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-titanium, 7305 title = {Ti-PETSc - an interface to PETSc from Titanium}, 7306 institution = {Berkeley}, 7307 author = {He, Yun and Liblit, Bun and Lin, Chang}, 7308 url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=9f7959be13337c735d52e5c0b0994bdea6d75a96}, 7309 year = {1999}, 7310 petsc_uses = {KSP}, 7311} 7312 7313@Unpublished{ ptatin-web-page, 7314 title = {ptatin3d}, 7315 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 7316 url = {https://bitbucket.org/jedbrown/ptatin3d}, 7317 year = {2018}, 7318 petsc_uses = {KSP} 7319} 7320 7321@Misc{ multiphase-web-page, 7322 author = {Q. Zou}, 7323 title = {Multiphase flow with {PETSc}}, 7324 institution = {LANL}, 7325 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 7326 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 7327 lab = {LANL}, 7328 petsc_uses = {KSP} 7329} 7330 7331@Misc{ electromag-web-page, 7332 title = {{EMSolve Web} page}, 7333 institution = {LLNL}, 7334 howpublished = {http://www.llnl.gov/casc/emsolve}, 7335 url = {http://www.Llnl.gov/casc/emsolve}, 7336 author = {Daniel {White et al.}}, 7337 lab = {LLNL}, 7338 petsc_uses = {KSP} 7339} 7340 7341@Unpublished{ fe-software-web-page, 7342 institution = {Kuleuven}, 7343 title = {Finite element software}, 7344 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 7345 petsc_uses = {KSP} 7346} 7347 7348@Misc{ petsc-web-page, 7349 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7350 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 7351 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7352 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7353 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7354 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7355 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7356 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7357 Zhang}, 7358 title = {{PETS}c {W}eb page}, 7359 url = {https://petsc.org/}, 7360 howpublished = {\url{https://petsc.org/}}, 7361 year = {2023} 7362} 7363 7364@Unpublished{ petsc-debian-package, 7365 author = {Adam C. Powell, IV}, 7366 title = {Debian package for PETSc}, 7367 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 7368 petsc_uses = {KSP} 7369} 7370 7371@Unpublished{ cactus, 7372 title = {Cactus Website}, 7373 url = {http://www.cactuscode.org/}, 7374 note = {Provides two interface to the PETSc solvers}, 7375 petsc_uses = {KSP} 7376} 7377 7378@Unpublished{ petsc-fem, 7379 author = {Mario Storti and Norberto Nigro}, 7380 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 7381 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 7382 url = {http://www.cimec.org.ar/petscfem}, 7383 petsc_uses = {KSP} 7384} 7385 7386@Misc{ fidap, 7387 title = {FIDAP 8.5}, 7388 howpublished = {\url{http://www.fluent.com}}, 7389 url = {http://www.fluent.com}, 7390 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 7391 solves.}, 7392 key = {FIDAP 8.5}, 7393 petsc_uses = {KSP} 7394} 7395 7396@Unpublished{ slepc, 7397 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7398 Vicente Hern\'andez and Vicent Vidal}, 7399 title = {{SLEPc} Website}, 7400 url = {http://slepc.upv.es/}, 7401 note = {Scalable Library for Eigenvalue Problem Computations}, 7402 petsc_uses = {KSP} 7403} 7404 7405@TechReport{ slepc-users-manual, 7406 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7407 Vicente Hern\'andez and Vicent Vidal}, 7408 title = {{SLEPc} Users Manual}, 7409 number = {DISC-II/24/02}, 7410 url = {http://slepc.upv.es/}, 7411 note = {Scalable Library for Eigenvalue Problem Computations}, 7412 petsc_uses = {KSP} 7413} 7414 7415@Misc{ deal.ii, 7416 title = {deal.II}, 7417 howpublished = {\url{http://www.dealii.org}}, 7418 url = {http://www.dealii.org}, 7419 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 7420 It allows PETSc linear algebra and solvers to be used underneath.}, 7421 key = {deal.II 5.0}, 7422 petsc_uses = {KSP} 7423} 7424 7425@Article{ bangerth2007deal, 7426 title = {{deal.II---A general-purpose object-oriented finite element library}}, 7427 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 7428 journal = {ACM Transactions on Mathematical Software (TOMS)}, 7429 volume = {33}, 7430 number = {4}, 7431 pages = {24--es}, 7432 issn = {0098-3500}, 7433 year = {2007}, 7434 publisher = {ACM}, 7435 petsc_uses = {KSP} 7436} 7437 7438@Misc{ globalarrays, 7439 author = {Jarek {Nieplocha et al.}}, 7440 title = {Global Arrays}, 7441 institution = {Pacific Northwest National Laboratories}, 7442 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 7443 url = {http://www.emsl.pnl.gov/docs/global}, 7444 note = {Global arrays can use PETSc linear solvers}, 7445 lab = {PNNL}, 7446 petsc_uses = {KSP} 7447} 7448 7449% LiteralHTML: 7450% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 7451% LiteralHTML: 7452@Article{ petsccommunity2022, 7453 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 7454 Community}, 7455 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 7456 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 7457 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 7458 and Hong Zhang and Junchao Zhang}, 7459 journal = {Computing in Science and Engineering}, 7460 volume = {24}, 7461 number = {03}, 7462 pages = {6--15}, 7463 issn = {1558-366X}, 7464 doi = {10.1109/MCSE.2022.3169974}, 7465 publisher = {IEEE Computer Society}, 7466 address = {Los Alamitos, CA, USA}, 7467 month = may, 7468 year = {2022}, 7469 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 7470 petsc_uses = {KSP} 7471} 7472 7473@Article{ brownknepleysmith14, 7474 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 7475 title = {Run-time extensibility and librarization of simulation software}, 7476 journal = {IEEE Computing in Science and Engineering}, 7477 month = jan, 7478 volume = {17}, 7479 number = {1}, 7480 pages = {38--45}, 7481 doi = {10.1109/MCSE.2014.95}, 7482 year = {2015}, 7483 petsc_uses = {KSP} 7484} 7485 7486@TechReport{ ass2012, 7487 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 7488 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 7489 institution = {Argonne National Laboratory}, 7490 type = {Preprint}, 7491 year = {2012}, 7492 number = {ANL/MCS-P2011-0112}, 7493 petsc_uses = {KSP} 7494} 7495 7496@TechReport{ clearyknepley99, 7497 author = {Andrew Cleary and Matthew G. Knepley}, 7498 title = {Solvers as Operators}, 7499 institution = {Lawrence Livermore National Laboratory}, 7500 type = {Technical Report}, 7501 number = {UCRL-ID-135342}, 7502 year = {1999}, 7503 petsc_uses = {KSP} 7504} 7505 7506@TechReport{ smcabbkz2012, 7507 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 7508 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 7509 title = {{PETSc's} software strategy for the design space of composable extreme-scale 7510 solvers}, 7511 institution = {Argonne National Laboratory}, 7512 type = {Preprint}, 7513 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 7514 year = {2012}, 7515 number = {ANL/MCS-P2059-0312}, 7516 petsc_uses = {KSP} 7517} 7518 7519@InProceedings{ mhwpmhs2009, 7520 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 7521 and G. E. Hammond and B. Smith}, 7522 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 7523 Toolkit {MPI} at Scale}, 7524 booktitle = {Cray Users Group Conference}, 7525 year = {2009}, 7526 petsc_uses = {KSP} 7527} 7528 7529@InProceedings{ msmhls2010, 7530 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 7531 Lichtner and B. F. Smith}, 7532 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 7533 {BlueGene} Architectures}, 7534 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 7535 year = {2010}, 7536 petsc_uses = {KSP} 7537} 7538 7539@InCollection{ msk2013, 7540 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 7541 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 7542 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7543 series = {Lecture Notes in Earth System Sciences}, 7544 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7545 Yaolin Shi}, 7546 doi = {10.1007/978-3-642-16405-7_7}, 7547 publisher = {Springer Berlin Heidelberg}, 7548 pages = {131--140}, 7549 year = {2013}, 7550 isbn = {978-3-642-16404-0}, 7551 petsc_uses = {KSP} 7552} 7553 7554@InCollection{ knepleyyuen13, 7555 author = {Matthew G. Knepley and David A. Yuen}, 7556 title = {Why Scientists and Engineers need {GPU}s today}, 7557 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7558 series = {Lecture Notes in Earth System Sciences}, 7559 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7560 Yaolin Shi}, 7561 doi = {10.1007/978-3-642-16405-7_1}, 7562 publisher = {Springer Berlin Heidelberg}, 7563 pages = {131--140}, 7564 year = {2013}, 7565 isbn = {978-3-642-16404-0}, 7566 petsc_uses = {KSP} 7567} 7568 7569@InCollection{ karpeevknepleybrune13, 7570 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 7571 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 7572 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7573 series = {Lecture Notes in Earth System Sciences}, 7574 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7575 Yaolin Shi}, 7576 doi = {10.1007/978-3-642-16405-7_30}, 7577 publisher = {Springer Berlin Heidelberg}, 7578 pages = {487--501}, 7579 year = {2013}, 7580 isbn = {978-3-642-16404-0}, 7581 petsc_uses = {KSP} 7582} 7583 7584@InCollection{ zhengetal13, 7585 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 7586 Variable Viscosity}, 7587 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7588 Zhang and Yaolin Shi}, 7589 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7590 series = {Lecture Notes in Earth System Sciences}, 7591 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7592 Yaolin Shi}, 7593 doi = {10.1007/978-3-642-16405-7_21}, 7594 publisher = {Springer Berlin Heidelberg}, 7595 pages = {321--333}, 7596 year = {2013}, 7597 isbn = {978-3-642-16404-0}, 7598 petsc_uses = {KSP} 7599} 7600 7601@Article{ zhengetal13b, 7602 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 7603 strongly variable viscosity based on {M}atlab and {CUDA}}, 7604 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7605 Zhang and Yaolin Shi}, 7606 journal = {IJHPCA}, 7607 volume = {28}, 7608 number = {1}, 7609 pages = {50--60}, 7610 doi = {10.1177/1094342013478640}, 7611 year = {2013}, 7612 petsc_uses = {KSP} 7613} 7614 7615@InBook{ s2011, 7616 author = {B. Smith}, 7617 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 7618 title = {Encyclopedia of Parallel Computing}, 7619 bookeditor = {D. Padua}, 7620 publisher = {Springer}, 7621 year = {2011}, 7622 petsc_uses = {KSP} 7623} 7624 7625@Article{ acostamejia06, 7626 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 7627 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 7628 journal = {Lecturas Matem\'aticas}, 7629 volume = {27}, 7630 year = {2006}, 7631 pages = {213--224}, 7632 petsc_uses = {KSP} 7633} 7634 7635@InProceedings{ quenettemoresisunterappelbe07, 7636 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 7637 title = {Explaining StGermain: An aspect oriented environment for building extensible 7638 computational mechanics modeling software}, 7639 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 7640 publisher = {IEEE}, 7641 pages = {1--8}, 7642 yerar = {2007}, 7643 petsc_uses = {KSP} 7644} 7645 7646@Article{ dfm1, 7647 title = {Vectorized sparse matrix multiply for compressed row storage format}, 7648 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 7649 journal = {Lecture Notes in Computer Science}, 7650 year = {2005}, 7651 pages = {99--106}, 7652 volume = {3514}, 7653 lab = {ORNL}, 7654 petsc_uses = {KSP} 7655} 7656 7657@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 7658 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 7659 Vandewalle and Stefaan Poedts}, 7660 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 7661 Scientific Computing Software}, 7662 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 7663 year = {2005}, 7664 note = {Lecture Notes in Computer Science}, 7665 volume = {3514}, 7666 publisher = {Springer-Verlag GmbH}, 7667 petsc_uses = {KSP} 7668} 7669 7670@InProceedings{ dalcin-paz-storti, 7671 author = {L. Dalcin and R. Paz and M. Storti}, 7672 title = {Desarrollo de Aplicaciones Paralelas en Python}, 7673 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 7674 Bariloche, Argentina}, 7675 year = {2004}, 7676 petsc_uses = {KSP} 7677} 7678 7679@Article{ mpi-python, 7680 author = {L. Dalcin and R. Paz and M. Storti}, 7681 title = {MPI for Python}, 7682 journal = {Journal of Parallel and Distributed Computing}, 7683 year = {2005}, 7684 petsc_uses = {KSP} 7685} 7686 7687@Unpublished{ hrv02a, 7688 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 7689 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7690 note = {Submited to VecPar 2002}, 7691 year = {2002}, 7692 petsc_uses = {KSP} 7693} 7694 7695@Article{ knyazev2007block, 7696 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 7697 {PETSc}}, 7698 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 7699 journal = {SIAM Journal on Scientific Computing}, 7700 volume = {29}, 7701 pages = {2224-2239}, 7702 doi = {10.1137/060661624}, 7703 year = {2007}, 7704 petsc_uses = {KSP} 7705} 7706 7707@MastersThesis{ aarrestad-master, 7708 author = {Asbjorn Hoiland Aarrestad}, 7709 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 7710 school = {University of Bergen}, 7711 month = aug, 7712 year = {2003}, 7713 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 7714 note = {Implemented Runge-Kutta methods using PETSc}, 7715 petsc_uses = {KSP} 7716} 7717 7718@PhDThesis{ kaushik-phd, 7719 author = {D. K. Kaushik}, 7720 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 7721 Differential Equations on Unstructured Grids}, 7722 school = {Old Dominion University}, 7723 month = dec, 7724 year = {2002}, 7725 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 7726 petsc_uses = {KSP} 7727} 7728 7729@TechReport{ rb1, 7730 author = {Rickard Bergstrom}, 7731 title = {Object Oriented Implementation of a General Finite Element Code}, 7732 number = {2002-13}, 7733 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 7734 year = {2002}, 7735 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 7736 note = {Discribes a finite element software package that uses PETSc for its solvers}, 7737 petsc_uses = {KSP} 7738} 7739 7740@InProceedings{ dbl1, 7741 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 7742 title = {A Parallel General Purpose Finite Element System}, 7743 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 7744 publisher = {SIAM}, 7745 year = {1999}, 7746 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 7747 note = {Describes software that uses PETSc for its parallel linear solves}, 7748 petsc_uses = {KSP} 7749} 7750 7751@Article{ p1, 7752 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 7753 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 7754 and B. Smith}, 7755 journal = {Parallel Computing}, 7756 year = {2002}, 7757 pages = {1811--1831}, 7758 volume = {28 (12)}, 7759 petsc_uses = {KSP} 7760} 7761 7762@Article{ automatic-ad, 7763 author = {Paul Hovland and Boyana Norris and Barry Smith}, 7764 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 7765 year = {2005}, 7766 journal = {Future Generation Computer Systems}, 7767 volume = {21}, 7768 number = {8}, 7769 pages = {1426--1438}, 7770 petsc_uses = {KSP} 7771} 7772 7773@TechReport{ remote-math, 7774 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 7775 Smith}, 7776 title = {Remote Access to Mathematical Software}, 7777 number = {ANL/MCS-P889-0601}, 7778 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7779 month = jun, 7780 year = {2001}, 7781 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 7782 petsc_uses = {KSP} 7783} 7784 7785@InProceedings{ gropp98, 7786 author = {William D. Gropp}, 7787 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 7788 publisher = {SIAM}, 7789 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7790 Scientific and Engineering Computing}, 7791 year = {1999}, 7792 pages = {21-29}, 7793 petsc_uses = {KSP} 7794} 7795 7796@InProceedings{ knepleysarin99, 7797 author = {Matthew Knepley and Vivek Sarin}, 7798 title = {Algorithm Development for Large Scale Computing}, 7799 publisher = {SIAM}, 7800 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7801 Scientific and Engineering Computing}, 7802 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}}, 7803 year = {1999}, 7804 petsc_uses = {KSP} 7805} 7806 7807@InBook{ bgms00, 7808 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 7809 chapter = {Software for the Scalable Solution of {PDEs}}, 7810 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 7811 title = {CRPC Handbook of Parallel Computing}, 7812 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 7813 and A. White}, 7814 publisher = {Morgan Kaufmann Publishers}, 7815 year = {2002}, 7816 petsc_uses = {KSP} 7817} 7818 7819@InProceedings{ hovland_norris_smith98, 7820 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 7821 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 7822 Computations}, 7823 publisher = {SIAM}, 7824 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7825 Scientific and Engineering Computing}, 7826 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 7827 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 7828 year = {1999}, 7829 pages = {129-137}, 7830 petsc_uses = {KSP} 7831} 7832 7833@InProceedings{ efficient, 7834 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7835 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 7836 Libraries}, 7837 booktitle = {Modern Software Tools in Scientific Computing}, 7838 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 7839 publisher = {Birkhauser Press}, 7840 pages = {163--202}, 7841 year = {1997}, 7842 petsc_uses = {KSP} 7843} 7844 7845% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 7846@TechReport{ petsc-user-ref, 7847 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7848 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 7849 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7850 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7851 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7852 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7853 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7854 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7855 Zhang}, 7856 title = {{PETSc/TAO} Users Manual}, 7857 institution = {Argonne National Laboratory}, 7858 number = {ANL-21/39 - Revision 3.20}, 7859 doi = {10.2172/1968587}, 7860 year = {2023} 7861} 7862 7863% url = {https://petsc.org/release} 7864@TechReport{ petsc-developers, 7865 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 7866 title = {{PETS}c Developers Guide}, 7867 institution = {Argonne National Laboratory}, 7868 number = {ANL-18/18}, 7869 year = {2018}, 7870 url = {https://petsc.org/release/developers}, 7871 petsc_uses = {KSP} 7872} 7873 7874@Unpublished{ alice-memory-snooper, 7875 author = {Ibrahima Ba and Barry~F. Smith}, 7876 title = {The {ALICE} Memory Snooper}, 7877 year = {1999}, 7878 petsc_uses = {KSP} 7879} 7880 7881@TechReport{ petsc-user-ref-polish, 7882 author = {Marcin Bojko and Piotr Krzyzanowski}, 7883 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 7884 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 7885 year = {1998}, 7886 note = {An introduction to PETSc in Polish}, 7887 petsc_uses = {KSP} 7888} 7889 7890@InProceedings{ abghmn00, 7891 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 7892 High-Performance Scientific Computing}, 7893 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 7894 Norris}, 7895 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 7896 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 7897 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 7898 Hasco\"{e}t and Uwe Naumann}, 7899 publisher = {Springer}, 7900 year = {2002}, 7901 petsc_uses = {KSP} 7902} 7903 7904@Unpublished{ petsc-mpi-paper, 7905 author = {Lois Curfman McInnes and Barry F. Smith}, 7906 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 7907 Libraries}, 7908 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 7909 month = jun, 7910 year = {1995}, 7911 petsc_uses = {KSP} 7912} 7913 7914@InProceedings{ miss-paper, 7915 author = {William D. Gropp and Barry F. Smith}, 7916 title = {Scalable, Extensible, and Portable Numerical Libraries}, 7917 publisher = {IEEE}, 7918 year = {1994}, 7919 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7920 address = {Mississippi State University}, 7921 pages = {87--93}, 7922 keyword = {numerical libraries, scientific computing, parallel computing}, 7923 petsc_uses = {KSP} 7924} 7925 7926@InProceedings{ snes-paper, 7927 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7928 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 7929 Minimization Problems}, 7930 publisher = {IEEE}, 7931 year = {1995}, 7932 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7933 address = {Mississippi State University}, 7934 pages = {60-67}, 7935 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 7936 petsc_uses = {KSP} 7937} 7938 7939@Article{ dsneutral, 7940 author = {Barry F. Smith and William D. Gropp}, 7941 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 7942 Sparse Linear Systems}, 7943 journal = {Scientific Programming}, 7944 volume = {5}, 7945 pages = {329--336}, 7946 key = {GroppSmith96 ! KSP design}, 7947 year = {1996}, 7948 petsc_uses = {KSP} 7949} 7950 7951@InProceedings{ bgms98, 7952 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7953 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 7954 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7955 Scientific and Engineering Computing}, 7956 publisher = {SIAM}, 7957 pages = {58-67}, 7958 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 7959 year = {1998}, 7960 petsc_uses = {KSP} 7961} 7962 7963@Article{ hkm98, 7964 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 7965 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 7966 {PDE} Computation}, 7967 journal = {Advances in Engineering Software}, 7968 volume = {29}, 7969 pages = {415-424}, 7970 year = {1998}, 7971 petsc_uses = {KSP} 7972} 7973 7974@TechReport{ pdpta99, 7975 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 7976 Smith}, 7977 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 7978 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 7979 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 7980 Vegas, Nevada}, 7981 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7982 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 7983 number = {ANL/MCS-P751-0599}, 7984 year = {1999}, 7985 petsc_uses = {KSP} 7986} 7987 7988@InProceedings{ bbh:com, 7989 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 7990 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 7991 Computing}}, 7992 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 7993 Euro-Par Conference, Munich, Germany, August/September 2000}, 7994 year = {2000}, 7995 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 7996 volume = {1900}, 7997 series = {Lecture Notes in Computer Science}, 7998 pages = {86--94}, 7999 address = {Berlin}, 8000 publisher = {Springer}, 8001 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 8002 petsc_uses = {KSP} 8003} 8004 8005@InProceedings{ overture00, 8006 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8007 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 8008 Components}, 8009 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 8010 booktitle = {Proceedings of the International Federation for Information Processing Working 8011 Conference on Software Architectures for Scientific Computing, Kluwer}, 8012 year = {2000}, 8013 pages = {57--68}, 8014 petsc_uses = {KSP} 8015} 8016 8017@TechReport{ smith97, 8018 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 8019 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 8020 number = {ANL/MCS-P701}, 8021 author = {Barry F. Smith}, 8022 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8023 petsc_uses = {KSP} 8024} 8025 8026@Article{ smith98, 8027 author = {Barry Smith}, 8028 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 8029 journal = {SIGNUM Newsletter}, 8030 year = {1998}, 8031 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 8032 petsc_uses = {KSP} 8033} 8034 8035@TechReport{ ad-petsc-tm, 8036 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 8037 {PETSc}}, 8038 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 8039 year = {1997}, 8040 type = {Technical Memorandum}, 8041 institution = {ANL}, 8042 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 8043 number = {ANL/MCS-TM-233}, 8044 petsc_uses = {KSP} 8045} 8046 8047% LiteralHTML: 8048% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 8049% LiteralHTML: 8050@PhDThesis{ klotzthesis2019, 8051 author = {Thomas S. Klotz}, 8052 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 8053 Biology}, 8054 school = {Rice University}, 8055 year = {2019}, 8056 petsc_uses = {KSP} 8057} 8058 8059@Article{ klotzbardhanknepley2018, 8060 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 8061 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 8062 journal = {Communications in Applied Mathematics and Computational Science}, 8063 note = {In review}, 8064 url = {https://arxiv.org/abs/1708.06028}, 8065 year = {2018}, 8066 petsc_uses = {KSP} 8067} 8068 8069@Misc{ brown2016, 8070 title = {Threading Tradeoffs in Domain Decomposition}, 8071 author = {Jed Brown}, 8072 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 8073 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 8074 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 8075 year = {2016}, 8076 petsc_uses = {KSP} 8077} 8078 8079@Article{ changnakshatralaknepleyjohnsson2017, 8080 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 8081 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 8082 Johnsson}, 8083 journal = {Concurency: Practice and Experience}, 8084 volume = {30}, 8085 number = {11}, 8086 eprint = {1705.03625}, 8087 doi = {10.1002/cpe.4401}, 8088 year = {2017}, 8089 petsc_uses = {KSP} 8090} 8091 8092@Article{ changfabienknepleymills2018, 8093 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 8094 spectrum analysis}, 8095 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 8096 journal = {SIAM Journal on Scientific Computing}, 8097 volume = {40}, 8098 number = {6}, 8099 pages = {C779--C802}, 8100 eprint = {1802.07832}, 8101 doi = {10.1137/18M1172260}, 8102 year = {2018}, 8103 petsc_uses = {KSP} 8104} 8105 8106@Article{ joshaghanichangnakshatralaknepley2019, 8107 title = {Composable solvers for the four-field double porosity/permeability model}, 8108 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 8109 Knepley}, 8110 journal = {Journal of Computational Physics}, 8111 volume = {386}, 8112 pages = {428--466}, 8113 doi = {10.1016/j.jcp.2019.02.020}, 8114 year = {2019}, 8115 petsc_uses = {KSP} 8116} 8117 8118@InProceedings{ barralknepleylangepiggottgorman2016, 8119 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 8120 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 8121 and Gerard J. Gorman}, 8122 booktitle = {25th International Meshing Roundtable}, 8123 editor = {Steve Owen and Hang Si}, 8124 month = sep, 8125 address = {Washington, DC}, 8126 pages = {1--5}, 8127 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 8128 year = {2016}, 8129 petsc_uses = {KSP} 8130} 8131 8132@Article{ adamsbrownknepleysamtaney2016, 8133 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 8134 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 8135 journal = {SIAM Journal on Scientific Computing}, 8136 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 8137 epub = {http://arxiv.org/abs/1406.7808}, 8138 volume = {8}, 8139 number = {4}, 8140 pages = {C426--C440}, 8141 doi = {10.1137/140975127}, 8142 year = {2016}, 8143 petsc_uses = {KSP} 8144} 8145 8146@InProceedings{ maysananruppknepleysmith2016, 8147 title = {Extreme-Scale Multigrid Components within {PETSc}}, 8148 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 8149 Smith}, 8150 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 8151 series = {PASC '16}, 8152 isbn = {978-1-4503-4126-4}, 8153 location = {Lausanne, Switzerland}, 8154 pages = {5:1--5:12}, 8155 articleno = {5}, 8156 numpages = {12}, 8157 doi = {10.1145/2929908.2929913}, 8158 acmid = {2929913}, 8159 publisher = {ACM}, 8160 address = {New York, NY, USA}, 8161 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 8162 preconditioning}, 8163 year = {2016}, 8164 petsc_uses = {KSP} 8165} 8166 8167@Article{ liu2015field, 8168 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 8169 author = {Lulu Liu and David E Keyes}, 8170 journal = {SIAM Journal on Scientific Computing}, 8171 volume = {37}, 8172 number = {3}, 8173 pages = {A1388--A1409}, 8174 year = {2015}, 8175 publisher = {SIAM}, 8176 petsc_uses = {KSP} 8177} 8178 8179@Article{ lujiaomissirlis2014, 8180 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 8181 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 8182 journal = {Numerical Linear Algebra with Applications}, 8183 volume = {21}, 8184 number = {2}, 8185 pages = {221--238}, 8186 year = {2014}, 8187 publisher = {Wiley Online Library}, 8188 petsc_uses = {KSP} 8189} 8190 8191@Article{ badiamartinprincipe2013, 8192 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 8193 solid mechanics}, 8194 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 8195 journal = {International Journal for Numerical Methods in Engineering}, 8196 volume = {96}, 8197 number = {4}, 8198 pages = {203--230}, 8199 year = {2013}, 8200 petsc_uses = {KSP} 8201} 8202 8203@Article{ morganknepleysananscott2016, 8204 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 8205 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 8206 journal = {Concurrency and Computation: Practice and Experience}, 8207 volume = {28}, 8208 pages = {4532--4542}, 8209 year = {2016}, 8210 url = {http://arxiv.org/abs/1602.04873}, 8211 doi = {10.1002/cpe.3820}, 8212 petsc_uses = {KSP} 8213} 8214 8215@Article{ morgansananknepleymills2020, 8216 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 8217 solvers}, 8218 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 8219 journal = {The International Journal of High Performance Computing Applications}, 8220 volume = {35}, 8221 issue = {1}, 8222 doi = {10.1177/1094342020966835}, 8223 url = {https://doi.org/10.1177/1094342020966835}, 8224 eprint = {https://doi.org/10.1177/1094342020966835}, 8225 year = {2020}, 8226 petsc_uses = {KSP} 8227} 8228 8229@Article{ msz2013, 8230 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 8231 author = {M. McCourt and B. F. Smith and H. Zhang}, 8232 journal = {SIAM Journal on Matrix Analysis and Applications}, 8233 year = {2015}, 8234 note = {To appear}, 8235 petsc_uses = {KSP} 8236} 8237 8238@Article{ bassi2014agglomeration, 8239 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 8240 free}, 8241 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 8242 journal = {Mathematical Models and Methods in Applied Sciences}, 8243 volume = {24}, 8244 number = {08}, 8245 pages = {1495--1539}, 8246 year = {2014}, 8247 publisher = {World Scientific}, 8248 petsc_uses = {KSP} 8249} 8250 8251@Article{ jhuranidemkowicz12, 8252 author = {{Jhurani}, C. and {Demkowicz}, L.}, 8253 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 8254 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 8255 journal = {Computer Methods in Applied Mechanics and Engineering}, 8256 volume = {213}, 8257 pages = {418-426}, 8258 year = {2012}, 8259 month = mar, 8260 doi = {10.1016/j.cma.2011.06.003}, 8261 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 8262 petsc_uses = {KSP} 8263} 8264 8265@Article{ yangcai11, 8266 author = {Yang, Haijian and Cai, Xiao-Chuan}, 8267 title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear 8268 Complementarity Problems}, 8269 journal = {J. Sci. Comput.}, 8270 issue_date = {May 2011}, 8271 volume = {47}, 8272 number = {2}, 8273 month = may, 8274 pages = {258--280}, 8275 year = {2011}, 8276 issn = {0885-7474}, 8277 numpages = {23}, 8278 doi = {10.1007/s10915-010-9436-4}, 8279 acmid = {1971246}, 8280 publisher = {Plenum Press}, 8281 address = {New York, NY, USA}, 8282 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 8283 preconditioners, Semismooth Newton, Two-level methods}, 8284 petsc_uses = {KSP} 8285} 8286 8287@Article{ rheinbach09, 8288 author = {Rheinbach, Oliver}, 8289 title = {Parallel Iterative Substructuring in Structural Mechanics}, 8290 journal = {Archives of Computational Methods in Engineering}, 8291 volume = {16}, 8292 number = {4}, 8293 pages = {425-463}, 8294 year = {2009}, 8295 issn = {1134-3060}, 8296 doi = {10.1007/s11831-009-9035-4}, 8297 publisher = {Springer Netherlands}, 8298 language = {English}, 8299 petsc_uses = {KSP} 8300} 8301 8302@Article{ knepleyterrel2013, 8303 author = {Matthew G. Knepley and Andy R. Terrel}, 8304 title = {Finite Element Integration on {GPUs}}, 8305 journal = {{ACM} Transactions on Mathematical Software}, 8306 volume = {39}, 8307 number = {2}, 8308 accepted = {17 April 2012}, 8309 year = {2013}, 8310 abstract = {We present a novel finite element integration method for low order elements on 8311 GPUs. We achieve more than 100GF for element integration on first order 8312 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 8313 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 8314 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 8315 url = {http://arxiv.org/abs/1103.0066}, 8316 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 8317 petsc_uses = {KSP} 8318} 8319 8320@Article{ knepleyruppterrel2016, 8321 title = {Finite Element Integration with Quadrature on the GPU}, 8322 journal = {ArXiv e-prints}, 8323 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 8324 version = {1}, 8325 date = {2016-07-14}, 8326 eprinttype = {arxiv}, 8327 eprintclass = {cs.MS}, 8328 eprint = {1607.04245v1}, 8329 petsc_uses = {KSP} 8330} 8331 8332@Article{ klawonnlanserrheinbach2014, 8333 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 8334 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 8335 journal = {SIAM Journal on Scientific Computing}, 8336 volume = {36}, 8337 number = {2}, 8338 pages = {A737--A765}, 8339 year = {2014}, 8340 petsc_uses = {KSP} 8341} 8342 8343@TechReport{ pbmkbsxt2012, 8344 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8345 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8346 year = {2013}, 8347 type = {Preprint}, 8348 number = {ANL/MCS-P2010-0112}, 8349 institution = {Argonne National Laboratory}, 8350 petsc_uses = {KSP} 8351} 8352 8353@Article{ bruneknepleysmithtu15, 8354 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8355 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8356 journal = {SIAM Review}, 8357 volume = {57}, 8358 number = {4}, 8359 pages = {535--565}, 8360 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 8361 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 8362 doi = {10.1137/130936725}, 8363 year = {2015}, 8364 petsc_uses = {KSP} 8365} 8366 8367@Article{ mszm2014, 8368 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 8369 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8370 volume = {40}, 8371 pages = {17--31}, 8372 year = {2014}, 8373 journal = {Parallel Computing}, 8374 doi = {10.1016/j.parco.2013.10.001}, 8375 petsc_uses = {KSP} 8376} 8377 8378@TechReport{ mszm2012, 8379 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 8380 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8381 year = {2012}, 8382 number = {ANL/MCS-P2097-0512}, 8383 institution = {Argonne National Laboratory}, 8384 petsc_uses = {KSP} 8385} 8386 8387@InProceedings{ bkmms2012, 8388 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 8389 F. Smith}, 8390 title = {Composable linear solvers for multiphysics}, 8391 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 8392 Computing} ({ISPDC} 2012)}, 8393 year = {2012}, 8394 doi = {10.1109/ISPDC.2012.16}, 8395 publisher = {IEEE Computer Society}, 8396 pages = {55--62}, 8397 petsc_uses = {KSP} 8398} 8399 8400@Article{ bourdinbucuroudet2009, 8401 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 8402 title = {Optimal Partitions for Eigenvalues}, 8403 journal = {SIAM J. Sci. Comput.}, 8404 volume = {31}, 8405 number = {6}, 8406 pages = {4100--4114}, 8407 year = {2009}, 8408 petsc_uses = {KSP} 8409} 8410 8411@InBook{ kimnbourdin2007, 8412 author = {J.-H. Kimn and Blaise Bourdin}, 8413 title = {Numerical implementation of overlapping balancing domain decomposition methods on 8414 unstructured meshes}, 8415 editor = {O. B. Widlund and D. E. Keyes}, 8416 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 8417 series = {Lecture Notes in Computational Science and Engineering}, 8418 number = {55}, 8419 publisher = {Springer-Verlag}, 8420 pages = {309--315}, 8421 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 8422 year = {2007}, 8423 petsc_uses = {KSP} 8424} 8425 8426@Article{ bjm2005, 8427 author = {AH Baker and ER Jessup and T Manteuffel}, 8428 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 8429 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 8430 year = {2005}, 8431 petsc_uses = {KSP} 8432} 8433 8434@Unpublished{ sundar-2008a, 8435 author = {R.S. Sampath and G. Biros}, 8436 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 8437 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8438 petsc_uses = {KSP} 8439} 8440 8441@Article{ sundar-2008, 8442 author = {H. Sundar and R.S. Sampath and G. Biros}, 8443 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 8444 journal = {SIAM Journal on Scientific Computing}, 8445 year = {2008}, 8446 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8447 petsc_uses = {KSP} 8448} 8449 8450@InProceedings{ sundar-2007, 8451 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8452 title = {Low-constant parallel algorithms for finite element simulations using linear 8453 octrees}, 8454 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 8455 year = {2007}, 8456 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8457 petsc_uses = {KSP} 8458} 8459 8460@InProceedings{ adams-98a, 8461 author = {Adams, Mark ~F.}, 8462 title = {A Parallel Maximal Independent Set Algorithm}, 8463 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 8464 year = {1998}, 8465 petsc_uses = {KSP} 8466} 8467 8468@Article{ akcelik2005ddd, 8469 title = {{Dynamic data-driven inversion for terascale simulations: real-time 8470 identification of airborne contaminants}}, 8471 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 8472 van Bloemen Waanders, B.}, 8473 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 8474 year = {2005}, 8475 publisher = {IEEE Computer Society Washington, DC, USA}, 8476 petsc_uses = {KSP} 8477} 8478 8479@InBook{ akcelik-2006, 8480 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 8481 Bloemen Waanders}, 8482 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 8483 title = {Frontiers of Parallel Computing}, 8484 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 8485 publisher = {SIAM}, 8486 year = {2006}, 8487 petsc_uses = {KSP} 8488} 8489 8490@Article{ dt, 8491 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 8492 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 8493 Convection Diffusion Equations}, 8494 journal = {The Journal of Supercomputing}, 8495 year = {2004}, 8496 pages = {235--253}, 8497 volume = {28}, 8498 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 8499 petsc_uses = {KSP} 8500} 8501 8502@PhDThesis{ hwang2004, 8503 author = {Feng-Nan Hwang}, 8504 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 8505 Computational Fluid Dynamics}, 8506 school = {University of Colorado at Boulder}, 8507 year = {2004}, 8508 petsc_uses = {KSP} 8509} 8510 8511@PhDThesis{ baker, 8512 author = {{A. H.} Baker}, 8513 title = {On improving the performance of the linear solver restarted {GMRES}}, 8514 school = {University of Colorado at Boulder}, 8515 year = {2003}, 8516 petsc_uses = {KSP} 8517} 8518 8519@TechReport{ klawonnrheinbach601, 8520 author = {Axel Klawonn and Oliver Rheinbach}, 8521 title = {A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional 8522 Linear Elasticity Using a Transformation of Basis}, 8523 institution = {Universit\"at Duisburg-Essen}, 8524 year = {2005}, 8525 type = {Technical Report}, 8526 number = {SM-E-601}, 8527 petsc_uses = {KSP} 8528} 8529 8530@TechReport{ klawonnrheinbach609, 8531 author = {Axel Klawonn and Oliver Rheinbach}, 8532 title = {Inexact FETI-DP Methods}, 8533 institution = {Universit\"at Duisburg-Essen}, 8534 year = {2005}, 8535 type = {Technical Report}, 8536 number = {SM-E-609}, 8537 petsc_uses = {KSP} 8538} 8539 8540@TechReport{ klawonnrheinbach607, 8541 author = {Axel Klawonn and Oliver Rheinbach}, 8542 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 8543 institution = {Universit\"at Duisburg-Essen}, 8544 year = {2005}, 8545 type = {Technical Report}, 8546 number = {SM-E-607}, 8547 petsc_uses = {KSP} 8548} 8549 8550@Article{ kul-natraj-pbp, 8551 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 8552 title = {Performance of a parallel mixed finite element implementation for fourth order 8553 clamped anisotropic plate bending problems in distributed memory environments}, 8554 journal = {Applied Mathematics and Computation}, 8555 volume = {155}, 8556 year = {2004}, 8557 number = {3}, 8558 pages = {753--777}, 8559 petsc_uses = {KSP} 8560} 8561 8562@Article{ bramkamp2006uej, 8563 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 8564 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 8565 journal = {Computers \& Fluids}, 8566 volume = {35}, 8567 number = {10}, 8568 pages = {1063--1073}, 8569 doi = {10.1016/j.compfluid.2005.10.003}, 8570 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 8571 derivation of the analytic flux Jacobian can become quite complicated depending on 8572 the complexity of the numerical flux calculation. Practically, the derivation of 8573 the exact Jacobian by hand is an unrealistic option because of the enormous 8574 man-hour investment needed. In this work, automatic differentiation is used to 8575 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 8576 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 8577 approximated by first-order forward differences. For a two-dimensional airfoil 8578 under three different flight conditions (quasi-incompressible flow, compressible 8579 subsonic flow, and transonic flow), we show that the robustness and performance of 8580 the present finite volume scheme is significantly improved by using exact 8581 Jacobians.}, 8582 year = {2006}, 8583 petsc_uses = {KSP} 8584} 8585 8586@Article{ shahbazi1, 8587 author = {Khosro Shahbazi}, 8588 title = {An explicit expression for the penalty parameter of the interior penalty method}, 8589 journal = {Journal of Computational Physics}, 8590 volume = {205}, 8591 year = {2005}, 8592 pages = {401--407}, 8593 petsc_uses = {KSP} 8594} 8595 8596@TechReport{ kk, 8597 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 8598 author = {Hans-Peter Kersken and Uwe Kuster}, 8599 year = {1999}, 8600 institution = {University of Stuttgart}, 8601 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 8602 number = {310}, 8603 petsc_uses = {KSP} 8604} 8605 8606@Article{ miha-mija, 8607 author = {M. D. Mihajlovi and S. Mijalkovi}, 8608 title = {A component decomposition preconditioning for 3D stress analysis problems}, 8609 journal = {Numerical Linear Algebra with Applications}, 8610 volume = {9}, 8611 year = {2002}, 8612 pages = {567--583}, 8613 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 8614 petsc_uses = {KSP} 8615} 8616 8617@Article{ bjm, 8618 author = {M Benzi and W Joubert and G Mateescu}, 8619 journal = {Electronic Transactions on Numerical Analysis}, 8620 year = {1999}, 8621 volume = {8}, 8622 pages = {88--114}, 8623 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 8624 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}, 8625 petsc_uses = {KSP} 8626} 8627 8628@PhDThesis{ hyde, 8629 author = {EMK Hyde}, 8630 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 8631 school = {Caltech}, 8632 year = {2003}, 8633 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 8634 petsc_uses = {KSP} 8635} 8636 8637@Article{ km2003, 8638 author = {A. Keese and H. G. Matthies}, 8639 journal = {Proceedings in Applied Mathematics and Mechanics}, 8640 year = {2003}, 8641 volume = {2}, 8642 pages = {485--486}, 8643 title = {Parallel Solution of Stochastic PDEs}, 8644 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 8645 petsc_uses = {KSP} 8646} 8647 8648@Article{ whszss, 8649 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 8650 and Otmar Scherzer and H. Siegfried Stiehl}, 8651 journal = {Real Time Imaging}, 8652 year = {2001}, 8653 volume = {7}, 8654 pages = {31--45}, 8655 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 8656 approaches}, 8657 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 8658 petsc_uses = {KSP} 8659} 8660 8661@TechReport{ baker1, 8662 title = {An Efficient Block Variant of GMRES}, 8663 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 8664 year = {2003}, 8665 type = {Technical Report}, 8666 institution = {University of Colorado, Boulder}, 8667 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 8668 number = {CU-CS-957-03}, 8669 petsc_uses = {KSP} 8670} 8671 8672@InProceedings{ mc2003, 8673 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 8674 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 8675 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8676 Methods}, 8677 pages = {639--646}, 8678 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8679 note = {}, 8680 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8681 year = {2003}, 8682 petsc_uses = {KSP} 8683} 8684 8685@InProceedings{ kt2003, 8686 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 8687 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 8688 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8689 Methods}, 8690 pages = {615--622}, 8691 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8692 note = {}, 8693 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8694 year = {2003}, 8695 petsc_uses = {KSP} 8696} 8697 8698@InProceedings{ krw2003, 8699 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 8700 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 8701 3D}, 8702 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8703 Methods}, 8704 pages = {361--368}, 8705 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8706 note = {}, 8707 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8708 year = {2003}, 8709 petsc_uses = {KSP} 8710} 8711 8712@InProceedings{ hc2003, 8713 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 8714 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 8715 Nonlinear Preconditioning}, 8716 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8717 Methods}, 8718 pages = {201--208}, 8719 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8720 note = {}, 8721 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8722 year = {2003}, 8723 petsc_uses = {KSP} 8724} 8725 8726@InProceedings{ g2003, 8727 author = {P. Goldfeld}, 8728 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 8729 (Generalized) {Stokes} and Parallel Implementation}, 8730 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8731 Methods}, 8732 pages = {209--216}, 8733 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8734 publisher = {National Autonomous University of Mexico (UNAM)}, 8735 note = {}, 8736 url = {http://www.ddm.org/DD14}, 8737 year = {2003}, 8738 petsc_uses = {KSP} 8739} 8740 8741@InProceedings{ dhv2003, 8742 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 8743 title = {Toward scalable FETI algorithm for variational inequalities with applications to 8744 composites}, 8745 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8746 Methods}, 8747 pages = {395--401}, 8748 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8749 publisher = {National Autonomous University of Mexico (UNAM)}, 8750 note = {}, 8751 url = {http://www.ddm.org/DD14}, 8752 year = {2003}, 8753 petsc_uses = {KSP} 8754} 8755 8756@InProceedings{ dhsv2002, 8757 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 8758 title = {Scalabilities of FETI for variational inequalities and contact shape 8759 optimization}, 8760 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8761 Methods}, 8762 pages = {359--367}, 8763 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8764 publisher = {CIMNE, Barcelona, Spain}, 8765 note = {}, 8766 url = {http://www.ddm.org/DD13}, 8767 year = {2002}, 8768 petsc_uses = {KSP} 8769} 8770 8771@InProceedings{ cky2002, 8772 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 8773 title = {A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked 8774 Duct Flows}, 8775 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8776 Methods}, 8777 pages = {343--350}, 8778 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8779 publisher = {CIMNE, Barcelona, Spain}, 8780 note = {}, 8781 url = {http://www.ddm.org/DD13}, 8782 year = {2002}, 8783 petsc_uses = {KSP} 8784} 8785 8786@Conference{ li-etal:03, 8787 author = {Li, Z. and Lanteri S. and Saad, Y.}, 8788 title = {Multiplicative-additive preconditioning combination for general sparse linear 8789 systems}, 8790 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 8791 Matrix Problems in Scientific and Industrial Applications}, 8792 address = {Napa, California, USA}, 8793 date = {october 27-29}, 8794 year = {2003}, 8795 petsc_uses = {KSP} 8796} 8797 8798@Article{ bashir2008hessian, 8799 title = {Hessian-based model reduction for large-scale systems with initial-condition 8800 inputs}, 8801 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 8802 J.}, 8803 journal = {International journal for numerical methods in engineering}, 8804 volume = {73}, 8805 number = {6}, 8806 pages = {844--868}, 8807 year = {2008}, 8808 publisher = {Wiley Online Library}, 8809 petsc_uses = {KSP} 8810} 8811 8812@Article{ bashir2007hessian, 8813 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 8814 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 8815 K.}, 8816 journal = {Computational Science--ICCS 2007}, 8817 pages = {1010--1017}, 8818 year = {2007}, 8819 publisher = {Springer}, 8820 petsc_uses = {KSP} 8821} 8822 8823@Article{ akcelik2011fast, 8824 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 8825 inverse problems based on low-rank partial {H}essian approximations}, 8826 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 8827 Waanders, B. and Wilcox, L.}, 8828 journal = {SIAM Journal on Scientific Computing}, 8829 volume = {33}, 8830 number = {1}, 8831 year = {2011}, 8832 petsc_uses = {KSP} 8833} 8834 8835@InProceedings{ ff2003, 8836 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 8837 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 8838 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 8839 year = {2003}, 8840 petsc_uses = {KSP} 8841} 8842 8843@InProceedings{ d2b2004, 8844 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 8845 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 8846 Ordering Strategies}, 8847 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 8848 year = {2004}, 8849 petsc_uses = {KSP} 8850} 8851 8852@InProceedings{ d2v2005, 8853 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8854 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 8855 Flow Equations}, 8856 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 8857 year = {2005}, 8858 petsc_uses = {KSP} 8859} 8860 8861@InProceedings{ dvs2006, 8862 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 8863 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 8864 Mixed Convection Equations}, 8865 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 8866 year = {2006}, 8867 petsc_uses = {KSP} 8868} 8869 8870@Article{ dsv2006, 8871 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8872 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 8873 Flow Equations}, 8874 journal = {Computational Fluid Dynamics}, 8875 year = {2006}, 8876 volume = {15}, 8877 number = {1}, 8878 petsc_uses = {KSP} 8879} 8880 8881@Article{ lahaye03, 8882 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 8883 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 8884 journal = {J. Comput. Appl. Math.}, 8885 year = {2004}, 8886 pages = {267--275}, 8887 volume = {168}, 8888 petsc_uses = {KSP} 8889} 8890 8891@TechReport{ brmn, 8892 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 8893 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 8894 year = {2002}, 8895 type = {Technical Report}, 8896 institution = {ANL}, 8897 number = {ANL/MCS-P993-0902}, 8898 note = {To appear in Future Generation Computer Systems}, 8899 petsc_uses = {KSP} 8900} 8901 8902@InProceedings{ mnbr, 8903 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 8904 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 8905 Algorithms}, 8906 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 8907 Mechanics}, 8908 year = {2003}, 8909 petsc_uses = {KSP} 8910} 8911 8912@InProceedings{ bmnr, 8913 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 8914 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 8915 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 8916 Applications, Lecture notes in Computer Science 2677}, 8917 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 8918 pages = {828--839}, 8919 year = {2003}, 8920 petsc_uses = {KSP} 8921} 8922 8923@Article{ ph03, 8924 author = {M. Pernice and R. D. Hornung}, 8925 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 8926 journal = {Computing and Visualization in Science}, 8927 year = {2003}, 8928 lab = {LANL}, 8929 petsc_uses = {KSP} 8930} 8931 8932@Article{ adams-02, 8933 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 8934 journal = {J. Comp. Phys.}, 8935 number = {2}, 8936 pages = {593-610}, 8937 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 8938 volume = {188}, 8939 year = {2003}, 8940 petsc_uses = {KSP} 8941} 8942 8943@InProceedings{ adams2001distributed, 8944 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 8945 smoothers}, 8946 author = {Adams, M.F.}, 8947 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 8948 pages = {14--14}, 8949 year = {2001}, 8950 organization = {IEEE}, 8951 petsc_uses = {KSP} 8952} 8953 8954@PhDThesis{ els01, 8955 author = {Ulrich Elsner}, 8956 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 8957 algorithms}, 8958 school = {Technical University Chemnitz}, 8959 year = {2002}, 8960 publisher = {Logos Verlag, Berlin}, 8961 isbn = {3-89722-923-4}, 8962 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 8963 different graph partitioning algorithms}, 8964 petsc_uses = {KSP} 8965} 8966 8967@TechReport{ ckk02, 8968 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 8969 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 8970 year = {2002}, 8971 type = {Technical Report}, 8972 institution = {ODU}, 8973 url = {http://www.math.odu.edu/\~{ }keyes}, 8974 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 8975 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 8976 Methods}, 8977 petsc_uses = {KSP} 8978} 8979 8980@Article{ gpw2002, 8981 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 8982 Heterogeneous Problems in Linear Elasticity}, 8983 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 8984 year = {2003}, 8985 pages = {283--324}, 8986 volume = {95}, 8987 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 8988 journal = {Numerische Mathematik}, 8989 petsc_uses = {KSP} 8990} 8991 8992@Article{ dh1, 8993 title = {Scalability and FETI based algorithm for large discretized variational 8994 inequalities}, 8995 author = {Z Dostal and D Horak}, 8996 year = {2003}, 8997 pages = {347--357}, 8998 volume = {61}, 8999 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 9000 journal = {Mathematics and Computers in Simulation}, 9001 petsc_uses = {KSP} 9002} 9003 9004@InProceedings{ dhsv1, 9005 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9006 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 9007 title = {36 Scalabilities of FETI for Variational Inequalities and Contact Shape 9008 Optimization}, 9009 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9010 Methods}, 9011 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9012 Kuznetsov}, 9013 petsc_uses = {KSP} 9014} 9015 9016@Article{ lahaye02, 9017 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 9018 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 9019 journal = {IEEEMAGN}, 9020 year = {2002}, 9021 volume = {38}, 9022 number = {2}, 9023 pages = {413-416}, 9024 petsc_uses = {KSP} 9025} 9026 9027@Article{ ckm01, 9028 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 9029 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 9030 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 9031 fluid dynamics}, 9032 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 9033 year = {2002}, 9034 volume = {40}, 9035 pages = {1463--1470}, 9036 petsc_uses = {KSP} 9037} 9038 9039@InProceedings{ cky01, 9040 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 9041 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 9042 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 9043 duct flow}, 9044 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9045 Methods}, 9046 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9047 Kuznetsov}, 9048 year = {2002}, 9049 petsc_uses = {KSP} 9050} 9051 9052@Article{ ck02, 9053 author = {X.-C. Cai and D. E. Keyes}, 9054 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 9055 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 9056 journal = {SIAM J. Sci. Comput.}, 9057 year = {2002}, 9058 pages = {183--200}, 9059 volume = {24}, 9060 petsc_uses = {KSP} 9061} 9062 9063@Article{ c04, 9064 author = {Feng-Nan Hwang and X.-C. Cai}, 9065 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 9066 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 9067 for incompressible {Navier-Stokes} equations}, 9068 journal = {Journal of Computational Physics}, 9069 year = {2005}, 9070 volume = {204}, 9071 pages = {666--691}, 9072 petsc_uses = {KSP} 9073} 9074 9075@Article{ hc06, 9076 author = {Feng-Nan Hwang and X.-C. Cai}, 9077 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 9078 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 9079 Algorithms}, 9080 journal = {Computer Methods in Applied Mechanics and Engineering}, 9081 year = {2006}, 9082 volume = {196}, 9083 pages = {1603--1611}, 9084 petsc_uses = {KSP} 9085} 9086 9087@InProceedings{ adams-01, 9088 author = {Mark F. Adams}, 9089 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 9090 Smoothers}, 9091 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 9092 address = {Denver, Colorado}, 9093 month = nov, 9094 year = {2001}, 9095 petsc_uses = {KSP} 9096} 9097 9098@Book{ 1dl, 9099 author = {Domenico Lahaye}, 9100 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 9101 Computations}, 9102 year = {2001}, 9103 publisher = {Katholieke Universiteit Leuven}, 9104 notes = {Thesis}, 9105 petsc_uses = {KSP} 9106} 9107 9108@Article{ adams-00, 9109 author = {Adams, M.~F.}, 9110 journal = {International Journal for Numerical Methods in Engineering}, 9111 number = {8}, 9112 pages = {1241-1262}, 9113 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 9114 Deformation Elasticity and Plasticity}, 9115 volume = {48}, 9116 year = {2000}, 9117 petsc_uses = {KSP} 9118} 9119 9120@Article{ adams2002evaluation, 9121 author = {Adams, M.~F.}, 9122 journal = {International Journal for Numerical Methods in Engineering}, 9123 number = {1}, 9124 pages = {519-534}, 9125 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 9126 Problems in Solid Mechanics}, 9127 volume = {55}, 9128 year = {2002}, 9129 petsc_uses = {KSP} 9130} 9131 9132@Article{ lahaye00, 9133 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 9134 title = {Algebraic Multigrid for Complex Symmetric Systems}, 9135 journal = {IEEEMAGN}, 9136 year = {2000}, 9137 volume = {36}, 9138 number = {4}, 9139 pages = {1535--1538}, 9140 petsc_uses = {KSP} 9141} 9142 9143@InProceedings{ adams-99c, 9144 author = {Mark F. Adams and J. Demmel}, 9145 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 9146 Finite Element Problems}, 9147 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 9148 address = {Portland, Oregon}, 9149 month = nov, 9150 year = {1999}, 9151 petsc_uses = {KSP} 9152} 9153 9154@Article{ chan95, 9155 author = {T. Chan and B. Smith and J. Zou}, 9156 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 9157 Grids}, 9158 journal = {Numer. Math.}, 9159 year = {1995}, 9160 volume = {73}, 9161 pages = {149--167}, 9162 petsc_uses = {KSP} 9163} 9164 9165@TechReport{ adams-csd-98-993, 9166 pages = {11}, 9167 year = {1998}, 9168 type = {Technical Report}, 9169 number = {CSD-98-993}, 9170 institution = {University of California, Berkeley}, 9171 title = {A Parallel Maximal Independent Set Algorithm}, 9172 bibdate = {March 11, 1998}, 9173 author = {Mark F. Adams and James Demmel}, 9174 abstract = {The parallel construction of maximal independent sets is a useful building block 9175 for many algorithms in the computational sciences, including graph coloring and 9176 multigrid coarse grid creation on unstructured meshes. We present an efficient 9177 asynchronous maximal independent set algorithm for use on parallel computers, for 9178 ``well partitioned'' graphs, that arise from finite element (FE) models. For 9179 appropriately partitioned bounded degree graphs, it is shown that the running time 9180 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 9181 improvement over the previous best P-RAM complexity for this class of graphs. We 9182 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 9183 model is indicative of the performance one can expect with practical partitions on 9184 graphs from FE problems.}, 9185 month = mar, 9186 petsc_uses = {KSP} 9187} 9188 9189@TechReport{ k676, 9190 year = {1994}, 9191 type = {Technical Report}, 9192 number = {TR1994-676}, 9193 institution = {New York University}, 9194 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 9195 Term}, 9196 author = {Axel Klawonn}, 9197 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 9198 petsc_uses = {KSP} 9199} 9200 9201@Book{ ak1, 9202 author = {Axel Klawonn}, 9203 title = {Preconditioners for Indefinite Problems}, 9204 year = {1995}, 9205 publisher = {Westfalishen Wilhelms-Universitat Munster}, 9206 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 9207 notes = {Thesis}, 9208 petsc_uses = {KSP} 9209} 9210 9211@TechReport{ knepleykarpeev05, 9212 pages = {41}, 9213 year = {2005}, 9214 type = {Technical Report}, 9215 number = {ANL/MCS-P1295-1005}, 9216 institution = {Argonne National Laboratory}, 9217 title = {Flexible Representation of Computational Meshes}, 9218 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9219 abstract = {}, 9220 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 9221 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 9222 month = oct, 9223 petsc_uses = {DMPlex} 9224} 9225 9226@TechReport{ knepleykarpeev07a, 9227 pages = {14}, 9228 year = {2007}, 9229 type = {Technical Report}, 9230 number = {ANL/MCS-P1455-0907}, 9231 institution = {Argonne National Laboratory}, 9232 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9233 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9234 abstract = {}, 9235 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 9236 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 9237 month = feb, 9238 petsc_uses = {DMPlex} 9239} 9240 9241@Article{ knepleykarpeev09, 9242 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9243 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9244 journal = {Scientific Programming}, 9245 volume = {17}, 9246 number = {3}, 9247 pages = {215--230}, 9248 year = {2009}, 9249 doi = {10.3233/SPR-2009-0249}, 9250 url = {http://arxiv.org/abs/0908.4427}, 9251 note = {\url{http://arxiv.org/abs/0908.4427}}, 9252 petsc_uses = {DMPlex} 9253} 9254 9255@Article{ biezuner2012computing, 9256 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 9257 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 9258 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 9259 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 9260 Sublinear Supersolutions}, 9261 journal = {Journal of Scientific Computing}, 9262 publisher = {Springer Netherlands}, 9263 issn = {0885-7474}, 9264 keyword = {Mathematics and Statistics}, 9265 pages = {180--201}, 9266 volume = {52}, 9267 issue = {1}, 9268 year = {2012}, 9269 doi = {10.1007/s10915-011-9540-0}, 9270 petsc_uses = {KSP} 9271} 9272 9273% LiteralHTML: 9274% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 9275% LiteralHTML: 9276@Book{ knepley2017, 9277 title = {Computational Science I}, 9278 author = {Matthew G. Knepley}, 9279 url = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}, 9280 note = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}}, 9281 publisher = {PETSc}, 9282 year = {2017}, 9283 petsc_uses = {KSP} 9284} 9285 9286@Article{ verleyeuser, 9287 title = {{User friendly permeability predicting software for technical textiles}}, 9288 author = {Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and 9289 Roose, D.}, 9290 journal = {status: published}, 9291 issn = {1560-6074}, 9292 publisher = {Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}, 9293 petsc_uses = {KSP} 9294} 9295 9296@Book{ pacheco, 9297 author = {Peter Pacheco}, 9298 title = {Parallel Programming with MPI}, 9299 year = {1997}, 9300 publisher = {Morgan-Kaufmann}, 9301 note = {Devotes a couple of sections to PETSc}, 9302 petsc_uses = {KSP} 9303} 9304 9305@Book{ 1sbg, 9306 author = {Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp}, 9307 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 9308 Differential Equations}, 9309 year = {1996}, 9310 publisher = {Cambridge University Press}, 9311 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 9312 petsc_uses = {KSP} 9313} 9314 9315@Misc{ petsc-fem:homepage, 9316 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 9317 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 9318 G. Rodriguez and G. Filippini}, 9319 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 9320 petsc_uses = {KSP} 9321} 9322 9323@Misc{ petsc4py-web-page, 9324 author = {Lisandro Dalcin}, 9325 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 9326 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 9327 note = {http://code.google.com/p/petsc4py/}, 9328 petsc_uses = {KSP} 9329} 9330 9331@Article{ libmeshpaper06, 9332 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 9333 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 9334 Simulations}}, 9335 journal = {Engineering with Computers}, 9336 volume = {22}, 9337 number = {3--4}, 9338 pages = {237--254}, 9339 year = {2006}, 9340 doi = {10.1007/s00366-006-0049-3}, 9341 petsc_uses = {KSP} 9342} 9343 9344@Misc{ sisiphus:homepage, 9345 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 9346 High-Resolution, Unstructured Simulations}, 9347 author = {T. {Tautges et al.}}, 9348 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 9349 petsc_uses = {KSP} 9350} 9351 9352@Misc{ pflotran:homepage, 9353 title = {{PFLOTRAN} project}, 9354 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 9355 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 9356 howpublished = {\url{http://pflotran.org/}}, 9357 petsc_uses = {KSP} 9358} 9359 9360@Misc{ pism:homepage, 9361 title = {{PISM}: A Parallel Ice Sheet Model}, 9362 author = {E. {Bueler et al.}}, 9363 howpublished = {\url{http://pism-docs.org}}, 9364 petsc_uses = {KSP} 9365} 9366 9367@Misc{ dohp:homepage, 9368 title = {Dohp: Dual order $hp$-finite elements}, 9369 author = {J. Brown}, 9370 howpublished = {\url{http://dohp.org}}, 9371 petsc_uses = {KSP} 9372} 9373 9374@Article{ mccourtrognlienetal12, 9375 title = {Improving parallel scalability for edge plasma transport simulations with neutral 9376 gas species}, 9377 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 9378 journal = {Computational Science and Discovery}, 9379 year = {2012}, 9380 volume = {5}, 9381 number = {014012}, 9382 doi = {10.1088/1749-4699/5/1/014012}, 9383 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 9384 2011)}, 9385 petsc_uses = {KSP} 9386} 9387 9388@Misc{ petclaw-github, 9389 title = {Pet{C}law Software}, 9390 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 9391 year = {2011}, 9392 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 9393 petsc_uses = {KSP} 9394} 9395 9396@Misc{ pyclaw-web-page, 9397 author = {Kyle T. Mandli and David I. Ketcheson and others}, 9398 title = {{PyClaw} software}, 9399 howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}}, 9400 url = {http://clawpack.github.io/doc/pyclaw/}, 9401 year = {2012}, 9402 petsc_uses = {KSP} 9403} 9404 9405@Article{ ketcheson2011highorder, 9406 title = {High-order wave propagation algorithms for general hyperbolic systems}, 9407 author = {Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.}, 9408 year = {2011}, 9409 note = {submitted}, 9410 petsc_uses = {KSP} 9411} 9412 9413@Article{ biros2005pln1, 9414 title = {{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained 9415 optimization. Part I: The {Krylov-Schur} solver}}, 9416 author = {Biros, G. and Ghattas, O.}, 9417 journal = {SIAM Journal on Scientific Computing}, 9418 volume = {27}, 9419 number = {2}, 9420 pages = {687--713}, 9421 year = {2005}, 9422 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9423 petsc_uses = {KSP} 9424} 9425 9426@Article{ biros2005pln2, 9427 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 9428 optimization. Part {II}: The {Lagrange Newton} solver, and its application to 9429 optimal control of steady viscous flows}, 9430 author = {Biros, G. and Ghattas, O.}, 9431 journal = {SIAM Journal on Scientific Computing}, 9432 volume = {27}, 9433 number = {2}, 9434 pages = {714--739}, 9435 year = {2005}, 9436 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9437 petsc_uses = {KSP} 9438} 9439 9440@Misc{ issm:homepage, 9441 title = {{I}ce {S}heet {S}ystem {M}odel}, 9442 author = {Eric Larour and Mathieu Morlighem and Helene Seroussi}, 9443 year = {2010}, 9444 note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}, 9445 petsc_uses = {KSP} 9446} 9447 9448@Article{ morlighem2010spatial, 9449 title = {Spatial patterns of basal drag inferred using control methods from a 9450 full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est 9451 {A}ntarctica}, 9452 author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and 9453 Aubry, D.}, 9454 journal = {Geophysical Research Letters}, 9455 volume = {37}, 9456 number = {14}, 9457 pages = {L14502}, 9458 year = {2010}, 9459 publisher = {American Geophysical Union}, 9460 petsc_uses = {KSP} 9461} 9462 9463@Article{ jardin2012plasmas, 9464 title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics 9465 of tokamak plasmas}, 9466 author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 9467 journal = {Computational Science \& Discovery}, 9468 volume = {5}, 9469 number = {1}, 9470 url = {http://stacks.iop.org/1749-4699/5/014002}, 9471 year = {2012}, 9472 petsc_uses = {KSP} 9473} 9474 9475@Article{ cmz2016, 9476 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 9477 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 9478 journal = {Journal of Scientific Computing}, 9479 publisher = {Springer}, 9480 pages = {803--825}, 9481 volume = {68}, 9482 issue = {2}, 9483 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 9484 doi = {10.1007/s10915-015-0159-4}, 9485 year = {2016}, 9486 note = {Also preprint ANL/MCS-P3039-0912}, 9487 petsc_uses = {KSP} 9488} 9489 9490@Article{ knepleybrownruppsmith13, 9491 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 9492 title = {Achieving High Performance with Unified Residual Evaluation}, 9493 journal = {ArXiv e-prints}, 9494 eprint = {1309.1204}, 9495 archiveprefix = {arXiv}, 9496 primaryclass = {cs.MS}, 9497 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 9498 Engineering, Finance, and Science}, 9499 year = {2013}, 9500 month = sep, 9501 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 9502 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9503 petsc_uses = {KSP} 9504} 9505 9506@Book{ fenicsbook, 9507 title = {Automated Solution of Differential Equations by the Finite Element Method: The 9508 FEniCS Book}, 9509 series = {Lecture Notes in Computational Science and Engineering}, 9510 volume = {84}, 9511 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 9512 publisher = {Springer}, 9513 isbn = {978-3-642-23098-1}, 9514 year = {2012}, 9515 petsc_uses = {KSP} 9516} 9517 9518@Article{ demidovahnertruppgottschling12, 9519 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 9520 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 9521 journal = {ArXiv e-prints}, 9522 archiveprefix = {arXiv}, 9523 eprint = {1212.6326}, 9524 primaryclass = {cs.MS}, 9525 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 9526 Parallel, and Cluster Computing, Physics - Computational Physics}, 9527 year = {2012}, 9528 month = dec, 9529 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 9530 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9531 petsc_uses = {KSP} 9532} 9533 9534@InProceedings{ viennacl, 9535 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 9536 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 9537 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 9538 year = {2010}, 9539 pages = {51-56}, 9540 petsc_uses = {KSP} 9541} 9542 9543@Article{ knepleybrownmcinnessmithruppadams2015, 9544 title = {Exascale Computing without Threads}, 9545 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9546 Karl Rupp and Mark Adams}, 9547 url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950}, 9548 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9549 Scientific Software Architecture for Portability and Performance}, 9550 doi = {10.6084/m9.figshare.5824950.v1}, 9551 year = {2015}, 9552 petsc_uses = {KSP} 9553} 9554 9555@Article{ knepleybrownmcinnessmithruppadams2015b, 9556 title = {Overview of the {PETSc} Library}, 9557 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9558 Karl Rupp and Mark Adams}, 9559 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 9560 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9561 Scientific Software Architecture for Portability and Performance}, 9562 year = {2015}, 9563 petsc_uses = {KSP} 9564} 9565 9566@InBook{ balaybrownknepleymcinnessmith2015, 9567 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 9568 Smith}, 9569 bookeditor = {J. Carver}, 9570 title = {Software Engineering for Science}, 9571 chapter = {Providing Mixed Language and Legacy Support within a Library}, 9572 publisher = {Taylor \& Francis}, 9573 year = {2015}, 9574 petsc_uses = {KSP} 9575} 9576 9577@Article{ ruppbalaybrownknepleymcinnessmith2015, 9578 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 9579 Software}, 9580 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 9581 McInnes and Barry F. Smith}, 9582 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 9583 Productivity Challenges}, 9584 journal = {ArXiv e-prints}, 9585 archiveprefix = {arXiv}, 9586 eprint = {1510.01122}, 9587 year = {2015}, 9588 petsc_uses = {KSP} 9589} 9590 9591@InProceedings{ knepley2013accurately, 9592 title = {Accurately Citing Software and Algorithms Used in Publications}, 9593 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 9594 F.}, 9595 year = {2013}, 9596 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 9597 (WSSSPE), held at SC13}, 9598 doi = {10.6084/m9.figshare.785731}, 9599 petsc_uses = {KSP} 9600} 9601 9602@InProceedings{ milleretal2013, 9603 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 9604 Strategies Developed for {FASTMath}}, 9605 author = {Mark C. 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Russo}, 10138 journal = {Journal of Scientific Computing}, 10139 year = {2005}, 10140 number = {1}, 10141 pages = {129--155}, 10142 volume = {25} 10143} 10144 10145@Article{ kennedy_2003, 10146 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 10147 author = {C.A. Kennedy and M.H. Carpenter}, 10148 journal = {Appl. Numer. Math.}, 10149 year = {2003}, 10150 number = {1-2}, 10151 pages = {139--181}, 10152 volume = {44}, 10153 doi = {10.1016/S0168-9274(02)00138-1}, 10154 publisher = {Elsevier Science Publishers B. 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Spiteri}, 10169 journal = {Applied Numerical Mathematics}, 10170 year = {1997}, 10171 pages = {151--167}, 10172 volume = {25} 10173} 10174 10175@Book{ ascherpetzold1998, 10176 title = {Computer methods for ordinary differential equations and differential-algebraic 10177 equations}, 10178 author = {Uri M Ascher and Linda R Petzold}, 10179 volume = {61}, 10180 publisher = {SIAM}, 10181 year = {1998} 10182} 10183 10184@Article{ colomesbadia2016, 10185 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 10186 equations}, 10187 author = {Oriol Colom{\'e}s and Santiago Badia}, 10188 journal = {International Journal for Numerical Methods in Engineering}, 10189 volume = {105}, 10190 number = {5}, 10191 pages = {372--400}, 10192 year = {2016} 10193} 10194 10195@Article{ sandu_1997, 10196 title = {Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: 10197 {R}osenbrock solvers}, 10198 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. 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Ketcheson and Chi Wang Shu}, 10233 title = {{High order strong stability preserving time discretizations}}, 10234 journal = {Journal of Scientific Computing}, 10235 volume = {38}, 10236 number = {3}, 10237 pages = {251--289}, 10238 doi = {10.1007/s10915-008-9239-z}, 10239 year = {2009} 10240} 10241 10242@Article{ ketcheson_2008, 10243 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 10244 Low-Storage Implementations}, 10245 author = {D.I. Ketcheson}, 10246 journal = {SIAM Journal on Scientific Computing}, 10247 year = {2008}, 10248 number = {4}, 10249 pages = {2113--2136}, 10250 volume = {30}, 10251 doi = {10.1137/07070485X}, 10252 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 10253 RungeKutta methods}, 10254 publisher = {SIAM} 10255} 10256 10257@Article{ jansen_2000, 10258 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 10259 equations with a stabilized finite element method}, 10260 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 10261 journal = {Computer Methods in Applied Mechanics and Engineering}, 10262 year = {2000}, 10263 number = {3}, 10264 pages = {305--319}, 10265 volume = {190}, 10266 publisher = {Elsevier} 10267} 10268 10269@Article{ butcher_2007, 10270 title = {Error propagation of general linear methods for ordinary differential equations}, 10271 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 10272 journal = {Journal of Complexity}, 10273 year = {2007}, 10274 number = {4-6}, 10275 pages = {560--580}, 10276 volume = {23}, 10277 abstract = {We discuss error propagation for general linear methods for ordinary differential 10278 equations up to terms of order p+2, where p is the order of the method. These 10279 results are then applied to the estimation of local discretization errors for 10280 methods of order p and for the adjacent order p+1. The results of numerical 10281 experiments confirm the reliability of these estimates. This research has 10282 applications in the design of robust stepsize and order changing strategies for 10283 algorithms based on general linear methods.}, 10284 doi = {10.1016/j.jco.2007.01.009}, 10285 issn = {0885-064X} 10286} 10287 10288@Article{ constantinescu_a2010a, 10289 title = {Extrapolated implicit-explicit time stepping}, 10290 author = {E.M. Constantinescu and A. Sandu}, 10291 journal = {SIAM Journal on Scientific Computing}, 10292 year = {2010}, 10293 number = {6}, 10294 pages = {4452-4477}, 10295 volume = {31}, 10296 comment = {Preprint \# ANL/MCS-P1612-0409}, 10297 doi = {10.1137/080732833} 10298} 10299 10300@InProceedings{ devito2011liszt, 10301 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 10302 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 10303 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 10304 Aiken, Alex and Duraisamy, Karthik and others}, 10305 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 10306 Networking, Storage and Analysis}, 10307 pages = {9}, 10308 year = {2011}, 10309 organization = {ACM} 10310} 10311 10312@Article{ devito2011designing, 10313 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 10314 author = {DeVito, Zachary and Hanrahan, Pat}, 10315 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 10316 year = {2011} 10317} 10318 10319@Misc{ pgasintro, 10320 author = {Tim Stitt}, 10321 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 10322 Model}, 10323 note = {\url{http://cnx.org/content/m20649/latest/}} 10324} 10325 10326@InProceedings{ el2006upc, 10327 title = {UPC: unified parallel C}, 10328 author = {El-Ghazawi, Tarek and Smith, Lauren}, 10329 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 10330 pages = {27}, 10331 year = {2006}, 10332 organization = {ACM} 10333} 10334 10335@InProceedings{ numrich1998co, 10336 title = {Co-Array Fortran for parallel programming}, 10337 author = {Numrich, Robert W and Reid, John}, 10338 booktitle = {ACM Sigplan Fortran Forum}, 10339 volume = {17}, 10340 number = {2}, 10341 pages = {1--31}, 10342 year = {1998}, 10343 organization = {ACM} 10344} 10345 10346@Article{ aiken1997titanium, 10347 title = {Titanium: A high-performance Java dialect}, 10348 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 10349 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 10350 Geoff and Semenzato, Luigi and others}, 10351 year = {1997} 10352} 10353 10354@Article{ charles2005x10, 10355 title = {X10: an object-oriented approach to non-uniform cluster computing}, 10356 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 10357 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 10358 Sarkar, Vivek}, 10359 journal = {Acm Sigplan Notices}, 10360 volume = {40}, 10361 number = {10}, 10362 pages = {519--538}, 10363 year = {2005}, 10364 publisher = {ACM} 10365} 10366 10367@Article{ chamberlain2007parallel, 10368 title = {Parallel programmability and the chapel language}, 10369 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 10370 journal = {International Journal of High Performance Computing Applications}, 10371 volume = {21}, 10372 number = {3}, 10373 pages = {291--312}, 10374 year = {2007}, 10375 publisher = {SAGE Publications} 10376} 10377 10378@InProceedings{ charmppoopsla93, 10379 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 10380 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 10381 editor = {Paepcke, A.}, 10382 fulleditor = {Paepcke, Andreas}, 10383 pages = {91--108}, 10384 month = sep, 10385 year = {1993}, 10386 booktitle = {{Proceedings of OOPSLA'93}}, 10387 publisher = {{ACM Press}} 10388} 10389 10390@InProceedings{ hewitt1973universal, 10391 title = {A universal modular actor formalism for artificial intelligence}, 10392 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 10393 booktitle = {Proceedings of the 3rd international joint conference on Artificial 10394 intelligence}, 10395 pages = {235--245}, 10396 year = {1973}, 10397 organization = {Morgan Kaufmann Publishers Inc.} 10398} 10399 10400@Book{ yonezawa1990abcl, 10401 title = {ABCL: an object-oriented concurrent system}, 10402 author = {Yonezawa, Akinori}, 10403 year = {1990}, 10404 publisher = {MIT press} 10405} 10406 10407@InProceedings{ dally1988object, 10408 title = {Object-oriented concurrent programming in CST}, 10409 author = {Dally, William J and Chien, Andrew A}, 10410 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 10411 applications: Architecture, software, computer systems, and general issues-Volume 10412 1}, 10413 pages = {434--439}, 10414 year = {1988}, 10415 organization = {ACM} 10416} 10417 10418@Article{ grimshaw1993easy, 10419 title = {Easy-to-use object-oriented parallel processing with Mentat}, 10420 author = {Grimshaw, Andrew S.}, 10421 journal = {Computer}, 10422 volume = {26}, 10423 number = {5}, 10424 pages = {39--51}, 10425 year = {1993}, 10426 publisher = {IEEE} 10427} 10428 10429@InProceedings{ gannon1991object, 10430 title = {Object oriented parallelism: pC++ ideas and experiments}, 10431 author = {Gannon, Dennis and Lee, JK}, 10432 booktitle = {Proceedings of}, 10433 pages = {13--23}, 10434 year = {1991} 10435} 10436 10437@InProceedings{ lau1992object, 10438 title = {An object-oriented class library for scalable parallel heuristic search}, 10439 author = {Lau, Wing-cheong and Singh, Vineet}, 10440 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 10441 pages = {252--267}, 10442 year = {1992}, 10443 organization = {Springer} 10444} 10445 10446@Book{ chase1989amber, 10447 title = {The Amber system: Parallel programming on a network of multiprocessors}, 10448 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 10449 Littlefield, Richard}, 10450 volume = {23}, 10451 number = {5}, 10452 year = {1989}, 10453 publisher = {ACM} 10454} 10455 10456@InProceedings{ kaiser2009parallex, 10457 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 10458 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 10459 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 10460 pages = {394--401}, 10461 year = {2009}, 10462 organization = {IEEE} 10463} 10464 10465@TechReport{ ipm, 10466 author = {Barry F. Smith}, 10467 title = {A New Parallel Programming Model for Computer Simulation}, 10468 institution = {Argonne National Laboratory}, 10469 year = {2014}, 10470 number = {ANL/MCS-P5135-0414} 10471} 10472 10473@Article{ groppsnir, 10474 author = {William Gropp and Marc Snir}, 10475 title = {Programming for Exascale Computers}, 10476 journal = {Computing in Science and Engineering}, 10477 volume = {15}, 10478 number = {6}, 10479 issn = {1521-9615}, 10480 year = {2013}, 10481 pages = {27-35}, 10482 doi = {10.1109/MCSE.2013.96}, 10483 publisher = {IEEE Computer Society}, 10484 address = {Los Alamitos, CA} 10485} 10486 10487@Book{ mpi3, 10488 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 10489 author = {Message Passing Interface Forum}, 10490 year = {2012}, 10491 publisher = {High Performance Computing Center Stuttgart (HLRS)} 10492} 10493 10494@Book{ openmp4, 10495 title = {OpenMP Application Program Interface, Version 4.0}, 10496 year = {2013}, 10497 publisher = {OpenMP Architecture Review Board} 10498} 10499 10500@InProceedings{ hartono2009annotation, 10501 title = {Annotation-based empirical performance tuning using {Orio}}, 10502 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 10503 booktitle = {Parallel \& Distributed Processing, 2009. IPDPS 2009. IEEE International 10504 Symposium on}, 10505 pages = {1--11}, 10506 year = {2009}, 10507 organization = {IEEE} 10508} 10509 10510@Book{ toselli2005domain, 10511 title = {Domain Decomposition Methods: Algorithms and Theory}, 10512 author = {Toselli, Andrea and Widlund, Olof B}, 10513 volume = {34}, 10514 year = {2005}, 10515 publisher = {Springer} 10516} 10517 10518@InBook{ st2016, 10519 author = {Barry F. Smith and Xumin Tu}, 10520 chapter = {Domain Decomposition}, 10521 title = {Encyclopedia of Applied and Computational Mathematics}, 10522 bookeditor = {B. Engquist}, 10523 publisher = {Springer}, 10524 pages = {375--381}, 10525 year = {2016} 10526} 10527 10528@TechReport{ saws, 10529 author = {Matt Otten and Jed Brown and Barry F. Smith}, 10530 title = {Scientific Application Web Server {(SAWs)} Users Manual}, 10531 institution = {Argonne National Laboratory}, 10532 year = {2013} 10533} 10534 10535@Article{ smith1997domain, 10536 title = {Domain Decomposition Methods for Partial Differential Equations}, 10537 author = {Smith, B.F.}, 10538 journal = {ICASE LARC Interdisciplinary Series in Science and Engineering}, 10539 volume = {4}, 10540 pages = {225--244}, 10541 year = {1997}, 10542 publisher = {Citeseer} 10543} 10544 10545@Article{ spillane2011abstract, 10546 title = {Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems 10547 in the overlaps}, 10548 author = {Spillane, N and Dolean, V and Hauret, P and Nataf, F and Pechstein, C and 10549 Scheichl, R}, 10550 journal = {NuMa-Report}, 10551 volume = {7}, 10552 pages = {2007}, 10553 year = {2011} 10554} 10555 10556@InProceedings{ jolivet2013scalabledd, 10557 title = {Scalable domain decomposition preconditioners for heterogeneous elliptic 10558 problems}, 10559 author = {Jolivet, Pierre and Hecht, Fr{\'e}d{\'e}ric and Nataf, Fr{\'e}d{\'e}ric and 10560 Prud'homme, Christophe}, 10561 booktitle = {Proceedings of SC13: International Conference for High Performance Computing, 10562 Networking, Storage and Analysis}, 10563 pages = {80}, 10564 year = {2013}, 10565 organization = {ACM} 10566} 10567 10568@Book{ ks2000, 10569 author = {D. Kinderlehrer and G. Stampacchia}, 10570 publisher = {Society for Industrial Mathematics}, 10571 title = {An Introduction to Variational Inequalities and Their Applications}, 10572 year = {2000} 10573} 10574 10575@Article{ wan2000energy, 10576 title = {An energy-minimizing interpolation for robust multigrid methods}, 10577 author = {Wan, W.L. and Chan, T.F. and Smith, B. F.}, 10578 journal = {SIAM Journal on Scientific Computing}, 10579 volume = {21}, 10580 number = {4}, 10581 pages = {1632--1649}, 10582 year = {2000}, 10583 publisher = {Philadelphia, PA: SIAM, c1993-} 10584} 10585 10586@Article{ chansmith1994, 10587 title = {Domain decomposition and multigrid algorithms for elliptic problems on 10588 unstructured meshes}, 10589 author = {Chan, T.F. and Smith, B.F.}, 10590 journal = {Electronic Transactions on Numerical Analysis}, 10591 volume = {2}, 10592 pages = {171--182}, 10593 year = {1994} 10594} 10595 10596@TechReport{ proto-fsp, 10597 author = {Venkatramani Balaji and Barry Smith and Brian Van Straalen and Priya Vashishta 10598 and Michael Zarnstorff and Michael Zika}, 10599 title = {Report of the {Proto-FSP} {Assessment Panel for the FSP}}, 10600 institution = {Princeton Plasma Physics Laboratory}, 10601 year = {2010}, 10602 url = {http://www.pppl.gov/fsp/documents/Proto-FSPAssessmentReport.pdf} 10603} 10604 10605@Article{ hirvijoki2021, 10606 title = {Structure-preserving marker-particle discretizations of {Coulomb} collisions for 10607 particle-in-cell codes}, 10608 journal = {Plasma Phys. Control. Fusion}, 10609 author = {Eero Hirvijoki}, 10610 note = {in press}, 10611 doi = {10.1088/1361-6587/abe884}, 10612 year = {2021} 10613} 10614 10615@Article{ ipsen2001, 10616 author = {Ilse C. F. Ipsen}, 10617 journal = {SIAM J. Sci. Comput.}, 10618 pages = {1050--1051}, 10619 volume = {23}, 10620 publisher = {SIAM}, 10621 title = {A Note on Preconditioning Nonsymmetric Matrices}, 10622 year = {2001} 10623} 10624 10625% Random papers on solvers for GPUs 10626@InProceedings{ gpus-suck, 10627 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. }, 10628 title = { On the Limits of {GPU} Acceleration}, 10629 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism}, 10630 year = {2010}, 10631 publisher = {USENIX} 10632} 10633 10634@InProceedings{ 882364, 10635 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter}, 10636 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid}, 10637 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers}, 10638 year = {2003}, 10639 isbn = {1-58113-709-5}, 10640 pages = {917--924}, 10641 location = {San Diego, California}, 10642 doi = {10.1145/1201775.882364}, 10643 publisher = {ACM}, 10644 address = {New York, NY} 10645} 10646 10647@Conference{ feng2008multigrid, 10648 author = {Feng, Z. and Li, P.}, 10649 booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008}, 10650 date-added = {2010-08-19 15:57:06 -0500}, 10651 date-modified = {2010-08-19 15:57:06 -0500}, 10652 pages = {647--654}, 10653 title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms}, 10654 year = {2008} 10655} 10656 10657@Conference{ goodnight2003multigrid, 10658 author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.}, 10659 booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware}, 10660 date-added = {2010-08-19 15:45:20 -0500}, 10661 date-modified = {2010-08-19 15:45:20 -0500}, 10662 organization = {Eurographics Association}, 10663 pages = {102--111}, 10664 title = {A multigrid solver for boundary value problems using programmable graphics 10665 hardware}, 10666 year = {2003} 10667} 10668 10669@Article{ buatois2007concurrent, 10670 author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.}, 10671 date-added = {2010-08-19 15:45:02 -0500}, 10672 date-modified = {2010-08-19 15:45:02 -0500}, 10673 journal = {High Performance Computing and Communications}, 10674 pages = {358--371}, 10675 publisher = {Citeseer}, 10676 title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}}, 10677 year = {2007} 10678} 10679 10680@Article{ joldes2010real, 10681 author = {Joldes, G.R. and Wittek, A. and Miller, K.}, 10682 date-added = {2010-08-19 15:44:41 -0500}, 10683 date-modified = {2010-08-19 15:44:41 -0500}, 10684 journal = {Computer Methods in Applied Mechanics and Engineering}, 10685 publisher = {Elsevier}, 10686 title = {Real-time nonlinear finite element computations on {GPU}-application to 10687 neurosurgical simulation}, 10688 year = {2010} 10689} 10690 10691@Misc{ aharon2005gpu, 10692 author = {Aharon, S.}, 10693 date-added = {2010-08-19 15:44:32 -0500}, 10694 date-modified = {2010-08-19 15:44:32 -0500}, 10695 month = apr, 10696 note = {US Patent App. 11/115,642}, 10697 publisher = {Google Patents}, 10698 title = {{GPU}-based Finite Element}, 10699 year = {2005} 10700} 10701 10702@Article{ cevahir2009fast, 10703 author = {Cevahir, A. and Nukada, A. and Matsuoka, S.}, 10704 date-added = {2010-08-19 15:44:01 -0500}, 10705 date-modified = {2010-08-19 15:44:01 -0500}, 10706 journal = {Computational Science--ICCS 2009}, 10707 pages = {893--903}, 10708 publisher = {Springer}, 10709 title = {Fast conjugate gradients with multiple {GPU}s}, 10710 year = {2009} 10711} 10712 10713@Article{ maier1995symmetric, 10714 author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.}, 10715 date-added = {2010-08-19 15:43:57 -0500}, 10716 date-modified = {2010-08-19 15:43:57 -0500}, 10717 journal = {Computational Mechanics}, 10718 number = {1}, 10719 pages = {115--129}, 10720 publisher = {Springer}, 10721 title = {Symmetric {G}alerkin boundary element method in plasticity and gradient 10722 plasticity}, 10723 volume = {17}, 10724 year = {1995} 10725} 10726 10727@Article{ corrigan-running, 10728 author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.}, 10729 date-added = {2010-08-19 15:43:47 -0500}, 10730 date-modified = {2010-08-19 15:43:47 -0500}, 10731 journal = {International Journal for Numerical Methods in Fluids}, 10732 publisher = {John Wiley \& Sons}, 10733 title = {Running unstructured grid based CFD solvers on modern graphics hardware} 10734} 10735 10736@InProceedings{ volkov08, 10737 author = {Vasily Volkov and James W. Demmel}, 10738 title = {Benchmarking GPUs to tune dense linear algebra}, 10739 booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)}, 10740 note = {\url{http://mc.stanford.edu/cgi-bin/images/6/65/SC08_Volkov_GPU.pdf}}, 10741 year = {2008} 10742} 10743 10744@TechReport{ cray-mvmult, 10745 author = {Guy~E. Blelloch and Michael~A. Heroux and Marco Zagha}, 10746 title = {Segmented Operations for Sparse Matrix Computation on Vector Multiprocessors}, 10747 institution = {School of Computer Science, Carnegie Mellon University}, 10748 number = {CMU-CS-93-173}, 10749 month = aug, 10750 year = {1993} 10751} 10752 10753@Conference{ bell2009implementing, 10754 author = {Bell, N. and Garland, M.}, 10755 booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage 10756 and Analysis}, 10757 date-added = {2010-08-19 15:43:42 -0500}, 10758 date-modified = {2010-08-19 15:43:42 -0500}, 10759 organization = {ACM}, 10760 pages = {1--11}, 10761 title = {Implementing sparse matrix-vector multiplication on throughput-oriented 10762 processors}, 10763 year = {2009} 10764} 10765 10766@Article{ bell2008efficient, 10767 author = {Bell, N. and Garland, M.}, 10768 date-added = {2010-08-19 15:43:36 -0500}, 10769 date-modified = {2010-08-19 15:43:36 -0500}, 10770 journal = {{NVIDIA} Corporation, {NVIDIA} Technical Report NVR-2008-004}, 10771 title = {Efficient sparse matrix-vector multiplication on {CUDA}}, 10772 year = {2008} 10773} 10774 10775@Article{ cohen-fast, 10776 author = {Cohen, J. and Molemaker, M.J.}, 10777 date-added = {2010-08-19 15:43:34 -0500}, 10778 date-modified = {2010-08-19 15:43:34 -0500}, 10779 journal = {Parallel Computational Fluid Dynamics: Recent Advances and Future Directions}, 10780 pages = {414}, 10781 publisher = {DEStech Publications}, 10782 title = {A fast double precision CFD code using CUDA} 10783} 10784 10785@Article{ kazhdan2008streaming, 10786 author = {Kazhdan, M. and Hoppe, H.}, 10787 date-added = {2010-08-19 15:43:32 -0500}, 10788 date-modified = {2010-08-19 15:43:32 -0500}, 10789 journal = {ACM Transactions on Graphics (TOG)}, 10790 number = {3}, 10791 pages = {21}, 10792 publisher = {ACM}, 10793 title = {Streaming multigrid for gradient-domain operations on large images}, 10794 volume = {27}, 10795 year = {2008} 10796} 10797 10798@Article{ bonnet1998symmetric, 10799 author = {Bonnet, M. and Maier, G. and Polizzotto, C.}, 10800 date-added = {2010-08-19 15:43:18 -0500}, 10801 date-modified = {2010-08-19 15:43:18 -0500}, 10802 journal = {Appl. Mech. Rev}, 10803 pages = {669--704}, 10804 title = {Symmetric {G}alerkin boundary element method.}, 10805 volume = {51}, 10806 year = {1998} 10807} 10808 10809@Conference{ zamith2007gpu, 10810 author = {Zamith, M. and Clua, E. and Pagliosa, P. and Conci, A. and Montenegro, A. and 10811 Valente, L.}, 10812 booktitle = {Proceedings of the VI Brazilian Symposium on Computer Games and Digital 10813 Entertainment}, 10814 date-added = {2010-08-19 15:43:14 -0500}, 10815 date-modified = {2010-08-19 15:43:14 -0500}, 10816 pages = {37--43}, 10817 title = {The {GPU} used as a math co-processor in real time applications}, 10818 year = {2007} 10819} 10820 10821@Article{ baskaran2009optimizing, 10822 author = {Baskaran, M.M. and Bordawekar, R.}, 10823 date-added = {2010-08-19 15:42:56 -0500}, 10824 date-modified = {2010-08-19 15:42:56 -0500}, 10825 journal = {IBM Research Report RC24704, IBM}, 10826 title = {Optimizing sparse matrix-vector multiplication on {GPU}s}, 10827 year = {2009} 10828} 10829 10830@Misc{ szeliski2006locally, 10831 author = {Szeliski, R.}, 10832 date-added = {2010-08-19 15:42:45 -0500}, 10833 date-modified = {2010-08-19 15:42:45 -0500}, 10834 month = jul, 10835 note = {US Patent App. 11/459,724}, 10836 publisher = {Google Patents}, 10837 title = {Locally adapted hierarchical basis preconditioning}, 10838 year = {2006} 10839} 10840 10841@Article{ jung2006cholesky, 10842 author = {Jung, J.H. and O'Leary, D.P.}, 10843 date-added = {2010-08-19 15:42:34 -0500}, 10844 date-modified = {2010-08-19 15:42:34 -0500}, 10845 journal = {Scholarly Paper, University of Maryland}, 10846 publisher = {Citeseer}, 10847 title = {Cholesky decomposition and linear programming on a {GPU}}, 10848 year = {2006} 10849} 10850 10851@Conference{ filipovic2009gpu, 10852 author = {Filipovic, J. and Peterlik, I. and Fousek, J.}, 10853 booktitle = {SAAHPC: Symposium on Application Accelerators in HPC}, 10854 date-added = {2010-08-19 15:42:33 -0500}, 10855 date-modified = {2010-08-19 15:42:33 -0500}, 10856 title = {{GPU} Acceleration of Equations Assembly in Finite Elements Method-Preliminary 10857 Results}, 10858 year = {2009} 10859} 10860 10861@Article{ taylor2009modelling, 10862 author = {Taylor, ZA and Comas, O. and Cheng, M. and Passenger, J. and Hawkes, DJ and 10863 Atkinson, D. and Ourselin, S.}, 10864 date-added = {2010-08-19 15:42:23 -0500}, 10865 date-modified = {2010-08-19 15:42:23 -0500}, 10866 journal = {Medical Image Analysis}, 10867 number = {2}, 10868 pages = {234--244}, 10869 publisher = {Elsevier}, 10870 title = {On modelling of anisotropic viscoelasticity for soft tissue simulation: Numerical 10871 solution and {GPU} execution}, 10872 volume = {13}, 10873 year = {2009} 10874} 10875 10876@Conference{ owens2007survey, 10877 author = {Owens, J.D. and Luebke, D. and Govindaraju, N. and Harris, M. and Kr{\\"u}ger, J. 10878 and Lefohn, A.E. and Purcell, T.J.}, 10879 booktitle = {Computer Graphics Forum}, 10880 date-added = {2010-08-19 15:42:21 -0500}, 10881 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Karpeyev}, 11555 title = {Geometric Integrators for Hamiltonian PDEs}, 11556 school = {Old Dominion University}, 11557 year = {2002} 11558} 11559 11560@InCollection{ fjp:ima, 11561 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 11562 title = {The Scalability of Mesh Improvement Algorithms}, 11563 booktitle = {Algorithms for Parallel Processing}, 11564 publisher = {Springer-Verlag}, 11565 volume = {105}, 11566 series = {The IMA Volumes in Mathematics and Its Applications}, 11567 editor = {Michael T.\ Heath and Abhiram Ranade and Robert S.\ Schreiber}, 11568 year = {1998}, 11569 pages = {185--212} 11570} 11571 11572@InProceedings{ poet, 11573 author = {Rob Armstrong and Alex Cheung}, 11574 title = {{POET} ({P}arallel {O}bject-Oriented {E}nvironment and {T}oolkit) and Frameworks 11575 for Scientific Distributed Computing}, 11576 booktitle = {Proceedings of {HICSS97}}, 11577 year = {1997} 11578} 11579 11580@Misc{ pseware-web-page, 11581 author = {}, 11582 title = {{PSEware} {Web} page}, 11583 note = {\url{http://www.extreme.indiana.edu/pseware}, Indiana University}, 11584 key = {{PSEware} {Web} page} 11585} 11586 11587@Article{ epperly2011high, 11588 title = {High-performance language interoperability for scientific computing through 11589 {B}abel}, 11590 author = {Epperly, Thomas GW and Kumfert, Gary and Dahlgren, Tamara and Ebner, Dietmar and 11591 Leek, Jim and Prantl, Adrian and Kohn, Scott}, 11592 journal = {International Journal of High Performance Computing Applications}, 11593 pages = {1094342011414036}, 11594 year = {2011}, 11595 publisher = {SAGE Publications} 11596} 11597 11598@Misc{ babel-web-page, 11599 author = {Tom Epperly and Tamara Dahlgren and Gary Kumfert}, 11600 title = {{Babel} {Web} page}, 11601 note = {\url{http://www.llnl.gov/CASC/components/babel.html}} 11602} 11603 11604@Misc{ infospheres-web-page, 11605 author = {K.~M. {Chandy et al.}}, 11606 title = {{Infospheres} {W}eb page}, 11607 note = {\url{http://www.infospheres.caltech.edu}}, 11608 key = {{Infospheres} {Web} page} 11609} 11610 11611@Misc{ hammond, 11612 author = {Glenn Hammond}, 11613 title = {{Sandia National Laboratory}, {C}omputations on {R}eactive {F}low, private 11614 communication} 11615} 11616 11617@Misc{ ornl, 11618 author = {Oak Ridge National Laboratory}, 11619 title = {Private communication via petsc-maint email support} 11620} 11621 11622@Unpublished{ cumulvs-web-page, 11623 author = {}, 11624 title = {{Cumulvs} {W}eb page}, 11625 note = {http://www.epm.ornl.gov/cs/cumulvs.html}, 11626 key = {{Cumulvs} {W}eb page} 11627} 11628 11629@Article{ nonlineargmres, 11630 author = {T. 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Markus}, 11696 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 11697 for {PDE} Based Applications}, 11698 year = {1994}, 11699 institution = {Department of Computer Sciences, Purdue University}, 11700 number = {CSD-TR-94-021} 11701} 11702 11703@Unpublished{ ilu-web-page, 11704 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 11705 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 11706 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 11707} 11708 11709@Unpublished{ doe2k-web-page, 11710 title = {{DOE2000 Initiative} {W}eb page}, 11711 note = {http://www.mcs.anl.gov/DOE2000}, 11712 key = {DOE2000 Initiative} 11713} 11714 11715@Misc{ pvode-web-page, 11716 title = {{PVODE} {W}eb Page}, 11717 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 11718 author = {A. {Hindmarsh et al.}} 11719} 11720 11721@Book{ szyperski97, 11722 author = {Clemens Szyperski}, 11723 title = {Component Software: Beyond Object-Oriented Programming}, 11724 publisher = {ACM Press}, 11725 address = {New York}, 11726 year = {1997} 11727} 11728 11729@Unpublished{ petsc:coloringuse, 11730 title = {Code for computing sparse {J}acobians}, 11731 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11732 institution = {Argonne National Laboratory} 11733} 11734 11735@Unpublished{ petsc:external, 11736 author = {B. F. {Smith et al.}}, 11737 title = {{External Software Used by PETSc}}, 11738 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11739 institution = {Argonne National Laboratory} 11740} 11741 11742@Unpublished{ petsc:use-by-external-packages, 11743 author = {B. F. {Smith et al.}}, 11744 title = {{Software Packages that Use or Interface to PETSc}}, 11745 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 11746 institution = {Argonne National Laboratory} 11747} 11748 11749@Unpublished{ petsc:prizes, 11750 author = {B. F. {Smith et al.}}, 11751 title = {{Prizes Won Using PETSc}}, 11752 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 11753 institution = {Argonne National Laboratory} 11754} 11755 11756@Unpublished{ petsc:csgf, 11757 author = {B. 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Ross}, 11881 publisher = {University of Toronto}, 11882 pages = {379--386}, 11883 year = {1994} 11884} 11885 11886@Article{ cs99, 11887 author = {X.-C. Cai and M. Sarkis}, 11888 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 11889 systems}, 11890 journal = {SIAM J. Scientific Computing}, 11891 year = {1999}, 11892 volume = {21}, 11893 pages = {792-797} 11894} 11895 11896@TechReport{ cs97a, 11897 author = {X.-C. Cai and M. Sarkis}, 11898 title = {A restricted additive {S}chwarz preconditioner for general sparse linear systems 11899 }, 11900 year = {1997}, 11901 institution = {Computer Science Department, University of Colorado-Boulder}, 11902 number = {CU-CS 843-97}, 11903 note = {(accepted by SIAM J. of Scientific Computing)} 11904} 11905 11906@Article{ cai2003restricted, 11907 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 11908 positive definite linear systems}, 11909 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 11910 journal = {SIAM Journal on Numerical Analysis}, 11911 volume = {41}, 11912 issue = {1}, 11913 pages = {1209--1231}, 11914 year = {2003}, 11915 doi = {10.1137/S0036142901389621} 11916} 11917 11918@TechReport{ caisaad, 11919 author = {Xiao-Chuan Cai and Youcef Saad}, 11920 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 11921 institution = {Army High Performance Computing Research Center, University of Minnesota }, 11922 year = {1993}, 11923 number = {Preprint 93-027 }, 11924 note = {SIAM J. 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Merlin}, 12004 title = {Parallel versions of {S}tones strongly implicit algorithm}, 12005 journal = {Concurrency and Computation: Practice and Experience}, 12006 pages = {1049--1062}, 12007 volumne = {13}, 12008 year = {2001} 12009} 12010 12011@Article{ p4-paper, 12012 author = {Ralph Butler and Ewing Lusk}, 12013 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 12014 journal = {Journal of Parallel Computing}, 12015 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 12016 Division preprint P362-0493)}, 12017 year = {1993} 12018} 12019 12020@TechReport{ picl, 12021 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 12022 title = {{PICL}: A portable instrumented communications library}, 12023 institution = {Oak Ridge National Laboratory}, 12024 number = {TM-11130}, 12025 year = {1990}, 12026 key = {PICL} 12027} 12028 12029@TechReport{ upshot, 12030 author = {Virginia Herrarte and Ewing Lusk}, 12031 title = {Studying Parallel Program Behavior with {U}pshot}, 12032 institution = {Argonne National Laboratory}, 12033 number = {ANL-91/15}, 12034 month = aug, 12035 year = {1991}, 12036 key = {Upshot} 12037} 12038 12039@TechReport{ p4-manual, 12040 author = {Ralph Butler and Ewing Lusk}, 12041 title = {User's Guide to the p4 Parallel Programming System}, 12042 institution = {Argonne National Laboratory}, 12043 number = {ANL-92/17}, 12044 month = oct, 12045 year = {1992}, 12046 key = {p4-Manual} 12047} 12048 12049@InProceedings{ oldparti, 12050 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 12051 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 12052 booktitle = {Proceedings of Supercomputing '93}, 12053 pages = {578--587}, 12054 year = {1993} 12055} 12056 12057@Article{ parti2, 12058 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 12059 and J. Saltz}, 12060 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 12061 journal = {ACM SIGPLAN Notices}, 12062 year = {1995}, 12063 pages = {68-79}, 12064 volume = {30}, 12065 number = {8} 12066} 12067 12068@Article{ parti3, 12069 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 12070 title = {Run-Time Parallelization and Scheduling of Loops}, 12071 journal = {IEEE Trans. Computers}, 12072 year = {1991}, 12073 pages = {604-612}, 12074 volume = {40}, 12075 number = {5} 12076} 12077 12078@InProceedings{ disz-lusk:wamtrace, 12079 author = {Terrence Disz and Ewing Lusk}, 12080 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 12081 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12082 year = {1987}, 12083 pages = {46--53} 12084} 12085 12086@InProceedings{ gorlick-kesselman:gauge, 12087 author = {Michael Gorlick and Carl Kesselman}, 12088 title = {Timing {Prolog} programs without Clocks}, 12089 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12090 year = {1996}, 12091 publisher = {Birkhauser} 12092} 12093 12094@TechReport{ aztec, 12095 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 12096 title = {Aztec User's Guide Version 1.1}, 12097 institution = {Sandia National Laboratories}, 12098 month = oct, 12099 year = {1995}, 12100 number = {SAND95/1559} 12101} 12102 12103@TechReport{ aztec2, 12104 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 12105 title = {Official {Aztec} User's Guide Version 2.1}, 12106 institution = {Sandia National Laboratories}, 12107 year = {1999} 12108} 12109 12110@Book{ taylor-chandy:pcn, 12111 author = {Chandy, M. and Taylor, S.}, 12112 title = {An Introduction to Parallel Programming}, 12113 year = {1991}, 12114 publisher = {Jones and Bartlett} 12115} 12116 12117@Book{ foster-taylor:strand, 12118 title = {Strand: New Concepts in Parallel Programming}, 12119 author = {Ian Foster and Stephen Taylor}, 12120 publisher = {Prentice-Hall}, 12121 adress = { Englewood Cliffs, New Jersey}, 12122 year = {1990} 12123} 12124 12125@Article{ aurora, 12126 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 12127 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 12128 Carlsson and A. Ciepielewski and B. Hausman}, 12129 title = {The Aurora OR-Parallel Prolog System}, 12130 journal = {New Generation Computing}, 12131 volume = {7}, 12132 number = {3}, 12133 year = {1990}, 12134 pages = {243--271} 12135} 12136 12137@TechReport{ roo, 12138 author = {E. Lusk and W. McCune and J. Slaney}, 12139 title = {Roo---a Parallel Theorem Prover}, 12140 institution = {Argonne National Laboratory}, 12141 number = {MCS--TM--149}, 12142 year = {1991} 12143} 12144 12145@TechReport{ heath-etheridge:vppp, 12146 author = {M. T. Heath and J. A. Etheridge}, 12147 title = {Visualizing the Performance of Parallel Programs}, 12148 institution = {Oak Ridge National Laboratory}, 12149 number = {ORNL TM-11813}, 12150 year = {1991} 12151} 12152 12153@TechReport{ chem:vis, 12154 author = {Ewing L. Lusk}, 12155 title = {Performance Visualization for Parallel Programs}, 12156 institution = {Argonne National Laboratory}, 12157 number = {ANL/MCS--P287--0192}, 12158 year = {1991}, 12159 note = {(to appear in {\em Theoretica Chimica Acta})} 12160} 12161 12162@TechReport{ picltrace, 12163 author = {P.~H.~Worley}, 12164 title = {A new {PICL} trace file format}, 12165 institution = {Oak Ridge National Laboratory}, 12166 number = {ORNL TM-12125}, 12167 month = jun, 12168 year = {1992} 12169} 12170 12171@InProceedings{ hideo, 12172 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 12173 title = {Inference of Phylogenetic trees using maximum likelihood}, 12174 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 12175 year = {1992}, 12176 pages = {247--262} 12177} 12178 12179@InProceedings{ dw90, 12180 author = {M. Dryja and O. Widlund}, 12181 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 12182 Problems}, 12183 booktitle = {Third International Symposium on Domain Decomposition Methods}, 12184 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 12185 year = {1990}, 12186 pages = {3-21}, 12187 publisher = {SIAM}, 12188 address = {Philadelphia}, 12189 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 12190 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 12191 references, good introduction to the theory. No computations}, 12192 key = {DryjaWidlund90 !AS} 12193} 12194 12195@Unpublished{ rosing, 12196 author = {Matt Rosing and Joel Saltz}, 12197 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 12198 key = {LowLatency}, 12199 note = {manuscript, 1992} 12200} 12201 12202@TechReport{ jp:incomplete, 12203 author = {Mark T. Jones and Paul E. Plassmann}, 12204 title = {An Improved Incomplete {C}holesky Factorization}, 12205 institution = {Argonne National Laboratory}, 12206 address = {Argonne, IL}, 12207 type = {Preprint}, 12208 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 12209 number = {MCS-P206-0191}, 12210 year = {1991}, 12211 key = {jones} 12212} 12213 12214@InCollection{ jp:ima, 12215 author = {Mark Jones and Paul Plassmann}, 12216 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 12217 booktitle = {Graph Theory and Sparse Matrix Computation}, 12218 publisher = {Springer-Verlag}, 12219 series = {The IMA Volumes in Mathematics and Its Applications}, 12220 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 12221 volume = {56}, 12222 year = {1993}, 12223 pages = {229--245} 12224} 12225 12226@Article{ pw98, 12227 author = {M. Pernice and H. F. Walker}, 12228 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 12229 journal = {SIAM J. Sci. Stat. Comput.}, 12230 year = {1998}, 12231 volume = {19}, 12232 pages = {302--318} 12233} 12234 12235@TechReport{ ysmp83, 12236 key = {Eisenstat}, 12237 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12238 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12239 institution = {Department of Computer Science, Yale University}, 12240 number = {YALE/DCS/RR-265}, 12241 month = apr, 12242 year = {1983} 12243} 12244 12245@InBook{ ysmp84, 12246 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12247 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12248 title = {Elliptic Problem Solvers II}, 12249 publisher = {Academic Press}, 12250 pages = {45--52}, 12251 editors = {G. Birkhoff and A. Schoenstadt}, 12252 year = {1984} 12253} 12254 12255@TechReport{ sparsekit, 12256 key = {Saad}, 12257 author = {Youcef Saad}, 12258 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 12259 institution = {Center for Supercomputing Research and Development, University of Illinois at 12260 Urbana-Champaign}, 12261 number = {1029}, 12262 year = {1990} 12263} 12264 12265@TechReport{ pde-user-ref, 12266 author = {Barry F. Smith}, 12267 title = {Extensible {PDE} Solvers Package Users Manual}, 12268 institution = {Argonne National Laboratory}, 12269 month = sep, 12270 year = {1994}, 12271 number = {ANL-93/40}, 12272 key = {Smith94 ! PDE} 12273} 12274 12275@TechReport{ bs-user-ref, 12276 author = {Mark T. Jones and Paul E. Plassmann}, 12277 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 12278 of Sparse Linear Systems}, 12279 institution = {Argonne National Laboratory}, 12280 month = dec, 12281 year = {1995}, 12282 number = {ANL-95/48} 12283} 12284 12285@TechReport{ snes-user-ref, 12286 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 12287 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 12288 institution = {Argonne National Laboratory}, 12289 month = feb, 12290 year = {1995}, 12291 number = {ANL/MCS-TM-193}, 12292 key = {GroppMcInnesSmith95 ! SNES} 12293} 12294 12295@TechReport{ sles-user-ref, 12296 author = {William D. Gropp and Barry F. Smith}, 12297 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 12298 institution = {Argonne National Laboratory}, 12299 month = mar, 12300 year = {1993}, 12301 number = {ANL-93/8}, 12302 key = {GroppSmith93 ! SLES} 12303} 12304 12305@TechReport{ chameleon-user-ref, 12306 author = {William D. Gropp and Barry F. Smith}, 12307 title = {Chameleon Parallel programming tools Users Manual}, 12308 institution = {Argonne National Laboratory}, 12309 month = mar, 12310 year = {1993}, 12311 number = {ANL-93/23}, 12312 key = {GroppSmith93 ! Chameleon} 12313} 12314 12315@Article{ euclid2, 12316 author = {D. Hysom and A. Pothen}, 12317 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 12318 journal = {SIAM J. Sci. Comput.}, 12319 volume = {22}, 12320 number = {6}, 12321 pages = {2194--2215} 12322} 12323 12324@TechReport{ euclid1, 12325 author = {D. Hysom and A. Pothen}, 12326 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 12327 Solution of Sparse Linear Systems)}, 12328 institution = {Old Dominion University}, 12329 year = {2001} 12330} 12331 12332@TechReport{ ksp-user-ref, 12333 author = {William D. Gropp and Barry F. Smith}, 12334 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 12335 Methods}, 12336 institution = {Argonne National Laboratory}, 12337 month = aug, 12338 year = {1993}, 12339 number = {ANL-93/30}, 12340 key = {GroppSmith93 ! KSP} 12341} 12342 12343@TechReport{ mpi-chameleon, 12344 author = {William D. Gropp and Ewing Lusk}, 12345 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 12346 institution = {Argonne National Laboratory}, 12347 month = dec, 12348 year = {1992}, 12349 number = {ANL-92/47}, 12350 key = {GroppLusk92 ! MPI} 12351} 12352 12353@TechReport{ blockcomm-fortran, 12354 author = {William D. Gropp}, 12355 title = {Block{C}omm for {F}ortran}, 12356 institution = {Argonne National Laboratory}, 12357 month = may, 12358 year = {1993}, 12359 number = {ANL-93/00 (to appear)}, 12360 key = {Gropp93 ! BlockComm} 12361} 12362 12363@TechReport{ autodocument, 12364 author = {William D. Gropp}, 12365 title = {Automatic documentation of {C} programs}, 12366 institution = {Argonne National Laboratory}, 12367 month = may, 12368 year = {1993}, 12369 number = {ANL-93/00}, 12370 key = {Gropp93 ! Autodoc} 12371} 12372 12373@TechReport{ zipcode, 12374 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 12375 Manfred Morari}, 12376 title = {The {Z}ipcode message-passing system}, 12377 institution = {Lawrence Livermore National Laboratory}, 12378 month = sep, 12379 year = {1992}, 12380 number = {Unpublished}, 12381 key = {Skjellum92 ! Zipcode} 12382} 12383 12384@Article{ paragraph, 12385 author = {Michael T. Heath and Jennifer Etheridge Finger}, 12386 title = {Visualizing performance of parallel programs}, 12387 journal = {IEEE Software}, 12388 volume = {8}, 12389 number = {5}, 12390 month = sep, 12391 year = {1991}, 12392 pages = {29--39}, 12393 key = {Heath91 ! Paragraph} 12394} 12395 12396@Article{ gropp90, 12397 author = {William Gropp and Edward Smith}, 12398 title = {Computational Fluid Dynamics on Parallel Processors}, 12399 journal = {Computers and Fluids}, 12400 volume = {18}, 12401 year = {1990}, 12402 pages = {289--304}, 12403 key = {Gropp90 ! performance} 12404} 12405 12406@Article{ foster92, 12407 author = {Ian Foster and William Gropp and Rick Stevens}, 12408 title = {The parallel scalability of the spectral transform method}, 12409 journal = {Monthly Weather Review}, 12410 volume = {120}, 12411 year = {1992}, 12412 pages = {835--850}, 12413 key = {Foster92 ! performance} 12414} 12415 12416@InBook{ fgn, 12417 author = {R. Freund and G. H. Golub and N. Nachtigal}, 12418 title = {Iterative Solution of Linear Systems}, 12419 series = {Acta Numerica}, 12420 year = {1992}, 12421 publisher = {Cambridge University Press}, 12422 pages = {57--100} 12423} 12424 12425@TechReport{ nachtigal90, 12426 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 12427 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12428 institution = {Massachusetts Institute of Technology}, 12429 month = mar, 12430 year = {1990}, 12431 number = {90-2}, 12432 key = {Nachtigal | Krylov} 12433} 12434 12435@Article{ nachtigal1992fnm, 12436 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12437 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 12438 journal = {SIAM Journal on Matrix Analysis and Applications}, 12439 volume = {13}, 12440 pages = {778}, 12441 year = {1992}, 12442 publisher = {SIAM} 12443} 12444 12445@TechReport{ embree1999descriptive, 12446 title = {How descriptive are {GMRES} convergence bounds}, 12447 author = {Embree, M.}, 12448 year = {1999}, 12449 number = {08}, 12450 institution = {Oxford University Computing Laboratory} 12451} 12452 12453@Article{ vorst92, 12454 author = {H. van der Vorst}, 12455 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 12456 of nonsymmetric linear systems}, 12457 journal = {SIAM J. Sci. Stat. Comput.}, 12458 year = {1992}, 12459 volume = {13}, 12460 pages = {631--644} 12461} 12462 12463@Article{ eisenstat81, 12464 author = {S. Eisenstat}, 12465 title = {Efficient Implementation of a Class of {CG} Methods}, 12466 journal = {SIAM J. Sci. Stat. Comput.}, 12467 year = {1981}, 12468 volume = {2}, 12469 pages = {1--4} 12470} 12471 12472@Manual{ ibm-essl, 12473 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 12474 Reference}, 12475 organization = {IBM}, 12476 year = {1992}, 12477 key = {IBM-ESSL} 12478} 12479 12480@Manual{ ibm-eui, 12481 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 12482 Release 2.0}, 12483 organization = {IBM}, 12484 month = jun, 12485 year = {1994}, 12486 key = {IBM-EUI} 12487} 12488 12489@Manual{ ibm-euih, 12490 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 12491 organization = {IBM}, 12492 author = {Peter Hochschild}, 12493 year = {1993}, 12494 key = {IBM-EUIH} 12495} 12496 12497@TechReport{ mpi, 12498 title = {Document for a Standard Message-Passing Interface}, 12499 author = {Message Passing Interface Forum}, 12500 institution = {University of Tennessee}, 12501 number = {CS-93-214}, 12502 month = nov, 12503 year = {1993}, 12504 key = {MPI Standard} 12505} 12506 12507@Unpublished{ mpi-final-web, 12508 author = {Message Passing Interface Forum}, 12509 title = {{MPI}: A Message-Passing Interface Standard}, 12510 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 12511 year = {1994}, 12512 month = may 12513} 12514 12515@Book{ hockney-jesshope, 12516 author = {R. W. Hockney and C. R. Jesshope}, 12517 title = {Parallel Computers 2}, 12518 publisher = {Adam Hilger}, 12519 year = {1988} 12520} 12521 12522@Book{ cm-fortran, 12523 author = {{Thinking Machines Corporation}}, 12524 title = {Users Manual for CM-Fortran}, 12525 publisher = {Thinking Machines Corporation}, 12526 year = {1993} 12527} 12528 12529@TechReport{ chang93, 12530 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 12531 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 12532 institution = {Yale Department of Computer Science}, 12533 number = {YALEU/DCS/RR-994}, 12534 month = nov, 12535 year = {1993}, 12536 key = {BDD|diag} 12537} 12538 12539@InProceedings{ gropplevine93, 12540 author = {N. Galbreath and W. Gropp and D. Levine}, 12541 title = {Applications-Driven Parallel {I/O}}, 12542 booktitle = {Proceedings of Supercomputing '93}, 12543 year = {1993}, 12544 pages = {462--471} 12545} 12546 12547@Book{ siegle85, 12548 author = {H. J. Siegel}, 12549 title = {Interconnection Networks for Large Scale Parallel Processing}, 12550 publisher = {Lexington Books}, 12551 year = {1985}, 12552 key = {Network Comparison} 12553} 12554 12555@Article{ lawrie75, 12556 author = {D. H. Lawrie}, 12557 title = {Access and alignment of data in an array processor}, 12558 journal = {IEEE Transactions on Computers}, 12559 volume = {C-24}, 12560 number = {12}, 12561 month = dec, 12562 year = {1975}, 12563 pages = {1145--1155}, 12564 key = {Omega Network} 12565} 12566 12567@Book{ knuth1986, 12568 title = {The {\TeX}{Book}}, 12569 author = {Donald Ervin Knuth and Duane Bibby}, 12570 volume = {1993}, 12571 year = {1986}, 12572 publisher = {Addison-Wesley Reading, Massachusetts} 12573} 12574 12575@Book{ lamport86, 12576 author = {Leslie Lamport}, 12577 title = {{LaTeX}: A document preparation system}, 12578 publisher = {Addison-Wesley}, 12579 year = {1986}, 12580 key = {Latex Manual} 12581} 12582 12583@InProceedings{ gropp-lusk:unix-tools, 12584 author = {William Gropp and Ewing Lusk}, 12585 title = {Scalable {U}nix Tools on Parallel Processors}, 12586 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 12587 publisher = {IEEE}, 12588 pages = {56--62} 12589} 12590 12591@InProceedings{ jp:bell_prize, 12592 author = {Mark Jones and Paul Plassmann}, 12593 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 12594 Applications}, 12595 booktitle = {Proceedings of Supercomputing '92}, 12596 publisher = {IEEE Computer Society Press}, 12597 year = {1992}, 12598 pages = {551--560} 12599} 12600 12601@COMMENT{WEB, CWEB references (for doctext)} 12602@TechReport{ web, 12603 author = {Donald E. Knuth}, 12604 title = {The {\tt WEB} system of structured documentation}, 12605 institution = {Computer Science Department, Stanford University}, 12606 year = {1983}, 12607 number = {980}, 12608 month = sep 12609} 12610 12611@Article{ literatepgm, 12612 author = {Donald E. Knuth}, 12613 title = {Literate Programming}, 12614 journal = {Computer Journal}, 12615 year = {1984}, 12616 volume = {27}, 12617 number = {2}, 12618 pages = {91--111} 12619} 12620 12621@Unpublished{ cweb-code, 12622 author = {Silvio Levy and Donald E. Knuth}, 12623 title = {CWEB}, 12624 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 12625} 12626 12627@Article{ jp:scalable, 12628 author = {Mark Jones and Paul Plassmann}, 12629 title = {Scalable Iterative Solution of Sparse Linear Systems}, 12630 journal = {Parallel Computing}, 12631 volume = {20}, 12632 number = {5}, 12633 month = may, 12634 year = {1994}, 12635 pages = {753--773} 12636} 12637 12638@Article{ jp:pcolor, 12639 author = {Mark T. Jones and Paul E. Plassmann}, 12640 title = {A Parallel Graph Coloring Heuristic}, 12641 journal = {SIAM J. Sci. Comput.}, 12642 volume = {14}, 12643 number = {3}, 12644 pages = {654-669}, 12645 year = {1993} 12646} 12647 12648@TechReport{ block_solve, 12649 author = {Mark T. Jones and Paul E. Plassmann}, 12650 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 12651 Sparse Linear Systems}, 12652 institution = {Argonne National Laboratory}, 12653 year = {1992}, 12654 number = {ANL-92/46}, 12655 key = {JonesPlassmann92 ! block_solve} 12656} 12657 12658@InProceedings{ supercond, 12659 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 12660 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 12661 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 12662 Conference}, 12663 month = feb, 12664 year = {1994}, 12665 key = {McInnesPalumbo94 ! superconductivity } 12666} 12667 12668@Unpublished{ preosti:93, 12669 author = {Gianfranco Preosti}, 12670 title = { }, 12671 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 12672 year = {1993}, 12673 key = {preosti93 ! GL-tilt3d} 12674} 12675 12676@Unpublished{ more:93, 12677 author = {Jorge J. Mor\'{e}}, 12678 title = { }, 12679 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 12680 {A}rgonne {N}ational {L}aboratory}, 12681 year = {1993}, 12682 key = {more93 ! MINPACK-2} 12683} 12684 12685@Article{ brownsaad:90, 12686 author = {Peter N. Brown and Youcef Saad}, 12687 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 12688 journal = {SIAM J. Sci. Stat. Comput.}, 12689 year = {1990}, 12690 volume = {11}, 12691 pages = {450-481} 12692} 12693 12694@Book{ using-mpi, 12695 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 12696 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 12697 publisher = {MIT Press}, 12698 year = {1994} 12699} 12700 12701@Book{ using-mpi2, 12702 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 12703 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 12704 publisher = {MIT Press}, 12705 year = {1999} 12706} 12707 12708@Article{ hs:52, 12709 author = {Magnus R. Hestenes and Eduard Steifel}, 12710 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 12711 journal = {J. Research of the National Bureau of Standards}, 12712 year = {1952}, 12713 volume = {49}, 12714 pages = {409-436} 12715} 12716 12717@Article{ ss:86, 12718 author = {Youcef Saad and Martin H. Schultz}, 12719 title = {{GMRES}: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear 12720 Systems}, 12721 journal = {SIAM J. Sci. Stat. Comput.}, 12722 year = {1986}, 12723 volume = {7}, 12724 pages = {856-869} 12725} 12726 12727@Article{ so:89, 12728 author = {Peter Sonneveld}, 12729 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 12730 journal = {SIAM J. Sci. Stat. Comput.}, 12731 year = {1989}, 12732 volume = {10}, 12733 pages = {36-52} 12734} 12735 12736@Article{ v:92, 12737 author = {{H. A.} {van der Vorst}}, 12738 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 12739 of nonsymmetric linear systems}, 12740 journal = {SIAM J. Sci. Stat. Comput.}, 12741 volume = {13}, 12742 year = {1992}, 12743 pages = {631-644} 12744} 12745 12746@Article{ f:93, 12747 author = {Roland W. Freund}, 12748 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 12749 Systems}, 12750 journal = {SIAM J. Sci. Stat. Comput.}, 12751 volume = {14}, 12752 year = {1993}, 12753 pages = {470-482} 12754} 12755 12756@Article{ ish:89, 12757 author = {S. Ishizuka}, 12758 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 12759 journal = {Combustion and Flame}, 12760 volume = {75}, 12761 year = {1989}, 12762 pages = {367-379} 12763} 12764 12765@Book{ williams89, 12766 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 12767 author = {F.A. Williams}, 12768 publisher = {Addison-Wesley}, 12769 year = {1989}, 12770 pages = {367-379} 12771} 12772 12773@Book{ ra75, 12774 author = {R. Aris}, 12775 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 12776 publisher = {Oxford}, 12777 year = {1975} 12778} 12779 12780@Book{ bebernes89, 12781 author = {J. Bebernes and D. Eberly}, 12782 title = {Mathematical Problems from Combustion Theory}, 12783 publisher = {Springer-Verlag}, 12784 series = {Applied Mathematical Sciences 83}, 12785 year = {1989} 12786} 12787 12788@InProceedings{ kikuchi89, 12789 author = {F. Kikuchi}, 12790 booktitle = { Computing Methods in Applied Sciences and Engineering}, 12791 editor = {R. Glowinski and J. L. Lions}, 12792 publisher = {Springer-Verlag}, 12793 series = {Lecture Notes in Mathematics}, 12794 title = {Finite element approximations to bifurcation problems of turning point type}, 12795 year = {1977} 12796} 12797 12798@Article{ rg85, 12799 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 12800 title = {Continuation-conjugate Gradient Methods fo the Least Squares Solution of 12801 Nonlinear Boundary Problems}, 12802 journal = {SIAM J. Sci. Stat. Comput.}, 12803 volume = {6}, 12804 year = {1985}, 12805 pages = {793-832} 12806} 12807 12808@InProceedings{ whitfield91, 12809 author = {D. Whitfield and L. Taylor}, 12810 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12811 Schemes}, 12812 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 12813 misc = {AIAA-91-1539}, 12814 pages = {134-145}, 12815 year = {1991} 12816} 12817 12818@InProceedings{ quinlan1, 12819 author = {M. Lemke and D. Quinlan}, 12820 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 12821 Architecture-Independent Development of Structured Grid Applications}, 12822 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 12823 publisher = {Springer Verlag}, 12824 year = {1992} 12825} 12826 12827@InProceedings{ quinlan2, 12828 author = {R. Parsons and D. Quinlan}, 12829 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 12830 Computations}, 12831 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 12832 year = {1994} 12833} 12834 12835% ***** Overview of functionality in Diffpack 12836@InBook{ dpoverview, 12837 author = {Bruaset, A. M. and Langtangen, H. P.}, 12838 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12839 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 12840 {Diffpack}}, 12841 publisher = {Birkh{\"{a}}user}, 12842 pages = {61--90}, 12843 year = {1997} 12844} 12845 12846% ***** Short overview of Diffpack 12847@InCollection{ dpoverview2, 12848 author = {Bruaset, A. M. and Langtangen, H. P.}, 12849 editor = {A. Sydow}, 12850 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 12851 and Applied Mathematics}, 12852 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 12853 pages = {553--558}, 12854 volume = {4}, 12855 year = {1997} 12856} 12857 12858% ***** Comprehensive documentation of Diffpack and 12859% associated numerical methods: 12860@Book{ dpbook, 12861 author = {H. P. Langtangen}, 12862 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 12863 Software. Part I}, 12864 series = {Lecture Notes in Computational Science and Engineering}, 12865 publisher = {Springer-Verlag}, 12866 year = {1998} 12867} 12868 12869% ***** Design issues of the linear solvers in Diffpack, serves also as a 12870% collection of examples on O-O in numerical computing 12871@Article{ ambhpl97a, 12872 author = {A. M. Bruaset and H. P. Langtangen }, 12873 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 12874 journal = {Transactions on Mathematical Software}, 12875 volume = {23 }, 12876 pages = {50--80}, 12877 year = {1997} 12878} 12879 12880@Misc{ dpurl, 12881 author = {{Diffpack Web page}}, 12882 howpublished = {\url{http://www.diffpack.com}} 12883} 12884 12885% ***** General intro to object-oriented numerics for "FORTRAN programmers" 12886@InCollection{ oonintro, 12887 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 12888 editor = {D{\ae}hlen, M. and Tveito, A.}, 12889 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12890 title = {Object-Oriented Numerics}, 12891 publisher = {Birkh{\"{a}}user}, 12892 year = {1997} 12893} 12894 12895% ***** Efficiency comparison: BLAS 1, Diffpack, C, 12896% and finite element applications (F77 vs Diffpack) 12897@InCollection{ dpefficiency, 12898 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 12899 H. P. and Miller, C. T.}, 12900 editor = {D{\ae}hlen, M. and Tveito, A.}, 12901 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12902 title = {On the Efficiency of {C++} in Scientific Computing}, 12903 publisher = {Birkh{\"{a}}user}, 12904 pages = {91--118}, 12905 year = {1997} 12906} 12907 12908% ***** Parallel concept in Diffpack: 12909@InCollection{ dpparallel, 12910 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 12911 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 12912 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 12913 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 12914 Simulators}, 12915 publisher = {Springer--Verlag}, 12916 series = {Lecture Notes in Computer Science}, 12917 pages = {161--168}, 12918 year = {1997} 12919} 12920 12921% ***** DD and ML methods in Diffpack: 12922@InCollection{ dpddml, 12923 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 12924 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 12925 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 12926 title = {Domain decomposition and multilevel methods in Diffpack}, 12927 year = {1997} 12928} 12929 12930@InProceedings{ bsca98, 12931 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 12932 Alexander}, 12933 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 12934 Optimization}, 12935 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12936 Scientific and Engineering Computing}, 12937 editor = {Mike Henderson et al.}, 12938 pages = {165-173}, 12939 year = {1998} 12940} 12941 12942@Book{ scalapack-user-guide, 12943 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 12944 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 12945 Stanley and D. Walker and R. C. Whaley}, 12946 title = {Sca{LAPACK} Users' Guide}, 12947 publisher = {SIAM}, 12948 address = {Philadelphia, PA}, 12949 year = {1997} 12950} 12951 12952@InProceedings{ keyes99, 12953 author = {D. E. Keyes}, 12954 title = {How Scalable is Domain Decomposition in Practice?}, 12955 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 12956 Methods}, 12957 editor = {C.-H. Lai et al.}, 12958 publisher = {Domain Decomposition Press, Bergen}, 12959 note = {To appear}, 12960 year = {1999} 12961} 12962 12963@Article{ fun3d, 12964 author = {W. K. Anderson and D. L. Bonhaus}, 12965 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 12966 grids}, 12967 journal = {Computers and Fluids}, 12968 year = {1994}, 12969 volume = {23}, 12970 pages = {1--21} 12971} 12972 12973% ------------------------------------------------------------------------- 12974% ------------------------------------------------------------------------- 12975@Article{ torczon, 12976 author = {Dennis, Jr., J. E. and V.~Torczon}, 12977 title = {Direct Search Methods on Parallel Machines}, 12978 journal = {SIAM J. Optimization}, 12979 volume = {1}, 12980 pages = {448--474}, 12981 year = {1991}, 12982 key = {Torczon !PDS} 12983} 12984 12985@InProceedings{ wt91, 12986 author = {D. L. Whitfield and L. K. Taylor}, 12987 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12988 Schemes}, 12989 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 12990 misc = {AIAA-91-1539}, 12991 pages = {134-145}, 12992 year = {1991} 12993} 12994 12995@Article{ ew96, 12996 author = {S. C. Eisenstat and H. F. Walker}, 12997 title = {Choosing the forcing terms in an inexact {N}ewton method}, 12998 journal = {SIAM J. Scientific Computing}, 12999 volume = {17}, 13000 year = {1996}, 13001 pages = {16--32} 13002} 13003 13004@Book{ thi93, 13005 author = {{Thinking Machines Corporation}}, 13006 title = {Users Manual for CM-Fortran}, 13007 publisher = {Thinking Machines Corporation}, 13008 year = {1993} 13009} 13010 13011@Book{ mortonmayers94, 13012 author = {K. W. Morton and D. F. Mayers}, 13013 title = {Numerical Solution of Partial Differential Equations}, 13014 publisher = {Press Syndicate of the University of Cambridge}, 13015 year = {1994} 13016} 13017 13018@Book{ heath97, 13019 author = {Michael T. Heath}, 13020 title = {Scientific Computing: An Introductory Survey}, 13021 publisher = {McGraw Hill}, 13022 year = {1997} 13023} 13024 13025@Article{ captools96, 13026 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 13027 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 13028 Performance on the Parallelization of Structured Mesh Codes}, 13029 journal = {Parallel Computing}, 13030 volume = {22}, 13031 pages = {197-226}, 13032 year = {1996} 13033} 13034 13035@Unpublished{ nastran-web-page, 13036 author = {{MSC Software Corporation}}, 13037 title = {{NASTRAN} {W}eb page}, 13038 note = {See {\tt http://www.mechsolutions.com\-/products\-/nastran/}} 13039} 13040 13041@Book{ hpf, 13042 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 13043 Zosel}, 13044 title = {The High Performance Fotran Handbook}, 13045 publisher = {MIT Press}, 13046 year = {1994} 13047} 13048 13049@InProceedings{ keyes98, 13050 author = {D. E. Keyes}, 13051 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 13052 Architectures}, 13053 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 13054 editors = {M. D. Salas and W. K. Anderson}, 13055 ppublisher = {Elsevier}, 13056 year = {1998} 13057} 13058 13059@InProceedings{ pooma-atlas, 13060 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 13061 J. V. W. Reynders and M. Tholburn}, 13062 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 13063 Applications}, 13064 year = {1995}, 13065 month = dec, 13066 booktitle = {Supercomputing '95 Proceedings} 13067} 13068 13069% --------------------------------------------------------------------------------- 13070% New bib entries for CRPC paper 13071@Misc{ mgnet-web-page, 13072 author = {Craig C. Douglas}, 13073 title = {{MGNet Web page}}, 13074 note = {See {\tt http://\-www.mgnet.org}} 13075} 13076 13077@Misc{ dagh-web-page, 13078 author = {M. Parashar and J. C. Browne}, 13079 title = {{DAGH Web page}}, 13080 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 13081} 13082 13083@Misc{ parasol-web-page, 13084 key = {PARASOL}, 13085 title = {{PARASOL Web page}}, 13086 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 13087} 13088 13089@Misc{ pooma-web-page, 13090 author = {{POOMA Web page}}, 13091 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 13092} 13093 13094@Misc{ mudpack-web-page, 13095 author = {John C. Adams}, 13096 title = {{MUDPACK Web page}}, 13097 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 13098} 13099 13100@Misc{ pellpack-web-page, 13101 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 13102 title = {{Parallel ELLPACK Web page}}, 13103 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 13104} 13105 13106@InProceedings{ pellpack95, 13107 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 13108 Catlin and S. Weerawarana and T.S. Papatheodorou}, 13109 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 13110 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 13111 address = {Albuquerque, NM}, 13112 year = {1995} 13113} 13114 13115@Misc{ nhse-web-page, 13116 author = {{National High-Performance Software Exchange Web page}}, 13117 note = {See {\tt http://\-www.nhse.org}} 13118} 13119 13120@Misc{ doug-web-page, 13121 author = {Mark J. Hagger and Linda Stals}, 13122 title = {{DOUG Web Page}}, 13123 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 13124} 13125 13126@TechReport{ doug97, 13127 author = {Mark J. Hagger}, 13128 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 13129 institution = {Mathematical Sciences, University of Bath}, 13130 year = {1997}, 13131 number = {9706}, 13132 note = {Advances in Computational Mathematics (to appear)} 13133} 13134 13135@Misc{ ug-web-page, 13136 author = {{UG Web Page}}, 13137 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 13138} 13139 13140@Article{ ug97, 13141 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 13142 Rentz-Reichert and C. Wieners}, 13143 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 13144 journal = {Computing and Visualization in Science}, 13145 year = {1997}, 13146 volume = {}, 13147 pages = {} 13148} 13149 13150@Misc{ vecfem-web-page, 13151 author = {Lutz Grosz}, 13152 title = {{VECFEM Web Page}}, 13153 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 13154} 13155 13156@Misc{ atlas-web-page, 13157 author = {R. Clint {Whaley et al.}}, 13158 title = {{ATLAS Web Page}}, 13159 howpublished = {\url{http://math-atlas.sourceforge.net}} 13160} 13161 13162@Misc{ fenics-web-page, 13163 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 13164 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 13165 title = {{FEniCS Web Page}}, 13166 note = {\url{http://www.fenicsproject.org}}, 13167 year = {2005} 13168} 13169 13170@Misc{ matlab-web-page, 13171 author = {{The} {MathWorks}}, 13172 title = {{Matlab} {Web} page}, 13173 url = {http://www.mathworks.com} 13174} 13175 13176@Misc{ phipac-web-page, 13177 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 13178 and D. Lam}, 13179 title = {{PHiPAC Web Page}}, 13180 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 13181} 13182 13183@InProceedings{ kelp, 13184 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 13185 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 13186 booktitle = {Irregular '96}, 13187 year = {1996} 13188} 13189 13190@Unpublished{ kelp-web-page, 13191 author = {Scott Baden}, 13192 title = {{KeLP} {W}eb page}, 13193 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 13194} 13195 13196@InProceedings{ hk99, 13197 author = {R. Hornung and S. Kohn}, 13198 title = {The Use of Object-Oriented Design Patterns in the {SAMRAI} Structured {AMR} 13199 Framework}, 13200 booktitle = {Proceedings of the SIAM Workshop on Object-Oriented Methods for Inter-Operable 13201 Scientific and Engineering Computing}, 13202 pages = {235-244}, 13203 year = {1999}, 13204 note = {See \url{http://www.llnl.gov/CASC/samrai}} 13205} 13206 13207@Unpublished{ samrai-web-page, 13208 title = {{SAMRAI} {W}eb Page}, 13209 author = {Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith}, 13210 note = {See {\tt http://www.llnl.gov/\-CASC/SAMRAI}} 13211} 13212 13213@Misc{ overture-web-page, 13214 author = {William Henshaw and Kyle Chand}, 13215 title = {{Overture} {W}eb page}, 13216 howpublished = {\url{http://www.llnl.gov/CASC/Overture}} 13217} 13218 13219@InProceedings{ overture99, 13220 author = {D.L. Brown and W.D. Henshaw and D.J. Quinlan}, 13221 title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations 13222 on Overlapping Grids}, 13223 publisher = {SIAM}, 13224 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 13225 Scientific and Engineering Computing}, 13226 year = {1999}, 13227 pages = {215-224}, 13228 note = {See \url{http://www.llnl.gov/CASC/Overture}} 13229} 13230 13231@InProceedings{ diffpack, 13232 author = {A.M. Bruaset and H.P. Langtangen}, 13233 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations: 13234 {D}iffpack}, 13235 booktitle = {Numerical Methods and Software Tools in Industrial Mathematics}, 13236 year = {1997}, 13237 pages = {61--90}, 13238 publisher = {Birkhauser Press} 13239} 13240 13241@Article{ dongarra:1984:ila, 13242 author = {J. J. Dongarra and F. G. Gustavson and A. Karp}, 13243 title = {Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline 13244 Machine}, 13245 journal = {SIAM Review}, 13246 volume = {26}, 13247 number = {1}, 13248 pages = {91--112}, 13249 month = jan, 13250 year = {1984}, 13251 coden = {SIREAD}, 13252 issn = {0036-1445 (print), 1095-7200 (electronic)}, 13253 mrclass = {65F10 (65F30)}, 13254 mrnumber = {85c:65032}, 13255 bibdate = {Mon Jan 20 1997}, 13256 abstract = {The authors examine common implementations of linear algebra algorithms, such as 13257 matrix-vector multiplication, matrix-matrix multiplication and the solution of 13258 linear equations. The different versions are examined for efficiency on a computer 13259 architecture which uses vector processing and has pipelined instruction execution. 13260 By using the advanced architectural features of such machines, one can usually 13261 achieve maximum performance, and tremendous improvements in terms of execution 13262 speed can be seen over conventional computers.}, 13263 classification= {723; 921}, 13264 journalabr = {SIAM Rev}, 13265 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 13266 mathematical programming; vector pipeline machine} 13267} 13268 13269@Book{ qv99, 13270 author = {Alfio Quarteroni and Alberto Valli}, 13271 title = {Domain Decomposition Methods for Partial Differential Equations}, 13272 publisher = {Oxford Science Publications}, 13273 address = {Oxford}, 13274 year = {1999} 13275} 13276 13277@Book{ ksv97, 13278 editor = {David E. Keyes and Ahmed Sameh and V. Venkatakrishnan}, 13279 title = {Parallel Numerical Algorithms}, 13280 publisher = {Kluwer Academic Publishers}, 13281 address = {the Netherlands}, 13282 year = {1997} 13283} 13284 13285@Book{ hackbusch94, 13286 author = {Wolfgang Hackbusch}, 13287 title = {Iterative Solution of Large Sparse Systems of Equations}, 13288 publisher = {Springer-Verlag}, 13289 address = {New York}, 13290 year = {1994} 13291} 13292 13293@Article{ hackbusch1980fast, 13294 title = {Fast solution of elliptic control problems}, 13295 author = {Hackbusch, W.}, 13296 journal = {Journal of Optimization Theory and Applications}, 13297 volume = {31}, 13298 number = {4}, 13299 pages = {565--581}, 13300 year = {1980}, 13301 publisher = {Springer} 13302} 13303 13304@Book{ hackbusch1985multi, 13305 title = {{Multi-grid methods and applications}}, 13306 author = {Hackbusch, W.}, 13307 isbn = {3540127615}, 13308 issn = {0179-3632}, 13309 year = {1985}, 13310 publisher = {Springer Verlag} 13311} 13312 13313@Book{ axelsson94, 13314 author = {Owe Axelsson}, 13315 title = {Iterative Solution Methods}, 13316 publisher = {Cambridge University Press}, 13317 address = {Cambridge}, 13318 year = {1994} 13319} 13320 13321@Book{ saad96, 13322 author = {Yousef Saad}, 13323 title = {Iterative Methods for Sparse Linear Systems}, 13324 publisher = {PWS Publishing Company}, 13325 address = {Boston}, 13326 year = {1996} 13327} 13328 13329@Book{ saad2003, 13330 title = {Iterative Methods for Sparse Linear Systems}, 13331 author = {Saad, Yousef}, 13332 doi = {10.1016/S1570-579X(01)80025-2}, 13333 edition = {2nd}, 13334 publisher = {SIAM}, 13335 year = {2003} 13336} 13337 13338@Book{ vandervorst03, 13339 author = {Henk A. {van der Vorst}}, 13340 title = {Iterative Krylov Methods for Large Linear Systems}, 13341 publisher = {Cambridge Monographs on Applied ahd Computational Mathematics}, 13342 year = {2003} 13343} 13344 13345@Book{ koniges00, 13346 editor = {Alice E. Koniges}, 13347 title = {Industrial Strength Parallel Computing}, 13348 publisher = {Morgan Kaufmann Publishers}, 13349 address = {San Francisco}, 13350 year = {2000} 13351} 13352 13353@Misc{ fftw-web-page, 13354 key = {Fftw}, 13355 title = {{FFTW} {Web} page}, 13356 note = {\texttt{http://www.fftw.org/}}, 13357 annote = {fast FFT. Parallel versions with MPI and Cilk} 13358} 13359 13360@InProceedings{ frigojohnson93, 13361 author = {Matteo Frigo and Steven G. Johnson}, 13362 title = {The Design and Implementation of {FFTW3}}, 13363 booktitle = {Proceedings of the IEEE}, 13364 volume = {93}, 13365 number = {2}, 13366 pages = {216--231}, 13367 year = {2005} 13368} 13369 13370@Book{ kelley95, 13371 author = {C. T. Kelley}, 13372 title = {Iterative Methods for Linear and Nonlinear Equations}, 13373 year = {1995}, 13374 publisher = {SIAM}, 13375 address = {Philadelphia} 13376} 13377 13378@Unpublished{ spai-web-page, 13379 title = {{SPAI} {W}eb {P}age}, 13380 note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/}, 13381 author = {Steven Bernard and Marcus Grote}, 13382 institution = {NASA Ames Research Center and ETH Zurich} 13383} 13384 13385@Article{ gh97, 13386 author = {M. J. Grote and T. Huckle}, 13387 title = {Parallel Preconditioning with Sparse Approximate Inverses}, 13388 year = {1997}, 13389 journal = {SIAM J. of Scient. Comput.}, 13390 volume = {18}, 13391 pages = {838-853} 13392} 13393 13394@Article{ zhang96, 13395 author = {Wen Zhang}, 13396 title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the 13397 simulation of a sintering process}, 13398 year = {1996}, 13399 journal = {Appl. Numer. Math.}, 13400 volume = {20}, 13401 pages = {235-244} 13402} 13403 13404@Article{ zhang98, 13405 author = {Wen Zhang and Ian Gladwell}, 13406 title = {The sintering of two particles by surface and grain boundary diffusion - a 13407 three-dimensional numerical study}, 13408 journal = {Comp. Mater. Sci.}, 13409 year = {1998}, 13410 volume = {12} 13411} 13412 13413@InProceedings{ mollerschwartzbach01, 13414 author = {Anders M\o{}ller and Michael I. Schwartzbach}, 13415 title = {The Pointer Assertion Logic Engine}, 13416 booktitle = {ACM Proceedings of PLDI'01}, 13417 year = {2001} 13418} 13419 13420@InProceedings{ klarlandschwartzbach97, 13421 author = {Nils Klarland and Michael I. Schwartzbach}, 13422 title = {A Domain-Specific Languages for Regular Sets of Strings and Trees}, 13423 booktitle = {Proceedings of the Conference on Domain-Specific Languages}, 13424 publisher = {USENIX}, 13425 month = oct, 13426 year = {1997}, 13427 address = {Santa Barbara, CA} 13428} 13429 13430@InProceedings{ conselmarlet98, 13431 author = {C. Consel and R. Marlet}, 13432 title = {Architecturing software using a methodology for language development}, 13433 booktitle = {Proceedings of the 10th International Symposium on Programming Languages, 13434 Implementations, Logics and Programs}, 13435 year = {1998}, 13436 pages = {170-174}, 13437 month = sep, 13438 address = {Pisa, Italy} 13439} 13440 13441@Misc{ sundials:homepage, 13442 author = {C. {Woodward et al.}}, 13443 title = {{SUNDIALS {W}eb page}}, 13444 howpublished = {\url{https://computation.llnl.gov/casc/sundials/main.html}} 13445} 13446 13447@article{gardner2022sundials, 13448 title = {Enabling new flexibility in the {SUNDIALS} suite of nonlinear and differential/algebraic equation solvers}, 13449 author = {Gardner, David J and Reynolds, Daniel R and Woodward, Carol S and Balos, Cody J}, 13450 journal = {ACM Transactions on Mathematical Software (TOMS)}, 13451 publisher = {ACM}, 13452 year = {2022}, 13453 doi = {10.1145/3539801} 13454} 13455 13456@Misc{ sundials-user-ref, 13457 title = {{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13458 note = {See \url{http://www.llnl.gov/CASC/sundials}}, 13459 author = {Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban 13460 and Dan Shumaker and Carol Woodward}, 13461 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 13462 number = {UCRL-JP-200037}, 13463 year = {2003} 13464} 13465 13466@Article{ sundials05, 13467 author = {A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 13468 and C. Woodward}, 13469 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13470 journal = {ACM Transactions on Mathematical Software}, 13471 volume = {31}, 13472 number = {3}, 13473 pages = {363--396}, 13474 year = {2005} 13475} 13476 13477@InProceedings{ serban2005cvodes, 13478 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 13479 author = {Serban, Radu and Hindmarsh, Alan C}, 13480 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 13481 Dynamics and Control, Long Beach, CA}, 13482 year = {2005} 13483} 13484 13485@Article{ pvode99, 13486 author = {G. Byrne and A. Hindmarsh}, 13487 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 13488 journal = {Int. J. High Perf. Comput. Apps.}, 13489 volume = {13}, 13490 number = {4}, 13491 year = {1999}, 13492 pages = {354 -- 365} 13493} 13494 13495@Article{ cvode95, 13496 author = {S. Cohen and A. Hindmarsh}, 13497 title = {{CVODE}, A Stiff/Nonstiff {ODE} Solver in {C}}, 13498 journal = {Computers in Physics}, 13499 volume = {10}, 13500 number = {2}, 13501 year = {1996}, 13502 pages = {138 -- 143} 13503} 13504 13505@TechReport{ ifpack, 13506 title = {Robust Algebraic Preconditioners using {IFPACK} 3.0}, 13507 author = {Marzio Sala and Michael Heroux}, 13508 institution = {Sandia National Laboratories}, 13509 number = {SAND2005-0662}, 13510 year = {2005} 13511} 13512 13513@TechReport{ kinsol-user-ref, 13514 title = {User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel 13515 Computers}, 13516 author = {Allan Taylor and Alan Hindmarsh}, 13517 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 13518 number = {UCRL-ID-131185}, 13519 year = {1998} 13520} 13521 13522@Article{ fiardmanteuffelmccormick98, 13523 author = {J.-M. Fiard and T. Manteuffel and S. McCormick}, 13524 title = {First-order system least squares {(FOSLS)} for convection-diffusion problems: 13525 numerical results}, 13526 journal = {SIAM J. Sci. Comp.}, 13527 year = {1998}, 13528 volume = {19}, 13529 pages = {1958--1979} 13530} 13531 13532@InProceedings{ vuduc02, 13533 author = {Richard Vuduc and James W. Demmel and Katherine A. Yelick and Shoaib Kamil and 13534 Rajesh Nishtala and Benjamin Lee}, 13535 title = {Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply}, 13536 booktitle = {Proceedings of Supercomputing}, 13537 year = {2002}, 13538 month = nov, 13539 address = {Baltimore} 13540} 13541 13542@Article{ beckerbraackrannacher1999, 13543 title = {Numerical simulation of laminar flames at low Mach number by adaptive finite 13544 elements}, 13545 author = {Roland Becker and Malte Braack and Rolf Rannacher}, 13546 journal = {Combustion Theory and Modelling}, 13547 volume = {3}, 13548 pages = {503--534}, 13549 year = {1999} 13550} 13551 13552@Article{ beckerrannacher01, 13553 author = {R. Becker and R. Rannacher}, 13554 title = {An optimal control approach to a posteriori error estimation in finite element 13555 methods}, 13556 journal = {Acta Numerica}, 13557 year = {2001}, 13558 volume = {10}, 13559 pages = {1--102} 13560} 13561 13562@Article{ babuskamiller84a, 13563 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13564 title = {The post-processing approach in the finite element method, {I}: Calculations of 13565 displacements, stresses, and other higher derivatives of the displacements}, 13566 journal = {Int. J. Numer. Meth. Eng.}, 13567 year = {1984}, 13568 volume = {20}, 13569 pages = {1085--1109} 13570} 13571 13572@Article{ babuskamiller84b, 13573 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13574 title = {The post-processing approach in the finite element method, {II}: The calculation 13575 of stress intensity factors}, 13576 journal = {Int. J. Numer. Meth. Eng.}, 13577 year = {1984}, 13578 volume = {20}, 13579 pages = {1111--1129} 13580} 13581 13582@Article{ babuskamiller84c, 13583 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13584 title = {The post-processing approach in the finite element method, {III}: A posteriori 13585 error estimation and adaptive mesh refinement}, 13586 journal = {Int. J. Numer. Meth. 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G. Kaper and T. J. 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Fishwick}, 14985 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 14986 to Interrelating Model Structures}, 14987 journal = {SCS Trans. on Simulation}, 14988 note = {Special Issue in Grand Challenges in Computer Simulation}, 14989 year = {2004} 14990} 14991 14992@Article{ fishwick03, 14993 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 14994 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 14995 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 14996 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 14997 year = {2003} 14998} 14999 15000@InProceedings{ kirner00, 15001 author = {T. G. Kirner and V. F. Martins}, 15002 title = {Development of an Information Visualization Tool Using Virtual Reality}, 15003 booktitle = {Proceedings of the 2000 ACM Symposium on Applied Computing}, 15004 year = {2000}, 15005 pages = {604--606} 15006} 15007 15008@InProceedings{ orso03, 15009 author = {A. Orso and J. Jones and M. J. Harrold}, 15010 title = {Visualization of Program-Execution Data for Deployed Software}, 15011 booktitle = {Proceedings of the 2003 ACM Symposium on Software Visualization}, 15012 year = {2003}, 15013 pages = {67--76} 15014} 15015 15016@Book{ tiller01, 15017 author = {M. Tiller}, 15018 title = {Introduction to Physical System Modeling with Modelica}, 15019 series = {Kluwer International Series inEngineering and Computer Science}, 15020 volume = {615}, 15021 publisher = {Kluwer}, 15022 year = {2001} 15023} 15024 15025@Article{ buck94, 15026 author = {J. Buck and S. Ha and E. Lee and D. Messerschmitt}, 15027 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 15028 journal = {Int. Journal of Computer Simulation}, 15029 volume = {4}, 15030 pages = {155--182}, 15031 year = {1994} 15032} 15033 15034@Article{ mu95, 15035 author = {M. Mu and J.R. Rice}, 15036 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 15037 journal = {Comp. Syst. Engr.}, 15038 volume = {6}, 15039 year = {1995}, 15040 pages = {87--95} 15041} 15042 15043@TechReport{ drashansky96, 15044 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 15045 author = {R. Drashansky and A. Joshi and J. R. Rice}, 15046 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 15047 year = {1996} 15048} 15049 15050@Article{ michopoulos05, 15051 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 15052 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 15053 journal = {Journal of Computing and Information Science in Engineering}, 15054 volume = {5}, 15055 issue = {3}, 15056 pages = {198--213}, 15057 year = {2005} 15058} 15059 15060@Article{ dubey09, 15061 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 15062 Multiphysics Simulation Code}, 15063 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 15064 Siegel and K. Weide}, 15065 journal = {Parallel Computing}, 15066 volume = {35}, 15067 issue = {10 -- 11}, 15068 pages = {512 -- 522}, 15069 year = {2009} 15070} 15071 15072@Book{ bottloring95, 15073 author = {Raoul Bott and Loring W. Tu}, 15074 title = {Differential Forms in Algebraic Topology}, 15075 publisher = {Springer}, 15076 year = {1995} 15077} 15078 15079@Book{ kobayashinomizu96, 15080 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 15081 title = {Foundations of Differential Geometry}, 15082 publisher = {Wiley-Interscience}, 15083 year = {1996} 15084} 15085 15086@Article{ hornungkohn02, 15087 author = {Richard D. Hornung and Scott R. Kohn}, 15088 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 15089 journal = {Concurrency and Computation: Practice and Experience}, 15090 volume = {14}, 15091 pages = {347--368}, 15092 year = {2002} 15093} 15094 15095@InProceedings{ concepts06, 15096 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 15097 Gabriel Dos Reis and Andrew Lumsdaine}, 15098 title = {Concepts: Linguistic Support for Generic Programming in C++}, 15099 booktitle = {Proceedings of OOPSLA 2006}, 15100 year = {2006}, 15101 pages = {???--???} 15102} 15103 15104@Book{ hatcher02, 15105 author = {Hatcher, Allen}, 15106 title = {Algebraic Topology}, 15107 publisher = {Cambridge University Press}, 15108 year = {2002} 15109} 15110 15111@Book{ gammahelmjohnsonvlissides95, 15112 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 15113 development, offering timeless and elegant solutions to common problems in 15114 software design. It describes patterns for managing object creation, composing 15115 objects into larger structures, and coordinating control flow between objects. The 15116 book provides numerous examples where using composition rather than inheritance 15117 can improve the reusability and flexibility of code. Note, though, that it's not a 15118 tutorial but a catalog that you can use to find an object-oriented design pattern 15119 that's appropriate for the needs of your particular application--a selection for 15120 virtuoso programmers who appreciate (or require) consistent, well-engineered 15121 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 15122 more valuable than ever! 15123 15124 Use the contents of the CD to create your own design documents and reusable 15125 components. The CD contains: 23 patterns you can cut and paste into your own 15126 design documents; sample code demonstrating pattern implementation; complete 15127 Design Patterns content in standard HTML format, with numerous hyperlinked 15128 cross-references; accessed through a standard web browser; Java-based dynamic 15129 search mechanism, enhancing online seach capabilities; graphical user environment, 15130 allowing ease of navigation. 15131 15132 First published in 1995, this landmark work on object-oriented software design 15133 presents a catalog of simple and succinct solutions to common design problems. 15134 Created by four experienced designers, the 23 patterns contained herein have 15135 become an essential resource for anyone developing reusable object-oriented 15136 software. In response to reader demand, the complete text and pattern catalog are 15137 now available on CD-ROM. This electronic version of Design Patterns enables 15138 programmers to install the book directly onto a computer or network for use as an 15139 online reference for creating reusable object-oriented software. 15140 15141 The authors first describe what patterns are and how they can help you in the 15142 design process. They then systematically name, explain, evaluate, and catalog 15143 recurring designs in object-oriented systems. All patterns are compiled from 15144 real-world examples and include code that demonstrates how they may be implemented 15145 in object-oriented programming languages such as C++ and Smalltalk. Readers who 15146 already own the book will want the CD to take advantage of its dynamic search 15147 mechanism and ready-to-install patterns.}}, 15148 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 15149 citeulike-article-id={115158}, 15150 howpublished = {Hardcover}, 15151 isbn = {0201633612}, 15152 keywords = {1995 algorithms architecture book books computer computing design design-pattern 15153 design-patterns design_patterns designpatterns development diplom entwurfsmuster 15154 four gang gof java mathgamespatterns no-tag object object-orientation 15155 object-oriented of oo-patterns oop oriented pattern patterns programming se 15156 software software-development software-engineering software_design 15157 softwareengineering standard}, 15158 month = jan, 15159 publisher = {{Addison-Wesley Professional}}, 15160 title = {Design Patterns}, 15161 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 15162 year = {1995} 15163} 15164 15165@InProceedings{ chaco95, 15166 author = {Bruce Hendrickson and Robert Leland}, 15167 title = {A multilevel algorithm for partitioning graphs}, 15168 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 15169 (CDROM)}, 15170 year = {1995}, 15171 isbn = {0-89791-816-9}, 15172 pages = {28}, 15173 location = {San Diego, California, United States}, 15174 doi = {10.1145/224170.224228}, 15175 publisher = {ACM Press}, 15176 address = {New York} 15177} 15178 15179@Book{ aleksandrov98, 15180 author = {Aleksandrov, Pavel S.}, 15181 title = {Combinatorial Topology}, 15182 publisher = {Dover}, 15183 volume = {3}, 15184 year = {1998} 15185} 15186 15187@Book{ steenrod99, 15188 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 15189 importance in modern physics--such as in gauge theory. This book, a succinct 15190 introduction to the subject by renown mathematician Norman Steenrod, was the first 15191 to present the subject systematically. 15192 15193 It begins with a general introduction to bundles, including such topics as 15194 differentiable manifolds and covering spaces. The author then provides brief 15195 surveys of advanced topics, such as homotopy theory and cohomology theory, before 15196 using them to study further properties of fibre bundles. The result is a classic 15197 and timeless work of great utility that will appeal to serious mathematicians and 15198 theoretical physicists alike. }}, 15199 author = {Steenrod, Norman}, 15200 citeulike-article-id={712999}, 15201 howpublished = {Paperback}, 15202 isbn = {0691005486}, 15203 keywords = {fibre_bundles topology}, 15204 month = apr, 15205 publisher = {{Princeton University Press}}, 15206 title = {The Topology of Fibre Bundles. (PMS-14)}, 15207 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 15208 year = {1999} 15209} 15210 15211@Book{ bredon97, 15212 author = {Bredon, Glen E.}, 15213 title = {Sheaf Theory}, 15214 publisher = {Springer}, 15215 pages = {524}, 15216 series = {Graduate Texts in Mathematics}, 15217 year = {1997} 15218} 15219 15220@TechReport{ tautgesmeyers04, 15221 title = {{MOAB}: A Mesh-Oriented Database}, 15222 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 15223 Ernst}, 15224 institution = {Sandia National Laboratories}, 15225 number = {SAND2004-1592}, 15226 month = apr, 15227 year = {2004} 15228} 15229 15230@Article{ tautges04, 15231 author = {Timothy J. Tautges}, 15232 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 15233 journal = {Engineering With Computers}, 15234 volume = {20}, 15235 pages = {286--293}, 15236 year = {2004} 15237} 15238 15239@InProceedings{ meyers02, 15240 author = {Ray Meyers et. al}, 15241 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 15242 booktitle = {8th International conference on numerical grid generation in computational field 15243 simulations}, 15244 month = jun, 15245 year = {2002} 15246} 15247 15248@InProceedings{ seolshepard05, 15249 author = {E. S. Seol and Mark S. Shephard}, 15250 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 15251 Analysis}, 15252 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 15253 year = {2005} 15254} 15255 15256@Article{ beallwalshshephard04, 15257 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 15258 title = {A comparison of techniques for geometry access related to mesh generation}, 15259 journal = {Engineering With Computers}, 15260 volume = {20}, 15261 number = {3}, 15262 pages = {210--221}, 15263 year = {2004} 15264} 15265 15266@Article{ careyandersoncarneskirk04, 15267 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 15268 Kirk}, 15269 title = {Some aspects of adaptive grid technology related to boundary and interior 15270 layers}, 15271 journal = {Journal of Computational Applied Mathematics}, 15272 volume = {166}, 15273 number = {1}, 15274 pages = {55--86}, 15275 year = {2004} 15276} 15277 15278@PhDThesis{ gralthesis, 15279 author = {Guntram Berti}, 15280 title = {Generic Software Components for Scientific Computing}, 15281 school = {TU Cottbus}, 15282 year = {2000}, 15283 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 15284} 15285 15286@Article{ whitehead1949, 15287 title = {Combinatorial homotopy. I}, 15288 author = {John HC Whitehead}, 15289 journal = {Bulletin of the American Mathematical Society}, 15290 volume = {55}, 15291 number = {3. P1}, 15292 pages = {213--245}, 15293 year = {1949}, 15294 publisher = {American Mathematical Society} 15295} 15296 15297@Article{ beylkincoifmanrokhlin91, 15298 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 15299 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 15300 journal = {Communications on Pure and Applied Mathematics}, 15301 volume = {44}, 15302 pages = {141--183}, 15303 year = {1991} 15304} 15305 15306@Book{ wesseling92, 15307 author = {Pieter Wesseling}, 15308 title = {An Introduction to Multigrid Methods}, 15309 publisher = {John Wiley and Sons}, 15310 year = {1992} 15311} 15312 15313@Book{ grakakos04, 15314 author = {Loukas Grakakos}, 15315 title = {Classical and Modern Fourier Analysis}, 15316 publisher = {Pearson Education}, 15317 address = {New Jersey}, 15318 year = {2004} 15319} 15320 15321@Misc{ hlib-web-page, 15322 key = {HLib}, 15323 title = {{HLib} {Web} page}, 15324 note = {{\texttt{http://www.hlib.org/}}}, 15325 annote = {Hierarchical matrices for fast integral transform} 15326} 15327 15328@Article{ hackbusch99, 15329 author = {Wolfgang Hackbusch}, 15330 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 15331 Introduction to {$\mathcal H$}-matrices}, 15332 journal = {Computing}, 15333 volume = {62}, 15334 pages = {89--108}, 15335 year = {1999} 15336} 15337 15338@TechReport{ kay1999green, 15339 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 15340 equations}, 15341 author = {Kay, D. and Loghin, D.}, 15342 year = {1999}, 15343 institution = {Oxford University Computing Laboratory}, 15344 number = {99/06} 15345} 15346 15347@Article{ bebendorf2003existence, 15348 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 15349 elliptic operators with {$L^\infty$}-coefficients}, 15350 author = {Bebendorf, M. and Hackbusch, W.}, 15351 journal = {Numerische Mathematik}, 15352 volume = {95}, 15353 number = {1}, 15354 pages = {1--28}, 15355 year = {2003}, 15356 publisher = {Springer} 15357} 15358 15359@Article{ hackbusch2005direct, 15360 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 15361 H$}-matrix approximation}, 15362 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 15363 journal = {Computing and Visualization in Science}, 15364 volume = {8}, 15365 number = {3}, 15366 pages = {179--188}, 15367 year = {2005}, 15368 publisher = {Springer} 15369} 15370 15371@TechReport{ duphof2003, 15372 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 15373 Logg and L. R. Scott}, 15374 title = {The {FE}ni{CS} project}, 15375 institution = {Chalmers Finite Element Center Preprint Series}, 15376 number = {2003--21}, 15377 year = {2003} 15378} 15379 15380@Article{ flame01, 15381 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 15382 Geijn}, 15383 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 15384 journal = {Transactions on Mathematical Software}, 15385 volume = {27}, 15386 number = {4}, 15387 year = {2001}, 15388 pages = {422--455} 15389} 15390 15391@Article{ puschel05, 15392 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 15393 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 15394 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 15395 Nick Rizzolo}, 15396 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 15397 journal = {Proceedings of the IEEE}, 15398 volume = {93}, 15399 number = {2}, 15400 year = {2005}, 15401 note = {special issue on "Program Generation, Optimization, and Adaptation"} 15402} 15403 15404@Article{ kirbylogg06, 15405 author = {Robert C. Kirby and Anders Logg}, 15406 title = {A compiler for variational forms}, 15407 journal = {ACM Transactions on Mathematical Software}, 15408 volume = {32}, 15409 number = {3}, 15410 year = {2006}, 15411 issn = {0098-3500}, 15412 pages = {417--444}, 15413 doi = {10.1145/1163641.1163644}, 15414 publisher = {ACM Press}, 15415 address = {New York, NY} 15416} 15417 15418@Article{ kirbylogg07, 15419 author = {Robert C. Kirby and Anders Logg}, 15420 title = {Efficient compilation of a class of variational forms}, 15421 journal = {ACM Transactions on Mathematical Software}, 15422 volume = {33}, 15423 number = {3}, 15424 year = {2007}, 15425 issn = {0098-3500}, 15426 pages = {17}, 15427 doi = {10.1145/1268769.1268771}, 15428 publisher = {ACM Press}, 15429 address = {New York, NY} 15430} 15431 15432@Article{ bankdupont81, 15433 author = {Randolph Bank and Todd Dupont}, 15434 title = {An optimal order process for solving finite element equations}, 15435 journal = {Mathematics of Computation}, 15436 volume = {36}, 15437 pages = {35--51}, 15438 year = {1981} 15439} 15440 15441@TechReport{ adams00, 15442 author = {Mark F. Adams}, 15443 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 15444 in solid mechanics}, 15445 institution = {UC Berkeley}, 15446 number = {CSD-00-1103}, 15447 year = {2000}, 15448 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 15449} 15450 15451@Article{ bergengradlhuelsemannruede06, 15452 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 15453 title = {A Massively Parallel Multigrid Method for Finite Elements}, 15454 journal = {Computing in Science \& Engineering}, 15455 volume = {8}, 15456 number = {6}, 15457 pages = {56--62}, 15458 year = {2006} 15459} 15460 15461@MastersThesis{ brunethesis08, 15462 author = {Peter R. Brune}, 15463 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 15464 school = {University of Chicago}, 15465 address = {Chicago, IL}, 15466 year = {2008}, 15467 month = feb 15468} 15469 15470@Article{ arnoldwinther02, 15471 author = {Douglas N. Arnold and Ragnar Winther}, 15472 title = {Mixed finite elements for elasticity}, 15473 journal = {Numerische Mathematik}, 15474 volume = {92}, 15475 number = {3}, 15476 month = sep, 15477 year = {2002}, 15478 pages = {401--419}, 15479 doi = {10.1007/s002110100348} 15480} 15481 15482@Article{ arnoldfalkwinther06, 15483 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 15484 title = {Finite element exterior calculus, homological techniques, and applications}, 15485 journal = {Acta Numerica}, 15486 year = {2006}, 15487 volume = {15}, 15488 pages = {1--155}, 15489 publisher = {Cambridge University Press}, 15490 doi = {10.1017/S0962492906210018} 15491} 15492 15493@Article{ kirby04, 15494 author = {Robert C. Kirby}, 15495 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 15496 functions}, 15497 journal = {ACM Transactions on Mathematical Software}, 15498 volume = {30}, 15499 number = {4}, 15500 year = {2004}, 15501 issn = {0098-3500}, 15502 pages = {502--516}, 15503 doi = {10.1145/1039813.1039820}, 15504 publisher = {ACM Press}, 15505 address = {New York, NY} 15506} 15507 15508@Article{ kirby06, 15509 author = {Robert C. Kirby}, 15510 title = {Optimizing {FIAT} with level 3 {BLAS}}, 15511 journal = {ACM Transactions on Mathematical Software}, 15512 volume = {32}, 15513 number = {2}, 15514 year = {2006}, 15515 issn = {0098-3500}, 15516 pages = {223--235}, 15517 doi = {10.1145/1141885.1141889}, 15518 publisher = {ACM Press}, 15519 address = {New York, NY} 15520} 15521 15522@Misc{ bluecrystal08, 15523 author = {{B}lue {C}rystal Cluster}, 15524 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 15525 year = {2008}, 15526 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 15527} 15528 15529@Article{ beylkin95, 15530 author = {Gregory Beylkin}, 15531 title = {On the Fast Fourier Transform of Functions With Singularities}, 15532 journal = {Applied and Computational Harmonic Analysis}, 15533 volume = {2}, 15534 pages = {363--381}, 15535 year = {1995} 15536} 15537 15538@InProceedings{ riehl08, 15539 author = {Jonathan Riehl}, 15540 title = {Implementing the MyFEM Embedded Domain-specific Language}, 15541 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 15542 Development (DSPD'08)}, 15543 address = {Nashville, TN}, 15544 year = {2008} 15545} 15546 15547@Article{ appel85, 15548 author = {Andrew W. Appel}, 15549 date-added = {2008-02-27 12:23:39 +0000}, 15550 date-modified = {2008-02-27 12:24:02 +0000}, 15551 doi = {10.1137/0906008}, 15552 journal = {SIAM Journal on Scientific and Statistical Computing}, 15553 keywords = {treecodes}, 15554 number = {1}, 15555 pages = {85-103}, 15556 publisher = {SIAM}, 15557 title = {An Efficient Program for Many-Body Simulation}, 15558 volume = {6}, 15559 year = {1985} 15560} 15561 15562@Article{ ewald21, 15563 author = {{Ewald}, P.~P.}, 15564 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 15565 journal = {Annalen der Physik}, 15566 year = {1921}, 15567 volume = {369}, 15568 pages = {253-287}, 15569 doi = {10.1002/andp.19213690304}, 15570 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 15571 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 15572} 15573 15574@Article{ greengardrokhlin87, 15575 author = {L. Greengard and V. Rokhlin}, 15576 date-added = {2008-02-15 18:43:55 +0000}, 15577 date-modified = {2008-02-26 20:09:11 +0000}, 15578 doi = {10.1016/0021-9991(87)90140-9}, 15579 journal = {J. Comput.\ Phys.}, 15580 keywords = {FMM}, 15581 number = {2}, 15582 pages = {325--348}, 15583 title = {A Fast Algorithm for Particle Simulations}, 15584 url = {citeseer.ist.psu.edu/greengard87fast.html}, 15585 volume = {73}, 15586 year = {1987}, 15587 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 15588} 15589 15590@Article{ greengardrokhlin97, 15591 author = {L. Greengard and V. Rokhlin}, 15592 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 15593 Dimensions}, 15594 journal = {Acta Numerica}, 15595 volume = {6}, 15596 year = {1997}, 15597 pages = {229--269} 15598} 15599 15600@Article{ luchenghuangmccammon06, 15601 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 15602 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 15603 systems}, 15604 journal = {PNAS}, 15605 doi = {10.1073/pnas.0605166103}, 15606 volume = {102}, 15607 number = {51}, 15608 year = {2006}, 15609 pages = {19314--19319} 15610} 15611 15612@Article{ schussnadlereisenberg01, 15613 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 15614 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 15615 from a molecular model}, 15616 journal = {Physical Review E}, 15617 volume = {64}, 15618 number = {3}, 15619 year = {2001} 15620} 15621 15622@Book{ hairerlubichwanner02, 15623 author = {E. Hairer and Ch. Lubich and G. Wanner}, 15624 title = {Geometric Numerical Integration}, 15625 publisher = {Springer-Verlag}, 15626 address = {Berlin Heidelberg}, 15627 year = {2002} 15628} 15629 15630@Article{ holstbakerwang00, 15631 author = {M. Holst and N. Baker and F. Wang}, 15632 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 15633 equation on massively parallel computers}, 15634 journal = {Journal of Computational Chemistry}, 15635 volume = {21}, 15636 year = {2000} 15637} 15638 15639@Book{ hockneyeastwood81, 15640 author = {R. Hockney and J. Eastwood}, 15641 title = {Computer simulation using particles}, 15642 publisher = {McGraw-Hill}, 15643 address = {New York}, 15644 year = {1981} 15645} 15646 15647@Article{ lutydavistironigunsteren94, 15648 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 15649 Gunsteren}, 15650 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 15651 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 15652 journal = {Molecular Simulation}, 15653 volume = {14}, 15654 number = {1}, 15655 year = {1994}, 15656 pages = {11--20} 15657} 15658 15659@Book{ briggshensonmccormick00, 15660 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 15661 title = {A Multigrid Tutorial (2nd ed.)}, 15662 year = {2000}, 15663 isbn = {0-89871-462-1}, 15664 publisher = {Society for Industrial and Applied Mathematics}, 15665 address = {Philadelphia, PA} 15666} 15667 15668@Article{ chartier2003spectral, 15669 title = {Spectral AMGe ($\rho$ AMGe)}, 15670 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 15671 McCormick, S and Ruge, J and Vassilevski, PS}, 15672 journal = {SIAM Journal on Scientific Computing}, 15673 volume = {25}, 15674 number = {1}, 15675 pages = {1--26}, 15676 year = {2003}, 15677 publisher = {SIAM} 15678} 15679 15680@Article{ galvis2010domain, 15681 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 15682 media}, 15683 author = {Galvis, Juan and Efendiev, Yalchin}, 15684 journal = {Multiscale Modeling \& Simulation}, 15685 volume = {8}, 15686 number = {4}, 15687 pages = {1461--1483}, 15688 year = {2010}, 15689 publisher = {SIAM} 15690} 15691 15692@Book{ brennerscott02, 15693 author = {Susanne~C. Brenner and L.~Ridgway Scott}, 15694 title = {The mathematical theory of finite element methods}, 15695 year = {2002}, 15696 isbn = {0-38795-451-1}, 15697 publisher = {Springer}, 15698 pages = {361} 15699} 15700 15701@Book{ trefethenbau97, 15702 author = {Lloyd N. Trefethen and David {Bau, III}}, 15703 title = {Numerical Linear Algebra}, 15704 publisher = {Society for Industrial and Applied Mathematics}, 15705 address = {Philadelphia, PA}, 15706 pages = {xii + 361}, 15707 year = {1997}, 15708 isbn = {0-89871-361-7}, 15709 isbn-13 = {978-0-89871-361-9}, 15710 lccn = {QA184 .T74 1997}, 15711 mrclass = {65-01 (65-02 65Fxx)}, 15712 mrnumber = {MR1444820 (98k:65002)}, 15713 mrreviewer = {Moody T. Chu}, 15714 bibdate = {Wed Jan 07 15:23:19 1998}, 15715 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 15716} 15717 15718@Article{ liptonreagan2014, 15719 title = {Quantum Algorithms via Linear Algebra: A Primer}, 15720 author = {Richard J Lipton and Kenneth W Regan}, 15721 pages = {206}, 15722 isbn = {978-0-26202-839-4}, 15723 year = {2014} 15724} 15725 15726@InProceedings{ rhea08, 15727 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 15728 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 15729 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 15730 booktitle = {Proceedings of IEEE/ACM SC '08}, 15731 year = {2008} 15732} 15733 15734@Misc{ bursteddewilcox09, 15735 author = {Carsten Burstedde and Lucas~C. Wilcox}, 15736 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 15737 note = {in preparation} 15738} 15739 15740@Article{ skeeltezcanhardy02, 15741 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 15742 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 15743 journal = {J. Comp. Chem.}, 15744 volume = {23}, 15745 pages = {673--684}, 15746 year = {2002} 15747} 15748 15749@Article{ verschelde99, 15750 author = {Jan Verschelde}, 15751 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 15752 homotopy continuation}, 15753 journal = {ACM Trans. Math. Softw.}, 15754 volume = {25}, 15755 number = {2}, 15756 issn = {0098-3500}, 15757 pages = {251--276}, 15758 doi = {10.1145/317275.317286}, 15759 publisher = {ACM}, 15760 address = {New York, NY}, 15761 year = {1999} 15762} 15763 15764@InProceedings{ sommeseverscheldewampler08, 15765 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 15766 title = {Solving Polynomial Systems Equation by Equation}, 15767 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 15768 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 15769 pages = {133--152}, 15770 publisher = {Springer-Verlag}, 15771 year = {2008} 15772} 15773 15774@Article{ phanthientanner77, 15775 author = {N. Phan-Thien and R.~I. Tanner}, 15776 title = {A new constitutive equation derived from network theory}, 15777 journal = {J. Non-Newt. Fluid Mech.}, 15778 volume = {2}, 15779 pages = {353}, 15780 year = {1977} 15781} 15782 15783@Manual{ sage, 15784 key = {SAGE}, 15785 author = {W.\thinspace{}A. Stein and others}, 15786 organization = {The Sage~Development Team}, 15787 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 15788 note = {{\tt http://www.sagemath.org}}, 15789 year = {2009} 15790} 15791 15792@Misc{ bateshauensteinsommesewampler06, 15793 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 15794 Wampler}, 15795 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 15796 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 15797} 15798 15799@Article{ archer09, 15800 author = {A. J. 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Keyes}, 15875 title = {{Fusion Simulation Project Workshop Report}}, 15876 month = jul, 15877 year = {2007}, 15878 note = {Available via 15879 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 15880} 15881 15882@Misc{ dahlburg02, 15883 author = {J. {Dahlburg (Chair)}}, 15884 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 15885 year = {2002}, 15886 note = {Available via 15887 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 15888} 15889 15890@Misc{ brown08, 15891 author = {D. {Brown (Chair)}}, 15892 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 15893 to the Future}}, 15894 year = {2008}, 15895 howpublished = {Office of Science, U.S. Department of Energy}, 15896 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 15897} 15898 15899@Misc{ crosscutting10, 15900 author = {D. Brown and P. {Messina (Chairs)}}, 15901 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 15902 Exascale}}, 15903 year = {2010}, 15904 howpublished = {Office of Science, U.S. Department of Energy}, 15905 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 15906} 15907 15908@Misc{ extreme-scale-solvers-workshop12, 15909 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 15910 L.C. McInnes and E. Ng and S. Wild}, 15911 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 15912 Architectures}, 15913 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 15914 note = {{Washington, DC}, March 8-9, 2012}, 15915 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 15916 year = {2012} 15917} 15918 15919@Misc{ monizrosner09, 15920 author = {{E. Moniz and R. Rosner}}, 15921 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 15922 and Simulation at the Extreme Scale}}, 15923 month = may, 15924 year = {2009}, 15925 note = {See 15926 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 15927} 15928 15929@Misc{ blanford08, 15930 author = {{R. Blandord (Chair)}}, 15931 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 15932 Computing at the Extreme Scale}}, 15933 month = dec, 15934 year = {2008}, 15935 note = {See 15936 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 15937} 15938 15939@Misc{ exascale07, 15940 author = {H. Simon and T. Zacharia and R. Stevens}, 15941 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 15942 year = {2007}, 15943 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 15944} 15945 15946@Misc{ ascrbreakthroughs08, 15947 author = {{Panel on Recent Significant Advancements in Computational Science}}, 15948 title = {Breakthroughs}, 15949 year = {2008}, 15950 note = {See 15951 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 15952} 15953 15954@Misc{ petsc-rd100-2009, 15955 author = {{R\&D Magazine}}, 15956 title = {{PETSc} {R}\&{D} 100 Award}, 15957 year = {2009}, 15958 note = {See 15959 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 15960} 15961 15962@Article{ compass-scidac08, 15963 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 15964 R. Ryne}, 15965 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 15966 Computational Science for Future Accelerators and Accelerator Technologies}, 15967 journal = {J. Phys.: Conf. Ser.}, 15968 volume = {125}, 15969 year = {2008}, 15970 pages = {012001}, 15971 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 15972} 15973 15974@Article{ compass-amundson-scidac08, 15975 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 15976 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 15977 Stoltz}, 15978 journal = {J. Phys.: Conf. Ser.}, 15979 volume = {125}, 15980 year = {2008} 15981} 15982 15983@InProceedings{ muszala09, 15984 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 15985 Simulations}, 15986 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 15987 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 15988 {(CBHPC 2009)}}, 15989 year = {2009} 15990} 15991 15992@Article{ gaston09, 15993 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 15994 Equations}, 15995 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 15996 journal = {Nuclear Engineering and Design}, 15997 volume = {239}, 15998 number = {10}, 15999 year = {2009}, 16000 pages = {1768 -- 1778} 16001} 16002 16003@Article{ gaston09b, 16004 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 16005 Engineering}, 16006 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 16007 and C. Permann and W. Taitano}, 16008 journal = {J. Phys.: Conf. 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Groen and S. Harfst and R. Izzard and J. Juric and 16038 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 16039 booktitle = {Proceedings of ICCS 2008}, 16040 year = {2008} 16041} 16042 16043@Article{ klocknerwarburtonbridgehesthaven09, 16044 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 16045 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 16046 journal = {J. Comput. Phys.}, 16047 volume = {228}, 16048 number = {21}, 16049 year = {2009}, 16050 issn = {0021-9991}, 16051 pages = {7863--7882}, 16052 doi = {10.1016/j.jcp.2009.06.041}, 16053 publisher = {Academic Press Professional}, 16054 address = {San Diego, CA} 16055} 16056 16057@PhDThesis{ rankin99, 16058 author = {Rankin, W. T.}, 16059 keywords = {FMM, parallel FMM}, 16060 school = {Department of Electrical and Computer Engineering, Duke University}, 16061 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 16062 year = {1999} 16063} 16064 16065@InProceedings{ warrensalmon93, 16066 abstract = {We report on an efficient adaptive N-body method which we have recently designed 16067 and implemented. The algorithm computes the forces on an arbitrary distribution of 16068 bodies in a time which scales as N log N with the particle number. The accuracy of 16069 the force calculations is analytically bounded, and can be adjusted via a user 16070 defined parameter between a few percent relative accuracy, down to machine 16071 arithmetic accuracy. Instead of using pointers to indicate the topology of the 16072 tree, we identify...}, 16073 address = {New York}, 16074 author = {Warren, Michael S. and Salmon, John K.}, 16075 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 16076 citeulike-article-id={580952}, 16077 keywords = {oct-tree}, 16078 pages = {12--21}, 16079 publisher = {ACM}, 16080 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 16081 year = {1993}, 16082 doi = {10.1145/169627.169640}, 16083 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 16084} 16085 16086@Unpublished{ cruzwccm10, 16087 author = {Felipe A. Cruz}, 16088 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 16089 note = {Presentation at WCCM 2010, Sydney Australia}, 16090 year = {2010} 16091} 16092 16093@Article{ mcguffee06, 16094 author = {S.~R. {McGuffee} and A.~H. Elcock}, 16095 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 16096 of salt, {pH}, point mutations, and protein concentration in simulations of 16097 1000-molecule systems}, 16098 journal = {Journal of the American Chemical Society}, 16099 volume = {128}, 16100 pages = {12098--12110}, 16101 year = {2006} 16102} 16103 16104@Article{ nilsencaihoylandlangtangen10, 16105 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 16106 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 16107 in Python}}, 16108 journal = {ArXiv e-prints}, 16109 archiveprefix = {arXiv}, 16110 eprint = {1002.0705}, 16111 primaryclass = {cs.DC}, 16112 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 16113 - Programming Languages}, 16114 year = {2010}, 16115 month = feb, 16116 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 16117 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16118} 16119 16120@Misc{ mcinnes:siam09:minisymposium, 16121 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 16122 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 16123 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 16124 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 16125 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 16126 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 16127 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 16128 Austin).} 16129} 16130 16131@Misc{ mcinnes:fsp-summary:feb2011, 16132 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 16133 title = {Solvers and Time Integration Breakout Summary}, 16134 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 16135 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 16136} 16137 16138@Misc{ dvi-materials:siamcse11, 16139 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 16140 Materials}, 16141 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 16142 Smith and L. Wang}, 16143 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 16144 and Engineering, March 3, 2011} 16145} 16146 16147@Misc{ jamroz:cemm10, 16148 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 16149 author = {B. Jamroz and S. Kruger and T. 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Tuminaro}, 16180 title = {Block preconditioners based on approximate commutators}, 16181 journal = {SIAM J. Sci. Comput.}, 16182 volume = {27}, 16183 number = {5}, 16184 year = {2006}, 16185 pages = {1651--1668} 16186} 16187 16188@Article{ braesssarazin1997, 16189 author = {Dietrich Braess and Regina Sarazin}, 16190 title = {An efficient smoother for the {Stokes} problem}, 16191 journal = {Applied Numerical Mathematics}, 16192 volume = {23}, 16193 number = {1}, 16194 year = {1997}, 16195 pages = {3--19}, 16196 doi = {10.1016/S0168-9274(96)00059-1} 16197} 16198 16199@Article{ wright2001large, 16200 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 16201 author = {Wright, T.G. and Trefethen, L.N.}, 16202 journal = {SIAM Journal on Scientific Computing}, 16203 volume = {23}, 16204 pages = {591}, 16205 year = {2001} 16206} 16207 16208@Misc{ wright2002eigtool, 16209 title = {Eig{T}ool}, 16210 author = {Wright, T.G. and Trefethen, LN}, 16211 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 16212 year = {2002} 16213} 16214 16215@Misc{ visit-web-site, 16216 key = {{VisIt}}, 16217 title = {{VisIt web site}}, 16218 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 16219 url = {http://wci.llnl.gov/codes/visit/}, 16220 year = {2011} 16221} 16222 16223@Book{ trefethen1996, 16224 title = {Finite difference and spectral methods for ordinary and partial differential 16225 equations}, 16226 author = {Lloyd Nicholas Trefethen}, 16227 year = {1996}, 16228 publisher = {Cornell University-Department of Computer Science and Center for Applied 16229 Mathematics} 16230} 16231 16232@Book{ trefethen2005spectra, 16233 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 16234 author = {Trefethen, L.N. and Embree, M.}, 16235 year = {2005}, 16236 publisher = {Princeton University Press} 16237} 16238 16239@Article{ gomez2010isogeometric, 16240 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 16241 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 16242 journal = {Computer Methods in Applied Mechanics and Engineering}, 16243 volume = {199}, 16244 number = {25-28}, 16245 pages = {1828--1840}, 16246 issn = {0045-7825}, 16247 year = {2010}, 16248 publisher = {Elsevier} 16249} 16250 16251@Article{ gomez2008isogeometric, 16252 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 16253 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 16254 journal = {Computer Methods in Applied Mechanics and Engineering}, 16255 volume = {197}, 16256 number = {49-50}, 16257 pages = {4333--4352}, 16258 year = {2008}, 16259 publisher = {Elsevier} 16260} 16261 16262@Misc{ fastmath:project, 16263 author = {Lori {Diachin (PI)}}, 16264 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 16265 (FASTMath) Institute}}, 16266 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 16267} 16268 16269@Misc{ exascale-software:proposal, 16270 author = {Peter {Beckman (PI)}}, 16271 title = {{Exascale Software Center}}, 16272 note = {proposal to DOE} 16273} 16274 16275@Misc{ imex:project, 16276 author = {Barry {Smith (PI)}}, 16277 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 16278 Multimodel PDEs}}, 16279 note = {DOE ASCR applied math project} 16280} 16281 16282@Misc{ intel-mic:website, 16283 author = {Intel}, 16284 title = {{Many Integrated Core Architecture}}, 16285 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 16286} 16287 16288@Article{ dudson:2009, 16289 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 16290 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 16291 journal = {Computer Physics Communications}, 16292 volume = {180}, 16293 pages = {1467}, 16294 year = {2009} 16295} 16296 16297@Article{ umansky:2009, 16298 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 16299 title = {{Status and verification of edge plasma turbulence code BOUT}}, 16300 journal = {Computer Physics Communications}, 16301 year = {2009}, 16302 volume = {180}, 16303 pages = {887-903} 16304} 16305 16306@Article{ xu:1998, 16307 author = {X.Q. Xu and R.H. Cohen}, 16308 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 16309 journal = {Computer Physics Communications}, 16310 year = {1998}, 16311 volume = {36}, 16312 number = {1-2}, 16313 pages = {158} 16314} 16315 16316@Article{ tron:1999, 16317 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 16318 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 16319 journal = {SIAM Journal on Optimization}, 16320 volume = {9}, 16321 number = {4}, 16322 pages = {1100-1127}, 16323 year = {1999} 16324} 16325 16326@Article{ stubenamg, 16327 author = {K. St\"{u}ben}, 16328 title = {A review of algebraic multigrid}, 16329 journal = {J. Comput. Appl. Math.}, 16330 volume = {128}, 16331 number = {1-2}, 16332 year = {2001}, 16333 issn = {0377-0427}, 16334 pages = {281--309}, 16335 doi = {10.1016/S0377-0427(00)00516-1}, 16336 publisher = {Elsevier Science Publishers B. V.}, 16337 address = {Amsterdam, The Netherlands, The Netherlands} 16338} 16339 16340@Article{ feuchtermg, 16341 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 16342 title = {Bridging the gap between geometric and algebraic multigrid methods}, 16343 journal = {Computing and visualization in science}, 16344 publisher = {Springer}, 16345 volume = {6}, 16346 number = {1}, 16347 year = {2003}, 16348 pages = {1--13} 16349} 16350 16351@Article{ chowmgsmoothness, 16352 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 16353 only attempts to interpolate in the directions of geometrical smoothness. These 16354 directions are determined by analyzing samples of algebraically smooth error, e. 16355 Neighboring grid points i and j are called smoothly coupled if e i and e j are 16356 consistently nearby in value. In addition, these dierences may be used to dene 16357 interpolation weights. These new ideas may be incorporated into the algebraic 16358 multigrid method. Test results show that the new method can have much lower grid 16359 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 16360 author = {Chow, Edmond}, 16361 citeulike-article-id={7675372}, 16362 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16363 journal = {American Journal of Mathematics}, 16364 keywords = {fem, multigrid}, 16365 pages = {197--215}, 16366 posted-at = {2010-08-17 23:29:51}, 16367 priority = {2}, 16368 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 16369 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16370 volume = {65}, 16371 year = {2001} 16372} 16373 16374@Article{ jonesamge, 16375 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 16376 elements) method based on element agglomeration. In the method, coarse grid 16377 elements are formed by agglomerating fine grid elements. Compatible interpolation 16378 operators are constructed which yield coarse grid basis functions with a minimal 16379 energy property. Heuristics based on interpolation quality measures are used to 16380 guide the agglomeration procedure. The performance of the resulting method is 16381 demonstrated in two-level numerical experiments.}}, 16382 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 16383 citeulike-article-id={8598569}, 16384 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16385 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 16386 journal = {SIAM Journal on Scientific Computing}, 16387 keywords = {amg, fem, multigrid}, 16388 number = {1}, 16389 pages = {109--133}, 16390 posted-at = {2011-01-13 18:05:55}, 16391 priority = {2}, 16392 publisher = {SIAM}, 16393 title = {{AMGE Based on Element Agglomeration}}, 16394 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16395 volume = {23}, 16396 year = {2001} 16397} 16398 16399@Article{ saad1993, 16400 author = {Saad, Youcef}, 16401 doi = {10.1137/0914028}, 16402 issn = {10648275}, 16403 journal = {SIAM Journal on Scientific Computing}, 16404 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 16405 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 16406 precondition-,preconditioned conju-,subject classi cations,variable 16407 preconditioners}, 16408 number = {2}, 16409 pages = {461--469}, 16410 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 16411 volume = {14}, 16412 year = {1993} 16413} 16414 16415@Misc{ path:homepage, 16416 author = {S. Dirkse and M. Ferris and T. Munson}, 16417 title = {{{PATH} {W}eb page}}, 16418 howpublished = {\url{http://pages.cs.wisc.edu/~ferris/path.html}} 16419} 16420 16421@Article{ ketcheson2008, 16422 author = {David I Ketcheson}, 16423 title = {Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with 16424 Low-Storage Implementations}, 16425 volume = {30}, 16426 journal = {SIAM Journal on Scientific Computing}, 16427 year = {2008}, 16428 pages = {2113--2136} 16429} 16430 16431@Article{ elman2009boundary, 16432 title = {{Boundary conditions in approximate commutator preconditioners for the 16433 Navier-Stokes equations}}, 16434 author = {Elman, H.C. and Tuminaro, R.}, 16435 journal = {Electronic Transactions on Numerical Analysis}, 16436 volume = {35}, 16437 pages = {257--280}, 16438 year = {2009} 16439} 16440 16441@Article{ elman2008tcp, 16442 title = {{A taxonomy and comparison of parallel block multi-level preconditioners for the 16443 incompressible Navier-Stokes equations}}, 16444 author = {Elman, H.C. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, 16445 R.}, 16446 journal = {Journal of Computational Physics}, 16447 volume = {227}, 16448 number = {1}, 16449 pages = {1790--1808}, 16450 year = {2008}, 16451 publisher = {Academic Press}, 16452 url = {http://chess.cs.umd.edu/~elman/papers/tax.pdf} 16453} 16454 16455@Article{ arioli2013, 16456 title = {Generalized {G}olub--{K}ahan bidiagonalization and stopping criteria}, 16457 author = {Arioli, Mario}, 16458 journal = {SIAM Journal on Matrix Analysis and Applications}, 16459 volume = {34}, 16460 number = {2}, 16461 pages = {571--592}, 16462 year = {2013}, 16463 publisher = {SIAM} 16464} 16465 16466@Book{ wesseling2009, 16467 title = {Principles of computational fluid dynamics}, 16468 author = {Wesseling, Pieter}, 16469 volume = {29}, 16470 year = {2009}, 16471 publisher = {Springer Science \& Business Media} 16472} 16473 16474@Article{ silvester2001efficient, 16475 title = {{Efficient preconditioning of the linearized Navier-Stokes equations for 16476 incompressible flow}}, 16477 author = {Silvester, D. and Elman, H. and Kay, D. and Wathen, A.}, 16478 journal = {Journal of Computational and Applied Mathematics}, 16479 volume = {128}, 16480 number = {1-2}, 16481 pages = {261--279}, 16482 issn = {0377-0427}, 16483 year = {2001}, 16484 publisher = {Elsevier} 16485} 16486 16487@Article{ elman1999bfbt, 16488 title = {{Preconditioning for the steady-state Navier-Stokes equations with low 16489 viscosity}}, 16490 author = {Elman, H.C.}, 16491 journal = {SIAM Journal on Scientific Computing}, 16492 volume = {20}, 16493 number = {4}, 16494 pages = {1299--1316}, 16495 issn = {1064-8275}, 16496 year = {1999}, 16497 publisher = {Citeseer} 16498} 16499 16500@Article{ elman2006bpb, 16501 title = {{Block preconditioners based on approximate commutators}}, 16502 author = {Elman, H. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, R.}, 16503 journal = {SIAM Journal on Scientific Computing}, 16504 volume = {27}, 16505 number = {5}, 16506 pages = {1651--1668}, 16507 year = {2006}, 16508 publisher = {Philadelphia, PA: SIAM, c1993-} 16509} 16510 16511@Article{ olshanskii2006analysis, 16512 title = {{Analysis of a Stokes interface problem}}, 16513 author = {Olshanskii, M.A. and Reusken, A.}, 16514 journal = {Numerische Mathematik}, 16515 volume = {103}, 16516 number = {1}, 16517 pages = {129--149}, 16518 issn = {0029-599X}, 16519 year = {2006}, 16520 publisher = {Springer} 16521} 16522 16523@Article{ patankar1972cph, 16524 title = {{A calculation procedure for heat, mass and momentum transfer in 16525 three-dimensional parabolic flows}}, 16526 author = {Patankar, S.V. and Spalding, D.B.}, 16527 journal = {Int. J. Heat Mass Transfer}, 16528 volume = {15}, 16529 pages = {1787--1806}, 16530 year = {1972} 16531} 16532 16533@Article{ rannacher1992simple, 16534 title = {{Simple nonconforming quadrilateral Stokes element}}, 16535 author = {Rannacher, R. and Turek, S.}, 16536 journal = {Numerical Methods for Partial Differential Equations}, 16537 volume = {8}, 16538 number = {2}, 16539 pages = {97--111}, 16540 issn = {1098-2426}, 16541 year = {1992}, 16542 publisher = {Wiley Online Library} 16543} 16544 16545@Article{ rannacher2000finite, 16546 title = {Finite Element Methods for the Incompressible {N}avier-{S}tokes Equations}, 16547 author = {Rannacher, R.}, 16548 journal = {Fundamental Directions in Mathematical Fluid Mechanics}, 16549 pages = {191}, 16550 isbn = {3764364149}, 16551 year = {2000}, 16552 publisher = {Birkhauser} 16553} 16554 16555@Article{ vanka1986block, 16556 title = {{Block-implicit multigrid solution of Navier-Stokes equations in primitive 16557 variables}}, 16558 author = {Vanka, S.P.}, 16559 journal = {Journal of Computational Physics}, 16560 volume = {65}, 16561 number = {1}, 16562 pages = {138--158}, 16563 issn = {0021-9991}, 16564 year = {1986}, 16565 publisher = {Elsevier} 16566} 16567 16568@Article{ eisenstat1983variational, 16569 title = {Variational iterative methods for nonsymmetric systems of linear equations}, 16570 author = {Eisenstat, S.C. and Elman, H.C. and Schultz, M.H.}, 16571 journal = {SIAM Journal on Numerical Analysis}, 16572 volume = {20}, 16573 number = {2}, 16574 pages = {345--357}, 16575 year = {1983}, 16576 publisher = {JSTOR} 16577} 16578 16579@InProceedings{ burstedde2008scalable, 16580 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16581 author = {Burstedde, C. and Ghattas, O. and Gurnis, M. and Stadler, G. and Tan, E. and Tu, 16582 T. and Wilcox, L.C. and Zhong, S.}, 16583 booktitle = {Proceedings of the 2008 ACM/IEEE conference on Supercomputing}, 16584 pages = {62}, 16585 year = {2008}, 16586 organization = {IEEE Press} 16587} 16588 16589@Article{ burstedde2009parallel, 16590 title = {Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes} 16591 flow problems}, 16592 author = {Burstedde, C. and Ghattas, O. and Stadler, G. and Tu, T. and Wilcox, L.C.}, 16593 journal = {Computer Methods in Applied Mechanics and Engineering}, 16594 volume = {198}, 16595 number = {21-26}, 16596 pages = {1691--1700}, 16597 year = {2009}, 16598 publisher = {Elsevier} 16599} 16600 16601@Article{ stadler2010dynamics, 16602 title = {The dynamics of plate tectonics and mantle flow: From local to global scales}, 16603 author = {Stadler, G. and Gurnis, M. and Burstedde, C. and Wilcox, L.C. and Alisic, L. and 16604 Ghattas, O.}, 16605 journal = {Science}, 16606 volume = {329}, 16607 number = {5995}, 16608 pages = {1033}, 16609 year = {2010}, 16610 publisher = {American Association for the Advancement of Science} 16611} 16612 16613@Article{ tackley2008modelling, 16614 title = {Modelling compressible mantle convection with large viscosity contrasts in a 16615 three-dimensional spherical shell using the yin-yang grid}, 16616 author = {Tackley, P.J.}, 16617 journal = {Physics of the Earth and Planetary Interiors}, 16618 volume = {171}, 16619 number = {1-4}, 16620 pages = {7--18}, 16621 year = {2008}, 16622 publisher = {Elsevier} 16623} 16624 16625@Article{ moresizhonggurnis96, 16626 author = {Louis N. Moresi and Shijie Zhong and Michael Gurnis}, 16627 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 16628 viscosity}, 16629 journal = {Physics of the Earth and Planetary Interiors}, 16630 volume = {97}, 16631 pages = {83-–94}, 16632 year = {1996} 16633} 16634 16635@Article{ moresisolomatov95, 16636 author = {Louis N. Moresi and V. S. Solomatov}, 16637 title = {Numerical investigation of {2D} convection with extremely large viscosity 16638 variations}, 16639 journal = {Physics of Fluids}, 16640 volume = {7}, 16641 number = {9}, 16642 pages = {2154-–2162}, 16643 year = {1995} 16644} 16645 16646@Article{ chenmolnar83, 16647 author = {W.-P. Chen and P. Molnar}, 16648 title = {Focal depths of intra-continental and intraplate earthquakes and their 16649 implications for the thermal and mechanical properties of the lithosphere}, 16650 journal = {Journal of Geophysical Research}, 16651 volume = {88}, 16652 pages = {4183–-4214}, 16653 year = {1983} 16654} 16655 16656@Article{ jackson02, 16657 author = {J. Jackson}, 16658 title = {Strength of the continental lithosphere: time to abandon the jelly sandwich?}, 16659 journal = {GSA Today}, 16660 volume = {12}, 16661 pages = {4–-10}, 16662 year = {2002} 16663} 16664 16665@Article{ burovwatts06, 16666 author = {E.B. Burov and A.B. Watts}, 16667 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 16668 brulee?}, 16669 journal = {GSA Today}, 16670 volume = {16}, 16671 pages = {4–-10}, 16672 year = {2006} 16673} 16674 16675@InProceedings{ yang:brent:2002, 16676 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 16677 Parallel Distributed Memory Architectures}, 16678 author = {Laurence T. Yang and Richard Brent}, 16679 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 16680 for Parallel Processing}, 16681 year = {2002}, 16682 publisher = {IEEE} 16683} 16684 16685@Article{ demmel2008communication, 16686 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 16687 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 16688 journal = {Arxiv preprint arXiv:0808.2664}, 16689 year = {2008} 16690} 16691 16692@Article{ demmel09, 16693 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 16694 title = {Communication-optimal Iterative Methods}, 16695 journal = {Journal of Physics: Conf. Series}, 16696 volume = {180}, 16697 year = {2009} 16698} 16699 16700@TechReport{ parms04, 16701 author = {Yousef Saad and Masha Sosonkina}, 16702 title = {{pARMS}: A package for the parallel iterative solution of general large sparse 16703 linear systems user's guide}, 16704 number = {UMSI2004-8}, 16705 institution = {Minnesota Supercomputer Institute, University of Minnesota}, 16706 year = {2004} 16707} 16708 16709@Article{ picard1890, 16710 author = {Emile Picard}, 16711 title = {M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la 16712 m\'ethode des approximations successives}, 16713 journal = {Journal De Math\'ematiques Pures et Appliqu\'ees}, 16714 volume = {4}, 16715 number = {6}, 16716 pages = {145--210}, 16717 year = {1890}, 16718 url = {http://math-doc.ujf-grenoble.fr/JMPA/PDF/JMPA_1890_4_6_A3_0.pdf} 16719} 16720 16721@Book{ rall1969, 16722 author = {Louis B. Rall}, 16723 title = {Computational solution of nonlinear operator equations}, 16724 publisher = {Krieger Pub Co.}, 16725 pages = {225}, 16726 year = {1969} 16727} 16728 16729@Article{ fletcherreeves1964, 16730 author = {R. Fletcher and C. M. Reeves}, 16731 title = {Function Minimization by Conjugate Gradients}, 16732 journal = {Computer Journal}, 16733 volume = {7}, 16734 pages = {149–-154}, 16735 year = {1964} 16736} 16737 16738@InBook{ mcinnesallanetal06, 16739 author = {Lois Curfman McInnes and Benjamin Allan and Robert Armstrong and Steven Benson 16740 and David Bernholdt and Tamara Dahlgren and Lori Diachin and Manojkumar Krishnan 16741 and James Kohl and Jay Larson and Sophia Lefantzi and Jarek Nieplocha and Boyana 16742 Norris and Steven Parker and Jaideep Ray and Shujia Zhou}, 16743 editor = {A.~M.~Bruaset and A.~Tveito}, 16744 title = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 16745 chapter = {Parallel {PDE}-Based Simulations Using the {Common Component Architecture}}, 16746 publisher = {Springer}, 16747 year = {2006}, 16748 number = {51}, 16749 series = {Lecture Notes in Computational Science and Engineering}, 16750 pages = {327--381}, 16751 doi = {10.1016/S0167-8191(02)00191-6} 16752} 16753 16754@Article{ cyrshadidtuminaro12, 16755 title = {Stabilization and scalable block preconditioning for the {Navier–Stokes} 16756 equations}, 16757 journal = {Journal of Computational Physics}, 16758 volume = {231}, 16759 number = {2}, 16760 pages = {345 - 363}, 16761 year = {2012}, 16762 issn = {0021-9991}, 16763 doi = {10.1016/j.jcp.2011.09.001}, 16764 author = {Eric C. Cyr and John N. Shadid and Raymond S. Tuminaro} 16765} 16766 16767@Article{ keyesmcinneswoodwardetal13, 16768 title = {Multiphysics Simulations: Challenges and Opportunities}, 16769 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 16770 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 16771 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 16772 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 16773 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 16774 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 16775 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 16776 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 16777 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 16778 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 16779 journal = {International Journal of High Performance Computing Applications}, 16780 month = feb, 16781 year = {2013}, 16782 volume = {27}, 16783 number = {1}, 16784 pages = {4--83}, 16785 doi = {10.1177/1094342012468181}, 16786 note = {Special issue}, 16787 abstract = {We consider multiphysics applications from algorithmic and architectural 16788 perspectives, where ``algorithmic'' includes both mathematical analysis and 16789 computational complexity and ``architectural'' includes both software and hardware 16790 environments. Many diverse multiphysics applications can be reduced, en route to 16791 their computational simulation, to a common algebraic coupling paradigm. 16792 Mathematical analysis of multiphysics coupling in this form is not always 16793 practical for realistic applications, but model problems representative of 16794 applications discussed herein can provide insight. A variety of software 16795 frameworks for multiphysics applications have been constructed and refined within 16796 disciplinary communities and executed on leading-edge computer systems. We examine 16797 several of these, expose some commonalities among them, and attempt to extrapolate 16798 best practices to future systems. From our study, we summarize challenges and 16799 forecast opportunities.} 16800} 16801 16802@Misc{ rosner10, 16803 author = {Robert {Rosner (Chair)}}, 16804 title = {{The Opportunities and Challenges of Exascale Computing}}, 16805 year = {2010}, 16806 howpublished = {Office of Science, U.S. Department of Energy}, 16807 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 16808} 16809 16810@Misc{ kogge2008exascale, 16811 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 16812 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 16813 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 16814 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 16815 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 16816 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 16817 howpublished = {DARPA}, 16818 year = {2008}, 16819 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 16820} 16821 16822@Misc{ doegrandchallengeworkshops, 16823 key = {Office of Science, U.S. Department of Energy}, 16824 title = {{Scientific Grand Challenges Workshop Series}}, 16825 howpublished = {Office of Science, U.S. Department of Energy, see 16826 \url{http://extremecomputing.labworks.org/workshops.stm}} 16827} 16828 16829@Misc{ lawrence2011, 16830 key = {Lawrence}, 16831 title = {{Ernest Orlando Lawrence Award Winners}}, 16832 howpublished = {U.S. Department of Energy, {\footnotesize 16833 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 16834 year = {2011} 16835} 16836 16837@Article{ murphy2000npi, 16838 title = {{A note on preconditioning for indefinite linear systems}}, 16839 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 16840 journal = {SIAM Journal on Scientific Computing}, 16841 volume = {21}, 16842 number = {6}, 16843 pages = {1969--1972}, 16844 year = {2000}, 16845 publisher = {Philadelphia, PA: SIAM, c1993-} 16846} 16847 16848@Article{ elman2011bouyancy, 16849 title = {Fast iterative solvers for buoyancy driven flow problems}, 16850 journal = {Journal of Computational Physics}, 16851 volume = {230}, 16852 number = {10}, 16853 pages = {3900 - 3914}, 16854 year = {2011}, 16855 note = {}, 16856 issn = {0021-9991}, 16857 doi = {10.1016/j.jcp.2011.02.014}, 16858 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 16859 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 16860 Adaptivity, Preconditioning, Algebraic multigrid} 16861} 16862 16863@Article{ dongarrabeckman11, 16864 author = {J. Dongarra and P. Beckman and et al.}, 16865 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 16866 journal = {Int. J. High Perf. Comput. 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Oliphant}, 17409 title = {Guide to Numpy}, 17410 publisher = {Trelgol}, 17411 year = {2008} 17412} 17413 17414@Misc{ pycuda, 17415 author = {Andreas Kl\"ockner}, 17416 title = {{PyCUDA}}, 17417 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 17418 year = {2011} 17419} 17420 17421@Misc{ pyopencl, 17422 author = {Andreas Kl\"ockner}, 17423 title = {{PyOpenCL}}, 17424 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 17425 year = {2011} 17426} 17427 17428@Article{ klockner2012, 17429 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 17430 Paul Ivanov and Ahmed Fasih}, 17431 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 17432 generation}, 17433 journal = {Parallel Computing}, 17434 volume = {38}, 17435 number = {3}, 17436 pages = {157--174}, 17437 year = {2012}, 17438 issn = {0167-8191}, 17439 doi = {10.1016/j.parco.2011.09.001} 17440} 17441 17442%%%%%% Matt Stuff %%%%%% 17443@Article{ morrabozdagknepleyrassvesselinov, 17444 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 17445 author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and 17446 Velimir Vesselinov}, 17447 journal = {Eos}, 17448 volume = {102}, 17449 doi = {10.1029/2021EO159258}, 17450 month = jun, 17451 year = {2021} 17452} 17453 17454@Misc{ knepley:icerm-workshop:2012, 17455 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 17456 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 17457 Models for Large-scale Simulations}, 17458 note = {Workshop sponsored by the Institute for Computational and Experimental Research 17459 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 17460 \url{http://icerm.brown.edu/tw12-1-exascale}}, 17461 year = {2012} 17462} 17463 17464@TechReport{ kirbyknepleyscott04, 17465 author = {Robert C. Kirby and Matthew G. Knepley and L. 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Ridgway Scott}, 17491 title = {Evaluation of the Action of Finite Element Operators}, 17492 type = {Technical Report}, 17493 number = {TR-2010-08}, 17494 institution = {University of Chicago}, 17495 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}, 17496 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}}, 17497 month = oct, 17498 year = {2010} 17499} 17500 17501@TechReport{ bruneknepleyscott11, 17502 author = {Peter R. Brune and Matthew G. Knepley and L. 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22337 22338@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 22339 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 22340 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 22341 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 22342 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 22343 pages = {1103}, 22344 year = {2018} 22345} 22346 22347@InProceedings{ barralangeloudiskramergormanpiggott2018, 22348 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 22349 modelling}, 22350 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 22351 and Matthew D Piggott}, 22352 booktitle = {EGU General Assembly Conference Abstracts}, 22353 volume = {20}, 22354 pages = {19168}, 22355 year = {2018} 22356} 22357 22358@Article{ principe2009, 22359 title = {{Mathematical models for thermally coupled low speed flows}}, 22360 author = {Javier Principe and Ramon Codina}, 22361 journal = {Advances in Theoretical and Applied Mechanics}, 22362 volume = {2}, 22363 number = {1-4}, 22364 pages = {93--112}, 22365 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 22366 year = {2009} 22367} 22368 22369@Book{ vandervorst2003, 22370 title = {Iterative {K}rylov Methods for Large Linear Systems}, 22371 author = {van der Vorst, H.}, 22372 isbn = {9780521818285}, 22373 publisher = {Cambridge University Press}, 22374 year = {2003} 22375} 22376 22377@Book{ peres2006, 22378 author = {Asher Peres}, 22379 title = {Quantum theory: concepts and methods}, 22380 volume = {57}, 22381 publisher = {Springer Science \& Business Media}, 22382 year = {2006} 22383} 22384 22385@Book{ kuttler2012, 22386 title = {Linear algebra: theory and applications}, 22387 author = {Kenneth Kuttler}, 22388 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 22389 year = {2012} 22390} 22391 22392@Book{ elman_silvester_wathen_2014, 22393 place = {Oxford}, 22394 title = {Finite elements and fast iterative solvers: with applications in incompressible 22395 fluid dynamics}, 22396 publisher = {Oxford University Press}, 22397 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 22398 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 22399 year = {2014} 22400} 22401 22402@Article{ alametal2007, 22403 title = {An evaluation of the ORNL Cray XT3}, 22404 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 22405 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 22406 journal = {International Journal of High Performance Computing Applications}, 22407 volume = {22}, 22408 number = {1}, 22409 pages = {52--80}, 22410 doi = {10.1177/1094342007085019}, 22411 year = {2007} 22412} 22413 22414@Article{ plazacarey2000, 22415 title = {Local refinement of simplicial grids based on the skeleton}, 22416 author = {Plaza, A. and Carey, Graham F.}, 22417 journal = {Applied Numerical Mathematics}, 22418 doi = {10.1016/S0168-9274(99)00022-7}, 22419 issn = {01689274}, 22420 volume = {32}, 22421 number = {2}, 22422 pages = {195--218}, 22423 year = {2000} 22424} 22425 22426@Article{ carsonstrakos2020, 22427 title = {On the cost of iterative computations}, 22428 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 22429 journal = {Phil. Trans. R. Soc. A}, 22430 volume = {378}, 22431 number = {20190050}, 22432 doi = {10.1098/rsta.2019.0050}, 22433 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 22434 year = {2020} 22435} 22436 22437@Article{ schoberl1999, 22438 title = {Multigrid methods for a parameter dependent problem in primal variables}, 22439 author = {Joachim Sch{\"o}berl}, 22440 journal = {Numerische Mathematik}, 22441 volume = {84}, 22442 number = {1}, 22443 pages = {97--119}, 22444 year = {1999} 22445} 22446 22447@Article{ wuleexuzikatanov2008, 22448 title = {Convergence analysis on iterative methods for semidefinite systems}, 22449 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 22450 journal = {Journal of Computational Mathematics}, 22451 pages = {797--815}, 22452 year = {2008} 22453} 22454 22455@Article{ maierrannacher2016, 22456 title = {Duality-based adaptivity in finite element discretization of heterogeneous 22457 multiscale problems}, 22458 author = {Maier, Matthias and Rannacher, Rolf}, 22459 journal = {Journal of Numerical Mathematics}, 22460 volume = {24}, 22461 number = {3}, 22462 pages = {167--187}, 22463 year = {2016} 22464} 22465 22466@Article{ maierrannacher2018, 22467 title = {A duality-based optimization approach for model adaptivity in heterogeneous 22468 multiscale problems}, 22469 author = {Maier, Matthias and Rannacher, Rolf}, 22470 journal = {Multiscale Modeling \& Simulation}, 22471 volume = {16}, 22472 number = {1}, 22473 pages = {412--428}, 22474 year = {2018} 22475} 22476 22477@Article{ margetismaierluskin2017, 22478 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 22479 metamaterial sheet}, 22480 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 22481 journal = {Studies in Applied Mathematics}, 22482 volume = {139}, 22483 number = {4}, 22484 pages = {599--625}, 22485 year = {2017} 22486} 22487 22488@Article{ maiermargetisluskin2017b, 22489 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 22490 approximation and validation}, 22491 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 22492 journal = {Journal of Computational Physics}, 22493 volume = {339}, 22494 pages = {126--145}, 22495 year = {2017} 22496} 22497 22498@Article{ maiermargetisluskin2018, 22499 title = {Generation of surface plasmon-polaritons by edge effects}, 22500 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 22501 journal = {Communications in Mathematical Sciences}, 22502 volume = {16}, 22503 number = {1}, 22504 pages = {77--95}, 22505 url = {http://arxiv.org/abs/1702.00848}, 22506 year = {2018} 22507} 22508 22509@Article{ maiermattheakiskaxirasluskinmargetis2018, 22510 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 22511 metamaterials}, 22512 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22513 Mitchell and Margetis, Dionisios}, 22514 journal = {Physical Review B}, 22515 volume = {97}, 22516 number = {3}, 22517 pages = {035307}, 22518 year = {2018} 22519} 22520 22521@Article{ maiermattheakiskaxirasluskinmargetis2019, 22522 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 22523 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22524 Mitchell and Margetis, Dionisios}, 22525 journal = {Proceedings of the Royal Society A}, 22526 volume = {475}, 22527 number = {2230}, 22528 pages = {20190220}, 22529 year = {2019} 22530} 22531 22532@Article{ maiermargetisluskin2020, 22533 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 22534 two scales}, 22535 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 22536 journal = {Physical Review B}, 22537 volume = {102}, 22538 number = {7}, 22539 pages = {075308}, 22540 year = {2020} 22541} 22542 22543@Article{ margetismaierstauberlowluskin2020, 22544 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 22545 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 22546 Luskin, Mitchell}, 22547 journal = {Journal of Physics A: Mathematical and Theoretical}, 22548 volume = {53}, 22549 number = {5}, 22550 pages = {055201}, 22551 year = {2020} 22552} 22553 22554@Article{ maiermargetismellet2020, 22555 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 22556 structures}, 22557 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 22558 journal = {Journal of Computational and Applied Mathematics}, 22559 volume = {377}, 22560 pages = {112909}, 22561 year = {2020} 22562} 22563 22564@Article{ maierkronbichler2021, 22565 title = {Efficient parallel 3D computation of the compressible Euler equations with an 22566 invariant-domain preserving second-order finite-element scheme}, 22567 author = {Maier, Matthias and Kronbichler, Martin}, 22568 journal = {ACM Transactions on Parallel Computing}, 22569 volume = {8}, 22570 number = {3}, 22571 pages = {1--30}, 22572 year = {2021} 22573} 22574 22575@Article{ guermondmaierpopovtomas2021, 22576 title = {Second-order invariant domain preserving approximation of the compressible 22577 Navier--Stokes equations}, 22578 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 22579 journal = {Computer Methods in Applied Mechanics and Engineering}, 22580 volume = {375}, 22581 pages = {113608}, 22582 year = {2021} 22583} 22584 22585@Article{ liliptonmaier2021, 22586 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 22587 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 22588 eprint = {2009.12166}, 22589 archiveprefix = {arXiv}, 22590 primaryclass = {phys.optics}, 22591 year = {2021} 22592} 22593 22594@Article{ songmaierluskin2020, 22595 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 22596 gradient-index graphene waveguides}, 22597 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22598 journal = {Journal of Computational Physics}, 22599 volume = {423}, 22600 pages = {109871}, 22601 year = {2020} 22602} 22603 22604@Article{ songmaierluskin2019, 22605 title = {Adaptive finite element simulations of waveguide configurations involving 22606 parallel 2D material sheets}, 22607 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22608 journal = {Computer Methods in Applied Mechanics and Engineering}, 22609 volume = {351}, 22610 pages = {20--34}, 22611 year = {2019} 22612} 22613 22614% 22615% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 22616% 22617% 22618@Unpublished{ rob1, 22619 author = {Rob Kunz}, 22620 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 22621 State University}, 22622 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 22623 sponsors = {U.S. Navy, NRC}, 22624 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 22625 simulations, including lake warming by power plants}, 22626 dates = {Oct 3 and 4, 2002}, 22627 email = {rfk@wt.arl.psu.edu} 22628} 22629 22630@Unpublished{ au1, 22631 author = {Feng Wang and William Appelbe}, 22632 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 22633 url = {http://www.vpac.org}, 22634 sponsors = { }, 22635 note = {Using PETSc for a Variety of Geophysical Simulations}, 22636 dates = {Nov 22, 2002} 22637} 22638 22639@Unpublished{ carl1, 22640 author = {Carl Sovinec}, 22641 institution = {Applied Physics, University of Wisconsin}, 22642 url = {http://nimrodteam.org}, 22643 sponsors = {DOE Office of Fusion Research}, 22644 note = {Investigating using PETSc for NIMROD}, 22645 dates = {Nov 21, 2002}, 22646 email = {sovinec@engr.wisc.edu} 22647} 22648 22649@Unpublished{ au1b, 22650 author = {Pablo Carrica and Robert Wilson}, 22651 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 22652 url = {http://}, 22653 sponsors = {Office of Naval Research}, 22654 note = {Using PETSc for a hydrodynamics of ships and submarines}, 22655 dates = {Sept, 2002}, 22656 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 22657} 22658 22659% ------------------- TAO References ---------------------- 22660@Article{ benson:2001:csp, 22661 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 22662 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 22663 journal = {{ACM} Transactions on Mathematical Software}, 22664 volume = {27}, 22665 number = {3}, 22666 month = sep, 22667 year = {2001}, 22668 pages = {361--376} 22669} 22670 22671@TechReport{ tao-user-ref-2000, 22672 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 22673 title = {{TAO} Users Manual}, 22674 year = {2000}, 22675 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22676 number = {ANL/MCS-TM-242}, 22677 note = {See \url{http://www.mcs.anl.gov/tao}} 22678} 22679 22680% ------------------- Optimization References ---------------------- 22681@Book{ optguide93, 22682 title = {Optimization Software Guide}, 22683 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 22684 publisher = {SIAM Publications}, 22685 address = {Philadelphia}, 22686 year = {1993} 22687} 22688 22689@InProceedings{ more84, 22690 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 22691 Hillstrom}, 22692 title = {The {MINPACK} Project}, 22693 booktitle = {Sources and Development of Mathematical Software}, 22694 editor = {Wayne R. Cowell}, 22695 year = {1984}, 22696 pages = {88--111} 22697} 22698 22699@Article{ steihaug:83, 22700 author = {Trond Steihaug}, 22701 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 22702 journal = {SIAM J. Numer. Anal.}, 22703 volume = {20}, 22704 year = {1983}, 22705 pages = {626--637}, 22706 key = {steihaug92 ! trust_region} 22707} 22708 22709@TechReport{ minpack2test, 22710 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 22711 title = {The {MINPACK-2} Test Problem Collection}, 22712 institution = {Argonne National Laboratory}, 22713 year = {1991}, 22714 number = {ANL/MCS-TM-150}, 22715 key = {more91 ! MINPACK-2} 22716} 22717 22718@TechReport{ hohmann:94, 22719 author = {Andreas Hohmann}, 22720 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 22721 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 22722 year = {1994}, 22723 number = {SC-94-4}, 22724 key = {Hohmann94} 22725} 22726 22727@TechReport{ meza:94, 22728 author = {Juan C. Meza}, 22729 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 22730 institution = {Sandia National Laboratory}, 22731 year = {1994}, 22732 number = {SAND94-8225}, 22733 key = {Meza94} 22734} 22735 22736@Book{ nw99, 22737 author = {Jorge Nocedal and Stephen J. Wright}, 22738 title = {Numerical Optimization}, 22739 year = {1999}, 22740 publisher = {Springer-Verlag}, 22741 address = {New York} 22742} 22743 22744@Book{ dennis:83, 22745 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 22746 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 22747 publisher = {Prentice-Hall, Inc.}, 22748 address = {Englewood Cliffs, NJ}, 22749 year = {1983} 22750} 22751 22752@TechReport{ more:92, 22753 author = {Jorge J. Mor\'{e} and David Thuente}, 22754 title = {Line search algorithms with guaranteed sufficient decrease}, 22755 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22756 year = {1992}, 22757 number = {MCS-P330-1092} 22758} 22759 22760@Article{ more-toraldo, 22761 author = {Jorge J. Mor\'e and G. Toraldo}, 22762 journal = {SIOPT}, 22763 pages = {93--113}, 22764 title = {On the solution of large quadratic programming problems with bound constraints}, 22765 volume = {1}, 22766 year = {1991} 22767} 22768 22769@Article{ byrd:1995:lma, 22770 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 22771 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 22772 journal = {SIAM Journal on Scientific Computing}, 22773 volume = {16}, 22774 number = {5}, 22775 pages = {1190--1208}, 22776 month = sep, 22777 year = {1995}, 22778 coden = {SJOCE3}, 22779 issn = {1064-8275 (print), 1095-7197 (electronic)}, 22780 mrclass = {90C30 (65K05)}, 22781 mrnumber = {96e:90039}, 22782 mrreviewer = {Henry Wolkowicz}, 22783 bibdate = {Fri Dec 4 16:17:35 MST 1998} 22784} 22785 22786@Article{ lin_c3, 22787 author = {C.-J. Lin and J. J. Mor\'e}, 22788 title = {Newton's method for large bound-constrained optimization problems}, 22789 year = {1999}, 22790 journal = {SIOPT}, 22791 volume = {9(4)}, 22792 pages = {1100--1127}, 22793 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 22794} 22795 22796@TechReport{ dolan2, 22797 author = {E. Dolan and J. J. Mor\'{e}}, 22798 title = {Benchmarking Optimization Software with Performance Profiles}, 22799 year = {2001}, 22800 month = jan, 22801 number = {ANL/MCS-P861-1200}, 22802 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22803 address = {Argonne, IL}, 22804 url = {http://www.mcs.anl.gov/~more/cops/} 22805} 22806 22807@InProceedings{ owlqn, 22808 author = {Galen Andrew and Jianfeng Gao}, 22809 title = {Scalable training of L1-regularized log-linear models}, 22810 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 22811 pages = {33--40}, 22812 year = {2007} 22813} 22814 22815@Article{ bmrm, 22816 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 22817 title = {Bundle methods for regularized risk minimization}, 22818 year = {2010}, 22819 journal = {Journal of Machine Learning Research}, 22820 volume = {11}, 22821 pages = {311--365} 22822} 22823 22824% ------------------- Component Software References ---------------------- 22825@InProceedings{ cca99, 22826 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 22827 McInnes and S. Parker and B. Smolinski}, 22828 title = {Toward a Common Component Architecture for High-Performance Scientific 22829 Computing}, 22830 booktitle = {Proceedings of {High Performance Distributed Computing}}, 22831 pages = {115--124}, 22832 year = {1999}, 22833 note = {See \url{http://cca-forum.org}} 22834} 22835 22836@Book{ szyperski98, 22837 author = {Clemens Szyperski}, 22838 title = {Component Software: Beyond Object-Oriented Programming}, 22839 publisher = {ACM Press}, 22840 address = {New York}, 22841 year = {1998} 22842} 22843 22844@Article{ broy98, 22845 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 22846 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 22847 Stal and Clemens Szyperski}, 22848 title = {What Characterizes a (Software) Component?}, 22849 journal = {Software -- Concepts and Tools}, 22850 publisher = {Springer-Verlag}, 22851 year = {1998}, 22852 volume = {19}, 22853 pages = {49--56} 22854} 22855 22856@Article{ componentware:94, 22857 author = {Jon Udell}, 22858 title = {Componentware}, 22859 journal = {Byte}, 22860 volume = {may}, 22861 pages = {46--56}, 22862 year = {1994}, 22863 key = {Udell94 ! componentware} 22864} 22865 22866@Misc{ cca-web-page, 22867 author = {{Common Component Architecture Forum}}, 22868 note = {See \url{http://cca-forum.org}} 22869} 22870 22871% --------------- References for Tools Used by TAO Developers ----------------- 22872 22873% 22874% tohtml: Used to generate on-line TAO users manual and manual pages 22875% 22876@TechReport{ tohtml, 22877 author = {William Gropp}, 22878 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 22879 institution = {Argonne National Laboratory}, 22880 number = {ANL/MCS-TM-00}, 22881 month = jan, 22882 year = {1995}, 22883 key = {tohtml} 22884} 22885 22886% 22887% doctext: Used to generate tex version of TAO manual pages 22888% 22889@TechReport{ doctext, 22890 author = {William Gropp}, 22891 title = {Users Manual for doctext: Producing documentation from {C} source code}, 22892 institution = {Argonne National Laboratory}, 22893 number = {ANL/MCS-TM-00}, 22894 month = jan, 22895 year = {1995}, 22896 key = {doctext} 22897} 22898 22899% 22900% bfort: Used to generate TAO Fortran interface 22901% 22902@TechReport{ bfort, 22903 author = {William Gropp}, 22904 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 22905 institution = {Argonne National Laboratory}, 22906 number = {ANL/MCS-TM-208}, 22907 month = mar, 22908 year = {1995}, 22909 key = {doctext} 22910} 22911 22912% ------------------------- PETSc References ------------------------------ 22913@InProceedings{ petsc, 22914 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 22915 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 22916 Libraries}, 22917 booktitle = {Modern Software Tools in Scientific Computing}, 22918 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 22919 publisher = {Birkhauser Press}, 22920 pages = {163--202}, 22921 year = {1997} 22922} 22923 22924% ------------------------- Misc Other References ------------------------------ 22925@Misc{ indeps-web-page, 22926 title = {{InDEPS} {W}eb page}, 22927 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 22928 author = {et al. Robert Armstrong}, 22929 institution = {Sandia National Laboratory}, 22930 key = {{InDEPS} {W}eb page} 22931} 22932 22933@Misc{ pooma, 22934 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 22935 chitectures}, 22936 year = {1996}, 22937 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 22938 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 22939} 22940 22941@Misc{ isis++-web-page, 22942 title = {{ISIS++} {W}eb Page}, 22943 note = {See \url{http://ca.sandia.gov/isis}}, 22944 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 22945 institution = {Sandia National Laboratories} 22946} 22947 22948@Misc{ trilinos-web-page, 22949 title = {{Trilinos} {W}eb Page}, 22950 note = {See 22951 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 22952 author = {Mike Heroux et al.}, 22953 institution = {Sandia National Laboratories} 22954} 22955 22956@Misc{ alice-web-page, 22957 title = {{ALICE} {W}eb page}, 22958 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 22959 Argonne National Laboratory}, 22960 key = {{ALICE} {W}eb page} 22961} 22962 22963@Misc{ autodiff-webpage, 22964 author = {{Computational Differentiation Project}}, 22965 note = {See \url{http://www.mcs.anl.gov/autodiff}} 22966} 22967 22968@Misc{ coool-home-page, 22969 author = {Lydia Deng and Wences Gouveia and John Scales}, 22970 title = {{The CWP Object-Oriented Optimization Library}}, 22971 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 22972} 22973 22974@Misc{ rice-inversion-home-page, 22975 author = {Mark S. Gokenbach and William W. Symes}, 22976 title = {{The Hilbert Class Library}}, 22977 note = {See \url{http://www.trip.caam.rice.edu/}} 22978} 22979 22980@Misc{ opt++-home-page, 22981 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 22982 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 22983} 22984 22985@Article{ gockenbach:1999:ccl, 22986 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 22987 title = {C++ Classes for Linking Optimization with Complex Simulations}, 22988 journal = {{ACM} Transactions on Mathematical Software}, 22989 volume = {25}, 22990 number = {2}, 22991 month = jun, 22992 year = {1999}, 22993 pages = {191-212}, 22994 abstract = {The object-oriented programming paradigm can be used to overcome the 22995 incompatibilities between off-the-shelf optimization software and application 22996 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 22997 objects arising in optimization problems, such as vectors, linear operators, and 22998 so forth, as C++ classes, making it possible to write optimization code in a 22999 natural fashion, while allowing application software such as simulators to use the 23000 most convenient data structures and programming style. In spite of the poor 23001 reputation C++ has for runtime performance, the use of mixed-language programming 23002 allows performance equal to that achieved by standard Fortran packages, as 23003 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 23004 accepted = {April 1999}, 23005 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 23006} 23007 23008@Misc{ neos-guide, 23009 author = {{The Optimization Software Guide}}, 23010 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 23011} 23012 23013@Article{ boyd, 23014 title = {Distributed optimization and statistical learning via the alternating direction 23015 method of multipliers}, 23016 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 23017 Jonathan and others}, 23018 journal = {Foundations and Trends{\textregistered} in Machine learning}, 23019 volume = {3}, 23020 number = {1}, 23021 pages = {1-122}, 23022 year = {2011}, 23023 publisher = {Now Publishers, Inc.} 23024} 23025 23026@Misc{ :alertsys, 23027 title = {page{ALERT}}, 23028 organization = {Alert Systems, Inc}, 23029 address = {Madison, Wisconsin}, 23030 note = {http://www.alertsys.com/} 23031} 23032 23033@Manual{ :cmfortran, 23034 title = {{CM} {F}ortran Language Reference Manual}, 23035 organization = {Thinking Machines Corporation}, 23036 year = {1994}, 23037 address = {Cambridge, MA} 23038} 23039 23040@Manual{ :cmmd, 23041 title = {{CMMD} Reference Manual, Version 3.0}, 23042 organization = {Thinking Machines Corporation}, 23043 year = {1993}, 23044 address = {Cambridge, MA} 23045} 23046 23047@Manual{ :cmssl, 23048 title = {{CMSSL} for {CM} {F}ortran}, 23049 volume = {I}, 23050 organization = {Thinking Machines Corporation}, 23051 year = {1994}, 23052 address = {Cambridge, MA} 23053} 23054 23055@Misc{ :condor, 23056 author = {M. Livny}, 23057 title = {{PI}, The {Condor} Project, High Throughput Computing}, 23058 howpublished = {www.cs.wisc.edu/condor} 23059} 23060 23061@Manual{ :connection, 23062 title = {Connection Machine {CM}--5 Technical Summary}, 23063 organization = {Thinking Machines Corporation}, 23064 year = {1993}, 23065 address = {Cambridge, MA} 23066} 23067 23068@Manual{ :cplex, 23069 title = {{CPLEX} Optimizer}, 23070 organization = {ILOG CPLEX Division}, 23071 address = {889 Alder Avenue, Incline Village, Nevada}, 23072 note = {http://www.cplex.com/} 23073} 23074 23075@Manual{ :cplextm, 23076 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 23077 (Version 2.0)}, 23078 organization = {CPLEX Optimization Inc.}, 23079 year = {1992}, 23080 address = {Incline Village, Nevada} 23081} 23082 23083@Misc{ :fatcop, 23084 author = {M. C. Ferris}, 23085 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 23086 Solver}, 23087 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 23088} 23089 23090@Misc{ :metaneos, 23091 author = {S. J. Wright}, 23092 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 23093 howpublished = {www-unix.mcs.anl.gov/metaneos} 23094} 23095 23096@InCollection{ gropp.more:optimization, 23097 author = {W. Gropp and J. J. Mor\'e}, 23098 title = {Optimization environments and the {NEOS} Server}, 23099 booktitle = {Approximation Theory and Optimization}, 23100 pages = {167--182}, 23101 publisher = {Cambridge University Press}, 23102 year = {1997}, 23103 editor = {M. D. Buhmann and A. Iserles} 23104} 23105 23106@Article{ czyzyk.mesnier.ea:neos, 23107 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 23108 title = {The {NEOS} Server}, 23109 journal = {IEEE Journal on Computational Science and Engineering}, 23110 volume = {5}, 23111 year = {1998}, 23112 pages = {68--75} 23113} 23114 23115@Book{ :osl, 23116 title = {Handbook for {IBM OSL}}, 23117 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 23118 year = {1994}, 23119 publisher = {Boyd and Fraser}, 23120 address = {Danvers, Massachusetts} 23121} 23122 23123@Manual{ :pro-matlab, 23124 title = {{PRO}--{MATLAB} User's Guide}, 23125 organization = {The MathWorks, Inc.}, 23126 year = {1989}, 23127 address = {21 Eliot Street, South Natick, MA 01760} 23128} 23129 23130@Misc{ :prostate, 23131 key = {Biomedical}, 23132 title = {Biomedical Business International Newsletter}, 23133 howpublished = {pp. 72--75}, 23134 year = {1996} 23135} 23136 23137@Misc{ :sipcase, 23138 key = {Natural}, 23139 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 23140 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 23141} 23142 23143@Book{ aarts.korst:simulated, 23144 author = {E. Aarts and J. Korst}, 23145 title = {Simulated Annealing and Boltzman Machines}, 23146 year = {1990}, 23147 publisher = {John Wiley \& Sons}, 23148 address = {Chichester} 23149} 23150 23151@TechReport{ aarts.laarhoven.ea:local-search-based, 23152 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 23153 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 23154 institution = {Centre for Quantitative Methods}, 23155 year = {1991}, 23156 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 23157 number = {106}, 23158 type = {CQM-Not} 23159} 23160 23161@Article{ aashtiani.magnanti:equilibria, 23162 author = {H. Z. Aashtiani and T. L. Magnanti}, 23163 title = {Equilibria on a congested transportation network}, 23164 journal = {SIAM Journal on Algebraic and Discrete Methods}, 23165 volume = {2}, 23166 year = {1981}, 23167 pages = {213--226} 23168} 23169 23170@Article{ ablow.brigham:analog, 23171 author = {C. M. Ablow and G. Brigham}, 23172 title = {An Analog Solution of Programming Problems}, 23173 journal = {Operations Research}, 23174 year = {1955}, 23175 volume = {3}, 23176 pages = {388--394} 23177} 23178 23179@Article{ achuthan.grabowski.ea:optimal, 23180 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 23181 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 23182 journal = {Opsearch}, 23183 year = {1981}, 23184 volume = {18}, 23185 pages = {117--138} 23186} 23187 23188@Book{ adelman.robinson:income, 23189 author = {I. Adelman and S. Robinson}, 23190 title = {Income Distribution Policy in Developing Countries}, 23191 publisher = {Stanford University Press}, 23192 year = {1978}, 23193 address = {Stanford, California} 23194} 23195 23196@Article{ adler.resende.ea:implementation, 23197 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 23198 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 23199 journal = {Mathematical Programming}, 23200 year = {1989}, 23201 volume = {44}, 23202 pages = {297--336} 23203} 23204 23205@TechReport{ aeberhard.coomans.ea:comparison, 23206 author = {S. Aeberhard and D. Coomans and O. de Vel}, 23207 title = {Comparison of Classifiers in High Dimensional Settings}, 23208 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 23209 University of North Queensland}, 23210 year = {1992}, 23211 number = {92-02}, 23212 type = {Technical Report} 23213} 23214 23215@Article{ aganagic.cottle:constructive, 23216 author = {M. Aganagi\'{c} and R. W. Cottle}, 23217 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 23218 Minors}, 23219 journal = {Mathematical Programming}, 23220 year = {1987}, 23221 volume = {37}, 23222 pages = {223--231} 23223} 23224 23225@TechReport{ aganagic:iterative, 23226 author = {M. Aganagi\'{c}}, 23227 title = {Iterative Methods for the Linear Complementarity Problem}, 23228 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 23229 University}, 23230 year = {1978}, 23231 type = {SOL}, 23232 number = {78-10}, 23233 address = {Stanford, California} 23234} 23235 23236@Book{ ahlfors:complex, 23237 author = {L. V. Ahlfors}, 23238 title = {Complex Analysis}, 23239 publisher = {McGraw--Hill Book Company}, 23240 address = {New York}, 23241 series = {International Series in Pure and Applied Mathematics}, 23242 edition = {Second}, 23243 year = {1966} 23244} 23245 23246@Article{ ahn:solution, 23247 author = {B--H. Ahn}, 23248 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 23249 journal = {Journal of Optimization Theory and Applications}, 23250 year = {1981}, 23251 volume = {33}, 23252 pages = {175--185} 23253} 23254 23255@Article{ al-fahed.stavroulakis.ea:hard, 23256 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 23257 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 23258 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 23259 volume = {71}, 23260 year = {1991}, 23261 pages = {257--265} 23262} 23263 23264@Article{ al-fahed.stavroulakis.ea:linear, 23265 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 23266 title = {A linear complementarity approach to the frictionless gripper}, 23267 journal = {International Journal of Robotic Research}, 23268 volume = {11}, 23269 year = {1992}, 23270 pages = {112--122} 23271} 23272 23273@Article{ al-khayyal.falk:jointly, 23274 author = {F. A. Al--Khayyal and J. E. Falk}, 23275 title = {Jointly Constrained Biconvex Programming}, 23276 journal = {Mathematics of Operations Research}, 23277 year = {1983}, 23278 volume = {8}, 23279 pages = {273--286} 23280} 23281 23282@Article{ al-khayyal.kyparisis:finite, 23283 author = {F. A. Al--Khayyal and J. Kyparisis}, 23284 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 23285 Inequalities}, 23286 journal = {Journal of Optimization Theory and Applications}, 23287 year = {1991}, 23288 volume = {70}, 23289 pages = {319--332} 23290} 23291 23292@PhDThesis{ al-khayyal:biconvex, 23293 author = {F. A. Al--Khayyal}, 23294 title = {Biconvex Programming and Biconcave Minimization}, 23295 year = {1977}, 23296 school = {The George Washington University} 23297} 23298 23299@Article{ alart.curnier:mixed, 23300 author = {P. Alart and A. Curnier}, 23301 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 23302 solution methods}, 23303 journal = {Computer Methods in Applied Mechanics and Engineering}, 23304 volume = {92}, 23305 year = {1991}, 23306 pages = {353--375} 23307} 23308 23309@Misc{ alexander.kellog.ea:piecewise, 23310 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 23311 title = {Piecewise smooth continuation}, 23312 howpublished = {Manuscript}, 23313 year = {1979} 23314} 23315 23316@InCollection{ alexander.li.ea:piecewise, 23317 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 23318 title = {Piecewise smooth homotopies}, 23319 booktitle = {Homotopy Methods and Global Convergence}, 23320 pages = {1--14}, 23321 publisher = {Plenum Press}, 23322 year = {1983}, 23323 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 23324 address = {New York} 23325} 23326 23327@InCollection{ alexander:topological, 23328 author = {J.~C. Alexander}, 23329 title = {The topological theory of an embedding method}, 23330 booktitle = {Continuation Methods}, 23331 pages = {37--68}, 23332 publisher = {Academic Press}, 23333 year = {1978}, 23334 editor = {H. Wacker}, 23335 address = {New York} 23336} 23337 23338@Book{ allen:probability, 23339 author = {A. O. Allen}, 23340 title = {Probability, Statistics and Queueing Theory}, 23341 publisher = {Academic Press}, 23342 year = {1990}, 23343 address = {London}, 23344 edition = {Second} 23345} 23346 23347@Book{ allgower.georg:numerical, 23348 author = {E. L. Allgower and K. Georg}, 23349 title = {Numerical Continuation Methods, An Introduction}, 23350 publisher = {Springer-Verlag}, 23351 year = {1990}, 23352 address = {Berlin} 23353} 23354 23355@InProceedings{ allgower.georg:predictor-corrector, 23356 crossref = {bachem.grotschel.ea:mathematical}, 23357 author = {E. L. Allgower and K. Georg}, 23358 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 23359 Zero Points of Nonlinear Mappings}, 23360 pages = {15--56} 23361} 23362 23363@Article{ aluffi-pentini.parisi.ea:algorithm, 23364 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 23365 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 23366 Algorithm}, 23367 journal = {ACM Transactions on Mathematical Software}, 23368 year = {1988}, 23369 volume = {14}, 23370 pages = {366--380} 23371} 23372 23373@Article{ anandalingam.friesz:hierarchical, 23374 author = {G. Anandalingam and T. L. Friesz}, 23375 title = {Hierarchical Optimization: An Introduction}, 23376 journal = {Annals of Operations Research}, 23377 year = {1992}, 23378 volume = {34}, 23379 pages = {1--11} 23380} 23381 23382@Article{ anandalingam.white:solution, 23383 author = {G. Anandalingam and D. J. White}, 23384 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 23385 Functions}, 23386 journal = {IEEE Transactions on Automatic Control}, 23387 year = {1990}, 23388 volume = {35}, 23389 number = {10}, 23390 pages = {1170--1173} 23391} 23392 23393@Article{ andersen.andersen:presolving, 23394 author = {E. Andersen and K. Andersen}, 23395 title = {Presolving in Linear Programming}, 23396 year = {1995}, 23397 journal = {Mathematical Programming}, 23398 volume = {71}, 23399 pages = {221--245} 23400} 23401 23402@InProceedings{ andersen.ye:homogeneous, 23403 author = {E. Andersen and Y. Ye}, 23404 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 23405 Equality Constraints}, 23406 crossref = {ferris.pang:complementarity}, 23407 pages = {1--11} 23408} 23409 23410@Book{ anderson.bai.ea:lapack, 23411 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 23412 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 23413 Sorensen}, 23414 title = {{LAPACK} User's Guide}, 23415 publisher = {SIAM}, 23416 year = {1995}, 23417 address = {Philadelphia, Pennsylvania}, 23418 edition = {Second} 23419} 23420 23421@Article{ anderson.ferris:direct, 23422 author = {E. J. Anderson and M. C. Ferris}, 23423 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 23424 year = {2001}, 23425 journal = {SIAM Journal on Optimization, forthcoming}, 23426 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 23427 key = {55} 23428} 23429 23430@InProceedings{ anderson.ferris:genetic, 23431 author = {E. J. Anderson and M. C. Ferris}, 23432 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 23433 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 23434 Waterloo, Ontario, Canada, May 28--30}, 23435 publisher = {University of Waterloo Press}, 23436 key = {14}, 23437 year = {1990} 23438} 23439 23440@Article{ anderson.ferris:genetic*1, 23441 author = {E. J. Anderson and M. C. Ferris}, 23442 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 23443 Problem}, 23444 journal = {ORSA Journal on Computing}, 23445 year = {1994}, 23446 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 23447 volume = {6}, 23448 pages = {161--173}, 23449 key = {22} 23450} 23451 23452@InProceedings{ anderson.ferris:parallel, 23453 author = {E. J. Anderson and M. C. Ferris}, 23454 title = {Parallel Genetic Algorithms in Optimization}, 23455 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 23456 Computing, Chicago, Illinois, December 11-13}, 23457 year = {1989}, 23458 key = {12} 23459} 23460 23461@Unpublished{ anderson.lewis:primal, 23462 author = {E. J. Anderson and A. S. Lewis}, 23463 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 23464 note = {In preparation} 23465} 23466 23467@Book{ anderson.nash:linear, 23468 author = {E. J. Anderson and P. Nash}, 23469 title = {Linear Programming in Infinite--Dimensional Spaces}, 23470 year = {1987}, 23471 publisher = {John Wiley \& Sons}, 23472 address = {Chichester} 23473} 23474 23475@InProceedings{ anderson:primal, 23476 author = {E. J. Anderson}, 23477 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 23478 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 23479 Programming, Cambridge, September 1984}, 23480 year = {1985}, 23481 editor = {E. J. Anderson and A. B. Philpott}, 23482 publisher = {Springer-Verlag}, 23483 address = {Berlin} 23484} 23485 23486@Article{ andradottir:method, 23487 author = {S. Andrad\'{o}ttir}, 23488 title = {A Method of Discrete Stochastic Optimization}, 23489 journal = {Management Science}, 23490 year = {1995}, 23491 volume = {41}, 23492 pages = {1946--1961} 23493} 23494 23495@Article{ andradottir:global, 23496 author = {S. Andrad\'{o}ttir}, 23497 title = {A Global Search Method for Discrete Stochastic Optimization}, 23498 journal = {SIAM Journal on Optimization}, 23499 year = {1996}, 23500 volume = {6}, 23501 pages = {513--530} 23502} 23503 23504@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 23505 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 23506 title = {An infeasible--interior--point predictor--corrector algorithm for the 23507 {P}$_x$--geometric {LCP}}, 23508 institution = {Department of Mathematics, The University of Iowa}, 23509 address = {Iowa City, Iowa}, 23510 year = {1994}, 23511 number = {62}, 23512 type = {Reports on Computational Mathematics} 23513} 23514 23515@TechReport{ anitescu.potra:formulating, 23516 author = {M. Anitescu and F. A. Potra}, 23517 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 23518 Linear Complementarity Problems}, 23519 institution = {Department of Mathematics, The University of Iowa}, 23520 year = {1996}, 23521 type = {Report}, 23522 number = {93}, 23523 address = {Iowa City, Iowa} 23524} 23525 23526@Article{ anstreicher.lee.ea:crashing, 23527 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 23528 title = {Crashing a Maximum-Weight Complementarity Basis}, 23529 journal = {Mathematical Programming}, 23530 year = {1992}, 23531 volume = {54}, 23532 pages = {281--294} 23533} 23534 23535@Article{ anstreicher:combined, 23536 author = {K. M. Anstreicher}, 23537 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 23538 programming}, 23539 journal = {Mathematical Programming}, 23540 year = {1991}, 23541 volume = {52}, 23542 pages = {429--440} 23543} 23544 23545@Article{ anstreicher:combined*1, 23546 author = {K. M. Anstreicher}, 23547 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 23548 journal = {Mathematical Programming}, 23549 year = {1989}, 23550 volume = {43}, 23551 pages = {209--223} 23552} 23553 23554@InCollection{ arbenz.gander.ea:remote, 23555 author = {P. Arbenz and W. Gander and M. Oettli}, 23556 title = {The Remote Computational System}, 23557 booktitle = {High-Performance Computation and Networks}, 23558 publisher = {Springer-Verlag}, 23559 year = {1996}, 23560 volume = {1067}, 23561 series = {Lecture Notes in Computer Science}, 23562 pages = {662--667} 23563} 23564 23565@InCollection{ arcus:comsoal, 23566 author = {A. L. Arcus}, 23567 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 23568 booktitle = {Readings in Production and Operations Management}, 23569 year = {1966}, 23570 editor = {E. S. Buffa}, 23571 publisher = {John Wiley \& Sons}, 23572 address = {New York} 23573} 23574 23575@TechReport{ arioli.chan.ea:computing, 23576 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 23577 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 23578 Optimization Calculations}, 23579 institution = {CERFACS}, 23580 year = {1993}, 23581 number = {TR/PA/93/34} 23582} 23583 23584@Article{ armijo:minimization, 23585 author = {L. Armijo}, 23586 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 23587 Derivatives}, 23588 journal = {Pacific Journal of Mathematics}, 23589 year = {1966}, 23590 volume = {16}, 23591 pages = {1--3} 23592} 23593 23594@Article{ arrow.debreu:existence, 23595 author = {K. Arrow and G. Debreu}, 23596 title = {Existence of Equilibrium for a Competitive Economy}, 23597 journal = {Econometrica}, 23598 year = {1954}, 23599 volume = {22}, 23600 pages = {265--290} 23601} 23602 23603@InCollection{ arrow.solow:gradient, 23604 author = {K. J. Arrow and R. M. Solow}, 23605 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 23606 booktitle = {Studies in Linear and Nonlinear Programming}, 23607 year = {1958}, 23608 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 23609 publisher = {Stanford University Press}, 23610 address = {Stanford, California}, 23611 pages = {166--176} 23612} 23613 23614@Book{ aubin.ekeland:nonlinear, 23615 author = {J.-P. Aubin and I. Ekeland}, 23616 title = {Applied nonlinear analysis}, 23617 publisher = {John Wiley \& Sons}, 23618 address = {New York}, 23619 year = {1984} 23620} 23621 23622@Article{ auchmuty:variational, 23623 author = {G. Auchmuty}, 23624 title = {Variational Principles for Variational Inequalities}, 23625 journal = {Numerical Functional Analysis and Optimization}, 23626 year = {1989}, 23627 volume = {10}, 23628 pages = {863--874} 23629} 23630 23631@Book{ auerbach.kotlikoff:dynamic, 23632 author = {A. J. Auerbach and L. J. Kotlikoff}, 23633 title = {Dynamic Fiscal Policy}, 23634 publisher = {Cambridge University Press}, 23635 address = {Cambridge, England}, 23636 year = {1987} 23637} 23638 23639@InProceedings{ ault.deutsch.ea:interpolating, 23640 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 23641 title = {Interpolating Subspaces in Approximation Theory}, 23642 booktitle = {Approximation Theory}, 23643 year = {1970}, 23644 editor = {A. Talbot}, 23645 publisher = {Academic Press}, 23646 address = {London} 23647} 23648 23649@Article{ auslender.crouzeix:global, 23650 author = {A. A. Auslender and J.--P. Crouzeix}, 23651 title = {Global Regularity Theorems}, 23652 journal = {Mathematics of Operations Research}, 23653 year = {1988}, 23654 volume = {13}, 23655 pages = {243--253} 23656} 23657 23658@Article{ auslender.haddou:interior-proximal, 23659 author = {A. Auslender and M. Haddou}, 23660 title = {An interior-proximal method for convex linearly constrained problems and its 23661 extension to variational inequalities}, 23662 year = {1995}, 23663 journal = {Mathematical Programming}, 23664 pages = {77--100}, 23665 volume = {71} 23666} 23667 23668@Article{ auslender:convergence, 23669 author = {A. Auslender}, 23670 title = {Convergence of stationary sequences for variational inequalities with maximal 23671 monotone operators}, 23672 journal = {Applied Mathematics and Optimization}, 23673 volume = {28}, 23674 year = {1993}, 23675 pages = {161--172} 23676} 23677 23678@Book{ auslender:optimization, 23679 author = {A. Auslender}, 23680 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 23681 year = {1976}, 23682 publisher = {Masson}, 23683 address = {Paris} 23684} 23685 23686@TechReport{ averick.carter.ea:minpack-2, 23687 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 23688 title = {The {MINPACK-2} Test Problem Collection}, 23689 institution = {Argonne National Laboratory}, 23690 year = {1992}, 23691 address = {Argonne, Illinois}, 23692 number = {MCS-P153-0692} 23693} 23694 23695@TechReport{ axline.billups.ea:guidelines, 23696 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 23697 title = {Guidelines for Software Security ({U})}, 23698 institution = {SNL}, 23699 year = {1989}, 23700 month = oct, 23701 address = {Albuquerque, New Mexico}, 23702 number = {SAND88-2955} 23703} 23704 23705@Article{ ayres.walter:greenhouse, 23706 author = {R. U. Ayres and J. Walter}, 23707 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 23708 journal = {Environmental and Resource Economics}, 23709 year = {1991}, 23710 volume = {1}, 23711 pages = {237--270} 23712} 23713 23714@PhDThesis{ bagley:behaviour, 23715 author = {J. D. Bagley}, 23716 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 23717 Algorithms}, 23718 year = {1967}, 23719 school = {University of Michigan} 23720} 23721 23722@Article{ bain.stewart:application, 23723 author = {R. S. Bain and W. E. Stewart}, 23724 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 23725 Algebraic Equation Systems}, 23726 journal = {Computers in Chemical Engineering}, 23727 year = {1991}, 23728 volume = {15}, 23729 pages = {203--208} 23730} 23731 23732@Article{ baker.lasdon:successive, 23733 author = {T. E. Baker and L. S. 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Mangasarian}, 23993 title = {Neural Network Training via Linear Programming}, 23994 booktitle = {Advances in Optimization and Parallel Computing}, 23995 year = {1992}, 23996 editor = {P. M. Pardalos}, 23997 publisher = {North Holland}, 23998 address = {Amsterdam}, 23999 pages = {56--67} 24000} 24001 24002@Article{ bennett.mangasarian:robust, 24003 author = {K. P. Bennett and O. L. Mangasarian}, 24004 title = {Robust Linear Programming Discrimination of Two Linearly Inseparable Sets}, 24005 journal = {Optimization Methods and Software}, 24006 year = {1992}, 24007 volume = {1}, 24008 pages = {23--34} 24009} 24010 24011@Article{ bennett.mangasarian:serial, 24012 author = {K. P. Bennett and O. L. Mangasarian}, 24013 title = {Serial and Parallel Multicategory Separation}, 24014 journal = {SIAM Journal on Optimization}, 24015 year = {1994}, 24016 volume = {4}, 24017 pages = {722--734} 24018} 24019 24020@TechReport{ bennett.wu.ea:support, 24021 author = {K. P. Bennett and D. Wu and L. 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Bertsekas}, 24177 title = {Nonlinear Programming}, 24178 publisher = {Athena Scientific}, 24179 year = {1995}, 24180 address = {Belmont, Massachusetts} 24181} 24182 24183@Article{ bertsekas:projected, 24184 author = {Dimitri P. Bertsekas}, 24185 title = {Projected {N}ewton Methods for Optimization Problems with Simple Constraints}, 24186 journal = {SIAM Journal on Control and Optimization}, 24187 year = {1982}, 24188 volume = {20}, 24189 pages = {221--246} 24190} 24191 24192@Article{ billups.dirkse.ea:comparison, 24193 author = {S. C. Billups and S. P. Dirkse and M. C. Ferris}, 24194 title = {A Comparison of Large Scale Mixed Complementarity Problem Solvers}, 24195 journal = {Computational Optimization and Applications}, 24196 year = {1997}, 24197 pages = {3--25}, 24198 volume = {7}, 24199 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps}, 24200 key = {51} 24201} 24202 24203@Article{ billups.ferris:convergence, 24204 author = {S. C. Billups and M. C. Ferris}, 24205 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 24206 Starting Points}, 24207 journal = {SIAM Journal on Optimization}, 24208 year = {1996}, 24209 volume = {6}, 24210 pages = {316--325}, 24211 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 24212 key = {34} 24213} 24214 24215@TechReport{ billups.ferris:convergence*1, 24216 author = {S. C. Billups and M. C. Ferris}, 24217 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 24218 Points}, 24219 institution = {Computer Sciences Department, University of Wisconsin}, 24220 year = {1993}, 24221 address = {Madison, Wisconsin}, 24222 number = {1180}, 24223 note = {Revised version in SIAM Journal on Optimization.} 24224} 24225 24226@Article{ billups.ferris:qpcomp, 24227 author = {S. C. Billups and M. C. Ferris}, 24228 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 24229 year = {1997}, 24230 journal = {Mathematical Programming}, 24231 pages = {533--562}, 24232 volume = {76}, 24233 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 24234 key = {47} 24235} 24236 24237@Article{ billups.ferris:solutions, 24238 author = {S. C. Billups and M. C. Ferris}, 24239 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 24240 journal = {Mathematics of Operations Research}, 24241 volume = {24}, 24242 pages = {219--236}, 24243 year = {1999}, 24244 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 24245 key = {42}, 24246 institution = {Computer Sciences Department, University of Wisconsin}, 24247 address = {Madison, Wisconsin}, 24248 type = {Mathematical Programming Technical Report}, 24249 number = {94--15} 24250} 24251 24252@TechReport{ billups.murata.ea:users, 24253 author = {S. C. Billups and K. K. 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Billups}, 24274 title = {Algorithms for Complementarity Problems and Generalized Equations}, 24275 school = {University of Wisconsin--Madison}, 24276 year = {1995}, 24277 address = {Madison, Wisconsin}, 24278 month = aug 24279} 24280 24281@MastersThesis{ billups:augmented, 24282 author = {S. C. Billups}, 24283 title = {An Augmented Jacobian Matrix Algorithm for Tracking Homotopy Zero Curves}, 24284 school = {Virginia Tech}, 24285 year = {1985}, 24286 address = {Blacksburg, Virginia} 24287} 24288 24289@TechReport{ billups:homotopy, 24290 author = {S. C. Billups}, 24291 title = {A Homotopy Based Algorithm for Mixed Complementarity Problems}, 24292 institution = {Department of Mathematics, University of Colorado}, 24293 year = {1998}, 24294 address = {Denver, Colorado} 24295} 24296 24297@Article{ billups:improving, 24298 author = {S. C. 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Dirkse}, 26477 title = {Robust Solution of Mixed Complementarity Problems}, 26478 school = {Computer Sciences Department, University of Wisconsin}, 26479 year = {1994}, 26480 address = {Madison, Wisconsin}, 26481 note = {Available from ftp://ftp.cs.wisc.edu/math-prog/tech-reports/}, 26482 annote = {Mathematical Programming Technical Report 94-12} 26483} 26484 26485@TechReport{ dixon.mills:neural, 26486 author = {L. C. Dixon and D. J. Mills}, 26487 title = {Neural Nets for Massively Parallel Optimisation}, 26488 institution = {Hatfield Polytechnic}, 26489 year = {1992}, 26490 address = {Hatfield, Hertforshire, England}, 26491 number = {Numerical Optimisation Centre Technical Report No. 259} 26492} 26493 26494@Article{ dontchev:local, 26495 author = {A. L. Dontchev}, 26496 title = {Local Convergence of the {N}ewton method for Generalized Equations}, 26497 journal = {C.R. Acad. Sci. 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Lucidi}, 27255 title = {Globally Convergent Methods for Nonlinear Equations}, 27256 institution = {Computer Sciences Department, University of Wisconsin}, 27257 year = {1991}, 27258 address = {Madison, Wisconsin}, 27259 number = {1030}, 27260 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1991/tr1030.ps}, 27261 key = {21} 27262} 27263 27264@Article{ ferris.lucidi:nonmonotone, 27265 author = {M. C. Ferris and S. Lucidi}, 27266 title = {Nonmonotone Stabilization Methods for Nonlinear Equations}, 27267 journal = {Journal of Optimization Theory and Applications}, 27268 year = {1994}, 27269 volume = {81}, 27270 pages = {53--71}, 27271 key = {30} 27272} 27273 27274@Article{ ferris.mangasarian:breast, 27275 author = {M. C. Ferris and O. L. Mangasarian}, 27276 title = {Breast Cancer Diagnosis via Linear Programming}, 27277 key = {50}, 27278 journal = {{IEEE} Computational Science and Engineering}, 27279 year = {1995}, 27280 volume = {2}, 27281 pages = {70--71} 27282} 27283 27284@Article{ ferris.mangasarian:error, 27285 author = {M. C. Ferris and O. L. Mangasarian}, 27286 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 27287 Inequalities}, 27288 journal = {Annals of Operations Research}, 27289 year = {1993}, 27290 volume = {47}, 27291 pages = {293--305}, 27292 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 27293 key = {24} 27294} 27295 27296@Article{ ferris.mangasarian:finite, 27297 author = {M. C. Ferris and O. L. Mangasarian}, 27298 title = {Finite Perturbation of Convex Programs}, 27299 journal = {Applied Mathematics and Optimization}, 27300 year = {1991}, 27301 volume = {23}, 27302 pages = {263--273}, 27303 key = {08} 27304} 27305 27306@Book{ ferris.mangasarian:linear, 27307 author = {M. C. Ferris and O. L. Mangasarian}, 27308 title = {Linear Programming via {MATLAB}}, 27309 publisher = {in preparation}, 27310 year = {1995}, 27311 address = {Madison, Wisconsin} 27312} 27313 27314@Article{ ferris.mangasarian:minimum, 27315 author = {M. C. Ferris and O. L. Mangasarian}, 27316 title = {Minimum Principle Sufficiency}, 27317 journal = {Mathematical Programming}, 27318 year = {1992}, 27319 volume = {57}, 27320 pages = {1--14}, 27321 key = {11} 27322} 27323 27324@Article{ ferris.mangasarian:parallel, 27325 author = {M. C. Ferris and O. L. Mangasarian}, 27326 title = {Parallel Constraint Distribution}, 27327 journal = {SIAM Journal on Optimization}, 27328 year = {1991}, 27329 volume = {1}, 27330 pages = {487--500}, 27331 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 27332 key = {18} 27333} 27334 27335@Article{ ferris.mangasarian:parallel*1, 27336 author = {M. C. Ferris and O. L. Mangasarian}, 27337 title = {Parallel Variable Distribution}, 27338 journal = {SIAM Journal on Optimization}, 27339 year = {1994}, 27340 volume = {4}, 27341 pages = {815--832}, 27342 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 27343 key = {31} 27344} 27345 27346@Article{ ferris.meeraus.ea:computing, 27347 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 27348 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 27349 journal = {Optimization Methods and Software}, 27350 year = {1999}, 27351 volume = {10}, 27352 pages = {669--685}, 27353 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 27354 key = {45} 27355} 27356 27357@Article{ ferris.mesnier.ea:neos, 27358 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 27359 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 27360 {I}nternet}, 27361 year = {2000}, 27362 journal = {{ACM} Transactions on Mathematical Software}, 27363 key = {54}, 27364 volume = {26}, 27365 pages = {1--18}, 27366 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 27367 institution = {Computer Sciences Department, University of Wisconsin}, 27368 address = {Madison, Wisconsin}, 27369 number = {96-08}, 27370 type = {Mathematical Programming Technical Report}, 27371 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 27372 Argonne National Laboratory}, 27373 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 27374 1996} 27375} 27376 27377@InCollection{ ferris.meyer:models, 27378 author = {M. C. Ferris and R. R. Meyer}, 27379 title = {Models and Solution for On-Demand Data Delivery Problems}, 27380 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 27381 key = {80}, 27382 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 27383 Problems}, 27384 editor = {P. M. Pardalos}, 27385 series = {Nonconvex Optimization and its Applications}, 27386 volume = {42}, 27387 address = {Dordrect}, 27388 year = {2000}, 27389 pages = {175--188}, 27390 publisher = {Kluwer}, 27391 type = {Mathematical Programming Technical Report}, 27392 institution = {Computer Sciences Department, University of Wisconsin}, 27393 number = {99-04} 27394} 27395 27396@InProceedings{ ferris.munson.ea:homotopy, 27397 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 27398 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 27399 booktitle = {Numerical Analysis 1999}, 27400 key = {88}, 27401 year = {2000}, 27402 editor = {D. F. Griffiths and G. A. Watson}, 27403 series = {Research Notes in Mathematics}, 27404 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 27405 address = {London}, 27406 pages = {143--167}, 27407 publisher = {Chapman and Hall}, 27408 institution = {Computer Sciences Department, University of Wisconsin}, 27409 number = {99-09}, 27410 type = {Mathematical Programming Technical Report} 27411} 27412 27413@TechReport{ ferris.munson.ea:practical, 27414 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 27415 title = {A Practical Approach to Sample-Path Simulation Optimization}, 27416 type = {Data Mining Institute Technical Report}, 27417 institution = {Computer Sciences Department, University of Wisconsin}, 27418 address = {Madison, Wisconsin}, 27419 year = {2000}, 27420 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 27421 number = {00-03}, 27422 key = {92}, 27423 annote = {To appear in WSC 2000} 27424} 27425 27426@InCollection{ ferris.munson:case, 27427 author = {M. C. Ferris and T. S. Munson}, 27428 title = {Case Studies in Complementarity: Improving Model Formulation}, 27429 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 27430 key = {73}, 27431 pages = {79--98}, 27432 publisher = {Springer Verlag}, 27433 year = {1999}, 27434 editor = {M. Th\'{e}ra and R. Tichatschke}, 27435 number = {477}, 27436 series = {Lecture Notes in Economics and Mathematical Systems}, 27437 address = {Berlin}, 27438 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 27439 type = {Mathematical Programming Technical Report}, 27440 institution = {Computer Sciences Department, University of Wisconsin} 27441} 27442 27443@Article{ ferris.munson:complementarity, 27444 author = {M. C. Ferris and T. S. Munson}, 27445 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 27446 year = {2000}, 27447 volume = {24}, 27448 pages = {165--188}, 27449 journal = {Journal of Economic Dynamics and Control}, 27450 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 27451 key = {70}, 27452 type = {Mathematical Programming Technical Report}, 27453 institution = {Computer Sciences Department, University of Wisconsin}, 27454 address = {Madison, Wisconsin}, 27455 number = {98-12} 27456} 27457 27458@Misc{ ferris.munson:condor, 27459 author = {M. C. Ferris and T. S. Munson}, 27460 title = {Condor Modeling Language Interface}, 27461 organization = {Computer Sciences Department, University of Wisconsin}, 27462 address = {Madison, Wisconsin}, 27463 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 27464} 27465 27466@Manual{ ferris.munson:gams, 27467 author = {M. C. Ferris and T. S. Munson}, 27468 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 27469 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 27470} 27471 27472@Article{ ferris.munson:interfaces, 27473 author = {M. C. Ferris and T. S. Munson}, 27474 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 27475 journal = {Computational Optimization and Applications}, 27476 volume = {12}, 27477 pages = {207--227}, 27478 year = {1999}, 27479 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 27480 key = {63}, 27481 institution = {Computer Sciences Department, University of Wisconsin}, 27482 address = {Madison, Wisconsin}, 27483 number = {97-12}, 27484 type = {Mathematical Programming Technical Report} 27485} 27486 27487@TechReport{ ferris.munson:interior, 27488 author = {M. C. Ferris and T. S. Munson}, 27489 title = {Interior Point Methods for Massive Support Vector Machines}, 27490 institution = {Computer Sciences Department, University of Wisconsin}, 27491 year = {2000}, 27492 key = {94}, 27493 type = {Data Mining Institute Technical Report}, 27494 number = {00-05}, 27495 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 27496 address = {Madison, Wisconsin}, 27497 annote = {Submitted to SIOPT} 27498} 27499 27500@Article{ ferris.munson:linear, 27501 author = {M. C. Ferris and T. S. Munson}, 27502 title = {Linear Programming for Emergency Broadcast Systems}, 27503 year = {1999}, 27504 journal = {{SIAG/OPT} Newsletter}, 27505 volume = {10}, 27506 pages = {6--8}, 27507 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 27508 key = {76}, 27509 type = {Mathematical Programming Technical Report}, 27510 institution = {Computer Sciences Department, University of Wisconsin}, 27511 address = {Madison, Wisconsin}, 27512 number = {98-20} 27513} 27514 27515@Article{ ferris.munson:modeling, 27516 author = {M. C. Ferris and T. S. Munson}, 27517 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 27518 year = {2000}, 27519 journal = {Mathematical Programming}, 27520 volume = {88}, 27521 pages = {487--506}, 27522 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 27523 key = {71}, 27524 type = {Mathematical Programming Technical Report}, 27525 institution = {Computer Sciences Department, University of Wisconsin}, 27526 address = {Madison, Wisconsin}, 27527 number = {98-13} 27528} 27529 27530@TechReport{ ferris.munson:preprocessing, 27531 author = {M. C. Ferris and T. S. Munson}, 27532 title = {Preprocessing Complementarity Problems}, 27533 type = {Mathematical Programming Technical Report}, 27534 institution = {Computer Sciences Department, University of Wisconsin}, 27535 address = {Madison, Wisconsin}, 27536 year = {1999}, 27537 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 27538 number = {99-07}, 27539 key = {86}, 27540 annote = {Submitted to ICCP 99} 27541} 27542 27543@TechReport{ ferris.munson:semismooth, 27544 author = {M. C. Ferris and T. S. Munson}, 27545 title = {Semismooth Support Vector Machines}, 27546 institution = {Computer Sciences Department, University of Wisconsin}, 27547 year = {2000}, 27548 key = {97}, 27549 type = {Data Mining Institute Technical Report}, 27550 number = {00-09}, 27551 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 27552 address = {Madison, Wisconsin}, 27553 annote = {Submitted to Math Prog B} 27554} 27555 27556@Article{ ferris.pang:engineering, 27557 author = {M. C. Ferris and J. S. Pang}, 27558 title = {Engineering and Economic Applications of Complementarity Problems}, 27559 year = {1997}, 27560 journal = {SIAM Review}, 27561 volume = {39}, 27562 pages = {669--713}, 27563 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 27564 key = {46} 27565} 27566 27567@Article{ ferris.pang:nondegenerate, 27568 author = {M. C. Ferris and J. S. Pang}, 27569 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 27570 journal = {SIAM Journal on Control and Optimization}, 27571 year = {1996}, 27572 volume = {34}, 27573 pages = {244--263}, 27574 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 27575 key = {35} 27576} 27577 27578@Article{ ferris.philpott:affine, 27579 author = {M. C. Ferris and A. B. Philpott}, 27580 title = {On Affine Scaling and Semi--Infinite Programming}, 27581 journal = {Mathematical Programming}, 27582 year = {1992}, 27583 volume = {56}, 27584 pages = {361--364}, 27585 key = {15} 27586} 27587 27588@Article{ ferris.philpott:interior, 27589 author = {M. C. Ferris and A. B. Philpott}, 27590 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 27591 journal = {Mathematical Programming}, 27592 year = {1989}, 27593 volume = {43}, 27594 pages = {257--276}, 27595 key = {04} 27596} 27597 27598@Article{ ferris.philpott:performance, 27599 author = {M. C. Ferris and A. B. Philpott}, 27600 title = {On the Performance of {K}armarkar's Algorithm}, 27601 journal = {Journal of the Operational Research Society}, 27602 year = {1988}, 27603 volume = {39}, 27604 pages = {257--270}, 27605 key = {03} 27606} 27607 27608@InCollection{ ferris.ralph:projected, 27609 author = {M. C. Ferris and D. Ralph}, 27610 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 27611 Maps}, 27612 booktitle = {Recent Advances in Nonsmooth Optimization}, 27613 publisher = {World Scientific Publishers}, 27614 year = {1995}, 27615 pages = {57--87}, 27616 editor = {D. Du and L. Qi and R. Womersley}, 27617 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 27618 key = {41} 27619} 27620 27621@Article{ ferris.ruszczynski:robust, 27622 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 27623 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 27624 year = {2000}, 27625 journal = {Networks}, 27626 volume = {35}, 27627 pages = {181--194}, 27628 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 27629 key = {60} 27630} 27631 27632@InCollection{ ferris.rutherford:accessing, 27633 author = {M. C. Ferris and T. F. Rutherford}, 27634 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 27635 booktitle = {Nonlinear Optimization and Applications}, 27636 key = {48}, 27637 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 27638 editor = {G. Di Pillo and F. Giannessi}, 27639 year = {1996}, 27640 pages = {141--153}, 27641 publisher = {Plenum Press}, 27642 address = {New York} 27643} 27644 27645@InCollection{ ferris.shepard:optimizing, 27646 author = {M. C. Ferris and D. M. Shepard}, 27647 title = {Optimization of Gamma Knife Radiosurgery}, 27648 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 27649 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 27650 publisher = {AMS}, 27651 year = {2000}, 27652 optseries = {DIMACS}, 27653 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 27654 key = {91}, 27655 type = {Data Mining Institute Technical Report}, 27656 institution = {Computer Sciences Department, University of Wisconsin}, 27657 address = {Madison, Wisconsin}, 27658 number = {00-01} 27659} 27660 27661@InCollection{ ferris.sinapiromsaran:formulating, 27662 author = {M. C. Ferris and K. Sinapiromsaran}, 27663 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 27664 booktitle = {Optimization}, 27665 key = {77}, 27666 publisher = {Springer-Verlag}, 27667 year = {2000}, 27668 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 27669 volume = {481}, 27670 series = {Lecture Notes in Economics and Mathematical Systems}, 27671 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 27672 type = {Mathematical Programming Technical Report}, 27673 institution = {Computer Sciences Department, University of Wisconsin}, 27674 address = {Madison, Wisconsin}, 27675 number = {98-21} 27676} 27677 27678@Article{ ferris.tin-loi:limit, 27679 author = {M. C. Ferris and F. Tin-Loi}, 27680 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 27681 Complementarity Constraints}, 27682 year = {2001}, 27683 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 27684 key = {78}, 27685 journal = {International Journal of Mechanical Sciences}, 27686 pages = {209--224}, 27687 volume = {43}, 27688 type = {Mathematical Programming Technical Report}, 27689 institution = {Computer Sciences Department, University of Wisconsin}, 27690 address = {Madison, Wisconsin}, 27691 number = {99-01} 27692} 27693 27694@Article{ ferris.tin-loi:nonlinear, 27695 author = {M. C. Ferris and F. Tin-Loi}, 27696 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 27697 Elastoplasticity}, 27698 year = {1998}, 27699 key = {64}, 27700 volume = {6}, 27701 pages = {857--870}, 27702 journal = {Structural Engineering and Mechanics} 27703} 27704 27705@Article{ ferris.tin-loi:solution, 27706 author = {M. C. Ferris and F. Tin-Loi}, 27707 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 27708 and Complementarity Constraints}, 27709 year = {1999}, 27710 journal = {Computer Methods in Applied Mechanics and Engineering}, 27711 volume = {174}, 27712 pages = {107--120}, 27713 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 27714 key = {66} 27715} 27716 27717@Article{ ferris.vlach:scheduling, 27718 author = {M. C. Ferris and M. Vlach}, 27719 title = {Scheduling with Earliness and Tardiness Penalties}, 27720 journal = {Naval Research Logistics Quarterly}, 27721 year = {1992}, 27722 volume = {39}, 27723 pages = {229--245}, 27724 key = {13} 27725} 27726 27727@TechReport{ ferris.zavriev:linear, 27728 author = {M. C. Ferris and S. K Zavriev}, 27729 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 27730 institution = {Computer Sciences Department, University of Wisconsin}, 27731 year = {1996}, 27732 key = {56}, 27733 address = {Madison, Wisconsin}, 27734 type = {Mathematical Programming Technical Report}, 27735 number = {96--12}, 27736 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 27737} 27738 27739@Article{ ferris:finite, 27740 author = {M. C. Ferris}, 27741 title = {Finite Termination of the Proximal Point Algorithm}, 27742 journal = {Mathematical Programming}, 27743 year = {1991}, 27744 volume = {50}, 27745 pages = {359--366}, 27746 key = {06} 27747} 27748 27749@Article{ ferris:iterative, 27750 author = {M. C. Ferris}, 27751 title = {Iterative Linear Programming Solution of Convex Programs}, 27752 journal = {Journal of Optimization Theory and Applications}, 27753 year = {1990}, 27754 volume = {65}, 27755 pages = {53--65}, 27756 key = {07} 27757} 27758 27759@Article{ ferris:linear, 27760 author = {M. C. Ferris}, 27761 title = {The Linear Complementarity Problem}, 27762 journal = {Bulletin of the American Mathematical Society}, 27763 year = {1993}, 27764 volume = {28}, 27765 pages = {169--175}, 27766 key = {27} 27767} 27768 27769@MastersThesis{ ferris:linear*1, 27770 author = {M. C. Ferris}, 27771 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 27772 Solving a Class of Structural Optimization Problems}, 27773 year = {1985}, 27774 school = {University of Cambridge}, 27775 address = {England}, 27776 key = {01} 27777} 27778 27779@TechReport{ ferris:matlab, 27780 author = {M. C. Ferris}, 27781 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 27782 institution = {Computer Sciences Department, University of Wisconsin}, 27783 year = {1998}, 27784 address = {Madison, Wisconsin}, 27785 type = {Mathematical Programming Technical Report}, 27786 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 27787 number = {98-19}, 27788 key = {75} 27789} 27790 27791@Article{ ferris:parallel, 27792 author = {M. C. Ferris}, 27793 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 27794 journal = {Mathematics of Operations Research}, 27795 year = {1994}, 27796 volume = {19}, 27797 pages = {645--658}, 27798 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 27799 key = {20} 27800} 27801 27802@TechReport{ ferris:parallel*1, 27803 author = {M. C. Ferris}, 27804 title = {Parallel Solution of Extremely Large Knapsack Problems}, 27805 institution = {Computer Sciences Department, University of Wisconsin}, 27806 year = {1989}, 27807 address = {Madison, Wisconsin}, 27808 number = {842}, 27809 key = {09} 27810} 27811 27812@PhDThesis{ ferris:weak, 27813 author = {M. C. Ferris}, 27814 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27815 year = {1988}, 27816 school = {University of Cambridge}, 27817 address = {England}, 27818 key = {02} 27819} 27820 27821@TechReport{ ferris:weak*1, 27822 author = {M. C. Ferris}, 27823 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27824 institution = {Computer Sciences Department, University of Wisconsin}, 27825 year = {1988}, 27826 address = {Madison, Wisconsin}, 27827 number = {779}, 27828 key = {05} 27829} 27830 27831@Book{ fiacco.mccormick:nonlinear, 27832 author = {A. V. Fiacco and G. P. McCormick}, 27833 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 27834 year = {1968}, 27835 publisher = {John Wiley \& Sons}, 27836 address = {New York}, 27837 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 27838} 27839 27840@Book{ fiacco:introduction, 27841 author = {A. V. Fiacco}, 27842 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 27843 year = {1983}, 27844 publisher = {Academic Press}, 27845 address = {New York} 27846} 27847 27848@Article{ fiedler.ptak:matrices, 27849 author = {M. Fiedler and V. Pt\'{a}k}, 27850 title = {On matrices with nonpositive off-diagonal elements and positive principal 27851 minors}, 27852 journal = {Czechoslovak Mathematics Journal}, 27853 volume = {12}, 27854 pages = {382--400}, 27855 year = {1962} 27856} 27857 27858@Article{ fischer.kanzow:finite, 27859 author = {A. Fischer and C. Kanzow}, 27860 title = {On Finite Termination of an Iterative Method for Linear Complementarity 27861 Problems}, 27862 journal = {Mathematical Programming}, 27863 volume = {74}, 27864 pages = {279--292}, 27865 year = {1996} 27866} 27867 27868@TechReport{ fischer:constrained, 27869 author = {A. Fischer}, 27870 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 27871 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 27872 year = {1995}, 27873 type = {Technical Report}, 27874 number = {MATH-NM-10-1995}, 27875 address = {Dresden} 27876} 27877 27878@Article{ fischer:local, 27879 author = {A. Fischer}, 27880 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 27881 weak conditions}, 27882 journal = {Optimization Methods and Software}, 27883 year = {1995}, 27884 volume = {6}, 27885 pages = {83--107} 27886} 27887 27888@InCollection{ fischer:ncp-function, 27889 author = {A. Fischer}, 27890 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 27891 booktitle = {Recent Advances in Nonsmooth Optimization}, 27892 publisher = {World Scientific Publishers}, 27893 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 27894 year = {1995}, 27895 pages = {88--105} 27896} 27897 27898@Article{ fischer:newton-type, 27899 author = {A. Fischer}, 27900 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 27901 Problems}, 27902 journal = {Journal of Optimization Theory and Applications}, 27903 year = {1995}, 27904 volume = {86}, 27905 pages = {585--608} 27906} 27907 27908@Article{ fischer:solution, 27909 author = {A. Fischer}, 27910 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 27911 Functions}, 27912 year = {1997}, 27913 journal = {Mathematical Programming}, 27914 pages = {513--532} 27915} 27916 27917@Article{ fischer:special, 27918 author = {A. Fischer}, 27919 title = {A Special {N}ewton--Type Optimization Method}, 27920 journal = {Optimization}, 27921 year = {1992}, 27922 volume = {24}, 27923 pages = {269--284} 27924} 27925 27926@Article{ fisher:use, 27927 author = {R. A. Fisher}, 27928 title = {The Use of Multiple Measurements in Taxonomic Problems}, 27929 journal = {Annual Eugenics}, 27930 year = {1936}, 27931 volume = {7}, 27932 number = {Part II}, 27933 pages = {179--188} 27934} 27935 27936@Book{ fishman:principles, 27937 author = {G. Fishman}, 27938 title = {Principles of Discrete Event Simulation}, 27939 publisher = {Wiley}, 27940 address = {New York, NY}, 27941 year = {1978} 27942} 27943 27944@Article{ fitchard.aldridge.ea:registration, 27945 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 27946 title = {Registration of Synthetic Tomographic Projection Data Sets Using 27947 Cross-Correlation}, 27948 journal = {Physics in Medicine and Biology}, 27949 year = {1998}, 27950 volume = {43}, 27951 pages = {1645--1657} 27952} 27953 27954@Article{ fletcher.matthews:stable, 27955 author = {R. Fletcher and S. P. J. Matthews}, 27956 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 27957 journal = {Mathematical Programming}, 27958 year = {1984}, 27959 volume = {30}, 27960 pages = {267--284} 27961} 27962 27963@TechReport{ fletcher.maza:nonlinear, 27964 author = {R. Fletcher and E. Sainz de la Maza}, 27965 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 27966 Programming}, 27967 institution = {Department of Mathematical Sciences}, 27968 year = {1987}, 27969 address = {The University, Dundee, Scotland}, 27970 number = {NA/100}, 27971 type = {Numerical Analysis Report} 27972} 27973 27974@InCollection{ fletcher:class, 27975 author = {R. Fletcher}, 27976 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 27977 Properties}, 27978 booktitle = {Integer and Nonlinear Programming}, 27979 year = {1970}, 27980 editor = {J. Abadie}, 27981 publisher = {North--Holland}, 27982 address = {Amsterdam}, 27983 pages = {157--173} 27984} 27985 27986@Article{ fletcher:exact, 27987 author = {R. 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Fletcher}, 28014 title = {Practical Methods of Optimization}, 28015 year = {1981}, 28016 publisher = {John Wiley \& Sons}, 28017 address = {Chichester}, 28018 volume = {1} 28019} 28020 28021@Book{ fletcher:practical*1, 28022 author = {R. Fletcher}, 28023 title = {Practical Methods of Optimization}, 28024 year = {1981}, 28025 publisher = {John Wiley \& Sons}, 28026 address = {Chichester}, 28027 volume = {2} 28028} 28029 28030@Book{ fletcher:practical*2, 28031 author = {R. Fletcher}, 28032 title = {Practical Methods of Optimization}, 28033 year = {1987}, 28034 publisher = {John Wiley \& Sons}, 28035 address = {New York}, 28036 edition = {second} 28037} 28038 28039@Unpublished{ fletcher:recent, 28040 author = {R. Fletcher}, 28041 title = {Recent Developments in Nonlinear Programming}, 28042 note = {Presentation at SOR 96, Braunchweig, Germany}, 28043 year = {1996} 28044} 28045 28046@InCollection{ fletcher:second, 28047 author = {R. 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Tomlin}, 28103 title = {Updating Triangular Factors of the Basis to Maintain Sparsity in the Product Form 28104 Simplex Method}, 28105 journal = {Mathematical Programming}, 28106 year = {1972}, 28107 volume = {2}, 28108 pages = {263--278} 28109} 28110 28111@TechReport{ forsgren.gill.ea:computing, 28112 author = {A. Forsgren and P. E. Gill and W. Murray}, 28113 title = {Computing Modified {N}ewton Directions using a Partial {C}holesky Factorization}, 28114 institution = {Department of Mathematics, Royal Institute of Technology}, 28115 year = {1993}, 28116 number = {TRITA-MAT-1993-9}, 28117 address = {Stockholm, Sweden} 28118} 28119 28120@TechReport{ forsgren.gill:primal-dual, 28121 author = {A. Forsgren and P. E. Gill}, 28122 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 28123 institution = {Department of Mathematics, University of California}, 28124 year = {1996}, 28125 type = {Report NA}, 28126 number = {96-3}, 28127 address = {San Diego} 28128} 28129 28130@InCollection{ fortin.glowinski:decomposition-coordination, 28131 author = {M. Fortin and R. Glowinski}, 28132 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 28133 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 28134 Problems}, 28135 publisher = {North-Holland}, 28136 year = {1983}, 28137 editor = {M. Fortin and R. Glowinski}, 28138 address = {Amsterdam} 28139} 28140 28141@Misc{ foster.kesselman:globus, 28142 author = {I. Foster and C. Kesselman}, 28143 title = {The Globus Project}, 28144 howpublished = {www.globus.org} 28145} 28146 28147@Article{ foster.kesselman:globus*1, 28148 author = {I. Foster and C. 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Gabriel}, 28404 title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and 28405 Extensions}, 28406 school = {The Johns Hopkins University}, 28407 year = {1992}, 28408 address = {Baltimore, Maryland} 28409} 28410 28411@Article{ gafni.bertsekas:two-metric, 28412 author = {E. M. Gafni and D. P. Bertsekas}, 28413 title = {Two-Metric Projection Methods for Constrained Optimization}, 28414 journal = {SIAM Journal on Control and Optimization}, 28415 year = {1984}, 28416 volume = {22}, 28417 pages = {936--964} 28418} 28419 28420@InProceedings{ gaivoronski:convergence, 28421 author = {A. A. Gaivoronski}, 28422 title = {Convergence of Parallel Backpropagation for Neural Networks}, 28423 booktitle = {SIAM Journal on Optimization}, 28424 year = {1994}, 28425 note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993, 28426 submitted} 28427} 28428 28429@Misc{ gaivoronski:private, 28430 author = {A. A. 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Gao}, 28474 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 28475 Conditions}, 28476 type = {Manuscript}, 28477 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 28478 month = oct, 28479 year = {1994} 28480} 28481 28482@Article{ garcia-palomares.mangasarian:superlinearly, 28483 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 28484 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 28485 Optimization Problems}, 28486 journal = {Mathematical Programming}, 28487 year = {1976}, 28488 volume = {11}, 28489 pages = {1--13} 28490} 28491 28492@Article{ garcia-palomares.restuccia:global, 28493 author = {U. M. {Garcia--Palomares} and A. Restuccia}, 28494 title = {A Global Quadratic Algorithm for Solving a System of Mixed Equations}, 28495 journal = {Mathematical Programming}, 28496 year = {1981}, 28497 volume = {21}, 28498 pages = {290--300} 28499} 28500 28501@InProceedings{ garcia-palomares:superlinearly, 28502 author = {U. M. {Garcia--Palomares}}, 28503 title = {Superlinearly Convergent Algorithms for Linearly Constrained Optimization}, 28504 crossref = {mangasarian.meyer.ea:nonlinear*2}, 28505 pages = {101--119} 28506} 28507 28508@Article{ garcia.gould:theorem, 28509 author = {C. B. Garcia and F. J. Gould}, 28510 title = {A Theorem on Homotopy Paths}, 28511 journal = {Mathematics of Operations Research}, 28512 year = {1978}, 28513 volume = {3}, 28514 pages = {282--289} 28515} 28516 28517@Book{ garcia.zangwill:pathways, 28518 author = {C. B. Garcia and W. I. Zangwill}, 28519 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 28520 year = {1981}, 28521 publisher = {Prentice-Hall, Inc}, 28522 address = {Englewood Cliffs, New Jersey} 28523} 28524 28525@Book{ garey.johnson:computers, 28526 author = {M. R. Garey and D. S. Johnson}, 28527 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 28528 year = {1979}, 28529 publisher = {W.H. Freeman and Company}, 28530 address = {San Francisco} 28531} 28532 28533@Article{ garey.tarjan.ea:one-processor, 28534 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 28535 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 28536 journal = {Mathematics of Operations Research}, 28537 year = {1988}, 28538 volume = {13}, 28539 pages = {330--348} 28540} 28541 28542@Book{ garfinkel.nemhauser:integer, 28543 author = {R. S. Garfinkel and G. L. Nemhauser}, 28544 title = {Integer Programming}, 28545 year = {1972}, 28546 publisher = {John Wiley \& Sons}, 28547 address = {New York} 28548} 28549 28550@Book{ gass:linear, 28551 author = {S. Gass}, 28552 title = {Linear Programming Methods and Applications}, 28553 edition = {Fifth}, 28554 publisher = {Boyd and Fraser Publishing Company}, 28555 address = {Danvers, Massachusetts}, 28556 year = {1985} 28557} 28558 28559@InProceedings{ gay:combining, 28560 author = {D. M. Gay}, 28561 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 28562 booktitle = {Sparse Matrix Proceedings 1978}, 28563 editor = {I. S. Duff and G. W. Stewart}, 28564 year = {1978}, 28565 organization = {SIAM}, 28566 address = {Philadelphia, Pennsylvania}, 28567 pages = {313--334} 28568} 28569 28570@Article{ gay:electronic, 28571 author = {D. M. Gay}, 28572 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 28573 journal = {{COAL} Newsletter}, 28574 year = {1985}, 28575 volume = {13}, 28576 pages = {10--12} 28577} 28578 28579@TechReport{ gay:hooking, 28580 author = {D. M. Gay}, 28581 title = {Hooking Your Solver to {AMPL}}, 28582 year = {1997}, 28583 institution = {Bell Laboratories}, 28584 address = {Murray Hill, New Jersey}, 28585 note = {Revised 1994, 1997} 28586} 28587 28588@Article{ gay:variant, 28589 author = {D. Gay}, 28590 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 28591 Form}, 28592 journal = {Mathematical Programming}, 28593 year = {1987}, 28594 volume = {37}, 28595 pages = {81--90} 28596} 28597 28598@Article{ geiger.kanzow:resolution, 28599 author = {C. Geiger and C. Kanzow}, 28600 title = {On the Resolution of Monotone Complementarity Problems}, 28601 journal = {Computational Optimization and Applications}, 28602 volume = {5}, 28603 year = {1996}, 28604 pages = {155--173} 28605} 28606 28607@Book{ geist.beguelin.ea:pvm, 28608 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 28609 V. S. Sunderam}, 28610 title = {{PVM}: Parallel Virtual Machine}, 28611 publisher = {MIT Press}, 28612 address = {Cambridge, Massachusetts}, 28613 year = {1994} 28614} 28615 28616@Article{ gendron.crainic:parallel, 28617 author = {B. Gendron and T. G. Crainic}, 28618 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 28619 journal = {Operations Research}, 28620 year = {1994}, 28621 volume = {42}, 28622 pages = {1042--1060} 28623} 28624 28625@Article{ george:automatic, 28626 author = {A. George}, 28627 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 28628 journal = {SIAM Journal on Numerical Analysis}, 28629 vol = {17}, 28630 pages = {740--751}, 28631 year = {1980} 28632} 28633 28634@InProceedings{ georges-schleuter:asparagos, 28635 crossref = {schaeffer:third}, 28636 author = {M. Georges--Schleuter}, 28637 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 28638 pages = {416--421} 28639} 28640 28641@Article{ georgiou:comments, 28642 author = {G. M. Georgiou}, 28643 title = {Comments On Hidden Nodes in Neural Nets}, 28644 journal = {IEEE Transactions on Circuits and Systems}, 28645 year = {1991}, 28646 volume = {38}, 28647 pages = {1410} 28648} 28649 28650@TechReport{ gertz.linderoth.ea:object-oriented, 28651 author = {M. Gertz and J. Linderoth and S. Wright}, 28652 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 28653 institution = {MCS Division, Argonne National Laboratory}, 28654 year = {in preparation} 28655} 28656 28657@Article{ ghellinck.vial:polynomial, 28658 author = {G. de Ghellinck and J.--Ph. Vial}, 28659 title = {A Polynomial {N}ewton Method for Linear Programming}, 28660 journal = {Algorithmica}, 28661 year = {1986}, 28662 volume = {1}, 28663 pages = {425--453} 28664} 28665 28666@InCollection{ gilbert.ng:predicting, 28667 author = {J. R. Gilbert and E. Ng}, 28668 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 28669 year = {1993}, 28670 booktitle = {Graph Theory and Sparse Matrix Computation}, 28671 editor = {A. George and J. Gilbert and J. Liu}, 28672 publisher = {Springer-Verlag} 28673} 28674 28675@Article{ gilbert-lemarechal, 28676 author = {J. C. Gilbert and C. 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Luo}, 31732 title = {Convergence Analysis of Primal--Dual Interior--Point Algorithms for Convex 31733 Quadratic Programs}, 31734 institution = {Communications Research Laboratory, McMaster University}, 31735 year = {1992}, 31736 address = {Hamilton, Ontario} 31737} 31738 31739@Article{ lustig.marsten.ea:computational, 31740 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31741 title = {Computational Experience with a Primal-Dual Interior Point Method for Linear 31742 Programming}, 31743 journal = {Linear Algebra and Its Applications}, 31744 year = {1991}, 31745 volume = {152}, 31746 pages = {191--222} 31747} 31748 31749@Article{ lustig.marsten.ea:implementing, 31750 author = {I. J. Lustig and R. E. Marsten and D. F. 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Madsen}, 31819 title = {Minimization of Nonlinear Approximation Functions}, 31820 year = {1985}, 31821 address = {Lyngby, Denmark}, 31822 school = {Institute of Numerical Analysis, Technical University of Denmark}, 31823 annote = {Dissertation} 31824} 31825 31826@Book{ magill.quinzii:theory, 31827 author = {M. Magill and M. Quinzii}, 31828 title = {Theory of Incomplete Markets}, 31829 publisher = {MIT Press}, 31830 year = {1996} 31831} 31832 31833@InCollection{ magnanti:models, 31834 author = {T. L. Magnanti}, 31835 title = {Models and Algorithms for Predicting Urban Traffic Equilibria}, 31836 booktitle = {Transportation Planning Models}, 31837 year = {1984}, 31838 editor = {M. Florian}, 31839 publisher = {North Holland}, 31840 pages = {153--186} 31841} 31842 31843@InCollection{ maguregui:modified, 31844 author = {J. Maguregui}, 31845 title = {A modified {N}ewton algorithm for functions over convex sets}, 31846 crossref = {mangasarian.meyer.ea:nonlinear*3}, 31847 pages = {461--473} 31848} 31849 31850@PhDThesis{ maguregui:regular, 31851 author = {J. Maguregui}, 31852 title = {Regular Multivalued Functions and Algorithmic Applications}, 31853 year = {1977}, 31854 address = {Madison, Wisconsin}, 31855 school = {Computer Sciences Department, University of Wisconsin} 31856} 31857 31858@Article{ mahey.oualibouch.ea:proximal, 31859 author = {P. Mahey and S. Oualibouch and D. T. Pham}, 31860 title = {Proximal Decomposition on the Graph of a Maximal Monotone Operator}, 31861 journal = {SIAM Journal on Optimization}, 31862 year = {1995}, 31863 volume = {5}, 31864 pages = {454--466} 31865} 31866 31867@Article{ mahey.pham:partial, 31868 author = {P. Mahey and D. T. Pham}, 31869 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 31870 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 31871 year = {1993}, 31872 volume = {27}, 31873 pages = {375--392} 31874} 31875 31876@InCollection{ maier.novati:shakedown, 31877 author = {G. Maier and G. Novati}, 31878 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 31879 geometric effects with reference to discrete structural models}, 31880 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 31881 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 31882 publisher = {Pineridge Press}, 31883 address = {Swansea}, 31884 year = {1990}, 31885 pages = {451--471} 31886} 31887 31888@Article{ maier:incremental, 31889 author = {G. Maier}, 31890 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 31891 Instabilizing Effects}, 31892 journal = {International Journal of Solids and Structures}, 31893 volume = {7}, 31894 year = {1971}, 31895 pages = {345--372} 31896} 31897 31898@InCollection{ maier:inverse, 31899 author = {G. Maier}, 31900 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 31901 booktitle = {Serie VIII}, 31902 publisher = {Academia Nazionale dei Lincei}, 31903 year = {1981}, 31904 volume = {LXX}, 31905 pages = {203--209} 31906} 31907 31908@Article{ maier:matrix, 31909 author = {G. Maier}, 31910 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 31911 yield planes}, 31912 journal = {Meccanica}, 31913 volume = {5}, 31914 year = {1970}, 31915 pages = {54--66} 31916} 31917 31918@Article{ maier:quadratic, 31919 author = {G. Maier}, 31920 title = {A quadratic programming approach for certain classes of nonlinear structural 31921 problems}, 31922 journal = {Meccanica}, 31923 volume = {3}, 31924 year = {1968}, 31925 pages = {121--130} 31926} 31927 31928@Book{ manber:introduction, 31929 author = {U. Manber}, 31930 title = {Introduction to Algorithms: {A} Creative Approach}, 31931 year = {1989}, 31932 publisher = {Addison-Wesley} 31933} 31934 31935@Article{ mangasarian.deleone:error, 31936 author = {O. L. Mangasarian and R. {De~Leone}}, 31937 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 31938 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 31939 journal = {Applied Mathematics and Optimization}, 31940 year = {1988}, 31941 volume = {17}, 31942 pages = {1--14} 31943} 31944 31945@Article{ mangasarian.deleone:parallel, 31946 author = {O. L. Mangasarian and R. {De~Leone}}, 31947 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 31948 Problems and Linear Programs}, 31949 journal = {Journal of Optimization Theory and Applications}, 31950 year = {1987}, 31951 volume = {54}, 31952 pages = {437--446} 31953} 31954 31955@Article{ mangasarian.fromovitz:fritz, 31956 author = {O. L. Mangasarian and S. Fromovitz}, 31957 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 31958 and inequality constraints}, 31959 journal = {Journal of Mathematical Analysis and its Applications}, 31960 year = {1967}, 31961 volume = {17}, 31962 pages = {37--47} 31963} 31964 31965@Article{ mangasarian.mclinden:simple, 31966 author = {O. L. Mangasarian and L. McLinden}, 31967 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 31968 Programs}, 31969 journal = {Mathematical Programming}, 31970 year = {1985}, 31971 volume = {32}, 31972 pages = {32--40} 31973} 31974 31975@Article{ mangasarian.meyer:nonlinear, 31976 author = {O. L. Mangasarian and R. R. Meyer}, 31977 title = {Nonlinear Perturbation of Linear Programs}, 31978 journal = {SIAM Journal on Control and Optimization}, 31979 year = {1979}, 31980 volume = {17}, 31981 pages = {745--752} 31982} 31983 31984@TechReport{ mangasarian.musicant:active, 31985 author = {O. L. Mangasarian and David R. Musicant}, 31986 title = {Active Set Support Vector Machine Classification}, 31987 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31988 year = {2000}, 31989 number = {00-04}, 31990 address = {Madison, Wisconsin} 31991} 31992 31993@TechReport{ mangasarian.musicant:lagrangian, 31994 author = {O. L. Mangasarian and D. R. Musicant}, 31995 title = {Lagrangian Support Vector Machines}, 31996 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31997 year = {2000}, 31998 number = {00-06}, 31999 address = {Madison, Wisconsin} 32000} 32001 32002@TechReport{ mangasarian.musicant:robust, 32003 author = {O. L. Mangasarian and David R. Musicant}, 32004 title = {Robust Linear and Support Vector Regression}, 32005 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 32006 year = {1999}, 32007 number = {99-09}, 32008 address = {Madison, Wisconsin} 32009} 32010 32011@Article{ mangasarian.musicant:successive, 32012 author = {O. L. Mangasarian and David R. Musicant}, 32013 title = {Successive Overrelaxation for Support Vector Machines}, 32014 journal = {IEEE Transactions on Neural Networks}, 32015 volume = {10}, 32016 year = {1999}, 32017 pages = {1032-1037} 32018} 32019 32020@Article{ mangasarian.pang:exact, 32021 author = {O. L. Mangasarian and J. S. Pang}, 32022 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 32023 Constraints}, 32024 journal = {Optimization}, 32025 year = {1997}, 32026 volume = {42}, 32027 pages = {1--8} 32028} 32029 32030@Article{ mangasarian.pang:extended, 32031 author = {O. L. Mangasarian and J. S. Pang}, 32032 title = {The Extended Linear Complementarity Problem}, 32033 journal = {SIAM Journal on Matrix Analysis and Applications}, 32034 year = {1994}, 32035 volume = {16} 32036} 32037 32038@Article{ mangasarian.ren:error, 32039 author = {O. L. Mangasarian and J. Ren}, 32040 title = {New error bounds for the nonlinear complementarity problem}, 32041 year = {1994}, 32042 volume = {1}, 32043 pages = {49--56}, 32044 journal = {Communications on Applied Nonlinear Analysis} 32045} 32046 32047@Article{ mangasarian.ren:improved, 32048 author = {O. L. Mangasarian and J. Ren}, 32049 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 32050 year = {1994}, 32051 volume = {66}, 32052 journal = {Mathematical Programming}, 32053 pages = {241--255} 32054} 32055 32056@InProceedings{ mangasarian.setiono.ea:pattern, 32057 crossref = {coleman.li:large-scale}, 32058 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 32059 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 32060 Diagnosis}, 32061 pages = {22--31} 32062} 32063 32064@Article{ mangasarian.shiau:error, 32065 author = {O. L. Mangasarian and T.--H. Shiau}, 32066 title = {Error Bounds for Monotone Linear Complementarity Problems}, 32067 journal = {Mathematical Programming}, 32068 year = {1986}, 32069 volume = {36}, 32070 pages = {81--89} 32071} 32072 32073@Article{ mangasarian.shiau:lipschitz, 32074 author = {O. L. Mangasarian and T.--H. Shiau}, 32075 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 32076 Complementarity Problems}, 32077 journal = {SIAM Journal on Control and Optimization}, 32078 year = {1987}, 32079 volume = {25}, 32080 pages = {583--595} 32081} 32082 32083@Article{ mangasarian.solodov:nonlinear, 32084 author = {O. L. Mangasarian and M. V. Solodov}, 32085 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 32086 journal = {Mathematical Programming}, 32087 year = {1993}, 32088 volume = {62}, 32089 pages = {277--298} 32090} 32091 32092@Article{ mangasarian.solodov:serial, 32093 author = {O. L. Mangasarian and M. V. Solodov}, 32094 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 32095 Minimization}, 32096 year = {1994}, 32097 journal = {Optimization Methods and Software}, 32098 volume = {4}, 32099 pages = {103--116} 32100} 32101 32102@Article{ mangasarian.street.ea:breast, 32103 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 32104 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 32105 journal = {Operations Research}, 32106 year = {1995}, 32107 volume = {43}, 32108 pages = {570--577} 32109} 32110 32111@Article{ mangasarian.wolberg:cancer, 32112 author = {O. L. Mangasarian and W. H. Wolberg}, 32113 title = {Cancer Diagnosis via Linear Programming}, 32114 journal = {SIAM News}, 32115 year = {1990}, 32116 volume = {23}, 32117 pages = {1 \& 18} 32118} 32119 32120@InCollection{ mangasarian:applications, 32121 author = {O. L. Mangasarian}, 32122 title = {Some Applications of Penalty Functions in Mathematical Programming}, 32123 booktitle = {Optimization and Related Fields}, 32124 year = {1986}, 32125 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 32126 publisher = {Springer-Verlag}, 32127 address = {Heidelberg}, 32128 pages = {307--329}, 32129 note = {Lecture Notes in Mathematics 1190} 32130} 32131 32132@Article{ mangasarian:characterization, 32133 author = {O. L. Mangasarian}, 32134 title = {Characterization of linear complementarity problems as linear programs}, 32135 journal = {Mathematical Programming Study}, 32136 year = {1978}, 32137 volume = {7}, 32138 pages = {74--87} 32139} 32140 32141@InProceedings{ mangasarian:condition, 32142 author = {O. L. Mangasarian}, 32143 title = {A condition number for linear inequalities and linear programs}, 32144 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 32145 1981}, 32146 year = {1981}, 32147 editor = {G. Bamberg and O. Opitz}, 32148 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 32149 address = {Konigstein}, 32150 pages = {3--15} 32151} 32152 32153@Article{ mangasarian:convergence, 32154 author = {O. L. Mangasarian}, 32155 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 32156 Symmetric Monotone Linear Complementarity Problem}, 32157 journal = {SIAM Journal on Optimization}, 32158 volume = {1}, 32159 pages = {114--122}, 32160 year = {1991} 32161} 32162 32163@Article{ mangasarian:equivalence, 32164 author = {O. L. Mangasarian}, 32165 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 32166 journal = {SIAM Journal on Applied Mathematics}, 32167 year = {1976}, 32168 volume = {31}, 32169 pages = {89--92} 32170} 32171 32172@Article{ mangasarian:error, 32173 author = {O. L. Mangasarian}, 32174 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 32175 journal = {ORSA Journal on Computing}, 32176 volume = {15}, 32177 pages = {187--192}, 32178 year = {1994} 32179} 32180 32181@Article{ mangasarian:error*1, 32182 author = {O. L. Mangasarian}, 32183 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 32184 journal = {Mathematical Programming}, 32185 year = {1990}, 32186 volume = {48}, 32187 pages = {437--445} 32188} 32189 32190@Article{ mangasarian:generalized, 32191 author = {O. L. Mangasarian}, 32192 title = {Generalized Linear Complementarity Problems as Linear Programs}, 32193 journal = {Methods of Operations Research}, 32194 year = {1979}, 32195 editor = {W. Oettli and F. Steffens}, 32196 volume = {31}, 32197 pages = {393--402} 32198} 32199 32200@InCollection{ mangasarian:generalized*1, 32201 author = {O. L. Mangasarian}, 32202 title = {Generalized Support Vector Machines}, 32203 year = {2000}, 32204 pages = {135-146}, 32205 booktitle = {Advances in Large Margin Classifiers}, 32206 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 32207 publisher = {MIT Press}, 32208 address = {Cambridge, MA} 32209} 32210 32211@Article{ mangasarian:global, 32212 author = {O. L. Mangasarian}, 32213 title = {Global error bounds for monotone affine variational inequality problems}, 32214 journal = {Linear Algebra and Its Applications}, 32215 year = {1992}, 32216 pages = {153--164} 32217} 32218 32219@InCollection{ mangasarian:least, 32220 author = {O. L. Mangasarian}, 32221 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 32222 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 32223 year = {1990}, 32224 publisher = {Oxford University Press}, 32225 address = {New York}, 32226 pages = {217--221} 32227} 32228 32229@Article{ mangasarian:least-norm, 32230 author = {O. L. Mangasarian}, 32231 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 32232 Problem}, 32233 journal = {Journal of Mathematical Analysis and Applications}, 32234 year = {1983}, 32235 volume = {92}, 32236 pages = {240--251} 32237} 32238 32239@Article{ mangasarian:linear, 32240 author = {O. L. Mangasarian}, 32241 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 32242 journal = {Mathematical Programming}, 32243 year = {1976}, 32244 volume = {10}, 32245 pages = {263--270} 32246} 32247 32248@Article{ mangasarian:linear*1, 32249 author = {O. L. Mangasarian}, 32250 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 32251 journal = {Operations Research}, 32252 year = {1965}, 32253 volume = {13}, 32254 pages = {444--452} 32255} 32256 32257@Article{ mangasarian:locally, 32258 author = {O. L. Mangasarian}, 32259 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 32260 Complementarity Problems}, 32261 journal = {Mathematical Programming}, 32262 year = {1980}, 32263 volume = {19}, 32264 pages = {200--212} 32265} 32266 32267@InCollection{ mangasarian:machine, 32268 author = {O. L. Mangasarian}, 32269 title = {Machine Learning via Polyhedral Concave Minimization}, 32270 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 32271 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 32272 pages = {175-188}, 32273 year = {1996}, 32274 address = {Heidelberg}, 32275 publisher = {Physica-Verlag A Springer-Verlag Company} 32276} 32277 32278@Article{ mangasarian:mathematical, 32279 author = {O. L. Mangasarian}, 32280 title = {Mathematical Programming in Neural Networks}, 32281 journal = {ORSA Journal on Computing}, 32282 volume = {5}, 32283 pages = {349--360}, 32284 year = {1993} 32285} 32286 32287@InProceedings{ mangasarian:mathematical*1, 32288 author = {O. L. Mangasarian}, 32289 title = {Mathematical Programming in Machine Learning}, 32290 booktitle = {Nonlinear Optimization and Applications}, 32291 editor = {G. Di Pillo and F. Giannessi}, 32292 publisher = {Plenum Publishing}, 32293 address = {New York}, 32294 pages = {283--295}, 32295 year = {1996} 32296} 32297 32298@Article{ mangasarian:mathematical*2, 32299 author = {O. L. Mangasarian}, 32300 title = {Mathematical Programming in Data Mining}, 32301 journal = {Data Mining and Knowledge Discovery}, 32302 volume = {1}, 32303 year = {1997}, 32304 pages = {183-201} 32305} 32306 32307@Article{ mangasarian:multi-surface, 32308 author = {O. L. Mangasarian}, 32309 title = {Multi-surface Method of Pattern Separation}, 32310 journal = {IEEE Transactions on Information Theory}, 32311 year = {1968}, 32312 volume = {IT-14}, 32313 pages = {801--807} 32314} 32315 32316@Book{ mangasarian:nonlinear, 32317 author = {O. L. Mangasarian}, 32318 title = {Nonlinear Programming}, 32319 year = {1969}, 32320 publisher = {McGraw--Hill}, 32321 address = {New York}, 32322 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 32323} 32324 32325@Article{ mangasarian:normal, 32326 author = {O. L. Mangasarian}, 32327 title = {Normal Solutions of Linear Programs}, 32328 journal = {Mathematical Programming Study}, 32329 year = {1984}, 32330 volume = {22}, 32331 pages = {206--216} 32332} 32333 32334@Article{ mangasarian:optimal, 32335 author = {O. L. Mangasarian}, 32336 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 32337 Linear Programs}, 32338 journal = {Journal of Optimization Theory and Applications}, 32339 year = {1981}, 32340 volume = {35}, 32341 pages = {123--128} 32342} 32343 32344@Article{ mangasarian:parallel, 32345 author = {O. L. Mangasarian}, 32346 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 32347 journal = {SIAM Journal on Control and Optimization}, 32348 volume = {33}, 32349 pages = {1916--1925}, 32350 year = {1995} 32351} 32352 32353@TechReport{ mangasarian:regularized, 32354 author = {O. L. 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Bonnans}, 34360 title = {Infeasible path following algorithms for linear complementarity problems}, 34361 institution = {INRIA}, 34362 year = {1994}, 34363 month = dec, 34364 number = {RR--2445}, 34365 type = {Research Report} 34366} 34367 34368@Article{ potra.sheng:large-step, 34369 author = {F. A. Potra and R. Sheng}, 34370 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 34371 year = {1997}, 34372 journal = {SIAM Journal on Optimization}, 34373 volume = {7}, 34374 pages = {318--335} 34375} 34376 34377@Article{ potra:infeasible, 34378 author = {F. A. Potra}, 34379 title = {An infeasible interior-point predictor-corrector algorithm for linear 34380 programming}, 34381 journal = {SIAM Journal on Optimization}, 34382 year = {1996}, 34383 volume = {6}, 34384 pages = {19--32} 34385} 34386 34387@TechReport{ potra:onl, 34388 author = {F. A. 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Pruyne}, 34530 title = {Resource Management Services for Parallel Applications}, 34531 school = {University of Wisconsin--Madison}, 34532 year = {1996}, 34533 address = {Madison, Wisconsin} 34534} 34535 34536@Book{ pshenichny.danilin:numerical, 34537 author = {B. N. Pshenichny and Yu. M. Danilin}, 34538 title = {Numerical Methods in Extremal Problems}, 34539 year = {1978}, 34540 publisher = {MIR Publishers}, 34541 address = {Moscow} 34542} 34543 34544@TechReport{ qi.chen:globally, 34545 author = {L. Qi and X. Chen}, 34546 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 34547 institution = {School of Mathematics, University of New South Wales}, 34548 year = {1993}, 34549 annote = {revised}, 34550 address = {Sydney} 34551} 34552 34553@Article{ qi.jiang:semismooth, 34554 author = {L. Qi and H. 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Rockafellar}, 35114 title = {Conjugate Duality and Optimization}, 35115 year = {1974}, 35116 publisher = {SIAM}, 35117 address = {Philadelphia, Pennsylvania}, 35118 volume = {16}, 35119 series = {Conference Board of the Mathematical Sciences} 35120} 35121 35122@Book{ rockafellar:convex, 35123 author = {R. T. Rockafellar}, 35124 title = {Convex Analysis}, 35125 year = {1970}, 35126 publisher = {Princeton University Press}, 35127 address = {Princeton, New Jersey} 35128} 35129 35130@Article{ rockafellar:first-, 35131 author = {R. T. Rockafellar}, 35132 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 35133 journal = {Transactions of the American Mathematical Society}, 35134 year = {1988}, 35135 volume = {307}, 35136 pages = {75--108} 35137} 35138 35139@InProceedings{ rockafellar:generalized, 35140 author = {R. T. Rockafellar}, 35141 title = {A Generalized Approach to Linear-Quadratic Programming}, 35142 booktitle = {Proceedings of the International Conference on Numerical Optimization and 35143 Applications}, 35144 year = {1986}, 35145 pages = {58--66}, 35146 note = {(Xi'an, China)} 35147} 35148 35149@InProceedings{ rockafellar:generalized*1, 35150 crossref = {bachem.grotschel.ea:mathematical}, 35151 author = {R. T. Rockafellar}, 35152 title = {Generalized Subgradients in Mathematical Programming}, 35153 pages = {368--390} 35154} 35155 35156@InCollection{ rockafellar:large-scale, 35157 author = {R. T. Rockafellar}, 35158 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 35159 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 35160 chapter = {15}, 35161 year = {1991}, 35162 editor = {S. Gomez and J. P. Hennart and R. A. 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Rockafellar}, 35222 title = {Network Flows and Monotropic Optimization}, 35223 publisher = {John Wiley}, 35224 year = {1984}, 35225 address = {New York} 35226} 35227 35228@Article{ rodrigues:mixed, 35229 author = {H. C. Rodrigues}, 35230 title = {A mixed variational formulation for shape optimization of solids with contact 35231 conditions}, 35232 journal = {Structural Optimization}, 35233 volume = {6}, 35234 year = {1993}, 35235 pages = {19--28} 35236} 35237 35238@Book{ rodrigues:obstacle, 35239 author = {J. F. Rodrigues}, 35240 title = {Obstacle Problems in Mathematical Physics}, 35241 publisher = {Elsevier Publishing Company}, 35242 address = {Amsterdam}, 35243 year = {1987} 35244} 35245 35246@Book{ roos.terlaky.ea:theory, 35247 author = {C. Roos and T. Terlaky and J.--Ph. 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{Fr\'{e}d\'{e}ric Alauzet}, 37901 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 37902 year = {2010} 37903} 37904 37905@Article{ chan1994qmrcgs, 37906 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 37907 systems}, 37908 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 37909 and Tong, Charles H}, 37910 journal = {SIAM Journal on Scientific Computing}, 37911 volume = {15}, 37912 number = {2}, 37913 pages = {338--347}, 37914 year = {1994}, 37915 publisher = {SIAM} 37916} 37917 37918@Article{ ghai2019comparison, 37919 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 37920 nonsymmetric linear systems}, 37921 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 37922 journal = {Numerical Linear Algebra with Applications}, 37923 volume = {26}, 37924 number = {1}, 37925 pages = {e2215}, 37926 year = {2019}, 37927 publisher = {Wiley Online Library} 37928} 37929 37930@Article{ mishrasalacknepley2022, 37931 title = {On the order of accuracy for finite difference approximations of partial 37932 differential equations using stencil composition}, 37933 author = {Abhishek Mishra and David Salac and Matthew G. Knepley}, 37934 journal = {International Journal on Numerical Methods in Engineering}, 37935 note = {Submitted}, 37936 year = {2022} 37937} 37938 37939@Article{ nathawaniknepley2022, 37940 title = {Droplet formation simulation using mixed finite elements}, 37941 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37942 journal = {Physics of Fluids}, 37943 volume = {34}, 37944 pages = {064105}, 37945 doi = {10.1063/5.0089752}, 37946 year = {2022} 37947} 37948 37949@InProceedings{ nathawaniknepley2022b, 37950 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 37951 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37952 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 37953 (ICCFD11)}, 37954 editor = {Christoph Brehm and Shishir Pandya}, 37955 number = {4103}, 37956 year = {2022} 37957} 37958 37959@Article{ nathawaniknepley2023, 37960 title = {One-dimensional model to simulate shear-induced droplet formation}, 37961 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37962 journal = {International Journal of Multiphase Flow}, 37963 note = {Submitted}, 37964 year = {2023} 37965} 37966 37967@InProceedings{ georgalisnathawaniknepleypatra2023, 37968 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 37969 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. Knepley and Abani 37970 Patra}, 37971 booktitle = {AIAA SciTech 2024}, 37972 note = {Accepted}, 37973 year = {2023} 37974} 37975 37976@Article{ brownbarrabeamsghaffariknepleymosesshakeristengelthompsonzhang2022, 37977 title = {Performance Portable Solid Mechanics via Matrix-Free $p$-Multigrid}, 37978 author = {Jed Brown and Valeria Barra and Natalie Beams and Leila Ghaffari and Matthew 37979 Knepley and William Moses and Rezgar Shakeri and Karen Stengel and Jeremy L. 37980 Thompson and Junchao Zhang}, 37981 doi = {10.48550/ARXIV.2204.01722}, 37982 url = {https://arxiv.org/abs/2204.01722}, 37983 publisher = {arXiv}, 37984 note = {Submitted}, 37985 year = {2022} 37986} 37987 37988@InCollection{ mayknepley2023, 37989 title = {Numerical Modeling of Subduction}, 37990 author = {Dave A. May and Matthew G. Knepley}, 37991 booktitle = {Dynamics of Plate Tectonics and Mantle Convection}, 37992 editor = {João C. Duarte}, 37993 pages = {539-571}, 37994 isbn = {978-0-323-85733-8}, 37995 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 37996 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 37997 year = {2023} 37998} 37999 38000@Article{ adamsknepley2023, 38001 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 38002 plasmas in {PETSc}}, 38003 author = {Mark F. Adams and Matthew G. Knepley}, 38004 url = {https://arxiv.org/abs/2302.10242}, 38005 note = {In preparation}, 38006 year = {2023}, 38007 petsc_uses = {DMPlex} 38008} 38009 38010@Article{ finnknepleypusztayadams2023, 38011 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 38012 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. Adams}, 38013 url = {https://arxiv.org/abs/2303.12620}, 38014 journal = {Communications in Applied Mathematics and Computational Science}, 38015 note = {Submitted}, 38016 year = {2023} 38017} 38018 38019@Article{ eggersdupont1994, 38020 title = {Drop formation in a one-dimensional approximation of the {Navier--Stokes} 38021 equation}, 38022 author = {Jens Eggers and Todd F. Dupont}, 38023 journal = {Journal of fluid mechanics}, 38024 volume = {262}, 38025 pages = {205--221}, 38026 year = {1994}, 38027 publisher = {Cambridge University Press} 38028} 38029 38030@PhDThesis{ pusztaythesis2023, 38031 title = {A Particle Basis Vlasov-Poisson-Landau Solver for Plasma Simulation in PETSc}, 38032 author = {Joseph V. Pusztay}, 38033 type = {{PhD} thesis}, 38034 school = {University at Buffalo, Department of Computer Science and Engineering}, 38035 address = {Buffalo, NY}, 38036 month = may, 38037 year = {2022} 38038} 38039 38040@PhDThesis{ finnthesis2023, 38041 title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau 38042 System}, 38043 author = {Daniel S. Finn}, 38044 type = {{PhD} thesis}, 38045 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38046 Engineering}, 38047 address = {Buffalo, NY}, 38048 month = may, 38049 year = {2023} 38050} 38051 38052@PhDThesis{ nathawanithesis2023, 38053 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 38054 author = {Darsh Kiritbhai Nathawani}, 38055 type = {{PhD} thesis}, 38056 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38057 Engineering}, 38058 address = {Buffalo, NY}, 38059 month = may, 38060 year = {2023} 38061} 38062 38063@article{MckayEriksonKozdon2019, 38064 title = {A computational method for earthquake cycles within anisotropic media}, 38065 author = {Maricela Best Mckay and Brittany A Erickson and Jeremy E Kozdon}, 38066 journal = {Geophysical Journal International}, 38067 volume = {219}, 38068 number = {2}, 38069 pages = {816--833}, 38070 year = {2019}, 38071} 38072 38073article{EricksonOReillyNordstrom2019, 38074 title = {Accuracy of stable, high-order finite difference methods for hyperbolic systems with non-smooth wave speeds}, 38075 author = {Brittany A Erickson and Ossian O’Reilly and Jan Nordstr{\"o}m}, 38076 journal = {Journal of Scientific Computing}, 38077 volume = {81}, 38078 pages = {2356--2387}, 38079 year = {2019}, 38080} 38081 38082@article{KozdonEricksonWilcox2021, 38083 title = {Hybridized summation-by-parts finite difference methods}, 38084 author = {Jeremy E Kozdon and Brittany A Erickson and Lucas C Wilcox}, 38085 journal = {Journal of Scientific Computing}, 38086 volume = {87}, 38087 number = {3}, 38088 pages = {85}, 38089 year = {2021}, 38090} 38091 38092@article{SEAS2022, 38093 title = {Community-driven code comparisons for three-dimensional dynamic modeling of sequences of earthquakes and aseismic slip}, 38094 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}, 38095 journal = {Journal of Geophysical Research: Solid Earth}, 38096 volume = {127}, 38097 number = {3}, 38098 pages = {e2021JB023519}, 38099 year = {2022}, 38100} 38101 38102@article{EricksonKozdonHarvey2022, 38103 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}, 38104 author = {Brittany A Erickson and Jeremy E Kozdon and Tobias Harvey}, 38105 journal = {Journal of Scientific Computing}, 38106 volume = {93}, 38107 number = {1}, 38108 pages = {17}, 38109 year = {2022}, 38110} 38111 38112@article{RuckerEriksonKarlstromLeeGopalakrishnan2022, 38113 title = {A Computational Framework for Time-Dependent Deformation in Viscoelastic Magmatic Systems}, 38114 author = {Cody Rucker and Brittany A Erickson and Leif Karlstrom and Brian Lee and Jay Gopalakrishnan}, 38115 journal = {Journal of Geophysical Research: Solid Earth}, 38116 volume = {127}, 38117 number = {9}, 38118 pages = {e2022JB024506}, 38119 year = {2022}, 38120} 38121 38122@article{HarveyEriksonKozdon2023, 38123 title = {A High-order Accurate Summation-by-Parts Finite Difference Method for Fully-dynamic Earthquake Sequence Simulations within Sedimentary Basins}, 38124 author = {Tobias W Harvey and Brittany A Erickson and Jeremy E Kozdon}, 38125 journal = {Journal of Geophysical Research: Solid Earth}, 38126 pages = {e2022JB025357}, 38127 year = {2023}, 38128} 38129 38130@article{SEAS2023, 38131 title = {Incorporating full elastodynamic effects and dipping fault geometries in community code verification exercises for simulations of earthquake sequences and aseismic slip {(SEAS)}}, 38132 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}, 38133 journal = {Bulletin of the Seismological Society of America}, 38134 volume = {113}, 38135 number = {2}, 38136 pages = {499--523}, 38137 year = {2023}, 38138} 38139
