1% 2% This file is formatted by: 3% bibtool petsc.bib -- expand.macros=on -- print.line.length=100 -- pass.comments=on 4% 5% If the reference uses PETSc, include a field listing components used, e.g. 6% petsc_uses = {KSP, SNES, TS, TAO}, 7% 8% For journal names, write out the full name, do not define abbreviations 9% 10% There are some additional historical comments below which may be of interest, 11% particularly in terms of notes about particularly impactful publications using PETSc. 12% 13 14% LiteralHTML: 15% LiteralHTML: <H2><center>Research and Publications that make use of PETSc</center></H2> 16% LiteralHTML: 17% LiteralHTML: <a name="nano"><H3><center>Nano-simulations</center></H3> 18% LiteralHTML: 19@article{WalkerNi2011, 20 title = {Anderson acceleration for fixed-point iterations}, 21 author = {Homer F Walker and Peng Ni}, 22 journal = {SIAM Journal on Numerical Analysis}, 23 volume = {49}, 24 number = {4}, 25 pages = {1715--1735}, 26 year = {2011}, 27 publisher = {SIAM} 28} 29@article{Hua2007, 30 title = {Numerical simulation of microdroplet formation in coflowing immiscible liquids}, 31 author = {Hua, Jinsong and Zhang, Baili and Lou, Jing}, 32 journal = {AIChE Journal}, 33 volume = {53}, 34 number = {10}, 35 pages = {2534--2548}, 36 year = {2007}, 37 publisher = {Wiley Online Library} 38} 39@Article{ openblas, 40 title = {OpenBLAS: A High Performance BLAS Library on Loongson 3A CPU}, 41 journal = {Journal of Software}, 42 volume = {22}, 43 pages = {208--216}, 44 year = {2011}, 45 url = {https://www.jos.org.cn/josen/article/abstract/11042}, 46 author = {ZHANG Xian-Yi and WANG Qian and ZHANG Yun-Quan Richard} 47} 48 49@Misc{ openblas-website, 50 title = {{OpenBLAS}}, 51 key = {OpenBLAS}, 52 howpublished = {\url{https://www.openblas.net}} 53} 54 55@Misc{ openacc-website, 56 title = {{OpenACC}}, 57 key = {OpenACC}, 58 howpublished = {\url{https://www.openacc.org}} 59} 60 61@Misc{ bueler2020petsc, 62 title = {PETSc for Partial Differential Equations: Numerical Solutions in C and Python}, 63 author = {Bueler, Ed}, 64 year = {2020}, 65 publisher = {SIAM}, 66 petsc_uses = {KSP} 67} 68 69@TechReport{ petscforgpuexascale, 70 title = {Toward Performance-Portable PETSc for GPU-based Exascale Systems}, 71 author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener 72 and Matthew Knepley and Scott E. Kruger and Hannah~Morgan and Todd Munson and Karl 73 Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang}, 74 institution = {Argonne National Laboratory}, 75 number = {ANL/MCS-P9401-1020}, 76 note = {\url{https://arxiv.org/abs/2011.00715}}, 77 year = {2020}, 78 petsc_uses = {KSP} 79} 80 81@Article{ mills2021, 82 title = {Toward performance-portable {PETS}c for {GPU}-based exascale systems}, 83 journal = {Parallel Computing}, 84 volume = {108}, 85 pages = {102831}, 86 year = {2021}, 87 issn = {0167-8191}, 88 doi = {https://doi.org/10.1016/j.parco.2021.102831}, 89 url = {https://www.sciencedirect.com/science/article/pii/S016781912100079X}, 90 author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener 91 and Matthew Knepley and Scott E. Kruger and Hannah Morgan and Todd Munson and Karl 92 Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang} 93} 94 95@Article{ rupp:2016:pis:2988256.2907944, 96 author = {Karl Rupp and Josef Weinbub and Ansgar J\"{u}ngel and Tibor Grasser}, 97 title = {Pipelined Iterative Solvers with Kernel Fusion for Graphics Processing Units}, 98 journal = {ACM Trans. Math. Softw.}, 99 issue_date = {September 2016}, 100 volume = {43}, 101 number = {2}, 102 month = aug, 103 year = {2016}, 104 issn = {0098-3500}, 105 pages = {11:1--11:27}, 106 articleno = {11}, 107 numpages = {27}, 108 doi = {10.1145/2907944}, 109 acmid = {2907944}, 110 publisher = {ACM}, 111 address = {New York, NY, USA}, 112 keywords = {BiCGStab method, CUDA, GMRES method, GPU, Iterative solvers, OpenCL, conjugate 113 gradient method}, 114 petsc_uses = {KSP} 115} 116 117@Article{ dalcin2011parallel, 118 title = {Parallel distributed computing using python}, 119 author = {Dalcin, Lisandro D and Paz, Rodrigo R and Kler, Pablo A and Cosimo, Alejandro}, 120 journal = {Advances in Water Resources}, 121 volume = {34}, 122 number = {9}, 123 pages = {1124--1139}, 124 year = {2011}, 125 publisher = {Elsevier}, 126 petsc_uses = {KSP} 127} 128 129@Article{ mendezpongaortiz2018, 130 title = {Diffusive molecular dynamics simulations of lithiation of silicon nanopillars}, 131 author = {JP Mendez and M Ponga and M Ortiz}, 132 journal = {Journal of the Mechanics and Physics of Solids}, 133 year = {2018}, 134 petsc_uses = {KSP} 135} 136 137@TechReport{ morgan2020evaluation, 138 title = {Evaluation of {PETS}c on a Heterogeneous Architecture, the {OLCF} {S}ummit 139 System: Part 1: Vector Node Performance}, 140 author = {Morgan, Hannah Mairs and Mills, Richard Tran and Smith, Barry}, 141 year = {2020}, 142 institution = {Argonne National Laboratory}, 143 url = {https://publications.anl.gov/anlpubs/2020/04/159190.pdf}, 144 petsc_uses = {KSP} 145} 146 147@TechReport{ pdeconstrainedspectraladjoints, 148 title = {PDE constrained optimization, error estimation and control with spectral elements 149 using PETSc and TAO}, 150 author = {Oana Marin and Emil Constantinescu and Barry Smith}, 151 type = {Preprint}, 152 number = {ANL/MCS-P9031-1117}, 153 institution = {ANL}, 154 month = nov, 155 year = {2017}, 156 petsc_uses = {KSP} 157} 158 159@InProceedings{ asc2013, 160 author = {S. Abhyankar and B. F. Smith and E. Constantinescu}, 161 title = {Evaluation of overlapping restricted additive Schwarz preconditioning for 162 parallel solution of very large power flow problems}, 163 booktitle = {HiPCNA-PG’13}, 164 year = {2013}, 165 petsc_uses = {KSP} 166} 167 168@InProceedings{ as2013, 169 author = {S. Abhyankar and B. F. Smith}, 170 title = {{PETSc:} An Advanced Math and Computing Framework for Rapidly Developing Parallel 171 Smart Grid Applications}, 172 booktitle = {Proceedings of the IEEE PES General Meeting}, 173 year = {2013}, 174 petsc_uses = {KSP} 175} 176 177@TechReport{ tspaper, 178 title = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library}, 179 author = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and 180 Barry F. Smith}, 181 type = {Preprint}, 182 number = {ANL/MCS-P5061-0114}, 183 institution = {ANL}, 184 month = jan, 185 year = {2014}, 186 petsc_uses = {KSP} 187} 188 189@TechReport{ abhyankaretal2018, 190 author = {Shrirang Abhyankar and Jed Brown and Emil M. Constantinescu and Debojyoti Ghosh 191 and Barry F. Smith and Hong Zhang}, 192 title = {{PETSc/TS}: {A} Modern Scalable {ODE/DAE} Solver Library}, 193 journal = {arXiv e-preprints}, 194 eprint = {1806.01437}, 195 archiveprefix = {arXiv}, 196 year = {2018}, 197 petsc_uses = {KSP} 198} 199 200@Article{ zhang2021cams, 201 title = {Optimal checkpointing for adjoint multistage time-stepping schemes}, 202 author = {Hong Zhang and Emil M. Constantinescu}, 203 journal = {arXiv e-preprints}, 204 eprint = {2202.11890}, 205 archiveprefix = {arXiv}, 206 year = {2022}, 207 petsc_uses = {KSP} 208} 209 210@InProceedings{ zhangconstantinescu2021b, 211 title = {Revolve-based adjoint checkpointing for multistage time integration}, 212 author = {Hong Zhang and Emil M. Constantinescu}, 213 booktitle = {Proceedings of the International Conference on Computational Science (ICCS)}, 214 month = jun, 215 year = {2021}, 216 petsc_uses = {KSP} 217} 218 219@Article{ zhang2022tsadjoint, 220 author = {Zhang, Hong and Constantinescu, Emil M. and Smith, Barry F.}, 221 title = {{PETSc TSAdjoint: A Discrete Adjoint ODE Solver for First-Order and Second-Order 222 Sensitivity Analysis}}, 223 journal = {SIAM Journal on Scientific Computing}, 224 volume = {44}, 225 number = {1}, 226 pages = {C1-C24}, 227 year = {2022}, 228 doi = {10.1137/21M140078X}, 229 petsc_uses = {KSP} 230} 231 232@TechReport{ bb2008, 233 author = {Tomasz Blachowicz and Bartlomiej Baron}, 234 title = {A graphical extension for the Windows version of the Parallel Finite Element 235 Micromagnetics Package (MagParExt)}, 236 url = {http://arxiv.org/abs/0807.2655}, 237 year = {2008}, 238 petsc_uses = {KSP} 239} 240 241@Article{ jacvgv2008, 242 author = {R. Y. Jaafar and A Asenjo and O Chubykalo-Fesenko and M Vazquez and E M Gonzalez 243 and J L Vicent}, 244 title = {Field induced vortex dynamics in magnetic Ni nanotriangles}, 245 journal = {Nanotechnology}, 246 volume = {19}, 247 year = {2008}, 248 doi = {10.1088/0957-4484/19/28/285717}, 249 petsc_uses = {KSP} 250} 251 252@Article{ yjdwh2008, 253 author = {Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He}, 254 title = {Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy}, 255 journal = {Journal of the Magnetics Society of Japan}, 256 volume = {32}, 257 year = {2008}, 258 pages = {50-53}, 259 url = {http://www.jstage.jst.go.jp/article/msjmag/32/2_1/32_50/_article}, 260 petsc_uses = {KSP} 261} 262 263@Article{ mtrtrsa2008, 264 author = {D. Makarov and S. Tibus and C. T. Rettner and T. Thomson and B. D. Terris and T. 265 Schrefl and M. Albrecht}, 266 title = {Magnetic strip patterns induced by focused ion beam irradiation}, 267 journal = {J. Appl. Phys.}, 268 volume = {103}, 269 year = {2008}, 270 doi = {10.1063/1.2894587}, 271 petsc_uses = {KSP} 272} 273 274@InProceedings{ tmrttsa2008, 275 author = {S. Tibus and D. Makarov and C. T. Rettner and T. Thomson and B. D. Terris and T. 276 Schrefl and M. Albrecht}, 277 title = {Patterning of magnetic films by focused ion beam irradiation}, 278 booktitle = {Intermag 2008 paper no. CM-05, submitted to IEEE Trans. Magn.}, 279 year = {2008}, 280 petsc_uses = {KSP} 281} 282 283@Article{ yjdbh2007, 284 author = {Lin Yuan and Jianju Jiang and Yongjiang di and Shaowei Bie and Huahui He}, 285 title = {Micromagnetic simulation of the magnetic dispersion angle and effective damping 286 factor for the single-phase soft magnetic films}, 287 journal = {J. Magn. Magn. Mater.}, 288 volume = {320}, 289 number = {7}, 290 pages = {1393-1397}, 291 doi = {10.1016/j.jmmm.2007.11.025}, 292 petsc_uses = {KSP} 293} 294 295@Article{ lxky2007, 296 author = {DENG Lian-wen and HUANG Xiao-zhong and ZH0U Ke-sheng and YANG}, 297 title = {Micromagnetic simulation and experimental study on microwave permeability of 298 nano-magnetic films}, 299 journal = {Transactions of Nonferrous Metals Society of China}, 300 year = {2007}, 301 pages = {756-759}, 302 url = {http://www.ysxbcn.com/icnfm2007/part2B/s0756.pdf}, 303 petsc_uses = {KSP} 304} 305 306@Article{ yjdwh2008a, 307 author = {Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He}, 308 title = {Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy}, 309 journal = {Journal of the Magnetics Society of Japan}, 310 volume = {32}, 311 year = {2008}, 312 pages = {50-53}, 313 doi = {10.3379/msjmag.32.50}, 314 petsc_uses = {KSP} 315} 316 317@Article{ lylw2007, 318 author = {Ching-Ming Lee and L. X. Ye and J. M. Lee and Te-Ho Wu}, 319 title = {Micromagnetic study of magnetization reversal in patterned DyFeCo thin films}, 320 journal = {Phys. Stat. Sol.}, 321 volume = {204}, 322 number = {12}, 323 pages = {4049-4052}, 324 year = {2007}, 325 doi = {10.1002/pssa.200777359}, 326 petsc_uses = {KSP} 327} 328 329@InProceedings{ sg2007, 330 author = {Simon Greaves}, 331 title = {Micromagnetic Simulations of Magnetic Recording Media}, 332 booktitle = {High Performance Computing on Vector Systems 2007}, 333 doi = {10.1007/978-3-540-74384-2_17}, 334 petsc_uses = {KSP} 335} 336 337@Article{ bsc2007, 338 author = {Nadjib Benatmane and Werner Scholz and T.W. Clinton}, 339 title = {Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings}, 340 journal = {IEEE Trans. Magn.}, 341 volume = {43}, 342 year = {2007}, 343 pages = {2884-2886}, 344 doi = {10.1109/TMAG.2007.892867}, 345 petsc_uses = {KSP} 346} 347 348@Article{ ffbf, 349 author = {T. Fischbacher and M. Franchin and G. Bordignon and H. Fangohr}, 350 title = {A Systematic Approach to Multiphysics Extensions of Finite-Element-Based 351 Micromagnetic Simulations: Nmag.}, 352 journal = {IEEE Trans. Magn. Volume}, 353 volume = {43}, 354 pages = {2896-2898}, 355 doi = {10.1109/TMAG.2007.893843}, 356 petsc_uses = {KSP} 357} 358 359@InBook{ dfssfs2006, 360 author = {R. Dittrich and J. Fidler and D. Suess and W. Schol and H. Forster, T. Schrefl}, 361 chapter = {Computational Aspects of Micromagnetics}, 362 title = {The Science of Hysteresis}, 363 editor = { G. Bertotti and I. Mayergoyz}, 364 url = {http://books.elsevier.com/us/elsevier/us/subindex.asp?maintarget=&isbn=0124808743}, 365 petsc_uses = {KSP} 366} 367 368@InBook{ fss, 369 author = {J. Fidler and T. Schrefl and W. Scholz}, 370 chapter = {Computational Micromagnetics}, 371 title = {Handbook of Theoretical and Computational Nanotechnology}, 372 editor = {M. Rieth and W. Schommers}, 373 url = {http://www.amazon.com/gp/product/158883042X}, 374 petsc_uses = {KSP} 375} 376 377@InBook{ shbsef, 378 author = {Thomas Schrefl and Gino Hrkac and Simon Bance and Dieter Suess and Otmar Ertl and 379 Josef Fidler}, 380 chapter = {Numerical Methods in Micromagnetics (Finite Element Method)}, 381 title = {Handbook of Magnetism and Advanced Magnetic Materials}, 382 editor = {Helmut Kronmueller and Stuart Parkin}, 383 doi = {10.1002/9780470022184.hmm203}, 384 petsc_uses = {KSP} 385} 386 387@InBook{ sfs, 388 author = {D. Suess and J. Fidler and T. Schrefl}, 389 chapter = {Micromagnetic Simulation of magnetic materials}, 390 title = {Handbook of Magnetic Materials}, 391 editor = {K. H. J. Buschow}, 392 url = {http://www.amazon.com/gp/product/0444518509}, 393 petsc_uses = {KSP} 394} 395 396@Article{ fsxzs, 397 author = {J. Fernandez-de-Castro and Xiao Shen and Jianhua Xue and Yuming Zhou and S. 398 Sharma}, 399 title = {Writer Flux Closure and Transition Degradation Mechanism in Perpendicular 400 Recording.}, 401 journal = {IEEE Trans. Magn. Volume}, 402 volume = {43}, 403 pages = {2175-2177}, 404 doi = {10.1109/TMAG.2007.893122}, 405 petsc_uses = {KSP} 406} 407 408@Article{ sb2006, 409 author = {W. Scholz and S. Batra}, 410 title = {Effect of write current waveform on magnetization and head field dynamics of 411 perpendicular recording heads}, 412 journal = {IEEE Trans. Magn.}, 413 volume = {42}, 414 year = {2006}, 415 pages = {2264--2266}, 416 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/ieee/scholz_2006_42_2264.pdf}, 417 petsc_uses = {KSP} 418} 419 420@Article{ bsr2006, 421 author = {S. Batra and W. Scholz and T. Roscamp}, 422 title = {Effect of thermal fluctuation field on the noise performance of a perpendicular 423 recording system}, 424 journal = {J. Appl. Phys.}, 425 volume = {99}, 426 year = {2006}, 427 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 428 petsc_uses = {KSP} 429} 430 431@InProceedings{ japios2006, 432 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 433 Subramanian}, 434 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 435 in systems with cubic and uniaxial anisotropy.}, 436 booktitle = {Intermag 2006 Conference}, 437 petsc_uses = {KSP} 438} 439 440@Article{ kbmb2006, 441 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 442 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 443 Perpendicular Recording Heads}, 444 journal = {IEEE Trans. Magn.}, 445 volume = {42}, 446 year = {2006}, 447 pages = {2428--2430}, 448 doi = {10.1109/TMAG.2006.879430}, 449 petsc_uses = {KSP} 450} 451 452@Article{ cclcw2006, 453 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 454 title = {Control of Domain Wall Motion in Permalloy Ring}, 455 journal = {IEEE Trans. Magn.}, 456 volume = {42}, 457 year = {2006}, 458 pages = {2960--2962}, 459 doi = {10.1109/TMAG.2006.878414}, 460 petsc_uses = {KSP} 461} 462 463@Article{ bfmfzczg2007, 464 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 465 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 466 title = {Micromagnetic modelling of ferromagnetic cones}, 467 journal = {J. Magn. Magn. Mater.}, 468 volume = {312}, 469 year = {2007}, 470 pages = {234-238}, 471 url = {http://eprints.soton.ac.uk/45900/}, 472 petsc_uses = {KSP} 473} 474 475@PhDThesis{ rb2005, 476 author = {Richard Boardman}, 477 title = {Computer simulation studies of magnetic nanostructures}, 478 school = {Computational Engineering and Design Group, School of Engineering Sciences, 479 University of Southampton, United Kingdom}, 480 year = {2005}, 481 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 482 petsc_uses = {KSP} 483} 484 485@InProceedings{ cwwy2006, 486 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 487 title = {MPI Performance Analysis Tools on Blue Gene/L}, 488 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 489 year = {2006}, 490 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 491 petsc_uses = {KSP} 492} 493 494@InProceedings{ ch2006, 495 author = {I.-H. Chung and J.K. Hollingsworth}, 496 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 497 Programs}, 498 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 499 pages = {45--56}, 500 doi = {10.1109/HPDC.2006.1652135}, 501 petsc_uses = {KSP} 502} 503 504@Article{ lkpl2005, 505 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 506 title = {Multibit MRAM using a pair of memory cells}, 507 journal = {IEEE Trans. Magn.}, 508 volume = {41}, 509 year = {2005}, 510 pages = {2670-2672}, 511 doi = {10.1109/TMAG.2005.855288}, 512 petsc_uses = {KSP} 513} 514 515@Article{ gscn2005, 516 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 517 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 518 journal = {Phys. Rev. B}, 519 volume = {71}, 520 year = {2005}, 521 doi = {10.1103/PhysRevB.71.144407}, 522 petsc_uses = {KSP} 523} 524 525@PhDThesis{ mda, 526 author = {Massimiliano d'Aquino}, 527 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 528 school = { Universita di Napoli Federico II.}, 529 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 530 petsc_uses = {KSP} 531} 532 533@TechReport{ ssdfssf2003, 534 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 535 Stehno and J. Fidler}, 536 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 537 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 538 petsc_uses = {KSP} 539} 540 541@InProceedings{ sb2006a, 542 author = {W. Scholz and S. Batra}, 543 title = {Effect of write current waveform on magnetization and head field dynamics of 544 perpendicular recording heads}, 545 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 546 petsc_uses = {KSP} 547} 548 549@Article{ scholz-batra1, 550 author = {W. Scholz and S. Batra}, 551 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 552 Recording}, 553 journal = {IEEE Trans. Magn.}, 554 note = {submitted}, 555 year = {2005}, 556 petsc_uses = {KSP} 557} 558 559@Article{ scholz-batra2, 560 author = {W. Scholz and S. Batra}, 561 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 562 journal = {IEEE Trans. Magn.}, 563 volume = {41}, 564 year = {2005}, 565 pages = {702-706}, 566 petsc_uses = {KSP} 567} 568 569@Article{ daquino-scholz1, 570 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 571 title = {Micromagnetic Analysis of Fast Precessional Switching}, 572 journal = {J. Magn. Magn. Mater.}, 573 volume = {290-291}, 574 year = {2005}, 575 pages = {510-513}, 576 petsc_uses = {KSP} 577} 578 579@Article{ aq-scholz-fid, 580 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 581 title = {Numerical and analytical study of fast precessional switching}, 582 journal = {J. Appl. Phys.}, 583 volume = {95}, 584 year = {2004}, 585 pages = {7055-7057}, 586 petsc_uses = {KSP} 587} 588 589@InProceedings{ gar-tabik-gar, 590 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 591 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 592 Scatterers}, 593 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 594 (PDP'04)}, 595 year = {2004}, 596 pages = {80--}, 597 petsc_uses = {KSP} 598} 599 600@InProceedings{ aq-scholz-mia, 601 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 602 title = {Analysis of fast precessional switching in magnetic thin films}, 603 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 604 year = {2004}, 605 pages = {257-260}, 606 petsc_uses = {KSP} 607} 608 609@Article{ scholz-fid-seus, 610 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 611 Dittrich and V. Tsiantos}, 612 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 613 Axes}, 614 journal = {J. Magn. Magn. Mater.}, 615 year = {2004}, 616 pages = {1524-1525}, 617 petsc_uses = {KSP} 618} 619 620@Article{ boardman-zimmerman, 621 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 622 Peter de Groot}, 623 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 624 journal = {Journal of Applied Physics}, 625 year = {2005}, 626 petsc_uses = {KSP} 627} 628 629@Article{ lim-kim-park, 630 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 631 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 632 journal = {IEEE Trans. Magn.}, 633 note = {submitted}, 634 petsc_uses = {KSP} 635} 636 637@Article{ scholz-suess2, 638 author = {W. Scholz and D. Suess and T. Schrefl and and J. Fidler}, 639 title = {Micromagnetic simulation of magnetization reversal in small particles with 640 surface anisotropy}, 641 journal = {J. Appl. Phys.}, 642 volume = {95}, 643 year = {2004}, 644 pages = {6807-6809}, 645 petsc_uses = {KSP} 646} 647 648@Article{ scholz-schrefl1, 649 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 650 Tsiantos}, 651 title = {Micromagnetic simulation of the pinning and depinning process in permanent 652 magnets}, 653 journal = {IEEE Trans. Magn.}, 654 volume = {39}, 655 year = {2003}, 656 pages = {2920-2922}, 657 petsc_uses = {KSP} 658} 659 660@Article{ scholz-guslienko, 661 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 662 W. Chantrell and J. Fidler}, 663 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 664 nanodots}, 665 journal = {J. Magn. Magn. Mater.}, 666 volume = {266}, 667 year = {2003}, 668 pages = {155-163}, 669 petsc_uses = {KSP} 670} 671 672@Article{ scholz1, 673 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 674 Forster and V. Tsiantos}, 675 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 676 journal = {Comp. Mat. Sci}, 677 year = {2003}, 678 pages = {366--383}, 679 volume = {28}, 680 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 681 petsc_uses = {KSP} 682} 683 684@PhDThesis{ scholz2, 685 author = {W. Scholz}, 686 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 687 school = {Vienna University of Technology, Vienna, Austria}, 688 year = {2003}, 689 petsc_uses = {KSP} 690} 691 692@Article{ scholz3, 693 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 694 Forster and J. Fidler}, 695 title = {Implementation of a high performance parallel finite element micromagnetics 696 package}, 697 journal = {J. Magn. Magn. Mater.}, 698 year = {2004}, 699 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 700 petsc_uses = {KSP} 701} 702 703% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 704@InBook{ zhanggladwell1, 705 author = {W. Zhang and I. Gladwell}, 706 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 707 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 708 year = {2000}, 709 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 710 Physics, vol. 552}, 711 publisher = {Springer}, 712 pages = {4190-}, 713 petsc_uses = {KSP} 714} 715 716@Article{ wolf1, 717 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 718 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 719 thin films}, 720 journal = {Phil. Mag. A}, 721 year = {2003}, 722 lab = {ANL}, 723 petsc_uses = {KSP} 724} 725 726@Article{ wolf2, 727 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 728 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 729 grain-boundary properties}, 730 journal = {Computational Materials Science}, 731 year = {2001}, 732 volume = {23}, 733 pages = {15--32}, 734 lab = {ANL}, 735 petsc_uses = {KSP} 736} 737 738@Article{ wolf3, 739 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 740 title = {Role of grain rotation in grain growth by mesoscale simulation}, 741 journal = {Phil. Mag. A}, 742 year = {2002}, 743 volume = {82}, 744 pages = {1271--1297}, 745 lab = {ANL}, 746 petsc_uses = {KSP} 747} 748 749% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 750@Article{ saut, 751 author = { Olivier Saut}, 752 title = {Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal}, 753 journal = {SIAM Journal on Scientific Computing}, 754 year = {2004}, 755 note = {submitted}, 756 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 757 petsc_uses = {KSP} 758} 759 760% LiteralHTML: 761% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 762% LiteralHTML: 763@InBook{ khanallorenziayachepennec2016, 764 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 765 of Brain Deformation in {Alzheimer's} Disease}, 766 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 767 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 768 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 769 Miller}, 770 pages = {167--176}, 771 isbn = {978-3-319-28329-6}, 772 doi = {10.1007/978-3-319-28329-6_15}, 773 publisher = {Springer International Publishing}, 774 year = {2016}, 775 petsc_uses = {KSP} 776} 777 778@Article{ ataseven, 779 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 780 title = {Parallel implementation of the accelerated BEM approach for EMSI of the human 781 brain}, 782 journal = {Medical and Biological Engineering and Computing}, 783 month = feb, 784 year = {2008}, 785 doi = {10.1007/s11517-008-0316-0}, 786 petsc_uses = {KSP} 787} 788 789@Article{ dennis-eberhart-03, 790 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 791 pages = {832-840}, 792 volume = {125}, 793 number = {6}, 794 title = {Finite-element simulation of cooling of realistic 3-D human head and neck}, 795 journal = {J Biomech Eng}, 796 year = {2003}, 797 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 798 petsc_uses = {KSP} 799} 800 801@Conference{ gu7174parallel, 802 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 803 frequency-domain small animal optical tomography}}, 804 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 805 booktitle = {Proc. of SPIE Vol}, 806 volume = {7174}, 807 number = {717406}, 808 pages = {1}, 809 petsc_uses = {KSP} 810} 811 812@Article{ barchanski2005using, 813 title = {{Using domain decomposition techniques for the calculation of low-frequency 814 electric current densities in high-resolution 3D human anatomy models}}, 815 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 816 T.}, 817 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 818 and Electronic Engineering}, 819 volume = {24}, 820 number = {2}, 821 pages = {458--467}, 822 issn = {0332-1649}, 823 year = {2005}, 824 publisher = {Emerald Group Publishing Limited}, 825 petsc_uses = {KSP} 826} 827 828@Article{ motrescurienen05, 829 author = {V. C. Motrescu and U. van Rienen}, 830 pages = {227--231}, 831 volume = {3}, 832 title = {Computation of currents induced by ELF electric fields in anisotropic human 833 tissues using the Finite Integration Technique}, 834 journal = {Advances in Radio Science}, 835 year = {2005}, 836 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 837 petsc_uses = {KSP} 838} 839 840@Article{ motrescurienen04, 841 author = {V. C. Motrescu and U. van Rienen}, 842 pages = {309--313}, 843 volume = {2}, 844 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 845 Integration Technique (FIT)}, 846 journal = {Advances in Radio Science}, 847 year = {2004}, 848 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 849 petsc_uses = {KSP} 850} 851 852@InProceedings{ dbl2, 853 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 854 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 855 booktitle = {ECCOMAS2000}, 856 year = {2000}, 857 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 858 petsc_uses = {KSP} 859} 860 861@Unpublished{ cell, 862 title = {Parallel Simulation Engines for Whole-Cell Models}, 863 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 864 Weber}, 865 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 866 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 867 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 868 year = {2001}, 869 petsc_uses = {KSP} 870} 871 872@Article{ barker2010two, 873 title = {Two-level Newton and hybrid Schwarz preconditioners for fluid-structure 874 interaction}, 875 author = {Barker, A.T. and Cai, X.C.}, 876 journal = {SIAM Journal on Scientific Computing}, 877 volume = {32}, 878 number = {4}, 879 pages = {2395--2417}, 880 year = {2010}, 881 publisher = {Society for Industrial and Applied Mathematics}, 882 petsc_uses = {KSP} 883} 884 885@Article{ barker2010scalable, 886 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 887 with application to blood flow modeling}, 888 author = {Barker, A.T. and Cai, X.C.}, 889 journal = {Journal of Computational Physics}, 890 volume = {229}, 891 number = {3}, 892 pages = {642--659}, 893 year = {2010}, 894 publisher = {Elsevier}, 895 petsc_uses = {KSP} 896} 897 898@Article{ barker2009nks, 899 title = {NKS for fully coupled fluid-structure interaction with application}, 900 author = {Barker, A.T. and Cai, X.C.}, 901 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 902 pages = {275--282}, 903 year = {2009}, 904 publisher = {Springer}, 905 petsc_uses = {KSP} 906} 907 908@Article{ mirams2013, 909 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 910 and Yi Cui and Gary R Mirams}, 911 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 912 to predict QT interval changes in the rabbit ventricular wedge}, 913 journal = {Journal of pharmacological and toxicological methods}, 914 volume = {68}, 915 number = {1}, 916 pages = {88--96}, 917 year = {2013}, 918 doi = {10.1016/j.vascn.2013.04.004}, 919 petsc_uses = {KSP} 920} 921 922% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 923% LiteralHTML: <center><img alt="" 924% LiteralHTML: src="images/spine0l.jpg"></center></p> 925% LiteralHTML: <center><img alt="" 926% LiteralHTML: src="images/vertebra.jpg"></center></p> 927% LiteralHTML:<font color="#FF0000"> 928% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 929% LiteralHTML:Understanding bone mechanical properties and how they may lead to 930% LiteralHTML:fractures is thus an important medical research activity. PETSc and 931% LiteralHTML:Prometheus have been used for extremely large scale finite element 932% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 933% LiteralHTML:team of doctors and computational scientists. This computation was 934% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 935% LiteralHTML:with over 4000 processors.</p> 936% LiteralHTML: </font> 937@Article{ arbenz2008scalable, 938 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 939 analysis of human bone structures}, 940 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 941 journal = {International Journal for Numerical Methods in Engineering}, 942 volume = {73}, 943 number = {7}, 944 pages = {927--947}, 945 year = {2008}, 946 publisher = {Wiley Online Library}, 947 petsc_uses = {KSP} 948} 949 950@InProceedings{ adams-04, 951 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 952 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 953 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 954 half a billion degrees of freedom}, 955 note = {Gordon Bell Award}, 956 year = {2004}, 957 petsc_uses = {KSP} 958} 959 960@InProceedings{ adams-03b, 961 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 962 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 963 Whole Bone Micro-Mechanics on the IBM SP}, 964 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 965 year = {2003}, 966 petsc_uses = {KSP} 967} 968 969@InProceedings{ oghattas2002, 970 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 971 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 972 booktitle = {Procceedings of SC2002}, 973 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 974 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 975 by time-dependent PDEs, and scalability results for an inverse wave propagation 976 problem of determining the material field of an acoustic medium. Using the 977 algorithm, they solved a synthetic inverse wave propagation problem though a 978 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 979 processors.}, 980 year = {2002}, 981 petsc_uses = {KSP} 982} 983 984% LiteralHTML: <a name="biology:cardiology"> 985% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 986% LiteralHTML: <center><img alt="" 987% LiteralHTML: src="images/heart.jpg"> 988% LiteralHTML: <img alt="" 989% LiteralHTML: src="images/pump.jpg"></center></p> 990% LiteralHTML: 991% LiteralHTML:<font color="#FF0000"> 992% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 993% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 994% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 995% LiteralHTML: through the heart. PETSc has been used by several research groups to 996% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 997% LiteralHTML: fully understand the developments of arrhthmias.</p> 998% LiteralHTML:</font> 999@InProceedings{ oghattas2000, 1000 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 1001 Walkington}, 1002 title = {A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic 1003 Interfaces}, 1004 booktitle = {Procceedings of SC2000}, 1005 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 1006 note = {Blood flow modeling at the microscale including effects on individual blood 1007 cells, for designing heart assist pumps, etc.}, 1008 year = {2000}, 1009 petsc_uses = {KSP} 1010} 1011 1012@InBook{ cfps2006, 1013 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 1014 editor = {A. Quarteroni et al.}, 1015 title = {Complex Systems in Biomedicine}, 1016 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 1017 publisher = {Springer-Verlag}, 1018 pages = {187--241}, 1019 year = {2006}, 1020 petsc_uses = {KSP} 1021} 1022 1023@InProceedings{ cfpst2007, 1024 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 1025 title = {Determining recovery times from transmembrane action potentials and unipolar 1026 electrograms in normal heart tissue}, 1027 booktitle = {FIMH07}, 1028 publisher = {Springer-Verlag}, 1029 volume = {4466}, 1030 pages = {139--149}, 1031 year = {2007}, 1032 petsc_uses = {KSP} 1033} 1034 1035@Article{ seemann2010framework, 1036 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 1037 Equations Using PETSc}}, 1038 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 1039 D{\\"o}ssel, O.}, 1040 journal = {Progress in Industrial Mathematics at ECMI 2008}, 1041 pages = {363--369}, 1042 year = {2010}, 1043 publisher = {Springer}, 1044 petsc_uses = {KSP} 1045} 1046 1047@InProceedings{ pft2005, 1048 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 1049 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 1050 Intramural Heterogeneity}, 1051 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 1052 pages = {267--277}, 1053 editors = {A. Frangi et al.}, 1054 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 1055 year = {2005}, 1056 petsc_uses = {KSP} 1057} 1058 1059@Article{ bgcp2005, 1060 author = {Boyce E. Griffith and Charles S. Peskin}, 1061 title = {On the order of accuracy of the immersed boundary method: Higher order 1062 convergence rates for sufficiently smooth problems}, 1063 journal = {Journal of Computational Physics}, 1064 year = {2005}, 1065 volume = {208}, 1066 pages = {75--105}, 1067 petsc_uses = {KSP} 1068} 1069 1070@Article{ griffith2007adaptive, 1071 title = {An adaptive, formally second order accurate version of the immersed boundary 1072 method}, 1073 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 1074 journal = {Journal of Computational Physics}, 1075 volume = {223}, 1076 number = {1}, 1077 pages = {10--49}, 1078 year = {2007}, 1079 publisher = {Elsevier}, 1080 petsc_uses = {KSP} 1081} 1082 1083@PhDThesis{ griffith05, 1084 author = {Boyce Griffith}, 1085 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 1086 parallel version of the immersed boundary method}, 1087 school = {New York University}, 1088 year = {2005}, 1089 petsc_uses = {KSP} 1090} 1091 1092@PhDThesis{ murillo, 1093 author = {Maria S. Murillo}, 1094 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 1095 Differential Equations with an Application in Computational Biology}, 1096 school = {University of Colorado at Boulder}, 1097 year = {2002}, 1098 petsc_uses = {KSP} 1099} 1100 1101@Article{ spv2004, 1102 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 1103 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 1104 journal = {IEEE Trans. Biomed. Eng}, 1105 year = {2004}, 1106 volume = {51}, 1107 pages = {1960--1968}, 1108 petsc_uses = {KSP} 1109} 1110 1111@Article{ vphl2003, 1112 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 1113 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 1114 journal = {J. Electrocardiol.}, 1115 year = {2003}, 1116 volume = {36}, 1117 pages = {69--74}, 1118 petsc_uses = {KSP} 1119} 1120 1121@InProceedings{ spbv2003, 1122 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and and E.J. Vigmond}, 1123 title = {Preconditioning Techniques for the Bidomain Equations}, 1124 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 1125 Methods}, 1126 pages = {571--580}, 1127 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 1128 note = {}, 1129 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 1130 year = {2003}, 1131 petsc_uses = {KSP} 1132} 1133 1134@Article{ franz-pavir-04, 1135 author = {P. Colli Franzone and L.~F. Pavarino}, 1136 title = {A parallel solver for reaction-diffusion systems in computational 1137 electrocardiology}, 1138 journal = {Mathematical Models and Methods in Applied Sciences}, 1139 year = {2004}, 1140 volume = {14}, 1141 number = {6}, 1142 pages = {883--912}, 1143 petsc_uses = {KSP} 1144} 1145 1146@Article{ franz-pavir-05, 1147 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 1148 title = {Simulating patterns of excitation, repolarization and action potential 1149 durationwith cardiac Bidomain and Monodomain models}, 1150 journal = {Mathematical Biosciences}, 1151 year = {2005}, 1152 volume = {197}, 1153 number = {1}, 1154 pages = {35--66}, 1155 petsc_uses = {KSP} 1156} 1157 1158@Article{ franz-pavir-06, 1159 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 1160 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 1161 the dispersion of cardiac repolarization and action potential duration: a 1162 simulation study}, 1163 journal = {Mathematical Biosciences}, 1164 year = {2006}, 1165 volume = {204}, 1166 number = {1}, 1167 pages = {132--165}, 1168 petsc_uses = {KSP} 1169} 1170 1171@InProceedings{ colli-franz-sim, 1172 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 1173 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 1174 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 1175 Mediterranean Conference on Medical and Biological Engineering}, 1176 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 1177 year = {2004}, 1178 petsc_uses = {KSP} 1179} 1180 1181@InProceedings{ pf2003, 1182 author = {Luca F. Pavarino and Piero Colli Franzone}, 1183 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 1184 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 1185 Methods}, 1186 pages = {669--776}, 1187 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 1188 note = {}, 1189 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 1190 year = {2003}, 1191 petsc_uses = {KSP} 1192} 1193 1194@Article{ maria-is04, 1195 author = {Maria Murillo and Xiao-Chuan Cai}, 1196 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 1197 activity of the heart}, 1198 journal = {Numerical Linear Algebra with Applications}, 1199 year = {2004}, 1200 volume = {11}, 1201 pages = {261 - 277}, 1202 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 1203 petsc_uses = {KSP} 1204} 1205 1206@Article{ murli2007monitoring, 1207 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 1208 Imaging in a Grid computing PSE}}, 1209 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 1210 and Lapegna, M.}, 1211 journal = {Grid-Based Problem Solving Environments}, 1212 pages = {421--432}, 1213 year = {2007}, 1214 publisher = {Springer}, 1215 petsc_uses = {KSP} 1216} 1217 1218@Article{ carracciuolo:2006:tpc, 1219 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 1220 title = {Towards a parallel component for imaging in PETSc programming environment: a case 1221 study in 3-D echocardiography}, 1222 journal = {Parallel Comput.}, 1223 volume = {32}, 1224 issue = {1}, 1225 month = jan, 1226 year = {2006}, 1227 issn = {0167-8191}, 1228 pages = {67--83}, 1229 numpages = {17}, 1230 doi = {10.1016/j.parco.2005.09.001}, 1231 acmid = {1141218}, 1232 publisher = {Elsevier Science Publishers B. V.}, 1233 address = {Amsterdam, The Netherlands, The Netherlands}, 1234 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 1235 component}, 1236 petsc_uses = {KSP} 1237} 1238 1239@Article{ damore2011integration, 1240 title = {Integration of emerging computer technologies for an efficient image sequences 1241 analysis}, 1242 journal = {Integrated Computer-Aided Engineering }, 1243 volume = {18}, 1244 number = {4}, 1245 pages = {365 - 378}, 1246 year = {2011}, 1247 note = {}, 1248 issn = {1875-8835}, 1249 doi = {10.3233/ICA-2011-0382}, 1250 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 1251 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 1252 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 1253 petsc_uses = {KSP} 1254} 1255 1256@InProceedings{ eth_biwi_00721, 1257 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and and G. 1258 Székely}, 1259 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 1260 a Schur Complement Preconditioner}, 1261 booktitle = {Euro-Par 2009 Parallel Processing}, 1262 year = {2009}, 1263 month = aug, 1264 pages = {747-759}, 1265 volume = {5704}, 1266 editor = {H. Sips and D. Epema and and H.-X. Lin}, 1267 series = {Lecture Notes in Computer Science}, 1268 publisher = {Springer}, 1269 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 1270 parallel Krylov solver}, 1271 petsc_uses = {KSP} 1272} 1273 1274% LiteralHTML: <a name="biology:imagingandsurgery"> 1275% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1276% LiteralHTML: <center><img alt="" 1277% LiteralHTML: src="images/brain.jpg"></center> 1278@Article{ ganser2004deformable, 1279 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 1280 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 1281 journal = {Medical Image Analysis}, 1282 volume = {8}, 1283 number = {1}, 1284 pages = {3--22}, 1285 year = {2004}, 1286 publisher = {Elsevier}, 1287 petsc_uses = {KSP} 1288} 1289 1290@Unpublished{ taccsurgery, 1291 title = {TACC supercomputer performs laser cancer surgery on canine}, 1292 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 1293 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 1294 Austin performed laser surgery on a dog in Houston without the intervention of a 1295 surgeon. The treatment was developed collaboratively by computational experts from 1296 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 1297 leading technologists from the M.D. Anderson Cancer Center in Houston, and 1298 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 1299 state-of-the-art thermal imaging technology, and advanced computational methods, 1300 dynamic, data-driven treatments are being pursued as a minimally invasive 1301 alternative to the standard treatment of cancer.}, 1302 petsc_uses = {KSP} 1303} 1304 1305@Article{ ffhbresso2008, 1306 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 1307 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 1308 Tinsley Oden}, 1309 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 1310 journal = {Engineering with Computers}, 1311 note = {Special issue on Computational Bioengineering}, 1312 year = {2008}, 1313 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 1314 petsc_uses = {KSP} 1315} 1316 1317@TechReport{ dobbhbbbdeffghkkps2008, 1318 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 1319 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 1320 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 1321 and S. Prudhomme and R. J. Stafford}, 1322 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 1323 Cancer}, 1324 year = {2008}, 1325 institution = {University of Texas at Austin}, 1326 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 1327 petsc_uses = {KSP} 1328} 1329 1330@Article{ ogdb2004, 1331 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 1332 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 1333 journal = {Physics in Medicine and Biology}, 1334 year = {2004}, 1335 volume = {49}, 1336 pages = {2955--2947}, 1337 petsc_uses = {KSP} 1338} 1339 1340@InProceedings{ majumdar11, 1341 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 1342 Baldridge and P. Krysl}, 1343 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 1344 booktitle = {ICCS 2005}, 1345 pages = {672--679}, 1346 editor = {V.S. Sunderam et al.}, 1347 year = {2005}, 1348 petsc_uses = {KSP} 1349} 1350 1351@Conference{ sermesant-etal:03, 1352 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 1353 Ayache, H.}, 1354 title = {A parallel implementation of non-rigid registration using a volumetric 1355 biomechanical model}, 1356 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 1357 address = {Philadelphia, PA, USA}, 1358 publisher = {Springer-Verlag}, 1359 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 1360 series = {Lecture Notes in Computer Science}, 1361 volume = {2717}, 1362 pages = {398-407}, 1363 date = {june 23-24}, 1364 year = {2003}, 1365 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 1366 petsc_uses = {KSP} 1367} 1368 1369@Conference{ sermesant-etal:04, 1370 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 1371 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 1372 title = {A Novel Nonrigid Registration Algorithm And Applications}, 1373 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 1374 address = {Philadelphia, PA, USA}, 1375 publisher = {Springer-Verlag}, 1376 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 1377 series = {Lecture Notes in Computer Science}, 1378 volume = {2208}, 1379 pages = {923}, 1380 year = {2003}, 1381 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 1382 petsc_uses = {KSP} 1383} 1384 1385@Article{ warfield-haker-talos-05, 1386 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 1387 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 1388 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 1389 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 1390 title = {Capturing intraoperative deformations: research experience at Brigham and Women's 1391 hospital}, 1392 journal = {Medical Image Analysis}, 1393 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 1394 year = {2005}, 1395 petsc_uses = {KSP} 1396} 1397 1398@Article{ brain3, 1399 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 1400 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 1401 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 1402 Deformation during Image Guided Neurosurgery}, 1403 journal = {Computing and Visualization in Science}, 1404 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 1405 year = {2002}, 1406 petsc_uses = {KSP} 1407} 1408 1409@Article{ brain2, 1410 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 1411 Kikinis and Simon K. Warfield}, 1412 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 1413 Element Biomechanical Model}, 1414 journal = {IEEE Transactions on Medical Imaging}, 1415 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 1416 year = {2001}, 1417 petsc_uses = {KSP} 1418} 1419 1420@InProceedings{ brain1, 1421 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 1422 Ferenc A. Jolesz and Ron Kikinis}, 1423 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 1424 Guided Neurosurgery}, 1425 booktitle = {Proceedings of SC2000}, 1426 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 1427 year = {2000}, 1428 petsc_uses = {KSP} 1429} 1430 1431@Article{ vanne06, 1432 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 1433 M. Lassas and M. Kalke}, 1434 title = {Parallelized Bayesian inversion for three-dimensional dental X-ray imaging}, 1435 journal = {IEEE Transactions on Medical Imaging}, 1436 volume = {25}, 1437 number = {2}, 1438 month = feb, 1439 year = {2006}, 1440 pages = {218--228}, 1441 petsc_uses = {KSP} 1442} 1443 1444@InProceedings{ knepleybardhan2015, 1445 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 1446 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 1447 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 1448 Exposition}, 1449 volume = {9}, 1450 pages = {V009T12A04}, 1451 doi = {10.1115/IMECE2015-53579}, 1452 year = {2015}, 1453 petsc_uses = {KSP} 1454} 1455 1456@InProceedings{ bardhanknepley2015, 1457 title = {Multiscale models and approximation algorithms for protein electrostatics}, 1458 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 1459 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 1460 volume = {61}, 1461 pages = {163--174}, 1462 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 1463 doi = {10.2495/BEM380131}, 1464 publisher = {WIT Press}, 1465 year = {2015}, 1466 petsc_uses = {KSP} 1467} 1468 1469% LiteralHTML: 1470% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 1471% LiteralHTML: 1472@InProceedings{ adamsbrennanknepleywang2022, 1473 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 1474 quench plasmas}, 1475 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 1476 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 1477 (IPDPS '22)}, 1478 doi = {10.1109/IPDPS53621.2022.00020}, 1479 year = {2022}, 1480 petsc_uses = {DMPlex} 1481} 1482 1483@Misc{ adamsknepleybrennan2021, 1484 title = {Runaway Electron Generation with High-Performance, Structure Preserving 1485 Discretization of Fokker-Plank-Landau}, 1486 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 1487 year = {2021}, 1488 petsc_uses = {KSP} 1489} 1490 1491@Article{ adamshirvijokiknepleybrownisaacmills2017, 1492 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 1493 Architectures}, 1494 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 1495 Isaac and Richard Mills}, 1496 journal = {SIAM Journal on Scientific Computing}, 1497 volume = {39}, 1498 number = {6}, 1499 pages = {C452--C465}, 1500 doi = {10.1137/17M1118828}, 1501 eprint = {1702.08880}, 1502 year = {2017}, 1503 petsc_uses = {KSP} 1504} 1505 1506@Article{ pusztayknepleyadams2022, 1507 title = {Conservative Projection Between FEM and Particle Bases}, 1508 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 1509 journal = {SIAM Journal on Scientific Computing}, 1510 volume = {44}, 1511 number = {4}, 1512 pages = {C310--C319}, 1513 doi = {10.1137/21M145407}, 1514 year = {2022} 1515} 1516 1517@Article{ hirvijoki2017, 1518 author = {Eero Hirvijoki and Mark F. Adams}, 1519 title = {Conservative discretization of the {Landau} collision integral}, 1520 journal = {Physics of Plasmas}, 1521 volume = {24}, 1522 number = {3}, 1523 pages = {032121}, 1524 doi = {10.1063/1.4979122}, 1525 year = {2017}, 1526 petsc_uses = {KSP} 1527} 1528 1529@Article{ mollenadamsknepleyhagerchang2021, 1530 title = {Implementation of higher-order velocity mapping between marker particles and grid 1531 in the particle-in-cell code XGC}, 1532 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 1533 S. Chang}, 1534 journal = {Journal of Plasma Physics}, 1535 eprint = {2012.11764}, 1536 doi = {10.1017/S0022377821000441}, 1537 year = {2021}, 1538 petsc_uses = {KSP} 1539} 1540 1541@Article{ lsmh2014, 1542 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 1543 title = {Comparison of particle trajectories and collision operators for collisional 1544 transport in nonaxisymmetric plasmas}, 1545 journal = { Physics of Plasmas}, 1546 volume = {21}, 1547 year = {2014}, 1548 petsc_uses = {KSP} 1549} 1550 1551@Article{ lpcep2014, 1552 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 1553 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 1554 pedestal}, 1555 journal = {Plasma Physics and Controlled Fusion}, 1556 volume = {56}, 1557 year = {2014}, 1558 petsc_uses = {KSP} 1559} 1560 1561@Article{ facets-scidac08, 1562 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 1563 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 1564 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 1565 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 1566 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 1567 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 1568 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 1569 Stotler and A. Pigarov}, 1570 journal = {J. Phys.: Conf. Ser.}, 1571 volume = {125}, 1572 year = {2008}, 1573 pages = {012040}, 1574 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 1575 petsc_uses = {KSP} 1576} 1577 1578@Article{ facets-scidac09, 1579 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 1580 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 1581 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 1582 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 1583 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 1584 and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar 1585 and A. Pigarov and H. Zhang}, 1586 journal = {J. Phys.: Conf. Ser.}, 1587 volume = {180}, 1588 year = {2009}, 1589 pages = {012056}, 1590 url = {http://iopscience.iop.org/1742-6596/180/1/012056}, 1591 petsc_uses = {KSP} 1592} 1593 1594@InProceedings{ facets-scidac10, 1595 title = {Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the 1596 {FACETS} Code}, 1597 author = {A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. 1598 Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. 1599 Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. 1600 Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. 1601 Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. 1602 Pigarov and H. Zhang}, 1603 booktitle = {Proceedings of SciDAC 2010 Conference}, 1604 year = {2010}, 1605 url = {http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf}, 1606 petsc_uses = {KSP} 1607} 1608 1609@InProceedings{ facets-fec2010, 1610 title = {Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using 1611 the {FACETS} Framework}, 1612 author = {J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina 1613 and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. 1614 McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang}, 1615 booktitle = {Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, 1616 Republic of Korea}, 1617 year = {2010}, 1618 petsc_uses = {KSP} 1619} 1620 1621@InProceedings{ facets-epdp2010, 1622 title = {{FACETS}: A Framework for Parallel Coupling of Fusion Components}, 1623 author = {J. Cary and A. Hakim and M. Miah and S. Kruger and A. Pletzer and S. Shasharina 1624 and S. Vadlamani and A. Pankin and R. Cohen and T. Epperly and T. Rognlien and R. 1625 Groebner and S. Balay and L. McInnes and H. Zhang}, 1626 booktitle = {Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on 1627 Parallel, Distributed and Network-Based Computing), Pisa, Italy}, 1628 year = {2010}, 1629 petsc_uses = {KSP} 1630} 1631 1632@Article{ carlssoncary09, 1633 author = {Johan Carlsson, John R. Cary}, 1634 title = {The hypersecant Jacobian approximation for quasi-Newton solves of sparse 1635 nonlinear systems}, 1636 journal = {arXiv}, 1637 year = {2009}, 1638 note = {http://arxiv.org/abs/0905.1054}, 1639 url = {http://arxiv.org/pdf/0905.1054v1}, 1640 petsc_uses = {KSP} 1641} 1642 1643@InProceedings{ oshahjs2006, 1644 author = {F. Ogando and A. Signell and J.A. Heikkinen and M. Aspn\"as and S. Henriksson and 1645 S.J. Janhunen and T.P. Kiviniemi}, 1646 title = {Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of 1647 application}, 1648 booktitle = {33rd EPS Conference on Plasma Phys.}, 1649 year = {2006}, 1650 url = {http://epsppd.epfl.ch/Roma/pdf/P4_153.pdf}, 1651 note = {European fusion code}, 1652 petsc_uses = {KSP} 1653} 1654 1655@Article{ zhu2006, 1656 author = {P. Zhu and A. Bhattacharjee and K. Germaschewski}, 1657 title = {Intermediate nonlinear evolution of the Parker instability: Formation of 1658 convection-induced discontinuities and absence of finite-time singularities}, 1659 journal = {Phys. Rev. Lett.}, 1660 volume = {96}, 1661 number = {065001}, 1662 year = {2006}, 1663 doi = {10.1103/PhysRevLett.96.065001}, 1664 petsc_uses = {KSP} 1665} 1666 1667@InProceedings{ ppc2005, 1668 author = {B. Philip and M. Pernice and L.Chacon}, 1669 title = {Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh 1670 Refinement}, 1671 booktitle = {Proceedings of the 16th International Conference on Domain Decomposition 1672 methods}, 1673 year = {2005}, 1674 lab = {LANL}, 1675 petsc_uses = {KSP} 1676} 1677 1678@Article{ pp2005, 1679 author = {M. Pernice and B. Philip}, 1680 title = {Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh 1681 Refinement}, 1682 year = {2005}, 1683 journal = {SIAM J. of Sci. Comput.}, 1684 lab = {LANL}, 1685 petsc_uses = {KSP} 1686} 1687 1688@Article{ gt2004, 1689 author = {A. H. Glasser and X. Z. Tang}, 1690 title = {The SEL macroscopic modeling code}, 1691 year = {2004}, 1692 journal = {Computer Physics Communications}, 1693 pages = {237--243}, 1694 volume = {164}, 1695 lab = {LANL}, 1696 petsc_uses = {KSP} 1697} 1698 1699@Article{ nl2006, 1700 author = {Y. Nishimura and Z.Lin}, 1701 title = {A finite element mesh in a tokamak edge geometry}, 1702 year = {2006}, 1703 journal = {Contributions to Plasma Physics}, 1704 volume = {22}, 1705 lab = {PPPL}, 1706 petsc_uses = {KSP} 1707} 1708 1709@Article{ nlle2004, 1710 author = {Y. Nishimura and Z.Lin and J.Lewandowski and S.Ethier}, 1711 title = {A finite element Poisson solver for gyrokinetic particle simulations in a global 1712 field aligned mesh}, 1713 year = {2006}, 1714 journal = {J. Comput. Phys.}, 1715 volume = {214}, 1716 pages = {657}, 1717 lab = {PPPL}, 1718 petsc_uses = {KSP} 1719} 1720 1721@InProceedings{ lnlle2004, 1722 author = {J.L.V Lewandowski and Y.Nishimura and W.W.Lee and Z.Lin and S. Ethier}, 1723 title = {Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons}, 1724 booktitle = {Sherwood Fusion Theory Conference, Missoula, MT}, 1725 year = {2004}, 1726 url = {http://www.sherwoodtheory.org/sherwood04/program/1e15.pdf}, 1727 lab = {PPPL}, 1728 petsc_uses = {KSP} 1729} 1730 1731@InProceedings{ nlclew2004, 1732 author = {Y. Nishimura and Z.Lin and L.Chen and J.Lewandowski and S.Ethier and W. Wang}, 1733 title = {Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron 1734 model}, 1735 booktitle = {Sherwood Fusion Theory Conference, Missoula, MT}, 1736 year = {2004}, 1737 url = {http://www.sherwoodtheory.org/sherwood04/program/1C32.pdf}, 1738 lab = {PPPL}, 1739 petsc_uses = {KSP} 1740} 1741 1742@Article{ tb1, 1743 author = {X.~Z.~Tang and A.~H.~Boozer}, 1744 title = {Numerical studies of a steady state axisymmetric co-axial helicity injection 1745 plasma}, 1746 journal = {Physics of Plasmas}, 1747 year = {2004}, 1748 pages = {171--185}, 1749 volume = {11}, 1750 lab = {LANL}, 1751 petsc_uses = {KSP} 1752} 1753 1754@Unpublished{ nlcw, 1755 title = {Inclusion of electromagnetic effects into gyrokinetic particle simulations}, 1756 author = {Y. Nishimura and Z.Lin and L.Chen and W. Wang}, 1757 note = {American Physical Society 45th Annual Meeting Division of Plasma Physics, 1758 Albuquerque, New Mexico, October 2003}, 1759 year = {2003}, 1760 petsc_uses = {KSP} 1761} 1762 1763@TechReport{ tang2001, 1764 author = {X. Z. Tang and G. Y. Fu and S. C. Jardin and L. L. Lowe and W. Park and H. R. 1765 Strauss}, 1766 title = {Resistive Magnetohydrodynamics Simulation of Fusion Plasmas}, 1767 year = {2001}, 1768 institution = {Princeton Plasma Physics Laboratory}, 1769 number = {PPPL-3532}, 1770 url = {http://www.pppl.gov/pub_report/2001/PPPL-3532.pdf}, 1771 note = {Presented at 10th Society for Industrial and Applied Mathematics (SIAM) 1772 Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, 1773 March 12-14, 2001.}, 1774 lab = {PPPL}, 1775 petsc_uses = {KSP} 1776} 1777 1778% LiteralHTML: 1779% LiteralHTML: <a name="geosciences"><H3><center>Geosciences</center></H3> 1780% LiteralHTML: 1781@Article{ valerathomasgarciacastillo2019, 1782 author = {Manuel Valera and Mary P. Thomas and Mariangel Garcia and Jose E. Castillo}, 1783 title = {Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear 1784 Coastal Ocean Model}, 1785 journal = {Journal of Marine Science and Engineering}, 1786 volume = {7}, 1787 number = {6}, 1788 article-number= {185}, 1789 url = {https://www.mdpi.com/2077-1312/7/6/185}, 1790 issn = {2077-1312}, 1791 doi = {10.3390/jmse7060185}, 1792 year = {2019}, 1793 petsc_uses = {KSP} 1794} 1795 1796@Article{ furuichimat2015, 1797 title = {Implicit solution of the material transport in Stokes flow simulation: Toward 1798 thermal convection simulation surrounded by free surface}, 1799 author = {Mikito Furuichi and Dave A May}, 1800 journal = {Computer Physics Communications}, 1801 volume = {192}, 1802 pages = {1--11}, 1803 year = {2015}, 1804 petsc_uses = {KSP} 1805} 1806 1807@Article{ sharplesmoresivelicjadamecmay2016, 1808 title = {Simulating faults and plate boundaries with a transversely isotropic plasticity 1809 model}, 1810 author = {Wendy Sharples and Louis N Moresi and Mirko Velic and Margarete A Jadamec and 1811 Dave A May}, 1812 journal = {Physics of the Earth and Planetary Interiors}, 1813 volume = {252}, 1814 pages = {77--90}, 1815 year = {2016}, 1816 petsc_uses = {KSP} 1817} 1818 1819@Article{ spiegelmanmaywilson2016, 1820 title = {On the solvability of incompressible Stokes with viscoplastic rheologies in 1821 geodynamics}, 1822 author = {Marc Spiegelman and Dave A May and Cian R Wilson}, 1823 journal = {Geochemistry, Geophysics, Geosystems}, 1824 volume = {17}, 1825 number = {6}, 1826 pages = {2213--2238}, 1827 year = {2016}, 1828 petsc_uses = {KSP} 1829} 1830 1831@Article{ buiteretal2016, 1832 title = {Benchmarking numerical models of brittle thrust wedges}, 1833 author = {Susanne JH Buiter and Guido Schreurs and Markus Albertz and Taras V Gerya and 1834 Boris Kaus and Walter Landry and Laetitia {Le Pourhiet} and Yury Mishin and David 1835 L Egholm and Michele Cooke and Bertrand Maillot and Cedric Thieulot and Tony Crook 1836 and Dave May and Pauline Souloumiac and Christopher Beaumont}, 1837 journal = {Journal of structural geology}, 1838 volume = {92}, 1839 pages = {140--177}, 1840 year = {2016}, 1841 petsc_uses = {KSP} 1842} 1843 1844@Article{ afanasievboehmdrielkrischerrietmannmayknepleyfichtner2019, 1845 title = {Modular and flexible spectral-element waveform modelling in two and three 1846 dimensions}, 1847 author = {Michael Afanasiev and Christian Boehm and Martin van Driel and Lion Krischer and 1848 Max Rietmann and Dave A. May and Matthew G. Knepley and Andreas Fichtner}, 1849 journal = {Geophysical Journal International}, 1850 volume = {216}, 1851 number = {3}, 1852 pages = {1675--1692}, 1853 doi = {10.1093/gji/ggy469}, 1854 year = {2019}, 1855 petsc_uses = {KSP} 1856} 1857 1858@Article{ haplaknepleyafanasievboehmdrielkrischerfichtner2020, 1859 title = {Fully Parallel Mesh {I/O} using {PETSc} {DMPlex} with an Application to Waveform 1860 Modeling}, 1861 author = {Vaclav Hapla and Matthew G. 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Snyder}, 2367 collaboration = {}, 2368 title = {Multiple-domain, simultaneous joint inversion of geophysical data with 2369 application to subsalt imaging}, 2370 publisher = {SEG}, 2371 year = {2011}, 2372 journal = {Geophysics}, 2373 volume = {76}, 2374 number = {3}, 2375 pages = {R69-R80}, 2376 keywords = {geophysical image processing; inverse problems; seismology}, 2377 doi = {10.1190/1.3554652}, 2378 petsc_uses = {KSP} 2379} 2380 2381@Article{ stefano:806, 2382 author = {Michele De Stefano}, 2383 collaboration = {}, 2384 title = {Simultaneous joint inversion for susceptibility and velocity}, 2385 publisher = {SEG}, 2386 year = {2011}, 2387 journal = {SEG Technical Program Expanded Abstracts}, 2388 volume = {30}, 2389 number = {1}, 2390 pages = {806-810}, 2391 keywords = {3D; imaging; inversion; magnetics; multiparameter}, 2392 doi = {10.1190/1.3628198}, 2393 petsc_uses = {KSP} 2394} 2395 2396@Article{ mayknepley2011, 2397 author = {Dave A. May and Matthew G. Knepley}, 2398 title = {Optimal, scalable forward models for computing gravity anomalies}, 2399 journal = {Geophysical Journal International}, 2400 volume = {187}, 2401 number = {1}, 2402 pages = {161--177}, 2403 url = {http://arxiv.org/abs/1107.5951}, 2404 note = {\url{http://arxiv.org/abs/1107.5951}}, 2405 year = {2011}, 2406 petsc_uses = {KSP} 2407} 2408 2409@InProceedings{ bourdinknepleymaurini2010, 2410 author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini}, 2411 title = {Numerical Simulation of Reservoir Stimulation - A Variational Approach}, 2412 booktitle = {Proceedings of the 37th Stanford Geothermal Workshop}, 2413 url = {https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}, 2414 note = {\url{https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}}, 2415 address = {Stanford, CA}, 2416 year = {2010}, 2417 petsc_uses = {KSP} 2418} 2419 2420@InProceedings{ bourdinknepleymaurini2010b, 2421 author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini}, 2422 title = {Secondary Thermal Cracks in {EGS}: a Variational Approach}, 2423 booktitle = {Proceedings of the 34th Annual Meeting of the Geothermal Resources Council}, 2424 url = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}, 2425 note = {\url{https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}}, 2426 address = {Sacramento, CA}, 2427 year = {2010}, 2428 petsc_uses = {KSP} 2429} 2430 2431@Article{ chen2007full, 2432 title = {Full 3D tomography for the crustal structure of the Los Angeles region}, 2433 author = {Chen, P. and Zhao, L. and Jordan, T.H.}, 2434 journal = {Bulletin of the Seismological Society of America}, 2435 volume = {97}, 2436 number = {4}, 2437 pages = {1094}, 2438 year = {2007}, 2439 publisher = {Seismol Soc America}, 2440 petsc_uses = {KSP} 2441} 2442 2443@Article{ brown2010ens, 2444 author = {Brown, Jed}, 2445 affiliation = {Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, 2446 Zürich, Switzerland}, 2447 title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}}, 2448 journal = {Journal of Scientific Computing}, 2449 publisher = {Springer Netherlands}, 2450 issn = {0885-7474}, 2451 keyword = {Mathematics and Statistics}, 2452 pages = {48-63}, 2453 volume = {45}, 2454 issue = {1}, 2455 doi = {10.1007/s10915-010-9396-8}, 2456 year = {2010}, 2457 petsc_uses = {KSP} 2458} 2459 2460@PhDThesis{ brown2011, 2461 title = {Computational methods for ice flow simulation}, 2462 author = {Jed Brown}, 2463 school = {ETH Z{\"u}rich}, 2464 year = {2011}, 2465 petsc_uses = {KSP} 2466} 2467 2468@Article{ brown2013tmeice, 2469 title = {Achieving textbook multigrid efficiency for hydrostatic ice flow}, 2470 author = {Jed Brown and Barry F. Smith and Aron Ahmadia}, 2471 journal = {SIAM Journal on Scientific Computing}, 2472 volume = {35}, 2473 number = {2}, 2474 year = {2013}, 2475 pages = {359--375}, 2476 doi = {10.1137/110834512}, 2477 note = {Also preprint ANL/MCS-P743-1298}, 2478 petsc_uses = {KSP} 2479} 2480 2481@InProceedings{ brown2013quasinewton, 2482 author = {Jed Brown and Peter Brune}, 2483 title = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type 2484 methods}, 2485 year = {2013}, 2486 booktitle = {International Conference on Mathematics and Computational Methods Applied to 2487 Nuclear Science and Engineering}, 2488 pages = {2554--2565}, 2489 petsc_uses = {KSP} 2490} 2491 2492@Misc{ spiegelman-siampp10, 2493 title = {Block Preconditioners and Advanced Software for Multiphysics Problems in Solid 2494 Earth Geodynamics}, 2495 author = {Marc Spiegelman}, 2496 note = {presentation at the 2010 SIAM Conference on Parallel Processing for Scientific 2497 Computing}, 2498 year = {2010}, 2499 petsc_uses = {KSP} 2500} 2501 2502@Article{ schauer2011a, 2503 author = {Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. 2504 Quintana-Ort\'{\i}}, 2505 title = {Large scale simulation of wave propagation in soils interacting with structures 2506 using {FEM} and {SBFEM}}, 2507 journal = {Journal of Computational Acoustics}, 2508 volume = {19}, 2509 number = {1}, 2510 pages = {75--93}, 2511 year = {2011}, 2512 doi = {10.1142/S0218396X11004316}, 2513 petsc_uses = {KSP} 2514} 2515 2516@Misc{ bsa2010, 2517 author = {J. Brown and B. Smith and A. Ahmadia}, 2518 title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow}, 2519 note = {submitted to SIAM Journal on Scientific Computing}, 2520 year = {2012}, 2521 petsc_uses = {KSP} 2522} 2523 2524@Article{ kellerkatz2016, 2525 title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere}, 2526 author = {Tobias Keller and Richard F. Katz}, 2527 journal = {Journal of Petrology}, 2528 doi = {10.1093/petrology/egw030}, 2529 url = {http://petrology.oxfordjournals.org/content/early/2016/07/15/petrology.egw030.abstract}, 2530 eprint = {http://petrology.oxfordjournals.org/content/early/2016/07/15/petrology.egw030.full.pdf+html}, 2531 year = {2016}, 2532 petsc_uses = {KSP} 2533} 2534 2535@Article{ weatherley12, 2536 author = {S. Weatherley and R.F. Katz}, 2537 title = {Melting and channelized magmatic flow in chemically heterogeneous, upwelling 2538 mantle}, 2539 journal = {Geochem.\ Geophys.\ Geosys.}, 2540 year = {2012}, 2541 volume = {13}, 2542 number = {1}, 2543 pages = {Q0AC18}, 2544 doi = {10.1029/2011GC003989}, 2545 petsc_uses = {KSP} 2546} 2547 2548@Article{ katz12, 2549 author = {R.F. Katz and S. Weatherley}, 2550 title = {Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges}, 2551 journal = {Earth\ Planet.\ Sci.\ Lett.}, 2552 year = {2012}, 2553 doi = {10.1016/j.epsl.2012.04.042}, 2554 volume = {335-336}, 2555 pages = {226-237}, 2556 petsc_uses = {KSP} 2557} 2558 2559@Article{ katz10b, 2560 author = {R.F. Katz}, 2561 title = {Porosity-driven convection and asymmetry beneath mid-ocean ridges}, 2562 journal = {Geochem.\ Geophys.\ Geosys.}, 2563 volume = {10}, 2564 number = {Q0AC07}, 2565 year = {2010}, 2566 doi = {10.1029/2010GC003282}, 2567 petsc_uses = {KSP} 2568} 2569 2570@Article{ england10, 2571 author = {P.C. England and R.F. Katz}, 2572 title = {Melting above the anhydrous solidus controls the location of volcanic arcs}, 2573 journal = {Nature}, 2574 year = {2010}, 2575 volume = {467}, 2576 pages = {700--703}, 2577 doi = {10.1038/nature09417}, 2578 petsc_uses = {KSP} 2579} 2580 2581@Article{ weatherley10, 2582 author = {S. Weatherley and R.F. Katz}, 2583 title = {Plate-Driven Mantle Dynamics and Global Patterns of Mid-Ocean Ridge Bathymetry}, 2584 journal = {Geochem.\ Geophys.\ Geosys.}, 2585 year = {2010}, 2586 volume = {11}, 2587 number = {10}, 2588 doi = {10.1029/2010GC003192}, 2589 petsc_uses = {KSP} 2590} 2591 2592@Article{ katz10, 2593 author = {R.F. Katz and M.G. Worster}, 2594 title = {The stability of ice-sheet grounding lines}, 2595 journal = {Proc.~Roy.~Soc.~A}, 2596 year = {2010}, 2597 volume = {466}, 2598 pages = {1597--1620}, 2599 doi = {10.1098/rspa.2009.0434}, 2600 url = {http://www.earth.ox.ac.uk/~richardk/publications/Katz_Worster_PRSA10.pdf}, 2601 petsc_uses = {KSP} 2602} 2603 2604@Article{ kyrkesmith2013stress, 2605 title = {Stress balances of ice streams in a vertically integrated, higher-order 2606 formulation}, 2607 author = {Kyrke-Smith, T.M. and Katz, R.F. and Fowler, A.C.}, 2608 journal = {Journal of Glaciology}, 2609 volume = {59}, 2610 number = {215}, 2611 pages = {449--466}, 2612 year = {2013}, 2613 doi = {10.3189/2013JoG12J140}, 2614 petsc_uses = {KSP} 2615} 2616 2617@Article{ takei2013anisotropy1, 2618 author = {Takei Y. and R.F. Katz}, 2619 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. 2620 Governing equations and linearised analysis}}, 2621 journal = {J.\ Fluid\ Mech.}, 2622 year = {2013}, 2623 volume = {734}, 2624 pages = {424-455}, 2625 doi = {10.1017/jfm.2013.482}, 2626 petsc_uses = {KSP} 2627} 2628 2629@Article{ katz2013anisotropy2, 2630 author = {Katz R.F. and Y. Takei}, 2631 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. 2632 Numerical solutions of the full equations}}, 2633 journal = {J.\ Fluid\ Mech.}, 2634 year = {2013}, 2635 volume = {734}, 2636 pages = {456-485}, 2637 doi = {10.1017/jfm.2013.483}, 2638 petsc_uses = {KSP} 2639} 2640 2641@Article{ kyrke-smith2014subglacial, 2642 author = {Kyrke-Smith, T.M. and R.F. Katz and A.C. 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Knepley}, 2865 title = {Modeling of Multiple Earthquake Cycles in Southern California Using the {SCEC} 2866 Community Fault Model}, 2867 booktitle = {Proceedings of Geosciences '08}, 2868 address = {Wellington, NZ}, 2869 month = nov, 2870 year = {2008}, 2871 petsc_uses = {KSP} 2872} 2873 2874@TechReport{ zhang07, 2875 title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for 2876 Tsunamis}, 2877 author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi}, 2878 type = {Preprint}, 2879 number = {ANL/MCS-P1459-0907}, 2880 institution = {ANL}, 2881 month = sep, 2882 year = {2007}, 2883 petsc_uses = {KSP} 2884} 2885 2886@Article{ katz08b, 2887 author = {Richard F. Katz}, 2888 title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic 2889 focusing at mid-ocean ridges}, 2890 journal = {J. Petrology}, 2891 year = {2008}, 2892 volume = {49}, 2893 pages = {2099--2121}, 2894 doi = {10.1093/petrology/egn058}, 2895 petsc_uses = {KSP} 2896} 2897 2898@Article{ hgrhkjvv2008, 2899 title = {On preconditioning for a parallel solution of the Richards equation}, 2900 author = {Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy 2901 Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena}, 2902 journal = {Computers and Geosciences}, 2903 volume = {34}, 2904 pages = {1958--1963}, 2905 year = {2008}, 2906 petsc_uses = {KSP} 2907} 2908 2909@Article{ maymoresi2008, 2910 title = {Preconditioned iterative methods for {Stokes} flow problems arising in 2911 computational geodynamics}, 2912 journal = {Physics of the Earth and Planetary Interiors}, 2913 volume = {171}, 2914 number = {1-4}, 2915 pages = {33--47}, 2916 year = {2008}, 2917 note = {{R}ecent Advances in Computational Geodynamics: Theory, Numerics and 2918 Applications}, 2919 issn = {0031-9201}, 2920 doi = {10.1016/j.pepi.2008.07.036}, 2921 author = {Dave A. May and Louis Moresi}, 2922 keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}, 2923 petsc_uses = {KSP} 2924} 2925 2926@Article{ kausmuhlhausmay2010, 2927 title = {A stabilization algorithm for geodynamic numerical simulations with a free 2928 surface}, 2929 author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May}, 2930 journal = {Physics of the Earth and Planetary Interiors}, 2931 volume = {181}, 2932 number = {1}, 2933 pages = {12--20}, 2934 year = {2010}, 2935 petsc_uses = {KSP} 2936} 2937 2938@Article{ duretzmaygeryatackley2011, 2939 title = {Discretization errors and free surface stabilization in the finite difference and 2940 marker-in-cell method for applied geodynamics: A numerical study}, 2941 author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley}, 2942 journal = {Geochemistry, Geophysics, Geosystems}, 2943 volume = {12}, 2944 number = {7}, 2945 year = {2011}, 2946 petsc_uses = {KSP} 2947} 2948 2949@Article{ furuichimaytackley2011, 2950 title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a 2951 {Schur} complement approach with mixed precision arithmetic}, 2952 author = {Mikito Furuichi and Dave A May and Paul J Tackley}, 2953 journal = {Journal of Computational Physics}, 2954 volume = {230}, 2955 number = {24}, 2956 pages = {8835--8851}, 2957 year = {2011}, 2958 petsc_uses = {KSP} 2959} 2960 2961@Article{ kellermaykaus2013, 2962 title = {Numerical modelling of magma dynamics coupled to tectonic deformation of 2963 lithosphere and crust}, 2964 author = {Tobias Keller and Dave A May and Boris JP Kaus}, 2965 journal = {Geophysical Journal International}, 2966 volume = {195}, 2967 number = {3}, 2968 pages = {1406--1442}, 2969 year = {2013}, 2970 petsc_uses = {KSP} 2971} 2972 2973@Article{ schellartfreemanstegmanmoresimay2007, 2974 title = {Evolution and diversity of subduction zones controlled by slab width}, 2975 author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A 2976 May}, 2977 journal = {Nature}, 2978 volume = {446}, 2979 number = {7133}, 2980 pages = {308--311}, 2981 year = {2007}, 2982 petsc_uses = {KSP} 2983} 2984 2985@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012, 2986 title = {A comparison of numerical surface topography calculations in geodynamic 2987 modelling: an evaluation of the sticky air method}, 2988 author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter 2989 and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley}, 2990 journal = {Geophysical Journal International}, 2991 volume = {189}, 2992 number = {1}, 2993 pages = {38--54}, 2994 year = {2012}, 2995 petsc_uses = {KSP} 2996} 2997 2998@Article{ stegmanfreemanschellartmoresimay2006, 2999 title = {Influence of trench width on subduction hinge retreat rates in 3-D models of slab 3000 rollback}, 3001 author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A 3002 May}, 3003 journal = {Geochemistry, Geophysics, Geosystems}, 3004 volume = {7}, 3005 number = {3}, 3006 year = {2006}, 3007 petsc_uses = {KSP} 3008} 3009 3010@InProceedings{ may2014ptatin, 3011 title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics}, 3012 author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}}, 3013 booktitle = {Proceedings of {SC14}: The {International Conference for High Performance 3014 Computing, Networking, Storage and Analysis}}, 3015 organization = {ACM}, 3016 pages = {274--284}, 3017 year = {2014}, 3018 doi = {10.1109/SC.2014.28}, 3019 petsc_uses = {KSP} 3020} 3021 3022@Article{ maybrownpourhiet2015, 3023 title = {A scalable, matrix-free multigrid preconditioner for finite element 3024 discretizations of heterogeneous {Stokes} flow}, 3025 author = {David A May and Jed Brown and Laetitia {Le Pourhiet}}, 3026 journal = {Computer Methods in Applied Mechanics and Engineering}, 3027 volume = {290}, 3028 pages = {496--523}, 3029 year = {2015}, 3030 doi = {10.1016/j.cma.2015.03.014}, 3031 petsc_uses = {KSP} 3032} 3033 3034@Article{ duretzmayyamato2016, 3035 title = {A free surface capturing discretization for the staggered grid finite difference 3036 scheme}, 3037 author = {Thibault Duretz and Dave A May and Philippe Yamato}, 3038 journal = {Geophysical Journal International}, 3039 volume = {204}, 3040 number = {3}, 3041 pages = {1518--1530}, 3042 year = {2016}, 3043 petsc_uses = {KSP} 3044} 3045 3046@Article{ rhebergenwellskatzwathen2014, 3047 author = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen}, 3048 title = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics}, 3049 journal = {SIAM J. Sci. Comput.}, 3050 volume = {36}, 3051 pages = {A1960--A1977}, 3052 year = {2014}, 3053 petsc_uses = {KSP} 3054} 3055 3056@Article{ katz08a, 3057 author = {R.F. Katz and M.G. Worster}, 3058 title = {Simulation of directional solidification, thermochemical convection, and chimney 3059 formation in a {H}ele-{S}haw cell}, 3060 journal = {J. Comp. Phys.}, 3061 volume = {227}, 3062 pages = {9823-9840}, 3063 year = {2008}, 3064 doi = {10.1016/j.jcp.2008.06.039}, 3065 petsc_uses = {KSP} 3066} 3067 3068@Article{ aabg2007, 3069 author = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas}, 3070 title = {Full waveform inversion for seismic velocity and anelastic losses in 3071 heterogeneous structures}, 3072 journal = {Bulletin of Seismological Society of America}, 3073 year = {2007}, 3074 volume = {97}, 3075 pages = {1990--2008}, 3076 petsc_uses = {KSP} 3077} 3078 3079@Article{ katz2006, 3080 author = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman}, 3081 title = {The dynamics of melt and shear localization in partially molten aggregates}, 3082 journal = {Nature}, 3083 year = {2006}, 3084 volume = {442}, 3085 pages = {676--679}, 3086 month = aug, 3087 day = {10}, 3088 url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}, 3089 petsc_uses = {KSP} 3090} 3091 3092@InProceedings{ mqrs2003, 3093 author = {Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl}, 3094 year = {2003}, 3095 title = {Parallel Preconditioning for Sedimentary Basin Simulations}, 3096 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 3097 Sozopol, Bulgaria, June 4-8, 2003}, 3098 petsc_uses = {KSP} 3099} 3100 3101@InProceedings{ lichtner1, 3102 author = {Chuan Lu and Peter C. Lichtner}, 3103 year = {2005}, 3104 title = {{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in 3105 Geologic Media}, 3106 booktitle = {Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL}, 3107 lab = {LANL}, 3108 petsc_uses = {KSP} 3109} 3110 3111@Article{ hammondlichtnermills2014, 3112 title = {Evaluating the Performance of Parallel Subsurface Simulators: An Illustrative 3113 Example with {PFLOTRAN}}, 3114 author = {Glenn E. Hammond and Peter C. Lichtner and Richard Tran Mills}, 3115 journal = {Water Resources Research}, 3116 volume = {50}, 3117 number = {1}, 3118 pages = {208--228}, 3119 doi = {10.1002/2012WR013483}, 3120 year = {2014}, 3121 petsc_uses = {KSP} 3122} 3123 3124@Article{ smw2003, 3125 author = {R. Scheichl and R. Masson and J. Wendebourg}, 3126 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 3127 journal = {Computational Geosciences}, 3128 year = {2003}, 3129 volume = {7}, 3130 pages = {295--318}, 3131 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 3132 petsc_uses = {KSP} 3133} 3134 3135@Article{ kees-miller-03, 3136 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 3137 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 3138 journal = {Computational Geosciences}, 3139 year = {2003}, 3140 volume = {7}, 3141 pages = {91--114}, 3142 petsc_uses = {KSP} 3143} 3144 3145@Article{ bk2003, 3146 author = {JN Buur and T Kuehnel}, 3147 title = {Improving depth imaging by automated model updating}, 3148 journal = {The Leading Edge}, 3149 year = {2003}, 3150 volume = {22}, 3151 pages = {310-318}, 3152 petsc_uses = {KSP} 3153} 3154 3155@Article{ frederickbuffett2016, 3156 title = {Submarine groundwater discharge as a possible formation mechanism for 3157 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 3158 author = {Jennifer M. Frederick and Bruce A. Buffett}, 3159 journal = {Journal of Geophysical Research: Solid Earth}, 3160 volume = {121}, 3161 number = {3}, 3162 pages = {1383--1404}, 3163 issn = {2169-9356}, 3164 doi = {10.1002/2015JB012627}, 3165 year = {2016}, 3166 petsc_uses = {KSP} 3167} 3168 3169% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3170% LiteralHTML:<font color="#FF0000"> 3171% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 3172% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 3173% LiteralHTML:variety of these simulations.</p> 3174% LiteralHTML:</font> 3175% LiteralHTML: 3176@InProceedings{ appelbe1, 3177 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 3178 year = {2003}, 3179 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 3180 computational methodology}, 3181 page = {781}, 3182 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 3183 Proceedings}, 3184 publisher = {Springer-Verlag}, 3185 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 3186 petsc_uses = {KSP} 3187} 3188 3189% LiteralHTML:<a name="katz"> 3190@InProceedings{ gd1, 3191 author = {Guillaume Dumont and Michel Kern}, 3192 title = {Parallelization of a 3D Seismic Migration Code with PETSc}, 3193 year = {1999}, 3194 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 3195 Computing}, 3196 petsc_uses = {KSP} 3197} 3198 3199% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 3200% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 3201% LiteralHTML:<font color="#FF0000"> 3202% LiteralHTML: Figures from the work of Richard Katz 3203@PhDThesis{ katzthesis, 3204 author = {R.F. Katz}, 3205 title = {The deep roots of volcanoes: models of magma dynamics with applications to 3206 subduction zones}, 3207 school = {Columbia University}, 3208 year = {2005}, 3209 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 3210 petsc_uses = {KSP} 3211} 3212 3213@InCollection{ knepleykatzsmith06, 3214 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 3215 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 3216 USA}, 3217 title = {Developing a Geodynamics Simulator with {PETSc}}, 3218 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 3219 series = {Lecture Notes in Computational Science and Engineering}, 3220 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 3221 publisher = {Springer Berlin Heidelberg}, 3222 isbn = {978-3-540-31619-0}, 3223 keyword = {Mathematics and Statistics}, 3224 pages = {413-438}, 3225 volume = {51}, 3226 doi = {10.1007/3-540-31619-1_12}, 3227 year = {2006}, 3228 petsc_uses = {KSP} 3229} 3230 3231@Article{ katz04, 3232 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 3233 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 3234 the global mid-ocean ridge system}, 3235 journal = {Geophys.\ Res.\ Letts.}, 3236 year = {2004}, 3237 volume = {31}, 3238 pages = {L15605}, 3239 petsc_uses = {KSP} 3240} 3241 3242@Article{ katz07, 3243 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 3244 Ethan Coon}, 3245 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 3246 Toolkit for Scientific Computation}}, 3247 journal = {Phys. Earth Planet. In.}, 3248 volume = {163}, 3249 pages = {52--68}, 3250 year = {2007}, 3251 petsc_uses = {KSP} 3252} 3253 3254@Article{ williams2006development, 3255 title = {{Development of a package for modeling stress in the lithosphere}}, 3256 author = {Williams, CA}, 3257 journal = {Eos Trans. AGU}, 3258 volume = {87}, 3259 pages = {36}, 3260 year = {2006}, 3261 petsc_uses = {KSP} 3262} 3263 3264@Article{ goverswortel05, 3265 author = {R. Govers and M.J.R. Wortel}, 3266 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 3267 journal = {Earth and Planetary Science Letters}, 3268 volume = {236/1-2}, 3269 pages = {505-523}, 3270 year = {2005}, 3271 petsc_uses = {KSP} 3272} 3273 3274@InProceedings{ snark2, 3275 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 3276 year = {2002}, 3277 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 3278 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 3279 petsc_uses = {KSP} 3280} 3281 3282@Article{ snark1, 3283 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 3284 Tan and Feng Wang}, 3285 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 3286 journal = {Submitted to Pure and Applied Geosciences}, 3287 petsc_uses = {KSP} 3288} 3289 3290@InProceedings{ earthquake2003, 3291 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 3292 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 3293 Tiankai Tu}, 3294 year = {2003}, 3295 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 3296 booktitle = {Proceedings of SC2003}, 3297 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 3298 petsc_uses = {KSP} 3299} 3300 3301@InProceedings{ stefano12, 3302 author = {Michele De Stefano}, 3303 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 3304 booktitle = {PIERS Proceedings}, 3305 month = aug, 3306 address = {Moscow, RUSSIA}, 3307 pages = {491--495}, 3308 year = {2012}, 3309 petsc_uses = {KSP} 3310} 3311 3312%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 3313 3314% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3315% LiteralHTML: <center><img alt="" 3316% LiteralHTML: src="images/ocean.jpg"></center></p> 3317@Article{ khatiwala07, 3318 author = {Khatiwala, S.}, 3319 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 3320 journal = {Glob. Biogeochem. Cycles}, 3321 volume = {21}, 3322 doi = {10.1029/2007GB002923}, 3323 year = {2007}, 3324 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 3325} 3326 3327@Article{ dks2004, 3328 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 3329 journal = {Ocean Modelling}, 3330 year = {2004}, 3331 volume = {6(2)}, 3332 pages = {125-150}, 3333 title = {A finite-element Ocean Model: Principles and Evaluation}, 3334 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}, 3335 petsc_uses = {KSP} 3336} 3337 3338@Article{ danilov1, 3339 author = {S. Danilov and G. Kivman and J. Schroter}, 3340 year = {2004}, 3341 title = {Evaluation of an eddy-permitting finite-element ocean model in the North 3342 Atlantic}, 3343 journal = {Ocean Modelling}, 3344 petsc_uses = {KSP} 3345} 3346 3347@Article{ nerger1, 3348 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 3349 year = {2004}, 3350 title = {Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to 3351 a Finite Element Model of the North Atlantic}, 3352 journal = {Journal of marine systems}, 3353 petsc_uses = {KSP} 3354} 3355 3356@Conference{ rakowsky2003self, 3357 title = {{A self-adaptive finite element model of the atmosphere}}, 3358 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 3359 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 3360 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 3361 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 3362 pages = {279}, 3363 isbn = {981238376X}, 3364 year = {2003}, 3365 organization = {World Scientific Pub Co}, 3366 petsc_uses = {KSP} 3367} 3368 3369@Article{ lauter3, 3370 author = {M. Lauter}, 3371 year = {2004}, 3372 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 3373 AtmosphArenmodell}, 3374 journal = {Berichte zur Polar- und Meeresforschung}, 3375 petsc_uses = {KSP} 3376} 3377 3378@Article{ lauter2, 3379 author = {M. Lauter and D. Handorf and K. Dethloff}, 3380 year = {2004}, 3381 title = {Unsteady analytical solutions of the spherical shallow water equations}, 3382 journal = {Journal of computational physics}, 3383 petsc_uses = {KSP} 3384} 3385 3386@PhDThesis{ lauter1, 3387 author = {M. Lauter}, 3388 year = {2004}, 3389 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 3390 AtmosphArenmodell}, 3391 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 3392 petsc_uses = {KSP} 3393} 3394 3395@Article{ frickenhaus1, 3396 author = {S. Frickenhaus and W. Hiller and M. Best}, 3397 year = {2005}, 3398 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 3399 parallel numerical atmosphere and ocean models}, 3400 journal = {Ocean Modelling}, 3401 volume = {10}, 3402 pages = {185--191}, 3403 petsc_uses = {KSP} 3404} 3405 3406@Article{ 0266-5611-24-3-034015, 3407 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 3408 title = {A Newton-CG method for large-scale three-dimensional elastic full-waveform 3409 seismic inversion}, 3410 journal = {Inverse Problems}, 3411 volume = {24}, 3412 number = {3}, 3413 pages = {034015 (26pp)}, 3414 url = {http://stacks.iop.org/0266-5611/24/034015}, 3415 year = {2008}, 3416 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 3417 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 3418 iterations with inner conjugate gradient linear iterations, globalized by an 3419 Armijo backtracking line search, solved on a sequence of finer grids and higher 3420 frequencies to remain in the vicinity of the global optimum, inexactly terminated 3421 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 3422 variation operator to capture sharp interfaces, finely discretized by finite 3423 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 3424 implemented in matrix-free fashion with adjoint-based computation of reduced 3425 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 3426 waveform storage, and partitioned spatially across processors to parallelize the 3427 solutions of the forward and adjoint wave equations and the evaluation of 3428 gradient-like information. Several numerical examples demonstrate the grid 3429 independence of linear and nonlinear iterations, the effectiveness of the 3430 preconditioner, the ability to solve inverse problems with up to 17 million 3431 inversion parameters on up to 2048 processors, the effectiveness of multiscale 3432 continuation in keeping iterates in the basin of attraction of the global minimum, 3433 and the ability to fit the observational data while reconstructing the model with 3434 reasonable resolution and capturing sharp interfaces.}, 3435 petsc_uses = {KSP} 3436} 3437 3438% LiteralHTML: 3439% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 3440% LiteralHTML: 3441% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3442% LiteralHTML:<font color="#FF0000"> 3443% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 3444% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 3445% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 3446% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 3447% LiteralHTML:for a variety of these simulations.</p> 3448% LiteralHTML:</font> 3449% LiteralHTML: 3450@Article{ mills2009modeling, 3451 title = {Modeling subsurface reactive flows using leadership-class computing}, 3452 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 3453 Mahinthakumar, G.K. and Smith, B.F.}, 3454 journal = {Journal of Physics: Conference Series}, 3455 volume = {180}, 3456 pages = {012062}, 3457 year = {2009}, 3458 publisher = {IOP Publishing}, 3459 petsc_uses = {KSP} 3460} 3461 3462@Conference{ mills2007simulating, 3463 title = {{Simulating subsurface flow and transport on ultrascale computers using 3464 PFLOTRAN}}, 3465 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 3466 booktitle = {Journal of Physics: Conference Series}, 3467 volume = {78}, 3468 pages = {012051}, 3469 year = {2007}, 3470 organization = {IOP Publishing}, 3471 petsc_uses = {KSP} 3472} 3473 3474@InProceedings{ mills2009, 3475 title = {Modeling subsurface reactive flows using leadership-class computing}, 3476 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 3477 Mahinthakmuar, G. and Smith, B.}, 3478 booktitle = {Journal of Physics: Conference Series}, 3479 volume = {180}, 3480 pages = {102062}, 3481 year = {2009}, 3482 organization = {IOP Publishing}, 3483 petsc_uses = {KSP} 3484} 3485 3486@Article{ guo2013parallel, 3487 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 3488 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 3489 }, 3490 journal = {Advances in Water Resources }, 3491 volume = {53}, 3492 number = {0}, 3493 pages = {101 - 108}, 3494 year = {2013}, 3495 note = {}, 3496 issn = {0309-1708}, 3497 doi = {10.1016/j.advwatres.2012.10.010}, 3498 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 3499 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 3500 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 3501 preconditioner}, 3502 petsc_uses = {KSP} 3503} 3504 3505@Unpublished{ stomp, 3506 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 3507 url = {http://stomp.pnl.gov/}, 3508 petsc_uses = {KSP} 3509} 3510 3511@InProceedings{ htfc2003, 3512 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 3513 title = {Methods and Experiences For Parallelizing Flood Models}, 3514 year = {2003}, 3515 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 3516 European PVM/MPI User's Group Meeting}, 3517 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 3518 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 3519 petsc_uses = {KSP} 3520} 3521 3522@InProceedings{ hulchy-tran-astalos-fmsip, 3523 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 3524 D.Froehlich}, 3525 title = {Flood Modeling System and Its Parallelization}, 3526 year = {2002}, 3527 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 3528 Engineering}, 3529 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 3530 petsc_uses = {KSP} 3531} 3532 3533@InProceedings{ gy1, 3534 author = {J. P. Gwo and G. T. Yeh}, 3535 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 3536 Transport at Watershed Scale}, 3537 year = {2004}, 3538 booktitle = {The International Conference on Computational Methods}, 3539 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 3540 petsc_uses = {KSP} 3541} 3542 3543@Conference{ cheng2009efficient, 3544 title = {{An efficient parallel method for large-scale groundwater flow equation based on 3545 PETSc}}, 3546 author = {Cheng, T. and Ji, X. and Wang, Q.}, 3547 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 3548 Conference on}, 3549 pages = {190--193}, 3550 organization = {IEEE}, 3551 petsc_uses = {KSP} 3552} 3553 3554@Unpublished{ sfrsm, 3555 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 3556 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 3557 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 3558 its linear solves}, 3559 petsc_uses = {KSP} 3560} 3561 3562% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3563@InProceedings{ bart_omar:sc05, 3564 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 3565 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 3566 title = {Dynamic data driven inversion for terascale simulations: real-time 3567 indentification of airborne contaminants}, 3568 booktitle = {Proceedings of SC2005}, 3569 organization = {IEEE/ACM}, 3570 address = {Seattle, WA}, 3571 year = {2005}, 3572 month = nov, 3573 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 3574 lab = {SNL}, 3575 petsc_uses = {KSP} 3576} 3577 3578@InProceedings{ anton-krassimir-lscc, 3579 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 3580 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 3581 Simulations}, 3582 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 3583 volume = {2907}, 3584 year = {2003}, 3585 publisher = {Springer-Verlag}, 3586 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 3587 petsc_uses = {KSP} 3588} 3589 3590@InProceedings{ aa2001, 3591 author = {Anton Antonov}, 3592 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 3593 year = {2001}, 3594 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 3595 Sozopol, Bulgaria}, 3596 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 3597 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 3598 petsc_uses = {KSP} 3599} 3600 3601% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3602@Article{ grassley-simmons-kercher-00, 3603 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 3604 year = {2000}, 3605 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 3606 reactive transport models}, 3607 journal = {Applied Geochemistry}, 3608 volume = {17}, 3609 pages = {699--708}, 3610 lab = {LLNL} 3611} 3612 3613@Article{ glassey-nitao-03, 3614 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 3615 and Carl I. Steefel and James R. Kercher}, 3616 year = {2003}, 3617 title = {The impact of climate change on vadose zone pore waters and its implication for 3618 long-term monitoring}, 3619 journal = {Computers and Geosciences}, 3620 volume = {29}, 3621 pages = {399-411}, 3622 lab = {LLNL}, 3623 petsc_uses = {KSP} 3624} 3625 3626@Article{ steefel-depaolo-lichtner-05, 3627 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 3628 year = {2005}, 3629 title = {Reactive transport modeling: An essential tool and a new research approach for 3630 the Earth sciences}, 3631 journal = {Earth and Planetary Science Letters}, 3632 lab = {LLNL,LANL}, 3633 petsc_uses = {KSP} 3634} 3635 3636% LiteralHTML:<a name="scalinglarge"> 3637% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3638% LiteralHTML: <center><img alt="" 3639% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 3640% LiteralHTML:<font color="#FF0000"> 3641% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 3642@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 3643 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 3644 Strategies for Large-Scale Numerical Simulations}, 3645 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 3646 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 3647 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 3648 Large-Scale Systems (scalA)}, 3649 pages = {65-72}, 3650 doi = {10.1109/ScalA.2018.00012}, 3651 month = nov, 3652 year = {2018}, 3653 petsc_uses = {KSP} 3654} 3655 3656@Article{ km2004, 3657 author = {A. Keese and H. G. Matthies}, 3658 journal = {Computers and Structures}, 3659 year = {2005}, 3660 volume = {83}, 3661 pages = {1033--1047}, 3662 title = {Hierarchical parallelisation for the solution of stochastic finite element 3663 equations}, 3664 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}, 3665 petsc_uses = {KSP} 3666} 3667 3668@Unpublished{ hvl2002, 3669 title = {Numerical Modeling of NAPL Source Zone Treatment}, 3670 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 3671 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 3672 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 3673 year = {2002}, 3674 lab = {LANL}, 3675 petsc_uses = {KSP} 3676} 3677 3678@PhDThesis{ hammond2003, 3679 author = {Glenn E. Hammond}, 3680 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 3681 Transport on Supercomputers}, 3682 school = {University of Illinois at Urbana-Champaign}, 3683 year = {2003}, 3684 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 3685 petsc_uses = {KSP} 3686} 3687 3688@Unpublished{ uk, 3689 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 3690 Scale Environmental Flows and Transport Processes}, 3691 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 3692 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 3693 buildings and in Green Bay. Used PETSc for its linear solvers}, 3694 year = {1999}, 3695 petsc_uses = {KSP} 3696} 3697 3698@InProceedings{ hammond2002, 3699 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 3700 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 3701 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 3702 year = {2002}, 3703 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 3704 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 3705 Resources, Delft, The Netherlands.}, 3706 lab = {LANL}, 3707 petsc_uses = {KSP} 3708} 3709 3710@TechReport{ steefel1, 3711 author = {C. I. Steefel}, 3712 title = {Software for modeling multicomponent, multidimensional reactive transport}, 3713 year = {2001}, 3714 institution = {Lawrence Livermore National Laboratory}, 3715 number = {UCRL-MA-143182}, 3716 lab = {LLNL}, 3717 petsc_uses = {KSP} 3718} 3719 3720@Article{ steefel2, 3721 author = {C. I. Steefel and A. C. Lasaga}, 3722 title = {A coupled model for transport of multiple chemical-species and kinetic 3723 precipitation dissolution reactions with application to reactive flow in 3724 single-phase hydrothermal systems}, 3725 journal = {Americal Journal of Science}, 3726 year = {1994}, 3727 pages = {529-592}, 3728 volume = {294}, 3729 number = {5}, 3730 petsc_uses = {KSP} 3731} 3732 3733@TechReport{ steefel3, 3734 author = {C. I. Steefel and S. B. Yabusaki}, 3735 title = {OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: 3736 User's manual and programmer's guide}, 3737 year = {1996}, 3738 institution = {Pacific Northwest National Laboratory}, 3739 number = {PNNL-11166}, 3740 lab = {PNNL}, 3741 petsc_uses = {KSP} 3742} 3743 3744@Article{ 2005hvl, 3745 author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner}, 3746 title = {Application of {J}acobian-free {N}ewton-{K}rylov with physics-based 3747 preconditioning to biogeochemical transport}, 3748 journal = {Advances in Water Resources}, 3749 year = {2005}, 3750 pages = {359--376}, 3751 volume = {28}, 3752 url = { 3753 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}, 3754 lab = {LANL}, 3755 petsc_uses = {KSP} 3756} 3757 3758@Article{ wang-zabar-05, 3759 author = {J Wang and N Zabaras}, 3760 journal = {Int. J. Heat and Mass Transfer}, 3761 title = {A Markov random field model of contamination source identification in porous 3762 media flow}, 3763 year = {2005}, 3764 petsc_uses = {KSP} 3765} 3766 3767@InBook{ kp1, 3768 author = {Jong G. Kim and Hyoung W. Park}, 3769 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 3770 Media}, 3771 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 3772 title = {Lecture Notes in Computer Science}, 3773 publisher = {Springer-Verlag}, 3774 volume = {3044}, 3775 year = {2004}, 3776 petsc_uses = {KSP} 3777} 3778 3779@Article{ 2001agusm...h32a06k, 3780 author = {{Kim}, J.~G. and {Kim}, J.}, 3781 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 3782 journal = {AGU Spring Meeting Abstracts}, 3783 year = {2001}, 3784 pages = {32-+}, 3785 petsc_uses = {KSP} 3786} 3787 3788@Article{ lzb2005, 3789 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 3790 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 3791 journal = {Journal of Hydraulic Engineering}, 3792 year = {2005}, 3793 volume = {131}, 3794 number = {4}, 3795 pages = {247--258}, 3796 petsc_uses = {KSP} 3797} 3798 3799@Article{ rao2005, 3800 author = {Prasada Rao}, 3801 title = {A parallel RMA2 model for simulating large-scale free surface flows}, 3802 journal = {Environmental Modelling and Software}, 3803 year = {2005}, 3804 pages = {47--53}, 3805 petsc_uses = {KSP} 3806} 3807 3808@InProceedings{ pr1, 3809 author = {Prasada Rao}, 3810 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 3811 Hydrodynamic Flows}, 3812 year = {2003}, 3813 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 3814 Conference}, 3815 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 3816 petsc_uses = {KSP} 3817} 3818 3819@InProceedings{ lichtner2004, 3820 author = {Peter C. Lichtner and Andrew Wolfsberg}, 3821 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 3822 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 3823 Challenge Supercomputing Problem}, 3824 year = {2004}, 3825 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 3826 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 3827 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 3828 lab = {LANL}, 3829 petsc_uses = {KSP} 3830} 3831 3832% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3833@Article{ aba01:petsc-app, 3834 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 3835 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 3836 journal = {Int. J. High Performance Computing Applications}, 3837 year = {2001}, 3838 volume = {15}, 3839 number = {1}, 3840 pages = {13--21}, 3841 petsc_uses = {KSP} 3842} 3843 3844@PhDThesis{ tjb200, 3845 author = {Thomas James Byer}, 3846 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 3847 Facilities}, 3848 school = {Stanford}, 3849 year = {2000}, 3850 petsc_uses = {KSP} 3851} 3852 3853@InProceedings{ puchyr2006, 3854 author = {Peter J. Puchyr}, 3855 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 3856 Win32 Cluster}, 3857 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 3858 note = {Paper number CIPC2006-207}, 3859 year = {2006}, 3860 petsc_uses = {KSP} 3861} 3862 3863@InProceedings{ texas98, 3864 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 3865 and G. A. Pope}, 3866 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 3867 Simulation}, 3868 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 3869 Symposium}, 3870 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 3871 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 3872 year = {1998}, 3873 petsc_uses = {KSP} 3874} 3875 3876% LiteralHTML: 3877% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 3878% LiteralHTML: 3879@Article{ farrellmitchellscottwechsung2021, 3880 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 3881 stationary incompressible {Navier-Stokes} equations}, 3882 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 3883 Wechsung}, 3884 journal = {The SMAI journal of computational mathematics}, 3885 volume = {7}, 3886 pages = {75--96}, 3887 year = {2021}, 3888 petsc_uses = {KSP} 3889} 3890 3891@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 3892 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 3893 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 3894 P MacLachlan and Ray S Tuminaro}, 3895 journal = {SIAM Journal on Scientific Computing}, 3896 number = {0}, 3897 pages = {S70--S91}, 3898 year = {2021}, 3899 petsc_uses = {KSP} 3900} 3901 3902@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 3903 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 3904 hyperelasticity}, 3905 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 3906 Oyar\'ua and Ricardo Ruiz-Baier}, 3907 journal = {Computer Methods in Applied Mechanics and Engineering}, 3908 volume = {374}, 3909 pages = {113562}, 3910 issn = {0045-7825}, 3911 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 3912 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 3913 year = {2021}, 3914 petsc_uses = {KSP} 3915} 3916 3917@Article{ farrellmitchellwechsung2018, 3918 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 3919 {Navier-Stokes} equations at high {Reynolds} number}, 3920 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 3921 journal = {SIAM Journal on Scientific Computing}, 3922 volume = {41}, 3923 number = {5}, 3924 eprint = {1810.03315}, 3925 pages = {A3073-A3096}, 3926 year = {2019}, 3927 petsc_uses = {KSP} 3928} 3929 3930@Article{ hevuikklaij2017, 3931 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 3932 discretized by a finite volume method}, 3933 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 3934 journal = {Journal of Numerical Mathematics}, 3935 volume = {25}, 3936 number = {2}, 3937 pages = {89--105}, 3938 year = {2017}, 3939 petsc_uses = {KSP} 3940} 3941 3942@InProceedings{ zou2015newton, 3943 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 3944 appearance/disappearance}, 3945 author = {Zou, L and Zhao, H and Zhang, H}, 3946 booktitle = {ANS 2015 Annual Meeting, June}, 3947 volume = {7}, 3948 number = {11}, 3949 year = {2015}, 3950 petsc_uses = {KSP} 3951} 3952 3953@Article{ guermond2009nonlinear, 3954 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 3955 Fourier/finite element technique and an interior penalty method}, 3956 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 3957 journal = {Journal of computational physics}, 3958 volume = {228}, 3959 number = {8}, 3960 pages = {2739--2757}, 3961 year = {2009}, 3962 publisher = {Elsevier}, 3963 petsc_uses = {KSP} 3964} 3965 3966@Article{ erzincanlisahin2015, 3967 title = {The numerical simulation of the wing kinematics effects on near wake topology and 3968 aerodynamic performance in hovering Drosophila flight}, 3969 author = {Belkis Erzincanli and Mehmet Sahin}, 3970 journal = {Computers \& Fluids}, 3971 volume = {122}, 3972 pages = {90--110}, 3973 year = {2015}, 3974 publisher = {Elsevier}, 3975 petsc_uses = {KSP} 3976} 3977 3978@Article{ ekensahin2015, 3979 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 3980 structure interaction problems}, 3981 author = {Ali Eken and Mehmet Sahin}, 3982 journal = {International Journal for Numerical Methods in Fluids}, 3983 year = {2015}, 3984 publisher = {Wiley Online Library}, 3985 petsc_uses = {KSP} 3986} 3987 3988@Article{ hwangsucai2015, 3989 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 3990 for transonic full potential equation}, 3991 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 3992 journal = {Computers \& Fluids}, 3993 volume = {110}, 3994 number = {30}, 3995 pages = {96--107}, 3996 year = {2015}, 3997 doi = {10.1016/j.compfluid.2014.04.005}, 3998 petsc_uses = {KSP} 3999} 4000 4001@Article{ yanghwangcai2016, 4002 title = {Nonlinear Preconditioning Techniques for Full-Space Lagrange--Newton Solution of 4003 PDE-Constrained Optimization Problems}, 4004 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 4005 journal = {SIAM Journal on Scientific Computing}, 4006 volume = {38}, 4007 number = {5}, 4008 pages = {A2756--A2778}, 4009 year = {2016}, 4010 petsc_uses = {KSP} 4011} 4012 4013@Article{ khanaidun2011, 4014 author = {Irfan Khan and Cyrus K. Aidun}, 4015 title = {Direct numerical simulation of saturated deformable porous media using parallel 4016 hybrid Lattice-Boltzmann and finite element method}, 4017 journal = {Int. J. Numer. Meth. Eng.}, 4018 volume = {86}, 4019 pages = {1379--1395}, 4020 year = {2011}, 4021 petsc_uses = {KSP} 4022} 4023 4024@Article{ khanaidun2014, 4025 author = {Irfan Khan and Cyrus K. Aidun}, 4026 title = {Modeling the deformation of saturate porous media using direct numerical 4027 simulation}, 4028 journal = {Int. J. Multiphase Flow}, 4029 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 4030 year = {2014}, 4031 petsc_uses = {KSP} 4032} 4033 4034@Article{ mofidi2014simulations, 4035 author = {A. Mofidi and P. M. Carrica}, 4036 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 4037 and Propeller}, 4038 journal = {Computers and Fluids}, 4039 pages = {191--203}, 4040 year = {2014}, 4041 petsc_uses = {KSP} 4042} 4043 4044@Article{ paik2014fluidstructure, 4045 author = {K. Paik and P. M. Carrica}, 4046 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 4047 Surface in a Rolling Tank}, 4048 journal = {Ocean Engineering}, 4049 pages = {201--212}, 4050 year = {2014}, 4051 petsc_uses = {KSP} 4052} 4053 4054@Article{ castro2013bubble, 4055 author = {A. M. Castro and P. M. Carrica}, 4056 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 4057 evaluation and numerical issues}, 4058 journal = {International Journal of Multiphase Flow 57}, 4059 pages = {131--150}, 4060 year = {2013}, 4061 petsc_uses = {KSP} 4062} 4063 4064@Article{ carrica2013turn, 4065 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 4066 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 4067 Dynamic Overset Grids}, 4068 journal = {Journal of Marine Science and Technology}, 4069 pages = {166--181}, 4070 year = {2013}, 4071 petsc_uses = {KSP} 4072} 4073 4074@Article{ castro2013eulerian, 4075 author = {A. M. Castro and P. M. Carrica}, 4076 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 4077 {Athena} {R}/V,}, 4078 journal = {International Shipbuilding Progress}, 4079 pages = {403--433}, 4080 year = {2013}, 4081 petsc_uses = {KSP} 4082} 4083 4084@Article{ chase2013overset, 4085 author = {N. Chase and T. Michael and P. M. Carrica}, 4086 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 4087 {Maneuvering} {Conditions}}, 4088 journal = {International Shipbuilding Progress}, 4089 pages = {171--205}, 4090 year = {2013}, 4091 petsc_uses = {KSP} 4092} 4093 4094@Article{ sadathosseini2013wu, 4095 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 4096 Stern}, 4097 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 4098 Free Surge Conditions in Short and Long Head Waves}, 4099 journal = {Ocean Engineering}, 4100 volume = {59}, 4101 pages = {240--273}, 4102 year = {2013}, 4103 petsc_uses = {KSP} 4104} 4105 4106@Article{ chase2013cfd, 4107 author = {N. Chase and P. M. Carrica}, 4108 title = {CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a 4109 Submarine}, 4110 journal = {Ocean Engineering}, 4111 pages = {68--80}, 4112 year = {2013}, 4113 petsc_uses = {KSP} 4114} 4115 4116@Article{ carrica2012cfd, 4117 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 4118 title = {CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 4119 of Moving Rudders and Rotating Propellers}, 4120 journal = {Computers and Fluids 53}, 4121 pages = {117--132}, 4122 year = {2012}, 4123 petsc_uses = {KSP} 4124} 4125 4126@Article{ sakamoto2012urans, 4127 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 4128 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 4129 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 4130 publisher = {Journal of Marine Science and Technology}, 4131 pages = {422--445}, 4132 year = {2012}, 4133 petsc_uses = {KSP} 4134} 4135 4136@Article{ sakamoto2012uransb, 4137 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 4138 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 4139 Analysis and Validation of Local Flow Characteristics}, 4140 journal = {Journal of Marine Science and Technology}, 4141 pages = {446--468}, 4142 year = {2012}, 4143 petsc_uses = {KSP} 4144} 4145 4146@Article{ li2012dynamic, 4147 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 4148 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 4149 journal = {Renewable Energy}, 4150 pages = {285--298}, 4151 year = {2012}, 4152 petsc_uses = {KSP} 4153} 4154 4155@Article{ huang2012a, 4156 author = {J. Huang and P. M. Carrica and F. Stern}, 4157 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 4158 journal = {International Journal for Numerical Methods in Fluids}, 4159 pages = {160--180}, 4160 year = {2012}, 4161 petsc_uses = {KSP} 4162} 4163 4164@Article{ huang2012b, 4165 author = {J. Huang and P. M. Carrica and F. Stern}, 4166 title = {A geometry-based level set method for curvilinear overset grids with application 4167 to ship hydrodynamics}, 4168 journal = {International Journal for Numerical Methods in Fluids}, 4169 pages = {494--521}, 4170 year = {2012}, 4171 petsc_uses = {KSP} 4172} 4173 4174@Article{ carrica2011computations, 4175 author = {P. M. Carrica and H. Fu and F. Stern}, 4176 title = {Computations of self-propulsion free to sink and trim and of motions in head 4177 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 4178 journal = {Applied Ocean Research}, 4179 pages = {309--320}, 4180 year = {2011}, 4181 petsc_uses = {KSP} 4182} 4183 4184@Article{ bhushan2011scalability, 4185 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 4186 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 4187 Using {CFDShip}-Iowa}, 4188 journal = {International Journal of High Performance Computing Applications}, 4189 pages = {466--487}, 4190 year = {2011}, 4191 petsc_uses = {KSP} 4192} 4193 4194@Article{ castro2011full, 4195 author = {A. M. Castro and P. M. Carrica and F. Stern}, 4196 title = {Full scale self-propulsion computations using discretized propeller for the 4197 {KRISO} container ship {KCS}}, 4198 journal = {Computers and Fluids}, 4199 pages = {35--47}, 4200 year = {2011}, 4201 petsc_uses = {KSP} 4202} 4203 4204@Article{ kandasamy2011multifidelity, 4205 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 4206 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 4207 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran 4208 for Low Wake}, 4209 journal = {Journal of Marine Science and Technology}, 4210 pages = {143--156}, 4211 year = {2011}, 4212 petsc_uses = {KSP} 4213} 4214 4215@Article{ kandasamy2011cfd, 4216 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 4217 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 4218 title = {CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran}, 4219 journal = {Journal of Marine Science and Technology}, 4220 pages = {157--167}, 4221 year = {2011}, 4222 petsc_uses = {KSP} 4223} 4224 4225@Article{ sadathosseini2011cfd, 4226 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 4227 and S. Yamamura and A. Mastuda}, 4228 title = {CFD System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 4229 Periodic Motion and Broaching}, 4230 journal = {Ocean Engineering}, 4231 pages = {88--110}, 4232 year = {2011}, 4233 petsc_uses = {KSP} 4234} 4235 4236@Article{ mosaviraad2010development, 4237 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 4238 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 4239 with Comparison to Regular Wave and Transient Wave Group Procedures Using 4240 {URANS}}, 4241 journal = {Ocean Engineering}, 4242 pages = {653--666}, 4243 year = {2010}, 4244 petsc_uses = {KSP} 4245} 4246 4247@Article{ carrica2010largescale, 4248 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4249 Stern}, 4250 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 4251 Heave Problems for a Surface Combatant}, 4252 journal = {Computers and Fluids}, 4253 pages = {1095--1111}, 4254 year = {2010}, 4255 petsc_uses = {KSP} 4256} 4257 4258@Article{ carrica2010selfpropulsion, 4259 author = {P. M. Carrica and A. M. Castro and F. Stern}, 4260 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 4261 with Dynamic Overset Grids}, 4262 journal = {Journal of Marine Science and Technology}, 4263 pages = {316--330}, 4264 year = {2010}, 4265 petsc_uses = {KSP} 4266} 4267 4268@Article{ ismail2010evaluation, 4269 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 4270 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 4271 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 4272 journal = {International Journal of Numerical Methods in Fluids}, 4273 pages = {850--886}, 4274 year = {2010}, 4275 petsc_uses = {KSP} 4276} 4277 4278@Article{ kandasamy2010integral, 4279 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 4280 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 4281 journal = {Journal of Fluids Engineering}, 4282 pages = {101103}, 4283 year = {2010}, 4284 petsc_uses = {KSP} 4285} 4286 4287@Article{ kirk:2014de, 4288 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 4289 title = {{Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) 4290 stabilized finite element flow solver}}, 4291 journal = {Computers {\&} Fluids}, 4292 year = {2014}, 4293 volume = {92}, 4294 number = {0}, 4295 pages = {281--292}, 4296 month = mar, 4297 petsc_uses = {KSP} 4298} 4299 4300@Article{ carracciuolo20111382, 4301 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 4302 in high performance computing environment}, 4303 journal = {Journal of Non-Newtonian Fluid Mechanics }, 4304 volume = {166}, 4305 number = {23--24}, 4306 pages = {1382--1395}, 4307 year = {2011}, 4308 issn = {0377-0257}, 4309 doi = {10.1016/j.jnnfm.2011.08.014}, 4310 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 4311 Maffettone and A. Murli}, 4312 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 4313 method, High performance computing}, 4314 petsc_uses = {KSP} 4315} 4316 4317@Article{ bungartzgatzhammerliebmehlneckel11, 4318 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 4319 Miriam and Neckel, Tobias}, 4320 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 4321 journal = {Computational Mechanics}, 4322 volume = {48}, 4323 number = {3}, 4324 pages = {365-376}, 4325 year = {2011}, 4326 issn = {0178-7675}, 4327 doi = {10.1007/s00466-011-0626-1}, 4328 publisher = {Springer-Verlag}, 4329 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 4330 Thermohydraulics; Two-phase flow}, 4331 language = {English}, 4332 petsc_uses = {KSP} 4333} 4334 4335@Article{ bpr:cfl, 4336 author = {H.~M. B{\"u}cker and B. Pollul and A. Rasch}, 4337 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 4338 Equations}}, 4339 journal = {International Journal for Numerical Methods in Fluids}, 4340 year = {2009}, 4341 volume = {59}, 4342 number = {1}, 4343 pages = {1--18}, 4344 doi = {10.1002/fld.1798}, 4345 petsc_uses = {KSP} 4346} 4347 4348@InBook{ bonfiglioli_campobasso_carpentieri_2010, 4349 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 4350 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 4351 preconditioned newton-krylov solver}, 4352 publisher = {Curran Associates}, 4353 year = {2010}, 4354 url = {http://www.proceedings.com/05932.html}, 4355 petsc_uses = {KSP} 4356} 4357 4358@Article{ bonfiglioli_rans_2005, 4359 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 4360 Bernardo}, 4361 title = {RANS simulations of a junction flow}, 4362 journal = {International Journal of Computational Fluid Dynamics}, 4363 volume = {19}, 4364 number = {2}, 4365 pages = {179-189}, 4366 year = {2005}, 4367 doi = {10.1080/10618560410001729126}, 4368 petsc_uses = {KSP} 4369} 4370 4371@InCollection{ bonfiglioli__carpentieri_rans_2008, 4372 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 4373 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 4374 Italy}, 4375 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 4376 Equations Using Fluctuation Splitting Schemes}, 4377 booktitle = {Numerical Mathematics and Advanced Applications}, 4378 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 4379 publisher = {Springer Berlin Heidelberg}, 4380 isbn = {978-3-540-69777-0}, 4381 pages = {151-158}, 4382 doi = {10.1007/978-3-540-69777-0_17}, 4383 year = {2008}, 4384 petsc_uses = {KSP} 4385} 4386 4387@InCollection{ bonfiglioli__carpentieri_ens_2007, 4388 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 4389 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 4390 Italy}, 4391 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 4392 Problems on Unstructured Grids}, 4393 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 4394 series = {Lecture Notes in Computer Science}, 4395 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 4396 publisher = {Springer Berlin / Heidelberg}, 4397 isbn = {978-3-540-75754-2}, 4398 pages = {676-685}, 4399 volume = {4699}, 4400 doi = {10.1007/978-3-540-75755-9_83}, 4401 year = {2007}, 4402 petsc_uses = {KSP} 4403} 4404 4405@Article{ terrelscottknepleykirby08, 4406 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 4407 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 4408 journal = {BIT}, 4409 volume = {48}, 4410 number = {2}, 4411 year = {2008}, 4412 petsc_uses = {KSP} 4413} 4414 4415@Article{ martamadermartinsweidealonso07, 4416 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 4417 J. Alonso}, 4418 title = {A methodology for the development of discrete adjoint solvers using automatic 4419 differentiation tools}, 4420 journal = {Computational Fluid Dyanmics}, 4421 volume = {21}, 4422 pages = {307--327}, 4423 year = {2007}, 4424 petsc_uses = {KSP} 4425} 4426 4427@TechReport{ avb2008, 4428 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 4429 title = {Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface 4430 Waves}, 4431 year = {2008}, 4432 institution = {University of Twente, the Netherlands}, 4433 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 4434 petsc_uses = {KSP} 4435} 4436 4437@InProceedings{ bdsm2005, 4438 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal}, 4439 title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids}, 4440 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit}, 4441 year = {2005}, 4442 url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}, 4443 petsc_uses = {KSP} 4444} 4445 4446@InProceedings{ ms2006, 4447 author = {S. Muller and Y. Stiriba}, 4448 title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR 4449 STEADY COMPRESSIBLE FLOWS}, 4450 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006}, 4451 year = {2006}, 4452 url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}, 4453 petsc_uses = {KSP} 4454} 4455 4456@Article{ araujoteixeiracunhagroth08, 4457 author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth}, 4458 title = {Parallel three-dimensional simulation of the injection molding process}, 4459 journal = {International Journal for Numerical Methods in Fluids}, 4460 year = {2008}, 4461 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 4462 petsc_uses = {KSP} 4463} 4464 4465@PhDThesis{ a2008, 4466 author = {A. Cubero}, 4467 title = {a parallel coupled algorithm for collocated grids and its application to Large 4468 Eddy Simulation of a turbulent wake}, 4469 school = {University of Zaragoza (Spain)}, 4470 year = {2008}, 4471 petsc_uses = {KSP} 4472} 4473 4474@Article{ afa2007, 4475 author = {A. Cubero and N. Fueyo}, 4476 title = {A Compact Momentum Interpolation Method for unsteady flows and relaxation}, 4477 journal = {Numerical Heat Transfer, part B-Fundamentals}, 4478 volume = {56}, 4479 number = {6}, 4480 pages = {507--529}, 4481 year = {2007}, 4482 url = {http://www.informaworld.com/smpp/content~content=a782025305~db=all~order=page}, 4483 petsc_uses = {KSP} 4484} 4485 4486@TechReport{ af2007, 4487 title = {Preconditioning based on a partially implicit implementation of Momentum 4488 Interpolation for coupled solvers}, 4489 institution = {Fluid Mechanics Group of the University of Zaragoza (Spain)}, 4490 year = {2007}, 4491 author = {A. Cubero and N. Fueyo}, 4492 petsc_uses = {KSP} 4493} 4494 4495@InCollection{ dwight2004, 4496 author = {Richard Dwight}, 4497 title = {Robust Mesh Deformation using the Linear Elasticity Equations}, 4498 booktitle = {Computational Fluid Dynamics 2006}, 4499 editor = {H. Deconinck and E. Dick}, 4500 publisher = {Springer}, 4501 year = {2006}, 4502 url = {http://www.maths.man.ac.uk/\~{ 4503 }rdwight/pub/rdwight-ICCFD4-LinElastDeformation-2006.pdf}, 4504 petsc_uses = {KSP} 4505} 4506 4507@InProceedings{ dwight2006, 4508 author = {Richard Dwight and Joel Brezillon}, 4509 title = {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based 4510 Optimization}, 4511 booktitle = {Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. 4512 AIAA-2006-0690}, 4513 year = {2006}, 4514 url = {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-AIAAReno-ApproxAdjoint.pdf}, 4515 petsc_uses = {KSP} 4516} 4517 4518@PhDThesis{ dwight2006a, 4519 author = {Richard Dwight}, 4520 title = {Efficiency Improvements of {RANS}-Based Analysis and Optimization using Implicit 4521 and Adjoint Methods on Unstructured Grids}, 4522 school = {School of Mathematics, University of Manchester}, 4523 year = {2006}, 4524 url = {http://www.maths.man.ac.uk/\~{ 4525 }rdwight/pub/rdwight-PhDThesis-ImplicitAndAdjoint.pdf}, 4526 petsc_uses = {KSP} 4527} 4528 4529@InProceedings{ lhdfrh, 4530 author = {M. Lauter and D. Handorf and K. Dethloff and S. Frickenhaus and N. Rakowsky and 4531 W. Hiller}, 4532 title = {An adaptive Lagrange-Galerkin shallow-water model on the sphere}, 4533 booktitle = {Workshop Proceedings Current Development in Shallow Water Models on the Sphere 4534 March, 10-14, 2003, Munich University of Technology, German}, 4535 year = {2003}, 4536 petsc_uses = {KSP} 4537} 4538 4539@InProceedings{ brios-ying-2002, 4540 author = {George Biros and Lexing Ying and Denis Zorin}, 4541 title = {The Embedded Boundary Integral Method (EBI) for the Incompressible 4542 {Navier-Stokes} equations}, 4543 booktitle = {IABEM 2002, International Association for Boundary Element Methods, UT Austin}, 4544 year = {2002}, 4545 petsc_uses = {KSP} 4546} 4547 4548@InProceedings{ mohsen-straatman-ins, 4549 author = {S.A. Mohsen Karimian and Anthony G. Straatman}, 4550 title = {Benchmarking of a {3D}, unstructured, finite volume code for incompressible 4551 {Navier-Stokes} equation on a cluster of distributed-memory computers}, 4552 booktitle = {Proceedings of the 19th International Symposium on High Performance Computing 4553 Systems and Applications}, 4554 pages = {11--16}, 4555 year = {2005}, 4556 url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046}, 4557 petsc_uses = {KSP} 4558} 4559 4560@TechReport{ bonglioli-icnmfd98, 4561 title = {Multidimensional Residual Distribution Schemes for the Pseudo-Compressible 4562 {Euler} and {Navier-Stokes} equations on Unstructured Meshes}, 4563 institution = {Universita della Basilicata via della Tecnica 3}, 4564 year = {1996}, 4565 author = {A. Bonglioli}, 4566 url = {http://www.unibas.it/utenti/bonfiglioli/icnmfd98.ps.gz}, 4567 petsc_uses = {KSP} 4568} 4569 4570@Article{ deng-piquet-ctf, 4571 author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"}, 4572 title = {A new fully coupled method for computing turbulent flows}, 4573 journal = {Computers and Fluids}, 4574 volume = {30}, 4575 pages = {445--472}, 4576 year = {2001}, 4577 petsc_uses = {KSP} 4578} 4579 4580@InProceedings{ knepleysarinsameh99b, 4581 title = {Multilevel Preconditioning for Parallel {CFD}}, 4582 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 4583 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 4584 Problems In Industrial Applications}, 4585 address = {Minneapolis, MN}, 4586 year = {1999}, 4587 petsc_uses = {KSP} 4588} 4589 4590@InProceedings{ garbey1, 4591 author = {M. Garbey and B. Hadri and W. Shyy.}, 4592 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 4593 Problems on the Grid}, 4594 booktitle = {Aerospace Sciences Meeting and Exhibit}, 4595 note = {Paper No. 2005-1386}, 4596 year = {2005}, 4597 petsc_uses = {KSP} 4598} 4599 4600@Article{ carrica2007unsteady, 4601 title = {An unsteady single-phase level set method for viscous free surface flows}, 4602 author = {Carrica, PM and Wilson, RV and Stern, F.}, 4603 journal = {International Journal for Numerical Methods in Fluids}, 4604 volume = {53}, 4605 number = {2}, 4606 pages = {229--256}, 4607 year = {2007}, 4608 publisher = {Chichester; New York: Wiley, c1981-}, 4609 petsc_uses = {KSP} 4610} 4611 4612@Article{ pctw2004, 4613 author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber}, 4614 title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of 4615 Spillways}, 4616 journal = {Journal of Hydraulic Research}, 4617 note = {accepted for publication}, 4618 year = {2004}, 4619 petsc_uses = {KSP} 4620} 4621 4622@Article{ wcs2004, 4623 author = {R. V. Wilson and P. M. Carrica and F. Stern}, 4624 title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface 4625 Combatant}, 4626 journal = {Computers and Fluids}, 4627 note = {in press}, 4628 year = {2004}, 4629 petsc_uses = {KSP} 4630} 4631 4632@Article{ cws2005, 4633 author = {P. M. Carrica and R. V. Wilson and F. Stern}, 4634 title = {Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem}, 4635 journal = {Computers and Fluids}, 4636 note = {accepted for publication}, 4637 year = {2005}, 4638 petsc_uses = {KSP} 4639} 4640 4641@Article{ chndss2010, 4642 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4643 Stern}, 4644 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 4645 Heave Problems for a Surface Combatant}, 4646 journal = {Computers and Fluids}, 4647 year = {2010}, 4648 volume = {39}, 4649 number = {7}, 4650 pages = {1095--1111}, 4651 petsc_uses = {KSP} 4652} 4653 4654@InProceedings{ chnkss2008, 4655 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4656 Stern}, 4657 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 4658 Grids}, 4659 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 4660 year = {2008}, 4661 petsc_uses = {KSP} 4662} 4663 4664@MastersThesis{ mtj, 4665 author = {M. T. Jozkowski}, 4666 title = {Application of Algebraic Multigrid Methods to the Solution of Stratified Flows 4667 About Submerged Bodies}, 4668 school = {The Pennsylvania State University}, 4669 year = {2005}, 4670 petsc_uses = {KSP} 4671} 4672 4673@Article{ pp, 4674 author = {E. G. Paterson and L. J. Peltier}, 4675 title = {Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and 4676 Wakes}, 4677 journal = {ASME Journal of Fluids Engineering}, 4678 note = {In press}, 4679 year = {2005}, 4680 petsc_uses = {KSP} 4681} 4682 4683@Article{ eps, 4684 author = {B. A. Edge and E. G. Paterson and G. Settles}, 4685 title = {Computational Study of the Wake and Contaminant Transport of a Walking Human}, 4686 journal = {ASME Journal of Fluids Engineering}, 4687 note = {In press}, 4688 year = {2005}, 4689 petsc_uses = {KSP} 4690} 4691 4692@InProceedings{ rp, 4693 author = {B. Racine and E. G. Paterson}, 4694 title = {Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines 4695 Using Unsteady {RANS} {CFD}}, 4696 booktitle = {35th AIAA Fluid Dynamics Conference and Exhibit}, 4697 year = {2005}, 4698 petsc_uses = {KSP} 4699} 4700 4701@InProceedings{ etpp, 4702 author = {B. A. Edge and M. F. Trujillo and E. G. Paterson and L. J. Peltier}, 4703 title = {Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids 4704 and DES}, 4705 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 4706 year = {2004}, 4707 petsc_uses = {KSP} 4708} 4709 4710@InProceedings{ pp8, 4711 author = {E. G. Paterson and L. J. Peltier}, 4712 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 4713 refinement grids and detached-eddy simulation}, 4714 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 4715 year = {2004}, 4716 petsc_uses = {KSP} 4717} 4718 4719@InProceedings{ mzwp, 4720 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 4721 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 4722 booktitle = {25th Symposium on Naval Hydrodynamics}, 4723 year = {2004}, 4724 petsc_uses = {KSP} 4725} 4726 4727@InProceedings{ ppph, 4728 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 4729 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 4730 booktitle = {25th Symposium on Naval Hydrodynamics}, 4731 year = {2004}, 4732 petsc_uses = {KSP} 4733} 4734 4735@InProceedings{ ppd, 4736 author = {E. G. Paterson and L. J. Peltier}, 4737 title = {Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes}, 4738 booktitle = {Symposium on LES Advancements and Applications, ASME FED Summer Meeting}, 4739 year = {2004}, 4740 petsc_uses = {KSP} 4741} 4742 4743@InProceedings{ bp, 4744 author = {W. J. Baker and E. G. and Paterson}, 4745 title = {Simulation of Steady Circulation Control for the General Aviation Circulation 4746 Control Wing}, 4747 booktitle = {NASA/ONR Workshop on Circulation Control}, 4748 year = {2004}, 4749 petsc_uses = {KSP} 4750} 4751 4752@InProceedings{ pb, 4753 author = {E. G. Paterson and W. J. Baker}, 4754 title = {RANS and Detached-Eddy Simulation of the NCCR airfoil}, 4755 booktitle = {NASA/ONR Workshop on Circulation Control}, 4756 year = {2004}, 4757 petsc_uses = {KSP} 4758} 4759 4760@InProceedings{ pb3, 4761 author = {E. G. Paterson and W. J. Baker}, 4762 title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control 4763 Surfaces}, 4764 booktitle = {42nd AIAA Aerospace Sciences Meeting}, 4765 year = {2004}, 4766 petsc_uses = {KSP} 4767} 4768 4769@InProceedings{ gid1, 4770 author = {G. Frank and J. D'Elia}, 4771 title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model}, 4772 year = {2004}, 4773 booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD}, 4774 url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf}, 4775 petsc_uses = {KSP} 4776} 4777 4778@InBook{ b1, 4779 author = {A.Bonfiglioli}, 4780 chapter = {On the use of the PETSc library for unstructured {CFD} applications}, 4781 year = {2001}, 4782 title = {Science and Supercomputing at CINECA}, 4783 pages = {397--400}, 4784 petsc_uses = {KSP} 4785} 4786 4787@InProceedings{ b2004, 4788 author = {L. A. Barba}, 4789 title = {Computing high-Reynolds number vortical flows: a highly accurate method with a 4790 fully meshless formulation}, 4791 year = {2004}, 4792 booktitle = {International Conference on Parallel CFD, Grand Canary, May 2004}, 4793 note = {Submitted}, 4794 petsc_uses = {KSP} 4795} 4796 4797@InProceedings{ bl2004, 4798 author = {L. A. Barba and A. Leonard}, 4799 title = {Computation of Viscous Vortices with Fully Meshless Method}, 4800 year = {2004}, 4801 booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004}, 4802 note = {Submitted}, 4803 petsc_uses = {KSP} 4804} 4805 4806@Article{ vws1, 4807 author = {B. G. M. Van Wachem and J. C. Schouten}, 4808 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 4809 Velocity}, 4810 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 4811 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 4812 Netherlands}, 4813 journal = {AIChE}, 4814 volumne = {48}, 4815 number = {12}, 4816 month = dec, 4817 year = {2002}, 4818 petsc_uses = {KSP} 4819} 4820 4821@TechReport{ lbam1, 4822 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 4823 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 4824 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 4825 di Bari Italy}, 4826 year = {2002}, 4827 number = {25/02}, 4828 petsc_uses = {KSP} 4829} 4830 4831@Article{ kees_miller_02, 4832 author = {C. E. Kees and C. T. Miller}, 4833 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 4834 journal = {Advances in Water Resources}, 4835 year = {2002}, 4836 volume = {25}, 4837 number = {2}, 4838 pages = {159-177.}, 4839 petsc_uses = {KSP} 4840} 4841 4842@InProceedings{ lepotmeersessers2001, 4843 author = {I. Lepot and F. Meers and J.A. Essers}, 4844 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 4845 Unstructured Meshes}, 4846 year = {2001}, 4847 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 4848 url = {http://www.ulg.ac.be/aerodyn}, 4849 petsc_uses = {KSP} 4850} 4851 4852@InProceedings{ knepley98, 4853 author = {Matthew Knepley and Denis Vanderstraeten}, 4854 title = {Parallel Building Blocks for Finite Element Simulations: Application to 4855 Solid-Liquid Mixture Flows}, 4856 booktitle = {Proceedings of Parallel CFD'97}, 4857 publisher = {Elsevier}, 4858 pages = {281--287}, 4859 year = {1998}, 4860 petsc_uses = {KSP} 4861} 4862 4863@InProceedings{ pcfd97, 4864 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. 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High Performance Computing Applications}, 4890 year = {2000}, 4891 volume = {14}, 4892 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 4893 pages = {102-136}, 4894 petsc_uses = {KSP} 4895} 4896 4897@InProceedings{ agkks-sc99, 4898 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 4899 Smith}, 4900 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 4901 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 4902 editor = {}, 4903 publisher = {}, 4904 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 4905 year = {1999}, 4906 note = {Winner of Gordon Bell Special Prize at SC 99}, 4907 petsc_uses = {KSP} 4908} 4909 4910@Article{ gkks01, 4911 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4912 title = {High Performance Parallel Implicit {CFD}}, 4913 journal = {Journal of Parallel Computing}, 4914 year = {2001}, 4915 volume = {27}, 4916 pages = {337-362}, 4917 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 4918 petsc_uses = {KSP} 4919} 4920 4921@Article{ cristea-sofonea-02, 4922 author = {Artur Cristea and Victor Sofonea}, 4923 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 4924 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 4925 Sciences, Information Sciences}, 4926 volume = {3}, 4927 number = {3}, 4928 year = {2002}, 4929 petsc_uses = {KSP} 4930} 4931 4932@Article{ cristea2, 4933 author = {Artur Cristea and Victor Sofonea}, 4934 title = {Two component lattice Boltzmann model with flux limiter techniques}, 4935 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 4936 Sciences, Information Sciences}, 4937 volume = {4}, 4938 number = {1}, 4939 year = {2003}, 4940 pages = {59--64}, 4941 petsc_uses = {KSP} 4942} 4943 4944@Article{ cristea1, 4945 author = {Artur Cristea and Victor Sofonea}, 4946 title = {Two component lattice Boltzmann model with flux limiters}, 4947 journal = {Central European Journal of Physics}, 4948 volume = {2}, 4949 number = {2}, 4950 year = {2004}, 4951 pages = {382--396}, 4952 petsc_uses = {KSP} 4953} 4954 4955@Article{ sofnea-lamura1, 4956 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 4957 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 4958 systems}, 4959 journal = {Physical Review E}, 4960 volume = {70}, 4961 number = {4}, 4962 year = {2004}, 4963 pages = {046702-1 / 046702-9}, 4964 petsc_uses = {KSP} 4965} 4966 4967@InProceedings{ gkks01b, 4968 author = {W. 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Smith}, 4982 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 4983 Code}, 4984 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 4985 (HiPC '2000)}, 4986 editor = {}, 4987 location = {Bangalore, India}, 4988 year = {2000}, 4989 pages = {395--404}, 4990 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 4991 petsc_uses = {KSP} 4992} 4993 4994@InProceedings{ gkks-sc00, 4995 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4996 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 4997 booktitle = {Proceedings of SC2000}, 4998 editor = {}, 4999 publisher = {IEEE Computer Society}, 5000 year = {2000}, 5001 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 5002 petsc_uses = {KSP} 5003} 5004 5005@InProceedings{ knepleysamehsarin99, 5006 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 5007 title = {Design of Large Scale Parallel Simulations}, 5008 booktitle = {Proceedings of Parallel CFD'99}, 5009 editors = {A. {Ecer et al.}}, 5010 publisher = {Elsevier}, 5011 year = {1999}, 5012 petsc_uses = {KSP} 5013} 5014 5015@InProceedings{ gkks-pcfd99, 5016 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 5017 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 5018 booktitle = {Proceedings of Parallel CFD'99}, 5019 editors = {A. {Ecer et al.}}, 5020 publisher = {Elsevier}, 5021 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 5022 year = {1999}, 5023 petsc_uses = {KSP} 5024} 5025 5026@InProceedings{ kks97, 5027 author = {D. K. Kaushik and D. E. Keyes and B. F. 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Smith}, 5042 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 5043 Incompressible Flows on Unstructured Grids}, 5044 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 5045 Methods}, 5046 editors = {C.-H. {Lai et al.}}, 5047 publisher = {Domain Decomposition Press, Bergen}, 5048 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 5049 year = {1999}, 5050 petsc_uses = {KSP} 5051} 5052 5053@InCollection{ kks97_cfd, 5054 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 5055 title = {Perspectives for {CFD} on Petaflops Systems}, 5056 booktitle = {CFD Review 1998}, 5057 editor = {M. Hafez and K. Oshima}, 5058 publisher = {World Scientific, Singapore}, 5059 pages = {1079--1096}, 5060 note = {}, 5061 year = {1998}, 5062 petsc_uses = {KSP} 5063} 5064 5065@Article{ hm99, 5066 author = {P. D. Hovland and L. C. McInnes}, 5067 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 5068 {PETSc}}, 5069 year = {2000}, 5070 journal = {Parallel Computing}, 5071 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 5072 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 5073 petsc_uses = {KSP} 5074} 5075 5076@InProceedings{ cruzbarbaknepley08, 5077 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 5078 title = {Fast Multipole Method for particle interactions: an open source parallel library 5079 component}, 5080 booktitle = {Proceedings of ParCFD2008}, 5081 year = {2008}, 5082 editor = {Tromeur-Dervout et. al.}, 5083 publisher = {Elsevier}, 5084 petsc_uses = {KSP} 5085} 5086 5087@Article{ hwangcai05, 5088 author = {F.-N. Hwang and X.-C. Cai}, 5089 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 5090 for incompressible {Navier-Stokes} equations}, 5091 journal = {J. Comput. Phys.}, 5092 volume = {204}, 5093 year = {2005}, 5094 pages = {666--691}, 5095 petsc_uses = {KSP} 5096} 5097 5098@Article{ barbaleonard07, 5099 author = {Lorena A Barba and Anthony Leonard}, 5100 title = {Emergence and evolution of tripole vortices from net-circulation initial 5101 conditions}, 5102 journal = {Phys. Fluids}, 5103 volume = {19}, 5104 pages = {017101}, 5105 year = {2007}, 5106 doi = {10.1063/1.2409734}, 5107 petsc_uses = {KSP} 5108} 5109 5110@Article{ barba07, 5111 author = {Lorena A Barba}, 5112 title = {Non-shielded multipolar vortices at high Reynolds number}, 5113 journal = {Phys. Rev. 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Ahmadia and Amal Alghamdi and 5322 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 5323 Emmett}, 5324 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 5325 journal = {SIAM Journal on Scientific Computing}, 5326 volume = {34}, 5327 number = {4}, 5328 pages = {C210--C231}, 5329 note = {\url{http://arxiv.org/abs/1111.6583}}, 5330 year = {2012}, 5331 petsc_uses = {KSP} 5332} 5333 5334% LiteralHTML: 5335% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 5336% LiteralHTML: 5337@Article{ sojkahorakhaplacermak2018, 5338 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 5339 decomposition method}, 5340 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 5341 journal = {Applied Mathematics and Computation}, 5342 volume = {319}, 5343 pages = {586--597}, 5344 year = {2018}, 5345 petsc_uses = {KSP} 5346} 5347 5348@Article{ chencai2014, 5349 title = {A parallel two-level domain decomposition based one-shot method for shape 5350 optimization problems}, 5351 author = {Rongliang Chen and Xiao‐Chuan Cai}, 5352 journal = {International Journal for Numerical Methods in Engineering}, 5353 volume = {99}, 5354 number = {13}, 5355 year = {2014}, 5356 doi = {10.1002/nme.4711}, 5357 petsc_uses = {KSP} 5358} 5359 5360@PhDThesis{ prudencio2005, 5361 author = {Ernesto Prudencio}, 5362 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 5363 for Optimization Problems Constrained by Partial Differential Equations}, 5364 school = {University of Colorado, Boulder}, 5365 year = {2005}, 5366 petsc_uses = {KSP} 5367} 5368 5369@Article{ prudenciocai2007, 5370 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 5371 for {PDE}-constrained optimization}, 5372 author = {Ernesto Prudencio and X. C. Cai}, 5373 journal = {SIAM J. Sci. Comp.}, 5374 volume = {29}, 5375 number = {3}, 5376 pages = {964--985}, 5377 year = {2007}, 5378 petsc_uses = {KSP} 5379} 5380 5381@Article{ prudenciobyrdcai2006, 5382 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 5383 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 5384 {PDE}-constrained Optimization Problems}, 5385 journal = {SIAM J. Sci. Comp.}, 5386 volume = {27}, 5387 pages = {1305--1328}, 5388 year = {2006}, 5389 petsc_uses = {KSP} 5390} 5391 5392@InProceedings{ prudenciobyrdcai2004, 5393 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 5394 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 5395 booktitle = {VECPAR 2004}, 5396 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 5397 publisher = {Springer}, 5398 pages = {569--582}, 5399 year = {2004}, 5400 petsc_uses = {KSP} 5401} 5402 5403@Article{ belhamadia-fortin-pcp, 5404 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 5405 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 5406 journal = {Journal of Computational Physics}, 5407 volume = {201}, 5408 pages = {753-770}, 5409 year = {2004}, 5410 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 5411 petsc_uses = {KSP} 5412} 5413 5414@Article{ biros00, 5415 author = {George Biros and Omar Ghattas}, 5416 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 5417 journal = {SIAG-Opt Views and News}, 5418 volume = {11}, 5419 number = {2}, 5420 year = {2000}, 5421 month = aug, 5422 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 5423 petsc_uses = {KSP} 5424} 5425 5426@Article{ bmm01, 5427 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 5428 journal = {ACM Transactions on Mathematical Software}, 5429 title = {A case study in the performance and scalability of optimization algorithms}, 5430 year = {2001}, 5431 volume = {27}, 5432 number = {3}, 5433 pages = {361--376}, 5434 petsc_uses = {KSP} 5435} 5436 5437@InProceedings{ oghattas1999, 5438 author = {George Biros and Omar Ghattas}, 5439 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 5440 incompressible flows}, 5441 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 5442 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 5443 year = {1999}, 5444 petsc_uses = {KSP} 5445} 5446 5447@InProceedings{ hkms00, 5448 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 5449 PDE-constrained Optimization}, 5450 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 5451 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 5452 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 5453 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 5454 Hasco\"{e}t and Uwe Naumann}, 5455 publisher = {Springer}, 5456 year = {2002}, 5457 petsc_uses = {KSP} 5458} 5459 5460% old version: replace with biros2005pln1 5461@TechReport{ bg011, 5462 author = {George Biros and Omar Ghattas}, 5463 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 5464 Part I: The Krylov-Schur Solver}, 5465 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 5466 year = {2001}, 5467 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 5468 petsc_uses = {KSP} 5469} 5470 5471% old version: replace with biros2005pln2 5472@TechReport{ bg012, 5473 author = {George Biros and Omar Ghattas}, 5474 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 5475 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 5476 Optimal Control of Steady Viscous Flows}, 5477 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 5478 year = {2001}, 5479 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 5480 petsc_uses = {KSP} 5481} 5482 5483% LiteralHTML: 5484% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 5485% LiteralHTML: 5486@InProceedings{ ly2003, 5487 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 5488 title = {A New Parallel Kernel-independent Fast Multipole Method}, 5489 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 5490 year = {2003}, 5491 note = {Winner of the Best Student Paper at SC2003}, 5492 petsc_uses = {KSP} 5493} 5494 5495@Article{ yokotabarbaknepley10, 5496 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 5497 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 5498 journal = {Computer Methods in Applied Mechanics and Engineering}, 5499 volume = {199}, 5500 number = {25-28}, 5501 pages = {1793--1804}, 5502 url = {http://arxiv.org/abs/0909.5413v1}, 5503 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 5504 year = {2010}, 5505 petsc_uses = {KSP} 5506} 5507 5508@Article{ cruzknepleybarba10, 5509 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 5510 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 5511 journal = {International Journal of Numerical Methods in Engineering}, 5512 volume = {85}, 5513 number = {4}, 5514 pages = {403--428}, 5515 url = {http://arxiv.org/abs/0905.2637}, 5516 note = {\url{http://arxiv.org/abs/0905.2637}}, 5517 year = {2010}, 5518 petsc_uses = {KSP} 5519} 5520 5521% LiteralHTML: 5522% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 5523% LiteralHTML: 5524@Article{ buchanpainumplebysmedleystevenson2012, 5525 title = {A sub-grid scale finite element agglomeration multigrid method with application 5526 to the Boltzmann transport equation}, 5527 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 5528 journal = {International Journal for Numerical Methods in Engineering}, 5529 volume = {92}, 5530 number = {3}, 5531 pages = {318--342}, 5532 year = {2012}, 5533 publisher = {Wiley Online Library}, 5534 petsc_uses = {KSP} 5535} 5536 5537@Article{ magoulesahamedsuzuki2015, 5538 title = {Green computing on graphics processing units}, 5539 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 5540 journal = {Concurrency and Computation: Practice and Experience}, 5541 year = {2015}, 5542 publisher = {Wiley Online Library}, 5543 petsc_uses = {KSP} 5544} 5545 5546@InProceedings{ yanrhodes11, 5547 author = {Yan, Baoqiang and Rhodes, Philip J.}, 5548 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 5549 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 5550 series = {ICPP '11}, 5551 pages = {355--364}, 5552 year = {2011}, 5553 isbn = {978-0-7695-4510-3}, 5554 numpages = {10}, 5555 doi = {10.1109/ICPP.2011.70}, 5556 acmid = {2066965}, 5557 publisher = {IEEE Computer Society}, 5558 address = {Washington, DC, USA}, 5559 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 5560 petsc_uses = {KSP} 5561} 5562 5563@Article{ hakansson2013mdstochasticliouville, 5564 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 5565 Stulz, Eugen}, 5566 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 5567 equation study}, 5568 journal = {Phys. Chem. Chem. Phys.}, 5569 year = {2013}, 5570 volume = {15}, 5571 issue = {26}, 5572 pages = {10930-10941}, 5573 publisher = {The Royal Society of Chemistry}, 5574 doi = {10.1039/C3CP50788B}, 5575 petsc_uses = {KSP} 5576} 5577 5578@Article{ hakansson2011stochasticliouville, 5579 author = {Hakansson, Par and Nair, Prasanth B.}, 5580 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 5581 form}, 5582 journal = {Phys. Chem. Chem. Phys.}, 5583 year = {2011}, 5584 volume = {13}, 5585 issue = {20}, 5586 pages = {9578-9589}, 5587 publisher = {The Royal Society of Chemistry}, 5588 doi = {10.1039/C1CP20400A}, 5589 petsc_uses = {KSP} 5590} 5591 5592@InProceedings{ wang:lee:scidac2011, 5593 author = {Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman 5594 McInnes and Todd Munson and Barry Smith}, 5595 title = {A Differential Variational Inequality Approach for the Simulation of 5596 Heterogeneous Materials}, 5597 booktitle = {Proceedings of SciDAC 2011 Conference}, 5598 year = {2011}, 5599 petsc_uses = {KSP} 5600} 5601 5602@Article{ bourdinlarsenrichardson2011, 5603 author = {Blaise Bourdin and Christopher Larsen and Casey Richardson}, 5604 title = {A time-discrete model for dynamic fracture based on crack regularization}, 5605 journal = {International Journal of Fracture}, 5606 volume = {168}, 5607 issue = {2}, 5608 pages = {133--143}, 5609 doi = {10.1007/s10704-010-9562-x}, 5610 year = {2011}, 5611 petsc_uses = {KSP} 5612} 5613 5614@Book{ bourdinfrancfortmarigo, 5615 author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo}, 5616 title = {The Variational Approach to Fracture}, 5617 publisher = {Springer}, 5618 year = {2008}, 5619 petsc_uses = {KSP} 5620} 5621 5622@Article{ bourdinfrancfortmarigo2008, 5623 author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo}, 5624 title = {The Variational Approach to Fracture}, 5625 journal = {J. Elasticity}, 5626 volume = {91}, 5627 issue = {1}, 5628 pages = {1--148}, 5629 doi = {10.1007/s10659-007-9107-3}, 5630 year = {2008}, 5631 petsc_uses = {KSP} 5632} 5633 5634@Article{ lahtinen2008spectrum, 5635 title = {Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model}, 5636 author = {Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, 5637 J.K.}, 5638 journal = {Annals of Physics}, 5639 volume = {323}, 5640 number = {9}, 5641 pages = {2286--2310}, 5642 year = {2008}, 5643 publisher = {Elsevier}, 5644 petsc_uses = {KSP} 5645} 5646 5647@InProceedings{ roark2004discriminative, 5648 title = {Discriminative language modeling with conditional random fields and the 5649 perceptron algorithm}, 5650 author = {Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.}, 5651 booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational 5652 Linguistics}, 5653 pages = {47}, 5654 year = {2004}, 5655 organization = {Association for Computational Linguistics}, 5656 petsc_uses = {KSP} 5657} 5658 5659@Article{ roark2007discriminative, 5660 title = {Discriminative n-gram language modeling}, 5661 author = {Roark, B. and Saraclar, M. and Collins, M.}, 5662 journal = {Computer Speech \& Language}, 5663 volume = {21}, 5664 number = {2}, 5665 pages = {373--392}, 5666 year = {2007}, 5667 publisher = {Elsevier}, 5668 petsc_uses = {KSP} 5669} 5670 5671@Conference{ garcia2011parallel, 5672 title = {{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D 5673 nanodevice simulators}}, 5674 author = {Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and 5675 Aldegunde, M.}, 5676 booktitle = {Electron Devices (CDE), 2011 Spanish Conference on}, 5677 pages = {1--4}, 5678 organization = {IEEE}, 5679 petsc_uses = {KSP} 5680} 5681 5682@Conference{ wesley2006parallel, 5683 title = {{A parallel artificial neural network implementation}}, 5684 author = {Wesley-Smith, I.}, 5685 booktitle = {Proceedings of The National Conference On Undergraduate Research (NCUR)}, 5686 year = {2006}, 5687 petsc_uses = {KSP} 5688} 5689 5690@Article{ hcsw1, 5691 author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu}, 5692 title = {Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional 5693 Poisson-Boltzmann equation in numerical simulation of colloidal particle 5694 interactions}, 5695 journal = {Computer Physics Communications}, 5696 volumne = {181}, 5697 year = {2010}, 5698 pages = {1529--1537}, 5699 petsc_uses = {KSP} 5700} 5701 5702@Article{ hh1, 5703 author = {C.-Y. Huang and F.-N. Hwang}, 5704 title = {Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for 5705 bifurcation analysis of incompressible sudden expansion flows}, 5706 journal = {Applied Numerical Mathematics}, 5707 volume = {60}, 5708 year = {2010}, 5709 pages = {738--751}, 5710 petsc_uses = {KSP} 5711} 5712 5713@Article{ hwhw1, 5714 author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. Wang}, 5715 title = {A parallel additive Schwarz preconditioned Jacobi-Davidson algorithm for 5716 polynomial eigenvalue problems in quantum dot simulation}, 5717 journal = {Journal of Computational Physics}, 5718 volume = {229}, 5719 year = {2010}, 5720 pages = {2932--2947}, 5721 petsc_uses = {KSP} 5722} 5723 5724@Article{ wei2011parallel, 5725 title = {{A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with 5726 Application in Quantum Dot Simulation}}, 5727 author = {Wei, Z.H. and Hwang, F.N. and Huang, T.M. and Wang, W.}, 5728 journal = {Domain Decomposition Methods in Science and Engineering XIX}, 5729 pages = {157--164}, 5730 year = {2011}, 5731 publisher = {Springer}, 5732 petsc_uses = {KSP} 5733} 5734 5735@Article{ flores2007sequential, 5736 title = {{Sequential and parallel resolution of the two-group transient neutron diffusion 5737 equation using second-degree iterative methods}}, 5738 author = {Flores-S{\'a}nchez, O. and Vidal, V. and Garc{\'\i}a, V. and Flores-S{\'a}nchez, P.}, 5739 journal = {High Performance Computing for Computational Science-VECPAR 2006}, 5740 pages = {426--438}, 5741 year = {2007}, 5742 publisher = {Springer}, 5743 petsc_uses = {KSP} 5744} 5745 5746@InProceedings{ gordonbell09, 5747 author = {Dinesh Kaushik and Michael Smith and Allan Wollaber and Barry Smith and Andrew 5748 Siegel and Won Sik Yang}, 5749 title = {Enabling High Fidelity Neutron Transport Simulations on Petascale Architectures}, 5750 booktitle = {ACM/IEEE Proceedings of SC2009: High Performance Networking and Computing}, 5751 note = {{SC'09 Gordon Bell} Prize Finalist}, 5752 year = {2009}, 5753 petsc_uses = {KSP} 5754} 5755 5756@Article{ knepleykarpeevdavidovitseisenberggillespie10, 5757 author = {Matthew G. Knepley and Dmitry A. Karpeev and Seth Davidovits and Robert~S. 5758 Eisenberg and Dirk Gillespie}, 5759 title = {An Efficient Algorithm for Classical Density Functional Theory in Three 5760 Dimensions: Ionic Solutions}, 5761 journal = {Journal of Physical Chemistry}, 5762 volume = {132}, 5763 number = {12}, 5764 pages = {124101--124111}, 5765 url = {http://arxiv.org/abs/0910.1531}, 5766 year = {2010}, 5767 petsc_uses = {KSP} 5768} 5769 5770@Article{ knepleykarpeeveisenberggillespie09, 5771 author = {{Knepley}, M.~G. and {Karpeev}, D.~A. and {Eisenberg}, R.~S. and {Gillespie}, 5772 D.}, 5773 title = {{Energetics of Calcium Selectivity: A Three-Dimensional Classical Density 5774 Functional Theory Approach}}, 5775 journal = {Biophysical Journal}, 5776 month = feb, 5777 volume = {96}, 5778 pages = {661}, 5779 doi = {10.1016/j.bpj.2008.12.3494}, 5780 year = {2009}, 5781 petsc_uses = {KSP} 5782} 5783 5784@Article{ scx2008, 5785 author = {SUWITO AND XIAO-CHUAN CAI AND YUNPING XI}, 5786 title = {PARALLEL FINITE ELEMENT METHOD FOR COUPLED CHLORIDE MOISTURE DIFFUSION IN 5787 CONCRETE}, 5788 journal = {INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING}, 5789 volume = {3}, 5790 number = {4}, 5791 year = {2006}, 5792 url = {http://www.math.ualberta.ca/ijnam/Volume-3-2006/No-4-06/2006-04-06.pdf}, 5793 petsc_uses = {KSP} 5794} 5795 5796@TechReport{ kdgs2008, 5797 year = {2008}, 5798 school = {Centro Internacional de Methodos Numericos en Ingenieria, Argentina}, 5799 title = {High Performance Simulations of Electrokinetic Flow and Transport in Microfluidic 5800 Chips}, 5801 author = {Pablo A. Klera and Lisandro D. Dalcin and Fabio A. Guarnieria and Mario A. 5802 Stortia}, 5803 url = {http://www.cimec.org.ar/ojs/index.php/cmm/article/view/1383}, 5804 petsc_uses = {KSP} 5805} 5806 5807@Article{ springerlink:10.1007/s10915-011-9551-x, 5808 author = {Schauer, Marco and Roman, Jose and Quintana-Ortí, Enrique and Langer, Sabine}, 5809 affiliation = {Institut für Angewandte Mechanik, Technische Universität Carolo-Wilhelmina zu 5810 Braunschweig, Spielmannstraße 11, 38106 Braunschweig, Germany}, 5811 title = {Parallel Computation of 3-D Soil-Structure Interaction in Time Domain with a 5812 Coupled FEM/SBFEM Approach}, 5813 journal = {Journal of Scientific Computing}, 5814 publisher = {Springer Netherlands}, 5815 issn = {0885-7474}, 5816 keyword = {Mathematics and Statistics}, 5817 pages = {1-22}, 5818 doi = {10.1007/s10915-011-9551-x}, 5819 petsc_uses = {KSP} 5820} 5821 5822@TechReport{ jj2007, 5823 author = {Boris Jeremic and Guanzhou Jie}, 5824 title = {Parallel Finite Element Computations for Soil-Foundation-Structure Interaction 5825 Problems Report}, 5826 institution = {UCD CompGeoMech 02--2007}, 5827 year = {2007}, 5828 url = {http://sokocalo.engr.ucdavis.edu/~jeremic/wwwpublications/CV-R23.pdf}, 5829 petsc_uses = {KSP} 5830} 5831 5832@Unpublished{ kuiper08, 5833 title = {Fast 3D frequency-dependent Radiative Transfer for Magneto-Hydrodynamics}, 5834 author = {Rolf Kuiper}, 5835 institution = {Max-Planck-Institute for Astronomy}, 5836 url = {http://www.mpia.de/~kuiper/MAKEMAKE.html}, 5837 year = {2008}, 5838 petsc_uses = {KSP} 5839} 5840 5841@Article{ williamson2012multidimensional, 5842 title = {Multidimensional multiphysics simulation of nuclear fuel behavior}, 5843 author = {Williamson, R.L. and Hales, J.D. and Novascone, S.R. and Tonks, M.R. and Gaston, 5844 D.R. and Permann, C.J. and Andrs, D. and Martineau, R.C.}, 5845 journal = {Journal of Nuclear Materials}, 5846 volume = {423}, 5847 number = {1}, 5848 pages = {149--163}, 5849 year = {2012}, 5850 publisher = {Elsevier}, 5851 petsc_uses = {KSP} 5852} 5853 5854@InProceedings{ kucukboyaci2015cobra, 5855 title = {COBRA-TF parallelization and application to PWR reactor core subchannel DNB 5856 analysis}, 5857 author = {Kucukboyaci, Vefa and Sung, Yixing and Salko, Robert}, 5858 booktitle = {Joint International Conference on Mathematics and Computation, Supercomputing in 5859 Nuclear Applications and the Monte Carlo Method}, 5860 pages = {1--18}, 5861 year = {2015}, 5862 petsc_uses = {KSP} 5863} 5864 5865@Article{ hales2012solving, 5866 title = {Solving Nonlinear Solid Mechanics Problems with the {J}acobian-{F}ree {N}ewton 5867 {K}rylov Method}, 5868 author = {Hales, J.D. and Novascone, S.R. and Williamson, R.L. and Gaston, D.R. and Tonks, 5869 M.R.}, 5870 journal = {Computer Modeling in Engineering \& Sciences(CMES)}, 5871 volume = {84}, 5872 number = {2}, 5873 pages = {123--153}, 5874 year = {2012}, 5875 publisher = {Tech Science Press}, 5876 petsc_uses = {KSP} 5877} 5878 5879@InProceedings{ srksyp2008, 5880 author = {M. A. Smith and C. Rabiti and D. Kaushik and B. Smith and W. S. Yang and G. 5881 Palmiotti}, 5882 title = {Fast reactor core simulations using the {UNIC} code}, 5883 booktitle = {Proceedings of the International Conference on the Physics of Reactors, Nuclear 5884 Power: A Sustainable Resource}, 5885 year = {2008}, 5886 petsc_uses = {KSP} 5887} 5888 5889@InProceedings{ psrlkssl2007, 5890 author = {G. Palmiotti and M. A. Smith and C. Rabiti and M. Leclere and D. Kaushik and A. 5891 Siegel and B. Smith and E. E. Lewis}, 5892 title = {{UNIC}: Ultimate Neutronic Investigation Code}, 5893 booktitle = {Joint International Topical Meeting on Mathematics and Computation and 5894 Supercomputing in Nuclear Applications}, 5895 year = {2007}, 5896 petsc_uses = {KSP} 5897} 5898 5899@InProceedings{ sprkssl2007, 5900 author = {M. A. Smith and G. Palmiotti and C. Rabiti and D. Kaushik and A. Siegel and B. 5901 Smith and E. E. Lewis}, 5902 title = {{PNFE} Component of the {UNIC} Code}, 5903 booktitle = {Joint International Topical Meeting on Mathematics and Computation and 5904 Supercomputing in Nuclear Applications}, 5905 year = {2007}, 5906 petsc_uses = {KSP} 5907} 5908 5909@InProceedings{ dc-oop-03, 5910 author = {H. Digonnet and T. Coupez}, 5911 title = {Object-oriented programming for fast-and-easy development of parallel 5912 applications in forming processes simulation}, 5913 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 5914 Mechanics}, 5915 year = {2003}, 5916 petsc_uses = {KSP} 5917} 5918 5919@InProceedings{ dc-cfm-03, 5920 author = {H. Digonnet and T. Coupez}, 5921 title = {Calcul parallele en mise en forme des materiaux}, 5922 booktitle = {XVIeme Congres Francais de Mecanique}, 5923 year = {2003}, 5924 petsc_uses = {KSP} 5925} 5926 5927@InProceedings{ dsc-pcsev-04, 5928 author = {H. Digonnet and L. Silva and T. Coupez}, 5929 title = {Parallel computation for solving efficiently viscoelastic fluid flow problems}, 5930 booktitle = {Proceedings of ECCOMAS 2004}, 5931 year = {2004}, 5932 petsc_uses = {KSP} 5933} 5934 5935@InProceedings{ dsc-pca3fs-04, 5936 author = {H. Digonnet and L. Silva and T. Coupez}, 5937 title = {Parallel computation applied to 3D FE simulation of polymer injection molding}, 5938 booktitle = {Proceedings of WCCM VI}, 5939 year = {2004}, 5940 petsc_uses = {KSP} 5941} 5942 5943@InProceedings{ dbcs-cpaac-05, 5944 author = {H. Digonnet and O. Basset and T. Coupez and L. Silva}, 5945 title = {Calcul parallele appliqu aux coulements de fluides complexe}, 5946 booktitle = {Proceedings of Eme Congres Francais de Mecanique}, 5947 year = {2005}, 5948 petsc_uses = {KSP} 5949} 5950 5951@Article{ sz2010, 5952 author = {B. Smith and H. Zhang}, 5953 title = {Sparse Triangular Solves for {ILU} Revisited: Data Layout Crucial to Better 5954 Performance}, 5955 journal = {International Journal of High Performance Computing Applications}, 5956 volume = {25}, 5957 number = {4}, 5958 pages = {386--391}, 5959 year = {2011}, 5960 petsc_uses = {KSP} 5961} 5962 5963@Article{ zssz2006, 5964 author = {H. Zhang and B. Smith and M. Sternberg and P. Zapol}, 5965 title = {{SIPs}: Shift-and-Invert Parallel Spectral Transformations}, 5966 journal = {TOMS}, 5967 url = {http://math.nist.gov/toms/Current.html#v33n2}, 5968 volumne = {33}, 5969 number = {2}, 5970 year = {2007}, 5971 petsc_uses = {KSP} 5972} 5973 5974@Article{ gs2006, 5975 author = {Fang Jin and Nivedita R. Gupta and Kathleen J. Stebe}, 5976 title = {The detachment of a viscous drop in a viscous solution in the presence of a 5977 soluble surfactant}, 5978 journal = {Phys. Fluids}, 5979 volume = {18}, 5980 year = {2006}, 5981 url = {http://scitation.aip.org/dbt/dbt.jsp?KEY=PHFLE6&Volume=LASTVOL&Issue=LASTISS}, 5982 petsc_uses = {KSP} 5983} 5984 5985@Article{ jmemsci, 5986 author = {Bo Zhou and Adam Powell}, 5987 title = {Phase Field Simulations of Liquid-Liquid Demixing During Immersion Precipitation 5988 of Polymeric Membranes in 2D and 3D}, 5989 journal = {J. 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Korres and Anastasios Tzavellas and Evangelos Galinas}, 6411 title = {A distributed implementation of multi-area power system state estimation on a 6412 cluster of computers }, 6413 journal = {Electric Power Systems Research }, 6414 volume = {102}, 6415 number = {0}, 6416 pages = {20 - 32}, 6417 year = {2013}, 6418 issn = {0378-7796}, 6419 doi = {10.1016/j.epsr.2013.04.002}, 6420 petsc_uses = {KSP} 6421} 6422 6423% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 6424% LiteralHTML:<font color="#FF0000"> 6425% LiteralHTML: Material failure, for example, cracking of steel beams resulting 6426% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 6427% LiteralHTML: are important for prediction and prevention. 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Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 6529 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 6530 Tolerance}, 6531 journal = {IEEE Transactions on Magnetics}, 6532 year = {2004}, 6533 volume = {40}, 6534 pages = {1306--1309}, 6535 petsc_uses = {KSP} 6536} 6537 6538@Article{ holst-lindblom-etal:2004, 6539 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 6540 Scheel and Lawrence E. Kidder}, 6541 title = {Optimal constraint projection for hyperbolic evolution systems, }, 6542 journal = {Phys. Rev. D}, 6543 year = {2004}, 6544 volume = {70}, 6545 pages = {084017}, 6546 petsc_uses = {KSP} 6547} 6548 6549@Article{ marm2005, 6550 author = {Matthew Anderson and Richard A. Matzner}, 6551 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 6552 journal = {Foundations of Physics}, 6553 volume = {35}, 6554 pages = {1572--9516}, 6555 year = {2005}, 6556 petsc_uses = {KSP} 6557} 6558 6559@Article{ cook-pfeiffer:2004, 6560 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 6561 title = {Excision boundary conditions for black hole initial data}, 6562 journal = {Phys. Rev. D}, 6563 volume = {70}, 6564 pages = {104016--24}, 6565 year = {2004}, 6566 petsc_uses = {KSP} 6567} 6568 6569@Article{ pfeiffer-kidder-etal:2005, 6570 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 6571 Shoemaker}, 6572 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 6573 journal = {Phys. Rev. D}, 6574 year = {2005}, 6575 volume = {71}, 6576 pages = {024020}, 6577 petsc_uses = {KSP} 6578} 6579 6580@Article{ pfeiffer-kidder-etal:2003, 6581 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 6582 Saul A.}, 6583 title = {A multidomain spectral method for solving elliptic equations}, 6584 journal = {CPC}, 6585 year = {2003}, 6586 volume = {152}, 6587 pages = {253--273}, 6588 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 6589 For a related online version, see arXiv:gr-qc/0202096}, 6590 petsc_uses = {KSP} 6591} 6592 6593@Article{ pfeiffer-cook-teukolsky:2002, 6594 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 6595 title = {Comparing initial-data sets for binary black hole}, 6596 journal = {PRD}, 6597 year = {2002}, 6598 volume = {66}, 6599 pages = {024047}, 6600 note = {for a related online version, seearXiv:gr-qc/0203085}, 6601 petsc_uses = {KSP} 6602} 6603 6604@PhDThesis{ pfeiffer:2003, 6605 author = {Pfeiffer, Harald P.}, 6606 title = {Initial Data for Black Hole Evolutions}, 6607 school = {Cornell University}, 6608 year = {2003}, 6609 petsc_uses = {KSP} 6610} 6611 6612@TechReport{ h1, 6613 author = {Erik Schnetter}, 6614 title = {A fast apparent horizon algorithm}, 6615 year = {2002}, 6616 number = {Arxiv preprint gr-qc/0206003}, 6617 url = {http://arxiv.org/pdf/gr-qc/0206003}, 6618 petsc_uses = {KSP} 6619} 6620 6621@Article{ h2, 6622 author = {Erik Schnetter}, 6623 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 6624 year = {2003}, 6625 journal = {Class. Quantum Grav.}, 6626 pages = {4719-4737}, 6627 volume = {20}, 6628 url = {http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf}, 6629 petsc_uses = {KSP} 6630} 6631 6632@Article{ adams-03a, 6633 author = {Adams, M.~F.}, 6634 journal = {Numerical Linear Algebra with Applications}, 6635 number = {2-3}, 6636 pages = {141-153}, 6637 title = {Algebraic multigrid methods for constrained linear systems with applications to 6638 contact problems in solid mechanics}, 6639 volume = {11}, 6640 year = {2004}, 6641 petsc_uses = {KSP} 6642} 6643 6644@Article{ vandesande1, 6645 author = {H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer}, 6646 journal = {IEEE TRANSACTIONS ON MAGNETICS}, 6647 year = {2003}, 6648 volume = {39}, 6649 pages = {1709--1712}, 6650 title = {Solving Nonlinear Magnetic Problems Using Newton Trust Region Methods}, 6651 petsc_uses = {KSP} 6652} 6653 6654@InProceedings{ vbde1, 6655 author = {Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith}, 6656 year = {2002}, 6657 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 6658 Uintah PSE}, 6659 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 6660 2002}, 6661 pages = {49-55}, 6662 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 6663 note = {Extended abstract}, 6664 petsc_uses = {KSP} 6665} 6666 6667@Unpublished{ ep1, 6668 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 6669 author = {Bradley R. Eccleston and Todd S. Palmer}, 6670 institution = {Department of Nuclear Engineering, Oregon State University}, 6671 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 6672 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 6673 Parallel Simulations}, 6674 year = {1999}, 6675 petsc_uses = {KSP} 6676} 6677 6678@InProceedings{ teo2007scalable, 6679 title = {A scalable modular convex solver for regularized risk minimization}, 6680 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 6681 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 6682 discovery and data mining}, 6683 pages = {727--736}, 6684 year = {2007}, 6685 organization = {ACM}, 6686 petsc_uses = {KSP} 6687} 6688 6689@InProceedings{ rm02, 6690 author = {Robert Malouf}, 6691 year = {2002}, 6692 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 6693 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 6694 (CoNLL-2002)}, 6695 pages = {49-55}, 6696 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 6697 petsc_uses = {KSP} 6698} 6699 6700@Unpublished{ hrv02, 6701 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 6702 author = {V. Hernandex and J. E. Roman and V. Vidal}, 6703 note = {Submitted to CMMSE}, 6704 petsc_uses = {KSP} 6705} 6706 6707@Article{ tmh2001, 6708 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 6709 journal = {Journal of Economic Dynamics and Control}, 6710 year = {2002}, 6711 volume = {26}, 6712 pages = {1499-1515}, 6713 title = {Solving finite difference schemes arising in trivariate option pricing}, 6714 petsc_uses = {KSP} 6715} 6716 6717@InProceedings{ a2, 6718 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 6719 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 6720 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6721 Methods}, 6722 editor = {C.-H. Lai et al.}, 6723 publisher = {Domain Decomposition Press, Bergen}, 6724 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 6725 year = {1999}, 6726 petsc_uses = {KSP} 6727} 6728 6729@Unpublished{ mmmdcmaa-web-page, 6730 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 6731 {A}coustics {W}eb Page}, 6732 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 6733 author = {David E. Keyes}, 6734 institution = {Old Dominion University}, 6735 petsc_uses = {KSP} 6736} 6737 6738@Conference{ liu2010parallelization, 6739 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 6740 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 6741 booktitle = {International Symposium on Parallel and Distributed Processing with 6742 Applications}, 6743 pages = {528--535}, 6744 year = {2010}, 6745 organization = {IEEE}, 6746 petsc_uses = {KSP} 6747} 6748 6749@Unpublished{ oil-reservoir-sim-web-page, 6750 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 6751 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 6752 institution = {University of Texas at Austin and Argonne National Laboratory}, 6753 key = {University of Texas at Austin and Argonne National Laboratory}, 6754 petsc_uses = {KSP} 6755} 6756 6757@Article{ tmh2001b, 6758 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 6759 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 6760 year = {2001}, 6761 volume = {37}, 6762 pages = {143--146}, 6763 title = {Adapting EMAP3D to parallel processing}, 6764 petsc_uses = {KSP} 6765} 6766 6767@Article{ harbury98, 6768 author = {HK Harbury and W Porod}, 6769 journal = {VLSI Design}, 6770 year = {1998}, 6771 volume = {6}, 6772 pages = {47--51}, 6773 title = {Parallel computation for electronic waves in quantum corrals}, 6774 petsc_uses = {KSP} 6775} 6776 6777@Article{ bludszuwei98, 6778 author = {Mark Bludszuweit}, 6779 journal = {Journal of Lightwave Technology}, 6780 year = {1998}, 6781 volume = {16}, 6782 number = {7}, 6783 pages = {1336--42}, 6784 title = {Mixed Finite Element Beam Propagation Method}, 6785 petsc_uses = {KSP} 6786} 6787 6788@Article{ s1, 6789 author = {J. L. Friedman and N. Stergioulas}, 6790 journal = {Astrophysics Journal}, 6791 year = {1998}, 6792 volume = {492}, 6793 number = {301}, 6794 pages = {}, 6795 title = {}, 6796 petsc_uses = {KSP} 6797} 6798 6799@Article{ s1a, 6800 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 6801 journal = {Astrophysics Journal}, 6802 year = {1999}, 6803 volume = {510}, 6804 number = {854}, 6805 pages = {}, 6806 title = {}, 6807 petsc_uses = {KSP} 6808} 6809 6810@PhDThesis{ s2, 6811 author = {N. Stergioulas}, 6812 title = {Ph. D. thesis}, 6813 year = {1996}, 6814 institution = {University of Wisconsin-Milwaukee}, 6815 petsc_uses = {KSP} 6816} 6817 6818@InProceedings{ coral1, 6819 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6820 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 6821 Parallel Computing Environment}, 6822 booktitle = {Proceedings of the Miami TEAM Workshop}, 6823 location = {Florida International University, Department of Electrical Engineering and 6824 Computing Science}, 6825 month = nov, 6826 year = {1993}, 6827 petsc_uses = {KSP} 6828} 6829 6830@InProceedings{ coral2, 6831 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6832 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 6833 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 6834 month = dec, 6835 year = {1994}, 6836 petsc_uses = {KSP} 6837} 6838 6839@InProceedings{ coral3, 6840 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6841 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 6842 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 6843 location = {Florida International University, Department of Electrical Engineering and 6844 Computing Science}, 6845 year = {1995}, 6846 petsc_uses = {KSP} 6847} 6848 6849@InProceedings{ mijalkovic, 6850 author = {Slobodan Mijalkovi\'{c}}, 6851 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 6852 Process Simulation}, 6853 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 6854 Gent, Belgium, September 27--30, 1999.}, 6855 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 6856 optvolume = {14}, 6857 optseries = {Lecture Notes in Computational Science and Engineering}, 6858 year = {2000}, 6859 publisher = {Springer}, 6860 address = {Berlin}, 6861 optpages = {179--184}, 6862 petsc_uses = {KSP} 6863} 6864 6865@Article{ bludszuwei98a, 6866 author = {Mark Bludszuweit}, 6867 journal = {Journal of Lightwave Technology}, 6868 year = {1998}, 6869 volume = {16}, 6870 number = {7}, 6871 pages = {1336--42}, 6872 title = {Mixed Finite Element Beam Propagation Method}, 6873 petsc_uses = {KSP} 6874} 6875 6876@Article{ gilli-pauletto-1998, 6877 author = {Manfred Gilli and Giorgio Pauletto}, 6878 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 6879 journal = {Computational Economics}, 6880 year = {2000}, 6881 volume = {16}, 6882 pages = {173--186}, 6883 petsc_uses = {KSP} 6884} 6885 6886% LiteralHTML: 6887% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 6888% LiteralHTML: 6889@Article{ collierdalcincalo2013, 6890 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 6891 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 6892 journal = {arxiv}, 6893 year = {2013}, 6894 number = {1305.4452}, 6895 note = {\url{http://arxiv.org/abs/1305.4452}}, 6896 petsc_uses = {KSP} 6897} 6898 6899@Article{ collierdalcinvignalcortescalo2016, 6900 title = {PetIGA: A framework for high-performance isogeometric analysis}, 6901 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 6902 Victor M. Calo}, 6903 journal = {Computer Methods in Applied Mechanics and Engineering}, 6904 year = {2016}, 6905 petsc_uses = {KSP} 6906} 6907 6908@Misc{ petiga-web-page, 6909 author = {N. Collier and L. Dalcin and V.M. Calo}, 6910 title = {{PetIGA} {W}eb page}, 6911 url = {https://bitbucket.org/dalcinl/petiga/}, 6912 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 6913 year = {2014}, 6914 petsc_uses = {KSP} 6915} 6916 6917@Article{ logg07, 6918 author = {Logg, Anders}, 6919 title = {Automating the Finite Element Method}, 6920 journal = {Archives of Computational Methods in Engineering}, 6921 volume = {14}, 6922 number = {2}, 6923 pages = {93-138}, 6924 year = {2007}, 6925 doi = {10.1007/s11831-007-9003-9}, 6926 publisher = {Kluwer Academic Publishers}, 6927 issn = {1134-3060}, 6928 language = {English}, 6929 petsc_uses = {KSP} 6930} 6931 6932@Article{ jezequelcouturierdenis12, 6933 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 6934 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 6935 versus the PETSc library}, 6936 journal = {The Journal of Supercomputing}, 6937 volume = {59}, 6938 number = {3}, 6939 pages = {1517-1532}, 6940 year = {2012}, 6941 issn = {0920-8542}, 6942 doi = {10.1007/s11227-011-0563-y}, 6943 publisher = {Springer US}, 6944 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 6945 Sparse linear solver}, 6946 language = {English}, 6947 petsc_uses = {KSP} 6948} 6949 6950@Unpublished{ feap-web-page, 6951 title = {FEAP: A Finite Element Analysis Program}, 6952 url = {http://www.ce.berkeley.edu/projects/feap/}, 6953 author = {FEAP Team}, 6954 note = {Uses PETSc linear solvers - iterative and direct}, 6955 petsc_uses = {KSP} 6956} 6957 6958@Unpublished{ parpre-web-page, 6959 title = {{ParPre} {W}eb {P}age}, 6960 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 6961 institution = {University of Tennessee}, 6962 author = {Victor Eijkhout}, 6963 note = {This is no longer supported. A set of preconditioners built on PETSc}, 6964 petsc_uses = {KSP} 6965} 6966 6967@Unpublished{ pism, 6968 title = {{PISM}: a Parallel Ice Sheet Model}, 6969 author = {{PISM Team}}, 6970 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 6971 Sheet Model). The thickness, temperature, velocity and age of the ice are all 6972 simulated, as is the deformation of the earth underneath the ice. New techniques 6973 for fast ice dynamics, earth deformation, and verification have are included.}, 6974 note = {\url{http://www.pism-docs.org/}}, 6975 petsc_uses = {KSP} 6976} 6977 6978@Unpublished{ oofem, 6979 title = {OOFEM - an object oriented finite element package}, 6980 author = {Borek Patzak}, 6981 url = {http://www.oofem.org}, 6982 petsc_uses = {KSP} 6983} 6984 6985@Unpublished{ dks2openfvm, 6986 title = {OpenFVM - a finite volume based general purpose CFD solver}, 6987 author = {Open source development}, 6988 url = {http://openfvm.sourceforge.net/}, 6989 petsc_uses = {KSP} 6990} 6991 6992@Unpublished{ sundar-2008w, 6993 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 6994 octree meshes}, 6995 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 6996 institution = {University of Pennsylvania}, 6997 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 6998 petsc_uses = {KSP} 6999} 7000 7001@Unpublished{ khatiwala07-software, 7002 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 7003 author = {Khatiwala, S.}, 7004 institution = {Columbia University}, 7005 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 7006 petsc_uses = {KSP} 7007} 7008 7009@InBook{ jiaolima99, 7010 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 7011 chapter = {SIFFEA:Scalable Integrated Framework for Finite Element Analysis}, 7012 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 7013 title = {Lecture Notes in Computer Science}, 7014 publisher = {Springer-Verlag}, 7015 volume = {1732}, 7016 year = {1999}, 7017 petsc_uses = {KSP} 7018} 7019 7020@Article{ crow1, 7021 author = {C. S. Crow IV}, 7022 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 7023 journal = {Hopkins Undergraduate Research Journal}, 7024 year = {2003}, 7025 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 7026 petsc_uses = {KSP} 7027} 7028 7029@Unpublished{ petsc-python, 7030 title = {PETSc for Python}, 7031 author = {L. Dalcin}, 7032 url = {https://petsc.org/main/petsc4py}, 7033 note = {Provides Python bindings for PETSc}, 7034} 7035 7036@Unpublished{ cfdship, 7037 title = {{CFDShip-Iowa}}, 7038 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 7039 institution = {University of Iowa}, 7040 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 7041 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 7042 structured grids, designed for ship applications}, 7043 petsc_uses = {KSP} 7044} 7045 7046@Unpublished{ bvw, 7047 title = {Multiflow}, 7048 author = {Berend van Wachem}, 7049 institution = {Mechanical Engineering - Chalmers University of Technology}, 7050 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 7051 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 7052 flows.}, 7053 petsc_uses = {KSP} 7054} 7055 7056@Unpublished{ dks2, 7057 title = {FENA - A Finite Element Model for the North Atlantic}, 7058 author = {Jens Schroeter}, 7059 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 7060 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 7061 petsc_uses = {KSP} 7062} 7063 7064@TechReport{ piwonski2010idea, 7065 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 7066 and Simulation in {3-D}}, 7067 author = {Piwonski, J. and Slawig, T.}, 7068 year = {2010}, 7069 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 7070 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 7071 petsc_uses = {KSP} 7072} 7073 7074@Unpublished{ metos3d-web, 7075 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 7076 author = {Piwonski, J. and Slawig, T.}, 7077 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 7078 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 7079 petsc_uses = {KSP} 7080} 7081 7082@Unpublished{ magpar, 7083 author = {W. Scholz}, 7084 title = {Magpar: Parallel Micromagnetics Code}, 7085 institution = {Vienna University of Technology}, 7086 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 7087 petsc_uses = {KSP} 7088} 7089 7090@Misc{ libmesh:sourceforge, 7091 author = {}, 7092 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 7093 equations on serial and parallel platforms}, 7094 note = {[Online]}, 7095 url = {http://libmesh.github.io}, 7096 petsc_uses = {KSP} 7097} 7098 7099@Misc{ moose-web-page, 7100 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 7101 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 7102 Gaston and John Peterson and Jason Miller}, 7103 institution = {Idaho National Laboratory}, 7104 howpublished = {\url{http://mooseframework.org}}, 7105 petsc_uses = {KSP} 7106} 7107 7108@Article{ gaston2009moose, 7109 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 7110 equations}, 7111 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 7112 journal = {Nuclear Engineering and Design}, 7113 volume = {239}, 7114 number = {10}, 7115 pages = {1768--1778}, 7116 year = {2009}, 7117 publisher = {Elsevier}, 7118 petsc_uses = {KSP} 7119} 7120 7121@Article{ tonks2012object, 7122 title = {An object-oriented finite element framework for multiphysics phase field 7123 simulations}, 7124 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 7125 journal = {Computational Materials Science}, 7126 volume = {51}, 7127 number = {1}, 7128 pages = {20--29}, 7129 year = {2012}, 7130 publisher = {Elsevier}, 7131 petsc_uses = {KSP} 7132} 7133 7134@Misc{ pylithmanual, 7135 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 7136 Strand and Charles Williams}, 7137 title = {{PyLith} User Manual Version 2.0.0}, 7138 year = {2014}, 7139 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 7140 petsc_uses = {KSP} 7141} 7142 7143@Misc{ pylith-web-page, 7144 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 7145 title = {{PyLith}}, 7146 year = {2012}, 7147 url = {http://geodynamics.org/resources/pylith/}, 7148 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 7149 petsc_uses = {KSP} 7150} 7151 7152@Misc{ galemanual, 7153 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 7154 title = {Gale User Manual Version 2.0.0}, 7155 year = {2011}, 7156 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 7157 petsc_uses = {KSP} 7158} 7159 7160@Unpublished{ underworld, 7161 author = {Louis Moresi}, 7162 title = {{UnderWorld}: A Geodynamics Modelling Code}, 7163 institution = {Monash University}, 7164 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 7165 petsc_uses = {KSP} 7166} 7167 7168@Article{ moresi2007computational, 7169 title = {Computational approaches to studying non-linear dynamics of the crust and 7170 mantle}, 7171 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 7172 M{\"u}hlhaus, H.B.}, 7173 journal = {Physics of the Earth and Planetary Interiors}, 7174 volume = {163}, 7175 number = {1-4}, 7176 pages = {69--82}, 7177 year = {2007}, 7178 publisher = {Elsevier}, 7179 petsc_uses = {KSP} 7180} 7181 7182@Article{ pitt2009chaste, 7183 title = {Chaste: a test-driven approach to software development for biological modelling}, 7184 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 7185 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 7186 and Walter, A. and others}, 7187 journal = {Computer Physics Communications}, 7188 volume = {180}, 7189 number = {12}, 7190 pages = {2452--2471}, 7191 year = {2009}, 7192 publisher = {Elsevier}, 7193 petsc_uses = {KSP} 7194} 7195 7196@Misc{ fenicsproject, 7197 title = {{The FEniCS project}}, 7198 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 7199 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 7200 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 7201 url = {http://fenicsproject.org}, 7202 year = {2011}, 7203 petsc_uses = {KSP} 7204} 7205 7206@Unpublished{ snark, 7207 title = {Snark: A suite of software for geoscientific applications and a philosophy of 7208 scientific software development}, 7209 institution = {Victorian Partnership for Advanced Computing}, 7210 url = {http://vpac.org/Snark}, 7211 petsc_uses = {KSP} 7212} 7213 7214@Misc{ imoose:sourceforge, 7215 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 7216 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 7217 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 7218 note = {[Online]}, 7219 url = {http://imoose.sourceforge.net}, 7220 petsc_uses = {KSP} 7221} 7222 7223@Unpublished{ fossi, 7224 author = {Stephan Frickenhaus}, 7225 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 7226 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 7227 codes}, 7228 institution = {AWI-Bremerhaven, Germanny}, 7229 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 7230 petsc_uses = {KSP} 7231} 7232 7233@Unpublished{ fun3dweb, 7234 author = {Dinesh Kaushik}, 7235 title = {PETSC-FUN3D Benchmark Page}, 7236 institution = {ODU/ANL}, 7237 url = {http://www.mcs.anl.gov/petsc-fun3d}, 7238 note = {CFD Benchmark of some solvers in PETSc}, 7239 petsc_uses = {KSP} 7240} 7241 7242@Unpublished{ scirun, 7243 author = {SCIRun Development Team}, 7244 title = {SCIRun}, 7245 institution = {University of Utah}, 7246 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 7247 note = {SCIRun now uses PETSc linear solvers}, 7248 petsc_uses = {KSP} 7249} 7250 7251@Misc{ prometheus, 7252 author = {Mark F. Adams}, 7253 title = {Prometheus - A scalable unstructured finite element solver}, 7254 institution = {Berkeley}, 7255 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 7256 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 7257 petsc_uses = {KSP} 7258} 7259 7260@Unpublished{ illuminator, 7261 author = {Adam C. Powell, IV}, 7262 title = {Illuminator Distributed Visualization Library}, 7263 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 7264 petsc_uses = {KSP} 7265} 7266 7267@Unpublished{ rheoplast, 7268 title = {RheoPlast Phase Field Multi-Physics Code}, 7269 author = {Adam Powell and David Dussault and Bo Zhou}, 7270 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 7271 petsc_uses = {KSP} 7272} 7273 7274@Misc{ tao-web-page, 7275 title = {{Toolkit for Advanced Optimization (TAO)} {W}eb Page}, 7276 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 7277 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 7278 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7279 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 7280 petsc_uses = {KSP} 7281} 7282 7283@TechReport{ tao-user-ref, 7284 title = {{Toolkit for Advanced Optimization (TAO) users manual}}, 7285 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 7286 and Steve Benson and Lois Curfman McInnes}, 7287 institution = {Argonne National Laboratory}, 7288 year = {2019}, 7289 number = {ANL/MCS-TM-322 - Rev 3.12}, 7290 petsc_uses = {KSP} 7291} 7292 7293% url = "http://www.mcs.anl.gov/tao", 7294@Unpublished{ mefpp-web-page, 7295 title = {{MEF++} {W}eb {P}age}, 7296 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 7297 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 7298 author = {Eric Chamberland}, 7299 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 7300 multiphysics}, 7301 petsc_uses = {KSP} 7302} 7303 7304@Unpublished{ tipetsc-web-page, 7305 title = {Ti-PETSc - an interface to PETSc from Titanium}, 7306 institution = {Berkeley}, 7307 url = {http://www.nersc.gov/\~{ }yunhe/cs267/final/paper.pdf}, 7308 petsc_uses = {KSP} 7309} 7310 7311@Unpublished{ ptatin-web-page, 7312 title = {ptatin3d}, 7313 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 7314 url = {https://bitbucket.org/jedbrown/ptatin3d}, 7315 year = {2018}, 7316 petsc_uses = {KSP} 7317} 7318 7319@Misc{ multiphase-web-page, 7320 author = {Q. Zou}, 7321 title = {Multiphase flow with {PETSc}}, 7322 institution = {LANL}, 7323 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 7324 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 7325 lab = {LANL}, 7326 petsc_uses = {KSP} 7327} 7328 7329@Misc{ electromag-web-page, 7330 title = {{EMSolve Web} page}, 7331 institution = {LLNL}, 7332 howpublished = {http://www.llnl.gov/casc/emsolve}, 7333 url = {http://www.Llnl.gov/casc/emsolve}, 7334 author = {Daniel {White et al.}}, 7335 lab = {LLNL}, 7336 petsc_uses = {KSP} 7337} 7338 7339@Unpublished{ fe-software-web-page, 7340 institution = {Kuleuven}, 7341 title = {Finite element software}, 7342 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 7343 petsc_uses = {KSP} 7344} 7345 7346@Misc{ petsc-web-page, 7347 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7348 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 7349 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7350 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7351 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7352 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7353 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7354 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7355 Zhang}, 7356 title = {{PETS}c {W}eb page}, 7357 url = {https://petsc.org/}, 7358 howpublished = {\url{https://petsc.org/}}, 7359 year = {2023} 7360} 7361 7362@Unpublished{ petsc-debian-package, 7363 author = {Adam C. Powell, IV}, 7364 title = {Debian package for PETSc}, 7365 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 7366 petsc_uses = {KSP} 7367} 7368 7369@Unpublished{ cactus, 7370 title = {Cactus Website}, 7371 url = {http://www.cactuscode.org/}, 7372 note = {Provides two interface to the PETSc solvers}, 7373 petsc_uses = {KSP} 7374} 7375 7376@Unpublished{ petsc-fem, 7377 author = {Mario Storti and Norberto Nigro}, 7378 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 7379 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 7380 url = {http://www.cimec.org.ar/petscfem}, 7381 petsc_uses = {KSP} 7382} 7383 7384@Misc{ fidap, 7385 title = {FIDAP 8.5}, 7386 howpublished = {\url{http://www.fluent.com}}, 7387 url = {http://www.fluent.com}, 7388 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 7389 solves.}, 7390 key = {FIDAP 8.5}, 7391 petsc_uses = {KSP} 7392} 7393 7394@Unpublished{ slepc, 7395 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7396 Vicente Hern\'andez and Vicent Vidal}, 7397 title = {{SLEPc} Website}, 7398 url = {http://slepc.upv.es/}, 7399 note = {Scalable Library for Eigenvalue Problem Computations}, 7400 petsc_uses = {KSP} 7401} 7402 7403@TechReport{ slepc-users-manual, 7404 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7405 Vicente Hern\'andez and Vicent Vidal}, 7406 title = {{SLEPc} Users Manual}, 7407 number = {DISC-II/24/02}, 7408 url = {http://slepc.upv.es/}, 7409 note = {Scalable Library for Eigenvalue Problem Computations}, 7410 petsc_uses = {KSP} 7411} 7412 7413@Misc{ deal.ii, 7414 title = {deal.II}, 7415 howpublished = {\url{http://www.dealii.org}}, 7416 url = {http://www.dealii.org}, 7417 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 7418 It allows PETSc linear algebra and solvers to be used underneath.}, 7419 key = {deal.II 5.0}, 7420 petsc_uses = {KSP} 7421} 7422 7423@Article{ bangerth2007deal, 7424 title = {{deal.II---A general-purpose object-oriented finite element library}}, 7425 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 7426 journal = {ACM Transactions on Mathematical Software (TOMS)}, 7427 volume = {33}, 7428 number = {4}, 7429 pages = {24--es}, 7430 issn = {0098-3500}, 7431 year = {2007}, 7432 publisher = {ACM}, 7433 petsc_uses = {KSP} 7434} 7435 7436@Misc{ globalarrays, 7437 author = {Jarek {Nieplocha et al.}}, 7438 title = {Global Arrays}, 7439 institution = {Pacific Northwest National Laboratories}, 7440 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 7441 url = {http://www.emsl.pnl.gov/docs/global}, 7442 note = {Global arrays can use PETSc linear solvers}, 7443 lab = {PNNL}, 7444 petsc_uses = {KSP} 7445} 7446 7447% LiteralHTML: 7448% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 7449% LiteralHTML: 7450@Article{ petsccommunity2022, 7451 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 7452 Community}, 7453 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 7454 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 7455 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 7456 and Hong Zhang and Junchao Zhang}, 7457 journal = {Computing in Science and Engineering}, 7458 volume = {24}, 7459 number = {03}, 7460 pages = {6--15}, 7461 issn = {1558-366X}, 7462 doi = {10.1109/MCSE.2022.3169974}, 7463 publisher = {IEEE Computer Society}, 7464 address = {Los Alamitos, CA, USA}, 7465 month = may, 7466 year = {2022}, 7467 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 7468 petsc_uses = {KSP} 7469} 7470 7471@Article{ brownknepleysmith14, 7472 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 7473 title = {Run-time extensibility and librarization of simulation software}, 7474 journal = {IEEE Computing in Science and Engineering}, 7475 month = jan, 7476 volume = {17}, 7477 number = {1}, 7478 pages = {38--45}, 7479 doi = {10.1109/MCSE.2014.95}, 7480 year = {2015}, 7481 petsc_uses = {KSP} 7482} 7483 7484@TechReport{ ass2012, 7485 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 7486 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 7487 institution = {Argonne National Laboratory}, 7488 type = {Preprint}, 7489 year = {2012}, 7490 number = {ANL/MCS-P2011-0112}, 7491 petsc_uses = {KSP} 7492} 7493 7494@TechReport{ clearyknepley99, 7495 author = {Andrew Cleary and Matthew G. Knepley}, 7496 title = {Solvers as Operators}, 7497 institution = {Lawrence Livermore National Laboratory}, 7498 type = {Technical Report}, 7499 number = {UCRL-ID-135342}, 7500 year = {1999}, 7501 petsc_uses = {KSP} 7502} 7503 7504@TechReport{ smcabbkz2012, 7505 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 7506 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 7507 title = {{PETSc's} software strategy for the design space of composable extreme-scale 7508 solvers}, 7509 institution = {Argonne National Laboratory}, 7510 type = {Preprint}, 7511 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 7512 year = {2012}, 7513 number = {ANL/MCS-P2059-0312}, 7514 petsc_uses = {KSP} 7515} 7516 7517@InProceedings{ mhwpmhs2009, 7518 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 7519 and G. E. Hammond and B. Smith}, 7520 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 7521 Toolkit {MPI} at Scale}, 7522 booktitle = {Cray Users Group Conference}, 7523 year = {2009}, 7524 petsc_uses = {KSP} 7525} 7526 7527@InProceedings{ msmhls2010, 7528 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 7529 Lichtner and B. F. Smith}, 7530 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 7531 {BlueGene} Architectures}, 7532 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 7533 year = {2010}, 7534 petsc_uses = {KSP} 7535} 7536 7537@InCollection{ msk2013, 7538 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 7539 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 7540 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7541 series = {Lecture Notes in Earth System Sciences}, 7542 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7543 Yaolin Shi}, 7544 doi = {10.1007/978-3-642-16405-7_7}, 7545 publisher = {Springer Berlin Heidelberg}, 7546 pages = {131--140}, 7547 year = {2013}, 7548 isbn = {978-3-642-16404-0}, 7549 petsc_uses = {KSP} 7550} 7551 7552@InCollection{ knepleyyuen13, 7553 author = {Matthew G. Knepley and David A. Yuen}, 7554 title = {Why Scientists and Engineers need {GPU}s today}, 7555 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7556 series = {Lecture Notes in Earth System Sciences}, 7557 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7558 Yaolin Shi}, 7559 doi = {10.1007/978-3-642-16405-7_1}, 7560 publisher = {Springer Berlin Heidelberg}, 7561 pages = {131--140}, 7562 year = {2013}, 7563 isbn = {978-3-642-16404-0}, 7564 petsc_uses = {KSP} 7565} 7566 7567@InCollection{ karpeevknepleybrune13, 7568 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 7569 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 7570 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7571 series = {Lecture Notes in Earth System Sciences}, 7572 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7573 Yaolin Shi}, 7574 doi = {10.1007/978-3-642-16405-7_30}, 7575 publisher = {Springer Berlin Heidelberg}, 7576 pages = {487--501}, 7577 year = {2013}, 7578 isbn = {978-3-642-16404-0}, 7579 petsc_uses = {KSP} 7580} 7581 7582@InCollection{ zhengetal13, 7583 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 7584 Variable Viscosity}, 7585 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7586 Zhang and Yaolin Shi}, 7587 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7588 series = {Lecture Notes in Earth System Sciences}, 7589 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7590 Yaolin Shi}, 7591 doi = {10.1007/978-3-642-16405-7_21}, 7592 publisher = {Springer Berlin Heidelberg}, 7593 pages = {321--333}, 7594 year = {2013}, 7595 isbn = {978-3-642-16404-0}, 7596 petsc_uses = {KSP} 7597} 7598 7599@Article{ zhengetal13b, 7600 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 7601 strongly variable viscosity based on {M}atlab and {CUDA}}, 7602 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7603 Zhang and Yaolin Shi}, 7604 journal = {IJHPCA}, 7605 volume = {28}, 7606 number = {1}, 7607 pages = {50--60}, 7608 doi = {10.1177/1094342013478640}, 7609 year = {2013}, 7610 petsc_uses = {KSP} 7611} 7612 7613@InBook{ s2011, 7614 author = {B. Smith}, 7615 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 7616 title = {Encyclopedia of Parallel Computing}, 7617 bookeditor = {D. Padua}, 7618 publisher = {Springer}, 7619 year = {2011}, 7620 petsc_uses = {KSP} 7621} 7622 7623@Article{ acostamejia06, 7624 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 7625 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 7626 journal = {Lecturas Matem\'aticas}, 7627 volume = {27}, 7628 year = {2006}, 7629 pages = {213--224}, 7630 petsc_uses = {KSP} 7631} 7632 7633@InProceedings{ quenettemoresisunterappelbe07, 7634 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 7635 title = {Explaining StGermain: An aspect oriented environment for building extensible 7636 computational mechanics modeling software}, 7637 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 7638 publisher = {IEEE}, 7639 pages = {1--8}, 7640 yerar = {2007}, 7641 petsc_uses = {KSP} 7642} 7643 7644@Article{ dfm1, 7645 title = {Vectorized sparse matrix multiply for compressed row storage format}, 7646 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 7647 journal = {Lecture Notes in Computer Science}, 7648 year = {2005}, 7649 pages = {99--106}, 7650 volume = {3514}, 7651 lab = {ORNL}, 7652 petsc_uses = {KSP} 7653} 7654 7655@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 7656 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 7657 Vandewalle and Stefaan Poedts}, 7658 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 7659 Scientific Computing Software}, 7660 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 7661 year = {2005}, 7662 note = {Lecture Notes in Computer Science}, 7663 volume = {3514}, 7664 publisher = {Springer-Verlag GmbH}, 7665 petsc_uses = {KSP} 7666} 7667 7668@InProceedings{ dalcin-paz-storti, 7669 author = {L. Dalcin and R. Paz and M. Storti}, 7670 title = {Desarrollo de Aplicaciones Paralelas en Python}, 7671 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 7672 Bariloche, Argentina}, 7673 year = {2004}, 7674 petsc_uses = {KSP} 7675} 7676 7677@Article{ mpi-python, 7678 author = {L. Dalcin and R. Paz and M. Storti}, 7679 title = {MPI for Python}, 7680 journal = {Journal of Parallel and Distributed Computing}, 7681 year = {2005}, 7682 petsc_uses = {KSP} 7683} 7684 7685@Unpublished{ hrv02a, 7686 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 7687 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7688 note = {Submited to VecPar 2002}, 7689 year = {2002}, 7690 petsc_uses = {KSP} 7691} 7692 7693@Article{ knyazev2007block, 7694 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 7695 {PETSc}}, 7696 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 7697 journal = {SIAM Journal on Scientific Computing}, 7698 volume = {29}, 7699 pages = {2224-2239}, 7700 doi = {10.1137/060661624}, 7701 year = {2007}, 7702 petsc_uses = {KSP} 7703} 7704 7705@MastersThesis{ aarrestad-master, 7706 author = {Asbjorn Hoiland Aarrestad}, 7707 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 7708 school = {University of Bergen}, 7709 month = aug, 7710 year = {2003}, 7711 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 7712 note = {Implemented Runge-Kutta methods using PETSc}, 7713 petsc_uses = {KSP} 7714} 7715 7716@PhDThesis{ kaushik-phd, 7717 author = {D. K. Kaushik}, 7718 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 7719 Differential Equations on Unstructured Grids}, 7720 school = {Old Dominion University}, 7721 month = dec, 7722 year = {2002}, 7723 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 7724 petsc_uses = {KSP} 7725} 7726 7727@TechReport{ rb1, 7728 author = {Rickard Bergstrom}, 7729 title = {Object Oriented Implementation of a General Finite Element Code}, 7730 number = {2002-13}, 7731 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 7732 year = {2002}, 7733 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 7734 note = {Discribes a finite element software package that uses PETSc for its solvers}, 7735 petsc_uses = {KSP} 7736} 7737 7738@InProceedings{ dbl1, 7739 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 7740 title = {A Parallel General Purpose Finite Element System}, 7741 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 7742 publisher = {SIAM}, 7743 year = {1999}, 7744 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 7745 note = {Describes software that uses PETSc for its parallel linear solves}, 7746 petsc_uses = {KSP} 7747} 7748 7749@Article{ p1, 7750 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 7751 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 7752 and B. Smith}, 7753 journal = {Parallel Computing}, 7754 year = {2002}, 7755 pages = {1811--1831}, 7756 volume = {28 (12)}, 7757 petsc_uses = {KSP} 7758} 7759 7760@Article{ automatic-ad, 7761 author = {Paul Hovland and Boyana Norris and Barry Smith}, 7762 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 7763 year = {2005}, 7764 journal = {Future Generation Computer Systems}, 7765 volume = {21}, 7766 number = {8}, 7767 pages = {1426--1438}, 7768 petsc_uses = {KSP} 7769} 7770 7771@TechReport{ remote-math, 7772 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 7773 Smith}, 7774 title = {Remote Access to Mathematical Software}, 7775 number = {ANL/MCS-P889-0601}, 7776 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7777 month = jun, 7778 year = {2001}, 7779 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 7780 petsc_uses = {KSP} 7781} 7782 7783@InProceedings{ gropp98, 7784 author = {William D. Gropp}, 7785 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 7786 publisher = {SIAM}, 7787 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7788 Scientific and Engineering Computing}, 7789 year = {1999}, 7790 pages = {21-29}, 7791 petsc_uses = {KSP} 7792} 7793 7794@InProceedings{ knepleysarin99, 7795 author = {Matthew Knepley and Vivek Sarin}, 7796 title = {Algorithm Development for Large Scale Computing}, 7797 publisher = {SIAM}, 7798 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7799 Scientific and Engineering Computing}, 7800 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}}, 7801 year = {1999}, 7802 petsc_uses = {KSP} 7803} 7804 7805@InBook{ bgms00, 7806 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 7807 chapter = {Software for the Scalable Solution of {PDEs}}, 7808 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 7809 title = {CRPC Handbook of Parallel Computing}, 7810 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 7811 and A. White}, 7812 publisher = {Morgan Kaufmann Publishers}, 7813 year = {2002}, 7814 petsc_uses = {KSP} 7815} 7816 7817@InProceedings{ hovland_norris_smith98, 7818 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 7819 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 7820 Computations}, 7821 publisher = {SIAM}, 7822 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7823 Scientific and Engineering Computing}, 7824 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 7825 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 7826 year = {1999}, 7827 pages = {129-137}, 7828 petsc_uses = {KSP} 7829} 7830 7831@InProceedings{ efficient, 7832 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7833 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 7834 Libraries}, 7835 booktitle = {Modern Software Tools in Scientific Computing}, 7836 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 7837 publisher = {Birkhauser Press}, 7838 pages = {163--202}, 7839 year = {1997}, 7840 petsc_uses = {KSP} 7841} 7842 7843% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 7844@TechReport{ petsc-user-ref, 7845 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7846 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 7847 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7848 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7849 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7850 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7851 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7852 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7853 Zhang}, 7854 title = {{PETSc/TAO} Users Manual}, 7855 institution = {Argonne National Laboratory}, 7856 number = {ANL-21/39 - Revision 3.20}, 7857 doi = {10.2172/1968587}, 7858 year = {2023} 7859} 7860 7861% url = {https://petsc.org/release} 7862@TechReport{ petsc-developers, 7863 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 7864 title = {{PETS}c Developers Guide}, 7865 institution = {Argonne National Laboratory}, 7866 number = {ANL-18/18}, 7867 year = {2018}, 7868 url = {https://petsc.org/release/developers}, 7869 petsc_uses = {KSP} 7870} 7871 7872@Unpublished{ alice-memory-snooper, 7873 author = {Ibrahima Ba and Barry~F. Smith}, 7874 title = {The {ALICE} Memory Snooper}, 7875 year = {1999}, 7876 petsc_uses = {KSP} 7877} 7878 7879@TechReport{ petsc-user-ref-polish, 7880 author = {Marcin Bojko and Piotr Krzyzanowski}, 7881 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 7882 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 7883 year = {1998}, 7884 note = {An introduction to PETSc in Polish}, 7885 petsc_uses = {KSP} 7886} 7887 7888@InProceedings{ abghmn00, 7889 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 7890 High-Performance Scientific Computing}, 7891 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 7892 Norris}, 7893 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 7894 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 7895 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 7896 Hasco\"{e}t and Uwe Naumann}, 7897 publisher = {Springer}, 7898 year = {2002}, 7899 petsc_uses = {KSP} 7900} 7901 7902@Unpublished{ petsc-mpi-paper, 7903 author = {Lois Curfman McInnes and Barry F. Smith}, 7904 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 7905 Libraries}, 7906 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 7907 month = jun, 7908 year = {1995}, 7909 petsc_uses = {KSP} 7910} 7911 7912@InProceedings{ miss-paper, 7913 author = {William D. Gropp and Barry F. Smith}, 7914 title = {Scalable, Extensible, and Portable Numerical Libraries}, 7915 publisher = {IEEE}, 7916 year = {1994}, 7917 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7918 address = {Mississippi State University}, 7919 pages = {87--93}, 7920 keyword = {numerical libraries, scientific computing, parallel computing}, 7921 petsc_uses = {KSP} 7922} 7923 7924@InProceedings{ snes-paper, 7925 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7926 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 7927 Minimization Problems}, 7928 publisher = {IEEE}, 7929 year = {1995}, 7930 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7931 address = {Mississippi State University}, 7932 pages = {60-67}, 7933 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 7934 petsc_uses = {KSP} 7935} 7936 7937@Article{ dsneutral, 7938 author = {Barry F. Smith and William D. Gropp}, 7939 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 7940 Sparse Linear Systems}, 7941 journal = {Scientific Programming}, 7942 volume = {5}, 7943 pages = {329--336}, 7944 key = {GroppSmith96 ! KSP design}, 7945 year = {1996}, 7946 petsc_uses = {KSP} 7947} 7948 7949@InProceedings{ bgms98, 7950 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7951 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 7952 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7953 Scientific and Engineering Computing}, 7954 publisher = {SIAM}, 7955 pages = {58-67}, 7956 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 7957 year = {1998}, 7958 petsc_uses = {KSP} 7959} 7960 7961@Article{ hkm98, 7962 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 7963 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 7964 {PDE} Computation}, 7965 journal = {Advances in Engineering Software}, 7966 volume = {29}, 7967 pages = {415-424}, 7968 year = {1998}, 7969 petsc_uses = {KSP} 7970} 7971 7972@TechReport{ pdpta99, 7973 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 7974 Smith}, 7975 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 7976 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 7977 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 7978 Vegas, Nevada}, 7979 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7980 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 7981 number = {ANL/MCS-P751-0599}, 7982 year = {1999}, 7983 petsc_uses = {KSP} 7984} 7985 7986@InProceedings{ bbh:com, 7987 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 7988 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 7989 Computing}}, 7990 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 7991 Euro-Par Conference, Munich, Germany, August/September 2000}, 7992 year = {2000}, 7993 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 7994 volume = {1900}, 7995 series = {Lecture Notes in Computer Science}, 7996 pages = {86--94}, 7997 address = {Berlin}, 7998 publisher = {Springer}, 7999 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 8000 petsc_uses = {KSP} 8001} 8002 8003@InProceedings{ overture00, 8004 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8005 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 8006 Components}, 8007 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 8008 booktitle = {Proceedings of the International Federation for Information Processing Working 8009 Conference on Software Architectures for Scientific Computing, Kluwer}, 8010 year = {2000}, 8011 pages = {57--68}, 8012 petsc_uses = {KSP} 8013} 8014 8015@TechReport{ smith97, 8016 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 8017 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 8018 number = {ANL/MCS-P701}, 8019 author = {Barry F. Smith}, 8020 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8021 petsc_uses = {KSP} 8022} 8023 8024@Article{ smith98, 8025 author = {Barry Smith}, 8026 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 8027 journal = {SIGNUM Newsletter}, 8028 year = {1998}, 8029 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 8030 petsc_uses = {KSP} 8031} 8032 8033@TechReport{ ad-petsc-tm, 8034 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 8035 {PETSc}}, 8036 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 8037 year = {1997}, 8038 type = {Technical Memorandum}, 8039 institution = {ANL}, 8040 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 8041 number = {ANL/MCS-TM-233}, 8042 petsc_uses = {KSP} 8043} 8044 8045% LiteralHTML: 8046% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 8047% LiteralHTML: 8048@PhDThesis{ klotzthesis2019, 8049 author = {Thomas S. Klotz}, 8050 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 8051 Biology}, 8052 school = {Rice University}, 8053 year = {2019}, 8054 petsc_uses = {KSP} 8055} 8056 8057@Article{ klotzbardhanknepley2018, 8058 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 8059 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 8060 journal = {Communications in Applied Mathematics and Computational Science}, 8061 note = {In review}, 8062 url = {https://arxiv.org/abs/1708.06028}, 8063 year = {2018}, 8064 petsc_uses = {KSP} 8065} 8066 8067@Misc{ brown2016, 8068 title = {Threading Tradeoffs in Domain Decomposition}, 8069 author = {Jed Brown}, 8070 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 8071 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 8072 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 8073 year = {2016}, 8074 petsc_uses = {KSP} 8075} 8076 8077@Article{ changnakshatralaknepleyjohnsson2017, 8078 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 8079 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 8080 Johnsson}, 8081 journal = {Concurency: Practice and Experience}, 8082 volume = {30}, 8083 number = {11}, 8084 eprint = {1705.03625}, 8085 doi = {10.1002/cpe.4401}, 8086 year = {2017}, 8087 petsc_uses = {KSP} 8088} 8089 8090@Article{ changfabienknepleymills2018, 8091 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 8092 spectrum analysis}, 8093 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 8094 journal = {SIAM Journal on Scientific Computing}, 8095 volume = {40}, 8096 number = {6}, 8097 pages = {C779--C802}, 8098 eprint = {1802.07832}, 8099 doi = {10.1137/18M1172260}, 8100 year = {2018}, 8101 petsc_uses = {KSP} 8102} 8103 8104@Article{ joshaghanichangnakshatralaknepley2019, 8105 title = {Composable solvers for the four-field double porosity/permeability model}, 8106 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 8107 Knepley}, 8108 journal = {Journal of Computational Physics}, 8109 volume = {386}, 8110 pages = {428--466}, 8111 doi = {10.1016/j.jcp.2019.02.020}, 8112 year = {2019}, 8113 petsc_uses = {KSP} 8114} 8115 8116@InProceedings{ barralknepleylangepiggottgorman2016, 8117 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 8118 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 8119 and Gerard J. Gorman}, 8120 booktitle = {25th International Meshing Roundtable}, 8121 editor = {Steve Owen and Hang Si}, 8122 month = sep, 8123 address = {Washington, DC}, 8124 pages = {1--5}, 8125 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 8126 year = {2016}, 8127 petsc_uses = {KSP} 8128} 8129 8130@Article{ adamsbrownknepleysamtaney2016, 8131 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 8132 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 8133 journal = {SIAM Journal on Scientific Computing}, 8134 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 8135 epub = {http://arxiv.org/abs/1406.7808}, 8136 volume = {8}, 8137 number = {4}, 8138 pages = {C426--C440}, 8139 doi = {10.1137/140975127}, 8140 year = {2016}, 8141 petsc_uses = {KSP} 8142} 8143 8144@InProceedings{ maysananruppknepleysmith2016, 8145 title = {Extreme-Scale Multigrid Components within {PETSc}}, 8146 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 8147 Smith}, 8148 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 8149 series = {PASC '16}, 8150 isbn = {978-1-4503-4126-4}, 8151 location = {Lausanne, Switzerland}, 8152 pages = {5:1--5:12}, 8153 articleno = {5}, 8154 numpages = {12}, 8155 doi = {10.1145/2929908.2929913}, 8156 acmid = {2929913}, 8157 publisher = {ACM}, 8158 address = {New York, NY, USA}, 8159 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 8160 preconditioning}, 8161 year = {2016}, 8162 petsc_uses = {KSP} 8163} 8164 8165@Article{ liu2015field, 8166 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 8167 author = {Lulu Liu and David E Keyes}, 8168 journal = {SIAM Journal on Scientific Computing}, 8169 volume = {37}, 8170 number = {3}, 8171 pages = {A1388--A1409}, 8172 year = {2015}, 8173 publisher = {SIAM}, 8174 petsc_uses = {KSP} 8175} 8176 8177@Article{ lujiaomissirlis2014, 8178 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 8179 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 8180 journal = {Numerical Linear Algebra with Applications}, 8181 volume = {21}, 8182 number = {2}, 8183 pages = {221--238}, 8184 year = {2014}, 8185 publisher = {Wiley Online Library}, 8186 petsc_uses = {KSP} 8187} 8188 8189@Article{ badiamartinprincipe2013, 8190 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 8191 solid mechanics}, 8192 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 8193 journal = {International Journal for Numerical Methods in Engineering}, 8194 volume = {96}, 8195 number = {4}, 8196 pages = {203--230}, 8197 year = {2013}, 8198 petsc_uses = {KSP} 8199} 8200 8201@Article{ morganknepleysananscott2016, 8202 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 8203 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 8204 journal = {Concurrency and Computation: Practice and Experience}, 8205 volume = {28}, 8206 pages = {4532--4542}, 8207 year = {2016}, 8208 url = {http://arxiv.org/abs/1602.04873}, 8209 doi = {10.1002/cpe.3820}, 8210 petsc_uses = {KSP} 8211} 8212 8213@Article{ morgansananknepleymills2020, 8214 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 8215 solvers}, 8216 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 8217 journal = {The International Journal of High Performance Computing Applications}, 8218 volume = {35}, 8219 issue = {1}, 8220 doi = {10.1177/1094342020966835}, 8221 url = {https://doi.org/10.1177/1094342020966835}, 8222 eprint = {https://doi.org/10.1177/1094342020966835}, 8223 year = {2020}, 8224 petsc_uses = {KSP} 8225} 8226 8227@Article{ msz2013, 8228 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 8229 author = {M. McCourt and B. F. Smith and H. Zhang}, 8230 journal = {SIAM Journal on Matrix Analysis and Applications}, 8231 year = {2015}, 8232 note = {To appear}, 8233 petsc_uses = {KSP} 8234} 8235 8236@Article{ bassi2014agglomeration, 8237 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 8238 free}, 8239 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 8240 journal = {Mathematical Models and Methods in Applied Sciences}, 8241 volume = {24}, 8242 number = {08}, 8243 pages = {1495--1539}, 8244 year = {2014}, 8245 publisher = {World Scientific}, 8246 petsc_uses = {KSP} 8247} 8248 8249@Article{ jhuranidemkowicz12, 8250 author = {{Jhurani}, C. and {Demkowicz}, L.}, 8251 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 8252 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 8253 journal = {Computer Methods in Applied Mechanics and Engineering}, 8254 volume = {213}, 8255 pages = {418-426}, 8256 year = {2012}, 8257 month = mar, 8258 doi = {10.1016/j.cma.2011.06.003}, 8259 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 8260 petsc_uses = {KSP} 8261} 8262 8263@Article{ yangcai11, 8264 author = {Yang, Haijian and Cai, Xiao-Chuan}, 8265 title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear 8266 Complementarity Problems}, 8267 journal = {J. Sci. Comput.}, 8268 issue_date = {May 2011}, 8269 volume = {47}, 8270 number = {2}, 8271 month = may, 8272 pages = {258--280}, 8273 year = {2011}, 8274 issn = {0885-7474}, 8275 numpages = {23}, 8276 doi = {10.1007/s10915-010-9436-4}, 8277 acmid = {1971246}, 8278 publisher = {Plenum Press}, 8279 address = {New York, NY, USA}, 8280 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 8281 preconditioners, Semismooth Newton, Two-level methods}, 8282 petsc_uses = {KSP} 8283} 8284 8285@Article{ rheinbach09, 8286 author = {Rheinbach, Oliver}, 8287 title = {Parallel Iterative Substructuring in Structural Mechanics}, 8288 journal = {Archives of Computational Methods in Engineering}, 8289 volume = {16}, 8290 number = {4}, 8291 pages = {425-463}, 8292 year = {2009}, 8293 issn = {1134-3060}, 8294 doi = {10.1007/s11831-009-9035-4}, 8295 publisher = {Springer Netherlands}, 8296 language = {English}, 8297 petsc_uses = {KSP} 8298} 8299 8300@Article{ knepleyterrel2013, 8301 author = {Matthew G. Knepley and Andy R. Terrel}, 8302 title = {Finite Element Integration on {GPUs}}, 8303 journal = {{ACM} Transactions on Mathematical Software}, 8304 volume = {39}, 8305 number = {2}, 8306 accepted = {17 April 2012}, 8307 year = {2013}, 8308 abstract = {We present a novel finite element integration method for low order elements on 8309 GPUs. We achieve more than 100GF for element integration on first order 8310 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 8311 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 8312 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 8313 url = {http://arxiv.org/abs/1103.0066}, 8314 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 8315 petsc_uses = {KSP} 8316} 8317 8318@Article{ knepleyruppterrel2016, 8319 title = {Finite Element Integration with Quadrature on the GPU}, 8320 journal = {ArXiv e-prints}, 8321 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 8322 version = {1}, 8323 date = {2016-07-14}, 8324 eprinttype = {arxiv}, 8325 eprintclass = {cs.MS}, 8326 eprint = {1607.04245v1}, 8327 petsc_uses = {KSP} 8328} 8329 8330@Article{ klawonnlanserrheinbach2014, 8331 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 8332 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 8333 journal = {SIAM Journal on Scientific Computing}, 8334 volume = {36}, 8335 number = {2}, 8336 pages = {A737--A765}, 8337 year = {2014}, 8338 petsc_uses = {KSP} 8339} 8340 8341@TechReport{ pbmkbsxt2012, 8342 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8343 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8344 year = {2013}, 8345 type = {Preprint}, 8346 number = {ANL/MCS-P2010-0112}, 8347 institution = {Argonne National Laboratory}, 8348 petsc_uses = {KSP} 8349} 8350 8351@Article{ bruneknepleysmithtu15, 8352 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8353 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8354 journal = {SIAM Review}, 8355 volume = {57}, 8356 number = {4}, 8357 pages = {535--565}, 8358 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 8359 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 8360 doi = {10.1137/130936725}, 8361 year = {2015}, 8362 petsc_uses = {KSP} 8363} 8364 8365@Article{ mszm2014, 8366 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 8367 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8368 volume = {40}, 8369 pages = {17--31}, 8370 year = {2014}, 8371 journal = {Parallel Computing}, 8372 doi = {10.1016/j.parco.2013.10.001}, 8373 petsc_uses = {KSP} 8374} 8375 8376@TechReport{ mszm2012, 8377 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 8378 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8379 year = {2012}, 8380 number = {ANL/MCS-P2097-0512}, 8381 institution = {Argonne National Laboratory}, 8382 petsc_uses = {KSP} 8383} 8384 8385@InProceedings{ bkmms2012, 8386 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 8387 F. Smith}, 8388 title = {Composable linear solvers for multiphysics}, 8389 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 8390 Computing} ({ISPDC} 2012)}, 8391 year = {2012}, 8392 doi = {10.1109/ISPDC.2012.16}, 8393 publisher = {IEEE Computer Society}, 8394 pages = {55--62}, 8395 petsc_uses = {KSP} 8396} 8397 8398@Article{ bourdinbucuroudet2009, 8399 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 8400 title = {Optimal Partitions for Eigenvalues}, 8401 journal = {SIAM J. Sci. Comput.}, 8402 volume = {31}, 8403 number = {6}, 8404 pages = {4100--4114}, 8405 year = {2009}, 8406 petsc_uses = {KSP} 8407} 8408 8409@InBook{ kimnbourdin2007, 8410 author = {J.-H. Kimn and Blaise Bourdin}, 8411 title = {Numerical implementation of overlapping balancing domain decomposition methods on 8412 unstructured meshes}, 8413 editor = {O. B. Widlund and D. E. Keyes}, 8414 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 8415 series = {Lecture Notes in Computational Science and Engineering}, 8416 number = {55}, 8417 publisher = {Springer-Verlag}, 8418 pages = {309--315}, 8419 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 8420 year = {2007}, 8421 petsc_uses = {KSP} 8422} 8423 8424@Article{ bjm2005, 8425 author = {AH Baker and ER Jessup and T Manteuffel}, 8426 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 8427 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 8428 year = {2005}, 8429 petsc_uses = {KSP} 8430} 8431 8432@Unpublished{ sundar-2008a, 8433 author = {R.S. Sampath and G. Biros}, 8434 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 8435 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8436 petsc_uses = {KSP} 8437} 8438 8439@Article{ sundar-2008, 8440 author = {H. Sundar and R.S. Sampath and G. Biros}, 8441 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 8442 journal = {SIAM Journal on Scientific Computing}, 8443 year = {2008}, 8444 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8445 petsc_uses = {KSP} 8446} 8447 8448@InProceedings{ sundar-2007, 8449 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8450 title = {Low-constant parallel algorithms for finite element simulations using linear 8451 octrees}, 8452 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 8453 year = {2007}, 8454 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8455 petsc_uses = {KSP} 8456} 8457 8458@InProceedings{ adams-98a, 8459 author = {Adams, Mark ~F.}, 8460 title = {A Parallel Maximal Independent Set Algorithm}, 8461 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 8462 year = {1998}, 8463 petsc_uses = {KSP} 8464} 8465 8466@Article{ akcelik2005ddd, 8467 title = {{Dynamic data-driven inversion for terascale simulations: real-time 8468 identification of airborne contaminants}}, 8469 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 8470 van Bloemen Waanders, B.}, 8471 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 8472 year = {2005}, 8473 publisher = {IEEE Computer Society Washington, DC, USA}, 8474 petsc_uses = {KSP} 8475} 8476 8477@InBook{ akcelik-2006, 8478 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 8479 Bloemen Waanders}, 8480 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 8481 title = {Frontiers of Parallel Computing}, 8482 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 8483 publisher = {SIAM}, 8484 year = {2006}, 8485 petsc_uses = {KSP} 8486} 8487 8488@Article{ dt, 8489 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 8490 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 8491 Convection Diffusion Equations}, 8492 journal = {The Journal of Supercomputing}, 8493 year = {2004}, 8494 pages = {235--253}, 8495 volume = {28}, 8496 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 8497 petsc_uses = {KSP} 8498} 8499 8500@PhDThesis{ hwang2004, 8501 author = {Feng-Nan Hwang}, 8502 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 8503 Computational Fluid Dynamics}, 8504 school = {University of Colorado at Boulder}, 8505 year = {2004}, 8506 petsc_uses = {KSP} 8507} 8508 8509@PhDThesis{ baker, 8510 author = {{A. H.} Baker}, 8511 title = {On improving the performance of the linear solver restarted {GMRES}}, 8512 school = {University of Colorado at Boulder}, 8513 year = {2003}, 8514 petsc_uses = {KSP} 8515} 8516 8517@TechReport{ klawonnrheinbach601, 8518 author = {Axel Klawonn and Oliver Rheinbach}, 8519 title = {A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional 8520 Linear Elasticity Using a Transformation of Basis}, 8521 institution = {Universit\"at Duisburg-Essen}, 8522 year = {2005}, 8523 type = {Technical Report}, 8524 number = {SM-E-601}, 8525 petsc_uses = {KSP} 8526} 8527 8528@TechReport{ klawonnrheinbach609, 8529 author = {Axel Klawonn and Oliver Rheinbach}, 8530 title = {Inexact FETI-DP Methods}, 8531 institution = {Universit\"at Duisburg-Essen}, 8532 year = {2005}, 8533 type = {Technical Report}, 8534 number = {SM-E-609}, 8535 petsc_uses = {KSP} 8536} 8537 8538@TechReport{ klawonnrheinbach607, 8539 author = {Axel Klawonn and Oliver Rheinbach}, 8540 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 8541 institution = {Universit\"at Duisburg-Essen}, 8542 year = {2005}, 8543 type = {Technical Report}, 8544 number = {SM-E-607}, 8545 petsc_uses = {KSP} 8546} 8547 8548@Article{ kul-natraj-pbp, 8549 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 8550 title = {Performance of a parallel mixed finite element implementation for fourth order 8551 clamped anisotropic plate bending problems in distributed memory environments}, 8552 journal = {Applied Mathematics and Computation}, 8553 volume = {155}, 8554 year = {2004}, 8555 number = {3}, 8556 pages = {753--777}, 8557 petsc_uses = {KSP} 8558} 8559 8560@Article{ bramkamp2006uej, 8561 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 8562 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 8563 journal = {Computers \& Fluids}, 8564 volume = {35}, 8565 number = {10}, 8566 pages = {1063--1073}, 8567 doi = {10.1016/j.compfluid.2005.10.003}, 8568 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 8569 derivation of the analytic flux Jacobian can become quite complicated depending on 8570 the complexity of the numerical flux calculation. Practically, the derivation of 8571 the exact Jacobian by hand is an unrealistic option because of the enormous 8572 man-hour investment needed. In this work, automatic differentiation is used to 8573 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 8574 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 8575 approximated by first-order forward differences. For a two-dimensional airfoil 8576 under three different flight conditions (quasi-incompressible flow, compressible 8577 subsonic flow, and transonic flow), we show that the robustness and performance of 8578 the present finite volume scheme is significantly improved by using exact 8579 Jacobians.}, 8580 year = {2006}, 8581 petsc_uses = {KSP} 8582} 8583 8584@Article{ shahbazi1, 8585 author = {Khosro Shahbazi}, 8586 title = {An explicit expression for the penalty parameter of the interior penalty method}, 8587 journal = {Journal of Computational Physics}, 8588 volume = {205}, 8589 year = {2005}, 8590 pages = {401--407}, 8591 petsc_uses = {KSP} 8592} 8593 8594@TechReport{ kk, 8595 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 8596 author = {Hans-Peter Kersken and Uwe Kuster}, 8597 year = {1999}, 8598 institution = {University of Stuttgart}, 8599 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 8600 number = {310}, 8601 petsc_uses = {KSP} 8602} 8603 8604@Article{ miha-mija, 8605 author = {M. D. Mihajlovi and S. Mijalkovi}, 8606 title = {A component decomposition preconditioning for 3D stress analysis problems}, 8607 journal = {Numerical Linear Algebra with Applications}, 8608 volume = {9}, 8609 year = {2002}, 8610 pages = {567--583}, 8611 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 8612 petsc_uses = {KSP} 8613} 8614 8615@Article{ bjm, 8616 author = {M Benzi and W Joubert and G Mateescu}, 8617 journal = {Electronic Transactions on Numerical Analysis}, 8618 year = {1999}, 8619 volume = {8}, 8620 pages = {88--114}, 8621 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 8622 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}, 8623 petsc_uses = {KSP} 8624} 8625 8626@PhDThesis{ hyde, 8627 author = {EMK Hyde}, 8628 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 8629 school = {Caltech}, 8630 year = {2003}, 8631 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 8632 petsc_uses = {KSP} 8633} 8634 8635@Article{ km2003, 8636 author = {A. Keese and H. G. Matthies}, 8637 journal = {Proceedings in Applied Mathematics and Mechanics}, 8638 year = {2003}, 8639 volume = {2}, 8640 pages = {485--486}, 8641 title = {Parallel Solution of Stochastic PDEs}, 8642 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 8643 petsc_uses = {KSP} 8644} 8645 8646@Article{ whszss, 8647 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 8648 and Otmar Scherzer and H. Siegfried Stiehl}, 8649 journal = {Real Time Imaging}, 8650 year = {2001}, 8651 volume = {7}, 8652 pages = {31--45}, 8653 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 8654 approaches}, 8655 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 8656 petsc_uses = {KSP} 8657} 8658 8659@TechReport{ baker1, 8660 title = {An Efficient Block Variant of GMRES}, 8661 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 8662 year = {2003}, 8663 type = {Technical Report}, 8664 institution = {University of Colorado, Boulder}, 8665 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 8666 number = {CU-CS-957-03}, 8667 petsc_uses = {KSP} 8668} 8669 8670@InProceedings{ mc2003, 8671 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 8672 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 8673 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8674 Methods}, 8675 pages = {639--646}, 8676 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8677 note = {}, 8678 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8679 year = {2003}, 8680 petsc_uses = {KSP} 8681} 8682 8683@InProceedings{ kt2003, 8684 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 8685 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 8686 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8687 Methods}, 8688 pages = {615--622}, 8689 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8690 note = {}, 8691 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8692 year = {2003}, 8693 petsc_uses = {KSP} 8694} 8695 8696@InProceedings{ krw2003, 8697 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 8698 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 8699 3D}, 8700 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8701 Methods}, 8702 pages = {361--368}, 8703 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8704 note = {}, 8705 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8706 year = {2003}, 8707 petsc_uses = {KSP} 8708} 8709 8710@InProceedings{ hc2003, 8711 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 8712 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 8713 Nonlinear Preconditioning}, 8714 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8715 Methods}, 8716 pages = {201--208}, 8717 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8718 note = {}, 8719 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8720 year = {2003}, 8721 petsc_uses = {KSP} 8722} 8723 8724@InProceedings{ g2003, 8725 author = {P. Goldfeld}, 8726 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 8727 (Generalized) {Stokes} and Parallel Implementation}, 8728 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8729 Methods}, 8730 pages = {209--216}, 8731 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8732 publisher = {National Autonomous University of Mexico (UNAM)}, 8733 note = {}, 8734 url = {http://www.ddm.org/DD14}, 8735 year = {2003}, 8736 petsc_uses = {KSP} 8737} 8738 8739@InProceedings{ dhv2003, 8740 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 8741 title = {Toward scalable FETI algorithm for variational inequalities with applications to 8742 composites}, 8743 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8744 Methods}, 8745 pages = {395--401}, 8746 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8747 publisher = {National Autonomous University of Mexico (UNAM)}, 8748 note = {}, 8749 url = {http://www.ddm.org/DD14}, 8750 year = {2003}, 8751 petsc_uses = {KSP} 8752} 8753 8754@InProceedings{ dhsv2002, 8755 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 8756 title = {Scalabilities of FETI for variational inequalities and contact shape 8757 optimization}, 8758 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8759 Methods}, 8760 pages = {359--367}, 8761 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8762 publisher = {CIMNE, Barcelona, Spain}, 8763 note = {}, 8764 url = {http://www.ddm.org/DD13}, 8765 year = {2002}, 8766 petsc_uses = {KSP} 8767} 8768 8769@InProceedings{ cky2002, 8770 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 8771 title = {A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked 8772 Duct Flows}, 8773 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8774 Methods}, 8775 pages = {343--350}, 8776 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8777 publisher = {CIMNE, Barcelona, Spain}, 8778 note = {}, 8779 url = {http://www.ddm.org/DD13}, 8780 year = {2002}, 8781 petsc_uses = {KSP} 8782} 8783 8784@Conference{ li-etal:03, 8785 author = {Li, Z. and Lanteri S. and Saad, Y.}, 8786 title = {Multiplicative-additive preconditioning combination for general sparse linear 8787 systems}, 8788 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 8789 Matrix Problems in Scientific and Industrial Applications}, 8790 address = {Napa, California, USA}, 8791 date = {october 27-29}, 8792 year = {2003}, 8793 petsc_uses = {KSP} 8794} 8795 8796@Article{ bashir2008hessian, 8797 title = {Hessian-based model reduction for large-scale systems with initial-condition 8798 inputs}, 8799 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 8800 J.}, 8801 journal = {International journal for numerical methods in engineering}, 8802 volume = {73}, 8803 number = {6}, 8804 pages = {844--868}, 8805 year = {2008}, 8806 publisher = {Wiley Online Library}, 8807 petsc_uses = {KSP} 8808} 8809 8810@Article{ bashir2007hessian, 8811 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 8812 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 8813 K.}, 8814 journal = {Computational Science--ICCS 2007}, 8815 pages = {1010--1017}, 8816 year = {2007}, 8817 publisher = {Springer}, 8818 petsc_uses = {KSP} 8819} 8820 8821@Article{ akcelik2011fast, 8822 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 8823 inverse problems based on low-rank partial {H}essian approximations}, 8824 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 8825 Waanders, B. and Wilcox, L.}, 8826 journal = {SIAM Journal on Scientific Computing}, 8827 volume = {33}, 8828 number = {1}, 8829 year = {2011}, 8830 petsc_uses = {KSP} 8831} 8832 8833@InProceedings{ ff2003, 8834 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 8835 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 8836 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 8837 year = {2003}, 8838 petsc_uses = {KSP} 8839} 8840 8841@InProceedings{ d2b2004, 8842 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 8843 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 8844 Ordering Strategies}, 8845 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 8846 year = {2004}, 8847 petsc_uses = {KSP} 8848} 8849 8850@InProceedings{ d2v2005, 8851 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8852 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 8853 Flow Equations}, 8854 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 8855 year = {2005}, 8856 petsc_uses = {KSP} 8857} 8858 8859@InProceedings{ dvs2006, 8860 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 8861 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 8862 Mixed Convection Equations}, 8863 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 8864 year = {2006}, 8865 petsc_uses = {KSP} 8866} 8867 8868@Article{ dsv2006, 8869 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8870 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 8871 Flow Equations}, 8872 journal = {Computational Fluid Dynamics}, 8873 year = {2006}, 8874 volume = {15}, 8875 number = {1}, 8876 petsc_uses = {KSP} 8877} 8878 8879@Article{ lahaye03, 8880 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 8881 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 8882 journal = {J. Comput. Appl. Math.}, 8883 year = {2004}, 8884 pages = {267--275}, 8885 volume = {168}, 8886 petsc_uses = {KSP} 8887} 8888 8889@TechReport{ brmn, 8890 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 8891 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 8892 year = {2002}, 8893 type = {Technical Report}, 8894 institution = {ANL}, 8895 number = {ANL/MCS-P993-0902}, 8896 note = {To appear in Future Generation Computer Systems}, 8897 petsc_uses = {KSP} 8898} 8899 8900@InProceedings{ mnbr, 8901 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 8902 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 8903 Algorithms}, 8904 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 8905 Mechanics}, 8906 year = {2003}, 8907 petsc_uses = {KSP} 8908} 8909 8910@InProceedings{ bmnr, 8911 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 8912 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 8913 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 8914 Applications, Lecture notes in Computer Science 2677}, 8915 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 8916 pages = {828--839}, 8917 year = {2003}, 8918 petsc_uses = {KSP} 8919} 8920 8921@Article{ ph03, 8922 author = {M. Pernice and R. D. Hornung}, 8923 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 8924 journal = {Computing and Visualization in Science}, 8925 year = {2003}, 8926 lab = {LANL}, 8927 petsc_uses = {KSP} 8928} 8929 8930@Article{ adams-02, 8931 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 8932 journal = {J. Comp. Phys.}, 8933 number = {2}, 8934 pages = {593-610}, 8935 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 8936 volume = {188}, 8937 year = {2003}, 8938 petsc_uses = {KSP} 8939} 8940 8941@InProceedings{ adams2001distributed, 8942 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 8943 smoothers}, 8944 author = {Adams, M.F.}, 8945 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 8946 pages = {14--14}, 8947 year = {2001}, 8948 organization = {IEEE}, 8949 petsc_uses = {KSP} 8950} 8951 8952@PhDThesis{ els01, 8953 author = {Ulrich Elsner}, 8954 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 8955 algorithms}, 8956 school = {Technical University Chemnitz}, 8957 year = {2002}, 8958 publisher = {Logos Verlag, Berlin}, 8959 isbn = {3-89722-923-4}, 8960 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 8961 different graph partitioning algorithms}, 8962 petsc_uses = {KSP} 8963} 8964 8965@TechReport{ ckk02, 8966 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 8967 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 8968 year = {2002}, 8969 type = {Technical Report}, 8970 institution = {ODU}, 8971 url = {http://www.math.odu.edu/\~{ }keyes}, 8972 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 8973 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 8974 Methods}, 8975 petsc_uses = {KSP} 8976} 8977 8978@Article{ gpw2002, 8979 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 8980 Heterogeneous Problems in Linear Elasticity}, 8981 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 8982 year = {2003}, 8983 pages = {283--324}, 8984 volume = {95}, 8985 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 8986 journal = {Numerische Mathematik}, 8987 petsc_uses = {KSP} 8988} 8989 8990@Article{ dh1, 8991 title = {Scalability and FETI based algorithm for large discretized variational 8992 inequalities}, 8993 author = {Z Dostal and D Horak}, 8994 year = {2003}, 8995 pages = {347--357}, 8996 volume = {61}, 8997 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 8998 journal = {Mathematics and Computers in Simulation}, 8999 petsc_uses = {KSP} 9000} 9001 9002@InProceedings{ dhsv1, 9003 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9004 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 9005 title = {36 Scalabilities of FETI for Variational Inequalities and Contact Shape 9006 Optimization}, 9007 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9008 Methods}, 9009 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9010 Kuznetsov}, 9011 petsc_uses = {KSP} 9012} 9013 9014@Article{ lahaye02, 9015 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 9016 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 9017 journal = {IEEEMAGN}, 9018 year = {2002}, 9019 volume = {38}, 9020 number = {2}, 9021 pages = {413-416}, 9022 petsc_uses = {KSP} 9023} 9024 9025@Article{ ckm01, 9026 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 9027 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 9028 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 9029 fluid dynamics}, 9030 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 9031 year = {2002}, 9032 volume = {40}, 9033 pages = {1463--1470}, 9034 petsc_uses = {KSP} 9035} 9036 9037@InProceedings{ cky01, 9038 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 9039 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 9040 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 9041 duct flow}, 9042 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9043 Methods}, 9044 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9045 Kuznetsov}, 9046 year = {2002}, 9047 petsc_uses = {KSP} 9048} 9049 9050@Article{ ck02, 9051 author = {X.-C. Cai and D. E. Keyes}, 9052 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 9053 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 9054 journal = {SIAM J. Sci. Comput.}, 9055 year = {2002}, 9056 pages = {183--200}, 9057 volume = {24}, 9058 petsc_uses = {KSP} 9059} 9060 9061@Article{ c04, 9062 author = {Feng-Nan Hwang and X.-C. Cai}, 9063 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 9064 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 9065 for incompressible {Navier-Stokes} equations}, 9066 journal = {Journal of Computational Physics}, 9067 year = {2005}, 9068 volume = {204}, 9069 pages = {666--691}, 9070 petsc_uses = {KSP} 9071} 9072 9073@Article{ hc06, 9074 author = {Feng-Nan Hwang and X.-C. Cai}, 9075 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 9076 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 9077 Algorithms}, 9078 journal = {Computer Methods in Applied Mechanics and Engineering}, 9079 year = {2006}, 9080 volume = {196}, 9081 pages = {1603--1611}, 9082 petsc_uses = {KSP} 9083} 9084 9085@InProceedings{ adams-01, 9086 author = {Mark F. Adams}, 9087 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 9088 Smoothers}, 9089 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 9090 address = {Denver, Colorado}, 9091 month = nov, 9092 year = {2001}, 9093 petsc_uses = {KSP} 9094} 9095 9096@Book{ 1dl, 9097 author = {Domenico Lahaye}, 9098 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 9099 Computations}, 9100 year = {2001}, 9101 publisher = {Katholieke Universiteit Leuven}, 9102 notes = {Thesis}, 9103 petsc_uses = {KSP} 9104} 9105 9106@Article{ adams-00, 9107 author = {Adams, M.~F.}, 9108 journal = {International Journal for Numerical Methods in Engineering}, 9109 number = {8}, 9110 pages = {1241-1262}, 9111 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 9112 Deformation Elasticity and Plasticity}, 9113 volume = {48}, 9114 year = {2000}, 9115 petsc_uses = {KSP} 9116} 9117 9118@Article{ adams2002evaluation, 9119 author = {Adams, M.~F.}, 9120 journal = {International Journal for Numerical Methods in Engineering}, 9121 number = {1}, 9122 pages = {519-534}, 9123 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 9124 Problems in Solid Mechanics}, 9125 volume = {55}, 9126 year = {2002}, 9127 petsc_uses = {KSP} 9128} 9129 9130@Article{ lahaye00, 9131 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 9132 title = {Algebraic Multigrid for Complex Symmetric Systems}, 9133 journal = {IEEEMAGN}, 9134 year = {2000}, 9135 volume = {36}, 9136 number = {4}, 9137 pages = {1535--1538}, 9138 petsc_uses = {KSP} 9139} 9140 9141@InProceedings{ adams-99c, 9142 author = {Mark F. Adams and J. Demmel}, 9143 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 9144 Finite Element Problems}, 9145 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 9146 address = {Portland, Oregon}, 9147 month = nov, 9148 year = {1999}, 9149 petsc_uses = {KSP} 9150} 9151 9152@Article{ chan95, 9153 author = {T. Chan and B. Smith and J. Zou}, 9154 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 9155 Grids}, 9156 journal = {Numer. Math.}, 9157 year = {1995}, 9158 volume = {73}, 9159 pages = {149--167}, 9160 petsc_uses = {KSP} 9161} 9162 9163@TechReport{ adams-csd-98-993, 9164 pages = {11}, 9165 year = {1998}, 9166 type = {Technical Report}, 9167 number = {CSD-98-993}, 9168 institution = {University of California, Berkeley}, 9169 title = {A Parallel Maximal Independent Set Algorithm}, 9170 bibdate = {March 11, 1998}, 9171 author = {Mark F. Adams and James Demmel}, 9172 abstract = {The parallel construction of maximal independent sets is a useful building block 9173 for many algorithms in the computational sciences, including graph coloring and 9174 multigrid coarse grid creation on unstructured meshes. We present an efficient 9175 asynchronous maximal independent set algorithm for use on parallel computers, for 9176 ``well partitioned'' graphs, that arise from finite element (FE) models. For 9177 appropriately partitioned bounded degree graphs, it is shown that the running time 9178 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 9179 improvement over the previous best P-RAM complexity for this class of graphs. We 9180 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 9181 model is indicative of the performance one can expect with practical partitions on 9182 graphs from FE problems.}, 9183 month = mar, 9184 petsc_uses = {KSP} 9185} 9186 9187@TechReport{ k676, 9188 year = {1994}, 9189 type = {Technical Report}, 9190 number = {TR1994-676}, 9191 institution = {New York University}, 9192 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 9193 Term}, 9194 author = {Axel Klawonn}, 9195 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 9196 petsc_uses = {KSP} 9197} 9198 9199@Book{ ak1, 9200 author = {Axel Klawonn}, 9201 title = {Preconditioners for Indefinite Problems}, 9202 year = {1995}, 9203 publisher = {Westfalishen Wilhelms-Universitat Munster}, 9204 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 9205 notes = {Thesis}, 9206 petsc_uses = {KSP} 9207} 9208 9209@TechReport{ knepleykarpeev05, 9210 pages = {41}, 9211 year = {2005}, 9212 type = {Technical Report}, 9213 number = {ANL/MCS-P1295-1005}, 9214 institution = {Argonne National Laboratory}, 9215 title = {Flexible Representation of Computational Meshes}, 9216 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9217 abstract = {}, 9218 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 9219 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 9220 month = oct, 9221 petsc_uses = {DMPlex} 9222} 9223 9224@TechReport{ knepleykarpeev07a, 9225 pages = {14}, 9226 year = {2007}, 9227 type = {Technical Report}, 9228 number = {ANL/MCS-P1455-0907}, 9229 institution = {Argonne National Laboratory}, 9230 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9231 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9232 abstract = {}, 9233 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 9234 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 9235 month = feb, 9236 petsc_uses = {DMPlex} 9237} 9238 9239@Article{ knepleykarpeev09, 9240 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9241 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9242 journal = {Scientific Programming}, 9243 volume = {17}, 9244 number = {3}, 9245 pages = {215--230}, 9246 year = {2009}, 9247 doi = {10.3233/SPR-2009-0249}, 9248 url = {http://arxiv.org/abs/0908.4427}, 9249 note = {\url{http://arxiv.org/abs/0908.4427}}, 9250 petsc_uses = {DMPlex} 9251} 9252 9253@Article{ biezuner2012computing, 9254 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 9255 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 9256 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 9257 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 9258 Sublinear Supersolutions}, 9259 journal = {Journal of Scientific Computing}, 9260 publisher = {Springer Netherlands}, 9261 issn = {0885-7474}, 9262 keyword = {Mathematics and Statistics}, 9263 pages = {180--201}, 9264 volume = {52}, 9265 issue = {1}, 9266 year = {2012}, 9267 doi = {10.1007/s10915-011-9540-0}, 9268 petsc_uses = {KSP} 9269} 9270 9271% LiteralHTML: 9272% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 9273% LiteralHTML: 9274@Book{ knepley2017, 9275 title = {Computational Science I}, 9276 author = {Matthew G. Knepley}, 9277 url = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}, 9278 note = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}}, 9279 publisher = {PETSc}, 9280 year = {2017}, 9281 petsc_uses = {KSP} 9282} 9283 9284@Article{ verleyeuser, 9285 title = {{User friendly permeability predicting software for technical textiles}}, 9286 author = {Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and 9287 Roose, D.}, 9288 journal = {status: published}, 9289 issn = {1560-6074}, 9290 publisher = {Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}, 9291 petsc_uses = {KSP} 9292} 9293 9294@Book{ pacheco, 9295 author = {Peter Pacheco}, 9296 title = {Parallel Programming with MPI}, 9297 year = {1997}, 9298 publisher = {Morgan-Kaufmann}, 9299 note = {Devotes a couple of sections to PETSc}, 9300 petsc_uses = {KSP} 9301} 9302 9303@Book{ 1sbg, 9304 author = {Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp}, 9305 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 9306 Differential Equations}, 9307 year = {1996}, 9308 publisher = {Cambridge University Press}, 9309 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 9310 petsc_uses = {KSP} 9311} 9312 9313@Misc{ petsc-fem:homepage, 9314 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 9315 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 9316 G. Rodriguez and G. Filippini}, 9317 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 9318 petsc_uses = {KSP} 9319} 9320 9321@Misc{ petsc4py-web-page, 9322 author = {Lisandro Dalcin}, 9323 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 9324 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 9325 note = {http://code.google.com/p/petsc4py/}, 9326 petsc_uses = {KSP} 9327} 9328 9329@Article{ libmeshpaper06, 9330 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 9331 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 9332 Simulations}}, 9333 journal = {Engineering with Computers}, 9334 volume = {22}, 9335 number = {3--4}, 9336 pages = {237--254}, 9337 year = {2006}, 9338 doi = {10.1007/s00366-006-0049-3}, 9339 petsc_uses = {KSP} 9340} 9341 9342@Misc{ sisiphus:homepage, 9343 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 9344 High-Resolution, Unstructured Simulations}, 9345 author = {T. {Tautges et al.}}, 9346 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 9347 petsc_uses = {KSP} 9348} 9349 9350@Misc{ pflotran:homepage, 9351 title = {{PFLOTRAN} project}, 9352 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 9353 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 9354 howpublished = {\url{http://pflotran.org/}}, 9355 petsc_uses = {KSP} 9356} 9357 9358@Misc{ pism:homepage, 9359 title = {{PISM}: A Parallel Ice Sheet Model}, 9360 author = {E. {Bueler et al.}}, 9361 howpublished = {\url{http://pism-docs.org}}, 9362 petsc_uses = {KSP} 9363} 9364 9365@Misc{ dohp:homepage, 9366 title = {Dohp: Dual order $hp$-finite elements}, 9367 author = {J. Brown}, 9368 howpublished = {\url{http://dohp.org}}, 9369 petsc_uses = {KSP} 9370} 9371 9372@Article{ mccourtrognlienetal12, 9373 title = {Improving parallel scalability for edge plasma transport simulations with neutral 9374 gas species}, 9375 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 9376 journal = {Computational Science and Discovery}, 9377 year = {2012}, 9378 volume = {5}, 9379 number = {014012}, 9380 doi = {10.1088/1749-4699/5/1/014012}, 9381 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 9382 2011)}, 9383 petsc_uses = {KSP} 9384} 9385 9386@Misc{ petclaw-github, 9387 title = {Pet{C}law Software}, 9388 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 9389 year = {2011}, 9390 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 9391 petsc_uses = {KSP} 9392} 9393 9394@Misc{ pyclaw-web-page, 9395 author = {Kyle T. Mandli and David I. Ketcheson and others}, 9396 title = {{PyClaw} software}, 9397 howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}}, 9398 url = {http://clawpack.github.io/doc/pyclaw/}, 9399 year = {2012}, 9400 petsc_uses = {KSP} 9401} 9402 9403@Article{ ketcheson2011highorder, 9404 title = {High-order wave propagation algorithms for general hyperbolic systems}, 9405 author = {Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.}, 9406 year = {2011}, 9407 note = {submitted}, 9408 petsc_uses = {KSP} 9409} 9410 9411@Article{ biros2005pln1, 9412 title = {{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained 9413 optimization. Part I: The {Krylov-Schur} solver}}, 9414 author = {Biros, G. and Ghattas, O.}, 9415 journal = {SIAM Journal on Scientific Computing}, 9416 volume = {27}, 9417 number = {2}, 9418 pages = {687--713}, 9419 year = {2005}, 9420 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9421 petsc_uses = {KSP} 9422} 9423 9424@Article{ biros2005pln2, 9425 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 9426 optimization. Part {II}: The {Lagrange Newton} solver, and its application to 9427 optimal control of steady viscous flows}, 9428 author = {Biros, G. and Ghattas, O.}, 9429 journal = {SIAM Journal on Scientific Computing}, 9430 volume = {27}, 9431 number = {2}, 9432 pages = {714--739}, 9433 year = {2005}, 9434 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9435 petsc_uses = {KSP} 9436} 9437 9438@Misc{ issm:homepage, 9439 title = {{I}ce {S}heet {S}ystem {M}odel}, 9440 author = {Eric Larour and Mathieu Morlighem and Helene Seroussi}, 9441 year = {2010}, 9442 note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}, 9443 petsc_uses = {KSP} 9444} 9445 9446@Article{ morlighem2010spatial, 9447 title = {Spatial patterns of basal drag inferred using control methods from a 9448 full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est 9449 {A}ntarctica}, 9450 author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and 9451 Aubry, D.}, 9452 journal = {Geophysical Research Letters}, 9453 volume = {37}, 9454 number = {14}, 9455 pages = {L14502}, 9456 year = {2010}, 9457 publisher = {American Geophysical Union}, 9458 petsc_uses = {KSP} 9459} 9460 9461@Article{ jardin2012plasmas, 9462 title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics 9463 of tokamak plasmas}, 9464 author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 9465 journal = {Computational Science \& Discovery}, 9466 volume = {5}, 9467 number = {1}, 9468 url = {http://stacks.iop.org/1749-4699/5/014002}, 9469 year = {2012}, 9470 petsc_uses = {KSP} 9471} 9472 9473@Article{ cmz2016, 9474 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 9475 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 9476 journal = {Journal of Scientific Computing}, 9477 publisher = {Springer}, 9478 pages = {803--825}, 9479 volume = {68}, 9480 issue = {2}, 9481 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 9482 doi = {10.1007/s10915-015-0159-4}, 9483 year = {2016}, 9484 note = {Also preprint ANL/MCS-P3039-0912}, 9485 petsc_uses = {KSP} 9486} 9487 9488@Article{ knepleybrownruppsmith13, 9489 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 9490 title = {Achieving High Performance with Unified Residual Evaluation}, 9491 journal = {ArXiv e-prints}, 9492 eprint = {1309.1204}, 9493 archiveprefix = {arXiv}, 9494 primaryclass = {cs.MS}, 9495 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 9496 Engineering, Finance, and Science}, 9497 year = {2013}, 9498 month = sep, 9499 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 9500 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9501 petsc_uses = {KSP} 9502} 9503 9504@Book{ fenicsbook, 9505 title = {Automated Solution of Differential Equations by the Finite Element Method: The 9506 FEniCS Book}, 9507 series = {Lecture Notes in Computational Science and Engineering}, 9508 volume = {84}, 9509 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 9510 publisher = {Springer}, 9511 isbn = {978-3-642-23098-1}, 9512 year = {2012}, 9513 petsc_uses = {KSP} 9514} 9515 9516@Article{ demidovahnertruppgottschling12, 9517 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 9518 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 9519 journal = {ArXiv e-prints}, 9520 archiveprefix = {arXiv}, 9521 eprint = {1212.6326}, 9522 primaryclass = {cs.MS}, 9523 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 9524 Parallel, and Cluster Computing, Physics - Computational Physics}, 9525 year = {2012}, 9526 month = dec, 9527 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 9528 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9529 petsc_uses = {KSP} 9530} 9531 9532@InProceedings{ viennacl, 9533 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 9534 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 9535 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 9536 year = {2010}, 9537 pages = {51-56}, 9538 petsc_uses = {KSP} 9539} 9540 9541@Article{ knepleybrownmcinnessmithruppadams2015, 9542 title = {Exascale Computing without Threads}, 9543 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9544 Karl Rupp and Mark Adams}, 9545 url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950}, 9546 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9547 Scientific Software Architecture for Portability and Performance}, 9548 doi = {10.6084/m9.figshare.5824950.v1}, 9549 year = {2015}, 9550 petsc_uses = {KSP} 9551} 9552 9553@Article{ knepleybrownmcinnessmithruppadams2015b, 9554 title = {Overview of the {PETSc} Library}, 9555 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9556 Karl Rupp and Mark Adams}, 9557 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 9558 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9559 Scientific Software Architecture for Portability and Performance}, 9560 year = {2015}, 9561 petsc_uses = {KSP} 9562} 9563 9564@InBook{ balaybrownknepleymcinnessmith2015, 9565 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 9566 Smith}, 9567 bookeditor = {J. Carver}, 9568 title = {Software Engineering for Science}, 9569 chapter = {Providing Mixed Language and Legacy Support within a Library}, 9570 publisher = {Taylor \& Francis}, 9571 year = {2015}, 9572 petsc_uses = {KSP} 9573} 9574 9575@Article{ ruppbalaybrownknepleymcinnessmith2015, 9576 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 9577 Software}, 9578 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 9579 McInnes and Barry F. Smith}, 9580 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 9581 Productivity Challenges}, 9582 journal = {ArXiv e-prints}, 9583 archiveprefix = {arXiv}, 9584 eprint = {1510.01122}, 9585 year = {2015}, 9586 petsc_uses = {KSP} 9587} 9588 9589@InProceedings{ knepley2013accurately, 9590 title = {Accurately Citing Software and Algorithms Used in Publications}, 9591 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 9592 F.}, 9593 year = {2013}, 9594 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 9595 (WSSSPE), held at SC13}, 9596 doi = {10.6084/m9.figshare.785731}, 9597 petsc_uses = {KSP} 9598} 9599 9600@InProceedings{ milleretal2013, 9601 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 9602 Strategies Developed for {FASTMath}}, 9603 author = {Mark C. 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Russo}, 10136 journal = {Journal of Scientific Computing}, 10137 year = {2005}, 10138 number = {1}, 10139 pages = {129--155}, 10140 volume = {25} 10141} 10142 10143@Article{ kennedy_2003, 10144 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 10145 author = {C.A. Kennedy and M.H. Carpenter}, 10146 journal = {Appl. Numer. Math.}, 10147 year = {2003}, 10148 number = {1-2}, 10149 pages = {139--181}, 10150 volume = {44}, 10151 doi = {10.1016/S0168-9274(02)00138-1}, 10152 publisher = {Elsevier Science Publishers B. 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Spiteri}, 10167 journal = {Applied Numerical Mathematics}, 10168 year = {1997}, 10169 pages = {151--167}, 10170 volume = {25} 10171} 10172 10173@Book{ ascherpetzold1998, 10174 title = {Computer methods for ordinary differential equations and differential-algebraic 10175 equations}, 10176 author = {Uri M Ascher and Linda R Petzold}, 10177 volume = {61}, 10178 publisher = {SIAM}, 10179 year = {1998} 10180} 10181 10182@Article{ colomesbadia2016, 10183 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 10184 equations}, 10185 author = {Oriol Colom{\'e}s and Santiago Badia}, 10186 journal = {International Journal for Numerical Methods in Engineering}, 10187 volume = {105}, 10188 number = {5}, 10189 pages = {372--400}, 10190 year = {2016} 10191} 10192 10193@Article{ sandu_1997, 10194 title = {Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: 10195 {R}osenbrock solvers}, 10196 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 10197 Potra}, 10198 journal = {Atmospheric Environment}, 10199 year = {1997}, 10200 number = {20}, 10201 pages = {3459--3472}, 10202 volume = {31}, 10203 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 10204 task is the integration of the stiff systems of ordinary differential equations 10205 describing the chemical transformations. It is therefore of interest to 10206 systematically search for stiff solvers which can be identified as close to 10207 optimal for atmospheric applications. In this paper we continue our investigation 10208 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 10209 and compare eight solvers on a set of seven box-models used in present day models. 10210 The focus is on Rosenbrock solvers. 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Ketcheson and Chi Wang Shu}, 10231 title = {{High order strong stability preserving time discretizations}}, 10232 journal = {Journal of Scientific Computing}, 10233 volume = {38}, 10234 number = {3}, 10235 pages = {251--289}, 10236 doi = {10.1007/s10915-008-9239-z}, 10237 year = {2009} 10238} 10239 10240@Article{ ketcheson_2008, 10241 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 10242 Low-Storage Implementations}, 10243 author = {D.I. Ketcheson}, 10244 journal = {SIAM Journal on Scientific Computing}, 10245 year = {2008}, 10246 number = {4}, 10247 pages = {2113--2136}, 10248 volume = {30}, 10249 doi = {10.1137/07070485X}, 10250 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 10251 RungeKutta methods}, 10252 publisher = {SIAM} 10253} 10254 10255@Article{ jansen_2000, 10256 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 10257 equations with a stabilized finite element method}, 10258 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 10259 journal = {Computer Methods in Applied Mechanics and Engineering}, 10260 year = {2000}, 10261 number = {3}, 10262 pages = {305--319}, 10263 volume = {190}, 10264 publisher = {Elsevier} 10265} 10266 10267@Article{ butcher_2007, 10268 title = {Error propagation of general linear methods for ordinary differential equations}, 10269 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 10270 journal = {Journal of Complexity}, 10271 year = {2007}, 10272 number = {4-6}, 10273 pages = {560--580}, 10274 volume = {23}, 10275 abstract = {We discuss error propagation for general linear methods for ordinary differential 10276 equations up to terms of order p+2, where p is the order of the method. These 10277 results are then applied to the estimation of local discretization errors for 10278 methods of order p and for the adjacent order p+1. The results of numerical 10279 experiments confirm the reliability of these estimates. This research has 10280 applications in the design of robust stepsize and order changing strategies for 10281 algorithms based on general linear methods.}, 10282 doi = {10.1016/j.jco.2007.01.009}, 10283 issn = {0885-064X} 10284} 10285 10286@Article{ constantinescu_a2010a, 10287 title = {Extrapolated implicit-explicit time stepping}, 10288 author = {E.M. Constantinescu and A. Sandu}, 10289 journal = {SIAM Journal on Scientific Computing}, 10290 year = {2010}, 10291 number = {6}, 10292 pages = {4452-4477}, 10293 volume = {31}, 10294 comment = {Preprint \# ANL/MCS-P1612-0409}, 10295 doi = {10.1137/080732833} 10296} 10297 10298@InProceedings{ devito2011liszt, 10299 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 10300 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 10301 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 10302 Aiken, Alex and Duraisamy, Karthik and others}, 10303 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 10304 Networking, Storage and Analysis}, 10305 pages = {9}, 10306 year = {2011}, 10307 organization = {ACM} 10308} 10309 10310@Article{ devito2011designing, 10311 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 10312 author = {DeVito, Zachary and Hanrahan, Pat}, 10313 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 10314 year = {2011} 10315} 10316 10317@Misc{ pgasintro, 10318 author = {Tim Stitt}, 10319 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 10320 Model}, 10321 note = {\url{http://cnx.org/content/m20649/latest/}} 10322} 10323 10324@InProceedings{ el2006upc, 10325 title = {UPC: unified parallel C}, 10326 author = {El-Ghazawi, Tarek and Smith, Lauren}, 10327 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 10328 pages = {27}, 10329 year = {2006}, 10330 organization = {ACM} 10331} 10332 10333@InProceedings{ numrich1998co, 10334 title = {Co-Array Fortran for parallel programming}, 10335 author = {Numrich, Robert W and Reid, John}, 10336 booktitle = {ACM Sigplan Fortran Forum}, 10337 volume = {17}, 10338 number = {2}, 10339 pages = {1--31}, 10340 year = {1998}, 10341 organization = {ACM} 10342} 10343 10344@Article{ aiken1997titanium, 10345 title = {Titanium: A high-performance Java dialect}, 10346 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 10347 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 10348 Geoff and Semenzato, Luigi and others}, 10349 year = {1997} 10350} 10351 10352@Article{ charles2005x10, 10353 title = {X10: an object-oriented approach to non-uniform cluster computing}, 10354 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 10355 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 10356 Sarkar, Vivek}, 10357 journal = {Acm Sigplan Notices}, 10358 volume = {40}, 10359 number = {10}, 10360 pages = {519--538}, 10361 year = {2005}, 10362 publisher = {ACM} 10363} 10364 10365@Article{ chamberlain2007parallel, 10366 title = {Parallel programmability and the chapel language}, 10367 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 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ICPPW'09. International Conference on}, 10458 pages = {394--401}, 10459 year = {2009}, 10460 organization = {IEEE} 10461} 10462 10463@TechReport{ ipm, 10464 author = {Barry F. Smith}, 10465 title = {A New Parallel Programming Model for Computer Simulation}, 10466 institution = {Argonne National Laboratory}, 10467 year = {2014}, 10468 number = {ANL/MCS-P5135-0414} 10469} 10470 10471@Article{ groppsnir, 10472 author = {William Gropp and Marc Snir}, 10473 title = {Programming for Exascale Computers}, 10474 journal = {Computing in Science and Engineering}, 10475 volume = {15}, 10476 number = {6}, 10477 issn = {1521-9615}, 10478 year = {2013}, 10479 pages = {27-35}, 10480 doi = {10.1109/MCSE.2013.96}, 10481 publisher = {IEEE Computer Society}, 10482 address = {Los Alamitos, CA} 10483} 10484 10485@Book{ mpi3, 10486 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 10487 author = {Message Passing Interface Forum}, 10488 year = {2012}, 10489 publisher = {High Performance Computing Center Stuttgart (HLRS)} 10490} 10491 10492@Book{ openmp4, 10493 title = {OpenMP Application Program Interface, Version 4.0}, 10494 year = {2013}, 10495 publisher = {OpenMP Architecture Review Board} 10496} 10497 10498@InProceedings{ hartono2009annotation, 10499 title = {Annotation-based empirical performance tuning using {Orio}}, 10500 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 10501 booktitle = {Parallel \& Distributed Processing, 2009. 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Smith}, 10528 title = {Scientific Application Web Server {(SAWs)} Users Manual}, 10529 institution = {Argonne National Laboratory}, 10530 year = {2013} 10531} 10532 10533@Article{ smith1997domain, 10534 title = {Domain Decomposition Methods for Partial Differential Equations}, 10535 author = {Smith, B.F.}, 10536 journal = {ICASE LARC Interdisciplinary Series in Science and Engineering}, 10537 volume = {4}, 10538 pages = {225--244}, 10539 year = {1997}, 10540 publisher = {Citeseer} 10541} 10542 10543@Article{ spillane2011abstract, 10544 title = {Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems 10545 in the overlaps}, 10546 author = {Spillane, N and Dolean, V and Hauret, P and Nataf, F and Pechstein, C and 10547 Scheichl, R}, 10548 journal = {NuMa-Report}, 10549 volume = {7}, 10550 pages = {2007}, 10551 year = {2011} 10552} 10553 10554@InProceedings{ jolivet2013scalabledd, 10555 title = {Scalable domain decomposition preconditioners for heterogeneous elliptic 10556 problems}, 10557 author = {Jolivet, Pierre and Hecht, Fr{\'e}d{\'e}ric and Nataf, Fr{\'e}d{\'e}ric and 10558 Prud'homme, Christophe}, 10559 booktitle = {Proceedings of SC13: International Conference for High Performance Computing, 10560 Networking, Storage and Analysis}, 10561 pages = {80}, 10562 year = {2013}, 10563 organization = {ACM} 10564} 10565 10566@Book{ ks2000, 10567 author = {D. Kinderlehrer and G. Stampacchia}, 10568 publisher = {Society for Industrial Mathematics}, 10569 title = {An Introduction to Variational Inequalities and Their Applications}, 10570 year = {2000} 10571} 10572 10573@Article{ wan2000energy, 10574 title = {An energy-minimizing interpolation for robust multigrid methods}, 10575 author = {Wan, W.L. and Chan, T.F. and Smith, B. F.}, 10576 journal = {SIAM Journal on Scientific Computing}, 10577 volume = {21}, 10578 number = {4}, 10579 pages = {1632--1649}, 10580 year = {2000}, 10581 publisher = {Philadelphia, PA: SIAM, c1993-} 10582} 10583 10584@Article{ chansmith1994, 10585 title = {Domain decomposition and multigrid algorithms for elliptic problems on 10586 unstructured meshes}, 10587 author = {Chan, T.F. and Smith, B.F.}, 10588 journal = {Electronic Transactions on Numerical Analysis}, 10589 volume = {2}, 10590 pages = {171--182}, 10591 year = {1994} 10592} 10593 10594@TechReport{ proto-fsp, 10595 author = {Venkatramani Balaji and Barry Smith and Brian Van Straalen and Priya Vashishta 10596 and Michael Zarnstorff and Michael Zika}, 10597 title = {Report of the {Proto-FSP} {Assessment Panel for the FSP}}, 10598 institution = {Princeton Plasma Physics Laboratory}, 10599 year = {2010}, 10600 url = {http://www.pppl.gov/fsp/documents/Proto-FSPAssessmentReport.pdf} 10601} 10602 10603@Article{ hirvijoki2021, 10604 title = {Structure-preserving marker-particle discretizations of {Coulomb} collisions for 10605 particle-in-cell codes}, 10606 journal = {Plasma Phys. Control. Fusion}, 10607 author = {Eero Hirvijoki}, 10608 note = {in press}, 10609 doi = {10.1088/1361-6587/abe884}, 10610 year = {2021} 10611} 10612 10613@Article{ ipsen2001, 10614 author = {Ilse C. F. Ipsen}, 10615 journal = {SIAM J. Sci. Comput.}, 10616 pages = {1050--1051}, 10617 volume = {23}, 10618 publisher = {SIAM}, 10619 title = {A Note on Preconditioning Nonsymmetric Matrices}, 10620 year = {2001} 10621} 10622 10623% Random papers on solvers for GPUs 10624@InProceedings{ gpus-suck, 10625 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. }, 10626 title = { On the Limits of {GPU} Acceleration}, 10627 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism}, 10628 year = {2010}, 10629 publisher = {USENIX} 10630} 10631 10632@InProceedings{ 882364, 10633 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter}, 10634 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid}, 10635 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers}, 10636 year = {2003}, 10637 isbn = {1-58113-709-5}, 10638 pages = {917--924}, 10639 location = {San Diego, California}, 10640 doi = {10.1145/1201775.882364}, 10641 publisher = {ACM}, 10642 address = {New York, NY} 10643} 10644 10645@Conference{ feng2008multigrid, 10646 author = {Feng, Z. and Li, P.}, 10647 booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008}, 10648 date-added = {2010-08-19 15:57:06 -0500}, 10649 date-modified = {2010-08-19 15:57:06 -0500}, 10650 pages = {647--654}, 10651 title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms}, 10652 year = {2008} 10653} 10654 10655@Conference{ goodnight2003multigrid, 10656 author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.}, 10657 booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware}, 10658 date-added = {2010-08-19 15:45:20 -0500}, 10659 date-modified = {2010-08-19 15:45:20 -0500}, 10660 organization = {Eurographics Association}, 10661 pages = {102--111}, 10662 title = {A multigrid solver for boundary value problems using programmable graphics 10663 hardware}, 10664 year = {2003} 10665} 10666 10667@Article{ buatois2007concurrent, 10668 author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.}, 10669 date-added = {2010-08-19 15:45:02 -0500}, 10670 date-modified = {2010-08-19 15:45:02 -0500}, 10671 journal = {High Performance Computing and Communications}, 10672 pages = {358--371}, 10673 publisher = {Citeseer}, 10674 title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}}, 10675 year = {2007} 10676} 10677 10678@Article{ joldes2010real, 10679 author = {Joldes, G.R. and Wittek, A. and Miller, K.}, 10680 date-added = {2010-08-19 15:44:41 -0500}, 10681 date-modified = {2010-08-19 15:44:41 -0500}, 10682 journal = {Computer Methods in Applied Mechanics and Engineering}, 10683 publisher = {Elsevier}, 10684 title = {Real-time nonlinear finite element computations on {GPU}-application to 10685 neurosurgical simulation}, 10686 year = {2010} 10687} 10688 10689@Misc{ aharon2005gpu, 10690 author = {Aharon, S.}, 10691 date-added = {2010-08-19 15:44:32 -0500}, 10692 date-modified = {2010-08-19 15:44:32 -0500}, 10693 month = apr, 10694 note = {US Patent App. 11/115,642}, 10695 publisher = {Google Patents}, 10696 title = {{GPU}-based Finite Element}, 10697 year = {2005} 10698} 10699 10700@Article{ cevahir2009fast, 10701 author = {Cevahir, A. and Nukada, A. and Matsuoka, S.}, 10702 date-added = {2010-08-19 15:44:01 -0500}, 10703 date-modified = {2010-08-19 15:44:01 -0500}, 10704 journal = {Computational Science--ICCS 2009}, 10705 pages = {893--903}, 10706 publisher = {Springer}, 10707 title = {Fast conjugate gradients with multiple {GPU}s}, 10708 year = {2009} 10709} 10710 10711@Article{ maier1995symmetric, 10712 author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.}, 10713 date-added = {2010-08-19 15:43:57 -0500}, 10714 date-modified = {2010-08-19 15:43:57 -0500}, 10715 journal = {Computational Mechanics}, 10716 number = {1}, 10717 pages = {115--129}, 10718 publisher = {Springer}, 10719 title = {Symmetric {G}alerkin boundary element method in plasticity and gradient 10720 plasticity}, 10721 volume = {17}, 10722 year = {1995} 10723} 10724 10725@Article{ corrigan-running, 10726 author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.}, 10727 date-added = {2010-08-19 15:43:47 -0500}, 10728 date-modified = {2010-08-19 15:43:47 -0500}, 10729 journal = {International Journal for Numerical Methods in Fluids}, 10730 publisher = {John Wiley \& Sons}, 10731 title = {Running unstructured grid based CFD solvers on modern graphics hardware} 10732} 10733 10734@InProceedings{ volkov08, 10735 author = {Vasily Volkov and James W. Demmel}, 10736 title = {Benchmarking GPUs to tune dense linear algebra}, 10737 booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)}, 10738 note = {\url{http://mc.stanford.edu/cgi-bin/images/6/65/SC08_Volkov_GPU.pdf}}, 10739 year = {2008} 10740} 10741 10742@TechReport{ cray-mvmult, 10743 author = {Guy~E. Blelloch and Michael~A. Heroux and Marco Zagha}, 10744 title = {Segmented Operations for Sparse Matrix Computation on Vector Multiprocessors}, 10745 institution = {School of Computer Science, Carnegie Mellon University}, 10746 number = {CMU-CS-93-173}, 10747 month = aug, 10748 year = {1993} 10749} 10750 10751@Conference{ bell2009implementing, 10752 author = {Bell, N. and Garland, M.}, 10753 booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage 10754 and Analysis}, 10755 date-added = {2010-08-19 15:43:42 -0500}, 10756 date-modified = {2010-08-19 15:43:42 -0500}, 10757 organization = {ACM}, 10758 pages = {1--11}, 10759 title = {Implementing sparse matrix-vector multiplication on throughput-oriented 10760 processors}, 10761 year = {2009} 10762} 10763 10764@Article{ bell2008efficient, 10765 author = {Bell, N. and Garland, M.}, 10766 date-added = {2010-08-19 15:43:36 -0500}, 10767 date-modified = {2010-08-19 15:43:36 -0500}, 10768 journal = {{NVIDIA} Corporation, {NVIDIA} Technical Report NVR-2008-004}, 10769 title = {Efficient sparse matrix-vector multiplication on {CUDA}}, 10770 year = {2008} 10771} 10772 10773@Article{ cohen-fast, 10774 author = {Cohen, J. and Molemaker, M.J.}, 10775 date-added = {2010-08-19 15:43:34 -0500}, 10776 date-modified = {2010-08-19 15:43:34 -0500}, 10777 journal = {Parallel Computational Fluid Dynamics: Recent Advances and Future Directions}, 10778 pages = {414}, 10779 publisher = {DEStech Publications}, 10780 title = {A fast double precision CFD code using CUDA} 10781} 10782 10783@Article{ kazhdan2008streaming, 10784 author = {Kazhdan, M. and Hoppe, H.}, 10785 date-added = {2010-08-19 15:43:32 -0500}, 10786 date-modified = {2010-08-19 15:43:32 -0500}, 10787 journal = {ACM Transactions on Graphics (TOG)}, 10788 number = {3}, 10789 pages = {21}, 10790 publisher = {ACM}, 10791 title = {Streaming multigrid for gradient-domain operations on large images}, 10792 volume = {27}, 10793 year = {2008} 10794} 10795 10796@Article{ bonnet1998symmetric, 10797 author = {Bonnet, M. and Maier, G. and Polizzotto, C.}, 10798 date-added = {2010-08-19 15:43:18 -0500}, 10799 date-modified = {2010-08-19 15:43:18 -0500}, 10800 journal = {Appl. Mech. Rev}, 10801 pages = {669--704}, 10802 title = {Symmetric {G}alerkin boundary element method.}, 10803 volume = {51}, 10804 year = {1998} 10805} 10806 10807@Conference{ zamith2007gpu, 10808 author = {Zamith, M. and Clua, E. and Pagliosa, P. and Conci, A. and Montenegro, A. and 10809 Valente, L.}, 10810 booktitle = {Proceedings of the VI Brazilian Symposium on Computer Games and Digital 10811 Entertainment}, 10812 date-added = {2010-08-19 15:43:14 -0500}, 10813 date-modified = {2010-08-19 15:43:14 -0500}, 10814 pages = {37--43}, 10815 title = {The {GPU} used as a math co-processor in real time applications}, 10816 year = {2007} 10817} 10818 10819@Article{ baskaran2009optimizing, 10820 author = {Baskaran, M.M. and Bordawekar, R.}, 10821 date-added = {2010-08-19 15:42:56 -0500}, 10822 date-modified = {2010-08-19 15:42:56 -0500}, 10823 journal = {IBM Research Report RC24704, IBM}, 10824 title = {Optimizing sparse matrix-vector multiplication on {GPU}s}, 10825 year = {2009} 10826} 10827 10828@Misc{ szeliski2006locally, 10829 author = {Szeliski, R.}, 10830 date-added = {2010-08-19 15:42:45 -0500}, 10831 date-modified = {2010-08-19 15:42:45 -0500}, 10832 month = jul, 10833 note = {US Patent App. 11/459,724}, 10834 publisher = {Google Patents}, 10835 title = {Locally adapted hierarchical basis preconditioning}, 10836 year = {2006} 10837} 10838 10839@Article{ jung2006cholesky, 10840 author = {Jung, J.H. and O'Leary, D.P.}, 10841 date-added = {2010-08-19 15:42:34 -0500}, 10842 date-modified = {2010-08-19 15:42:34 -0500}, 10843 journal = {Scholarly Paper, University of Maryland}, 10844 publisher = {Citeseer}, 10845 title = {Cholesky decomposition and linear programming on a {GPU}}, 10846 year = {2006} 10847} 10848 10849@Conference{ filipovic2009gpu, 10850 author = {Filipovic, J. and Peterlik, I. and Fousek, J.}, 10851 booktitle = {SAAHPC: Symposium on Application Accelerators in HPC}, 10852 date-added = {2010-08-19 15:42:33 -0500}, 10853 date-modified = {2010-08-19 15:42:33 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Karpeyev}, 11553 title = {Geometric Integrators for Hamiltonian PDEs}, 11554 school = {Old Dominion University}, 11555 year = {2002} 11556} 11557 11558@InCollection{ fjp:ima, 11559 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 11560 title = {The Scalability of Mesh Improvement Algorithms}, 11561 booktitle = {Algorithms for Parallel Processing}, 11562 publisher = {Springer-Verlag}, 11563 volume = {105}, 11564 series = {The IMA Volumes in Mathematics and Its Applications}, 11565 editor = {Michael T.\ Heath and Abhiram Ranade and Robert S.\ Schreiber}, 11566 year = {1998}, 11567 pages = {185--212} 11568} 11569 11570@InProceedings{ poet, 11571 author = {Rob Armstrong and Alex Cheung}, 11572 title = {{POET} ({P}arallel {O}bject-Oriented {E}nvironment and {T}oolkit) and Frameworks 11573 for Scientific Distributed Computing}, 11574 booktitle = {Proceedings of {HICSS97}}, 11575 year = {1997} 11576} 11577 11578@Misc{ pseware-web-page, 11579 author = {}, 11580 title = {{PSEware} {Web} page}, 11581 note = {\url{http://www.extreme.indiana.edu/pseware}, Indiana University}, 11582 key = {{PSEware} {Web} page} 11583} 11584 11585@Article{ epperly2011high, 11586 title = {High-performance language interoperability for scientific computing through 11587 {B}abel}, 11588 author = {Epperly, Thomas GW and Kumfert, Gary and Dahlgren, Tamara and Ebner, Dietmar and 11589 Leek, Jim and Prantl, Adrian and Kohn, Scott}, 11590 journal = {International Journal of High Performance Computing Applications}, 11591 pages = {1094342011414036}, 11592 year = {2011}, 11593 publisher = {SAGE Publications} 11594} 11595 11596@Misc{ babel-web-page, 11597 author = {Tom Epperly and Tamara Dahlgren and Gary Kumfert}, 11598 title = {{Babel} {Web} page}, 11599 note = {\url{http://www.llnl.gov/CASC/components/babel.html}} 11600} 11601 11602@Misc{ infospheres-web-page, 11603 author = {K.~M. {Chandy et al.}}, 11604 title = {{Infospheres} {W}eb page}, 11605 note = {\url{http://www.infospheres.caltech.edu}}, 11606 key = {{Infospheres} {Web} page} 11607} 11608 11609@Misc{ hammond, 11610 author = {Glenn Hammond}, 11611 title = {{Sandia National Laboratory}, {C}omputations on {R}eactive {F}low, private 11612 communication} 11613} 11614 11615@Misc{ ornl, 11616 author = {Oak Ridge National Laboratory}, 11617 title = {Private communication via petsc-maint email support} 11618} 11619 11620@Unpublished{ cumulvs-web-page, 11621 author = {}, 11622 title = {{Cumulvs} {W}eb page}, 11623 note = {http://www.epm.ornl.gov/cs/cumulvs.html}, 11624 key = {{Cumulvs} {W}eb page} 11625} 11626 11627@Article{ nonlineargmres, 11628 author = {T. 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Markus}, 11694 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 11695 for {PDE} Based Applications}, 11696 year = {1994}, 11697 institution = {Department of Computer Sciences, Purdue University}, 11698 number = {CSD-TR-94-021} 11699} 11700 11701@Unpublished{ ilu-web-page, 11702 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 11703 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 11704 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 11705} 11706 11707@Unpublished{ doe2k-web-page, 11708 title = {{DOE2000 Initiative} {W}eb page}, 11709 note = {http://www.mcs.anl.gov/DOE2000}, 11710 key = {DOE2000 Initiative} 11711} 11712 11713@Misc{ pvode-web-page, 11714 title = {{PVODE} {W}eb Page}, 11715 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 11716 author = {A. {Hindmarsh et al.}} 11717} 11718 11719@Book{ szyperski97, 11720 author = {Clemens Szyperski}, 11721 title = {Component Software: Beyond Object-Oriented Programming}, 11722 publisher = {ACM Press}, 11723 address = {New York}, 11724 year = {1997} 11725} 11726 11727@Unpublished{ petsc:coloringuse, 11728 title = {Code for computing sparse {J}acobians}, 11729 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11730 institution = {Argonne National Laboratory} 11731} 11732 11733@Unpublished{ petsc:external, 11734 author = {B. F. {Smith et al.}}, 11735 title = {{External Software Used by PETSc}}, 11736 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11737 institution = {Argonne National Laboratory} 11738} 11739 11740@Unpublished{ petsc:use-by-external-packages, 11741 author = {B. F. {Smith et al.}}, 11742 title = {{Software Packages that Use or Interface to PETSc}}, 11743 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 11744 institution = {Argonne National Laboratory} 11745} 11746 11747@Unpublished{ petsc:prizes, 11748 author = {B. F. {Smith et al.}}, 11749 title = {{Prizes Won Using PETSc}}, 11750 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 11751 institution = {Argonne National Laboratory} 11752} 11753 11754@Unpublished{ petsc:csgf, 11755 author = {B. 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Ross}, 11879 publisher = {University of Toronto}, 11880 pages = {379--386}, 11881 year = {1994} 11882} 11883 11884@Article{ cs99, 11885 author = {X.-C. Cai and M. Sarkis}, 11886 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 11887 systems}, 11888 journal = {SIAM J. Scientific Computing}, 11889 year = {1999}, 11890 volume = {21}, 11891 pages = {792-797} 11892} 11893 11894@TechReport{ cs97a, 11895 author = {X.-C. Cai and M. Sarkis}, 11896 title = {A restricted additive {S}chwarz preconditioner for general sparse linear systems 11897 }, 11898 year = {1997}, 11899 institution = {Computer Science Department, University of Colorado-Boulder}, 11900 number = {CU-CS 843-97}, 11901 note = {(accepted by SIAM J. of Scientific Computing)} 11902} 11903 11904@Article{ cai2003restricted, 11905 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 11906 positive definite linear systems}, 11907 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 11908 journal = {SIAM Journal on Numerical Analysis}, 11909 volume = {41}, 11910 issue = {1}, 11911 pages = {1209--1231}, 11912 year = {2003}, 11913 doi = {10.1137/S0036142901389621} 11914} 11915 11916@TechReport{ caisaad, 11917 author = {Xiao-Chuan Cai and Youcef Saad}, 11918 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 11919 institution = {Army High Performance Computing Research Center, University of Minnesota }, 11920 year = {1993}, 11921 number = {Preprint 93-027 }, 11922 note = {SIAM J. 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Merlin}, 12002 title = {Parallel versions of {S}tones strongly implicit algorithm}, 12003 journal = {Concurrency and Computation: Practice and Experience}, 12004 pages = {1049--1062}, 12005 volumne = {13}, 12006 year = {2001} 12007} 12008 12009@Article{ p4-paper, 12010 author = {Ralph Butler and Ewing Lusk}, 12011 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 12012 journal = {Journal of Parallel Computing}, 12013 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 12014 Division preprint P362-0493)}, 12015 year = {1993} 12016} 12017 12018@TechReport{ picl, 12019 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 12020 title = {{PICL}: A portable instrumented communications library}, 12021 institution = {Oak Ridge National Laboratory}, 12022 number = {TM-11130}, 12023 year = {1990}, 12024 key = {PICL} 12025} 12026 12027@TechReport{ upshot, 12028 author = {Virginia Herrarte and Ewing Lusk}, 12029 title = {Studying Parallel Program Behavior with {U}pshot}, 12030 institution = {Argonne National Laboratory}, 12031 number = {ANL-91/15}, 12032 month = aug, 12033 year = {1991}, 12034 key = {Upshot} 12035} 12036 12037@TechReport{ p4-manual, 12038 author = {Ralph Butler and Ewing Lusk}, 12039 title = {User's Guide to the p4 Parallel Programming System}, 12040 institution = {Argonne National Laboratory}, 12041 number = {ANL-92/17}, 12042 month = oct, 12043 year = {1992}, 12044 key = {p4-Manual} 12045} 12046 12047@InProceedings{ oldparti, 12048 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 12049 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 12050 booktitle = {Proceedings of Supercomputing '93}, 12051 pages = {578--587}, 12052 year = {1993} 12053} 12054 12055@Article{ parti2, 12056 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 12057 and J. Saltz}, 12058 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 12059 journal = {ACM SIGPLAN Notices}, 12060 year = {1995}, 12061 pages = {68-79}, 12062 volume = {30}, 12063 number = {8} 12064} 12065 12066@Article{ parti3, 12067 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 12068 title = {Run-Time Parallelization and Scheduling of Loops}, 12069 journal = {IEEE Trans. Computers}, 12070 year = {1991}, 12071 pages = {604-612}, 12072 volume = {40}, 12073 number = {5} 12074} 12075 12076@InProceedings{ disz-lusk:wamtrace, 12077 author = {Terrence Disz and Ewing Lusk}, 12078 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 12079 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12080 year = {1987}, 12081 pages = {46--53} 12082} 12083 12084@InProceedings{ gorlick-kesselman:gauge, 12085 author = {Michael Gorlick and Carl Kesselman}, 12086 title = {Timing {Prolog} programs without Clocks}, 12087 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12088 year = {1996}, 12089 publisher = {Birkhauser} 12090} 12091 12092@TechReport{ aztec, 12093 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 12094 title = {Aztec User's Guide Version 1.1}, 12095 institution = {Sandia National Laboratories}, 12096 month = oct, 12097 year = {1995}, 12098 number = {SAND95/1559} 12099} 12100 12101@TechReport{ aztec2, 12102 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 12103 title = {Official {Aztec} User's Guide Version 2.1}, 12104 institution = {Sandia National Laboratories}, 12105 year = {1999} 12106} 12107 12108@Book{ taylor-chandy:pcn, 12109 author = {Chandy, M. and Taylor, S.}, 12110 title = {An Introduction to Parallel Programming}, 12111 year = {1991}, 12112 publisher = {Jones and Bartlett} 12113} 12114 12115@Book{ foster-taylor:strand, 12116 title = {Strand: New Concepts in Parallel Programming}, 12117 author = {Ian Foster and Stephen Taylor}, 12118 publisher = {Prentice-Hall}, 12119 adress = { Englewood Cliffs, New Jersey}, 12120 year = {1990} 12121} 12122 12123@Article{ aurora, 12124 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 12125 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 12126 Carlsson and A. Ciepielewski and B. Hausman}, 12127 title = {The Aurora OR-Parallel Prolog System}, 12128 journal = {New Generation Computing}, 12129 volume = {7}, 12130 number = {3}, 12131 year = {1990}, 12132 pages = {243--271} 12133} 12134 12135@TechReport{ roo, 12136 author = {E. Lusk and W. McCune and J. Slaney}, 12137 title = {Roo---a Parallel Theorem Prover}, 12138 institution = {Argonne National Laboratory}, 12139 number = {MCS--TM--149}, 12140 year = {1991} 12141} 12142 12143@TechReport{ heath-etheridge:vppp, 12144 author = {M. T. Heath and J. A. Etheridge}, 12145 title = {Visualizing the Performance of Parallel Programs}, 12146 institution = {Oak Ridge National Laboratory}, 12147 number = {ORNL TM-11813}, 12148 year = {1991} 12149} 12150 12151@TechReport{ chem:vis, 12152 author = {Ewing L. Lusk}, 12153 title = {Performance Visualization for Parallel Programs}, 12154 institution = {Argonne National Laboratory}, 12155 number = {ANL/MCS--P287--0192}, 12156 year = {1991}, 12157 note = {(to appear in {\em Theoretica Chimica Acta})} 12158} 12159 12160@TechReport{ picltrace, 12161 author = {P.~H.~Worley}, 12162 title = {A new {PICL} trace file format}, 12163 institution = {Oak Ridge National Laboratory}, 12164 number = {ORNL TM-12125}, 12165 month = jun, 12166 year = {1992} 12167} 12168 12169@InProceedings{ hideo, 12170 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 12171 title = {Inference of Phylogenetic trees using maximum likelihood}, 12172 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 12173 year = {1992}, 12174 pages = {247--262} 12175} 12176 12177@InProceedings{ dw90, 12178 author = {M. Dryja and O. Widlund}, 12179 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 12180 Problems}, 12181 booktitle = {Third International Symposium on Domain Decomposition Methods}, 12182 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 12183 year = {1990}, 12184 pages = {3-21}, 12185 publisher = {SIAM}, 12186 address = {Philadelphia}, 12187 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 12188 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 12189 references, good introduction to the theory. No computations}, 12190 key = {DryjaWidlund90 !AS} 12191} 12192 12193@Unpublished{ rosing, 12194 author = {Matt Rosing and Joel Saltz}, 12195 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 12196 key = {LowLatency}, 12197 note = {manuscript, 1992} 12198} 12199 12200@TechReport{ jp:incomplete, 12201 author = {Mark T. Jones and Paul E. Plassmann}, 12202 title = {An Improved Incomplete {C}holesky Factorization}, 12203 institution = {Argonne National Laboratory}, 12204 address = {Argonne, IL}, 12205 type = {Preprint}, 12206 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 12207 number = {MCS-P206-0191}, 12208 year = {1991}, 12209 key = {jones} 12210} 12211 12212@InCollection{ jp:ima, 12213 author = {Mark Jones and Paul Plassmann}, 12214 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 12215 booktitle = {Graph Theory and Sparse Matrix Computation}, 12216 publisher = {Springer-Verlag}, 12217 series = {The IMA Volumes in Mathematics and Its Applications}, 12218 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 12219 volume = {56}, 12220 year = {1993}, 12221 pages = {229--245} 12222} 12223 12224@Article{ pw98, 12225 author = {M. Pernice and H. F. Walker}, 12226 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 12227 journal = {SIAM J. Sci. Stat. Comput.}, 12228 year = {1998}, 12229 volume = {19}, 12230 pages = {302--318} 12231} 12232 12233@TechReport{ ysmp83, 12234 key = {Eisenstat}, 12235 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12236 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12237 institution = {Department of Computer Science, Yale University}, 12238 number = {YALE/DCS/RR-265}, 12239 month = apr, 12240 year = {1983} 12241} 12242 12243@InBook{ ysmp84, 12244 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12245 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12246 title = {Elliptic Problem Solvers II}, 12247 publisher = {Academic Press}, 12248 pages = {45--52}, 12249 editors = {G. Birkhoff and A. Schoenstadt}, 12250 year = {1984} 12251} 12252 12253@TechReport{ sparsekit, 12254 key = {Saad}, 12255 author = {Youcef Saad}, 12256 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 12257 institution = {Center for Supercomputing Research and Development, University of Illinois at 12258 Urbana-Champaign}, 12259 number = {1029}, 12260 year = {1990} 12261} 12262 12263@TechReport{ pde-user-ref, 12264 author = {Barry F. Smith}, 12265 title = {Extensible {PDE} Solvers Package Users Manual}, 12266 institution = {Argonne National Laboratory}, 12267 month = sep, 12268 year = {1994}, 12269 number = {ANL-93/40}, 12270 key = {Smith94 ! PDE} 12271} 12272 12273@TechReport{ bs-user-ref, 12274 author = {Mark T. Jones and Paul E. Plassmann}, 12275 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 12276 of Sparse Linear Systems}, 12277 institution = {Argonne National Laboratory}, 12278 month = dec, 12279 year = {1995}, 12280 number = {ANL-95/48} 12281} 12282 12283@TechReport{ snes-user-ref, 12284 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 12285 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 12286 institution = {Argonne National Laboratory}, 12287 month = feb, 12288 year = {1995}, 12289 number = {ANL/MCS-TM-193}, 12290 key = {GroppMcInnesSmith95 ! SNES} 12291} 12292 12293@TechReport{ sles-user-ref, 12294 author = {William D. Gropp and Barry F. Smith}, 12295 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 12296 institution = {Argonne National Laboratory}, 12297 month = mar, 12298 year = {1993}, 12299 number = {ANL-93/8}, 12300 key = {GroppSmith93 ! SLES} 12301} 12302 12303@TechReport{ chameleon-user-ref, 12304 author = {William D. Gropp and Barry F. Smith}, 12305 title = {Chameleon Parallel programming tools Users Manual}, 12306 institution = {Argonne National Laboratory}, 12307 month = mar, 12308 year = {1993}, 12309 number = {ANL-93/23}, 12310 key = {GroppSmith93 ! Chameleon} 12311} 12312 12313@Article{ euclid2, 12314 author = {D. Hysom and A. Pothen}, 12315 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 12316 journal = {SIAM J. Sci. Comput.}, 12317 volume = {22}, 12318 number = {6}, 12319 pages = {2194--2215} 12320} 12321 12322@TechReport{ euclid1, 12323 author = {D. Hysom and A. Pothen}, 12324 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 12325 Solution of Sparse Linear Systems)}, 12326 institution = {Old Dominion University}, 12327 year = {2001} 12328} 12329 12330@TechReport{ ksp-user-ref, 12331 author = {William D. Gropp and Barry F. Smith}, 12332 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 12333 Methods}, 12334 institution = {Argonne National Laboratory}, 12335 month = aug, 12336 year = {1993}, 12337 number = {ANL-93/30}, 12338 key = {GroppSmith93 ! KSP} 12339} 12340 12341@TechReport{ mpi-chameleon, 12342 author = {William D. Gropp and Ewing Lusk}, 12343 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 12344 institution = {Argonne National Laboratory}, 12345 month = dec, 12346 year = {1992}, 12347 number = {ANL-92/47}, 12348 key = {GroppLusk92 ! MPI} 12349} 12350 12351@TechReport{ blockcomm-fortran, 12352 author = {William D. Gropp}, 12353 title = {Block{C}omm for {F}ortran}, 12354 institution = {Argonne National Laboratory}, 12355 month = may, 12356 year = {1993}, 12357 number = {ANL-93/00 (to appear)}, 12358 key = {Gropp93 ! BlockComm} 12359} 12360 12361@TechReport{ autodocument, 12362 author = {William D. Gropp}, 12363 title = {Automatic documentation of {C} programs}, 12364 institution = {Argonne National Laboratory}, 12365 month = may, 12366 year = {1993}, 12367 number = {ANL-93/00}, 12368 key = {Gropp93 ! Autodoc} 12369} 12370 12371@TechReport{ zipcode, 12372 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 12373 Manfred Morari}, 12374 title = {The {Z}ipcode message-passing system}, 12375 institution = {Lawrence Livermore National Laboratory}, 12376 month = sep, 12377 year = {1992}, 12378 number = {Unpublished}, 12379 key = {Skjellum92 ! Zipcode} 12380} 12381 12382@Article{ paragraph, 12383 author = {Michael T. Heath and Jennifer Etheridge Finger}, 12384 title = {Visualizing performance of parallel programs}, 12385 journal = {IEEE Software}, 12386 volume = {8}, 12387 number = {5}, 12388 month = sep, 12389 year = {1991}, 12390 pages = {29--39}, 12391 key = {Heath91 ! Paragraph} 12392} 12393 12394@Article{ gropp90, 12395 author = {William Gropp and Edward Smith}, 12396 title = {Computational Fluid Dynamics on Parallel Processors}, 12397 journal = {Computers and Fluids}, 12398 volume = {18}, 12399 year = {1990}, 12400 pages = {289--304}, 12401 key = {Gropp90 ! performance} 12402} 12403 12404@Article{ foster92, 12405 author = {Ian Foster and William Gropp and Rick Stevens}, 12406 title = {The parallel scalability of the spectral transform method}, 12407 journal = {Monthly Weather Review}, 12408 volume = {120}, 12409 year = {1992}, 12410 pages = {835--850}, 12411 key = {Foster92 ! performance} 12412} 12413 12414@InBook{ fgn, 12415 author = {R. Freund and G. H. Golub and N. Nachtigal}, 12416 title = {Iterative Solution of Linear Systems}, 12417 series = {Acta Numerica}, 12418 year = {1992}, 12419 publisher = {Cambridge University Press}, 12420 pages = {57--100} 12421} 12422 12423@TechReport{ nachtigal90, 12424 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 12425 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12426 institution = {Massachusetts Institute of Technology}, 12427 month = mar, 12428 year = {1990}, 12429 number = {90-2}, 12430 key = {Nachtigal | Krylov} 12431} 12432 12433@Article{ nachtigal1992fnm, 12434 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12435 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 12436 journal = {SIAM Journal on Matrix Analysis and Applications}, 12437 volume = {13}, 12438 pages = {778}, 12439 year = {1992}, 12440 publisher = {SIAM} 12441} 12442 12443@TechReport{ embree1999descriptive, 12444 title = {How descriptive are {GMRES} convergence bounds}, 12445 author = {Embree, M.}, 12446 year = {1999}, 12447 number = {08}, 12448 institution = {Oxford University Computing Laboratory} 12449} 12450 12451@Article{ vorst92, 12452 author = {H. van der Vorst}, 12453 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 12454 of nonsymmetric linear systems}, 12455 journal = {SIAM J. Sci. Stat. Comput.}, 12456 year = {1992}, 12457 volume = {13}, 12458 pages = {631--644} 12459} 12460 12461@Article{ eisenstat81, 12462 author = {S. Eisenstat}, 12463 title = {Efficient Implementation of a Class of {CG} Methods}, 12464 journal = {SIAM J. Sci. Stat. Comput.}, 12465 year = {1981}, 12466 volume = {2}, 12467 pages = {1--4} 12468} 12469 12470@Manual{ ibm-essl, 12471 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 12472 Reference}, 12473 organization = {IBM}, 12474 year = {1992}, 12475 key = {IBM-ESSL} 12476} 12477 12478@Manual{ ibm-eui, 12479 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 12480 Release 2.0}, 12481 organization = {IBM}, 12482 month = jun, 12483 year = {1994}, 12484 key = {IBM-EUI} 12485} 12486 12487@Manual{ ibm-euih, 12488 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 12489 organization = {IBM}, 12490 author = {Peter Hochschild}, 12491 year = {1993}, 12492 key = {IBM-EUIH} 12493} 12494 12495@TechReport{ mpi, 12496 title = {Document for a Standard Message-Passing Interface}, 12497 author = {Message Passing Interface Forum}, 12498 institution = {University of Tennessee}, 12499 number = {CS-93-214}, 12500 month = nov, 12501 year = {1993}, 12502 key = {MPI Standard} 12503} 12504 12505@Unpublished{ mpi-final-web, 12506 author = {Message Passing Interface Forum}, 12507 title = {{MPI}: A Message-Passing Interface Standard}, 12508 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 12509 year = {1994}, 12510 month = may 12511} 12512 12513@Book{ hockney-jesshope, 12514 author = {R. W. Hockney and C. R. Jesshope}, 12515 title = {Parallel Computers 2}, 12516 publisher = {Adam Hilger}, 12517 year = {1988} 12518} 12519 12520@Book{ cm-fortran, 12521 author = {{Thinking Machines Corporation}}, 12522 title = {Users Manual for CM-Fortran}, 12523 publisher = {Thinking Machines Corporation}, 12524 year = {1993} 12525} 12526 12527@TechReport{ chang93, 12528 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 12529 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 12530 institution = {Yale Department of Computer Science}, 12531 number = {YALEU/DCS/RR-994}, 12532 month = nov, 12533 year = {1993}, 12534 key = {BDD|diag} 12535} 12536 12537@InProceedings{ gropplevine93, 12538 author = {N. Galbreath and W. Gropp and D. Levine}, 12539 title = {Applications-Driven Parallel {I/O}}, 12540 booktitle = {Proceedings of Supercomputing '93}, 12541 year = {1993}, 12542 pages = {462--471} 12543} 12544 12545@Book{ siegle85, 12546 author = {H. J. Siegel}, 12547 title = {Interconnection Networks for Large Scale Parallel Processing}, 12548 publisher = {Lexington Books}, 12549 year = {1985}, 12550 key = {Network Comparison} 12551} 12552 12553@Article{ lawrie75, 12554 author = {D. H. Lawrie}, 12555 title = {Access and alignment of data in an array processor}, 12556 journal = {IEEE Transactions on Computers}, 12557 volume = {C-24}, 12558 number = {12}, 12559 month = dec, 12560 year = {1975}, 12561 pages = {1145--1155}, 12562 key = {Omega Network} 12563} 12564 12565@Book{ knuth1986, 12566 title = {The {\TeX}{Book}}, 12567 author = {Donald Ervin Knuth and Duane Bibby}, 12568 volume = {1993}, 12569 year = {1986}, 12570 publisher = {Addison-Wesley Reading, Massachusetts} 12571} 12572 12573@Book{ lamport86, 12574 author = {Leslie Lamport}, 12575 title = {{LaTeX}: A document preparation system}, 12576 publisher = {Addison-Wesley}, 12577 year = {1986}, 12578 key = {Latex Manual} 12579} 12580 12581@InProceedings{ gropp-lusk:unix-tools, 12582 author = {William Gropp and Ewing Lusk}, 12583 title = {Scalable {U}nix Tools on Parallel Processors}, 12584 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 12585 publisher = {IEEE}, 12586 pages = {56--62} 12587} 12588 12589@InProceedings{ jp:bell_prize, 12590 author = {Mark Jones and Paul Plassmann}, 12591 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 12592 Applications}, 12593 booktitle = {Proceedings of Supercomputing '92}, 12594 publisher = {IEEE Computer Society Press}, 12595 year = {1992}, 12596 pages = {551--560} 12597} 12598 12599@COMMENT{WEB, CWEB references (for doctext)} 12600@TechReport{ web, 12601 author = {Donald E. Knuth}, 12602 title = {The {\tt WEB} system of structured documentation}, 12603 institution = {Computer Science Department, Stanford University}, 12604 year = {1983}, 12605 number = {980}, 12606 month = sep 12607} 12608 12609@Article{ literatepgm, 12610 author = {Donald E. Knuth}, 12611 title = {Literate Programming}, 12612 journal = {Computer Journal}, 12613 year = {1984}, 12614 volume = {27}, 12615 number = {2}, 12616 pages = {91--111} 12617} 12618 12619@Unpublished{ cweb-code, 12620 author = {Silvio Levy and Donald E. Knuth}, 12621 title = {CWEB}, 12622 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 12623} 12624 12625@Article{ jp:scalable, 12626 author = {Mark Jones and Paul Plassmann}, 12627 title = {Scalable Iterative Solution of Sparse Linear Systems}, 12628 journal = {Parallel Computing}, 12629 volume = {20}, 12630 number = {5}, 12631 month = may, 12632 year = {1994}, 12633 pages = {753--773} 12634} 12635 12636@Article{ jp:pcolor, 12637 author = {Mark T. Jones and Paul E. Plassmann}, 12638 title = {A Parallel Graph Coloring Heuristic}, 12639 journal = {SIAM J. Sci. Comput.}, 12640 volume = {14}, 12641 number = {3}, 12642 pages = {654-669}, 12643 year = {1993} 12644} 12645 12646@TechReport{ block_solve, 12647 author = {Mark T. Jones and Paul E. Plassmann}, 12648 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 12649 Sparse Linear Systems}, 12650 institution = {Argonne National Laboratory}, 12651 year = {1992}, 12652 number = {ANL-92/46}, 12653 key = {JonesPlassmann92 ! block_solve} 12654} 12655 12656@InProceedings{ supercond, 12657 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 12658 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 12659 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 12660 Conference}, 12661 month = feb, 12662 year = {1994}, 12663 key = {McInnesPalumbo94 ! superconductivity } 12664} 12665 12666@Unpublished{ preosti:93, 12667 author = {Gianfranco Preosti}, 12668 title = { }, 12669 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 12670 year = {1993}, 12671 key = {preosti93 ! GL-tilt3d} 12672} 12673 12674@Unpublished{ more:93, 12675 author = {Jorge J. Mor\'{e}}, 12676 title = { }, 12677 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 12678 {A}rgonne {N}ational {L}aboratory}, 12679 year = {1993}, 12680 key = {more93 ! MINPACK-2} 12681} 12682 12683@Article{ brownsaad:90, 12684 author = {Peter N. Brown and Youcef Saad}, 12685 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 12686 journal = {SIAM J. Sci. Stat. Comput.}, 12687 year = {1990}, 12688 volume = {11}, 12689 pages = {450-481} 12690} 12691 12692@Book{ using-mpi, 12693 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 12694 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 12695 publisher = {MIT Press}, 12696 year = {1994} 12697} 12698 12699@Book{ using-mpi2, 12700 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 12701 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 12702 publisher = {MIT Press}, 12703 year = {1999} 12704} 12705 12706@Article{ hs:52, 12707 author = {Magnus R. Hestenes and Eduard Steifel}, 12708 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 12709 journal = {J. Research of the National Bureau of Standards}, 12710 year = {1952}, 12711 volume = {49}, 12712 pages = {409-436} 12713} 12714 12715@Article{ ss:86, 12716 author = {Youcef Saad and Martin H. Schultz}, 12717 title = {{GMRES}: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear 12718 Systems}, 12719 journal = {SIAM J. Sci. Stat. Comput.}, 12720 year = {1986}, 12721 volume = {7}, 12722 pages = {856-869} 12723} 12724 12725@Article{ so:89, 12726 author = {Peter Sonneveld}, 12727 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 12728 journal = {SIAM J. Sci. Stat. Comput.}, 12729 year = {1989}, 12730 volume = {10}, 12731 pages = {36-52} 12732} 12733 12734@Article{ v:92, 12735 author = {{H. A.} {van der Vorst}}, 12736 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 12737 of nonsymmetric linear systems}, 12738 journal = {SIAM J. Sci. Stat. Comput.}, 12739 volume = {13}, 12740 year = {1992}, 12741 pages = {631-644} 12742} 12743 12744@Article{ f:93, 12745 author = {Roland W. Freund}, 12746 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 12747 Systems}, 12748 journal = {SIAM J. Sci. Stat. Comput.}, 12749 volume = {14}, 12750 year = {1993}, 12751 pages = {470-482} 12752} 12753 12754@Article{ ish:89, 12755 author = {S. Ishizuka}, 12756 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 12757 journal = {Combustion and Flame}, 12758 volume = {75}, 12759 year = {1989}, 12760 pages = {367-379} 12761} 12762 12763@Book{ williams89, 12764 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 12765 author = {F.A. Williams}, 12766 publisher = {Addison-Wesley}, 12767 year = {1989}, 12768 pages = {367-379} 12769} 12770 12771@Book{ ra75, 12772 author = {R. Aris}, 12773 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 12774 publisher = {Oxford}, 12775 year = {1975} 12776} 12777 12778@Book{ bebernes89, 12779 author = {J. Bebernes and D. Eberly}, 12780 title = {Mathematical Problems from Combustion Theory}, 12781 publisher = {Springer-Verlag}, 12782 series = {Applied Mathematical Sciences 83}, 12783 year = {1989} 12784} 12785 12786@InProceedings{ kikuchi89, 12787 author = {F. Kikuchi}, 12788 booktitle = { Computing Methods in Applied Sciences and Engineering}, 12789 editor = {R. Glowinski and J. L. Lions}, 12790 publisher = {Springer-Verlag}, 12791 series = {Lecture Notes in Mathematics}, 12792 title = {Finite element approximations to bifurcation problems of turning point type}, 12793 year = {1977} 12794} 12795 12796@Article{ rg85, 12797 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 12798 title = {Continuation-conjugate Gradient Methods fo the Least Squares Solution of 12799 Nonlinear Boundary Problems}, 12800 journal = {SIAM J. Sci. Stat. Comput.}, 12801 volume = {6}, 12802 year = {1985}, 12803 pages = {793-832} 12804} 12805 12806@InProceedings{ whitfield91, 12807 author = {D. Whitfield and L. Taylor}, 12808 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12809 Schemes}, 12810 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 12811 misc = {AIAA-91-1539}, 12812 pages = {134-145}, 12813 year = {1991} 12814} 12815 12816@InProceedings{ quinlan1, 12817 author = {M. Lemke and D. Quinlan}, 12818 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 12819 Architecture-Independent Development of Structured Grid Applications}, 12820 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 12821 publisher = {Springer Verlag}, 12822 year = {1992} 12823} 12824 12825@InProceedings{ quinlan2, 12826 author = {R. Parsons and D. Quinlan}, 12827 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 12828 Computations}, 12829 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 12830 year = {1994} 12831} 12832 12833% ***** Overview of functionality in Diffpack 12834@InBook{ dpoverview, 12835 author = {Bruaset, A. M. and Langtangen, H. P.}, 12836 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12837 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 12838 {Diffpack}}, 12839 publisher = {Birkh{\"{a}}user}, 12840 pages = {61--90}, 12841 year = {1997} 12842} 12843 12844% ***** Short overview of Diffpack 12845@InCollection{ dpoverview2, 12846 author = {Bruaset, A. M. and Langtangen, H. P.}, 12847 editor = {A. Sydow}, 12848 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 12849 and Applied Mathematics}, 12850 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 12851 pages = {553--558}, 12852 volume = {4}, 12853 year = {1997} 12854} 12855 12856% ***** Comprehensive documentation of Diffpack and 12857% associated numerical methods: 12858@Book{ dpbook, 12859 author = {H. P. Langtangen}, 12860 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 12861 Software. Part I}, 12862 series = {Lecture Notes in Computational Science and Engineering}, 12863 publisher = {Springer-Verlag}, 12864 year = {1998} 12865} 12866 12867% ***** Design issues of the linear solvers in Diffpack, serves also as a 12868% collection of examples on O-O in numerical computing 12869@Article{ ambhpl97a, 12870 author = {A. M. Bruaset and H. P. Langtangen }, 12871 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 12872 journal = {Transactions on Mathematical Software}, 12873 volume = {23 }, 12874 pages = {50--80}, 12875 year = {1997} 12876} 12877 12878@Misc{ dpurl, 12879 author = {{Diffpack Web page}}, 12880 howpublished = {\url{http://www.diffpack.com}} 12881} 12882 12883% ***** General intro to object-oriented numerics for "FORTRAN programmers" 12884@InCollection{ oonintro, 12885 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 12886 editor = {D{\ae}hlen, M. and Tveito, A.}, 12887 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12888 title = {Object-Oriented Numerics}, 12889 publisher = {Birkh{\"{a}}user}, 12890 year = {1997} 12891} 12892 12893% ***** Efficiency comparison: BLAS 1, Diffpack, C, 12894% and finite element applications (F77 vs Diffpack) 12895@InCollection{ dpefficiency, 12896 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 12897 H. P. and Miller, C. T.}, 12898 editor = {D{\ae}hlen, M. and Tveito, A.}, 12899 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12900 title = {On the Efficiency of {C++} in Scientific Computing}, 12901 publisher = {Birkh{\"{a}}user}, 12902 pages = {91--118}, 12903 year = {1997} 12904} 12905 12906% ***** Parallel concept in Diffpack: 12907@InCollection{ dpparallel, 12908 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 12909 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 12910 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 12911 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 12912 Simulators}, 12913 publisher = {Springer--Verlag}, 12914 series = {Lecture Notes in Computer Science}, 12915 pages = {161--168}, 12916 year = {1997} 12917} 12918 12919% ***** DD and ML methods in Diffpack: 12920@InCollection{ dpddml, 12921 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 12922 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 12923 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 12924 title = {Domain decomposition and multilevel methods in Diffpack}, 12925 year = {1997} 12926} 12927 12928@InProceedings{ bsca98, 12929 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 12930 Alexander}, 12931 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 12932 Optimization}, 12933 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12934 Scientific and Engineering Computing}, 12935 editor = {Mike Henderson et al.}, 12936 pages = {165-173}, 12937 year = {1998} 12938} 12939 12940@Book{ scalapack-user-guide, 12941 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 12942 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 12943 Stanley and D. Walker and R. C. Whaley}, 12944 title = {Sca{LAPACK} Users' Guide}, 12945 publisher = {SIAM}, 12946 address = {Philadelphia, PA}, 12947 year = {1997} 12948} 12949 12950@InProceedings{ keyes99, 12951 author = {D. E. Keyes}, 12952 title = {How Scalable is Domain Decomposition in Practice?}, 12953 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 12954 Methods}, 12955 editor = {C.-H. Lai et al.}, 12956 publisher = {Domain Decomposition Press, Bergen}, 12957 note = {To appear}, 12958 year = {1999} 12959} 12960 12961@Article{ fun3d, 12962 author = {W. K. Anderson and D. L. Bonhaus}, 12963 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 12964 grids}, 12965 journal = {Computers and Fluids}, 12966 year = {1994}, 12967 volume = {23}, 12968 pages = {1--21} 12969} 12970 12971% ------------------------------------------------------------------------- 12972% ------------------------------------------------------------------------- 12973@Article{ torczon, 12974 author = {Dennis, Jr., J. E. and V.~Torczon}, 12975 title = {Direct Search Methods on Parallel Machines}, 12976 journal = {SIAM J. Optimization}, 12977 volume = {1}, 12978 pages = {448--474}, 12979 year = {1991}, 12980 key = {Torczon !PDS} 12981} 12982 12983@InProceedings{ wt91, 12984 author = {D. L. Whitfield and L. K. Taylor}, 12985 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12986 Schemes}, 12987 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 12988 misc = {AIAA-91-1539}, 12989 pages = {134-145}, 12990 year = {1991} 12991} 12992 12993@Article{ ew96, 12994 author = {S. C. Eisenstat and H. F. Walker}, 12995 title = {Choosing the forcing terms in an inexact {N}ewton method}, 12996 journal = {SIAM J. Scientific Computing}, 12997 volume = {17}, 12998 year = {1996}, 12999 pages = {16--32} 13000} 13001 13002@Book{ thi93, 13003 author = {{Thinking Machines Corporation}}, 13004 title = {Users Manual for CM-Fortran}, 13005 publisher = {Thinking Machines Corporation}, 13006 year = {1993} 13007} 13008 13009@Book{ mortonmayers94, 13010 author = {K. W. Morton and D. F. Mayers}, 13011 title = {Numerical Solution of Partial Differential Equations}, 13012 publisher = {Press Syndicate of the University of Cambridge}, 13013 year = {1994} 13014} 13015 13016@Book{ heath97, 13017 author = {Michael T. Heath}, 13018 title = {Scientific Computing: An Introductory Survey}, 13019 publisher = {McGraw Hill}, 13020 year = {1997} 13021} 13022 13023@Article{ captools96, 13024 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 13025 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 13026 Performance on the Parallelization of Structured Mesh Codes}, 13027 journal = {Parallel Computing}, 13028 volume = {22}, 13029 pages = {197-226}, 13030 year = {1996} 13031} 13032 13033@Unpublished{ nastran-web-page, 13034 author = {{MSC Software Corporation}}, 13035 title = {{NASTRAN} {W}eb page}, 13036 note = {See {\tt http://www.mechsolutions.com\-/products\-/nastran/}} 13037} 13038 13039@Book{ hpf, 13040 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 13041 Zosel}, 13042 title = {The High Performance Fotran Handbook}, 13043 publisher = {MIT Press}, 13044 year = {1994} 13045} 13046 13047@InProceedings{ keyes98, 13048 author = {D. E. Keyes}, 13049 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 13050 Architectures}, 13051 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 13052 editors = {M. D. Salas and W. K. Anderson}, 13053 ppublisher = {Elsevier}, 13054 year = {1998} 13055} 13056 13057@InProceedings{ pooma-atlas, 13058 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 13059 J. V. W. Reynders and M. Tholburn}, 13060 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 13061 Applications}, 13062 year = {1995}, 13063 month = dec, 13064 booktitle = {Supercomputing '95 Proceedings} 13065} 13066 13067% --------------------------------------------------------------------------------- 13068% New bib entries for CRPC paper 13069@Misc{ mgnet-web-page, 13070 author = {Craig C. Douglas}, 13071 title = {{MGNet Web page}}, 13072 note = {See {\tt http://\-www.mgnet.org}} 13073} 13074 13075@Misc{ dagh-web-page, 13076 author = {M. Parashar and J. C. Browne}, 13077 title = {{DAGH Web page}}, 13078 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 13079} 13080 13081@Misc{ parasol-web-page, 13082 key = {PARASOL}, 13083 title = {{PARASOL Web page}}, 13084 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 13085} 13086 13087@Misc{ pooma-web-page, 13088 author = {{POOMA Web page}}, 13089 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 13090} 13091 13092@Misc{ mudpack-web-page, 13093 author = {John C. Adams}, 13094 title = {{MUDPACK Web page}}, 13095 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 13096} 13097 13098@Misc{ pellpack-web-page, 13099 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 13100 title = {{Parallel ELLPACK Web page}}, 13101 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 13102} 13103 13104@InProceedings{ pellpack95, 13105 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 13106 Catlin and S. Weerawarana and T.S. Papatheodorou}, 13107 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 13108 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 13109 address = {Albuquerque, NM}, 13110 year = {1995} 13111} 13112 13113@Misc{ nhse-web-page, 13114 author = {{National High-Performance Software Exchange Web page}}, 13115 note = {See {\tt http://\-www.nhse.org}} 13116} 13117 13118@Misc{ doug-web-page, 13119 author = {Mark J. Hagger and Linda Stals}, 13120 title = {{DOUG Web Page}}, 13121 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 13122} 13123 13124@TechReport{ doug97, 13125 author = {Mark J. Hagger}, 13126 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 13127 institution = {Mathematical Sciences, University of Bath}, 13128 year = {1997}, 13129 number = {9706}, 13130 note = {Advances in Computational Mathematics (to appear)} 13131} 13132 13133@Misc{ ug-web-page, 13134 author = {{UG Web Page}}, 13135 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 13136} 13137 13138@Article{ ug97, 13139 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 13140 Rentz-Reichert and C. Wieners}, 13141 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 13142 journal = {Computing and Visualization in Science}, 13143 year = {1997}, 13144 volume = {}, 13145 pages = {} 13146} 13147 13148@Misc{ vecfem-web-page, 13149 author = {Lutz Grosz}, 13150 title = {{VECFEM Web Page}}, 13151 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 13152} 13153 13154@Misc{ atlas-web-page, 13155 author = {R. Clint {Whaley et al.}}, 13156 title = {{ATLAS Web Page}}, 13157 howpublished = {\url{http://math-atlas.sourceforge.net}} 13158} 13159 13160@Misc{ fenics-web-page, 13161 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 13162 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 13163 title = {{FEniCS Web Page}}, 13164 note = {\url{http://www.fenicsproject.org}}, 13165 year = {2005} 13166} 13167 13168@Misc{ matlab-web-page, 13169 author = {{The} {MathWorks}}, 13170 title = {{Matlab} {Web} page}, 13171 url = {http://www.mathworks.com} 13172} 13173 13174@Misc{ phipac-web-page, 13175 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 13176 and D. Lam}, 13177 title = {{PHiPAC Web Page}}, 13178 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 13179} 13180 13181@InProceedings{ kelp, 13182 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 13183 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 13184 booktitle = {Irregular '96}, 13185 year = {1996} 13186} 13187 13188@Unpublished{ kelp-web-page, 13189 author = {Scott Baden}, 13190 title = {{KeLP} {W}eb page}, 13191 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 13192} 13193 13194@InProceedings{ hk99, 13195 author = {R. Hornung and S. Kohn}, 13196 title = {The Use of Object-Oriented Design Patterns in the {SAMRAI} Structured {AMR} 13197 Framework}, 13198 booktitle = {Proceedings of the SIAM Workshop on Object-Oriented Methods for Inter-Operable 13199 Scientific and Engineering Computing}, 13200 pages = {235-244}, 13201 year = {1999}, 13202 note = {See \url{http://www.llnl.gov/CASC/samrai}} 13203} 13204 13205@Unpublished{ samrai-web-page, 13206 title = {{SAMRAI} {W}eb Page}, 13207 author = {Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith}, 13208 note = {See {\tt http://www.llnl.gov/\-CASC/SAMRAI}} 13209} 13210 13211@Misc{ overture-web-page, 13212 author = {William Henshaw and Kyle Chand}, 13213 title = {{Overture} {W}eb page}, 13214 howpublished = {\url{http://www.llnl.gov/CASC/Overture}} 13215} 13216 13217@InProceedings{ overture99, 13218 author = {D.L. Brown and W.D. Henshaw and D.J. Quinlan}, 13219 title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations 13220 on Overlapping Grids}, 13221 publisher = {SIAM}, 13222 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 13223 Scientific and Engineering Computing}, 13224 year = {1999}, 13225 pages = {215-224}, 13226 note = {See \url{http://www.llnl.gov/CASC/Overture}} 13227} 13228 13229@InProceedings{ diffpack, 13230 author = {A.M. Bruaset and H.P. Langtangen}, 13231 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations: 13232 {D}iffpack}, 13233 booktitle = {Numerical Methods and Software Tools in Industrial Mathematics}, 13234 year = {1997}, 13235 pages = {61--90}, 13236 publisher = {Birkhauser Press} 13237} 13238 13239@Article{ dongarra:1984:ila, 13240 author = {J. J. Dongarra and F. G. Gustavson and A. Karp}, 13241 title = {Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline 13242 Machine}, 13243 journal = {SIAM Review}, 13244 volume = {26}, 13245 number = {1}, 13246 pages = {91--112}, 13247 month = jan, 13248 year = {1984}, 13249 coden = {SIREAD}, 13250 issn = {0036-1445 (print), 1095-7200 (electronic)}, 13251 mrclass = {65F10 (65F30)}, 13252 mrnumber = {85c:65032}, 13253 bibdate = {Mon Jan 20 1997}, 13254 abstract = {The authors examine common implementations of linear algebra algorithms, such as 13255 matrix-vector multiplication, matrix-matrix multiplication and the solution of 13256 linear equations. The different versions are examined for efficiency on a computer 13257 architecture which uses vector processing and has pipelined instruction execution. 13258 By using the advanced architectural features of such machines, one can usually 13259 achieve maximum performance, and tremendous improvements in terms of execution 13260 speed can be seen over conventional computers.}, 13261 classification= {723; 921}, 13262 journalabr = {SIAM Rev}, 13263 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 13264 mathematical programming; vector pipeline machine} 13265} 13266 13267@Book{ qv99, 13268 author = {Alfio Quarteroni and Alberto Valli}, 13269 title = {Domain Decomposition Methods for Partial Differential Equations}, 13270 publisher = {Oxford Science Publications}, 13271 address = {Oxford}, 13272 year = {1999} 13273} 13274 13275@Book{ ksv97, 13276 editor = {David E. Keyes and Ahmed Sameh and V. Venkatakrishnan}, 13277 title = {Parallel Numerical Algorithms}, 13278 publisher = {Kluwer Academic Publishers}, 13279 address = {the Netherlands}, 13280 year = {1997} 13281} 13282 13283@Book{ hackbusch94, 13284 author = {Wolfgang Hackbusch}, 13285 title = {Iterative Solution of Large Sparse Systems of Equations}, 13286 publisher = {Springer-Verlag}, 13287 address = {New York}, 13288 year = {1994} 13289} 13290 13291@Article{ hackbusch1980fast, 13292 title = {Fast solution of elliptic control problems}, 13293 author = {Hackbusch, W.}, 13294 journal = {Journal of Optimization Theory and Applications}, 13295 volume = {31}, 13296 number = {4}, 13297 pages = {565--581}, 13298 year = {1980}, 13299 publisher = {Springer} 13300} 13301 13302@Book{ hackbusch1985multi, 13303 title = {{Multi-grid methods and applications}}, 13304 author = {Hackbusch, W.}, 13305 isbn = {3540127615}, 13306 issn = {0179-3632}, 13307 year = {1985}, 13308 publisher = {Springer Verlag} 13309} 13310 13311@Book{ axelsson94, 13312 author = {Owe Axelsson}, 13313 title = {Iterative Solution Methods}, 13314 publisher = {Cambridge University Press}, 13315 address = {Cambridge}, 13316 year = {1994} 13317} 13318 13319@Book{ saad96, 13320 author = {Yousef Saad}, 13321 title = {Iterative Methods for Sparse Linear Systems}, 13322 publisher = {PWS Publishing Company}, 13323 address = {Boston}, 13324 year = {1996} 13325} 13326 13327@Book{ saad2003, 13328 title = {Iterative Methods for Sparse Linear Systems}, 13329 author = {Saad, Yousef}, 13330 doi = {10.1016/S1570-579X(01)80025-2}, 13331 edition = {2nd}, 13332 publisher = {SIAM}, 13333 year = {2003} 13334} 13335 13336@Book{ vandervorst03, 13337 author = {Henk A. {van der Vorst}}, 13338 title = {Iterative Krylov Methods for Large Linear Systems}, 13339 publisher = {Cambridge Monographs on Applied ahd Computational Mathematics}, 13340 year = {2003} 13341} 13342 13343@Book{ koniges00, 13344 editor = {Alice E. Koniges}, 13345 title = {Industrial Strength Parallel Computing}, 13346 publisher = {Morgan Kaufmann Publishers}, 13347 address = {San Francisco}, 13348 year = {2000} 13349} 13350 13351@Misc{ fftw-web-page, 13352 key = {Fftw}, 13353 title = {{FFTW} {Web} page}, 13354 note = {\texttt{http://www.fftw.org/}}, 13355 annote = {fast FFT. Parallel versions with MPI and Cilk} 13356} 13357 13358@InProceedings{ frigojohnson93, 13359 author = {Matteo Frigo and Steven G. Johnson}, 13360 title = {The Design and Implementation of {FFTW3}}, 13361 booktitle = {Proceedings of the IEEE}, 13362 volume = {93}, 13363 number = {2}, 13364 pages = {216--231}, 13365 year = {2005} 13366} 13367 13368@Book{ kelley95, 13369 author = {C. T. Kelley}, 13370 title = {Iterative Methods for Linear and Nonlinear Equations}, 13371 year = {1995}, 13372 publisher = {SIAM}, 13373 address = {Philadelphia} 13374} 13375 13376@Unpublished{ spai-web-page, 13377 title = {{SPAI} {W}eb {P}age}, 13378 note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/}, 13379 author = {Steven Bernard and Marcus Grote}, 13380 institution = {NASA Ames Research Center and ETH Zurich} 13381} 13382 13383@Article{ gh97, 13384 author = {M. J. Grote and T. Huckle}, 13385 title = {Parallel Preconditioning with Sparse Approximate Inverses}, 13386 year = {1997}, 13387 journal = {SIAM J. of Scient. Comput.}, 13388 volume = {18}, 13389 pages = {838-853} 13390} 13391 13392@Article{ zhang96, 13393 author = {Wen Zhang}, 13394 title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the 13395 simulation of a sintering process}, 13396 year = {1996}, 13397 journal = {Appl. Numer. Math.}, 13398 volume = {20}, 13399 pages = {235-244} 13400} 13401 13402@Article{ zhang98, 13403 author = {Wen Zhang and Ian Gladwell}, 13404 title = {The sintering of two particles by surface and grain boundary diffusion - a 13405 three-dimensional numerical study}, 13406 journal = {Comp. Mater. Sci.}, 13407 year = {1998}, 13408 volume = {12} 13409} 13410 13411@InProceedings{ mollerschwartzbach01, 13412 author = {Anders M\o{}ller and Michael I. Schwartzbach}, 13413 title = {The Pointer Assertion Logic Engine}, 13414 booktitle = {ACM Proceedings of PLDI'01}, 13415 year = {2001} 13416} 13417 13418@InProceedings{ klarlandschwartzbach97, 13419 author = {Nils Klarland and Michael I. Schwartzbach}, 13420 title = {A Domain-Specific Languages for Regular Sets of Strings and Trees}, 13421 booktitle = {Proceedings of the Conference on Domain-Specific Languages}, 13422 publisher = {USENIX}, 13423 month = oct, 13424 year = {1997}, 13425 address = {Santa Barbara, CA} 13426} 13427 13428@InProceedings{ conselmarlet98, 13429 author = {C. Consel and R. Marlet}, 13430 title = {Architecturing software using a methodology for language development}, 13431 booktitle = {Proceedings of the 10th International Symposium on Programming Languages, 13432 Implementations, Logics and Programs}, 13433 year = {1998}, 13434 pages = {170-174}, 13435 month = sep, 13436 address = {Pisa, Italy} 13437} 13438 13439@Misc{ sundials:homepage, 13440 author = {C. {Woodward et al.}}, 13441 title = {{SUNDIALS {W}eb page}}, 13442 howpublished = {\url{https://computation.llnl.gov/casc/sundials/main.html}} 13443} 13444 13445@article{gardner2022sundials, 13446 title = {Enabling new flexibility in the {SUNDIALS} suite of nonlinear and differential/algebraic equation solvers}, 13447 author = {Gardner, David J and Reynolds, Daniel R and Woodward, Carol S and Balos, Cody J}, 13448 journal = {ACM Transactions on Mathematical Software (TOMS)}, 13449 publisher = {ACM}, 13450 year = {2022}, 13451 doi = {10.1145/3539801} 13452} 13453 13454@Misc{ sundials-user-ref, 13455 title = {{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13456 note = {See \url{http://www.llnl.gov/CASC/sundials}}, 13457 author = {Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban 13458 and Dan Shumaker and Carol Woodward}, 13459 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 13460 number = {UCRL-JP-200037}, 13461 year = {2003} 13462} 13463 13464@Article{ sundials05, 13465 author = {A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 13466 and C. Woodward}, 13467 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13468 journal = {ACM Transactions on Mathematical Software}, 13469 volume = {31}, 13470 number = {3}, 13471 pages = {363--396}, 13472 year = {2005} 13473} 13474 13475@InProceedings{ serban2005cvodes, 13476 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 13477 author = {Serban, Radu and Hindmarsh, Alan C}, 13478 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 13479 Dynamics and Control, Long Beach, CA}, 13480 year = {2005} 13481} 13482 13483@Article{ pvode99, 13484 author = {G. Byrne and A. Hindmarsh}, 13485 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 13486 journal = {Int. J. High Perf. Comput. Apps.}, 13487 volume = {13}, 13488 number = {4}, 13489 year = {1999}, 13490 pages = {354 -- 365} 13491} 13492 13493@Article{ cvode95, 13494 author = {S. Cohen and A. Hindmarsh}, 13495 title = {{CVODE}, A Stiff/Nonstiff {ODE} Solver in {C}}, 13496 journal = {Computers in Physics}, 13497 volume = {10}, 13498 number = {2}, 13499 year = {1996}, 13500 pages = {138 -- 143} 13501} 13502 13503@TechReport{ ifpack, 13504 title = {Robust Algebraic Preconditioners using {IFPACK} 3.0}, 13505 author = {Marzio Sala and Michael Heroux}, 13506 institution = {Sandia National Laboratories}, 13507 number = {SAND2005-0662}, 13508 year = {2005} 13509} 13510 13511@TechReport{ kinsol-user-ref, 13512 title = {User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel 13513 Computers}, 13514 author = {Allan Taylor and Alan Hindmarsh}, 13515 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 13516 number = {UCRL-ID-131185}, 13517 year = {1998} 13518} 13519 13520@Article{ fiardmanteuffelmccormick98, 13521 author = {J.-M. Fiard and T. Manteuffel and S. McCormick}, 13522 title = {First-order system least squares {(FOSLS)} for convection-diffusion problems: 13523 numerical results}, 13524 journal = {SIAM J. Sci. Comp.}, 13525 year = {1998}, 13526 volume = {19}, 13527 pages = {1958--1979} 13528} 13529 13530@InProceedings{ vuduc02, 13531 author = {Richard Vuduc and James W. Demmel and Katherine A. Yelick and Shoaib Kamil and 13532 Rajesh Nishtala and Benjamin Lee}, 13533 title = {Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply}, 13534 booktitle = {Proceedings of Supercomputing}, 13535 year = {2002}, 13536 month = nov, 13537 address = {Baltimore} 13538} 13539 13540@Article{ beckerbraackrannacher1999, 13541 title = {Numerical simulation of laminar flames at low Mach number by adaptive finite 13542 elements}, 13543 author = {Roland Becker and Malte Braack and Rolf Rannacher}, 13544 journal = {Combustion Theory and Modelling}, 13545 volume = {3}, 13546 pages = {503--534}, 13547 year = {1999} 13548} 13549 13550@Article{ beckerrannacher01, 13551 author = {R. Becker and R. Rannacher}, 13552 title = {An optimal control approach to a posteriori error estimation in finite element 13553 methods}, 13554 journal = {Acta Numerica}, 13555 year = {2001}, 13556 volume = {10}, 13557 pages = {1--102} 13558} 13559 13560@Article{ babuskamiller84a, 13561 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13562 title = {The post-processing approach in the finite element method, {I}: Calculations of 13563 displacements, stresses, and other higher derivatives of the displacements}, 13564 journal = {Int. J. Numer. Meth. Eng.}, 13565 year = {1984}, 13566 volume = {20}, 13567 pages = {1085--1109} 13568} 13569 13570@Article{ babuskamiller84b, 13571 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13572 title = {The post-processing approach in the finite element method, {II}: The calculation 13573 of stress intensity factors}, 13574 journal = {Int. J. Numer. Meth. Eng.}, 13575 year = {1984}, 13576 volume = {20}, 13577 pages = {1111--1129} 13578} 13579 13580@Article{ babuskamiller84c, 13581 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13582 title = {The post-processing approach in the finite element method, {III}: A posteriori 13583 error estimation and adaptive mesh refinement}, 13584 journal = {Int. J. Numer. Meth. 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Fishwick}, 14983 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 14984 to Interrelating Model Structures}, 14985 journal = {SCS Trans. on Simulation}, 14986 note = {Special Issue in Grand Challenges in Computer Simulation}, 14987 year = {2004} 14988} 14989 14990@Article{ fishwick03, 14991 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 14992 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 14993 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 14994 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 14995 year = {2003} 14996} 14997 14998@InProceedings{ kirner00, 14999 author = {T. G. Kirner and V. F. Martins}, 15000 title = {Development of an Information Visualization Tool Using Virtual Reality}, 15001 booktitle = {Proceedings of the 2000 ACM Symposium on Applied Computing}, 15002 year = {2000}, 15003 pages = {604--606} 15004} 15005 15006@InProceedings{ orso03, 15007 author = {A. Orso and J. Jones and M. J. Harrold}, 15008 title = {Visualization of Program-Execution Data for Deployed Software}, 15009 booktitle = {Proceedings of the 2003 ACM Symposium on Software Visualization}, 15010 year = {2003}, 15011 pages = {67--76} 15012} 15013 15014@Book{ tiller01, 15015 author = {M. Tiller}, 15016 title = {Introduction to Physical System Modeling with Modelica}, 15017 series = {Kluwer International Series inEngineering and Computer Science}, 15018 volume = {615}, 15019 publisher = {Kluwer}, 15020 year = {2001} 15021} 15022 15023@Article{ buck94, 15024 author = {J. Buck and S. Ha and E. Lee and D. Messerschmitt}, 15025 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 15026 journal = {Int. Journal of Computer Simulation}, 15027 volume = {4}, 15028 pages = {155--182}, 15029 year = {1994} 15030} 15031 15032@Article{ mu95, 15033 author = {M. Mu and J.R. Rice}, 15034 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 15035 journal = {Comp. Syst. Engr.}, 15036 volume = {6}, 15037 year = {1995}, 15038 pages = {87--95} 15039} 15040 15041@TechReport{ drashansky96, 15042 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 15043 author = {R. Drashansky and A. Joshi and J. R. Rice}, 15044 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 15045 year = {1996} 15046} 15047 15048@Article{ michopoulos05, 15049 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 15050 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 15051 journal = {Journal of Computing and Information Science in Engineering}, 15052 volume = {5}, 15053 issue = {3}, 15054 pages = {198--213}, 15055 year = {2005} 15056} 15057 15058@Article{ dubey09, 15059 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 15060 Multiphysics Simulation Code}, 15061 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 15062 Siegel and K. Weide}, 15063 journal = {Parallel Computing}, 15064 volume = {35}, 15065 issue = {10 -- 11}, 15066 pages = {512 -- 522}, 15067 year = {2009} 15068} 15069 15070@Book{ bottloring95, 15071 author = {Raoul Bott and Loring W. Tu}, 15072 title = {Differential Forms in Algebraic Topology}, 15073 publisher = {Springer}, 15074 year = {1995} 15075} 15076 15077@Book{ kobayashinomizu96, 15078 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 15079 title = {Foundations of Differential Geometry}, 15080 publisher = {Wiley-Interscience}, 15081 year = {1996} 15082} 15083 15084@Article{ hornungkohn02, 15085 author = {Richard D. Hornung and Scott R. Kohn}, 15086 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 15087 journal = {Concurrency and Computation: Practice and Experience}, 15088 volume = {14}, 15089 pages = {347--368}, 15090 year = {2002} 15091} 15092 15093@InProceedings{ concepts06, 15094 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 15095 Gabriel Dos Reis and Andrew Lumsdaine}, 15096 title = {Concepts: Linguistic Support for Generic Programming in C++}, 15097 booktitle = {Proceedings of OOPSLA 2006}, 15098 year = {2006}, 15099 pages = {???--???} 15100} 15101 15102@Book{ hatcher02, 15103 author = {Hatcher, Allen}, 15104 title = {Algebraic Topology}, 15105 publisher = {Cambridge University Press}, 15106 year = {2002} 15107} 15108 15109@Book{ gammahelmjohnsonvlissides95, 15110 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 15111 development, offering timeless and elegant solutions to common problems in 15112 software design. It describes patterns for managing object creation, composing 15113 objects into larger structures, and coordinating control flow between objects. The 15114 book provides numerous examples where using composition rather than inheritance 15115 can improve the reusability and flexibility of code. Note, though, that it's not a 15116 tutorial but a catalog that you can use to find an object-oriented design pattern 15117 that's appropriate for the needs of your particular application--a selection for 15118 virtuoso programmers who appreciate (or require) consistent, well-engineered 15119 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 15120 more valuable than ever! 15121 15122 Use the contents of the CD to create your own design documents and reusable 15123 components. The CD contains: 23 patterns you can cut and paste into your own 15124 design documents; sample code demonstrating pattern implementation; complete 15125 Design Patterns content in standard HTML format, with numerous hyperlinked 15126 cross-references; accessed through a standard web browser; Java-based dynamic 15127 search mechanism, enhancing online seach capabilities; graphical user environment, 15128 allowing ease of navigation. 15129 15130 First published in 1995, this landmark work on object-oriented software design 15131 presents a catalog of simple and succinct solutions to common design problems. 15132 Created by four experienced designers, the 23 patterns contained herein have 15133 become an essential resource for anyone developing reusable object-oriented 15134 software. In response to reader demand, the complete text and pattern catalog are 15135 now available on CD-ROM. This electronic version of Design Patterns enables 15136 programmers to install the book directly onto a computer or network for use as an 15137 online reference for creating reusable object-oriented software. 15138 15139 The authors first describe what patterns are and how they can help you in the 15140 design process. They then systematically name, explain, evaluate, and catalog 15141 recurring designs in object-oriented systems. All patterns are compiled from 15142 real-world examples and include code that demonstrates how they may be implemented 15143 in object-oriented programming languages such as C++ and Smalltalk. Readers who 15144 already own the book will want the CD to take advantage of its dynamic search 15145 mechanism and ready-to-install patterns.}}, 15146 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 15147 citeulike-article-id={115158}, 15148 howpublished = {Hardcover}, 15149 isbn = {0201633612}, 15150 keywords = {1995 algorithms architecture book books computer computing design design-pattern 15151 design-patterns design_patterns designpatterns development diplom entwurfsmuster 15152 four gang gof java mathgamespatterns no-tag object object-orientation 15153 object-oriented of oo-patterns oop oriented pattern patterns programming se 15154 software software-development software-engineering software_design 15155 softwareengineering standard}, 15156 month = jan, 15157 publisher = {{Addison-Wesley Professional}}, 15158 title = {Design Patterns}, 15159 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 15160 year = {1995} 15161} 15162 15163@InProceedings{ chaco95, 15164 author = {Bruce Hendrickson and Robert Leland}, 15165 title = {A multilevel algorithm for partitioning graphs}, 15166 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 15167 (CDROM)}, 15168 year = {1995}, 15169 isbn = {0-89791-816-9}, 15170 pages = {28}, 15171 location = {San Diego, California, United States}, 15172 doi = {10.1145/224170.224228}, 15173 publisher = {ACM Press}, 15174 address = {New York} 15175} 15176 15177@Book{ aleksandrov98, 15178 author = {Aleksandrov, Pavel S.}, 15179 title = {Combinatorial Topology}, 15180 publisher = {Dover}, 15181 volume = {3}, 15182 year = {1998} 15183} 15184 15185@Book{ steenrod99, 15186 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 15187 importance in modern physics--such as in gauge theory. This book, a succinct 15188 introduction to the subject by renown mathematician Norman Steenrod, was the first 15189 to present the subject systematically. 15190 15191 It begins with a general introduction to bundles, including such topics as 15192 differentiable manifolds and covering spaces. The author then provides brief 15193 surveys of advanced topics, such as homotopy theory and cohomology theory, before 15194 using them to study further properties of fibre bundles. The result is a classic 15195 and timeless work of great utility that will appeal to serious mathematicians and 15196 theoretical physicists alike. }}, 15197 author = {Steenrod, Norman}, 15198 citeulike-article-id={712999}, 15199 howpublished = {Paperback}, 15200 isbn = {0691005486}, 15201 keywords = {fibre_bundles topology}, 15202 month = apr, 15203 publisher = {{Princeton University Press}}, 15204 title = {The Topology of Fibre Bundles. (PMS-14)}, 15205 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 15206 year = {1999} 15207} 15208 15209@Book{ bredon97, 15210 author = {Bredon, Glen E.}, 15211 title = {Sheaf Theory}, 15212 publisher = {Springer}, 15213 pages = {524}, 15214 series = {Graduate Texts in Mathematics}, 15215 year = {1997} 15216} 15217 15218@TechReport{ tautgesmeyers04, 15219 title = {{MOAB}: A Mesh-Oriented Database}, 15220 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 15221 Ernst}, 15222 institution = {Sandia National Laboratories}, 15223 number = {SAND2004-1592}, 15224 month = apr, 15225 year = {2004} 15226} 15227 15228@Article{ tautges04, 15229 author = {Timothy J. Tautges}, 15230 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 15231 journal = {Engineering With Computers}, 15232 volume = {20}, 15233 pages = {286--293}, 15234 year = {2004} 15235} 15236 15237@InProceedings{ meyers02, 15238 author = {Ray Meyers et. al}, 15239 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 15240 booktitle = {8th International conference on numerical grid generation in computational field 15241 simulations}, 15242 month = jun, 15243 year = {2002} 15244} 15245 15246@InProceedings{ seolshepard05, 15247 author = {E. S. Seol and Mark S. Shephard}, 15248 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 15249 Analysis}, 15250 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 15251 year = {2005} 15252} 15253 15254@Article{ beallwalshshephard04, 15255 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 15256 title = {A comparison of techniques for geometry access related to mesh generation}, 15257 journal = {Engineering With Computers}, 15258 volume = {20}, 15259 number = {3}, 15260 pages = {210--221}, 15261 year = {2004} 15262} 15263 15264@Article{ careyandersoncarneskirk04, 15265 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 15266 Kirk}, 15267 title = {Some aspects of adaptive grid technology related to boundary and interior 15268 layers}, 15269 journal = {Journal of Computational Applied Mathematics}, 15270 volume = {166}, 15271 number = {1}, 15272 pages = {55--86}, 15273 year = {2004} 15274} 15275 15276@PhDThesis{ gralthesis, 15277 author = {Guntram Berti}, 15278 title = {Generic Software Components for Scientific Computing}, 15279 school = {TU Cottbus}, 15280 year = {2000}, 15281 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 15282} 15283 15284@Article{ whitehead1949, 15285 title = {Combinatorial homotopy. I}, 15286 author = {John HC Whitehead}, 15287 journal = {Bulletin of the American Mathematical Society}, 15288 volume = {55}, 15289 number = {3. P1}, 15290 pages = {213--245}, 15291 year = {1949}, 15292 publisher = {American Mathematical Society} 15293} 15294 15295@Article{ beylkincoifmanrokhlin91, 15296 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 15297 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 15298 journal = {Communications on Pure and Applied Mathematics}, 15299 volume = {44}, 15300 pages = {141--183}, 15301 year = {1991} 15302} 15303 15304@Book{ wesseling92, 15305 author = {Pieter Wesseling}, 15306 title = {An Introduction to Multigrid Methods}, 15307 publisher = {John Wiley and Sons}, 15308 year = {1992} 15309} 15310 15311@Book{ grakakos04, 15312 author = {Loukas Grakakos}, 15313 title = {Classical and Modern Fourier Analysis}, 15314 publisher = {Pearson Education}, 15315 address = {New Jersey}, 15316 year = {2004} 15317} 15318 15319@Misc{ hlib-web-page, 15320 key = {HLib}, 15321 title = {{HLib} {Web} page}, 15322 note = {{\texttt{http://www.hlib.org/}}}, 15323 annote = {Hierarchical matrices for fast integral transform} 15324} 15325 15326@Article{ hackbusch99, 15327 author = {Wolfgang Hackbusch}, 15328 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 15329 Introduction to {$\mathcal H$}-matrices}, 15330 journal = {Computing}, 15331 volume = {62}, 15332 pages = {89--108}, 15333 year = {1999} 15334} 15335 15336@TechReport{ kay1999green, 15337 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 15338 equations}, 15339 author = {Kay, D. and Loghin, D.}, 15340 year = {1999}, 15341 institution = {Oxford University Computing Laboratory}, 15342 number = {99/06} 15343} 15344 15345@Article{ bebendorf2003existence, 15346 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 15347 elliptic operators with {$L^\infty$}-coefficients}, 15348 author = {Bebendorf, M. and Hackbusch, W.}, 15349 journal = {Numerische Mathematik}, 15350 volume = {95}, 15351 number = {1}, 15352 pages = {1--28}, 15353 year = {2003}, 15354 publisher = {Springer} 15355} 15356 15357@Article{ hackbusch2005direct, 15358 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 15359 H$}-matrix approximation}, 15360 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 15361 journal = {Computing and Visualization in Science}, 15362 volume = {8}, 15363 number = {3}, 15364 pages = {179--188}, 15365 year = {2005}, 15366 publisher = {Springer} 15367} 15368 15369@TechReport{ duphof2003, 15370 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 15371 Logg and L. R. Scott}, 15372 title = {The {FE}ni{CS} project}, 15373 institution = {Chalmers Finite Element Center Preprint Series}, 15374 number = {2003--21}, 15375 year = {2003} 15376} 15377 15378@Article{ flame01, 15379 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 15380 Geijn}, 15381 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 15382 journal = {Transactions on Mathematical Software}, 15383 volume = {27}, 15384 number = {4}, 15385 year = {2001}, 15386 pages = {422--455} 15387} 15388 15389@Article{ puschel05, 15390 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 15391 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 15392 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 15393 Nick Rizzolo}, 15394 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 15395 journal = {Proceedings of the IEEE}, 15396 volume = {93}, 15397 number = {2}, 15398 year = {2005}, 15399 note = {special issue on "Program Generation, Optimization, and Adaptation"} 15400} 15401 15402@Article{ kirbylogg06, 15403 author = {Robert C. Kirby and Anders Logg}, 15404 title = {A compiler for variational forms}, 15405 journal = {ACM Transactions on Mathematical Software}, 15406 volume = {32}, 15407 number = {3}, 15408 year = {2006}, 15409 issn = {0098-3500}, 15410 pages = {417--444}, 15411 doi = {10.1145/1163641.1163644}, 15412 publisher = {ACM Press}, 15413 address = {New York, NY} 15414} 15415 15416@Article{ kirbylogg07, 15417 author = {Robert C. Kirby and Anders Logg}, 15418 title = {Efficient compilation of a class of variational forms}, 15419 journal = {ACM Transactions on Mathematical Software}, 15420 volume = {33}, 15421 number = {3}, 15422 year = {2007}, 15423 issn = {0098-3500}, 15424 pages = {17}, 15425 doi = {10.1145/1268769.1268771}, 15426 publisher = {ACM Press}, 15427 address = {New York, NY} 15428} 15429 15430@Article{ bankdupont81, 15431 author = {Randolph Bank and Todd Dupont}, 15432 title = {An optimal order process for solving finite element equations}, 15433 journal = {Mathematics of Computation}, 15434 volume = {36}, 15435 pages = {35--51}, 15436 year = {1981} 15437} 15438 15439@TechReport{ adams00, 15440 author = {Mark F. Adams}, 15441 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 15442 in solid mechanics}, 15443 institution = {UC Berkeley}, 15444 number = {CSD-00-1103}, 15445 year = {2000}, 15446 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 15447} 15448 15449@Article{ bergengradlhuelsemannruede06, 15450 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 15451 title = {A Massively Parallel Multigrid Method for Finite Elements}, 15452 journal = {Computing in Science \& Engineering}, 15453 volume = {8}, 15454 number = {6}, 15455 pages = {56--62}, 15456 year = {2006} 15457} 15458 15459@MastersThesis{ brunethesis08, 15460 author = {Peter R. Brune}, 15461 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 15462 school = {University of Chicago}, 15463 address = {Chicago, IL}, 15464 year = {2008}, 15465 month = feb 15466} 15467 15468@Article{ arnoldwinther02, 15469 author = {Douglas N. Arnold and Ragnar Winther}, 15470 title = {Mixed finite elements for elasticity}, 15471 journal = {Numerische Mathematik}, 15472 volume = {92}, 15473 number = {3}, 15474 month = sep, 15475 year = {2002}, 15476 pages = {401--419}, 15477 doi = {10.1007/s002110100348} 15478} 15479 15480@Article{ arnoldfalkwinther06, 15481 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 15482 title = {Finite element exterior calculus, homological techniques, and applications}, 15483 journal = {Acta Numerica}, 15484 year = {2006}, 15485 volume = {15}, 15486 pages = {1--155}, 15487 publisher = {Cambridge University Press}, 15488 doi = {10.1017/S0962492906210018} 15489} 15490 15491@Article{ kirby04, 15492 author = {Robert C. Kirby}, 15493 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 15494 functions}, 15495 journal = {ACM Transactions on Mathematical Software}, 15496 volume = {30}, 15497 number = {4}, 15498 year = {2004}, 15499 issn = {0098-3500}, 15500 pages = {502--516}, 15501 doi = {10.1145/1039813.1039820}, 15502 publisher = {ACM Press}, 15503 address = {New York, NY} 15504} 15505 15506@Article{ kirby06, 15507 author = {Robert C. Kirby}, 15508 title = {Optimizing {FIAT} with level 3 {BLAS}}, 15509 journal = {ACM Transactions on Mathematical Software}, 15510 volume = {32}, 15511 number = {2}, 15512 year = {2006}, 15513 issn = {0098-3500}, 15514 pages = {223--235}, 15515 doi = {10.1145/1141885.1141889}, 15516 publisher = {ACM Press}, 15517 address = {New York, NY} 15518} 15519 15520@Misc{ bluecrystal08, 15521 author = {{B}lue {C}rystal Cluster}, 15522 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 15523 year = {2008}, 15524 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 15525} 15526 15527@Article{ beylkin95, 15528 author = {Gregory Beylkin}, 15529 title = {On the Fast Fourier Transform of Functions With Singularities}, 15530 journal = {Applied and Computational Harmonic Analysis}, 15531 volume = {2}, 15532 pages = {363--381}, 15533 year = {1995} 15534} 15535 15536@InProceedings{ riehl08, 15537 author = {Jonathan Riehl}, 15538 title = {Implementing the MyFEM Embedded Domain-specific Language}, 15539 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 15540 Development (DSPD'08)}, 15541 address = {Nashville, TN}, 15542 year = {2008} 15543} 15544 15545@Article{ appel85, 15546 author = {Andrew W. Appel}, 15547 date-added = {2008-02-27 12:23:39 +0000}, 15548 date-modified = {2008-02-27 12:24:02 +0000}, 15549 doi = {10.1137/0906008}, 15550 journal = {SIAM Journal on Scientific and Statistical Computing}, 15551 keywords = {treecodes}, 15552 number = {1}, 15553 pages = {85-103}, 15554 publisher = {SIAM}, 15555 title = {An Efficient Program for Many-Body Simulation}, 15556 volume = {6}, 15557 year = {1985} 15558} 15559 15560@Article{ ewald21, 15561 author = {{Ewald}, P.~P.}, 15562 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 15563 journal = {Annalen der Physik}, 15564 year = {1921}, 15565 volume = {369}, 15566 pages = {253-287}, 15567 doi = {10.1002/andp.19213690304}, 15568 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 15569 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 15570} 15571 15572@Article{ greengardrokhlin87, 15573 author = {L. Greengard and V. Rokhlin}, 15574 date-added = {2008-02-15 18:43:55 +0000}, 15575 date-modified = {2008-02-26 20:09:11 +0000}, 15576 doi = {10.1016/0021-9991(87)90140-9}, 15577 journal = {J. Comput.\ Phys.}, 15578 keywords = {FMM}, 15579 number = {2}, 15580 pages = {325--348}, 15581 title = {A Fast Algorithm for Particle Simulations}, 15582 url = {citeseer.ist.psu.edu/greengard87fast.html}, 15583 volume = {73}, 15584 year = {1987}, 15585 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 15586} 15587 15588@Article{ greengardrokhlin97, 15589 author = {L. Greengard and V. Rokhlin}, 15590 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 15591 Dimensions}, 15592 journal = {Acta Numerica}, 15593 volume = {6}, 15594 year = {1997}, 15595 pages = {229--269} 15596} 15597 15598@Article{ luchenghuangmccammon06, 15599 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 15600 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 15601 systems}, 15602 journal = {PNAS}, 15603 doi = {10.1073/pnas.0605166103}, 15604 volume = {102}, 15605 number = {51}, 15606 year = {2006}, 15607 pages = {19314--19319} 15608} 15609 15610@Article{ schussnadlereisenberg01, 15611 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 15612 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 15613 from a molecular model}, 15614 journal = {Physical Review E}, 15615 volume = {64}, 15616 number = {3}, 15617 year = {2001} 15618} 15619 15620@Book{ hairerlubichwanner02, 15621 author = {E. Hairer and Ch. Lubich and G. Wanner}, 15622 title = {Geometric Numerical Integration}, 15623 publisher = {Springer-Verlag}, 15624 address = {Berlin Heidelberg}, 15625 year = {2002} 15626} 15627 15628@Article{ holstbakerwang00, 15629 author = {M. Holst and N. Baker and F. Wang}, 15630 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 15631 equation on massively parallel computers}, 15632 journal = {Journal of Computational Chemistry}, 15633 volume = {21}, 15634 year = {2000} 15635} 15636 15637@Book{ hockneyeastwood81, 15638 author = {R. Hockney and J. Eastwood}, 15639 title = {Computer simulation using particles}, 15640 publisher = {McGraw-Hill}, 15641 address = {New York}, 15642 year = {1981} 15643} 15644 15645@Article{ lutydavistironigunsteren94, 15646 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. 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Brenner and L.~Ridgway Scott}, 15692 title = {The mathematical theory of finite element methods}, 15693 year = {2002}, 15694 isbn = {0-38795-451-1}, 15695 publisher = {Springer}, 15696 pages = {361} 15697} 15698 15699@Book{ trefethenbau97, 15700 author = {Lloyd N. Trefethen and David {Bau, III}}, 15701 title = {Numerical Linear Algebra}, 15702 publisher = {Society for Industrial and Applied Mathematics}, 15703 address = {Philadelphia, PA}, 15704 pages = {xii + 361}, 15705 year = {1997}, 15706 isbn = {0-89871-361-7}, 15707 isbn-13 = {978-0-89871-361-9}, 15708 lccn = {QA184 .T74 1997}, 15709 mrclass = {65-01 (65-02 65Fxx)}, 15710 mrnumber = {MR1444820 (98k:65002)}, 15711 mrreviewer = {Moody T. Chu}, 15712 bibdate = {Wed Jan 07 15:23:19 1998}, 15713 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 15714} 15715 15716@Article{ liptonreagan2014, 15717 title = {Quantum Algorithms via Linear Algebra: A Primer}, 15718 author = {Richard J Lipton and Kenneth W Regan}, 15719 pages = {206}, 15720 isbn = {978-0-26202-839-4}, 15721 year = {2014} 15722} 15723 15724@InProceedings{ rhea08, 15725 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 15726 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 15727 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 15728 booktitle = {Proceedings of IEEE/ACM SC '08}, 15729 year = {2008} 15730} 15731 15732@Misc{ bursteddewilcox09, 15733 author = {Carsten Burstedde and Lucas~C. Wilcox}, 15734 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 15735 note = {in preparation} 15736} 15737 15738@Article{ skeeltezcanhardy02, 15739 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 15740 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 15741 journal = {J. Comp. Chem.}, 15742 volume = {23}, 15743 pages = {673--684}, 15744 year = {2002} 15745} 15746 15747@Article{ verschelde99, 15748 author = {Jan Verschelde}, 15749 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 15750 homotopy continuation}, 15751 journal = {ACM Trans. Math. Softw.}, 15752 volume = {25}, 15753 number = {2}, 15754 issn = {0098-3500}, 15755 pages = {251--276}, 15756 doi = {10.1145/317275.317286}, 15757 publisher = {ACM}, 15758 address = {New York, NY}, 15759 year = {1999} 15760} 15761 15762@InProceedings{ sommeseverscheldewampler08, 15763 author = {Andrew J. Sommese and Jan Verschelde and Charles W. 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Rosner}}, 15919 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 15920 and Simulation at the Extreme Scale}}, 15921 month = may, 15922 year = {2009}, 15923 note = {See 15924 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 15925} 15926 15927@Misc{ blanford08, 15928 author = {{R. Blandord (Chair)}}, 15929 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 15930 Computing at the Extreme Scale}}, 15931 month = dec, 15932 year = {2008}, 15933 note = {See 15934 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 15935} 15936 15937@Misc{ exascale07, 15938 author = {H. Simon and T. Zacharia and R. 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Ryne}, 15963 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 15964 Computational Science for Future Accelerators and Accelerator Technologies}, 15965 journal = {J. Phys.: Conf. Ser.}, 15966 volume = {125}, 15967 year = {2008}, 15968 pages = {012001}, 15969 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 15970} 15971 15972@Article{ compass-amundson-scidac08, 15973 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 15974 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 15975 Stoltz}, 15976 journal = {J. Phys.: Conf. Ser.}, 15977 volume = {125}, 15978 year = {2008} 15979} 15980 15981@InProceedings{ muszala09, 15982 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 15983 Simulations}, 15984 author = {S. Muszala and J. Amundson and L. C. McInnes and B. 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T.}, 16057 keywords = {FMM, parallel FMM}, 16058 school = {Department of Electrical and Computer Engineering, Duke University}, 16059 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 16060 year = {1999} 16061} 16062 16063@InProceedings{ warrensalmon93, 16064 abstract = {We report on an efficient adaptive N-body method which we have recently designed 16065 and implemented. The algorithm computes the forces on an arbitrary distribution of 16066 bodies in a time which scales as N log N with the particle number. The accuracy of 16067 the force calculations is analytically bounded, and can be adjusted via a user 16068 defined parameter between a few percent relative accuracy, down to machine 16069 arithmetic accuracy. Instead of using pointers to indicate the topology of the 16070 tree, we identify...}, 16071 address = {New York}, 16072 author = {Warren, Michael S. and Salmon, John K.}, 16073 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 16074 citeulike-article-id={580952}, 16075 keywords = {oct-tree}, 16076 pages = {12--21}, 16077 publisher = {ACM}, 16078 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 16079 year = {1993}, 16080 doi = {10.1145/169627.169640}, 16081 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 16082} 16083 16084@Unpublished{ cruzwccm10, 16085 author = {Felipe A. Cruz}, 16086 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 16087 note = {Presentation at WCCM 2010, Sydney Australia}, 16088 year = {2010} 16089} 16090 16091@Article{ mcguffee06, 16092 author = {S.~R. {McGuffee} and A.~H. 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Tuminaro}, 16178 title = {Block preconditioners based on approximate commutators}, 16179 journal = {SIAM J. Sci. Comput.}, 16180 volume = {27}, 16181 number = {5}, 16182 year = {2006}, 16183 pages = {1651--1668} 16184} 16185 16186@Article{ braesssarazin1997, 16187 author = {Dietrich Braess and Regina Sarazin}, 16188 title = {An efficient smoother for the {Stokes} problem}, 16189 journal = {Applied Numerical Mathematics}, 16190 volume = {23}, 16191 number = {1}, 16192 year = {1997}, 16193 pages = {3--19}, 16194 doi = {10.1016/S0168-9274(96)00059-1} 16195} 16196 16197@Article{ wright2001large, 16198 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 16199 author = {Wright, T.G. and Trefethen, L.N.}, 16200 journal = {SIAM Journal on Scientific Computing}, 16201 volume = {23}, 16202 pages = {591}, 16203 year = {2001} 16204} 16205 16206@Misc{ wright2002eigtool, 16207 title = {Eig{T}ool}, 16208 author = {Wright, T.G. and Trefethen, LN}, 16209 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 16210 year = {2002} 16211} 16212 16213@Misc{ visit-web-site, 16214 key = {{VisIt}}, 16215 title = {{VisIt web site}}, 16216 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 16217 url = {http://wci.llnl.gov/codes/visit/}, 16218 year = {2011} 16219} 16220 16221@Book{ trefethen1996, 16222 title = {Finite difference and spectral methods for ordinary and partial differential 16223 equations}, 16224 author = {Lloyd Nicholas Trefethen}, 16225 year = {1996}, 16226 publisher = {Cornell University-Department of Computer Science and Center for Applied 16227 Mathematics} 16228} 16229 16230@Book{ trefethen2005spectra, 16231 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 16232 author = {Trefethen, L.N. and Embree, M.}, 16233 year = {2005}, 16234 publisher = {Princeton University Press} 16235} 16236 16237@Article{ gomez2010isogeometric, 16238 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 16239 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 16240 journal = {Computer Methods in Applied Mechanics and Engineering}, 16241 volume = {199}, 16242 number = {25-28}, 16243 pages = {1828--1840}, 16244 issn = {0045-7825}, 16245 year = {2010}, 16246 publisher = {Elsevier} 16247} 16248 16249@Article{ gomez2008isogeometric, 16250 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 16251 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 16252 journal = {Computer Methods in Applied Mechanics and Engineering}, 16253 volume = {197}, 16254 number = {49-50}, 16255 pages = {4333--4352}, 16256 year = {2008}, 16257 publisher = {Elsevier} 16258} 16259 16260@Misc{ fastmath:project, 16261 author = {Lori {Diachin (PI)}}, 16262 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 16263 (FASTMath) Institute}}, 16264 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 16265} 16266 16267@Misc{ exascale-software:proposal, 16268 author = {Peter {Beckman (PI)}}, 16269 title = {{Exascale Software Center}}, 16270 note = {proposal to DOE} 16271} 16272 16273@Misc{ imex:project, 16274 author = {Barry {Smith (PI)}}, 16275 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 16276 Multimodel PDEs}}, 16277 note = {DOE ASCR applied math project} 16278} 16279 16280@Misc{ intel-mic:website, 16281 author = {Intel}, 16282 title = {{Many Integrated Core Architecture}}, 16283 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 16284} 16285 16286@Article{ dudson:2009, 16287 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 16288 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 16289 journal = {Computer Physics Communications}, 16290 volume = {180}, 16291 pages = {1467}, 16292 year = {2009} 16293} 16294 16295@Article{ umansky:2009, 16296 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 16297 title = {{Status and verification of edge plasma turbulence code BOUT}}, 16298 journal = {Computer Physics Communications}, 16299 year = {2009}, 16300 volume = {180}, 16301 pages = {887-903} 16302} 16303 16304@Article{ xu:1998, 16305 author = {X.Q. Xu and R.H. Cohen}, 16306 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 16307 journal = {Computer Physics Communications}, 16308 year = {1998}, 16309 volume = {36}, 16310 number = {1-2}, 16311 pages = {158} 16312} 16313 16314@Article{ tron:1999, 16315 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 16316 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 16317 journal = {SIAM Journal on Optimization}, 16318 volume = {9}, 16319 number = {4}, 16320 pages = {1100-1127}, 16321 year = {1999} 16322} 16323 16324@Article{ stubenamg, 16325 author = {K. St\"{u}ben}, 16326 title = {A review of algebraic multigrid}, 16327 journal = {J. Comput. Appl. Math.}, 16328 volume = {128}, 16329 number = {1-2}, 16330 year = {2001}, 16331 issn = {0377-0427}, 16332 pages = {281--309}, 16333 doi = {10.1016/S0377-0427(00)00516-1}, 16334 publisher = {Elsevier Science Publishers B. V.}, 16335 address = {Amsterdam, The Netherlands, The Netherlands} 16336} 16337 16338@Article{ feuchtermg, 16339 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 16340 title = {Bridging the gap between geometric and algebraic multigrid methods}, 16341 journal = {Computing and visualization in science}, 16342 publisher = {Springer}, 16343 volume = {6}, 16344 number = {1}, 16345 year = {2003}, 16346 pages = {1--13} 16347} 16348 16349@Article{ chowmgsmoothness, 16350 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 16351 only attempts to interpolate in the directions of geometrical smoothness. These 16352 directions are determined by analyzing samples of algebraically smooth error, e. 16353 Neighboring grid points i and j are called smoothly coupled if e i and e j are 16354 consistently nearby in value. In addition, these dierences may be used to dene 16355 interpolation weights. These new ideas may be incorporated into the algebraic 16356 multigrid method. Test results show that the new method can have much lower grid 16357 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 16358 author = {Chow, Edmond}, 16359 citeulike-article-id={7675372}, 16360 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16361 journal = {American Journal of Mathematics}, 16362 keywords = {fem, multigrid}, 16363 pages = {197--215}, 16364 posted-at = {2010-08-17 23:29:51}, 16365 priority = {2}, 16366 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 16367 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16368 volume = {65}, 16369 year = {2001} 16370} 16371 16372@Article{ jonesamge, 16373 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 16374 elements) method based on element agglomeration. In the method, coarse grid 16375 elements are formed by agglomerating fine grid elements. Compatible interpolation 16376 operators are constructed which yield coarse grid basis functions with a minimal 16377 energy property. Heuristics based on interpolation quality measures are used to 16378 guide the agglomeration procedure. The performance of the resulting method is 16379 demonstrated in two-level numerical experiments.}}, 16380 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 16381 citeulike-article-id={8598569}, 16382 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16383 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 16384 journal = {SIAM Journal on Scientific Computing}, 16385 keywords = {amg, fem, multigrid}, 16386 number = {1}, 16387 pages = {109--133}, 16388 posted-at = {2011-01-13 18:05:55}, 16389 priority = {2}, 16390 publisher = {SIAM}, 16391 title = {{AMGE Based on Element Agglomeration}}, 16392 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16393 volume = {23}, 16394 year = {2001} 16395} 16396 16397@Article{ saad1993, 16398 author = {Saad, Youcef}, 16399 doi = {10.1137/0914028}, 16400 issn = {10648275}, 16401 journal = {SIAM Journal on Scientific Computing}, 16402 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 16403 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 16404 precondition-,preconditioned conju-,subject classi cations,variable 16405 preconditioners}, 16406 number = {2}, 16407 pages = {461--469}, 16408 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 16409 volume = {14}, 16410 year = {1993} 16411} 16412 16413@Misc{ path:homepage, 16414 author = {S. Dirkse and M. Ferris and T. Munson}, 16415 title = {{{PATH} {W}eb page}}, 16416 howpublished = {\url{http://pages.cs.wisc.edu/~ferris/path.html}} 16417} 16418 16419@Article{ ketcheson2008, 16420 author = {David I Ketcheson}, 16421 title = {Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with 16422 Low-Storage Implementations}, 16423 volume = {30}, 16424 journal = {SIAM Journal on Scientific Computing}, 16425 year = {2008}, 16426 pages = {2113--2136} 16427} 16428 16429@Article{ elman2009boundary, 16430 title = {{Boundary conditions in approximate commutator preconditioners for the 16431 Navier-Stokes equations}}, 16432 author = {Elman, H.C. and Tuminaro, R.}, 16433 journal = {Electronic Transactions on Numerical Analysis}, 16434 volume = {35}, 16435 pages = {257--280}, 16436 year = {2009} 16437} 16438 16439@Article{ elman2008tcp, 16440 title = {{A taxonomy and comparison of parallel block multi-level preconditioners for the 16441 incompressible Navier-Stokes equations}}, 16442 author = {Elman, H.C. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, 16443 R.}, 16444 journal = {Journal of Computational Physics}, 16445 volume = {227}, 16446 number = {1}, 16447 pages = {1790--1808}, 16448 year = {2008}, 16449 publisher = {Academic Press}, 16450 url = {http://chess.cs.umd.edu/~elman/papers/tax.pdf} 16451} 16452 16453@Article{ arioli2013, 16454 title = {Generalized {G}olub--{K}ahan bidiagonalization and stopping criteria}, 16455 author = {Arioli, Mario}, 16456 journal = {SIAM Journal on Matrix Analysis and Applications}, 16457 volume = {34}, 16458 number = {2}, 16459 pages = {571--592}, 16460 year = {2013}, 16461 publisher = {SIAM} 16462} 16463 16464@Book{ wesseling2009, 16465 title = {Principles of computational fluid dynamics}, 16466 author = {Wesseling, Pieter}, 16467 volume = {29}, 16468 year = {2009}, 16469 publisher = {Springer Science \& Business Media} 16470} 16471 16472@Article{ silvester2001efficient, 16473 title = {{Efficient preconditioning of the linearized Navier-Stokes equations for 16474 incompressible flow}}, 16475 author = {Silvester, D. and Elman, H. and Kay, D. and Wathen, A.}, 16476 journal = {Journal of Computational and Applied Mathematics}, 16477 volume = {128}, 16478 number = {1-2}, 16479 pages = {261--279}, 16480 issn = {0377-0427}, 16481 year = {2001}, 16482 publisher = {Elsevier} 16483} 16484 16485@Article{ elman1999bfbt, 16486 title = {{Preconditioning for the steady-state Navier-Stokes equations with low 16487 viscosity}}, 16488 author = {Elman, H.C.}, 16489 journal = {SIAM Journal on Scientific Computing}, 16490 volume = {20}, 16491 number = {4}, 16492 pages = {1299--1316}, 16493 issn = {1064-8275}, 16494 year = {1999}, 16495 publisher = {Citeseer} 16496} 16497 16498@Article{ elman2006bpb, 16499 title = {{Block preconditioners based on approximate commutators}}, 16500 author = {Elman, H. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, R.}, 16501 journal = {SIAM Journal on Scientific Computing}, 16502 volume = {27}, 16503 number = {5}, 16504 pages = {1651--1668}, 16505 year = {2006}, 16506 publisher = {Philadelphia, PA: SIAM, c1993-} 16507} 16508 16509@Article{ olshanskii2006analysis, 16510 title = {{Analysis of a Stokes interface problem}}, 16511 author = {Olshanskii, M.A. and Reusken, A.}, 16512 journal = {Numerische Mathematik}, 16513 volume = {103}, 16514 number = {1}, 16515 pages = {129--149}, 16516 issn = {0029-599X}, 16517 year = {2006}, 16518 publisher = {Springer} 16519} 16520 16521@Article{ patankar1972cph, 16522 title = {{A calculation procedure for heat, mass and momentum transfer in 16523 three-dimensional parabolic flows}}, 16524 author = {Patankar, S.V. and Spalding, D.B.}, 16525 journal = {Int. J. Heat Mass Transfer}, 16526 volume = {15}, 16527 pages = {1787--1806}, 16528 year = {1972} 16529} 16530 16531@Article{ rannacher1992simple, 16532 title = {{Simple nonconforming quadrilateral Stokes element}}, 16533 author = {Rannacher, R. and Turek, S.}, 16534 journal = {Numerical Methods for Partial Differential Equations}, 16535 volume = {8}, 16536 number = {2}, 16537 pages = {97--111}, 16538 issn = {1098-2426}, 16539 year = {1992}, 16540 publisher = {Wiley Online Library} 16541} 16542 16543@Article{ rannacher2000finite, 16544 title = {Finite Element Methods for the Incompressible {N}avier-{S}tokes Equations}, 16545 author = {Rannacher, R.}, 16546 journal = {Fundamental Directions in Mathematical Fluid Mechanics}, 16547 pages = {191}, 16548 isbn = {3764364149}, 16549 year = {2000}, 16550 publisher = {Birkhauser} 16551} 16552 16553@Article{ vanka1986block, 16554 title = {{Block-implicit multigrid solution of Navier-Stokes equations in primitive 16555 variables}}, 16556 author = {Vanka, S.P.}, 16557 journal = {Journal of Computational Physics}, 16558 volume = {65}, 16559 number = {1}, 16560 pages = {138--158}, 16561 issn = {0021-9991}, 16562 year = {1986}, 16563 publisher = {Elsevier} 16564} 16565 16566@Article{ eisenstat1983variational, 16567 title = {Variational iterative methods for nonsymmetric systems of linear equations}, 16568 author = {Eisenstat, S.C. and Elman, H.C. and Schultz, M.H.}, 16569 journal = {SIAM Journal on Numerical Analysis}, 16570 volume = {20}, 16571 number = {2}, 16572 pages = {345--357}, 16573 year = {1983}, 16574 publisher = {JSTOR} 16575} 16576 16577@InProceedings{ burstedde2008scalable, 16578 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16579 author = {Burstedde, C. and Ghattas, O. and Gurnis, M. and Stadler, G. and Tan, E. and Tu, 16580 T. and Wilcox, L.C. and Zhong, S.}, 16581 booktitle = {Proceedings of the 2008 ACM/IEEE conference on Supercomputing}, 16582 pages = {62}, 16583 year = {2008}, 16584 organization = {IEEE Press} 16585} 16586 16587@Article{ burstedde2009parallel, 16588 title = {Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes} 16589 flow problems}, 16590 author = {Burstedde, C. and Ghattas, O. and Stadler, G. and Tu, T. and Wilcox, L.C.}, 16591 journal = {Computer Methods in Applied Mechanics and Engineering}, 16592 volume = {198}, 16593 number = {21-26}, 16594 pages = {1691--1700}, 16595 year = {2009}, 16596 publisher = {Elsevier} 16597} 16598 16599@Article{ stadler2010dynamics, 16600 title = {The dynamics of plate tectonics and mantle flow: From local to global scales}, 16601 author = {Stadler, G. and Gurnis, M. and Burstedde, C. and Wilcox, L.C. and Alisic, L. and 16602 Ghattas, O.}, 16603 journal = {Science}, 16604 volume = {329}, 16605 number = {5995}, 16606 pages = {1033}, 16607 year = {2010}, 16608 publisher = {American Association for the Advancement of Science} 16609} 16610 16611@Article{ tackley2008modelling, 16612 title = {Modelling compressible mantle convection with large viscosity contrasts in a 16613 three-dimensional spherical shell using the yin-yang grid}, 16614 author = {Tackley, P.J.}, 16615 journal = {Physics of the Earth and Planetary Interiors}, 16616 volume = {171}, 16617 number = {1-4}, 16618 pages = {7--18}, 16619 year = {2008}, 16620 publisher = {Elsevier} 16621} 16622 16623@Article{ moresizhonggurnis96, 16624 author = {Louis N. Moresi and Shijie Zhong and Michael Gurnis}, 16625 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 16626 viscosity}, 16627 journal = {Physics of the Earth and Planetary Interiors}, 16628 volume = {97}, 16629 pages = {83-–94}, 16630 year = {1996} 16631} 16632 16633@Article{ moresisolomatov95, 16634 author = {Louis N. Moresi and V. S. Solomatov}, 16635 title = {Numerical investigation of {2D} convection with extremely large viscosity 16636 variations}, 16637 journal = {Physics of Fluids}, 16638 volume = {7}, 16639 number = {9}, 16640 pages = {2154-–2162}, 16641 year = {1995} 16642} 16643 16644@Article{ chenmolnar83, 16645 author = {W.-P. Chen and P. Molnar}, 16646 title = {Focal depths of intra-continental and intraplate earthquakes and their 16647 implications for the thermal and mechanical properties of the lithosphere}, 16648 journal = {Journal of Geophysical Research}, 16649 volume = {88}, 16650 pages = {4183–-4214}, 16651 year = {1983} 16652} 16653 16654@Article{ jackson02, 16655 author = {J. Jackson}, 16656 title = {Strength of the continental lithosphere: time to abandon the jelly sandwich?}, 16657 journal = {GSA Today}, 16658 volume = {12}, 16659 pages = {4–-10}, 16660 year = {2002} 16661} 16662 16663@Article{ burovwatts06, 16664 author = {E.B. Burov and A.B. Watts}, 16665 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 16666 brulee?}, 16667 journal = {GSA Today}, 16668 volume = {16}, 16669 pages = {4–-10}, 16670 year = {2006} 16671} 16672 16673@InProceedings{ yang:brent:2002, 16674 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 16675 Parallel Distributed Memory Architectures}, 16676 author = {Laurence T. Yang and Richard Brent}, 16677 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 16678 for Parallel Processing}, 16679 year = {2002}, 16680 publisher = {IEEE} 16681} 16682 16683@Article{ demmel2008communication, 16684 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 16685 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 16686 journal = {Arxiv preprint arXiv:0808.2664}, 16687 year = {2008} 16688} 16689 16690@Article{ demmel09, 16691 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 16692 title = {Communication-optimal Iterative Methods}, 16693 journal = {Journal of Physics: Conf. Series}, 16694 volume = {180}, 16695 year = {2009} 16696} 16697 16698@TechReport{ parms04, 16699 author = {Yousef Saad and Masha Sosonkina}, 16700 title = {{pARMS}: A package for the parallel iterative solution of general large sparse 16701 linear systems user's guide}, 16702 number = {UMSI2004-8}, 16703 institution = {Minnesota Supercomputer Institute, University of Minnesota}, 16704 year = {2004} 16705} 16706 16707@Article{ picard1890, 16708 author = {Emile Picard}, 16709 title = {M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la 16710 m\'ethode des approximations successives}, 16711 journal = {Journal De Math\'ematiques Pures et Appliqu\'ees}, 16712 volume = {4}, 16713 number = {6}, 16714 pages = {145--210}, 16715 year = {1890}, 16716 url = {http://math-doc.ujf-grenoble.fr/JMPA/PDF/JMPA_1890_4_6_A3_0.pdf} 16717} 16718 16719@Book{ rall1969, 16720 author = {Louis B. Rall}, 16721 title = {Computational solution of nonlinear operator equations}, 16722 publisher = {Krieger Pub Co.}, 16723 pages = {225}, 16724 year = {1969} 16725} 16726 16727@Article{ fletcherreeves1964, 16728 author = {R. Fletcher and C. M. Reeves}, 16729 title = {Function Minimization by Conjugate Gradients}, 16730 journal = {Computer Journal}, 16731 volume = {7}, 16732 pages = {149–-154}, 16733 year = {1964} 16734} 16735 16736@InBook{ mcinnesallanetal06, 16737 author = {Lois Curfman McInnes and Benjamin Allan and Robert Armstrong and Steven Benson 16738 and David Bernholdt and Tamara Dahlgren and Lori Diachin and Manojkumar Krishnan 16739 and James Kohl and Jay Larson and Sophia Lefantzi and Jarek Nieplocha and Boyana 16740 Norris and Steven Parker and Jaideep Ray and Shujia Zhou}, 16741 editor = {A.~M.~Bruaset and A.~Tveito}, 16742 title = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 16743 chapter = {Parallel {PDE}-Based Simulations Using the {Common Component Architecture}}, 16744 publisher = {Springer}, 16745 year = {2006}, 16746 number = {51}, 16747 series = {Lecture Notes in Computational Science and Engineering}, 16748 pages = {327--381}, 16749 doi = {10.1016/S0167-8191(02)00191-6} 16750} 16751 16752@Article{ cyrshadidtuminaro12, 16753 title = {Stabilization and scalable block preconditioning for the {Navier–Stokes} 16754 equations}, 16755 journal = {Journal of Computational Physics}, 16756 volume = {231}, 16757 number = {2}, 16758 pages = {345 - 363}, 16759 year = {2012}, 16760 issn = {0021-9991}, 16761 doi = {10.1016/j.jcp.2011.09.001}, 16762 author = {Eric C. Cyr and John N. Shadid and Raymond S. Tuminaro} 16763} 16764 16765@Article{ keyesmcinneswoodwardetal13, 16766 title = {Multiphysics Simulations: Challenges and Opportunities}, 16767 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 16768 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 16769 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 16770 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 16771 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 16772 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 16773 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 16774 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 16775 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 16776 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 16777 journal = {International Journal of High Performance Computing Applications}, 16778 month = feb, 16779 year = {2013}, 16780 volume = {27}, 16781 number = {1}, 16782 pages = {4--83}, 16783 doi = {10.1177/1094342012468181}, 16784 note = {Special issue}, 16785 abstract = {We consider multiphysics applications from algorithmic and architectural 16786 perspectives, where ``algorithmic'' includes both mathematical analysis and 16787 computational complexity and ``architectural'' includes both software and hardware 16788 environments. Many diverse multiphysics applications can be reduced, en route to 16789 their computational simulation, to a common algebraic coupling paradigm. 16790 Mathematical analysis of multiphysics coupling in this form is not always 16791 practical for realistic applications, but model problems representative of 16792 applications discussed herein can provide insight. A variety of software 16793 frameworks for multiphysics applications have been constructed and refined within 16794 disciplinary communities and executed on leading-edge computer systems. We examine 16795 several of these, expose some commonalities among them, and attempt to extrapolate 16796 best practices to future systems. From our study, we summarize challenges and 16797 forecast opportunities.} 16798} 16799 16800@Misc{ rosner10, 16801 author = {Robert {Rosner (Chair)}}, 16802 title = {{The Opportunities and Challenges of Exascale Computing}}, 16803 year = {2010}, 16804 howpublished = {Office of Science, U.S. Department of Energy}, 16805 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 16806} 16807 16808@Misc{ kogge2008exascale, 16809 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 16810 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 16811 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 16812 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 16813 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 16814 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 16815 howpublished = {DARPA}, 16816 year = {2008}, 16817 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 16818} 16819 16820@Misc{ doegrandchallengeworkshops, 16821 key = {Office of Science, U.S. Department of Energy}, 16822 title = {{Scientific Grand Challenges Workshop Series}}, 16823 howpublished = {Office of Science, U.S. Department of Energy, see 16824 \url{http://extremecomputing.labworks.org/workshops.stm}} 16825} 16826 16827@Misc{ lawrence2011, 16828 key = {Lawrence}, 16829 title = {{Ernest Orlando Lawrence Award Winners}}, 16830 howpublished = {U.S. Department of Energy, {\footnotesize 16831 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 16832 year = {2011} 16833} 16834 16835@Article{ murphy2000npi, 16836 title = {{A note on preconditioning for indefinite linear systems}}, 16837 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 16838 journal = {SIAM Journal on Scientific Computing}, 16839 volume = {21}, 16840 number = {6}, 16841 pages = {1969--1972}, 16842 year = {2000}, 16843 publisher = {Philadelphia, PA: SIAM, c1993-} 16844} 16845 16846@Article{ elman2011bouyancy, 16847 title = {Fast iterative solvers for buoyancy driven flow problems}, 16848 journal = {Journal of Computational Physics}, 16849 volume = {230}, 16850 number = {10}, 16851 pages = {3900 - 3914}, 16852 year = {2011}, 16853 note = {}, 16854 issn = {0021-9991}, 16855 doi = {10.1016/j.jcp.2011.02.014}, 16856 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 16857 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 16858 Adaptivity, Preconditioning, Algebraic multigrid} 16859} 16860 16861@Article{ dongarrabeckman11, 16862 author = {J. Dongarra and P. Beckman and et al.}, 16863 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 16864 journal = {Int. J. High Perf. Comput. 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Oliphant}, 17407 title = {Guide to Numpy}, 17408 publisher = {Trelgol}, 17409 year = {2008} 17410} 17411 17412@Misc{ pycuda, 17413 author = {Andreas Kl\"ockner}, 17414 title = {{PyCUDA}}, 17415 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 17416 year = {2011} 17417} 17418 17419@Misc{ pyopencl, 17420 author = {Andreas Kl\"ockner}, 17421 title = {{PyOpenCL}}, 17422 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 17423 year = {2011} 17424} 17425 17426@Article{ klockner2012, 17427 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 17428 Paul Ivanov and Ahmed Fasih}, 17429 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 17430 generation}, 17431 journal = {Parallel Computing}, 17432 volume = {38}, 17433 number = {3}, 17434 pages = {157--174}, 17435 year = {2012}, 17436 issn = {0167-8191}, 17437 doi = {10.1016/j.parco.2011.09.001} 17438} 17439 17440%%%%%% Matt Stuff %%%%%% 17441@Article{ morrabozdagknepleyrassvesselinov, 17442 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 17443 author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and 17444 Velimir Vesselinov}, 17445 journal = {Eos}, 17446 volume = {102}, 17447 doi = {10.1029/2021EO159258}, 17448 month = jun, 17449 year = {2021} 17450} 17451 17452@Misc{ knepley:icerm-workshop:2012, 17453 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 17454 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 17455 Models for Large-scale Simulations}, 17456 note = {Workshop sponsored by the Institute for Computational and Experimental Research 17457 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 17458 \url{http://icerm.brown.edu/tw12-1-exascale}}, 17459 year = {2012} 17460} 17461 17462@TechReport{ kirbyknepleyscott04, 17463 author = {Robert C. Kirby and Matthew G. Knepley and L. 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Ridgway Scott}, 17489 title = {Evaluation of the Action of Finite Element Operators}, 17490 type = {Technical Report}, 17491 number = {TR-2010-08}, 17492 institution = {University of Chicago}, 17493 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}, 17494 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}}, 17495 month = oct, 17496 year = {2010} 17497} 17498 17499@TechReport{ bruneknepleyscott11, 17500 author = {Peter R. Brune and Matthew G. Knepley and L. 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Yuen and Huai 17513 Zhang and Yaolin Shi}, 17514 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 17515 strongly variable viscosity based on {Matlab} and {CUDA}}, 17516 type = {Research Report}, 17517 number = {UMSI 2011/33}, 17518 institution = {University of Minnesota Supercomputing Institute}, 17519 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 17520 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 17521 month = mar, 17522 year = {2011} 17523} 17524 17525@InProceedings{ zheng2010, 17526 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. 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22335 22336@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 22337 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 22338 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 22339 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 22340 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 22341 pages = {1103}, 22342 year = {2018} 22343} 22344 22345@InProceedings{ barralangeloudiskramergormanpiggott2018, 22346 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 22347 modelling}, 22348 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 22349 and Matthew D Piggott}, 22350 booktitle = {EGU General Assembly Conference Abstracts}, 22351 volume = {20}, 22352 pages = {19168}, 22353 year = {2018} 22354} 22355 22356@Article{ principe2009, 22357 title = {{Mathematical models for thermally coupled low speed flows}}, 22358 author = {Javier Principe and Ramon Codina}, 22359 journal = {Advances in Theoretical and Applied Mechanics}, 22360 volume = {2}, 22361 number = {1-4}, 22362 pages = {93--112}, 22363 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 22364 year = {2009} 22365} 22366 22367@Book{ vandervorst2003, 22368 title = {Iterative {K}rylov Methods for Large Linear Systems}, 22369 author = {van der Vorst, H.}, 22370 isbn = {9780521818285}, 22371 publisher = {Cambridge University Press}, 22372 year = {2003} 22373} 22374 22375@Book{ peres2006, 22376 author = {Asher Peres}, 22377 title = {Quantum theory: concepts and methods}, 22378 volume = {57}, 22379 publisher = {Springer Science \& Business Media}, 22380 year = {2006} 22381} 22382 22383@Book{ kuttler2012, 22384 title = {Linear algebra: theory and applications}, 22385 author = {Kenneth Kuttler}, 22386 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 22387 year = {2012} 22388} 22389 22390@Book{ elman_silvester_wathen_2014, 22391 place = {Oxford}, 22392 title = {Finite elements and fast iterative solvers: with applications in incompressible 22393 fluid dynamics}, 22394 publisher = {Oxford University Press}, 22395 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 22396 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 22397 year = {2014} 22398} 22399 22400@Article{ alametal2007, 22401 title = {An evaluation of the ORNL Cray XT3}, 22402 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 22403 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 22404 journal = {International Journal of High Performance Computing Applications}, 22405 volume = {22}, 22406 number = {1}, 22407 pages = {52--80}, 22408 doi = {10.1177/1094342007085019}, 22409 year = {2007} 22410} 22411 22412@Article{ plazacarey2000, 22413 title = {Local refinement of simplicial grids based on the skeleton}, 22414 author = {Plaza, A. and Carey, Graham F.}, 22415 journal = {Applied Numerical Mathematics}, 22416 doi = {10.1016/S0168-9274(99)00022-7}, 22417 issn = {01689274}, 22418 volume = {32}, 22419 number = {2}, 22420 pages = {195--218}, 22421 year = {2000} 22422} 22423 22424@Article{ carsonstrakos2020, 22425 title = {On the cost of iterative computations}, 22426 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 22427 journal = {Phil. Trans. R. Soc. A}, 22428 volume = {378}, 22429 number = {20190050}, 22430 doi = {10.1098/rsta.2019.0050}, 22431 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 22432 year = {2020} 22433} 22434 22435@Article{ schoberl1999, 22436 title = {Multigrid methods for a parameter dependent problem in primal variables}, 22437 author = {Joachim Sch{\"o}berl}, 22438 journal = {Numerische Mathematik}, 22439 volume = {84}, 22440 number = {1}, 22441 pages = {97--119}, 22442 year = {1999} 22443} 22444 22445@Article{ wuleexuzikatanov2008, 22446 title = {Convergence analysis on iterative methods for semidefinite systems}, 22447 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 22448 journal = {Journal of Computational Mathematics}, 22449 pages = {797--815}, 22450 year = {2008} 22451} 22452 22453@Article{ maierrannacher2016, 22454 title = {Duality-based adaptivity in finite element discretization of heterogeneous 22455 multiscale problems}, 22456 author = {Maier, Matthias and Rannacher, Rolf}, 22457 journal = {Journal of Numerical Mathematics}, 22458 volume = {24}, 22459 number = {3}, 22460 pages = {167--187}, 22461 year = {2016} 22462} 22463 22464@Article{ maierrannacher2018, 22465 title = {A duality-based optimization approach for model adaptivity in heterogeneous 22466 multiscale problems}, 22467 author = {Maier, Matthias and Rannacher, Rolf}, 22468 journal = {Multiscale Modeling \& Simulation}, 22469 volume = {16}, 22470 number = {1}, 22471 pages = {412--428}, 22472 year = {2018} 22473} 22474 22475@Article{ margetismaierluskin2017, 22476 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 22477 metamaterial sheet}, 22478 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 22479 journal = {Studies in Applied Mathematics}, 22480 volume = {139}, 22481 number = {4}, 22482 pages = {599--625}, 22483 year = {2017} 22484} 22485 22486@Article{ maiermargetisluskin2017b, 22487 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 22488 approximation and validation}, 22489 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 22490 journal = {Journal of Computational Physics}, 22491 volume = {339}, 22492 pages = {126--145}, 22493 year = {2017} 22494} 22495 22496@Article{ maiermargetisluskin2018, 22497 title = {Generation of surface plasmon-polaritons by edge effects}, 22498 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 22499 journal = {Communications in Mathematical Sciences}, 22500 volume = {16}, 22501 number = {1}, 22502 pages = {77--95}, 22503 url = {http://arxiv.org/abs/1702.00848}, 22504 year = {2018} 22505} 22506 22507@Article{ maiermattheakiskaxirasluskinmargetis2018, 22508 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 22509 metamaterials}, 22510 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22511 Mitchell and Margetis, Dionisios}, 22512 journal = {Physical Review B}, 22513 volume = {97}, 22514 number = {3}, 22515 pages = {035307}, 22516 year = {2018} 22517} 22518 22519@Article{ maiermattheakiskaxirasluskinmargetis2019, 22520 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 22521 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22522 Mitchell and Margetis, Dionisios}, 22523 journal = {Proceedings of the Royal Society A}, 22524 volume = {475}, 22525 number = {2230}, 22526 pages = {20190220}, 22527 year = {2019} 22528} 22529 22530@Article{ maiermargetisluskin2020, 22531 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 22532 two scales}, 22533 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 22534 journal = {Physical Review B}, 22535 volume = {102}, 22536 number = {7}, 22537 pages = {075308}, 22538 year = {2020} 22539} 22540 22541@Article{ margetismaierstauberlowluskin2020, 22542 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 22543 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 22544 Luskin, Mitchell}, 22545 journal = {Journal of Physics A: Mathematical and Theoretical}, 22546 volume = {53}, 22547 number = {5}, 22548 pages = {055201}, 22549 year = {2020} 22550} 22551 22552@Article{ maiermargetismellet2020, 22553 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 22554 structures}, 22555 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 22556 journal = {Journal of Computational and Applied Mathematics}, 22557 volume = {377}, 22558 pages = {112909}, 22559 year = {2020} 22560} 22561 22562@Article{ maierkronbichler2021, 22563 title = {Efficient parallel 3D computation of the compressible Euler equations with an 22564 invariant-domain preserving second-order finite-element scheme}, 22565 author = {Maier, Matthias and Kronbichler, Martin}, 22566 journal = {ACM Transactions on Parallel Computing}, 22567 volume = {8}, 22568 number = {3}, 22569 pages = {1--30}, 22570 year = {2021} 22571} 22572 22573@Article{ guermondmaierpopovtomas2021, 22574 title = {Second-order invariant domain preserving approximation of the compressible 22575 Navier--Stokes equations}, 22576 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 22577 journal = {Computer Methods in Applied Mechanics and Engineering}, 22578 volume = {375}, 22579 pages = {113608}, 22580 year = {2021} 22581} 22582 22583@Article{ liliptonmaier2021, 22584 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 22585 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 22586 eprint = {2009.12166}, 22587 archiveprefix = {arXiv}, 22588 primaryclass = {phys.optics}, 22589 year = {2021} 22590} 22591 22592@Article{ songmaierluskin2020, 22593 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 22594 gradient-index graphene waveguides}, 22595 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22596 journal = {Journal of Computational Physics}, 22597 volume = {423}, 22598 pages = {109871}, 22599 year = {2020} 22600} 22601 22602@Article{ songmaierluskin2019, 22603 title = {Adaptive finite element simulations of waveguide configurations involving 22604 parallel 2D material sheets}, 22605 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22606 journal = {Computer Methods in Applied Mechanics and Engineering}, 22607 volume = {351}, 22608 pages = {20--34}, 22609 year = {2019} 22610} 22611 22612% 22613% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 22614% 22615% 22616@Unpublished{ rob1, 22617 author = {Rob Kunz}, 22618 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 22619 State University}, 22620 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 22621 sponsors = {U.S. Navy, NRC}, 22622 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 22623 simulations, including lake warming by power plants}, 22624 dates = {Oct 3 and 4, 2002}, 22625 email = {rfk@wt.arl.psu.edu} 22626} 22627 22628@Unpublished{ au1, 22629 author = {Feng Wang and William Appelbe}, 22630 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 22631 url = {http://www.vpac.org}, 22632 sponsors = { }, 22633 note = {Using PETSc for a Variety of Geophysical Simulations}, 22634 dates = {Nov 22, 2002} 22635} 22636 22637@Unpublished{ carl1, 22638 author = {Carl Sovinec}, 22639 institution = {Applied Physics, University of Wisconsin}, 22640 url = {http://nimrodteam.org}, 22641 sponsors = {DOE Office of Fusion Research}, 22642 note = {Investigating using PETSc for NIMROD}, 22643 dates = {Nov 21, 2002}, 22644 email = {sovinec@engr.wisc.edu} 22645} 22646 22647@Unpublished{ au1b, 22648 author = {Pablo Carrica and Robert Wilson}, 22649 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 22650 url = {http://}, 22651 sponsors = {Office of Naval Research}, 22652 note = {Using PETSc for a hydrodynamics of ships and submarines}, 22653 dates = {Sept, 2002}, 22654 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 22655} 22656 22657% ------------------- TAO References ---------------------- 22658@Article{ benson:2001:csp, 22659 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 22660 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 22661 journal = {{ACM} Transactions on Mathematical Software}, 22662 volume = {27}, 22663 number = {3}, 22664 month = sep, 22665 year = {2001}, 22666 pages = {361--376} 22667} 22668 22669@TechReport{ tao-user-ref-2000, 22670 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 22671 title = {{TAO} Users Manual}, 22672 year = {2000}, 22673 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22674 number = {ANL/MCS-TM-242}, 22675 note = {See \url{http://www.mcs.anl.gov/tao}} 22676} 22677 22678% ------------------- Optimization References ---------------------- 22679@Book{ optguide93, 22680 title = {Optimization Software Guide}, 22681 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 22682 publisher = {SIAM Publications}, 22683 address = {Philadelphia}, 22684 year = {1993} 22685} 22686 22687@InProceedings{ more84, 22688 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 22689 Hillstrom}, 22690 title = {The {MINPACK} Project}, 22691 booktitle = {Sources and Development of Mathematical Software}, 22692 editor = {Wayne R. Cowell}, 22693 year = {1984}, 22694 pages = {88--111} 22695} 22696 22697@Article{ steihaug:83, 22698 author = {Trond Steihaug}, 22699 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 22700 journal = {SIAM J. Numer. Anal.}, 22701 volume = {20}, 22702 year = {1983}, 22703 pages = {626--637}, 22704 key = {steihaug92 ! trust_region} 22705} 22706 22707@TechReport{ minpack2test, 22708 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 22709 title = {The {MINPACK-2} Test Problem Collection}, 22710 institution = {Argonne National Laboratory}, 22711 year = {1991}, 22712 number = {ANL/MCS-TM-150}, 22713 key = {more91 ! MINPACK-2} 22714} 22715 22716@TechReport{ hohmann:94, 22717 author = {Andreas Hohmann}, 22718 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 22719 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 22720 year = {1994}, 22721 number = {SC-94-4}, 22722 key = {Hohmann94} 22723} 22724 22725@TechReport{ meza:94, 22726 author = {Juan C. Meza}, 22727 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 22728 institution = {Sandia National Laboratory}, 22729 year = {1994}, 22730 number = {SAND94-8225}, 22731 key = {Meza94} 22732} 22733 22734@Book{ nw99, 22735 author = {Jorge Nocedal and Stephen J. Wright}, 22736 title = {Numerical Optimization}, 22737 year = {1999}, 22738 publisher = {Springer-Verlag}, 22739 address = {New York} 22740} 22741 22742@Book{ dennis:83, 22743 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 22744 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 22745 publisher = {Prentice-Hall, Inc.}, 22746 address = {Englewood Cliffs, NJ}, 22747 year = {1983} 22748} 22749 22750@TechReport{ more:92, 22751 author = {Jorge J. Mor\'{e} and David Thuente}, 22752 title = {Line search algorithms with guaranteed sufficient decrease}, 22753 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22754 year = {1992}, 22755 number = {MCS-P330-1092} 22756} 22757 22758@Article{ more-toraldo, 22759 author = {Jorge J. Mor\'e and G. Toraldo}, 22760 journal = {SIOPT}, 22761 pages = {93--113}, 22762 title = {On the solution of large quadratic programming problems with bound constraints}, 22763 volume = {1}, 22764 year = {1991} 22765} 22766 22767@Article{ byrd:1995:lma, 22768 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 22769 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 22770 journal = {SIAM Journal on Scientific Computing}, 22771 volume = {16}, 22772 number = {5}, 22773 pages = {1190--1208}, 22774 month = sep, 22775 year = {1995}, 22776 coden = {SJOCE3}, 22777 issn = {1064-8275 (print), 1095-7197 (electronic)}, 22778 mrclass = {90C30 (65K05)}, 22779 mrnumber = {96e:90039}, 22780 mrreviewer = {Henry Wolkowicz}, 22781 bibdate = {Fri Dec 4 16:17:35 MST 1998} 22782} 22783 22784@Article{ lin_c3, 22785 author = {C.-J. Lin and J. J. Mor\'e}, 22786 title = {Newton's method for large bound-constrained optimization problems}, 22787 year = {1999}, 22788 journal = {SIOPT}, 22789 volume = {9(4)}, 22790 pages = {1100--1127}, 22791 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 22792} 22793 22794@TechReport{ dolan2, 22795 author = {E. Dolan and J. J. Mor\'{e}}, 22796 title = {Benchmarking Optimization Software with Performance Profiles}, 22797 year = {2001}, 22798 month = jan, 22799 number = {ANL/MCS-P861-1200}, 22800 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22801 address = {Argonne, IL}, 22802 url = {http://www.mcs.anl.gov/~more/cops/} 22803} 22804 22805@InProceedings{ owlqn, 22806 author = {Galen Andrew and Jianfeng Gao}, 22807 title = {Scalable training of L1-regularized log-linear models}, 22808 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 22809 pages = {33--40}, 22810 year = {2007} 22811} 22812 22813@Article{ bmrm, 22814 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 22815 title = {Bundle methods for regularized risk minimization}, 22816 year = {2010}, 22817 journal = {Journal of Machine Learning Research}, 22818 volume = {11}, 22819 pages = {311--365} 22820} 22821 22822% ------------------- Component Software References ---------------------- 22823@InProceedings{ cca99, 22824 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 22825 McInnes and S. Parker and B. Smolinski}, 22826 title = {Toward a Common Component Architecture for High-Performance Scientific 22827 Computing}, 22828 booktitle = {Proceedings of {High Performance Distributed Computing}}, 22829 pages = {115--124}, 22830 year = {1999}, 22831 note = {See \url{http://cca-forum.org}} 22832} 22833 22834@Book{ szyperski98, 22835 author = {Clemens Szyperski}, 22836 title = {Component Software: Beyond Object-Oriented Programming}, 22837 publisher = {ACM Press}, 22838 address = {New York}, 22839 year = {1998} 22840} 22841 22842@Article{ broy98, 22843 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 22844 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 22845 Stal and Clemens Szyperski}, 22846 title = {What Characterizes a (Software) Component?}, 22847 journal = {Software -- Concepts and Tools}, 22848 publisher = {Springer-Verlag}, 22849 year = {1998}, 22850 volume = {19}, 22851 pages = {49--56} 22852} 22853 22854@Article{ componentware:94, 22855 author = {Jon Udell}, 22856 title = {Componentware}, 22857 journal = {Byte}, 22858 volume = {may}, 22859 pages = {46--56}, 22860 year = {1994}, 22861 key = {Udell94 ! componentware} 22862} 22863 22864@Misc{ cca-web-page, 22865 author = {{Common Component Architecture Forum}}, 22866 note = {See \url{http://cca-forum.org}} 22867} 22868 22869% --------------- References for Tools Used by TAO Developers ----------------- 22870 22871% 22872% tohtml: Used to generate on-line TAO users manual and manual pages 22873% 22874@TechReport{ tohtml, 22875 author = {William Gropp}, 22876 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 22877 institution = {Argonne National Laboratory}, 22878 number = {ANL/MCS-TM-00}, 22879 month = jan, 22880 year = {1995}, 22881 key = {tohtml} 22882} 22883 22884% 22885% doctext: Used to generate tex version of TAO manual pages 22886% 22887@TechReport{ doctext, 22888 author = {William Gropp}, 22889 title = {Users Manual for doctext: Producing documentation from {C} source code}, 22890 institution = {Argonne National Laboratory}, 22891 number = {ANL/MCS-TM-00}, 22892 month = jan, 22893 year = {1995}, 22894 key = {doctext} 22895} 22896 22897% 22898% bfort: Used to generate TAO Fortran interface 22899% 22900@TechReport{ bfort, 22901 author = {William Gropp}, 22902 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 22903 institution = {Argonne National Laboratory}, 22904 number = {ANL/MCS-TM-208}, 22905 month = mar, 22906 year = {1995}, 22907 key = {doctext} 22908} 22909 22910% ------------------------- PETSc References ------------------------------ 22911@InProceedings{ petsc, 22912 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 22913 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 22914 Libraries}, 22915 booktitle = {Modern Software Tools in Scientific Computing}, 22916 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 22917 publisher = {Birkhauser Press}, 22918 pages = {163--202}, 22919 year = {1997} 22920} 22921 22922% ------------------------- Misc Other References ------------------------------ 22923@Misc{ indeps-web-page, 22924 title = {{InDEPS} {W}eb page}, 22925 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 22926 author = {et al. Robert Armstrong}, 22927 institution = {Sandia National Laboratory}, 22928 key = {{InDEPS} {W}eb page} 22929} 22930 22931@Misc{ pooma, 22932 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 22933 chitectures}, 22934 year = {1996}, 22935 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 22936 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 22937} 22938 22939@Misc{ isis++-web-page, 22940 title = {{ISIS++} {W}eb Page}, 22941 note = {See \url{http://ca.sandia.gov/isis}}, 22942 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 22943 institution = {Sandia National Laboratories} 22944} 22945 22946@Misc{ trilinos-web-page, 22947 title = {{Trilinos} {W}eb Page}, 22948 note = {See 22949 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 22950 author = {Mike Heroux et al.}, 22951 institution = {Sandia National Laboratories} 22952} 22953 22954@Misc{ alice-web-page, 22955 title = {{ALICE} {W}eb page}, 22956 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 22957 Argonne National Laboratory}, 22958 key = {{ALICE} {W}eb page} 22959} 22960 22961@Misc{ autodiff-webpage, 22962 author = {{Computational Differentiation Project}}, 22963 note = {See \url{http://www.mcs.anl.gov/autodiff}} 22964} 22965 22966@Misc{ coool-home-page, 22967 author = {Lydia Deng and Wences Gouveia and John Scales}, 22968 title = {{The CWP Object-Oriented Optimization Library}}, 22969 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 22970} 22971 22972@Misc{ rice-inversion-home-page, 22973 author = {Mark S. Gokenbach and William W. Symes}, 22974 title = {{The Hilbert Class Library}}, 22975 note = {See \url{http://www.trip.caam.rice.edu/}} 22976} 22977 22978@Misc{ opt++-home-page, 22979 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 22980 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 22981} 22982 22983@Article{ gockenbach:1999:ccl, 22984 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 22985 title = {C++ Classes for Linking Optimization with Complex Simulations}, 22986 journal = {{ACM} Transactions on Mathematical Software}, 22987 volume = {25}, 22988 number = {2}, 22989 month = jun, 22990 year = {1999}, 22991 pages = {191-212}, 22992 abstract = {The object-oriented programming paradigm can be used to overcome the 22993 incompatibilities between off-the-shelf optimization software and application 22994 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 22995 objects arising in optimization problems, such as vectors, linear operators, and 22996 so forth, as C++ classes, making it possible to write optimization code in a 22997 natural fashion, while allowing application software such as simulators to use the 22998 most convenient data structures and programming style. In spite of the poor 22999 reputation C++ has for runtime performance, the use of mixed-language programming 23000 allows performance equal to that achieved by standard Fortran packages, as 23001 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 23002 accepted = {April 1999}, 23003 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 23004} 23005 23006@Misc{ neos-guide, 23007 author = {{The Optimization Software Guide}}, 23008 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 23009} 23010 23011@Article{ boyd, 23012 title = {Distributed optimization and statistical learning via the alternating direction 23013 method of multipliers}, 23014 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 23015 Jonathan and others}, 23016 journal = {Foundations and Trends{\textregistered} in Machine learning}, 23017 volume = {3}, 23018 number = {1}, 23019 pages = {1-122}, 23020 year = {2011}, 23021 publisher = {Now Publishers, Inc.} 23022} 23023 23024@Misc{ :alertsys, 23025 title = {page{ALERT}}, 23026 organization = {Alert Systems, Inc}, 23027 address = {Madison, Wisconsin}, 23028 note = {http://www.alertsys.com/} 23029} 23030 23031@Manual{ :cmfortran, 23032 title = {{CM} {F}ortran Language Reference Manual}, 23033 organization = {Thinking Machines Corporation}, 23034 year = {1994}, 23035 address = {Cambridge, MA} 23036} 23037 23038@Manual{ :cmmd, 23039 title = {{CMMD} Reference Manual, Version 3.0}, 23040 organization = {Thinking Machines Corporation}, 23041 year = {1993}, 23042 address = {Cambridge, MA} 23043} 23044 23045@Manual{ :cmssl, 23046 title = {{CMSSL} for {CM} {F}ortran}, 23047 volume = {I}, 23048 organization = {Thinking Machines Corporation}, 23049 year = {1994}, 23050 address = {Cambridge, MA} 23051} 23052 23053@Misc{ :condor, 23054 author = {M. Livny}, 23055 title = {{PI}, The {Condor} Project, High Throughput Computing}, 23056 howpublished = {www.cs.wisc.edu/condor} 23057} 23058 23059@Manual{ :connection, 23060 title = {Connection Machine {CM}--5 Technical Summary}, 23061 organization = {Thinking Machines Corporation}, 23062 year = {1993}, 23063 address = {Cambridge, MA} 23064} 23065 23066@Manual{ :cplex, 23067 title = {{CPLEX} Optimizer}, 23068 organization = {ILOG CPLEX Division}, 23069 address = {889 Alder Avenue, Incline Village, Nevada}, 23070 note = {http://www.cplex.com/} 23071} 23072 23073@Manual{ :cplextm, 23074 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 23075 (Version 2.0)}, 23076 organization = {CPLEX Optimization Inc.}, 23077 year = {1992}, 23078 address = {Incline Village, Nevada} 23079} 23080 23081@Misc{ :fatcop, 23082 author = {M. C. Ferris}, 23083 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 23084 Solver}, 23085 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 23086} 23087 23088@Misc{ :metaneos, 23089 author = {S. J. Wright}, 23090 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 23091 howpublished = {www-unix.mcs.anl.gov/metaneos} 23092} 23093 23094@InCollection{ gropp.more:optimization, 23095 author = {W. Gropp and J. J. Mor\'e}, 23096 title = {Optimization environments and the {NEOS} Server}, 23097 booktitle = {Approximation Theory and Optimization}, 23098 pages = {167--182}, 23099 publisher = {Cambridge University Press}, 23100 year = {1997}, 23101 editor = {M. D. Buhmann and A. Iserles} 23102} 23103 23104@Article{ czyzyk.mesnier.ea:neos, 23105 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 23106 title = {The {NEOS} Server}, 23107 journal = {IEEE Journal on Computational Science and Engineering}, 23108 volume = {5}, 23109 year = {1998}, 23110 pages = {68--75} 23111} 23112 23113@Book{ :osl, 23114 title = {Handbook for {IBM OSL}}, 23115 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 23116 year = {1994}, 23117 publisher = {Boyd and Fraser}, 23118 address = {Danvers, Massachusetts} 23119} 23120 23121@Manual{ :pro-matlab, 23122 title = {{PRO}--{MATLAB} User's Guide}, 23123 organization = {The MathWorks, Inc.}, 23124 year = {1989}, 23125 address = {21 Eliot Street, South Natick, MA 01760} 23126} 23127 23128@Misc{ :prostate, 23129 key = {Biomedical}, 23130 title = {Biomedical Business International Newsletter}, 23131 howpublished = {pp. 72--75}, 23132 year = {1996} 23133} 23134 23135@Misc{ :sipcase, 23136 key = {Natural}, 23137 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 23138 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 23139} 23140 23141@Book{ aarts.korst:simulated, 23142 author = {E. Aarts and J. Korst}, 23143 title = {Simulated Annealing and Boltzman Machines}, 23144 year = {1990}, 23145 publisher = {John Wiley \& Sons}, 23146 address = {Chichester} 23147} 23148 23149@TechReport{ aarts.laarhoven.ea:local-search-based, 23150 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 23151 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 23152 institution = {Centre for Quantitative Methods}, 23153 year = {1991}, 23154 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 23155 number = {106}, 23156 type = {CQM-Not} 23157} 23158 23159@Article{ aashtiani.magnanti:equilibria, 23160 author = {H. Z. Aashtiani and T. L. Magnanti}, 23161 title = {Equilibria on a congested transportation network}, 23162 journal = {SIAM Journal on Algebraic and Discrete Methods}, 23163 volume = {2}, 23164 year = {1981}, 23165 pages = {213--226} 23166} 23167 23168@Article{ ablow.brigham:analog, 23169 author = {C. M. Ablow and G. Brigham}, 23170 title = {An Analog Solution of Programming Problems}, 23171 journal = {Operations Research}, 23172 year = {1955}, 23173 volume = {3}, 23174 pages = {388--394} 23175} 23176 23177@Article{ achuthan.grabowski.ea:optimal, 23178 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 23179 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 23180 journal = {Opsearch}, 23181 year = {1981}, 23182 volume = {18}, 23183 pages = {117--138} 23184} 23185 23186@Book{ adelman.robinson:income, 23187 author = {I. Adelman and S. Robinson}, 23188 title = {Income Distribution Policy in Developing Countries}, 23189 publisher = {Stanford University Press}, 23190 year = {1978}, 23191 address = {Stanford, California} 23192} 23193 23194@Article{ adler.resende.ea:implementation, 23195 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 23196 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 23197 journal = {Mathematical Programming}, 23198 year = {1989}, 23199 volume = {44}, 23200 pages = {297--336} 23201} 23202 23203@TechReport{ aeberhard.coomans.ea:comparison, 23204 author = {S. Aeberhard and D. Coomans and O. de Vel}, 23205 title = {Comparison of Classifiers in High Dimensional Settings}, 23206 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 23207 University of North Queensland}, 23208 year = {1992}, 23209 number = {92-02}, 23210 type = {Technical Report} 23211} 23212 23213@Article{ aganagic.cottle:constructive, 23214 author = {M. Aganagi\'{c} and R. W. Cottle}, 23215 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 23216 Minors}, 23217 journal = {Mathematical Programming}, 23218 year = {1987}, 23219 volume = {37}, 23220 pages = {223--231} 23221} 23222 23223@TechReport{ aganagic:iterative, 23224 author = {M. Aganagi\'{c}}, 23225 title = {Iterative Methods for the Linear Complementarity Problem}, 23226 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 23227 University}, 23228 year = {1978}, 23229 type = {SOL}, 23230 number = {78-10}, 23231 address = {Stanford, California} 23232} 23233 23234@Book{ ahlfors:complex, 23235 author = {L. V. Ahlfors}, 23236 title = {Complex Analysis}, 23237 publisher = {McGraw--Hill Book Company}, 23238 address = {New York}, 23239 series = {International Series in Pure and Applied Mathematics}, 23240 edition = {Second}, 23241 year = {1966} 23242} 23243 23244@Article{ ahn:solution, 23245 author = {B--H. Ahn}, 23246 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 23247 journal = {Journal of Optimization Theory and Applications}, 23248 year = {1981}, 23249 volume = {33}, 23250 pages = {175--185} 23251} 23252 23253@Article{ al-fahed.stavroulakis.ea:hard, 23254 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 23255 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 23256 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 23257 volume = {71}, 23258 year = {1991}, 23259 pages = {257--265} 23260} 23261 23262@Article{ al-fahed.stavroulakis.ea:linear, 23263 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 23264 title = {A linear complementarity approach to the frictionless gripper}, 23265 journal = {International Journal of Robotic Research}, 23266 volume = {11}, 23267 year = {1992}, 23268 pages = {112--122} 23269} 23270 23271@Article{ al-khayyal.falk:jointly, 23272 author = {F. A. Al--Khayyal and J. E. Falk}, 23273 title = {Jointly Constrained Biconvex Programming}, 23274 journal = {Mathematics of Operations Research}, 23275 year = {1983}, 23276 volume = {8}, 23277 pages = {273--286} 23278} 23279 23280@Article{ al-khayyal.kyparisis:finite, 23281 author = {F. A. Al--Khayyal and J. Kyparisis}, 23282 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 23283 Inequalities}, 23284 journal = {Journal of Optimization Theory and Applications}, 23285 year = {1991}, 23286 volume = {70}, 23287 pages = {319--332} 23288} 23289 23290@PhDThesis{ al-khayyal:biconvex, 23291 author = {F. A. Al--Khayyal}, 23292 title = {Biconvex Programming and Biconcave Minimization}, 23293 year = {1977}, 23294 school = {The George Washington University} 23295} 23296 23297@Article{ alart.curnier:mixed, 23298 author = {P. Alart and A. Curnier}, 23299 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 23300 solution methods}, 23301 journal = {Computer Methods in Applied Mechanics and Engineering}, 23302 volume = {92}, 23303 year = {1991}, 23304 pages = {353--375} 23305} 23306 23307@Misc{ alexander.kellog.ea:piecewise, 23308 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 23309 title = {Piecewise smooth continuation}, 23310 howpublished = {Manuscript}, 23311 year = {1979} 23312} 23313 23314@InCollection{ alexander.li.ea:piecewise, 23315 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 23316 title = {Piecewise smooth homotopies}, 23317 booktitle = {Homotopy Methods and Global Convergence}, 23318 pages = {1--14}, 23319 publisher = {Plenum Press}, 23320 year = {1983}, 23321 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 23322 address = {New York} 23323} 23324 23325@InCollection{ alexander:topological, 23326 author = {J.~C. Alexander}, 23327 title = {The topological theory of an embedding method}, 23328 booktitle = {Continuation Methods}, 23329 pages = {37--68}, 23330 publisher = {Academic Press}, 23331 year = {1978}, 23332 editor = {H. Wacker}, 23333 address = {New York} 23334} 23335 23336@Book{ allen:probability, 23337 author = {A. O. Allen}, 23338 title = {Probability, Statistics and Queueing Theory}, 23339 publisher = {Academic Press}, 23340 year = {1990}, 23341 address = {London}, 23342 edition = {Second} 23343} 23344 23345@Book{ allgower.georg:numerical, 23346 author = {E. L. Allgower and K. Georg}, 23347 title = {Numerical Continuation Methods, An Introduction}, 23348 publisher = {Springer-Verlag}, 23349 year = {1990}, 23350 address = {Berlin} 23351} 23352 23353@InProceedings{ allgower.georg:predictor-corrector, 23354 crossref = {bachem.grotschel.ea:mathematical}, 23355 author = {E. L. Allgower and K. Georg}, 23356 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 23357 Zero Points of Nonlinear Mappings}, 23358 pages = {15--56} 23359} 23360 23361@Article{ aluffi-pentini.parisi.ea:algorithm, 23362 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 23363 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 23364 Algorithm}, 23365 journal = {ACM Transactions on Mathematical Software}, 23366 year = {1988}, 23367 volume = {14}, 23368 pages = {366--380} 23369} 23370 23371@Article{ anandalingam.friesz:hierarchical, 23372 author = {G. Anandalingam and T. L. Friesz}, 23373 title = {Hierarchical Optimization: An Introduction}, 23374 journal = {Annals of Operations Research}, 23375 year = {1992}, 23376 volume = {34}, 23377 pages = {1--11} 23378} 23379 23380@Article{ anandalingam.white:solution, 23381 author = {G. Anandalingam and D. J. White}, 23382 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 23383 Functions}, 23384 journal = {IEEE Transactions on Automatic Control}, 23385 year = {1990}, 23386 volume = {35}, 23387 number = {10}, 23388 pages = {1170--1173} 23389} 23390 23391@Article{ andersen.andersen:presolving, 23392 author = {E. Andersen and K. Andersen}, 23393 title = {Presolving in Linear Programming}, 23394 year = {1995}, 23395 journal = {Mathematical Programming}, 23396 volume = {71}, 23397 pages = {221--245} 23398} 23399 23400@InProceedings{ andersen.ye:homogeneous, 23401 author = {E. Andersen and Y. Ye}, 23402 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 23403 Equality Constraints}, 23404 crossref = {ferris.pang:complementarity}, 23405 pages = {1--11} 23406} 23407 23408@Book{ anderson.bai.ea:lapack, 23409 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 23410 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 23411 Sorensen}, 23412 title = {{LAPACK} User's Guide}, 23413 publisher = {SIAM}, 23414 year = {1995}, 23415 address = {Philadelphia, Pennsylvania}, 23416 edition = {Second} 23417} 23418 23419@Article{ anderson.ferris:direct, 23420 author = {E. J. Anderson and M. C. Ferris}, 23421 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 23422 year = {2001}, 23423 journal = {SIAM Journal on Optimization, forthcoming}, 23424 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 23425 key = {55} 23426} 23427 23428@InProceedings{ anderson.ferris:genetic, 23429 author = {E. J. Anderson and M. C. Ferris}, 23430 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 23431 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 23432 Waterloo, Ontario, Canada, May 28--30}, 23433 publisher = {University of Waterloo Press}, 23434 key = {14}, 23435 year = {1990} 23436} 23437 23438@Article{ anderson.ferris:genetic*1, 23439 author = {E. J. Anderson and M. C. Ferris}, 23440 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 23441 Problem}, 23442 journal = {ORSA Journal on Computing}, 23443 year = {1994}, 23444 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 23445 volume = {6}, 23446 pages = {161--173}, 23447 key = {22} 23448} 23449 23450@InProceedings{ anderson.ferris:parallel, 23451 author = {E. J. Anderson and M. C. Ferris}, 23452 title = {Parallel Genetic Algorithms in Optimization}, 23453 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 23454 Computing, Chicago, Illinois, December 11-13}, 23455 year = {1989}, 23456 key = {12} 23457} 23458 23459@Unpublished{ anderson.lewis:primal, 23460 author = {E. J. Anderson and A. S. Lewis}, 23461 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 23462 note = {In preparation} 23463} 23464 23465@Book{ anderson.nash:linear, 23466 author = {E. J. Anderson and P. Nash}, 23467 title = {Linear Programming in Infinite--Dimensional Spaces}, 23468 year = {1987}, 23469 publisher = {John Wiley \& Sons}, 23470 address = {Chichester} 23471} 23472 23473@InProceedings{ anderson:primal, 23474 author = {E. J. Anderson}, 23475 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 23476 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 23477 Programming, Cambridge, September 1984}, 23478 year = {1985}, 23479 editor = {E. J. Anderson and A. B. Philpott}, 23480 publisher = {Springer-Verlag}, 23481 address = {Berlin} 23482} 23483 23484@Article{ andradottir:method, 23485 author = {S. Andrad\'{o}ttir}, 23486 title = {A Method of Discrete Stochastic Optimization}, 23487 journal = {Management Science}, 23488 year = {1995}, 23489 volume = {41}, 23490 pages = {1946--1961} 23491} 23492 23493@Article{ andradottir:global, 23494 author = {S. Andrad\'{o}ttir}, 23495 title = {A Global Search Method for Discrete Stochastic Optimization}, 23496 journal = {SIAM Journal on Optimization}, 23497 year = {1996}, 23498 volume = {6}, 23499 pages = {513--530} 23500} 23501 23502@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 23503 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 23504 title = {An infeasible--interior--point predictor--corrector algorithm for the 23505 {P}$_x$--geometric {LCP}}, 23506 institution = {Department of Mathematics, The University of Iowa}, 23507 address = {Iowa City, Iowa}, 23508 year = {1994}, 23509 number = {62}, 23510 type = {Reports on Computational Mathematics} 23511} 23512 23513@TechReport{ anitescu.potra:formulating, 23514 author = {M. Anitescu and F. A. Potra}, 23515 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 23516 Linear Complementarity Problems}, 23517 institution = {Department of Mathematics, The University of Iowa}, 23518 year = {1996}, 23519 type = {Report}, 23520 number = {93}, 23521 address = {Iowa City, Iowa} 23522} 23523 23524@Article{ anstreicher.lee.ea:crashing, 23525 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 23526 title = {Crashing a Maximum-Weight Complementarity Basis}, 23527 journal = {Mathematical Programming}, 23528 year = {1992}, 23529 volume = {54}, 23530 pages = {281--294} 23531} 23532 23533@Article{ anstreicher:combined, 23534 author = {K. M. Anstreicher}, 23535 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 23536 programming}, 23537 journal = {Mathematical Programming}, 23538 year = {1991}, 23539 volume = {52}, 23540 pages = {429--440} 23541} 23542 23543@Article{ anstreicher:combined*1, 23544 author = {K. M. Anstreicher}, 23545 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 23546 journal = {Mathematical Programming}, 23547 year = {1989}, 23548 volume = {43}, 23549 pages = {209--223} 23550} 23551 23552@InCollection{ arbenz.gander.ea:remote, 23553 author = {P. Arbenz and W. Gander and M. Oettli}, 23554 title = {The Remote Computational System}, 23555 booktitle = {High-Performance Computation and Networks}, 23556 publisher = {Springer-Verlag}, 23557 year = {1996}, 23558 volume = {1067}, 23559 series = {Lecture Notes in Computer Science}, 23560 pages = {662--667} 23561} 23562 23563@InCollection{ arcus:comsoal, 23564 author = {A. L. Arcus}, 23565 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 23566 booktitle = {Readings in Production and Operations Management}, 23567 year = {1966}, 23568 editor = {E. S. Buffa}, 23569 publisher = {John Wiley \& Sons}, 23570 address = {New York} 23571} 23572 23573@TechReport{ arioli.chan.ea:computing, 23574 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 23575 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 23576 Optimization Calculations}, 23577 institution = {CERFACS}, 23578 year = {1993}, 23579 number = {TR/PA/93/34} 23580} 23581 23582@Article{ armijo:minimization, 23583 author = {L. Armijo}, 23584 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 23585 Derivatives}, 23586 journal = {Pacific Journal of Mathematics}, 23587 year = {1966}, 23588 volume = {16}, 23589 pages = {1--3} 23590} 23591 23592@Article{ arrow.debreu:existence, 23593 author = {K. Arrow and G. Debreu}, 23594 title = {Existence of Equilibrium for a Competitive Economy}, 23595 journal = {Econometrica}, 23596 year = {1954}, 23597 volume = {22}, 23598 pages = {265--290} 23599} 23600 23601@InCollection{ arrow.solow:gradient, 23602 author = {K. J. Arrow and R. M. Solow}, 23603 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 23604 booktitle = {Studies in Linear and Nonlinear Programming}, 23605 year = {1958}, 23606 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 23607 publisher = {Stanford University Press}, 23608 address = {Stanford, California}, 23609 pages = {166--176} 23610} 23611 23612@Book{ aubin.ekeland:nonlinear, 23613 author = {J.-P. Aubin and I. Ekeland}, 23614 title = {Applied nonlinear analysis}, 23615 publisher = {John Wiley \& Sons}, 23616 address = {New York}, 23617 year = {1984} 23618} 23619 23620@Article{ auchmuty:variational, 23621 author = {G. Auchmuty}, 23622 title = {Variational Principles for Variational Inequalities}, 23623 journal = {Numerical Functional Analysis and Optimization}, 23624 year = {1989}, 23625 volume = {10}, 23626 pages = {863--874} 23627} 23628 23629@Book{ auerbach.kotlikoff:dynamic, 23630 author = {A. J. Auerbach and L. J. Kotlikoff}, 23631 title = {Dynamic Fiscal Policy}, 23632 publisher = {Cambridge University Press}, 23633 address = {Cambridge, England}, 23634 year = {1987} 23635} 23636 23637@InProceedings{ ault.deutsch.ea:interpolating, 23638 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 23639 title = {Interpolating Subspaces in Approximation Theory}, 23640 booktitle = {Approximation Theory}, 23641 year = {1970}, 23642 editor = {A. Talbot}, 23643 publisher = {Academic Press}, 23644 address = {London} 23645} 23646 23647@Article{ auslender.crouzeix:global, 23648 author = {A. A. Auslender and J.--P. Crouzeix}, 23649 title = {Global Regularity Theorems}, 23650 journal = {Mathematics of Operations Research}, 23651 year = {1988}, 23652 volume = {13}, 23653 pages = {243--253} 23654} 23655 23656@Article{ auslender.haddou:interior-proximal, 23657 author = {A. Auslender and M. Haddou}, 23658 title = {An interior-proximal method for convex linearly constrained problems and its 23659 extension to variational inequalities}, 23660 year = {1995}, 23661 journal = {Mathematical Programming}, 23662 pages = {77--100}, 23663 volume = {71} 23664} 23665 23666@Article{ auslender:convergence, 23667 author = {A. Auslender}, 23668 title = {Convergence of stationary sequences for variational inequalities with maximal 23669 monotone operators}, 23670 journal = {Applied Mathematics and Optimization}, 23671 volume = {28}, 23672 year = {1993}, 23673 pages = {161--172} 23674} 23675 23676@Book{ auslender:optimization, 23677 author = {A. Auslender}, 23678 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 23679 year = {1976}, 23680 publisher = {Masson}, 23681 address = {Paris} 23682} 23683 23684@TechReport{ averick.carter.ea:minpack-2, 23685 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 23686 title = {The {MINPACK-2} Test Problem Collection}, 23687 institution = {Argonne National Laboratory}, 23688 year = {1992}, 23689 address = {Argonne, Illinois}, 23690 number = {MCS-P153-0692} 23691} 23692 23693@TechReport{ axline.billups.ea:guidelines, 23694 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 23695 title = {Guidelines for Software Security ({U})}, 23696 institution = {SNL}, 23697 year = {1989}, 23698 month = oct, 23699 address = {Albuquerque, New Mexico}, 23700 number = {SAND88-2955} 23701} 23702 23703@Article{ ayres.walter:greenhouse, 23704 author = {R. U. Ayres and J. Walter}, 23705 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 23706 journal = {Environmental and Resource Economics}, 23707 year = {1991}, 23708 volume = {1}, 23709 pages = {237--270} 23710} 23711 23712@PhDThesis{ bagley:behaviour, 23713 author = {J. D. Bagley}, 23714 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 23715 Algorithms}, 23716 year = {1967}, 23717 school = {University of Michigan} 23718} 23719 23720@Article{ bain.stewart:application, 23721 author = {R. S. Bain and W. E. Stewart}, 23722 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 23723 Algebraic Equation Systems}, 23724 journal = {Computers in Chemical Engineering}, 23725 year = {1991}, 23726 volume = {15}, 23727 pages = {203--208} 23728} 23729 23730@Article{ baker.lasdon:successive, 23731 author = {T. E. Baker and L. S. 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Ferris}, 24203 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 24204 Starting Points}, 24205 journal = {SIAM Journal on Optimization}, 24206 year = {1996}, 24207 volume = {6}, 24208 pages = {316--325}, 24209 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 24210 key = {34} 24211} 24212 24213@TechReport{ billups.ferris:convergence*1, 24214 author = {S. C. Billups and M. C. Ferris}, 24215 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 24216 Points}, 24217 institution = {Computer Sciences Department, University of Wisconsin}, 24218 year = {1993}, 24219 address = {Madison, Wisconsin}, 24220 number = {1180}, 24221 note = {Revised version in SIAM Journal on Optimization.} 24222} 24223 24224@Article{ billups.ferris:qpcomp, 24225 author = {S. C. Billups and M. C. Ferris}, 24226 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 24227 year = {1997}, 24228 journal = {Mathematical Programming}, 24229 pages = {533--562}, 24230 volume = {76}, 24231 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 24232 key = {47} 24233} 24234 24235@Article{ billups.ferris:solutions, 24236 author = {S. C. Billups and M. C. Ferris}, 24237 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 24238 journal = {Mathematics of Operations Research}, 24239 volume = {24}, 24240 pages = {219--236}, 24241 year = {1999}, 24242 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 24243 key = {42}, 24244 institution = {Computer Sciences Department, University of Wisconsin}, 24245 address = {Madison, Wisconsin}, 24246 type = {Mathematical Programming Technical Report}, 24247 number = {94--15} 24248} 24249 24250@TechReport{ billups.murata.ea:users, 24251 author = {S. C. Billups and K. K. 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Billups}, 24272 title = {Algorithms for Complementarity Problems and Generalized Equations}, 24273 school = {University of Wisconsin--Madison}, 24274 year = {1995}, 24275 address = {Madison, Wisconsin}, 24276 month = aug 24277} 24278 24279@MastersThesis{ billups:augmented, 24280 author = {S. C. Billups}, 24281 title = {An Augmented Jacobian Matrix Algorithm for Tracking Homotopy Zero Curves}, 24282 school = {Virginia Tech}, 24283 year = {1985}, 24284 address = {Blacksburg, Virginia} 24285} 24286 24287@TechReport{ billups:homotopy, 24288 author = {S. C. Billups}, 24289 title = {A Homotopy Based Algorithm for Mixed Complementarity Problems}, 24290 institution = {Department of Mathematics, University of Colorado}, 24291 year = {1998}, 24292 address = {Denver, Colorado} 24293} 24294 24295@Article{ billups:improving, 24296 author = {S. C. 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Dirkse}, 26475 title = {Robust Solution of Mixed Complementarity Problems}, 26476 school = {Computer Sciences Department, University of Wisconsin}, 26477 year = {1994}, 26478 address = {Madison, Wisconsin}, 26479 note = {Available from ftp://ftp.cs.wisc.edu/math-prog/tech-reports/}, 26480 annote = {Mathematical Programming Technical Report 94-12} 26481} 26482 26483@TechReport{ dixon.mills:neural, 26484 author = {L. C. Dixon and D. J. Mills}, 26485 title = {Neural Nets for Massively Parallel Optimisation}, 26486 institution = {Hatfield Polytechnic}, 26487 year = {1992}, 26488 address = {Hatfield, Hertforshire, England}, 26489 number = {Numerical Optimisation Centre Technical Report No. 259} 26490} 26491 26492@Article{ dontchev:local, 26493 author = {A. L. Dontchev}, 26494 title = {Local Convergence of the {N}ewton method for Generalized Equations}, 26495 journal = {C.R. Acad. Sci. 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Lucidi}, 27253 title = {Globally Convergent Methods for Nonlinear Equations}, 27254 institution = {Computer Sciences Department, University of Wisconsin}, 27255 year = {1991}, 27256 address = {Madison, Wisconsin}, 27257 number = {1030}, 27258 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1991/tr1030.ps}, 27259 key = {21} 27260} 27261 27262@Article{ ferris.lucidi:nonmonotone, 27263 author = {M. C. Ferris and S. Lucidi}, 27264 title = {Nonmonotone Stabilization Methods for Nonlinear Equations}, 27265 journal = {Journal of Optimization Theory and Applications}, 27266 year = {1994}, 27267 volume = {81}, 27268 pages = {53--71}, 27269 key = {30} 27270} 27271 27272@Article{ ferris.mangasarian:breast, 27273 author = {M. C. Ferris and O. L. Mangasarian}, 27274 title = {Breast Cancer Diagnosis via Linear Programming}, 27275 key = {50}, 27276 journal = {{IEEE} Computational Science and Engineering}, 27277 year = {1995}, 27278 volume = {2}, 27279 pages = {70--71} 27280} 27281 27282@Article{ ferris.mangasarian:error, 27283 author = {M. C. Ferris and O. L. Mangasarian}, 27284 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 27285 Inequalities}, 27286 journal = {Annals of Operations Research}, 27287 year = {1993}, 27288 volume = {47}, 27289 pages = {293--305}, 27290 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 27291 key = {24} 27292} 27293 27294@Article{ ferris.mangasarian:finite, 27295 author = {M. C. Ferris and O. L. Mangasarian}, 27296 title = {Finite Perturbation of Convex Programs}, 27297 journal = {Applied Mathematics and Optimization}, 27298 year = {1991}, 27299 volume = {23}, 27300 pages = {263--273}, 27301 key = {08} 27302} 27303 27304@Book{ ferris.mangasarian:linear, 27305 author = {M. C. Ferris and O. L. Mangasarian}, 27306 title = {Linear Programming via {MATLAB}}, 27307 publisher = {in preparation}, 27308 year = {1995}, 27309 address = {Madison, Wisconsin} 27310} 27311 27312@Article{ ferris.mangasarian:minimum, 27313 author = {M. C. Ferris and O. L. Mangasarian}, 27314 title = {Minimum Principle Sufficiency}, 27315 journal = {Mathematical Programming}, 27316 year = {1992}, 27317 volume = {57}, 27318 pages = {1--14}, 27319 key = {11} 27320} 27321 27322@Article{ ferris.mangasarian:parallel, 27323 author = {M. C. Ferris and O. L. Mangasarian}, 27324 title = {Parallel Constraint Distribution}, 27325 journal = {SIAM Journal on Optimization}, 27326 year = {1991}, 27327 volume = {1}, 27328 pages = {487--500}, 27329 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 27330 key = {18} 27331} 27332 27333@Article{ ferris.mangasarian:parallel*1, 27334 author = {M. C. Ferris and O. L. Mangasarian}, 27335 title = {Parallel Variable Distribution}, 27336 journal = {SIAM Journal on Optimization}, 27337 year = {1994}, 27338 volume = {4}, 27339 pages = {815--832}, 27340 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 27341 key = {31} 27342} 27343 27344@Article{ ferris.meeraus.ea:computing, 27345 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 27346 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 27347 journal = {Optimization Methods and Software}, 27348 year = {1999}, 27349 volume = {10}, 27350 pages = {669--685}, 27351 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 27352 key = {45} 27353} 27354 27355@Article{ ferris.mesnier.ea:neos, 27356 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 27357 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 27358 {I}nternet}, 27359 year = {2000}, 27360 journal = {{ACM} Transactions on Mathematical Software}, 27361 key = {54}, 27362 volume = {26}, 27363 pages = {1--18}, 27364 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 27365 institution = {Computer Sciences Department, University of Wisconsin}, 27366 address = {Madison, Wisconsin}, 27367 number = {96-08}, 27368 type = {Mathematical Programming Technical Report}, 27369 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 27370 Argonne National Laboratory}, 27371 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 27372 1996} 27373} 27374 27375@InCollection{ ferris.meyer:models, 27376 author = {M. C. Ferris and R. R. Meyer}, 27377 title = {Models and Solution for On-Demand Data Delivery Problems}, 27378 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 27379 key = {80}, 27380 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 27381 Problems}, 27382 editor = {P. M. Pardalos}, 27383 series = {Nonconvex Optimization and its Applications}, 27384 volume = {42}, 27385 address = {Dordrect}, 27386 year = {2000}, 27387 pages = {175--188}, 27388 publisher = {Kluwer}, 27389 type = {Mathematical Programming Technical Report}, 27390 institution = {Computer Sciences Department, University of Wisconsin}, 27391 number = {99-04} 27392} 27393 27394@InProceedings{ ferris.munson.ea:homotopy, 27395 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 27396 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 27397 booktitle = {Numerical Analysis 1999}, 27398 key = {88}, 27399 year = {2000}, 27400 editor = {D. F. Griffiths and G. A. Watson}, 27401 series = {Research Notes in Mathematics}, 27402 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 27403 address = {London}, 27404 pages = {143--167}, 27405 publisher = {Chapman and Hall}, 27406 institution = {Computer Sciences Department, University of Wisconsin}, 27407 number = {99-09}, 27408 type = {Mathematical Programming Technical Report} 27409} 27410 27411@TechReport{ ferris.munson.ea:practical, 27412 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 27413 title = {A Practical Approach to Sample-Path Simulation Optimization}, 27414 type = {Data Mining Institute Technical Report}, 27415 institution = {Computer Sciences Department, University of Wisconsin}, 27416 address = {Madison, Wisconsin}, 27417 year = {2000}, 27418 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 27419 number = {00-03}, 27420 key = {92}, 27421 annote = {To appear in WSC 2000} 27422} 27423 27424@InCollection{ ferris.munson:case, 27425 author = {M. C. Ferris and T. S. Munson}, 27426 title = {Case Studies in Complementarity: Improving Model Formulation}, 27427 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 27428 key = {73}, 27429 pages = {79--98}, 27430 publisher = {Springer Verlag}, 27431 year = {1999}, 27432 editor = {M. Th\'{e}ra and R. Tichatschke}, 27433 number = {477}, 27434 series = {Lecture Notes in Economics and Mathematical Systems}, 27435 address = {Berlin}, 27436 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 27437 type = {Mathematical Programming Technical Report}, 27438 institution = {Computer Sciences Department, University of Wisconsin} 27439} 27440 27441@Article{ ferris.munson:complementarity, 27442 author = {M. C. Ferris and T. S. Munson}, 27443 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 27444 year = {2000}, 27445 volume = {24}, 27446 pages = {165--188}, 27447 journal = {Journal of Economic Dynamics and Control}, 27448 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 27449 key = {70}, 27450 type = {Mathematical Programming Technical Report}, 27451 institution = {Computer Sciences Department, University of Wisconsin}, 27452 address = {Madison, Wisconsin}, 27453 number = {98-12} 27454} 27455 27456@Misc{ ferris.munson:condor, 27457 author = {M. C. Ferris and T. S. Munson}, 27458 title = {Condor Modeling Language Interface}, 27459 organization = {Computer Sciences Department, University of Wisconsin}, 27460 address = {Madison, Wisconsin}, 27461 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 27462} 27463 27464@Manual{ ferris.munson:gams, 27465 author = {M. C. Ferris and T. S. Munson}, 27466 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 27467 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 27468} 27469 27470@Article{ ferris.munson:interfaces, 27471 author = {M. C. Ferris and T. S. Munson}, 27472 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 27473 journal = {Computational Optimization and Applications}, 27474 volume = {12}, 27475 pages = {207--227}, 27476 year = {1999}, 27477 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 27478 key = {63}, 27479 institution = {Computer Sciences Department, University of Wisconsin}, 27480 address = {Madison, Wisconsin}, 27481 number = {97-12}, 27482 type = {Mathematical Programming Technical Report} 27483} 27484 27485@TechReport{ ferris.munson:interior, 27486 author = {M. C. Ferris and T. S. Munson}, 27487 title = {Interior Point Methods for Massive Support Vector Machines}, 27488 institution = {Computer Sciences Department, University of Wisconsin}, 27489 year = {2000}, 27490 key = {94}, 27491 type = {Data Mining Institute Technical Report}, 27492 number = {00-05}, 27493 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 27494 address = {Madison, Wisconsin}, 27495 annote = {Submitted to SIOPT} 27496} 27497 27498@Article{ ferris.munson:linear, 27499 author = {M. C. Ferris and T. S. Munson}, 27500 title = {Linear Programming for Emergency Broadcast Systems}, 27501 year = {1999}, 27502 journal = {{SIAG/OPT} Newsletter}, 27503 volume = {10}, 27504 pages = {6--8}, 27505 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 27506 key = {76}, 27507 type = {Mathematical Programming Technical Report}, 27508 institution = {Computer Sciences Department, University of Wisconsin}, 27509 address = {Madison, Wisconsin}, 27510 number = {98-20} 27511} 27512 27513@Article{ ferris.munson:modeling, 27514 author = {M. C. Ferris and T. S. Munson}, 27515 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 27516 year = {2000}, 27517 journal = {Mathematical Programming}, 27518 volume = {88}, 27519 pages = {487--506}, 27520 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 27521 key = {71}, 27522 type = {Mathematical Programming Technical Report}, 27523 institution = {Computer Sciences Department, University of Wisconsin}, 27524 address = {Madison, Wisconsin}, 27525 number = {98-13} 27526} 27527 27528@TechReport{ ferris.munson:preprocessing, 27529 author = {M. C. Ferris and T. S. Munson}, 27530 title = {Preprocessing Complementarity Problems}, 27531 type = {Mathematical Programming Technical Report}, 27532 institution = {Computer Sciences Department, University of Wisconsin}, 27533 address = {Madison, Wisconsin}, 27534 year = {1999}, 27535 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 27536 number = {99-07}, 27537 key = {86}, 27538 annote = {Submitted to ICCP 99} 27539} 27540 27541@TechReport{ ferris.munson:semismooth, 27542 author = {M. C. Ferris and T. S. Munson}, 27543 title = {Semismooth Support Vector Machines}, 27544 institution = {Computer Sciences Department, University of Wisconsin}, 27545 year = {2000}, 27546 key = {97}, 27547 type = {Data Mining Institute Technical Report}, 27548 number = {00-09}, 27549 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 27550 address = {Madison, Wisconsin}, 27551 annote = {Submitted to Math Prog B} 27552} 27553 27554@Article{ ferris.pang:engineering, 27555 author = {M. C. Ferris and J. S. Pang}, 27556 title = {Engineering and Economic Applications of Complementarity Problems}, 27557 year = {1997}, 27558 journal = {SIAM Review}, 27559 volume = {39}, 27560 pages = {669--713}, 27561 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 27562 key = {46} 27563} 27564 27565@Article{ ferris.pang:nondegenerate, 27566 author = {M. C. Ferris and J. S. Pang}, 27567 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 27568 journal = {SIAM Journal on Control and Optimization}, 27569 year = {1996}, 27570 volume = {34}, 27571 pages = {244--263}, 27572 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 27573 key = {35} 27574} 27575 27576@Article{ ferris.philpott:affine, 27577 author = {M. C. Ferris and A. B. Philpott}, 27578 title = {On Affine Scaling and Semi--Infinite Programming}, 27579 journal = {Mathematical Programming}, 27580 year = {1992}, 27581 volume = {56}, 27582 pages = {361--364}, 27583 key = {15} 27584} 27585 27586@Article{ ferris.philpott:interior, 27587 author = {M. C. Ferris and A. B. Philpott}, 27588 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 27589 journal = {Mathematical Programming}, 27590 year = {1989}, 27591 volume = {43}, 27592 pages = {257--276}, 27593 key = {04} 27594} 27595 27596@Article{ ferris.philpott:performance, 27597 author = {M. C. Ferris and A. B. Philpott}, 27598 title = {On the Performance of {K}armarkar's Algorithm}, 27599 journal = {Journal of the Operational Research Society}, 27600 year = {1988}, 27601 volume = {39}, 27602 pages = {257--270}, 27603 key = {03} 27604} 27605 27606@InCollection{ ferris.ralph:projected, 27607 author = {M. C. Ferris and D. Ralph}, 27608 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 27609 Maps}, 27610 booktitle = {Recent Advances in Nonsmooth Optimization}, 27611 publisher = {World Scientific Publishers}, 27612 year = {1995}, 27613 pages = {57--87}, 27614 editor = {D. Du and L. Qi and R. Womersley}, 27615 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 27616 key = {41} 27617} 27618 27619@Article{ ferris.ruszczynski:robust, 27620 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 27621 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 27622 year = {2000}, 27623 journal = {Networks}, 27624 volume = {35}, 27625 pages = {181--194}, 27626 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 27627 key = {60} 27628} 27629 27630@InCollection{ ferris.rutherford:accessing, 27631 author = {M. C. Ferris and T. F. Rutherford}, 27632 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 27633 booktitle = {Nonlinear Optimization and Applications}, 27634 key = {48}, 27635 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 27636 editor = {G. Di Pillo and F. Giannessi}, 27637 year = {1996}, 27638 pages = {141--153}, 27639 publisher = {Plenum Press}, 27640 address = {New York} 27641} 27642 27643@InCollection{ ferris.shepard:optimizing, 27644 author = {M. C. Ferris and D. M. Shepard}, 27645 title = {Optimization of Gamma Knife Radiosurgery}, 27646 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 27647 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 27648 publisher = {AMS}, 27649 year = {2000}, 27650 optseries = {DIMACS}, 27651 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 27652 key = {91}, 27653 type = {Data Mining Institute Technical Report}, 27654 institution = {Computer Sciences Department, University of Wisconsin}, 27655 address = {Madison, Wisconsin}, 27656 number = {00-01} 27657} 27658 27659@InCollection{ ferris.sinapiromsaran:formulating, 27660 author = {M. C. Ferris and K. Sinapiromsaran}, 27661 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 27662 booktitle = {Optimization}, 27663 key = {77}, 27664 publisher = {Springer-Verlag}, 27665 year = {2000}, 27666 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 27667 volume = {481}, 27668 series = {Lecture Notes in Economics and Mathematical Systems}, 27669 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 27670 type = {Mathematical Programming Technical Report}, 27671 institution = {Computer Sciences Department, University of Wisconsin}, 27672 address = {Madison, Wisconsin}, 27673 number = {98-21} 27674} 27675 27676@Article{ ferris.tin-loi:limit, 27677 author = {M. C. Ferris and F. Tin-Loi}, 27678 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 27679 Complementarity Constraints}, 27680 year = {2001}, 27681 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 27682 key = {78}, 27683 journal = {International Journal of Mechanical Sciences}, 27684 pages = {209--224}, 27685 volume = {43}, 27686 type = {Mathematical Programming Technical Report}, 27687 institution = {Computer Sciences Department, University of Wisconsin}, 27688 address = {Madison, Wisconsin}, 27689 number = {99-01} 27690} 27691 27692@Article{ ferris.tin-loi:nonlinear, 27693 author = {M. C. Ferris and F. Tin-Loi}, 27694 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 27695 Elastoplasticity}, 27696 year = {1998}, 27697 key = {64}, 27698 volume = {6}, 27699 pages = {857--870}, 27700 journal = {Structural Engineering and Mechanics} 27701} 27702 27703@Article{ ferris.tin-loi:solution, 27704 author = {M. C. Ferris and F. Tin-Loi}, 27705 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 27706 and Complementarity Constraints}, 27707 year = {1999}, 27708 journal = {Computer Methods in Applied Mechanics and Engineering}, 27709 volume = {174}, 27710 pages = {107--120}, 27711 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 27712 key = {66} 27713} 27714 27715@Article{ ferris.vlach:scheduling, 27716 author = {M. C. Ferris and M. Vlach}, 27717 title = {Scheduling with Earliness and Tardiness Penalties}, 27718 journal = {Naval Research Logistics Quarterly}, 27719 year = {1992}, 27720 volume = {39}, 27721 pages = {229--245}, 27722 key = {13} 27723} 27724 27725@TechReport{ ferris.zavriev:linear, 27726 author = {M. C. Ferris and S. K Zavriev}, 27727 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 27728 institution = {Computer Sciences Department, University of Wisconsin}, 27729 year = {1996}, 27730 key = {56}, 27731 address = {Madison, Wisconsin}, 27732 type = {Mathematical Programming Technical Report}, 27733 number = {96--12}, 27734 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 27735} 27736 27737@Article{ ferris:finite, 27738 author = {M. C. Ferris}, 27739 title = {Finite Termination of the Proximal Point Algorithm}, 27740 journal = {Mathematical Programming}, 27741 year = {1991}, 27742 volume = {50}, 27743 pages = {359--366}, 27744 key = {06} 27745} 27746 27747@Article{ ferris:iterative, 27748 author = {M. C. Ferris}, 27749 title = {Iterative Linear Programming Solution of Convex Programs}, 27750 journal = {Journal of Optimization Theory and Applications}, 27751 year = {1990}, 27752 volume = {65}, 27753 pages = {53--65}, 27754 key = {07} 27755} 27756 27757@Article{ ferris:linear, 27758 author = {M. C. Ferris}, 27759 title = {The Linear Complementarity Problem}, 27760 journal = {Bulletin of the American Mathematical Society}, 27761 year = {1993}, 27762 volume = {28}, 27763 pages = {169--175}, 27764 key = {27} 27765} 27766 27767@MastersThesis{ ferris:linear*1, 27768 author = {M. C. Ferris}, 27769 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 27770 Solving a Class of Structural Optimization Problems}, 27771 year = {1985}, 27772 school = {University of Cambridge}, 27773 address = {England}, 27774 key = {01} 27775} 27776 27777@TechReport{ ferris:matlab, 27778 author = {M. C. Ferris}, 27779 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 27780 institution = {Computer Sciences Department, University of Wisconsin}, 27781 year = {1998}, 27782 address = {Madison, Wisconsin}, 27783 type = {Mathematical Programming Technical Report}, 27784 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 27785 number = {98-19}, 27786 key = {75} 27787} 27788 27789@Article{ ferris:parallel, 27790 author = {M. C. Ferris}, 27791 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 27792 journal = {Mathematics of Operations Research}, 27793 year = {1994}, 27794 volume = {19}, 27795 pages = {645--658}, 27796 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 27797 key = {20} 27798} 27799 27800@TechReport{ ferris:parallel*1, 27801 author = {M. C. Ferris}, 27802 title = {Parallel Solution of Extremely Large Knapsack Problems}, 27803 institution = {Computer Sciences Department, University of Wisconsin}, 27804 year = {1989}, 27805 address = {Madison, Wisconsin}, 27806 number = {842}, 27807 key = {09} 27808} 27809 27810@PhDThesis{ ferris:weak, 27811 author = {M. C. Ferris}, 27812 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27813 year = {1988}, 27814 school = {University of Cambridge}, 27815 address = {England}, 27816 key = {02} 27817} 27818 27819@TechReport{ ferris:weak*1, 27820 author = {M. C. Ferris}, 27821 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27822 institution = {Computer Sciences Department, University of Wisconsin}, 27823 year = {1988}, 27824 address = {Madison, Wisconsin}, 27825 number = {779}, 27826 key = {05} 27827} 27828 27829@Book{ fiacco.mccormick:nonlinear, 27830 author = {A. V. Fiacco and G. P. McCormick}, 27831 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 27832 year = {1968}, 27833 publisher = {John Wiley \& Sons}, 27834 address = {New York}, 27835 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 27836} 27837 27838@Book{ fiacco:introduction, 27839 author = {A. V. Fiacco}, 27840 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 27841 year = {1983}, 27842 publisher = {Academic Press}, 27843 address = {New York} 27844} 27845 27846@Article{ fiedler.ptak:matrices, 27847 author = {M. Fiedler and V. Pt\'{a}k}, 27848 title = {On matrices with nonpositive off-diagonal elements and positive principal 27849 minors}, 27850 journal = {Czechoslovak Mathematics Journal}, 27851 volume = {12}, 27852 pages = {382--400}, 27853 year = {1962} 27854} 27855 27856@Article{ fischer.kanzow:finite, 27857 author = {A. Fischer and C. Kanzow}, 27858 title = {On Finite Termination of an Iterative Method for Linear Complementarity 27859 Problems}, 27860 journal = {Mathematical Programming}, 27861 volume = {74}, 27862 pages = {279--292}, 27863 year = {1996} 27864} 27865 27866@TechReport{ fischer:constrained, 27867 author = {A. Fischer}, 27868 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 27869 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 27870 year = {1995}, 27871 type = {Technical Report}, 27872 number = {MATH-NM-10-1995}, 27873 address = {Dresden} 27874} 27875 27876@Article{ fischer:local, 27877 author = {A. Fischer}, 27878 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 27879 weak conditions}, 27880 journal = {Optimization Methods and Software}, 27881 year = {1995}, 27882 volume = {6}, 27883 pages = {83--107} 27884} 27885 27886@InCollection{ fischer:ncp-function, 27887 author = {A. Fischer}, 27888 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 27889 booktitle = {Recent Advances in Nonsmooth Optimization}, 27890 publisher = {World Scientific Publishers}, 27891 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 27892 year = {1995}, 27893 pages = {88--105} 27894} 27895 27896@Article{ fischer:newton-type, 27897 author = {A. Fischer}, 27898 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 27899 Problems}, 27900 journal = {Journal of Optimization Theory and Applications}, 27901 year = {1995}, 27902 volume = {86}, 27903 pages = {585--608} 27904} 27905 27906@Article{ fischer:solution, 27907 author = {A. Fischer}, 27908 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 27909 Functions}, 27910 year = {1997}, 27911 journal = {Mathematical Programming}, 27912 pages = {513--532} 27913} 27914 27915@Article{ fischer:special, 27916 author = {A. Fischer}, 27917 title = {A Special {N}ewton--Type Optimization Method}, 27918 journal = {Optimization}, 27919 year = {1992}, 27920 volume = {24}, 27921 pages = {269--284} 27922} 27923 27924@Article{ fisher:use, 27925 author = {R. A. Fisher}, 27926 title = {The Use of Multiple Measurements in Taxonomic Problems}, 27927 journal = {Annual Eugenics}, 27928 year = {1936}, 27929 volume = {7}, 27930 number = {Part II}, 27931 pages = {179--188} 27932} 27933 27934@Book{ fishman:principles, 27935 author = {G. Fishman}, 27936 title = {Principles of Discrete Event Simulation}, 27937 publisher = {Wiley}, 27938 address = {New York, NY}, 27939 year = {1978} 27940} 27941 27942@Article{ fitchard.aldridge.ea:registration, 27943 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 27944 title = {Registration of Synthetic Tomographic Projection Data Sets Using 27945 Cross-Correlation}, 27946 journal = {Physics in Medicine and Biology}, 27947 year = {1998}, 27948 volume = {43}, 27949 pages = {1645--1657} 27950} 27951 27952@Article{ fletcher.matthews:stable, 27953 author = {R. Fletcher and S. P. J. Matthews}, 27954 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 27955 journal = {Mathematical Programming}, 27956 year = {1984}, 27957 volume = {30}, 27958 pages = {267--284} 27959} 27960 27961@TechReport{ fletcher.maza:nonlinear, 27962 author = {R. Fletcher and E. Sainz de la Maza}, 27963 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 27964 Programming}, 27965 institution = {Department of Mathematical Sciences}, 27966 year = {1987}, 27967 address = {The University, Dundee, Scotland}, 27968 number = {NA/100}, 27969 type = {Numerical Analysis Report} 27970} 27971 27972@InCollection{ fletcher:class, 27973 author = {R. Fletcher}, 27974 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 27975 Properties}, 27976 booktitle = {Integer and Nonlinear Programming}, 27977 year = {1970}, 27978 editor = {J. Abadie}, 27979 publisher = {North--Holland}, 27980 address = {Amsterdam}, 27981 pages = {157--173} 27982} 27983 27984@Article{ fletcher:exact, 27985 author = {R. 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Fletcher}, 28012 title = {Practical Methods of Optimization}, 28013 year = {1981}, 28014 publisher = {John Wiley \& Sons}, 28015 address = {Chichester}, 28016 volume = {1} 28017} 28018 28019@Book{ fletcher:practical*1, 28020 author = {R. Fletcher}, 28021 title = {Practical Methods of Optimization}, 28022 year = {1981}, 28023 publisher = {John Wiley \& Sons}, 28024 address = {Chichester}, 28025 volume = {2} 28026} 28027 28028@Book{ fletcher:practical*2, 28029 author = {R. Fletcher}, 28030 title = {Practical Methods of Optimization}, 28031 year = {1987}, 28032 publisher = {John Wiley \& Sons}, 28033 address = {New York}, 28034 edition = {second} 28035} 28036 28037@Unpublished{ fletcher:recent, 28038 author = {R. Fletcher}, 28039 title = {Recent Developments in Nonlinear Programming}, 28040 note = {Presentation at SOR 96, Braunchweig, Germany}, 28041 year = {1996} 28042} 28043 28044@InCollection{ fletcher:second, 28045 author = {R. 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Tomlin}, 28101 title = {Updating Triangular Factors of the Basis to Maintain Sparsity in the Product Form 28102 Simplex Method}, 28103 journal = {Mathematical Programming}, 28104 year = {1972}, 28105 volume = {2}, 28106 pages = {263--278} 28107} 28108 28109@TechReport{ forsgren.gill.ea:computing, 28110 author = {A. Forsgren and P. E. Gill and W. Murray}, 28111 title = {Computing Modified {N}ewton Directions using a Partial {C}holesky Factorization}, 28112 institution = {Department of Mathematics, Royal Institute of Technology}, 28113 year = {1993}, 28114 number = {TRITA-MAT-1993-9}, 28115 address = {Stockholm, Sweden} 28116} 28117 28118@TechReport{ forsgren.gill:primal-dual, 28119 author = {A. Forsgren and P. E. Gill}, 28120 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 28121 institution = {Department of Mathematics, University of California}, 28122 year = {1996}, 28123 type = {Report NA}, 28124 number = {96-3}, 28125 address = {San Diego} 28126} 28127 28128@InCollection{ fortin.glowinski:decomposition-coordination, 28129 author = {M. Fortin and R. Glowinski}, 28130 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 28131 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 28132 Problems}, 28133 publisher = {North-Holland}, 28134 year = {1983}, 28135 editor = {M. Fortin and R. Glowinski}, 28136 address = {Amsterdam} 28137} 28138 28139@Misc{ foster.kesselman:globus, 28140 author = {I. Foster and C. Kesselman}, 28141 title = {The Globus Project}, 28142 howpublished = {www.globus.org} 28143} 28144 28145@Article{ foster.kesselman:globus*1, 28146 author = {I. Foster and C. 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Gabriel}, 28402 title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and 28403 Extensions}, 28404 school = {The Johns Hopkins University}, 28405 year = {1992}, 28406 address = {Baltimore, Maryland} 28407} 28408 28409@Article{ gafni.bertsekas:two-metric, 28410 author = {E. M. Gafni and D. P. Bertsekas}, 28411 title = {Two-Metric Projection Methods for Constrained Optimization}, 28412 journal = {SIAM Journal on Control and Optimization}, 28413 year = {1984}, 28414 volume = {22}, 28415 pages = {936--964} 28416} 28417 28418@InProceedings{ gaivoronski:convergence, 28419 author = {A. A. Gaivoronski}, 28420 title = {Convergence of Parallel Backpropagation for Neural Networks}, 28421 booktitle = {SIAM Journal on Optimization}, 28422 year = {1994}, 28423 note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993, 28424 submitted} 28425} 28426 28427@Misc{ gaivoronski:private, 28428 author = {A. A. 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Gao}, 28472 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 28473 Conditions}, 28474 type = {Manuscript}, 28475 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 28476 month = oct, 28477 year = {1994} 28478} 28479 28480@Article{ garcia-palomares.mangasarian:superlinearly, 28481 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 28482 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 28483 Optimization Problems}, 28484 journal = {Mathematical Programming}, 28485 year = {1976}, 28486 volume = {11}, 28487 pages = {1--13} 28488} 28489 28490@Article{ garcia-palomares.restuccia:global, 28491 author = {U. M. {Garcia--Palomares} and A. Restuccia}, 28492 title = {A Global Quadratic Algorithm for Solving a System of Mixed Equations}, 28493 journal = {Mathematical Programming}, 28494 year = {1981}, 28495 volume = {21}, 28496 pages = {290--300} 28497} 28498 28499@InProceedings{ garcia-palomares:superlinearly, 28500 author = {U. M. {Garcia--Palomares}}, 28501 title = {Superlinearly Convergent Algorithms for Linearly Constrained Optimization}, 28502 crossref = {mangasarian.meyer.ea:nonlinear*2}, 28503 pages = {101--119} 28504} 28505 28506@Article{ garcia.gould:theorem, 28507 author = {C. B. Garcia and F. J. Gould}, 28508 title = {A Theorem on Homotopy Paths}, 28509 journal = {Mathematics of Operations Research}, 28510 year = {1978}, 28511 volume = {3}, 28512 pages = {282--289} 28513} 28514 28515@Book{ garcia.zangwill:pathways, 28516 author = {C. B. Garcia and W. I. Zangwill}, 28517 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 28518 year = {1981}, 28519 publisher = {Prentice-Hall, Inc}, 28520 address = {Englewood Cliffs, New Jersey} 28521} 28522 28523@Book{ garey.johnson:computers, 28524 author = {M. R. Garey and D. S. Johnson}, 28525 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 28526 year = {1979}, 28527 publisher = {W.H. Freeman and Company}, 28528 address = {San Francisco} 28529} 28530 28531@Article{ garey.tarjan.ea:one-processor, 28532 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 28533 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 28534 journal = {Mathematics of Operations Research}, 28535 year = {1988}, 28536 volume = {13}, 28537 pages = {330--348} 28538} 28539 28540@Book{ garfinkel.nemhauser:integer, 28541 author = {R. S. Garfinkel and G. L. Nemhauser}, 28542 title = {Integer Programming}, 28543 year = {1972}, 28544 publisher = {John Wiley \& Sons}, 28545 address = {New York} 28546} 28547 28548@Book{ gass:linear, 28549 author = {S. Gass}, 28550 title = {Linear Programming Methods and Applications}, 28551 edition = {Fifth}, 28552 publisher = {Boyd and Fraser Publishing Company}, 28553 address = {Danvers, Massachusetts}, 28554 year = {1985} 28555} 28556 28557@InProceedings{ gay:combining, 28558 author = {D. M. Gay}, 28559 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 28560 booktitle = {Sparse Matrix Proceedings 1978}, 28561 editor = {I. S. Duff and G. W. Stewart}, 28562 year = {1978}, 28563 organization = {SIAM}, 28564 address = {Philadelphia, Pennsylvania}, 28565 pages = {313--334} 28566} 28567 28568@Article{ gay:electronic, 28569 author = {D. M. Gay}, 28570 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 28571 journal = {{COAL} Newsletter}, 28572 year = {1985}, 28573 volume = {13}, 28574 pages = {10--12} 28575} 28576 28577@TechReport{ gay:hooking, 28578 author = {D. M. Gay}, 28579 title = {Hooking Your Solver to {AMPL}}, 28580 year = {1997}, 28581 institution = {Bell Laboratories}, 28582 address = {Murray Hill, New Jersey}, 28583 note = {Revised 1994, 1997} 28584} 28585 28586@Article{ gay:variant, 28587 author = {D. Gay}, 28588 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 28589 Form}, 28590 journal = {Mathematical Programming}, 28591 year = {1987}, 28592 volume = {37}, 28593 pages = {81--90} 28594} 28595 28596@Article{ geiger.kanzow:resolution, 28597 author = {C. Geiger and C. Kanzow}, 28598 title = {On the Resolution of Monotone Complementarity Problems}, 28599 journal = {Computational Optimization and Applications}, 28600 volume = {5}, 28601 year = {1996}, 28602 pages = {155--173} 28603} 28604 28605@Book{ geist.beguelin.ea:pvm, 28606 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 28607 V. S. Sunderam}, 28608 title = {{PVM}: Parallel Virtual Machine}, 28609 publisher = {MIT Press}, 28610 address = {Cambridge, Massachusetts}, 28611 year = {1994} 28612} 28613 28614@Article{ gendron.crainic:parallel, 28615 author = {B. Gendron and T. G. Crainic}, 28616 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 28617 journal = {Operations Research}, 28618 year = {1994}, 28619 volume = {42}, 28620 pages = {1042--1060} 28621} 28622 28623@Article{ george:automatic, 28624 author = {A. George}, 28625 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 28626 journal = {SIAM Journal on Numerical Analysis}, 28627 vol = {17}, 28628 pages = {740--751}, 28629 year = {1980} 28630} 28631 28632@InProceedings{ georges-schleuter:asparagos, 28633 crossref = {schaeffer:third}, 28634 author = {M. Georges--Schleuter}, 28635 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 28636 pages = {416--421} 28637} 28638 28639@Article{ georgiou:comments, 28640 author = {G. M. Georgiou}, 28641 title = {Comments On Hidden Nodes in Neural Nets}, 28642 journal = {IEEE Transactions on Circuits and Systems}, 28643 year = {1991}, 28644 volume = {38}, 28645 pages = {1410} 28646} 28647 28648@TechReport{ gertz.linderoth.ea:object-oriented, 28649 author = {M. Gertz and J. Linderoth and S. Wright}, 28650 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 28651 institution = {MCS Division, Argonne National Laboratory}, 28652 year = {in preparation} 28653} 28654 28655@Article{ ghellinck.vial:polynomial, 28656 author = {G. de Ghellinck and J.--Ph. Vial}, 28657 title = {A Polynomial {N}ewton Method for Linear Programming}, 28658 journal = {Algorithmica}, 28659 year = {1986}, 28660 volume = {1}, 28661 pages = {425--453} 28662} 28663 28664@InCollection{ gilbert.ng:predicting, 28665 author = {J. R. Gilbert and E. Ng}, 28666 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 28667 year = {1993}, 28668 booktitle = {Graph Theory and Sparse Matrix Computation}, 28669 editor = {A. George and J. Gilbert and J. Liu}, 28670 publisher = {Springer-Verlag} 28671} 28672 28673@Article{ gilbert-lemarechal, 28674 author = {J. C. Gilbert and C. 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Tseng}, 31671 title = {On the Convergence Rate of Dual Ascent Methods for Strictly Convex Minimization}, 31672 journal = {Mathematics of Operations Research}, 31673 year = {1993}, 31674 volume = {18}, 31675 pages = {846--867} 31676} 31677 31678@Article{ luo.tseng:error, 31679 author = {Z.--Q. Luo and P. Tseng}, 31680 title = {Error Bound and Convergence Analysis of Matrix Splitting Algorithms for the 31681 Affine Variational Inequality Problem}, 31682 journal = {SIAM Journal on Optimization}, 31683 year = {1992}, 31684 volume = {2}, 31685 pages = {43--54} 31686} 31687 31688@Article{ luo.tseng:error*1, 31689 author = {Z.-Q. Luo and P. Tseng}, 31690 title = {Error Bound and Reduced Gradient Projection Algorithms for Convex Minimization 31691 Over a Polyhedral Set}, 31692 journal = {SIAM Journal on Optimization}, 31693 year = {1993}, 31694 volume = {3}, 31695 pages = {43--59} 31696} 31697 31698@Article{ luo.tseng:error*2, 31699 author = {Z.-Q. Luo and P. 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Luo}, 31730 title = {Convergence Analysis of Primal--Dual Interior--Point Algorithms for Convex 31731 Quadratic Programs}, 31732 institution = {Communications Research Laboratory, McMaster University}, 31733 year = {1992}, 31734 address = {Hamilton, Ontario} 31735} 31736 31737@Article{ lustig.marsten.ea:computational, 31738 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31739 title = {Computational Experience with a Primal-Dual Interior Point Method for Linear 31740 Programming}, 31741 journal = {Linear Algebra and Its Applications}, 31742 year = {1991}, 31743 volume = {152}, 31744 pages = {191--222} 31745} 31746 31747@Article{ lustig.marsten.ea:implementing, 31748 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31749 title = {On implementing {M}ehrotra's predictor-corrector interior point method for linear 31750 programming}, 31751 journal = {SIAM Journal on Optimization}, 31752 year = {1992}, 31753 volume = {2}, 31754 pages = {435--449} 31755} 31756 31757@Article{ lustig.marsten.ea:interior-point, 31758 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31759 title = {Interior-Point Methods for Linear Programming: Computational State of the Art}, 31760 journal = {ORSA Journal on Computing}, 31761 year = {1994}, 31762 volume = {6}, 31763 number = {1}, 31764 pages = {1--38} 31765} 31766 31767@Article{ lyman.wolbarst:optimization, 31768 author = {J. T. Lyman and A. B. 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Madsen}, 31817 title = {Minimization of Nonlinear Approximation Functions}, 31818 year = {1985}, 31819 address = {Lyngby, Denmark}, 31820 school = {Institute of Numerical Analysis, Technical University of Denmark}, 31821 annote = {Dissertation} 31822} 31823 31824@Book{ magill.quinzii:theory, 31825 author = {M. Magill and M. Quinzii}, 31826 title = {Theory of Incomplete Markets}, 31827 publisher = {MIT Press}, 31828 year = {1996} 31829} 31830 31831@InCollection{ magnanti:models, 31832 author = {T. L. Magnanti}, 31833 title = {Models and Algorithms for Predicting Urban Traffic Equilibria}, 31834 booktitle = {Transportation Planning Models}, 31835 year = {1984}, 31836 editor = {M. Florian}, 31837 publisher = {North Holland}, 31838 pages = {153--186} 31839} 31840 31841@InCollection{ maguregui:modified, 31842 author = {J. Maguregui}, 31843 title = {A modified {N}ewton algorithm for functions over convex sets}, 31844 crossref = {mangasarian.meyer.ea:nonlinear*3}, 31845 pages = {461--473} 31846} 31847 31848@PhDThesis{ maguregui:regular, 31849 author = {J. Maguregui}, 31850 title = {Regular Multivalued Functions and Algorithmic Applications}, 31851 year = {1977}, 31852 address = {Madison, Wisconsin}, 31853 school = {Computer Sciences Department, University of Wisconsin} 31854} 31855 31856@Article{ mahey.oualibouch.ea:proximal, 31857 author = {P. Mahey and S. Oualibouch and D. T. Pham}, 31858 title = {Proximal Decomposition on the Graph of a Maximal Monotone Operator}, 31859 journal = {SIAM Journal on Optimization}, 31860 year = {1995}, 31861 volume = {5}, 31862 pages = {454--466} 31863} 31864 31865@Article{ mahey.pham:partial, 31866 author = {P. Mahey and D. T. Pham}, 31867 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 31868 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 31869 year = {1993}, 31870 volume = {27}, 31871 pages = {375--392} 31872} 31873 31874@InCollection{ maier.novati:shakedown, 31875 author = {G. Maier and G. Novati}, 31876 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 31877 geometric effects with reference to discrete structural models}, 31878 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 31879 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 31880 publisher = {Pineridge Press}, 31881 address = {Swansea}, 31882 year = {1990}, 31883 pages = {451--471} 31884} 31885 31886@Article{ maier:incremental, 31887 author = {G. Maier}, 31888 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 31889 Instabilizing Effects}, 31890 journal = {International Journal of Solids and Structures}, 31891 volume = {7}, 31892 year = {1971}, 31893 pages = {345--372} 31894} 31895 31896@InCollection{ maier:inverse, 31897 author = {G. Maier}, 31898 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 31899 booktitle = {Serie VIII}, 31900 publisher = {Academia Nazionale dei Lincei}, 31901 year = {1981}, 31902 volume = {LXX}, 31903 pages = {203--209} 31904} 31905 31906@Article{ maier:matrix, 31907 author = {G. Maier}, 31908 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 31909 yield planes}, 31910 journal = {Meccanica}, 31911 volume = {5}, 31912 year = {1970}, 31913 pages = {54--66} 31914} 31915 31916@Article{ maier:quadratic, 31917 author = {G. Maier}, 31918 title = {A quadratic programming approach for certain classes of nonlinear structural 31919 problems}, 31920 journal = {Meccanica}, 31921 volume = {3}, 31922 year = {1968}, 31923 pages = {121--130} 31924} 31925 31926@Book{ manber:introduction, 31927 author = {U. Manber}, 31928 title = {Introduction to Algorithms: {A} Creative Approach}, 31929 year = {1989}, 31930 publisher = {Addison-Wesley} 31931} 31932 31933@Article{ mangasarian.deleone:error, 31934 author = {O. L. Mangasarian and R. {De~Leone}}, 31935 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 31936 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 31937 journal = {Applied Mathematics and Optimization}, 31938 year = {1988}, 31939 volume = {17}, 31940 pages = {1--14} 31941} 31942 31943@Article{ mangasarian.deleone:parallel, 31944 author = {O. L. Mangasarian and R. {De~Leone}}, 31945 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 31946 Problems and Linear Programs}, 31947 journal = {Journal of Optimization Theory and Applications}, 31948 year = {1987}, 31949 volume = {54}, 31950 pages = {437--446} 31951} 31952 31953@Article{ mangasarian.fromovitz:fritz, 31954 author = {O. L. Mangasarian and S. Fromovitz}, 31955 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 31956 and inequality constraints}, 31957 journal = {Journal of Mathematical Analysis and its Applications}, 31958 year = {1967}, 31959 volume = {17}, 31960 pages = {37--47} 31961} 31962 31963@Article{ mangasarian.mclinden:simple, 31964 author = {O. L. Mangasarian and L. McLinden}, 31965 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 31966 Programs}, 31967 journal = {Mathematical Programming}, 31968 year = {1985}, 31969 volume = {32}, 31970 pages = {32--40} 31971} 31972 31973@Article{ mangasarian.meyer:nonlinear, 31974 author = {O. L. Mangasarian and R. R. Meyer}, 31975 title = {Nonlinear Perturbation of Linear Programs}, 31976 journal = {SIAM Journal on Control and Optimization}, 31977 year = {1979}, 31978 volume = {17}, 31979 pages = {745--752} 31980} 31981 31982@TechReport{ mangasarian.musicant:active, 31983 author = {O. L. Mangasarian and David R. Musicant}, 31984 title = {Active Set Support Vector Machine Classification}, 31985 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31986 year = {2000}, 31987 number = {00-04}, 31988 address = {Madison, Wisconsin} 31989} 31990 31991@TechReport{ mangasarian.musicant:lagrangian, 31992 author = {O. L. Mangasarian and D. R. Musicant}, 31993 title = {Lagrangian Support Vector Machines}, 31994 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31995 year = {2000}, 31996 number = {00-06}, 31997 address = {Madison, Wisconsin} 31998} 31999 32000@TechReport{ mangasarian.musicant:robust, 32001 author = {O. L. Mangasarian and David R. Musicant}, 32002 title = {Robust Linear and Support Vector Regression}, 32003 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 32004 year = {1999}, 32005 number = {99-09}, 32006 address = {Madison, Wisconsin} 32007} 32008 32009@Article{ mangasarian.musicant:successive, 32010 author = {O. L. Mangasarian and David R. Musicant}, 32011 title = {Successive Overrelaxation for Support Vector Machines}, 32012 journal = {IEEE Transactions on Neural Networks}, 32013 volume = {10}, 32014 year = {1999}, 32015 pages = {1032-1037} 32016} 32017 32018@Article{ mangasarian.pang:exact, 32019 author = {O. L. Mangasarian and J. S. Pang}, 32020 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 32021 Constraints}, 32022 journal = {Optimization}, 32023 year = {1997}, 32024 volume = {42}, 32025 pages = {1--8} 32026} 32027 32028@Article{ mangasarian.pang:extended, 32029 author = {O. L. Mangasarian and J. S. Pang}, 32030 title = {The Extended Linear Complementarity Problem}, 32031 journal = {SIAM Journal on Matrix Analysis and Applications}, 32032 year = {1994}, 32033 volume = {16} 32034} 32035 32036@Article{ mangasarian.ren:error, 32037 author = {O. L. Mangasarian and J. Ren}, 32038 title = {New error bounds for the nonlinear complementarity problem}, 32039 year = {1994}, 32040 volume = {1}, 32041 pages = {49--56}, 32042 journal = {Communications on Applied Nonlinear Analysis} 32043} 32044 32045@Article{ mangasarian.ren:improved, 32046 author = {O. L. Mangasarian and J. Ren}, 32047 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 32048 year = {1994}, 32049 volume = {66}, 32050 journal = {Mathematical Programming}, 32051 pages = {241--255} 32052} 32053 32054@InProceedings{ mangasarian.setiono.ea:pattern, 32055 crossref = {coleman.li:large-scale}, 32056 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 32057 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 32058 Diagnosis}, 32059 pages = {22--31} 32060} 32061 32062@Article{ mangasarian.shiau:error, 32063 author = {O. L. Mangasarian and T.--H. Shiau}, 32064 title = {Error Bounds for Monotone Linear Complementarity Problems}, 32065 journal = {Mathematical Programming}, 32066 year = {1986}, 32067 volume = {36}, 32068 pages = {81--89} 32069} 32070 32071@Article{ mangasarian.shiau:lipschitz, 32072 author = {O. L. Mangasarian and T.--H. Shiau}, 32073 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 32074 Complementarity Problems}, 32075 journal = {SIAM Journal on Control and Optimization}, 32076 year = {1987}, 32077 volume = {25}, 32078 pages = {583--595} 32079} 32080 32081@Article{ mangasarian.solodov:nonlinear, 32082 author = {O. L. Mangasarian and M. V. Solodov}, 32083 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 32084 journal = {Mathematical Programming}, 32085 year = {1993}, 32086 volume = {62}, 32087 pages = {277--298} 32088} 32089 32090@Article{ mangasarian.solodov:serial, 32091 author = {O. L. Mangasarian and M. V. Solodov}, 32092 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 32093 Minimization}, 32094 year = {1994}, 32095 journal = {Optimization Methods and Software}, 32096 volume = {4}, 32097 pages = {103--116} 32098} 32099 32100@Article{ mangasarian.street.ea:breast, 32101 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 32102 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 32103 journal = {Operations Research}, 32104 year = {1995}, 32105 volume = {43}, 32106 pages = {570--577} 32107} 32108 32109@Article{ mangasarian.wolberg:cancer, 32110 author = {O. L. Mangasarian and W. H. Wolberg}, 32111 title = {Cancer Diagnosis via Linear Programming}, 32112 journal = {SIAM News}, 32113 year = {1990}, 32114 volume = {23}, 32115 pages = {1 \& 18} 32116} 32117 32118@InCollection{ mangasarian:applications, 32119 author = {O. L. Mangasarian}, 32120 title = {Some Applications of Penalty Functions in Mathematical Programming}, 32121 booktitle = {Optimization and Related Fields}, 32122 year = {1986}, 32123 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 32124 publisher = {Springer-Verlag}, 32125 address = {Heidelberg}, 32126 pages = {307--329}, 32127 note = {Lecture Notes in Mathematics 1190} 32128} 32129 32130@Article{ mangasarian:characterization, 32131 author = {O. L. Mangasarian}, 32132 title = {Characterization of linear complementarity problems as linear programs}, 32133 journal = {Mathematical Programming Study}, 32134 year = {1978}, 32135 volume = {7}, 32136 pages = {74--87} 32137} 32138 32139@InProceedings{ mangasarian:condition, 32140 author = {O. L. Mangasarian}, 32141 title = {A condition number for linear inequalities and linear programs}, 32142 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 32143 1981}, 32144 year = {1981}, 32145 editor = {G. Bamberg and O. Opitz}, 32146 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 32147 address = {Konigstein}, 32148 pages = {3--15} 32149} 32150 32151@Article{ mangasarian:convergence, 32152 author = {O. L. Mangasarian}, 32153 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 32154 Symmetric Monotone Linear Complementarity Problem}, 32155 journal = {SIAM Journal on Optimization}, 32156 volume = {1}, 32157 pages = {114--122}, 32158 year = {1991} 32159} 32160 32161@Article{ mangasarian:equivalence, 32162 author = {O. L. Mangasarian}, 32163 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 32164 journal = {SIAM Journal on Applied Mathematics}, 32165 year = {1976}, 32166 volume = {31}, 32167 pages = {89--92} 32168} 32169 32170@Article{ mangasarian:error, 32171 author = {O. L. Mangasarian}, 32172 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 32173 journal = {ORSA Journal on Computing}, 32174 volume = {15}, 32175 pages = {187--192}, 32176 year = {1994} 32177} 32178 32179@Article{ mangasarian:error*1, 32180 author = {O. L. Mangasarian}, 32181 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 32182 journal = {Mathematical Programming}, 32183 year = {1990}, 32184 volume = {48}, 32185 pages = {437--445} 32186} 32187 32188@Article{ mangasarian:generalized, 32189 author = {O. L. Mangasarian}, 32190 title = {Generalized Linear Complementarity Problems as Linear Programs}, 32191 journal = {Methods of Operations Research}, 32192 year = {1979}, 32193 editor = {W. Oettli and F. Steffens}, 32194 volume = {31}, 32195 pages = {393--402} 32196} 32197 32198@InCollection{ mangasarian:generalized*1, 32199 author = {O. L. Mangasarian}, 32200 title = {Generalized Support Vector Machines}, 32201 year = {2000}, 32202 pages = {135-146}, 32203 booktitle = {Advances in Large Margin Classifiers}, 32204 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 32205 publisher = {MIT Press}, 32206 address = {Cambridge, MA} 32207} 32208 32209@Article{ mangasarian:global, 32210 author = {O. L. Mangasarian}, 32211 title = {Global error bounds for monotone affine variational inequality problems}, 32212 journal = {Linear Algebra and Its Applications}, 32213 year = {1992}, 32214 pages = {153--164} 32215} 32216 32217@InCollection{ mangasarian:least, 32218 author = {O. L. Mangasarian}, 32219 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 32220 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 32221 year = {1990}, 32222 publisher = {Oxford University Press}, 32223 address = {New York}, 32224 pages = {217--221} 32225} 32226 32227@Article{ mangasarian:least-norm, 32228 author = {O. L. Mangasarian}, 32229 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 32230 Problem}, 32231 journal = {Journal of Mathematical Analysis and Applications}, 32232 year = {1983}, 32233 volume = {92}, 32234 pages = {240--251} 32235} 32236 32237@Article{ mangasarian:linear, 32238 author = {O. L. Mangasarian}, 32239 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 32240 journal = {Mathematical Programming}, 32241 year = {1976}, 32242 volume = {10}, 32243 pages = {263--270} 32244} 32245 32246@Article{ mangasarian:linear*1, 32247 author = {O. L. Mangasarian}, 32248 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 32249 journal = {Operations Research}, 32250 year = {1965}, 32251 volume = {13}, 32252 pages = {444--452} 32253} 32254 32255@Article{ mangasarian:locally, 32256 author = {O. L. Mangasarian}, 32257 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 32258 Complementarity Problems}, 32259 journal = {Mathematical Programming}, 32260 year = {1980}, 32261 volume = {19}, 32262 pages = {200--212} 32263} 32264 32265@InCollection{ mangasarian:machine, 32266 author = {O. L. Mangasarian}, 32267 title = {Machine Learning via Polyhedral Concave Minimization}, 32268 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 32269 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 32270 pages = {175-188}, 32271 year = {1996}, 32272 address = {Heidelberg}, 32273 publisher = {Physica-Verlag A Springer-Verlag Company} 32274} 32275 32276@Article{ mangasarian:mathematical, 32277 author = {O. L. Mangasarian}, 32278 title = {Mathematical Programming in Neural Networks}, 32279 journal = {ORSA Journal on Computing}, 32280 volume = {5}, 32281 pages = {349--360}, 32282 year = {1993} 32283} 32284 32285@InProceedings{ mangasarian:mathematical*1, 32286 author = {O. L. Mangasarian}, 32287 title = {Mathematical Programming in Machine Learning}, 32288 booktitle = {Nonlinear Optimization and Applications}, 32289 editor = {G. Di Pillo and F. Giannessi}, 32290 publisher = {Plenum Publishing}, 32291 address = {New York}, 32292 pages = {283--295}, 32293 year = {1996} 32294} 32295 32296@Article{ mangasarian:mathematical*2, 32297 author = {O. L. Mangasarian}, 32298 title = {Mathematical Programming in Data Mining}, 32299 journal = {Data Mining and Knowledge Discovery}, 32300 volume = {1}, 32301 year = {1997}, 32302 pages = {183-201} 32303} 32304 32305@Article{ mangasarian:multi-surface, 32306 author = {O. L. Mangasarian}, 32307 title = {Multi-surface Method of Pattern Separation}, 32308 journal = {IEEE Transactions on Information Theory}, 32309 year = {1968}, 32310 volume = {IT-14}, 32311 pages = {801--807} 32312} 32313 32314@Book{ mangasarian:nonlinear, 32315 author = {O. L. Mangasarian}, 32316 title = {Nonlinear Programming}, 32317 year = {1969}, 32318 publisher = {McGraw--Hill}, 32319 address = {New York}, 32320 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 32321} 32322 32323@Article{ mangasarian:normal, 32324 author = {O. L. Mangasarian}, 32325 title = {Normal Solutions of Linear Programs}, 32326 journal = {Mathematical Programming Study}, 32327 year = {1984}, 32328 volume = {22}, 32329 pages = {206--216} 32330} 32331 32332@Article{ mangasarian:optimal, 32333 author = {O. L. Mangasarian}, 32334 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 32335 Linear Programs}, 32336 journal = {Journal of Optimization Theory and Applications}, 32337 year = {1981}, 32338 volume = {35}, 32339 pages = {123--128} 32340} 32341 32342@Article{ mangasarian:parallel, 32343 author = {O. L. Mangasarian}, 32344 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 32345 journal = {SIAM Journal on Control and Optimization}, 32346 volume = {33}, 32347 pages = {1916--1925}, 32348 year = {1995} 32349} 32350 32351@TechReport{ mangasarian:regularized, 32352 author = {O. L. 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Pruyne}, 34528 title = {Resource Management Services for Parallel Applications}, 34529 school = {University of Wisconsin--Madison}, 34530 year = {1996}, 34531 address = {Madison, Wisconsin} 34532} 34533 34534@Book{ pshenichny.danilin:numerical, 34535 author = {B. N. Pshenichny and Yu. M. Danilin}, 34536 title = {Numerical Methods in Extremal Problems}, 34537 year = {1978}, 34538 publisher = {MIR Publishers}, 34539 address = {Moscow} 34540} 34541 34542@TechReport{ qi.chen:globally, 34543 author = {L. Qi and X. Chen}, 34544 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 34545 institution = {School of Mathematics, University of New South Wales}, 34546 year = {1993}, 34547 annote = {revised}, 34548 address = {Sydney} 34549} 34550 34551@Article{ qi.jiang:semismooth, 34552 author = {L. Qi and H. 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Rockafellar}, 35112 title = {Conjugate Duality and Optimization}, 35113 year = {1974}, 35114 publisher = {SIAM}, 35115 address = {Philadelphia, Pennsylvania}, 35116 volume = {16}, 35117 series = {Conference Board of the Mathematical Sciences} 35118} 35119 35120@Book{ rockafellar:convex, 35121 author = {R. T. Rockafellar}, 35122 title = {Convex Analysis}, 35123 year = {1970}, 35124 publisher = {Princeton University Press}, 35125 address = {Princeton, New Jersey} 35126} 35127 35128@Article{ rockafellar:first-, 35129 author = {R. T. Rockafellar}, 35130 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 35131 journal = {Transactions of the American Mathematical Society}, 35132 year = {1988}, 35133 volume = {307}, 35134 pages = {75--108} 35135} 35136 35137@InProceedings{ rockafellar:generalized, 35138 author = {R. T. Rockafellar}, 35139 title = {A Generalized Approach to Linear-Quadratic Programming}, 35140 booktitle = {Proceedings of the International Conference on Numerical Optimization and 35141 Applications}, 35142 year = {1986}, 35143 pages = {58--66}, 35144 note = {(Xi'an, China)} 35145} 35146 35147@InProceedings{ rockafellar:generalized*1, 35148 crossref = {bachem.grotschel.ea:mathematical}, 35149 author = {R. T. Rockafellar}, 35150 title = {Generalized Subgradients in Mathematical Programming}, 35151 pages = {368--390} 35152} 35153 35154@InCollection{ rockafellar:large-scale, 35155 author = {R. T. Rockafellar}, 35156 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 35157 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 35158 chapter = {15}, 35159 year = {1991}, 35160 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 35161 publisher = {SIAM Publications}, 35162 pages = {247--261} 35163} 35164 35165@Article{ rockafellar:linear-quadratic, 35166 author = {R. T. Rockafellar}, 35167 title = {Linear-Quadratic Programming and Optimal Control}, 35168 journal = {SIAM Journal on Control and Optimization}, 35169 year = {1987}, 35170 volume = {25}, 35171 pages = {781--814} 35172} 35173 35174@Article{ rockafellar:maximality, 35175 author = {R. T. Rockafellar}, 35176 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 35177 journal = {Transactions of the American Mathematical Society}, 35178 year = {1970}, 35179 volume = {149}, 35180 pages = {75--88} 35181} 35182 35183@InCollection{ rockafellar:monotone, 35184 author = {R. T. Rockafellar}, 35185 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 35186 crossref = {mangasarian.meyer.ea:nonlinear*3}, 35187 pages = {1--26} 35188} 35189 35190@Article{ rockafellar:monotone*1, 35191 author = {R. T. 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Rockafellar}, 35220 title = {Network Flows and Monotropic Optimization}, 35221 publisher = {John Wiley}, 35222 year = {1984}, 35223 address = {New York} 35224} 35225 35226@Article{ rodrigues:mixed, 35227 author = {H. C. Rodrigues}, 35228 title = {A mixed variational formulation for shape optimization of solids with contact 35229 conditions}, 35230 journal = {Structural Optimization}, 35231 volume = {6}, 35232 year = {1993}, 35233 pages = {19--28} 35234} 35235 35236@Book{ rodrigues:obstacle, 35237 author = {J. F. Rodrigues}, 35238 title = {Obstacle Problems in Mathematical Physics}, 35239 publisher = {Elsevier Publishing Company}, 35240 address = {Amsterdam}, 35241 year = {1987} 35242} 35243 35244@Book{ roos.terlaky.ea:theory, 35245 author = {C. Roos and T. Terlaky and J.--Ph. Vial}, 35246 title = {Theory and Algorithms for Linear Optimization: An Interior-Point Approach}, 35247 publisher = {John Wiley \& Sons}, 35248 year = {1997}, 35249 address = {Chichester} 35250} 35251 35252@TechReport{ rosa:decomposition, 35253 author = {C. H. Rosa}, 35254 title = {A Decomposition Technique for Equilibrium Programming under Uncertainty}, 35255 institution = {IIASA}, 35256 year = {1996}, 35257 number = {WP-96-013}, 35258 address = {A-2361 Laxenburg, Austria} 35259} 35260 35261@Article{ rosen.lane.ea:treatment, 35262 author = {I. Rosen and R. Lane and S. Morrill and J. Belli}, 35263 title = {Treatment Plan Optimization Using Linear Programming}, 35264 journal = {Medical Physics}, 35265 year = {1990}, 35266 volume = {18}, 35267 number = {2}, 35268 pages = {141--152} 35269} 35270 35271@TechReport{ rosenblatt:perceptron-a, 35272 author = {F. 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Waterloo}, 37871 year = {2021} 37872} 37873 37874@Article{ brookshughes1982, 37875 title = {Streamline upwind/{Petrov-Galerkin} formulations for convection dominated flows 37876 with particular emphasis on the incompressible {Navier-Stokes} equations}, 37877 author = {Alexander N Brooks and Thomas JR Hughes}, 37878 journal = {Computer methods in applied mechanics and engineering}, 37879 volume = {32}, 37880 number = {1-3}, 37881 pages = {199--259}, 37882 year = {1982}, 37883 publisher = {Elsevier} 37884} 37885 37886@InProceedings{ suhisaac2020, 37887 title = {Evaluation of a minimally synchronous algorithm for 2: 1 octree balance}, 37888 author = {Hansol Suh and Tobin Isaac}, 37889 booktitle = {SC20: International Conference for High Performance Computing, Networking, 37890 Storage and Analysis}, 37891 pages = {1--12}, 37892 year = {2020}, 37893 organization = {IEEE} 37894} 37895 37896@Misc{ alauzet2010, 37897 title = {Metric-Based Anisotropic Mesh Adaptation}, 37898 author = {Fr\'{e}d\'{e}ric Alauzet}, 37899 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 37900 year = {2010} 37901} 37902 37903@Article{ chan1994qmrcgs, 37904 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 37905 systems}, 37906 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 37907 and Tong, Charles H}, 37908 journal = {SIAM Journal on Scientific Computing}, 37909 volume = {15}, 37910 number = {2}, 37911 pages = {338--347}, 37912 year = {1994}, 37913 publisher = {SIAM} 37914} 37915 37916@Article{ ghai2019comparison, 37917 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 37918 nonsymmetric linear systems}, 37919 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 37920 journal = {Numerical Linear Algebra with Applications}, 37921 volume = {26}, 37922 number = {1}, 37923 pages = {e2215}, 37924 year = {2019}, 37925 publisher = {Wiley Online Library} 37926} 37927 37928@Article{ mishrasalacknepley2022, 37929 title = {On the order of accuracy for finite difference approximations of partial 37930 differential equations using stencil composition}, 37931 author = {Abhishek Mishra and David Salac and Matthew G. Knepley}, 37932 journal = {International Journal on Numerical Methods in Engineering}, 37933 note = {Submitted}, 37934 year = {2022} 37935} 37936 37937@Article{ nathawaniknepley2022, 37938 title = {Droplet formation simulation using mixed finite elements}, 37939 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37940 journal = {Physics of Fluids}, 37941 volume = {34}, 37942 pages = {064105}, 37943 doi = {10.1063/5.0089752}, 37944 year = {2022} 37945} 37946 37947@InProceedings{ nathawaniknepley2022b, 37948 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 37949 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37950 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 37951 (ICCFD11)}, 37952 editor = {Christoph Brehm and Shishir Pandya}, 37953 number = {4103}, 37954 year = {2022} 37955} 37956 37957@Article{ nathawaniknepley2023, 37958 title = {One-dimensional model to simulate shear-induced droplet formation}, 37959 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37960 journal = {International Journal of Multiphase Flow}, 37961 note = {Submitted}, 37962 year = {2023} 37963} 37964 37965@InProceedings{ georgalisnathawaniknepleypatra2023, 37966 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 37967 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. Knepley and Abani 37968 Patra}, 37969 booktitle = {AIAA SciTech 2024}, 37970 note = {Accepted}, 37971 year = {2023} 37972} 37973 37974@Article{ brownbarrabeamsghaffariknepleymosesshakeristengelthompsonzhang2022, 37975 title = {Performance Portable Solid Mechanics via Matrix-Free $p$-Multigrid}, 37976 author = {Jed Brown and Valeria Barra and Natalie Beams and Leila Ghaffari and Matthew 37977 Knepley and William Moses and Rezgar Shakeri and Karen Stengel and Jeremy L. 37978 Thompson and Junchao Zhang}, 37979 doi = {10.48550/ARXIV.2204.01722}, 37980 url = {https://arxiv.org/abs/2204.01722}, 37981 publisher = {arXiv}, 37982 note = {Submitted}, 37983 year = {2022} 37984} 37985 37986@InCollection{ mayknepley2023, 37987 title = {Numerical Modeling of Subduction}, 37988 author = {Dave A. May and Matthew G. Knepley}, 37989 booktitle = {Dynamics of Plate Tectonics and Mantle Convection}, 37990 editor = {João C. Duarte}, 37991 pages = {539-571}, 37992 isbn = {978-0-323-85733-8}, 37993 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 37994 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 37995 year = {2023} 37996} 37997 37998@Article{ adamsknepley2023, 37999 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 38000 plasmas in {PETSc}}, 38001 author = {Mark F. Adams and Matthew G. Knepley}, 38002 url = {https://arxiv.org/abs/2302.10242}, 38003 note = {In preparation}, 38004 year = {2023}, 38005 petsc_uses = {DMPlex} 38006} 38007 38008@Article{ finnknepleypusztayadams2023, 38009 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 38010 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. Adams}, 38011 url = {https://arxiv.org/abs/2303.12620}, 38012 journal = {Communications in Applied Mathematics and Computational Science}, 38013 note = {Submitted}, 38014 year = {2023} 38015} 38016 38017@Article{ eggersdupont1994, 38018 title = {Drop formation in a one-dimensional approximation of the {Navier--Stokes} 38019 equation}, 38020 author = {Jens Eggers and Todd F. Dupont}, 38021 journal = {Journal of fluid mechanics}, 38022 volume = {262}, 38023 pages = {205--221}, 38024 year = {1994}, 38025 publisher = {Cambridge University Press} 38026} 38027 38028@PhDThesis{ pusztaythesis2023, 38029 title = {A Particle Basis Vlasov-Poisson-Landau Solver for Plasma Simulation in PETSc}, 38030 author = {Joseph V. Pusztay}, 38031 type = {{PhD} thesis}, 38032 school = {University at Buffalo, Department of Computer Science and Engineering}, 38033 address = {Buffalo, NY}, 38034 month = may, 38035 year = {2022} 38036} 38037 38038@PhDThesis{ finnthesis2023, 38039 title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau 38040 System}, 38041 author = {Daniel S. Finn}, 38042 type = {{PhD} thesis}, 38043 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38044 Engineering}, 38045 address = {Buffalo, NY}, 38046 month = may, 38047 year = {2023} 38048} 38049 38050@PhDThesis{ nathawanithesis2023, 38051 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 38052 author = {Darsh Kiritbhai Nathawani}, 38053 type = {{PhD} thesis}, 38054 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38055 Engineering}, 38056 address = {Buffalo, NY}, 38057 month = may, 38058 year = {2023} 38059} 38060 38061@article{MckayEriksonKozdon2019, 38062 title = {A computational method for earthquake cycles within anisotropic media}, 38063 author = {Maricela Best Mckay and Brittany A Erickson and Jeremy E Kozdon}, 38064 journal = {Geophysical Journal International}, 38065 volume = {219}, 38066 number = {2}, 38067 pages = {816--833}, 38068 year = {2019}, 38069} 38070 38071article{EricksonOReillyNordstrom2019, 38072 title = {Accuracy of stable, high-order finite difference methods for hyperbolic systems with non-smooth wave speeds}, 38073 author = {Brittany A Erickson and Ossian O’Reilly and Jan Nordstr{\"o}m}, 38074 journal = {Journal of Scientific Computing}, 38075 volume = {81}, 38076 pages = {2356--2387}, 38077 year = {2019}, 38078} 38079 38080@article{KozdonEricksonWilcox2021, 38081 title = {Hybridized summation-by-parts finite difference methods}, 38082 author = {Jeremy E Kozdon and Brittany A Erickson and Lucas C Wilcox}, 38083 journal = {Journal of Scientific Computing}, 38084 volume = {87}, 38085 number = {3}, 38086 pages = {85}, 38087 year = {2021}, 38088} 38089 38090@article{SEAS2022, 38091 title = {Community-driven code comparisons for three-dimensional dynamic modeling of sequences of earthquakes and aseismic slip}, 38092 author = {Junle Jiang and Brittany A Erickson and Val{\`e}re R Lambert and Jean-Paul Ampuero and Ryosuke Ando and Sylvain D Barbot and Camilla Cattania and Luca Dal Zilio and Benchun Duan and Eric M Dunham and Alice-Agnes Gabriel and Nadia Lapusta and Duo Li and Meng Li and Dunyu Liu and Yajing Liu and So Ozawa and Casper Pranger and Ylona van Dinther}, 38093 journal = {Journal of Geophysical Research: Solid Earth}, 38094 volume = {127}, 38095 number = {3}, 38096 pages = {e2021JB023519}, 38097 year = {2022}, 38098} 38099 38100@article{EricksonKozdonHarvey2022, 38101 title = {A non-stiff summation-by-parts finite difference method for the scalar wave equation in second order form: Characteristic boundary conditions and nonlinear interfaces}, 38102 author = {Brittany A Erickson and Jeremy E Kozdon and Tobias Harvey}, 38103 journal = {Journal of Scientific Computing}, 38104 volume = {93}, 38105 number = {1}, 38106 pages = {17}, 38107 year = {2022}, 38108} 38109 38110@article{RuckerEriksonKarlstromLeeGopalakrishnan2022, 38111 title = {A Computational Framework for Time-Dependent Deformation in Viscoelastic Magmatic Systems}, 38112 author = {Cody Rucker and Brittany A Erickson and Leif Karlstrom and Brian Lee and Jay Gopalakrishnan}, 38113 journal = {Journal of Geophysical Research: Solid Earth}, 38114 volume = {127}, 38115 number = {9}, 38116 pages = {e2022JB024506}, 38117 year = {2022}, 38118} 38119 38120@article{HarveyEriksonKozdon2023, 38121 title = {A High-order Accurate Summation-by-Parts Finite Difference Method for Fully-dynamic Earthquake Sequence Simulations within Sedimentary Basins}, 38122 author = {Tobias W Harvey and Brittany A Erickson and Jeremy E Kozdon}, 38123 journal = {Journal of Geophysical Research: Solid Earth}, 38124 pages = {e2022JB025357}, 38125 year = {2023}, 38126} 38127 38128@article{SEAS2023, 38129 title = {Incorporating full elastodynamic effects and dipping fault geometries in community code verification exercises for simulations of earthquake sequences and aseismic slip {(SEAS)}}, 38130 author = {Brittany A Erickson and Junle Jiang and Val{\`e}re Lambert and Sylvain D Barbot and Mohamed Abdelmeguid and Martin Almquist and Jean-Paul Ampuero and Ryosuke Ando and Camilla Cattania and Alexandre Chen and Luca Dal Zilio and Shuai Deng and Eric M. Dunham and Ahmed E. Elbanna and Alice‐Agnes Gabriel and Tobias W. Harvey and Yihe Huang and Yoshihiro Kaneko and Jeremy E. Kozdon and Nadia Lapusta and Duo Li and Meng Li and Chao Liang and Yajing Liu and So Ozawa and Andrea Perez‐Silva and Casper Pranger and Paul Segall and Yudong Sun and Prithvi Thakur and Carsten Uphoff and Ylona van Dinther and Yuyun Yang}, 38131 journal = {Bulletin of the Seismological Society of America}, 38132 volume = {113}, 38133 number = {2}, 38134 pages = {499--523}, 38135 year = {2023}, 38136} 38137
