},
journal = {International Journal for Numerical Methods in Fluids},
volume = {53},
number = {2},
pages = {229--256},
year = {2007},
publisher = {Chichester; New York: Wiley, c1981-},
petsc_uses = {KSP}
}
@Article{ pctw2004,
author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber},
title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of
Spillways},
journal = {Journal of Hydraulic Research},
note = {accepted for publication},
year = {2004},
petsc_uses = {KSP}
}
@Article{ wcs2004,
author = {R. V. Wilson and P. M. Carrica and F. Stern},
title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface
Combatant},
journal = {Computers and Fluids},
note = {in press},
year = {2004},
petsc_uses = {KSP}
}
@Article{ cws2005,
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},
note = {accepted for publication},
year = {2005},
petsc_uses = {KSP}
}
@Article{ chndss2010,
author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F.
Stern},
title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and
Heave Problems for a Surface Combatant},
journal = {Computers and Fluids},
year = {2010},
volume = {39},
number = {7},
pages = {1095--1111},
petsc_uses = {KSP}
}
@InProceedings{ chnkss2008,
author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F.
Stern},
title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear
Grids},
booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea},
year = {2008},
petsc_uses = {KSP}
}
@MastersThesis{ mtj,
author = {M. T. Jozkowski},
title = {Application of Algebraic Multigrid Methods to the Solution of Stratified Flows
About Submerged Bodies},
school = {The Pennsylvania State University},
year = {2005},
petsc_uses = {KSP}
}
@Article{ pp,
author = {E. G. Paterson and L. J. Peltier},
title = {Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and
Wakes},
journal = {ASME Journal of Fluids Engineering},
note = {In press},
year = {2005},
petsc_uses = {KSP}
}
@Article{ eps,
author = {B. A. Edge and E. G. Paterson and G. Settles},
title = {Computational Study of the Wake and Contaminant Transport of a Walking Human},
journal = {ASME Journal of Fluids Engineering},
note = {In press},
year = {2005},
petsc_uses = {KSP}
}
@InProceedings{ rp,
author = {B. Racine and E. G. Paterson},
title = {Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines
Using Unsteady {RANS} {CFD}},
booktitle = {35th AIAA Fluid Dynamics Conference and Exhibit},
year = {2005},
petsc_uses = {KSP}
}
@InProceedings{ etpp,
author = {B. A. Edge and M. F. Trujillo and E. G. Paterson and L. J. Peltier},
title = {Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids
and DES},
booktitle = {7th Overset Composite Grid and Solution Technology Symposium},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ pp8,
author = {E. G. Paterson and L. J. Peltier},
title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset
refinement grids and detached-eddy simulation},
booktitle = {7th Overset Composite Grid and Solution Technology Symposium},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ mzwp,
author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson},
title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles},
booktitle = {25th Symposium on Naval Hydrodynamics},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ ppph,
author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric},
title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing},
booktitle = {25th Symposium on Naval Hydrodynamics},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ ppd,
author = {E. G. Paterson and L. J. Peltier},
title = {Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes},
booktitle = {Symposium on LES Advancements and Applications, ASME FED Summer Meeting},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ bp,
author = {W. J. Baker and E. G. and Paterson},
title = {Simulation of Steady Circulation Control for the General Aviation Circulation
Control Wing},
booktitle = {NASA/ONR Workshop on Circulation Control},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ pb,
author = {E. G. Paterson and W. J. Baker},
title = {RANS and Detached-Eddy Simulation of the NCCR airfoil},
booktitle = {NASA/ONR Workshop on Circulation Control},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ pb3,
author = {E. G. Paterson and W. J. Baker},
title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control
Surfaces},
booktitle = {42nd AIAA Aerospace Sciences Meeting},
year = {2004},
petsc_uses = {KSP}
}
@InProceedings{ gid1,
author = {G. Frank and J. D'Elia},
title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model},
year = {2004},
booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD},
url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf},
petsc_uses = {KSP}
}
@InBook{ b1,
author = {A.Bonfiglioli},
chapter = {On the use of the PETSc library for unstructured {CFD} applications},
year = {2001},
title = {Science and Supercomputing at CINECA},
pages = {397--400},
petsc_uses = {KSP}
}
@InProceedings{ b2004,
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},
petsc_uses = {KSP}
}
@InProceedings{ bl2004,
author = {L. A. Barba and A. Leonard},
title = {Computation of Viscous Vortices with Fully Meshless Method},
year = {2004},
booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004},
note = {Submitted},
petsc_uses = {KSP}
}
@Article{ vws1,
author = {B. G. M. Van Wachem and J. C. Schouten},
title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise
Velocity},
institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering
and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The
Netherlands},
journal = {AIChE},
volumne = {48},
number = {12},
month = dec,
year = {2002},
petsc_uses = {KSP}
}
@TechReport{ lbam1,
author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi},
title = {Precondizionatori paralleli per la fluidodinamica computazionale},
institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico
di Bari Italy},
year = {2002},
number = {25/02},
petsc_uses = {KSP}
}
@Article{ kees_miller_02,
author = {C. E. Kees and C. T. Miller},
title = {Higher Order Time Integration Methods for Two-Phase Flow},
journal = {Advances in Water Resources},
year = {2002},
volume = {25},
number = {2},
pages = {159-177.},
petsc_uses = {KSP}
}
@InProceedings{ lepotmeersessers2001,
author = {I. Lepot and F. Meers and J.A. Essers},
title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D
Unstructured Meshes},
year = {2001},
booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001},
url = {http://www.ulg.ac.be/aerodyn},
petsc_uses = {KSP}
}
@InProceedings{ knepley98,
author = {Matthew Knepley and Denis Vanderstraeten},
title = {Parallel Building Blocks for Finite Element Simulations: Application to
Solid-Liquid Mixture Flows},
booktitle = {Proceedings of Parallel CFD'97},
publisher = {Elsevier},
pages = {281--287},
year = {1998},
petsc_uses = {KSP}
}
@InProceedings{ pcfd97,
author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri},
title = {Parallel Implicit {PDE} Computations: Algorithms and Software},
publisher = {Elsevier},
year = {1998},
booktitle = {Proceedings of Parallel CFD'97},
pages = {333-344},
petsc_uses = {KSP}
}
@InProceedings{ knepleysamehsari98,
author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin},
title = {Parallel Simulation of Particulate Flows},
booktitle = {Solving Irregularly Structured Problems in Parallel},
editors = {A. Ferreira et al},
year = {1998},
series = {Lecture Notes in Computer Science},
volume = {1457},
pages = {226--237},
petsc_uses = {KSP}
}
@Article{ gkmt98,
author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri},
title = {Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel
Implicit {CFD}},
journal = {Int. J. High Performance Computing Applications},
year = {2000},
volume = {14},
url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z},
pages = {102-136},
petsc_uses = {KSP}
}
@InProceedings{ agkks-sc99,
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},
petsc_uses = {KSP}
}
@Article{ gkks01,
author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith},
title = {High Performance Parallel Implicit {CFD}},
journal = {Journal of Parallel Computing},
year = {2001},
volume = {27},
pages = {337-362},
url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf},
petsc_uses = {KSP}
}
@Article{ cristea-sofonea-02,
author = {Artur Cristea and Victor Sofonea},
title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems},
journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical
Sciences, Information Sciences},
volume = {3},
number = {3},
year = {2002},
petsc_uses = {KSP}
}
@Article{ cristea2,
author = {Artur Cristea and Victor Sofonea},
title = {Two component lattice Boltzmann model with flux limiter techniques},
journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical
Sciences, Information Sciences},
volume = {4},
number = {1},
year = {2003},
pages = {59--64},
petsc_uses = {KSP}
}
@Article{ cristea1,
author = {Artur Cristea and Victor Sofonea},
title = {Two component lattice Boltzmann model with flux limiters},
journal = {Central European Journal of Physics},
volume = {2},
number = {2},
year = {2004},
pages = {382--396},
petsc_uses = {KSP}
}
@Article{ sofnea-lamura1,
author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea},
title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor
systems},
journal = {Physical Review E},
volume = {70},
number = {4},
year = {2004},
pages = {046702-1 / 046702-9},
petsc_uses = {KSP}
}
@InProceedings{ gkks01b,
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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
year = {1999},
petsc_uses = {KSP}
}
@InProceedings{ gkks-pcfd99,
author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith},
title = {Towards Realistic Performance Bounds for Implicit {CFD} codes},
booktitle = {Proceedings of Parallel CFD'99},
editors = {A. {Ecer et al.}},
publisher = {Elsevier},
url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf},
year = {1999},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InCollection{ kks97_cfd,
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 = {},
year = {1998},
petsc_uses = {KSP}
}
@Article{ hm99,
author = {P. D. Hovland and L. C. McInnes},
title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and
{PETSc}},
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''},
petsc_uses = {KSP}
}
@InProceedings{ cruzbarbaknepley08,
author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley},
title = {Fast Multipole Method for particle interactions: an open source parallel library
component},
booktitle = {Proceedings of ParCFD2008},
year = {2008},
editor = {Tromeur-Dervout et. al.},
publisher = {Elsevier},
petsc_uses = {KSP}
}
@Article{ hwangcai05,
author = {F.-N. Hwang and X.-C. Cai},
title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm
for incompressible {Navier-Stokes} equations},
journal = {J. Comput. Phys.},
volume = {204},
year = {2005},
pages = {666--691},
petsc_uses = {KSP}
}
@Article{ barbaleonard07,
author = {Lorena A Barba and Anthony Leonard},
title = {Emergence and evolution of tripole vortices from net-circulation initial
conditions},
journal = {Phys. Fluids},
volume = {19},
pages = {017101},
year = {2007},
doi = {10.1063/1.2409734},
petsc_uses = {KSP}
}
@Article{ barba07,
author = {Lorena A Barba},
title = {Non-shielded multipolar vortices at high Reynolds number},
journal = {Phys. Rev. E},
volume = {73},
pages = {065303},
year = {2006},
doi = {10.1103/PhysRevE.73.065303},
petsc_uses = {KSP}
}
@Article{ schofield2010multi,
title = {Multi-material incompressible flow simulation using the moment-of-fluid method},
author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and
Lowrie, R.B. and Swartz, B.K.},
journal = {International Journal for Numerical Methods in Fluids},
volume = {63},
number = {8},
pages = {931--952},
year = {2010},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Wave propagation and the Helmholtz equation
% LiteralHTML:
% LiteralHTML: article{DeGersem99,
% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du},
% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids},
% LiteralHTML: }
@Article{ nagler2014,
title = {Sound transmission through a poroelastic layered panel},
author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff},
journal = {Computational Mechanics},
volume = {53},
number = {4},
pages = {549--560},
issn = {1432-0924},
doi = {10.1007/s00466-013-0916-x},
year = {2014},
petsc_uses = {KSP}
}
@Article{ sheikh2013,
author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.},
title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel
deflation},
journal = {Numerical Linear Algebra with Applications},
volume = {20},
number = {4},
issn = {1099-1506},
doi = {10.1002/nla.1882},
pages = {645--662},
keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier
analysis},
year = {2013},
petsc_uses = {KSP}
}
@InProceedings{ silence,
author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J.
Fuenmayor},
title = {A parallel computing approach for solving the Helmholtz equation in 3D domains:
Application to the study of acoustic behaviour of silencers},
year = {2004},
booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering
(ECCOMAS)},
petsc_uses = {KSP}
}
@Article{ degersem99,
author = {H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer},
title = {Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods
to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations},
journal = {COMPEL},
year = {1999},
volume = {18},
number = {3},
pages = {298--310},
bibdate = {},
petsc_uses = {KSP}
}
@InProceedings{ widlund-wave-98,
author = {Olof B. Widlund},
title = {Schwarz Methods for {H}elmholtz's Equation},
booktitle = {Mathematical and Numerical Aspects of Wave Propagation},
editor = {John A. DeSanto},
year = {1998},
publisher = {SIAM},
pages = {620--622},
address = {Philadelphia},
note = {Proceedings of the Fourth International Conference on Mathematical and Numerical
Aspects of Wave Propagation, Golden, Colorado, June 1--5},
petsc_uses = {KSP}
}
@InProceedings{ toselli-wave-98,
author = {Andrea Toselli},
title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media},
booktitle = {Mathematical and Numerical Aspects of Wave Propagation},
editor = {John A. DeSanto},
year = {1998},
publisher = {SIAM},
address = {Philadelphia},
pages = {540--542},
note = {Proceedings of the Fourth International Conference on Mathematical and Numerical
Aspects of Wave Propagation, Golden, Colorado, June 1--5},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Optimization
% LiteralHTML:
@Article{ sojkahorakhaplacermak2018,
title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain
decomposition method},
author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k},
journal = {Applied Mathematics and Computation},
volume = {319},
pages = {586--597},
year = {2018},
petsc_uses = {KSP}
}
@Article{ chencai2014,
title = {A parallel two-level domain decomposition based one-shot method for shape
optimization problems},
author = {Rongliang Chen and Xiao‐Chuan Cai},
journal = {International Journal for Numerical Methods in Engineering},
volume = {99},
number = {13},
year = {2014},
doi = {10.1002/nme.4711},
petsc_uses = {KSP}
}
@PhDThesis{ prudencio2005,
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},
petsc_uses = {KSP}
}
@Article{ prudenciocai2007,
title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing
for {PDE}-constrained optimization},
author = {Ernesto Prudencio and X. C. Cai},
journal = {SIAM J. Sci. Comp.},
volume = {29},
number = {3},
pages = {964--985},
year = {2007},
petsc_uses = {KSP}
}
@Article{ prudenciobyrdcai2006,
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},
petsc_uses = {KSP}
}
@InProceedings{ prudenciobyrdcai2004,
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},
pages = {569--582},
year = {2004},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = aug,
url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% 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},
petsc_uses = {KSP}
}
% 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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Fast Algorithms
% LiteralHTML:
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Other Application Areas
% LiteralHTML:
@Article{ buchanpainumplebysmedleystevenson2012,
title = {A sub-grid scale finite element agglomeration multigrid method with application
to the Boltzmann transport equation},
author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson},
journal = {International Journal for Numerical Methods in Engineering},
volume = {92},
number = {3},
pages = {318--342},
year = {2012},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
@Article{ magoulesahamedsuzuki2015,
title = {Green computing on graphics processing units},
author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki},
journal = {Concurrency and Computation: Practice and Experience},
year = {2015},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
@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},
doi = {10.1109/ICPP.2011.70},
acmid = {2066965},
publisher = {IEEE Computer Society},
address = {Washington, DC, USA},
keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
year = {2011},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/s10659-007-9107-3},
year = {2008},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ hcsw1,
author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu},
title = {Parallel {N}ewton--{K}rylov--{S}chwarz algorithms for the three-dimensional
{P}oisson--{B}oltzmann equation in numerical simulation of colloidal particle
interactions},
journal = {Computer Physics Communications},
volumne = {181},
year = {2010},
pages = {1529--1537},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
year = {2010},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/s10915-011-9551-x},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2008},
petsc_uses = {KSP}
}
@Article{ williamson2012multidimensional,
title = {Multidimensional multiphysics simulation of nuclear fuel behavior},
author = {Williamson, R.L. and Hales, J.D. and Novascone, S.R. and Tonks, M.R. and Gaston,
D.R. and Permann, C.J. and Andrs, D. and Martineau, R.C.},
journal = {Journal of Nuclear Materials},
volume = {423},
number = {1},
pages = {149--163},
year = {2012},
publisher = {Elsevier},
petsc_uses = {KSP}
}
@InProceedings{ kucukboyaci2015cobra,
title = {COBRA-TF parallelization and application to PWR reactor core subchannel DNB
analysis},
author = {Kucukboyaci, Vefa and Sung, Yixing and Salko, Robert},
booktitle = {Joint International Conference on Mathematics and Computation, Supercomputing in
Nuclear Applications and the Monte Carlo Method},
pages = {1--18},
year = {2015},
petsc_uses = {KSP}
}
@Article{ hales2012solving,
title = {Solving Nonlinear Solid Mechanics Problems with the {J}acobian-{F}ree {N}ewton
{K}rylov Method},
author = {Hales, J.D. and Novascone, S.R. and Williamson, R.L. and Gaston, D.R. and Tonks,
M.R.},
journal = {Computer Modeling in Engineering \& Sciences(CMES)},
volume = {84},
number = {2},
pages = {123--153},
year = {2012},
publisher = {Tech Science Press},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1016/j.memsci.2005.05.030},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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/},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ bonfi-palma-pas-05,
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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ ovtchinnikovcai04,
author = {S. Ovtchinnikov and X.-C. Cai},
journal = {Numer. Lin. Alg. Applics},
volume = {11},
title = {One-level {N}ewton--{K}rylov--{S}chwarz algorithm for unsteady nonlinear radiation
diffusion problem},
year = {2004},
pages = {867--881},
petsc_uses = {KSP}
}
@Article{ mixedstress,
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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2004},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ idema2013towards,
title = {Towards faster solution of large power flow problems},
author = {Idema, Reijer and Papaefthymiou, Georgios and Lahaye, Domenico and Vuik, Cornelis
and van der Sluis, Lou},
journal = {Power Systems, IEEE Transactions on},
volume = {28},
number = {4},
pages = {4918--4925},
year = {2013},
publisher = {IEEE},
petsc_uses = {KSP}
}
@Article{ 6026245,
author = {Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.},
journal = {Power Systems, IEEE Transactions on},
title = {Scalable Newton-Krylov Solver for Very Large Power Flow Problems},
year = {2012},
month = feb,
volume = {27},
number = {1},
pages = {390-396},
doi = {10.1109/TPWRS.2011.2165860},
issn = {0885-8950},
petsc_uses = {KSP}
}
@Book{ idema2014computational,
title = {Computational Methods in Power System Analysis},
author = {Idema, Reijer and Lahaye, Domenico JP},
year = {2014},
publisher = {Springer},
petsc_uses = {KSP}
}
@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 = {2011},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InProceedings{ abhyankarhipcna11-2,
author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang},
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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ korrestzavellasgalinas2013,
author = {George N. Korres and Anastasios Tzavellas and Evangelos Galinas},
title = {A distributed implementation of multi-area power system state estimation on a
cluster of computers },
journal = {Electric Power Systems Research },
volume = {102},
number = {0},
pages = {20 - 32},
year = {2013},
issn = {0378-7796},
doi = {10.1016/j.epsr.2013.04.002},
petsc_uses = {KSP}
}
% LiteralHTML:
|
% LiteralHTML:
% LiteralHTML: Material failure, for example, cracking of steel beams resulting
% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations
% LiteralHTML: are important for prediction and prevention. PETSc has been used
% LiteralHTML: in a variety of studies of material failure.
% LiteralHTML:
% LiteralHTML:
@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},
petsc_uses = {KSP}
}
@InProceedings{ gray1,
author = {J. Gray 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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {},
petsc_uses = {KSP}
}
% LiteralHTML:
|
@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},
petsc_uses = {KSP}
}
@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 = {2003},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
year = {2005},
volume = {71},
pages = {024020},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@PhDThesis{ pfeiffer:2003,
author = {Pfeiffer, Harald P.},
title = {Initial Data for Black Hole Evolutions},
school = {Cornell University},
year = {2003},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 {N}ewton Trust Region Methods},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {1999},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ s1,
author = {J. L. Friedman and N. Stergioulas},
journal = {Astrophysics Journal},
year = {1998},
volume = {492},
number = {301},
pages = {},
title = {},
petsc_uses = {KSP}
}
@Article{ s1a,
author = {S. M. Morsink and N. Stergioulas and S. Blattnig},
journal = {Astrophysics Journal},
year = {1999},
volume = {510},
number = {854},
pages = {},
title = {},
petsc_uses = {KSP}
}
@PhDThesis{ s2,
author = {N. Stergioulas},
title = {Ph. D. thesis},
year = {1996},
institution = {University of Wisconsin-Milwaukee},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Software Packages that use or interface to PETSc
% LiteralHTML:
@Article{ collierdalcincalo2013,
title = {{PetIGA}: High-Performance Isogeometric Analysis},
author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo},
journal = {arxiv},
year = {2013},
number = {1305.4452},
note = {\url{http://arxiv.org/abs/1305.4452}},
petsc_uses = {KSP}
}
@Article{ collierdalcinvignalcortescalo2016,
title = {PetIGA: A framework for high-performance isogeometric analysis},
author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and
Victor M. Calo},
journal = {Computer Methods in Applied Mechanics and Engineering},
year = {2016},
petsc_uses = {KSP}
}
@Misc{ petiga-web-page,
author = {N. Collier and L. Dalcin and V.M. Calo},
title = {{PetIGA} {W}eb page},
url = {https://bitbucket.org/dalcinl/petiga/},
howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}},
year = {2014},
petsc_uses = {KSP}
}
@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},
publisher = {Kluwer Academic Publishers},
issn = {1134-3060},
language = {English},
petsc_uses = {KSP}
}
@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},
publisher = {Springer US},
keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method;
Sparse linear solver},
language = {English},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Unpublished{ pism,
title = {{PISM}: a Parallel Ice Sheet Model},
author = {{PISM Team}},
abstract = {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.},
note = {\url{http://www.pism-docs.org/}},
petsc_uses = {KSP}
}
@Unpublished{ oofem,
title = {OOFEM - an object oriented finite element package},
author = {Borek Patzak},
url = {http://www.oofem.org},
petsc_uses = {KSP}
}
@Unpublished{ dks2openfvm,
title = {OpenFVM - a finite volume based general purpose CFD solver},
author = {Open source development},
url = {http://openfvm.sourceforge.net/},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {1999},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Unpublished{ petsc-python,
title = {PETSc for Python},
author = {L. Dalcin},
url = {https://petsc.org/main/petsc4py},
note = {Provides Python bindings for PETSc},
}
@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},
petsc_uses = {KSP}
}
@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.},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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/},
petsc_uses = {KSP}
}
@Unpublished{ magpar,
author = {W. Scholz},
title = {Magpar: Parallel Micromagnetics Code},
institution = {Vienna University of Technology},
url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/},
petsc_uses = {KSP}
}
@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.github.io},
petsc_uses = {KSP}
}
@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}},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 2.0.0},
year = {2014},
url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf},
petsc_uses = {KSP}
}
@Misc{ pylith-web-page,
author = {Brad Aagaard and Matthew G. Knepley and Charles Williams},
title = {{PyLith}},
year = {2012},
url = {http://geodynamics.org/resources/pylith/},
howpublished = {\url{http://geodynamics.org/resources/pylith/}},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Unpublished{ underworld,
author = {Louis Moresi},
title = {{UnderWorld}: A Geodynamics Modelling Code},
institution = {Monash University},
url = {http://www.mcc.monash.edu/twiki/view/Codes},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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/},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Unpublished{ illuminator,
author = {Adam C. Powell, IV},
title = {Illuminator Distributed Visualization Library},
url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Misc{ tao-web-page,
title = {{Toolkit for Advanced Optimization ({TAO})} {W}eb Page},
author = {Alp Dener and Adam Denchfield and 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}},
petsc_uses = {KSP}
}
@TechReport{ tao-user-ref,
title = {{Toolkit for Advanced Optimization ({TAO}) users manual}},
author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild
and Steve Benson and Lois Curfman McInnes},
institution = {Argonne National Laboratory},
year = {2019},
number = {ANL/MCS-TM-322 - Rev 3.12},
petsc_uses = {KSP}
}
% 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},
petsc_uses = {KSP}
}
@Unpublished{ tipetsc-titanium,
title = {Ti-PETSc - an interface to PETSc from Titanium},
institution = {Berkeley},
author = {He, Yun and Liblit, Bun and Lin, Chang},
url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=9f7959be13337c735d52e5c0b0994bdea6d75a96},
year = {1999},
petsc_uses = {KSP},
}
@Unpublished{ ptatin-web-page,
title = {ptatin3d},
author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan},
url = {https://bitbucket.org/jedbrown/ptatin3d},
year = {2018},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Unpublished{ fe-software-web-page,
institution = {Kuleuven},
title = {Finite element software},
url = {http://www.esat.kuleuven.ac.be/elen/research/software-development},
petsc_uses = {KSP}
}
@Misc{ petsc-web-page,
author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed
Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro
Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D.
Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev
and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and
Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell
and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich
and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao
Zhang},
title = {{PETS}c {W}eb page},
url = {https://petsc.org/},
howpublished = {\url{https://petsc.org/}},
year = {2025}
}
@Unpublished{ petsc-debian-package,
author = {Adam C. Powell, IV},
title = {Debian package for PETSc},
url = {http://lyre.mit.edu/\~{ }powell/petsc.html},
petsc_uses = {KSP}
}
@Unpublished{ cactus,
title = {Cactus Website},
url = {http://www.cactuscode.org/},
note = {Provides two interface to the PETSc solvers},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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} Website},
url = {http://slepc.upv.es/},
note = {Scalable Library for Eigenvalue Problem Computations},
petsc_uses = {KSP}
}
@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://slepc.upv.es/},
note = {Scalable Library for Eigenvalue Problem Computations},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Software Engineering
% LiteralHTML:
@Article{ petsccommunity2022,
title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User
Community},
author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob
Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin
and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang
and Hong Zhang and Junchao Zhang},
journal = {Computing in Science and Engineering},
volume = {24},
number = {03},
pages = {6--15},
issn = {1558-366X},
doi = {10.1109/MCSE.2022.3169974},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
month = may,
year = {2022},
url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043},
petsc_uses = {KSP}
}
@Article{ brownknepleysmith14,
author = {Jed Brown and Matthew G. Knepley and Barry Smith},
title = {Run-time extensibility and librarization of simulation software},
journal = {IEEE Computing in Science and Engineering},
month = jan,
volume = {17},
number = {1},
pages = {38--45},
doi = {10.1109/MCSE.2014.95},
year = {2015},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/978-3-642-16405-7_7},
publisher = {Springer Berlin Heidelberg},
pages = {131--140},
year = {2013},
isbn = {978-3-642-16404-0},
petsc_uses = {KSP}
}
@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},
publisher = {Springer Berlin Heidelberg},
pages = {131--140},
year = {2013},
isbn = {978-3-642-16404-0},
petsc_uses = {KSP}
}
@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},
publisher = {Springer Berlin Heidelberg},
pages = {487--501},
year = {2013},
isbn = {978-3-642-16404-0},
petsc_uses = {KSP}
}
@InCollection{ zhengetal13,
title = {{GPU} Implementation of Multigrid Solver for {S}tokes 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},
publisher = {Springer Berlin Heidelberg},
pages = {321--333},
year = {2013},
isbn = {978-3-642-16404-0},
petsc_uses = {KSP}
}
@Article{ zhengetal13b,
title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with
strongly variable viscosity based on {M}atlab and {CUDA}},
author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai
Zhang and Yaolin Shi},
journal = {IJHPCA},
volume = {28},
number = {1},
pages = {50--60},
doi = {10.1177/1094342013478640},
year = {2013},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2002},
petsc_uses = {KSP}
}
@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},
doi = {10.1137/060661624},
year = {2007},
petsc_uses = {KSP}
}
@MastersThesis{ aarrestad-master,
author = {Asbjorn Hoiland Aarrestad},
title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers},
school = {University of Bergen},
month = aug,
year = {2003},
url = {http://www.parallab.uib.no/projects/molecul/matrix/},
note = {Implemented Runge-Kutta methods using PETSc},
petsc_uses = {KSP}
}
@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 = dec,
year = {2002},
url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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)},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = jun,
year = {2001},
url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2002},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% 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 Steven Benson and Jed
Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro
Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D.
Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev
and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and
Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell
and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich
and Barry~F. Smith and Hansol Suh and Stefano Zampini and Hong Zhang and Hong Zhang
and Junchao Zhang},
title = {{PETSc/TAO} Users Manual},
institution = {Argonne National Laboratory},
number = {ANL-21/39 - Revision 3.24},
doi = {10.2172/2998643},
year = {2025}
}
% url = {https://petsc.org/release}
@TechReport{ petsc-developers,
author = {Scott Kruger and Patrick Sanan and Barry~F. Smith},
title = {{PETS}c Developers Guide},
institution = {Argonne National Laboratory},
number = {ANL-18/18},
year = {2018},
url = {https://petsc.org/release/developers},
petsc_uses = {KSP}
}
@Unpublished{ alice-memory-snooper,
author = {Ibrahima Ba and Barry~F. Smith},
title = {The {ALICE} Memory Snooper},
year = {1999},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z},
year = {1998},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Algorithm design and analysis
% LiteralHTML:
@PhDThesis{ klotzthesis2019,
author = {Thomas S. Klotz},
title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular
Biology},
school = {Rice University},
year = {2019},
petsc_uses = {KSP}
}
@Article{ klotzbardhanknepley2018,
title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling},
author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley},
journal = {arXiv e-prints},
eprint = {1708.06028},
archiveprefix = {arXiv},
primaryclass = {math.na},
year = {2018},
note = {\url{http://arxiv.org/abs/1708.06028}},
petsc_uses = {KSP}
}
@Misc{ brown2016,
title = {Threading Tradeoffs in Domain Decomposition},
author = {Jed Brown},
note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium,
\url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}},
url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf},
year = {2016},
petsc_uses = {KSP}
}
@Article{ changnakshatralaknepleyjohnsson2017,
title = {A performance spectrum for parallel computational frameworks that solve {PDEs}},
author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart
Johnsson},
journal = {Concurency: Practice and Experience},
volume = {30},
number = {11},
eprint = {1705.03625},
doi = {10.1002/cpe.4401},
year = {2017},
petsc_uses = {KSP}
}
@Article{ changfabienknepleymills2018,
title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)}
spectrum analysis},
author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills},
journal = {SIAM Journal on Scientific Computing},
volume = {40},
number = {6},
pages = {C779--C802},
eprint = {1802.07832},
doi = {10.1137/18M1172260},
year = {2018},
petsc_uses = {KSP}
}
@Article{ joshaghanichangnakshatralaknepley2019,
title = {Composable solvers for the four-field double porosity/permeability model},
author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G.
Knepley},
journal = {Journal of Computational Physics},
volume = {386},
pages = {428--466},
doi = {10.1016/j.jcp.2019.02.020},
year = {2019},
petsc_uses = {KSP}
}
@InProceedings{ barralknepleylangepiggottgorman2016,
title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}},
author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott
and Gerard J. Gorman},
booktitle = {25th International Meshing Roundtable},
editor = {Steve Owen and Hang Si},
month = sep,
address = {Washington, DC},
pages = {1--5},
url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf},
year = {2016},
petsc_uses = {KSP}
}
@Article{ adamsbrownknepleysamtaney2016,
title = {Segmental Refinement: A Multigrid Technique for Data Locality},
author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney},
journal = {SIAM Journal on Scientific Computing},
url = {http://epubs.siam.org/toc/sjoce3/38/4 },
epub = {http://arxiv.org/abs/1406.7808},
volume = {8},
number = {4},
pages = {C426--C440},
doi = {10.1137/140975127},
year = {2016},
petsc_uses = {KSP}
}
@InProceedings{ maysananruppknepleysmith2016,
title = {Extreme-Scale Multigrid Components within {PETSc}},
author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F.
Smith},
booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}},
series = {PASC '16},
isbn = {978-1-4503-4126-4},
location = {Lausanne, Switzerland},
pages = {5:1--5:12},
articleno = {5},
numpages = {12},
doi = {10.1145/2929908.2929913},
acmid = {2929913},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing,
preconditioning},
year = {2016},
petsc_uses = {KSP}
}
@Article{ liu2015field,
title = {Field-Split Preconditioned Inexact Newton Algorithms},
author = {Lulu Liu and David E Keyes},
journal = {SIAM Journal on Scientific Computing},
volume = {37},
number = {3},
pages = {A1388--A1409},
year = {2015},
publisher = {SIAM},
petsc_uses = {KSP}
}
@Article{ lujiaomissirlis2014,
title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers},
author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis},
journal = {Numerical Linear Algebra with Applications},
volume = {21},
number = {2},
pages = {221--238},
year = {2014},
publisher = {Wiley Online Library},
petsc_uses = {KSP}
}
@Article{ badiamartinprincipe2013,
title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and
solid mechanics},
author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe},
journal = {International Journal for Numerical Methods in Engineering},
volume = {96},
number = {4},
pages = {203--230},
year = {2013},
petsc_uses = {KSP}
}
@Article{ morganknepleysananscott2016,
title = {A Stochastic Performance Model for Pipelined {Krylov} Methods},
author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott},
journal = {Concurrency and Computation: Practice and Experience},
volume = {28},
pages = {4532--4542},
year = {2016},
url = {http://arxiv.org/abs/1602.04873},
doi = {10.1002/cpe.3820},
petsc_uses = {KSP}
}
@Article{ morgansananknepleymills2020,
title = {Understanding performance variability in standard and pipelined parallel {Krylov}
solvers},
author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills},
journal = {The International Journal of High Performance Computing Applications},
volume = {35},
issue = {1},
doi = {10.1177/1094342020966835},
url = {https://doi.org/10.1177/1094342020966835},
eprint = {https://doi.org/10.1177/1094342020966835},
year = {2020},
petsc_uses = {KSP}
}
@Article{ msz2013,
title = {Efficient Sparse Matrix-Matrix Products Using Colorings},
author = {M. McCourt and B. F. Smith and H. Zhang},
journal = {SIAM Journal on Matrix Analysis and Applications},
year = {2015},
note = {To appear},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ yangcai11,
author = {Yang, Haijian and Cai, Xiao-Chuan},
title = {Parallel Two-Grid Semismooth {N}ewton--{K}rylov--{S}chwarz 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},
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},
petsc_uses = {KSP}
}
@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},
publisher = {Springer Netherlands},
language = {English},
petsc_uses = {KSP}
}
@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 = {no. 10, \url{http://arxiv.org/abs/1103.0066}},
petsc_uses = {KSP}
}
@Article{ knepleyruppterrel2016,
title = {Finite Element Integration with Quadrature on the GPU},
journal = {ArXiv e-prints},
author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel},
version = {1},
date = {2016-07-14},
eprinttype = {arxiv},
eprintclass = {cs.MS},
eprint = {1607.04245v1},
petsc_uses = {KSP}
}
@Article{ klawonnlanserrheinbach2014,
title = {Nonlinear {FETI-DP} and {BDDC} Methods},
author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach},
journal = {SIAM Journal on Scientific Computing},
volume = {36},
number = {2},
pages = {A737--A765},
year = {2014},
petsc_uses = {KSP}
}
@Article{ bruneknepleysmithtu15,
title = {Composing Scalable Nonlinear Algebraic Solvers},
author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu},
journal = {SIAM Review},
volume = {57},
number = {4},
pages = {535--565},
note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}},
url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf},
doi = {10.1137/130936725},
year = {2015},
petsc_uses = {KSP}
}
@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},
volume = {40},
pages = {17--31},
year = {2014},
journal = {Parallel Computing},
doi = {10.1016/j.parco.2013.10.001},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InProceedings{ bkmms2012,
author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry
F. Smith},
title = {Composable linear solvers for multiphysics},
booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed
Computing} ({ISPDC} 2012)},
year = {2012},
doi = {10.1109/ISPDC.2012.16},
publisher = {IEEE Computer Society},
pages = {55--62},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = {2004},
petsc_uses = {KSP}
}
@PhDThesis{ baker,
author = {{A. H.} Baker},
title = {On improving the performance of the linear solver restarted {GMRES}},
school = {University of Colorado at Boulder},
year = {2003},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@InProceedings{ cky2002,
author = {Xiao-Chuan Cai and David E. Keyes and David P. Young},
title = {A Nonlinear Additive {S}chwarz Preconditioned Inexact {N}ewton 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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = nov,
year = {2001},
petsc_uses = {KSP}
}
@Book{ 1dl,
author = {Domenico Lahaye},
title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field
Computations},
year = {2001},
publisher = {Katholieke Universiteit Leuven},
notes = {Thesis},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = nov,
year = {1999},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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,
petsc_uses = {KSP}
}
@Article{ benzigolubliesen2005,
title = {Numerical solution of saddle point problems},
author = {Michele Benzi and Gene H. Golub and J\"org Liesen},
volume = {14},
journal = {Acta Numerica},
pages = {1-–137},
doi = {10.1017/S0962492904000212},
year = {2005}
}
@Article{ mardal2011preconditioning,
title = {Preconditioning discretizations of systems of partial differential equations},
author = {Kent-Andre Mardal and Ragnar Winther},
journal = {Numerical Linear Algebra with Applications},
volume = {18},
number = {1},
pages = {1--40},
year = {2011}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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 = oct,
petsc_uses = {DMPlex}
}
@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 = feb,
petsc_uses = {DMPlex}
}
@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}},
petsc_uses = {DMPlex}
}
@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},
doi = {10.1007/s10915-011-9540-0},
petsc_uses = {KSP}
}
% LiteralHTML:
% LiteralHTML: Books
% LiteralHTML:
@Book{ knepley2017,
title = {Computational Science I},
author = {Matthew G. Knepley},
url = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf},
note = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}},
publisher = {PETSc},
year = {2017},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Book{ pacheco,
author = {Peter Pacheco},
title = {Parallel Programming with MPI},
year = {1997},
publisher = {Morgan-Kaufmann},
note = {Devotes a couple of sections to PETSc},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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}},
petsc_uses = {KSP}
}
@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/},
petsc_uses = {KSP}
}
@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},
doi = {10.1007/s00366-006-0049-3},
petsc_uses = {KSP}
}
@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}},
petsc_uses = {KSP}
}
@Misc{ pflotran:homepage,
title = {{PFLOTRAN} project},
author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra
and Jitendra Kumar and Peter Lichtner and Richard Mills},
howpublished = {\url{http://pflotran.org/}},
petsc_uses = {KSP}
}
@Misc{ pism:homepage,
title = {{PISM}: A Parallel Ice Sheet Model},
author = {E. {Bueler et al.}},
howpublished = {\url{http://pism-docs.org}},
petsc_uses = {KSP}
}
@Misc{ dohp:homepage,
title = {Dohp: Dual order $hp$-finite elements},
author = {J. Brown},
howpublished = {\url{http://dohp.org}},
petsc_uses = {KSP}
}
@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)},
petsc_uses = {KSP}
}
@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}},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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}}},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ cmz2016,
title = {Analysis and Practical Use of Flexible {BiCGStab}},
author = {Jie Chen and Lois Curfman McInnes and Hong Zhang},
journal = {Journal of Scientific Computing},
publisher = {Springer},
pages = {803--825},
volume = {68},
issue = {2},
url = {http://link.springer.com/article/10.1007/s10915-015-0159-4},
doi = {10.1007/s10915-015-0159-4},
year = {2016},
note = {Also preprint ANL/MCS-P3039-0912},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@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},
petsc_uses = {KSP}
}
@Article{ knepleybrownmcinnessmithruppadams2015,
title = {Exascale Computing without Threads},
author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and
Karl Rupp and Mark Adams},
url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950},
note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on
Scientific Software Architecture for Portability and Performance},
doi = {10.6084/m9.figshare.5824950.v1},
year = {2015},
petsc_uses = {KSP}
}
@Article{ knepleybrownmcinnessmithruppadams2015b,
title = {Overview of the {PETSc} Library},
author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and
Karl Rupp and Mark Adams},
url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf},
note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on
Scientific Software Architecture for Portability and Performance},
year = {2015},
petsc_uses = {KSP}
}
@InCollection{ balaybrownknepleymcinnessmith2015,
author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry
Smith},
title = {Providing Mixed Language and Legacy Support within a Library},
editor = {J. Carver},
booktitle = {Software Engineering for Science},
publisher = {Taylor \& Francis},
year = {2015},
petsc_uses = {KSP}
}
@Article{ ruppbalaybrownknepleymcinnessmith2015,
title = {On The Evolution Of User Support Topics in Computational Science and Engineering
Software},
author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman
McInnes and Barry F. Smith},
note = {Whitepaper for Computational Science \& Engineering Software Sustainability and
Productivity Challenges},
journal = {ArXiv e-prints},
archiveprefix = {arXiv},
eprint = {1510.01122},
year = {2015},
petsc_uses = {KSP}
}
@InProceedings{ knepley2013accurately,
title = {Accurately Citing Software and Algorithms Used in Publications},
author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry
F.},
year = {2013},
booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences
(WSSSPE), held at SC13},
doi = {10.6084/m9.figshare.785731},
petsc_uses = {KSP}
}
@InProceedings{ milleretal2013,
title = {Package Management Practice Essential for Interoperability: Lessons Learned and
Strategies Developed for {FASTMath}},
author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and
Barry Smith},
year = {2013},
booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences
(WSSSPE), held at SC13},
doi = {10.6084/m9.figshare.789055},
petsc_uses = {KSP}
}
@TechReport{ dudsonetal2012,
title = {Improved Nonlinear Solvers in {BOUT++}},
author = {Ben Dudson and Sean Farley and Lois Curfman McInnes},
institution = {Argonne National Laboratory},
number = {ANL/MCS-P3025-0812},
year = {2012},
petsc_uses = {KSP}
}
@Misc{ brown13,
author = {J. Brown},
title = {Scalable Repository Workflows},
note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale
Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}},
year = {2013},
petsc_uses = {KSP}
}
@Misc{ starforest11,
title = {Star forests as a parallel communication model},
author = {Jed Brown},
url = {https://jedbrown.org/files/StarForest.pdf},
year = {2011},
petsc_uses = {KSP}
}
@Misc{ brownknepleysmith13,
author = {J. Brown and M. Knepley and B. Smith},
title = {Run-time Extensibility: Anything Less is Unsustainable},
note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale
Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}},
year = {2013},
petsc_uses = {KSP}
}
@Article{ jzhaoyliwkliu15,
author = {J. Zhao and Y. Li and W.K. Liu},
title = {Predicting band structure of 3{D} mechanical metamaterials with complex geometry
via {XFEM}},
journal = {Computational Mechanics},
year = {2015},
url = {http://link.springer.com/article/10.1007/s00466-015-1129-2},
petsc_uses = {KSP}
}
@Article{ alisic14,
author = {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen},
title = {Compaction around a rigid, circular inclusion in partially molten rock},
journal = {J. Geophys. Res.},
year = {2014},
volume = {119},
number = {7},
pages = {5903-5920},
doi = {10.1002/2013JB010906},
petsc_uses = {KSP}
}
@Article{ rhebergen14,
author = {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen},
title = {Analysis of block preconditioners for models of coupled magma mantle dynamics},
journal = {SIAM J. Sci. Comp.},
year = {2014},
volume = {36},
number = {4},
pages = {1960-1977},
doi = {10.1137/130946678},
petsc_uses = {KSP}
}
@Article{ allwright14,
author = {J. Allwright and R.F. Katz},
title = {Pipe Poiseuille flow of viscously anisotropic, partially molten rock},
journal = {Geophys. J. Int.},
year = {2014},
volume = {199},
number = {3},
pages = {1608--1624},
doi = {10.1093/gji/ggu345},
petsc_uses = {KSP}
}
@Misc{ gropp10,
author = {William D. Gropp},
title = {Update on libraries for {B}lue {W}aters},
address = {Bordeaux, France},
year = {2010},
url = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf},
petsc_uses = {KSP}
}
@InProceedings{ mayknepley2017,
title = {{DMSwarm}: Particles in {PETSc}},
author = {Dave A May and Matthew G Knepley},
booktitle = {EGU General Assembly Conference Abstracts},
volume = {19},
pages = {10133},
year = {2017},
petsc_uses = {KSP}
}
@InProceedings{ adamsbrownknepley2013,
author = {Mark F. Adams and Jed Brown and Matthew G. Knepley},
title = {Low-communication techniques for extreme-scale multilevel solvers},
booktitle = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC},
organization = {DOE Office of Advanced Scientific Computing Research},
year = {2013},
petsc_uses = {KSP}
}
@Article{ bhallagriffithknepleyadamsguy2017,
title = {Scalable smoothing strategies for a geometric multigrid method for the immersed
boundary equations},
author = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F.
Adams and Robert D. Guy},
journal = {arXiv e-prints},
eprint = {1612.02208},
year = {2017},
note = {\url{http://arxiv.org/abs/1612.02208}},
petsc_uses = {KSP}
}
@Article{ zampini2016pcbddc,
title = {{PCBDDC}: a class of robust dual-primal methods in {PETSc}},
author = {Zampini, Stefano},
journal = {SIAM Journal on Scientific Computing},
volume = {38},
number = {5},
pages = {S282--S306},
year = {2016},
publisher = {SIAM},
petsc_uses = {KSP}
}
@Article{ jolivetromanzampini2020,
title = {{KSPHPDDM} and {PCHPDDM}: extending {PETSc} with advanced {Krylov} methods and
robust multilevel overlapping {Schwarz} preconditioners},
author = {Pierre Jolivet and Jose Roman and Stefano Zampini},
journal = {Computers and Mathematics with Applications},
volume = {84},
pages = {277--295},
year = {2021}
}
@Article{ zampinitu2017,
title = {Multilevel {BDDC} deluxe algorithms with adaptive coarse spaces for flow in
porous media},
author = {Stefano Zampini and Xuemin Tu},
journal = {SIAM Journal of Scientific Computing},
volume = {39},
number = {4},
pages = {A1389--A1415},
year = {2017}
}
@Article{ ohwidlundzampinidohrmann2017,
title = {{BDDC} algorithms with deluxe scaling and adaptive selection of primal
constraints for {Raviart-Thomas} vector fields},
author = {D.-S. Oh and Olof B. Widlund and Stefano Zampini and Clark Dohrmann},
journal = {Mathematics of Computation},
volume = {87},
number = {310},
pages = {659--692},
year = {2017}
}
@Article{ veigapavarinoscacchiwidlundzampini2016,
title = {Adaptive selection of primal constraints for isogeometric {BDDC} deluxe
preconditioners},
author = {L. Beirao Da Veiga and Luca F. Pavarino and S. Scacchi and Olof B. Widlund and
Stefano Zampini},
journal = {SIAM Journal of Scientific Computing},
volume = {39},
number = {1},
pages = {A281--A302},
year = {2016}
}
@Article{ pavarinoscacchiwidlundzampini2018,
title = {Isogeometric {BDDC} deluxe preconditioners for linear elasticity for isogeometric
analysis},
author = {Luca F. Pavarino and S. Scacchi and Olof B. Widlund and Stefano Zampini},
journal = {Mathematical Models and Methods in Applied Sciences},
volume = {28},
number = {7},
pages = {1337--1370},
year = {2018}
}
@Article{ bergervergiatwaisman2017,
title = {An overlapping Domain Decomposition preconditioning method for monolithic
solution of shear bands},
author = {Luc Berger-Vergiat and Haim Waisman},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {318},
pages = {33--60},
year = {2017},
petsc_uses = {KSP}
}
@Article{ abhyankarmaldonadosmithzhang2020,
title = {{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics
Simulations},
author = {S. Abhyankar and G. Betrie and D.A. Maldonado and L.C. McInnes and B. Smith and
H. Zhang},
journal = {ACM Transactions on Mathematical Software},
volume = {46},
number = {1},
year = {2020},
doi = {10.1145/3344587},
petsc_uses = {KSP}
}
@InProceedings{ zhangellpack2018,
author = {Hong Zhang and Richard T. Mills and Karl Rupp and Barry F. Smith},
title = {Vectorized Parallel Sparse Matrix-Vector Multiplication in {PETSc} Using
{AVX-512}},
booktitle = {Proceedings of the 47th International Conference on Parallel Processing},
year = {2018},
petsc_uses = {KSP}
}
@Misc{ petsc-user-meetings:website,
title = {{PETSc User Meetings}},
key = {PETSc User Meetings},
howpublished = {\url{https://petsc.org/release/community/meetings/meeting}},
petsc_uses = {KSP}
}
@Article{ flexible-bicgstab-chen16,
title = {Analysis and Practical Use of Flexible {BiCGStab}},
author = {J. Chen and L.C. McInnes and H. Zhang},
journal = {Journal of Scientific Computing},
volume = {68},
number = {2},
month = jul,
year = {2016},
pages = {803--825},
doi = {10.1007/s10915-015-0159-4},
petsc_uses = {KSP}
}
@Misc{ petsc-extensibility2016,
author = {M. Knepley and D. A. May and J. Brown and B. Smith},
title = {{Extensibility in PETSc}},
note = {SIAM News, available via
\url{https://sinews.siam.org/Details-Page/extensibility-in-petsc}},
year = {2016},
petsc_uses = {KSP}
}
@Misc{ error-estimation-whitepaper2017,
author = {E. Constantinescu and O. Marin and T. Munson and B. Smith and H. Zhang},
title = {End-to-end error estimation and control},
note = {whitepaper for 2017 ASCR Applied Mathematics PI Meeting},
doi = {10.6084/m9.figshare.5339866},
year = {2017},
petsc_uses = {KSP}
}
@Misc{ petsc-user-support15,
title = {On the Evolution of User Support Topics in Computational Science and Engineering
Software},
author = {K. Rupp and S. Balay and J. Brown and M. Knepley and L. C. McInnes and B. Smith},
note = {Workshop on CSE Software Sustainability and Productivity (CSESSP) Challenges, Oct
15-16, 2015},
year = {2015},
petsc_uses = {KSP}
}
@InBook{ petsc-mixed-language-support2016,
title = {Numerical Library Support for High-Performance Mixed Language Applications and
Legacy Code},
author = {S. Balay and J. Brown and M. Knepley and L.C. McInnes and B. Smith},
booktitle = {Software Engineering for Science},
editors = {J. Carver et al.},
publisher = {CRC Press},
pages = {201--214},
year = {2016},
petsc_uses = {KSP}
}
@InProceedings{ konolige2018parallel,
title = {A Parallel Solver for Graph {L}aplacians},
author = {Tristan Konolige and Jed Brown},
booktitle = {Proceedings of the Platform for Advanced Scientific Computing (PASC)},
doi = {10.1145/3218176.3218227},
note = {Best Paper Award},
archiveprefix = {arXiv},
eprint = {1705.06266},
year = {2018},
petsc_uses = {KSP}
}
@InProceedings{ werner-kimn2019,
title = {Parallel implementation of {AC} optimal power flow and time-constrained optimal
power flow using high-performance computing},
author = {Alex Werner and Kapil Duwadi and Nicholas Stegmeier and Timothy M. Hansen and
Jung-Han Kimn},
booktitle = {IEEE 9th Annual Computing and Communication Workshop and Conference (CCWC 2019)},
note = {Best Paper in Track},
year = {2019},
petsc_uses = {KSP}
}
@MastersThesis{ rinaldo-ceresoli18,
author = {Stefano Guido Rinaldo and Andrea Ceresoli},
title = {Newton–Krylov–Schwarz Methods for Distributed Power Flow and Related
Applications},
school = {Politecnico di Milano},
year = {2018},
month = apr,
petsc_uses = {KSP}
}
@Article{ sananschneppmay2016,
title = {Pipelined, Flexible {K}rylov Subspace Methods},
author = {P. Sanan and S. M. Schnepp and D. A. May},
journal = {SIAM Journal on Scientific Computing},
volume = {38},
number = {5},
pages = {C441-C470},
year = {2016},
doi = {10.1137/15M1049130},
petsc_uses = {KSP}
}
@Article{ petscsf2022,
author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and
Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and
Smith, Barry F. and Zampini, Stefano},
journal = {IEEE Transactions on Parallel and Distributed Systems},
title = {The {PetscSF} Scalable Communication Layer},
year = {2022},
volume = {33},
number = {4},
pages = {842-853},
doi = {10.1109/TPDS.2021.3084070}
}
@Article{ brandt2000,
title = {General highly accurate algebraic coarsening},
author = {Achi Brandt},
journal = {Electronic Transactions on Numerical Analysis},
volume = {10},
number = {9680},
pages = {1--20},
issn = {10689613},
year = {2000}
}
@Article{ dalcinpazklercosimo2011,
title = {Parallel distributed computing using Python},
author = {Lisandro D. Dalcin and Rodrigo R. Paz and Pablo A. Kler and Alejandro Cosimo},
journal = {Advances in Water Resources},
volume = {34},
number = {9},
pages = {1124 - 1139},
note = {New Computational Methods and Software Tools},
issn = {0309-1708},
doi = {10.1016/j.advwatres.2011.04.013},
year = {2011}
}
@Article{ behnelbradshawcitrodalcinseljebotnsmith2011,
title = {Cython: The Best of Both Worlds},
author = {Behnel,Stefan and Bradshaw,Robert and Citro,Craig and Dalcin,Lisandro and
Seljebotn,Dag Sverre and Smith,Kurt },
journal = {Computing in Science \& Engineering},
volume = {13},
number = {2},
pages = {31-39},
doi = {10.1109/MCSE.2010.118},
year = {2011}
}
@Article{ dalcinpazstorti2005,
title = {MPI for Python},
author = {Lisandro Dalcín and Rodrigo Paz and Mario Storti},
journal = {Journal of Parallel and Distributed Computing},
volume = {65},
number = {9},
pages = {1108 - 1115},
issn = {0743-7315},
doi = {10.1016/j.jpdc.2005.03.010},
year = {2005}
}
@Article{ dalcincolliervignalcortescalo2016,
title = {PetIGA: A framework for high-performance isogeometric analysis},
author = {Lisandro Dalcin and Nathan Collier and P. Vignal and A.M.A. Cortes and Victor M.
Calo},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {308},
pages = {151 - 181},
issn = {0045-7825},
doi = {10.1016/j.cma.2016.05.011},
year = {2016}
}
@Article{ collierpardodalcinpaszynskicalo2012,
title = {The cost of continuity: A study of the performance of isogeometric finite
elements using direct solvers},
author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M.
Calo},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {213-216},
pages = {353 - 361},
issn = {0045-7825},
doi = {10.1016/j.cma.2011.11.002},
year = {2012}
}
@Article{ collierdalcinpardocalo2013,
title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite
Elements},
author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo},
journal = {SIAM Journal on Scientific Computing},
volume = {35},
number = {2},
pages = {A767-A784},
doi = {10.1137/120881038},
year = {2013}
}
@Article{ dunning2017jump,
title = {{JuMP}: a modeling language for mathematical optimization},
author = {Dunning, Iain and Huchette, Joey and Lubin, Miles},
journal = {SIAM Review},
volume = {59},
number = {2},
pages = {295--320},
year = {2017},
publisher = {SIAM}
}
@InProceedings{ prudencioschulz2011,
title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for
Estimation, Simulation and Optimization},
author = {Ernesto E Prudencio and Karl W Schulz},
booktitle = {European Conference on Parallel Processing},
pages = {398--407},
year = {2011}
}
@Misc{ rol-website,
key = {ROL},
title = {{Rapid Optimization Library} Website},
howpublished = {\url{https://trilinos.org/packages/rol}},
year = {2018}
}
@Article{ more1994line,
title = {Line search algorithms with guaranteed sufficient decrease},
author = {Mor{\'e}, Jorge J and Thuente, David J},
journal = {ACM Transactions on Mathematical Software},
volume = {20},
number = {3},
pages = {286--307},
year = {1994},
publisher = {ACM}
}
@Article{ griewank2000algorithm,
title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or
adjoint mode of computational differentiation},
author = {Griewank, Andreas and Walther, Andrea},
journal = {ACM Transactions on Mathematical Software},
volume = {26},
number = {1},
pages = {19--45},
year = {2000},
publisher = {ACM}
}
@Article{ metcalf2011seven,
title = {The seven ages of fortran},
author = {Metcalf, Michael},
journal = {Journal of Computer Science \& Technology},
volume = {11},
year = {2011}
}
@Article{ giraldo_2013,
title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified
model of the atmosphere {(NUMA)}},
author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu},
journal = {SIAM Journal on Scientific Computing},
year = {2013},
number = {5},
pages = {B1162-B1194},
volume = {35},
doi = {10.1137/120876034}
}
@Article{ constantinescu_tr2016b,
author = {Constantinescu, E.M.},
title = {Estimating Global Errors in Time Stepping},
journal = {ArXiv e-prints},
archiveprefix = {arXiv},
eprint = {1503.05166},
primaryclass = {math.NA},
keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70},
year = {2016},
month = mar,
adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@Article{ pareschi_2005,
title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems
with Relaxation},
author = {L. Pareschi and G. Russo},
journal = {Journal of Scientific Computing},
year = {2005},
number = {1},
pages = {129--155},
volume = {25}
}
@Article{ kennedy_2003,
title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations},
author = {C.A. Kennedy and M.H. Carpenter},
journal = {Appl. Numer. Math.},
year = {2003},
number = {1-2},
pages = {139--181},
volume = {44},
doi = {10.1016/S0168-9274(02)00138-1},
publisher = {Elsevier Science Publishers B. V.}
}
@Unpublished{ boscarino_tr2011,
title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic
equations in the diffusion limit},
author = {Boscarino, S. and Pareschi, L. and Russo, G.},
note = {Arxiv preprint arXiv:1110.4375},
year = {2011}
}
@Article{ ascher_1997,
title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential
equations},
author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri},
journal = {Applied Numerical Mathematics},
year = {1997},
pages = {151--167},
volume = {25}
}
@Book{ ascherpetzold1998,
title = {Computer methods for ordinary differential equations and differential-algebraic
equations},
author = {Uri M Ascher and Linda R Petzold},
volume = {61},
publisher = {SIAM},
year = {1998}
}
@Article{ colomesbadia2016,
title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes}
equations},
author = {Oriol Colom{\'e}s and Santiago Badia},
journal = {International Journal for Numerical Methods in Engineering},
volume = {105},
number = {5},
pages = {372--400},
year = {2016}
}
@Article{ sandu_1997,
title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry problems {II}:
{R}osenbrock solvers},
author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A.
Potra},
journal = {Atmospheric Environment},
year = {1997},
number = {20},
pages = {3459--3472},
volume = {31},
abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major
task is the integration of the stiff systems of ordinary differential equations
describing the chemical transformations. It is therefore of interest to
systematically search for stiff solvers which can be identified as close to
optimal for atmospheric applications. In this paper we continue our investigation
from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85)
and compare eight solvers on a set of seven box-models used in present day models.
The focus is on Rosenbrock solvers. These turn out to be very well suited for our
application when they are provided with highly efficient sparse matrix techniques
to economize on the linear algebra. Two of the Rosenbrock solvers tested are from
the literature, viz. and 4, and two are new and specially developed for air
quality applications, viz. 3 and 3. }
}
@Article{ rang_2005,
title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic
equations of index 1},
author = {Rang, J. and Angermann, L.},
journal = {BIT Numerical Mathematics},
year = {2005},
number = {4},
pages = {761--787},
volume = {45},
publisher = {Springer},
doi = {10.1007/s10543-005-0035-y}
}
@article{rang2015improved,
title = {Improved traditional {R}osenbrock--{W}anner methods for stiff {ODE}s and {DAE}s},
author = {Rang, Joachim},
journal = {Journal of Computational and Applied Mathematics},
volume = {286},
pages = {128--144},
year = {2015},
publisher = {Elsevier},
doi = {10.1016/j.cam.2015.03.010}
}
@Article{ gottliebketchesonshu2009,
author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu},
title = {{High order strong stability preserving time discretizations}},
journal = {Journal of Scientific Computing},
volume = {38},
number = {3},
pages = {251--289},
doi = {10.1007/s10915-008-9239-z},
year = {2009}
}
@Article{ ZhouGuoShu2001,
title = {Numerical study on Landau damping},
author = {Tie Zhou and Yan Guo and Chi Wang Shu},
journal = {Physica D: Nonlinear Phenomena},
volume = {157},
issue = {4},
pages = {322-333},
doi = {10.1016/S0167-2789(01)00289-5},
issn = {01672789},
year = {2001}
}
@Article{ ketcheson_2008,
title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with
Low-Storage Implementations},
author = {D.I. Ketcheson},
journal = {SIAM Journal on Scientific Computing},
year = {2008},
number = {4},
pages = {2113--2136},
volume = {30},
doi = {10.1137/07070485X},
keywords = {method of lines, strong stability-preserving, monotonicity, low-storage,
RungeKutta methods},
publisher = {SIAM}
}
@Article{ jansen_2000,
title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes
equations with a stabilized finite element method},
author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.},
journal = {Computer Methods in Applied Mechanics and Engineering},
year = {2000},
number = {3},
pages = {305--319},
volume = {190},
publisher = {Elsevier}
}
@Article{ butcher_2007,
title = {Error propagation of general linear methods for ordinary differential equations},
author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright},
journal = {Journal of Complexity},
year = {2007},
number = {4-6},
pages = {560--580},
volume = {23},
abstract = {We discuss error propagation for general linear methods for ordinary differential
equations up to terms of order p+2, where p is the order of the method. These
results are then applied to the estimation of local discretization errors for
methods of order p and for the adjacent order p+1. The results of numerical
experiments confirm the reliability of these estimates. This research has
applications in the design of robust stepsize and order changing strategies for
algorithms based on general linear methods.},
doi = {10.1016/j.jco.2007.01.009},
issn = {0885-064X}
}
@Article{ constantinescu_a2010a,
title = {Extrapolated implicit-explicit time stepping},
author = {E.M. Constantinescu and A. Sandu},
journal = {SIAM Journal on Scientific Computing},
year = {2010},
number = {6},
pages = {4452-4477},
volume = {31},
comment = {Preprint \# ANL/MCS-P1612-0409},
doi = {10.1137/080732833}
}
@InProceedings{ devito2011liszt,
title = {Liszt: a domain specific language for building portable mesh-based PDE solvers},
author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen
and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and
Aiken, Alex and Duraisamy, Karthik and others},
booktitle = {Proceedings of 2011 International Conference for High Performance Computing,
Networking, Storage and Analysis},
pages = {9},
year = {2011},
organization = {ACM}
}
@Article{ devito2011designing,
title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers},
author = {DeVito, Zachary and Hanrahan, Pat},
journal = {Scientific Discovery through Advanced Computing Program (SciDAC)},
year = {2011}
}
@Misc{ pgasintro,
author = {Tim Stitt},
title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming
Model},
note = {\url{http://cnx.org/content/m20649/latest/}}
}
@InProceedings{ el2006upc,
title = {UPC: unified parallel C},
author = {El-Ghazawi, Tarek and Smith, Lauren},
booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing},
pages = {27},
year = {2006},
organization = {ACM}
}
@InProceedings{ numrich1998co,
title = {Co-Array Fortran for parallel programming},
author = {Numrich, Robert W and Reid, John},
booktitle = {ACM Sigplan Fortran Forum},
volume = {17},
number = {2},
pages = {1--31},
year = {1998},
organization = {ACM}
}
@Article{ aiken1997titanium,
title = {Titanium: A high-performance Java dialect},
author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger,
Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike,
Geoff and Semenzato, Luigi and others},
year = {1997}
}
@Article{ charles2005x10,
title = {X10: an object-oriented approach to non-uniform cluster computing},
author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa,
Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and
Sarkar, Vivek},
journal = {Acm Sigplan Notices},
volume = {40},
number = {10},
pages = {519--538},
year = {2005},
publisher = {ACM}
}
@Article{ chamberlain2007parallel,
title = {Parallel programmability and the chapel language},
author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P},
journal = {International Journal of High Performance Computing Applications},
volume = {21},
number = {3},
pages = {291--312},
year = {2007},
publisher = {SAGE Publications}
}
@InProceedings{ charmppoopsla93,
author = {{Kal\'{e}}, L.V. and Krishnan, S.},
title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}},
editor = {Paepcke, A.},
fulleditor = {Paepcke, Andreas},
pages = {91--108},
month = sep,
year = {1993},
booktitle = {{Proceedings of OOPSLA'93}},
publisher = {{ACM Press}}
}
@InProceedings{ hewitt1973universal,
title = {A universal modular actor formalism for artificial intelligence},
author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard},
booktitle = {Proceedings of the 3rd international joint conference on Artificial
intelligence},
pages = {235--245},
year = {1973},
organization = {Morgan Kaufmann Publishers Inc.}
}
@Book{ yonezawa1990abcl,
title = {ABCL: an object-oriented concurrent system},
author = {Yonezawa, Akinori},
year = {1990},
publisher = {MIT press}
}
@InProceedings{ dally1988object,
title = {Object-oriented concurrent programming in CST},
author = {Dally, William J and Chien, Andrew A},
booktitle = {Proceedings of the third conference on Hypercube concurrent computers and
applications: Architecture, software, computer systems, and general issues-Volume
1},
pages = {434--439},
year = {1988},
organization = {ACM}
}
@Article{ grimshaw1993easy,
title = {Easy-to-use object-oriented parallel processing with Mentat},
author = {Grimshaw, Andrew S.},
journal = {Computer},
volume = {26},
number = {5},
pages = {39--51},
year = {1993},
publisher = {IEEE}
}
@InProceedings{ gannon1991object,
title = {Object oriented parallelism: pC++ ideas and experiments},
author = {Gannon, Dennis and Lee, JK},
booktitle = {Proceedings of},
pages = {13--23},
year = {1991}
}
@InProceedings{ lau1992object,
title = {An object-oriented class library for scalable parallel heuristic search},
author = {Lau, Wing-cheong and Singh, Vineet},
booktitle = {ECOOP’92 European Conference on Object-Oriented Programming},
pages = {252--267},
year = {1992},
organization = {Springer}
}
@Book{ chase1989amber,
title = {The Amber system: Parallel programming on a network of multiprocessors},
author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and
Littlefield, Richard},
volume = {23},
number = {5},
year = {1989},
publisher = {ACM}
}
@InProceedings{ kaiser2009parallex,
title = {Parallex an advanced parallel execution model for scaling-impaired applications},
author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas},
booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on},
pages = {394--401},
year = {2009},
organization = {IEEE}
}
@TechReport{ ipm,
author = {Barry F. Smith},
title = {A New Parallel Programming Model for Computer Simulation},
institution = {Argonne National Laboratory},
year = {2014},
number = {ANL/MCS-P5135-0414}
}
@Article{ groppsnir,
author = {William Gropp and Marc Snir},
title = {Programming for Exascale Computers},
journal = {Computing in Science and Engineering},
volume = {15},
number = {6},
issn = {1521-9615},
year = {2013},
pages = {27-35},
doi = {10.1109/MCSE.2013.96},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA}
}
@Book{ mpi3,
title = {MPI: A Message-Passing Interface Standard, Version 3.0},
author = {Message Passing Interface Forum},
year = {2012},
publisher = {High Performance Computing Center Stuttgart (HLRS)}
}
@Book{ openmp4,
title = {OpenMP Application Program Interface, Version 4.0},
year = {2013},
publisher = {OpenMP Architecture Review Board}
}
@InProceedings{ hartono2009annotation,
title = {Annotation-based empirical performance tuning using {Orio}},
author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy},
booktitle = {Parallel \& Distributed Processing, 2009. IPDPS 2009. IEEE International
Symposium on},
pages = {1--11},
year = {2009},
organization = {IEEE}
}
@Book{ toselli2005domain,
title = {Domain Decomposition Methods: Algorithms and Theory},
author = {Toselli, Andrea and Widlund, Olof B},
volume = {34},
year = {2005},
publisher = {Springer}
}
@InBook{ st2016,
author = {Barry F. Smith and Xumin Tu},
chapter = {Domain Decomposition},
title = {Encyclopedia of Applied and Computational Mathematics},
bookeditor = {B. Engquist},
publisher = {Springer},
pages = {375--381},
year = {2016}
}
@TechReport{ saws,
author = {Matt Otten and Jed Brown and Barry F. Smith},
title = {Scientific Application Web Server {(SAWs)} Users Manual},
institution = {Argonne National Laboratory},
year = {2013}
}
@Article{ smith1997domain,
title = {Domain Decomposition Methods for Partial Differential Equations},
author = {Smith, B.F.},
journal = {ICASE LARC Interdisciplinary Series in Science and Engineering},
volume = {4},
pages = {225--244},
year = {1997},
publisher = {Citeseer}
}
@Article{ spillane2011abstract,
title = {Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems
in the overlaps},
author = {Spillane, N and Dolean, V and Hauret, P and Nataf, F and Pechstein, C and
Scheichl, R},
journal = {NuMa-Report},
volume = {7},
pages = {2007},
year = {2011}
}
@InProceedings{ jolivet2013scalabledd,
title = {Scalable domain decomposition preconditioners for heterogeneous elliptic
problems},
author = {Jolivet, Pierre and Hecht, Fr{\'e}d{\'e}ric and Nataf, Fr{\'e}d{\'e}ric and
Prud'homme, Christophe},
booktitle = {Proceedings of SC13: International Conference for High Performance Computing,
Networking, Storage and Analysis},
pages = {80},
year = {2013},
organization = {ACM}
}
@Book{ ks2000,
author = {D. Kinderlehrer and G. Stampacchia},
publisher = {Society for Industrial Mathematics},
title = {An Introduction to Variational Inequalities and Their Applications},
year = {2000}
}
@Article{ wan2000energy,
title = {An energy-minimizing interpolation for robust multigrid methods},
author = {Wan, W.L. and Chan, T.F. and Smith, B. F.},
journal = {SIAM Journal on Scientific Computing},
volume = {21},
number = {4},
pages = {1632--1649},
year = {2000},
publisher = {Philadelphia, PA: SIAM, c1993-}
}
@Article{ chansmith1994,
title = {Domain decomposition and multigrid algorithms for elliptic problems on
unstructured meshes},
author = {Chan, T.F. and Smith, B.F.},
journal = {Electronic Transactions on Numerical Analysis},
volume = {2},
pages = {171--182},
year = {1994}
}
@TechReport{ proto-fsp,
author = {Venkatramani Balaji and Barry Smith and Brian Van Straalen and Priya Vashishta
and Michael Zarnstorff and Michael Zika},
title = {Report of the {Proto-FSP} {Assessment Panel for the FSP}},
institution = {Princeton Plasma Physics Laboratory},
year = {2010},
url = {http://www.pppl.gov/fsp/documents/Proto-FSPAssessmentReport.pdf}
}
@Article{ hirvijoki2021,
title = {Structure-preserving marker-particle discretizations of {Coulomb} collisions for
particle-in-cell codes},
journal = {Plasma Phys. Control. Fusion},
author = {Eero Hirvijoki},
note = {in press},
doi = {10.1088/1361-6587/abe884},
year = {2021}
}
@Article{ ipsen2001,
author = {Ilse C. F. Ipsen},
journal = {SIAM J. Sci. Comput.},
pages = {1050--1051},
volume = {23},
publisher = {SIAM},
title = {A Note on Preconditioning Nonsymmetric Matrices},
year = {2001}
}
% Random papers on solvers for GPUs
@InProceedings{ gpus-suck,
author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. },
title = { On the Limits of {GPU} Acceleration},
booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism},
year = {2010},
publisher = {USENIX}
}
@InProceedings{ 882364,
author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter},
title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid},
booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers},
year = {2003},
isbn = {1-58113-709-5},
pages = {917--924},
location = {San Diego, California},
doi = {10.1145/1201775.882364},
publisher = {ACM},
address = {New York, NY}
}
@Conference{ feng2008multigrid,
author = {Feng, Z. and Li, P.},
booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008},
date-added = {2010-08-19 15:57:06 -0500},
date-modified = {2010-08-19 15:57:06 -0500},
pages = {647--654},
title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms},
year = {2008}
}
@Conference{ goodnight2003multigrid,
author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.},
booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware},
date-added = {2010-08-19 15:45:20 -0500},
date-modified = {2010-08-19 15:45:20 -0500},
organization = {Eurographics Association},
pages = {102--111},
title = {A multigrid solver for boundary value problems using programmable graphics
hardware},
year = {2003}
}
@Article{ buatois2007concurrent,
author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.},
date-added = {2010-08-19 15:45:02 -0500},
date-modified = {2010-08-19 15:45:02 -0500},
journal = {High Performance Computing and Communications},
pages = {358--371},
publisher = {Citeseer},
title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}},
year = {2007}
}
@Article{ joldes2010real,
author = {Joldes, G.R. and Wittek, A. and Miller, K.},
date-added = {2010-08-19 15:44:41 -0500},
date-modified = {2010-08-19 15:44:41 -0500},
journal = {Computer Methods in Applied Mechanics and Engineering},
publisher = {Elsevier},
title = {Real-time nonlinear finite element computations on {GPU}-application to
neurosurgical simulation},
year = {2010}
}
@Misc{ aharon2005gpu,
author = {Aharon, S.},
date-added = {2010-08-19 15:44:32 -0500},
date-modified = {2010-08-19 15:44:32 -0500},
month = apr,
note = {US Patent App. 11/115,642},
publisher = {Google Patents},
title = {{GPU}-based Finite Element},
year = {2005}
}
@Article{ cevahir2009fast,
author = {Cevahir, A. and Nukada, A. and Matsuoka, S.},
date-added = {2010-08-19 15:44:01 -0500},
date-modified = {2010-08-19 15:44:01 -0500},
journal = {Computational Science--ICCS 2009},
pages = {893--903},
publisher = {Springer},
title = {Fast conjugate gradients with multiple {GPU}s},
year = {2009}
}
@Article{ maier1995symmetric,
author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.},
date-added = {2010-08-19 15:43:57 -0500},
date-modified = {2010-08-19 15:43:57 -0500},
journal = {Computational Mechanics},
number = {1},
pages = {115--129},
publisher = {Springer},
title = {Symmetric {G}alerkin boundary element method in plasticity and gradient
plasticity},
volume = {17},
year = {1995}
}
@Article{ corrigan-running,
author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.},
date-added = {2010-08-19 15:43:47 -0500},
date-modified = {2010-08-19 15:43:47 -0500},
journal = {International Journal for Numerical Methods in Fluids},
publisher = {John Wiley \& Sons},
title = {Running unstructured grid based CFD solvers on modern graphics hardware}
}
@InProceedings{ volkov08,
author = {Vasily Volkov and James W. Demmel},
title = {Benchmarking GPUs to tune dense linear algebra},
booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)},
note = {\url{http://mc.stanford.edu/cgi-bin/images/6/65/SC08_Volkov_GPU.pdf}},
year = {2008}
}
@TechReport{ cray-mvmult,
author = {Guy~E. Blelloch and Michael~A. Heroux and Marco Zagha},
title = {Segmented Operations for Sparse Matrix Computation on Vector Multiprocessors},
institution = {School of Computer Science, Carnegie Mellon University},
number = {CMU-CS-93-173},
month = aug,
year = {1993}
}
@Conference{ bell2009implementing,
author = {Bell, N. and Garland, M.},
booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage
and Analysis},
date-added = {2010-08-19 15:43:42 -0500},
date-modified = {2010-08-19 15:43:42 -0500},
organization = {ACM},
pages = {1--11},
title = {Implementing sparse matrix-vector multiplication on throughput-oriented
processors},
year = {2009}
}
@Article{ bell2008efficient,
author = {Bell, N. and Garland, M.},
date-added = {2010-08-19 15:43:36 -0500},
date-modified = {2010-08-19 15:43:36 -0500},
journal = {{NVIDIA} Corporation, {NVIDIA} Technical Report NVR-2008-004},
title = {Efficient sparse matrix-vector multiplication on {CUDA}},
year = {2008}
}
@Article{ cohen-fast,
author = {Cohen, J. and Molemaker, M.J.},
date-added = {2010-08-19 15:43:34 -0500},
date-modified = {2010-08-19 15:43:34 -0500},
journal = {Parallel Computational Fluid Dynamics: Recent Advances and Future Directions},
pages = {414},
publisher = {DEStech Publications},
title = {A fast double precision CFD code using CUDA}
}
@Article{ kazhdan2008streaming,
author = {Kazhdan, M. and Hoppe, H.},
date-added = {2010-08-19 15:43:32 -0500},
date-modified = {2010-08-19 15:43:32 -0500},
journal = {ACM Transactions on Graphics (TOG)},
number = {3},
pages = {21},
publisher = {ACM},
title = {Streaming multigrid for gradient-domain operations on large images},
volume = {27},
year = {2008}
}
@Article{ bonnet1998symmetric,
author = {Bonnet, M. and Maier, G. and Polizzotto, C.},
date-added = {2010-08-19 15:43:18 -0500},
date-modified = {2010-08-19 15:43:18 -0500},
journal = {Appl. Mech. Rev},
pages = {669--704},
title = {Symmetric {G}alerkin boundary element method.},
volume = {51},
year = {1998}
}
@Conference{ zamith2007gpu,
author = {Zamith, M. and Clua, E. and Pagliosa, P. and Conci, A. and Montenegro, A. and
Valente, L.},
booktitle = {Proceedings of the VI Brazilian Symposium on Computer Games and Digital
Entertainment},
date-added = {2010-08-19 15:43:14 -0500},
date-modified = {2010-08-19 15:43:14 -0500},
pages = {37--43},
title = {The {GPU} used as a math co-processor in real time applications},
year = {2007}
}
@Article{ baskaran2009optimizing,
author = {Baskaran, M.M. and Bordawekar, R.},
date-added = {2010-08-19 15:42:56 -0500},
date-modified = {2010-08-19 15:42:56 -0500},
journal = {IBM Research Report RC24704, IBM},
title = {Optimizing sparse matrix-vector multiplication on {GPU}s},
year = {2009}
}
@Misc{ szeliski2006locally,
author = {Szeliski, R.},
date-added = {2010-08-19 15:42:45 -0500},
date-modified = {2010-08-19 15:42:45 -0500},
month = jul,
note = {US Patent App. 11/459,724},
publisher = {Google Patents},
title = {Locally adapted hierarchical basis preconditioning},
year = {2006}
}
@Article{ jung2006cholesky,
author = {Jung, J.H. and O'Leary, D.P.},
date-added = {2010-08-19 15:42:34 -0500},
date-modified = {2010-08-19 15:42:34 -0500},
journal = {Scholarly Paper, University of Maryland},
publisher = {Citeseer},
title = {Cholesky decomposition and linear programming on a {GPU}},
year = {2006}
}
@Conference{ filipovic2009gpu,
author = {Filipovic, J. and Peterlik, I. and Fousek, J.},
booktitle = {SAAHPC: Symposium on Application Accelerators in HPC},
date-added = {2010-08-19 15:42:33 -0500},
date-modified = {2010-08-19 15:42:33 -0500},
title = {{GPU} Acceleration of Equations Assembly in Finite Elements Method-Preliminary
Results},
year = {2009}
}
@Article{ taylor2009modelling,
author = {Taylor, ZA and Comas, O. and Cheng, M. and Passenger, J. and Hawkes, DJ and
Atkinson, D. and Ourselin, S.},
date-added = {2010-08-19 15:42:23 -0500},
date-modified = {2010-08-19 15:42:23 -0500},
journal = {Medical Image Analysis},
number = {2},
pages = {234--244},
publisher = {Elsevier},
title = {On modelling of anisotropic viscoelasticity for soft tissue simulation: Numerical
solution and {GPU} execution},
volume = {13},
year = {2009}
}
@Conference{ owens2007survey,
author = {Owens, J.D. and Luebke, D. and Govindaraju, N. and Harris, M. and Kr{\\"u}ger, J.
and Lefohn, A.E. and Purcell, T.J.},
booktitle = {Computer Graphics Forum},
date-added = {2010-08-19 15:42:21 -0500},
date-modified = {2010-08-19 15:42:21 -0500},
number = {1},
organization = {John Wiley \& Sons},
pages = {80--113},
title = {A survey of general-purpose computation on graphics hardware},
volume = {26},
year = {2007}
}
@Article{ strzodka2005scientific,
author = {Strzodka, R. and Doggett, M. and Kolb, A.},
date-added = {2010-08-19 15:42:18 -0500},
date-modified = {2010-08-19 15:42:18 -0500},
journal = {Simulation Modelling Practice and Theory},
number = {8},
pages = {667--680},
publisher = {Elsevier},
title = {Scientific computation for simulations on programmable graphics hardware},
volume = {13},
year = {2005}
}
@Conference{ rumpf2001using,
author = {Rumpf, M. and Strzodka, R.},
booktitle = {Proc. of IASTED Visualization, Imaging and Image Processing Conference
(VIIP-01)},
date-added = {2010-08-19 15:42:15 -0500},
date-modified = {2010-08-19 15:42:15 -0500},
organization = {Citeseer},
pages = {193--202},
title = {Using graphics cards for quantized FEM computations},
year = {2001}
}
@Article{ sirtori1992galerkin,
author = {Sirtori, S. and Maier, G. and Novati, G. and Miccoli, S.},
date-added = {2010-08-19 15:42:14 -0500},
date-modified = {2010-08-19 15:42:14 -0500},
journal = {International Journal for Numerical Methods in Engineering},
number = {2},
pages = {255--282},
publisher = {John Wiley \& Sons},
title = {A {G}alerkin symmetric boundary-element method in elasticity: formulation and
implementation},
volume = {35},
year = {1992}
}
@Article{ tejada2005large,
author = {Tejada, E. and Ertl, T.},
date-added = {2010-08-19 15:42:09 -0500},
date-modified = {2010-08-19 15:42:09 -0500},
journal = {Simulation Modelling Practice and Theory},
number = {8},
pages = {703--715},
publisher = {Elsevier},
title = {Large steps in {GPU}-based deformable bodies simulation},
volume = {13},
year = {2005}
}
@Article{ goddeke2008using,
author = {Goddeke, D. and Strzodka, R. and Mohd-Yusof, J. and McCormick, P. and Wobker, H.
and Becker, C. and Turek, S.},
date-added = {2010-08-19 15:42:06 -0500},
date-modified = {2010-08-19 15:42:06 -0500},
journal = {International Journal of Computational Science and Engineering},
number = {1},
pages = {36--55},
publisher = {Inderscience},
title = {Using {GPU}s to improve multigrid solver performance on a cluster},
volume = {4},
year = {2008}
}
@Article{ garland2008parallel,
author = {Garland, M. and Le Grand, S. and Nickolls, J. and Anderson, J. and Hardwick, J.
and Morton, S. and Phillips, E. and Zhang, Y. and Volkov, V.},
date-added = {2010-08-19 15:41:51 -0500},
date-modified = {2010-08-19 15:41:51 -0500},
journal = {IEEE Micro},
number = {4},
pages = {13--27},
title = {Parallel computing experiences with CUDA},
volume = {28},
year = {2008}
}
@Article{ wong1985method,
author = {Wong, SH and Ciric, IR},
date-added = {2010-08-19 15:41:48 -0500},
date-modified = {2010-08-19 15:41:48 -0500},
journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical
and Electronic Engineering},
publisher = {MCB UP Ltd},
title = {Method of conformal transformation for the finite-element solution of
axisymmetric exterior-field problems},
volume = {4},
year = {1985}
}
@Article{ turek-feast,
author = {Turek, S. and G{\\"o}ddeke, D. and Becker, C. and Buijssen, S.H.M. and Wobker,
H.},
date-added = {2010-08-19 15:41:47 -0500},
date-modified = {2010-08-19 15:41:47 -0500},
journal = {Concurrency and Computation: Practice and Experience},
publisher = {John Wiley \& Sons},
title = {FEAST-realization of hardware-oriented numerics for HPC simulations with finite
elements}
}
@Article{ abedi2006space,
author = {Abedi, R. and Petracovici, B. and Haber, R.B.},
date-added = {2010-08-19 15:41:46 -0500},
date-modified = {2010-08-19 15:41:46 -0500},
journal = {Computer Methods in Applied Mechanics and Engineering},
number = {25-28},
pages = {3247--3273},
publisher = {Elsevier},
title = {A space-time discontinuous {G}alerkin method for linearized elastodynamics with
element-wise momentum balance},
volume = {195},
year = {2006}
}
@Conference{ georgii2005interactiveb,
author = {Georgii, J. and Westermann, R.},
booktitle = {Proceedings of VMV},
date-added = {2010-08-19 15:41:36 -0500},
date-modified = {2010-08-19 15:41:36 -0500},
title = {Interactive simulation and rendering of heterogeneous deformable bodies},
year = {2005}
}
@Article{ mosegaard2005gpu,
author = {Mosegaard, J. and others},
date-added = {2010-08-19 15:41:35 -0500},
date-modified = {2010-08-19 15:41:35 -0500},
publisher = {IEEE Computer Society},
title = {{GPU} accelerated surgical simulators for complex morphology},
year = {2005}
}
@Article{ meyer2007particle,
author = {Meyer, M. and Nelson, B. and Kirby, R. and Whitaker, R.},
date-added = {2010-08-19 15:41:33 -0500},
date-modified = {2010-08-19 15:41:33 -0500},
journal = {IEEE Transactions on Visualization and Computer Graphics},
pages = {1015--1026},
publisher = {Published by the IEEE Computer Society},
title = {Particle systems for efficient and accurate high-order finite element
visualization},
year = {2007}
}
@Conference{ rumpf2001nonlinear,
author = {Rumpf, M. and Strzodka, R.},
booktitle = {Data Visualization 2001: proceedings of the Joint Eurographics-IEEE TCVG
Symposium on Visualization in Ascona, Switzerland, May 28-30, 2001},
date-added = {2010-08-19 15:41:29 -0500},
date-modified = {2010-08-19 15:41:29 -0500},
organization = {Springer Verlag Wien},
pages = {75},
title = {Nonlinear diffusion in graphics hardware},
year = {2001}
}
@Article{ georgii2005interactive,
author = {Georgii, J. and Echtler, F. and Westermann, R.},
date-added = {2010-08-19 15:41:28 -0500},
date-modified = {2010-08-19 15:41:28 -0500},
journal = {Simulation and Visualisation},
pages = {247--258},
publisher = {Citeseer},
title = {Interactive simulation of deformable bodies on {GPU}s},
volume = {2005},
year = {2005}
}
@Article{ harish2007accelerating,
author = {Harish, P. and Narayanan, P.},
date-added = {2010-08-19 15:41:27 -0500},
date-modified = {2010-08-19 15:41:27 -0500},
journal = {High Performance Computing--HiPC 2007},
pages = {197--208},
publisher = {Springer},
title = {Accelerating large graph algorithms on the {GPU} using CUDA},
year = {2007}
}
@Article{ keunings1995parallel,
author = {Keunings, R.},
date-added = {2010-08-19 15:41:19 -0500},
date-modified = {2010-08-19 15:41:19 -0500},
journal = {Computers and Chemical Engineering},
number = {6},
pages = {647--670},
publisher = {Oxford; New York: Pergamon Press, 1977-},
title = {Parallel finite element algorithms applied to computational rheology},
volume = {19},
year = {1995}
}
@Conference{ taylor2007real,
author = {Taylor, Z.A. and Cheng, M. and Ourselin, S.},
booktitle = {Proceedings of the 10th international conference on Medical image computing and
computer-assisted intervention-Volume Part I},
date-added = {2010-08-19 15:41:17 -0500},
date-modified = {2010-08-19 15:41:17 -0500},
organization = {Springer-Verlag},
pages = {701--708},
title = {Real-time nonlinear finite element analysis for surgical simulation using
graphics processing units},
year = {2007}
}
@Article{ liu2000finite,
author = {Liu, R. and Li, DY},
date-added = {2010-08-19 15:41:16 -0500},
date-modified = {2010-08-19 15:41:16 -0500},
journal = {Materials Science and Engineering A},
number = {1-2},
pages = {169--175},
publisher = {Elsevier},
title = {A finite element model study on wear resistance of pseudoelastic {TiNi} alloy},
volume = {277},
year = {2000}
}
@Conference{ kakadiaris1994active,
author = {Kakadiaris, I.A. and Metaxas, D. and Bajcsy, R.},
booktitle = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
date-added = {2010-08-19 15:41:15 -0500},
date-modified = {2010-08-19 15:41:15 -0500},
organization = {Citeseer},
pages = {980--980},
title = {Active part-decomposition, shape, and motion estimation of articulated objects: A
physics-based approach},
year = {1994}
}
@Conference{ de2004gpu,
author = {De Pascale, M. and De Pascale, G. and Prattichizzo, D. and Barbagli, F.},
booktitle = {Proceedings of Eurohaptics},
date-added = {2010-08-19 15:41:14 -0500},
date-modified = {2010-08-19 15:41:14 -0500},
organization = {Citeseer},
pages = {44--51},
title = {A {GPU}-friendly method for haptic and graphic rendering of deformable objects},
volume = {2004},
year = {2004}
}
@Book{ taflove1995computational,
author = {Taflove, A. and Hagness, S.C.},
date-added = {2010-08-19 15:41:14 -0500},
date-modified = {2010-08-19 15:41:14 -0500},
publisher = {Artech House Norwood, MA},
title = {Computational electrodynamics},
year = {1995}
}
@Conference{ galoppo2005lu,
author = {Galoppo, N. and Govindaraju, N.K. and Henson, M. and Manocha, D.},
booktitle = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing},
date-added = {2010-08-19 15:41:13 -0500},
date-modified = {2010-08-19 15:41:13 -0500},
organization = {IEEE Computer Society},
pages = {3},
title = {{LU-GPU}: Efficient algorithms for solving dense linear systems on graphics
hardware},
year = {2005}
}
@Conference{ ryoo2008optimization,
author = {Ryoo, S. and Rodrigues, C.I. and Baghsorkhi, S.S. and Stone, S.S. and Kirk, D.B.
and Hwu, W.W.},
booktitle = {Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of
parallel programming},
date-added = {2010-08-19 15:41:12 -0500},
date-modified = {2010-08-19 15:41:12 -0500},
organization = {ACM},
pages = {73--82},
title = {Optimization principles and application performance evaluation of a multithreaded
{GPU} using CUDA},
year = {2008}
}
@Conference{ micikevicius20093d,
author = {Micikevicius, P.},
booktitle = {Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing
Units},
date-added = {2010-08-19 15:41:11 -0500},
date-modified = {2010-08-19 15:41:11 -0500},
organization = {ACM},
pages = {79--84},
title = {3D finite difference computation on {GPU}s using {CUDA}},
year = {2009}
}
@Conference{ zhou2004pixel,
author = {Zhou, Y. and Garland, M. and Haber, R.},
booktitle = {IEEE Visualization, 2004},
date-added = {2010-08-19 15:41:03 -0500},
date-modified = {2010-08-19 15:41:03 -0500},
pages = {425--432},
title = {Pixel-exact rendering of spacetime finite element solutions},
year = {2004}
}
@Article{ komatitsch2009porting,
author = {Komatitsch, D. and Mich{\'e}a, D. and Erlebacher, G.},
date-added = {2010-08-19 15:41:01 -0500},
date-modified = {2010-08-19 15:41:01 -0500},
journal = {Journal of Parallel and Distributed Computing},
number = {5},
pages = {451--460},
publisher = {Elsevier},
title = {Porting a high-order finite-element earthquake modeling application to NVIDIA
graphics cards using CUDA},
volume = {69},
year = {2009}
}
@Article{ komatitsch1998spectral,
author = {Komatitsch, D. and Vilotte, J.P.},
date-added = {2010-08-19 15:40:59 -0500},
date-modified = {2010-08-19 15:40:59 -0500},
journal = {Bulletin of the Seismological Society of America},
number = {2},
pages = {368--392},
publisher = {[El Cerrito, Calif., etc., Seismological Society of America, etc.]},
title = {The spectral element method: {A}n efficient tool to simulate the seismic response
of 2D and 3D geological structures},
volume = {88},
year = {1998}
}
@Article{ wu2005improved,
author = {Wu, W. and Heng, P.A.},
date-added = {2010-08-19 15:40:59 -0500},
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@Conference{ bolz2003sparse,
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year = {2004}
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% ----------------------------------------------------------------------------------------------------------------
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volume = {198(2)}
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@TechReport{ daly2012interagency,
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Computing},
year = {2002},
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year = {1994},
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author = {Clemens Szyperski},
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@Unpublished{ petsc:external,
author = {B. F. {Smith et al.}},
title = {{External Software Used by PETSc}},
note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}},
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author = {B. F. {Smith et al.}},
title = {{Software Packages that Use or Interface to PETSc}},
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institution = {Argonne National Laboratory}
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@Unpublished{ petsc:prizes,
author = {B. F. {Smith et al.}},
title = {{Prizes Won Using PETSc}},
note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}},
institution = {Argonne National Laboratory}
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author = {B. F. {Smith et al.}},
title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}},
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institution = {Argonne National Laboratory}
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title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes
{W}eb Page},
note = {http://www.asci.uchicago.edu},
author = {R. {Rosner et al.}},
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@Unpublished{ esi-web-page,
title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page},
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author = {R. {Clay et al.}}
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@Unpublished{ infobus-web-page,
title = {{I}nfo{B}us {W}eb Page},
note = {http://www.java.sun.com/beans/infobus},
key = {infobus}
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@Unpublished{ xray-web-page,
title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic
{S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)},
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Scientific and Engineering Computing},
year = {1999},
pages = {30-39}
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author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens},
title = {Divorcing Language Dependencies from a Scientific Software Library},
publisher = {SIAM},
booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing},
year = {2001}
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author = {Lori Freitag and Mark Jones and Paul Plassmann},
title = {Component Integration for Unstructured Mesh Algorithms and Software},
publisher = {SIAM},
booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable
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year = {1999},
pages = {215-224}
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@Book{ templates,
author = {R. Barrett and M. Berry and T. F. Chan and J. Demmel and J. Donato and J.
Dongarra and V. Eijkhout and R. Pozo and C. Romine and H. Van der Vorst },
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year = {1994},
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author = {M. Parashar and J. C. Browne and C. Edwards and K. Klimkowski},
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@TechReport{ parasha,
author = {M. Parashar and J. C. Browne},
title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement
Techniques},
institution = {Department of Computer Science, University of Texas at Austin},
year = {1995}
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author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang},
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journal = {Parallel Computing},
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author = {Greg Burns and Raja Daoud and James Vaigl},
title = {{LAM}: An Open Cluster Environment for {MPI}},
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year = {1993},
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@Misc{ mpich-web-page,
author = {William Gropp and {et. al.}},
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author = {MPI Forum},
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number = {3/4},
year = {1994},
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key = {NAS Parallel Benchmarks},
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author = {H. L. Stone},
title = {Iterative solution of implicit approximations of multidimensional partial
differential equations},
journal = {SIAM J. Numerical Analysis},
pages = {87--113},
volumne = {5},
year = {1968}
}
@Article{ parallelstones,
author = {J. S. Reeve and A. D. Scurr and J. H. Merlin},
title = {Parallel versions of {S}tones strongly implicit algorithm},
journal = {Concurrency and Computation: Practice and Experience},
pages = {1049--1062},
volumne = {13},
year = {2001}
}
@Article{ p4-paper,
author = {Ralph Butler and Ewing Lusk},
title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System},
journal = {Journal of Parallel Computing},
note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science
Division preprint P362-0493)},
year = {1993}
}
@TechReport{ picl,
author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley},
title = {{PICL}: A portable instrumented communications library},
institution = {Oak Ridge National Laboratory},
number = {TM-11130},
year = {1990},
key = {PICL}
}
@TechReport{ upshot,
author = {Virginia Herrarte and Ewing Lusk},
title = {Studying Parallel Program Behavior with {U}pshot},
institution = {Argonne National Laboratory},
number = {ANL-91/15},
month = aug,
year = {1991},
key = {Upshot}
}
@TechReport{ p4-manual,
author = {Ralph Butler and Ewing Lusk},
title = {User's Guide to the p4 Parallel Programming System},
institution = {Argonne National Laboratory},
number = {ANL-92/17},
month = oct,
year = {1992},
key = {p4-Manual}
}
@InProceedings{ oldparti,
author = {Gagan Agrawal and Alan Sussman and Joel Saltz},
title = {Compiler and Runtime Support for Unstructured and Block Structured Problems},
booktitle = {Proceedings of Supercomputing '93},
pages = {578--587},
year = {1993}
}
@Article{ parti2,
author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers
and J. Saltz},
title = {Efficient Support for Irregular Applications on Distributed Memory Machines},
journal = {ACM SIGPLAN Notices},
year = {1995},
pages = {68-79},
volume = {30},
number = {8}
}
@Article{ parti3,
author = {J. Saltz and R. Mirchandaney and K. Crowley},
title = {Run-Time Parallelization and Scheduling of Loops},
journal = {IEEE Trans. Computers},
year = {1991},
pages = {604-612},
volume = {40},
number = {5}
}
@InProceedings{ disz-lusk:wamtrace,
author = {Terrence Disz and Ewing Lusk},
title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs},
booktitle = {Proceedings of the 1987 Symposium on Logic Programming},
year = {1987},
pages = {46--53}
}
@InProceedings{ gorlick-kesselman:gauge,
author = {Michael Gorlick and Carl Kesselman},
title = {Timing {Prolog} programs without Clocks},
booktitle = {Proceedings of the 1987 Symposium on Logic Programming},
year = {1996},
publisher = {Birkhauser}
}
@TechReport{ aztec,
author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro},
title = {Aztec User's Guide Version 1.1},
institution = {Sandia National Laboratories},
month = oct,
year = {1995},
number = {SAND95/1559}
}
@TechReport{ aztec2,
author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid},
title = {Official {Aztec} User's Guide Version 2.1},
institution = {Sandia National Laboratories},
year = {1999}
}
@Book{ taylor-chandy:pcn,
author = {Chandy, M. and Taylor, S.},
title = {An Introduction to Parallel Programming},
year = {1991},
publisher = {Jones and Bartlett}
}
@Book{ foster-taylor:strand,
title = {Strand: New Concepts in Parallel Programming},
author = {Ian Foster and Stephen Taylor},
publisher = {Prentice-Hall},
adress = { Englewood Cliffs, New Jersey},
year = {1990}
}
@Article{ aurora,
author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and
D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M.
Carlsson and A. Ciepielewski and B. Hausman},
title = {The Aurora OR-Parallel Prolog System},
journal = {New Generation Computing},
volume = {7},
number = {3},
year = {1990},
pages = {243--271}
}
@TechReport{ roo,
author = {E. Lusk and W. McCune and J. Slaney},
title = {Roo---a Parallel Theorem Prover},
institution = {Argonne National Laboratory},
number = {MCS--TM--149},
year = {1991}
}
@TechReport{ heath-etheridge:vppp,
author = {M. T. Heath and J. A. Etheridge},
title = {Visualizing the Performance of Parallel Programs},
institution = {Oak Ridge National Laboratory},
number = {ORNL TM-11813},
year = {1991}
}
@TechReport{ chem:vis,
author = {Ewing L. Lusk},
title = {Performance Visualization for Parallel Programs},
institution = {Argonne National Laboratory},
number = {ANL/MCS--P287--0192},
year = {1991},
note = {(to appear in {\em Theoretica Chimica Acta})}
}
@TechReport{ picltrace,
author = {P.~H.~Worley},
title = {A new {PICL} trace file format},
institution = {Oak Ridge National Laboratory},
number = {ORNL TM-12125},
month = jun,
year = {1992}
}
@InProceedings{ hideo,
author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek},
title = {Inference of Phylogenetic trees using maximum likelihood},
booktitle = {Proceedings of the First Intel Delta Applications Workshop},
year = {1992},
pages = {247--262}
}
@InProceedings{ dw90,
author = {M. Dryja and O. Widlund},
title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic
Problems},
booktitle = {Third International Symposium on Domain Decomposition Methods},
editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund},
year = {1990},
pages = {3-21},
publisher = {SIAM},
address = {Philadelphia},
annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how
many approaches may be cast in the form of additive {S}chwarz-subspace form. 58
references, good introduction to the theory. No computations},
key = {DryjaWidlund90 !AS}
}
@Unpublished{ rosing,
author = {Matt Rosing and Joel Saltz},
title = {Low Latency Messages on Distributed Memory Multiprocessors},
key = {LowLatency},
note = {manuscript, 1992}
}
@TechReport{ jp:incomplete,
author = {Mark T. Jones and Paul E. Plassmann},
title = {An Improved Incomplete {C}holesky Factorization},
institution = {Argonne National Laboratory},
address = {Argonne, IL},
type = {Preprint},
note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})},
number = {MCS-P206-0191},
year = {1991},
key = {jones}
}
@InCollection{ jp:ima,
author = {Mark Jones and Paul Plassmann},
title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems},
booktitle = {Graph Theory and Sparse Matrix Computation},
publisher = {Springer-Verlag},
series = {The IMA Volumes in Mathematics and Its Applications},
editor = {Alan George and John Gilbert and Joseph W.H.~Liu},
volume = {56},
year = {1993},
pages = {229--245}
}
@Article{ pw98,
author = {M. Pernice and H. F. Walker},
title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems},
journal = {SIAM J. Sci. Stat. Comput.},
year = {1998},
volume = {19},
pages = {302--318}
}
@TechReport{ ysmp83,
key = {Eisenstat},
author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman},
title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage},
institution = {Department of Computer Science, Yale University},
number = {YALE/DCS/RR-265},
month = apr,
year = {1983}
}
@InBook{ ysmp84,
author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman},
chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage},
title = {Elliptic Problem Solvers II},
publisher = {Academic Press},
pages = {45--52},
editors = {G. Birkhoff and A. Schoenstadt},
year = {1984}
}
@TechReport{ sparsekit,
key = {Saad},
author = {Youcef Saad},
title = {{SPARSKIT}, a basic tool kit for sparse matrix computations},
institution = {Center for Supercomputing Research and Development, University of Illinois at
Urbana-Champaign},
number = {1029},
year = {1990}
}
@TechReport{ pde-user-ref,
author = {Barry F. Smith},
title = {Extensible {PDE} Solvers Package Users Manual},
institution = {Argonne National Laboratory},
month = sep,
year = {1994},
number = {ANL-93/40},
key = {Smith94 ! PDE}
}
@TechReport{ bs-user-ref,
author = {Mark T. Jones and Paul E. Plassmann},
title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution
of Sparse Linear Systems},
institution = {Argonne National Laboratory},
month = dec,
year = {1995},
number = {ANL-95/48}
}
@TechReport{ snes-user-ref,
author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith},
title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package},
institution = {Argonne National Laboratory},
month = feb,
year = {1995},
number = {ANL/MCS-TM-193},
key = {GroppMcInnesSmith95 ! SNES}
}
@TechReport{ sles-user-ref,
author = {William D. Gropp and Barry F. Smith},
title = {{S}implified {L}inear {E}quation {S}olvers Users Manual},
institution = {Argonne National Laboratory},
month = mar,
year = {1993},
number = {ANL-93/8},
key = {GroppSmith93 ! SLES}
}
@TechReport{ chameleon-user-ref,
author = {William D. Gropp and Barry F. Smith},
title = {Chameleon Parallel programming tools Users Manual},
institution = {Argonne National Laboratory},
month = mar,
year = {1993},
number = {ANL-93/23},
key = {GroppSmith93 ! Chameleon}
}
@Article{ euclid2,
author = {D. Hysom and A. Pothen},
title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning},
journal = {SIAM J. Sci. Comput.},
volume = {22},
number = {6},
pages = {2194--2215}
}
@TechReport{ euclid1,
author = {D. Hysom and A. Pothen},
title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel
Solution of Sparse Linear Systems)},
institution = {Old Dominion University},
year = {2001}
}
@TechReport{ ksp-user-ref,
author = {William D. Gropp and Barry F. Smith},
title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space
Methods},
institution = {Argonne National Laboratory},
month = aug,
year = {1993},
number = {ANL-93/30},
key = {GroppSmith93 ! KSP}
}
@TechReport{ mpi-chameleon,
author = {William D. Gropp and Ewing Lusk},
title = {A Test Implementation of the {MPI} Draft Message-Passing Standard},
institution = {Argonne National Laboratory},
month = dec,
year = {1992},
number = {ANL-92/47},
key = {GroppLusk92 ! MPI}
}
@TechReport{ blockcomm-fortran,
author = {William D. Gropp},
title = {Block{C}omm for {F}ortran},
institution = {Argonne National Laboratory},
month = may,
year = {1993},
number = {ANL-93/00 (to appear)},
key = {Gropp93 ! BlockComm}
}
@TechReport{ autodocument,
author = {William D. Gropp},
title = {Automatic documentation of {C} programs},
institution = {Argonne National Laboratory},
month = may,
year = {1993},
number = {ANL-93/00},
key = {Gropp93 ! Autodoc}
}
@TechReport{ zipcode,
author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and
Manfred Morari},
title = {The {Z}ipcode message-passing system},
institution = {Lawrence Livermore National Laboratory},
month = sep,
year = {1992},
number = {Unpublished},
key = {Skjellum92 ! Zipcode}
}
@Article{ paragraph,
author = {Michael T. Heath and Jennifer Etheridge Finger},
title = {Visualizing performance of parallel programs},
journal = {IEEE Software},
volume = {8},
number = {5},
month = sep,
year = {1991},
pages = {29--39},
key = {Heath91 ! Paragraph}
}
@Article{ gropp90,
author = {William Gropp and Edward Smith},
title = {Computational Fluid Dynamics on Parallel Processors},
journal = {Computers and Fluids},
volume = {18},
year = {1990},
pages = {289--304},
key = {Gropp90 ! performance}
}
@Article{ foster92,
author = {Ian Foster and William Gropp and Rick Stevens},
title = {The parallel scalability of the spectral transform method},
journal = {Monthly Weather Review},
volume = {120},
year = {1992},
pages = {835--850},
key = {Foster92 ! performance}
}
@InBook{ fgn,
author = {R. Freund and G. H. Golub and N. Nachtigal},
title = {Iterative Solution of Linear Systems},
series = {Acta Numerica},
year = {1992},
publisher = {Cambridge University Press},
pages = {57--100}
}
@TechReport{ nachtigal90,
author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen},
title = {How Fast are Nonsymmetric Matrix Iterations?},
institution = {Massachusetts Institute of Technology},
month = mar,
year = {1990},
number = {90-2},
key = {Nachtigal | Krylov}
}
@Article{ nachtigal1992fnm,
title = {How Fast are Nonsymmetric Matrix Iterations?},
author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.},
journal = {SIAM Journal on Matrix Analysis and Applications},
volume = {13},
pages = {778},
year = {1992},
publisher = {SIAM}
}
@TechReport{ embree1999descriptive,
title = {How descriptive are {GMRES} convergence bounds},
author = {Embree, M.},
year = {1999},
number = {08},
institution = {Oxford University Computing Laboratory}
}
@Article{ vorst92,
author = {H. van der Vorst},
title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution
of nonsymmetric linear systems},
journal = {SIAM J. Sci. Stat. Comput.},
year = {1992},
volume = {13},
pages = {631--644}
}
@Article{ eisenstat81,
author = {S. Eisenstat},
title = {Efficient Implementation of a Class of {CG} Methods},
journal = {SIAM J. Sci. Stat. Comput.},
year = {1981},
volume = {2},
pages = {1--4}
}
@Manual{ ibm-essl,
title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and
Reference},
organization = {IBM},
year = {1992},
key = {IBM-ESSL}
}
@Manual{ ibm-eui,
title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference
Release 2.0},
organization = {IBM},
month = jun,
year = {1994},
key = {IBM-EUI}
}
@Manual{ ibm-euih,
title = {Using {EUIH}: An Experimental {EUI} Implementation},
organization = {IBM},
author = {Peter Hochschild},
year = {1993},
key = {IBM-EUIH}
}
@TechReport{ mpi,
title = {Document for a Standard Message-Passing Interface},
author = {Message Passing Interface Forum},
institution = {University of Tennessee},
number = {CS-93-214},
month = nov,
year = {1993},
key = {MPI Standard}
}
@Unpublished{ mpi-final-web,
author = {Message Passing Interface Forum},
title = {{MPI}: A Message-Passing Interface Standard},
note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html},
year = {1994},
month = may
}
@Book{ hockney-jesshope,
author = {R. W. Hockney and C. R. Jesshope},
title = {Parallel Computers 2},
publisher = {Adam Hilger},
year = {1988}
}
@Book{ cm-fortran,
author = {{Thinking Machines Corporation}},
title = {Users Manual for CM-Fortran},
publisher = {Thinking Machines Corporation},
year = {1993}
}
@TechReport{ chang93,
title = {Experiments and Bounds on Block Diagonal Preconditioning},
author = {Mark Yan-Ming Chang and Martin H. Schultz},
institution = {Yale Department of Computer Science},
number = {YALEU/DCS/RR-994},
month = nov,
year = {1993},
key = {BDD|diag}
}
@InProceedings{ gropplevine93,
author = {N. Galbreath and W. Gropp and D. Levine},
title = {Applications-Driven Parallel {I/O}},
booktitle = {Proceedings of Supercomputing '93},
year = {1993},
pages = {462--471}
}
@Book{ siegle85,
author = {H. J. Siegel},
title = {Interconnection Networks for Large Scale Parallel Processing},
publisher = {Lexington Books},
year = {1985},
key = {Network Comparison}
}
@Article{ lawrie75,
author = {D. H. Lawrie},
title = {Access and alignment of data in an array processor},
journal = {IEEE Transactions on Computers},
volume = {C-24},
number = {12},
month = dec,
year = {1975},
pages = {1145--1155},
key = {Omega Network}
}
@Book{ knuth1986,
title = {The {\TeX}{Book}},
author = {Donald Ervin Knuth and Duane Bibby},
volume = {1993},
year = {1986},
publisher = {Addison-Wesley Reading, Massachusetts}
}
@Book{ lamport86,
author = {Leslie Lamport},
title = {{LaTeX}: A document preparation system},
publisher = {Addison-Wesley},
year = {1986},
key = {Latex Manual}
}
@InProceedings{ gropp-lusk:unix-tools,
author = {William Gropp and Ewing Lusk},
title = {Scalable {U}nix Tools on Parallel Processors},
booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference},
publisher = {IEEE},
pages = {56--62}
}
@InProceedings{ jp:bell_prize,
author = {Mark Jones and Paul Plassmann},
title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel
Applications},
booktitle = {Proceedings of Supercomputing '92},
publisher = {IEEE Computer Society Press},
year = {1992},
pages = {551--560}
}
@COMMENT{WEB, CWEB references (for doctext)}
@TechReport{ web,
author = {Donald E. Knuth},
title = {The {\tt WEB} system of structured documentation},
institution = {Computer Science Department, Stanford University},
year = {1983},
number = {980},
month = sep
}
@Article{ literatepgm,
author = {Donald E. Knuth},
title = {Literate Programming},
journal = {Computer Journal},
year = {1984},
volume = {27},
number = {2},
pages = {91--111}
}
@Unpublished{ cweb-code,
author = {Silvio Levy and Donald E. Knuth},
title = {CWEB},
note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb}
}
@Article{ jp:scalable,
author = {Mark Jones and Paul Plassmann},
title = {Scalable Iterative Solution of Sparse Linear Systems},
journal = {Parallel Computing},
volume = {20},
number = {5},
month = may,
year = {1994},
pages = {753--773}
}
@Article{ jp:pcolor,
author = {Mark T. Jones and Paul E. Plassmann},
title = {A Parallel Graph Coloring Heuristic},
journal = {SIAM J. Sci. Comput.},
volume = {14},
number = {3},
pages = {654-669},
year = {1993}
}
@TechReport{ block_solve,
author = {Mark T. Jones and Paul E. Plassmann},
title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of
Sparse Linear Systems},
institution = {Argonne National Laboratory},
year = {1992},
number = {ANL-92/46},
key = {JonesPlassmann92 ! block_solve}
}
@InProceedings{ supercond,
author = {Lois Curfman Mc{I}nnes and Mario Palumbo},
title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model},
booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications
Conference},
month = feb,
year = {1994},
key = {McInnesPalumbo94 ! superconductivity }
}
@Unpublished{ preosti:93,
author = {Gianfranco Preosti},
title = { },
note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity},
year = {1993},
key = {preosti93 ! GL-tilt3d}
}
@Unpublished{ more:93,
author = {Jorge J. Mor\'{e}},
title = { },
note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision,
{A}rgonne {N}ational {L}aboratory},
year = {1993},
key = {more93 ! MINPACK-2}
}
@Article{ brownsaad:90,
author = {Peter N. Brown and Youcef Saad},
title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations},
journal = {SIAM J. Sci. Stat. Comput.},
year = {1990},
volume = {11},
pages = {450-481}
}
@Book{ using-mpi,
author = {William Gropp and Ewing Lusk and Anthony Skjellum},
title = {Using MPI: Portable Parallel Programming with the Message Passing Interface},
publisher = {MIT Press},
year = {1994}
}
@Book{ using-mpi2,
author = {William Gropp and Ewing Lusk and Rajeev Thakur},
title = {Using MPI 2: Advanced Features of the Message Passing Interface},
publisher = {MIT Press},
year = {1999}
}
@Article{ hs:52,
author = {Magnus R. Hestenes and Eduard Steifel},
title = {Methods of Conjugate Gradients for Solving Linear Systems},
journal = {J. Research of the National Bureau of Standards},
year = {1952},
volume = {49},
pages = {409-436}
}
@Article{ so:89,
author = {Peter Sonneveld},
title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems},
journal = {SIAM J. Sci. Stat. Comput.},
year = {1989},
volume = {10},
pages = {36-52}
}
@Article{ v:92,
author = {{H. A.} {van der Vorst}},
title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution
of nonsymmetric linear systems},
journal = {SIAM J. Sci. Stat. Comput.},
volume = {13},
year = {1992},
pages = {631-644}
}
@Article{ f:93,
author = {Roland W. Freund},
title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear
Systems},
journal = {SIAM J. Sci. Stat. Comput.},
volume = {14},
year = {1993},
pages = {470-482}
}
@Article{ ish:89,
author = {S. Ishizuka},
title = {An Experimental Study on Extinction and Stablity of Tubular Flames},
journal = {Combustion and Flame},
volume = {75},
year = {1989},
pages = {367-379}
}
@Book{ williams89,
title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems},
author = {F.A. Williams},
publisher = {Addison-Wesley},
year = {1989},
pages = {367-379}
}
@Book{ ra75,
author = {R. Aris},
title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts},
publisher = {Oxford},
year = {1975}
}
@Book{ bebernes89,
author = {J. Bebernes and D. Eberly},
title = {Mathematical Problems from Combustion Theory},
publisher = {Springer-Verlag},
series = {Applied Mathematical Sciences 83},
year = {1989}
}
@InProceedings{ kikuchi89,
author = {F. Kikuchi},
booktitle = { Computing Methods in Applied Sciences and Engineering},
editor = {R. Glowinski and J. L. Lions},
publisher = {Springer-Verlag},
series = {Lecture Notes in Mathematics},
title = {Finite element approximations to bifurcation problems of turning point type},
year = {1977}
}
@Article{ rg85,
author = {R. Glowinski and H.B. Keller and L. Reinhart},
title = {Continuation-conjugate Gradient Methods for the Least Squares Solution of
Nonlinear Boundary Problems},
journal = {SIAM J. Sci. Stat. Comput.},
volume = {6},
year = {1985},
pages = {793-832}
}
@InProceedings{ whitfield91,
author = {D. Whitfield and L. Taylor},
title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split
Schemes},
booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference},
misc = {AIAA-91-1539},
pages = {134-145},
year = {1991}
}
@InProceedings{ quinlan1,
author = {M. Lemke and D. Quinlan},
title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for
Architecture-Independent Development of Structured Grid Applications},
booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science},
publisher = {Springer Verlag},
year = {1992}
}
@InProceedings{ quinlan2,
author = {R. Parsons and D. Quinlan},
title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference
Computations},
booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference},
year = {1994}
}
% ***** Overview of functionality in Diffpack
@InBook{ dpoverview,
author = {Bruaset, A. M. and Langtangen, H. P.},
booktitle = {Mathematical Models and Software Tools in Industrial Mathematics},
title = {A Comprehensive Set of Tools for Solving Partial Differential Equations;
{Diffpack}},
publisher = {Birkh{\"{a}}user},
pages = {61--90},
year = {1997}
}
% ***** Short overview of Diffpack
@InCollection{ dpoverview2,
author = {Bruaset, A. M. and Langtangen, H. P.},
editor = {A. Sydow},
booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling
and Applied Mathematics},
title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers},
pages = {553--558},
volume = {4},
year = {1997}
}
% ***** Comprehensive documentation of Diffpack and
% associated numerical methods:
@Book{ dpbook,
author = {H. P. Langtangen},
title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and
Software. Part I},
series = {Lecture Notes in Computational Science and Engineering},
publisher = {Springer-Verlag},
year = {1998}
}
% ***** Design issues of the linear solvers in Diffpack, serves also as a
% collection of examples on O-O in numerical computing
@Article{ ambhpl97a,
author = {A. M. Bruaset and H. P. Langtangen },
title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}},
journal = {Transactions on Mathematical Software},
volume = {23 },
pages = {50--80},
year = {1997}
}
@Misc{ dpurl,
author = {{Diffpack Web page}},
howpublished = {\url{http://www.diffpack.com}}
}
% ***** General intro to object-oriented numerics for "FORTRAN programmers"
@InCollection{ oonintro,
author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen},
editor = {D{\ae}hlen, M. and Tveito, A.},
booktitle = {Mathematical Models and Software Tools in Industrial Mathematics},
title = {Object-Oriented Numerics},
publisher = {Birkh{\"{a}}user},
year = {1997}
}
% ***** Efficiency comparison: BLAS 1, Diffpack, C,
% and finite element applications (F77 vs Diffpack)
@InCollection{ dpefficiency,
author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen,
H. P. and Miller, C. T.},
editor = {D{\ae}hlen, M. and Tveito, A.},
booktitle = {Mathematical Models and Software Tools in Industrial Mathematics},
title = {On the Efficiency of {C++} in Scientific Computing},
publisher = {Birkh{\"{a}}user},
pages = {91--118},
year = {1997}
}
% ***** Parallel concept in Diffpack:
@InCollection{ dpparallel,
author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito},
editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn},
booktitle = {Scientific Computing in Object-Oriented Parallel Environments},
title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential
Simulators},
publisher = {Springer--Verlag},
series = {Lecture Notes in Computer Science},
pages = {161--168},
year = {1997}
}
% ***** DD and ML methods in Diffpack:
@InCollection{ dpddml,
author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch},
editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes},
booktitle = {Proceedings of the 9th Conference on Domain Decomposition},
title = {Domain decomposition and multilevel methods in Diffpack},
year = {1997}
}
@InProceedings{ bsca98,
author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David
Alexander},
title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear
Optimization},
booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable
Scientific and Engineering Computing},
editor = {Mike Henderson et al.},
pages = {165-173},
year = {1998}
}
@Book{ scalapack-user-guide,
author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I.
Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K.
Stanley and D. Walker and R. C. Whaley},
title = {Sca{LAPACK} Users' Guide},
publisher = {SIAM},
address = {Philadelphia, PA},
year = {1997}
}
@InProceedings{ keyes99,
author = {D. E. Keyes},
title = {How Scalable is Domain Decomposition in Practice?},
booktitle = {Proceedings of the 11th International Conference on Domain Decomposition
Methods},
editor = {C.-H. Lai et al.},
publisher = {Domain Decomposition Press, Bergen},
note = {To appear},
year = {1999}
}
@Article{ fun3d,
author = {W. K. Anderson and D. L. Bonhaus},
title = {An implicit upwind algorithm for computing turbulent flows on unstructured
grids},
journal = {Computers and Fluids},
year = {1994},
volume = {23},
pages = {1--21}
}
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
@Article{ torczon,
author = {Dennis, Jr., J. E. and V.~Torczon},
title = {Direct Search Methods on Parallel Machines},
journal = {SIAM J. Optimization},
volume = {1},
pages = {448--474},
year = {1991},
key = {Torczon !PDS}
}
@InProceedings{ wt91,
author = {D. L. Whitfield and L. K. Taylor},
title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split
Schemes},
booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference},
misc = {AIAA-91-1539},
pages = {134-145},
year = {1991}
}
@Article{ ew96,
author = {S. C. Eisenstat and H. F. Walker},
title = {Choosing the forcing terms in an inexact {N}ewton method},
journal = {SIAM J. Scientific Computing},
volume = {17},
year = {1996},
pages = {16--32}
}
@Book{ thi93,
author = {{Thinking Machines Corporation}},
title = {Users Manual for CM-Fortran},
publisher = {Thinking Machines Corporation},
year = {1993}
}
@Book{ mortonmayers94,
author = {K. W. Morton and D. F. Mayers},
title = {Numerical Solution of Partial Differential Equations},
publisher = {Press Syndicate of the University of Cambridge},
year = {1994}
}
@Book{ heath97,
author = {Michael T. Heath},
title = {Scientific Computing: An Introductory Survey},
publisher = {McGraw Hill},
year = {1997}
}
@Article{ captools96,
author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett},
title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and
Performance on the Parallelization of Structured Mesh Codes},
journal = {Parallel Computing},
volume = {22},
pages = {197-226},
year = {1996}
}
@Misc{ nastran-web-page,
author = {{MSC Software Corporation}},
title = {{NASTRAN} {W}eb page},
howpublished = {\url{http://www.mechsolutions.com/products/nastran/}},
year = {2024}
}
@Book{ hpf,
author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E.
Zosel},
title = {The High Performance Fotran Handbook},
publisher = {MIT Press},
year = {1994}
}
@InProceedings{ keyes98,
author = {D. E. Keyes},
title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed
Architectures},
booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century},
editors = {M. D. Salas and W. K. Anderson},
ppublisher = {Elsevier},
year = {1998}
}
@InProceedings{ pooma-atlas,
author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and
J. V. W. Reynders and M. Tholburn},
title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific
Applications},
year = {1995},
month = dec,
booktitle = {Supercomputing '95 Proceedings}
}
% ---------------------------------------------------------------------------------
% New bib entries for CRPC paper
@Misc{ mgnet-web-page,
author = {Craig C. Douglas},
title = {{MGNet Web page}},
note = {See {\tt http://\-www.mgnet.org}}
}
@Misc{ dagh-web-page,
author = {M. Parashar and J. C. Browne},
title = {{DAGH Web page}},
note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}}
}
@Misc{ parasol-web-page,
key = {PARASOL},
title = {{PARASOL Web page}},
note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}}
}
@Misc{ pooma-web-page,
author = {{POOMA Web page}},
note = {See {\tt http://\-www.acl.lanl.gov/pooma}}
}
@Misc{ mudpack-web-page,
author = {John C. Adams},
title = {{MUDPACK Web page}},
note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}}
}
@Misc{ pellpack-web-page,
author = {Elias Houstis and John Rice and Apostolos Hadjidimos},
title = {{Parallel ELLPACK Web page}},
note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}}
}
@InProceedings{ pellpack95,
author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C.
Catlin and S. Weerawarana and T.S. Papatheodorou},
title = {Parallel {ELLPACK} Elliptic {PDE} Solvers},
booktitle = {Proceedings of INTEL Supercomputer User's Group Conference},
address = {Albuquerque, NM},
year = {1995}
}
@Misc{ nhse-web-page,
author = {{National High-Performance Software Exchange Web page}},
note = {See {\tt http://\-www.nhse.org}}
}
@Misc{ doug-web-page,
author = {Mark J. Hagger and Linda Stals},
title = {{DOUG Web Page}},
note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}}
}
@TechReport{ doug97,
author = {Mark J. Hagger},
title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}},
institution = {Mathematical Sciences, University of Bath},
year = {1997},
number = {9706},
note = {Advances in Computational Mathematics (to appear)}
}
@Misc{ ug-web-page,
author = {{UG Web Page}},
note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}}
}
@Article{ ug97,
author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H.
Rentz-Reichert and C. Wieners},
title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations},
journal = {Computing and Visualization in Science},
year = {1997},
volume = {},
pages = {}
}
@Misc{ vecfem-web-page,
author = {Lutz Grosz},
title = {{VECFEM Web Page}},
note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}}
}
@Misc{ atlas-web-page,
author = {R. Clint {Whaley et al.}},
title = {{ATLAS Web Page}},
howpublished = {\url{http://math-atlas.sourceforge.net}}
}
@Misc{ fenics-web-page,
author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C.
Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott},
title = {{FEniCS Web Page}},
note = {\url{http://www.fenicsproject.org}},
year = {2005}
}
@Misc{ matlab-web-page,
author = {{The} {MathWorks}},
title = {{Matlab} {Web} page},
url = {http://www.mathworks.com}
}
@Misc{ phipac-web-page,
author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin
and D. Lam},
title = {{PHiPAC Web Page}},
note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}}
}
@InProceedings{ kelp,
author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn},
title = {Flexible Communication Mechanisms for Dynamic Structured Applications},
booktitle = {Irregular '96},
year = {1996}
}
@Unpublished{ kelp-web-page,
author = {Scott Baden},
title = {{KeLP} {W}eb page},
note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}}
}
@InProceedings{ hk99,
author = {R. Hornung and S. Kohn},
title = {The Use of Object-Oriented Design Patterns in the {SAMRAI} Structured {AMR}
Framework},
booktitle = {Proceedings of the SIAM Workshop on Object-Oriented Methods for Inter-Operable
Scientific and Engineering Computing},
pages = {235-244},
year = {1999},
note = {See \url{http://www.llnl.gov/CASC/samrai}}
}
@Unpublished{ samrai-web-page,
title = {{SAMRAI} {W}eb Page},
author = {Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith},
note = {See {\tt http://www.llnl.gov/\-CASC/SAMRAI}}
}
@Misc{ overture-web-page,
author = {William Henshaw and Kyle Chand},
title = {{Overture} {W}eb page},
howpublished = {\url{http://www.llnl.gov/CASC/Overture}}
}
@InProceedings{ overture99,
author = {D.L. Brown and W.D. Henshaw and D.J. Quinlan},
title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations
on Overlapping Grids},
publisher = {SIAM},
booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable
Scientific and Engineering Computing},
year = {1999},
pages = {215-224},
note = {See \url{http://www.llnl.gov/CASC/Overture}}
}
@InProceedings{ diffpack,
author = {A.M. Bruaset and H.P. Langtangen},
title = {A Comprehensive Set of Tools for Solving Partial Differential Equations:
{D}iffpack},
booktitle = {Numerical Methods and Software Tools in Industrial Mathematics},
year = {1997},
pages = {61--90},
publisher = {Birkhauser Press}
}
@Article{ dongarra:1984:ila,
author = {J. J. Dongarra and F. G. Gustavson and A. Karp},
title = {Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline
Machine},
journal = {SIAM Review},
volume = {26},
number = {1},
pages = {91--112},
month = jan,
year = {1984},
coden = {SIREAD},
issn = {0036-1445 (print), 1095-7200 (electronic)},
mrclass = {65F10 (65F30)},
mrnumber = {85c:65032},
bibdate = {Mon Jan 20 1997},
abstract = {The authors examine common implementations of linear algebra algorithms, such as
matrix-vector multiplication, matrix-matrix multiplication and the solution of
linear equations. The different versions are examined for efficiency on a computer
architecture which uses vector processing and has pipelined instruction execution.
By using the advanced architectural features of such machines, one can usually
achieve maximum performance, and tremendous improvements in terms of execution
speed can be seen over conventional computers.},
classification= {723; 921},
journalabr = {SIAM Rev},
keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms;
mathematical programming; vector pipeline machine}
}
@Book{ qv99,
author = {Alfio Quarteroni and Alberto Valli},
title = {Domain Decomposition Methods for Partial Differential Equations},
publisher = {Oxford Science Publications},
address = {Oxford},
year = {1999}
}
@Book{ ksv97,
editor = {David E. Keyes and Ahmed Sameh and V. Venkatakrishnan},
title = {Parallel Numerical Algorithms},
publisher = {Kluwer Academic Publishers},
address = {the Netherlands},
year = {1997}
}
@Book{ hackbusch94,
author = {Wolfgang Hackbusch},
title = {Iterative Solution of Large Sparse Systems of Equations},
publisher = {Springer-Verlag},
address = {New York},
year = {1994}
}
@Article{ hackbusch1980fast,
title = {Fast solution of elliptic control problems},
author = {Hackbusch, W.},
journal = {Journal of Optimization Theory and Applications},
volume = {31},
number = {4},
pages = {565--581},
year = {1980},
publisher = {Springer}
}
@Book{ hackbusch1985multi,
title = {{Multi-grid methods and applications}},
author = {Hackbusch, W.},
isbn = {3540127615},
issn = {0179-3632},
year = {1985},
publisher = {Springer Verlag}
}
@Book{ axelsson94,
author = {Owe Axelsson},
title = {Iterative Solution Methods},
publisher = {Cambridge University Press},
address = {Cambridge},
year = {1994}
}
@Book{ saad96,
author = {Yousef Saad},
title = {Iterative Methods for Sparse Linear Systems},
publisher = {PWS Publishing Company},
address = {Boston},
year = {1996}
}
@Book{ saad2003,
title = {Iterative Methods for Sparse Linear Systems},
author = {Saad, Yousef},
doi = {10.1016/S1570-579X(01)80025-2},
edition = {2nd},
publisher = {SIAM},
year = {2003}
}
@Book{ vandervorst03,
author = {Henk A. {van der Vorst}},
title = {Iterative Krylov Methods for Large Linear Systems},
publisher = {Cambridge Monographs on Applied ahd Computational Mathematics},
year = {2003}
}
@Book{ koniges00,
editor = {Alice E. Koniges},
title = {Industrial Strength Parallel Computing},
publisher = {Morgan Kaufmann Publishers},
address = {San Francisco},
year = {2000}
}
@Misc{ fftw-web-page,
key = {Fftw},
title = {{FFTW} {Web} page},
note = {\texttt{http://www.fftw.org/}},
annote = {fast FFT. Parallel versions with MPI and Cilk}
}
@InProceedings{ frigojohnson93,
author = {Matteo Frigo and Steven G. Johnson},
title = {The Design and Implementation of {FFTW3}},
booktitle = {Proceedings of the IEEE},
volume = {93},
number = {2},
pages = {216--231},
year = {2005}
}
@Book{ kelley95,
author = {C. T. Kelley},
title = {Iterative Methods for Linear and Nonlinear Equations},
year = {1995},
publisher = {SIAM},
address = {Philadelphia}
}
@Unpublished{ spai-web-page,
title = {{SPAI} {W}eb {P}age},
note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/},
author = {Steven Bernard and Marcus Grote},
institution = {NASA Ames Research Center and ETH Zurich}
}
@Article{ gh97,
author = {M. J. Grote and T. Huckle},
title = {Parallel Preconditioning with Sparse Approximate Inverses},
year = {1997},
journal = {SIAM J. of Scient. Comput.},
volume = {18},
pages = {838-853}
}
@Article{ zhang96,
author = {Wen Zhang},
title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the
simulation of a sintering process},
year = {1996},
journal = {Appl. Numer. Math.},
volume = {20},
pages = {235-244}
}
@Article{ zhang98,
author = {Wen Zhang and Ian Gladwell},
title = {The sintering of two particles by surface and grain boundary diffusion - a
three-dimensional numerical study},
journal = {Comp. Mater. Sci.},
year = {1998},
volume = {12}
}
@InProceedings{ mollerschwartzbach01,
author = {Anders M\o{}ller and Michael I. Schwartzbach},
title = {The Pointer Assertion Logic Engine},
booktitle = {ACM Proceedings of PLDI'01},
year = {2001}
}
@InProceedings{ klarlandschwartzbach97,
author = {Nils Klarland and Michael I. Schwartzbach},
title = {A Domain-Specific Languages for Regular Sets of Strings and Trees},
booktitle = {Proceedings of the Conference on Domain-Specific Languages},
publisher = {USENIX},
month = oct,
year = {1997},
address = {Santa Barbara, CA}
}
@InProceedings{ conselmarlet98,
author = {C. Consel and R. Marlet},
title = {Architecturing software using a methodology for language development},
booktitle = {Proceedings of the 10th International Symposium on Programming Languages,
Implementations, Logics and Programs},
year = {1998},
pages = {170-174},
month = sep,
address = {Pisa, Italy}
}
@Misc{ sundials:homepage,
author = {C. {Woodward et al.}},
title = {{SUNDIALS {W}eb page}},
howpublished = {\url{https://computation.llnl.gov/casc/sundials/main.html}}
}
@article{gardner2022sundials,
title = {Enabling new flexibility in the {SUNDIALS} suite of nonlinear and differential/algebraic equation solvers},
author = {Gardner, David J and Reynolds, Daniel R and Woodward, Carol S and Balos, Cody J},
journal = {ACM Transactions on Mathematical Software (TOMS)},
publisher = {ACM},
year = {2022},
doi = {10.1145/3539801}
}
@Misc{ sundials-user-ref,
title = {{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers},
note = {See \url{http://www.llnl.gov/CASC/sundials}},
author = {Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban
and Dan Shumaker and Carol Woodward},
institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory},
number = {UCRL-JP-200037},
year = {2003}
}
@Article{ sundials05,
author = {A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker
and C. Woodward},
title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers},
journal = {ACM Transactions on Mathematical Software},
volume = {31},
number = {3},
pages = {363--396},
year = {2005}
}
@InProceedings{ serban2005cvodes,
title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}},
author = {Serban, Radu and Hindmarsh, Alan C},
booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear
Dynamics and Control, Long Beach, CA},
year = {2005}
}
@Article{ pvode99,
author = {G. Byrne and A. Hindmarsh},
title = {{PVODE}, An {ODE} Solver for Parallel Computers},
journal = {Int. J. High Perf. Comput. Apps.},
volume = {13},
number = {4},
year = {1999},
pages = {354 -- 365}
}
@Article{ cvode95,
author = {S. Cohen and A. Hindmarsh},
title = {{CVODE}, A Stiff/Nonstiff {ODE} Solver in {C}},
journal = {Computers in Physics},
volume = {10},
number = {2},
year = {1996},
pages = {138 -- 143}
}
@TechReport{ ifpack,
title = {Robust Algebraic Preconditioners using {IFPACK} 3.0},
author = {Marzio Sala and Michael Heroux},
institution = {Sandia National Laboratories},
number = {SAND2005-0662},
year = {2005}
}
@TechReport{ kinsol-user-ref,
title = {User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel
Computers},
author = {Allan Taylor and Alan Hindmarsh},
institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory},
number = {UCRL-ID-131185},
year = {1998}
}
@Article{ fiardmanteuffelmccormick98,
author = {J.-M. Fiard and T. Manteuffel and S. McCormick},
title = {First-order system least squares {(FOSLS)} for convection-diffusion problems:
numerical results},
journal = {SIAM J. Sci. Comp.},
year = {1998},
volume = {19},
pages = {1958--1979}
}
@InProceedings{ vuduc02,
author = {Richard Vuduc and James W. Demmel and Katherine A. Yelick and Shoaib Kamil and
Rajesh Nishtala and Benjamin Lee},
title = {Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply},
booktitle = {Proceedings of Supercomputing},
year = {2002},
month = nov,
address = {Baltimore}
}
@Article{ beckerbraackrannacher1999,
title = {Numerical simulation of laminar flames at low Mach number by adaptive finite
elements},
author = {Roland Becker and Malte Braack and Rolf Rannacher},
journal = {Combustion Theory and Modelling},
volume = {3},
pages = {503--534},
year = {1999}
}
@Article{ beckerrannacher01,
author = {R. Becker and R. Rannacher},
title = {An optimal control approach to a posteriori error estimation in finite element
methods},
journal = {Acta Numerica},
year = {2001},
volume = {10},
pages = {1--102}
}
@Article{ babuskamiller84a,
author = {I. Babu$\check{s}$ka and A.D. Miller},
title = {The post-processing approach in the finite element method, {I}: Calculations of
displacements, stresses, and other higher derivatives of the displacements},
journal = {Int. J. Numer. Meth. Eng.},
year = {1984},
volume = {20},
pages = {1085--1109}
}
@Article{ babuskamiller84b,
author = {I. Babu$\check{s}$ka and A.D. Miller},
title = {The post-processing approach in the finite element method, {II}: The calculation
of stress intensity factors},
journal = {Int. J. Numer. Meth. Eng.},
year = {1984},
volume = {20},
pages = {1111--1129}
}
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title = {{TC}hem: {A} Software Toolkit for the Analysis of Complex Kinetic Models},
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author = {Y. Zhou},
title = {Eigenvalue Computation from the Optimization Perspective: On {Jacobi-Davidson,
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institution = {Argonne National Laboratory},
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year = {2003}
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Hu and Tamara Kolda and Richard Lehoucq and Kevin Long and Roger Pawlowski and
Eric Phipps and Andrew Salinger and Heidi Thornquist and Ray Tuminaro and James
Willenbring and Alan Williams},
institution = {Sandia National Laboratories},
number = {SAND2003-2927},
year = {2003}
}
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year = {2003}
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% -----------------------------------------------------------------------
% Model coupling refs
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volume = {5},
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pages = {198--213},
year = {2005}
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title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel
Multiphysics Simulation Code},
author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A.
Siegel and K. Weide},
journal = {Parallel Computing},
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issue = {10 -- 11},
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year = {2009}
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@Book{ bottloring95,
author = {Raoul Bott and Loring W. Tu},
title = {Differential Forms in Algebraic Topology},
publisher = {Springer},
year = {1995}
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author = {Shoshichi Kobayashi and Katsumi Nomizu},
title = {Foundations of Differential Geometry},
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year = {1996}
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author = {Richard D. Hornung and Scott R. Kohn},
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author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and
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title = {Concepts: Linguistic Support for Generic Programming in C++},
booktitle = {Proceedings of OOPSLA 2006},
year = {2006},
pages = {???--???}
}
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author = {Hatcher, Allen},
title = {Algebraic Topology},
publisher = {Cambridge University Press},
year = {2002}
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@Book{ gammahelmjohnsonvlissides95,
abstract = {{Design Patterns is a modern classic in the literature of object-oriented
development, offering timeless and elegant solutions to common problems in
software design. It describes patterns for managing object creation, composing
objects into larger structures, and coordinating control flow between objects. The
book provides numerous examples where using composition rather than inheritance
can improve the reusability and flexibility of code. Note, though, that it's not a
tutorial but a catalog that you can use to find an object-oriented design pattern
that's appropriate for the needs of your particular application--a selection for
virtuoso programmers who appreciate (or require) consistent, well-engineered
object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is
more valuable than ever!
Use the contents of the CD to create your own design documents and reusable
components. The CD contains: 23 patterns you can cut and paste into your own
design documents; sample code demonstrating pattern implementation; complete
Design Patterns content in standard HTML format, with numerous hyperlinked
cross-references; accessed through a standard web browser; Java-based dynamic
search mechanism, enhancing online search capabilities; graphical user environment,
allowing ease of navigation.
First published in 1995, this landmark work on object-oriented software design
presents a catalog of simple and succinct solutions to common design problems.
Created by four experienced designers, the 23 patterns contained herein have
become an essential resource for anyone developing reusable object-oriented
software. In response to reader demand, the complete text and pattern catalog are
now available on CD-ROM. This electronic version of Design Patterns enables
programmers to install the book directly onto a computer or network for use as an
online reference for creating reusable object-oriented software.
The authors first describe what patterns are and how they can help you in the
design process. They then systematically name, explain, evaluate, and catalog
recurring designs in object-oriented systems. All patterns are compiled from
real-world examples and include code that demonstrates how they may be implemented
in object-oriented programming languages such as C++ and Smalltalk. Readers who
already own the book will want the CD to take advantage of its dynamic search
mechanism and ready-to-install patterns.}},
author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John},
citeulike-article-id={115158},
howpublished = {Hardcover},
isbn = {0201633612},
keywords = {1995 algorithms architecture book books computer computing design design-pattern
design-patterns design_patterns designpatterns development diplom entwurfsmuster
four gang gof java mathgamespatterns no-tag object object-orientation
object-oriented of oo-patterns oop oriented pattern patterns programming se
software software-development software-engineering software_design
softwareengineering standard},
month = jan,
publisher = {{Addison-Wesley Professional}},
title = {Design Patterns},
url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612},
year = {1995}
}
@InProceedings{ chaco95,
author = {Bruce Hendrickson and Robert Leland},
title = {A multilevel algorithm for partitioning graphs},
booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing
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year = {1995},
isbn = {0-89791-816-9},
pages = {28},
location = {San Diego, California, United States},
doi = {10.1145/224170.224228},
publisher = {ACM Press},
address = {New York}
}
@Book{ aleksandrov98,
author = {Aleksandrov, Pavel S.},
title = {Combinatorial Topology},
publisher = {Dover},
volume = {3},
year = {1998}
}
@Book{ steenrod99,
abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great
importance in modern physics--such as in gauge theory. This book, a succinct
introduction to the subject by renown mathematician Norman Steenrod, was the first
to present the subject systematically.
It begins with a general introduction to bundles, including such topics as
differentiable manifolds and covering spaces. The author then provides brief
surveys of advanced topics, such as homotopy theory and cohomology theory, before
using them to study further properties of fibre bundles. The result is a classic
and timeless work of great utility that will appeal to serious mathematicians and
theoretical physicists alike. }},
author = {Steenrod, Norman},
citeulike-article-id={712999},
howpublished = {Paperback},
isbn = {0691005486},
keywords = {fibre_bundles topology},
month = apr,
publisher = {{Princeton University Press}},
title = {The Topology of Fibre Bundles. (PMS-14)},
url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486},
year = {1999}
}
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author = {Bredon, Glen E.},
title = {Sheaf Theory},
publisher = {Springer},
pages = {524},
series = {Graduate Texts in Mathematics},
year = {1997}
}
@TechReport{ tautgesmeyers04,
title = {{MOAB}: A Mesh-Oriented Database},
author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey
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institution = {Sandia National Laboratories},
number = {SAND2004-1592},
month = apr,
year = {2004}
}
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author = {Timothy J. Tautges},
title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation},
journal = {Engineering With Computers},
volume = {20},
pages = {286--293},
year = {2004}
}
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author = {Ray Meyers et. al},
title = {{SNL} Implementation of the {TSTT} Mesh Interface},
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month = jun,
year = {2002}
}
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author = {E. S. Seol and Mark S. Shephard},
title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive
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year = {2005}
}
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title = {3D anisotropic mesh adaptation by mesh modification},
author = {Xiangrong Li and Mark S Shephard and Mark W Beall},
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pages = {4915--4950},
year = {2005},
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title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry},
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journal = {Engineering with Computers},
volume = {30},
pages = {271--286},
year = {2014},
}
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author = {Mark W. Beall and Joe Walsh and Mark S. Shephard},
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journal = {Engineering With Computers},
volume = {20},
number = {3},
pages = {210--221},
year = {2004}
}
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author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S.
Kirk},
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pages = {55--86},
year = {2004}
}
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author = {Guntram Berti},
title = {Generic Software Components for Scientific Computing},
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year = {2000},
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title = {Combinatorial homotopy. I},
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author = {Pieter Wesseling},
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author = {Loukas Grakakos},
title = {Classical and Modern Fourier Analysis},
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key = {HLib},
title = {{HLib} {Web} page},
note = {{\texttt{http://www.hlib.org/}}},
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author = {Wolfgang Hackbusch},
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title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes
equations},
author = {Kay, D. and Loghin, D.},
year = {1999},
institution = {Oxford University Computing Laboratory},
number = {99/06}
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title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of
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year = {2003},
publisher = {Springer}
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title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal
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pages = {179--188},
year = {2005},
publisher = {Springer}
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author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A.
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title = {The {FE}ni{CS} project},
institution = {Chalmers Finite Element Center Preprint Series},
number = {2003--21},
year = {2003}
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author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de
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volume = {27},
number = {4},
year = {2001},
pages = {422--455}
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author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua
and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and
Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and
Nick Rizzolo},
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author = {Robert C. Kirby and Anders Logg},
title = {A compiler for variational forms},
journal = {ACM Transactions on Mathematical Software},
volume = {32},
number = {3},
year = {2006},
issn = {0098-3500},
pages = {417--444},
doi = {10.1145/1163641.1163644},
publisher = {ACM Press},
address = {New York, NY}
}
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author = {Robert C. Kirby and Anders Logg},
title = {Efficient compilation of a class of variational forms},
journal = {ACM Transactions on Mathematical Software},
volume = {33},
number = {3},
year = {2007},
issn = {0098-3500},
pages = {17},
doi = {10.1145/1268769.1268771},
publisher = {ACM Press},
address = {New York, NY}
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author = {Randolph Bank and Todd Dupont},
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author = {Mark F. Adams},
title = {Evaluation of three unstructured multigrid methods on 3D finite element problems
in solid mechanics},
institution = {UC Berkeley},
number = {CSD-00-1103},
year = {2000},
url = {citeseer.ist.psu.edu/article/adams00evaluation.html}
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author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude},
title = {A Massively Parallel Multigrid Method for Finite Elements},
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volume = {8},
number = {6},
pages = {56--62},
year = {2006}
}
@MastersThesis{ brunethesis08,
author = {Peter R. Brune},
title = {Enabling Unstructured Multigrid Under the Sieve Framework},
school = {University of Chicago},
address = {Chicago, IL},
year = {2008},
month = feb
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author = {Douglas N. Arnold and Ragnar Winther},
title = {Mixed finite elements for elasticity},
journal = {Numerische Mathematik},
volume = {92},
number = {3},
month = sep,
year = {2002},
pages = {401--419},
doi = {10.1007/s002110100348}
}
@Article{ arnoldfalkwinther06,
author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther},
title = {Finite element exterior calculus, homological techniques, and applications},
journal = {Acta Numerica},
year = {2006},
volume = {15},
pages = {1--155},
publisher = {Cambridge University Press},
doi = {10.1017/S0962492906210018}
}
@Article{ kirby04,
author = {Robert C. Kirby},
title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis
functions},
journal = {ACM Transactions on Mathematical Software},
volume = {30},
number = {4},
year = {2004},
issn = {0098-3500},
pages = {502--516},
doi = {10.1145/1039813.1039820},
publisher = {ACM Press},
address = {New York, NY}
}
@Article{ kirby06,
author = {Robert C. Kirby},
title = {Optimizing {FIAT} with level 3 {BLAS}},
journal = {ACM Transactions on Mathematical Software},
volume = {32},
number = {2},
year = {2006},
issn = {0098-3500},
pages = {223--235},
doi = {10.1145/1141885.1141889},
publisher = {ACM Press},
address = {New York, NY}
}
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author = {{B}lue {C}rystal Cluster},
title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}},
year = {2008},
note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}}
}
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author = {Gregory Beylkin},
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journal = {Applied and Computational Harmonic Analysis},
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pages = {363--381},
year = {1995}
}
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author = {Jonathan Riehl},
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address = {Nashville, TN},
year = {2008}
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date-added = {2008-02-27 12:23:39 +0000},
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journal = {SIAM Journal on Scientific and Statistical Computing},
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year = {1985}
}
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author = {{Ewald}, P.~P.},
title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}},
journal = {Annalen der Physik},
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volume = {369},
pages = {253-287},
doi = {10.1002/andp.19213690304},
adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
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author = {L. Greengard and V. Rokhlin},
date-added = {2008-02-15 18:43:55 +0000},
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journal = {J. Comput.\ Phys.},
keywords = {FMM},
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title = {A Fast Algorithm for Particle Simulations},
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author = {L. Greengard and V. Rokhlin},
title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three
Dimensions},
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@Article{ luchenghuangmccammon06,
author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon},
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@Article{ schussnadlereisenberg01,
author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg},
title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel
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author = {E. Hairer and Ch. Lubich and G. Wanner},
title = {Geometric Numerical Integration},
publisher = {Springer-Verlag},
address = {Berlin Heidelberg},
year = {2002}
}
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author = {M. Holst and N. Baker and F. Wang},
title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann
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year = {2000}
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author = {R. Hockney and J. Eastwood},
title = {Computer simulation using particles},
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@Article{ lutydavistironigunsteren94,
author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van
Gunsteren},
title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for
Calculating Electrostatic Interactions in Periodic Molecular Systems},
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pages = {11--20}
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author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.},
title = {A Multigrid Tutorial (2nd ed.)},
year = {2000},
isbn = {0-89871-462-1},
publisher = {Society for Industrial and Applied Mathematics},
address = {Philadelphia, PA}
}
@Article{ chartier2003spectral,
title = {Spectral AMGe ($\rho$ AMGe)},
author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and
McCormick, S and Ruge, J and Vassilevski, PS},
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volume = {25},
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year = {2003},
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@Article{ galvis2010domain,
title = {Domain decomposition preconditioners for multiscale flows in high-contrast
media},
author = {Galvis, Juan and Efendiev, Yalchin},
journal = {Multiscale Modeling \& Simulation},
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number = {4},
pages = {1461--1483},
year = {2010},
publisher = {SIAM}
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@Book{ brennerscott02,
author = {Susanne~C. Brenner and L.~Ridgway Scott},
title = {The mathematical theory of finite element methods},
year = {2002},
isbn = {0-38795-451-1},
publisher = {Springer},
pages = {361}
}
@Book{ trefethenbau97,
author = {Lloyd N. Trefethen and David {Bau, III}},
title = {Numerical Linear Algebra},
publisher = {Society for Industrial and Applied Mathematics},
address = {Philadelphia, PA},
pages = {xii + 361},
year = {1997},
isbn = {0-89871-361-7},
isbn-13 = {978-0-89871-361-9},
lccn = {QA184 .T74 1997},
mrclass = {65-01 (65-02 65Fxx)},
mrnumber = {MR1444820 (98k:65002)},
mrreviewer = {Moody T. Chu},
bibdate = {Wed Jan 07 15:23:19 1998},
bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib}
}
@Article{ liptonreagan2014,
title = {Quantum Algorithms via Linear Algebra: A Primer},
author = {Richard J Lipton and Kenneth W Regan},
pages = {206},
isbn = {978-0-26202-839-4},
year = {2014}
}
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author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh
Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong},
title = {Scalable adaptive mantle convection simulation on petascale supercomputers},
booktitle = {Proceedings of IEEE/ACM SC '08},
year = {2008}
}
@Misc{ bursteddewilcox09,
author = {Carsten Burstedde and Lucas~C. Wilcox},
title = {The p4est library: A parallel scalable forest of adaptive octrees},
note = {in preparation}
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@Article{ skeeltezcanhardy02,
author = {R. D. Skeel and I. Tezcan and D. J. Hardy},
title = {Multiple Grid Methods for Classical Molecular Dynamics},
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author = {Jan Verschelde},
title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by
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volume = {25},
number = {2},
issn = {0098-3500},
pages = {251--276},
doi = {10.1145/317275.317286},
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}
@InProceedings{ sommeseverscheldewampler08,
author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler},
title = {Solving Polynomial Systems Equation by Equation},
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editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese},
pages = {133--152},
publisher = {Springer-Verlag},
year = {2008}
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@Article{ phanthientanner77,
author = {N. Phan-Thien and R.~I. Tanner},
title = {A new constitutive equation derived from network theory},
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year = {1977}
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@Manual{ sage,
key = {SAGE},
author = {W.\thinspace{}A. Stein and others},
organization = {The Sage~Development Team},
title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)},
note = {{\tt http://www.sagemath.org}},
year = {2009}
}
@Misc{ bateshauensteinsommesewampler06,
author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W.
Wampler},
title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry},
howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini}
}
@Article{ archer09,
author = {A. J. Archer},
collaboration = {},
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volume = {130},
number = {1},
eid = {014509},
numpages = {8},
pages = {014509},
keywords = {colloids; continuum mechanics; density functional theory; free energy; glass
transition; statistical distributions; stochastic processes},
doi = {10.1063/1.3054633}
}
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author = {Hanswalter Giesekus},
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pages = {361--385}
}
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author = {D.~D. Joseph},
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publisher = {Springer},
address = {New York, NY},
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author = {J.~G. Oldroyd},
title = {On the Formulation of Rheological Equations of State},
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volume = {200},
year = {1950},
pages = {523--541}
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author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur},
title = {Predicting Memory-Access Cost Based on Data-Access Patterns},
booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego},
year = {2004}
}
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author = {C. Pozrikidis},
title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation},
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pages = {675},
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isbn = {0792373510}
}
@Misc{ kritzkeyesfsp07,
author = {A. Kritz and D. Keyes},
title = {{Fusion Simulation Project Workshop Report}},
month = jul,
year = {2007},
note = {Available via
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}
@Misc{ dahlburg02,
author = {J. {Dahlburg (Chair)}},
title = {{Final Report of the FESAC ISOFS SubCommittee}},
year = {2002},
note = {Available via
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}
@Misc{ brown08,
author = {D. {Brown (Chair)}},
title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View
to the Future}},
year = {2008},
howpublished = {Office of Science, U.S. Department of Energy},
url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf}
}
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author = {D. Brown and P. {Messina (Chairs)}},
title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the
Exascale}},
year = {2010},
howpublished = {Office of Science, U.S. Department of Energy},
url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf}
}
@Misc{ extreme-scale-solvers-workshop12,
author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and
L.C. McInnes and E. Ng and S. Wild},
title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future
Architectures},
howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy},
note = {{Washington, DC}, March 8-9, 2012},
url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf},
year = {2012}
}
@Misc{ monizrosner09,
author = {{E. Moniz and R. Rosner}},
title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling
and Simulation at the Extreme Scale}},
month = may,
year = {2009},
note = {See
\url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}}
}
@Misc{ blanford08,
author = {{R. Blandord (Chair)}},
title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of
Computing at the Extreme Scale}},
month = dec,
year = {2008},
note = {See
\url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}}
}
@Misc{ exascale07,
author = {H. Simon and T. Zacharia and R. Stevens},
title = {{Modeling and Simulation at the Exascale for Energy and the Environment}},
year = {2007},
note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}}
}
@Misc{ ascrbreakthroughs08,
author = {{Panel on Recent Significant Advancements in Computational Science}},
title = {Breakthroughs},
year = {2008},
note = {See
\url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}}
}
@Misc{ petsc-rd100-2009,
author = {{R\&D Magazine}},
title = {{PETSc} {R}\&{D} 100 Award},
year = {2009},
note = {See
\url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}}
}
@Article{ compass-scidac08,
author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and
R. Ryne},
title = {Community Petascale Project for Accelerator Science and Simulation: Advancing
Computational Science for Future Accelerators and Accelerator Technologies},
journal = {J. Phys.: Conf. Ser.},
volume = {125},
year = {2008},
pages = {012001},
url = {http://iopscience.iop.org/1742-6596/125/1/012001}
}
@Article{ compass-amundson-scidac08,
title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications},
author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P.
Stoltz},
journal = {J. Phys.: Conf. Ser.},
volume = {125},
year = {2008}
}
@InProceedings{ muszala09,
title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator
Simulations},
author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris},
booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing
{(CBHPC 2009)}},
year = {2009}
}
@Article{ gaston09,
title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear
Equations},
author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie},
journal = {Nuclear Engineering and Design},
volume = {239},
number = {10},
year = {2009},
pages = {1768 -- 1778}
}
@Article{ gaston09b,
title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear
Engineering},
author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park
and C. Permann and W. Taitano},
journal = {J. Phys.: Conf. Ser.},
volume = {180},
year = {2009},
pages = {012012}
}
@Article{ newman09,
title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen
Diffusion in {UO$_2$} Nuclear Fuel Rods},
author = {Chris Newman and Glen Hansen and Derek Gaston},
journal = {Journal of Nuclear Materials},
volume = {392},
issue = {1},
year = {2009},
pages = {6 -- 15}
}
@Misc{ www:fenics,
author = {{FE}ni{CS}},
title = {{FE}ni{CS} Project},
howpublished = {\url{http://www.fenics.org/}},
year = {2018}
}
@InProceedings{ zwart08,
title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical
Systems},
author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut
and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E.
Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and
S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp},
booktitle = {Proceedings of ICCS 2008},
year = {2008}
}
@Article{ klocknerwarburtonbridgehesthaven09,
author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.},
title = {Nodal discontinuous {G}alerkin methods on graphics processors},
journal = {J. Comput. Phys.},
volume = {228},
number = {21},
year = {2009},
issn = {0021-9991},
pages = {7863--7882},
doi = {10.1016/j.jcp.2009.06.041},
publisher = {Academic Press Professional},
address = {San Diego, CA}
}
@PhDThesis{ rankin99,
author = {Rankin, W. T.},
keywords = {FMM, parallel FMM},
school = {Department of Electrical and Computer Engineering, Duke University},
title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms},
year = {1999}
}
@InProceedings{ warrensalmon93,
abstract = {We report on an efficient adaptive N-body method which we have recently designed
and implemented. The algorithm computes the forces on an arbitrary distribution of
bodies in a time which scales as N log N with the particle number. The accuracy of
the force calculations is analytically bounded, and can be adjusted via a user
defined parameter between a few percent relative accuracy, down to machine
arithmetic accuracy. Instead of using pointers to indicate the topology of the
tree, we identify...},
address = {New York},
author = {Warren, Michael S. and Salmon, John K.},
booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing},
citeulike-article-id={580952},
keywords = {oct-tree},
pages = {12--21},
publisher = {ACM},
title = {A parallel hashed Oct-Tree {N}-body algorithm},
year = {1993},
doi = {10.1145/169627.169640},
url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100}
}
@Unpublished{ cruzwccm10,
author = {Felipe A. Cruz},
title = {Heterogeneous extension of the PetFMM a Fast Multipole Library},
note = {Presentation at WCCM 2010, Sydney Australia},
year = {2010}
}
@Article{ mcguffee06,
author = {S.~R. {McGuffee} and A.~H. Elcock},
title = {Atomistically detailed simulations of concentrated protein solutions: the effects
of salt, {pH}, point mutations, and protein concentration in simulations of
1000-molecule systems},
journal = {Journal of the American Chemical Society},
volume = {128},
pages = {12098--12110},
year = {2006}
}
@Article{ nilsencaihoylandlangtangen10,
author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.},
title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach
in Python}},
journal = {ArXiv e-prints},
archiveprefix = {arXiv},
eprint = {1002.0705},
primaryclass = {cs.DC},
keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science
- Programming Languages},
year = {2010},
month = feb,
adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@Misc{ mcinnes:siam09:minisymposium,
title = {Implicit Nonlinear Solvers in Multimodel Simulations},
author = {L. C. McInnes and C. {Woodward (co-organizers)}},
note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009,
Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J.
White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ.
of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll
(INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at
Austin).}
}
@Misc{ mcinnes:fsp-summary:feb2011,
author = {Lois Curfman McInnes and Luis Chacon and John Shadid},
title = {Solvers and Time Integration Breakout Summary},
note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see
\url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}}
}
@Misc{ dvi-materials:siamcse11,
title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous
Materials},
author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F.
Smith and L. Wang},
note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science
and Engineering, March 3, 2011}
}
@Misc{ jamroz:cemm10,
title = {{JFNK} within the semi-implicit scheme in {NIMROD}},
author = {B. Jamroz and S. Kruger and T. Austin},
note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010}
}
@Misc{ kruger:feb4-2011,
title = {personal communication},
author = {S. Kruger},
note = {February, 2011}
}
@Article{ elman1996,
author = {H.C. Elman},
title = {Preconditioning for the steady-state {Navier-Stokes} equations for low
viscosity},
journal = {SIAM J. Sci. Comput.},
volume = {20},
year = {1996},
pages = {1299--1316}
}
@Article{ kayloghinwathen2002,
author = {D. Kay and D. Loghin and A. Wathen},
title = {A preconditioning for the steady-state {Navier-Stokes} equations},
journal = {SIAM J. Sci. Comput.},
volume = {24},
year = {2002},
pages = {237--256}
}
@Article{ elmanhowleshadidshuttleworthtuminaro2006,
author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro},
title = {Block preconditioners based on approximate commutators},
journal = {SIAM J. Sci. Comput.},
volume = {27},
number = {5},
year = {2006},
pages = {1651--1668}
}
@Article{ braesssarazin1997,
author = {Dietrich Braess and Regina Sarazin},
title = {An efficient smoother for the {Stokes} problem},
journal = {Applied Numerical Mathematics},
volume = {23},
number = {1},
year = {1997},
pages = {3--19},
doi = {10.1016/S0168-9274(96)00059-1}
}
@Article{ wright2001large,
title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}},
author = {Wright, T.G. and Trefethen, L.N.},
journal = {SIAM Journal on Scientific Computing},
volume = {23},
pages = {591},
year = {2001}
}
@Misc{ wright2002eigtool,
title = {Eig{T}ool},
author = {Wright, T.G. and Trefethen, LN},
howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}},
year = {2002}
}
@Misc{ visit-web-site,
key = {{VisIt}},
title = {{VisIt web site}},
howpublished = {\url{http://wci.llnl.gov/codes/visit/}},
url = {http://wci.llnl.gov/codes/visit/},
year = {2011}
}
@Book{ trefethen1996,
title = {Finite difference and spectral methods for ordinary and partial differential
equations},
author = {Lloyd Nicholas Trefethen},
year = {1996},
publisher = {Cornell University-Department of Computer Science and Center for Applied
Mathematics}
}
@Book{ trefethen2005spectra,
title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators},
author = {Trefethen, L.N. and Embree, M.},
year = {2005},
publisher = {Princeton University Press}
}
@Article{ gomez2010isogeometric,
title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations},
author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {199},
number = {25-28},
pages = {1828--1840},
issn = {0045-7825},
year = {2010},
publisher = {Elsevier}
}
@Article{ gomez2008isogeometric,
title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model},
author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {197},
number = {49-50},
pages = {4333--4352},
year = {2008},
publisher = {Elsevier}
}
@Misc{ fastmath:project,
author = {Lori {Diachin (PI)}},
title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics
(FASTMath) Institute}},
howpublished = {\url{https://fastmath-scidac.llnl.gov}}
}
@Misc{ exascale-software:proposal,
author = {Peter {Beckman (PI)}},
title = {{Exascale Software Center}},
note = {proposal to DOE}
}
@Misc{ imex:project,
author = {Barry {Smith (PI)}},
title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent
Multimodel PDEs}},
note = {DOE ASCR applied math project}
}
@Misc{ intel-mic:website,
author = {Intel},
title = {{Many Integrated Core Architecture}},
note = {\url{http://www.intel.com/technology/architecture-silicon/mic}}
}
@Article{ dudson:2009,
author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson},
title = {{{BOUT++:}} a framework for parallel plasma fluid simulations},
journal = {Computer Physics Communications},
volume = {180},
pages = {1467},
year = {2009}
}
@Article{ umansky:2009,
author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra},
title = {{Status and verification of edge plasma turbulence code BOUT}},
journal = {Computer Physics Communications},
year = {2009},
volume = {180},
pages = {887-903}
}
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author = {X.Q. Xu and R.H. Cohen},
title = {{Scrape-Off Layer Turbulence Theory and Simulations}},
journal = {Computer Physics Communications},
year = {1998},
volume = {36},
number = {1-2},
pages = {158}
}
@Article{ tron:1999,
title = {Newton's Method for Large Bound-constrained Optimization Problems},
author = {Chih-Jen Lin and Jorge Mor\'{e}},
journal = {SIAM Journal on Optimization},
volume = {9},
number = {4},
pages = {1100-1127},
year = {1999}
}
@Article{ stubenamg,
author = {K. St\"{u}ben},
title = {A review of algebraic multigrid},
journal = {J. Comput. Appl. Math.},
volume = {128},
number = {1-2},
year = {2001},
issn = {0377-0427},
pages = {281--309},
doi = {10.1016/S0377-0427(00)00516-1},
publisher = {Elsevier Science Publishers B. V.},
address = {Amsterdam, The Netherlands, The Netherlands}
}
@Article{ feuchtermg,
author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum},
title = {Bridging the gap between geometric and algebraic multigrid methods},
journal = {Computing and visualization in science},
publisher = {Springer},
volume = {6},
number = {1},
year = {2003},
pages = {1--13}
}
@Article{ chowmgsmoothness,
abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that
only attempts to interpolate in the directions of geometrical smoothness. These
directions are determined by analyzing samples of algebraically smooth error, e.
Neighboring grid points i and j are called smoothly coupled if e i and e j are
consistently nearby in value. In addition, these dierences may be used to dene
interpolation weights. These new ideas may be incorporated into the algebraic
multigrid method. Test results show that the new method can have much lower grid
and operator complexities compared to AMG, leading to lower solve timings. 1 },
author = {Chow, Edmond},
citeulike-article-id={7675372},
citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
journal = {American Journal of Mathematics},
keywords = {fem, multigrid},
pages = {197--215},
posted-at = {2010-08-17 23:29:51},
priority = {2},
title = {An Unstructured Multigrid Method Based on Geometric Smoothness},
url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
volume = {65},
year = {2001}
}
@Article{ jonesamge,
abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite
elements) method based on element agglomeration. In the method, coarse grid
elements are formed by agglomerating fine grid elements. Compatible interpolation
operators are constructed which yield coarse grid basis functions with a minimal
energy property. Heuristics based on interpolation quality measures are used to
guide the agglomeration procedure. The performance of the resulting method is
demonstrated in two-level numerical experiments.}},
author = {Jones, Jim E. and Vassilevski, Panayot S.},
citeulike-article-id={8598569},
citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109},
journal = {SIAM Journal on Scientific Computing},
keywords = {amg, fem, multigrid},
number = {1},
pages = {109--133},
posted-at = {2011-01-13 18:05:55},
priority = {2},
publisher = {SIAM},
title = {{AMGE Based on Element Agglomeration}},
url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
volume = {23},
year = {2001}
}
@Article{ saad1993,
author = {Saad, Youcef},
doi = {10.1137/0914028},
issn = {10648275},
journal = {SIAM Journal on Scientific Computing},
keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose
iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of
precondition-,preconditioned conju-,subject classi cations,variable
preconditioners},
number = {2},
pages = {461--469},
title = {{A flexible inner-outer preconditioned GMRES algorithm}},
volume = {14},
year = {1993}
}
@Misc{ path:homepage,
author = {S. Dirkse and M. Ferris and T. Munson},
title = {{{PATH} {W}eb page}},
howpublished = {\url{http://pages.cs.wisc.edu/~ferris/path.html}}
}
@Article{ ketcheson2008,
author = {David I Ketcheson},
title = {Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with
Low-Storage Implementations},
volume = {30},
journal = {SIAM Journal on Scientific Computing},
year = {2008},
pages = {2113--2136}
}
@Article{ elman2009boundary,
title = {{Boundary conditions in approximate commutator preconditioners for the
Navier-Stokes equations}},
author = {Elman, H.C. and Tuminaro, R.},
journal = {Electronic Transactions on Numerical Analysis},
volume = {35},
pages = {257--280},
year = {2009}
}
@Article{ elman2008tcp,
title = {{A taxonomy and comparison of parallel block multi-level preconditioners for the
incompressible Navier-Stokes equations}},
author = {Elman, H.C. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro,
R.},
journal = {Journal of Computational Physics},
volume = {227},
number = {1},
pages = {1790--1808},
year = {2008},
publisher = {Academic Press},
url = {https://www.osti.gov/biblio/920807/}
}
@Article{ arioli2013,
title = {Generalized {G}olub--{K}ahan bidiagonalization and stopping criteria},
author = {Arioli, Mario},
journal = {SIAM Journal on Matrix Analysis and Applications},
volume = {34},
number = {2},
pages = {571--592},
year = {2013},
publisher = {SIAM}
}
@Book{ wesseling2009,
title = {Principles of computational fluid dynamics},
author = {Wesseling, Pieter},
volume = {29},
year = {2009},
publisher = {Springer Science \& Business Media}
}
@Article{ silvester2001efficient,
title = {{Efficient preconditioning of the linearized Navier-Stokes equations for
incompressible flow}},
author = {Silvester, D. and Elman, H. and Kay, D. and Wathen, A.},
journal = {Journal of Computational and Applied Mathematics},
volume = {128},
number = {1-2},
pages = {261--279},
issn = {0377-0427},
year = {2001},
publisher = {Elsevier}
}
@Article{ elman1999bfbt,
title = {{Preconditioning for the steady-state Navier-Stokes equations with low
viscosity}},
author = {Elman, H.C.},
journal = {SIAM Journal on Scientific Computing},
volume = {20},
number = {4},
pages = {1299--1316},
issn = {1064-8275},
year = {1999},
publisher = {Citeseer}
}
@Article{ elman2006bpb,
title = {{Block preconditioners based on approximate commutators}},
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title = {Scalable adaptive mantle convection simulation on petascale supercomputers},
author = {Burstedde, C. and Ghattas, O. and Gurnis, M. and Stadler, G. and Tan, E. and Tu,
T. and Wilcox, L.C. and Zhong, S.},
booktitle = {Proceedings of the 2008 ACM/IEEE conference on Supercomputing},
pages = {62},
year = {2008},
organization = {IEEE Press}
}
@Article{ burstedde2009parallel,
title = {Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes}
flow problems},
author = {Burstedde, C. and Ghattas, O. and Stadler, G. and Tu, T. and Wilcox, L.C.},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {198},
number = {21-26},
pages = {1691--1700},
year = {2009},
publisher = {Elsevier}
}
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title = {The dynamics of plate tectonics and mantle flow: From local to global scales},
author = {Stadler, G. and Gurnis, M. and Burstedde, C. and Wilcox, L.C. and Alisic, L. and
Ghattas, O.},
journal = {Science},
volume = {329},
number = {5995},
pages = {1033},
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publisher = {American Association for the Advancement of Science}
}
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title = {Modelling compressible mantle convection with large viscosity contrasts in a
three-dimensional spherical shell using the yin-yang grid},
author = {Tackley, P.J.},
journal = {Physics of the Earth and Planetary Interiors},
volume = {171},
number = {1-4},
pages = {7--18},
year = {2008},
publisher = {Elsevier}
}
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author = {Louis N. Moresi and Shijie Zhong and Michael Gurnis},
title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying
viscosity},
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volume = {97},
pages = {83-–94},
year = {1996}
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author = {Louis N. Moresi and V. S. Solomatov},
title = {Numerical investigation of {2D} convection with extremely large viscosity
variations},
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year = {1995}
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author = {W.-P. Chen and P. Molnar},
title = {Focal depths of intra-continental and intraplate earthquakes and their
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year = {1983}
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author = {J. Jackson},
title = {Strength of the continental lithosphere: time to abandon the jelly sandwich?},
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year = {2002}
}
@Article{ burovwatts06,
author = {E.B. Burov and A.B. Watts},
title = {The long-term strength of continental lithosphere: jelly sandwich or creme
brulee?},
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year = {2006}
}
@InProceedings{ yang:brent:2002,
title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on
Parallel Distributed Memory Architectures},
author = {Laurence T. Yang and Richard Brent},
booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures
for Parallel Processing},
year = {2002},
publisher = {IEEE}
}
@Article{ demmel2008communication,
title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations},
author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.},
journal = {Arxiv preprint arXiv:0808.2664},
year = {2008}
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author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick},
title = {Communication-optimal Iterative Methods},
journal = {Journal of Physics: Conf. Series},
volume = {180},
year = {2009}
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author = {Yousef Saad and Masha Sosonkina},
title = {{pARMS}: A package for the parallel iterative solution of general large sparse
linear systems user's guide},
number = {UMSI2004-8},
institution = {Minnesota Supercomputer Institute, University of Minnesota},
year = {2004}
}
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author = {Emile Picard},
title = {M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la
m\'ethode des approximations successives},
journal = {Journal De Math\'ematiques Pures et Appliqu\'ees},
volume = {4},
number = {6},
pages = {145--210},
year = {1890},
url = {http://math-doc.ujf-grenoble.fr/JMPA/PDF/JMPA_1890_4_6_A3_0.pdf}
}
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author = {Louis B. Rall},
title = {Computational solution of nonlinear operator equations},
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author = {R. Fletcher and C. M. Reeves},
title = {Function Minimization by Conjugate Gradients},
journal = {Computer Journal},
volume = {7},
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@InBook{ mcinnesallanetal06,
author = {Lois Curfman McInnes and Benjamin Allan and Robert Armstrong and Steven Benson
and David Bernholdt and Tamara Dahlgren and Lori Diachin and Manojkumar Krishnan
and James Kohl and Jay Larson and Sophia Lefantzi and Jarek Nieplocha and Boyana
Norris and Steven Parker and Jaideep Ray and Shujia Zhou},
editor = {A.~M.~Bruaset and A.~Tveito},
title = {Numerical Solution of Partial Differential Equations on Parallel Computers},
chapter = {Parallel {PDE}-Based Simulations Using the {Common Component Architecture}},
publisher = {Springer},
year = {2006},
number = {51},
series = {Lecture Notes in Computational Science and Engineering},
pages = {327--381},
doi = {10.1016/S0167-8191(02)00191-6}
}
@Article{ cyrshadidtuminaro12,
title = {Stabilization and scalable block preconditioning for the {Navier–Stokes}
equations},
journal = {Journal of Computational Physics},
volume = {231},
number = {2},
pages = {345 - 363},
year = {2012},
issn = {0021-9991},
doi = {10.1016/j.jcp.2011.09.001},
author = {Eric C. Cyr and John N. Shadid and Raymond S. Tuminaro}
}
@Article{ keyesmcinneswoodwardetal13,
title = {Multiphysics Simulations: Challenges and Opportunities},
author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and
Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and
Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel
Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin
Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras
and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein
and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and
Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich
R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and
Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth},
journal = {International Journal of High Performance Computing Applications},
month = feb,
year = {2013},
volume = {27},
number = {1},
pages = {4--83},
doi = {10.1177/1094342012468181},
note = {Special issue},
abstract = {We consider multiphysics applications from algorithmic and architectural
perspectives, where ``algorithmic'' includes both mathematical analysis and
computational complexity and ``architectural'' includes both software and hardware
environments. Many diverse multiphysics applications can be reduced, en route to
their computational simulation, to a common algebraic coupling paradigm.
Mathematical analysis of multiphysics coupling in this form is not always
practical for realistic applications, but model problems representative of
applications discussed herein can provide insight. A variety of software
frameworks for multiphysics applications have been constructed and refined within
disciplinary communities and executed on leading-edge computer systems. We examine
several of these, expose some commonalities among them, and attempt to extrapolate
best practices to future systems. From our study, we summarize challenges and
forecast opportunities.}
}
@Misc{ rosner10,
author = {Robert {Rosner (Chair)}},
title = {{The Opportunities and Challenges of Exascale Computing}},
year = {2010},
howpublished = {Office of Science, U.S. Department of Energy},
url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf}
}
@Misc{ kogge2008exascale,
title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems},
author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian
Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod
and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein
and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan
Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick},
howpublished = {DARPA},
year = {2008},
url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf}
}
@Misc{ doegrandchallengeworkshops,
key = {Office of Science, U.S. Department of Energy},
title = {{Scientific Grand Challenges Workshop Series}},
howpublished = {Office of Science, U.S. Department of Energy, see
\url{http://extremecomputing.labworks.org/workshops.stm}}
}
@Misc{ lawrence2011,
key = {Lawrence},
title = {{Ernest Orlando Lawrence Award Winners}},
howpublished = {U.S. Department of Energy, {\footnotesize
\url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}},
year = {2011}
}
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title = {{A note on preconditioning for indefinite linear systems}},
author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.},
journal = {SIAM Journal on Scientific Computing},
volume = {21},
number = {6},
pages = {1969--1972},
year = {2000},
publisher = {Philadelphia, PA: SIAM, c1993-}
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title = {Fast iterative solvers for buoyancy driven flow problems},
journal = {Journal of Computational Physics},
volume = {230},
number = {10},
pages = {3900 - 3914},
year = {2011},
note = {},
issn = {0021-9991},
doi = {10.1016/j.jcp.2011.02.014},
author = {Howard Elman and Milan Mihajlovic and David Silvester},
keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping,
Adaptivity, Preconditioning, Algebraic multigrid}
}
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author = {J. Dongarra and P. Beckman and et al.},
title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap},
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year = {2011},
pages = {3--60}
}
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title = {Energy optimization of algebraic multigrid bases},
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pages = {205--228},
year = {1999},
publisher = {Springer}
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title = {Algebraic multigrid by smoothed aggregation for second and fourth order elliptic
problems},
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volume = {56},
number = {3},
pages = {179--196},
year = {1996},
publisher = {Springer}
}
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title = {Convergence of algebraic multigrid based on smoothed aggregation},
author = {Van{\v{e}}ek, P. and Brezina, M. and Mandel, J.},
journal = {Numerische Mathematik},
volume = {88},
number = {3},
pages = {559--579},
year = {2001},
publisher = {Springer}
}
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title = {Algebraic multigrid methods based on compatible relaxation and energy
minimization},
author = {Brannick, J. and Zikatanov, L.},
journal = {Domain decomposition methods in science and engineering XVI},
pages = {15--26},
year = {2007},
publisher = {Springer}
}
@Article{ brannickfalgout2010,
title = {{Compatible Relaxation and Coarsening in Algebraic Multigrid}},
author = {James J. Brannick and Robert D. Falgout},
journal = {SIAM Journal on Scientific Computing},
volume = {32},
number = {3},
pages = {1393--1416},
url = {http://epubs.siam.org/doi/10.1137/090772216},
doi = {10.1137/090772216},
issn = {1064-8275},
year = {2010}
}
@Article{ xu2004energy,
title = {On an energy minimizing basis for algebraic multigrid methods},
author = {Xu, J. and Zikatanov, L.},
journal = {Computing and Visualization in Science},
volume = {7},
number = {3},
pages = {121--127},
year = {2004},
publisher = {Springer}
}
@Article{ dblp:journals/toms/bakerhlt09,
author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist},
title = {Anasazi software for the numerical solution of large-scale eigenvalue problems},
journal = {ACM Trans. Math. Softw.},
volume = {36},
number = {3},
year = {2009},
doi = {10.1145/1527286.1527287},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@Article{ dblp:journals/siamsc/yanggbllhn05,
author = {Chao Yang and Weiguo Gao and Zhaojun Bai and Xiaoye S. Li and Lie-Quan Lee and
Parry Husbands and Esmond G. Ng},
title = {An Algebraic Substructuring Method for Large-Scale Eigenvalue Calculation},
journal = {SIAM J. Scientific Computing},
volume = {27},
number = {3},
year = {2005},
pages = {873-892},
doi = {10.1137/040613767},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@TechReport{ ml-guide,
author = {M.W. Gee and C.M. Siefert and J.J. Hu and R.S. Tuminaro and M.G. Sala},
title = {{ML} 5.0 Smoothed Aggregation User's Guide},
institution = {Sandia National Laboratories},
year = {2006},
number = {SAND2006-2649}
}
@Article{ brannick06,
title = {An energy-based AMG coarsening strategy},
volume = {13},
doi = {10.1002/nla.480},
number = {2-3},
journal = {Numerical Linear Algebra with Applications},
author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S
and Ruge, J},
year = {2006},
pages = {133--148}
}
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author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.},
title = {A new perspective on strength measures in algebraic multigrid},
journal = {Numerical Linear Algebra with Applications},
volume = {17},
number = {4},
pages = {713--733},
year = {2010},
publisher = {John Wiley \& Sons, Ltd.},
issn = {1099-1506},
doi = {10.1002/nla.669}
}
@Article{ olson11,
author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.},
title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy
Minimization},
journal = {SIAM J. Sci. Comput.},
issue_date = {April 2011},
volume = {33},
issue = {2},
month = apr,
year = {2011},
issn = {1064-8275},
pages = {966--991},
numpages = {26},
doi = {10.1137/100803031},
acmid = {2078825},
publisher = {Society for Industrial and Applied Mathematics},
address = {Philadelphia, PA},
keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed
aggregation}
}
@Article{ dorit2011,
author = {Dorit Ron and Ilya Safro and Achi Brandt},
title = {Relaxation-Based Coarsening and Multiscale Graph Organization},
journal = {Multiscale Modeling {\&} Simulation},
volume = {9},
number = {1},
year = {2011},
pages = {407-423},
doi = {10.1137/100791142}
}
@Article{ chen2011algebraic,
title = {Algebraic distance on graphs},
author = {Chen, Jie and Safro, Ilya},
journal = {SIAM Journal on Scientific Computing},
volume = {33},
number = {6},
pages = {3468--3490},
year = {2011},
publisher = {SIAM}
}
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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}
}
@Article{ adams03a,
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{ adams-10a,
author = {M. ~F. Adams and Ravi Samtaney and Achi Brandt},
doi = {10.1016/j.jcp.2010.04.024},
issn = {0021-9991},
journal = {Journal of Computational Physics},
keywords = {Implicit magnetohydrodynamics},
number = {18},
pages = {6208 - 6219},
title = {Toward textbook multigrid efficiency for fully implicit resistive
magnetohydrodynamics},
volume = {229},
year = {2010}
}
@InProceedings{ adams98,
address = {Copper Mountain, CO},
author = {Adams, M.~F.},
booktitle = {Proceedings 5th Copper Mountain Conference on Iterative Methods},
title = {A Parallel Maximal Independent Set Algorithm},
year = {1998}
}
@InProceedings{ madaypatera89,
author = {Y. Maday and A. T. Patera},
title = {Spectral element methods for the {Navier-Stokes} equations},
editor = {A. K. Noor and J. T. Oden},
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@Article{ mishra2012mlmcfvm,
title = {Multi-level {M}onte {C}arlo finite volume methods for nonlinear systems of
conservation laws in multi-dimensions},
journal = {Journal of Computational Physics},
volume = {231},
number = {8},
pages = {3365--3388},
year = {2012},
issn = {0021-9991},
doi = {10.1016/j.jcp.2012.01.011},
author = {S. Mishra and Ch. Schwab and J. {\v S}ukys},
keywords = {Conservation laws, Euler, MHD, Uncertainty quantification, Multi-level Monte
Carlo, Parallelization}
}
@Article{ barth2011mlmcfe,
author = {Barth, Andrea and Schwab, Christoph and Zollinger, Nathaniel},
affiliation = {ETH Zentrum, Seminar für Angewandte Mathematik, Rämistrasse 101, 8092 Zurich,
Switzerland},
title = {Multi-Level {M}onte {C}arlo Finite Element method for elliptic {PDE}s with
stochastic coefficients},
journal = {Numerische Mathematik},
publisher = {Springer Berlin / Heidelberg},
issn = {0029-599X},
keyword = {Mathematics and Statistics},
pages = {123-161},
volume = {119},
issue = {1},
doi = {10.1007/s00211-011-0377-0},
year = {2011}
}
@Article{ nguyen2011hybridizable,
title = {Hybridizable discontinuous {G}alerkin methods},
author = {Nguyen, N.C. and Peraire, J. and Cockburn, B.},
journal = {Spectral and High Order Methods for Partial Differential Equations},
pages = {63--84},
year = {2011},
publisher = {Springer}
}
@Misc{ snyder-scidac3:proposal,
author = {Philip {Snyder (PI)}},
title = {{Plasma Edge Advanced Computation (PEAC) Center}},
note = {proposal to DOE SciDAC3},
month = oct,
year = {2011}
}
@Misc{ wirth-scidac3:proposal,
author = {Brian {Wirth (PI)}},
title = {{Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier
through Leadership Class Computing}},
note = {proposal to DOE SciDAC3},
month = oct,
year = {2011}
}
@Misc{ cary-scidac3:proposal,
author = {John {Cary (PI)}},
title = {{Integrated Multiscale Modeling for Plasma Analysis and Control of Tokamak
Stability (IMMPACTS)}},
note = {proposal to DOE SciDAC3},
month = oct,
year = {2011}
}
@Misc{ vashista-scidac3:proposal,
author = {Priya {Vashista (PI)}},
title = {{Design of Damage-Tolerance Material Interfaces for Extreme
Stress-Temperature-Corrosion Environments: Algorithms and Methods for
Multi-Petaflops Simulations}},
note = {proposal to DOE SciDAC3},
month = mar,
year = {2012}
}
@Article{ elemental2012,
author = {Jack Poulson and Bryan Marker and Jeff R. Hammond and Nichols A. Romero and
Robert {v}an~{d}e~{G}eijn},
title = {Elemental: A New Framework for Distributed Memory Dense Matrix Computations},
journal = {{ACM} Transactions on Mathematical Software},
volume = {39},
number = {2},
year = {2013}
}
@Misc{ elemental-web-page,
author = {Jack Poulson},
title = {Elemental: Distributed memory dense linear algebra},
howpublished = {\url{http://libelemental.org}},
url = {http://libelemental.org/},
year = {2015}
}
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title = {A Science-based Case for Large-scale Simulation},
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publisher = {U.S. Department of Energy},
year = {2004},
url = {http://www.pnl.gov/scales}
}
@InProceedings{ cilk95,
address = {Santa Barbara, California},
author = {Robert D. Blumofe and Christopher F. Joerg and Bradley C. Kuszmaul and Charles E.
Leiserson and Keith H. Randall and Yuli Zhou},
booktitle = {Proceedings of the Fifth ACM SIGPLAN Symposium on Principles and Practice of
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month = jul,
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title = {{Cilk}: An Efficient Multithreaded Runtime System},
year = {1995}
}
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author = {Julian Seward},
title = {Valgrind},
url = {http://valgrind.org/},
howpublished = {\url{http://valgrind.org/}},
year = {2012}
}
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author = {C.~L. Lawson and R.~J. Hanson and D. Kincaid and F.~T. Krogh},
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@TechReport{ lapack90,
author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J.
Du~Croz and A. Greenbaum and S. Hammarling and A. McKenney and D. Sorensen},
title = {{LAPACK}: A portable linear algebra library for high-performance computers},
institution = {Computer Science Dept., University of Tennessee},
number = {CS-90-105},
month = may,
year = {1990}
}
@TechReport{ nvidiafermi,
author = {NVIDIA},
title = {{NVIDIA}'s Next Generation {CUDA} Compute Architecture: {F}ermi},
institution = {NVIDIA},
year = {2009}
}
@Misc{ intelmic,
author = {Many Core Group, Cambridge University},
title = {Intel Many Integrated Core Architecture},
howpublished = {\url{http://www.many-core.group.cam.ac.uk/ukgpucc2/talks/Elgar.pdf}},
month = dec,
year = {2010}
}
@Article{ abusufahkucklawrie81,
author = {W. Abu-Sufah and D.~J. Kuck and D.~H. Lawrie},
title = {On the Performance Enhancement of Paging Systems Through Program Analysis and
Transformations},
journal = {IEEE Trans. Comput.},
volume = {30},
number = {5},
pages = {341--356},
year = {1981}
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@InProceedings{ guobikshandifraguelagarzaranpadua08,
author = {Guo, Jia and Bikshandi, Ganesh and Fraguela, Basilio B. and Garzaran, Maria J.
and Padua, David},
title = {Programming with tiles},
booktitle = {Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of
parallel programming},
series = {PPoPP '08},
year = {2008},
isbn = {978-1-59593-795-7},
location = {Salt Lake City, UT},
pages = {111--122},
numpages = {12},
doi = {10.1145/1345206.1345225},
acmid = {1345225},
publisher = {ACM},
address = {New York, NY}
}
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journal = {International Journal of High Performance Computing Applications},
year = {2004},
title = {Sparse Tiling for Stationary Iterative Methods},
month = feb,
publisher = {Sage Publications},
pages = {95-114},
volume = {18},
number = {1},
author = {Michelle Mills Strout and Larry Carter and Jeanne Ferrante and Barbara Kreaseck}
}
@Misc{ openclstandard,
author = {Khronos Group},
title = {{OpenCL} 1.2 Specification},
howpublished = {\url{http://www.khronos.org/registry/cl/specs/opencl-1.2.pdf}},
url = {http://www.khronos.org/registry/cl/specs/opencl-1.2.pdf},
year = {2011}
}
@Misc{ stlguide,
author = {SGI},
title = {Standard Template Library Programmer's Guide},
howpublished = {\url{http://www.sgi.com/tech/stl/}},
url = {http://www.sgi.com/tech/stl/},
year = {2011}
}
@Book{ stepanov09,
author = {Alexander Stepanov and Paul McJones},
title = {Elements of Programming},
publisher = {Addison-Wesley},
isbn = {978-0-321-63537-2},
year = {2009}
}
@Article{ bangerthhartmannkanschat2007,
author = {W. Bangerth and R. Hartmann and G. Kanschat},
title = {{deal.II} -- a General Purpose Object Oriented Finite Element Library},
journal = {ACM Trans. Math. Softw.},
year = {2007},
volume = {33},
number = {4},
pages = {24/1--24/27}
}
@Misc{ dealii-web-page,
author = {W. Bangerth and R. Hartmann and G. Kanschat},
title = {{deal.II}},
howpublished = {\url{http://www.dealii.org/}},
url = {http://www.dealii.org/},
year = {2012}
}
@InBook{ siek2012,
title = {The C++0x ``Concepts'' Effort},
author = {Jeremy G. Siek},
editor = {Jeremy Gibbons},
booktitle = {Generic and Indexed Programming: International Spring School, SSGIP 2010, Oxford,
UK, March 22-26, 2010, Revised Lectures},
pages = {175--216},
isbn = {978-3-642-32202-0},
doi = {10.1007/978-3-642-32202-0_4},
url = {http://arxiv.org/abs/1201.0027},
note = {\url{http://arxiv.org/abs/1201.0027}},
publisher = {Springer Berlin Heidelberg},
year = {2012}
}
@Misc{ sharpclaw,
note = {\url{http://numerics.kaust.edu.sa/sharpclaw}},
author = {Ketcheson, D. I. and Parsani, M.},
keywords = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic
PDEs,sharpclaw,software},
mendeley-tags = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic
PDEs,sharpclaw,software},
title = {{SharpClaw software}},
year = {2011}
}
@Book{ leveque2002,
title = {Finite volume methods for hyperbolic problems},
author = {Randall J LeVeque},
volume = {31},
year = {2002}
}
@Misc{ clawpack45,
note = {\url{http://www.clawpack.org}},
author = {LeVeque, R. J. and Berger, M. J.},
keywords = {clawpack,finite volumes,hyperbolic PDEs,software},
mendeley-tags = {clawpack,finite volumes,hyperbolic PDEs,software},
title = {{Clawpack Software version 4.5}},
url = {www.clawpack.org},
year = {2011}
}
@Article{ nilsen2010,
archiveprefix = {arXiv},
arxivid = {arXiv:1002.0705v1},
author = {Nilsen, J.K. and Cai, X. and H{\o}yland, Bj{\o} rn and Langtangen, H. P.},
eprint = {arXiv:1002.0705v1},
file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the
parallelization of scientific codes by a function-centric approach in
Python.pdf:pdf},
journal = {Computational Science \& Discovery},
keywords = {parallel,programming,python,software},
mendeley-tags = {parallel,programming,python,software},
pages = {015003},
publisher = {IOP Publishing},
title = {{Simplifying the parallelization of scientific codes by a function-centric
approach in Python}},
url = {http://iopscience.iop.org/1749-4699/3/1/015003},
volume = {3},
year = {2010}
}
@Book{ langtangen09,
author = {Hans Petter Langtangen},
title = {Python Scripting for Computational Science},
publisher = {Springer},
series = {Texts in Computational Science and Engineering},
pages = {784},
isbn = {3540739157},
year = {2009}
}
@Book{ numpyguide,
author = {Travis E. Oliphant},
title = {Guide to {N}umpy},
publisher = {Trelgol},
year = {2008}
}
@Misc{ pycuda,
author = {Andreas Kl\"ockner},
title = {{PyCUDA}},
howpublished = {\url{http://mathema.tician.de/software/pycuda}},
year = {2011}
}
@Misc{ pyopencl,
author = {Andreas Kl\"ockner},
title = {{PyOpenCL}},
howpublished = {\url{http://mathema.tician.de/software/pyopencl}},
year = {2011}
}
@Article{ klockner2012,
author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and
Paul Ivanov and Ahmed Fasih},
title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code
generation},
journal = {Parallel Computing},
volume = {38},
number = {3},
pages = {157--174},
year = {2012},
issn = {0167-8191},
doi = {10.1016/j.parco.2011.09.001}
}
%%%%%% Matt Stuff %%%%%%
@Article{ morrabozdagknepleyrassvesselinov,
title = {A Tectonic Shift in Analytics and Computing Is Coming},
author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and
Velimir Vesselinov},
journal = {Eos},
volume = {102},
doi = {10.1029/2021EO159258},
month = {Jun},
year = {2021}
}
@Misc{ knepley:icerm-workshop:2012,
author = {David Keyes and Matthew Knepley and Katherine Yelick},
title = {Synchronization-reducing and Communication-reducing Algorithms and Programming
Models for Large-scale Simulations},
note = {Workshop sponsored by the Institute for Computational and Experimental Research
in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI,
\url{http://icerm.brown.edu/tw12-1-exascale}},
year = {2012}
}
@TechReport{ kirbyknepleyscott04,
author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
title = {Optimal Evaluation of Finite Element Matrices},
type = {Technical Report},
number = {TR-2004-04},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}},
pages = {14},
month = may,
year = {2004}
}
@TechReport{ kirbyknepleyscott10,
author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
title = {Languages and Compilers for Variational Forms},
type = {Technical Report},
number = {TR-2010-09},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09}},
month = oct,
year = {2010}
}
@TechReport{ kirbyknepleyscott10b,
author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
title = {Evaluation of the Action of Finite Element Operators},
type = {Technical Report},
number = {TR-2010-08},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}},
month = oct,
year = {2010}
}
@TechReport{ bruneknepleyscott11,
author = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott},
title = {Exponential grids in high-dimensional space},
type = {Technical Report},
number = {TR-2011-07},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}},
month = dec,
year = {2011}
}
@TechReport{ zheng11,
author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai
Zhang and Yaolin Shi},
title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with
strongly variable viscosity based on {Matlab} and {CUDA}},
type = {Research Report},
number = {UMSI 2011/33},
institution = {University of Minnesota Supercomputing Institute},
url = {http://static.msi.umn.edu/rreports/2011/33.pdf},
note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}},
month = mar,
year = {2011}
}
@InProceedings{ zheng2010,
author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai
Zhang and Yaolin Shi},
title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
note = {Fall Meeting Supplemental, Abstract IN41A-1350},
year = {2010}
}
@InCollection{ terrelkirbyknepleyscott12,
author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott
and Garth N. Wells},
title = {Finite elements for incompressible fluids},
editors = {A. Logg and K.A. Mardal and G. N. Wells},
booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
pages = {163--169},
publisher = {Springer-Verlag},
year = {2012}
}
@InCollection{ mardalhaga12,
author = {Kent-Andre Mardal and Joachim Berdal Haga},
title = {Block preconditioning of systems of PDEs},
editors = {A. Logg and K.A. Mardal and G. N. Wells},
booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
pages = {643--655},
publisher = {Springer-Verlag},
year = {2012}
}
@InCollection{ kirbyknepleyloggscottterrel12,
author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott and
Andy R. Terrel},
title = {Discrete optimization of finite element matrix evaluation},
editors = {A. Logg and K.A. Mardal and G. N. Wells},
booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
pages = {385--397},
publisher = {Springer-Verlag},
year = {2012}
}
@InCollection{ kirby12,
author = {Robert C. Kirby},
title = {{FIAT}: Numerical Construction of Finite Element Basis Functions},
editors = {A. Logg and K.A. Mardal and G. N. Wells},
booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
publisher = {Springer-Verlag},
year = {2012}
}
@Article{ brownconveryhotesknepleypetropolous1993,
author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and
Labros Petropolous},
title = {Closed strings with low harmonics and kinks},
journal = {Physical Review D},
volume = {48},
number = {6},
year = {1993}
}
@Article{ minimax1996,
title = {MiniMax: What has been learned thus far},
author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and
Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and
C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M.
Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and
M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. Pruneau},
journal = {Nuovo Cimento},
volume = {19},
number = {1},
pages = {1045--1049},
year = {1996}
}
@Article{ minimax1997,
author = {Minimax Collaboration},
title = {Analysis of Charged Particle/Photon Correlations in Hadronic Multiparticle
Production},
journal = {Physical Review D},
volume = {55},
number = {9},
year = {1997}
}
@Article{ minimax2000,
author = {Minimax Collaboration},
title = {Search for disoriented chiral condensate at the {Fermilab} {Tevatron}},
journal = {Physical Review D},
volume = {61},
number = {3},
year = {2000}
}
@Article{ kirbyknepleyloggscott05,
author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott},
title = {Optimizing the evaluation of finite element matrices},
journal = {SIAM Journal on Scientific Computing},
volume = {27},
number = {3},
pages = {741--758},
year = {2005}
}
@Article{ bardhanknepleyanitescu2008,
author = {Jaydeep P. Bardhan and Matthew G. Knepley and Mihai Anitescu},
title = {Bounding the Electrostatic Free Energies Associated with Linear Continuum Models
of Molecular Solvation},
journal = {Journal of Chemical Physics},
volume = {130},
number = {10},
pages = {104108},
note = {Selected for the March 15, 2009 issue of Virtual Journal of Biological Physics
Research},
doi = {10.1063/1.3081148},
year = {2008}
}
%Poster at Biophysical Society Fall Meeting
@Article{ bardhanknepley2017,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a
Hydration-Shell {Poisson}-{Boltzmann} Model},
journal = {Biophysical Journal},
volume = {110},
number = {3},
note = {Fall Meeting Supplemental, Abstract DI14A-08},
doi = {10.1016/j.bpj.2015.11.1766},
year = {2017}
}
@Article{ tabrizirahimigoossensknepleybardhan2018,
title = {Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer
Interface Condition (SLIC) Continuum Dielectric Model},
author = {Amirhossein Molavi Tabrizi and Ali Mehdizadeh Rahimi and Spencer Goossens and
Matthew G. Knepley and Jaydeep P. Bardhan},
journal = {International Journal of Quantum Chemistry},
note = {Accepted},
year = {2018}
}
@Article{ knepley2010,
author = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. J. and Donoho, D.
and Fomel, S. and Friedlander, M. P. and Gerstein, M. and Mitchell, I. and
Ouellette, L. L. and Bramble, N. W. and Brown, P. O. and Carey, V. and DeNardis,
L. and Gentleman, R. and {Gezelter, J}, D. and Goodman, A. and Moore, J. E. and
Pasquale, F. A. and Rolnick, J. and Seringhaus, M. and Subramanian, R.},
title = {{Reproducible Research: addressing the need for data and code sharing in
computational science}},
journal = {Computing in Science and Engineering},
volume = {12},
number = {5},
pages = {8--13},
url = {http://www.bepress.com/cgi/viewcontent.cgi?article=1034\&context=sagmb},
year = {2010}
}
@Article{ ketchesonahmadiaknepley2011,
title = {Conference Review: High Performance Computing and Hybrid Programming Concepts for
Hyperbolic PDE Codes},
author = {David I. Ketcheson and Aron Ahmadia and Matthew G. Knepley},
journal = {SIAM News},
volume = {44},
number = {7},
month = sep,
note = {\url{http://www.siam.org/pdf/news/1912.pdf}},
year = {2011}
}
@Article{ yokotabardhanknepleybarbahamada2011,
author = {Rio Yokota and Jaydeep P. Bardhan and Matthew G. Knepley and L.A. Barba and
Tsuyoshi Hamada},
title = {Biomolecular electrostatics using a fast multipole {BEM} on up to 512 {GPU}s and
a billion unknowns},
journal = {Computer Physics Communications},
volume = {182},
number = {6},
pages = {1272--1283},
year = {2011},
issn = {0010-4655},
doi = {10.1016/j.cpc.2011.02.013},
url = {http://arxiv.org/abs/1007.4591}
}
@Article{ bardhanknepley2011,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Mathematical Analysis of the {BIBEE} Approximation for Molecular Solvation: Exact
Results for Spherical Inclusions},
journal = {Journal of Chemical Physics},
volume = {135},
number = {12},
pages = {124107--124117},
url = {http://arxiv.org/abs/1109.0651},
note = {\url{http://arxiv.org/abs/1109.0651}},
year = {2011}
}
@Article{ bruneknepleyscott2013,
author = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott},
title = {Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and
Graded Meshes},
journal = {SIAM Journal on Scientific Computing},
url = {http://arxiv.org/abs/1104.0261},
note = {\url{http://arxiv.org/abs/1104.0261}},
volume = {35},
number = {1},
pages = {A173--A191},
year = {2013}
}
@Article{ bardhanknepley2012a,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Computational science and re-discovery: open-source implementations of
ellipsoidal harmonics for problems in potential theory},
journal = {Computational Science \& Discovery},
volume = {5},
pages = {014006},
note = {\url{http://arxiv.org/abs/1204.0267}},
doi = {10.1088/1749-4699/5/1/014006},
year = {2012}
}
@Article{ kreienkampetal2013,
author = {Amy Kreienkamp and Lucy Y. Liu and Mona S. Minkara and Matthew G. Knepley and
Jaydeep P. Bardhan and Mala L. Radhakrishnan},
title = {Analysis of fast boundary-integral approximations for modeling electrostatic
contributions of molecular binding},
journal = {Molecular Based Mathematical Biology},
volume = {1},
pages = {124--150},
doi = {10.2478/mlbmb-2013-0007},
issn = {2299-3266},
month = jun,
note = {\url{http://www.degruyter.com/view/j/mlbmb.2012.1.issue/mlbmb-2013-0007/mlbmb-2013-0007.xml}},
year = {2013}
}
@Article{ bardhanknepleybrune2015,
author = {Jaydeep P. Bardhan and Matthew G. Knepley and Peter R. Brune},
title = {Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of
Boundary-Integral Operators},
journal = {Molecular Based Mathematical Biology},
volume = {3},
number = {1},
pages = {1--22},
doi = {10.1515/mlbmb-2015-0001},
year = {2015}
}
@Article{ bardhanknepley14,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary
Conditions},
journal = {Journal of Chemical Physics},
volume = {141},
number = {13},
pages = {131103},
doi = {10.1063/1.4897324},
year = {2014}
}
@InProceedings{ bardhantejaniwieckowskiramaswamyknepley2015,
title = {A Nonlinear Boundary Condition for Continuum Models of Biomolecular
Electrostatics},
author = {Jaydeep P. Bardhan and D. A. Tejani and N. S. Wieckowski and A. Ramaswamy and
Matthew G. Knepley},
booktitle = {Proceedings of PIERS},
pages = {1215--1221},
month = jul,
url = {http://piers.org/piersproceedings/piers2015PragueProc.php?start=250},
year = {2015}
}
@Article{ tabriziknepleybardhan2016,
title = {Generalising the mean spherical approximation as a multiscale, nonlinear boundary
condition at the solute-solvent interface},
author = {Amirhossein Molavi Tabrizi and Matthew G. Knepley and Jaydeep P. Bardhan},
journal = {Molecular Physics},
volume = {114},
number = {16-17},
pages = {2558--2567},
doi = {10.1080/00268976.2016.1198503},
year = {2016}
}
% http://tex.stackexchange.com/questions/155532/biblatex-and-pubmed-pubmed-central-ids
@Article{ tabrizigoossensrahimiknepleybardhan2017,
title = {Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and
Mixtures Using a Solvation-Layer Interface Condition},
author = {Amirhossein Molavi Tabrizi and Spencer Goossens and Ali Mehdizadeh Rahimi and
Matthew G. Knepley and Jaydeep P. Bardhan},
journal = {Journal of Chemical Physics},
volume = {146},
number = {9},
pages = {094103},
url = {http://scitation.aip.org/content/aip/journal/jcp/146/9/10.1063/1.4977037},
eprint = {https://arxiv.org/abs/1611.02150},
doi = {10.1063/1.4977037},
note = {PMCID: PMC5336475},
year = {2017}
}
@Article{ tabrizigoossenscooperknepleybardhan2017,
title = {Extending the Solvation-Layer Interface Condition {(SLIC)} Continum Electrostatic
Model to Linearized {Poisson}-{Boltzmann} Solvent},
author = {Amirhossein Molavi Tabrizi and Spencer Goossens and Christopher D. Cooper and
Matthew G. Knepley and Jaydeep P. Bardhan},
number = {6},
pages = {2897--2914},
journal = {Journal of Chemical Theory and Computation},
year = {2017}
}
@InProceedings{ mcclanahan2011,
author = {McClanahan, C and Czechowski, Kent and Battaglino, Casey and Iyer, K and Yeung, P
K and Vuduc, Richard},
booktitle = {Proc. ACM/IEEE Conf. Supercomputing (SC)},
title = {{Prospects for scalable 3D FFTs on heterogeneous exascale systems}},
url = {http://mcclanahoochie.com/blog/wp-content/uploads/2011/01/fft-sc11.pdf},
year = {2011}
}
@Article{ ghyselsashbymeerbergenvanroose2013,
author = {Ghysels, P. and Ashby, T.J. and Meerbergen, K. and Vanroose, W.},
title = {Hiding global communication latency in the {GMRES} algorithm on massively
parallel machines},
journal = {SIAM Journal on Scientific Computing},
volume = {35},
number = {1},
pages = {C48--C71},
year = {2013}
}
@Article{ ghyselsvanroose2014,
author = {P. Ghysels and W. Vanroose},
title = {Hiding Global Synchronization Latency in the Preconditioned Conjugate Gradient
Algorithm},
journal = {Parallel Computing},
volume = {40},
number = {7},
pages = {224--238},
note = {7th Workshop on Parallel Matrix Algorithms and Applications},
doi = {10.1016/j.parco.2013.06.001},
year = {2014}
}
@InProceedings{ strzodkagoddeke06,
author = {R. Strzodka and D. G\"oddeke},
title = {Pipelined Mixed Precision Algorithms on {FPGA}s for Fast and Accurate PDE Solvers
from Low Precision Components},
booktitle = {Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom
Computing Machines},
note = {FCCM ’06},
pages = {259--270},
year = {2006},
organization = {IEEE Computer Society}
}
@InCollection{ jacquesnicolasvollaire12,
author = {T. Jacques and L. Nicolas and C. Vollaire},
title = {Electromagnetic Scattering with the Boundary Integral Method on {MIMD} Systems},
editors = {P. Sloot, M. Bubak, A. Hoekstra, and B. Hertzberger},
booktitle = {High-Performance Computing and Networking},
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multiscale problems},
author = {Maier, Matthias and Rannacher, Rolf},
journal = {Journal of Numerical Mathematics},
volume = {24},
number = {3},
pages = {167--187},
year = {2016}
}
@Article{ maierrannacher2018,
title = {A duality-based optimization approach for model adaptivity in heterogeneous
multiscale problems},
author = {Maier, Matthias and Rannacher, Rolf},
journal = {Multiscale Modeling \& Simulation},
volume = {16},
number = {1},
pages = {412--428},
year = {2018}
}
@Article{ margetismaierluskin2017,
title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite
metamaterial sheet},
author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell},
journal = {Studies in Applied Mathematics},
volume = {139},
number = {4},
pages = {599--625},
year = {2017}
}
@Article{ maiermargetisluskin2017b,
title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element
approximation and validation},
author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell},
journal = {Journal of Computational Physics},
volume = {339},
pages = {126--145},
year = {2017}
}
@Article{ maiermargetisluskin2018,
title = {Generation of surface plasmon-polaritons by edge effects},
author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin},
journal = {Communications in Mathematical Sciences},
volume = {16},
number = {1},
pages = {77--95},
url = {http://arxiv.org/abs/1702.00848},
year = {2018}
}
@Article{ maiermattheakiskaxirasluskinmargetis2018,
title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic
metamaterials},
author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin,
Mitchell and Margetis, Dionisios},
journal = {Physical Review B},
volume = {97},
number = {3},
pages = {035307},
year = {2018}
}
@Article{ maiermattheakiskaxirasluskinmargetis2019,
title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect},
author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin,
Mitchell and Margetis, Dionisios},
journal = {Proceedings of the Royal Society A},
volume = {475},
number = {2230},
pages = {20190220},
year = {2019}
}
@Article{ maiermargetisluskin2020,
title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of
two scales},
author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios},
journal = {Physical Review B},
volume = {102},
number = {7},
pages = {075308},
year = {2020}
}
@Article{ margetismaierstauberlowluskin2020,
title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials},
author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and
Luskin, Mitchell},
journal = {Journal of Physics A: Mathematical and Theoretical},
volume = {53},
number = {5},
pages = {055201},
year = {2020}
}
@Article{ maiermargetismellet2020,
title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic
structures},
author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine},
journal = {Journal of Computational and Applied Mathematics},
volume = {377},
pages = {112909},
year = {2020}
}
@Article{ maierkronbichler2021,
title = {Efficient parallel 3D computation of the compressible Euler equations with an
invariant-domain preserving second-order finite-element scheme},
author = {Maier, Matthias and Kronbichler, Martin},
journal = {ACM Transactions on Parallel Computing},
volume = {8},
number = {3},
pages = {1--30},
year = {2021}
}
@Article{ guermondmaierpopovtomas2021,
title = {Second-order invariant domain preserving approximation of the compressible
Navier--Stokes equations},
author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {375},
pages = {113608},
year = {2021}
}
@Article{ liliptonmaier2021,
title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals},
author = {Li, Wei and Lipton, Robert and Maier, Matthias},
eprint = {2009.12166},
archiveprefix = {arXiv},
primaryclass = {phys.optics},
year = {2021}
}
@Article{ songmaierluskin2020,
title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling
gradient-index graphene waveguides},
author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell},
journal = {Journal of Computational Physics},
volume = {423},
pages = {109871},
year = {2020}
}
@Article{ songmaierluskin2019,
title = {Adaptive finite element simulations of waveguide configurations involving
parallel 2D material sheets},
author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {351},
pages = {20--34},
year = {2019}
}
%
% Users Who have Visited ANL for Consulting on PETSc
%
%
@Unpublished{ rob1,
author = {Rob Kunz},
institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania
State University},
url = {http://www.arl.psu.edu/areas/compmech/compmech.html},
sponsors = {U.S. Navy, NRC},
note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD
simulations, including lake warming by power plants},
dates = {Oct 3 and 4, 2002},
email = {rfk@wt.arl.psu.edu}
}
@Unpublished{ au1,
author = {Feng Wang and William Appelbe},
institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia},
url = {http://www.vpac.org},
sponsors = { },
note = {Using PETSc for a Variety of Geophysical Simulations},
dates = {Nov 22, 2002}
}
@Unpublished{ carl1,
author = {Carl Sovinec},
institution = {Applied Physics, University of Wisconsin},
url = {http://nimrodteam.org},
sponsors = {DOE Office of Fusion Research},
note = {Investigating using PETSc for NIMROD},
dates = {Nov 21, 2002},
email = {sovinec@engr.wisc.edu}
}
@Unpublished{ au1b,
author = {Pablo Carrica and Robert Wilson},
institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa},
url = {http://},
sponsors = {Office of Naval Research},
note = {Using PETSc for a hydrodynamics of ships and submarines},
dates = {Sept, 2002},
email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu}
}
% ------------------- TAO References ----------------------
@Article{ benson:2001:csp,
author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'},
title = {A Case Study in the Performance and Scalability of Optimization Algorithms},
journal = {{ACM} Transactions on Mathematical Software},
volume = {27},
number = {3},
month = sep,
year = {2001},
pages = {361--376}
}
@TechReport{ tao-user-ref-2000,
author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}},
title = {{TAO} Users Manual},
year = {2000},
institution = {Mathematics and Computer Science Division, Argonne National Laboratory},
number = {ANL/MCS-TM-242},
note = {See \url{http://www.mcs.anl.gov/tao}}
}
% ------------------- Optimization References ----------------------
@Book{ optguide93,
title = {Optimization Software Guide},
author = {Jorge J. Mor\'{e} and Stephen J. Wright},
publisher = {SIAM Publications},
address = {Philadelphia},
year = {1993}
}
@InProceedings{ more84,
author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E.
Hillstrom},
title = {The {MINPACK} Project},
booktitle = {Sources and Development of Mathematical Software},
editor = {Wayne R. Cowell},
year = {1984},
pages = {88--111}
}
@Article{ steihaug:83,
author = {Trond Steihaug},
title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization},
journal = {SIAM J. Numer. Anal.},
volume = {20},
year = {1983},
pages = {626--637},
key = {steihaug92 ! trust_region}
}
@TechReport{ minpack2test,
author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}},
title = {The {MINPACK-2} Test Problem Collection},
institution = {Argonne National Laboratory},
year = {1991},
number = {ANL/MCS-TM-150},
key = {more91 ! MINPACK-2}
}
@TechReport{ hohmann:94,
author = {Andreas Hohmann},
title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods},
institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin},
year = {1994},
number = {SC-94-4},
key = {Hohmann94}
}
@TechReport{ meza:94,
author = {Juan C. Meza},
title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization},
institution = {Sandia National Laboratory},
year = {1994},
number = {SAND94-8225},
key = {Meza94}
}
@Book{ dennis:83,
author = {J. E. {Dennis Jr.} and Robert B. Schnabel},
title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations},
publisher = {Prentice-Hall, Inc.},
address = {Englewood Cliffs, NJ},
year = {1983}
}
@TechReport{ more:92,
author = {Jorge J. Mor\'{e} and David Thuente},
title = {Line search algorithms with guaranteed sufficient decrease},
institution = {Mathematics and Computer Science Division, Argonne National Laboratory},
year = {1992},
number = {MCS-P330-1092}
}
@Article{ more-toraldo,
author = {Jorge J. Mor\'e and G. Toraldo},
journal = {SIOPT},
pages = {93--113},
title = {On the solution of large quadratic programming problems with bound constraints},
volume = {1},
year = {1991}
}
@Article{ byrd:1995:lma,
author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu},
title = {A Limited Memory Algorithm for Bound Constrained Optimization},
journal = {SIAM Journal on Scientific Computing},
volume = {16},
number = {5},
pages = {1190--1208},
month = sep,
year = {1995},
coden = {SJOCE3},
issn = {1064-8275 (print), 1095-7197 (electronic)},
mrclass = {90C30 (65K05)},
mrnumber = {96e:90039},
mrreviewer = {Henry Wolkowicz},
bibdate = {Fri Dec 4 16:17:35 MST 1998}
}
@Article{ lin_c3,
author = {C.-J. Lin and J. J. Mor\'e},
title = {Newton's method for large bound-constrained optimization problems},
year = {1999},
journal = {SIOPT},
volume = {9(4)},
pages = {1100--1127},
url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz}
}
@TechReport{ dolan2,
author = {E. Dolan and J. J. Mor\'{e}},
title = {Benchmarking Optimization Software with Performance Profiles},
year = {2001},
month = jan,
number = {ANL/MCS-P861-1200},
institution = {Mathematics and Computer Science Division, Argonne National Laboratory},
address = {Argonne, IL},
url = {http://www.mcs.anl.gov/~more/cops/}
}
@InProceedings{ owlqn,
author = {Galen Andrew and Jianfeng Gao},
title = {Scalable training of L1-regularized log-linear models},
booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)},
pages = {33--40},
year = {2007}
}
@Article{ bmrm,
author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le},
title = {Bundle methods for regularized risk minimization},
year = {2010},
journal = {Journal of Machine Learning Research},
volume = {11},
pages = {311--365}
}
% ------------------- Component Software References ----------------------
@InProceedings{ cca99,
author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C.
McInnes and S. Parker and B. Smolinski},
title = {Toward a Common Component Architecture for High-Performance Scientific
Computing},
booktitle = {Proceedings of {High Performance Distributed Computing}},
pages = {115--124},
year = {1999},
note = {See \url{http://cca-forum.org}}
}
@Book{ szyperski98,
author = {Clemens Szyperski},
title = {Component Software: Beyond Object-Oriented Programming},
publisher = {ACM Press},
address = {New York},
year = {1998}
}
@Article{ broy98,
author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and
Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael
Stal and Clemens Szyperski},
title = {What Characterizes a (Software) Component?},
journal = {Software -- Concepts and Tools},
publisher = {Springer-Verlag},
year = {1998},
volume = {19},
pages = {49--56}
}
@Article{ componentware:94,
author = {Jon Udell},
title = {Componentware},
journal = {Byte},
volume = {may},
pages = {46--56},
year = {1994},
key = {Udell94 ! componentware}
}
@Misc{ cca-web-page,
author = {{Common Component Architecture Forum}},
note = {See \url{http://cca-forum.org}}
}
% --------------- References for Tools Used by TAO Developers -----------------
%
% tohtml: Used to generate on-line TAO users manual and manual pages
%
@TechReport{ tohtml,
author = {William Gropp},
title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}},
institution = {Argonne National Laboratory},
number = {ANL/MCS-TM-00},
month = jan,
year = {1995},
key = {tohtml}
}
%
% doctext: Used to generate tex version of TAO manual pages
%
@TechReport{ doctext,
author = {William Gropp},
title = {Users Manual for doctext: Producing documentation from {C} source code},
institution = {Argonne National Laboratory},
number = {ANL/MCS-TM-00},
month = jan,
year = {1995},
key = {doctext}
}
% ------------------------- PETSc References ------------------------------
@InProceedings{ petsc,
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}
}
% ------------------------- Misc Other References ------------------------------
@Misc{ indeps-web-page,
title = {{InDEPS} {W}eb page},
note = {http://z.ca.sandia.gov/\~{ }indeps/},
author = {et al. Robert Armstrong},
institution = {Sandia National Laboratory},
key = {{InDEPS} {W}eb page}
}
@Misc{ pooma,
title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar
chitectures},
year = {1996},
author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn and M. S.
S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey}
}
@Misc{ isis++-web-page,
title = {{ISIS++} {W}eb Page},
note = {See \url{http://ca.sandia.gov/isis}},
author = {Robert L. Clay and Kyran Mish and Alan B. Williams},
institution = {Sandia National Laboratories}
}
@Misc{ trilinos-web-page,
title = {{Trilinos} {W}eb Page},
note = {See
\url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}},
author = {Mike Heroux et al.},
institution = {Sandia National Laboratories}
}
@Misc{ alice-web-page,
title = {{ALICE} {W}eb page},
note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division,
Argonne National Laboratory},
key = {{ALICE} {W}eb page}
}
@Misc{ autodiff-webpage,
author = {{Computational Differentiation Project}},
note = {See \url{http://www.mcs.anl.gov/autodiff}}
}
@Misc{ coool-home-page,
author = {Lydia Deng and Wences Gouveia and John Scales},
title = {{The CWP Object-Oriented Optimization Library}},
note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}}
}
@Misc{ rice-inversion-home-page,
author = {Mark S. Gokenbach and William W. Symes},
title = {{The Hilbert Class Library}},
note = {See \url{http://www.trip.caam.rice.edu/}}
}
@Misc{ opt++-home-page,
author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}},
note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}}
}
@Article{ gockenbach:1999:ccl,
author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes},
title = {C++ Classes for Linking Optimization with Complex Simulations},
journal = {{ACM} Transactions on Mathematical Software},
volume = {25},
number = {2},
month = jun,
year = {1999},
pages = {191-212},
abstract = {The object-oriented programming paradigm can be used to overcome the
incompatibilities between off-the-shelf optimization software and application
software. The Hilbert Class Library (HCL) defines the fundamental mathematical
objects arising in optimization problems, such as vectors, linear operators, and
so forth, as C++ classes, making it possible to write optimization code in a
natural fashion, while allowing application software such as simulators to use the
most convenient data structures and programming style. In spite of the poor
reputation C++ has for runtime performance, the use of mixed-language programming
allows performance equal to that achieved by standard Fortran packages, as
comparisons with the popular code LBFGS and ARPACK demonstrate.},
accepted = {April 1999},
url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/}
}
@Misc{ neos-guide,
author = {{The Optimization Software Guide}},
note = {See \url{http://www.mcs.anl.gov/otc/Guide/}}
}
@Article{ boyd,
title = {Distributed optimization and statistical learning via the alternating direction
method of multipliers},
author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein,
Jonathan and others},
journal = {Foundations and Trends{\textregistered} in Machine learning},
volume = {3},
number = {1},
pages = {1-122},
year = {2011},
publisher = {Now Publishers, Inc.}
}
@Misc{ :alertsys,
title = {page{ALERT}},
organization = {Alert Systems, Inc},
address = {Madison, Wisconsin},
note = {http://www.alertsys.com/}
}
@Manual{ :cmfortran,
title = {{CM} {F}ortran Language Reference Manual},
organization = {Thinking Machines Corporation},
year = {1994},
address = {Cambridge, MA}
}
@Manual{ :cmmd,
title = {{CMMD} Reference Manual, Version 3.0},
organization = {Thinking Machines Corporation},
year = {1993},
address = {Cambridge, MA}
}
@Manual{ :cmssl,
title = {{CMSSL} for {CM} {F}ortran},
volume = {I},
organization = {Thinking Machines Corporation},
year = {1994},
address = {Cambridge, MA}
}
@Misc{ :condor,
author = {M. Livny},
title = {{PI}, The {Condor} Project, High Throughput Computing},
howpublished = {www.cs.wisc.edu/condor}
}
@Manual{ :connection,
title = {Connection Machine {CM}--5 Technical Summary},
organization = {Thinking Machines Corporation},
year = {1993},
address = {Cambridge, MA}
}
@Manual{ :cplex,
title = {{CPLEX} Optimizer},
organization = {ILOG CPLEX Division},
address = {889 Alder Avenue, Incline Village, Nevada},
note = {http://www.cplex.com/}
}
@Manual{ :cplextm,
title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer
(Version 2.0)},
organization = {CPLEX Optimization Inc.},
year = {1992},
address = {Incline Village, Nevada}
}
@Misc{ :fatcop,
author = {M. C. Ferris},
title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming
Solver},
howpublished = {www.cs.wisc.edu/math-prog/fatcop}
}
@Misc{ :metaneos,
author = {S. J. Wright},
title = {{metaNEOS}: Metacomputing Environments for Optimization},
howpublished = {www-unix.mcs.anl.gov/metaneos}
}
@InCollection{ gropp.more:optimization,
author = {W. Gropp and J. J. Mor\'e},
title = {Optimization environments and the {NEOS} Server},
booktitle = {Approximation Theory and Optimization},
pages = {167--182},
publisher = {Cambridge University Press},
year = {1997},
editor = {M. D. Buhmann and A. Iserles}
}
@Article{ czyzyk.mesnier.ea:neos,
author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e},
title = {The {NEOS} Server},
journal = {IEEE Journal on Computational Science and Engineering},
volume = {5},
year = {1998},
pages = {68--75}
}
@Book{ :osl,
title = {Handbook for {IBM OSL}},
author = {M. S. Hung and W. O. Rom and A. D. Warren},
year = {1994},
publisher = {Boyd and Fraser},
address = {Danvers, Massachusetts}
}
@Manual{ :pro-matlab,
title = {{PRO}--{MATLAB} User's Guide},
organization = {The MathWorks, Inc.},
year = {1989},
address = {21 Eliot Street, South Natick, MA 01760}
}
@Misc{ :prostate,
key = {Biomedical},
title = {Biomedical Business International Newsletter},
howpublished = {pp. 72--75},
year = {1996}
}
@Misc{ :sipcase,
key = {Natural},
title = {Natural Gas Planning: An Application of Stochastic Linear Programming},
howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html}
}
@Book{ aarts.korst:simulated,
author = {E. Aarts and J. Korst},
title = {Simulated Annealing and Boltzman Machines},
year = {1990},
publisher = {John Wiley \& Sons},
address = {Chichester}
}
@TechReport{ aarts.laarhoven.ea:local-search-based,
author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder},
title = {Local-Search-Based Algorithms for Job Shop Scheduling},
institution = {Centre for Quantitative Methods},
year = {1991},
address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven},
number = {106},
type = {CQM-Not}
}
@Article{ aashtiani.magnanti:equilibria,
author = {H. Z. Aashtiani and T. L. Magnanti},
title = {Equilibria on a congested transportation network},
journal = {SIAM Journal on Algebraic and Discrete Methods},
volume = {2},
year = {1981},
pages = {213--226}
}
@Article{ ablow.brigham:analog,
author = {C. M. Ablow and G. Brigham},
title = {An Analog Solution of Programming Problems},
journal = {Operations Research},
year = {1955},
volume = {3},
pages = {388--394}
}
@Article{ achuthan.grabowski.ea:optimal,
author = {N. R. Achuthan and J. Grabowski and J. B. Sidney},
title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties},
journal = {Opsearch},
year = {1981},
volume = {18},
pages = {117--138}
}
@Book{ adelman.robinson:income,
author = {I. Adelman and S. Robinson},
title = {Income Distribution Policy in Developing Countries},
publisher = {Stanford University Press},
year = {1978},
address = {Stanford, California}
}
@Article{ adler.resende.ea:implementation,
author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar},
title = {An Implementation of {K}armarkar's Algorithm for Linear Programming},
journal = {Mathematical Programming},
year = {1989},
volume = {44},
pages = {297--336}
}
@TechReport{ aeberhard.coomans.ea:comparison,
author = {S. Aeberhard and D. Coomans and O. de Vel},
title = {Comparison of Classifiers in High Dimensional Settings},
institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook
University of North Queensland},
year = {1992},
number = {92-02},
type = {Technical Report}
}
@Article{ aganagic.cottle:constructive,
author = {M. Aganagi\'{c} and R. W. Cottle},
title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal
Minors},
journal = {Mathematical Programming},
year = {1987},
volume = {37},
pages = {223--231}
}
@TechReport{ aganagic:iterative,
author = {M. Aganagi\'{c}},
title = {Iterative Methods for the Linear Complementarity Problem},
institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford
University},
year = {1978},
type = {SOL},
number = {78-10},
address = {Stanford, California}
}
@Book{ ahlfors:complex,
author = {L. V. Ahlfors},
title = {Complex Analysis},
publisher = {McGraw--Hill Book Company},
address = {New York},
series = {International Series in Pure and Applied Mathematics},
edition = {Second},
year = {1966}
}
@Article{ ahn:solution,
author = {B--H. Ahn},
title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods},
journal = {Journal of Optimization Theory and Applications},
year = {1981},
volume = {33},
pages = {175--185}
}
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institution = {Department of Mathematics, The University of Iowa},
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year = {1994},
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opttype = {RPI Math Report},
optnumber = {98-100},
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author = {A. B. Berkelaar and B. Jansen and C. Roos and T. Terlaky},
title = {Basis and Tripartition Identification for Quadratic Programming and Linear
Complementarity Problems},
institution = {Department of Econometrics and Operations Research},
year = {1996},
address = {Erasmus University, Rotterdam, The Netherlands}
}
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title = {Distributed Asynchronous Relaxation Methods for the Convex Network Flow Problem},
journal = {SIAM Journal on Control and Optimization},
year = {1987},
volume = {25},
pages = {74--85}
}
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author = {D. P. Bertsekas and E. M. Gafni},
title = {Projection Methods for Variational Inequalities with Application to the Traffic
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journal = {Mathematical Programming Study},
year = {1982},
volume = {17},
pages = {139--159}
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title = {Relaxation Methods for Network Flow Problems with Convex Arc Costs},
journal = {SIAM Journal on Control and Optimization},
year = {1987},
volume = {25},
pages = {1219--1243}
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author = {D. P. Bertsekas and P. Tseng},
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note = {Manuscript}
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year = {1991},
volume = {16},
pages = {580--595}
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author = {D. P. Bertsekas and J. N. Tsitsiklis},
title = {Parallel and Distributed Computation: Numerical Methods},
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year = {1989},
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author = {D. P. Bertsekas},
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title = {Dynamic Programming and Optimal Control},
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address = {Belmont MA}
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year = {1982},
volume = {36},
pages = {221--252}
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year = {1976},
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title = {Necessary and Sufficient Conditions for a Penalty Method to be Exact},
journal = {Mathematical Programming},
year = {1975},
volume = {9},
pages = {87--99}
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author = {D. P. Bertsekas},
title = {Nonlinear Programming},
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year = {1995},
address = {Belmont, Massachusetts}
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author = {Dimitri P. Bertsekas},
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year = {1982},
volume = {20},
pages = {221--246}
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year = {1997},
pages = {3--25},
volume = {7},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps},
key = {51}
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year = {1996},
volume = {6},
pages = {316--325},
url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps},
key = {34}
}
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author = {S. C. Billups and M. C. Ferris},
title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting
Points},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1993},
address = {Madison, Wisconsin},
number = {1180},
note = {Revised version in SIAM Journal on Optimization.}
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author = {S. C. Billups and M. C. Ferris},
title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems},
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journal = {Mathematical Programming},
pages = {533--562},
volume = {76},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps},
key = {47}
}
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volume = {24},
pages = {219--236},
year = {1999},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps},
key = {42},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
type = {Mathematical Programming Technical Report},
number = {94--15}
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address = {Albuquerque, New Mexico},
number = {SAND91--1482}
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institution = {Department of Mathematics, University of Colorado},
year = {1999},
address = {Denver, Colorado}
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author = {S. C. Billups},
title = {Algorithms for Complementarity Problems and Generalized Equations},
school = {University of Wisconsin--Madison},
year = {1995},
address = {Madison, Wisconsin},
month = aug
}
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author = {S. C. Billups},
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year = {1998},
address = {Denver, Colorado}
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pages = {153--176}
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type = {Mathematical Programming Technical Report},
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address = {Madison, Wisconsin}
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author = {P. S. Bradley and O. L. Mangasarian and W. N. Street},
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year = {1995},
type = {Mathematical Programming Technical Report},
number = {95-21},
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author = {R. S. Burachik and A. N. Iusem},
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institution = {Instituto de Matem\'{a}tica Pura e Aplicada},
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type = {Working Paper},
address = {Rio de Janeiro}
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year = {1998},
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volume = {8},
pages = {197--216}
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key = {38}
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year = {1996},
type = {Technical Report}
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number = {99-11}
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author = {Q. Chen and M. C. Ferris},
title = {{FATCOP}: {A} Fault Tolerant {C}ondor-{PVM} Mixed Integer Program Solver},
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institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
year = {1999},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/99-05.ps},
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key = {81},
annote = {Submitted to {\em SIOPT}}
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author = {Y. Chen and M. Florian},
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year = {1994}
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@Misc{ condon.dahl.ea:implementing,
author = {T. Condon and H. Dahl and S. Devarajan},
title = {Implementing a Computable General Equilibrium Model on {GAMS} -- The {C}ameroon
Model},
year = {1987},
howpublished = {{DRD} Discussion Paper 290},
note = {The World Bank, Washington DC}
}
@Book{ conn.gould.ea:lancelot,
author = {A. R. Conn and N. I. M. Gould and Ph. L. Toint},
title = {{LANCELOT}: {A} {F}ortran package for Large--Scale Nonlinear Optimization
(Release {A})},
year = {1992},
publisher = {Springer Verlag},
address = {Heidelberg, Berlin},
series = {Springer Series in Computational Mathematics},
number = {17}
}
@Article{ conn.gould.ea:numerical,
author = {A. R. Conn and N. I. M. Gould and Ph. L. Toint},
title = {Numerical Experiments with the {LANCELOT} Package (Release {A}) for Large-Scale
Nonlinear Optimization},
journal = {Mathematical Programming},
year = {1996},
volume = {75},
pages = {73--110}
}
@Book{ cgt,
author = {A. R. Conn and N. I. M. Gould and Ph. L. Toint},
title = {Trust-Region Methods},
year = {2000},
publisher = {SIAM},
address = {Philadelphia, Pennsylvania}
}
@InCollection{ conn.toint:algorithm,
author = {A. R. Conn and Ph. L. Toint},
title = {An Algorithm using Quadratic Interpolation for Unconstrained Derivative Free
Optimization},
booktitle = {Nonlinear Optimization and Applications},
editor = {G. Di Pillo and F. Giannessi},
year = {1996},
publisher = {Plenum Press},
address = {New York}
}
@Article{ conry.seireg:mathematical,
author = {T. F. Conry and A. Seireg},
title = {A Mathematical Programming Method for Design for Elastic Bodies in Contact},
journal = {{ASME} Transactions Journal of Applied Mechanics},
volume = {93},
year = {1971},
pages = {387--392}
}
@Article{ cook.gerards.ea:sensitivity,
author = {W. Cook and A. M. H. Gerards and A. Schrijver and \'{E}. Tardos},
title = {Sensitivity Results in Integer Linear Programming},
journal = {Mathematical Programming},
year = {1986},
volume = {34},
pages = {251--264}
}
@Article{ cook:taxonomy,
author = {S. A. Cook},
title = {A Taxonomy of Problems with Fast Parallel Algorithms},
journal = {Information and Control},
year = {1985},
volume = {64},
pages = {2--22}
}
@Article{ cooper:gradient,
author = {R. E. M. Cooper},
title = {A gradient method of optimizing external-beam radiotherapy treatment plans},
journal = {Radiology},
year = {1978},
volume = {128},
pages = {235--243}
}
@Article{ cormack:problem,
author = {A. M. Cormack},
title = {A problem in roatation therapy with x-rays},
journal = {International Journal of Radiation Oncology, Biology and Physics},
year = {1987},
volume = {13},
pages = {623--630}
}
@Article{ cormack:problem*1,
author = {A. M. Cormack},
title = {A problem in roatation therapy with x-rays2: dose distributions with an axis of
symmetry},
journal = {International Journal of Radiation Oncology, Biology and Physics},
year = {1987},
volume = {13},
pages = {1921--1925}
}
@Article{ cottle.dantzig:complementary,
author = {R. W. Cottle and G. B. Dantzig},
title = {Complementary Pivot Theory of Mathematical Programming},
journal = {Linear Algebra and Its Applications},
year = {1968},
volume = {1},
pages = {103--125}
}
@Article{ cottle.dantzig:generalization,
author = {R. W. Cottle and G. B. Dantzig},
title = {A Generalization of the Linear Complementarity Problem},
journal = {Journal of Combinatorial Theory},
year = {1970},
volume = {8},
pages = {79--90}
}
@Book{ cottle.giannessi.ea:variational,
author = {R. W. Cottle and F. Giannessi and J.--L. Lions},
title = {Variational Inequalities and Complementarity Problems: Theory and Applications},
year = {1980},
publisher = {John Wiley \& Sons},
address = {New York}
}
@InCollection{ cottle.goheen:special,
author = {R. W. Cottle and M. S. Goheen},
title = {A Special Class of Large Quadratic Programs},
pages = {361--390},
crossref = {mangasarian.meyer.ea:nonlinear*3}
}
@Article{ cottle.golub.ea:solution,
author = {R. W. Cottle and G. H. Golub and R. S. Sacher},
title = {On the Solution of Large Structured Complementarity Problems: The Block
Partitioned Case},
journal = {Applied Mathematics and Optimization},
year = {1978},
volume = {4},
pages = {347--363}
}
@Book{ cottle.pang.ea:linear,
author = {R. W. Cottle and J. S. Pang and R. E. Stone},
title = {The Linear Complementarity Problem},
year = {1992},
publisher = {Academic Press},
address = {Boston}
}
@Article{ cottle.pang.ea:sufficient,
author = {R. W. Cottle and J. S. Pang and V. Venkateswaran},
title = {Sufficient Matrices and the Linear Complementarity Problem},
journal = {Linear Algebra and Its Applications},
year = {1989},
volume = {114/115},
pages = {231--249}
}
@PhDThesis{ cottle:nonlinear,
author = {R. W. Cottle},
title = {Nonlinear programs with positively bounded {J}acobians},
school = {Department of Mathematics, University of California},
year = {1964},
address = {Berkeley, California}
}
@Article{ cottle:nonlinear*1,
author = {R. W. Cottle},
title = {Nonlinear programs with positively bounded {J}acobians},
journal = {Journal of the Society for Industrial and Applied Mathematics},
volume = {14},
year = {1966},
pages = {147--158}
}
@InCollection{ cottle:principal,
author = {R. W. Cottle},
title = {The principal pivoting method of quadratic programming},
booktitle = {Mathematics of the Decision Sciences, Part 1},
publisher = {American Mathematical Society},
editor = {G. B. Dantzig and Jr. A. F. Veinott},
address = {Providence, Rhode Island},
year = {1968},
pages = {144--162}
}
@Unpublished{ courant:calculus,
author = {R. Courant},
title = {Calculus of Variations and Supplementary Notes and Exercises},
year = {1956},
note = {Supplementary notes by M. Kruskal and H. Rubin, revised and amended by J. Moser,
New York University}
}
@Article{ courant:variational,
author = {R. Courant},
title = {Variational Methods for the Solution of Problems of Equilibrium and Vibration},
journal = {Bulletin of the American Mathematical Society},
year = {1943},
volume = {49},
pages = {1--23}
}
@Book{ cristianini.shawe-taylor:introduction,
author = {N. Cristianini and J. Shawe-Taylor},
title = {An Introduction to Support Vector Machines},
publisher = {Cambridge University Press},
address = {Cambridge},
year = {2000}
}
@Article{ cromme:strong,
author = {L. Cromme},
title = {Strong Uniqueness},
journal = {Numerische Mathematik},
year = {1978},
volume = {29},
pages = {179--193}
}
@Article{ crowder.johnson.ea:solving,
author = {H. Crowder and E. L. Johnson and M. W. Padberg},
title = {Solving Large Scale Zero-One Linear Programming Problems},
journal = {Operations Research},
year = {1983},
volume = {31},
pages = {803--834}
}
@Article{ cryer.dempster:equivalence,
author = {C. W. Cryer and M. A. H. Dempster},
title = {Equivalence of Linear Complementarity Problems and Linear Programs in Vector
Lattice {H}ilbert Spaces},
journal = {SIAM Journal on Control and Optimization},
year = {1980},
volume = {18},
pages = {76--89}
}
@Article{ cryer:method,
author = {C. W. Cryer},
title = {The method of {C}hristopherson for solving free boundary problems for infinite
journal bearings by means of finite differences},
journal = {Mathematics of Computation},
volume = {25},
year = {1971},
pages = {435--553}
}
@Article{ cryer:solution,
author = {C. W. Cryer},
title = {The Solution of a Quadratic Programming Problem Using Systematic Overrelaxation},
journal = {SIAM Journal on Control and Optimization},
year = {1971},
volume = {9},
pages = {385--392}
}
@Article{ cryer:solution*1,
author = {C. W. Cryer},
title = {The Solution of a Quadratic Programming Using Systematic Overrelaxation},
journal = {SIAM Journal on Control},
year = {1971},
volume = {9},
pages = {385--392}
}
@Manual{ culler:split-c,
author = {D. Culler},
title = {The Split--{C} Programming Language},
organization = {Computer Science Department, University of California, Berkeley}
}
@InProceedings{ cun.denker.ea:optimal,
author = {Y. le Cun and J. S. Denker and S. A. Solla},
title = {Optimal Brain Damage},
booktitle = {Advances in Neural Information Processing Systems II {(Denver 1989)}},
year = {1990},
editor = {D. S. Touretzky},
publisher = {Morgan Kaufmann},
address = {San Mateo, California},
pages = {598--605}
}
@TechReport{ czyzyk.mehrotra.ea:pcx,
author = {J. Czyzyk and S. Mehrotra and S. J. Wright},
title = {{PCx} Users Guide},
institution = {Optimization Technology Center, Argonne National Laboratory and Northwestern
University},
year = {1996},
type = {Technical Report},
number = {OTC 96/01}
}
@TechReport{ czyzyk.mesnier.ea:network-enabled,
address = {Argonne, Illinois},
author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e},
institution = {Argonne National Laboratory},
number = {MCS-P615-0996},
title = {The {N}etwork-{E}nabled {O}ptimization {S}erver},
type = {Preprint},
year = {1996}
}
@Article{ czyzyk.wisniewski.ea:optimization,
title = {Optimization Case Studies in the {NEOS} Guide},
author = {J. Czyzyk and T. Wisniewski and S. J. Wright},
journal = {SIAM Review},
volume = {41},
pages = {148--163},
year = {1999}
}
@Article{ dai.laan.ea:simplicial,
author = {Y. Dai and G. van der Laan and A. J. J. Talman and Y. Yamamoto},
title = {A Simplicial Algorithm for the Nonlinear Stationary Problem on an Unbounded
Polyhedron},
journal = {SIAM Journal on Optimization},
year = {1991},
volume = {1},
pages = {151--165}
}
@Article{ dai.talman:linear,
author = {Y. Dai and D. Talman},
title = {Linear Stationary Point Problems on Unbounded Polyhedra},
journal = {Mathematics of Operations Research},
year = {1993},
pages = {635--644}
}
@Book{ daniel:approximate,
author = {J. W. Daniel},
title = {The approximate minimization of functionals},
year = {1971},
publisher = {Prentice-Hall, Inc},
address = {Englewood Cliffs, New Jersey}
}
@Article{ danskin:theory,
author = {J. M. Danskin},
title = {The Theory of Min--Max, with Applications},
journal = {SIAM Journal on Applied Mathematics},
year = {1964},
volume = {14},
pages = {641--664}
}
@Book{ danskin:theory*1,
author = {J. M. Danskin},
title = {The Theory of Min--Max},
year = {1967},
publisher = {Springer-Verlag},
address = {New York}
}
@InCollection{ dantzig.cottle:positive,
author = {G. B. Dantzig and R. W. Cottle},
title = {Positive (semi-)definite programming},
booktitle = {Nonlinear Programming},
publisher = {North-Holland},
editor = {J. Abadie},
address = {Amsterdam},
year = {1967},
pages = {55--73}
}
@Article{ dantzig.manne:complementarity,
author = {G. B. Dantzig and A. S. Manne},
title = {A Complementarity Algorithm for an Optimal Captial Path with Invariant
Proportions},
journal = {Journal of Economic Theory},
year = {1974},
volume = {9},
pages = {312--323}
}
@Article{ dantzig.wolfe:decomposition,
author = {G. B. Dantzig and P. Wolfe},
title = {Decomposition Principle for Linear Programs},
journal = {Operations Research},
year = {1960},
volume = {8},
pages = {101--111}
}
@Book{ dantzig:linear,
author = {G. B. Dantzig},
title = {Linear Programming and Extensions},
year = {1963},
publisher = {Princeton University Press},
address = {Princeton, New Jersey}
}
@Manual{ dash:xpress-mp,
title = {{XPRESS-MP} User Guide},
organization = {Dash Associates},
address = {Blisworth House, Blisworth, Northants, UK},
note = {http://www.dashopt.com/}
}
@Book{ davis:handbook,
author = {L. D. Davis},
title = {The Handbook of Genetic Algorithms},
year = {1990},
publisher = {Van Nostrand Reinhold}
}
@TechReport{ davis:users,
author = {T. A. Davis},
title = {Users' guide for the unsymmetric-pattern multifrontal Package ({UMFPACK})},
type = {{Technical Report}},
year = {1993},
institution = {Computer and Information Sciences Department, University of Florida},
address = {Gainesville, Florida}
}
@TechReport{ dax:computation,
author = {A. Dax},
title = {The Computation of Descent Directions at Degenerate Points},
institution = {Hydrological Service of Israel},
year = {1985},
type = {Technical Report}
}
@Article{ dax:note,
author = {A. Dax},
title = {A Note on Optimality Conditions for the Euclidean Multifacility Location
Problem},
journal = {Mathematical Programming},
year = {1986},
volume = {36},
pages = {72--80}
}
@Article{ deasy:multiple,
author = {J. O. Deasy},
title = {Multiple local minima in radiotherapy optimization problems with dose volume
constraints},
journal = {Medical Physics},
year = {1997},
optvolume = {24},
optnumber = {7},
optpages = {1157-1161}
}
@Article{ deboor.ron:computational,
author = {C. {deBoor} and A. Ron},
title = {Computational Aspects of Polynomial Interpolation in Several Variables},
journal = {Mathematics of Computation},
year = {1992},
volume = {58},
pages = {705--727}
}
@Article{ debremaecker.ferris.ea:compressional,
author = {J.--C. {De~Bremaecker} and M. C. Ferris and D. Ralph},
title = {Compressional Fractures considered as Contact Problems and Mixed Complementarity
Problems},
year = {2000},
key = {82},
journal = {Engineering Fracture Mechanics},
volume = {66},
pages = {287--303}
}
@Article{ debremaecker.ferris:comparison,
author = {J.--C. {De~Bremaecker} and M. C. Ferris},
title = {A Comparison of Two Algorithms for Solving Closed Crack Problems},
year = {2000},
key = {90},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/00-01.ps},
journal = {Engineering Fracture Mechanics},
volume = {66},
pages = {601--605},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {00-01}
}
@Article{ dedonato.maier:mathematical,
author = {O. {De~Donato} and G. Maier},
title = {Mathematical programming methods for the inelastic analysis of reinforced
concrete frames allowing for limited rotation capacity},
journal = {International Journal for Numerical Methods in Engineering},
volume = {4},
year = {1972},
pages = {307--329}
}
@Book{ deimling:nonlinear,
author = {K. Deimling},
title = {Nonlinear Functional Analysis},
publisher = {Springer-Verlag},
year = {1985}
}
@PhDThesis{ dejong:analysis,
author = {K. A. De~Jong},
title = {An Analysis of the Behavior of a Class of Genetic Adaptive Systems},
year = {1975},
school = {University of Michigan},
note = {Dissertation Abstracts International 36(10), 5140B}
}
@Article{ deleone.mangasarian.ea:multi-sweep,
author = {R. {De~Leone} and O. L. Mangasarian and T.-H. Shiau},
title = {Multi-Sweep Asynchronous Parallel Successive Overelaxation for the Nonsymmetric
Linear Complementarity Problem},
journal = {Annals of Operations Research},
year = {1990},
volume = {22},
pages = {43--54}
}
@InCollection{ deleone.mangasarian:serial,
author = {R. {De~Leone} and O. L. Mangasarian},
title = {Serial and Parallel Solution of Large Scale Linear Programs by Augmented
{L}agrangian Successive Overrelaxation},
booktitle = {Optimization, Parallel Processing and Applications},
publisher = {Springer-Verlag},
year = {1988},
editor = {A. Kurzhanski and K. Neumann and D. Pallaschke},
volume = {304},
series = {Lecture Notes in Economics and Mathematical Systems},
pages = {103--124},
address = {Berlin}
}
@TechReport{ deluca.facchinei.ea:combining,
author = {T. {De~Luca} and F. Facchinei and C. Kanzow},
title = {Combining Equation-Based Methods for the Solution of Large-Scale Nonlinear
Complementarity Problems: Theory and Numerical Results},
type = {Preprint},
institution = {Institute of Applied Mathematics, University of Hamburg},
year = {1996}
}
@TechReport{ deluca.facchinei.ea:general,
author = {T. {De~Luca} and F. Facchinei and C. Kanzow},
title = {A General Framework for Solving Nonlinear Complementarity Problems: Theory and
Numerical Results},
type = {Preprint},
institution = {Institute of Applied Mathematics, University of Hamburg},
year = {1997}
}
@Article{ deluca.facchinei.ea:semismooth,
author = {T. {De~Luca} and F. Facchinei and C. Kanzow},
title = {A Semismooth Equation Approach to the Solution of Nonlinear Complementarity
Problems},
journal = {Mathematical Programming},
volume = {75},
pages = {407--439},
year = {1996}
}
@Article{ deluca.facchinei.ea:theoretical,
author = {T. {De~Luca} and F. Facchinei and C. Kanzow},
title = {A Theoretical and Numerical Comparison of some Semismooth Algorithms for
Complementarity Problems},
year = {1999},
journal = {Computational Optimization and Applications, forthcoming}
}
@Article{ demarzo.eaves:computing,
author = {P. M. DeMarzo and B. C. Eaves},
title = {Computing Equilibria of {GEI} by Relocalization on a Grassmann Manifold},
journal = {Journal of Mathematical Economics},
year = {1996},
volume = {26},
pages = {479--497}
}
@Article{ dembo.steihaug:truncated,
author = {R. S. Dembo and T. Steihaug},
title = {Truncated {N}ewton Method Algorithms for Large--Scale Unconstrained
Optimization},
journal = {Mathematical Programming},
year = {1983},
volume = {26},
pages = {190--212}
}
@Article{ dembo:performance,
author = {R. S. Dembo},
title = {The Performance of {NLPNET}, {A} Large--Scale Nonlinear Network Optimizer},
journal = {Mathematical Programming Study},
year = {1986},
volume = {26},
pages = {245--248}
}
@Article{ demoor.vandenberghe.ea:generalized,
author = {B. {De~Moor} and L. Vandenberghe and J. Vandewalle},
title = {The generalized linear complementarity problem and an algorithm to find all its
solutions},
journal = {Mathematical Programming},
volume = {57},
year = {1992},
pages = {415--426}
}
@Book{ demyanov.vasilev:nondifferentiable,
author = {V. F. Dem\'{y}anov and L. V. Vasil\'{e}v},
title = {Nondifferentiable Optimization},
publisher = {Optimization Software, Inc.},
year = {1985},
address = {New York}
}
@Article{ dennis.torczon:direct,
author = {J. E. Dennis and V. Torczon},
title = {Direct Search Methods on Parallel Machines},
journal = {SIAM Journal on Optimization},
year = {1991},
volume = {1},
pages = {448--474}
}
@TechReport{ depierro.iusem:convergence,
author = {A. R. {De~Pierro} and A. N. Iusem},
title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite
Linear Complementarity Problems},
institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao},
year = {1990},
address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil}
}
@Article{ depierro.iusem:relaxed,
author = {A. R. {De~Pierro} and A. N. Iusem},
title = {A Relaxed Version of {B}regman's Method for Convex Programming},
journal = {Journal of Optimization Theory and Applications},
year = {1986},
volume = {51},
pages = {421--440}
}
@Book{ dervis.melo.ea:general,
author = {K. Dervis and J. de Melo and S. Robinson},
title = {General Equilibrium Models of Development Policy},
publisher = {Cambridge University Press},
year = {1982},
address = {Cambridge, England}
}
@Article{ deschutter.demoor:minimal,
author = {B. {De~Schutter} and B. {De~Moor}},
title = {Minimal Realization in the Max Algebra is an Extended Linear Complementarity
Problem},
journal = {Systems \& Control Letters},
year = {1995},
pages = {103--111}
}
@Article{ desilets.golden.ea:predicting,
author = {L. DeSilets and B. Golden and Q. Wang and R. Kumar},
title = {Predicting Salinity in the {C}hesapeake {B}ay Using Backpropagation},
journal = {Computers \& Operations Research},
year = {1992},
volume = {19},
pages = {277--285}
}
@PhDThesis{ desilva:sensitivity,
author = {A. H. DeSilva},
title = {Sensitivity Formulas for Nonlinear Factorable Programming and their Application
to the Solution of an Implicitly Defined Optimization Model of {US} Crude Oil
Production},
school = {George Washington University},
address = {Washington, D.C.},
year = {1978}
}
@TechReport{ dijkstra:cooperating,
author = {E. W. Dijkstra},
title = {Cooperating Sequential Processes},
institution = {Technological University},
year = {1965},
address = {Eindhoven, The Netherlands},
number = {EWD--123},
type = {Technical Report}
}
@Article{ dikin:iterative,
author = {I. I. Dikin},
title = {Iterative Solution of Problems of Linear and Quadratic Programming},
journal = {Soviet Mathematics Doklady},
year = {1967},
volume = {8},
pages = {674--675}
}
@InCollection{ dipillo.grippo.ea:class,
author = {G. Di~Pillo and L. Grippo and F. Lampariello},
title = {A Class of Methods for the Solution of Optimization Problems with Inequalities},
booktitle = {System Modelling and Optimization},
year = {1981},
editor = {R. F. Drenick and F. Kozin},
publisher = {Springer-Verlag},
address = {Berlin}
}
@Article{ dipillo.grippo:augmented,
author = {G. Di~Pillo and L. Grippo},
title = {An Augmented {L}agrangian for Inequality Constraints in Nonlinear Programming
Problems},
journal = {Journal of Optimization Theory and Applications},
year = {1982},
volume = {36},
pages = {495--519}
}
@Article{ dipillo.grippo:class,
author = {G. Di~Pillo and L. Grippo},
title = {A New Class of Augmented {L}agrangians in Nonlinear Programming},
journal = {SIAM Journal on Control and Optimization},
year = {1979},
volume = {17},
pages = {618--628}
}
@Article{ dipillo.grippo:continuously,
author = {G. Di~Pillo and L. Grippo},
title = {A Continuously Differentiable Exact Penalty Function for Nonlinear Programming
Problems with Inequality Constraints},
journal = {SIAM Journal on Control and Optimization},
year = {1985},
volume = {23},
pages = {72--84}
}
@Article{ dipillo.grippo:exact,
author = {G. Di~Pillo and L. Grippo},
title = {An Exact Penalty Method with Global Convergence Properties for Nonlinear
Programming Problems},
journal = {Mathematical Programming},
year = {1986},
volume = {36},
pages = {1--18}
}
@TechReport{ dirkse.ferris.ea:gams,
author = {S. P. Dirkse and M. C. Ferris and P. V. Preckel and T. Rutherford},
title = {The {GAMS} Callable Program Library for Variational and Complementarity Solvers},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1994},
address = {Madison, Wisconsin},
number = {94-07},
type = {Mathematical Programming Technical Report},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/94-07.ps},
key = {25}
}
@InProceedings{ dirkse.ferris:crash,
crossref = {ferris.pang:complementarity},
author = {S. P. Dirkse and M. C. Ferris},
title = {Crash Techniques for Large-Scale Complementarity Problems},
pages = {40--61},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-22.ps},
key = {52}
}
@Article{ dirkse.ferris:mcplib,
author = {S. P. Dirkse and M. C. Ferris},
title = {{MCPLIB}: {A} Collection of Nonlinear Mixed Complementarity Problems},
journal = {Optimization Methods and Software},
pages = {319--345},
volume = {5},
year = {1995},
url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1994/tr1215.ps},
key = {36}
}
@InCollection{ dirkse.ferris:modeling,
author = {S. P. Dirkse and M. C. Ferris},
title = {Modeling and Solution Environments for {MPEC}: {GAMS} \& {MATLAB}},
year = {1999},
pages = {127--148},
editor = {M. Fukushima and L. Qi},
booktitle = {Reformulation: Nonsmooth, Piecewise Smooth, Semismooth and Smoothing Methods},
publisher = {Kluwer Academic Publishers},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/97-09.ps},
key = {62}
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key = {61},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/97-06.ps}
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year = {1994},
address = {Madison, Wisconsin},
note = {Available from ftp://ftp.cs.wisc.edu/math-prog/tech-reports/},
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key = {87},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/99-08.ps},
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address = {Madison, Wisconsin},
number = {99-08},
type = {Mathematical Programming Technical Report},
annote = {Submitted to }
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author = {D. L. Eager and M. C. Ferris and M. K. Vernon},
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year = {1999},
type = {Technical Report},
number = {1402},
address = {Madison, Wisconsin},
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year = {1999},
booktitle = {Multimedia Computing and Networking, Proceedings of {SPIE}},
volume = {3654},
address = {Bellingham, Washington},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-10.ps},
key = {69},
pages = {301--316},
annote = {18 percent acceptance rate}
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journal = {Performance Evaluation},
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key = {72},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-15.ps},
volume = {42},
pages = {163--185}
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year = {1991},
number = {608},
address = {Clemson, South Carolina}
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year = {1991},
note = {To appear}
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year = {1998},
institution = {Computer Sciences Department, University of Wisconsin},
note = {In preparation}
}
@Article{ ferris.horn:partitioning,
author = {M. C. Ferris and J. D. Horn},
title = {Partitioning Mathematical Programs for Parallel Solution},
year = {1998},
volume = {80},
pages = {35--62},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/tr1232.ps},
journal = {Mathematical Programming},
key = {40}
}
@Article{ ferris.kanzow.ea:feasible,
author = {M. C. Ferris and C. Kanzow and T. S. Munson},
title = {Feasible Descent Algorithms for Mixed Complementarity Problems},
year = {1999},
journal = {Mathematical Programming},
volume = {86},
pages = {475--497},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-04.ps},
key = {67}
}
@InCollection{ ferris.kanzow:complementarity,
author = {M. C. Ferris and C. Kanzow},
title = {Complementarity and Related Problems: {A} Survey},
booktitle = {Handbook of Applied Optimization, forthcoming},
key = {74},
publisher = {Oxford University Press},
year = {2000},
editor = {P. M. Pardalos and M. G. C. Resende},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-17.ps},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {98-17},
type = {Mathematical Programming Technical Report}
}
@Article{ ferris.lucidi.ea:nonmonotone,
author = {M. C. Ferris and S. Lucidi and M. Roma},
title = {Nonmonotone Curvilinear Stabilization Techniques for Unconstrained Optimization},
journal = {Computational Optimization and Applications},
volume = {6},
pages = {117--136},
year = {1996},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/94-16.ps},
key = {43}
}
@TechReport{ ferris.lucidi:globally,
author = {M. C. Ferris and S. Lucidi},
title = {Globally Convergent Methods for Nonlinear Equations},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1991},
address = {Madison, Wisconsin},
number = {1030},
url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1991/tr1030.ps},
key = {21}
}
@Article{ ferris.lucidi:nonmonotone,
author = {M. C. Ferris and S. Lucidi},
title = {Nonmonotone Stabilization Methods for Nonlinear Equations},
journal = {Journal of Optimization Theory and Applications},
year = {1994},
volume = {81},
pages = {53--71},
key = {30}
}
@Article{ ferris.mangasarian:breast,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Breast Cancer Diagnosis via Linear Programming},
key = {50},
journal = {{IEEE} Computational Science and Engineering},
year = {1995},
volume = {2},
pages = {70--71}
}
@Article{ ferris.mangasarian:error,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational
Inequalities},
journal = {Annals of Operations Research},
year = {1993},
volume = {47},
pages = {293--305},
url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps},
key = {24}
}
@Article{ ferris.mangasarian:finite,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Finite Perturbation of Convex Programs},
journal = {Applied Mathematics and Optimization},
year = {1991},
volume = {23},
pages = {263--273},
key = {08}
}
@Book{ ferris.mangasarian:linear,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Linear Programming via {MATLAB}},
publisher = {in preparation},
year = {1995},
address = {Madison, Wisconsin}
}
@Article{ ferris.mangasarian:minimum,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Minimum Principle Sufficiency},
journal = {Mathematical Programming},
year = {1992},
volume = {57},
pages = {1--14},
key = {11}
}
@Article{ ferris.mangasarian:parallel,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Parallel Constraint Distribution},
journal = {SIAM Journal on Optimization},
year = {1991},
volume = {1},
pages = {487--500},
url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps},
key = {18}
}
@Article{ ferris.mangasarian:parallel*1,
author = {M. C. Ferris and O. L. Mangasarian},
title = {Parallel Variable Distribution},
journal = {SIAM Journal on Optimization},
year = {1994},
volume = {4},
pages = {815--832},
url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps},
key = {31}
}
@Article{ ferris.meeraus.ea:computing,
title = {Computing {W}ardropian Equilibrium in a Complementarity Framework},
author = {M. C. Ferris and A. Meeraus and T. F. Rutherford},
journal = {Optimization Methods and Software},
year = {1999},
volume = {10},
pages = {669--685},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps},
key = {45}
}
@Article{ ferris.mesnier.ea:neos,
author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}},
title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the
{I}nternet},
year = {2000},
journal = {{ACM} Transactions on Mathematical Software},
key = {54},
volume = {26},
pages = {1--18},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {96-08},
type = {Mathematical Programming Technical Report},
note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division,
Argonne National Laboratory},
annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH},
1996}
}
@InCollection{ ferris.meyer:models,
author = {M. C. Ferris and R. R. Meyer},
title = {Models and Solution for On-Demand Data Delivery Problems},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps},
key = {80},
booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete
Problems},
editor = {P. M. Pardalos},
series = {Nonconvex Optimization and its Applications},
volume = {42},
address = {Dordrect},
year = {2000},
pages = {175--188},
publisher = {Kluwer},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
number = {99-04}
}
@InProceedings{ ferris.munson.ea:homotopy,
author = {M. C. Ferris and T. S. Munson and D. Ralph},
title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver},
booktitle = {Numerical Analysis 1999},
key = {88},
year = {2000},
editor = {D. F. Griffiths and G. A. Watson},
series = {Research Notes in Mathematics},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps},
address = {London},
pages = {143--167},
publisher = {Chapman and Hall},
institution = {Computer Sciences Department, University of Wisconsin},
number = {99-09},
type = {Mathematical Programming Technical Report}
}
@TechReport{ ferris.munson.ea:practical,
author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran},
title = {A Practical Approach to Sample-Path Simulation Optimization},
type = {Data Mining Institute Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
year = {2000},
url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps},
number = {00-03},
key = {92},
annote = {To appear in WSC 2000}
}
@InCollection{ ferris.munson:case,
author = {M. C. Ferris and T. S. Munson},
title = {Case Studies in Complementarity: Improving Model Formulation},
booktitle = {Ill--Posed Variational Problems and Regularization Techniques},
key = {73},
pages = {79--98},
publisher = {Springer Verlag},
year = {1999},
editor = {M. Th\'{e}ra and R. Tichatschke},
number = {477},
series = {Lecture Notes in Economics and Mathematical Systems},
address = {Berlin},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin}
}
@Article{ ferris.munson:complementarity,
author = {M. C. Ferris and T. S. Munson},
title = {Complementarity Problems in {GAMS} and the {PATH} Solver},
year = {2000},
volume = {24},
pages = {165--188},
journal = {Journal of Economic Dynamics and Control},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps},
key = {70},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {98-12}
}
@Misc{ ferris.munson:condor,
author = {M. C. Ferris and T. S. Munson},
title = {Condor Modeling Language Interface},
organization = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
note = {ftp://ftp.cs.wisc.edu/math-prog/condor}
}
@Manual{ ferris.munson:gams,
author = {M. C. Ferris and T. S. Munson},
title = {{GAMS}/{PATH} User Guide: Version 4.3},
organization = {Department of Computer Sciences, University of Wisconsin, Madison}
}
@Article{ ferris.munson:interfaces,
author = {M. C. Ferris and T. S. Munson},
title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage},
journal = {Computational Optimization and Applications},
volume = {12},
pages = {207--227},
year = {1999},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps},
key = {63},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {97-12},
type = {Mathematical Programming Technical Report}
}
@TechReport{ ferris.munson:interior,
author = {M. C. Ferris and T. S. Munson},
title = {Interior Point Methods for Massive Support Vector Machines},
institution = {Computer Sciences Department, University of Wisconsin},
year = {2000},
key = {94},
type = {Data Mining Institute Technical Report},
number = {00-05},
url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps},
address = {Madison, Wisconsin},
annote = {Submitted to SIOPT}
}
@Article{ ferris.munson:linear,
author = {M. C. Ferris and T. S. Munson},
title = {Linear Programming for Emergency Broadcast Systems},
year = {1999},
journal = {{SIAG/OPT} Newsletter},
volume = {10},
pages = {6--8},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps},
key = {76},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {98-20}
}
@Article{ ferris.munson:modeling,
author = {M. C. Ferris and T. S. Munson},
title = {Modeling Languages and {C}ondor: Metacomputing for Optimization},
year = {2000},
journal = {Mathematical Programming},
volume = {88},
pages = {487--506},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps},
key = {71},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {98-13}
}
@TechReport{ ferris.munson:preprocessing,
author = {M. C. Ferris and T. S. Munson},
title = {Preprocessing Complementarity Problems},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
year = {1999},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps},
number = {99-07},
key = {86},
annote = {Submitted to ICCP 99}
}
@TechReport{ ferris.munson:semismooth,
author = {M. C. Ferris and T. S. Munson},
title = {Semismooth Support Vector Machines},
institution = {Computer Sciences Department, University of Wisconsin},
year = {2000},
key = {97},
type = {Data Mining Institute Technical Report},
number = {00-09},
url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps},
address = {Madison, Wisconsin},
annote = {Submitted to Math Prog B}
}
@Article{ ferris.pang:engineering,
author = {M. C. Ferris and J. S. Pang},
title = {Engineering and Economic Applications of Complementarity Problems},
year = {1997},
journal = {SIAM Review},
volume = {39},
pages = {669--713},
url = {http: //www.siam.org/journals/sirev/39-4/28596.html},
key = {46}
}
@Article{ ferris.pang:nondegenerate,
author = {M. C. Ferris and J. S. Pang},
title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities},
journal = {SIAM Journal on Control and Optimization},
year = {1996},
volume = {34},
pages = {244--263},
url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps},
key = {35}
}
@Article{ ferris.philpott:affine,
author = {M. C. Ferris and A. B. Philpott},
title = {On Affine Scaling and Semi--Infinite Programming},
journal = {Mathematical Programming},
year = {1992},
volume = {56},
pages = {361--364},
key = {15}
}
@Article{ ferris.philpott:interior,
author = {M. C. Ferris and A. B. Philpott},
title = {An Interior Point Algorithm for Semi--Infinite Linear Programming},
journal = {Mathematical Programming},
year = {1989},
volume = {43},
pages = {257--276},
key = {04}
}
@Article{ ferris.philpott:performance,
author = {M. C. Ferris and A. B. Philpott},
title = {On the Performance of {K}armarkar's Algorithm},
journal = {Journal of the Operational Research Society},
year = {1988},
volume = {39},
pages = {257--270},
key = {03}
}
@InCollection{ ferris.ralph:projected,
author = {M. C. Ferris and D. Ralph},
title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal
Maps},
booktitle = {Recent Advances in Nonsmooth Optimization},
publisher = {World Scientific Publishers},
year = {1995},
pages = {57--87},
editor = {D. Du and L. Qi and R. Womersley},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps},
key = {41}
}
@Article{ ferris.ruszczynski:robust,
author = {M. C. Ferris and A. Ruszczy{\'{n}}ski},
title = {Robust Path Choice and Vehicle Guidance in Networks with Failures},
year = {2000},
journal = {Networks},
volume = {35},
pages = {181--194},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps},
key = {60}
}
@InCollection{ ferris.rutherford:accessing,
author = {M. C. Ferris and T. F. Rutherford},
title = {Accessing Realistic Complementarity Problems within {Matlab}},
booktitle = {Nonlinear Optimization and Applications},
key = {48},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps},
editor = {G. Di Pillo and F. Giannessi},
year = {1996},
pages = {141--153},
publisher = {Plenum Press},
address = {New York}
}
@InCollection{ ferris.shepard:optimizing,
author = {M. C. Ferris and D. M. Shepard},
title = {Optimization of Gamma Knife Radiosurgery},
booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming},
editor = {D.-Z. Du and P. Pardolas and J. Wang},
publisher = {AMS},
year = {2000},
optseries = {DIMACS},
url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps},
key = {91},
type = {Data Mining Institute Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {00-01}
}
@InCollection{ ferris.sinapiromsaran:formulating,
author = {M. C. Ferris and K. Sinapiromsaran},
title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems},
booktitle = {Optimization},
key = {77},
publisher = {Springer-Verlag},
year = {2000},
editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings},
volume = {481},
series = {Lecture Notes in Economics and Mathematical Systems},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {98-21}
}
@Article{ ferris.tin-loi:limit,
author = {M. C. Ferris and F. Tin-Loi},
title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with
Complementarity Constraints},
year = {2001},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps},
key = {78},
journal = {International Journal of Mechanical Sciences},
pages = {209--224},
volume = {43},
type = {Mathematical Programming Technical Report},
institution = {Computer Sciences Department, University of Wisconsin},
address = {Madison, Wisconsin},
number = {99-01}
}
@Article{ ferris.tin-loi:nonlinear,
author = {M. C. Ferris and F. Tin-Loi},
title = {Nonlinear Programming Approach for a Class of Inverse Problems in
Elastoplasticity},
year = {1998},
key = {64},
volume = {6},
pages = {857--870},
journal = {Structural Engineering and Mechanics}
}
@Article{ ferris.tin-loi:solution,
author = {M. C. Ferris and F. Tin-Loi},
title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement
and Complementarity Constraints},
year = {1999},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {174},
pages = {107--120},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps},
key = {66}
}
@Article{ ferris.vlach:scheduling,
author = {M. C. Ferris and M. Vlach},
title = {Scheduling with Earliness and Tardiness Penalties},
journal = {Naval Research Logistics Quarterly},
year = {1992},
volume = {39},
pages = {229--245},
key = {13}
}
@TechReport{ ferris.zavriev:linear,
author = {M. C. Ferris and S. K Zavriev},
title = {The Linear Convergence of a Successive Linear Programming Algorithm},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1996},
key = {56},
address = {Madison, Wisconsin},
type = {Mathematical Programming Technical Report},
number = {96--12},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps}
}
@Article{ ferris:finite,
author = {M. C. Ferris},
title = {Finite Termination of the Proximal Point Algorithm},
journal = {Mathematical Programming},
year = {1991},
volume = {50},
pages = {359--366},
key = {06}
}
@Article{ ferris:iterative,
author = {M. C. Ferris},
title = {Iterative Linear Programming Solution of Convex Programs},
journal = {Journal of Optimization Theory and Applications},
year = {1990},
volume = {65},
pages = {53--65},
key = {07}
}
@Article{ ferris:linear,
author = {M. C. Ferris},
title = {The Linear Complementarity Problem},
journal = {Bulletin of the American Mathematical Society},
year = {1993},
volume = {28},
pages = {169--175},
key = {27}
}
@MastersThesis{ ferris:linear*1,
author = {M. C. Ferris},
title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for
Solving a Class of Structural Optimization Problems},
year = {1985},
school = {University of Cambridge},
address = {England},
key = {01}
}
@TechReport{ ferris:matlab,
author = {M. C. Ferris},
title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1998},
address = {Madison, Wisconsin},
type = {Mathematical Programming Technical Report},
url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps},
number = {98-19},
key = {75}
}
@Article{ ferris:parallel,
author = {M. C. Ferris},
title = {Parallel Constraint Distribution for Convex Quadratic Programs},
journal = {Mathematics of Operations Research},
year = {1994},
volume = {19},
pages = {645--658},
url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps},
key = {20}
}
@TechReport{ ferris:parallel*1,
author = {M. C. Ferris},
title = {Parallel Solution of Extremely Large Knapsack Problems},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1989},
address = {Madison, Wisconsin},
number = {842},
key = {09}
}
@PhDThesis{ ferris:weak,
author = {M. C. Ferris},
title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming},
year = {1988},
school = {University of Cambridge},
address = {England},
key = {02}
}
@TechReport{ ferris:weak*1,
author = {M. C. Ferris},
title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1988},
address = {Madison, Wisconsin},
number = {779},
key = {05}
}
@Book{ fiacco.mccormick:nonlinear,
author = {A. V. Fiacco and G. P. McCormick},
title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques},
year = {1968},
publisher = {John Wiley \& Sons},
address = {New York},
note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990}
}
@Book{ fiacco:introduction,
author = {A. V. Fiacco},
title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming},
year = {1983},
publisher = {Academic Press},
address = {New York}
}
@Article{ fiedler.ptak:matrices,
author = {M. Fiedler and V. Pt\'{a}k},
title = {On matrices with nonpositive off-diagonal elements and positive principal
minors},
journal = {Czechoslovak Mathematics Journal},
volume = {12},
pages = {382--400},
year = {1962}
}
@Article{ fischer.kanzow:finite,
author = {A. Fischer and C. Kanzow},
title = {On Finite Termination of an Iterative Method for Linear Complementarity
Problems},
journal = {Mathematical Programming},
volume = {74},
pages = {279--292},
year = {1996}
}
@TechReport{ fischer:constrained,
author = {A. Fischer},
title = {A New Constrained Optimization Reformulation for Complementarity Problems},
institution = {Institute of Numerical Mathematics, Technical University of Dresden},
year = {1995},
type = {Technical Report},
number = {MATH-NM-10-1995},
address = {Dresden}
}
@Article{ fischer:local,
author = {A. Fischer},
title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under
weak conditions},
journal = {Optimization Methods and Software},
year = {1995},
volume = {6},
pages = {83--107}
}
@InCollection{ fischer:ncp-function,
author = {A. Fischer},
title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems},
booktitle = {Recent Advances in Nonsmooth Optimization},
publisher = {World Scientific Publishers},
editor = {D. Z. Du and L. Qi and R. S. Womersley},
year = {1995},
pages = {88--105}
}
@Article{ fischer:newton-type,
author = {A. Fischer},
title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity
Problems},
journal = {Journal of Optimization Theory and Applications},
year = {1995},
volume = {86},
pages = {585--608}
}
@Article{ fischer:solution,
author = {A. Fischer},
title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian
Functions},
year = {1997},
journal = {Mathematical Programming},
pages = {513--532}
}
@Article{ fischer:special,
author = {A. Fischer},
title = {A Special {N}ewton--Type Optimization Method},
journal = {Optimization},
year = {1992},
volume = {24},
pages = {269--284}
}
@Article{ fisher:use,
author = {R. A. Fisher},
title = {The Use of Multiple Measurements in Taxonomic Problems},
journal = {Annual Eugenics},
year = {1936},
volume = {7},
number = {Part II},
pages = {179--188}
}
@Book{ fishman:principles,
author = {G. Fishman},
title = {Principles of Discrete Event Simulation},
publisher = {Wiley},
address = {New York, NY},
year = {1978}
}
@Article{ fitchard.aldridge.ea:registration,
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title = {Registration of Synthetic Tomographic Projection Data Sets Using
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journal = {Physics in Medicine and Biology},
year = {1998},
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pages = {1645--1657}
}
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year = {1984},
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pages = {267--284}
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author = {R. Fletcher and E. Sainz de la Maza},
title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear
Programming},
institution = {Department of Mathematical Sciences},
year = {1987},
address = {The University, Dundee, Scotland},
number = {NA/100},
type = {Numerical Analysis Report}
}
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title = {A Class of Methods for Nonlinear Programming with Termination and Convergence
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year = {1970},
editor = {J. Abadie},
publisher = {North--Holland},
address = {Amsterdam},
pages = {157--173}
}
@Article{ fletcher:exact,
author = {R. Fletcher},
title = {An Exact Penalty Function for Nonlinear Programming with Inequalities},
journal = {Mathematical Programming},
year = {1973},
volume = {5},
pages = {129--150}
}
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year = {1968},
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pages = {392--399}
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@InProceedings{ fletcher:penalty,
crossref = {bachem.grotschel.ea:mathematical},
author = {R. Fletcher},
title = {Penalty Functions},
pages = {87--114}
}
@Book{ fletcher:practical,
author = {R. Fletcher},
title = {Practical Methods of Optimization},
year = {1981},
publisher = {John Wiley \& Sons},
address = {Chichester},
volume = {1}
}
@Book{ fletcher:practical*1,
author = {R. Fletcher},
title = {Practical Methods of Optimization},
year = {1981},
publisher = {John Wiley \& Sons},
address = {Chichester},
volume = {2}
}
@Book{ fletcher:practical*2,
author = {R. Fletcher},
title = {Practical Methods of Optimization},
year = {1987},
publisher = {John Wiley \& Sons},
address = {New York},
edition = {second}
}
@Unpublished{ fletcher:recent,
author = {R. Fletcher},
title = {Recent Developments in Nonlinear Programming},
note = {Presentation at SOR 96, Braunchweig, Germany},
year = {1996}
}
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author = {R. Fletcher},
title = {Second Order Correction for Nondifferentiable Optimization},
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year = {1982},
editor = {G. A. Watson},
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title = {Mathematical programming applications in national, regional, and urban planning},
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address = {Tokyo},
year = {1989}
}
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author = {M. Florian},
title = {Nonlinear Cost Network Models in Transportation Analysis},
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year = {1986},
volume = {26},
pages = {167--196}
}
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crossref = {schaeffer:third},
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title = {Varying the Probability of Mutation in the Genetic Algorithm},
pages = {422--427}
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author = {J. J. Forrest and D. Goldfarb},
title = {Steepest--Edge Simplex Algorithms for Linear Programming},
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year = {1992},
volume = {57},
pages = {341--374}
}
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author = {J. J. H. Forrest and J. A. Tomlin},
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year = {1972},
volume = {2},
pages = {263--278}
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@TechReport{ forsgren.gill.ea:computing,
author = {A. Forsgren and P. E. Gill and W. Murray},
title = {Computing Modified {N}ewton Directions using a Partial {C}holesky Factorization},
institution = {Department of Mathematics, Royal Institute of Technology},
year = {1993},
number = {TRITA-MAT-1993-9},
address = {Stockholm, Sweden}
}
@TechReport{ forsgren.gill:primal-dual,
author = {A. Forsgren and P. E. Gill},
title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming},
institution = {Department of Mathematics, University of California},
year = {1996},
type = {Report NA},
number = {96-3},
address = {San Diego}
}
@InCollection{ fortin.glowinski:decomposition-coordination,
author = {M. Fortin and R. Glowinski},
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year = {1983},
editor = {M. Fortin and R. Glowinski},
address = {Amsterdam}
}
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howpublished = {www.globus.org}
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volume = {11},
pages = {115--128},
year = {1997}
}
@Book{ foster.kesselman:grid,
editor = {I. Foster and C. Kesselman},
title = {The Grid: Blueprint for a Future Computing Infrastructure},
publisher = {Morgan Kaufmann Publishers},
year = {1999}
}
@Book{ fourer.gay.ea:ampl,
author = {R. Fourer and D. M. Gay and B. W. Kernighan},
title = {{AMPL}: {A} Modeling Language for Mathematical Programming},
year = {1993},
publisher = {Duxbury Press}
}
@Article{ fourer.gay.ea:modeling,
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title = {A Modeling Language for Mathematical Programming},
journal = {Management Science},
year = {1990},
volume = {36},
pages = {519--554}
}
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year = {1995},
volume = {22},
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pages = {1911--1921}
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institution = {Stanford University},
year = {1988},
number = {{SOL} 88.16},
type = {Technical Report}
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@InCollection{ francois.mcdonald.ea:uruguay,
author = {J. F. Francois and B. McDonald and H. Nordstrom},
title = {The {U}ruguay Round: {A} Numerically Based Qualitative Assessment},
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address = {New York},
editors = {W. Martin and L. A. Winters},
publisher = {Cambridge University Press}
}
@InCollection{ francois.mcdonald.ea:uruguay*1,
author = {J. F. Francois and B. McDonald and H. Nordstrom},
title = {The {U}ruguay Round: {A} Global Analysis},
booktitle = {Challenges and Opportunities for East Asian Trade},
address = {Cambridge},
editors = {D. Robertson},
publisher = {Cambridge University Press}
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year = {1996},
volume = {22},
pages = {46--77}
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year = {1996},
editor = {L. Saitta},
publisher = {Morgan Kaufmann}
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author = {Robert M. Freund and Michael J. Todd},
title = {Barrier functions and interior-point algorithms for linear programming with
zero-, one-, or two-sided bounds on the variables},
year = {1992},
month = jul
}
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year = {1983},
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author = {K. R. Frisch},
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author = {K. Fukunaga},
title = {Statistical Pattern Recognition},
year = {1990},
publisher = {Academic Press},
address = {New York}
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author = {M. Fukushima and Z.--Q. Luo and J. S. Pang},
title = {A Globally Convergent Sequential Quadratic Programming Algorithm for Mathematical
Programs with Linear Complementarity Constraints},
journal = {Computational Optimization and Applications},
year = {1998},
volume = {10},
pages = {5--34}
}
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author = {M. Fukushima},
title = {Equivalent Differentiable Optimization Problems and Descent Methods for
Asymmetric Variational Inequality Problems},
journal = {Mathematical Programming},
year = {1992},
volume = {53},
pages = {99--110}
}
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author = {M. Fukushima},
title = {The Primal {D}ouglas-{R}achford Splitting Algorithm for a Class of Monotone
Mappings with Application to the Traffic Equilibrium Problem},
journal = {Mathematical Programming},
year = {1996},
volume = {72},
pages = {1--15}
}
@Article{ gabay.mercier:dual,
author = {D. Gabay and B. Mercier},
title = {A Dual Algorithm for the Solution of Nonlinear Variational Inequalities via
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year = {1976},
volume = {2},
pages = {17--48}
}
@InCollection{ gabay:applications,
author = {D. Gabay},
title = {Applications of the Method of Multipliers to Variational Inequalities},
booktitle = {Augmented {L}agrangian Methods: Applications to the Solution of Boundary Value
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publisher = {North-Holland},
year = {1983},
editor = {M. Fortin and R. Glowinski},
address = {Amsterdam}
}
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note = {Draft, 1995}
}
@TechReport{ gabriel.kydes:nonlinear,
author = {S. A. Gabriel and A. S. Kydes},
title = {A Nonlinear Complementarity Approach for Solving the National Energy Modeling
System},
institution = {Mathematics and Computer Science Division, Argonne National Laboratory},
year = {1995},
type = {Preprint},
number = {MCS-P504-0395},
address = {Argonne, Illinois},
month = mar
}
@InProceedings{ gabriel.more:smoothing,
crossref = {ferris.pang:complementarity},
author = {S. A. Gabriel and J. J. Mor\'{e}},
title = {Smoothing of Mixed Complementarity Problems}
}
@Article{ gabriel.pang:inexact,
author = {S. A. Gabriel and J. S. Pang},
title = {An Inexact {NE/SQP} Method for Solving the Nonlinear Complementarity Problem},
journal = {Computational Optimization and Applications},
year = {1992},
volume = {1},
pages = {67--91}
}
@InCollection{ gabriel.pang:trust,
author = {S. A. Gabriel and J. S. Pang},
title = {A Trust Region Method for Constrained Nonsmooth Equations},
booktitle = {Large--Scale Optimization: State of the Art},
publisher = {Kluwer Academic Publishers},
year = {1994},
editor = {W. W. Hager and D. W. Hearn and P. M. Pardalos},
pages = {159--186}
}
@PhDThesis{ gabriel:algorithms,
author = {S. A. Gabriel},
title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and
Extensions},
school = {The Johns Hopkins University},
year = {1992},
address = {Baltimore, Maryland}
}
@Article{ gafni.bertsekas:two-metric,
author = {E. M. Gafni and D. P. Bertsekas},
title = {Two-Metric Projection Methods for Constrained Optimization},
journal = {SIAM Journal on Control and Optimization},
year = {1984},
volume = {22},
pages = {936--964}
}
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author = {A. A. Gaivoronski},
title = {Convergence of Parallel Backpropagation for Neural Networks},
booktitle = {SIAM Journal on Optimization},
year = {1994},
note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993,
submitted}
}
@Misc{ gaivoronski:private,
author = {A. A. Gaivoronski},
title = {Private Communication},
year = {1992},
month = nov,
address = {ITALTEL, Milan}
}
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author = {S. I. Gallant},
title = {Neural Network Learning and Expert Systems},
year = {1993},
publisher = {MIT Press},
address = {Cambridge, Massachusetts}
}
@InProceedings{ ganti.gehrke.ea:framework,
author = {V. Ganti and J. Gehrke and R. Ramakrishnan},
title = {A Framework for Measuring Changes in Data Characteristics},
booktitle = {Proceedings of the Eighteenth ACM SIGACT-SIGMOD-SIGART Symposium on Principles of
Database Systems, May 31 - June 2, 1999, Philadelphia, Pennsylvania},
publisher = {ACM Press},
year = {1999},
isbn = {1-58113-062-7},
pages = {126--137}
}
@Book{ ganz:gamma,
author = {J. C. Ganz},
title = {Gamma Knife Surgery},
publisher = {Springer-Verlag Wien},
year = {1997},
address = {Austria}
}
@TechReport{ gao:nonlinear,
author = {Y. Gao},
title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral
Conditions},
type = {Manuscript},
institution = {Department of Mathematics, Virginia Polytechnic Institute and State University},
month = oct,
year = {1994}
}
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author = {U. M. {Garcia--Palomares} and O. L. Mangasarian},
title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained
Optimization Problems},
journal = {Mathematical Programming},
year = {1976},
volume = {11},
pages = {1--13}
}
@Article{ garcia-palomares.restuccia:global,
author = {U. M. {Garcia--Palomares} and A. Restuccia},
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journal = {Mathematical Programming},
year = {1981},
volume = {21},
pages = {290--300}
}
@InProceedings{ garcia-palomares:superlinearly,
author = {U. M. {Garcia--Palomares}},
title = {Superlinearly Convergent Algorithms for Linearly Constrained Optimization},
crossref = {mangasarian.meyer.ea:nonlinear*2},
pages = {101--119}
}
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year = {1978},
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pages = {282--289}
}
@Book{ garcia.zangwill:pathways,
author = {C. B. Garcia and W. I. Zangwill},
title = {Pathways to Solutions, Fixed Points, and Equilibria},
year = {1981},
publisher = {Prentice-Hall, Inc},
address = {Englewood Cliffs, New Jersey}
}
@Book{ garey.johnson:computers,
author = {M. R. Garey and D. S. Johnson},
title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness},
year = {1979},
publisher = {W.H. Freeman and Company},
address = {San Francisco}
}
@Article{ garey.tarjan.ea:one-processor,
author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong},
title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties},
journal = {Mathematics of Operations Research},
year = {1988},
volume = {13},
pages = {330--348}
}
@Book{ garfinkel.nemhauser:integer,
author = {R. S. Garfinkel and G. L. Nemhauser},
title = {Integer Programming},
year = {1972},
publisher = {John Wiley \& Sons},
address = {New York}
}
@Book{ gass:linear,
author = {S. Gass},
title = {Linear Programming Methods and Applications},
edition = {Fifth},
publisher = {Boyd and Fraser Publishing Company},
address = {Danvers, Massachusetts},
year = {1985}
}
@InProceedings{ gay:combining,
author = {D. M. Gay},
title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases},
booktitle = {Sparse Matrix Proceedings 1978},
editor = {I. S. Duff and G. W. Stewart},
year = {1978},
organization = {SIAM},
address = {Philadelphia, Pennsylvania},
pages = {313--334}
}
@Article{ gay:electronic,
author = {D. M. Gay},
title = {Electronic Mail Distribution of Linear Programming Test Problems},
journal = {{COAL} Newsletter},
year = {1985},
volume = {13},
pages = {10--12}
}
@TechReport{ gay:hooking,
author = {D. M. Gay},
title = {Hooking Your Solver to {AMPL}},
year = {1997},
institution = {Bell Laboratories},
address = {Murray Hill, New Jersey},
note = {Revised 1994, 1997}
}
@Article{ gay:variant,
author = {D. Gay},
title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard
Form},
journal = {Mathematical Programming},
year = {1987},
volume = {37},
pages = {81--90}
}
@Article{ geiger.kanzow:resolution,
author = {C. Geiger and C. Kanzow},
title = {On the Resolution of Monotone Complementarity Problems},
journal = {Computational Optimization and Applications},
volume = {5},
year = {1996},
pages = {155--173}
}
@Book{ geist.beguelin.ea:pvm,
author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and
V. S. Sunderam},
title = {{PVM}: Parallel Virtual Machine},
publisher = {MIT Press},
address = {Cambridge, Massachusetts},
year = {1994}
}
@Article{ gendron.crainic:parallel,
author = {B. Gendron and T. G. Crainic},
title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis},
journal = {Operations Research},
year = {1994},
volume = {42},
pages = {1042--1060}
}
@Article{ george:automatic,
author = {A. George},
title = {An automatic one-way dissection algorithm for irregular finite-element problems},
journal = {SIAM Journal on Numerical Analysis},
vol = {17},
pages = {740--751},
year = {1980}
}
@InProceedings{ georges-schleuter:asparagos,
crossref = {schaeffer:third},
author = {M. Georges--Schleuter},
title = {Asparagos: An Asynchronous Parallel Genetic Algorithm},
pages = {416--421}
}
@Article{ georgiou:comments,
author = {G. M. Georgiou},
title = {Comments On Hidden Nodes in Neural Nets},
journal = {IEEE Transactions on Circuits and Systems},
year = {1991},
volume = {38},
pages = {1410}
}
@TechReport{ gertz.linderoth.ea:object-oriented,
author = {M. Gertz and J. Linderoth and S. Wright},
title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming},
institution = {MCS Division, Argonne National Laboratory},
year = {in preparation}
}
@Article{ ghellinck.vial:polynomial,
author = {G. de Ghellinck and J.--Ph. Vial},
title = {A Polynomial {N}ewton Method for Linear Programming},
journal = {Algorithmica},
year = {1986},
volume = {1},
pages = {425--453}
}
@InCollection{ gilbert.ng:predicting,
author = {J. R. Gilbert and E. Ng},
title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations},
year = {1993},
booktitle = {Graph Theory and Sparse Matrix Computation},
editor = {A. George and J. Gilbert and J. Liu},
publisher = {Springer-Verlag}
}
@Article{ gilbert-lemarechal,
author = {J. C. Gilbert and C. Lemarechal},
title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms},
journal = {Mathematical Programming},
year = {1989},
volume = {45},
pages = {407--434}
}
@Article{ gill.murray.ea:computing,
author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright},
title = {Computing Forward-Difference Intervals for Numerical Optimization},
journal = {SIAM Journal on Scientific and Statistical Computing},
year = {1983},
volume = {4},
pages = {310--321}
}
@Article{ gill.murray.ea:maintaining,
author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright},
title = {Maintaining {LU} Factors of a General Sparse Matrix},
year = {1987},
journal = {Linear Algebra and Its Applications},
volume = {88/89},
pages = {239--270}
}
@Book{ gill.murray.ea:practical,
author = {P. E. Gill and W. Murray and M. H. Wright},
title = {Practical Optimization},
year = {1981},
publisher = {Academic Press},
address = {London}
}
@Article{ gill.murray.ea:practical*1,
author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright},
title = {A Practical Anti-Cycling Procedure for Linearly Constrained Optimization},
journal = {Mathematical Programming},
year = {1989},
volume = {45},
pages = {437--474}
}
@Article{ gill.murray.ea:projected,
author = {P. E. Gill and W. Murray and M. A. Saunders and J. A. Tomlin and M. H. Wright},
title = {On Projected {N}ewton Barrier Methods for Linear Programming and an Equivalence
to {K}armarkar's Projective Method},
journal = {Mathematical Programming},
year = {1986},
volume = {36},
pages = {183--209}
}
@Article{ gill.murray:newton-type,
author = {P. E. Gill and W. Murray},
title = {{N}ewton--Type Methods for Unconstrained and Linearly Constrained Optimization},
journal = {Mathematical Programming},
year = {1974},
volume = {7},
pages = {311--350}
}
@InProceedings{ gill.murray:nonlinear,
author = {P. E. Gill and W. Murray},
title = {Nonlinear Least Squares and Nonlinearly Constrained Optimization},
booktitle = {Numerical Analysis, Dundee 1975},
year = {1976},
editor = {G. A. Watson},
publisher = {Springer-Verlag},
address = {Berlin},
note = {Lecture Notes in Mathematics 506}
}
@Book{ ginsburgh.waelbroeck:activity,
author = {V. Ginsburgh and J. Waelbroeck},
title = {Activity Analysis and General Equilibrium Modelling},
publisher = {North--Holland},
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institution = {Institute of Applied Mathematics, University of Hamburg},
type = {Preprint},
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address = {Hamburg, Germany}
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institution = {Institute of Applied Mathematics, University of Hamburg},
year = {1997},
type = {Preprint},
address = {Hamburg, Germany}
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year = {1995}
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number = {95-064},
address = {Minnesota},
year = {1995}
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author = {A. J. King},
title = {{SP/OSL} Version 1.0 Stochastic Programming Interface Library User's Guide},
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year = {1994},
number = {RC 19757},
address = {Yorktown Heights, New York}
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year = {1996},
volume = {88},
pages = {233--236}
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volume = {30},
year = {1988},
pages = {1185--1198}
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year = {1992},
pages = {249--269}
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year = {1996}
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year = {1988}
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@TechReport{ klarbring:large,
author = {A. Klarbring},
title = {Large Displacement Frictional Contact: a Continuum Framework for Finite Element
Discretization},
number = {LiTH-IKP-R-798},
institution = {Department of Mechanical Engineering, Link{\"o}ping Institute of Technology},
address = {Link{\"o}ping},
year = {1994}
}
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year = {1986},
pages = {175--200}
}
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address = {Lausanne},
year = {1992},
pages = {409--422}
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author = {A. Klarbring},
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address = {Southampton},
year = {1993},
pages = {233--264}
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year = {1986}
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pages = {869--887}
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year = {1991},
volume = {16},
pages = {754--774}
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@TechReport{ kojima.megiddo.ea:primal-dual,
author = {M. Kojima and N. Megiddo and S. Mizuno},
title = {A primal-dual exterior point algorithm for linear programming},
institution = {IBM Alamaden Research Center},
year = {1991},
number = {RJ 8500},
address = {San Jose, California}
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@Book{ kojima.megiddo.ea:unified,
author = {M. Kojima and N. Megiddo and T. Noma and A. Yoshise},
title = {A Unified Approach to Interior Point Algorithms for Linear Complementarity
Problems},
year = {1991},
publisher = {Springer-Verlag},
address = {Berlin},
volume = {538},
series = {Lecture Notes in Computer Science}
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year = {1989},
volume = {43},
pages = {107--113}
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@TechReport{ kojima.mizuno.ea:infeasible,
author = {M. Kojima and S. Mizuno and M. Todd},
title = {Infeasible interior-point primal-dual potential-reduction algorithms for linear
programming},
institution = {School of Operations Research and Industrial Engineering, Cornell University},
year = {1992},
number = {1023},
address = {Ithaca, New York},
month = aug
}
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journal = {Mathematical Programming},
year = {1991},
volume = {50},
pages = {331--342}
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year = {1989},
volume = {44},
pages = {1--20}
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year = {1994}
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author = {K. O. Kortanek and M. Shi},
title = {Remarks on `Convergence Results and Numerical Experiments on a Linear Programming
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institution = {College of Business Administration, University of Iowa},
year = {1987},
address = {Iowa City},
number = {87--1},
type = {Working Paper}
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author = {K. O. Kortanek},
title = {Vector--Supercomputer Experiments with the Linear Programming Scaling Algorithm},
institution = {College of Business Administration, University of Iowa},
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number = {87--2},
type = {Working Paper}
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author = {E. L. Lawler and J. K. Lenstra and A. H. G. Rinnooy Kan and D. B. Shmoys},
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institution = {Centre for Mathematics and Computer Science},
year = {1989},
address = {P.O. Box 4079, 1009 AB Amsterdam, The Netherlands},
number = {BS--R89xx}
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number = {TR93-1},
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title = {Linearly Convergent Descent Methods for Unconstrained Minimization of Convex
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institution = {Department of Mathematics and Statistics, Old Dominion University},
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institution = {Communications Research Laboratory, McMaster University},
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address = {Hamilton, Ontario}
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@TechReport{ mangasarian.musicant:active,
author = {O. L. Mangasarian and David R. Musicant},
title = {Active Set Support Vector Machine Classification},
institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin},
year = {2000},
number = {00-04},
address = {Madison, Wisconsin}
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@TechReport{ mangasarian.musicant:lagrangian,
author = {O. L. Mangasarian and D. R. Musicant},
title = {Lagrangian Support Vector Machines},
institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin},
year = {2000},
number = {00-06},
address = {Madison, Wisconsin}
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@TechReport{ mangasarian.musicant:robust,
author = {O. L. Mangasarian and David R. Musicant},
title = {Robust Linear and Support Vector Regression},
institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin},
year = {1999},
number = {99-09},
address = {Madison, Wisconsin}
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@Article{ mangasarian.musicant:successive,
author = {O. L. Mangasarian and David R. Musicant},
title = {Successive Overrelaxation for Support Vector Machines},
journal = {IEEE Transactions on Neural Networks},
volume = {10},
year = {1999},
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year = {1997},
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pages = {1--8}
}
@Article{ mangasarian.pang:extended,
author = {O. L. Mangasarian and J. S. Pang},
title = {The Extended Linear Complementarity Problem},
journal = {SIAM Journal on Matrix Analysis and Applications},
year = {1994},
volume = {16}
}
@Article{ mangasarian.ren:error,
author = {O. L. Mangasarian and J. Ren},
title = {New error bounds for the nonlinear complementarity problem},
year = {1994},
volume = {1},
pages = {49--56},
journal = {Communications on Applied Nonlinear Analysis}
}
@Article{ mangasarian.ren:improved,
author = {O. L. Mangasarian and J. Ren},
title = {New Improved Error Bounds for the Linear Complementarity Problem},
year = {1994},
volume = {66},
journal = {Mathematical Programming},
pages = {241--255}
}
@InProceedings{ mangasarian.setiono.ea:pattern,
crossref = {coleman.li:large-scale},
author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg},
title = {Pattern Recognition via Linear Programming: Theory and Application to Medical
Diagnosis},
pages = {22--31}
}
@Article{ mangasarian.shiau:error,
author = {O. L. Mangasarian and T.--H. Shiau},
title = {Error Bounds for Monotone Linear Complementarity Problems},
journal = {Mathematical Programming},
year = {1986},
volume = {36},
pages = {81--89}
}
@Article{ mangasarian.shiau:lipschitz,
author = {O. L. Mangasarian and T.--H. Shiau},
title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and
Complementarity Problems},
journal = {SIAM Journal on Control and Optimization},
year = {1987},
volume = {25},
pages = {583--595}
}
@Article{ mangasarian.solodov:nonlinear,
author = {O. L. Mangasarian and M. V. Solodov},
title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization},
journal = {Mathematical Programming},
year = {1993},
volume = {62},
pages = {277--298}
}
@Article{ mangasarian.solodov:serial,
author = {O. L. Mangasarian and M. V. Solodov},
title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed
Minimization},
year = {1994},
journal = {Optimization Methods and Software},
volume = {4},
pages = {103--116}
}
@Article{ mangasarian.street.ea:breast,
author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg},
title = {Breast Cancer Diagnosis and Prognosis via Linear Programming},
journal = {Operations Research},
year = {1995},
volume = {43},
pages = {570--577}
}
@Article{ mangasarian.wolberg:cancer,
author = {O. L. Mangasarian and W. H. Wolberg},
title = {Cancer Diagnosis via Linear Programming},
journal = {SIAM News},
year = {1990},
volume = {23},
pages = {1 \& 18}
}
@InCollection{ mangasarian:applications,
author = {O. L. Mangasarian},
title = {Some Applications of Penalty Functions in Mathematical Programming},
booktitle = {Optimization and Related Fields},
year = {1986},
editor = {R. Conti and E. De~Giorgi and F. Giannessi},
publisher = {Springer-Verlag},
address = {Heidelberg},
pages = {307--329},
note = {Lecture Notes in Mathematics 1190}
}
@Article{ mangasarian:characterization,
author = {O. L. Mangasarian},
title = {Characterization of linear complementarity problems as linear programs},
journal = {Mathematical Programming Study},
year = {1978},
volume = {7},
pages = {74--87}
}
@InProceedings{ mangasarian:condition,
author = {O. L. Mangasarian},
title = {A condition number for linear inequalities and linear programs},
booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September
1981},
year = {1981},
editor = {G. Bamberg and O. Opitz},
publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein},
address = {Konigstein},
pages = {3--15}
}
@Article{ mangasarian:convergence,
author = {O. L. Mangasarian},
title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the
Symmetric Monotone Linear Complementarity Problem},
journal = {SIAM Journal on Optimization},
volume = {1},
pages = {114--122},
year = {1991}
}
@Article{ mangasarian:equivalence,
author = {O. L. Mangasarian},
title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations},
journal = {SIAM Journal on Applied Mathematics},
year = {1976},
volume = {31},
pages = {89--92}
}
@Article{ mangasarian:error,
author = {O. L. Mangasarian},
title = {Error Bounds for Inconsistent Linear Inequalities and Programs},
journal = {ORSA Journal on Computing},
volume = {15},
pages = {187--192},
year = {1994}
}
@Article{ mangasarian:error*1,
author = {O. L. Mangasarian},
title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems},
journal = {Mathematical Programming},
year = {1990},
volume = {48},
pages = {437--445}
}
@Article{ mangasarian:generalized,
author = {O. L. Mangasarian},
title = {Generalized Linear Complementarity Problems as Linear Programs},
journal = {Methods of Operations Research},
year = {1979},
editor = {W. Oettli and F. Steffens},
volume = {31},
pages = {393--402}
}
@InCollection{ mangasarian:generalized*1,
author = {O. L. Mangasarian},
title = {Generalized Support Vector Machines},
year = {2000},
pages = {135-146},
booktitle = {Advances in Large Margin Classifiers},
editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans},
publisher = {MIT Press},
address = {Cambridge, MA}
}
@Article{ mangasarian:global,
author = {O. L. Mangasarian},
title = {Global error bounds for monotone affine variational inequality problems},
journal = {Linear Algebra and Its Applications},
year = {1992},
pages = {153--164}
}
@InCollection{ mangasarian:least,
author = {O. L. Mangasarian},
title = {Least Norm Solution of Non--Monotone Complementarity Problems},
booktitle = {Functional Analysis, Optimization and Mathematical Economics},
year = {1990},
publisher = {Oxford University Press},
address = {New York},
pages = {217--221}
}
@Article{ mangasarian:least-norm,
author = {O. L. Mangasarian},
title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization
Problem},
journal = {Journal of Mathematical Analysis and Applications},
year = {1983},
volume = {92},
pages = {240--251}
}
@Article{ mangasarian:linear,
author = {O. L. Mangasarian},
title = {Linear Complementarity Problems Solvable by a Single Linear Program},
journal = {Mathematical Programming},
year = {1976},
volume = {10},
pages = {263--270}
}
@Article{ mangasarian:linear*1,
author = {O. L. Mangasarian},
title = {Linear and Nonlinear Separation of Patterns by Linear Programming},
journal = {Operations Research},
year = {1965},
volume = {13},
pages = {444--452}
}
@Article{ mangasarian:locally,
author = {O. L. Mangasarian},
title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear
Complementarity Problems},
journal = {Mathematical Programming},
year = {1980},
volume = {19},
pages = {200--212}
}
@InCollection{ mangasarian:machine,
author = {O. L. Mangasarian},
title = {Machine Learning via Polyhedral Concave Minimization},
editor = {H. Fischer and B. Riedmueller and S. Schaeffler},
booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter},
pages = {175-188},
year = {1996},
address = {Heidelberg},
publisher = {Physica-Verlag A Springer-Verlag Company}
}
@Article{ mangasarian:mathematical,
author = {O. L. Mangasarian},
title = {Mathematical Programming in Neural Networks},
journal = {ORSA Journal on Computing},
volume = {5},
pages = {349--360},
year = {1993}
}
@InProceedings{ mangasarian:mathematical*1,
author = {O. L. Mangasarian},
title = {Mathematical Programming in Machine Learning},
booktitle = {Nonlinear Optimization and Applications},
editor = {G. Di Pillo and F. Giannessi},
publisher = {Plenum Publishing},
address = {New York},
pages = {283--295},
year = {1996}
}
@Article{ mangasarian:mathematical*2,
author = {O. L. Mangasarian},
title = {Mathematical Programming in Data Mining},
journal = {Data Mining and Knowledge Discovery},
volume = {1},
year = {1997},
pages = {183-201}
}
@Article{ mangasarian:multi-surface,
author = {O. L. Mangasarian},
title = {Multi-surface Method of Pattern Separation},
journal = {IEEE Transactions on Information Theory},
year = {1968},
volume = {IT-14},
pages = {801--807}
}
@Book{ mangasarian:nonlinear,
author = {O. L. Mangasarian},
title = {Nonlinear Programming},
year = {1969},
publisher = {McGraw--Hill},
address = {New York},
note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994}
}
@Article{ mangasarian:normal,
author = {O. L. Mangasarian},
title = {Normal Solutions of Linear Programs},
journal = {Mathematical Programming Study},
year = {1984},
volume = {22},
pages = {206--216}
}
@Article{ mangasarian:optimal,
author = {O. L. Mangasarian},
title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of
Linear Programs},
journal = {Journal of Optimization Theory and Applications},
year = {1981},
volume = {35},
pages = {123--128}
}
@Article{ mangasarian:parallel,
author = {O. L. Mangasarian},
title = {Parallel Gradient Distribution in Unconstrained Optimization},
journal = {SIAM Journal on Control and Optimization},
volume = {33},
pages = {1916--1925},
year = {1995}
}
@TechReport{ mangasarian:regularized,
author = {O. L. Mangasarian},
title = {Regularized Linear Programs with Equilibrium Constraints},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1997},
address = {Madison, Wisconsin},
type = {Mathematical Programming Technical Report},
number = {97--13},
url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/97-13.ps}
}
@Article{ mangasarian:simple,
author = {O. L. Mangasarian},
title = {A Simple Characterization of Solution Sets of Convex Programs},
journal = {Operations Research Letters},
year = {1988},
volume = {7},
pages = {21--26}
}
@Article{ mangasarian:solution,
author = {O. L. Mangasarian},
title = {Solution of Symmetric Linear Complementarity Problems by Iterative Methods},
journal = {Journal of Optimization Theory and Applications},
year = {1977},
month = aug,
volume = {22},
pages = {465--485}
}
@Article{ mangasarian:stable,
author = {O. L. Mangasarian},
title = {A Stable Theorem of the Alternative: An Extension of the {G}ordan Theorem},
journal = {Linear Algebra and Its Applications},
year = {1981},
volume = {41},
pages = {209--223}
}
@Article{ mangasarian:sufficiency,
author = {O. L. Mangasarian},
title = {Sufficiency of Exact Penalty Minimization},
journal = {SIAM Journal on Control and Optimization},
year = {1985},
month = jan,
volume = {23},
pages = {30--37}
}
@Article{ mangasarian:unconstrained,
author = {O. L. Mangasarian},
title = {Unconstrained {L}agrangians in Nonlinear Programming},
journal = {SIAM Journal on Control and Optimization},
year = {1975},
volume = {13},
pages = {772--791}
}
@Book{ manne.richels:buying,
author = {A. S. Manne and R. G. Richels},
title = {Buying Greenhouse Insurance: The Economics of Carbon Dioxide Emission Limits},
publisher = {MIT Press},
year = {1992},
address = {Cambridge MA}
}
@Article{ manne.richels:global,
author = {A. S. Manne and R. G. Richels},
title = {Global {CO2} Emission Reductions - the Impacts of Rising Energy Costs},
journal = {The Energy Journal},
year = {1991},
volume = {12},
pages = {87--107}
}
@Article{ manne.richels:international,
author = {A. S. Manne and R. G. Richels},
title = {International Trade in Carbon Emission Rights: {A} Decomposition Procedure},
journal = {Economic Review},
year = {1991},
volume = {81},
pages = {135--139}
}
@Article{ manne.rutherford:international,
author = {A. S. Manne and T. F. Rutherford},
title = {International Trade in Oil, Gas and Carbon Emission Rights: An Intertemporal
General Equilibrium Model},
journal = {The Energy Journal},
year = {1993},
volume = {14},
pages = {1--20}
}
@InCollection{ manne:eta-macro,
author = {A. S. Manne},
title = {{ETA}-{M}acro: {A} {M}odel of Energy-Economy Interactions},
booktitle = {Modeling Energy-Economy Interactions},
year = {1977},
editor = {C. J. Hitch},
publisher = {Resources for the Future},
address = {Washington DC}
}
@PhDThesis{ maratos:exact,
author = {N. Maratos},
title = {Exact Penalty Function Algorithms for Finite Dimensional and Control Optimization
Problems},
year = {1978},
school = {Imperial College, University of London}
}
@Article{ marcotte.dussault:note,
author = {P. Marcotte and J.--P. Dussault},
title = {A Note on a Globally Convergent {N}ewton Method for Solving Monotone Variational
Inequalities},
journal = {Operations Research Letters},
year = {1987},
volume = {6},
pages = {35--42}
}
@Article{ marcotte.zhu:exact,
author = {P. Marcotte and D. L. Zhu},
title = {Exact and Inexact Penalty Methods for the Generalized Bilevel Programming
Problem},
journal = {Mathematical Programming},
year = {1996},
volume = {74},
pages = {141--158}
}
@Article{ marcotte:algorithm,
author = {P. Marcotte},
title = {A New Algorithm for Solving Variational Inequalities with Application to the
Traffic Assignment Problem},
journal = {Mathematical Programming},
year = {1985},
volume = {33},
pages = {339--351}
}
@Article{ marcotte:application,
author = {P. Marcotte},
title = {Application of {K}hobotov's Algorithm to Variational Inequalities and Network
Equilibrium Problems},
journal = {Information Systems and Operational Research},
year = {1991},
volume = {29},
pages = {258--270}
}
@Article{ marcotte:network,
author = {P. Marcotte},
title = {Network Design Problem with Congestion Effects: {A} Case of Bilevel Programming},
journal = {Mathematical Programming},
year = {1986},
volume = {34},
pages = {142--162}
}
@Article{ markusen.rutherford.ea:el,
author = {J. R. Markusen and T. F. Rutherford and L. Hunter},
title = {El libre comercio en {A}merica del {N}orte y la produccion de automoviles},
journal = {Cuadernos Economicos de Ice},
year = {1995},
volume = {59},
pages = {57--68}
}
@Article{ markusen.rutherford.ea:trade,
author = {J. R. Markusen and T. F. Rutherford and L. Hunter},
title = {Trade liberalization in a multinational-dominated industry},
journal = {Journal of International Economics},
year = {1995},
volume = {38},
pages = {95--118}
}
@Article{ markusen.rutherford:discrete,
author = {J. R. Markusen and T. F. Rutherford},
title = {Discrete plant-location decisions in an applied general equilibrium model of
trade liberalization},
journal = {Weltwirtshchaftliches Archiv},
year = {1994}
}
@Article{ markusen.wigle:nash,
author = {J. Markusen and R. Wigle},
title = {Nash Equilibrium Tariffs for the {U}nited {S}tates and {C}anada: The Roles of
Country Size, Scale Economies and Capital Mobility},
journal = {Journal of Political Mobility},
year = {1989},
volume = {97},
pages = {368--386}
}
@Article{ marquardt:algorithm,
author = {D. W. Marquardt},
title = {An Algorithm for Least--Squares Estimation of Nonlinear Parameters},
journal = {SIAM Journal on Applied Mathematics},
year = {1963},
volume = {11},
pages = {431--441}
}
@Article{ martello.toth:algorithm,
author = {S. Martello and P. Toth},
title = {A New Algorithm for the 0--1 Knapsack Problem},
journal = {Management Science},
year = {1988},
volume = {34},
pages = {633--644}
}
@InCollection{ martello.toth:algorithms,
author = {S. Martello and P. Toth},
title = {Algorithms for Knapsack Problems},
booktitle = {Surveys in Combinatorial Optimization},
year = {1987},
editor = {S. Martello and G. Laporte and M. Minoux and C. Ribeiro},
publisher = {Annals of Discrete Mathematics 31, North--Holland},
address = {Amsterdam}
}
@Article{ martello.toth:mixture,
author = {S. Martello and P. Toth},
title = {A Mixture of Dynamic Programming and Branch--and--Bound for the Subset--Sum
Problem},
journal = {Management Science},
year = {1984},
volume = {30},
pages = {765--771}
}
@Article{ martello.toth:worst-case,
author = {S. Martello and P. Toth},
title = {Worst--Case Analysis of Greedy Algorithms for the Subset Sum Problem},
journal = {Mathematical Programming},
year = {1984},
volume = {28},
pages = {198--205}
}
@Article{ martinet:regularisation,
author = {Bernard Martinet},
title = {Regularisation d'Inequations Variationelles par Approximations Successives},
journal = {Revue Fran\c{c}aise d'Informatique et Recherche Operationelle},
year = {1970},
volume = {4},
pages = {154--159}
}
@Article{ maskin.tirole:theory,
author = {E. Maskin and J. Tirole},
title = {A theory of Dynamic Oligopoly, {I}: Overview and quantity competition with large
fixed costs},
journal = {Econometrica},
volume = {56},
year = {1988},
pages = {549--569}
}
@Article{ maskin.tirole:theory*1,
author = {E. Maskin and J. Tirole},
title = {A theory of Dynamic Oligopoly, {II}: Price competition, Kinked demand curves, and
Edgeworth cycles},
journal = {Econometrica},
volume = {56},
year = {1988},
pages = {571--579}
}
@Article{ maskus.rutherford.ea:economic,
author = {K. Maskus and T. F. Rutherford and S. Selby},
title = {Economic Implications of Changes in Labor Standards: a Computational Analysis for
{M}exico},
journal = {North American Journal of Economics and Finance},
year = {1996}
}
@Article{ mastor:experimental,
author = {A. A. Mastor},
title = {An Experimental Investigation and Comparative Evaluation of Production Line
Balancing Techniques},
journal = {Management Science},
year = {1970},
volume = {16},
pages = {728--746}
}
@Article{ mathias.pang:error,
author = {R. Mathias and J. S. Pang},
title = {Error bounds for the linear complementarity problem with a {P}-matrix},
journal = {Linear Algebra and Its Applications},
year = {1990},
volume = {132},
pages = {123--136}
}
@Article{ mathiesen:algorithm,
author = {L. Mathiesen},
title = {An Algorithm based on a Sequence of Linear Complementarity Problems applied to a
{W}alrasian Equilibrium Model: An Example},
journal = {Mathematical Programming},
year = {1987},
volume = {37},
pages = {1--18}
}
@Article{ mathiesen:computation,
author = {L. Mathiesen},
title = {Computation of Economic Equilibria by a Sequence of Linear Complementarity
Problems},
journal = {Mathematical Programming Study},
year = {1985},
volume = {23},
pages = {144--162}
}
@Article{ mathiesen:computational,
author = {L. Mathiesen},
title = {Computational Experience in Solving Equilibrium Models by a Sequence of Linear
Complementarity Problems},
journal = {Operations Research},
year = {1985},
volume = {33},
pages = {1225--1250}
}
@Book{ matlab:users,
author = {{MATLAB}},
title = {User's Guide},
year = {1992},
publisher = {The MathWorks, Inc.}
}
@Book{ mcclelland.rummelhart:explorations,
author = {J. L. McClelland and D. E. Rummelhart},
title = {Explorations in Parallel Distributed Processing: {A} Handbook of Models,
Programs, and Exercises},
year = {1987},
publisher = {MIT Press},
address = {Cambridge, Massachusetts}
}
@Article{ mccormick:modification,
author = {G. P. McCormick},
title = {A Modification of {A}rmijo's Step--Size Rule for Negative Curvature},
journal = {Mathematical Programming},
year = {1977},
volume = {13},
pages = {111--115}
}
@Book{ mccormick:nonlinear,
author = {G. P. McCormick},
title = {Nonlinear Programming: Theory, Algorithms and Applications},
year = {1983},
publisher = {John Wiley \& Sons},
address = {New York}
}
@Article{ mcculloch.pitts:logical,
author = {W. McCulloch and W. Pitts},
title = {A Logical Calculus of the Ideas Immanent in Nervous Activity},
journal = {Bulletin of Mathematical Biophysics},
year = {1943},
volume = {7},
pages = {115--133}
}
@TechReport{ mckenna.zenios:optimal,
author = {M. McKenna and S. A. Zenios},
title = {An Optimal Parallel Implementation of a Quadratic Transportation Algorithm},
institution = {Thinking Machines Corporation},
year = {1990},
type = {Working Paper},
address = {Cambridge, MA}
}
@Article{ mckinnon:convergence,
author = {K. I. M. McKinnon},
title = {Convergence of the {N}elder-{M}ead Simplex Method to a Nonstationary Point},
journal = {SIAM Journal on Optimization},
year = {1998},
volume = {9},
pages = {148--158}
}
@Article{ mcshane.monma.ea:implementation,
author = {K. A. McShane and C. L. Monma and D. F. Shanno},
title = {An implementation of a primal-dual interior point method for linear programming},
journal = {ORSA Journal of Computing},
year = {1989},
volume = {1},
pages = {70--83}
}
@PhDThesis{ medhi:decomposition,
author = {D. Medhi},
title = {Decomposition of Structured Large--Scale Optimization Problems and Parallel
Optimization},
school = {Computer Sciences Department, University of Wisconsin},
year = {1987},
address = {Madison, Wisconsin},
note = {Technical Report 718}
}
@Article{ medhi:parallel,
author = {D. Medhi},
title = {Parallel Bundle-Based Decomposition for Large-Scale Structured Mathematical
Programming Problems},
journal = {Annals of Operations Research},
year = {1990},
volume = {22},
pages = {101--127}
}
@Article{ megiddo:complexity,
author = {N. Megiddo},
title = {On the complexity of polyhedral separability},
journal = {Discrete and Computational Geometry},
year = {1988},
volume = {3},
pages = {325--337}
}
@Article{ megiddo:finding,
author = {N. Megiddo},
title = {On Finding Primal-- and Dual--Optimal Bases},
journal = {ORSA Journal on Computing},
year = {1991},
volume = {3},
pages = {63--65}
}
@Article{ mehrotra:implementation,
author = {S. Mehrotra},
title = {On the implementation of a primal-dual interior point method},
journal = {SIAM Journal on Optimization},
year = {1992},
volume = {2},
pages = {575--601}
}
@PhDThesis{ merrill:applications,
author = {O. H. Merrill},
title = {Application and Extensions of an Algorithm that Computes Fixed Points of Upper
Semicontinuous Point to Set Mappings},
year = {1972},
school = {University of Michigan}
}
@Article{ merten.muller:variance,
author = {A. G. Merten and M. E. Muller},
title = {Variance Minimization in Single Machine Sequencing Problems},
journal = {Management Science},
year = {1972},
volume = {18},
pages = {518--528}
}
@TechReport{ meyer:continuity,
author = {R. R. Meyer},
title = {Continuity Properties of Linear Programs},
institution = {Computer Sciences Department, University of Wisconsin},
year = {1979},
address = {Madison, Wisconsin},
number = {373}
}
@Article{ miersemann.mittelmann:continuation,
author = {E. Miersemann and H. D. Mittelmann},
title = {Continuation for Parametrized Nonlinear Variational Inequalities},
journal = {Journal of Computational and Applied Mathematics},
year = {1989},
volume = {26},
pages = {23--34}
}
@Article{ mifflin:semismooth,
author = {R. Mifflin},
title = {Semismooth and semiconvex functions in constrained optimization},
journal = {SIAM Journal on Control and Optimization},
year = {1977},
volume = {15},
pages = {957--972}
}
@Article{ mifflin:stable,
author = {R. Mifflin},
title = {A Stable Method for Solving Certain Constrained Least Squares Problems},
journal = {Mathematical Programming},
vol = {16},
pages = {141--158},
year = {1979}
}
@Book{ miller:survival,
author = {Jr. R. G. Miller},
title = {Survival Analysis},
year = {1981},
publisher = {John Wiley \& Sons},
address = {New York}
}
@Book{ minsky.papert:perceptrons,
author = {M. Minsky and S. Papert},
title = {Perceptrons: An Introduction to Computational Geometry},
year = {1969},
publisher = {MIT Press},
address = {Cambridge, Massachusetts}
}
@Article{ minty:monotone,
author = {G. J. Minty},
title = {Monotone (Nonlinear) Operators in {H}ilbert Space},
journal = {Duke Mathematics Journal},
year = {1962},
volume = {29},
pages = {341--346}
}
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year = {1994},
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number = {1006},
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pages = {340--357}
}
@Article{ paige.saunders:lsqr,
author = {C. C. Paige and M. A. Saunders},
title = {{LSQR}: An Algorithm for Sparse Linear Equations and Sparse Least Squares},
journal = {{ACM} Transactions on Mathematical Software},
year = {1982},
volume = {8},
pages = {43--71}
}
@Article{ paige.saunders:solution,
author = {C. C. Paige and M. A. Saunders},
title = {Solution of Sparse Indefinite Systems of Linear Equations},
journal = {SIAM Journal on Numerical Analysis},
year = {1975},
volume = {12},
pages = {617--629}
}
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author = {F. Palacios--Gomez and L. Lasdon and M. Engquist},
title = {Nonlinear Optimization by Successive Linear Programming},
journal = {Management Science},
year = {1982},
volume = {28},
pages = {1106--1120}
}
@Article{ palomares.mangasarian:superlinearly,
author = {U. M. Garcia Palomares and O. L. Mangasarian},
title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained
Optimization Problems},
journal = {Mathematical Programming},
year = {1976},
volume = {11},
pages = {1--13}
}
@Article{ panagiotopoulos.al-fahed:robot,
author = {P. D. Panagiotopoulos and A. M. Al-Fahed},
title = {Robot Hand Grasping and Related Problems: Optimal Contol and Identification},
journal = {The International Journal of Robotics Research},
year = {1994},
volume = {13},
pages = {127--136}
}
@Book{ panagiotopoulos:hemivariational,
author = {P. D. Panagiotopoulos},
title = {Hemivariational Inequalities},
publisher = {Springer-Verlag},
address = {Berlin},
year = {1993}
}
@Book{ panagiotopoulos:inequality,
author = {P. D. Panagiotopoulos},
title = {Inequality Problems in Mechanics and Applications},
publisher = {Birkh{\"{a}}user},
address = {Boston},
year = {1985}
}
@Article{ pang.chan:iterative,
author = {J. S. Pang and D. Chan},
title = {Iterative Methods for Variational and Complementarity Problems},
journal = {Mathematical Programming},
year = {1982},
volume = {24},
pages = {284--313}
}
@Article{ pang.gabriel:nesqp,
author = {J. S. Pang and S. A. Gabriel},
title = {{NE/SQP}: {A} Robust Algorithm for the Nonlinear Complementarity Problem},
journal = {Mathematical Programming},
year = {1993},
volume = {60},
pages = {295--338}
}
@Article{ pang.han.ea:minimization,
author = {J. S. Pang and S.--P. Han and N. Rangaraj},
title = {Minimization of Locally {L}ipschitzian Functions},
journal = {SIAM Journal on Optimization},
year = {1991},
volume = {1},
pages = {57--82}
}
@Article{ pang.qi:nonsmooth,
author = {J. S. Pang and L. Qi},
title = {Nonsmooth Equations: Motivation and Algorithms},
journal = {SIAM Journal on Optimization},
year = {1993},
volume = {3},
pages = {443--465}
}
@Article{ pang.trinkle.ea:complementarity,
author = {J. S. Pang and J. C. Trinkle and G. Lo},
title = {A Complementarity Approach to a Quasistatic Multi-Rigid-Body Contact Problem},
journal = {Computational Optimization and Applications},
volume = {5},
pages = {97--138},
year = {1996}
}
@Article{ pang.trinkle:complementarity,
author = {J. S. Pang and J. C. Trinkle},
title = {Complementarity Formulations and Existence of Solutions of Multi-Rigid-Body
Contact Problems with {C}oulomb Friction},
year = {1996},
journal = {Mathematical Programming},
volume = {73},
pages = {199--226}
}
@TechReport{ pang.wang:embedding,
author = {J. S. Pang and Z. P. Wang},
title = {Embedding Methods for Variational Inequality and Nonlinear Complementarity
Problems},
institution = {Department of Mathematical Sciences, The Johns Hopkins University},
year = {1990},
address = {Baltimore, Maryland}
}
@TechReport{ pang.yang:parallel,
author = {J. S. Pang and J. M. Yang},
title = {Parallel {N}ewton Methods for the Nonlinear Complementarity Problem},
institution = {Department of Mathematical Sciences, The Johns Hopkins University},
year = {1987},
address = {Baltimore, Maryland},
type = {Manuscript}
}
@Article{ pang.yu:linearized,
author = {J. S. Pang and C. S. Yu},
title = {Linearized Simplicial Decomposition Methods for Computing Traffic Equilibria on
Networks},
journal = {Networks},
volume = {14},
pages = {427--438},
year = {1984}
}
@Article{ pang:b-differentiable,
author = {J. S. Pang},
title = {A {B}--Differentiable Equation Based, Globally and Locally Quadratically
Convergent Algorithm for Nonlinear Programs, Complementarity and Variational
Inequality Problems},
journal = {Mathematical Programming},
year = {1991},
volume = {51},
pages = {101--132}
}
@InCollection{ pang:complementarity,
author = {J. S. Pang},
title = {Complementarity Problems},
booktitle = {Handbook in Global Optimization},
publisher = {Kluwer Academic Publishers},
year = {1994},
editor = {R. Horst and P. Pardalos},
address = {Boston}
}
@Article{ pang:convergence,
author = {J. S. Pang},
title = {On the Convergence of a Basic Iterative Method for the Implicit Complementarity
Problem},
journal = {Journal of Optimization Theory and Applications},
year = {1982},
volume = {37},
pages = {149--162}
}
@Article{ pang:convergence*1,
author = {J. S. Pang},
title = {Convergence of Splitting and {N}ewton Methods for Complementarity Problems: An
Application of some Sensitivity Results},
journal = {Mathematical Programming},
year = {1993},
volume = {58},
pages = {149--160}
}
@Article{ pang:inexact,
author = {J. S. Pang},
title = {Inexact {N}ewton Methods for the Nonlinear Complementarity Problem},
journal = {Mathematical Programming},
year = {1986},
volume = {36},
pages = {54--71}
}
@Article{ pang:more,
author = {J. S. Pang},
title = {More Results on the Convergence of Iterative Methods for the Symmetric Linear
Complementarity Problem},
journal = {Journal of Optimization Theory and Applications},
year = {1986},
volume = {49},
pages = {107--134}
}
@Article{ pang:more*1,
author = {J. S. Pang},
title = {More Results on the Convergence of Iterative Methods for Symmetric Linear
Complementarity Problems},
journal = {Journal of Optimization Theory and Applications},
year = {1986},
volume = {49},
pages = {107--134}
}
@Article{ pang:necessary,
author = {J. S. Pang},
title = {Necessary and Sufficient Conditions for the Convergence of Iterative Methods for
the Linear Complementarity Problem},
journal = {Journal of Optimization Theory and Applications},
year = {1984},
volume = {42},
pages = {1--17}
}
@Article{ pang:newtons,
author = {J. S. Pang},
title = {{N}ewton's Method for {B}--Differentiable Equations},
journal = {Mathematics of Operations Research},
year = {1990},
volume = {15},
pages = {311--341}
}
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author = {J. S. Pang},
title = {A Posteriori Error Bound for the Linearly--Constrained Variational Inequality
Problem},
journal = {Mathematics of Operations Research},
year = {1987},
volume = {12},
pages = {474--484}
}
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author = {J. F. A. D. Pantoja and D. Q. Mayne},
title = {Sequential Quadratic Programming Algorithm for Discrete Optimal Control Problems
with Control Inequality Constraints},
journal = {International Journal on Control},
year = {1991},
volume = {53},
pages = {823--836}
}
@Book{ papadimitriou.steiglitz:combinatorial,
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title = {Combinatorial Optimization: Algorithms and Complexity},
year = {1982},
publisher = {Prentice-Hall, Inc},
address = {Englewood Cliffs, New Jersey}
}
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Reckwerdt},
title = {Investigation of the convolution method for polyenergetic spectra},
journal = {Medical Physics},
year = {1993},
volume = {20},
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pages = {1327--1336}
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@Article{ parisot:resolution,
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title = {{R}\'{e}solution Num\'{e}rique Approach\'{e}e du Probl\`{e}me de Programmation
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pages = {227--259}
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@Article{ parker.cave.ea:comparison,
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year = {1985},
volume = {175},
pages = {231--237}
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@InProceedings{ parker:optimal,
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title = {Optimal Algorithms for Adaptive Networks: Second Order Direct Propagation, and
Second Order Hebbian Learning},
booktitle = {Proceedings of the IEEE First International Conference on Neural Networks: Volume
II},
year = {1987},
address = {San Diego:IEEE},
pages = {593--600}
}
@Book{ pascali.sburlan:nonlinear,
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title = {Nonlinear Mappings of Monotone Type},
publisher = {Editura Academeie},
year = {1978}
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author = {G. B. Passty},
title = {Ergodic convergence to a zero of the sum of monotone operators in {H}ilbert
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journal = {Journal of Mathematical Analysis and Applications},
year = {1979},
volume = {72},
pages = {383--390}
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@Article{ peaceman.rachford:numerical,
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year = {1955},
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pages = {28--41}
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@Book{ peck.tiesberg:global,
author = {S. Peck and T. Tiesberg},
title = {Global Warming Uncertainties and the Value of Information: An Analysis Using
{CETA}},
publisher = {The Electric Power Institute},
year = {1992},
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@TechReport{ peng:convexity,
author = {J. -M. Peng},
title = {The Convexity of the Implicit {L}agrangian},
institution = {State Key Laboratory of Scientific and Engineering Computing, Academic Sinica},
year = {1995},
type = {Technical Report},
address = {Beijing}
}
@Article{ peng:equivalence,
author = {J. -M. Peng},
title = {Equivalence of Variational Inequality Problems to Unconstrained Optimization},
journal = {Mathematical Programming},
year = {1997},
volume = {78},
pages = {347--356}
}
@Article{ pennisi:taking,
author = {E. Pennisi},
title = {Taking a structured approach to understanding proteins},
journal = {Science},
year = {1998},
volume = {279},
pages = {978--979}
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author = {J. P. Penot},
title = {On regularity conditions in mathematical programming},
journal = {Mathematical Programming Study},
year = {1982},
volume = {17},
pages = {28--66}
}
@Book{ perez:principles,
author = {C. A. Perez and L. W. Brady},
title = {Principles and practice of radiotherapy},
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year = {1998},
address = {Philadelphia},
edition = {3rd}
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title = {International Trade in Carbon Emission Rights and Basic Materials: General
Equilibrium Calculations for 2020},
journal = {Scandinavian Journal of Economics},
year = {1993}
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author = {C. Perroni and T. Rutherford},
title = {Regular Flexibility of Nested {CES} Functions},
journal = {European Economic Review},
year = {1995},
volume = {39},
pages = {335--343}
}
@InCollection{ perroni.wigle:environmental,
author = {C. Perroni and R. M. Wigle},
title = {Environmental Policy Modeling},
booktitle = {Global Trade Analysis: Modeling and Applications},
publisher = {Cambridge University Press},
year = {1996},
editor = {T. Hertel}
}
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journal = {SIAM Review},
year = {1973},
volume = {15},
pages = {639--654}
}
@PhDThesis{ petersson:optimization,
author = {J. Petersson},
title = {Optimization of Structures in Unilateral Contact},
type = {{L}ink{\"o}ping Studies in Science and Technology, Dissertations},
number = {397},
school = {Division of Mechanics, Department of Mechanical Engineering, Link{\"o}ping
University},
address = {Link{\"o}ping, Sweden},
year = {1995}
}
@Book{ petri:modelling,
author = {P. Petri},
title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence},
publisher = {Harvard University Press},
year = {1984}
}
@InProceedings{ petrzykowski:application,
author = {T. Petrzykowski},
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year = {1962},
publisher = {North--Holland},
address = {Amsterdam},
pages = {185--189}
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crossref = {grefenstette:genetic},
author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette},
title = {A Parallel Genetic Algorithm},
pages = {155--161}
}
@InProceedings{ pettey.leuze:theoretical,
crossref = {schaeffer:third},
author = {C. C. Pettey and M. R. Leuze},
title = {A Theoretical Investigation of a Parallel Genetic Algorithm},
pages = {398--405}
}
@Book{ pfeiffer.glocker:multibody,
author = {F. Pfeiffer and C. Glocker},
title = {Multibody Dynamics with Unilateral Contact},
year = {1996},
publisher = {John Wiley \& Sons}
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@TechReport{ pierro.iusem:convergence,
author = {A. R. de Pierro and A. N. Iusem},
title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite
Linear Complementarity Problems},
institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao},
year = {1990},
address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil}
}
@InCollection{ pillo.grippo.ea:class,
author = {G. Di Pillo and L. Grippo and F. Lampariello},
title = {A Class of Methods for the Solution of Optimization Problems with Inequalities},
booktitle = {System Modelling and Optimization},
year = {1981},
editor = {R. F. Drenick and F. Kozin},
publisher = {Springer-Verlag},
address = {Berlin}
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author = {G. Di Pillo and L. Grippo},
title = {An Augmented {L}agrangian for Inequality Constraints in Nonlinear Programming
Problems},
journal = {Journal of Optimization Theory and Applications},
year = {1982},
volume = {36},
pages = {495--519}
}
@Article{ pillo.grippo:class,
author = {G. Di Pillo and L. Grippo},
title = {A New Class of Augmented {L}agrangians in Nonlinear Programming},
journal = {SIAM Journal on Control and Optimization},
year = {1979},
volume = {17},
pages = {618--628}
}
@Article{ pillo.grippo:continuously,
author = {G. Di Pillo and L. Grippo},
title = {A Continuously Differentiable Exact Penalty Function for Nonlinear Programming
Problems with Inequality Constraints},
journal = {SIAM Journal on Control and Optimization},
year = {1985},
volume = {23},
pages = {72--84}
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@Article{ pillo.grippo:exact,
author = {G. Di Pillo and L. Grippo},
title = {An Exact Penalty Method with Global Convergence Properties for Nonlinear
Programming Problems},
journal = {Mathematical Programming},
year = {1986},
volume = {36},
pages = {1--18}
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@InProceedings{ plambeck.fu.ea:throughput,
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editor = {J. Schoen},
year = {1993},
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pages = {70--75}
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author = {E. L. Plambeck and B. --R. Fu and S.M. Robinson and R. Suri},
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journal = {Mathematical Programming},
year = {1996},
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pages = {137--176}
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author = {J. Platt},
title = {Sequential Minimal Optimization: A Fast Algorithm for Training Support Vector
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editor = {Bernhard {Sch\"olkopf} and Christopher J. C. Burges and Alexander J. Smola},
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publisher = {MIT Press},
pages = {185-208},
year = {1999}
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@Book{ poincare:sur,
author = {H. Poincar\'{e}},
title = {Sur les Courbes {D}\'{e}fin\'{e}es par une \'{E}quation Differentielle {I}},
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@Book{ polak:computational,
author = {E. Polak},
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year = {1971},
publisher = {Academic Press},
address = {New York}
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pages = {337--349}
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pages = {740--751},
note = {(Russian)}
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year = {1973},
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pages = {42--58}
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@Book{ polyak:introduction,
author = {B. T. Polyak},
title = {Introduction to Optimization},
year = {1987},
publisher = {Optimization Software, Inc.},
address = {Publications Division, New York}
}
@Unpublished{ polyak:methods,
author = {R. A. Polyak},
title = {On the Methods of Centers},
year = {1988},
note = {Unpublished manuscript}
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@Unpublished{ polyak:sharp,
author = {B. T. Polyak},
title = {Sharp Minima},
year = {1979},
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Problems with Constraints},
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Programming},
year = {1982},
address = {Bonn}
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@Article{ polychronopoulos.tsitsiklis:analysis,
author = {G. H. Polychronopoulos and J. N. Tsitsiklis},
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pages = {133--143}
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author = {F. A. Potra and J. F. Bonnans},
title = {Infeasible path following algorithms for linear complementarity problems},
institution = {INRIA},
year = {1994},
month = dec,
number = {RR--2445},
type = {Research Report}
}
@Article{ potra.sheng:large-step,
author = {F. A. Potra and R. Sheng},
title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}},
year = {1997},
journal = {SIAM Journal on Optimization},
volume = {7},
pages = {318--335}
}
@Article{ potra:infeasible,
author = {F. A. Potra},
title = {An infeasible interior-point predictor-corrector algorithm for linear
programming},
journal = {SIAM Journal on Optimization},
year = {1996},
volume = {6},
pages = {19--32}
}
@TechReport{ potra:onl,
author = {F. A. Potra},
title = {An ${O}(n{L})$ infeasible--interior--point algorithm for {LCP} with quadratic
convergence.},
institution = {Department of Mathematics, The University of Iowa},
address = {Iowa City, Iowa},
year = {1994},
number = {50},
type = {Reports on Computational Mathematics}
}
@TechReport{ potra:predictor-corrector,
author = {F. A. Potra},
title = {On a predictor-corrector method for solving linear programs from infeasible
starting points},
institution = {Department of Mathematics, University of Iowa},
address = {Iowa City, Iowa},
year = {1992},
number = {34},
type = {Reports on Computational Mathematics}
}
@TechReport{ potra:quadratically,
author = {F. A. Potra},
title = {A quadratically convergent infeasible interior-point algorithm for linear
programming},
institution = {Department of Mathematics, University of Iowa},
year = {1992},
number = {28},
address = {Iowa City, Iowa},
month = jul
}
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author = {M. J. D. Powell},
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Optimization Calculations},
crossref = {mangasarian.meyer.ea:nonlinear*3},
pages = {27--63}
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@InProceedings{ powell:direct,
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publisher = {Kluwer Academic Publishers},
pages = {51--67},
address = {Dordrecht, The Netherlands}
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@InCollection{ powell:hybrid,
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@TechReport{ powell:karmarkars,
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title = {{K}armarkar's algorithm: a view from nonlinear programming},
institution = {Department of Applied Mathematics and Theoretical Physics, University of
Cambridge},
year = {1989},
month = nov,
address = {Cambridge, CB3 9EW, England}
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title = {Stochastic Programming},
publisher = {Kluwer Academic Publishers},
year = {1995},
address = {Dordrecht, The Netherlands}
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@Book{ press.flannery.ea:numerical,
author = {William H. Press and Brian P. Flannery and Saul A. Teukolsky and William T.
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pages = {67--85}
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publisher = {Springer-Verlag},
year = {1995},
editor = {D. G. Feitelson and L. Rudolph},
volume = {949},
series = {Lecture Notes in Computer Science}
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author = {J. C. Pruyne},
title = {Resource Management Services for Parallel Applications},
school = {University of Wisconsin--Madison},
year = {1996},
address = {Madison, Wisconsin}
}
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author = {L. Qi and X. Chen},
title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations},
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year = {1993},
annote = {revised},
address = {Sydney}
}
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author = {L. Qi and H. Jiang},
title = {Semismooth {K}arush--{K}uhn--{T}ucker Equations and Convergence Analysis of
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pages = {301--325},
year = {1997}
}
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author = {H. -D. Qi and J. -M. Peng},
title = {A New Unconstrained Optimization Approach for Nonlinear Complementarity
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institution = {State Key Laboratory of Scientific and Engineering Computing, Academic Sinica},
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address = {Beijing}
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address = {Dordrecht}
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year = {1993},
volume = {58},
pages = {353--368}
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year = {1993},
volume = {18},
pages = {227--244}
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author = {L. Qi},
title = {Regular pseudo-smooth {NCP} and {BVIP} functions and globally and quadratically
convergent generalized {N}ewton methods for complementarity and variational
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institution = {School of Mathematics, University of New South Wales},
year = {1997},
type = {Applied Mathematics Report},
number = {AMR 97/14},
address = {Sydney, Australia}
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pages = {671--677}
}
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volume = {22},
pages = {1041--1050},
year = {1994}
}
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Path Search},
journal = {Mathematics of Operations Research},
year = {1994},
volume = {19},
pages = {352--389}
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@InProceedings{ ralph:piecewise,
author = {D. Ralph},
title = {A Piecewise Sequential Quadratic Programming Method for Mathematical Programs
with Linear Complementarity Constraints},
booktitle = {Proceedings of the Seventh Conference on Computational Techniques and
Applications (CTAC95)},
year = {1996}
}
@PhDThesis{ raman:integration,
author = {R. Raman},
title = {Integration of logic and heuristic knowledge in discrete optimization techniques
for process systems.},
address = {Pittsburgh, Pennsylvania},
year = {1993},
school = {Department of Chemical Engineering, Carnegie Mellon University}
}
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author = {Narayan Rangaraj},
title = {Nonsmooth Optimization: Algorithms and Applications},
year = {1990},
address = {Baltimore, MD},
school = {Department of Mathematical Sciences, The Johns Hopkins University}
}
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year = {1997},
editor = {D. D. Leavitt and G. Starkshall},
publisher = {Medical Physics Publishing},
address = {St. Louis, Missouri},
pages = {420--422}
}
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journal = {Mathematical Programming},
year = {1982},
volume = {24},
pages = {55--69}
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title = {Combinatorial Algorithms: Theory and Practice},
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address = {Englewood Cliffs, New Jersey}
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author = {J. A. Reinoza},
title = {A Degree for Generalized Equations},
year = {1979},
address = {Madison, Wisconsin},
school = {University of Wisconsin}
}
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year = {1985},
volume = {31},
pages = {307--320}
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author = {J. Ren},
title = {Computable Error Bounds in Mathematical Programming},
school = {Computer Sciences Department, University of Wisconsin},
year = {1993},
address = {Madison, Wisconsin},
note = {Technical Report 1173}
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title = {A Polynomial--Time Algorithm, based on {N}ewton's method, for Linear
Programming},
journal = {Mathematical Programming},
year = {1988},
volume = {40},
pages = {59--94}
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author = {H. Robbins and S. Monro},
title = {A Stochastic Approximation Method},
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year = {1951},
volume = {22},
pages = {400--407}
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author = {S. M. Robinson},
title = {Analysis of Sample-Path Optimization},
journal = {Mathematics of Operations Research},
year = {1996},
volume = {21},
pages = {513--528}
}
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author = {S. M. Robinson},
title = {Bundle-Based Decomposition: Conditions for Convergence},
booktitle = {Analyse Non Lin\'{e}aire},
year = {1989},
editor = {H. Attouch and J. P. Aubin and F. Clarke and I. Ekeland},
publisher = {Gauthier-Villaars},
address = {Paris},
pages = {435--447}
}
@InCollection{ robinson:bundle-based*1,
author = {S. M. Robinson},
title = {Bundle-Based Decomposition: Description and Preliminary Results},
booktitle = {System Modeling and Optimization},
year = {1986},
editor = {A Pr\'{e}kopa and J. Szelezc\'{a}n and B. Straazicky},
publisher = {Springer-Verlag},
address = {Berlin},
pages = {751--756},
volume = {84},
series = {Lecture Notes in Control and Information Sciences}
}
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author = {S. M. Robinson},
title = {Some Continuity Properties of Polyhedral Multifunctions},
journal = {Mathematical Programming Study},
year = {1981},
volume = {14},
pages = {206--214}
}
@Article{ robinson:extension,
author = {S. M. Robinson},
title = {Extension of {N}ewton's Method to Nonlinear Functions with Values in a Cone},
journal = {Numerische Mathematik},
year = {1972},
volume = {19},
pages = {341--347}
}
@InCollection{ robinson:generalized,
crossref = {bachem.grotschel.ea:mathematical},
author = {S. M. Robinson},
title = {Generalized Equations},
pages = {346--367}
}
@Article{ robinson:generalized*1,
author = {S. M. Robinson},
title = {Generalized Equations and their Solution: {P}art {I}: Basic Theory},
journal = {Mathematical Programming Study},
year = {1979},
volume = {10},
pages = {128--141}
}
@InCollection{ robinson:homeomorphism,
author = {S. M. Robinson},
title = {Homeomorphism Conditions for Normal Maps of Polyhedra},
booktitle = {Optimization and Nonlinear Analysis},
year = {1992},
editor = {A. Ioffe and M. Marcus and S. Reich},
publisher = {Longman},
address = {Harlow, Essex, England},
pages = {240--248},
series = {Pitman Research Notes in Mathematics Series No. 244}
}
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author = {S. M. Robinson},
title = {An Implicit--Function Theorem for a Class of Nonsmooth Functions},
journal = {Mathematics of Operations Research},
year = {1991},
volume = {16},
pages = {292--309}
}
@Article{ robinson:local*1,
author = {S. M. Robinson},
title = {Local Epi--Continuity and Local Optimization},
journal = {Mathematical Programming},
year = {1987},
volume = {37},
pages = {208--222}
}
@Article{ robinson:local*2,
author = {S. M. Robinson},
title = {Local Structure of Feasible Sets in Nonlinear Programming, {P}art~{II}:
Nondegeneracy},
journal = {Mathematical Programming Study},
year = {1984},
volume = {22},
pages = {217--230}
}
@Article{ robinson:local*3,
author = {S. M. Robinson},
title = {Local Structure of Feasible Sets in Nonlinear Programming, {P}art~{III}:
Stability and Sensitivity},
journal = {Mathematical Programming Study},
year = {1987},
volume = {30},
pages = {45--66}
}
@Article{ robinson:mathematical,
author = {S. M. Robinson},
title = {Mathematical Foundations of Nonsmooth Embedding Methods},
journal = {Mathematical Programming},
year = {1990},
volume = {48},
pages = {221--229}
}
@Article{ robinson:newtons,
author = {S. M. Robinson},
title = {{N}ewton's Method for a Class of Nonsmooth Functions},
journal = {Set Valued Analysis},
year = {1994},
volume = {2},
pages = {291--305}
}
@Article{ robinson:nonsingularity,
author = {S. M. Robinson},
title = {Nonsingularity and Symmetry for Linear Normal Maps},
journal = {Mathematical Programming},
year = {1993},
volume = {62},
pages = {415--425}
}
@InCollection{ robinson:nonsmooth,
author = {S. M. Robinson},
title = {Nonsmooth Continuation for Generalized Equations},
year = {1997},
pages = {282--291},
editors = {P. Gritzmann and R. Horst and E. Sachs and R. Tichatschke},
booktitle = {Recent Advances in Optimization},
series = {Lecture Notes in Economics and Mathematical Systems},
volume = {452},
publisher = {Springer-Verlag},
address = {Heidelberg}
}
@Article{ robinson:normal,
author = {S. M. Robinson},
title = {Normal Maps Induced by Linear Transformations},
journal = {Mathematics of Operations Research},
year = {1992},
volume = {17},
pages = {691--714}
}
@Article{ robinson:normed,
author = {S. M. Robinson},
title = {Normed Convex Processes},
journal = {Transactions of the American Mathematical Society},
year = {1972},
volume = {174},
pages = {127--140}
}
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author = {S. M. Robinson},
title = {A reduction method for variational inequalities},
journal = {Mathematical Programming},
year = {1998},
volume = {80},
pages = {161--169}
}
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author = {S. M. Robinson},
title = {Regularity and stability for convex multivalued functions},
journal = {Mathematics of Operations Research},
year = {1976},
volume = {1},
pages = {130--143}
}
@Unpublished{ robinson:shadow,
author = {S. M. Robinson},
title = {Shadow {JUNK} for biblio file},
year = {1800}
}
@Article{ robinson:shadow*1,
author = {S. M. Robinson},
title = {Shadow Prices for Measures of Effectiveness {I}: Linear Model},
journal = {Operations Research},
year = {1993},
volume = {41},
pages = {518--535}
}
@Article{ robinson:shadow*2,
author = {S. M. Robinson},
title = {Shadow Prices for Measures of Effectiveness {II}: General Model},
journal = {Operations Research},
year = {1993},
volume = {41},
pages = {536--548}
}
@Unpublished{ robinson:stability,
author = {S. M. Robinson},
title = {Stability {JUNK} for biblio file},
year = {1800}
}
@Article{ robinson:stability*1,
author = {S. M. Robinson},
title = {Stability theory for systems of inequalities, {P}art {I}: linear systems},
journal = {SIAM Journal on Numerical Analysis},
year = {1975},
volume = {12},
pages = {754--769}
}
@Article{ robinson:stability*2,
author = {S. M. Robinson},
title = {Stability theory for systems of inequalities, {P}art {II}: Differentiable
Nonlinear Systems},
journal = {SIAM Journal on Numerical Analysis},
year = {1976},
volume = {13},
pages = {497--513}
}
@Article{ robinson:strongly,
author = {S. M. Robinson},
title = {Strongly Regular Generalized Equations},
journal = {Mathematics of Operations Research},
year = {1980},
volume = {5},
pages = {43--62}
}
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author = {R. T. Rockafellar and R. J.--B. Wets},
title = {Generalized Linear-Quadratic Problems of Deterministic and Stochastic Optimal
Control in Discrete Time},
journal = {SIAM Journal on Control and Optimization},
year = {1990},
volume = {28},
pages = {810--822}
}
@Article{ rockafellar.wets:lagrangian,
author = {R. T. Rockafellar and R. J.--B. Wets},
title = {A {L}agrangian Finite Generation Technique for Solving Linear-Quadratic Problems
in Stochastic Programming},
journal = {Mathematical Programming Study},
year = {1986},
volume = {28},
pages = {63--93}
}
@InCollection{ rockafellar.wets:linear-quadratic,
author = {R. T. Rockafellar and R. J.--B. Wets},
title = {Linear-Quadratic Programming Problems with Stochastic Penalties: the Finite
Generation Algorithm},
booktitle = {Stochastic Optimization},
publisher = {Springer-Verlag},
year = {1987},
editor = {V. I. Arkin and A. Shiraer and R. J.--B. Wets},
series = {Lecture Notes in Control and Information Sciences, IIASA Series No. 81},
pages = {545--560},
address = {New York, Berlin}
}
@Article{ rockafellar.wets:scenarios,
author = {R. T. Rockafellar and R. J.--B. Wets},
title = {Scenarios and Policy Aggregation in Optimization under Uncertainty},
journal = {Mathematics of Operations Research},
year = {1991},
volume = {10},
pages = {119--147}
}
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author = {R. T. Rockafellar},
title = {New Applications of Duality in Convex Programming},
booktitle = {Proceedings of the Fourth Conference on Probability},
year = {1971},
address = {Brasov, Romania}
}
@Article{ rockafellar:augmented,
author = {R. T. Rockafellar},
title = {Augmented {L}agrange Multiplier Functions and Duality in Nonconvex Programming},
journal = {SIAM Journal on Control and Optimization},
year = {1974},
volume = {12},
pages = {268--285}
}
@Article{ rockafellar:augmented*1,
author = {R. T. Rockafellar},
title = {Augmented {L}agrangians and Applications of the Proximal Point Algorithm in
Convex Programming},
journal = {Mathematics of Operations Research},
year = {1976},
volume = {1},
pages = {97--116}
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author = {R. T. Rockafellar},
title = {Characterization of the subdifferentials of convex functions},
journal = {Pacific Journal of Mathematics},
year = {1966},
volume = {17},
number = {3},
pages = {497--510}
}
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author = {R. T. Rockafellar},
title = {Computational Schemes for Large--Scale Problems in Extended Linear--Quadratic
Programming},
journal = {Mathematical Programming},
year = {1990},
volume = {48},
pages = {447--474}
}
@Book{ rockafellar:conjugate,
author = {R. T. Rockafellar},
title = {Conjugate Duality and Optimization},
year = {1974},
publisher = {SIAM},
address = {Philadelphia, Pennsylvania},
volume = {16},
series = {Conference Board of the Mathematical Sciences}
}
@Book{ rockafellar:convex,
author = {R. T. Rockafellar},
title = {Convex Analysis},
year = {1970},
publisher = {Princeton University Press},
address = {Princeton, New Jersey}
}
@Article{ rockafellar:first-,
author = {R. T. Rockafellar},
title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming},
journal = {Transactions of the American Mathematical Society},
year = {1988},
volume = {307},
pages = {75--108}
}
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author = {R. T. Rockafellar},
title = {A Generalized Approach to Linear-Quadratic Programming},
booktitle = {Proceedings of the International Conference on Numerical Optimization and
Applications},
year = {1986},
pages = {58--66},
note = {(Xi'an, China)}
}
@InProceedings{ rockafellar:generalized*1,
crossref = {bachem.grotschel.ea:mathematical},
author = {R. T. Rockafellar},
title = {Generalized Subgradients in Mathematical Programming},
pages = {368--390}
}
@InCollection{ rockafellar:large-scale,
author = {R. T. Rockafellar},
title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization},
booktitle = {Advances in Numerical Partial Differential Equations and Optimization},
chapter = {15},
year = {1991},
editor = {S. Gomez and J. P. Hennart and R. A. Tapia},
publisher = {SIAM Publications},
pages = {247--261}
}
@Article{ rockafellar:linear-quadratic,
author = {R. T. Rockafellar},
title = {Linear-Quadratic Programming and Optimal Control},
journal = {SIAM Journal on Control and Optimization},
year = {1987},
volume = {25},
pages = {781--814}
}
@Article{ rockafellar:maximality,
author = {R. T. Rockafellar},
title = {On the Maximality of Sums of Nonlinear Monotone Operators},
journal = {Transactions of the American Mathematical Society},
year = {1970},
volume = {149},
pages = {75--88}
}
@InCollection{ rockafellar:monotone,
author = {R. T. Rockafellar},
title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming},
crossref = {mangasarian.meyer.ea:nonlinear*3},
pages = {1--26}
}
@Article{ rockafellar:monotone*1,
author = {R. T. Rockafellar},
title = {Monotone Operators and the Proximal Point Algorithm},
journal = {SIAM Journal on Control and Optimization},
year = {1976},
volume = {14},
pages = {877--898}
}
@Article{ rockafellar:multiplier,
author = {R. T. Rockafellar},
title = {The Multiplier Method of {H}estenes and {P}owell Applied to Convex Programming},
journal = {Journal of Optimization Theory and Applications},
year = {1973},
volume = {12},
pages = {555--562}
}
@Article{ rockafellar:multistage,
author = {R. T. Rockafellar},
title = {Multistage Convex Programming and Discrete-Time Optimal Control},
journal = {Control and Cybernetics},
year = {1988},
volume = {17},
number = {2-3},
pages = {225--245}
}
@Book{ rockafellar:network,
author = {R. T. Rockafellar},
title = {Network Flows and Monotropic Optimization},
publisher = {John Wiley},
year = {1984},
address = {New York}
}
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author = {H. C. Rodrigues},
title = {A mixed variational formulation for shape optimization of solids with contact
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journal = {Structural Optimization},
volume = {6},
year = {1993},
pages = {19--28}
}
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author = {J. F. Rodrigues},
title = {Obstacle Problems in Mathematical Physics},
publisher = {Elsevier Publishing Company},
address = {Amsterdam},
year = {1987}
}
@Book{ roos.terlaky.ea:theory,
author = {C. Roos and T. Terlaky and J.--Ph. Vial},
title = {Theory and Algorithms for Linear Optimization: An Interior-Point Approach},
publisher = {John Wiley \& Sons},
year = {1997},
address = {Chichester}
}
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author = {C. H. Rosa},
title = {A Decomposition Technique for Equilibrium Programming under Uncertainty},
institution = {IIASA},
year = {1996},
number = {WP-96-013},
address = {A-2361 Laxenburg, Austria}
}
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author = {I. Rosen and R. Lane and S. Morrill and J. Belli},
title = {Treatment Plan Optimization Using Linear Programming},
journal = {Medical Physics},
year = {1990},
volume = {18},
number = {2},
pages = {141--152}
}
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author = {F. Rosenblatt},
title = {The perceptron--a perceiving and recognizing automaton},
institution = {Cornell Aeronautical Laboratory},
year = {1957},
month = jan,
address = {Ithaca, New York},
number = {85-460-1}
}
@Book{ rosenblatt:principles,
author = {F. Rosenblatt},
title = {Principles of Neurodynamics},
year = {1962},
publisher = {Spartan Books},
address = {New York}
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@InProceedings{ rosenblatt:two,
author = {F. Rosenblatt},
title = {Two theorems of statistical separability in the perceptron},
booktitle = {Proceedings of Symposium Held at National Physical Laboratory, November 1958},
year = {1959},
publisher = {{HMS} Stationery Office},
address = {London},
volume = {1}
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author = {H. H. Rosenbrock},
title = {Automatic Method for Finding the Greatest or Least Value of a Function},
journal = {Computer Journal},
year = {1960},
volume = {3},
pages = {175--184}
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author = {A. Roy and S. Mukhopadhyay},
title = {Pattern Classification Using Linear Programming},
journal = {ORSA Journal on Computing},
year = {1990},
volume = {3},
pages = {66--80}
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@Book{ rubinstein:monte,
author = {R. Rubinstein},
title = {Monte Carlo Optimization, Simulation, and Sensitivity Analysis of Queueing
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publisher = {Wiley},
address = {New York, NY},
year = {1986}
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@Article{ ruchala.olivera.ea:comparison,
author = {K. J. Ruchala and G. H. Olivera and T. R. Mackie},
title = {A Comparison of Maximum-Likelihood and Iterative Filtered Backprojection
Reconstruction Algorithms for Megavoltage {CT} on a Tomotherapy System},
journal = {Physics in Medicine and Biology, forthcoming},
year = {1999}
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author = {W. Rudin},
title = {Principles of Mathematical Analysis},
year = {1976},
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edition = {Third}
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@Book{ rudin:real,
author = {W. Rudin},
title = {Real and Complex Analysis},
year = {1974},
publisher = {McGraw--Hill},
address = {Tokyo, Japan},
edition = {Second}
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author = {W. H. Wolberg and K. P. Bennett and O. L. Mangasarian},
title = {Breast Cancer Diagnosis and Prognostic Determination from Cell Analysis},
institution = {Departments of Surgery and Human Oncology and Computer Sciences, University of
Wisconsin},
year = {1992},
address = {Madison, WI 53706},
type = {Manuscript}
}
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author = {W. H. Wolberg and O. L. Mangasarian},
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journal = {Proceedings of the National Academy of Sciences,U.S.A.},
year = {1990},
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year = {1991},
note = {Computer Sciences Department, University of Wisconsin, Madison, ftp: //ftp. cs.
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author = {W. H. Wolberg and W. N. Street and O. L. Mangasarian},
title = {Breast Cytology Diagnosis via Digital Image Analysis},
journal = {Analytical and Quantitative Cytology and Histology},
year = {1993},
volume = {15},
number = {6},
pages = {396--404}
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@Unpublished{ wolberg.street.ea:wdbc,
author = {W. H. Wolberg and W. N. Street and O. L. Mangasarian},
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year = {1995},
note = {Computer Sciences Department, University of Wisconsin, Madison, ftp: //ftp.
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}
@Unpublished{ wolberg.street.ea:wpbc,
author = {W. H. Wolberg and W. N. Street and O. L. Mangasarian},
title = {{WPBC: Wisconsin Prognostic Breast Cancer Database}},
year = {1995},
note = {Computer Sciences Department, University of Wisconsin, Madison, ftp: //ftp.
cs.wisc.edu/math-prog/cpo-dataset/machine-learn/WPBC/}
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pages = {815--838}
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author = {S. J. Wright and Y. Zhang},
title = {A Superquadratic Infeasible--Interior--Point Method for linear complementarity
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institution = {Argonne National Laboratory},
year = {1994},
annote = {revised},
number = {MCS--P418--0294},
address = {Argonne, Illinois},
type = {Preprint}
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author = {S. E. Wright},
title = {{DYNFGM}: Dynamic Finite Generation Method},
institution = {Department of Mathematics, University of Washington},
year = {1989},
address = {Seattle, Washington}
}
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pages = {29--51},
year = {1994}
}
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pages = {79--106}
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author = {S. J. Wright},
title = {A Path--Following Infeasible--Interior--Point Algorithm for Linear and Quadratic
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institution = {Argonne National Laboratory},
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address = {Argonne, Illinois}
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author = {S. J. Wright},
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address = {Philadelphia, Pennsylvania}
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author = {S. J. Wright},
title = {On Reduced Convex QP Formulations of Monotone LCP Problems},
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address = {Argonne, Illinois}
}
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pages = {91--104}
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author = {S. Xu},
title = {The Global Linear Convergence of an Infeasible Non-Interior Path-Following
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institution = {Department of Mathematics, University of Washington},
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type = {Technical Report},
address = {Seattle, WA}
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pages = {469--492}
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institution = {Department of Applied Mathematics and Physics, Kyoto University},
year = {1996},
type = {Technical Report},
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type = {report},
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address = {Philadelphia, PA}
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author = {S. A. Zenios and R. Qi and E. D. Chajakis},
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institution = {Decision Sciences Department, Wharton School, University of Pennsylvania},
year = {1990},
type = {report},
number = {89-10-02},
address = {Philadelphia, PA}
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year = {1993},
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pages = {413--422},
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@TechReport{ zhang.zhang:superlinear,
author = {Y. Zhang and D. Zhang},
title = {Superlinear convergence of infeasible interior-point methods for linear
programming},
institution = {Department of Mathematics and Statistics, University of Maryland},
year = {1992},
number = {92-15},
address = {Baltimore County, Maryland}
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pages = {208--227}
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volume = {4},
pages = {208--227}
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@Article{ bacuta2006,
title = {A unified approach for Uzawa algorithms},
author = {Constantin Bacuta},
journal = {SIAM Journal on Numerical Analysis},
volume = {44},
number = {6},
pages = {2633--2649},
year = {2006}
}
@Article{ manteuffelrugesouthworth2018,
title = {Nonsymmetric algebraic multigrid based on local approximate ideal restriction
(AIR)},
author = {Thomas A Manteuffel and John Ruge and Ben S Southworth},
journal = {SIAM Journal on Scientific Computing},
volume = {40},
number = {6},
pages = {A4105--A4130},
year = {2018}
}
@Article{ manteuffelmunzenmaierrugesouthworth2019,
title = {Nonsymmetric reduction-based algebraic multigrid},
author = {Thomas A Manteuffel and Steffen M\"unzenmaier and John Ruge and Ben S Southworth},
journal = {SIAM Journal on Scientific Computing},
volume = {41},
number = {5},
pages = {S242--S268},
year = {2019}
}
@PhDThesis{ sivas2021,
title = {Preconditioning of HDG for the Navier–Stokes Equations},
author = {Abdullah Ali Sivas},
department = {Applied Mathematics},
institution = {University of Waterloo},
year = {2021}
}
@Article{ brookshughes1982,
title = {Streamline upwind/{Petrov-Galerkin} formulations for convection dominated flows
with particular emphasis on the incompressible {Navier-Stokes} equations},
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volume = {32},
number = {1-3},
pages = {199--259},
year = {1982},
publisher = {Elsevier}
}
@InProceedings{ suhisaac2020,
title = {Evaluation of a minimally synchronous algorithm for 2: 1 octree balance},
author = {Hansol Suh and Tobin Isaac},
booktitle = {SC20: International Conference for High Performance Computing, Networking,
Storage and Analysis},
pages = {1--12},
year = {2020},
organization = {IEEE}
}
@Misc{ alauzet2010,
title = {Metric-Based Anisotropic Mesh Adaptation},
author = {Fr\'{e}d\'{e}ric Alauzet},
howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}},
year = {2010}
}
@Article{ chan1994qmrcgs,
title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric
systems},
author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd
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@Article{ ghai2019comparison,
title = {A comparison of preconditioned {K}rylov subspace methods for large-scale
nonsymmetric linear systems},
author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin},
journal = {Numerical Linear Algebra with Applications},
volume = {26},
number = {1},
pages = {e2215},
year = {2019},
publisher = {Wiley Online Library}
}
@Article{ mishrasalacknepley2025,
title = {Stencil Composition for Finite Difference Approximations of Partial Differential Equations},
author = {Abhishek Mishra and David Salac and Matthew G. Knepley},
journal = {SIAM Journal on Scientific Computing},
volume = {47},
number = {2},
doi = {10.1137/23M1596478},
year = {2025}
}
@Article{ nathawaniknepley2022,
title = {Droplet formation simulation using mixed finite elements},
author = {Darsh K. Nathawani and Matthew G. Knepley},
journal = {Physics of Fluids},
volume = {34},
pages = {064105},
doi = {10.1063/5.0089752},
year = {2022}
}
@InProceedings{ nathawaniknepley2022b,
title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method},
author = {Darsh K. Nathawani and Matthew G. Knepley},
booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11
(ICCFD11)},
editor = {Christoph Brehm and Shishir Pandya},
number = {4103},
year = {2022}
}
@Article{ nathawaniknepley2023,
title = {A one-dimensional mathematical model for shear-induced droplet formation in co-flowing fluids},
author = {Darsh K. Nathawani and Matthew G. Knepley},
journal = {Theoretical and Computational Fluid Dynamics},
url = {https://rdcu.be/dFtlR},
doi = {10.1007/s00162-024-00690-5},
year = {2024}
}
@InProceedings{ georgalisnathawaniknepleypatra2023,
title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors},
author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. Knepley and Abani
Patra},
booktitle = {AIAA SciTech 2024},
note = {Accepted},
year = {2023}
}
@Article{ brownbarrabeamsghaffariknepleymosesshakeristengelthompsonzhang2022,
title = {Performance Portable Solid Mechanics via Matrix-Free $p$-Multigrid},
author = {Jed Brown and Valeria Barra and Natalie Beams and Leila Ghaffari and Matthew
Knepley and William Moses and Rezgar Shakeri and Karen Stengel and Jeremy L.
Thompson and Junchao Zhang},
doi = {10.48550/ARXIV.2204.01722},
url = {https://arxiv.org/abs/2204.01722},
publisher = {arXiv},
note = {Submitted},
year = {2022}
}
@InCollection{ mayknepley2023,
title = {Numerical Modeling of Subduction},
author = {Dave A. May and Matthew G. Knepley},
booktitle = {Dynamics of Plate Tectonics and Mantle Convection},
editor = {João C. Duarte},
pages = {539-571},
isbn = {978-0-323-85733-8},
doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2},
url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202},
year = {2023}
}
@Article{ adamswangmersonhucksknepley2024,
title = {A performance portable, fully implicit {Landau} collision operator with batched linear solvers},
author = {Mark F. Adams and Peng Wang and Jacob Merson and Kevin Hucks and Matthew G. Knepley},
journal = {SIAM Journal on Scientific Computing},
volume = {47},
number = {2},
pages = {B360-B381},
doi = {10.1137/24M1640252},
url = {https://arxiv.org/abs/2209.03228},
year = {2025},
petsc_uses = {DMPlex}
}
@Article{ adamsknepley2023,
title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized
plasmas in {PETSc}},
author = {Mark F. Adams and Matthew G. Knepley},
url = {https://arxiv.org/abs/2302.10242},
note = {In preparation},
year = {2023},
petsc_uses = {DMPlex}
}
@Article{ finnknepleypusztayadams2023,
title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}},
author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. Adams},
url = {https://arxiv.org/abs/2303.12620},
journal = {Communications in Applied Mathematics and Computational Science},
volume = {18},
number = {1},
pages = {135--152},
doi = {10.2140/camcos.2023.18.135},
year = {2023},
petsc_uses = {DMPlex}
}
@Article{ adamsfinnknepleypusztay2025,
title = {A projection method for particle resampling},
author = {Mark F. Adams and Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay},
url = {https://arxiv.org/abs/2501.13681},
journal = {Computer Physics Communications},
note = {Submitted},
year = {2025},
petsc_uses = {DMPlex}
}
@Article{ finnpusztayknepleyadams2026,
title = {Structure Preservation using Discrete Gradients in the Vlasov-Poisson-Landau System},
author = {Daniel S. Finn and Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams},
journal = {Journal of Computational Physics},
pages = {114749},
year = {2026},
petsc_uses = {DMPlex}
}
@Article{ hamhaplaknepleymitchellsagiyama2024,
title = {Efficient N-to-M Checkpointing Algorithm for Finite Element Simulations},
author = {David A. Ham and Vaclav Hapla and Matthew G. Knepley and Lawrence Mitchell and Koki Sagiyama},
journal = {SIAM Journal on Scientific Computing},
volume = {46},
number = {6},
url = {https://arXiv.org/abs/2401.05868},
doi = {10.1137/23M161372},
year = {2024},
petsc_uses = {DMPlex}
}
@InProceedings{ retfalviknepleydesjardin2025,
title = {Performance Modeling and Scaling of PETSc based Direct Numerical Simulations for Hybrid Rocket Boundary Layers},
author = {Kolos Retfalvi and Matthew G. Knepley and Paul E. DesJardin},
booktitle = {Proceedings of the ASME 2025, Fluids Engineering Division Summer Meeting},
note = {Accepted},
year = {2025}
}
@Article{ retfalviwhitesidesmcgurnknepleydesjardin2025,
title = {Direct Numerical Simulations for Hybrid Rocket Boundary Layers: Performance Modeling and Scaling},
author = {Kolos Retfalvi and Russell Whitesides and Matthew McGurn and Matthew G. Knepley and Paul E. DesJardin},
journal = {International Journal of High Performance Computing Applications},
doi = {10.1177/10943420251374921},
year = {2025}
}
@Article{ knepley2025,
title = {Transformations of Computational Meshes},
author = {Matthew G. Knepley},
journal = {Engineering with Computers},
doi = {10.1007/s00366-025-02175-3},
url = {https://link.springer.com/content/pdf/10.1007/s00366-025-02175-3.pdf},
year = {2025},
petsc_uses = {DMPlex}
}
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@PhDThesis{ pusztaythesis2023,
title = {A Particle Basis Vlasov-Poisson-Landau Solver for Plasma Simulation in PETSc},
author = {Joseph V. Pusztay},
type = {{PhD} thesis},
school = {University at Buffalo, Department of Computer Science and Engineering},
address = {Buffalo, NY},
month = may,
year = {2022}
}
@PhDThesis{ finnthesis2023,
title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau
System},
author = {Daniel S. Finn},
type = {{PhD} thesis},
school = {University at Buffalo, Program in Computational and Data-Enabled Science and
Engineering},
address = {Buffalo, NY},
month = may,
year = {2023}
}
@PhDThesis{ nathawanithesis2023,
title = {Droplet Formation: One-dimensional Mathematical Model and Computations},
author = {Darsh Kiritbhai Nathawani},
type = {{PhD} thesis},
school = {University at Buffalo, Program in Computational and Data-Enabled Science and
Engineering},
address = {Buffalo, NY},
month = may,
year = {2023}
}
@PhDThesis{ dentonthesis2022,
title = {Geometry Aware Mesh Topologies},
author = {Brandon Lee Denton},
type = {{PhD} thesis},
school = {University at Buffalo, Department of Mechanical and Aerospace Engineering},
address = {Buffalo, NY},
month = may,
year = {2022}
}
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year = {2020}
}
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title = {On the famous unpublished preprint ``{Methods} of integration which preserve the contact transformation property of the {Hamilton} equations'' by {Ren\'e De Vogelaere}},
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eprint = {2003.12268},
archivePrefix = {arXiv},
primaryClass = {math.NA},
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year = {2020}
}
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title = {{Compatible Discrete Operator} schemes on polyhedral meshes for elliptic and {Stokes} equations},
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year = {2014}
}
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@Inbook{ shapero2025,
author = {Daniel Shapero},
title = {Linear-algebraic representation and transformation of unstructured meshes},
booktitle = {Proceedings of the 2025 SIAM International Meshing Roundtable (IMR)},
chapter = {},
pages = {154--166},
doi = {10.1137/1.9781611978575.13},
URL = {https://epubs.siam.org/doi/abs/10.1137/1.9781611978575.13},
eprint = {https://epubs.siam.org/doi/pdf/10.1137/1.9781611978575.13},
year = {2025}
}
@article{MckayEriksonKozdon2019,
title = {A computational method for earthquake cycles within anisotropic media},
author = {Maricela Best Mckay and Brittany A Erickson and Jeremy E Kozdon},
journal = {Geophysical Journal International},
volume = {219},
number = {2},
pages = {816--833},
year = {2019},
}
@article{EricksonOReillyNordstrom2019,
title = {Accuracy of stable, high-order finite difference methods for hyperbolic systems with non-smooth wave speeds},
author = {Brittany A Erickson and Ossian O’Reilly and Jan Nordstr{\"o}m},
journal = {Journal of Scientific Computing},
volume = {81},
pages = {2356--2387},
year = {2019},
}
@article{KozdonEricksonWilcox2021,
title = {Hybridized summation-by-parts finite difference methods},
author = {Jeremy E Kozdon and Brittany A Erickson and Lucas C Wilcox},
journal = {Journal of Scientific Computing},
volume = {87},
number = {3},
pages = {85},
year = {2021},
}
@article{SEAS2022,
title = {Community-driven code comparisons for three-dimensional dynamic modeling of sequences of earthquakes and aseismic slip},
author = {Junle Jiang and Brittany A Erickson and Val{\`e}re R Lambert and Jean-Paul Ampuero and Ryosuke Ando and Sylvain D Barbot and Camilla Cattania and Luca Dal Zilio and Benchun Duan and Eric M Dunham and Alice-Agnes Gabriel and Nadia Lapusta and Duo Li and Meng Li and Dunyu Liu and Yajing Liu and So Ozawa and Casper Pranger and Ylona van Dinther},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {127},
number = {3},
pages = {e2021JB023519},
year = {2022},
}
@article{EricksonKozdonHarvey2022,
title = {A non-stiff summation-by-parts finite difference method for the scalar wave equation in second order form: Characteristic boundary conditions and nonlinear interfaces},
author = {Brittany A Erickson and Jeremy E Kozdon and Tobias Harvey},
journal = {Journal of Scientific Computing},
volume = {93},
number = {1},
pages = {17},
year = {2022},
}
@article{RuckerEriksonKarlstromLeeGopalakrishnan2022,
title = {A Computational Framework for Time-Dependent Deformation in Viscoelastic Magmatic Systems},
author = {Cody Rucker and Brittany A Erickson and Leif Karlstrom and Brian Lee and Jay Gopalakrishnan},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {127},
number = {9},
pages = {e2022JB024506},
year = {2022},
}
@article{HarveyEriksonKozdon2023,
title = {A High-order Accurate Summation-by-Parts Finite Difference Method for Fully-dynamic Earthquake Sequence Simulations within Sedimentary Basins},
author = {Tobias W Harvey and Brittany A Erickson and Jeremy E Kozdon},
journal = {Journal of Geophysical Research: Solid Earth},
pages = {e2022JB025357},
year = {2023},
}
@article{SEAS2023,
title = {Incorporating full elastodynamic effects and dipping fault geometries in community code verification exercises for simulations of earthquake sequences and aseismic slip {(SEAS)}},
author = {Brittany A Erickson and Junle Jiang and Val{\`e}re Lambert and Sylvain D Barbot and Mohamed Abdelmeguid and Martin Almquist and Jean-Paul Ampuero and Ryosuke Ando and Camilla Cattania and Alexandre Chen and Luca Dal Zilio and Shuai Deng and Eric M. Dunham and Ahmed E. Elbanna and Alice‐Agnes Gabriel and Tobias W. Harvey and Yihe Huang and Yoshihiro Kaneko and Jeremy E. Kozdon and Nadia Lapusta and Duo Li and Meng Li and Chao Liang and Yajing Liu and So Ozawa and Andrea Perez‐Silva and Casper Pranger and Paul Segall and Yudong Sun and Prithvi Thakur and Carsten Uphoff and Ylona van Dinther and Yuyun Yang},
journal = {Bulletin of the Seismological Society of America},
volume = {113},
number = {2},
pages = {499--523},
year = {2023},
}
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title = {On solving large-scale limited-memory quasi-{N}ewton equations},
author = {Erway, Jennifer B and Marcia, Roummel F},
journal = {Linear Algebra and its Applications},
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pages = {196--225},
year = {2017},
publisher = {Elsevier},
}
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year={2008},
month=jun,
pages={1353-1368},
}
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title={A Unified Library of Nonlinear Solution Schemes},
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DOI={10.1115/1.4006992},
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@InProceedings{ beallwalshshephard2003,
title = {Accessing {CAD} Geometry for Mesh Generation},
author = {Mark W. Beall and Joe Walsh and Mark S. Shephard},
booktitle = {Proceedings of the 12th International Meshing Roundtable},
month = sep,
address = {Santa Fe, NM},
pages = {33--42},
year = {2003}
}
@article{ MoresiMansourGiordaniKnepleyKnightGraciosaGollapalliLuBeucher2025,
title = {Underworld3: Mathematically Self-Describing Modelling in Python for Desktop, HPC and Cloud},
author = {Louis Moresi and John Mansour and Julian Giordani and Matt Knepley and Ben Knight and Juan Carlos Graciosa and Thyagarajulu Gollapalli and Neng Lu and Romain Beucher},
journal = {The Journal of Open Source Software},
doi = {10.21105/joss.07831},
year = {2025},
petsc_uses = {DMPlex}
}
@Article{ rdycore,
title = {Development of a River Dynamical Core for E3sm to Simulate Compound Flooding on Exascale-Class Heterogeneous Supercomputers},
author = {Gautam Bisht and Donghui Xu and Jeffrey Johnson and Jed Brown and Matthew G. Knepley and Mark F Adams and Dongyu Feng and Dalei Hao and Darren Engwirda and Mukesh Kumar and Zeli Tan},
journal = {Environmental Modelling \& Software},
note = {Accepted},
year = {2025}
}
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@article{ mcintyrechensquiremeyrandsimon2025,
title = {Evidence for the Helicity Barrier from Measurements of the Turbulence Transition Range in the Solar Wind},
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journal = {Phys. Rev. X},
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doi = {10.1103/PhysRevX.15.031008},
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year = {2025}
}
@article{ huangdongwang2025,
title = {Machine-learning heat flux closure for multi-moment fluid modeling of nonlinear {Landau} damping},
author = {Ziyu Huang and Chuanfei Dong and Liang Wang},
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number = {11},
pages = {e2419073122},
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