Revision 477e44bbb558b1357d86363677accbb4bcdfaabc authored by Fande Kong on 19 July 2022, 22:06:52 UTC, committed by Satish Balay on 19 July 2022, 22:19:37 UTC
Reproducible with: ./configure --with-mpi=0 --download-fblaslapack --with-debugging=no Linker output after filtering: ld: warning: could not create compact unwind for _dgeev_: registers 27 and 28 not saved contiguously in frame ld: warning: could not create compact unwind for _dgebak_: registers 25 and 26 not saved contiguously in frame
1 parent 3bd2ae8
petsc.bib
%
% If the reference uses PETSc, include a field listing components used, e.g.
% petsc_uses = {KSP, SNES, TS, TAO},
%
% For journal names, write out the full name, instead of defining abbreviations
% (despite some historical usage of abbreviations below).
%
% There are some additional historical comments below which may be of interest,
% particularly in terms of notes about particularly impactful publications using PETSc.
%
% LiteralHTML:
% LiteralHTML: <H2><center>Research and Publications that make use of PETSc</center></H2>
% LiteralHTML:
% LiteralHTML: <a name="nano"><H3><center>Nano-simulations</center></H3>
% LiteralHTML:
@misc{bueler2020petsc,
title={PETSc for Partial Differential Equations: Numerical Solutions in C and Python},
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{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 = {November},
year = {2017},
petsc_uses={KSP},
}
@INPROCEEDINGS{asc2013,
author = "S. Abhyankar and B. F. Smith and E. Constantinescu",
title = "Evaluation of overlapping restricted additive Schwarz preconditioning for parallel solution of very large power flow problems",
booktitle = "HiPCNA-PG’13",
year = 2013,
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 = {January},
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{ZhangConstantinescu2021,
title = {Optimal checkpointing for adjoint multistage time-stepping schemes},
author = {Hong Zhang and Emil M. Constantinescu},
journal = {SIAM Journal on Scientific Computing},
note = {submitted},
year = {2021},
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 = {June},
year = {2021},
petsc_uses={KSP},
}
@techreport{ZhangConstantinescuSmith2019,
author = {Hong Zhang and Emil M. Constantinescu and Barry F. Smith},
title = {{PETSc TSAdjoint}: a discrete adjoint {ODE} solver for first-order and second-order sensitivity analysis},
journal = {arXiv e-preprints},
eprint = {1912.07696},
archivePrefix = {arXiv},
year = {2019},
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 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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@article{saut,
author = { Olivier Saut},
title = "Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal",
journal = "SIAM Journal on Scientific Computing",
year = 2004,
note = "submitted",
url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf},
petsc_uses={KSP},
}
% LiteralHTML:
% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3>
% 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 = {February},
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 Newton and hybrid Schwarz preconditioners for fluid-structure interaction},
author={Barker, A.T. and Cai, X.C.},
journal={SIAM Journal on Scientific Computing},
volume={32},
number={4},
pages={2395--2417},
year={2010},
publisher={Society for Industrial and Applied Mathematics},
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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/spine0l.jpg"></center></p>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/vertebra.jpg"></center></p>
% LiteralHTML:<font color="#FF0000">
% 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.</p>
% LiteralHTML: </font>
@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: <a name="biology:cardiology">
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/heart.jpg">
% LiteralHTML: <img alt=""
% LiteralHTML: src="images/pump.jpg"></center></p>
% LiteralHTML:
% LiteralHTML:<font color="#FF0000">
% 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.</p>
% LiteralHTML:</font>
@inproceedings{oghattas2000,
author = "J. Antaki and G. Belloch and O. Ghattas and I. Malcevic
and G. Miller and N. Walkington",
title = "A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic
Interfaces",
booktitle = "Procceedings of SC2000",
url ="http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf",
note = "Blood flow modeling at the microscale including effects on individual blood cells,
for designing heart assist pumps, etc.",
year = "2000",
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 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 = {January},
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 and G. Székely},
title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using a Schur Complement Preconditioner},
booktitle = {Euro-Par 2009 Parallel Processing},
year = {2009},
month = {August},
pages = {747-759},
volume = {5704},
editor = {H. Sips and D. Epema and and H.-X. Lin},
series = {Lecture Notes in Computer Science},
publisher = {Springer},
keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, parallel Krylov solver},
petsc_uses={KSP},
}
% LiteralHTML: <a name="biology:imagingandsurgery">
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/brain.jpg"></center>
@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 Brigham and Women's hospital",
journal = "Medical Image Analysis",
url ="http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf",
year = "2005",
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 Bayesian inversion for three-dimensional dental X-ray imaging",
journal = "IEEE Transactions on Medical Imaging",
volume = "25",
number = "2",
month = "February",
year = "2006",
pages = "218--228",
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},
}
% LiteralHTML:
% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3>
% LiteralHTML:
@article{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)},
note = {Accepted},
year = {2022},
petsc_uses={DMPlex},
}
@misc{AdamsKnepleyBrennan2021,
title = {Runaway Electron Generation with High-Performance, Structure Preserving Discretization of Fokker-Plank-Landau},
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},
note = {Accepted},
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},
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 Jacobian approximation for quasi-Newton solves of sparse nonlinear systems},
journal = {arXiv},
year = {2009},
note = {http://arxiv.org/abs/0905.1054},
url = {http://arxiv.org/pdf/0905.1054v1},
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 Parker 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 Poisson 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},
}
% LiteralHTML:
% LiteralHTML: <a name="geosciences"><H3><center>Geosciences</center></H3>
% LiteralHTML:
@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 Stokes 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 Galerkin 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 {YoungOppenheimDimant2017,
author = {Matthew A. Young and Meers M. Oppenheim and Yakov S. Dimant},
title = {Hybrid simulations of coupled Farley-Buneman/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 Mars' 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 = {ACM Transaction on Mathematical Software},
eprint = {1508.02470},
note = {In review},
year = {2017},
petsc_uses={KSP},
}
@eprint{KnepleyLangeGorman2017,
title = {Unstructured Overlapping Mesh Distribution in Parallel},
author = {Matthew G. Knepley and Michael Lange and Gerard J. Gorman},
journal = {arXiv},
eprint = {1506.06194},
note = {submitted},
year = {2017},
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 = {April},
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 = {January},
address = {Seattle, WA},
pages = {1--5},
url = {http://imr.sandia.gov/papers/imr31/2026_imr31RJ_Wallwork.pdf},
year = {2022},
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},
year = {2021},
petsc_uses={KSP,DMPlex},
}
@article{FarrellMitchellScottWechsung2022,
title = {Robust multigrid methods for nearly incompressible elasticity using macro elements},
author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian Wechsung},
journal = {IMA Journal of Numerical Analysis},
issn = {0272-4979},
doi = {10.1093/imanum/drab083},
url = {https://doi.org/10.1093/imanum/drab083},
year = {2022},
petsc_uses={KSP,DMPlex},
}
@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}},
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volume = {9},
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doi = {10.5194/gmd-9-3803-2016},
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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},
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doi = {10.1007/978-3-642-38750-0_21},
year = {2013},
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year = 2014,
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publisher = {Springer},
year = 2014,
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@unpublished{Leon-Baldelli-Bourdin-2014a,
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Month = {08},
Note = {Submitted.},
Title = {On the asymptotic derivation of Winkler-type energies from {3D} elasticity},
Year = {2014},
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Volume = {70},
Year = {2014},
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Volume = {Submitted},
Year = {2014},
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Booktitle = {Proceedings of the 38th Workshop on Geothermal Reservoir Engineering Stanford University, Stanford, CA},
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Year = {2013},
petsc_uses={KSP},
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Pages = {75-91},
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experiments and numerical simulations using a two-dimensional variational approach},
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Year = {2013},
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Pages = {2360--2379},
Title = {A variational approach to the fracture of brittle thin films under out of plane loading},
Volume = {61},
Year = {2013},
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}
@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},
}
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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.},
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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},
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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},
}
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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},
}
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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 = {http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf},
note = {\url{http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf}},
address = {Stanford, CA},
year = {2010},
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},
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volume={97},
number={4},
pages={1094},
year={2007},
publisher={Seismol Soc America},
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@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
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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
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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
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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},
}
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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 euler atmospheric equations},
year={2014},
month={Sept},
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 Southern California Using the {SCEC} Community Fault Model},
booktitle = {Proceedings of Geosciences '08},
address = {Wellington, NZ},
month = {November},
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 = {September},
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 Richards equation",
author = "Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena",
journal = "Computers and Geosciences",
volume = "34",
pages = "1958--1963",
year = "2008",
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 = {August},
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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML:<font color="#FF0000">
% 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.</p>
% LiteralHTML:</font>
% 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:<a name="katz">
@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: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg">
% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p>
% LiteralHTML:<font color="#FF0000">
% 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 = {August},
address = {Moscow, RUSSIA},
pages = {491--495},
year = {2012},
petsc_uses={KSP},
}
%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY=
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/ocean.jpg"></center></p>
@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 North Atlantic},
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 Kalman Filter and the SEIK Filter applied to a Finite Element Model of the North Atlantic},
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 Newton-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: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3>
% LiteralHTML:
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML:<font color="#FF0000">
% 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.</p>
% LiteralHTML:</font>
% 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 = {November},
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},
}
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@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},
}
% LiteralHTML:<a name="scalinglarge">
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/scalinglarge.jpg"></center></p>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML: Sample <strong>strong scaling</strong> 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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@Article{aba01:petsc-app,
author = {Jason Abate and Peng Wang and Kamy Sepehrnoori},
title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s},
journal = "Int. J. High Performance Computing Applications",
year = 2001,
volume = 15,
number = 1,
pages = {13--21},
month = {Spring},
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: <a name="cfd"><H3><center>CFD</center></H3>
% 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 Drosophila 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 Lagrange--Newton 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-Boltzmann 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 Catamaran 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 Catamaran",
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 Navier--Stokes (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},
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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",
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journal ="International Journal for Numerical Methods in Fluids",
year = 2009,
volume = 59,
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petsc_uses={KSP},
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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},
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petsc_uses={KSP},
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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},
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petsc_uses={KSP},
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@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},
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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},
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@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",
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volume = 21,
pages = "307--327",
year = 2007,
petsc_uses={KSP},
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@techreport{avb2008,
Author = "V.R. Ambati and J.J.W. van der Vegt and O. Bokhove",
TITLE = "Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface Waves",
year = 2008,
INSTITUTION = "University of Twente, the Netherlands",
url = "http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf",
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},
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@Article{AraujoTeixeiraCunhaGroth08,
Author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth},
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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",
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year = 2007,
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petsc_uses={KSP},
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@TechReport{af2007,
title = "Preconditioning based on a partially implicit implementation of Momentum Interpolation for coupled solvers",
institution = "Fluid Mechanics Group of the University of Zaragoza (Spain)",
year = "2007",
author = "A. Cubero and N. Fueyo",
petsc_uses={KSP},
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@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},
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@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},
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@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
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booktitle = "Proceedings of the 19th International Symposium on High Performance Computing Systems and
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year = 2005,
url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046},
petsc_uses={KSP},
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@TechReport{bonglioli-icnmfd98,
title = "Multidimensional Residual Distribution Schemes for the Pseudo-Compressible {Euler}
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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},
}
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Author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"},
TITLE = "A new fully coupled method for computing turbulent flows",
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pages = "445--472",
year = 2001,
petsc_uses={KSP},
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@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},
month = {June},
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",
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year = 2005,
petsc_uses={KSP},
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@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},
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@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",
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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},
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petsc_uses={KSP},
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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,
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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,
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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",
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year = 2005,
petsc_uses={KSP},
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@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},
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@InProceedings{etpp,
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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 = "December",
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},
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volume = 25,
number = 2,
pages = {159-177.},
petsc_uses={KSP},
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@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},
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@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: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3>
% 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: <a name="optimization"><H3><center>Optimization</center></H3>
% 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="august",
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: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3>
% 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: <a name="otherapps"><H3><center>Other Application Areas</center></H3>
% 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",
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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},
}
@book{BourdinFrancfortMarigo,
author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo},
title = {The Variational Approach to Fracture},
publisher = {Springer},
year = {2008},
petsc_uses={KSP},
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@article{BourdinFrancfortMarigo2008,
author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo},
title = {The Variational Approach to Fracture},
journal = {J. Elasticity},
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pages = {1--148},
doi = {10.1007/s10659-007-9107-3},
year = {2008},
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@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},
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year={2008},
publisher={Elsevier},
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@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},
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title={Discriminative n-gram language modeling},
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year={2007},
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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},
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@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},
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author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu},
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year = 2010,
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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},
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year = 2010,
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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},
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year = 2010,
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@article{wei2011parallel,
title={{A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with Application in Quantum Dot Simulation}},
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journal={Domain Decomposition Methods in Science and Engineering XIX},
pages={157--164},
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publisher={Springer},
petsc_uses={KSP},
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@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},
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@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},
}
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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}},
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@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",
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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},
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@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},
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@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.},
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volume={423},
number={1},
pages={149--163},
year={2012},
publisher={Elsevier},
petsc_uses={KSP},
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@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},
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@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},
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@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",
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year = 2011,
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@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",
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number = 2,
year = 2007,
petsc_uses={KSP},
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@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},
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@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 Newton-Krylov-Schwarz 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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML:<font color="#FF0000">
% 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.</p>
% LiteralHTML:</font>
% 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 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: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@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 Newton 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: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3>
% 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 and R. Paz and M. Storti",
institution = "International Center for Computer Methods in Engineering",
url = "http://www.cimec.org.ar/python",
note = "Provides Python bindings for PETSc via SWIG",
petsc_uses={KSP},
}
@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/cig/software/pylith/},
howpublished = {\url{http://geodynamics.org/cig/software/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-web-page,
title = "Ti-PETSc - an interface to PETSc from Titanium",
Institution = "Berkeley",
url = "http://www.nersc.gov/\~{ }yunhe/cs267/final/paper.pdf",
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 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 = {2021},
}
@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} Homepage",
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: <a name="software"><H3><center>Software Engineering</center></H3>
% LiteralHTML:
@article{PETScCommunity2021,
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},
url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043},
doi = {10.6084/m9.figshare.16523043.v1},
note = {Accepted},
year = {2021},
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 = "August",
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 = "December",
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= "June",
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 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 = {{PETSc/TAO} Users Manual},
institution = {Argonne National Laboratory},
number = {ANL-21/39 - Revision 3.16},
year = {2021},
}
% url = {http://www.mcs.anl.gov/petsc}
@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 = {http://www.mcs.anl.gov/petsc},
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: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3>
% 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 = {Communications in Applied Mathematics and Computational Science},
note = {In review},
url = {https://arxiv.org/abs/1708.06028},
year = {2018},
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 = {September},
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 Newton-Krylov-Schwarz Method for Nonlinear Complementarity Problems},
journal = {J. Sci. Comput.},
issue_date = {May 2011},
volume = {47},
number = {2},
month = may,
pages = {258--280},
year = {2011},
issn = {0885-7474},
numpages = {23},
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},
}
@online{KnepleyRuppTerrel2016,
title = {Finite Element Integration with Quadrature on the GPU},
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},
}
@techreport{pbmkbsxt2012,
title = "Composing Scalable Nonlinear Algebraic Solvers",
author = "Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu",
year = 2013,
type = "Preprint",
number = "ANL/MCS-P2010-0112",
institution = "Argonne National Laboratory",
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 Schwarz Preconditioned Inexact Newton Method for Shocked Duct Flows",
BOOKTITLE = "Proceedings of the 13th International Conference on
Domain Decomposition Methods",
PAGES = "343--350",
EDITOR = "N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov",
PUBLISHER = "CIMNE, Barcelona, Spain",
NOTE = "",
URL = "http://www.ddm.org/DD13",
YEAR = "2002",
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 = {November},
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 = {November},
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 # " 11,",
petsc_uses={KSP},
}
@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 = {October},
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 = "February",
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: <a name="books"><H3><center>Books</center></H3>
% 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},
}
@inbook{BalayBrownKnepleyMcInnesSmith2015,
author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry Smith},
bookeditor = {J. Carver},
title = {Software Engineering for Science},
chapter = {Providing Mixed Language and Legacy Support within a Library},
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},
}
@article{SSM2016,
author = {P. Sanan and S.M. Schnepp and D.A. May},
title = {Pipelined, Flexible {Krylov} Subspace Methods},
journal = {SIAM Journal on Scientific Computing},
volume = {38},
number = {5},
pages = {C441-C470},
year = {2016},
doi = {10.1137/15M1049130},
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 = {Advances in Computational Mathematics},
eprint = {1612.02208},
note = {In review},
year = {2017},
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{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{http://www.mcs.anl.gov/petsc/meetings}",
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 = {July},
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 = {April},
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}
}
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title={Line search algorithms with guaranteed sufficient decrease},
author={Mor{\'e}, Jorge J and Thuente, David J},
journal={ACM Transactions on Mathematical Software},
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number={3},
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year={1994},
publisher={ACM}
}
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title={Algorithm 799: revolve: an implementation of checkpointing for the reverse or adjoint mode of computational differentiation},
author={Griewank, Andreas and Walther, Andrea},
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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},
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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},
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Year = {1997},
Pages = {151--167},
Volume = {25}
}
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title = {Computer methods for ordinary differential equations and differential-algebraic equations},
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publisher = {SIAM},
year = {1998}
}
@article{ColomesBadia2016,
title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} equations},
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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}
}
@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{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}
}
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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}
}
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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}
}
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title={Liszt: a domain specific language for building portable mesh-based PDE solvers},
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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/}}
}
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author={El-Ghazawi, Tarek and Smith, Lauren},
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pages={27},
year={2006},
organization={ACM}
}
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year={2007},
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@inproceedings{dally1988object,
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@book{chase1989amber,
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year={2009},
organization={IEEE}
}
@TechReport{ipm,
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year={2012},
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@book{openmp4,
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title={Annotation-based empirical performance tuning using {Orio}},
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pages={1--11},
year={2009},
organization={IEEE}
}
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title="Domain Decomposition Methods: Algorithms and Theory",
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year={2005},
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pages={375--381},
year = "2016"
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@TechReport{ saws,
Author = "Matt Otten and Jed Brown and Barry F. Smith",
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Year = 2013
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year={2011}
}
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title={Scalable domain decomposition preconditioners for heterogeneous elliptic problems},
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booktitle={Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis},
pages={80},
year={2013},
organization={ACM}
}
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Year = {2000}
}
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title={An energy-minimizing interpolation for robust multigrid methods},
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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 # {~27},
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 # {~25},
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},
Date-Modified = {2010-08-19 15:40:59 -0500},
Journal = {The Visual Computer},
Number = {8},
Pages = {707--716},
Publisher = {Springer},
Title = {An improved scheme of an interactive finite element model for 3D soft-tissue cutting and deformation},
Volume = {21},
Year = {2005}}
@article{taylor2008high,
Author = {Taylor, Z.A. and Cheng, M. and Ourselin, S.},
Date-Added = {2010-08-19 15:40:57 -0500},
Date-Modified = {2010-08-19 15:40:57 -0500},
Journal = {IEEE transactions on medical imaging},
Number = {5},
Pages = {650},
Title = {High-speed nonlinear finite element analysis for surgical simulation using graphics processing units.},
Volume = {27},
Year = {2008}}
@conference{bolz2003sparse,
Author = {Bolz, J. and Farmer, I. and Grinspun, E. and Schr{\\"o}oder, P.},
Booktitle = {ACM SIGGRAPH 2003 Papers},
Date-Added = {2010-08-19 15:40:55 -0500},
Date-Modified = {2010-08-19 15:40:55 -0500},
Organization = {ACM},
Pages = {924},
Title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid},
Year = {2003}}
@article{wu2004hybrid,
Author = {Wu, W. and Heng, P.A.},
Date-Added = {2010-08-19 15:40:54 -0500},
Date-Modified = {2010-08-19 15:40:54 -0500},
Journal = {Computer Animation and Virtual Worlds},
Number = {3-4},
Pages = {219--227},
Publisher = {John Wiley \& Sons},
Title = {A hybrid condensed finite element model with {GPU} acceleration for interactive 3D soft tissue cutting},
Volume = {15},
Year = {2004}}
% ----------------------------------------------------------------------------------------------------------------
@TechReport{davis97,
author = "T. Davis",
title = "The {U}niversity of {F}lorida Sparse Matrix Collection",
institution = "University of Florida",
year = 1997
}
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Author = {Davis, T. A. and Hu, Y.},
title = {The {U}niversity of {F}lorida sparse matrix collection},
Journal = {ACM Transactions on Mathematical Software},
Volume = {38},
Issue = {1},
Year = {2011},
Pages = {1--25}
}
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title={Algorithm 832: {UMFPACK} V4.3---An Unsymmetric-Pattern Multifrontal Method},
author={Davis, Timothy A},
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volume={30},
number={2},
pages={196--199},
year={2004},
publisher={ACM}
}
@TechReport{streams,
author = {J. D. McCalpin},
title = {{STREAM}: Sustainable memory bandwidth in high performance computers},
institution = {University of Virginia},
url = {http://www.cs.virginia.edu/stream},
year = {1995}
}
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journal = "Numer. Math.",
volume = "52",
year = "1988",
pages = "251--277",
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title = "Convergence of the multigrid full approximation scheme
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journal = "Numer. Math.",
volume = "53",
year = "1988",
pages = "663--686",
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title = {Multigrid Net; http://www.mgnet.org/},
author = {Craig Douglas},
note = {Contains enormous bibliography on multigrid publications},
year = 2009
}
@unpublished{copper,
title = {Fourteenth Copper Mountain Conference on Multigrid Methods},
author = {},
note = {Held bi-annually},
year = 2009
}
@BOOK{wessling1992,
AUTHOR="Pieter Wesseling",
TITLE="An Introduction to Multigrid Methods",
YEAR="2004",
PUBLISHER="R. T. Edwards"
}
@BOOK{bhm2000,
AUTHOR="William L. Briggs and Van Emden Henson and Steve F. McCormick",
TITLE="A Multigrid Tutorial",
YEAR="2000",
PUBLISHER="SIAM",
}
@book{trottenberg2001multigrid,
title={{Multigrid}},
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isbn={012701070X},
year={2001},
publisher={Academic Press}
}
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author = "Achi Brandt",
title = "Multigrid Techniques: 1984 Guide with Applications for Fluid Dynamics",
institution = "Gesellschaft fur Mathematik und Dataenverarbeitung",
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year = 1984
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pages={857},
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AUTHOR = "T. Washio and C. W. Oosterlee",
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VOLUME = "21",
PAGES = "1670--1690",
YEAR = "2000"
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YEAR = "2005"
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@Misc{fusion:report,
title = "{Report of the Fusion Energy Sciences Advisory Committee Burning Plasma Strategy Panel}",
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@Misc{hecrtf:report,
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@Misc{ pseware-web-page,
author = "",
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key = "{PSEware} {Web} page",
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@Misc{ babel-web-page,
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@Misc{ infospheres-web-page,
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author = "Glenn Hammond",
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author = "Oak Ridge National Laboratory",
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year = 2004,
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@Article{cumulvs97,
author = "G. A. Geist and J. A. Kohl and P. M. Papadopoulos",
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@techreport{daly2012interagency,
author={John Daly and Bill Harrod and Thuc Hoang and Lucy Nowell and Bob Adolf and Shekhar Borkar and Nathan DeBardeleben and Mootaz Elnozahy and Mike Heroux and David Rogers and Rob Ross and Vivek Sarkar and Martin Schulz and Marc Snir and Paul Woodward},
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@techreport{ szyld,
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institution = "Department of Mathematics, Temple University",
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@techreport{ pdelab,
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title = "{I}nter-{L}anguage {U}nification Reference Manual",
note = "ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation",
}
@Unpublished{doe2k-web-page,
title = "{DOE2000 Initiative} {W}eb page",
note = "http://www.mcs.anl.gov/DOE2000",
key = "DOE2000 Initiative",
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@Misc{pvode-web-page,
title = "{PVODE} {W}eb Page",
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@BOOK{szyperski97,
AUTHOR = "Clemens Szyperski",
TITLE = "Component Software: Beyond Object-Oriented Programming",
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@Unpublished{petsc:coloringuse,
title = "Code for computing sparse {J}acobians",
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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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@Unpublished{petsc:use-by-external-packages,
author = {B. F. {Smith et al.}},
title = "{Software Packages that Use or Interface to PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}",
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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}",
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author = {B. F. {Smith et al.}},
title = "{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}",
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@Unpublished{flash-web-page,
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",
note = "http://z.ca.sandia.gov/esi",
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"
}
@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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@INPROCEEDINGS{ kohn98,
AUTHOR= "Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski",
TITLE= "Language Interoperability Mechanisms for High-Performance Scientific Applications",
PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
year = 1999,
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@INPROCEEDINGS{ kohn01,
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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@INPROCEEDINGS{ freitag_jones_plassmann98,
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 Scientific and Engineering Computing",
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 },
TITLE = {Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods},
PUBLISHER = {SIAM},
YEAR = {1994},
ADDRESS = {Philadelphia, PA}
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@InProceedings{parasha2,
author = {M. Parashar and J. C. Browne and C. Edwards and K. Klimkowski},
title = { A Common Data Management Infrastructure for Parallel Adaptive
Algorithms for {PDE} Solutions},
booktitle = {SC97 Proceedings},
publisher = "IEEE Computer Society Press",
year = {1997}
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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"
}
@Article{parti,
author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang},
title = {Communication Optimizations for Irregular
Scientific Computations on Distributed Memory Architectures},
journal = {Journal of Parallel and Distributed Computing},
year = {1994},
volume = {22},
pages = {462--478}
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author = {G. Agrawal and A. Sussman and J. Saltz},
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journal = {IEEE Trans. on Parallel and Distributed Systems},
volume = {6},
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year = "1995"
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@Article{gropp-lusk-doss-skjellum,
author = { William Gropp and Ewing Lusk and Nathan Doss and Anthony
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author = "Greg Burns and Raja Daoud and James Vaigl",
title = "{LAM}: An Open Cluster Environment for {MPI}",
booktitle = "Proceedings of Supercomputing Symposium '94",
editor = "John W. Ross",
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year = "1999",
volume = "21",
pages = "792-797"
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@TechReport( cs97a,
AUTHOR = "X.-C. Cai and M. Sarkis",
TITLE = "A restricted additive {S}chwarz preconditioner for general sparse linear systems ",
YEAR = 1997,
Institution = "Computer Science Department,
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Number = "CU-CS 843-97",
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@article{cai2003restricted,
title={Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric positive definite linear systems},
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volume=41,
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pages={1209--1231},
year=2003,
doi={10.1137/S0036142901389621}
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@TECHREPORT{caisaad,
AUTHOR="Xiao-Chuan Cai and Youcef Saad",
TITLE="Overlapping domain decomposition algorithms for
general sparse matrices",
INSTITUTION="Army High Performance Computing
Research Center, University of Minnesota ",
YEAR="1993",
NUMBER="Preprint 93-027 ",
NOTE= "SIAM J. Sci. Comp. (submitted)"
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@BOOK{ruminations,
AUTHOR="Andrew Koenig and Barbara Moo",
TITLE="Ruminations on C++",
YEAR="1996",
PUBLISHER="Addison-Wesley"
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@BOOK{mpi-complete,
AUTHOR="Marc Snir and Steve Otto and Steven Huss-Lederman and David
Walker and Jack Dongarra",
TITLE="{MPI}: The Complete Reference",
YEAR="1995",
PUBLISHER="MIT Press"
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@Unpublished{ tcl-tk-web-page,
title = "{Tcl/Tk} {W}orld {W}ide {W}eb page",
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month = Aug
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author = {William Gropp and {et. al.}},
title = {{MPICH} {W}eb page},
key = "MPICH",
url = {http://www.mpich.org},
howpublished = {\url{http://www.mpich.org}},
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@article{MPI-final,
author = {MPI Forum},
Title = "{MPI}: A Message-Passing Interface Standard",
Journal = "International J. Supercomputing Applications",
Volume = 8,
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Year = 1994,
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@Unpublished{ npb-web-page,
key = "NAS Parallel Benchmarks",
title = "{NAS} {P}arallel {B}enchmarks {W}eb page",
note = "http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html",
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TITLE = "Computer Solution of Large Sparse Positive Definite Systems",
AUTHOR= "Alan George and Joseph W. Liu",
PUBLISHER = "Prentice-Hall",
YEAR = 1981,
KEY = "SparseDirect"
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@book{ p4-book,
TITLE = "Portable Programs for Parallel Processors",
PUBLISHER = "Holt, Rinehart, {and} Winston",
YEAR = 1987,
AUTHOR = "James Boyle and Ralph Butler and Terrence Disz and
Barnett Glickfeld and Ewing Lusk and Ross Overbeek and
James Patterson and Rick Stevens",
KEY = "P4Book"
}
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author = "H. L. Stone",
title = "Iterative solution of implicit approximations of multidimensional partial differential equations",
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author = "J. S. Reeve and A. D. Scurr and J. H. Merlin",
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@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
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Year = 1993
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@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-Chanpaign",
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 varient 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{ss:86,
author="Youcef Saad and Martin H. Schultz",
title="{GMRES}: A Generalized Minimal Residual Algorithm
for Solving Nonsymmetric Linear Systems",
journal = "SIAM J. Sci. Stat. Comput.",
year=1986,
volume=7,
pages="856-869"}
@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 fo 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
}
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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" }
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volume=23,
pages="1--21"
}
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
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author = "D. L. Whitfield and L. K. Taylor",
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Author = "{MSC Software Corporation}",
title = "{NASTRAN} {W}eb page",
note = "See {\tt http://www.mechsolutions.com\-/products\-/nastran/}"
}
@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"
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@inproceedings{keyes98,
AUTHOR = "D. E. Keyes",
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YEAR = "1998"
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author = "S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and
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month = "December",
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% ---------------------------------------------------------------------------------
% 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}",
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year = "2005"
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@misc{matlab-web-page,
author = {{The} {MathWorks}},
title = {{Matlab} {Web} page},
url = {http://www.mathworks.com}
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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}"
}
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Author = "A.M. Bruaset and H.P. Langtangen",
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Year = 1997,
pages = "61--90",
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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",
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key = {Fftw},
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@inproceedings{KlarlandSchwartzbach97,
AUTHOR = "Nils Klarland and Michael I. Schwartzbach",
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MONTH = "September",
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}"
}
@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",
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year = 2003
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number = 3,
pages = "363--396",
year = 2005
}
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title={{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}},
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year={2005}
}
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year = 1999,
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@techreport{ifpack,
title = "Robust Algebraic Preconditioners using {IFPACK} 3.0",
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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",
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@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",
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YEAR = "2002",
MONTH = "November",
ADDRESS = "Baltimore"
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@article{BeckerBraackRannacher1999,
title = {Numerical simulation of laminar flames at low Mach number by adaptive finite elements},
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year = {1999}
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@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
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journal = "Int. J. Numer. Meth. Eng.",
year = "1984",
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pages = {1111--1129}
}
@article{BabuskaMiller84c,
author = "I. Babu$\check{s}$ka and A.D. Miller",
title = "The post-processing approach in the finite element method, {III}: A posteriori error estimation and adaptive
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}
@unpublished{jtb-web-page,
title = "{The Java Tree Builder}",
note = "See \url{http://www.cs.purdue.edu/jtb}",
author = "Jens Palsberg",
institution = "Purdue University"
}
@unpublished{Palsberg98,
title = "Why Visitors?",
note = "See \url{http://www.cs.purdue.edu/jtb/whyvisitors}",
author = "Jens Palsberg",
institution = "Purdue University",
year = "1998"
}
@unpublished{ply-web-page,
title = "{PLY (Python Lex-Yacc)}",
note = "\url{http://systems.cs.chicago.edu/ply}",
author = "David Beazley",
institution = "University of Chicago"
}
@misc{adic-web-page,
title = "{ADIC Web page}",
note = "\url{http://www.mcs.anl.gov/autodiff}",
author = "Paul Hovland and Uwe Naumann and Boyana Norris",
institution = "Argonne National Laboratory"
}
@article{Naumann02,
author = "Uwe Naumann",
title = "Optimal accumulation of {J}acobian matrices by elimination methods on the dual computational graph",
journal = "Mathematical Programming (to appear)",
note = "Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002",
year = "2003"
}
@article{kaper1,
author = "H. G. Kaper and T. J. Kaper",
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Institution = {Department of Computer Science, University of Minnesota},
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Note = {http://www.cs.umn.edu/~metis},
Number = {97-060},
Title = {{ParMETIS}: Parallel graph partitioning and sparse matrix ordering library},
Year = {1997}
}
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note = "Columbia University, in preparation",
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key = "{Advanced CompuTational Software (ACTS) Web page}",
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% -----------------------------------------------------------------------
% Model coupling refs
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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 seach 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.}},
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citeulike-article-id = {115158},
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month = {January},
publisher = {{Addison-Wesley Professional}},
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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.
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author = {Chow, Edmond},
citeulike-article-id = {7675372},
citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
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priority = {2},
title = {An Unstructured Multigrid Method Based on Geometric Smoothness},
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citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
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pages = {109--133},
posted-at = {2011-01-13 18:05:55},
priority = {2},
publisher = {SIAM},
title = {{AMGE Based on Element Agglomeration}},
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pages = {461--469},
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year = {2002}
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@article{BurovWatts06,
author = {E.B. Burov and A.B. Watts},
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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}
}
@article{demmel09,
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
}
@TechReport( parms04,
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,
)
@article{Picard1890,
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},
publisher = {Krieger Pub Co.},
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year = {1969}
}
@article{FletcherReeves1964,
author = {R. Fletcher and C. M. Reeves},
title = {Function Minimization by Conjugate Gradients},
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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
}
@article{murphy2000npi,
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-}
}
@article{elman2011bouyancy,
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}
}
@ARTICLE{DongarraBeckman11,
AUTHOR={J. Dongarra and P. Beckman and et al.},
TITLE={The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap},
JOURNAL={Int. J. High Perf. Comput. Applics.},
VOLUME={25},
YEAR={2011},
PAGES={3--60}
}
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title={Energy optimization of algebraic multigrid bases},
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year={1999},
publisher={Springer}
}
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pages={179--196},
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publisher={Springer}
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@article{vanek2001convergence,
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}
}
@article{brannick2007algebraic,
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}
}
@article{Olson10,
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}
}
@inproceedings{Adams04,
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 = {March},
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}
}
@book{ScalesReport,
title = {A Science-based Case for Large-scale Simulation},
editor = {D. E. Keyes},
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 Parallel Programming (PPoPP)},
day = {19--21},
month = jul,
pages = {207--216},
title = {{Cilk}: An Efficient Multithreaded Runtime System},
year = {1995}
}
@misc{valgrind-web-page,
author = {Julian Seward},
title = {Valgrind},
url = {http://valgrind.org/},
howpublished = {\url{http://valgrind.org/}},
year = {2012}
}
@article{BLAS79,
author = {C.~L. Lawson and R.~J. Hanson and D. Kincaid and F.~T. Krogh},
title = {Basic linear algebra subprograms for Fortran usage},
journal = {ACM Transactions on Mathematical Software},
volume = {5},
pages = {308--323},
year = {1979}
}
@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 = {December},
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},
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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},
}
@article{Strout04,
Journal = {International Journal of High Performance Computing Applications},
Year = {2004},
Title = {Sparse Tiling for Stationary Iterative Methods},
Month = {February},
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 Numpy},
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 = {June},
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 = {October},
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 = {October},
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 = {December},
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 = {March},
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{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\&amp;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 = {September},
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 = {June},
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 = {July},
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},
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}
}
@techreport{Ghysels_Ashby_Meerbergen_Vanroose_2012,
Author = {Ghysels, P. and Ashby, T.J. and Meerbergen, K. and Vanroose, W.},
Institution = {Intel Exascience Lab},
Address= {Leuven, Belgium},
Number = {04.2012.1},
Type = {Tech. report},
Title = {Hiding global communication latency in the {GMRES} algorithm on massively parallel machines},
url = {http://twna.ua.ac.be/sites/twna.ua.ac.be/files/latency_gmres.pdf},
Year = {2012}
}
@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},
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publisher = {Springer},
year = {1999}
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@inproceedings{HoeflerLumsdaineRehm07,
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booktitle = {Proceedings of the 2007 International Conference on High Performance Computing, Networking, Storage and Analysis, SC07},
location = {Reno, NV},
publisher = {IEEE Computer Society/ACM},
source = {http://www.unixer.de/~htor/publications/},
month = {Nov.},
year = {2007}
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author = {T. Hoefler and C. Siebert and A. Lumsdaine},
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booktitle = {Proceedings of the 2010 ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP'10)},
month = {Jan.},
location = {Bangalore, India},
publisher = {ACM},
isbn = {978-1-60558-708-0},
source = {http://www.unixer.de/~htor/publications/},
pages = {159--168},
year = {2010},
}
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year={2016},
publisher={ACM}
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D. Osei-Kuffuor and J. Sarich and B. Smith and J. Willenbring and U.M. Yang},
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year = 2017,
note = {available via \url{https://arxiv.org/abs/1702.08425}}
}
@misc{deal.II:website,
title = "{{deal.II}: An open-source finite element library}",
author = "Wolfgang Bangerth and others",
howpublished="\url{http://www.dealii.org}",
year = 2018
}
@misc{fission-gas-scidac:website,
title = "{Simulation of Fission Gas in Uranium Oxide Nuclear Fuel}",
author = "A. David {Andersson (PI)}",
howpublished="SciDAC project, \url{https://collab.cels.anl.gov/display/FissionGasSciDAC2}",
year = 2018
}
@misc{tokamak-disruption-scidac:project,
title = "{Tokamak Disruption Simulation}",
author = "Xianzhu {Tang (PI)}",
howpublished="SciDAC project",
year = 2018
}
@inproceedings{duplyakin2018memory,
title={Evaluating Active Learning with Cost and Memory Awareness},
author={Duplyakin, Dmitry and Brown, Jed and Calhoun, Donna},
booktitle={2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
pages={214--223},
year={2018},
organization={IEEE},
pdf={https://jedbrown.org/files/DuplyakinBrownCalhoun-ActiveLearningCostMemoryAware-2018.pdf}
}
@InProceedings{duplyakin2016active,
author = "Dmitry Duplyakin and Jed Brown and Robert Ricci",
title = "Active Learning in Performance Analysis",
booktitle = "Proceedings of the IEEE Cluster Conference",
year = 2016,
month = Sep,
url = "http://www.flux.utah.edu/paper/duplyakin-cluster16",
pdf = {https://jedbrown.org/files/DuplyakinBrownRicci-ActiveLearningPerformanceAnalysis-2016.pdf}
}
@misc{XGC1:website,
title = "{XGC1 project website}",
author = "C. S. Chang and others",
howpublished="\url{https://epsi.pppl.gov/computing/xgc-1}",
year = 2018
}
@misc{WDMApp-Bhattacharjee-ECP:website,
title = "{WDMApp: High-Fidelity Whole Device Modeling of Magnetically Confined Fusion Plasmas}",
author = "A. Bhattacharjee and others",
note = "ECP application project",
howpublished = "\url{https://www.exascaleproject.org/activity/energy-applications}",
year = 2018
}
@misc{subsurface-Steefel-ECP:website,
title = "{Subsurface: Exascale Subsurface Simulator of Coupled Flow, Transport, Reactions, and Mechanics}",
note = "ECP application project",
author = "C. Steefel and others",
howpublished="\url{https://www.exascaleproject.org/activity/earth-space-science-applications}",
year = 2018
}
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title = "High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration",
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year = 2014,
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year={2012}
}
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pages = {612--632},
year = {2011},
}
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title = {Large displacement body-fitted {FSI} simulations using a mesh-connectivity-change moving mesh strategy},
author = {Nicolas Barral and Fr{\'e}d{\'e}ric Alauzet},
booktitle = {44th AIAA Fluid Dynamics Conference},
pages = {2773},
year = {2014}
}
@inproceedings{BarralAlauzetLoseille2015,
title = {Metric-based anisotropic mesh adaptation for three-dimensional time-dependent problems involving moving geometries},
author = {Nicolas Barral and Fr{\'e}d{\'e}ric Alauzet and Adrien Loseille},
booktitle = {53rd AIAA Aerospace Sciences Meeting},
pages = {2039},
year = {2015}
}
@article{BarralOlivierAlauzet2017,
title = {Time-accurate anisotropic mesh adaptation for three-dimensional time-dependent problems with body-fitted moving geometries},
author = {Nicolas Barral and G{\'e}raldine Olivier and Fr{\'e}d{\'e}ric Alauzet},
journal = {Journal of Computational Physics},
volume = {331},
pages = {157--187},
year = {2017},
}
@article{IbanezBarralKrakosLoseilleMichalPark2017,
title = {First Benchmark of the Unstructured Grid Adaptation Working Group},
author = {Daniel Ibanez and Nicolas Barral and Joshua Krakos and Adrien Loseille and Todd Michal and Mike Park},
journal = {Procedia engineering},
volume = {203},
pages = {154--166},
year = {2017}
}
@inproceedings{ParkBarralIbanezKamenetskiyKrakosMichalLoseille2018,
title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows},
author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and Joshua A Krakos and Todd R Michal and Adrien Loseille},
booktitle = {2018 AIAA Aerospace Sciences Meeting},
pages = {1103},
year = {2018}
}
@inproceedings{BarralAngeloudisKramerGormanPiggott2018,
title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics modelling},
author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman and Matthew D Piggott},
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volume = {20},
pages = {19168},
year = {2018}
}
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title = {{Mathematical models for thermally coupled low speed flows}},
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year = {2009}
}
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title = {Iterative {K}rylov Methods for Large Linear Systems},
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year = {2003},
}
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author = {Asher Peres},
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year = {2006}
}
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title = {Linear algebra: theory and applications},
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year = {2012}
}
@book{elman_silvester_wathen_2014,
place = {Oxford},
title = {Finite elements and fast iterative solvers: with applications in incompressible fluid dynamics},
publisher = {Oxford University Press},
author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.},
url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&},
year = {2014}
}
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title = {An evaluation of the ORNL Cray XT3},
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journal = {International Journal of High Performance Computing Applications},
volume = {22},
number = {1},
pages = {52--80},
doi = {10.1177/1094342007085019},
year = {2007}
}
@article{PlazaCarey2000,
title = {Local refinement of simplicial grids based on the skeleton},
author = {Plaza, A. and Carey, Graham F.},
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pages = {195--218},
year = {2000}
}
@article{CarsonStrakos2020,
title = {On the cost of iterative computations},
author = {Eric Carson and Zden\v{e}k Strako\v{s}},
journal = {Phil. Trans. R. Soc. A},
volume = {378},
number = {20190050},
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year = {2020}
}
@article{Schoberl1999,
title = {Multigrid methods for a parameter dependent problem in primal variables},
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pages = {97--119},
year = {1999}
}
@article{WuLeeXuZikatanov2008,
title = {Convergence analysis on iterative methods for semidefinite systems},
author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov},
journal = {Journal of Computational Mathematics},
pages = {797--815},
year = {2008},
}
@article{MaierRannacher2016,
title={Duality-based adaptivity in finite element discretization of heterogeneous 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}
}
%
% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3>
%
%
@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"
}
@String{AJ = "Astrophysics J."}
@String{PC = "Parallel Computing"}
@String{AIAAJ = "AIAA J."}
@String{LAA = "Linear Algebra and Applications"}
@String{JCP = "J. Computational Physics"}
@String{JPDC = "J. Parallel and Distributed Computing"}
@String{ANM = "Applied Numerical Mathematics"}
@String{SIAPMA = "SIAM J. Applied Mathematics"}
@String{SICOMP = "SIAM J. Computing"}
@String{SIMAX = "SIAM J. Matrix Analysis and Applications"}
@String{SINUM = "SIAM J. Numerical Analysis"}
@String{SIREV = "SIAM Review"}
@String{SISSC = "SIAM J. Scientific and Statistical Computing"}
@String{SISC = "SIAM J. Scientific Computing"}
@String{SIOPT = "SIAM J. Optimization"}
@String{NumMath = "Numerische Mathematik"}
@String{MathComp = "Mathematics of Computation"}
@String{IJNMF = "International J. for Numerical Methods in Fluids"}
@String{Impact = "Impact of Computing in Science and Engineering"}
@String{CPC = "Computer Physics Communications"}
@String{jota = "J. Optimization Theory and Applications"}
@String{ZaMM = "Zeitschrift f\:{u}r angewandte Mathematik und
Mechanik"}
% ------------------- 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{NW99,
author = "Jorge Nocedal and Stephen J. Wright",
title = "Numerical Optimization",
year = "1999",
publisher = "Springer-Verlag",
address = "New York",
}
@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",
}
%
% bfort: Used to generate TAO Fortran interface
%
@TechReport{bfort,
author = "William Gropp",
title = "Users Manual for bfort: Producing {F}ortran interfaces
to {C} source code",
institution = "Argonne National Laboratory",
number = "ANL/MCS-TM-208",
month = MAR,
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 a nd 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."
}
@String{academic = "Academic Press"}
@String{acmtoms = "{ACM} Transactions on Mathematical Software"}
@String{addison = "Addison-Wesley"}
@String{amopt = "Applied Mathematics and Optimization"}
@String{asmebiomech = "Journal of Biomechanical Engineering"}
@String{annor = "Annals of Operations Research"}
@String{bullams = "Bulletin of the American Mathematical Society"}
@String{coap = "Computational Optimization and Applications"}
@String{dmitr = "Data Mining Institute Technical Report"}
@String{ftpsrc = "Available from
ftp://ftp.cs.wisc.edu/math-prog/tech-reports/"}
@String{jacm = "Journal of Associated Computing Machinery"}
@String{jmaa = "Journal of Mathematical Analysis and its
Applications"}
@String{joc = "INFORMS Journal on Computing"}
@String{jota = "Journal of Optimization Theory and Applications"}
@String{kluwer = "Kluwer Academic Publishers"}
@String{laa = "Linear Algebra and Its Applications"}
@String{madison = "Madison, Wisconsin"}
@String{mansci = "Management Science"}
@String{mathcomp = "Mathematics of Computation"}
@String{mathor = "Mathematics of Operations Research"}
@String{mathprog = "Mathematical Programming"}
@String{mathprogstudy = "Mathematical Programming Study"}
@String{mptr = "Mathematical Programming Technical Report"}
@String{navres = "Naval Research Logistics Quarterly"}
@String{northholland = "North-Holland"}
@String{nummath = "Numerische Mathematik"}
@String{ojc = "ORSA Journal on Computing"}
@String{oms = "Optimization Methods and Software"}
@String{opres = "Operations Research"}
@String{opreslet = "Operations Research Letters"}
@String{prenticehall = "Prentice-Hall, Inc"}
@String{siamath = "SIAM Journal on Applied Mathematics"}
@String{sicon = "SIAM Journal on Control and Optimization"}
@String{simax = "SIAM Journal on Matrix Analysis and Applications"}
@String{sina = "SIAM Journal on Numerical Analysis"}
@String{siopt = "SIAM Journal on Optimization"}
@String{sisc = "SIAM Journal on Scientific Computing"}
@String{sissc = "SIAM Journal on Scientific and Statistical Computing"}
@String{smd = "Soviet Mathematics Doklady"}
@String{springer = "Springer-Verlag"}
@String{transams = "Transactions of the American Mathematical Society"}
@String{transport = "Transportation Research"}
@String{uwcs = "Computer Sciences Department, University of
Wisconsin"}
@String{wiley = "John Wiley \& Sons"}
@Misc{:alertsys,
title = "page{ALERT}",
organization = "Alert Systems, Inc",
address = madison,
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 = wiley,
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 = opres,
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 = mathprog,
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 = mathprog,
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 = jota,
year = "1981",
volume = "33",
pages = "175--185",
}
@Article{al-fahed.stavroulakis.ea:hard,
author = "A. M. Al-Fahed and G. E. Stavroulakis and P. D.
Panagiotopoulos",
title = "Hard and soft fingered robot grippers. The linear
complementarity approach",
journal = "Zeitschrift f{\"{u}}r Angewandte Mathematik und
Mechanik",
volume = "71",
year = "1991",
pages = "257--265",
}
@Article{al-fahed.stavroulakis.ea:linear,
author = "A. M. Al-Fahed and G. E. Stavroulakis and P. D.
Panagiotopoulos",
title = "A linear complementarity approach to the frictionless
gripper",
journal = "International Journal of Robotic Research",
volume = "11",
year = "1992",
pages = "112--122",
}
@Article{al-khayyal.falk:jointly,
author = "F. A. Al--Khayyal and J. E. Falk",
title = "Jointly Constrained Biconvex Programming",
journal = mathor,
year = "1983",
volume = "8",
pages = "273--286",
}
@Article{al-khayyal.kyparisis:finite,
author = "F. A. Al--Khayyal and J. Kyparisis",
title = "Finite Convergence of Algorithms for Nonlinear
Programs and Variational Inequalities",
journal = jota,
year = "1991",
volume = "70",
pages = "319--332",
}
@PhdThesis{al-khayyal:biconvex,
author = "F. A. Al--Khayyal",
title = "Biconvex Programming and Biconcave Minimization",
year = "1977",
school = "The George Washington University",
}
@Article{alart.curnier:mixed,
author = "P. Alart and A. Curnier",
title = "A mixed formulation for frictional contact problems
prone to {N}ewton like solution methods",
journal = "Computer Methods in Applied Mechanics and
Engineering",
volume = "92",
year = "1991",
pages = "353--375",
}
@Misc{alexander.kellog.ea:piecewise,
author = "J.~C. Alexander and R.~B. Kellog and T.-Y. Li and
J~.A. Yorke",
title = "Piecewise smooth continuation",
howpublished = "Manuscript",
year = "1979",
}
@InCollection{alexander.li.ea:piecewise,
author = "J.~C. Alexander and T.-Y. Li and J~.A. Yorke",
title = "Piecewise smooth homotopies",
booktitle = "Homotopy Methods and Global Convergence",
pages = "1--14",
publisher = "Plenum Press",
year = "1983",
editor = "B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and
M.~J. Todd",
address = "New York",
}
@InCollection{alexander:topological,
author = "J.~C. Alexander",
title = "The topological theory of an embedding method",
booktitle = "Continuation Methods",
pages = "37--68",
publisher = "Academic Press",
year = "1978",
editor = "H. Wacker",
address = "New York",
}
@Book{allen:probability,
author = {A. O. Allen},
title = {Probability, Statistics and Queueing Theory},
publisher = {Academic Press},
year = 1990,
address = {London},
edition = {Second}
}
@Book{allgower.georg:numerical,
author = "E. L. Allgower and K. Georg",
title = "Numerical Continuation Methods, An Introduction",
publisher = "Springer-Verlag",
year = "1990",
address = "Berlin",
}
@InProceedings{allgower.georg:predictor-corrector,
crossref = "bachem.grotschel.ea:mathematical",
author = "E. L. Allgower and K. Georg",
title = "Predictor--Corrector and Simplicial Methods for
Approximating Fixed Points and Zero Points of Nonlinear
Mappings",
pages = "15--56",
}
@Article{aluffi-pentini.parisi.ea:algorithm,
author = "F. Aluffi-Pentini and V. Parisi and F. Zirilli",
title = "Algorithm 667: {SIGMA}- {A} Stochastic-Integration
Global Minimization Algorithm",
journal = "ACM Transactions on Mathematical Software",
year = "1988",
volume = "14",
pages = "366--380",
}
@Article{anandalingam.friesz:hierarchical,
author = "G. Anandalingam and T. L. Friesz",
title = "Hierarchical Optimization: An Introduction",
journal = annor,
year = "1992",
volume = "34",
pages = "1--11",
}
@Article{anandalingam.white:solution,
author = "G. Anandalingam and D. J. White",
title = "A Solution Method for the Linear Static Stackelberg
Problem Using Penalty Functions",
journal = "IEEE Transactions on Automatic Control",
year = "1990",
volume = "35",
number = "10",
pages = "1170--1173",
}
@Article{andersen.andersen:presolving,
author = "E. Andersen and K. Andersen",
title = "Presolving in Linear Programming",
year = "1995",
journal = mathprog,
volume = "71",
pages = "221--245",
}
@InProceedings{andersen.ye:homogeneous,
author = "E. Andersen and Y. Ye",
title = "On a Homogeneous Algorithm for a Monotone
Complementarity Problem with Nonlinear Equality
Constraints",
crossref = "ferris.pang:complementarity",
pages = "1--11",
}
@Book{anderson.bai.ea:lapack,
author = "E. Anderson and Z. Bai and C. Bischof and J. Demmel
and J. Dongarra and J. Du Cros and A. Greenbaum and S.
Hammarling and A. McKenney and S. Ostrouchov and D.
Sorensen",
title = "{LAPACK} User's Guide",
publisher = "SIAM",
year = "1995",
address = "Philadelphia, Pennsylvania",
edition = "Second",
}
@Article{anderson.ferris:direct,
author = "E. J. Anderson and M. C. Ferris",
title = "A Direct Search Algorithm for Optimization with Noisy Function Evaluations",
year = 2001,
journal = "SIAM Journal on Optimization, forthcoming",
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps",
key = "55",
}
@InProceedings{anderson.ferris:genetic,
author = "E. J. Anderson and M. C. Ferris",
title = "A Genetic Algorithm for the Assembly Line Balancing Problem",
booktitle = "Proceedings of the Integer Programming / Combinatorial Optimization Conference, Waterloo, Ontario, Canada, May 28--30",
publisher = "University of Waterloo Press",
key = "14",
year = "1990"
}
@Article{anderson.ferris:genetic*1,
author = "E. J. Anderson and M. C. Ferris",
title = "Genetic Algorithms for Combinatorial Optimization: The
Assembly Line Balancing Problem",
journal = ojc,
year = "1994",
URL = "ftp:
//ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps",
volume = "6",
pages = "161--173",
key = "22",
}
@InProceedings{anderson.ferris:parallel,
author = "E. J. Anderson and M. C. Ferris",
title = "Parallel Genetic Algorithms in Optimization",
booktitle = "Proceedings of the Fourth SIAM conference on Parallel
Processing for Scientific Computing, Chicago, Illinois,
December 11-13",
year = "1989",
key = "12",
}
@Unpublished{anderson.lewis:primal,
author = "E. J. Anderson and A. S. Lewis",
title = "A New Primal Algorithm for Semi-Infinite Linear
Programming",
note = "In preparation",
}
@Book{anderson.nash:linear,
author = "E. J. Anderson and P. Nash",
title = "Linear Programming in Infinite--Dimensional Spaces",
year = "1987",
publisher = wiley,
address = "Chichester",
}
@InProceedings{anderson:primal,
author = "E. J. Anderson",
title = "A New Primal Algorithm for Semi-Infinite Linear
Programming",
booktitle = "Proceedings of an International Symposium on Infinite
Dimensional Linear Programming, Cambridge, September
1984",
year = "1985",
editor = "E. J. Anderson and A. B. Philpott",
publisher = springer,
address = "Berlin",
}
@Article{andradottir:method,
author = "S. Andrad\'{o}ttir",
title = "A Method of Discrete Stochastic Optimization",
journal = mansci,
year = "1995",
volume = "41",
pages = "1946--1961",
}
@Article{andradottir:global,
author = "S. Andrad\'{o}ttir",
title = "A Global Search Method for Discrete Stochastic Optimization",
journal = siopt,
year = "1996",
volume = "6",
pages = "513--530",
}
@TechReport{anitescu.lesaja.ea:infeasible-interior-point,
author = "M. Anitescu and G. Lesaja and F. A. Potra",
title = "An infeasible--interior--point predictor--corrector
algorithm for the {P}$_x$--geometric {LCP}",
institution = "Department of Mathematics, The University of Iowa",
address = "Iowa City, Iowa",
year = "1994",
number = "62",
type = "Reports on Computational Mathematics",
}
@TechReport{anitescu.potra:formulating,
author = "M. Anitescu and F. A. Potra",
title = "Formulating Dynamic Multi-Rigid-Body Contact Problems
with Friction as Solvable Linear Complementarity
Problems",
institution = "Department of Mathematics, The University of Iowa",
year = "1996",
type = "Report",
number = "93",
address = "Iowa City, Iowa",
}
@Article{anstreicher.lee.ea:crashing,
author = "K. M. Anstreicher and J. Lee and T. F. Rutherford",
title = "Crashing a Maximum-Weight Complementarity Basis",
journal = mathprog,
year = "1992",
volume = "54",
pages = "281--294",
}
@Article{anstreicher:combined,
author = "K. M. Anstreicher",
title = "A combined phase {I}--phase {II} scaled potential
algorithm for linear programming",
journal = mathprog,
year = "1991",
volume = "52",
pages = "429--440",
}
@Article{anstreicher:combined*1,
author = "K. M. Anstreicher",
title = "A combined phase {I}--phase {II} projective algorithm
for linear programming",
journal = mathprog,
year = "1989",
volume = "43",
pages = "209--223",
}
@InCollection{arbenz.gander.ea:remote,
author = "P. Arbenz and W. Gander and M. Oettli",
title = "The Remote Computational System",
booktitle = "High-Performance Computation and Networks",
publisher = springer,
year = "1996",
volume = "1067",
series = "Lecture Notes in Computer Science",
pages = "662--667",
}
@InCollection{arcus:comsoal,
author = "A. L. Arcus",
title = "{COMSOAL}: {A} Computer Method of Sequencing
Operations for Assembly Lines",
booktitle = "Readings in Production and Operations Management",
year = "1966",
editor = "E. S. Buffa",
publisher = wiley,
address = "New York",
}
@TechReport{arioli.chan.ea:computing,
author = "M. Arioli and T. F. Chan and I. S. Duff and N. I. M.
Gould and J. K. Reid",
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@TechReport{bennett.wu.ea:support,
author = "K. P. Bennett and D. Wu and L. Auslender",
title = "On Support Vector Decision Trees for Database
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institution = "Department of Mathematical Sciences, Rensselaer
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year = "1998",
OPTkey = "",
OPTtype = "RPI Math Report",
OPTnumber = "98-100",
OPTaddress = "Troy, New York",
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OPTnote = "",
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author = "A. B. Berkelaar and B. Jansen and C. Roos and T.
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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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author = "D. P. Bertsekas and J. N. Tsitsiklis",
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year = "1982",
publisher = academic,
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title = "Dynamic Programming and Optimal Control",
publisher = "Athena Scientific",
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@Book{bertsekas:nonlinear,
author = "D. P. Bertsekas",
title = "Nonlinear Programming",
publisher = "Athena Scientific",
year = "1995",
address = "Belmont, Massachusetts",
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author = "S. C. Billups and S. P. Dirkse and M. C. Ferris",
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journal = coap,
year = "1997",
pages = "3--25",
volume = "7",
URL = "ftp:
//ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps",
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@Article{billups.ferris:convergence,
author = "S. C. Billups and M. C. Ferris",
title = "Convergence of an Infeasible Interior--Point Algorithm
from Arbitrary Positive Starting Points",
journal = siopt,
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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@TechReport{billups.ferris:convergence*1,
author = "S. C. Billups and M. C. Ferris",
title = "Convergence of Infeasible Interior--Point Algorithms
from Arbitrary Starting Points",
institution = uwcs,
year = "1993",
address = madison,
number = "1180",
note = "Revised version in SIAM Journal on Optimization.",
}
@Article{billups.ferris:qpcomp,
author = "S. C. Billups and M. C. Ferris",
title = "{QPCOMP}: {A} Quadratic Program Based Solver for Mixed
Complementarity Problems",
year = "1997",
journal = mathprog,
pages = "533--562",
volume = "76",
URL = "ftp:
//ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps",
key = "47",
}
@Article{billups.ferris:solutions,
author = "S. C. Billups and M. C. Ferris",
title = "Solutions to Affine Generalized Equations Using
Proximal Mappings",
journal = mathor,
volume = "24",
pages = "219--236",
year = "1999",
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps",
key = "42",
institution = uwcs,
address = madison,
type = mptr,
number = "94--15",
}
@TechReport{billups.murata.ea:users,
author = "S. C. Billups and K. K. Murata and K. E. Washington and D. L. Y. Louie",
title = "User's manual for {CONTAIN--HWR/0}, Rev. 1: {A} Computer Code for the Analysis of Heavy Water Nuclear Reactor Containments Under Accident Conditions",
institution = "SNL",
year = "1994",
month = jan,
address = "Albuquerque, New Mexico",
number = "SAND91--1482",
}
@TechReport{billups.speight.ea:nonmonotone,
author = "S. C. Billups and A. L. Speight and L. T. Watson",
title = "Nonmonotone Path Following Methods for Nonsmooth
Equations and Complementarity Problems",
institution = "Department of Mathematics, University of Colorado",
year = "1999",
address = "Denver, Colorado",
}
@PhdThesis{billups:algorithms,
author = "S. C. Billups",
title = "Algorithms for Complementarity Problems and
Generalized Equations",
school = "University of Wisconsin--Madison",
year = "1995",
address = "Madison, Wisconsin",
month = aug,
}
@MastersThesis{billups:augmented,
author = "S. C. Billups",
title = "An Augmented Jacobian Matrix Algorithm for Tracking
Homotopy Zero Curves",
school = "Virginia Tech",
year = "1985",
address = "Blacksburg, Virginia",
}
@TechReport{billups:homotopy,
author = "S. C. Billups",
title = "A Homotopy Based Algorithm for Mixed Complementarity Problems",
institution = "Department of Mathematics, University of Colorado",
year = "1998",
address = "Denver, Colorado",
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@Article{billups:improving,
author = "S. C. Billups",
title = "Improving the Robustness of Descent-Based Methods for Semi-Smooth Equations Using Proximal Perturbations",
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volume = 87,
pages = "153--176"
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@TechReport{bischof.carle.ea:adifor,
author = "C. Bischof and A. Carle and P. Khademi and A. Mauer
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institution = "Argonne National Laboratory",
year = "1995",
address = "Argonne, Illinois",
number = "ANL/MCS--TM--192",
type = "Mathematics and Computer Science Division Report",
}
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author = "J. Bisschop and R. Entriken",
title = "{AIMMS} -- The Modeling System",
year = "1993",
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Savelsbergh",
title = "{MIPLIB} 3.0",
howpublished = "http://www.caam.rice.edu/\~bixby/miplib/miplib.html",
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@InProceedings{bjorkman.klarbring.ea:sequential,
author = "G. Bj{\"{o}}rkman and A. Klarbring and T. Larsson and
M. R{\"{o}}nnqvist and B. Sj{\"{o}}din",
title = "Sequential quadratic programming for non-linear
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editor = "J. Herskovits",
booktitle = "Structural Optimization 93, The World Congress on
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volume = "2",
year = "1993",
pages = "301--308",
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@Article{bjorkman:path,
author = "G. Bj{\"o}rkman",
title = "Path Following and Critical Points for Contact
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pages = "231--246",
year = "1992",
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author = "G. Bj{\"o}rkman",
title = "The Solution of Large Displacement Frictionless
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type = "{Technical Report}",
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institution = "Computer and Information Sciences Department,
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author = "A. Dax",
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@Article{debremaecker.ferris.ea:compressional,
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key = "90",
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/00-01.ps",
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pages = "601--605",
institution = uwcs,
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author = "K. A. De~Jong",
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@TechReport{deluca.facchinei.ea:combining,
author = "T. {De~Luca} and F. Facchinei and C. Kanzow",
title = "Combining Equation-Based Methods for the Solution of
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type = "Preprint",
institution = "Institute of Applied Mathematics, University of
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year = "1996",
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@TechReport{deluca.facchinei.ea:general,
author = "T. {De~Luca} and F. Facchinei and C. Kanzow",
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year = "1997",
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author = "T. {De~Luca} and F. Facchinei and C. Kanzow",
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journal = mathprog,
volume = "75",
pages = "407--439",
year = "1996",
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@Article{deluca.facchinei.ea:theoretical,
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institution = "Instituto de Matematica, Elasticita e Ciencia da
Computacao",
year = "1990",
address = "Universidade Estadual de Campinas, CP 6065, Campinas,
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author = "G. Di~Pillo and L. Grippo and F. Lampariello",
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@TechReport{dirkse.ferris.ea:gams,
author = "S. P. Dirkse and M. C. Ferris and P. V. Preckel and T.
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institution = uwcs,
year = "1994",
address = madison,
number = "94-07",
type = mptr,
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
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pages = "40--61",
URL = "ftp:
//ftp.cs.wisc.edu/math-prog/tech-reports/95-22.ps",
key = "52",
}
@Article{dirkse.ferris:mcplib,
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year = "1995",
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key = "36",
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@InCollection{dirkse.ferris:modeling,
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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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@Article{dirkse.ferris:path,
author = "S. P. Dirkse and M. C. Ferris",
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year = "1995",
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key = "39",
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@InCollection{dirkse.ferris:traffic,
author = "S. P. Dirkse and M. C. Ferris",
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key = "61",
URL = "ftp:
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address = madison,
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annote = "Mathematical Programming Technical Report 94-12",
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@TechReport{dixon.mills:neural,
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@Article{dsouza.meyer.ea:mixed,
author = "W. D. D'Souza and R. R. Meyer and M. C. Ferris and B.
R. Thomadsen",
title = "Mixed Integer Programming Models for Prostate
Brachytherapy Treatment Optimization",
journal = "Medical Physics",
year = "1999",
key = "85",
volume = "26",
number = "6",
pages = "1099",
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@TechReport{dsouza.meyer.ea:mixed*1,
author = "W. D. D'Souza and R. R. Meyer and M. C. Ferris and B.
R. Thomadsen",
title = "Mixed Integer Programming Models for Prostate
Brachytherapy Treatment Optimization",
year = "1999",
key = "87",
URL = "ftp:
//ftp.cs.wisc.edu/math-prog/tech-reports/99-08.ps",
institution = uwcs,
address = madison,
number = "99-08",
type = mptr,
annote = "Submitted to ",
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@Article{dsouza.meyer.ea:iterative,
author = "W. D. D'Souza and R. R. Meyer and B. R. Thomadsen and M. C. Ferris",
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journal = "Physics and Medicine in Biology, forthcoming",
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@TechReport{eager.ferris.ea:models,
author = "D. L. Eager and M. C. Ferris and M. K. Vernon",
title = "Models for Optimized Regional Caching in Heterogeneous
Video-On-Demand Systems",
institution = uwcs,
year = "1999",
type = "Technical Report",
number = "1402",
address = madison,
URL = "http:
//www.cs.wisc.edu/tech-reports/reports/1999/tr1402.ps.Z",
key = "84",
}
@InProceedings{eager.ferris.ea:optimized,
author = "D. L. Eager and M. C. Ferris and M. K. Vernon",
title = "Optimized Regional Caching for On-Demand Data Delivery",
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",
}
@Article{eager.ferris.ea:optimized*1,
author = {D. L. Eager and M. C. Ferris and M. K. Vernon},
title = {Optimized Caching in Systems with Heterogeneous Client Populations},
journal = {Performance Evaluation},
year = {2000},
key = {72},
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-15.ps",
volume = {42},
pages = {163--185},
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@InProceedings{eager.vernon:dynamic,
author = "D. L. Eager and M. K. Vernon",
title = "Dynamic Skyscraper Broadcasts for Video-On-Demand",
year = "1998",
booktitle = "Proceedings of the 4th International Workshop on
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pages = "18--32",
address = "Istanbul, Turkey",
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volume = "6",
pages = "475--484",
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@Article{eaves.rothblum:relationships,
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author = "B. C. Eaves",
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year = "1978",
volume = "7",
pages = "1--14",
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@InCollection{eaves:computing*1,
author = "B. C. Eaves",
title = "Computing Stationary Points, Again",
pages = "391--405",
crossref = "mangasarian.meyer.ea:nonlinear*3",
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journal = mathprog,
year = "1972",
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address = "Providence, RI",
pages = "73--143",
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author = "A. A. Ebiefung and M. M. Kostreva",
title = "{Z}--Matrices annd the Generalized Linear
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institution = "Department of Mathematical Sciences, Clemson
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year = "1991",
number = "608",
address = "Clemson, South Carolina",
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title={A Semismooth {N}ewton Method for Variational Inequalities: {T}he Case of Box Constraints},
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volume={92},
pages={76},
year={1997}
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@TechReport{facchinei.fischer.ea:simply,
author = "F. Facchinei and A. Fischer and C. Kanzow and J. -M.
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institution = "University of Hamburg",
year = "1996",
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volume = "85",
pages = "107--134",
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volume = "92",
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@TechReport{facchinei.pang:total,
author = "F. Facchinei and J. S. Pang",
title = "Total stability of variational inequalities",
institution = "Universit\'a di Roma ``La Sapienza'', Dipartimento di
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type = "Manuscript",
address = "Roma, Italy",
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year = "1997",
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author = "F. Facchinei and J. Soares",
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author = "G. Fang and B. Geiser and T. R. Mackie",
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author = "M. C. Ferris and R. Fourer and D. M. Gay",
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journal = siopt,
volume = "9",
pages = "991--1009",
year = "1999",
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-02.ps",
key = "65",
institution = uwcs,
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@TechReport{ferris.horn:NLP2MCP,
author = "M. C. Ferris and J. D. Horn",
title = "{NLP2MCP}: Automatic conversion of nonlinear programs
into mixed complementarity problems",
year = "1998",
institution = uwcs,
note = "In preparation",
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@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 = mathprog,
key = "40",
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@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 = mathprog,
volume = "86",
pages = "475--497",
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key = "67",
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@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 = uwcs,
address = madison,
number = "98-17",
type = mptr
}
@Article{ferris.lucidi.ea:nonmonotone,
author = "M. C. Ferris and S. Lucidi and M. Roma",
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pages = "117--136",
year = "1996",
URL = "ftp:
//ftp.cs.wisc.edu/math-prog/tech-reports/94-16.ps",
key = "43",
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@TechReport{ferris.lucidi:globally,
author = "M. C. Ferris and S. Lucidi",
title = "Globally Convergent Methods for Nonlinear Equations",
institution = uwcs,
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key = "21",
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@Article{ferris.lucidi:nonmonotone,
author = "M. C. Ferris and S. Lucidi",
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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 = annor,
year = "1993",
volume = "47",
pages = "293--305",
URL = "ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps",
key = "24",
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@Article{ferris.mangasarian:finite,
author = "M. C. Ferris and O. L. Mangasarian",
title = "Finite Perturbation of Convex Programs",
journal = amopt,
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 = mathprog,
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 = siopt,
year = "1991",
volume = "1",
pages = "487--500",
URL = "ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps",
key = "18",
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@Article{ferris.mangasarian:parallel*1,
author = "M. C. Ferris and O. L. Mangasarian",
title = "Parallel Variable Distribution",
journal = siopt,
year = "1994",
volume = "4",
pages = "815--832",
URL = "ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps",
key = "31",
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@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 = uwcs,
address = madison,
number = "96-08",
type = mptr,
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 = mptr,
institution = uwcs,
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 = uwcs,
number = "99-09",
type = mptr,
}
@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 = dmitr,
institution = uwcs,
address = madison,
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 = mptr,
institution = uwcs,
}
@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 = mptr,
institution = uwcs,
address = madison,
number = "98-12",
}
@Misc{ferris.munson:condor,
author = "M. C. Ferris and T. S. Munson",
title = "Condor Modeling Language Interface",
organization = uwcs,
address = madison,
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 = coap,
volume = "12",
pages = "207--227",
year = "1999",
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps",
key = "63",
institution = uwcs,
address = madison,
number = "97-12",
type = mptr,
}
@TechReport{ferris.munson:interior,
author = {M. C. Ferris and T. S. Munson},
title = {Interior Point Methods for Massive Support Vector Machines},
institution = uwcs,
year = 2000,
key = 94,
type = dmitr,
number = {00-05},
URL = "ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps",
address = madison,
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 = mptr,
institution = uwcs,
address = madison,
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 = mathprog,
volume = 88,
pages = "487--506",
URL = "ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps",
key = "71",
type = mptr,
institution = uwcs,
address = madison,
number = "98-13",
}
@TechReport{ferris.munson:preprocessing,
author = "M. C. Ferris and T. S. Munson",
title = "Preprocessing Complementarity Problems",
type = mptr,
institution = uwcs,
address = madison,
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 = uwcs,
year = 2000,
key = 97,
type = dmitr,
number = {00-09},
URL = "ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps",
address = madison,
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 = sicon,
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 = mathprog,
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 = mathprog,
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 = dmitr,
institution = uwcs,
address = madison,
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,
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 = mptr,
institution = uwcs,
address = madison,
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 = mptr,
institution = uwcs,
address = madison,
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 = navres,
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 = uwcs,
year = "1996",
key = "56",
address = madison,
type = mptr,
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 = mathprog,
year = "1991",
volume = "50",
pages = "359--366",
key = "06",
}
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author = "M. C. Ferris",
title = "Iterative Linear Programming Solution of Convex Programs",
journal = jota,
year = "1990",
volume = "65",
pages = "53--65",
key = "07",
}
@Article{ferris:linear,
author = "M. C. Ferris",
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journal = bullams,
year = "1993",
volume = "28",
pages = "169--175",
key = "27",
}
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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 = uwcs,
year = "1998",
address = madison,
type = mptr,
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 = mathor,
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 = uwcs,
year = "1989",
address = madison,
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 = uwcs,
year = "1988",
address = madison,
number = "779",
key = "05",
}
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@Article{fischer.kanzow:finite,
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volume = "74",
pages = "279--292",
year = "1996",
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@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",
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year = "1995",
volume = "6",
pages = "83--107",
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@InCollection{fischer:ncp-function,
author = "A. Fischer",
title = "An {NCP}--Function and its Use for the Solution of
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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",
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@Article{fischer:newton-type,
author = "A. Fischer",
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volume = "86",
pages = "585--608",
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@Article{fischer:solution,
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pages = "513--532",
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author = "E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt
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@TechReport{fletcher.maza:nonlinear,
author = "R. Fletcher and E. Sainz de la Maza",
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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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crossref = "bachem.grotschel.ea:mathematical",
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title = "Penalty Functions",
pages = "87--114",
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@Book{fletcher:practical,
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author = "R. Fletcher",
title = "Practical Methods of Optimization",
year = "1981",
publisher = wiley,
address = "Chichester",
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@Book{fletcher:practical*2,
author = "R. Fletcher",
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publisher = wiley,
address = "New York",
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@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",
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@InProceedings{fogarty:varying,
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@Article{forrest.goldfarb:steepest-edge,
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@Article{forrest.tomlin:updating,
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@TechReport{forsgren.gill.ea:computing,
author = "A. Forsgren and P. E. Gill and W. Murray",
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{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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author = "I. Foster and C. Kesselman",
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pages = "115--128",
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@Book{foster.kesselman:grid,
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publisher = "Duxbury Press",
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@Article{fourer.gay.ea:modeling,
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institution = "Stanford University",
year = "1988",
number = "{SOL} 88.16",
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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",
booktitle = "The {U}ruguay Round and the Developing Economies",
address = "New York",
editors = "W. Martin and L. A. Winters",
publisher = "Cambridge University Press",
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@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",
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year = "1992",
month = jul,
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@Article{friesz.tobin.ea:nonlinear,
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@Unpublished{frisch:logarithmic,
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@Book{fukunaga:statistical,
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@Article{gabay.mercier:dual,
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@InCollection{gabay:applications,
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year = "1983",
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Asymmetric, Elastic Traffic Equilibrium Problem",
note = "Draft, 1995",
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@TechReport{gabriel.kydes:nonlinear,
author = "S. A. Gabriel and A. S. Kydes",
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year = "1995",
type = "Preprint",
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month = mar,
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author = "S. A. Gabriel and J. J. Mor\'{e}",
title = "Smoothing of Mixed Complementarity Problems",
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journal = "Computational Optimization and Applications",
year = "1992",
volume = "1",
pages = "67--91",
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@InCollection{gabriel.pang:trust,
author = "S. A. Gabriel and J. S. Pang",
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publisher = kluwer,
year = "1994",
editor = "W. W. Hager and D. W. Hearn and P. M. Pardalos",
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@PhdThesis{gabriel:algorithms,
author = "S. A. Gabriel",
title = "Algorithms for the Nonlinear Complementarity Problem:
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school = "The Johns Hopkins University",
year = "1992",
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author = "S. Gom\'{e}z and C. Barr\'{o}n",
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institution = "Department of Mechanical Engineering, Link{\"o}ping
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institution = "School of Operations Research and Industrial
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number = "1023",
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number = 5,
pages = "1339--1346"
}
@InProceedings{luo.tseng:class,
author = "Z.-Q. Luo and P. Tseng",
title = "A New Class of Merit Functions for the Nonlinear
Complementarity Problem",
crossref = "ferris.pang:complementarity",
pages = "204--225",
}
@Article{luo.tseng:convergence,
author = "Z.-Q. Luo and P. Tseng",
title = "On the Convergence of the Coordinate Descent Method
for Convex Differentiable Minimization",
journal = jota,
year = "1992",
volume = "72",
pages = "7--35",
}
@Article{luo.tseng:convergence*1,
author = "Z.-Q. Luo and P. Tseng",
title = "On the Convergence of a Matrix Splitting Algorithm for
the Symmetric Monotone Linear Complementarity Problem",
journal = "SIAM Journal on Control and Optimization",
year = "1991",
volume = "29",
pages = "1037--1060",
}
@Article{luo.tseng:convergence*2,
author = "Z.-Q. Luo and P. Tseng",
title = "On the Convergence Rate of Dual Ascent Methods for
Strictly Convex Minimization",
journal = mathor,
year = "1993",
volume = "18",
pages = "846--867",
}
@Article{luo.tseng:error,
author = "Z.--Q. Luo and P. Tseng",
title = "Error Bound and Convergence Analysis of Matrix
Splitting Algorithms for the Affine Variational
Inequality Problem",
journal = siopt,
year = "1992",
volume = "2",
pages = "43--54",
}
@Article{luo.tseng:error*1,
author = "Z.-Q. Luo and P. Tseng",
title = "Error Bound and Reduced Gradient Projection Algorithms
for Convex Minimization Over a Polyhedral Set",
journal = siopt,
year = "1993",
volume = "3",
pages = "43--59",
}
@Article{luo.tseng:error*2,
author = "Z.-Q. Luo and P. Tseng",
title = "Error Bounds and Convergence Analysis of Feasible
Descent Methods: {A} General Approach",
journal = annor,
year = "1993",
volume = "46",
pages = "157--178",
}
@Article{luo.tseng:global,
author = "Z.-Q. Luo and P. Tseng",
title = "On Global Error Bound for a Class of Monotone Affine
Variational Inequality Problems",
journal = opreslet,
year = "1992",
volume = "11",
pages = "159--165",
}
@Article{luo.tseng:linear,
author = "Z.-Q. Luo and P. Tseng",
title = "On the linear convergence of descent methods for
convex essentially smooth minimization",
journal = sicon,
year = "1992",
volume = "30",
pages = "408--425",
}
@TechReport{luo:convergence,
author = "Z.-Q. Luo",
title = "Convergence Analysis of Primal--Dual Interior--Point
Algorithms for Convex Quadratic Programs",
institution = "Communications Research Laboratory, McMaster
University",
year = "1992",
address = "Hamilton, Ontario",
}
@Article{lustig.marsten.ea:computational,
author = "I. J. Lustig and R. E. Marsten and D. F. Shanno",
title = "Computational Experience with a Primal-Dual Interior
Point Method for Linear Programming",
journal = laa,
year = "1991",
volume = "152",
pages = "191--222",
}
@Article{lustig.marsten.ea:implementing,
author = "I. J. Lustig and R. E. Marsten and D. F. Shanno",
title = "On implementing {M}ehrotra's predictor-corrector
interior point method for linear programming",
journal = siopt,
year = "1992",
volume = "2",
pages = "435--449",
}
@Article{lustig.marsten.ea:interior-point,
author = "I. J. Lustig and R. E. Marsten and D. F. Shanno",
title = "Interior-Point Methods for Linear Programming:
Computational State of the Art",
journal = ojc,
year = "1994",
volume = "6",
number = "1",
pages = "1--38",
}
@Article{lyman.wolbarst:optimization,
author = "J. T. Lyman and A. B. Wolbarst",
title = "Optimization of Radiation Therapy {IV}: {A} Dose
Volume Histogram Reduction Algorithm",
journal = "International Journal of Radiation Oncology, Biology
and Physics",
year = "1989",
volume = "17",
pages = "433--436",
}
@Article{mackie.holmes.ea:tomotherapy*1,
author = "T. R. Mackie and T. Holmes and S. Swerdloff and P.
Reckwerdt and J. O. Deasy and J. Yang and B. Paliwal
and T. Kinsella",
title = "Tomotherapy: a new concept for the delivery of dynamic
conformal radiotherapy",
journal = "Medical Physics",
year = "1993",
volume = "20",
number = "6",
pages = "1709--1719",
}
@Article{mackie.holmes.ea:tomotherapy*2,
author = "T. R. Mackie and T. W. Holmes and P. J. Reckwerdt and
J. Yang",
title = "Tomotherapy: Optimized Planning and Delivery of
Radiation Therapy",
journal = "Int. J. of Imaging Systems and Technology",
year = "1995",
volume = "6",
pages = "43--55",
}
@Article{mackie.scrimger.ea:convolution,
author = "T. R. Mackie and J. W. Scrimger and J. J. Batista",
title = "A convolution method of calculating dose from 15 Me{V}
x-rays",
journal = "Medical Physics",
year = "1985",
volume = "12",
pages = "188--196",
}
@Article{mackinnon:technique,
author = "James G. Mac{K}innon",
title = "A Technique for the Solution of Spatial Equilibrium
Models",
journal = "Journal of Regional Science",
year = "1976",
volume = "16",
pages = "293--307",
}
@PhdThesis{madsen:minimization,
author = "K. Madsen",
title = "Minimization of Nonlinear Approximation Functions",
year = "1985",
address = "Lyngby, Denmark",
school = "Institute of Numerical Analysis, Technical University
of Denmark",
annote = "Dissertation",
}
@Book{magill.quinzii:theory,
author = "M. Magill and M. Quinzii",
title = "Theory of Incomplete Markets",
publisher = "MIT Press",
year = "1996",
}
@InCollection{magnanti:models,
author = "T. L. Magnanti",
title = "Models and Algorithms for Predicting Urban Traffic
Equilibria",
booktitle = "Transportation Planning Models",
year = "1984",
editor = "M. Florian",
publisher = "North Holland",
pages = "153--186",
}
@InCollection{maguregui:modified,
author = "J. Maguregui",
title = "A modified {N}ewton algorithm for functions over
convex sets",
crossref = "mangasarian.meyer.ea:nonlinear*3",
pages = "461--473",
}
@PhdThesis{maguregui:regular,
author = "J. Maguregui",
title = "Regular Multivalued Functions and Algorithmic
Applications",
year = "1977",
address = madison,
school = uwcs,
}
@Article{mahey.oualibouch.ea:proximal,
author = "P. Mahey and S. Oualibouch and D. T. Pham",
title = "Proximal Decomposition on the Graph of a Maximal
Monotone Operator",
journal = siopt,
year = "1995",
volume = "5",
pages = "454--466",
}
@Article{mahey.pham:partial,
author = "P. Mahey and D. T. Pham",
title = "Partial Regularization of the Sum of Two Maximal
Monotone Operators",
journal = "{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique",
year = "1993",
volume = "27",
pages = "375--392",
}
@InCollection{maier.novati:shakedown,
author = "G. Maier and G. Novati",
title = "A shakedown and bounding theory allowing for nonlinear
hardening and second order geometric effects with
reference to discrete structural models",
editors = "J. A. K{\"{o}}nig and M. Kleiber",
booktitle = "Inelastic Solids and Structures, A. Sawczuk memorial
volume",
publisher = "Pineridge Press",
address = "Swansea",
year = "1990",
pages = "451--471",
}
@Article{maier:incremental,
author = "G. Maier",
title = "Incremental Plastic Analysis in the Presence of Large
Displacement and Physical Instabilizing Effects",
journal = "International Journal of Solids and Structures",
volume = "7",
year = "1971",
pages = "345--372",
}
@InCollection{maier:inverse,
author = "G. Maier",
title = "Inverse Problems in Engineering Plasticity: {A}
Quadratic Programming Approach",
booktitle = "Serie VIII",
publisher = "Academia Nazionale dei Lincei",
year = "1981",
volume = "LXX",
pages = "203--209",
}
@Article{maier:matrix,
author = "G. Maier",
title = "A matrix structural theory of piecewise linear
elastoplasticity with interacting yield planes",
journal = "Meccanica",
volume = "5",
year = "1970",
pages = "54--66",
}
@Article{maier:quadratic,
author = "G. Maier",
title = "A quadratic programming approach for certain classes
of nonlinear structural problems",
journal = "Meccanica",
volume = "3",
year = "1968",
pages = "121--130",
}
@Book{manber:introduction,
author = "U. Manber",
title = "Introduction to Algorithms: {A} Creative Approach",
year = "1989",
publisher = addison,
}
@Article{mangasarian.deleone:error,
author = "O. L. Mangasarian and R. {De~Leone}",
title = "Error Bounds for Strongly Convex Programs and
(Super)linearly Convergent Iterative Schemes for the
Least 2--norm Solution of Linear Programs",
journal = "Applied Mathematics and Optimization",
year = "1988",
volume = "17",
pages = "1--14",
}
@Article{mangasarian.deleone:parallel,
author = "O. L. Mangasarian and R. {De~Leone}",
title = "Parallel Successive Overrelaxation Methods for
Symmetric Linear Complementarity Problems and Linear
Programs",
journal = jota,
year = "1987",
volume = "54",
pages = "437--446",
}
@Article{mangasarian.fromovitz:fritz,
author = "O. L. Mangasarian and S. Fromovitz",
title = "The {F}ritz {J}ohn necessary optimality conditions in
the presence of equality and inequality constraints",
journal = jmaa,
year = "1967",
volume = "17",
pages = "37--47",
}
@Article{mangasarian.mclinden:simple,
author = "O. L. Mangasarian and L. McLinden",
title = "Simple Bounds for Solutions of Monotone
Complementarity Problems and Convex Programs",
journal = mathprog,
year = "1985",
volume = "32",
pages = "32--40",
}
@Article{mangasarian.meyer:nonlinear,
author = "O. L. Mangasarian and R. R. Meyer",
title = "Nonlinear Perturbation of Linear Programs",
journal = sicon,
year = "1979",
volume = "17",
pages = "745--752",
}
@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",
}
@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",
}
@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",
}
@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,
pages = {1032-1037},
}
@Article{mangasarian.pang:exact,
author = "O. L. Mangasarian and J. S. Pang",
title = "Exact Penalty Functions for Mathematical Programs with
Linear Complementarity Constraints",
journal = "Optimization",
year = "1997",
volume = "42",
pages = "1--8",
}
@Article{mangasarian.pang:extended,
author = "O. L. Mangasarian and J. S. Pang",
title = "The Extended Linear Complementarity Problem",
journal = simax,
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 = mathprog,
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 = mathprog,
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 = sicon,
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 = mathprog,
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 = oms,
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 = opres,
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,
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 = siopt,
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 = siamath,
year = "1976",
volume = "31",
pages = "89--92",
}
@Article{mangasarian:error,
author = "O. L. Mangasarian",
title = "Error Bounds for Inconsistent Linear Inequalities and
Programs",
journal = ojc,
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 = mathprog,
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 = laa,
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 = mathprog,
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 = ojc,
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 = jota,
year = "1981",
volume = "35",
pages = "123--128",
}
@Article{mangasarian:parallel,
author = "O. L. Mangasarian",
title = "Parallel Gradient Distribution in Unconstrained
Optimization",
journal = sicon,
volume = "33",
pages = "1916--1925",
year = "1995",
}
@TechReport{mangasarian:regularized,
author = "O. L. Mangasarian",
title = "Regularized Linear Programs with Equilibrium
Constraints",
institution = uwcs,
year = "1997",
address = madison,
type = mptr,
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 = opreslet,
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 = jota,
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 = laa,
year = "1981",
volume = "41",
pages = "209--223",
}
@Article{mangasarian:sufficiency,
author = "O. L. Mangasarian",
title = "Sufficiency of Exact Penalty Minimization",
journal = sicon,
year = "1985",
month = jan,
volume = "23",
pages = "30--37",
}
@Article{mangasarian:unconstrained,
author = "O. L. Mangasarian",
title = "Unconstrained {L}agrangians in Nonlinear Programming",
journal = sicon,
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",
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