1% 2% This file is formatted by: 3% bibtool petsc.bib -- expand.macros=on -- print.line.length=100 -- pass.comments=on 4% 5% If the reference uses PETSc, include a field listing components used, e.g. 6% petsc_uses = {KSP, SNES, TS, TAO}, 7% 8% For journal names, write out the full name, do not define abbreviations 9% 10% There are some additional historical comments below which may be of interest, 11% particularly in terms of notes about particularly impactful publications using PETSc. 12% 13 14% LiteralHTML: 15% LiteralHTML: <H2><center>Research and Publications that make use of PETSc</center></H2> 16% LiteralHTML: 17% LiteralHTML: <a name="nano"><H3><center>Nano-simulations</center></H3> 18% LiteralHTML: 19@Article{ openblas, 20 title = {OpenBLAS: A High Performance BLAS Library on Loongson 3A CPU}, 21 journal = {Journal of Software}, 22 volume = {22}, 23 pages = {208--216}, 24 year = {2011}, 25 url = {https://www.jos.org.cn/josen/article/abstract/11042}, 26 author = {ZHANG Xian-Yi and WANG Qian and ZHANG Yun-Quan Richard} 27} 28 29@Misc{ openblas-website, 30 title = {{OpenBLAS}}, 31 key = {OpeBLAS}, 32 howpublished = {\url{https://www.openblas.net}} 33} 34 35@Misc{ openacc-website, 36 title = {{OpenACC}}, 37 key = {OpenACC}, 38 howpublished = {\url{https://www.openacc.org}} 39} 40 41@Misc{ bueler2020petsc, 42 title = {PETSc for Partial Differential Equations: Numerical Solutions in C and Python}, 43 author = {Bueler, Ed}, 44 year = {2020}, 45 publisher = {SIAM}, 46 petsc_uses = {KSP} 47} 48 49@TechReport{ petscforgpuexascale, 50 title = {Toward Performance-Portable PETSc for GPU-based Exascale Systems}, 51 author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener 52 and Matthew Knepley and Scott E. Kruger and Hannah~Morgan and Todd Munson and Karl 53 Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang}, 54 institution = {Argonne National Laboratory}, 55 number = {ANL/MCS-P9401-1020}, 56 note = {\url{https://arxiv.org/abs/2011.00715}}, 57 year = {2020}, 58 petsc_uses = {KSP} 59} 60 61@Article{ mills2021, 62 title = {Toward performance-portable {PETS}c for {GPU}-based exascale systems}, 63 journal = {Parallel Computing}, 64 volume = {108}, 65 pages = {102831}, 66 year = {2021}, 67 issn = {0167-8191}, 68 doi = {https://doi.org/10.1016/j.parco.2021.102831}, 69 url = {https://www.sciencedirect.com/science/article/pii/S016781912100079X}, 70 author = {Richard Tran Mills and Mark F. Adams and Satish Balay and Jed Brown and Alp Dener 71 and Matthew Knepley and Scott E. Kruger and Hannah Morgan and Todd Munson and Karl 72 Rupp and Barry F. Smith and Stefano Zampini and Hong Zhang and Junchao Zhang} 73} 74 75@Article{ rupp:2016:pis:2988256.2907944, 76 author = {Karl Rupp and Josef Weinbub and Ansgar J\"{u}ngel and Tibor Grasser}, 77 title = {Pipelined Iterative Solvers with Kernel Fusion for Graphics Processing Units}, 78 journal = {ACM Trans. Math. Softw.}, 79 issue_date = {September 2016}, 80 volume = {43}, 81 number = {2}, 82 month = {Aug}, 83 year = {2016}, 84 issn = {0098-3500}, 85 pages = {11:1--11:27}, 86 articleno = {11}, 87 numpages = {27}, 88 doi = {10.1145/2907944}, 89 acmid = {2907944}, 90 publisher = {ACM}, 91 address = {New York, NY, USA}, 92 keywords = {BiCGStab method, CUDA, GMRES method, GPU, Iterative solvers, OpenCL, conjugate 93 gradient method}, 94 petsc_uses = {KSP} 95} 96 97@Article{ dalcin2011parallel, 98 title = {Parallel distributed computing using python}, 99 author = {Dalcin, Lisandro D and Paz, Rodrigo R and Kler, Pablo A and Cosimo, Alejandro}, 100 journal = {Advances in Water Resources}, 101 volume = {34}, 102 number = {9}, 103 pages = {1124--1139}, 104 year = {2011}, 105 publisher = {Elsevier}, 106 petsc_uses = {KSP} 107} 108 109@Article{ mendezpongaortiz2018, 110 title = {Diffusive molecular dynamics simulations of lithiation of silicon nanopillars}, 111 author = {JP Mendez and M Ponga and M Ortiz}, 112 journal = {Journal of the Mechanics and Physics of Solids}, 113 year = {2018}, 114 petsc_uses = {KSP} 115} 116 117@TechReport{ morgan2020evaluation, 118 title = {Evaluation of {PETS}c on a Heterogeneous Architecture, the {OLCF} {S}ummit 119 System: Part 1: Vector Node Performance}, 120 author = {Morgan, Hannah Mairs and Mills, Richard Tran and Smith, Barry}, 121 year = {2020}, 122 institution = {Argonne National Laboratory}, 123 url = {https://publications.anl.gov/anlpubs/2020/04/159190.pdf}, 124 petsc_uses = {KSP} 125} 126 127@TechReport{ pdeconstrainedspectraladjoints, 128 title = {PDE constrained optimization, error estimation and control with spectral elements 129 using PETSc and TAO}, 130 author = {Oana Marin and Emil Constantinescu and Barry Smith}, 131 type = {Preprint}, 132 number = {ANL/MCS-P9031-1117}, 133 institution = {ANL}, 134 month = {November}, 135 year = {2017}, 136 petsc_uses = {KSP} 137} 138 139@InProceedings{ asc2013, 140 author = {S. Abhyankar and B. F. Smith and E. Constantinescu}, 141 title = {Evaluation of overlapping restricted additive Schwarz preconditioning for 142 parallel solution of very large power flow problems}, 143 booktitle = {HiPCNA-PG’13}, 144 year = {2013}, 145 petsc_uses = {KSP} 146} 147 148@InProceedings{ as2013, 149 author = {S. Abhyankar and B. F. Smith}, 150 title = {{PETSc:} An Advanced Math and Computing Framework for Rapidly Developing Parallel 151 Smart Grid Applications}, 152 booktitle = {Proceedings of the IEEE PES General Meeting}, 153 year = {2013}, 154 petsc_uses = {KSP} 155} 156 157@TechReport{ tspaper, 158 title = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library}, 159 author = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and 160 Barry F. Smith}, 161 type = {Preprint}, 162 number = {ANL/MCS-P5061-0114}, 163 institution = {ANL}, 164 month = {January}, 165 year = {2014}, 166 petsc_uses = {KSP} 167} 168 169@TechReport{ abhyankaretal2018, 170 author = {Shrirang Abhyankar and Jed Brown and Emil M. Constantinescu and Debojyoti Ghosh 171 and Barry F. Smith and Hong Zhang}, 172 title = {{PETSc/TS}: {A} Modern Scalable {ODE/DAE} Solver Library}, 173 journal = {arXiv e-preprints}, 174 eprint = {1806.01437}, 175 archiveprefix = {arXiv}, 176 year = {2018}, 177 petsc_uses = {KSP} 178} 179 180@Article{ zhang2021cams, 181 title = {Optimal checkpointing for adjoint multistage time-stepping schemes}, 182 author = {Hong Zhang and Emil M. Constantinescu}, 183 journal = {arXiv e-preprints}, 184 eprint = {2202.11890}, 185 archiveprefix = {arXiv}, 186 year = {2022}, 187 petsc_uses = {KSP} 188} 189 190@InProceedings{ zhangconstantinescu2021b, 191 title = {Revolve-based adjoint checkpointing for multistage time integration}, 192 author = {Hong Zhang and Emil M. Constantinescu}, 193 booktitle = {Proceedings of the International Conference on Computational Science (ICCS)}, 194 month = {June}, 195 year = {2021}, 196 petsc_uses = {KSP} 197} 198 199@Article{ zhang2022tsadjoint, 200 author = {Zhang, Hong and Constantinescu, Emil M. and Smith, Barry F.}, 201 title = {{PETSc TSAdjoint: A Discrete Adjoint ODE Solver for First-Order and Second-Order 202 Sensitivity Analysis}}, 203 journal = {SIAM Journal on Scientific Computing}, 204 volume = {44}, 205 number = {1}, 206 pages = {C1-C24}, 207 year = {2022}, 208 doi = {10.1137/21M140078X}, 209 petsc_uses = {KSP} 210} 211 212@TechReport{ bb2008, 213 author = {Tomasz Blachowicz and Bartlomiej Baron}, 214 title = {A graphical extension for the Windows version of the Parallel Finite Element 215 Micromagnetics Package (MagParExt)}, 216 url = {http://arxiv.org/abs/0807.2655}, 217 year = {2008}, 218 petsc_uses = {KSP} 219} 220 221@Article{ jacvgv2008, 222 author = {R. Y. Jaafar and A Asenjo and O Chubykalo-Fesenko and M Vazquez and E M Gonzalez 223 and J L Vicent}, 224 title = {Field induced vortex dynamics in magnetic Ni nanotriangles}, 225 journal = {Nanotechnology}, 226 volume = {19}, 227 year = {2008}, 228 doi = {10.1088/0957-4484/19/28/285717}, 229 petsc_uses = {KSP} 230} 231 232@Article{ yjdwh2008, 233 author = {Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He}, 234 title = {Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy}, 235 journal = {Journal of the Magnetics Society of Japan}, 236 volume = {32}, 237 year = {2008}, 238 pages = {50-53}, 239 url = {http://www.jstage.jst.go.jp/article/msjmag/32/2_1/32_50/_article}, 240 petsc_uses = {KSP} 241} 242 243@Article{ mtrtrsa2008, 244 author = {D. Makarov and S. Tibus and C. T. Rettner and T. Thomson and B. D. Terris and T. 245 Schrefl and M. Albrecht}, 246 title = {Magnetic strip patterns induced by focused ion beam irradiation}, 247 journal = {J. Appl. Phys.}, 248 volume = {103}, 249 year = {2008}, 250 doi = {10.1063/1.2894587}, 251 petsc_uses = {KSP} 252} 253 254@InProceedings{ tmrttsa2008, 255 author = {S. Tibus and D. Makarov and C. T. Rettner and T. Thomson and B. D. Terris and T. 256 Schrefl and M. Albrecht}, 257 title = {Patterning of magnetic films by focused ion beam irradiation}, 258 booktitle = {Intermag 2008 paper no. CM-05, submitted to IEEE Trans. Magn.}, 259 year = {2008}, 260 petsc_uses = {KSP} 261} 262 263@Article{ yjdbh2007, 264 author = {Lin Yuan and Jianju Jiang and Yongjiang di and Shaowei Bie and Huahui He}, 265 title = {Micromagnetic simulation of the magnetic dispersion angle and effective damping 266 factor for the single-phase soft magnetic films}, 267 journal = {J. Magn. Magn. Mater.}, 268 volume = {320}, 269 number = {7}, 270 pages = {1393-1397}, 271 doi = {10.1016/j.jmmm.2007.11.025}, 272 petsc_uses = {KSP} 273} 274 275@Article{ lxky2007, 276 author = {DENG Lian-wen and HUANG Xiao-zhong and ZH0U Ke-sheng and YANG}, 277 title = {Micromagnetic simulation and experimental study on microwave permeability of 278 nano-magnetic films}, 279 journal = {Transactions of Nonferrous Metals Society of China}, 280 year = {2007}, 281 pages = {756-759}, 282 url = {http://www.ysxbcn.com/icnfm2007/part2B/s0756.pdf}, 283 petsc_uses = {KSP} 284} 285 286@Article{ yjdwh2008a, 287 author = {Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He}, 288 title = {Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy}, 289 journal = {Journal of the Magnetics Society of Japan}, 290 volume = {32}, 291 year = {2008}, 292 pages = {50-53}, 293 doi = {10.3379/msjmag.32.50}, 294 petsc_uses = {KSP} 295} 296 297@Article{ lylw2007, 298 author = {Ching-Ming Lee and L. X. Ye and J. M. Lee and Te-Ho Wu}, 299 title = {Micromagnetic study of magnetization reversal in patterned DyFeCo thin films}, 300 journal = {Phys. Stat. Sol.}, 301 volume = {204}, 302 number = {12}, 303 pages = {4049-4052}, 304 year = {2007}, 305 doi = {10.1002/pssa.200777359}, 306 petsc_uses = {KSP} 307} 308 309@InProceedings{ sg2007, 310 author = {Simon Greaves}, 311 title = {Micromagnetic Simulations of Magnetic Recording Media}, 312 booktitle = {High Performance Computing on Vector Systems 2007}, 313 doi = {10.1007/978-3-540-74384-2_17}, 314 petsc_uses = {KSP} 315} 316 317@Article{ bsc2007, 318 author = {Nadjib Benatmane and Werner Scholz and T.W. Clinton}, 319 title = {Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings}, 320 journal = {IEEE Trans. Magn.}, 321 volume = {43}, 322 year = {2007}, 323 pages = {2884-2886}, 324 doi = {10.1109/TMAG.2007.892867}, 325 petsc_uses = {KSP} 326} 327 328@Article{ ffbf, 329 author = {T. Fischbacher and M. Franchin and G. Bordignon and H. Fangohr}, 330 title = {A Systematic Approach to Multiphysics Extensions of Finite-Element-Based 331 Micromagnetic Simulations: Nmag.}, 332 journal = {IEEE Trans. Magn. Volume}, 333 volume = {43}, 334 pages = {2896-2898}, 335 doi = {10.1109/TMAG.2007.893843}, 336 petsc_uses = {KSP} 337} 338 339@InBook{ dfssfs2006, 340 author = {R. Dittrich and J. Fidler and D. Suess and W. Schol and H. Forster, T. Schrefl}, 341 chapter = {Computational Aspects of Micromagnetics}, 342 title = {The Science of Hysteresis}, 343 editor = { G. Bertotti and I. Mayergoyz}, 344 url = {http://books.elsevier.com/us/elsevier/us/subindex.asp?maintarget=&isbn=0124808743}, 345 petsc_uses = {KSP} 346} 347 348@InBook{ fss, 349 author = {J. Fidler and T. Schrefl and W. Scholz}, 350 chapter = {Computational Micromagnetics}, 351 title = {Handbook of Theoretical and Computational Nanotechnology}, 352 editor = {M. Rieth and W. Schommers}, 353 url = {http://www.amazon.com/gp/product/158883042X}, 354 petsc_uses = {KSP} 355} 356 357@InBook{ shbsef, 358 author = {Thomas Schrefl and Gino Hrkac and Simon Bance and Dieter Suess and Otmar Ertl and 359 Josef Fidler}, 360 chapter = {Numerical Methods in Micromagnetics (Finite Element Method)}, 361 title = {Handbook of Magnetism and Advanced Magnetic Materials}, 362 editor = {Helmut Kronmueller and Stuart Parkin}, 363 doi = {10.1002/9780470022184.hmm203}, 364 petsc_uses = {KSP} 365} 366 367@InBook{ sfs, 368 author = {D. Suess and J. Fidler and T. Schrefl}, 369 chapter = {Micromagnetic Simulation of magnetic materials}, 370 title = {Handbook of Magnetic Materials}, 371 editor = {K. H. J. Buschow}, 372 url = {http://www.amazon.com/gp/product/0444518509}, 373 petsc_uses = {KSP} 374} 375 376@Article{ fsxzs, 377 author = {J. Fernandez-de-Castro and Xiao Shen and Jianhua Xue and Yuming Zhou and S. 378 Sharma}, 379 title = {Writer Flux Closure and Transition Degradation Mechanism in Perpendicular 380 Recording.}, 381 journal = {IEEE Trans. Magn. Volume}, 382 volume = {43}, 383 pages = {2175-2177}, 384 doi = {10.1109/TMAG.2007.893122}, 385 petsc_uses = {KSP} 386} 387 388@Article{ sb2006, 389 author = {W. Scholz and S. Batra}, 390 title = {Effect of write current waveform on magnetization and head field dynamics of 391 perpendicular recording heads}, 392 journal = {IEEE Trans. Magn.}, 393 volume = {42}, 394 year = {2006}, 395 pages = {2264--2266}, 396 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/ieee/scholz_2006_42_2264.pdf}, 397 petsc_uses = {KSP} 398} 399 400@Article{ bsr2006, 401 author = {S. Batra and W. Scholz and T. Roscamp}, 402 title = {Effect of thermal fluctuation field on the noise performance of a perpendicular 403 recording system}, 404 journal = {J. Appl. Phys.}, 405 volume = {99}, 406 year = {2006}, 407 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 408 petsc_uses = {KSP} 409} 410 411@InProceedings{ japios2006, 412 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 413 Subramanian}, 414 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 415 in systems with cubic and uniaxial anisotropy.}, 416 booktitle = {Intermag 2006 Conference}, 417 petsc_uses = {KSP} 418} 419 420@Article{ kbmb2006, 421 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 422 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 423 Perpendicular Recording Heads}, 424 journal = {IEEE Trans. Magn.}, 425 volume = {42}, 426 year = {2006}, 427 pages = {2428--2430}, 428 doi = {10.1109/TMAG.2006.879430}, 429 petsc_uses = {KSP} 430} 431 432@Article{ cclcw2006, 433 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 434 title = {Control of Domain Wall Motion in Permalloy Ring}, 435 journal = {IEEE Trans. Magn.}, 436 volume = {42}, 437 year = {2006}, 438 pages = {2960--2962}, 439 doi = {10.1109/TMAG.2006.878414}, 440 petsc_uses = {KSP} 441} 442 443@Article{ bfmfzczg2007, 444 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 445 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 446 title = {Micromagnetic modelling of ferromagnetic cones}, 447 journal = {J. Magn. Magn. Mater.}, 448 volume = {312}, 449 year = {2007}, 450 pages = {234-238}, 451 url = {http://eprints.soton.ac.uk/45900/}, 452 petsc_uses = {KSP} 453} 454 455@PhDThesis{ rb2005, 456 author = {Richard Boardman}, 457 title = {Computer simulation studies of magnetic nanostructures}, 458 school = {Computational Engineering and Design Group, School of Engineering Sciences, 459 University of Southampton, United Kingdom}, 460 year = {2005}, 461 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 462 petsc_uses = {KSP} 463} 464 465@InProceedings{ cwwy2006, 466 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 467 title = {MPI Performance Analysis Tools on Blue Gene/L}, 468 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 469 year = {2006}, 470 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 471 petsc_uses = {KSP} 472} 473 474@InProceedings{ ch2006, 475 author = {I.-H. Chung and J.K. Hollingsworth}, 476 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 477 Programs}, 478 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 479 pages = {45--56}, 480 doi = {10.1109/HPDC.2006.1652135}, 481 petsc_uses = {KSP} 482} 483 484@Article{ lkpl2005, 485 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 486 title = {Multibit MRAM using a pair of memory cells}, 487 journal = {IEEE Trans. Magn.}, 488 volume = {41}, 489 year = {2005}, 490 pages = {2670-2672}, 491 doi = {10.1109/TMAG.2005.855288}, 492 petsc_uses = {KSP} 493} 494 495@Article{ gscn2005, 496 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 497 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 498 journal = {Phys. Rev. B}, 499 volume = {71}, 500 year = {2005}, 501 doi = {10.1103/PhysRevB.71.144407}, 502 petsc_uses = {KSP} 503} 504 505@PhDThesis{ mda, 506 author = {Massimiliano d'Aquino}, 507 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 508 school = { Universita di Napoli Federico II.}, 509 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 510 petsc_uses = {KSP} 511} 512 513@TechReport{ ssdfssf2003, 514 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 515 Stehno and J. Fidler}, 516 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 517 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 518 petsc_uses = {KSP} 519} 520 521@InProceedings{ sb2006a, 522 author = {W. Scholz and S. Batra}, 523 title = {Effect of write current waveform on magnetization and head field dynamics of 524 perpendicular recording heads}, 525 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 526 petsc_uses = {KSP} 527} 528 529@Article{ scholz-batra1, 530 author = {W. Scholz and S. Batra}, 531 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 532 Recording}, 533 journal = {IEEE Trans. Magn.}, 534 note = {submitted}, 535 year = {2005}, 536 petsc_uses = {KSP} 537} 538 539@Article{ scholz-batra2, 540 author = {W. Scholz and S. Batra}, 541 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 542 journal = {IEEE Trans. Magn.}, 543 volume = {41}, 544 year = {2005}, 545 pages = {702-706}, 546 petsc_uses = {KSP} 547} 548 549@Article{ daquino-scholz1, 550 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 551 title = {Micromagnetic Analysis of Fast Precessional Switching}, 552 journal = {J. Magn. Magn. Mater.}, 553 volume = {290-291}, 554 year = {2005}, 555 pages = {510-513}, 556 petsc_uses = {KSP} 557} 558 559@Article{ aq-scholz-fid, 560 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 561 title = {Numerical and analytical study of fast precessional switching}, 562 journal = {J. Appl. Phys.}, 563 volume = {95}, 564 year = {2004}, 565 pages = {7055-7057}, 566 petsc_uses = {KSP} 567} 568 569@InProceedings{ gar-tabik-gar, 570 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 571 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 572 Scatterers}, 573 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 574 (PDP'04)}, 575 year = {2004}, 576 pages = {80--}, 577 petsc_uses = {KSP} 578} 579 580@InProceedings{ aq-scholz-mia, 581 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 582 title = {Analysis of fast precessional switching in magnetic thin films}, 583 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 584 year = {2004}, 585 pages = {257-260}, 586 petsc_uses = {KSP} 587} 588 589@Article{ scholz-fid-seus, 590 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 591 Dittrich and V. Tsiantos}, 592 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 593 Axes}, 594 journal = {J. Magn. Magn. Mater.}, 595 year = {2004}, 596 pages = {1524-1525}, 597 petsc_uses = {KSP} 598} 599 600@Article{ boardman-zimmerman, 601 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 602 Peter de Groot}, 603 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 604 journal = {Journal of Applied Physics}, 605 year = {2005}, 606 petsc_uses = {KSP} 607} 608 609@Article{ lim-kim-park, 610 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 611 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 612 journal = {IEEE Trans. Magn.}, 613 note = {submitted}, 614 petsc_uses = {KSP} 615} 616 617@Article{ scholz-suess2, 618 author = {W. Scholz and D. Suess and T. Schrefl and and J. Fidler}, 619 title = {Micromagnetic simulation of magnetization reversal in small particles with 620 surface anisotropy}, 621 journal = {J. Appl. Phys.}, 622 volume = {95}, 623 year = {2004}, 624 pages = {6807-6809}, 625 petsc_uses = {KSP} 626} 627 628@Article{ scholz-schrefl1, 629 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 630 Tsiantos}, 631 title = {Micromagnetic simulation of the pinning and depinning process in permanent 632 magnets}, 633 journal = {IEEE Trans. Magn.}, 634 volume = {39}, 635 year = {2003}, 636 pages = {2920-2922}, 637 petsc_uses = {KSP} 638} 639 640@Article{ scholz-guslienko, 641 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 642 W. Chantrell and J. Fidler}, 643 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 644 nanodots}, 645 journal = {J. Magn. Magn. Mater.}, 646 volume = {266}, 647 year = {2003}, 648 pages = {155-163}, 649 petsc_uses = {KSP} 650} 651 652@Article{ scholz1, 653 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 654 Forster and V. Tsiantos}, 655 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 656 journal = {Comp. Mat. Sci}, 657 year = {2003}, 658 pages = {366--383}, 659 volume = {28}, 660 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 661 petsc_uses = {KSP} 662} 663 664@PhDThesis{ scholz2, 665 author = {W. Scholz}, 666 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 667 school = {Vienna University of Technology, Vienna, Austria}, 668 year = {2003}, 669 petsc_uses = {KSP} 670} 671 672@Article{ scholz3, 673 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 674 Forster and J. Fidler}, 675 title = {Implementation of a high performance parallel finite element micromagnetics 676 package}, 677 journal = {J. Magn. Magn. Mater.}, 678 year = {2004}, 679 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 680 petsc_uses = {KSP} 681} 682 683% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 684@InBook{ zhanggladwell1, 685 author = {W. Zhang and I. Gladwell}, 686 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 687 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 688 year = {2000}, 689 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 690 Physics, vol. 552}, 691 publisher = {Springer}, 692 pages = {4190-}, 693 petsc_uses = {KSP} 694} 695 696@Article{ wolf1, 697 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 698 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 699 thin films}, 700 journal = {Phil. Mag. A}, 701 year = {2003}, 702 lab = {ANL}, 703 petsc_uses = {KSP} 704} 705 706@Article{ wolf2, 707 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 708 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 709 grain-boundary properties}, 710 journal = {Computational Materials Science}, 711 year = {2001}, 712 volume = {23}, 713 pages = {15--32}, 714 lab = {ANL}, 715 petsc_uses = {KSP} 716} 717 718@Article{ wolf3, 719 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 720 title = {Role of grain rotation in grain growth by mesoscale simulation}, 721 journal = {Phil. Mag. A}, 722 year = {2002}, 723 volume = {82}, 724 pages = {1271--1297}, 725 lab = {ANL}, 726 petsc_uses = {KSP} 727} 728 729% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 730@Article{ saut, 731 author = { Olivier Saut}, 732 title = {Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal}, 733 journal = {SIAM Journal on Scientific Computing}, 734 year = {2004}, 735 note = {submitted}, 736 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 737 petsc_uses = {KSP} 738} 739 740% LiteralHTML: 741% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 742% LiteralHTML: 743@InBook{ khanallorenziayachepennec2016, 744 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 745 of Brain Deformation in {Alzheimer's} Disease}, 746 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 747 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 748 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 749 Miller}, 750 pages = {167--176}, 751 isbn = {978-3-319-28329-6}, 752 doi = {10.1007/978-3-319-28329-6_15}, 753 publisher = {Springer International Publishing}, 754 year = {2016}, 755 petsc_uses = {KSP} 756} 757 758@Article{ ataseven, 759 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 760 title = {Parallel implementation of the accelerated BEM approach for EMSI of the human 761 brain}, 762 journal = {Medical and Biological Engineering and Computing}, 763 month = {February}, 764 year = {2008}, 765 doi = {10.1007/s11517-008-0316-0}, 766 petsc_uses = {KSP} 767} 768 769@Article{ dennis-eberhart-03, 770 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 771 pages = {832-840}, 772 volume = {125}, 773 number = {6}, 774 title = {Finite-element simulation of cooling of realistic 3-D human head and neck}, 775 journal = {J Biomech Eng}, 776 year = {2003}, 777 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 778 petsc_uses = {KSP} 779} 780 781@Conference{ gu7174parallel, 782 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 783 frequency-domain small animal optical tomography}}, 784 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 785 booktitle = {Proc. of SPIE Vol}, 786 volume = {7174}, 787 number = {717406}, 788 pages = {1}, 789 petsc_uses = {KSP} 790} 791 792@Article{ barchanski2005using, 793 title = {{Using domain decomposition techniques for the calculation of low-frequency 794 electric current densities in high-resolution 3D human anatomy models}}, 795 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 796 T.}, 797 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 798 and Electronic Engineering}, 799 volume = {24}, 800 number = {2}, 801 pages = {458--467}, 802 issn = {0332-1649}, 803 year = {2005}, 804 publisher = {Emerald Group Publishing Limited}, 805 petsc_uses = {KSP} 806} 807 808@Article{ motrescurienen05, 809 author = {V. C. Motrescu and U. van Rienen}, 810 pages = {227--231}, 811 volume = {3}, 812 title = {Computation of currents induced by ELF electric fields in anisotropic human 813 tissues using the Finite Integration Technique}, 814 journal = {Advances in Radio Science}, 815 year = {2005}, 816 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 817 petsc_uses = {KSP} 818} 819 820@Article{ motrescurienen04, 821 author = {V. C. Motrescu and U. van Rienen}, 822 pages = {309--313}, 823 volume = {2}, 824 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 825 Integration Technique (FIT)}, 826 journal = {Advances in Radio Science}, 827 year = {2004}, 828 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 829 petsc_uses = {KSP} 830} 831 832@InProceedings{ dbl2, 833 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 834 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 835 booktitle = {ECCOMAS2000}, 836 year = {2000}, 837 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 838 petsc_uses = {KSP} 839} 840 841@Unpublished{ cell, 842 title = {Parallel Simulation Engines for Whole-Cell Models}, 843 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 844 Weber}, 845 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 846 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 847 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 848 year = {2001}, 849 petsc_uses = {KSP} 850} 851 852@Article{ barker2010two, 853 title = {Two-level Newton and hybrid Schwarz preconditioners for fluid-structure 854 interaction}, 855 author = {Barker, A.T. and Cai, X.C.}, 856 journal = {SIAM Journal on Scientific Computing}, 857 volume = {32}, 858 number = {4}, 859 pages = {2395--2417}, 860 year = {2010}, 861 publisher = {Society for Industrial and Applied Mathematics}, 862 petsc_uses = {KSP} 863} 864 865@Article{ barker2010scalable, 866 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 867 with application to blood flow modeling}, 868 author = {Barker, A.T. and Cai, X.C.}, 869 journal = {Journal of Computational Physics}, 870 volume = {229}, 871 number = {3}, 872 pages = {642--659}, 873 year = {2010}, 874 publisher = {Elsevier}, 875 petsc_uses = {KSP} 876} 877 878@Article{ barker2009nks, 879 title = {NKS for fully coupled fluid-structure interaction with application}, 880 author = {Barker, A.T. and Cai, X.C.}, 881 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 882 pages = {275--282}, 883 year = {2009}, 884 publisher = {Springer}, 885 petsc_uses = {KSP} 886} 887 888@Article{ mirams2013, 889 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 890 and Yi Cui and Gary R Mirams}, 891 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 892 to predict QT interval changes in the rabbit ventricular wedge}, 893 journal = {Journal of pharmacological and toxicological methods}, 894 volume = {68}, 895 number = {1}, 896 pages = {88--96}, 897 year = {2013}, 898 doi = {10.1016/j.vascn.2013.04.004}, 899 petsc_uses = {KSP} 900} 901 902% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 903% LiteralHTML: <center><img alt="" 904% LiteralHTML: src="images/spine0l.jpg"></center></p> 905% LiteralHTML: <center><img alt="" 906% LiteralHTML: src="images/vertebra.jpg"></center></p> 907% LiteralHTML:<font color="#FF0000"> 908% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 909% LiteralHTML:Understanding bone mechanical properties and how they may lead to 910% LiteralHTML:fractures is thus an important medical research activity. PETSc and 911% LiteralHTML:Prometheus have been used for extremely large scale finite element 912% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 913% LiteralHTML:team of doctors and computational scientists. This computation was 914% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 915% LiteralHTML:with over 4000 processors.</p> 916% LiteralHTML: </font> 917@Article{ arbenz2008scalable, 918 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 919 analysis of human bone structures}, 920 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 921 journal = {International Journal for Numerical Methods in Engineering}, 922 volume = {73}, 923 number = {7}, 924 pages = {927--947}, 925 year = {2008}, 926 publisher = {Wiley Online Library}, 927 petsc_uses = {KSP} 928} 929 930@InProceedings{ adams-04, 931 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 932 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 933 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 934 half a billion degrees of freedom}, 935 note = {Gordon Bell Award}, 936 year = {2004}, 937 petsc_uses = {KSP} 938} 939 940@InProceedings{ adams-03b, 941 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 942 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 943 Whole Bone Micro-Mechanics on the IBM SP}, 944 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 945 year = {2003}, 946 petsc_uses = {KSP} 947} 948 949@InProceedings{ oghattas2002, 950 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 951 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 952 booktitle = {Procceedings of SC2002}, 953 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 954 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 955 by time-dependent PDEs, and scalability results for an inverse wave propagation 956 problem of determining the material field of an acoustic medium. Using the 957 algorithm, they solved a synthetic inverse wave propagation problem though a 958 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 959 processors.}, 960 year = {2002}, 961 petsc_uses = {KSP} 962} 963 964% LiteralHTML: <a name="biology:cardiology"> 965% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 966% LiteralHTML: <center><img alt="" 967% LiteralHTML: src="images/heart.jpg"> 968% LiteralHTML: <img alt="" 969% LiteralHTML: src="images/pump.jpg"></center></p> 970% LiteralHTML: 971% LiteralHTML:<font color="#FF0000"> 972% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 973% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 974% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 975% LiteralHTML: through the heart. PETSc has been used by several research groups to 976% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 977% LiteralHTML: fully understand the developments of arrhthmias.</p> 978% LiteralHTML:</font> 979@InProceedings{ oghattas2000, 980 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 981 Walkington}, 982 title = {A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic 983 Interfaces}, 984 booktitle = {Procceedings of SC2000}, 985 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 986 note = {Blood flow modeling at the microscale including effects on individual blood 987 cells, for designing heart assist pumps, etc.}, 988 year = {2000}, 989 petsc_uses = {KSP} 990} 991 992@InBook{ cfps2006, 993 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 994 editor = {A. Quarteroni et al.}, 995 title = {Complex Systems in Biomedicine}, 996 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 997 publisher = {Springer-Verlag}, 998 pages = {187--241}, 999 year = {2006}, 1000 petsc_uses = {KSP} 1001} 1002 1003@InProceedings{ cfpst2007, 1004 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 1005 title = {Determining recovery times from transmembrane action potentials and unipolar 1006 electrograms in normal heart tissue}, 1007 booktitle = {FIMH07}, 1008 publisher = {Springer-Verlag}, 1009 volume = {4466}, 1010 pages = {139--149}, 1011 year = {2007}, 1012 petsc_uses = {KSP} 1013} 1014 1015@Article{ seemann2010framework, 1016 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 1017 Equations Using PETSc}}, 1018 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 1019 D{\\"o}ssel, O.}, 1020 journal = {Progress in Industrial Mathematics at ECMI 2008}, 1021 pages = {363--369}, 1022 year = {2010}, 1023 publisher = {Springer}, 1024 petsc_uses = {KSP} 1025} 1026 1027@InProceedings{ pft2005, 1028 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 1029 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 1030 Intramural Heterogeneity}, 1031 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 1032 pages = {267--277}, 1033 editors = {A. Frangi et al.}, 1034 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 1035 year = {2005}, 1036 petsc_uses = {KSP} 1037} 1038 1039@Article{ bgcp2005, 1040 author = {Boyce E. Griffith and Charles S. Peskin}, 1041 title = {On the order of accuracy of the immersed boundary method: Higher order 1042 convergence rates for sufficiently smooth problems}, 1043 journal = {Journal of Computational Physics}, 1044 year = {2005}, 1045 volume = {208}, 1046 pages = {75--105}, 1047 petsc_uses = {KSP} 1048} 1049 1050@Article{ griffith2007adaptive, 1051 title = {An adaptive, formally second order accurate version of the immersed boundary 1052 method}, 1053 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 1054 journal = {Journal of Computational Physics}, 1055 volume = {223}, 1056 number = {1}, 1057 pages = {10--49}, 1058 year = {2007}, 1059 publisher = {Elsevier}, 1060 petsc_uses = {KSP} 1061} 1062 1063@PhDThesis{ griffith05, 1064 author = {Boyce Griffith}, 1065 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 1066 parallel version of the immersed boundary method}, 1067 school = {New York University}, 1068 year = {2005}, 1069 petsc_uses = {KSP} 1070} 1071 1072@PhDThesis{ murillo, 1073 author = {Maria S. Murillo}, 1074 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 1075 Differential Equations with an Application in Computational Biology}, 1076 school = {University of Colorado at Boulder}, 1077 year = {2002}, 1078 petsc_uses = {KSP} 1079} 1080 1081@Article{ spv2004, 1082 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 1083 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 1084 journal = {IEEE Trans. Biomed. Eng}, 1085 year = {2004}, 1086 volume = {51}, 1087 pages = {1960--1968}, 1088 petsc_uses = {KSP} 1089} 1090 1091@Article{ vphl2003, 1092 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 1093 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 1094 journal = {J. Electrocardiol.}, 1095 year = {2003}, 1096 volume = {36}, 1097 pages = {69--74}, 1098 petsc_uses = {KSP} 1099} 1100 1101@InProceedings{ spbv2003, 1102 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and and E.J. Vigmond}, 1103 title = {Preconditioning Techniques for the Bidomain Equations}, 1104 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 1105 Methods}, 1106 pages = {571--580}, 1107 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 1108 note = {}, 1109 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 1110 year = {2003}, 1111 petsc_uses = {KSP} 1112} 1113 1114@Article{ franz-pavir-04, 1115 author = {P. Colli Franzone and L.~F. Pavarino}, 1116 title = {A parallel solver for reaction-diffusion systems in computational 1117 electrocardiology}, 1118 journal = {Mathematical Models and Methods in Applied Sciences}, 1119 year = {2004}, 1120 volume = {14}, 1121 number = {6}, 1122 pages = {883--912}, 1123 petsc_uses = {KSP} 1124} 1125 1126@Article{ franz-pavir-05, 1127 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 1128 title = {Simulating patterns of excitation, repolarization and action potential 1129 durationwith cardiac Bidomain and Monodomain models}, 1130 journal = {Mathematical Biosciences}, 1131 year = {2005}, 1132 volume = {197}, 1133 number = {1}, 1134 pages = {35--66}, 1135 petsc_uses = {KSP} 1136} 1137 1138@Article{ franz-pavir-06, 1139 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 1140 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 1141 the dispersion of cardiac repolarization and action potential duration: a 1142 simulation study}, 1143 journal = {Mathematical Biosciences}, 1144 year = {2006}, 1145 volume = {204}, 1146 number = {1}, 1147 pages = {132--165}, 1148 petsc_uses = {KSP} 1149} 1150 1151@InProceedings{ colli-franz-sim, 1152 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 1153 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 1154 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 1155 Mediterranean Conference on Medical and Biological Engineering}, 1156 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 1157 year = {2004}, 1158 petsc_uses = {KSP} 1159} 1160 1161@InProceedings{ pf2003, 1162 author = {Luca F. Pavarino and Piero Colli Franzone}, 1163 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 1164 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 1165 Methods}, 1166 pages = {669--776}, 1167 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 1168 note = {}, 1169 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 1170 year = {2003}, 1171 petsc_uses = {KSP} 1172} 1173 1174@Article{ maria-is04, 1175 author = {Maria Murillo and Xiao-Chuan Cai}, 1176 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 1177 activity of the heart}, 1178 journal = {Numerical Linear Algebra with Applications}, 1179 year = {2004}, 1180 volume = {11}, 1181 pages = {261 - 277}, 1182 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 1183 petsc_uses = {KSP} 1184} 1185 1186@Article{ murli2007monitoring, 1187 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 1188 Imaging in a Grid computing PSE}}, 1189 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 1190 and Lapegna, M.}, 1191 journal = {Grid-Based Problem Solving Environments}, 1192 pages = {421--432}, 1193 year = {2007}, 1194 publisher = {Springer}, 1195 petsc_uses = {KSP} 1196} 1197 1198@Article{ carracciuolo:2006:tpc, 1199 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 1200 title = {Towards a parallel component for imaging in PETSc programming environment: a case 1201 study in 3-D echocardiography}, 1202 journal = {Parallel Comput.}, 1203 volume = {32}, 1204 issue = {1}, 1205 month = {January}, 1206 year = {2006}, 1207 issn = {0167-8191}, 1208 pages = {67--83}, 1209 numpages = {17}, 1210 doi = {10.1016/j.parco.2005.09.001}, 1211 acmid = {1141218}, 1212 publisher = {Elsevier Science Publishers B. V.}, 1213 address = {Amsterdam, The Netherlands, The Netherlands}, 1214 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 1215 component}, 1216 petsc_uses = {KSP} 1217} 1218 1219@Article{ damore2011integration, 1220 title = {Integration of emerging computer technologies for an efficient image sequences 1221 analysis}, 1222 journal = {Integrated Computer-Aided Engineering }, 1223 volume = {18}, 1224 number = {4}, 1225 pages = {365 - 378}, 1226 year = {2011}, 1227 note = {}, 1228 issn = {1875-8835}, 1229 doi = {10.3233/ICA-2011-0382}, 1230 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 1231 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 1232 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 1233 petsc_uses = {KSP} 1234} 1235 1236@InProceedings{ eth_biwi_00721, 1237 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and and G. 1238 Székely}, 1239 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 1240 a Schur Complement Preconditioner}, 1241 booktitle = {Euro-Par 2009 Parallel Processing}, 1242 year = {2009}, 1243 month = {August}, 1244 pages = {747-759}, 1245 volume = {5704}, 1246 editor = {H. Sips and D. Epema and and H.-X. Lin}, 1247 series = {Lecture Notes in Computer Science}, 1248 publisher = {Springer}, 1249 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 1250 parallel Krylov solver}, 1251 petsc_uses = {KSP} 1252} 1253 1254% LiteralHTML: <a name="biology:imagingandsurgery"> 1255% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1256% LiteralHTML: <center><img alt="" 1257% LiteralHTML: src="images/brain.jpg"></center> 1258@Article{ ganser2004deformable, 1259 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 1260 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 1261 journal = {Medical Image Analysis}, 1262 volume = {8}, 1263 number = {1}, 1264 pages = {3--22}, 1265 year = {2004}, 1266 publisher = {Elsevier}, 1267 petsc_uses = {KSP} 1268} 1269 1270@Unpublished{ taccsurgery, 1271 title = {TACC supercomputer performs laser cancer surgery on canine}, 1272 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 1273 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 1274 Austin performed laser surgery on a dog in Houston without the intervention of a 1275 surgeon. The treatment was developed collaboratively by computational experts from 1276 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 1277 leading technologists from the M.D. Anderson Cancer Center in Houston, and 1278 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 1279 state-of-the-art thermal imaging technology, and advanced computational methods, 1280 dynamic, data-driven treatments are being pursued as a minimally invasive 1281 alternative to the standard treatment of cancer.}, 1282 petsc_uses = {KSP} 1283} 1284 1285@Article{ ffhbresso2008, 1286 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 1287 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 1288 Tinsley Oden}, 1289 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 1290 journal = {Engineering with Computers}, 1291 note = {Special issue on Computational Bioengineering}, 1292 year = {2008}, 1293 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 1294 petsc_uses = {KSP} 1295} 1296 1297@TechReport{ dobbhbbbdeffghkkps2008, 1298 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 1299 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 1300 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 1301 and S. Prudhomme and R. J. Stafford}, 1302 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 1303 Cancer}, 1304 year = {2008}, 1305 institution = {University of Texas at Austin}, 1306 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 1307 petsc_uses = {KSP} 1308} 1309 1310@Article{ ogdb2004, 1311 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 1312 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 1313 journal = {Physics in Medicine and Biology}, 1314 year = {2004}, 1315 volume = {49}, 1316 pages = {2955--2947}, 1317 petsc_uses = {KSP} 1318} 1319 1320@InProceedings{ majumdar11, 1321 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 1322 Baldridge and P. Krysl}, 1323 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 1324 booktitle = {ICCS 2005}, 1325 pages = {672--679}, 1326 editor = {V.S. Sunderam et al.}, 1327 year = {2005}, 1328 petsc_uses = {KSP} 1329} 1330 1331@Conference{ sermesant-etal:03, 1332 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 1333 Ayache, H.}, 1334 title = {A parallel implementation of non-rigid registration using a volumetric 1335 biomechanical model}, 1336 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 1337 address = {Philadelphia, PA, USA}, 1338 publisher = {Springer-Verlag}, 1339 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 1340 series = {Lecture Notes in Computer Science}, 1341 volume = {2717}, 1342 pages = {398-407}, 1343 date = {june 23-24}, 1344 year = {2003}, 1345 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 1346 petsc_uses = {KSP} 1347} 1348 1349@Conference{ sermesant-etal:04, 1350 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 1351 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 1352 title = {A Novel Nonrigid Registration Algorithm And Applications}, 1353 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 1354 address = {Philadelphia, PA, USA}, 1355 publisher = {Springer-Verlag}, 1356 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 1357 series = {Lecture Notes in Computer Science}, 1358 volume = {2208}, 1359 pages = {923}, 1360 year = {2003}, 1361 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 1362 petsc_uses = {KSP} 1363} 1364 1365@Article{ warfield-haker-talos-05, 1366 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 1367 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 1368 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 1369 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 1370 title = {Capturing intraoperative deformations: research experience at Brigham and Women's 1371 hospital}, 1372 journal = {Medical Image Analysis}, 1373 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 1374 year = {2005}, 1375 petsc_uses = {KSP} 1376} 1377 1378@Article{ brain3, 1379 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 1380 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 1381 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 1382 Deformation during Image Guided Neurosurgery}, 1383 journal = {Computing and Visualization in Science}, 1384 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 1385 year = {2002}, 1386 petsc_uses = {KSP} 1387} 1388 1389@Article{ brain2, 1390 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 1391 Kikinis and Simon K. Warfield}, 1392 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 1393 Element Biomechanical Model}, 1394 journal = {IEEE Transactions on Medical Imaging}, 1395 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 1396 year = {2001}, 1397 petsc_uses = {KSP} 1398} 1399 1400@InProceedings{ brain1, 1401 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 1402 Ferenc A. Jolesz and Ron Kikinis}, 1403 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 1404 Guided Neurosurgery}, 1405 booktitle = {Proceedings of SC2000}, 1406 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 1407 year = {2000}, 1408 petsc_uses = {KSP} 1409} 1410 1411@Article{ vanne06, 1412 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 1413 M. Lassas and M. Kalke}, 1414 title = {Parallelized Bayesian inversion for three-dimensional dental X-ray imaging}, 1415 journal = {IEEE Transactions on Medical Imaging}, 1416 volume = {25}, 1417 number = {2}, 1418 month = {February}, 1419 year = {2006}, 1420 pages = {218--228}, 1421 petsc_uses = {KSP} 1422} 1423 1424@InProceedings{ knepleybardhan2015, 1425 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 1426 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 1427 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 1428 Exposition}, 1429 volume = {9}, 1430 pages = {V009T12A04}, 1431 doi = {10.1115/IMECE2015-53579}, 1432 year = {2015}, 1433 petsc_uses = {KSP} 1434} 1435 1436@InProceedings{ bardhanknepley2015, 1437 title = {Multiscale models and approximation algorithms for protein electrostatics}, 1438 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 1439 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 1440 volume = {61}, 1441 pages = {163--174}, 1442 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 1443 doi = {10.2495/BEM380131}, 1444 publisher = {WIT Press}, 1445 year = {2015}, 1446 petsc_uses = {KSP} 1447} 1448 1449% LiteralHTML: 1450% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 1451% LiteralHTML: 1452@InProceedings{ adamsbrennanknepleywang2022, 1453 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 1454 quench plasmas}, 1455 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 1456 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 1457 (IPDPS '22)}, 1458 doi = {10.1109/IPDPS53621.2022.00020}, 1459 year = {2022}, 1460 petsc_uses = {DMPlex} 1461} 1462 1463@Misc{ adamsknepleybrennan2021, 1464 title = {Runaway Electron Generation with High-Performance, Structure Preserving 1465 Discretization of Fokker-Plank-Landau}, 1466 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 1467 year = {2021}, 1468 petsc_uses = {KSP} 1469} 1470 1471@Article{ adamshirvijokiknepleybrownisaacmills2017, 1472 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 1473 Architectures}, 1474 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 1475 Isaac and Richard Mills}, 1476 journal = {SIAM Journal on Scientific Computing}, 1477 volume = {39}, 1478 number = {6}, 1479 pages = {C452--C465}, 1480 doi = {10.1137/17M1118828}, 1481 eprint = {1702.08880}, 1482 year = {2017}, 1483 petsc_uses = {KSP} 1484} 1485 1486@Article{ pusztayknepleyadams2022, 1487 title = {Conservative Projection Between FEM and Particle Bases}, 1488 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 1489 journal = {SIAM Journal on Scientific Computing}, 1490 volume = {44}, 1491 number = {4}, 1492 pages = {C310--C319}, 1493 doi = {10.1137/21M145407}, 1494 year = {2022} 1495} 1496 1497@Article{ hirvijoki2017, 1498 author = {Eero Hirvijoki and Mark F. Adams}, 1499 title = {Conservative discretization of the {Landau} collision integral}, 1500 journal = {Physics of Plasmas}, 1501 volume = {24}, 1502 number = {3}, 1503 pages = {032121}, 1504 doi = {10.1063/1.4979122}, 1505 year = {2017}, 1506 petsc_uses = {KSP} 1507} 1508 1509@Article{ mollenadamsknepleyhagerchang2021, 1510 title = {Implementation of higher-order velocity mapping between marker particles and grid 1511 in the particle-in-cell code XGC}, 1512 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 1513 S. Chang}, 1514 journal = {Journal of Plasma Physics}, 1515 eprint = {2012.11764}, 1516 doi = {10.1017/S0022377821000441}, 1517 year = {2021}, 1518 petsc_uses = {KSP} 1519} 1520 1521@Article{ lsmh2014, 1522 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 1523 title = {Comparison of particle trajectories and collision operators for collisional 1524 transport in nonaxisymmetric plasmas}, 1525 journal = { Physics of Plasmas}, 1526 volume = {21}, 1527 year = {2014}, 1528 petsc_uses = {KSP} 1529} 1530 1531@Article{ lpcep2014, 1532 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 1533 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 1534 pedestal}, 1535 journal = {Plasma Physics and Controlled Fusion}, 1536 volume = {56}, 1537 year = {2014}, 1538 petsc_uses = {KSP} 1539} 1540 1541@Article{ facets-scidac08, 1542 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 1543 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 1544 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 1545 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 1546 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 1547 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 1548 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 1549 Stotler and A. Pigarov}, 1550 journal = {J. Phys.: Conf. Ser.}, 1551 volume = {125}, 1552 year = {2008}, 1553 pages = {012040}, 1554 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 1555 petsc_uses = {KSP} 1556} 1557 1558@Article{ facets-scidac09, 1559 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 1560 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 1561 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 1562 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 1563 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 1564 and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar 1565 and A. Pigarov and H. Zhang}, 1566 journal = {J. Phys.: Conf. Ser.}, 1567 volume = {180}, 1568 year = {2009}, 1569 pages = {012056}, 1570 url = {http://iopscience.iop.org/1742-6596/180/1/012056}, 1571 petsc_uses = {KSP} 1572} 1573 1574@InProceedings{ facets-scidac10, 1575 title = {Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the 1576 {FACETS} Code}, 1577 author = {A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. 1578 Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. 1579 Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. 1580 Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. 1581 Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. 1582 Pigarov and H. Zhang}, 1583 booktitle = {Proceedings of SciDAC 2010 Conference}, 1584 year = {2010}, 1585 url = {http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf}, 1586 petsc_uses = {KSP} 1587} 1588 1589@InProceedings{ facets-fec2010, 1590 title = {Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using 1591 the {FACETS} Framework}, 1592 author = {J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina 1593 and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. 1594 McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang}, 1595 booktitle = {Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, 1596 Republic of Korea}, 1597 year = {2010}, 1598 petsc_uses = {KSP} 1599} 1600 1601@InProceedings{ facets-epdp2010, 1602 title = {{FACETS}: A Framework for Parallel Coupling of Fusion Components}, 1603 author = {J. Cary and A. Hakim and M. Miah and S. Kruger and A. Pletzer and S. Shasharina 1604 and S. Vadlamani and A. Pankin and R. Cohen and T. Epperly and T. Rognlien and R. 1605 Groebner and S. Balay and L. McInnes and H. Zhang}, 1606 booktitle = {Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on 1607 Parallel, Distributed and Network-Based Computing), Pisa, Italy}, 1608 year = {2010}, 1609 petsc_uses = {KSP} 1610} 1611 1612@Article{ carlssoncary09, 1613 author = {Johan Carlsson, John R. Cary}, 1614 title = {The hypersecant Jacobian approximation for quasi-Newton solves of sparse 1615 nonlinear systems}, 1616 journal = {arXiv}, 1617 year = {2009}, 1618 note = {http://arxiv.org/abs/0905.1054}, 1619 url = {http://arxiv.org/pdf/0905.1054v1}, 1620 petsc_uses = {KSP} 1621} 1622 1623@InProceedings{ oshahjs2006, 1624 author = {F. Ogando and A. Signell and J.A. Heikkinen and M. Aspn\"as and S. Henriksson and 1625 S.J. Janhunen and T.P. Kiviniemi}, 1626 title = {Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of 1627 application}, 1628 booktitle = {33rd EPS Conference on Plasma Phys.}, 1629 year = {2006}, 1630 url = {http://epsppd.epfl.ch/Roma/pdf/P4_153.pdf}, 1631 note = {European fusion code}, 1632 petsc_uses = {KSP} 1633} 1634 1635@Article{ zhu2006, 1636 author = {P. Zhu and A. Bhattacharjee and K. Germaschewski}, 1637 title = {Intermediate nonlinear evolution of the Parker instability: Formation of 1638 convection-induced discontinuities and absence of finite-time singularities}, 1639 journal = {Phys. Rev. Lett.}, 1640 volume = {96}, 1641 number = {065001}, 1642 year = {2006}, 1643 doi = {10.1103/PhysRevLett.96.065001}, 1644 petsc_uses = {KSP} 1645} 1646 1647@InProceedings{ ppc2005, 1648 author = {B. Philip and M. Pernice and L.Chacon}, 1649 title = {Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh 1650 Refinement}, 1651 booktitle = {Proceedings of the 16th International Conference on Domain Decomposition 1652 methods}, 1653 year = {2005}, 1654 lab = {LANL}, 1655 petsc_uses = {KSP} 1656} 1657 1658@Article{ pp2005, 1659 author = {M. Pernice and B. Philip}, 1660 title = {Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh 1661 Refinement}, 1662 year = {2005}, 1663 journal = {SIAM J. of Sci. Comput.}, 1664 lab = {LANL}, 1665 petsc_uses = {KSP} 1666} 1667 1668@Article{ gt2004, 1669 author = {A. H. Glasser and X. Z. Tang}, 1670 title = {The SEL macroscopic modeling code}, 1671 year = {2004}, 1672 journal = {Computer Physics Communications}, 1673 pages = {237--243}, 1674 volume = {164}, 1675 lab = {LANL}, 1676 petsc_uses = {KSP} 1677} 1678 1679@Article{ nl2006, 1680 author = {Y. Nishimura and Z.Lin}, 1681 title = {A finite element mesh in a tokamak edge geometry}, 1682 year = {2006}, 1683 journal = {Contributions to Plasma Physics}, 1684 volume = {22}, 1685 lab = {PPPL}, 1686 petsc_uses = {KSP} 1687} 1688 1689@Article{ nlle2004, 1690 author = {Y. Nishimura and Z.Lin and J.Lewandowski and S.Ethier}, 1691 title = {A finite element Poisson solver for gyrokinetic particle simulations in a global 1692 field aligned mesh}, 1693 year = {2006}, 1694 journal = {J. Comput. Phys.}, 1695 volume = {214}, 1696 pages = {657}, 1697 lab = {PPPL}, 1698 petsc_uses = {KSP} 1699} 1700 1701@InProceedings{ lnlle2004, 1702 author = {J.L.V Lewandowski and Y.Nishimura and W.W.Lee and Z.Lin and S. Ethier}, 1703 title = {Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons}, 1704 booktitle = {Sherwood Fusion Theory Conference, Missoula, MT}, 1705 year = {2004}, 1706 url = {http://www.sherwoodtheory.org/sherwood04/program/1e15.pdf}, 1707 lab = {PPPL}, 1708 petsc_uses = {KSP} 1709} 1710 1711@InProceedings{ nlclew2004, 1712 author = {Y. Nishimura and Z.Lin and L.Chen and J.Lewandowski and S.Ethier and W. Wang}, 1713 title = {Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron 1714 model}, 1715 booktitle = {Sherwood Fusion Theory Conference, Missoula, MT}, 1716 year = {2004}, 1717 url = {http://www.sherwoodtheory.org/sherwood04/program/1C32.pdf}, 1718 lab = {PPPL}, 1719 petsc_uses = {KSP} 1720} 1721 1722@Article{ tb1, 1723 author = {X.~Z.~Tang and A.~H.~Boozer}, 1724 title = {Numerical studies of a steady state axisymmetric co-axial helicity injection 1725 plasma}, 1726 journal = {Physics of Plasmas}, 1727 year = {2004}, 1728 pages = {171--185}, 1729 volume = {11}, 1730 lab = {LANL}, 1731 petsc_uses = {KSP} 1732} 1733 1734@Unpublished{ nlcw, 1735 title = {Inclusion of electromagnetic effects into gyrokinetic particle simulations}, 1736 author = {Y. Nishimura and Z.Lin and L.Chen and W. Wang}, 1737 note = {American Physical Society 45th Annual Meeting Division of Plasma Physics, 1738 Albuquerque, New Mexico, October 2003}, 1739 year = {2003}, 1740 petsc_uses = {KSP} 1741} 1742 1743@TechReport{ tang2001, 1744 author = {X. Z. Tang and G. Y. Fu and S. C. Jardin and L. L. Lowe and W. Park and H. R. 1745 Strauss}, 1746 title = {Resistive Magnetohydrodynamics Simulation of Fusion Plasmas}, 1747 year = {2001}, 1748 institution = {Princeton Plasma Physics Laboratory}, 1749 number = {PPPL-3532}, 1750 url = {http://www.pppl.gov/pub_report/2001/PPPL-3532.pdf}, 1751 note = {Presented at 10th Society for Industrial and Applied Mathematics (SIAM) 1752 Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, 1753 March 12-14, 2001.}, 1754 lab = {PPPL}, 1755 petsc_uses = {KSP} 1756} 1757 1758% LiteralHTML: 1759% LiteralHTML: <a name="geosciences"><H3><center>Geosciences</center></H3> 1760% LiteralHTML: 1761@Article{ valerathomasgarciacastillo2019, 1762 author = {Manuel Valera and Mary P. Thomas and Mariangel Garcia and Jose E. Castillo}, 1763 title = {Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear 1764 Coastal Ocean Model}, 1765 journal = {Journal of Marine Science and Engineering}, 1766 volume = {7}, 1767 number = {6}, 1768 article-number= {185}, 1769 url = {https://www.mdpi.com/2077-1312/7/6/185}, 1770 issn = {2077-1312}, 1771 doi = {10.3390/jmse7060185}, 1772 year = {2019}, 1773 petsc_uses = {KSP} 1774} 1775 1776@Article{ furuichimat2015, 1777 title = {Implicit solution of the material transport in Stokes flow simulation: Toward 1778 thermal convection simulation surrounded by free surface}, 1779 author = {Mikito Furuichi and Dave A May}, 1780 journal = {Computer Physics Communications}, 1781 volume = {192}, 1782 pages = {1--11}, 1783 year = {2015}, 1784 petsc_uses = {KSP} 1785} 1786 1787@Article{ sharplesmoresivelicjadamecmay2016, 1788 title = {Simulating faults and plate boundaries with a transversely isotropic plasticity 1789 model}, 1790 author = {Wendy Sharples and Louis N Moresi and Mirko Velic and Margarete A Jadamec and 1791 Dave A May}, 1792 journal = {Physics of the Earth and Planetary Interiors}, 1793 volume = {252}, 1794 pages = {77--90}, 1795 year = {2016}, 1796 petsc_uses = {KSP} 1797} 1798 1799@Article{ spiegelmanmaywilson2016, 1800 title = {On the solvability of incompressible Stokes with viscoplastic rheologies in 1801 geodynamics}, 1802 author = {Marc Spiegelman and Dave A May and Cian R Wilson}, 1803 journal = {Geochemistry, Geophysics, Geosystems}, 1804 volume = {17}, 1805 number = {6}, 1806 pages = {2213--2238}, 1807 year = {2016}, 1808 petsc_uses = {KSP} 1809} 1810 1811@Article{ buiteretal2016, 1812 title = {Benchmarking numerical models of brittle thrust wedges}, 1813 author = {Susanne JH Buiter and Guido Schreurs and Markus Albertz and Taras V Gerya and 1814 Boris Kaus and Walter Landry and Laetitia {Le Pourhiet} and Yury Mishin and David 1815 L Egholm and Michele Cooke and Bertrand Maillot and Cedric Thieulot and Tony Crook 1816 and Dave May and Pauline Souloumiac and Christopher Beaumont}, 1817 journal = {Journal of structural geology}, 1818 volume = {92}, 1819 pages = {140--177}, 1820 year = {2016}, 1821 petsc_uses = {KSP} 1822} 1823 1824@Article{ afanasievboehmdrielkrischerrietmannmayknepleyfichtner2019, 1825 title = {Modular and flexible spectral-element waveform modelling in two and three 1826 dimensions}, 1827 author = {Michael Afanasiev and Christian Boehm and Martin van Driel and Lion Krischer and 1828 Max Rietmann and Dave A. May and Matthew G. Knepley and Andreas Fichtner}, 1829 journal = {Geophysical Journal International}, 1830 volume = {216}, 1831 number = {3}, 1832 pages = {1675--1692}, 1833 doi = {10.1093/gji/ggy469}, 1834 year = {2019}, 1835 petsc_uses = {KSP} 1836} 1837 1838@Article{ haplaknepleyafanasievboehmdrielkrischerfichtner2020, 1839 title = {Fully Parallel Mesh {I/O} using {PETSc} {DMPlex} with an Application to Waveform 1840 Modeling}, 1841 author = {Vaclav Hapla and Matthew G. Knepley and Michael Afanasiev and Christian Boehm and 1842 Martin van Driel and Lion Krischer and Andreas Fichtner}, 1843 journal = {SIAM Journal on Scientific Computing}, 1844 volume = {43}, 1845 number = {2}, 1846 pages = {C127--C153}, 1847 eprint = {http://arxiv.org/abs/2004.08729}, 1848 doi = {10.1137/20M1332748}, 1849 year = {2021}, 1850 petsc_uses = {KSP} 1851} 1852 1853@Article{ parsani2021, 1854 title = {High-order accurate entropy-stable discontinuous collocated Galerkin methods with 1855 the summation-by-parts property for compressible CFD frameworks: Scalable SSDC 1856 algorithms and flow solver}, 1857 author = {Matteo Parsani and Radouan Boukharfane and Irving Reyna Nolasco and David C. {Del 1858 Rey Fernández} and Stefano Zampini and Bilel Hadri and Lisandro Dalcin}, 1859 journal = {Journal of Computational Physics}, 1860 volume = {424}, 1861 pages = {109844}, 1862 issn = {0021-9991}, 1863 doi = {https://doi.org/10.1016/j.jcp.2020.109844}, 1864 url = {http://www.sciencedirect.com/science/article/pii/S0021999120306185}, 1865 year = {2021}, 1866 petsc_uses = {KSP} 1867} 1868 1869@Article{ ambartsumyanbouakaramthanhghattaskeyesstadlerturkiyyahzampini2020, 1870 title = {Hierarchical matrix approximations of {Hessians} arising in inverse problems 1871 governed by {PDEs}}, 1872 author = {I. 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Weatherley}, 2530 title = {Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges}, 2531 journal = {Earth\ Planet.\ Sci.\ Lett.}, 2532 year = {2012}, 2533 doi = {10.1016/j.epsl.2012.04.042}, 2534 volume = {335-336}, 2535 pages = {226-237}, 2536 petsc_uses = {KSP} 2537} 2538 2539@Article{ katz10b, 2540 author = {R.F. Katz}, 2541 title = {Porosity-driven convection and asymmetry beneath mid-ocean ridges}, 2542 journal = {Geochem.\ Geophys.\ Geosys.}, 2543 volume = {10}, 2544 number = {Q0AC07}, 2545 year = {2010}, 2546 doi = {10.1029/2010GC003282}, 2547 petsc_uses = {KSP} 2548} 2549 2550@Article{ england10, 2551 author = {P.C. England and R.F. Katz}, 2552 title = {Melting above the anhydrous solidus controls the location of volcanic arcs}, 2553 journal = {Nature}, 2554 year = {2010}, 2555 volume = {467}, 2556 pages = {700--703}, 2557 doi = {10.1038/nature09417}, 2558 petsc_uses = {KSP} 2559} 2560 2561@Article{ weatherley10, 2562 author = {S. Weatherley and R.F. Katz}, 2563 title = {Plate-Driven Mantle Dynamics and Global Patterns of Mid-Ocean Ridge Bathymetry}, 2564 journal = {Geochem.\ Geophys.\ Geosys.}, 2565 year = {2010}, 2566 volume = {11}, 2567 number = {10}, 2568 doi = {10.1029/2010GC003192}, 2569 petsc_uses = {KSP} 2570} 2571 2572@Article{ katz10, 2573 author = {R.F. Katz and M.G. Worster}, 2574 title = {The stability of ice-sheet grounding lines}, 2575 journal = {Proc.~Roy.~Soc.~A}, 2576 year = {2010}, 2577 volume = {466}, 2578 pages = {1597--1620}, 2579 doi = {10.1098/rspa.2009.0434}, 2580 url = {http://www.earth.ox.ac.uk/~richardk/publications/Katz_Worster_PRSA10.pdf}, 2581 petsc_uses = {KSP} 2582} 2583 2584@Article{ kyrkesmith2013stress, 2585 title = {Stress balances of ice streams in a vertically integrated, higher-order 2586 formulation}, 2587 author = {Kyrke-Smith, T.M. and Katz, R.F. and Fowler, A.C.}, 2588 journal = {Journal of Glaciology}, 2589 volume = {59}, 2590 number = {215}, 2591 pages = {449--466}, 2592 year = {2013}, 2593 doi = {10.3189/2013JoG12J140}, 2594 petsc_uses = {KSP} 2595} 2596 2597@Article{ takei2013anisotropy1, 2598 author = {Takei Y. and R.F. Katz}, 2599 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. 2600 Governing equations and linearised analysis}}, 2601 journal = {J.\ Fluid\ Mech.}, 2602 year = {2013}, 2603 volume = {734}, 2604 pages = {424-455}, 2605 doi = {10.1017/jfm.2013.482}, 2606 petsc_uses = {KSP} 2607} 2608 2609@Article{ katz2013anisotropy2, 2610 author = {Katz R.F. and Y. Takei}, 2611 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. 2612 Numerical solutions of the full equations}}, 2613 journal = {J.\ Fluid\ Mech.}, 2614 year = {2013}, 2615 volume = {734}, 2616 pages = {456-485}, 2617 doi = {10.1017/jfm.2013.483}, 2618 petsc_uses = {KSP} 2619} 2620 2621@Article{ kyrke-smith2014subglacial, 2622 author = {Kyrke-Smith, T.M. and R.F. Katz and A.C. Fowler}, 2623 title = {Subglacial hydrology and the formation of ice streams}, 2624 journal = {Proc.\ Roy.\ Soc.\ A}, 2625 year = {2014}, 2626 volume = {470}, 2627 number = {2161}, 2628 doi = {10.1098/rspa.2013.0494}, 2629 petsc_uses = {KSP} 2630} 2631 2632@Article{ spiegelmanwilsonvankeken2013, 2633 author = {{Spiegelman}, M.~W. and {Wilson}, C.~R. and {Van Keken}, P.~E. }, 2634 title = {{TerraFERMA: The Transparent Finite Element Rapid Model Assembler for 2635 multi-physics problems in the solid Earth sciences}}, 2636 journal = {AGU Fall Meeting Abstracts}, 2637 keywords = {0560 COMPUTATIONAL GEOPHYSICS Numerical solutions, 1902 INFORMATICS Community 2638 modeling frameworks, 1906 INFORMATICS Computational models, algorithms}, 2639 year = {2013}, 2640 month = dec, 2641 pages = {A2208}, 2642 adsurl = {http://adsabs.harvard.edu/abs/2013AGUFMDI31A2208S}, 2643 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 2644 petsc_uses = {KSP} 2645} 2646 2647@Article{ bueler2009shallow, 2648 title = {{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled 2649 ice sheet model}}, 2650 author = {Ed Bueler and Jed Brown}, 2651 journal = {Journal of Geophysical Research-Earth Surface}, 2652 volume = {114}, 2653 number = {F3}, 2654 pages = {F03008}, 2655 year = {2009}, 2656 publisher = {American Geophysical Union}, 2657 petsc_uses = {KSP} 2658} 2659 2660@Article{ bueler2007est, 2661 title = {{Exact solutions to the thermomechanically coupled shallow ice approximation: 2662 effective tools for verification}}, 2663 author = {Ed Bueler and Jed Brown and Craig Lingle}, 2664 journal = {J. Glaciol}, 2665 volume = {53}, 2666 pages = {499--516}, 2667 year = {2007}, 2668 petsc_uses = {KSP} 2669} 2670 2671@Article{ bueler2007fcv, 2672 title = {{Fast computation of a viscoelastic deformable Earth model for ice-sheet 2673 simulations}}, 2674 author = {Ed Bueler and Craig S. Lingle and Jed Brown}, 2675 journal = {Ann. Glaciol}, 2676 volume = {46}, 2677 pages = {97--105}, 2678 year = {2007}, 2679 petsc_uses = {KSP} 2680} 2681 2682@Article{ bueler2005iso, 2683 author = {Ed Bueler and Craig S. Lingle and Jed A. Kallen-Brown and David N. Covey and 2684 Latrice N. Bowman}, 2685 title = {Exact solutions and numerical verification for isothermal ice sheets}, 2686 journal = {J. 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Williams}, 2751 journal = {Journal of Geophysical Research: Solid Earth}, 2752 volume = {118}, 2753 number = {6}, 2754 pages = {3059--3079}, 2755 issn = {2169-9356}, 2756 doi = {10.1002/jgrb.50217}, 2757 keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics}, 2758 year = {2013}, 2759 petsc_uses = {KSP} 2760} 2761 2762@InProceedings{ aagaardknepleywilliams11, 2763 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 2764 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 2765 Deformation}, 2766 booktitle = {Eos Transactions of the AGU}, 2767 organization = {American Geophysical Union}, 2768 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 2769 year = {2011}, 2770 petsc_uses = {KSP} 2771} 2772 2773@InProceedings{ knepley10b, 2774 author = {Matthew G. {Knepley}}, 2775 title = {Acceleration of low order finite element computation with {GPUs} (Invited)}, 2776 booktitle = {Eos Transactions of the AGU}, 2777 organization = {American Geophysical Union}, 2778 note = {Fall Meeting Supplemental, Abstract IN44A-01}, 2779 year = {2010}, 2780 petsc_uses = {KSP} 2781} 2782 2783@InProceedings{ mayknepleygurnis09, 2784 author = {Dave A. May and Matthew G. Knepley and Michael Gurnis}, 2785 title = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}}, 2786 booktitle = {Eos Transactions of the AGU}, 2787 organization = {American Geophysical Union}, 2788 note = {Fall Meeting Supplemental, Abstract P31A-A1241}, 2789 year = {2009}, 2790 petsc_uses = {KSP} 2791} 2792 2793@InProceedings{ yuenknepleyerlebacherwright09, 2794 author = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright}, 2795 title = {The Coming Role of {GPU} in Computational Geodynamics}, 2796 booktitle = {Eos Transactions of the AGU}, 2797 organization = {American Geophysical Union}, 2798 note = {Fall Meeting Supplemental, Abstract DI22A-05}, 2799 year = {2009}, 2800 petsc_uses = {KSP} 2801} 2802 2803@InProceedings{ aagaardknepleywilliams08, 2804 author = {Brad Aagaard and Charles A. Williams and Matthew G. Knepley}, 2805 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 2806 Deformation}, 2807 booktitle = {Eos Transactions of the AGU}, 2808 organization = {American Geophysical Union}, 2809 volume = {89}, 2810 number = {53}, 2811 note = {Fall Meeting Supplemental, Abstract T41A-1925}, 2812 year = {2007}, 2813 petsc_uses = {KSP} 2814} 2815 2816@InProceedings{ aagaardknepleywilliams07, 2817 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 2818 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 2819 Deformation}, 2820 booktitle = {Eos Transactions of the AGU}, 2821 organization = {American Geophysical Union}, 2822 volume = {88}, 2823 number = {52}, 2824 note = {Fall Meeting Supplemental, Abstract T21B-1798}, 2825 year = {2007}, 2826 petsc_uses = {KSP} 2827} 2828 2829@InProceedings{ aagaardknepleywilliams05, 2830 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 2831 title = {Development of software for studying earthquakes across multiple spatial and 2832 temporal scales by coupling quasi-static and dynamic simulations}, 2833 booktitle = {Eos Transactions of the AGU}, 2834 organization = {American Geophysical Union}, 2835 volume = {86}, 2836 number = {52}, 2837 note = {Fall Meeting Supplemental, Abstract S53A-1072}, 2838 year = {2005}, 2839 petsc_uses = {KSP} 2840} 2841 2842@InProceedings{ williamsgablehagermeadeaagaardknepley08, 2843 author = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and 2844 Brad Aagaard and Matthew G. Knepley}, 2845 title = {Modeling of Multiple Earthquake Cycles in Southern California Using the {SCEC} 2846 Community Fault Model}, 2847 booktitle = {Proceedings of Geosciences '08}, 2848 address = {Wellington, NZ}, 2849 month = {November}, 2850 year = {2008}, 2851 petsc_uses = {KSP} 2852} 2853 2854@TechReport{ zhang07, 2855 title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for 2856 Tsunamis}, 2857 author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi}, 2858 type = {Preprint}, 2859 number = {ANL/MCS-P1459-0907}, 2860 institution = {ANL}, 2861 month = {September}, 2862 year = {2007}, 2863 petsc_uses = {KSP} 2864} 2865 2866@Article{ katz08b, 2867 author = {Richard F. Katz}, 2868 title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic 2869 focusing at mid-ocean ridges}, 2870 journal = {J. Petrology}, 2871 year = {2008}, 2872 volume = {49}, 2873 pages = {2099--2121}, 2874 doi = {10.1093/petrology/egn058}, 2875 petsc_uses = {KSP} 2876} 2877 2878@Article{ hgrhkjvv2008, 2879 title = {On preconditioning for a parallel solution of the Richards equation}, 2880 author = {Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy 2881 Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena}, 2882 journal = {Computers and Geosciences}, 2883 volume = {34}, 2884 pages = {1958--1963}, 2885 year = {2008}, 2886 petsc_uses = {KSP} 2887} 2888 2889@Article{ maymoresi2008, 2890 title = {Preconditioned iterative methods for {Stokes} flow problems arising in 2891 computational geodynamics}, 2892 journal = {Physics of the Earth and Planetary Interiors}, 2893 volume = {171}, 2894 number = {1-4}, 2895 pages = {33--47}, 2896 year = {2008}, 2897 note = {{R}ecent Advances in Computational Geodynamics: Theory, Numerics and 2898 Applications}, 2899 issn = {0031-9201}, 2900 doi = {10.1016/j.pepi.2008.07.036}, 2901 author = {Dave A. May and Louis Moresi}, 2902 keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}, 2903 petsc_uses = {KSP} 2904} 2905 2906@Article{ kausmuhlhausmay2010, 2907 title = {A stabilization algorithm for geodynamic numerical simulations with a free 2908 surface}, 2909 author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May}, 2910 journal = {Physics of the Earth and Planetary Interiors}, 2911 volume = {181}, 2912 number = {1}, 2913 pages = {12--20}, 2914 year = {2010}, 2915 petsc_uses = {KSP} 2916} 2917 2918@Article{ duretzmaygeryatackley2011, 2919 title = {Discretization errors and free surface stabilization in the finite difference and 2920 marker-in-cell method for applied geodynamics: A numerical study}, 2921 author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley}, 2922 journal = {Geochemistry, Geophysics, Geosystems}, 2923 volume = {12}, 2924 number = {7}, 2925 year = {2011}, 2926 petsc_uses = {KSP} 2927} 2928 2929@Article{ furuichimaytackley2011, 2930 title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a 2931 {Schur} complement approach with mixed precision arithmetic}, 2932 author = {Mikito Furuichi and Dave A May and Paul J Tackley}, 2933 journal = {Journal of Computational Physics}, 2934 volume = {230}, 2935 number = {24}, 2936 pages = {8835--8851}, 2937 year = {2011}, 2938 petsc_uses = {KSP} 2939} 2940 2941@Article{ kellermaykaus2013, 2942 title = {Numerical modelling of magma dynamics coupled to tectonic deformation of 2943 lithosphere and crust}, 2944 author = {Tobias Keller and Dave A May and Boris JP Kaus}, 2945 journal = {Geophysical Journal International}, 2946 volume = {195}, 2947 number = {3}, 2948 pages = {1406--1442}, 2949 year = {2013}, 2950 petsc_uses = {KSP} 2951} 2952 2953@Article{ schellartfreemanstegmanmoresimay2007, 2954 title = {Evolution and diversity of subduction zones controlled by slab width}, 2955 author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A 2956 May}, 2957 journal = {Nature}, 2958 volume = {446}, 2959 number = {7133}, 2960 pages = {308--311}, 2961 year = {2007}, 2962 petsc_uses = {KSP} 2963} 2964 2965@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012, 2966 title = {A comparison of numerical surface topography calculations in geodynamic 2967 modelling: an evaluation of the sticky air method}, 2968 author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter 2969 and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley}, 2970 journal = {Geophysical Journal International}, 2971 volume = {189}, 2972 number = {1}, 2973 pages = {38--54}, 2974 year = {2012}, 2975 petsc_uses = {KSP} 2976} 2977 2978@Article{ stegmanfreemanschellartmoresimay2006, 2979 title = {Influence of trench width on subduction hinge retreat rates in 3-D models of slab 2980 rollback}, 2981 author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A 2982 May}, 2983 journal = {Geochemistry, Geophysics, Geosystems}, 2984 volume = {7}, 2985 number = {3}, 2986 year = {2006}, 2987 petsc_uses = {KSP} 2988} 2989 2990@InProceedings{ may2014ptatin, 2991 title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics}, 2992 author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}}, 2993 booktitle = {Proceedings of {SC14}: The {International Conference for High Performance 2994 Computing, Networking, Storage and Analysis}}, 2995 organization = {ACM}, 2996 pages = {274--284}, 2997 year = {2014}, 2998 doi = {10.1109/SC.2014.28}, 2999 petsc_uses = {KSP} 3000} 3001 3002@Article{ maybrownpourhiet2015, 3003 title = {A scalable, matrix-free multigrid preconditioner for finite element 3004 discretizations of heterogeneous {Stokes} flow}, 3005 author = {David A May and Jed Brown and Laetitia {Le Pourhiet}}, 3006 journal = {Computer Methods in Applied Mechanics and Engineering}, 3007 volume = {290}, 3008 pages = {496--523}, 3009 year = {2015}, 3010 doi = {10.1016/j.cma.2015.03.014}, 3011 petsc_uses = {KSP} 3012} 3013 3014@Article{ duretzmayyamato2016, 3015 title = {A free surface capturing discretization for the staggered grid finite difference 3016 scheme}, 3017 author = {Thibault Duretz and Dave A May and Philippe Yamato}, 3018 journal = {Geophysical Journal International}, 3019 volume = {204}, 3020 number = {3}, 3021 pages = {1518--1530}, 3022 year = {2016}, 3023 petsc_uses = {KSP} 3024} 3025 3026@Article{ rhebergenwellskatzwathen2014, 3027 author = {Sander Rhebergen and Garth N. 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Katz and Marc Spiegelman and Benjamin Holtzman}, 3061 title = {The dynamics of melt and shear localization in partially molten aggregates}, 3062 journal = {Nature}, 3063 year = {2006}, 3064 volume = {442}, 3065 pages = {676--679}, 3066 month = {August}, 3067 day = {10}, 3068 url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}, 3069 petsc_uses = {KSP} 3070} 3071 3072@InProceedings{ mqrs2003, 3073 author = {Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl}, 3074 year = {2003}, 3075 title = {Parallel Preconditioning for Sedimentary Basin Simulations}, 3076 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 3077 Sozopol, Bulgaria, June 4-8, 2003}, 3078 petsc_uses = {KSP} 3079} 3080 3081@InProceedings{ lichtner1, 3082 author = {Chuan Lu and Peter C. 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Wendebourg}, 3106 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 3107 journal = {Computational Geosciences}, 3108 year = {2003}, 3109 volume = {7}, 3110 pages = {295--318}, 3111 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 3112 petsc_uses = {KSP} 3113} 3114 3115@Article{ kees-miller-03, 3116 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 3117 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 3118 journal = {Computational Geosciences}, 3119 year = {2003}, 3120 volume = {7}, 3121 pages = {91--114}, 3122 petsc_uses = {KSP} 3123} 3124 3125@Article{ bk2003, 3126 author = {JN Buur and T Kuehnel}, 3127 title = {Improving depth imaging by automated model updating}, 3128 journal = {The Leading Edge}, 3129 year = {2003}, 3130 volume = {22}, 3131 pages = {310-318}, 3132 petsc_uses = {KSP} 3133} 3134 3135@Article{ frederickbuffett2016, 3136 title = {Submarine groundwater discharge as a possible formation mechanism for 3137 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 3138 author = {Jennifer M. Frederick and Bruce A. Buffett}, 3139 journal = {Journal of Geophysical Research: Solid Earth}, 3140 volume = {121}, 3141 number = {3}, 3142 pages = {1383--1404}, 3143 issn = {2169-9356}, 3144 doi = {10.1002/2015JB012627}, 3145 year = {2016}, 3146 petsc_uses = {KSP} 3147} 3148 3149% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3150% LiteralHTML:<font color="#FF0000"> 3151% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 3152% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 3153% LiteralHTML:variety of these simulations.</p> 3154% LiteralHTML:</font> 3155% LiteralHTML: 3156@InProceedings{ appelbe1, 3157 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 3158 year = {2003}, 3159 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 3160 computational methodology}, 3161 page = {781}, 3162 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 3163 Proceedings}, 3164 publisher = {Springer-Verlag}, 3165 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 3166 petsc_uses = {KSP} 3167} 3168 3169% LiteralHTML:<a name="katz"> 3170@InProceedings{ gd1, 3171 author = {Guillaume Dumont and Michel Kern}, 3172 title = {Parallelization of a 3D Seismic Migration Code with PETSc}, 3173 year = {1999}, 3174 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 3175 Computing}, 3176 petsc_uses = {KSP} 3177} 3178 3179% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 3180% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 3181% LiteralHTML:<font color="#FF0000"> 3182% LiteralHTML: Figures from the work of Richard Katz 3183@PhDThesis{ katzthesis, 3184 author = {R.F. Katz}, 3185 title = {The deep roots of volcanoes: models of magma dynamics with applications to 3186 subduction zones}, 3187 school = {Columbia University}, 3188 year = {2005}, 3189 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 3190 petsc_uses = {KSP} 3191} 3192 3193@InCollection{ knepleykatzsmith06, 3194 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 3195 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 3196 USA}, 3197 title = {Developing a Geodynamics Simulator with {PETSc}}, 3198 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 3199 series = {Lecture Notes in Computational Science and Engineering}, 3200 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 3201 publisher = {Springer Berlin Heidelberg}, 3202 isbn = {978-3-540-31619-0}, 3203 keyword = {Mathematics and Statistics}, 3204 pages = {413-438}, 3205 volume = {51}, 3206 doi = {10.1007/3-540-31619-1_12}, 3207 year = {2006}, 3208 petsc_uses = {KSP} 3209} 3210 3211@Article{ katz04, 3212 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 3213 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 3214 the global mid-ocean ridge system}, 3215 journal = {Geophys.\ Res.\ Letts.}, 3216 year = {2004}, 3217 volume = {31}, 3218 pages = {L15605}, 3219 petsc_uses = {KSP} 3220} 3221 3222@Article{ katz07, 3223 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 3224 Ethan Coon}, 3225 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 3226 Toolkit for Scientific Computation}}, 3227 journal = {Phys. Earth Planet. In.}, 3228 volume = {163}, 3229 pages = {52--68}, 3230 year = {2007}, 3231 petsc_uses = {KSP} 3232} 3233 3234@Article{ williams2006development, 3235 title = {{Development of a package for modeling stress in the lithosphere}}, 3236 author = {Williams, CA}, 3237 journal = {Eos Trans. AGU}, 3238 volume = {87}, 3239 pages = {36}, 3240 year = {2006}, 3241 petsc_uses = {KSP} 3242} 3243 3244@Article{ goverswortel05, 3245 author = {R. Govers and M.J.R. Wortel}, 3246 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 3247 journal = {Earth and Planetary Science Letters}, 3248 volume = {236/1-2}, 3249 pages = {505-523}, 3250 year = {2005}, 3251 petsc_uses = {KSP} 3252} 3253 3254@InProceedings{ snark2, 3255 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 3256 year = {2002}, 3257 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 3258 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 3259 petsc_uses = {KSP} 3260} 3261 3262@Article{ snark1, 3263 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 3264 Tan and Feng Wang}, 3265 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 3266 journal = {Submitted to Pure and Applied Geosciences}, 3267 petsc_uses = {KSP} 3268} 3269 3270@InProceedings{ earthquake2003, 3271 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 3272 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 3273 Tiankai Tu}, 3274 year = {2003}, 3275 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 3276 booktitle = {Proceedings of SC2003}, 3277 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 3278 petsc_uses = {KSP} 3279} 3280 3281@InProceedings{ stefano12, 3282 author = {Michele De Stefano}, 3283 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 3284 booktitle = {PIERS Proceedings}, 3285 month = {August}, 3286 address = {Moscow, RUSSIA}, 3287 pages = {491--495}, 3288 year = {2012}, 3289 petsc_uses = {KSP} 3290} 3291 3292%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 3293 3294% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3295% LiteralHTML: <center><img alt="" 3296% LiteralHTML: src="images/ocean.jpg"></center></p> 3297@Article{ khatiwala07, 3298 author = {Khatiwala, S.}, 3299 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 3300 journal = {Glob. Biogeochem. Cycles}, 3301 volume = {21}, 3302 doi = {10.1029/2007GB002923}, 3303 year = {2007}, 3304 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 3305} 3306 3307@Article{ dks2004, 3308 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 3309 journal = {Ocean Modelling}, 3310 year = {2004}, 3311 volume = {6(2)}, 3312 pages = {125-150}, 3313 title = {A finite-element Ocean Model: Principles and Evaluation}, 3314 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}, 3315 petsc_uses = {KSP} 3316} 3317 3318@Article{ danilov1, 3319 author = {S. Danilov and G. Kivman and J. Schroter}, 3320 year = {2004}, 3321 title = {Evaluation of an eddy-permitting finite-element ocean model in the North 3322 Atlantic}, 3323 journal = {Ocean Modelling}, 3324 petsc_uses = {KSP} 3325} 3326 3327@Article{ nerger1, 3328 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 3329 year = {2004}, 3330 title = {Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to 3331 a Finite Element Model of the North Atlantic}, 3332 journal = {Journal of marine systems}, 3333 petsc_uses = {KSP} 3334} 3335 3336@Conference{ rakowsky2003self, 3337 title = {{A self-adaptive finite element model of the atmosphere}}, 3338 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 3339 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 3340 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 3341 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 3342 pages = {279}, 3343 isbn = {981238376X}, 3344 year = {2003}, 3345 organization = {World Scientific Pub Co}, 3346 petsc_uses = {KSP} 3347} 3348 3349@Article{ lauter3, 3350 author = {M. Lauter}, 3351 year = {2004}, 3352 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 3353 AtmosphArenmodell}, 3354 journal = {Berichte zur Polar- und Meeresforschung}, 3355 petsc_uses = {KSP} 3356} 3357 3358@Article{ lauter2, 3359 author = {M. Lauter and D. Handorf and K. Dethloff}, 3360 year = {2004}, 3361 title = {Unsteady analytical solutions of the spherical shallow water equations}, 3362 journal = {Journal of computational physics}, 3363 petsc_uses = {KSP} 3364} 3365 3366@PhDThesis{ lauter1, 3367 author = {M. Lauter}, 3368 year = {2004}, 3369 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 3370 AtmosphArenmodell}, 3371 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 3372 petsc_uses = {KSP} 3373} 3374 3375@Article{ frickenhaus1, 3376 author = {S. Frickenhaus and W. Hiller and M. Best}, 3377 year = {2005}, 3378 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 3379 parallel numerical atmosphere and ocean models}, 3380 journal = {Ocean Modelling}, 3381 volume = {10}, 3382 pages = {185--191}, 3383 petsc_uses = {KSP} 3384} 3385 3386@Article{ 0266-5611-24-3-034015, 3387 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 3388 title = {A Newton-CG method for large-scale three-dimensional elastic full-waveform 3389 seismic inversion}, 3390 journal = {Inverse Problems}, 3391 volume = {24}, 3392 number = {3}, 3393 pages = {034015 (26pp)}, 3394 url = {http://stacks.iop.org/0266-5611/24/034015}, 3395 year = {2008}, 3396 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 3397 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 3398 iterations with inner conjugate gradient linear iterations, globalized by an 3399 Armijo backtracking line search, solved on a sequence of finer grids and higher 3400 frequencies to remain in the vicinity of the global optimum, inexactly terminated 3401 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 3402 variation operator to capture sharp interfaces, finely discretized by finite 3403 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 3404 implemented in matrix-free fashion with adjoint-based computation of reduced 3405 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 3406 waveform storage, and partitioned spatially across processors to parallelize the 3407 solutions of the forward and adjoint wave equations and the evaluation of 3408 gradient-like information. Several numerical examples demonstrate the grid 3409 independence of linear and nonlinear iterations, the effectiveness of the 3410 preconditioner, the ability to solve inverse problems with up to 17 million 3411 inversion parameters on up to 2048 processors, the effectiveness of multiscale 3412 continuation in keeping iterates in the basin of attraction of the global minimum, 3413 and the ability to fit the observational data while reconstructing the model with 3414 reasonable resolution and capturing sharp interfaces.}, 3415 petsc_uses = {KSP} 3416} 3417 3418% LiteralHTML: 3419% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 3420% LiteralHTML: 3421% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3422% LiteralHTML:<font color="#FF0000"> 3423% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 3424% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 3425% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 3426% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 3427% LiteralHTML:for a variety of these simulations.</p> 3428% LiteralHTML:</font> 3429% LiteralHTML: 3430@Article{ mills2009modeling, 3431 title = {Modeling subsurface reactive flows using leadership-class computing}, 3432 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 3433 Mahinthakumar, G.K. and Smith, B.F.}, 3434 journal = {Journal of Physics: Conference Series}, 3435 volume = {180}, 3436 pages = {012062}, 3437 year = {2009}, 3438 publisher = {IOP Publishing}, 3439 petsc_uses = {KSP} 3440} 3441 3442@Conference{ mills2007simulating, 3443 title = {{Simulating subsurface flow and transport on ultrascale computers using 3444 PFLOTRAN}}, 3445 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 3446 booktitle = {Journal of Physics: Conference Series}, 3447 volume = {78}, 3448 pages = {012051}, 3449 year = {2007}, 3450 organization = {IOP Publishing}, 3451 petsc_uses = {KSP} 3452} 3453 3454@InProceedings{ mills2009, 3455 title = {Modeling subsurface reactive flows using leadership-class computing}, 3456 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 3457 Mahinthakmuar, G. and Smith, B.}, 3458 booktitle = {Journal of Physics: Conference Series}, 3459 volume = {180}, 3460 pages = {102062}, 3461 year = {2009}, 3462 organization = {IOP Publishing}, 3463 petsc_uses = {KSP} 3464} 3465 3466@Article{ guo2013parallel, 3467 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 3468 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 3469 }, 3470 journal = {Advances in Water Resources }, 3471 volume = {53}, 3472 number = {0}, 3473 pages = {101 - 108}, 3474 year = {2013}, 3475 note = {}, 3476 issn = {0309-1708}, 3477 doi = {10.1016/j.advwatres.2012.10.010}, 3478 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 3479 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 3480 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 3481 preconditioner}, 3482 petsc_uses = {KSP} 3483} 3484 3485@Unpublished{ stomp, 3486 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 3487 url = {http://stomp.pnl.gov/}, 3488 petsc_uses = {KSP} 3489} 3490 3491@InProceedings{ htfc2003, 3492 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 3493 title = {Methods and Experiences For Parallelizing Flood Models}, 3494 year = {2003}, 3495 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 3496 European PVM/MPI User's Group Meeting}, 3497 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 3498 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 3499 petsc_uses = {KSP} 3500} 3501 3502@InProceedings{ hulchy-tran-astalos-fmsip, 3503 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 3504 D.Froehlich}, 3505 title = {Flood Modeling System and Its Parallelization}, 3506 year = {2002}, 3507 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 3508 Engineering}, 3509 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 3510 petsc_uses = {KSP} 3511} 3512 3513@InProceedings{ gy1, 3514 author = {J. P. Gwo and G. T. Yeh}, 3515 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 3516 Transport at Watershed Scale}, 3517 year = {2004}, 3518 booktitle = {The International Conference on Computational Methods}, 3519 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 3520 petsc_uses = {KSP} 3521} 3522 3523@Conference{ cheng2009efficient, 3524 title = {{An efficient parallel method for large-scale groundwater flow equation based on 3525 PETSc}}, 3526 author = {Cheng, T. and Ji, X. and Wang, Q.}, 3527 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 3528 Conference on}, 3529 pages = {190--193}, 3530 organization = {IEEE}, 3531 petsc_uses = {KSP} 3532} 3533 3534@Unpublished{ sfrsm, 3535 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 3536 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 3537 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 3538 its linear solves}, 3539 petsc_uses = {KSP} 3540} 3541 3542% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3543@InProceedings{ bart_omar:sc05, 3544 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 3545 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 3546 title = {Dynamic data driven inversion for terascale simulations: real-time 3547 indentification of airborne contaminants}, 3548 booktitle = {Proceedings of SC2005}, 3549 organization = {IEEE/ACM}, 3550 address = {Seattle, WA}, 3551 year = {2005}, 3552 month = {November}, 3553 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 3554 lab = {SNL}, 3555 petsc_uses = {KSP} 3556} 3557 3558@InProceedings{ anton-krassimir-lscc, 3559 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 3560 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 3561 Simulations}, 3562 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 3563 volume = {2907}, 3564 year = {2003}, 3565 publisher = {Springer-Verlag}, 3566 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 3567 petsc_uses = {KSP} 3568} 3569 3570@InProceedings{ aa2001, 3571 author = {Anton Antonov}, 3572 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 3573 year = {2001}, 3574 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 3575 Sozopol, Bulgaria}, 3576 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 3577 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 3578 petsc_uses = {KSP} 3579} 3580 3581% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3582@Article{ grassley-simmons-kercher-00, 3583 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 3584 year = {2000}, 3585 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 3586 reactive transport models}, 3587 journal = {Applied Geochemistry}, 3588 volume = {17}, 3589 pages = {699--708}, 3590 lab = {LLNL} 3591} 3592 3593@Article{ glassey-nitao-03, 3594 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 3595 and Carl I. Steefel and James R. Kercher}, 3596 year = {2003}, 3597 title = {The impact of climate change on vadose zone pore waters and its implication for 3598 long-term monitoring}, 3599 journal = {Computers and Geosciences}, 3600 volume = {29}, 3601 pages = {399-411}, 3602 lab = {LLNL}, 3603 petsc_uses = {KSP} 3604} 3605 3606@Article{ steefel-depaolo-lichtner-05, 3607 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 3608 year = {2005}, 3609 title = {Reactive transport modeling: An essential tool and a new research approach for 3610 the Earth sciences}, 3611 journal = {Earth and Planetary Science Letters}, 3612 lab = {LLNL,LANL}, 3613 petsc_uses = {KSP} 3614} 3615 3616% LiteralHTML:<a name="scalinglarge"> 3617% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3618% LiteralHTML: <center><img alt="" 3619% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 3620% LiteralHTML:<font color="#FF0000"> 3621% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 3622@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 3623 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 3624 Strategies for Large-Scale Numerical Simulations}, 3625 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 3626 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 3627 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 3628 Large-Scale Systems (scalA)}, 3629 pages = {65-72}, 3630 doi = {10.1109/ScalA.2018.00012}, 3631 month = {Nov}, 3632 year = {2018}, 3633 petsc_uses = {KSP} 3634} 3635 3636@Article{ km2004, 3637 author = {A. Keese and H. G. Matthies}, 3638 journal = {Computers and Structures}, 3639 year = {2005}, 3640 volume = {83}, 3641 pages = {1033--1047}, 3642 title = {Hierarchical parallelisation for the solution of stochastic finite element 3643 equations}, 3644 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}, 3645 petsc_uses = {KSP} 3646} 3647 3648@Unpublished{ hvl2002, 3649 title = {Numerical Modeling of NAPL Source Zone Treatment}, 3650 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 3651 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 3652 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 3653 year = {2002}, 3654 lab = {LANL}, 3655 petsc_uses = {KSP} 3656} 3657 3658@PhDThesis{ hammond2003, 3659 author = {Glenn E. Hammond}, 3660 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 3661 Transport on Supercomputers}, 3662 school = {University of Illinois at Urbana-Champaign}, 3663 year = {2003}, 3664 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 3665 petsc_uses = {KSP} 3666} 3667 3668@Unpublished{ uk, 3669 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 3670 Scale Environmental Flows and Transport Processes}, 3671 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 3672 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 3673 buildings and in Green Bay. Used PETSc for its linear solvers}, 3674 year = {1999}, 3675 petsc_uses = {KSP} 3676} 3677 3678@InProceedings{ hammond2002, 3679 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 3680 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 3681 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 3682 year = {2002}, 3683 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 3684 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 3685 Resources, Delft, The Netherlands.}, 3686 lab = {LANL}, 3687 petsc_uses = {KSP} 3688} 3689 3690@TechReport{ steefel1, 3691 author = {C. I. Steefel}, 3692 title = {Software for modeling multicomponent, multidimensional reactive transport}, 3693 year = {2001}, 3694 institution = {Lawrence Livermore National Laboratory}, 3695 number = {UCRL-MA-143182}, 3696 lab = {LLNL}, 3697 petsc_uses = {KSP} 3698} 3699 3700@Article{ steefel2, 3701 author = {C. I. Steefel and A. C. Lasaga}, 3702 title = {A coupled model for transport of multiple chemical-species and kinetic 3703 precipitation dissolution reactions with application to reactive flow in 3704 single-phase hydrothermal systems}, 3705 journal = {Americal Journal of Science}, 3706 year = {1994}, 3707 pages = {529-592}, 3708 volume = {294}, 3709 number = {5}, 3710 petsc_uses = {KSP} 3711} 3712 3713@TechReport{ steefel3, 3714 author = {C. I. Steefel and S. B. Yabusaki}, 3715 title = {OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: 3716 User's manual and programmer's guide}, 3717 year = {1996}, 3718 institution = {Pacific Northwest National Laboratory}, 3719 number = {PNNL-11166}, 3720 lab = {PNNL}, 3721 petsc_uses = {KSP} 3722} 3723 3724@Article{ 2005hvl, 3725 author = {G. E. Hammond and A.J. Valocchi and P.C. 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Park}, 3749 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 3750 Media}, 3751 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 3752 title = {Lecture Notes in Computer Science}, 3753 publisher = {Springer-Verlag}, 3754 volume = {3044}, 3755 year = {2004}, 3756 petsc_uses = {KSP} 3757} 3758 3759@Article{ 2001agusm...h32a06k, 3760 author = {{Kim}, J.~G. and {Kim}, J.}, 3761 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 3762 journal = {AGU Spring Meeting Abstracts}, 3763 year = {2001}, 3764 pages = {32-+}, 3765 petsc_uses = {KSP} 3766} 3767 3768@Article{ lzb2005, 3769 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 3770 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 3771 journal = {Journal of Hydraulic Engineering}, 3772 year = {2005}, 3773 volume = {131}, 3774 number = {4}, 3775 pages = {247--258}, 3776 petsc_uses = {KSP} 3777} 3778 3779@Article{ rao2005, 3780 author = {Prasada Rao}, 3781 title = {A parallel RMA2 model for simulating large-scale free surface flows}, 3782 journal = {Environmental Modelling and Software}, 3783 year = {2005}, 3784 pages = {47--53}, 3785 petsc_uses = {KSP} 3786} 3787 3788@InProceedings{ pr1, 3789 author = {Prasada Rao}, 3790 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 3791 Hydrodynamic Flows}, 3792 year = {2003}, 3793 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 3794 Conference}, 3795 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 3796 petsc_uses = {KSP} 3797} 3798 3799@InProceedings{ lichtner2004, 3800 author = {Peter C. Lichtner and Andrew Wolfsberg}, 3801 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 3802 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 3803 Challenge Supercomputing Problem}, 3804 year = {2004}, 3805 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 3806 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 3807 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 3808 lab = {LANL}, 3809 petsc_uses = {KSP} 3810} 3811 3812% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 3813@Article{ aba01:petsc-app, 3814 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 3815 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 3816 journal = {Int. J. High Performance Computing Applications}, 3817 year = {2001}, 3818 volume = {15}, 3819 number = {1}, 3820 pages = {13--21}, 3821 month = {Spring}, 3822 petsc_uses = {KSP} 3823} 3824 3825@PhDThesis{ tjb200, 3826 author = {Thomas James Byer}, 3827 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 3828 Facilities}, 3829 school = {Stanford}, 3830 year = {2000}, 3831 petsc_uses = {KSP} 3832} 3833 3834@InProceedings{ puchyr2006, 3835 author = {Peter J. Puchyr}, 3836 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 3837 Win32 Cluster}, 3838 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 3839 note = {Paper number CIPC2006-207}, 3840 year = {2006}, 3841 petsc_uses = {KSP} 3842} 3843 3844@InProceedings{ texas98, 3845 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 3846 and G. A. Pope}, 3847 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 3848 Simulation}, 3849 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 3850 Symposium}, 3851 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 3852 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 3853 year = {1998}, 3854 petsc_uses = {KSP} 3855} 3856 3857% LiteralHTML: 3858% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 3859% LiteralHTML: 3860@Article{ farrellmitchellscottwechsung2021, 3861 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 3862 stationary incompressible {Navier-Stokes} equations}, 3863 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 3864 Wechsung}, 3865 journal = {The SMAI journal of computational mathematics}, 3866 volume = {7}, 3867 pages = {75--96}, 3868 year = {2021}, 3869 petsc_uses = {KSP} 3870} 3871 3872@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 3873 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 3874 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 3875 P MacLachlan and Ray S Tuminaro}, 3876 journal = {SIAM Journal on Scientific Computing}, 3877 number = {0}, 3878 pages = {S70--S91}, 3879 year = {2021}, 3880 petsc_uses = {KSP} 3881} 3882 3883@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 3884 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 3885 hyperelasticity}, 3886 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 3887 Oyar\'ua and Ricardo Ruiz-Baier}, 3888 journal = {Computer Methods in Applied Mechanics and Engineering}, 3889 volume = {374}, 3890 pages = {113562}, 3891 issn = {0045-7825}, 3892 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 3893 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 3894 year = {2021}, 3895 petsc_uses = {KSP} 3896} 3897 3898@Article{ farrellmitchellwechsung2018, 3899 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 3900 {Navier-Stokes} equations at high {Reynolds} number}, 3901 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 3902 journal = {SIAM Journal on Scientific Computing}, 3903 volume = {41}, 3904 number = {5}, 3905 eprint = {1810.03315}, 3906 pages = {A3073-A3096}, 3907 year = {2019}, 3908 petsc_uses = {KSP} 3909} 3910 3911@Article{ hevuikklaij2017, 3912 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 3913 discretized by a finite volume method}, 3914 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 3915 journal = {Journal of Numerical Mathematics}, 3916 volume = {25}, 3917 number = {2}, 3918 pages = {89--105}, 3919 year = {2017}, 3920 petsc_uses = {KSP} 3921} 3922 3923@InProceedings{ zou2015newton, 3924 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 3925 appearance/disappearance}, 3926 author = {Zou, L and Zhao, H and Zhang, H}, 3927 booktitle = {ANS 2015 Annual Meeting, June}, 3928 volume = {7}, 3929 number = {11}, 3930 year = {2015}, 3931 petsc_uses = {KSP} 3932} 3933 3934@Article{ guermond2009nonlinear, 3935 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 3936 Fourier/finite element technique and an interior penalty method}, 3937 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 3938 journal = {Journal of computational physics}, 3939 volume = {228}, 3940 number = {8}, 3941 pages = {2739--2757}, 3942 year = {2009}, 3943 publisher = {Elsevier}, 3944 petsc_uses = {KSP} 3945} 3946 3947@Article{ erzincanlisahin2015, 3948 title = {The numerical simulation of the wing kinematics effects on near wake topology and 3949 aerodynamic performance in hovering Drosophila flight}, 3950 author = {Belkis Erzincanli and Mehmet Sahin}, 3951 journal = {Computers \& Fluids}, 3952 volume = {122}, 3953 pages = {90--110}, 3954 year = {2015}, 3955 publisher = {Elsevier}, 3956 petsc_uses = {KSP} 3957} 3958 3959@Article{ ekensahin2015, 3960 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 3961 structure interaction problems}, 3962 author = {Ali Eken and Mehmet Sahin}, 3963 journal = {International Journal for Numerical Methods in Fluids}, 3964 year = {2015}, 3965 publisher = {Wiley Online Library}, 3966 petsc_uses = {KSP} 3967} 3968 3969@Article{ hwangsucai2015, 3970 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 3971 for transonic full potential equation}, 3972 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 3973 journal = {Computers \& Fluids}, 3974 volume = {110}, 3975 number = {30}, 3976 pages = {96--107}, 3977 year = {2015}, 3978 doi = {10.1016/j.compfluid.2014.04.005}, 3979 petsc_uses = {KSP} 3980} 3981 3982@Article{ yanghwangcai2016, 3983 title = {Nonlinear Preconditioning Techniques for Full-Space Lagrange--Newton Solution of 3984 PDE-Constrained Optimization Problems}, 3985 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 3986 journal = {SIAM Journal on Scientific Computing}, 3987 volume = {38}, 3988 number = {5}, 3989 pages = {A2756--A2778}, 3990 year = {2016}, 3991 petsc_uses = {KSP} 3992} 3993 3994@Article{ khanaidun2011, 3995 author = {Irfan Khan and Cyrus K. Aidun}, 3996 title = {Direct numerical simulation of saturated deformable porous media using parallel 3997 hybrid Lattice-Boltzmann and finite element method}, 3998 journal = {Int. J. Numer. Meth. Eng.}, 3999 volume = {86}, 4000 pages = {1379--1395}, 4001 year = {2011}, 4002 petsc_uses = {KSP} 4003} 4004 4005@Article{ khanaidun2014, 4006 author = {Irfan Khan and Cyrus K. Aidun}, 4007 title = {Modeling the deformation of saturate porous media using direct numerical 4008 simulation}, 4009 journal = {Int. J. Multiphase Flow}, 4010 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 4011 year = {2014}, 4012 petsc_uses = {KSP} 4013} 4014 4015@Article{ mofidi2014simulations, 4016 author = {A. Mofidi and P. M. Carrica}, 4017 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 4018 and Propeller}, 4019 journal = {Computers and Fluids}, 4020 pages = {191--203}, 4021 year = {2014}, 4022 petsc_uses = {KSP} 4023} 4024 4025@Article{ paik2014fluidstructure, 4026 author = {K. Paik and P. M. Carrica}, 4027 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 4028 Surface in a Rolling Tank}, 4029 journal = {Ocean Engineering}, 4030 pages = {201--212}, 4031 year = {2014}, 4032 petsc_uses = {KSP} 4033} 4034 4035@Article{ castro2013bubble, 4036 author = {A. M. Castro and P. M. Carrica}, 4037 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 4038 evaluation and numerical issues}, 4039 journal = {International Journal of Multiphase Flow 57}, 4040 pages = {131--150}, 4041 year = {2013}, 4042 petsc_uses = {KSP} 4043} 4044 4045@Article{ carrica2013turn, 4046 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 4047 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 4048 Dynamic Overset Grids}, 4049 journal = {Journal of Marine Science and Technology}, 4050 pages = {166--181}, 4051 year = {2013}, 4052 petsc_uses = {KSP} 4053} 4054 4055@Article{ castro2013eulerian, 4056 author = {A. M. Castro and P. M. Carrica}, 4057 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 4058 {Athena} {R}/V,}, 4059 journal = {International Shipbuilding Progress}, 4060 pages = {403--433}, 4061 year = {2013}, 4062 petsc_uses = {KSP} 4063} 4064 4065@Article{ chase2013overset, 4066 author = {N. Chase and T. Michael and P. M. Carrica}, 4067 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 4068 {Maneuvering} {Conditions}}, 4069 journal = {International Shipbuilding Progress}, 4070 pages = {171--205}, 4071 year = {2013}, 4072 petsc_uses = {KSP} 4073} 4074 4075@Article{ sadathosseini2013wu, 4076 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 4077 Stern}, 4078 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 4079 Free Surge Conditions in Short and Long Head Waves}, 4080 journal = {Ocean Engineering}, 4081 volume = {59}, 4082 pages = {240--273}, 4083 year = {2013}, 4084 petsc_uses = {KSP} 4085} 4086 4087@Article{ chase2013cfd, 4088 author = {N. Chase and P. M. Carrica}, 4089 title = {CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a 4090 Submarine}, 4091 journal = {Ocean Engineering}, 4092 pages = {68--80}, 4093 year = {2013}, 4094 petsc_uses = {KSP} 4095} 4096 4097@Article{ carrica2012cfd, 4098 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 4099 title = {CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 4100 of Moving Rudders and Rotating Propellers}, 4101 journal = {Computers and Fluids 53}, 4102 pages = {117--132}, 4103 year = {2012}, 4104 petsc_uses = {KSP} 4105} 4106 4107@Article{ sakamoto2012urans, 4108 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 4109 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 4110 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 4111 publisher = {Journal of Marine Science and Technology}, 4112 pages = {422--445}, 4113 year = {2012}, 4114 petsc_uses = {KSP} 4115} 4116 4117@Article{ sakamoto2012uransb, 4118 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 4119 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 4120 Analysis and Validation of Local Flow Characteristics}, 4121 journal = {Journal of Marine Science and Technology}, 4122 pages = {446--468}, 4123 year = {2012}, 4124 petsc_uses = {KSP} 4125} 4126 4127@Article{ li2012dynamic, 4128 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 4129 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 4130 journal = {Renewable Energy}, 4131 pages = {285--298}, 4132 year = {2012}, 4133 petsc_uses = {KSP} 4134} 4135 4136@Article{ huang2012a, 4137 author = {J. Huang and P. M. Carrica and F. Stern}, 4138 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 4139 journal = {International Journal for Numerical Methods in Fluids}, 4140 pages = {160--180}, 4141 year = {2012}, 4142 petsc_uses = {KSP} 4143} 4144 4145@Article{ huang2012b, 4146 author = {J. Huang and P. M. Carrica and F. Stern}, 4147 title = {A geometry-based level set method for curvilinear overset grids with application 4148 to ship hydrodynamics}, 4149 journal = {International Journal for Numerical Methods in Fluids}, 4150 pages = {494--521}, 4151 year = {2012}, 4152 petsc_uses = {KSP} 4153} 4154 4155@Article{ carrica2011computations, 4156 author = {P. M. Carrica and H. Fu and F. Stern}, 4157 title = {Computations of self-propulsion free to sink and trim and of motions in head 4158 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 4159 journal = {Applied Ocean Research}, 4160 pages = {309--320}, 4161 year = {2011}, 4162 petsc_uses = {KSP} 4163} 4164 4165@Article{ bhushan2011scalability, 4166 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 4167 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 4168 Using {CFDShip}-Iowa}, 4169 journal = {International Journal of High Performance Computing Applications}, 4170 pages = {466--487}, 4171 year = {2011}, 4172 petsc_uses = {KSP} 4173} 4174 4175@Article{ castro2011full, 4176 author = {A. M. Castro and P. M. Carrica and F. Stern}, 4177 title = {Full scale self-propulsion computations using discretized propeller for the 4178 {KRISO} container ship {KCS}}, 4179 journal = {Computers and Fluids}, 4180 pages = {35--47}, 4181 year = {2011}, 4182 petsc_uses = {KSP} 4183} 4184 4185@Article{ kandasamy2011multifidelity, 4186 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 4187 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 4188 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran 4189 for Low Wake}, 4190 journal = {Journal of Marine Science and Technology}, 4191 pages = {143--156}, 4192 year = {2011}, 4193 petsc_uses = {KSP} 4194} 4195 4196@Article{ kandasamy2011cfd, 4197 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 4198 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 4199 title = {CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran}, 4200 journal = {Journal of Marine Science and Technology}, 4201 pages = {157--167}, 4202 year = {2011}, 4203 petsc_uses = {KSP} 4204} 4205 4206@Article{ sadathosseini2011cfd, 4207 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 4208 and S. Yamamura and A. Mastuda}, 4209 title = {CFD System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 4210 Periodic Motion and Broaching}, 4211 journal = {Ocean Engineering}, 4212 pages = {88--110}, 4213 year = {2011}, 4214 petsc_uses = {KSP} 4215} 4216 4217@Article{ mosaviraad2010development, 4218 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 4219 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 4220 with Comparison to Regular Wave and Transient Wave Group Procedures Using 4221 {URANS}}, 4222 journal = {Ocean Engineering}, 4223 pages = {653--666}, 4224 year = {2010}, 4225 petsc_uses = {KSP} 4226} 4227 4228@Article{ carrica2010largescale, 4229 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4230 Stern}, 4231 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 4232 Heave Problems for a Surface Combatant}, 4233 journal = {Computers and Fluids}, 4234 pages = {1095--1111}, 4235 year = {2010}, 4236 petsc_uses = {KSP} 4237} 4238 4239@Article{ carrica2010selfpropulsion, 4240 author = {P. M. Carrica and A. M. Castro and F. Stern}, 4241 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 4242 with Dynamic Overset Grids}, 4243 journal = {Journal of Marine Science and Technology}, 4244 pages = {316--330}, 4245 year = {2010}, 4246 petsc_uses = {KSP} 4247} 4248 4249@Article{ ismail2010evaluation, 4250 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 4251 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 4252 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 4253 journal = {International Journal of Numerical Methods in Fluids}, 4254 pages = {850--886}, 4255 year = {2010}, 4256 petsc_uses = {KSP} 4257} 4258 4259@Article{ kandasamy2010integral, 4260 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 4261 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 4262 journal = {Journal of Fluids Engineering}, 4263 pages = {101103}, 4264 year = {2010}, 4265 petsc_uses = {KSP} 4266} 4267 4268@Article{ kirk:2014de, 4269 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 4270 title = {{Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) 4271 stabilized finite element flow solver}}, 4272 journal = {Computers {\&} Fluids}, 4273 year = {2014}, 4274 volume = {92}, 4275 number = {0}, 4276 pages = {281--292}, 4277 month = mar, 4278 petsc_uses = {KSP} 4279} 4280 4281@Article{ carracciuolo20111382, 4282 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 4283 in high performance computing environment}, 4284 journal = {Journal of Non-Newtonian Fluid Mechanics }, 4285 volume = {166}, 4286 number = {23--24}, 4287 pages = {1382--1395}, 4288 year = {2011}, 4289 issn = {0377-0257}, 4290 doi = {10.1016/j.jnnfm.2011.08.014}, 4291 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 4292 Maffettone and A. Murli}, 4293 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 4294 method, High performance computing}, 4295 petsc_uses = {KSP} 4296} 4297 4298@Article{ bungartzgatzhammerliebmehlneckel11, 4299 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 4300 Miriam and Neckel, Tobias}, 4301 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 4302 journal = {Computational Mechanics}, 4303 volume = {48}, 4304 number = {3}, 4305 pages = {365-376}, 4306 year = {2011}, 4307 issn = {0178-7675}, 4308 doi = {10.1007/s00466-011-0626-1}, 4309 publisher = {Springer-Verlag}, 4310 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 4311 Thermohydraulics; Two-phase flow}, 4312 language = {English}, 4313 petsc_uses = {KSP} 4314} 4315 4316@Article{ bpr:cfl, 4317 author = {H.~M. B{\"u}cker and B. Pollul and A. Rasch}, 4318 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 4319 Equations}}, 4320 journal = {International Journal for Numerical Methods in Fluids}, 4321 year = {2009}, 4322 volume = {59}, 4323 number = {1}, 4324 pages = {1--18}, 4325 doi = {10.1002/fld.1798}, 4326 petsc_uses = {KSP} 4327} 4328 4329@InBook{ bonfiglioli_campobasso_carpentieri_2010, 4330 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 4331 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 4332 preconditioned newton-krylov solver}, 4333 publisher = {Curran Associates}, 4334 year = {2010}, 4335 url = {http://www.proceedings.com/05932.html}, 4336 petsc_uses = {KSP} 4337} 4338 4339@Article{ bonfiglioli_rans_2005, 4340 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 4341 Bernardo}, 4342 title = {RANS simulations of a junction flow}, 4343 journal = {International Journal of Computational Fluid Dynamics}, 4344 volume = {19}, 4345 number = {2}, 4346 pages = {179-189}, 4347 year = {2005}, 4348 doi = {10.1080/10618560410001729126}, 4349 petsc_uses = {KSP} 4350} 4351 4352@InCollection{ bonfiglioli__carpentieri_rans_2008, 4353 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 4354 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 4355 Italy}, 4356 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 4357 Equations Using Fluctuation Splitting Schemes}, 4358 booktitle = {Numerical Mathematics and Advanced Applications}, 4359 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 4360 publisher = {Springer Berlin Heidelberg}, 4361 isbn = {978-3-540-69777-0}, 4362 pages = {151-158}, 4363 doi = {10.1007/978-3-540-69777-0_17}, 4364 year = {2008}, 4365 petsc_uses = {KSP} 4366} 4367 4368@InCollection{ bonfiglioli__carpentieri_ens_2007, 4369 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 4370 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 4371 Italy}, 4372 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 4373 Problems on Unstructured Grids}, 4374 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 4375 series = {Lecture Notes in Computer Science}, 4376 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 4377 publisher = {Springer Berlin / Heidelberg}, 4378 isbn = {978-3-540-75754-2}, 4379 pages = {676-685}, 4380 volume = {4699}, 4381 doi = {10.1007/978-3-540-75755-9_83}, 4382 year = {2007}, 4383 petsc_uses = {KSP} 4384} 4385 4386@Article{ terrelscottknepleykirby08, 4387 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 4388 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 4389 journal = {BIT}, 4390 volume = {48}, 4391 number = {2}, 4392 year = {2008}, 4393 petsc_uses = {KSP} 4394} 4395 4396@Article{ martamadermartinsweidealonso07, 4397 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 4398 J. Alonso}, 4399 title = {A methodology for the development of discrete adjoint solvers using automatic 4400 differentiation tools}, 4401 journal = {Computational Fluid Dyanmics}, 4402 volume = {21}, 4403 pages = {307--327}, 4404 year = {2007}, 4405 petsc_uses = {KSP} 4406} 4407 4408@TechReport{ avb2008, 4409 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 4410 title = {Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface 4411 Waves}, 4412 year = {2008}, 4413 institution = {University of Twente, the Netherlands}, 4414 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 4415 petsc_uses = {KSP} 4416} 4417 4418@InProceedings{ bdsm2005, 4419 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal}, 4420 title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids}, 4421 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit}, 4422 year = {2005}, 4423 url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}, 4424 petsc_uses = {KSP} 4425} 4426 4427@InProceedings{ ms2006, 4428 author = {S. Muller and Y. Stiriba}, 4429 title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR 4430 STEADY COMPRESSIBLE FLOWS}, 4431 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006}, 4432 year = {2006}, 4433 url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}, 4434 petsc_uses = {KSP} 4435} 4436 4437@Article{ araujoteixeiracunhagroth08, 4438 author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth}, 4439 title = {Parallel three-dimensional simulation of the injection molding process}, 4440 journal = {International Journal for Numerical Methods in Fluids}, 4441 year = {2008}, 4442 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 4443 petsc_uses = {KSP} 4444} 4445 4446@PhDThesis{ a2008, 4447 author = {A. Cubero}, 4448 title = {a parallel coupled algorithm for collocated grids and its application to Large 4449 Eddy Simulation of a turbulent wake}, 4450 school = {University of Zaragoza (Spain)}, 4451 year = {2008}, 4452 petsc_uses = {KSP} 4453} 4454 4455@Article{ afa2007, 4456 author = {A. Cubero and N. Fueyo}, 4457 title = {A Compact Momentum Interpolation Method for unsteady flows and relaxation}, 4458 journal = {Numerical Heat Transfer, part B-Fundamentals}, 4459 volume = {56}, 4460 number = {6}, 4461 pages = {507--529}, 4462 year = {2007}, 4463 url = {http://www.informaworld.com/smpp/content~content=a782025305~db=all~order=page}, 4464 petsc_uses = {KSP} 4465} 4466 4467@TechReport{ af2007, 4468 title = {Preconditioning based on a partially implicit implementation of Momentum 4469 Interpolation for coupled solvers}, 4470 institution = {Fluid Mechanics Group of the University of Zaragoza (Spain)}, 4471 year = {2007}, 4472 author = {A. Cubero and N. Fueyo}, 4473 petsc_uses = {KSP} 4474} 4475 4476@InCollection{ dwight2004, 4477 author = {Richard Dwight}, 4478 title = {Robust Mesh Deformation using the Linear Elasticity Equations}, 4479 booktitle = {Computational Fluid Dynamics 2006}, 4480 editor = {H. Deconinck and E. Dick}, 4481 publisher = {Springer}, 4482 year = {2006}, 4483 url = {http://www.maths.man.ac.uk/\~{ 4484 }rdwight/pub/rdwight-ICCFD4-LinElastDeformation-2006.pdf}, 4485 petsc_uses = {KSP} 4486} 4487 4488@InProceedings{ dwight2006, 4489 author = {Richard Dwight and Joel Brezillon}, 4490 title = {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based 4491 Optimization}, 4492 booktitle = {Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. 4493 AIAA-2006-0690}, 4494 year = {2006}, 4495 url = {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-AIAAReno-ApproxAdjoint.pdf}, 4496 petsc_uses = {KSP} 4497} 4498 4499@PhDThesis{ dwight2006a, 4500 author = {Richard Dwight}, 4501 title = {Efficiency Improvements of {RANS}-Based Analysis and Optimization using Implicit 4502 and Adjoint Methods on Unstructured Grids}, 4503 school = {School of Mathematics, University of Manchester}, 4504 year = {2006}, 4505 url = {http://www.maths.man.ac.uk/\~{ 4506 }rdwight/pub/rdwight-PhDThesis-ImplicitAndAdjoint.pdf}, 4507 petsc_uses = {KSP} 4508} 4509 4510@InProceedings{ lhdfrh, 4511 author = {M. Lauter and D. Handorf and K. Dethloff and S. Frickenhaus and N. Rakowsky and 4512 W. Hiller}, 4513 title = {An adaptive Lagrange-Galerkin shallow-water model on the sphere}, 4514 booktitle = {Workshop Proceedings Current Development in Shallow Water Models on the Sphere 4515 March, 10-14, 2003, Munich University of Technology, German}, 4516 year = {2003}, 4517 petsc_uses = {KSP} 4518} 4519 4520@InProceedings{ brios-ying-2002, 4521 author = {George Biros and Lexing Ying and Denis Zorin}, 4522 title = {The Embedded Boundary Integral Method (EBI) for the Incompressible 4523 {Navier-Stokes} equations}, 4524 booktitle = {IABEM 2002, International Association for Boundary Element Methods, UT Austin}, 4525 year = {2002}, 4526 petsc_uses = {KSP} 4527} 4528 4529@InProceedings{ mohsen-straatman-ins, 4530 author = {S.A. Mohsen Karimian and Anthony G. Straatman}, 4531 title = {Benchmarking of a {3D}, unstructured, finite volume code for incompressible 4532 {Navier-Stokes} equation on a cluster of distributed-memory computers}, 4533 booktitle = {Proceedings of the 19th International Symposium on High Performance Computing 4534 Systems and Applications}, 4535 pages = {11--16}, 4536 year = {2005}, 4537 url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046}, 4538 petsc_uses = {KSP} 4539} 4540 4541@TechReport{ bonglioli-icnmfd98, 4542 title = {Multidimensional Residual Distribution Schemes for the Pseudo-Compressible 4543 {Euler} and {Navier-Stokes} equations on Unstructured Meshes}, 4544 institution = {Universita della Basilicata via della Tecnica 3}, 4545 year = {1996}, 4546 author = {A. Bonglioli}, 4547 url = {http://www.unibas.it/utenti/bonfiglioli/icnmfd98.ps.gz}, 4548 petsc_uses = {KSP} 4549} 4550 4551@Article{ deng-piquet-ctf, 4552 author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"}, 4553 title = {A new fully coupled method for computing turbulent flows}, 4554 journal = {Computers and Fluids}, 4555 volume = {30}, 4556 pages = {445--472}, 4557 year = {2001}, 4558 petsc_uses = {KSP} 4559} 4560 4561@InProceedings{ knepleysarinsameh99b, 4562 title = {Multilevel Preconditioning for Parallel {CFD}}, 4563 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 4564 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 4565 Problems In Industrial Applications}, 4566 address = {Minneapolis, MN}, 4567 month = {June}, 4568 year = {1999}, 4569 petsc_uses = {KSP} 4570} 4571 4572@InProceedings{ garbey1, 4573 author = {M. Garbey and B. Hadri and W. Shyy.}, 4574 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 4575 Problems on the Grid}, 4576 booktitle = {Aerospace Sciences Meeting and Exhibit}, 4577 note = {Paper No. 2005-1386}, 4578 year = {2005}, 4579 petsc_uses = {KSP} 4580} 4581 4582@Article{ carrica2007unsteady, 4583 title = {An unsteady single-phase level set method for viscous free surface flows}, 4584 author = {Carrica, PM and Wilson, RV and Stern, F.}, 4585 journal = {International Journal for Numerical Methods in Fluids}, 4586 volume = {53}, 4587 number = {2}, 4588 pages = {229--256}, 4589 year = {2007}, 4590 publisher = {Chichester; New York: Wiley, c1981-}, 4591 petsc_uses = {KSP} 4592} 4593 4594@Article{ pctw2004, 4595 author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber}, 4596 title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of 4597 Spillways}, 4598 journal = {Journal of Hydraulic Research}, 4599 note = {accepted for publication}, 4600 year = {2004}, 4601 petsc_uses = {KSP} 4602} 4603 4604@Article{ wcs2004, 4605 author = {R. V. Wilson and P. M. Carrica and F. Stern}, 4606 title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface 4607 Combatant}, 4608 journal = {Computers and Fluids}, 4609 note = {in press}, 4610 year = {2004}, 4611 petsc_uses = {KSP} 4612} 4613 4614@Article{ cws2005, 4615 author = {P. M. Carrica and R. V. Wilson and F. Stern}, 4616 title = {Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem}, 4617 journal = {Computers and Fluids}, 4618 note = {accepted for publication}, 4619 year = {2005}, 4620 petsc_uses = {KSP} 4621} 4622 4623@Article{ chndss2010, 4624 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4625 Stern}, 4626 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 4627 Heave Problems for a Surface Combatant}, 4628 journal = {Computers and Fluids}, 4629 year = {2010}, 4630 volume = {39}, 4631 number = {7}, 4632 pages = {1095--1111}, 4633 petsc_uses = {KSP} 4634} 4635 4636@InProceedings{ chnkss2008, 4637 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 4638 Stern}, 4639 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 4640 Grids}, 4641 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 4642 year = {2008}, 4643 petsc_uses = {KSP} 4644} 4645 4646@MastersThesis{ mtj, 4647 author = {M. T. Jozkowski}, 4648 title = {Application of Algebraic Multigrid Methods to the Solution of Stratified Flows 4649 About Submerged Bodies}, 4650 school = {The Pennsylvania State University}, 4651 year = {2005}, 4652 petsc_uses = {KSP} 4653} 4654 4655@Article{ pp, 4656 author = {E. G. Paterson and L. J. Peltier}, 4657 title = {Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and 4658 Wakes}, 4659 journal = {ASME Journal of Fluids Engineering}, 4660 note = {In press}, 4661 year = {2005}, 4662 petsc_uses = {KSP} 4663} 4664 4665@Article{ eps, 4666 author = {B. A. Edge and E. G. Paterson and G. Settles}, 4667 title = {Computational Study of the Wake and Contaminant Transport of a Walking Human}, 4668 journal = {ASME Journal of Fluids Engineering}, 4669 note = {In press}, 4670 year = {2005}, 4671 petsc_uses = {KSP} 4672} 4673 4674@InProceedings{ rp, 4675 author = {B. Racine and E. G. Paterson}, 4676 title = {Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines 4677 Using Unsteady {RANS} {CFD}}, 4678 booktitle = {35th AIAA Fluid Dynamics Conference and Exhibit}, 4679 year = {2005}, 4680 petsc_uses = {KSP} 4681} 4682 4683@InProceedings{ etpp, 4684 author = {B. A. Edge and M. F. Trujillo and E. G. Paterson and L. J. Peltier}, 4685 title = {Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids 4686 and DES}, 4687 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 4688 year = {2004}, 4689 petsc_uses = {KSP} 4690} 4691 4692@InProceedings{ pp8, 4693 author = {E. G. Paterson and L. J. Peltier}, 4694 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 4695 refinement grids and detached-eddy simulation}, 4696 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 4697 year = {2004}, 4698 petsc_uses = {KSP} 4699} 4700 4701@InProceedings{ mzwp, 4702 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 4703 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 4704 booktitle = {25th Symposium on Naval Hydrodynamics}, 4705 year = {2004}, 4706 petsc_uses = {KSP} 4707} 4708 4709@InProceedings{ ppph, 4710 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 4711 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 4712 booktitle = {25th Symposium on Naval Hydrodynamics}, 4713 year = {2004}, 4714 petsc_uses = {KSP} 4715} 4716 4717@InProceedings{ ppd, 4718 author = {E. G. Paterson and L. J. Peltier}, 4719 title = {Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes}, 4720 booktitle = {Symposium on LES Advancements and Applications, ASME FED Summer Meeting}, 4721 year = {2004}, 4722 petsc_uses = {KSP} 4723} 4724 4725@InProceedings{ bp, 4726 author = {W. J. Baker and E. G. and Paterson}, 4727 title = {Simulation of Steady Circulation Control for the General Aviation Circulation 4728 Control Wing}, 4729 booktitle = {NASA/ONR Workshop on Circulation Control}, 4730 year = {2004}, 4731 petsc_uses = {KSP} 4732} 4733 4734@InProceedings{ pb, 4735 author = {E. G. Paterson and W. J. Baker}, 4736 title = {RANS and Detached-Eddy Simulation of the NCCR airfoil}, 4737 booktitle = {NASA/ONR Workshop on Circulation Control}, 4738 year = {2004}, 4739 petsc_uses = {KSP} 4740} 4741 4742@InProceedings{ pb3, 4743 author = {E. G. Paterson and W. J. Baker}, 4744 title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control 4745 Surfaces}, 4746 booktitle = {42nd AIAA Aerospace Sciences Meeting}, 4747 year = {2004}, 4748 petsc_uses = {KSP} 4749} 4750 4751@InProceedings{ gid1, 4752 author = {G. Frank and J. D'Elia}, 4753 title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model}, 4754 year = {2004}, 4755 booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD}, 4756 url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf}, 4757 petsc_uses = {KSP} 4758} 4759 4760@InBook{ b1, 4761 author = {A.Bonfiglioli}, 4762 chapter = {On the use of the PETSc library for unstructured {CFD} applications}, 4763 year = {2001}, 4764 title = {Science and Supercomputing at CINECA}, 4765 pages = {397--400}, 4766 petsc_uses = {KSP} 4767} 4768 4769@InProceedings{ b2004, 4770 author = {L. A. Barba}, 4771 title = {Computing high-Reynolds number vortical flows: a highly accurate method with a 4772 fully meshless formulation}, 4773 year = {2004}, 4774 booktitle = {International Conference on Parallel CFD, Grand Canary, May 2004}, 4775 note = {Submitted}, 4776 petsc_uses = {KSP} 4777} 4778 4779@InProceedings{ bl2004, 4780 author = {L. A. Barba and A. Leonard}, 4781 title = {Computation of Viscous Vortices with Fully Meshless Method}, 4782 year = {2004}, 4783 booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004}, 4784 note = {Submitted}, 4785 petsc_uses = {KSP} 4786} 4787 4788@Article{ vws1, 4789 author = {B. G. M. Van Wachem and J. C. Schouten}, 4790 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 4791 Velocity}, 4792 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 4793 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 4794 Netherlands}, 4795 journal = {AIChE}, 4796 volumne = {48}, 4797 number = {12}, 4798 month = {December}, 4799 year = {2002}, 4800 petsc_uses = {KSP} 4801} 4802 4803@TechReport{ lbam1, 4804 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 4805 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 4806 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 4807 di Bari Italy}, 4808 year = {2002}, 4809 number = {25/02}, 4810 petsc_uses = {KSP} 4811} 4812 4813@Article{ kees_miller_02, 4814 author = {C. E. Kees and C. T. Miller}, 4815 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 4816 journal = {Advances in Water Resources}, 4817 year = {2002}, 4818 volume = {25}, 4819 number = {2}, 4820 pages = {159-177.}, 4821 petsc_uses = {KSP} 4822} 4823 4824@InProceedings{ lepotmeersessers2001, 4825 author = {I. Lepot and F. Meers and J.A. Essers}, 4826 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 4827 Unstructured Meshes}, 4828 year = {2001}, 4829 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 4830 url = {http://www.ulg.ac.be/aerodyn}, 4831 petsc_uses = {KSP} 4832} 4833 4834@InProceedings{ knepley98, 4835 author = {Matthew Knepley and Denis Vanderstraeten}, 4836 title = {Parallel Building Blocks for Finite Element Simulations: Application to 4837 Solid-Liquid Mixture Flows}, 4838 booktitle = {Proceedings of Parallel CFD'97}, 4839 publisher = {Elsevier}, 4840 pages = {281--287}, 4841 year = {1998}, 4842 petsc_uses = {KSP} 4843} 4844 4845@InProceedings{ pcfd97, 4846 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 4847 title = {Parallel Implicit {PDE} Computations: Algorithms and Software}, 4848 publisher = {Elsevier}, 4849 year = {1998}, 4850 booktitle = {Proceedings of Parallel CFD'97}, 4851 pages = {333-344}, 4852 petsc_uses = {KSP} 4853} 4854 4855@InProceedings{ knepleysamehsari98, 4856 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 4857 title = {Parallel Simulation of Particulate Flows}, 4858 booktitle = {Solving Irregularly Structured Problems in Parallel}, 4859 editors = {A. Ferreira et al}, 4860 year = {1998}, 4861 series = {Lecture Notes in Computer Science}, 4862 volume = {1457}, 4863 pages = {226--237}, 4864 petsc_uses = {KSP} 4865} 4866 4867@Article{ gkmt98, 4868 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 4869 title = {Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel 4870 Implicit {CFD}}, 4871 journal = {Int. J. High Performance Computing Applications}, 4872 year = {2000}, 4873 volume = {14}, 4874 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 4875 pages = {102-136}, 4876 petsc_uses = {KSP} 4877} 4878 4879@InProceedings{ agkks-sc99, 4880 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 4881 Smith}, 4882 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 4883 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 4884 editor = {}, 4885 publisher = {}, 4886 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 4887 year = {1999}, 4888 note = {Winner of Gordon Bell Special Prize at SC 99}, 4889 petsc_uses = {KSP} 4890} 4891 4892@Article{ gkks01, 4893 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4894 title = {High Performance Parallel Implicit {CFD}}, 4895 journal = {Journal of Parallel Computing}, 4896 year = {2001}, 4897 volume = {27}, 4898 pages = {337-362}, 4899 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 4900 petsc_uses = {KSP} 4901} 4902 4903@Article{ cristea-sofonea-02, 4904 author = {Artur Cristea and Victor Sofonea}, 4905 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 4906 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 4907 Sciences, Information Sciences}, 4908 volume = {3}, 4909 number = {3}, 4910 year = {2002}, 4911 petsc_uses = {KSP} 4912} 4913 4914@Article{ cristea2, 4915 author = {Artur Cristea and Victor Sofonea}, 4916 title = {Two component lattice Boltzmann model with flux limiter techniques}, 4917 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 4918 Sciences, Information Sciences}, 4919 volume = {4}, 4920 number = {1}, 4921 year = {2003}, 4922 pages = {59--64}, 4923 petsc_uses = {KSP} 4924} 4925 4926@Article{ cristea1, 4927 author = {Artur Cristea and Victor Sofonea}, 4928 title = {Two component lattice Boltzmann model with flux limiters}, 4929 journal = {Central European Journal of Physics}, 4930 volume = {2}, 4931 number = {2}, 4932 year = {2004}, 4933 pages = {382--396}, 4934 petsc_uses = {KSP} 4935} 4936 4937@Article{ sofnea-lamura1, 4938 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 4939 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 4940 systems}, 4941 journal = {Physical Review E}, 4942 volume = {70}, 4943 number = {4}, 4944 year = {2004}, 4945 pages = {046702-1 / 046702-9}, 4946 petsc_uses = {KSP} 4947} 4948 4949@InProceedings{ gkks01b, 4950 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4951 title = {Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}}, 4952 booktitle = {Proceedings of the First MIT Conference on Computational Fluid and Solid 4953 Mechanics}, 4954 editor = {}, 4955 location = {Cambridge, MA}, 4956 year = {2001}, 4957 month = jun, 4958 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf}, 4959 petsc_uses = {KSP} 4960} 4961 4962@InProceedings{ gkks00, 4963 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4964 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 4965 Code}, 4966 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 4967 (HiPC '2000)}, 4968 editor = {}, 4969 location = {Bangalore, India}, 4970 year = {2000}, 4971 pages = {395--404}, 4972 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 4973 petsc_uses = {KSP} 4974} 4975 4976@InProceedings{ gkks-sc00, 4977 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 4978 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 4979 booktitle = {Proceedings of SC2000}, 4980 editor = {}, 4981 publisher = {IEEE Computer Society}, 4982 year = {2000}, 4983 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 4984 petsc_uses = {KSP} 4985} 4986 4987@InProceedings{ knepleysamehsarin99, 4988 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 4989 title = {Design of Large Scale Parallel Simulations}, 4990 booktitle = {Proceedings of Parallel CFD'99}, 4991 editors = {A. {Ecer et al.}}, 4992 publisher = {Elsevier}, 4993 year = {1999}, 4994 petsc_uses = {KSP} 4995} 4996 4997@InProceedings{ gkks-pcfd99, 4998 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 4999 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 5000 booktitle = {Proceedings of Parallel CFD'99}, 5001 editors = {A. {Ecer et al.}}, 5002 publisher = {Elsevier}, 5003 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 5004 year = {1999}, 5005 petsc_uses = {KSP} 5006} 5007 5008@InProceedings{ kks97, 5009 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 5010 title = {On the Interaction of Architecture and Algorithm in the Domain-Based 5011 Parallelization of an Unstructured Grid Incompressible Flow Code}, 5012 booktitle = {Proceedings of the 10th International Conference on Domain Decomposition 5013 Methods}, 5014 editor = {J. Mandel et al.}, 5015 pages = {311--319}, 5016 publisher = {Wiley}, 5017 note = {}, 5018 year = {1997}, 5019 petsc_uses = {KSP} 5020} 5021 5022@InProceedings{ kks99, 5023 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 5024 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 5025 Incompressible Flows on Unstructured Grids}, 5026 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 5027 Methods}, 5028 editors = {C.-H. {Lai et al.}}, 5029 publisher = {Domain Decomposition Press, Bergen}, 5030 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 5031 year = {1999}, 5032 petsc_uses = {KSP} 5033} 5034 5035@InCollection{ kks97_cfd, 5036 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 5037 title = {Perspectives for {CFD} on Petaflops Systems}, 5038 booktitle = {CFD Review 1998}, 5039 editor = {M. Hafez and K. Oshima}, 5040 publisher = {World Scientific, Singapore}, 5041 pages = {1079--1096}, 5042 note = {}, 5043 year = {1998}, 5044 petsc_uses = {KSP} 5045} 5046 5047@Article{ hm99, 5048 author = {P. D. Hovland and L. C. McInnes}, 5049 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 5050 {PETSc}}, 5051 year = {2000}, 5052 journal = {Parallel Computing}, 5053 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 5054 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 5055 petsc_uses = {KSP} 5056} 5057 5058@InProceedings{ cruzbarbaknepley08, 5059 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 5060 title = {Fast Multipole Method for particle interactions: an open source parallel library 5061 component}, 5062 booktitle = {Proceedings of ParCFD2008}, 5063 year = {2008}, 5064 editor = {Tromeur-Dervout et. al.}, 5065 publisher = {Elsevier}, 5066 petsc_uses = {KSP} 5067} 5068 5069@Article{ hwangcai05, 5070 author = {F.-N. Hwang and X.-C. Cai}, 5071 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 5072 for incompressible {Navier-Stokes} equations}, 5073 journal = {J. Comput. Phys.}, 5074 volume = {204}, 5075 year = {2005}, 5076 pages = {666--691}, 5077 petsc_uses = {KSP} 5078} 5079 5080@Article{ barbaleonard07, 5081 author = {Lorena A Barba and Anthony Leonard}, 5082 title = {Emergence and evolution of tripole vortices from net-circulation initial 5083 conditions}, 5084 journal = {Phys. Fluids}, 5085 volume = {19}, 5086 pages = {017101}, 5087 year = {2007}, 5088 doi = {10.1063/1.2409734}, 5089 petsc_uses = {KSP} 5090} 5091 5092@Article{ barba07, 5093 author = {Lorena A Barba}, 5094 title = {Non-shielded multipolar vortices at high Reynolds number}, 5095 journal = {Phys. Rev. E}, 5096 volume = {73}, 5097 pages = {065303}, 5098 year = {2006}, 5099 doi = {10.1103/PhysRevE.73.065303}, 5100 petsc_uses = {KSP} 5101} 5102 5103@Article{ schofield2010multi, 5104 title = {Multi-material incompressible flow simulation using the moment-of-fluid method}, 5105 author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and 5106 Lowrie, R.B. and Swartz, B.K.}, 5107 journal = {International Journal for Numerical Methods in Fluids}, 5108 volume = {63}, 5109 number = {8}, 5110 pages = {931--952}, 5111 year = {2010}, 5112 publisher = {Wiley Online Library}, 5113 petsc_uses = {KSP} 5114} 5115 5116% LiteralHTML: 5117% LiteralHTML: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3> 5118% LiteralHTML: 5119% LiteralHTML: article{DeGersem99, 5120% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, 5121% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, 5122% LiteralHTML: } 5123@Article{ nagler2014, 5124 title = {Sound transmission through a poroelastic layered panel}, 5125 author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff}, 5126 journal = {Computational Mechanics}, 5127 volume = {53}, 5128 number = {4}, 5129 pages = {549--560}, 5130 issn = {1432-0924}, 5131 doi = {10.1007/s00466-013-0916-x}, 5132 year = {2014}, 5133 petsc_uses = {KSP} 5134} 5135 5136@Article{ sheikh2013, 5137 author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.}, 5138 title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel 5139 deflation}, 5140 journal = {Numerical Linear Algebra with Applications}, 5141 volume = {20}, 5142 number = {4}, 5143 issn = {1099-1506}, 5144 doi = {10.1002/nla.1882}, 5145 pages = {645--662}, 5146 keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier 5147 analysis}, 5148 year = {2013}, 5149 petsc_uses = {KSP} 5150} 5151 5152@InProceedings{ silence, 5153 author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. 5154 Fuenmayor}, 5155 title = {A parallel computing approach for solving the Helmholtz equation in 3D domains: 5156 Application to the study of acoustic behaviour of silencers}, 5157 year = {2004}, 5158 booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering 5159 (ECCOMAS)}, 5160 petsc_uses = {KSP} 5161} 5162 5163@Article{ degersem99, 5164 author = {H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer}, 5165 title = {Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods 5166 to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations}, 5167 journal = {COMPEL}, 5168 year = {1999}, 5169 volume = {18}, 5170 number = {3}, 5171 pages = {298--310}, 5172 bibdate = {}, 5173 petsc_uses = {KSP} 5174} 5175 5176@InProceedings{ widlund-wave-98, 5177 author = {Olof B. Widlund}, 5178 title = {Schwarz Methods for {H}elmholtz's Equation}, 5179 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 5180 editor = {John A. DeSanto}, 5181 year = {1998}, 5182 publisher = {SIAM}, 5183 pages = {620--622}, 5184 address = {Philadelphia}, 5185 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 5186 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 5187 petsc_uses = {KSP} 5188} 5189 5190@InProceedings{ toselli-wave-98, 5191 author = {Andrea Toselli}, 5192 title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media}, 5193 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 5194 editor = {John A. DeSanto}, 5195 year = {1998}, 5196 publisher = {SIAM}, 5197 address = {Philadelphia}, 5198 pages = {540--542}, 5199 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 5200 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 5201 petsc_uses = {KSP} 5202} 5203 5204@InProceedings{ mcinnes-wave-98, 5205 author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes}, 5206 title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods}, 5207 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 5208 editor = {John A. DeSanto}, 5209 year = {1998}, 5210 publisher = {SIAM}, 5211 address = {Philadelphia}, 5212 pages = {623--625}, 5213 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 5214 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 5215 petsc_uses = {KSP} 5216} 5217 5218@InProceedings{ mska98, 5219 author = {L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi}, 5220 title = {Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the 5221 Parallel Computation of {H}elmholtz Problems}, 5222 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 5223 editor = {J. Mandel et al.}, 5224 publisher = {AMS}, 5225 pages = {349--357}, 5226 year = {1998}, 5227 petsc_uses = {KSP} 5228} 5229 5230@InProceedings{ ccew98, 5231 author = {X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund}, 5232 title = {Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation}, 5233 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 5234 editor = {J. Mandel et al.}, 5235 publisher = {AMS}, 5236 pages = {437-445}, 5237 year = {1998}, 5238 petsc_uses = {KSP} 5239} 5240 5241@InProceedings{ ra98a, 5242 author = {R. Susan-Resiga and H. M. Atassi}, 5243 title = {Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic 5244 Problems}, 5245 booktitle = {Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference}, 5246 publisher = {AIAA}, 5247 pages = {86-96}, 5248 note = {AIAA paper 98-2218}, 5249 year = {1998}, 5250 petsc_uses = {KSP} 5251} 5252 5253@InProceedings{ ar98c, 5254 author = {H. M. Atassi and R. Susan-Resiga}, 5255 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: 5256 General Formulation}, 5257 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 5258 publisher = {ASME}, 5259 note = {NCA-25}, 5260 pages = {375-379}, 5261 year = {1998}, 5262 petsc_uses = {KSP} 5263} 5264 5265@InProceedings{ ra98b, 5266 author = {R. Susan-Resiga and H. M. Atassi}, 5267 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: 5268 Numerical Implementation and Applications}, 5269 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 5270 publisher = {ASME}, 5271 note = {NCA-25}, 5272 pages = {381 -388}, 5273 year = {1998}, 5274 petsc_uses = {KSP} 5275} 5276 5277@InProceedings{ cai-dd10-98, 5278 author = {Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. 5279 Widlund}, 5280 title = {Overlapping {S}chwarz methods for solving {H}elmholtz's Equation}, 5281 booktitle = {Domain Decomposition Methods 10}, 5282 editors = {Jan Mandel and Charbel Farhat and Xiao-Chuan Cai}, 5283 series = {Contemporary Mathematics}, 5284 volume = {218}, 5285 publisher = {American Mathematical Society}, 5286 address = {Providence, Rhode Island}, 5287 year = {1998}, 5288 pages = {437--445}, 5289 petsc_uses = {KSP} 5290} 5291 5292@InProceedings{ alghamdi2011petclaw, 5293 title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython}, 5294 booktitle = {Proceedings of SpringSim 2011}, 5295 publisher = {ACM}, 5296 author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and 5297 Kyle T. Mandli and Lisandro Dalcin}, 5298 year = {2011}, 5299 petsc_uses = {KSP} 5300} 5301 5302@Article{ pyclaw2012, 5303 author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and 5304 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 5305 Emmett}, 5306 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 5307 journal = {SIAM Journal on Scientific Computing}, 5308 volume = {34}, 5309 number = {4}, 5310 pages = {C210--C231}, 5311 note = {\url{http://arxiv.org/abs/1111.6583}}, 5312 year = {2012}, 5313 petsc_uses = {KSP} 5314} 5315 5316% LiteralHTML: 5317% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 5318% LiteralHTML: 5319@Article{ sojkahorakhaplacermak2018, 5320 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 5321 decomposition method}, 5322 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 5323 journal = {Applied Mathematics and Computation}, 5324 volume = {319}, 5325 pages = {586--597}, 5326 year = {2018}, 5327 petsc_uses = {KSP} 5328} 5329 5330@Article{ chencai2014, 5331 title = {A parallel two-level domain decomposition based one-shot method for shape 5332 optimization problems}, 5333 author = {Rongliang Chen and Xiao‐Chuan Cai}, 5334 journal = {International Journal for Numerical Methods in Engineering}, 5335 volume = {99}, 5336 number = {13}, 5337 year = {2014}, 5338 doi = {10.1002/nme.4711}, 5339 petsc_uses = {KSP} 5340} 5341 5342@PhDThesis{ prudencio2005, 5343 author = {Ernesto Prudencio}, 5344 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 5345 for Optimization Problems Constrained by Partial Differential Equations}, 5346 school = {University of Colorado, Boulder}, 5347 year = {2005}, 5348 petsc_uses = {KSP} 5349} 5350 5351@Article{ prudenciocai2007, 5352 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 5353 for {PDE}-constrained optimization}, 5354 author = {Ernesto Prudencio and X. C. Cai}, 5355 journal = {SIAM J. Sci. Comp.}, 5356 volume = {29}, 5357 number = {3}, 5358 pages = {964--985}, 5359 year = {2007}, 5360 petsc_uses = {KSP} 5361} 5362 5363@Article{ prudenciobyrdcai2006, 5364 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 5365 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 5366 {PDE}-constrained Optimization Problems}, 5367 journal = {SIAM J. Sci. Comp.}, 5368 volume = {27}, 5369 pages = {1305--1328}, 5370 year = {2006}, 5371 petsc_uses = {KSP} 5372} 5373 5374@InProceedings{ prudenciobyrdcai2004, 5375 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 5376 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 5377 booktitle = {VECPAR 2004}, 5378 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 5379 publisher = {Springer}, 5380 pages = {569--582}, 5381 year = {2004}, 5382 petsc_uses = {KSP} 5383} 5384 5385@Article{ belhamadia-fortin-pcp, 5386 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 5387 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 5388 journal = {Journal of Computational Physics}, 5389 volume = {201}, 5390 pages = {753-770}, 5391 year = {2004}, 5392 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 5393 petsc_uses = {KSP} 5394} 5395 5396@Article{ biros00, 5397 author = {George Biros and Omar Ghattas}, 5398 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 5399 journal = {SIAG-Opt Views and News}, 5400 volume = {11}, 5401 number = {2}, 5402 year = {2000}, 5403 month = {august}, 5404 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 5405 petsc_uses = {KSP} 5406} 5407 5408@Article{ bmm01, 5409 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 5410 journal = {ACM Transactions on Mathematical Software}, 5411 title = {A case study in the performance and scalability of optimization algorithms}, 5412 year = {2001}, 5413 volume = {27}, 5414 number = {3}, 5415 pages = {361--376}, 5416 petsc_uses = {KSP} 5417} 5418 5419@InProceedings{ oghattas1999, 5420 author = {George Biros and Omar Ghattas}, 5421 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 5422 incompressible flows}, 5423 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 5424 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 5425 year = {1999}, 5426 petsc_uses = {KSP} 5427} 5428 5429@InProceedings{ hkms00, 5430 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 5431 PDE-constrained Optimization}, 5432 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 5433 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 5434 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 5435 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 5436 Hasco\"{e}t and Uwe Naumann}, 5437 publisher = {Springer}, 5438 year = {2002}, 5439 petsc_uses = {KSP} 5440} 5441 5442% old version: replace with biros2005pln1 5443@TechReport{ bg011, 5444 author = {George Biros and Omar Ghattas}, 5445 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 5446 Part I: The Krylov-Schur Solver}, 5447 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 5448 year = {2001}, 5449 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 5450 petsc_uses = {KSP} 5451} 5452 5453% old version: replace with biros2005pln2 5454@TechReport{ bg012, 5455 author = {George Biros and Omar Ghattas}, 5456 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 5457 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 5458 Optimal Control of Steady Viscous Flows}, 5459 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 5460 year = {2001}, 5461 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 5462 petsc_uses = {KSP} 5463} 5464 5465% LiteralHTML: 5466% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 5467% LiteralHTML: 5468@InProceedings{ ly2003, 5469 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 5470 title = {A New Parallel Kernel-independent Fast Multipole Method}, 5471 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 5472 year = {2003}, 5473 note = {Winner of the Best Student Paper at SC2003}, 5474 petsc_uses = {KSP} 5475} 5476 5477@Article{ yokotabarbaknepley10, 5478 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 5479 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 5480 journal = {Computer Methods in Applied Mechanics and Engineering}, 5481 volume = {199}, 5482 number = {25-28}, 5483 pages = {1793--1804}, 5484 url = {http://arxiv.org/abs/0909.5413v1}, 5485 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 5486 year = {2010}, 5487 petsc_uses = {KSP} 5488} 5489 5490@Article{ cruzknepleybarba10, 5491 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 5492 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 5493 journal = {International Journal of Numerical Methods in Engineering}, 5494 volume = {85}, 5495 number = {4}, 5496 pages = {403--428}, 5497 url = {http://arxiv.org/abs/0905.2637}, 5498 note = {\url{http://arxiv.org/abs/0905.2637}}, 5499 year = {2010}, 5500 petsc_uses = {KSP} 5501} 5502 5503% LiteralHTML: 5504% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 5505% LiteralHTML: 5506@Article{ buchanpainumplebysmedleystevenson2012, 5507 title = {A sub-grid scale finite element agglomeration multigrid method with application 5508 to the Boltzmann transport equation}, 5509 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 5510 journal = {International Journal for Numerical Methods in Engineering}, 5511 volume = {92}, 5512 number = {3}, 5513 pages = {318--342}, 5514 year = {2012}, 5515 publisher = {Wiley Online Library}, 5516 petsc_uses = {KSP} 5517} 5518 5519@Article{ magoulesahamedsuzuki2015, 5520 title = {Green computing on graphics processing units}, 5521 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 5522 journal = {Concurrency and Computation: Practice and Experience}, 5523 year = {2015}, 5524 publisher = {Wiley Online Library}, 5525 petsc_uses = {KSP} 5526} 5527 5528@InProceedings{ yanrhodes11, 5529 author = {Yan, Baoqiang and Rhodes, Philip J.}, 5530 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 5531 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 5532 series = {ICPP '11}, 5533 pages = {355--364}, 5534 year = {2011}, 5535 isbn = {978-0-7695-4510-3}, 5536 numpages = {10}, 5537 doi = {10.1109/ICPP.2011.70}, 5538 acmid = {2066965}, 5539 publisher = {IEEE Computer Society}, 5540 address = {Washington, DC, USA}, 5541 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 5542 petsc_uses = {KSP} 5543} 5544 5545@Article{ hakansson2013mdstochasticliouville, 5546 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 5547 Stulz, Eugen}, 5548 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 5549 equation study}, 5550 journal = {Phys. Chem. Chem. Phys.}, 5551 year = {2013}, 5552 volume = {15}, 5553 issue = {26}, 5554 pages = {10930-10941}, 5555 publisher = {The Royal Society of Chemistry}, 5556 doi = {10.1039/C3CP50788B}, 5557 petsc_uses = {KSP} 5558} 5559 5560@Article{ hakansson2011stochasticliouville, 5561 author = {Hakansson, Par and Nair, Prasanth B.}, 5562 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 5563 form}, 5564 journal = {Phys. Chem. Chem. 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Tarucha and John Fettig and Nahil Sobh}, 6099 title = {Spin configurations in circular and rectangular vertical quantum dots in a 6100 magnetic field: Three-dimensional self-consistent simulation}, 6101 year = {2005}, 6102 number = {Arxiv preprint cond-mat/0506585}, 6103 url = {http://arxiv.org/pdf/cond-mat/0506585}, 6104 petsc_uses = {KSP} 6105} 6106 6107@InProceedings{ richard-smedley-03, 6108 author = {Richard P. Smedley-Stevenson}, 6109 title = {PARALLEL THERMAL RADIATION TRANSPORT IN TWO DIMENSIONS}, 6110 year = {2003}, 6111 booktitle = {18th International Conference on Transport Theory (18 ICTT)}, 6112 url = {http://www.iprj.uerj.br/\~{ }ricardob/Evento_Cientifico_html/poster03j.pdf}, 6113 petsc_uses = {KSP} 6114} 6115 6116@Article{ guan-godoy-ravaioli-03, 6117 author = {D. Guan and A. Godoy and U. Ravaioli and F. 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Cooke}, 6182 title = {Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three 6183 Dimensions}, 6184 year = {2004}, 6185 booktitle = {40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit}, 6186 url = {http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282}, 6187 petsc_uses = {KSP} 6188} 6189 6190@InProceedings{ allard-gouranton-ipts2002, 6191 author = {Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin}, 6192 title = {Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster}, 6193 year = {2002}, 6194 booktitle = {Immersive Projection Technology Symposium}, 6195 url = {http://www-id.imag.fr/\~{ }allardj/files/ipts2002.pdf}, 6196 petsc_uses = {KSP} 6197} 6198 6199@Article{ icc, 6200 author = {D Ioan and G Ciuprina and C Ciobotaru}, 6201 title = {Hybrid and concurrent algorithms for nonlinear magnetic field problems}, 6202 journal = {IEEE Transactions on Magnetics}, 6203 year = {2000}, 6204 url = {http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/20/19005/00877735.pdf}, 6205 petsc_uses = {KSP} 6206} 6207 6208@InProceedings{ hs1, 6209 author = {Brian J. Henz and Dale R. Shires}, 6210 title = {Development and Performance Analysis of a Parallel Finite Element Application 6211 Implemented in an Object-Oriented Programming Framework}, 6212 year = {2003}, 6213 booktitle = {PDPTA 2003}, 6214 pages = {1286-1292}, 6215 note = {Resin Transfer Modeling}, 6216 petsc_uses = {KSP} 6217} 6218 6219@TechReport{ b2000, 6220 author = {Rickard Bergstrom}, 6221 title = {Least-Squares Finite Element Methods for Electromagnetic Applications}, 6222 year = {2000}, 6223 institution = {Chalmers}, 6224 number = {2000-05}, 6225 url = {http://www.phi.chalmers.se/pub/preprints/ps/phiprint-2000-05.ps}, 6226 petsc_uses = {KSP} 6227} 6228 6229@Article{ fs2004, 6230 author = {Petri Fast and Michael J. Shelley}, 6231 title = {A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele 6232 Shaw Flow}, 6233 journal = {Journal of Computational Physics}, 6234 year = {2004}, 6235 volume = {195}, 6236 url = {http://www.math.nyu.edu/faculty/shelley/papers/FS2004.pdf}, 6237 pages = {117-142}, 6238 petsc_uses = {KSP} 6239} 6240 6241@MastersThesis{ wallach, 6242 author = {Hanna Wallach}, 6243 title = {Efficient Training of Conditional Random Fields}, 6244 school = {University of Edinburgh}, 6245 year = {2002}, 6246 url = {http://scholar.google.com/url?sa=U&q=http://www.hcrc.ed.ac.uk/\~{ 6247 }osborne/msc-projects/wallach.ps.gz}, 6248 petsc_uses = {KSP} 6249} 6250 6251@Article{ something, 6252 author = {T Rylander and A Bondeson}, 6253 title = {Stability of explicit-implicit hybrid time-stepping schemes for Maxwells 6254 equations}, 6255 journal = {Journal of Computational Physics}, 6256 year = {2002}, 6257 volume = {179}, 6258 pages = {426-438}, 6259 petsc_uses = {KSP} 6260} 6261 6262@TechReport{ uf1, 6263 author = {Uwe Fabricius}, 6264 title = {Comparison of two implementations of AMG-preconditioned CG considering an 6265 electrostatic problem}, 6266 year = {2004}, 6267 institution = {Friedrich Alexander Universitat Erlangen Nurnberg Germany}, 6268 url = {http://www10.informatik.uni-erlangen.de/de/Publications/TechnicalReports/TechRep04-1.pdf}, 6269 number = {04-1}, 6270 petsc_uses = {KSP} 6271} 6272 6273@InBook{ sg1, 6274 author = {Natalia Seoane and A.J.Garca-Loureiro}, 6275 chapter = {Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity 6276 Equation}, 6277 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=h0xlulyhugck3y2gnt2l&referrer=parent&backto=issue,79,112;journal,212,1787;linkingpublicationresults,1:105633,1}, 6278 title = {Lecture Notes in Computer Science}, 6279 publisher = {Springer-Verlag}, 6280 volume = {3037}, 6281 year = {2004}, 6282 petsc_uses = {KSP} 6283} 6284 6285@Article{ nikyilmazgivisheikhipope10, 6286 author = {M. B. Nik and S. L. Yilmaz and P. Givi and M. R. H. Sheikhi and S. B. Pope}, 6287 title = {Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function}, 6288 journal = {AIAA Journal}, 6289 volume = {48}, 6290 number = {7}, 6291 pages = {1513--1522}, 6292 year = {2010}, 6293 petsc_uses = {KSP} 6294} 6295 6296@Article{ nikyilmazsheikhigivi10, 6297 author = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi}, 6298 title = {Grid Resolution Effects on VSFMDF/LES}, 6299 journal = {Flow, Turbulence and Combustion}, 6300 doi = {10.1007/s10494-010-9272-5}, 6301 year = {2010}, 6302 petsc_uses = {KSP} 6303} 6304 6305@Article{ idema2013towards, 6306 title = {Towards faster solution of large power flow problems}, 6307 author = {Idema, Reijer and Papaefthymiou, Georgios and Lahaye, Domenico and Vuik, Cornelis 6308 and van der Sluis, Lou}, 6309 journal = {Power Systems, IEEE Transactions on}, 6310 volume = {28}, 6311 number = {4}, 6312 pages = {4918--4925}, 6313 year = {2013}, 6314 publisher = {IEEE}, 6315 petsc_uses = {KSP} 6316} 6317 6318@Article{ 6026245, 6319 author = {Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.}, 6320 journal = {Power Systems, IEEE Transactions on}, 6321 title = {Scalable Newton-Krylov Solver for Very Large Power Flow Problems}, 6322 year = {2012}, 6323 month = {Feb}, 6324 volume = {27}, 6325 number = {1}, 6326 pages = {390-396}, 6327 doi = {10.1109/TPWRS.2011.2165860}, 6328 issn = {0885-8950}, 6329 petsc_uses = {KSP} 6330} 6331 6332@Book{ idema2014computational, 6333 title = {Computational Methods in Power System Analysis}, 6334 author = {Idema, Reijer and Lahaye, Domenico JP}, 6335 year = {2014}, 6336 publisher = {Springer}, 6337 petsc_uses = {KSP} 6338} 6339 6340@PhDThesis{ abhyankar2011thesis, 6341 author = {Shrirang Abhyankar}, 6342 title = {Development of an implicitly coupled electromechanical and electromagnetic 6343 transients simulator for power systems}, 6344 school = {Illinois Institute of Technology}, 6345 year = {2011}, 6346 petsc_uses = {KSP} 6347} 6348 6349@InProceedings{ abhyankarhipcna11-1, 6350 author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck}, 6351 title = {Using {PETSc} to develop scalable applications for next-generation power grid}, 6352 year = {2011}, 6353 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 6354 Networking and Analytics for the Power Grid}, 6355 url = {http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf}, 6356 publisher = {ACM}, 6357 petsc_uses = {KSP} 6358} 6359 6360@InProceedings{ abhyankarhipcna11-2, 6361 author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang}, 6362 title = {Development of a parallel three-phase transient stability simulator for power 6363 systems}, 6364 year = {2011}, 6365 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 6366 Networking and Analytics for the Power Grid}, 6367 publisher = {ACM}, 6368 petsc_uses = {KSP} 6369} 6370 6371@InProceedings{ abhyankarpesgeneral2012, 6372 author = {Shrirang Abhyankar and A. Flueck}, 6373 title = {An implicitly-coupled solution approach for combined electromechanical and 6374 electromagnetic transients simulation}, 6375 year = {2012}, 6376 booktitle = {Proceedings of the IEEE PES General Meeting}, 6377 publisher = {IEEE}, 6378 petsc_uses = {KSP} 6379} 6380 6381@Article{ idemalahayevuiksluis2012, 6382 author = {Reijer Idema and Domenico Lahaye and Cornelis Vuik and Lou van der Sluis}, 6383 title = {Scalable Newton-Krylov solver for very large Power Flow problems}, 6384 journal = {IEEE Transactions on Power Systems}, 6385 year = {2012}, 6386 volume = {27}, 6387 pages = {390-396}, 6388 petsc_uses = {KSP} 6389} 6390 6391@Article{ korrestzavellasgalinas2013, 6392 author = {George N. Korres and Anastasios Tzavellas and Evangelos Galinas}, 6393 title = {A distributed implementation of multi-area power system state estimation on a 6394 cluster of computers }, 6395 journal = {Electric Power Systems Research }, 6396 volume = {102}, 6397 number = {0}, 6398 pages = {20 - 32}, 6399 year = {2013}, 6400 issn = {0378-7796}, 6401 doi = {10.1016/j.epsr.2013.04.002}, 6402 petsc_uses = {KSP} 6403} 6404 6405% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 6406% LiteralHTML:<font color="#FF0000"> 6407% LiteralHTML: Material failure, for example, cracking of steel beams resulting 6408% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 6409% LiteralHTML: are important for prediction and prevention. PETSc has been used 6410% LiteralHTML: in a variety of studies of material failure.</p> 6411% LiteralHTML:</font> 6412% LiteralHTML: 6413@InProceedings{ gray2, 6414 author = {Yuan He and Joshua Gray and Richard Braatz and Richard Alkire}, 6415 title = {Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel}, 6416 year = {2004}, 6417 booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}, 6418 petsc_uses = {KSP} 6419} 6420 6421@InProceedings{ gray1, 6422 author = {J. Gray and and C. Homescu and L. Petzold and Richard Alkire}, 6423 title = {Algorithms and Computing Architectures for Solving Differential-Algebraic 6424 Equation Systems Typically Encountered in Models of Corrosion Pit Initiation}, 6425 year = {2003}, 6426 booktitle = {Abstracts of the Electrochemical Society 204th meeting}, 6427 petsc_uses = {KSP} 6428} 6429 6430@InProceedings{ crack2, 6431 author = {Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. 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Ingraffea}, 6452 title = {Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation}, 6453 booktitle = {International Conference ON Computational Engineering and Sciences}, 6454 year = {2002}, 6455 url = {http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf}, 6456 petsc_uses = {KSP} 6457} 6458 6459@InProceedings{ crack, 6460 author = {Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and 6461 Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris 6462 Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis 6463 and Paul A. Wawrzynek}, 6464 title = {Parallel FEM Simulation of Crack Propagation}, 6465 booktitle = {Proceedings of Irregular 2000}, 6466 url = {http://www.cs.cornell.edu/stodghil/papers/irregular00.ps}, 6467 year = {2000}, 6468 petsc_uses = {KSP} 6469} 6470 6471@InProceedings{ beaudoin98, 6472 author = {A. J. 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Balkema Publishers}, 6483 address = {Rotterdam, Netherlands}, 6484 month = jun, 6485 optpages = {}, 6486 petsc_uses = {KSP} 6487} 6488 6489% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 6490@TechReport{ defordheld1, 6491 author = {JF DeFord and BL Held}, 6492 title = {RF3P-A New Parallel Driven Frequency Electromagnetic Solver}, 6493 year = {2002}, 6494 institution = {Simulation Technology and Applied Research}, 6495 url = {http://www.staarinc.com/support/papers/aces2002.pdf}, 6496 note = {Discusses their parallel commercial solver that uses PETSc}, 6497 petsc_uses = {KSP} 6498} 6499 6500@PhDThesis{ sande2003, 6501 author = {Hans Vande Sande}, 6502 title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic 6503 Quasi-Static Electromagnetic Systems}, 6504 school = {Katholieke Universiteit Leuven, Belgium}, 6505 year = {2003}, 6506 petsc_uses = {KSP} 6507} 6508 6509@Article{ sdchh2004, 6510 author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 6511 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 6512 Tolerance}, 6513 journal = {IEEE Transactions on Magnetics}, 6514 year = {2004}, 6515 volume = {40}, 6516 pages = {1306--1309}, 6517 petsc_uses = {KSP} 6518} 6519 6520@Article{ holst-lindblom-etal:2004, 6521 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 6522 Scheel and Lawrence E. Kidder}, 6523 title = {Optimal constraint projection for hyperbolic evolution systems, }, 6524 journal = {Phys. Rev. D}, 6525 year = {2004}, 6526 volume = {70}, 6527 pages = {084017}, 6528 petsc_uses = {KSP} 6529} 6530 6531@Article{ marm2005, 6532 author = {Matthew Anderson and Richard A. Matzner}, 6533 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 6534 journal = {Foundations of Physics}, 6535 volume = {35}, 6536 pages = {1572--9516}, 6537 year = {2005}, 6538 petsc_uses = {KSP} 6539} 6540 6541@Article{ cook-pfeiffer:2004, 6542 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 6543 title = {Excision boundary conditions for black hole initial data}, 6544 journal = {Phys. Rev. D}, 6545 volume = {70}, 6546 pages = {104016--24}, 6547 year = {2004}, 6548 petsc_uses = {KSP} 6549} 6550 6551@Article{ pfeiffer-kidder-etal:2005, 6552 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 6553 Shoemaker}, 6554 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 6555 journal = {Phys. Rev. D}, 6556 year = {2005}, 6557 volume = {71}, 6558 pages = {024020}, 6559 petsc_uses = {KSP} 6560} 6561 6562@Article{ pfeiffer-kidder-etal:2003, 6563 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 6564 Saul A.}, 6565 title = {A multidomain spectral method for solving elliptic equations}, 6566 journal = {CPC}, 6567 year = {2003}, 6568 volume = {152}, 6569 pages = {253--273}, 6570 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 6571 For a related online version, see arXiv:gr-qc/0202096}, 6572 petsc_uses = {KSP} 6573} 6574 6575@Article{ pfeiffer-cook-teukolsky:2002, 6576 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 6577 title = {Comparing initial-data sets for binary black hole}, 6578 journal = {PRD}, 6579 year = {2002}, 6580 volume = {66}, 6581 pages = {024047}, 6582 note = {for a related online version, seearXiv:gr-qc/0203085}, 6583 petsc_uses = {KSP} 6584} 6585 6586@PhDThesis{ pfeiffer:2003, 6587 author = {Pfeiffer, Harald P.}, 6588 title = {Initial Data for Black Hole Evolutions}, 6589 school = {Cornell University}, 6590 year = {2003}, 6591 petsc_uses = {KSP} 6592} 6593 6594@TechReport{ h1, 6595 author = {Erik Schnetter}, 6596 title = {A fast apparent horizon algorithm}, 6597 year = {2002}, 6598 number = {Arxiv preprint gr-qc/0206003}, 6599 url = {http://arxiv.org/pdf/gr-qc/0206003}, 6600 petsc_uses = {KSP} 6601} 6602 6603@Article{ h2, 6604 author = {Erik Schnetter}, 6605 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 6606 year = {2003}, 6607 journal = {Class. 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Smith}, 6638 year = {2002}, 6639 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 6640 Uintah PSE}, 6641 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 6642 2002}, 6643 pages = {49-55}, 6644 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 6645 note = {Extended abstract}, 6646 petsc_uses = {KSP} 6647} 6648 6649@Unpublished{ ep1, 6650 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 6651 author = {Bradley R. Eccleston and Todd S. Palmer}, 6652 institution = {Department of Nuclear Engineering, Oregon State University}, 6653 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 6654 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 6655 Parallel Simulations}, 6656 year = {1999}, 6657 petsc_uses = {KSP} 6658} 6659 6660@InProceedings{ teo2007scalable, 6661 title = {A scalable modular convex solver for regularized risk minimization}, 6662 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 6663 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 6664 discovery and data mining}, 6665 pages = {727--736}, 6666 year = {2007}, 6667 organization = {ACM}, 6668 petsc_uses = {KSP} 6669} 6670 6671@InProceedings{ rm02, 6672 author = {Robert Malouf}, 6673 year = {2002}, 6674 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 6675 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 6676 (CoNLL-2002)}, 6677 pages = {49-55}, 6678 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 6679 petsc_uses = {KSP} 6680} 6681 6682@Unpublished{ hrv02, 6683 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 6684 author = {V. Hernandex and J. E. Roman and V. Vidal}, 6685 note = {Submitted to CMMSE}, 6686 petsc_uses = {KSP} 6687} 6688 6689@Article{ tmh2001, 6690 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 6691 journal = {Journal of Economic Dynamics and Control}, 6692 year = {2002}, 6693 volume = {26}, 6694 pages = {1499-1515}, 6695 title = {Solving finite difference schemes arising in trivariate option pricing}, 6696 petsc_uses = {KSP} 6697} 6698 6699@InProceedings{ a2, 6700 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 6701 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 6702 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6703 Methods}, 6704 editor = {C.-H. Lai et al.}, 6705 publisher = {Domain Decomposition Press, Bergen}, 6706 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 6707 year = {1999}, 6708 petsc_uses = {KSP} 6709} 6710 6711@Unpublished{ mmmdcmaa-web-page, 6712 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 6713 {A}coustics {W}eb Page}, 6714 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 6715 author = {David E. Keyes}, 6716 institution = {Old Dominion University}, 6717 petsc_uses = {KSP} 6718} 6719 6720@Conference{ liu2010parallelization, 6721 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 6722 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 6723 booktitle = {International Symposium on Parallel and Distributed Processing with 6724 Applications}, 6725 pages = {528--535}, 6726 year = {2010}, 6727 organization = {IEEE}, 6728 petsc_uses = {KSP} 6729} 6730 6731@Unpublished{ oil-reservoir-sim-web-page, 6732 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 6733 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 6734 institution = {University of Texas at Austin and Argonne National Laboratory}, 6735 key = {University of Texas at Austin and Argonne National Laboratory}, 6736 petsc_uses = {KSP} 6737} 6738 6739@Article{ tmh2001b, 6740 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 6741 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 6742 year = {2001}, 6743 volume = {37}, 6744 pages = {143--146}, 6745 title = {Adapting EMAP3D to parallel processing}, 6746 petsc_uses = {KSP} 6747} 6748 6749@Article{ harbury98, 6750 author = {HK Harbury and W Porod}, 6751 journal = {VLSI Design}, 6752 year = {1998}, 6753 volume = {6}, 6754 pages = {47--51}, 6755 title = {Parallel computation for electronic waves in quantum corrals}, 6756 petsc_uses = {KSP} 6757} 6758 6759@Article{ bludszuwei98, 6760 author = {Mark Bludszuweit}, 6761 journal = {Journal of Lightwave Technology}, 6762 year = {1998}, 6763 volume = {16}, 6764 number = {7}, 6765 pages = {1336--42}, 6766 title = {Mixed Finite Element Beam Propagation Method}, 6767 petsc_uses = {KSP} 6768} 6769 6770@Article{ s1, 6771 author = {J. L. Friedman and N. Stergioulas}, 6772 journal = {Astrophysics Journal}, 6773 year = {1998}, 6774 volume = {492}, 6775 number = {301}, 6776 pages = {}, 6777 title = {}, 6778 petsc_uses = {KSP} 6779} 6780 6781@Article{ s1a, 6782 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 6783 journal = {Astrophysics Journal}, 6784 year = {1999}, 6785 volume = {510}, 6786 number = {854}, 6787 pages = {}, 6788 title = {}, 6789 petsc_uses = {KSP} 6790} 6791 6792@PhDThesis{ s2, 6793 author = {N. Stergioulas}, 6794 title = {Ph. D. thesis}, 6795 year = {1996}, 6796 institution = {University of Wisconsin-Milwaukee}, 6797 petsc_uses = {KSP} 6798} 6799 6800@InProceedings{ coral1, 6801 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6802 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 6803 Parallel Computing Environment}, 6804 booktitle = {Proceedings of the Miami TEAM Workshop}, 6805 location = {Florida International University, Department of Electrical Engineering and 6806 Computing Science}, 6807 month = nov, 6808 year = {1993}, 6809 petsc_uses = {KSP} 6810} 6811 6812@InProceedings{ coral2, 6813 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6814 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 6815 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 6816 month = dec, 6817 year = {1994}, 6818 petsc_uses = {KSP} 6819} 6820 6821@InProceedings{ coral3, 6822 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 6823 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 6824 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 6825 location = {Florida International University, Department of Electrical Engineering and 6826 Computing Science}, 6827 year = {1995}, 6828 petsc_uses = {KSP} 6829} 6830 6831@InProceedings{ mijalkovic, 6832 author = {Slobodan Mijalkovi\'{c}}, 6833 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 6834 Process Simulation}, 6835 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 6836 Gent, Belgium, September 27--30, 1999.}, 6837 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 6838 optvolume = {14}, 6839 optseries = {Lecture Notes in Computational Science and Engineering}, 6840 year = {2000}, 6841 publisher = {Springer}, 6842 address = {Berlin}, 6843 optpages = {179--184}, 6844 petsc_uses = {KSP} 6845} 6846 6847@Article{ bludszuwei98a, 6848 author = {Mark Bludszuweit}, 6849 journal = {Journal of Lightwave Technology}, 6850 year = {1998}, 6851 volume = {16}, 6852 number = {7}, 6853 pages = {1336--42}, 6854 title = {Mixed Finite Element Beam Propagation Method}, 6855 petsc_uses = {KSP} 6856} 6857 6858@Article{ gilli-pauletto-1998, 6859 author = {Manfred Gilli and Giorgio Pauletto}, 6860 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 6861 journal = {Computational Economics}, 6862 year = {2000}, 6863 volume = {16}, 6864 pages = {173--186}, 6865 petsc_uses = {KSP} 6866} 6867 6868% LiteralHTML: 6869% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 6870% LiteralHTML: 6871@Article{ collierdalcincalo2013, 6872 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 6873 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 6874 journal = {arxiv}, 6875 year = {2013}, 6876 number = {1305.4452}, 6877 note = {\url{http://arxiv.org/abs/1305.4452}}, 6878 petsc_uses = {KSP} 6879} 6880 6881@Article{ collierdalcinvignalcortescalo2016, 6882 title = {PetIGA: A framework for high-performance isogeometric analysis}, 6883 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 6884 Victor M. Calo}, 6885 journal = {Computer Methods in Applied Mechanics and Engineering}, 6886 year = {2016}, 6887 petsc_uses = {KSP} 6888} 6889 6890@Misc{ petiga-web-page, 6891 author = {N. Collier and L. Dalcin and V.M. Calo}, 6892 title = {{PetIGA} {W}eb page}, 6893 url = {https://bitbucket.org/dalcinl/petiga/}, 6894 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 6895 year = {2014}, 6896 petsc_uses = {KSP} 6897} 6898 6899@Article{ logg07, 6900 author = {Logg, Anders}, 6901 title = {Automating the Finite Element Method}, 6902 journal = {Archives of Computational Methods in Engineering}, 6903 volume = {14}, 6904 number = {2}, 6905 pages = {93-138}, 6906 year = {2007}, 6907 doi = {10.1007/s11831-007-9003-9}, 6908 publisher = {Kluwer Academic Publishers}, 6909 issn = {1134-3060}, 6910 language = {English}, 6911 petsc_uses = {KSP} 6912} 6913 6914@Article{ jezequelcouturierdenis12, 6915 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 6916 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 6917 versus the PETSc library}, 6918 journal = {The Journal of Supercomputing}, 6919 volume = {59}, 6920 number = {3}, 6921 pages = {1517-1532}, 6922 year = {2012}, 6923 issn = {0920-8542}, 6924 doi = {10.1007/s11227-011-0563-y}, 6925 publisher = {Springer US}, 6926 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 6927 Sparse linear solver}, 6928 language = {English}, 6929 petsc_uses = {KSP} 6930} 6931 6932@Unpublished{ feap-web-page, 6933 title = {FEAP: A Finite Element Analysis Program}, 6934 url = {http://www.ce.berkeley.edu/projects/feap/}, 6935 author = {FEAP Team}, 6936 note = {Uses PETSc linear solvers - iterative and direct}, 6937 petsc_uses = {KSP} 6938} 6939 6940@Unpublished{ parpre-web-page, 6941 title = {{ParPre} {W}eb {P}age}, 6942 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 6943 institution = {University of Tennessee}, 6944 author = {Victor Eijkhout}, 6945 note = {This is no longer supported. A set of preconditioners built on PETSc}, 6946 petsc_uses = {KSP} 6947} 6948 6949@Unpublished{ pism, 6950 title = {{PISM}: a Parallel Ice Sheet Model}, 6951 author = {{PISM Team}}, 6952 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 6953 Sheet Model). The thickness, temperature, velocity and age of the ice are all 6954 simulated, as is the deformation of the earth underneath the ice. New techniques 6955 for fast ice dynamics, earth deformation, and verification have are included.}, 6956 note = {\url{http://www.pism-docs.org/}}, 6957 petsc_uses = {KSP} 6958} 6959 6960@Unpublished{ oofem, 6961 title = {OOFEM - an object oriented finite element package}, 6962 author = {Borek Patzak}, 6963 url = {http://www.oofem.org}, 6964 petsc_uses = {KSP} 6965} 6966 6967@Unpublished{ dks2openfvm, 6968 title = {OpenFVM - a finite volume based general purpose CFD solver}, 6969 author = {Open source development}, 6970 url = {http://openfvm.sourceforge.net/}, 6971 petsc_uses = {KSP} 6972} 6973 6974@Unpublished{ sundar-2008w, 6975 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 6976 octree meshes}, 6977 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 6978 institution = {University of Pennsylvania}, 6979 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 6980 petsc_uses = {KSP} 6981} 6982 6983@Unpublished{ khatiwala07-software, 6984 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 6985 author = {Khatiwala, S.}, 6986 institution = {Columbia University}, 6987 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 6988 petsc_uses = {KSP} 6989} 6990 6991@InBook{ jiaolima99, 6992 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 6993 chapter = {SIFFEA:Scalable Integrated Framework for Finite Element Analysis}, 6994 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 6995 title = {Lecture Notes in Computer Science}, 6996 publisher = {Springer-Verlag}, 6997 volume = {1732}, 6998 year = {1999}, 6999 petsc_uses = {KSP} 7000} 7001 7002@Article{ crow1, 7003 author = {C. S. Crow IV}, 7004 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 7005 journal = {Hopkins Undergraduate Research Journal}, 7006 year = {2003}, 7007 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 7008 petsc_uses = {KSP} 7009} 7010 7011@Unpublished{ petsc-python, 7012 title = {PETSc for Python}, 7013 author = {L. Dalcin}, 7014 url = {https://petsc.org/main/petsc4py}, 7015 note = {Provides Python bindings for PETSc}, 7016} 7017 7018@Unpublished{ cfdship, 7019 title = {{CFDShip-Iowa}}, 7020 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 7021 institution = {University of Iowa}, 7022 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 7023 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 7024 structured grids, designed for ship applications}, 7025 petsc_uses = {KSP} 7026} 7027 7028@Unpublished{ bvw, 7029 title = {Multiflow}, 7030 author = {Berend van Wachem}, 7031 institution = {Mechanical Engineering - Chalmers University of Technology}, 7032 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 7033 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 7034 flows.}, 7035 petsc_uses = {KSP} 7036} 7037 7038@Unpublished{ dks2, 7039 title = {FENA - A Finite Element Model for the North Atlantic}, 7040 author = {Jens Schroeter}, 7041 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 7042 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 7043 petsc_uses = {KSP} 7044} 7045 7046@TechReport{ piwonski2010idea, 7047 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 7048 and Simulation in {3-D}}, 7049 author = {Piwonski, J. and Slawig, T.}, 7050 year = {2010}, 7051 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 7052 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 7053 petsc_uses = {KSP} 7054} 7055 7056@Unpublished{ metos3d-web, 7057 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 7058 author = {Piwonski, J. and Slawig, T.}, 7059 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 7060 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 7061 petsc_uses = {KSP} 7062} 7063 7064@Unpublished{ magpar, 7065 author = {W. Scholz}, 7066 title = {Magpar: Parallel Micromagnetics Code}, 7067 institution = {Vienna University of Technology}, 7068 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 7069 petsc_uses = {KSP} 7070} 7071 7072@Misc{ libmesh:sourceforge, 7073 author = {}, 7074 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 7075 equations on serial and parallel platforms}, 7076 note = {[Online]}, 7077 url = {http://libmesh.github.io}, 7078 petsc_uses = {KSP} 7079} 7080 7081@Misc{ moose-web-page, 7082 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 7083 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 7084 Gaston and John Peterson and Jason Miller}, 7085 institution = {Idaho National Laboratory}, 7086 howpublished = {\url{http://mooseframework.org}}, 7087 petsc_uses = {KSP} 7088} 7089 7090@Article{ gaston2009moose, 7091 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 7092 equations}, 7093 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 7094 journal = {Nuclear Engineering and Design}, 7095 volume = {239}, 7096 number = {10}, 7097 pages = {1768--1778}, 7098 year = {2009}, 7099 publisher = {Elsevier}, 7100 petsc_uses = {KSP} 7101} 7102 7103@Article{ tonks2012object, 7104 title = {An object-oriented finite element framework for multiphysics phase field 7105 simulations}, 7106 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 7107 journal = {Computational Materials Science}, 7108 volume = {51}, 7109 number = {1}, 7110 pages = {20--29}, 7111 year = {2012}, 7112 publisher = {Elsevier}, 7113 petsc_uses = {KSP} 7114} 7115 7116@Misc{ pylithmanual, 7117 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 7118 Strand and Charles Williams}, 7119 title = {{PyLith} User Manual Version 2.0.0}, 7120 year = {2014}, 7121 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 7122 petsc_uses = {KSP} 7123} 7124 7125@Misc{ pylith-web-page, 7126 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 7127 title = {{PyLith}}, 7128 year = {2012}, 7129 url = {http://geodynamics.org/resources/pylith/}, 7130 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 7131 petsc_uses = {KSP} 7132} 7133 7134@Misc{ galemanual, 7135 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 7136 title = {Gale User Manual Version 2.0.0}, 7137 year = {2011}, 7138 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 7139 petsc_uses = {KSP} 7140} 7141 7142@Unpublished{ underworld, 7143 author = {Louis Moresi}, 7144 title = {{UnderWorld}: A Geodynamics Modelling Code}, 7145 institution = {Monash University}, 7146 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 7147 petsc_uses = {KSP} 7148} 7149 7150@Article{ moresi2007computational, 7151 title = {Computational approaches to studying non-linear dynamics of the crust and 7152 mantle}, 7153 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 7154 M{\"u}hlhaus, H.B.}, 7155 journal = {Physics of the Earth and Planetary Interiors}, 7156 volume = {163}, 7157 number = {1-4}, 7158 pages = {69--82}, 7159 year = {2007}, 7160 publisher = {Elsevier}, 7161 petsc_uses = {KSP} 7162} 7163 7164@Article{ pitt2009chaste, 7165 title = {Chaste: a test-driven approach to software development for biological modelling}, 7166 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 7167 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 7168 and Walter, A. and others}, 7169 journal = {Computer Physics Communications}, 7170 volume = {180}, 7171 number = {12}, 7172 pages = {2452--2471}, 7173 year = {2009}, 7174 publisher = {Elsevier}, 7175 petsc_uses = {KSP} 7176} 7177 7178@Misc{ fenicsproject, 7179 title = {{The FEniCS project}}, 7180 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 7181 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 7182 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 7183 url = {http://fenicsproject.org}, 7184 year = {2011}, 7185 petsc_uses = {KSP} 7186} 7187 7188@Unpublished{ snark, 7189 title = {Snark: A suite of software for geoscientific applications and a philosophy of 7190 scientific software development}, 7191 institution = {Victorian Partnership for Advanced Computing}, 7192 url = {http://vpac.org/Snark}, 7193 petsc_uses = {KSP} 7194} 7195 7196@Misc{ imoose:sourceforge, 7197 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 7198 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 7199 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 7200 note = {[Online]}, 7201 url = {http://imoose.sourceforge.net}, 7202 petsc_uses = {KSP} 7203} 7204 7205@Unpublished{ fossi, 7206 author = {Stephan Frickenhaus}, 7207 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 7208 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 7209 codes}, 7210 institution = {AWI-Bremerhaven, Germanny}, 7211 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 7212 petsc_uses = {KSP} 7213} 7214 7215@Unpublished{ fun3dweb, 7216 author = {Dinesh Kaushik}, 7217 title = {PETSC-FUN3D Benchmark Page}, 7218 institution = {ODU/ANL}, 7219 url = {http://www.mcs.anl.gov/petsc-fun3d}, 7220 note = {CFD Benchmark of some solvers in PETSc}, 7221 petsc_uses = {KSP} 7222} 7223 7224@Unpublished{ scirun, 7225 author = {SCIRun Development Team}, 7226 title = {SCIRun}, 7227 institution = {University of Utah}, 7228 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 7229 note = {SCIRun now uses PETSc linear solvers}, 7230 petsc_uses = {KSP} 7231} 7232 7233@Misc{ prometheus, 7234 author = {Mark F. Adams}, 7235 title = {Prometheus - A scalable unstructured finite element solver}, 7236 institution = {Berkeley}, 7237 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 7238 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 7239 petsc_uses = {KSP} 7240} 7241 7242@Unpublished{ illuminator, 7243 author = {Adam C. Powell, IV}, 7244 title = {Illuminator Distributed Visualization Library}, 7245 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 7246 petsc_uses = {KSP} 7247} 7248 7249@Unpublished{ rheoplast, 7250 title = {RheoPlast Phase Field Multi-Physics Code}, 7251 author = {Adam Powell and David Dussault and Bo Zhou}, 7252 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 7253 petsc_uses = {KSP} 7254} 7255 7256@Misc{ tao-web-page, 7257 title = {{Toolkit for Advanced Optimization (TAO)} {W}eb Page}, 7258 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 7259 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 7260 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7261 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 7262 petsc_uses = {KSP} 7263} 7264 7265@TechReport{ tao-user-ref, 7266 title = {{Toolkit for Advanced Optimization (TAO) users manual}}, 7267 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 7268 and Steve Benson and Lois Curfman McInnes}, 7269 institution = {Argonne National Laboratory}, 7270 year = {2019}, 7271 number = {ANL/MCS-TM-322 - Rev 3.12}, 7272 petsc_uses = {KSP} 7273} 7274 7275% url = "http://www.mcs.anl.gov/tao", 7276@Unpublished{ mefpp-web-page, 7277 title = {{MEF++} {W}eb {P}age}, 7278 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 7279 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 7280 author = {Eric Chamberland}, 7281 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 7282 multiphysics}, 7283 petsc_uses = {KSP} 7284} 7285 7286@Unpublished{ tipetsc-web-page, 7287 title = {Ti-PETSc - an interface to PETSc from Titanium}, 7288 institution = {Berkeley}, 7289 url = {http://www.nersc.gov/\~{ }yunhe/cs267/final/paper.pdf}, 7290 petsc_uses = {KSP} 7291} 7292 7293@Unpublished{ ptatin-web-page, 7294 title = {ptatin3d}, 7295 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 7296 url = {https://bitbucket.org/jedbrown/ptatin3d}, 7297 year = {2018}, 7298 petsc_uses = {KSP} 7299} 7300 7301@Misc{ multiphase-web-page, 7302 author = {Q. Zou}, 7303 title = {Multiphase flow with {PETSc}}, 7304 institution = {LANL}, 7305 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 7306 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 7307 lab = {LANL}, 7308 petsc_uses = {KSP} 7309} 7310 7311@Misc{ electromag-web-page, 7312 title = {{EMSolve Web} page}, 7313 institution = {LLNL}, 7314 howpublished = {http://www.llnl.gov/casc/emsolve}, 7315 url = {http://www.Llnl.gov/casc/emsolve}, 7316 author = {Daniel {White et al.}}, 7317 lab = {LLNL}, 7318 petsc_uses = {KSP} 7319} 7320 7321@Unpublished{ fe-software-web-page, 7322 institution = {Kuleuven}, 7323 title = {Finite element software}, 7324 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 7325 petsc_uses = {KSP} 7326} 7327 7328@Misc{ petsc-web-page, 7329 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7330 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 7331 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7332 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7333 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7334 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7335 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7336 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7337 Zhang}, 7338 title = {{PETS}c {W}eb page}, 7339 url = {https://petsc.org/}, 7340 howpublished = {\url{https://petsc.org/}}, 7341 year = {2023} 7342} 7343 7344@Unpublished{ petsc-debian-package, 7345 author = {Adam C. Powell, IV}, 7346 title = {Debian package for PETSc}, 7347 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 7348 petsc_uses = {KSP} 7349} 7350 7351@Unpublished{ cactus, 7352 title = {Cactus Website}, 7353 url = {http://www.cactuscode.org/}, 7354 note = {Provides two interface to the PETSc solvers}, 7355 petsc_uses = {KSP} 7356} 7357 7358@Unpublished{ petsc-fem, 7359 author = {Mario Storti and Norberto Nigro}, 7360 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 7361 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 7362 url = {http://www.cimec.org.ar/petscfem}, 7363 petsc_uses = {KSP} 7364} 7365 7366@Misc{ fidap, 7367 title = {FIDAP 8.5}, 7368 howpublished = {\url{http://www.fluent.com}}, 7369 url = {http://www.fluent.com}, 7370 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 7371 solves.}, 7372 key = {FIDAP 8.5}, 7373 petsc_uses = {KSP} 7374} 7375 7376@Unpublished{ slepc, 7377 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7378 Vicente Hern\'andez and Vicent Vidal}, 7379 title = {{SLEPc} Website}, 7380 url = {http://slepc.upv.es/}, 7381 note = {Scalable Library for Eigenvalue Problem Computations}, 7382 petsc_uses = {KSP} 7383} 7384 7385@TechReport{ slepc-users-manual, 7386 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 7387 Vicente Hern\'andez and Vicent Vidal}, 7388 title = {{SLEPc} Users Manual}, 7389 number = {DISC-II/24/02}, 7390 url = {http://slepc.upv.es/}, 7391 note = {Scalable Library for Eigenvalue Problem Computations}, 7392 petsc_uses = {KSP} 7393} 7394 7395@Misc{ deal.ii, 7396 title = {deal.II}, 7397 howpublished = {\url{http://www.dealii.org}}, 7398 url = {http://www.dealii.org}, 7399 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 7400 It allows PETSc linear algebra and solvers to be used underneath.}, 7401 key = {deal.II 5.0}, 7402 petsc_uses = {KSP} 7403} 7404 7405@Article{ bangerth2007deal, 7406 title = {{deal.II---A general-purpose object-oriented finite element library}}, 7407 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 7408 journal = {ACM Transactions on Mathematical Software (TOMS)}, 7409 volume = {33}, 7410 number = {4}, 7411 pages = {24--es}, 7412 issn = {0098-3500}, 7413 year = {2007}, 7414 publisher = {ACM}, 7415 petsc_uses = {KSP} 7416} 7417 7418@Misc{ globalarrays, 7419 author = {Jarek {Nieplocha et al.}}, 7420 title = {Global Arrays}, 7421 institution = {Pacific Northwest National Laboratories}, 7422 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 7423 url = {http://www.emsl.pnl.gov/docs/global}, 7424 note = {Global arrays can use PETSc linear solvers}, 7425 lab = {PNNL}, 7426 petsc_uses = {KSP} 7427} 7428 7429% LiteralHTML: 7430% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 7431% LiteralHTML: 7432@Article{ petsccommunity2022, 7433 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 7434 Community}, 7435 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 7436 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 7437 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 7438 and Hong Zhang and Junchao Zhang}, 7439 journal = {Computing in Science and Engineering}, 7440 volume = {24}, 7441 number = {03}, 7442 pages = {6--15}, 7443 issn = {1558-366X}, 7444 doi = {10.1109/MCSE.2022.3169974}, 7445 publisher = {IEEE Computer Society}, 7446 address = {Los Alamitos, CA, USA}, 7447 month = {may}, 7448 year = {2022}, 7449 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 7450 petsc_uses = {KSP} 7451} 7452 7453@Article{ brownknepleysmith14, 7454 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 7455 title = {Run-time extensibility and librarization of simulation software}, 7456 journal = {IEEE Computing in Science and Engineering}, 7457 month = {Jan}, 7458 volume = {17}, 7459 number = {1}, 7460 pages = {38--45}, 7461 doi = {10.1109/MCSE.2014.95}, 7462 year = {2015}, 7463 petsc_uses = {KSP} 7464} 7465 7466@TechReport{ ass2012, 7467 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 7468 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 7469 institution = {Argonne National Laboratory}, 7470 type = {Preprint}, 7471 year = {2012}, 7472 number = {ANL/MCS-P2011-0112}, 7473 petsc_uses = {KSP} 7474} 7475 7476@TechReport{ clearyknepley99, 7477 author = {Andrew Cleary and Matthew G. Knepley}, 7478 title = {Solvers as Operators}, 7479 institution = {Lawrence Livermore National Laboratory}, 7480 type = {Technical Report}, 7481 number = {UCRL-ID-135342}, 7482 year = {1999}, 7483 petsc_uses = {KSP} 7484} 7485 7486@TechReport{ smcabbkz2012, 7487 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 7488 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 7489 title = {{PETSc's} software strategy for the design space of composable extreme-scale 7490 solvers}, 7491 institution = {Argonne National Laboratory}, 7492 type = {Preprint}, 7493 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 7494 year = {2012}, 7495 number = {ANL/MCS-P2059-0312}, 7496 petsc_uses = {KSP} 7497} 7498 7499@InProceedings{ mhwpmhs2009, 7500 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 7501 and G. E. Hammond and B. Smith}, 7502 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 7503 Toolkit {MPI} at Scale}, 7504 booktitle = {Cray Users Group Conference}, 7505 year = {2009}, 7506 petsc_uses = {KSP} 7507} 7508 7509@InProceedings{ msmhls2010, 7510 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 7511 Lichtner and B. F. Smith}, 7512 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 7513 {BlueGene} Architectures}, 7514 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 7515 year = {2010}, 7516 petsc_uses = {KSP} 7517} 7518 7519@InCollection{ msk2013, 7520 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 7521 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 7522 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7523 series = {Lecture Notes in Earth System Sciences}, 7524 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7525 Yaolin Shi}, 7526 doi = {10.1007/978-3-642-16405-7_7}, 7527 publisher = {Springer Berlin Heidelberg}, 7528 pages = {131--140}, 7529 year = {2013}, 7530 isbn = {978-3-642-16404-0}, 7531 petsc_uses = {KSP} 7532} 7533 7534@InCollection{ knepleyyuen13, 7535 author = {Matthew G. Knepley and David A. Yuen}, 7536 title = {Why Scientists and Engineers need {GPU}s today}, 7537 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7538 series = {Lecture Notes in Earth System Sciences}, 7539 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7540 Yaolin Shi}, 7541 doi = {10.1007/978-3-642-16405-7_1}, 7542 publisher = {Springer Berlin Heidelberg}, 7543 pages = {131--140}, 7544 year = {2013}, 7545 isbn = {978-3-642-16404-0}, 7546 petsc_uses = {KSP} 7547} 7548 7549@InCollection{ karpeevknepleybrune13, 7550 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 7551 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 7552 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7553 series = {Lecture Notes in Earth System Sciences}, 7554 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7555 Yaolin Shi}, 7556 doi = {10.1007/978-3-642-16405-7_30}, 7557 publisher = {Springer Berlin Heidelberg}, 7558 pages = {487--501}, 7559 year = {2013}, 7560 isbn = {978-3-642-16404-0}, 7561 petsc_uses = {KSP} 7562} 7563 7564@InCollection{ zhengetal13, 7565 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 7566 Variable Viscosity}, 7567 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7568 Zhang and Yaolin Shi}, 7569 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 7570 series = {Lecture Notes in Earth System Sciences}, 7571 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 7572 Yaolin Shi}, 7573 doi = {10.1007/978-3-642-16405-7_21}, 7574 publisher = {Springer Berlin Heidelberg}, 7575 pages = {321--333}, 7576 year = {2013}, 7577 isbn = {978-3-642-16404-0}, 7578 petsc_uses = {KSP} 7579} 7580 7581@Article{ zhengetal13b, 7582 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 7583 strongly variable viscosity based on {M}atlab and {CUDA}}, 7584 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 7585 Zhang and Yaolin Shi}, 7586 journal = {IJHPCA}, 7587 volume = {28}, 7588 number = {1}, 7589 pages = {50--60}, 7590 doi = {10.1177/1094342013478640}, 7591 year = {2013}, 7592 petsc_uses = {KSP} 7593} 7594 7595@InBook{ s2011, 7596 author = {B. Smith}, 7597 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 7598 title = {Encyclopedia of Parallel Computing}, 7599 bookeditor = {D. Padua}, 7600 publisher = {Springer}, 7601 year = {2011}, 7602 petsc_uses = {KSP} 7603} 7604 7605@Article{ acostamejia06, 7606 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 7607 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 7608 journal = {Lecturas Matem\'aticas}, 7609 volume = {27}, 7610 year = {2006}, 7611 pages = {213--224}, 7612 petsc_uses = {KSP} 7613} 7614 7615@InProceedings{ quenettemoresisunterappelbe07, 7616 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 7617 title = {Explaining StGermain: An aspect oriented environment for building extensible 7618 computational mechanics modeling software}, 7619 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 7620 publisher = {IEEE}, 7621 pages = {1--8}, 7622 yerar = {2007}, 7623 petsc_uses = {KSP} 7624} 7625 7626@Article{ dfm1, 7627 title = {Vectorized sparse matrix multiply for compressed row storage format}, 7628 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 7629 journal = {Lecture Notes in Computer Science}, 7630 year = {2005}, 7631 pages = {99--106}, 7632 volume = {3514}, 7633 lab = {ORNL}, 7634 petsc_uses = {KSP} 7635} 7636 7637@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 7638 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 7639 Vandewalle and Stefaan Poedts}, 7640 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 7641 Scientific Computing Software}, 7642 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 7643 year = {2005}, 7644 note = {Lecture Notes in Computer Science}, 7645 volume = {3514}, 7646 publisher = {Springer-Verlag GmbH}, 7647 petsc_uses = {KSP} 7648} 7649 7650@InProceedings{ dalcin-paz-storti, 7651 author = {L. Dalcin and R. Paz and M. Storti}, 7652 title = {Desarrollo de Aplicaciones Paralelas en Python}, 7653 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 7654 Bariloche, Argentina}, 7655 year = {2004}, 7656 petsc_uses = {KSP} 7657} 7658 7659@Article{ mpi-python, 7660 author = {L. Dalcin and R. Paz and M. Storti}, 7661 title = {MPI for Python}, 7662 journal = {Journal of Parallel and Distributed Computing}, 7663 year = {2005}, 7664 petsc_uses = {KSP} 7665} 7666 7667@Unpublished{ hrv02a, 7668 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 7669 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7670 note = {Submited to VecPar 2002}, 7671 year = {2002}, 7672 petsc_uses = {KSP} 7673} 7674 7675@Article{ knyazev2007block, 7676 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 7677 {PETSc}}, 7678 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 7679 journal = {SIAM Journal on Scientific Computing}, 7680 volume = {29}, 7681 pages = {2224-2239}, 7682 doi = {10.1137/060661624}, 7683 year = {2007}, 7684 petsc_uses = {KSP} 7685} 7686 7687@MastersThesis{ aarrestad-master, 7688 author = {Asbjorn Hoiland Aarrestad}, 7689 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 7690 school = {University of Bergen}, 7691 month = {August}, 7692 year = {2003}, 7693 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 7694 note = {Implemented Runge-Kutta methods using PETSc}, 7695 petsc_uses = {KSP} 7696} 7697 7698@PhDThesis{ kaushik-phd, 7699 author = {D. K. Kaushik}, 7700 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 7701 Differential Equations on Unstructured Grids}, 7702 school = {Old Dominion University}, 7703 month = {December}, 7704 year = {2002}, 7705 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 7706 petsc_uses = {KSP} 7707} 7708 7709@TechReport{ rb1, 7710 author = {Rickard Bergstrom}, 7711 title = {Object Oriented Implementation of a General Finite Element Code}, 7712 number = {2002-13}, 7713 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 7714 year = {2002}, 7715 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 7716 note = {Discribes a finite element software package that uses PETSc for its solvers}, 7717 petsc_uses = {KSP} 7718} 7719 7720@InProceedings{ dbl1, 7721 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 7722 title = {A Parallel General Purpose Finite Element System}, 7723 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 7724 publisher = {SIAM}, 7725 year = {1999}, 7726 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 7727 note = {Describes software that uses PETSc for its parallel linear solves}, 7728 petsc_uses = {KSP} 7729} 7730 7731@Article{ p1, 7732 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 7733 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 7734 and B. Smith}, 7735 journal = {Parallel Computing}, 7736 year = {2002}, 7737 pages = {1811--1831}, 7738 volume = {28 (12)}, 7739 petsc_uses = {KSP} 7740} 7741 7742@Article{ automatic-ad, 7743 author = {Paul Hovland and Boyana Norris and Barry Smith}, 7744 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 7745 year = {2005}, 7746 journal = {Future Generation Computer Systems}, 7747 volume = {21}, 7748 number = {8}, 7749 pages = {1426--1438}, 7750 petsc_uses = {KSP} 7751} 7752 7753@TechReport{ remote-math, 7754 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 7755 Smith}, 7756 title = {Remote Access to Mathematical Software}, 7757 number = {ANL/MCS-P889-0601}, 7758 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7759 month = {June}, 7760 year = {2001}, 7761 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 7762 petsc_uses = {KSP} 7763} 7764 7765@InProceedings{ gropp98, 7766 author = {William D. Gropp}, 7767 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 7768 publisher = {SIAM}, 7769 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7770 Scientific and Engineering Computing}, 7771 year = {1999}, 7772 pages = {21-29}, 7773 petsc_uses = {KSP} 7774} 7775 7776@InProceedings{ knepleysarin99, 7777 author = {Matthew Knepley and Vivek Sarin}, 7778 title = {Algorithm Development for Large Scale Computing}, 7779 publisher = {SIAM}, 7780 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7781 Scientific and Engineering Computing}, 7782 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}}, 7783 year = {1999}, 7784 petsc_uses = {KSP} 7785} 7786 7787@InBook{ bgms00, 7788 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 7789 chapter = {Software for the Scalable Solution of {PDEs}}, 7790 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 7791 title = {CRPC Handbook of Parallel Computing}, 7792 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 7793 and A. White}, 7794 publisher = {Morgan Kaufmann Publishers}, 7795 year = {2002}, 7796 petsc_uses = {KSP} 7797} 7798 7799@InProceedings{ hovland_norris_smith98, 7800 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 7801 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 7802 Computations}, 7803 publisher = {SIAM}, 7804 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7805 Scientific and Engineering Computing}, 7806 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 7807 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 7808 year = {1999}, 7809 pages = {129-137}, 7810 petsc_uses = {KSP} 7811} 7812 7813@InProceedings{ efficient, 7814 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7815 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 7816 Libraries}, 7817 booktitle = {Modern Software Tools in Scientific Computing}, 7818 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 7819 publisher = {Birkhauser Press}, 7820 pages = {163--202}, 7821 year = {1997}, 7822 petsc_uses = {KSP} 7823} 7824 7825% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 7826@TechReport{ petsc-user-ref, 7827 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 7828 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 7829 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 7830 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 7831 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 7832 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 7833 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 7834 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 7835 Zhang}, 7836 title = {{PETSc/TAO} Users Manual}, 7837 institution = {Argonne National Laboratory}, 7838 number = {ANL-21/39 - Revision 3.19}, 7839 doi = {10.2172/1968587}, 7840 year = {2023} 7841} 7842 7843% url = {https://petsc.org/release} 7844@TechReport{ petsc-developers, 7845 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 7846 title = {{PETS}c Developers Guide}, 7847 institution = {Argonne National Laboratory}, 7848 number = {ANL-18/18}, 7849 year = {2018}, 7850 url = {https://petsc.org/release/developers}, 7851 petsc_uses = {KSP} 7852} 7853 7854@Unpublished{ alice-memory-snooper, 7855 author = {Ibrahima Ba and Barry~F. Smith}, 7856 title = {The {ALICE} Memory Snooper}, 7857 year = {1999}, 7858 petsc_uses = {KSP} 7859} 7860 7861@TechReport{ petsc-user-ref-polish, 7862 author = {Marcin Bojko and Piotr Krzyzanowski}, 7863 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 7864 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 7865 year = {1998}, 7866 note = {An introduction to PETSc in Polish}, 7867 petsc_uses = {KSP} 7868} 7869 7870@InProceedings{ abghmn00, 7871 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 7872 High-Performance Scientific Computing}, 7873 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 7874 Norris}, 7875 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 7876 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 7877 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 7878 Hasco\"{e}t and Uwe Naumann}, 7879 publisher = {Springer}, 7880 year = {2002}, 7881 petsc_uses = {KSP} 7882} 7883 7884@Unpublished{ petsc-mpi-paper, 7885 author = {Lois Curfman McInnes and Barry F. Smith}, 7886 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 7887 Libraries}, 7888 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 7889 month = June, 7890 year = {1995}, 7891 petsc_uses = {KSP} 7892} 7893 7894@InProceedings{ miss-paper, 7895 author = {William D. Gropp and Barry F. Smith}, 7896 title = {Scalable, Extensible, and Portable Numerical Libraries}, 7897 publisher = {IEEE}, 7898 year = {1994}, 7899 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7900 address = {Mississippi State University}, 7901 pages = {87--93}, 7902 keyword = {numerical libraries, scientific computing, parallel computing}, 7903 petsc_uses = {KSP} 7904} 7905 7906@InProceedings{ snes-paper, 7907 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7908 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 7909 Minimization Problems}, 7910 publisher = {IEEE}, 7911 year = {1995}, 7912 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 7913 address = {Mississippi State University}, 7914 pages = {60-67}, 7915 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 7916 petsc_uses = {KSP} 7917} 7918 7919@Article{ dsneutral, 7920 author = {Barry F. Smith and William D. Gropp}, 7921 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 7922 Sparse Linear Systems}, 7923 journal = {Scientific Programming}, 7924 volume = {5}, 7925 pages = {329--336}, 7926 key = {GroppSmith96 ! KSP design}, 7927 year = {1996}, 7928 petsc_uses = {KSP} 7929} 7930 7931@InProceedings{ bgms98, 7932 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 7933 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 7934 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 7935 Scientific and Engineering Computing}, 7936 publisher = {SIAM}, 7937 pages = {58-67}, 7938 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 7939 year = {1998}, 7940 petsc_uses = {KSP} 7941} 7942 7943@Article{ hkm98, 7944 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 7945 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 7946 {PDE} Computation}, 7947 journal = {Advances in Engineering Software}, 7948 volume = {29}, 7949 pages = {415-424}, 7950 year = {1998}, 7951 petsc_uses = {KSP} 7952} 7953 7954@TechReport{ pdpta99, 7955 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 7956 Smith}, 7957 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 7958 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 7959 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 7960 Vegas, Nevada}, 7961 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 7962 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 7963 number = {ANL/MCS-P751-0599}, 7964 year = {1999}, 7965 petsc_uses = {KSP} 7966} 7967 7968@InProceedings{ bbh:com, 7969 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 7970 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 7971 Computing}}, 7972 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 7973 Euro-Par Conference, Munich, Germany, August/September 2000}, 7974 year = {2000}, 7975 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 7976 volume = {1900}, 7977 series = {Lecture Notes in Computer Science}, 7978 pages = {86--94}, 7979 address = {Berlin}, 7980 publisher = {Springer}, 7981 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 7982 petsc_uses = {KSP} 7983} 7984 7985@InProceedings{ overture00, 7986 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 7987 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 7988 Components}, 7989 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 7990 booktitle = {Proceedings of the International Federation for Information Processing Working 7991 Conference on Software Architectures for Scientific Computing, Kluwer}, 7992 year = {2000}, 7993 pages = {57--68}, 7994 petsc_uses = {KSP} 7995} 7996 7997@TechReport{ smith97, 7998 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 7999 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 8000 number = {ANL/MCS-P701}, 8001 author = {Barry F. Smith}, 8002 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8003 petsc_uses = {KSP} 8004} 8005 8006@Article{ smith98, 8007 author = {Barry Smith}, 8008 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 8009 journal = {SIGNUM Newsletter}, 8010 year = {1998}, 8011 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 8012 petsc_uses = {KSP} 8013} 8014 8015@TechReport{ ad-petsc-tm, 8016 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 8017 {PETSc}}, 8018 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 8019 year = {1997}, 8020 type = {Technical Memorandum}, 8021 institution = {ANL}, 8022 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 8023 number = {ANL/MCS-TM-233}, 8024 petsc_uses = {KSP} 8025} 8026 8027% LiteralHTML: 8028% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 8029% LiteralHTML: 8030@PhDThesis{ klotzthesis2019, 8031 author = {Thomas S. Klotz}, 8032 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 8033 Biology}, 8034 school = {Rice University}, 8035 year = {2019}, 8036 petsc_uses = {KSP} 8037} 8038 8039@Article{ klotzbardhanknepley2018, 8040 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 8041 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 8042 journal = {Communications in Applied Mathematics and Computational Science}, 8043 note = {In review}, 8044 url = {https://arxiv.org/abs/1708.06028}, 8045 year = {2018}, 8046 petsc_uses = {KSP} 8047} 8048 8049@Misc{ brown2016, 8050 title = {Threading Tradeoffs in Domain Decomposition}, 8051 author = {Jed Brown}, 8052 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 8053 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 8054 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 8055 year = {2016}, 8056 petsc_uses = {KSP} 8057} 8058 8059@Article{ changnakshatralaknepleyjohnsson2017, 8060 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 8061 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 8062 Johnsson}, 8063 journal = {Concurency: Practice and Experience}, 8064 volume = {30}, 8065 number = {11}, 8066 eprint = {1705.03625}, 8067 doi = {10.1002/cpe.4401}, 8068 year = {2017}, 8069 petsc_uses = {KSP} 8070} 8071 8072@Article{ changfabienknepleymills2018, 8073 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 8074 spectrum analysis}, 8075 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 8076 journal = {SIAM Journal on Scientific Computing}, 8077 volume = {40}, 8078 number = {6}, 8079 pages = {C779--C802}, 8080 eprint = {1802.07832}, 8081 doi = {10.1137/18M1172260}, 8082 year = {2018}, 8083 petsc_uses = {KSP} 8084} 8085 8086@Article{ joshaghanichangnakshatralaknepley2019, 8087 title = {Composable solvers for the four-field double porosity/permeability model}, 8088 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 8089 Knepley}, 8090 journal = {Journal of Computational Physics}, 8091 volume = {386}, 8092 pages = {428--466}, 8093 doi = {10.1016/j.jcp.2019.02.020}, 8094 year = {2019}, 8095 petsc_uses = {KSP} 8096} 8097 8098@InProceedings{ barralknepleylangepiggottgorman2016, 8099 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 8100 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 8101 and Gerard J. Gorman}, 8102 booktitle = {25th International Meshing Roundtable}, 8103 editor = {Steve Owen and Hang Si}, 8104 month = {September}, 8105 address = {Washington, DC}, 8106 pages = {1--5}, 8107 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 8108 year = {2016}, 8109 petsc_uses = {KSP} 8110} 8111 8112@Article{ adamsbrownknepleysamtaney2016, 8113 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 8114 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 8115 journal = {SIAM Journal on Scientific Computing}, 8116 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 8117 epub = {http://arxiv.org/abs/1406.7808}, 8118 volume = {8}, 8119 number = {4}, 8120 pages = {C426--C440}, 8121 doi = {10.1137/140975127}, 8122 year = {2016}, 8123 petsc_uses = {KSP} 8124} 8125 8126@InProceedings{ maysananruppknepleysmith2016, 8127 title = {Extreme-Scale Multigrid Components within {PETSc}}, 8128 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 8129 Smith}, 8130 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 8131 series = {PASC '16}, 8132 isbn = {978-1-4503-4126-4}, 8133 location = {Lausanne, Switzerland}, 8134 pages = {5:1--5:12}, 8135 articleno = {5}, 8136 numpages = {12}, 8137 doi = {10.1145/2929908.2929913}, 8138 acmid = {2929913}, 8139 publisher = {ACM}, 8140 address = {New York, NY, USA}, 8141 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 8142 preconditioning}, 8143 year = {2016}, 8144 petsc_uses = {KSP} 8145} 8146 8147@Article{ liu2015field, 8148 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 8149 author = {Lulu Liu and David E Keyes}, 8150 journal = {SIAM Journal on Scientific Computing}, 8151 volume = {37}, 8152 number = {3}, 8153 pages = {A1388--A1409}, 8154 year = {2015}, 8155 publisher = {SIAM}, 8156 petsc_uses = {KSP} 8157} 8158 8159@Article{ lujiaomissirlis2014, 8160 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 8161 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 8162 journal = {Numerical Linear Algebra with Applications}, 8163 volume = {21}, 8164 number = {2}, 8165 pages = {221--238}, 8166 year = {2014}, 8167 publisher = {Wiley Online Library}, 8168 petsc_uses = {KSP} 8169} 8170 8171@Article{ badiamartinprincipe2013, 8172 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 8173 solid mechanics}, 8174 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 8175 journal = {International Journal for Numerical Methods in Engineering}, 8176 volume = {96}, 8177 number = {4}, 8178 pages = {203--230}, 8179 year = {2013}, 8180 petsc_uses = {KSP} 8181} 8182 8183@Article{ morganknepleysananscott2016, 8184 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 8185 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 8186 journal = {Concurrency and Computation: Practice and Experience}, 8187 volume = {28}, 8188 pages = {4532--4542}, 8189 year = {2016}, 8190 url = {http://arxiv.org/abs/1602.04873}, 8191 doi = {10.1002/cpe.3820}, 8192 petsc_uses = {KSP} 8193} 8194 8195@Article{ morgansananknepleymills2020, 8196 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 8197 solvers}, 8198 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 8199 journal = {The International Journal of High Performance Computing Applications}, 8200 volume = {35}, 8201 issue = {1}, 8202 doi = {10.1177/1094342020966835}, 8203 url = {https://doi.org/10.1177/1094342020966835}, 8204 eprint = {https://doi.org/10.1177/1094342020966835}, 8205 year = {2020}, 8206 petsc_uses = {KSP} 8207} 8208 8209@Article{ msz2013, 8210 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 8211 author = {M. McCourt and B. F. Smith and H. Zhang}, 8212 journal = {SIAM Journal on Matrix Analysis and Applications}, 8213 year = {2015}, 8214 note = {To appear}, 8215 petsc_uses = {KSP} 8216} 8217 8218@Article{ bassi2014agglomeration, 8219 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 8220 free}, 8221 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 8222 journal = {Mathematical Models and Methods in Applied Sciences}, 8223 volume = {24}, 8224 number = {08}, 8225 pages = {1495--1539}, 8226 year = {2014}, 8227 publisher = {World Scientific}, 8228 petsc_uses = {KSP} 8229} 8230 8231@Article{ jhuranidemkowicz12, 8232 author = {{Jhurani}, C. and {Demkowicz}, L.}, 8233 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 8234 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 8235 journal = {Computer Methods in Applied Mechanics and Engineering}, 8236 volume = {213}, 8237 pages = {418-426}, 8238 year = {2012}, 8239 month = mar, 8240 doi = {10.1016/j.cma.2011.06.003}, 8241 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 8242 petsc_uses = {KSP} 8243} 8244 8245@Article{ yangcai11, 8246 author = {Yang, Haijian and Cai, Xiao-Chuan}, 8247 title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear 8248 Complementarity Problems}, 8249 journal = {J. Sci. Comput.}, 8250 issue_date = {May 2011}, 8251 volume = {47}, 8252 number = {2}, 8253 month = may, 8254 pages = {258--280}, 8255 year = {2011}, 8256 issn = {0885-7474}, 8257 numpages = {23}, 8258 doi = {10.1007/s10915-010-9436-4}, 8259 acmid = {1971246}, 8260 publisher = {Plenum Press}, 8261 address = {New York, NY, USA}, 8262 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 8263 preconditioners, Semismooth Newton, Two-level methods}, 8264 petsc_uses = {KSP} 8265} 8266 8267@Article{ rheinbach09, 8268 author = {Rheinbach, Oliver}, 8269 title = {Parallel Iterative Substructuring in Structural Mechanics}, 8270 journal = {Archives of Computational Methods in Engineering}, 8271 volume = {16}, 8272 number = {4}, 8273 pages = {425-463}, 8274 year = {2009}, 8275 issn = {1134-3060}, 8276 doi = {10.1007/s11831-009-9035-4}, 8277 publisher = {Springer Netherlands}, 8278 language = {English}, 8279 petsc_uses = {KSP} 8280} 8281 8282@Article{ knepleyterrel2013, 8283 author = {Matthew G. Knepley and Andy R. Terrel}, 8284 title = {Finite Element Integration on {GPUs}}, 8285 journal = {{ACM} Transactions on Mathematical Software}, 8286 volume = {39}, 8287 number = {2}, 8288 accepted = {17 April 2012}, 8289 year = {2013}, 8290 abstract = {We present a novel finite element integration method for low order elements on 8291 GPUs. We achieve more than 100GF for element integration on first order 8292 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 8293 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 8294 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 8295 url = {http://arxiv.org/abs/1103.0066}, 8296 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 8297 petsc_uses = {KSP} 8298} 8299 8300@Article{ knepleyruppterrel2016, 8301 title = {Finite Element Integration with Quadrature on the GPU}, 8302 journal = {ArXiv e-prints}, 8303 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 8304 version = {1}, 8305 date = {2016-07-14}, 8306 eprinttype = {arxiv}, 8307 eprintclass = {cs.MS}, 8308 eprint = {1607.04245v1}, 8309 petsc_uses = {KSP} 8310} 8311 8312@Article{ klawonnlanserrheinbach2014, 8313 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 8314 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 8315 journal = {SIAM Journal on Scientific Computing}, 8316 volume = {36}, 8317 number = {2}, 8318 pages = {A737--A765}, 8319 year = {2014}, 8320 petsc_uses = {KSP} 8321} 8322 8323@TechReport{ pbmkbsxt2012, 8324 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8325 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8326 year = {2013}, 8327 type = {Preprint}, 8328 number = {ANL/MCS-P2010-0112}, 8329 institution = {Argonne National Laboratory}, 8330 petsc_uses = {KSP} 8331} 8332 8333@Article{ bruneknepleysmithtu15, 8334 title = {Composing Scalable Nonlinear Algebraic Solvers}, 8335 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 8336 journal = {SIAM Review}, 8337 volume = {57}, 8338 number = {4}, 8339 pages = {535--565}, 8340 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 8341 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 8342 doi = {10.1137/130936725}, 8343 year = {2015}, 8344 petsc_uses = {KSP} 8345} 8346 8347@Article{ mszm2014, 8348 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 8349 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8350 volume = {40}, 8351 pages = {17--31}, 8352 year = {2014}, 8353 journal = {Parallel Computing}, 8354 doi = {10.1016/j.parco.2013.10.001}, 8355 petsc_uses = {KSP} 8356} 8357 8358@TechReport{ mszm2012, 8359 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 8360 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 8361 year = {2012}, 8362 number = {ANL/MCS-P2097-0512}, 8363 institution = {Argonne National Laboratory}, 8364 petsc_uses = {KSP} 8365} 8366 8367@InProceedings{ bkmms2012, 8368 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 8369 F. Smith}, 8370 title = {Composable linear solvers for multiphysics}, 8371 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 8372 Computing} ({ISPDC} 2012)}, 8373 year = {2012}, 8374 doi = {10.1109/ISPDC.2012.16}, 8375 publisher = {IEEE Computer Society}, 8376 pages = {55--62}, 8377 petsc_uses = {KSP} 8378} 8379 8380@Article{ bourdinbucuroudet2009, 8381 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 8382 title = {Optimal Partitions for Eigenvalues}, 8383 journal = {SIAM J. Sci. Comput.}, 8384 volume = {31}, 8385 number = {6}, 8386 pages = {4100--4114}, 8387 year = {2009}, 8388 petsc_uses = {KSP} 8389} 8390 8391@InBook{ kimnbourdin2007, 8392 author = {J.-H. Kimn and Blaise Bourdin}, 8393 title = {Numerical implementation of overlapping balancing domain decomposition methods on 8394 unstructured meshes}, 8395 editor = {O. B. Widlund and D. E. Keyes}, 8396 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 8397 series = {Lecture Notes in Computational Science and Engineering}, 8398 number = {55}, 8399 publisher = {Springer-Verlag}, 8400 pages = {309--315}, 8401 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 8402 year = {2007}, 8403 petsc_uses = {KSP} 8404} 8405 8406@Article{ bjm2005, 8407 author = {AH Baker and ER Jessup and T Manteuffel}, 8408 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 8409 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 8410 year = {2005}, 8411 petsc_uses = {KSP} 8412} 8413 8414@Unpublished{ sundar-2008a, 8415 author = {R.S. Sampath and G. Biros}, 8416 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 8417 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8418 petsc_uses = {KSP} 8419} 8420 8421@Article{ sundar-2008, 8422 author = {H. Sundar and R.S. Sampath and G. Biros}, 8423 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 8424 journal = {SIAM Journal on Scientific Computing}, 8425 year = {2008}, 8426 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8427 petsc_uses = {KSP} 8428} 8429 8430@InProceedings{ sundar-2007, 8431 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8432 title = {Low-constant parallel algorithms for finite element simulations using linear 8433 octrees}, 8434 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 8435 year = {2007}, 8436 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 8437 petsc_uses = {KSP} 8438} 8439 8440@InProceedings{ adams-98a, 8441 author = {Adams, Mark ~F.}, 8442 title = {A Parallel Maximal Independent Set Algorithm}, 8443 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 8444 year = {1998}, 8445 petsc_uses = {KSP} 8446} 8447 8448@Article{ akcelik2005ddd, 8449 title = {{Dynamic data-driven inversion for terascale simulations: real-time 8450 identification of airborne contaminants}}, 8451 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 8452 van Bloemen Waanders, B.}, 8453 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 8454 year = {2005}, 8455 publisher = {IEEE Computer Society Washington, DC, USA}, 8456 petsc_uses = {KSP} 8457} 8458 8459@InBook{ akcelik-2006, 8460 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 8461 Bloemen Waanders}, 8462 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 8463 title = {Frontiers of Parallel Computing}, 8464 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 8465 publisher = {SIAM}, 8466 year = {2006}, 8467 petsc_uses = {KSP} 8468} 8469 8470@Article{ dt, 8471 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 8472 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 8473 Convection Diffusion Equations}, 8474 journal = {The Journal of Supercomputing}, 8475 year = {2004}, 8476 pages = {235--253}, 8477 volume = {28}, 8478 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 8479 petsc_uses = {KSP} 8480} 8481 8482@PhDThesis{ hwang2004, 8483 author = {Feng-Nan Hwang}, 8484 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 8485 Computational Fluid Dynamics}, 8486 school = {University of Colorado at Boulder}, 8487 year = {2004}, 8488 petsc_uses = {KSP} 8489} 8490 8491@PhDThesis{ baker, 8492 author = {{A. H.} Baker}, 8493 title = {On improving the performance of the linear solver restarted {GMRES}}, 8494 school = {University of Colorado at Boulder}, 8495 year = {2003}, 8496 petsc_uses = {KSP} 8497} 8498 8499@TechReport{ klawonnrheinbach601, 8500 author = {Axel Klawonn and Oliver Rheinbach}, 8501 title = {A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional 8502 Linear Elasticity Using a Transformation of Basis}, 8503 institution = {Universit\"at Duisburg-Essen}, 8504 year = {2005}, 8505 type = {Technical Report}, 8506 number = {SM-E-601}, 8507 petsc_uses = {KSP} 8508} 8509 8510@TechReport{ klawonnrheinbach609, 8511 author = {Axel Klawonn and Oliver Rheinbach}, 8512 title = {Inexact FETI-DP Methods}, 8513 institution = {Universit\"at Duisburg-Essen}, 8514 year = {2005}, 8515 type = {Technical Report}, 8516 number = {SM-E-609}, 8517 petsc_uses = {KSP} 8518} 8519 8520@TechReport{ klawonnrheinbach607, 8521 author = {Axel Klawonn and Oliver Rheinbach}, 8522 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 8523 institution = {Universit\"at Duisburg-Essen}, 8524 year = {2005}, 8525 type = {Technical Report}, 8526 number = {SM-E-607}, 8527 petsc_uses = {KSP} 8528} 8529 8530@Article{ kul-natraj-pbp, 8531 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 8532 title = {Performance of a parallel mixed finite element implementation for fourth order 8533 clamped anisotropic plate bending problems in distributed memory environments}, 8534 journal = {Applied Mathematics and Computation}, 8535 volume = {155}, 8536 year = {2004}, 8537 number = {3}, 8538 pages = {753--777}, 8539 petsc_uses = {KSP} 8540} 8541 8542@Article{ bramkamp2006uej, 8543 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 8544 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 8545 journal = {Computers \& Fluids}, 8546 volume = {35}, 8547 number = {10}, 8548 pages = {1063--1073}, 8549 doi = {10.1016/j.compfluid.2005.10.003}, 8550 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 8551 derivation of the analytic flux Jacobian can become quite complicated depending on 8552 the complexity of the numerical flux calculation. Practically, the derivation of 8553 the exact Jacobian by hand is an unrealistic option because of the enormous 8554 man-hour investment needed. In this work, automatic differentiation is used to 8555 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 8556 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 8557 approximated by first-order forward differences. For a two-dimensional airfoil 8558 under three different flight conditions (quasi-incompressible flow, compressible 8559 subsonic flow, and transonic flow), we show that the robustness and performance of 8560 the present finite volume scheme is significantly improved by using exact 8561 Jacobians.}, 8562 year = {2006}, 8563 petsc_uses = {KSP} 8564} 8565 8566@Article{ shahbazi1, 8567 author = {Khosro Shahbazi}, 8568 title = {An explicit expression for the penalty parameter of the interior penalty method}, 8569 journal = {Journal of Computational Physics}, 8570 volume = {205}, 8571 year = {2005}, 8572 pages = {401--407}, 8573 petsc_uses = {KSP} 8574} 8575 8576@TechReport{ kk, 8577 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 8578 author = {Hans-Peter Kersken and Uwe Kuster}, 8579 year = {1999}, 8580 institution = {University of Stuttgart}, 8581 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 8582 number = {310}, 8583 petsc_uses = {KSP} 8584} 8585 8586@Article{ miha-mija, 8587 author = {M. D. Mihajlovi and S. Mijalkovi}, 8588 title = {A component decomposition preconditioning for 3D stress analysis problems}, 8589 journal = {Numerical Linear Algebra with Applications}, 8590 volume = {9}, 8591 year = {2002}, 8592 pages = {567--583}, 8593 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 8594 petsc_uses = {KSP} 8595} 8596 8597@Article{ bjm, 8598 author = {M Benzi and W Joubert and G Mateescu}, 8599 journal = {Electronic Transactions on Numerical Analysis}, 8600 year = {1999}, 8601 volume = {8}, 8602 pages = {88--114}, 8603 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 8604 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}, 8605 petsc_uses = {KSP} 8606} 8607 8608@PhDThesis{ hyde, 8609 author = {EMK Hyde}, 8610 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 8611 school = {Caltech}, 8612 year = {2003}, 8613 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 8614 petsc_uses = {KSP} 8615} 8616 8617@Article{ km2003, 8618 author = {A. Keese and H. G. Matthies}, 8619 journal = {Proceedings in Applied Mathematics and Mechanics}, 8620 year = {2003}, 8621 volume = {2}, 8622 pages = {485--486}, 8623 title = {Parallel Solution of Stochastic PDEs}, 8624 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 8625 petsc_uses = {KSP} 8626} 8627 8628@Article{ whszss, 8629 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 8630 and Otmar Scherzer and H. Siegfried Stiehl}, 8631 journal = {Real Time Imaging}, 8632 year = {2001}, 8633 volume = {7}, 8634 pages = {31--45}, 8635 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 8636 approaches}, 8637 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 8638 petsc_uses = {KSP} 8639} 8640 8641@TechReport{ baker1, 8642 title = {An Efficient Block Variant of GMRES}, 8643 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 8644 year = {2003}, 8645 type = {Technical Report}, 8646 institution = {University of Colorado, Boulder}, 8647 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 8648 number = {CU-CS-957-03}, 8649 petsc_uses = {KSP} 8650} 8651 8652@InProceedings{ mc2003, 8653 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 8654 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 8655 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8656 Methods}, 8657 pages = {639--646}, 8658 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8659 note = {}, 8660 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8661 year = {2003}, 8662 petsc_uses = {KSP} 8663} 8664 8665@InProceedings{ kt2003, 8666 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 8667 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 8668 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8669 Methods}, 8670 pages = {615--622}, 8671 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8672 note = {}, 8673 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8674 year = {2003}, 8675 petsc_uses = {KSP} 8676} 8677 8678@InProceedings{ krw2003, 8679 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 8680 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 8681 3D}, 8682 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8683 Methods}, 8684 pages = {361--368}, 8685 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8686 note = {}, 8687 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8688 year = {2003}, 8689 petsc_uses = {KSP} 8690} 8691 8692@InProceedings{ hc2003, 8693 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 8694 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 8695 Nonlinear Preconditioning}, 8696 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 8697 Methods}, 8698 pages = {201--208}, 8699 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 8700 note = {}, 8701 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 8702 year = {2003}, 8703 petsc_uses = {KSP} 8704} 8705 8706@InProceedings{ g2003, 8707 author = {P. Goldfeld}, 8708 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 8709 (Generalized) {Stokes} and Parallel Implementation}, 8710 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8711 Methods}, 8712 pages = {209--216}, 8713 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8714 publisher = {National Autonomous University of Mexico (UNAM)}, 8715 note = {}, 8716 url = {http://www.ddm.org/DD14}, 8717 year = {2003}, 8718 petsc_uses = {KSP} 8719} 8720 8721@InProceedings{ dhv2003, 8722 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 8723 title = {Toward scalable FETI algorithm for variational inequalities with applications to 8724 composites}, 8725 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 8726 Methods}, 8727 pages = {395--401}, 8728 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 8729 publisher = {National Autonomous University of Mexico (UNAM)}, 8730 note = {}, 8731 url = {http://www.ddm.org/DD14}, 8732 year = {2003}, 8733 petsc_uses = {KSP} 8734} 8735 8736@InProceedings{ dhsv2002, 8737 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 8738 title = {Scalabilities of FETI for variational inequalities and contact shape 8739 optimization}, 8740 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8741 Methods}, 8742 pages = {359--367}, 8743 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8744 publisher = {CIMNE, Barcelona, Spain}, 8745 note = {}, 8746 url = {http://www.ddm.org/DD13}, 8747 year = {2002}, 8748 petsc_uses = {KSP} 8749} 8750 8751@InProceedings{ cky2002, 8752 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 8753 title = {A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked 8754 Duct Flows}, 8755 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8756 Methods}, 8757 pages = {343--350}, 8758 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 8759 publisher = {CIMNE, Barcelona, Spain}, 8760 note = {}, 8761 url = {http://www.ddm.org/DD13}, 8762 year = {2002}, 8763 petsc_uses = {KSP} 8764} 8765 8766@Conference{ li-etal:03, 8767 author = {Li, Z. and Lanteri S. and Saad, Y.}, 8768 title = {Multiplicative-additive preconditioning combination for general sparse linear 8769 systems}, 8770 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 8771 Matrix Problems in Scientific and Industrial Applications}, 8772 address = {Napa, California, USA}, 8773 date = {october 27-29}, 8774 year = {2003}, 8775 petsc_uses = {KSP} 8776} 8777 8778@Article{ bashir2008hessian, 8779 title = {Hessian-based model reduction for large-scale systems with initial-condition 8780 inputs}, 8781 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 8782 J.}, 8783 journal = {International journal for numerical methods in engineering}, 8784 volume = {73}, 8785 number = {6}, 8786 pages = {844--868}, 8787 year = {2008}, 8788 publisher = {Wiley Online Library}, 8789 petsc_uses = {KSP} 8790} 8791 8792@Article{ bashir2007hessian, 8793 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 8794 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 8795 K.}, 8796 journal = {Computational Science--ICCS 2007}, 8797 pages = {1010--1017}, 8798 year = {2007}, 8799 publisher = {Springer}, 8800 petsc_uses = {KSP} 8801} 8802 8803@Article{ akcelik2011fast, 8804 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 8805 inverse problems based on low-rank partial {H}essian approximations}, 8806 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 8807 Waanders, B. and Wilcox, L.}, 8808 journal = {SIAM Journal on Scientific Computing}, 8809 volume = {33}, 8810 number = {1}, 8811 year = {2011}, 8812 petsc_uses = {KSP} 8813} 8814 8815@InProceedings{ ff2003, 8816 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 8817 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 8818 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 8819 year = {2003}, 8820 petsc_uses = {KSP} 8821} 8822 8823@InProceedings{ d2b2004, 8824 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 8825 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 8826 Ordering Strategies}, 8827 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 8828 year = {2004}, 8829 petsc_uses = {KSP} 8830} 8831 8832@InProceedings{ d2v2005, 8833 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8834 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 8835 Flow Equations}, 8836 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 8837 year = {2005}, 8838 petsc_uses = {KSP} 8839} 8840 8841@InProceedings{ dvs2006, 8842 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 8843 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 8844 Mixed Convection Equations}, 8845 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 8846 year = {2006}, 8847 petsc_uses = {KSP} 8848} 8849 8850@Article{ dsv2006, 8851 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 8852 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 8853 Flow Equations}, 8854 journal = {Computational Fluid Dynamics}, 8855 year = {2006}, 8856 volume = {15}, 8857 number = {1}, 8858 petsc_uses = {KSP} 8859} 8860 8861@Article{ lahaye03, 8862 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 8863 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 8864 journal = {J. Comput. Appl. Math.}, 8865 year = {2004}, 8866 pages = {267--275}, 8867 volume = {168}, 8868 petsc_uses = {KSP} 8869} 8870 8871@TechReport{ brmn, 8872 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 8873 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 8874 year = {2002}, 8875 type = {Technical Report}, 8876 institution = {ANL}, 8877 number = {ANL/MCS-P993-0902}, 8878 note = {To appear in Future Generation Computer Systems}, 8879 petsc_uses = {KSP} 8880} 8881 8882@InProceedings{ mnbr, 8883 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 8884 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 8885 Algorithms}, 8886 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 8887 Mechanics}, 8888 year = {2003}, 8889 petsc_uses = {KSP} 8890} 8891 8892@InProceedings{ bmnr, 8893 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 8894 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 8895 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 8896 Applications, Lecture notes in Computer Science 2677}, 8897 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 8898 pages = {828--839}, 8899 year = {2003}, 8900 petsc_uses = {KSP} 8901} 8902 8903@Article{ ph03, 8904 author = {M. Pernice and R. D. Hornung}, 8905 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 8906 journal = {Computing and Visualization in Science}, 8907 year = {2003}, 8908 lab = {LANL}, 8909 petsc_uses = {KSP} 8910} 8911 8912@Article{ adams-02, 8913 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 8914 journal = {J. Comp. Phys.}, 8915 number = {2}, 8916 pages = {593-610}, 8917 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 8918 volume = {188}, 8919 year = {2003}, 8920 petsc_uses = {KSP} 8921} 8922 8923@InProceedings{ adams2001distributed, 8924 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 8925 smoothers}, 8926 author = {Adams, M.F.}, 8927 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 8928 pages = {14--14}, 8929 year = {2001}, 8930 organization = {IEEE}, 8931 petsc_uses = {KSP} 8932} 8933 8934@PhDThesis{ els01, 8935 author = {Ulrich Elsner}, 8936 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 8937 algorithms}, 8938 school = {Technical University Chemnitz}, 8939 year = {2002}, 8940 publisher = {Logos Verlag, Berlin}, 8941 isbn = {3-89722-923-4}, 8942 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 8943 different graph partitioning algorithms}, 8944 petsc_uses = {KSP} 8945} 8946 8947@TechReport{ ckk02, 8948 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 8949 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 8950 year = {2002}, 8951 type = {Technical Report}, 8952 institution = {ODU}, 8953 url = {http://www.math.odu.edu/\~{ }keyes}, 8954 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 8955 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 8956 Methods}, 8957 petsc_uses = {KSP} 8958} 8959 8960@Article{ gpw2002, 8961 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 8962 Heterogeneous Problems in Linear Elasticity}, 8963 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 8964 year = {2003}, 8965 pages = {283--324}, 8966 volume = {95}, 8967 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 8968 journal = {Numerische Mathematik}, 8969 petsc_uses = {KSP} 8970} 8971 8972@Article{ dh1, 8973 title = {Scalability and FETI based algorithm for large discretized variational 8974 inequalities}, 8975 author = {Z Dostal and D Horak}, 8976 year = {2003}, 8977 pages = {347--357}, 8978 volume = {61}, 8979 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 8980 journal = {Mathematics and Computers in Simulation}, 8981 petsc_uses = {KSP} 8982} 8983 8984@InProceedings{ dhsv1, 8985 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 8986 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 8987 title = {36 Scalabilities of FETI for Variational Inequalities and Contact Shape 8988 Optimization}, 8989 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 8990 Methods}, 8991 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 8992 Kuznetsov}, 8993 petsc_uses = {KSP} 8994} 8995 8996@Article{ lahaye02, 8997 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 8998 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 8999 journal = {IEEEMAGN}, 9000 year = {2002}, 9001 volume = {38}, 9002 number = {2}, 9003 pages = {413-416}, 9004 petsc_uses = {KSP} 9005} 9006 9007@Article{ ckm01, 9008 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 9009 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 9010 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 9011 fluid dynamics}, 9012 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 9013 year = {2002}, 9014 volume = {40}, 9015 pages = {1463--1470}, 9016 petsc_uses = {KSP} 9017} 9018 9019@InProceedings{ cky01, 9020 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 9021 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 9022 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 9023 duct flow}, 9024 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9025 Methods}, 9026 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9027 Kuznetsov}, 9028 year = {2002}, 9029 petsc_uses = {KSP} 9030} 9031 9032@Article{ ck02, 9033 author = {X.-C. Cai and D. E. Keyes}, 9034 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 9035 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 9036 journal = {SIAM J. Sci. Comput.}, 9037 year = {2002}, 9038 pages = {183--200}, 9039 volume = {24}, 9040 petsc_uses = {KSP} 9041} 9042 9043@Article{ c04, 9044 author = {Feng-Nan Hwang and X.-C. Cai}, 9045 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 9046 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 9047 for incompressible {Navier-Stokes} equations}, 9048 journal = {Journal of Computational Physics}, 9049 year = {2005}, 9050 volume = {204}, 9051 pages = {666--691}, 9052 petsc_uses = {KSP} 9053} 9054 9055@Article{ hc06, 9056 author = {Feng-Nan Hwang and X.-C. Cai}, 9057 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 9058 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 9059 Algorithms}, 9060 journal = {Computer Methods in Applied Mechanics and Engineering}, 9061 year = {2006}, 9062 volume = {196}, 9063 pages = {1603--1611}, 9064 petsc_uses = {KSP} 9065} 9066 9067@InProceedings{ adams-01, 9068 author = {Mark F. Adams}, 9069 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 9070 Smoothers}, 9071 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 9072 address = {Denver, Colorado}, 9073 month = {November}, 9074 year = {2001}, 9075 petsc_uses = {KSP} 9076} 9077 9078@Book{ 1dl, 9079 author = {Domenico Lahaye}, 9080 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 9081 Computations}, 9082 year = {2001}, 9083 publisher = {Katholieke Universiteit Leuven}, 9084 notes = {Thesis}, 9085 petsc_uses = {KSP} 9086} 9087 9088@Article{ adams-00, 9089 author = {Adams, M.~F.}, 9090 journal = {International Journal for Numerical Methods in Engineering}, 9091 number = {8}, 9092 pages = {1241-1262}, 9093 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 9094 Deformation Elasticity and Plasticity}, 9095 volume = {48}, 9096 year = {2000}, 9097 petsc_uses = {KSP} 9098} 9099 9100@Article{ adams2002evaluation, 9101 author = {Adams, M.~F.}, 9102 journal = {International Journal for Numerical Methods in Engineering}, 9103 number = {1}, 9104 pages = {519-534}, 9105 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 9106 Problems in Solid Mechanics}, 9107 volume = {55}, 9108 year = {2002}, 9109 petsc_uses = {KSP} 9110} 9111 9112@Article{ lahaye00, 9113 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 9114 title = {Algebraic Multigrid for Complex Symmetric Systems}, 9115 journal = {IEEEMAGN}, 9116 year = {2000}, 9117 volume = {36}, 9118 number = {4}, 9119 pages = {1535--1538}, 9120 petsc_uses = {KSP} 9121} 9122 9123@InProceedings{ adams-99c, 9124 author = {Mark F. Adams and J. Demmel}, 9125 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 9126 Finite Element Problems}, 9127 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 9128 address = {Portland, Oregon}, 9129 month = {November}, 9130 year = {1999}, 9131 petsc_uses = {KSP} 9132} 9133 9134@Article{ chan95, 9135 author = {T. Chan and B. Smith and J. Zou}, 9136 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 9137 Grids}, 9138 journal = {Numer. Math.}, 9139 year = {1995}, 9140 volume = {73}, 9141 pages = {149--167}, 9142 petsc_uses = {KSP} 9143} 9144 9145@TechReport{ adams-csd-98-993, 9146 pages = {11}, 9147 year = {1998}, 9148 type = {Technical Report}, 9149 number = {CSD-98-993}, 9150 institution = {University of California, Berkeley}, 9151 title = {A Parallel Maximal Independent Set Algorithm}, 9152 bibdate = {March 11, 1998}, 9153 author = {Mark F. Adams and James Demmel}, 9154 abstract = {The parallel construction of maximal independent sets is a useful building block 9155 for many algorithms in the computational sciences, including graph coloring and 9156 multigrid coarse grid creation on unstructured meshes. We present an efficient 9157 asynchronous maximal independent set algorithm for use on parallel computers, for 9158 ``well partitioned'' graphs, that arise from finite element (FE) models. For 9159 appropriately partitioned bounded degree graphs, it is shown that the running time 9160 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 9161 improvement over the previous best P-RAM complexity for this class of graphs. We 9162 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 9163 model is indicative of the performance one can expect with practical partitions on 9164 graphs from FE problems.}, 9165 month = mar # { 11,}, 9166 petsc_uses = {KSP} 9167} 9168 9169@TechReport{ k676, 9170 year = {1994}, 9171 type = {Technical Report}, 9172 number = {TR1994-676}, 9173 institution = {New York University}, 9174 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 9175 Term}, 9176 author = {Axel Klawonn}, 9177 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 9178 petsc_uses = {KSP} 9179} 9180 9181@Book{ ak1, 9182 author = {Axel Klawonn}, 9183 title = {Preconditioners for Indefinite Problems}, 9184 year = {1995}, 9185 publisher = {Westfalishen Wilhelms-Universitat Munster}, 9186 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 9187 notes = {Thesis}, 9188 petsc_uses = {KSP} 9189} 9190 9191@TechReport{ knepleykarpeev05, 9192 pages = {41}, 9193 year = {2005}, 9194 type = {Technical Report}, 9195 number = {ANL/MCS-P1295-1005}, 9196 institution = {Argonne National Laboratory}, 9197 title = {Flexible Representation of Computational Meshes}, 9198 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9199 abstract = {}, 9200 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 9201 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 9202 month = {October}, 9203 petsc_uses = {DMPlex} 9204} 9205 9206@TechReport{ knepleykarpeev07a, 9207 pages = {14}, 9208 year = {2007}, 9209 type = {Technical Report}, 9210 number = {ANL/MCS-P1455-0907}, 9211 institution = {Argonne National Laboratory}, 9212 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9213 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9214 abstract = {}, 9215 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 9216 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 9217 month = {February}, 9218 petsc_uses = {DMPlex} 9219} 9220 9221@Article{ knepleykarpeev09, 9222 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 9223 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 9224 journal = {Scientific Programming}, 9225 volume = {17}, 9226 number = {3}, 9227 pages = {215--230}, 9228 year = {2009}, 9229 doi = {10.3233/SPR-2009-0249}, 9230 url = {http://arxiv.org/abs/0908.4427}, 9231 note = {\url{http://arxiv.org/abs/0908.4427}}, 9232 petsc_uses = {DMPlex} 9233} 9234 9235@Article{ biezuner2012computing, 9236 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 9237 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 9238 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 9239 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 9240 Sublinear Supersolutions}, 9241 journal = {Journal of Scientific Computing}, 9242 publisher = {Springer Netherlands}, 9243 issn = {0885-7474}, 9244 keyword = {Mathematics and Statistics}, 9245 pages = {180--201}, 9246 volume = {52}, 9247 issue = {1}, 9248 year = {2012}, 9249 doi = {10.1007/s10915-011-9540-0}, 9250 petsc_uses = {KSP} 9251} 9252 9253% LiteralHTML: 9254% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 9255% LiteralHTML: 9256@Book{ knepley2017, 9257 title = {Computational Science I}, 9258 author = {Matthew G. Knepley}, 9259 url = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}, 9260 note = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}}, 9261 publisher = {PETSc}, 9262 year = {2017}, 9263 petsc_uses = {KSP} 9264} 9265 9266@Article{ verleyeuser, 9267 title = {{User friendly permeability predicting software for technical textiles}}, 9268 author = {Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and 9269 Roose, D.}, 9270 journal = {status: published}, 9271 issn = {1560-6074}, 9272 publisher = {Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}, 9273 petsc_uses = {KSP} 9274} 9275 9276@Book{ pacheco, 9277 author = {Peter Pacheco}, 9278 title = {Parallel Programming with MPI}, 9279 year = {1997}, 9280 publisher = {Morgan-Kaufmann}, 9281 note = {Devotes a couple of sections to PETSc}, 9282 petsc_uses = {KSP} 9283} 9284 9285@Book{ 1sbg, 9286 author = {Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp}, 9287 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 9288 Differential Equations}, 9289 year = {1996}, 9290 publisher = {Cambridge University Press}, 9291 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 9292 petsc_uses = {KSP} 9293} 9294 9295@Misc{ petsc-fem:homepage, 9296 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 9297 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 9298 G. Rodriguez and G. Filippini}, 9299 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 9300 petsc_uses = {KSP} 9301} 9302 9303@Misc{ petsc4py-web-page, 9304 author = {Lisandro Dalcin}, 9305 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 9306 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 9307 note = {http://code.google.com/p/petsc4py/}, 9308 petsc_uses = {KSP} 9309} 9310 9311@Article{ libmeshpaper06, 9312 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 9313 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 9314 Simulations}}, 9315 journal = {Engineering with Computers}, 9316 volume = {22}, 9317 number = {3--4}, 9318 pages = {237--254}, 9319 year = {2006}, 9320 doi = {10.1007/s00366-006-0049-3}, 9321 petsc_uses = {KSP} 9322} 9323 9324@Misc{ sisiphus:homepage, 9325 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 9326 High-Resolution, Unstructured Simulations}, 9327 author = {T. {Tautges et al.}}, 9328 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 9329 petsc_uses = {KSP} 9330} 9331 9332@Misc{ pflotran:homepage, 9333 title = {{PFLOTRAN} project}, 9334 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 9335 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 9336 howpublished = {\url{http://pflotran.org/}}, 9337 petsc_uses = {KSP} 9338} 9339 9340@Misc{ pism:homepage, 9341 title = {{PISM}: A Parallel Ice Sheet Model}, 9342 author = {E. {Bueler et al.}}, 9343 howpublished = {\url{http://pism-docs.org}}, 9344 petsc_uses = {KSP} 9345} 9346 9347@Misc{ dohp:homepage, 9348 title = {Dohp: Dual order $hp$-finite elements}, 9349 author = {J. Brown}, 9350 howpublished = {\url{http://dohp.org}}, 9351 petsc_uses = {KSP} 9352} 9353 9354@Article{ mccourtrognlienetal12, 9355 title = {Improving parallel scalability for edge plasma transport simulations with neutral 9356 gas species}, 9357 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 9358 journal = {Computational Science and Discovery}, 9359 year = {2012}, 9360 volume = {5}, 9361 number = {014012}, 9362 doi = {10.1088/1749-4699/5/1/014012}, 9363 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 9364 2011)}, 9365 petsc_uses = {KSP} 9366} 9367 9368@Misc{ petclaw-github, 9369 title = {Pet{C}law Software}, 9370 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 9371 year = {2011}, 9372 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 9373 petsc_uses = {KSP} 9374} 9375 9376@Misc{ pyclaw-web-page, 9377 author = {Kyle T. Mandli and David I. Ketcheson and others}, 9378 title = {{PyClaw} software}, 9379 howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}}, 9380 url = {http://clawpack.github.io/doc/pyclaw/}, 9381 year = {2012}, 9382 petsc_uses = {KSP} 9383} 9384 9385@Article{ ketcheson2011highorder, 9386 title = {High-order wave propagation algorithms for general hyperbolic systems}, 9387 author = {Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.}, 9388 year = {2011}, 9389 note = {submitted}, 9390 petsc_uses = {KSP} 9391} 9392 9393@Article{ biros2005pln1, 9394 title = {{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained 9395 optimization. Part I: The {Krylov-Schur} solver}}, 9396 author = {Biros, G. and Ghattas, O.}, 9397 journal = {SIAM Journal on Scientific Computing}, 9398 volume = {27}, 9399 number = {2}, 9400 pages = {687--713}, 9401 year = {2005}, 9402 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9403 petsc_uses = {KSP} 9404} 9405 9406@Article{ biros2005pln2, 9407 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 9408 optimization. Part {II}: The {Lagrange Newton} solver, and its application to 9409 optimal control of steady viscous flows}, 9410 author = {Biros, G. and Ghattas, O.}, 9411 journal = {SIAM Journal on Scientific Computing}, 9412 volume = {27}, 9413 number = {2}, 9414 pages = {714--739}, 9415 year = {2005}, 9416 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 9417 petsc_uses = {KSP} 9418} 9419 9420@Misc{ issm:homepage, 9421 title = {{I}ce {S}heet {S}ystem {M}odel}, 9422 author = {Eric Larour and Mathieu Morlighem and Helene Seroussi}, 9423 year = {2010}, 9424 note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}, 9425 petsc_uses = {KSP} 9426} 9427 9428@Article{ morlighem2010spatial, 9429 title = {Spatial patterns of basal drag inferred using control methods from a 9430 full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est 9431 {A}ntarctica}, 9432 author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and 9433 Aubry, D.}, 9434 journal = {Geophysical Research Letters}, 9435 volume = {37}, 9436 number = {14}, 9437 pages = {L14502}, 9438 year = {2010}, 9439 publisher = {American Geophysical Union}, 9440 petsc_uses = {KSP} 9441} 9442 9443@Article{ jardin2012plasmas, 9444 title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics 9445 of tokamak plasmas}, 9446 author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 9447 journal = {Computational Science \& Discovery}, 9448 volume = {5}, 9449 number = {1}, 9450 url = {http://stacks.iop.org/1749-4699/5/014002}, 9451 year = {2012}, 9452 petsc_uses = {KSP} 9453} 9454 9455@Article{ cmz2016, 9456 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 9457 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 9458 journal = {Journal of Scientific Computing}, 9459 publisher = {Springer}, 9460 pages = {803--825}, 9461 volume = {68}, 9462 issue = {2}, 9463 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 9464 doi = {10.1007/s10915-015-0159-4}, 9465 year = {2016}, 9466 note = {Also preprint ANL/MCS-P3039-0912}, 9467 petsc_uses = {KSP} 9468} 9469 9470@Article{ knepleybrownruppsmith13, 9471 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 9472 title = {Achieving High Performance with Unified Residual Evaluation}, 9473 journal = {ArXiv e-prints}, 9474 eprint = {1309.1204}, 9475 archiveprefix = {arXiv}, 9476 primaryclass = {cs.MS}, 9477 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 9478 Engineering, Finance, and Science}, 9479 year = {2013}, 9480 month = sep, 9481 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 9482 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9483 petsc_uses = {KSP} 9484} 9485 9486@Book{ fenicsbook, 9487 title = {Automated Solution of Differential Equations by the Finite Element Method: The 9488 FEniCS Book}, 9489 series = {Lecture Notes in Computational Science and Engineering}, 9490 volume = {84}, 9491 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 9492 publisher = {Springer}, 9493 isbn = {978-3-642-23098-1}, 9494 year = {2012}, 9495 petsc_uses = {KSP} 9496} 9497 9498@Article{ demidovahnertruppgottschling12, 9499 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 9500 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 9501 journal = {ArXiv e-prints}, 9502 archiveprefix = {arXiv}, 9503 eprint = {1212.6326}, 9504 primaryclass = {cs.MS}, 9505 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 9506 Parallel, and Cluster Computing, Physics - Computational Physics}, 9507 year = {2012}, 9508 month = dec, 9509 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 9510 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 9511 petsc_uses = {KSP} 9512} 9513 9514@InProceedings{ viennacl, 9515 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 9516 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 9517 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 9518 year = {2010}, 9519 pages = {51-56}, 9520 petsc_uses = {KSP} 9521} 9522 9523@Article{ knepleybrownmcinnessmithruppadams2015, 9524 title = {Exascale Computing without Threads}, 9525 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9526 Karl Rupp and Mark Adams}, 9527 url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950}, 9528 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9529 Scientific Software Architecture for Portability and Performance}, 9530 doi = {10.6084/m9.figshare.5824950.v1}, 9531 year = {2015}, 9532 petsc_uses = {KSP} 9533} 9534 9535@Article{ knepleybrownmcinnessmithruppadams2015b, 9536 title = {Overview of the {PETSc} Library}, 9537 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 9538 Karl Rupp and Mark Adams}, 9539 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 9540 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 9541 Scientific Software Architecture for Portability and Performance}, 9542 year = {2015}, 9543 petsc_uses = {KSP} 9544} 9545 9546@InBook{ balaybrownknepleymcinnessmith2015, 9547 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 9548 Smith}, 9549 bookeditor = {J. Carver}, 9550 title = {Software Engineering for Science}, 9551 chapter = {Providing Mixed Language and Legacy Support within a Library}, 9552 publisher = {Taylor \& Francis}, 9553 year = {2015}, 9554 petsc_uses = {KSP} 9555} 9556 9557@Article{ ruppbalaybrownknepleymcinnessmith2015, 9558 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 9559 Software}, 9560 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 9561 McInnes and Barry F. Smith}, 9562 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 9563 Productivity Challenges}, 9564 journal = {ArXiv e-prints}, 9565 archiveprefix = {arXiv}, 9566 eprint = {1510.01122}, 9567 year = {2015}, 9568 petsc_uses = {KSP} 9569} 9570 9571@InProceedings{ knepley2013accurately, 9572 title = {Accurately Citing Software and Algorithms Used in Publications}, 9573 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 9574 F.}, 9575 year = {2013}, 9576 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 9577 (WSSSPE), held at SC13}, 9578 doi = {10.6084/m9.figshare.785731}, 9579 petsc_uses = {KSP} 9580} 9581 9582@InProceedings{ milleretal2013, 9583 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 9584 Strategies Developed for {FASTMath}}, 9585 author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and 9586 Barry Smith}, 9587 year = {2013}, 9588 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 9589 (WSSSPE), held at SC13}, 9590 doi = {10.6084/m9.figshare.789055}, 9591 petsc_uses = {KSP} 9592} 9593 9594@TechReport{ dudsonetal2012, 9595 title = {Improved Nonlinear Solvers in {BOUT++}}, 9596 author = {Ben Dudson and Sean Farley and Lois Curfman McInnes}, 9597 institution = {Argonne National Laboratory}, 9598 number = {ANL/MCS-P3025-0812}, 9599 year = {2012}, 9600 petsc_uses = {KSP} 9601} 9602 9603@Misc{ brown13, 9604 author = {J. Brown}, 9605 title = {Scalable Repository Workflows}, 9606 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 9607 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 9608 year = {2013}, 9609 petsc_uses = {KSP} 9610} 9611 9612@Misc{ starforest11, 9613 title = {Star forests as a parallel communication model}, 9614 author = {Jed Brown}, 9615 url = {https://jedbrown.org/files/StarForest.pdf}, 9616 year = {2011}, 9617 petsc_uses = {KSP} 9618} 9619 9620@Misc{ brownknepleysmith13, 9621 author = {J. Brown and M. Knepley and B. Smith}, 9622 title = {Run-time Extensibility: Anything Less is Unsustainable}, 9623 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 9624 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 9625 year = {2013}, 9626 petsc_uses = {KSP} 9627} 9628 9629@Article{ jzhaoyliwkliu15, 9630 author = {J. Zhao and Y. Li and W.K. Liu}, 9631 title = {Predicting band structure of 3{D} mechanical metamaterials with complex geometry 9632 via {XFEM}}, 9633 journal = {Computational Mechanics}, 9634 year = {2015}, 9635 url = {http://link.springer.com/article/10.1007/s00466-015-1129-2}, 9636 petsc_uses = {KSP} 9637} 9638 9639@Article{ alisic14, 9640 author = {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen}, 9641 title = {Compaction around a rigid, circular inclusion in partially molten rock}, 9642 journal = {J. Geophys. Res.}, 9643 year = {2014}, 9644 volume = {119}, 9645 number = {7}, 9646 pages = {5903-5920}, 9647 doi = {10.1002/2013JB010906}, 9648 petsc_uses = {KSP} 9649} 9650 9651@Article{ rhebergen14, 9652 author = {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen}, 9653 title = {Analysis of block preconditioners for models of coupled magma mantle dynamics}, 9654 journal = {SIAM J. Sci. Comp.}, 9655 year = {2014}, 9656 volume = {36}, 9657 number = {4}, 9658 pages = {1960-1977}, 9659 doi = {10.1137/130946678}, 9660 petsc_uses = {KSP} 9661} 9662 9663@Article{ allwright14, 9664 author = {J. Allwright and R.F. Katz}, 9665 title = {Pipe Poiseuille flow of viscously anisotropic, partially molten rock}, 9666 journal = {Geophys. J. Int.}, 9667 year = {2014}, 9668 volume = {199}, 9669 number = {3}, 9670 pages = {1608--1624}, 9671 doi = {10.1093/gji/ggu345}, 9672 petsc_uses = {KSP} 9673} 9674 9675@Misc{ gropp10, 9676 author = {William D. Gropp}, 9677 title = {Update on libraries for {B}lue {W}aters}, 9678 address = {Bordeaux, France}, 9679 year = {2010}, 9680 url = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf}, 9681 petsc_uses = {KSP} 9682} 9683 9684@Article{ ssm2016, 9685 author = {P. Sanan and S.M. Schnepp and D.A. May}, 9686 title = {Pipelined, Flexible {Krylov} Subspace Methods}, 9687 journal = {SIAM Journal on Scientific Computing}, 9688 volume = {38}, 9689 number = {5}, 9690 pages = {C441-C470}, 9691 year = {2016}, 9692 doi = {10.1137/15M1049130}, 9693 petsc_uses = {KSP} 9694} 9695 9696@InProceedings{ mayknepley2017, 9697 title = {{DMSwarm}: Particles in {PETSc}}, 9698 author = {Dave A May and Matthew G Knepley}, 9699 booktitle = {EGU General Assembly Conference Abstracts}, 9700 volume = {19}, 9701 pages = {10133}, 9702 year = {2017}, 9703 petsc_uses = {KSP} 9704} 9705 9706@InProceedings{ adamsbrownknepley2013, 9707 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley}, 9708 title = {Low-communication techniques for extreme-scale multilevel solvers}, 9709 booktitle = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC}, 9710 organization = {DOE Office of Advanced Scientific Computing Research}, 9711 year = {2013}, 9712 petsc_uses = {KSP} 9713} 9714 9715@Article{ bhallagriffithknepleyadamsguy2017, 9716 title = {Scalable smoothing strategies for a geometric multigrid method for the immersed 9717 boundary equations}, 9718 author = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F. 9719 Adams and Robert D. Guy}, 9720 journal = {Advances in Computational Mathematics}, 9721 eprint = {1612.02208}, 9722 note = {In review}, 9723 year = {2017}, 9724 petsc_uses = {KSP} 9725} 9726 9727@Article{ zampini2016pcbddc, 9728 title = {{PCBDDC}: a class of robust dual-primal methods in {PETSc}}, 9729 author = {Zampini, Stefano}, 9730 journal = {SIAM Journal on Scientific Computing}, 9731 volume = {38}, 9732 number = {5}, 9733 pages = {S282--S306}, 9734 year = {2016}, 9735 publisher = {SIAM}, 9736 petsc_uses = {KSP} 9737} 9738 9739@Article{ jolivetromanzampini2020, 9740 title = {{KSPHPDDM} and {PCHPDDM}: extending {PETSc} with advanced {Krylov} methods and 9741 robust multilevel overlapping {Schwarz} preconditioners}, 9742 author = {Pierre Jolivet and Jose Roman and Stefano Zampini}, 9743 journal = {Computers and Mathematics with Applications}, 9744 volume = {84}, 9745 pages = {277--295}, 9746 year = {2020} 9747} 9748 9749@Article{ zampinitu2017, 9750 title = {Multilevel {BDDC} deluxe algorithms with adaptive coarse spaces for flow in 9751 porous media}, 9752 author = {Stefano Zampini and Xuemin Tu}, 9753 journal = {SIAM Journal of Scientific Computing}, 9754 volume = {39}, 9755 number = {4}, 9756 pages = {A1389--A1415}, 9757 year = {2017} 9758} 9759 9760@Article{ ohwidlundzampinidohrmann2017, 9761 title = {{BDDC} algorithms with deluxe scaling and adaptive selection of primal 9762 constraints for {Raviart-Thomas} vector fields}, 9763 author = {D.-S. Oh and Olof B. Widlund and Stefano Zampini and Clark Dohrmann}, 9764 journal = {Mathematics of Computation}, 9765 volume = {87}, 9766 number = {310}, 9767 pages = {659--692}, 9768 year = {2017} 9769} 9770 9771@Article{ veigapavarinoscacchiwidlundzampini2016, 9772 title = {Adaptive selection of primal constraints for isogeometric {BDDC} deluxe 9773 preconditioners}, 9774 author = {L. Beirao Da Veiga and Luca F. Pavarino and S. Scacchi and Olof B. Widlund and 9775 Stefano Zampini}, 9776 journal = {SIAM Journal of Scientific Computing}, 9777 volume = {39}, 9778 number = {1}, 9779 pages = {A281--A302}, 9780 year = {2016} 9781} 9782 9783@Article{ pavarinoscacchiwidlundzampini2018, 9784 title = {Isogeometric {BDDC} deluxe preconditioners for linear elasticity for isogeometric 9785 analysis}, 9786 author = {Luca F. Pavarino and S. Scacchi and Olof B. Widlund and Stefano Zampini}, 9787 journal = {Mathematical Models and Methods in Applied Sciences}, 9788 volume = {28}, 9789 number = {7}, 9790 pages = {1337--1370}, 9791 year = {2018} 9792} 9793 9794@Article{ bergervergiatwaisman2017, 9795 title = {An overlapping Domain Decomposition preconditioning method for monolithic 9796 solution of shear bands}, 9797 author = {Luc Berger-Vergiat and Haim Waisman}, 9798 journal = {Computer Methods in Applied Mechanics and Engineering}, 9799 volume = {318}, 9800 pages = {33--60}, 9801 year = {2017}, 9802 petsc_uses = {KSP} 9803} 9804 9805@Article{ abhyankarmaldonadosmithzhang2020, 9806 title = {{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics 9807 Simulations}, 9808 author = {S. Abhyankar and G. Betrie and D.A. Maldonado and L.C. McInnes and B. Smith and 9809 H. 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May}, 9923 journal = {SIAM Journal on Scientific Computing}, 9924 volume = {38}, 9925 number = {5}, 9926 pages = {C441-C470}, 9927 year = {2016}, 9928 doi = {10.1137/15M1049130}, 9929 petsc_uses = {KSP} 9930} 9931 9932@Article{ petscsf2022, 9933 author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and 9934 Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and 9935 Smith, Barry F. and Zampini, Stefano}, 9936 journal = {IEEE Transactions on Parallel and Distributed Systems}, 9937 title = {The {PetscSF} Scalable Communication Layer}, 9938 year = {2022}, 9939 volume = {33}, 9940 number = {4}, 9941 pages = {842-853}, 9942 doi = {10.1109/TPDS.2021.3084070} 9943} 9944 9945@Article{ brandt2000, 9946 title = {General highly accurate algebraic coarsening}, 9947 author = {Achi Brandt}, 9948 journal = {Electronic Transactions on Numerical Analysis}, 9949 volume = {10}, 9950 number = {9680}, 9951 pages = {1--20}, 9952 issn = {10689613}, 9953 year = {2000} 9954} 9955 9956@Article{ dalcinpazklercosimo2011, 9957 title = {Parallel distributed computing using Python}, 9958 author = {Lisandro D. 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Kler and Alejandro Cosimo}, 9959 journal = {Advances in Water Resources}, 9960 volume = {34}, 9961 number = {9}, 9962 pages = {1124 - 1139}, 9963 note = {New Computational Methods and Software Tools}, 9964 issn = {0309-1708}, 9965 doi = {10.1016/j.advwatres.2011.04.013}, 9966 year = {2011} 9967} 9968 9969@Article{ behnelbradshawcitrodalcinseljebotnsmith2011, 9970 title = {Cython: The Best of Both Worlds}, 9971 author = {Behnel,Stefan and Bradshaw,Robert and Citro,Craig and Dalcin,Lisandro and 9972 Seljebotn,Dag Sverre and Smith,Kurt }, 9973 journal = {Computing in Science \& Engineering}, 9974 volume = {13}, 9975 number = {2}, 9976 pages = {31-39}, 9977 doi = {10.1109/MCSE.2010.118}, 9978 year = {2011} 9979} 9980 9981@Article{ dalcinpazstorti2005, 9982 title = {MPI for Python}, 9983 author = {Lisandro Dalcín and Rodrigo Paz and Mario Storti}, 9984 journal = {Journal of Parallel and Distributed Computing}, 9985 volume = {65}, 9986 number = {9}, 9987 pages = {1108 - 1115}, 9988 issn = {0743-7315}, 9989 doi = {10.1016/j.jpdc.2005.03.010}, 9990 year = {2005} 9991} 9992 9993@Article{ dalcincolliervignalcortescalo2016, 9994 title = {PetIGA: A framework for high-performance isogeometric analysis}, 9995 author = {Lisandro Dalcin and Nathan Collier and P. Vignal and A.M.A. Cortes and Victor M. 9996 Calo}, 9997 journal = {Computer Methods in Applied Mechanics and Engineering}, 9998 volume = {308}, 9999 pages = {151 - 181}, 10000 issn = {0045-7825}, 10001 doi = {10.1016/j.cma.2016.05.011}, 10002 year = {2016} 10003} 10004 10005@Article{ collierpardodalcinpaszynskicalo2012, 10006 title = {The cost of continuity: A study of the performance of isogeometric finite 10007 elements using direct solvers}, 10008 author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M. 10009 Calo}, 10010 journal = {Computer Methods in Applied Mechanics and Engineering}, 10011 volume = {213-216}, 10012 pages = {353 - 361}, 10013 issn = {0045-7825}, 10014 doi = {10.1016/j.cma.2011.11.002}, 10015 year = {2012} 10016} 10017 10018@Article{ collierdalcinpardocalo2013, 10019 title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite 10020 Elements}, 10021 author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo}, 10022 journal = {SIAM Journal on Scientific Computing}, 10023 volume = {35}, 10024 number = {2}, 10025 pages = {A767-A784}, 10026 doi = {10.1137/120881038}, 10027 year = {2013} 10028} 10029 10030@Article{ dunning2017jump, 10031 title = {{JuMP}: a modeling language for mathematical optimization}, 10032 author = {Dunning, Iain and Huchette, Joey and Lubin, Miles}, 10033 journal = {SIAM Review}, 10034 volume = {59}, 10035 number = {2}, 10036 pages = {295--320}, 10037 year = {2017}, 10038 publisher = {SIAM} 10039} 10040 10041@InProceedings{ prudencioschulz2011, 10042 title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for 10043 Estimation, Simulation and Optimization}, 10044 author = {Ernesto E Prudencio and Karl W Schulz}, 10045 booktitle = {European Conference on Parallel Processing}, 10046 pages = {398--407}, 10047 year = {2011} 10048} 10049 10050@Misc{ rol-website, 10051 key = {ROL}, 10052 title = {{Rapid Optimization Library} Website}, 10053 howpublished = {\url{https://trilinos.org/packages/rol}}, 10054 year = {2018} 10055} 10056 10057@Article{ more1994line, 10058 title = {Line search algorithms with guaranteed sufficient decrease}, 10059 author = {Mor{\'e}, Jorge J and Thuente, David J}, 10060 journal = {ACM Transactions on Mathematical Software}, 10061 volume = {20}, 10062 number = {3}, 10063 pages = {286--307}, 10064 year = {1994}, 10065 publisher = {ACM} 10066} 10067 10068@Article{ griewank2000algorithm, 10069 title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or 10070 adjoint mode of computational differentiation}, 10071 author = {Griewank, Andreas and Walther, Andrea}, 10072 journal = {ACM Transactions on Mathematical Software}, 10073 volume = {26}, 10074 number = {1}, 10075 pages = {19--45}, 10076 year = {2000}, 10077 publisher = {ACM} 10078} 10079 10080@Article{ metcalf2011seven, 10081 title = {The seven ages of fortran}, 10082 author = {Metcalf, Michael}, 10083 journal = {Journal of Computer Science \& Technology}, 10084 volume = {11}, 10085 year = {2011} 10086} 10087 10088@Article{ giraldo_2013, 10089 title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified 10090 model of the atmosphere {(NUMA)}}, 10091 author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu}, 10092 journal = {SIAM Journal on Scientific Computing}, 10093 year = {2013}, 10094 number = {5}, 10095 pages = {B1162-B1194}, 10096 volume = {35}, 10097 doi = {10.1137/120876034} 10098} 10099 10100@Article{ constantinescu_tr2016b, 10101 author = {Constantinescu, E.M.}, 10102 title = {Estimating Global Errors in Time Stepping}, 10103 journal = {ArXiv e-prints}, 10104 archiveprefix = {arXiv}, 10105 eprint = {1503.05166}, 10106 primaryclass = {math.NA}, 10107 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70}, 10108 year = {2016}, 10109 month = mar, 10110 adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C}, 10111 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 10112} 10113 10114@Article{ pareschi_2005, 10115 title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems 10116 with Relaxation}, 10117 author = {L. Pareschi and G. Russo}, 10118 journal = {Journal of Scientific Computing}, 10119 year = {2005}, 10120 number = {1}, 10121 pages = {129--155}, 10122 volume = {25} 10123} 10124 10125@Article{ kennedy_2003, 10126 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 10127 author = {C.A. Kennedy and M.H. Carpenter}, 10128 journal = {Appl. Numer. Math.}, 10129 year = {2003}, 10130 number = {1-2}, 10131 pages = {139--181}, 10132 volume = {44}, 10133 doi = {10.1016/S0168-9274(02)00138-1}, 10134 publisher = {Elsevier Science Publishers B. V.} 10135} 10136 10137@Unpublished{ boscarino_tr2011, 10138 title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic 10139 equations in the diffusion limit}, 10140 author = {Boscarino, S. and Pareschi, L. and Russo, G.}, 10141 note = {Arxiv preprint arXiv:1110.4375}, 10142 year = {2011} 10143} 10144 10145@Article{ ascher_1997, 10146 title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential 10147 equations}, 10148 author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri}, 10149 journal = {Applied Numerical Mathematics}, 10150 year = {1997}, 10151 pages = {151--167}, 10152 volume = {25} 10153} 10154 10155@Book{ ascherpetzold1998, 10156 title = {Computer methods for ordinary differential equations and differential-algebraic 10157 equations}, 10158 author = {Uri M Ascher and Linda R Petzold}, 10159 volume = {61}, 10160 publisher = {SIAM}, 10161 year = {1998} 10162} 10163 10164@Article{ colomesbadia2016, 10165 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 10166 equations}, 10167 author = {Oriol Colom{\'e}s and Santiago Badia}, 10168 journal = {International Journal for Numerical Methods in Engineering}, 10169 volume = {105}, 10170 number = {5}, 10171 pages = {372--400}, 10172 year = {2016} 10173} 10174 10175@Article{ sandu_1997, 10176 title = {Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: 10177 {R}osenbrock solvers}, 10178 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 10179 Potra}, 10180 journal = {Atmospheric Environment}, 10181 year = {1997}, 10182 number = {20}, 10183 pages = {3459--3472}, 10184 volume = {31}, 10185 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 10186 task is the integration of the stiff systems of ordinary differential equations 10187 describing the chemical transformations. It is therefore of interest to 10188 systematically search for stiff solvers which can be identified as close to 10189 optimal for atmospheric applications. In this paper we continue our investigation 10190 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 10191 and compare eight solvers on a set of seven box-models used in present day models. 10192 The focus is on Rosenbrock solvers. These turn out to be very well suited for our 10193 application when they are provided with highly efficient sparse matrix techniques 10194 to economize on the linear algebra. Two of the Rosenbrock solvers tested are from 10195 the literature, viz. and 4, and two are new and specially developed for air 10196 quality applications, viz. 3 and 3. } 10197} 10198 10199@Article{ rang_2005, 10200 title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic 10201 equations of index 1}, 10202 author = {Rang, J. and Angermann, L.}, 10203 journal = {BIT Numerical Mathematics}, 10204 year = {2005}, 10205 number = {4}, 10206 pages = {761--787}, 10207 volume = {45}, 10208 publisher = {Springer} 10209} 10210 10211@Article{ gottliebketchesonshu2009, 10212 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 10213 title = {{High order strong stability preserving time discretizations}}, 10214 journal = {Journal of Scientific Computing}, 10215 volume = {38}, 10216 number = {3}, 10217 pages = {251--289}, 10218 doi = {10.1007/s10915-008-9239-z}, 10219 year = {2009} 10220} 10221 10222@Article{ ketcheson_2008, 10223 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 10224 Low-Storage Implementations}, 10225 author = {D.I. Ketcheson}, 10226 journal = {SIAM Journal on Scientific Computing}, 10227 year = {2008}, 10228 number = {4}, 10229 pages = {2113--2136}, 10230 volume = {30}, 10231 doi = {10.1137/07070485X}, 10232 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 10233 RungeKutta methods}, 10234 publisher = {SIAM} 10235} 10236 10237@Article{ jansen_2000, 10238 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 10239 equations with a stabilized finite element method}, 10240 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 10241 journal = {Computer Methods in Applied Mechanics and Engineering}, 10242 year = {2000}, 10243 number = {3}, 10244 pages = {305--319}, 10245 volume = {190}, 10246 publisher = {Elsevier} 10247} 10248 10249@Article{ butcher_2007, 10250 title = {Error propagation of general linear methods for ordinary differential equations}, 10251 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 10252 journal = {Journal of Complexity}, 10253 year = {2007}, 10254 number = {4-6}, 10255 pages = {560--580}, 10256 volume = {23}, 10257 abstract = {We discuss error propagation for general linear methods for ordinary differential 10258 equations up to terms of order p+2, where p is the order of the method. These 10259 results are then applied to the estimation of local discretization errors for 10260 methods of order p and for the adjacent order p+1. The results of numerical 10261 experiments confirm the reliability of these estimates. This research has 10262 applications in the design of robust stepsize and order changing strategies for 10263 algorithms based on general linear methods.}, 10264 doi = {10.1016/j.jco.2007.01.009}, 10265 issn = {0885-064X} 10266} 10267 10268@Article{ constantinescu_a2010a, 10269 title = {Extrapolated implicit-explicit time stepping}, 10270 author = {E.M. Constantinescu and A. Sandu}, 10271 journal = {SIAM Journal on Scientific Computing}, 10272 year = {2010}, 10273 number = {6}, 10274 pages = {4452-4477}, 10275 volume = {31}, 10276 comment = {Preprint \# ANL/MCS-P1612-0409}, 10277 doi = {10.1137/080732833} 10278} 10279 10280@InProceedings{ devito2011liszt, 10281 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 10282 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 10283 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 10284 Aiken, Alex and Duraisamy, Karthik and others}, 10285 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 10286 Networking, Storage and Analysis}, 10287 pages = {9}, 10288 year = {2011}, 10289 organization = {ACM} 10290} 10291 10292@Article{ devito2011designing, 10293 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 10294 author = {DeVito, Zachary and Hanrahan, Pat}, 10295 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 10296 year = {2011} 10297} 10298 10299@Misc{ pgasintro, 10300 author = {Tim Stitt}, 10301 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 10302 Model}, 10303 note = {\url{http://cnx.org/content/m20649/latest/}} 10304} 10305 10306@InProceedings{ el2006upc, 10307 title = {UPC: unified parallel C}, 10308 author = {El-Ghazawi, Tarek and Smith, Lauren}, 10309 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 10310 pages = {27}, 10311 year = {2006}, 10312 organization = {ACM} 10313} 10314 10315@InProceedings{ numrich1998co, 10316 title = {Co-Array Fortran for parallel programming}, 10317 author = {Numrich, Robert W and Reid, John}, 10318 booktitle = {ACM Sigplan Fortran Forum}, 10319 volume = {17}, 10320 number = {2}, 10321 pages = {1--31}, 10322 year = {1998}, 10323 organization = {ACM} 10324} 10325 10326@Article{ aiken1997titanium, 10327 title = {Titanium: A high-performance Java dialect}, 10328 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 10329 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 10330 Geoff and Semenzato, Luigi and others}, 10331 year = {1997} 10332} 10333 10334@Article{ charles2005x10, 10335 title = {X10: an object-oriented approach to non-uniform cluster computing}, 10336 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 10337 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 10338 Sarkar, Vivek}, 10339 journal = {Acm Sigplan Notices}, 10340 volume = {40}, 10341 number = {10}, 10342 pages = {519--538}, 10343 year = {2005}, 10344 publisher = {ACM} 10345} 10346 10347@Article{ chamberlain2007parallel, 10348 title = {Parallel programmability and the chapel language}, 10349 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 10350 journal = {International Journal of High Performance Computing Applications}, 10351 volume = {21}, 10352 number = {3}, 10353 pages = {291--312}, 10354 year = {2007}, 10355 publisher = {SAGE Publications} 10356} 10357 10358@InProceedings{ charmppoopsla93, 10359 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 10360 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 10361 editor = {Paepcke, A.}, 10362 fulleditor = {Paepcke, Andreas}, 10363 pages = {91--108}, 10364 month = {September}, 10365 year = {1993}, 10366 booktitle = {{Proceedings of OOPSLA'93}}, 10367 publisher = {{ACM Press}} 10368} 10369 10370@InProceedings{ hewitt1973universal, 10371 title = {A universal modular actor formalism for artificial intelligence}, 10372 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 10373 booktitle = {Proceedings of the 3rd international joint conference on Artificial 10374 intelligence}, 10375 pages = {235--245}, 10376 year = {1973}, 10377 organization = {Morgan Kaufmann Publishers Inc.} 10378} 10379 10380@Book{ yonezawa1990abcl, 10381 title = {ABCL: an object-oriented concurrent system}, 10382 author = {Yonezawa, Akinori}, 10383 year = {1990}, 10384 publisher = {MIT press} 10385} 10386 10387@InProceedings{ dally1988object, 10388 title = {Object-oriented concurrent programming in CST}, 10389 author = {Dally, William J and Chien, Andrew A}, 10390 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 10391 applications: Architecture, software, computer systems, and general issues-Volume 10392 1}, 10393 pages = {434--439}, 10394 year = {1988}, 10395 organization = {ACM} 10396} 10397 10398@Article{ grimshaw1993easy, 10399 title = {Easy-to-use object-oriented parallel processing with Mentat}, 10400 author = {Grimshaw, Andrew S.}, 10401 journal = {Computer}, 10402 volume = {26}, 10403 number = {5}, 10404 pages = {39--51}, 10405 year = {1993}, 10406 publisher = {IEEE} 10407} 10408 10409@InProceedings{ gannon1991object, 10410 title = {Object oriented parallelism: pC++ ideas and experiments}, 10411 author = {Gannon, Dennis and Lee, JK}, 10412 booktitle = {Proceedings of}, 10413 pages = {13--23}, 10414 year = {1991} 10415} 10416 10417@InProceedings{ lau1992object, 10418 title = {An object-oriented class library for scalable parallel heuristic search}, 10419 author = {Lau, Wing-cheong and Singh, Vineet}, 10420 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 10421 pages = {252--267}, 10422 year = {1992}, 10423 organization = {Springer} 10424} 10425 10426@Book{ chase1989amber, 10427 title = {The Amber system: Parallel programming on a network of multiprocessors}, 10428 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 10429 Littlefield, Richard}, 10430 volume = {23}, 10431 number = {5}, 10432 year = {1989}, 10433 publisher = {ACM} 10434} 10435 10436@InProceedings{ kaiser2009parallex, 10437 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 10438 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 10439 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 10440 pages = {394--401}, 10441 year = {2009}, 10442 organization = {IEEE} 10443} 10444 10445@TechReport{ ipm, 10446 author = {Barry F. Smith}, 10447 title = {A New Parallel Programming Model for Computer Simulation}, 10448 institution = {Argonne National Laboratory}, 10449 year = {2014}, 10450 number = {ANL/MCS-P5135-0414} 10451} 10452 10453@Article{ groppsnir, 10454 author = {William Gropp and Marc Snir}, 10455 title = {Programming for Exascale Computers}, 10456 journal = {Computing in Science and Engineering}, 10457 volume = {15}, 10458 number = {6}, 10459 issn = {1521-9615}, 10460 year = {2013}, 10461 pages = {27-35}, 10462 doi = {10.1109/MCSE.2013.96}, 10463 publisher = {IEEE Computer Society}, 10464 address = {Los Alamitos, CA} 10465} 10466 10467@Book{ mpi3, 10468 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 10469 author = {Message Passing Interface Forum}, 10470 year = {2012}, 10471 publisher = {High Performance Computing Center Stuttgart (HLRS)} 10472} 10473 10474@Book{ openmp4, 10475 title = {OpenMP Application Program Interface, Version 4.0}, 10476 year = {2013}, 10477 publisher = {OpenMP Architecture Review Board} 10478} 10479 10480@InProceedings{ hartono2009annotation, 10481 title = {Annotation-based empirical performance tuning using {Orio}}, 10482 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 10483 booktitle = {Parallel \& Distributed Processing, 2009. 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Control. Fusion}, 10589 author = {Eero Hirvijoki}, 10590 note = {in press}, 10591 doi = {10.1088/1361-6587/abe884}, 10592 year = {2021} 10593} 10594 10595@Article{ ipsen2001, 10596 author = {Ilse C. F. Ipsen}, 10597 journal = {SIAM J. Sci. Comput.}, 10598 pages = {1050--1051}, 10599 volume = {23}, 10600 publisher = {SIAM}, 10601 title = {A Note on Preconditioning Nonsymmetric Matrices}, 10602 year = {2001} 10603} 10604 10605% Random papers on solvers for GPUs 10606@InProceedings{ gpus-suck, 10607 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. }, 10608 title = { On the Limits of {GPU} Acceleration}, 10609 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism}, 10610 year = {2010}, 10611 publisher = {USENIX} 10612} 10613 10614@InProceedings{ 882364, 10615 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter}, 10616 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid}, 10617 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers}, 10618 year = {2003}, 10619 isbn = {1-58113-709-5}, 10620 pages = {917--924}, 10621 location = {San Diego, California}, 10622 doi = {10.1145/1201775.882364}, 10623 publisher = {ACM}, 10624 address = {New York, NY} 10625} 10626 10627@Conference{ feng2008multigrid, 10628 author = {Feng, Z. and Li, P.}, 10629 booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008}, 10630 date-added = {2010-08-19 15:57:06 -0500}, 10631 date-modified = {2010-08-19 15:57:06 -0500}, 10632 pages = {647--654}, 10633 title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms}, 10634 year = {2008} 10635} 10636 10637@Conference{ goodnight2003multigrid, 10638 author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.}, 10639 booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware}, 10640 date-added = {2010-08-19 15:45:20 -0500}, 10641 date-modified = {2010-08-19 15:45:20 -0500}, 10642 organization = {Eurographics Association}, 10643 pages = {102--111}, 10644 title = {A multigrid solver for boundary value problems using programmable graphics 10645 hardware}, 10646 year = {2003} 10647} 10648 10649@Article{ buatois2007concurrent, 10650 author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.}, 10651 date-added = {2010-08-19 15:45:02 -0500}, 10652 date-modified = {2010-08-19 15:45:02 -0500}, 10653 journal = {High Performance Computing and Communications}, 10654 pages = {358--371}, 10655 publisher = {Citeseer}, 10656 title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}}, 10657 year = {2007} 10658} 10659 10660@Article{ joldes2010real, 10661 author = {Joldes, G.R. and Wittek, A. and Miller, K.}, 10662 date-added = {2010-08-19 15:44:41 -0500}, 10663 date-modified = {2010-08-19 15:44:41 -0500}, 10664 journal = {Computer Methods in Applied Mechanics and Engineering}, 10665 publisher = {Elsevier}, 10666 title = {Real-time nonlinear finite element computations on {GPU}-application to 10667 neurosurgical simulation}, 10668 year = {2010} 10669} 10670 10671@Misc{ aharon2005gpu, 10672 author = {Aharon, S.}, 10673 date-added = {2010-08-19 15:44:32 -0500}, 10674 date-modified = {2010-08-19 15:44:32 -0500}, 10675 month = apr # {~27}, 10676 note = {US Patent App. 11/115,642}, 10677 publisher = {Google Patents}, 10678 title = {{GPU}-based Finite Element}, 10679 year = {2005} 10680} 10681 10682@Article{ cevahir2009fast, 10683 author = {Cevahir, A. and Nukada, A. and Matsuoka, S.}, 10684 date-added = {2010-08-19 15:44:01 -0500}, 10685 date-modified = {2010-08-19 15:44:01 -0500}, 10686 journal = {Computational Science--ICCS 2009}, 10687 pages = {893--903}, 10688 publisher = {Springer}, 10689 title = {Fast conjugate gradients with multiple {GPU}s}, 10690 year = {2009} 10691} 10692 10693@Article{ maier1995symmetric, 10694 author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.}, 10695 date-added = {2010-08-19 15:43:57 -0500}, 10696 date-modified = {2010-08-19 15:43:57 -0500}, 10697 journal = {Computational Mechanics}, 10698 number = {1}, 10699 pages = {115--129}, 10700 publisher = {Springer}, 10701 title = {Symmetric {G}alerkin boundary element method in plasticity and gradient 10702 plasticity}, 10703 volume = {17}, 10704 year = {1995} 10705} 10706 10707@Article{ corrigan-running, 10708 author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.}, 10709 date-added = {2010-08-19 15:43:47 -0500}, 10710 date-modified = {2010-08-19 15:43:47 -0500}, 10711 journal = {International Journal for Numerical Methods in Fluids}, 10712 publisher = {John Wiley \& Sons}, 10713 title = {Running unstructured grid based CFD solvers on modern graphics hardware} 10714} 10715 10716@InProceedings{ volkov08, 10717 author = {Vasily Volkov and James W. 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Markus}, 11675 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 11676 for {PDE} Based Applications}, 11677 year = {1994}, 11678 institution = {Department of Computer Sciences, Purdue University}, 11679 number = {CSD-TR-94-021} 11680} 11681 11682@Unpublished{ ilu-web-page, 11683 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 11684 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 11685 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 11686} 11687 11688@Unpublished{ doe2k-web-page, 11689 title = {{DOE2000 Initiative} {W}eb page}, 11690 note = {http://www.mcs.anl.gov/DOE2000}, 11691 key = {DOE2000 Initiative} 11692} 11693 11694@Misc{ pvode-web-page, 11695 title = {{PVODE} {W}eb Page}, 11696 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 11697 author = {A. {Hindmarsh et al.}} 11698} 11699 11700@Book{ szyperski97, 11701 author = {Clemens Szyperski}, 11702 title = {Component Software: Beyond Object-Oriented Programming}, 11703 publisher = {ACM Press}, 11704 address = {New York}, 11705 year = {1997} 11706} 11707 11708@Unpublished{ petsc:coloringuse, 11709 title = {Code for computing sparse {J}acobians}, 11710 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11711 institution = {Argonne National Laboratory} 11712} 11713 11714@Unpublished{ petsc:external, 11715 author = {B. F. {Smith et al.}}, 11716 title = {{External Software Used by PETSc}}, 11717 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 11718 institution = {Argonne National Laboratory} 11719} 11720 11721@Unpublished{ petsc:use-by-external-packages, 11722 author = {B. F. {Smith et al.}}, 11723 title = {{Software Packages that Use or Interface to PETSc}}, 11724 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 11725 institution = {Argonne National Laboratory} 11726} 11727 11728@Unpublished{ petsc:prizes, 11729 author = {B. F. {Smith et al.}}, 11730 title = {{Prizes Won Using PETSc}}, 11731 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 11732 institution = {Argonne National Laboratory} 11733} 11734 11735@Unpublished{ petsc:csgf, 11736 author = {B. F. {Smith et al.}}, 11737 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 11738 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 11739 institution = {Argonne National Laboratory} 11740} 11741 11742@Unpublished{ flash-web-page, 11743 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 11744 {W}eb Page}, 11745 note = {http://www.asci.uchicago.edu}, 11746 author = {R. {Rosner et al.}}, 11747 institution = {University of Chicago} 11748} 11749 11750@Unpublished{ esi-web-page, 11751 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 11752 note = {http://z.ca.sandia.gov/esi}, 11753 author = {R. {Clay et al.}} 11754} 11755 11756@Unpublished{ infobus-web-page, 11757 title = {{I}nfo{B}us {W}eb Page}, 11758 note = {http://www.java.sun.com/beans/infobus}, 11759 key = {infobus} 11760} 11761 11762@Unpublished{ xray-web-page, 11763 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 11764 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 11765 note = {http://www.mcs.anl.gov/xray/}, 11766 institution = {Argonne National Laboratory} 11767} 11768 11769@InProceedings{ kohn98, 11770 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 11771 title = {Language Interoperability Mechanisms for High-Performance Scientific 11772 Applications}, 11773 publisher = {SIAM}, 11774 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 11775 Scientific and Engineering Computing}, 11776 year = {1999}, 11777 pages = {30-39} 11778} 11779 11780@InProceedings{ kohn01, 11781 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 11782 title = {Divorcing Language Dependencies from a Scientific Software Library}, 11783 publisher = {SIAM}, 11784 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 11785 year = {2001} 11786} 11787 11788@InProceedings{ freitag_jones_plassmann98, 11789 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 11790 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 11791 publisher = {SIAM}, 11792 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 11793 Scientific and Engineering Computing}, 11794 year = {1999}, 11795 pages = {215-224} 11796} 11797 11798@Book{ templates, 11799 author = {R. 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Browne}, 11819 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 11820 Techniques}, 11821 institution = {Department of Computer Science, University of Texas at Austin}, 11822 year = {1995} 11823} 11824 11825@Article{ parti, 11826 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 11827 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 11828 Memory Architectures}, 11829 journal = {Journal of Parallel and Distributed Computing}, 11830 year = {1994}, 11831 volume = {22}, 11832 pages = {462--478} 11833} 11834 11835@Article{ mparti, 11836 author = {G. Agrawal and A. Sussman and J. Saltz}, 11837 title = {An Integrated Runtime and Compile-time Approach for Parallelizing Structured and 11838 Block Structured Applications}, 11839 journal = {IEEE Trans. on Parallel and Distributed Systems}, 11840 volume = {6}, 11841 number = {7}, 11842 year = {1995} 11843} 11844 11845@Article{ gropp-lusk-doss-skjellum, 11846 author = { William Gropp and Ewing Lusk and Nathan Doss and Anthony Skjellum}, 11847 title = {A high-performance, portable implementation of the {MPI} Message Passing 11848 Interface standard}, 11849 journal = {Parallel Computing}, 11850 year = {1996}, 11851 volume = {22}, 11852 pages = {789--828} 11853} 11854 11855@InProceedings{ lam, 11856 author = {Greg Burns and Raja Daoud and James Vaigl}, 11857 title = {{LAM}: An Open Cluster Environment for {MPI}}, 11858 booktitle = {Proceedings of Supercomputing Symposium '94}, 11859 editor = {John W. Ross}, 11860 publisher = {University of Toronto}, 11861 pages = {379--386}, 11862 year = {1994} 11863} 11864 11865@Article{ cs99, 11866 author = {X.-C. Cai and M. Sarkis}, 11867 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 11868 systems}, 11869 journal = {SIAM J. Scientific Computing}, 11870 year = {1999}, 11871 volume = {21}, 11872 pages = {792-797} 11873} 11874 11875@TechReport{ cs97a, 11876 author = {X.-C. Cai and M. Sarkis}, 11877 title = {A restricted additive {S}chwarz preconditioner for general sparse linear systems 11878 }, 11879 year = {1997}, 11880 institution = {Computer Science Department, University of Colorado-Boulder}, 11881 number = {CU-CS 843-97}, 11882 note = {(accepted by SIAM J. of Scientific Computing)} 11883} 11884 11885@Article{ cai2003restricted, 11886 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 11887 positive definite linear systems}, 11888 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 11889 journal = {SIAM Journal on Numerical Analysis}, 11890 volume = {41}, 11891 issue = {1}, 11892 pages = {1209--1231}, 11893 year = {2003}, 11894 doi = {10.1137/S0036142901389621} 11895} 11896 11897@TechReport{ caisaad, 11898 author = {Xiao-Chuan Cai and Youcef Saad}, 11899 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 11900 institution = {Army High Performance Computing Research Center, University of Minnesota }, 11901 year = {1993}, 11902 number = {Preprint 93-027 }, 11903 note = {SIAM J. Sci. Comp. (submitted)} 11904} 11905 11906@Book{ ruminations, 11907 author = {Andrew Koenig and Barbara Moo}, 11908 title = {Ruminations on C++}, 11909 year = {1996}, 11910 publisher = {Addison-Wesley} 11911} 11912 11913@Book{ mpi-complete, 11914 author = {Marc Snir and Steve Otto and Steven Huss-Lederman and David Walker and Jack 11915 Dongarra}, 11916 title = {{MPI}: The Complete Reference}, 11917 year = {1995}, 11918 publisher = {MIT Press} 11919} 11920 11921@Unpublished{ tcl-tk-web-page, 11922 title = {{Tcl/Tk} {W}orld {W}ide {W}eb page}, 11923 note = {http://www.sunlabs.com/research/tcl/}, 11924 year = {1996}, 11925 month = aug 11926} 11927 11928@Misc{ mpich-web-page, 11929 author = {William Gropp and {et. al.}}, 11930 title = {{MPICH} {W}eb page}, 11931 key = {MPICH}, 11932 url = {http://www.mpich.org}, 11933 howpublished = {\url{http://www.mpich.org}} 11934} 11935 11936@Article{ mpi-final, 11937 author = {MPI Forum}, 11938 title = {{MPI}: A Message-Passing Interface Standard}, 11939 journal = {International J. Supercomputing Applications}, 11940 volume = {8}, 11941 number = {3/4}, 11942 year = {1994}, 11943 key = {MPI Standard - final} 11944} 11945 11946@Unpublished{ npb-web-page, 11947 key = {NAS Parallel Benchmarks}, 11948 title = {{NAS} {P}arallel {B}enchmarks {W}eb page}, 11949 note = {http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html}, 11950 year = {1996}, 11951 month = dec 11952} 11953 11954@Book{ george81, 11955 title = {Computer Solution of Large Sparse Positive Definite Systems}, 11956 author = {Alan George and Joseph W. Liu}, 11957 publisher = {Prentice-Hall}, 11958 year = {1981}, 11959 key = {SparseDirect} 11960} 11961 11962@Book{ p4-book, 11963 title = {Portable Programs for Parallel Processors}, 11964 publisher = {Holt, Rinehart, {and} Winston}, 11965 year = {1987}, 11966 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 11967 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 11968 key = {P4Book} 11969} 11970 11971@Article{ stones, 11972 author = {H. L. Stone}, 11973 title = {Iterative solution of implicit approximations of multidimensional partial 11974 differential equations}, 11975 journal = {SIAM J. Numerical Analysis}, 11976 pages = {87--113}, 11977 volumne = {5}, 11978 year = {1968} 11979} 11980 11981@Article{ parallelstones, 11982 author = {J. S. Reeve and A. D. Scurr and J. H. Merlin}, 11983 title = {Parallel versions of {S}tones strongly implicit algorithm}, 11984 journal = {Concurrency and Computation: Practice and Experience}, 11985 pages = {1049--1062}, 11986 volumne = {13}, 11987 year = {2001} 11988} 11989 11990@Article{ p4-paper, 11991 author = {Ralph Butler and Ewing Lusk}, 11992 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 11993 journal = {Journal of Parallel Computing}, 11994 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 11995 Division preprint P362-0493)}, 11996 year = {1993} 11997} 11998 11999@TechReport{ picl, 12000 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 12001 title = {{PICL}: A portable instrumented communications library}, 12002 institution = {Oak Ridge National Laboratory}, 12003 number = {TM-11130}, 12004 year = {1990}, 12005 key = {PICL} 12006} 12007 12008@TechReport{ upshot, 12009 author = {Virginia Herrarte and Ewing Lusk}, 12010 title = {Studying Parallel Program Behavior with {U}pshot}, 12011 institution = {Argonne National Laboratory}, 12012 number = {ANL-91/15}, 12013 month = aug, 12014 year = {1991}, 12015 key = {Upshot} 12016} 12017 12018@TechReport{ p4-manual, 12019 author = {Ralph Butler and Ewing Lusk}, 12020 title = {User's Guide to the p4 Parallel Programming System}, 12021 institution = {Argonne National Laboratory}, 12022 number = {ANL-92/17}, 12023 month = oct, 12024 year = {1992}, 12025 key = {p4-Manual} 12026} 12027 12028@InProceedings{ oldparti, 12029 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 12030 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 12031 booktitle = {Proceedings of Supercomputing '93}, 12032 pages = {578--587}, 12033 year = {1993} 12034} 12035 12036@Article{ parti2, 12037 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 12038 and J. Saltz}, 12039 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 12040 journal = {ACM SIGPLAN Notices}, 12041 year = {1995}, 12042 pages = {68-79}, 12043 volume = {30}, 12044 number = {8} 12045} 12046 12047@Article{ parti3, 12048 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 12049 title = {Run-Time Parallelization and Scheduling of Loops}, 12050 journal = {IEEE Trans. Computers}, 12051 year = {1991}, 12052 pages = {604-612}, 12053 volume = {40}, 12054 number = {5} 12055} 12056 12057@InProceedings{ disz-lusk:wamtrace, 12058 author = {Terrence Disz and Ewing Lusk}, 12059 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 12060 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12061 year = {1987}, 12062 pages = {46--53} 12063} 12064 12065@InProceedings{ gorlick-kesselman:gauge, 12066 author = {Michael Gorlick and Carl Kesselman}, 12067 title = {Timing {Prolog} programs without Clocks}, 12068 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 12069 year = {1996}, 12070 publisher = {Birkhauser} 12071} 12072 12073@TechReport{ aztec, 12074 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 12075 title = {Aztec User's Guide Version 1.1}, 12076 institution = {Sandia National Laboratories}, 12077 month = oct, 12078 year = {1995}, 12079 number = {SAND95/1559} 12080} 12081 12082@TechReport{ aztec2, 12083 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 12084 title = {Official {Aztec} User's Guide Version 2.1}, 12085 institution = {Sandia National Laboratories}, 12086 year = {1999} 12087} 12088 12089@Book{ taylor-chandy:pcn, 12090 author = {Chandy, M. and Taylor, S.}, 12091 title = {An Introduction to Parallel Programming}, 12092 year = {1991}, 12093 publisher = {Jones and Bartlett} 12094} 12095 12096@Book{ foster-taylor:strand, 12097 title = {Strand: New Concepts in Parallel Programming}, 12098 author = {Ian Foster and Stephen Taylor}, 12099 publisher = {Prentice-Hall}, 12100 adress = { Englewood Cliffs, New Jersey}, 12101 year = {1990} 12102} 12103 12104@Article{ aurora, 12105 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 12106 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 12107 Carlsson and A. Ciepielewski and B. Hausman}, 12108 title = {The Aurora OR-Parallel Prolog System}, 12109 journal = {New Generation Computing}, 12110 volume = {7}, 12111 number = {3}, 12112 year = {1990}, 12113 pages = {243--271} 12114} 12115 12116@TechReport{ roo, 12117 author = {E. Lusk and W. McCune and J. Slaney}, 12118 title = {Roo---a Parallel Theorem Prover}, 12119 institution = {Argonne National Laboratory}, 12120 number = {MCS--TM--149}, 12121 year = {1991} 12122} 12123 12124@TechReport{ heath-etheridge:vppp, 12125 author = {M. T. Heath and J. A. Etheridge}, 12126 title = {Visualizing the Performance of Parallel Programs}, 12127 institution = {Oak Ridge National Laboratory}, 12128 number = {ORNL TM-11813}, 12129 year = {1991} 12130} 12131 12132@TechReport{ chem:vis, 12133 author = {Ewing L. Lusk}, 12134 title = {Performance Visualization for Parallel Programs}, 12135 institution = {Argonne National Laboratory}, 12136 number = {ANL/MCS--P287--0192}, 12137 year = {1991}, 12138 note = {(to appear in {\em Theoretica Chimica Acta})} 12139} 12140 12141@TechReport{ picltrace, 12142 author = {P.~H.~Worley}, 12143 title = {A new {PICL} trace file format}, 12144 institution = {Oak Ridge National Laboratory}, 12145 number = {ORNL TM-12125}, 12146 month = jun, 12147 year = {1992} 12148} 12149 12150@InProceedings{ hideo, 12151 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 12152 title = {Inference of Phylogenetic trees using maximum likelihood}, 12153 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 12154 year = {1992}, 12155 pages = {247--262} 12156} 12157 12158@InProceedings{ dw90, 12159 author = {M. Dryja and O. Widlund}, 12160 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 12161 Problems}, 12162 booktitle = {Third International Symposium on Domain Decomposition Methods}, 12163 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 12164 year = {1990}, 12165 pages = {3-21}, 12166 publisher = {SIAM}, 12167 address = {Philadelphia}, 12168 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 12169 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 12170 references, good introduction to the theory. No computations}, 12171 key = {DryjaWidlund90 !AS} 12172} 12173 12174@Unpublished{ rosing, 12175 author = {Matt Rosing and Joel Saltz}, 12176 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 12177 key = {LowLatency}, 12178 note = {manuscript, 1992} 12179} 12180 12181@TechReport{ jp:incomplete, 12182 author = {Mark T. Jones and Paul E. Plassmann}, 12183 title = {An Improved Incomplete {C}holesky Factorization}, 12184 institution = {Argonne National Laboratory}, 12185 address = {Argonne, IL}, 12186 type = {Preprint}, 12187 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 12188 number = {MCS-P206-0191}, 12189 year = {1991}, 12190 key = {jones} 12191} 12192 12193@InCollection{ jp:ima, 12194 author = {Mark Jones and Paul Plassmann}, 12195 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 12196 booktitle = {Graph Theory and Sparse Matrix Computation}, 12197 publisher = {Springer-Verlag}, 12198 series = {The IMA Volumes in Mathematics and Its Applications}, 12199 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 12200 volume = {56}, 12201 year = {1993}, 12202 pages = {229--245} 12203} 12204 12205@Article{ pw98, 12206 author = {M. Pernice and H. F. Walker}, 12207 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 12208 journal = {SIAM J. Sci. Stat. Comput.}, 12209 year = {1998}, 12210 volume = {19}, 12211 pages = {302--318} 12212} 12213 12214@TechReport{ ysmp83, 12215 key = {Eisenstat}, 12216 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12217 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12218 institution = {Department of Computer Science, Yale University}, 12219 number = {YALE/DCS/RR-265}, 12220 month = apr, 12221 year = {1983} 12222} 12223 12224@InBook{ ysmp84, 12225 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 12226 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 12227 title = {Elliptic Problem Solvers II}, 12228 publisher = {Academic Press}, 12229 pages = {45--52}, 12230 editors = {G. Birkhoff and A. Schoenstadt}, 12231 year = {1984} 12232} 12233 12234@TechReport{ sparsekit, 12235 key = {Saad}, 12236 author = {Youcef Saad}, 12237 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 12238 institution = {Center for Supercomputing Research and Development, University of Illinois at 12239 Urbana-Champaign}, 12240 number = {1029}, 12241 year = {1990} 12242} 12243 12244@TechReport{ pde-user-ref, 12245 author = {Barry F. Smith}, 12246 title = {Extensible {PDE} Solvers Package Users Manual}, 12247 institution = {Argonne National Laboratory}, 12248 month = sep, 12249 year = {1994}, 12250 number = {ANL-93/40}, 12251 key = {Smith94 ! PDE} 12252} 12253 12254@TechReport{ bs-user-ref, 12255 author = {Mark T. Jones and Paul E. Plassmann}, 12256 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 12257 of Sparse Linear Systems}, 12258 institution = {Argonne National Laboratory}, 12259 month = dec, 12260 year = {1995}, 12261 number = {ANL-95/48} 12262} 12263 12264@TechReport{ snes-user-ref, 12265 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 12266 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 12267 institution = {Argonne National Laboratory}, 12268 month = feb, 12269 year = {1995}, 12270 number = {ANL/MCS-TM-193}, 12271 key = {GroppMcInnesSmith95 ! SNES} 12272} 12273 12274@TechReport{ sles-user-ref, 12275 author = {William D. Gropp and Barry F. Smith}, 12276 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 12277 institution = {Argonne National Laboratory}, 12278 month = mar, 12279 year = {1993}, 12280 number = {ANL-93/8}, 12281 key = {GroppSmith93 ! SLES} 12282} 12283 12284@TechReport{ chameleon-user-ref, 12285 author = {William D. Gropp and Barry F. Smith}, 12286 title = {Chameleon Parallel programming tools Users Manual}, 12287 institution = {Argonne National Laboratory}, 12288 month = mar, 12289 year = {1993}, 12290 number = {ANL-93/23}, 12291 key = {GroppSmith93 ! Chameleon} 12292} 12293 12294@Article{ euclid2, 12295 author = {D. Hysom and A. Pothen}, 12296 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 12297 journal = {SIAM J. Sci. Comput.}, 12298 volume = {22}, 12299 number = {6}, 12300 pages = {2194--2215} 12301} 12302 12303@TechReport{ euclid1, 12304 author = {D. Hysom and A. Pothen}, 12305 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 12306 Solution of Sparse Linear Systems)}, 12307 institution = {Old Dominion University}, 12308 year = {2001} 12309} 12310 12311@TechReport{ ksp-user-ref, 12312 author = {William D. Gropp and Barry F. Smith}, 12313 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 12314 Methods}, 12315 institution = {Argonne National Laboratory}, 12316 month = aug, 12317 year = {1993}, 12318 number = {ANL-93/30}, 12319 key = {GroppSmith93 ! KSP} 12320} 12321 12322@TechReport{ mpi-chameleon, 12323 author = {William D. Gropp and Ewing Lusk}, 12324 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 12325 institution = {Argonne National Laboratory}, 12326 month = dec, 12327 year = {1992}, 12328 number = {ANL-92/47}, 12329 key = {GroppLusk92 ! MPI} 12330} 12331 12332@TechReport{ blockcomm-fortran, 12333 author = {William D. Gropp}, 12334 title = {Block{C}omm for {F}ortran}, 12335 institution = {Argonne National Laboratory}, 12336 month = may, 12337 year = {1993}, 12338 number = {ANL-93/00 (to appear)}, 12339 key = {Gropp93 ! BlockComm} 12340} 12341 12342@TechReport{ autodocument, 12343 author = {William D. Gropp}, 12344 title = {Automatic documentation of {C} programs}, 12345 institution = {Argonne National Laboratory}, 12346 month = may, 12347 year = {1993}, 12348 number = {ANL-93/00}, 12349 key = {Gropp93 ! Autodoc} 12350} 12351 12352@TechReport{ zipcode, 12353 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 12354 Manfred Morari}, 12355 title = {The {Z}ipcode message-passing system}, 12356 institution = {Lawrence Livermore National Laboratory}, 12357 month = sep, 12358 year = {1992}, 12359 number = {Unpublished}, 12360 key = {Skjellum92 ! Zipcode} 12361} 12362 12363@Article{ paragraph, 12364 author = {Michael T. Heath and Jennifer Etheridge Finger}, 12365 title = {Visualizing performance of parallel programs}, 12366 journal = {IEEE Software}, 12367 volume = {8}, 12368 number = {5}, 12369 month = sep, 12370 year = {1991}, 12371 pages = {29--39}, 12372 key = {Heath91 ! Paragraph} 12373} 12374 12375@Article{ gropp90, 12376 author = {William Gropp and Edward Smith}, 12377 title = {Computational Fluid Dynamics on Parallel Processors}, 12378 journal = {Computers and Fluids}, 12379 volume = {18}, 12380 year = {1990}, 12381 pages = {289--304}, 12382 key = {Gropp90 ! performance} 12383} 12384 12385@Article{ foster92, 12386 author = {Ian Foster and William Gropp and Rick Stevens}, 12387 title = {The parallel scalability of the spectral transform method}, 12388 journal = {Monthly Weather Review}, 12389 volume = {120}, 12390 year = {1992}, 12391 pages = {835--850}, 12392 key = {Foster92 ! performance} 12393} 12394 12395@InBook{ fgn, 12396 author = {R. Freund and G. H. Golub and N. Nachtigal}, 12397 title = {Iterative Solution of Linear Systems}, 12398 series = {Acta Numerica}, 12399 year = {1992}, 12400 publisher = {Cambridge University Press}, 12401 pages = {57--100} 12402} 12403 12404@TechReport{ nachtigal90, 12405 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 12406 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12407 institution = {Massachusetts Institute of Technology}, 12408 month = mar, 12409 year = {1990}, 12410 number = {90-2}, 12411 key = {Nachtigal | Krylov} 12412} 12413 12414@Article{ nachtigal1992fnm, 12415 title = {How Fast are Nonsymmetric Matrix Iterations?}, 12416 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 12417 journal = {SIAM Journal on Matrix Analysis and Applications}, 12418 volume = {13}, 12419 pages = {778}, 12420 year = {1992}, 12421 publisher = {SIAM} 12422} 12423 12424@TechReport{ embree1999descriptive, 12425 title = {How descriptive are {GMRES} convergence bounds}, 12426 author = {Embree, M.}, 12427 year = {1999}, 12428 number = {08}, 12429 institution = {Oxford University Computing Laboratory} 12430} 12431 12432@Article{ vorst92, 12433 author = {H. van der Vorst}, 12434 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 12435 of nonsymmetric linear systems}, 12436 journal = {SIAM J. Sci. Stat. Comput.}, 12437 year = {1992}, 12438 volume = {13}, 12439 pages = {631--644} 12440} 12441 12442@Article{ eisenstat81, 12443 author = {S. Eisenstat}, 12444 title = {Efficient Implementation of a Class of {CG} Methods}, 12445 journal = {SIAM J. Sci. Stat. Comput.}, 12446 year = {1981}, 12447 volume = {2}, 12448 pages = {1--4} 12449} 12450 12451@Manual{ ibm-essl, 12452 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 12453 Reference}, 12454 organization = {IBM}, 12455 year = {1992}, 12456 key = {IBM-ESSL} 12457} 12458 12459@Manual{ ibm-eui, 12460 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 12461 Release 2.0}, 12462 organization = {IBM}, 12463 month = jun, 12464 year = {1994}, 12465 key = {IBM-EUI} 12466} 12467 12468@Manual{ ibm-euih, 12469 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 12470 organization = {IBM}, 12471 author = {Peter Hochschild}, 12472 year = {1993}, 12473 key = {IBM-EUIH} 12474} 12475 12476@TechReport{ mpi, 12477 title = {Document for a Standard Message-Passing Interface}, 12478 author = {Message Passing Interface Forum}, 12479 institution = {University of Tennessee}, 12480 number = {CS-93-214}, 12481 month = nov, 12482 year = {1993}, 12483 key = {MPI Standard} 12484} 12485 12486@Unpublished{ mpi-final-web, 12487 author = {Message Passing Interface Forum}, 12488 title = {{MPI}: A Message-Passing Interface Standard}, 12489 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 12490 year = {1994}, 12491 month = may 12492} 12493 12494@Book{ hockney-jesshope, 12495 author = {R. W. Hockney and C. R. Jesshope}, 12496 title = {Parallel Computers 2}, 12497 publisher = {Adam Hilger}, 12498 year = {1988} 12499} 12500 12501@Book{ cm-fortran, 12502 author = {{Thinking Machines Corporation}}, 12503 title = {Users Manual for CM-Fortran}, 12504 publisher = {Thinking Machines Corporation}, 12505 year = {1993} 12506} 12507 12508@TechReport{ chang93, 12509 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 12510 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 12511 institution = {Yale Department of Computer Science}, 12512 number = {YALEU/DCS/RR-994}, 12513 month = nov, 12514 year = {1993}, 12515 key = {BDD|diag} 12516} 12517 12518@InProceedings{ gropplevine93, 12519 author = {N. Galbreath and W. Gropp and D. Levine}, 12520 title = {Applications-Driven Parallel {I/O}}, 12521 booktitle = {Proceedings of Supercomputing '93}, 12522 year = {1993}, 12523 pages = {462--471} 12524} 12525 12526@Book{ siegle85, 12527 author = {H. J. Siegel}, 12528 title = {Interconnection Networks for Large Scale Parallel Processing}, 12529 publisher = {Lexington Books}, 12530 year = {1985}, 12531 key = {Network Comparison} 12532} 12533 12534@Article{ lawrie75, 12535 author = {D. H. Lawrie}, 12536 title = {Access and alignment of data in an array processor}, 12537 journal = {IEEE Transactions on Computers}, 12538 volume = {C-24}, 12539 number = {12}, 12540 month = dec, 12541 year = {1975}, 12542 pages = {1145--1155}, 12543 key = {Omega Network} 12544} 12545 12546@Book{ knuth1986, 12547 title = {The {\TeX}{Book}}, 12548 author = {Donald Ervin Knuth and Duane Bibby}, 12549 volume = {1993}, 12550 year = {1986}, 12551 publisher = {Addison-Wesley Reading, Massachusetts} 12552} 12553 12554@Book{ lamport86, 12555 author = {Leslie Lamport}, 12556 title = {{LaTeX}: A document preparation system}, 12557 publisher = {Addison-Wesley}, 12558 year = {1986}, 12559 key = {Latex Manual} 12560} 12561 12562@InProceedings{ gropp-lusk:unix-tools, 12563 author = {William Gropp and Ewing Lusk}, 12564 title = {Scalable {U}nix Tools on Parallel Processors}, 12565 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 12566 publisher = {IEEE}, 12567 pages = {56--62} 12568} 12569 12570@InProceedings{ jp:bell_prize, 12571 author = {Mark Jones and Paul Plassmann}, 12572 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 12573 Applications}, 12574 booktitle = {Proceedings of Supercomputing '92}, 12575 publisher = {IEEE Computer Society Press}, 12576 year = {1992}, 12577 pages = {551--560} 12578} 12579 12580@COMMENT{WEB, CWEB references (for doctext)} 12581@TechReport{ web, 12582 author = {Donald E. Knuth}, 12583 title = {The {\tt WEB} system of structured documentation}, 12584 institution = {Computer Science Department, Stanford University}, 12585 year = {1983}, 12586 number = {980}, 12587 month = sep 12588} 12589 12590@Article{ literatepgm, 12591 author = {Donald E. Knuth}, 12592 title = {Literate Programming}, 12593 journal = {Computer Journal}, 12594 year = {1984}, 12595 volume = {27}, 12596 number = {2}, 12597 pages = {91--111} 12598} 12599 12600@Unpublished{ cweb-code, 12601 author = {Silvio Levy and Donald E. Knuth}, 12602 title = {CWEB}, 12603 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 12604} 12605 12606@Article{ jp:scalable, 12607 author = {Mark Jones and Paul Plassmann}, 12608 title = {Scalable Iterative Solution of Sparse Linear Systems}, 12609 journal = {Parallel Computing}, 12610 volume = {20}, 12611 number = {5}, 12612 month = {May}, 12613 year = {1994}, 12614 pages = {753--773} 12615} 12616 12617@Article{ jp:pcolor, 12618 author = {Mark T. Jones and Paul E. Plassmann}, 12619 title = {A Parallel Graph Coloring Heuristic}, 12620 journal = {SIAM J. Sci. Comput.}, 12621 volume = {14}, 12622 number = {3}, 12623 pages = {654-669}, 12624 year = {1993} 12625} 12626 12627@TechReport{ block_solve, 12628 author = {Mark T. Jones and Paul E. Plassmann}, 12629 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 12630 Sparse Linear Systems}, 12631 institution = {Argonne National Laboratory}, 12632 year = {1992}, 12633 number = {ANL-92/46}, 12634 key = {JonesPlassmann92 ! block_solve} 12635} 12636 12637@InProceedings{ supercond, 12638 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 12639 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 12640 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 12641 Conference}, 12642 month = feb, 12643 year = {1994}, 12644 key = {McInnesPalumbo94 ! superconductivity } 12645} 12646 12647@Unpublished{ preosti:93, 12648 author = {Gianfranco Preosti}, 12649 title = { }, 12650 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 12651 year = {1993}, 12652 key = {preosti93 ! GL-tilt3d} 12653} 12654 12655@Unpublished{ more:93, 12656 author = {Jorge J. Mor\'{e}}, 12657 title = { }, 12658 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 12659 {A}rgonne {N}ational {L}aboratory}, 12660 year = {1993}, 12661 key = {more93 ! MINPACK-2} 12662} 12663 12664@Article{ brownsaad:90, 12665 author = {Peter N. Brown and Youcef Saad}, 12666 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 12667 journal = {SIAM J. Sci. Stat. Comput.}, 12668 year = {1990}, 12669 volume = {11}, 12670 pages = {450-481} 12671} 12672 12673@Book{ using-mpi, 12674 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 12675 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 12676 publisher = {MIT Press}, 12677 year = {1994} 12678} 12679 12680@Book{ using-mpi2, 12681 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 12682 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 12683 publisher = {MIT Press}, 12684 year = {1999} 12685} 12686 12687@Article{ hs:52, 12688 author = {Magnus R. Hestenes and Eduard Steifel}, 12689 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 12690 journal = {J. Research of the National Bureau of Standards}, 12691 year = {1952}, 12692 volume = {49}, 12693 pages = {409-436} 12694} 12695 12696@Article{ ss:86, 12697 author = {Youcef Saad and Martin H. Schultz}, 12698 title = {{GMRES}: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear 12699 Systems}, 12700 journal = {SIAM J. Sci. Stat. Comput.}, 12701 year = {1986}, 12702 volume = {7}, 12703 pages = {856-869} 12704} 12705 12706@Article{ so:89, 12707 author = {Peter Sonneveld}, 12708 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 12709 journal = {SIAM J. Sci. Stat. Comput.}, 12710 year = {1989}, 12711 volume = {10}, 12712 pages = {36-52} 12713} 12714 12715@Article{ v:92, 12716 author = {{H. A.} {van der Vorst}}, 12717 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 12718 of nonsymmetric linear systems}, 12719 journal = {SIAM J. Sci. Stat. Comput.}, 12720 volume = {13}, 12721 year = {1992}, 12722 pages = {631-644} 12723} 12724 12725@Article{ f:93, 12726 author = {Roland W. Freund}, 12727 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 12728 Systems}, 12729 journal = {SIAM J. Sci. Stat. Comput.}, 12730 volume = {14}, 12731 year = {1993}, 12732 pages = {470-482} 12733} 12734 12735@Article{ ish:89, 12736 author = {S. Ishizuka}, 12737 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 12738 journal = {Combustion and Flame}, 12739 volume = {75}, 12740 year = {1989}, 12741 pages = {367-379} 12742} 12743 12744@Book{ williams89, 12745 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 12746 author = {F.A. Williams}, 12747 publisher = {Addison-Wesley}, 12748 year = {1989}, 12749 pages = {367-379} 12750} 12751 12752@Book{ ra75, 12753 author = {R. Aris}, 12754 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 12755 publisher = {Oxford}, 12756 year = {1975} 12757} 12758 12759@Book{ bebernes89, 12760 author = {J. Bebernes and D. Eberly}, 12761 title = {Mathematical Problems from Combustion Theory}, 12762 publisher = {Springer-Verlag}, 12763 series = {Applied Mathematical Sciences 83}, 12764 year = {1989} 12765} 12766 12767@InProceedings{ kikuchi89, 12768 author = {F. Kikuchi}, 12769 booktitle = { Computing Methods in Applied Sciences and Engineering}, 12770 editor = {R. Glowinski and J. L. Lions}, 12771 publisher = {Springer-Verlag}, 12772 series = {Lecture Notes in Mathematics}, 12773 title = {Finite element approximations to bifurcation problems of turning point type}, 12774 year = {1977} 12775} 12776 12777@Article{ rg85, 12778 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 12779 title = {Continuation-conjugate Gradient Methods fo the Least Squares Solution of 12780 Nonlinear Boundary Problems}, 12781 journal = {SIAM J. Sci. Stat. Comput.}, 12782 volume = {6}, 12783 year = {1985}, 12784 pages = {793-832} 12785} 12786 12787@InProceedings{ whitfield91, 12788 author = {D. Whitfield and L. Taylor}, 12789 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12790 Schemes}, 12791 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 12792 misc = {AIAA-91-1539}, 12793 pages = {134-145}, 12794 year = {1991} 12795} 12796 12797@InProceedings{ quinlan1, 12798 author = {M. Lemke and D. Quinlan}, 12799 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 12800 Architecture-Independent Development of Structured Grid Applications}, 12801 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 12802 publisher = {Springer Verlag}, 12803 year = {1992} 12804} 12805 12806@InProceedings{ quinlan2, 12807 author = {R. Parsons and D. Quinlan}, 12808 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 12809 Computations}, 12810 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 12811 year = {1994} 12812} 12813 12814% ***** Overview of functionality in Diffpack 12815@InBook{ dpoverview, 12816 author = {Bruaset, A. M. and Langtangen, H. P.}, 12817 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12818 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 12819 {Diffpack}}, 12820 publisher = {Birkh{\"{a}}user}, 12821 pages = {61--90}, 12822 year = {1997} 12823} 12824 12825% ***** Short overview of Diffpack 12826@InCollection{ dpoverview2, 12827 author = {Bruaset, A. M. and Langtangen, H. P.}, 12828 editor = {A. Sydow}, 12829 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 12830 and Applied Mathematics}, 12831 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 12832 pages = {553--558}, 12833 volume = {4}, 12834 year = {1997} 12835} 12836 12837% ***** Comprehensive documentation of Diffpack and 12838% associated numerical methods: 12839@Book{ dpbook, 12840 author = {H. P. Langtangen}, 12841 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 12842 Software. Part I}, 12843 series = {Lecture Notes in Computational Science and Engineering}, 12844 publisher = {Springer-Verlag}, 12845 year = {1998} 12846} 12847 12848% ***** Design issues of the linear solvers in Diffpack, serves also as a 12849% collection of examples on O-O in numerical computing 12850@Article{ ambhpl97a, 12851 author = {A. M. Bruaset and H. P. Langtangen }, 12852 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 12853 journal = {Transactions on Mathematical Software}, 12854 volume = {23 }, 12855 pages = {50--80}, 12856 year = {1997} 12857} 12858 12859@Misc{ dpurl, 12860 author = {{Diffpack Web page}}, 12861 howpublished = {\url{http://www.diffpack.com}} 12862} 12863 12864% ***** General intro to object-oriented numerics for "FORTRAN programmers" 12865@InCollection{ oonintro, 12866 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 12867 editor = {D{\ae}hlen, M. and Tveito, A.}, 12868 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12869 title = {Object-Oriented Numerics}, 12870 publisher = {Birkh{\"{a}}user}, 12871 year = {1997} 12872} 12873 12874% ***** Efficiency comparison: BLAS 1, Diffpack, C, 12875% and finite element applications (F77 vs Diffpack) 12876@InCollection{ dpefficiency, 12877 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 12878 H. P. and Miller, C. T.}, 12879 editor = {D{\ae}hlen, M. and Tveito, A.}, 12880 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 12881 title = {On the Efficiency of {C++} in Scientific Computing}, 12882 publisher = {Birkh{\"{a}}user}, 12883 pages = {91--118}, 12884 year = {1997} 12885} 12886 12887% ***** Parallel concept in Diffpack: 12888@InCollection{ dpparallel, 12889 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 12890 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 12891 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 12892 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 12893 Simulators}, 12894 publisher = {Springer--Verlag}, 12895 series = {Lecture Notes in Computer Science}, 12896 pages = {161--168}, 12897 year = {1997} 12898} 12899 12900% ***** DD and ML methods in Diffpack: 12901@InCollection{ dpddml, 12902 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 12903 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 12904 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 12905 title = {Domain decomposition and multilevel methods in Diffpack}, 12906 year = {1997} 12907} 12908 12909@InProceedings{ bsca98, 12910 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 12911 Alexander}, 12912 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 12913 Optimization}, 12914 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12915 Scientific and Engineering Computing}, 12916 editor = {Mike Henderson et al.}, 12917 pages = {165-173}, 12918 year = {1998} 12919} 12920 12921@Book{ scalapack-user-guide, 12922 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 12923 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 12924 Stanley and D. Walker and R. C. Whaley}, 12925 title = {Sca{LAPACK} Users' Guide}, 12926 publisher = {SIAM}, 12927 address = {Philadelphia, PA}, 12928 year = {1997} 12929} 12930 12931@InProceedings{ keyes99, 12932 author = {D. E. Keyes}, 12933 title = {How Scalable is Domain Decomposition in Practice?}, 12934 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 12935 Methods}, 12936 editor = {C.-H. Lai et al.}, 12937 publisher = {Domain Decomposition Press, Bergen}, 12938 note = {To appear}, 12939 year = {1999} 12940} 12941 12942@Article{ fun3d, 12943 author = {W. K. Anderson and D. L. Bonhaus}, 12944 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 12945 grids}, 12946 journal = {Computers and Fluids}, 12947 year = {1994}, 12948 volume = {23}, 12949 pages = {1--21} 12950} 12951 12952% ------------------------------------------------------------------------- 12953% ------------------------------------------------------------------------- 12954@Article{ torczon, 12955 author = {Dennis, Jr., J. E. and V.~Torczon}, 12956 title = {Direct Search Methods on Parallel Machines}, 12957 journal = {SIAM J. Optimization}, 12958 volume = {1}, 12959 pages = {448--474}, 12960 year = {1991}, 12961 key = {Torczon !PDS} 12962} 12963 12964@InProceedings{ wt91, 12965 author = {D. L. Whitfield and L. K. Taylor}, 12966 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 12967 Schemes}, 12968 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 12969 misc = {AIAA-91-1539}, 12970 pages = {134-145}, 12971 year = {1991} 12972} 12973 12974@Article{ ew96, 12975 author = {S. C. Eisenstat and H. F. Walker}, 12976 title = {Choosing the forcing terms in an inexact {N}ewton method}, 12977 journal = {SIAM J. Scientific Computing}, 12978 volume = {17}, 12979 year = {1996}, 12980 pages = {16--32} 12981} 12982 12983@Book{ thi93, 12984 author = {{Thinking Machines Corporation}}, 12985 title = {Users Manual for CM-Fortran}, 12986 publisher = {Thinking Machines Corporation}, 12987 year = {1993} 12988} 12989 12990@Book{ mortonmayers94, 12991 author = {K. W. Morton and D. F. Mayers}, 12992 title = {Numerical Solution of Partial Differential Equations}, 12993 publisher = {Press Syndicate of the University of Cambridge}, 12994 year = {1994} 12995} 12996 12997@Book{ heath97, 12998 author = {Michael T. Heath}, 12999 title = {Scientific Computing: An Introductory Survey}, 13000 publisher = {McGraw Hill}, 13001 year = {1997} 13002} 13003 13004@Article{ captools96, 13005 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 13006 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 13007 Performance on the Parallelization of Structured Mesh Codes}, 13008 journal = {Parallel Computing}, 13009 volume = {22}, 13010 pages = {197-226}, 13011 year = {1996} 13012} 13013 13014@Unpublished{ nastran-web-page, 13015 author = {{MSC Software Corporation}}, 13016 title = {{NASTRAN} {W}eb page}, 13017 note = {See {\tt http://www.mechsolutions.com\-/products\-/nastran/}} 13018} 13019 13020@Book{ hpf, 13021 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 13022 Zosel}, 13023 title = {The High Performance Fotran Handbook}, 13024 publisher = {MIT Press}, 13025 year = {1994} 13026} 13027 13028@InProceedings{ keyes98, 13029 author = {D. E. Keyes}, 13030 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 13031 Architectures}, 13032 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 13033 editors = {M. D. Salas and W. K. Anderson}, 13034 ppublisher = {Elsevier}, 13035 year = {1998} 13036} 13037 13038@InProceedings{ pooma-atlas, 13039 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 13040 J. V. W. Reynders and M. Tholburn}, 13041 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 13042 Applications}, 13043 year = {1995}, 13044 month = {December}, 13045 booktitle = {Supercomputing '95 Proceedings} 13046} 13047 13048% --------------------------------------------------------------------------------- 13049% New bib entries for CRPC paper 13050@Misc{ mgnet-web-page, 13051 author = {Craig C. Douglas}, 13052 title = {{MGNet Web page}}, 13053 note = {See {\tt http://\-www.mgnet.org}} 13054} 13055 13056@Misc{ dagh-web-page, 13057 author = {M. Parashar and J. C. Browne}, 13058 title = {{DAGH Web page}}, 13059 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 13060} 13061 13062@Misc{ parasol-web-page, 13063 key = {PARASOL}, 13064 title = {{PARASOL Web page}}, 13065 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 13066} 13067 13068@Misc{ pooma-web-page, 13069 author = {{POOMA Web page}}, 13070 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 13071} 13072 13073@Misc{ mudpack-web-page, 13074 author = {John C. Adams}, 13075 title = {{MUDPACK Web page}}, 13076 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 13077} 13078 13079@Misc{ pellpack-web-page, 13080 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 13081 title = {{Parallel ELLPACK Web page}}, 13082 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 13083} 13084 13085@InProceedings{ pellpack95, 13086 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 13087 Catlin and S. Weerawarana and T.S. Papatheodorou}, 13088 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 13089 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 13090 address = {Albuquerque, NM}, 13091 year = {1995} 13092} 13093 13094@Misc{ nhse-web-page, 13095 author = {{National High-Performance Software Exchange Web page}}, 13096 note = {See {\tt http://\-www.nhse.org}} 13097} 13098 13099@Misc{ doug-web-page, 13100 author = {Mark J. Hagger and Linda Stals}, 13101 title = {{DOUG Web Page}}, 13102 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 13103} 13104 13105@TechReport{ doug97, 13106 author = {Mark J. Hagger}, 13107 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 13108 institution = {Mathematical Sciences, University of Bath}, 13109 year = {1997}, 13110 number = {9706}, 13111 note = {Advances in Computational Mathematics (to appear)} 13112} 13113 13114@Misc{ ug-web-page, 13115 author = {{UG Web Page}}, 13116 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 13117} 13118 13119@Article{ ug97, 13120 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 13121 Rentz-Reichert and C. Wieners}, 13122 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 13123 journal = {Computing and Visualization in Science}, 13124 year = {1997}, 13125 volume = {}, 13126 pages = {} 13127} 13128 13129@Misc{ vecfem-web-page, 13130 author = {Lutz Grosz}, 13131 title = {{VECFEM Web Page}}, 13132 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 13133} 13134 13135@Misc{ atlas-web-page, 13136 author = {R. Clint {Whaley et al.}}, 13137 title = {{ATLAS Web Page}}, 13138 howpublished = {\url{http://math-atlas.sourceforge.net}} 13139} 13140 13141@Misc{ fenics-web-page, 13142 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 13143 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 13144 title = {{FEniCS Web Page}}, 13145 note = {\url{http://www.fenicsproject.org}}, 13146 year = {2005} 13147} 13148 13149@Misc{ matlab-web-page, 13150 author = {{The} {MathWorks}}, 13151 title = {{Matlab} {Web} page}, 13152 url = {http://www.mathworks.com} 13153} 13154 13155@Misc{ phipac-web-page, 13156 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 13157 and D. Lam}, 13158 title = {{PHiPAC Web Page}}, 13159 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 13160} 13161 13162@InProceedings{ kelp, 13163 author = {Stephan J. Fink and Scott B. Baden and Scott R. 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Quinlan}, 13200 title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations 13201 on Overlapping Grids}, 13202 publisher = {SIAM}, 13203 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 13204 Scientific and Engineering Computing}, 13205 year = {1999}, 13206 pages = {215-224}, 13207 note = {See \url{http://www.llnl.gov/CASC/Overture}} 13208} 13209 13210@InProceedings{ diffpack, 13211 author = {A.M. Bruaset and H.P. Langtangen}, 13212 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations: 13213 {D}iffpack}, 13214 booktitle = {Numerical Methods and Software Tools in Industrial Mathematics}, 13215 year = {1997}, 13216 pages = {61--90}, 13217 publisher = {Birkhauser Press} 13218} 13219 13220@Article{ dongarra:1984:ila, 13221 author = {J. J. Dongarra and F. G. Gustavson and A. Karp}, 13222 title = {Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline 13223 Machine}, 13224 journal = {SIAM Review}, 13225 volume = {26}, 13226 number = {1}, 13227 pages = {91--112}, 13228 month = jan, 13229 year = {1984}, 13230 coden = {SIREAD}, 13231 issn = {0036-1445 (print), 1095-7200 (electronic)}, 13232 mrclass = {65F10 (65F30)}, 13233 mrnumber = {85c:65032}, 13234 bibdate = {Mon Jan 20 1997}, 13235 abstract = {The authors examine common implementations of linear algebra algorithms, such as 13236 matrix-vector multiplication, matrix-matrix multiplication and the solution of 13237 linear equations. The different versions are examined for efficiency on a computer 13238 architecture which uses vector processing and has pipelined instruction execution. 13239 By using the advanced architectural features of such machines, one can usually 13240 achieve maximum performance, and tremendous improvements in terms of execution 13241 speed can be seen over conventional computers.}, 13242 classification= {723; 921}, 13243 journalabr = {SIAM Rev}, 13244 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 13245 mathematical programming; vector pipeline machine} 13246} 13247 13248@Book{ qv99, 13249 author = {Alfio Quarteroni and Alberto Valli}, 13250 title = {Domain Decomposition Methods for Partial Differential Equations}, 13251 publisher = {Oxford Science Publications}, 13252 address = {Oxford}, 13253 year = {1999} 13254} 13255 13256@Book{ ksv97, 13257 editor = {David E. Keyes and Ahmed Sameh and V. 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Koniges}, 13326 title = {Industrial Strength Parallel Computing}, 13327 publisher = {Morgan Kaufmann Publishers}, 13328 address = {San Francisco}, 13329 year = {2000} 13330} 13331 13332@Misc{ fftw-web-page, 13333 key = {Fftw}, 13334 title = {{FFTW} {Web} page}, 13335 note = {\texttt{http://www.fftw.org/}}, 13336 annote = {fast FFT. Parallel versions with MPI and Cilk} 13337} 13338 13339@InProceedings{ frigojohnson93, 13340 author = {Matteo Frigo and Steven G. Johnson}, 13341 title = {The Design and Implementation of {FFTW3}}, 13342 booktitle = {Proceedings of the IEEE}, 13343 volume = {93}, 13344 number = {2}, 13345 pages = {216--231}, 13346 year = {2005} 13347} 13348 13349@Book{ kelley95, 13350 author = {C. T. Kelley}, 13351 title = {Iterative Methods for Linear and Nonlinear Equations}, 13352 year = {1995}, 13353 publisher = {SIAM}, 13354 address = {Philadelphia} 13355} 13356 13357@Unpublished{ spai-web-page, 13358 title = {{SPAI} {W}eb {P}age}, 13359 note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/}, 13360 author = {Steven Bernard and Marcus Grote}, 13361 institution = {NASA Ames Research Center and ETH Zurich} 13362} 13363 13364@Article{ gh97, 13365 author = {M. J. Grote and T. Huckle}, 13366 title = {Parallel Preconditioning with Sparse Approximate Inverses}, 13367 year = {1997}, 13368 journal = {SIAM J. of Scient. Comput.}, 13369 volume = {18}, 13370 pages = {838-853} 13371} 13372 13373@Article{ zhang96, 13374 author = {Wen Zhang}, 13375 title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the 13376 simulation of a sintering process}, 13377 year = {1996}, 13378 journal = {Appl. Numer. 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Schwartzbach}, 13401 title = {A Domain-Specific Languages for Regular Sets of Strings and Trees}, 13402 booktitle = {Proceedings of the Conference on Domain-Specific Languages}, 13403 publisher = {USENIX}, 13404 month = {October}, 13405 year = {1997}, 13406 address = {Santa Barbara, CA} 13407} 13408 13409@InProceedings{ conselmarlet98, 13410 author = {C. Consel and R. Marlet}, 13411 title = {Architecturing software using a methodology for language development}, 13412 booktitle = {Proceedings of the 10th International Symposium on Programming Languages, 13413 Implementations, Logics and Programs}, 13414 year = {1998}, 13415 pages = {170-174}, 13416 month = {September}, 13417 address = {Pisa, Italy} 13418} 13419 13420@Misc{ sundials:homepage, 13421 author = {C. {Woodward et al.}}, 13422 title = {{SUNDIALS {W}eb page}}, 13423 howpublished = {\url{https://computation.llnl.gov/casc/sundials/main.html}} 13424} 13425 13426@article{gardner2022sundials, 13427 title = {Enabling new flexibility in the {SUNDIALS} suite of nonlinear and differential/algebraic equation solvers}, 13428 author = {Gardner, David J and Reynolds, Daniel R and Woodward, Carol S and Balos, Cody J}, 13429 journal = {ACM Transactions on Mathematical Software (TOMS)}, 13430 publisher = {ACM}, 13431 year = {2022}, 13432 doi = {10.1145/3539801} 13433} 13434 13435@Misc{ sundials-user-ref, 13436 title = {{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13437 note = {See \url{http://www.llnl.gov/CASC/sundials}}, 13438 author = {Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban 13439 and Dan Shumaker and Carol Woodward}, 13440 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 13441 number = {UCRL-JP-200037}, 13442 year = {2003} 13443} 13444 13445@Article{ sundials05, 13446 author = {A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 13447 and C. Woodward}, 13448 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 13449 journal = {ACM Transactions on Mathematical Software}, 13450 volume = {31}, 13451 number = {3}, 13452 pages = {363--396}, 13453 year = {2005} 13454} 13455 13456@InProceedings{ serban2005cvodes, 13457 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 13458 author = {Serban, Radu and Hindmarsh, Alan C}, 13459 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 13460 Dynamics and Control, Long Beach, CA}, 13461 year = {2005} 13462} 13463 13464@Article{ pvode99, 13465 author = {G. Byrne and A. Hindmarsh}, 13466 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 13467 journal = {Int. J. High Perf. Comput. 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Babu$\check{s}$ka and A.D. Miller}, 13543 title = {The post-processing approach in the finite element method, {I}: Calculations of 13544 displacements, stresses, and other higher derivatives of the displacements}, 13545 journal = {Int. J. Numer. Meth. Eng.}, 13546 year = {1984}, 13547 volume = {20}, 13548 pages = {1085--1109} 13549} 13550 13551@Article{ babuskamiller84b, 13552 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13553 title = {The post-processing approach in the finite element method, {II}: The calculation 13554 of stress intensity factors}, 13555 journal = {Int. J. Numer. Meth. Eng.}, 13556 year = {1984}, 13557 volume = {20}, 13558 pages = {1111--1129} 13559} 13560 13561@Article{ babuskamiller84c, 13562 author = {I. Babu$\check{s}$ka and A.D. Miller}, 13563 title = {The post-processing approach in the finite element method, {III}: A posteriori 13564 error estimation and adaptive mesh refinement}, 13565 journal = {Int. J. Numer. Meth. Eng.}, 13566 year = {1984}, 13567 volume = {20}, 13568 pages = {2311--2324} 13569} 13570 13571@Unpublished{ jtb-web-page, 13572 title = {{The Java Tree Builder}}, 13573 note = {See \url{http://www.cs.purdue.edu/jtb}}, 13574 author = {Jens Palsberg}, 13575 institution = {Purdue University} 13576} 13577 13578@Unpublished{ palsberg98, 13579 title = {Why Visitors?}, 13580 note = {See \url{http://www.cs.purdue.edu/jtb/whyvisitors}}, 13581 author = {Jens Palsberg}, 13582 institution = {Purdue University}, 13583 year = {1998} 13584} 13585 13586@Unpublished{ ply-web-page, 13587 title = {{PLY (Python Lex-Yacc)}}, 13588 note = {\url{http://systems.cs.chicago.edu/ply}}, 13589 author = {David Beazley}, 13590 institution = {University of Chicago} 13591} 13592 13593@Misc{ adic-web-page, 13594 title = {{ADIC Web page}}, 13595 note = {\url{http://www.mcs.anl.gov/autodiff}}, 13596 author = {Paul Hovland and Uwe Naumann and Boyana Norris}, 13597 institution = {Argonne National Laboratory} 13598} 13599 13600@Article{ naumann02, 13601 author = {Uwe Naumann}, 13602 title = {Optimal accumulation of {J}acobian matrices by elimination methods on the dual 13603 computational graph}, 13604 journal = {Mathematical Programming (to appear)}, 13605 note = {Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002}, 13606 year = {2003} 13607} 13608 13609@Article{ kaper1, 13610 author = {H. G. Kaper and T. J. Kaper}, 13611 title = {Asymptotic Analysis of Two Reduction Methods for Systems of Chemical Reactions}, 13612 journal = {Physica D}, 13613 year = {2002}, 13614 pages = {66--93}, 13615 volume = {165} 13616} 13617 13618@Misc{ veltisto-web-page, 13619 author = {George Biros}, 13620 title = {{Veltisto Web page}}, 13621 note = {\url{http://www.cs.nyu.edu/~biros/veltisto}} 13622} 13623 13624@Article{ karypiskumar98, 13625 author = {George Karypis and Vipin Kumar}, 13626 title = {A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix 13627 Ordering}, 13628 journal = {Journal of Parallel and Distributed Computing}, 13629 volume = {48}, 13630 pages = {71--85}, 13631 year = {1998} 13632} 13633 13634@TechReport{ karypiskumar97, 13635 author = {Karypis, George and Kumar, V.}, 13636 institution = {Department of Computer Science, University of Minnesota}, 13637 keywords = {graph partitioning; ParMetis}, 13638 note = {http://www.cs.umn.edu/~metis}, 13639 number = {97-060}, 13640 title = {{ParMETIS}: Parallel graph partitioning and sparse matrix ordering library}, 13641 year = {1997} 13642} 13643 13644@Misc{ parmetis-web-page, 13645 author = {George {Karypis et al.}}, 13646 title = {{ParMETIS Web page}}, 13647 note = {\url{http://www.cs.umn.edu/~karypis/metis/parmetis}}, 13648 year = {2005} 13649} 13650 13651@Misc{ sparskit-web-page, 13652 author = {Yousef {Saad et al.}}, 13653 title = {{SPARSKIT Web page}}, 13654 note = {\url{http://www.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html}} 13655} 13656 13657@Misc{ dscpack-web-page, 13658 author = {Padma Raghavan}, 13659 title = {{DSCPACK Web page}}, 13660 note = {\url{http://www.cse.psu.edu/~raghavan/Dscpack}} 13661} 13662 13663@Misc{ gaussian-web-page, 13664 author = {}, 13665 title = {{Gaussian Web page}}, 13666 note = {\url{http://gaussian.com}}, 13667 key = {{Gaussian} {Web} page} 13668} 13669 13670@Book{ lapack-user-guide, 13671 author = {E. Anderson and Z. Bai and C. Bischof and S. Blackford and J. Demmel and J. 13672 Dongarra and J. Du Cris and A. Greenbaum and S. Hammarling and A. McKenney and D. 13673 Sorensen}, 13674 title = {LAPACK Users' Guide, Third Edition}, 13675 publisher = {SIAM}, 13676 year = {1999} 13677} 13678 13679@Manual{ nwchem4.1, 13680 author = {High Performance Computational Chemistry Group}, 13681 title = {{NWChem}, A Computational Chemistry Package for Parallel Computers, Version 4.1}, 13682 year = {2002}, 13683 organization = {Pacific Northwest National Laboratory}, 13684 address = {Richland, Washington 99325-0999 USA}, 13685 note = {See \url{http://www.emsl.pnl.gov/pub/docs/nwchem/}} 13686} 13687 13688@TechReport{ tchem, 13689 title = {{TC}hem: {A} Software Toolkit for the Analysis of Complex Kinetic Models}, 13690 author = {Cosmin Safta and Habib Najm and Omar Knio}, 13691 institution = {Sandia National Laboratories}, 13692 number = {SAND2011-3282}, 13693 year = {2011} 13694} 13695 13696@Misc{ scidac-web-page, 13697 author = {}, 13698 title = {{{SciDAC Initiative Web page}}}, 13699 note = {\url{http://www.osti.gov/scidac}}, 13700 key = {{SciDAC Initiative Web page}} 13701} 13702 13703@Misc{ cmrs:homepage, 13704 author = {Amitava {Bhattacharjee (PI)}}, 13705 title = {{Center for Magnetic Reconnection Studies}}, 13706 howpublished = {\url{http://www.physics.uiowa.edu/cmrs}} 13707} 13708 13709@Misc{ tops:homepage, 13710 author = {David {Keyes (PI)}}, 13711 title = {{Towards Optimal Petascale Simulations (TOPS) Center}}, 13712 howpublished = {\url{http://scalablesolvers.org}} 13713} 13714 13715@Misc{ tstt:homepage, 13716 author = {David Brown and Jim Glimm and Lori Freitag}, 13717 title = {{Terascale Simulation Tools and Technology (TSTT) Center}}, 13718 howpublished = {\url{http://www.tstt-scidac.org}}, 13719 year = {2005} 13720} 13721 13722@Misc{ petsc:applications, 13723 author = {B. F. {Smith et al.}}, 13724 title = {{Scientific Applications Using {PETSc}}}, 13725 howpublished = {\url{http://www.mcs.anl.gov/petsc/publications}} 13726} 13727 13728@Misc{ petsc:users, 13729 author = {B. F. {Smith et al.}}, 13730 title = {{PETSc User Statistics}}, 13731 howpublished = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/usage.html}} 13732} 13733 13734@Misc{ cemm:homepage, 13735 author = {Steve {Jardin (PI)}}, 13736 title = {{Center for Extended MHD Modeling}}, 13737 howpublished = {\url{http://w3.pppl.gov/CEMM}} 13738} 13739 13740@Misc{ m3d:homepage, 13741 author = {Steve {Jardin et al.}}, 13742 title = {{M3D Web page}}, 13743 howpublished = {\url{http://w3.pppl.gov/m3d}} 13744} 13745 13746@Misc{ nimrod:homepage, 13747 author = {Carl R. {Sovinec et al.}}, 13748 title = {{NIMROD Web page}}, 13749 howpublished = {http://nimrodteam.org} 13750} 13751 13752@Misc{ grace-web-page, 13753 author = {Manish {Parashar et al.}}, 13754 title = {{GrACE Web Page}}, 13755 howpublished = {\url{http://www.caip.rutgers.edu/~parashar/TASSL/Projects/GrACE}} 13756} 13757 13758@Misc{ accel1, 13759 title = {Advanced Computing for 21st Century Accelerator Science and Technology Web page}, 13760 howpublished = {\url{http://scidac.nersc.gov/accelerator/}}, 13761 author = {K. Ko and R. Ryne (PIs)} 13762} 13763 13764@Unpublished{ katzspiegelman03, 13765 author = {Richard F. Katz and Marc Spiegelman}, 13766 title = {A semi-{L}agrangian {C}rank-{N}icholson algorithm for the numerical solution of 13767 advection-diffusion problems}, 13768 note = {Columbia University, in preparation} 13769} 13770 13771@Misc{ acts:homepage, 13772 author = {}, 13773 title = {{Advanced CompuTational Software (ACTS) Web page}}, 13774 howpublished = {\url{http://acts.nersc.gov}}, 13775 key = {{Advanced CompuTational Software (ACTS) Web page}} 13776} 13777 13778@Article{ superlu99, 13779 author = {James W. Demmel and Stanley C. Eisenstat and John R. Gilbert and Xiaoye S. Li and 13780 Joseph W. H. Liu}, 13781 title = {A supernodal approach to sparse partial pivoting}, 13782 journal = {SIAM J. Matrix Analysis and Applications}, 13783 year = {1999}, 13784 volume = {20}, 13785 number = {3}, 13786 pages = {720-755} 13787} 13788 13789@Misc{ superlu:homepage, 13790 author = {J. 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Wilson}, 14581 title = {{BOUT++}: A Framework for Parallel Plasma Fluid Simulations}, 14582 journal = {Computer Physics Communications}, 14583 year = {2009}, 14584 volume = {180}, 14585 issue = {9}, 14586 pages = {1467 -- 1480}, 14587 note = {} 14588} 14589 14590@Article{ tempest, 14591 author = {Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and M.R. Dorr and J.A. Hittinger 14592 and G. Kerbel and W.M. Nevins and T. Rognlien}, 14593 title = {Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST}, 14594 journal = {Bull. Am. Phys. Soc. }, 14595 year = {2005}, 14596 volume = {50}, 14597 number = {86}, 14598 pages = {CP1}, 14599 note = {} 14600} 14601 14602@Article{ ccahpc, 14603 author = {David E. Bernholdt and Benjamin A. Allan and Robert Armstrong and Felipe Bertrand 14604 and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif 14605 and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James 14606 A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia 14607 Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek 14608 Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende 14609 and Theresa L. Windus and Shujia Zhou}, 14610 title = {A Component Architecture for High-Performance Scientific Computing}, 14611 journal = {Intl. J. High-Perf. Computing Appl.}, 14612 volume = {20}, 14613 pages = {163--202}, 14614 year = {2006}, 14615 note = {ACTS Collection special issue} 14616} 14617 14618@Misc{ cca-forum:homepage, 14619 author = {{Common Component Architecture Forum}}, 14620 note = {\url{http://www.cca-forum.org}}, 14621 year = {2010} 14622} 14623 14624@Misc{ petsc:driven-cavity-example, 14625 title = {{PETSc Driven Cavity Example Code}}, 14626 author = {B. F. {Smith et al.}}, 14627 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 14628} 14629 14630@Misc{ petsc-dm:webpage, 14631 author = {B. F. {Smith et al.}}, 14632 title = {{PETSc DM Webpage}}, 14633 howpublished = {\url{https://petsc.org/release/manualpages/DM/}}, 14634 year = {2018} 14635} 14636 14637@Misc{ unic-ref, 14638 author = {Giuseppe Palmiotti}, 14639 title = {{UNIC} Neutronics Software}, 14640 note = {Nuclear Engineering Division, Argonne National Laboratory} 14641} 14642 14643% ----------------------------------------------------------------------- 14644% Model coupling refs 14645@Book{ greve-blatter, 14646 author = {Ralf Greve and Heinz Blatter}, 14647 title = {Dynamics of Ice Sheets and Glaciers}, 14648 series = {Advances in Geophysical and Environmental Mechanics and Mathematics}, 14649 publisher = {Springer}, 14650 year = {2009} 14651} 14652 14653@Misc{ doe-isicles, 14654 key = {ISICLES}, 14655 title = {Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}}, 14656 howpublished = {\url{http://www.csm.ornl.gov/ISICLES/index.html}} 14657} 14658 14659@Article{ safta2011tchem, 14660 title = {TChem-a software toolkit for the analysis of complex kinetic models}, 14661 author = {Safta, Cosmin and Najm, Habib N and Knio, Omar}, 14662 journal = {Sandia Report, SAND2011-3282}, 14663 year = {2011} 14664} 14665 14666@Misc{ chemkin-website, 14667 key = {chemkin}, 14668 title = {ANSYS Chemkin-Pro Website}, 14669 howpublished = {\url{http://www.ansys.com/products/fluids/ansys-chemkin-pro}}, 14670 year = {2017} 14671} 14672 14673@Misc{ mct-website, 14674 key = {MCT}, 14675 title = {{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite}, 14676 howpublished = {\url{http://www.mcs.anl.gov/mct}} 14677} 14678 14679@Article{ larson:05, 14680 author = {Jay Larson and Robert Jacob and Everest Ong}, 14681 title = {{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building 14682 Multi-Physics Parallel Coupled Models}, 14683 journal = {Int. 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Keyes}, 14770 title = {Multi-domain multi-model formulation for compressible flows: Conservative 14771 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 14772 note = {AIAA Paper 99-0784}, 14773 year = {1999} 14774} 14775 14776@Article{ peszynska, 14777 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 14778 title = {Mortar upscaling for multiphysics flow in porous media}, 14779 journal = {Computational Geosciences} 14780} 14781 14782@TechReport{ wheeler00, 14783 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 14784 title = {A distributed computing portal for coupling multi-physics and multiple domains in 14785 porous media}, 14786 institution = {University of Texas at Austin}, 14787 number = {TICAM 00-03}, 14788 year = {2000} 14789} 14790 14791@TechReport{ peszynska00, 14792 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 14793 title = {Multiphysics Coupling of Codes}, 14794 institution = {University of Texas at Austin}, 14795 number = {TICAM 00-02}, 14796 year = {2000} 14797} 14798 14799@Article{ joshaghanijoodatnakshatrala2019, 14800 title = {A stabilized mixed discontinuous Galerkin formulation for double 14801 porosity/permeability model}, 14802 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 14803 journal = {Computer Methods in Applied Mechanics and Engineering}, 14804 volume = {352}, 14805 pages = {508--560}, 14806 year = {2019} 14807} 14808 14809@InProceedings{ cai99, 14810 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 14811 title = {An explicit multi-model compressible flow formulation based on the full potential 14812 equation and the {Euler} equations on {3D} unstructured meshes}, 14813 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 14814 Methods}, 14815 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 14816 year = {1999} 14817} 14818 14819@Article{ he05, 14820 author = {Yun He and Chris H. Q. Ding}, 14821 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 14822 Architectures}, 14823 year = {2005}, 14824 volume = {19}, 14825 pages = {329--240}, 14826 number = {3}, 14827 journal = {Int. Journal of High Performance Computing Applications} 14828} 14829 14830@InProceedings{ uiuc-rocket-center02, 14831 author = {W. A. Dick and M. T. Heath}, 14832 title = {Whole System Simulation of Solid Propellant Rockets}, 14833 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 14834 month = {July}, 14835 year = {2002} 14836} 14837 14838@InProceedings{ toth04, 14839 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 14840 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 14841 Oehmke}, 14842 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 14843 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 14844 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 14845 Sun-Earth Connection}, 14846 year = {2004}, 14847 publisher = {Elsevier}, 14848 pages = {383--397} 14849} 14850 14851@Misc{ csdrm:web, 14852 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 14853 Shepherd}, 14854 title = {{Center for Simulation of Dynamic Response of Materials}}, 14855 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 14856} 14857 14858@Misc{ csar:web, 14859 author = {M. {Heath (Director)}}, 14860 title = {{Center for Simulation of Advanced Rockets}}, 14861 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 14862} 14863 14864@Misc{ csafe:web, 14865 author = {D. {Pershing (Director)}}, 14866 title = {{Center for Simulation of Accidental Fires and Explosions}}, 14867 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 14868} 14869 14870@Misc{ cits:web, 14871 author = {P. {Moin (Director)}}, 14872 title = {{Center for Integrated Turbulence Simulations}}, 14873 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 14874} 14875 14876@Misc{ flash:web, 14877 author = {D. {Lamb (Director)}}, 14878 title = {{Center for Integrated Turbulence Simulations}}, 14879 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 14880} 14881 14882@TechReport{ utah-csafe03, 14883 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 14884 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 14885 Problems, Part 1: Algorithm Development}, 14886 institution = {University of Utah, Center for the Simulation of Accidental Fires and 14887 Explosions}, 14888 year = {2003} 14889} 14890 14891@InBook{ shepherd07, 14892 author = {M. Shepherd and E. Seol and B. FrantzDale}, 14893 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 14894 year = {2007}, 14895 booktitle = {CRC Handbook of Dynamic System Modeling}, 14896 publisher = {Wiley}, 14897 pages = {1--41}, 14898 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 14899} 14900 14901@InProceedings{ cactus02, 14902 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 14903 Radke and Edward Seidel and John Shalf}, 14904 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 14905 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 14906 year = {2002}, 14907 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 14908} 14909 14910@Misc{ cactus:homepage, 14911 author = {G. {Allen et al.}}, 14912 title = {{Cactus Web page}}, 14913 howpublished = {\url{http://cactuscode.org}} 14914} 14915 14916@Misc{ open-grid-forum:web, 14917 key = {{Open Grid Forum}}, 14918 title = {{Open Grid Forum}}, 14919 note = {See \url{http://www.ogf.org}} 14920} 14921 14922@Misc{ nox:web, 14923 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 14924 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 14925 note = {See \url{http://software.sandia.gov/nox}} 14926} 14927 14928@Misc{ chombo:web, 14929 author = {P. {Colella (PI)}}, 14930 title = {{Chombo}}, 14931 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 14932} 14933 14934@Article{ lanzkron96, 14935 author = {P. 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Messerschmitt}, 15006 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 15007 journal = {Int. Journal of Computer Simulation}, 15008 volume = {4}, 15009 pages = {155--182}, 15010 year = {1994} 15011} 15012 15013@Article{ mu95, 15014 author = {M. Mu and J.R. Rice}, 15015 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 15016 journal = {Comp. Syst. Engr.}, 15017 volume = {6}, 15018 year = {1995}, 15019 pages = {87--95} 15020} 15021 15022@TechReport{ drashansky96, 15023 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 15024 author = {R. Drashansky and A. Joshi and J. R. Rice}, 15025 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 15026 year = {1996} 15027} 15028 15029@Article{ michopoulos05, 15030 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 15031 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 15032 journal = {Journal of Computing and Information Science in Engineering}, 15033 volume = {5}, 15034 issue = {3}, 15035 pages = {198--213}, 15036 year = {2005} 15037} 15038 15039@Article{ dubey09, 15040 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 15041 Multiphysics Simulation Code}, 15042 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 15043 Siegel and K. Weide}, 15044 journal = {Parallel Computing}, 15045 volume = {35}, 15046 issue = {10 -- 11}, 15047 pages = {512 -- 522}, 15048 year = {2009} 15049} 15050 15051@Book{ bottloring95, 15052 author = {Raoul Bott and Loring W. Tu}, 15053 title = {Differential Forms in Algebraic Topology}, 15054 publisher = {Springer}, 15055 year = {1995} 15056} 15057 15058@Book{ kobayashinomizu96, 15059 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 15060 title = {Foundations of Differential Geometry}, 15061 publisher = {Wiley-Interscience}, 15062 year = {1996} 15063} 15064 15065@Article{ hornungkohn02, 15066 author = {Richard D. Hornung and Scott R. Kohn}, 15067 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 15068 journal = {Concurrency and Computation: Practice and Experience}, 15069 volume = {14}, 15070 pages = {347--368}, 15071 year = {2002} 15072} 15073 15074@InProceedings{ concepts06, 15075 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 15076 Gabriel Dos Reis and Andrew Lumsdaine}, 15077 title = {Concepts: Linguistic Support for Generic Programming in C++}, 15078 booktitle = {Proceedings of OOPSLA 2006}, 15079 year = {2006}, 15080 pages = {???--???} 15081} 15082 15083@Book{ hatcher02, 15084 author = {Hatcher, Allen}, 15085 title = {Algebraic Topology}, 15086 publisher = {Cambridge University Press}, 15087 year = {2002} 15088} 15089 15090@Book{ gammahelmjohnsonvlissides95, 15091 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 15092 development, offering timeless and elegant solutions to common problems in 15093 software design. It describes patterns for managing object creation, composing 15094 objects into larger structures, and coordinating control flow between objects. The 15095 book provides numerous examples where using composition rather than inheritance 15096 can improve the reusability and flexibility of code. Note, though, that it's not a 15097 tutorial but a catalog that you can use to find an object-oriented design pattern 15098 that's appropriate for the needs of your particular application--a selection for 15099 virtuoso programmers who appreciate (or require) consistent, well-engineered 15100 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 15101 more valuable than ever! 15102 15103 Use the contents of the CD to create your own design documents and reusable 15104 components. The CD contains: 23 patterns you can cut and paste into your own 15105 design documents; sample code demonstrating pattern implementation; complete 15106 Design Patterns content in standard HTML format, with numerous hyperlinked 15107 cross-references; accessed through a standard web browser; Java-based dynamic 15108 search mechanism, enhancing online seach capabilities; graphical user environment, 15109 allowing ease of navigation. 15110 15111 First published in 1995, this landmark work on object-oriented software design 15112 presents a catalog of simple and succinct solutions to common design problems. 15113 Created by four experienced designers, the 23 patterns contained herein have 15114 become an essential resource for anyone developing reusable object-oriented 15115 software. In response to reader demand, the complete text and pattern catalog are 15116 now available on CD-ROM. This electronic version of Design Patterns enables 15117 programmers to install the book directly onto a computer or network for use as an 15118 online reference for creating reusable object-oriented software. 15119 15120 The authors first describe what patterns are and how they can help you in the 15121 design process. They then systematically name, explain, evaluate, and catalog 15122 recurring designs in object-oriented systems. All patterns are compiled from 15123 real-world examples and include code that demonstrates how they may be implemented 15124 in object-oriented programming languages such as C++ and Smalltalk. Readers who 15125 already own the book will want the CD to take advantage of its dynamic search 15126 mechanism and ready-to-install patterns.}}, 15127 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 15128 citeulike-article-id={115158}, 15129 howpublished = {Hardcover}, 15130 isbn = {0201633612}, 15131 keywords = {1995 algorithms architecture book books computer computing design design-pattern 15132 design-patterns design_patterns designpatterns development diplom entwurfsmuster 15133 four gang gof java mathgamespatterns no-tag object object-orientation 15134 object-oriented of oo-patterns oop oriented pattern patterns programming se 15135 software software-development software-engineering software_design 15136 softwareengineering standard}, 15137 month = {January}, 15138 publisher = {{Addison-Wesley Professional}}, 15139 title = {Design Patterns}, 15140 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 15141 year = {1995} 15142} 15143 15144@InProceedings{ chaco95, 15145 author = {Bruce Hendrickson and Robert Leland}, 15146 title = {A multilevel algorithm for partitioning graphs}, 15147 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 15148 (CDROM)}, 15149 year = {1995}, 15150 isbn = {0-89791-816-9}, 15151 pages = {28}, 15152 location = {San Diego, California, United States}, 15153 doi = {10.1145/224170.224228}, 15154 publisher = {ACM Press}, 15155 address = {New York} 15156} 15157 15158@Book{ aleksandrov98, 15159 author = {Aleksandrov, Pavel S.}, 15160 title = {Combinatorial Topology}, 15161 publisher = {Dover}, 15162 volume = {3}, 15163 year = {1998} 15164} 15165 15166@Book{ steenrod99, 15167 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 15168 importance in modern physics--such as in gauge theory. This book, a succinct 15169 introduction to the subject by renown mathematician Norman Steenrod, was the first 15170 to present the subject systematically. 15171 15172 It begins with a general introduction to bundles, including such topics as 15173 differentiable manifolds and covering spaces. The author then provides brief 15174 surveys of advanced topics, such as homotopy theory and cohomology theory, before 15175 using them to study further properties of fibre bundles. The result is a classic 15176 and timeless work of great utility that will appeal to serious mathematicians and 15177 theoretical physicists alike. }}, 15178 author = {Steenrod, Norman}, 15179 citeulike-article-id={712999}, 15180 howpublished = {Paperback}, 15181 isbn = {0691005486}, 15182 keywords = {fibre_bundles topology}, 15183 month = {April}, 15184 publisher = {{Princeton University Press}}, 15185 title = {The Topology of Fibre Bundles. (PMS-14)}, 15186 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 15187 year = {1999} 15188} 15189 15190@Book{ bredon97, 15191 author = {Bredon, Glen E.}, 15192 title = {Sheaf Theory}, 15193 publisher = {Springer}, 15194 pages = {524}, 15195 series = {Graduate Texts in Mathematics}, 15196 year = {1997} 15197} 15198 15199@TechReport{ tautgesmeyers04, 15200 title = {{MOAB}: A Mesh-Oriented Database}, 15201 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 15202 Ernst}, 15203 institution = {Sandia National Laboratories}, 15204 number = {SAND2004-1592}, 15205 month = {April}, 15206 year = {2004} 15207} 15208 15209@Article{ tautges04, 15210 author = {Timothy J. Tautges}, 15211 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 15212 journal = {Engineering With Computers}, 15213 volume = {20}, 15214 pages = {286--293}, 15215 year = {2004} 15216} 15217 15218@InProceedings{ meyers02, 15219 author = {Ray Meyers et. al}, 15220 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 15221 booktitle = {8th International conference on numerical grid generation in computational field 15222 simulations}, 15223 month = {June}, 15224 year = {2002} 15225} 15226 15227@InProceedings{ seolshepard05, 15228 author = {E. S. Seol and Mark S. Shephard}, 15229 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 15230 Analysis}, 15231 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 15232 year = {2005} 15233} 15234 15235@Article{ beallwalshshephard04, 15236 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 15237 title = {A comparison of techniques for geometry access related to mesh generation}, 15238 journal = {Engineering With Computers}, 15239 volume = {20}, 15240 number = {3}, 15241 pages = {210--221}, 15242 year = {2004} 15243} 15244 15245@Article{ careyandersoncarneskirk04, 15246 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 15247 Kirk}, 15248 title = {Some aspects of adaptive grid technology related to boundary and interior 15249 layers}, 15250 journal = {Journal of Computational Applied Mathematics}, 15251 volume = {166}, 15252 number = {1}, 15253 pages = {55--86}, 15254 year = {2004} 15255} 15256 15257@PhDThesis{ gralthesis, 15258 author = {Guntram Berti}, 15259 title = {Generic Software Components for Scientific Computing}, 15260 school = {TU Cottbus}, 15261 year = {2000}, 15262 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 15263} 15264 15265@Article{ whitehead1949, 15266 title = {Combinatorial homotopy. I}, 15267 author = {John HC Whitehead}, 15268 journal = {Bulletin of the American Mathematical Society}, 15269 volume = {55}, 15270 number = {3. P1}, 15271 pages = {213--245}, 15272 year = {1949}, 15273 publisher = {American Mathematical Society} 15274} 15275 15276@Article{ beylkincoifmanrokhlin91, 15277 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 15278 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 15279 journal = {Communications on Pure and Applied Mathematics}, 15280 volume = {44}, 15281 pages = {141--183}, 15282 year = {1991} 15283} 15284 15285@Book{ wesseling92, 15286 author = {Pieter Wesseling}, 15287 title = {An Introduction to Multigrid Methods}, 15288 publisher = {John Wiley and Sons}, 15289 year = {1992} 15290} 15291 15292@Book{ grakakos04, 15293 author = {Loukas Grakakos}, 15294 title = {Classical and Modern Fourier Analysis}, 15295 publisher = {Pearson Education}, 15296 address = {New Jersey}, 15297 year = {2004} 15298} 15299 15300@Misc{ hlib-web-page, 15301 key = {HLib}, 15302 title = {{HLib} {Web} page}, 15303 note = {{\texttt{http://www.hlib.org/}}}, 15304 annote = {Hierarchical matrices for fast integral transform} 15305} 15306 15307@Article{ hackbusch99, 15308 author = {Wolfgang Hackbusch}, 15309 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 15310 Introduction to {$\mathcal H$}-matrices}, 15311 journal = {Computing}, 15312 volume = {62}, 15313 pages = {89--108}, 15314 year = {1999} 15315} 15316 15317@TechReport{ kay1999green, 15318 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 15319 equations}, 15320 author = {Kay, D. and Loghin, D.}, 15321 year = {1999}, 15322 institution = {Oxford University Computing Laboratory}, 15323 number = {99/06} 15324} 15325 15326@Article{ bebendorf2003existence, 15327 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 15328 elliptic operators with {$L^\infty$}-coefficients}, 15329 author = {Bebendorf, M. and Hackbusch, W.}, 15330 journal = {Numerische Mathematik}, 15331 volume = {95}, 15332 number = {1}, 15333 pages = {1--28}, 15334 year = {2003}, 15335 publisher = {Springer} 15336} 15337 15338@Article{ hackbusch2005direct, 15339 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 15340 H$}-matrix approximation}, 15341 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 15342 journal = {Computing and Visualization in Science}, 15343 volume = {8}, 15344 number = {3}, 15345 pages = {179--188}, 15346 year = {2005}, 15347 publisher = {Springer} 15348} 15349 15350@TechReport{ duphof2003, 15351 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 15352 Logg and L. R. Scott}, 15353 title = {The {FE}ni{CS} project}, 15354 institution = {Chalmers Finite Element Center Preprint Series}, 15355 number = {2003--21}, 15356 year = {2003} 15357} 15358 15359@Article{ flame01, 15360 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 15361 Geijn}, 15362 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 15363 journal = {Transactions on Mathematical Software}, 15364 volume = {27}, 15365 number = {4}, 15366 year = {2001}, 15367 pages = {422--455} 15368} 15369 15370@Article{ puschel05, 15371 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 15372 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 15373 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 15374 Nick Rizzolo}, 15375 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 15376 journal = {Proceedings of the IEEE}, 15377 volume = {93}, 15378 number = {2}, 15379 year = {2005}, 15380 note = {special issue on "Program Generation, Optimization, and Adaptation"} 15381} 15382 15383@Article{ kirbylogg06, 15384 author = {Robert C. Kirby and Anders Logg}, 15385 title = {A compiler for variational forms}, 15386 journal = {ACM Transactions on Mathematical Software}, 15387 volume = {32}, 15388 number = {3}, 15389 year = {2006}, 15390 issn = {0098-3500}, 15391 pages = {417--444}, 15392 doi = {10.1145/1163641.1163644}, 15393 publisher = {ACM Press}, 15394 address = {New York, NY} 15395} 15396 15397@Article{ kirbylogg07, 15398 author = {Robert C. Kirby and Anders Logg}, 15399 title = {Efficient compilation of a class of variational forms}, 15400 journal = {ACM Transactions on Mathematical Software}, 15401 volume = {33}, 15402 number = {3}, 15403 year = {2007}, 15404 issn = {0098-3500}, 15405 pages = {17}, 15406 doi = {10.1145/1268769.1268771}, 15407 publisher = {ACM Press}, 15408 address = {New York, NY} 15409} 15410 15411@Article{ bankdupont81, 15412 author = {Randolph Bank and Todd Dupont}, 15413 title = {An optimal order process for solving finite element equations}, 15414 journal = {Mathematics of Computation}, 15415 volume = {36}, 15416 pages = {35--51}, 15417 year = {1981} 15418} 15419 15420@TechReport{ adams00, 15421 author = {Mark F. Adams}, 15422 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 15423 in solid mechanics}, 15424 institution = {UC Berkeley}, 15425 number = {CSD-00-1103}, 15426 year = {2000}, 15427 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 15428} 15429 15430@Article{ bergengradlhuelsemannruede06, 15431 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 15432 title = {A Massively Parallel Multigrid Method for Finite Elements}, 15433 journal = {Computing in Science \& Engineering}, 15434 volume = {8}, 15435 number = {6}, 15436 pages = {56--62}, 15437 year = {2006} 15438} 15439 15440@MastersThesis{ brunethesis08, 15441 author = {Peter R. Brune}, 15442 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 15443 school = {University of Chicago}, 15444 address = {Chicago, IL}, 15445 year = {2008}, 15446 month = {February} 15447} 15448 15449@Article{ arnoldwinther02, 15450 author = {Douglas N. Arnold and Ragnar Winther}, 15451 title = {Mixed finite elements for elasticity}, 15452 journal = {Numerische Mathematik}, 15453 volume = {92}, 15454 number = {3}, 15455 month = {September}, 15456 year = {2002}, 15457 pages = {401--419}, 15458 doi = {10.1007/s002110100348} 15459} 15460 15461@Article{ arnoldfalkwinther06, 15462 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 15463 title = {Finite element exterior calculus, homological techniques, and applications}, 15464 journal = {Acta Numerica}, 15465 year = {2006}, 15466 volume = {15}, 15467 pages = {1--155}, 15468 publisher = {Cambridge University Press}, 15469 doi = {10.1017/S0962492906210018} 15470} 15471 15472@Article{ kirby04, 15473 author = {Robert C. Kirby}, 15474 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 15475 functions}, 15476 journal = {ACM Transactions on Mathematical Software}, 15477 volume = {30}, 15478 number = {4}, 15479 year = {2004}, 15480 issn = {0098-3500}, 15481 pages = {502--516}, 15482 doi = {10.1145/1039813.1039820}, 15483 publisher = {ACM Press}, 15484 address = {New York, NY} 15485} 15486 15487@Article{ kirby06, 15488 author = {Robert C. Kirby}, 15489 title = {Optimizing {FIAT} with level 3 {BLAS}}, 15490 journal = {ACM Transactions on Mathematical Software}, 15491 volume = {32}, 15492 number = {2}, 15493 year = {2006}, 15494 issn = {0098-3500}, 15495 pages = {223--235}, 15496 doi = {10.1145/1141885.1141889}, 15497 publisher = {ACM Press}, 15498 address = {New York, NY} 15499} 15500 15501@Misc{ bluecrystal08, 15502 author = {{B}lue {C}rystal Cluster}, 15503 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 15504 year = {2008}, 15505 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 15506} 15507 15508@Article{ beylkin95, 15509 author = {Gregory Beylkin}, 15510 title = {On the Fast Fourier Transform of Functions With Singularities}, 15511 journal = {Applied and Computational Harmonic Analysis}, 15512 volume = {2}, 15513 pages = {363--381}, 15514 year = {1995} 15515} 15516 15517@InProceedings{ riehl08, 15518 author = {Jonathan Riehl}, 15519 title = {Implementing the MyFEM Embedded Domain-specific Language}, 15520 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 15521 Development (DSPD'08)}, 15522 address = {Nashville, TN}, 15523 year = {2008} 15524} 15525 15526@Article{ appel85, 15527 author = {Andrew W. Appel}, 15528 date-added = {2008-02-27 12:23:39 +0000}, 15529 date-modified = {2008-02-27 12:24:02 +0000}, 15530 doi = {10.1137/0906008}, 15531 journal = {SIAM Journal on Scientific and Statistical Computing}, 15532 keywords = {treecodes}, 15533 number = {1}, 15534 pages = {85-103}, 15535 publisher = {SIAM}, 15536 title = {An Efficient Program for Many-Body Simulation}, 15537 volume = {6}, 15538 year = {1985} 15539} 15540 15541@Article{ ewald21, 15542 author = {{Ewald}, P.~P.}, 15543 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 15544 journal = {Annalen der Physik}, 15545 year = {1921}, 15546 volume = {369}, 15547 pages = {253-287}, 15548 doi = {10.1002/andp.19213690304}, 15549 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 15550 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 15551} 15552 15553@Article{ greengardrokhlin87, 15554 author = {L. Greengard and V. Rokhlin}, 15555 date-added = {2008-02-15 18:43:55 +0000}, 15556 date-modified = {2008-02-26 20:09:11 +0000}, 15557 doi = {10.1016/0021-9991(87)90140-9}, 15558 journal = {J. Comput.\ Phys.}, 15559 keywords = {FMM}, 15560 number = {2}, 15561 pages = {325--348}, 15562 title = {A Fast Algorithm for Particle Simulations}, 15563 url = {citeseer.ist.psu.edu/greengard87fast.html}, 15564 volume = {73}, 15565 year = {1987}, 15566 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 15567} 15568 15569@Article{ greengardrokhlin97, 15570 author = {L. Greengard and V. Rokhlin}, 15571 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 15572 Dimensions}, 15573 journal = {Acta Numerica}, 15574 volume = {6}, 15575 year = {1997}, 15576 pages = {229--269} 15577} 15578 15579@Article{ luchenghuangmccammon06, 15580 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 15581 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 15582 systems}, 15583 journal = {PNAS}, 15584 doi = {10.1073/pnas.0605166103}, 15585 volume = {102}, 15586 number = {51}, 15587 year = {2006}, 15588 pages = {19314--19319} 15589} 15590 15591@Article{ schussnadlereisenberg01, 15592 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 15593 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 15594 from a molecular model}, 15595 journal = {Physical Review E}, 15596 volume = {64}, 15597 number = {3}, 15598 year = {2001} 15599} 15600 15601@Book{ hairerlubichwanner02, 15602 author = {E. Hairer and Ch. Lubich and G. Wanner}, 15603 title = {Geometric Numerical Integration}, 15604 publisher = {Springer-Verlag}, 15605 address = {Berlin Heidelberg}, 15606 year = {2002} 15607} 15608 15609@Article{ holstbakerwang00, 15610 author = {M. Holst and N. Baker and F. Wang}, 15611 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 15612 equation on massively parallel computers}, 15613 journal = {Journal of Computational Chemistry}, 15614 volume = {21}, 15615 year = {2000} 15616} 15617 15618@Book{ hockneyeastwood81, 15619 author = {R. Hockney and J. Eastwood}, 15620 title = {Computer simulation using particles}, 15621 publisher = {McGraw-Hill}, 15622 address = {New York}, 15623 year = {1981} 15624} 15625 15626@Article{ lutydavistironigunsteren94, 15627 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 15628 Gunsteren}, 15629 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 15630 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 15631 journal = {Molecular Simulation}, 15632 volume = {14}, 15633 number = {1}, 15634 year = {1994}, 15635 pages = {11--20} 15636} 15637 15638@Book{ briggshensonmccormick00, 15639 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 15640 title = {A Multigrid Tutorial (2nd ed.)}, 15641 year = {2000}, 15642 isbn = {0-89871-462-1}, 15643 publisher = {Society for Industrial and Applied Mathematics}, 15644 address = {Philadelphia, PA} 15645} 15646 15647@Article{ chartier2003spectral, 15648 title = {Spectral AMGe ($\rho$ AMGe)}, 15649 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 15650 McCormick, S and Ruge, J and Vassilevski, PS}, 15651 journal = {SIAM Journal on Scientific Computing}, 15652 volume = {25}, 15653 number = {1}, 15654 pages = {1--26}, 15655 year = {2003}, 15656 publisher = {SIAM} 15657} 15658 15659@Article{ galvis2010domain, 15660 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 15661 media}, 15662 author = {Galvis, Juan and Efendiev, Yalchin}, 15663 journal = {Multiscale Modeling \& Simulation}, 15664 volume = {8}, 15665 number = {4}, 15666 pages = {1461--1483}, 15667 year = {2010}, 15668 publisher = {SIAM} 15669} 15670 15671@Book{ brennerscott02, 15672 author = {Susanne~C. Brenner and L.~Ridgway Scott}, 15673 title = {The mathematical theory of finite element methods}, 15674 year = {2002}, 15675 isbn = {0-38795-451-1}, 15676 publisher = {Springer}, 15677 pages = {361} 15678} 15679 15680@Book{ trefethenbau97, 15681 author = {Lloyd N. Trefethen and David {Bau, III}}, 15682 title = {Numerical Linear Algebra}, 15683 publisher = {Society for Industrial and Applied Mathematics}, 15684 address = {Philadelphia, PA}, 15685 pages = {xii + 361}, 15686 year = {1997}, 15687 isbn = {0-89871-361-7}, 15688 isbn-13 = {978-0-89871-361-9}, 15689 lccn = {QA184 .T74 1997}, 15690 mrclass = {65-01 (65-02 65Fxx)}, 15691 mrnumber = {MR1444820 (98k:65002)}, 15692 mrreviewer = {Moody T. Chu}, 15693 bibdate = {Wed Jan 07 15:23:19 1998}, 15694 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 15695} 15696 15697@Article{ liptonreagan2014, 15698 title = {Quantum Algorithms via Linear Algebra: A Primer}, 15699 author = {Richard J Lipton and Kenneth W Regan}, 15700 pages = {206}, 15701 isbn = {978-0-26202-839-4}, 15702 year = {2014} 15703} 15704 15705@InProceedings{ rhea08, 15706 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 15707 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 15708 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 15709 booktitle = {Proceedings of IEEE/ACM SC '08}, 15710 year = {2008} 15711} 15712 15713@Misc{ bursteddewilcox09, 15714 author = {Carsten Burstedde and Lucas~C. Wilcox}, 15715 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 15716 note = {in preparation} 15717} 15718 15719@Article{ skeeltezcanhardy02, 15720 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 15721 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 15722 journal = {J. Comp. Chem.}, 15723 volume = {23}, 15724 pages = {673--684}, 15725 year = {2002} 15726} 15727 15728@Article{ verschelde99, 15729 author = {Jan Verschelde}, 15730 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 15731 homotopy continuation}, 15732 journal = {ACM Trans. Math. Softw.}, 15733 volume = {25}, 15734 number = {2}, 15735 issn = {0098-3500}, 15736 pages = {251--276}, 15737 doi = {10.1145/317275.317286}, 15738 publisher = {ACM}, 15739 address = {New York, NY}, 15740 year = {1999} 15741} 15742 15743@InProceedings{ sommeseverscheldewampler08, 15744 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 15745 title = {Solving Polynomial Systems Equation by Equation}, 15746 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 15747 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 15748 pages = {133--152}, 15749 publisher = {Springer-Verlag}, 15750 year = {2008} 15751} 15752 15753@Article{ phanthientanner77, 15754 author = {N. Phan-Thien and R.~I. Tanner}, 15755 title = {A new constitutive equation derived from network theory}, 15756 journal = {J. Non-Newt. Fluid Mech.}, 15757 volume = {2}, 15758 pages = {353}, 15759 year = {1977} 15760} 15761 15762@Manual{ sage, 15763 key = {SAGE}, 15764 author = {W.\thinspace{}A. Stein and others}, 15765 organization = {The Sage~Development Team}, 15766 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 15767 note = {{\tt http://www.sagemath.org}}, 15768 year = {2009} 15769} 15770 15771@Misc{ bateshauensteinsommesewampler06, 15772 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 15773 Wampler}, 15774 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 15775 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 15776} 15777 15778@Article{ archer09, 15779 author = {A. J. Archer}, 15780 collaboration = {}, 15781 title = {Dynamical density functional theory for molecular and colloidal fluids: A 15782 microscopic approach to fluid mechanics}, 15783 publisher = {AIP}, 15784 year = {2009}, 15785 journal = {The Journal of Chemical Physics}, 15786 volume = {130}, 15787 number = {1}, 15788 eid = {014509}, 15789 numpages = {8}, 15790 pages = {014509}, 15791 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 15792 transition; statistical distributions; stochastic processes}, 15793 doi = {10.1063/1.3054633} 15794} 15795 15796@Article{ giesekus1966, 15797 author = {Hanswalter Giesekus}, 15798 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 15799 journal = {Rheologica Acta}, 15800 publisher = {Springer Berlin / Heidelberg}, 15801 volume = {5}, 15802 number = {1}, 15803 month = {March}, 15804 year = {1966}, 15805 doi = {10.1007/BF01973575}, 15806 pages = {29-35} 15807} 15808 15809@Article{ baaijens98, 15810 author = {F.P. Baaijens}, 15811 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 15812 journal = {Journal of Non-Newtonian Fluid Mechanics}, 15813 volume = {79}, 15814 year = {1998}, 15815 pages = {361--385} 15816} 15817 15818@Book{ joseph90, 15819 author = {D.~D. Joseph}, 15820 title = {Fluid Dynamics of Viscoelastic Liquids}, 15821 publisher = {Springer}, 15822 address = {New York, NY}, 15823 year = {1990} 15824} 15825 15826@Article{ oldroyd50, 15827 author = {J.~G. Oldroyd}, 15828 title = {On the Formulation of Rheological Equations of State}, 15829 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 15830 Sciences}, 15831 volume = {200}, 15832 year = {1950}, 15833 pages = {523--541} 15834} 15835 15836@InProceedings{ bynasungroppthakur04, 15837 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 15838 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 15839 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 15840 year = {2004} 15841} 15842 15843@Book{ pozrikidis07, 15844 author = {C. Pozrikidis}, 15845 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 15846 publisher = {Kluwer (Springer)}, 15847 pages = {675}, 15848 year = {2001}, 15849 isbn = {0792373510} 15850} 15851 15852@Misc{ kritzkeyesfsp07, 15853 author = {A. Kritz and D. Keyes}, 15854 title = {{Fusion Simulation Project Workshop Report}}, 15855 month = {July}, 15856 year = {2007}, 15857 note = {Available via 15858 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 15859} 15860 15861@Misc{ dahlburg02, 15862 author = {J. {Dahlburg (Chair)}}, 15863 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 15864 year = {2002}, 15865 note = {Available via 15866 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 15867} 15868 15869@Misc{ brown08, 15870 author = {D. {Brown (Chair)}}, 15871 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 15872 to the Future}}, 15873 year = {2008}, 15874 howpublished = {Office of Science, U.S. Department of Energy}, 15875 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 15876} 15877 15878@Misc{ crosscutting10, 15879 author = {D. Brown and P. {Messina (Chairs)}}, 15880 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 15881 Exascale}}, 15882 year = {2010}, 15883 howpublished = {Office of Science, U.S. Department of Energy}, 15884 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 15885} 15886 15887@Misc{ extreme-scale-solvers-workshop12, 15888 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 15889 L.C. McInnes and E. Ng and S. Wild}, 15890 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 15891 Architectures}, 15892 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 15893 note = {{Washington, DC}, March 8-9, 2012}, 15894 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 15895 year = {2012} 15896} 15897 15898@Misc{ monizrosner09, 15899 author = {{E. Moniz and R. Rosner}}, 15900 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 15901 and Simulation at the Extreme Scale}}, 15902 month = {May}, 15903 year = {2009}, 15904 note = {See 15905 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 15906} 15907 15908@Misc{ blanford08, 15909 author = {{R. Blandord (Chair)}}, 15910 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 15911 Computing at the Extreme Scale}}, 15912 month = {Dec}, 15913 year = {2008}, 15914 note = {See 15915 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 15916} 15917 15918@Misc{ exascale07, 15919 author = {H. Simon and T. Zacharia and R. Stevens}, 15920 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 15921 year = {2007}, 15922 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 15923} 15924 15925@Misc{ ascrbreakthroughs08, 15926 author = {{Panel on Recent Significant Advancements in Computational Science}}, 15927 title = {Breakthroughs}, 15928 year = {2008}, 15929 note = {See 15930 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 15931} 15932 15933@Misc{ petsc-rd100-2009, 15934 author = {{R\&D Magazine}}, 15935 title = {{PETSc} {R}\&{D} 100 Award}, 15936 year = {2009}, 15937 note = {See 15938 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 15939} 15940 15941@Article{ compass-scidac08, 15942 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 15943 R. Ryne}, 15944 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 15945 Computational Science for Future Accelerators and Accelerator Technologies}, 15946 journal = {J. Phys.: Conf. Ser.}, 15947 volume = {125}, 15948 year = {2008}, 15949 pages = {012001}, 15950 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 15951} 15952 15953@Article{ compass-amundson-scidac08, 15954 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 15955 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 15956 Stoltz}, 15957 journal = {J. Phys.: Conf. Ser.}, 15958 volume = {125}, 15959 year = {2008} 15960} 15961 15962@InProceedings{ muszala09, 15963 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 15964 Simulations}, 15965 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 15966 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 15967 {(CBHPC 2009)}}, 15968 year = {2009} 15969} 15970 15971@Article{ gaston09, 15972 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 15973 Equations}, 15974 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 15975 journal = {Nuclear Engineering and Design}, 15976 volume = {239}, 15977 number = {10}, 15978 year = {2009}, 15979 pages = {1768 -- 1778} 15980} 15981 15982@Article{ gaston09b, 15983 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 15984 Engineering}, 15985 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 15986 and C. Permann and W. Taitano}, 15987 journal = {J. Phys.: Conf. Ser.}, 15988 volume = {180}, 15989 year = {2009}, 15990 pages = {012012} 15991} 15992 15993@Article{ newman09, 15994 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 15995 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 15996 author = {Chris Newman and Glen Hansen and Derek Gaston}, 15997 journal = {Journal of Nuclear Materials}, 15998 volume = {392}, 15999 issue = {1}, 16000 year = {2009}, 16001 pages = {6 -- 15} 16002} 16003 16004@Misc{ www:fenics, 16005 author = {{FE}ni{CS}}, 16006 title = {{FE}ni{CS} Project}, 16007 howpublished = {\url{http://www.fenics.org/}}, 16008 year = {2018} 16009} 16010 16011@InProceedings{ zwart08, 16012 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 16013 Systems}, 16014 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 16015 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 16016 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 16017 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 16018 booktitle = {Proceedings of ICCS 2008}, 16019 year = {2008} 16020} 16021 16022@Article{ klocknerwarburtonbridgehesthaven09, 16023 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 16024 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 16025 journal = {J. Comput. Phys.}, 16026 volume = {228}, 16027 number = {21}, 16028 year = {2009}, 16029 issn = {0021-9991}, 16030 pages = {7863--7882}, 16031 doi = {10.1016/j.jcp.2009.06.041}, 16032 publisher = {Academic Press Professional}, 16033 address = {San Diego, CA} 16034} 16035 16036@PhDThesis{ rankin99, 16037 author = {Rankin, W. T.}, 16038 keywords = {FMM, parallel FMM}, 16039 school = {Department of Electrical and Computer Engineering, Duke University}, 16040 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 16041 year = {1999} 16042} 16043 16044@InProceedings{ warrensalmon93, 16045 abstract = {We report on an efficient adaptive N-body method which we have recently designed 16046 and implemented. The algorithm computes the forces on an arbitrary distribution of 16047 bodies in a time which scales as N log N with the particle number. The accuracy of 16048 the force calculations is analytically bounded, and can be adjusted via a user 16049 defined parameter between a few percent relative accuracy, down to machine 16050 arithmetic accuracy. Instead of using pointers to indicate the topology of the 16051 tree, we identify...}, 16052 address = {New York}, 16053 author = {Warren, Michael S. and Salmon, John K.}, 16054 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 16055 citeulike-article-id={580952}, 16056 keywords = {oct-tree}, 16057 pages = {12--21}, 16058 publisher = {ACM}, 16059 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 16060 year = {1993}, 16061 doi = {10.1145/169627.169640}, 16062 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 16063} 16064 16065@Unpublished{ cruzwccm10, 16066 author = {Felipe A. Cruz}, 16067 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 16068 note = {Presentation at WCCM 2010, Sydney Australia}, 16069 year = {2010} 16070} 16071 16072@Article{ mcguffee06, 16073 author = {S.~R. {McGuffee} and A.~H. Elcock}, 16074 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 16075 of salt, {pH}, point mutations, and protein concentration in simulations of 16076 1000-molecule systems}, 16077 journal = {Journal of the American Chemical Society}, 16078 volume = {128}, 16079 pages = {12098--12110}, 16080 year = {2006} 16081} 16082 16083@Article{ nilsencaihoylandlangtangen10, 16084 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 16085 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 16086 in Python}}, 16087 journal = {ArXiv e-prints}, 16088 archiveprefix = {arXiv}, 16089 eprint = {1002.0705}, 16090 primaryclass = {cs.DC}, 16091 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 16092 - Programming Languages}, 16093 year = {2010}, 16094 month = feb, 16095 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 16096 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16097} 16098 16099@Misc{ mcinnes:siam09:minisymposium, 16100 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 16101 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 16102 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 16103 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 16104 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 16105 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 16106 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 16107 Austin).} 16108} 16109 16110@Misc{ mcinnes:fsp-summary:feb2011, 16111 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 16112 title = {Solvers and Time Integration Breakout Summary}, 16113 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 16114 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 16115} 16116 16117@Misc{ dvi-materials:siamcse11, 16118 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 16119 Materials}, 16120 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 16121 Smith and L. Wang}, 16122 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 16123 and Engineering, March 3, 2011} 16124} 16125 16126@Misc{ jamroz:cemm10, 16127 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 16128 author = {B. Jamroz and S. Kruger and T. Austin}, 16129 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 16130} 16131 16132@Misc{ kruger:feb4-2011, 16133 title = {personal communication}, 16134 author = {S. Kruger}, 16135 note = {February, 2011} 16136} 16137 16138@Article{ elman1996, 16139 author = {H.C. Elman}, 16140 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 16141 viscosity}, 16142 journal = {SIAM J. Sci. Comput.}, 16143 volume = {20}, 16144 year = {1996}, 16145 pages = {1299--1316} 16146} 16147 16148@Article{ kayloghinwathen2002, 16149 author = {D. Kay and D. Loghin and A. Wathen}, 16150 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 16151 journal = {SIAM J. Sci. Comput.}, 16152 volume = {24}, 16153 year = {2002}, 16154 pages = {237--256} 16155} 16156 16157@Article{ elmanhowleshadidshuttleworthtuminaro2006, 16158 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 16159 title = {Block preconditioners based on approximate commutators}, 16160 journal = {SIAM J. Sci. Comput.}, 16161 volume = {27}, 16162 number = {5}, 16163 year = {2006}, 16164 pages = {1651--1668} 16165} 16166 16167@Article{ braesssarazin1997, 16168 author = {Dietrich Braess and Regina Sarazin}, 16169 title = {An efficient smoother for the {Stokes} problem}, 16170 journal = {Applied Numerical Mathematics}, 16171 volume = {23}, 16172 number = {1}, 16173 year = {1997}, 16174 pages = {3--19}, 16175 doi = {10.1016/S0168-9274(96)00059-1} 16176} 16177 16178@Article{ wright2001large, 16179 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 16180 author = {Wright, T.G. and Trefethen, L.N.}, 16181 journal = {SIAM Journal on Scientific Computing}, 16182 volume = {23}, 16183 pages = {591}, 16184 year = {2001} 16185} 16186 16187@Misc{ wright2002eigtool, 16188 title = {Eig{T}ool}, 16189 author = {Wright, T.G. and Trefethen, LN}, 16190 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 16191 year = {2002} 16192} 16193 16194@Misc{ visit-web-site, 16195 key = {{VisIt}}, 16196 title = {{VisIt web site}}, 16197 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 16198 url = {http://wci.llnl.gov/codes/visit/}, 16199 year = {2011} 16200} 16201 16202@Book{ trefethen1996, 16203 title = {Finite difference and spectral methods for ordinary and partial differential 16204 equations}, 16205 author = {Lloyd Nicholas Trefethen}, 16206 year = {1996}, 16207 publisher = {Cornell University-Department of Computer Science and Center for Applied 16208 Mathematics} 16209} 16210 16211@Book{ trefethen2005spectra, 16212 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 16213 author = {Trefethen, L.N. and Embree, M.}, 16214 year = {2005}, 16215 publisher = {Princeton University Press} 16216} 16217 16218@Article{ gomez2010isogeometric, 16219 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 16220 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 16221 journal = {Computer Methods in Applied Mechanics and Engineering}, 16222 volume = {199}, 16223 number = {25-28}, 16224 pages = {1828--1840}, 16225 issn = {0045-7825}, 16226 year = {2010}, 16227 publisher = {Elsevier} 16228} 16229 16230@Article{ gomez2008isogeometric, 16231 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 16232 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 16233 journal = {Computer Methods in Applied Mechanics and Engineering}, 16234 volume = {197}, 16235 number = {49-50}, 16236 pages = {4333--4352}, 16237 year = {2008}, 16238 publisher = {Elsevier} 16239} 16240 16241@Misc{ fastmath:project, 16242 author = {Lori {Diachin (PI)}}, 16243 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 16244 (FASTMath) Institute}}, 16245 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 16246} 16247 16248@Misc{ exascale-software:proposal, 16249 author = {Peter {Beckman (PI)}}, 16250 title = {{Exascale Software Center}}, 16251 note = {proposal to DOE} 16252} 16253 16254@Misc{ imex:project, 16255 author = {Barry {Smith (PI)}}, 16256 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 16257 Multimodel PDEs}}, 16258 note = {DOE ASCR applied math project} 16259} 16260 16261@Misc{ intel-mic:website, 16262 author = {Intel}, 16263 title = {{Many Integrated Core Architecture}}, 16264 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 16265} 16266 16267@Article{ dudson:2009, 16268 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 16269 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 16270 journal = {Computer Physics Communications}, 16271 volume = {180}, 16272 pages = {1467}, 16273 year = {2009} 16274} 16275 16276@Article{ umansky:2009, 16277 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 16278 title = {{Status and verification of edge plasma turbulence code BOUT}}, 16279 journal = {Computer Physics Communications}, 16280 year = {2009}, 16281 volume = {180}, 16282 pages = {887-903} 16283} 16284 16285@Article{ xu:1998, 16286 author = {X.Q. Xu and R.H. Cohen}, 16287 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 16288 journal = {Computer Physics Communications}, 16289 year = {1998}, 16290 volume = {36}, 16291 number = {1-2}, 16292 pages = {158} 16293} 16294 16295@Article{ tron:1999, 16296 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 16297 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 16298 journal = {SIAM Journal on Optimization}, 16299 volume = {9}, 16300 number = {4}, 16301 pages = {1100-1127}, 16302 year = {1999} 16303} 16304 16305@Article{ stubenamg, 16306 author = {K. St\"{u}ben}, 16307 title = {A review of algebraic multigrid}, 16308 journal = {J. Comput. Appl. Math.}, 16309 volume = {128}, 16310 number = {1-2}, 16311 year = {2001}, 16312 issn = {0377-0427}, 16313 pages = {281--309}, 16314 doi = {10.1016/S0377-0427(00)00516-1}, 16315 publisher = {Elsevier Science Publishers B. V.}, 16316 address = {Amsterdam, The Netherlands, The Netherlands} 16317} 16318 16319@Article{ feuchtermg, 16320 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 16321 title = {Bridging the gap between geometric and algebraic multigrid methods}, 16322 journal = {Computing and visualization in science}, 16323 publisher = {Springer}, 16324 volume = {6}, 16325 number = {1}, 16326 year = {2003}, 16327 pages = {1--13} 16328} 16329 16330@Article{ chowmgsmoothness, 16331 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 16332 only attempts to interpolate in the directions of geometrical smoothness. These 16333 directions are determined by analyzing samples of algebraically smooth error, e. 16334 Neighboring grid points i and j are called smoothly coupled if e i and e j are 16335 consistently nearby in value. In addition, these dierences may be used to dene 16336 interpolation weights. These new ideas may be incorporated into the algebraic 16337 multigrid method. Test results show that the new method can have much lower grid 16338 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 16339 author = {Chow, Edmond}, 16340 citeulike-article-id={7675372}, 16341 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16342 journal = {American Journal of Mathematics}, 16343 keywords = {fem, multigrid}, 16344 pages = {197--215}, 16345 posted-at = {2010-08-17 23:29:51}, 16346 priority = {2}, 16347 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 16348 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 16349 volume = {65}, 16350 year = {2001} 16351} 16352 16353@Article{ jonesamge, 16354 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 16355 elements) method based on element agglomeration. In the method, coarse grid 16356 elements are formed by agglomerating fine grid elements. Compatible interpolation 16357 operators are constructed which yield coarse grid basis functions with a minimal 16358 energy property. Heuristics based on interpolation quality measures are used to 16359 guide the agglomeration procedure. The performance of the resulting method is 16360 demonstrated in two-level numerical experiments.}}, 16361 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 16362 citeulike-article-id={8598569}, 16363 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16364 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 16365 journal = {SIAM Journal on Scientific Computing}, 16366 keywords = {amg, fem, multigrid}, 16367 number = {1}, 16368 pages = {109--133}, 16369 posted-at = {2011-01-13 18:05:55}, 16370 priority = {2}, 16371 publisher = {SIAM}, 16372 title = {{AMGE Based on Element Agglomeration}}, 16373 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 16374 volume = {23}, 16375 year = {2001} 16376} 16377 16378@Article{ saad1993, 16379 author = {Saad, Youcef}, 16380 doi = {10.1137/0914028}, 16381 issn = {10648275}, 16382 journal = {SIAM Journal on Scientific Computing}, 16383 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 16384 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 16385 precondition-,preconditioned conju-,subject classi cations,variable 16386 preconditioners}, 16387 number = {2}, 16388 pages = {461--469}, 16389 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 16390 volume = {14}, 16391 year = {1993} 16392} 16393 16394@Misc{ path:homepage, 16395 author = {S. Dirkse and M. Ferris and T. 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Moresi and Shijie Zhong and Michael Gurnis}, 16606 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 16607 viscosity}, 16608 journal = {Physics of the Earth and Planetary Interiors}, 16609 volume = {97}, 16610 pages = {83-–94}, 16611 year = {1996} 16612} 16613 16614@Article{ moresisolomatov95, 16615 author = {Louis N. Moresi and V. S. Solomatov}, 16616 title = {Numerical investigation of {2D} convection with extremely large viscosity 16617 variations}, 16618 journal = {Physics of Fluids}, 16619 volume = {7}, 16620 number = {9}, 16621 pages = {2154-–2162}, 16622 year = {1995} 16623} 16624 16625@Article{ chenmolnar83, 16626 author = {W.-P. Chen and P. 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Watts}, 16646 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 16647 brulee?}, 16648 journal = {GSA Today}, 16649 volume = {16}, 16650 pages = {4–-10}, 16651 year = {2006} 16652} 16653 16654@InProceedings{ yang:brent:2002, 16655 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 16656 Parallel Distributed Memory Architectures}, 16657 author = {Laurence T. Yang and Richard Brent}, 16658 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 16659 for Parallel Processing}, 16660 year = {2002}, 16661 publisher = {IEEE} 16662} 16663 16664@Article{ demmel2008communication, 16665 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 16666 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 16667 journal = {Arxiv preprint arXiv:0808.2664}, 16668 year = {2008} 16669} 16670 16671@Article{ demmel09, 16672 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 16673 title = {Communication-optimal Iterative Methods}, 16674 journal = {Journal of Physics: Conf. 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Rall}, 16702 title = {Computational solution of nonlinear operator equations}, 16703 publisher = {Krieger Pub Co.}, 16704 pages = {225}, 16705 year = {1969} 16706} 16707 16708@Article{ fletcherreeves1964, 16709 author = {R. Fletcher and C. M. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 16744} 16745 16746@Article{ keyesmcinneswoodwardetal13, 16747 title = {Multiphysics Simulations: Challenges and Opportunities}, 16748 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 16749 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 16750 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 16751 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 16752 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 16753 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 16754 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 16755 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 16756 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 16757 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 16758 journal = {International Journal of High Performance Computing Applications}, 16759 month = {Feb}, 16760 year = {2013}, 16761 volume = {27}, 16762 number = {1}, 16763 pages = {4--83}, 16764 doi = {10.1177/1094342012468181}, 16765 note = {Special issue}, 16766 abstract = {We consider multiphysics applications from algorithmic and architectural 16767 perspectives, where ``algorithmic'' includes both mathematical analysis and 16768 computational complexity and ``architectural'' includes both software and hardware 16769 environments. Many diverse multiphysics applications can be reduced, en route to 16770 their computational simulation, to a common algebraic coupling paradigm. 16771 Mathematical analysis of multiphysics coupling in this form is not always 16772 practical for realistic applications, but model problems representative of 16773 applications discussed herein can provide insight. A variety of software 16774 frameworks for multiphysics applications have been constructed and refined within 16775 disciplinary communities and executed on leading-edge computer systems. We examine 16776 several of these, expose some commonalities among them, and attempt to extrapolate 16777 best practices to future systems. From our study, we summarize challenges and 16778 forecast opportunities.} 16779} 16780 16781@Misc{ rosner10, 16782 author = {Robert {Rosner (Chair)}}, 16783 title = {{The Opportunities and Challenges of Exascale Computing}}, 16784 year = {2010}, 16785 howpublished = {Office of Science, U.S. Department of Energy}, 16786 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 16787} 16788 16789@Misc{ kogge2008exascale, 16790 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 16791 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 16792 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 16793 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 16794 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 16795 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 16796 howpublished = {DARPA}, 16797 year = {2008}, 16798 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 16799} 16800 16801@Misc{ doegrandchallengeworkshops, 16802 key = {Office of Science, U.S. Department of Energy}, 16803 title = {{Scientific Grand Challenges Workshop Series}}, 16804 howpublished = {Office of Science, U.S. Department of Energy, see 16805 \url{http://extremecomputing.labworks.org/workshops.stm}} 16806} 16807 16808@Misc{ lawrence2011, 16809 key = {Lawrence}, 16810 title = {{Ernest Orlando Lawrence Award Winners}}, 16811 howpublished = {U.S. Department of Energy, {\footnotesize 16812 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 16813 year = {2011} 16814} 16815 16816@Article{ murphy2000npi, 16817 title = {{A note on preconditioning for indefinite linear systems}}, 16818 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 16819 journal = {SIAM Journal on Scientific Computing}, 16820 volume = {21}, 16821 number = {6}, 16822 pages = {1969--1972}, 16823 year = {2000}, 16824 publisher = {Philadelphia, PA: SIAM, c1993-} 16825} 16826 16827@Article{ elman2011bouyancy, 16828 title = {Fast iterative solvers for buoyancy driven flow problems}, 16829 journal = {Journal of Computational Physics}, 16830 volume = {230}, 16831 number = {10}, 16832 pages = {3900 - 3914}, 16833 year = {2011}, 16834 note = {}, 16835 issn = {0021-9991}, 16836 doi = {10.1016/j.jcp.2011.02.014}, 16837 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 16838 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 16839 Adaptivity, Preconditioning, Algebraic multigrid} 16840} 16841 16842@Article{ dongarrabeckman11, 16843 author = {J. Dongarra and P. Beckman and et al.}, 16844 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 16845 journal = {Int. J. High Perf. Comput. 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Brannick and Robert D. Falgout}, 16898 journal = {SIAM Journal on Scientific Computing}, 16899 volume = {32}, 16900 number = {3}, 16901 pages = {1393--1416}, 16902 url = {http://epubs.siam.org/doi/10.1137/090772216}, 16903 doi = {10.1137/090772216}, 16904 issn = {1064-8275}, 16905 year = {2010} 16906} 16907 16908@Article{ xu2004energy, 16909 title = {On an energy minimizing basis for algebraic multigrid methods}, 16910 author = {Xu, J. and Zikatanov, L.}, 16911 journal = {Computing and Visualization in Science}, 16912 volume = {7}, 16913 number = {3}, 16914 pages = {121--127}, 16915 year = {2004}, 16916 publisher = {Springer} 16917} 16918 16919@Article{ dblp:journals/toms/bakerhlt09, 16920 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 16921 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 16922 journal = {ACM Trans. Math. Softw.}, 16923 volume = {36}, 16924 number = {3}, 16925 year = {2009}, 16926 doi = {10.1145/1527286.1527287}, 16927 bibsource = {DBLP, http://dblp.uni-trier.de} 16928} 16929 16930@Article{ dblp:journals/siamsc/yanggbllhn05, 16931 author = {Chao Yang and Weiguo Gao and Zhaojun Bai and Xiaoye S. Li and Lie-Quan Lee and 16932 Parry Husbands and Esmond G. Ng}, 16933 title = {An Algebraic Substructuring Method for Large-Scale Eigenvalue Calculation}, 16934 journal = {SIAM J. Scientific Computing}, 16935 volume = {27}, 16936 number = {3}, 16937 year = {2005}, 16938 pages = {873-892}, 16939 doi = {10.1137/040613767}, 16940 bibsource = {DBLP, http://dblp.uni-trier.de} 16941} 16942 16943@TechReport{ ml-guide, 16944 author = {M.W. Gee and C.M. Siefert and J.J. Hu and R.S. Tuminaro and M.G. Sala}, 16945 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 16946 institution = {Sandia National Laboratories}, 16947 year = {2006}, 16948 number = {SAND2006-2649} 16949} 16950 16951@Article{ brannick06, 16952 title = {An energy-based AMG coarsening strategy}, 16953 volume = {13}, 16954 doi = {10.1002/nla.480}, 16955 number = {2-3}, 16956 journal = {Numerical Linear Algebra with Applications}, 16957 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 16958 and Ruge, J}, 16959 year = {2006}, 16960 pages = {133--148} 16961} 16962 16963@Article{ olson10, 16964 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 16965 title = {A new perspective on strength measures in algebraic multigrid}, 16966 journal = {Numerical Linear Algebra with Applications}, 16967 volume = {17}, 16968 number = {4}, 16969 pages = {713--733}, 16970 year = {2010}, 16971 publisher = {John Wiley \& Sons, Ltd.}, 16972 issn = {1099-1506}, 16973 doi = {10.1002/nla.669} 16974} 16975 16976@Article{ olson11, 16977 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 16978 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 16979 Minimization}, 16980 journal = {SIAM J. Sci. Comput.}, 16981 issue_date = {April 2011}, 16982 volume = {33}, 16983 issue = {2}, 16984 month = apr, 16985 year = {2011}, 16986 issn = {1064-8275}, 16987 pages = {966--991}, 16988 numpages = {26}, 16989 doi = {10.1137/100803031}, 16990 acmid = {2078825}, 16991 publisher = {Society for Industrial and Applied Mathematics}, 16992 address = {Philadelphia, PA}, 16993 keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed 16994 aggregation} 16995} 16996 16997@Article{ dorit2011, 16998 author = {Dorit Ron and Ilya Safro and Achi Brandt}, 16999 title = {Relaxation-Based Coarsening and Multiscale Graph Organization}, 17000 journal = {Multiscale Modeling {\&} Simulation}, 17001 volume = {9}, 17002 number = {1}, 17003 year = {2011}, 17004 pages = {407-423}, 17005 doi = {10.1137/100791142} 17006} 17007 17008@Article{ chen2011algebraic, 17009 title = {Algebraic distance on graphs}, 17010 author = {Chen, Jie and Safro, Ilya}, 17011 journal = {SIAM Journal on Scientific Computing}, 17012 volume = {33}, 17013 number = {6}, 17014 pages = {3468--3490}, 17015 year = {2011}, 17016 publisher = {SIAM} 17017} 17018 17019@InProceedings{ adams04, 17020 author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.}, 17021 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 17022 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 17023 half a billion degrees of freedom}, 17024 note = {Gordon Bell Award}, 17025 year = {2004} 17026} 17027 17028@Article{ adams03a, 17029 author = {Adams, M.~F.}, 17030 journal = {Numerical Linear Algebra with Applications}, 17031 number = {2-3}, 17032 pages = {141-153}, 17033 title = {Algebraic multigrid methods for constrained linear systems with applications to 17034 contact problems in solid mechanics}, 17035 volume = {11}, 17036 year = {2004} 17037} 17038 17039@Article{ adams-10a, 17040 author = {M. ~F. Adams and Ravi Samtaney and Achi Brandt}, 17041 doi = {10.1016/j.jcp.2010.04.024}, 17042 issn = {0021-9991}, 17043 journal = {Journal of Computational Physics}, 17044 keywords = {Implicit magnetohydrodynamics}, 17045 number = {18}, 17046 pages = {6208 - 6219}, 17047 title = {Toward textbook multigrid efficiency for fully implicit resistive 17048 magnetohydrodynamics}, 17049 volume = {229}, 17050 year = {2010} 17051} 17052 17053@InProceedings{ adams98, 17054 address = {Copper Mountain, CO}, 17055 author = {Adams, M.~F.}, 17056 booktitle = {Proceedings 5th Copper Mountain Conference on Iterative Methods}, 17057 title = {A Parallel Maximal Independent Set Algorithm}, 17058 year = {1998} 17059} 17060 17061@InProceedings{ madaypatera89, 17062 author = {Y. Maday and A. T. Patera}, 17063 title = {Spectral element methods for the {Navier-Stokes} equations}, 17064 editor = {A. K. Noor and J. T. 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P.}, 17360 eprint = {arXiv:1002.0705v1}, 17361 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 17362 parallelization of scientific codes by a function-centric approach in 17363 Python.pdf:pdf}, 17364 journal = {Computational Science \& Discovery}, 17365 keywords = {parallel,programming,python,software}, 17366 mendeley-tags = {parallel,programming,python,software}, 17367 pages = {015003}, 17368 publisher = {IOP Publishing}, 17369 title = {{Simplifying the parallelization of scientific codes by a function-centric 17370 approach in Python}}, 17371 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 17372 volume = {3}, 17373 year = {2010} 17374} 17375 17376@Book{ langtangen09, 17377 author = {Hans Petter Langtangen}, 17378 title = {Python Scripting for Computational Science}, 17379 publisher = {Springer}, 17380 series = {Texts in Computational Science and Engineering}, 17381 pages = {784}, 17382 isbn = {3540739157}, 17383 year = {2009} 17384} 17385 17386@Book{ numpyguide, 17387 author = {Travis E. 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Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 17569 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. Pruneau}, 17570 journal = {Nuovo Cimento}, 17571 volume = {19}, 17572 number = {1}, 17573 pages = {1045--1049}, 17574 year = {1996} 17575} 17576 17577@Article{ minimax1997, 17578 author = {Minimax Collaboration}, 17579 title = {Analysis of Charged Particle/Photon Correlations in Hadronic Multiparticle 17580 Production}, 17581 journal = {Physical Review D}, 17582 volume = {55}, 17583 number = {9}, 17584 year = {1997} 17585} 17586 17587@Article{ minimax2000, 17588 author = {Minimax Collaboration}, 17589 title = {Search for disoriented chiral condensate at the {Fermilab} {Tevatron}}, 17590 journal = {Physical Review D}, 17591 volume = {61}, 17592 number = {3}, 17593 year = {2000} 17594} 17595 17596@Article{ kirbyknepleyloggscott05, 17597 author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. 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Knepley}, 17623 title = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a 17624 Hydration-Shell {Poisson}-{Boltzmann} Model}, 17625 journal = {Biophysical Journal}, 17626 volume = {110}, 17627 number = {3}, 17628 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 17629 doi = {10.1016/j.bpj.2015.11.1766}, 17630 year = {2017} 17631} 17632 17633@Article{ tabrizirahimigoossensknepleybardhan2018, 17634 title = {Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer 17635 Interface Condition (SLIC) Continuum Dielectric Model}, 17636 author = {Amirhossein Molavi Tabrizi and Ali Mehdizadeh Rahimi and Spencer Goossens and 17637 Matthew G. Knepley and Jaydeep P. Bardhan}, 17638 journal = {International Journal of Quantum Chemistry}, 17639 note = {Accepted}, 17640 year = {2018} 17641} 17642 17643@Article{ knepley2010, 17644 author = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. 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A}, 22409 volume = {378}, 22410 number = {20190050}, 22411 doi = {10.1098/rsta.2019.0050}, 22412 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 22413 year = {2020} 22414} 22415 22416@Article{ schoberl1999, 22417 title = {Multigrid methods for a parameter dependent problem in primal variables}, 22418 author = {Joachim Sch{\"o}berl}, 22419 journal = {Numerische Mathematik}, 22420 volume = {84}, 22421 number = {1}, 22422 pages = {97--119}, 22423 year = {1999} 22424} 22425 22426@Article{ wuleexuzikatanov2008, 22427 title = {Convergence analysis on iterative methods for semidefinite systems}, 22428 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 22429 journal = {Journal of Computational Mathematics}, 22430 pages = {797--815}, 22431 year = {2008} 22432} 22433 22434@Article{ maierrannacher2016, 22435 title = {Duality-based adaptivity in finite element discretization of heterogeneous 22436 multiscale problems}, 22437 author = {Maier, Matthias and Rannacher, Rolf}, 22438 journal = {Journal of Numerical Mathematics}, 22439 volume = {24}, 22440 number = {3}, 22441 pages = {167--187}, 22442 year = {2016} 22443} 22444 22445@Article{ maierrannacher2018, 22446 title = {A duality-based optimization approach for model adaptivity in heterogeneous 22447 multiscale problems}, 22448 author = {Maier, Matthias and Rannacher, Rolf}, 22449 journal = {Multiscale Modeling \& Simulation}, 22450 volume = {16}, 22451 number = {1}, 22452 pages = {412--428}, 22453 year = {2018} 22454} 22455 22456@Article{ margetismaierluskin2017, 22457 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 22458 metamaterial sheet}, 22459 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 22460 journal = {Studies in Applied Mathematics}, 22461 volume = {139}, 22462 number = {4}, 22463 pages = {599--625}, 22464 year = {2017} 22465} 22466 22467@Article{ maiermargetisluskin2017b, 22468 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 22469 approximation and validation}, 22470 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 22471 journal = {Journal of Computational Physics}, 22472 volume = {339}, 22473 pages = {126--145}, 22474 year = {2017} 22475} 22476 22477@Article{ maiermargetisluskin2018, 22478 title = {Generation of surface plasmon-polaritons by edge effects}, 22479 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 22480 journal = {Communications in Mathematical Sciences}, 22481 volume = {16}, 22482 number = {1}, 22483 pages = {77--95}, 22484 url = {http://arxiv.org/abs/1702.00848}, 22485 year = {2018} 22486} 22487 22488@Article{ maiermattheakiskaxirasluskinmargetis2018, 22489 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 22490 metamaterials}, 22491 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22492 Mitchell and Margetis, Dionisios}, 22493 journal = {Physical Review B}, 22494 volume = {97}, 22495 number = {3}, 22496 pages = {035307}, 22497 year = {2018} 22498} 22499 22500@Article{ maiermattheakiskaxirasluskinmargetis2019, 22501 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 22502 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 22503 Mitchell and Margetis, Dionisios}, 22504 journal = {Proceedings of the Royal Society A}, 22505 volume = {475}, 22506 number = {2230}, 22507 pages = {20190220}, 22508 year = {2019} 22509} 22510 22511@Article{ maiermargetisluskin2020, 22512 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 22513 two scales}, 22514 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 22515 journal = {Physical Review B}, 22516 volume = {102}, 22517 number = {7}, 22518 pages = {075308}, 22519 year = {2020} 22520} 22521 22522@Article{ margetismaierstauberlowluskin2020, 22523 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 22524 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 22525 Luskin, Mitchell}, 22526 journal = {Journal of Physics A: Mathematical and Theoretical}, 22527 volume = {53}, 22528 number = {5}, 22529 pages = {055201}, 22530 year = {2020} 22531} 22532 22533@Article{ maiermargetismellet2020, 22534 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 22535 structures}, 22536 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 22537 journal = {Journal of Computational and Applied Mathematics}, 22538 volume = {377}, 22539 pages = {112909}, 22540 year = {2020} 22541} 22542 22543@Article{ maierkronbichler2021, 22544 title = {Efficient parallel 3D computation of the compressible Euler equations with an 22545 invariant-domain preserving second-order finite-element scheme}, 22546 author = {Maier, Matthias and Kronbichler, Martin}, 22547 journal = {ACM Transactions on Parallel Computing}, 22548 volume = {8}, 22549 number = {3}, 22550 pages = {1--30}, 22551 year = {2021} 22552} 22553 22554@Article{ guermondmaierpopovtomas2021, 22555 title = {Second-order invariant domain preserving approximation of the compressible 22556 Navier--Stokes equations}, 22557 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 22558 journal = {Computer Methods in Applied Mechanics and Engineering}, 22559 volume = {375}, 22560 pages = {113608}, 22561 year = {2021} 22562} 22563 22564@Article{ liliptonmaier2021, 22565 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 22566 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 22567 eprint = {2009.12166}, 22568 archiveprefix = {arXiv}, 22569 primaryclass = {phys.optics}, 22570 year = {2021} 22571} 22572 22573@Article{ songmaierluskin2020, 22574 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 22575 gradient-index graphene waveguides}, 22576 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22577 journal = {Journal of Computational Physics}, 22578 volume = {423}, 22579 pages = {109871}, 22580 year = {2020} 22581} 22582 22583@Article{ songmaierluskin2019, 22584 title = {Adaptive finite element simulations of waveguide configurations involving 22585 parallel 2D material sheets}, 22586 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 22587 journal = {Computer Methods in Applied Mechanics and Engineering}, 22588 volume = {351}, 22589 pages = {20--34}, 22590 year = {2019} 22591} 22592 22593% 22594% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 22595% 22596% 22597@Unpublished{ rob1, 22598 author = {Rob Kunz}, 22599 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 22600 State University}, 22601 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 22602 sponsors = {U.S. Navy, NRC}, 22603 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 22604 simulations, including lake warming by power plants}, 22605 dates = {Oct 3 and 4, 2002}, 22606 email = {rfk@wt.arl.psu.edu} 22607} 22608 22609@Unpublished{ au1, 22610 author = {Feng Wang and William Appelbe}, 22611 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 22612 url = {http://www.vpac.org}, 22613 sponsors = { }, 22614 note = {Using PETSc for a Variety of Geophysical Simulations}, 22615 dates = {Nov 22, 2002} 22616} 22617 22618@Unpublished{ carl1, 22619 author = {Carl Sovinec}, 22620 institution = {Applied Physics, University of Wisconsin}, 22621 url = {http://nimrodteam.org}, 22622 sponsors = {DOE Office of Fusion Research}, 22623 note = {Investigating using PETSc for NIMROD}, 22624 dates = {Nov 21, 2002}, 22625 email = {sovinec@engr.wisc.edu} 22626} 22627 22628@Unpublished{ au1b, 22629 author = {Pablo Carrica and Robert Wilson}, 22630 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 22631 url = {http://}, 22632 sponsors = {Office of Naval Research}, 22633 note = {Using PETSc for a hydrodynamics of ships and submarines}, 22634 dates = {Sept, 2002}, 22635 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 22636} 22637 22638% ------------------- TAO References ---------------------- 22639@Article{ benson:2001:csp, 22640 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 22641 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 22642 journal = {{ACM} Transactions on Mathematical Software}, 22643 volume = {27}, 22644 number = {3}, 22645 month = sep, 22646 year = {2001}, 22647 pages = {361--376} 22648} 22649 22650@TechReport{ tao-user-ref-2000, 22651 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 22652 title = {{TAO} Users Manual}, 22653 year = {2000}, 22654 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22655 number = {ANL/MCS-TM-242}, 22656 note = {See \url{http://www.mcs.anl.gov/tao}} 22657} 22658 22659% ------------------- Optimization References ---------------------- 22660@Book{ optguide93, 22661 title = {Optimization Software Guide}, 22662 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 22663 publisher = {SIAM Publications}, 22664 address = {Philadelphia}, 22665 year = {1993} 22666} 22667 22668@InProceedings{ more84, 22669 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 22670 Hillstrom}, 22671 title = {The {MINPACK} Project}, 22672 booktitle = {Sources and Development of Mathematical Software}, 22673 editor = {Wayne R. Cowell}, 22674 year = {1984}, 22675 pages = {88--111} 22676} 22677 22678@Article{ steihaug:83, 22679 author = {Trond Steihaug}, 22680 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 22681 journal = {SIAM J. Numer. Anal.}, 22682 volume = {20}, 22683 year = {1983}, 22684 pages = {626--637}, 22685 key = {steihaug92 ! trust_region} 22686} 22687 22688@TechReport{ minpack2test, 22689 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 22690 title = {The {MINPACK-2} Test Problem Collection}, 22691 institution = {Argonne National Laboratory}, 22692 year = {1991}, 22693 number = {ANL/MCS-TM-150}, 22694 key = {more91 ! MINPACK-2} 22695} 22696 22697@TechReport{ hohmann:94, 22698 author = {Andreas Hohmann}, 22699 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 22700 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 22701 year = {1994}, 22702 number = {SC-94-4}, 22703 key = {Hohmann94} 22704} 22705 22706@TechReport{ meza:94, 22707 author = {Juan C. Meza}, 22708 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 22709 institution = {Sandia National Laboratory}, 22710 year = {1994}, 22711 number = {SAND94-8225}, 22712 key = {Meza94} 22713} 22714 22715@Book{ nw99, 22716 author = {Jorge Nocedal and Stephen J. Wright}, 22717 title = {Numerical Optimization}, 22718 year = {1999}, 22719 publisher = {Springer-Verlag}, 22720 address = {New York} 22721} 22722 22723@Book{ dennis:83, 22724 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 22725 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 22726 publisher = {Prentice-Hall, Inc.}, 22727 address = {Englewood Cliffs, NJ}, 22728 year = {1983} 22729} 22730 22731@TechReport{ more:92, 22732 author = {Jorge J. Mor\'{e} and David Thuente}, 22733 title = {Line search algorithms with guaranteed sufficient decrease}, 22734 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22735 year = {1992}, 22736 number = {MCS-P330-1092} 22737} 22738 22739@Article{ more-toraldo, 22740 author = {Jorge J. Mor\'e and G. Toraldo}, 22741 journal = {SIOPT}, 22742 pages = {93--113}, 22743 title = {On the solution of large quadratic programming problems with bound constraints}, 22744 volume = {1}, 22745 year = {1991} 22746} 22747 22748@Article{ byrd:1995:lma, 22749 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 22750 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 22751 journal = {SIAM Journal on Scientific Computing}, 22752 volume = {16}, 22753 number = {5}, 22754 pages = {1190--1208}, 22755 month = sep, 22756 year = {1995}, 22757 coden = {SJOCE3}, 22758 issn = {1064-8275 (print), 1095-7197 (electronic)}, 22759 mrclass = {90C30 (65K05)}, 22760 mrnumber = {96e:90039}, 22761 mrreviewer = {Henry Wolkowicz}, 22762 bibdate = {Fri Dec 4 16:17:35 MST 1998} 22763} 22764 22765@Article{ lin_c3, 22766 author = {C.-J. Lin and J. J. Mor\'e}, 22767 title = {Newton's method for large bound-constrained optimization problems}, 22768 year = {1999}, 22769 journal = {SIOPT}, 22770 volume = {9(4)}, 22771 pages = {1100--1127}, 22772 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 22773} 22774 22775@TechReport{ dolan2, 22776 author = {E. Dolan and J. J. Mor\'{e}}, 22777 title = {Benchmarking Optimization Software with Performance Profiles}, 22778 year = {2001}, 22779 month = jan, 22780 number = {ANL/MCS-P861-1200}, 22781 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 22782 address = {Argonne, IL}, 22783 url = {http://www.mcs.anl.gov/~more/cops/} 22784} 22785 22786@InProceedings{ owlqn, 22787 author = {Galen Andrew and Jianfeng Gao}, 22788 title = {Scalable training of L1-regularized log-linear models}, 22789 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 22790 pages = {33--40}, 22791 year = {2007} 22792} 22793 22794@Article{ bmrm, 22795 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 22796 title = {Bundle methods for regularized risk minimization}, 22797 year = {2010}, 22798 journal = {Journal of Machine Learning Research}, 22799 volume = {11}, 22800 pages = {311--365} 22801} 22802 22803% ------------------- Component Software References ---------------------- 22804@InProceedings{ cca99, 22805 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 22806 McInnes and S. Parker and B. Smolinski}, 22807 title = {Toward a Common Component Architecture for High-Performance Scientific 22808 Computing}, 22809 booktitle = {Proceedings of {High Performance Distributed Computing}}, 22810 pages = {115--124}, 22811 year = {1999}, 22812 note = {See \url{http://cca-forum.org}} 22813} 22814 22815@Book{ szyperski98, 22816 author = {Clemens Szyperski}, 22817 title = {Component Software: Beyond Object-Oriented Programming}, 22818 publisher = {ACM Press}, 22819 address = {New York}, 22820 year = {1998} 22821} 22822 22823@Article{ broy98, 22824 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 22825 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 22826 Stal and Clemens Szyperski}, 22827 title = {What Characterizes a (Software) Component?}, 22828 journal = {Software -- Concepts and Tools}, 22829 publisher = {Springer-Verlag}, 22830 year = {1998}, 22831 volume = {19}, 22832 pages = {49--56} 22833} 22834 22835@Article{ componentware:94, 22836 author = {Jon Udell}, 22837 title = {Componentware}, 22838 journal = {Byte}, 22839 volume = {May}, 22840 pages = {46--56}, 22841 year = {1994}, 22842 key = {Udell94 ! componentware} 22843} 22844 22845@Misc{ cca-web-page, 22846 author = {{Common Component Architecture Forum}}, 22847 note = {See \url{http://cca-forum.org}} 22848} 22849 22850% --------------- References for Tools Used by TAO Developers ----------------- 22851 22852% 22853% tohtml: Used to generate on-line TAO users manual and manual pages 22854% 22855@TechReport{ tohtml, 22856 author = {William Gropp}, 22857 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 22858 institution = {Argonne National Laboratory}, 22859 number = {ANL/MCS-TM-00}, 22860 month = jan, 22861 year = {1995}, 22862 key = {tohtml} 22863} 22864 22865% 22866% doctext: Used to generate tex version of TAO manual pages 22867% 22868@TechReport{ doctext, 22869 author = {William Gropp}, 22870 title = {Users Manual for doctext: Producing documentation from {C} source code}, 22871 institution = {Argonne National Laboratory}, 22872 number = {ANL/MCS-TM-00}, 22873 month = jan, 22874 year = {1995}, 22875 key = {doctext} 22876} 22877 22878% 22879% bfort: Used to generate TAO Fortran interface 22880% 22881@TechReport{ bfort, 22882 author = {William Gropp}, 22883 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 22884 institution = {Argonne National Laboratory}, 22885 number = {ANL/MCS-TM-208}, 22886 month = mar, 22887 year = {1995}, 22888 key = {doctext} 22889} 22890 22891% ------------------------- PETSc References ------------------------------ 22892@InProceedings{ petsc, 22893 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 22894 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 22895 Libraries}, 22896 booktitle = {Modern Software Tools in Scientific Computing}, 22897 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 22898 publisher = {Birkhauser Press}, 22899 pages = {163--202}, 22900 year = {1997} 22901} 22902 22903% ------------------------- Misc Other References ------------------------------ 22904@Misc{ indeps-web-page, 22905 title = {{InDEPS} {W}eb page}, 22906 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 22907 author = {et al. Robert Armstrong}, 22908 institution = {Sandia National Laboratory}, 22909 key = {{InDEPS} {W}eb page} 22910} 22911 22912@Misc{ pooma, 22913 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 22914 chitectures}, 22915 year = {1996}, 22916 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 22917 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 22918} 22919 22920@Misc{ isis++-web-page, 22921 title = {{ISIS++} {W}eb Page}, 22922 note = {See \url{http://ca.sandia.gov/isis}}, 22923 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 22924 institution = {Sandia National Laboratories} 22925} 22926 22927@Misc{ trilinos-web-page, 22928 title = {{Trilinos} {W}eb Page}, 22929 note = {See 22930 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 22931 author = {Mike Heroux et al.}, 22932 institution = {Sandia National Laboratories} 22933} 22934 22935@Misc{ alice-web-page, 22936 title = {{ALICE} {W}eb page}, 22937 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 22938 Argonne National Laboratory}, 22939 key = {{ALICE} {W}eb page} 22940} 22941 22942@Misc{ autodiff-webpage, 22943 author = {{Computational Differentiation Project}}, 22944 note = {See \url{http://www.mcs.anl.gov/autodiff}} 22945} 22946 22947@Misc{ coool-home-page, 22948 author = {Lydia Deng and Wences Gouveia and John Scales}, 22949 title = {{The CWP Object-Oriented Optimization Library}}, 22950 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 22951} 22952 22953@Misc{ rice-inversion-home-page, 22954 author = {Mark S. Gokenbach and William W. Symes}, 22955 title = {{The Hilbert Class Library}}, 22956 note = {See \url{http://www.trip.caam.rice.edu/}} 22957} 22958 22959@Misc{ opt++-home-page, 22960 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 22961 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 22962} 22963 22964@Article{ gockenbach:1999:ccl, 22965 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 22966 title = {C++ Classes for Linking Optimization with Complex Simulations}, 22967 journal = {{ACM} Transactions on Mathematical Software}, 22968 volume = {25}, 22969 number = {2}, 22970 month = jun, 22971 year = {1999}, 22972 pages = {191-212}, 22973 abstract = {The object-oriented programming paradigm can be used to overcome the 22974 incompatibilities between off-the-shelf optimization software and application 22975 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 22976 objects arising in optimization problems, such as vectors, linear operators, and 22977 so forth, as C++ classes, making it possible to write optimization code in a 22978 natural fashion, while allowing application software such as simulators to use the 22979 most convenient data structures and programming style. In spite of the poor 22980 reputation C++ has for runtime performance, the use of mixed-language programming 22981 allows performance equal to that achieved by standard Fortran packages, as 22982 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 22983 accepted = {April 1999}, 22984 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 22985} 22986 22987@Misc{ neos-guide, 22988 author = {{The Optimization Software Guide}}, 22989 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 22990} 22991 22992@Article{ boyd, 22993 title = {Distributed optimization and statistical learning via the alternating direction 22994 method of multipliers}, 22995 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 22996 Jonathan and others}, 22997 journal = {Foundations and Trends{\textregistered} in Machine learning}, 22998 volume = {3}, 22999 number = {1}, 23000 pages = {1-122}, 23001 year = {2011}, 23002 publisher = {Now Publishers, Inc.} 23003} 23004 23005@Misc{ :alertsys, 23006 title = {page{ALERT}}, 23007 organization = {Alert Systems, Inc}, 23008 address = {Madison, Wisconsin}, 23009 note = {http://www.alertsys.com/} 23010} 23011 23012@Manual{ :cmfortran, 23013 title = {{CM} {F}ortran Language Reference Manual}, 23014 organization = {Thinking Machines Corporation}, 23015 year = {1994}, 23016 address = {Cambridge, MA} 23017} 23018 23019@Manual{ :cmmd, 23020 title = {{CMMD} Reference Manual, Version 3.0}, 23021 organization = {Thinking Machines Corporation}, 23022 year = {1993}, 23023 address = {Cambridge, MA} 23024} 23025 23026@Manual{ :cmssl, 23027 title = {{CMSSL} for {CM} {F}ortran}, 23028 volume = {I}, 23029 organization = {Thinking Machines Corporation}, 23030 year = {1994}, 23031 address = {Cambridge, MA} 23032} 23033 23034@Misc{ :condor, 23035 author = {M. Livny}, 23036 title = {{PI}, The {Condor} Project, High Throughput Computing}, 23037 howpublished = {www.cs.wisc.edu/condor} 23038} 23039 23040@Manual{ :connection, 23041 title = {Connection Machine {CM}--5 Technical Summary}, 23042 organization = {Thinking Machines Corporation}, 23043 year = {1993}, 23044 address = {Cambridge, MA} 23045} 23046 23047@Manual{ :cplex, 23048 title = {{CPLEX} Optimizer}, 23049 organization = {ILOG CPLEX Division}, 23050 address = {889 Alder Avenue, Incline Village, Nevada}, 23051 note = {http://www.cplex.com/} 23052} 23053 23054@Manual{ :cplextm, 23055 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 23056 (Version 2.0)}, 23057 organization = {CPLEX Optimization Inc.}, 23058 year = {1992}, 23059 address = {Incline Village, Nevada} 23060} 23061 23062@Misc{ :fatcop, 23063 author = {M. C. Ferris}, 23064 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 23065 Solver}, 23066 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 23067} 23068 23069@Misc{ :metaneos, 23070 author = {S. J. Wright}, 23071 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 23072 howpublished = {www-unix.mcs.anl.gov/metaneos} 23073} 23074 23075@InCollection{ gropp.more:optimization, 23076 author = {W. Gropp and J. J. Mor\'e}, 23077 title = {Optimization environments and the {NEOS} Server}, 23078 booktitle = {Approximation Theory and Optimization}, 23079 pages = {167--182}, 23080 publisher = {Cambridge University Press}, 23081 year = {1997}, 23082 editor = {M. D. Buhmann and A. Iserles} 23083} 23084 23085@Article{ czyzyk.mesnier.ea:neos, 23086 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 23087 title = {The {NEOS} Server}, 23088 journal = {IEEE Journal on Computational Science and Engineering}, 23089 volume = {5}, 23090 year = {1998}, 23091 pages = {68--75} 23092} 23093 23094@Book{ :osl, 23095 title = {Handbook for {IBM OSL}}, 23096 author = {M. S. Hung and W. O. Rom and A. D. 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Ferris}, 23402 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 23403 year = {2001}, 23404 journal = {SIAM Journal on Optimization, forthcoming}, 23405 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 23406 key = {55} 23407} 23408 23409@InProceedings{ anderson.ferris:genetic, 23410 author = {E. J. Anderson and M. C. Ferris}, 23411 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 23412 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 23413 Waterloo, Ontario, Canada, May 28--30}, 23414 publisher = {University of Waterloo Press}, 23415 key = {14}, 23416 year = {1990} 23417} 23418 23419@Article{ anderson.ferris:genetic*1, 23420 author = {E. J. Anderson and M. C. 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Nash}, 23448 title = {Linear Programming in Infinite--Dimensional Spaces}, 23449 year = {1987}, 23450 publisher = {John Wiley \& Sons}, 23451 address = {Chichester} 23452} 23453 23454@InProceedings{ anderson:primal, 23455 author = {E. J. Anderson}, 23456 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 23457 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 23458 Programming, Cambridge, September 1984}, 23459 year = {1985}, 23460 editor = {E. J. Anderson and A. B. Philpott}, 23461 publisher = {Springer-Verlag}, 23462 address = {Berlin} 23463} 23464 23465@Article{ andradottir:method, 23466 author = {S. Andrad\'{o}ttir}, 23467 title = {A Method of Discrete Stochastic Optimization}, 23468 journal = {Management Science}, 23469 year = {1995}, 23470 volume = {41}, 23471 pages = {1946--1961} 23472} 23473 23474@Article{ andradottir:global, 23475 author = {S. 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Walter}, 23686 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 23687 journal = {Environmental and Resource Economics}, 23688 year = {1991}, 23689 volume = {1}, 23690 pages = {237--270} 23691} 23692 23693@PhDThesis{ bagley:behaviour, 23694 author = {J. D. Bagley}, 23695 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 23696 Algorithms}, 23697 year = {1967}, 23698 school = {University of Michigan} 23699} 23700 23701@Article{ bain.stewart:application, 23702 author = {R. S. Bain and W. E. Stewart}, 23703 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 23704 Algebraic Equation Systems}, 23705 journal = {Computers in Chemical Engineering}, 23706 year = {1991}, 23707 volume = {15}, 23708 pages = {203--208} 23709} 23710 23711@Article{ baker.lasdon:successive, 23712 author = {T. E. Baker and L. S. 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Whalley}, 23738 title = {A General Equilibrium Model for Tax Policy Evaluation}, 23739 publisher = {The University of Chicago Press}, 23740 year = {1985}, 23741 series = {National Bureau of Economic Research Monograph} 23742} 23743 23744@InProceedings{ balog.angelos.ea:dose, 23745 author = {J. Balog and L. Angelos and T. R. Mackie and P. Reckwerdt}, 23746 title = {Dose Computation for a One-Dimensional Multileaf Collimator}, 23747 booktitle = {Proceedings of the XII International Conference on the Use of Computers in 23748 Radiation Therapy, Salt Lake City}, 23749 year = {1997}, 23750 editor = {D. D. Leavitt and G. Starkshall}, 23751 publisher = {Medical Physics Publishing}, 23752 address = {St. Louis, Missouri}, 23753 pages = {323--326} 23754} 23755 23756@Article{ baraff:fast, 23757 author = {D. 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Model analysis and 25321 optimality conditions}, 25322 type = {Publication}, 25323 number = {CRT-94-56}, 25324 institution = {Centre de Recherche sur les Transports, Universit\'e de Montr\'eal}, 25325 address = {Montr\'eal, Canada}, 25326 year = {1994} 25327} 25328 25329@Article{ chen.harker:continuation, 25330 author = {B. Chen and P. T. Harker}, 25331 title = {A Continuation Method for Monotone Variational Inequalities}, 25332 journal = {Mathematical Programming}, 25333 volume = {69}, 25334 pages = {237--253}, 25335 year = {1995} 25336} 25337 25338@Article{ chen.harker:non-interior, 25339 author = {B. Chen and P. T. Harker}, 25340 title = {A Non-Interior-Point Continuation Method for Linear Complementarity Problems}, 25341 journal = {SIAM Journal on Matrix Analysis and Applications}, 25342 year = {1993}, 25343 volume = {14}, 25344 pages = {1168--1190} 25345} 25346 25347@Article{ chen.harker:smooth, 25348 author = {B. Chen and P. T. 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Mangasarian}, 27277 title = {Finite Perturbation of Convex Programs}, 27278 journal = {Applied Mathematics and Optimization}, 27279 year = {1991}, 27280 volume = {23}, 27281 pages = {263--273}, 27282 key = {08} 27283} 27284 27285@Book{ ferris.mangasarian:linear, 27286 author = {M. C. Ferris and O. L. Mangasarian}, 27287 title = {Linear Programming via {MATLAB}}, 27288 publisher = {in preparation}, 27289 year = {1995}, 27290 address = {Madison, Wisconsin} 27291} 27292 27293@Article{ ferris.mangasarian:minimum, 27294 author = {M. C. Ferris and O. L. Mangasarian}, 27295 title = {Minimum Principle Sufficiency}, 27296 journal = {Mathematical Programming}, 27297 year = {1992}, 27298 volume = {57}, 27299 pages = {1--14}, 27300 key = {11} 27301} 27302 27303@Article{ ferris.mangasarian:parallel, 27304 author = {M. C. Ferris and O. L. Mangasarian}, 27305 title = {Parallel Constraint Distribution}, 27306 journal = {SIAM Journal on Optimization}, 27307 year = {1991}, 27308 volume = {1}, 27309 pages = {487--500}, 27310 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 27311 key = {18} 27312} 27313 27314@Article{ ferris.mangasarian:parallel*1, 27315 author = {M. C. Ferris and O. L. Mangasarian}, 27316 title = {Parallel Variable Distribution}, 27317 journal = {SIAM Journal on Optimization}, 27318 year = {1994}, 27319 volume = {4}, 27320 pages = {815--832}, 27321 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 27322 key = {31} 27323} 27324 27325@Article{ ferris.meeraus.ea:computing, 27326 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 27327 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 27328 journal = {Optimization Methods and Software}, 27329 year = {1999}, 27330 volume = {10}, 27331 pages = {669--685}, 27332 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 27333 key = {45} 27334} 27335 27336@Article{ ferris.mesnier.ea:neos, 27337 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 27338 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 27339 {I}nternet}, 27340 year = {2000}, 27341 journal = {{ACM} Transactions on Mathematical Software}, 27342 key = {54}, 27343 volume = {26}, 27344 pages = {1--18}, 27345 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 27346 institution = {Computer Sciences Department, University of Wisconsin}, 27347 address = {Madison, Wisconsin}, 27348 number = {96-08}, 27349 type = {Mathematical Programming Technical Report}, 27350 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 27351 Argonne National Laboratory}, 27352 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 27353 1996} 27354} 27355 27356@InCollection{ ferris.meyer:models, 27357 author = {M. C. Ferris and R. R. Meyer}, 27358 title = {Models and Solution for On-Demand Data Delivery Problems}, 27359 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 27360 key = {80}, 27361 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 27362 Problems}, 27363 editor = {P. M. Pardalos}, 27364 series = {Nonconvex Optimization and its Applications}, 27365 volume = {42}, 27366 address = {Dordrect}, 27367 year = {2000}, 27368 pages = {175--188}, 27369 publisher = {Kluwer}, 27370 type = {Mathematical Programming Technical Report}, 27371 institution = {Computer Sciences Department, University of Wisconsin}, 27372 number = {99-04} 27373} 27374 27375@InProceedings{ ferris.munson.ea:homotopy, 27376 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 27377 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 27378 booktitle = {Numerical Analysis 1999}, 27379 key = {88}, 27380 year = {2000}, 27381 editor = {D. F. Griffiths and G. A. Watson}, 27382 series = {Research Notes in Mathematics}, 27383 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 27384 address = {London}, 27385 pages = {143--167}, 27386 publisher = {Chapman and Hall}, 27387 institution = {Computer Sciences Department, University of Wisconsin}, 27388 number = {99-09}, 27389 type = {Mathematical Programming Technical Report} 27390} 27391 27392@TechReport{ ferris.munson.ea:practical, 27393 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 27394 title = {A Practical Approach to Sample-Path Simulation Optimization}, 27395 type = {Data Mining Institute Technical Report}, 27396 institution = {Computer Sciences Department, University of Wisconsin}, 27397 address = {Madison, Wisconsin}, 27398 year = {2000}, 27399 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 27400 number = {00-03}, 27401 key = {92}, 27402 annote = {To appear in WSC 2000} 27403} 27404 27405@InCollection{ ferris.munson:case, 27406 author = {M. C. Ferris and T. S. Munson}, 27407 title = {Case Studies in Complementarity: Improving Model Formulation}, 27408 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 27409 key = {73}, 27410 pages = {79--98}, 27411 publisher = {Springer Verlag}, 27412 year = {1999}, 27413 editor = {M. Th\'{e}ra and R. Tichatschke}, 27414 number = {477}, 27415 series = {Lecture Notes in Economics and Mathematical Systems}, 27416 address = {Berlin}, 27417 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 27418 type = {Mathematical Programming Technical Report}, 27419 institution = {Computer Sciences Department, University of Wisconsin} 27420} 27421 27422@Article{ ferris.munson:complementarity, 27423 author = {M. C. Ferris and T. S. Munson}, 27424 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 27425 year = {2000}, 27426 volume = {24}, 27427 pages = {165--188}, 27428 journal = {Journal of Economic Dynamics and Control}, 27429 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 27430 key = {70}, 27431 type = {Mathematical Programming Technical Report}, 27432 institution = {Computer Sciences Department, University of Wisconsin}, 27433 address = {Madison, Wisconsin}, 27434 number = {98-12} 27435} 27436 27437@Misc{ ferris.munson:condor, 27438 author = {M. C. Ferris and T. S. Munson}, 27439 title = {Condor Modeling Language Interface}, 27440 organization = {Computer Sciences Department, University of Wisconsin}, 27441 address = {Madison, Wisconsin}, 27442 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 27443} 27444 27445@Manual{ ferris.munson:gams, 27446 author = {M. C. Ferris and T. S. Munson}, 27447 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 27448 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 27449} 27450 27451@Article{ ferris.munson:interfaces, 27452 author = {M. C. Ferris and T. S. Munson}, 27453 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 27454 journal = {Computational Optimization and Applications}, 27455 volume = {12}, 27456 pages = {207--227}, 27457 year = {1999}, 27458 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 27459 key = {63}, 27460 institution = {Computer Sciences Department, University of Wisconsin}, 27461 address = {Madison, Wisconsin}, 27462 number = {97-12}, 27463 type = {Mathematical Programming Technical Report} 27464} 27465 27466@TechReport{ ferris.munson:interior, 27467 author = {M. C. Ferris and T. S. Munson}, 27468 title = {Interior Point Methods for Massive Support Vector Machines}, 27469 institution = {Computer Sciences Department, University of Wisconsin}, 27470 year = {2000}, 27471 key = {94}, 27472 type = {Data Mining Institute Technical Report}, 27473 number = {00-05}, 27474 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 27475 address = {Madison, Wisconsin}, 27476 annote = {Submitted to SIOPT} 27477} 27478 27479@Article{ ferris.munson:linear, 27480 author = {M. C. Ferris and T. S. Munson}, 27481 title = {Linear Programming for Emergency Broadcast Systems}, 27482 year = {1999}, 27483 journal = {{SIAG/OPT} Newsletter}, 27484 volume = {10}, 27485 pages = {6--8}, 27486 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 27487 key = {76}, 27488 type = {Mathematical Programming Technical Report}, 27489 institution = {Computer Sciences Department, University of Wisconsin}, 27490 address = {Madison, Wisconsin}, 27491 number = {98-20} 27492} 27493 27494@Article{ ferris.munson:modeling, 27495 author = {M. C. Ferris and T. S. Munson}, 27496 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 27497 year = {2000}, 27498 journal = {Mathematical Programming}, 27499 volume = {88}, 27500 pages = {487--506}, 27501 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 27502 key = {71}, 27503 type = {Mathematical Programming Technical Report}, 27504 institution = {Computer Sciences Department, University of Wisconsin}, 27505 address = {Madison, Wisconsin}, 27506 number = {98-13} 27507} 27508 27509@TechReport{ ferris.munson:preprocessing, 27510 author = {M. C. Ferris and T. S. Munson}, 27511 title = {Preprocessing Complementarity Problems}, 27512 type = {Mathematical Programming Technical Report}, 27513 institution = {Computer Sciences Department, University of Wisconsin}, 27514 address = {Madison, Wisconsin}, 27515 year = {1999}, 27516 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 27517 number = {99-07}, 27518 key = {86}, 27519 annote = {Submitted to ICCP 99} 27520} 27521 27522@TechReport{ ferris.munson:semismooth, 27523 author = {M. C. Ferris and T. S. Munson}, 27524 title = {Semismooth Support Vector Machines}, 27525 institution = {Computer Sciences Department, University of Wisconsin}, 27526 year = {2000}, 27527 key = {97}, 27528 type = {Data Mining Institute Technical Report}, 27529 number = {00-09}, 27530 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 27531 address = {Madison, Wisconsin}, 27532 annote = {Submitted to Math Prog B} 27533} 27534 27535@Article{ ferris.pang:engineering, 27536 author = {M. C. Ferris and J. S. Pang}, 27537 title = {Engineering and Economic Applications of Complementarity Problems}, 27538 year = {1997}, 27539 journal = {SIAM Review}, 27540 volume = {39}, 27541 pages = {669--713}, 27542 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 27543 key = {46} 27544} 27545 27546@Article{ ferris.pang:nondegenerate, 27547 author = {M. C. Ferris and J. S. Pang}, 27548 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 27549 journal = {SIAM Journal on Control and Optimization}, 27550 year = {1996}, 27551 volume = {34}, 27552 pages = {244--263}, 27553 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 27554 key = {35} 27555} 27556 27557@Article{ ferris.philpott:affine, 27558 author = {M. C. Ferris and A. B. Philpott}, 27559 title = {On Affine Scaling and Semi--Infinite Programming}, 27560 journal = {Mathematical Programming}, 27561 year = {1992}, 27562 volume = {56}, 27563 pages = {361--364}, 27564 key = {15} 27565} 27566 27567@Article{ ferris.philpott:interior, 27568 author = {M. C. Ferris and A. B. Philpott}, 27569 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 27570 journal = {Mathematical Programming}, 27571 year = {1989}, 27572 volume = {43}, 27573 pages = {257--276}, 27574 key = {04} 27575} 27576 27577@Article{ ferris.philpott:performance, 27578 author = {M. C. Ferris and A. B. Philpott}, 27579 title = {On the Performance of {K}armarkar's Algorithm}, 27580 journal = {Journal of the Operational Research Society}, 27581 year = {1988}, 27582 volume = {39}, 27583 pages = {257--270}, 27584 key = {03} 27585} 27586 27587@InCollection{ ferris.ralph:projected, 27588 author = {M. C. Ferris and D. Ralph}, 27589 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 27590 Maps}, 27591 booktitle = {Recent Advances in Nonsmooth Optimization}, 27592 publisher = {World Scientific Publishers}, 27593 year = {1995}, 27594 pages = {57--87}, 27595 editor = {D. Du and L. Qi and R. Womersley}, 27596 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 27597 key = {41} 27598} 27599 27600@Article{ ferris.ruszczynski:robust, 27601 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 27602 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 27603 year = {2000}, 27604 journal = {Networks}, 27605 volume = {35}, 27606 pages = {181--194}, 27607 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 27608 key = {60} 27609} 27610 27611@InCollection{ ferris.rutherford:accessing, 27612 author = {M. C. Ferris and T. F. Rutherford}, 27613 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 27614 booktitle = {Nonlinear Optimization and Applications}, 27615 key = {48}, 27616 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 27617 editor = {G. Di Pillo and F. Giannessi}, 27618 year = {1996}, 27619 pages = {141--153}, 27620 publisher = {Plenum Press}, 27621 address = {New York} 27622} 27623 27624@InCollection{ ferris.shepard:optimizing, 27625 author = {M. C. Ferris and D. M. Shepard}, 27626 title = {Optimization of Gamma Knife Radiosurgery}, 27627 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 27628 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 27629 publisher = {AMS}, 27630 year = {2000}, 27631 optseries = {DIMACS}, 27632 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 27633 key = {91}, 27634 type = {Data Mining Institute Technical Report}, 27635 institution = {Computer Sciences Department, University of Wisconsin}, 27636 address = {Madison, Wisconsin}, 27637 number = {00-01} 27638} 27639 27640@InCollection{ ferris.sinapiromsaran:formulating, 27641 author = {M. C. Ferris and K. Sinapiromsaran}, 27642 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 27643 booktitle = {Optimization}, 27644 key = {77}, 27645 publisher = {Springer-Verlag}, 27646 year = {2000}, 27647 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 27648 volume = {481}, 27649 series = {Lecture Notes in Economics and Mathematical Systems}, 27650 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 27651 type = {Mathematical Programming Technical Report}, 27652 institution = {Computer Sciences Department, University of Wisconsin}, 27653 address = {Madison, Wisconsin}, 27654 number = {98-21} 27655} 27656 27657@Article{ ferris.tin-loi:limit, 27658 author = {M. C. Ferris and F. Tin-Loi}, 27659 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 27660 Complementarity Constraints}, 27661 year = {2001}, 27662 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 27663 key = {78}, 27664 journal = {International Journal of Mechanical Sciences}, 27665 pages = {209--224}, 27666 volume = {43}, 27667 type = {Mathematical Programming Technical Report}, 27668 institution = {Computer Sciences Department, University of Wisconsin}, 27669 address = {Madison, Wisconsin}, 27670 number = {99-01} 27671} 27672 27673@Article{ ferris.tin-loi:nonlinear, 27674 author = {M. C. Ferris and F. Tin-Loi}, 27675 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 27676 Elastoplasticity}, 27677 year = {1998}, 27678 key = {64}, 27679 volume = {6}, 27680 pages = {857--870}, 27681 journal = {Structural Engineering and Mechanics} 27682} 27683 27684@Article{ ferris.tin-loi:solution, 27685 author = {M. C. Ferris and F. Tin-Loi}, 27686 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 27687 and Complementarity Constraints}, 27688 year = {1999}, 27689 journal = {Computer Methods in Applied Mechanics and Engineering}, 27690 volume = {174}, 27691 pages = {107--120}, 27692 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 27693 key = {66} 27694} 27695 27696@Article{ ferris.vlach:scheduling, 27697 author = {M. C. Ferris and M. Vlach}, 27698 title = {Scheduling with Earliness and Tardiness Penalties}, 27699 journal = {Naval Research Logistics Quarterly}, 27700 year = {1992}, 27701 volume = {39}, 27702 pages = {229--245}, 27703 key = {13} 27704} 27705 27706@TechReport{ ferris.zavriev:linear, 27707 author = {M. C. Ferris and S. K Zavriev}, 27708 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 27709 institution = {Computer Sciences Department, University of Wisconsin}, 27710 year = {1996}, 27711 key = {56}, 27712 address = {Madison, Wisconsin}, 27713 type = {Mathematical Programming Technical Report}, 27714 number = {96--12}, 27715 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 27716} 27717 27718@Article{ ferris:finite, 27719 author = {M. C. Ferris}, 27720 title = {Finite Termination of the Proximal Point Algorithm}, 27721 journal = {Mathematical Programming}, 27722 year = {1991}, 27723 volume = {50}, 27724 pages = {359--366}, 27725 key = {06} 27726} 27727 27728@Article{ ferris:iterative, 27729 author = {M. C. Ferris}, 27730 title = {Iterative Linear Programming Solution of Convex Programs}, 27731 journal = {Journal of Optimization Theory and Applications}, 27732 year = {1990}, 27733 volume = {65}, 27734 pages = {53--65}, 27735 key = {07} 27736} 27737 27738@Article{ ferris:linear, 27739 author = {M. C. Ferris}, 27740 title = {The Linear Complementarity Problem}, 27741 journal = {Bulletin of the American Mathematical Society}, 27742 year = {1993}, 27743 volume = {28}, 27744 pages = {169--175}, 27745 key = {27} 27746} 27747 27748@MastersThesis{ ferris:linear*1, 27749 author = {M. C. Ferris}, 27750 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 27751 Solving a Class of Structural Optimization Problems}, 27752 year = {1985}, 27753 school = {University of Cambridge}, 27754 address = {England}, 27755 key = {01} 27756} 27757 27758@TechReport{ ferris:matlab, 27759 author = {M. C. Ferris}, 27760 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 27761 institution = {Computer Sciences Department, University of Wisconsin}, 27762 year = {1998}, 27763 address = {Madison, Wisconsin}, 27764 type = {Mathematical Programming Technical Report}, 27765 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 27766 number = {98-19}, 27767 key = {75} 27768} 27769 27770@Article{ ferris:parallel, 27771 author = {M. C. Ferris}, 27772 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 27773 journal = {Mathematics of Operations Research}, 27774 year = {1994}, 27775 volume = {19}, 27776 pages = {645--658}, 27777 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 27778 key = {20} 27779} 27780 27781@TechReport{ ferris:parallel*1, 27782 author = {M. C. Ferris}, 27783 title = {Parallel Solution of Extremely Large Knapsack Problems}, 27784 institution = {Computer Sciences Department, University of Wisconsin}, 27785 year = {1989}, 27786 address = {Madison, Wisconsin}, 27787 number = {842}, 27788 key = {09} 27789} 27790 27791@PhDThesis{ ferris:weak, 27792 author = {M. C. Ferris}, 27793 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27794 year = {1988}, 27795 school = {University of Cambridge}, 27796 address = {England}, 27797 key = {02} 27798} 27799 27800@TechReport{ ferris:weak*1, 27801 author = {M. C. Ferris}, 27802 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 27803 institution = {Computer Sciences Department, University of Wisconsin}, 27804 year = {1988}, 27805 address = {Madison, Wisconsin}, 27806 number = {779}, 27807 key = {05} 27808} 27809 27810@Book{ fiacco.mccormick:nonlinear, 27811 author = {A. V. Fiacco and G. P. McCormick}, 27812 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 27813 year = {1968}, 27814 publisher = {John Wiley \& Sons}, 27815 address = {New York}, 27816 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 27817} 27818 27819@Book{ fiacco:introduction, 27820 author = {A. V. Fiacco}, 27821 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 27822 year = {1983}, 27823 publisher = {Academic Press}, 27824 address = {New York} 27825} 27826 27827@Article{ fiedler.ptak:matrices, 27828 author = {M. Fiedler and V. Pt\'{a}k}, 27829 title = {On matrices with nonpositive off-diagonal elements and positive principal 27830 minors}, 27831 journal = {Czechoslovak Mathematics Journal}, 27832 volume = {12}, 27833 pages = {382--400}, 27834 year = {1962} 27835} 27836 27837@Article{ fischer.kanzow:finite, 27838 author = {A. Fischer and C. Kanzow}, 27839 title = {On Finite Termination of an Iterative Method for Linear Complementarity 27840 Problems}, 27841 journal = {Mathematical Programming}, 27842 volume = {74}, 27843 pages = {279--292}, 27844 year = {1996} 27845} 27846 27847@TechReport{ fischer:constrained, 27848 author = {A. Fischer}, 27849 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 27850 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 27851 year = {1995}, 27852 type = {Technical Report}, 27853 number = {MATH-NM-10-1995}, 27854 address = {Dresden} 27855} 27856 27857@Article{ fischer:local, 27858 author = {A. Fischer}, 27859 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 27860 weak conditions}, 27861 journal = {Optimization Methods and Software}, 27862 year = {1995}, 27863 volume = {6}, 27864 pages = {83--107} 27865} 27866 27867@InCollection{ fischer:ncp-function, 27868 author = {A. Fischer}, 27869 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 27870 booktitle = {Recent Advances in Nonsmooth Optimization}, 27871 publisher = {World Scientific Publishers}, 27872 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 27873 year = {1995}, 27874 pages = {88--105} 27875} 27876 27877@Article{ fischer:newton-type, 27878 author = {A. Fischer}, 27879 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 27880 Problems}, 27881 journal = {Journal of Optimization Theory and Applications}, 27882 year = {1995}, 27883 volume = {86}, 27884 pages = {585--608} 27885} 27886 27887@Article{ fischer:solution, 27888 author = {A. Fischer}, 27889 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 27890 Functions}, 27891 year = {1997}, 27892 journal = {Mathematical Programming}, 27893 pages = {513--532} 27894} 27895 27896@Article{ fischer:special, 27897 author = {A. Fischer}, 27898 title = {A Special {N}ewton--Type Optimization Method}, 27899 journal = {Optimization}, 27900 year = {1992}, 27901 volume = {24}, 27902 pages = {269--284} 27903} 27904 27905@Article{ fisher:use, 27906 author = {R. A. Fisher}, 27907 title = {The Use of Multiple Measurements in Taxonomic Problems}, 27908 journal = {Annual Eugenics}, 27909 year = {1936}, 27910 volume = {7}, 27911 number = {Part II}, 27912 pages = {179--188} 27913} 27914 27915@Book{ fishman:principles, 27916 author = {G. Fishman}, 27917 title = {Principles of Discrete Event Simulation}, 27918 publisher = {Wiley}, 27919 address = {New York, NY}, 27920 year = {1978} 27921} 27922 27923@Article{ fitchard.aldridge.ea:registration, 27924 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 27925 title = {Registration of Synthetic Tomographic Projection Data Sets Using 27926 Cross-Correlation}, 27927 journal = {Physics in Medicine and Biology}, 27928 year = {1998}, 27929 volume = {43}, 27930 pages = {1645--1657} 27931} 27932 27933@Article{ fletcher.matthews:stable, 27934 author = {R. Fletcher and S. P. J. Matthews}, 27935 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 27936 journal = {Mathematical Programming}, 27937 year = {1984}, 27938 volume = {30}, 27939 pages = {267--284} 27940} 27941 27942@TechReport{ fletcher.maza:nonlinear, 27943 author = {R. Fletcher and E. Sainz de la Maza}, 27944 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 27945 Programming}, 27946 institution = {Department of Mathematical Sciences}, 27947 year = {1987}, 27948 address = {The University, Dundee, Scotland}, 27949 number = {NA/100}, 27950 type = {Numerical Analysis Report} 27951} 27952 27953@InCollection{ fletcher:class, 27954 author = {R. Fletcher}, 27955 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 27956 Properties}, 27957 booktitle = {Integer and Nonlinear Programming}, 27958 year = {1970}, 27959 editor = {J. Abadie}, 27960 publisher = {North--Holland}, 27961 address = {Amsterdam}, 27962 pages = {157--173} 27963} 27964 27965@Article{ fletcher:exact, 27966 author = {R. Fletcher}, 27967 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 27968 journal = {Mathematical Programming}, 27969 year = {1973}, 27970 volume = {5}, 27971 pages = {129--150} 27972} 27973 27974@Article{ fletcher:generalized, 27975 author = {R. Fletcher}, 27976 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 27977 Equations}, 27978 journal = {The Computer Journal}, 27979 year = {1968}, 27980 volume = {10}, 27981 pages = {392--399} 27982} 27983 27984@InProceedings{ fletcher:penalty, 27985 crossref = {bachem.grotschel.ea:mathematical}, 27986 author = {R. Fletcher}, 27987 title = {Penalty Functions}, 27988 pages = {87--114} 27989} 27990 27991@Book{ fletcher:practical, 27992 author = {R. Fletcher}, 27993 title = {Practical Methods of Optimization}, 27994 year = {1981}, 27995 publisher = {John Wiley \& Sons}, 27996 address = {Chichester}, 27997 volume = {1} 27998} 27999 28000@Book{ fletcher:practical*1, 28001 author = {R. Fletcher}, 28002 title = {Practical Methods of Optimization}, 28003 year = {1981}, 28004 publisher = {John Wiley \& Sons}, 28005 address = {Chichester}, 28006 volume = {2} 28007} 28008 28009@Book{ fletcher:practical*2, 28010 author = {R. Fletcher}, 28011 title = {Practical Methods of Optimization}, 28012 year = {1987}, 28013 publisher = {John Wiley \& Sons}, 28014 address = {New York}, 28015 edition = {second} 28016} 28017 28018@Unpublished{ fletcher:recent, 28019 author = {R. Fletcher}, 28020 title = {Recent Developments in Nonlinear Programming}, 28021 note = {Presentation at SOR 96, Braunchweig, Germany}, 28022 year = {1996} 28023} 28024 28025@InCollection{ fletcher:second, 28026 author = {R. Fletcher}, 28027 title = {Second Order Correction for Nondifferentiable Optimization}, 28028 booktitle = {Numerical Analysis}, 28029 year = {1982}, 28030 editor = {G. A. Watson}, 28031 publisher = {Springer-Verlag}, 28032 address = {Berlin}, 28033 pages = {85--114} 28034} 28035 28036@InCollection{ florian:mathematical, 28037 author = {M. Florian}, 28038 title = {Mathematical programming applications in national, regional, and urban planning}, 28039 editors = {M. Iri and K. Tanabe}, 28040 booktitle = {Mathematical Programming: Recent Developments and Applications}, 28041 publisher = {Kluwer Academic Publishers}, 28042 address = {Tokyo}, 28043 year = {1989} 28044} 28045 28046@Article{ florian:nonlinear, 28047 author = {M. Florian}, 28048 title = {Nonlinear Cost Network Models in Transportation Analysis}, 28049 journal = {Mathematical Programming Study}, 28050 year = {1986}, 28051 volume = {26}, 28052 pages = {167--196} 28053} 28054 28055@Article{ flynn:computer, 28056 author = {M.~J. Flynn}, 28057 title = {Some Computer Organizations and their Effectiveness}, 28058 journal = {IEEE Transactions on Computers}, 28059 year = {1972}, 28060 volume = {C-21}, 28061 pages = {948--960} 28062} 28063 28064@InProceedings{ fogarty:varying, 28065 crossref = {schaeffer:third}, 28066 author = {T. C. Fogarty}, 28067 title = {Varying the Probability of Mutation in the Genetic Algorithm}, 28068 pages = {422--427} 28069} 28070 28071@Article{ forrest.goldfarb:steepest-edge, 28072 author = {J. J. Forrest and D. Goldfarb}, 28073 title = {Steepest--Edge Simplex Algorithms for Linear Programming}, 28074 journal = {Mathematical Programming}, 28075 year = {1992}, 28076 volume = {57}, 28077 pages = {341--374} 28078} 28079 28080@Article{ forrest.tomlin:updating, 28081 author = {J. J. H. Forrest and J. A. Tomlin}, 28082 title = {Updating Triangular Factors of the Basis to Maintain Sparsity in the Product Form 28083 Simplex Method}, 28084 journal = {Mathematical Programming}, 28085 year = {1972}, 28086 volume = {2}, 28087 pages = {263--278} 28088} 28089 28090@TechReport{ forsgren.gill.ea:computing, 28091 author = {A. Forsgren and P. E. Gill and W. Murray}, 28092 title = {Computing Modified {N}ewton Directions using a Partial {C}holesky Factorization}, 28093 institution = {Department of Mathematics, Royal Institute of Technology}, 28094 year = {1993}, 28095 number = {TRITA-MAT-1993-9}, 28096 address = {Stockholm, Sweden} 28097} 28098 28099@TechReport{ forsgren.gill:primal-dual, 28100 author = {A. Forsgren and P. E. Gill}, 28101 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 28102 institution = {Department of Mathematics, University of California}, 28103 year = {1996}, 28104 type = {Report NA}, 28105 number = {96-3}, 28106 address = {San Diego} 28107} 28108 28109@InCollection{ fortin.glowinski:decomposition-coordination, 28110 author = {M. Fortin and R. Glowinski}, 28111 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 28112 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 28113 Problems}, 28114 publisher = {North-Holland}, 28115 year = {1983}, 28116 editor = {M. Fortin and R. Glowinski}, 28117 address = {Amsterdam} 28118} 28119 28120@Misc{ foster.kesselman:globus, 28121 author = {I. Foster and C. Kesselman}, 28122 title = {The Globus Project}, 28123 howpublished = {www.globus.org} 28124} 28125 28126@Article{ foster.kesselman:globus*1, 28127 author = {I. Foster and C. Kesselman}, 28128 title = {Globus: A Metacomputing Infrastructure Toolkit}, 28129 journal = {International Journal of Supercomputer Applications}, 28130 volume = {11}, 28131 pages = {115--128}, 28132 year = {1997} 28133} 28134 28135@Book{ foster.kesselman:grid, 28136 editor = {I. Foster and C. Kesselman}, 28137 title = {The Grid: Blueprint for a Future Computing Infrastructure}, 28138 publisher = {Morgan Kaufmann Publishers}, 28139 year = {1999} 28140} 28141 28142@Book{ fourer.gay.ea:ampl, 28143 author = {R. Fourer and D. M. Gay and B. W. Kernighan}, 28144 title = {{AMPL}: {A} Modeling Language for Mathematical Programming}, 28145 year = {1993}, 28146 publisher = {Duxbury Press} 28147} 28148 28149@Article{ fourer.gay.ea:modeling, 28150 author = {R. Fourer and D. M. Gay and B. W. 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Gabriel}, 28383 title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and 28384 Extensions}, 28385 school = {The Johns Hopkins University}, 28386 year = {1992}, 28387 address = {Baltimore, Maryland} 28388} 28389 28390@Article{ gafni.bertsekas:two-metric, 28391 author = {E. M. Gafni and D. P. Bertsekas}, 28392 title = {Two-Metric Projection Methods for Constrained Optimization}, 28393 journal = {SIAM Journal on Control and Optimization}, 28394 year = {1984}, 28395 volume = {22}, 28396 pages = {936--964} 28397} 28398 28399@InProceedings{ gaivoronski:convergence, 28400 author = {A. A. Gaivoronski}, 28401 title = {Convergence of Parallel Backpropagation for Neural Networks}, 28402 booktitle = {SIAM Journal on Optimization}, 28403 year = {1994}, 28404 note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993, 28405 submitted} 28406} 28407 28408@Misc{ gaivoronski:private, 28409 author = {A. A. 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Gao}, 28453 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 28454 Conditions}, 28455 type = {Manuscript}, 28456 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 28457 month = oct, 28458 year = {1994} 28459} 28460 28461@Article{ garcia-palomares.mangasarian:superlinearly, 28462 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 28463 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 28464 Optimization Problems}, 28465 journal = {Mathematical Programming}, 28466 year = {1976}, 28467 volume = {11}, 28468 pages = {1--13} 28469} 28470 28471@Article{ garcia-palomares.restuccia:global, 28472 author = {U. M. {Garcia--Palomares} and A. Restuccia}, 28473 title = {A Global Quadratic Algorithm for Solving a System of Mixed Equations}, 28474 journal = {Mathematical Programming}, 28475 year = {1981}, 28476 volume = {21}, 28477 pages = {290--300} 28478} 28479 28480@InProceedings{ garcia-palomares:superlinearly, 28481 author = {U. M. {Garcia--Palomares}}, 28482 title = {Superlinearly Convergent Algorithms for Linearly Constrained Optimization}, 28483 crossref = {mangasarian.meyer.ea:nonlinear*2}, 28484 pages = {101--119} 28485} 28486 28487@Article{ garcia.gould:theorem, 28488 author = {C. B. Garcia and F. J. Gould}, 28489 title = {A Theorem on Homotopy Paths}, 28490 journal = {Mathematics of Operations Research}, 28491 year = {1978}, 28492 volume = {3}, 28493 pages = {282--289} 28494} 28495 28496@Book{ garcia.zangwill:pathways, 28497 author = {C. B. Garcia and W. I. Zangwill}, 28498 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 28499 year = {1981}, 28500 publisher = {Prentice-Hall, Inc}, 28501 address = {Englewood Cliffs, New Jersey} 28502} 28503 28504@Book{ garey.johnson:computers, 28505 author = {M. R. Garey and D. S. Johnson}, 28506 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 28507 year = {1979}, 28508 publisher = {W.H. Freeman and Company}, 28509 address = {San Francisco} 28510} 28511 28512@Article{ garey.tarjan.ea:one-processor, 28513 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 28514 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 28515 journal = {Mathematics of Operations Research}, 28516 year = {1988}, 28517 volume = {13}, 28518 pages = {330--348} 28519} 28520 28521@Book{ garfinkel.nemhauser:integer, 28522 author = {R. S. Garfinkel and G. L. Nemhauser}, 28523 title = {Integer Programming}, 28524 year = {1972}, 28525 publisher = {John Wiley \& Sons}, 28526 address = {New York} 28527} 28528 28529@Book{ gass:linear, 28530 author = {S. Gass}, 28531 title = {Linear Programming Methods and Applications}, 28532 edition = {Fifth}, 28533 publisher = {Boyd and Fraser Publishing Company}, 28534 address = {Danvers, Massachusetts}, 28535 year = {1985} 28536} 28537 28538@InProceedings{ gay:combining, 28539 author = {D. M. Gay}, 28540 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 28541 booktitle = {Sparse Matrix Proceedings 1978}, 28542 editor = {I. S. Duff and G. W. Stewart}, 28543 year = {1978}, 28544 organization = {SIAM}, 28545 address = {Philadelphia, Pennsylvania}, 28546 pages = {313--334} 28547} 28548 28549@Article{ gay:electronic, 28550 author = {D. M. Gay}, 28551 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 28552 journal = {{COAL} Newsletter}, 28553 year = {1985}, 28554 volume = {13}, 28555 pages = {10--12} 28556} 28557 28558@TechReport{ gay:hooking, 28559 author = {D. M. Gay}, 28560 title = {Hooking Your Solver to {AMPL}}, 28561 year = {1997}, 28562 institution = {Bell Laboratories}, 28563 address = {Murray Hill, New Jersey}, 28564 note = {Revised 1994, 1997} 28565} 28566 28567@Article{ gay:variant, 28568 author = {D. Gay}, 28569 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 28570 Form}, 28571 journal = {Mathematical Programming}, 28572 year = {1987}, 28573 volume = {37}, 28574 pages = {81--90} 28575} 28576 28577@Article{ geiger.kanzow:resolution, 28578 author = {C. Geiger and C. Kanzow}, 28579 title = {On the Resolution of Monotone Complementarity Problems}, 28580 journal = {Computational Optimization and Applications}, 28581 volume = {5}, 28582 year = {1996}, 28583 pages = {155--173} 28584} 28585 28586@Book{ geist.beguelin.ea:pvm, 28587 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 28588 V. S. Sunderam}, 28589 title = {{PVM}: Parallel Virtual Machine}, 28590 publisher = {MIT Press}, 28591 address = {Cambridge, Massachusetts}, 28592 year = {1994} 28593} 28594 28595@Article{ gendron.crainic:parallel, 28596 author = {B. Gendron and T. G. Crainic}, 28597 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 28598 journal = {Operations Research}, 28599 year = {1994}, 28600 volume = {42}, 28601 pages = {1042--1060} 28602} 28603 28604@Article{ george:automatic, 28605 author = {A. George}, 28606 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 28607 journal = {SIAM Journal on Numerical Analysis}, 28608 vol = {17}, 28609 pages = {740--751}, 28610 year = {1980} 28611} 28612 28613@InProceedings{ georges-schleuter:asparagos, 28614 crossref = {schaeffer:third}, 28615 author = {M. Georges--Schleuter}, 28616 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 28617 pages = {416--421} 28618} 28619 28620@Article{ georgiou:comments, 28621 author = {G. M. Georgiou}, 28622 title = {Comments On Hidden Nodes in Neural Nets}, 28623 journal = {IEEE Transactions on Circuits and Systems}, 28624 year = {1991}, 28625 volume = {38}, 28626 pages = {1410} 28627} 28628 28629@TechReport{ gertz.linderoth.ea:object-oriented, 28630 author = {M. Gertz and J. Linderoth and S. Wright}, 28631 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 28632 institution = {MCS Division, Argonne National Laboratory}, 28633 year = {in preparation} 28634} 28635 28636@Article{ ghellinck.vial:polynomial, 28637 author = {G. de Ghellinck and J.--Ph. Vial}, 28638 title = {A Polynomial {N}ewton Method for Linear Programming}, 28639 journal = {Algorithmica}, 28640 year = {1986}, 28641 volume = {1}, 28642 pages = {425--453} 28643} 28644 28645@InCollection{ gilbert.ng:predicting, 28646 author = {J. R. Gilbert and E. Ng}, 28647 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 28648 year = {1993}, 28649 booktitle = {Graph Theory and Sparse Matrix Computation}, 28650 editor = {A. George and J. Gilbert and J. Liu}, 28651 publisher = {Springer-Verlag} 28652} 28653 28654@Article{ gilbert-lemarechal, 28655 author = {J. C. Gilbert and C. Lemarechal}, 28656 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 28657 journal = {Mathematical Programming}, 28658 year = {1989}, 28659 volume = {45}, 28660 pages = {407--434} 28661} 28662 28663@Article{ gill.murray.ea:computing, 28664 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 28665 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 28666 journal = {SIAM Journal on Scientific and Statistical Computing}, 28667 year = {1983}, 28668 volume = {4}, 28669 pages = {310--321} 28670} 28671 28672@Article{ gill.murray.ea:maintaining, 28673 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 28674 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 28675 year = {1987}, 28676 journal = {Linear Algebra and Its Applications}, 28677 volume = {88/89}, 28678 pages = {239--270} 28679} 28680 28681@Book{ gill.murray.ea:practical, 28682 author = {P. E. Gill and W. Murray and M. H. 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Tseng}, 31652 title = {On the Convergence Rate of Dual Ascent Methods for Strictly Convex Minimization}, 31653 journal = {Mathematics of Operations Research}, 31654 year = {1993}, 31655 volume = {18}, 31656 pages = {846--867} 31657} 31658 31659@Article{ luo.tseng:error, 31660 author = {Z.--Q. Luo and P. Tseng}, 31661 title = {Error Bound and Convergence Analysis of Matrix Splitting Algorithms for the 31662 Affine Variational Inequality Problem}, 31663 journal = {SIAM Journal on Optimization}, 31664 year = {1992}, 31665 volume = {2}, 31666 pages = {43--54} 31667} 31668 31669@Article{ luo.tseng:error*1, 31670 author = {Z.-Q. Luo and P. Tseng}, 31671 title = {Error Bound and Reduced Gradient Projection Algorithms for Convex Minimization 31672 Over a Polyhedral Set}, 31673 journal = {SIAM Journal on Optimization}, 31674 year = {1993}, 31675 volume = {3}, 31676 pages = {43--59} 31677} 31678 31679@Article{ luo.tseng:error*2, 31680 author = {Z.-Q. Luo and P. Tseng}, 31681 title = {Error Bounds and Convergence Analysis of Feasible Descent Methods: {A} General 31682 Approach}, 31683 journal = {Annals of Operations Research}, 31684 year = {1993}, 31685 volume = {46}, 31686 pages = {157--178} 31687} 31688 31689@Article{ luo.tseng:global, 31690 author = {Z.-Q. Luo and P. Tseng}, 31691 title = {On Global Error Bound for a Class of Monotone Affine Variational Inequality 31692 Problems}, 31693 journal = {Operations Research Letters}, 31694 year = {1992}, 31695 volume = {11}, 31696 pages = {159--165} 31697} 31698 31699@Article{ luo.tseng:linear, 31700 author = {Z.-Q. Luo and P. Tseng}, 31701 title = {On the linear convergence of descent methods for convex essentially smooth 31702 minimization}, 31703 journal = {SIAM Journal on Control and Optimization}, 31704 year = {1992}, 31705 volume = {30}, 31706 pages = {408--425} 31707} 31708 31709@TechReport{ luo:convergence, 31710 author = {Z.-Q. Luo}, 31711 title = {Convergence Analysis of Primal--Dual Interior--Point Algorithms for Convex 31712 Quadratic Programs}, 31713 institution = {Communications Research Laboratory, McMaster University}, 31714 year = {1992}, 31715 address = {Hamilton, Ontario} 31716} 31717 31718@Article{ lustig.marsten.ea:computational, 31719 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31720 title = {Computational Experience with a Primal-Dual Interior Point Method for Linear 31721 Programming}, 31722 journal = {Linear Algebra and Its Applications}, 31723 year = {1991}, 31724 volume = {152}, 31725 pages = {191--222} 31726} 31727 31728@Article{ lustig.marsten.ea:implementing, 31729 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31730 title = {On implementing {M}ehrotra's predictor-corrector interior point method for linear 31731 programming}, 31732 journal = {SIAM Journal on Optimization}, 31733 year = {1992}, 31734 volume = {2}, 31735 pages = {435--449} 31736} 31737 31738@Article{ lustig.marsten.ea:interior-point, 31739 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 31740 title = {Interior-Point Methods for Linear Programming: Computational State of the Art}, 31741 journal = {ORSA Journal on Computing}, 31742 year = {1994}, 31743 volume = {6}, 31744 number = {1}, 31745 pages = {1--38} 31746} 31747 31748@Article{ lyman.wolbarst:optimization, 31749 author = {J. T. Lyman and A. B. 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Madsen}, 31798 title = {Minimization of Nonlinear Approximation Functions}, 31799 year = {1985}, 31800 address = {Lyngby, Denmark}, 31801 school = {Institute of Numerical Analysis, Technical University of Denmark}, 31802 annote = {Dissertation} 31803} 31804 31805@Book{ magill.quinzii:theory, 31806 author = {M. Magill and M. Quinzii}, 31807 title = {Theory of Incomplete Markets}, 31808 publisher = {MIT Press}, 31809 year = {1996} 31810} 31811 31812@InCollection{ magnanti:models, 31813 author = {T. L. Magnanti}, 31814 title = {Models and Algorithms for Predicting Urban Traffic Equilibria}, 31815 booktitle = {Transportation Planning Models}, 31816 year = {1984}, 31817 editor = {M. Florian}, 31818 publisher = {North Holland}, 31819 pages = {153--186} 31820} 31821 31822@InCollection{ maguregui:modified, 31823 author = {J. Maguregui}, 31824 title = {A modified {N}ewton algorithm for functions over convex sets}, 31825 crossref = {mangasarian.meyer.ea:nonlinear*3}, 31826 pages = {461--473} 31827} 31828 31829@PhDThesis{ maguregui:regular, 31830 author = {J. Maguregui}, 31831 title = {Regular Multivalued Functions and Algorithmic Applications}, 31832 year = {1977}, 31833 address = {Madison, Wisconsin}, 31834 school = {Computer Sciences Department, University of Wisconsin} 31835} 31836 31837@Article{ mahey.oualibouch.ea:proximal, 31838 author = {P. Mahey and S. Oualibouch and D. T. Pham}, 31839 title = {Proximal Decomposition on the Graph of a Maximal Monotone Operator}, 31840 journal = {SIAM Journal on Optimization}, 31841 year = {1995}, 31842 volume = {5}, 31843 pages = {454--466} 31844} 31845 31846@Article{ mahey.pham:partial, 31847 author = {P. Mahey and D. T. Pham}, 31848 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 31849 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 31850 year = {1993}, 31851 volume = {27}, 31852 pages = {375--392} 31853} 31854 31855@InCollection{ maier.novati:shakedown, 31856 author = {G. Maier and G. Novati}, 31857 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 31858 geometric effects with reference to discrete structural models}, 31859 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 31860 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 31861 publisher = {Pineridge Press}, 31862 address = {Swansea}, 31863 year = {1990}, 31864 pages = {451--471} 31865} 31866 31867@Article{ maier:incremental, 31868 author = {G. Maier}, 31869 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 31870 Instabilizing Effects}, 31871 journal = {International Journal of Solids and Structures}, 31872 volume = {7}, 31873 year = {1971}, 31874 pages = {345--372} 31875} 31876 31877@InCollection{ maier:inverse, 31878 author = {G. Maier}, 31879 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 31880 booktitle = {Serie VIII}, 31881 publisher = {Academia Nazionale dei Lincei}, 31882 year = {1981}, 31883 volume = {LXX}, 31884 pages = {203--209} 31885} 31886 31887@Article{ maier:matrix, 31888 author = {G. Maier}, 31889 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 31890 yield planes}, 31891 journal = {Meccanica}, 31892 volume = {5}, 31893 year = {1970}, 31894 pages = {54--66} 31895} 31896 31897@Article{ maier:quadratic, 31898 author = {G. Maier}, 31899 title = {A quadratic programming approach for certain classes of nonlinear structural 31900 problems}, 31901 journal = {Meccanica}, 31902 volume = {3}, 31903 year = {1968}, 31904 pages = {121--130} 31905} 31906 31907@Book{ manber:introduction, 31908 author = {U. Manber}, 31909 title = {Introduction to Algorithms: {A} Creative Approach}, 31910 year = {1989}, 31911 publisher = {Addison-Wesley} 31912} 31913 31914@Article{ mangasarian.deleone:error, 31915 author = {O. L. Mangasarian and R. {De~Leone}}, 31916 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 31917 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 31918 journal = {Applied Mathematics and Optimization}, 31919 year = {1988}, 31920 volume = {17}, 31921 pages = {1--14} 31922} 31923 31924@Article{ mangasarian.deleone:parallel, 31925 author = {O. L. Mangasarian and R. {De~Leone}}, 31926 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 31927 Problems and Linear Programs}, 31928 journal = {Journal of Optimization Theory and Applications}, 31929 year = {1987}, 31930 volume = {54}, 31931 pages = {437--446} 31932} 31933 31934@Article{ mangasarian.fromovitz:fritz, 31935 author = {O. L. Mangasarian and S. Fromovitz}, 31936 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 31937 and inequality constraints}, 31938 journal = {Journal of Mathematical Analysis and its Applications}, 31939 year = {1967}, 31940 volume = {17}, 31941 pages = {37--47} 31942} 31943 31944@Article{ mangasarian.mclinden:simple, 31945 author = {O. L. Mangasarian and L. McLinden}, 31946 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 31947 Programs}, 31948 journal = {Mathematical Programming}, 31949 year = {1985}, 31950 volume = {32}, 31951 pages = {32--40} 31952} 31953 31954@Article{ mangasarian.meyer:nonlinear, 31955 author = {O. L. Mangasarian and R. R. Meyer}, 31956 title = {Nonlinear Perturbation of Linear Programs}, 31957 journal = {SIAM Journal on Control and Optimization}, 31958 year = {1979}, 31959 volume = {17}, 31960 pages = {745--752} 31961} 31962 31963@TechReport{ mangasarian.musicant:active, 31964 author = {O. L. Mangasarian and David R. Musicant}, 31965 title = {Active Set Support Vector Machine Classification}, 31966 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31967 year = {2000}, 31968 number = {00-04}, 31969 address = {Madison, Wisconsin} 31970} 31971 31972@TechReport{ mangasarian.musicant:lagrangian, 31973 author = {O. L. Mangasarian and D. R. Musicant}, 31974 title = {Lagrangian Support Vector Machines}, 31975 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31976 year = {2000}, 31977 number = {00-06}, 31978 address = {Madison, Wisconsin} 31979} 31980 31981@TechReport{ mangasarian.musicant:robust, 31982 author = {O. L. Mangasarian and David R. Musicant}, 31983 title = {Robust Linear and Support Vector Regression}, 31984 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 31985 year = {1999}, 31986 number = {99-09}, 31987 address = {Madison, Wisconsin} 31988} 31989 31990@Article{ mangasarian.musicant:successive, 31991 author = {O. L. Mangasarian and David R. Musicant}, 31992 title = {Successive Overrelaxation for Support Vector Machines}, 31993 journal = {IEEE Transactions on Neural Networks}, 31994 volume = {10}, 31995 year = {1999}, 31996 pages = {1032-1037} 31997} 31998 31999@Article{ mangasarian.pang:exact, 32000 author = {O. L. Mangasarian and J. S. Pang}, 32001 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 32002 Constraints}, 32003 journal = {Optimization}, 32004 year = {1997}, 32005 volume = {42}, 32006 pages = {1--8} 32007} 32008 32009@Article{ mangasarian.pang:extended, 32010 author = {O. L. Mangasarian and J. S. Pang}, 32011 title = {The Extended Linear Complementarity Problem}, 32012 journal = {SIAM Journal on Matrix Analysis and Applications}, 32013 year = {1994}, 32014 volume = {16} 32015} 32016 32017@Article{ mangasarian.ren:error, 32018 author = {O. L. Mangasarian and J. Ren}, 32019 title = {New error bounds for the nonlinear complementarity problem}, 32020 year = {1994}, 32021 volume = {1}, 32022 pages = {49--56}, 32023 journal = {Communications on Applied Nonlinear Analysis} 32024} 32025 32026@Article{ mangasarian.ren:improved, 32027 author = {O. L. Mangasarian and J. Ren}, 32028 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 32029 year = {1994}, 32030 volume = {66}, 32031 journal = {Mathematical Programming}, 32032 pages = {241--255} 32033} 32034 32035@InProceedings{ mangasarian.setiono.ea:pattern, 32036 crossref = {coleman.li:large-scale}, 32037 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 32038 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 32039 Diagnosis}, 32040 pages = {22--31} 32041} 32042 32043@Article{ mangasarian.shiau:error, 32044 author = {O. L. Mangasarian and T.--H. Shiau}, 32045 title = {Error Bounds for Monotone Linear Complementarity Problems}, 32046 journal = {Mathematical Programming}, 32047 year = {1986}, 32048 volume = {36}, 32049 pages = {81--89} 32050} 32051 32052@Article{ mangasarian.shiau:lipschitz, 32053 author = {O. L. Mangasarian and T.--H. Shiau}, 32054 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 32055 Complementarity Problems}, 32056 journal = {SIAM Journal on Control and Optimization}, 32057 year = {1987}, 32058 volume = {25}, 32059 pages = {583--595} 32060} 32061 32062@Article{ mangasarian.solodov:nonlinear, 32063 author = {O. L. Mangasarian and M. V. Solodov}, 32064 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 32065 journal = {Mathematical Programming}, 32066 year = {1993}, 32067 volume = {62}, 32068 pages = {277--298} 32069} 32070 32071@Article{ mangasarian.solodov:serial, 32072 author = {O. L. Mangasarian and M. V. Solodov}, 32073 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 32074 Minimization}, 32075 year = {1994}, 32076 journal = {Optimization Methods and Software}, 32077 volume = {4}, 32078 pages = {103--116} 32079} 32080 32081@Article{ mangasarian.street.ea:breast, 32082 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 32083 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 32084 journal = {Operations Research}, 32085 year = {1995}, 32086 volume = {43}, 32087 pages = {570--577} 32088} 32089 32090@Article{ mangasarian.wolberg:cancer, 32091 author = {O. L. Mangasarian and W. H. Wolberg}, 32092 title = {Cancer Diagnosis via Linear Programming}, 32093 journal = {SIAM News}, 32094 year = {1990}, 32095 volume = {23}, 32096 pages = {1 \& 18} 32097} 32098 32099@InCollection{ mangasarian:applications, 32100 author = {O. L. Mangasarian}, 32101 title = {Some Applications of Penalty Functions in Mathematical Programming}, 32102 booktitle = {Optimization and Related Fields}, 32103 year = {1986}, 32104 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 32105 publisher = {Springer-Verlag}, 32106 address = {Heidelberg}, 32107 pages = {307--329}, 32108 note = {Lecture Notes in Mathematics 1190} 32109} 32110 32111@Article{ mangasarian:characterization, 32112 author = {O. L. Mangasarian}, 32113 title = {Characterization of linear complementarity problems as linear programs}, 32114 journal = {Mathematical Programming Study}, 32115 year = {1978}, 32116 volume = {7}, 32117 pages = {74--87} 32118} 32119 32120@InProceedings{ mangasarian:condition, 32121 author = {O. L. Mangasarian}, 32122 title = {A condition number for linear inequalities and linear programs}, 32123 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 32124 1981}, 32125 year = {1981}, 32126 editor = {G. Bamberg and O. Opitz}, 32127 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 32128 address = {Konigstein}, 32129 pages = {3--15} 32130} 32131 32132@Article{ mangasarian:convergence, 32133 author = {O. L. Mangasarian}, 32134 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 32135 Symmetric Monotone Linear Complementarity Problem}, 32136 journal = {SIAM Journal on Optimization}, 32137 volume = {1}, 32138 pages = {114--122}, 32139 year = {1991} 32140} 32141 32142@Article{ mangasarian:equivalence, 32143 author = {O. L. Mangasarian}, 32144 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 32145 journal = {SIAM Journal on Applied Mathematics}, 32146 year = {1976}, 32147 volume = {31}, 32148 pages = {89--92} 32149} 32150 32151@Article{ mangasarian:error, 32152 author = {O. L. Mangasarian}, 32153 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 32154 journal = {ORSA Journal on Computing}, 32155 volume = {15}, 32156 pages = {187--192}, 32157 year = {1994} 32158} 32159 32160@Article{ mangasarian:error*1, 32161 author = {O. L. Mangasarian}, 32162 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 32163 journal = {Mathematical Programming}, 32164 year = {1990}, 32165 volume = {48}, 32166 pages = {437--445} 32167} 32168 32169@Article{ mangasarian:generalized, 32170 author = {O. L. Mangasarian}, 32171 title = {Generalized Linear Complementarity Problems as Linear Programs}, 32172 journal = {Methods of Operations Research}, 32173 year = {1979}, 32174 editor = {W. Oettli and F. Steffens}, 32175 volume = {31}, 32176 pages = {393--402} 32177} 32178 32179@InCollection{ mangasarian:generalized*1, 32180 author = {O. L. Mangasarian}, 32181 title = {Generalized Support Vector Machines}, 32182 year = {2000}, 32183 pages = {135-146}, 32184 booktitle = {Advances in Large Margin Classifiers}, 32185 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 32186 publisher = {MIT Press}, 32187 address = {Cambridge, MA} 32188} 32189 32190@Article{ mangasarian:global, 32191 author = {O. L. Mangasarian}, 32192 title = {Global error bounds for monotone affine variational inequality problems}, 32193 journal = {Linear Algebra and Its Applications}, 32194 year = {1992}, 32195 pages = {153--164} 32196} 32197 32198@InCollection{ mangasarian:least, 32199 author = {O. L. Mangasarian}, 32200 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 32201 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 32202 year = {1990}, 32203 publisher = {Oxford University Press}, 32204 address = {New York}, 32205 pages = {217--221} 32206} 32207 32208@Article{ mangasarian:least-norm, 32209 author = {O. L. Mangasarian}, 32210 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 32211 Problem}, 32212 journal = {Journal of Mathematical Analysis and Applications}, 32213 year = {1983}, 32214 volume = {92}, 32215 pages = {240--251} 32216} 32217 32218@Article{ mangasarian:linear, 32219 author = {O. L. Mangasarian}, 32220 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 32221 journal = {Mathematical Programming}, 32222 year = {1976}, 32223 volume = {10}, 32224 pages = {263--270} 32225} 32226 32227@Article{ mangasarian:linear*1, 32228 author = {O. L. Mangasarian}, 32229 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 32230 journal = {Operations Research}, 32231 year = {1965}, 32232 volume = {13}, 32233 pages = {444--452} 32234} 32235 32236@Article{ mangasarian:locally, 32237 author = {O. L. Mangasarian}, 32238 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 32239 Complementarity Problems}, 32240 journal = {Mathematical Programming}, 32241 year = {1980}, 32242 volume = {19}, 32243 pages = {200--212} 32244} 32245 32246@InCollection{ mangasarian:machine, 32247 author = {O. L. Mangasarian}, 32248 title = {Machine Learning via Polyhedral Concave Minimization}, 32249 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 32250 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 32251 pages = {175-188}, 32252 year = {1996}, 32253 address = {Heidelberg}, 32254 publisher = {Physica-Verlag A Springer-Verlag Company} 32255} 32256 32257@Article{ mangasarian:mathematical, 32258 author = {O. L. Mangasarian}, 32259 title = {Mathematical Programming in Neural Networks}, 32260 journal = {ORSA Journal on Computing}, 32261 volume = {5}, 32262 pages = {349--360}, 32263 year = {1993} 32264} 32265 32266@InProceedings{ mangasarian:mathematical*1, 32267 author = {O. L. Mangasarian}, 32268 title = {Mathematical Programming in Machine Learning}, 32269 booktitle = {Nonlinear Optimization and Applications}, 32270 editor = {G. Di Pillo and F. Giannessi}, 32271 publisher = {Plenum Publishing}, 32272 address = {New York}, 32273 pages = {283--295}, 32274 year = {1996} 32275} 32276 32277@Article{ mangasarian:mathematical*2, 32278 author = {O. L. Mangasarian}, 32279 title = {Mathematical Programming in Data Mining}, 32280 journal = {Data Mining and Knowledge Discovery}, 32281 volume = {1}, 32282 year = {1997}, 32283 pages = {183-201} 32284} 32285 32286@Article{ mangasarian:multi-surface, 32287 author = {O. L. Mangasarian}, 32288 title = {Multi-surface Method of Pattern Separation}, 32289 journal = {IEEE Transactions on Information Theory}, 32290 year = {1968}, 32291 volume = {IT-14}, 32292 pages = {801--807} 32293} 32294 32295@Book{ mangasarian:nonlinear, 32296 author = {O. L. Mangasarian}, 32297 title = {Nonlinear Programming}, 32298 year = {1969}, 32299 publisher = {McGraw--Hill}, 32300 address = {New York}, 32301 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 32302} 32303 32304@Article{ mangasarian:normal, 32305 author = {O. L. Mangasarian}, 32306 title = {Normal Solutions of Linear Programs}, 32307 journal = {Mathematical Programming Study}, 32308 year = {1984}, 32309 volume = {22}, 32310 pages = {206--216} 32311} 32312 32313@Article{ mangasarian:optimal, 32314 author = {O. L. Mangasarian}, 32315 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 32316 Linear Programs}, 32317 journal = {Journal of Optimization Theory and Applications}, 32318 year = {1981}, 32319 volume = {35}, 32320 pages = {123--128} 32321} 32322 32323@Article{ mangasarian:parallel, 32324 author = {O. L. Mangasarian}, 32325 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 32326 journal = {SIAM Journal on Control and Optimization}, 32327 volume = {33}, 32328 pages = {1916--1925}, 32329 year = {1995} 32330} 32331 32332@TechReport{ mangasarian:regularized, 32333 author = {O. L. 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Petri}, 34106 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 34107 publisher = {Harvard University Press}, 34108 year = {1984} 34109} 34110 34111@InProceedings{ petrzykowski:application, 34112 author = {T. Petrzykowski}, 34113 title = {Application of the Steepest Ascent Method to Concave Programming}, 34114 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 34115 year = {1962}, 34116 publisher = {North--Holland}, 34117 address = {Amsterdam}, 34118 pages = {185--189} 34119} 34120 34121@InProceedings{ pettey.leuze.ea:parallel, 34122 crossref = {grefenstette:genetic}, 34123 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 34124 title = {A Parallel Genetic Algorithm}, 34125 pages = {155--161} 34126} 34127 34128@InProceedings{ pettey.leuze:theoretical, 34129 crossref = {schaeffer:third}, 34130 author = {C. C. Pettey and M. R. 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Bonnans}, 34339 title = {Infeasible path following algorithms for linear complementarity problems}, 34340 institution = {INRIA}, 34341 year = {1994}, 34342 month = dec, 34343 number = {RR--2445}, 34344 type = {Research Report} 34345} 34346 34347@Article{ potra.sheng:large-step, 34348 author = {F. A. Potra and R. Sheng}, 34349 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 34350 year = {1997}, 34351 journal = {SIAM Journal on Optimization}, 34352 volume = {7}, 34353 pages = {318--335} 34354} 34355 34356@Article{ potra:infeasible, 34357 author = {F. A. Potra}, 34358 title = {An infeasible interior-point predictor-corrector algorithm for linear 34359 programming}, 34360 journal = {SIAM Journal on Optimization}, 34361 year = {1996}, 34362 volume = {6}, 34363 pages = {19--32} 34364} 34365 34366@TechReport{ potra:onl, 34367 author = {F. A. 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Pruyne}, 34509 title = {Resource Management Services for Parallel Applications}, 34510 school = {University of Wisconsin--Madison}, 34511 year = {1996}, 34512 address = {Madison, Wisconsin} 34513} 34514 34515@Book{ pshenichny.danilin:numerical, 34516 author = {B. N. Pshenichny and Yu. M. Danilin}, 34517 title = {Numerical Methods in Extremal Problems}, 34518 year = {1978}, 34519 publisher = {MIR Publishers}, 34520 address = {Moscow} 34521} 34522 34523@TechReport{ qi.chen:globally, 34524 author = {L. Qi and X. Chen}, 34525 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 34526 institution = {School of Mathematics, University of New South Wales}, 34527 year = {1993}, 34528 annote = {revised}, 34529 address = {Sydney} 34530} 34531 34532@Article{ qi.jiang:semismooth, 34533 author = {L. Qi and H. 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Rockafellar}, 35120 title = {A Generalized Approach to Linear-Quadratic Programming}, 35121 booktitle = {Proceedings of the International Conference on Numerical Optimization and 35122 Applications}, 35123 year = {1986}, 35124 pages = {58--66}, 35125 note = {(Xi'an, China)} 35126} 35127 35128@InProceedings{ rockafellar:generalized*1, 35129 crossref = {bachem.grotschel.ea:mathematical}, 35130 author = {R. T. Rockafellar}, 35131 title = {Generalized Subgradients in Mathematical Programming}, 35132 pages = {368--390} 35133} 35134 35135@InCollection{ rockafellar:large-scale, 35136 author = {R. T. Rockafellar}, 35137 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 35138 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 35139 chapter = {15}, 35140 year = {1991}, 35141 editor = {S. Gomez and J. P. Hennart and R. A. 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Rockafellar}, 35201 title = {Network Flows and Monotropic Optimization}, 35202 publisher = {John Wiley}, 35203 year = {1984}, 35204 address = {New York} 35205} 35206 35207@Article{ rodrigues:mixed, 35208 author = {H. C. Rodrigues}, 35209 title = {A mixed variational formulation for shape optimization of solids with contact 35210 conditions}, 35211 journal = {Structural Optimization}, 35212 volume = {6}, 35213 year = {1993}, 35214 pages = {19--28} 35215} 35216 35217@Book{ rodrigues:obstacle, 35218 author = {J. F. Rodrigues}, 35219 title = {Obstacle Problems in Mathematical Physics}, 35220 publisher = {Elsevier Publishing Company}, 35221 address = {Amsterdam}, 35222 year = {1987} 35223} 35224 35225@Book{ roos.terlaky.ea:theory, 35226 author = {C. Roos and T. Terlaky and J.--Ph. Vial}, 35227 title = {Theory and Algorithms for Linear Optimization: An Interior-Point Approach}, 35228 publisher = {John Wiley \& Sons}, 35229 year = {1997}, 35230 address = {Chichester} 35231} 35232 35233@TechReport{ rosa:decomposition, 35234 author = {C. H. Rosa}, 35235 title = {A Decomposition Technique for Equilibrium Programming under Uncertainty}, 35236 institution = {IIASA}, 35237 year = {1996}, 35238 number = {WP-96-013}, 35239 address = {A-2361 Laxenburg, Austria} 35240} 35241 35242@Article{ rosen.lane.ea:treatment, 35243 author = {I. Rosen and R. Lane and S. Morrill and J. Belli}, 35244 title = {Treatment Plan Optimization Using Linear Programming}, 35245 journal = {Medical Physics}, 35246 year = {1990}, 35247 volume = {18}, 35248 number = {2}, 35249 pages = {141--152} 35250} 35251 35252@TechReport{ rosenblatt:perceptron-a, 35253 author = {F. 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{Fr\'{e}d\'{e}ric Alauzet}, 37881 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 37882 year = {2010} 37883} 37884 37885@Article{ chan1994qmrcgs, 37886 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 37887 systems}, 37888 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 37889 and Tong, Charles H}, 37890 journal = {SIAM Journal on Scientific Computing}, 37891 volume = {15}, 37892 number = {2}, 37893 pages = {338--347}, 37894 year = {1994}, 37895 publisher = {SIAM} 37896} 37897 37898@Article{ ghai2019comparison, 37899 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 37900 nonsymmetric linear systems}, 37901 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 37902 journal = {Numerical Linear Algebra with Applications}, 37903 volume = {26}, 37904 number = {1}, 37905 pages = {e2215}, 37906 year = {2019}, 37907 publisher = {Wiley 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Knepley}, 37914 journal = {International Journal on Numerical Methods in Engineering}, 37915 note = {Submitted}, 37916 year = {2022} 37917} 37918 37919@Article{ nathawaniknepley2022, 37920 title = {Droplet formation simulation using mixed finite elements}, 37921 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37922 journal = {Physics of Fluids}, 37923 volume = {34}, 37924 pages = {064105}, 37925 doi = {10.1063/5.0089752}, 37926 year = {2022} 37927} 37928 37929@InProceedings{ nathawaniknepley2022b, 37930 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 37931 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37932 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 37933 (ICCFD11)}, 37934 editor = {Christoph Brehm and Shishir Pandya}, 37935 number = {4103}, 37936 year = {2022} 37937} 37938 37939@Article{ nathawaniknepley2023, 37940 title = {One-dimensional model to simulate shear-induced droplet formation}, 37941 author = {Darsh K. Nathawani and Matthew G. Knepley}, 37942 journal = {Physics of Fluids}, 37943 note = {Submitted}, 37944 year = {2023} 37945} 37946 37947@Article{ georgalisnathawaniknepleypatra2023, 37948 title = {Uncertainty quantification of droplet atomization and pinch-off with {Gaussian 37949 Processes}}, 37950 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. 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Duarte}, 37973 pages = {539-571}, 37974 isbn = {978-0-323-85733-8}, 37975 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 37976 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 37977 year = {2023} 37978} 37979 37980@Article{ adamsknepley2023, 37981 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 37982 plasmas in {PETSc}}, 37983 author = {Mark F. Adams and Matthew G. Knepley}, 37984 url = {https://arxiv.org/abs/2302.10242}, 37985 note = {In preparation}, 37986 year = {2023}, 37987 petsc_uses = {DMPlex} 37988} 37989 37990@Article{ finnknepleypusztayadams2023, 37991 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 37992 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. 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Pusztay}, 38013 type = {{PhD} thesis}, 38014 school = {University at Buffalo, Department of Computer Science and Engineering}, 38015 address = {Buffalo, NY}, 38016 month = {May}, 38017 year = {2022} 38018} 38019 38020@PhDThesis{ finnthesis2023, 38021 title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau 38022 System}, 38023 author = {Daniel S. Finn}, 38024 type = {{PhD} thesis}, 38025 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38026 Engineering}, 38027 address = {Buffalo, NY}, 38028 month = {May}, 38029 year = {2023} 38030} 38031 38032@PhDThesis{ nathawanithesis2023, 38033 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 38034 author = {Darsh Kiritbhai Nathawani}, 38035 type = {{PhD} thesis}, 38036 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 38037 Engineering}, 38038 address = {Buffalo, NY}, 38039 month = {May}, 38040 year = {2023} 38041} 38042
