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{veldhuizen1984d, 20 title = {{D}-stability and {K}aps-{R}entrop-methods}, 21 author = {Veldhuizen, M van}, 22 journal = {Computing}, 23 volume = {32}, 24 number = {3}, 25 pages = {229--237}, 26 year = {1984}, 27 publisher = {Springer} 28} 29 30@article{shampine1982implementation, 31 title = {Implementation of {R}osenbrock methods}, 32 author = {Shampine, Lawrence F}, 33 journal = {ACM Transactions on Mathematical Software (TOMS)}, 34 volume = {8}, 35 number = {2}, 36 pages = {93--113}, 37 year = {1982}, 38 publisher = {ACM New York, NY, USA} 39} 40 41@book{wanner1996solving, 42 title = {Solving ordinary differential equations {II}}, 43 author = {Wanner, Gerhard and Hairer, Ernst}, 44 volume = {375}, 45 year = {1996}, 46 publisher = {Springer Berlin Heidelberg New York} 47} 48 49@article{kaps1979generalized, 50 title = {Generalized {R}unge--{K}utta methods of order four with stepsize control for stiff ordinary differential equations}, 51 author = {Kaps, Peter and Rentrop, Peter}, 52 journal = {Numerische Mathematik}, 53 volume = {33}, 54 pages = {55--68}, 55 year = {1979}, 56 publisher = {Springer} 57} 58 59@book{butcher2016numerical, 60 title = {Numerical methods for ordinary differential equations}, 61 author = {Butcher, John Charles}, 62 year = {2016}, 63 publisher = {John Wiley \& Sons} 64} 65 66@article{chung1993, 67 author = {Chung, J. and Hulbert, G. M.}, 68 title = {A Time Integration Algorithm for Structural Dynamics With Improved Numerical Dissipation: The Generalized-alpha Method}, 69 journal = {Journal of Applied Mechanics}, 70 volume = {60}, 71 number = {2}, 72 pages = {371-375}, 73 year = {1993}, 74 month = {06}, 75 issn = {0021-8936}, 76 doi = {10.1115/1.2900803}, 77 url = {https://doi.org/10.1115/1.2900803}, 78 eprint = {https://asmedigitalcollection.asme.org/appliedmechanics/article-pdf/60/2/371/5463014/371\_1.pdf}, 79} 80 81@article{hosea1996analysis, 82 title = {Analysis and implementation of {TR-BDF2}}, 83 author = {Hosea, ME and Shampine, LF}, 84 journal = {Applied Numerical Mathematics}, 85 volume = {20}, 86 number = {1-2}, 87 pages = {21--37}, 88 year = {1996}, 89 publisher = {Elsevier} 90} 91 92@article{kennedy2019diagonally, 93 title = {Diagonally implicit {R}unge--{K}utta methods for stiff {ODE}s}, 94 author = {Kennedy, Christopher A and Carpenter, Mark H}, 95 journal = {Applied Numerical Mathematics}, 96 volume = {146}, 97 pages = {221--244}, 98 year = {2019}, 99 publisher = {Elsevier} 100} 101 102@inproceedings{xu2017adaptive, 103 title = {Adaptive relaxed {ADMM}: Convergence theory and practical implementation}, 104 author = {Xu, Zheng and Figueiredo, Mario AT and Yuan, Xiaoming and Studer, Christoph and Goldstein, Tom}, 105 booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition}, 106 pages = {7389--7398}, 107 year = {2017} 108} 109 110@article{hindmarsh1996time, 111 title = {Time-step limits for stable solutions of the ice-sheet equation}, 112 author = {Hindmarsh, Richard CA and Payne, Antony J}, 113 journal = {Annals of Glaciology}, 114 volume = {23}, 115 pages = {74--85}, 116 year = {1996}, 117 publisher = {Cambridge University Press} 118} 119 120@article{benson2006flexible, 121 title = {Flexible complementarity solvers for large-scale applications}, 122 author = {Benson, Steven J and Munson, Todd S}, 123 journal = {Optimization Methods and Software}, 124 volume = {21}, 125 number = {1}, 126 pages = {155--168}, 127 year = {2006}, 128 publisher ={Taylor \& Francis} 129} 130 131@article{byrd1994representations, 132 title = {Representations of quasi-{N}ewton matrices and their use in limited memory methods}, 133 author = {Byrd, Richard H and Nocedal, Jorge and Schnabel, Robert B}, 134 journal = {Mathematical Programming}, 135 volume = {63}, 136 number = {1-3}, 137 pages = {129--156}, 138 year = {1994}, 139 publisher = {Springer} 140} 141 142@article{gilbert1989some, 143 title = {Some numerical experiments with variable-storage quasi-{N}ewton algorithms}, 144 author = {Gilbert, Jean Charles and Lemar{\'e}chal, Claude}, 145 journal = {Mathematical programming}, 146 volume = {45}, 147 number = {1-3}, 148 pages = {407--435}, 149 year = {1989}, 150 publisher = {Springer} 151} 152 153@inproceedings{dener2019accelerating, 154 title = {Accelerating limited-memory quasi-{N}ewton convergence for large-scale optimization}, 155 author = {Dener, Alp and Munson, Todd}, 156 booktitle = {Computational Science--ICCS 2019: 19th International Conference, Faro, Portugal, June 12--14, 2019, Proceedings, Part III 19}, 157 pages = {495--507}, 158 year = {2019}, 159 organization = {Springer} 160} 161 162@article{park2021linear, 163 title = {Linear and nonlinear solvers for simulating multiphase flow within large-scale engineered subsurface systems}, 164 author = {Park, Heeho D and Hammond, Glenn E and Valocchi, Albert J and LaForce, Tara}, 165 journal = {Advances in Water Resources}, 166 volume = {156}, 167 pages = {104029}, 168 year = {2021}, 169 publisher = {Elsevier} 170} 171 172@inproceedings{va1981design, 173 title = {Design of optimally smoothing multi-stage schemes for the {E}uler equations}, 174 author = {Van Leer, Bram and Tai, Chang-Hsien and Powell, Kenneth}, 175 booktitle = {9th Computational Fluid Dynamics Conference}, 176 pages = {1933}, 177 year = {1981} 178} 179 180@article{pierce1997preconditioned, 181 title = {Preconditioned multigrid methods for compressible flow calculations on stretched meshes}, 182 author = {Pierce, Niles A and Giles, Michael B}, 183 journal = {Journal of Computational Physics}, 184 volume = {136}, 185 number = {2}, 186 pages = {425--445}, 187 year = {1997}, 188 publisher = {Elsevier} 189} 190 191@article{kong2016highly, 192 title = {A highly scalable multilevel {S}chwarz method with boundary geometry preserving coarse spaces for {3D} elasticity problems on domains with complex geometry}, 193 author = {Kong, Fande and Cai, Xiao-Chuan}, 194 journal = {SIAM Journal on Scientific Computing}, 195 volume = {38}, 196 number = {2}, 197 pages = {C73--C95}, 198 year = {2016}, 199 publisher = {SIAM} 200} 201 202@inproceedings{gutierrez2017accommodating, 203 title = {Accommodating thread-level heterogeneity in coupled parallel applications}, 204 author = {Guti{\'e}rrez, Samuel K and Davis, Kei and Arnold, Dorian C and Baker, Randal S and Robey, Robert W and McCormick, Patrick and 205 Holladay, Daniel and Dahl, Jon A and Zerr, R Joe and Weik, Florian and others}, 206 booktitle = {2017 {IEEE} International Parallel and Distributed Processing Symposium ({IPDPS})}, 207 pages = {469--478}, 208 year = {2017}, 209 organization = {IEEE} 210} 211 212@article{heroux2011bi, 213 title = {Bi-modal MPI and MPI+ threads computing on scalable multicore systems}, 214 author = {Heroux, Michael A and Brightwell, R and Wolf, Michael M}, 215 journal = {IJHPCA (Submitted)}, 216 year = {2011} 217} 218 219@inproceedings{bozdaug2005parallel, 220 title = {A parallel distance-2 graph coloring algorithm for distributed memory computers}, 221 author = {Bozda{\u{g}}, Doruk and Catalyurek, Umit and Gebremedhin, Assefaw H and Manne, Fredrik and Boman, Erik G and {\"O}zg{\"u}ner, F{\"u}sun}, 222 booktitle = {International conference on high performance computing and communications}, 223 pages = {796--806}, 224 year = {2005}, 225 organization = {Springer} 226} 227 228@article{dohrmann2009overlapping, 229 title = {An overlapping {S}chwarz algorithm for almost incompressible elasticity}, 230 author = {Dohrmann, Clark R and Widlund, Olof B}, 231 journal = {SIAM journal on numerical analysis}, 232 volume = {47}, 233 number = {4}, 234 pages = {2897--2923}, 235 year = {2009}, 236 publisher = {SIAM} 237} 238 239@article{dohrmann2008domain, 240 title = {Domain decomposition for less regular subdomains: Overlapping {S}chwarz in two dimensions}, 241 author = {Dohrmann, Clark R and Klawonn, Axel and Widlund, Olof B}, 242 journal = {SIAM journal on numerical analysis}, 243 volume = {46}, 244 number = {4}, 245 pages = {2153--2168}, 246 year = {2008}, 247 publisher = {SIAM} 248} 249 250@incollection{dohrmann2008family, 251 title = {A family of energy minimizing coarse spaces for overlapping {S}chwarz preconditioners}, 252 author = {Dohrmann, Clark R and Klawonn, Axel and Widlund, Olof B}, 253 booktitle = {Domain decomposition methods in science and engineering XVII}, 254 pages = {247--254}, 255 year = {2008}, 256 publisher = {Springer} 257} 258 259@book{dohrmann2008extending, 260 title = {Extending theory for domain decomposition algorithms to irregular subdomains}, 261 author = {Dohrmann, Clark R and Klawonn, Axel and Widlund, Olof B}, 262 year = {2008}, 263 publisher = {Springer} 264} 265 266@article{dryja1994schwarz, 267 title = {{S}chwarz analysis of iterative substructuring algorithms for elliptic problems in three dimensions}, 268 author = {Dryja, Maksymilian and Smith, Barry F and Widlund, Olof B}, 269 journal = {SIAM journal on numerical analysis}, 270 volume = {31}, 271 number = {6}, 272 pages = {1662--1694}, 273 year = {1994}, 274 publisher = {SIAM} 275} 276 277@book{smith1990domain, 278 title = {Domain decomposition algorithms for the partial differential equations of linear elasticity}, 279 author = {Smith, Barry F}, 280 year = {1990}, 281 publisher = {New York University} 282} 283 284@article{bramble1989construction, 285 title = {The construction of preconditioners for elliptic problems by substructuring. {IV}}, 286 author = {Bramble, James H and Pasciak, Joseph E and Schatz, Alfred H}, 287 journal = {Mathematics of Computation}, 288 volume = {53}, 289 number = {187}, 290 pages = {1--24}, 291 year = {1989} 292} 293 294@article{kaczmarz1937angenaherte, 295 title = {Angenaherte auflosung von systemen linearer gleichungen}, 296 author = {Kaczmarz, Stefan}, 297 journal = {Bull. Int. Acad. Pol. Sic. Let., Cl. Sci. Math. Nat.}, 298 pages = {355--357}, 299 year = {1937} 300} 301 302@article{nataf2022recent, 303 title = {Recent advances in domain decomposition methods for large-scale saddle point problems}, 304 author = {Nataf, Fr{\'e}d{\'e}ric and Tournier, Pierre-Henri}, 305 journal = {Comptes Rendus. M{\'e}canique}, 306 volume = {350}, 307 number = {S1}, 308 pages = {1--15}, 309 year = {2022} 310} 311 312@article{al2022robustpd, 313 title = {A robust algebraic multilevel domain decomposition preconditioner for sparse symmetric positive definite matrices}, 314 author = {Al Daas, Hussam and Jolivet, Pierre}, 315 journal = {SIAM Journal on Scientific Computing}, 316 volume = {44}, 317 number = {4}, 318 pages = {A2582--A2598}, 319 year = {2022}, 320 publisher = {SIAM} 321} 322 323@article{al2022robust, 324 title = {A robust algebraic domain decomposition preconditioner for sparse normal equations}, 325 author = {Al Daas, Hussam and Jolivet, Pierre and Scott, Jennifer A}, 326 journal = {SIAM Journal on Scientific Computing}, 327 volume = {44}, 328 number = {3}, 329 pages = {A1047--A1068}, 330 year = {2022}, 331 publisher = {SIAM} 332} 333 334@article{al2021multilevel, 335 title = {A multilevel {S}chwarz preconditioner based on a hierarchy of robust coarse spaces}, 336 author = {Al Daas, Hussam and Grigori, Laura and Jolivet, Pierre and Tournier, Pierre-Henri}, 337 journal = {SIAM Journal on Scientific Computing}, 338 volume = {43}, 339 number = {3}, 340 pages = {A1907--A1928}, 341 year = {2021}, 342 publisher = {SIAM} 343} 344 345@book{dolean2015introduction, 346 title = {An introduction to domain decomposition methods: algorithms, theory, and parallel implementation}, 347 author = {Dolean, Victorita and Jolivet, Pierre and Nataf, Fr{\'e}d{\'e}ric}, 348 year = {2015}, 349 publisher = {SIAM} 350} 351 352@article{spillane2011robust, 353 title = {A robust two-level domain decomposition preconditioner for systems of {PDE}s}, 354 author = {Spillane, Nicole and Dolean, Victorita and Hauret, Patrice and Nataf, Fr{\'e}d{\'e}ric and Pechstein, Clemens and Scheichl, Robert}, 355 journal = {Comptes Rendus Mathematique}, 356 volume = {349}, 357 number = {23-24}, 358 pages = {1255--1259}, 359 year = {2011}, 360 publisher = {Elsevier} 361} 362 363@article{kong2020highly, 364 title = {A Highly Parallel Multilevel {N}ewton--{K}rylov--{S}chwarz Method with Subspace-Based Coarsening and 365 Partition-Based Balancing for the Multigroup Neutron Transport Equation on Three-Dimensional Unstructured Meshes}, 366 author = {Kong, Fande and Wang, Yaqi and Gaston, Derek R and Permann, Cody J and Slaughter, Andrew E and Lindsay, 367 Alexander D and DeHart, Mark D and Martineau, Richard C}, 368 journal = {SIAM Journal on Scientific Computing}, 369 volume = {42}, 370 number = {5}, 371 pages = {C193--C220}, 372 year = {2020}, 373 publisher = {SIAM} 374} 375 376@article{ipsen2001note, 377 title = {A note on preconditioning nonsymmetric matrices}, 378 author = {Ipsen, Ilse CF}, 379 journal = {SIAM Journal on Scientific Computing}, 380 volume = {23}, 381 number = {3}, 382 pages = {1050--1051}, 383 year = {2001}, 384 publisher = {SIAM} 385} 386 387@article{murphy2000note, 388 title = {A note on preconditioning for indefinite linear systems}, 389 author = {Murphy, Malcolm F and Golub, Gene H and Wathen, Andrew J}, 390 journal = {SIAM Journal on Scientific Computing}, 391 volume = {21}, 392 number = {6}, 393 pages = {1969--1972}, 394 year = {2000}, 395 publisher = {SIAM} 396} 397 398@article{oliphant1961implicit, 399 title = {An implicit, numerical method for solving two-dimensional time-dependent diffusion problems}, 400 author = {Oliphant, Thomas A}, 401 journal = {Quarterly of Applied mathematics}, 402 volume = {19}, 403 number = {3}, 404 pages = {221--229}, 405 year = {1961} 406} 407 408@article{dupont1968approximate, 409 title = {An approximate factorization procedure for solving self-adjoint elliptic difference equations}, 410 author = {Dupont, Todd and Kendall, Richard P and Rachford, Jr, HH}, 411 journal = {SIAM Journal on Numerical Analysis}, 412 volume = {5}, 413 number = {3}, 414 pages = {559--573}, 415 year = {1968}, 416 publisher = {SIAM} 417} 418 419@inproceedings{manteuffel1979shifted, 420 title = {Shifted incomplete {C}holesky factorization}, 421 author = {Manteuffel, Thomas A}, 422 booktitle = {Sparse Matrix Proceedings 1978}, 423 pages = {41--61}, 424 year = {1979}, 425 organization = {SIAM, Philadelphia, PA} 426} 427 428@incollection{chan1997approximate, 429 title = {Approximate and incomplete factorizations}, 430 author = {Chan, Tony F and Van Der Vorst, Henk A}, 431 booktitle = {Parallel numerical algorithms}, 432 pages = {167--202}, 433 year = {1997}, 434 publisher = {Springer} 435} 436 437@article{mandel2008multispace, 438 title = {Multispace and multilevel {BDDC}}, 439 author = {Mandel, Jan and Soused{\'\i}k, Bed{\v{r}}ich and Dohrmann, Clark R}, 440 journal = {Computing}, 441 volume = {83}, 442 number = {2-3}, 443 pages = {55--85}, 444 year = {2008}, 445 publisher = {Springer} 446} 447 448@article{klawonn2006dual, 449 title = {Dual-primal {FETI} methods for linear elasticity}, 450 author = {Klawonn, Axel and Widlund, Olof B}, 451 journal = {Communications on Pure and Applied Mathematics: A Journal Issued by the Courant Institute of Mathematical Sciences}, 452 volume = {59}, 453 number = {11}, 454 pages = {1523--1572}, 455 year = {2006}, 456 publisher = {Wiley Online Library} 457} 458 459@article{dohrmann2007approximate, 460 title = {An approximate {BDDC} preconditioner}, 461 author = {Dohrmann, Clark R}, 462 journal = {Numerical Linear Algebra with Applications}, 463 volume = {14}, 464 number = {2}, 465 pages = {149--168}, 466 year = {2007}, 467 publisher = {Wiley Online Library} 468} 469 470@book{dryja1987additive, 471 title = {An additive variant of the {S}chwarz alternating method for the case of many subregions}, 472 author = {Dryja, Maksymilian and Widlund, Olof}, 473 year = {1987}, 474 publisher = {Ultracomputer Research Laboratory, Univ., Courant Inst. of Mathematical~…} 475} 476 477@article{couturier2016tsirm, 478 title = {{TSIRM}: A two-stage iteration with least-squares residual minimization algorithm to solve large sparse linear and nonlinear systems}, 479 author = {Couturier, Rapha{\"e}l and Khodja, Lilia Ziane and Guyeux, Christophe}, 480 journal = {Journal of Computational Science}, 481 volume = {17}, 482 pages = {535--546}, 483 year = {2016}, 484 publisher = {Elsevier} 485} 486 487@article{chan1998transpose, 488 title = {Transpose-free formulations of Lanczos-type methods for nonsymmetric linear systems}, 489 author = {Chan, Tony F and De Pillis, Lisette and Van Der Vorst, Henk}, 490 journal = {Numerical Algorithms}, 491 volume = {17}, 492 pages = {51--66}, 493 year = {1998}, 494 publisher = {Springer} 495} 496 497@article{catabriga2006performance, 498 title = {Performance of {LCD} iterative method in the finite element and finite difference solution of convection--diffusion equations}, 499 author = {Catabriga, L and Valli, AMP and Melotti, BZ and Pessoa, LM and Coutinho, ALGA}, 500 journal = {Communications in numerical methods in engineering}, 501 volume = {22}, 502 number = {6}, 503 pages = {643--656}, 504 year = {2006}, 505 publisher = {Wiley Online Library} 506} 507 508@article{catabriga2004evaluating, 509 title = {Evaluating the {LCD} algorithm for solving linear systems of equations arising from implicit {SUPG} formulation of compressible flows}, 510 author = {Catabriga, Lucia and Coutinho, Alvaro LGA and Franca, Leopoldo P}, 511 journal = {International Journal for Numerical Methods in Engineering}, 512 volume = {60}, 513 number = {9}, 514 pages = {1513--1534}, 515 year = {2004}, 516 publisher = {Wiley Online Library} 517} 518 519@article{dai2004study, 520 title = {Study on semi-conjugate direction methods for non-symmetric systems}, 521 author = {Dai, Yu-Hong and Yuan, Jinyun}, 522 journal = {International journal for numerical methods in engineering}, 523 volume = {60}, 524 number = {8}, 525 pages = {1383--1399}, 526 year = {2004}, 527 publisher = {Wiley Online Library} 528} 529 530@article{yuan2004semi, 531 title = {Semi-conjugate direction methods for real positive definite systems}, 532 author = {Yuan, JY and Golub, Gene H and Plemmons, Robert J and Cecilio, WAG}, 533 journal = {BIT Numerical Mathematics}, 534 volume = {44}, 535 pages = {189--207}, 536 year = {2004}, 537 publisher = {Springer} 538} 539 540@article{ji2017breakdown, 541 title = {A breakdown-free block conjugate gradient method}, 542 author = {Ji, Hao and Li, Yaohang}, 543 journal = {BIT Numerical Mathematics}, 544 volume = {57}, 545 pages = {379--403}, 546 year = {2017}, 547 publisher = {Springer} 548} 549 550@inproceedings{jolivet2016block, 551 title = {Block iterative methods and recycling for improved scalability of linear solvers}, 552 author = {Jolivet, Pierre and Tournier, Pierre-Henri}, 553 booktitle = {SC'16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis}, 554 pages = {190--203}, 555 year = {2016}, 556 organization = {IEEE} 557} 558 559@article{calandra2013modified, 560 title = {A modified block flexible {GMRES} method with deflation at each iteration for the solution of non-{H}ermitian linear systems with multiple right-hand sides}, 561 author = {Calandra, Henri and Gratton, Serge and Lago, Rafael and Vasseur, Xavier and Carvalho, Luiz Mariano}, 562 journal = {SIAM Journal on Scientific Computing}, 563 volume = {35}, 564 number = {5}, 565 pages = {S345--S367}, 566 year = {2013}, 567 publisher = {SIAM} 568} 569 570@article{o1980block, 571 title = {The block conjugate gradient algorithm and related methods}, 572 author = {O'Leary, Dianne P}, 573 journal = {Linear algebra and its applications}, 574 volume = {29}, 575 pages = {293--322}, 576 year = {1980}, 577 publisher = {Elsevier} 578} 579 580@article{erhel1996restarted, 581 title = {Restarted {GMRES} preconditioned by deflation}, 582 author = {Erhel, Jocelyne and Burrage, Kevin and Pohl, Bert}, 583 journal = {Journal of computational and applied mathematics}, 584 volume = {69}, 585 number = {2}, 586 pages = {303--318}, 587 year = {1996}, 588 publisher = {Elsevier} 589} 590 591@article{bai1994newton, 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621@article{demmel2012communication, 622 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 623 author = {Demmel, James and Grigori, Laura and Hoemmen, Mark and Langou, Julien}, 624 journal = {SIAM Journal on Scientific Computing}, 625 volume = {34}, 626 number = {1}, 627 pages = {A206--A239}, 628 year = {2012}, 629 publisher = {SIAM} 630} 631 632@article{philippe2012generation, 633 title = {On the generation of {K}rylov subspace bases}, 634 author = {Philippe, Bernard and Reichel, Lothar}, 635 journal = {Applied Numerical Mathematics}, 636 volume = {62}, 637 number = {9}, 638 pages = {1171--1186}, 639 year = {2012}, 640 publisher = {Elsevier} 641} 642 643@article{wakam2013memory, 644 title = {Memory efficient hybrid algebraic solvers for linear systems arising from compressible flows}, 645 author = {Wakam, D{\'e}sir{\'e} Nuentsa and Pacull, Fran{\c{c}}ois}, 646 journal = {Computers \& Fluids}, 647 volume = {80}, 648 pages = {158--167}, 649 year = {2013}, 650 publisher = {Elsevier} 651} 652 653@misc{wakam2011parallelism, 654 title = {Parallelism and robustness in {GMRES} with the {N}ewton basis and the deflated restarting}, 655 author = {Wakam, D{\'e}sir{\'e} Nuentsa and Erhel, Jocelyne}, 656 year = {2011}, 657 url = {https://hal.inria.fr/inria-00638247/en} 658} 659 660@article{tu2015feti, 661 title = {A {FETI-DP} type domain decomposition algorithm for three-dimensional incompressible {S}tokes equations}, 662 author = {Tu, Xuemin and Li, Jing}, 663 journal = {SIAM Journal on Numerical Analysis}, 664 volume = {53}, 665 number = {2}, 666 pages = {720--742}, 667 year = {2015}, 668 publisher = {SIAM} 669} 670 671@article{farhat2001feti, 672 title = {{FETI-DP}: a dual--primal unified {FETI} method—part {I}: A faster alternative to the two-level {FETI} method}, 673 author = {Farhat, Charbel and Lesoinne, Michel and LeTallec, Patrick and Pierson, Kendall and Rixen, Daniel}, 674 journal = {International journal for numerical methods in 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Appl. Phys.}, 1391 volume = {99}, 1392 year = {2006}, 1393 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 1394 petsc_uses = {KSP} 1395} 1396 1397@InProceedings{ japios2006, 1398 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 1399 Subramanian}, 1400 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 1401 in systems with cubic and uniaxial anisotropy.}, 1402 booktitle = {Intermag 2006 Conference}, 1403 petsc_uses = {KSP} 1404} 1405 1406@Article{ kbmb2006, 1407 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 1408 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 1409 Perpendicular Recording Heads}, 1410 journal = {IEEE Trans. Magn.}, 1411 volume = {42}, 1412 year = {2006}, 1413 pages = {2428--2430}, 1414 doi = {10.1109/TMAG.2006.879430}, 1415 petsc_uses = {KSP} 1416} 1417 1418@Article{ cclcw2006, 1419 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 1420 title = {Control of Domain Wall Motion in Permalloy Ring}, 1421 journal = {IEEE Trans. Magn.}, 1422 volume = {42}, 1423 year = {2006}, 1424 pages = {2960--2962}, 1425 doi = {10.1109/TMAG.2006.878414}, 1426 petsc_uses = {KSP} 1427} 1428 1429@Article{ bfmfzczg2007, 1430 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 1431 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 1432 title = {Micromagnetic modelling of ferromagnetic cones}, 1433 journal = {J. Magn. Magn. Mater.}, 1434 volume = {312}, 1435 year = {2007}, 1436 pages = {234-238}, 1437 url = {http://eprints.soton.ac.uk/45900/}, 1438 petsc_uses = {KSP} 1439} 1440 1441@PhDThesis{ rb2005, 1442 author = {Richard Boardman}, 1443 title = {Computer simulation studies of magnetic nanostructures}, 1444 school = {Computational Engineering and Design Group, School of Engineering Sciences, 1445 University of Southampton, United Kingdom}, 1446 year = {2005}, 1447 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 1448 petsc_uses = {KSP} 1449} 1450 1451@InProceedings{ cwwy2006, 1452 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 1453 title = {MPI Performance Analysis Tools on Blue Gene/L}, 1454 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 1455 year = {2006}, 1456 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 1457 petsc_uses = {KSP} 1458} 1459 1460@InProceedings{ ch2006, 1461 author = {I.-H. Chung and J.K. Hollingsworth}, 1462 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 1463 Programs}, 1464 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 1465 pages = {45--56}, 1466 doi = {10.1109/HPDC.2006.1652135}, 1467 petsc_uses = {KSP} 1468} 1469 1470@Article{ lkpl2005, 1471 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1472 title = {Multibit {MRAM} using a pair of memory cells}, 1473 journal = {IEEE Trans. Magn.}, 1474 volume = {41}, 1475 year = {2005}, 1476 pages = {2670-2672}, 1477 doi = {10.1109/TMAG.2005.855288}, 1478 petsc_uses = {KSP} 1479} 1480 1481@Article{ gscn2005, 1482 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 1483 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 1484 journal = {Phys. Rev. B}, 1485 volume = {71}, 1486 year = {2005}, 1487 doi = {10.1103/PhysRevB.71.144407}, 1488 petsc_uses = {KSP} 1489} 1490 1491@PhDThesis{ mda, 1492 author = {Massimiliano d'Aquino}, 1493 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 1494 school = { Universita di Napoli Federico II.}, 1495 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 1496 petsc_uses = {KSP} 1497} 1498 1499@TechReport{ ssdfssf2003, 1500 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 1501 Stehno and J. Fidler}, 1502 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 1503 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 1504 petsc_uses = {KSP} 1505} 1506 1507@InProceedings{ sb2006a, 1508 author = {W. Scholz and S. Batra}, 1509 title = {Effect of write current waveform on magnetization and head field dynamics of 1510 perpendicular recording heads}, 1511 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 1512 petsc_uses = {KSP} 1513} 1514 1515@Article{ scholz-batra1, 1516 author = {W. Scholz and S. Batra}, 1517 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 1518 Recording}, 1519 journal = {IEEE Trans. Magn.}, 1520 note = {submitted}, 1521 year = {2005}, 1522 petsc_uses = {KSP} 1523} 1524 1525@Article{ scholz-batra2, 1526 author = {W. Scholz and S. Batra}, 1527 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 1528 journal = {IEEE Trans. Magn.}, 1529 volume = {41}, 1530 year = {2005}, 1531 pages = {702-706}, 1532 petsc_uses = {KSP} 1533} 1534 1535@Article{ daquino-scholz1, 1536 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1537 title = {Micromagnetic Analysis of Fast Precessional Switching}, 1538 journal = {J. Magn. Magn. Mater.}, 1539 volume = {290-291}, 1540 year = {2005}, 1541 pages = {510-513}, 1542 petsc_uses = {KSP} 1543} 1544 1545@Article{ aq-scholz-fid, 1546 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1547 title = {Numerical and analytical study of fast precessional switching}, 1548 journal = {J. Appl. Phys.}, 1549 volume = {95}, 1550 year = {2004}, 1551 pages = {7055-7057}, 1552 petsc_uses = {KSP} 1553} 1554 1555@InProceedings{ gar-tabik-gar, 1556 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 1557 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 1558 Scatterers}, 1559 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 1560 (PDP'04)}, 1561 year = {2004}, 1562 pages = {80--}, 1563 petsc_uses = {KSP} 1564} 1565 1566@InProceedings{ aq-scholz-mia, 1567 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 1568 title = {Analysis of fast precessional switching in magnetic thin films}, 1569 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 1570 year = {2004}, 1571 pages = {257-260}, 1572 petsc_uses = {KSP} 1573} 1574 1575@Article{ scholz-fid-seus, 1576 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 1577 Dittrich and V. Tsiantos}, 1578 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 1579 Axes}, 1580 journal = {J. Magn. Magn. Mater.}, 1581 year = {2004}, 1582 pages = {1524-1525}, 1583 petsc_uses = {KSP} 1584} 1585 1586@Article{ boardman-zimmerman, 1587 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 1588 Peter de Groot}, 1589 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 1590 journal = {Journal of Applied Physics}, 1591 year = {2005}, 1592 petsc_uses = {KSP} 1593} 1594 1595@Article{ lim-kim-park, 1596 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1597 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 1598 journal = {IEEE Trans. Magn.}, 1599 note = {submitted}, 1600 petsc_uses = {KSP} 1601} 1602 1603@Article{ scholz-suess2, 1604 author = {W. Scholz and D. Suess and T. Schrefl and J. Fidler}, 1605 title = {Micromagnetic simulation of magnetization reversal in small particles with 1606 surface anisotropy}, 1607 journal = {J. Appl. Phys.}, 1608 volume = {95}, 1609 year = {2004}, 1610 pages = {6807-6809}, 1611 petsc_uses = {KSP} 1612} 1613 1614@Article{ scholz-schrefl1, 1615 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 1616 Tsiantos}, 1617 title = {Micromagnetic simulation of the pinning and depinning process in permanent 1618 magnets}, 1619 journal = {IEEE Trans. Magn.}, 1620 volume = {39}, 1621 year = {2003}, 1622 pages = {2920-2922}, 1623 petsc_uses = {KSP} 1624} 1625 1626@Article{ scholz-guslienko, 1627 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 1628 W. Chantrell and J. Fidler}, 1629 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 1630 nanodots}, 1631 journal = {J. Magn. Magn. Mater.}, 1632 volume = {266}, 1633 year = {2003}, 1634 pages = {155-163}, 1635 petsc_uses = {KSP} 1636} 1637 1638@Article{ scholz1, 1639 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 1640 Forster and V. Tsiantos}, 1641 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1642 journal = {Comp. Mat. Sci}, 1643 year = {2003}, 1644 pages = {366--383}, 1645 volume = {28}, 1646 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 1647 petsc_uses = {KSP} 1648} 1649 1650@PhDThesis{ scholz2, 1651 author = {W. Scholz}, 1652 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1653 school = {Vienna University of Technology, Vienna, Austria}, 1654 year = {2003}, 1655 petsc_uses = {KSP} 1656} 1657 1658@Article{ scholz3, 1659 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 1660 Forster and J. Fidler}, 1661 title = {Implementation of a high performance parallel finite element micromagnetics 1662 package}, 1663 journal = {J. Magn. Magn. Mater.}, 1664 year = {2004}, 1665 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 1666 petsc_uses = {KSP} 1667} 1668 1669% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1670@InBook{ zhanggladwell1, 1671 author = {W. Zhang and I. Gladwell}, 1672 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 1673 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 1674 year = {2000}, 1675 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 1676 Physics, vol. 552}, 1677 publisher = {Springer}, 1678 pages = {4190-}, 1679 petsc_uses = {KSP} 1680} 1681 1682@Article{ wolf1, 1683 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 1684 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 1685 thin films}, 1686 journal = {Phil. Mag. A}, 1687 year = {2003}, 1688 lab = {ANL}, 1689 petsc_uses = {KSP} 1690} 1691 1692@Article{ wolf2, 1693 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 1694 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 1695 grain-boundary properties}, 1696 journal = {Computational Materials Science}, 1697 year = {2001}, 1698 volume = {23}, 1699 pages = {15--32}, 1700 lab = {ANL}, 1701 petsc_uses = {KSP} 1702} 1703 1704@Article{ wolf3, 1705 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 1706 title = {Role of grain rotation in grain growth by mesoscale simulation}, 1707 journal = {Phil. Mag. A}, 1708 year = {2002}, 1709 volume = {82}, 1710 pages = {1271--1297}, 1711 lab = {ANL}, 1712 petsc_uses = {KSP} 1713} 1714 1715% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1716@Article{ saut, 1717 author = { Olivier Saut}, 1718 title = {Bidimensional Study of the {M}axwell-{B}loch Model in a Nonlinear Crystal}, 1719 journal = {SIAM Journal on Scientific Computing}, 1720 year = {2004}, 1721 note = {submitted}, 1722 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 1723 petsc_uses = {KSP} 1724} 1725 1726% LiteralHTML: 1727% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 1728% LiteralHTML: 1729@InBook{ khanallorenziayachepennec2016, 1730 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 1731 of Brain Deformation in {Alzheimer's} Disease}, 1732 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 1733 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 1734 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 1735 Miller}, 1736 pages = {167--176}, 1737 isbn = {978-3-319-28329-6}, 1738 doi = {10.1007/978-3-319-28329-6_15}, 1739 publisher = {Springer International Publishing}, 1740 year = {2016}, 1741 petsc_uses = {KSP} 1742} 1743 1744@Article{ ataseven, 1745 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 1746 title = {Parallel implementation of the accelerated {BEM} approach for {EMSI} of the human 1747 brain}, 1748 journal = {Medical and Biological Engineering and Computing}, 1749 month = feb, 1750 year = {2008}, 1751 doi = {10.1007/s11517-008-0316-0}, 1752 petsc_uses = {KSP} 1753} 1754 1755@Article{ dennis-eberhart-03, 1756 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 1757 pages = {832-840}, 1758 volume = {125}, 1759 number = {6}, 1760 title = {Finite-element simulation of cooling of realistic {3-D} human head and neck}, 1761 journal = {J Biomech Eng}, 1762 year = {2003}, 1763 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 1764 petsc_uses = {KSP} 1765} 1766 1767@Conference{ gu7174parallel, 1768 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 1769 frequency-domain small animal optical tomography}}, 1770 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 1771 booktitle = {Proc. of SPIE Vol}, 1772 volume = {7174}, 1773 number = {717406}, 1774 pages = {1}, 1775 petsc_uses = {KSP} 1776} 1777 1778@Article{ barchanski2005using, 1779 title = {{Using domain decomposition techniques for the calculation of low-frequency 1780 electric current densities in high-resolution 3D human anatomy models}}, 1781 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 1782 T.}, 1783 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 1784 and Electronic Engineering}, 1785 volume = {24}, 1786 number = {2}, 1787 pages = {458--467}, 1788 issn = {0332-1649}, 1789 year = {2005}, 1790 publisher = {Emerald Group Publishing Limited}, 1791 petsc_uses = {KSP} 1792} 1793 1794@Article{ motrescurienen05, 1795 author = {V. C. Motrescu and U. van Rienen}, 1796 pages = {227--231}, 1797 volume = {3}, 1798 title = {Computation of currents induced by {ELF} electric fields in anisotropic human 1799 tissues using the Finite Integration Technique}, 1800 journal = {Advances in Radio Science}, 1801 year = {2005}, 1802 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 1803 petsc_uses = {KSP} 1804} 1805 1806@Article{ motrescurienen04, 1807 author = {V. C. Motrescu and U. van Rienen}, 1808 pages = {309--313}, 1809 volume = {2}, 1810 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 1811 Integration Technique (FIT)}, 1812 journal = {Advances in Radio Science}, 1813 year = {2004}, 1814 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 1815 petsc_uses = {KSP} 1816} 1817 1818@InProceedings{ dbl2, 1819 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 1820 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 1821 booktitle = {ECCOMAS2000}, 1822 year = {2000}, 1823 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 1824 petsc_uses = {KSP} 1825} 1826 1827@Unpublished{ cell, 1828 title = {Parallel Simulation Engines for Whole-Cell Models}, 1829 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 1830 Weber}, 1831 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 1832 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 1833 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 1834 year = {2001}, 1835 petsc_uses = {KSP} 1836} 1837 1838@Article{ barker2010two, 1839 title = {Two-level {N}ewton and hybrid {S}chwarz preconditioners for fluid-structure 1840 interaction}, 1841 author = {Barker, A.T. and Cai, X.C.}, 1842 journal = {SIAM Journal on Scientific Computing}, 1843 volume = {32}, 1844 number = {4}, 1845 pages = {2395--2417}, 1846 year = {2010}, 1847 publisher = {Society for Industrial and Applied Mathematics}, 1848 petsc_uses = {KSP} 1849} 1850 1851@Article{ barker2010scalable, 1852 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 1853 with application to blood flow modeling}, 1854 author = {Barker, A.T. and Cai, X.C.}, 1855 journal = {Journal of Computational Physics}, 1856 volume = {229}, 1857 number = {3}, 1858 pages = {642--659}, 1859 year = {2010}, 1860 publisher = {Elsevier}, 1861 petsc_uses = {KSP} 1862} 1863 1864@Article{ barker2009nks, 1865 title = {{NKS} for fully coupled fluid-structure interaction with application}, 1866 author = {Barker, A.T. and Cai, X.C.}, 1867 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 1868 pages = {275--282}, 1869 year = {2009}, 1870 publisher = {Springer}, 1871 petsc_uses = {KSP} 1872} 1873 1874@Article{ mirams2013, 1875 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 1876 and Yi Cui and Gary R Mirams}, 1877 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 1878 to predict {QT} interval changes in the rabbit ventricular wedge}, 1879 journal = {Journal of pharmacological and toxicological methods}, 1880 volume = {68}, 1881 number = {1}, 1882 pages = {88--96}, 1883 year = {2013}, 1884 doi = {10.1016/j.vascn.2013.04.004}, 1885 petsc_uses = {KSP} 1886} 1887 1888% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1889% LiteralHTML: <center><img alt="" 1890% LiteralHTML: src="images/spine0l.jpg"></center></p> 1891% LiteralHTML: <center><img alt="" 1892% LiteralHTML: src="images/vertebra.jpg"></center></p> 1893% LiteralHTML:<font color="#FF0000"> 1894% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 1895% LiteralHTML:Understanding bone mechanical properties and how they may lead to 1896% LiteralHTML:fractures is thus an important medical research activity. PETSc and 1897% LiteralHTML:Prometheus have been used for extremely large scale finite element 1898% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 1899% LiteralHTML:team of doctors and computational scientists. This computation was 1900% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 1901% LiteralHTML:with over 4000 processors.</p> 1902% LiteralHTML: </font> 1903@Article{ arbenz2008scalable, 1904 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 1905 analysis of human bone structures}, 1906 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 1907 journal = {International Journal for Numerical Methods in Engineering}, 1908 volume = {73}, 1909 number = {7}, 1910 pages = {927--947}, 1911 year = {2008}, 1912 publisher = {Wiley Online Library}, 1913 petsc_uses = {KSP} 1914} 1915 1916@InProceedings{ adams-04, 1917 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1918 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 1919 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 1920 half a billion degrees of freedom}, 1921 note = {Gordon Bell Award}, 1922 year = {2004}, 1923 petsc_uses = {KSP} 1924} 1925 1926@InProceedings{ adams-03b, 1927 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1928 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 1929 Whole Bone Micro-Mechanics on the {IBM SP}}, 1930 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 1931 year = {2003}, 1932 petsc_uses = {KSP} 1933} 1934 1935@InProceedings{ oghattas2002, 1936 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 1937 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 1938 booktitle = {Procceedings of SC2002}, 1939 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 1940 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 1941 by time-dependent PDEs, and scalability results for an inverse wave propagation 1942 problem of determining the material field of an acoustic medium. Using the 1943 algorithm, they solved a synthetic inverse wave propagation problem though a 1944 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 1945 processors.}, 1946 year = {2002}, 1947 petsc_uses = {KSP} 1948} 1949 1950% LiteralHTML: <a name="biology:cardiology"> 1951% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1952% LiteralHTML: <center><img alt="" 1953% LiteralHTML: src="images/heart.jpg"> 1954% LiteralHTML: <img alt="" 1955% LiteralHTML: src="images/pump.jpg"></center></p> 1956% LiteralHTML: 1957% LiteralHTML:<font color="#FF0000"> 1958% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 1959% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 1960% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 1961% LiteralHTML: through the heart. PETSc has been used by several research groups to 1962% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 1963% LiteralHTML: fully understand the developments of arrhthmias.</p> 1964% LiteralHTML:</font> 1965@InProceedings{ oghattas2000, 1966 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 1967 Walkington}, 1968 title = {A Parallel Dynamic-Mesh {L}agrangian Method for Simulation of Flows with Dynamic 1969 Interfaces}, 1970 booktitle = {Procceedings of SC2000}, 1971 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 1972 note = {Blood flow modeling at the microscale including effects on individual blood 1973 cells, for designing heart assist pumps, etc.}, 1974 year = {2000}, 1975 petsc_uses = {KSP} 1976} 1977 1978@InBook{ cfps2006, 1979 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 1980 editor = {A. Quarteroni et al.}, 1981 title = {Complex Systems in Biomedicine}, 1982 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 1983 publisher = {Springer-Verlag}, 1984 pages = {187--241}, 1985 year = {2006}, 1986 petsc_uses = {KSP} 1987} 1988 1989@InProceedings{ cfpst2007, 1990 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 1991 title = {Determining recovery times from transmembrane action potentials and unipolar 1992 electrograms in normal heart tissue}, 1993 booktitle = {FIMH07}, 1994 publisher = {Springer-Verlag}, 1995 volume = {4466}, 1996 pages = {139--149}, 1997 year = {2007}, 1998 petsc_uses = {KSP} 1999} 2000 2001@Article{ seemann2010framework, 2002 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 2003 Equations Using PETSc}}, 2004 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 2005 D{\\"o}ssel, O.}, 2006 journal = {Progress in Industrial Mathematics at ECMI 2008}, 2007 pages = {363--369}, 2008 year = {2010}, 2009 publisher = {Springer}, 2010 petsc_uses = {KSP} 2011} 2012 2013@InProceedings{ pft2005, 2014 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 2015 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 2016 Intramural Heterogeneity}, 2017 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 2018 pages = {267--277}, 2019 editors = {A. Frangi et al.}, 2020 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 2021 year = {2005}, 2022 petsc_uses = {KSP} 2023} 2024 2025@Article{ bgcp2005, 2026 author = {Boyce E. Griffith and Charles S. Peskin}, 2027 title = {On the order of accuracy of the immersed boundary method: Higher order 2028 convergence rates for sufficiently smooth problems}, 2029 journal = {Journal of Computational Physics}, 2030 year = {2005}, 2031 volume = {208}, 2032 pages = {75--105}, 2033 petsc_uses = {KSP} 2034} 2035 2036@Article{ griffith2007adaptive, 2037 title = {An adaptive, formally second order accurate version of the immersed boundary 2038 method}, 2039 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 2040 journal = {Journal of Computational Physics}, 2041 volume = {223}, 2042 number = {1}, 2043 pages = {10--49}, 2044 year = {2007}, 2045 publisher = {Elsevier}, 2046 petsc_uses = {KSP} 2047} 2048 2049@PhDThesis{ griffith05, 2050 author = {Boyce Griffith}, 2051 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 2052 parallel version of the immersed boundary method}, 2053 school = {New York University}, 2054 year = {2005}, 2055 petsc_uses = {KSP} 2056} 2057 2058@PhDThesis{ murillo, 2059 author = {Maria S. Murillo}, 2060 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 2061 Differential Equations with an Application in Computational Biology}, 2062 school = {University of Colorado at Boulder}, 2063 year = {2002}, 2064 petsc_uses = {KSP} 2065} 2066 2067@Article{ spv2004, 2068 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 2069 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 2070 journal = {IEEE Trans. Biomed. Eng}, 2071 year = {2004}, 2072 volume = {51}, 2073 pages = {1960--1968}, 2074 petsc_uses = {KSP} 2075} 2076 2077@Article{ vphl2003, 2078 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 2079 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 2080 journal = {J. Electrocardiol.}, 2081 year = {2003}, 2082 volume = {36}, 2083 pages = {69--74}, 2084 petsc_uses = {KSP} 2085} 2086 2087@InProceedings{ spbv2003, 2088 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and E.J. Vigmond}, 2089 title = {Preconditioning Techniques for the Bidomain Equations}, 2090 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2091 Methods}, 2092 pages = {571--580}, 2093 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2094 note = {}, 2095 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2096 year = {2003}, 2097 petsc_uses = {KSP} 2098} 2099 2100@Article{ franz-pavir-04, 2101 author = {P. Colli Franzone and L.~F. Pavarino}, 2102 title = {A parallel solver for reaction-diffusion systems in computational 2103 electrocardiology}, 2104 journal = {Mathematical Models and Methods in Applied Sciences}, 2105 year = {2004}, 2106 volume = {14}, 2107 number = {6}, 2108 pages = {883--912}, 2109 petsc_uses = {KSP} 2110} 2111 2112@Article{ franz-pavir-05, 2113 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2114 title = {Simulating patterns of excitation, repolarization and action potential 2115 durationwith cardiac Bidomain and Monodomain models}, 2116 journal = {Mathematical Biosciences}, 2117 year = {2005}, 2118 volume = {197}, 2119 number = {1}, 2120 pages = {35--66}, 2121 petsc_uses = {KSP} 2122} 2123 2124@Article{ franz-pavir-06, 2125 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2126 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 2127 the dispersion of cardiac repolarization and action potential duration: a 2128 simulation study}, 2129 journal = {Mathematical Biosciences}, 2130 year = {2006}, 2131 volume = {204}, 2132 number = {1}, 2133 pages = {132--165}, 2134 petsc_uses = {KSP} 2135} 2136 2137@InProceedings{ colli-franz-sim, 2138 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 2139 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 2140 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 2141 Mediterranean Conference on Medical and Biological Engineering}, 2142 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 2143 year = {2004}, 2144 petsc_uses = {KSP} 2145} 2146 2147@InProceedings{ pf2003, 2148 author = {Luca F. Pavarino and Piero Colli Franzone}, 2149 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 2150 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2151 Methods}, 2152 pages = {669--776}, 2153 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2154 note = {}, 2155 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2156 year = {2003}, 2157 petsc_uses = {KSP} 2158} 2159 2160@Article{ maria-is04, 2161 author = {Maria Murillo and Xiao-Chuan Cai}, 2162 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 2163 activity of the heart}, 2164 journal = {Numerical Linear Algebra with Applications}, 2165 year = {2004}, 2166 volume = {11}, 2167 pages = {261 - 277}, 2168 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 2169 petsc_uses = {KSP} 2170} 2171 2172@Article{ murli2007monitoring, 2173 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 2174 Imaging in a Grid computing PSE}}, 2175 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 2176 and Lapegna, M.}, 2177 journal = {Grid-Based Problem Solving Environments}, 2178 pages = {421--432}, 2179 year = {2007}, 2180 publisher = {Springer}, 2181 petsc_uses = {KSP} 2182} 2183 2184@Article{ carracciuolo:2006:tpc, 2185 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 2186 title = {Towards a parallel component for imaging in {PETSc} programming environment: a case 2187 study in {3-D} echocardiography}, 2188 journal = {Parallel Comput.}, 2189 volume = {32}, 2190 issue = {1}, 2191 month = jan, 2192 year = {2006}, 2193 issn = {0167-8191}, 2194 pages = {67--83}, 2195 numpages = {17}, 2196 doi = {10.1016/j.parco.2005.09.001}, 2197 acmid = {1141218}, 2198 publisher = {Elsevier Science Publishers B. V.}, 2199 address = {Amsterdam, The Netherlands, The Netherlands}, 2200 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 2201 component}, 2202 petsc_uses = {KSP} 2203} 2204 2205@Article{ damore2011integration, 2206 title = {Integration of emerging computer technologies for an efficient image sequences 2207 analysis}, 2208 journal = {Integrated Computer-Aided Engineering }, 2209 volume = {18}, 2210 number = {4}, 2211 pages = {365 - 378}, 2212 year = {2011}, 2213 note = {}, 2214 issn = {1875-8835}, 2215 doi = {10.3233/ICA-2011-0382}, 2216 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 2217 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 2218 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 2219 petsc_uses = {KSP} 2220} 2221 2222@InProceedings{ eth_biwi_00721, 2223 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and G. 2224 Székely}, 2225 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 2226 a {S}chur Complement Preconditioner}, 2227 booktitle = {Euro-Par 2009 Parallel Processing}, 2228 year = {2009}, 2229 month = aug, 2230 pages = {747-759}, 2231 volume = {5704}, 2232 editor = {H. Sips and D. Epema and H.-X. Lin}, 2233 series = {Lecture Notes in Computer Science}, 2234 publisher = {Springer}, 2235 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 2236 parallel Krylov solver}, 2237 petsc_uses = {KSP} 2238} 2239 2240% LiteralHTML: <a name="biology:imagingandsurgery"> 2241% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 2242% LiteralHTML: <center><img alt="" 2243% LiteralHTML: src="images/brain.jpg"></center> 2244@Article{ ganser2004deformable, 2245 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 2246 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 2247 journal = {Medical Image Analysis}, 2248 volume = {8}, 2249 number = {1}, 2250 pages = {3--22}, 2251 year = {2004}, 2252 publisher = {Elsevier}, 2253 petsc_uses = {KSP} 2254} 2255 2256@Unpublished{ taccsurgery, 2257 title = {{TACC} supercomputer performs laser cancer surgery on canine}, 2258 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 2259 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 2260 Austin performed laser surgery on a dog in Houston without the intervention of a 2261 surgeon. The treatment was developed collaboratively by computational experts from 2262 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 2263 leading technologists from the M.D. Anderson Cancer Center in Houston, and 2264 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 2265 state-of-the-art thermal imaging technology, and advanced computational methods, 2266 dynamic, data-driven treatments are being pursued as a minimally invasive 2267 alternative to the standard treatment of cancer.}, 2268 petsc_uses = {KSP} 2269} 2270 2271@Article{ ffhbresso2008, 2272 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 2273 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 2274 Tinsley Oden}, 2275 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 2276 journal = {Engineering with Computers}, 2277 note = {Special issue on Computational Bioengineering}, 2278 year = {2008}, 2279 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 2280 petsc_uses = {KSP} 2281} 2282 2283@TechReport{ dobbhbbbdeffghkkps2008, 2284 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 2285 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 2286 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 2287 and S. Prudhomme and R. J. Stafford}, 2288 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 2289 Cancer}, 2290 year = {2008}, 2291 institution = {University of Texas at Austin}, 2292 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 2293 petsc_uses = {KSP} 2294} 2295 2296@Article{ ogdb2004, 2297 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 2298 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 2299 journal = {Physics in Medicine and Biology}, 2300 year = {2004}, 2301 volume = {49}, 2302 pages = {2955--2947}, 2303 petsc_uses = {KSP} 2304} 2305 2306@InProceedings{ majumdar11, 2307 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 2308 Baldridge and P. Krysl}, 2309 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 2310 booktitle = {ICCS 2005}, 2311 pages = {672--679}, 2312 editor = {V.S. Sunderam et al.}, 2313 year = {2005}, 2314 petsc_uses = {KSP} 2315} 2316 2317@Conference{ sermesant-etal:03, 2318 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 2319 Ayache, H.}, 2320 title = {A parallel implementation of non-rigid registration using a volumetric 2321 biomechanical model}, 2322 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 2323 address = {Philadelphia, PA, USA}, 2324 publisher = {Springer-Verlag}, 2325 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2326 series = {Lecture Notes in Computer Science}, 2327 volume = {2717}, 2328 pages = {398-407}, 2329 date = {june 23-24}, 2330 year = {2003}, 2331 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 2332 petsc_uses = {KSP} 2333} 2334 2335@Conference{ sermesant-etal:04, 2336 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 2337 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 2338 title = {A Novel Nonrigid Registration Algorithm And Applications}, 2339 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 2340 address = {Philadelphia, PA, USA}, 2341 publisher = {Springer-Verlag}, 2342 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2343 series = {Lecture Notes in Computer Science}, 2344 volume = {2208}, 2345 pages = {923}, 2346 year = {2003}, 2347 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 2348 petsc_uses = {KSP} 2349} 2350 2351@Article{ warfield-haker-talos-05, 2352 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 2353 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 2354 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 2355 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 2356 title = {Capturing intraoperative deformations: research experience at {B}righam and {W}omen's 2357 hospital}, 2358 journal = {Medical Image Analysis}, 2359 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 2360 year = {2005}, 2361 petsc_uses = {KSP} 2362} 2363 2364@Article{ brain3, 2365 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 2366 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 2367 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 2368 Deformation during Image Guided Neurosurgery}, 2369 journal = {Computing and Visualization in Science}, 2370 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 2371 year = {2002}, 2372 petsc_uses = {KSP} 2373} 2374 2375@Article{ brain2, 2376 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 2377 Kikinis and Simon K. Warfield}, 2378 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 2379 Element Biomechanical Model}, 2380 journal = {IEEE Transactions on Medical Imaging}, 2381 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 2382 year = {2001}, 2383 petsc_uses = {KSP} 2384} 2385 2386@InProceedings{ brain1, 2387 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 2388 Ferenc A. Jolesz and Ron Kikinis}, 2389 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 2390 Guided Neurosurgery}, 2391 booktitle = {Proceedings of SC2000}, 2392 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 2393 year = {2000}, 2394 petsc_uses = {KSP} 2395} 2396 2397@Article{ vanne06, 2398 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 2399 M. Lassas and M. Kalke}, 2400 title = {Parallelized {B}ayesian inversion for three-dimensional dental {X}-ray imaging}, 2401 journal = {IEEE Transactions on Medical Imaging}, 2402 volume = {25}, 2403 number = {2}, 2404 month = feb, 2405 year = {2006}, 2406 pages = {218--228}, 2407 petsc_uses = {KSP} 2408} 2409 2410@InProceedings{ knepleybardhan2015, 2411 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 2412 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 2413 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 2414 Exposition}, 2415 volume = {9}, 2416 pages = {V009T12A04}, 2417 doi = {10.1115/IMECE2015-53579}, 2418 year = {2015}, 2419 petsc_uses = {KSP} 2420} 2421 2422@InProceedings{ bardhanknepley2015, 2423 title = {Multiscale models and approximation algorithms for protein electrostatics}, 2424 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 2425 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 2426 volume = {61}, 2427 pages = {163--174}, 2428 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 2429 doi = {10.2495/BEM380131}, 2430 publisher = {WIT Press}, 2431 year = {2015}, 2432 petsc_uses = {KSP} 2433} 2434 2435% LiteralHTML: 2436% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 2437% LiteralHTML: 2438@InProceedings{ adamsbrennanknepleywang2022, 2439 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 2440 quench plasmas}, 2441 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 2442 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 2443 (IPDPS '22)}, 2444 doi = {10.1109/IPDPS53621.2022.00020}, 2445 year = {2022}, 2446 petsc_uses = {DMPlex} 2447} 2448 2449@Misc{ adamsknepleybrennan2021, 2450 title = {Runaway Electron Generation with High-Performance, Structure Preserving 2451 Discretization of {F}okker--{P}lank--{L}andau}, 2452 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 2453 year = {2021}, 2454 petsc_uses = {KSP} 2455} 2456 2457@Article{ adamshirvijokiknepleybrownisaacmills2017, 2458 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 2459 Architectures}, 2460 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 2461 Isaac and Richard Mills}, 2462 journal = {SIAM Journal on Scientific Computing}, 2463 volume = {39}, 2464 number = {6}, 2465 pages = {C452--C465}, 2466 doi = {10.1137/17M1118828}, 2467 eprint = {1702.08880}, 2468 year = {2017}, 2469 petsc_uses = {KSP} 2470} 2471 2472@Article{ pusztayknepleyadams2022, 2473 title = {Conservative Projection Between {FEM} and Particle Bases}, 2474 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 2475 journal = {SIAM Journal on Scientific Computing}, 2476 volume = {44}, 2477 number = {4}, 2478 pages = {C310--C319}, 2479 doi = {10.1137/21M145407}, 2480 year = {2022} 2481} 2482 2483@Article{ hirvijoki2017, 2484 author = {Eero Hirvijoki and Mark F. Adams}, 2485 title = {Conservative discretization of the {Landau} collision integral}, 2486 journal = {Physics of Plasmas}, 2487 volume = {24}, 2488 number = {3}, 2489 pages = {032121}, 2490 doi = {10.1063/1.4979122}, 2491 year = {2017}, 2492 petsc_uses = {KSP} 2493} 2494 2495@Article{ mollenadamsknepleyhagerchang2021, 2496 title = {Implementation of higher-order velocity mapping between marker particles and grid 2497 in the particle-in-cell code {XGC}}, 2498 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 2499 S. Chang}, 2500 journal = {Journal of Plasma Physics}, 2501 volume = {87}, 2502 number = {2}, 2503 pages = {905870229}, 2504 eprint = {2012.11764}, 2505 doi = {10.1017/S0022377821000441}, 2506 year = {2021}, 2507 petsc_uses = {KSP} 2508} 2509 2510@Article{ lsmh2014, 2511 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 2512 title = {Comparison of particle trajectories and collision operators for collisional 2513 transport in nonaxisymmetric plasmas}, 2514 journal = { Physics of Plasmas}, 2515 volume = {21}, 2516 year = {2014}, 2517 petsc_uses = {KSP} 2518} 2519 2520@Article{ lpcep2014, 2521 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 2522 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 2523 pedestal}, 2524 journal = {Plasma Physics and Controlled Fusion}, 2525 volume = {56}, 2526 year = {2014}, 2527 petsc_uses = {KSP} 2528} 2529 2530@Article{ facets-scidac08, 2531 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 2532 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 2533 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 2534 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 2535 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 2536 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 2537 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 2538 Stotler and A. Pigarov}, 2539 journal = {J. Phys.: Conf. Ser.}, 2540 volume = {125}, 2541 year = {2008}, 2542 pages = {012040}, 2543 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 2544 petsc_uses = {KSP} 2545} 2546 2547@Article{ facets-scidac09, 2548 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 2549 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 2550 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 2551 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 2552 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 2553 and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar 2554 and A. Pigarov and H. Zhang}, 2555 journal = {J. Phys.: Conf. Ser.}, 2556 volume = {180}, 2557 year = {2009}, 2558 pages = {012056}, 2559 url = {http://iopscience.iop.org/1742-6596/180/1/012056}, 2560 petsc_uses = {KSP} 2561} 2562 2563@InProceedings{ facets-scidac10, 2564 title = {Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the 2565 {FACETS} Code}, 2566 author = {A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. 2567 Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. 2568 Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. 2569 Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. 2570 Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. 2571 Pigarov and H. 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Brubeck}, 3219 school = {Oxford University}, 3220 year = {2022} 3221} 3222 3223@Misc{ firedrakeproject, 3224 title = {{The {F}iredrake project}}, 3225 author = {David A Ham and Firedrake Team}, 3226 url = {http://firedrakeproject.org}, 3227 year = {2022}, 3228 petsc_uses = {KSP} 3229} 3230 3231@Article{ rathgeberhammitchelllangeluporinimcraeberceamarkallkelly2016, 3232 title = {Firedrake: automating the finite element method by composing abstractions}, 3233 author = {Florian Rathgeber and David A Ham and Lawrence Mitchell and Michael Lange and 3234 Fabio Luporini and Andrew TT McRae and Gheorghe-Teodor Bercea and Graham R Markall 3235 and Paul HJ Kelly}, 3236 journal = {ACM Transactions on Mathematical Software (TOMS)}, 3237 volume = {43}, 3238 number = {3}, 3239 pages = {24}, 3240 year = {2016}, 3241 petsc_uses = {KSP} 3242} 3243 3244@Article{ mitchellmuller2016, 3245 title = {High level implementation of geometric multigrid solvers for finite element 3246 problems: Applications in atmospheric modelling}, 3247 author = {Lawrence Mitchell and Eike Hermann M{\"u}ller}, 3248 journal = {Journal of Computational Physics}, 3249 volume = {327}, 3250 pages = {1--18}, 3251 year = {2016}, 3252 petsc_uses = {KSP} 3253} 3254 3255@Article{ mcraeberceamitchellhamcotter2016, 3256 title = {Automated generation and symbolic manipulation of tensor product finite 3257 elements}, 3258 author = {Andrew TT McRae and Gheorghe-Teodor Bercea and Lawrence Mitchell and David A Ham 3259 and Colin J Cotter}, 3260 journal = {SIAM Journal on Scientific Computing}, 3261 volume = {38}, 3262 number = {5}, 3263 pages = {S25--S47}, 3264 year = {2016}, 3265 petsc_uses = {KSP} 3266} 3267 3268@Article{ berceamcraehammitchellrathgebernardiluporinikelly2016, 3269 title = {A structure-exploiting numbering algorithm for finite elements on extruded 3270 meshes, and its performance evaluation in {Firedrake}}, 3271 author = {Gheorghe-Teodor Bercea and Andrew TT McRae and David A Ham and Lawrence Mitchell 3272 and Florian Rathgeber and L. Nardi and Fabio Luporini and Paul HJ Kelly}, 3273 journal = {Geoscientific Model Development}, 3274 volume = {9}, 3275 number = {10}, 3276 pages = {3803--3815}, 3277 doi = {10.5194/gmd-9-3803-2016}, 3278 year = {2016}, 3279 petsc_uses = {KSP} 3280} 3281 3282@InProceedings{ markallrathgebermitchellloriantbertollihamkelly2013, 3283 author = {Graham R. Markall and Florian Rathgeber and Lawrence Mitchell and Nicolas Loriant 3284 and Carlo Bertolli and David A. Ham and Paul HJ Kelly}, 3285 editor = {Julian Martin Kunkel and Thomas Ludwig and Hans Werner Meuer}, 3286 title = {Performance-Portable Finite Element Assembly Using {PyOP2} and {FEniCS}}, 3287 booktitle = {Proceedings of 28th International Supercomputing Conference, ISC 2013}, 3288 publisher = {Springer Berlin Heidelberg}, 3289 pages = {279--289}, 3290 isbn = {978-3-642-38750-0}, 3291 doi = {10.1007/978-3-642-38750-0_21}, 3292 year = {2013}, 3293 petsc_uses = {KSP} 3294} 3295 3296@Article{ kirbymitchell2017, 3297 title = {Solver composition across the {PDE}/linear algebra barrier}, 3298 author = {Robert C Kirby and Lawrence Mitchell}, 3299 journal = {arXiv preprint arXiv:1706.01346}, 3300 year = {2017}, 3301 petsc_uses = {KSP} 3302} 3303 3304@Article{ saibaba2012application, 3305 title = {Application of hierarchical matrices to linear inverse problems in 3306 geostatistics}, 3307 author = {Saibaba, Arvind Krishna and Ambikasaran, Sivaram and Yue Li, J and Kitanidis, 3308 Peter K and Darve, Eric F}, 3309 journal = {Oil and Gas Science and Technology-Revue de l'IFP-Institut Francais du Petrole}, 3310 volume = {67}, 3311 number = {5}, 3312 pages = {857}, 3313 year = {2012}, 3314 petsc_uses = {KSP} 3315} 3316 3317@Article{ collignonkausmayfernandez14, 3318 author = {Collignon, M. and Kaus, B. and May, D.A. and Fern\'andez, N.}, 3319 title = {Influences of surface processes on fold growth during {3-D} detachment folding}, 3320 journal = {Geochem Geophy Geosy}, 3321 year = {2014}, 3322 petsc_uses = {KSP} 3323} 3324 3325@Article{ fernandezkaus14, 3326 author = {Fern\'andez, N. and Kaus, B.}, 3327 title = {Fold interaction and wavelength selection in {3D} models of multilayer detachment 3328 folding}, 3329 journal = {Tectonophysics}, 3330 year = {2014}, 3331 petsc_uses = {KSP} 3332} 3333 3334@Article{ baumannkauspopov14, 3335 author = {Baumann, T. and Kaus, B. 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Snyder}, 3518 collaboration = {}, 3519 title = {Multiple-domain, simultaneous joint inversion of geophysical data with 3520 application to subsalt imaging}, 3521 publisher = {SEG}, 3522 year = {2011}, 3523 journal = {Geophysics}, 3524 volume = {76}, 3525 number = {3}, 3526 pages = {R69-R80}, 3527 keywords = {geophysical image processing; inverse problems; seismology}, 3528 doi = {10.1190/1.3554652}, 3529 petsc_uses = {KSP} 3530} 3531 3532@Article{ stefano:806, 3533 author = {Michele De Stefano}, 3534 collaboration = {}, 3535 title = {Simultaneous joint inversion for susceptibility and velocity}, 3536 publisher = {SEG}, 3537 year = {2011}, 3538 journal = {SEG Technical Program Expanded Abstracts}, 3539 volume = {30}, 3540 number = {1}, 3541 pages = {806-810}, 3542 keywords = {3D; imaging; inversion; magnetics; multiparameter}, 3543 doi = {10.1190/1.3628198}, 3544 petsc_uses = {KSP} 3545} 3546 3547@Article{ mayknepley2011, 3548 author = {Dave A. May and Matthew G. Knepley}, 3549 title = {Optimal, scalable forward models for computing gravity anomalies}, 3550 journal = {Geophysical Journal International}, 3551 volume = {187}, 3552 number = {1}, 3553 pages = {161--177}, 3554 url = {http://arxiv.org/abs/1107.5951}, 3555 note = {\url{http://arxiv.org/abs/1107.5951}}, 3556 year = {2011}, 3557 petsc_uses = {KSP} 3558} 3559 3560@InProceedings{ bourdinknepleymaurini2010, 3561 author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini}, 3562 title = {Numerical Simulation of Reservoir Stimulation - A Variational Approach}, 3563 booktitle = {Proceedings of the 37th Stanford Geothermal Workshop}, 3564 url = {https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}, 3565 note = {\url{https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}}, 3566 address = {Stanford, CA}, 3567 year = {2010}, 3568 petsc_uses = {KSP} 3569} 3570 3571@InProceedings{ bourdinknepleymaurini2010b, 3572 author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini}, 3573 title = {Secondary Thermal Cracks in {EGS}: a Variational Approach}, 3574 booktitle = {Proceedings of the 34th Annual Meeting of the Geothermal Resources Council}, 3575 url = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}, 3576 note = {\url{https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}}, 3577 address = {Sacramento, CA}, 3578 year = {2010}, 3579 petsc_uses = {KSP} 3580} 3581 3582@Article{ chen2007full, 3583 title = {Full {3D} tomography for the crustal structure of the {Los Angeles} region}, 3584 author = {Chen, P. and Zhao, L. and Jordan, T.H.}, 3585 journal = {Bulletin of the Seismological Society of America}, 3586 volume = {97}, 3587 number = {4}, 3588 pages = {1094}, 3589 year = {2007}, 3590 publisher = {Seismol Soc America}, 3591 petsc_uses = {KSP} 3592} 3593 3594@Article{ brown2010ens, 3595 author = {Brown, Jed}, 3596 affiliation = {Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, 3597 Zürich, Switzerland}, 3598 title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}}, 3599 journal = {Journal of Scientific Computing}, 3600 publisher = {Springer Netherlands}, 3601 issn = {0885-7474}, 3602 keyword = {Mathematics and Statistics}, 3603 pages = {48-63}, 3604 volume = {45}, 3605 issue = {1}, 3606 doi = {10.1007/s10915-010-9396-8}, 3607 year = {2010}, 3608 petsc_uses = {KSP} 3609} 3610 3611@PhDThesis{ brown2011, 3612 title = {Computational methods for ice flow simulation}, 3613 author = {Jed Brown}, 3614 school = {ETH Z{\"u}rich}, 3615 year = {2011}, 3616 petsc_uses = {KSP} 3617} 3618 3619@Article{ brown2013tmeice, 3620 title = {Achieving textbook multigrid efficiency for hydrostatic ice flow}, 3621 author = {Jed Brown and Barry F. Smith and Aron Ahmadia}, 3622 journal = {SIAM Journal on Scientific Computing}, 3623 volume = {35}, 3624 number = {2}, 3625 year = {2013}, 3626 pages = {359--375}, 3627 doi = {10.1137/110834512}, 3628 note = {Also preprint ANL/MCS-P743-1298}, 3629 petsc_uses = {KSP} 3630} 3631 3632@InProceedings{ brown2013quasinewton, 3633 author = {Jed Brown and Peter Brune}, 3634 title = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type 3635 methods}, 3636 year = {2013}, 3637 booktitle = {International Conference on Mathematics and Computational Methods Applied to 3638 Nuclear Science and Engineering}, 3639 pages = {2554--2565}, 3640 petsc_uses = {KSP} 3641} 3642 3643@Misc{ spiegelman-siampp10, 3644 title = {Block Preconditioners and Advanced Software for Multiphysics Problems in Solid 3645 Earth Geodynamics}, 3646 author = {Marc Spiegelman}, 3647 note = {presentation at the 2010 SIAM Conference on Parallel Processing for Scientific 3648 Computing}, 3649 year = {2010}, 3650 petsc_uses = {KSP} 3651} 3652 3653@Article{ schauer2011a, 3654 author = {Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. 3655 Quintana-Ort\'{\i}}, 3656 title = {Large scale simulation of wave propagation in soils interacting with structures 3657 using {FEM} and {SBFEM}}, 3658 journal = {Journal of Computational Acoustics}, 3659 volume = {19}, 3660 number = {1}, 3661 pages = {75--93}, 3662 year = {2011}, 3663 doi = {10.1142/S0218396X11004316}, 3664 petsc_uses = {KSP} 3665} 3666 3667@Misc{ bsa2010, 3668 author = {J. Brown and B. Smith and A. Ahmadia}, 3669 title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow}, 3670 note = {submitted to SIAM Journal on Scientific Computing}, 3671 year = {2012}, 3672 petsc_uses = {KSP} 3673} 3674 3675@Article{ kellerkatz2016, 3676 title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere}, 3677 author = {Tobias Keller and Richard F. 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Weatherley}, 3701 title = {Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges}, 3702 journal = {Earth\ Planet.\ Sci.\ Lett.}, 3703 year = {2012}, 3704 doi = {10.1016/j.epsl.2012.04.042}, 3705 volume = {335-336}, 3706 pages = {226-237}, 3707 petsc_uses = {KSP} 3708} 3709 3710@Article{ katz10b, 3711 author = {R.F. Katz}, 3712 title = {Porosity-driven convection and asymmetry beneath mid-ocean ridges}, 3713 journal = {Geochem.\ Geophys.\ Geosys.}, 3714 volume = {10}, 3715 number = {Q0AC07}, 3716 year = {2010}, 3717 doi = {10.1029/2010GC003282}, 3718 petsc_uses = {KSP} 3719} 3720 3721@Article{ england10, 3722 author = {P.C. England and R.F. Katz}, 3723 title = {Melting above the anhydrous solidus controls the location of volcanic arcs}, 3724 journal = {Nature}, 3725 year = {2010}, 3726 volume = {467}, 3727 pages = {700--703}, 3728 doi = {10.1038/nature09417}, 3729 petsc_uses = {KSP} 3730} 3731 3732@Article{ weatherley10, 3733 author = {S. Weatherley and R.F. 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Katz}, 3770 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. 3771 Governing equations and linearised analysis}}, 3772 journal = {J.\ Fluid\ Mech.}, 3773 year = {2013}, 3774 volume = {734}, 3775 pages = {424-455}, 3776 doi = {10.1017/jfm.2013.482}, 3777 petsc_uses = {KSP} 3778} 3779 3780@Article{ katz2013anisotropy2, 3781 author = {Katz R.F. and Y. Takei}, 3782 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. 3783 Numerical solutions of the full equations}}, 3784 journal = {J.\ Fluid\ Mech.}, 3785 year = {2013}, 3786 volume = {734}, 3787 pages = {456-485}, 3788 doi = {10.1017/jfm.2013.483}, 3789 petsc_uses = {KSP} 3790} 3791 3792@Article{ kyrke-smith2014subglacial, 3793 author = {Kyrke-Smith, T.M. and R.F. Katz and A.C. 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Glaciol.}, 3858 volume = {51}, 3859 number = {173}, 3860 pages = {291--306}, 3861 year = {2005}, 3862 petsc_uses = {KSP} 3863} 3864 3865@Article{ chao2008programming, 3866 title = {{Programming on Numerical Simulation of Tsunami with PETSc and FEPG}}, 3867 author = {Chao-fan, Z. and Yao-lin, S.}, 3868 journal = {Earthquake}, 3869 year = {2008}, 3870 petsc_uses = {KSP} 3871} 3872 3873@Article{ marti2014, 3874 author = {Marti, P. and Schaeffer, N. and Hollerbach, R. and Cébron, D. and Nore, C. and 3875 Luddens, F. and Guermond, J.-L. and Aubert, J. and Takehiro, S. and Sasaki, Y. and 3876 Hayashi, Y.-Y. and Simitev, R. and Busse, F. and Vantieghem, S. and Jackson, A.}, 3877 title = {Full sphere hydrodynamic and dynamo benchmarks}, 3878 journal = {Geophysical Journal International}, 3879 year = {2014}, 3880 doi = {10.1093/gji/ggt518}, 3881 url = {http://gji.oxfordjournals.org/content/early/2014/01/26/gji.ggt518.abstract}, 3882 petsc_uses = {KSP} 3883} 3884 3885@InProceedings{ ganfulukyangxueyang2013, 3886 author = {Gan, Lin and Fu, Haohuan and Luk, Wayne and Yang, Chao and Xue, Wei and Yang, 3887 Guangwen}, 3888 title = {Global Atmospheric Simulation on a Reconfigurable Platform}, 3889 booktitle = {Proceedings of the 2013 IEEE 21st Annual International Symposium on 3890 Field-Programmable Custom Computing Machines}, 3891 series = {FCCM '13}, 3892 pages = {230--}, 3893 year = {2013}, 3894 isbn = {978-0-7695-4969-9}, 3895 doi = {10.1109/FCCM.2013.26}, 3896 acmid = {2495688}, 3897 publisher = {IEEE Computer Society}, 3898 petsc_uses = {KSP} 3899} 3900 3901@InProceedings{ ganfuchaolukxuemencerhuangyang2014, 3902 author = {Lin Gan and Haohuan Fu and Chao Yang and Luk, W. and Wei Xue and Mencer, O. and 3903 Xiaomeng Huang and Guangwen Yang}, 3904 booktitle = {Field Programmable Logic and Applications (FPL), 2014 24th International 3905 Conference on}, 3906 title = {A highly-efficient and green data flow engine for solving {E}uler atmospheric 3907 equations}, 3908 year = {2014}, 3909 month = sep, 3910 pages = {1-6}, 3911 doi = {10.1109/FPL.2014.6927462}, 3912 petsc_uses = {KSP} 3913} 3914 3915%Aagaard, B., Williams, C., Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), EarthScope National Meeting, Austin, Texas, May 17–20. 3916%Aagaard, B., Williams, C., and Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), Southern California Earthquake Center Annual Meeting, Palm Springs, California, September 11–14. 3917%Aagaard, B., Williams, C., and Knepley, M. (2012). PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation (abstract), Seismological Society of America Annual Meeting, San Diego, California, April 17-19. 3918@Article{ aagaardknepleywilliams13, 3919 title = {A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element 3920 Models of Quasi-static and Dynamic Crustal Deformation}, 3921 author = {Brad T. Aagaard and Matthew G. Knepley and Charles A. Williams}, 3922 journal = {Journal of Geophysical Research: Solid Earth}, 3923 volume = {118}, 3924 number = {6}, 3925 pages = {3059--3079}, 3926 issn = {2169-9356}, 3927 doi = {10.1002/jgrb.50217}, 3928 keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics}, 3929 year = {2013}, 3930 petsc_uses = {KSP} 3931} 3932 3933@InProceedings{ aagaardknepleywilliams11, 3934 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3935 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3936 Deformation}, 3937 booktitle = {Eos Transactions of the AGU}, 3938 organization = {American Geophysical Union}, 3939 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 3940 year = {2011}, 3941 petsc_uses = {KSP} 3942} 3943 3944@InProceedings{ knepley10b, 3945 author = {Matthew G. {Knepley}}, 3946 title = {Acceleration of low order finite element computation with {GPUs} (Invited)}, 3947 booktitle = {Eos Transactions of the AGU}, 3948 organization = {American Geophysical Union}, 3949 note = {Fall Meeting Supplemental, Abstract IN44A-01}, 3950 year = {2010}, 3951 petsc_uses = {KSP} 3952} 3953 3954@InProceedings{ mayknepleygurnis09, 3955 author = {Dave A. May and Matthew G. Knepley and Michael Gurnis}, 3956 title = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}}, 3957 booktitle = {Eos Transactions of the AGU}, 3958 organization = {American Geophysical Union}, 3959 note = {Fall Meeting Supplemental, Abstract P31A-A1241}, 3960 year = {2009}, 3961 petsc_uses = {KSP} 3962} 3963 3964@InProceedings{ yuenknepleyerlebacherwright09, 3965 author = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright}, 3966 title = {The Coming Role of {GPU} in Computational Geodynamics}, 3967 booktitle = {Eos Transactions of the AGU}, 3968 organization = {American Geophysical Union}, 3969 note = {Fall Meeting Supplemental, Abstract DI22A-05}, 3970 year = {2009}, 3971 petsc_uses = {KSP} 3972} 3973 3974@InProceedings{ aagaardknepleywilliams08, 3975 author = {Brad Aagaard and Charles A. Williams and Matthew G. Knepley}, 3976 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3977 Deformation}, 3978 booktitle = {Eos Transactions of the AGU}, 3979 organization = {American Geophysical Union}, 3980 volume = {89}, 3981 number = {53}, 3982 note = {Fall Meeting Supplemental, Abstract T41A-1925}, 3983 year = {2007}, 3984 petsc_uses = {KSP} 3985} 3986 3987@InProceedings{ aagaardknepleywilliams07, 3988 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3989 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3990 Deformation}, 3991 booktitle = {Eos Transactions of the AGU}, 3992 organization = {American Geophysical Union}, 3993 volume = {88}, 3994 number = {52}, 3995 note = {Fall Meeting Supplemental, Abstract T21B-1798}, 3996 year = {2007}, 3997 petsc_uses = {KSP} 3998} 3999 4000@InProceedings{ aagaardknepleywilliams05, 4001 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 4002 title = {Development of software for studying earthquakes across multiple spatial and 4003 temporal scales by coupling quasi-static and dynamic simulations}, 4004 booktitle = {Eos Transactions of the AGU}, 4005 organization = {American Geophysical Union}, 4006 volume = {86}, 4007 number = {52}, 4008 note = {Fall Meeting Supplemental, Abstract S53A-1072}, 4009 year = {2005}, 4010 petsc_uses = {KSP} 4011} 4012 4013@InProceedings{ williamsgablehagermeadeaagaardknepley08, 4014 author = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and 4015 Brad Aagaard and Matthew G. Knepley}, 4016 title = {Modeling of Multiple Earthquake Cycles in {S}outhern {C}alifornia Using the {SCEC} 4017 Community Fault Model}, 4018 booktitle = {Proceedings of Geosciences '08}, 4019 address = {Wellington, NZ}, 4020 month = nov, 4021 year = {2008}, 4022 petsc_uses = {KSP} 4023} 4024 4025@TechReport{ zhang07, 4026 title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for 4027 Tsunamis}, 4028 author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi}, 4029 type = {Preprint}, 4030 number = {ANL/MCS-P1459-0907}, 4031 institution = {ANL}, 4032 month = sep, 4033 year = {2007}, 4034 petsc_uses = {KSP} 4035} 4036 4037@Article{ katz08b, 4038 author = {Richard F. Katz}, 4039 title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic 4040 focusing at mid-ocean ridges}, 4041 journal = {J. Petrology}, 4042 year = {2008}, 4043 volume = {49}, 4044 pages = {2099--2121}, 4045 doi = {10.1093/petrology/egn058}, 4046 petsc_uses = {KSP} 4047} 4048 4049@Article{ hgrhkjvv2008, 4050 title = {On preconditioning for a parallel solution of the {R}ichards equation}, 4051 author = {Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy 4052 Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena}, 4053 journal = {Computers and Geosciences}, 4054 volume = {34}, 4055 pages = {1958--1963}, 4056 year = {2008}, 4057 petsc_uses = {KSP} 4058} 4059 4060@Article{ maymoresi2008, 4061 title = {Preconditioned iterative methods for {Stokes} flow problems arising in 4062 computational geodynamics}, 4063 journal = {Physics of the Earth and Planetary Interiors}, 4064 volume = {171}, 4065 number = {1-4}, 4066 pages = {33--47}, 4067 year = {2008}, 4068 note = {{R}ecent Advances in Computational Geodynamics: Theory, Numerics and 4069 Applications}, 4070 issn = {0031-9201}, 4071 doi = {10.1016/j.pepi.2008.07.036}, 4072 author = {Dave A. May and Louis Moresi}, 4073 keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}, 4074 petsc_uses = {KSP} 4075} 4076 4077@Article{ kausmuhlhausmay2010, 4078 title = {A stabilization algorithm for geodynamic numerical simulations with a free 4079 surface}, 4080 author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May}, 4081 journal = {Physics of the Earth and Planetary Interiors}, 4082 volume = {181}, 4083 number = {1}, 4084 pages = {12--20}, 4085 year = {2010}, 4086 petsc_uses = {KSP} 4087} 4088 4089@Article{ duretzmaygeryatackley2011, 4090 title = {Discretization errors and free surface stabilization in the finite difference and 4091 marker-in-cell method for applied geodynamics: A numerical study}, 4092 author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley}, 4093 journal = {Geochemistry, Geophysics, Geosystems}, 4094 volume = {12}, 4095 number = {7}, 4096 year = {2011}, 4097 petsc_uses = {KSP} 4098} 4099 4100@Article{ furuichimaytackley2011, 4101 title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a 4102 {Schur} complement approach with mixed precision arithmetic}, 4103 author = {Mikito Furuichi and Dave A May and Paul J Tackley}, 4104 journal = {Journal of Computational Physics}, 4105 volume = {230}, 4106 number = {24}, 4107 pages = {8835--8851}, 4108 year = {2011}, 4109 petsc_uses = {KSP} 4110} 4111 4112@Article{ kellermaykaus2013, 4113 title = {Numerical modelling of magma dynamics coupled to tectonic deformation of 4114 lithosphere and crust}, 4115 author = {Tobias Keller and Dave A May and Boris JP Kaus}, 4116 journal = {Geophysical Journal International}, 4117 volume = {195}, 4118 number = {3}, 4119 pages = {1406--1442}, 4120 year = {2013}, 4121 petsc_uses = {KSP} 4122} 4123 4124@Article{ schellartfreemanstegmanmoresimay2007, 4125 title = {Evolution and diversity of subduction zones controlled by slab width}, 4126 author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A 4127 May}, 4128 journal = {Nature}, 4129 volume = {446}, 4130 number = {7133}, 4131 pages = {308--311}, 4132 year = {2007}, 4133 petsc_uses = {KSP} 4134} 4135 4136@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012, 4137 title = {A comparison of numerical surface topography calculations in geodynamic 4138 modelling: an evaluation of the sticky air method}, 4139 author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter 4140 and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley}, 4141 journal = {Geophysical Journal International}, 4142 volume = {189}, 4143 number = {1}, 4144 pages = {38--54}, 4145 year = {2012}, 4146 petsc_uses = {KSP} 4147} 4148 4149@Article{ stegmanfreemanschellartmoresimay2006, 4150 title = {Influence of trench width on subduction hinge retreat rates in {3-D} models of slab 4151 rollback}, 4152 author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A 4153 May}, 4154 journal = {Geochemistry, Geophysics, Geosystems}, 4155 volume = {7}, 4156 number = {3}, 4157 year = {2006}, 4158 petsc_uses = {KSP} 4159} 4160 4161@InProceedings{ may2014ptatin, 4162 title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics}, 4163 author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}}, 4164 booktitle = {Proceedings of {SC14}: The {International Conference for High Performance 4165 Computing, Networking, Storage and Analysis}}, 4166 organization = {ACM}, 4167 pages = {274--284}, 4168 year = {2014}, 4169 doi = {10.1109/SC.2014.28}, 4170 petsc_uses = {KSP} 4171} 4172 4173@Article{ maybrownpourhiet2015, 4174 title = {A scalable, matrix-free multigrid preconditioner for finite element 4175 discretizations of heterogeneous {Stokes} flow}, 4176 author = {David A May and Jed Brown and Laetitia {Le Pourhiet}}, 4177 journal = {Computer Methods in Applied Mechanics and Engineering}, 4178 volume = {290}, 4179 pages = {496--523}, 4180 year = {2015}, 4181 doi = {10.1016/j.cma.2015.03.014}, 4182 petsc_uses = {KSP} 4183} 4184 4185@Article{ duretzmayyamato2016, 4186 title = {A free surface capturing discretization for the staggered grid finite difference 4187 scheme}, 4188 author = {Thibault Duretz and Dave A May and Philippe Yamato}, 4189 journal = {Geophysical Journal International}, 4190 volume = {204}, 4191 number = {3}, 4192 pages = {1518--1530}, 4193 year = {2016}, 4194 petsc_uses = {KSP} 4195} 4196 4197@Article{ rhebergenwellskatzwathen2014, 4198 author = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen}, 4199 title = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics}, 4200 journal = {SIAM J. Sci. Comput.}, 4201 volume = {36}, 4202 pages = {A1960--A1977}, 4203 year = {2014}, 4204 petsc_uses = {KSP} 4205} 4206 4207@Article{ katz08a, 4208 author = {R.F. Katz and M.G. Worster}, 4209 title = {Simulation of directional solidification, thermochemical convection, and chimney 4210 formation in a {H}ele-{S}haw cell}, 4211 journal = {J. Comp. Phys.}, 4212 volume = {227}, 4213 pages = {9823-9840}, 4214 year = {2008}, 4215 doi = {10.1016/j.jcp.2008.06.039}, 4216 petsc_uses = {KSP} 4217} 4218 4219@Article{ aabg2007, 4220 author = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas}, 4221 title = {Full waveform inversion for seismic velocity and anelastic losses in 4222 heterogeneous structures}, 4223 journal = {Bulletin of Seismological Society of America}, 4224 year = {2007}, 4225 volume = {97}, 4226 pages = {1990--2008}, 4227 petsc_uses = {KSP} 4228} 4229 4230@Article{ katz2006, 4231 author = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman}, 4232 title = {The dynamics of melt and shear localization in partially molten aggregates}, 4233 journal = {Nature}, 4234 year = {2006}, 4235 volume = {442}, 4236 pages = {676--679}, 4237 month = aug, 4238 day = {10}, 4239 url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}, 4240 petsc_uses = {KSP} 4241} 4242 4243@InProceedings{ mqrs2003, 4244 author = {Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl}, 4245 year = {2003}, 4246 title = {Parallel Preconditioning for Sedimentary Basin Simulations}, 4247 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 4248 Sozopol, Bulgaria, June 4-8, 2003}, 4249 petsc_uses = {KSP} 4250} 4251 4252@InProceedings{ lichtner1, 4253 author = {Chuan Lu and Peter C. Lichtner}, 4254 year = {2005}, 4255 title = {{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in 4256 Geologic Media}, 4257 booktitle = {Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL}, 4258 lab = {LANL}, 4259 petsc_uses = {KSP} 4260} 4261 4262@Article{ hammondlichtnermills2014, 4263 title = {Evaluating the Performance of Parallel Subsurface Simulators: An Illustrative 4264 Example with {PFLOTRAN}}, 4265 author = {Glenn E. Hammond and Peter C. Lichtner and Richard Tran Mills}, 4266 journal = {Water Resources Research}, 4267 volume = {50}, 4268 number = {1}, 4269 pages = {208--228}, 4270 doi = {10.1002/2012WR013483}, 4271 year = {2014}, 4272 petsc_uses = {KSP} 4273} 4274 4275@Article{ smw2003, 4276 author = {R. Scheichl and R. Masson and J. Wendebourg}, 4277 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 4278 journal = {Computational Geosciences}, 4279 year = {2003}, 4280 volume = {7}, 4281 pages = {295--318}, 4282 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 4283 petsc_uses = {KSP} 4284} 4285 4286@Article{ kees-miller-03, 4287 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 4288 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 4289 journal = {Computational Geosciences}, 4290 year = {2003}, 4291 volume = {7}, 4292 pages = {91--114}, 4293 petsc_uses = {KSP} 4294} 4295 4296@Article{ bk2003, 4297 author = {JN Buur and T Kuehnel}, 4298 title = {Improving depth imaging by automated model updating}, 4299 journal = {The Leading Edge}, 4300 year = {2003}, 4301 volume = {22}, 4302 pages = {310-318}, 4303 petsc_uses = {KSP} 4304} 4305 4306@Article{ frederickbuffett2016, 4307 title = {Submarine groundwater discharge as a possible formation mechanism for 4308 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 4309 author = {Jennifer M. Frederick and Bruce A. Buffett}, 4310 journal = {Journal of Geophysical Research: Solid Earth}, 4311 volume = {121}, 4312 number = {3}, 4313 pages = {1383--1404}, 4314 issn = {2169-9356}, 4315 doi = {10.1002/2015JB012627}, 4316 year = {2016}, 4317 petsc_uses = {KSP} 4318} 4319 4320% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4321% LiteralHTML:<font color="#FF0000"> 4322% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 4323% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 4324% LiteralHTML:variety of these simulations.</p> 4325% LiteralHTML:</font> 4326% LiteralHTML: 4327@InProceedings{ appelbe1, 4328 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4329 year = {2003}, 4330 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 4331 computational methodology}, 4332 page = {781}, 4333 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 4334 Proceedings}, 4335 publisher = {Springer-Verlag}, 4336 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 4337 petsc_uses = {KSP} 4338} 4339 4340% LiteralHTML:<a name="katz"> 4341@InProceedings{ gd1, 4342 author = {Guillaume Dumont and Michel Kern}, 4343 title = {Parallelization of a {3D} Seismic Migration Code with {PETSc}}, 4344 year = {1999}, 4345 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 4346 Computing}, 4347 petsc_uses = {KSP} 4348} 4349 4350% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 4351% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 4352% LiteralHTML:<font color="#FF0000"> 4353% LiteralHTML: Figures from the work of Richard Katz 4354@PhDThesis{ katzthesis, 4355 author = {R.F. Katz}, 4356 title = {The deep roots of volcanoes: models of magma dynamics with applications to 4357 subduction zones}, 4358 school = {Columbia University}, 4359 year = {2005}, 4360 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 4361 petsc_uses = {KSP} 4362} 4363 4364@InCollection{ knepleykatzsmith06, 4365 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 4366 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 4367 USA}, 4368 title = {Developing a Geodynamics Simulator with {PETSc}}, 4369 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 4370 series = {Lecture Notes in Computational Science and Engineering}, 4371 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 4372 publisher = {Springer Berlin Heidelberg}, 4373 isbn = {978-3-540-31619-0}, 4374 keyword = {Mathematics and Statistics}, 4375 pages = {413-438}, 4376 volume = {51}, 4377 doi = {10.1007/3-540-31619-1_12}, 4378 year = {2006}, 4379 petsc_uses = {KSP} 4380} 4381 4382@Article{ katz04, 4383 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 4384 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 4385 the global mid-ocean ridge system}, 4386 journal = {Geophys.\ Res.\ Letts.}, 4387 year = {2004}, 4388 volume = {31}, 4389 pages = {L15605}, 4390 petsc_uses = {KSP} 4391} 4392 4393@Article{ katz07, 4394 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 4395 Ethan Coon}, 4396 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 4397 Toolkit for Scientific Computation}}, 4398 journal = {Phys. Earth Planet. In.}, 4399 volume = {163}, 4400 pages = {52--68}, 4401 year = {2007}, 4402 petsc_uses = {KSP} 4403} 4404 4405@Article{ williams2006development, 4406 title = {{Development of a package for modeling stress in the lithosphere}}, 4407 author = {Williams, CA}, 4408 journal = {Eos Trans. AGU}, 4409 volume = {87}, 4410 pages = {36}, 4411 year = {2006}, 4412 petsc_uses = {KSP} 4413} 4414 4415@Article{ goverswortel05, 4416 author = {R. Govers and M.J.R. Wortel}, 4417 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 4418 journal = {Earth and Planetary Science Letters}, 4419 volume = {236/1-2}, 4420 pages = {505-523}, 4421 year = {2005}, 4422 petsc_uses = {KSP} 4423} 4424 4425@InProceedings{ snark2, 4426 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4427 year = {2002}, 4428 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 4429 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 4430 petsc_uses = {KSP} 4431} 4432 4433@Article{ snark1, 4434 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 4435 Tan and Feng Wang}, 4436 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 4437 journal = {Submitted to Pure and Applied Geosciences}, 4438 petsc_uses = {KSP} 4439} 4440 4441@InProceedings{ earthquake2003, 4442 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 4443 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 4444 Tiankai Tu}, 4445 year = {2003}, 4446 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 4447 booktitle = {Proceedings of SC2003}, 4448 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 4449 petsc_uses = {KSP} 4450} 4451 4452@InProceedings{ stefano12, 4453 author = {Michele De Stefano}, 4454 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 4455 booktitle = {PIERS Proceedings}, 4456 month = aug, 4457 address = {Moscow, RUSSIA}, 4458 pages = {491--495}, 4459 year = {2012}, 4460 petsc_uses = {KSP} 4461} 4462 4463%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 4464 4465% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4466% LiteralHTML: <center><img alt="" 4467% LiteralHTML: src="images/ocean.jpg"></center></p> 4468@Article{ khatiwala07, 4469 author = {Khatiwala, S.}, 4470 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 4471 journal = {Glob. Biogeochem. Cycles}, 4472 volume = {21}, 4473 doi = {10.1029/2007GB002923}, 4474 year = {2007}, 4475 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 4476} 4477 4478@Article{ dks2004, 4479 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 4480 journal = {Ocean Modelling}, 4481 year = {2004}, 4482 volume = {6(2)}, 4483 pages = {125-150}, 4484 title = {A finite-element Ocean Model: Principles and Evaluation}, 4485 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}, 4486 petsc_uses = {KSP} 4487} 4488 4489@Article{ danilov1, 4490 author = {S. Danilov and G. Kivman and J. Schroter}, 4491 year = {2004}, 4492 title = {Evaluation of an eddy-permitting finite-element ocean model in the {N}orth 4493 {A}tlantic}, 4494 journal = {Ocean Modelling}, 4495 petsc_uses = {KSP} 4496} 4497 4498@Article{ nerger1, 4499 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 4500 year = {2004}, 4501 title = {Data Assimilation with the Ensemble {K}alman Filter and the {SEIK} Filter applied to 4502 a Finite Element Model of the {N}orth {A}tlantic}, 4503 journal = {Journal of marine systems}, 4504 petsc_uses = {KSP} 4505} 4506 4507@Conference{ rakowsky2003self, 4508 title = {{A self-adaptive finite element model of the atmosphere}}, 4509 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 4510 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 4511 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 4512 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 4513 pages = {279}, 4514 isbn = {981238376X}, 4515 year = {2003}, 4516 organization = {World Scientific Pub Co}, 4517 petsc_uses = {KSP} 4518} 4519 4520@Article{ lauter3, 4521 author = {M. Lauter}, 4522 year = {2004}, 4523 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4524 AtmosphArenmodell}, 4525 journal = {Berichte zur Polar- und Meeresforschung}, 4526 petsc_uses = {KSP} 4527} 4528 4529@Article{ lauter2, 4530 author = {M. Lauter and D. Handorf and K. Dethloff}, 4531 year = {2004}, 4532 title = {Unsteady analytical solutions of the spherical shallow water equations}, 4533 journal = {Journal of computational physics}, 4534 petsc_uses = {KSP} 4535} 4536 4537@PhDThesis{ lauter1, 4538 author = {M. Lauter}, 4539 year = {2004}, 4540 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4541 AtmosphArenmodell}, 4542 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 4543 petsc_uses = {KSP} 4544} 4545 4546@Article{ frickenhaus1, 4547 author = {S. Frickenhaus and W. Hiller and M. Best}, 4548 year = {2005}, 4549 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 4550 parallel numerical atmosphere and ocean models}, 4551 journal = {Ocean Modelling}, 4552 volume = {10}, 4553 pages = {185--191}, 4554 petsc_uses = {KSP} 4555} 4556 4557@Article{ 0266-5611-24-3-034015, 4558 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 4559 title = {A {N}ewton-{CG} method for large-scale three-dimensional elastic full-waveform 4560 seismic inversion}, 4561 journal = {Inverse Problems}, 4562 volume = {24}, 4563 number = {3}, 4564 pages = {034015 (26pp)}, 4565 url = {http://stacks.iop.org/0266-5611/24/034015}, 4566 year = {2008}, 4567 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 4568 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 4569 iterations with inner conjugate gradient linear iterations, globalized by an 4570 Armijo backtracking line search, solved on a sequence of finer grids and higher 4571 frequencies to remain in the vicinity of the global optimum, inexactly terminated 4572 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 4573 variation operator to capture sharp interfaces, finely discretized by finite 4574 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 4575 implemented in matrix-free fashion with adjoint-based computation of reduced 4576 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 4577 waveform storage, and partitioned spatially across processors to parallelize the 4578 solutions of the forward and adjoint wave equations and the evaluation of 4579 gradient-like information. Several numerical examples demonstrate the grid 4580 independence of linear and nonlinear iterations, the effectiveness of the 4581 preconditioner, the ability to solve inverse problems with up to 17 million 4582 inversion parameters on up to 2048 processors, the effectiveness of multiscale 4583 continuation in keeping iterates in the basin of attraction of the global minimum, 4584 and the ability to fit the observational data while reconstructing the model with 4585 reasonable resolution and capturing sharp interfaces.}, 4586 petsc_uses = {KSP} 4587} 4588 4589% LiteralHTML: 4590% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 4591% LiteralHTML: 4592% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4593% LiteralHTML:<font color="#FF0000"> 4594% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 4595% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 4596% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 4597% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 4598% LiteralHTML:for a variety of these simulations.</p> 4599% LiteralHTML:</font> 4600% LiteralHTML: 4601@Article{ mills2009modeling, 4602 title = {Modeling subsurface reactive flows using leadership-class computing}, 4603 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4604 Mahinthakumar, G.K. and Smith, B.F.}, 4605 journal = {Journal of Physics: Conference Series}, 4606 volume = {180}, 4607 pages = {012062}, 4608 year = {2009}, 4609 publisher = {IOP Publishing}, 4610 petsc_uses = {KSP} 4611} 4612 4613@Conference{ mills2007simulating, 4614 title = {{Simulating subsurface flow and transport on ultrascale computers using 4615 PFLOTRAN}}, 4616 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 4617 booktitle = {Journal of Physics: Conference Series}, 4618 volume = {78}, 4619 pages = {012051}, 4620 year = {2007}, 4621 organization = {IOP Publishing}, 4622 petsc_uses = {KSP} 4623} 4624 4625@InProceedings{ mills2009, 4626 title = {Modeling subsurface reactive flows using leadership-class computing}, 4627 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4628 Mahinthakmuar, G. and Smith, B.}, 4629 booktitle = {Journal of Physics: Conference Series}, 4630 volume = {180}, 4631 pages = {102062}, 4632 year = {2009}, 4633 organization = {IOP Publishing}, 4634 petsc_uses = {KSP} 4635} 4636 4637@Article{ guo2013parallel, 4638 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 4639 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 4640 }, 4641 journal = {Advances in Water Resources }, 4642 volume = {53}, 4643 number = {0}, 4644 pages = {101 - 108}, 4645 year = {2013}, 4646 note = {}, 4647 issn = {0309-1708}, 4648 doi = {10.1016/j.advwatres.2012.10.010}, 4649 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 4650 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 4651 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 4652 preconditioner}, 4653 petsc_uses = {KSP} 4654} 4655 4656@Unpublished{ stomp, 4657 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 4658 url = {http://stomp.pnl.gov/}, 4659 petsc_uses = {KSP} 4660} 4661 4662@InProceedings{ htfc2003, 4663 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 4664 title = {Methods and Experiences For Parallelizing Flood Models}, 4665 year = {2003}, 4666 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 4667 European PVM/MPI User's Group Meeting}, 4668 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 4669 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 4670 petsc_uses = {KSP} 4671} 4672 4673@InProceedings{ hulchy-tran-astalos-fmsip, 4674 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 4675 D.Froehlich}, 4676 title = {Flood Modeling System and Its Parallelization}, 4677 year = {2002}, 4678 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 4679 Engineering}, 4680 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 4681 petsc_uses = {KSP} 4682} 4683 4684@InProceedings{ gy1, 4685 author = {J. P. Gwo and G. T. Yeh}, 4686 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 4687 Transport at Watershed Scale}, 4688 year = {2004}, 4689 booktitle = {The International Conference on Computational Methods}, 4690 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 4691 petsc_uses = {KSP} 4692} 4693 4694@Conference{ cheng2009efficient, 4695 title = {{An efficient parallel method for large-scale groundwater flow equation based on 4696 PETSc}}, 4697 author = {Cheng, T. and Ji, X. and Wang, Q.}, 4698 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 4699 Conference on}, 4700 pages = {190--193}, 4701 organization = {IEEE}, 4702 petsc_uses = {KSP} 4703} 4704 4705@Unpublished{ sfrsm, 4706 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 4707 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 4708 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 4709 its linear solves}, 4710 petsc_uses = {KSP} 4711} 4712 4713% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4714@InProceedings{ bart_omar:sc05, 4715 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 4716 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 4717 title = {Dynamic data driven inversion for terascale simulations: real-time 4718 indentification of airborne contaminants}, 4719 booktitle = {Proceedings of SC2005}, 4720 organization = {IEEE/ACM}, 4721 address = {Seattle, WA}, 4722 year = {2005}, 4723 month = nov, 4724 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 4725 lab = {SNL}, 4726 petsc_uses = {KSP} 4727} 4728 4729@InProceedings{ anton-krassimir-lscc, 4730 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 4731 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 4732 Simulations}, 4733 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 4734 volume = {2907}, 4735 year = {2003}, 4736 publisher = {Springer-Verlag}, 4737 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 4738 petsc_uses = {KSP} 4739} 4740 4741@InProceedings{ aa2001, 4742 author = {Anton Antonov}, 4743 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 4744 year = {2001}, 4745 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 4746 Sozopol, Bulgaria}, 4747 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 4748 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 4749 petsc_uses = {KSP} 4750} 4751 4752% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4753@Article{ grassley-simmons-kercher-00, 4754 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 4755 year = {2000}, 4756 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 4757 reactive transport models}, 4758 journal = {Applied Geochemistry}, 4759 volume = {17}, 4760 pages = {699--708}, 4761 lab = {LLNL} 4762} 4763 4764@Article{ glassey-nitao-03, 4765 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 4766 and Carl I. Steefel and James R. Kercher}, 4767 year = {2003}, 4768 title = {The impact of climate change on vadose zone pore waters and its implication for 4769 long-term monitoring}, 4770 journal = {Computers and Geosciences}, 4771 volume = {29}, 4772 pages = {399-411}, 4773 lab = {LLNL}, 4774 petsc_uses = {KSP} 4775} 4776 4777@Article{ steefel-depaolo-lichtner-05, 4778 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 4779 year = {2005}, 4780 title = {Reactive transport modeling: An essential tool and a new research approach for 4781 the Earth sciences}, 4782 journal = {Earth and Planetary Science Letters}, 4783 lab = {LLNL,LANL}, 4784 petsc_uses = {KSP} 4785} 4786 4787% LiteralHTML:<a name="scalinglarge"> 4788% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4789% LiteralHTML: <center><img alt="" 4790% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 4791% LiteralHTML:<font color="#FF0000"> 4792% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 4793@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 4794 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 4795 Strategies for Large-Scale Numerical Simulations}, 4796 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 4797 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 4798 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 4799 Large-Scale Systems (scalA)}, 4800 pages = {65-72}, 4801 doi = {10.1109/ScalA.2018.00012}, 4802 month = nov, 4803 year = {2018}, 4804 petsc_uses = {KSP} 4805} 4806 4807@Article{ km2004, 4808 author = {A. Keese and H. G. Matthies}, 4809 journal = {Computers and Structures}, 4810 year = {2005}, 4811 volume = {83}, 4812 pages = {1033--1047}, 4813 title = {Hierarchical parallelisation for the solution of stochastic finite element 4814 equations}, 4815 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}, 4816 petsc_uses = {KSP} 4817} 4818 4819@Unpublished{ hvl2002, 4820 title = {Numerical Modeling of {NAPL} Source Zone Treatment}, 4821 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 4822 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 4823 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 4824 year = {2002}, 4825 lab = {LANL}, 4826 petsc_uses = {KSP} 4827} 4828 4829@PhDThesis{ hammond2003, 4830 author = {Glenn E. Hammond}, 4831 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 4832 Transport on Supercomputers}, 4833 school = {University of Illinois at Urbana-Champaign}, 4834 year = {2003}, 4835 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 4836 petsc_uses = {KSP} 4837} 4838 4839@Unpublished{ uk, 4840 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 4841 Scale Environmental Flows and Transport Processes}, 4842 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 4843 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 4844 buildings and in Green Bay. Used PETSc for its linear solvers}, 4845 year = {1999}, 4846 petsc_uses = {KSP} 4847} 4848 4849@InProceedings{ hammond2002, 4850 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 4851 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 4852 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 4853 year = {2002}, 4854 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 4855 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 4856 Resources, Delft, The Netherlands.}, 4857 lab = {LANL}, 4858 petsc_uses = {KSP} 4859} 4860 4861@TechReport{ steefel1, 4862 author = {C. I. Steefel}, 4863 title = {Software for modeling multicomponent, multidimensional reactive transport}, 4864 year = {2001}, 4865 institution = {Lawrence Livermore National Laboratory}, 4866 number = {UCRL-MA-143182}, 4867 lab = {LLNL}, 4868 petsc_uses = {KSP} 4869} 4870 4871@Article{ steefel2, 4872 author = {C. I. Steefel and A. C. Lasaga}, 4873 title = {A coupled model for transport of multiple chemical-species and kinetic 4874 precipitation dissolution reactions with application to reactive flow in 4875 single-phase hydrothermal systems}, 4876 journal = {Americal Journal of Science}, 4877 year = {1994}, 4878 pages = {529-592}, 4879 volume = {294}, 4880 number = {5}, 4881 petsc_uses = {KSP} 4882} 4883 4884@TechReport{ steefel3, 4885 author = {C. I. Steefel and S. B. Yabusaki}, 4886 title = {{OS3D/GIMRT}, Software for Multicomponent-Multidimensional reactive transport: 4887 User's manual and programmer's guide}, 4888 year = {1996}, 4889 institution = {Pacific Northwest National Laboratory}, 4890 number = {PNNL-11166}, 4891 lab = {PNNL}, 4892 petsc_uses = {KSP} 4893} 4894 4895@Article{ 2005hvl, 4896 author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner}, 4897 title = {Application of {J}acobian-free {N}ewton-{K}rylov with physics-based 4898 preconditioning to biogeochemical transport}, 4899 journal = {Advances in Water Resources}, 4900 year = {2005}, 4901 pages = {359--376}, 4902 volume = {28}, 4903 url = { 4904 http://www.sciencedirect.com/science?_ob=IssueURL&_tockey=%23TOC%235953%232005%23999719995%23576651%23FLA%23Volume_28,_Issue_4,_Pages_315-427_(April_2005)&_auth=y&view=c&_acct=C000059129&_version=1&_urlVersion=0&_userid=2914253&md5=0d485527443c6192356cc508e1621002}, 4905 lab = {LANL}, 4906 petsc_uses = {KSP} 4907} 4908 4909@Article{ wang-zabar-05, 4910 author = {J Wang and N Zabaras}, 4911 journal = {Int. J. Heat and Mass Transfer}, 4912 title = {A Markov random field model of contamination source identification in porous 4913 media flow}, 4914 year = {2005}, 4915 petsc_uses = {KSP} 4916} 4917 4918@InBook{ kp1, 4919 author = {Jong G. Kim and Hyoung W. Park}, 4920 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 4921 Media}, 4922 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 4923 title = {Lecture Notes in Computer Science}, 4924 publisher = {Springer-Verlag}, 4925 volume = {3044}, 4926 year = {2004}, 4927 petsc_uses = {KSP} 4928} 4929 4930@Article{ 2001agusm...h32a06k, 4931 author = {{Kim}, J.~G. and {Kim}, J.}, 4932 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 4933 journal = {AGU Spring Meeting Abstracts}, 4934 year = {2001}, 4935 pages = {32-+}, 4936 petsc_uses = {KSP} 4937} 4938 4939@Article{ lzb2005, 4940 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 4941 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 4942 journal = {Journal of Hydraulic Engineering}, 4943 year = {2005}, 4944 volume = {131}, 4945 number = {4}, 4946 pages = {247--258}, 4947 petsc_uses = {KSP} 4948} 4949 4950@Article{ rao2005, 4951 author = {Prasada Rao}, 4952 title = {A parallel {RMA2} model for simulating large-scale free surface flows}, 4953 journal = {Environmental Modelling and Software}, 4954 year = {2005}, 4955 pages = {47--53}, 4956 petsc_uses = {KSP} 4957} 4958 4959@InProceedings{ pr1, 4960 author = {Prasada Rao}, 4961 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 4962 Hydrodynamic Flows}, 4963 year = {2003}, 4964 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 4965 Conference}, 4966 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 4967 petsc_uses = {KSP} 4968} 4969 4970@InProceedings{ lichtner2004, 4971 author = {Peter C. Lichtner and Andrew Wolfsberg}, 4972 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 4973 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 4974 Challenge Supercomputing Problem}, 4975 year = {2004}, 4976 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 4977 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 4978 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 4979 lab = {LANL}, 4980 petsc_uses = {KSP} 4981} 4982 4983% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4984@Article{ aba01:petsc-app, 4985 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 4986 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 4987 journal = {Int. J. High Performance Computing Applications}, 4988 year = {2001}, 4989 volume = {15}, 4990 number = {1}, 4991 pages = {13--21}, 4992 petsc_uses = {KSP} 4993} 4994 4995@PhDThesis{ tjb200, 4996 author = {Thomas James Byer}, 4997 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 4998 Facilities}, 4999 school = {Stanford}, 5000 year = {2000}, 5001 petsc_uses = {KSP} 5002} 5003 5004@InProceedings{ puchyr2006, 5005 author = {Peter J. Puchyr}, 5006 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 5007 {Win32} Cluster}, 5008 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 5009 note = {Paper number CIPC2006-207}, 5010 year = {2006}, 5011 petsc_uses = {KSP} 5012} 5013 5014@InProceedings{ texas98, 5015 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 5016 and G. A. Pope}, 5017 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 5018 Simulation}, 5019 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 5020 Symposium}, 5021 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 5022 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 5023 year = {1998}, 5024 petsc_uses = {KSP} 5025} 5026 5027% LiteralHTML: 5028% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 5029% LiteralHTML: 5030@Article{ farrellmitchellscottwechsung2021, 5031 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 5032 stationary incompressible {Navier-Stokes} equations}, 5033 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 5034 Wechsung}, 5035 journal = {The SMAI journal of computational mathematics}, 5036 volume = {7}, 5037 pages = {75--96}, 5038 year = {2021}, 5039 petsc_uses = {KSP} 5040} 5041 5042@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 5043 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 5044 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 5045 P MacLachlan and Ray S Tuminaro}, 5046 journal = {SIAM Journal on Scientific Computing}, 5047 number = {0}, 5048 pages = {S70--S91}, 5049 year = {2021}, 5050 petsc_uses = {KSP} 5051} 5052 5053@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 5054 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 5055 hyperelasticity}, 5056 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 5057 Oyar\'ua and Ricardo Ruiz-Baier}, 5058 journal = {Computer Methods in Applied Mechanics and Engineering}, 5059 volume = {374}, 5060 pages = {113562}, 5061 issn = {0045-7825}, 5062 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 5063 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 5064 year = {2021}, 5065 petsc_uses = {KSP} 5066} 5067 5068@Article{ farrellmitchellwechsung2018, 5069 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 5070 {Navier-Stokes} equations at high {Reynolds} number}, 5071 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 5072 journal = {SIAM Journal on Scientific Computing}, 5073 volume = {41}, 5074 number = {5}, 5075 eprint = {1810.03315}, 5076 pages = {A3073-A3096}, 5077 year = {2019}, 5078 petsc_uses = {KSP} 5079} 5080 5081@Article{ hevuikklaij2017, 5082 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 5083 discretized by a finite volume method}, 5084 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 5085 journal = {Journal of Numerical Mathematics}, 5086 volume = {25}, 5087 number = {2}, 5088 pages = {89--105}, 5089 year = {2017}, 5090 petsc_uses = {KSP} 5091} 5092 5093@InProceedings{ zou2015newton, 5094 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 5095 appearance/disappearance}, 5096 author = {Zou, L and Zhao, H and Zhang, H}, 5097 booktitle = {ANS 2015 Annual Meeting, June}, 5098 volume = {7}, 5099 number = {11}, 5100 year = {2015}, 5101 petsc_uses = {KSP} 5102} 5103 5104@Article{ guermond2009nonlinear, 5105 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 5106 Fourier/finite element technique and an interior penalty method}, 5107 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 5108 journal = {Journal of computational physics}, 5109 volume = {228}, 5110 number = {8}, 5111 pages = {2739--2757}, 5112 year = {2009}, 5113 publisher = {Elsevier}, 5114 petsc_uses = {KSP} 5115} 5116 5117@Article{ erzincanlisahin2015, 5118 title = {The numerical simulation of the wing kinematics effects on near wake topology and 5119 aerodynamic performance in hovering {D}rosophila flight}, 5120 author = {Belkis Erzincanli and Mehmet Sahin}, 5121 journal = {Computers \& Fluids}, 5122 volume = {122}, 5123 pages = {90--110}, 5124 year = {2015}, 5125 publisher = {Elsevier}, 5126 petsc_uses = {KSP} 5127} 5128 5129@Article{ ekensahin2015, 5130 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 5131 structure interaction problems}, 5132 author = {Ali Eken and Mehmet Sahin}, 5133 journal = {International Journal for Numerical Methods in Fluids}, 5134 year = {2015}, 5135 publisher = {Wiley Online Library}, 5136 petsc_uses = {KSP} 5137} 5138 5139@Article{ hwangsucai2015, 5140 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 5141 for transonic full potential equation}, 5142 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 5143 journal = {Computers \& Fluids}, 5144 volume = {110}, 5145 number = {30}, 5146 pages = {96--107}, 5147 year = {2015}, 5148 doi = {10.1016/j.compfluid.2014.04.005}, 5149 petsc_uses = {KSP} 5150} 5151 5152@Article{ yanghwangcai2016, 5153 title = {Nonlinear Preconditioning Techniques for Full-Space {L}agrange--{N}ewton Solution of 5154 {PDE}-Constrained Optimization Problems}, 5155 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 5156 journal = {SIAM Journal on Scientific Computing}, 5157 volume = {38}, 5158 number = {5}, 5159 pages = {A2756--A2778}, 5160 year = {2016}, 5161 petsc_uses = {KSP} 5162} 5163 5164@Article{ khanaidun2011, 5165 author = {Irfan Khan and Cyrus K. Aidun}, 5166 title = {Direct numerical simulation of saturated deformable porous media using parallel 5167 hybrid Lattice-{B}oltzmann and finite element method}, 5168 journal = {Int. J. Numer. Meth. Eng.}, 5169 volume = {86}, 5170 pages = {1379--1395}, 5171 year = {2011}, 5172 petsc_uses = {KSP} 5173} 5174 5175@Article{ khanaidun2014, 5176 author = {Irfan Khan and Cyrus K. Aidun}, 5177 title = {Modeling the deformation of saturate porous media using direct numerical 5178 simulation}, 5179 journal = {Int. J. Multiphase Flow}, 5180 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 5181 year = {2014}, 5182 petsc_uses = {KSP} 5183} 5184 5185@Article{ mofidi2014simulations, 5186 author = {A. Mofidi and P. M. Carrica}, 5187 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 5188 and Propeller}, 5189 journal = {Computers and Fluids}, 5190 pages = {191--203}, 5191 year = {2014}, 5192 petsc_uses = {KSP} 5193} 5194 5195@Article{ paik2014fluidstructure, 5196 author = {K. Paik and P. M. Carrica}, 5197 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 5198 Surface in a Rolling Tank}, 5199 journal = {Ocean Engineering}, 5200 pages = {201--212}, 5201 year = {2014}, 5202 petsc_uses = {KSP} 5203} 5204 5205@Article{ castro2013bubble, 5206 author = {A. M. Castro and P. M. Carrica}, 5207 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 5208 evaluation and numerical issues}, 5209 journal = {International Journal of Multiphase Flow 57}, 5210 pages = {131--150}, 5211 year = {2013}, 5212 petsc_uses = {KSP} 5213} 5214 5215@Article{ carrica2013turn, 5216 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 5217 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 5218 Dynamic Overset Grids}, 5219 journal = {Journal of Marine Science and Technology}, 5220 pages = {166--181}, 5221 year = {2013}, 5222 petsc_uses = {KSP} 5223} 5224 5225@Article{ castro2013eulerian, 5226 author = {A. M. Castro and P. M. Carrica}, 5227 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 5228 {Athena} {R}/V,}, 5229 journal = {International Shipbuilding Progress}, 5230 pages = {403--433}, 5231 year = {2013}, 5232 petsc_uses = {KSP} 5233} 5234 5235@Article{ chase2013overset, 5236 author = {N. Chase and T. Michael and P. M. Carrica}, 5237 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 5238 {Maneuvering} {Conditions}}, 5239 journal = {International Shipbuilding Progress}, 5240 pages = {171--205}, 5241 year = {2013}, 5242 petsc_uses = {KSP} 5243} 5244 5245@Article{ sadathosseini2013wu, 5246 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 5247 Stern}, 5248 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 5249 Free Surge Conditions in Short and Long Head Waves}, 5250 journal = {Ocean Engineering}, 5251 volume = {59}, 5252 pages = {240--273}, 5253 year = {2013}, 5254 petsc_uses = {KSP} 5255} 5256 5257@Article{ chase2013cfd, 5258 author = {N. Chase and P. M. Carrica}, 5259 title = {{CFD} Simulations of a Submarine Propeller and Application to Self-Propulsion of a 5260 Submarine}, 5261 journal = {Ocean Engineering}, 5262 pages = {68--80}, 5263 year = {2013}, 5264 petsc_uses = {KSP} 5265} 5266 5267@Article{ carrica2012cfd, 5268 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 5269 title = {{CFD} Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 5270 of Moving Rudders and Rotating Propellers}, 5271 journal = {Computers and Fluids 53}, 5272 pages = {117--132}, 5273 year = {2012}, 5274 petsc_uses = {KSP} 5275} 5276 5277@Article{ sakamoto2012urans, 5278 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5279 title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 5280 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 5281 publisher = {Journal of Marine Science and Technology}, 5282 pages = {422--445}, 5283 year = {2012}, 5284 petsc_uses = {KSP} 5285} 5286 5287@Article{ sakamoto2012uransb, 5288 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5289 title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 5290 Analysis and Validation of Local Flow Characteristics}, 5291 journal = {Journal of Marine Science and Technology}, 5292 pages = {446--468}, 5293 year = {2012}, 5294 petsc_uses = {KSP} 5295} 5296 5297@Article{ li2012dynamic, 5298 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 5299 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 5300 journal = {Renewable Energy}, 5301 pages = {285--298}, 5302 year = {2012}, 5303 petsc_uses = {KSP} 5304} 5305 5306@Article{ huang2012a, 5307 author = {J. Huang and P. M. Carrica and F. Stern}, 5308 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 5309 journal = {International Journal for Numerical Methods in Fluids}, 5310 pages = {160--180}, 5311 year = {2012}, 5312 petsc_uses = {KSP} 5313} 5314 5315@Article{ huang2012b, 5316 author = {J. Huang and P. M. Carrica and F. Stern}, 5317 title = {A geometry-based level set method for curvilinear overset grids with application 5318 to ship hydrodynamics}, 5319 journal = {International Journal for Numerical Methods in Fluids}, 5320 pages = {494--521}, 5321 year = {2012}, 5322 petsc_uses = {KSP} 5323} 5324 5325@Article{ carrica2011computations, 5326 author = {P. M. Carrica and H. Fu and F. Stern}, 5327 title = {Computations of self-propulsion free to sink and trim and of motions in head 5328 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 5329 journal = {Applied Ocean Research}, 5330 pages = {309--320}, 5331 year = {2011}, 5332 petsc_uses = {KSP} 5333} 5334 5335@Article{ bhushan2011scalability, 5336 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 5337 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 5338 Using {CFDShip}-Iowa}, 5339 journal = {International Journal of High Performance Computing Applications}, 5340 pages = {466--487}, 5341 year = {2011}, 5342 petsc_uses = {KSP} 5343} 5344 5345@Article{ castro2011full, 5346 author = {A. M. Castro and P. M. Carrica and F. Stern}, 5347 title = {Full scale self-propulsion computations using discretized propeller for the 5348 {KRISO} container ship {KCS}}, 5349 journal = {Computers and Fluids}, 5350 pages = {35--47}, 5351 year = {2011}, 5352 petsc_uses = {KSP} 5353} 5354 5355@Article{ kandasamy2011multifidelity, 5356 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5357 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5358 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing {C}atamaran 5359 for Low Wake}, 5360 journal = {Journal of Marine Science and Technology}, 5361 pages = {143--156}, 5362 year = {2011}, 5363 petsc_uses = {KSP} 5364} 5365 5366@Article{ kandasamy2011cfd, 5367 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5368 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5369 title = {{CFD} Validation Studies for a High-speed Foil-assisted Semi-planing {C}atamaran}, 5370 journal = {Journal of Marine Science and Technology}, 5371 pages = {157--167}, 5372 year = {2011}, 5373 petsc_uses = {KSP} 5374} 5375 5376@Article{ sadathosseini2011cfd, 5377 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 5378 and S. Yamamura and A. Mastuda}, 5379 title = {{CFD} System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 5380 Periodic Motion and Broaching}, 5381 journal = {Ocean Engineering}, 5382 pages = {88--110}, 5383 year = {2011}, 5384 petsc_uses = {KSP} 5385} 5386 5387@Article{ mosaviraad2010development, 5388 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 5389 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 5390 with Comparison to Regular Wave and Transient Wave Group Procedures Using 5391 {URANS}}, 5392 journal = {Ocean Engineering}, 5393 pages = {653--666}, 5394 year = {2010}, 5395 petsc_uses = {KSP} 5396} 5397 5398@Article{ carrica2010largescale, 5399 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5400 Stern}, 5401 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5402 Heave Problems for a Surface Combatant}, 5403 journal = {Computers and Fluids}, 5404 pages = {1095--1111}, 5405 year = {2010}, 5406 petsc_uses = {KSP} 5407} 5408 5409@Article{ carrica2010selfpropulsion, 5410 author = {P. M. Carrica and A. M. Castro and F. Stern}, 5411 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 5412 with Dynamic Overset Grids}, 5413 journal = {Journal of Marine Science and Technology}, 5414 pages = {316--330}, 5415 year = {2010}, 5416 petsc_uses = {KSP} 5417} 5418 5419@Article{ ismail2010evaluation, 5420 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 5421 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 5422 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 5423 journal = {International Journal of Numerical Methods in Fluids}, 5424 pages = {850--886}, 5425 year = {2010}, 5426 petsc_uses = {KSP} 5427} 5428 5429@Article{ kandasamy2010integral, 5430 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 5431 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 5432 journal = {Journal of Fluids Engineering}, 5433 pages = {101103}, 5434 year = {2010}, 5435 petsc_uses = {KSP} 5436} 5437 5438@Article{ kirk:2014de, 5439 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 5440 title = {{Modeling hypersonic entry with the fully-implicit {N}avier--{S}tokes (FIN-S) 5441 stabilized finite element flow solver}}, 5442 journal = {Computers {\&} Fluids}, 5443 year = {2014}, 5444 volume = {92}, 5445 number = {0}, 5446 pages = {281--292}, 5447 month = mar, 5448 petsc_uses = {KSP} 5449} 5450 5451@Article{ carracciuolo20111382, 5452 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 5453 in high performance computing environment}, 5454 journal = {Journal of Non-Newtonian Fluid Mechanics }, 5455 volume = {166}, 5456 number = {23--24}, 5457 pages = {1382--1395}, 5458 year = {2011}, 5459 issn = {0377-0257}, 5460 doi = {10.1016/j.jnnfm.2011.08.014}, 5461 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 5462 Maffettone and A. Murli}, 5463 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 5464 method, High performance computing}, 5465 petsc_uses = {KSP} 5466} 5467 5468@Article{ bungartzgatzhammerliebmehlneckel11, 5469 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 5470 Miriam and Neckel, Tobias}, 5471 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 5472 journal = {Computational Mechanics}, 5473 volume = {48}, 5474 number = {3}, 5475 pages = {365-376}, 5476 year = {2011}, 5477 issn = {0178-7675}, 5478 doi = {10.1007/s00466-011-0626-1}, 5479 publisher = {Springer-Verlag}, 5480 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 5481 Thermohydraulics; Two-phase flow}, 5482 language = {English}, 5483 petsc_uses = {KSP} 5484} 5485 5486@Article{ bpr:cfl, 5487 author = {H.~M. B{\"u}cker and B. Pollul and A. Rasch}, 5488 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 5489 Equations}}, 5490 journal = {International Journal for Numerical Methods in Fluids}, 5491 year = {2009}, 5492 volume = {59}, 5493 number = {1}, 5494 pages = {1--18}, 5495 doi = {10.1002/fld.1798}, 5496 petsc_uses = {KSP} 5497} 5498 5499@InBook{ bonfiglioli_campobasso_carpentieri_2010, 5500 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 5501 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 5502 preconditioned newton-krylov solver}, 5503 publisher = {Curran Associates}, 5504 year = {2010}, 5505 url = {http://www.proceedings.com/05932.html}, 5506 petsc_uses = {KSP} 5507} 5508 5509@Article{ bonfiglioli_rans_2005, 5510 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 5511 Bernardo}, 5512 title = {RANS simulations of a junction flow}, 5513 journal = {International Journal of Computational Fluid Dynamics}, 5514 volume = {19}, 5515 number = {2}, 5516 pages = {179-189}, 5517 year = {2005}, 5518 doi = {10.1080/10618560410001729126}, 5519 petsc_uses = {KSP} 5520} 5521 5522@InCollection{ bonfiglioli__carpentieri_rans_2008, 5523 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 5524 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 5525 Italy}, 5526 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 5527 Equations Using Fluctuation Splitting Schemes}, 5528 booktitle = {Numerical Mathematics and Advanced Applications}, 5529 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 5530 publisher = {Springer Berlin Heidelberg}, 5531 isbn = {978-3-540-69777-0}, 5532 pages = {151-158}, 5533 doi = {10.1007/978-3-540-69777-0_17}, 5534 year = {2008}, 5535 petsc_uses = {KSP} 5536} 5537 5538@InCollection{ bonfiglioli__carpentieri_ens_2007, 5539 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 5540 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 5541 Italy}, 5542 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 5543 Problems on Unstructured Grids}, 5544 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 5545 series = {Lecture Notes in Computer Science}, 5546 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 5547 publisher = {Springer Berlin / Heidelberg}, 5548 isbn = {978-3-540-75754-2}, 5549 pages = {676-685}, 5550 volume = {4699}, 5551 doi = {10.1007/978-3-540-75755-9_83}, 5552 year = {2007}, 5553 petsc_uses = {KSP} 5554} 5555 5556@Article{ terrelscottknepleykirby08, 5557 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 5558 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 5559 journal = {BIT}, 5560 volume = {48}, 5561 number = {2}, 5562 year = {2008}, 5563 petsc_uses = {KSP} 5564} 5565 5566@Article{ martamadermartinsweidealonso07, 5567 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 5568 J. Alonso}, 5569 title = {A methodology for the development of discrete adjoint solvers using automatic 5570 differentiation tools}, 5571 journal = {Computational Fluid Dyanmics}, 5572 volume = {21}, 5573 pages = {307--327}, 5574 year = {2007}, 5575 petsc_uses = {KSP} 5576} 5577 5578@TechReport{ avb2008, 5579 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 5580 title = {Variational Space-time (Dis)continuous {G}alerkin Method for Linear Free Surface 5581 Waves}, 5582 year = {2008}, 5583 institution = {University of Twente, the Netherlands}, 5584 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 5585 petsc_uses = {KSP} 5586} 5587 5588@InProceedings{ bdsm2005, 5589 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal}, 5590 title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids}, 5591 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit}, 5592 year = {2005}, 5593 url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}, 5594 petsc_uses = {KSP} 5595} 5596 5597@InProceedings{ ms2006, 5598 author = {S. Muller and Y. Stiriba}, 5599 title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR 5600 STEADY COMPRESSIBLE FLOWS}, 5601 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006}, 5602 year = {2006}, 5603 url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}, 5604 petsc_uses = {KSP} 5605} 5606 5607@Article{ araujoteixeiracunhagroth08, 5608 author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth}, 5609 title = {Parallel three-dimensional simulation of the injection molding process}, 5610 journal = {International Journal for Numerical Methods in Fluids}, 5611 year = {2008}, 5612 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 5613 petsc_uses = {KSP} 5614} 5615 5616@PhDThesis{ a2008, 5617 author = {A. Cubero}, 5618 title = {a parallel coupled algorithm for collocated grids and its application to Large 5619 Eddy Simulation of a turbulent wake}, 5620 school = {University of Zaragoza (Spain)}, 5621 year = {2008}, 5622 petsc_uses = {KSP} 5623} 5624 5625@Article{ afa2007, 5626 author = {A. Cubero and N. 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Lauter and D. Handorf and K. Dethloff and S. Frickenhaus and N. Rakowsky and 5682 W. Hiller}, 5683 title = {An adaptive Lagrange-Galerkin shallow-water model on the sphere}, 5684 booktitle = {Workshop Proceedings Current Development in Shallow Water Models on the Sphere 5685 March, 10-14, 2003, Munich University of Technology, German}, 5686 year = {2003}, 5687 petsc_uses = {KSP} 5688} 5689 5690@InProceedings{ brios-ying-2002, 5691 author = {George Biros and Lexing Ying and Denis Zorin}, 5692 title = {The Embedded Boundary Integral Method (EBI) for the Incompressible 5693 {Navier-Stokes} equations}, 5694 booktitle = {IABEM 2002, International Association for Boundary Element Methods, UT Austin}, 5695 year = {2002}, 5696 petsc_uses = {KSP} 5697} 5698 5699@InProceedings{ mohsen-straatman-ins, 5700 author = {S.A. Mohsen Karimian and Anthony G. 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Visonneau"}, 5723 title = {A new fully coupled method for computing turbulent flows}, 5724 journal = {Computers and Fluids}, 5725 volume = {30}, 5726 pages = {445--472}, 5727 year = {2001}, 5728 petsc_uses = {KSP} 5729} 5730 5731@InProceedings{ knepleysarinsameh99b, 5732 title = {Multilevel Preconditioning for Parallel {CFD}}, 5733 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 5734 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 5735 Problems In Industrial Applications}, 5736 address = {Minneapolis, MN}, 5737 year = {1999}, 5738 petsc_uses = {KSP} 5739} 5740 5741@InProceedings{ garbey1, 5742 author = {M. Garbey and B. Hadri and W. Shyy.}, 5743 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 5744 Problems on the Grid}, 5745 booktitle = {Aerospace Sciences Meeting and Exhibit}, 5746 note = {Paper No. 2005-1386}, 5747 year = {2005}, 5748 petsc_uses = {KSP} 5749} 5750 5751@Article{ carrica2007unsteady, 5752 title = {An unsteady single-phase level set method for viscous free surface flows}, 5753 author = {Carrica, PM and Wilson, RV and Stern, F.}, 5754 journal = {International Journal for Numerical Methods in Fluids}, 5755 volume = {53}, 5756 number = {2}, 5757 pages = {229--256}, 5758 year = {2007}, 5759 publisher = {Chichester; New York: Wiley, c1981-}, 5760 petsc_uses = {KSP} 5761} 5762 5763@Article{ pctw2004, 5764 author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber}, 5765 title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of 5766 Spillways}, 5767 journal = {Journal of Hydraulic Research}, 5768 note = {accepted for publication}, 5769 year = {2004}, 5770 petsc_uses = {KSP} 5771} 5772 5773@Article{ wcs2004, 5774 author = {R. V. Wilson and P. M. Carrica and F. Stern}, 5775 title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface 5776 Combatant}, 5777 journal = {Computers and Fluids}, 5778 note = {in press}, 5779 year = {2004}, 5780 petsc_uses = {KSP} 5781} 5782 5783@Article{ cws2005, 5784 author = {P. M. Carrica and R. V. Wilson and F. Stern}, 5785 title = {Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem}, 5786 journal = {Computers and Fluids}, 5787 note = {accepted for publication}, 5788 year = {2005}, 5789 petsc_uses = {KSP} 5790} 5791 5792@Article{ chndss2010, 5793 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5794 Stern}, 5795 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5796 Heave Problems for a Surface Combatant}, 5797 journal = {Computers and Fluids}, 5798 year = {2010}, 5799 volume = {39}, 5800 number = {7}, 5801 pages = {1095--1111}, 5802 petsc_uses = {KSP} 5803} 5804 5805@InProceedings{ chnkss2008, 5806 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5807 Stern}, 5808 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 5809 Grids}, 5810 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 5811 year = {2008}, 5812 petsc_uses = {KSP} 5813} 5814 5815@MastersThesis{ mtj, 5816 author = {M. T. 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Paterson}, 5845 title = {Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines 5846 Using Unsteady {RANS} {CFD}}, 5847 booktitle = {35th AIAA Fluid Dynamics Conference and Exhibit}, 5848 year = {2005}, 5849 petsc_uses = {KSP} 5850} 5851 5852@InProceedings{ etpp, 5853 author = {B. A. Edge and M. F. Trujillo and E. G. Paterson and L. J. Peltier}, 5854 title = {Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids 5855 and DES}, 5856 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 5857 year = {2004}, 5858 petsc_uses = {KSP} 5859} 5860 5861@InProceedings{ pp8, 5862 author = {E. G. Paterson and L. J. Peltier}, 5863 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 5864 refinement grids and detached-eddy simulation}, 5865 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 5866 year = {2004}, 5867 petsc_uses = {KSP} 5868} 5869 5870@InProceedings{ mzwp, 5871 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 5872 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 5873 booktitle = {25th Symposium on Naval Hydrodynamics}, 5874 year = {2004}, 5875 petsc_uses = {KSP} 5876} 5877 5878@InProceedings{ ppph, 5879 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 5880 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 5881 booktitle = {25th Symposium on Naval Hydrodynamics}, 5882 year = {2004}, 5883 petsc_uses = {KSP} 5884} 5885 5886@InProceedings{ ppd, 5887 author = {E. G. Paterson and L. J. 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Baker}, 5913 title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control 5914 Surfaces}, 5915 booktitle = {42nd AIAA Aerospace Sciences Meeting}, 5916 year = {2004}, 5917 petsc_uses = {KSP} 5918} 5919 5920@InProceedings{ gid1, 5921 author = {G. Frank and J. D'Elia}, 5922 title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model}, 5923 year = {2004}, 5924 booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD}, 5925 url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf}, 5926 petsc_uses = {KSP} 5927} 5928 5929@InBook{ b1, 5930 author = {A.Bonfiglioli}, 5931 chapter = {On the use of the PETSc library for unstructured {CFD} applications}, 5932 year = {2001}, 5933 title = {Science and Supercomputing at CINECA}, 5934 pages = {397--400}, 5935 petsc_uses = {KSP} 5936} 5937 5938@InProceedings{ b2004, 5939 author = {L. A. Barba}, 5940 title = {Computing high-Reynolds number vortical flows: a highly accurate method with a 5941 fully meshless formulation}, 5942 year = {2004}, 5943 booktitle = {International Conference on Parallel CFD, Grand Canary, May 2004}, 5944 note = {Submitted}, 5945 petsc_uses = {KSP} 5946} 5947 5948@InProceedings{ bl2004, 5949 author = {L. A. Barba and A. Leonard}, 5950 title = {Computation of Viscous Vortices with Fully Meshless Method}, 5951 year = {2004}, 5952 booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004}, 5953 note = {Submitted}, 5954 petsc_uses = {KSP} 5955} 5956 5957@Article{ vws1, 5958 author = {B. G. M. Van Wachem and J. C. Schouten}, 5959 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 5960 Velocity}, 5961 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 5962 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 5963 Netherlands}, 5964 journal = {AIChE}, 5965 volumne = {48}, 5966 number = {12}, 5967 month = dec, 5968 year = {2002}, 5969 petsc_uses = {KSP} 5970} 5971 5972@TechReport{ lbam1, 5973 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 5974 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 5975 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 5976 di Bari Italy}, 5977 year = {2002}, 5978 number = {25/02}, 5979 petsc_uses = {KSP} 5980} 5981 5982@Article{ kees_miller_02, 5983 author = {C. E. Kees and C. T. Miller}, 5984 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 5985 journal = {Advances in Water Resources}, 5986 year = {2002}, 5987 volume = {25}, 5988 number = {2}, 5989 pages = {159-177.}, 5990 petsc_uses = {KSP} 5991} 5992 5993@InProceedings{ lepotmeersessers2001, 5994 author = {I. Lepot and F. Meers and J.A. Essers}, 5995 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 5996 Unstructured Meshes}, 5997 year = {2001}, 5998 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 5999 url = {http://www.ulg.ac.be/aerodyn}, 6000 petsc_uses = {KSP} 6001} 6002 6003@InProceedings{ knepley98, 6004 author = {Matthew Knepley and Denis Vanderstraeten}, 6005 title = {Parallel Building Blocks for Finite Element Simulations: Application to 6006 Solid-Liquid Mixture Flows}, 6007 booktitle = {Proceedings of Parallel CFD'97}, 6008 publisher = {Elsevier}, 6009 pages = {281--287}, 6010 year = {1998}, 6011 petsc_uses = {KSP} 6012} 6013 6014@InProceedings{ pcfd97, 6015 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 6016 title = {Parallel Implicit {PDE} Computations: Algorithms and Software}, 6017 publisher = {Elsevier}, 6018 year = {1998}, 6019 booktitle = {Proceedings of Parallel CFD'97}, 6020 pages = {333-344}, 6021 petsc_uses = {KSP} 6022} 6023 6024@InProceedings{ knepleysamehsari98, 6025 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 6026 title = {Parallel Simulation of Particulate Flows}, 6027 booktitle = {Solving Irregularly Structured Problems in Parallel}, 6028 editors = {A. Ferreira et al}, 6029 year = {1998}, 6030 series = {Lecture Notes in Computer Science}, 6031 volume = {1457}, 6032 pages = {226--237}, 6033 petsc_uses = {KSP} 6034} 6035 6036@Article{ gkmt98, 6037 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 6038 title = {Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel 6039 Implicit {CFD}}, 6040 journal = {Int. J. High Performance Computing Applications}, 6041 year = {2000}, 6042 volume = {14}, 6043 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 6044 pages = {102-136}, 6045 petsc_uses = {KSP} 6046} 6047 6048@InProceedings{ agkks-sc99, 6049 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 6050 Smith}, 6051 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 6052 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 6053 editor = {}, 6054 publisher = {}, 6055 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 6056 year = {1999}, 6057 note = {Winner of Gordon Bell Special Prize at SC 99}, 6058 petsc_uses = {KSP} 6059} 6060 6061@Article{ gkks01, 6062 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6063 title = {High Performance Parallel Implicit {CFD}}, 6064 journal = {Journal of Parallel Computing}, 6065 year = {2001}, 6066 volume = {27}, 6067 pages = {337-362}, 6068 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 6069 petsc_uses = {KSP} 6070} 6071 6072@Article{ cristea-sofonea-02, 6073 author = {Artur Cristea and Victor Sofonea}, 6074 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 6075 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 6076 Sciences, Information Sciences}, 6077 volume = {3}, 6078 number = {3}, 6079 year = {2002}, 6080 petsc_uses = {KSP} 6081} 6082 6083@Article{ cristea2, 6084 author = {Artur Cristea and Victor Sofonea}, 6085 title = {Two component lattice Boltzmann model with flux limiter techniques}, 6086 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 6087 Sciences, Information Sciences}, 6088 volume = {4}, 6089 number = {1}, 6090 year = {2003}, 6091 pages = {59--64}, 6092 petsc_uses = {KSP} 6093} 6094 6095@Article{ cristea1, 6096 author = {Artur Cristea and Victor Sofonea}, 6097 title = {Two component lattice Boltzmann model with flux limiters}, 6098 journal = {Central European Journal of Physics}, 6099 volume = {2}, 6100 number = {2}, 6101 year = {2004}, 6102 pages = {382--396}, 6103 petsc_uses = {KSP} 6104} 6105 6106@Article{ sofnea-lamura1, 6107 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 6108 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 6109 systems}, 6110 journal = {Physical Review E}, 6111 volume = {70}, 6112 number = {4}, 6113 year = {2004}, 6114 pages = {046702-1 / 046702-9}, 6115 petsc_uses = {KSP} 6116} 6117 6118@InProceedings{ gkks01b, 6119 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6120 title = {Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}}, 6121 booktitle = {Proceedings of the First MIT Conference on Computational Fluid and Solid 6122 Mechanics}, 6123 editor = {}, 6124 location = {Cambridge, MA}, 6125 year = {2001}, 6126 month = jun, 6127 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf}, 6128 petsc_uses = {KSP} 6129} 6130 6131@InProceedings{ gkks00, 6132 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6133 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 6134 Code}, 6135 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 6136 (HiPC '2000)}, 6137 editor = {}, 6138 location = {Bangalore, India}, 6139 year = {2000}, 6140 pages = {395--404}, 6141 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 6142 petsc_uses = {KSP} 6143} 6144 6145@InProceedings{ gkks-sc00, 6146 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6147 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 6148 booktitle = {Proceedings of SC2000}, 6149 editor = {}, 6150 publisher = {IEEE Computer Society}, 6151 year = {2000}, 6152 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 6153 petsc_uses = {KSP} 6154} 6155 6156@InProceedings{ knepleysamehsarin99, 6157 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 6158 title = {Design of Large Scale Parallel Simulations}, 6159 booktitle = {Proceedings of Parallel CFD'99}, 6160 editors = {A. {Ecer et al.}}, 6161 publisher = {Elsevier}, 6162 year = {1999}, 6163 petsc_uses = {KSP} 6164} 6165 6166@InProceedings{ gkks-pcfd99, 6167 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 6168 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 6169 booktitle = {Proceedings of Parallel CFD'99}, 6170 editors = {A. {Ecer et al.}}, 6171 publisher = {Elsevier}, 6172 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 6173 year = {1999}, 6174 petsc_uses = {KSP} 6175} 6176 6177@InProceedings{ kks97, 6178 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6179 title = {On the Interaction of Architecture and Algorithm in the Domain-Based 6180 Parallelization of an Unstructured Grid Incompressible Flow Code}, 6181 booktitle = {Proceedings of the 10th International Conference on Domain Decomposition 6182 Methods}, 6183 editor = {J. Mandel et al.}, 6184 pages = {311--319}, 6185 publisher = {Wiley}, 6186 note = {}, 6187 year = {1997}, 6188 petsc_uses = {KSP} 6189} 6190 6191@InProceedings{ kks99, 6192 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6193 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 6194 Incompressible Flows on Unstructured Grids}, 6195 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6196 Methods}, 6197 editors = {C.-H. {Lai et al.}}, 6198 publisher = {Domain Decomposition Press, Bergen}, 6199 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 6200 year = {1999}, 6201 petsc_uses = {KSP} 6202} 6203 6204@InCollection{ kks97_cfd, 6205 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 6206 title = {Perspectives for {CFD} on Petaflops Systems}, 6207 booktitle = {CFD Review 1998}, 6208 editor = {M. Hafez and K. Oshima}, 6209 publisher = {World Scientific, Singapore}, 6210 pages = {1079--1096}, 6211 note = {}, 6212 year = {1998}, 6213 petsc_uses = {KSP} 6214} 6215 6216@Article{ hm99, 6217 author = {P. D. Hovland and L. C. McInnes}, 6218 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 6219 {PETSc}}, 6220 year = {2000}, 6221 journal = {Parallel Computing}, 6222 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 6223 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 6224 petsc_uses = {KSP} 6225} 6226 6227@InProceedings{ cruzbarbaknepley08, 6228 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 6229 title = {Fast Multipole Method for particle interactions: an open source parallel library 6230 component}, 6231 booktitle = {Proceedings of ParCFD2008}, 6232 year = {2008}, 6233 editor = {Tromeur-Dervout et. al.}, 6234 publisher = {Elsevier}, 6235 petsc_uses = {KSP} 6236} 6237 6238@Article{ hwangcai05, 6239 author = {F.-N. Hwang and X.-C. Cai}, 6240 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 6241 for incompressible {Navier-Stokes} equations}, 6242 journal = {J. Comput. Phys.}, 6243 volume = {204}, 6244 year = {2005}, 6245 pages = {666--691}, 6246 petsc_uses = {KSP} 6247} 6248 6249@Article{ barbaleonard07, 6250 author = {Lorena A Barba and Anthony Leonard}, 6251 title = {Emergence and evolution of tripole vortices from net-circulation initial 6252 conditions}, 6253 journal = {Phys. Fluids}, 6254 volume = {19}, 6255 pages = {017101}, 6256 year = {2007}, 6257 doi = {10.1063/1.2409734}, 6258 petsc_uses = {KSP} 6259} 6260 6261@Article{ barba07, 6262 author = {Lorena A Barba}, 6263 title = {Non-shielded multipolar vortices at high Reynolds number}, 6264 journal = {Phys. Rev. E}, 6265 volume = {73}, 6266 pages = {065303}, 6267 year = {2006}, 6268 doi = {10.1103/PhysRevE.73.065303}, 6269 petsc_uses = {KSP} 6270} 6271 6272@Article{ schofield2010multi, 6273 title = {Multi-material incompressible flow simulation using the moment-of-fluid method}, 6274 author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and 6275 Lowrie, R.B. and Swartz, B.K.}, 6276 journal = {International Journal for Numerical Methods in Fluids}, 6277 volume = {63}, 6278 number = {8}, 6279 pages = {931--952}, 6280 year = {2010}, 6281 publisher = {Wiley Online Library}, 6282 petsc_uses = {KSP} 6283} 6284 6285% LiteralHTML: 6286% LiteralHTML: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3> 6287% LiteralHTML: 6288% LiteralHTML: article{DeGersem99, 6289% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, 6290% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, 6291% LiteralHTML: } 6292@Article{ nagler2014, 6293 title = {Sound transmission through a poroelastic layered panel}, 6294 author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff}, 6295 journal = {Computational Mechanics}, 6296 volume = {53}, 6297 number = {4}, 6298 pages = {549--560}, 6299 issn = {1432-0924}, 6300 doi = {10.1007/s00466-013-0916-x}, 6301 year = {2014}, 6302 petsc_uses = {KSP} 6303} 6304 6305@Article{ sheikh2013, 6306 author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.}, 6307 title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel 6308 deflation}, 6309 journal = {Numerical Linear Algebra with Applications}, 6310 volume = {20}, 6311 number = {4}, 6312 issn = {1099-1506}, 6313 doi = {10.1002/nla.1882}, 6314 pages = {645--662}, 6315 keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier 6316 analysis}, 6317 year = {2013}, 6318 petsc_uses = {KSP} 6319} 6320 6321@InProceedings{ silence, 6322 author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. 6323 Fuenmayor}, 6324 title = {A parallel computing approach for solving the Helmholtz equation in 3D domains: 6325 Application to the study of acoustic behaviour of silencers}, 6326 year = {2004}, 6327 booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering 6328 (ECCOMAS)}, 6329 petsc_uses = {KSP} 6330} 6331 6332@Article{ degersem99, 6333 author = {H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer}, 6334 title = {Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods 6335 to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations}, 6336 journal = {COMPEL}, 6337 year = {1999}, 6338 volume = {18}, 6339 number = {3}, 6340 pages = {298--310}, 6341 bibdate = {}, 6342 petsc_uses = {KSP} 6343} 6344 6345@InProceedings{ widlund-wave-98, 6346 author = {Olof B. Widlund}, 6347 title = {Schwarz Methods for {H}elmholtz's Equation}, 6348 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6349 editor = {John A. DeSanto}, 6350 year = {1998}, 6351 publisher = {SIAM}, 6352 pages = {620--622}, 6353 address = {Philadelphia}, 6354 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6355 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6356 petsc_uses = {KSP} 6357} 6358 6359@InProceedings{ toselli-wave-98, 6360 author = {Andrea Toselli}, 6361 title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media}, 6362 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6363 editor = {John A. DeSanto}, 6364 year = {1998}, 6365 publisher = {SIAM}, 6366 address = {Philadelphia}, 6367 pages = {540--542}, 6368 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6369 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6370 petsc_uses = {KSP} 6371} 6372 6373@InProceedings{ mcinnes-wave-98, 6374 author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes}, 6375 title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods}, 6376 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6377 editor = {John A. DeSanto}, 6378 year = {1998}, 6379 publisher = {SIAM}, 6380 address = {Philadelphia}, 6381 pages = {623--625}, 6382 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6383 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6384 petsc_uses = {KSP} 6385} 6386 6387@InProceedings{ mska98, 6388 author = {L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi}, 6389 title = {Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the 6390 Parallel Computation of {H}elmholtz Problems}, 6391 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6392 editor = {J. Mandel et al.}, 6393 publisher = {AMS}, 6394 pages = {349--357}, 6395 year = {1998}, 6396 petsc_uses = {KSP} 6397} 6398 6399@InProceedings{ ccew98, 6400 author = {X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund}, 6401 title = {Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation}, 6402 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6403 editor = {J. Mandel et al.}, 6404 publisher = {AMS}, 6405 pages = {437-445}, 6406 year = {1998}, 6407 petsc_uses = {KSP} 6408} 6409 6410@InProceedings{ ra98a, 6411 author = {R. Susan-Resiga and H. M. Atassi}, 6412 title = {Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic 6413 Problems}, 6414 booktitle = {Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference}, 6415 publisher = {AIAA}, 6416 pages = {86-96}, 6417 note = {AIAA paper 98-2218}, 6418 year = {1998}, 6419 petsc_uses = {KSP} 6420} 6421 6422@InProceedings{ ar98c, 6423 author = {H. M. Atassi and R. Susan-Resiga}, 6424 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: 6425 General Formulation}, 6426 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6427 publisher = {ASME}, 6428 note = {NCA-25}, 6429 pages = {375-379}, 6430 year = {1998}, 6431 petsc_uses = {KSP} 6432} 6433 6434@InProceedings{ ra98b, 6435 author = {R. Susan-Resiga and H. M. Atassi}, 6436 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: 6437 Numerical Implementation and Applications}, 6438 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6439 publisher = {ASME}, 6440 note = {NCA-25}, 6441 pages = {381 -388}, 6442 year = {1998}, 6443 petsc_uses = {KSP} 6444} 6445 6446@InProceedings{ cai-dd10-98, 6447 author = {Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. 6448 Widlund}, 6449 title = {Overlapping {S}chwarz methods for solving {H}elmholtz's Equation}, 6450 booktitle = {Domain Decomposition Methods 10}, 6451 editors = {Jan Mandel and Charbel Farhat and Xiao-Chuan Cai}, 6452 series = {Contemporary Mathematics}, 6453 volume = {218}, 6454 publisher = {American Mathematical Society}, 6455 address = {Providence, Rhode Island}, 6456 year = {1998}, 6457 pages = {437--445}, 6458 petsc_uses = {KSP} 6459} 6460 6461@InProceedings{ alghamdi2011petclaw, 6462 title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython}, 6463 booktitle = {Proceedings of SpringSim 2011}, 6464 publisher = {ACM}, 6465 author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and 6466 Kyle T. Mandli and Lisandro Dalcin}, 6467 year = {2011}, 6468 petsc_uses = {KSP} 6469} 6470 6471@Article{ pyclaw2012, 6472 author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and 6473 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 6474 Emmett}, 6475 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 6476 journal = {SIAM Journal on Scientific Computing}, 6477 volume = {34}, 6478 number = {4}, 6479 pages = {C210--C231}, 6480 note = {\url{http://arxiv.org/abs/1111.6583}}, 6481 year = {2012}, 6482 petsc_uses = {KSP} 6483} 6484 6485% LiteralHTML: 6486% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 6487% LiteralHTML: 6488@Article{ sojkahorakhaplacermak2018, 6489 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 6490 decomposition method}, 6491 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 6492 journal = {Applied Mathematics and Computation}, 6493 volume = {319}, 6494 pages = {586--597}, 6495 year = {2018}, 6496 petsc_uses = {KSP} 6497} 6498 6499@Article{ chencai2014, 6500 title = {A parallel two-level domain decomposition based one-shot method for shape 6501 optimization problems}, 6502 author = {Rongliang Chen and Xiao‐Chuan Cai}, 6503 journal = {International Journal for Numerical Methods in Engineering}, 6504 volume = {99}, 6505 number = {13}, 6506 year = {2014}, 6507 doi = {10.1002/nme.4711}, 6508 petsc_uses = {KSP} 6509} 6510 6511@PhDThesis{ prudencio2005, 6512 author = {Ernesto Prudencio}, 6513 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 6514 for Optimization Problems Constrained by Partial Differential Equations}, 6515 school = {University of Colorado, Boulder}, 6516 year = {2005}, 6517 petsc_uses = {KSP} 6518} 6519 6520@Article{ prudenciocai2007, 6521 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 6522 for {PDE}-constrained optimization}, 6523 author = {Ernesto Prudencio and X. C. Cai}, 6524 journal = {SIAM J. Sci. Comp.}, 6525 volume = {29}, 6526 number = {3}, 6527 pages = {964--985}, 6528 year = {2007}, 6529 petsc_uses = {KSP} 6530} 6531 6532@Article{ prudenciobyrdcai2006, 6533 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6534 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 6535 {PDE}-constrained Optimization Problems}, 6536 journal = {SIAM J. Sci. Comp.}, 6537 volume = {27}, 6538 pages = {1305--1328}, 6539 year = {2006}, 6540 petsc_uses = {KSP} 6541} 6542 6543@InProceedings{ prudenciobyrdcai2004, 6544 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 6545 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6546 booktitle = {VECPAR 2004}, 6547 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 6548 publisher = {Springer}, 6549 pages = {569--582}, 6550 year = {2004}, 6551 petsc_uses = {KSP} 6552} 6553 6554@Article{ belhamadia-fortin-pcp, 6555 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 6556 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 6557 journal = {Journal of Computational Physics}, 6558 volume = {201}, 6559 pages = {753-770}, 6560 year = {2004}, 6561 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 6562 petsc_uses = {KSP} 6563} 6564 6565@Article{ biros00, 6566 author = {George Biros and Omar Ghattas}, 6567 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 6568 journal = {SIAG-Opt Views and News}, 6569 volume = {11}, 6570 number = {2}, 6571 year = {2000}, 6572 month = aug, 6573 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 6574 petsc_uses = {KSP} 6575} 6576 6577@Article{ bmm01, 6578 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 6579 journal = {ACM Transactions on Mathematical Software}, 6580 title = {A case study in the performance and scalability of optimization algorithms}, 6581 year = {2001}, 6582 volume = {27}, 6583 number = {3}, 6584 pages = {361--376}, 6585 petsc_uses = {KSP} 6586} 6587 6588@InProceedings{ oghattas1999, 6589 author = {George Biros and Omar Ghattas}, 6590 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 6591 incompressible flows}, 6592 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 6593 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 6594 year = {1999}, 6595 petsc_uses = {KSP} 6596} 6597 6598@InProceedings{ hkms00, 6599 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 6600 PDE-constrained Optimization}, 6601 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 6602 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 6603 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 6604 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 6605 Hasco\"{e}t and Uwe Naumann}, 6606 publisher = {Springer}, 6607 year = {2002}, 6608 petsc_uses = {KSP} 6609} 6610 6611% old version: replace with biros2005pln1 6612@TechReport{ bg011, 6613 author = {George Biros and Omar Ghattas}, 6614 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 6615 Part I: The Krylov-Schur Solver}, 6616 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6617 year = {2001}, 6618 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 6619 petsc_uses = {KSP} 6620} 6621 6622% old version: replace with biros2005pln2 6623@TechReport{ bg012, 6624 author = {George Biros and Omar Ghattas}, 6625 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 6626 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 6627 Optimal Control of Steady Viscous Flows}, 6628 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6629 year = {2001}, 6630 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 6631 petsc_uses = {KSP} 6632} 6633 6634% LiteralHTML: 6635% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 6636% LiteralHTML: 6637@InProceedings{ ly2003, 6638 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 6639 title = {A New Parallel Kernel-independent Fast Multipole Method}, 6640 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 6641 year = {2003}, 6642 note = {Winner of the Best Student Paper at SC2003}, 6643 petsc_uses = {KSP} 6644} 6645 6646@Article{ yokotabarbaknepley10, 6647 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 6648 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 6649 journal = {Computer Methods in Applied Mechanics and Engineering}, 6650 volume = {199}, 6651 number = {25-28}, 6652 pages = {1793--1804}, 6653 url = {http://arxiv.org/abs/0909.5413v1}, 6654 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 6655 year = {2010}, 6656 petsc_uses = {KSP} 6657} 6658 6659@Article{ cruzknepleybarba10, 6660 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 6661 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 6662 journal = {International Journal of Numerical Methods in Engineering}, 6663 volume = {85}, 6664 number = {4}, 6665 pages = {403--428}, 6666 url = {http://arxiv.org/abs/0905.2637}, 6667 note = {\url{http://arxiv.org/abs/0905.2637}}, 6668 year = {2010}, 6669 petsc_uses = {KSP} 6670} 6671 6672% LiteralHTML: 6673% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 6674% LiteralHTML: 6675@Article{ buchanpainumplebysmedleystevenson2012, 6676 title = {A sub-grid scale finite element agglomeration multigrid method with application 6677 to the Boltzmann transport equation}, 6678 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 6679 journal = {International Journal for Numerical Methods in Engineering}, 6680 volume = {92}, 6681 number = {3}, 6682 pages = {318--342}, 6683 year = {2012}, 6684 publisher = {Wiley Online Library}, 6685 petsc_uses = {KSP} 6686} 6687 6688@Article{ magoulesahamedsuzuki2015, 6689 title = {Green computing on graphics processing units}, 6690 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 6691 journal = {Concurrency and Computation: Practice and Experience}, 6692 year = {2015}, 6693 publisher = {Wiley Online Library}, 6694 petsc_uses = {KSP} 6695} 6696 6697@InProceedings{ yanrhodes11, 6698 author = {Yan, Baoqiang and Rhodes, Philip J.}, 6699 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 6700 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 6701 series = {ICPP '11}, 6702 pages = {355--364}, 6703 year = {2011}, 6704 isbn = {978-0-7695-4510-3}, 6705 numpages = {10}, 6706 doi = {10.1109/ICPP.2011.70}, 6707 acmid = {2066965}, 6708 publisher = {IEEE Computer Society}, 6709 address = {Washington, DC, USA}, 6710 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 6711 petsc_uses = {KSP} 6712} 6713 6714@Article{ hakansson2013mdstochasticliouville, 6715 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 6716 Stulz, Eugen}, 6717 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 6718 equation study}, 6719 journal = {Phys. Chem. Chem. Phys.}, 6720 year = {2013}, 6721 volume = {15}, 6722 issue = {26}, 6723 pages = {10930-10941}, 6724 publisher = {The Royal Society of Chemistry}, 6725 doi = {10.1039/C3CP50788B}, 6726 petsc_uses = {KSP} 6727} 6728 6729@Article{ hakansson2011stochasticliouville, 6730 author = {Hakansson, Par and Nair, Prasanth B.}, 6731 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 6732 form}, 6733 journal = {Phys. Chem. Chem. Phys.}, 6734 year = {2011}, 6735 volume = {13}, 6736 issue = {20}, 6737 pages = {9578-9589}, 6738 publisher = {The Royal Society of Chemistry}, 6739 doi = {10.1039/C1CP20400A}, 6740 petsc_uses = {KSP} 6741} 6742 6743@InProceedings{ wang:lee:scidac2011, 6744 author = {Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman 6745 McInnes and Todd Munson and Barry Smith}, 6746 title = {A Differential Variational Inequality Approach for the Simulation of 6747 Heterogeneous Materials}, 6748 booktitle = {Proceedings of SciDAC 2011 Conference}, 6749 year = {2011}, 6750 petsc_uses = {KSP} 6751} 6752 6753@Article{ bourdinlarsenrichardson2011, 6754 author = {Blaise Bourdin and Christopher Larsen and Casey Richardson}, 6755 title = {A time-discrete model for dynamic fracture based on crack regularization}, 6756 journal = {International Journal of Fracture}, 6757 volume = {168}, 6758 issue = {2}, 6759 pages = {133--143}, 6760 doi = {10.1007/s10704-010-9562-x}, 6761 year = {2011}, 6762 petsc_uses = {KSP} 6763} 6764 6765@Article{ bourdinfrancfortmarigo2008, 6766 author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo}, 6767 title = {The Variational Approach to Fracture}, 6768 journal = {J. Elasticity}, 6769 volume = {91}, 6770 issue = {1}, 6771 pages = {1--148}, 6772 doi = {10.1007/s10659-007-9107-3}, 6773 year = {2008}, 6774 petsc_uses = {KSP} 6775} 6776 6777@Article{ lahtinen2008spectrum, 6778 title = {Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model}, 6779 author = {Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, 6780 J.K.}, 6781 journal = {Annals of Physics}, 6782 volume = {323}, 6783 number = {9}, 6784 pages = {2286--2310}, 6785 year = {2008}, 6786 publisher = {Elsevier}, 6787 petsc_uses = {KSP} 6788} 6789 6790@InProceedings{ roark2004discriminative, 6791 title = {Discriminative language modeling with conditional random fields and the 6792 perceptron algorithm}, 6793 author = {Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.}, 6794 booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational 6795 Linguistics}, 6796 pages = {47}, 6797 year = {2004}, 6798 organization = {Association for Computational Linguistics}, 6799 petsc_uses = {KSP} 6800} 6801 6802@Article{ roark2007discriminative, 6803 title = {Discriminative n-gram language modeling}, 6804 author = {Roark, B. and Saraclar, M. and Collins, M.}, 6805 journal = {Computer Speech \& Language}, 6806 volume = {21}, 6807 number = {2}, 6808 pages = {373--392}, 6809 year = {2007}, 6810 publisher = {Elsevier}, 6811 petsc_uses = {KSP} 6812} 6813 6814@Conference{ garcia2011parallel, 6815 title = {{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D 6816 nanodevice simulators}}, 6817 author = {Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and 6818 Aldegunde, M.}, 6819 booktitle = {Electron Devices (CDE), 2011 Spanish Conference on}, 6820 pages = {1--4}, 6821 organization = {IEEE}, 6822 petsc_uses = {KSP} 6823} 6824 6825@Conference{ wesley2006parallel, 6826 title = {{A parallel artificial neural network implementation}}, 6827 author = {Wesley-Smith, I.}, 6828 booktitle = {Proceedings of The National Conference On Undergraduate Research (NCUR)}, 6829 year = {2006}, 6830 petsc_uses = {KSP} 6831} 6832 6833@Article{ hcsw1, 6834 author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu}, 6835 title = {Parallel {N}ewton--{K}rylov--{S}chwarz algorithms for the three-dimensional 6836 {P}oisson--{B}oltzmann equation in numerical simulation of colloidal particle 6837 interactions}, 6838 journal = {Computer Physics Communications}, 6839 volumne = {181}, 6840 year = {2010}, 6841 pages = {1529--1537}, 6842 petsc_uses = {KSP} 6843} 6844 6845@Article{ hh1, 6846 author = {C.-Y. Huang and F.-N. Hwang}, 6847 title = {Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for 6848 bifurcation analysis of incompressible sudden expansion flows}, 6849 journal = {Applied Numerical Mathematics}, 6850 volume = {60}, 6851 year = {2010}, 6852 pages = {738--751}, 6853 petsc_uses = {KSP} 6854} 6855 6856@Article{ hwhw1, 6857 author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. 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Cooke}, 7343 title = {Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three 7344 Dimensions}, 7345 year = {2004}, 7346 booktitle = {40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit}, 7347 url = {http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282}, 7348 petsc_uses = {KSP} 7349} 7350 7351@InProceedings{ allard-gouranton-ipts2002, 7352 author = {Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin}, 7353 title = {Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster}, 7354 year = {2002}, 7355 booktitle = {Immersive Projection Technology Symposium}, 7356 url = {http://www-id.imag.fr/\~{ }allardj/files/ipts2002.pdf}, 7357 petsc_uses = {KSP} 7358} 7359 7360@Article{ icc, 7361 author = {D Ioan and G Ciuprina and C Ciobotaru}, 7362 title = {Hybrid and concurrent algorithms for nonlinear magnetic field problems}, 7363 journal = {IEEE Transactions on Magnetics}, 7364 year = {2000}, 7365 url = {http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/20/19005/00877735.pdf}, 7366 petsc_uses = {KSP} 7367} 7368 7369@InProceedings{ hs1, 7370 author = {Brian J. Henz and Dale R. Shires}, 7371 title = {Development and Performance Analysis of a Parallel Finite Element Application 7372 Implemented in an Object-Oriented Programming Framework}, 7373 year = {2003}, 7374 booktitle = {PDPTA 2003}, 7375 pages = {1286-1292}, 7376 note = {Resin Transfer Modeling}, 7377 petsc_uses = {KSP} 7378} 7379 7380@TechReport{ b2000, 7381 author = {Rickard Bergstrom}, 7382 title = {Least-Squares Finite Element Methods for Electromagnetic Applications}, 7383 year = {2000}, 7384 institution = {Chalmers}, 7385 number = {2000-05}, 7386 url = {http://www.phi.chalmers.se/pub/preprints/ps/phiprint-2000-05.ps}, 7387 petsc_uses = {KSP} 7388} 7389 7390@Article{ fs2004, 7391 author = {Petri Fast and Michael J. Shelley}, 7392 title = {A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele 7393 Shaw Flow}, 7394 journal = {Journal of Computational Physics}, 7395 year = {2004}, 7396 volume = {195}, 7397 url = {http://www.math.nyu.edu/faculty/shelley/papers/FS2004.pdf}, 7398 pages = {117-142}, 7399 petsc_uses = {KSP} 7400} 7401 7402@MastersThesis{ wallach, 7403 author = {Hanna Wallach}, 7404 title = {Efficient Training of Conditional Random Fields}, 7405 school = {University of Edinburgh}, 7406 year = {2002}, 7407 url = {http://scholar.google.com/url?sa=U&q=http://www.hcrc.ed.ac.uk/\~{ 7408 }osborne/msc-projects/wallach.ps.gz}, 7409 petsc_uses = {KSP} 7410} 7411 7412@Article{ something, 7413 author = {T Rylander and A Bondeson}, 7414 title = {Stability of explicit-implicit hybrid time-stepping schemes for Maxwells 7415 equations}, 7416 journal = {Journal of Computational Physics}, 7417 year = {2002}, 7418 volume = {179}, 7419 pages = {426-438}, 7420 petsc_uses = {KSP} 7421} 7422 7423@TechReport{ uf1, 7424 author = {Uwe Fabricius}, 7425 title = {Comparison of two implementations of {AMG}-preconditioned {CG} considering an 7426 electrostatic problem}, 7427 year = {2004}, 7428 institution = {Friedrich Alexander Universitat Erlangen Nurnberg Germany}, 7429 url = {http://www10.informatik.uni-erlangen.de/de/Publications/TechnicalReports/TechRep04-1.pdf}, 7430 number = {04-1}, 7431 petsc_uses = {KSP} 7432} 7433 7434@InBook{ sg1, 7435 author = {Natalia Seoane and A.J.Garca-Loureiro}, 7436 chapter = {Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity 7437 Equation}, 7438 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=h0xlulyhugck3y2gnt2l&referrer=parent&backto=issue,79,112;journal,212,1787;linkingpublicationresults,1:105633,1}, 7439 title = {Lecture Notes in Computer Science}, 7440 publisher = {Springer-Verlag}, 7441 volume = {3037}, 7442 year = {2004}, 7443 petsc_uses = {KSP} 7444} 7445 7446@Article{ nikyilmazgivisheikhipope10, 7447 author = {M. B. Nik and S. L. Yilmaz and P. Givi and M. R. H. Sheikhi and S. B. Pope}, 7448 title = {Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function}, 7449 journal = {AIAA Journal}, 7450 volume = {48}, 7451 number = {7}, 7452 pages = {1513--1522}, 7453 year = {2010}, 7454 petsc_uses = {KSP} 7455} 7456 7457@Article{ nikyilmazsheikhigivi10, 7458 author = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi}, 7459 title = {Grid Resolution Effects on VSFMDF/LES}, 7460 journal = {Flow, Turbulence and Combustion}, 7461 doi = {10.1007/s10494-010-9272-5}, 7462 year = {2010}, 7463 petsc_uses = {KSP} 7464} 7465 7466@Article{ idema2013towards, 7467 title = {Towards faster solution of large power flow problems}, 7468 author = {Idema, Reijer and Papaefthymiou, Georgios and Lahaye, Domenico and Vuik, Cornelis 7469 and van der Sluis, Lou}, 7470 journal = {Power Systems, IEEE Transactions on}, 7471 volume = {28}, 7472 number = {4}, 7473 pages = {4918--4925}, 7474 year = {2013}, 7475 publisher = {IEEE}, 7476 petsc_uses = {KSP} 7477} 7478 7479@Article{ 6026245, 7480 author = {Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.}, 7481 journal = {Power Systems, IEEE Transactions on}, 7482 title = {Scalable Newton-Krylov Solver for Very Large Power Flow Problems}, 7483 year = {2012}, 7484 month = feb, 7485 volume = {27}, 7486 number = {1}, 7487 pages = {390-396}, 7488 doi = {10.1109/TPWRS.2011.2165860}, 7489 issn = {0885-8950}, 7490 petsc_uses = {KSP} 7491} 7492 7493@Book{ idema2014computational, 7494 title = {Computational Methods in Power System Analysis}, 7495 author = {Idema, Reijer and Lahaye, Domenico JP}, 7496 year = {2014}, 7497 publisher = {Springer}, 7498 petsc_uses = {KSP} 7499} 7500 7501@PhDThesis{ abhyankar2011thesis, 7502 author = {Shrirang Abhyankar}, 7503 title = {Development of an implicitly coupled electromechanical and electromagnetic 7504 transients simulator for power systems}, 7505 school = {Illinois Institute of Technology}, 7506 year = {2011}, 7507 petsc_uses = {KSP} 7508} 7509 7510@InProceedings{ abhyankarhipcna11-1, 7511 author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck}, 7512 title = {Using {PETSc} to develop scalable applications for next-generation power grid}, 7513 year = {2011}, 7514 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 7515 Networking and Analytics for the Power Grid}, 7516 url = {http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf}, 7517 publisher = {ACM}, 7518 petsc_uses = {KSP} 7519} 7520 7521@InProceedings{ abhyankarhipcna11-2, 7522 author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang}, 7523 title = {Development of a parallel three-phase transient stability simulator for power 7524 systems}, 7525 year = {2011}, 7526 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 7527 Networking and Analytics for the Power Grid}, 7528 publisher = {ACM}, 7529 petsc_uses = {KSP} 7530} 7531 7532@InProceedings{ abhyankarpesgeneral2012, 7533 author = {Shrirang Abhyankar and A. Flueck}, 7534 title = {An implicitly-coupled solution approach for combined electromechanical and 7535 electromagnetic transients simulation}, 7536 year = {2012}, 7537 booktitle = {Proceedings of the IEEE PES General Meeting}, 7538 publisher = {IEEE}, 7539 petsc_uses = {KSP} 7540} 7541 7542@Article{ idemalahayevuiksluis2012, 7543 author = {Reijer Idema and Domenico Lahaye and Cornelis Vuik and Lou van der Sluis}, 7544 title = {Scalable Newton-Krylov solver for very large Power Flow problems}, 7545 journal = {IEEE Transactions on Power Systems}, 7546 year = {2012}, 7547 volume = {27}, 7548 pages = {390-396}, 7549 petsc_uses = {KSP} 7550} 7551 7552@Article{ korrestzavellasgalinas2013, 7553 author = {George N. Korres and Anastasios Tzavellas and Evangelos Galinas}, 7554 title = {A distributed implementation of multi-area power system state estimation on a 7555 cluster of computers }, 7556 journal = {Electric Power Systems Research }, 7557 volume = {102}, 7558 number = {0}, 7559 pages = {20 - 32}, 7560 year = {2013}, 7561 issn = {0378-7796}, 7562 doi = {10.1016/j.epsr.2013.04.002}, 7563 petsc_uses = {KSP} 7564} 7565 7566% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7567% LiteralHTML:<font color="#FF0000"> 7568% LiteralHTML: Material failure, for example, cracking of steel beams resulting 7569% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 7570% LiteralHTML: are important for prediction and prevention. PETSc has been used 7571% LiteralHTML: in a variety of studies of material failure.</p> 7572% LiteralHTML:</font> 7573% LiteralHTML: 7574@InProceedings{ gray2, 7575 author = {Yuan He and Joshua Gray and Richard Braatz and Richard Alkire}, 7576 title = {Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel}, 7577 year = {2004}, 7578 booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}, 7579 petsc_uses = {KSP} 7580} 7581 7582@InProceedings{ gray1, 7583 author = {J. Gray and C. Homescu and L. Petzold and Richard Alkire}, 7584 title = {Algorithms and Computing Architectures for Solving Differential-Algebraic 7585 Equation Systems Typically Encountered in Models of Corrosion Pit Initiation}, 7586 year = {2003}, 7587 booktitle = {Abstracts of the Electrochemical Society 204th meeting}, 7588 petsc_uses = {KSP} 7589} 7590 7591@InProceedings{ crack2, 7592 author = {Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. Wawrzynek}, 7593 title = {A multiscale modeling approach to crack initiation in metallic polycrystals}, 7594 booktitle = {44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials 7595 Conference}, 7596 url = {http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=TRD&recid=A0325099AH}, 7597 year = {2003}, 7598 petsc_uses = {KSP} 7599} 7600 7601@TechReport{ hdams1, 7602 author = {Gerd Heber and Andrew J. Dolgert and Maxirn Alt and Karen A. Mazurkiewicz and 7603 Lynd Stringer}, 7604 title = {Fracture Mechanics on the Intel Itanium Architecture}, 7605 year = {2001}, 7606 institution = {Intel Corporation}, 7607 url = {http://cedar.intel.com/media/pdf/scs/cptconitanium.pdf}, 7608 petsc_uses = {KSP} 7609} 7610 7611@InProceedings{ ihwi, 7612 author = {E. Iesulauro and G. Heber and P. A. Wawrzynek and A. R. Ingraffea}, 7613 title = {Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation}, 7614 booktitle = {International Conference ON Computational Engineering and Sciences}, 7615 year = {2002}, 7616 url = {http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf}, 7617 petsc_uses = {KSP} 7618} 7619 7620@InProceedings{ crack, 7621 author = {Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and 7622 Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris 7623 Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis 7624 and Paul A. Wawrzynek}, 7625 title = {Parallel FEM Simulation of Crack Propagation}, 7626 booktitle = {Proceedings of Irregular 2000}, 7627 url = {http://www.cs.cornell.edu/stodghil/papers/irregular00.ps}, 7628 year = {2000}, 7629 petsc_uses = {KSP} 7630} 7631 7632@InProceedings{ beaudoin98, 7633 author = {A. J. Beaudoin}, 7634 title = {Use of Polycrystal Plasticity Theory in Assessing Material Performance}, 7635 booktitle = {Simulation of materials processing: Theory, methods, and applications - 7636 Proceedings of the Sixth International Conference, NUMIFORM'98}, 7637 editor = {J. Hu\'etink and F. P. T. Baaijens}, 7638 optvolume = {}, 7639 optnumber = {}, 7640 optseries = {}, 7641 year = {1998}, 7642 optorganization={}, 7643 publisher = {A. A. Balkema Publishers}, 7644 address = {Rotterdam, Netherlands}, 7645 month = jun, 7646 optpages = {}, 7647 petsc_uses = {KSP} 7648} 7649 7650% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7651@TechReport{ defordheld1, 7652 author = {JF DeFord and BL Held}, 7653 title = {RF3P-A New Parallel Driven Frequency Electromagnetic Solver}, 7654 year = {2002}, 7655 institution = {Simulation Technology and Applied Research}, 7656 url = {http://www.staarinc.com/support/papers/aces2002.pdf}, 7657 note = {Discusses their parallel commercial solver that uses PETSc}, 7658 petsc_uses = {KSP} 7659} 7660 7661@PhDThesis{ sande2003, 7662 author = {Hans Vande Sande}, 7663 title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic 7664 Quasi-Static Electromagnetic Systems}, 7665 school = {Katholieke Universiteit Leuven, Belgium}, 7666 year = {2003}, 7667 petsc_uses = {KSP} 7668} 7669 7670@Article{ sdchh2004, 7671 author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 7672 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 7673 Tolerance}, 7674 journal = {IEEE Transactions on Magnetics}, 7675 year = {2004}, 7676 volume = {40}, 7677 pages = {1306--1309}, 7678 petsc_uses = {KSP} 7679} 7680 7681@Article{ holst-lindblom-etal:2004, 7682 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 7683 Scheel and Lawrence E. Kidder}, 7684 title = {Optimal constraint projection for hyperbolic evolution systems, }, 7685 journal = {Phys. Rev. D}, 7686 year = {2004}, 7687 volume = {70}, 7688 pages = {084017}, 7689 petsc_uses = {KSP} 7690} 7691 7692@Article{ marm2005, 7693 author = {Matthew Anderson and Richard A. Matzner}, 7694 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 7695 journal = {Foundations of Physics}, 7696 volume = {35}, 7697 pages = {1572--9516}, 7698 year = {2005}, 7699 petsc_uses = {KSP} 7700} 7701 7702@Article{ cook-pfeiffer:2004, 7703 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 7704 title = {Excision boundary conditions for black hole initial data}, 7705 journal = {Phys. Rev. D}, 7706 volume = {70}, 7707 pages = {104016--24}, 7708 year = {2004}, 7709 petsc_uses = {KSP} 7710} 7711 7712@Article{ pfeiffer-kidder-etal:2005, 7713 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 7714 Shoemaker}, 7715 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 7716 journal = {Phys. Rev. D}, 7717 year = {2005}, 7718 volume = {71}, 7719 pages = {024020}, 7720 petsc_uses = {KSP} 7721} 7722 7723@Article{ pfeiffer-kidder-etal:2003, 7724 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 7725 Saul A.}, 7726 title = {A multidomain spectral method for solving elliptic equations}, 7727 journal = {CPC}, 7728 year = {2003}, 7729 volume = {152}, 7730 pages = {253--273}, 7731 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 7732 For a related online version, see arXiv:gr-qc/0202096}, 7733 petsc_uses = {KSP} 7734} 7735 7736@Article{ pfeiffer-cook-teukolsky:2002, 7737 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 7738 title = {Comparing initial-data sets for binary black hole}, 7739 journal = {PRD}, 7740 year = {2002}, 7741 volume = {66}, 7742 pages = {024047}, 7743 note = {for a related online version, seearXiv:gr-qc/0203085}, 7744 petsc_uses = {KSP} 7745} 7746 7747@PhDThesis{ pfeiffer:2003, 7748 author = {Pfeiffer, Harald P.}, 7749 title = {Initial Data for Black Hole Evolutions}, 7750 school = {Cornell University}, 7751 year = {2003}, 7752 petsc_uses = {KSP} 7753} 7754 7755@TechReport{ h1, 7756 author = {Erik Schnetter}, 7757 title = {A fast apparent horizon algorithm}, 7758 year = {2002}, 7759 number = {Arxiv preprint gr-qc/0206003}, 7760 url = {http://arxiv.org/pdf/gr-qc/0206003}, 7761 petsc_uses = {KSP} 7762} 7763 7764@Article{ h2, 7765 author = {Erik Schnetter}, 7766 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 7767 year = {2003}, 7768 journal = {Class. Quantum Grav.}, 7769 pages = {4719-4737}, 7770 volume = {20}, 7771 url = {http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf}, 7772 petsc_uses = {KSP} 7773} 7774 7775@Article{ adams-03a, 7776 author = {Adams, M.~F.}, 7777 journal = {Numerical Linear Algebra with Applications}, 7778 number = {2-3}, 7779 pages = {141-153}, 7780 title = {Algebraic multigrid methods for constrained linear systems with applications to 7781 contact problems in solid mechanics}, 7782 volume = {11}, 7783 year = {2004}, 7784 petsc_uses = {KSP} 7785} 7786 7787@Article{ vandesande1, 7788 author = {H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer}, 7789 journal = {IEEE TRANSACTIONS ON MAGNETICS}, 7790 year = {2003}, 7791 volume = {39}, 7792 pages = {1709--1712}, 7793 title = {Solving Nonlinear Magnetic Problems Using {N}ewton Trust Region Methods}, 7794 petsc_uses = {KSP} 7795} 7796 7797@InProceedings{ vbde1, 7798 author = {Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith}, 7799 year = {2002}, 7800 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 7801 Uintah PSE}, 7802 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 7803 2002}, 7804 pages = {49-55}, 7805 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 7806 note = {Extended abstract}, 7807 petsc_uses = {KSP} 7808} 7809 7810@Unpublished{ ep1, 7811 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 7812 author = {Bradley R. Eccleston and Todd S. Palmer}, 7813 institution = {Department of Nuclear Engineering, Oregon State University}, 7814 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 7815 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 7816 Parallel Simulations}, 7817 year = {1999}, 7818 petsc_uses = {KSP} 7819} 7820 7821@InProceedings{ teo2007scalable, 7822 title = {A scalable modular convex solver for regularized risk minimization}, 7823 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 7824 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 7825 discovery and data mining}, 7826 pages = {727--736}, 7827 year = {2007}, 7828 organization = {ACM}, 7829 petsc_uses = {KSP} 7830} 7831 7832@InProceedings{ rm02, 7833 author = {Robert Malouf}, 7834 year = {2002}, 7835 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 7836 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 7837 (CoNLL-2002)}, 7838 pages = {49-55}, 7839 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 7840 petsc_uses = {KSP} 7841} 7842 7843@Unpublished{ hrv02, 7844 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 7845 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7846 note = {Submitted to CMMSE}, 7847 petsc_uses = {KSP} 7848} 7849 7850@Article{ tmh2001, 7851 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 7852 journal = {Journal of Economic Dynamics and Control}, 7853 year = {2002}, 7854 volume = {26}, 7855 pages = {1499-1515}, 7856 title = {Solving finite difference schemes arising in trivariate option pricing}, 7857 petsc_uses = {KSP} 7858} 7859 7860@InProceedings{ a2, 7861 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 7862 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 7863 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 7864 Methods}, 7865 editor = {C.-H. Lai et al.}, 7866 publisher = {Domain Decomposition Press, Bergen}, 7867 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 7868 year = {1999}, 7869 petsc_uses = {KSP} 7870} 7871 7872@Unpublished{ mmmdcmaa-web-page, 7873 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 7874 {A}coustics {W}eb Page}, 7875 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 7876 author = {David E. Keyes}, 7877 institution = {Old Dominion University}, 7878 petsc_uses = {KSP} 7879} 7880 7881@Conference{ liu2010parallelization, 7882 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 7883 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 7884 booktitle = {International Symposium on Parallel and Distributed Processing with 7885 Applications}, 7886 pages = {528--535}, 7887 year = {2010}, 7888 organization = {IEEE}, 7889 petsc_uses = {KSP} 7890} 7891 7892@Unpublished{ oil-reservoir-sim-web-page, 7893 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 7894 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 7895 institution = {University of Texas at Austin and Argonne National Laboratory}, 7896 key = {University of Texas at Austin and Argonne National Laboratory}, 7897 petsc_uses = {KSP} 7898} 7899 7900@Article{ tmh2001b, 7901 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 7902 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 7903 year = {2001}, 7904 volume = {37}, 7905 pages = {143--146}, 7906 title = {Adapting EMAP3D to parallel processing}, 7907 petsc_uses = {KSP} 7908} 7909 7910@Article{ harbury98, 7911 author = {HK Harbury and W Porod}, 7912 journal = {VLSI Design}, 7913 year = {1998}, 7914 volume = {6}, 7915 pages = {47--51}, 7916 title = {Parallel computation for electronic waves in quantum corrals}, 7917 petsc_uses = {KSP} 7918} 7919 7920@Article{ bludszuwei98, 7921 author = {Mark Bludszuweit}, 7922 journal = {Journal of Lightwave Technology}, 7923 year = {1998}, 7924 volume = {16}, 7925 number = {7}, 7926 pages = {1336--42}, 7927 title = {Mixed Finite Element Beam Propagation Method}, 7928 petsc_uses = {KSP} 7929} 7930 7931@Article{ s1, 7932 author = {J. L. Friedman and N. Stergioulas}, 7933 journal = {Astrophysics Journal}, 7934 year = {1998}, 7935 volume = {492}, 7936 number = {301}, 7937 pages = {}, 7938 title = {}, 7939 petsc_uses = {KSP} 7940} 7941 7942@Article{ s1a, 7943 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 7944 journal = {Astrophysics Journal}, 7945 year = {1999}, 7946 volume = {510}, 7947 number = {854}, 7948 pages = {}, 7949 title = {}, 7950 petsc_uses = {KSP} 7951} 7952 7953@PhDThesis{ s2, 7954 author = {N. Stergioulas}, 7955 title = {Ph. D. thesis}, 7956 year = {1996}, 7957 institution = {University of Wisconsin-Milwaukee}, 7958 petsc_uses = {KSP} 7959} 7960 7961@InProceedings{ coral1, 7962 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7963 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 7964 Parallel Computing Environment}, 7965 booktitle = {Proceedings of the Miami TEAM Workshop}, 7966 location = {Florida International University, Department of Electrical Engineering and 7967 Computing Science}, 7968 month = nov, 7969 year = {1993}, 7970 petsc_uses = {KSP} 7971} 7972 7973@InProceedings{ coral2, 7974 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7975 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 7976 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 7977 month = dec, 7978 year = {1994}, 7979 petsc_uses = {KSP} 7980} 7981 7982@InProceedings{ coral3, 7983 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7984 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 7985 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 7986 location = {Florida International University, Department of Electrical Engineering and 7987 Computing Science}, 7988 year = {1995}, 7989 petsc_uses = {KSP} 7990} 7991 7992@InProceedings{ mijalkovic, 7993 author = {Slobodan Mijalkovi\'{c}}, 7994 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 7995 Process Simulation}, 7996 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 7997 Gent, Belgium, September 27--30, 1999.}, 7998 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 7999 optvolume = {14}, 8000 optseries = {Lecture Notes in Computational Science and Engineering}, 8001 year = {2000}, 8002 publisher = {Springer}, 8003 address = {Berlin}, 8004 optpages = {179--184}, 8005 petsc_uses = {KSP} 8006} 8007 8008@Article{ bludszuwei98a, 8009 author = {Mark Bludszuweit}, 8010 journal = {Journal of Lightwave Technology}, 8011 year = {1998}, 8012 volume = {16}, 8013 number = {7}, 8014 pages = {1336--42}, 8015 title = {Mixed Finite Element Beam Propagation Method}, 8016 petsc_uses = {KSP} 8017} 8018 8019@Article{ gilli-pauletto-1998, 8020 author = {Manfred Gilli and Giorgio Pauletto}, 8021 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 8022 journal = {Computational Economics}, 8023 year = {2000}, 8024 volume = {16}, 8025 pages = {173--186}, 8026 petsc_uses = {KSP} 8027} 8028 8029% LiteralHTML: 8030% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 8031% LiteralHTML: 8032@Article{ collierdalcincalo2013, 8033 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 8034 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 8035 journal = {arxiv}, 8036 year = {2013}, 8037 number = {1305.4452}, 8038 note = {\url{http://arxiv.org/abs/1305.4452}}, 8039 petsc_uses = {KSP} 8040} 8041 8042@Article{ collierdalcinvignalcortescalo2016, 8043 title = {PetIGA: A framework for high-performance isogeometric analysis}, 8044 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 8045 Victor M. Calo}, 8046 journal = {Computer Methods in Applied Mechanics and Engineering}, 8047 year = {2016}, 8048 petsc_uses = {KSP} 8049} 8050 8051@Misc{ petiga-web-page, 8052 author = {N. Collier and L. Dalcin and V.M. Calo}, 8053 title = {{PetIGA} {W}eb page}, 8054 url = {https://bitbucket.org/dalcinl/petiga/}, 8055 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 8056 year = {2014}, 8057 petsc_uses = {KSP} 8058} 8059 8060@Article{ logg07, 8061 author = {Logg, Anders}, 8062 title = {Automating the Finite Element Method}, 8063 journal = {Archives of Computational Methods in Engineering}, 8064 volume = {14}, 8065 number = {2}, 8066 pages = {93-138}, 8067 year = {2007}, 8068 doi = {10.1007/s11831-007-9003-9}, 8069 publisher = {Kluwer Academic Publishers}, 8070 issn = {1134-3060}, 8071 language = {English}, 8072 petsc_uses = {KSP} 8073} 8074 8075@Article{ jezequelcouturierdenis12, 8076 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 8077 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 8078 versus the PETSc library}, 8079 journal = {The Journal of Supercomputing}, 8080 volume = {59}, 8081 number = {3}, 8082 pages = {1517-1532}, 8083 year = {2012}, 8084 issn = {0920-8542}, 8085 doi = {10.1007/s11227-011-0563-y}, 8086 publisher = {Springer US}, 8087 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 8088 Sparse linear solver}, 8089 language = {English}, 8090 petsc_uses = {KSP} 8091} 8092 8093@Unpublished{ feap-web-page, 8094 title = {FEAP: A Finite Element Analysis Program}, 8095 url = {http://www.ce.berkeley.edu/projects/feap/}, 8096 author = {FEAP Team}, 8097 note = {Uses PETSc linear solvers - iterative and direct}, 8098 petsc_uses = {KSP} 8099} 8100 8101@Unpublished{ parpre-web-page, 8102 title = {{ParPre} {W}eb {P}age}, 8103 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 8104 institution = {University of Tennessee}, 8105 author = {Victor Eijkhout}, 8106 note = {This is no longer supported. A set of preconditioners built on PETSc}, 8107 petsc_uses = {KSP} 8108} 8109 8110@Unpublished{ pism, 8111 title = {{PISM}: a Parallel Ice Sheet Model}, 8112 author = {{PISM Team}}, 8113 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 8114 Sheet Model). The thickness, temperature, velocity and age of the ice are all 8115 simulated, as is the deformation of the earth underneath the ice. New techniques 8116 for fast ice dynamics, earth deformation, and verification have are included.}, 8117 note = {\url{http://www.pism-docs.org/}}, 8118 petsc_uses = {KSP} 8119} 8120 8121@Unpublished{ oofem, 8122 title = {OOFEM - an object oriented finite element package}, 8123 author = {Borek Patzak}, 8124 url = {http://www.oofem.org}, 8125 petsc_uses = {KSP} 8126} 8127 8128@Unpublished{ dks2openfvm, 8129 title = {OpenFVM - a finite volume based general purpose CFD solver}, 8130 author = {Open source development}, 8131 url = {http://openfvm.sourceforge.net/}, 8132 petsc_uses = {KSP} 8133} 8134 8135@Unpublished{ sundar-2008w, 8136 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 8137 octree meshes}, 8138 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8139 institution = {University of Pennsylvania}, 8140 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 8141 petsc_uses = {KSP} 8142} 8143 8144@Unpublished{ khatiwala07-software, 8145 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 8146 author = {Khatiwala, S.}, 8147 institution = {Columbia University}, 8148 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 8149 petsc_uses = {KSP} 8150} 8151 8152@InBook{ jiaolima99, 8153 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 8154 chapter = {{SIFFEA}:Scalable Integrated Framework for Finite Element Analysis}, 8155 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 8156 title = {Lecture Notes in Computer Science}, 8157 publisher = {Springer-Verlag}, 8158 volume = {1732}, 8159 year = {1999}, 8160 petsc_uses = {KSP} 8161} 8162 8163@Article{ crow1, 8164 author = {C. S. Crow IV}, 8165 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 8166 journal = {Hopkins Undergraduate Research Journal}, 8167 year = {2003}, 8168 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 8169 petsc_uses = {KSP} 8170} 8171 8172@Unpublished{ petsc-python, 8173 title = {PETSc for Python}, 8174 author = {L. Dalcin}, 8175 url = {https://petsc.org/main/petsc4py}, 8176 note = {Provides Python bindings for PETSc}, 8177} 8178 8179@Unpublished{ cfdship, 8180 title = {{CFDShip-Iowa}}, 8181 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 8182 institution = {University of Iowa}, 8183 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 8184 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 8185 structured grids, designed for ship applications}, 8186 petsc_uses = {KSP} 8187} 8188 8189@Unpublished{ bvw, 8190 title = {Multiflow}, 8191 author = {Berend van Wachem}, 8192 institution = {Mechanical Engineering - Chalmers University of Technology}, 8193 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 8194 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 8195 flows.}, 8196 petsc_uses = {KSP} 8197} 8198 8199@Unpublished{ dks2, 8200 title = {FENA - A Finite Element Model for the North Atlantic}, 8201 author = {Jens Schroeter}, 8202 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 8203 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 8204 petsc_uses = {KSP} 8205} 8206 8207@TechReport{ piwonski2010idea, 8208 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 8209 and Simulation in {3-D}}, 8210 author = {Piwonski, J. and Slawig, T.}, 8211 year = {2010}, 8212 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8213 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 8214 petsc_uses = {KSP} 8215} 8216 8217@Unpublished{ metos3d-web, 8218 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 8219 author = {Piwonski, J. and Slawig, T.}, 8220 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8221 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 8222 petsc_uses = {KSP} 8223} 8224 8225@Unpublished{ magpar, 8226 author = {W. Scholz}, 8227 title = {Magpar: Parallel Micromagnetics Code}, 8228 institution = {Vienna University of Technology}, 8229 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 8230 petsc_uses = {KSP} 8231} 8232 8233@Misc{ libmesh:sourceforge, 8234 author = {}, 8235 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 8236 equations on serial and parallel platforms}, 8237 note = {[Online]}, 8238 url = {http://libmesh.github.io}, 8239 petsc_uses = {KSP} 8240} 8241 8242@Misc{ moose-web-page, 8243 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 8244 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 8245 Gaston and John Peterson and Jason Miller}, 8246 institution = {Idaho National Laboratory}, 8247 howpublished = {\url{http://mooseframework.org}}, 8248 petsc_uses = {KSP} 8249} 8250 8251@Article{ gaston2009moose, 8252 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 8253 equations}, 8254 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 8255 journal = {Nuclear Engineering and Design}, 8256 volume = {239}, 8257 number = {10}, 8258 pages = {1768--1778}, 8259 year = {2009}, 8260 publisher = {Elsevier}, 8261 petsc_uses = {KSP} 8262} 8263 8264@Article{ tonks2012object, 8265 title = {An object-oriented finite element framework for multiphysics phase field 8266 simulations}, 8267 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 8268 journal = {Computational Materials Science}, 8269 volume = {51}, 8270 number = {1}, 8271 pages = {20--29}, 8272 year = {2012}, 8273 publisher = {Elsevier}, 8274 petsc_uses = {KSP} 8275} 8276 8277@Misc{ pylithmanual, 8278 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 8279 Strand and Charles Williams}, 8280 title = {{PyLith} User Manual Version 2.0.0}, 8281 year = {2014}, 8282 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 8283 petsc_uses = {KSP} 8284} 8285 8286@Misc{ pylith-web-page, 8287 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 8288 title = {{PyLith}}, 8289 year = {2012}, 8290 url = {http://geodynamics.org/resources/pylith/}, 8291 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 8292 petsc_uses = {KSP} 8293} 8294 8295@Misc{ galemanual, 8296 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 8297 title = {Gale User Manual Version 2.0.0}, 8298 year = {2011}, 8299 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 8300 petsc_uses = {KSP} 8301} 8302 8303@Unpublished{ underworld, 8304 author = {Louis Moresi}, 8305 title = {{UnderWorld}: A Geodynamics Modelling Code}, 8306 institution = {Monash University}, 8307 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 8308 petsc_uses = {KSP} 8309} 8310 8311@Article{ moresi2007computational, 8312 title = {Computational approaches to studying non-linear dynamics of the crust and 8313 mantle}, 8314 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 8315 M{\"u}hlhaus, H.B.}, 8316 journal = {Physics of the Earth and Planetary Interiors}, 8317 volume = {163}, 8318 number = {1-4}, 8319 pages = {69--82}, 8320 year = {2007}, 8321 publisher = {Elsevier}, 8322 petsc_uses = {KSP} 8323} 8324 8325@Article{ pitt2009chaste, 8326 title = {Chaste: a test-driven approach to software development for biological modelling}, 8327 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 8328 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 8329 and Walter, A. and others}, 8330 journal = {Computer Physics Communications}, 8331 volume = {180}, 8332 number = {12}, 8333 pages = {2452--2471}, 8334 year = {2009}, 8335 publisher = {Elsevier}, 8336 petsc_uses = {KSP} 8337} 8338 8339@Misc{ fenicsproject, 8340 title = {{The FEniCS project}}, 8341 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 8342 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 8343 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 8344 url = {http://fenicsproject.org}, 8345 year = {2011}, 8346 petsc_uses = {KSP} 8347} 8348 8349@Unpublished{ snark, 8350 title = {Snark: A suite of software for geoscientific applications and a philosophy of 8351 scientific software development}, 8352 institution = {Victorian Partnership for Advanced Computing}, 8353 url = {http://vpac.org/Snark}, 8354 petsc_uses = {KSP} 8355} 8356 8357@Misc{ imoose:sourceforge, 8358 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 8359 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 8360 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 8361 note = {[Online]}, 8362 url = {http://imoose.sourceforge.net}, 8363 petsc_uses = {KSP} 8364} 8365 8366@Unpublished{ fossi, 8367 author = {Stephan Frickenhaus}, 8368 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 8369 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 8370 codes}, 8371 institution = {AWI-Bremerhaven, Germanny}, 8372 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 8373 petsc_uses = {KSP} 8374} 8375 8376@Unpublished{ fun3dweb, 8377 author = {Dinesh Kaushik}, 8378 title = {PETSC-FUN3D Benchmark Page}, 8379 institution = {ODU/ANL}, 8380 url = {http://www.mcs.anl.gov/petsc-fun3d}, 8381 note = {CFD Benchmark of some solvers in PETSc}, 8382 petsc_uses = {KSP} 8383} 8384 8385@Unpublished{ scirun, 8386 author = {SCIRun Development Team}, 8387 title = {SCIRun}, 8388 institution = {University of Utah}, 8389 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 8390 note = {SCIRun now uses PETSc linear solvers}, 8391 petsc_uses = {KSP} 8392} 8393 8394@Misc{ prometheus, 8395 author = {Mark F. Adams}, 8396 title = {Prometheus - A scalable unstructured finite element solver}, 8397 institution = {Berkeley}, 8398 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 8399 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 8400 petsc_uses = {KSP} 8401} 8402 8403@Unpublished{ illuminator, 8404 author = {Adam C. Powell, IV}, 8405 title = {Illuminator Distributed Visualization Library}, 8406 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 8407 petsc_uses = {KSP} 8408} 8409 8410@Unpublished{ rheoplast, 8411 title = {RheoPlast Phase Field Multi-Physics Code}, 8412 author = {Adam Powell and David Dussault and Bo Zhou}, 8413 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 8414 petsc_uses = {KSP} 8415} 8416 8417@Misc{ tao-web-page, 8418 title = {{Toolkit for Advanced Optimization ({TAO})} {W}eb Page}, 8419 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8420 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 8421 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8422 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 8423 petsc_uses = {KSP} 8424} 8425 8426@TechReport{ tao-user-ref, 8427 title = {{Toolkit for Advanced Optimization ({TAO}) users manual}}, 8428 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8429 and Steve Benson and Lois Curfman McInnes}, 8430 institution = {Argonne National Laboratory}, 8431 year = {2019}, 8432 number = {ANL/MCS-TM-322 - Rev 3.12}, 8433 petsc_uses = {KSP} 8434} 8435 8436% url = "http://www.mcs.anl.gov/tao", 8437@Unpublished{ mefpp-web-page, 8438 title = {{MEF++} {W}eb {P}age}, 8439 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 8440 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 8441 author = {Eric Chamberland}, 8442 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 8443 multiphysics}, 8444 petsc_uses = {KSP} 8445} 8446 8447@Unpublished{ tipetsc-titanium, 8448 title = {Ti-PETSc - an interface to PETSc from Titanium}, 8449 institution = {Berkeley}, 8450 author = {He, Yun and Liblit, Bun and Lin, Chang}, 8451 url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=9f7959be13337c735d52e5c0b0994bdea6d75a96}, 8452 year = {1999}, 8453 petsc_uses = {KSP}, 8454} 8455 8456@Unpublished{ ptatin-web-page, 8457 title = {ptatin3d}, 8458 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 8459 url = {https://bitbucket.org/jedbrown/ptatin3d}, 8460 year = {2018}, 8461 petsc_uses = {KSP} 8462} 8463 8464@Misc{ multiphase-web-page, 8465 author = {Q. Zou}, 8466 title = {Multiphase flow with {PETSc}}, 8467 institution = {LANL}, 8468 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 8469 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 8470 lab = {LANL}, 8471 petsc_uses = {KSP} 8472} 8473 8474@Misc{ electromag-web-page, 8475 title = {{EMSolve Web} page}, 8476 institution = {LLNL}, 8477 howpublished = {http://www.llnl.gov/casc/emsolve}, 8478 url = {http://www.Llnl.gov/casc/emsolve}, 8479 author = {Daniel {White et al.}}, 8480 lab = {LLNL}, 8481 petsc_uses = {KSP} 8482} 8483 8484@Unpublished{ fe-software-web-page, 8485 institution = {Kuleuven}, 8486 title = {Finite element software}, 8487 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 8488 petsc_uses = {KSP} 8489} 8490 8491@Misc{ petsc-web-page, 8492 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8493 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 8494 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8495 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8496 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 8497 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 8498 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 8499 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 8500 Zhang}, 8501 title = {{PETS}c {W}eb page}, 8502 url = {https://petsc.org/}, 8503 howpublished = {\url{https://petsc.org/}}, 8504 year = {2024} 8505} 8506 8507@Unpublished{ petsc-debian-package, 8508 author = {Adam C. Powell, IV}, 8509 title = {Debian package for PETSc}, 8510 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 8511 petsc_uses = {KSP} 8512} 8513 8514@Unpublished{ cactus, 8515 title = {Cactus Website}, 8516 url = {http://www.cactuscode.org/}, 8517 note = {Provides two interface to the PETSc solvers}, 8518 petsc_uses = {KSP} 8519} 8520 8521@Unpublished{ petsc-fem, 8522 author = {Mario Storti and Norberto Nigro}, 8523 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 8524 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 8525 url = {http://www.cimec.org.ar/petscfem}, 8526 petsc_uses = {KSP} 8527} 8528 8529@Misc{ fidap, 8530 title = {FIDAP 8.5}, 8531 howpublished = {\url{http://www.fluent.com}}, 8532 url = {http://www.fluent.com}, 8533 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 8534 solves.}, 8535 key = {FIDAP 8.5}, 8536 petsc_uses = {KSP} 8537} 8538 8539@Unpublished{ slepc, 8540 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8541 Vicente Hern\'andez and Vicent Vidal}, 8542 title = {{SLEPc} Website}, 8543 url = {http://slepc.upv.es/}, 8544 note = {Scalable Library for Eigenvalue Problem Computations}, 8545 petsc_uses = {KSP} 8546} 8547 8548@TechReport{ slepc-users-manual, 8549 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8550 Vicente Hern\'andez and Vicent Vidal}, 8551 title = {{SLEPc} Users Manual}, 8552 number = {DISC-II/24/02}, 8553 url = {http://slepc.upv.es/}, 8554 note = {Scalable Library for Eigenvalue Problem Computations}, 8555 petsc_uses = {KSP} 8556} 8557 8558@Misc{ deal.ii, 8559 title = {deal.II}, 8560 howpublished = {\url{http://www.dealii.org}}, 8561 url = {http://www.dealii.org}, 8562 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 8563 It allows PETSc linear algebra and solvers to be used underneath.}, 8564 key = {deal.II 5.0}, 8565 petsc_uses = {KSP} 8566} 8567 8568@Article{ bangerth2007deal, 8569 title = {{deal.II---A general-purpose object-oriented finite element library}}, 8570 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 8571 journal = {ACM Transactions on Mathematical Software (TOMS)}, 8572 volume = {33}, 8573 number = {4}, 8574 pages = {24--es}, 8575 issn = {0098-3500}, 8576 year = {2007}, 8577 publisher = {ACM}, 8578 petsc_uses = {KSP} 8579} 8580 8581@Misc{ globalarrays, 8582 author = {Jarek {Nieplocha et al.}}, 8583 title = {Global Arrays}, 8584 institution = {Pacific Northwest National Laboratories}, 8585 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 8586 url = {http://www.emsl.pnl.gov/docs/global}, 8587 note = {Global arrays can use PETSc linear solvers}, 8588 lab = {PNNL}, 8589 petsc_uses = {KSP} 8590} 8591 8592% LiteralHTML: 8593% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 8594% LiteralHTML: 8595@Article{ petsccommunity2022, 8596 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 8597 Community}, 8598 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 8599 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 8600 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 8601 and Hong Zhang and Junchao Zhang}, 8602 journal = {Computing in Science and Engineering}, 8603 volume = {24}, 8604 number = {03}, 8605 pages = {6--15}, 8606 issn = {1558-366X}, 8607 doi = {10.1109/MCSE.2022.3169974}, 8608 publisher = {IEEE Computer Society}, 8609 address = {Los Alamitos, CA, USA}, 8610 month = may, 8611 year = {2022}, 8612 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 8613 petsc_uses = {KSP} 8614} 8615 8616@Article{ brownknepleysmith14, 8617 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 8618 title = {Run-time extensibility and librarization of simulation software}, 8619 journal = {IEEE Computing in Science and Engineering}, 8620 month = jan, 8621 volume = {17}, 8622 number = {1}, 8623 pages = {38--45}, 8624 doi = {10.1109/MCSE.2014.95}, 8625 year = {2015}, 8626 petsc_uses = {KSP} 8627} 8628 8629@TechReport{ ass2012, 8630 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 8631 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 8632 institution = {Argonne National Laboratory}, 8633 type = {Preprint}, 8634 year = {2012}, 8635 number = {ANL/MCS-P2011-0112}, 8636 petsc_uses = {KSP} 8637} 8638 8639@TechReport{ clearyknepley99, 8640 author = {Andrew Cleary and Matthew G. Knepley}, 8641 title = {Solvers as Operators}, 8642 institution = {Lawrence Livermore National Laboratory}, 8643 type = {Technical Report}, 8644 number = {UCRL-ID-135342}, 8645 year = {1999}, 8646 petsc_uses = {KSP} 8647} 8648 8649@TechReport{ smcabbkz2012, 8650 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 8651 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 8652 title = {{PETSc's} software strategy for the design space of composable extreme-scale 8653 solvers}, 8654 institution = {Argonne National Laboratory}, 8655 type = {Preprint}, 8656 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 8657 year = {2012}, 8658 number = {ANL/MCS-P2059-0312}, 8659 petsc_uses = {KSP} 8660} 8661 8662@InProceedings{ mhwpmhs2009, 8663 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 8664 and G. E. Hammond and B. Smith}, 8665 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 8666 Toolkit {MPI} at Scale}, 8667 booktitle = {Cray Users Group Conference}, 8668 year = {2009}, 8669 petsc_uses = {KSP} 8670} 8671 8672@InProceedings{ msmhls2010, 8673 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 8674 Lichtner and B. F. Smith}, 8675 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 8676 {BlueGene} Architectures}, 8677 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 8678 year = {2010}, 8679 petsc_uses = {KSP} 8680} 8681 8682@InCollection{ msk2013, 8683 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 8684 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 8685 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8686 series = {Lecture Notes in Earth System Sciences}, 8687 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8688 Yaolin Shi}, 8689 doi = {10.1007/978-3-642-16405-7_7}, 8690 publisher = {Springer Berlin Heidelberg}, 8691 pages = {131--140}, 8692 year = {2013}, 8693 isbn = {978-3-642-16404-0}, 8694 petsc_uses = {KSP} 8695} 8696 8697@InCollection{ knepleyyuen13, 8698 author = {Matthew G. Knepley and David A. Yuen}, 8699 title = {Why Scientists and Engineers need {GPU}s today}, 8700 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8701 series = {Lecture Notes in Earth System Sciences}, 8702 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8703 Yaolin Shi}, 8704 doi = {10.1007/978-3-642-16405-7_1}, 8705 publisher = {Springer Berlin Heidelberg}, 8706 pages = {131--140}, 8707 year = {2013}, 8708 isbn = {978-3-642-16404-0}, 8709 petsc_uses = {KSP} 8710} 8711 8712@InCollection{ karpeevknepleybrune13, 8713 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 8714 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 8715 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8716 series = {Lecture Notes in Earth System Sciences}, 8717 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8718 Yaolin Shi}, 8719 doi = {10.1007/978-3-642-16405-7_30}, 8720 publisher = {Springer Berlin Heidelberg}, 8721 pages = {487--501}, 8722 year = {2013}, 8723 isbn = {978-3-642-16404-0}, 8724 petsc_uses = {KSP} 8725} 8726 8727@InCollection{ zhengetal13, 8728 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 8729 Variable Viscosity}, 8730 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8731 Zhang and Yaolin Shi}, 8732 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8733 series = {Lecture Notes in Earth System Sciences}, 8734 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8735 Yaolin Shi}, 8736 doi = {10.1007/978-3-642-16405-7_21}, 8737 publisher = {Springer Berlin Heidelberg}, 8738 pages = {321--333}, 8739 year = {2013}, 8740 isbn = {978-3-642-16404-0}, 8741 petsc_uses = {KSP} 8742} 8743 8744@Article{ zhengetal13b, 8745 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 8746 strongly variable viscosity based on {M}atlab and {CUDA}}, 8747 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8748 Zhang and Yaolin Shi}, 8749 journal = {IJHPCA}, 8750 volume = {28}, 8751 number = {1}, 8752 pages = {50--60}, 8753 doi = {10.1177/1094342013478640}, 8754 year = {2013}, 8755 petsc_uses = {KSP} 8756} 8757 8758@InBook{ s2011, 8759 author = {B. Smith}, 8760 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 8761 title = {Encyclopedia of Parallel Computing}, 8762 bookeditor = {D. Padua}, 8763 publisher = {Springer}, 8764 year = {2011}, 8765 petsc_uses = {KSP} 8766} 8767 8768@Article{ acostamejia06, 8769 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 8770 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 8771 journal = {Lecturas Matem\'aticas}, 8772 volume = {27}, 8773 year = {2006}, 8774 pages = {213--224}, 8775 petsc_uses = {KSP} 8776} 8777 8778@InProceedings{ quenettemoresisunterappelbe07, 8779 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 8780 title = {Explaining StGermain: An aspect oriented environment for building extensible 8781 computational mechanics modeling software}, 8782 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 8783 publisher = {IEEE}, 8784 pages = {1--8}, 8785 yerar = {2007}, 8786 petsc_uses = {KSP} 8787} 8788 8789@Article{ dfm1, 8790 title = {Vectorized sparse matrix multiply for compressed row storage format}, 8791 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 8792 journal = {Lecture Notes in Computer Science}, 8793 year = {2005}, 8794 pages = {99--106}, 8795 volume = {3514}, 8796 lab = {ORNL}, 8797 petsc_uses = {KSP} 8798} 8799 8800@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 8801 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 8802 Vandewalle and Stefaan Poedts}, 8803 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 8804 Scientific Computing Software}, 8805 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 8806 year = {2005}, 8807 note = {Lecture Notes in Computer Science}, 8808 volume = {3514}, 8809 publisher = {Springer-Verlag GmbH}, 8810 petsc_uses = {KSP} 8811} 8812 8813@InProceedings{ dalcin-paz-storti, 8814 author = {L. Dalcin and R. Paz and M. Storti}, 8815 title = {Desarrollo de Aplicaciones Paralelas en Python}, 8816 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 8817 Bariloche, Argentina}, 8818 year = {2004}, 8819 petsc_uses = {KSP} 8820} 8821 8822@Article{ mpi-python, 8823 author = {L. Dalcin and R. Paz and M. Storti}, 8824 title = {MPI for Python}, 8825 journal = {Journal of Parallel and Distributed Computing}, 8826 year = {2005}, 8827 petsc_uses = {KSP} 8828} 8829 8830@Unpublished{ hrv02a, 8831 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 8832 author = {V. Hernandex and J. E. Roman and V. Vidal}, 8833 note = {Submited to VecPar 2002}, 8834 year = {2002}, 8835 petsc_uses = {KSP} 8836} 8837 8838@Article{ knyazev2007block, 8839 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 8840 {PETSc}}, 8841 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 8842 journal = {SIAM Journal on Scientific Computing}, 8843 volume = {29}, 8844 pages = {2224-2239}, 8845 doi = {10.1137/060661624}, 8846 year = {2007}, 8847 petsc_uses = {KSP} 8848} 8849 8850@MastersThesis{ aarrestad-master, 8851 author = {Asbjorn Hoiland Aarrestad}, 8852 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 8853 school = {University of Bergen}, 8854 month = aug, 8855 year = {2003}, 8856 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 8857 note = {Implemented Runge-Kutta methods using PETSc}, 8858 petsc_uses = {KSP} 8859} 8860 8861@PhDThesis{ kaushik-phd, 8862 author = {D. K. Kaushik}, 8863 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 8864 Differential Equations on Unstructured Grids}, 8865 school = {Old Dominion University}, 8866 month = dec, 8867 year = {2002}, 8868 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 8869 petsc_uses = {KSP} 8870} 8871 8872@TechReport{ rb1, 8873 author = {Rickard Bergstrom}, 8874 title = {Object Oriented Implementation of a General Finite Element Code}, 8875 number = {2002-13}, 8876 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 8877 year = {2002}, 8878 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 8879 note = {Discribes a finite element software package that uses PETSc for its solvers}, 8880 petsc_uses = {KSP} 8881} 8882 8883@InProceedings{ dbl1, 8884 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 8885 title = {A Parallel General Purpose Finite Element System}, 8886 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 8887 publisher = {SIAM}, 8888 year = {1999}, 8889 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 8890 note = {Describes software that uses PETSc for its parallel linear solves}, 8891 petsc_uses = {KSP} 8892} 8893 8894@Article{ p1, 8895 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 8896 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 8897 and B. Smith}, 8898 journal = {Parallel Computing}, 8899 year = {2002}, 8900 pages = {1811--1831}, 8901 volume = {28 (12)}, 8902 petsc_uses = {KSP} 8903} 8904 8905@Article{ automatic-ad, 8906 author = {Paul Hovland and Boyana Norris and Barry Smith}, 8907 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 8908 year = {2005}, 8909 journal = {Future Generation Computer Systems}, 8910 volume = {21}, 8911 number = {8}, 8912 pages = {1426--1438}, 8913 petsc_uses = {KSP} 8914} 8915 8916@TechReport{ remote-math, 8917 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 8918 Smith}, 8919 title = {Remote Access to Mathematical Software}, 8920 number = {ANL/MCS-P889-0601}, 8921 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8922 month = jun, 8923 year = {2001}, 8924 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 8925 petsc_uses = {KSP} 8926} 8927 8928@InProceedings{ gropp98, 8929 author = {William D. Gropp}, 8930 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 8931 publisher = {SIAM}, 8932 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8933 Scientific and Engineering Computing}, 8934 year = {1999}, 8935 pages = {21-29}, 8936 petsc_uses = {KSP} 8937} 8938 8939@InProceedings{ knepleysarin99, 8940 author = {Matthew Knepley and Vivek Sarin}, 8941 title = {Algorithm Development for Large Scale Computing}, 8942 publisher = {SIAM}, 8943 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8944 Scientific and Engineering Computing}, 8945 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}}, 8946 year = {1999}, 8947 petsc_uses = {KSP} 8948} 8949 8950@InBook{ bgms00, 8951 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8952 chapter = {Software for the Scalable Solution of {PDEs}}, 8953 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 8954 title = {CRPC Handbook of Parallel Computing}, 8955 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 8956 and A. White}, 8957 publisher = {Morgan Kaufmann Publishers}, 8958 year = {2002}, 8959 petsc_uses = {KSP} 8960} 8961 8962@InProceedings{ hovland_norris_smith98, 8963 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 8964 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 8965 Computations}, 8966 publisher = {SIAM}, 8967 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8968 Scientific and Engineering Computing}, 8969 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 8970 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 8971 year = {1999}, 8972 pages = {129-137}, 8973 petsc_uses = {KSP} 8974} 8975 8976@InProceedings{ efficient, 8977 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 8978 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 8979 Libraries}, 8980 booktitle = {Modern Software Tools in Scientific Computing}, 8981 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 8982 publisher = {Birkhauser Press}, 8983 pages = {163--202}, 8984 year = {1997}, 8985 petsc_uses = {KSP} 8986} 8987 8988% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 8989@TechReport{ petsc-user-ref, 8990 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8991 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 8992 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8993 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8994 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 8995 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 8996 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 8997 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 8998 Zhang}, 8999 title = {{PETSc/TAO} Users Manual}, 9000 institution = {Argonne National Laboratory}, 9001 number = {ANL-21/39 - Revision 3.21}, 9002 doi = {10.2172/2205494}, 9003 year = {2024} 9004} 9005 9006% url = {https://petsc.org/release} 9007@TechReport{ petsc-developers, 9008 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 9009 title = {{PETS}c Developers Guide}, 9010 institution = {Argonne National Laboratory}, 9011 number = {ANL-18/18}, 9012 year = {2018}, 9013 url = {https://petsc.org/release/developers}, 9014 petsc_uses = {KSP} 9015} 9016 9017@Unpublished{ alice-memory-snooper, 9018 author = {Ibrahima Ba and Barry~F. Smith}, 9019 title = {The {ALICE} Memory Snooper}, 9020 year = {1999}, 9021 petsc_uses = {KSP} 9022} 9023 9024@TechReport{ petsc-user-ref-polish, 9025 author = {Marcin Bojko and Piotr Krzyzanowski}, 9026 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 9027 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 9028 year = {1998}, 9029 note = {An introduction to PETSc in Polish}, 9030 petsc_uses = {KSP} 9031} 9032 9033@InProceedings{ abghmn00, 9034 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 9035 High-Performance Scientific Computing}, 9036 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 9037 Norris}, 9038 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 9039 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 9040 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 9041 Hasco\"{e}t and Uwe Naumann}, 9042 publisher = {Springer}, 9043 year = {2002}, 9044 petsc_uses = {KSP} 9045} 9046 9047@Unpublished{ petsc-mpi-paper, 9048 author = {Lois Curfman McInnes and Barry F. Smith}, 9049 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 9050 Libraries}, 9051 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 9052 month = jun, 9053 year = {1995}, 9054 petsc_uses = {KSP} 9055} 9056 9057@InProceedings{ miss-paper, 9058 author = {William D. Gropp and Barry F. Smith}, 9059 title = {Scalable, Extensible, and Portable Numerical Libraries}, 9060 publisher = {IEEE}, 9061 year = {1994}, 9062 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 9063 address = {Mississippi State University}, 9064 pages = {87--93}, 9065 keyword = {numerical libraries, scientific computing, parallel computing}, 9066 petsc_uses = {KSP} 9067} 9068 9069@InProceedings{ snes-paper, 9070 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 9071 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 9072 Minimization Problems}, 9073 publisher = {IEEE}, 9074 year = {1995}, 9075 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 9076 address = {Mississippi State University}, 9077 pages = {60-67}, 9078 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 9079 petsc_uses = {KSP} 9080} 9081 9082@Article{ dsneutral, 9083 author = {Barry F. Smith and William D. Gropp}, 9084 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 9085 Sparse Linear Systems}, 9086 journal = {Scientific Programming}, 9087 volume = {5}, 9088 pages = {329--336}, 9089 key = {GroppSmith96 ! KSP design}, 9090 year = {1996}, 9091 petsc_uses = {KSP} 9092} 9093 9094@InProceedings{ bgms98, 9095 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 9096 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 9097 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 9098 Scientific and Engineering Computing}, 9099 publisher = {SIAM}, 9100 pages = {58-67}, 9101 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 9102 year = {1998}, 9103 petsc_uses = {KSP} 9104} 9105 9106@Article{ hkm98, 9107 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 9108 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 9109 {PDE} Computation}, 9110 journal = {Advances in Engineering Software}, 9111 volume = {29}, 9112 pages = {415-424}, 9113 year = {1998}, 9114 petsc_uses = {KSP} 9115} 9116 9117@TechReport{ pdpta99, 9118 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 9119 Smith}, 9120 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 9121 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 9122 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 9123 Vegas, Nevada}, 9124 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 9125 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 9126 number = {ANL/MCS-P751-0599}, 9127 year = {1999}, 9128 petsc_uses = {KSP} 9129} 9130 9131@InProceedings{ bbh:com, 9132 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 9133 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 9134 Computing}}, 9135 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 9136 Euro-Par Conference, Munich, Germany, August/September 2000}, 9137 year = {2000}, 9138 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 9139 volume = {1900}, 9140 series = {Lecture Notes in Computer Science}, 9141 pages = {86--94}, 9142 address = {Berlin}, 9143 publisher = {Springer}, 9144 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 9145 petsc_uses = {KSP} 9146} 9147 9148@InProceedings{ overture00, 9149 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 9150 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 9151 Components}, 9152 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 9153 booktitle = {Proceedings of the International Federation for Information Processing Working 9154 Conference on Software Architectures for Scientific Computing, Kluwer}, 9155 year = {2000}, 9156 pages = {57--68}, 9157 petsc_uses = {KSP} 9158} 9159 9160@TechReport{ smith97, 9161 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 9162 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 9163 number = {ANL/MCS-P701}, 9164 author = {Barry F. Smith}, 9165 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 9166 petsc_uses = {KSP} 9167} 9168 9169@Article{ smith98, 9170 author = {Barry Smith}, 9171 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 9172 journal = {SIGNUM Newsletter}, 9173 year = {1998}, 9174 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 9175 petsc_uses = {KSP} 9176} 9177 9178@TechReport{ ad-petsc-tm, 9179 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 9180 {PETSc}}, 9181 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 9182 year = {1997}, 9183 type = {Technical Memorandum}, 9184 institution = {ANL}, 9185 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 9186 number = {ANL/MCS-TM-233}, 9187 petsc_uses = {KSP} 9188} 9189 9190% LiteralHTML: 9191% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 9192% LiteralHTML: 9193@PhDThesis{ klotzthesis2019, 9194 author = {Thomas S. Klotz}, 9195 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 9196 Biology}, 9197 school = {Rice University}, 9198 year = {2019}, 9199 petsc_uses = {KSP} 9200} 9201 9202@Article{ klotzbardhanknepley2018, 9203 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 9204 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 9205 journal = {arXiv e-prints}, 9206 eprint = {1708.06028}, 9207 archiveprefix = {arXiv}, 9208 primaryclass = {math.na}, 9209 year = {2018}, 9210 note = {\url{http://arxiv.org/abs/1708.06028}}, 9211 petsc_uses = {KSP} 9212} 9213 9214@Misc{ brown2016, 9215 title = {Threading Tradeoffs in Domain Decomposition}, 9216 author = {Jed Brown}, 9217 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 9218 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 9219 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 9220 year = {2016}, 9221 petsc_uses = {KSP} 9222} 9223 9224@Article{ changnakshatralaknepleyjohnsson2017, 9225 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 9226 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 9227 Johnsson}, 9228 journal = {Concurency: Practice and Experience}, 9229 volume = {30}, 9230 number = {11}, 9231 eprint = {1705.03625}, 9232 doi = {10.1002/cpe.4401}, 9233 year = {2017}, 9234 petsc_uses = {KSP} 9235} 9236 9237@Article{ changfabienknepleymills2018, 9238 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 9239 spectrum analysis}, 9240 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 9241 journal = {SIAM Journal on Scientific Computing}, 9242 volume = {40}, 9243 number = {6}, 9244 pages = {C779--C802}, 9245 eprint = {1802.07832}, 9246 doi = {10.1137/18M1172260}, 9247 year = {2018}, 9248 petsc_uses = {KSP} 9249} 9250 9251@Article{ joshaghanichangnakshatralaknepley2019, 9252 title = {Composable solvers for the four-field double porosity/permeability model}, 9253 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 9254 Knepley}, 9255 journal = {Journal of Computational Physics}, 9256 volume = {386}, 9257 pages = {428--466}, 9258 doi = {10.1016/j.jcp.2019.02.020}, 9259 year = {2019}, 9260 petsc_uses = {KSP} 9261} 9262 9263@InProceedings{ barralknepleylangepiggottgorman2016, 9264 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 9265 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 9266 and Gerard J. Gorman}, 9267 booktitle = {25th International Meshing Roundtable}, 9268 editor = {Steve Owen and Hang Si}, 9269 month = sep, 9270 address = {Washington, DC}, 9271 pages = {1--5}, 9272 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 9273 year = {2016}, 9274 petsc_uses = {KSP} 9275} 9276 9277@Article{ adamsbrownknepleysamtaney2016, 9278 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 9279 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 9280 journal = {SIAM Journal on Scientific Computing}, 9281 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 9282 epub = {http://arxiv.org/abs/1406.7808}, 9283 volume = {8}, 9284 number = {4}, 9285 pages = {C426--C440}, 9286 doi = {10.1137/140975127}, 9287 year = {2016}, 9288 petsc_uses = {KSP} 9289} 9290 9291@InProceedings{ maysananruppknepleysmith2016, 9292 title = {Extreme-Scale Multigrid Components within {PETSc}}, 9293 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 9294 Smith}, 9295 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 9296 series = {PASC '16}, 9297 isbn = {978-1-4503-4126-4}, 9298 location = {Lausanne, Switzerland}, 9299 pages = {5:1--5:12}, 9300 articleno = {5}, 9301 numpages = {12}, 9302 doi = {10.1145/2929908.2929913}, 9303 acmid = {2929913}, 9304 publisher = {ACM}, 9305 address = {New York, NY, USA}, 9306 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 9307 preconditioning}, 9308 year = {2016}, 9309 petsc_uses = {KSP} 9310} 9311 9312@Article{ liu2015field, 9313 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 9314 author = {Lulu Liu and David E Keyes}, 9315 journal = {SIAM Journal on Scientific Computing}, 9316 volume = {37}, 9317 number = {3}, 9318 pages = {A1388--A1409}, 9319 year = {2015}, 9320 publisher = {SIAM}, 9321 petsc_uses = {KSP} 9322} 9323 9324@Article{ lujiaomissirlis2014, 9325 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 9326 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 9327 journal = {Numerical Linear Algebra with Applications}, 9328 volume = {21}, 9329 number = {2}, 9330 pages = {221--238}, 9331 year = {2014}, 9332 publisher = {Wiley Online Library}, 9333 petsc_uses = {KSP} 9334} 9335 9336@Article{ badiamartinprincipe2013, 9337 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 9338 solid mechanics}, 9339 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 9340 journal = {International Journal for Numerical Methods in Engineering}, 9341 volume = {96}, 9342 number = {4}, 9343 pages = {203--230}, 9344 year = {2013}, 9345 petsc_uses = {KSP} 9346} 9347 9348@Article{ morganknepleysananscott2016, 9349 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 9350 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 9351 journal = {Concurrency and Computation: Practice and Experience}, 9352 volume = {28}, 9353 pages = {4532--4542}, 9354 year = {2016}, 9355 url = {http://arxiv.org/abs/1602.04873}, 9356 doi = {10.1002/cpe.3820}, 9357 petsc_uses = {KSP} 9358} 9359 9360@Article{ morgansananknepleymills2020, 9361 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 9362 solvers}, 9363 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 9364 journal = {The International Journal of High Performance Computing Applications}, 9365 volume = {35}, 9366 issue = {1}, 9367 doi = {10.1177/1094342020966835}, 9368 url = {https://doi.org/10.1177/1094342020966835}, 9369 eprint = {https://doi.org/10.1177/1094342020966835}, 9370 year = {2020}, 9371 petsc_uses = {KSP} 9372} 9373 9374@Article{ msz2013, 9375 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 9376 author = {M. McCourt and B. F. Smith and H. Zhang}, 9377 journal = {SIAM Journal on Matrix Analysis and Applications}, 9378 year = {2015}, 9379 note = {To appear}, 9380 petsc_uses = {KSP} 9381} 9382 9383@Article{ bassi2014agglomeration, 9384 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 9385 free}, 9386 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 9387 journal = {Mathematical Models and Methods in Applied Sciences}, 9388 volume = {24}, 9389 number = {08}, 9390 pages = {1495--1539}, 9391 year = {2014}, 9392 publisher = {World Scientific}, 9393 petsc_uses = {KSP} 9394} 9395 9396@Article{ jhuranidemkowicz12, 9397 author = {{Jhurani}, C. and {Demkowicz}, L.}, 9398 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 9399 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 9400 journal = {Computer Methods in Applied Mechanics and Engineering}, 9401 volume = {213}, 9402 pages = {418-426}, 9403 year = {2012}, 9404 month = mar, 9405 doi = {10.1016/j.cma.2011.06.003}, 9406 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 9407 petsc_uses = {KSP} 9408} 9409 9410@Article{ yangcai11, 9411 author = {Yang, Haijian and Cai, Xiao-Chuan}, 9412 title = {Parallel Two-Grid Semismooth {N}ewton--{K}rylov--{S}chwarz Method for Nonlinear 9413 Complementarity Problems}, 9414 journal = {J. Sci. Comput.}, 9415 issue_date = {May 2011}, 9416 volume = {47}, 9417 number = {2}, 9418 month = may, 9419 pages = {258--280}, 9420 year = {2011}, 9421 issn = {0885-7474}, 9422 numpages = {23}, 9423 doi = {10.1007/s10915-010-9436-4}, 9424 acmid = {1971246}, 9425 publisher = {Plenum Press}, 9426 address = {New York, NY, USA}, 9427 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 9428 preconditioners, Semismooth Newton, Two-level methods}, 9429 petsc_uses = {KSP} 9430} 9431 9432@Article{ rheinbach09, 9433 author = {Rheinbach, Oliver}, 9434 title = {Parallel Iterative Substructuring in Structural Mechanics}, 9435 journal = {Archives of Computational Methods in Engineering}, 9436 volume = {16}, 9437 number = {4}, 9438 pages = {425-463}, 9439 year = {2009}, 9440 issn = {1134-3060}, 9441 doi = {10.1007/s11831-009-9035-4}, 9442 publisher = {Springer Netherlands}, 9443 language = {English}, 9444 petsc_uses = {KSP} 9445} 9446 9447@Article{ knepleyterrel2013, 9448 author = {Matthew G. Knepley and Andy R. Terrel}, 9449 title = {Finite Element Integration on {GPUs}}, 9450 journal = {{ACM} Transactions on Mathematical Software}, 9451 volume = {39}, 9452 number = {2}, 9453 accepted = {17 April 2012}, 9454 year = {2013}, 9455 abstract = {We present a novel finite element integration method for low order elements on 9456 GPUs. We achieve more than 100GF for element integration on first order 9457 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 9458 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 9459 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 9460 url = {http://arxiv.org/abs/1103.0066}, 9461 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 9462 petsc_uses = {KSP} 9463} 9464 9465@Article{ knepleyruppterrel2016, 9466 title = {Finite Element Integration with Quadrature on the GPU}, 9467 journal = {ArXiv e-prints}, 9468 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 9469 version = {1}, 9470 date = {2016-07-14}, 9471 eprinttype = {arxiv}, 9472 eprintclass = {cs.MS}, 9473 eprint = {1607.04245v1}, 9474 petsc_uses = {KSP} 9475} 9476 9477@Article{ klawonnlanserrheinbach2014, 9478 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 9479 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 9480 journal = {SIAM Journal on Scientific Computing}, 9481 volume = {36}, 9482 number = {2}, 9483 pages = {A737--A765}, 9484 year = {2014}, 9485 petsc_uses = {KSP} 9486} 9487 9488@Article{ bruneknepleysmithtu15, 9489 title = {Composing Scalable Nonlinear Algebraic Solvers}, 9490 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 9491 journal = {SIAM Review}, 9492 volume = {57}, 9493 number = {4}, 9494 pages = {535--565}, 9495 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 9496 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 9497 doi = {10.1137/130936725}, 9498 year = {2015}, 9499 petsc_uses = {KSP} 9500} 9501 9502@Article{ mszm2014, 9503 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 9504 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9505 volume = {40}, 9506 pages = {17--31}, 9507 year = {2014}, 9508 journal = {Parallel Computing}, 9509 doi = {10.1016/j.parco.2013.10.001}, 9510 petsc_uses = {KSP} 9511} 9512 9513@TechReport{ mszm2012, 9514 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 9515 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9516 year = {2012}, 9517 number = {ANL/MCS-P2097-0512}, 9518 institution = {Argonne National Laboratory}, 9519 petsc_uses = {KSP} 9520} 9521 9522@InProceedings{ bkmms2012, 9523 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 9524 F. Smith}, 9525 title = {Composable linear solvers for multiphysics}, 9526 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 9527 Computing} ({ISPDC} 2012)}, 9528 year = {2012}, 9529 doi = {10.1109/ISPDC.2012.16}, 9530 publisher = {IEEE Computer Society}, 9531 pages = {55--62}, 9532 petsc_uses = {KSP} 9533} 9534 9535@Article{ bourdinbucuroudet2009, 9536 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 9537 title = {Optimal Partitions for Eigenvalues}, 9538 journal = {SIAM J. Sci. Comput.}, 9539 volume = {31}, 9540 number = {6}, 9541 pages = {4100--4114}, 9542 year = {2009}, 9543 petsc_uses = {KSP} 9544} 9545 9546@InBook{ kimnbourdin2007, 9547 author = {J.-H. Kimn and Blaise Bourdin}, 9548 title = {Numerical implementation of overlapping balancing domain decomposition methods on 9549 unstructured meshes}, 9550 editor = {O. B. Widlund and D. E. Keyes}, 9551 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 9552 series = {Lecture Notes in Computational Science and Engineering}, 9553 number = {55}, 9554 publisher = {Springer-Verlag}, 9555 pages = {309--315}, 9556 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 9557 year = {2007}, 9558 petsc_uses = {KSP} 9559} 9560 9561@Article{ bjm2005, 9562 author = {AH Baker and ER Jessup and T Manteuffel}, 9563 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 9564 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 9565 year = {2005}, 9566 petsc_uses = {KSP} 9567} 9568 9569@Unpublished{ sundar-2008a, 9570 author = {R.S. Sampath and G. Biros}, 9571 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 9572 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9573 petsc_uses = {KSP} 9574} 9575 9576@Article{ sundar-2008, 9577 author = {H. Sundar and R.S. Sampath and G. Biros}, 9578 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 9579 journal = {SIAM Journal on Scientific Computing}, 9580 year = {2008}, 9581 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9582 petsc_uses = {KSP} 9583} 9584 9585@InProceedings{ sundar-2007, 9586 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 9587 title = {Low-constant parallel algorithms for finite element simulations using linear 9588 octrees}, 9589 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 9590 year = {2007}, 9591 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9592 petsc_uses = {KSP} 9593} 9594 9595@InProceedings{ adams-98a, 9596 author = {Adams, Mark ~F.}, 9597 title = {A Parallel Maximal Independent Set Algorithm}, 9598 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 9599 year = {1998}, 9600 petsc_uses = {KSP} 9601} 9602 9603@Article{ akcelik2005ddd, 9604 title = {{Dynamic data-driven inversion for terascale simulations: real-time 9605 identification of airborne contaminants}}, 9606 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 9607 van Bloemen Waanders, B.}, 9608 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 9609 year = {2005}, 9610 publisher = {IEEE Computer Society Washington, DC, USA}, 9611 petsc_uses = {KSP} 9612} 9613 9614@InBook{ akcelik-2006, 9615 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 9616 Bloemen Waanders}, 9617 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 9618 title = {Frontiers of Parallel Computing}, 9619 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 9620 publisher = {SIAM}, 9621 year = {2006}, 9622 petsc_uses = {KSP} 9623} 9624 9625@Article{ dt, 9626 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 9627 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 9628 Convection Diffusion Equations}, 9629 journal = {The Journal of Supercomputing}, 9630 year = {2004}, 9631 pages = {235--253}, 9632 volume = {28}, 9633 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 9634 petsc_uses = {KSP} 9635} 9636 9637@PhDThesis{ hwang2004, 9638 author = {Feng-Nan Hwang}, 9639 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 9640 Computational Fluid Dynamics}, 9641 school = {University of Colorado at Boulder}, 9642 year = {2004}, 9643 petsc_uses = {KSP} 9644} 9645 9646@PhDThesis{ baker, 9647 author = {{A. H.} Baker}, 9648 title = {On improving the performance of the linear solver restarted {GMRES}}, 9649 school = {University of Colorado at Boulder}, 9650 year = {2003}, 9651 petsc_uses = {KSP} 9652} 9653 9654@TechReport{ klawonnrheinbach601, 9655 author = {Axel Klawonn and Oliver Rheinbach}, 9656 title = {A Parallel Implementation of Dual-Primal {FETI-DP} Methods for Three Dimensional 9657 Linear Elasticity Using a Transformation of Basis}, 9658 institution = {Universit\"at Duisburg-Essen}, 9659 year = {2005}, 9660 type = {Technical Report}, 9661 number = {SM-E-601}, 9662 petsc_uses = {KSP} 9663} 9664 9665@TechReport{ klawonnrheinbach609, 9666 author = {Axel Klawonn and Oliver Rheinbach}, 9667 title = {Inexact FETI-DP Methods}, 9668 institution = {Universit\"at Duisburg-Essen}, 9669 year = {2005}, 9670 type = {Technical Report}, 9671 number = {SM-E-609}, 9672 petsc_uses = {KSP} 9673} 9674 9675@TechReport{ klawonnrheinbach607, 9676 author = {Axel Klawonn and Oliver Rheinbach}, 9677 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 9678 institution = {Universit\"at Duisburg-Essen}, 9679 year = {2005}, 9680 type = {Technical Report}, 9681 number = {SM-E-607}, 9682 petsc_uses = {KSP} 9683} 9684 9685@Article{ kul-natraj-pbp, 9686 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 9687 title = {Performance of a parallel mixed finite element implementation for fourth order 9688 clamped anisotropic plate bending problems in distributed memory environments}, 9689 journal = {Applied Mathematics and Computation}, 9690 volume = {155}, 9691 year = {2004}, 9692 number = {3}, 9693 pages = {753--777}, 9694 petsc_uses = {KSP} 9695} 9696 9697@Article{ bramkamp2006uej, 9698 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 9699 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 9700 journal = {Computers \& Fluids}, 9701 volume = {35}, 9702 number = {10}, 9703 pages = {1063--1073}, 9704 doi = {10.1016/j.compfluid.2005.10.003}, 9705 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 9706 derivation of the analytic flux Jacobian can become quite complicated depending on 9707 the complexity of the numerical flux calculation. Practically, the derivation of 9708 the exact Jacobian by hand is an unrealistic option because of the enormous 9709 man-hour investment needed. In this work, automatic differentiation is used to 9710 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 9711 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 9712 approximated by first-order forward differences. For a two-dimensional airfoil 9713 under three different flight conditions (quasi-incompressible flow, compressible 9714 subsonic flow, and transonic flow), we show that the robustness and performance of 9715 the present finite volume scheme is significantly improved by using exact 9716 Jacobians.}, 9717 year = {2006}, 9718 petsc_uses = {KSP} 9719} 9720 9721@Article{ shahbazi1, 9722 author = {Khosro Shahbazi}, 9723 title = {An explicit expression for the penalty parameter of the interior penalty method}, 9724 journal = {Journal of Computational Physics}, 9725 volume = {205}, 9726 year = {2005}, 9727 pages = {401--407}, 9728 petsc_uses = {KSP} 9729} 9730 9731@TechReport{ kk, 9732 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 9733 author = {Hans-Peter Kersken and Uwe Kuster}, 9734 year = {1999}, 9735 institution = {University of Stuttgart}, 9736 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 9737 number = {310}, 9738 petsc_uses = {KSP} 9739} 9740 9741@Article{ miha-mija, 9742 author = {M. D. Mihajlovi and S. Mijalkovi}, 9743 title = {A component decomposition preconditioning for 3D stress analysis problems}, 9744 journal = {Numerical Linear Algebra with Applications}, 9745 volume = {9}, 9746 year = {2002}, 9747 pages = {567--583}, 9748 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 9749 petsc_uses = {KSP} 9750} 9751 9752@Article{ bjm, 9753 author = {M Benzi and W Joubert and G Mateescu}, 9754 journal = {Electronic Transactions on Numerical Analysis}, 9755 year = {1999}, 9756 volume = {8}, 9757 pages = {88--114}, 9758 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 9759 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}, 9760 petsc_uses = {KSP} 9761} 9762 9763@PhDThesis{ hyde, 9764 author = {EMK Hyde}, 9765 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 9766 school = {Caltech}, 9767 year = {2003}, 9768 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 9769 petsc_uses = {KSP} 9770} 9771 9772@Article{ km2003, 9773 author = {A. Keese and H. G. Matthies}, 9774 journal = {Proceedings in Applied Mathematics and Mechanics}, 9775 year = {2003}, 9776 volume = {2}, 9777 pages = {485--486}, 9778 title = {Parallel Solution of Stochastic PDEs}, 9779 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 9780 petsc_uses = {KSP} 9781} 9782 9783@Article{ whszss, 9784 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 9785 and Otmar Scherzer and H. Siegfried Stiehl}, 9786 journal = {Real Time Imaging}, 9787 year = {2001}, 9788 volume = {7}, 9789 pages = {31--45}, 9790 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 9791 approaches}, 9792 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 9793 petsc_uses = {KSP} 9794} 9795 9796@TechReport{ baker1, 9797 title = {An Efficient Block Variant of GMRES}, 9798 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 9799 year = {2003}, 9800 type = {Technical Report}, 9801 institution = {University of Colorado, Boulder}, 9802 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 9803 number = {CU-CS-957-03}, 9804 petsc_uses = {KSP} 9805} 9806 9807@InProceedings{ mc2003, 9808 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 9809 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 9810 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9811 Methods}, 9812 pages = {639--646}, 9813 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9814 note = {}, 9815 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9816 year = {2003}, 9817 petsc_uses = {KSP} 9818} 9819 9820@InProceedings{ kt2003, 9821 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 9822 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 9823 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9824 Methods}, 9825 pages = {615--622}, 9826 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9827 note = {}, 9828 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9829 year = {2003}, 9830 petsc_uses = {KSP} 9831} 9832 9833@InProceedings{ krw2003, 9834 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 9835 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 9836 3D}, 9837 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9838 Methods}, 9839 pages = {361--368}, 9840 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9841 note = {}, 9842 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9843 year = {2003}, 9844 petsc_uses = {KSP} 9845} 9846 9847@InProceedings{ hc2003, 9848 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 9849 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 9850 Nonlinear Preconditioning}, 9851 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9852 Methods}, 9853 pages = {201--208}, 9854 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9855 note = {}, 9856 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9857 year = {2003}, 9858 petsc_uses = {KSP} 9859} 9860 9861@InProceedings{ g2003, 9862 author = {P. Goldfeld}, 9863 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 9864 (Generalized) {Stokes} and Parallel Implementation}, 9865 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9866 Methods}, 9867 pages = {209--216}, 9868 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9869 publisher = {National Autonomous University of Mexico (UNAM)}, 9870 note = {}, 9871 url = {http://www.ddm.org/DD14}, 9872 year = {2003}, 9873 petsc_uses = {KSP} 9874} 9875 9876@InProceedings{ dhv2003, 9877 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 9878 title = {Toward scalable {FETI} algorithm for variational inequalities with applications to 9879 composites}, 9880 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9881 Methods}, 9882 pages = {395--401}, 9883 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9884 publisher = {National Autonomous University of Mexico (UNAM)}, 9885 note = {}, 9886 url = {http://www.ddm.org/DD14}, 9887 year = {2003}, 9888 petsc_uses = {KSP} 9889} 9890 9891@InProceedings{ dhsv2002, 9892 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9893 title = {Scalabilities of {FETI} for variational inequalities and contact shape 9894 optimization}, 9895 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9896 Methods}, 9897 pages = {359--367}, 9898 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9899 publisher = {CIMNE, Barcelona, Spain}, 9900 note = {}, 9901 url = {http://www.ddm.org/DD13}, 9902 year = {2002}, 9903 petsc_uses = {KSP} 9904} 9905 9906@InProceedings{ cky2002, 9907 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 9908 title = {A Nonlinear Additive {S}chwarz Preconditioned Inexact {N}ewton Method for Shocked 9909 Duct Flows}, 9910 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9911 Methods}, 9912 pages = {343--350}, 9913 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9914 publisher = {CIMNE, Barcelona, Spain}, 9915 note = {}, 9916 url = {http://www.ddm.org/DD13}, 9917 year = {2002}, 9918 petsc_uses = {KSP} 9919} 9920 9921@Conference{ li-etal:03, 9922 author = {Li, Z. and Lanteri S. and Saad, Y.}, 9923 title = {Multiplicative-additive preconditioning combination for general sparse linear 9924 systems}, 9925 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 9926 Matrix Problems in Scientific and Industrial Applications}, 9927 address = {Napa, California, USA}, 9928 date = {october 27-29}, 9929 year = {2003}, 9930 petsc_uses = {KSP} 9931} 9932 9933@Article{ bashir2008hessian, 9934 title = {Hessian-based model reduction for large-scale systems with initial-condition 9935 inputs}, 9936 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 9937 J.}, 9938 journal = {International journal for numerical methods in engineering}, 9939 volume = {73}, 9940 number = {6}, 9941 pages = {844--868}, 9942 year = {2008}, 9943 publisher = {Wiley Online Library}, 9944 petsc_uses = {KSP} 9945} 9946 9947@Article{ bashir2007hessian, 9948 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 9949 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 9950 K.}, 9951 journal = {Computational Science--ICCS 2007}, 9952 pages = {1010--1017}, 9953 year = {2007}, 9954 publisher = {Springer}, 9955 petsc_uses = {KSP} 9956} 9957 9958@Article{ akcelik2011fast, 9959 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 9960 inverse problems based on low-rank partial {H}essian approximations}, 9961 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 9962 Waanders, B. and Wilcox, L.}, 9963 journal = {SIAM Journal on Scientific Computing}, 9964 volume = {33}, 9965 number = {1}, 9966 year = {2011}, 9967 petsc_uses = {KSP} 9968} 9969 9970@InProceedings{ ff2003, 9971 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 9972 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 9973 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 9974 year = {2003}, 9975 petsc_uses = {KSP} 9976} 9977 9978@InProceedings{ d2b2004, 9979 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 9980 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 9981 Ordering Strategies}, 9982 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 9983 year = {2004}, 9984 petsc_uses = {KSP} 9985} 9986 9987@InProceedings{ d2v2005, 9988 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 9989 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 9990 Flow Equations}, 9991 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 9992 year = {2005}, 9993 petsc_uses = {KSP} 9994} 9995 9996@InProceedings{ dvs2006, 9997 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 9998 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 9999 Mixed Convection Equations}, 10000 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 10001 year = {2006}, 10002 petsc_uses = {KSP} 10003} 10004 10005@Article{ dsv2006, 10006 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 10007 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 10008 Flow Equations}, 10009 journal = {Computational Fluid Dynamics}, 10010 year = {2006}, 10011 volume = {15}, 10012 number = {1}, 10013 petsc_uses = {KSP} 10014} 10015 10016@Article{ lahaye03, 10017 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 10018 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 10019 journal = {J. Comput. Appl. Math.}, 10020 year = {2004}, 10021 pages = {267--275}, 10022 volume = {168}, 10023 petsc_uses = {KSP} 10024} 10025 10026@TechReport{ brmn, 10027 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 10028 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 10029 year = {2002}, 10030 type = {Technical Report}, 10031 institution = {ANL}, 10032 number = {ANL/MCS-P993-0902}, 10033 note = {To appear in Future Generation Computer Systems}, 10034 petsc_uses = {KSP} 10035} 10036 10037@InProceedings{ mnbr, 10038 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 10039 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 10040 Algorithms}, 10041 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 10042 Mechanics}, 10043 year = {2003}, 10044 petsc_uses = {KSP} 10045} 10046 10047@InProceedings{ bmnr, 10048 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 10049 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 10050 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 10051 Applications, Lecture notes in Computer Science 2677}, 10052 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 10053 pages = {828--839}, 10054 year = {2003}, 10055 petsc_uses = {KSP} 10056} 10057 10058@Article{ ph03, 10059 author = {M. Pernice and R. D. Hornung}, 10060 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 10061 journal = {Computing and Visualization in Science}, 10062 year = {2003}, 10063 lab = {LANL}, 10064 petsc_uses = {KSP} 10065} 10066 10067@Article{ adams-02, 10068 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 10069 journal = {J. Comp. Phys.}, 10070 number = {2}, 10071 pages = {593-610}, 10072 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 10073 volume = {188}, 10074 year = {2003}, 10075 petsc_uses = {KSP} 10076} 10077 10078@InProceedings{ adams2001distributed, 10079 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 10080 smoothers}, 10081 author = {Adams, M.F.}, 10082 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 10083 pages = {14--14}, 10084 year = {2001}, 10085 organization = {IEEE}, 10086 petsc_uses = {KSP} 10087} 10088 10089@PhDThesis{ els01, 10090 author = {Ulrich Elsner}, 10091 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 10092 algorithms}, 10093 school = {Technical University Chemnitz}, 10094 year = {2002}, 10095 publisher = {Logos Verlag, Berlin}, 10096 isbn = {3-89722-923-4}, 10097 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 10098 different graph partitioning algorithms}, 10099 petsc_uses = {KSP} 10100} 10101 10102@TechReport{ ckk02, 10103 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 10104 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 10105 year = {2002}, 10106 type = {Technical Report}, 10107 institution = {ODU}, 10108 url = {http://www.math.odu.edu/\~{ }keyes}, 10109 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 10110 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 10111 Methods}, 10112 petsc_uses = {KSP} 10113} 10114 10115@Article{ gpw2002, 10116 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 10117 Heterogeneous Problems in Linear Elasticity}, 10118 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 10119 year = {2003}, 10120 pages = {283--324}, 10121 volume = {95}, 10122 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 10123 journal = {Numerische Mathematik}, 10124 petsc_uses = {KSP} 10125} 10126 10127@Article{ dh1, 10128 title = {Scalability and FETI based algorithm for large discretized variational 10129 inequalities}, 10130 author = {Z Dostal and D Horak}, 10131 year = {2003}, 10132 pages = {347--357}, 10133 volume = {61}, 10134 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 10135 journal = {Mathematics and Computers in Simulation}, 10136 petsc_uses = {KSP} 10137} 10138 10139@InProceedings{ dhsv1, 10140 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 10141 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 10142 title = {36 Scalabilities of {FETI} for Variational Inequalities and Contact Shape 10143 Optimization}, 10144 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 10145 Methods}, 10146 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10147 Kuznetsov}, 10148 petsc_uses = {KSP} 10149} 10150 10151@Article{ lahaye02, 10152 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 10153 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 10154 journal = {IEEEMAGN}, 10155 year = {2002}, 10156 volume = {38}, 10157 number = {2}, 10158 pages = {413-416}, 10159 petsc_uses = {KSP} 10160} 10161 10162@Article{ ckm01, 10163 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 10164 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 10165 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 10166 fluid dynamics}, 10167 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 10168 year = {2002}, 10169 volume = {40}, 10170 pages = {1463--1470}, 10171 petsc_uses = {KSP} 10172} 10173 10174@InProceedings{ cky01, 10175 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 10176 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 10177 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 10178 duct flow}, 10179 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 10180 Methods}, 10181 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10182 Kuznetsov}, 10183 year = {2002}, 10184 petsc_uses = {KSP} 10185} 10186 10187@Article{ ck02, 10188 author = {X.-C. Cai and D. E. Keyes}, 10189 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 10190 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 10191 journal = {SIAM J. Sci. Comput.}, 10192 year = {2002}, 10193 pages = {183--200}, 10194 volume = {24}, 10195 petsc_uses = {KSP} 10196} 10197 10198@Article{ c04, 10199 author = {Feng-Nan Hwang and X.-C. Cai}, 10200 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 10201 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 10202 for incompressible {Navier-Stokes} equations}, 10203 journal = {Journal of Computational Physics}, 10204 year = {2005}, 10205 volume = {204}, 10206 pages = {666--691}, 10207 petsc_uses = {KSP} 10208} 10209 10210@Article{ hc06, 10211 author = {Feng-Nan Hwang and X.-C. Cai}, 10212 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 10213 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 10214 Algorithms}, 10215 journal = {Computer Methods in Applied Mechanics and Engineering}, 10216 year = {2006}, 10217 volume = {196}, 10218 pages = {1603--1611}, 10219 petsc_uses = {KSP} 10220} 10221 10222@InProceedings{ adams-01, 10223 author = {Mark F. Adams}, 10224 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 10225 Smoothers}, 10226 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 10227 address = {Denver, Colorado}, 10228 month = nov, 10229 year = {2001}, 10230 petsc_uses = {KSP} 10231} 10232 10233@Book{ 1dl, 10234 author = {Domenico Lahaye}, 10235 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 10236 Computations}, 10237 year = {2001}, 10238 publisher = {Katholieke Universiteit Leuven}, 10239 notes = {Thesis}, 10240 petsc_uses = {KSP} 10241} 10242 10243@Article{ adams-00, 10244 author = {Adams, M.~F.}, 10245 journal = {International Journal for Numerical Methods in Engineering}, 10246 number = {8}, 10247 pages = {1241-1262}, 10248 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 10249 Deformation Elasticity and Plasticity}, 10250 volume = {48}, 10251 year = {2000}, 10252 petsc_uses = {KSP} 10253} 10254 10255@Article{ adams2002evaluation, 10256 author = {Adams, M.~F.}, 10257 journal = {International Journal for Numerical Methods in Engineering}, 10258 number = {1}, 10259 pages = {519-534}, 10260 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 10261 Problems in Solid Mechanics}, 10262 volume = {55}, 10263 year = {2002}, 10264 petsc_uses = {KSP} 10265} 10266 10267@Article{ lahaye00, 10268 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 10269 title = {Algebraic Multigrid for Complex Symmetric Systems}, 10270 journal = {IEEEMAGN}, 10271 year = {2000}, 10272 volume = {36}, 10273 number = {4}, 10274 pages = {1535--1538}, 10275 petsc_uses = {KSP} 10276} 10277 10278@InProceedings{ adams-99c, 10279 author = {Mark F. Adams and J. Demmel}, 10280 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 10281 Finite Element Problems}, 10282 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 10283 address = {Portland, Oregon}, 10284 month = nov, 10285 year = {1999}, 10286 petsc_uses = {KSP} 10287} 10288 10289@Article{ chan95, 10290 author = {T. Chan and B. Smith and J. Zou}, 10291 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 10292 Grids}, 10293 journal = {Numer. Math.}, 10294 year = {1995}, 10295 volume = {73}, 10296 pages = {149--167}, 10297 petsc_uses = {KSP} 10298} 10299 10300@TechReport{ adams-csd-98-993, 10301 pages = {11}, 10302 year = {1998}, 10303 type = {Technical Report}, 10304 number = {CSD-98-993}, 10305 institution = {University of California, Berkeley}, 10306 title = {A Parallel Maximal Independent Set Algorithm}, 10307 bibdate = {March 11, 1998}, 10308 author = {Mark F. Adams and James Demmel}, 10309 abstract = {The parallel construction of maximal independent sets is a useful building block 10310 for many algorithms in the computational sciences, including graph coloring and 10311 multigrid coarse grid creation on unstructured meshes. We present an efficient 10312 asynchronous maximal independent set algorithm for use on parallel computers, for 10313 ``well partitioned'' graphs, that arise from finite element (FE) models. For 10314 appropriately partitioned bounded degree graphs, it is shown that the running time 10315 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 10316 improvement over the previous best P-RAM complexity for this class of graphs. We 10317 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 10318 model is indicative of the performance one can expect with practical partitions on 10319 graphs from FE problems.}, 10320 month = mar, 10321 petsc_uses = {KSP} 10322} 10323 10324@Article{ benzigolubliesen2005, 10325 title = {Numerical solution of saddle point problems}, 10326 author = {Michele Benzi and Gene H. Golub and J\"org Liesen}, 10327 volume = {14}, 10328 journal = {Acta Numerica}, 10329 pages = {1-–137}, 10330 doi = {10.1017/S0962492904000212}, 10331 year = {2005} 10332} 10333 10334@Article{ mardal2011preconditioning, 10335 title = {Preconditioning discretizations of systems of partial differential equations}, 10336 author = {Kent-Andre Mardal and Ragnar Winther}, 10337 journal = {Numerical Linear Algebra with Applications}, 10338 volume = {18}, 10339 number = {1}, 10340 pages = {1--40}, 10341 year = {2011} 10342} 10343 10344@TechReport{ k676, 10345 year = {1994}, 10346 type = {Technical Report}, 10347 number = {TR1994-676}, 10348 institution = {New York University}, 10349 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 10350 Term}, 10351 author = {Axel Klawonn}, 10352 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 10353 petsc_uses = {KSP} 10354} 10355 10356@Book{ ak1, 10357 author = {Axel Klawonn}, 10358 title = {Preconditioners for Indefinite Problems}, 10359 year = {1995}, 10360 publisher = {Westfalishen Wilhelms-Universitat Munster}, 10361 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 10362 notes = {Thesis}, 10363 petsc_uses = {KSP} 10364} 10365 10366@TechReport{ knepleykarpeev05, 10367 pages = {41}, 10368 year = {2005}, 10369 type = {Technical Report}, 10370 number = {ANL/MCS-P1295-1005}, 10371 institution = {Argonne National Laboratory}, 10372 title = {Flexible Representation of Computational Meshes}, 10373 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10374 abstract = {}, 10375 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 10376 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 10377 month = oct, 10378 petsc_uses = {DMPlex} 10379} 10380 10381@TechReport{ knepleykarpeev07a, 10382 pages = {14}, 10383 year = {2007}, 10384 type = {Technical Report}, 10385 number = {ANL/MCS-P1455-0907}, 10386 institution = {Argonne National Laboratory}, 10387 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10388 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10389 abstract = {}, 10390 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 10391 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 10392 month = feb, 10393 petsc_uses = {DMPlex} 10394} 10395 10396@Article{ knepleykarpeev09, 10397 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10398 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10399 journal = {Scientific Programming}, 10400 volume = {17}, 10401 number = {3}, 10402 pages = {215--230}, 10403 year = {2009}, 10404 doi = {10.3233/SPR-2009-0249}, 10405 url = {http://arxiv.org/abs/0908.4427}, 10406 note = {\url{http://arxiv.org/abs/0908.4427}}, 10407 petsc_uses = {DMPlex} 10408} 10409 10410@Article{ biezuner2012computing, 10411 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 10412 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 10413 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 10414 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 10415 Sublinear Supersolutions}, 10416 journal = {Journal of Scientific Computing}, 10417 publisher = {Springer Netherlands}, 10418 issn = {0885-7474}, 10419 keyword = {Mathematics and Statistics}, 10420 pages = {180--201}, 10421 volume = {52}, 10422 issue = {1}, 10423 year = {2012}, 10424 doi = {10.1007/s10915-011-9540-0}, 10425 petsc_uses = {KSP} 10426} 10427 10428% LiteralHTML: 10429% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 10430% LiteralHTML: 10431@Book{ knepley2017, 10432 title = {Computational Science I}, 10433 author = {Matthew G. 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Smith and Petter Bj{\o}rstad and William D. Gropp}, 10462 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 10463 Differential Equations}, 10464 year = {1996}, 10465 publisher = {Cambridge University Press}, 10466 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 10467 petsc_uses = {KSP} 10468} 10469 10470@Misc{ petsc-fem:homepage, 10471 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 10472 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 10473 G. Rodriguez and G. Filippini}, 10474 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 10475 petsc_uses = {KSP} 10476} 10477 10478@Misc{ petsc4py-web-page, 10479 author = {Lisandro Dalcin}, 10480 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 10481 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 10482 note = {http://code.google.com/p/petsc4py/}, 10483 petsc_uses = {KSP} 10484} 10485 10486@Article{ libmeshpaper06, 10487 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 10488 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 10489 Simulations}}, 10490 journal = {Engineering with Computers}, 10491 volume = {22}, 10492 number = {3--4}, 10493 pages = {237--254}, 10494 year = {2006}, 10495 doi = {10.1007/s00366-006-0049-3}, 10496 petsc_uses = {KSP} 10497} 10498 10499@Misc{ sisiphus:homepage, 10500 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 10501 High-Resolution, Unstructured Simulations}, 10502 author = {T. {Tautges et al.}}, 10503 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 10504 petsc_uses = {KSP} 10505} 10506 10507@Misc{ pflotran:homepage, 10508 title = {{PFLOTRAN} project}, 10509 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 10510 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 10511 howpublished = {\url{http://pflotran.org/}}, 10512 petsc_uses = {KSP} 10513} 10514 10515@Misc{ pism:homepage, 10516 title = {{PISM}: A Parallel Ice Sheet Model}, 10517 author = {E. {Bueler et al.}}, 10518 howpublished = {\url{http://pism-docs.org}}, 10519 petsc_uses = {KSP} 10520} 10521 10522@Misc{ dohp:homepage, 10523 title = {Dohp: Dual order $hp$-finite elements}, 10524 author = {J. Brown}, 10525 howpublished = {\url{http://dohp.org}}, 10526 petsc_uses = {KSP} 10527} 10528 10529@Article{ mccourtrognlienetal12, 10530 title = {Improving parallel scalability for edge plasma transport simulations with neutral 10531 gas species}, 10532 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 10533 journal = {Computational Science and Discovery}, 10534 year = {2012}, 10535 volume = {5}, 10536 number = {014012}, 10537 doi = {10.1088/1749-4699/5/1/014012}, 10538 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 10539 2011)}, 10540 petsc_uses = {KSP} 10541} 10542 10543@Misc{ petclaw-github, 10544 title = {Pet{C}law Software}, 10545 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 10546 year = {2011}, 10547 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 10548 petsc_uses = {KSP} 10549} 10550 10551@Misc{ pyclaw-web-page, 10552 author = {Kyle T. Mandli and David I. 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Part I: The {Krylov-Schur} solver}}, 10571 author = {Biros, G. and Ghattas, O.}, 10572 journal = {SIAM Journal on Scientific Computing}, 10573 volume = {27}, 10574 number = {2}, 10575 pages = {687--713}, 10576 year = {2005}, 10577 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 10578 petsc_uses = {KSP} 10579} 10580 10581@Article{ biros2005pln2, 10582 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 10583 optimization. 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C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 10622 journal = {Computational Science \& Discovery}, 10623 volume = {5}, 10624 number = {1}, 10625 url = {http://stacks.iop.org/1749-4699/5/014002}, 10626 year = {2012}, 10627 petsc_uses = {KSP} 10628} 10629 10630@Article{ cmz2016, 10631 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 10632 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 10633 journal = {Journal of Scientific Computing}, 10634 publisher = {Springer}, 10635 pages = {803--825}, 10636 volume = {68}, 10637 issue = {2}, 10638 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 10639 doi = {10.1007/s10915-015-0159-4}, 10640 year = {2016}, 10641 note = {Also preprint ANL/MCS-P3039-0912}, 10642 petsc_uses = {KSP} 10643} 10644 10645@Article{ knepleybrownruppsmith13, 10646 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 10647 title = {Achieving High Performance with Unified Residual Evaluation}, 10648 journal = {ArXiv e-prints}, 10649 eprint = {1309.1204}, 10650 archiveprefix = {arXiv}, 10651 primaryclass = {cs.MS}, 10652 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 10653 Engineering, Finance, and Science}, 10654 year = {2013}, 10655 month = sep, 10656 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 10657 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10658 petsc_uses = {KSP} 10659} 10660 10661@Book{ fenicsbook, 10662 title = {Automated Solution of Differential Equations by the Finite Element Method: The 10663 FEniCS Book}, 10664 series = {Lecture Notes in Computational Science and Engineering}, 10665 volume = {84}, 10666 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 10667 publisher = {Springer}, 10668 isbn = {978-3-642-23098-1}, 10669 year = {2012}, 10670 petsc_uses = {KSP} 10671} 10672 10673@Article{ demidovahnertruppgottschling12, 10674 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 10675 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 10676 journal = {ArXiv e-prints}, 10677 archiveprefix = {arXiv}, 10678 eprint = {1212.6326}, 10679 primaryclass = {cs.MS}, 10680 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 10681 Parallel, and Cluster Computing, Physics - Computational Physics}, 10682 year = {2012}, 10683 month = dec, 10684 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 10685 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10686 petsc_uses = {KSP} 10687} 10688 10689@InProceedings{ viennacl, 10690 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 10691 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 10692 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 10693 year = {2010}, 10694 pages = {51-56}, 10695 petsc_uses = {KSP} 10696} 10697 10698@Article{ knepleybrownmcinnessmithruppadams2015, 10699 title = {Exascale Computing without Threads}, 10700 author = {Matthew G. 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Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 10713 Karl Rupp and Mark Adams}, 10714 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 10715 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 10716 Scientific Software Architecture for Portability and Performance}, 10717 year = {2015}, 10718 petsc_uses = {KSP} 10719} 10720 10721@InCollection{ balaybrownknepleymcinnessmith2015, 10722 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 10723 Smith}, 10724 title = {Providing Mixed Language and Legacy Support within a Library}, 10725 editor = {J. Carver}, 10726 booktitle = {Software Engineering for Science}, 10727 publisher = {Taylor \& Francis}, 10728 year = {2015}, 10729 petsc_uses = {KSP} 10730} 10731 10732@Article{ ruppbalaybrownknepleymcinnessmith2015, 10733 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 10734 Software}, 10735 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 10736 McInnes and Barry F. Smith}, 10737 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 10738 Productivity Challenges}, 10739 journal = {ArXiv e-prints}, 10740 archiveprefix = {arXiv}, 10741 eprint = {1510.01122}, 10742 year = {2015}, 10743 petsc_uses = {KSP} 10744} 10745 10746@InProceedings{ knepley2013accurately, 10747 title = {Accurately Citing Software and Algorithms Used in Publications}, 10748 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 10749 F.}, 10750 year = {2013}, 10751 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10752 (WSSSPE), held at SC13}, 10753 doi = {10.6084/m9.figshare.785731}, 10754 petsc_uses = {KSP} 10755} 10756 10757@InProceedings{ milleretal2013, 10758 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 10759 Strategies Developed for {FASTMath}}, 10760 author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and 10761 Barry Smith}, 10762 year = {2013}, 10763 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10764 (WSSSPE), held at SC13}, 10765 doi = {10.6084/m9.figshare.789055}, 10766 petsc_uses = {KSP} 10767} 10768 10769@TechReport{ dudsonetal2012, 10770 title = {Improved Nonlinear Solvers in {BOUT++}}, 10771 author = {Ben Dudson and Sean Farley and Lois Curfman McInnes}, 10772 institution = {Argonne National Laboratory}, 10773 number = {ANL/MCS-P3025-0812}, 10774 year = {2012}, 10775 petsc_uses = {KSP} 10776} 10777 10778@Misc{ brown13, 10779 author = {J. Brown}, 10780 title = {Scalable Repository Workflows}, 10781 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 10782 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 10783 year = {2013}, 10784 petsc_uses = {KSP} 10785} 10786 10787@Misc{ starforest11, 10788 title = {Star forests as a parallel communication model}, 10789 author = {Jed Brown}, 10790 url = {https://jedbrown.org/files/StarForest.pdf}, 10791 year = {2011}, 10792 petsc_uses = {KSP} 10793} 10794 10795@Misc{ brownknepleysmith13, 10796 author = {J. Brown and M. Knepley and B. Smith}, 10797 title = {Run-time Extensibility: Anything Less is Unsustainable}, 10798 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 10799 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 10800 year = {2013}, 10801 petsc_uses = {KSP} 10802} 10803 10804@Article{ jzhaoyliwkliu15, 10805 author = {J. Zhao and Y. Li and W.K. Liu}, 10806 title = {Predicting band structure of 3{D} mechanical metamaterials with complex geometry 10807 via {XFEM}}, 10808 journal = {Computational Mechanics}, 10809 year = {2015}, 10810 url = {http://link.springer.com/article/10.1007/s00466-015-1129-2}, 10811 petsc_uses = {KSP} 10812} 10813 10814@Article{ alisic14, 10815 author = {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen}, 10816 title = {Compaction around a rigid, circular inclusion in partially molten rock}, 10817 journal = {J. Geophys. Res.}, 10818 year = {2014}, 10819 volume = {119}, 10820 number = {7}, 10821 pages = {5903-5920}, 10822 doi = {10.1002/2013JB010906}, 10823 petsc_uses = {KSP} 10824} 10825 10826@Article{ rhebergen14, 10827 author = {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen}, 10828 title = {Analysis of block preconditioners for models of coupled magma mantle dynamics}, 10829 journal = {SIAM J. Sci. Comp.}, 10830 year = {2014}, 10831 volume = {36}, 10832 number = {4}, 10833 pages = {1960-1977}, 10834 doi = {10.1137/130946678}, 10835 petsc_uses = {KSP} 10836} 10837 10838@Article{ allwright14, 10839 author = {J. Allwright and R.F. Katz}, 10840 title = {Pipe Poiseuille flow of viscously anisotropic, partially molten rock}, 10841 journal = {Geophys. J. Int.}, 10842 year = {2014}, 10843 volume = {199}, 10844 number = {3}, 10845 pages = {1608--1624}, 10846 doi = {10.1093/gji/ggu345}, 10847 petsc_uses = {KSP} 10848} 10849 10850@Misc{ gropp10, 10851 author = {William D. Gropp}, 10852 title = {Update on libraries for {B}lue {W}aters}, 10853 address = {Bordeaux, France}, 10854 year = {2010}, 10855 url = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf}, 10856 petsc_uses = {KSP} 10857} 10858 10859@InProceedings{ mayknepley2017, 10860 title = {{DMSwarm}: Particles in {PETSc}}, 10861 author = {Dave A May and Matthew G Knepley}, 10862 booktitle = {EGU General Assembly Conference Abstracts}, 10863 volume = {19}, 10864 pages = {10133}, 10865 year = {2017}, 10866 petsc_uses = {KSP} 10867} 10868 10869@InProceedings{ adamsbrownknepley2013, 10870 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley}, 10871 title = {Low-communication techniques for extreme-scale multilevel solvers}, 10872 booktitle = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC}, 10873 organization = {DOE Office of Advanced Scientific Computing Research}, 10874 year = {2013}, 10875 petsc_uses = {KSP} 10876} 10877 10878@Article{ bhallagriffithknepleyadamsguy2017, 10879 title = {Scalable smoothing strategies for a geometric multigrid method for the immersed 10880 boundary equations}, 10881 author = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F. 10882 Adams and Robert D. Guy}, 10883 journal = {arXiv e-prints}, 10884 eprint = {1612.02208}, 10885 year = {2017}, 10886 note = {\url{http://arxiv.org/abs/1612.02208}}, 10887 petsc_uses = {KSP} 10888} 10889 10890@Article{ zampini2016pcbddc, 10891 title = {{PCBDDC}: a class of robust dual-primal methods in {PETSc}}, 10892 author = {Zampini, Stefano}, 10893 journal = {SIAM Journal on Scientific Computing}, 10894 volume = {38}, 10895 number = {5}, 10896 pages = {S282--S306}, 10897 year = {2016}, 10898 publisher = {SIAM}, 10899 petsc_uses = {KSP} 10900} 10901 10902@Article{ jolivetromanzampini2020, 10903 title = {{KSPHPDDM} and {PCHPDDM}: extending {PETSc} with advanced {Krylov} methods and 10904 robust multilevel overlapping {Schwarz} preconditioners}, 10905 author = {Pierre Jolivet and Jose Roman and Stefano Zampini}, 10906 journal = {Computers and Mathematics with Applications}, 10907 volume = {84}, 10908 pages = {277--295}, 10909 year = {2020} 10910} 10911 10912@Article{ zampinitu2017, 10913 title = {Multilevel {BDDC} deluxe algorithms with adaptive coarse spaces for flow in 10914 porous media}, 10915 author = {Stefano Zampini and Xuemin Tu}, 10916 journal = {SIAM Journal of Scientific Computing}, 10917 volume = {39}, 10918 number = {4}, 10919 pages = {A1389--A1415}, 10920 year = {2017} 10921} 10922 10923@Article{ ohwidlundzampinidohrmann2017, 10924 title = {{BDDC} algorithms with deluxe scaling and adaptive selection of primal 10925 constraints for {Raviart-Thomas} vector fields}, 10926 author = {D.-S. Oh and Olof B. Widlund and Stefano Zampini and Clark Dohrmann}, 10927 journal = {Mathematics of Computation}, 10928 volume = {87}, 10929 number = {310}, 10930 pages = {659--692}, 10931 year = {2017} 10932} 10933 10934@Article{ veigapavarinoscacchiwidlundzampini2016, 10935 title = {Adaptive selection of primal constraints for isogeometric {BDDC} deluxe 10936 preconditioners}, 10937 author = {L. Beirao Da Veiga and Luca F. Pavarino and S. Scacchi and Olof B. Widlund and 10938 Stefano Zampini}, 10939 journal = {SIAM Journal of Scientific Computing}, 10940 volume = {39}, 10941 number = {1}, 10942 pages = {A281--A302}, 10943 year = {2016} 10944} 10945 10946@Article{ pavarinoscacchiwidlundzampini2018, 10947 title = {Isogeometric {BDDC} deluxe preconditioners for linear elasticity for isogeometric 10948 analysis}, 10949 author = {Luca F. Pavarino and S. Scacchi and Olof B. Widlund and Stefano Zampini}, 10950 journal = {Mathematical Models and Methods in Applied Sciences}, 10951 volume = {28}, 10952 number = {7}, 10953 pages = {1337--1370}, 10954 year = {2018} 10955} 10956 10957@Article{ bergervergiatwaisman2017, 10958 title = {An overlapping Domain Decomposition preconditioning method for monolithic 10959 solution of shear bands}, 10960 author = {Luc Berger-Vergiat and Haim Waisman}, 10961 journal = {Computer Methods in Applied Mechanics and Engineering}, 10962 volume = {318}, 10963 pages = {33--60}, 10964 year = {2017}, 10965 petsc_uses = {KSP} 10966} 10967 10968@Article{ abhyankarmaldonadosmithzhang2020, 10969 title = {{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics 10970 Simulations}, 10971 author = {S. Abhyankar and G. Betrie and D.A. Maldonado and L.C. McInnes and B. Smith and 10972 H. 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Hansen and 11066 Jung-Han Kimn}, 11067 booktitle = {IEEE 9th Annual Computing and Communication Workshop and Conference (CCWC 2019)}, 11068 note = {Best Paper in Track}, 11069 year = {2019}, 11070 petsc_uses = {KSP} 11071} 11072 11073@MastersThesis{ rinaldo-ceresoli18, 11074 author = {Stefano Guido Rinaldo and Andrea Ceresoli}, 11075 title = {Newton–Krylov–Schwarz Methods for Distributed Power Flow and Related 11076 Applications}, 11077 school = {Politecnico di Milano}, 11078 year = {2018}, 11079 month = apr, 11080 petsc_uses = {KSP} 11081} 11082 11083@Article{ sananschneppmay2016, 11084 title = {Pipelined, Flexible {K}rylov Subspace Methods}, 11085 author = {P. Sanan and S. M. Schnepp and D. A. May}, 11086 journal = {SIAM Journal on Scientific Computing}, 11087 volume = {38}, 11088 number = {5}, 11089 pages = {C441-C470}, 11090 year = {2016}, 11091 doi = {10.1137/15M1049130}, 11092 petsc_uses = {KSP} 11093} 11094 11095@Article{ petscsf2022, 11096 author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and 11097 Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and 11098 Smith, Barry F. and Zampini, Stefano}, 11099 journal = {IEEE Transactions on Parallel and Distributed Systems}, 11100 title = {The {PetscSF} Scalable Communication Layer}, 11101 year = {2022}, 11102 volume = {33}, 11103 number = {4}, 11104 pages = {842-853}, 11105 doi = {10.1109/TPDS.2021.3084070} 11106} 11107 11108@Article{ brandt2000, 11109 title = {General highly accurate algebraic coarsening}, 11110 author = {Achi Brandt}, 11111 journal = {Electronic Transactions on Numerical Analysis}, 11112 volume = {10}, 11113 number = {9680}, 11114 pages = {1--20}, 11115 issn = {10689613}, 11116 year = {2000} 11117} 11118 11119@Article{ dalcinpazklercosimo2011, 11120 title = {Parallel distributed computing using Python}, 11121 author = {Lisandro D. Dalcin and Rodrigo R. Paz and Pablo A. Kler and Alejandro Cosimo}, 11122 journal = {Advances in Water Resources}, 11123 volume = {34}, 11124 number = {9}, 11125 pages = {1124 - 1139}, 11126 note = {New Computational Methods and Software Tools}, 11127 issn = {0309-1708}, 11128 doi = {10.1016/j.advwatres.2011.04.013}, 11129 year = {2011} 11130} 11131 11132@Article{ behnelbradshawcitrodalcinseljebotnsmith2011, 11133 title = {Cython: The Best of Both Worlds}, 11134 author = {Behnel,Stefan and Bradshaw,Robert and Citro,Craig and Dalcin,Lisandro and 11135 Seljebotn,Dag Sverre and Smith,Kurt }, 11136 journal = {Computing in Science \& Engineering}, 11137 volume = {13}, 11138 number = {2}, 11139 pages = {31-39}, 11140 doi = {10.1109/MCSE.2010.118}, 11141 year = {2011} 11142} 11143 11144@Article{ dalcinpazstorti2005, 11145 title = {MPI for Python}, 11146 author = {Lisandro Dalcín and Rodrigo Paz and Mario Storti}, 11147 journal = {Journal of Parallel and Distributed Computing}, 11148 volume = {65}, 11149 number = {9}, 11150 pages = {1108 - 1115}, 11151 issn = {0743-7315}, 11152 doi = {10.1016/j.jpdc.2005.03.010}, 11153 year = {2005} 11154} 11155 11156@Article{ dalcincolliervignalcortescalo2016, 11157 title = {PetIGA: A framework for high-performance isogeometric analysis}, 11158 author = {Lisandro Dalcin and Nathan Collier and P. Vignal and A.M.A. Cortes and Victor M. 11159 Calo}, 11160 journal = {Computer Methods in Applied Mechanics and Engineering}, 11161 volume = {308}, 11162 pages = {151 - 181}, 11163 issn = {0045-7825}, 11164 doi = {10.1016/j.cma.2016.05.011}, 11165 year = {2016} 11166} 11167 11168@Article{ collierpardodalcinpaszynskicalo2012, 11169 title = {The cost of continuity: A study of the performance of isogeometric finite 11170 elements using direct solvers}, 11171 author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M. 11172 Calo}, 11173 journal = {Computer Methods in Applied Mechanics and Engineering}, 11174 volume = {213-216}, 11175 pages = {353 - 361}, 11176 issn = {0045-7825}, 11177 doi = {10.1016/j.cma.2011.11.002}, 11178 year = {2012} 11179} 11180 11181@Article{ collierdalcinpardocalo2013, 11182 title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite 11183 Elements}, 11184 author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo}, 11185 journal = {SIAM Journal on Scientific Computing}, 11186 volume = {35}, 11187 number = {2}, 11188 pages = {A767-A784}, 11189 doi = {10.1137/120881038}, 11190 year = {2013} 11191} 11192 11193@Article{ dunning2017jump, 11194 title = {{JuMP}: a modeling language for mathematical optimization}, 11195 author = {Dunning, Iain and Huchette, Joey and Lubin, Miles}, 11196 journal = {SIAM Review}, 11197 volume = {59}, 11198 number = {2}, 11199 pages = {295--320}, 11200 year = {2017}, 11201 publisher = {SIAM} 11202} 11203 11204@InProceedings{ prudencioschulz2011, 11205 title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for 11206 Estimation, Simulation and Optimization}, 11207 author = {Ernesto E Prudencio and Karl W Schulz}, 11208 booktitle = {European Conference on Parallel Processing}, 11209 pages = {398--407}, 11210 year = {2011} 11211} 11212 11213@Misc{ rol-website, 11214 key = {ROL}, 11215 title = {{Rapid Optimization Library} Website}, 11216 howpublished = {\url{https://trilinos.org/packages/rol}}, 11217 year = {2018} 11218} 11219 11220@Article{ more1994line, 11221 title = {Line search algorithms with guaranteed sufficient decrease}, 11222 author = {Mor{\'e}, Jorge J and Thuente, David J}, 11223 journal = {ACM Transactions on Mathematical Software}, 11224 volume = {20}, 11225 number = {3}, 11226 pages = {286--307}, 11227 year = {1994}, 11228 publisher = {ACM} 11229} 11230 11231@Article{ griewank2000algorithm, 11232 title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or 11233 adjoint mode of computational differentiation}, 11234 author = {Griewank, Andreas and Walther, Andrea}, 11235 journal = {ACM Transactions on Mathematical Software}, 11236 volume = {26}, 11237 number = {1}, 11238 pages = {19--45}, 11239 year = {2000}, 11240 publisher = {ACM} 11241} 11242 11243@Article{ metcalf2011seven, 11244 title = {The seven ages of fortran}, 11245 author = {Metcalf, Michael}, 11246 journal = {Journal of Computer Science \& Technology}, 11247 volume = {11}, 11248 year = {2011} 11249} 11250 11251@Article{ giraldo_2013, 11252 title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified 11253 model of the atmosphere {(NUMA)}}, 11254 author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu}, 11255 journal = {SIAM Journal on Scientific Computing}, 11256 year = {2013}, 11257 number = {5}, 11258 pages = {B1162-B1194}, 11259 volume = {35}, 11260 doi = {10.1137/120876034} 11261} 11262 11263@Article{ constantinescu_tr2016b, 11264 author = {Constantinescu, E.M.}, 11265 title = {Estimating Global Errors in Time Stepping}, 11266 journal = {ArXiv e-prints}, 11267 archiveprefix = {arXiv}, 11268 eprint = {1503.05166}, 11269 primaryclass = {math.NA}, 11270 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70}, 11271 year = {2016}, 11272 month = mar, 11273 adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C}, 11274 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 11275} 11276 11277@Article{ pareschi_2005, 11278 title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems 11279 with Relaxation}, 11280 author = {L. Pareschi and G. Russo}, 11281 journal = {Journal of Scientific Computing}, 11282 year = {2005}, 11283 number = {1}, 11284 pages = {129--155}, 11285 volume = {25} 11286} 11287 11288@Article{ kennedy_2003, 11289 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 11290 author = {C.A. Kennedy and M.H. Carpenter}, 11291 journal = {Appl. Numer. Math.}, 11292 year = {2003}, 11293 number = {1-2}, 11294 pages = {139--181}, 11295 volume = {44}, 11296 doi = {10.1016/S0168-9274(02)00138-1}, 11297 publisher = {Elsevier Science Publishers B. V.} 11298} 11299 11300@Unpublished{ boscarino_tr2011, 11301 title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic 11302 equations in the diffusion limit}, 11303 author = {Boscarino, S. and Pareschi, L. and Russo, G.}, 11304 note = {Arxiv preprint arXiv:1110.4375}, 11305 year = {2011} 11306} 11307 11308@Article{ ascher_1997, 11309 title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential 11310 equations}, 11311 author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri}, 11312 journal = {Applied Numerical Mathematics}, 11313 year = {1997}, 11314 pages = {151--167}, 11315 volume = {25} 11316} 11317 11318@Book{ ascherpetzold1998, 11319 title = {Computer methods for ordinary differential equations and differential-algebraic 11320 equations}, 11321 author = {Uri M Ascher and Linda R Petzold}, 11322 volume = {61}, 11323 publisher = {SIAM}, 11324 year = {1998} 11325} 11326 11327@Article{ colomesbadia2016, 11328 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 11329 equations}, 11330 author = {Oriol Colom{\'e}s and Santiago Badia}, 11331 journal = {International Journal for Numerical Methods in Engineering}, 11332 volume = {105}, 11333 number = {5}, 11334 pages = {372--400}, 11335 year = {2016} 11336} 11337 11338@Article{ sandu_1997, 11339 title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry problems {II}: 11340 {R}osenbrock solvers}, 11341 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 11342 Potra}, 11343 journal = {Atmospheric Environment}, 11344 year = {1997}, 11345 number = {20}, 11346 pages = {3459--3472}, 11347 volume = {31}, 11348 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 11349 task is the integration of the stiff systems of ordinary differential equations 11350 describing the chemical transformations. It is therefore of interest to 11351 systematically search for stiff solvers which can be identified as close to 11352 optimal for atmospheric applications. In this paper we continue our investigation 11353 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 11354 and compare eight solvers on a set of seven box-models used in present day models. 11355 The focus is on Rosenbrock solvers. These turn out to be very well suited for our 11356 application when they are provided with highly efficient sparse matrix techniques 11357 to economize on the linear algebra. Two of the Rosenbrock solvers tested are from 11358 the literature, viz. and 4, and two are new and specially developed for air 11359 quality applications, viz. 3 and 3. } 11360} 11361 11362@Article{ rang_2005, 11363 title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic 11364 equations of index 1}, 11365 author = {Rang, J. and Angermann, L.}, 11366 journal = {BIT Numerical Mathematics}, 11367 year = {2005}, 11368 number = {4}, 11369 pages = {761--787}, 11370 volume = {45}, 11371 publisher = {Springer}, 11372 doi = {10.1007/s10543-005-0035-y} 11373} 11374 11375@article{rang2015improved, 11376 title = {Improved traditional {R}osenbrock--{W}anner methods for stiff {ODE}s and {DAE}s}, 11377 author = {Rang, Joachim}, 11378 journal = {Journal of Computational and Applied Mathematics}, 11379 volume = {286}, 11380 pages = {128--144}, 11381 year = {2015}, 11382 publisher = {Elsevier}, 11383 doi = {10.1016/j.cam.2015.03.010} 11384} 11385 11386@Article{ gottliebketchesonshu2009, 11387 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 11388 title = {{High order strong stability preserving time discretizations}}, 11389 journal = {Journal of Scientific Computing}, 11390 volume = {38}, 11391 number = {3}, 11392 pages = {251--289}, 11393 doi = {10.1007/s10915-008-9239-z}, 11394 year = {2009} 11395} 11396 11397@Article{ ketcheson_2008, 11398 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 11399 Low-Storage Implementations}, 11400 author = {D.I. Ketcheson}, 11401 journal = {SIAM Journal on Scientific Computing}, 11402 year = {2008}, 11403 number = {4}, 11404 pages = {2113--2136}, 11405 volume = {30}, 11406 doi = {10.1137/07070485X}, 11407 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 11408 RungeKutta methods}, 11409 publisher = {SIAM} 11410} 11411 11412@Article{ jansen_2000, 11413 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 11414 equations with a stabilized finite element method}, 11415 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 11416 journal = {Computer Methods in Applied Mechanics and Engineering}, 11417 year = {2000}, 11418 number = {3}, 11419 pages = {305--319}, 11420 volume = {190}, 11421 publisher = {Elsevier} 11422} 11423 11424@Article{ butcher_2007, 11425 title = {Error propagation of general linear methods for ordinary differential equations}, 11426 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 11427 journal = {Journal of Complexity}, 11428 year = {2007}, 11429 number = {4-6}, 11430 pages = {560--580}, 11431 volume = {23}, 11432 abstract = {We discuss error propagation for general linear methods for ordinary differential 11433 equations up to terms of order p+2, where p is the order of the method. These 11434 results are then applied to the estimation of local discretization errors for 11435 methods of order p and for the adjacent order p+1. The results of numerical 11436 experiments confirm the reliability of these estimates. This research has 11437 applications in the design of robust stepsize and order changing strategies for 11438 algorithms based on general linear methods.}, 11439 doi = {10.1016/j.jco.2007.01.009}, 11440 issn = {0885-064X} 11441} 11442 11443@Article{ constantinescu_a2010a, 11444 title = {Extrapolated implicit-explicit time stepping}, 11445 author = {E.M. Constantinescu and A. Sandu}, 11446 journal = {SIAM Journal on Scientific Computing}, 11447 year = {2010}, 11448 number = {6}, 11449 pages = {4452-4477}, 11450 volume = {31}, 11451 comment = {Preprint \# ANL/MCS-P1612-0409}, 11452 doi = {10.1137/080732833} 11453} 11454 11455@InProceedings{ devito2011liszt, 11456 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 11457 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 11458 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 11459 Aiken, Alex and Duraisamy, Karthik and others}, 11460 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 11461 Networking, Storage and Analysis}, 11462 pages = {9}, 11463 year = {2011}, 11464 organization = {ACM} 11465} 11466 11467@Article{ devito2011designing, 11468 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 11469 author = {DeVito, Zachary and Hanrahan, Pat}, 11470 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 11471 year = {2011} 11472} 11473 11474@Misc{ pgasintro, 11475 author = {Tim Stitt}, 11476 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 11477 Model}, 11478 note = {\url{http://cnx.org/content/m20649/latest/}} 11479} 11480 11481@InProceedings{ el2006upc, 11482 title = {UPC: unified parallel C}, 11483 author = {El-Ghazawi, Tarek and Smith, Lauren}, 11484 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 11485 pages = {27}, 11486 year = {2006}, 11487 organization = {ACM} 11488} 11489 11490@InProceedings{ numrich1998co, 11491 title = {Co-Array Fortran for parallel programming}, 11492 author = {Numrich, Robert W and Reid, John}, 11493 booktitle = {ACM Sigplan Fortran Forum}, 11494 volume = {17}, 11495 number = {2}, 11496 pages = {1--31}, 11497 year = {1998}, 11498 organization = {ACM} 11499} 11500 11501@Article{ aiken1997titanium, 11502 title = {Titanium: A high-performance Java dialect}, 11503 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 11504 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 11505 Geoff and Semenzato, Luigi and others}, 11506 year = {1997} 11507} 11508 11509@Article{ charles2005x10, 11510 title = {X10: an object-oriented approach to non-uniform cluster computing}, 11511 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 11512 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 11513 Sarkar, Vivek}, 11514 journal = {Acm Sigplan Notices}, 11515 volume = {40}, 11516 number = {10}, 11517 pages = {519--538}, 11518 year = {2005}, 11519 publisher = {ACM} 11520} 11521 11522@Article{ chamberlain2007parallel, 11523 title = {Parallel programmability and the chapel language}, 11524 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 11525 journal = {International Journal of High Performance Computing Applications}, 11526 volume = {21}, 11527 number = {3}, 11528 pages = {291--312}, 11529 year = {2007}, 11530 publisher = {SAGE Publications} 11531} 11532 11533@InProceedings{ charmppoopsla93, 11534 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 11535 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 11536 editor = {Paepcke, A.}, 11537 fulleditor = {Paepcke, Andreas}, 11538 pages = {91--108}, 11539 month = sep, 11540 year = {1993}, 11541 booktitle = {{Proceedings of OOPSLA'93}}, 11542 publisher = {{ACM Press}} 11543} 11544 11545@InProceedings{ hewitt1973universal, 11546 title = {A universal modular actor formalism for artificial intelligence}, 11547 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 11548 booktitle = {Proceedings of the 3rd international joint conference on Artificial 11549 intelligence}, 11550 pages = {235--245}, 11551 year = {1973}, 11552 organization = {Morgan Kaufmann Publishers Inc.} 11553} 11554 11555@Book{ yonezawa1990abcl, 11556 title = {ABCL: an object-oriented concurrent system}, 11557 author = {Yonezawa, Akinori}, 11558 year = {1990}, 11559 publisher = {MIT press} 11560} 11561 11562@InProceedings{ dally1988object, 11563 title = {Object-oriented concurrent programming in CST}, 11564 author = {Dally, William J and Chien, Andrew A}, 11565 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 11566 applications: Architecture, software, computer systems, and general issues-Volume 11567 1}, 11568 pages = {434--439}, 11569 year = {1988}, 11570 organization = {ACM} 11571} 11572 11573@Article{ grimshaw1993easy, 11574 title = {Easy-to-use object-oriented parallel processing with Mentat}, 11575 author = {Grimshaw, Andrew S.}, 11576 journal = {Computer}, 11577 volume = {26}, 11578 number = {5}, 11579 pages = {39--51}, 11580 year = {1993}, 11581 publisher = {IEEE} 11582} 11583 11584@InProceedings{ gannon1991object, 11585 title = {Object oriented parallelism: pC++ ideas and experiments}, 11586 author = {Gannon, Dennis and Lee, JK}, 11587 booktitle = {Proceedings of}, 11588 pages = {13--23}, 11589 year = {1991} 11590} 11591 11592@InProceedings{ lau1992object, 11593 title = {An object-oriented class library for scalable parallel heuristic search}, 11594 author = {Lau, Wing-cheong and Singh, Vineet}, 11595 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 11596 pages = {252--267}, 11597 year = {1992}, 11598 organization = {Springer} 11599} 11600 11601@Book{ chase1989amber, 11602 title = {The Amber system: Parallel programming on a network of multiprocessors}, 11603 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 11604 Littlefield, Richard}, 11605 volume = {23}, 11606 number = {5}, 11607 year = {1989}, 11608 publisher = {ACM} 11609} 11610 11611@InProceedings{ kaiser2009parallex, 11612 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 11613 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 11614 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 11615 pages = {394--401}, 11616 year = {2009}, 11617 organization = {IEEE} 11618} 11619 11620@TechReport{ ipm, 11621 author = {Barry F. Smith}, 11622 title = {A New Parallel Programming Model for Computer Simulation}, 11623 institution = {Argonne National Laboratory}, 11624 year = {2014}, 11625 number = {ANL/MCS-P5135-0414} 11626} 11627 11628@Article{ groppsnir, 11629 author = {William Gropp and Marc Snir}, 11630 title = {Programming for Exascale Computers}, 11631 journal = {Computing in Science and Engineering}, 11632 volume = {15}, 11633 number = {6}, 11634 issn = {1521-9615}, 11635 year = {2013}, 11636 pages = {27-35}, 11637 doi = {10.1109/MCSE.2013.96}, 11638 publisher = {IEEE Computer Society}, 11639 address = {Los Alamitos, CA} 11640} 11641 11642@Book{ mpi3, 11643 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 11644 author = {Message Passing Interface Forum}, 11645 year = {2012}, 11646 publisher = {High Performance Computing Center Stuttgart (HLRS)} 11647} 11648 11649@Book{ openmp4, 11650 title = {OpenMP Application Program Interface, Version 4.0}, 11651 year = {2013}, 11652 publisher = {OpenMP Architecture Review Board} 11653} 11654 11655@InProceedings{ hartono2009annotation, 11656 title = {Annotation-based empirical performance tuning using {Orio}}, 11657 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 11658 booktitle = {Parallel \& Distributed Processing, 2009. 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Markus}, 12851 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 12852 for {PDE} Based Applications}, 12853 year = {1994}, 12854 institution = {Department of Computer Sciences, Purdue University}, 12855 number = {CSD-TR-94-021} 12856} 12857 12858@Unpublished{ ilu-web-page, 12859 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 12860 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 12861 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 12862} 12863 12864@Unpublished{ doe2k-web-page, 12865 title = {{DOE2000 Initiative} {W}eb page}, 12866 note = {http://www.mcs.anl.gov/DOE2000}, 12867 key = {DOE2000 Initiative} 12868} 12869 12870@Misc{ pvode-web-page, 12871 title = {{PVODE} {W}eb Page}, 12872 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 12873 author = {A. {Hindmarsh et al.}} 12874} 12875 12876@Book{ szyperski97, 12877 author = {Clemens Szyperski}, 12878 title = {Component Software: Beyond Object-Oriented Programming}, 12879 publisher = {ACM Press}, 12880 address = {New York}, 12881 year = {1997} 12882} 12883 12884@Unpublished{ petsc:coloringuse, 12885 title = {Code for computing sparse {J}acobians}, 12886 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12887 institution = {Argonne National Laboratory} 12888} 12889 12890@Unpublished{ petsc:external, 12891 author = {B. F. {Smith et al.}}, 12892 title = {{External Software Used by PETSc}}, 12893 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12894 institution = {Argonne National Laboratory} 12895} 12896 12897@Unpublished{ petsc:use-by-external-packages, 12898 author = {B. F. {Smith et al.}}, 12899 title = {{Software Packages that Use or Interface to PETSc}}, 12900 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 12901 institution = {Argonne National Laboratory} 12902} 12903 12904@Unpublished{ petsc:prizes, 12905 author = {B. F. {Smith et al.}}, 12906 title = {{Prizes Won Using PETSc}}, 12907 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12908 institution = {Argonne National Laboratory} 12909} 12910 12911@Unpublished{ petsc:csgf, 12912 author = {B. F. {Smith et al.}}, 12913 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 12914 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12915 institution = {Argonne National Laboratory} 12916} 12917 12918@Unpublished{ flash-web-page, 12919 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 12920 {W}eb Page}, 12921 note = {http://www.asci.uchicago.edu}, 12922 author = {R. {Rosner et al.}}, 12923 institution = {University of Chicago} 12924} 12925 12926@Unpublished{ esi-web-page, 12927 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 12928 note = {http://z.ca.sandia.gov/esi}, 12929 author = {R. {Clay et al.}} 12930} 12931 12932@Unpublished{ infobus-web-page, 12933 title = {{I}nfo{B}us {W}eb Page}, 12934 note = {http://www.java.sun.com/beans/infobus}, 12935 key = {infobus} 12936} 12937 12938@Unpublished{ xray-web-page, 12939 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 12940 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 12941 note = {http://www.mcs.anl.gov/xray/}, 12942 institution = {Argonne National Laboratory} 12943} 12944 12945@InProceedings{ kohn98, 12946 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 12947 title = {Language Interoperability Mechanisms for High-Performance Scientific 12948 Applications}, 12949 publisher = {SIAM}, 12950 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12951 Scientific and Engineering Computing}, 12952 year = {1999}, 12953 pages = {30-39} 12954} 12955 12956@InProceedings{ kohn01, 12957 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 12958 title = {Divorcing Language Dependencies from a Scientific Software Library}, 12959 publisher = {SIAM}, 12960 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 12961 year = {2001} 12962} 12963 12964@InProceedings{ freitag_jones_plassmann98, 12965 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 12966 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 12967 publisher = {SIAM}, 12968 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12969 Scientific and Engineering Computing}, 12970 year = {1999}, 12971 pages = {215-224} 12972} 12973 12974@Book{ templates, 12975 author = {R. 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Browne}, 12995 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 12996 Techniques}, 12997 institution = {Department of Computer Science, University of Texas at Austin}, 12998 year = {1995} 12999} 13000 13001@Article{ parti, 13002 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 13003 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 13004 Memory Architectures}, 13005 journal = {Journal of Parallel and Distributed Computing}, 13006 year = {1994}, 13007 volume = {22}, 13008 pages = {462--478} 13009} 13010 13011@Article{ mparti, 13012 author = {G. Agrawal and A. Sussman and J. 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Ross}, 13036 publisher = {University of Toronto}, 13037 pages = {379--386}, 13038 year = {1994} 13039} 13040 13041@Article{ cs99, 13042 author = {X.-C. Cai and M. Sarkis}, 13043 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 13044 systems}, 13045 journal = {SIAM J. Scientific Computing}, 13046 year = {1999}, 13047 volume = {21}, 13048 pages = {792-797} 13049} 13050 13051@Article{ cai2003restricted, 13052 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 13053 positive definite linear systems}, 13054 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 13055 journal = {SIAM Journal on Numerical Analysis}, 13056 volume = {41}, 13057 issue = {1}, 13058 pages = {1209--1231}, 13059 year = {2003}, 13060 doi = {10.1137/S0036142901389621} 13061} 13062 13063@TechReport{ caisaad, 13064 author = {Xiao-Chuan Cai and Youcef Saad}, 13065 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 13066 institution = {Army High Performance Computing Research Center, University of Minnesota }, 13067 year = {1993}, 13068 number = {Preprint 93-027 }, 13069 note = {SIAM J. Sci. Comp. 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Merlin}, 13149 title = {Parallel versions of {S}tones strongly implicit algorithm}, 13150 journal = {Concurrency and Computation: Practice and Experience}, 13151 pages = {1049--1062}, 13152 volumne = {13}, 13153 year = {2001} 13154} 13155 13156@Article{ p4-paper, 13157 author = {Ralph Butler and Ewing Lusk}, 13158 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 13159 journal = {Journal of Parallel Computing}, 13160 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 13161 Division preprint P362-0493)}, 13162 year = {1993} 13163} 13164 13165@TechReport{ picl, 13166 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 13167 title = {{PICL}: A portable instrumented communications library}, 13168 institution = {Oak Ridge National Laboratory}, 13169 number = {TM-11130}, 13170 year = {1990}, 13171 key = {PICL} 13172} 13173 13174@TechReport{ upshot, 13175 author = {Virginia Herrarte and Ewing Lusk}, 13176 title = {Studying Parallel Program Behavior with {U}pshot}, 13177 institution = {Argonne National Laboratory}, 13178 number = {ANL-91/15}, 13179 month = aug, 13180 year = {1991}, 13181 key = {Upshot} 13182} 13183 13184@TechReport{ p4-manual, 13185 author = {Ralph Butler and Ewing Lusk}, 13186 title = {User's Guide to the p4 Parallel Programming System}, 13187 institution = {Argonne National Laboratory}, 13188 number = {ANL-92/17}, 13189 month = oct, 13190 year = {1992}, 13191 key = {p4-Manual} 13192} 13193 13194@InProceedings{ oldparti, 13195 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 13196 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 13197 booktitle = {Proceedings of Supercomputing '93}, 13198 pages = {578--587}, 13199 year = {1993} 13200} 13201 13202@Article{ parti2, 13203 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 13204 and J. Saltz}, 13205 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 13206 journal = {ACM SIGPLAN Notices}, 13207 year = {1995}, 13208 pages = {68-79}, 13209 volume = {30}, 13210 number = {8} 13211} 13212 13213@Article{ parti3, 13214 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 13215 title = {Run-Time Parallelization and Scheduling of Loops}, 13216 journal = {IEEE Trans. Computers}, 13217 year = {1991}, 13218 pages = {604-612}, 13219 volume = {40}, 13220 number = {5} 13221} 13222 13223@InProceedings{ disz-lusk:wamtrace, 13224 author = {Terrence Disz and Ewing Lusk}, 13225 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 13226 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13227 year = {1987}, 13228 pages = {46--53} 13229} 13230 13231@InProceedings{ gorlick-kesselman:gauge, 13232 author = {Michael Gorlick and Carl Kesselman}, 13233 title = {Timing {Prolog} programs without Clocks}, 13234 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13235 year = {1996}, 13236 publisher = {Birkhauser} 13237} 13238 13239@TechReport{ aztec, 13240 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 13241 title = {Aztec User's Guide Version 1.1}, 13242 institution = {Sandia National Laboratories}, 13243 month = oct, 13244 year = {1995}, 13245 number = {SAND95/1559} 13246} 13247 13248@TechReport{ aztec2, 13249 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 13250 title = {Official {Aztec} User's Guide Version 2.1}, 13251 institution = {Sandia National Laboratories}, 13252 year = {1999} 13253} 13254 13255@Book{ taylor-chandy:pcn, 13256 author = {Chandy, M. and Taylor, S.}, 13257 title = {An Introduction to Parallel Programming}, 13258 year = {1991}, 13259 publisher = {Jones and Bartlett} 13260} 13261 13262@Book{ foster-taylor:strand, 13263 title = {Strand: New Concepts in Parallel Programming}, 13264 author = {Ian Foster and Stephen Taylor}, 13265 publisher = {Prentice-Hall}, 13266 adress = { Englewood Cliffs, New Jersey}, 13267 year = {1990} 13268} 13269 13270@Article{ aurora, 13271 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 13272 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 13273 Carlsson and A. Ciepielewski and B. Hausman}, 13274 title = {The Aurora OR-Parallel Prolog System}, 13275 journal = {New Generation Computing}, 13276 volume = {7}, 13277 number = {3}, 13278 year = {1990}, 13279 pages = {243--271} 13280} 13281 13282@TechReport{ roo, 13283 author = {E. Lusk and W. McCune and J. Slaney}, 13284 title = {Roo---a Parallel Theorem Prover}, 13285 institution = {Argonne National Laboratory}, 13286 number = {MCS--TM--149}, 13287 year = {1991} 13288} 13289 13290@TechReport{ heath-etheridge:vppp, 13291 author = {M. T. Heath and J. A. Etheridge}, 13292 title = {Visualizing the Performance of Parallel Programs}, 13293 institution = {Oak Ridge National Laboratory}, 13294 number = {ORNL TM-11813}, 13295 year = {1991} 13296} 13297 13298@TechReport{ chem:vis, 13299 author = {Ewing L. Lusk}, 13300 title = {Performance Visualization for Parallel Programs}, 13301 institution = {Argonne National Laboratory}, 13302 number = {ANL/MCS--P287--0192}, 13303 year = {1991}, 13304 note = {(to appear in {\em Theoretica Chimica Acta})} 13305} 13306 13307@TechReport{ picltrace, 13308 author = {P.~H.~Worley}, 13309 title = {A new {PICL} trace file format}, 13310 institution = {Oak Ridge National Laboratory}, 13311 number = {ORNL TM-12125}, 13312 month = jun, 13313 year = {1992} 13314} 13315 13316@InProceedings{ hideo, 13317 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 13318 title = {Inference of Phylogenetic trees using maximum likelihood}, 13319 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 13320 year = {1992}, 13321 pages = {247--262} 13322} 13323 13324@InProceedings{ dw90, 13325 author = {M. Dryja and O. Widlund}, 13326 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 13327 Problems}, 13328 booktitle = {Third International Symposium on Domain Decomposition Methods}, 13329 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 13330 year = {1990}, 13331 pages = {3-21}, 13332 publisher = {SIAM}, 13333 address = {Philadelphia}, 13334 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 13335 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 13336 references, good introduction to the theory. No computations}, 13337 key = {DryjaWidlund90 !AS} 13338} 13339 13340@Unpublished{ rosing, 13341 author = {Matt Rosing and Joel Saltz}, 13342 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 13343 key = {LowLatency}, 13344 note = {manuscript, 1992} 13345} 13346 13347@TechReport{ jp:incomplete, 13348 author = {Mark T. Jones and Paul E. Plassmann}, 13349 title = {An Improved Incomplete {C}holesky Factorization}, 13350 institution = {Argonne National Laboratory}, 13351 address = {Argonne, IL}, 13352 type = {Preprint}, 13353 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 13354 number = {MCS-P206-0191}, 13355 year = {1991}, 13356 key = {jones} 13357} 13358 13359@InCollection{ jp:ima, 13360 author = {Mark Jones and Paul Plassmann}, 13361 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 13362 booktitle = {Graph Theory and Sparse Matrix Computation}, 13363 publisher = {Springer-Verlag}, 13364 series = {The IMA Volumes in Mathematics and Its Applications}, 13365 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 13366 volume = {56}, 13367 year = {1993}, 13368 pages = {229--245} 13369} 13370 13371@Article{ pw98, 13372 author = {M. Pernice and H. F. Walker}, 13373 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 13374 journal = {SIAM J. Sci. Stat. Comput.}, 13375 year = {1998}, 13376 volume = {19}, 13377 pages = {302--318} 13378} 13379 13380@TechReport{ ysmp83, 13381 key = {Eisenstat}, 13382 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13383 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13384 institution = {Department of Computer Science, Yale University}, 13385 number = {YALE/DCS/RR-265}, 13386 month = apr, 13387 year = {1983} 13388} 13389 13390@InBook{ ysmp84, 13391 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13392 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13393 title = {Elliptic Problem Solvers II}, 13394 publisher = {Academic Press}, 13395 pages = {45--52}, 13396 editors = {G. Birkhoff and A. Schoenstadt}, 13397 year = {1984} 13398} 13399 13400@TechReport{ sparsekit, 13401 key = {Saad}, 13402 author = {Youcef Saad}, 13403 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 13404 institution = {Center for Supercomputing Research and Development, University of Illinois at 13405 Urbana-Champaign}, 13406 number = {1029}, 13407 year = {1990} 13408} 13409 13410@TechReport{ pde-user-ref, 13411 author = {Barry F. Smith}, 13412 title = {Extensible {PDE} Solvers Package Users Manual}, 13413 institution = {Argonne National Laboratory}, 13414 month = sep, 13415 year = {1994}, 13416 number = {ANL-93/40}, 13417 key = {Smith94 ! PDE} 13418} 13419 13420@TechReport{ bs-user-ref, 13421 author = {Mark T. Jones and Paul E. Plassmann}, 13422 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 13423 of Sparse Linear Systems}, 13424 institution = {Argonne National Laboratory}, 13425 month = dec, 13426 year = {1995}, 13427 number = {ANL-95/48} 13428} 13429 13430@TechReport{ snes-user-ref, 13431 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 13432 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 13433 institution = {Argonne National Laboratory}, 13434 month = feb, 13435 year = {1995}, 13436 number = {ANL/MCS-TM-193}, 13437 key = {GroppMcInnesSmith95 ! SNES} 13438} 13439 13440@TechReport{ sles-user-ref, 13441 author = {William D. Gropp and Barry F. Smith}, 13442 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 13443 institution = {Argonne National Laboratory}, 13444 month = mar, 13445 year = {1993}, 13446 number = {ANL-93/8}, 13447 key = {GroppSmith93 ! 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Smith}, 13479 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 13480 Methods}, 13481 institution = {Argonne National Laboratory}, 13482 month = aug, 13483 year = {1993}, 13484 number = {ANL-93/30}, 13485 key = {GroppSmith93 ! KSP} 13486} 13487 13488@TechReport{ mpi-chameleon, 13489 author = {William D. Gropp and Ewing Lusk}, 13490 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 13491 institution = {Argonne National Laboratory}, 13492 month = dec, 13493 year = {1992}, 13494 number = {ANL-92/47}, 13495 key = {GroppLusk92 ! MPI} 13496} 13497 13498@TechReport{ blockcomm-fortran, 13499 author = {William D. Gropp}, 13500 title = {Block{C}omm for {F}ortran}, 13501 institution = {Argonne National Laboratory}, 13502 month = may, 13503 year = {1993}, 13504 number = {ANL-93/00 (to appear)}, 13505 key = {Gropp93 ! BlockComm} 13506} 13507 13508@TechReport{ autodocument, 13509 author = {William D. Gropp}, 13510 title = {Automatic documentation of {C} programs}, 13511 institution = {Argonne National Laboratory}, 13512 month = may, 13513 year = {1993}, 13514 number = {ANL-93/00}, 13515 key = {Gropp93 ! Autodoc} 13516} 13517 13518@TechReport{ zipcode, 13519 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 13520 Manfred Morari}, 13521 title = {The {Z}ipcode message-passing system}, 13522 institution = {Lawrence Livermore National Laboratory}, 13523 month = sep, 13524 year = {1992}, 13525 number = {Unpublished}, 13526 key = {Skjellum92 ! Zipcode} 13527} 13528 13529@Article{ paragraph, 13530 author = {Michael T. Heath and Jennifer Etheridge Finger}, 13531 title = {Visualizing performance of parallel programs}, 13532 journal = {IEEE Software}, 13533 volume = {8}, 13534 number = {5}, 13535 month = sep, 13536 year = {1991}, 13537 pages = {29--39}, 13538 key = {Heath91 ! Paragraph} 13539} 13540 13541@Article{ gropp90, 13542 author = {William Gropp and Edward Smith}, 13543 title = {Computational Fluid Dynamics on Parallel Processors}, 13544 journal = {Computers and Fluids}, 13545 volume = {18}, 13546 year = {1990}, 13547 pages = {289--304}, 13548 key = {Gropp90 ! performance} 13549} 13550 13551@Article{ foster92, 13552 author = {Ian Foster and William Gropp and Rick Stevens}, 13553 title = {The parallel scalability of the spectral transform method}, 13554 journal = {Monthly Weather Review}, 13555 volume = {120}, 13556 year = {1992}, 13557 pages = {835--850}, 13558 key = {Foster92 ! performance} 13559} 13560 13561@InBook{ fgn, 13562 author = {R. Freund and G. H. Golub and N. Nachtigal}, 13563 title = {Iterative Solution of Linear Systems}, 13564 series = {Acta Numerica}, 13565 year = {1992}, 13566 publisher = {Cambridge University Press}, 13567 pages = {57--100} 13568} 13569 13570@TechReport{ nachtigal90, 13571 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 13572 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13573 institution = {Massachusetts Institute of Technology}, 13574 month = mar, 13575 year = {1990}, 13576 number = {90-2}, 13577 key = {Nachtigal | Krylov} 13578} 13579 13580@Article{ nachtigal1992fnm, 13581 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13582 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 13583 journal = {SIAM Journal on Matrix Analysis and Applications}, 13584 volume = {13}, 13585 pages = {778}, 13586 year = {1992}, 13587 publisher = {SIAM} 13588} 13589 13590@TechReport{ embree1999descriptive, 13591 title = {How descriptive are {GMRES} convergence bounds}, 13592 author = {Embree, M.}, 13593 year = {1999}, 13594 number = {08}, 13595 institution = {Oxford University Computing Laboratory} 13596} 13597 13598@Article{ vorst92, 13599 author = {H. van der Vorst}, 13600 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 13601 of nonsymmetric linear systems}, 13602 journal = {SIAM J. Sci. Stat. Comput.}, 13603 year = {1992}, 13604 volume = {13}, 13605 pages = {631--644} 13606} 13607 13608@Article{ eisenstat81, 13609 author = {S. Eisenstat}, 13610 title = {Efficient Implementation of a Class of {CG} Methods}, 13611 journal = {SIAM J. Sci. Stat. Comput.}, 13612 year = {1981}, 13613 volume = {2}, 13614 pages = {1--4} 13615} 13616 13617@Manual{ ibm-essl, 13618 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 13619 Reference}, 13620 organization = {IBM}, 13621 year = {1992}, 13622 key = {IBM-ESSL} 13623} 13624 13625@Manual{ ibm-eui, 13626 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 13627 Release 2.0}, 13628 organization = {IBM}, 13629 month = jun, 13630 year = {1994}, 13631 key = {IBM-EUI} 13632} 13633 13634@Manual{ ibm-euih, 13635 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 13636 organization = {IBM}, 13637 author = {Peter Hochschild}, 13638 year = {1993}, 13639 key = {IBM-EUIH} 13640} 13641 13642@TechReport{ mpi, 13643 title = {Document for a Standard Message-Passing Interface}, 13644 author = {Message Passing Interface Forum}, 13645 institution = {University of Tennessee}, 13646 number = {CS-93-214}, 13647 month = nov, 13648 year = {1993}, 13649 key = {MPI Standard} 13650} 13651 13652@Unpublished{ mpi-final-web, 13653 author = {Message Passing Interface Forum}, 13654 title = {{MPI}: A Message-Passing Interface Standard}, 13655 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 13656 year = {1994}, 13657 month = may 13658} 13659 13660@Book{ hockney-jesshope, 13661 author = {R. W. Hockney and C. R. Jesshope}, 13662 title = {Parallel Computers 2}, 13663 publisher = {Adam Hilger}, 13664 year = {1988} 13665} 13666 13667@Book{ cm-fortran, 13668 author = {{Thinking Machines Corporation}}, 13669 title = {Users Manual for CM-Fortran}, 13670 publisher = {Thinking Machines Corporation}, 13671 year = {1993} 13672} 13673 13674@TechReport{ chang93, 13675 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 13676 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 13677 institution = {Yale Department of Computer Science}, 13678 number = {YALEU/DCS/RR-994}, 13679 month = nov, 13680 year = {1993}, 13681 key = {BDD|diag} 13682} 13683 13684@InProceedings{ gropplevine93, 13685 author = {N. Galbreath and W. Gropp and D. Levine}, 13686 title = {Applications-Driven Parallel {I/O}}, 13687 booktitle = {Proceedings of Supercomputing '93}, 13688 year = {1993}, 13689 pages = {462--471} 13690} 13691 13692@Book{ siegle85, 13693 author = {H. J. Siegel}, 13694 title = {Interconnection Networks for Large Scale Parallel Processing}, 13695 publisher = {Lexington Books}, 13696 year = {1985}, 13697 key = {Network Comparison} 13698} 13699 13700@Article{ lawrie75, 13701 author = {D. H. Lawrie}, 13702 title = {Access and alignment of data in an array processor}, 13703 journal = {IEEE Transactions on Computers}, 13704 volume = {C-24}, 13705 number = {12}, 13706 month = dec, 13707 year = {1975}, 13708 pages = {1145--1155}, 13709 key = {Omega Network} 13710} 13711 13712@Book{ knuth1986, 13713 title = {The {\TeX}{Book}}, 13714 author = {Donald Ervin Knuth and Duane Bibby}, 13715 volume = {1993}, 13716 year = {1986}, 13717 publisher = {Addison-Wesley Reading, Massachusetts} 13718} 13719 13720@Book{ lamport86, 13721 author = {Leslie Lamport}, 13722 title = {{LaTeX}: A document preparation system}, 13723 publisher = {Addison-Wesley}, 13724 year = {1986}, 13725 key = {Latex Manual} 13726} 13727 13728@InProceedings{ gropp-lusk:unix-tools, 13729 author = {William Gropp and Ewing Lusk}, 13730 title = {Scalable {U}nix Tools on Parallel Processors}, 13731 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 13732 publisher = {IEEE}, 13733 pages = {56--62} 13734} 13735 13736@InProceedings{ jp:bell_prize, 13737 author = {Mark Jones and Paul Plassmann}, 13738 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 13739 Applications}, 13740 booktitle = {Proceedings of Supercomputing '92}, 13741 publisher = {IEEE Computer Society Press}, 13742 year = {1992}, 13743 pages = {551--560} 13744} 13745 13746@COMMENT{WEB, CWEB references (for doctext)} 13747@TechReport{ web, 13748 author = {Donald E. Knuth}, 13749 title = {The {\tt WEB} system of structured documentation}, 13750 institution = {Computer Science Department, Stanford University}, 13751 year = {1983}, 13752 number = {980}, 13753 month = sep 13754} 13755 13756@Article{ literatepgm, 13757 author = {Donald E. Knuth}, 13758 title = {Literate Programming}, 13759 journal = {Computer Journal}, 13760 year = {1984}, 13761 volume = {27}, 13762 number = {2}, 13763 pages = {91--111} 13764} 13765 13766@Unpublished{ cweb-code, 13767 author = {Silvio Levy and Donald E. Knuth}, 13768 title = {CWEB}, 13769 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 13770} 13771 13772@Article{ jp:scalable, 13773 author = {Mark Jones and Paul Plassmann}, 13774 title = {Scalable Iterative Solution of Sparse Linear Systems}, 13775 journal = {Parallel Computing}, 13776 volume = {20}, 13777 number = {5}, 13778 month = may, 13779 year = {1994}, 13780 pages = {753--773} 13781} 13782 13783@Article{ jp:pcolor, 13784 author = {Mark T. Jones and Paul E. Plassmann}, 13785 title = {A Parallel Graph Coloring Heuristic}, 13786 journal = {SIAM J. Sci. Comput.}, 13787 volume = {14}, 13788 number = {3}, 13789 pages = {654-669}, 13790 year = {1993} 13791} 13792 13793@TechReport{ block_solve, 13794 author = {Mark T. Jones and Paul E. Plassmann}, 13795 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 13796 Sparse Linear Systems}, 13797 institution = {Argonne National Laboratory}, 13798 year = {1992}, 13799 number = {ANL-92/46}, 13800 key = {JonesPlassmann92 ! block_solve} 13801} 13802 13803@InProceedings{ supercond, 13804 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 13805 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 13806 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 13807 Conference}, 13808 month = feb, 13809 year = {1994}, 13810 key = {McInnesPalumbo94 ! superconductivity } 13811} 13812 13813@Unpublished{ preosti:93, 13814 author = {Gianfranco Preosti}, 13815 title = { }, 13816 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 13817 year = {1993}, 13818 key = {preosti93 ! GL-tilt3d} 13819} 13820 13821@Unpublished{ more:93, 13822 author = {Jorge J. Mor\'{e}}, 13823 title = { }, 13824 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 13825 {A}rgonne {N}ational {L}aboratory}, 13826 year = {1993}, 13827 key = {more93 ! MINPACK-2} 13828} 13829 13830@Article{ brownsaad:90, 13831 author = {Peter N. Brown and Youcef Saad}, 13832 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 13833 journal = {SIAM J. Sci. Stat. Comput.}, 13834 year = {1990}, 13835 volume = {11}, 13836 pages = {450-481} 13837} 13838 13839@Book{ using-mpi, 13840 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 13841 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 13842 publisher = {MIT Press}, 13843 year = {1994} 13844} 13845 13846@Book{ using-mpi2, 13847 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 13848 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 13849 publisher = {MIT Press}, 13850 year = {1999} 13851} 13852 13853@Article{ hs:52, 13854 author = {Magnus R. Hestenes and Eduard Steifel}, 13855 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 13856 journal = {J. Research of the National Bureau of Standards}, 13857 year = {1952}, 13858 volume = {49}, 13859 pages = {409-436} 13860} 13861 13862@Article{ so:89, 13863 author = {Peter Sonneveld}, 13864 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 13865 journal = {SIAM J. Sci. Stat. Comput.}, 13866 year = {1989}, 13867 volume = {10}, 13868 pages = {36-52} 13869} 13870 13871@Article{ v:92, 13872 author = {{H. A.} {van der Vorst}}, 13873 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 13874 of nonsymmetric linear systems}, 13875 journal = {SIAM J. Sci. Stat. Comput.}, 13876 volume = {13}, 13877 year = {1992}, 13878 pages = {631-644} 13879} 13880 13881@Article{ f:93, 13882 author = {Roland W. Freund}, 13883 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 13884 Systems}, 13885 journal = {SIAM J. Sci. Stat. Comput.}, 13886 volume = {14}, 13887 year = {1993}, 13888 pages = {470-482} 13889} 13890 13891@Article{ ish:89, 13892 author = {S. Ishizuka}, 13893 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 13894 journal = {Combustion and Flame}, 13895 volume = {75}, 13896 year = {1989}, 13897 pages = {367-379} 13898} 13899 13900@Book{ williams89, 13901 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 13902 author = {F.A. Williams}, 13903 publisher = {Addison-Wesley}, 13904 year = {1989}, 13905 pages = {367-379} 13906} 13907 13908@Book{ ra75, 13909 author = {R. Aris}, 13910 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 13911 publisher = {Oxford}, 13912 year = {1975} 13913} 13914 13915@Book{ bebernes89, 13916 author = {J. Bebernes and D. Eberly}, 13917 title = {Mathematical Problems from Combustion Theory}, 13918 publisher = {Springer-Verlag}, 13919 series = {Applied Mathematical Sciences 83}, 13920 year = {1989} 13921} 13922 13923@InProceedings{ kikuchi89, 13924 author = {F. Kikuchi}, 13925 booktitle = { Computing Methods in Applied Sciences and Engineering}, 13926 editor = {R. Glowinski and J. L. Lions}, 13927 publisher = {Springer-Verlag}, 13928 series = {Lecture Notes in Mathematics}, 13929 title = {Finite element approximations to bifurcation problems of turning point type}, 13930 year = {1977} 13931} 13932 13933@Article{ rg85, 13934 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 13935 title = {Continuation-conjugate Gradient Methods for the Least Squares Solution of 13936 Nonlinear Boundary Problems}, 13937 journal = {SIAM J. Sci. Stat. Comput.}, 13938 volume = {6}, 13939 year = {1985}, 13940 pages = {793-832} 13941} 13942 13943@InProceedings{ whitfield91, 13944 author = {D. Whitfield and L. Taylor}, 13945 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13946 Schemes}, 13947 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 13948 misc = {AIAA-91-1539}, 13949 pages = {134-145}, 13950 year = {1991} 13951} 13952 13953@InProceedings{ quinlan1, 13954 author = {M. Lemke and D. Quinlan}, 13955 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 13956 Architecture-Independent Development of Structured Grid Applications}, 13957 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 13958 publisher = {Springer Verlag}, 13959 year = {1992} 13960} 13961 13962@InProceedings{ quinlan2, 13963 author = {R. Parsons and D. Quinlan}, 13964 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 13965 Computations}, 13966 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 13967 year = {1994} 13968} 13969 13970% ***** Overview of functionality in Diffpack 13971@InBook{ dpoverview, 13972 author = {Bruaset, A. M. and Langtangen, H. P.}, 13973 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13974 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 13975 {Diffpack}}, 13976 publisher = {Birkh{\"{a}}user}, 13977 pages = {61--90}, 13978 year = {1997} 13979} 13980 13981% ***** Short overview of Diffpack 13982@InCollection{ dpoverview2, 13983 author = {Bruaset, A. M. and Langtangen, H. P.}, 13984 editor = {A. Sydow}, 13985 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 13986 and Applied Mathematics}, 13987 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 13988 pages = {553--558}, 13989 volume = {4}, 13990 year = {1997} 13991} 13992 13993% ***** Comprehensive documentation of Diffpack and 13994% associated numerical methods: 13995@Book{ dpbook, 13996 author = {H. P. Langtangen}, 13997 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 13998 Software. Part I}, 13999 series = {Lecture Notes in Computational Science and Engineering}, 14000 publisher = {Springer-Verlag}, 14001 year = {1998} 14002} 14003 14004% ***** Design issues of the linear solvers in Diffpack, serves also as a 14005% collection of examples on O-O in numerical computing 14006@Article{ ambhpl97a, 14007 author = {A. M. Bruaset and H. P. Langtangen }, 14008 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 14009 journal = {Transactions on Mathematical Software}, 14010 volume = {23 }, 14011 pages = {50--80}, 14012 year = {1997} 14013} 14014 14015@Misc{ dpurl, 14016 author = {{Diffpack Web page}}, 14017 howpublished = {\url{http://www.diffpack.com}} 14018} 14019 14020% ***** General intro to object-oriented numerics for "FORTRAN programmers" 14021@InCollection{ oonintro, 14022 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 14023 editor = {D{\ae}hlen, M. and Tveito, A.}, 14024 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14025 title = {Object-Oriented Numerics}, 14026 publisher = {Birkh{\"{a}}user}, 14027 year = {1997} 14028} 14029 14030% ***** Efficiency comparison: BLAS 1, Diffpack, C, 14031% and finite element applications (F77 vs Diffpack) 14032@InCollection{ dpefficiency, 14033 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 14034 H. P. and Miller, C. T.}, 14035 editor = {D{\ae}hlen, M. and Tveito, A.}, 14036 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14037 title = {On the Efficiency of {C++} in Scientific Computing}, 14038 publisher = {Birkh{\"{a}}user}, 14039 pages = {91--118}, 14040 year = {1997} 14041} 14042 14043% ***** Parallel concept in Diffpack: 14044@InCollection{ dpparallel, 14045 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 14046 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 14047 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 14048 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 14049 Simulators}, 14050 publisher = {Springer--Verlag}, 14051 series = {Lecture Notes in Computer Science}, 14052 pages = {161--168}, 14053 year = {1997} 14054} 14055 14056% ***** DD and ML methods in Diffpack: 14057@InCollection{ dpddml, 14058 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 14059 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 14060 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 14061 title = {Domain decomposition and multilevel methods in Diffpack}, 14062 year = {1997} 14063} 14064 14065@InProceedings{ bsca98, 14066 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 14067 Alexander}, 14068 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 14069 Optimization}, 14070 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14071 Scientific and Engineering Computing}, 14072 editor = {Mike Henderson et al.}, 14073 pages = {165-173}, 14074 year = {1998} 14075} 14076 14077@Book{ scalapack-user-guide, 14078 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 14079 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 14080 Stanley and D. Walker and R. C. Whaley}, 14081 title = {Sca{LAPACK} Users' Guide}, 14082 publisher = {SIAM}, 14083 address = {Philadelphia, PA}, 14084 year = {1997} 14085} 14086 14087@InProceedings{ keyes99, 14088 author = {D. E. Keyes}, 14089 title = {How Scalable is Domain Decomposition in Practice?}, 14090 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 14091 Methods}, 14092 editor = {C.-H. Lai et al.}, 14093 publisher = {Domain Decomposition Press, Bergen}, 14094 note = {To appear}, 14095 year = {1999} 14096} 14097 14098@Article{ fun3d, 14099 author = {W. K. Anderson and D. L. Bonhaus}, 14100 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 14101 grids}, 14102 journal = {Computers and Fluids}, 14103 year = {1994}, 14104 volume = {23}, 14105 pages = {1--21} 14106} 14107 14108% ------------------------------------------------------------------------- 14109% ------------------------------------------------------------------------- 14110@Article{ torczon, 14111 author = {Dennis, Jr., J. E. and V.~Torczon}, 14112 title = {Direct Search Methods on Parallel Machines}, 14113 journal = {SIAM J. Optimization}, 14114 volume = {1}, 14115 pages = {448--474}, 14116 year = {1991}, 14117 key = {Torczon !PDS} 14118} 14119 14120@InProceedings{ wt91, 14121 author = {D. L. Whitfield and L. K. Taylor}, 14122 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 14123 Schemes}, 14124 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 14125 misc = {AIAA-91-1539}, 14126 pages = {134-145}, 14127 year = {1991} 14128} 14129 14130@Article{ ew96, 14131 author = {S. C. Eisenstat and H. F. Walker}, 14132 title = {Choosing the forcing terms in an inexact {N}ewton method}, 14133 journal = {SIAM J. Scientific Computing}, 14134 volume = {17}, 14135 year = {1996}, 14136 pages = {16--32} 14137} 14138 14139@Book{ thi93, 14140 author = {{Thinking Machines Corporation}}, 14141 title = {Users Manual for CM-Fortran}, 14142 publisher = {Thinking Machines Corporation}, 14143 year = {1993} 14144} 14145 14146@Book{ mortonmayers94, 14147 author = {K. W. Morton and D. F. Mayers}, 14148 title = {Numerical Solution of Partial Differential Equations}, 14149 publisher = {Press Syndicate of the University of Cambridge}, 14150 year = {1994} 14151} 14152 14153@Book{ heath97, 14154 author = {Michael T. Heath}, 14155 title = {Scientific Computing: An Introductory Survey}, 14156 publisher = {McGraw Hill}, 14157 year = {1997} 14158} 14159 14160@Article{ captools96, 14161 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 14162 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 14163 Performance on the Parallelization of Structured Mesh Codes}, 14164 journal = {Parallel Computing}, 14165 volume = {22}, 14166 pages = {197-226}, 14167 year = {1996} 14168} 14169 14170@Misc{ nastran-web-page, 14171 author = {{MSC Software Corporation}}, 14172 title = {{NASTRAN} {W}eb page}, 14173 howpublished = {\url{http://www.mechsolutions.com/products/nastran/}}, 14174 year = {2024} 14175} 14176 14177@Book{ hpf, 14178 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 14179 Zosel}, 14180 title = {The High Performance Fotran Handbook}, 14181 publisher = {MIT Press}, 14182 year = {1994} 14183} 14184 14185@InProceedings{ keyes98, 14186 author = {D. E. Keyes}, 14187 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 14188 Architectures}, 14189 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 14190 editors = {M. D. Salas and W. K. Anderson}, 14191 ppublisher = {Elsevier}, 14192 year = {1998} 14193} 14194 14195@InProceedings{ pooma-atlas, 14196 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14197 J. V. W. Reynders and M. Tholburn}, 14198 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14199 Applications}, 14200 year = {1995}, 14201 month = dec, 14202 booktitle = {Supercomputing '95 Proceedings} 14203} 14204 14205% --------------------------------------------------------------------------------- 14206% New bib entries for CRPC paper 14207@Misc{ mgnet-web-page, 14208 author = {Craig C. Douglas}, 14209 title = {{MGNet Web page}}, 14210 note = {See {\tt http://\-www.mgnet.org}} 14211} 14212 14213@Misc{ dagh-web-page, 14214 author = {M. Parashar and J. C. Browne}, 14215 title = {{DAGH Web page}}, 14216 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14217} 14218 14219@Misc{ parasol-web-page, 14220 key = {PARASOL}, 14221 title = {{PARASOL Web page}}, 14222 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14223} 14224 14225@Misc{ pooma-web-page, 14226 author = {{POOMA Web page}}, 14227 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14228} 14229 14230@Misc{ mudpack-web-page, 14231 author = {John C. Adams}, 14232 title = {{MUDPACK Web page}}, 14233 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14234} 14235 14236@Misc{ pellpack-web-page, 14237 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14238 title = {{Parallel ELLPACK Web page}}, 14239 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14240} 14241 14242@InProceedings{ pellpack95, 14243 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14244 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14245 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14246 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14247 address = {Albuquerque, NM}, 14248 year = {1995} 14249} 14250 14251@Misc{ nhse-web-page, 14252 author = {{National High-Performance Software Exchange Web page}}, 14253 note = {See {\tt http://\-www.nhse.org}} 14254} 14255 14256@Misc{ doug-web-page, 14257 author = {Mark J. Hagger and Linda Stals}, 14258 title = {{DOUG Web Page}}, 14259 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14260} 14261 14262@TechReport{ doug97, 14263 author = {Mark J. Hagger}, 14264 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14265 institution = {Mathematical Sciences, University of Bath}, 14266 year = {1997}, 14267 number = {9706}, 14268 note = {Advances in Computational Mathematics (to appear)} 14269} 14270 14271@Misc{ ug-web-page, 14272 author = {{UG Web Page}}, 14273 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14274} 14275 14276@Article{ ug97, 14277 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14278 Rentz-Reichert and C. Wieners}, 14279 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14280 journal = {Computing and Visualization in Science}, 14281 year = {1997}, 14282 volume = {}, 14283 pages = {} 14284} 14285 14286@Misc{ vecfem-web-page, 14287 author = {Lutz Grosz}, 14288 title = {{VECFEM Web Page}}, 14289 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14290} 14291 14292@Misc{ atlas-web-page, 14293 author = {R. Clint {Whaley et al.}}, 14294 title = {{ATLAS Web Page}}, 14295 howpublished = {\url{http://math-atlas.sourceforge.net}} 14296} 14297 14298@Misc{ fenics-web-page, 14299 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14300 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14301 title = {{FEniCS Web Page}}, 14302 note = {\url{http://www.fenicsproject.org}}, 14303 year = {2005} 14304} 14305 14306@Misc{ matlab-web-page, 14307 author = {{The} {MathWorks}}, 14308 title = {{Matlab} {Web} page}, 14309 url = {http://www.mathworks.com} 14310} 14311 14312@Misc{ phipac-web-page, 14313 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14314 and D. Lam}, 14315 title = {{PHiPAC Web Page}}, 14316 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14317} 14318 14319@InProceedings{ kelp, 14320 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14321 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14322 booktitle = {Irregular '96}, 14323 year = {1996} 14324} 14325 14326@Unpublished{ kelp-web-page, 14327 author = {Scott Baden}, 14328 title = {{KeLP} {W}eb page}, 14329 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14330} 14331 14332@InProceedings{ hk99, 14333 author = {R. Hornung and S. 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The different versions are examined for efficiency on a computer 14395 architecture which uses vector processing and has pipelined instruction execution. 14396 By using the advanced architectural features of such machines, one can usually 14397 achieve maximum performance, and tremendous improvements in terms of execution 14398 speed can be seen over conventional computers.}, 14399 classification= {723; 921}, 14400 journalabr = {SIAM Rev}, 14401 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 14402 mathematical programming; vector pipeline machine} 14403} 14404 14405@Book{ qv99, 14406 author = {Alfio Quarteroni and Alberto Valli}, 14407 title = {Domain Decomposition Methods for Partial Differential Equations}, 14408 publisher = {Oxford Science Publications}, 14409 address = {Oxford}, 14410 year = {1999} 14411} 14412 14413@Book{ ksv97, 14414 editor = {David E. Keyes and Ahmed Sameh and V. 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Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 14604 and C. Woodward}, 14605 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 14606 journal = {ACM Transactions on Mathematical Software}, 14607 volume = {31}, 14608 number = {3}, 14609 pages = {363--396}, 14610 year = {2005} 14611} 14612 14613@InProceedings{ serban2005cvodes, 14614 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 14615 author = {Serban, Radu and Hindmarsh, Alan C}, 14616 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 14617 Dynamics and Control, Long Beach, CA}, 14618 year = {2005} 14619} 14620 14621@Article{ pvode99, 14622 author = {G. Byrne and A. Hindmarsh}, 14623 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 14624 journal = {Int. J. High Perf. Comput. 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Softw.}, 15683 volume = {31}, 15684 year = {2005}, 15685 pages = {326--350} 15686} 15687 15688@Unpublished{ compass:homepage, 15689 author = {Panagiotis {Spentzouris (PI)}}, 15690 title = {Community Petascale Project for Accelerator Science and Simulation (ComPASS)}, 15691 note = {SciDAC2 project, see \url{https://compass.fnal.gov/}} 15692} 15693 15694@Unpublished{ cmsnf:homepage, 15695 author = {{Todd Allen, Director}}, 15696 title = {{Center for Materials Science of Nuclear Fuel}}, 15697 note = {Energy Frontier Research Center, see 15698 \url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}} 15699} 15700 15701@Unpublished{ dvi-materials:project, 15702 author = {{L.~C.} {McInnes (PI)}}, 15703 title = {Large-Scale Differential Variational Inequalities for Heterogeneous Materials}, 15704 note = {{SciDAC}-e project}, 15705 year = {2011} 15706} 15707 15708@Misc{ scidac:homepage, 15709 author = {{DOE Office of Science}}, 15710 title = {{Scientific Discovery through Advanced Computing}}, 15711 year = {2007}, 15712 howpublished = {\url{http://www.scidac.gov}} 15713} 15714 15715@Misc{ corba, 15716 author = {{Object Management Group}}, 15717 year = {2007}, 15718 title = {{Common Object Request Broker Architecture (CORBA)}}, 15719 howpublished = {\url{http://www.corba.org}} 15720} 15721 15722@Article{ uedge, 15723 author = {T.~D. 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Wilson}, 15745 title = {{BOUT++}: A Framework for Parallel Plasma Fluid Simulations}, 15746 journal = {Computer Physics Communications}, 15747 year = {2009}, 15748 volume = {180}, 15749 issue = {9}, 15750 pages = {1467 -- 1480}, 15751 note = {} 15752} 15753 15754@Article{ tempest, 15755 author = {Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and M.R. Dorr and J.A. Hittinger 15756 and G. Kerbel and W.M. Nevins and T. Rognlien}, 15757 title = {Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST}, 15758 journal = {Bull. Am. Phys. Soc. }, 15759 year = {2005}, 15760 volume = {50}, 15761 number = {86}, 15762 pages = {CP1}, 15763 note = {} 15764} 15765 15766@Article{ ccahpc, 15767 author = {David E. Bernholdt and Benjamin A. Allan and Robert Armstrong and Felipe Bertrand 15768 and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif 15769 and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James 15770 A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia 15771 Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek 15772 Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende 15773 and Theresa L. Windus and Shujia Zhou}, 15774 title = {A Component Architecture for High-Performance Scientific Computing}, 15775 journal = {Intl. J. High-Perf. Computing Appl.}, 15776 volume = {20}, 15777 pages = {163--202}, 15778 year = {2006}, 15779 note = {ACTS Collection special issue} 15780} 15781 15782@Misc{ cca-forum:homepage, 15783 author = {{Common Component Architecture Forum}}, 15784 note = {\url{http://www.cca-forum.org}}, 15785 year = {2010} 15786} 15787 15788@Misc{ petsc:driven-cavity-example, 15789 title = {{PETSc Driven Cavity Example Code}}, 15790 author = {B. F. {Smith et al.}}, 15791 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 15792} 15793 15794@Misc{ petsc-dm:webpage, 15795 author = {B. F. {Smith et al.}}, 15796 title = {{PETSc DM Webpage}}, 15797 howpublished = {\url{https://petsc.org/release/manualpages/DM/}}, 15798 year = {2018} 15799} 15800 15801@Misc{ unic-ref, 15802 author = {Giuseppe Palmiotti}, 15803 title = {{UNIC} Neutronics Software}, 15804 note = {Nuclear Engineering Division, Argonne National Laboratory} 15805} 15806 15807% ----------------------------------------------------------------------- 15808% Model coupling refs 15809@Book{ greve-blatter, 15810 author = {Ralf Greve and Heinz Blatter}, 15811 title = {Dynamics of Ice Sheets and Glaciers}, 15812 series = {Advances in Geophysical and Environmental Mechanics and Mathematics}, 15813 publisher = {Springer}, 15814 year = {2009} 15815} 15816 15817@Misc{ doe-isicles, 15818 key = {ISICLES}, 15819 title = {Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}}, 15820 howpublished = {\url{http://www.csm.ornl.gov/ISICLES/index.html}} 15821} 15822 15823@Article{ safta2011tchem, 15824 title = {TChem-a software toolkit for the analysis of complex kinetic models}, 15825 author = {Safta, Cosmin and Najm, Habib N and Knio, Omar}, 15826 journal = {Sandia Report, SAND2011-3282}, 15827 year = {2011} 15828} 15829 15830@Misc{ chemkin-website, 15831 key = {chemkin}, 15832 title = {ANSYS Chemkin-Pro Website}, 15833 howpublished = {\url{http://www.ansys.com/products/fluids/ansys-chemkin-pro}}, 15834 year = {2017} 15835} 15836 15837@Misc{ mct-website, 15838 key = {MCT}, 15839 title = {{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite}, 15840 howpublished = {\url{http://www.mcs.anl.gov/mct}} 15841} 15842 15843@Article{ larson:05, 15844 author = {Jay Larson and Robert Jacob and Everest Ong}, 15845 title = {{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building 15846 Multi-Physics Parallel Coupled Models}, 15847 journal = {Int. 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Dongarra and C. J. K. Tan}, 15909 series = {Lecture Notes in Computer Science}, 15910 volume = {2073}, 15911 publisher = {Springer-Verlag} 15912} 15913 15914@InProceedings{ lefantzi03, 15915 author = {S. Lefantzi and J. Ray}, 15916 year = {2003}, 15917 title = {A Component-based Scientific Toolkit for Reacting Flows}, 15918 booktitle = {Proc. Second MIT Conference on Computational Fluid and Solid Mechanics}, 15919 volume = {2}, 15920 publisher = {Elsevier} 15921} 15922 15923@Article{ boville98, 15924 author = {B. A. Boville and P. R. Gent}, 15925 title = {The {NCAR} Climate System Model, Version One}, 15926 journal = {Journal of Climate}, 15927 volume = {11}, 15928 year = {1998}, 15929 pages = {1115--1130} 15930} 15931 15932@Misc{ paraschivoiu99, 15933 author = {M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes}, 15934 title = {Multi-domain multi-model formulation for compressible flows: Conservative 15935 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 15936 note = {AIAA Paper 99-0784}, 15937 year = {1999} 15938} 15939 15940@Article{ peszynska, 15941 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 15942 title = {Mortar upscaling for multiphysics flow in porous media}, 15943 journal = {Computational Geosciences} 15944} 15945 15946@TechReport{ wheeler00, 15947 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 15948 title = {A distributed computing portal for coupling multi-physics and multiple domains in 15949 porous media}, 15950 institution = {University of Texas at Austin}, 15951 number = {TICAM 00-03}, 15952 year = {2000} 15953} 15954 15955@TechReport{ peszynska00, 15956 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 15957 title = {Multiphysics Coupling of Codes}, 15958 institution = {University of Texas at Austin}, 15959 number = {TICAM 00-02}, 15960 year = {2000} 15961} 15962 15963@Article{ joshaghanijoodatnakshatrala2019, 15964 title = {A stabilized mixed discontinuous Galerkin formulation for double 15965 porosity/permeability model}, 15966 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 15967 journal = {Computer Methods in Applied Mechanics and Engineering}, 15968 volume = {352}, 15969 pages = {508--560}, 15970 year = {2019} 15971} 15972 15973@InProceedings{ cai99, 15974 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 15975 title = {An explicit multi-model compressible flow formulation based on the full potential 15976 equation and the {Euler} equations on {3D} unstructured meshes}, 15977 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 15978 Methods}, 15979 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 15980 year = {1999} 15981} 15982 15983@Article{ he05, 15984 author = {Yun He and Chris H. Q. Ding}, 15985 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 15986 Architectures}, 15987 year = {2005}, 15988 volume = {19}, 15989 pages = {329--240}, 15990 number = {3}, 15991 journal = {Int. Journal of High Performance Computing Applications} 15992} 15993 15994@InProceedings{ uiuc-rocket-center02, 15995 author = {W. A. Dick and M. T. Heath}, 15996 title = {Whole System Simulation of Solid Propellant Rockets}, 15997 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 15998 month = jul, 15999 year = {2002} 16000} 16001 16002@InProceedings{ toth04, 16003 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 16004 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 16005 Oehmke}, 16006 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 16007 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 16008 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 16009 Sun-Earth Connection}, 16010 year = {2004}, 16011 publisher = {Elsevier}, 16012 pages = {383--397} 16013} 16014 16015@Misc{ csdrm:web, 16016 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 16017 Shepherd}, 16018 title = {{Center for Simulation of Dynamic Response of Materials}}, 16019 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 16020} 16021 16022@Misc{ csar:web, 16023 author = {M. {Heath (Director)}}, 16024 title = {{Center for Simulation of Advanced Rockets}}, 16025 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 16026} 16027 16028@Misc{ csafe:web, 16029 author = {D. {Pershing (Director)}}, 16030 title = {{Center for Simulation of Accidental Fires and Explosions}}, 16031 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 16032} 16033 16034@Misc{ cits:web, 16035 author = {P. {Moin (Director)}}, 16036 title = {{Center for Integrated Turbulence Simulations}}, 16037 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 16038} 16039 16040@Misc{ flash:web, 16041 author = {D. {Lamb (Director)}}, 16042 title = {{Center for Integrated Turbulence Simulations}}, 16043 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 16044} 16045 16046@TechReport{ utah-csafe03, 16047 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 16048 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 16049 Problems, Part 1: Algorithm Development}, 16050 institution = {University of Utah, Center for the Simulation of Accidental Fires and 16051 Explosions}, 16052 year = {2003} 16053} 16054 16055@InBook{ shepherd07, 16056 author = {M. Shepherd and E. Seol and B. FrantzDale}, 16057 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 16058 year = {2007}, 16059 booktitle = {CRC Handbook of Dynamic System Modeling}, 16060 publisher = {Wiley}, 16061 pages = {1--41}, 16062 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 16063} 16064 16065@InProceedings{ cactus02, 16066 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 16067 Radke and Edward Seidel and John Shalf}, 16068 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 16069 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 16070 year = {2002}, 16071 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 16072} 16073 16074@Misc{ cactus:homepage, 16075 author = {G. {Allen et al.}}, 16076 title = {{Cactus Web page}}, 16077 howpublished = {\url{http://cactuscode.org}} 16078} 16079 16080@Misc{ open-grid-forum:web, 16081 key = {{Open Grid Forum}}, 16082 title = {{Open Grid Forum}}, 16083 note = {See \url{http://www.ogf.org}} 16084} 16085 16086@Misc{ nox:web, 16087 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 16088 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 16089 note = {See \url{http://software.sandia.gov/nox}} 16090} 16091 16092@Misc{ chombo:web, 16093 author = {P. {Colella (PI)}}, 16094 title = {{Chombo}}, 16095 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 16096} 16097 16098@Article{ lanzkron96, 16099 author = {P. J. Lanzkron and D. J. Rose and J. T. Wilkes}, 16100 title = {An Analysis of Approximate Nonlinear Elimination}, 16101 journal = {SIAM J. Sci. Comput.}, 16102 volume = {17}, 16103 year = {1996}, 16104 pages = {538--559} 16105} 16106 16107@Article{ jiang95, 16108 author = {J. Jiang and P. Forsyth}, 16109 title = {Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} 16110 Equations}, 16111 journal = {Computers and Fluids}, 16112 volume = {24}, 16113 pages = {753--770}, 16114 year = {1995} 16115} 16116 16117@Article{ young90, 16118 author = {D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant}, 16119 title = {Global Convergence of Inexact {Newton} Methods for Transonic Flow}, 16120 journal = {Int. J. Numer. Methods Fluids}, 16121 volume = {11}, 16122 pages = {1075--1095}, 16123 year = {1990} 16124} 16125 16126@Article{ fishwick04, 16127 author = {Paul A. Fishwick}, 16128 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 16129 to Interrelating Model Structures}, 16130 journal = {SCS Trans. on Simulation}, 16131 note = {Special Issue in Grand Challenges in Computer Simulation}, 16132 year = {2004} 16133} 16134 16135@Article{ fishwick03, 16136 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 16137 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 16138 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 16139 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 16140 year = {2003} 16141} 16142 16143@InProceedings{ kirner00, 16144 author = {T. G. Kirner and V. F. Martins}, 16145 title = {Development of an Information Visualization Tool Using Virtual Reality}, 16146 booktitle = {Proceedings of the 2000 ACM Symposium on Applied Computing}, 16147 year = {2000}, 16148 pages = {604--606} 16149} 16150 16151@InProceedings{ orso03, 16152 author = {A. Orso and J. Jones and M. J. Harrold}, 16153 title = {Visualization of Program-Execution Data for Deployed Software}, 16154 booktitle = {Proceedings of the 2003 ACM Symposium on Software Visualization}, 16155 year = {2003}, 16156 pages = {67--76} 16157} 16158 16159@Book{ tiller01, 16160 author = {M. Tiller}, 16161 title = {Introduction to Physical System Modeling with Modelica}, 16162 series = {Kluwer International Series inEngineering and Computer Science}, 16163 volume = {615}, 16164 publisher = {Kluwer}, 16165 year = {2001} 16166} 16167 16168@Article{ buck94, 16169 author = {J. Buck and S. Ha and E. Lee and D. Messerschmitt}, 16170 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 16171 journal = {Int. Journal of Computer Simulation}, 16172 volume = {4}, 16173 pages = {155--182}, 16174 year = {1994} 16175} 16176 16177@Article{ mu95, 16178 author = {M. Mu and J.R. Rice}, 16179 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 16180 journal = {Comp. Syst. Engr.}, 16181 volume = {6}, 16182 year = {1995}, 16183 pages = {87--95} 16184} 16185 16186@TechReport{ drashansky96, 16187 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 16188 author = {R. Drashansky and A. Joshi and J. R. Rice}, 16189 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 16190 year = {1996} 16191} 16192 16193@Article{ michopoulos05, 16194 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 16195 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 16196 journal = {Journal of Computing and Information Science in Engineering}, 16197 volume = {5}, 16198 issue = {3}, 16199 pages = {198--213}, 16200 year = {2005} 16201} 16202 16203@Article{ dubey09, 16204 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16205 Multiphysics Simulation Code}, 16206 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16207 Siegel and K. Weide}, 16208 journal = {Parallel Computing}, 16209 volume = {35}, 16210 issue = {10 -- 11}, 16211 pages = {512 -- 522}, 16212 year = {2009} 16213} 16214 16215@Book{ bottloring95, 16216 author = {Raoul Bott and Loring W. Tu}, 16217 title = {Differential Forms in Algebraic Topology}, 16218 publisher = {Springer}, 16219 year = {1995} 16220} 16221 16222@Book{ kobayashinomizu96, 16223 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16224 title = {Foundations of Differential Geometry}, 16225 publisher = {Wiley-Interscience}, 16226 year = {1996} 16227} 16228 16229@Article{ hornungkohn02, 16230 author = {Richard D. Hornung and Scott R. Kohn}, 16231 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16232 journal = {Concurrency and Computation: Practice and Experience}, 16233 volume = {14}, 16234 pages = {347--368}, 16235 year = {2002} 16236} 16237 16238@InProceedings{ concepts06, 16239 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16240 Gabriel Dos Reis and Andrew Lumsdaine}, 16241 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16242 booktitle = {Proceedings of OOPSLA 2006}, 16243 year = {2006}, 16244 pages = {???--???} 16245} 16246 16247@Book{ hatcher02, 16248 author = {Hatcher, Allen}, 16249 title = {Algebraic Topology}, 16250 publisher = {Cambridge University Press}, 16251 year = {2002} 16252} 16253 16254@Book{ gammahelmjohnsonvlissides95, 16255 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16256 development, offering timeless and elegant solutions to common problems in 16257 software design. It describes patterns for managing object creation, composing 16258 objects into larger structures, and coordinating control flow between objects. The 16259 book provides numerous examples where using composition rather than inheritance 16260 can improve the reusability and flexibility of code. Note, though, that it's not a 16261 tutorial but a catalog that you can use to find an object-oriented design pattern 16262 that's appropriate for the needs of your particular application--a selection for 16263 virtuoso programmers who appreciate (or require) consistent, well-engineered 16264 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16265 more valuable than ever! 16266 16267 Use the contents of the CD to create your own design documents and reusable 16268 components. The CD contains: 23 patterns you can cut and paste into your own 16269 design documents; sample code demonstrating pattern implementation; complete 16270 Design Patterns content in standard HTML format, with numerous hyperlinked 16271 cross-references; accessed through a standard web browser; Java-based dynamic 16272 search mechanism, enhancing online search capabilities; graphical user environment, 16273 allowing ease of navigation. 16274 16275 First published in 1995, this landmark work on object-oriented software design 16276 presents a catalog of simple and succinct solutions to common design problems. 16277 Created by four experienced designers, the 23 patterns contained herein have 16278 become an essential resource for anyone developing reusable object-oriented 16279 software. In response to reader demand, the complete text and pattern catalog are 16280 now available on CD-ROM. This electronic version of Design Patterns enables 16281 programmers to install the book directly onto a computer or network for use as an 16282 online reference for creating reusable object-oriented software. 16283 16284 The authors first describe what patterns are and how they can help you in the 16285 design process. They then systematically name, explain, evaluate, and catalog 16286 recurring designs in object-oriented systems. All patterns are compiled from 16287 real-world examples and include code that demonstrates how they may be implemented 16288 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16289 already own the book will want the CD to take advantage of its dynamic search 16290 mechanism and ready-to-install patterns.}}, 16291 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16292 citeulike-article-id={115158}, 16293 howpublished = {Hardcover}, 16294 isbn = {0201633612}, 16295 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16296 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16297 four gang gof java mathgamespatterns no-tag object object-orientation 16298 object-oriented of oo-patterns oop oriented pattern patterns programming se 16299 software software-development software-engineering software_design 16300 softwareengineering standard}, 16301 month = jan, 16302 publisher = {{Addison-Wesley Professional}}, 16303 title = {Design Patterns}, 16304 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16305 year = {1995} 16306} 16307 16308@InProceedings{ chaco95, 16309 author = {Bruce Hendrickson and Robert Leland}, 16310 title = {A multilevel algorithm for partitioning graphs}, 16311 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16312 (CDROM)}, 16313 year = {1995}, 16314 isbn = {0-89791-816-9}, 16315 pages = {28}, 16316 location = {San Diego, California, United States}, 16317 doi = {10.1145/224170.224228}, 16318 publisher = {ACM Press}, 16319 address = {New York} 16320} 16321 16322@Book{ aleksandrov98, 16323 author = {Aleksandrov, Pavel S.}, 16324 title = {Combinatorial Topology}, 16325 publisher = {Dover}, 16326 volume = {3}, 16327 year = {1998} 16328} 16329 16330@Book{ steenrod99, 16331 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16332 importance in modern physics--such as in gauge theory. This book, a succinct 16333 introduction to the subject by renown mathematician Norman Steenrod, was the first 16334 to present the subject systematically. 16335 16336 It begins with a general introduction to bundles, including such topics as 16337 differentiable manifolds and covering spaces. The author then provides brief 16338 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16339 using them to study further properties of fibre bundles. The result is a classic 16340 and timeless work of great utility that will appeal to serious mathematicians and 16341 theoretical physicists alike. }}, 16342 author = {Steenrod, Norman}, 16343 citeulike-article-id={712999}, 16344 howpublished = {Paperback}, 16345 isbn = {0691005486}, 16346 keywords = {fibre_bundles topology}, 16347 month = apr, 16348 publisher = {{Princeton University Press}}, 16349 title = {The Topology of Fibre Bundles. (PMS-14)}, 16350 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16351 year = {1999} 16352} 16353 16354@Book{ bredon97, 16355 author = {Bredon, Glen E.}, 16356 title = {Sheaf Theory}, 16357 publisher = {Springer}, 16358 pages = {524}, 16359 series = {Graduate Texts in Mathematics}, 16360 year = {1997} 16361} 16362 16363@TechReport{ tautgesmeyers04, 16364 title = {{MOAB}: A Mesh-Oriented Database}, 16365 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16366 Ernst}, 16367 institution = {Sandia National Laboratories}, 16368 number = {SAND2004-1592}, 16369 month = apr, 16370 year = {2004} 16371} 16372 16373@Article{ tautges04, 16374 author = {Timothy J. Tautges}, 16375 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16376 journal = {Engineering With Computers}, 16377 volume = {20}, 16378 pages = {286--293}, 16379 year = {2004} 16380} 16381 16382@InProceedings{ meyers02, 16383 author = {Ray Meyers et. al}, 16384 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16385 booktitle = {8th International conference on numerical grid generation in computational field 16386 simulations}, 16387 month = jun, 16388 year = {2002} 16389} 16390 16391@InProceedings{ seolshepard05, 16392 author = {E. S. Seol and Mark S. Shephard}, 16393 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16394 Analysis}, 16395 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16396 year = {2005} 16397} 16398 16399@Article{ lishephardbeall2005, 16400 title = {3D anisotropic mesh adaptation by mesh modification}, 16401 author = {Xiangrong Li and Mark S Shephard and Mark W Beall}, 16402 journal = {Computer methods in applied mechanics and engineering}, 16403 volume = {194}, 16404 number = {48-49}, 16405 pages = {4915--4950}, 16406 year = {2005}, 16407} 16408 16409@Article{ lushephardtendulkarbeall2014, 16410 title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry}, 16411 author = {Qiukai Lu and Mark S Shephard and Saurabh Tendulkar and Mark W Beall}, 16412 journal = {Engineering with Computers}, 16413 volume = {30}, 16414 pages = {271--286}, 16415 year = {2014}, 16416} 16417 16418@Article{ beallwalshshephard04, 16419 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16420 title = {A comparison of techniques for geometry access related to mesh generation}, 16421 journal = {Engineering With Computers}, 16422 volume = {20}, 16423 number = {3}, 16424 pages = {210--221}, 16425 year = {2004} 16426} 16427 16428@Article{ careyandersoncarneskirk04, 16429 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16430 Kirk}, 16431 title = {Some aspects of adaptive grid technology related to boundary and interior 16432 layers}, 16433 journal = {Journal of Computational Applied Mathematics}, 16434 volume = {166}, 16435 number = {1}, 16436 pages = {55--86}, 16437 year = {2004} 16438} 16439 16440@PhDThesis{ gralthesis, 16441 author = {Guntram Berti}, 16442 title = {Generic Software Components for Scientific Computing}, 16443 school = {TU Cottbus}, 16444 year = {2000}, 16445 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16446} 16447 16448@Article{ whitehead1949, 16449 title = {Combinatorial homotopy. I}, 16450 author = {John HC Whitehead}, 16451 journal = {Bulletin of the American Mathematical Society}, 16452 volume = {55}, 16453 number = {3. P1}, 16454 pages = {213--245}, 16455 year = {1949}, 16456 publisher = {American Mathematical Society} 16457} 16458 16459@Article{ beylkincoifmanrokhlin91, 16460 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16461 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16462 journal = {Communications on Pure and Applied Mathematics}, 16463 volume = {44}, 16464 pages = {141--183}, 16465 year = {1991} 16466} 16467 16468@Book{ wesseling92, 16469 author = {Pieter Wesseling}, 16470 title = {An Introduction to Multigrid Methods}, 16471 publisher = {John Wiley and Sons}, 16472 year = {1992} 16473} 16474 16475@Book{ grakakos04, 16476 author = {Loukas Grakakos}, 16477 title = {Classical and Modern Fourier Analysis}, 16478 publisher = {Pearson Education}, 16479 address = {New Jersey}, 16480 year = {2004} 16481} 16482 16483@Misc{ hlib-web-page, 16484 key = {HLib}, 16485 title = {{HLib} {Web} page}, 16486 note = {{\texttt{http://www.hlib.org/}}}, 16487 annote = {Hierarchical matrices for fast integral transform} 16488} 16489 16490@Article{ hackbusch99, 16491 author = {Wolfgang Hackbusch}, 16492 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16493 Introduction to {$\mathcal H$}-matrices}, 16494 journal = {Computing}, 16495 volume = {62}, 16496 pages = {89--108}, 16497 year = {1999} 16498} 16499 16500@TechReport{ kay1999green, 16501 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16502 equations}, 16503 author = {Kay, D. and Loghin, D.}, 16504 year = {1999}, 16505 institution = {Oxford University Computing Laboratory}, 16506 number = {99/06} 16507} 16508 16509@Article{ bebendorf2003existence, 16510 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16511 elliptic operators with {$L^\infty$}-coefficients}, 16512 author = {Bebendorf, M. and Hackbusch, W.}, 16513 journal = {Numerische Mathematik}, 16514 volume = {95}, 16515 number = {1}, 16516 pages = {1--28}, 16517 year = {2003}, 16518 publisher = {Springer} 16519} 16520 16521@Article{ hackbusch2005direct, 16522 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16523 H$}-matrix approximation}, 16524 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16525 journal = {Computing and Visualization in Science}, 16526 volume = {8}, 16527 number = {3}, 16528 pages = {179--188}, 16529 year = {2005}, 16530 publisher = {Springer} 16531} 16532 16533@TechReport{ duphof2003, 16534 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16535 Logg and L. R. Scott}, 16536 title = {The {FE}ni{CS} project}, 16537 institution = {Chalmers Finite Element Center Preprint Series}, 16538 number = {2003--21}, 16539 year = {2003} 16540} 16541 16542@Article{ flame01, 16543 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16544 Geijn}, 16545 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16546 journal = {Transactions on Mathematical Software}, 16547 volume = {27}, 16548 number = {4}, 16549 year = {2001}, 16550 pages = {422--455} 16551} 16552 16553@Article{ puschel05, 16554 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16555 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16556 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16557 Nick Rizzolo}, 16558 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16559 journal = {Proceedings of the IEEE}, 16560 volume = {93}, 16561 number = {2}, 16562 year = {2005}, 16563 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16564} 16565 16566@Article{ kirbylogg06, 16567 author = {Robert C. Kirby and Anders Logg}, 16568 title = {A compiler for variational forms}, 16569 journal = {ACM Transactions on Mathematical Software}, 16570 volume = {32}, 16571 number = {3}, 16572 year = {2006}, 16573 issn = {0098-3500}, 16574 pages = {417--444}, 16575 doi = {10.1145/1163641.1163644}, 16576 publisher = {ACM Press}, 16577 address = {New York, NY} 16578} 16579 16580@Article{ kirbylogg07, 16581 author = {Robert C. Kirby and Anders Logg}, 16582 title = {Efficient compilation of a class of variational forms}, 16583 journal = {ACM Transactions on Mathematical Software}, 16584 volume = {33}, 16585 number = {3}, 16586 year = {2007}, 16587 issn = {0098-3500}, 16588 pages = {17}, 16589 doi = {10.1145/1268769.1268771}, 16590 publisher = {ACM Press}, 16591 address = {New York, NY} 16592} 16593 16594@Article{ bankdupont81, 16595 author = {Randolph Bank and Todd Dupont}, 16596 title = {An optimal order process for solving finite element equations}, 16597 journal = {Mathematics of Computation}, 16598 volume = {36}, 16599 pages = {35--51}, 16600 year = {1981} 16601} 16602 16603@TechReport{ adams00, 16604 author = {Mark F. Adams}, 16605 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16606 in solid mechanics}, 16607 institution = {UC Berkeley}, 16608 number = {CSD-00-1103}, 16609 year = {2000}, 16610 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16611} 16612 16613@Article{ bergengradlhuelsemannruede06, 16614 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16615 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16616 journal = {Computing in Science \& Engineering}, 16617 volume = {8}, 16618 number = {6}, 16619 pages = {56--62}, 16620 year = {2006} 16621} 16622 16623@MastersThesis{ brunethesis08, 16624 author = {Peter R. Brune}, 16625 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16626 school = {University of Chicago}, 16627 address = {Chicago, IL}, 16628 year = {2008}, 16629 month = feb 16630} 16631 16632@Article{ arnoldwinther02, 16633 author = {Douglas N. Arnold and Ragnar Winther}, 16634 title = {Mixed finite elements for elasticity}, 16635 journal = {Numerische Mathematik}, 16636 volume = {92}, 16637 number = {3}, 16638 month = sep, 16639 year = {2002}, 16640 pages = {401--419}, 16641 doi = {10.1007/s002110100348} 16642} 16643 16644@Article{ arnoldfalkwinther06, 16645 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16646 title = {Finite element exterior calculus, homological techniques, and applications}, 16647 journal = {Acta Numerica}, 16648 year = {2006}, 16649 volume = {15}, 16650 pages = {1--155}, 16651 publisher = {Cambridge University Press}, 16652 doi = {10.1017/S0962492906210018} 16653} 16654 16655@Article{ kirby04, 16656 author = {Robert C. Kirby}, 16657 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 16658 functions}, 16659 journal = {ACM Transactions on Mathematical Software}, 16660 volume = {30}, 16661 number = {4}, 16662 year = {2004}, 16663 issn = {0098-3500}, 16664 pages = {502--516}, 16665 doi = {10.1145/1039813.1039820}, 16666 publisher = {ACM Press}, 16667 address = {New York, NY} 16668} 16669 16670@Article{ kirby06, 16671 author = {Robert C. Kirby}, 16672 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16673 journal = {ACM Transactions on Mathematical Software}, 16674 volume = {32}, 16675 number = {2}, 16676 year = {2006}, 16677 issn = {0098-3500}, 16678 pages = {223--235}, 16679 doi = {10.1145/1141885.1141889}, 16680 publisher = {ACM Press}, 16681 address = {New York, NY} 16682} 16683 16684@Misc{ bluecrystal08, 16685 author = {{B}lue {C}rystal Cluster}, 16686 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16687 year = {2008}, 16688 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16689} 16690 16691@Article{ beylkin95, 16692 author = {Gregory Beylkin}, 16693 title = {On the Fast Fourier Transform of Functions With Singularities}, 16694 journal = {Applied and Computational Harmonic Analysis}, 16695 volume = {2}, 16696 pages = {363--381}, 16697 year = {1995} 16698} 16699 16700@InProceedings{ riehl08, 16701 author = {Jonathan Riehl}, 16702 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16703 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16704 Development (DSPD'08)}, 16705 address = {Nashville, TN}, 16706 year = {2008} 16707} 16708 16709@Article{ appel85, 16710 author = {Andrew W. Appel}, 16711 date-added = {2008-02-27 12:23:39 +0000}, 16712 date-modified = {2008-02-27 12:24:02 +0000}, 16713 doi = {10.1137/0906008}, 16714 journal = {SIAM Journal on Scientific and Statistical Computing}, 16715 keywords = {treecodes}, 16716 number = {1}, 16717 pages = {85-103}, 16718 publisher = {SIAM}, 16719 title = {An Efficient Program for Many-Body Simulation}, 16720 volume = {6}, 16721 year = {1985} 16722} 16723 16724@Article{ ewald21, 16725 author = {{Ewald}, P.~P.}, 16726 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 16727 journal = {Annalen der Physik}, 16728 year = {1921}, 16729 volume = {369}, 16730 pages = {253-287}, 16731 doi = {10.1002/andp.19213690304}, 16732 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 16733 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16734} 16735 16736@Article{ greengardrokhlin87, 16737 author = {L. Greengard and V. Rokhlin}, 16738 date-added = {2008-02-15 18:43:55 +0000}, 16739 date-modified = {2008-02-26 20:09:11 +0000}, 16740 doi = {10.1016/0021-9991(87)90140-9}, 16741 journal = {J. Comput.\ Phys.}, 16742 keywords = {FMM}, 16743 number = {2}, 16744 pages = {325--348}, 16745 title = {A Fast Algorithm for Particle Simulations}, 16746 url = {citeseer.ist.psu.edu/greengard87fast.html}, 16747 volume = {73}, 16748 year = {1987}, 16749 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 16750} 16751 16752@Article{ greengardrokhlin97, 16753 author = {L. Greengard and V. Rokhlin}, 16754 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 16755 Dimensions}, 16756 journal = {Acta Numerica}, 16757 volume = {6}, 16758 year = {1997}, 16759 pages = {229--269} 16760} 16761 16762@Article{ luchenghuangmccammon06, 16763 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 16764 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 16765 systems}, 16766 journal = {PNAS}, 16767 doi = {10.1073/pnas.0605166103}, 16768 volume = {102}, 16769 number = {51}, 16770 year = {2006}, 16771 pages = {19314--19319} 16772} 16773 16774@Article{ schussnadlereisenberg01, 16775 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 16776 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 16777 from a molecular model}, 16778 journal = {Physical Review E}, 16779 volume = {64}, 16780 number = {3}, 16781 year = {2001} 16782} 16783 16784@Book{ hairerlubichwanner02, 16785 author = {E. Hairer and Ch. Lubich and G. Wanner}, 16786 title = {Geometric Numerical Integration}, 16787 publisher = {Springer-Verlag}, 16788 address = {Berlin Heidelberg}, 16789 year = {2002} 16790} 16791 16792@Article{ holstbakerwang00, 16793 author = {M. Holst and N. Baker and F. Wang}, 16794 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 16795 equation on massively parallel computers}, 16796 journal = {Journal of Computational Chemistry}, 16797 volume = {21}, 16798 year = {2000} 16799} 16800 16801@Book{ hockneyeastwood81, 16802 author = {R. Hockney and J. Eastwood}, 16803 title = {Computer simulation using particles}, 16804 publisher = {McGraw-Hill}, 16805 address = {New York}, 16806 year = {1981} 16807} 16808 16809@Article{ lutydavistironigunsteren94, 16810 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 16811 Gunsteren}, 16812 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 16813 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 16814 journal = {Molecular Simulation}, 16815 volume = {14}, 16816 number = {1}, 16817 year = {1994}, 16818 pages = {11--20} 16819} 16820 16821@Book{ briggshensonmccormick00, 16822 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 16823 title = {A Multigrid Tutorial (2nd ed.)}, 16824 year = {2000}, 16825 isbn = {0-89871-462-1}, 16826 publisher = {Society for Industrial and Applied Mathematics}, 16827 address = {Philadelphia, PA} 16828} 16829 16830@Article{ chartier2003spectral, 16831 title = {Spectral AMGe ($\rho$ AMGe)}, 16832 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 16833 McCormick, S and Ruge, J and Vassilevski, PS}, 16834 journal = {SIAM Journal on Scientific Computing}, 16835 volume = {25}, 16836 number = {1}, 16837 pages = {1--26}, 16838 year = {2003}, 16839 publisher = {SIAM} 16840} 16841 16842@Article{ galvis2010domain, 16843 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 16844 media}, 16845 author = {Galvis, Juan and Efendiev, Yalchin}, 16846 journal = {Multiscale Modeling \& Simulation}, 16847 volume = {8}, 16848 number = {4}, 16849 pages = {1461--1483}, 16850 year = {2010}, 16851 publisher = {SIAM} 16852} 16853 16854@Book{ brennerscott02, 16855 author = {Susanne~C. Brenner and L.~Ridgway Scott}, 16856 title = {The mathematical theory of finite element methods}, 16857 year = {2002}, 16858 isbn = {0-38795-451-1}, 16859 publisher = {Springer}, 16860 pages = {361} 16861} 16862 16863@Book{ trefethenbau97, 16864 author = {Lloyd N. Trefethen and David {Bau, III}}, 16865 title = {Numerical Linear Algebra}, 16866 publisher = {Society for Industrial and Applied Mathematics}, 16867 address = {Philadelphia, PA}, 16868 pages = {xii + 361}, 16869 year = {1997}, 16870 isbn = {0-89871-361-7}, 16871 isbn-13 = {978-0-89871-361-9}, 16872 lccn = {QA184 .T74 1997}, 16873 mrclass = {65-01 (65-02 65Fxx)}, 16874 mrnumber = {MR1444820 (98k:65002)}, 16875 mrreviewer = {Moody T. Chu}, 16876 bibdate = {Wed Jan 07 15:23:19 1998}, 16877 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16878} 16879 16880@Article{ liptonreagan2014, 16881 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16882 author = {Richard J Lipton and Kenneth W Regan}, 16883 pages = {206}, 16884 isbn = {978-0-26202-839-4}, 16885 year = {2014} 16886} 16887 16888@InProceedings{ rhea08, 16889 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16890 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16891 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16892 booktitle = {Proceedings of IEEE/ACM SC '08}, 16893 year = {2008} 16894} 16895 16896@Misc{ bursteddewilcox09, 16897 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16898 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16899 note = {in preparation} 16900} 16901 16902@Article{ skeeltezcanhardy02, 16903 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16904 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16905 journal = {J. Comp. Chem.}, 16906 volume = {23}, 16907 pages = {673--684}, 16908 year = {2002} 16909} 16910 16911@Article{ verschelde99, 16912 author = {Jan Verschelde}, 16913 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16914 homotopy continuation}, 16915 journal = {ACM Trans. Math. Softw.}, 16916 volume = {25}, 16917 number = {2}, 16918 issn = {0098-3500}, 16919 pages = {251--276}, 16920 doi = {10.1145/317275.317286}, 16921 publisher = {ACM}, 16922 address = {New York, NY}, 16923 year = {1999} 16924} 16925 16926@InProceedings{ sommeseverscheldewampler08, 16927 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16928 title = {Solving Polynomial Systems Equation by Equation}, 16929 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16930 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16931 pages = {133--152}, 16932 publisher = {Springer-Verlag}, 16933 year = {2008} 16934} 16935 16936@Article{ phanthientanner77, 16937 author = {N. Phan-Thien and R.~I. Tanner}, 16938 title = {A new constitutive equation derived from network theory}, 16939 journal = {J. Non-Newt. Fluid Mech.}, 16940 volume = {2}, 16941 pages = {353}, 16942 year = {1977} 16943} 16944 16945@Manual{ sage, 16946 key = {SAGE}, 16947 author = {W.\thinspace{}A. Stein and others}, 16948 organization = {The Sage~Development Team}, 16949 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16950 note = {{\tt http://www.sagemath.org}}, 16951 year = {2009} 16952} 16953 16954@Misc{ bateshauensteinsommesewampler06, 16955 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16956 Wampler}, 16957 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16958 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16959} 16960 16961@Article{ archer09, 16962 author = {A. J. Archer}, 16963 collaboration = {}, 16964 title = {Dynamical density functional theory for molecular and colloidal fluids: A 16965 microscopic approach to fluid mechanics}, 16966 publisher = {AIP}, 16967 year = {2009}, 16968 journal = {The Journal of Chemical Physics}, 16969 volume = {130}, 16970 number = {1}, 16971 eid = {014509}, 16972 numpages = {8}, 16973 pages = {014509}, 16974 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 16975 transition; statistical distributions; stochastic processes}, 16976 doi = {10.1063/1.3054633} 16977} 16978 16979@Article{ giesekus1966, 16980 author = {Hanswalter Giesekus}, 16981 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 16982 journal = {Rheologica Acta}, 16983 publisher = {Springer Berlin / Heidelberg}, 16984 volume = {5}, 16985 number = {1}, 16986 month = mar, 16987 year = {1966}, 16988 doi = {10.1007/BF01973575}, 16989 pages = {29-35} 16990} 16991 16992@Article{ baaijens98, 16993 author = {F.P. Baaijens}, 16994 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 16995 journal = {Journal of Non-Newtonian Fluid Mechanics}, 16996 volume = {79}, 16997 year = {1998}, 16998 pages = {361--385} 16999} 17000 17001@Book{ joseph90, 17002 author = {D.~D. Joseph}, 17003 title = {Fluid Dynamics of Viscoelastic Liquids}, 17004 publisher = {Springer}, 17005 address = {New York, NY}, 17006 year = {1990} 17007} 17008 17009@Article{ oldroyd50, 17010 author = {J.~G. Oldroyd}, 17011 title = {On the Formulation of Rheological Equations of State}, 17012 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 17013 Sciences}, 17014 volume = {200}, 17015 year = {1950}, 17016 pages = {523--541} 17017} 17018 17019@InProceedings{ bynasungroppthakur04, 17020 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 17021 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 17022 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 17023 year = {2004} 17024} 17025 17026@Book{ pozrikidis07, 17027 author = {C. Pozrikidis}, 17028 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 17029 publisher = {Kluwer (Springer)}, 17030 pages = {675}, 17031 year = {2001}, 17032 isbn = {0792373510} 17033} 17034 17035@Misc{ kritzkeyesfsp07, 17036 author = {A. Kritz and D. Keyes}, 17037 title = {{Fusion Simulation Project Workshop Report}}, 17038 month = jul, 17039 year = {2007}, 17040 note = {Available via 17041 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 17042} 17043 17044@Misc{ dahlburg02, 17045 author = {J. {Dahlburg (Chair)}}, 17046 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 17047 year = {2002}, 17048 note = {Available via 17049 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 17050} 17051 17052@Misc{ brown08, 17053 author = {D. {Brown (Chair)}}, 17054 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 17055 to the Future}}, 17056 year = {2008}, 17057 howpublished = {Office of Science, U.S. Department of Energy}, 17058 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 17059} 17060 17061@Misc{ crosscutting10, 17062 author = {D. Brown and P. {Messina (Chairs)}}, 17063 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 17064 Exascale}}, 17065 year = {2010}, 17066 howpublished = {Office of Science, U.S. Department of Energy}, 17067 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 17068} 17069 17070@Misc{ extreme-scale-solvers-workshop12, 17071 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 17072 L.C. McInnes and E. Ng and S. Wild}, 17073 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 17074 Architectures}, 17075 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 17076 note = {{Washington, DC}, March 8-9, 2012}, 17077 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 17078 year = {2012} 17079} 17080 17081@Misc{ monizrosner09, 17082 author = {{E. Moniz and R. Rosner}}, 17083 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 17084 and Simulation at the Extreme Scale}}, 17085 month = may, 17086 year = {2009}, 17087 note = {See 17088 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 17089} 17090 17091@Misc{ blanford08, 17092 author = {{R. Blandord (Chair)}}, 17093 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 17094 Computing at the Extreme Scale}}, 17095 month = dec, 17096 year = {2008}, 17097 note = {See 17098 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 17099} 17100 17101@Misc{ exascale07, 17102 author = {H. Simon and T. Zacharia and R. Stevens}, 17103 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 17104 year = {2007}, 17105 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 17106} 17107 17108@Misc{ ascrbreakthroughs08, 17109 author = {{Panel on Recent Significant Advancements in Computational Science}}, 17110 title = {Breakthroughs}, 17111 year = {2008}, 17112 note = {See 17113 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 17114} 17115 17116@Misc{ petsc-rd100-2009, 17117 author = {{R\&D Magazine}}, 17118 title = {{PETSc} {R}\&{D} 100 Award}, 17119 year = {2009}, 17120 note = {See 17121 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 17122} 17123 17124@Article{ compass-scidac08, 17125 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 17126 R. Ryne}, 17127 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 17128 Computational Science for Future Accelerators and Accelerator Technologies}, 17129 journal = {J. Phys.: Conf. Ser.}, 17130 volume = {125}, 17131 year = {2008}, 17132 pages = {012001}, 17133 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 17134} 17135 17136@Article{ compass-amundson-scidac08, 17137 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 17138 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 17139 Stoltz}, 17140 journal = {J. Phys.: Conf. Ser.}, 17141 volume = {125}, 17142 year = {2008} 17143} 17144 17145@InProceedings{ muszala09, 17146 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 17147 Simulations}, 17148 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 17149 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 17150 {(CBHPC 2009)}}, 17151 year = {2009} 17152} 17153 17154@Article{ gaston09, 17155 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 17156 Equations}, 17157 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 17158 journal = {Nuclear Engineering and Design}, 17159 volume = {239}, 17160 number = {10}, 17161 year = {2009}, 17162 pages = {1768 -- 1778} 17163} 17164 17165@Article{ gaston09b, 17166 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 17167 Engineering}, 17168 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 17169 and C. Permann and W. Taitano}, 17170 journal = {J. Phys.: Conf. Ser.}, 17171 volume = {180}, 17172 year = {2009}, 17173 pages = {012012} 17174} 17175 17176@Article{ newman09, 17177 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 17178 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 17179 author = {Chris Newman and Glen Hansen and Derek Gaston}, 17180 journal = {Journal of Nuclear Materials}, 17181 volume = {392}, 17182 issue = {1}, 17183 year = {2009}, 17184 pages = {6 -- 15} 17185} 17186 17187@Misc{ www:fenics, 17188 author = {{FE}ni{CS}}, 17189 title = {{FE}ni{CS} Project}, 17190 howpublished = {\url{http://www.fenics.org/}}, 17191 year = {2018} 17192} 17193 17194@InProceedings{ zwart08, 17195 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 17196 Systems}, 17197 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 17198 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 17199 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 17200 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 17201 booktitle = {Proceedings of ICCS 2008}, 17202 year = {2008} 17203} 17204 17205@Article{ klocknerwarburtonbridgehesthaven09, 17206 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 17207 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 17208 journal = {J. Comput. Phys.}, 17209 volume = {228}, 17210 number = {21}, 17211 year = {2009}, 17212 issn = {0021-9991}, 17213 pages = {7863--7882}, 17214 doi = {10.1016/j.jcp.2009.06.041}, 17215 publisher = {Academic Press Professional}, 17216 address = {San Diego, CA} 17217} 17218 17219@PhDThesis{ rankin99, 17220 author = {Rankin, W. T.}, 17221 keywords = {FMM, parallel FMM}, 17222 school = {Department of Electrical and Computer Engineering, Duke University}, 17223 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17224 year = {1999} 17225} 17226 17227@InProceedings{ warrensalmon93, 17228 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17229 and implemented. The algorithm computes the forces on an arbitrary distribution of 17230 bodies in a time which scales as N log N with the particle number. The accuracy of 17231 the force calculations is analytically bounded, and can be adjusted via a user 17232 defined parameter between a few percent relative accuracy, down to machine 17233 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17234 tree, we identify...}, 17235 address = {New York}, 17236 author = {Warren, Michael S. and Salmon, John K.}, 17237 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17238 citeulike-article-id={580952}, 17239 keywords = {oct-tree}, 17240 pages = {12--21}, 17241 publisher = {ACM}, 17242 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17243 year = {1993}, 17244 doi = {10.1145/169627.169640}, 17245 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17246} 17247 17248@Unpublished{ cruzwccm10, 17249 author = {Felipe A. Cruz}, 17250 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17251 note = {Presentation at WCCM 2010, Sydney Australia}, 17252 year = {2010} 17253} 17254 17255@Article{ mcguffee06, 17256 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17257 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17258 of salt, {pH}, point mutations, and protein concentration in simulations of 17259 1000-molecule systems}, 17260 journal = {Journal of the American Chemical Society}, 17261 volume = {128}, 17262 pages = {12098--12110}, 17263 year = {2006} 17264} 17265 17266@Article{ nilsencaihoylandlangtangen10, 17267 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17268 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17269 in Python}}, 17270 journal = {ArXiv e-prints}, 17271 archiveprefix = {arXiv}, 17272 eprint = {1002.0705}, 17273 primaryclass = {cs.DC}, 17274 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17275 - Programming Languages}, 17276 year = {2010}, 17277 month = feb, 17278 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17279 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17280} 17281 17282@Misc{ mcinnes:siam09:minisymposium, 17283 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17284 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17285 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17286 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17287 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17288 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17289 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17290 Austin).} 17291} 17292 17293@Misc{ mcinnes:fsp-summary:feb2011, 17294 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17295 title = {Solvers and Time Integration Breakout Summary}, 17296 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17297 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17298} 17299 17300@Misc{ dvi-materials:siamcse11, 17301 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17302 Materials}, 17303 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17304 Smith and L. Wang}, 17305 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17306 and Engineering, March 3, 2011} 17307} 17308 17309@Misc{ jamroz:cemm10, 17310 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17311 author = {B. Jamroz and S. Kruger and T. Austin}, 17312 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17313} 17314 17315@Misc{ kruger:feb4-2011, 17316 title = {personal communication}, 17317 author = {S. Kruger}, 17318 note = {February, 2011} 17319} 17320 17321@Article{ elman1996, 17322 author = {H.C. Elman}, 17323 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17324 viscosity}, 17325 journal = {SIAM J. Sci. Comput.}, 17326 volume = {20}, 17327 year = {1996}, 17328 pages = {1299--1316} 17329} 17330 17331@Article{ kayloghinwathen2002, 17332 author = {D. Kay and D. Loghin and A. Wathen}, 17333 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17334 journal = {SIAM J. Sci. Comput.}, 17335 volume = {24}, 17336 year = {2002}, 17337 pages = {237--256} 17338} 17339 17340@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17341 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17342 title = {Block preconditioners based on approximate commutators}, 17343 journal = {SIAM J. Sci. Comput.}, 17344 volume = {27}, 17345 number = {5}, 17346 year = {2006}, 17347 pages = {1651--1668} 17348} 17349 17350@Article{ braesssarazin1997, 17351 author = {Dietrich Braess and Regina Sarazin}, 17352 title = {An efficient smoother for the {Stokes} problem}, 17353 journal = {Applied Numerical Mathematics}, 17354 volume = {23}, 17355 number = {1}, 17356 year = {1997}, 17357 pages = {3--19}, 17358 doi = {10.1016/S0168-9274(96)00059-1} 17359} 17360 17361@Article{ wright2001large, 17362 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17363 author = {Wright, T.G. and Trefethen, L.N.}, 17364 journal = {SIAM Journal on Scientific Computing}, 17365 volume = {23}, 17366 pages = {591}, 17367 year = {2001} 17368} 17369 17370@Misc{ wright2002eigtool, 17371 title = {Eig{T}ool}, 17372 author = {Wright, T.G. and Trefethen, LN}, 17373 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17374 year = {2002} 17375} 17376 17377@Misc{ visit-web-site, 17378 key = {{VisIt}}, 17379 title = {{VisIt web site}}, 17380 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17381 url = {http://wci.llnl.gov/codes/visit/}, 17382 year = {2011} 17383} 17384 17385@Book{ trefethen1996, 17386 title = {Finite difference and spectral methods for ordinary and partial differential 17387 equations}, 17388 author = {Lloyd Nicholas Trefethen}, 17389 year = {1996}, 17390 publisher = {Cornell University-Department of Computer Science and Center for Applied 17391 Mathematics} 17392} 17393 17394@Book{ trefethen2005spectra, 17395 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17396 author = {Trefethen, L.N. and Embree, M.}, 17397 year = {2005}, 17398 publisher = {Princeton University Press} 17399} 17400 17401@Article{ gomez2010isogeometric, 17402 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17403 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17404 journal = {Computer Methods in Applied Mechanics and Engineering}, 17405 volume = {199}, 17406 number = {25-28}, 17407 pages = {1828--1840}, 17408 issn = {0045-7825}, 17409 year = {2010}, 17410 publisher = {Elsevier} 17411} 17412 17413@Article{ gomez2008isogeometric, 17414 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17415 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17416 journal = {Computer Methods in Applied Mechanics and Engineering}, 17417 volume = {197}, 17418 number = {49-50}, 17419 pages = {4333--4352}, 17420 year = {2008}, 17421 publisher = {Elsevier} 17422} 17423 17424@Misc{ fastmath:project, 17425 author = {Lori {Diachin (PI)}}, 17426 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17427 (FASTMath) Institute}}, 17428 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17429} 17430 17431@Misc{ exascale-software:proposal, 17432 author = {Peter {Beckman (PI)}}, 17433 title = {{Exascale Software Center}}, 17434 note = {proposal to DOE} 17435} 17436 17437@Misc{ imex:project, 17438 author = {Barry {Smith (PI)}}, 17439 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17440 Multimodel PDEs}}, 17441 note = {DOE ASCR applied math project} 17442} 17443 17444@Misc{ intel-mic:website, 17445 author = {Intel}, 17446 title = {{Many Integrated Core Architecture}}, 17447 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17448} 17449 17450@Article{ dudson:2009, 17451 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17452 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17453 journal = {Computer Physics Communications}, 17454 volume = {180}, 17455 pages = {1467}, 17456 year = {2009} 17457} 17458 17459@Article{ umansky:2009, 17460 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17461 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17462 journal = {Computer Physics Communications}, 17463 year = {2009}, 17464 volume = {180}, 17465 pages = {887-903} 17466} 17467 17468@Article{ xu:1998, 17469 author = {X.Q. Xu and R.H. Cohen}, 17470 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17471 journal = {Computer Physics Communications}, 17472 year = {1998}, 17473 volume = {36}, 17474 number = {1-2}, 17475 pages = {158} 17476} 17477 17478@Article{ tron:1999, 17479 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17480 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17481 journal = {SIAM Journal on Optimization}, 17482 volume = {9}, 17483 number = {4}, 17484 pages = {1100-1127}, 17485 year = {1999} 17486} 17487 17488@Article{ stubenamg, 17489 author = {K. St\"{u}ben}, 17490 title = {A review of algebraic multigrid}, 17491 journal = {J. Comput. Appl. Math.}, 17492 volume = {128}, 17493 number = {1-2}, 17494 year = {2001}, 17495 issn = {0377-0427}, 17496 pages = {281--309}, 17497 doi = {10.1016/S0377-0427(00)00516-1}, 17498 publisher = {Elsevier Science Publishers B. V.}, 17499 address = {Amsterdam, The Netherlands, The Netherlands} 17500} 17501 17502@Article{ feuchtermg, 17503 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17504 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17505 journal = {Computing and visualization in science}, 17506 publisher = {Springer}, 17507 volume = {6}, 17508 number = {1}, 17509 year = {2003}, 17510 pages = {1--13} 17511} 17512 17513@Article{ chowmgsmoothness, 17514 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17515 only attempts to interpolate in the directions of geometrical smoothness. These 17516 directions are determined by analyzing samples of algebraically smooth error, e. 17517 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17518 consistently nearby in value. In addition, these dierences may be used to dene 17519 interpolation weights. These new ideas may be incorporated into the algebraic 17520 multigrid method. Test results show that the new method can have much lower grid 17521 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17522 author = {Chow, Edmond}, 17523 citeulike-article-id={7675372}, 17524 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17525 journal = {American Journal of Mathematics}, 17526 keywords = {fem, multigrid}, 17527 pages = {197--215}, 17528 posted-at = {2010-08-17 23:29:51}, 17529 priority = {2}, 17530 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17531 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17532 volume = {65}, 17533 year = {2001} 17534} 17535 17536@Article{ jonesamge, 17537 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17538 elements) method based on element agglomeration. In the method, coarse grid 17539 elements are formed by agglomerating fine grid elements. Compatible interpolation 17540 operators are constructed which yield coarse grid basis functions with a minimal 17541 energy property. Heuristics based on interpolation quality measures are used to 17542 guide the agglomeration procedure. The performance of the resulting method is 17543 demonstrated in two-level numerical experiments.}}, 17544 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17545 citeulike-article-id={8598569}, 17546 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17547 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17548 journal = {SIAM Journal on Scientific Computing}, 17549 keywords = {amg, fem, multigrid}, 17550 number = {1}, 17551 pages = {109--133}, 17552 posted-at = {2011-01-13 18:05:55}, 17553 priority = {2}, 17554 publisher = {SIAM}, 17555 title = {{AMGE Based on Element Agglomeration}}, 17556 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17557 volume = {23}, 17558 year = {2001} 17559} 17560 17561@Article{ saad1993, 17562 author = {Saad, Youcef}, 17563 doi = {10.1137/0914028}, 17564 issn = {10648275}, 17565 journal = {SIAM Journal on Scientific Computing}, 17566 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17567 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17568 precondition-,preconditioned conju-,subject classi cations,variable 17569 preconditioners}, 17570 number = {2}, 17571 pages = {461--469}, 17572 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17573 volume = {14}, 17574 year = {1993} 17575} 17576 17577@Misc{ path:homepage, 17578 author = {S. Dirkse and M. Ferris and T. 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Moresi and Shijie Zhong and Michael Gurnis}, 17789 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 17790 viscosity}, 17791 journal = {Physics of the Earth and Planetary Interiors}, 17792 volume = {97}, 17793 pages = {83-–94}, 17794 year = {1996} 17795} 17796 17797@Article{ moresisolomatov95, 17798 author = {Louis N. Moresi and V. S. Solomatov}, 17799 title = {Numerical investigation of {2D} convection with extremely large viscosity 17800 variations}, 17801 journal = {Physics of Fluids}, 17802 volume = {7}, 17803 number = {9}, 17804 pages = {2154-–2162}, 17805 year = {1995} 17806} 17807 17808@Article{ chenmolnar83, 17809 author = {W.-P. Chen and P. 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Watts}, 17829 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 17830 brulee?}, 17831 journal = {GSA Today}, 17832 volume = {16}, 17833 pages = {4–-10}, 17834 year = {2006} 17835} 17836 17837@InProceedings{ yang:brent:2002, 17838 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 17839 Parallel Distributed Memory Architectures}, 17840 author = {Laurence T. Yang and Richard Brent}, 17841 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 17842 for Parallel Processing}, 17843 year = {2002}, 17844 publisher = {IEEE} 17845} 17846 17847@Article{ demmel2008communication, 17848 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 17849 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 17850 journal = {Arxiv preprint arXiv:0808.2664}, 17851 year = {2008} 17852} 17853 17854@Article{ demmel09, 17855 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 17856 title = {Communication-optimal Iterative Methods}, 17857 journal = {Journal of Physics: Conf. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 17927} 17928 17929@Article{ keyesmcinneswoodwardetal13, 17930 title = {Multiphysics Simulations: Challenges and Opportunities}, 17931 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17932 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17933 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17934 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17935 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17936 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17937 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17938 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17939 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17940 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17941 journal = {International Journal of High Performance Computing Applications}, 17942 month = feb, 17943 year = {2013}, 17944 volume = {27}, 17945 number = {1}, 17946 pages = {4--83}, 17947 doi = {10.1177/1094342012468181}, 17948 note = {Special issue}, 17949 abstract = {We consider multiphysics applications from algorithmic and architectural 17950 perspectives, where ``algorithmic'' includes both mathematical analysis and 17951 computational complexity and ``architectural'' includes both software and hardware 17952 environments. Many diverse multiphysics applications can be reduced, en route to 17953 their computational simulation, to a common algebraic coupling paradigm. 17954 Mathematical analysis of multiphysics coupling in this form is not always 17955 practical for realistic applications, but model problems representative of 17956 applications discussed herein can provide insight. A variety of software 17957 frameworks for multiphysics applications have been constructed and refined within 17958 disciplinary communities and executed on leading-edge computer systems. We examine 17959 several of these, expose some commonalities among them, and attempt to extrapolate 17960 best practices to future systems. From our study, we summarize challenges and 17961 forecast opportunities.} 17962} 17963 17964@Misc{ rosner10, 17965 author = {Robert {Rosner (Chair)}}, 17966 title = {{The Opportunities and Challenges of Exascale Computing}}, 17967 year = {2010}, 17968 howpublished = {Office of Science, U.S. Department of Energy}, 17969 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17970} 17971 17972@Misc{ kogge2008exascale, 17973 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 17974 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 17975 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 17976 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 17977 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 17978 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 17979 howpublished = {DARPA}, 17980 year = {2008}, 17981 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 17982} 17983 17984@Misc{ doegrandchallengeworkshops, 17985 key = {Office of Science, U.S. Department of Energy}, 17986 title = {{Scientific Grand Challenges Workshop Series}}, 17987 howpublished = {Office of Science, U.S. Department of Energy, see 17988 \url{http://extremecomputing.labworks.org/workshops.stm}} 17989} 17990 17991@Misc{ lawrence2011, 17992 key = {Lawrence}, 17993 title = {{Ernest Orlando Lawrence Award Winners}}, 17994 howpublished = {U.S. Department of Energy, {\footnotesize 17995 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 17996 year = {2011} 17997} 17998 17999@Article{ murphy2000npi, 18000 title = {{A note on preconditioning for indefinite linear systems}}, 18001 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 18002 journal = {SIAM Journal on Scientific Computing}, 18003 volume = {21}, 18004 number = {6}, 18005 pages = {1969--1972}, 18006 year = {2000}, 18007 publisher = {Philadelphia, PA: SIAM, c1993-} 18008} 18009 18010@Article{ elman2011bouyancy, 18011 title = {Fast iterative solvers for buoyancy driven flow problems}, 18012 journal = {Journal of Computational Physics}, 18013 volume = {230}, 18014 number = {10}, 18015 pages = {3900 - 3914}, 18016 year = {2011}, 18017 note = {}, 18018 issn = {0021-9991}, 18019 doi = {10.1016/j.jcp.2011.02.014}, 18020 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 18021 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 18022 Adaptivity, Preconditioning, Algebraic multigrid} 18023} 18024 18025@Article{ dongarrabeckman11, 18026 author = {J. Dongarra and P. Beckman and et al.}, 18027 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 18028 journal = {Int. J. High Perf. Comput. 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Brannick and Robert D. Falgout}, 18081 journal = {SIAM Journal on Scientific Computing}, 18082 volume = {32}, 18083 number = {3}, 18084 pages = {1393--1416}, 18085 url = {http://epubs.siam.org/doi/10.1137/090772216}, 18086 doi = {10.1137/090772216}, 18087 issn = {1064-8275}, 18088 year = {2010} 18089} 18090 18091@Article{ xu2004energy, 18092 title = {On an energy minimizing basis for algebraic multigrid methods}, 18093 author = {Xu, J. and Zikatanov, L.}, 18094 journal = {Computing and Visualization in Science}, 18095 volume = {7}, 18096 number = {3}, 18097 pages = {121--127}, 18098 year = {2004}, 18099 publisher = {Springer} 18100} 18101 18102@Article{ dblp:journals/toms/bakerhlt09, 18103 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 18104 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 18105 journal = {ACM Trans. Math. 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Sala}, 18128 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 18129 institution = {Sandia National Laboratories}, 18130 year = {2006}, 18131 number = {SAND2006-2649} 18132} 18133 18134@Article{ brannick06, 18135 title = {An energy-based AMG coarsening strategy}, 18136 volume = {13}, 18137 doi = {10.1002/nla.480}, 18138 number = {2-3}, 18139 journal = {Numerical Linear Algebra with Applications}, 18140 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 18141 and Ruge, J}, 18142 year = {2006}, 18143 pages = {133--148} 18144} 18145 18146@Article{ olson10, 18147 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 18148 title = {A new perspective on strength measures in algebraic multigrid}, 18149 journal = {Numerical Linear Algebra with Applications}, 18150 volume = {17}, 18151 number = {4}, 18152 pages = {713--733}, 18153 year = {2010}, 18154 publisher = {John Wiley \& Sons, Ltd.}, 18155 issn = {1099-1506}, 18156 doi = {10.1002/nla.669} 18157} 18158 18159@Article{ olson11, 18160 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 18161 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 18162 Minimization}, 18163 journal = {SIAM J. Sci. 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P.}, 18543 eprint = {arXiv:1002.0705v1}, 18544 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 18545 parallelization of scientific codes by a function-centric approach in 18546 Python.pdf:pdf}, 18547 journal = {Computational Science \& Discovery}, 18548 keywords = {parallel,programming,python,software}, 18549 mendeley-tags = {parallel,programming,python,software}, 18550 pages = {015003}, 18551 publisher = {IOP Publishing}, 18552 title = {{Simplifying the parallelization of scientific codes by a function-centric 18553 approach in Python}}, 18554 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 18555 volume = {3}, 18556 year = {2010} 18557} 18558 18559@Book{ langtangen09, 18560 author = {Hans Petter Langtangen}, 18561 title = {Python Scripting for Computational Science}, 18562 publisher = {Springer}, 18563 series = {Texts in Computational Science and Engineering}, 18564 pages = {784}, 18565 isbn = {3540739157}, 18566 year = {2009} 18567} 18568 18569@Book{ numpyguide, 18570 author = {Travis E. Oliphant}, 18571 title = {Guide to {N}umpy}, 18572 publisher = {Trelgol}, 18573 year = {2008} 18574} 18575 18576@Misc{ pycuda, 18577 author = {Andreas Kl\"ockner}, 18578 title = {{PyCUDA}}, 18579 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 18580 year = {2011} 18581} 18582 18583@Misc{ pyopencl, 18584 author = {Andreas Kl\"ockner}, 18585 title = {{PyOpenCL}}, 18586 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 18587 year = {2011} 18588} 18589 18590@Article{ klockner2012, 18591 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 18592 Paul Ivanov and Ahmed Fasih}, 18593 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 18594 generation}, 18595 journal = {Parallel Computing}, 18596 volume = {38}, 18597 number = {3}, 18598 pages = {157--174}, 18599 year = {2012}, 18600 issn = {0167-8191}, 18601 doi = {10.1016/j.parco.2011.09.001} 18602} 18603 18604%%%%%% Matt Stuff %%%%%% 18605@Article{ morrabozdagknepleyrassvesselinov, 18606 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 18607 author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and 18608 Velimir Vesselinov}, 18609 journal = {Eos}, 18610 volume = {102}, 18611 doi = {10.1029/2021EO159258}, 18612 month = {Jun}, 18613 year = {2021} 18614} 18615 18616@Misc{ knepley:icerm-workshop:2012, 18617 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 18618 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 18619 Models for Large-scale Simulations}, 18620 note = {Workshop sponsored by the Institute for Computational and Experimental Research 18621 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 18622 \url{http://icerm.brown.edu/tw12-1-exascale}}, 18623 year = {2012} 18624} 18625 18626@TechReport{ kirbyknepleyscott04, 18627 author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott}, 18628 title = {Optimal Evaluation of Finite Element Matrices}, 18629 type = {Technical Report}, 18630 number = {TR-2004-04}, 18631 institution = {University of Chicago}, 18632 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}, 18633 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}}, 18634 pages = {14}, 18635 month = may, 18636 year = {2004} 18637} 18638 18639@TechReport{ kirbyknepleyscott10, 18640 author = {Robert C. Kirby and Matthew G. Knepley and L. 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Yuen and Huai 18677 Zhang and Yaolin Shi}, 18678 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 18679 strongly variable viscosity based on {Matlab} and {CUDA}}, 18680 type = {Research Report}, 18681 number = {UMSI 2011/33}, 18682 institution = {University of Minnesota Supercomputing Institute}, 18683 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 18684 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 18685 month = mar, 18686 year = {2011} 18687} 18688 18689@InProceedings{ zheng2010, 18690 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai 18691 Zhang and Yaolin Shi}, 18692 title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients}, 18693 booktitle = {Eos Transactions of the AGU}, 18694 organization = {American Geophysical Union}, 18695 note = {Fall Meeting Supplemental, Abstract IN41A-1350}, 18696 year = {2010} 18697} 18698 18699@InCollection{ terrelkirbyknepleyscott12, 18700 author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott 18701 and Garth N. Wells}, 18702 title = {Finite elements for incompressible fluids}, 18703 editors = {A. Logg and K.A. Mardal and G. N. 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Terrel}, 18727 title = {Discrete optimization of finite element matrix evaluation}, 18728 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18729 booktitle = {Automated solutions of differential equations by the finite element method}, 18730 series = {Lecture Notes in Computational Science and Engineering}, 18731 volume = {84}, 18732 pages = {385--397}, 18733 publisher = {Springer-Verlag}, 18734 year = {2012} 18735} 18736 18737@InCollection{ kirby12, 18738 author = {Robert C. Kirby}, 18739 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 18740 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18741 booktitle = {Automated solutions of differential equations by the finite element method}, 18742 series = {Lecture Notes in Computational Science and Engineering}, 18743 volume = {84}, 18744 publisher = {Springer-Verlag}, 18745 year = {2012} 18746} 18747 18748@Article{ brownconveryhotesknepleypetropolous1993, 18749 author = {Robert W. 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23586 23587@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 23588 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 23589 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 23590 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 23591 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 23592 pages = {1103}, 23593 year = {2018} 23594} 23595 23596@InProceedings{ barralangeloudiskramergormanpiggott2018, 23597 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 23598 modelling}, 23599 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 23600 and Matthew D Piggott}, 23601 booktitle = {EGU General Assembly Conference Abstracts}, 23602 volume = {20}, 23603 pages = {19168}, 23604 year = {2018} 23605} 23606 23607@Article{ principe2009, 23608 title = {{Mathematical models for thermally coupled low speed flows}}, 23609 author = {Javier Principe and Ramon Codina}, 23610 journal = {Advances in Theoretical and Applied Mechanics}, 23611 volume = {2}, 23612 number = {1-4}, 23613 pages = {93--112}, 23614 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 23615 year = {2009} 23616} 23617 23618@Book{ vandervorst2003, 23619 title = {Iterative {K}rylov Methods for Large Linear Systems}, 23620 author = {van der Vorst, H.}, 23621 isbn = {9780521818285}, 23622 publisher = {Cambridge University Press}, 23623 year = {2003} 23624} 23625 23626@Book{ peres2006, 23627 author = {Asher Peres}, 23628 title = {Quantum theory: concepts and methods}, 23629 volume = {57}, 23630 publisher = {Springer Science \& Business Media}, 23631 year = {2006} 23632} 23633 23634@Book{ kuttler2012, 23635 title = {Linear algebra: theory and applications}, 23636 author = {Kenneth Kuttler}, 23637 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 23638 year = {2012} 23639} 23640 23641@Book{ elman_silvester_wathen_2014, 23642 place = {Oxford}, 23643 title = {Finite elements and fast iterative solvers: with applications in incompressible 23644 fluid dynamics}, 23645 publisher = {Oxford University Press}, 23646 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 23647 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 23648 year = {2014} 23649} 23650 23651@Article{ alametal2007, 23652 title = {An evaluation of the ORNL Cray XT3}, 23653 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 23654 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 23655 journal = {International Journal of High Performance Computing Applications}, 23656 volume = {22}, 23657 number = {1}, 23658 pages = {52--80}, 23659 doi = {10.1177/1094342007085019}, 23660 year = {2007} 23661} 23662 23663@Article{ plazacarey2000, 23664 title = {Local refinement of simplicial grids based on the skeleton}, 23665 author = {Plaza, A. and Carey, Graham F.}, 23666 journal = {Applied Numerical Mathematics}, 23667 doi = {10.1016/S0168-9274(99)00022-7}, 23668 issn = {01689274}, 23669 volume = {32}, 23670 number = {2}, 23671 pages = {195--218}, 23672 year = {2000} 23673} 23674 23675@Article{ carsonstrakos2020, 23676 title = {On the cost of iterative computations}, 23677 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 23678 journal = {Phil. Trans. R. Soc. A}, 23679 volume = {378}, 23680 number = {20190050}, 23681 doi = {10.1098/rsta.2019.0050}, 23682 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 23683 year = {2020} 23684} 23685 23686@Article{ schoberl1999, 23687 title = {Multigrid methods for a parameter dependent problem in primal variables}, 23688 author = {Joachim Sch{\"o}berl}, 23689 journal = {Numerische Mathematik}, 23690 volume = {84}, 23691 number = {1}, 23692 pages = {97--119}, 23693 year = {1999} 23694} 23695 23696@Article{ wuleexuzikatanov2008, 23697 title = {Convergence analysis on iterative methods for semidefinite systems}, 23698 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 23699 journal = {Journal of Computational Mathematics}, 23700 pages = {797--815}, 23701 year = {2008} 23702} 23703 23704@Article{ maierrannacher2016, 23705 title = {Duality-based adaptivity in finite element discretization of heterogeneous 23706 multiscale problems}, 23707 author = {Maier, Matthias and Rannacher, Rolf}, 23708 journal = {Journal of Numerical Mathematics}, 23709 volume = {24}, 23710 number = {3}, 23711 pages = {167--187}, 23712 year = {2016} 23713} 23714 23715@Article{ maierrannacher2018, 23716 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23717 multiscale problems}, 23718 author = {Maier, Matthias and Rannacher, Rolf}, 23719 journal = {Multiscale Modeling \& Simulation}, 23720 volume = {16}, 23721 number = {1}, 23722 pages = {412--428}, 23723 year = {2018} 23724} 23725 23726@Article{ margetismaierluskin2017, 23727 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23728 metamaterial sheet}, 23729 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23730 journal = {Studies in Applied Mathematics}, 23731 volume = {139}, 23732 number = {4}, 23733 pages = {599--625}, 23734 year = {2017} 23735} 23736 23737@Article{ maiermargetisluskin2017b, 23738 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23739 approximation and validation}, 23740 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23741 journal = {Journal of Computational Physics}, 23742 volume = {339}, 23743 pages = {126--145}, 23744 year = {2017} 23745} 23746 23747@Article{ maiermargetisluskin2018, 23748 title = {Generation of surface plasmon-polaritons by edge effects}, 23749 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23750 journal = {Communications in Mathematical Sciences}, 23751 volume = {16}, 23752 number = {1}, 23753 pages = {77--95}, 23754 url = {http://arxiv.org/abs/1702.00848}, 23755 year = {2018} 23756} 23757 23758@Article{ maiermattheakiskaxirasluskinmargetis2018, 23759 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23760 metamaterials}, 23761 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23762 Mitchell and Margetis, Dionisios}, 23763 journal = {Physical Review B}, 23764 volume = {97}, 23765 number = {3}, 23766 pages = {035307}, 23767 year = {2018} 23768} 23769 23770@Article{ maiermattheakiskaxirasluskinmargetis2019, 23771 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23772 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23773 Mitchell and Margetis, Dionisios}, 23774 journal = {Proceedings of the Royal Society A}, 23775 volume = {475}, 23776 number = {2230}, 23777 pages = {20190220}, 23778 year = {2019} 23779} 23780 23781@Article{ maiermargetisluskin2020, 23782 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23783 two scales}, 23784 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23785 journal = {Physical Review B}, 23786 volume = {102}, 23787 number = {7}, 23788 pages = {075308}, 23789 year = {2020} 23790} 23791 23792@Article{ margetismaierstauberlowluskin2020, 23793 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 23794 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 23795 Luskin, Mitchell}, 23796 journal = {Journal of Physics A: Mathematical and Theoretical}, 23797 volume = {53}, 23798 number = {5}, 23799 pages = {055201}, 23800 year = {2020} 23801} 23802 23803@Article{ maiermargetismellet2020, 23804 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 23805 structures}, 23806 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 23807 journal = {Journal of Computational and Applied Mathematics}, 23808 volume = {377}, 23809 pages = {112909}, 23810 year = {2020} 23811} 23812 23813@Article{ maierkronbichler2021, 23814 title = {Efficient parallel 3D computation of the compressible Euler equations with an 23815 invariant-domain preserving second-order finite-element scheme}, 23816 author = {Maier, Matthias and Kronbichler, Martin}, 23817 journal = {ACM Transactions on Parallel Computing}, 23818 volume = {8}, 23819 number = {3}, 23820 pages = {1--30}, 23821 year = {2021} 23822} 23823 23824@Article{ guermondmaierpopovtomas2021, 23825 title = {Second-order invariant domain preserving approximation of the compressible 23826 Navier--Stokes equations}, 23827 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 23828 journal = {Computer Methods in Applied Mechanics and Engineering}, 23829 volume = {375}, 23830 pages = {113608}, 23831 year = {2021} 23832} 23833 23834@Article{ liliptonmaier2021, 23835 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 23836 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 23837 eprint = {2009.12166}, 23838 archiveprefix = {arXiv}, 23839 primaryclass = {phys.optics}, 23840 year = {2021} 23841} 23842 23843@Article{ songmaierluskin2020, 23844 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 23845 gradient-index graphene waveguides}, 23846 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23847 journal = {Journal of Computational Physics}, 23848 volume = {423}, 23849 pages = {109871}, 23850 year = {2020} 23851} 23852 23853@Article{ songmaierluskin2019, 23854 title = {Adaptive finite element simulations of waveguide configurations involving 23855 parallel 2D material sheets}, 23856 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23857 journal = {Computer Methods in Applied Mechanics and Engineering}, 23858 volume = {351}, 23859 pages = {20--34}, 23860 year = {2019} 23861} 23862 23863% 23864% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23865% 23866% 23867@Unpublished{ rob1, 23868 author = {Rob Kunz}, 23869 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23870 State University}, 23871 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23872 sponsors = {U.S. Navy, NRC}, 23873 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23874 simulations, including lake warming by power plants}, 23875 dates = {Oct 3 and 4, 2002}, 23876 email = {rfk@wt.arl.psu.edu} 23877} 23878 23879@Unpublished{ au1, 23880 author = {Feng Wang and William Appelbe}, 23881 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23882 url = {http://www.vpac.org}, 23883 sponsors = { }, 23884 note = {Using PETSc for a Variety of Geophysical Simulations}, 23885 dates = {Nov 22, 2002} 23886} 23887 23888@Unpublished{ carl1, 23889 author = {Carl Sovinec}, 23890 institution = {Applied Physics, University of Wisconsin}, 23891 url = {http://nimrodteam.org}, 23892 sponsors = {DOE Office of Fusion Research}, 23893 note = {Investigating using PETSc for NIMROD}, 23894 dates = {Nov 21, 2002}, 23895 email = {sovinec@engr.wisc.edu} 23896} 23897 23898@Unpublished{ au1b, 23899 author = {Pablo Carrica and Robert Wilson}, 23900 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23901 url = {http://}, 23902 sponsors = {Office of Naval Research}, 23903 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23904 dates = {Sept, 2002}, 23905 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23906} 23907 23908% ------------------- TAO References ---------------------- 23909@Article{ benson:2001:csp, 23910 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 23911 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 23912 journal = {{ACM} Transactions on Mathematical Software}, 23913 volume = {27}, 23914 number = {3}, 23915 month = sep, 23916 year = {2001}, 23917 pages = {361--376} 23918} 23919 23920@TechReport{ tao-user-ref-2000, 23921 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 23922 title = {{TAO} Users Manual}, 23923 year = {2000}, 23924 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23925 number = {ANL/MCS-TM-242}, 23926 note = {See \url{http://www.mcs.anl.gov/tao}} 23927} 23928 23929% ------------------- Optimization References ---------------------- 23930@Book{ optguide93, 23931 title = {Optimization Software Guide}, 23932 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 23933 publisher = {SIAM Publications}, 23934 address = {Philadelphia}, 23935 year = {1993} 23936} 23937 23938@InProceedings{ more84, 23939 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 23940 Hillstrom}, 23941 title = {The {MINPACK} Project}, 23942 booktitle = {Sources and Development of Mathematical Software}, 23943 editor = {Wayne R. Cowell}, 23944 year = {1984}, 23945 pages = {88--111} 23946} 23947 23948@Article{ steihaug:83, 23949 author = {Trond Steihaug}, 23950 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 23951 journal = {SIAM J. Numer. Anal.}, 23952 volume = {20}, 23953 year = {1983}, 23954 pages = {626--637}, 23955 key = {steihaug92 ! trust_region} 23956} 23957 23958@TechReport{ minpack2test, 23959 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 23960 title = {The {MINPACK-2} Test Problem Collection}, 23961 institution = {Argonne National Laboratory}, 23962 year = {1991}, 23963 number = {ANL/MCS-TM-150}, 23964 key = {more91 ! MINPACK-2} 23965} 23966 23967@TechReport{ hohmann:94, 23968 author = {Andreas Hohmann}, 23969 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 23970 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 23971 year = {1994}, 23972 number = {SC-94-4}, 23973 key = {Hohmann94} 23974} 23975 23976@TechReport{ meza:94, 23977 author = {Juan C. Meza}, 23978 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 23979 institution = {Sandia National Laboratory}, 23980 year = {1994}, 23981 number = {SAND94-8225}, 23982 key = {Meza94} 23983} 23984 23985@Book{ dennis:83, 23986 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 23987 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 23988 publisher = {Prentice-Hall, Inc.}, 23989 address = {Englewood Cliffs, NJ}, 23990 year = {1983} 23991} 23992 23993@TechReport{ more:92, 23994 author = {Jorge J. Mor\'{e} and David Thuente}, 23995 title = {Line search algorithms with guaranteed sufficient decrease}, 23996 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23997 year = {1992}, 23998 number = {MCS-P330-1092} 23999} 24000 24001@Article{ more-toraldo, 24002 author = {Jorge J. Mor\'e and G. Toraldo}, 24003 journal = {SIOPT}, 24004 pages = {93--113}, 24005 title = {On the solution of large quadratic programming problems with bound constraints}, 24006 volume = {1}, 24007 year = {1991} 24008} 24009 24010@Article{ byrd:1995:lma, 24011 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 24012 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 24013 journal = {SIAM Journal on Scientific Computing}, 24014 volume = {16}, 24015 number = {5}, 24016 pages = {1190--1208}, 24017 month = sep, 24018 year = {1995}, 24019 coden = {SJOCE3}, 24020 issn = {1064-8275 (print), 1095-7197 (electronic)}, 24021 mrclass = {90C30 (65K05)}, 24022 mrnumber = {96e:90039}, 24023 mrreviewer = {Henry Wolkowicz}, 24024 bibdate = {Fri Dec 4 16:17:35 MST 1998} 24025} 24026 24027@Article{ lin_c3, 24028 author = {C.-J. Lin and J. J. Mor\'e}, 24029 title = {Newton's method for large bound-constrained optimization problems}, 24030 year = {1999}, 24031 journal = {SIOPT}, 24032 volume = {9(4)}, 24033 pages = {1100--1127}, 24034 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 24035} 24036 24037@TechReport{ dolan2, 24038 author = {E. Dolan and J. J. Mor\'{e}}, 24039 title = {Benchmarking Optimization Software with Performance Profiles}, 24040 year = {2001}, 24041 month = jan, 24042 number = {ANL/MCS-P861-1200}, 24043 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24044 address = {Argonne, IL}, 24045 url = {http://www.mcs.anl.gov/~more/cops/} 24046} 24047 24048@InProceedings{ owlqn, 24049 author = {Galen Andrew and Jianfeng Gao}, 24050 title = {Scalable training of L1-regularized log-linear models}, 24051 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 24052 pages = {33--40}, 24053 year = {2007} 24054} 24055 24056@Article{ bmrm, 24057 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 24058 title = {Bundle methods for regularized risk minimization}, 24059 year = {2010}, 24060 journal = {Journal of Machine Learning Research}, 24061 volume = {11}, 24062 pages = {311--365} 24063} 24064 24065% ------------------- Component Software References ---------------------- 24066@InProceedings{ cca99, 24067 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 24068 McInnes and S. Parker and B. Smolinski}, 24069 title = {Toward a Common Component Architecture for High-Performance Scientific 24070 Computing}, 24071 booktitle = {Proceedings of {High Performance Distributed Computing}}, 24072 pages = {115--124}, 24073 year = {1999}, 24074 note = {See \url{http://cca-forum.org}} 24075} 24076 24077@Book{ szyperski98, 24078 author = {Clemens Szyperski}, 24079 title = {Component Software: Beyond Object-Oriented Programming}, 24080 publisher = {ACM Press}, 24081 address = {New York}, 24082 year = {1998} 24083} 24084 24085@Article{ broy98, 24086 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 24087 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 24088 Stal and Clemens Szyperski}, 24089 title = {What Characterizes a (Software) Component?}, 24090 journal = {Software -- Concepts and Tools}, 24091 publisher = {Springer-Verlag}, 24092 year = {1998}, 24093 volume = {19}, 24094 pages = {49--56} 24095} 24096 24097@Article{ componentware:94, 24098 author = {Jon Udell}, 24099 title = {Componentware}, 24100 journal = {Byte}, 24101 volume = {may}, 24102 pages = {46--56}, 24103 year = {1994}, 24104 key = {Udell94 ! componentware} 24105} 24106 24107@Misc{ cca-web-page, 24108 author = {{Common Component Architecture Forum}}, 24109 note = {See \url{http://cca-forum.org}} 24110} 24111 24112% --------------- References for Tools Used by TAO Developers ----------------- 24113 24114% 24115% tohtml: Used to generate on-line TAO users manual and manual pages 24116% 24117@TechReport{ tohtml, 24118 author = {William Gropp}, 24119 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 24120 institution = {Argonne National Laboratory}, 24121 number = {ANL/MCS-TM-00}, 24122 month = jan, 24123 year = {1995}, 24124 key = {tohtml} 24125} 24126 24127% 24128% doctext: Used to generate tex version of TAO manual pages 24129% 24130@TechReport{ doctext, 24131 author = {William Gropp}, 24132 title = {Users Manual for doctext: Producing documentation from {C} source code}, 24133 institution = {Argonne National Laboratory}, 24134 number = {ANL/MCS-TM-00}, 24135 month = jan, 24136 year = {1995}, 24137 key = {doctext} 24138} 24139 24140% 24141% bfort: Used to generate TAO Fortran interface 24142% 24143@TechReport{ bfort, 24144 author = {William Gropp}, 24145 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 24146 institution = {Argonne National Laboratory}, 24147 number = {ANL/MCS-TM-208}, 24148 month = mar, 24149 year = {1995}, 24150 key = {doctext} 24151} 24152 24153% ------------------------- PETSc References ------------------------------ 24154@InProceedings{ petsc, 24155 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 24156 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 24157 Libraries}, 24158 booktitle = {Modern Software Tools in Scientific Computing}, 24159 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 24160 publisher = {Birkhauser Press}, 24161 pages = {163--202}, 24162 year = {1997} 24163} 24164 24165% ------------------------- Misc Other References ------------------------------ 24166@Misc{ indeps-web-page, 24167 title = {{InDEPS} {W}eb page}, 24168 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 24169 author = {et al. Robert Armstrong}, 24170 institution = {Sandia National Laboratory}, 24171 key = {{InDEPS} {W}eb page} 24172} 24173 24174@Misc{ pooma, 24175 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 24176 chitectures}, 24177 year = {1996}, 24178 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 24179 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 24180} 24181 24182@Misc{ isis++-web-page, 24183 title = {{ISIS++} {W}eb Page}, 24184 note = {See \url{http://ca.sandia.gov/isis}}, 24185 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 24186 institution = {Sandia National Laboratories} 24187} 24188 24189@Misc{ trilinos-web-page, 24190 title = {{Trilinos} {W}eb Page}, 24191 note = {See 24192 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 24193 author = {Mike Heroux et al.}, 24194 institution = {Sandia National Laboratories} 24195} 24196 24197@Misc{ alice-web-page, 24198 title = {{ALICE} {W}eb page}, 24199 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 24200 Argonne National Laboratory}, 24201 key = {{ALICE} {W}eb page} 24202} 24203 24204@Misc{ autodiff-webpage, 24205 author = {{Computational Differentiation Project}}, 24206 note = {See \url{http://www.mcs.anl.gov/autodiff}} 24207} 24208 24209@Misc{ coool-home-page, 24210 author = {Lydia Deng and Wences Gouveia and John Scales}, 24211 title = {{The CWP Object-Oriented Optimization Library}}, 24212 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 24213} 24214 24215@Misc{ rice-inversion-home-page, 24216 author = {Mark S. Gokenbach and William W. Symes}, 24217 title = {{The Hilbert Class Library}}, 24218 note = {See \url{http://www.trip.caam.rice.edu/}} 24219} 24220 24221@Misc{ opt++-home-page, 24222 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 24223 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 24224} 24225 24226@Article{ gockenbach:1999:ccl, 24227 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 24228 title = {C++ Classes for Linking Optimization with Complex Simulations}, 24229 journal = {{ACM} Transactions on Mathematical Software}, 24230 volume = {25}, 24231 number = {2}, 24232 month = jun, 24233 year = {1999}, 24234 pages = {191-212}, 24235 abstract = {The object-oriented programming paradigm can be used to overcome the 24236 incompatibilities between off-the-shelf optimization software and application 24237 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 24238 objects arising in optimization problems, such as vectors, linear operators, and 24239 so forth, as C++ classes, making it possible to write optimization code in a 24240 natural fashion, while allowing application software such as simulators to use the 24241 most convenient data structures and programming style. In spite of the poor 24242 reputation C++ has for runtime performance, the use of mixed-language programming 24243 allows performance equal to that achieved by standard Fortran packages, as 24244 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 24245 accepted = {April 1999}, 24246 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 24247} 24248 24249@Misc{ neos-guide, 24250 author = {{The Optimization Software Guide}}, 24251 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 24252} 24253 24254@Article{ boyd, 24255 title = {Distributed optimization and statistical learning via the alternating direction 24256 method of multipliers}, 24257 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 24258 Jonathan and others}, 24259 journal = {Foundations and Trends{\textregistered} in Machine learning}, 24260 volume = {3}, 24261 number = {1}, 24262 pages = {1-122}, 24263 year = {2011}, 24264 publisher = {Now Publishers, Inc.} 24265} 24266 24267@Misc{ :alertsys, 24268 title = {page{ALERT}}, 24269 organization = {Alert Systems, Inc}, 24270 address = {Madison, Wisconsin}, 24271 note = {http://www.alertsys.com/} 24272} 24273 24274@Manual{ :cmfortran, 24275 title = {{CM} {F}ortran Language Reference Manual}, 24276 organization = {Thinking Machines Corporation}, 24277 year = {1994}, 24278 address = {Cambridge, MA} 24279} 24280 24281@Manual{ :cmmd, 24282 title = {{CMMD} Reference Manual, Version 3.0}, 24283 organization = {Thinking Machines Corporation}, 24284 year = {1993}, 24285 address = {Cambridge, MA} 24286} 24287 24288@Manual{ :cmssl, 24289 title = {{CMSSL} for {CM} {F}ortran}, 24290 volume = {I}, 24291 organization = {Thinking Machines Corporation}, 24292 year = {1994}, 24293 address = {Cambridge, MA} 24294} 24295 24296@Misc{ :condor, 24297 author = {M. Livny}, 24298 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24299 howpublished = {www.cs.wisc.edu/condor} 24300} 24301 24302@Manual{ :connection, 24303 title = {Connection Machine {CM}--5 Technical Summary}, 24304 organization = {Thinking Machines Corporation}, 24305 year = {1993}, 24306 address = {Cambridge, MA} 24307} 24308 24309@Manual{ :cplex, 24310 title = {{CPLEX} Optimizer}, 24311 organization = {ILOG CPLEX Division}, 24312 address = {889 Alder Avenue, Incline Village, Nevada}, 24313 note = {http://www.cplex.com/} 24314} 24315 24316@Manual{ :cplextm, 24317 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24318 (Version 2.0)}, 24319 organization = {CPLEX Optimization Inc.}, 24320 year = {1992}, 24321 address = {Incline Village, Nevada} 24322} 24323 24324@Misc{ :fatcop, 24325 author = {M. C. Ferris}, 24326 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24327 Solver}, 24328 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24329} 24330 24331@Misc{ :metaneos, 24332 author = {S. J. Wright}, 24333 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24334 howpublished = {www-unix.mcs.anl.gov/metaneos} 24335} 24336 24337@InCollection{ gropp.more:optimization, 24338 author = {W. Gropp and J. J. Mor\'e}, 24339 title = {Optimization environments and the {NEOS} Server}, 24340 booktitle = {Approximation Theory and Optimization}, 24341 pages = {167--182}, 24342 publisher = {Cambridge University Press}, 24343 year = {1997}, 24344 editor = {M. D. Buhmann and A. Iserles} 24345} 24346 24347@Article{ czyzyk.mesnier.ea:neos, 24348 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24349 title = {The {NEOS} Server}, 24350 journal = {IEEE Journal on Computational Science and Engineering}, 24351 volume = {5}, 24352 year = {1998}, 24353 pages = {68--75} 24354} 24355 24356@Book{ :osl, 24357 title = {Handbook for {IBM OSL}}, 24358 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24359 year = {1994}, 24360 publisher = {Boyd and Fraser}, 24361 address = {Danvers, Massachusetts} 24362} 24363 24364@Manual{ :pro-matlab, 24365 title = {{PRO}--{MATLAB} User's Guide}, 24366 organization = {The MathWorks, Inc.}, 24367 year = {1989}, 24368 address = {21 Eliot Street, South Natick, MA 01760} 24369} 24370 24371@Misc{ :prostate, 24372 key = {Biomedical}, 24373 title = {Biomedical Business International Newsletter}, 24374 howpublished = {pp. 72--75}, 24375 year = {1996} 24376} 24377 24378@Misc{ :sipcase, 24379 key = {Natural}, 24380 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24381 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24382} 24383 24384@Book{ aarts.korst:simulated, 24385 author = {E. Aarts and J. Korst}, 24386 title = {Simulated Annealing and Boltzman Machines}, 24387 year = {1990}, 24388 publisher = {John Wiley \& Sons}, 24389 address = {Chichester} 24390} 24391 24392@TechReport{ aarts.laarhoven.ea:local-search-based, 24393 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 24394 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 24395 institution = {Centre for Quantitative Methods}, 24396 year = {1991}, 24397 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 24398 number = {106}, 24399 type = {CQM-Not} 24400} 24401 24402@Article{ aashtiani.magnanti:equilibria, 24403 author = {H. Z. Aashtiani and T. L. Magnanti}, 24404 title = {Equilibria on a congested transportation network}, 24405 journal = {SIAM Journal on Algebraic and Discrete Methods}, 24406 volume = {2}, 24407 year = {1981}, 24408 pages = {213--226} 24409} 24410 24411@Article{ ablow.brigham:analog, 24412 author = {C. M. Ablow and G. Brigham}, 24413 title = {An Analog Solution of Programming Problems}, 24414 journal = {Operations Research}, 24415 year = {1955}, 24416 volume = {3}, 24417 pages = {388--394} 24418} 24419 24420@Article{ achuthan.grabowski.ea:optimal, 24421 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 24422 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 24423 journal = {Opsearch}, 24424 year = {1981}, 24425 volume = {18}, 24426 pages = {117--138} 24427} 24428 24429@Book{ adelman.robinson:income, 24430 author = {I. Adelman and S. Robinson}, 24431 title = {Income Distribution Policy in Developing Countries}, 24432 publisher = {Stanford University Press}, 24433 year = {1978}, 24434 address = {Stanford, California} 24435} 24436 24437@Article{ adler.resende.ea:implementation, 24438 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 24439 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 24440 journal = {Mathematical Programming}, 24441 year = {1989}, 24442 volume = {44}, 24443 pages = {297--336} 24444} 24445 24446@TechReport{ aeberhard.coomans.ea:comparison, 24447 author = {S. Aeberhard and D. Coomans and O. de Vel}, 24448 title = {Comparison of Classifiers in High Dimensional Settings}, 24449 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 24450 University of North Queensland}, 24451 year = {1992}, 24452 number = {92-02}, 24453 type = {Technical Report} 24454} 24455 24456@Article{ aganagic.cottle:constructive, 24457 author = {M. Aganagi\'{c} and R. W. Cottle}, 24458 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 24459 Minors}, 24460 journal = {Mathematical Programming}, 24461 year = {1987}, 24462 volume = {37}, 24463 pages = {223--231} 24464} 24465 24466@TechReport{ aganagic:iterative, 24467 author = {M. Aganagi\'{c}}, 24468 title = {Iterative Methods for the Linear Complementarity Problem}, 24469 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 24470 University}, 24471 year = {1978}, 24472 type = {SOL}, 24473 number = {78-10}, 24474 address = {Stanford, California} 24475} 24476 24477@Book{ ahlfors:complex, 24478 author = {L. V. Ahlfors}, 24479 title = {Complex Analysis}, 24480 publisher = {McGraw--Hill Book Company}, 24481 address = {New York}, 24482 series = {International Series in Pure and Applied Mathematics}, 24483 edition = {Second}, 24484 year = {1966} 24485} 24486 24487@Article{ ahn:solution, 24488 author = {B--H. Ahn}, 24489 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 24490 journal = {Journal of Optimization Theory and Applications}, 24491 year = {1981}, 24492 volume = {33}, 24493 pages = {175--185} 24494} 24495 24496@Article{ al-fahed.stavroulakis.ea:hard, 24497 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24498 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 24499 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 24500 volume = {71}, 24501 year = {1991}, 24502 pages = {257--265} 24503} 24504 24505@Article{ al-fahed.stavroulakis.ea:linear, 24506 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24507 title = {A linear complementarity approach to the frictionless gripper}, 24508 journal = {International Journal of Robotic Research}, 24509 volume = {11}, 24510 year = {1992}, 24511 pages = {112--122} 24512} 24513 24514@Article{ al-khayyal.falk:jointly, 24515 author = {F. A. Al--Khayyal and J. E. Falk}, 24516 title = {Jointly Constrained Biconvex Programming}, 24517 journal = {Mathematics of Operations Research}, 24518 year = {1983}, 24519 volume = {8}, 24520 pages = {273--286} 24521} 24522 24523@Article{ al-khayyal.kyparisis:finite, 24524 author = {F. A. Al--Khayyal and J. Kyparisis}, 24525 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 24526 Inequalities}, 24527 journal = {Journal of Optimization Theory and Applications}, 24528 year = {1991}, 24529 volume = {70}, 24530 pages = {319--332} 24531} 24532 24533@PhDThesis{ al-khayyal:biconvex, 24534 author = {F. A. Al--Khayyal}, 24535 title = {Biconvex Programming and Biconcave Minimization}, 24536 year = {1977}, 24537 school = {The George Washington University} 24538} 24539 24540@Article{ alart.curnier:mixed, 24541 author = {P. Alart and A. Curnier}, 24542 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 24543 solution methods}, 24544 journal = {Computer Methods in Applied Mechanics and Engineering}, 24545 volume = {92}, 24546 year = {1991}, 24547 pages = {353--375} 24548} 24549 24550@Misc{ alexander.kellog.ea:piecewise, 24551 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 24552 title = {Piecewise smooth continuation}, 24553 howpublished = {Manuscript}, 24554 year = {1979} 24555} 24556 24557@InCollection{ alexander.li.ea:piecewise, 24558 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 24559 title = {Piecewise smooth homotopies}, 24560 booktitle = {Homotopy Methods and Global Convergence}, 24561 pages = {1--14}, 24562 publisher = {Plenum Press}, 24563 year = {1983}, 24564 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 24565 address = {New York} 24566} 24567 24568@InCollection{ alexander:topological, 24569 author = {J.~C. Alexander}, 24570 title = {The topological theory of an embedding method}, 24571 booktitle = {Continuation Methods}, 24572 pages = {37--68}, 24573 publisher = {Academic Press}, 24574 year = {1978}, 24575 editor = {H. Wacker}, 24576 address = {New York} 24577} 24578 24579@Book{ allen:probability, 24580 author = {A. O. Allen}, 24581 title = {Probability, Statistics and Queueing Theory}, 24582 publisher = {Academic Press}, 24583 year = {1990}, 24584 address = {London}, 24585 edition = {Second} 24586} 24587 24588@Book{ allgower.georg:numerical, 24589 author = {E. L. Allgower and K. Georg}, 24590 title = {Numerical Continuation Methods, An Introduction}, 24591 publisher = {Springer-Verlag}, 24592 year = {1990}, 24593 address = {Berlin} 24594} 24595 24596@InProceedings{ allgower.georg:predictor-corrector, 24597 crossref = {bachem.grotschel.ea:mathematical}, 24598 author = {E. L. Allgower and K. Georg}, 24599 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 24600 Zero Points of Nonlinear Mappings}, 24601 pages = {15--56} 24602} 24603 24604@Article{ aluffi-pentini.parisi.ea:algorithm, 24605 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 24606 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 24607 Algorithm}, 24608 journal = {ACM Transactions on Mathematical Software}, 24609 year = {1988}, 24610 volume = {14}, 24611 pages = {366--380} 24612} 24613 24614@Article{ anandalingam.friesz:hierarchical, 24615 author = {G. Anandalingam and T. L. Friesz}, 24616 title = {Hierarchical Optimization: An Introduction}, 24617 journal = {Annals of Operations Research}, 24618 year = {1992}, 24619 volume = {34}, 24620 pages = {1--11} 24621} 24622 24623@Article{ anandalingam.white:solution, 24624 author = {G. Anandalingam and D. J. White}, 24625 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 24626 Functions}, 24627 journal = {IEEE Transactions on Automatic Control}, 24628 year = {1990}, 24629 volume = {35}, 24630 number = {10}, 24631 pages = {1170--1173} 24632} 24633 24634@Article{ andersen.andersen:presolving, 24635 author = {E. Andersen and K. Andersen}, 24636 title = {Presolving in Linear Programming}, 24637 year = {1995}, 24638 journal = {Mathematical Programming}, 24639 volume = {71}, 24640 pages = {221--245} 24641} 24642 24643@InProceedings{ andersen.ye:homogeneous, 24644 author = {E. Andersen and Y. Ye}, 24645 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 24646 Equality Constraints}, 24647 crossref = {ferris.pang:complementarity}, 24648 pages = {1--11} 24649} 24650 24651@Book{ anderson.bai.ea:lapack, 24652 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 24653 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 24654 Sorensen}, 24655 title = {{LAPACK} User's Guide}, 24656 publisher = {SIAM}, 24657 year = {1995}, 24658 address = {Philadelphia, Pennsylvania}, 24659 edition = {Second} 24660} 24661 24662@Article{ anderson.ferris:direct, 24663 author = {E. J. Anderson and M. C. Ferris}, 24664 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 24665 year = {2001}, 24666 journal = {SIAM Journal on Optimization, forthcoming}, 24667 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 24668 key = {55} 24669} 24670 24671@InProceedings{ anderson.ferris:genetic, 24672 author = {E. J. Anderson and M. C. Ferris}, 24673 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 24674 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 24675 Waterloo, Ontario, Canada, May 28--30}, 24676 publisher = {University of Waterloo Press}, 24677 key = {14}, 24678 year = {1990} 24679} 24680 24681@Article{ anderson.ferris:genetic*1, 24682 author = {E. J. Anderson and M. C. Ferris}, 24683 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 24684 Problem}, 24685 journal = {ORSA Journal on Computing}, 24686 year = {1994}, 24687 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 24688 volume = {6}, 24689 pages = {161--173}, 24690 key = {22} 24691} 24692 24693@InProceedings{ anderson.ferris:parallel, 24694 author = {E. J. Anderson and M. C. Ferris}, 24695 title = {Parallel Genetic Algorithms in Optimization}, 24696 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 24697 Computing, Chicago, Illinois, December 11-13}, 24698 year = {1989}, 24699 key = {12} 24700} 24701 24702@Unpublished{ anderson.lewis:primal, 24703 author = {E. J. Anderson and A. S. Lewis}, 24704 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24705 note = {In preparation} 24706} 24707 24708@Book{ anderson.nash:linear, 24709 author = {E. J. Anderson and P. Nash}, 24710 title = {Linear Programming in Infinite--Dimensional Spaces}, 24711 year = {1987}, 24712 publisher = {John Wiley \& Sons}, 24713 address = {Chichester} 24714} 24715 24716@InProceedings{ anderson:primal, 24717 author = {E. J. Anderson}, 24718 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24719 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 24720 Programming, Cambridge, September 1984}, 24721 year = {1985}, 24722 editor = {E. J. Anderson and A. B. Philpott}, 24723 publisher = {Springer-Verlag}, 24724 address = {Berlin} 24725} 24726 24727@Article{ andradottir:method, 24728 author = {S. Andrad\'{o}ttir}, 24729 title = {A Method of Discrete Stochastic Optimization}, 24730 journal = {Management Science}, 24731 year = {1995}, 24732 volume = {41}, 24733 pages = {1946--1961} 24734} 24735 24736@Article{ andradottir:global, 24737 author = {S. Andrad\'{o}ttir}, 24738 title = {A Global Search Method for Discrete Stochastic Optimization}, 24739 journal = {SIAM Journal on Optimization}, 24740 year = {1996}, 24741 volume = {6}, 24742 pages = {513--530} 24743} 24744 24745@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 24746 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 24747 title = {An infeasible--interior--point predictor--corrector algorithm for the 24748 {P}$_x$--geometric {LCP}}, 24749 institution = {Department of Mathematics, The University of Iowa}, 24750 address = {Iowa City, Iowa}, 24751 year = {1994}, 24752 number = {62}, 24753 type = {Reports on Computational Mathematics} 24754} 24755 24756@TechReport{ anitescu.potra:formulating, 24757 author = {M. Anitescu and F. A. Potra}, 24758 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 24759 Linear Complementarity Problems}, 24760 institution = {Department of Mathematics, The University of Iowa}, 24761 year = {1996}, 24762 type = {Report}, 24763 number = {93}, 24764 address = {Iowa City, Iowa} 24765} 24766 24767@Article{ anstreicher.lee.ea:crashing, 24768 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 24769 title = {Crashing a Maximum-Weight Complementarity Basis}, 24770 journal = {Mathematical Programming}, 24771 year = {1992}, 24772 volume = {54}, 24773 pages = {281--294} 24774} 24775 24776@Article{ anstreicher:combined, 24777 author = {K. M. Anstreicher}, 24778 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 24779 programming}, 24780 journal = {Mathematical Programming}, 24781 year = {1991}, 24782 volume = {52}, 24783 pages = {429--440} 24784} 24785 24786@Article{ anstreicher:combined*1, 24787 author = {K. M. Anstreicher}, 24788 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 24789 journal = {Mathematical Programming}, 24790 year = {1989}, 24791 volume = {43}, 24792 pages = {209--223} 24793} 24794 24795@InCollection{ arbenz.gander.ea:remote, 24796 author = {P. Arbenz and W. Gander and M. Oettli}, 24797 title = {The Remote Computational System}, 24798 booktitle = {High-Performance Computation and Networks}, 24799 publisher = {Springer-Verlag}, 24800 year = {1996}, 24801 volume = {1067}, 24802 series = {Lecture Notes in Computer Science}, 24803 pages = {662--667} 24804} 24805 24806@InCollection{ arcus:comsoal, 24807 author = {A. L. Arcus}, 24808 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 24809 booktitle = {Readings in Production and Operations Management}, 24810 year = {1966}, 24811 editor = {E. S. Buffa}, 24812 publisher = {John Wiley \& Sons}, 24813 address = {New York} 24814} 24815 24816@TechReport{ arioli.chan.ea:computing, 24817 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 24818 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 24819 Optimization Calculations}, 24820 institution = {CERFACS}, 24821 year = {1993}, 24822 number = {TR/PA/93/34} 24823} 24824 24825@Article{ armijo:minimization, 24826 author = {L. Armijo}, 24827 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 24828 Derivatives}, 24829 journal = {Pacific Journal of Mathematics}, 24830 year = {1966}, 24831 volume = {16}, 24832 pages = {1--3} 24833} 24834 24835@Article{ arrow.debreu:existence, 24836 author = {K. Arrow and G. Debreu}, 24837 title = {Existence of Equilibrium for a Competitive Economy}, 24838 journal = {Econometrica}, 24839 year = {1954}, 24840 volume = {22}, 24841 pages = {265--290} 24842} 24843 24844@InCollection{ arrow.solow:gradient, 24845 author = {K. J. Arrow and R. M. Solow}, 24846 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 24847 booktitle = {Studies in Linear and Nonlinear Programming}, 24848 year = {1958}, 24849 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 24850 publisher = {Stanford University Press}, 24851 address = {Stanford, California}, 24852 pages = {166--176} 24853} 24854 24855@Book{ aubin.ekeland:nonlinear, 24856 author = {J.-P. Aubin and I. Ekeland}, 24857 title = {Applied nonlinear analysis}, 24858 publisher = {John Wiley \& Sons}, 24859 address = {New York}, 24860 year = {1984} 24861} 24862 24863@Article{ auchmuty:variational, 24864 author = {G. Auchmuty}, 24865 title = {Variational Principles for Variational Inequalities}, 24866 journal = {Numerical Functional Analysis and Optimization}, 24867 year = {1989}, 24868 volume = {10}, 24869 pages = {863--874} 24870} 24871 24872@Book{ auerbach.kotlikoff:dynamic, 24873 author = {A. J. Auerbach and L. J. Kotlikoff}, 24874 title = {Dynamic Fiscal Policy}, 24875 publisher = {Cambridge University Press}, 24876 address = {Cambridge, England}, 24877 year = {1987} 24878} 24879 24880@InProceedings{ ault.deutsch.ea:interpolating, 24881 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 24882 title = {Interpolating Subspaces in Approximation Theory}, 24883 booktitle = {Approximation Theory}, 24884 year = {1970}, 24885 editor = {A. Talbot}, 24886 publisher = {Academic Press}, 24887 address = {London} 24888} 24889 24890@Article{ auslender.crouzeix:global, 24891 author = {A. A. Auslender and J.--P. Crouzeix}, 24892 title = {Global Regularity Theorems}, 24893 journal = {Mathematics of Operations Research}, 24894 year = {1988}, 24895 volume = {13}, 24896 pages = {243--253} 24897} 24898 24899@Article{ auslender.haddou:interior-proximal, 24900 author = {A. Auslender and M. Haddou}, 24901 title = {An interior-proximal method for convex linearly constrained problems and its 24902 extension to variational inequalities}, 24903 year = {1995}, 24904 journal = {Mathematical Programming}, 24905 pages = {77--100}, 24906 volume = {71} 24907} 24908 24909@Article{ auslender:convergence, 24910 author = {A. Auslender}, 24911 title = {Convergence of stationary sequences for variational inequalities with maximal 24912 monotone operators}, 24913 journal = {Applied Mathematics and Optimization}, 24914 volume = {28}, 24915 year = {1993}, 24916 pages = {161--172} 24917} 24918 24919@Book{ auslender:optimization, 24920 author = {A. Auslender}, 24921 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 24922 year = {1976}, 24923 publisher = {Masson}, 24924 address = {Paris} 24925} 24926 24927@TechReport{ averick.carter.ea:minpack-2, 24928 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 24929 title = {The {MINPACK-2} Test Problem Collection}, 24930 institution = {Argonne National Laboratory}, 24931 year = {1992}, 24932 address = {Argonne, Illinois}, 24933 number = {MCS-P153-0692} 24934} 24935 24936@TechReport{ axline.billups.ea:guidelines, 24937 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 24938 title = {Guidelines for Software Security ({U})}, 24939 institution = {SNL}, 24940 year = {1989}, 24941 month = oct, 24942 address = {Albuquerque, New Mexico}, 24943 number = {SAND88-2955} 24944} 24945 24946@Article{ ayres.walter:greenhouse, 24947 author = {R. U. Ayres and J. Walter}, 24948 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 24949 journal = {Environmental and Resource Economics}, 24950 year = {1991}, 24951 volume = {1}, 24952 pages = {237--270} 24953} 24954 24955@PhDThesis{ bagley:behaviour, 24956 author = {J. D. Bagley}, 24957 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 24958 Algorithms}, 24959 year = {1967}, 24960 school = {University of Michigan} 24961} 24962 24963@Article{ bain.stewart:application, 24964 author = {R. S. Bain and W. E. Stewart}, 24965 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 24966 Algebraic Equation Systems}, 24967 journal = {Computers in Chemical Engineering}, 24968 year = {1991}, 24969 volume = {15}, 24970 pages = {203--208} 24971} 24972 24973@Article{ baker.lasdon:successive, 24974 author = {T. E. Baker and L. S. 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Bertsekas}, 25418 title = {Nonlinear Programming}, 25419 publisher = {Athena Scientific}, 25420 year = {1995}, 25421 address = {Belmont, Massachusetts} 25422} 25423 25424@Article{ bertsekas:projected, 25425 author = {Dimitri P. Bertsekas}, 25426 title = {Projected {N}ewton Methods for Optimization Problems with Simple Constraints}, 25427 journal = {SIAM Journal on Control and Optimization}, 25428 year = {1982}, 25429 volume = {20}, 25430 pages = {221--246} 25431} 25432 25433@Article{ billups.dirkse.ea:comparison, 25434 author = {S. C. Billups and S. P. Dirkse and M. C. Ferris}, 25435 title = {A Comparison of Large Scale Mixed Complementarity Problem Solvers}, 25436 journal = {Computational Optimization and Applications}, 25437 year = {1997}, 25438 pages = {3--25}, 25439 volume = {7}, 25440 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps}, 25441 key = {51} 25442} 25443 25444@Article{ billups.ferris:convergence, 25445 author = {S. C. Billups and M. C. Ferris}, 25446 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 25447 Starting Points}, 25448 journal = {SIAM Journal on Optimization}, 25449 year = {1996}, 25450 volume = {6}, 25451 pages = {316--325}, 25452 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 25453 key = {34} 25454} 25455 25456@TechReport{ billups.ferris:convergence*1, 25457 author = {S. C. Billups and M. C. Ferris}, 25458 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 25459 Points}, 25460 institution = {Computer Sciences Department, University of Wisconsin}, 25461 year = {1993}, 25462 address = {Madison, Wisconsin}, 25463 number = {1180}, 25464 note = {Revised version in SIAM Journal on Optimization.} 25465} 25466 25467@Article{ billups.ferris:qpcomp, 25468 author = {S. C. Billups and M. C. Ferris}, 25469 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 25470 year = {1997}, 25471 journal = {Mathematical Programming}, 25472 pages = {533--562}, 25473 volume = {76}, 25474 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 25475 key = {47} 25476} 25477 25478@Article{ billups.ferris:solutions, 25479 author = {S. C. Billups and M. C. Ferris}, 25480 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 25481 journal = {Mathematics of Operations Research}, 25482 volume = {24}, 25483 pages = {219--236}, 25484 year = {1999}, 25485 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 25486 key = {42}, 25487 institution = {Computer Sciences Department, University of Wisconsin}, 25488 address = {Madison, Wisconsin}, 25489 type = {Mathematical Programming Technical Report}, 25490 number = {94--15} 25491} 25492 25493@TechReport{ billups.murata.ea:users, 25494 author = {S. C. Billups and K. K. 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Mangasarian}, 28509 title = {Breast Cancer Diagnosis via Linear Programming}, 28510 key = {50}, 28511 journal = {{IEEE} Computational Science and Engineering}, 28512 year = {1995}, 28513 volume = {2}, 28514 pages = {70--71} 28515} 28516 28517@Article{ ferris.mangasarian:error, 28518 author = {M. C. Ferris and O. L. Mangasarian}, 28519 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 28520 Inequalities}, 28521 journal = {Annals of Operations Research}, 28522 year = {1993}, 28523 volume = {47}, 28524 pages = {293--305}, 28525 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 28526 key = {24} 28527} 28528 28529@Article{ ferris.mangasarian:finite, 28530 author = {M. C. Ferris and O. L. Mangasarian}, 28531 title = {Finite Perturbation of Convex Programs}, 28532 journal = {Applied Mathematics and Optimization}, 28533 year = {1991}, 28534 volume = {23}, 28535 pages = {263--273}, 28536 key = {08} 28537} 28538 28539@Book{ ferris.mangasarian:linear, 28540 author = {M. C. Ferris and O. L. Mangasarian}, 28541 title = {Linear Programming via {MATLAB}}, 28542 publisher = {in preparation}, 28543 year = {1995}, 28544 address = {Madison, Wisconsin} 28545} 28546 28547@Article{ ferris.mangasarian:minimum, 28548 author = {M. C. Ferris and O. L. Mangasarian}, 28549 title = {Minimum Principle Sufficiency}, 28550 journal = {Mathematical Programming}, 28551 year = {1992}, 28552 volume = {57}, 28553 pages = {1--14}, 28554 key = {11} 28555} 28556 28557@Article{ ferris.mangasarian:parallel, 28558 author = {M. C. Ferris and O. L. Mangasarian}, 28559 title = {Parallel Constraint Distribution}, 28560 journal = {SIAM Journal on Optimization}, 28561 year = {1991}, 28562 volume = {1}, 28563 pages = {487--500}, 28564 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28565 key = {18} 28566} 28567 28568@Article{ ferris.mangasarian:parallel*1, 28569 author = {M. C. Ferris and O. L. Mangasarian}, 28570 title = {Parallel Variable Distribution}, 28571 journal = {SIAM Journal on Optimization}, 28572 year = {1994}, 28573 volume = {4}, 28574 pages = {815--832}, 28575 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28576 key = {31} 28577} 28578 28579@Article{ ferris.meeraus.ea:computing, 28580 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28581 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28582 journal = {Optimization Methods and Software}, 28583 year = {1999}, 28584 volume = {10}, 28585 pages = {669--685}, 28586 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28587 key = {45} 28588} 28589 28590@Article{ ferris.mesnier.ea:neos, 28591 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28592 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28593 {I}nternet}, 28594 year = {2000}, 28595 journal = {{ACM} Transactions on Mathematical Software}, 28596 key = {54}, 28597 volume = {26}, 28598 pages = {1--18}, 28599 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28600 institution = {Computer Sciences Department, University of Wisconsin}, 28601 address = {Madison, Wisconsin}, 28602 number = {96-08}, 28603 type = {Mathematical Programming Technical Report}, 28604 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28605 Argonne National Laboratory}, 28606 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28607 1996} 28608} 28609 28610@InCollection{ ferris.meyer:models, 28611 author = {M. C. Ferris and R. R. Meyer}, 28612 title = {Models and Solution for On-Demand Data Delivery Problems}, 28613 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28614 key = {80}, 28615 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28616 Problems}, 28617 editor = {P. M. Pardalos}, 28618 series = {Nonconvex Optimization and its Applications}, 28619 volume = {42}, 28620 address = {Dordrect}, 28621 year = {2000}, 28622 pages = {175--188}, 28623 publisher = {Kluwer}, 28624 type = {Mathematical Programming Technical Report}, 28625 institution = {Computer Sciences Department, University of Wisconsin}, 28626 number = {99-04} 28627} 28628 28629@InProceedings{ ferris.munson.ea:homotopy, 28630 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28631 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28632 booktitle = {Numerical Analysis 1999}, 28633 key = {88}, 28634 year = {2000}, 28635 editor = {D. F. Griffiths and G. A. Watson}, 28636 series = {Research Notes in Mathematics}, 28637 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28638 address = {London}, 28639 pages = {143--167}, 28640 publisher = {Chapman and Hall}, 28641 institution = {Computer Sciences Department, University of Wisconsin}, 28642 number = {99-09}, 28643 type = {Mathematical Programming Technical Report} 28644} 28645 28646@TechReport{ ferris.munson.ea:practical, 28647 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28648 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28649 type = {Data Mining Institute Technical Report}, 28650 institution = {Computer Sciences Department, University of Wisconsin}, 28651 address = {Madison, Wisconsin}, 28652 year = {2000}, 28653 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28654 number = {00-03}, 28655 key = {92}, 28656 annote = {To appear in WSC 2000} 28657} 28658 28659@InCollection{ ferris.munson:case, 28660 author = {M. C. Ferris and T. S. Munson}, 28661 title = {Case Studies in Complementarity: Improving Model Formulation}, 28662 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28663 key = {73}, 28664 pages = {79--98}, 28665 publisher = {Springer Verlag}, 28666 year = {1999}, 28667 editor = {M. Th\'{e}ra and R. Tichatschke}, 28668 number = {477}, 28669 series = {Lecture Notes in Economics and Mathematical Systems}, 28670 address = {Berlin}, 28671 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28672 type = {Mathematical Programming Technical Report}, 28673 institution = {Computer Sciences Department, University of Wisconsin} 28674} 28675 28676@Article{ ferris.munson:complementarity, 28677 author = {M. C. Ferris and T. S. Munson}, 28678 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28679 year = {2000}, 28680 volume = {24}, 28681 pages = {165--188}, 28682 journal = {Journal of Economic Dynamics and Control}, 28683 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28684 key = {70}, 28685 type = {Mathematical Programming Technical Report}, 28686 institution = {Computer Sciences Department, University of Wisconsin}, 28687 address = {Madison, Wisconsin}, 28688 number = {98-12} 28689} 28690 28691@Misc{ ferris.munson:condor, 28692 author = {M. C. Ferris and T. S. Munson}, 28693 title = {Condor Modeling Language Interface}, 28694 organization = {Computer Sciences Department, University of Wisconsin}, 28695 address = {Madison, Wisconsin}, 28696 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28697} 28698 28699@Manual{ ferris.munson:gams, 28700 author = {M. C. Ferris and T. S. Munson}, 28701 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28702 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28703} 28704 28705@Article{ ferris.munson:interfaces, 28706 author = {M. C. Ferris and T. S. Munson}, 28707 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28708 journal = {Computational Optimization and Applications}, 28709 volume = {12}, 28710 pages = {207--227}, 28711 year = {1999}, 28712 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28713 key = {63}, 28714 institution = {Computer Sciences Department, University of Wisconsin}, 28715 address = {Madison, Wisconsin}, 28716 number = {97-12}, 28717 type = {Mathematical Programming Technical Report} 28718} 28719 28720@TechReport{ ferris.munson:interior, 28721 author = {M. C. Ferris and T. S. Munson}, 28722 title = {Interior Point Methods for Massive Support Vector Machines}, 28723 institution = {Computer Sciences Department, University of Wisconsin}, 28724 year = {2000}, 28725 key = {94}, 28726 type = {Data Mining Institute Technical Report}, 28727 number = {00-05}, 28728 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28729 address = {Madison, Wisconsin}, 28730 annote = {Submitted to SIOPT} 28731} 28732 28733@Article{ ferris.munson:linear, 28734 author = {M. C. Ferris and T. S. Munson}, 28735 title = {Linear Programming for Emergency Broadcast Systems}, 28736 year = {1999}, 28737 journal = {{SIAG/OPT} Newsletter}, 28738 volume = {10}, 28739 pages = {6--8}, 28740 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28741 key = {76}, 28742 type = {Mathematical Programming Technical Report}, 28743 institution = {Computer Sciences Department, University of Wisconsin}, 28744 address = {Madison, Wisconsin}, 28745 number = {98-20} 28746} 28747 28748@Article{ ferris.munson:modeling, 28749 author = {M. C. Ferris and T. S. Munson}, 28750 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28751 year = {2000}, 28752 journal = {Mathematical Programming}, 28753 volume = {88}, 28754 pages = {487--506}, 28755 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28756 key = {71}, 28757 type = {Mathematical Programming Technical Report}, 28758 institution = {Computer Sciences Department, University of Wisconsin}, 28759 address = {Madison, Wisconsin}, 28760 number = {98-13} 28761} 28762 28763@TechReport{ ferris.munson:preprocessing, 28764 author = {M. C. Ferris and T. S. Munson}, 28765 title = {Preprocessing Complementarity Problems}, 28766 type = {Mathematical Programming Technical Report}, 28767 institution = {Computer Sciences Department, University of Wisconsin}, 28768 address = {Madison, Wisconsin}, 28769 year = {1999}, 28770 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28771 number = {99-07}, 28772 key = {86}, 28773 annote = {Submitted to ICCP 99} 28774} 28775 28776@TechReport{ ferris.munson:semismooth, 28777 author = {M. C. Ferris and T. S. Munson}, 28778 title = {Semismooth Support Vector Machines}, 28779 institution = {Computer Sciences Department, University of Wisconsin}, 28780 year = {2000}, 28781 key = {97}, 28782 type = {Data Mining Institute Technical Report}, 28783 number = {00-09}, 28784 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28785 address = {Madison, Wisconsin}, 28786 annote = {Submitted to Math Prog B} 28787} 28788 28789@Article{ ferris.pang:engineering, 28790 author = {M. C. Ferris and J. S. Pang}, 28791 title = {Engineering and Economic Applications of Complementarity Problems}, 28792 year = {1997}, 28793 journal = {SIAM Review}, 28794 volume = {39}, 28795 pages = {669--713}, 28796 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28797 key = {46} 28798} 28799 28800@Article{ ferris.pang:nondegenerate, 28801 author = {M. C. Ferris and J. S. Pang}, 28802 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28803 journal = {SIAM Journal on Control and Optimization}, 28804 year = {1996}, 28805 volume = {34}, 28806 pages = {244--263}, 28807 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28808 key = {35} 28809} 28810 28811@Article{ ferris.philpott:affine, 28812 author = {M. C. Ferris and A. B. Philpott}, 28813 title = {On Affine Scaling and Semi--Infinite Programming}, 28814 journal = {Mathematical Programming}, 28815 year = {1992}, 28816 volume = {56}, 28817 pages = {361--364}, 28818 key = {15} 28819} 28820 28821@Article{ ferris.philpott:interior, 28822 author = {M. C. Ferris and A. B. Philpott}, 28823 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28824 journal = {Mathematical Programming}, 28825 year = {1989}, 28826 volume = {43}, 28827 pages = {257--276}, 28828 key = {04} 28829} 28830 28831@Article{ ferris.philpott:performance, 28832 author = {M. C. Ferris and A. B. Philpott}, 28833 title = {On the Performance of {K}armarkar's Algorithm}, 28834 journal = {Journal of the Operational Research Society}, 28835 year = {1988}, 28836 volume = {39}, 28837 pages = {257--270}, 28838 key = {03} 28839} 28840 28841@InCollection{ ferris.ralph:projected, 28842 author = {M. C. Ferris and D. Ralph}, 28843 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28844 Maps}, 28845 booktitle = {Recent Advances in Nonsmooth Optimization}, 28846 publisher = {World Scientific Publishers}, 28847 year = {1995}, 28848 pages = {57--87}, 28849 editor = {D. Du and L. Qi and R. Womersley}, 28850 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28851 key = {41} 28852} 28853 28854@Article{ ferris.ruszczynski:robust, 28855 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28856 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28857 year = {2000}, 28858 journal = {Networks}, 28859 volume = {35}, 28860 pages = {181--194}, 28861 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28862 key = {60} 28863} 28864 28865@InCollection{ ferris.rutherford:accessing, 28866 author = {M. C. Ferris and T. F. Rutherford}, 28867 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28868 booktitle = {Nonlinear Optimization and Applications}, 28869 key = {48}, 28870 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28871 editor = {G. Di Pillo and F. Giannessi}, 28872 year = {1996}, 28873 pages = {141--153}, 28874 publisher = {Plenum Press}, 28875 address = {New York} 28876} 28877 28878@InCollection{ ferris.shepard:optimizing, 28879 author = {M. C. Ferris and D. M. Shepard}, 28880 title = {Optimization of Gamma Knife Radiosurgery}, 28881 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28882 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28883 publisher = {AMS}, 28884 year = {2000}, 28885 optseries = {DIMACS}, 28886 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28887 key = {91}, 28888 type = {Data Mining Institute Technical Report}, 28889 institution = {Computer Sciences Department, University of Wisconsin}, 28890 address = {Madison, Wisconsin}, 28891 number = {00-01} 28892} 28893 28894@InCollection{ ferris.sinapiromsaran:formulating, 28895 author = {M. C. Ferris and K. Sinapiromsaran}, 28896 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28897 booktitle = {Optimization}, 28898 key = {77}, 28899 publisher = {Springer-Verlag}, 28900 year = {2000}, 28901 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28902 volume = {481}, 28903 series = {Lecture Notes in Economics and Mathematical Systems}, 28904 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28905 type = {Mathematical Programming Technical Report}, 28906 institution = {Computer Sciences Department, University of Wisconsin}, 28907 address = {Madison, Wisconsin}, 28908 number = {98-21} 28909} 28910 28911@Article{ ferris.tin-loi:limit, 28912 author = {M. C. Ferris and F. Tin-Loi}, 28913 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28914 Complementarity Constraints}, 28915 year = {2001}, 28916 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28917 key = {78}, 28918 journal = {International Journal of Mechanical Sciences}, 28919 pages = {209--224}, 28920 volume = {43}, 28921 type = {Mathematical Programming Technical Report}, 28922 institution = {Computer Sciences Department, University of Wisconsin}, 28923 address = {Madison, Wisconsin}, 28924 number = {99-01} 28925} 28926 28927@Article{ ferris.tin-loi:nonlinear, 28928 author = {M. C. Ferris and F. Tin-Loi}, 28929 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28930 Elastoplasticity}, 28931 year = {1998}, 28932 key = {64}, 28933 volume = {6}, 28934 pages = {857--870}, 28935 journal = {Structural Engineering and Mechanics} 28936} 28937 28938@Article{ ferris.tin-loi:solution, 28939 author = {M. C. Ferris and F. Tin-Loi}, 28940 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28941 and Complementarity Constraints}, 28942 year = {1999}, 28943 journal = {Computer Methods in Applied Mechanics and Engineering}, 28944 volume = {174}, 28945 pages = {107--120}, 28946 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 28947 key = {66} 28948} 28949 28950@Article{ ferris.vlach:scheduling, 28951 author = {M. C. Ferris and M. Vlach}, 28952 title = {Scheduling with Earliness and Tardiness Penalties}, 28953 journal = {Naval Research Logistics Quarterly}, 28954 year = {1992}, 28955 volume = {39}, 28956 pages = {229--245}, 28957 key = {13} 28958} 28959 28960@TechReport{ ferris.zavriev:linear, 28961 author = {M. C. Ferris and S. K Zavriev}, 28962 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 28963 institution = {Computer Sciences Department, University of Wisconsin}, 28964 year = {1996}, 28965 key = {56}, 28966 address = {Madison, Wisconsin}, 28967 type = {Mathematical Programming Technical Report}, 28968 number = {96--12}, 28969 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 28970} 28971 28972@Article{ ferris:finite, 28973 author = {M. C. Ferris}, 28974 title = {Finite Termination of the Proximal Point Algorithm}, 28975 journal = {Mathematical Programming}, 28976 year = {1991}, 28977 volume = {50}, 28978 pages = {359--366}, 28979 key = {06} 28980} 28981 28982@Article{ ferris:iterative, 28983 author = {M. C. Ferris}, 28984 title = {Iterative Linear Programming Solution of Convex Programs}, 28985 journal = {Journal of Optimization Theory and Applications}, 28986 year = {1990}, 28987 volume = {65}, 28988 pages = {53--65}, 28989 key = {07} 28990} 28991 28992@Article{ ferris:linear, 28993 author = {M. C. Ferris}, 28994 title = {The Linear Complementarity Problem}, 28995 journal = {Bulletin of the American Mathematical Society}, 28996 year = {1993}, 28997 volume = {28}, 28998 pages = {169--175}, 28999 key = {27} 29000} 29001 29002@MastersThesis{ ferris:linear*1, 29003 author = {M. C. Ferris}, 29004 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 29005 Solving a Class of Structural Optimization Problems}, 29006 year = {1985}, 29007 school = {University of Cambridge}, 29008 address = {England}, 29009 key = {01} 29010} 29011 29012@TechReport{ ferris:matlab, 29013 author = {M. C. Ferris}, 29014 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 29015 institution = {Computer Sciences Department, University of Wisconsin}, 29016 year = {1998}, 29017 address = {Madison, Wisconsin}, 29018 type = {Mathematical Programming Technical Report}, 29019 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 29020 number = {98-19}, 29021 key = {75} 29022} 29023 29024@Article{ ferris:parallel, 29025 author = {M. C. Ferris}, 29026 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 29027 journal = {Mathematics of Operations Research}, 29028 year = {1994}, 29029 volume = {19}, 29030 pages = {645--658}, 29031 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 29032 key = {20} 29033} 29034 29035@TechReport{ ferris:parallel*1, 29036 author = {M. C. Ferris}, 29037 title = {Parallel Solution of Extremely Large Knapsack Problems}, 29038 institution = {Computer Sciences Department, University of Wisconsin}, 29039 year = {1989}, 29040 address = {Madison, Wisconsin}, 29041 number = {842}, 29042 key = {09} 29043} 29044 29045@PhDThesis{ ferris:weak, 29046 author = {M. C. Ferris}, 29047 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29048 year = {1988}, 29049 school = {University of Cambridge}, 29050 address = {England}, 29051 key = {02} 29052} 29053 29054@TechReport{ ferris:weak*1, 29055 author = {M. C. Ferris}, 29056 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29057 institution = {Computer Sciences Department, University of Wisconsin}, 29058 year = {1988}, 29059 address = {Madison, Wisconsin}, 29060 number = {779}, 29061 key = {05} 29062} 29063 29064@Book{ fiacco.mccormick:nonlinear, 29065 author = {A. V. Fiacco and G. P. McCormick}, 29066 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 29067 year = {1968}, 29068 publisher = {John Wiley \& Sons}, 29069 address = {New York}, 29070 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 29071} 29072 29073@Book{ fiacco:introduction, 29074 author = {A. V. Fiacco}, 29075 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 29076 year = {1983}, 29077 publisher = {Academic Press}, 29078 address = {New York} 29079} 29080 29081@Article{ fiedler.ptak:matrices, 29082 author = {M. Fiedler and V. Pt\'{a}k}, 29083 title = {On matrices with nonpositive off-diagonal elements and positive principal 29084 minors}, 29085 journal = {Czechoslovak Mathematics Journal}, 29086 volume = {12}, 29087 pages = {382--400}, 29088 year = {1962} 29089} 29090 29091@Article{ fischer.kanzow:finite, 29092 author = {A. Fischer and C. Kanzow}, 29093 title = {On Finite Termination of an Iterative Method for Linear Complementarity 29094 Problems}, 29095 journal = {Mathematical Programming}, 29096 volume = {74}, 29097 pages = {279--292}, 29098 year = {1996} 29099} 29100 29101@TechReport{ fischer:constrained, 29102 author = {A. Fischer}, 29103 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 29104 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 29105 year = {1995}, 29106 type = {Technical Report}, 29107 number = {MATH-NM-10-1995}, 29108 address = {Dresden} 29109} 29110 29111@Article{ fischer:local, 29112 author = {A. Fischer}, 29113 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 29114 weak conditions}, 29115 journal = {Optimization Methods and Software}, 29116 year = {1995}, 29117 volume = {6}, 29118 pages = {83--107} 29119} 29120 29121@InCollection{ fischer:ncp-function, 29122 author = {A. Fischer}, 29123 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 29124 booktitle = {Recent Advances in Nonsmooth Optimization}, 29125 publisher = {World Scientific Publishers}, 29126 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 29127 year = {1995}, 29128 pages = {88--105} 29129} 29130 29131@Article{ fischer:newton-type, 29132 author = {A. Fischer}, 29133 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 29134 Problems}, 29135 journal = {Journal of Optimization Theory and Applications}, 29136 year = {1995}, 29137 volume = {86}, 29138 pages = {585--608} 29139} 29140 29141@Article{ fischer:solution, 29142 author = {A. Fischer}, 29143 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 29144 Functions}, 29145 year = {1997}, 29146 journal = {Mathematical Programming}, 29147 pages = {513--532} 29148} 29149 29150@Article{ fischer:special, 29151 author = {A. Fischer}, 29152 title = {A Special {N}ewton--Type Optimization Method}, 29153 journal = {Optimization}, 29154 year = {1992}, 29155 volume = {24}, 29156 pages = {269--284} 29157} 29158 29159@Article{ fisher:use, 29160 author = {R. A. Fisher}, 29161 title = {The Use of Multiple Measurements in Taxonomic Problems}, 29162 journal = {Annual Eugenics}, 29163 year = {1936}, 29164 volume = {7}, 29165 number = {Part II}, 29166 pages = {179--188} 29167} 29168 29169@Book{ fishman:principles, 29170 author = {G. Fishman}, 29171 title = {Principles of Discrete Event Simulation}, 29172 publisher = {Wiley}, 29173 address = {New York, NY}, 29174 year = {1978} 29175} 29176 29177@Article{ fitchard.aldridge.ea:registration, 29178 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 29179 title = {Registration of Synthetic Tomographic Projection Data Sets Using 29180 Cross-Correlation}, 29181 journal = {Physics in Medicine and Biology}, 29182 year = {1998}, 29183 volume = {43}, 29184 pages = {1645--1657} 29185} 29186 29187@Article{ fletcher.matthews:stable, 29188 author = {R. Fletcher and S. P. J. Matthews}, 29189 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 29190 journal = {Mathematical Programming}, 29191 year = {1984}, 29192 volume = {30}, 29193 pages = {267--284} 29194} 29195 29196@TechReport{ fletcher.maza:nonlinear, 29197 author = {R. Fletcher and E. Sainz de la Maza}, 29198 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 29199 Programming}, 29200 institution = {Department of Mathematical Sciences}, 29201 year = {1987}, 29202 address = {The University, Dundee, Scotland}, 29203 number = {NA/100}, 29204 type = {Numerical Analysis Report} 29205} 29206 29207@InCollection{ fletcher:class, 29208 author = {R. Fletcher}, 29209 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 29210 Properties}, 29211 booktitle = {Integer and Nonlinear Programming}, 29212 year = {1970}, 29213 editor = {J. Abadie}, 29214 publisher = {North--Holland}, 29215 address = {Amsterdam}, 29216 pages = {157--173} 29217} 29218 29219@Article{ fletcher:exact, 29220 author = {R. Fletcher}, 29221 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 29222 journal = {Mathematical Programming}, 29223 year = {1973}, 29224 volume = {5}, 29225 pages = {129--150} 29226} 29227 29228@Article{ fletcher:generalized, 29229 author = {R. Fletcher}, 29230 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 29231 Equations}, 29232 journal = {The Computer Journal}, 29233 year = {1968}, 29234 volume = {10}, 29235 pages = {392--399} 29236} 29237 29238@InProceedings{ fletcher:penalty, 29239 crossref = {bachem.grotschel.ea:mathematical}, 29240 author = {R. Fletcher}, 29241 title = {Penalty Functions}, 29242 pages = {87--114} 29243} 29244 29245@Book{ fletcher:practical, 29246 author = {R. Fletcher}, 29247 title = {Practical Methods of Optimization}, 29248 year = {1981}, 29249 publisher = {John Wiley \& Sons}, 29250 address = {Chichester}, 29251 volume = {1} 29252} 29253 29254@Book{ fletcher:practical*1, 29255 author = {R. Fletcher}, 29256 title = {Practical Methods of Optimization}, 29257 year = {1981}, 29258 publisher = {John Wiley \& Sons}, 29259 address = {Chichester}, 29260 volume = {2} 29261} 29262 29263@Book{ fletcher:practical*2, 29264 author = {R. Fletcher}, 29265 title = {Practical Methods of Optimization}, 29266 year = {1987}, 29267 publisher = {John Wiley \& Sons}, 29268 address = {New York}, 29269 edition = {second} 29270} 29271 29272@Unpublished{ fletcher:recent, 29273 author = {R. Fletcher}, 29274 title = {Recent Developments in Nonlinear Programming}, 29275 note = {Presentation at SOR 96, Braunchweig, Germany}, 29276 year = {1996} 29277} 29278 29279@InCollection{ fletcher:second, 29280 author = {R. 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Gill}, 29355 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 29356 institution = {Department of Mathematics, University of California}, 29357 year = {1996}, 29358 type = {Report NA}, 29359 number = {96-3}, 29360 address = {San Diego} 29361} 29362 29363@InCollection{ fortin.glowinski:decomposition-coordination, 29364 author = {M. Fortin and R. Glowinski}, 29365 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 29366 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 29367 Problems}, 29368 publisher = {North-Holland}, 29369 year = {1983}, 29370 editor = {M. Fortin and R. Glowinski}, 29371 address = {Amsterdam} 29372} 29373 29374@Misc{ foster.kesselman:globus, 29375 author = {I. Foster and C. Kesselman}, 29376 title = {The Globus Project}, 29377 howpublished = {www.globus.org} 29378} 29379 29380@Article{ foster.kesselman:globus*1, 29381 author = {I. Foster and C. 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Gao}, 29707 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 29708 Conditions}, 29709 type = {Manuscript}, 29710 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 29711 month = oct, 29712 year = {1994} 29713} 29714 29715@Article{ garcia-palomares.mangasarian:superlinearly, 29716 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 29717 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 29718 Optimization Problems}, 29719 journal = {Mathematical Programming}, 29720 year = {1976}, 29721 volume = {11}, 29722 pages = {1--13} 29723} 29724 29725@Article{ garcia-palomares.restuccia:global, 29726 author = {U. M. {Garcia--Palomares} and A. 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Zangwill}, 29752 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 29753 year = {1981}, 29754 publisher = {Prentice-Hall, Inc}, 29755 address = {Englewood Cliffs, New Jersey} 29756} 29757 29758@Book{ garey.johnson:computers, 29759 author = {M. R. Garey and D. S. Johnson}, 29760 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 29761 year = {1979}, 29762 publisher = {W.H. Freeman and Company}, 29763 address = {San Francisco} 29764} 29765 29766@Article{ garey.tarjan.ea:one-processor, 29767 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 29768 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 29769 journal = {Mathematics of Operations Research}, 29770 year = {1988}, 29771 volume = {13}, 29772 pages = {330--348} 29773} 29774 29775@Book{ garfinkel.nemhauser:integer, 29776 author = {R. S. Garfinkel and G. L. Nemhauser}, 29777 title = {Integer Programming}, 29778 year = {1972}, 29779 publisher = {John Wiley \& Sons}, 29780 address = {New York} 29781} 29782 29783@Book{ gass:linear, 29784 author = {S. Gass}, 29785 title = {Linear Programming Methods and Applications}, 29786 edition = {Fifth}, 29787 publisher = {Boyd and Fraser Publishing Company}, 29788 address = {Danvers, Massachusetts}, 29789 year = {1985} 29790} 29791 29792@InProceedings{ gay:combining, 29793 author = {D. M. Gay}, 29794 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 29795 booktitle = {Sparse Matrix Proceedings 1978}, 29796 editor = {I. S. Duff and G. W. Stewart}, 29797 year = {1978}, 29798 organization = {SIAM}, 29799 address = {Philadelphia, Pennsylvania}, 29800 pages = {313--334} 29801} 29802 29803@Article{ gay:electronic, 29804 author = {D. M. Gay}, 29805 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 29806 journal = {{COAL} Newsletter}, 29807 year = {1985}, 29808 volume = {13}, 29809 pages = {10--12} 29810} 29811 29812@TechReport{ gay:hooking, 29813 author = {D. M. Gay}, 29814 title = {Hooking Your Solver to {AMPL}}, 29815 year = {1997}, 29816 institution = {Bell Laboratories}, 29817 address = {Murray Hill, New Jersey}, 29818 note = {Revised 1994, 1997} 29819} 29820 29821@Article{ gay:variant, 29822 author = {D. Gay}, 29823 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 29824 Form}, 29825 journal = {Mathematical Programming}, 29826 year = {1987}, 29827 volume = {37}, 29828 pages = {81--90} 29829} 29830 29831@Article{ geiger.kanzow:resolution, 29832 author = {C. Geiger and C. Kanzow}, 29833 title = {On the Resolution of Monotone Complementarity Problems}, 29834 journal = {Computational Optimization and Applications}, 29835 volume = {5}, 29836 year = {1996}, 29837 pages = {155--173} 29838} 29839 29840@Book{ geist.beguelin.ea:pvm, 29841 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 29842 V. S. Sunderam}, 29843 title = {{PVM}: Parallel Virtual Machine}, 29844 publisher = {MIT Press}, 29845 address = {Cambridge, Massachusetts}, 29846 year = {1994} 29847} 29848 29849@Article{ gendron.crainic:parallel, 29850 author = {B. Gendron and T. G. Crainic}, 29851 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 29852 journal = {Operations Research}, 29853 year = {1994}, 29854 volume = {42}, 29855 pages = {1042--1060} 29856} 29857 29858@Article{ george:automatic, 29859 author = {A. George}, 29860 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 29861 journal = {SIAM Journal on Numerical Analysis}, 29862 vol = {17}, 29863 pages = {740--751}, 29864 year = {1980} 29865} 29866 29867@InProceedings{ georges-schleuter:asparagos, 29868 crossref = {schaeffer:third}, 29869 author = {M. Georges--Schleuter}, 29870 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 29871 pages = {416--421} 29872} 29873 29874@Article{ georgiou:comments, 29875 author = {G. M. Georgiou}, 29876 title = {Comments On Hidden Nodes in Neural Nets}, 29877 journal = {IEEE Transactions on Circuits and Systems}, 29878 year = {1991}, 29879 volume = {38}, 29880 pages = {1410} 29881} 29882 29883@TechReport{ gertz.linderoth.ea:object-oriented, 29884 author = {M. Gertz and J. Linderoth and S. Wright}, 29885 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 29886 institution = {MCS Division, Argonne National Laboratory}, 29887 year = {in preparation} 29888} 29889 29890@Article{ ghellinck.vial:polynomial, 29891 author = {G. de Ghellinck and J.--Ph. Vial}, 29892 title = {A Polynomial {N}ewton Method for Linear Programming}, 29893 journal = {Algorithmica}, 29894 year = {1986}, 29895 volume = {1}, 29896 pages = {425--453} 29897} 29898 29899@InCollection{ gilbert.ng:predicting, 29900 author = {J. R. Gilbert and E. Ng}, 29901 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 29902 year = {1993}, 29903 booktitle = {Graph Theory and Sparse Matrix Computation}, 29904 editor = {A. George and J. Gilbert and J. Liu}, 29905 publisher = {Springer-Verlag} 29906} 29907 29908@Article{ gilbert-lemarechal, 29909 author = {J. C. Gilbert and C. 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Maier}, 33153 title = {A quadratic programming approach for certain classes of nonlinear structural 33154 problems}, 33155 journal = {Meccanica}, 33156 volume = {3}, 33157 year = {1968}, 33158 pages = {121--130} 33159} 33160 33161@Book{ manber:introduction, 33162 author = {U. Manber}, 33163 title = {Introduction to Algorithms: {A} Creative Approach}, 33164 year = {1989}, 33165 publisher = {Addison-Wesley} 33166} 33167 33168@Article{ mangasarian.deleone:error, 33169 author = {O. L. Mangasarian and R. {De~Leone}}, 33170 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 33171 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 33172 journal = {Applied Mathematics and Optimization}, 33173 year = {1988}, 33174 volume = {17}, 33175 pages = {1--14} 33176} 33177 33178@Article{ mangasarian.deleone:parallel, 33179 author = {O. L. Mangasarian and R. {De~Leone}}, 33180 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 33181 Problems and Linear Programs}, 33182 journal = {Journal of Optimization Theory and Applications}, 33183 year = {1987}, 33184 volume = {54}, 33185 pages = {437--446} 33186} 33187 33188@Article{ mangasarian.fromovitz:fritz, 33189 author = {O. L. Mangasarian and S. Fromovitz}, 33190 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 33191 and inequality constraints}, 33192 journal = {Journal of Mathematical Analysis and its Applications}, 33193 year = {1967}, 33194 volume = {17}, 33195 pages = {37--47} 33196} 33197 33198@Article{ mangasarian.mclinden:simple, 33199 author = {O. L. Mangasarian and L. McLinden}, 33200 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 33201 Programs}, 33202 journal = {Mathematical Programming}, 33203 year = {1985}, 33204 volume = {32}, 33205 pages = {32--40} 33206} 33207 33208@Article{ mangasarian.meyer:nonlinear, 33209 author = {O. L. Mangasarian and R. R. Meyer}, 33210 title = {Nonlinear Perturbation of Linear Programs}, 33211 journal = {SIAM Journal on Control and Optimization}, 33212 year = {1979}, 33213 volume = {17}, 33214 pages = {745--752} 33215} 33216 33217@TechReport{ mangasarian.musicant:active, 33218 author = {O. L. Mangasarian and David R. Musicant}, 33219 title = {Active Set Support Vector Machine Classification}, 33220 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33221 year = {2000}, 33222 number = {00-04}, 33223 address = {Madison, Wisconsin} 33224} 33225 33226@TechReport{ mangasarian.musicant:lagrangian, 33227 author = {O. L. Mangasarian and D. R. Musicant}, 33228 title = {Lagrangian Support Vector Machines}, 33229 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33230 year = {2000}, 33231 number = {00-06}, 33232 address = {Madison, Wisconsin} 33233} 33234 33235@TechReport{ mangasarian.musicant:robust, 33236 author = {O. L. Mangasarian and David R. Musicant}, 33237 title = {Robust Linear and Support Vector Regression}, 33238 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33239 year = {1999}, 33240 number = {99-09}, 33241 address = {Madison, Wisconsin} 33242} 33243 33244@Article{ mangasarian.musicant:successive, 33245 author = {O. L. Mangasarian and David R. Musicant}, 33246 title = {Successive Overrelaxation for Support Vector Machines}, 33247 journal = {IEEE Transactions on Neural Networks}, 33248 volume = {10}, 33249 year = {1999}, 33250 pages = {1032-1037} 33251} 33252 33253@Article{ mangasarian.pang:exact, 33254 author = {O. L. Mangasarian and J. S. Pang}, 33255 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 33256 Constraints}, 33257 journal = {Optimization}, 33258 year = {1997}, 33259 volume = {42}, 33260 pages = {1--8} 33261} 33262 33263@Article{ mangasarian.pang:extended, 33264 author = {O. L. Mangasarian and J. S. Pang}, 33265 title = {The Extended Linear Complementarity Problem}, 33266 journal = {SIAM Journal on Matrix Analysis and Applications}, 33267 year = {1994}, 33268 volume = {16} 33269} 33270 33271@Article{ mangasarian.ren:error, 33272 author = {O. L. Mangasarian and J. Ren}, 33273 title = {New error bounds for the nonlinear complementarity problem}, 33274 year = {1994}, 33275 volume = {1}, 33276 pages = {49--56}, 33277 journal = {Communications on Applied Nonlinear Analysis} 33278} 33279 33280@Article{ mangasarian.ren:improved, 33281 author = {O. L. Mangasarian and J. Ren}, 33282 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 33283 year = {1994}, 33284 volume = {66}, 33285 journal = {Mathematical Programming}, 33286 pages = {241--255} 33287} 33288 33289@InProceedings{ mangasarian.setiono.ea:pattern, 33290 crossref = {coleman.li:large-scale}, 33291 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 33292 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 33293 Diagnosis}, 33294 pages = {22--31} 33295} 33296 33297@Article{ mangasarian.shiau:error, 33298 author = {O. L. Mangasarian and T.--H. Shiau}, 33299 title = {Error Bounds for Monotone Linear Complementarity Problems}, 33300 journal = {Mathematical Programming}, 33301 year = {1986}, 33302 volume = {36}, 33303 pages = {81--89} 33304} 33305 33306@Article{ mangasarian.shiau:lipschitz, 33307 author = {O. L. Mangasarian and T.--H. Shiau}, 33308 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 33309 Complementarity Problems}, 33310 journal = {SIAM Journal on Control and Optimization}, 33311 year = {1987}, 33312 volume = {25}, 33313 pages = {583--595} 33314} 33315 33316@Article{ mangasarian.solodov:nonlinear, 33317 author = {O. L. Mangasarian and M. V. Solodov}, 33318 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 33319 journal = {Mathematical Programming}, 33320 year = {1993}, 33321 volume = {62}, 33322 pages = {277--298} 33323} 33324 33325@Article{ mangasarian.solodov:serial, 33326 author = {O. L. Mangasarian and M. V. Solodov}, 33327 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 33328 Minimization}, 33329 year = {1994}, 33330 journal = {Optimization Methods and Software}, 33331 volume = {4}, 33332 pages = {103--116} 33333} 33334 33335@Article{ mangasarian.street.ea:breast, 33336 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 33337 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 33338 journal = {Operations Research}, 33339 year = {1995}, 33340 volume = {43}, 33341 pages = {570--577} 33342} 33343 33344@Article{ mangasarian.wolberg:cancer, 33345 author = {O. L. Mangasarian and W. H. Wolberg}, 33346 title = {Cancer Diagnosis via Linear Programming}, 33347 journal = {SIAM News}, 33348 year = {1990}, 33349 volume = {23}, 33350 pages = {1 \& 18} 33351} 33352 33353@InCollection{ mangasarian:applications, 33354 author = {O. L. Mangasarian}, 33355 title = {Some Applications of Penalty Functions in Mathematical Programming}, 33356 booktitle = {Optimization and Related Fields}, 33357 year = {1986}, 33358 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 33359 publisher = {Springer-Verlag}, 33360 address = {Heidelberg}, 33361 pages = {307--329}, 33362 note = {Lecture Notes in Mathematics 1190} 33363} 33364 33365@Article{ mangasarian:characterization, 33366 author = {O. L. Mangasarian}, 33367 title = {Characterization of linear complementarity problems as linear programs}, 33368 journal = {Mathematical Programming Study}, 33369 year = {1978}, 33370 volume = {7}, 33371 pages = {74--87} 33372} 33373 33374@InProceedings{ mangasarian:condition, 33375 author = {O. L. Mangasarian}, 33376 title = {A condition number for linear inequalities and linear programs}, 33377 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 33378 1981}, 33379 year = {1981}, 33380 editor = {G. Bamberg and O. Opitz}, 33381 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 33382 address = {Konigstein}, 33383 pages = {3--15} 33384} 33385 33386@Article{ mangasarian:convergence, 33387 author = {O. L. Mangasarian}, 33388 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 33389 Symmetric Monotone Linear Complementarity Problem}, 33390 journal = {SIAM Journal on Optimization}, 33391 volume = {1}, 33392 pages = {114--122}, 33393 year = {1991} 33394} 33395 33396@Article{ mangasarian:equivalence, 33397 author = {O. L. Mangasarian}, 33398 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 33399 journal = {SIAM Journal on Applied Mathematics}, 33400 year = {1976}, 33401 volume = {31}, 33402 pages = {89--92} 33403} 33404 33405@Article{ mangasarian:error, 33406 author = {O. L. Mangasarian}, 33407 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 33408 journal = {ORSA Journal on Computing}, 33409 volume = {15}, 33410 pages = {187--192}, 33411 year = {1994} 33412} 33413 33414@Article{ mangasarian:error*1, 33415 author = {O. L. Mangasarian}, 33416 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 33417 journal = {Mathematical Programming}, 33418 year = {1990}, 33419 volume = {48}, 33420 pages = {437--445} 33421} 33422 33423@Article{ mangasarian:generalized, 33424 author = {O. L. Mangasarian}, 33425 title = {Generalized Linear Complementarity Problems as Linear Programs}, 33426 journal = {Methods of Operations Research}, 33427 year = {1979}, 33428 editor = {W. Oettli and F. Steffens}, 33429 volume = {31}, 33430 pages = {393--402} 33431} 33432 33433@InCollection{ mangasarian:generalized*1, 33434 author = {O. L. Mangasarian}, 33435 title = {Generalized Support Vector Machines}, 33436 year = {2000}, 33437 pages = {135-146}, 33438 booktitle = {Advances in Large Margin Classifiers}, 33439 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 33440 publisher = {MIT Press}, 33441 address = {Cambridge, MA} 33442} 33443 33444@Article{ mangasarian:global, 33445 author = {O. L. Mangasarian}, 33446 title = {Global error bounds for monotone affine variational inequality problems}, 33447 journal = {Linear Algebra and Its Applications}, 33448 year = {1992}, 33449 pages = {153--164} 33450} 33451 33452@InCollection{ mangasarian:least, 33453 author = {O. L. Mangasarian}, 33454 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 33455 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 33456 year = {1990}, 33457 publisher = {Oxford University Press}, 33458 address = {New York}, 33459 pages = {217--221} 33460} 33461 33462@Article{ mangasarian:least-norm, 33463 author = {O. L. Mangasarian}, 33464 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 33465 Problem}, 33466 journal = {Journal of Mathematical Analysis and Applications}, 33467 year = {1983}, 33468 volume = {92}, 33469 pages = {240--251} 33470} 33471 33472@Article{ mangasarian:linear, 33473 author = {O. L. Mangasarian}, 33474 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 33475 journal = {Mathematical Programming}, 33476 year = {1976}, 33477 volume = {10}, 33478 pages = {263--270} 33479} 33480 33481@Article{ mangasarian:linear*1, 33482 author = {O. L. Mangasarian}, 33483 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 33484 journal = {Operations Research}, 33485 year = {1965}, 33486 volume = {13}, 33487 pages = {444--452} 33488} 33489 33490@Article{ mangasarian:locally, 33491 author = {O. L. Mangasarian}, 33492 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 33493 Complementarity Problems}, 33494 journal = {Mathematical Programming}, 33495 year = {1980}, 33496 volume = {19}, 33497 pages = {200--212} 33498} 33499 33500@InCollection{ mangasarian:machine, 33501 author = {O. L. Mangasarian}, 33502 title = {Machine Learning via Polyhedral Concave Minimization}, 33503 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 33504 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 33505 pages = {175-188}, 33506 year = {1996}, 33507 address = {Heidelberg}, 33508 publisher = {Physica-Verlag A Springer-Verlag Company} 33509} 33510 33511@Article{ mangasarian:mathematical, 33512 author = {O. L. Mangasarian}, 33513 title = {Mathematical Programming in Neural Networks}, 33514 journal = {ORSA Journal on Computing}, 33515 volume = {5}, 33516 pages = {349--360}, 33517 year = {1993} 33518} 33519 33520@InProceedings{ mangasarian:mathematical*1, 33521 author = {O. L. Mangasarian}, 33522 title = {Mathematical Programming in Machine Learning}, 33523 booktitle = {Nonlinear Optimization and Applications}, 33524 editor = {G. Di Pillo and F. Giannessi}, 33525 publisher = {Plenum Publishing}, 33526 address = {New York}, 33527 pages = {283--295}, 33528 year = {1996} 33529} 33530 33531@Article{ mangasarian:mathematical*2, 33532 author = {O. L. Mangasarian}, 33533 title = {Mathematical Programming in Data Mining}, 33534 journal = {Data Mining and Knowledge Discovery}, 33535 volume = {1}, 33536 year = {1997}, 33537 pages = {183-201} 33538} 33539 33540@Article{ mangasarian:multi-surface, 33541 author = {O. L. Mangasarian}, 33542 title = {Multi-surface Method of Pattern Separation}, 33543 journal = {IEEE Transactions on Information Theory}, 33544 year = {1968}, 33545 volume = {IT-14}, 33546 pages = {801--807} 33547} 33548 33549@Book{ mangasarian:nonlinear, 33550 author = {O. L. Mangasarian}, 33551 title = {Nonlinear Programming}, 33552 year = {1969}, 33553 publisher = {McGraw--Hill}, 33554 address = {New York}, 33555 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 33556} 33557 33558@Article{ mangasarian:normal, 33559 author = {O. L. Mangasarian}, 33560 title = {Normal Solutions of Linear Programs}, 33561 journal = {Mathematical Programming Study}, 33562 year = {1984}, 33563 volume = {22}, 33564 pages = {206--216} 33565} 33566 33567@Article{ mangasarian:optimal, 33568 author = {O. L. Mangasarian}, 33569 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 33570 Linear Programs}, 33571 journal = {Journal of Optimization Theory and Applications}, 33572 year = {1981}, 33573 volume = {35}, 33574 pages = {123--128} 33575} 33576 33577@Article{ mangasarian:parallel, 33578 author = {O. L. Mangasarian}, 33579 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 33580 journal = {SIAM Journal on Control and Optimization}, 33581 volume = {33}, 33582 pages = {1916--1925}, 33583 year = {1995} 33584} 33585 33586@TechReport{ mangasarian:regularized, 33587 author = {O. L. 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Brady}, 35305 title = {Principles and practice of radiotherapy}, 35306 publisher = {Lippincott-Raven}, 35307 year = {1998}, 35308 address = {Philadelphia}, 35309 edition = {3rd} 35310} 35311 35312@Article{ perroni.rutherford:international, 35313 author = {C. Perroni and T. Rutherford}, 35314 title = {International Trade in Carbon Emission Rights and Basic Materials: General 35315 Equilibrium Calculations for 2020}, 35316 journal = {Scandinavian Journal of Economics}, 35317 year = {1993} 35318} 35319 35320@Article{ perroni.rutherford:regular, 35321 author = {C. Perroni and T. Rutherford}, 35322 title = {Regular Flexibility of Nested {CES} Functions}, 35323 journal = {European Economic Review}, 35324 year = {1995}, 35325 volume = {39}, 35326 pages = {335--343} 35327} 35328 35329@InCollection{ perroni.wigle:environmental, 35330 author = {C. Perroni and R. M. 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Petri}, 35360 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35361 publisher = {Harvard University Press}, 35362 year = {1984} 35363} 35364 35365@InProceedings{ petrzykowski:application, 35366 author = {T. Petrzykowski}, 35367 title = {Application of the Steepest Ascent Method to Concave Programming}, 35368 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35369 year = {1962}, 35370 publisher = {North--Holland}, 35371 address = {Amsterdam}, 35372 pages = {185--189} 35373} 35374 35375@InProceedings{ pettey.leuze.ea:parallel, 35376 crossref = {grefenstette:genetic}, 35377 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35378 title = {A Parallel Genetic Algorithm}, 35379 pages = {155--161} 35380} 35381 35382@InProceedings{ pettey.leuze:theoretical, 35383 crossref = {schaeffer:third}, 35384 author = {C. C. Pettey and M. R. Leuze}, 35385 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35386 pages = {398--405} 35387} 35388 35389@Book{ pfeiffer.glocker:multibody, 35390 author = {F. Pfeiffer and C. Glocker}, 35391 title = {Multibody Dynamics with Unilateral Contact}, 35392 year = {1996}, 35393 publisher = {John Wiley \& Sons} 35394} 35395 35396@TechReport{ pierro.iusem:convergence, 35397 author = {A. R. de Pierro and A. N. Iusem}, 35398 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35399 Linear Complementarity Problems}, 35400 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35401 year = {1990}, 35402 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35403} 35404 35405@InCollection{ pillo.grippo.ea:class, 35406 author = {G. Di Pillo and L. Grippo and F. 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Grippo}, 35427 title = {A New Class of Augmented {L}agrangians in Nonlinear Programming}, 35428 journal = {SIAM Journal on Control and Optimization}, 35429 year = {1979}, 35430 volume = {17}, 35431 pages = {618--628} 35432} 35433 35434@Article{ pillo.grippo:continuously, 35435 author = {G. Di Pillo and L. Grippo}, 35436 title = {A Continuously Differentiable Exact Penalty Function for Nonlinear Programming 35437 Problems with Inequality Constraints}, 35438 journal = {SIAM Journal on Control and Optimization}, 35439 year = {1985}, 35440 volume = {23}, 35441 pages = {72--84} 35442} 35443 35444@Article{ pillo.grippo:exact, 35445 author = {G. Di Pillo and L. Grippo}, 35446 title = {An Exact Penalty Method with Global Convergence Properties for Nonlinear 35447 Programming Problems}, 35448 journal = {Mathematical Programming}, 35449 year = {1986}, 35450 volume = {36}, 35451 pages = {1--18} 35452} 35453 35454@InProceedings{ plambeck.fu.ea:throughput, 35455 author = {E. L. 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Computational Mathematics and Mathematical Physics}, 35534 year = {1973}, 35535 volume = {13}, 35536 pages = {42--58} 35537} 35538 35539@Article{ polyak:conjugate, 35540 author = {B. T. Polyak}, 35541 title = {The conjugate gradient method in extremal problems}, 35542 journal = {USSR Computational Mathematics and Mathematical Physics}, 35543 year = {1969}, 35544 volume = {9}, 35545 pages = {94--112}, 35546 note = {Translated from Russian} 35547} 35548 35549@Book{ polyak:introduction, 35550 author = {B. T. Polyak}, 35551 title = {Introduction to Optimization}, 35552 year = {1987}, 35553 publisher = {Optimization Software, Inc.}, 35554 address = {Publications Division, New York} 35555} 35556 35557@Unpublished{ polyak:methods, 35558 author = {R. A. Polyak}, 35559 title = {On the Methods of Centers}, 35560 year = {1988}, 35561 note = {Unpublished manuscript} 35562} 35563 35564@Unpublished{ polyak:sharp, 35565 author = {B. T. Polyak}, 35566 title = {Sharp Minima}, 35567 year = {1979}, 35568 note = {A Talk given at the {IIASA} Workshop on Generalized {L}agrangians and their 35569 Applications, {IIASA}, Laxenburg, Austria} 35570} 35571 35572@InProceedings{ polyak:smooth, 35573 author = {R. A. Polyak}, 35574 title = {Smooth Optimization Methods for Solving Nonlinear Extremal and Equilibrium 35575 Problems with Constraints}, 35576 booktitle = {Abstracts of the Papers of the 11th International Symposium on Mathematical 35577 Programming}, 35578 year = {1982}, 35579 address = {Bonn} 35580} 35581 35582@Article{ polychronopoulos.tsitsiklis:analysis, 35583 author = {G. H. Polychronopoulos and J. N. Tsitsiklis}, 35584 title = {Stochastic Shortest Path Problems with Recourse}, 35585 journal = {Networks}, 35586 year = {1996}, 35587 volume = {27}, 35588 pages = {133--143} 35589} 35590 35591@TechReport{ potra.bonnans:infeasible, 35592 author = {F. A. Potra and J. F. Bonnans}, 35593 title = {Infeasible path following algorithms for linear complementarity problems}, 35594 institution = {INRIA}, 35595 year = {1994}, 35596 month = dec, 35597 number = {RR--2445}, 35598 type = {Research Report} 35599} 35600 35601@Article{ potra.sheng:large-step, 35602 author = {F. A. Potra and R. Sheng}, 35603 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 35604 year = {1997}, 35605 journal = {SIAM Journal on Optimization}, 35606 volume = {7}, 35607 pages = {318--335} 35608} 35609 35610@Article{ potra:infeasible, 35611 author = {F. A. Potra}, 35612 title = {An infeasible interior-point predictor-corrector algorithm for linear 35613 programming}, 35614 journal = {SIAM Journal on Optimization}, 35615 year = {1996}, 35616 volume = {6}, 35617 pages = {19--32} 35618} 35619 35620@TechReport{ potra:onl, 35621 author = {F. A. Potra}, 35622 title = {An ${O}(n{L})$ infeasible--interior--point algorithm for {LCP} with quadratic 35623 convergence.}, 35624 institution = {Department of Mathematics, The University of Iowa}, 35625 address = {Iowa City, Iowa}, 35626 year = {1994}, 35627 number = {50}, 35628 type = {Reports on Computational Mathematics} 35629} 35630 35631@TechReport{ potra:predictor-corrector, 35632 author = {F. A. Potra}, 35633 title = {On a predictor-corrector method for solving linear programs from infeasible 35634 starting points}, 35635 institution = {Department of Mathematics, University of Iowa}, 35636 address = {Iowa City, Iowa}, 35637 year = {1992}, 35638 number = {34}, 35639 type = {Reports on Computational Mathematics} 35640} 35641 35642@TechReport{ potra:quadratically, 35643 author = {F. A. Potra}, 35644 title = {A quadratically convergent infeasible interior-point algorithm for linear 35645 programming}, 35646 institution = {Department of Mathematics, University of Iowa}, 35647 year = {1992}, 35648 number = {28}, 35649 address = {Iowa City, Iowa}, 35650 month = jul 35651} 35652 35653@InCollection{ powell:convergence, 35654 author = {M. J. D. Powell}, 35655 title = {The Convergence of Variable Metric Methods for Nonlinearly Constrained 35656 Optimization Calculations}, 35657 crossref = {mangasarian.meyer.ea:nonlinear*3}, 35658 pages = {27--63} 35659} 35660 35661@InProceedings{ powell:direct, 35662 author = {M. J. D. Powell}, 35663 title = {A Direct Search Optimization Method that Models the Objective and Constraint 35664 Functions by Linear Interpolation}, 35665 booktitle = {Advances in Optimization and Numerical Analysis, Proceedings of the Sixth 35666 Workshop on Optimization and Numerical Analysis, Oaxaca, Mexico}, 35667 volume = {275}, 35668 year = {1994}, 35669 publisher = {Kluwer Academic Publishers}, 35670 pages = {51--67}, 35671 address = {Dordrecht, The Netherlands} 35672} 35673 35674@Article{ powell:efficient, 35675 author = {M. J. D. Powell}, 35676 title = {An Efficient Method for Finding the Minimum of a Function of Several Variables 35677 without Calculating Derivatives}, 35678 journal = {Computer Journal}, 35679 year = {1964}, 35680 volume = {17}, 35681 pages = {155--162} 35682} 35683 35684@InCollection{ powell:general, 35685 author = {M. J. D. 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Powell}, 35706 title = {{K}armarkar's algorithm: a view from nonlinear programming}, 35707 institution = {Department of Applied Mathematics and Theoretical Physics, University of 35708 Cambridge}, 35709 year = {1989}, 35710 month = nov, 35711 address = {Cambridge, CB3 9EW, England} 35712} 35713 35714@InCollection{ powell:method, 35715 author = {M. J. D. Powell}, 35716 title = {A Method for Nonlinear Constraints in Minimization Problems}, 35717 booktitle = {Optimization}, 35718 year = {1969}, 35719 editor = {R. Fletcher}, 35720 publisher = {Academic Press}, 35721 address = {London}, 35722 pages = {283--298} 35723} 35724 35725@Book{ prekopa:stochastic, 35726 author = {A. Pr{\'{e}}kopa}, 35727 title = {Stochastic Programming}, 35728 publisher = {Kluwer Academic Publishers}, 35729 year = {1995}, 35730 address = {Dordrecht, The Netherlands} 35731} 35732 35733@Book{ press.flannery.ea:numerical, 35734 author = {William H. Press and Brian P. Flannery and Saul A. Teukolsky and William T. 35735 Vetterling}, 35736 title = {Numerical Recipes : the Art of Scientific Computing}, 35737 publisher = {Cambridge University Press}, 35738 year = {1988} 35739} 35740 35741@Article{ pruyne.livny:interfacing, 35742 author = {J. Pruyne and M. Livny}, 35743 title = {Interfacing {C}ondor and {PVM} to Harness the Cycles of Workstation Clusters}, 35744 journal = {Journal on Future Generations of Computer Systems}, 35745 volume = {12}, 35746 year = {1996}, 35747 pages = {67--85} 35748} 35749 35750@InCollection{ pruyne.livny:parallel, 35751 author = {J. Pruyne and M. Livny}, 35752 title = {Parallel Processing on Dynamic Resources using {CARMI}}, 35753 booktitle = {Job Scheduling Strategies for Parallel Processing}, 35754 publisher = {Springer-Verlag}, 35755 year = {1995}, 35756 editor = {D. G. Feitelson and L. Rudolph}, 35757 volume = {949}, 35758 series = {Lecture Notes in Computer Science} 35759} 35760 35761@PhDThesis{ pruyne:resource, 35762 author = {J. C. Pruyne}, 35763 title = {Resource Management Services for Parallel Applications}, 35764 school = {University of Wisconsin--Madison}, 35765 year = {1996}, 35766 address = {Madison, Wisconsin} 35767} 35768 35769@Book{ pshenichny.danilin:numerical, 35770 author = {B. N. Pshenichny and Yu. M. Danilin}, 35771 title = {Numerical Methods in Extremal Problems}, 35772 year = {1978}, 35773 publisher = {MIR Publishers}, 35774 address = {Moscow} 35775} 35776 35777@TechReport{ qi.chen:globally, 35778 author = {L. Qi and X. Chen}, 35779 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 35780 institution = {School of Mathematics, University of New South Wales}, 35781 year = {1993}, 35782 annote = {revised}, 35783 address = {Sydney} 35784} 35785 35786@Article{ qi.jiang:semismooth, 35787 author = {L. Qi and H. Jiang}, 35788 title = {Semismooth {K}arush--{K}uhn--{T}ucker Equations and Convergence Analysis of 35789 {N}ewton Methods and Quasi--{N}ewton Methods for Solving these Equations}, 35790 journal = {Mathematics of Operations Research}, 35791 volume = {22}, 35792 pages = {301--325}, 35793 year = {1997} 35794} 35795 35796@TechReport{ qi.peng:unconstrained, 35797 author = {H. -D. Qi and J. -M. Peng}, 35798 title = {A New Unconstrained Optimization Approach for Nonlinear Complementarity 35799 Problems}, 35800 institution = {State Key Laboratory of Scientific and Engineering Computing, Academic Sinica}, 35801 year = {1996}, 35802 type = {Technical Report}, 35803 address = {Beijing} 35804} 35805 35806@InCollection{ qi.sun:survey, 35807 author = {L. Qi and D. Sun}, 35808 title = {A Survey of Some Nonsmooth Equations and Smoothing {N}ewton Methods}, 35809 year = {1999}, 35810 editor = {A. Eberhard and B. Glover and R. Hill and D. Ralph}, 35811 booktitle = {Progress in Optimization}, 35812 pages = {121--146}, 35813 series = {Applied Optimization}, 35814 volume = {30}, 35815 publisher = {Kluwer Academic Publishers}, 35816 address = {Dordrecht} 35817} 35818 35819@Article{ qi.sun:nonsmooth, 35820 author = {L. Qi and J. Sun}, 35821 title = {A Nonsmooth Version of {N}ewton's Method}, 35822 journal = {Mathematical Programming}, 35823 year = {1993}, 35824 volume = {58}, 35825 pages = {353--368} 35826} 35827 35828@Article{ qi:convergence, 35829 author = {L. Qi}, 35830 title = {Convergence Analysis of Some Algorithms for Solving Nonsmooth Equations}, 35831 journal = {Mathematics of Operations Research}, 35832 year = {1993}, 35833 volume = {18}, 35834 pages = {227--244} 35835} 35836 35837@TechReport{ qi:regular, 35838 author = {L. 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Rockafellar}, 36347 title = {Conjugate Duality and Optimization}, 36348 year = {1974}, 36349 publisher = {SIAM}, 36350 address = {Philadelphia, Pennsylvania}, 36351 volume = {16}, 36352 series = {Conference Board of the Mathematical Sciences} 36353} 36354 36355@Book{ rockafellar:convex, 36356 author = {R. T. Rockafellar}, 36357 title = {Convex Analysis}, 36358 year = {1970}, 36359 publisher = {Princeton University Press}, 36360 address = {Princeton, New Jersey} 36361} 36362 36363@Article{ rockafellar:first-, 36364 author = {R. T. Rockafellar}, 36365 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 36366 journal = {Transactions of the American Mathematical Society}, 36367 year = {1988}, 36368 volume = {307}, 36369 pages = {75--108} 36370} 36371 36372@InProceedings{ rockafellar:generalized, 36373 author = {R. T. Rockafellar}, 36374 title = {A Generalized Approach to Linear-Quadratic Programming}, 36375 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36376 Applications}, 36377 year = {1986}, 36378 pages = {58--66}, 36379 note = {(Xi'an, China)} 36380} 36381 36382@InProceedings{ rockafellar:generalized*1, 36383 crossref = {bachem.grotschel.ea:mathematical}, 36384 author = {R. T. Rockafellar}, 36385 title = {Generalized Subgradients in Mathematical Programming}, 36386 pages = {368--390} 36387} 36388 36389@InCollection{ rockafellar:large-scale, 36390 author = {R. T. Rockafellar}, 36391 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36392 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36393 chapter = {15}, 36394 year = {1991}, 36395 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 36396 publisher = {SIAM Publications}, 36397 pages = {247--261} 36398} 36399 36400@Article{ rockafellar:linear-quadratic, 36401 author = {R. T. Rockafellar}, 36402 title = {Linear-Quadratic Programming and Optimal Control}, 36403 journal = {SIAM Journal on Control and Optimization}, 36404 year = {1987}, 36405 volume = {25}, 36406 pages = {781--814} 36407} 36408 36409@Article{ rockafellar:maximality, 36410 author = {R. T. Rockafellar}, 36411 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 36412 journal = {Transactions of the American Mathematical Society}, 36413 year = {1970}, 36414 volume = {149}, 36415 pages = {75--88} 36416} 36417 36418@InCollection{ rockafellar:monotone, 36419 author = {R. T. Rockafellar}, 36420 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 36421 crossref = {mangasarian.meyer.ea:nonlinear*3}, 36422 pages = {1--26} 36423} 36424 36425@Article{ rockafellar:monotone*1, 36426 author = {R. T. Rockafellar}, 36427 title = {Monotone Operators and the Proximal Point Algorithm}, 36428 journal = {SIAM Journal on Control and Optimization}, 36429 year = {1976}, 36430 volume = {14}, 36431 pages = {877--898} 36432} 36433 36434@Article{ rockafellar:multiplier, 36435 author = {R. T. Rockafellar}, 36436 title = {The Multiplier Method of {H}estenes and {P}owell Applied to Convex Programming}, 36437 journal = {Journal of Optimization Theory and Applications}, 36438 year = {1973}, 36439 volume = {12}, 36440 pages = {555--562} 36441} 36442 36443@Article{ rockafellar:multistage, 36444 author = {R. T. Rockafellar}, 36445 title = {Multistage Convex Programming and Discrete-Time Optimal Control}, 36446 journal = {Control and Cybernetics}, 36447 year = {1988}, 36448 volume = {17}, 36449 number = {2-3}, 36450 pages = {225--245} 36451} 36452 36453@Book{ rockafellar:network, 36454 author = {R. T. Rockafellar}, 36455 title = {Network Flows and Monotropic Optimization}, 36456 publisher = {John Wiley}, 36457 year = {1984}, 36458 address = {New York} 36459} 36460 36461@Article{ rodrigues:mixed, 36462 author = {H. C. Rodrigues}, 36463 title = {A mixed variational formulation for shape optimization of solids with contact 36464 conditions}, 36465 journal = {Structural Optimization}, 36466 volume = {6}, 36467 year = {1993}, 36468 pages = {19--28} 36469} 36470 36471@Book{ rodrigues:obstacle, 36472 author = {J. F. Rodrigues}, 36473 title = {Obstacle Problems in Mathematical Physics}, 36474 publisher = {Elsevier Publishing Company}, 36475 address = {Amsterdam}, 36476 year = {1987} 36477} 36478 36479@Book{ roos.terlaky.ea:theory, 36480 author = {C. Roos and T. Terlaky and J.--Ph. 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{Fr\'{e}d\'{e}ric Alauzet}, 39134 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 39135 year = {2010} 39136} 39137 39138@Article{ chan1994qmrcgs, 39139 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 39140 systems}, 39141 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 39142 and Tong, Charles H}, 39143 journal = {SIAM Journal on Scientific Computing}, 39144 volume = {15}, 39145 number = {2}, 39146 pages = {338--347}, 39147 year = {1994}, 39148 publisher = {SIAM} 39149} 39150 39151@Article{ ghai2019comparison, 39152 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 39153 nonsymmetric linear systems}, 39154 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 39155 journal = {Numerical Linear Algebra with Applications}, 39156 volume = {26}, 39157 number = {1}, 39158 pages = {e2215}, 39159 year = {2019}, 39160 publisher = {Wiley 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Knepley}, 39167 journal = {International Journal on Numerical Methods in Engineering}, 39168 note = {Submitted}, 39169 year = {2022} 39170} 39171 39172@Article{ nathawaniknepley2022, 39173 title = {Droplet formation simulation using mixed finite elements}, 39174 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39175 journal = {Physics of Fluids}, 39176 volume = {34}, 39177 pages = {064105}, 39178 doi = {10.1063/5.0089752}, 39179 year = {2022} 39180} 39181 39182@InProceedings{ nathawaniknepley2022b, 39183 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 39184 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39185 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 39186 (ICCFD11)}, 39187 editor = {Christoph Brehm and Shishir Pandya}, 39188 number = {4103}, 39189 year = {2022} 39190} 39191 39192@Article{ nathawaniknepley2023, 39193 title = {A one-dimensional mathematical model for shear-induced droplet formation in co-flowing fluids}, 39194 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39195 journal = {Theoretical and Computational Fluid Dynamics}, 39196 url = {https://rdcu.be/dFtlR}, 39197 doi = {10.1007/s00162-024-00690-5}, 39198 year = {2024} 39199} 39200 39201@InProceedings{ georgalisnathawaniknepleypatra2023, 39202 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 39203 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. Knepley and Abani 39204 Patra}, 39205 booktitle = {AIAA SciTech 2024}, 39206 note = {Accepted}, 39207 year = {2023} 39208} 39209 39210@Article{ brownbarrabeamsghaffariknepleymosesshakeristengelthompsonzhang2022, 39211 title = {Performance Portable Solid Mechanics via Matrix-Free $p$-Multigrid}, 39212 author = {Jed Brown and Valeria Barra and Natalie Beams and Leila Ghaffari and Matthew 39213 Knepley and William Moses and Rezgar Shakeri and Karen Stengel and Jeremy L. 39214 Thompson and Junchao Zhang}, 39215 doi = {10.48550/ARXIV.2204.01722}, 39216 url = {https://arxiv.org/abs/2204.01722}, 39217 publisher = {arXiv}, 39218 note = {Submitted}, 39219 year = {2022} 39220} 39221 39222@InCollection{ mayknepley2023, 39223 title = {Numerical Modeling of Subduction}, 39224 author = {Dave A. May and Matthew G. Knepley}, 39225 booktitle = {Dynamics of Plate Tectonics and Mantle Convection}, 39226 editor = {João C. Duarte}, 39227 pages = {539-571}, 39228 isbn = {978-0-323-85733-8}, 39229 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 39230 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 39231 year = {2023} 39232} 39233 39234@Article{ adamsknepley2023, 39235 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 39236 plasmas in {PETSc}}, 39237 author = {Mark F. Adams and Matthew G. Knepley}, 39238 url = {https://arxiv.org/abs/2302.10242}, 39239 note = {In preparation}, 39240 year = {2023}, 39241 petsc_uses = {DMPlex} 39242} 39243 39244@Article{ finnknepleypusztayadams2023, 39245 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 39246 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. 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Finn}, 39291 type = {{PhD} thesis}, 39292 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 39293 Engineering}, 39294 address = {Buffalo, NY}, 39295 month = may, 39296 year = {2023} 39297} 39298 39299@PhDThesis{ nathawanithesis2023, 39300 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 39301 author = {Darsh Kiritbhai Nathawani}, 39302 type = {{PhD} thesis}, 39303 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 39304 Engineering}, 39305 address = {Buffalo, NY}, 39306 month = may, 39307 year = {2023} 39308} 39309 39310@article{MckayEriksonKozdon2019, 39311 title = {A computational method for earthquake cycles within anisotropic media}, 39312 author = {Maricela Best Mckay and Brittany A Erickson and Jeremy E Kozdon}, 39313 journal = {Geophysical Journal International}, 39314 volume = {219}, 39315 number = {2}, 39316 pages = {816--833}, 39317 year = {2019}, 39318} 39319 39320@article{EricksonOReillyNordstrom2019, 39321 title = {Accuracy of stable, high-order finite difference methods for hyperbolic systems with non-smooth wave speeds}, 39322 author = {Brittany A Erickson and Ossian O’Reilly and Jan Nordstr{\"o}m}, 39323 journal = {Journal of Scientific Computing}, 39324 volume = {81}, 39325 pages = {2356--2387}, 39326 year = {2019}, 39327} 39328 39329@article{KozdonEricksonWilcox2021, 39330 title = {Hybridized summation-by-parts finite difference methods}, 39331 author = {Jeremy E Kozdon and Brittany A Erickson and Lucas C Wilcox}, 39332 journal = {Journal of Scientific Computing}, 39333 volume = {87}, 39334 number = {3}, 39335 pages = {85}, 39336 year = {2021}, 39337} 39338 39339@article{SEAS2022, 39340 title = {Community-driven code comparisons for three-dimensional dynamic modeling of sequences of earthquakes and aseismic slip}, 39341 author = {Junle Jiang and Brittany A Erickson and Val{\`e}re R Lambert and Jean-Paul Ampuero and Ryosuke Ando and Sylvain D Barbot and Camilla Cattania and Luca Dal Zilio and Benchun Duan and Eric M Dunham and Alice-Agnes Gabriel and Nadia Lapusta and Duo Li and Meng Li and Dunyu Liu and Yajing Liu and So Ozawa and Casper Pranger and Ylona van Dinther}, 39342 journal = {Journal of Geophysical Research: Solid Earth}, 39343 volume = {127}, 39344 number = {3}, 39345 pages = {e2021JB023519}, 39346 year = {2022}, 39347} 39348 39349@article{EricksonKozdonHarvey2022, 39350 title = {A non-stiff summation-by-parts finite difference method for the scalar wave equation in second order form: Characteristic boundary conditions and nonlinear interfaces}, 39351 author = {Brittany A Erickson and Jeremy E Kozdon and Tobias Harvey}, 39352 journal = {Journal of Scientific Computing}, 39353 volume = {93}, 39354 number = {1}, 39355 pages = {17}, 39356 year = {2022}, 39357} 39358 39359@article{RuckerEriksonKarlstromLeeGopalakrishnan2022, 39360 title = {A Computational Framework for Time-Dependent Deformation in Viscoelastic Magmatic Systems}, 39361 author = {Cody Rucker and Brittany A Erickson and Leif Karlstrom and Brian Lee and Jay Gopalakrishnan}, 39362 journal = {Journal of Geophysical Research: Solid Earth}, 39363 volume = {127}, 39364 number = {9}, 39365 pages = {e2022JB024506}, 39366 year = {2022}, 39367} 39368 39369@article{HarveyEriksonKozdon2023, 39370 title = {A High-order Accurate Summation-by-Parts Finite Difference Method for Fully-dynamic Earthquake Sequence Simulations within Sedimentary Basins}, 39371 author = {Tobias W Harvey and Brittany A Erickson and Jeremy E Kozdon}, 39372 journal = {Journal of Geophysical Research: Solid Earth}, 39373 pages = {e2022JB025357}, 39374 year = {2023}, 39375} 39376 39377@article{SEAS2023, 39378 title = {Incorporating full elastodynamic effects and dipping fault geometries in community code verification exercises for simulations of earthquake sequences and aseismic slip {(SEAS)}}, 39379 author = {Brittany A Erickson and Junle Jiang and Val{\`e}re Lambert and Sylvain D Barbot and Mohamed Abdelmeguid and Martin Almquist and Jean-Paul Ampuero and Ryosuke Ando and Camilla Cattania and Alexandre Chen and Luca Dal Zilio and Shuai Deng and Eric M. 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