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@Misc{ bueler2020petsc, 20 title = {PETSc for Partial Differential Equations: Numerical Solutions in C and Python}, 21 author = {Bueler, Ed}, 22 year = {2020}, 23 publisher = {SIAM}, 24 petsc_uses = {KSP} 25} 26 27@TechReport{ petscforgpuexascale, 28 title = {Toward Performance-Portable PETSc for GPU-based Exascale Systems}, 29 author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener 30 and Matthew Knepley and Scott E. Kruger and Hannah~Morgan and Todd Munson and Karl 31 Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang}, 32 institution = {Argonne National Laboratory}, 33 number = {ANL/MCS-P9401-1020}, 34 note = {\url{https://arxiv.org/abs/2011.00715}}, 35 year = {2020}, 36 petsc_uses = {KSP} 37} 38 39@Article{ mills2021, 40 title = {Toward performance-portable {PETS}c for {GPU}-based exascale systems}, 41 journal = {Parallel Computing}, 42 volume = {108}, 43 pages = {102831}, 44 year = {2021}, 45 issn = {0167-8191}, 46 doi = {https://doi.org/10.1016/j.parco.2021.102831}, 47 url = {https://www.sciencedirect.com/science/article/pii/S016781912100079X}, 48 author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener 49 and Matthew Knepley and Scott E. Kruger and Hannah Morgan and Todd Munson and Karl 50 Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang} 51} 52 53@Article{ rupp:2016:pis:2988256.2907944, 54 author = {Karl Rupp and Josef Weinbub and Ansgar J\"{u}ngel and Tibor Grasser}, 55 title = {Pipelined Iterative Solvers with Kernel Fusion for Graphics Processing Units}, 56 journal = {ACM Trans. Math. Softw.}, 57 issue_date = {September 2016}, 58 volume = {43}, 59 number = {2}, 60 month = {Aug}, 61 year = {2016}, 62 issn = {0098-3500}, 63 pages = {11:1--11:27}, 64 articleno = {11}, 65 numpages = {27}, 66 doi = {10.1145/2907944}, 67 acmid = {2907944}, 68 publisher = {ACM}, 69 address = {New York, NY, USA}, 70 keywords = {BiCGStab method, CUDA, GMRES method, GPU, Iterative solvers, OpenCL, conjugate 71 gradient method}, 72 petsc_uses = {KSP} 73} 74 75@Article{ dalcin2011parallel, 76 title = {Parallel distributed computing using python}, 77 author = {Dalcin, Lisandro D and Paz, Rodrigo R and Kler, Pablo A and Cosimo, Alejandro}, 78 journal = {Advances in Water Resources}, 79 volume = {34}, 80 number = {9}, 81 pages = {1124--1139}, 82 year = {2011}, 83 publisher = {Elsevier}, 84 petsc_uses = {KSP} 85} 86 87@Article{ mendezpongaortiz2018, 88 title = {Diffusive molecular dynamics simulations of lithiation of silicon nanopillars}, 89 author = {JP Mendez and M Ponga and M Ortiz}, 90 journal = {Journal of the Mechanics and Physics of Solids}, 91 year = {2018}, 92 petsc_uses = {KSP} 93} 94 95@TechReport{ morgan2020evaluation, 96 title = {Evaluation of {PETS}c on a Heterogeneous Architecture, the {OLCF} {S}ummit 97 System: Part 1: Vector Node Performance}, 98 author = {Morgan, Hannah Mairs and Mills, Richard Tran and Smith, Barry}, 99 year = {2020}, 100 institution = {Argonne National Laboratory}, 101 url = {https://publications.anl.gov/anlpubs/2020/04/159190.pdf}, 102 petsc_uses = {KSP} 103} 104 105@TechReport{ pdeconstrainedspectraladjoints, 106 title = {PDE constrained optimization, error estimation and control with spectral elements 107 using PETSc and TAO}, 108 author = {Oana Marin and Emil Constantinescu and Barry Smith}, 109 type = {Preprint}, 110 number = {ANL/MCS-P9031-1117}, 111 institution = {ANL}, 112 month = {November}, 113 year = {2017}, 114 petsc_uses = {KSP} 115} 116 117@InProceedings{ asc2013, 118 author = {S. Abhyankar and B. F. Smith and E. Constantinescu}, 119 title = {Evaluation of overlapping restricted additive Schwarz preconditioning for 120 parallel solution of very large power flow problems}, 121 booktitle = {HiPCNA-PG’13}, 122 year = {2013}, 123 petsc_uses = {KSP} 124} 125 126@InProceedings{ as2013, 127 author = {S. Abhyankar and B. F. Smith}, 128 title = {{PETSc:} An Advanced Math and Computing Framework for Rapidly Developing Parallel 129 Smart Grid Applications}, 130 booktitle = {Proceedings of the IEEE PES General Meeting}, 131 year = {2013}, 132 petsc_uses = {KSP} 133} 134 135@TechReport{ tspaper, 136 title = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library}, 137 author = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and 138 Barry F. Smith}, 139 type = {Preprint}, 140 number = {ANL/MCS-P5061-0114}, 141 institution = {ANL}, 142 month = {January}, 143 year = {2014}, 144 petsc_uses = {KSP} 145} 146 147@TechReport{ abhyankaretal2018, 148 author = {Shrirang Abhyankar and Jed Brown and Emil M. Constantinescu and Debojyoti Ghosh 149 and Barry F. Smith and Hong Zhang}, 150 title = {{PETSc/TS}: {A} Modern Scalable {ODE/DAE} Solver Library}, 151 journal = {arXiv e-preprints}, 152 eprint = {1806.01437}, 153 archiveprefix = {arXiv}, 154 year = {2018}, 155 petsc_uses = {KSP} 156} 157 158@Article{ zhang2021cams, 159 title = {Optimal checkpointing for adjoint multistage time-stepping schemes}, 160 author = {Hong Zhang and Emil M. Constantinescu}, 161 journal = {arXiv e-preprints}, 162 eprint = {2202.11890}, 163 archiveprefix = {arXiv}, 164 year = {2022}, 165 petsc_uses = {KSP} 166} 167 168@InProceedings{ zhangconstantinescu2021b, 169 title = {Revolve-based adjoint checkpointing for multistage time integration}, 170 author = {Hong Zhang and Emil M. Constantinescu}, 171 booktitle = {Proceedings of the International Conference on Computational Science (ICCS)}, 172 month = {June}, 173 year = {2021}, 174 petsc_uses = {KSP} 175} 176 177@Article{ zhang2022tsadjoint, 178 author = {Zhang, Hong and Constantinescu, Emil M. and Smith, Barry F.}, 179 title = {{PETSc TSAdjoint: A Discrete Adjoint ODE Solver for First-Order and Second-Order 180 Sensitivity Analysis}}, 181 journal = {SIAM Journal on Scientific Computing}, 182 volume = {44}, 183 number = {1}, 184 pages = {C1-C24}, 185 year = {2022}, 186 doi = {10.1137/21M140078X}, 187 petsc_uses = {KSP} 188} 189 190@TechReport{ bb2008, 191 author = {Tomasz Blachowicz and Bartlomiej Baron}, 192 title = {A graphical extension for the Windows version of the Parallel Finite Element 193 Micromagnetics Package (MagParExt)}, 194 url = {http://arxiv.org/abs/0807.2655}, 195 year = {2008}, 196 petsc_uses = {KSP} 197} 198 199@Article{ jacvgv2008, 200 author = {R. Y. Jaafar and A Asenjo and O Chubykalo-Fesenko and M Vazquez and E M Gonzalez 201 and J L Vicent}, 202 title = {Field induced vortex dynamics in magnetic Ni nanotriangles}, 203 journal = {Nanotechnology}, 204 volume = {19}, 205 year = {2008}, 206 doi = {10.1088/0957-4484/19/28/285717}, 207 petsc_uses = {KSP} 208} 209 210@Article{ yjdwh2008, 211 author = {Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He}, 212 title = {Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy}, 213 journal = {Journal of the Magnetics Society of Japan}, 214 volume = {32}, 215 year = {2008}, 216 pages = {50-53}, 217 url = {http://www.jstage.jst.go.jp/article/msjmag/32/2_1/32_50/_article}, 218 petsc_uses = {KSP} 219} 220 221@Article{ mtrtrsa2008, 222 author = {D. Makarov and S. Tibus and C. T. Rettner and T. Thomson and B. D. Terris and T. 223 Schrefl and M. Albrecht}, 224 title = {Magnetic strip patterns induced by focused ion beam irradiation}, 225 journal = {J. Appl. Phys.}, 226 volume = {103}, 227 year = {2008}, 228 doi = {10.1063/1.2894587}, 229 petsc_uses = {KSP} 230} 231 232@InProceedings{ tmrttsa2008, 233 author = {S. Tibus and D. Makarov and C. T. Rettner and T. Thomson and B. D. Terris and T. 234 Schrefl and M. Albrecht}, 235 title = {Patterning of magnetic films by focused ion beam irradiation}, 236 booktitle = {Intermag 2008 paper no. CM-05, submitted to IEEE Trans. Magn.}, 237 year = {2008}, 238 petsc_uses = {KSP} 239} 240 241@Article{ yjdbh2007, 242 author = {Lin Yuan and Jianju Jiang and Yongjiang di and Shaowei Bie and Huahui He}, 243 title = {Micromagnetic simulation of the magnetic dispersion angle and effective damping 244 factor for the single-phase soft magnetic films}, 245 journal = {J. Magn. Magn. Mater.}, 246 volume = {320}, 247 number = {7}, 248 pages = {1393-1397}, 249 doi = {10.1016/j.jmmm.2007.11.025}, 250 petsc_uses = {KSP} 251} 252 253@Article{ lxky2007, 254 author = {DENG Lian-wen and HUANG Xiao-zhong and ZH0U Ke-sheng and YANG}, 255 title = {Micromagnetic simulation and experimental study on microwave permeability of 256 nano-magnetic films}, 257 journal = {Transactions of Nonferrous Metals Society of China}, 258 year = {2007}, 259 pages = {756-759}, 260 url = {http://www.ysxbcn.com/icnfm2007/part2B/s0756.pdf}, 261 petsc_uses = {KSP} 262} 263 264@Article{ yjdwh2008a, 265 author = {Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He}, 266 title = {Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy}, 267 journal = {Journal of the Magnetics Society of Japan}, 268 volume = {32}, 269 year = {2008}, 270 pages = {50-53}, 271 doi = {10.3379/msjmag.32.50}, 272 petsc_uses = {KSP} 273} 274 275@Article{ lylw2007, 276 author = {Ching-Ming Lee and L. X. Ye and J. M. Lee and Te-Ho Wu}, 277 title = {Micromagnetic study of magnetization reversal in patterned DyFeCo thin films}, 278 journal = {Phys. Stat. Sol.}, 279 volume = {204}, 280 number = {12}, 281 pages = {4049-4052}, 282 year = {2007}, 283 doi = {10.1002/pssa.200777359}, 284 petsc_uses = {KSP} 285} 286 287@InProceedings{ sg2007, 288 author = {Simon Greaves}, 289 title = {Micromagnetic Simulations of Magnetic Recording Media}, 290 booktitle = {High Performance Computing on Vector Systems 2007}, 291 doi = {10.1007/978-3-540-74384-2_17}, 292 petsc_uses = {KSP} 293} 294 295@Article{ bsc2007, 296 author = {Nadjib Benatmane and Werner Scholz and T.W. Clinton}, 297 title = {Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings}, 298 journal = {IEEE Trans. Magn.}, 299 volume = {43}, 300 year = {2007}, 301 pages = {2884-2886}, 302 doi = {10.1109/TMAG.2007.892867}, 303 petsc_uses = {KSP} 304} 305 306@Article{ ffbf, 307 author = {T. Fischbacher and M. Franchin and G. Bordignon and H. Fangohr}, 308 title = {A Systematic Approach to Multiphysics Extensions of Finite-Element-Based 309 Micromagnetic Simulations: Nmag.}, 310 journal = {IEEE Trans. Magn. Volume}, 311 volume = {43}, 312 pages = {2896-2898}, 313 doi = {10.1109/TMAG.2007.893843}, 314 petsc_uses = {KSP} 315} 316 317@InBook{ dfssfs2006, 318 author = {R. Dittrich and J. Fidler and D. Suess and W. Schol and H. Forster, T. Schrefl}, 319 chapter = {Computational Aspects of Micromagnetics}, 320 title = {The Science of Hysteresis}, 321 editor = { G. Bertotti and I. Mayergoyz}, 322 url = {http://books.elsevier.com/us/elsevier/us/subindex.asp?maintarget=&isbn=0124808743}, 323 petsc_uses = {KSP} 324} 325 326@InBook{ fss, 327 author = {J. Fidler and T. Schrefl and W. Scholz}, 328 chapter = {Computational Micromagnetics}, 329 title = {Handbook of Theoretical and Computational Nanotechnology}, 330 editor = {M. Rieth and W. Schommers}, 331 url = {http://www.amazon.com/gp/product/158883042X}, 332 petsc_uses = {KSP} 333} 334 335@InBook{ shbsef, 336 author = {Thomas Schrefl and Gino Hrkac and Simon Bance and Dieter Suess and Otmar Ertl and 337 Josef Fidler}, 338 chapter = {Numerical Methods in Micromagnetics (Finite Element Method)}, 339 title = {Handbook of Magnetism and Advanced Magnetic Materials}, 340 editor = {Helmut Kronmueller and Stuart Parkin}, 341 doi = {10.1002/9780470022184.hmm203}, 342 petsc_uses = {KSP} 343} 344 345@InBook{ sfs, 346 author = {D. Suess and J. Fidler and T. Schrefl}, 347 chapter = {Micromagnetic Simulation of magnetic materials}, 348 title = {Handbook of Magnetic Materials}, 349 editor = {K. H. J. Buschow}, 350 url = {http://www.amazon.com/gp/product/0444518509}, 351 petsc_uses = {KSP} 352} 353 354@Article{ fsxzs, 355 author = {J. Fernandez-de-Castro and Xiao Shen and Jianhua Xue and Yuming Zhou and S. 356 Sharma}, 357 title = {Writer Flux Closure and Transition Degradation Mechanism in Perpendicular 358 Recording.}, 359 journal = {IEEE Trans. Magn. Volume}, 360 volume = {43}, 361 pages = {2175-2177}, 362 doi = {10.1109/TMAG.2007.893122}, 363 petsc_uses = {KSP} 364} 365 366@Article{ sb2006, 367 author = {W. Scholz and S. Batra}, 368 title = {Effect of write current waveform on magnetization and head field dynamics of 369 perpendicular recording heads}, 370 journal = {IEEE Trans. Magn.}, 371 volume = {42}, 372 year = {2006}, 373 pages = {2264--2266}, 374 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/ieee/scholz_2006_42_2264.pdf}, 375 petsc_uses = {KSP} 376} 377 378@Article{ bsr2006, 379 author = {S. Batra and W. Scholz and T. Roscamp}, 380 title = {Effect of thermal fluctuation field on the noise performance of a perpendicular 381 recording system}, 382 journal = {J. Appl. Phys.}, 383 volume = {99}, 384 year = {2006}, 385 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 386 petsc_uses = {KSP} 387} 388 389@InProceedings{ japios2006, 390 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 391 Subramanian}, 392 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 393 in systems with cubic and uniaxial anisotropy.}, 394 booktitle = {Intermag 2006 Conference}, 395 petsc_uses = {KSP} 396} 397 398@Article{ kbmb2006, 399 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 400 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 401 Perpendicular Recording Heads}, 402 journal = {IEEE Trans. Magn.}, 403 volume = {42}, 404 year = {2006}, 405 pages = {2428--2430}, 406 doi = {10.1109/TMAG.2006.879430}, 407 petsc_uses = {KSP} 408} 409 410@Article{ cclcw2006, 411 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 412 title = {Control of Domain Wall Motion in Permalloy Ring}, 413 journal = {IEEE Trans. Magn.}, 414 volume = {42}, 415 year = {2006}, 416 pages = {2960--2962}, 417 doi = {10.1109/TMAG.2006.878414}, 418 petsc_uses = {KSP} 419} 420 421@Article{ bfmfzczg2007, 422 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 423 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 424 title = {Micromagnetic modelling of ferromagnetic cones}, 425 journal = {J. Magn. Magn. Mater.}, 426 volume = {312}, 427 year = {2007}, 428 pages = {234-238}, 429 url = {http://eprints.soton.ac.uk/45900/}, 430 petsc_uses = {KSP} 431} 432 433@PhDThesis{ rb2005, 434 author = {Richard Boardman}, 435 title = {Computer simulation studies of magnetic nanostructures}, 436 school = {Computational Engineering and Design Group, School of Engineering Sciences, 437 University of Southampton, United Kingdom}, 438 year = {2005}, 439 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 440 petsc_uses = {KSP} 441} 442 443@InProceedings{ cwwy2006, 444 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 445 title = {MPI Performance Analysis Tools on Blue Gene/L}, 446 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 447 year = {2006}, 448 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 449 petsc_uses = {KSP} 450} 451 452@InProceedings{ ch2006, 453 author = {I.-H. Chung and J.K. Hollingsworth}, 454 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 455 Programs}, 456 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 457 pages = {45--56}, 458 doi = {10.1109/HPDC.2006.1652135}, 459 petsc_uses = {KSP} 460} 461 462@Article{ lkpl2005, 463 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 464 title = {Multibit MRAM using a pair of memory cells}, 465 journal = {IEEE Trans. Magn.}, 466 volume = {41}, 467 year = {2005}, 468 pages = {2670-2672}, 469 doi = {10.1109/TMAG.2005.855288}, 470 petsc_uses = {KSP} 471} 472 473@Article{ gscn2005, 474 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 475 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 476 journal = {Phys. Rev. B}, 477 volume = {71}, 478 year = {2005}, 479 doi = {10.1103/PhysRevB.71.144407}, 480 petsc_uses = {KSP} 481} 482 483@PhDThesis{ mda, 484 author = {Massimiliano d'Aquino}, 485 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 486 school = { Universita di Napoli Federico II.}, 487 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 488 petsc_uses = {KSP} 489} 490 491@TechReport{ ssdfssf2003, 492 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 493 Stehno and J. Fidler}, 494 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 495 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 496 petsc_uses = {KSP} 497} 498 499@InProceedings{ sb2006a, 500 author = {W. Scholz and S. Batra}, 501 title = {Effect of write current waveform on magnetization and head field dynamics of 502 perpendicular recording heads}, 503 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 504 petsc_uses = {KSP} 505} 506 507@Article{ scholz-batra1, 508 author = {W. Scholz and S. Batra}, 509 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 510 Recording}, 511 journal = {IEEE Trans. Magn.}, 512 note = {submitted}, 513 year = {2005}, 514 petsc_uses = {KSP} 515} 516 517@Article{ scholz-batra2, 518 author = {W. Scholz and S. Batra}, 519 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 520 journal = {IEEE Trans. Magn.}, 521 volume = {41}, 522 year = {2005}, 523 pages = {702-706}, 524 petsc_uses = {KSP} 525} 526 527@Article{ daquino-scholz1, 528 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 529 title = {Micromagnetic Analysis of Fast Precessional Switching}, 530 journal = {J. Magn. Magn. Mater.}, 531 volume = {290-291}, 532 year = {2005}, 533 pages = {510-513}, 534 petsc_uses = {KSP} 535} 536 537@Article{ aq-scholz-fid, 538 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 539 title = {Numerical and analytical study of fast precessional switching}, 540 journal = {J. Appl. Phys.}, 541 volume = {95}, 542 year = {2004}, 543 pages = {7055-7057}, 544 petsc_uses = {KSP} 545} 546 547@InProceedings{ gar-tabik-gar, 548 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 549 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 550 Scatterers}, 551 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 552 (PDP'04)}, 553 year = {2004}, 554 pages = {80--}, 555 petsc_uses = {KSP} 556} 557 558@InProceedings{ aq-scholz-mia, 559 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 560 title = {Analysis of fast precessional switching in magnetic thin films}, 561 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 562 year = {2004}, 563 pages = {257-260}, 564 petsc_uses = {KSP} 565} 566 567@Article{ scholz-fid-seus, 568 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 569 Dittrich and V. Tsiantos}, 570 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 571 Axes}, 572 journal = {J. Magn. Magn. Mater.}, 573 year = {2004}, 574 pages = {1524-1525}, 575 petsc_uses = {KSP} 576} 577 578@Article{ boardman-zimmerman, 579 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 580 Peter de Groot}, 581 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 582 journal = {Journal of Applied Physics}, 583 year = {2005}, 584 petsc_uses = {KSP} 585} 586 587@Article{ lim-kim-park, 588 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 589 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 590 journal = {IEEE Trans. Magn.}, 591 note = {submitted}, 592 petsc_uses = {KSP} 593} 594 595@Article{ scholz-suess2, 596 author = {W. Scholz and D. Suess and T. Schrefl and and J. Fidler}, 597 title = {Micromagnetic simulation of magnetization reversal in small particles with 598 surface anisotropy}, 599 journal = {J. Appl. Phys.}, 600 volume = {95}, 601 year = {2004}, 602 pages = {6807-6809}, 603 petsc_uses = {KSP} 604} 605 606@Article{ scholz-schrefl1, 607 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 608 Tsiantos}, 609 title = {Micromagnetic simulation of the pinning and depinning process in permanent 610 magnets}, 611 journal = {IEEE Trans. Magn.}, 612 volume = {39}, 613 year = {2003}, 614 pages = {2920-2922}, 615 petsc_uses = {KSP} 616} 617 618@Article{ scholz-guslienko, 619 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 620 W. Chantrell and J. Fidler}, 621 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 622 nanodots}, 623 journal = {J. Magn. Magn. Mater.}, 624 volume = {266}, 625 year = {2003}, 626 pages = {155-163}, 627 petsc_uses = {KSP} 628} 629 630@Article{ scholz1, 631 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 632 Forster and V. Tsiantos}, 633 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 634 journal = {Comp. Mat. Sci}, 635 year = {2003}, 636 pages = {366--383}, 637 volume = {28}, 638 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 639 petsc_uses = {KSP} 640} 641 642@PhDThesis{ scholz2, 643 author = {W. Scholz}, 644 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 645 school = {Vienna University of Technology, Vienna, Austria}, 646 year = {2003}, 647 petsc_uses = {KSP} 648} 649 650@Article{ scholz3, 651 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 652 Forster and J. Fidler}, 653 title = {Implementation of a high performance parallel finite element micromagnetics 654 package}, 655 journal = {J. Magn. Magn. Mater.}, 656 year = {2004}, 657 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 658 petsc_uses = {KSP} 659} 660 661% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 662@InBook{ zhanggladwell1, 663 author = {W. Zhang and I. Gladwell}, 664 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 665 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 666 year = {2000}, 667 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 668 Physics, vol. 552}, 669 publisher = {Springer}, 670 pages = {4190-}, 671 petsc_uses = {KSP} 672} 673 674@Article{ wolf1, 675 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 676 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 677 thin films}, 678 journal = {Phil. Mag. A}, 679 year = {2003}, 680 lab = {ANL}, 681 petsc_uses = {KSP} 682} 683 684@Article{ wolf2, 685 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 686 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 687 grain-boundary properties}, 688 journal = {Computational Materials Science}, 689 year = {2001}, 690 volume = {23}, 691 pages = {15--32}, 692 lab = {ANL}, 693 petsc_uses = {KSP} 694} 695 696@Article{ wolf3, 697 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 698 title = {Role of grain rotation in grain growth by mesoscale simulation}, 699 journal = {Phil. Mag. A}, 700 year = {2002}, 701 volume = {82}, 702 pages = {1271--1297}, 703 lab = {ANL}, 704 petsc_uses = {KSP} 705} 706 707% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 708@Article{ saut, 709 author = { Olivier Saut}, 710 title = {Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal}, 711 journal = {SIAM Journal on Scientific Computing}, 712 year = {2004}, 713 note = {submitted}, 714 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 715 petsc_uses = {KSP} 716} 717 718% LiteralHTML: 719% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 720% LiteralHTML: 721@InBook{ khanallorenziayachepennec2016, 722 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 723 of Brain Deformation in {Alzheimer's} Disease}, 724 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 725 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 726 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 727 Miller}, 728 pages = {167--176}, 729 isbn = {978-3-319-28329-6}, 730 doi = {10.1007/978-3-319-28329-6_15}, 731 publisher = {Springer International Publishing}, 732 year = {2016}, 733 petsc_uses = {KSP} 734} 735 736@Article{ ataseven, 737 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 738 title = {Parallel implementation of the accelerated BEM approach for EMSI of the human 739 brain}, 740 journal = {Medical and Biological Engineering and Computing}, 741 month = {February}, 742 year = {2008}, 743 doi = {10.1007/s11517-008-0316-0}, 744 petsc_uses = {KSP} 745} 746 747@Article{ dennis-eberhart-03, 748 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 749 pages = {832-840}, 750 volume = {125}, 751 number = {6}, 752 title = {Finite-element simulation of cooling of realistic 3-D human head and neck}, 753 journal = {J Biomech Eng}, 754 year = {2003}, 755 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 756 petsc_uses = {KSP} 757} 758 759@Conference{ gu7174parallel, 760 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 761 frequency-domain small animal optical tomography}}, 762 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 763 booktitle = {Proc. of SPIE Vol}, 764 volume = {7174}, 765 number = {717406}, 766 pages = {1}, 767 petsc_uses = {KSP} 768} 769 770@Article{ barchanski2005using, 771 title = {{Using domain decomposition techniques for the calculation of low-frequency 772 electric current densities in high-resolution 3D human anatomy models}}, 773 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 774 T.}, 775 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 776 and Electronic Engineering}, 777 volume = {24}, 778 number = {2}, 779 pages = {458--467}, 780 issn = {0332-1649}, 781 year = {2005}, 782 publisher = {Emerald Group Publishing Limited}, 783 petsc_uses = {KSP} 784} 785 786@Article{ motrescurienen05, 787 author = {V. C. Motrescu and U. van Rienen}, 788 pages = {227--231}, 789 volume = {3}, 790 title = {Computation of currents induced by ELF electric fields in anisotropic human 791 tissues using the Finite Integration Technique}, 792 journal = {Advances in Radio Science}, 793 year = {2005}, 794 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 795 petsc_uses = {KSP} 796} 797 798@Article{ motrescurienen04, 799 author = {V. C. Motrescu and U. van Rienen}, 800 pages = {309--313}, 801 volume = {2}, 802 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 803 Integration Technique (FIT)}, 804 journal = {Advances in Radio Science}, 805 year = {2004}, 806 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 807 petsc_uses = {KSP} 808} 809 810@InProceedings{ dbl2, 811 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 812 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 813 booktitle = {ECCOMAS2000}, 814 year = {2000}, 815 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 816 petsc_uses = {KSP} 817} 818 819@Unpublished{ cell, 820 title = {Parallel Simulation Engines for Whole-Cell Models}, 821 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 822 Weber}, 823 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 824 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 825 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 826 year = {2001}, 827 petsc_uses = {KSP} 828} 829 830@Article{ barker2010two, 831 title = {Two-level Newton and hybrid Schwarz preconditioners for fluid-structure 832 interaction}, 833 author = {Barker, A.T. and Cai, X.C.}, 834 journal = {SIAM Journal on Scientific Computing}, 835 volume = {32}, 836 number = {4}, 837 pages = {2395--2417}, 838 year = {2010}, 839 publisher = {Society for Industrial and Applied Mathematics}, 840 petsc_uses = {KSP} 841} 842 843@Article{ barker2010scalable, 844 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 845 with application to blood flow modeling}, 846 author = {Barker, A.T. and Cai, X.C.}, 847 journal = {Journal of Computational Physics}, 848 volume = {229}, 849 number = {3}, 850 pages = {642--659}, 851 year = {2010}, 852 publisher = {Elsevier}, 853 petsc_uses = {KSP} 854} 855 856@Article{ barker2009nks, 857 title = {NKS for fully coupled fluid-structure interaction with application}, 858 author = {Barker, A.T. and Cai, X.C.}, 859 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 860 pages = {275--282}, 861 year = {2009}, 862 publisher = {Springer}, 863 petsc_uses = {KSP} 864} 865 866@Article{ mirams2013, 867 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 868 and Yi Cui and Gary R Mirams}, 869 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 870 to predict QT interval changes in the rabbit ventricular wedge}, 871 journal = {Journal of pharmacological and toxicological methods}, 872 volume = {68}, 873 number = {1}, 874 pages = {88--96}, 875 year = {2013}, 876 doi = {10.1016/j.vascn.2013.04.004}, 877 petsc_uses = {KSP} 878} 879 880% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 881% LiteralHTML: <center><img alt="" 882% LiteralHTML: src="images/spine0l.jpg"></center></p> 883% LiteralHTML: <center><img alt="" 884% LiteralHTML: src="images/vertebra.jpg"></center></p> 885% LiteralHTML:<font color="#FF0000"> 886% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 887% LiteralHTML:Understanding bone mechanical properties and how they may lead to 888% LiteralHTML:fractures is thus an important medical research activity. PETSc and 889% LiteralHTML:Prometheus have been used for extremely large scale finite element 890% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 891% LiteralHTML:team of doctors and computational scientists. This computation was 892% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 893% LiteralHTML:with over 4000 processors.</p> 894% LiteralHTML: </font> 895@Article{ arbenz2008scalable, 896 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 897 analysis of human bone structures}, 898 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 899 journal = {International Journal for Numerical Methods in Engineering}, 900 volume = {73}, 901 number = {7}, 902 pages = {927--947}, 903 year = {2008}, 904 publisher = {Wiley Online Library}, 905 petsc_uses = {KSP} 906} 907 908@InProceedings{ adams-04, 909 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 910 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 911 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 912 half a billion degrees of freedom}, 913 note = {Gordon Bell Award}, 914 year = {2004}, 915 petsc_uses = {KSP} 916} 917 918@InProceedings{ adams-03b, 919 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 920 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 921 Whole Bone Micro-Mechanics on the IBM SP}, 922 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 923 year = {2003}, 924 petsc_uses = {KSP} 925} 926 927@InProceedings{ oghattas2002, 928 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 929 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 930 booktitle = {Procceedings of SC2002}, 931 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 932 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 933 by time-dependent PDEs, and scalability results for an inverse wave propagation 934 problem of determining the material field of an acoustic medium. Using the 935 algorithm, they solved a synthetic inverse wave propagation problem though a 936 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 937 processors.}, 938 year = {2002}, 939 petsc_uses = {KSP} 940} 941 942% LiteralHTML: <a name="biology:cardiology"> 943% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 944% LiteralHTML: <center><img alt="" 945% LiteralHTML: src="images/heart.jpg"> 946% LiteralHTML: <img alt="" 947% LiteralHTML: src="images/pump.jpg"></center></p> 948% LiteralHTML: 949% LiteralHTML:<font color="#FF0000"> 950% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 951% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 952% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 953% LiteralHTML: through the heart. PETSc has been used by several research groups to 954% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 955% LiteralHTML: fully understand the developments of arrhthmias.</p> 956% LiteralHTML:</font> 957@InProceedings{ oghattas2000, 958 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 959 Walkington}, 960 title = {A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic 961 Interfaces}, 962 booktitle = {Procceedings of SC2000}, 963 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 964 note = {Blood flow modeling at the microscale including effects on individual blood 965 cells, for designing heart assist pumps, etc.}, 966 year = {2000}, 967 petsc_uses = {KSP} 968} 969 970@InBook{ cfps2006, 971 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 972 editor = {A. Quarteroni et al.}, 973 title = {Complex Systems in Biomedicine}, 974 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 975 publisher = {Springer-Verlag}, 976 pages = {187--241}, 977 year = {2006}, 978 petsc_uses = {KSP} 979} 980 981@InProceedings{ cfpst2007, 982 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 983 title = {Determining recovery times from transmembrane action potentials and unipolar 984 electrograms in normal heart tissue}, 985 booktitle = {FIMH07}, 986 publisher = {Springer-Verlag}, 987 volume = {4466}, 988 pages = {139--149}, 989 year = {2007}, 990 petsc_uses = {KSP} 991} 992 993@Article{ seemann2010framework, 994 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 995 Equations Using PETSc}}, 996 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 997 D{\\"o}ssel, O.}, 998 journal = {Progress in Industrial Mathematics at ECMI 2008}, 999 pages = {363--369}, 1000 year = {2010}, 1001 publisher = {Springer}, 1002 petsc_uses = {KSP} 1003} 1004 1005@InProceedings{ pft2005, 1006 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 1007 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 1008 Intramural Heterogeneity}, 1009 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 1010 pages = {267--277}, 1011 editors = {A. Frangi et al.}, 1012 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 1013 year = {2005}, 1014 petsc_uses = {KSP} 1015} 1016 1017@Article{ bgcp2005, 1018 author = {Boyce E. Griffith and Charles S. Peskin}, 1019 title = {On the order of accuracy of the immersed boundary method: Higher order 1020 convergence rates for sufficiently smooth problems}, 1021 journal = {Journal of Computational Physics}, 1022 year = {2005}, 1023 volume = {208}, 1024 pages = {75--105}, 1025 petsc_uses = {KSP} 1026} 1027 1028@Article{ griffith2007adaptive, 1029 title = {An adaptive, formally second order accurate version of the immersed boundary 1030 method}, 1031 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 1032 journal = {Journal of Computational Physics}, 1033 volume = {223}, 1034 number = {1}, 1035 pages = {10--49}, 1036 year = {2007}, 1037 publisher = {Elsevier}, 1038 petsc_uses = {KSP} 1039} 1040 1041@PhDThesis{ griffith05, 1042 author = {Boyce Griffith}, 1043 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 1044 parallel version of the immersed boundary method}, 1045 school = {New York University}, 1046 year = {2005}, 1047 petsc_uses = {KSP} 1048} 1049 1050@PhDThesis{ murillo, 1051 author = {Maria S. Murillo}, 1052 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 1053 Differential Equations with an Application in Computational Biology}, 1054 school = {University of Colorado at Boulder}, 1055 year = {2002}, 1056 petsc_uses = {KSP} 1057} 1058 1059@Article{ spv2004, 1060 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 1061 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 1062 journal = {IEEE Trans. Biomed. Eng}, 1063 year = {2004}, 1064 volume = {51}, 1065 pages = {1960--1968}, 1066 petsc_uses = {KSP} 1067} 1068 1069@Article{ vphl2003, 1070 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 1071 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 1072 journal = {J. Electrocardiol.}, 1073 year = {2003}, 1074 volume = {36}, 1075 pages = {69--74}, 1076 petsc_uses = {KSP} 1077} 1078 1079@InProceedings{ spbv2003, 1080 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and and E.J. Vigmond}, 1081 title = {Preconditioning Techniques for the Bidomain Equations}, 1082 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 1083 Methods}, 1084 pages = {571--580}, 1085 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 1086 note = {}, 1087 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 1088 year = {2003}, 1089 petsc_uses = {KSP} 1090} 1091 1092@Article{ franz-pavir-04, 1093 author = {P. Colli Franzone and L.~F. Pavarino}, 1094 title = {A parallel solver for reaction-diffusion systems in computational 1095 electrocardiology}, 1096 journal = {Mathematical Models and Methods in Applied Sciences}, 1097 year = {2004}, 1098 volume = {14}, 1099 number = {6}, 1100 pages = {883--912}, 1101 petsc_uses = {KSP} 1102} 1103 1104@Article{ franz-pavir-05, 1105 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 1106 title = {Simulating patterns of excitation, repolarization and action potential 1107 durationwith cardiac Bidomain and Monodomain models}, 1108 journal = {Mathematical Biosciences}, 1109 year = {2005}, 1110 volume = {197}, 1111 number = {1}, 1112 pages = {35--66}, 1113 petsc_uses = {KSP} 1114} 1115 1116@Article{ franz-pavir-06, 1117 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 1118 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 1119 the dispersion of cardiac repolarization and action potential duration: a 1120 simulation study}, 1121 journal = {Mathematical Biosciences}, 1122 year = {2006}, 1123 volume = {204}, 1124 number = {1}, 1125 pages = {132--165}, 1126 petsc_uses = {KSP} 1127} 1128 1129@InProceedings{ colli-franz-sim, 1130 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 1131 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 1132 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 1133 Mediterranean Conference on Medical and Biological Engineering}, 1134 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 1135 year = {2004}, 1136 petsc_uses = {KSP} 1137} 1138 1139@InProceedings{ pf2003, 1140 author = {Luca F. Pavarino and Piero Colli Franzone}, 1141 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 1142 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 1143 Methods}, 1144 pages = {669--776}, 1145 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 1146 note = {}, 1147 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 1148 year = {2003}, 1149 petsc_uses = {KSP} 1150} 1151 1152@Article{ maria-is04, 1153 author = {Maria Murillo and Xiao-Chuan Cai}, 1154 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 1155 activity of the heart}, 1156 journal = {Numerical Linear Algebra with Applications}, 1157 year = {2004}, 1158 volume = {11}, 1159 pages = {261 - 277}, 1160 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 1161 petsc_uses = {KSP} 1162} 1163 1164@Article{ murli2007monitoring, 1165 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 1166 Imaging in a Grid computing PSE}}, 1167 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 1168 and Lapegna, M.}, 1169 journal = {Grid-Based Problem Solving Environments}, 1170 pages = {421--432}, 1171 year = {2007}, 1172 publisher = {Springer}, 1173 petsc_uses = {KSP} 1174} 1175 1176@Article{ carracciuolo:2006:tpc, 1177 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 1178 title = {Towards a parallel component for imaging in PETSc programming environment: a case 1179 study in 3-D echocardiography}, 1180 journal = {Parallel Comput.}, 1181 volume = {32}, 1182 issue = {1}, 1183 month = {January}, 1184 year = {2006}, 1185 issn = {0167-8191}, 1186 pages = {67--83}, 1187 numpages = {17}, 1188 doi = {10.1016/j.parco.2005.09.001}, 1189 acmid = {1141218}, 1190 publisher = {Elsevier Science Publishers B. V.}, 1191 address = {Amsterdam, The Netherlands, The Netherlands}, 1192 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 1193 component}, 1194 petsc_uses = {KSP} 1195} 1196 1197@Article{ damore2011integration, 1198 title = {Integration of emerging computer technologies for an efficient image sequences 1199 analysis}, 1200 journal = {Integrated Computer-Aided Engineering }, 1201 volume = {18}, 1202 number = {4}, 1203 pages = {365 - 378}, 1204 year = {2011}, 1205 note = {}, 1206 issn = {1875-8835}, 1207 doi = {10.3233/ICA-2011-0382}, 1208 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 1209 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 1210 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 1211 petsc_uses = {KSP} 1212} 1213 1214@InProceedings{ eth_biwi_00721, 1215 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and and G. 1216 Székely}, 1217 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 1218 a Schur Complement Preconditioner}, 1219 booktitle = {Euro-Par 2009 Parallel Processing}, 1220 year = {2009}, 1221 month = {August}, 1222 pages = {747-759}, 1223 volume = {5704}, 1224 editor = {H. Sips and D. Epema and and H.-X. Lin}, 1225 series = {Lecture Notes in Computer Science}, 1226 publisher = {Springer}, 1227 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 1228 parallel Krylov solver}, 1229 petsc_uses = {KSP} 1230} 1231 1232% LiteralHTML: <a name="biology:imagingandsurgery"> 1233% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1234% LiteralHTML: <center><img alt="" 1235% LiteralHTML: src="images/brain.jpg"></center> 1236@Article{ ganser2004deformable, 1237 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 1238 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 1239 journal = {Medical Image Analysis}, 1240 volume = {8}, 1241 number = {1}, 1242 pages = {3--22}, 1243 year = {2004}, 1244 publisher = {Elsevier}, 1245 petsc_uses = {KSP} 1246} 1247 1248@Unpublished{ taccsurgery, 1249 title = {TACC supercomputer performs laser cancer surgery on canine}, 1250 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 1251 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 1252 Austin performed laser surgery on a dog in Houston without the intervention of a 1253 surgeon. The treatment was developed collaboratively by computational experts from 1254 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 1255 leading technologists from the M.D. Anderson Cancer Center in Houston, and 1256 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 1257 state-of-the-art thermal imaging technology, and advanced computational methods, 1258 dynamic, data-driven treatments are being pursued as a minimally invasive 1259 alternative to the standard treatment of cancer.}, 1260 petsc_uses = {KSP} 1261} 1262 1263@Article{ ffhbresso2008, 1264 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 1265 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 1266 Tinsley Oden}, 1267 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 1268 journal = {Engineering with Computers}, 1269 note = {Special issue on Computational Bioengineering}, 1270 year = {2008}, 1271 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 1272 petsc_uses = {KSP} 1273} 1274 1275@TechReport{ dobbhbbbdeffghkkps2008, 1276 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 1277 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 1278 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 1279 and S. Prudhomme and R. J. Stafford}, 1280 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 1281 Cancer}, 1282 year = {2008}, 1283 institution = {University of Texas at Austin}, 1284 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 1285 petsc_uses = {KSP} 1286} 1287 1288@Article{ ogdb2004, 1289 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 1290 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 1291 journal = {Physics in Medicine and Biology}, 1292 year = {2004}, 1293 volume = {49}, 1294 pages = {2955--2947}, 1295 petsc_uses = {KSP} 1296} 1297 1298@InProceedings{ majumdar11, 1299 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 1300 Baldridge and P. Krysl}, 1301 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 1302 booktitle = {ICCS 2005}, 1303 pages = {672--679}, 1304 editor = {V.S. Sunderam et al.}, 1305 year = {2005}, 1306 petsc_uses = {KSP} 1307} 1308 1309@Conference{ sermesant-etal:03, 1310 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 1311 Ayache, H.}, 1312 title = {A parallel implementation of non-rigid registration using a volumetric 1313 biomechanical model}, 1314 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 1315 address = {Philadelphia, PA, USA}, 1316 publisher = {Springer-Verlag}, 1317 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 1318 series = {Lecture Notes in Computer Science}, 1319 volume = {2717}, 1320 pages = {398-407}, 1321 date = {june 23-24}, 1322 year = {2003}, 1323 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 1324 petsc_uses = {KSP} 1325} 1326 1327@Conference{ sermesant-etal:04, 1328 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 1329 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 1330 title = {A Novel Nonrigid Registration Algorithm And Applications}, 1331 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 1332 address = {Philadelphia, PA, USA}, 1333 publisher = {Springer-Verlag}, 1334 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 1335 series = {Lecture Notes in Computer Science}, 1336 volume = {2208}, 1337 pages = {923}, 1338 year = {2003}, 1339 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 1340 petsc_uses = {KSP} 1341} 1342 1343@Article{ warfield-haker-talos-05, 1344 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 1345 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 1346 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 1347 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 1348 title = {Capturing intraoperative deformations: research experience at Brigham and Women's 1349 hospital}, 1350 journal = {Medical Image Analysis}, 1351 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 1352 year = {2005}, 1353 petsc_uses = {KSP} 1354} 1355 1356@Article{ brain3, 1357 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 1358 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 1359 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 1360 Deformation during Image Guided Neurosurgery}, 1361 journal = {Computing and Visualization in Science}, 1362 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 1363 year = {2002}, 1364 petsc_uses = {KSP} 1365} 1366 1367@Article{ brain2, 1368 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 1369 Kikinis and Simon K. Warfield}, 1370 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 1371 Element Biomechanical Model}, 1372 journal = {IEEE Transactions on Medical Imaging}, 1373 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 1374 year = {2001}, 1375 petsc_uses = {KSP} 1376} 1377 1378@InProceedings{ brain1, 1379 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 1380 Ferenc A. Jolesz and Ron Kikinis}, 1381 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 1382 Guided Neurosurgery}, 1383 booktitle = {Proceedings of SC2000}, 1384 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 1385 year = {2000}, 1386 petsc_uses = {KSP} 1387} 1388 1389@Article{ vanne06, 1390 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 1391 M. Lassas and M. Kalke}, 1392 title = {Parallelized Bayesian inversion for three-dimensional dental X-ray imaging}, 1393 journal = {IEEE Transactions on Medical Imaging}, 1394 volume = {25}, 1395 number = {2}, 1396 month = {February}, 1397 year = {2006}, 1398 pages = {218--228}, 1399 petsc_uses = {KSP} 1400} 1401 1402@InProceedings{ knepleybardhan2015, 1403 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 1404 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 1405 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 1406 Exposition}, 1407 volume = {9}, 1408 pages = {V009T12A04}, 1409 doi = {10.1115/IMECE2015-53579}, 1410 year = {2015}, 1411 petsc_uses = {KSP} 1412} 1413 1414@InProceedings{ bardhanknepley2015, 1415 title = {Multiscale models and approximation algorithms for protein electrostatics}, 1416 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 1417 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 1418 volume = {61}, 1419 pages = {163--174}, 1420 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 1421 doi = {10.2495/BEM380131}, 1422 publisher = {WIT Press}, 1423 year = {2015}, 1424 petsc_uses = {KSP} 1425} 1426 1427% LiteralHTML: 1428% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 1429% LiteralHTML: 1430@InProceedings{ adamsbrennanknepleywang2022, 1431 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 1432 quench plasmas}, 1433 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 1434 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 1435 (IPDPS '22)}, 1436 doi = {10.1109/IPDPS53621.2022.00020}, 1437 year = {2022}, 1438 petsc_uses = {DMPlex} 1439} 1440 1441@Misc{ adamsknepleybrennan2021, 1442 title = {Runaway Electron Generation with High-Performance, Structure Preserving 1443 Discretization of Fokker-Plank-Landau}, 1444 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 1445 year = {2021}, 1446 petsc_uses = {KSP} 1447} 1448 1449@Article{ adamshirvijokiknepleybrownisaacmills2017, 1450 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 1451 Architectures}, 1452 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 1453 Isaac and Richard Mills}, 1454 journal = {SIAM Journal on Scientific Computing}, 1455 volume = {39}, 1456 number = {6}, 1457 pages = {C452--C465}, 1458 doi = {10.1137/17M1118828}, 1459 eprint = {1702.08880}, 1460 year = {2017}, 1461 petsc_uses = {KSP} 1462} 1463 1464@Article{ pusztayknepleyadams2022, 1465 title = {Conservative Projection Between FEM and Particle Bases}, 1466 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 1467 journal = {SIAM Journal on Scientific Computing}, 1468 volume = {44}, 1469 number = {4}, 1470 pages = {C310--C319}, 1471 doi = {10.1137/21M145407}, 1472 year = {2022} 1473} 1474 1475@Article{ hirvijoki2017, 1476 author = {Eero Hirvijoki and Mark F. Adams}, 1477 title = {Conservative discretization of the {Landau} collision integral}, 1478 journal = {Physics of Plasmas}, 1479 volume = {24}, 1480 number = {3}, 1481 pages = {032121}, 1482 doi = {10.1063/1.4979122}, 1483 year = {2017}, 1484 petsc_uses = {KSP} 1485} 1486 1487@Article{ mollenadamsknepleyhagerchang2021, 1488 title = {Implementation of higher-order velocity mapping between marker particles and grid 1489 in the particle-in-cell code XGC}, 1490 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 1491 S. Chang}, 1492 journal = {Journal of Plasma Physics}, 1493 eprint = {2012.11764}, 1494 doi = {10.1017/S0022377821000441}, 1495 year = {2021}, 1496 petsc_uses = {KSP} 1497} 1498 1499@Article{ lsmh2014, 1500 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 1501 title = {Comparison of particle trajectories and collision operators for collisional 1502 transport in nonaxisymmetric plasmas}, 1503 journal = { Physics of Plasmas}, 1504 volume = {21}, 1505 year = {2014}, 1506 petsc_uses = {KSP} 1507} 1508 1509@Article{ lpcep2014, 1510 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 1511 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 1512 pedestal}, 1513 journal = {Plasma Physics and Controlled Fusion}, 1514 volume = {56}, 1515 year = {2014}, 1516 petsc_uses = {KSP} 1517} 1518 1519@Article{ facets-scidac08, 1520 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 1521 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 1522 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 1523 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 1524 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 1525 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 1526 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 1527 Stotler and A. Pigarov}, 1528 journal = {J. Phys.: Conf. Ser.}, 1529 volume = {125}, 1530 year = {2008}, 1531 pages = {012040}, 1532 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 1533 petsc_uses = {KSP} 1534} 1535 1536@Article{ facets-scidac09, 1537 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 1538 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 1539 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 1540 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 1541 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 1542 and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar 1543 and A. Pigarov and H. Zhang}, 1544 journal = {J. Phys.: Conf. Ser.}, 1545 volume = {180}, 1546 year = {2009}, 1547 pages = {012056}, 1548 url = {http://iopscience.iop.org/1742-6596/180/1/012056}, 1549 petsc_uses = {KSP} 1550} 1551 1552@InProceedings{ facets-scidac10, 1553 title = {Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the 1554 {FACETS} Code}, 1555 author = {A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. 1556 Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. 1557 Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. 1558 Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. 1559 Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. 1560 Pigarov and H. Zhang}, 1561 booktitle = {Proceedings of SciDAC 2010 Conference}, 1562 year = {2010}, 1563 url = {http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf}, 1564 petsc_uses = {KSP} 1565} 1566 1567@InProceedings{ facets-fec2010, 1568 title = {Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using 1569 the {FACETS} Framework}, 1570 author = {J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina 1571 and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. 1572 McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang}, 1573 booktitle = {Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, 1574 Republic of Korea}, 1575 year = {2010}, 1576 petsc_uses = {KSP} 1577} 1578 1579@InProceedings{ facets-epdp2010, 1580 title = {{FACETS}: A Framework for Parallel Coupling of Fusion Components}, 1581 author = {J. Cary and A. Hakim and M. Miah and S. Kruger and A. Pletzer and S. Shasharina 1582 and S. Vadlamani and A. Pankin and R. Cohen and T. Epperly and T. Rognlien and R. 1583 Groebner and S. Balay and L. McInnes and H. Zhang}, 1584 booktitle = {Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on 1585 Parallel, Distributed and Network-Based Computing), Pisa, Italy}, 1586 year = {2010}, 1587 petsc_uses = {KSP} 1588} 1589 1590@Article{ carlssoncary09, 1591 author = {Johan Carlsson, John R. Cary}, 1592 title = {The hypersecant Jacobian approximation for quasi-Newton solves of sparse 1593 nonlinear systems}, 1594 journal = {arXiv}, 1595 year = {2009}, 1596 note = {http://arxiv.org/abs/0905.1054}, 1597 url = {http://arxiv.org/pdf/0905.1054v1}, 1598 petsc_uses = {KSP} 1599} 1600 1601@InProceedings{ oshahjs2006, 1602 author = {F. Ogando and A. Signell and J.A. Heikkinen and M. Aspn\"as and S. Henriksson and 1603 S.J. Janhunen and T.P. Kiviniemi}, 1604 title = {Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of 1605 application}, 1606 booktitle = {33rd EPS Conference on Plasma Phys.}, 1607 year = {2006}, 1608 url = {http://epsppd.epfl.ch/Roma/pdf/P4_153.pdf}, 1609 note = {European fusion code}, 1610 petsc_uses = {KSP} 1611} 1612 1613@Article{ zhu2006, 1614 author = {P. Zhu and A. Bhattacharjee and K. Germaschewski}, 1615 title = {Intermediate nonlinear evolution of the Parker instability: Formation of 1616 convection-induced discontinuities and absence of finite-time singularities}, 1617 journal = {Phys. Rev. Lett.}, 1618 volume = {96}, 1619 number = {065001}, 1620 year = {2006}, 1621 doi = {10.1103/PhysRevLett.96.065001}, 1622 petsc_uses = {KSP} 1623} 1624 1625@InProceedings{ ppc2005, 1626 author = {B. Philip and M. Pernice and L.Chacon}, 1627 title = {Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh 1628 Refinement}, 1629 booktitle = {Proceedings of the 16th International Conference on Domain Decomposition 1630 methods}, 1631 year = {2005}, 1632 lab = {LANL}, 1633 petsc_uses = {KSP} 1634} 1635 1636@Article{ pp2005, 1637 author = {M. Pernice and B. Philip}, 1638 title = {Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh 1639 Refinement}, 1640 year = {2005}, 1641 journal = {SIAM J. of Sci. Comput.}, 1642 lab = {LANL}, 1643 petsc_uses = {KSP} 1644} 1645 1646@Article{ gt2004, 1647 author = {A. H. Glasser and X. Z. Tang}, 1648 title = {The SEL macroscopic modeling code}, 1649 year = {2004}, 1650 journal = {Computer Physics Communications}, 1651 pages = {237--243}, 1652 volume = {164}, 1653 lab = {LANL}, 1654 petsc_uses = {KSP} 1655} 1656 1657@Article{ nl2006, 1658 author = {Y. Nishimura and Z.Lin}, 1659 title = {A finite element mesh in a tokamak edge geometry}, 1660 year = {2006}, 1661 journal = {Contributions to Plasma Physics}, 1662 volume = {22}, 1663 lab = {PPPL}, 1664 petsc_uses = {KSP} 1665} 1666 1667@Article{ nlle2004, 1668 author = {Y. Nishimura and Z.Lin and J.Lewandowski and S.Ethier}, 1669 title = {A finite element Poisson solver for gyrokinetic particle simulations in a global 1670 field aligned mesh}, 1671 year = {2006}, 1672 journal = {J. Comput. Phys.}, 1673 volume = {214}, 1674 pages = {657}, 1675 lab = {PPPL}, 1676 petsc_uses = {KSP} 1677} 1678 1679@InProceedings{ lnlle2004, 1680 author = {J.L.V Lewandowski and Y.Nishimura and W.W.Lee and Z.Lin and S. Ethier}, 1681 title = {Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons}, 1682 booktitle = {Sherwood Fusion Theory Conference, Missoula, MT}, 1683 year = {2004}, 1684 url = {http://www.sherwoodtheory.org/sherwood04/program/1e15.pdf}, 1685 lab = {PPPL}, 1686 petsc_uses = {KSP} 1687} 1688 1689@InProceedings{ nlclew2004, 1690 author = {Y. Nishimura and Z.Lin and L.Chen and J.Lewandowski and S.Ethier and W. Wang}, 1691 title = {Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron 1692 model}, 1693 booktitle = {Sherwood Fusion Theory Conference, Missoula, MT}, 1694 year = {2004}, 1695 url = {http://www.sherwoodtheory.org/sherwood04/program/1C32.pdf}, 1696 lab = {PPPL}, 1697 petsc_uses = {KSP} 1698} 1699 1700@Article{ tb1, 1701 author = {X.~Z.~Tang and A.~H.~Boozer}, 1702 title = {Numerical studies of a steady state axisymmetric co-axial helicity injection 1703 plasma}, 1704 journal = {Physics of Plasmas}, 1705 year = {2004}, 1706 pages = {171--185}, 1707 volume = {11}, 1708 lab = {LANL}, 1709 petsc_uses = {KSP} 1710} 1711 1712@Unpublished{ nlcw, 1713 title = {Inclusion of electromagnetic effects into gyrokinetic particle simulations}, 1714 author = {Y. Nishimura and Z.Lin and L.Chen and W. Wang}, 1715 note = {American Physical Society 45th Annual Meeting Division of Plasma Physics, 1716 Albuquerque, New Mexico, October 2003}, 1717 year = {2003}, 1718 petsc_uses = {KSP} 1719} 1720 1721@TechReport{ tang2001, 1722 author = {X. Z. Tang and G. Y. Fu and S. C. Jardin and L. L. Lowe and W. Park and H. R. 1723 Strauss}, 1724 title = {Resistive Magnetohydrodynamics Simulation of Fusion Plasmas}, 1725 year = {2001}, 1726 institution = {Princeton Plasma Physics Laboratory}, 1727 number = {PPPL-3532}, 1728 url = {http://www.pppl.gov/pub_report/2001/PPPL-3532.pdf}, 1729 note = {Presented at 10th Society for Industrial and Applied Mathematics (SIAM) 1730 Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, 1731 March 12-14, 2001.}, 1732 lab = {PPPL}, 1733 petsc_uses = {KSP} 1734} 1735 1736% LiteralHTML: 1737% LiteralHTML: <a name="geosciences"><H3><center>Geosciences</center></H3> 1738% LiteralHTML: 1739@Article{ valerathomasgarciacastillo2019, 1740 author = {Manuel Valera and Mary P. Thomas and Mariangel Garcia and Jose E. Castillo}, 1741 title = {Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear 1742 Coastal Ocean Model}, 1743 journal = {Journal of Marine Science and Engineering}, 1744 volume = {7}, 1745 number = {6}, 1746 article-number= {185}, 1747 url = {https://www.mdpi.com/2077-1312/7/6/185}, 1748 issn = {2077-1312}, 1749 doi = {10.3390/jmse7060185}, 1750 year = {2019}, 1751 petsc_uses = {KSP} 1752} 1753 1754@Article{ furuichimat2015, 1755 title = {Implicit solution of the material transport in Stokes flow simulation: Toward 1756 thermal convection simulation surrounded by free surface}, 1757 author = {Mikito Furuichi and Dave A May}, 1758 journal = {Computer Physics Communications}, 1759 volume = {192}, 1760 pages = {1--11}, 1761 year = {2015}, 1762 petsc_uses = {KSP} 1763} 1764 1765@Article{ sharplesmoresivelicjadamecmay2016, 1766 title = {Simulating faults and plate boundaries with a transversely isotropic plasticity 1767 model}, 1768 author = {Wendy Sharples and Louis N Moresi and Mirko Velic and Margarete A Jadamec and 1769 Dave A May}, 1770 journal = {Physics of the Earth and Planetary Interiors}, 1771 volume = {252}, 1772 pages = {77--90}, 1773 year = {2016}, 1774 petsc_uses = {KSP} 1775} 1776 1777@Article{ spiegelmanmaywilson2016, 1778 title = {On the solvability of incompressible Stokes with viscoplastic rheologies in 1779 geodynamics}, 1780 author = {Marc Spiegelman and Dave A May and Cian R Wilson}, 1781 journal = {Geochemistry, Geophysics, Geosystems}, 1782 volume = {17}, 1783 number = {6}, 1784 pages = {2213--2238}, 1785 year = {2016}, 1786 petsc_uses = {KSP} 1787} 1788 1789@Article{ buiteretal2016, 1790 title = {Benchmarking numerical models of brittle thrust wedges}, 1791 author = {Susanne JH Buiter and Guido Schreurs and Markus Albertz and Taras V Gerya and 1792 Boris Kaus and Walter Landry and Laetitia {Le Pourhiet} and Yury Mishin and David 1793 L Egholm and Michele Cooke and Bertrand Maillot and Cedric Thieulot and Tony Crook 1794 and Dave May and Pauline Souloumiac and Christopher Beaumont}, 1795 journal = {Journal of structural geology}, 1796 volume = {92}, 1797 pages = {140--177}, 1798 year = {2016}, 1799 petsc_uses = {KSP} 1800} 1801 1802@Article{ afanasievboehmdrielkrischerrietmannmayknepleyfichtner2019, 1803 title = {Modular and flexible spectral-element waveform modelling in two and three 1804 dimensions}, 1805 author = {Michael Afanasiev and Christian Boehm and Martin van Driel and Lion Krischer and 1806 Max Rietmann and Dave A. May and Matthew G. Knepley and Andreas Fichtner}, 1807 journal = {Geophysical Journal International}, 1808 volume = {216}, 1809 number = {3}, 1810 pages = {1675--1692}, 1811 doi = {10.1093/gji/ggy469}, 1812 year = {2019}, 1813 petsc_uses = {KSP} 1814} 1815 1816@Article{ haplaknepleyafanasievboehmdrielkrischerfichtner2020, 1817 title = {Fully Parallel Mesh {I/O} using {PETSc} {DMPlex} with an Application to Waveform 1818 Modeling}, 1819 author = {Vaclav Hapla and Matthew G. Knepley and Michael Afanasiev and Christian Boehm and 1820 Martin van Driel and Lion Krischer and Andreas Fichtner}, 1821 journal = {SIAM Journal on Scientific Computing}, 1822 volume = {43}, 1823 number = {2}, 1824 pages = {C127--C153}, 1825 eprint = {http://arxiv.org/abs/2004.08729}, 1826 doi = {10.1137/20M1332748}, 1827 year = {2021}, 1828 petsc_uses = {KSP} 1829} 1830 1831@Article{ parsani2021, 1832 title = {High-order accurate entropy-stable discontinuous collocated Galerkin methods with 1833 the summation-by-parts property for compressible CFD frameworks: Scalable SSDC 1834 algorithms and flow solver}, 1835 author = {Matteo Parsani and Radouan Boukharfane and Irving Reyna Nolasco and David C. {Del 1836 Rey Fernández} and Stefano Zampini and Bilel Hadri and Lisandro Dalcin}, 1837 journal = {Journal of Computational Physics}, 1838 volume = {424}, 1839 pages = {109844}, 1840 issn = {0021-9991}, 1841 doi = {https://doi.org/10.1016/j.jcp.2020.109844}, 1842 url = {http://www.sciencedirect.com/science/article/pii/S0021999120306185}, 1843 year = {2021}, 1844 petsc_uses = {KSP} 1845} 1846 1847@Article{ ambartsumyanbouakaramthanhghattaskeyesstadlerturkiyyahzampini2020, 1848 title = {Hierarchical matrix approximations of {Hessians} arising in inverse problems 1849 governed by {PDEs}}, 1850 author = {I. Ambartsumyan and W. Bouakaram and Than Bui-Thanh and Omar Ghattas and David 1851 Keyes and Georg Stadler and George Turkiyyah and Stefano Zampini}, 1852 journal = {SIAM Journal of Scientific Computing}, 1853 volume = {42}, 1854 number = {5}, 1855 pages = {A3397--A3426}, 1856 year = {2020} 1857} 1858 1859@Article{ zampinibouakaramturkiyyahkniokeyes2022, 1860 title = {H2Opus: a distributed memory {multi-GPU} software for non-local operators}, 1861 author = {Stefano Zampini and W. Bouakaram and George Turkiyyah and O. Knio and David E. 1862 Keyes}, 1863 journal = {Advances on Computational Mathematics}, 1864 note = {In press}, 1865 year = {2022} 1866} 1867 1868@Article{ dassizampiniscacchi2022, 1869 title = {Robust and scalable adaptive {BDDC} preconditioners for virtual element 1870 discretizations of elliptic equations in mixed form}, 1871 author = {F. Dassi and Stefano Zampini and S. 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Smith and Aron Ahmadia}, 2429 journal = {SIAM Journal on Scientific Computing}, 2430 volume = {35}, 2431 number = {2}, 2432 year = {2013}, 2433 pages = {359--375}, 2434 doi = {10.1137/110834512}, 2435 note = {Also preprint ANL/MCS-P743-1298}, 2436 petsc_uses = {KSP} 2437} 2438 2439@InProceedings{ brown2013quasinewton, 2440 author = {Jed Brown and Peter Brune}, 2441 title = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type 2442 methods}, 2443 year = {2013}, 2444 booktitle = {International Conference on Mathematics and Computational Methods Applied to 2445 Nuclear Science and Engineering}, 2446 pages = {2554--2565}, 2447 petsc_uses = {KSP} 2448} 2449 2450@Misc{ spiegelman-siampp10, 2451 title = {Block Preconditioners and Advanced Software for Multiphysics Problems in Solid 2452 Earth Geodynamics}, 2453 author = {Marc Spiegelman}, 2454 note = {presentation at the 2010 SIAM Conference on Parallel Processing for Scientific 2455 Computing}, 2456 year = {2010}, 2457 petsc_uses = {KSP} 2458} 2459 2460@Article{ schauer2011a, 2461 author = {Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. 2462 Quintana-Ort\'{\i}}, 2463 title = {Large scale simulation of wave propagation in soils interacting with structures 2464 using {FEM} and {SBFEM}}, 2465 journal = {Journal of Computational Acoustics}, 2466 volume = {19}, 2467 number = {1}, 2468 pages = {75--93}, 2469 year = {2011}, 2470 doi = {10.1142/S0218396X11004316}, 2471 petsc_uses = {KSP} 2472} 2473 2474@Misc{ bsa2010, 2475 author = {J. Brown and B. Smith and A. Ahmadia}, 2476 title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow}, 2477 note = {submitted to SIAM Journal on Scientific Computing}, 2478 year = {2012}, 2479 petsc_uses = {KSP} 2480} 2481 2482@Article{ kellerkatz2016, 2483 title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere}, 2484 author = {Tobias Keller and Richard F. 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Wendebourg}, 3084 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 3085 journal = {Computational Geosciences}, 3086 year = {2003}, 3087 volume = {7}, 3088 pages = {295--318}, 3089 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 3090 petsc_uses = {KSP} 3091} 3092 3093@Article{ kees-miller-03, 3094 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 3095 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 3096 journal = {Computational Geosciences}, 3097 year = {2003}, 3098 volume = {7}, 3099 pages = {91--114}, 3100 petsc_uses = {KSP} 3101} 3102 3103@Article{ bk2003, 3104 author = {JN Buur and T Kuehnel}, 3105 title = {Improving depth imaging by automated model updating}, 3106 journal = {The Leading Edge}, 3107 year = {2003}, 3108 volume = {22}, 3109 pages = {310-318}, 3110 petsc_uses = {KSP} 3111} 3112 3113@Article{ frederickbuffett2016, 3114 title = {Submarine groundwater discharge as a possible formation mechanism for 3115 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 3116 author = {Jennifer M. Frederick and Bruce A. Buffett}, 3117 journal = {Journal of Geophysical Research: Solid Earth}, 3118 volume = {121}, 3119 number = {3}, 3120 pages = {1383--1404}, 3121 issn = {2169-9356}, 3122 doi = {10.1002/2015JB012627}, 3123 year = {2016}, 3124 petsc_uses = {KSP} 3125} 3126 3127% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3128% LiteralHTML:<font color="#FF0000"> 3129% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 3130% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 3131% LiteralHTML:variety of these simulations.</p> 3132% LiteralHTML:</font> 3133% LiteralHTML: 3134@InProceedings{ appelbe1, 3135 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 3136 year = {2003}, 3137 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 3138 computational methodology}, 3139 page = {781}, 3140 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 3141 Proceedings}, 3142 publisher = {Springer-Verlag}, 3143 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 3144 petsc_uses = {KSP} 3145} 3146 3147% LiteralHTML:<a name="katz"> 3148@InProceedings{ gd1, 3149 author = {Guillaume Dumont and Michel Kern}, 3150 title = {Parallelization of a 3D Seismic Migration Code with PETSc}, 3151 year = {1999}, 3152 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 3153 Computing}, 3154 petsc_uses = {KSP} 3155} 3156 3157% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 3158% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 3159% LiteralHTML:<font color="#FF0000"> 3160% LiteralHTML: Figures from the work of Richard Katz 3161@PhDThesis{ katzthesis, 3162 author = {R.F. Katz}, 3163 title = {The deep roots of volcanoes: models of magma dynamics with applications to 3164 subduction zones}, 3165 school = {Columbia University}, 3166 year = {2005}, 3167 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 3168 petsc_uses = {KSP} 3169} 3170 3171@InCollection{ knepleykatzsmith06, 3172 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 3173 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 3174 USA}, 3175 title = {Developing a Geodynamics Simulator with {PETSc}}, 3176 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 3177 series = {Lecture Notes in Computational Science and Engineering}, 3178 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 3179 publisher = {Springer Berlin Heidelberg}, 3180 isbn = {978-3-540-31619-0}, 3181 keyword = {Mathematics and Statistics}, 3182 pages = {413-438}, 3183 volume = {51}, 3184 doi = {10.1007/3-540-31619-1_12}, 3185 year = {2006}, 3186 petsc_uses = {KSP} 3187} 3188 3189@Article{ katz04, 3190 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 3191 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 3192 the global mid-ocean ridge system}, 3193 journal = {Geophys.\ Res.\ Letts.}, 3194 year = {2004}, 3195 volume = {31}, 3196 pages = {L15605}, 3197 petsc_uses = {KSP} 3198} 3199 3200@Article{ katz07, 3201 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 3202 Ethan Coon}, 3203 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 3204 Toolkit for Scientific Computation}}, 3205 journal = {Phys. Earth Planet. In.}, 3206 volume = {163}, 3207 pages = {52--68}, 3208 year = {2007}, 3209 petsc_uses = {KSP} 3210} 3211 3212@Article{ williams2006development, 3213 title = {{Development of a package for modeling stress in the lithosphere}}, 3214 author = {Williams, CA}, 3215 journal = {Eos Trans. AGU}, 3216 volume = {87}, 3217 pages = {36}, 3218 year = {2006}, 3219 petsc_uses = {KSP} 3220} 3221 3222@Article{ goverswortel05, 3223 author = {R. Govers and M.J.R. Wortel}, 3224 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 3225 journal = {Earth and Planetary Science Letters}, 3226 volume = {236/1-2}, 3227 pages = {505-523}, 3228 year = {2005}, 3229 petsc_uses = {KSP} 3230} 3231 3232@InProceedings{ snark2, 3233 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 3234 year = {2002}, 3235 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 3236 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 3237 petsc_uses = {KSP} 3238} 3239 3240@Article{ snark1, 3241 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 3242 Tan and Feng Wang}, 3243 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 3244 journal = {Submitted to Pure and Applied Geosciences}, 3245 petsc_uses = {KSP} 3246} 3247 3248@InProceedings{ earthquake2003, 3249 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 3250 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 3251 Tiankai Tu}, 3252 year = {2003}, 3253 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 3254 booktitle = {Proceedings of SC2003}, 3255 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 3256 petsc_uses = {KSP} 3257} 3258 3259@InProceedings{ stefano12, 3260 author = {Michele De Stefano}, 3261 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 3262 booktitle = {PIERS Proceedings}, 3263 month = {August}, 3264 address = {Moscow, RUSSIA}, 3265 pages = {491--495}, 3266 year = {2012}, 3267 petsc_uses = {KSP} 3268} 3269 3270%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 3271 3272% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3273% LiteralHTML: <center><img alt="" 3274% LiteralHTML: src="images/ocean.jpg"></center></p> 3275@Article{ khatiwala07, 3276 author = {Khatiwala, S.}, 3277 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 3278 journal = {Glob. Biogeochem. Cycles}, 3279 volume = {21}, 3280 doi = {10.1029/2007GB002923}, 3281 year = {2007}, 3282 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 3283} 3284 3285@Article{ dks2004, 3286 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 3287 journal = {Ocean Modelling}, 3288 year = {2004}, 3289 volume = {6(2)}, 3290 pages = {125-150}, 3291 title = {A finite-element Ocean Model: Principles and Evaluation}, 3292 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}, 3293 petsc_uses = {KSP} 3294} 3295 3296@Article{ danilov1, 3297 author = {S. Danilov and G. Kivman and J. Schroter}, 3298 year = {2004}, 3299 title = {Evaluation of an eddy-permitting finite-element ocean model in the North 3300 Atlantic}, 3301 journal = {Ocean Modelling}, 3302 petsc_uses = {KSP} 3303} 3304 3305@Article{ nerger1, 3306 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 3307 year = {2004}, 3308 title = {Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to 3309 a Finite Element Model of the North Atlantic}, 3310 journal = {Journal of marine systems}, 3311 petsc_uses = {KSP} 3312} 3313 3314@Conference{ rakowsky2003self, 3315 title = {{A self-adaptive finite element model of the atmosphere}}, 3316 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 3317 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 3318 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 3319 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 3320 pages = {279}, 3321 isbn = {981238376X}, 3322 year = {2003}, 3323 organization = {World Scientific Pub Co}, 3324 petsc_uses = {KSP} 3325} 3326 3327@Article{ lauter3, 3328 author = {M. Lauter}, 3329 year = {2004}, 3330 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 3331 AtmosphArenmodell}, 3332 journal = {Berichte zur Polar- und Meeresforschung}, 3333 petsc_uses = {KSP} 3334} 3335 3336@Article{ lauter2, 3337 author = {M. Lauter and D. Handorf and K. Dethloff}, 3338 year = {2004}, 3339 title = {Unsteady analytical solutions of the spherical shallow water equations}, 3340 journal = {Journal of computational physics}, 3341 petsc_uses = {KSP} 3342} 3343 3344@PhDThesis{ lauter1, 3345 author = {M. Lauter}, 3346 year = {2004}, 3347 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 3348 AtmosphArenmodell}, 3349 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 3350 petsc_uses = {KSP} 3351} 3352 3353@Article{ frickenhaus1, 3354 author = {S. Frickenhaus and W. Hiller and M. Best}, 3355 year = {2005}, 3356 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 3357 parallel numerical atmosphere and ocean models}, 3358 journal = {Ocean Modelling}, 3359 volume = {10}, 3360 pages = {185--191}, 3361 petsc_uses = {KSP} 3362} 3363 3364@Article{ 0266-5611-24-3-034015, 3365 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 3366 title = {A Newton-CG method for large-scale three-dimensional elastic full-waveform 3367 seismic inversion}, 3368 journal = {Inverse Problems}, 3369 volume = {24}, 3370 number = {3}, 3371 pages = {034015 (26pp)}, 3372 url = {http://stacks.iop.org/0266-5611/24/034015}, 3373 year = {2008}, 3374 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 3375 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 3376 iterations with inner conjugate gradient linear iterations, globalized by an 3377 Armijo backtracking line search, solved on a sequence of finer grids and higher 3378 frequencies to remain in the vicinity of the global optimum, inexactly terminated 3379 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 3380 variation operator to capture sharp interfaces, finely discretized by finite 3381 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 3382 implemented in matrix-free fashion with adjoint-based computation of reduced 3383 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 3384 waveform storage, and partitioned spatially across processors to parallelize the 3385 solutions of the forward and adjoint wave equations and the evaluation of 3386 gradient-like information. Several numerical examples demonstrate the grid 3387 independence of linear and nonlinear iterations, the effectiveness of the 3388 preconditioner, the ability to solve inverse problems with up to 17 million 3389 inversion parameters on up to 2048 processors, the effectiveness of multiscale 3390 continuation in keeping iterates in the basin of attraction of the global minimum, 3391 and the ability to fit the observational data while reconstructing the model with 3392 reasonable resolution and capturing sharp interfaces.}, 3393 petsc_uses = {KSP} 3394} 3395 3396% LiteralHTML: 3397% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 3398% LiteralHTML: 3399% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3400% LiteralHTML:<font color="#FF0000"> 3401% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 3402% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 3403% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 3404% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 3405% LiteralHTML:for a variety of these simulations.</p> 3406% LiteralHTML:</font> 3407% LiteralHTML: 3408@Article{ mills2009modeling, 3409 title = {Modeling subsurface reactive flows using leadership-class computing}, 3410 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 3411 Mahinthakumar, G.K. and Smith, B.F.}, 3412 journal = {Journal of Physics: Conference Series}, 3413 volume = {180}, 3414 pages = {012062}, 3415 year = {2009}, 3416 publisher = {IOP Publishing}, 3417 petsc_uses = {KSP} 3418} 3419 3420@Conference{ mills2007simulating, 3421 title = {{Simulating subsurface flow and transport on ultrascale computers using 3422 PFLOTRAN}}, 3423 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 3424 booktitle = {Journal of Physics: Conference Series}, 3425 volume = {78}, 3426 pages = {012051}, 3427 year = {2007}, 3428 organization = {IOP Publishing}, 3429 petsc_uses = {KSP} 3430} 3431 3432@InProceedings{ mills2009, 3433 title = {Modeling subsurface reactive flows using leadership-class computing}, 3434 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 3435 Mahinthakmuar, G. and Smith, B.}, 3436 booktitle = {Journal of Physics: Conference Series}, 3437 volume = {180}, 3438 pages = {102062}, 3439 year = {2009}, 3440 organization = {IOP Publishing}, 3441 petsc_uses = {KSP} 3442} 3443 3444@Article{ guo2013parallel, 3445 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 3446 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 3447 }, 3448 journal = {Advances in Water Resources }, 3449 volume = {53}, 3450 number = {0}, 3451 pages = {101 - 108}, 3452 year = {2013}, 3453 note = {}, 3454 issn = {0309-1708}, 3455 doi = {10.1016/j.advwatres.2012.10.010}, 3456 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 3457 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 3458 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 3459 preconditioner}, 3460 petsc_uses = {KSP} 3461} 3462 3463@Unpublished{ stomp, 3464 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 3465 url = {http://stomp.pnl.gov/}, 3466 petsc_uses = {KSP} 3467} 3468 3469@InProceedings{ htfc2003, 3470 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 3471 title = {Methods and Experiences For Parallelizing Flood Models}, 3472 year = {2003}, 3473 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 3474 European PVM/MPI User's Group Meeting}, 3475 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 3476 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 3477 petsc_uses = {KSP} 3478} 3479 3480@InProceedings{ hulchy-tran-astalos-fmsip, 3481 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 3482 D.Froehlich}, 3483 title = {Flood Modeling System and Its Parallelization}, 3484 year = {2002}, 3485 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 3486 Engineering}, 3487 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 3488 petsc_uses = {KSP} 3489} 3490 3491@InProceedings{ gy1, 3492 author = {J. P. Gwo and G. T. Yeh}, 3493 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 3494 Transport at Watershed Scale}, 3495 year = {2004}, 3496 booktitle = {The International Conference on Computational Methods}, 3497 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 3498 petsc_uses = {KSP} 3499} 3500 3501@Conference{ cheng2009efficient, 3502 title = {{An efficient parallel method for large-scale groundwater flow equation based on 3503 PETSc}}, 3504 author = {Cheng, T. and Ji, X. and Wang, Q.}, 3505 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 3506 Conference on}, 3507 pages = {190--193}, 3508 organization = {IEEE}, 3509 petsc_uses = {KSP} 3510} 3511 3512@Unpublished{ sfrsm, 3513 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 3514 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 3515 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 3516 its linear solves}, 3517 petsc_uses = {KSP} 3518} 3519 3520% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3521@InProceedings{ bart_omar:sc05, 3522 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 3523 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 3524 title = {Dynamic data driven inversion for terascale simulations: real-time 3525 indentification of airborne contaminants}, 3526 booktitle = {Proceedings of SC2005}, 3527 organization = {IEEE/ACM}, 3528 address = {Seattle, WA}, 3529 year = {2005}, 3530 month = {November}, 3531 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 3532 lab = {SNL}, 3533 petsc_uses = {KSP} 3534} 3535 3536@InProceedings{ anton-krassimir-lscc, 3537 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 3538 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 3539 Simulations}, 3540 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 3541 volume = {2907}, 3542 year = {2003}, 3543 publisher = {Springer-Verlag}, 3544 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 3545 petsc_uses = {KSP} 3546} 3547 3548@InProceedings{ aa2001, 3549 author = {Anton Antonov}, 3550 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 3551 year = {2001}, 3552 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 3553 Sozopol, Bulgaria}, 3554 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 3555 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 3556 petsc_uses = {KSP} 3557} 3558 3559% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3560@Article{ grassley-simmons-kercher-00, 3561 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 3562 year = {2000}, 3563 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 3564 reactive transport models}, 3565 journal = {Applied Geochemistry}, 3566 volume = {17}, 3567 pages = {699--708}, 3568 lab = {LLNL} 3569} 3570 3571@Article{ glassey-nitao-03, 3572 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 3573 and Carl I. Steefel and James R. Kercher}, 3574 year = {2003}, 3575 title = {The impact of climate change on vadose zone pore waters and its implication for 3576 long-term monitoring}, 3577 journal = {Computers and Geosciences}, 3578 volume = {29}, 3579 pages = {399-411}, 3580 lab = {LLNL}, 3581 petsc_uses = {KSP} 3582} 3583 3584@Article{ steefel-depaolo-lichtner-05, 3585 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 3586 year = {2005}, 3587 title = {Reactive transport modeling: An essential tool and a new research approach for 3588 the Earth sciences}, 3589 journal = {Earth and Planetary Science Letters}, 3590 lab = {LLNL,LANL}, 3591 petsc_uses = {KSP} 3592} 3593 3594% LiteralHTML:<a name="scalinglarge"> 3595% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3596% LiteralHTML: <center><img alt="" 3597% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 3598% LiteralHTML:<font color="#FF0000"> 3599% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 3600@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 3601 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 3602 Strategies for Large-Scale Numerical Simulations}, 3603 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 3604 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 3605 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 3606 Large-Scale Systems (scalA)}, 3607 pages = {65-72}, 3608 doi = {10.1109/ScalA.2018.00012}, 3609 month = {Nov}, 3610 year = {2018}, 3611 petsc_uses = {KSP} 3612} 3613 3614@Article{ km2004, 3615 author = {A. Keese and H. G. Matthies}, 3616 journal = {Computers and Structures}, 3617 year = {2005}, 3618 volume = {83}, 3619 pages = {1033--1047}, 3620 title = {Hierarchical parallelisation for the solution of stochastic finite element 3621 equations}, 3622 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}, 3623 petsc_uses = {KSP} 3624} 3625 3626@Unpublished{ hvl2002, 3627 title = {Numerical Modeling of NAPL Source Zone Treatment}, 3628 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 3629 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 3630 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 3631 year = {2002}, 3632 lab = {LANL}, 3633 petsc_uses = {KSP} 3634} 3635 3636@PhDThesis{ hammond2003, 3637 author = {Glenn E. Hammond}, 3638 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 3639 Transport on Supercomputers}, 3640 school = {University of Illinois at Urbana-Champaign}, 3641 year = {2003}, 3642 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 3643 petsc_uses = {KSP} 3644} 3645 3646@Unpublished{ uk, 3647 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 3648 Scale Environmental Flows and Transport Processes}, 3649 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 3650 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 3651 buildings and in Green Bay. Used PETSc for its linear solvers}, 3652 year = {1999}, 3653 petsc_uses = {KSP} 3654} 3655 3656@InProceedings{ hammond2002, 3657 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 3658 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 3659 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 3660 year = {2002}, 3661 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 3662 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 3663 Resources, Delft, The Netherlands.}, 3664 lab = {LANL}, 3665 petsc_uses = {KSP} 3666} 3667 3668@TechReport{ steefel1, 3669 author = {C. I. Steefel}, 3670 title = {Software for modeling multicomponent, multidimensional reactive transport}, 3671 year = {2001}, 3672 institution = {Lawrence Livermore National Laboratory}, 3673 number = {UCRL-MA-143182}, 3674 lab = {LLNL}, 3675 petsc_uses = {KSP} 3676} 3677 3678@Article{ steefel2, 3679 author = {C. I. Steefel and A. C. Lasaga}, 3680 title = {A coupled model for transport of multiple chemical-species and kinetic 3681 precipitation dissolution reactions with application to reactive flow in 3682 single-phase hydrothermal systems}, 3683 journal = {Americal Journal of Science}, 3684 year = {1994}, 3685 pages = {529-592}, 3686 volume = {294}, 3687 number = {5}, 3688 petsc_uses = {KSP} 3689} 3690 3691@TechReport{ steefel3, 3692 author = {C. I. Steefel and S. B. Yabusaki}, 3693 title = {OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: 3694 User's manual and programmer's guide}, 3695 year = {1996}, 3696 institution = {Pacific Northwest National Laboratory}, 3697 number = {PNNL-11166}, 3698 lab = {PNNL}, 3699 petsc_uses = {KSP} 3700} 3701 3702@Article{ 2005hvl, 3703 author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner}, 3704 title = {Application of {J}acobian-free {N}ewton-{K}rylov with physics-based 3705 preconditioning to biogeochemical transport}, 3706 journal = {Advances in Water Resources}, 3707 year = {2005}, 3708 pages = {359--376}, 3709 volume = {28}, 3710 url = { 3711 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}, 3712 lab = {LANL}, 3713 petsc_uses = {KSP} 3714} 3715 3716@Article{ wang-zabar-05, 3717 author = {J Wang and N Zabaras}, 3718 journal = {Int. J. Heat and Mass Transfer}, 3719 title = {A Markov random field model of contamination source identification in porous 3720 media flow}, 3721 year = {2005}, 3722 petsc_uses = {KSP} 3723} 3724 3725@InBook{ kp1, 3726 author = {Jong G. Kim and Hyoung W. Park}, 3727 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 3728 Media}, 3729 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 3730 title = {Lecture Notes in Computer Science}, 3731 publisher = {Springer-Verlag}, 3732 volume = {3044}, 3733 year = {2004}, 3734 petsc_uses = {KSP} 3735} 3736 3737@Article{ 2001agusm...h32a06k, 3738 author = {{Kim}, J.~G. and {Kim}, J.}, 3739 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 3740 journal = {AGU Spring Meeting Abstracts}, 3741 year = {2001}, 3742 pages = {32-+}, 3743 petsc_uses = {KSP} 3744} 3745 3746@Article{ lzb2005, 3747 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 3748 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 3749 journal = {Journal of Hydraulic Engineering}, 3750 year = {2005}, 3751 volume = {131}, 3752 number = {4}, 3753 pages = {247--258}, 3754 petsc_uses = {KSP} 3755} 3756 3757@Article{ rao2005, 3758 author = {Prasada Rao}, 3759 title = {A parallel RMA2 model for simulating large-scale free surface flows}, 3760 journal = {Environmental Modelling and Software}, 3761 year = {2005}, 3762 pages = {47--53}, 3763 petsc_uses = {KSP} 3764} 3765 3766@InProceedings{ pr1, 3767 author = {Prasada Rao}, 3768 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 3769 Hydrodynamic Flows}, 3770 year = {2003}, 3771 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 3772 Conference}, 3773 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 3774 petsc_uses = {KSP} 3775} 3776 3777@InProceedings{ lichtner2004, 3778 author = {Peter C. Lichtner and Andrew Wolfsberg}, 3779 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 3780 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 3781 Challenge Supercomputing Problem}, 3782 year = {2004}, 3783 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 3784 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 3785 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 3786 lab = {LANL}, 3787 petsc_uses = {KSP} 3788} 3789 3790% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3791@Article{ aba01:petsc-app, 3792 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 3793 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 3794 journal = {Int. J. High Performance Computing Applications}, 3795 year = {2001}, 3796 volume = {15}, 3797 number = {1}, 3798 pages = {13--21}, 3799 month = {Spring}, 3800 petsc_uses = {KSP} 3801} 3802 3803@PhDThesis{ tjb200, 3804 author = {Thomas James Byer}, 3805 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 3806 Facilities}, 3807 school = {Stanford}, 3808 year = {2000}, 3809 petsc_uses = {KSP} 3810} 3811 3812@InProceedings{ puchyr2006, 3813 author = {Peter J. Puchyr}, 3814 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 3815 Win32 Cluster}, 3816 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 3817 note = {Paper number CIPC2006-207}, 3818 year = {2006}, 3819 petsc_uses = {KSP} 3820} 3821 3822@InProceedings{ texas98, 3823 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 3824 and G. A. Pope}, 3825 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 3826 Simulation}, 3827 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 3828 Symposium}, 3829 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 3830 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 3831 year = {1998}, 3832 petsc_uses = {KSP} 3833} 3834 3835% LiteralHTML: 3836% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 3837% LiteralHTML: 3838@Article{ farrellmitchellscottwechsung2021, 3839 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 3840 stationary incompressible {Navier-Stokes} equations}, 3841 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 3842 Wechsung}, 3843 journal = {The SMAI journal of computational mathematics}, 3844 volume = {7}, 3845 pages = {75--96}, 3846 year = {2021}, 3847 petsc_uses = {KSP} 3848} 3849 3850@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 3851 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 3852 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 3853 P MacLachlan and Ray S Tuminaro}, 3854 journal = {SIAM Journal on Scientific Computing}, 3855 number = {0}, 3856 pages = {S70--S91}, 3857 year = {2021}, 3858 petsc_uses = {KSP} 3859} 3860 3861@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 3862 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 3863 hyperelasticity}, 3864 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 3865 Oyar\'ua and Ricardo Ruiz-Baier}, 3866 journal = {Computer Methods in Applied Mechanics and Engineering}, 3867 volume = {374}, 3868 pages = {113562}, 3869 issn = {0045-7825}, 3870 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 3871 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 3872 year = {2021}, 3873 petsc_uses = {KSP} 3874} 3875 3876@Article{ farrellmitchellwechsung2018, 3877 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 3878 {Navier-Stokes} equations at high {Reynolds} number}, 3879 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 3880 journal = {SIAM Journal on Scientific Computing}, 3881 volume = {41}, 3882 number = {5}, 3883 eprint = {1810.03315}, 3884 pages = {A3073-A3096}, 3885 year = {2019}, 3886 petsc_uses = {KSP} 3887} 3888 3889@Article{ hevuikklaij2017, 3890 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 3891 discretized by a finite volume method}, 3892 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 3893 journal = {Journal of Numerical Mathematics}, 3894 volume = {25}, 3895 number = {2}, 3896 pages = {89--105}, 3897 year = {2017}, 3898 petsc_uses = {KSP} 3899} 3900 3901@InProceedings{ zou2015newton, 3902 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 3903 appearance/disappearance}, 3904 author = {Zou, L and Zhao, H and Zhang, H}, 3905 booktitle = {ANS 2015 Annual Meeting, June}, 3906 volume = {7}, 3907 number = {11}, 3908 year = {2015}, 3909 petsc_uses = {KSP} 3910} 3911 3912@Article{ guermond2009nonlinear, 3913 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 3914 Fourier/finite element technique and an interior penalty method}, 3915 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 3916 journal = {Journal of computational physics}, 3917 volume = {228}, 3918 number = {8}, 3919 pages = {2739--2757}, 3920 year = {2009}, 3921 publisher = {Elsevier}, 3922 petsc_uses = {KSP} 3923} 3924 3925@Article{ erzincanlisahin2015, 3926 title = {The numerical simulation of the wing kinematics effects on near wake topology and 3927 aerodynamic performance in hovering Drosophila flight}, 3928 author = {Belkis Erzincanli and Mehmet Sahin}, 3929 journal = {Computers \& Fluids}, 3930 volume = {122}, 3931 pages = {90--110}, 3932 year = {2015}, 3933 publisher = {Elsevier}, 3934 petsc_uses = {KSP} 3935} 3936 3937@Article{ ekensahin2015, 3938 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 3939 structure interaction problems}, 3940 author = {Ali Eken and Mehmet Sahin}, 3941 journal = {International Journal for Numerical Methods in Fluids}, 3942 year = {2015}, 3943 publisher = {Wiley Online Library}, 3944 petsc_uses = {KSP} 3945} 3946 3947@Article{ hwangsucai2015, 3948 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 3949 for transonic full potential equation}, 3950 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 3951 journal = {Computers \& Fluids}, 3952 volume = {110}, 3953 number = {30}, 3954 pages = {96--107}, 3955 year = {2015}, 3956 doi = {10.1016/j.compfluid.2014.04.005}, 3957 petsc_uses = {KSP} 3958} 3959 3960@Article{ yanghwangcai2016, 3961 title = {Nonlinear Preconditioning Techniques for Full-Space Lagrange--Newton Solution of 3962 PDE-Constrained Optimization Problems}, 3963 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 3964 journal = {SIAM Journal on Scientific Computing}, 3965 volume = {38}, 3966 number = {5}, 3967 pages = {A2756--A2778}, 3968 year = {2016}, 3969 petsc_uses = {KSP} 3970} 3971 3972@Article{ khanaidun2011, 3973 author = {Irfan Khan and Cyrus K. Aidun}, 3974 title = {Direct numerical simulation of saturated deformable porous media using parallel 3975 hybrid Lattice-Boltzmann and finite element method}, 3976 journal = {Int. J. Numer. Meth. Eng.}, 3977 volume = {86}, 3978 pages = {1379--1395}, 3979 year = {2011}, 3980 petsc_uses = {KSP} 3981} 3982 3983@Article{ khanaidun2014, 3984 author = {Irfan Khan and Cyrus K. Aidun}, 3985 title = {Modeling the deformation of saturate porous media using direct numerical 3986 simulation}, 3987 journal = {Int. J. Multiphase Flow}, 3988 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 3989 year = {2014}, 3990 petsc_uses = {KSP} 3991} 3992 3993@Article{ mofidi2014simulations, 3994 author = {A. Mofidi and P. M. Carrica}, 3995 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 3996 and Propeller}, 3997 journal = {Computers and Fluids}, 3998 pages = {191--203}, 3999 year = {2014}, 4000 petsc_uses = {KSP} 4001} 4002 4003@Article{ paik2014fluidstructure, 4004 author = {K. Paik and P. M. Carrica}, 4005 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 4006 Surface in a Rolling Tank}, 4007 journal = {Ocean Engineering}, 4008 pages = {201--212}, 4009 year = {2014}, 4010 petsc_uses = {KSP} 4011} 4012 4013@Article{ castro2013bubble, 4014 author = {A. M. Castro and P. M. Carrica}, 4015 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 4016 evaluation and numerical issues}, 4017 journal = {International Journal of Multiphase Flow 57}, 4018 pages = {131--150}, 4019 year = {2013}, 4020 petsc_uses = {KSP} 4021} 4022 4023@Article{ carrica2013turn, 4024 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 4025 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 4026 Dynamic Overset Grids}, 4027 journal = {Journal of Marine Science and Technology}, 4028 pages = {166--181}, 4029 year = {2013}, 4030 petsc_uses = {KSP} 4031} 4032 4033@Article{ castro2013eulerian, 4034 author = {A. M. Castro and P. M. Carrica}, 4035 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 4036 {Athena} {R}/V,}, 4037 journal = {International Shipbuilding Progress}, 4038 pages = {403--433}, 4039 year = {2013}, 4040 petsc_uses = {KSP} 4041} 4042 4043@Article{ chase2013overset, 4044 author = {N. Chase and T. Michael and P. M. Carrica}, 4045 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 4046 {Maneuvering} {Conditions}}, 4047 journal = {International Shipbuilding Progress}, 4048 pages = {171--205}, 4049 year = {2013}, 4050 petsc_uses = {KSP} 4051} 4052 4053@Article{ sadathosseini2013wu, 4054 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 4055 Stern}, 4056 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 4057 Free Surge Conditions in Short and Long Head Waves}, 4058 journal = {Ocean Engineering}, 4059 volume = {59}, 4060 pages = {240--273}, 4061 year = {2013}, 4062 petsc_uses = {KSP} 4063} 4064 4065@Article{ chase2013cfd, 4066 author = {N. Chase and P. M. Carrica}, 4067 title = {CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a 4068 Submarine}, 4069 journal = {Ocean Engineering}, 4070 pages = {68--80}, 4071 year = {2013}, 4072 petsc_uses = {KSP} 4073} 4074 4075@Article{ carrica2012cfd, 4076 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 4077 title = {CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 4078 of Moving Rudders and Rotating Propellers}, 4079 journal = {Computers and Fluids 53}, 4080 pages = {117--132}, 4081 year = {2012}, 4082 petsc_uses = {KSP} 4083} 4084 4085@Article{ sakamoto2012urans, 4086 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 4087 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 4088 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 4089 publisher = {Journal of Marine Science and Technology}, 4090 pages = {422--445}, 4091 year = {2012}, 4092 petsc_uses = {KSP} 4093} 4094 4095@Article{ sakamoto2012uransb, 4096 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 4097 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 4098 Analysis and Validation of Local Flow Characteristics}, 4099 journal = {Journal of Marine Science and Technology}, 4100 pages = {446--468}, 4101 year = {2012}, 4102 petsc_uses = {KSP} 4103} 4104 4105@Article{ li2012dynamic, 4106 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 4107 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 4108 journal = {Renewable Energy}, 4109 pages = {285--298}, 4110 year = {2012}, 4111 petsc_uses = {KSP} 4112} 4113 4114@Article{ huang2012a, 4115 author = {J. Huang and P. M. Carrica and F. Stern}, 4116 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 4117 journal = {International Journal for Numerical Methods in Fluids}, 4118 pages = {160--180}, 4119 year = {2012}, 4120 petsc_uses = {KSP} 4121} 4122 4123@Article{ huang2012b, 4124 author = {J. Huang and P. M. Carrica and F. Stern}, 4125 title = {A geometry-based level set method for curvilinear overset grids with application 4126 to ship hydrodynamics}, 4127 journal = {International Journal for Numerical Methods in Fluids}, 4128 pages = {494--521}, 4129 year = {2012}, 4130 petsc_uses = {KSP} 4131} 4132 4133@Article{ carrica2011computations, 4134 author = {P. M. Carrica and H. Fu and F. Stern}, 4135 title = {Computations of self-propulsion free to sink and trim and of motions in head 4136 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 4137 journal = {Applied Ocean Research}, 4138 pages = {309--320}, 4139 year = {2011}, 4140 petsc_uses = {KSP} 4141} 4142 4143@Article{ bhushan2011scalability, 4144 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 4145 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 4146 Using {CFDShip}-Iowa}, 4147 journal = {International Journal of High Performance Computing Applications}, 4148 pages = {466--487}, 4149 year = {2011}, 4150 petsc_uses = {KSP} 4151} 4152 4153@Article{ castro2011full, 4154 author = {A. M. Castro and P. M. Carrica and F. Stern}, 4155 title = {Full scale self-propulsion computations using discretized propeller for the 4156 {KRISO} container ship {KCS}}, 4157 journal = {Computers and Fluids}, 4158 pages = {35--47}, 4159 year = {2011}, 4160 petsc_uses = {KSP} 4161} 4162 4163@Article{ kandasamy2011multifidelity, 4164 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 4165 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 4166 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran 4167 for Low Wake}, 4168 journal = {Journal of Marine Science and Technology}, 4169 pages = {143--156}, 4170 year = {2011}, 4171 petsc_uses = {KSP} 4172} 4173 4174@Article{ kandasamy2011cfd, 4175 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 4176 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 4177 title = {CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran}, 4178 journal = {Journal of Marine Science and Technology}, 4179 pages = {157--167}, 4180 year = {2011}, 4181 petsc_uses = {KSP} 4182} 4183 4184@Article{ sadathosseini2011cfd, 4185 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 4186 and S. Yamamura and A. Mastuda}, 4187 title = {CFD System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 4188 Periodic Motion and Broaching}, 4189 journal = {Ocean Engineering}, 4190 pages = {88--110}, 4191 year = {2011}, 4192 petsc_uses = {KSP} 4193} 4194 4195@Article{ mosaviraad2010development, 4196 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 4197 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 4198 with Comparison to Regular Wave and Transient Wave Group Procedures Using 4199 {URANS}}, 4200 journal = {Ocean Engineering}, 4201 pages = {653--666}, 4202 year = {2010}, 4203 petsc_uses = {KSP} 4204} 4205 4206@Article{ carrica2010largescale, 4207 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4208 Stern}, 4209 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 4210 Heave Problems for a Surface Combatant}, 4211 journal = {Computers and Fluids}, 4212 pages = {1095--1111}, 4213 year = {2010}, 4214 petsc_uses = {KSP} 4215} 4216 4217@Article{ carrica2010selfpropulsion, 4218 author = {P. M. Carrica and A. M. Castro and F. Stern}, 4219 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 4220 with Dynamic Overset Grids}, 4221 journal = {Journal of Marine Science and Technology}, 4222 pages = {316--330}, 4223 year = {2010}, 4224 petsc_uses = {KSP} 4225} 4226 4227@Article{ ismail2010evaluation, 4228 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 4229 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 4230 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 4231 journal = {International Journal of Numerical Methods in Fluids}, 4232 pages = {850--886}, 4233 year = {2010}, 4234 petsc_uses = {KSP} 4235} 4236 4237@Article{ kandasamy2010integral, 4238 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 4239 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 4240 journal = {Journal of Fluids Engineering}, 4241 pages = {101103}, 4242 year = {2010}, 4243 petsc_uses = {KSP} 4244} 4245 4246@Article{ kirk:2014de, 4247 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 4248 title = {{Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) 4249 stabilized finite element flow solver}}, 4250 journal = {Computers {\&} Fluids}, 4251 year = {2014}, 4252 volume = {92}, 4253 number = {0}, 4254 pages = {281--292}, 4255 month = mar, 4256 petsc_uses = {KSP} 4257} 4258 4259@Article{ carracciuolo20111382, 4260 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 4261 in high performance computing environment}, 4262 journal = {Journal of Non-Newtonian Fluid Mechanics }, 4263 volume = {166}, 4264 number = {23--24}, 4265 pages = {1382--1395}, 4266 year = {2011}, 4267 issn = {0377-0257}, 4268 doi = {10.1016/j.jnnfm.2011.08.014}, 4269 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 4270 Maffettone and A. Murli}, 4271 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 4272 method, High performance computing}, 4273 petsc_uses = {KSP} 4274} 4275 4276@Article{ bungartzgatzhammerliebmehlneckel11, 4277 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 4278 Miriam and Neckel, Tobias}, 4279 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 4280 journal = {Computational Mechanics}, 4281 volume = {48}, 4282 number = {3}, 4283 pages = {365-376}, 4284 year = {2011}, 4285 issn = {0178-7675}, 4286 doi = {10.1007/s00466-011-0626-1}, 4287 publisher = {Springer-Verlag}, 4288 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 4289 Thermohydraulics; Two-phase flow}, 4290 language = {English}, 4291 petsc_uses = {KSP} 4292} 4293 4294@Article{ bpr:cfl, 4295 author = {H.~M. B{\"u}cker and B. Pollul and A. Rasch}, 4296 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 4297 Equations}}, 4298 journal = {International Journal for Numerical Methods in Fluids}, 4299 year = {2009}, 4300 volume = {59}, 4301 number = {1}, 4302 pages = {1--18}, 4303 doi = {10.1002/fld.1798}, 4304 petsc_uses = {KSP} 4305} 4306 4307@InBook{ bonfiglioli_campobasso_carpentieri_2010, 4308 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 4309 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 4310 preconditioned newton-krylov solver}, 4311 publisher = {Curran Associates}, 4312 year = {2010}, 4313 url = {http://www.proceedings.com/05932.html}, 4314 petsc_uses = {KSP} 4315} 4316 4317@Article{ bonfiglioli_rans_2005, 4318 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 4319 Bernardo}, 4320 title = {RANS simulations of a junction flow}, 4321 journal = {International Journal of Computational Fluid Dynamics}, 4322 volume = {19}, 4323 number = {2}, 4324 pages = {179-189}, 4325 year = {2005}, 4326 doi = {10.1080/10618560410001729126}, 4327 petsc_uses = {KSP} 4328} 4329 4330@InCollection{ bonfiglioli__carpentieri_rans_2008, 4331 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 4332 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 4333 Italy}, 4334 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 4335 Equations Using Fluctuation Splitting Schemes}, 4336 booktitle = {Numerical Mathematics and Advanced Applications}, 4337 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 4338 publisher = {Springer Berlin Heidelberg}, 4339 isbn = {978-3-540-69777-0}, 4340 pages = {151-158}, 4341 doi = {10.1007/978-3-540-69777-0_17}, 4342 year = {2008}, 4343 petsc_uses = {KSP} 4344} 4345 4346@InCollection{ bonfiglioli__carpentieri_ens_2007, 4347 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 4348 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 4349 Italy}, 4350 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 4351 Problems on Unstructured Grids}, 4352 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 4353 series = {Lecture Notes in Computer Science}, 4354 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 4355 publisher = {Springer Berlin / Heidelberg}, 4356 isbn = {978-3-540-75754-2}, 4357 pages = {676-685}, 4358 volume = {4699}, 4359 doi = {10.1007/978-3-540-75755-9_83}, 4360 year = {2007}, 4361 petsc_uses = {KSP} 4362} 4363 4364@Article{ terrelscottknepleykirby08, 4365 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 4366 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 4367 journal = {BIT}, 4368 volume = {48}, 4369 number = {2}, 4370 year = {2008}, 4371 petsc_uses = {KSP} 4372} 4373 4374@Article{ martamadermartinsweidealonso07, 4375 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 4376 J. Alonso}, 4377 title = {A methodology for the development of discrete adjoint solvers using automatic 4378 differentiation tools}, 4379 journal = {Computational Fluid Dyanmics}, 4380 volume = {21}, 4381 pages = {307--327}, 4382 year = {2007}, 4383 petsc_uses = {KSP} 4384} 4385 4386@TechReport{ avb2008, 4387 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 4388 title = {Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface 4389 Waves}, 4390 year = {2008}, 4391 institution = {University of Twente, the Netherlands}, 4392 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 4393 petsc_uses = {KSP} 4394} 4395 4396@InProceedings{ bdsm2005, 4397 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal}, 4398 title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids}, 4399 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit}, 4400 year = {2005}, 4401 url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}, 4402 petsc_uses = {KSP} 4403} 4404 4405@InProceedings{ ms2006, 4406 author = {S. Muller and Y. Stiriba}, 4407 title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR 4408 STEADY COMPRESSIBLE FLOWS}, 4409 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006}, 4410 year = {2006}, 4411 url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}, 4412 petsc_uses = {KSP} 4413} 4414 4415@Article{ araujoteixeiracunhagroth08, 4416 author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth}, 4417 title = {Parallel three-dimensional simulation of the injection molding process}, 4418 journal = {International Journal for Numerical Methods in Fluids}, 4419 year = {2008}, 4420 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 4421 petsc_uses = {KSP} 4422} 4423 4424@PhDThesis{ a2008, 4425 author = {A. Cubero}, 4426 title = {a parallel coupled algorithm for collocated grids and its application to Large 4427 Eddy Simulation of a turbulent wake}, 4428 school = {University of Zaragoza (Spain)}, 4429 year = {2008}, 4430 petsc_uses = {KSP} 4431} 4432 4433@Article{ afa2007, 4434 author = {A. Cubero and N. Fueyo}, 4435 title = {A Compact Momentum Interpolation Method for unsteady flows and relaxation}, 4436 journal = {Numerical Heat Transfer, part B-Fundamentals}, 4437 volume = {56}, 4438 number = {6}, 4439 pages = {507--529}, 4440 year = {2007}, 4441 url = {http://www.informaworld.com/smpp/content~content=a782025305~db=all~order=page}, 4442 petsc_uses = {KSP} 4443} 4444 4445@TechReport{ af2007, 4446 title = {Preconditioning based on a partially implicit implementation of Momentum 4447 Interpolation for coupled solvers}, 4448 institution = {Fluid Mechanics Group of the University of Zaragoza (Spain)}, 4449 year = {2007}, 4450 author = {A. Cubero and N. Fueyo}, 4451 petsc_uses = {KSP} 4452} 4453 4454@InCollection{ dwight2004, 4455 author = {Richard Dwight}, 4456 title = {Robust Mesh Deformation using the Linear Elasticity Equations}, 4457 booktitle = {Computational Fluid Dynamics 2006}, 4458 editor = {H. Deconinck and E. Dick}, 4459 publisher = {Springer}, 4460 year = {2006}, 4461 url = {http://www.maths.man.ac.uk/\~{ 4462 }rdwight/pub/rdwight-ICCFD4-LinElastDeformation-2006.pdf}, 4463 petsc_uses = {KSP} 4464} 4465 4466@InProceedings{ dwight2006, 4467 author = {Richard Dwight and Joel Brezillon}, 4468 title = {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based 4469 Optimization}, 4470 booktitle = {Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. 4471 AIAA-2006-0690}, 4472 year = {2006}, 4473 url = {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-AIAAReno-ApproxAdjoint.pdf}, 4474 petsc_uses = {KSP} 4475} 4476 4477@PhDThesis{ dwight2006a, 4478 author = {Richard Dwight}, 4479 title = {Efficiency Improvements of {RANS}-Based Analysis and Optimization using Implicit 4480 and Adjoint Methods on Unstructured Grids}, 4481 school = {School of Mathematics, University of Manchester}, 4482 year = {2006}, 4483 url = {http://www.maths.man.ac.uk/\~{ 4484 }rdwight/pub/rdwight-PhDThesis-ImplicitAndAdjoint.pdf}, 4485 petsc_uses = {KSP} 4486} 4487 4488@InProceedings{ lhdfrh, 4489 author = {M. Lauter and D. Handorf and K. Dethloff and S. Frickenhaus and N. Rakowsky and 4490 W. Hiller}, 4491 title = {An adaptive Lagrange-Galerkin shallow-water model on the sphere}, 4492 booktitle = {Workshop Proceedings Current Development in Shallow Water Models on the Sphere 4493 March, 10-14, 2003, Munich University of Technology, German}, 4494 year = {2003}, 4495 petsc_uses = {KSP} 4496} 4497 4498@InProceedings{ brios-ying-2002, 4499 author = {George Biros and Lexing Ying and Denis Zorin}, 4500 title = {The Embedded Boundary Integral Method (EBI) for the Incompressible 4501 {Navier-Stokes} equations}, 4502 booktitle = {IABEM 2002, International Association for Boundary Element Methods, UT Austin}, 4503 year = {2002}, 4504 petsc_uses = {KSP} 4505} 4506 4507@InProceedings{ mohsen-straatman-ins, 4508 author = {S.A. Mohsen Karimian and Anthony G. Straatman}, 4509 title = {Benchmarking of a {3D}, unstructured, finite volume code for incompressible 4510 {Navier-Stokes} equation on a cluster of distributed-memory computers}, 4511 booktitle = {Proceedings of the 19th International Symposium on High Performance Computing 4512 Systems and Applications}, 4513 pages = {11--16}, 4514 year = {2005}, 4515 url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046}, 4516 petsc_uses = {KSP} 4517} 4518 4519@TechReport{ bonglioli-icnmfd98, 4520 title = {Multidimensional Residual Distribution Schemes for the Pseudo-Compressible 4521 {Euler} and {Navier-Stokes} equations on Unstructured Meshes}, 4522 institution = {Universita della Basilicata via della Tecnica 3}, 4523 year = {1996}, 4524 author = {A. Bonglioli}, 4525 url = {http://www.unibas.it/utenti/bonfiglioli/icnmfd98.ps.gz}, 4526 petsc_uses = {KSP} 4527} 4528 4529@Article{ deng-piquet-ctf, 4530 author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"}, 4531 title = {A new fully coupled method for computing turbulent flows}, 4532 journal = {Computers and Fluids}, 4533 volume = {30}, 4534 pages = {445--472}, 4535 year = {2001}, 4536 petsc_uses = {KSP} 4537} 4538 4539@InProceedings{ knepleysarinsameh99b, 4540 title = {Multilevel Preconditioning for Parallel {CFD}}, 4541 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 4542 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 4543 Problems In Industrial Applications}, 4544 address = {Minneapolis, MN}, 4545 month = {June}, 4546 year = {1999}, 4547 petsc_uses = {KSP} 4548} 4549 4550@InProceedings{ garbey1, 4551 author = {M. Garbey and B. Hadri and W. Shyy.}, 4552 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 4553 Problems on the Grid}, 4554 booktitle = {Aerospace Sciences Meeting and Exhibit}, 4555 note = {Paper No. 2005-1386}, 4556 year = {2005}, 4557 petsc_uses = {KSP} 4558} 4559 4560@Article{ carrica2007unsteady, 4561 title = {An unsteady single-phase level set method for viscous free surface flows}, 4562 author = {Carrica, PM and Wilson, RV and Stern, F.}, 4563 journal = {International Journal for Numerical Methods in Fluids}, 4564 volume = {53}, 4565 number = {2}, 4566 pages = {229--256}, 4567 year = {2007}, 4568 publisher = {Chichester; New York: Wiley, c1981-}, 4569 petsc_uses = {KSP} 4570} 4571 4572@Article{ pctw2004, 4573 author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber}, 4574 title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of 4575 Spillways}, 4576 journal = {Journal of Hydraulic Research}, 4577 note = {accepted for publication}, 4578 year = {2004}, 4579 petsc_uses = {KSP} 4580} 4581 4582@Article{ wcs2004, 4583 author = {R. V. Wilson and P. M. Carrica and F. Stern}, 4584 title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface 4585 Combatant}, 4586 journal = {Computers and Fluids}, 4587 note = {in press}, 4588 year = {2004}, 4589 petsc_uses = {KSP} 4590} 4591 4592@Article{ cws2005, 4593 author = {P. M. Carrica and R. V. Wilson and F. Stern}, 4594 title = {Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem}, 4595 journal = {Computers and Fluids}, 4596 note = {accepted for publication}, 4597 year = {2005}, 4598 petsc_uses = {KSP} 4599} 4600 4601@Article{ chndss2010, 4602 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4603 Stern}, 4604 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 4605 Heave Problems for a Surface Combatant}, 4606 journal = {Computers and Fluids}, 4607 year = {2010}, 4608 volume = {39}, 4609 number = {7}, 4610 pages = {1095--1111}, 4611 petsc_uses = {KSP} 4612} 4613 4614@InProceedings{ chnkss2008, 4615 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4616 Stern}, 4617 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 4618 Grids}, 4619 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 4620 year = {2008}, 4621 petsc_uses = {KSP} 4622} 4623 4624@MastersThesis{ mtj, 4625 author = {M. T. Jozkowski}, 4626 title = {Application of Algebraic Multigrid Methods to the Solution of Stratified Flows 4627 About Submerged Bodies}, 4628 school = {The Pennsylvania State University}, 4629 year = {2005}, 4630 petsc_uses = {KSP} 4631} 4632 4633@Article{ pp, 4634 author = {E. G. Paterson and L. J. Peltier}, 4635 title = {Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and 4636 Wakes}, 4637 journal = {ASME Journal of Fluids Engineering}, 4638 note = {In press}, 4639 year = {2005}, 4640 petsc_uses = {KSP} 4641} 4642 4643@Article{ eps, 4644 author = {B. A. Edge and E. G. Paterson and G. Settles}, 4645 title = {Computational Study of the Wake and Contaminant Transport of a Walking Human}, 4646 journal = {ASME Journal of Fluids Engineering}, 4647 note = {In press}, 4648 year = {2005}, 4649 petsc_uses = {KSP} 4650} 4651 4652@InProceedings{ rp, 4653 author = {B. Racine and E. G. Paterson}, 4654 title = {Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines 4655 Using Unsteady {RANS} {CFD}}, 4656 booktitle = {35th AIAA Fluid Dynamics Conference and Exhibit}, 4657 year = {2005}, 4658 petsc_uses = {KSP} 4659} 4660 4661@InProceedings{ etpp, 4662 author = {B. A. Edge and M. F. Trujillo and E. G. Paterson and L. J. Peltier}, 4663 title = {Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids 4664 and DES}, 4665 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 4666 year = {2004}, 4667 petsc_uses = {KSP} 4668} 4669 4670@InProceedings{ pp8, 4671 author = {E. G. Paterson and L. J. Peltier}, 4672 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 4673 refinement grids and detached-eddy simulation}, 4674 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 4675 year = {2004}, 4676 petsc_uses = {KSP} 4677} 4678 4679@InProceedings{ mzwp, 4680 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 4681 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 4682 booktitle = {25th Symposium on Naval Hydrodynamics}, 4683 year = {2004}, 4684 petsc_uses = {KSP} 4685} 4686 4687@InProceedings{ ppph, 4688 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 4689 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 4690 booktitle = {25th Symposium on Naval Hydrodynamics}, 4691 year = {2004}, 4692 petsc_uses = {KSP} 4693} 4694 4695@InProceedings{ ppd, 4696 author = {E. G. Paterson and L. J. Peltier}, 4697 title = {Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes}, 4698 booktitle = {Symposium on LES Advancements and Applications, ASME FED Summer Meeting}, 4699 year = {2004}, 4700 petsc_uses = {KSP} 4701} 4702 4703@InProceedings{ bp, 4704 author = {W. J. Baker and E. G. and Paterson}, 4705 title = {Simulation of Steady Circulation Control for the General Aviation Circulation 4706 Control Wing}, 4707 booktitle = {NASA/ONR Workshop on Circulation Control}, 4708 year = {2004}, 4709 petsc_uses = {KSP} 4710} 4711 4712@InProceedings{ pb, 4713 author = {E. G. Paterson and W. J. Baker}, 4714 title = {RANS and Detached-Eddy Simulation of the NCCR airfoil}, 4715 booktitle = {NASA/ONR Workshop on Circulation Control}, 4716 year = {2004}, 4717 petsc_uses = {KSP} 4718} 4719 4720@InProceedings{ pb3, 4721 author = {E. G. Paterson and W. J. Baker}, 4722 title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control 4723 Surfaces}, 4724 booktitle = {42nd AIAA Aerospace Sciences Meeting}, 4725 year = {2004}, 4726 petsc_uses = {KSP} 4727} 4728 4729@InProceedings{ gid1, 4730 author = {G. Frank and J. D'Elia}, 4731 title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model}, 4732 year = {2004}, 4733 booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD}, 4734 url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf}, 4735 petsc_uses = {KSP} 4736} 4737 4738@InBook{ b1, 4739 author = {A.Bonfiglioli}, 4740 chapter = {On the use of the PETSc library for unstructured {CFD} applications}, 4741 year = {2001}, 4742 title = {Science and Supercomputing at CINECA}, 4743 pages = {397--400}, 4744 petsc_uses = {KSP} 4745} 4746 4747@InProceedings{ b2004, 4748 author = {L. A. Barba}, 4749 title = {Computing high-Reynolds number vortical flows: a highly accurate method with a 4750 fully meshless formulation}, 4751 year = {2004}, 4752 booktitle = {International Conference on Parallel CFD, Grand Canary, May 2004}, 4753 note = {Submitted}, 4754 petsc_uses = {KSP} 4755} 4756 4757@InProceedings{ bl2004, 4758 author = {L. A. Barba and A. Leonard}, 4759 title = {Computation of Viscous Vortices with Fully Meshless Method}, 4760 year = {2004}, 4761 booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004}, 4762 note = {Submitted}, 4763 petsc_uses = {KSP} 4764} 4765 4766@Article{ vws1, 4767 author = {B. G. M. Van Wachem and J. C. Schouten}, 4768 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 4769 Velocity}, 4770 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 4771 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 4772 Netherlands}, 4773 journal = {AIChE}, 4774 volumne = {48}, 4775 number = {12}, 4776 month = {December}, 4777 year = {2002}, 4778 petsc_uses = {KSP} 4779} 4780 4781@TechReport{ lbam1, 4782 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 4783 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 4784 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 4785 di Bari Italy}, 4786 year = {2002}, 4787 number = {25/02}, 4788 petsc_uses = {KSP} 4789} 4790 4791@Article{ kees_miller_02, 4792 author = {C. E. Kees and C. T. Miller}, 4793 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 4794 journal = {Advances in Water Resources}, 4795 year = {2002}, 4796 volume = {25}, 4797 number = {2}, 4798 pages = {159-177.}, 4799 petsc_uses = {KSP} 4800} 4801 4802@InProceedings{ lepotmeersessers2001, 4803 author = {I. Lepot and F. Meers and J.A. Essers}, 4804 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 4805 Unstructured Meshes}, 4806 year = {2001}, 4807 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 4808 url = {http://www.ulg.ac.be/aerodyn}, 4809 petsc_uses = {KSP} 4810} 4811 4812@InProceedings{ knepley98, 4813 author = {Matthew Knepley and Denis Vanderstraeten}, 4814 title = {Parallel Building Blocks for Finite Element Simulations: Application to 4815 Solid-Liquid Mixture Flows}, 4816 booktitle = {Proceedings of Parallel CFD'97}, 4817 publisher = {Elsevier}, 4818 pages = {281--287}, 4819 year = {1998}, 4820 petsc_uses = {KSP} 4821} 4822 4823@InProceedings{ pcfd97, 4824 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 4825 title = {Parallel Implicit {PDE} Computations: Algorithms and Software}, 4826 publisher = {Elsevier}, 4827 year = {1998}, 4828 booktitle = {Proceedings of Parallel CFD'97}, 4829 pages = {333-344}, 4830 petsc_uses = {KSP} 4831} 4832 4833@InProceedings{ knepleysamehsari98, 4834 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 4835 title = {Parallel Simulation of Particulate Flows}, 4836 booktitle = {Solving Irregularly Structured Problems in Parallel}, 4837 editors = {A. Ferreira et al}, 4838 year = {1998}, 4839 series = {Lecture Notes in Computer Science}, 4840 volume = {1457}, 4841 pages = {226--237}, 4842 petsc_uses = {KSP} 4843} 4844 4845@Article{ gkmt98, 4846 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 4847 title = {Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel 4848 Implicit {CFD}}, 4849 journal = {Int. J. High Performance Computing Applications}, 4850 year = {2000}, 4851 volume = {14}, 4852 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 4853 pages = {102-136}, 4854 petsc_uses = {KSP} 4855} 4856 4857@InProceedings{ agkks-sc99, 4858 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 4859 Smith}, 4860 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 4861 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 4862 editor = {}, 4863 publisher = {}, 4864 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 4865 year = {1999}, 4866 note = {Winner of Gordon Bell Special Prize at SC 99}, 4867 petsc_uses = {KSP} 4868} 4869 4870@Article{ gkks01, 4871 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4872 title = {High Performance Parallel Implicit {CFD}}, 4873 journal = {Journal of Parallel Computing}, 4874 year = {2001}, 4875 volume = {27}, 4876 pages = {337-362}, 4877 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 4878 petsc_uses = {KSP} 4879} 4880 4881@Article{ cristea-sofonea-02, 4882 author = {Artur Cristea and Victor Sofonea}, 4883 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 4884 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 4885 Sciences, Information Sciences}, 4886 volume = {3}, 4887 number = {3}, 4888 year = {2002}, 4889 petsc_uses = {KSP} 4890} 4891 4892@Article{ cristea2, 4893 author = {Artur Cristea and Victor Sofonea}, 4894 title = {Two component lattice Boltzmann model with flux limiter techniques}, 4895 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 4896 Sciences, Information Sciences}, 4897 volume = {4}, 4898 number = {1}, 4899 year = {2003}, 4900 pages = {59--64}, 4901 petsc_uses = {KSP} 4902} 4903 4904@Article{ cristea1, 4905 author = {Artur Cristea and Victor Sofonea}, 4906 title = {Two component lattice Boltzmann model with flux limiters}, 4907 journal = {Central European Journal of Physics}, 4908 volume = {2}, 4909 number = {2}, 4910 year = {2004}, 4911 pages = {382--396}, 4912 petsc_uses = {KSP} 4913} 4914 4915@Article{ sofnea-lamura1, 4916 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 4917 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 4918 systems}, 4919 journal = {Physical Review E}, 4920 volume = {70}, 4921 number = {4}, 4922 year = {2004}, 4923 pages = {046702-1 / 046702-9}, 4924 petsc_uses = {KSP} 4925} 4926 4927@InProceedings{ gkks01b, 4928 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4929 title = {Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}}, 4930 booktitle = {Proceedings of the First MIT Conference on Computational Fluid and Solid 4931 Mechanics}, 4932 editor = {}, 4933 location = {Cambridge, MA}, 4934 year = {2001}, 4935 month = jun, 4936 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf}, 4937 petsc_uses = {KSP} 4938} 4939 4940@InProceedings{ gkks00, 4941 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4942 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 4943 Code}, 4944 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 4945 (HiPC '2000)}, 4946 editor = {}, 4947 location = {Bangalore, India}, 4948 year = {2000}, 4949 pages = {395--404}, 4950 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 4951 petsc_uses = {KSP} 4952} 4953 4954@InProceedings{ gkks-sc00, 4955 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4956 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 4957 booktitle = {Proceedings of SC2000}, 4958 editor = {}, 4959 publisher = {IEEE Computer Society}, 4960 year = {2000}, 4961 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 4962 petsc_uses = {KSP} 4963} 4964 4965@InProceedings{ knepleysamehsarin99, 4966 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 4967 title = {Design of Large Scale Parallel Simulations}, 4968 booktitle = {Proceedings of Parallel CFD'99}, 4969 editors = {A. {Ecer et al.}}, 4970 publisher = {Elsevier}, 4971 year = {1999}, 4972 petsc_uses = {KSP} 4973} 4974 4975@InProceedings{ gkks-pcfd99, 4976 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 4977 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 4978 booktitle = {Proceedings of Parallel CFD'99}, 4979 editors = {A. {Ecer et al.}}, 4980 publisher = {Elsevier}, 4981 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 4982 year = {1999}, 4983 petsc_uses = {KSP} 4984} 4985 4986@InProceedings{ kks97, 4987 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4988 title = {On the Interaction of Architecture and Algorithm in the Domain-Based 4989 Parallelization of an Unstructured Grid Incompressible Flow Code}, 4990 booktitle = {Proceedings of the 10th International Conference on Domain Decomposition 4991 Methods}, 4992 editor = {J. Mandel et al.}, 4993 pages = {311--319}, 4994 publisher = {Wiley}, 4995 note = {}, 4996 year = {1997}, 4997 petsc_uses = {KSP} 4998} 4999 5000@InProceedings{ kks99, 5001 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 5002 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 5003 Incompressible Flows on Unstructured Grids}, 5004 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 5005 Methods}, 5006 editors = {C.-H. {Lai et al.}}, 5007 publisher = {Domain Decomposition Press, Bergen}, 5008 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 5009 year = {1999}, 5010 petsc_uses = {KSP} 5011} 5012 5013@InCollection{ kks97_cfd, 5014 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 5015 title = {Perspectives for {CFD} on Petaflops Systems}, 5016 booktitle = {CFD Review 1998}, 5017 editor = {M. Hafez and K. Oshima}, 5018 publisher = {World Scientific, Singapore}, 5019 pages = {1079--1096}, 5020 note = {}, 5021 year = {1998}, 5022 petsc_uses = {KSP} 5023} 5024 5025@Article{ hm99, 5026 author = {P. D. Hovland and L. C. McInnes}, 5027 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 5028 {PETSc}}, 5029 year = {2000}, 5030 journal = {Parallel Computing}, 5031 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 5032 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 5033 petsc_uses = {KSP} 5034} 5035 5036@InProceedings{ cruzbarbaknepley08, 5037 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 5038 title = {Fast Multipole Method for particle interactions: an open source parallel library 5039 component}, 5040 booktitle = {Proceedings of ParCFD2008}, 5041 year = {2008}, 5042 editor = {Tromeur-Dervout et. al.}, 5043 publisher = {Elsevier}, 5044 petsc_uses = {KSP} 5045} 5046 5047@Article{ hwangcai05, 5048 author = {F.-N. Hwang and X.-C. Cai}, 5049 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 5050 for incompressible {Navier-Stokes} equations}, 5051 journal = {J. Comput. Phys.}, 5052 volume = {204}, 5053 year = {2005}, 5054 pages = {666--691}, 5055 petsc_uses = {KSP} 5056} 5057 5058@Article{ barbaleonard07, 5059 author = {Lorena A Barba and Anthony Leonard}, 5060 title = {Emergence and evolution of tripole vortices from net-circulation initial 5061 conditions}, 5062 journal = {Phys. Fluids}, 5063 volume = {19}, 5064 pages = {017101}, 5065 year = {2007}, 5066 doi = {10.1063/1.2409734}, 5067 petsc_uses = {KSP} 5068} 5069 5070@Article{ barba07, 5071 author = {Lorena A Barba}, 5072 title = {Non-shielded multipolar vortices at high Reynolds number}, 5073 journal = {Phys. Rev. E}, 5074 volume = {73}, 5075 pages = {065303}, 5076 year = {2006}, 5077 doi = {10.1103/PhysRevE.73.065303}, 5078 petsc_uses = {KSP} 5079} 5080 5081@Article{ schofield2010multi, 5082 title = {Multi-material incompressible flow simulation using the moment-of-fluid method}, 5083 author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and 5084 Lowrie, R.B. and Swartz, B.K.}, 5085 journal = {International Journal for Numerical Methods in Fluids}, 5086 volume = {63}, 5087 number = {8}, 5088 pages = {931--952}, 5089 year = {2010}, 5090 publisher = {Wiley Online Library}, 5091 petsc_uses = {KSP} 5092} 5093 5094% LiteralHTML: 5095% LiteralHTML: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3> 5096% LiteralHTML: 5097% LiteralHTML: article{DeGersem99, 5098% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, 5099% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, 5100% LiteralHTML: } 5101@Article{ nagler2014, 5102 title = {Sound transmission through a poroelastic layered panel}, 5103 author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff}, 5104 journal = {Computational Mechanics}, 5105 volume = {53}, 5106 number = {4}, 5107 pages = {549--560}, 5108 issn = {1432-0924}, 5109 doi = {10.1007/s00466-013-0916-x}, 5110 year = {2014}, 5111 petsc_uses = {KSP} 5112} 5113 5114@Article{ sheikh2013, 5115 author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.}, 5116 title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel 5117 deflation}, 5118 journal = {Numerical Linear Algebra with Applications}, 5119 volume = {20}, 5120 number = {4}, 5121 issn = {1099-1506}, 5122 doi = {10.1002/nla.1882}, 5123 pages = {645--662}, 5124 keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier 5125 analysis}, 5126 year = {2013}, 5127 petsc_uses = {KSP} 5128} 5129 5130@InProceedings{ silence, 5131 author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. 5132 Fuenmayor}, 5133 title = {A parallel computing approach for solving the Helmholtz equation in 3D domains: 5134 Application to the study of acoustic behaviour of silencers}, 5135 year = {2004}, 5136 booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering 5137 (ECCOMAS)}, 5138 petsc_uses = {KSP} 5139} 5140 5141@Article{ degersem99, 5142 author = {H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer}, 5143 title = {Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods 5144 to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations}, 5145 journal = {COMPEL}, 5146 year = {1999}, 5147 volume = {18}, 5148 number = {3}, 5149 pages = {298--310}, 5150 bibdate = {}, 5151 petsc_uses = {KSP} 5152} 5153 5154@InProceedings{ widlund-wave-98, 5155 author = {Olof B. Widlund}, 5156 title = {Schwarz Methods for {H}elmholtz's Equation}, 5157 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 5158 editor = {John A. DeSanto}, 5159 year = {1998}, 5160 publisher = {SIAM}, 5161 pages = {620--622}, 5162 address = {Philadelphia}, 5163 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 5164 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 5165 petsc_uses = {KSP} 5166} 5167 5168@InProceedings{ toselli-wave-98, 5169 author = {Andrea Toselli}, 5170 title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media}, 5171 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 5172 editor = {John A. DeSanto}, 5173 year = {1998}, 5174 publisher = {SIAM}, 5175 address = {Philadelphia}, 5176 pages = {540--542}, 5177 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 5178 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 5179 petsc_uses = {KSP} 5180} 5181 5182@InProceedings{ mcinnes-wave-98, 5183 author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes}, 5184 title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods}, 5185 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 5186 editor = {John A. DeSanto}, 5187 year = {1998}, 5188 publisher = {SIAM}, 5189 address = {Philadelphia}, 5190 pages = {623--625}, 5191 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 5192 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 5193 petsc_uses = {KSP} 5194} 5195 5196@InProceedings{ mska98, 5197 author = {L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi}, 5198 title = {Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the 5199 Parallel Computation of {H}elmholtz Problems}, 5200 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 5201 editor = {J. Mandel et al.}, 5202 publisher = {AMS}, 5203 pages = {349--357}, 5204 year = {1998}, 5205 petsc_uses = {KSP} 5206} 5207 5208@InProceedings{ ccew98, 5209 author = {X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund}, 5210 title = {Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation}, 5211 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 5212 editor = {J. Mandel et al.}, 5213 publisher = {AMS}, 5214 pages = {437-445}, 5215 year = {1998}, 5216 petsc_uses = {KSP} 5217} 5218 5219@InProceedings{ ra98a, 5220 author = {R. Susan-Resiga and H. M. Atassi}, 5221 title = {Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic 5222 Problems}, 5223 booktitle = {Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference}, 5224 publisher = {AIAA}, 5225 pages = {86-96}, 5226 note = {AIAA paper 98-2218}, 5227 year = {1998}, 5228 petsc_uses = {KSP} 5229} 5230 5231@InProceedings{ ar98c, 5232 author = {H. M. Atassi and R. Susan-Resiga}, 5233 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: 5234 General Formulation}, 5235 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 5236 publisher = {ASME}, 5237 note = {NCA-25}, 5238 pages = {375-379}, 5239 year = {1998}, 5240 petsc_uses = {KSP} 5241} 5242 5243@InProceedings{ ra98b, 5244 author = {R. Susan-Resiga and H. M. Atassi}, 5245 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: 5246 Numerical Implementation and Applications}, 5247 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 5248 publisher = {ASME}, 5249 note = {NCA-25}, 5250 pages = {381 -388}, 5251 year = {1998}, 5252 petsc_uses = {KSP} 5253} 5254 5255@InProceedings{ cai-dd10-98, 5256 author = {Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. 5257 Widlund}, 5258 title = {Overlapping {S}chwarz methods for solving {H}elmholtz's Equation}, 5259 booktitle = {Domain Decomposition Methods 10}, 5260 editors = {Jan Mandel and Charbel Farhat and Xiao-Chuan Cai}, 5261 series = {Contemporary Mathematics}, 5262 volume = {218}, 5263 publisher = {American Mathematical Society}, 5264 address = {Providence, Rhode Island}, 5265 year = {1998}, 5266 pages = {437--445}, 5267 petsc_uses = {KSP} 5268} 5269 5270@InProceedings{ alghamdi2011petclaw, 5271 title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython}, 5272 booktitle = {Proceedings of SpringSim 2011}, 5273 publisher = {ACM}, 5274 author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and 5275 Kyle T. Mandli and Lisandro Dalcin}, 5276 year = {2011}, 5277 petsc_uses = {KSP} 5278} 5279 5280@Article{ pyclaw2012, 5281 author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and 5282 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 5283 Emmett}, 5284 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 5285 journal = {SIAM Journal on Scientific Computing}, 5286 volume = {34}, 5287 number = {4}, 5288 pages = {C210--C231}, 5289 note = {\url{http://arxiv.org/abs/1111.6583}}, 5290 year = {2012}, 5291 petsc_uses = {KSP} 5292} 5293 5294% LiteralHTML: 5295% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 5296% LiteralHTML: 5297@Article{ sojkahorakhaplacermak2018, 5298 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 5299 decomposition method}, 5300 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 5301 journal = {Applied Mathematics and Computation}, 5302 volume = {319}, 5303 pages = {586--597}, 5304 year = {2018}, 5305 petsc_uses = {KSP} 5306} 5307 5308@Article{ chencai2014, 5309 title = {A parallel two-level domain decomposition based one-shot method for shape 5310 optimization problems}, 5311 author = {Rongliang Chen and Xiao‐Chuan Cai}, 5312 journal = {International Journal for Numerical Methods in Engineering}, 5313 volume = {99}, 5314 number = {13}, 5315 year = {2014}, 5316 doi = {10.1002/nme.4711}, 5317 petsc_uses = {KSP} 5318} 5319 5320@PhDThesis{ prudencio2005, 5321 author = {Ernesto Prudencio}, 5322 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 5323 for Optimization Problems Constrained by Partial Differential Equations}, 5324 school = {University of Colorado, Boulder}, 5325 year = {2005}, 5326 petsc_uses = {KSP} 5327} 5328 5329@Article{ prudenciocai2007, 5330 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 5331 for {PDE}-constrained optimization}, 5332 author = {Ernesto Prudencio and X. C. Cai}, 5333 journal = {SIAM J. Sci. Comp.}, 5334 volume = {29}, 5335 number = {3}, 5336 pages = {964--985}, 5337 year = {2007}, 5338 petsc_uses = {KSP} 5339} 5340 5341@Article{ prudenciobyrdcai2006, 5342 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 5343 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 5344 {PDE}-constrained Optimization Problems}, 5345 journal = {SIAM J. Sci. Comp.}, 5346 volume = {27}, 5347 pages = {1305--1328}, 5348 year = {2006}, 5349 petsc_uses = {KSP} 5350} 5351 5352@InProceedings{ prudenciobyrdcai2004, 5353 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 5354 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 5355 booktitle = {VECPAR 2004}, 5356 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 5357 publisher = {Springer}, 5358 pages = {569--582}, 5359 year = {2004}, 5360 petsc_uses = {KSP} 5361} 5362 5363@Article{ belhamadia-fortin-pcp, 5364 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 5365 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 5366 journal = {Journal of Computational Physics}, 5367 volume = {201}, 5368 pages = {753-770}, 5369 year = {2004}, 5370 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 5371 petsc_uses = {KSP} 5372} 5373 5374@Article{ biros00, 5375 author = {George Biros and Omar Ghattas}, 5376 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 5377 journal = {SIAG-Opt Views and News}, 5378 volume = {11}, 5379 number = {2}, 5380 year = {2000}, 5381 month = {august}, 5382 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 5383 petsc_uses = {KSP} 5384} 5385 5386@Article{ bmm01, 5387 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 5388 journal = {ACM Transactions on Mathematical Software}, 5389 title = {A case study in the performance and scalability of optimization algorithms}, 5390 year = {2001}, 5391 volume = {27}, 5392 number = {3}, 5393 pages = {361--376}, 5394 petsc_uses = {KSP} 5395} 5396 5397@InProceedings{ oghattas1999, 5398 author = {George Biros and Omar Ghattas}, 5399 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 5400 incompressible flows}, 5401 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 5402 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 5403 year = {1999}, 5404 petsc_uses = {KSP} 5405} 5406 5407@InProceedings{ hkms00, 5408 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 5409 PDE-constrained Optimization}, 5410 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 5411 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 5412 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 5413 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 5414 Hasco\"{e}t and Uwe Naumann}, 5415 publisher = {Springer}, 5416 year = {2002}, 5417 petsc_uses = {KSP} 5418} 5419 5420% old version: replace with biros2005pln1 5421@TechReport{ bg011, 5422 author = {George Biros and Omar Ghattas}, 5423 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 5424 Part I: The Krylov-Schur Solver}, 5425 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 5426 year = {2001}, 5427 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 5428 petsc_uses = {KSP} 5429} 5430 5431% old version: replace with biros2005pln2 5432@TechReport{ bg012, 5433 author = {George Biros and Omar Ghattas}, 5434 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 5435 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 5436 Optimal Control of Steady Viscous Flows}, 5437 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 5438 year = {2001}, 5439 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 5440 petsc_uses = {KSP} 5441} 5442 5443% LiteralHTML: 5444% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 5445% LiteralHTML: 5446@InProceedings{ ly2003, 5447 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 5448 title = {A New Parallel Kernel-independent Fast Multipole Method}, 5449 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 5450 year = {2003}, 5451 note = {Winner of the Best Student Paper at SC2003}, 5452 petsc_uses = {KSP} 5453} 5454 5455@Article{ yokotabarbaknepley10, 5456 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 5457 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 5458 journal = {Computer Methods in Applied Mechanics and Engineering}, 5459 volume = {199}, 5460 number = {25-28}, 5461 pages = {1793--1804}, 5462 url = {http://arxiv.org/abs/0909.5413v1}, 5463 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 5464 year = {2010}, 5465 petsc_uses = {KSP} 5466} 5467 5468@Article{ cruzknepleybarba10, 5469 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 5470 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 5471 journal = {International Journal of Numerical Methods in Engineering}, 5472 volume = {85}, 5473 number = {4}, 5474 pages = {403--428}, 5475 url = {http://arxiv.org/abs/0905.2637}, 5476 note = {\url{http://arxiv.org/abs/0905.2637}}, 5477 year = {2010}, 5478 petsc_uses = {KSP} 5479} 5480 5481% LiteralHTML: 5482% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 5483% LiteralHTML: 5484@Article{ buchanpainumplebysmedleystevenson2012, 5485 title = {A sub-grid scale finite element agglomeration multigrid method with application 5486 to the Boltzmann transport equation}, 5487 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 5488 journal = {International Journal for Numerical Methods in Engineering}, 5489 volume = {92}, 5490 number = {3}, 5491 pages = {318--342}, 5492 year = {2012}, 5493 publisher = {Wiley Online Library}, 5494 petsc_uses = {KSP} 5495} 5496 5497@Article{ magoulesahamedsuzuki2015, 5498 title = {Green computing on graphics processing units}, 5499 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 5500 journal = {Concurrency and Computation: Practice and Experience}, 5501 year = {2015}, 5502 publisher = {Wiley Online Library}, 5503 petsc_uses = {KSP} 5504} 5505 5506@InProceedings{ yanrhodes11, 5507 author = {Yan, Baoqiang and Rhodes, Philip J.}, 5508 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 5509 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 5510 series = {ICPP '11}, 5511 pages = {355--364}, 5512 year = {2011}, 5513 isbn = {978-0-7695-4510-3}, 5514 numpages = {10}, 5515 doi = {10.1109/ICPP.2011.70}, 5516 acmid = {2066965}, 5517 publisher = {IEEE Computer Society}, 5518 address = {Washington, DC, USA}, 5519 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 5520 petsc_uses = {KSP} 5521} 5522 5523@Article{ hakansson2013mdstochasticliouville, 5524 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 5525 Stulz, Eugen}, 5526 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 5527 equation study}, 5528 journal = {Phys. Chem. Chem. Phys.}, 5529 year = {2013}, 5530 volume = {15}, 5531 issue = {26}, 5532 pages = {10930-10941}, 5533 publisher = {The Royal Society of Chemistry}, 5534 doi = {10.1039/C3CP50788B}, 5535 petsc_uses = {KSP} 5536} 5537 5538@Article{ hakansson2011stochasticliouville, 5539 author = {Hakansson, Par and Nair, Prasanth B.}, 5540 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 5541 form}, 5542 journal = {Phys. Chem. Chem. 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Tarucha and John Fettig and Nahil Sobh}, 6077 title = {Spin configurations in circular and rectangular vertical quantum dots in a 6078 magnetic field: Three-dimensional self-consistent simulation}, 6079 year = {2005}, 6080 number = {Arxiv preprint cond-mat/0506585}, 6081 url = {http://arxiv.org/pdf/cond-mat/0506585}, 6082 petsc_uses = {KSP} 6083} 6084 6085@InProceedings{ richard-smedley-03, 6086 author = {Richard P. Smedley-Stevenson}, 6087 title = {PARALLEL THERMAL RADIATION TRANSPORT IN TWO DIMENSIONS}, 6088 year = {2003}, 6089 booktitle = {18th International Conference on Transport Theory (18 ICTT)}, 6090 url = {http://www.iprj.uerj.br/\~{ }ricardob/Evento_Cientifico_html/poster03j.pdf}, 6091 petsc_uses = {KSP} 6092} 6093 6094@Article{ guan-godoy-ravaioli-03, 6095 author = {D. Guan and A. Godoy and U. Ravaioli and F. 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Cooke}, 6160 title = {Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three 6161 Dimensions}, 6162 year = {2004}, 6163 booktitle = {40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit}, 6164 url = {http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282}, 6165 petsc_uses = {KSP} 6166} 6167 6168@InProceedings{ allard-gouranton-ipts2002, 6169 author = {Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin}, 6170 title = {Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster}, 6171 year = {2002}, 6172 booktitle = {Immersive Projection Technology Symposium}, 6173 url = {http://www-id.imag.fr/\~{ }allardj/files/ipts2002.pdf}, 6174 petsc_uses = {KSP} 6175} 6176 6177@Article{ icc, 6178 author = {D Ioan and G Ciuprina and C Ciobotaru}, 6179 title = {Hybrid and concurrent algorithms for nonlinear magnetic field problems}, 6180 journal = {IEEE Transactions on Magnetics}, 6181 year = {2000}, 6182 url = {http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/20/19005/00877735.pdf}, 6183 petsc_uses = {KSP} 6184} 6185 6186@InProceedings{ hs1, 6187 author = {Brian J. 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B. Nik and S. L. Yilmaz and P. Givi and M. R. H. Sheikhi and S. B. Pope}, 6265 title = {Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function}, 6266 journal = {AIAA Journal}, 6267 volume = {48}, 6268 number = {7}, 6269 pages = {1513--1522}, 6270 year = {2010}, 6271 petsc_uses = {KSP} 6272} 6273 6274@Article{ nikyilmazsheikhigivi10, 6275 author = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi}, 6276 title = {Grid Resolution Effects on VSFMDF/LES}, 6277 journal = {Flow, Turbulence and Combustion}, 6278 doi = {10.1007/s10494-010-9272-5}, 6279 year = {2010}, 6280 petsc_uses = {KSP} 6281} 6282 6283@Article{ idema2013towards, 6284 title = {Towards faster solution of large power flow problems}, 6285 author = {Idema, Reijer and Papaefthymiou, Georgios and Lahaye, Domenico and Vuik, Cornelis 6286 and van der Sluis, Lou}, 6287 journal = {Power Systems, IEEE Transactions on}, 6288 volume = {28}, 6289 number = {4}, 6290 pages = {4918--4925}, 6291 year = {2013}, 6292 publisher = {IEEE}, 6293 petsc_uses = {KSP} 6294} 6295 6296@Article{ 6026245, 6297 author = {Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.}, 6298 journal = {Power Systems, IEEE Transactions on}, 6299 title = {Scalable Newton-Krylov Solver for Very Large Power Flow Problems}, 6300 year = {2012}, 6301 month = {Feb}, 6302 volume = {27}, 6303 number = {1}, 6304 pages = {390-396}, 6305 doi = {10.1109/TPWRS.2011.2165860}, 6306 issn = {0885-8950}, 6307 petsc_uses = {KSP} 6308} 6309 6310@Book{ idema2014computational, 6311 title = {Computational Methods in Power System Analysis}, 6312 author = {Idema, Reijer and Lahaye, Domenico JP}, 6313 year = {2014}, 6314 publisher = {Springer}, 6315 petsc_uses = {KSP} 6316} 6317 6318@PhDThesis{ abhyankar2011thesis, 6319 author = {Shrirang Abhyankar}, 6320 title = {Development of an implicitly coupled electromechanical and electromagnetic 6321 transients simulator for power systems}, 6322 school = {Illinois Institute of Technology}, 6323 year = {2011}, 6324 petsc_uses = {KSP} 6325} 6326 6327@InProceedings{ abhyankarhipcna11-1, 6328 author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck}, 6329 title = {Using {PETSc} to develop scalable applications for next-generation power grid}, 6330 year = {2011}, 6331 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 6332 Networking and Analytics for the Power Grid}, 6333 url = {http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf}, 6334 publisher = {ACM}, 6335 petsc_uses = {KSP} 6336} 6337 6338@InProceedings{ abhyankarhipcna11-2, 6339 author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang}, 6340 title = {Development of a parallel three-phase transient stability simulator for power 6341 systems}, 6342 year = {2011}, 6343 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 6344 Networking and Analytics for the Power Grid}, 6345 publisher = {ACM}, 6346 petsc_uses = {KSP} 6347} 6348 6349@InProceedings{ abhyankarpesgeneral2012, 6350 author = {Shrirang Abhyankar and A. Flueck}, 6351 title = {An implicitly-coupled solution approach for combined electromechanical and 6352 electromagnetic transients simulation}, 6353 year = {2012}, 6354 booktitle = {Proceedings of the IEEE PES General Meeting}, 6355 publisher = {IEEE}, 6356 petsc_uses = {KSP} 6357} 6358 6359@Article{ idemalahayevuiksluis2012, 6360 author = {Reijer Idema and Domenico Lahaye and Cornelis Vuik and Lou van der Sluis}, 6361 title = {Scalable Newton-Krylov solver for very large Power Flow problems}, 6362 journal = {IEEE Transactions on Power Systems}, 6363 year = {2012}, 6364 volume = {27}, 6365 pages = {390-396}, 6366 petsc_uses = {KSP} 6367} 6368 6369@Article{ korrestzavellasgalinas2013, 6370 author = {George N. Korres and Anastasios Tzavellas and Evangelos Galinas}, 6371 title = {A distributed implementation of multi-area power system state estimation on a 6372 cluster of computers }, 6373 journal = {Electric Power Systems Research }, 6374 volume = {102}, 6375 number = {0}, 6376 pages = {20 - 32}, 6377 year = {2013}, 6378 issn = {0378-7796}, 6379 doi = {10.1016/j.epsr.2013.04.002}, 6380 petsc_uses = {KSP} 6381} 6382 6383% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 6384% LiteralHTML:<font color="#FF0000"> 6385% LiteralHTML: Material failure, for example, cracking of steel beams resulting 6386% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 6387% LiteralHTML: are important for prediction and prevention. PETSc has been used 6388% LiteralHTML: in a variety of studies of material failure.</p> 6389% LiteralHTML:</font> 6390% LiteralHTML: 6391@InProceedings{ gray2, 6392 author = {Yuan He and Joshua Gray and Richard Braatz and Richard Alkire}, 6393 title = {Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel}, 6394 year = {2004}, 6395 booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}, 6396 petsc_uses = {KSP} 6397} 6398 6399@InProceedings{ gray1, 6400 author = {J. Gray and and C. Homescu and L. Petzold and Richard Alkire}, 6401 title = {Algorithms and Computing Architectures for Solving Differential-Algebraic 6402 Equation Systems Typically Encountered in Models of Corrosion Pit Initiation}, 6403 year = {2003}, 6404 booktitle = {Abstracts of the Electrochemical Society 204th meeting}, 6405 petsc_uses = {KSP} 6406} 6407 6408@InProceedings{ crack2, 6409 author = {Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. 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Ingraffea}, 6430 title = {Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation}, 6431 booktitle = {International Conference ON Computational Engineering and Sciences}, 6432 year = {2002}, 6433 url = {http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf}, 6434 petsc_uses = {KSP} 6435} 6436 6437@InProceedings{ crack, 6438 author = {Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and 6439 Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris 6440 Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis 6441 and Paul A. Wawrzynek}, 6442 title = {Parallel FEM Simulation of Crack Propagation}, 6443 booktitle = {Proceedings of Irregular 2000}, 6444 url = {http://www.cs.cornell.edu/stodghil/papers/irregular00.ps}, 6445 year = {2000}, 6446 petsc_uses = {KSP} 6447} 6448 6449@InProceedings{ beaudoin98, 6450 author = {A. J. Beaudoin}, 6451 title = {Use of Polycrystal Plasticity Theory in Assessing Material Performance}, 6452 booktitle = {Simulation of materials processing: Theory, methods, and applications - 6453 Proceedings of the Sixth International Conference, NUMIFORM'98}, 6454 editor = {J. Hu\'etink and F. P. T. Baaijens}, 6455 optvolume = {}, 6456 optnumber = {}, 6457 optseries = {}, 6458 year = {1998}, 6459 optorganization={}, 6460 publisher = {A. A. Balkema Publishers}, 6461 address = {Rotterdam, Netherlands}, 6462 month = jun, 6463 optpages = {}, 6464 petsc_uses = {KSP} 6465} 6466 6467% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 6468@TechReport{ defordheld1, 6469 author = {JF DeFord and BL Held}, 6470 title = {RF3P-A New Parallel Driven Frequency Electromagnetic Solver}, 6471 year = {2002}, 6472 institution = {Simulation Technology and Applied Research}, 6473 url = {http://www.staarinc.com/support/papers/aces2002.pdf}, 6474 note = {Discusses their parallel commercial solver that uses PETSc}, 6475 petsc_uses = {KSP} 6476} 6477 6478@PhDThesis{ sande2003, 6479 author = {Hans Vande Sande}, 6480 title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic 6481 Quasi-Static Electromagnetic Systems}, 6482 school = {Katholieke Universiteit Leuven, Belgium}, 6483 year = {2003}, 6484 petsc_uses = {KSP} 6485} 6486 6487@Article{ sdchh2004, 6488 author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 6489 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 6490 Tolerance}, 6491 journal = {IEEE Transactions on Magnetics}, 6492 year = {2004}, 6493 volume = {40}, 6494 pages = {1306--1309}, 6495 petsc_uses = {KSP} 6496} 6497 6498@Article{ holst-lindblom-etal:2004, 6499 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 6500 Scheel and Lawrence E. Kidder}, 6501 title = {Optimal constraint projection for hyperbolic evolution systems, }, 6502 journal = {Phys. Rev. D}, 6503 year = {2004}, 6504 volume = {70}, 6505 pages = {084017}, 6506 petsc_uses = {KSP} 6507} 6508 6509@Article{ marm2005, 6510 author = {Matthew Anderson and Richard A. Matzner}, 6511 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 6512 journal = {Foundations of Physics}, 6513 volume = {35}, 6514 pages = {1572--9516}, 6515 year = {2005}, 6516 petsc_uses = {KSP} 6517} 6518 6519@Article{ cook-pfeiffer:2004, 6520 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 6521 title = {Excision boundary conditions for black hole initial data}, 6522 journal = {Phys. Rev. D}, 6523 volume = {70}, 6524 pages = {104016--24}, 6525 year = {2004}, 6526 petsc_uses = {KSP} 6527} 6528 6529@Article{ pfeiffer-kidder-etal:2005, 6530 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 6531 Shoemaker}, 6532 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 6533 journal = {Phys. Rev. D}, 6534 year = {2005}, 6535 volume = {71}, 6536 pages = {024020}, 6537 petsc_uses = {KSP} 6538} 6539 6540@Article{ pfeiffer-kidder-etal:2003, 6541 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 6542 Saul A.}, 6543 title = {A multidomain spectral method for solving elliptic equations}, 6544 journal = {CPC}, 6545 year = {2003}, 6546 volume = {152}, 6547 pages = {253--273}, 6548 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 6549 For a related online version, see arXiv:gr-qc/0202096}, 6550 petsc_uses = {KSP} 6551} 6552 6553@Article{ pfeiffer-cook-teukolsky:2002, 6554 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 6555 title = {Comparing initial-data sets for binary black hole}, 6556 journal = {PRD}, 6557 year = {2002}, 6558 volume = {66}, 6559 pages = {024047}, 6560 note = {for a related online version, seearXiv:gr-qc/0203085}, 6561 petsc_uses = {KSP} 6562} 6563 6564@PhDThesis{ pfeiffer:2003, 6565 author = {Pfeiffer, Harald P.}, 6566 title = {Initial Data for Black Hole Evolutions}, 6567 school = {Cornell University}, 6568 year = {2003}, 6569 petsc_uses = {KSP} 6570} 6571 6572@TechReport{ h1, 6573 author = {Erik Schnetter}, 6574 title = {A fast apparent horizon algorithm}, 6575 year = {2002}, 6576 number = {Arxiv preprint gr-qc/0206003}, 6577 url = {http://arxiv.org/pdf/gr-qc/0206003}, 6578 petsc_uses = {KSP} 6579} 6580 6581@Article{ h2, 6582 author = {Erik Schnetter}, 6583 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 6584 year = {2003}, 6585 journal = {Class. 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Smith}, 6616 year = {2002}, 6617 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 6618 Uintah PSE}, 6619 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 6620 2002}, 6621 pages = {49-55}, 6622 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 6623 note = {Extended abstract}, 6624 petsc_uses = {KSP} 6625} 6626 6627@Unpublished{ ep1, 6628 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 6629 author = {Bradley R. Eccleston and Todd S. Palmer}, 6630 institution = {Department of Nuclear Engineering, Oregon State University}, 6631 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 6632 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 6633 Parallel Simulations}, 6634 year = {1999}, 6635 petsc_uses = {KSP} 6636} 6637 6638@InProceedings{ teo2007scalable, 6639 title = {A scalable modular convex solver for regularized risk minimization}, 6640 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 6641 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 6642 discovery and data mining}, 6643 pages = {727--736}, 6644 year = {2007}, 6645 organization = {ACM}, 6646 petsc_uses = {KSP} 6647} 6648 6649@InProceedings{ rm02, 6650 author = {Robert Malouf}, 6651 year = {2002}, 6652 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 6653 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 6654 (CoNLL-2002)}, 6655 pages = {49-55}, 6656 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 6657 petsc_uses = {KSP} 6658} 6659 6660@Unpublished{ hrv02, 6661 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 6662 author = {V. Hernandex and J. E. Roman and V. Vidal}, 6663 note = {Submitted to CMMSE}, 6664 petsc_uses = {KSP} 6665} 6666 6667@Article{ tmh2001, 6668 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 6669 journal = {Journal of Economic Dynamics and Control}, 6670 year = {2002}, 6671 volume = {26}, 6672 pages = {1499-1515}, 6673 title = {Solving finite difference schemes arising in trivariate option pricing}, 6674 petsc_uses = {KSP} 6675} 6676 6677@InProceedings{ a2, 6678 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 6679 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 6680 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6681 Methods}, 6682 editor = {C.-H. Lai et al.}, 6683 publisher = {Domain Decomposition Press, Bergen}, 6684 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 6685 year = {1999}, 6686 petsc_uses = {KSP} 6687} 6688 6689@Unpublished{ mmmdcmaa-web-page, 6690 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 6691 {A}coustics {W}eb Page}, 6692 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 6693 author = {David E. Keyes}, 6694 institution = {Old Dominion University}, 6695 petsc_uses = {KSP} 6696} 6697 6698@Conference{ liu2010parallelization, 6699 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 6700 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 6701 booktitle = {International Symposium on Parallel and Distributed Processing with 6702 Applications}, 6703 pages = {528--535}, 6704 year = {2010}, 6705 organization = {IEEE}, 6706 petsc_uses = {KSP} 6707} 6708 6709@Unpublished{ oil-reservoir-sim-web-page, 6710 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 6711 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 6712 institution = {University of Texas at Austin and Argonne National Laboratory}, 6713 key = {University of Texas at Austin and Argonne National Laboratory}, 6714 petsc_uses = {KSP} 6715} 6716 6717@Article{ tmh2001b, 6718 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 6719 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 6720 year = {2001}, 6721 volume = {37}, 6722 pages = {143--146}, 6723 title = {Adapting EMAP3D to parallel processing}, 6724 petsc_uses = {KSP} 6725} 6726 6727@Article{ harbury98, 6728 author = {HK Harbury and W Porod}, 6729 journal = {VLSI Design}, 6730 year = {1998}, 6731 volume = {6}, 6732 pages = {47--51}, 6733 title = {Parallel computation for electronic waves in quantum corrals}, 6734 petsc_uses = {KSP} 6735} 6736 6737@Article{ bludszuwei98, 6738 author = {Mark Bludszuweit}, 6739 journal = {Journal of Lightwave Technology}, 6740 year = {1998}, 6741 volume = {16}, 6742 number = {7}, 6743 pages = {1336--42}, 6744 title = {Mixed Finite Element Beam Propagation Method}, 6745 petsc_uses = {KSP} 6746} 6747 6748@Article{ s1, 6749 author = {J. L. Friedman and N. Stergioulas}, 6750 journal = {Astrophysics Journal}, 6751 year = {1998}, 6752 volume = {492}, 6753 number = {301}, 6754 pages = {}, 6755 title = {}, 6756 petsc_uses = {KSP} 6757} 6758 6759@Article{ s1a, 6760 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 6761 journal = {Astrophysics Journal}, 6762 year = {1999}, 6763 volume = {510}, 6764 number = {854}, 6765 pages = {}, 6766 title = {}, 6767 petsc_uses = {KSP} 6768} 6769 6770@PhDThesis{ s2, 6771 author = {N. Stergioulas}, 6772 title = {Ph. D. thesis}, 6773 year = {1996}, 6774 institution = {University of Wisconsin-Milwaukee}, 6775 petsc_uses = {KSP} 6776} 6777 6778@InProceedings{ coral1, 6779 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6780 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 6781 Parallel Computing Environment}, 6782 booktitle = {Proceedings of the Miami TEAM Workshop}, 6783 location = {Florida International University, Department of Electrical Engineering and 6784 Computing Science}, 6785 month = nov, 6786 year = {1993}, 6787 petsc_uses = {KSP} 6788} 6789 6790@InProceedings{ coral2, 6791 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6792 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 6793 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 6794 month = dec, 6795 year = {1994}, 6796 petsc_uses = {KSP} 6797} 6798 6799@InProceedings{ coral3, 6800 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6801 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 6802 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 6803 location = {Florida International University, Department of Electrical Engineering and 6804 Computing Science}, 6805 year = {1995}, 6806 petsc_uses = {KSP} 6807} 6808 6809@InProceedings{ mijalkovic, 6810 author = {Slobodan Mijalkovi\'{c}}, 6811 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 6812 Process Simulation}, 6813 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 6814 Gent, Belgium, September 27--30, 1999.}, 6815 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 6816 optvolume = {14}, 6817 optseries = {Lecture Notes in Computational Science and Engineering}, 6818 year = {2000}, 6819 publisher = {Springer}, 6820 address = {Berlin}, 6821 optpages = {179--184}, 6822 petsc_uses = {KSP} 6823} 6824 6825@Article{ bludszuwei98a, 6826 author = {Mark Bludszuweit}, 6827 journal = {Journal of Lightwave Technology}, 6828 year = {1998}, 6829 volume = {16}, 6830 number = {7}, 6831 pages = {1336--42}, 6832 title = {Mixed Finite Element Beam Propagation Method}, 6833 petsc_uses = {KSP} 6834} 6835 6836@Article{ gilli-pauletto-1998, 6837 author = {Manfred Gilli and Giorgio Pauletto}, 6838 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 6839 journal = {Computational Economics}, 6840 year = {2000}, 6841 volume = {16}, 6842 pages = {173--186}, 6843 petsc_uses = {KSP} 6844} 6845 6846% LiteralHTML: 6847% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 6848% LiteralHTML: 6849@Article{ collierdalcincalo2013, 6850 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 6851 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 6852 journal = {arxiv}, 6853 year = {2013}, 6854 number = {1305.4452}, 6855 note = {\url{http://arxiv.org/abs/1305.4452}}, 6856 petsc_uses = {KSP} 6857} 6858 6859@Article{ collierdalcinvignalcortescalo2016, 6860 title = {PetIGA: A framework for high-performance isogeometric analysis}, 6861 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 6862 Victor M. Calo}, 6863 journal = {Computer Methods in Applied Mechanics and Engineering}, 6864 year = {2016}, 6865 petsc_uses = {KSP} 6866} 6867 6868@Misc{ petiga-web-page, 6869 author = {N. Collier and L. Dalcin and V.M. Calo}, 6870 title = {{PetIGA} {W}eb page}, 6871 url = {https://bitbucket.org/dalcinl/petiga/}, 6872 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 6873 year = {2014}, 6874 petsc_uses = {KSP} 6875} 6876 6877@Article{ logg07, 6878 author = {Logg, Anders}, 6879 title = {Automating the Finite Element Method}, 6880 journal = {Archives of Computational Methods in Engineering}, 6881 volume = {14}, 6882 number = {2}, 6883 pages = {93-138}, 6884 year = {2007}, 6885 doi = {10.1007/s11831-007-9003-9}, 6886 publisher = {Kluwer Academic Publishers}, 6887 issn = {1134-3060}, 6888 language = {English}, 6889 petsc_uses = {KSP} 6890} 6891 6892@Article{ jezequelcouturierdenis12, 6893 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 6894 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 6895 versus the PETSc library}, 6896 journal = {The Journal of Supercomputing}, 6897 volume = {59}, 6898 number = {3}, 6899 pages = {1517-1532}, 6900 year = {2012}, 6901 issn = {0920-8542}, 6902 doi = {10.1007/s11227-011-0563-y}, 6903 publisher = {Springer US}, 6904 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 6905 Sparse linear solver}, 6906 language = {English}, 6907 petsc_uses = {KSP} 6908} 6909 6910@Unpublished{ feap-web-page, 6911 title = {FEAP: A Finite Element Analysis Program}, 6912 url = {http://www.ce.berkeley.edu/projects/feap/}, 6913 author = {FEAP Team}, 6914 note = {Uses PETSc linear solvers - iterative and direct}, 6915 petsc_uses = {KSP} 6916} 6917 6918@Unpublished{ parpre-web-page, 6919 title = {{ParPre} {W}eb {P}age}, 6920 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 6921 institution = {University of Tennessee}, 6922 author = {Victor Eijkhout}, 6923 note = {This is no longer supported. A set of preconditioners built on PETSc}, 6924 petsc_uses = {KSP} 6925} 6926 6927@Unpublished{ pism, 6928 title = {{PISM}: a Parallel Ice Sheet Model}, 6929 author = {{PISM Team}}, 6930 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 6931 Sheet Model). The thickness, temperature, velocity and age of the ice are all 6932 simulated, as is the deformation of the earth underneath the ice. New techniques 6933 for fast ice dynamics, earth deformation, and verification have are included.}, 6934 note = {\url{http://www.pism-docs.org/}}, 6935 petsc_uses = {KSP} 6936} 6937 6938@Unpublished{ oofem, 6939 title = {OOFEM - an object oriented finite element package}, 6940 author = {Borek Patzak}, 6941 url = {http://www.oofem.org}, 6942 petsc_uses = {KSP} 6943} 6944 6945@Unpublished{ dks2openfvm, 6946 title = {OpenFVM - a finite volume based general purpose CFD solver}, 6947 author = {Open source development}, 6948 url = {http://openfvm.sourceforge.net/}, 6949 petsc_uses = {KSP} 6950} 6951 6952@Unpublished{ sundar-2008w, 6953 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 6954 octree meshes}, 6955 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 6956 institution = {University of Pennsylvania}, 6957 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 6958 petsc_uses = {KSP} 6959} 6960 6961@Unpublished{ khatiwala07-software, 6962 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 6963 author = {Khatiwala, S.}, 6964 institution = {Columbia University}, 6965 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 6966 petsc_uses = {KSP} 6967} 6968 6969@InBook{ jiaolima99, 6970 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 6971 chapter = {SIFFEA:Scalable Integrated Framework for Finite Element Analysis}, 6972 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 6973 title = {Lecture Notes in Computer Science}, 6974 publisher = {Springer-Verlag}, 6975 volume = {1732}, 6976 year = {1999}, 6977 petsc_uses = {KSP} 6978} 6979 6980@Article{ crow1, 6981 author = {C. S. Crow IV}, 6982 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 6983 journal = {Hopkins Undergraduate Research Journal}, 6984 year = {2003}, 6985 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 6986 petsc_uses = {KSP} 6987} 6988 6989@Unpublished{ petsc-python, 6990 title = {PETSc for Python}, 6991 author = {L. Dalcin and R. Paz and M. Storti}, 6992 institution = {International Center for Computer Methods in Engineering}, 6993 url = {http://www.cimec.org.ar/python}, 6994 note = {Provides Python bindings for PETSc via SWIG}, 6995 petsc_uses = {KSP} 6996} 6997 6998@Unpublished{ cfdship, 6999 title = {{CFDShip-Iowa}}, 7000 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 7001 institution = {University of Iowa}, 7002 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 7003 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 7004 structured grids, designed for ship applications}, 7005 petsc_uses = {KSP} 7006} 7007 7008@Unpublished{ bvw, 7009 title = {Multiflow}, 7010 author = {Berend van Wachem}, 7011 institution = {Mechanical Engineering - Chalmers University of Technology}, 7012 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 7013 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 7014 flows.}, 7015 petsc_uses = {KSP} 7016} 7017 7018@Unpublished{ dks2, 7019 title = {FENA - A Finite Element Model for the North Atlantic}, 7020 author = {Jens Schroeter}, 7021 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 7022 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 7023 petsc_uses = {KSP} 7024} 7025 7026@TechReport{ piwonski2010idea, 7027 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 7028 and Simulation in {3-D}}, 7029 author = {Piwonski, J. and Slawig, T.}, 7030 year = {2010}, 7031 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 7032 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 7033 petsc_uses = {KSP} 7034} 7035 7036@Unpublished{ metos3d-web, 7037 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 7038 author = {Piwonski, J. and Slawig, T.}, 7039 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 7040 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 7041 petsc_uses = {KSP} 7042} 7043 7044@Unpublished{ magpar, 7045 author = {W. Scholz}, 7046 title = {Magpar: Parallel Micromagnetics Code}, 7047 institution = {Vienna University of Technology}, 7048 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 7049 petsc_uses = {KSP} 7050} 7051 7052@Misc{ libmesh:sourceforge, 7053 author = {}, 7054 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 7055 equations on serial and parallel platforms}, 7056 note = {[Online]}, 7057 url = {http://libmesh.github.io}, 7058 petsc_uses = {KSP} 7059} 7060 7061@Misc{ moose-web-page, 7062 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 7063 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 7064 Gaston and John Peterson and Jason Miller}, 7065 institution = {Idaho National Laboratory}, 7066 howpublished = {\url{http://mooseframework.org}}, 7067 petsc_uses = {KSP} 7068} 7069 7070@Article{ gaston2009moose, 7071 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 7072 equations}, 7073 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 7074 journal = {Nuclear Engineering and Design}, 7075 volume = {239}, 7076 number = {10}, 7077 pages = {1768--1778}, 7078 year = {2009}, 7079 publisher = {Elsevier}, 7080 petsc_uses = {KSP} 7081} 7082 7083@Article{ tonks2012object, 7084 title = {An object-oriented finite element framework for multiphysics phase field 7085 simulations}, 7086 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 7087 journal = {Computational Materials Science}, 7088 volume = {51}, 7089 number = {1}, 7090 pages = {20--29}, 7091 year = {2012}, 7092 publisher = {Elsevier}, 7093 petsc_uses = {KSP} 7094} 7095 7096@Misc{ pylithmanual, 7097 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 7098 Strand and Charles Williams}, 7099 title = {{PyLith} User Manual Version 2.0.0}, 7100 year = {2014}, 7101 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 7102 petsc_uses = {KSP} 7103} 7104 7105@Misc{ pylith-web-page, 7106 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 7107 title = {{PyLith}}, 7108 year = {2012}, 7109 url = {http://geodynamics.org/resources/pylith/}, 7110 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 7111 petsc_uses = {KSP} 7112} 7113 7114@Misc{ galemanual, 7115 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 7116 title = {Gale User Manual Version 2.0.0}, 7117 year = {2011}, 7118 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 7119 petsc_uses = {KSP} 7120} 7121 7122@Unpublished{ underworld, 7123 author = {Louis Moresi}, 7124 title = {{UnderWorld}: A Geodynamics Modelling Code}, 7125 institution = {Monash University}, 7126 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 7127 petsc_uses = {KSP} 7128} 7129 7130@Article{ moresi2007computational, 7131 title = {Computational approaches to studying non-linear dynamics of the crust and 7132 mantle}, 7133 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 7134 M{\"u}hlhaus, H.B.}, 7135 journal = {Physics of the Earth and Planetary Interiors}, 7136 volume = {163}, 7137 number = {1-4}, 7138 pages = {69--82}, 7139 year = {2007}, 7140 publisher = {Elsevier}, 7141 petsc_uses = {KSP} 7142} 7143 7144@Article{ pitt2009chaste, 7145 title = {Chaste: a test-driven approach to software development for biological modelling}, 7146 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 7147 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 7148 and Walter, A. and others}, 7149 journal = {Computer Physics Communications}, 7150 volume = {180}, 7151 number = {12}, 7152 pages = {2452--2471}, 7153 year = {2009}, 7154 publisher = {Elsevier}, 7155 petsc_uses = {KSP} 7156} 7157 7158@Misc{ fenicsproject, 7159 title = {{The FEniCS project}}, 7160 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 7161 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 7162 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 7163 url = {http://fenicsproject.org}, 7164 year = {2011}, 7165 petsc_uses = {KSP} 7166} 7167 7168@Unpublished{ snark, 7169 title = {Snark: A suite of software for geoscientific applications and a philosophy of 7170 scientific software development}, 7171 institution = {Victorian Partnership for Advanced Computing}, 7172 url = {http://vpac.org/Snark}, 7173 petsc_uses = {KSP} 7174} 7175 7176@Misc{ imoose:sourceforge, 7177 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 7178 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 7179 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 7180 note = {[Online]}, 7181 url = {http://imoose.sourceforge.net}, 7182 petsc_uses = {KSP} 7183} 7184 7185@Unpublished{ fossi, 7186 author = {Stephan Frickenhaus}, 7187 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 7188 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 7189 codes}, 7190 institution = {AWI-Bremerhaven, Germanny}, 7191 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 7192 petsc_uses = {KSP} 7193} 7194 7195@Unpublished{ fun3dweb, 7196 author = {Dinesh Kaushik}, 7197 title = {PETSC-FUN3D Benchmark Page}, 7198 institution = {ODU/ANL}, 7199 url = {http://www.mcs.anl.gov/petsc-fun3d}, 7200 note = {CFD Benchmark of some solvers in PETSc}, 7201 petsc_uses = {KSP} 7202} 7203 7204@Unpublished{ scirun, 7205 author = {SCIRun Development Team}, 7206 title = {SCIRun}, 7207 institution = {University of Utah}, 7208 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 7209 note = {SCIRun now uses PETSc linear solvers}, 7210 petsc_uses = {KSP} 7211} 7212 7213@Misc{ prometheus, 7214 author = {Mark F. Adams}, 7215 title = {Prometheus - A scalable unstructured finite element solver}, 7216 institution = {Berkeley}, 7217 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 7218 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 7219 petsc_uses = {KSP} 7220} 7221 7222@Unpublished{ illuminator, 7223 author = {Adam C. Powell, IV}, 7224 title = {Illuminator Distributed Visualization Library}, 7225 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 7226 petsc_uses = {KSP} 7227} 7228 7229@Unpublished{ rheoplast, 7230 title = {RheoPlast Phase Field Multi-Physics Code}, 7231 author = {Adam Powell and David Dussault and Bo Zhou}, 7232 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 7233 petsc_uses = {KSP} 7234} 7235 7236@Misc{ tao-web-page, 7237 title = {{Toolkit for Advanced Optimization (TAO)} {W}eb Page}, 7238 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 7239 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 7240 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7241 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 7242 petsc_uses = {KSP} 7243} 7244 7245@TechReport{ tao-user-ref, 7246 title = {{Toolkit for Advanced Optimization (TAO) users manual}}, 7247 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 7248 and Steve Benson and Lois Curfman McInnes}, 7249 institution = {Argonne National Laboratory}, 7250 year = {2019}, 7251 number = {ANL/MCS-TM-322 - Rev 3.12}, 7252 petsc_uses = {KSP} 7253} 7254 7255% url = "http://www.mcs.anl.gov/tao", 7256@Unpublished{ mefpp-web-page, 7257 title = {{MEF++} {W}eb {P}age}, 7258 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 7259 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 7260 author = {Eric Chamberland}, 7261 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 7262 multiphysics}, 7263 petsc_uses = {KSP} 7264} 7265 7266@Unpublished{ tipetsc-web-page, 7267 title = {Ti-PETSc - an interface to PETSc from Titanium}, 7268 institution = {Berkeley}, 7269 url = {http://www.nersc.gov/\~{ }yunhe/cs267/final/paper.pdf}, 7270 petsc_uses = {KSP} 7271} 7272 7273@Unpublished{ ptatin-web-page, 7274 title = {ptatin3d}, 7275 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 7276 url = {https://bitbucket.org/jedbrown/ptatin3d}, 7277 year = {2018}, 7278 petsc_uses = {KSP} 7279} 7280 7281@Misc{ multiphase-web-page, 7282 author = {Q. Zou}, 7283 title = {Multiphase flow with {PETSc}}, 7284 institution = {LANL}, 7285 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 7286 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 7287 lab = {LANL}, 7288 petsc_uses = {KSP} 7289} 7290 7291@Misc{ electromag-web-page, 7292 title = {{EMSolve Web} page}, 7293 institution = {LLNL}, 7294 howpublished = {http://www.llnl.gov/casc/emsolve}, 7295 url = {http://www.Llnl.gov/casc/emsolve}, 7296 author = {Daniel {White et al.}}, 7297 lab = {LLNL}, 7298 petsc_uses = {KSP} 7299} 7300 7301@Unpublished{ fe-software-web-page, 7302 institution = {Kuleuven}, 7303 title = {Finite element software}, 7304 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 7305 petsc_uses = {KSP} 7306} 7307 7308@Misc{ petsc-web-page, 7309 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7310 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 7311 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7312 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7313 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7314 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7315 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7316 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7317 Zhang}, 7318 title = {{PETS}c {W}eb page}, 7319 url = {https://petsc.org/}, 7320 howpublished = {\url{https://petsc.org/}}, 7321 year = {2023} 7322} 7323 7324@Unpublished{ petsc-debian-package, 7325 author = {Adam C. Powell, IV}, 7326 title = {Debian package for PETSc}, 7327 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 7328 petsc_uses = {KSP} 7329} 7330 7331@Unpublished{ cactus, 7332 title = {Cactus Website}, 7333 url = {http://www.cactuscode.org/}, 7334 note = {Provides two interface to the PETSc solvers}, 7335 petsc_uses = {KSP} 7336} 7337 7338@Unpublished{ petsc-fem, 7339 author = {Mario Storti and Norberto Nigro}, 7340 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 7341 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 7342 url = {http://www.cimec.org.ar/petscfem}, 7343 petsc_uses = {KSP} 7344} 7345 7346@Misc{ fidap, 7347 title = {FIDAP 8.5}, 7348 howpublished = {\url{http://www.fluent.com}}, 7349 url = {http://www.fluent.com}, 7350 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 7351 solves.}, 7352 key = {FIDAP 8.5}, 7353 petsc_uses = {KSP} 7354} 7355 7356@Unpublished{ slepc, 7357 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7358 Vicente Hern\'andez and Vicent Vidal}, 7359 title = {{SLEPc} Homepage}, 7360 url = {http://slepc.upv.es/}, 7361 note = {Scalable Library for Eigenvalue Problem Computations}, 7362 petsc_uses = {KSP} 7363} 7364 7365@TechReport{ slepc-users-manual, 7366 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7367 Vicente Hern\'andez and Vicent Vidal}, 7368 title = {{SLEPc} Users Manual}, 7369 number = {DISC-II/24/02}, 7370 url = {http://slepc.upv.es/}, 7371 note = {Scalable Library for Eigenvalue Problem Computations}, 7372 petsc_uses = {KSP} 7373} 7374 7375@Misc{ deal.ii, 7376 title = {deal.II}, 7377 howpublished = {\url{http://www.dealii.org}}, 7378 url = {http://www.dealii.org}, 7379 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 7380 It allows PETSc linear algebra and solvers to be used underneath.}, 7381 key = {deal.II 5.0}, 7382 petsc_uses = {KSP} 7383} 7384 7385@Article{ bangerth2007deal, 7386 title = {{deal.II---A general-purpose object-oriented finite element library}}, 7387 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 7388 journal = {ACM Transactions on Mathematical Software (TOMS)}, 7389 volume = {33}, 7390 number = {4}, 7391 pages = {24--es}, 7392 issn = {0098-3500}, 7393 year = {2007}, 7394 publisher = {ACM}, 7395 petsc_uses = {KSP} 7396} 7397 7398@Misc{ globalarrays, 7399 author = {Jarek {Nieplocha et al.}}, 7400 title = {Global Arrays}, 7401 institution = {Pacific Northwest National Laboratories}, 7402 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 7403 url = {http://www.emsl.pnl.gov/docs/global}, 7404 note = {Global arrays can use PETSc linear solvers}, 7405 lab = {PNNL}, 7406 petsc_uses = {KSP} 7407} 7408 7409% LiteralHTML: 7410% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 7411% LiteralHTML: 7412@Article{ petsccommunity2022, 7413 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 7414 Community}, 7415 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 7416 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 7417 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 7418 and Hong Zhang and Junchao Zhang}, 7419 journal = {Computing in Science and Engineering}, 7420 volume = {24}, 7421 number = {03}, 7422 pages = {6--15}, 7423 issn = {1558-366X}, 7424 doi = {10.1109/MCSE.2022.3169974}, 7425 publisher = {IEEE Computer Society}, 7426 address = {Los Alamitos, CA, USA}, 7427 month = {may}, 7428 year = {2022}, 7429 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 7430 petsc_uses = {KSP} 7431} 7432 7433@Article{ brownknepleysmith14, 7434 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 7435 title = {Run-time extensibility and librarization of simulation software}, 7436 journal = {IEEE Computing in Science and Engineering}, 7437 month = {Jan}, 7438 volume = {17}, 7439 number = {1}, 7440 pages = {38--45}, 7441 doi = {10.1109/MCSE.2014.95}, 7442 year = {2015}, 7443 petsc_uses = {KSP} 7444} 7445 7446@TechReport{ ass2012, 7447 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 7448 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 7449 institution = {Argonne National Laboratory}, 7450 type = {Preprint}, 7451 year = {2012}, 7452 number = {ANL/MCS-P2011-0112}, 7453 petsc_uses = {KSP} 7454} 7455 7456@TechReport{ clearyknepley99, 7457 author = {Andrew Cleary and Matthew G. Knepley}, 7458 title = {Solvers as Operators}, 7459 institution = {Lawrence Livermore National Laboratory}, 7460 type = {Technical Report}, 7461 number = {UCRL-ID-135342}, 7462 year = {1999}, 7463 petsc_uses = {KSP} 7464} 7465 7466@TechReport{ smcabbkz2012, 7467 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 7468 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 7469 title = {{PETSc's} software strategy for the design space of composable extreme-scale 7470 solvers}, 7471 institution = {Argonne National Laboratory}, 7472 type = {Preprint}, 7473 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 7474 year = {2012}, 7475 number = {ANL/MCS-P2059-0312}, 7476 petsc_uses = {KSP} 7477} 7478 7479@InProceedings{ mhwpmhs2009, 7480 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 7481 and G. E. Hammond and B. Smith}, 7482 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 7483 Toolkit {MPI} at Scale}, 7484 booktitle = {Cray Users Group Conference}, 7485 year = {2009}, 7486 petsc_uses = {KSP} 7487} 7488 7489@InProceedings{ msmhls2010, 7490 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 7491 Lichtner and B. F. Smith}, 7492 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 7493 {BlueGene} Architectures}, 7494 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 7495 year = {2010}, 7496 petsc_uses = {KSP} 7497} 7498 7499@InCollection{ msk2013, 7500 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 7501 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 7502 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7503 series = {Lecture Notes in Earth System Sciences}, 7504 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7505 Yaolin Shi}, 7506 doi = {10.1007/978-3-642-16405-7_7}, 7507 publisher = {Springer Berlin Heidelberg}, 7508 pages = {131--140}, 7509 year = {2013}, 7510 isbn = {978-3-642-16404-0}, 7511 petsc_uses = {KSP} 7512} 7513 7514@InCollection{ knepleyyuen13, 7515 author = {Matthew G. Knepley and David A. Yuen}, 7516 title = {Why Scientists and Engineers need {GPU}s today}, 7517 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7518 series = {Lecture Notes in Earth System Sciences}, 7519 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7520 Yaolin Shi}, 7521 doi = {10.1007/978-3-642-16405-7_1}, 7522 publisher = {Springer Berlin Heidelberg}, 7523 pages = {131--140}, 7524 year = {2013}, 7525 isbn = {978-3-642-16404-0}, 7526 petsc_uses = {KSP} 7527} 7528 7529@InCollection{ karpeevknepleybrune13, 7530 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 7531 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 7532 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7533 series = {Lecture Notes in Earth System Sciences}, 7534 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7535 Yaolin Shi}, 7536 doi = {10.1007/978-3-642-16405-7_30}, 7537 publisher = {Springer Berlin Heidelberg}, 7538 pages = {487--501}, 7539 year = {2013}, 7540 isbn = {978-3-642-16404-0}, 7541 petsc_uses = {KSP} 7542} 7543 7544@InCollection{ zhengetal13, 7545 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 7546 Variable Viscosity}, 7547 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7548 Zhang and Yaolin Shi}, 7549 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7550 series = {Lecture Notes in Earth System Sciences}, 7551 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7552 Yaolin Shi}, 7553 doi = {10.1007/978-3-642-16405-7_21}, 7554 publisher = {Springer Berlin Heidelberg}, 7555 pages = {321--333}, 7556 year = {2013}, 7557 isbn = {978-3-642-16404-0}, 7558 petsc_uses = {KSP} 7559} 7560 7561@Article{ zhengetal13b, 7562 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 7563 strongly variable viscosity based on {M}atlab and {CUDA}}, 7564 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7565 Zhang and Yaolin Shi}, 7566 journal = {IJHPCA}, 7567 volume = {28}, 7568 number = {1}, 7569 pages = {50--60}, 7570 doi = {10.1177/1094342013478640}, 7571 year = {2013}, 7572 petsc_uses = {KSP} 7573} 7574 7575@InBook{ s2011, 7576 author = {B. Smith}, 7577 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 7578 title = {Encyclopedia of Parallel Computing}, 7579 bookeditor = {D. Padua}, 7580 publisher = {Springer}, 7581 year = {2011}, 7582 petsc_uses = {KSP} 7583} 7584 7585@Article{ acostamejia06, 7586 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 7587 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 7588 journal = {Lecturas Matem\'aticas}, 7589 volume = {27}, 7590 year = {2006}, 7591 pages = {213--224}, 7592 petsc_uses = {KSP} 7593} 7594 7595@InProceedings{ quenettemoresisunterappelbe07, 7596 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 7597 title = {Explaining StGermain: An aspect oriented environment for building extensible 7598 computational mechanics modeling software}, 7599 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 7600 publisher = {IEEE}, 7601 pages = {1--8}, 7602 yerar = {2007}, 7603 petsc_uses = {KSP} 7604} 7605 7606@Article{ dfm1, 7607 title = {Vectorized sparse matrix multiply for compressed row storage format}, 7608 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 7609 journal = {Lecture Notes in Computer Science}, 7610 year = {2005}, 7611 pages = {99--106}, 7612 volume = {3514}, 7613 lab = {ORNL}, 7614 petsc_uses = {KSP} 7615} 7616 7617@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 7618 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 7619 Vandewalle and Stefaan Poedts}, 7620 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 7621 Scientific Computing Software}, 7622 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 7623 year = {2005}, 7624 note = {Lecture Notes in Computer Science}, 7625 volume = {3514}, 7626 publisher = {Springer-Verlag GmbH}, 7627 petsc_uses = {KSP} 7628} 7629 7630@InProceedings{ dalcin-paz-storti, 7631 author = {L. Dalcin and R. Paz and M. Storti}, 7632 title = {Desarrollo de Aplicaciones Paralelas en Python}, 7633 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 7634 Bariloche, Argentina}, 7635 year = {2004}, 7636 petsc_uses = {KSP} 7637} 7638 7639@Article{ mpi-python, 7640 author = {L. Dalcin and R. Paz and M. Storti}, 7641 title = {MPI for Python}, 7642 journal = {Journal of Parallel and Distributed Computing}, 7643 year = {2005}, 7644 petsc_uses = {KSP} 7645} 7646 7647@Unpublished{ hrv02a, 7648 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 7649 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7650 note = {Submited to VecPar 2002}, 7651 year = {2002}, 7652 petsc_uses = {KSP} 7653} 7654 7655@Article{ knyazev2007block, 7656 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 7657 {PETSc}}, 7658 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 7659 journal = {SIAM Journal on Scientific Computing}, 7660 volume = {29}, 7661 pages = {2224-2239}, 7662 doi = {10.1137/060661624}, 7663 year = {2007}, 7664 petsc_uses = {KSP} 7665} 7666 7667@MastersThesis{ aarrestad-master, 7668 author = {Asbjorn Hoiland Aarrestad}, 7669 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 7670 school = {University of Bergen}, 7671 month = {August}, 7672 year = {2003}, 7673 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 7674 note = {Implemented Runge-Kutta methods using PETSc}, 7675 petsc_uses = {KSP} 7676} 7677 7678@PhDThesis{ kaushik-phd, 7679 author = {D. K. Kaushik}, 7680 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 7681 Differential Equations on Unstructured Grids}, 7682 school = {Old Dominion University}, 7683 month = {December}, 7684 year = {2002}, 7685 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 7686 petsc_uses = {KSP} 7687} 7688 7689@TechReport{ rb1, 7690 author = {Rickard Bergstrom}, 7691 title = {Object Oriented Implementation of a General Finite Element Code}, 7692 number = {2002-13}, 7693 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 7694 year = {2002}, 7695 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 7696 note = {Discribes a finite element software package that uses PETSc for its solvers}, 7697 petsc_uses = {KSP} 7698} 7699 7700@InProceedings{ dbl1, 7701 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 7702 title = {A Parallel General Purpose Finite Element System}, 7703 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 7704 publisher = {SIAM}, 7705 year = {1999}, 7706 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 7707 note = {Describes software that uses PETSc for its parallel linear solves}, 7708 petsc_uses = {KSP} 7709} 7710 7711@Article{ p1, 7712 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 7713 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 7714 and B. Smith}, 7715 journal = {Parallel Computing}, 7716 year = {2002}, 7717 pages = {1811--1831}, 7718 volume = {28 (12)}, 7719 petsc_uses = {KSP} 7720} 7721 7722@Article{ automatic-ad, 7723 author = {Paul Hovland and Boyana Norris and Barry Smith}, 7724 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 7725 year = {2005}, 7726 journal = {Future Generation Computer Systems}, 7727 volume = {21}, 7728 number = {8}, 7729 pages = {1426--1438}, 7730 petsc_uses = {KSP} 7731} 7732 7733@TechReport{ remote-math, 7734 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 7735 Smith}, 7736 title = {Remote Access to Mathematical Software}, 7737 number = {ANL/MCS-P889-0601}, 7738 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7739 month = {June}, 7740 year = {2001}, 7741 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 7742 petsc_uses = {KSP} 7743} 7744 7745@InProceedings{ gropp98, 7746 author = {William D. Gropp}, 7747 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 7748 publisher = {SIAM}, 7749 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7750 Scientific and Engineering Computing}, 7751 year = {1999}, 7752 pages = {21-29}, 7753 petsc_uses = {KSP} 7754} 7755 7756@InProceedings{ knepleysarin99, 7757 author = {Matthew Knepley and Vivek Sarin}, 7758 title = {Algorithm Development for Large Scale Computing}, 7759 publisher = {SIAM}, 7760 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7761 Scientific and Engineering Computing}, 7762 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}}, 7763 year = {1999}, 7764 petsc_uses = {KSP} 7765} 7766 7767@InBook{ bgms00, 7768 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 7769 chapter = {Software for the Scalable Solution of {PDEs}}, 7770 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 7771 title = {CRPC Handbook of Parallel Computing}, 7772 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 7773 and A. White}, 7774 publisher = {Morgan Kaufmann Publishers}, 7775 year = {2002}, 7776 petsc_uses = {KSP} 7777} 7778 7779@InProceedings{ hovland_norris_smith98, 7780 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 7781 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 7782 Computations}, 7783 publisher = {SIAM}, 7784 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7785 Scientific and Engineering Computing}, 7786 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 7787 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 7788 year = {1999}, 7789 pages = {129-137}, 7790 petsc_uses = {KSP} 7791} 7792 7793@InProceedings{ efficient, 7794 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7795 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 7796 Libraries}, 7797 booktitle = {Modern Software Tools in Scientific Computing}, 7798 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 7799 publisher = {Birkhauser Press}, 7800 pages = {163--202}, 7801 year = {1997}, 7802 petsc_uses = {KSP} 7803} 7804 7805% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 7806@TechReport{ petsc-user-ref, 7807 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7808 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 7809 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7810 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7811 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7812 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7813 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7814 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7815 Zhang}, 7816 title = {{PETSc/TAO} Users Manual}, 7817 institution = {Argonne National Laboratory}, 7818 number = {ANL-21/39 - Revision 3.19}, 7819 doi = {10.2172/1968587}, 7820 year = {2023} 7821} 7822 7823% url = {https://petsc.org/release} 7824@TechReport{ petsc-developers, 7825 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 7826 title = {{PETS}c Developers Guide}, 7827 institution = {Argonne National Laboratory}, 7828 number = {ANL-18/18}, 7829 year = {2018}, 7830 url = {https://petsc.org/release/developers}, 7831 petsc_uses = {KSP} 7832} 7833 7834@Unpublished{ alice-memory-snooper, 7835 author = {Ibrahima Ba and Barry~F. Smith}, 7836 title = {The {ALICE} Memory Snooper}, 7837 year = {1999}, 7838 petsc_uses = {KSP} 7839} 7840 7841@TechReport{ petsc-user-ref-polish, 7842 author = {Marcin Bojko and Piotr Krzyzanowski}, 7843 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 7844 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 7845 year = {1998}, 7846 note = {An introduction to PETSc in Polish}, 7847 petsc_uses = {KSP} 7848} 7849 7850@InProceedings{ abghmn00, 7851 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 7852 High-Performance Scientific Computing}, 7853 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 7854 Norris}, 7855 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 7856 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 7857 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 7858 Hasco\"{e}t and Uwe Naumann}, 7859 publisher = {Springer}, 7860 year = {2002}, 7861 petsc_uses = {KSP} 7862} 7863 7864@Unpublished{ petsc-mpi-paper, 7865 author = {Lois Curfman McInnes and Barry F. Smith}, 7866 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 7867 Libraries}, 7868 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 7869 month = jun, 7870 year = {1995}, 7871 petsc_uses = {KSP} 7872} 7873 7874@InProceedings{ miss-paper, 7875 author = {William D. Gropp and Barry F. Smith}, 7876 title = {Scalable, Extensible, and Portable Numerical Libraries}, 7877 publisher = {IEEE}, 7878 year = {1994}, 7879 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7880 address = {Mississippi State University}, 7881 pages = {87--93}, 7882 keyword = {numerical libraries, scientific computing, parallel computing}, 7883 petsc_uses = {KSP} 7884} 7885 7886@InProceedings{ snes-paper, 7887 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7888 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 7889 Minimization Problems}, 7890 publisher = {IEEE}, 7891 year = {1995}, 7892 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7893 address = {Mississippi State University}, 7894 pages = {60-67}, 7895 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 7896 petsc_uses = {KSP} 7897} 7898 7899@Article{ dsneutral, 7900 author = {Barry F. Smith and William D. Gropp}, 7901 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 7902 Sparse Linear Systems}, 7903 journal = {Scientific Programming}, 7904 volume = {5}, 7905 pages = {329--336}, 7906 key = {GroppSmith96 ! KSP design}, 7907 year = {1996}, 7908 petsc_uses = {KSP} 7909} 7910 7911@InProceedings{ bgms98, 7912 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7913 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 7914 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7915 Scientific and Engineering Computing}, 7916 publisher = {SIAM}, 7917 pages = {58-67}, 7918 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 7919 year = {1998}, 7920 petsc_uses = {KSP} 7921} 7922 7923@Article{ hkm98, 7924 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 7925 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 7926 {PDE} Computation}, 7927 journal = {Advances in Engineering Software}, 7928 volume = {29}, 7929 pages = {415-424}, 7930 year = {1998}, 7931 petsc_uses = {KSP} 7932} 7933 7934@TechReport{ pdpta99, 7935 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 7936 Smith}, 7937 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 7938 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 7939 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 7940 Vegas, Nevada}, 7941 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7942 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 7943 number = {ANL/MCS-P751-0599}, 7944 year = {1999}, 7945 petsc_uses = {KSP} 7946} 7947 7948@InProceedings{ bbh:com, 7949 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 7950 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 7951 Computing}}, 7952 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 7953 Euro-Par Conference, Munich, Germany, August/September 2000}, 7954 year = {2000}, 7955 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 7956 volume = {1900}, 7957 series = {Lecture Notes in Computer Science}, 7958 pages = {86--94}, 7959 address = {Berlin}, 7960 publisher = {Springer}, 7961 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 7962 petsc_uses = {KSP} 7963} 7964 7965@InProceedings{ overture00, 7966 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 7967 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 7968 Components}, 7969 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 7970 booktitle = {Proceedings of the International Federation for Information Processing Working 7971 Conference on Software Architectures for Scientific Computing, Kluwer}, 7972 year = {2000}, 7973 pages = {57--68}, 7974 petsc_uses = {KSP} 7975} 7976 7977@TechReport{ smith97, 7978 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 7979 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 7980 number = {ANL/MCS-P701}, 7981 author = {Barry F. Smith}, 7982 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7983 petsc_uses = {KSP} 7984} 7985 7986@Article{ smith98, 7987 author = {Barry Smith}, 7988 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 7989 journal = {SIGNUM Newsletter}, 7990 year = {1998}, 7991 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 7992 petsc_uses = {KSP} 7993} 7994 7995@TechReport{ ad-petsc-tm, 7996 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 7997 {PETSc}}, 7998 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 7999 year = {1997}, 8000 type = {Technical Memorandum}, 8001 institution = {ANL}, 8002 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 8003 number = {ANL/MCS-TM-233}, 8004 petsc_uses = {KSP} 8005} 8006 8007% LiteralHTML: 8008% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 8009% LiteralHTML: 8010@PhDThesis{ klotzthesis2019, 8011 author = {Thomas S. Klotz}, 8012 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 8013 Biology}, 8014 school = {Rice University}, 8015 year = {2019}, 8016 petsc_uses = {KSP} 8017} 8018 8019@Article{ klotzbardhanknepley2018, 8020 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 8021 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 8022 journal = {Communications in Applied Mathematics and Computational Science}, 8023 note = {In review}, 8024 url = {https://arxiv.org/abs/1708.06028}, 8025 year = {2018}, 8026 petsc_uses = {KSP} 8027} 8028 8029@Misc{ brown2016, 8030 title = {Threading Tradeoffs in Domain Decomposition}, 8031 author = {Jed Brown}, 8032 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 8033 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 8034 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 8035 year = {2016}, 8036 petsc_uses = {KSP} 8037} 8038 8039@Article{ changnakshatralaknepleyjohnsson2017, 8040 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 8041 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 8042 Johnsson}, 8043 journal = {Concurency: Practice and Experience}, 8044 volume = {30}, 8045 number = {11}, 8046 eprint = {1705.03625}, 8047 doi = {10.1002/cpe.4401}, 8048 year = {2017}, 8049 petsc_uses = {KSP} 8050} 8051 8052@Article{ changfabienknepleymills2018, 8053 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 8054 spectrum analysis}, 8055 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 8056 journal = {SIAM Journal on Scientific Computing}, 8057 volume = {40}, 8058 number = {6}, 8059 pages = {C779--C802}, 8060 eprint = {1802.07832}, 8061 doi = {10.1137/18M1172260}, 8062 year = {2018}, 8063 petsc_uses = {KSP} 8064} 8065 8066@Article{ joshaghanichangnakshatralaknepley2019, 8067 title = {Composable solvers for the four-field double porosity/permeability model}, 8068 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 8069 Knepley}, 8070 journal = {Journal of Computational Physics}, 8071 volume = {386}, 8072 pages = {428--466}, 8073 doi = {10.1016/j.jcp.2019.02.020}, 8074 year = {2019}, 8075 petsc_uses = {KSP} 8076} 8077 8078@InProceedings{ barralknepleylangepiggottgorman2016, 8079 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 8080 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 8081 and Gerard J. Gorman}, 8082 booktitle = {25th International Meshing Roundtable}, 8083 editor = {Steve Owen and Hang Si}, 8084 month = {September}, 8085 address = {Washington, DC}, 8086 pages = {1--5}, 8087 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 8088 year = {2016}, 8089 petsc_uses = {KSP} 8090} 8091 8092@Article{ adamsbrownknepleysamtaney2016, 8093 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 8094 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 8095 journal = {SIAM Journal on Scientific Computing}, 8096 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 8097 epub = {http://arxiv.org/abs/1406.7808}, 8098 volume = {8}, 8099 number = {4}, 8100 pages = {C426--C440}, 8101 doi = {10.1137/140975127}, 8102 year = {2016}, 8103 petsc_uses = {KSP} 8104} 8105 8106@InProceedings{ maysananruppknepleysmith2016, 8107 title = {Extreme-Scale Multigrid Components within {PETSc}}, 8108 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 8109 Smith}, 8110 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 8111 series = {PASC '16}, 8112 isbn = {978-1-4503-4126-4}, 8113 location = {Lausanne, Switzerland}, 8114 pages = {5:1--5:12}, 8115 articleno = {5}, 8116 numpages = {12}, 8117 doi = {10.1145/2929908.2929913}, 8118 acmid = {2929913}, 8119 publisher = {ACM}, 8120 address = {New York, NY, USA}, 8121 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 8122 preconditioning}, 8123 year = {2016}, 8124 petsc_uses = {KSP} 8125} 8126 8127@Article{ liu2015field, 8128 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 8129 author = {Lulu Liu and David E Keyes}, 8130 journal = {SIAM Journal on Scientific Computing}, 8131 volume = {37}, 8132 number = {3}, 8133 pages = {A1388--A1409}, 8134 year = {2015}, 8135 publisher = {SIAM}, 8136 petsc_uses = {KSP} 8137} 8138 8139@Article{ lujiaomissirlis2014, 8140 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 8141 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 8142 journal = {Numerical Linear Algebra with Applications}, 8143 volume = {21}, 8144 number = {2}, 8145 pages = {221--238}, 8146 year = {2014}, 8147 publisher = {Wiley Online Library}, 8148 petsc_uses = {KSP} 8149} 8150 8151@Article{ badiamartinprincipe2013, 8152 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 8153 solid mechanics}, 8154 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 8155 journal = {International Journal for Numerical Methods in Engineering}, 8156 volume = {96}, 8157 number = {4}, 8158 pages = {203--230}, 8159 year = {2013}, 8160 petsc_uses = {KSP} 8161} 8162 8163@Article{ morganknepleysananscott2016, 8164 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 8165 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 8166 journal = {Concurrency and Computation: Practice and Experience}, 8167 volume = {28}, 8168 pages = {4532--4542}, 8169 year = {2016}, 8170 url = {http://arxiv.org/abs/1602.04873}, 8171 doi = {10.1002/cpe.3820}, 8172 petsc_uses = {KSP} 8173} 8174 8175@Article{ morgansananknepleymills2020, 8176 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 8177 solvers}, 8178 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 8179 journal = {The International Journal of High Performance Computing Applications}, 8180 volume = {35}, 8181 issue = {1}, 8182 doi = {10.1177/1094342020966835}, 8183 url = {https://doi.org/10.1177/1094342020966835}, 8184 eprint = {https://doi.org/10.1177/1094342020966835}, 8185 year = {2020}, 8186 petsc_uses = {KSP} 8187} 8188 8189@Article{ msz2013, 8190 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 8191 author = {M. McCourt and B. F. Smith and H. Zhang}, 8192 journal = {SIAM Journal on Matrix Analysis and Applications}, 8193 year = {2015}, 8194 note = {To appear}, 8195 petsc_uses = {KSP} 8196} 8197 8198@Article{ bassi2014agglomeration, 8199 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 8200 free}, 8201 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 8202 journal = {Mathematical Models and Methods in Applied Sciences}, 8203 volume = {24}, 8204 number = {08}, 8205 pages = {1495--1539}, 8206 year = {2014}, 8207 publisher = {World Scientific}, 8208 petsc_uses = {KSP} 8209} 8210 8211@Article{ jhuranidemkowicz12, 8212 author = {{Jhurani}, C. and {Demkowicz}, L.}, 8213 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 8214 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 8215 journal = {Computer Methods in Applied Mechanics and Engineering}, 8216 volume = {213}, 8217 pages = {418-426}, 8218 year = {2012}, 8219 month = mar, 8220 doi = {10.1016/j.cma.2011.06.003}, 8221 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 8222 petsc_uses = {KSP} 8223} 8224 8225@Article{ yangcai11, 8226 author = {Yang, Haijian and Cai, Xiao-Chuan}, 8227 title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear 8228 Complementarity Problems}, 8229 journal = {J. Sci. Comput.}, 8230 issue_date = {May 2011}, 8231 volume = {47}, 8232 number = {2}, 8233 month = may, 8234 pages = {258--280}, 8235 year = {2011}, 8236 issn = {0885-7474}, 8237 numpages = {23}, 8238 doi = {10.1007/s10915-010-9436-4}, 8239 acmid = {1971246}, 8240 publisher = {Plenum Press}, 8241 address = {New York, NY, USA}, 8242 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 8243 preconditioners, Semismooth Newton, Two-level methods}, 8244 petsc_uses = {KSP} 8245} 8246 8247@Article{ rheinbach09, 8248 author = {Rheinbach, Oliver}, 8249 title = {Parallel Iterative Substructuring in Structural Mechanics}, 8250 journal = {Archives of Computational Methods in Engineering}, 8251 volume = {16}, 8252 number = {4}, 8253 pages = {425-463}, 8254 year = {2009}, 8255 issn = {1134-3060}, 8256 doi = {10.1007/s11831-009-9035-4}, 8257 publisher = {Springer Netherlands}, 8258 language = {English}, 8259 petsc_uses = {KSP} 8260} 8261 8262@Article{ knepleyterrel2013, 8263 author = {Matthew G. Knepley and Andy R. Terrel}, 8264 title = {Finite Element Integration on {GPUs}}, 8265 journal = {{ACM} Transactions on Mathematical Software}, 8266 volume = {39}, 8267 number = {2}, 8268 accepted = {17 April 2012}, 8269 year = {2013}, 8270 abstract = {We present a novel finite element integration method for low order elements on 8271 GPUs. We achieve more than 100GF for element integration on first order 8272 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 8273 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 8274 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 8275 url = {http://arxiv.org/abs/1103.0066}, 8276 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 8277 petsc_uses = {KSP} 8278} 8279 8280@Article{ knepleyruppterrel2016, 8281 title = {Finite Element Integration with Quadrature on the GPU}, 8282 journal = {ArXiv e-prints}, 8283 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 8284 version = {1}, 8285 date = {2016-07-14}, 8286 eprinttype = {arxiv}, 8287 eprintclass = {cs.MS}, 8288 eprint = {1607.04245v1}, 8289 petsc_uses = {KSP} 8290} 8291 8292@Article{ klawonnlanserrheinbach2014, 8293 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 8294 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 8295 journal = {SIAM Journal on Scientific Computing}, 8296 volume = {36}, 8297 number = {2}, 8298 pages = {A737--A765}, 8299 year = {2014}, 8300 petsc_uses = {KSP} 8301} 8302 8303@TechReport{ pbmkbsxt2012, 8304 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8305 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8306 year = {2013}, 8307 type = {Preprint}, 8308 number = {ANL/MCS-P2010-0112}, 8309 institution = {Argonne National Laboratory}, 8310 petsc_uses = {KSP} 8311} 8312 8313@Article{ bruneknepleysmithtu15, 8314 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8315 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8316 journal = {SIAM Review}, 8317 volume = {57}, 8318 number = {4}, 8319 pages = {535--565}, 8320 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 8321 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 8322 doi = {10.1137/130936725}, 8323 year = {2015}, 8324 petsc_uses = {KSP} 8325} 8326 8327@Article{ mszm2014, 8328 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 8329 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8330 volume = {40}, 8331 pages = {17--31}, 8332 year = {2014}, 8333 journal = {Parallel Computing}, 8334 doi = {10.1016/j.parco.2013.10.001}, 8335 petsc_uses = {KSP} 8336} 8337 8338@TechReport{ mszm2012, 8339 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 8340 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8341 year = {2012}, 8342 number = {ANL/MCS-P2097-0512}, 8343 institution = {Argonne National Laboratory}, 8344 petsc_uses = {KSP} 8345} 8346 8347@InProceedings{ bkmms2012, 8348 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 8349 F. Smith}, 8350 title = {Composable linear solvers for multiphysics}, 8351 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 8352 Computing} ({ISPDC} 2012)}, 8353 year = {2012}, 8354 doi = {10.1109/ISPDC.2012.16}, 8355 publisher = {IEEE Computer Society}, 8356 pages = {55--62}, 8357 petsc_uses = {KSP} 8358} 8359 8360@Article{ bourdinbucuroudet2009, 8361 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 8362 title = {Optimal Partitions for Eigenvalues}, 8363 journal = {SIAM J. Sci. Comput.}, 8364 volume = {31}, 8365 number = {6}, 8366 pages = {4100--4114}, 8367 year = {2009}, 8368 petsc_uses = {KSP} 8369} 8370 8371@InBook{ kimnbourdin2007, 8372 author = {J.-H. Kimn and Blaise Bourdin}, 8373 title = {Numerical implementation of overlapping balancing domain decomposition methods on 8374 unstructured meshes}, 8375 editor = {O. B. Widlund and D. E. Keyes}, 8376 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 8377 series = {Lecture Notes in Computational Science and Engineering}, 8378 number = {55}, 8379 publisher = {Springer-Verlag}, 8380 pages = {309--315}, 8381 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 8382 year = {2007}, 8383 petsc_uses = {KSP} 8384} 8385 8386@Article{ bjm2005, 8387 author = {AH Baker and ER Jessup and T Manteuffel}, 8388 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 8389 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 8390 year = {2005}, 8391 petsc_uses = {KSP} 8392} 8393 8394@Unpublished{ sundar-2008a, 8395 author = {R.S. Sampath and G. Biros}, 8396 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 8397 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8398 petsc_uses = {KSP} 8399} 8400 8401@Article{ sundar-2008, 8402 author = {H. Sundar and R.S. Sampath and G. Biros}, 8403 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 8404 journal = {SIAM Journal on Scientific Computing}, 8405 year = {2008}, 8406 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8407 petsc_uses = {KSP} 8408} 8409 8410@InProceedings{ sundar-2007, 8411 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8412 title = {Low-constant parallel algorithms for finite element simulations using linear 8413 octrees}, 8414 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 8415 year = {2007}, 8416 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8417 petsc_uses = {KSP} 8418} 8419 8420@InProceedings{ adams-98a, 8421 author = {Adams, Mark ~F.}, 8422 title = {A Parallel Maximal Independent Set Algorithm}, 8423 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 8424 year = {1998}, 8425 petsc_uses = {KSP} 8426} 8427 8428@Article{ akcelik2005ddd, 8429 title = {{Dynamic data-driven inversion for terascale simulations: real-time 8430 identification of airborne contaminants}}, 8431 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 8432 van Bloemen Waanders, B.}, 8433 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 8434 year = {2005}, 8435 publisher = {IEEE Computer Society Washington, DC, USA}, 8436 petsc_uses = {KSP} 8437} 8438 8439@InBook{ akcelik-2006, 8440 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 8441 Bloemen Waanders}, 8442 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 8443 title = {Frontiers of Parallel Computing}, 8444 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 8445 publisher = {SIAM}, 8446 year = {2006}, 8447 petsc_uses = {KSP} 8448} 8449 8450@Article{ dt, 8451 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 8452 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 8453 Convection Diffusion Equations}, 8454 journal = {The Journal of Supercomputing}, 8455 year = {2004}, 8456 pages = {235--253}, 8457 volume = {28}, 8458 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 8459 petsc_uses = {KSP} 8460} 8461 8462@PhDThesis{ hwang2004, 8463 author = {Feng-Nan Hwang}, 8464 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 8465 Computational Fluid Dynamics}, 8466 school = {University of Colorado at Boulder}, 8467 year = {2004}, 8468 petsc_uses = {KSP} 8469} 8470 8471@PhDThesis{ baker, 8472 author = {{A. H.} Baker}, 8473 title = {On improving the performance of the linear solver restarted {GMRES}}, 8474 school = {University of Colorado at Boulder}, 8475 year = {2003}, 8476 petsc_uses = {KSP} 8477} 8478 8479@TechReport{ klawonnrheinbach601, 8480 author = {Axel Klawonn and Oliver Rheinbach}, 8481 title = {A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional 8482 Linear Elasticity Using a Transformation of Basis}, 8483 institution = {Universit\"at Duisburg-Essen}, 8484 year = {2005}, 8485 type = {Technical Report}, 8486 number = {SM-E-601}, 8487 petsc_uses = {KSP} 8488} 8489 8490@TechReport{ klawonnrheinbach609, 8491 author = {Axel Klawonn and Oliver Rheinbach}, 8492 title = {Inexact FETI-DP Methods}, 8493 institution = {Universit\"at Duisburg-Essen}, 8494 year = {2005}, 8495 type = {Technical Report}, 8496 number = {SM-E-609}, 8497 petsc_uses = {KSP} 8498} 8499 8500@TechReport{ klawonnrheinbach607, 8501 author = {Axel Klawonn and Oliver Rheinbach}, 8502 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 8503 institution = {Universit\"at Duisburg-Essen}, 8504 year = {2005}, 8505 type = {Technical Report}, 8506 number = {SM-E-607}, 8507 petsc_uses = {KSP} 8508} 8509 8510@Article{ kul-natraj-pbp, 8511 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 8512 title = {Performance of a parallel mixed finite element implementation for fourth order 8513 clamped anisotropic plate bending problems in distributed memory environments}, 8514 journal = {Applied Mathematics and Computation}, 8515 volume = {155}, 8516 year = {2004}, 8517 number = {3}, 8518 pages = {753--777}, 8519 petsc_uses = {KSP} 8520} 8521 8522@Article{ bramkamp2006uej, 8523 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 8524 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 8525 journal = {Computers \& Fluids}, 8526 volume = {35}, 8527 number = {10}, 8528 pages = {1063--1073}, 8529 doi = {10.1016/j.compfluid.2005.10.003}, 8530 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 8531 derivation of the analytic flux Jacobian can become quite complicated depending on 8532 the complexity of the numerical flux calculation. Practically, the derivation of 8533 the exact Jacobian by hand is an unrealistic option because of the enormous 8534 man-hour investment needed. In this work, automatic differentiation is used to 8535 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 8536 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 8537 approximated by first-order forward differences. For a two-dimensional airfoil 8538 under three different flight conditions (quasi-incompressible flow, compressible 8539 subsonic flow, and transonic flow), we show that the robustness and performance of 8540 the present finite volume scheme is significantly improved by using exact 8541 Jacobians.}, 8542 year = {2006}, 8543 petsc_uses = {KSP} 8544} 8545 8546@Article{ shahbazi1, 8547 author = {Khosro Shahbazi}, 8548 title = {An explicit expression for the penalty parameter of the interior penalty method}, 8549 journal = {Journal of Computational Physics}, 8550 volume = {205}, 8551 year = {2005}, 8552 pages = {401--407}, 8553 petsc_uses = {KSP} 8554} 8555 8556@TechReport{ kk, 8557 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 8558 author = {Hans-Peter Kersken and Uwe Kuster}, 8559 year = {1999}, 8560 institution = {University of Stuttgart}, 8561 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 8562 number = {310}, 8563 petsc_uses = {KSP} 8564} 8565 8566@Article{ miha-mija, 8567 author = {M. D. Mihajlovi and S. Mijalkovi}, 8568 title = {A component decomposition preconditioning for 3D stress analysis problems}, 8569 journal = {Numerical Linear Algebra with Applications}, 8570 volume = {9}, 8571 year = {2002}, 8572 pages = {567--583}, 8573 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 8574 petsc_uses = {KSP} 8575} 8576 8577@Article{ bjm, 8578 author = {M Benzi and W Joubert and G Mateescu}, 8579 journal = {Electronic Transactions on Numerical Analysis}, 8580 year = {1999}, 8581 volume = {8}, 8582 pages = {88--114}, 8583 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 8584 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}, 8585 petsc_uses = {KSP} 8586} 8587 8588@PhDThesis{ hyde, 8589 author = {EMK Hyde}, 8590 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 8591 school = {Caltech}, 8592 year = {2003}, 8593 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 8594 petsc_uses = {KSP} 8595} 8596 8597@Article{ km2003, 8598 author = {A. Keese and H. G. Matthies}, 8599 journal = {Proceedings in Applied Mathematics and Mechanics}, 8600 year = {2003}, 8601 volume = {2}, 8602 pages = {485--486}, 8603 title = {Parallel Solution of Stochastic PDEs}, 8604 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 8605 petsc_uses = {KSP} 8606} 8607 8608@Article{ whszss, 8609 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 8610 and Otmar Scherzer and H. Siegfried Stiehl}, 8611 journal = {Real Time Imaging}, 8612 year = {2001}, 8613 volume = {7}, 8614 pages = {31--45}, 8615 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 8616 approaches}, 8617 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 8618 petsc_uses = {KSP} 8619} 8620 8621@TechReport{ baker1, 8622 title = {An Efficient Block Variant of GMRES}, 8623 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 8624 year = {2003}, 8625 type = {Technical Report}, 8626 institution = {University of Colorado, Boulder}, 8627 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 8628 number = {CU-CS-957-03}, 8629 petsc_uses = {KSP} 8630} 8631 8632@InProceedings{ mc2003, 8633 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 8634 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 8635 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8636 Methods}, 8637 pages = {639--646}, 8638 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8639 note = {}, 8640 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8641 year = {2003}, 8642 petsc_uses = {KSP} 8643} 8644 8645@InProceedings{ kt2003, 8646 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 8647 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 8648 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8649 Methods}, 8650 pages = {615--622}, 8651 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8652 note = {}, 8653 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8654 year = {2003}, 8655 petsc_uses = {KSP} 8656} 8657 8658@InProceedings{ krw2003, 8659 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 8660 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 8661 3D}, 8662 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8663 Methods}, 8664 pages = {361--368}, 8665 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8666 note = {}, 8667 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8668 year = {2003}, 8669 petsc_uses = {KSP} 8670} 8671 8672@InProceedings{ hc2003, 8673 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 8674 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 8675 Nonlinear Preconditioning}, 8676 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8677 Methods}, 8678 pages = {201--208}, 8679 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8680 note = {}, 8681 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8682 year = {2003}, 8683 petsc_uses = {KSP} 8684} 8685 8686@InProceedings{ g2003, 8687 author = {P. Goldfeld}, 8688 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 8689 (Generalized) {Stokes} and Parallel Implementation}, 8690 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8691 Methods}, 8692 pages = {209--216}, 8693 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8694 publisher = {National Autonomous University of Mexico (UNAM)}, 8695 note = {}, 8696 url = {http://www.ddm.org/DD14}, 8697 year = {2003}, 8698 petsc_uses = {KSP} 8699} 8700 8701@InProceedings{ dhv2003, 8702 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 8703 title = {Toward scalable FETI algorithm for variational inequalities with applications to 8704 composites}, 8705 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8706 Methods}, 8707 pages = {395--401}, 8708 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8709 publisher = {National Autonomous University of Mexico (UNAM)}, 8710 note = {}, 8711 url = {http://www.ddm.org/DD14}, 8712 year = {2003}, 8713 petsc_uses = {KSP} 8714} 8715 8716@InProceedings{ dhsv2002, 8717 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 8718 title = {Scalabilities of FETI for variational inequalities and contact shape 8719 optimization}, 8720 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8721 Methods}, 8722 pages = {359--367}, 8723 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8724 publisher = {CIMNE, Barcelona, Spain}, 8725 note = {}, 8726 url = {http://www.ddm.org/DD13}, 8727 year = {2002}, 8728 petsc_uses = {KSP} 8729} 8730 8731@InProceedings{ cky2002, 8732 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 8733 title = {A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked 8734 Duct Flows}, 8735 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8736 Methods}, 8737 pages = {343--350}, 8738 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8739 publisher = {CIMNE, Barcelona, Spain}, 8740 note = {}, 8741 url = {http://www.ddm.org/DD13}, 8742 year = {2002}, 8743 petsc_uses = {KSP} 8744} 8745 8746@Conference{ li-etal:03, 8747 author = {Li, Z. and Lanteri S. and Saad, Y.}, 8748 title = {Multiplicative-additive preconditioning combination for general sparse linear 8749 systems}, 8750 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 8751 Matrix Problems in Scientific and Industrial Applications}, 8752 address = {Napa, California, USA}, 8753 date = {october 27-29}, 8754 year = {2003}, 8755 petsc_uses = {KSP} 8756} 8757 8758@Article{ bashir2008hessian, 8759 title = {Hessian-based model reduction for large-scale systems with initial-condition 8760 inputs}, 8761 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 8762 J.}, 8763 journal = {International journal for numerical methods in engineering}, 8764 volume = {73}, 8765 number = {6}, 8766 pages = {844--868}, 8767 year = {2008}, 8768 publisher = {Wiley Online Library}, 8769 petsc_uses = {KSP} 8770} 8771 8772@Article{ bashir2007hessian, 8773 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 8774 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 8775 K.}, 8776 journal = {Computational Science--ICCS 2007}, 8777 pages = {1010--1017}, 8778 year = {2007}, 8779 publisher = {Springer}, 8780 petsc_uses = {KSP} 8781} 8782 8783@Article{ akcelik2011fast, 8784 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 8785 inverse problems based on low-rank partial {H}essian approximations}, 8786 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 8787 Waanders, B. and Wilcox, L.}, 8788 journal = {SIAM Journal on Scientific Computing}, 8789 volume = {33}, 8790 number = {1}, 8791 year = {2011}, 8792 petsc_uses = {KSP} 8793} 8794 8795@InProceedings{ ff2003, 8796 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 8797 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 8798 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 8799 year = {2003}, 8800 petsc_uses = {KSP} 8801} 8802 8803@InProceedings{ d2b2004, 8804 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 8805 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 8806 Ordering Strategies}, 8807 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 8808 year = {2004}, 8809 petsc_uses = {KSP} 8810} 8811 8812@InProceedings{ d2v2005, 8813 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8814 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 8815 Flow Equations}, 8816 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 8817 year = {2005}, 8818 petsc_uses = {KSP} 8819} 8820 8821@InProceedings{ dvs2006, 8822 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 8823 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 8824 Mixed Convection Equations}, 8825 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 8826 year = {2006}, 8827 petsc_uses = {KSP} 8828} 8829 8830@Article{ dsv2006, 8831 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8832 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 8833 Flow Equations}, 8834 journal = {Computational Fluid Dynamics}, 8835 year = {2006}, 8836 volume = {15}, 8837 number = {1}, 8838 petsc_uses = {KSP} 8839} 8840 8841@Article{ lahaye03, 8842 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 8843 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 8844 journal = {J. Comput. Appl. Math.}, 8845 year = {2004}, 8846 pages = {267--275}, 8847 volume = {168}, 8848 petsc_uses = {KSP} 8849} 8850 8851@TechReport{ brmn, 8852 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 8853 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 8854 year = {2002}, 8855 type = {Technical Report}, 8856 institution = {ANL}, 8857 number = {ANL/MCS-P993-0902}, 8858 note = {To appear in Future Generation Computer Systems}, 8859 petsc_uses = {KSP} 8860} 8861 8862@InProceedings{ mnbr, 8863 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 8864 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 8865 Algorithms}, 8866 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 8867 Mechanics}, 8868 year = {2003}, 8869 petsc_uses = {KSP} 8870} 8871 8872@InProceedings{ bmnr, 8873 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 8874 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 8875 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 8876 Applications, Lecture notes in Computer Science 2677}, 8877 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 8878 pages = {828--839}, 8879 year = {2003}, 8880 petsc_uses = {KSP} 8881} 8882 8883@Article{ ph03, 8884 author = {M. Pernice and R. D. Hornung}, 8885 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 8886 journal = {Computing and Visualization in Science}, 8887 year = {2003}, 8888 lab = {LANL}, 8889 petsc_uses = {KSP} 8890} 8891 8892@Article{ adams-02, 8893 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 8894 journal = {J. Comp. Phys.}, 8895 number = {2}, 8896 pages = {593-610}, 8897 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 8898 volume = {188}, 8899 year = {2003}, 8900 petsc_uses = {KSP} 8901} 8902 8903@InProceedings{ adams2001distributed, 8904 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 8905 smoothers}, 8906 author = {Adams, M.F.}, 8907 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 8908 pages = {14--14}, 8909 year = {2001}, 8910 organization = {IEEE}, 8911 petsc_uses = {KSP} 8912} 8913 8914@PhDThesis{ els01, 8915 author = {Ulrich Elsner}, 8916 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 8917 algorithms}, 8918 school = {Technical University Chemnitz}, 8919 year = {2002}, 8920 publisher = {Logos Verlag, Berlin}, 8921 isbn = {3-89722-923-4}, 8922 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 8923 different graph partitioning algorithms}, 8924 petsc_uses = {KSP} 8925} 8926 8927@TechReport{ ckk02, 8928 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 8929 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 8930 year = {2002}, 8931 type = {Technical Report}, 8932 institution = {ODU}, 8933 url = {http://www.math.odu.edu/\~{ }keyes}, 8934 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 8935 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 8936 Methods}, 8937 petsc_uses = {KSP} 8938} 8939 8940@Article{ gpw2002, 8941 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 8942 Heterogeneous Problems in Linear Elasticity}, 8943 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 8944 year = {2003}, 8945 pages = {283--324}, 8946 volume = {95}, 8947 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 8948 journal = {Numerische Mathematik}, 8949 petsc_uses = {KSP} 8950} 8951 8952@Article{ dh1, 8953 title = {Scalability and FETI based algorithm for large discretized variational 8954 inequalities}, 8955 author = {Z Dostal and D Horak}, 8956 year = {2003}, 8957 pages = {347--357}, 8958 volume = {61}, 8959 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 8960 journal = {Mathematics and Computers in Simulation}, 8961 petsc_uses = {KSP} 8962} 8963 8964@InProceedings{ dhsv1, 8965 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 8966 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 8967 title = {36 Scalabilities of FETI for Variational Inequalities and Contact Shape 8968 Optimization}, 8969 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8970 Methods}, 8971 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 8972 Kuznetsov}, 8973 petsc_uses = {KSP} 8974} 8975 8976@Article{ lahaye02, 8977 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 8978 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 8979 journal = {IEEEMAGN}, 8980 year = {2002}, 8981 volume = {38}, 8982 number = {2}, 8983 pages = {413-416}, 8984 petsc_uses = {KSP} 8985} 8986 8987@Article{ ckm01, 8988 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 8989 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 8990 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 8991 fluid dynamics}, 8992 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 8993 year = {2002}, 8994 volume = {40}, 8995 pages = {1463--1470}, 8996 petsc_uses = {KSP} 8997} 8998 8999@InProceedings{ cky01, 9000 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 9001 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 9002 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 9003 duct flow}, 9004 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9005 Methods}, 9006 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9007 Kuznetsov}, 9008 year = {2002}, 9009 petsc_uses = {KSP} 9010} 9011 9012@Article{ ck02, 9013 author = {X.-C. Cai and D. E. Keyes}, 9014 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 9015 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 9016 journal = {SIAM J. Sci. Comput.}, 9017 year = {2002}, 9018 pages = {183--200}, 9019 volume = {24}, 9020 petsc_uses = {KSP} 9021} 9022 9023@Article{ c04, 9024 author = {Feng-Nan Hwang and X.-C. Cai}, 9025 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 9026 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 9027 for incompressible {Navier-Stokes} equations}, 9028 journal = {Journal of Computational Physics}, 9029 year = {2005}, 9030 volume = {204}, 9031 pages = {666--691}, 9032 petsc_uses = {KSP} 9033} 9034 9035@Article{ hc06, 9036 author = {Feng-Nan Hwang and X.-C. Cai}, 9037 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 9038 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 9039 Algorithms}, 9040 journal = {Computer Methods in Applied Mechanics and Engineering}, 9041 year = {2006}, 9042 volume = {196}, 9043 pages = {1603--1611}, 9044 petsc_uses = {KSP} 9045} 9046 9047@InProceedings{ adams-01, 9048 author = {Mark F. Adams}, 9049 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 9050 Smoothers}, 9051 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 9052 address = {Denver, Colorado}, 9053 month = {November}, 9054 year = {2001}, 9055 petsc_uses = {KSP} 9056} 9057 9058@Book{ 1dl, 9059 author = {Domenico Lahaye}, 9060 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 9061 Computations}, 9062 year = {2001}, 9063 publisher = {Katholieke Universiteit Leuven}, 9064 notes = {Thesis}, 9065 petsc_uses = {KSP} 9066} 9067 9068@Article{ adams-00, 9069 author = {Adams, M.~F.}, 9070 journal = {International Journal for Numerical Methods in Engineering}, 9071 number = {8}, 9072 pages = {1241-1262}, 9073 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 9074 Deformation Elasticity and Plasticity}, 9075 volume = {48}, 9076 year = {2000}, 9077 petsc_uses = {KSP} 9078} 9079 9080@Article{ adams2002evaluation, 9081 author = {Adams, M.~F.}, 9082 journal = {International Journal for Numerical Methods in Engineering}, 9083 number = {1}, 9084 pages = {519-534}, 9085 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 9086 Problems in Solid Mechanics}, 9087 volume = {55}, 9088 year = {2002}, 9089 petsc_uses = {KSP} 9090} 9091 9092@Article{ lahaye00, 9093 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 9094 title = {Algebraic Multigrid for Complex Symmetric Systems}, 9095 journal = {IEEEMAGN}, 9096 year = {2000}, 9097 volume = {36}, 9098 number = {4}, 9099 pages = {1535--1538}, 9100 petsc_uses = {KSP} 9101} 9102 9103@InProceedings{ adams-99c, 9104 author = {Mark F. Adams and J. Demmel}, 9105 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 9106 Finite Element Problems}, 9107 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 9108 address = {Portland, Oregon}, 9109 month = {November}, 9110 year = {1999}, 9111 petsc_uses = {KSP} 9112} 9113 9114@Article{ chan95, 9115 author = {T. Chan and B. Smith and J. Zou}, 9116 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 9117 Grids}, 9118 journal = {Numer. Math.}, 9119 year = {1995}, 9120 volume = {73}, 9121 pages = {149--167}, 9122 petsc_uses = {KSP} 9123} 9124 9125@TechReport{ adams-csd-98-993, 9126 pages = {11}, 9127 year = {1998}, 9128 type = {Technical Report}, 9129 number = {CSD-98-993}, 9130 institution = {University of California, Berkeley}, 9131 title = {A Parallel Maximal Independent Set Algorithm}, 9132 bibdate = {March 11, 1998}, 9133 author = {Mark F. Adams and James Demmel}, 9134 abstract = {The parallel construction of maximal independent sets is a useful building block 9135 for many algorithms in the computational sciences, including graph coloring and 9136 multigrid coarse grid creation on unstructured meshes. We present an efficient 9137 asynchronous maximal independent set algorithm for use on parallel computers, for 9138 ``well partitioned'' graphs, that arise from finite element (FE) models. For 9139 appropriately partitioned bounded degree graphs, it is shown that the running time 9140 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 9141 improvement over the previous best P-RAM complexity for this class of graphs. We 9142 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 9143 model is indicative of the performance one can expect with practical partitions on 9144 graphs from FE problems.}, 9145 month = mar # { 11,}, 9146 petsc_uses = {KSP} 9147} 9148 9149@TechReport{ k676, 9150 year = {1994}, 9151 type = {Technical Report}, 9152 number = {TR1994-676}, 9153 institution = {New York University}, 9154 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 9155 Term}, 9156 author = {Axel Klawonn}, 9157 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 9158 petsc_uses = {KSP} 9159} 9160 9161@Book{ ak1, 9162 author = {Axel Klawonn}, 9163 title = {Preconditioners for Indefinite Problems}, 9164 year = {1995}, 9165 publisher = {Westfalishen Wilhelms-Universitat Munster}, 9166 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 9167 notes = {Thesis}, 9168 petsc_uses = {KSP} 9169} 9170 9171@TechReport{ knepleykarpeev05, 9172 pages = {41}, 9173 year = {2005}, 9174 type = {Technical Report}, 9175 number = {ANL/MCS-P1295-1005}, 9176 institution = {Argonne National Laboratory}, 9177 title = {Flexible Representation of Computational Meshes}, 9178 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9179 abstract = {}, 9180 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 9181 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 9182 month = {October}, 9183 petsc_uses = {DMPlex} 9184} 9185 9186@TechReport{ knepleykarpeev07a, 9187 pages = {14}, 9188 year = {2007}, 9189 type = {Technical Report}, 9190 number = {ANL/MCS-P1455-0907}, 9191 institution = {Argonne National Laboratory}, 9192 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9193 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9194 abstract = {}, 9195 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 9196 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 9197 month = {February}, 9198 petsc_uses = {DMPlex} 9199} 9200 9201@Article{ knepleykarpeev09, 9202 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9203 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9204 journal = {Scientific Programming}, 9205 volume = {17}, 9206 number = {3}, 9207 pages = {215--230}, 9208 year = {2009}, 9209 doi = {10.3233/SPR-2009-0249}, 9210 url = {http://arxiv.org/abs/0908.4427}, 9211 note = {\url{http://arxiv.org/abs/0908.4427}}, 9212 petsc_uses = {DMPlex} 9213} 9214 9215@Article{ biezuner2012computing, 9216 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 9217 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 9218 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 9219 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 9220 Sublinear Supersolutions}, 9221 journal = {Journal of Scientific Computing}, 9222 publisher = {Springer Netherlands}, 9223 issn = {0885-7474}, 9224 keyword = {Mathematics and Statistics}, 9225 pages = {180--201}, 9226 volume = {52}, 9227 issue = {1}, 9228 year = {2012}, 9229 doi = {10.1007/s10915-011-9540-0}, 9230 petsc_uses = {KSP} 9231} 9232 9233% LiteralHTML: 9234% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 9235% LiteralHTML: 9236@Book{ knepley2017, 9237 title = {Computational Science I}, 9238 author = {Matthew G. Knepley}, 9239 url = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}, 9240 note = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}}, 9241 publisher = {PETSc}, 9242 year = {2017}, 9243 petsc_uses = {KSP} 9244} 9245 9246@Article{ verleyeuser, 9247 title = {{User friendly permeability predicting software for technical textiles}}, 9248 author = {Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and 9249 Roose, D.}, 9250 journal = {status: published}, 9251 issn = {1560-6074}, 9252 publisher = {Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}, 9253 petsc_uses = {KSP} 9254} 9255 9256@Book{ pacheco, 9257 author = {Peter Pacheco}, 9258 title = {Parallel Programming with MPI}, 9259 year = {1997}, 9260 publisher = {Morgan-Kaufmann}, 9261 note = {Devotes a couple of sections to PETSc}, 9262 petsc_uses = {KSP} 9263} 9264 9265@Book{ 1sbg, 9266 author = {Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp}, 9267 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 9268 Differential Equations}, 9269 year = {1996}, 9270 publisher = {Cambridge University Press}, 9271 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 9272 petsc_uses = {KSP} 9273} 9274 9275@Misc{ petsc-fem:homepage, 9276 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 9277 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 9278 G. Rodriguez and G. Filippini}, 9279 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 9280 petsc_uses = {KSP} 9281} 9282 9283@Misc{ petsc4py-web-page, 9284 author = {Lisandro Dalcin}, 9285 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 9286 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 9287 note = {http://code.google.com/p/petsc4py/}, 9288 petsc_uses = {KSP} 9289} 9290 9291@Article{ libmeshpaper06, 9292 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 9293 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 9294 Simulations}}, 9295 journal = {Engineering with Computers}, 9296 volume = {22}, 9297 number = {3--4}, 9298 pages = {237--254}, 9299 year = {2006}, 9300 doi = {10.1007/s00366-006-0049-3}, 9301 petsc_uses = {KSP} 9302} 9303 9304@Misc{ sisiphus:homepage, 9305 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 9306 High-Resolution, Unstructured Simulations}, 9307 author = {T. {Tautges et al.}}, 9308 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 9309 petsc_uses = {KSP} 9310} 9311 9312@Misc{ pflotran:homepage, 9313 title = {{PFLOTRAN} project}, 9314 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 9315 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 9316 howpublished = {\url{http://pflotran.org/}}, 9317 petsc_uses = {KSP} 9318} 9319 9320@Misc{ pism:homepage, 9321 title = {{PISM}: A Parallel Ice Sheet Model}, 9322 author = {E. {Bueler et al.}}, 9323 howpublished = {\url{http://pism-docs.org}}, 9324 petsc_uses = {KSP} 9325} 9326 9327@Misc{ dohp:homepage, 9328 title = {Dohp: Dual order $hp$-finite elements}, 9329 author = {J. Brown}, 9330 howpublished = {\url{http://dohp.org}}, 9331 petsc_uses = {KSP} 9332} 9333 9334@Article{ mccourtrognlienetal12, 9335 title = {Improving parallel scalability for edge plasma transport simulations with neutral 9336 gas species}, 9337 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 9338 journal = {Computational Science and Discovery}, 9339 year = {2012}, 9340 volume = {5}, 9341 number = {014012}, 9342 doi = {10.1088/1749-4699/5/1/014012}, 9343 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 9344 2011)}, 9345 petsc_uses = {KSP} 9346} 9347 9348@Misc{ petclaw-github, 9349 title = {Pet{C}law Software}, 9350 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 9351 year = {2011}, 9352 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 9353 petsc_uses = {KSP} 9354} 9355 9356@Misc{ pyclaw-web-page, 9357 author = {Kyle T. Mandli and David I. Ketcheson and others}, 9358 title = {{PyClaw} software}, 9359 howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}}, 9360 url = {http://clawpack.github.io/doc/pyclaw/}, 9361 year = {2012}, 9362 petsc_uses = {KSP} 9363} 9364 9365@Article{ ketcheson2011highorder, 9366 title = {High-order wave propagation algorithms for general hyperbolic systems}, 9367 author = {Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.}, 9368 year = {2011}, 9369 note = {submitted}, 9370 petsc_uses = {KSP} 9371} 9372 9373@Article{ biros2005pln1, 9374 title = {{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained 9375 optimization. Part I: The {Krylov-Schur} solver}}, 9376 author = {Biros, G. and Ghattas, O.}, 9377 journal = {SIAM Journal on Scientific Computing}, 9378 volume = {27}, 9379 number = {2}, 9380 pages = {687--713}, 9381 year = {2005}, 9382 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9383 petsc_uses = {KSP} 9384} 9385 9386@Article{ biros2005pln2, 9387 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 9388 optimization. Part {II}: The {Lagrange Newton} solver, and its application to 9389 optimal control of steady viscous flows}, 9390 author = {Biros, G. and Ghattas, O.}, 9391 journal = {SIAM Journal on Scientific Computing}, 9392 volume = {27}, 9393 number = {2}, 9394 pages = {714--739}, 9395 year = {2005}, 9396 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9397 petsc_uses = {KSP} 9398} 9399 9400@Misc{ issm:homepage, 9401 title = {{I}ce {S}heet {S}ystem {M}odel}, 9402 author = {Eric Larour and Mathieu Morlighem and Helene Seroussi}, 9403 year = {2010}, 9404 note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}, 9405 petsc_uses = {KSP} 9406} 9407 9408@Article{ morlighem2010spatial, 9409 title = {Spatial patterns of basal drag inferred using control methods from a 9410 full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est 9411 {A}ntarctica}, 9412 author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and 9413 Aubry, D.}, 9414 journal = {Geophysical Research Letters}, 9415 volume = {37}, 9416 number = {14}, 9417 pages = {L14502}, 9418 year = {2010}, 9419 publisher = {American Geophysical Union}, 9420 petsc_uses = {KSP} 9421} 9422 9423@Article{ jardin2012plasmas, 9424 title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics 9425 of tokamak plasmas}, 9426 author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 9427 journal = {Computational Science \& Discovery}, 9428 volume = {5}, 9429 number = {1}, 9430 url = {http://stacks.iop.org/1749-4699/5/014002}, 9431 year = {2012}, 9432 petsc_uses = {KSP} 9433} 9434 9435@Article{ cmz2016, 9436 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 9437 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 9438 journal = {Journal of Scientific Computing}, 9439 publisher = {Springer}, 9440 pages = {803--825}, 9441 volume = {68}, 9442 issue = {2}, 9443 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 9444 doi = {10.1007/s10915-015-0159-4}, 9445 year = {2016}, 9446 note = {Also preprint ANL/MCS-P3039-0912}, 9447 petsc_uses = {KSP} 9448} 9449 9450@Article{ knepleybrownruppsmith13, 9451 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 9452 title = {Achieving High Performance with Unified Residual Evaluation}, 9453 journal = {ArXiv e-prints}, 9454 eprint = {1309.1204}, 9455 archiveprefix = {arXiv}, 9456 primaryclass = {cs.MS}, 9457 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 9458 Engineering, Finance, and Science}, 9459 year = {2013}, 9460 month = sep, 9461 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 9462 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9463 petsc_uses = {KSP} 9464} 9465 9466@Book{ fenicsbook, 9467 title = {Automated Solution of Differential Equations by the Finite Element Method: The 9468 FEniCS Book}, 9469 series = {Lecture Notes in Computational Science and Engineering}, 9470 volume = {84}, 9471 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 9472 publisher = {Springer}, 9473 isbn = {978-3-642-23098-1}, 9474 year = {2012}, 9475 petsc_uses = {KSP} 9476} 9477 9478@Article{ demidovahnertruppgottschling12, 9479 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 9480 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 9481 journal = {ArXiv e-prints}, 9482 archiveprefix = {arXiv}, 9483 eprint = {1212.6326}, 9484 primaryclass = {cs.MS}, 9485 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 9486 Parallel, and Cluster Computing, Physics - Computational Physics}, 9487 year = {2012}, 9488 month = dec, 9489 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 9490 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9491 petsc_uses = {KSP} 9492} 9493 9494@InProceedings{ viennacl, 9495 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 9496 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 9497 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 9498 year = {2010}, 9499 pages = {51-56}, 9500 petsc_uses = {KSP} 9501} 9502 9503@Article{ knepleybrownmcinnessmithruppadams2015, 9504 title = {Exascale Computing without Threads}, 9505 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9506 Karl Rupp and Mark Adams}, 9507 url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950}, 9508 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9509 Scientific Software Architecture for Portability and Performance}, 9510 doi = {10.6084/m9.figshare.5824950.v1}, 9511 year = {2015}, 9512 petsc_uses = {KSP} 9513} 9514 9515@Article{ knepleybrownmcinnessmithruppadams2015b, 9516 title = {Overview of the {PETSc} Library}, 9517 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9518 Karl Rupp and Mark Adams}, 9519 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 9520 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9521 Scientific Software Architecture for Portability and Performance}, 9522 year = {2015}, 9523 petsc_uses = {KSP} 9524} 9525 9526@InBook{ balaybrownknepleymcinnessmith2015, 9527 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 9528 Smith}, 9529 bookeditor = {J. Carver}, 9530 title = {Software Engineering for Science}, 9531 chapter = {Providing Mixed Language and Legacy Support within a Library}, 9532 publisher = {Taylor \& Francis}, 9533 year = {2015}, 9534 petsc_uses = {KSP} 9535} 9536 9537@Article{ ruppbalaybrownknepleymcinnessmith2015, 9538 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 9539 Software}, 9540 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 9541 McInnes and Barry F. Smith}, 9542 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 9543 Productivity Challenges}, 9544 journal = {ArXiv e-prints}, 9545 archiveprefix = {arXiv}, 9546 eprint = {1510.01122}, 9547 year = {2015}, 9548 petsc_uses = {KSP} 9549} 9550 9551@InProceedings{ knepley2013accurately, 9552 title = {Accurately Citing Software and Algorithms Used in Publications}, 9553 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 9554 F.}, 9555 year = {2013}, 9556 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 9557 (WSSSPE), held at SC13}, 9558 doi = {10.6084/m9.figshare.785731}, 9559 petsc_uses = {KSP} 9560} 9561 9562@InProceedings{ milleretal2013, 9563 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 9564 Strategies Developed for {FASTMath}}, 9565 author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and 9566 Barry Smith}, 9567 year = {2013}, 9568 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 9569 (WSSSPE), held at SC13}, 9570 doi = {10.6084/m9.figshare.789055}, 9571 petsc_uses = {KSP} 9572} 9573 9574@TechReport{ dudsonetal2012, 9575 title = {Improved Nonlinear Solvers in {BOUT++}}, 9576 author = {Ben Dudson and Sean Farley and Lois Curfman McInnes}, 9577 institution = {Argonne National Laboratory}, 9578 number = {ANL/MCS-P3025-0812}, 9579 year = {2012}, 9580 petsc_uses = {KSP} 9581} 9582 9583@Misc{ brown13, 9584 author = {J. Brown}, 9585 title = {Scalable Repository Workflows}, 9586 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 9587 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 9588 year = {2013}, 9589 petsc_uses = {KSP} 9590} 9591 9592@Misc{ starforest11, 9593 title = {Star forests as a parallel communication model}, 9594 author = {Jed Brown}, 9595 url = {https://jedbrown.org/files/StarForest.pdf}, 9596 year = {2011}, 9597 petsc_uses = {KSP} 9598} 9599 9600@Misc{ brownknepleysmith13, 9601 author = {J. Brown and M. Knepley and B. Smith}, 9602 title = {Run-time Extensibility: Anything Less is Unsustainable}, 9603 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 9604 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 9605 year = {2013}, 9606 petsc_uses = {KSP} 9607} 9608 9609@Article{ jzhaoyliwkliu15, 9610 author = {J. Zhao and Y. Li and W.K. Liu}, 9611 title = {Predicting band structure of 3{D} mechanical metamaterials with complex geometry 9612 via {XFEM}}, 9613 journal = {Computational Mechanics}, 9614 year = {2015}, 9615 url = {http://link.springer.com/article/10.1007/s00466-015-1129-2}, 9616 petsc_uses = {KSP} 9617} 9618 9619@Article{ alisic14, 9620 author = {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen}, 9621 title = {Compaction around a rigid, circular inclusion in partially molten rock}, 9622 journal = {J. Geophys. Res.}, 9623 year = {2014}, 9624 volume = {119}, 9625 number = {7}, 9626 pages = {5903-5920}, 9627 doi = {10.1002/2013JB010906}, 9628 petsc_uses = {KSP} 9629} 9630 9631@Article{ rhebergen14, 9632 author = {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen}, 9633 title = {Analysis of block preconditioners for models of coupled magma mantle dynamics}, 9634 journal = {SIAM J. Sci. Comp.}, 9635 year = {2014}, 9636 volume = {36}, 9637 number = {4}, 9638 pages = {1960-1977}, 9639 doi = {10.1137/130946678}, 9640 petsc_uses = {KSP} 9641} 9642 9643@Article{ allwright14, 9644 author = {J. Allwright and R.F. Katz}, 9645 title = {Pipe Poiseuille flow of viscously anisotropic, partially molten rock}, 9646 journal = {Geophys. J. Int.}, 9647 year = {2014}, 9648 volume = {199}, 9649 number = {3}, 9650 pages = {1608--1624}, 9651 doi = {10.1093/gji/ggu345}, 9652 petsc_uses = {KSP} 9653} 9654 9655@Misc{ gropp10, 9656 author = {William D. Gropp}, 9657 title = {Update on libraries for {B}lue {W}aters}, 9658 address = {Bordeaux, France}, 9659 year = {2010}, 9660 url = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf}, 9661 petsc_uses = {KSP} 9662} 9663 9664@Article{ ssm2016, 9665 author = {P. Sanan and S.M. Schnepp and D.A. May}, 9666 title = {Pipelined, Flexible {Krylov} Subspace Methods}, 9667 journal = {SIAM Journal on Scientific Computing}, 9668 volume = {38}, 9669 number = {5}, 9670 pages = {C441-C470}, 9671 year = {2016}, 9672 doi = {10.1137/15M1049130}, 9673 petsc_uses = {KSP} 9674} 9675 9676@InProceedings{ mayknepley2017, 9677 title = {{DMSwarm}: Particles in {PETSc}}, 9678 author = {Dave A May and Matthew G Knepley}, 9679 booktitle = {EGU General Assembly Conference Abstracts}, 9680 volume = {19}, 9681 pages = {10133}, 9682 year = {2017}, 9683 petsc_uses = {KSP} 9684} 9685 9686@InProceedings{ adamsbrownknepley2013, 9687 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley}, 9688 title = {Low-communication techniques for extreme-scale multilevel solvers}, 9689 booktitle = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC}, 9690 organization = {DOE Office of Advanced Scientific Computing Research}, 9691 year = {2013}, 9692 petsc_uses = {KSP} 9693} 9694 9695@Article{ bhallagriffithknepleyadamsguy2017, 9696 title = {Scalable smoothing strategies for a geometric multigrid method for the immersed 9697 boundary equations}, 9698 author = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F. 9699 Adams and Robert D. Guy}, 9700 journal = {Advances in Computational Mathematics}, 9701 eprint = {1612.02208}, 9702 note = {In review}, 9703 year = {2017}, 9704 petsc_uses = {KSP} 9705} 9706 9707@Article{ zampini2016pcbddc, 9708 title = {{PCBDDC}: a class of robust dual-primal methods in {PETSc}}, 9709 author = {Zampini, Stefano}, 9710 journal = {SIAM Journal on Scientific Computing}, 9711 volume = {38}, 9712 number = {5}, 9713 pages = {S282--S306}, 9714 year = {2016}, 9715 publisher = {SIAM}, 9716 petsc_uses = {KSP} 9717} 9718 9719@Article{ jolivetromanzampini2020, 9720 title = {{KSPHPDDM} and {PCHPDDM}: extending {PETSc} with advanced {Krylov} methods and 9721 robust multilevel overlapping {Schwarz} preconditioners}, 9722 author = {Pierre Jolivet and Jose Roman and Stefano Zampini}, 9723 journal = {Computers and Mathematics with Applications}, 9724 volume = {84}, 9725 pages = {277--295}, 9726 year = {2020} 9727} 9728 9729@Article{ zampinitu2017, 9730 title = {Multilevel {BDDC} deluxe algorithms with adaptive coarse spaces for flow in 9731 porous media}, 9732 author = {Stefano Zampini and Xuemin Tu}, 9733 journal = {SIAM Journal of Scientific Computing}, 9734 volume = {39}, 9735 number = {4}, 9736 pages = {A1389--A1415}, 9737 year = {2017} 9738} 9739 9740@Article{ ohwidlundzampinidohrmann2017, 9741 title = {{BDDC} algorithms with deluxe scaling and adaptive selection of primal 9742 constraints for {Raviart-Thomas} vector fields}, 9743 author = {D.-S. Oh and Olof B. Widlund and Stefano Zampini and Clark Dohrmann}, 9744 journal = {Mathematics of Computation}, 9745 volume = {87}, 9746 number = {310}, 9747 pages = {659--692}, 9748 year = {2017} 9749} 9750 9751@Article{ veigapavarinoscacchiwidlundzampini2016, 9752 title = {Adaptive selection of primal constraints for isogeometric {BDDC} deluxe 9753 preconditioners}, 9754 author = {L. Beirao Da Veiga and Luca F. Pavarino and S. Scacchi and Olof B. Widlund and 9755 Stefano Zampini}, 9756 journal = {SIAM Journal of Scientific Computing}, 9757 volume = {39}, 9758 number = {1}, 9759 pages = {A281--A302}, 9760 year = {2016} 9761} 9762 9763@Article{ pavarinoscacchiwidlundzampini2018, 9764 title = {Isogeometric {BDDC} deluxe preconditioners for linear elasticity for isogeometric 9765 analysis}, 9766 author = {Luca F. Pavarino and S. Scacchi and Olof B. Widlund and Stefano Zampini}, 9767 journal = {Mathematical Models and Methods in Applied Sciences}, 9768 volume = {28}, 9769 number = {7}, 9770 pages = {1337--1370}, 9771 year = {2018} 9772} 9773 9774@Article{ bergervergiatwaisman2017, 9775 title = {An overlapping Domain Decomposition preconditioning method for monolithic 9776 solution of shear bands}, 9777 author = {Luc Berger-Vergiat and Haim Waisman}, 9778 journal = {Computer Methods in Applied Mechanics and Engineering}, 9779 volume = {318}, 9780 pages = {33--60}, 9781 year = {2017}, 9782 petsc_uses = {KSP} 9783} 9784 9785@Article{ abhyankarmaldonadosmithzhang2020, 9786 title = {{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics 9787 Simulations}, 9788 author = {S. Abhyankar and G. Betrie and D.A. Maldonado and L.C. McInnes and B. Smith and 9789 H. 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May}, 9903 journal = {SIAM Journal on Scientific Computing}, 9904 volume = {38}, 9905 number = {5}, 9906 pages = {C441-C470}, 9907 year = {2016}, 9908 doi = {10.1137/15M1049130}, 9909 petsc_uses = {KSP} 9910} 9911 9912@Article{ petscsf2022, 9913 author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and 9914 Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and 9915 Smith, Barry F. and Zampini, Stefano}, 9916 journal = {IEEE Transactions on Parallel and Distributed Systems}, 9917 title = {The {PetscSF} Scalable Communication Layer}, 9918 year = {2022}, 9919 volume = {33}, 9920 number = {4}, 9921 pages = {842-853}, 9922 doi = {10.1109/TPDS.2021.3084070} 9923} 9924 9925@Article{ brandt2000, 9926 title = {General highly accurate algebraic coarsening}, 9927 author = {Achi Brandt}, 9928 journal = {Electronic Transactions on Numerical Analysis}, 9929 volume = {10}, 9930 number = {9680}, 9931 pages = {1--20}, 9932 issn = {10689613}, 9933 year = {2000} 9934} 9935 9936@Article{ dalcinpazklercosimo2011, 9937 title = {Parallel distributed computing using Python}, 9938 author = {Lisandro D. 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Kler and Alejandro Cosimo}, 9939 journal = {Advances in Water Resources}, 9940 volume = {34}, 9941 number = {9}, 9942 pages = {1124 - 1139}, 9943 note = {New Computational Methods and Software Tools}, 9944 issn = {0309-1708}, 9945 doi = {10.1016/j.advwatres.2011.04.013}, 9946 year = {2011} 9947} 9948 9949@Article{ behnelbradshawcitrodalcinseljebotnsmith2011, 9950 title = {Cython: The Best of Both Worlds}, 9951 author = {Behnel,Stefan and Bradshaw,Robert and Citro,Craig and Dalcin,Lisandro and 9952 Seljebotn,Dag Sverre and Smith,Kurt }, 9953 journal = {Computing in Science \& Engineering}, 9954 volume = {13}, 9955 number = {2}, 9956 pages = {31-39}, 9957 doi = {10.1109/MCSE.2010.118}, 9958 year = {2011} 9959} 9960 9961@Article{ dalcinpazstorti2005, 9962 title = {MPI for Python}, 9963 author = {Lisandro Dalcín and Rodrigo Paz and Mario Storti}, 9964 journal = {Journal of Parallel and Distributed Computing}, 9965 volume = {65}, 9966 number = {9}, 9967 pages = {1108 - 1115}, 9968 issn = {0743-7315}, 9969 doi = {10.1016/j.jpdc.2005.03.010}, 9970 year = {2005} 9971} 9972 9973@Article{ dalcincolliervignalcortescalo2016, 9974 title = {PetIGA: A framework for high-performance isogeometric analysis}, 9975 author = {Lisandro Dalcin and Nathan Collier and P. Vignal and A.M.A. Cortes and Victor M. 9976 Calo}, 9977 journal = {Computer Methods in Applied Mechanics and Engineering}, 9978 volume = {308}, 9979 pages = {151 - 181}, 9980 issn = {0045-7825}, 9981 doi = {10.1016/j.cma.2016.05.011}, 9982 year = {2016} 9983} 9984 9985@Article{ collierpardodalcinpaszynskicalo2012, 9986 title = {The cost of continuity: A study of the performance of isogeometric finite 9987 elements using direct solvers}, 9988 author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M. 9989 Calo}, 9990 journal = {Computer Methods in Applied Mechanics and Engineering}, 9991 volume = {213-216}, 9992 pages = {353 - 361}, 9993 issn = {0045-7825}, 9994 doi = {10.1016/j.cma.2011.11.002}, 9995 year = {2012} 9996} 9997 9998@Article{ collierdalcinpardocalo2013, 9999 title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite 10000 Elements}, 10001 author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo}, 10002 journal = {SIAM Journal on Scientific Computing}, 10003 volume = {35}, 10004 number = {2}, 10005 pages = {A767-A784}, 10006 doi = {10.1137/120881038}, 10007 year = {2013} 10008} 10009 10010@Article{ dunning2017jump, 10011 title = {{JuMP}: a modeling language for mathematical optimization}, 10012 author = {Dunning, Iain and Huchette, Joey and Lubin, Miles}, 10013 journal = {SIAM Review}, 10014 volume = {59}, 10015 number = {2}, 10016 pages = {295--320}, 10017 year = {2017}, 10018 publisher = {SIAM} 10019} 10020 10021@InProceedings{ prudencioschulz2011, 10022 title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for 10023 Estimation, Simulation and Optimization}, 10024 author = {Ernesto E Prudencio and Karl W Schulz}, 10025 booktitle = {European Conference on Parallel Processing}, 10026 pages = {398--407}, 10027 year = {2011} 10028} 10029 10030@Misc{ rol-website, 10031 key = {ROL}, 10032 title = {{Rapid Optimization Library} Website}, 10033 howpublished = {\url{https://trilinos.org/packages/rol}}, 10034 year = {2018} 10035} 10036 10037@Article{ more1994line, 10038 title = {Line search algorithms with guaranteed sufficient decrease}, 10039 author = {Mor{\'e}, Jorge J and Thuente, David J}, 10040 journal = {ACM Transactions on Mathematical Software}, 10041 volume = {20}, 10042 number = {3}, 10043 pages = {286--307}, 10044 year = {1994}, 10045 publisher = {ACM} 10046} 10047 10048@Article{ griewank2000algorithm, 10049 title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or 10050 adjoint mode of computational differentiation}, 10051 author = {Griewank, Andreas and Walther, Andrea}, 10052 journal = {ACM Transactions on Mathematical Software}, 10053 volume = {26}, 10054 number = {1}, 10055 pages = {19--45}, 10056 year = {2000}, 10057 publisher = {ACM} 10058} 10059 10060@Article{ metcalf2011seven, 10061 title = {The seven ages of fortran}, 10062 author = {Metcalf, Michael}, 10063 journal = {Journal of Computer Science \& Technology}, 10064 volume = {11}, 10065 year = {2011} 10066} 10067 10068@Article{ giraldo_2013, 10069 title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified 10070 model of the atmosphere {(NUMA)}}, 10071 author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu}, 10072 journal = {SIAM Journal on Scientific Computing}, 10073 year = {2013}, 10074 number = {5}, 10075 pages = {B1162-B1194}, 10076 volume = {35}, 10077 doi = {10.1137/120876034} 10078} 10079 10080@Article{ constantinescu_tr2016b, 10081 author = {Constantinescu, E.M.}, 10082 title = {Estimating Global Errors in Time Stepping}, 10083 journal = {ArXiv e-prints}, 10084 archiveprefix = {arXiv}, 10085 eprint = {1503.05166}, 10086 primaryclass = {math.NA}, 10087 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70}, 10088 year = {2016}, 10089 month = mar, 10090 adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C}, 10091 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 10092} 10093 10094@Article{ pareschi_2005, 10095 title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems 10096 with Relaxation}, 10097 author = {L. Pareschi and G. Russo}, 10098 journal = {Journal of Scientific Computing}, 10099 year = {2005}, 10100 number = {1}, 10101 pages = {129--155}, 10102 volume = {25} 10103} 10104 10105@Article{ kennedy_2003, 10106 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 10107 author = {C.A. Kennedy and M.H. Carpenter}, 10108 journal = {Appl. Numer. Math.}, 10109 year = {2003}, 10110 number = {1-2}, 10111 pages = {139--181}, 10112 volume = {44}, 10113 doi = {10.1016/S0168-9274(02)00138-1}, 10114 publisher = {Elsevier Science Publishers B. V.} 10115} 10116 10117@Unpublished{ boscarino_tr2011, 10118 title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic 10119 equations in the diffusion limit}, 10120 author = {Boscarino, S. and Pareschi, L. and Russo, G.}, 10121 note = {Arxiv preprint arXiv:1110.4375}, 10122 year = {2011} 10123} 10124 10125@Article{ ascher_1997, 10126 title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential 10127 equations}, 10128 author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri}, 10129 journal = {Applied Numerical Mathematics}, 10130 year = {1997}, 10131 pages = {151--167}, 10132 volume = {25} 10133} 10134 10135@Book{ ascherpetzold1998, 10136 title = {Computer methods for ordinary differential equations and differential-algebraic 10137 equations}, 10138 author = {Uri M Ascher and Linda R Petzold}, 10139 volume = {61}, 10140 publisher = {SIAM}, 10141 year = {1998} 10142} 10143 10144@Article{ colomesbadia2016, 10145 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 10146 equations}, 10147 author = {Oriol Colom{\'e}s and Santiago Badia}, 10148 journal = {International Journal for Numerical Methods in Engineering}, 10149 volume = {105}, 10150 number = {5}, 10151 pages = {372--400}, 10152 year = {2016} 10153} 10154 10155@Article{ sandu_1997, 10156 title = {Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: 10157 {R}osenbrock solvers}, 10158 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 10159 Potra}, 10160 journal = {Atmospheric Environment}, 10161 year = {1997}, 10162 number = {20}, 10163 pages = {3459--3472}, 10164 volume = {31}, 10165 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 10166 task is the integration of the stiff systems of ordinary differential equations 10167 describing the chemical transformations. It is therefore of interest to 10168 systematically search for stiff solvers which can be identified as close to 10169 optimal for atmospheric applications. In this paper we continue our investigation 10170 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 10171 and compare eight solvers on a set of seven box-models used in present day models. 10172 The focus is on Rosenbrock solvers. These turn out to be very well suited for our 10173 application when they are provided with highly efficient sparse matrix techniques 10174 to economize on the linear algebra. Two of the Rosenbrock solvers tested are from 10175 the literature, viz. and 4, and two are new and specially developed for air 10176 quality applications, viz. 3 and 3. } 10177} 10178 10179@Article{ rang_2005, 10180 title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic 10181 equations of index 1}, 10182 author = {Rang, J. and Angermann, L.}, 10183 journal = {BIT Numerical Mathematics}, 10184 year = {2005}, 10185 number = {4}, 10186 pages = {761--787}, 10187 volume = {45}, 10188 publisher = {Springer} 10189} 10190 10191@Article{ gottliebketchesonshu2009, 10192 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 10193 title = {{High order strong stability preserving time discretizations}}, 10194 journal = {Journal of Scientific Computing}, 10195 volume = {38}, 10196 number = {3}, 10197 pages = {251--289}, 10198 doi = {10.1007/s10915-008-9239-z}, 10199 year = {2009} 10200} 10201 10202@Article{ ketcheson_2008, 10203 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 10204 Low-Storage Implementations}, 10205 author = {D.I. Ketcheson}, 10206 journal = {SIAM Journal on Scientific Computing}, 10207 year = {2008}, 10208 number = {4}, 10209 pages = {2113--2136}, 10210 volume = {30}, 10211 doi = {10.1137/07070485X}, 10212 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 10213 RungeKutta methods}, 10214 publisher = {SIAM} 10215} 10216 10217@Article{ jansen_2000, 10218 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 10219 equations with a stabilized finite element method}, 10220 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 10221 journal = {Computer Methods in Applied Mechanics and Engineering}, 10222 year = {2000}, 10223 number = {3}, 10224 pages = {305--319}, 10225 volume = {190}, 10226 publisher = {Elsevier} 10227} 10228 10229@Article{ butcher_2007, 10230 title = {Error propagation of general linear methods for ordinary differential equations}, 10231 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 10232 journal = {Journal of Complexity}, 10233 year = {2007}, 10234 number = {4-6}, 10235 pages = {560--580}, 10236 volume = {23}, 10237 abstract = {We discuss error propagation for general linear methods for ordinary differential 10238 equations up to terms of order p+2, where p is the order of the method. These 10239 results are then applied to the estimation of local discretization errors for 10240 methods of order p and for the adjacent order p+1. The results of numerical 10241 experiments confirm the reliability of these estimates. This research has 10242 applications in the design of robust stepsize and order changing strategies for 10243 algorithms based on general linear methods.}, 10244 doi = {10.1016/j.jco.2007.01.009}, 10245 issn = {0885-064X} 10246} 10247 10248@Article{ constantinescu_a2010a, 10249 title = {Extrapolated implicit-explicit time stepping}, 10250 author = {E.M. Constantinescu and A. Sandu}, 10251 journal = {SIAM Journal on Scientific Computing}, 10252 year = {2010}, 10253 number = {6}, 10254 pages = {4452-4477}, 10255 volume = {31}, 10256 comment = {Preprint \# ANL/MCS-P1612-0409}, 10257 doi = {10.1137/080732833} 10258} 10259 10260@InProceedings{ devito2011liszt, 10261 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 10262 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 10263 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 10264 Aiken, Alex and Duraisamy, Karthik and others}, 10265 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 10266 Networking, Storage and Analysis}, 10267 pages = {9}, 10268 year = {2011}, 10269 organization = {ACM} 10270} 10271 10272@Article{ devito2011designing, 10273 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 10274 author = {DeVito, Zachary and Hanrahan, Pat}, 10275 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 10276 year = {2011} 10277} 10278 10279@Misc{ pgasintro, 10280 author = {Tim Stitt}, 10281 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 10282 Model}, 10283 note = {\url{http://cnx.org/content/m20649/latest/}} 10284} 10285 10286@InProceedings{ el2006upc, 10287 title = {UPC: unified parallel C}, 10288 author = {El-Ghazawi, Tarek and Smith, Lauren}, 10289 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 10290 pages = {27}, 10291 year = {2006}, 10292 organization = {ACM} 10293} 10294 10295@InProceedings{ numrich1998co, 10296 title = {Co-Array Fortran for parallel programming}, 10297 author = {Numrich, Robert W and Reid, John}, 10298 booktitle = {ACM Sigplan Fortran Forum}, 10299 volume = {17}, 10300 number = {2}, 10301 pages = {1--31}, 10302 year = {1998}, 10303 organization = {ACM} 10304} 10305 10306@Article{ aiken1997titanium, 10307 title = {Titanium: A high-performance Java dialect}, 10308 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 10309 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 10310 Geoff and Semenzato, Luigi and others}, 10311 year = {1997} 10312} 10313 10314@Article{ charles2005x10, 10315 title = {X10: an object-oriented approach to non-uniform cluster computing}, 10316 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 10317 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 10318 Sarkar, Vivek}, 10319 journal = {Acm Sigplan Notices}, 10320 volume = {40}, 10321 number = {10}, 10322 pages = {519--538}, 10323 year = {2005}, 10324 publisher = {ACM} 10325} 10326 10327@Article{ chamberlain2007parallel, 10328 title = {Parallel programmability and the chapel language}, 10329 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 10330 journal = {International Journal of High Performance Computing Applications}, 10331 volume = {21}, 10332 number = {3}, 10333 pages = {291--312}, 10334 year = {2007}, 10335 publisher = {SAGE Publications} 10336} 10337 10338@InProceedings{ charmppoopsla93, 10339 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 10340 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 10341 editor = {Paepcke, A.}, 10342 fulleditor = {Paepcke, Andreas}, 10343 pages = {91--108}, 10344 month = {September}, 10345 year = {1993}, 10346 booktitle = {{Proceedings of OOPSLA'93}}, 10347 publisher = {{ACM Press}} 10348} 10349 10350@InProceedings{ hewitt1973universal, 10351 title = {A universal modular actor formalism for artificial intelligence}, 10352 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 10353 booktitle = {Proceedings of the 3rd international joint conference on Artificial 10354 intelligence}, 10355 pages = {235--245}, 10356 year = {1973}, 10357 organization = {Morgan Kaufmann Publishers Inc.} 10358} 10359 10360@Book{ yonezawa1990abcl, 10361 title = {ABCL: an object-oriented concurrent system}, 10362 author = {Yonezawa, Akinori}, 10363 year = {1990}, 10364 publisher = {MIT press} 10365} 10366 10367@InProceedings{ dally1988object, 10368 title = {Object-oriented concurrent programming in CST}, 10369 author = {Dally, William J and Chien, Andrew A}, 10370 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 10371 applications: Architecture, software, computer systems, and general issues-Volume 10372 1}, 10373 pages = {434--439}, 10374 year = {1988}, 10375 organization = {ACM} 10376} 10377 10378@Article{ grimshaw1993easy, 10379 title = {Easy-to-use object-oriented parallel processing with Mentat}, 10380 author = {Grimshaw, Andrew S.}, 10381 journal = {Computer}, 10382 volume = {26}, 10383 number = {5}, 10384 pages = {39--51}, 10385 year = {1993}, 10386 publisher = {IEEE} 10387} 10388 10389@InProceedings{ gannon1991object, 10390 title = {Object oriented parallelism: pC++ ideas and experiments}, 10391 author = {Gannon, Dennis and Lee, JK}, 10392 booktitle = {Proceedings of}, 10393 pages = {13--23}, 10394 year = {1991} 10395} 10396 10397@InProceedings{ lau1992object, 10398 title = {An object-oriented class library for scalable parallel heuristic search}, 10399 author = {Lau, Wing-cheong and Singh, Vineet}, 10400 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 10401 pages = {252--267}, 10402 year = {1992}, 10403 organization = {Springer} 10404} 10405 10406@Book{ chase1989amber, 10407 title = {The Amber system: Parallel programming on a network of multiprocessors}, 10408 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 10409 Littlefield, Richard}, 10410 volume = {23}, 10411 number = {5}, 10412 year = {1989}, 10413 publisher = {ACM} 10414} 10415 10416@InProceedings{ kaiser2009parallex, 10417 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 10418 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 10419 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 10420 pages = {394--401}, 10421 year = {2009}, 10422 organization = {IEEE} 10423} 10424 10425@TechReport{ ipm, 10426 author = {Barry F. Smith}, 10427 title = {A New Parallel Programming Model for Computer Simulation}, 10428 institution = {Argonne National Laboratory}, 10429 year = {2014}, 10430 number = {ANL/MCS-P5135-0414} 10431} 10432 10433@Article{ groppsnir, 10434 author = {William Gropp and Marc Snir}, 10435 title = {Programming for Exascale Computers}, 10436 journal = {Computing in Science and Engineering}, 10437 volume = {15}, 10438 number = {6}, 10439 issn = {1521-9615}, 10440 year = {2013}, 10441 pages = {27-35}, 10442 doi = {10.1109/MCSE.2013.96}, 10443 publisher = {IEEE Computer Society}, 10444 address = {Los Alamitos, CA} 10445} 10446 10447@Book{ mpi3, 10448 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 10449 author = {Message Passing Interface Forum}, 10450 year = {2012}, 10451 publisher = {High Performance Computing Center Stuttgart (HLRS)} 10452} 10453 10454@Book{ openmp4, 10455 title = {OpenMP Application Program Interface, Version 4.0}, 10456 year = {2013}, 10457 publisher = {OpenMP Architecture Review Board} 10458} 10459 10460@InProceedings{ hartono2009annotation, 10461 title = {Annotation-based empirical performance tuning using {Orio}}, 10462 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 10463 booktitle = {Parallel \& Distributed Processing, 2009. 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Control. Fusion}, 10569 author = {Eero Hirvijoki}, 10570 note = {in press}, 10571 doi = {10.1088/1361-6587/abe884}, 10572 year = {2021} 10573} 10574 10575@Article{ ipsen2001, 10576 author = {Ilse C. F. Ipsen}, 10577 journal = {SIAM J. Sci. Comput.}, 10578 pages = {1050--1051}, 10579 volume = {23}, 10580 publisher = {SIAM}, 10581 title = {A Note on Preconditioning Nonsymmetric Matrices}, 10582 year = {2001} 10583} 10584 10585% Random papers on solvers for GPUs 10586@InProceedings{ gpus-suck, 10587 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. }, 10588 title = { On the Limits of {GPU} Acceleration}, 10589 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism}, 10590 year = {2010}, 10591 publisher = {USENIX} 10592} 10593 10594@InProceedings{ 882364, 10595 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter}, 10596 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid}, 10597 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers}, 10598 year = {2003}, 10599 isbn = {1-58113-709-5}, 10600 pages = {917--924}, 10601 location = {San Diego, California}, 10602 doi = {10.1145/1201775.882364}, 10603 publisher = {ACM}, 10604 address = {New York, NY} 10605} 10606 10607@Conference{ feng2008multigrid, 10608 author = {Feng, Z. and Li, P.}, 10609 booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008}, 10610 date-added = {2010-08-19 15:57:06 -0500}, 10611 date-modified = {2010-08-19 15:57:06 -0500}, 10612 pages = {647--654}, 10613 title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms}, 10614 year = {2008} 10615} 10616 10617@Conference{ goodnight2003multigrid, 10618 author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.}, 10619 booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware}, 10620 date-added = {2010-08-19 15:45:20 -0500}, 10621 date-modified = {2010-08-19 15:45:20 -0500}, 10622 organization = {Eurographics Association}, 10623 pages = {102--111}, 10624 title = {A multigrid solver for boundary value problems using programmable graphics 10625 hardware}, 10626 year = {2003} 10627} 10628 10629@Article{ buatois2007concurrent, 10630 author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.}, 10631 date-added = {2010-08-19 15:45:02 -0500}, 10632 date-modified = {2010-08-19 15:45:02 -0500}, 10633 journal = {High Performance Computing and Communications}, 10634 pages = {358--371}, 10635 publisher = {Citeseer}, 10636 title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}}, 10637 year = {2007} 10638} 10639 10640@Article{ joldes2010real, 10641 author = {Joldes, G.R. and Wittek, A. and Miller, K.}, 10642 date-added = {2010-08-19 15:44:41 -0500}, 10643 date-modified = {2010-08-19 15:44:41 -0500}, 10644 journal = {Computer Methods in Applied Mechanics and Engineering}, 10645 publisher = {Elsevier}, 10646 title = {Real-time nonlinear finite element computations on {GPU}-application to 10647 neurosurgical simulation}, 10648 year = {2010} 10649} 10650 10651@Misc{ aharon2005gpu, 10652 author = {Aharon, S.}, 10653 date-added = {2010-08-19 15:44:32 -0500}, 10654 date-modified = {2010-08-19 15:44:32 -0500}, 10655 month = apr # {~27}, 10656 note = {US Patent App. 11/115,642}, 10657 publisher = {Google Patents}, 10658 title = {{GPU}-based Finite Element}, 10659 year = {2005} 10660} 10661 10662@Article{ cevahir2009fast, 10663 author = {Cevahir, A. and Nukada, A. and Matsuoka, S.}, 10664 date-added = {2010-08-19 15:44:01 -0500}, 10665 date-modified = {2010-08-19 15:44:01 -0500}, 10666 journal = {Computational Science--ICCS 2009}, 10667 pages = {893--903}, 10668 publisher = {Springer}, 10669 title = {Fast conjugate gradients with multiple {GPU}s}, 10670 year = {2009} 10671} 10672 10673@Article{ maier1995symmetric, 10674 author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.}, 10675 date-added = {2010-08-19 15:43:57 -0500}, 10676 date-modified = {2010-08-19 15:43:57 -0500}, 10677 journal = {Computational Mechanics}, 10678 number = {1}, 10679 pages = {115--129}, 10680 publisher = {Springer}, 10681 title = {Symmetric {G}alerkin boundary element method in plasticity and gradient 10682 plasticity}, 10683 volume = {17}, 10684 year = {1995} 10685} 10686 10687@Article{ corrigan-running, 10688 author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.}, 10689 date-added = {2010-08-19 15:43:47 -0500}, 10690 date-modified = {2010-08-19 15:43:47 -0500}, 10691 journal = {International Journal for Numerical Methods in Fluids}, 10692 publisher = {John Wiley \& Sons}, 10693 title = {Running unstructured grid based CFD solvers on modern graphics hardware} 10694} 10695 10696@InProceedings{ volkov08, 10697 author = {Vasily Volkov and James W. 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Markus}, 11655 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 11656 for {PDE} Based Applications}, 11657 year = {1994}, 11658 institution = {Department of Computer Sciences, Purdue University}, 11659 number = {CSD-TR-94-021} 11660} 11661 11662@Unpublished{ ilu-web-page, 11663 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 11664 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 11665 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 11666} 11667 11668@Unpublished{ doe2k-web-page, 11669 title = {{DOE2000 Initiative} {W}eb page}, 11670 note = {http://www.mcs.anl.gov/DOE2000}, 11671 key = {DOE2000 Initiative} 11672} 11673 11674@Misc{ pvode-web-page, 11675 title = {{PVODE} {W}eb Page}, 11676 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 11677 author = {A. {Hindmarsh et al.}} 11678} 11679 11680@Book{ szyperski97, 11681 author = {Clemens Szyperski}, 11682 title = {Component Software: Beyond Object-Oriented Programming}, 11683 publisher = {ACM Press}, 11684 address = {New York}, 11685 year = {1997} 11686} 11687 11688@Unpublished{ petsc:coloringuse, 11689 title = {Code for computing sparse {J}acobians}, 11690 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11691 institution = {Argonne National Laboratory} 11692} 11693 11694@Unpublished{ petsc:external, 11695 author = {B. F. {Smith et al.}}, 11696 title = {{External Software Used by PETSc}}, 11697 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11698 institution = {Argonne National Laboratory} 11699} 11700 11701@Unpublished{ petsc:use-by-external-packages, 11702 author = {B. F. {Smith et al.}}, 11703 title = {{Software Packages that Use or Interface to PETSc}}, 11704 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 11705 institution = {Argonne National Laboratory} 11706} 11707 11708@Unpublished{ petsc:prizes, 11709 author = {B. F. {Smith et al.}}, 11710 title = {{Prizes Won Using PETSc}}, 11711 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 11712 institution = {Argonne National Laboratory} 11713} 11714 11715@Unpublished{ petsc:csgf, 11716 author = {B. F. {Smith et al.}}, 11717 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 11718 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 11719 institution = {Argonne National Laboratory} 11720} 11721 11722@Unpublished{ flash-web-page, 11723 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 11724 {W}eb Page}, 11725 note = {http://www.asci.uchicago.edu}, 11726 author = {R. {Rosner et al.}}, 11727 institution = {University of Chicago} 11728} 11729 11730@Unpublished{ esi-web-page, 11731 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 11732 note = {http://z.ca.sandia.gov/esi}, 11733 author = {R. {Clay et al.}} 11734} 11735 11736@Unpublished{ infobus-web-page, 11737 title = {{I}nfo{B}us {W}eb Page}, 11738 note = {http://www.java.sun.com/beans/infobus}, 11739 key = {infobus} 11740} 11741 11742@Unpublished{ xray-web-page, 11743 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 11744 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 11745 note = {http://www.mcs.anl.gov/xray/}, 11746 institution = {Argonne National Laboratory} 11747} 11748 11749@InProceedings{ kohn98, 11750 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 11751 title = {Language Interoperability Mechanisms for High-Performance Scientific 11752 Applications}, 11753 publisher = {SIAM}, 11754 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 11755 Scientific and Engineering Computing}, 11756 year = {1999}, 11757 pages = {30-39} 11758} 11759 11760@InProceedings{ kohn01, 11761 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 11762 title = {Divorcing Language Dependencies from a Scientific Software Library}, 11763 publisher = {SIAM}, 11764 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 11765 year = {2001} 11766} 11767 11768@InProceedings{ freitag_jones_plassmann98, 11769 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 11770 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 11771 publisher = {SIAM}, 11772 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 11773 Scientific and Engineering Computing}, 11774 year = {1999}, 11775 pages = {215-224} 11776} 11777 11778@Book{ templates, 11779 author = {R. 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Browne}, 11799 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 11800 Techniques}, 11801 institution = {Department of Computer Science, University of Texas at Austin}, 11802 year = {1995} 11803} 11804 11805@Article{ parti, 11806 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 11807 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 11808 Memory Architectures}, 11809 journal = {Journal of Parallel and Distributed Computing}, 11810 year = {1994}, 11811 volume = {22}, 11812 pages = {462--478} 11813} 11814 11815@Article{ mparti, 11816 author = {G. Agrawal and A. Sussman and J. Saltz}, 11817 title = {An Integrated Runtime and Compile-time Approach for Parallelizing Structured and 11818 Block Structured Applications}, 11819 journal = {IEEE Trans. on Parallel and Distributed Systems}, 11820 volume = {6}, 11821 number = {7}, 11822 year = {1995} 11823} 11824 11825@Article{ gropp-lusk-doss-skjellum, 11826 author = { William Gropp and Ewing Lusk and Nathan Doss and Anthony Skjellum}, 11827 title = {A high-performance, portable implementation of the {MPI} Message Passing 11828 Interface standard}, 11829 journal = {Parallel Computing}, 11830 year = {1996}, 11831 volume = {22}, 11832 pages = {789--828} 11833} 11834 11835@InProceedings{ lam, 11836 author = {Greg Burns and Raja Daoud and James Vaigl}, 11837 title = {{LAM}: An Open Cluster Environment for {MPI}}, 11838 booktitle = {Proceedings of Supercomputing Symposium '94}, 11839 editor = {John W. Ross}, 11840 publisher = {University of Toronto}, 11841 pages = {379--386}, 11842 year = {1994} 11843} 11844 11845@Article{ cs99, 11846 author = {X.-C. Cai and M. Sarkis}, 11847 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 11848 systems}, 11849 journal = {SIAM J. Scientific Computing}, 11850 year = {1999}, 11851 volume = {21}, 11852 pages = {792-797} 11853} 11854 11855@TechReport{ cs97a, 11856 author = {X.-C. Cai and M. Sarkis}, 11857 title = {A restricted additive {S}chwarz preconditioner for general sparse linear systems 11858 }, 11859 year = {1997}, 11860 institution = {Computer Science Department, University of Colorado-Boulder}, 11861 number = {CU-CS 843-97}, 11862 note = {(accepted by SIAM J. of Scientific Computing)} 11863} 11864 11865@Article{ cai2003restricted, 11866 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 11867 positive definite linear systems}, 11868 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 11869 journal = {SIAM Journal on Numerical Analysis}, 11870 volume = {41}, 11871 issue = {1}, 11872 pages = {1209--1231}, 11873 year = {2003}, 11874 doi = {10.1137/S0036142901389621} 11875} 11876 11877@TechReport{ caisaad, 11878 author = {Xiao-Chuan Cai and Youcef Saad}, 11879 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 11880 institution = {Army High Performance Computing Research Center, University of Minnesota }, 11881 year = {1993}, 11882 number = {Preprint 93-027 }, 11883 note = {SIAM J. Sci. Comp. (submitted)} 11884} 11885 11886@Book{ ruminations, 11887 author = {Andrew Koenig and Barbara Moo}, 11888 title = {Ruminations on C++}, 11889 year = {1996}, 11890 publisher = {Addison-Wesley} 11891} 11892 11893@Book{ mpi-complete, 11894 author = {Marc Snir and Steve Otto and Steven Huss-Lederman and David Walker and Jack 11895 Dongarra}, 11896 title = {{MPI}: The Complete Reference}, 11897 year = {1995}, 11898 publisher = {MIT Press} 11899} 11900 11901@Unpublished{ tcl-tk-web-page, 11902 title = {{Tcl/Tk} {W}orld {W}ide {W}eb page}, 11903 note = {http://www.sunlabs.com/research/tcl/}, 11904 year = {1996}, 11905 month = aug 11906} 11907 11908@Misc{ mpich-web-page, 11909 author = {William Gropp and {et. al.}}, 11910 title = {{MPICH} {W}eb page}, 11911 key = {MPICH}, 11912 url = {http://www.mpich.org}, 11913 howpublished = {\url{http://www.mpich.org}} 11914} 11915 11916@Article{ mpi-final, 11917 author = {MPI Forum}, 11918 title = {{MPI}: A Message-Passing Interface Standard}, 11919 journal = {International J. Supercomputing Applications}, 11920 volume = {8}, 11921 number = {3/4}, 11922 year = {1994}, 11923 key = {MPI Standard - final} 11924} 11925 11926@Unpublished{ npb-web-page, 11927 key = {NAS Parallel Benchmarks}, 11928 title = {{NAS} {P}arallel {B}enchmarks {W}eb page}, 11929 note = {http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html}, 11930 year = {1996}, 11931 month = dec 11932} 11933 11934@Book{ george81, 11935 title = {Computer Solution of Large Sparse Positive Definite Systems}, 11936 author = {Alan George and Joseph W. Liu}, 11937 publisher = {Prentice-Hall}, 11938 year = {1981}, 11939 key = {SparseDirect} 11940} 11941 11942@Book{ p4-book, 11943 title = {Portable Programs for Parallel Processors}, 11944 publisher = {Holt, Rinehart, {and} Winston}, 11945 year = {1987}, 11946 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 11947 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 11948 key = {P4Book} 11949} 11950 11951@Article{ stones, 11952 author = {H. L. Stone}, 11953 title = {Iterative solution of implicit approximations of multidimensional partial 11954 differential equations}, 11955 journal = {SIAM J. Numerical Analysis}, 11956 pages = {87--113}, 11957 volumne = {5}, 11958 year = {1968} 11959} 11960 11961@Article{ parallelstones, 11962 author = {J. S. Reeve and A. D. Scurr and J. H. Merlin}, 11963 title = {Parallel versions of {S}tones strongly implicit algorithm}, 11964 journal = {Concurrency and Computation: Practice and Experience}, 11965 pages = {1049--1062}, 11966 volumne = {13}, 11967 year = {2001} 11968} 11969 11970@Article{ p4-paper, 11971 author = {Ralph Butler and Ewing Lusk}, 11972 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 11973 journal = {Journal of Parallel Computing}, 11974 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 11975 Division preprint P362-0493)}, 11976 year = {1993} 11977} 11978 11979@TechReport{ picl, 11980 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 11981 title = {{PICL}: A portable instrumented communications library}, 11982 institution = {Oak Ridge National Laboratory}, 11983 number = {TM-11130}, 11984 year = {1990}, 11985 key = {PICL} 11986} 11987 11988@TechReport{ upshot, 11989 author = {Virginia Herrarte and Ewing Lusk}, 11990 title = {Studying Parallel Program Behavior with {U}pshot}, 11991 institution = {Argonne National Laboratory}, 11992 number = {ANL-91/15}, 11993 month = aug, 11994 year = {1991}, 11995 key = {Upshot} 11996} 11997 11998@TechReport{ p4-manual, 11999 author = {Ralph Butler and Ewing Lusk}, 12000 title = {User's Guide to the p4 Parallel Programming System}, 12001 institution = {Argonne National Laboratory}, 12002 number = {ANL-92/17}, 12003 month = oct, 12004 year = {1992}, 12005 key = {p4-Manual} 12006} 12007 12008@InProceedings{ oldparti, 12009 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 12010 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 12011 booktitle = {Proceedings of Supercomputing '93}, 12012 pages = {578--587}, 12013 year = {1993} 12014} 12015 12016@Article{ parti2, 12017 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 12018 and J. Saltz}, 12019 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 12020 journal = {ACM SIGPLAN Notices}, 12021 year = {1995}, 12022 pages = {68-79}, 12023 volume = {30}, 12024 number = {8} 12025} 12026 12027@Article{ parti3, 12028 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 12029 title = {Run-Time Parallelization and Scheduling of Loops}, 12030 journal = {IEEE Trans. Computers}, 12031 year = {1991}, 12032 pages = {604-612}, 12033 volume = {40}, 12034 number = {5} 12035} 12036 12037@InProceedings{ disz-lusk:wamtrace, 12038 author = {Terrence Disz and Ewing Lusk}, 12039 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 12040 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12041 year = {1987}, 12042 pages = {46--53} 12043} 12044 12045@InProceedings{ gorlick-kesselman:gauge, 12046 author = {Michael Gorlick and Carl Kesselman}, 12047 title = {Timing {Prolog} programs without Clocks}, 12048 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12049 year = {1996}, 12050 publisher = {Birkhauser} 12051} 12052 12053@TechReport{ aztec, 12054 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 12055 title = {Aztec User's Guide Version 1.1}, 12056 institution = {Sandia National Laboratories}, 12057 month = oct, 12058 year = {1995}, 12059 number = {SAND95/1559} 12060} 12061 12062@TechReport{ aztec2, 12063 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 12064 title = {Official {Aztec} User's Guide Version 2.1}, 12065 institution = {Sandia National Laboratories}, 12066 year = {1999} 12067} 12068 12069@Book{ taylor-chandy:pcn, 12070 author = {Chandy, M. and Taylor, S.}, 12071 title = {An Introduction to Parallel Programming}, 12072 year = {1991}, 12073 publisher = {Jones and Bartlett} 12074} 12075 12076@Book{ foster-taylor:strand, 12077 title = {Strand: New Concepts in Parallel Programming}, 12078 author = {Ian Foster and Stephen Taylor}, 12079 publisher = {Prentice-Hall}, 12080 adress = { Englewood Cliffs, New Jersey}, 12081 year = {1990} 12082} 12083 12084@Article{ aurora, 12085 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 12086 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 12087 Carlsson and A. Ciepielewski and B. Hausman}, 12088 title = {The Aurora OR-Parallel Prolog System}, 12089 journal = {New Generation Computing}, 12090 volume = {7}, 12091 number = {3}, 12092 year = {1990}, 12093 pages = {243--271} 12094} 12095 12096@TechReport{ roo, 12097 author = {E. Lusk and W. McCune and J. Slaney}, 12098 title = {Roo---a Parallel Theorem Prover}, 12099 institution = {Argonne National Laboratory}, 12100 number = {MCS--TM--149}, 12101 year = {1991} 12102} 12103 12104@TechReport{ heath-etheridge:vppp, 12105 author = {M. T. Heath and J. A. Etheridge}, 12106 title = {Visualizing the Performance of Parallel Programs}, 12107 institution = {Oak Ridge National Laboratory}, 12108 number = {ORNL TM-11813}, 12109 year = {1991} 12110} 12111 12112@TechReport{ chem:vis, 12113 author = {Ewing L. Lusk}, 12114 title = {Performance Visualization for Parallel Programs}, 12115 institution = {Argonne National Laboratory}, 12116 number = {ANL/MCS--P287--0192}, 12117 year = {1991}, 12118 note = {(to appear in {\em Theoretica Chimica Acta})} 12119} 12120 12121@TechReport{ picltrace, 12122 author = {P.~H.~Worley}, 12123 title = {A new {PICL} trace file format}, 12124 institution = {Oak Ridge National Laboratory}, 12125 number = {ORNL TM-12125}, 12126 month = jun, 12127 year = {1992} 12128} 12129 12130@InProceedings{ hideo, 12131 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 12132 title = {Inference of Phylogenetic trees using maximum likelihood}, 12133 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 12134 year = {1992}, 12135 pages = {247--262} 12136} 12137 12138@InProceedings{ dw90, 12139 author = {M. Dryja and O. Widlund}, 12140 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 12141 Problems}, 12142 booktitle = {Third International Symposium on Domain Decomposition Methods}, 12143 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 12144 year = {1990}, 12145 pages = {3-21}, 12146 publisher = {SIAM}, 12147 address = {Philadelphia}, 12148 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 12149 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 12150 references, good introduction to the theory. No computations}, 12151 key = {DryjaWidlund90 !AS} 12152} 12153 12154@Unpublished{ rosing, 12155 author = {Matt Rosing and Joel Saltz}, 12156 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 12157 key = {LowLatency}, 12158 note = {manuscript, 1992} 12159} 12160 12161@TechReport{ jp:incomplete, 12162 author = {Mark T. Jones and Paul E. Plassmann}, 12163 title = {An Improved Incomplete {C}holesky Factorization}, 12164 institution = {Argonne National Laboratory}, 12165 address = {Argonne, IL}, 12166 type = {Preprint}, 12167 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 12168 number = {MCS-P206-0191}, 12169 year = {1991}, 12170 key = {jones} 12171} 12172 12173@InCollection{ jp:ima, 12174 author = {Mark Jones and Paul Plassmann}, 12175 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 12176 booktitle = {Graph Theory and Sparse Matrix Computation}, 12177 publisher = {Springer-Verlag}, 12178 series = {The IMA Volumes in Mathematics and Its Applications}, 12179 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 12180 volume = {56}, 12181 year = {1993}, 12182 pages = {229--245} 12183} 12184 12185@Article{ pw98, 12186 author = {M. Pernice and H. F. Walker}, 12187 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 12188 journal = {SIAM J. Sci. Stat. Comput.}, 12189 year = {1998}, 12190 volume = {19}, 12191 pages = {302--318} 12192} 12193 12194@TechReport{ ysmp83, 12195 key = {Eisenstat}, 12196 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12197 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12198 institution = {Department of Computer Science, Yale University}, 12199 number = {YALE/DCS/RR-265}, 12200 month = apr, 12201 year = {1983} 12202} 12203 12204@InBook{ ysmp84, 12205 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12206 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12207 title = {Elliptic Problem Solvers II}, 12208 publisher = {Academic Press}, 12209 pages = {45--52}, 12210 editors = {G. Birkhoff and A. Schoenstadt}, 12211 year = {1984} 12212} 12213 12214@TechReport{ sparsekit, 12215 key = {Saad}, 12216 author = {Youcef Saad}, 12217 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 12218 institution = {Center for Supercomputing Research and Development, University of Illinois at 12219 Urbana-Champaign}, 12220 number = {1029}, 12221 year = {1990} 12222} 12223 12224@TechReport{ pde-user-ref, 12225 author = {Barry F. Smith}, 12226 title = {Extensible {PDE} Solvers Package Users Manual}, 12227 institution = {Argonne National Laboratory}, 12228 month = sep, 12229 year = {1994}, 12230 number = {ANL-93/40}, 12231 key = {Smith94 ! PDE} 12232} 12233 12234@TechReport{ bs-user-ref, 12235 author = {Mark T. Jones and Paul E. Plassmann}, 12236 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 12237 of Sparse Linear Systems}, 12238 institution = {Argonne National Laboratory}, 12239 month = dec, 12240 year = {1995}, 12241 number = {ANL-95/48} 12242} 12243 12244@TechReport{ snes-user-ref, 12245 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 12246 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 12247 institution = {Argonne National Laboratory}, 12248 month = feb, 12249 year = {1995}, 12250 number = {ANL/MCS-TM-193}, 12251 key = {GroppMcInnesSmith95 ! SNES} 12252} 12253 12254@TechReport{ sles-user-ref, 12255 author = {William D. Gropp and Barry F. Smith}, 12256 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 12257 institution = {Argonne National Laboratory}, 12258 month = mar, 12259 year = {1993}, 12260 number = {ANL-93/8}, 12261 key = {GroppSmith93 ! SLES} 12262} 12263 12264@TechReport{ chameleon-user-ref, 12265 author = {William D. Gropp and Barry F. Smith}, 12266 title = {Chameleon Parallel programming tools Users Manual}, 12267 institution = {Argonne National Laboratory}, 12268 month = mar, 12269 year = {1993}, 12270 number = {ANL-93/23}, 12271 key = {GroppSmith93 ! Chameleon} 12272} 12273 12274@Article{ euclid2, 12275 author = {D. Hysom and A. Pothen}, 12276 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 12277 journal = {SIAM J. Sci. Comput.}, 12278 volume = {22}, 12279 number = {6}, 12280 pages = {2194--2215} 12281} 12282 12283@TechReport{ euclid1, 12284 author = {D. Hysom and A. Pothen}, 12285 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 12286 Solution of Sparse Linear Systems)}, 12287 institution = {Old Dominion University}, 12288 year = {2001} 12289} 12290 12291@TechReport{ ksp-user-ref, 12292 author = {William D. Gropp and Barry F. Smith}, 12293 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 12294 Methods}, 12295 institution = {Argonne National Laboratory}, 12296 month = aug, 12297 year = {1993}, 12298 number = {ANL-93/30}, 12299 key = {GroppSmith93 ! KSP} 12300} 12301 12302@TechReport{ mpi-chameleon, 12303 author = {William D. Gropp and Ewing Lusk}, 12304 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 12305 institution = {Argonne National Laboratory}, 12306 month = dec, 12307 year = {1992}, 12308 number = {ANL-92/47}, 12309 key = {GroppLusk92 ! MPI} 12310} 12311 12312@TechReport{ blockcomm-fortran, 12313 author = {William D. Gropp}, 12314 title = {Block{C}omm for {F}ortran}, 12315 institution = {Argonne National Laboratory}, 12316 month = may, 12317 year = {1993}, 12318 number = {ANL-93/00 (to appear)}, 12319 key = {Gropp93 ! BlockComm} 12320} 12321 12322@TechReport{ autodocument, 12323 author = {William D. Gropp}, 12324 title = {Automatic documentation of {C} programs}, 12325 institution = {Argonne National Laboratory}, 12326 month = may, 12327 year = {1993}, 12328 number = {ANL-93/00}, 12329 key = {Gropp93 ! Autodoc} 12330} 12331 12332@TechReport{ zipcode, 12333 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 12334 Manfred Morari}, 12335 title = {The {Z}ipcode message-passing system}, 12336 institution = {Lawrence Livermore National Laboratory}, 12337 month = sep, 12338 year = {1992}, 12339 number = {Unpublished}, 12340 key = {Skjellum92 ! Zipcode} 12341} 12342 12343@Article{ paragraph, 12344 author = {Michael T. Heath and Jennifer Etheridge Finger}, 12345 title = {Visualizing performance of parallel programs}, 12346 journal = {IEEE Software}, 12347 volume = {8}, 12348 number = {5}, 12349 month = sep, 12350 year = {1991}, 12351 pages = {29--39}, 12352 key = {Heath91 ! Paragraph} 12353} 12354 12355@Article{ gropp90, 12356 author = {William Gropp and Edward Smith}, 12357 title = {Computational Fluid Dynamics on Parallel Processors}, 12358 journal = {Computers and Fluids}, 12359 volume = {18}, 12360 year = {1990}, 12361 pages = {289--304}, 12362 key = {Gropp90 ! performance} 12363} 12364 12365@Article{ foster92, 12366 author = {Ian Foster and William Gropp and Rick Stevens}, 12367 title = {The parallel scalability of the spectral transform method}, 12368 journal = {Monthly Weather Review}, 12369 volume = {120}, 12370 year = {1992}, 12371 pages = {835--850}, 12372 key = {Foster92 ! performance} 12373} 12374 12375@InBook{ fgn, 12376 author = {R. Freund and G. H. Golub and N. Nachtigal}, 12377 title = {Iterative Solution of Linear Systems}, 12378 series = {Acta Numerica}, 12379 year = {1992}, 12380 publisher = {Cambridge University Press}, 12381 pages = {57--100} 12382} 12383 12384@TechReport{ nachtigal90, 12385 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 12386 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12387 institution = {Massachusetts Institute of Technology}, 12388 month = mar, 12389 year = {1990}, 12390 number = {90-2}, 12391 key = {Nachtigal | Krylov} 12392} 12393 12394@Article{ nachtigal1992fnm, 12395 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12396 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 12397 journal = {SIAM Journal on Matrix Analysis and Applications}, 12398 volume = {13}, 12399 pages = {778}, 12400 year = {1992}, 12401 publisher = {SIAM} 12402} 12403 12404@TechReport{ embree1999descriptive, 12405 title = {How descriptive are {GMRES} convergence bounds}, 12406 author = {Embree, M.}, 12407 year = {1999}, 12408 number = {08}, 12409 institution = {Oxford University Computing Laboratory} 12410} 12411 12412@Article{ vorst92, 12413 author = {H. van der Vorst}, 12414 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 12415 of nonsymmetric linear systems}, 12416 journal = {SIAM J. Sci. Stat. Comput.}, 12417 year = {1992}, 12418 volume = {13}, 12419 pages = {631--644} 12420} 12421 12422@Article{ eisenstat81, 12423 author = {S. Eisenstat}, 12424 title = {Efficient Implementation of a Class of {CG} Methods}, 12425 journal = {SIAM J. Sci. Stat. Comput.}, 12426 year = {1981}, 12427 volume = {2}, 12428 pages = {1--4} 12429} 12430 12431@Manual{ ibm-essl, 12432 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 12433 Reference}, 12434 organization = {IBM}, 12435 year = {1992}, 12436 key = {IBM-ESSL} 12437} 12438 12439@Manual{ ibm-eui, 12440 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 12441 Release 2.0}, 12442 organization = {IBM}, 12443 month = jun, 12444 year = {1994}, 12445 key = {IBM-EUI} 12446} 12447 12448@Manual{ ibm-euih, 12449 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 12450 organization = {IBM}, 12451 author = {Peter Hochschild}, 12452 year = {1993}, 12453 key = {IBM-EUIH} 12454} 12455 12456@TechReport{ mpi, 12457 title = {Document for a Standard Message-Passing Interface}, 12458 author = {Message Passing Interface Forum}, 12459 institution = {University of Tennessee}, 12460 number = {CS-93-214}, 12461 month = nov, 12462 year = {1993}, 12463 key = {MPI Standard} 12464} 12465 12466@Unpublished{ mpi-final-web, 12467 author = {Message Passing Interface Forum}, 12468 title = {{MPI}: A Message-Passing Interface Standard}, 12469 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 12470 year = {1994}, 12471 month = may 12472} 12473 12474@Book{ hockney-jesshope, 12475 author = {R. W. Hockney and C. R. Jesshope}, 12476 title = {Parallel Computers 2}, 12477 publisher = {Adam Hilger}, 12478 year = {1988} 12479} 12480 12481@Book{ cm-fortran, 12482 author = {{Thinking Machines Corporation}}, 12483 title = {Users Manual for CM-Fortran}, 12484 publisher = {Thinking Machines Corporation}, 12485 year = {1993} 12486} 12487 12488@TechReport{ chang93, 12489 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 12490 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 12491 institution = {Yale Department of Computer Science}, 12492 number = {YALEU/DCS/RR-994}, 12493 month = nov, 12494 year = {1993}, 12495 key = {BDD|diag} 12496} 12497 12498@InProceedings{ gropplevine93, 12499 author = {N. Galbreath and W. Gropp and D. Levine}, 12500 title = {Applications-Driven Parallel {I/O}}, 12501 booktitle = {Proceedings of Supercomputing '93}, 12502 year = {1993}, 12503 pages = {462--471} 12504} 12505 12506@Book{ siegle85, 12507 author = {H. J. Siegel}, 12508 title = {Interconnection Networks for Large Scale Parallel Processing}, 12509 publisher = {Lexington Books}, 12510 year = {1985}, 12511 key = {Network Comparison} 12512} 12513 12514@Article{ lawrie75, 12515 author = {D. H. Lawrie}, 12516 title = {Access and alignment of data in an array processor}, 12517 journal = {IEEE Transactions on Computers}, 12518 volume = {C-24}, 12519 number = {12}, 12520 month = dec, 12521 year = {1975}, 12522 pages = {1145--1155}, 12523 key = {Omega Network} 12524} 12525 12526@Book{ knuth1986, 12527 title = {The {\TeX}{Book}}, 12528 author = {Donald Ervin Knuth and Duane Bibby}, 12529 volume = {1993}, 12530 year = {1986}, 12531 publisher = {Addison-Wesley Reading, Massachusetts} 12532} 12533 12534@Book{ lamport86, 12535 author = {Leslie Lamport}, 12536 title = {{LaTeX}: A document preparation system}, 12537 publisher = {Addison-Wesley}, 12538 year = {1986}, 12539 key = {Latex Manual} 12540} 12541 12542@InProceedings{ gropp-lusk:unix-tools, 12543 author = {William Gropp and Ewing Lusk}, 12544 title = {Scalable {U}nix Tools on Parallel Processors}, 12545 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 12546 publisher = {IEEE}, 12547 pages = {56--62} 12548} 12549 12550@InProceedings{ jp:bell_prize, 12551 author = {Mark Jones and Paul Plassmann}, 12552 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 12553 Applications}, 12554 booktitle = {Proceedings of Supercomputing '92}, 12555 publisher = {IEEE Computer Society Press}, 12556 year = {1992}, 12557 pages = {551--560} 12558} 12559 12560@COMMENT{WEB, CWEB references (for doctext)} 12561@TechReport{ web, 12562 author = {Donald E. Knuth}, 12563 title = {The {\tt WEB} system of structured documentation}, 12564 institution = {Computer Science Department, Stanford University}, 12565 year = {1983}, 12566 number = {980}, 12567 month = sep 12568} 12569 12570@Article{ literatepgm, 12571 author = {Donald E. Knuth}, 12572 title = {Literate Programming}, 12573 journal = {Computer Journal}, 12574 year = {1984}, 12575 volume = {27}, 12576 number = {2}, 12577 pages = {91--111} 12578} 12579 12580@Unpublished{ cweb-code, 12581 author = {Silvio Levy and Donald E. Knuth}, 12582 title = {CWEB}, 12583 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 12584} 12585 12586@Article{ jp:scalable, 12587 author = {Mark Jones and Paul Plassmann}, 12588 title = {Scalable Iterative Solution of Sparse Linear Systems}, 12589 journal = {Parallel Computing}, 12590 volume = {20}, 12591 number = {5}, 12592 month = {May}, 12593 year = {1994}, 12594 pages = {753--773} 12595} 12596 12597@Article{ jp:pcolor, 12598 author = {Mark T. Jones and Paul E. Plassmann}, 12599 title = {A Parallel Graph Coloring Heuristic}, 12600 journal = {SIAM J. Sci. Comput.}, 12601 volume = {14}, 12602 number = {3}, 12603 pages = {654-669}, 12604 year = {1993} 12605} 12606 12607@TechReport{ block_solve, 12608 author = {Mark T. Jones and Paul E. Plassmann}, 12609 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 12610 Sparse Linear Systems}, 12611 institution = {Argonne National Laboratory}, 12612 year = {1992}, 12613 number = {ANL-92/46}, 12614 key = {JonesPlassmann92 ! block_solve} 12615} 12616 12617@InProceedings{ supercond, 12618 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 12619 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 12620 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 12621 Conference}, 12622 month = feb, 12623 year = {1994}, 12624 key = {McInnesPalumbo94 ! superconductivity } 12625} 12626 12627@Unpublished{ preosti:93, 12628 author = {Gianfranco Preosti}, 12629 title = { }, 12630 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 12631 year = {1993}, 12632 key = {preosti93 ! GL-tilt3d} 12633} 12634 12635@Unpublished{ more:93, 12636 author = {Jorge J. Mor\'{e}}, 12637 title = { }, 12638 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 12639 {A}rgonne {N}ational {L}aboratory}, 12640 year = {1993}, 12641 key = {more93 ! MINPACK-2} 12642} 12643 12644@Article{ brownsaad:90, 12645 author = {Peter N. Brown and Youcef Saad}, 12646 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 12647 journal = {SIAM J. Sci. Stat. Comput.}, 12648 year = {1990}, 12649 volume = {11}, 12650 pages = {450-481} 12651} 12652 12653@Book{ using-mpi, 12654 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 12655 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 12656 publisher = {MIT Press}, 12657 year = {1994} 12658} 12659 12660@Book{ using-mpi2, 12661 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 12662 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 12663 publisher = {MIT Press}, 12664 year = {1999} 12665} 12666 12667@Article{ hs:52, 12668 author = {Magnus R. Hestenes and Eduard Steifel}, 12669 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 12670 journal = {J. Research of the National Bureau of Standards}, 12671 year = {1952}, 12672 volume = {49}, 12673 pages = {409-436} 12674} 12675 12676@Article{ ss:86, 12677 author = {Youcef Saad and Martin H. Schultz}, 12678 title = {{GMRES}: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear 12679 Systems}, 12680 journal = {SIAM J. Sci. Stat. Comput.}, 12681 year = {1986}, 12682 volume = {7}, 12683 pages = {856-869} 12684} 12685 12686@Article{ so:89, 12687 author = {Peter Sonneveld}, 12688 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 12689 journal = {SIAM J. Sci. Stat. Comput.}, 12690 year = {1989}, 12691 volume = {10}, 12692 pages = {36-52} 12693} 12694 12695@Article{ v:92, 12696 author = {{H. A.} {van der Vorst}}, 12697 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 12698 of nonsymmetric linear systems}, 12699 journal = {SIAM J. Sci. Stat. Comput.}, 12700 volume = {13}, 12701 year = {1992}, 12702 pages = {631-644} 12703} 12704 12705@Article{ f:93, 12706 author = {Roland W. Freund}, 12707 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 12708 Systems}, 12709 journal = {SIAM J. Sci. Stat. Comput.}, 12710 volume = {14}, 12711 year = {1993}, 12712 pages = {470-482} 12713} 12714 12715@Article{ ish:89, 12716 author = {S. Ishizuka}, 12717 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 12718 journal = {Combustion and Flame}, 12719 volume = {75}, 12720 year = {1989}, 12721 pages = {367-379} 12722} 12723 12724@Book{ williams89, 12725 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 12726 author = {F.A. Williams}, 12727 publisher = {Addison-Wesley}, 12728 year = {1989}, 12729 pages = {367-379} 12730} 12731 12732@Book{ ra75, 12733 author = {R. Aris}, 12734 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 12735 publisher = {Oxford}, 12736 year = {1975} 12737} 12738 12739@Book{ bebernes89, 12740 author = {J. Bebernes and D. Eberly}, 12741 title = {Mathematical Problems from Combustion Theory}, 12742 publisher = {Springer-Verlag}, 12743 series = {Applied Mathematical Sciences 83}, 12744 year = {1989} 12745} 12746 12747@InProceedings{ kikuchi89, 12748 author = {F. Kikuchi}, 12749 booktitle = { Computing Methods in Applied Sciences and Engineering}, 12750 editor = {R. Glowinski and J. L. Lions}, 12751 publisher = {Springer-Verlag}, 12752 series = {Lecture Notes in Mathematics}, 12753 title = {Finite element approximations to bifurcation problems of turning point type}, 12754 year = {1977} 12755} 12756 12757@Article{ rg85, 12758 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 12759 title = {Continuation-conjugate Gradient Methods fo the Least Squares Solution of 12760 Nonlinear Boundary Problems}, 12761 journal = {SIAM J. Sci. Stat. Comput.}, 12762 volume = {6}, 12763 year = {1985}, 12764 pages = {793-832} 12765} 12766 12767@InProceedings{ whitfield91, 12768 author = {D. Whitfield and L. Taylor}, 12769 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12770 Schemes}, 12771 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 12772 misc = {AIAA-91-1539}, 12773 pages = {134-145}, 12774 year = {1991} 12775} 12776 12777@InProceedings{ quinlan1, 12778 author = {M. Lemke and D. Quinlan}, 12779 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 12780 Architecture-Independent Development of Structured Grid Applications}, 12781 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 12782 publisher = {Springer Verlag}, 12783 year = {1992} 12784} 12785 12786@InProceedings{ quinlan2, 12787 author = {R. Parsons and D. Quinlan}, 12788 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 12789 Computations}, 12790 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 12791 year = {1994} 12792} 12793 12794% ***** Overview of functionality in Diffpack 12795@InBook{ dpoverview, 12796 author = {Bruaset, A. M. and Langtangen, H. P.}, 12797 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12798 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 12799 {Diffpack}}, 12800 publisher = {Birkh{\"{a}}user}, 12801 pages = {61--90}, 12802 year = {1997} 12803} 12804 12805% ***** Short overview of Diffpack 12806@InCollection{ dpoverview2, 12807 author = {Bruaset, A. M. and Langtangen, H. P.}, 12808 editor = {A. Sydow}, 12809 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 12810 and Applied Mathematics}, 12811 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 12812 pages = {553--558}, 12813 volume = {4}, 12814 year = {1997} 12815} 12816 12817% ***** Comprehensive documentation of Diffpack and 12818% associated numerical methods: 12819@Book{ dpbook, 12820 author = {H. P. Langtangen}, 12821 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 12822 Software. Part I}, 12823 series = {Lecture Notes in Computational Science and Engineering}, 12824 publisher = {Springer-Verlag}, 12825 year = {1998} 12826} 12827 12828% ***** Design issues of the linear solvers in Diffpack, serves also as a 12829% collection of examples on O-O in numerical computing 12830@Article{ ambhpl97a, 12831 author = {A. M. Bruaset and H. P. Langtangen }, 12832 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 12833 journal = {Transactions on Mathematical Software}, 12834 volume = {23 }, 12835 pages = {50--80}, 12836 year = {1997} 12837} 12838 12839@Misc{ dpurl, 12840 author = {{Diffpack Web page}}, 12841 howpublished = {\url{http://www.diffpack.com}} 12842} 12843 12844% ***** General intro to object-oriented numerics for "FORTRAN programmers" 12845@InCollection{ oonintro, 12846 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 12847 editor = {D{\ae}hlen, M. and Tveito, A.}, 12848 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12849 title = {Object-Oriented Numerics}, 12850 publisher = {Birkh{\"{a}}user}, 12851 year = {1997} 12852} 12853 12854% ***** Efficiency comparison: BLAS 1, Diffpack, C, 12855% and finite element applications (F77 vs Diffpack) 12856@InCollection{ dpefficiency, 12857 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 12858 H. P. and Miller, C. T.}, 12859 editor = {D{\ae}hlen, M. and Tveito, A.}, 12860 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12861 title = {On the Efficiency of {C++} in Scientific Computing}, 12862 publisher = {Birkh{\"{a}}user}, 12863 pages = {91--118}, 12864 year = {1997} 12865} 12866 12867% ***** Parallel concept in Diffpack: 12868@InCollection{ dpparallel, 12869 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 12870 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 12871 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 12872 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 12873 Simulators}, 12874 publisher = {Springer--Verlag}, 12875 series = {Lecture Notes in Computer Science}, 12876 pages = {161--168}, 12877 year = {1997} 12878} 12879 12880% ***** DD and ML methods in Diffpack: 12881@InCollection{ dpddml, 12882 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 12883 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 12884 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 12885 title = {Domain decomposition and multilevel methods in Diffpack}, 12886 year = {1997} 12887} 12888 12889@InProceedings{ bsca98, 12890 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 12891 Alexander}, 12892 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 12893 Optimization}, 12894 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12895 Scientific and Engineering Computing}, 12896 editor = {Mike Henderson et al.}, 12897 pages = {165-173}, 12898 year = {1998} 12899} 12900 12901@Book{ scalapack-user-guide, 12902 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 12903 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 12904 Stanley and D. Walker and R. C. Whaley}, 12905 title = {Sca{LAPACK} Users' Guide}, 12906 publisher = {SIAM}, 12907 address = {Philadelphia, PA}, 12908 year = {1997} 12909} 12910 12911@InProceedings{ keyes99, 12912 author = {D. E. Keyes}, 12913 title = {How Scalable is Domain Decomposition in Practice?}, 12914 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 12915 Methods}, 12916 editor = {C.-H. Lai et al.}, 12917 publisher = {Domain Decomposition Press, Bergen}, 12918 note = {To appear}, 12919 year = {1999} 12920} 12921 12922@Article{ fun3d, 12923 author = {W. K. Anderson and D. L. Bonhaus}, 12924 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 12925 grids}, 12926 journal = {Computers and Fluids}, 12927 year = {1994}, 12928 volume = {23}, 12929 pages = {1--21} 12930} 12931 12932% ------------------------------------------------------------------------- 12933% ------------------------------------------------------------------------- 12934@Article{ torczon, 12935 author = {Dennis, Jr., J. E. and V.~Torczon}, 12936 title = {Direct Search Methods on Parallel Machines}, 12937 journal = {SIAM J. Optimization}, 12938 volume = {1}, 12939 pages = {448--474}, 12940 year = {1991}, 12941 key = {Torczon !PDS} 12942} 12943 12944@InProceedings{ wt91, 12945 author = {D. L. Whitfield and L. K. Taylor}, 12946 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12947 Schemes}, 12948 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 12949 misc = {AIAA-91-1539}, 12950 pages = {134-145}, 12951 year = {1991} 12952} 12953 12954@Article{ ew96, 12955 author = {S. C. Eisenstat and H. F. Walker}, 12956 title = {Choosing the forcing terms in an inexact {N}ewton method}, 12957 journal = {SIAM J. Scientific Computing}, 12958 volume = {17}, 12959 year = {1996}, 12960 pages = {16--32} 12961} 12962 12963@Book{ thi93, 12964 author = {{Thinking Machines Corporation}}, 12965 title = {Users Manual for CM-Fortran}, 12966 publisher = {Thinking Machines Corporation}, 12967 year = {1993} 12968} 12969 12970@Book{ mortonmayers94, 12971 author = {K. W. Morton and D. F. Mayers}, 12972 title = {Numerical Solution of Partial Differential Equations}, 12973 publisher = {Press Syndicate of the University of Cambridge}, 12974 year = {1994} 12975} 12976 12977@Book{ heath97, 12978 author = {Michael T. Heath}, 12979 title = {Scientific Computing: An Introductory Survey}, 12980 publisher = {McGraw Hill}, 12981 year = {1997} 12982} 12983 12984@Article{ captools96, 12985 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 12986 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 12987 Performance on the Parallelization of Structured Mesh Codes}, 12988 journal = {Parallel Computing}, 12989 volume = {22}, 12990 pages = {197-226}, 12991 year = {1996} 12992} 12993 12994@Unpublished{ nastran-web-page, 12995 author = {{MSC Software Corporation}}, 12996 title = {{NASTRAN} {W}eb page}, 12997 note = {See {\tt http://www.mechsolutions.com\-/products\-/nastran/}} 12998} 12999 13000@Book{ hpf, 13001 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 13002 Zosel}, 13003 title = {The High Performance Fotran Handbook}, 13004 publisher = {MIT Press}, 13005 year = {1994} 13006} 13007 13008@InProceedings{ keyes98, 13009 author = {D. E. Keyes}, 13010 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 13011 Architectures}, 13012 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 13013 editors = {M. D. Salas and W. K. Anderson}, 13014 ppublisher = {Elsevier}, 13015 year = {1998} 13016} 13017 13018@InProceedings{ pooma-atlas, 13019 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 13020 J. V. W. Reynders and M. Tholburn}, 13021 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 13022 Applications}, 13023 year = {1995}, 13024 month = {December}, 13025 booktitle = {Supercomputing '95 Proceedings} 13026} 13027 13028% --------------------------------------------------------------------------------- 13029% New bib entries for CRPC paper 13030@Misc{ mgnet-web-page, 13031 author = {Craig C. Douglas}, 13032 title = {{MGNet Web page}}, 13033 note = {See {\tt http://\-www.mgnet.org}} 13034} 13035 13036@Misc{ dagh-web-page, 13037 author = {M. Parashar and J. C. Browne}, 13038 title = {{DAGH Web page}}, 13039 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 13040} 13041 13042@Misc{ parasol-web-page, 13043 key = {PARASOL}, 13044 title = {{PARASOL Web page}}, 13045 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 13046} 13047 13048@Misc{ pooma-web-page, 13049 author = {{POOMA Web page}}, 13050 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 13051} 13052 13053@Misc{ mudpack-web-page, 13054 author = {John C. Adams}, 13055 title = {{MUDPACK Web page}}, 13056 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 13057} 13058 13059@Misc{ pellpack-web-page, 13060 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 13061 title = {{Parallel ELLPACK Web page}}, 13062 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 13063} 13064 13065@InProceedings{ pellpack95, 13066 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 13067 Catlin and S. Weerawarana and T.S. Papatheodorou}, 13068 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 13069 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 13070 address = {Albuquerque, NM}, 13071 year = {1995} 13072} 13073 13074@Misc{ nhse-web-page, 13075 author = {{National High-Performance Software Exchange Web page}}, 13076 note = {See {\tt http://\-www.nhse.org}} 13077} 13078 13079@Misc{ doug-web-page, 13080 author = {Mark J. Hagger and Linda Stals}, 13081 title = {{DOUG Web Page}}, 13082 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 13083} 13084 13085@TechReport{ doug97, 13086 author = {Mark J. Hagger}, 13087 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 13088 institution = {Mathematical Sciences, University of Bath}, 13089 year = {1997}, 13090 number = {9706}, 13091 note = {Advances in Computational Mathematics (to appear)} 13092} 13093 13094@Misc{ ug-web-page, 13095 author = {{UG Web Page}}, 13096 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 13097} 13098 13099@Article{ ug97, 13100 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 13101 Rentz-Reichert and C. Wieners}, 13102 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 13103 journal = {Computing and Visualization in Science}, 13104 year = {1997}, 13105 volume = {}, 13106 pages = {} 13107} 13108 13109@Misc{ vecfem-web-page, 13110 author = {Lutz Grosz}, 13111 title = {{VECFEM Web Page}}, 13112 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 13113} 13114 13115@Misc{ atlas-web-page, 13116 author = {R. Clint {Whaley et al.}}, 13117 title = {{ATLAS Web Page}}, 13118 howpublished = {\url{http://math-atlas.sourceforge.net}} 13119} 13120 13121@Misc{ fenics-web-page, 13122 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 13123 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 13124 title = {{FEniCS Web Page}}, 13125 note = {\url{http://www.fenicsproject.org}}, 13126 year = {2005} 13127} 13128 13129@Misc{ matlab-web-page, 13130 author = {{The} {MathWorks}}, 13131 title = {{Matlab} {Web} page}, 13132 url = {http://www.mathworks.com} 13133} 13134 13135@Misc{ phipac-web-page, 13136 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 13137 and D. Lam}, 13138 title = {{PHiPAC Web Page}}, 13139 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 13140} 13141 13142@InProceedings{ kelp, 13143 author = {Stephan J. Fink and Scott B. Baden and Scott R. 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Quinlan}, 13180 title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations 13181 on Overlapping Grids}, 13182 publisher = {SIAM}, 13183 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 13184 Scientific and Engineering Computing}, 13185 year = {1999}, 13186 pages = {215-224}, 13187 note = {See \url{http://www.llnl.gov/CASC/Overture}} 13188} 13189 13190@InProceedings{ diffpack, 13191 author = {A.M. Bruaset and H.P. Langtangen}, 13192 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations: 13193 {D}iffpack}, 13194 booktitle = {Numerical Methods and Software Tools in Industrial Mathematics}, 13195 year = {1997}, 13196 pages = {61--90}, 13197 publisher = {Birkhauser Press} 13198} 13199 13200@Article{ dongarra:1984:ila, 13201 author = {J. J. Dongarra and F. G. Gustavson and A. 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The different versions are examined for efficiency on a computer 13218 architecture which uses vector processing and has pipelined instruction execution. 13219 By using the advanced architectural features of such machines, one can usually 13220 achieve maximum performance, and tremendous improvements in terms of execution 13221 speed can be seen over conventional computers.}, 13222 classification= {723; 921}, 13223 journalabr = {SIAM Rev}, 13224 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 13225 mathematical programming; vector pipeline machine} 13226} 13227 13228@Book{ qv99, 13229 author = {Alfio Quarteroni and Alberto Valli}, 13230 title = {Domain Decomposition Methods for Partial Differential Equations}, 13231 publisher = {Oxford Science Publications}, 13232 address = {Oxford}, 13233 year = {1999} 13234} 13235 13236@Book{ ksv97, 13237 editor = {David E. Keyes and Ahmed Sameh and V. 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Koniges}, 13306 title = {Industrial Strength Parallel Computing}, 13307 publisher = {Morgan Kaufmann Publishers}, 13308 address = {San Francisco}, 13309 year = {2000} 13310} 13311 13312@Misc{ fftw-web-page, 13313 key = {Fftw}, 13314 title = {{FFTW} {Web} page}, 13315 note = {\texttt{http://www.fftw.org/}}, 13316 annote = {fast FFT. Parallel versions with MPI and Cilk} 13317} 13318 13319@InProceedings{ frigojohnson93, 13320 author = {Matteo Frigo and Steven G. Johnson}, 13321 title = {The Design and Implementation of {FFTW3}}, 13322 booktitle = {Proceedings of the IEEE}, 13323 volume = {93}, 13324 number = {2}, 13325 pages = {216--231}, 13326 year = {2005} 13327} 13328 13329@Book{ kelley95, 13330 author = {C. T. Kelley}, 13331 title = {Iterative Methods for Linear and Nonlinear Equations}, 13332 year = {1995}, 13333 publisher = {SIAM}, 13334 address = {Philadelphia} 13335} 13336 13337@Unpublished{ spai-web-page, 13338 title = {{SPAI} {W}eb {P}age}, 13339 note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/}, 13340 author = {Steven Bernard and Marcus Grote}, 13341 institution = {NASA Ames Research Center and ETH Zurich} 13342} 13343 13344@Article{ gh97, 13345 author = {M. J. Grote and T. Huckle}, 13346 title = {Parallel Preconditioning with Sparse Approximate Inverses}, 13347 year = {1997}, 13348 journal = {SIAM J. of Scient. Comput.}, 13349 volume = {18}, 13350 pages = {838-853} 13351} 13352 13353@Article{ zhang96, 13354 author = {Wen Zhang}, 13355 title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the 13356 simulation of a sintering process}, 13357 year = {1996}, 13358 journal = {Appl. Numer. Math.}, 13359 volume = {20}, 13360 pages = {235-244} 13361} 13362 13363@Article{ zhang98, 13364 author = {Wen Zhang and Ian Gladwell}, 13365 title = {The sintering of two particles by surface and grain boundary diffusion - a 13366 three-dimensional numerical study}, 13367 journal = {Comp. Mater. Sci.}, 13368 year = {1998}, 13369 volume = {12} 13370} 13371 13372@InProceedings{ mollerschwartzbach01, 13373 author = {Anders M\o{}ller and Michael I. Schwartzbach}, 13374 title = {The Pointer Assertion Logic Engine}, 13375 booktitle = {ACM Proceedings of PLDI'01}, 13376 year = {2001} 13377} 13378 13379@InProceedings{ klarlandschwartzbach97, 13380 author = {Nils Klarland and Michael I. Schwartzbach}, 13381 title = {A Domain-Specific Languages for Regular Sets of Strings and Trees}, 13382 booktitle = {Proceedings of the Conference on Domain-Specific Languages}, 13383 publisher = {USENIX}, 13384 month = {October}, 13385 year = {1997}, 13386 address = {Santa Barbara, CA} 13387} 13388 13389@InProceedings{ conselmarlet98, 13390 author = {C. Consel and R. Marlet}, 13391 title = {Architecturing software using a methodology for language development}, 13392 booktitle = {Proceedings of the 10th International Symposium on Programming Languages, 13393 Implementations, Logics and Programs}, 13394 year = {1998}, 13395 pages = {170-174}, 13396 month = {September}, 13397 address = {Pisa, Italy} 13398} 13399 13400@Misc{ sundials:homepage, 13401 author = {C. {Woodward et al.}}, 13402 title = {{SUNDIALS {W}eb page}}, 13403 howpublished = {\url{https://computation.llnl.gov/casc/sundials/main.html}} 13404} 13405 13406@Misc{ sundials-user-ref, 13407 title = {{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13408 note = {See \url{http://www.llnl.gov/CASC/sundials}}, 13409 author = {Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban 13410 and Dan Shumaker and Carol Woodward}, 13411 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 13412 number = {UCRL-JP-200037}, 13413 year = {2003} 13414} 13415 13416@Article{ sundials05, 13417 author = {A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 13418 and C. Woodward}, 13419 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13420 journal = {ACM Transactions on Mathematical Software}, 13421 volume = {31}, 13422 number = {3}, 13423 pages = {363--396}, 13424 year = {2005} 13425} 13426 13427@InProceedings{ serban2005cvodes, 13428 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 13429 author = {Serban, Radu and Hindmarsh, Alan C}, 13430 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 13431 Dynamics and Control, Long Beach, CA}, 13432 year = {2005} 13433} 13434 13435@Article{ pvode99, 13436 author = {G. Byrne and A. Hindmarsh}, 13437 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 13438 journal = {Int. J. High Perf. Comput. Apps.}, 13439 volume = {13}, 13440 number = {4}, 13441 year = {1999}, 13442 pages = {354 -- 365} 13443} 13444 13445@Article{ cvode95, 13446 author = {S. Cohen and A. 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Babu$\check{s}$ka and A.D. Miller}, 13514 title = {The post-processing approach in the finite element method, {I}: Calculations of 13515 displacements, stresses, and other higher derivatives of the displacements}, 13516 journal = {Int. J. Numer. Meth. Eng.}, 13517 year = {1984}, 13518 volume = {20}, 13519 pages = {1085--1109} 13520} 13521 13522@Article{ babuskamiller84b, 13523 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13524 title = {The post-processing approach in the finite element method, {II}: The calculation 13525 of stress intensity factors}, 13526 journal = {Int. J. Numer. Meth. Eng.}, 13527 year = {1984}, 13528 volume = {20}, 13529 pages = {1111--1129} 13530} 13531 13532@Article{ babuskamiller84c, 13533 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13534 title = {The post-processing approach in the finite element method, {III}: A posteriori 13535 error estimation and adaptive mesh refinement}, 13536 journal = {Int. J. Numer. Meth. Eng.}, 13537 year = {1984}, 13538 volume = {20}, 13539 pages = {2311--2324} 13540} 13541 13542@Unpublished{ jtb-web-page, 13543 title = {{The Java Tree Builder}}, 13544 note = {See \url{http://www.cs.purdue.edu/jtb}}, 13545 author = {Jens Palsberg}, 13546 institution = {Purdue University} 13547} 13548 13549@Unpublished{ palsberg98, 13550 title = {Why Visitors?}, 13551 note = {See \url{http://www.cs.purdue.edu/jtb/whyvisitors}}, 13552 author = {Jens Palsberg}, 13553 institution = {Purdue University}, 13554 year = {1998} 13555} 13556 13557@Unpublished{ ply-web-page, 13558 title = {{PLY (Python Lex-Yacc)}}, 13559 note = {\url{http://systems.cs.chicago.edu/ply}}, 13560 author = {David Beazley}, 13561 institution = {University of Chicago} 13562} 13563 13564@Misc{ adic-web-page, 13565 title = {{ADIC Web page}}, 13566 note = {\url{http://www.mcs.anl.gov/autodiff}}, 13567 author = {Paul Hovland and Uwe Naumann and Boyana Norris}, 13568 institution = {Argonne National Laboratory} 13569} 13570 13571@Article{ naumann02, 13572 author = {Uwe Naumann}, 13573 title = {Optimal accumulation of {J}acobian matrices by elimination methods on the dual 13574 computational graph}, 13575 journal = {Mathematical Programming (to appear)}, 13576 note = {Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002}, 13577 year = {2003} 13578} 13579 13580@Article{ kaper1, 13581 author = {H. 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Anderson and Z. Bai and C. Bischof and S. Blackford and J. Demmel and J. 13643 Dongarra and J. Du Cris and A. Greenbaum and S. Hammarling and A. McKenney and D. 13644 Sorensen}, 13645 title = {LAPACK Users' Guide, Third Edition}, 13646 publisher = {SIAM}, 13647 year = {1999} 13648} 13649 13650@Manual{ nwchem4.1, 13651 author = {High Performance Computational Chemistry Group}, 13652 title = {{NWChem}, A Computational Chemistry Package for Parallel Computers, Version 4.1}, 13653 year = {2002}, 13654 organization = {Pacific Northwest National Laboratory}, 13655 address = {Richland, Washington 99325-0999 USA}, 13656 note = {See \url{http://www.emsl.pnl.gov/pub/docs/nwchem/}} 13657} 13658 13659@TechReport{ tchem, 13660 title = {{TC}hem: {A} Software Toolkit for the Analysis of Complex Kinetic Models}, 13661 author = {Cosmin Safta and Habib Najm and Omar Knio}, 13662 institution = {Sandia National Laboratories}, 13663 number = {SAND2011-3282}, 13664 year = {2011} 13665} 13666 13667@Misc{ scidac-web-page, 13668 author = {}, 13669 title = {{{SciDAC Initiative Web page}}}, 13670 note = {\url{http://www.osti.gov/scidac}}, 13671 key = {{SciDAC Initiative Web page}} 13672} 13673 13674@Misc{ cmrs:homepage, 13675 author = {Amitava {Bhattacharjee (PI)}}, 13676 title = {{Center for Magnetic Reconnection Studies}}, 13677 howpublished = {\url{http://www.physics.uiowa.edu/cmrs}} 13678} 13679 13680@Misc{ tops:homepage, 13681 author = {David {Keyes (PI)}}, 13682 title = {{Towards Optimal Petascale Simulations (TOPS) Center}}, 13683 howpublished = {\url{http://scalablesolvers.org}} 13684} 13685 13686@Misc{ tstt:homepage, 13687 author = {David Brown and Jim Glimm and Lori Freitag}, 13688 title = {{Terascale Simulation Tools and Technology (TSTT) Center}}, 13689 howpublished = {\url{http://www.tstt-scidac.org}}, 13690 year = {2005} 13691} 13692 13693@Misc{ petsc:applications, 13694 author = {B. F. {Smith et al.}}, 13695 title = {{Scientific Applications Using {PETSc}}}, 13696 howpublished = {\url{http://www.mcs.anl.gov/petsc/publications}} 13697} 13698 13699@Misc{ petsc:users, 13700 author = {B. 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Ko and R. Ryne (PIs)} 13733} 13734 13735@Unpublished{ katzspiegelman03, 13736 author = {Richard F. Katz and Marc Spiegelman}, 13737 title = {A semi-{L}agrangian {C}rank-{N}icholson algorithm for the numerical solution of 13738 advection-diffusion problems}, 13739 note = {Columbia University, in preparation} 13740} 13741 13742@Misc{ acts:homepage, 13743 author = {}, 13744 title = {{Advanced CompuTational Software (ACTS) Web page}}, 13745 howpublished = {\url{http://acts.nersc.gov}}, 13746 key = {{Advanced CompuTational Software (ACTS) Web page}} 13747} 13748 13749@Article{ superlu99, 13750 author = {James W. Demmel and Stanley C. Eisenstat and John R. Gilbert and Xiaoye S. Li and 13751 Joseph W. H. Liu}, 13752 title = {A supernodal approach to sparse partial pivoting}, 13753 journal = {SIAM J. Matrix Analysis and Applications}, 13754 year = {1999}, 13755 volume = {20}, 13756 number = {3}, 13757 pages = {720-755} 13758} 13759 13760@Misc{ superlu:homepage, 13761 author = {J. 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F. {Smith et al.}}, 14598 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 14599} 14600 14601@Misc{ petsc-dm:webpage, 14602 author = {B. 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Pool and J. 14824 Shepherd}, 14825 title = {{Center for Simulation of Dynamic Response of Materials}}, 14826 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 14827} 14828 14829@Misc{ csar:web, 14830 author = {M. {Heath (Director)}}, 14831 title = {{Center for Simulation of Advanced Rockets}}, 14832 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 14833} 14834 14835@Misc{ csafe:web, 14836 author = {D. {Pershing (Director)}}, 14837 title = {{Center for Simulation of Accidental Fires and Explosions}}, 14838 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 14839} 14840 14841@Misc{ cits:web, 14842 author = {P. {Moin (Director)}}, 14843 title = {{Center for Integrated Turbulence Simulations}}, 14844 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 14845} 14846 14847@Misc{ flash:web, 14848 author = {D. {Lamb (Director)}}, 14849 title = {{Center for Integrated Turbulence Simulations}}, 14850 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 14851} 14852 14853@TechReport{ utah-csafe03, 14854 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 14855 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 14856 Problems, Part 1: Algorithm Development}, 14857 institution = {University of Utah, Center for the Simulation of Accidental Fires and 14858 Explosions}, 14859 year = {2003} 14860} 14861 14862@InBook{ shepherd07, 14863 author = {M. Shepherd and E. Seol and B. FrantzDale}, 14864 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 14865 year = {2007}, 14866 booktitle = {CRC Handbook of Dynamic System Modeling}, 14867 publisher = {Wiley}, 14868 pages = {1--41}, 14869 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 14870} 14871 14872@InProceedings{ cactus02, 14873 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 14874 Radke and Edward Seidel and John Shalf}, 14875 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 14876 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 14877 year = {2002}, 14878 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 14879} 14880 14881@Misc{ cactus:homepage, 14882 author = {G. {Allen et al.}}, 14883 title = {{Cactus Web page}}, 14884 howpublished = {\url{http://cactuscode.org}} 14885} 14886 14887@Misc{ open-grid-forum:web, 14888 key = {{Open Grid Forum}}, 14889 title = {{Open Grid Forum}}, 14890 note = {See \url{http://www.ogf.org}} 14891} 14892 14893@Misc{ nox:web, 14894 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 14895 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 14896 note = {See \url{http://software.sandia.gov/nox}} 14897} 14898 14899@Misc{ chombo:web, 14900 author = {P. {Colella (PI)}}, 14901 title = {{Chombo}}, 14902 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 14903} 14904 14905@Article{ lanzkron96, 14906 author = {P. 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Michopoulos and Charbel Farhat and Jacob Fish}, 15003 journal = {Journal of Computing and Information Science in Engineering}, 15004 volume = {5}, 15005 issue = {3}, 15006 pages = {198--213}, 15007 year = {2005} 15008} 15009 15010@Article{ dubey09, 15011 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 15012 Multiphysics Simulation Code}, 15013 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 15014 Siegel and K. Weide}, 15015 journal = {Parallel Computing}, 15016 volume = {35}, 15017 issue = {10 -- 11}, 15018 pages = {512 -- 522}, 15019 year = {2009} 15020} 15021 15022@Book{ bottloring95, 15023 author = {Raoul Bott and Loring W. Tu}, 15024 title = {Differential Forms in Algebraic Topology}, 15025 publisher = {Springer}, 15026 year = {1995} 15027} 15028 15029@Book{ kobayashinomizu96, 15030 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 15031 title = {Foundations of Differential Geometry}, 15032 publisher = {Wiley-Interscience}, 15033 year = {1996} 15034} 15035 15036@Article{ hornungkohn02, 15037 author = {Richard D. Hornung and Scott R. Kohn}, 15038 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 15039 journal = {Concurrency and Computation: Practice and Experience}, 15040 volume = {14}, 15041 pages = {347--368}, 15042 year = {2002} 15043} 15044 15045@InProceedings{ concepts06, 15046 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 15047 Gabriel Dos Reis and Andrew Lumsdaine}, 15048 title = {Concepts: Linguistic Support for Generic Programming in C++}, 15049 booktitle = {Proceedings of OOPSLA 2006}, 15050 year = {2006}, 15051 pages = {???--???} 15052} 15053 15054@Book{ hatcher02, 15055 author = {Hatcher, Allen}, 15056 title = {Algebraic Topology}, 15057 publisher = {Cambridge University Press}, 15058 year = {2002} 15059} 15060 15061@Book{ gammahelmjohnsonvlissides95, 15062 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 15063 development, offering timeless and elegant solutions to common problems in 15064 software design. It describes patterns for managing object creation, composing 15065 objects into larger structures, and coordinating control flow between objects. The 15066 book provides numerous examples where using composition rather than inheritance 15067 can improve the reusability and flexibility of code. Note, though, that it's not a 15068 tutorial but a catalog that you can use to find an object-oriented design pattern 15069 that's appropriate for the needs of your particular application--a selection for 15070 virtuoso programmers who appreciate (or require) consistent, well-engineered 15071 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 15072 more valuable than ever! 15073 15074 Use the contents of the CD to create your own design documents and reusable 15075 components. The CD contains: 23 patterns you can cut and paste into your own 15076 design documents; sample code demonstrating pattern implementation; complete 15077 Design Patterns content in standard HTML format, with numerous hyperlinked 15078 cross-references; accessed through a standard web browser; Java-based dynamic 15079 search mechanism, enhancing online seach capabilities; graphical user environment, 15080 allowing ease of navigation. 15081 15082 First published in 1995, this landmark work on object-oriented software design 15083 presents a catalog of simple and succinct solutions to common design problems. 15084 Created by four experienced designers, the 23 patterns contained herein have 15085 become an essential resource for anyone developing reusable object-oriented 15086 software. In response to reader demand, the complete text and pattern catalog are 15087 now available on CD-ROM. This electronic version of Design Patterns enables 15088 programmers to install the book directly onto a computer or network for use as an 15089 online reference for creating reusable object-oriented software. 15090 15091 The authors first describe what patterns are and how they can help you in the 15092 design process. They then systematically name, explain, evaluate, and catalog 15093 recurring designs in object-oriented systems. All patterns are compiled from 15094 real-world examples and include code that demonstrates how they may be implemented 15095 in object-oriented programming languages such as C++ and Smalltalk. Readers who 15096 already own the book will want the CD to take advantage of its dynamic search 15097 mechanism and ready-to-install patterns.}}, 15098 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 15099 citeulike-article-id={115158}, 15100 howpublished = {Hardcover}, 15101 isbn = {0201633612}, 15102 keywords = {1995 algorithms architecture book books computer computing design design-pattern 15103 design-patterns design_patterns designpatterns development diplom entwurfsmuster 15104 four gang gof java mathgamespatterns no-tag object object-orientation 15105 object-oriented of oo-patterns oop oriented pattern patterns programming se 15106 software software-development software-engineering software_design 15107 softwareengineering standard}, 15108 month = {January}, 15109 publisher = {{Addison-Wesley Professional}}, 15110 title = {Design Patterns}, 15111 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 15112 year = {1995} 15113} 15114 15115@InProceedings{ chaco95, 15116 author = {Bruce Hendrickson and Robert Leland}, 15117 title = {A multilevel algorithm for partitioning graphs}, 15118 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 15119 (CDROM)}, 15120 year = {1995}, 15121 isbn = {0-89791-816-9}, 15122 pages = {28}, 15123 location = {San Diego, California, United States}, 15124 doi = {10.1145/224170.224228}, 15125 publisher = {ACM Press}, 15126 address = {New York} 15127} 15128 15129@Book{ aleksandrov98, 15130 author = {Aleksandrov, Pavel S.}, 15131 title = {Combinatorial Topology}, 15132 publisher = {Dover}, 15133 volume = {3}, 15134 year = {1998} 15135} 15136 15137@Book{ steenrod99, 15138 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 15139 importance in modern physics--such as in gauge theory. This book, a succinct 15140 introduction to the subject by renown mathematician Norman Steenrod, was the first 15141 to present the subject systematically. 15142 15143 It begins with a general introduction to bundles, including such topics as 15144 differentiable manifolds and covering spaces. The author then provides brief 15145 surveys of advanced topics, such as homotopy theory and cohomology theory, before 15146 using them to study further properties of fibre bundles. The result is a classic 15147 and timeless work of great utility that will appeal to serious mathematicians and 15148 theoretical physicists alike. }}, 15149 author = {Steenrod, Norman}, 15150 citeulike-article-id={712999}, 15151 howpublished = {Paperback}, 15152 isbn = {0691005486}, 15153 keywords = {fibre_bundles topology}, 15154 month = {April}, 15155 publisher = {{Princeton University Press}}, 15156 title = {The Topology of Fibre Bundles. (PMS-14)}, 15157 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 15158 year = {1999} 15159} 15160 15161@Book{ bredon97, 15162 author = {Bredon, Glen E.}, 15163 title = {Sheaf Theory}, 15164 publisher = {Springer}, 15165 pages = {524}, 15166 series = {Graduate Texts in Mathematics}, 15167 year = {1997} 15168} 15169 15170@TechReport{ tautgesmeyers04, 15171 title = {{MOAB}: A Mesh-Oriented Database}, 15172 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 15173 Ernst}, 15174 institution = {Sandia National Laboratories}, 15175 number = {SAND2004-1592}, 15176 month = {April}, 15177 year = {2004} 15178} 15179 15180@Article{ tautges04, 15181 author = {Timothy J. Tautges}, 15182 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 15183 journal = {Engineering With Computers}, 15184 volume = {20}, 15185 pages = {286--293}, 15186 year = {2004} 15187} 15188 15189@InProceedings{ meyers02, 15190 author = {Ray Meyers et. al}, 15191 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 15192 booktitle = {8th International conference on numerical grid generation in computational field 15193 simulations}, 15194 month = {June}, 15195 year = {2002} 15196} 15197 15198@InProceedings{ seolshepard05, 15199 author = {E. S. Seol and Mark S. Shephard}, 15200 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 15201 Analysis}, 15202 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 15203 year = {2005} 15204} 15205 15206@Article{ beallwalshshephard04, 15207 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 15208 title = {A comparison of techniques for geometry access related to mesh generation}, 15209 journal = {Engineering With Computers}, 15210 volume = {20}, 15211 number = {3}, 15212 pages = {210--221}, 15213 year = {2004} 15214} 15215 15216@Article{ careyandersoncarneskirk04, 15217 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 15218 Kirk}, 15219 title = {Some aspects of adaptive grid technology related to boundary and interior 15220 layers}, 15221 journal = {Journal of Computational Applied Mathematics}, 15222 volume = {166}, 15223 number = {1}, 15224 pages = {55--86}, 15225 year = {2004} 15226} 15227 15228@PhDThesis{ gralthesis, 15229 author = {Guntram Berti}, 15230 title = {Generic Software Components for Scientific Computing}, 15231 school = {TU Cottbus}, 15232 year = {2000}, 15233 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 15234} 15235 15236@Article{ whitehead1949, 15237 title = {Combinatorial homotopy. I}, 15238 author = {John HC Whitehead}, 15239 journal = {Bulletin of the American Mathematical Society}, 15240 volume = {55}, 15241 number = {3. P1}, 15242 pages = {213--245}, 15243 year = {1949}, 15244 publisher = {American Mathematical Society} 15245} 15246 15247@Article{ beylkincoifmanrokhlin91, 15248 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 15249 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 15250 journal = {Communications on Pure and Applied Mathematics}, 15251 volume = {44}, 15252 pages = {141--183}, 15253 year = {1991} 15254} 15255 15256@Book{ wesseling92, 15257 author = {Pieter Wesseling}, 15258 title = {An Introduction to Multigrid Methods}, 15259 publisher = {John Wiley and Sons}, 15260 year = {1992} 15261} 15262 15263@Book{ grakakos04, 15264 author = {Loukas Grakakos}, 15265 title = {Classical and Modern Fourier Analysis}, 15266 publisher = {Pearson Education}, 15267 address = {New Jersey}, 15268 year = {2004} 15269} 15270 15271@Misc{ hlib-web-page, 15272 key = {HLib}, 15273 title = {{HLib} {Web} page}, 15274 note = {{\texttt{http://www.hlib.org/}}}, 15275 annote = {Hierarchical matrices for fast integral transform} 15276} 15277 15278@Article{ hackbusch99, 15279 author = {Wolfgang Hackbusch}, 15280 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 15281 Introduction to {$\mathcal H$}-matrices}, 15282 journal = {Computing}, 15283 volume = {62}, 15284 pages = {89--108}, 15285 year = {1999} 15286} 15287 15288@TechReport{ kay1999green, 15289 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 15290 equations}, 15291 author = {Kay, D. and Loghin, D.}, 15292 year = {1999}, 15293 institution = {Oxford University Computing Laboratory}, 15294 number = {99/06} 15295} 15296 15297@Article{ bebendorf2003existence, 15298 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 15299 elliptic operators with {$L^\infty$}-coefficients}, 15300 author = {Bebendorf, M. and Hackbusch, W.}, 15301 journal = {Numerische Mathematik}, 15302 volume = {95}, 15303 number = {1}, 15304 pages = {1--28}, 15305 year = {2003}, 15306 publisher = {Springer} 15307} 15308 15309@Article{ hackbusch2005direct, 15310 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 15311 H$}-matrix approximation}, 15312 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 15313 journal = {Computing and Visualization in Science}, 15314 volume = {8}, 15315 number = {3}, 15316 pages = {179--188}, 15317 year = {2005}, 15318 publisher = {Springer} 15319} 15320 15321@TechReport{ duphof2003, 15322 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 15323 Logg and L. R. Scott}, 15324 title = {The {FE}ni{CS} project}, 15325 institution = {Chalmers Finite Element Center Preprint Series}, 15326 number = {2003--21}, 15327 year = {2003} 15328} 15329 15330@Article{ flame01, 15331 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 15332 Geijn}, 15333 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 15334 journal = {Transactions on Mathematical Software}, 15335 volume = {27}, 15336 number = {4}, 15337 year = {2001}, 15338 pages = {422--455} 15339} 15340 15341@Article{ puschel05, 15342 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 15343 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 15344 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 15345 Nick Rizzolo}, 15346 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 15347 journal = {Proceedings of the IEEE}, 15348 volume = {93}, 15349 number = {2}, 15350 year = {2005}, 15351 note = {special issue on "Program Generation, Optimization, and Adaptation"} 15352} 15353 15354@Article{ kirbylogg06, 15355 author = {Robert C. Kirby and Anders Logg}, 15356 title = {A compiler for variational forms}, 15357 journal = {ACM Transactions on Mathematical Software}, 15358 volume = {32}, 15359 number = {3}, 15360 year = {2006}, 15361 issn = {0098-3500}, 15362 pages = {417--444}, 15363 doi = {10.1145/1163641.1163644}, 15364 publisher = {ACM Press}, 15365 address = {New York, NY} 15366} 15367 15368@Article{ kirbylogg07, 15369 author = {Robert C. Kirby and Anders Logg}, 15370 title = {Efficient compilation of a class of variational forms}, 15371 journal = {ACM Transactions on Mathematical Software}, 15372 volume = {33}, 15373 number = {3}, 15374 year = {2007}, 15375 issn = {0098-3500}, 15376 pages = {17}, 15377 doi = {10.1145/1268769.1268771}, 15378 publisher = {ACM Press}, 15379 address = {New York, NY} 15380} 15381 15382@Article{ bankdupont81, 15383 author = {Randolph Bank and Todd Dupont}, 15384 title = {An optimal order process for solving finite element equations}, 15385 journal = {Mathematics of Computation}, 15386 volume = {36}, 15387 pages = {35--51}, 15388 year = {1981} 15389} 15390 15391@TechReport{ adams00, 15392 author = {Mark F. Adams}, 15393 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 15394 in solid mechanics}, 15395 institution = {UC Berkeley}, 15396 number = {CSD-00-1103}, 15397 year = {2000}, 15398 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 15399} 15400 15401@Article{ bergengradlhuelsemannruede06, 15402 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 15403 title = {A Massively Parallel Multigrid Method for Finite Elements}, 15404 journal = {Computing in Science \& Engineering}, 15405 volume = {8}, 15406 number = {6}, 15407 pages = {56--62}, 15408 year = {2006} 15409} 15410 15411@MastersThesis{ brunethesis08, 15412 author = {Peter R. Brune}, 15413 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 15414 school = {University of Chicago}, 15415 address = {Chicago, IL}, 15416 year = {2008}, 15417 month = {February} 15418} 15419 15420@Article{ arnoldwinther02, 15421 author = {Douglas N. Arnold and Ragnar Winther}, 15422 title = {Mixed finite elements for elasticity}, 15423 journal = {Numerische Mathematik}, 15424 volume = {92}, 15425 number = {3}, 15426 month = {September}, 15427 year = {2002}, 15428 pages = {401--419}, 15429 doi = {10.1007/s002110100348} 15430} 15431 15432@Article{ arnoldfalkwinther06, 15433 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 15434 title = {Finite element exterior calculus, homological techniques, and applications}, 15435 journal = {Acta Numerica}, 15436 year = {2006}, 15437 volume = {15}, 15438 pages = {1--155}, 15439 publisher = {Cambridge University Press}, 15440 doi = {10.1017/S0962492906210018} 15441} 15442 15443@Article{ kirby04, 15444 author = {Robert C. Kirby}, 15445 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 15446 functions}, 15447 journal = {ACM Transactions on Mathematical Software}, 15448 volume = {30}, 15449 number = {4}, 15450 year = {2004}, 15451 issn = {0098-3500}, 15452 pages = {502--516}, 15453 doi = {10.1145/1039813.1039820}, 15454 publisher = {ACM Press}, 15455 address = {New York, NY} 15456} 15457 15458@Article{ kirby06, 15459 author = {Robert C. Kirby}, 15460 title = {Optimizing {FIAT} with level 3 {BLAS}}, 15461 journal = {ACM Transactions on Mathematical Software}, 15462 volume = {32}, 15463 number = {2}, 15464 year = {2006}, 15465 issn = {0098-3500}, 15466 pages = {223--235}, 15467 doi = {10.1145/1141885.1141889}, 15468 publisher = {ACM Press}, 15469 address = {New York, NY} 15470} 15471 15472@Misc{ bluecrystal08, 15473 author = {{B}lue {C}rystal Cluster}, 15474 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 15475 year = {2008}, 15476 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 15477} 15478 15479@Article{ beylkin95, 15480 author = {Gregory Beylkin}, 15481 title = {On the Fast Fourier Transform of Functions With Singularities}, 15482 journal = {Applied and Computational Harmonic Analysis}, 15483 volume = {2}, 15484 pages = {363--381}, 15485 year = {1995} 15486} 15487 15488@InProceedings{ riehl08, 15489 author = {Jonathan Riehl}, 15490 title = {Implementing the MyFEM Embedded Domain-specific Language}, 15491 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 15492 Development (DSPD'08)}, 15493 address = {Nashville, TN}, 15494 year = {2008} 15495} 15496 15497@Article{ appel85, 15498 author = {Andrew W. Appel}, 15499 date-added = {2008-02-27 12:23:39 +0000}, 15500 date-modified = {2008-02-27 12:24:02 +0000}, 15501 doi = {10.1137/0906008}, 15502 journal = {SIAM Journal on Scientific and Statistical Computing}, 15503 keywords = {treecodes}, 15504 number = {1}, 15505 pages = {85-103}, 15506 publisher = {SIAM}, 15507 title = {An Efficient Program for Many-Body Simulation}, 15508 volume = {6}, 15509 year = {1985} 15510} 15511 15512@Article{ ewald21, 15513 author = {{Ewald}, P.~P.}, 15514 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 15515 journal = {Annalen der Physik}, 15516 year = {1921}, 15517 volume = {369}, 15518 pages = {253-287}, 15519 doi = {10.1002/andp.19213690304}, 15520 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 15521 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 15522} 15523 15524@Article{ greengardrokhlin87, 15525 author = {L. Greengard and V. Rokhlin}, 15526 date-added = {2008-02-15 18:43:55 +0000}, 15527 date-modified = {2008-02-26 20:09:11 +0000}, 15528 doi = {10.1016/0021-9991(87)90140-9}, 15529 journal = {J. Comput.\ Phys.}, 15530 keywords = {FMM}, 15531 number = {2}, 15532 pages = {325--348}, 15533 title = {A Fast Algorithm for Particle Simulations}, 15534 url = {citeseer.ist.psu.edu/greengard87fast.html}, 15535 volume = {73}, 15536 year = {1987}, 15537 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 15538} 15539 15540@Article{ greengardrokhlin97, 15541 author = {L. Greengard and V. Rokhlin}, 15542 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 15543 Dimensions}, 15544 journal = {Acta Numerica}, 15545 volume = {6}, 15546 year = {1997}, 15547 pages = {229--269} 15548} 15549 15550@Article{ luchenghuangmccammon06, 15551 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 15552 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 15553 systems}, 15554 journal = {PNAS}, 15555 doi = {10.1073/pnas.0605166103}, 15556 volume = {102}, 15557 number = {51}, 15558 year = {2006}, 15559 pages = {19314--19319} 15560} 15561 15562@Article{ schussnadlereisenberg01, 15563 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 15564 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 15565 from a molecular model}, 15566 journal = {Physical Review E}, 15567 volume = {64}, 15568 number = {3}, 15569 year = {2001} 15570} 15571 15572@Book{ hairerlubichwanner02, 15573 author = {E. Hairer and Ch. Lubich and G. Wanner}, 15574 title = {Geometric Numerical Integration}, 15575 publisher = {Springer-Verlag}, 15576 address = {Berlin Heidelberg}, 15577 year = {2002} 15578} 15579 15580@Article{ holstbakerwang00, 15581 author = {M. Holst and N. Baker and F. Wang}, 15582 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 15583 equation on massively parallel computers}, 15584 journal = {Journal of Computational Chemistry}, 15585 volume = {21}, 15586 year = {2000} 15587} 15588 15589@Book{ hockneyeastwood81, 15590 author = {R. Hockney and J. Eastwood}, 15591 title = {Computer simulation using particles}, 15592 publisher = {McGraw-Hill}, 15593 address = {New York}, 15594 year = {1981} 15595} 15596 15597@Article{ lutydavistironigunsteren94, 15598 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 15599 Gunsteren}, 15600 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 15601 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 15602 journal = {Molecular Simulation}, 15603 volume = {14}, 15604 number = {1}, 15605 year = {1994}, 15606 pages = {11--20} 15607} 15608 15609@Book{ briggshensonmccormick00, 15610 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 15611 title = {A Multigrid Tutorial (2nd ed.)}, 15612 year = {2000}, 15613 isbn = {0-89871-462-1}, 15614 publisher = {Society for Industrial and Applied Mathematics}, 15615 address = {Philadelphia, PA} 15616} 15617 15618@Article{ chartier2003spectral, 15619 title = {Spectral AMGe ($\rho$ AMGe)}, 15620 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 15621 McCormick, S and Ruge, J and Vassilevski, PS}, 15622 journal = {SIAM Journal on Scientific Computing}, 15623 volume = {25}, 15624 number = {1}, 15625 pages = {1--26}, 15626 year = {2003}, 15627 publisher = {SIAM} 15628} 15629 15630@Article{ galvis2010domain, 15631 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 15632 media}, 15633 author = {Galvis, Juan and Efendiev, Yalchin}, 15634 journal = {Multiscale Modeling \& Simulation}, 15635 volume = {8}, 15636 number = {4}, 15637 pages = {1461--1483}, 15638 year = {2010}, 15639 publisher = {SIAM} 15640} 15641 15642@Book{ brennerscott02, 15643 author = {Susanne~C. Brenner and L.~Ridgway Scott}, 15644 title = {The mathematical theory of finite element methods}, 15645 year = {2002}, 15646 isbn = {0-38795-451-1}, 15647 publisher = {Springer}, 15648 pages = {361} 15649} 15650 15651@Book{ trefethenbau97, 15652 author = {Lloyd N. Trefethen and David {Bau, III}}, 15653 title = {Numerical Linear Algebra}, 15654 publisher = {Society for Industrial and Applied Mathematics}, 15655 address = {Philadelphia, PA}, 15656 pages = {xii + 361}, 15657 year = {1997}, 15658 isbn = {0-89871-361-7}, 15659 isbn-13 = {978-0-89871-361-9}, 15660 lccn = {QA184 .T74 1997}, 15661 mrclass = {65-01 (65-02 65Fxx)}, 15662 mrnumber = {MR1444820 (98k:65002)}, 15663 mrreviewer = {Moody T. Chu}, 15664 bibdate = {Wed Jan 07 15:23:19 1998}, 15665 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 15666} 15667 15668@Article{ liptonreagan2014, 15669 title = {Quantum Algorithms via Linear Algebra: A Primer}, 15670 author = {Richard J Lipton and Kenneth W Regan}, 15671 pages = {206}, 15672 isbn = {978-0-26202-839-4}, 15673 year = {2014} 15674} 15675 15676@InProceedings{ rhea08, 15677 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 15678 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 15679 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 15680 booktitle = {Proceedings of IEEE/ACM SC '08}, 15681 year = {2008} 15682} 15683 15684@Misc{ bursteddewilcox09, 15685 author = {Carsten Burstedde and Lucas~C. Wilcox}, 15686 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 15687 note = {in preparation} 15688} 15689 15690@Article{ skeeltezcanhardy02, 15691 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 15692 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 15693 journal = {J. Comp. Chem.}, 15694 volume = {23}, 15695 pages = {673--684}, 15696 year = {2002} 15697} 15698 15699@Article{ verschelde99, 15700 author = {Jan Verschelde}, 15701 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 15702 homotopy continuation}, 15703 journal = {ACM Trans. Math. Softw.}, 15704 volume = {25}, 15705 number = {2}, 15706 issn = {0098-3500}, 15707 pages = {251--276}, 15708 doi = {10.1145/317275.317286}, 15709 publisher = {ACM}, 15710 address = {New York, NY}, 15711 year = {1999} 15712} 15713 15714@InProceedings{ sommeseverscheldewampler08, 15715 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 15716 title = {Solving Polynomial Systems Equation by Equation}, 15717 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 15718 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 15719 pages = {133--152}, 15720 publisher = {Springer-Verlag}, 15721 year = {2008} 15722} 15723 15724@Article{ phanthientanner77, 15725 author = {N. Phan-Thien and R.~I. Tanner}, 15726 title = {A new constitutive equation derived from network theory}, 15727 journal = {J. Non-Newt. Fluid Mech.}, 15728 volume = {2}, 15729 pages = {353}, 15730 year = {1977} 15731} 15732 15733@Manual{ sage, 15734 key = {SAGE}, 15735 author = {W.\thinspace{}A. Stein and others}, 15736 organization = {The Sage~Development Team}, 15737 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 15738 note = {{\tt http://www.sagemath.org}}, 15739 year = {2009} 15740} 15741 15742@Misc{ bateshauensteinsommesewampler06, 15743 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 15744 Wampler}, 15745 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 15746 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 15747} 15748 15749@Article{ archer09, 15750 author = {A. J. Archer}, 15751 collaboration = {}, 15752 title = {Dynamical density functional theory for molecular and colloidal fluids: A 15753 microscopic approach to fluid mechanics}, 15754 publisher = {AIP}, 15755 year = {2009}, 15756 journal = {The Journal of Chemical Physics}, 15757 volume = {130}, 15758 number = {1}, 15759 eid = {014509}, 15760 numpages = {8}, 15761 pages = {014509}, 15762 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 15763 transition; statistical distributions; stochastic processes}, 15764 doi = {10.1063/1.3054633} 15765} 15766 15767@Article{ giesekus1966, 15768 author = {Hanswalter Giesekus}, 15769 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 15770 journal = {Rheologica Acta}, 15771 publisher = {Springer Berlin / Heidelberg}, 15772 volume = {5}, 15773 number = {1}, 15774 month = {March}, 15775 year = {1966}, 15776 doi = {10.1007/BF01973575}, 15777 pages = {29-35} 15778} 15779 15780@Article{ baaijens98, 15781 author = {F.P. Baaijens}, 15782 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 15783 journal = {Journal of Non-Newtonian Fluid Mechanics}, 15784 volume = {79}, 15785 year = {1998}, 15786 pages = {361--385} 15787} 15788 15789@Book{ joseph90, 15790 author = {D.~D. Joseph}, 15791 title = {Fluid Dynamics of Viscoelastic Liquids}, 15792 publisher = {Springer}, 15793 address = {New York, NY}, 15794 year = {1990} 15795} 15796 15797@Article{ oldroyd50, 15798 author = {J.~G. Oldroyd}, 15799 title = {On the Formulation of Rheological Equations of State}, 15800 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 15801 Sciences}, 15802 volume = {200}, 15803 year = {1950}, 15804 pages = {523--541} 15805} 15806 15807@InProceedings{ bynasungroppthakur04, 15808 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 15809 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 15810 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 15811 year = {2004} 15812} 15813 15814@Book{ pozrikidis07, 15815 author = {C. Pozrikidis}, 15816 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 15817 publisher = {Kluwer (Springer)}, 15818 pages = {675}, 15819 year = {2001}, 15820 isbn = {0792373510} 15821} 15822 15823@Misc{ kritzkeyesfsp07, 15824 author = {A. Kritz and D. Keyes}, 15825 title = {{Fusion Simulation Project Workshop Report}}, 15826 month = {July}, 15827 year = {2007}, 15828 note = {Available via 15829 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 15830} 15831 15832@Misc{ dahlburg02, 15833 author = {J. {Dahlburg (Chair)}}, 15834 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 15835 year = {2002}, 15836 note = {Available via 15837 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 15838} 15839 15840@Misc{ brown08, 15841 author = {D. {Brown (Chair)}}, 15842 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 15843 to the Future}}, 15844 year = {2008}, 15845 howpublished = {Office of Science, U.S. Department of Energy}, 15846 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 15847} 15848 15849@Misc{ crosscutting10, 15850 author = {D. Brown and P. {Messina (Chairs)}}, 15851 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 15852 Exascale}}, 15853 year = {2010}, 15854 howpublished = {Office of Science, U.S. Department of Energy}, 15855 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 15856} 15857 15858@Misc{ extreme-scale-solvers-workshop12, 15859 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 15860 L.C. McInnes and E. Ng and S. Wild}, 15861 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 15862 Architectures}, 15863 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 15864 note = {{Washington, DC}, March 8-9, 2012}, 15865 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 15866 year = {2012} 15867} 15868 15869@Misc{ monizrosner09, 15870 author = {{E. Moniz and R. Rosner}}, 15871 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 15872 and Simulation at the Extreme Scale}}, 15873 month = {May}, 15874 year = {2009}, 15875 note = {See 15876 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 15877} 15878 15879@Misc{ blanford08, 15880 author = {{R. Blandord (Chair)}}, 15881 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 15882 Computing at the Extreme Scale}}, 15883 month = {Dec}, 15884 year = {2008}, 15885 note = {See 15886 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 15887} 15888 15889@Misc{ exascale07, 15890 author = {H. Simon and T. Zacharia and R. Stevens}, 15891 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 15892 year = {2007}, 15893 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 15894} 15895 15896@Misc{ ascrbreakthroughs08, 15897 author = {{Panel on Recent Significant Advancements in Computational Science}}, 15898 title = {Breakthroughs}, 15899 year = {2008}, 15900 note = {See 15901 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 15902} 15903 15904@Misc{ petsc-rd100-2009, 15905 author = {{R\&D Magazine}}, 15906 title = {{PETSc} {R}\&{D} 100 Award}, 15907 year = {2009}, 15908 note = {See 15909 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 15910} 15911 15912@Article{ compass-scidac08, 15913 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 15914 R. Ryne}, 15915 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 15916 Computational Science for Future Accelerators and Accelerator Technologies}, 15917 journal = {J. Phys.: Conf. Ser.}, 15918 volume = {125}, 15919 year = {2008}, 15920 pages = {012001}, 15921 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 15922} 15923 15924@Article{ compass-amundson-scidac08, 15925 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 15926 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 15927 Stoltz}, 15928 journal = {J. Phys.: Conf. Ser.}, 15929 volume = {125}, 15930 year = {2008} 15931} 15932 15933@InProceedings{ muszala09, 15934 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 15935 Simulations}, 15936 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 15937 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 15938 {(CBHPC 2009)}}, 15939 year = {2009} 15940} 15941 15942@Article{ gaston09, 15943 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 15944 Equations}, 15945 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 15946 journal = {Nuclear Engineering and Design}, 15947 volume = {239}, 15948 number = {10}, 15949 year = {2009}, 15950 pages = {1768 -- 1778} 15951} 15952 15953@Article{ gaston09b, 15954 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 15955 Engineering}, 15956 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 15957 and C. Permann and W. Taitano}, 15958 journal = {J. Phys.: Conf. Ser.}, 15959 volume = {180}, 15960 year = {2009}, 15961 pages = {012012} 15962} 15963 15964@Article{ newman09, 15965 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 15966 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 15967 author = {Chris Newman and Glen Hansen and Derek Gaston}, 15968 journal = {Journal of Nuclear Materials}, 15969 volume = {392}, 15970 issue = {1}, 15971 year = {2009}, 15972 pages = {6 -- 15} 15973} 15974 15975@Misc{ www:fenics, 15976 author = {{FE}ni{CS}}, 15977 title = {{FE}ni{CS} Project}, 15978 howpublished = {\url{http://www.fenics.org/}}, 15979 year = {2018} 15980} 15981 15982@InProceedings{ zwart08, 15983 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 15984 Systems}, 15985 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 15986 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 15987 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 15988 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 15989 booktitle = {Proceedings of ICCS 2008}, 15990 year = {2008} 15991} 15992 15993@Article{ klocknerwarburtonbridgehesthaven09, 15994 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 15995 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 15996 journal = {J. Comput. Phys.}, 15997 volume = {228}, 15998 number = {21}, 15999 year = {2009}, 16000 issn = {0021-9991}, 16001 pages = {7863--7882}, 16002 doi = {10.1016/j.jcp.2009.06.041}, 16003 publisher = {Academic Press Professional}, 16004 address = {San Diego, CA} 16005} 16006 16007@PhDThesis{ rankin99, 16008 author = {Rankin, W. T.}, 16009 keywords = {FMM, parallel FMM}, 16010 school = {Department of Electrical and Computer Engineering, Duke University}, 16011 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 16012 year = {1999} 16013} 16014 16015@InProceedings{ warrensalmon93, 16016 abstract = {We report on an efficient adaptive N-body method which we have recently designed 16017 and implemented. The algorithm computes the forces on an arbitrary distribution of 16018 bodies in a time which scales as N log N with the particle number. The accuracy of 16019 the force calculations is analytically bounded, and can be adjusted via a user 16020 defined parameter between a few percent relative accuracy, down to machine 16021 arithmetic accuracy. Instead of using pointers to indicate the topology of the 16022 tree, we identify...}, 16023 address = {New York}, 16024 author = {Warren, Michael S. and Salmon, John K.}, 16025 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 16026 citeulike-article-id={580952}, 16027 keywords = {oct-tree}, 16028 pages = {12--21}, 16029 publisher = {ACM}, 16030 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 16031 year = {1993}, 16032 doi = {10.1145/169627.169640}, 16033 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 16034} 16035 16036@Unpublished{ cruzwccm10, 16037 author = {Felipe A. Cruz}, 16038 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 16039 note = {Presentation at WCCM 2010, Sydney Australia}, 16040 year = {2010} 16041} 16042 16043@Article{ mcguffee06, 16044 author = {S.~R. {McGuffee} and A.~H. Elcock}, 16045 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 16046 of salt, {pH}, point mutations, and protein concentration in simulations of 16047 1000-molecule systems}, 16048 journal = {Journal of the American Chemical Society}, 16049 volume = {128}, 16050 pages = {12098--12110}, 16051 year = {2006} 16052} 16053 16054@Article{ nilsencaihoylandlangtangen10, 16055 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 16056 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 16057 in Python}}, 16058 journal = {ArXiv e-prints}, 16059 archiveprefix = {arXiv}, 16060 eprint = {1002.0705}, 16061 primaryclass = {cs.DC}, 16062 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 16063 - Programming Languages}, 16064 year = {2010}, 16065 month = feb, 16066 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 16067 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16068} 16069 16070@Misc{ mcinnes:siam09:minisymposium, 16071 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 16072 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 16073 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 16074 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 16075 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 16076 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 16077 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 16078 Austin).} 16079} 16080 16081@Misc{ mcinnes:fsp-summary:feb2011, 16082 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 16083 title = {Solvers and Time Integration Breakout Summary}, 16084 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 16085 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 16086} 16087 16088@Misc{ dvi-materials:siamcse11, 16089 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 16090 Materials}, 16091 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 16092 Smith and L. Wang}, 16093 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 16094 and Engineering, March 3, 2011} 16095} 16096 16097@Misc{ jamroz:cemm10, 16098 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 16099 author = {B. Jamroz and S. Kruger and T. Austin}, 16100 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 16101} 16102 16103@Misc{ kruger:feb4-2011, 16104 title = {personal communication}, 16105 author = {S. Kruger}, 16106 note = {February, 2011} 16107} 16108 16109@Article{ elman1996, 16110 author = {H.C. Elman}, 16111 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 16112 viscosity}, 16113 journal = {SIAM J. Sci. Comput.}, 16114 volume = {20}, 16115 year = {1996}, 16116 pages = {1299--1316} 16117} 16118 16119@Article{ kayloghinwathen2002, 16120 author = {D. Kay and D. Loghin and A. Wathen}, 16121 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 16122 journal = {SIAM J. Sci. Comput.}, 16123 volume = {24}, 16124 year = {2002}, 16125 pages = {237--256} 16126} 16127 16128@Article{ elmanhowleshadidshuttleworthtuminaro2006, 16129 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 16130 title = {Block preconditioners based on approximate commutators}, 16131 journal = {SIAM J. Sci. Comput.}, 16132 volume = {27}, 16133 number = {5}, 16134 year = {2006}, 16135 pages = {1651--1668} 16136} 16137 16138@Article{ braesssarazin1997, 16139 author = {Dietrich Braess and Regina Sarazin}, 16140 title = {An efficient smoother for the {Stokes} problem}, 16141 journal = {Applied Numerical Mathematics}, 16142 volume = {23}, 16143 number = {1}, 16144 year = {1997}, 16145 pages = {3--19}, 16146 doi = {10.1016/S0168-9274(96)00059-1} 16147} 16148 16149@Article{ wright2001large, 16150 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 16151 author = {Wright, T.G. and Trefethen, L.N.}, 16152 journal = {SIAM Journal on Scientific Computing}, 16153 volume = {23}, 16154 pages = {591}, 16155 year = {2001} 16156} 16157 16158@Misc{ wright2002eigtool, 16159 title = {Eig{T}ool}, 16160 author = {Wright, T.G. and Trefethen, LN}, 16161 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 16162 year = {2002} 16163} 16164 16165@Misc{ visit-web-site, 16166 key = {{VisIt}}, 16167 title = {{VisIt web site}}, 16168 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 16169 url = {http://wci.llnl.gov/codes/visit/}, 16170 year = {2011} 16171} 16172 16173@Book{ trefethen1996, 16174 title = {Finite difference and spectral methods for ordinary and partial differential 16175 equations}, 16176 author = {Lloyd Nicholas Trefethen}, 16177 year = {1996}, 16178 publisher = {Cornell University-Department of Computer Science and Center for Applied 16179 Mathematics} 16180} 16181 16182@Book{ trefethen2005spectra, 16183 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 16184 author = {Trefethen, L.N. and Embree, M.}, 16185 year = {2005}, 16186 publisher = {Princeton University Press} 16187} 16188 16189@Article{ gomez2010isogeometric, 16190 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 16191 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 16192 journal = {Computer Methods in Applied Mechanics and Engineering}, 16193 volume = {199}, 16194 number = {25-28}, 16195 pages = {1828--1840}, 16196 issn = {0045-7825}, 16197 year = {2010}, 16198 publisher = {Elsevier} 16199} 16200 16201@Article{ gomez2008isogeometric, 16202 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 16203 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 16204 journal = {Computer Methods in Applied Mechanics and Engineering}, 16205 volume = {197}, 16206 number = {49-50}, 16207 pages = {4333--4352}, 16208 year = {2008}, 16209 publisher = {Elsevier} 16210} 16211 16212@Misc{ fastmath:project, 16213 author = {Lori {Diachin (PI)}}, 16214 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 16215 (FASTMath) Institute}}, 16216 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 16217} 16218 16219@Misc{ exascale-software:proposal, 16220 author = {Peter {Beckman (PI)}}, 16221 title = {{Exascale Software Center}}, 16222 note = {proposal to DOE} 16223} 16224 16225@Misc{ imex:project, 16226 author = {Barry {Smith (PI)}}, 16227 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 16228 Multimodel PDEs}}, 16229 note = {DOE ASCR applied math project} 16230} 16231 16232@Misc{ intel-mic:website, 16233 author = {Intel}, 16234 title = {{Many Integrated Core Architecture}}, 16235 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 16236} 16237 16238@Article{ dudson:2009, 16239 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 16240 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 16241 journal = {Computer Physics Communications}, 16242 volume = {180}, 16243 pages = {1467}, 16244 year = {2009} 16245} 16246 16247@Article{ umansky:2009, 16248 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 16249 title = {{Status and verification of edge plasma turbulence code BOUT}}, 16250 journal = {Computer Physics Communications}, 16251 year = {2009}, 16252 volume = {180}, 16253 pages = {887-903} 16254} 16255 16256@Article{ xu:1998, 16257 author = {X.Q. Xu and R.H. Cohen}, 16258 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 16259 journal = {Computer Physics Communications}, 16260 year = {1998}, 16261 volume = {36}, 16262 number = {1-2}, 16263 pages = {158} 16264} 16265 16266@Article{ tron:1999, 16267 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 16268 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 16269 journal = {SIAM Journal on Optimization}, 16270 volume = {9}, 16271 number = {4}, 16272 pages = {1100-1127}, 16273 year = {1999} 16274} 16275 16276@Article{ stubenamg, 16277 author = {K. St\"{u}ben}, 16278 title = {A review of algebraic multigrid}, 16279 journal = {J. Comput. Appl. Math.}, 16280 volume = {128}, 16281 number = {1-2}, 16282 year = {2001}, 16283 issn = {0377-0427}, 16284 pages = {281--309}, 16285 doi = {10.1016/S0377-0427(00)00516-1}, 16286 publisher = {Elsevier Science Publishers B. V.}, 16287 address = {Amsterdam, The Netherlands, The Netherlands} 16288} 16289 16290@Article{ feuchtermg, 16291 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 16292 title = {Bridging the gap between geometric and algebraic multigrid methods}, 16293 journal = {Computing and visualization in science}, 16294 publisher = {Springer}, 16295 volume = {6}, 16296 number = {1}, 16297 year = {2003}, 16298 pages = {1--13} 16299} 16300 16301@Article{ chowmgsmoothness, 16302 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 16303 only attempts to interpolate in the directions of geometrical smoothness. These 16304 directions are determined by analyzing samples of algebraically smooth error, e. 16305 Neighboring grid points i and j are called smoothly coupled if e i and e j are 16306 consistently nearby in value. In addition, these dierences may be used to dene 16307 interpolation weights. These new ideas may be incorporated into the algebraic 16308 multigrid method. Test results show that the new method can have much lower grid 16309 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 16310 author = {Chow, Edmond}, 16311 citeulike-article-id={7675372}, 16312 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16313 journal = {American Journal of Mathematics}, 16314 keywords = {fem, multigrid}, 16315 pages = {197--215}, 16316 posted-at = {2010-08-17 23:29:51}, 16317 priority = {2}, 16318 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 16319 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16320 volume = {65}, 16321 year = {2001} 16322} 16323 16324@Article{ jonesamge, 16325 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 16326 elements) method based on element agglomeration. In the method, coarse grid 16327 elements are formed by agglomerating fine grid elements. Compatible interpolation 16328 operators are constructed which yield coarse grid basis functions with a minimal 16329 energy property. Heuristics based on interpolation quality measures are used to 16330 guide the agglomeration procedure. The performance of the resulting method is 16331 demonstrated in two-level numerical experiments.}}, 16332 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 16333 citeulike-article-id={8598569}, 16334 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16335 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 16336 journal = {SIAM Journal on Scientific Computing}, 16337 keywords = {amg, fem, multigrid}, 16338 number = {1}, 16339 pages = {109--133}, 16340 posted-at = {2011-01-13 18:05:55}, 16341 priority = {2}, 16342 publisher = {SIAM}, 16343 title = {{AMGE Based on Element Agglomeration}}, 16344 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16345 volume = {23}, 16346 year = {2001} 16347} 16348 16349@Article{ saad1993, 16350 author = {Saad, Youcef}, 16351 doi = {10.1137/0914028}, 16352 issn = {10648275}, 16353 journal = {SIAM Journal on Scientific Computing}, 16354 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 16355 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 16356 precondition-,preconditioned conju-,subject classi cations,variable 16357 preconditioners}, 16358 number = {2}, 16359 pages = {461--469}, 16360 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 16361 volume = {14}, 16362 year = {1993} 16363} 16364 16365@Misc{ path:homepage, 16366 author = {S. Dirkse and M. Ferris and T. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 16715} 16716 16717@Article{ keyesmcinneswoodwardetal13, 16718 title = {Multiphysics Simulations: Challenges and Opportunities}, 16719 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 16720 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 16721 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 16722 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 16723 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 16724 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 16725 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 16726 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 16727 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 16728 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 16729 journal = {International Journal of High Performance Computing Applications}, 16730 month = {Feb}, 16731 year = {2013}, 16732 volume = {27}, 16733 number = {1}, 16734 pages = {4--83}, 16735 doi = {10.1177/1094342012468181}, 16736 note = {Special issue}, 16737 abstract = {We consider multiphysics applications from algorithmic and architectural 16738 perspectives, where ``algorithmic'' includes both mathematical analysis and 16739 computational complexity and ``architectural'' includes both software and hardware 16740 environments. Many diverse multiphysics applications can be reduced, en route to 16741 their computational simulation, to a common algebraic coupling paradigm. 16742 Mathematical analysis of multiphysics coupling in this form is not always 16743 practical for realistic applications, but model problems representative of 16744 applications discussed herein can provide insight. A variety of software 16745 frameworks for multiphysics applications have been constructed and refined within 16746 disciplinary communities and executed on leading-edge computer systems. We examine 16747 several of these, expose some commonalities among them, and attempt to extrapolate 16748 best practices to future systems. From our study, we summarize challenges and 16749 forecast opportunities.} 16750} 16751 16752@Misc{ rosner10, 16753 author = {Robert {Rosner (Chair)}}, 16754 title = {{The Opportunities and Challenges of Exascale Computing}}, 16755 year = {2010}, 16756 howpublished = {Office of Science, U.S. Department of Energy}, 16757 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 16758} 16759 16760@Misc{ kogge2008exascale, 16761 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 16762 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 16763 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 16764 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 16765 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 16766 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 16767 howpublished = {DARPA}, 16768 year = {2008}, 16769 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 16770} 16771 16772@Misc{ doegrandchallengeworkshops, 16773 key = {Office of Science, U.S. Department of Energy}, 16774 title = {{Scientific Grand Challenges Workshop Series}}, 16775 howpublished = {Office of Science, U.S. Department of Energy, see 16776 \url{http://extremecomputing.labworks.org/workshops.stm}} 16777} 16778 16779@Misc{ lawrence2011, 16780 key = {Lawrence}, 16781 title = {{Ernest Orlando Lawrence Award Winners}}, 16782 howpublished = {U.S. Department of Energy, {\footnotesize 16783 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 16784 year = {2011} 16785} 16786 16787@Article{ murphy2000npi, 16788 title = {{A note on preconditioning for indefinite linear systems}}, 16789 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 16790 journal = {SIAM Journal on Scientific Computing}, 16791 volume = {21}, 16792 number = {6}, 16793 pages = {1969--1972}, 16794 year = {2000}, 16795 publisher = {Philadelphia, PA: SIAM, c1993-} 16796} 16797 16798@Article{ elman2011bouyancy, 16799 title = {Fast iterative solvers for buoyancy driven flow problems}, 16800 journal = {Journal of Computational Physics}, 16801 volume = {230}, 16802 number = {10}, 16803 pages = {3900 - 3914}, 16804 year = {2011}, 16805 note = {}, 16806 issn = {0021-9991}, 16807 doi = {10.1016/j.jcp.2011.02.014}, 16808 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 16809 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 16810 Adaptivity, Preconditioning, Algebraic multigrid} 16811} 16812 16813@Article{ dongarrabeckman11, 16814 author = {J. Dongarra and P. Beckman and et al.}, 16815 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 16816 journal = {Int. J. High Perf. Comput. 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Brannick and Robert D. Falgout}, 16869 journal = {SIAM Journal on Scientific Computing}, 16870 volume = {32}, 16871 number = {3}, 16872 pages = {1393--1416}, 16873 url = {http://epubs.siam.org/doi/10.1137/090772216}, 16874 doi = {10.1137/090772216}, 16875 issn = {1064-8275}, 16876 year = {2010} 16877} 16878 16879@Article{ xu2004energy, 16880 title = {On an energy minimizing basis for algebraic multigrid methods}, 16881 author = {Xu, J. and Zikatanov, L.}, 16882 journal = {Computing and Visualization in Science}, 16883 volume = {7}, 16884 number = {3}, 16885 pages = {121--127}, 16886 year = {2004}, 16887 publisher = {Springer} 16888} 16889 16890@Article{ dblp:journals/toms/bakerhlt09, 16891 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 16892 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 16893 journal = {ACM Trans. Math. 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Sala}, 16916 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 16917 institution = {Sandia National Laboratories}, 16918 year = {2006}, 16919 number = {SAND2006-2649} 16920} 16921 16922@Article{ brannick06, 16923 title = {An energy-based AMG coarsening strategy}, 16924 volume = {13}, 16925 doi = {10.1002/nla.480}, 16926 number = {2-3}, 16927 journal = {Numerical Linear Algebra with Applications}, 16928 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 16929 and Ruge, J}, 16930 year = {2006}, 16931 pages = {133--148} 16932} 16933 16934@Article{ olson10, 16935 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 16936 title = {A new perspective on strength measures in algebraic multigrid}, 16937 journal = {Numerical Linear Algebra with Applications}, 16938 volume = {17}, 16939 number = {4}, 16940 pages = {713--733}, 16941 year = {2010}, 16942 publisher = {John Wiley \& Sons, Ltd.}, 16943 issn = {1099-1506}, 16944 doi = {10.1002/nla.669} 16945} 16946 16947@Article{ olson11, 16948 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 16949 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 16950 Minimization}, 16951 journal = {SIAM J. Sci. Comput.}, 16952 issue_date = {April 2011}, 16953 volume = {33}, 16954 issue = {2}, 16955 month = apr, 16956 year = {2011}, 16957 issn = {1064-8275}, 16958 pages = {966--991}, 16959 numpages = {26}, 16960 doi = {10.1137/100803031}, 16961 acmid = {2078825}, 16962 publisher = {Society for Industrial and Applied Mathematics}, 16963 address = {Philadelphia, PA}, 16964 keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed 16965 aggregation} 16966} 16967 16968@Article{ dorit2011, 16969 author = {Dorit Ron and Ilya Safro and Achi Brandt}, 16970 title = {Relaxation-Based Coarsening and Multiscale Graph Organization}, 16971 journal = {Multiscale Modeling {\&} Simulation}, 16972 volume = {9}, 16973 number = {1}, 16974 year = {2011}, 16975 pages = {407-423}, 16976 doi = {10.1137/100791142} 16977} 16978 16979@Article{ chen2011algebraic, 16980 title = {Algebraic distance on graphs}, 16981 author = {Chen, Jie and Safro, Ilya}, 16982 journal = {SIAM Journal on Scientific Computing}, 16983 volume = {33}, 16984 number = {6}, 16985 pages = {3468--3490}, 16986 year = {2011}, 16987 publisher = {SIAM} 16988} 16989 16990@InProceedings{ adams04, 16991 author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.}, 16992 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 16993 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 16994 half a billion degrees of freedom}, 16995 note = {Gordon Bell Award}, 16996 year = {2004} 16997} 16998 16999@Article{ adams03a, 17000 author = {Adams, M.~F.}, 17001 journal = {Numerical Linear Algebra with Applications}, 17002 number = {2-3}, 17003 pages = {141-153}, 17004 title = {Algebraic multigrid methods for constrained linear systems with applications to 17005 contact problems in solid mechanics}, 17006 volume = {11}, 17007 year = {2004} 17008} 17009 17010@Article{ adams-10a, 17011 author = {M. ~F. 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P.}, 17331 eprint = {arXiv:1002.0705v1}, 17332 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 17333 parallelization of scientific codes by a function-centric approach in 17334 Python.pdf:pdf}, 17335 journal = {Computational Science \& Discovery}, 17336 keywords = {parallel,programming,python,software}, 17337 mendeley-tags = {parallel,programming,python,software}, 17338 pages = {015003}, 17339 publisher = {IOP Publishing}, 17340 title = {{Simplifying the parallelization of scientific codes by a function-centric 17341 approach in Python}}, 17342 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 17343 volume = {3}, 17344 year = {2010} 17345} 17346 17347@Book{ langtangen09, 17348 author = {Hans Petter Langtangen}, 17349 title = {Python Scripting for Computational Science}, 17350 publisher = {Springer}, 17351 series = {Texts in Computational Science and Engineering}, 17352 pages = {784}, 17353 isbn = {3540739157}, 17354 year = {2009} 17355} 17356 17357@Book{ numpyguide, 17358 author = {Travis E. 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Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott and 17502 Andy R. Terrel}, 17503 title = {Discrete optimization of finite element matrix evaluation}, 17504 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 17505 booktitle = {Automated solutions of differential equations by the finite element method}, 17506 series = {Lecture Notes in Computational Science and Engineering}, 17507 volume = {84}, 17508 pages = {385--397}, 17509 publisher = {Springer-Verlag}, 17510 year = {2012} 17511} 17512 17513@InCollection{ kirby12, 17514 author = {Robert C. Kirby}, 17515 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 17516 editors = {A. Logg and K.A. Mardal and G. N. 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Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 17540 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. Pruneau}, 17541 journal = {Nuovo Cimento}, 17542 volume = {19}, 17543 number = {1}, 17544 pages = {1045--1049}, 17545 year = {1996} 17546} 17547 17548@Article{ minimax1997, 17549 author = {Minimax Collaboration}, 17550 title = {Analysis of Charged Particle/Photon Correlations in Hadronic Multiparticle 17551 Production}, 17552 journal = {Physical Review D}, 17553 volume = {55}, 17554 number = {9}, 17555 year = {1997} 17556} 17557 17558@Article{ minimax2000, 17559 author = {Minimax Collaboration}, 17560 title = {Search for disoriented chiral condensate at the {Fermilab} {Tevatron}}, 17561 journal = {Physical Review D}, 17562 volume = {61}, 17563 number = {3}, 17564 year = {2000} 17565} 17566 17567@Article{ kirbyknepleyloggscott05, 17568 author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. 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Knepley}, 17594 title = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a 17595 Hydration-Shell {Poisson}-{Boltzmann} Model}, 17596 journal = {Biophysical Journal}, 17597 volume = {110}, 17598 number = {3}, 17599 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 17600 doi = {10.1016/j.bpj.2015.11.1766}, 17601 year = {2017} 17602} 17603 17604@Article{ tabrizirahimigoossensknepleybardhan2018, 17605 title = {Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer 17606 Interface Condition (SLIC) Continuum Dielectric Model}, 17607 author = {Amirhossein Molavi Tabrizi and Ali Mehdizadeh Rahimi and Spencer Goossens and 17608 Matthew G. Knepley and Jaydeep P. Bardhan}, 17609 journal = {International Journal of Quantum Chemistry}, 17610 note = {Accepted}, 17611 year = {2018} 17612} 17613 17614@Article{ knepley2010, 17615 author = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. 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A}, 22380 volume = {378}, 22381 number = {20190050}, 22382 doi = {10.1098/rsta.2019.0050}, 22383 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 22384 year = {2020} 22385} 22386 22387@Article{ schoberl1999, 22388 title = {Multigrid methods for a parameter dependent problem in primal variables}, 22389 author = {Joachim Sch{\"o}berl}, 22390 journal = {Numerische Mathematik}, 22391 volume = {84}, 22392 number = {1}, 22393 pages = {97--119}, 22394 year = {1999} 22395} 22396 22397@Article{ wuleexuzikatanov2008, 22398 title = {Convergence analysis on iterative methods for semidefinite systems}, 22399 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 22400 journal = {Journal of Computational Mathematics}, 22401 pages = {797--815}, 22402 year = {2008} 22403} 22404 22405@Article{ maierrannacher2016, 22406 title = {Duality-based adaptivity in finite element discretization of heterogeneous 22407 multiscale problems}, 22408 author = {Maier, Matthias and Rannacher, Rolf}, 22409 journal = {Journal of Numerical Mathematics}, 22410 volume = {24}, 22411 number = {3}, 22412 pages = {167--187}, 22413 year = {2016} 22414} 22415 22416@Article{ maierrannacher2018, 22417 title = {A duality-based optimization approach for model adaptivity in heterogeneous 22418 multiscale problems}, 22419 author = {Maier, Matthias and Rannacher, Rolf}, 22420 journal = {Multiscale Modeling \& Simulation}, 22421 volume = {16}, 22422 number = {1}, 22423 pages = {412--428}, 22424 year = {2018} 22425} 22426 22427@Article{ margetismaierluskin2017, 22428 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 22429 metamaterial sheet}, 22430 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 22431 journal = {Studies in Applied Mathematics}, 22432 volume = {139}, 22433 number = {4}, 22434 pages = {599--625}, 22435 year = {2017} 22436} 22437 22438@Article{ maiermargetisluskin2017b, 22439 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 22440 approximation and validation}, 22441 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 22442 journal = {Journal of Computational Physics}, 22443 volume = {339}, 22444 pages = {126--145}, 22445 year = {2017} 22446} 22447 22448@Article{ maiermargetisluskin2018, 22449 title = {Generation of surface plasmon-polaritons by edge effects}, 22450 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 22451 journal = {Communications in Mathematical Sciences}, 22452 volume = {16}, 22453 number = {1}, 22454 pages = {77--95}, 22455 url = {http://arxiv.org/abs/1702.00848}, 22456 year = {2018} 22457} 22458 22459@Article{ maiermattheakiskaxirasluskinmargetis2018, 22460 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 22461 metamaterials}, 22462 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22463 Mitchell and Margetis, Dionisios}, 22464 journal = {Physical Review B}, 22465 volume = {97}, 22466 number = {3}, 22467 pages = {035307}, 22468 year = {2018} 22469} 22470 22471@Article{ maiermattheakiskaxirasluskinmargetis2019, 22472 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 22473 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22474 Mitchell and Margetis, Dionisios}, 22475 journal = {Proceedings of the Royal Society A}, 22476 volume = {475}, 22477 number = {2230}, 22478 pages = {20190220}, 22479 year = {2019} 22480} 22481 22482@Article{ maiermargetisluskin2020, 22483 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 22484 two scales}, 22485 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 22486 journal = {Physical Review B}, 22487 volume = {102}, 22488 number = {7}, 22489 pages = {075308}, 22490 year = {2020} 22491} 22492 22493@Article{ margetismaierstauberlowluskin2020, 22494 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 22495 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 22496 Luskin, Mitchell}, 22497 journal = {Journal of Physics A: Mathematical and Theoretical}, 22498 volume = {53}, 22499 number = {5}, 22500 pages = {055201}, 22501 year = {2020} 22502} 22503 22504@Article{ maiermargetismellet2020, 22505 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 22506 structures}, 22507 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 22508 journal = {Journal of Computational and Applied Mathematics}, 22509 volume = {377}, 22510 pages = {112909}, 22511 year = {2020} 22512} 22513 22514@Article{ maierkronbichler2021, 22515 title = {Efficient parallel 3D computation of the compressible Euler equations with an 22516 invariant-domain preserving second-order finite-element scheme}, 22517 author = {Maier, Matthias and Kronbichler, Martin}, 22518 journal = {ACM Transactions on Parallel Computing}, 22519 volume = {8}, 22520 number = {3}, 22521 pages = {1--30}, 22522 year = {2021} 22523} 22524 22525@Article{ guermondmaierpopovtomas2021, 22526 title = {Second-order invariant domain preserving approximation of the compressible 22527 Navier--Stokes equations}, 22528 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 22529 journal = {Computer Methods in Applied Mechanics and Engineering}, 22530 volume = {375}, 22531 pages = {113608}, 22532 year = {2021} 22533} 22534 22535@Article{ liliptonmaier2021, 22536 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 22537 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 22538 eprint = {2009.12166}, 22539 archiveprefix = {arXiv}, 22540 primaryclass = {phys.optics}, 22541 year = {2021} 22542} 22543 22544@Article{ songmaierluskin2020, 22545 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 22546 gradient-index graphene waveguides}, 22547 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22548 journal = {Journal of Computational Physics}, 22549 volume = {423}, 22550 pages = {109871}, 22551 year = {2020} 22552} 22553 22554@Article{ songmaierluskin2019, 22555 title = {Adaptive finite element simulations of waveguide configurations involving 22556 parallel 2D material sheets}, 22557 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22558 journal = {Computer Methods in Applied Mechanics and Engineering}, 22559 volume = {351}, 22560 pages = {20--34}, 22561 year = {2019} 22562} 22563 22564% 22565% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 22566% 22567% 22568@Unpublished{ rob1, 22569 author = {Rob Kunz}, 22570 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 22571 State University}, 22572 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 22573 sponsors = {U.S. Navy, NRC}, 22574 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 22575 simulations, including lake warming by power plants}, 22576 dates = {Oct 3 and 4, 2002}, 22577 email = {rfk@wt.arl.psu.edu} 22578} 22579 22580@Unpublished{ au1, 22581 author = {Feng Wang and William Appelbe}, 22582 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 22583 url = {http://www.vpac.org}, 22584 sponsors = { }, 22585 note = {Using PETSc for a Variety of Geophysical Simulations}, 22586 dates = {Nov 22, 2002} 22587} 22588 22589@Unpublished{ carl1, 22590 author = {Carl Sovinec}, 22591 institution = {Applied Physics, University of Wisconsin}, 22592 url = {http://nimrodteam.org}, 22593 sponsors = {DOE Office of Fusion Research}, 22594 note = {Investigating using PETSc for NIMROD}, 22595 dates = {Nov 21, 2002}, 22596 email = {sovinec@engr.wisc.edu} 22597} 22598 22599@Unpublished{ au1b, 22600 author = {Pablo Carrica and Robert Wilson}, 22601 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 22602 url = {http://}, 22603 sponsors = {Office of Naval Research}, 22604 note = {Using PETSc for a hydrodynamics of ships and submarines}, 22605 dates = {Sept, 2002}, 22606 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 22607} 22608 22609% ------------------- TAO References ---------------------- 22610@Article{ benson:2001:csp, 22611 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 22612 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 22613 journal = {{ACM} Transactions on Mathematical Software}, 22614 volume = {27}, 22615 number = {3}, 22616 month = sep, 22617 year = {2001}, 22618 pages = {361--376} 22619} 22620 22621@TechReport{ tao-user-ref-2000, 22622 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 22623 title = {{TAO} Users Manual}, 22624 year = {2000}, 22625 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22626 number = {ANL/MCS-TM-242}, 22627 note = {See \url{http://www.mcs.anl.gov/tao}} 22628} 22629 22630% ------------------- Optimization References ---------------------- 22631@Book{ optguide93, 22632 title = {Optimization Software Guide}, 22633 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 22634 publisher = {SIAM Publications}, 22635 address = {Philadelphia}, 22636 year = {1993} 22637} 22638 22639@InProceedings{ more84, 22640 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 22641 Hillstrom}, 22642 title = {The {MINPACK} Project}, 22643 booktitle = {Sources and Development of Mathematical Software}, 22644 editor = {Wayne R. Cowell}, 22645 year = {1984}, 22646 pages = {88--111} 22647} 22648 22649@Article{ steihaug:83, 22650 author = {Trond Steihaug}, 22651 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 22652 journal = {SIAM J. Numer. Anal.}, 22653 volume = {20}, 22654 year = {1983}, 22655 pages = {626--637}, 22656 key = {steihaug92 ! trust_region} 22657} 22658 22659@TechReport{ minpack2test, 22660 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 22661 title = {The {MINPACK-2} Test Problem Collection}, 22662 institution = {Argonne National Laboratory}, 22663 year = {1991}, 22664 number = {ANL/MCS-TM-150}, 22665 key = {more91 ! MINPACK-2} 22666} 22667 22668@TechReport{ hohmann:94, 22669 author = {Andreas Hohmann}, 22670 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 22671 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 22672 year = {1994}, 22673 number = {SC-94-4}, 22674 key = {Hohmann94} 22675} 22676 22677@TechReport{ meza:94, 22678 author = {Juan C. Meza}, 22679 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 22680 institution = {Sandia National Laboratory}, 22681 year = {1994}, 22682 number = {SAND94-8225}, 22683 key = {Meza94} 22684} 22685 22686@Book{ nw99, 22687 author = {Jorge Nocedal and Stephen J. Wright}, 22688 title = {Numerical Optimization}, 22689 year = {1999}, 22690 publisher = {Springer-Verlag}, 22691 address = {New York} 22692} 22693 22694@Book{ dennis:83, 22695 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 22696 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 22697 publisher = {Prentice-Hall, Inc.}, 22698 address = {Englewood Cliffs, NJ}, 22699 year = {1983} 22700} 22701 22702@TechReport{ more:92, 22703 author = {Jorge J. Mor\'{e} and David Thuente}, 22704 title = {Line search algorithms with guaranteed sufficient decrease}, 22705 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22706 year = {1992}, 22707 number = {MCS-P330-1092} 22708} 22709 22710@Article{ more-toraldo, 22711 author = {Jorge J. Mor\'e and G. Toraldo}, 22712 journal = {SIOPT}, 22713 pages = {93--113}, 22714 title = {On the solution of large quadratic programming problems with bound constraints}, 22715 volume = {1}, 22716 year = {1991} 22717} 22718 22719@Article{ byrd:1995:lma, 22720 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 22721 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 22722 journal = {SIAM Journal on Scientific Computing}, 22723 volume = {16}, 22724 number = {5}, 22725 pages = {1190--1208}, 22726 month = sep, 22727 year = {1995}, 22728 coden = {SJOCE3}, 22729 issn = {1064-8275 (print), 1095-7197 (electronic)}, 22730 mrclass = {90C30 (65K05)}, 22731 mrnumber = {96e:90039}, 22732 mrreviewer = {Henry Wolkowicz}, 22733 bibdate = {Fri Dec 4 16:17:35 MST 1998} 22734} 22735 22736@Article{ lin_c3, 22737 author = {C.-J. Lin and J. J. Mor\'e}, 22738 title = {Newton's method for large bound-constrained optimization problems}, 22739 year = {1999}, 22740 journal = {SIOPT}, 22741 volume = {9(4)}, 22742 pages = {1100--1127}, 22743 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 22744} 22745 22746@TechReport{ dolan2, 22747 author = {E. Dolan and J. J. Mor\'{e}}, 22748 title = {Benchmarking Optimization Software with Performance Profiles}, 22749 year = {2001}, 22750 month = jan, 22751 number = {ANL/MCS-P861-1200}, 22752 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22753 address = {Argonne, IL}, 22754 url = {http://www.mcs.anl.gov/~more/cops/} 22755} 22756 22757@InProceedings{ owlqn, 22758 author = {Galen Andrew and Jianfeng Gao}, 22759 title = {Scalable training of L1-regularized log-linear models}, 22760 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 22761 pages = {33--40}, 22762 year = {2007} 22763} 22764 22765@Article{ bmrm, 22766 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 22767 title = {Bundle methods for regularized risk minimization}, 22768 year = {2010}, 22769 journal = {Journal of Machine Learning Research}, 22770 volume = {11}, 22771 pages = {311--365} 22772} 22773 22774% ------------------- Component Software References ---------------------- 22775@InProceedings{ cca99, 22776 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 22777 McInnes and S. Parker and B. Smolinski}, 22778 title = {Toward a Common Component Architecture for High-Performance Scientific 22779 Computing}, 22780 booktitle = {Proceedings of {High Performance Distributed Computing}}, 22781 pages = {115--124}, 22782 year = {1999}, 22783 note = {See \url{http://cca-forum.org}} 22784} 22785 22786@Book{ szyperski98, 22787 author = {Clemens Szyperski}, 22788 title = {Component Software: Beyond Object-Oriented Programming}, 22789 publisher = {ACM Press}, 22790 address = {New York}, 22791 year = {1998} 22792} 22793 22794@Article{ broy98, 22795 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 22796 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 22797 Stal and Clemens Szyperski}, 22798 title = {What Characterizes a (Software) Component?}, 22799 journal = {Software -- Concepts and Tools}, 22800 publisher = {Springer-Verlag}, 22801 year = {1998}, 22802 volume = {19}, 22803 pages = {49--56} 22804} 22805 22806@Article{ componentware:94, 22807 author = {Jon Udell}, 22808 title = {Componentware}, 22809 journal = {Byte}, 22810 volume = {May}, 22811 pages = {46--56}, 22812 year = {1994}, 22813 key = {Udell94 ! componentware} 22814} 22815 22816@Misc{ cca-web-page, 22817 author = {{Common Component Architecture Forum}}, 22818 note = {See \url{http://cca-forum.org}} 22819} 22820 22821% --------------- References for Tools Used by TAO Developers ----------------- 22822 22823% 22824% tohtml: Used to generate on-line TAO users manual and manual pages 22825% 22826@TechReport{ tohtml, 22827 author = {William Gropp}, 22828 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 22829 institution = {Argonne National Laboratory}, 22830 number = {ANL/MCS-TM-00}, 22831 month = jan, 22832 year = {1995}, 22833 key = {tohtml} 22834} 22835 22836% 22837% doctext: Used to generate tex version of TAO manual pages 22838% 22839@TechReport{ doctext, 22840 author = {William Gropp}, 22841 title = {Users Manual for doctext: Producing documentation from {C} source code}, 22842 institution = {Argonne National Laboratory}, 22843 number = {ANL/MCS-TM-00}, 22844 month = jan, 22845 year = {1995}, 22846 key = {doctext} 22847} 22848 22849% 22850% bfort: Used to generate TAO Fortran interface 22851% 22852@TechReport{ bfort, 22853 author = {William Gropp}, 22854 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 22855 institution = {Argonne National Laboratory}, 22856 number = {ANL/MCS-TM-208}, 22857 month = mar, 22858 year = {1995}, 22859 key = {doctext} 22860} 22861 22862% ------------------------- PETSc References ------------------------------ 22863@InProceedings{ petsc, 22864 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 22865 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 22866 Libraries}, 22867 booktitle = {Modern Software Tools in Scientific Computing}, 22868 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 22869 publisher = {Birkhauser Press}, 22870 pages = {163--202}, 22871 year = {1997} 22872} 22873 22874% ------------------------- Misc Other References ------------------------------ 22875@Misc{ indeps-web-page, 22876 title = {{InDEPS} {W}eb page}, 22877 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 22878 author = {et al. Robert Armstrong}, 22879 institution = {Sandia National Laboratory}, 22880 key = {{InDEPS} {W}eb page} 22881} 22882 22883@Misc{ pooma, 22884 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 22885 chitectures}, 22886 year = {1996}, 22887 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 22888 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 22889} 22890 22891@Misc{ isis++-web-page, 22892 title = {{ISIS++} {W}eb Page}, 22893 note = {See \url{http://ca.sandia.gov/isis}}, 22894 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 22895 institution = {Sandia National Laboratories} 22896} 22897 22898@Misc{ trilinos-web-page, 22899 title = {{Trilinos} {W}eb Page}, 22900 note = {See 22901 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 22902 author = {Mike Heroux et al.}, 22903 institution = {Sandia National Laboratories} 22904} 22905 22906@Misc{ alice-web-page, 22907 title = {{ALICE} {W}eb page}, 22908 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 22909 Argonne National Laboratory}, 22910 key = {{ALICE} {W}eb page} 22911} 22912 22913@Misc{ autodiff-webpage, 22914 author = {{Computational Differentiation Project}}, 22915 note = {See \url{http://www.mcs.anl.gov/autodiff}} 22916} 22917 22918@Misc{ coool-home-page, 22919 author = {Lydia Deng and Wences Gouveia and John Scales}, 22920 title = {{The CWP Object-Oriented Optimization Library}}, 22921 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 22922} 22923 22924@Misc{ rice-inversion-home-page, 22925 author = {Mark S. Gokenbach and William W. Symes}, 22926 title = {{The Hilbert Class Library}}, 22927 note = {See \url{http://www.trip.caam.rice.edu/}} 22928} 22929 22930@Misc{ opt++-home-page, 22931 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 22932 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 22933} 22934 22935@Article{ gockenbach:1999:ccl, 22936 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 22937 title = {C++ Classes for Linking Optimization with Complex Simulations}, 22938 journal = {{ACM} Transactions on Mathematical Software}, 22939 volume = {25}, 22940 number = {2}, 22941 month = jun, 22942 year = {1999}, 22943 pages = {191-212}, 22944 abstract = {The object-oriented programming paradigm can be used to overcome the 22945 incompatibilities between off-the-shelf optimization software and application 22946 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 22947 objects arising in optimization problems, such as vectors, linear operators, and 22948 so forth, as C++ classes, making it possible to write optimization code in a 22949 natural fashion, while allowing application software such as simulators to use the 22950 most convenient data structures and programming style. In spite of the poor 22951 reputation C++ has for runtime performance, the use of mixed-language programming 22952 allows performance equal to that achieved by standard Fortran packages, as 22953 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 22954 accepted = {April 1999}, 22955 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 22956} 22957 22958@Misc{ neos-guide, 22959 author = {{The Optimization Software Guide}}, 22960 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 22961} 22962 22963@Article{ boyd, 22964 title = {Distributed optimization and statistical learning via the alternating direction 22965 method of multipliers}, 22966 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 22967 Jonathan and others}, 22968 journal = {Foundations and Trends{\textregistered} in Machine learning}, 22969 volume = {3}, 22970 number = {1}, 22971 pages = {1-122}, 22972 year = {2011}, 22973 publisher = {Now Publishers, Inc.} 22974} 22975 22976@Misc{ :alertsys, 22977 title = {page{ALERT}}, 22978 organization = {Alert Systems, Inc}, 22979 address = {Madison, Wisconsin}, 22980 note = {http://www.alertsys.com/} 22981} 22982 22983@Manual{ :cmfortran, 22984 title = {{CM} {F}ortran Language Reference Manual}, 22985 organization = {Thinking Machines Corporation}, 22986 year = {1994}, 22987 address = {Cambridge, MA} 22988} 22989 22990@Manual{ :cmmd, 22991 title = {{CMMD} Reference Manual, Version 3.0}, 22992 organization = {Thinking Machines Corporation}, 22993 year = {1993}, 22994 address = {Cambridge, MA} 22995} 22996 22997@Manual{ :cmssl, 22998 title = {{CMSSL} for {CM} {F}ortran}, 22999 volume = {I}, 23000 organization = {Thinking Machines Corporation}, 23001 year = {1994}, 23002 address = {Cambridge, MA} 23003} 23004 23005@Misc{ :condor, 23006 author = {M. Livny}, 23007 title = {{PI}, The {Condor} Project, High Throughput Computing}, 23008 howpublished = {www.cs.wisc.edu/condor} 23009} 23010 23011@Manual{ :connection, 23012 title = {Connection Machine {CM}--5 Technical Summary}, 23013 organization = {Thinking Machines Corporation}, 23014 year = {1993}, 23015 address = {Cambridge, MA} 23016} 23017 23018@Manual{ :cplex, 23019 title = {{CPLEX} Optimizer}, 23020 organization = {ILOG CPLEX Division}, 23021 address = {889 Alder Avenue, Incline Village, Nevada}, 23022 note = {http://www.cplex.com/} 23023} 23024 23025@Manual{ :cplextm, 23026 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 23027 (Version 2.0)}, 23028 organization = {CPLEX Optimization Inc.}, 23029 year = {1992}, 23030 address = {Incline Village, Nevada} 23031} 23032 23033@Misc{ :fatcop, 23034 author = {M. C. Ferris}, 23035 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 23036 Solver}, 23037 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 23038} 23039 23040@Misc{ :metaneos, 23041 author = {S. J. Wright}, 23042 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 23043 howpublished = {www-unix.mcs.anl.gov/metaneos} 23044} 23045 23046@InCollection{ gropp.more:optimization, 23047 author = {W. Gropp and J. J. Mor\'e}, 23048 title = {Optimization environments and the {NEOS} Server}, 23049 booktitle = {Approximation Theory and Optimization}, 23050 pages = {167--182}, 23051 publisher = {Cambridge University Press}, 23052 year = {1997}, 23053 editor = {M. D. Buhmann and A. Iserles} 23054} 23055 23056@Article{ czyzyk.mesnier.ea:neos, 23057 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 23058 title = {The {NEOS} Server}, 23059 journal = {IEEE Journal on Computational Science and Engineering}, 23060 volume = {5}, 23061 year = {1998}, 23062 pages = {68--75} 23063} 23064 23065@Book{ :osl, 23066 title = {Handbook for {IBM OSL}}, 23067 author = {M. S. Hung and W. O. Rom and A. D. 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Nash}, 23419 title = {Linear Programming in Infinite--Dimensional Spaces}, 23420 year = {1987}, 23421 publisher = {John Wiley \& Sons}, 23422 address = {Chichester} 23423} 23424 23425@InProceedings{ anderson:primal, 23426 author = {E. J. Anderson}, 23427 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 23428 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 23429 Programming, Cambridge, September 1984}, 23430 year = {1985}, 23431 editor = {E. J. Anderson and A. B. Philpott}, 23432 publisher = {Springer-Verlag}, 23433 address = {Berlin} 23434} 23435 23436@Article{ andradottir:method, 23437 author = {S. Andrad\'{o}ttir}, 23438 title = {A Method of Discrete Stochastic Optimization}, 23439 journal = {Management Science}, 23440 year = {1995}, 23441 volume = {41}, 23442 pages = {1946--1961} 23443} 23444 23445@Article{ andradottir:global, 23446 author = {S. 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Walter}, 23657 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 23658 journal = {Environmental and Resource Economics}, 23659 year = {1991}, 23660 volume = {1}, 23661 pages = {237--270} 23662} 23663 23664@PhDThesis{ bagley:behaviour, 23665 author = {J. D. Bagley}, 23666 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 23667 Algorithms}, 23668 year = {1967}, 23669 school = {University of Michigan} 23670} 23671 23672@Article{ bain.stewart:application, 23673 author = {R. S. Bain and W. E. Stewart}, 23674 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 23675 Algebraic Equation Systems}, 23676 journal = {Computers in Chemical Engineering}, 23677 year = {1991}, 23678 volume = {15}, 23679 pages = {203--208} 23680} 23681 23682@Article{ baker.lasdon:successive, 23683 author = {T. E. Baker and L. S. 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Whalley}, 23709 title = {A General Equilibrium Model for Tax Policy Evaluation}, 23710 publisher = {The University of Chicago Press}, 23711 year = {1985}, 23712 series = {National Bureau of Economic Research Monograph} 23713} 23714 23715@InProceedings{ balog.angelos.ea:dose, 23716 author = {J. Balog and L. Angelos and T. R. Mackie and P. Reckwerdt}, 23717 title = {Dose Computation for a One-Dimensional Multileaf Collimator}, 23718 booktitle = {Proceedings of the XII International Conference on the Use of Computers in 23719 Radiation Therapy, Salt Lake City}, 23720 year = {1997}, 23721 editor = {D. D. Leavitt and G. Starkshall}, 23722 publisher = {Medical Physics Publishing}, 23723 address = {St. Louis, Missouri}, 23724 pages = {323--326} 23725} 23726 23727@Article{ baraff:fast, 23728 author = {D. 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Model analysis and 25292 optimality conditions}, 25293 type = {Publication}, 25294 number = {CRT-94-56}, 25295 institution = {Centre de Recherche sur les Transports, Universit\'e de Montr\'eal}, 25296 address = {Montr\'eal, Canada}, 25297 year = {1994} 25298} 25299 25300@Article{ chen.harker:continuation, 25301 author = {B. Chen and P. T. Harker}, 25302 title = {A Continuation Method for Monotone Variational Inequalities}, 25303 journal = {Mathematical Programming}, 25304 volume = {69}, 25305 pages = {237--253}, 25306 year = {1995} 25307} 25308 25309@Article{ chen.harker:non-interior, 25310 author = {B. Chen and P. T. Harker}, 25311 title = {A Non-Interior-Point Continuation Method for Linear Complementarity Problems}, 25312 journal = {SIAM Journal on Matrix Analysis and Applications}, 25313 year = {1993}, 25314 volume = {14}, 25315 pages = {1168--1190} 25316} 25317 25318@Article{ chen.harker:smooth, 25319 author = {B. Chen and P. T. 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Mangasarian}, 27248 title = {Finite Perturbation of Convex Programs}, 27249 journal = {Applied Mathematics and Optimization}, 27250 year = {1991}, 27251 volume = {23}, 27252 pages = {263--273}, 27253 key = {08} 27254} 27255 27256@Book{ ferris.mangasarian:linear, 27257 author = {M. C. Ferris and O. L. Mangasarian}, 27258 title = {Linear Programming via {MATLAB}}, 27259 publisher = {in preparation}, 27260 year = {1995}, 27261 address = {Madison, Wisconsin} 27262} 27263 27264@Article{ ferris.mangasarian:minimum, 27265 author = {M. C. Ferris and O. L. Mangasarian}, 27266 title = {Minimum Principle Sufficiency}, 27267 journal = {Mathematical Programming}, 27268 year = {1992}, 27269 volume = {57}, 27270 pages = {1--14}, 27271 key = {11} 27272} 27273 27274@Article{ ferris.mangasarian:parallel, 27275 author = {M. C. Ferris and O. L. Mangasarian}, 27276 title = {Parallel Constraint Distribution}, 27277 journal = {SIAM Journal on Optimization}, 27278 year = {1991}, 27279 volume = {1}, 27280 pages = {487--500}, 27281 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 27282 key = {18} 27283} 27284 27285@Article{ ferris.mangasarian:parallel*1, 27286 author = {M. C. Ferris and O. L. Mangasarian}, 27287 title = {Parallel Variable Distribution}, 27288 journal = {SIAM Journal on Optimization}, 27289 year = {1994}, 27290 volume = {4}, 27291 pages = {815--832}, 27292 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 27293 key = {31} 27294} 27295 27296@Article{ ferris.meeraus.ea:computing, 27297 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 27298 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 27299 journal = {Optimization Methods and Software}, 27300 year = {1999}, 27301 volume = {10}, 27302 pages = {669--685}, 27303 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 27304 key = {45} 27305} 27306 27307@Article{ ferris.mesnier.ea:neos, 27308 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 27309 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 27310 {I}nternet}, 27311 year = {2000}, 27312 journal = {{ACM} Transactions on Mathematical Software}, 27313 key = {54}, 27314 volume = {26}, 27315 pages = {1--18}, 27316 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 27317 institution = {Computer Sciences Department, University of Wisconsin}, 27318 address = {Madison, Wisconsin}, 27319 number = {96-08}, 27320 type = {Mathematical Programming Technical Report}, 27321 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 27322 Argonne National Laboratory}, 27323 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 27324 1996} 27325} 27326 27327@InCollection{ ferris.meyer:models, 27328 author = {M. C. Ferris and R. R. Meyer}, 27329 title = {Models and Solution for On-Demand Data Delivery Problems}, 27330 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 27331 key = {80}, 27332 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 27333 Problems}, 27334 editor = {P. M. Pardalos}, 27335 series = {Nonconvex Optimization and its Applications}, 27336 volume = {42}, 27337 address = {Dordrect}, 27338 year = {2000}, 27339 pages = {175--188}, 27340 publisher = {Kluwer}, 27341 type = {Mathematical Programming Technical Report}, 27342 institution = {Computer Sciences Department, University of Wisconsin}, 27343 number = {99-04} 27344} 27345 27346@InProceedings{ ferris.munson.ea:homotopy, 27347 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 27348 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 27349 booktitle = {Numerical Analysis 1999}, 27350 key = {88}, 27351 year = {2000}, 27352 editor = {D. F. Griffiths and G. A. Watson}, 27353 series = {Research Notes in Mathematics}, 27354 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 27355 address = {London}, 27356 pages = {143--167}, 27357 publisher = {Chapman and Hall}, 27358 institution = {Computer Sciences Department, University of Wisconsin}, 27359 number = {99-09}, 27360 type = {Mathematical Programming Technical Report} 27361} 27362 27363@TechReport{ ferris.munson.ea:practical, 27364 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 27365 title = {A Practical Approach to Sample-Path Simulation Optimization}, 27366 type = {Data Mining Institute Technical Report}, 27367 institution = {Computer Sciences Department, University of Wisconsin}, 27368 address = {Madison, Wisconsin}, 27369 year = {2000}, 27370 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 27371 number = {00-03}, 27372 key = {92}, 27373 annote = {To appear in WSC 2000} 27374} 27375 27376@InCollection{ ferris.munson:case, 27377 author = {M. C. Ferris and T. S. Munson}, 27378 title = {Case Studies in Complementarity: Improving Model Formulation}, 27379 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 27380 key = {73}, 27381 pages = {79--98}, 27382 publisher = {Springer Verlag}, 27383 year = {1999}, 27384 editor = {M. Th\'{e}ra and R. Tichatschke}, 27385 number = {477}, 27386 series = {Lecture Notes in Economics and Mathematical Systems}, 27387 address = {Berlin}, 27388 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 27389 type = {Mathematical Programming Technical Report}, 27390 institution = {Computer Sciences Department, University of Wisconsin} 27391} 27392 27393@Article{ ferris.munson:complementarity, 27394 author = {M. C. Ferris and T. S. Munson}, 27395 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 27396 year = {2000}, 27397 volume = {24}, 27398 pages = {165--188}, 27399 journal = {Journal of Economic Dynamics and Control}, 27400 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 27401 key = {70}, 27402 type = {Mathematical Programming Technical Report}, 27403 institution = {Computer Sciences Department, University of Wisconsin}, 27404 address = {Madison, Wisconsin}, 27405 number = {98-12} 27406} 27407 27408@Misc{ ferris.munson:condor, 27409 author = {M. C. Ferris and T. S. Munson}, 27410 title = {Condor Modeling Language Interface}, 27411 organization = {Computer Sciences Department, University of Wisconsin}, 27412 address = {Madison, Wisconsin}, 27413 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 27414} 27415 27416@Manual{ ferris.munson:gams, 27417 author = {M. C. Ferris and T. S. Munson}, 27418 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 27419 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 27420} 27421 27422@Article{ ferris.munson:interfaces, 27423 author = {M. C. Ferris and T. S. Munson}, 27424 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 27425 journal = {Computational Optimization and Applications}, 27426 volume = {12}, 27427 pages = {207--227}, 27428 year = {1999}, 27429 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 27430 key = {63}, 27431 institution = {Computer Sciences Department, University of Wisconsin}, 27432 address = {Madison, Wisconsin}, 27433 number = {97-12}, 27434 type = {Mathematical Programming Technical Report} 27435} 27436 27437@TechReport{ ferris.munson:interior, 27438 author = {M. C. Ferris and T. S. Munson}, 27439 title = {Interior Point Methods for Massive Support Vector Machines}, 27440 institution = {Computer Sciences Department, University of Wisconsin}, 27441 year = {2000}, 27442 key = {94}, 27443 type = {Data Mining Institute Technical Report}, 27444 number = {00-05}, 27445 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 27446 address = {Madison, Wisconsin}, 27447 annote = {Submitted to SIOPT} 27448} 27449 27450@Article{ ferris.munson:linear, 27451 author = {M. C. Ferris and T. S. Munson}, 27452 title = {Linear Programming for Emergency Broadcast Systems}, 27453 year = {1999}, 27454 journal = {{SIAG/OPT} Newsletter}, 27455 volume = {10}, 27456 pages = {6--8}, 27457 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 27458 key = {76}, 27459 type = {Mathematical Programming Technical Report}, 27460 institution = {Computer Sciences Department, University of Wisconsin}, 27461 address = {Madison, Wisconsin}, 27462 number = {98-20} 27463} 27464 27465@Article{ ferris.munson:modeling, 27466 author = {M. C. Ferris and T. S. Munson}, 27467 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 27468 year = {2000}, 27469 journal = {Mathematical Programming}, 27470 volume = {88}, 27471 pages = {487--506}, 27472 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 27473 key = {71}, 27474 type = {Mathematical Programming Technical Report}, 27475 institution = {Computer Sciences Department, University of Wisconsin}, 27476 address = {Madison, Wisconsin}, 27477 number = {98-13} 27478} 27479 27480@TechReport{ ferris.munson:preprocessing, 27481 author = {M. C. Ferris and T. S. Munson}, 27482 title = {Preprocessing Complementarity Problems}, 27483 type = {Mathematical Programming Technical Report}, 27484 institution = {Computer Sciences Department, University of Wisconsin}, 27485 address = {Madison, Wisconsin}, 27486 year = {1999}, 27487 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 27488 number = {99-07}, 27489 key = {86}, 27490 annote = {Submitted to ICCP 99} 27491} 27492 27493@TechReport{ ferris.munson:semismooth, 27494 author = {M. C. Ferris and T. S. Munson}, 27495 title = {Semismooth Support Vector Machines}, 27496 institution = {Computer Sciences Department, University of Wisconsin}, 27497 year = {2000}, 27498 key = {97}, 27499 type = {Data Mining Institute Technical Report}, 27500 number = {00-09}, 27501 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 27502 address = {Madison, Wisconsin}, 27503 annote = {Submitted to Math Prog B} 27504} 27505 27506@Article{ ferris.pang:engineering, 27507 author = {M. C. Ferris and J. S. Pang}, 27508 title = {Engineering and Economic Applications of Complementarity Problems}, 27509 year = {1997}, 27510 journal = {SIAM Review}, 27511 volume = {39}, 27512 pages = {669--713}, 27513 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 27514 key = {46} 27515} 27516 27517@Article{ ferris.pang:nondegenerate, 27518 author = {M. C. Ferris and J. S. Pang}, 27519 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 27520 journal = {SIAM Journal on Control and Optimization}, 27521 year = {1996}, 27522 volume = {34}, 27523 pages = {244--263}, 27524 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 27525 key = {35} 27526} 27527 27528@Article{ ferris.philpott:affine, 27529 author = {M. C. Ferris and A. B. Philpott}, 27530 title = {On Affine Scaling and Semi--Infinite Programming}, 27531 journal = {Mathematical Programming}, 27532 year = {1992}, 27533 volume = {56}, 27534 pages = {361--364}, 27535 key = {15} 27536} 27537 27538@Article{ ferris.philpott:interior, 27539 author = {M. C. Ferris and A. B. Philpott}, 27540 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 27541 journal = {Mathematical Programming}, 27542 year = {1989}, 27543 volume = {43}, 27544 pages = {257--276}, 27545 key = {04} 27546} 27547 27548@Article{ ferris.philpott:performance, 27549 author = {M. C. Ferris and A. B. Philpott}, 27550 title = {On the Performance of {K}armarkar's Algorithm}, 27551 journal = {Journal of the Operational Research Society}, 27552 year = {1988}, 27553 volume = {39}, 27554 pages = {257--270}, 27555 key = {03} 27556} 27557 27558@InCollection{ ferris.ralph:projected, 27559 author = {M. C. Ferris and D. Ralph}, 27560 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 27561 Maps}, 27562 booktitle = {Recent Advances in Nonsmooth Optimization}, 27563 publisher = {World Scientific Publishers}, 27564 year = {1995}, 27565 pages = {57--87}, 27566 editor = {D. Du and L. Qi and R. Womersley}, 27567 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 27568 key = {41} 27569} 27570 27571@Article{ ferris.ruszczynski:robust, 27572 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 27573 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 27574 year = {2000}, 27575 journal = {Networks}, 27576 volume = {35}, 27577 pages = {181--194}, 27578 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 27579 key = {60} 27580} 27581 27582@InCollection{ ferris.rutherford:accessing, 27583 author = {M. C. Ferris and T. F. Rutherford}, 27584 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 27585 booktitle = {Nonlinear Optimization and Applications}, 27586 key = {48}, 27587 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 27588 editor = {G. Di Pillo and F. Giannessi}, 27589 year = {1996}, 27590 pages = {141--153}, 27591 publisher = {Plenum Press}, 27592 address = {New York} 27593} 27594 27595@InCollection{ ferris.shepard:optimizing, 27596 author = {M. C. Ferris and D. M. Shepard}, 27597 title = {Optimization of Gamma Knife Radiosurgery}, 27598 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 27599 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 27600 publisher = {AMS}, 27601 year = {2000}, 27602 optseries = {DIMACS}, 27603 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 27604 key = {91}, 27605 type = {Data Mining Institute Technical Report}, 27606 institution = {Computer Sciences Department, University of Wisconsin}, 27607 address = {Madison, Wisconsin}, 27608 number = {00-01} 27609} 27610 27611@InCollection{ ferris.sinapiromsaran:formulating, 27612 author = {M. C. Ferris and K. Sinapiromsaran}, 27613 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 27614 booktitle = {Optimization}, 27615 key = {77}, 27616 publisher = {Springer-Verlag}, 27617 year = {2000}, 27618 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 27619 volume = {481}, 27620 series = {Lecture Notes in Economics and Mathematical Systems}, 27621 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 27622 type = {Mathematical Programming Technical Report}, 27623 institution = {Computer Sciences Department, University of Wisconsin}, 27624 address = {Madison, Wisconsin}, 27625 number = {98-21} 27626} 27627 27628@Article{ ferris.tin-loi:limit, 27629 author = {M. C. Ferris and F. Tin-Loi}, 27630 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 27631 Complementarity Constraints}, 27632 year = {2001}, 27633 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 27634 key = {78}, 27635 journal = {International Journal of Mechanical Sciences}, 27636 pages = {209--224}, 27637 volume = {43}, 27638 type = {Mathematical Programming Technical Report}, 27639 institution = {Computer Sciences Department, University of Wisconsin}, 27640 address = {Madison, Wisconsin}, 27641 number = {99-01} 27642} 27643 27644@Article{ ferris.tin-loi:nonlinear, 27645 author = {M. C. Ferris and F. Tin-Loi}, 27646 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 27647 Elastoplasticity}, 27648 year = {1998}, 27649 key = {64}, 27650 volume = {6}, 27651 pages = {857--870}, 27652 journal = {Structural Engineering and Mechanics} 27653} 27654 27655@Article{ ferris.tin-loi:solution, 27656 author = {M. C. Ferris and F. Tin-Loi}, 27657 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 27658 and Complementarity Constraints}, 27659 year = {1999}, 27660 journal = {Computer Methods in Applied Mechanics and Engineering}, 27661 volume = {174}, 27662 pages = {107--120}, 27663 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 27664 key = {66} 27665} 27666 27667@Article{ ferris.vlach:scheduling, 27668 author = {M. C. Ferris and M. Vlach}, 27669 title = {Scheduling with Earliness and Tardiness Penalties}, 27670 journal = {Naval Research Logistics Quarterly}, 27671 year = {1992}, 27672 volume = {39}, 27673 pages = {229--245}, 27674 key = {13} 27675} 27676 27677@TechReport{ ferris.zavriev:linear, 27678 author = {M. C. Ferris and S. K Zavriev}, 27679 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 27680 institution = {Computer Sciences Department, University of Wisconsin}, 27681 year = {1996}, 27682 key = {56}, 27683 address = {Madison, Wisconsin}, 27684 type = {Mathematical Programming Technical Report}, 27685 number = {96--12}, 27686 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 27687} 27688 27689@Article{ ferris:finite, 27690 author = {M. C. Ferris}, 27691 title = {Finite Termination of the Proximal Point Algorithm}, 27692 journal = {Mathematical Programming}, 27693 year = {1991}, 27694 volume = {50}, 27695 pages = {359--366}, 27696 key = {06} 27697} 27698 27699@Article{ ferris:iterative, 27700 author = {M. C. Ferris}, 27701 title = {Iterative Linear Programming Solution of Convex Programs}, 27702 journal = {Journal of Optimization Theory and Applications}, 27703 year = {1990}, 27704 volume = {65}, 27705 pages = {53--65}, 27706 key = {07} 27707} 27708 27709@Article{ ferris:linear, 27710 author = {M. C. Ferris}, 27711 title = {The Linear Complementarity Problem}, 27712 journal = {Bulletin of the American Mathematical Society}, 27713 year = {1993}, 27714 volume = {28}, 27715 pages = {169--175}, 27716 key = {27} 27717} 27718 27719@MastersThesis{ ferris:linear*1, 27720 author = {M. C. Ferris}, 27721 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 27722 Solving a Class of Structural Optimization Problems}, 27723 year = {1985}, 27724 school = {University of Cambridge}, 27725 address = {England}, 27726 key = {01} 27727} 27728 27729@TechReport{ ferris:matlab, 27730 author = {M. C. Ferris}, 27731 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 27732 institution = {Computer Sciences Department, University of Wisconsin}, 27733 year = {1998}, 27734 address = {Madison, Wisconsin}, 27735 type = {Mathematical Programming Technical Report}, 27736 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 27737 number = {98-19}, 27738 key = {75} 27739} 27740 27741@Article{ ferris:parallel, 27742 author = {M. C. Ferris}, 27743 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 27744 journal = {Mathematics of Operations Research}, 27745 year = {1994}, 27746 volume = {19}, 27747 pages = {645--658}, 27748 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 27749 key = {20} 27750} 27751 27752@TechReport{ ferris:parallel*1, 27753 author = {M. C. Ferris}, 27754 title = {Parallel Solution of Extremely Large Knapsack Problems}, 27755 institution = {Computer Sciences Department, University of Wisconsin}, 27756 year = {1989}, 27757 address = {Madison, Wisconsin}, 27758 number = {842}, 27759 key = {09} 27760} 27761 27762@PhDThesis{ ferris:weak, 27763 author = {M. C. Ferris}, 27764 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27765 year = {1988}, 27766 school = {University of Cambridge}, 27767 address = {England}, 27768 key = {02} 27769} 27770 27771@TechReport{ ferris:weak*1, 27772 author = {M. C. Ferris}, 27773 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27774 institution = {Computer Sciences Department, University of Wisconsin}, 27775 year = {1988}, 27776 address = {Madison, Wisconsin}, 27777 number = {779}, 27778 key = {05} 27779} 27780 27781@Book{ fiacco.mccormick:nonlinear, 27782 author = {A. V. Fiacco and G. P. McCormick}, 27783 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 27784 year = {1968}, 27785 publisher = {John Wiley \& Sons}, 27786 address = {New York}, 27787 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 27788} 27789 27790@Book{ fiacco:introduction, 27791 author = {A. V. Fiacco}, 27792 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 27793 year = {1983}, 27794 publisher = {Academic Press}, 27795 address = {New York} 27796} 27797 27798@Article{ fiedler.ptak:matrices, 27799 author = {M. Fiedler and V. Pt\'{a}k}, 27800 title = {On matrices with nonpositive off-diagonal elements and positive principal 27801 minors}, 27802 journal = {Czechoslovak Mathematics Journal}, 27803 volume = {12}, 27804 pages = {382--400}, 27805 year = {1962} 27806} 27807 27808@Article{ fischer.kanzow:finite, 27809 author = {A. Fischer and C. Kanzow}, 27810 title = {On Finite Termination of an Iterative Method for Linear Complementarity 27811 Problems}, 27812 journal = {Mathematical Programming}, 27813 volume = {74}, 27814 pages = {279--292}, 27815 year = {1996} 27816} 27817 27818@TechReport{ fischer:constrained, 27819 author = {A. Fischer}, 27820 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 27821 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 27822 year = {1995}, 27823 type = {Technical Report}, 27824 number = {MATH-NM-10-1995}, 27825 address = {Dresden} 27826} 27827 27828@Article{ fischer:local, 27829 author = {A. Fischer}, 27830 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 27831 weak conditions}, 27832 journal = {Optimization Methods and Software}, 27833 year = {1995}, 27834 volume = {6}, 27835 pages = {83--107} 27836} 27837 27838@InCollection{ fischer:ncp-function, 27839 author = {A. Fischer}, 27840 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 27841 booktitle = {Recent Advances in Nonsmooth Optimization}, 27842 publisher = {World Scientific Publishers}, 27843 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 27844 year = {1995}, 27845 pages = {88--105} 27846} 27847 27848@Article{ fischer:newton-type, 27849 author = {A. Fischer}, 27850 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 27851 Problems}, 27852 journal = {Journal of Optimization Theory and Applications}, 27853 year = {1995}, 27854 volume = {86}, 27855 pages = {585--608} 27856} 27857 27858@Article{ fischer:solution, 27859 author = {A. Fischer}, 27860 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 27861 Functions}, 27862 year = {1997}, 27863 journal = {Mathematical Programming}, 27864 pages = {513--532} 27865} 27866 27867@Article{ fischer:special, 27868 author = {A. Fischer}, 27869 title = {A Special {N}ewton--Type Optimization Method}, 27870 journal = {Optimization}, 27871 year = {1992}, 27872 volume = {24}, 27873 pages = {269--284} 27874} 27875 27876@Article{ fisher:use, 27877 author = {R. A. Fisher}, 27878 title = {The Use of Multiple Measurements in Taxonomic Problems}, 27879 journal = {Annual Eugenics}, 27880 year = {1936}, 27881 volume = {7}, 27882 number = {Part II}, 27883 pages = {179--188} 27884} 27885 27886@Book{ fishman:principles, 27887 author = {G. Fishman}, 27888 title = {Principles of Discrete Event Simulation}, 27889 publisher = {Wiley}, 27890 address = {New York, NY}, 27891 year = {1978} 27892} 27893 27894@Article{ fitchard.aldridge.ea:registration, 27895 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 27896 title = {Registration of Synthetic Tomographic Projection Data Sets Using 27897 Cross-Correlation}, 27898 journal = {Physics in Medicine and Biology}, 27899 year = {1998}, 27900 volume = {43}, 27901 pages = {1645--1657} 27902} 27903 27904@Article{ fletcher.matthews:stable, 27905 author = {R. Fletcher and S. P. J. Matthews}, 27906 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 27907 journal = {Mathematical Programming}, 27908 year = {1984}, 27909 volume = {30}, 27910 pages = {267--284} 27911} 27912 27913@TechReport{ fletcher.maza:nonlinear, 27914 author = {R. Fletcher and E. Sainz de la Maza}, 27915 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 27916 Programming}, 27917 institution = {Department of Mathematical Sciences}, 27918 year = {1987}, 27919 address = {The University, Dundee, Scotland}, 27920 number = {NA/100}, 27921 type = {Numerical Analysis Report} 27922} 27923 27924@InCollection{ fletcher:class, 27925 author = {R. Fletcher}, 27926 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 27927 Properties}, 27928 booktitle = {Integer and Nonlinear Programming}, 27929 year = {1970}, 27930 editor = {J. Abadie}, 27931 publisher = {North--Holland}, 27932 address = {Amsterdam}, 27933 pages = {157--173} 27934} 27935 27936@Article{ fletcher:exact, 27937 author = {R. Fletcher}, 27938 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 27939 journal = {Mathematical Programming}, 27940 year = {1973}, 27941 volume = {5}, 27942 pages = {129--150} 27943} 27944 27945@Article{ fletcher:generalized, 27946 author = {R. Fletcher}, 27947 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 27948 Equations}, 27949 journal = {The Computer Journal}, 27950 year = {1968}, 27951 volume = {10}, 27952 pages = {392--399} 27953} 27954 27955@InProceedings{ fletcher:penalty, 27956 crossref = {bachem.grotschel.ea:mathematical}, 27957 author = {R. Fletcher}, 27958 title = {Penalty Functions}, 27959 pages = {87--114} 27960} 27961 27962@Book{ fletcher:practical, 27963 author = {R. Fletcher}, 27964 title = {Practical Methods of Optimization}, 27965 year = {1981}, 27966 publisher = {John Wiley \& Sons}, 27967 address = {Chichester}, 27968 volume = {1} 27969} 27970 27971@Book{ fletcher:practical*1, 27972 author = {R. Fletcher}, 27973 title = {Practical Methods of Optimization}, 27974 year = {1981}, 27975 publisher = {John Wiley \& Sons}, 27976 address = {Chichester}, 27977 volume = {2} 27978} 27979 27980@Book{ fletcher:practical*2, 27981 author = {R. Fletcher}, 27982 title = {Practical Methods of Optimization}, 27983 year = {1987}, 27984 publisher = {John Wiley \& Sons}, 27985 address = {New York}, 27986 edition = {second} 27987} 27988 27989@Unpublished{ fletcher:recent, 27990 author = {R. Fletcher}, 27991 title = {Recent Developments in Nonlinear Programming}, 27992 note = {Presentation at SOR 96, Braunchweig, Germany}, 27993 year = {1996} 27994} 27995 27996@InCollection{ fletcher:second, 27997 author = {R. Fletcher}, 27998 title = {Second Order Correction for Nondifferentiable Optimization}, 27999 booktitle = {Numerical Analysis}, 28000 year = {1982}, 28001 editor = {G. A. Watson}, 28002 publisher = {Springer-Verlag}, 28003 address = {Berlin}, 28004 pages = {85--114} 28005} 28006 28007@InCollection{ florian:mathematical, 28008 author = {M. Florian}, 28009 title = {Mathematical programming applications in national, regional, and urban planning}, 28010 editors = {M. Iri and K. Tanabe}, 28011 booktitle = {Mathematical Programming: Recent Developments and Applications}, 28012 publisher = {Kluwer Academic Publishers}, 28013 address = {Tokyo}, 28014 year = {1989} 28015} 28016 28017@Article{ florian:nonlinear, 28018 author = {M. Florian}, 28019 title = {Nonlinear Cost Network Models in Transportation Analysis}, 28020 journal = {Mathematical Programming Study}, 28021 year = {1986}, 28022 volume = {26}, 28023 pages = {167--196} 28024} 28025 28026@Article{ flynn:computer, 28027 author = {M.~J. Flynn}, 28028 title = {Some Computer Organizations and their Effectiveness}, 28029 journal = {IEEE Transactions on Computers}, 28030 year = {1972}, 28031 volume = {C-21}, 28032 pages = {948--960} 28033} 28034 28035@InProceedings{ fogarty:varying, 28036 crossref = {schaeffer:third}, 28037 author = {T. C. Fogarty}, 28038 title = {Varying the Probability of Mutation in the Genetic Algorithm}, 28039 pages = {422--427} 28040} 28041 28042@Article{ forrest.goldfarb:steepest-edge, 28043 author = {J. J. Forrest and D. Goldfarb}, 28044 title = {Steepest--Edge Simplex Algorithms for Linear Programming}, 28045 journal = {Mathematical Programming}, 28046 year = {1992}, 28047 volume = {57}, 28048 pages = {341--374} 28049} 28050 28051@Article{ forrest.tomlin:updating, 28052 author = {J. J. H. Forrest and J. A. Tomlin}, 28053 title = {Updating Triangular Factors of the Basis to Maintain Sparsity in the Product Form 28054 Simplex Method}, 28055 journal = {Mathematical Programming}, 28056 year = {1972}, 28057 volume = {2}, 28058 pages = {263--278} 28059} 28060 28061@TechReport{ forsgren.gill.ea:computing, 28062 author = {A. Forsgren and P. E. Gill and W. Murray}, 28063 title = {Computing Modified {N}ewton Directions using a Partial {C}holesky Factorization}, 28064 institution = {Department of Mathematics, Royal Institute of Technology}, 28065 year = {1993}, 28066 number = {TRITA-MAT-1993-9}, 28067 address = {Stockholm, Sweden} 28068} 28069 28070@TechReport{ forsgren.gill:primal-dual, 28071 author = {A. Forsgren and P. E. Gill}, 28072 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 28073 institution = {Department of Mathematics, University of California}, 28074 year = {1996}, 28075 type = {Report NA}, 28076 number = {96-3}, 28077 address = {San Diego} 28078} 28079 28080@InCollection{ fortin.glowinski:decomposition-coordination, 28081 author = {M. Fortin and R. Glowinski}, 28082 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 28083 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 28084 Problems}, 28085 publisher = {North-Holland}, 28086 year = {1983}, 28087 editor = {M. Fortin and R. Glowinski}, 28088 address = {Amsterdam} 28089} 28090 28091@Misc{ foster.kesselman:globus, 28092 author = {I. Foster and C. Kesselman}, 28093 title = {The Globus Project}, 28094 howpublished = {www.globus.org} 28095} 28096 28097@Article{ foster.kesselman:globus*1, 28098 author = {I. Foster and C. Kesselman}, 28099 title = {Globus: A Metacomputing Infrastructure Toolkit}, 28100 journal = {International Journal of Supercomputer Applications}, 28101 volume = {11}, 28102 pages = {115--128}, 28103 year = {1997} 28104} 28105 28106@Book{ foster.kesselman:grid, 28107 editor = {I. Foster and C. Kesselman}, 28108 title = {The Grid: Blueprint for a Future Computing Infrastructure}, 28109 publisher = {Morgan Kaufmann Publishers}, 28110 year = {1999} 28111} 28112 28113@Book{ fourer.gay.ea:ampl, 28114 author = {R. Fourer and D. M. Gay and B. W. Kernighan}, 28115 title = {{AMPL}: {A} Modeling Language for Mathematical Programming}, 28116 year = {1993}, 28117 publisher = {Duxbury Press} 28118} 28119 28120@Article{ fourer.gay.ea:modeling, 28121 author = {R. Fourer and D. M. Gay and B. W. 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Gabriel}, 28354 title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and 28355 Extensions}, 28356 school = {The Johns Hopkins University}, 28357 year = {1992}, 28358 address = {Baltimore, Maryland} 28359} 28360 28361@Article{ gafni.bertsekas:two-metric, 28362 author = {E. M. Gafni and D. P. Bertsekas}, 28363 title = {Two-Metric Projection Methods for Constrained Optimization}, 28364 journal = {SIAM Journal on Control and Optimization}, 28365 year = {1984}, 28366 volume = {22}, 28367 pages = {936--964} 28368} 28369 28370@InProceedings{ gaivoronski:convergence, 28371 author = {A. A. Gaivoronski}, 28372 title = {Convergence of Parallel Backpropagation for Neural Networks}, 28373 booktitle = {SIAM Journal on Optimization}, 28374 year = {1994}, 28375 note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993, 28376 submitted} 28377} 28378 28379@Misc{ gaivoronski:private, 28380 author = {A. A. 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Gao}, 28424 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 28425 Conditions}, 28426 type = {Manuscript}, 28427 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 28428 month = oct, 28429 year = {1994} 28430} 28431 28432@Article{ garcia-palomares.mangasarian:superlinearly, 28433 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 28434 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 28435 Optimization Problems}, 28436 journal = {Mathematical Programming}, 28437 year = {1976}, 28438 volume = {11}, 28439 pages = {1--13} 28440} 28441 28442@Article{ garcia-palomares.restuccia:global, 28443 author = {U. M. {Garcia--Palomares} and A. Restuccia}, 28444 title = {A Global Quadratic Algorithm for Solving a System of Mixed Equations}, 28445 journal = {Mathematical Programming}, 28446 year = {1981}, 28447 volume = {21}, 28448 pages = {290--300} 28449} 28450 28451@InProceedings{ garcia-palomares:superlinearly, 28452 author = {U. M. {Garcia--Palomares}}, 28453 title = {Superlinearly Convergent Algorithms for Linearly Constrained Optimization}, 28454 crossref = {mangasarian.meyer.ea:nonlinear*2}, 28455 pages = {101--119} 28456} 28457 28458@Article{ garcia.gould:theorem, 28459 author = {C. B. Garcia and F. J. Gould}, 28460 title = {A Theorem on Homotopy Paths}, 28461 journal = {Mathematics of Operations Research}, 28462 year = {1978}, 28463 volume = {3}, 28464 pages = {282--289} 28465} 28466 28467@Book{ garcia.zangwill:pathways, 28468 author = {C. B. Garcia and W. I. Zangwill}, 28469 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 28470 year = {1981}, 28471 publisher = {Prentice-Hall, Inc}, 28472 address = {Englewood Cliffs, New Jersey} 28473} 28474 28475@Book{ garey.johnson:computers, 28476 author = {M. R. Garey and D. S. Johnson}, 28477 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 28478 year = {1979}, 28479 publisher = {W.H. Freeman and Company}, 28480 address = {San Francisco} 28481} 28482 28483@Article{ garey.tarjan.ea:one-processor, 28484 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 28485 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 28486 journal = {Mathematics of Operations Research}, 28487 year = {1988}, 28488 volume = {13}, 28489 pages = {330--348} 28490} 28491 28492@Book{ garfinkel.nemhauser:integer, 28493 author = {R. S. Garfinkel and G. L. Nemhauser}, 28494 title = {Integer Programming}, 28495 year = {1972}, 28496 publisher = {John Wiley \& Sons}, 28497 address = {New York} 28498} 28499 28500@Book{ gass:linear, 28501 author = {S. Gass}, 28502 title = {Linear Programming Methods and Applications}, 28503 edition = {Fifth}, 28504 publisher = {Boyd and Fraser Publishing Company}, 28505 address = {Danvers, Massachusetts}, 28506 year = {1985} 28507} 28508 28509@InProceedings{ gay:combining, 28510 author = {D. M. Gay}, 28511 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 28512 booktitle = {Sparse Matrix Proceedings 1978}, 28513 editor = {I. S. Duff and G. W. Stewart}, 28514 year = {1978}, 28515 organization = {SIAM}, 28516 address = {Philadelphia, Pennsylvania}, 28517 pages = {313--334} 28518} 28519 28520@Article{ gay:electronic, 28521 author = {D. M. Gay}, 28522 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 28523 journal = {{COAL} Newsletter}, 28524 year = {1985}, 28525 volume = {13}, 28526 pages = {10--12} 28527} 28528 28529@TechReport{ gay:hooking, 28530 author = {D. M. Gay}, 28531 title = {Hooking Your Solver to {AMPL}}, 28532 year = {1997}, 28533 institution = {Bell Laboratories}, 28534 address = {Murray Hill, New Jersey}, 28535 note = {Revised 1994, 1997} 28536} 28537 28538@Article{ gay:variant, 28539 author = {D. Gay}, 28540 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 28541 Form}, 28542 journal = {Mathematical Programming}, 28543 year = {1987}, 28544 volume = {37}, 28545 pages = {81--90} 28546} 28547 28548@Article{ geiger.kanzow:resolution, 28549 author = {C. Geiger and C. Kanzow}, 28550 title = {On the Resolution of Monotone Complementarity Problems}, 28551 journal = {Computational Optimization and Applications}, 28552 volume = {5}, 28553 year = {1996}, 28554 pages = {155--173} 28555} 28556 28557@Book{ geist.beguelin.ea:pvm, 28558 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 28559 V. S. Sunderam}, 28560 title = {{PVM}: Parallel Virtual Machine}, 28561 publisher = {MIT Press}, 28562 address = {Cambridge, Massachusetts}, 28563 year = {1994} 28564} 28565 28566@Article{ gendron.crainic:parallel, 28567 author = {B. Gendron and T. G. Crainic}, 28568 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 28569 journal = {Operations Research}, 28570 year = {1994}, 28571 volume = {42}, 28572 pages = {1042--1060} 28573} 28574 28575@Article{ george:automatic, 28576 author = {A. George}, 28577 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 28578 journal = {SIAM Journal on Numerical Analysis}, 28579 vol = {17}, 28580 pages = {740--751}, 28581 year = {1980} 28582} 28583 28584@InProceedings{ georges-schleuter:asparagos, 28585 crossref = {schaeffer:third}, 28586 author = {M. Georges--Schleuter}, 28587 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 28588 pages = {416--421} 28589} 28590 28591@Article{ georgiou:comments, 28592 author = {G. M. Georgiou}, 28593 title = {Comments On Hidden Nodes in Neural Nets}, 28594 journal = {IEEE Transactions on Circuits and Systems}, 28595 year = {1991}, 28596 volume = {38}, 28597 pages = {1410} 28598} 28599 28600@TechReport{ gertz.linderoth.ea:object-oriented, 28601 author = {M. Gertz and J. Linderoth and S. Wright}, 28602 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 28603 institution = {MCS Division, Argonne National Laboratory}, 28604 year = {in preparation} 28605} 28606 28607@Article{ ghellinck.vial:polynomial, 28608 author = {G. de Ghellinck and J.--Ph. Vial}, 28609 title = {A Polynomial {N}ewton Method for Linear Programming}, 28610 journal = {Algorithmica}, 28611 year = {1986}, 28612 volume = {1}, 28613 pages = {425--453} 28614} 28615 28616@InCollection{ gilbert.ng:predicting, 28617 author = {J. R. Gilbert and E. Ng}, 28618 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 28619 year = {1993}, 28620 booktitle = {Graph Theory and Sparse Matrix Computation}, 28621 editor = {A. George and J. Gilbert and J. Liu}, 28622 publisher = {Springer-Verlag} 28623} 28624 28625@Article{ gilbert-lemarechal, 28626 author = {J. C. Gilbert and C. Lemarechal}, 28627 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 28628 journal = {Mathematical Programming}, 28629 year = {1989}, 28630 volume = {45}, 28631 pages = {407--434} 28632} 28633 28634@Article{ gill.murray.ea:computing, 28635 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 28636 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 28637 journal = {SIAM Journal on Scientific and Statistical Computing}, 28638 year = {1983}, 28639 volume = {4}, 28640 pages = {310--321} 28641} 28642 28643@Article{ gill.murray.ea:maintaining, 28644 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 28645 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 28646 year = {1987}, 28647 journal = {Linear Algebra and Its Applications}, 28648 volume = {88/89}, 28649 pages = {239--270} 28650} 28651 28652@Book{ gill.murray.ea:practical, 28653 author = {P. E. Gill and W. Murray and M. H. 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Tseng}, 31623 title = {On the Convergence Rate of Dual Ascent Methods for Strictly Convex Minimization}, 31624 journal = {Mathematics of Operations Research}, 31625 year = {1993}, 31626 volume = {18}, 31627 pages = {846--867} 31628} 31629 31630@Article{ luo.tseng:error, 31631 author = {Z.--Q. Luo and P. Tseng}, 31632 title = {Error Bound and Convergence Analysis of Matrix Splitting Algorithms for the 31633 Affine Variational Inequality Problem}, 31634 journal = {SIAM Journal on Optimization}, 31635 year = {1992}, 31636 volume = {2}, 31637 pages = {43--54} 31638} 31639 31640@Article{ luo.tseng:error*1, 31641 author = {Z.-Q. Luo and P. Tseng}, 31642 title = {Error Bound and Reduced Gradient Projection Algorithms for Convex Minimization 31643 Over a Polyhedral Set}, 31644 journal = {SIAM Journal on Optimization}, 31645 year = {1993}, 31646 volume = {3}, 31647 pages = {43--59} 31648} 31649 31650@Article{ luo.tseng:error*2, 31651 author = {Z.-Q. Luo and P. Tseng}, 31652 title = {Error Bounds and Convergence Analysis of Feasible Descent Methods: {A} General 31653 Approach}, 31654 journal = {Annals of Operations Research}, 31655 year = {1993}, 31656 volume = {46}, 31657 pages = {157--178} 31658} 31659 31660@Article{ luo.tseng:global, 31661 author = {Z.-Q. Luo and P. Tseng}, 31662 title = {On Global Error Bound for a Class of Monotone Affine Variational Inequality 31663 Problems}, 31664 journal = {Operations Research Letters}, 31665 year = {1992}, 31666 volume = {11}, 31667 pages = {159--165} 31668} 31669 31670@Article{ luo.tseng:linear, 31671 author = {Z.-Q. Luo and P. Tseng}, 31672 title = {On the linear convergence of descent methods for convex essentially smooth 31673 minimization}, 31674 journal = {SIAM Journal on Control and Optimization}, 31675 year = {1992}, 31676 volume = {30}, 31677 pages = {408--425} 31678} 31679 31680@TechReport{ luo:convergence, 31681 author = {Z.-Q. Luo}, 31682 title = {Convergence Analysis of Primal--Dual Interior--Point Algorithms for Convex 31683 Quadratic Programs}, 31684 institution = {Communications Research Laboratory, McMaster University}, 31685 year = {1992}, 31686 address = {Hamilton, Ontario} 31687} 31688 31689@Article{ lustig.marsten.ea:computational, 31690 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31691 title = {Computational Experience with a Primal-Dual Interior Point Method for Linear 31692 Programming}, 31693 journal = {Linear Algebra and Its Applications}, 31694 year = {1991}, 31695 volume = {152}, 31696 pages = {191--222} 31697} 31698 31699@Article{ lustig.marsten.ea:implementing, 31700 author = {I. J. Lustig and R. E. Marsten and D. F. 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Madsen}, 31769 title = {Minimization of Nonlinear Approximation Functions}, 31770 year = {1985}, 31771 address = {Lyngby, Denmark}, 31772 school = {Institute of Numerical Analysis, Technical University of Denmark}, 31773 annote = {Dissertation} 31774} 31775 31776@Book{ magill.quinzii:theory, 31777 author = {M. Magill and M. Quinzii}, 31778 title = {Theory of Incomplete Markets}, 31779 publisher = {MIT Press}, 31780 year = {1996} 31781} 31782 31783@InCollection{ magnanti:models, 31784 author = {T. L. Magnanti}, 31785 title = {Models and Algorithms for Predicting Urban Traffic Equilibria}, 31786 booktitle = {Transportation Planning Models}, 31787 year = {1984}, 31788 editor = {M. Florian}, 31789 publisher = {North Holland}, 31790 pages = {153--186} 31791} 31792 31793@InCollection{ maguregui:modified, 31794 author = {J. Maguregui}, 31795 title = {A modified {N}ewton algorithm for functions over convex sets}, 31796 crossref = {mangasarian.meyer.ea:nonlinear*3}, 31797 pages = {461--473} 31798} 31799 31800@PhDThesis{ maguregui:regular, 31801 author = {J. Maguregui}, 31802 title = {Regular Multivalued Functions and Algorithmic Applications}, 31803 year = {1977}, 31804 address = {Madison, Wisconsin}, 31805 school = {Computer Sciences Department, University of Wisconsin} 31806} 31807 31808@Article{ mahey.oualibouch.ea:proximal, 31809 author = {P. Mahey and S. Oualibouch and D. T. Pham}, 31810 title = {Proximal Decomposition on the Graph of a Maximal Monotone Operator}, 31811 journal = {SIAM Journal on Optimization}, 31812 year = {1995}, 31813 volume = {5}, 31814 pages = {454--466} 31815} 31816 31817@Article{ mahey.pham:partial, 31818 author = {P. Mahey and D. T. Pham}, 31819 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 31820 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 31821 year = {1993}, 31822 volume = {27}, 31823 pages = {375--392} 31824} 31825 31826@InCollection{ maier.novati:shakedown, 31827 author = {G. Maier and G. Novati}, 31828 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 31829 geometric effects with reference to discrete structural models}, 31830 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 31831 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 31832 publisher = {Pineridge Press}, 31833 address = {Swansea}, 31834 year = {1990}, 31835 pages = {451--471} 31836} 31837 31838@Article{ maier:incremental, 31839 author = {G. Maier}, 31840 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 31841 Instabilizing Effects}, 31842 journal = {International Journal of Solids and Structures}, 31843 volume = {7}, 31844 year = {1971}, 31845 pages = {345--372} 31846} 31847 31848@InCollection{ maier:inverse, 31849 author = {G. Maier}, 31850 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 31851 booktitle = {Serie VIII}, 31852 publisher = {Academia Nazionale dei Lincei}, 31853 year = {1981}, 31854 volume = {LXX}, 31855 pages = {203--209} 31856} 31857 31858@Article{ maier:matrix, 31859 author = {G. Maier}, 31860 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 31861 yield planes}, 31862 journal = {Meccanica}, 31863 volume = {5}, 31864 year = {1970}, 31865 pages = {54--66} 31866} 31867 31868@Article{ maier:quadratic, 31869 author = {G. Maier}, 31870 title = {A quadratic programming approach for certain classes of nonlinear structural 31871 problems}, 31872 journal = {Meccanica}, 31873 volume = {3}, 31874 year = {1968}, 31875 pages = {121--130} 31876} 31877 31878@Book{ manber:introduction, 31879 author = {U. Manber}, 31880 title = {Introduction to Algorithms: {A} Creative Approach}, 31881 year = {1989}, 31882 publisher = {Addison-Wesley} 31883} 31884 31885@Article{ mangasarian.deleone:error, 31886 author = {O. L. Mangasarian and R. {De~Leone}}, 31887 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 31888 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 31889 journal = {Applied Mathematics and Optimization}, 31890 year = {1988}, 31891 volume = {17}, 31892 pages = {1--14} 31893} 31894 31895@Article{ mangasarian.deleone:parallel, 31896 author = {O. L. Mangasarian and R. {De~Leone}}, 31897 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 31898 Problems and Linear Programs}, 31899 journal = {Journal of Optimization Theory and Applications}, 31900 year = {1987}, 31901 volume = {54}, 31902 pages = {437--446} 31903} 31904 31905@Article{ mangasarian.fromovitz:fritz, 31906 author = {O. L. Mangasarian and S. Fromovitz}, 31907 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 31908 and inequality constraints}, 31909 journal = {Journal of Mathematical Analysis and its Applications}, 31910 year = {1967}, 31911 volume = {17}, 31912 pages = {37--47} 31913} 31914 31915@Article{ mangasarian.mclinden:simple, 31916 author = {O. L. Mangasarian and L. McLinden}, 31917 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 31918 Programs}, 31919 journal = {Mathematical Programming}, 31920 year = {1985}, 31921 volume = {32}, 31922 pages = {32--40} 31923} 31924 31925@Article{ mangasarian.meyer:nonlinear, 31926 author = {O. L. Mangasarian and R. R. Meyer}, 31927 title = {Nonlinear Perturbation of Linear Programs}, 31928 journal = {SIAM Journal on Control and Optimization}, 31929 year = {1979}, 31930 volume = {17}, 31931 pages = {745--752} 31932} 31933 31934@TechReport{ mangasarian.musicant:active, 31935 author = {O. L. Mangasarian and David R. Musicant}, 31936 title = {Active Set Support Vector Machine Classification}, 31937 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31938 year = {2000}, 31939 number = {00-04}, 31940 address = {Madison, Wisconsin} 31941} 31942 31943@TechReport{ mangasarian.musicant:lagrangian, 31944 author = {O. L. Mangasarian and D. R. Musicant}, 31945 title = {Lagrangian Support Vector Machines}, 31946 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31947 year = {2000}, 31948 number = {00-06}, 31949 address = {Madison, Wisconsin} 31950} 31951 31952@TechReport{ mangasarian.musicant:robust, 31953 author = {O. L. Mangasarian and David R. Musicant}, 31954 title = {Robust Linear and Support Vector Regression}, 31955 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31956 year = {1999}, 31957 number = {99-09}, 31958 address = {Madison, Wisconsin} 31959} 31960 31961@Article{ mangasarian.musicant:successive, 31962 author = {O. L. Mangasarian and David R. Musicant}, 31963 title = {Successive Overrelaxation for Support Vector Machines}, 31964 journal = {IEEE Transactions on Neural Networks}, 31965 volume = {10}, 31966 year = {1999}, 31967 pages = {1032-1037} 31968} 31969 31970@Article{ mangasarian.pang:exact, 31971 author = {O. L. Mangasarian and J. S. Pang}, 31972 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 31973 Constraints}, 31974 journal = {Optimization}, 31975 year = {1997}, 31976 volume = {42}, 31977 pages = {1--8} 31978} 31979 31980@Article{ mangasarian.pang:extended, 31981 author = {O. L. Mangasarian and J. S. Pang}, 31982 title = {The Extended Linear Complementarity Problem}, 31983 journal = {SIAM Journal on Matrix Analysis and Applications}, 31984 year = {1994}, 31985 volume = {16} 31986} 31987 31988@Article{ mangasarian.ren:error, 31989 author = {O. L. Mangasarian and J. Ren}, 31990 title = {New error bounds for the nonlinear complementarity problem}, 31991 year = {1994}, 31992 volume = {1}, 31993 pages = {49--56}, 31994 journal = {Communications on Applied Nonlinear Analysis} 31995} 31996 31997@Article{ mangasarian.ren:improved, 31998 author = {O. L. Mangasarian and J. Ren}, 31999 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 32000 year = {1994}, 32001 volume = {66}, 32002 journal = {Mathematical Programming}, 32003 pages = {241--255} 32004} 32005 32006@InProceedings{ mangasarian.setiono.ea:pattern, 32007 crossref = {coleman.li:large-scale}, 32008 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 32009 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 32010 Diagnosis}, 32011 pages = {22--31} 32012} 32013 32014@Article{ mangasarian.shiau:error, 32015 author = {O. L. Mangasarian and T.--H. Shiau}, 32016 title = {Error Bounds for Monotone Linear Complementarity Problems}, 32017 journal = {Mathematical Programming}, 32018 year = {1986}, 32019 volume = {36}, 32020 pages = {81--89} 32021} 32022 32023@Article{ mangasarian.shiau:lipschitz, 32024 author = {O. L. Mangasarian and T.--H. Shiau}, 32025 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 32026 Complementarity Problems}, 32027 journal = {SIAM Journal on Control and Optimization}, 32028 year = {1987}, 32029 volume = {25}, 32030 pages = {583--595} 32031} 32032 32033@Article{ mangasarian.solodov:nonlinear, 32034 author = {O. L. Mangasarian and M. V. Solodov}, 32035 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 32036 journal = {Mathematical Programming}, 32037 year = {1993}, 32038 volume = {62}, 32039 pages = {277--298} 32040} 32041 32042@Article{ mangasarian.solodov:serial, 32043 author = {O. L. Mangasarian and M. V. Solodov}, 32044 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 32045 Minimization}, 32046 year = {1994}, 32047 journal = {Optimization Methods and Software}, 32048 volume = {4}, 32049 pages = {103--116} 32050} 32051 32052@Article{ mangasarian.street.ea:breast, 32053 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 32054 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 32055 journal = {Operations Research}, 32056 year = {1995}, 32057 volume = {43}, 32058 pages = {570--577} 32059} 32060 32061@Article{ mangasarian.wolberg:cancer, 32062 author = {O. L. Mangasarian and W. H. Wolberg}, 32063 title = {Cancer Diagnosis via Linear Programming}, 32064 journal = {SIAM News}, 32065 year = {1990}, 32066 volume = {23}, 32067 pages = {1 \& 18} 32068} 32069 32070@InCollection{ mangasarian:applications, 32071 author = {O. L. Mangasarian}, 32072 title = {Some Applications of Penalty Functions in Mathematical Programming}, 32073 booktitle = {Optimization and Related Fields}, 32074 year = {1986}, 32075 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 32076 publisher = {Springer-Verlag}, 32077 address = {Heidelberg}, 32078 pages = {307--329}, 32079 note = {Lecture Notes in Mathematics 1190} 32080} 32081 32082@Article{ mangasarian:characterization, 32083 author = {O. L. Mangasarian}, 32084 title = {Characterization of linear complementarity problems as linear programs}, 32085 journal = {Mathematical Programming Study}, 32086 year = {1978}, 32087 volume = {7}, 32088 pages = {74--87} 32089} 32090 32091@InProceedings{ mangasarian:condition, 32092 author = {O. L. Mangasarian}, 32093 title = {A condition number for linear inequalities and linear programs}, 32094 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 32095 1981}, 32096 year = {1981}, 32097 editor = {G. Bamberg and O. Opitz}, 32098 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 32099 address = {Konigstein}, 32100 pages = {3--15} 32101} 32102 32103@Article{ mangasarian:convergence, 32104 author = {O. L. Mangasarian}, 32105 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 32106 Symmetric Monotone Linear Complementarity Problem}, 32107 journal = {SIAM Journal on Optimization}, 32108 volume = {1}, 32109 pages = {114--122}, 32110 year = {1991} 32111} 32112 32113@Article{ mangasarian:equivalence, 32114 author = {O. L. Mangasarian}, 32115 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 32116 journal = {SIAM Journal on Applied Mathematics}, 32117 year = {1976}, 32118 volume = {31}, 32119 pages = {89--92} 32120} 32121 32122@Article{ mangasarian:error, 32123 author = {O. L. Mangasarian}, 32124 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 32125 journal = {ORSA Journal on Computing}, 32126 volume = {15}, 32127 pages = {187--192}, 32128 year = {1994} 32129} 32130 32131@Article{ mangasarian:error*1, 32132 author = {O. L. Mangasarian}, 32133 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 32134 journal = {Mathematical Programming}, 32135 year = {1990}, 32136 volume = {48}, 32137 pages = {437--445} 32138} 32139 32140@Article{ mangasarian:generalized, 32141 author = {O. L. Mangasarian}, 32142 title = {Generalized Linear Complementarity Problems as Linear Programs}, 32143 journal = {Methods of Operations Research}, 32144 year = {1979}, 32145 editor = {W. Oettli and F. Steffens}, 32146 volume = {31}, 32147 pages = {393--402} 32148} 32149 32150@InCollection{ mangasarian:generalized*1, 32151 author = {O. L. Mangasarian}, 32152 title = {Generalized Support Vector Machines}, 32153 year = {2000}, 32154 pages = {135-146}, 32155 booktitle = {Advances in Large Margin Classifiers}, 32156 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 32157 publisher = {MIT Press}, 32158 address = {Cambridge, MA} 32159} 32160 32161@Article{ mangasarian:global, 32162 author = {O. L. Mangasarian}, 32163 title = {Global error bounds for monotone affine variational inequality problems}, 32164 journal = {Linear Algebra and Its Applications}, 32165 year = {1992}, 32166 pages = {153--164} 32167} 32168 32169@InCollection{ mangasarian:least, 32170 author = {O. L. Mangasarian}, 32171 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 32172 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 32173 year = {1990}, 32174 publisher = {Oxford University Press}, 32175 address = {New York}, 32176 pages = {217--221} 32177} 32178 32179@Article{ mangasarian:least-norm, 32180 author = {O. L. Mangasarian}, 32181 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 32182 Problem}, 32183 journal = {Journal of Mathematical Analysis and Applications}, 32184 year = {1983}, 32185 volume = {92}, 32186 pages = {240--251} 32187} 32188 32189@Article{ mangasarian:linear, 32190 author = {O. L. Mangasarian}, 32191 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 32192 journal = {Mathematical Programming}, 32193 year = {1976}, 32194 volume = {10}, 32195 pages = {263--270} 32196} 32197 32198@Article{ mangasarian:linear*1, 32199 author = {O. L. Mangasarian}, 32200 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 32201 journal = {Operations Research}, 32202 year = {1965}, 32203 volume = {13}, 32204 pages = {444--452} 32205} 32206 32207@Article{ mangasarian:locally, 32208 author = {O. L. Mangasarian}, 32209 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 32210 Complementarity Problems}, 32211 journal = {Mathematical Programming}, 32212 year = {1980}, 32213 volume = {19}, 32214 pages = {200--212} 32215} 32216 32217@InCollection{ mangasarian:machine, 32218 author = {O. L. Mangasarian}, 32219 title = {Machine Learning via Polyhedral Concave Minimization}, 32220 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 32221 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 32222 pages = {175-188}, 32223 year = {1996}, 32224 address = {Heidelberg}, 32225 publisher = {Physica-Verlag A Springer-Verlag Company} 32226} 32227 32228@Article{ mangasarian:mathematical, 32229 author = {O. L. Mangasarian}, 32230 title = {Mathematical Programming in Neural Networks}, 32231 journal = {ORSA Journal on Computing}, 32232 volume = {5}, 32233 pages = {349--360}, 32234 year = {1993} 32235} 32236 32237@InProceedings{ mangasarian:mathematical*1, 32238 author = {O. L. Mangasarian}, 32239 title = {Mathematical Programming in Machine Learning}, 32240 booktitle = {Nonlinear Optimization and Applications}, 32241 editor = {G. Di Pillo and F. Giannessi}, 32242 publisher = {Plenum Publishing}, 32243 address = {New York}, 32244 pages = {283--295}, 32245 year = {1996} 32246} 32247 32248@Article{ mangasarian:mathematical*2, 32249 author = {O. L. Mangasarian}, 32250 title = {Mathematical Programming in Data Mining}, 32251 journal = {Data Mining and Knowledge Discovery}, 32252 volume = {1}, 32253 year = {1997}, 32254 pages = {183-201} 32255} 32256 32257@Article{ mangasarian:multi-surface, 32258 author = {O. L. Mangasarian}, 32259 title = {Multi-surface Method of Pattern Separation}, 32260 journal = {IEEE Transactions on Information Theory}, 32261 year = {1968}, 32262 volume = {IT-14}, 32263 pages = {801--807} 32264} 32265 32266@Book{ mangasarian:nonlinear, 32267 author = {O. L. Mangasarian}, 32268 title = {Nonlinear Programming}, 32269 year = {1969}, 32270 publisher = {McGraw--Hill}, 32271 address = {New York}, 32272 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 32273} 32274 32275@Article{ mangasarian:normal, 32276 author = {O. L. Mangasarian}, 32277 title = {Normal Solutions of Linear Programs}, 32278 journal = {Mathematical Programming Study}, 32279 year = {1984}, 32280 volume = {22}, 32281 pages = {206--216} 32282} 32283 32284@Article{ mangasarian:optimal, 32285 author = {O. L. Mangasarian}, 32286 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 32287 Linear Programs}, 32288 journal = {Journal of Optimization Theory and Applications}, 32289 year = {1981}, 32290 volume = {35}, 32291 pages = {123--128} 32292} 32293 32294@Article{ mangasarian:parallel, 32295 author = {O. L. Mangasarian}, 32296 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 32297 journal = {SIAM Journal on Control and Optimization}, 32298 volume = {33}, 32299 pages = {1916--1925}, 32300 year = {1995} 32301} 32302 32303@TechReport{ mangasarian:regularized, 32304 author = {O. L. 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Petri}, 34077 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 34078 publisher = {Harvard University Press}, 34079 year = {1984} 34080} 34081 34082@InProceedings{ petrzykowski:application, 34083 author = {T. Petrzykowski}, 34084 title = {Application of the Steepest Ascent Method to Concave Programming}, 34085 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 34086 year = {1962}, 34087 publisher = {North--Holland}, 34088 address = {Amsterdam}, 34089 pages = {185--189} 34090} 34091 34092@InProceedings{ pettey.leuze.ea:parallel, 34093 crossref = {grefenstette:genetic}, 34094 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 34095 title = {A Parallel Genetic Algorithm}, 34096 pages = {155--161} 34097} 34098 34099@InProceedings{ pettey.leuze:theoretical, 34100 crossref = {schaeffer:third}, 34101 author = {C. C. Pettey and M. R. Leuze}, 34102 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 34103 pages = {398--405} 34104} 34105 34106@Book{ pfeiffer.glocker:multibody, 34107 author = {F. Pfeiffer and C. Glocker}, 34108 title = {Multibody Dynamics with Unilateral Contact}, 34109 year = {1996}, 34110 publisher = {John Wiley \& Sons} 34111} 34112 34113@TechReport{ pierro.iusem:convergence, 34114 author = {A. R. de Pierro and A. N. Iusem}, 34115 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 34116 Linear Complementarity Problems}, 34117 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 34118 year = {1990}, 34119 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 34120} 34121 34122@InCollection{ pillo.grippo.ea:class, 34123 author = {G. Di Pillo and L. Grippo and F. 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Bonnans}, 34310 title = {Infeasible path following algorithms for linear complementarity problems}, 34311 institution = {INRIA}, 34312 year = {1994}, 34313 month = dec, 34314 number = {RR--2445}, 34315 type = {Research Report} 34316} 34317 34318@Article{ potra.sheng:large-step, 34319 author = {F. A. Potra and R. Sheng}, 34320 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 34321 year = {1997}, 34322 journal = {SIAM Journal on Optimization}, 34323 volume = {7}, 34324 pages = {318--335} 34325} 34326 34327@Article{ potra:infeasible, 34328 author = {F. A. Potra}, 34329 title = {An infeasible interior-point predictor-corrector algorithm for linear 34330 programming}, 34331 journal = {SIAM Journal on Optimization}, 34332 year = {1996}, 34333 volume = {6}, 34334 pages = {19--32} 34335} 34336 34337@TechReport{ potra:onl, 34338 author = {F. A. 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Pruyne}, 34480 title = {Resource Management Services for Parallel Applications}, 34481 school = {University of Wisconsin--Madison}, 34482 year = {1996}, 34483 address = {Madison, Wisconsin} 34484} 34485 34486@Book{ pshenichny.danilin:numerical, 34487 author = {B. N. Pshenichny and Yu. M. Danilin}, 34488 title = {Numerical Methods in Extremal Problems}, 34489 year = {1978}, 34490 publisher = {MIR Publishers}, 34491 address = {Moscow} 34492} 34493 34494@TechReport{ qi.chen:globally, 34495 author = {L. Qi and X. Chen}, 34496 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 34497 institution = {School of Mathematics, University of New South Wales}, 34498 year = {1993}, 34499 annote = {revised}, 34500 address = {Sydney} 34501} 34502 34503@Article{ qi.jiang:semismooth, 34504 author = {L. Qi and H. 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Rockafellar}, 35172 title = {Network Flows and Monotropic Optimization}, 35173 publisher = {John Wiley}, 35174 year = {1984}, 35175 address = {New York} 35176} 35177 35178@Article{ rodrigues:mixed, 35179 author = {H. C. Rodrigues}, 35180 title = {A mixed variational formulation for shape optimization of solids with contact 35181 conditions}, 35182 journal = {Structural Optimization}, 35183 volume = {6}, 35184 year = {1993}, 35185 pages = {19--28} 35186} 35187 35188@Book{ rodrigues:obstacle, 35189 author = {J. F. Rodrigues}, 35190 title = {Obstacle Problems in Mathematical Physics}, 35191 publisher = {Elsevier Publishing Company}, 35192 address = {Amsterdam}, 35193 year = {1987} 35194} 35195 35196@Book{ roos.terlaky.ea:theory, 35197 author = {C. Roos and T. Terlaky and J.--Ph. 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{Fr\'{e}d\'{e}ric Alauzet}, 37852 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 37853 year = {2010} 37854} 37855 37856@Article{ chan1994qmrcgs, 37857 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 37858 systems}, 37859 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 37860 and Tong, Charles H}, 37861 journal = {SIAM Journal on Scientific Computing}, 37862 volume = {15}, 37863 number = {2}, 37864 pages = {338--347}, 37865 year = {1994}, 37866 publisher = {SIAM} 37867} 37868 37869@Article{ ghai2019comparison, 37870 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 37871 nonsymmetric linear systems}, 37872 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 37873 journal = {Numerical Linear Algebra with Applications}, 37874 volume = {26}, 37875 number = {1}, 37876 pages = {e2215}, 37877 year = {2019}, 37878 publisher = {Wiley 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Knepley}, 37885 journal = {International Journal on Numerical Methods in Engineering}, 37886 note = {Submitted}, 37887 year = {2022} 37888} 37889 37890@Article{ nathawaniknepley2022, 37891 title = {Droplet formation simulation using mixed finite elements}, 37892 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37893 journal = {Physics of Fluids}, 37894 volume = {34}, 37895 pages = {064105}, 37896 doi = {10.1063/5.0089752}, 37897 year = {2022} 37898} 37899 37900@InProceedings{ nathawaniknepley2022b, 37901 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 37902 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37903 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 37904 (ICCFD11)}, 37905 editor = {Christoph Brehm and Shishir Pandya}, 37906 number = {4103}, 37907 year = {2022} 37908} 37909 37910@Article{ nathawaniknepley2023, 37911 title = {One-dimensional model to simulate shear-induced droplet formation}, 37912 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37913 journal = {Physics of Fluids}, 37914 note = {Submitted}, 37915 year = {2023} 37916} 37917 37918@Article{ georgalisnathawaniknepleypatra2023, 37919 title = {Uncertainty quantification of droplet atomization and pinch-off with {Gaussian 37920 Processes}}, 37921 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. 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Pusztay}, 37984 type = {{PhD} thesis}, 37985 school = {University at Buffalo, Department of Computer Science and Engineering}, 37986 address = {Buffalo, NY}, 37987 month = {May}, 37988 year = {2022} 37989} 37990 37991@PhDThesis{ finnthesis2023, 37992 title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau 37993 System}, 37994 author = {Daniel S. Finn}, 37995 type = {{PhD} thesis}, 37996 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 37997 Engineering}, 37998 address = {Buffalo, NY}, 37999 month = {May}, 38000 year = {2023} 38001} 38002 38003@PhDThesis{ nathawanithesis2023, 38004 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 38005 author = {Darsh Kiritbhai Nathawani}, 38006 type = {{PhD} thesis}, 38007 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38008 Engineering}, 38009 address = {Buffalo, NY}, 38010 month = {May}, 38011 year = {2023} 38012} 38013
