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} 11373 11374@Article{ gottliebketchesonshu2009, 11375 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 11376 title = {{High order strong stability preserving time discretizations}}, 11377 journal = {Journal of Scientific Computing}, 11378 volume = {38}, 11379 number = {3}, 11380 pages = {251--289}, 11381 doi = {10.1007/s10915-008-9239-z}, 11382 year = {2009} 11383} 11384 11385@Article{ ketcheson_2008, 11386 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 11387 Low-Storage Implementations}, 11388 author = {D.I. Ketcheson}, 11389 journal = {SIAM Journal on Scientific Computing}, 11390 year = {2008}, 11391 number = {4}, 11392 pages = {2113--2136}, 11393 volume = {30}, 11394 doi = {10.1137/07070485X}, 11395 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 11396 RungeKutta methods}, 11397 publisher = {SIAM} 11398} 11399 11400@Article{ jansen_2000, 11401 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 11402 equations with a stabilized finite element method}, 11403 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 11404 journal = {Computer Methods in Applied Mechanics and Engineering}, 11405 year = {2000}, 11406 number = {3}, 11407 pages = {305--319}, 11408 volume = {190}, 11409 publisher = {Elsevier} 11410} 11411 11412@Article{ butcher_2007, 11413 title = {Error propagation of general linear methods for ordinary differential equations}, 11414 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 11415 journal = {Journal of Complexity}, 11416 year = {2007}, 11417 number = {4-6}, 11418 pages = {560--580}, 11419 volume = {23}, 11420 abstract = {We discuss error propagation for general linear methods for ordinary differential 11421 equations up to terms of order p+2, where p is the order of the method. These 11422 results are then applied to the estimation of local discretization errors for 11423 methods of order p and for the adjacent order p+1. The results of numerical 11424 experiments confirm the reliability of these estimates. This research has 11425 applications in the design of robust stepsize and order changing strategies for 11426 algorithms based on general linear methods.}, 11427 doi = {10.1016/j.jco.2007.01.009}, 11428 issn = {0885-064X} 11429} 11430 11431@Article{ constantinescu_a2010a, 11432 title = {Extrapolated implicit-explicit time stepping}, 11433 author = {E.M. Constantinescu and A. Sandu}, 11434 journal = {SIAM Journal on Scientific Computing}, 11435 year = {2010}, 11436 number = {6}, 11437 pages = {4452-4477}, 11438 volume = {31}, 11439 comment = {Preprint \# ANL/MCS-P1612-0409}, 11440 doi = {10.1137/080732833} 11441} 11442 11443@InProceedings{ devito2011liszt, 11444 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 11445 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 11446 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 11447 Aiken, Alex and Duraisamy, Karthik and others}, 11448 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 11449 Networking, Storage and Analysis}, 11450 pages = {9}, 11451 year = {2011}, 11452 organization = {ACM} 11453} 11454 11455@Article{ devito2011designing, 11456 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 11457 author = {DeVito, Zachary and Hanrahan, Pat}, 11458 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 11459 year = {2011} 11460} 11461 11462@Misc{ pgasintro, 11463 author = {Tim Stitt}, 11464 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 11465 Model}, 11466 note = {\url{http://cnx.org/content/m20649/latest/}} 11467} 11468 11469@InProceedings{ el2006upc, 11470 title = {UPC: unified parallel C}, 11471 author = {El-Ghazawi, Tarek and Smith, Lauren}, 11472 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 11473 pages = {27}, 11474 year = {2006}, 11475 organization = {ACM} 11476} 11477 11478@InProceedings{ numrich1998co, 11479 title = {Co-Array Fortran for parallel programming}, 11480 author = {Numrich, Robert W and Reid, John}, 11481 booktitle = {ACM Sigplan Fortran Forum}, 11482 volume = {17}, 11483 number = {2}, 11484 pages = {1--31}, 11485 year = {1998}, 11486 organization = {ACM} 11487} 11488 11489@Article{ aiken1997titanium, 11490 title = {Titanium: A high-performance Java dialect}, 11491 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 11492 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 11493 Geoff and Semenzato, Luigi and others}, 11494 year = {1997} 11495} 11496 11497@Article{ charles2005x10, 11498 title = {X10: an object-oriented approach to non-uniform cluster computing}, 11499 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 11500 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 11501 Sarkar, Vivek}, 11502 journal = {Acm Sigplan Notices}, 11503 volume = {40}, 11504 number = {10}, 11505 pages = {519--538}, 11506 year = {2005}, 11507 publisher = {ACM} 11508} 11509 11510@Article{ chamberlain2007parallel, 11511 title = {Parallel programmability and the chapel language}, 11512 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 11513 journal = {International Journal of High Performance Computing Applications}, 11514 volume = {21}, 11515 number = {3}, 11516 pages = {291--312}, 11517 year = {2007}, 11518 publisher = {SAGE Publications} 11519} 11520 11521@InProceedings{ charmppoopsla93, 11522 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 11523 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 11524 editor = {Paepcke, A.}, 11525 fulleditor = {Paepcke, Andreas}, 11526 pages = {91--108}, 11527 month = sep, 11528 year = {1993}, 11529 booktitle = {{Proceedings of OOPSLA'93}}, 11530 publisher = {{ACM Press}} 11531} 11532 11533@InProceedings{ hewitt1973universal, 11534 title = {A universal modular actor formalism for artificial intelligence}, 11535 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 11536 booktitle = {Proceedings of the 3rd international joint conference on Artificial 11537 intelligence}, 11538 pages = {235--245}, 11539 year = {1973}, 11540 organization = {Morgan Kaufmann Publishers Inc.} 11541} 11542 11543@Book{ yonezawa1990abcl, 11544 title = {ABCL: an object-oriented concurrent system}, 11545 author = {Yonezawa, Akinori}, 11546 year = {1990}, 11547 publisher = {MIT press} 11548} 11549 11550@InProceedings{ dally1988object, 11551 title = {Object-oriented concurrent programming in CST}, 11552 author = {Dally, William J and Chien, Andrew A}, 11553 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 11554 applications: Architecture, software, computer systems, and general issues-Volume 11555 1}, 11556 pages = {434--439}, 11557 year = {1988}, 11558 organization = {ACM} 11559} 11560 11561@Article{ grimshaw1993easy, 11562 title = {Easy-to-use object-oriented parallel processing with Mentat}, 11563 author = {Grimshaw, Andrew S.}, 11564 journal = {Computer}, 11565 volume = {26}, 11566 number = {5}, 11567 pages = {39--51}, 11568 year = {1993}, 11569 publisher = {IEEE} 11570} 11571 11572@InProceedings{ gannon1991object, 11573 title = {Object oriented parallelism: pC++ ideas and experiments}, 11574 author = {Gannon, Dennis and Lee, JK}, 11575 booktitle = {Proceedings of}, 11576 pages = {13--23}, 11577 year = {1991} 11578} 11579 11580@InProceedings{ lau1992object, 11581 title = {An object-oriented class library for scalable parallel heuristic search}, 11582 author = {Lau, Wing-cheong and Singh, Vineet}, 11583 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 11584 pages = {252--267}, 11585 year = {1992}, 11586 organization = {Springer} 11587} 11588 11589@Book{ chase1989amber, 11590 title = {The Amber system: Parallel programming on a network of multiprocessors}, 11591 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 11592 Littlefield, Richard}, 11593 volume = {23}, 11594 number = {5}, 11595 year = {1989}, 11596 publisher = {ACM} 11597} 11598 11599@InProceedings{ kaiser2009parallex, 11600 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 11601 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 11602 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 11603 pages = {394--401}, 11604 year = {2009}, 11605 organization = {IEEE} 11606} 11607 11608@TechReport{ ipm, 11609 author = {Barry F. Smith}, 11610 title = {A New Parallel Programming Model for Computer Simulation}, 11611 institution = {Argonne National Laboratory}, 11612 year = {2014}, 11613 number = {ANL/MCS-P5135-0414} 11614} 11615 11616@Article{ groppsnir, 11617 author = {William Gropp and Marc Snir}, 11618 title = {Programming for Exascale Computers}, 11619 journal = {Computing in Science and Engineering}, 11620 volume = {15}, 11621 number = {6}, 11622 issn = {1521-9615}, 11623 year = {2013}, 11624 pages = {27-35}, 11625 doi = {10.1109/MCSE.2013.96}, 11626 publisher = {IEEE Computer Society}, 11627 address = {Los Alamitos, CA} 11628} 11629 11630@Book{ mpi3, 11631 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 11632 author = {Message Passing Interface Forum}, 11633 year = {2012}, 11634 publisher = {High Performance Computing Center Stuttgart (HLRS)} 11635} 11636 11637@Book{ openmp4, 11638 title = {OpenMP Application Program Interface, Version 4.0}, 11639 year = {2013}, 11640 publisher = {OpenMP Architecture Review Board} 11641} 11642 11643@InProceedings{ hartono2009annotation, 11644 title = {Annotation-based empirical performance tuning using {Orio}}, 11645 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 11646 booktitle = {Parallel \& Distributed Processing, 2009. 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Markus}, 12839 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 12840 for {PDE} Based Applications}, 12841 year = {1994}, 12842 institution = {Department of Computer Sciences, Purdue University}, 12843 number = {CSD-TR-94-021} 12844} 12845 12846@Unpublished{ ilu-web-page, 12847 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 12848 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 12849 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 12850} 12851 12852@Unpublished{ doe2k-web-page, 12853 title = {{DOE2000 Initiative} {W}eb page}, 12854 note = {http://www.mcs.anl.gov/DOE2000}, 12855 key = {DOE2000 Initiative} 12856} 12857 12858@Misc{ pvode-web-page, 12859 title = {{PVODE} {W}eb Page}, 12860 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 12861 author = {A. {Hindmarsh et al.}} 12862} 12863 12864@Book{ szyperski97, 12865 author = {Clemens Szyperski}, 12866 title = {Component Software: Beyond Object-Oriented Programming}, 12867 publisher = {ACM Press}, 12868 address = {New York}, 12869 year = {1997} 12870} 12871 12872@Unpublished{ petsc:coloringuse, 12873 title = {Code for computing sparse {J}acobians}, 12874 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12875 institution = {Argonne National Laboratory} 12876} 12877 12878@Unpublished{ petsc:external, 12879 author = {B. F. {Smith et al.}}, 12880 title = {{External Software Used by PETSc}}, 12881 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12882 institution = {Argonne National Laboratory} 12883} 12884 12885@Unpublished{ petsc:use-by-external-packages, 12886 author = {B. F. {Smith et al.}}, 12887 title = {{Software Packages that Use or Interface to PETSc}}, 12888 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 12889 institution = {Argonne National Laboratory} 12890} 12891 12892@Unpublished{ petsc:prizes, 12893 author = {B. F. {Smith et al.}}, 12894 title = {{Prizes Won Using PETSc}}, 12895 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12896 institution = {Argonne National Laboratory} 12897} 12898 12899@Unpublished{ petsc:csgf, 12900 author = {B. F. {Smith et al.}}, 12901 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 12902 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12903 institution = {Argonne National Laboratory} 12904} 12905 12906@Unpublished{ flash-web-page, 12907 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 12908 {W}eb Page}, 12909 note = {http://www.asci.uchicago.edu}, 12910 author = {R. {Rosner et al.}}, 12911 institution = {University of Chicago} 12912} 12913 12914@Unpublished{ esi-web-page, 12915 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 12916 note = {http://z.ca.sandia.gov/esi}, 12917 author = {R. {Clay et al.}} 12918} 12919 12920@Unpublished{ infobus-web-page, 12921 title = {{I}nfo{B}us {W}eb Page}, 12922 note = {http://www.java.sun.com/beans/infobus}, 12923 key = {infobus} 12924} 12925 12926@Unpublished{ xray-web-page, 12927 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 12928 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 12929 note = {http://www.mcs.anl.gov/xray/}, 12930 institution = {Argonne National Laboratory} 12931} 12932 12933@InProceedings{ kohn98, 12934 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 12935 title = {Language Interoperability Mechanisms for High-Performance Scientific 12936 Applications}, 12937 publisher = {SIAM}, 12938 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12939 Scientific and Engineering Computing}, 12940 year = {1999}, 12941 pages = {30-39} 12942} 12943 12944@InProceedings{ kohn01, 12945 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 12946 title = {Divorcing Language Dependencies from a Scientific Software Library}, 12947 publisher = {SIAM}, 12948 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 12949 year = {2001} 12950} 12951 12952@InProceedings{ freitag_jones_plassmann98, 12953 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 12954 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 12955 publisher = {SIAM}, 12956 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12957 Scientific and Engineering Computing}, 12958 year = {1999}, 12959 pages = {215-224} 12960} 12961 12962@Book{ templates, 12963 author = {R. Barrett and M. Berry and T. F. Chan and J. Demmel and J. Donato and J. 12964 Dongarra and V. Eijkhout and R. Pozo and C. Romine and H. Van der Vorst }, 12965 title = {Templates for the Solution of Linear Systems: Building Blocks for Iterative 12966 Methods}, 12967 publisher = {SIAM}, 12968 year = {1994}, 12969 address = {Philadelphia, PA} 12970} 12971 12972@InProceedings{ parasha2, 12973 author = {M. Parashar and J. C. Browne and C. Edwards and K. Klimkowski}, 12974 title = { A Common Data Management Infrastructure for Parallel Adaptive Algorithms for 12975 {PDE} Solutions}, 12976 booktitle = {SC97 Proceedings}, 12977 publisher = {IEEE Computer Society Press}, 12978 year = {1997} 12979} 12980 12981@TechReport{ parasha, 12982 author = {M. Parashar and J. C. Browne}, 12983 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 12984 Techniques}, 12985 institution = {Department of Computer Science, University of Texas at Austin}, 12986 year = {1995} 12987} 12988 12989@Article{ parti, 12990 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 12991 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 12992 Memory Architectures}, 12993 journal = {Journal of Parallel and Distributed Computing}, 12994 year = {1994}, 12995 volume = {22}, 12996 pages = {462--478} 12997} 12998 12999@Article{ mparti, 13000 author = {G. Agrawal and A. Sussman and J. 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Ross}, 13024 publisher = {University of Toronto}, 13025 pages = {379--386}, 13026 year = {1994} 13027} 13028 13029@Article{ cs99, 13030 author = {X.-C. Cai and M. Sarkis}, 13031 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 13032 systems}, 13033 journal = {SIAM J. Scientific Computing}, 13034 year = {1999}, 13035 volume = {21}, 13036 pages = {792-797} 13037} 13038 13039@Article{ cai2003restricted, 13040 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 13041 positive definite linear systems}, 13042 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 13043 journal = {SIAM Journal on Numerical Analysis}, 13044 volume = {41}, 13045 issue = {1}, 13046 pages = {1209--1231}, 13047 year = {2003}, 13048 doi = {10.1137/S0036142901389621} 13049} 13050 13051@TechReport{ caisaad, 13052 author = {Xiao-Chuan Cai and Youcef Saad}, 13053 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 13054 institution = {Army High Performance Computing Research Center, University of Minnesota }, 13055 year = {1993}, 13056 number = {Preprint 93-027 }, 13057 note = {SIAM J. Sci. Comp. 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Supercomputing Applications}, 13094 volume = {8}, 13095 number = {3/4}, 13096 year = {1994}, 13097 key = {MPI Standard - final} 13098} 13099 13100@Unpublished{ npb-web-page, 13101 key = {NAS Parallel Benchmarks}, 13102 title = {{NAS} {P}arallel {B}enchmarks {W}eb page}, 13103 note = {http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html}, 13104 year = {1996}, 13105 month = dec 13106} 13107 13108@Book{ george81, 13109 title = {Computer Solution of Large Sparse Positive Definite Systems}, 13110 author = {Alan George and Joseph W. Liu}, 13111 publisher = {Prentice-Hall}, 13112 year = {1981}, 13113 key = {SparseDirect} 13114} 13115 13116@Book{ p4-book, 13117 title = {Portable Programs for Parallel Processors}, 13118 publisher = {Holt, Rinehart, {and} Winston}, 13119 year = {1987}, 13120 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 13121 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 13122 key = {P4Book} 13123} 13124 13125@Article{ stones, 13126 author = {H. L. Stone}, 13127 title = {Iterative solution of implicit approximations of multidimensional partial 13128 differential equations}, 13129 journal = {SIAM J. Numerical Analysis}, 13130 pages = {87--113}, 13131 volumne = {5}, 13132 year = {1968} 13133} 13134 13135@Article{ parallelstones, 13136 author = {J. S. Reeve and A. D. Scurr and J. H. Merlin}, 13137 title = {Parallel versions of {S}tones strongly implicit algorithm}, 13138 journal = {Concurrency and Computation: Practice and Experience}, 13139 pages = {1049--1062}, 13140 volumne = {13}, 13141 year = {2001} 13142} 13143 13144@Article{ p4-paper, 13145 author = {Ralph Butler and Ewing Lusk}, 13146 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 13147 journal = {Journal of Parallel Computing}, 13148 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 13149 Division preprint P362-0493)}, 13150 year = {1993} 13151} 13152 13153@TechReport{ picl, 13154 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 13155 title = {{PICL}: A portable instrumented communications library}, 13156 institution = {Oak Ridge National Laboratory}, 13157 number = {TM-11130}, 13158 year = {1990}, 13159 key = {PICL} 13160} 13161 13162@TechReport{ upshot, 13163 author = {Virginia Herrarte and Ewing Lusk}, 13164 title = {Studying Parallel Program Behavior with {U}pshot}, 13165 institution = {Argonne National Laboratory}, 13166 number = {ANL-91/15}, 13167 month = aug, 13168 year = {1991}, 13169 key = {Upshot} 13170} 13171 13172@TechReport{ p4-manual, 13173 author = {Ralph Butler and Ewing Lusk}, 13174 title = {User's Guide to the p4 Parallel Programming System}, 13175 institution = {Argonne National Laboratory}, 13176 number = {ANL-92/17}, 13177 month = oct, 13178 year = {1992}, 13179 key = {p4-Manual} 13180} 13181 13182@InProceedings{ oldparti, 13183 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 13184 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 13185 booktitle = {Proceedings of Supercomputing '93}, 13186 pages = {578--587}, 13187 year = {1993} 13188} 13189 13190@Article{ parti2, 13191 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 13192 and J. Saltz}, 13193 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 13194 journal = {ACM SIGPLAN Notices}, 13195 year = {1995}, 13196 pages = {68-79}, 13197 volume = {30}, 13198 number = {8} 13199} 13200 13201@Article{ parti3, 13202 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 13203 title = {Run-Time Parallelization and Scheduling of Loops}, 13204 journal = {IEEE Trans. Computers}, 13205 year = {1991}, 13206 pages = {604-612}, 13207 volume = {40}, 13208 number = {5} 13209} 13210 13211@InProceedings{ disz-lusk:wamtrace, 13212 author = {Terrence Disz and Ewing Lusk}, 13213 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 13214 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13215 year = {1987}, 13216 pages = {46--53} 13217} 13218 13219@InProceedings{ gorlick-kesselman:gauge, 13220 author = {Michael Gorlick and Carl Kesselman}, 13221 title = {Timing {Prolog} programs without Clocks}, 13222 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13223 year = {1996}, 13224 publisher = {Birkhauser} 13225} 13226 13227@TechReport{ aztec, 13228 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 13229 title = {Aztec User's Guide Version 1.1}, 13230 institution = {Sandia National Laboratories}, 13231 month = oct, 13232 year = {1995}, 13233 number = {SAND95/1559} 13234} 13235 13236@TechReport{ aztec2, 13237 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 13238 title = {Official {Aztec} User's Guide Version 2.1}, 13239 institution = {Sandia National Laboratories}, 13240 year = {1999} 13241} 13242 13243@Book{ taylor-chandy:pcn, 13244 author = {Chandy, M. and Taylor, S.}, 13245 title = {An Introduction to Parallel Programming}, 13246 year = {1991}, 13247 publisher = {Jones and Bartlett} 13248} 13249 13250@Book{ foster-taylor:strand, 13251 title = {Strand: New Concepts in Parallel Programming}, 13252 author = {Ian Foster and Stephen Taylor}, 13253 publisher = {Prentice-Hall}, 13254 adress = { Englewood Cliffs, New Jersey}, 13255 year = {1990} 13256} 13257 13258@Article{ aurora, 13259 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 13260 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 13261 Carlsson and A. Ciepielewski and B. Hausman}, 13262 title = {The Aurora OR-Parallel Prolog System}, 13263 journal = {New Generation Computing}, 13264 volume = {7}, 13265 number = {3}, 13266 year = {1990}, 13267 pages = {243--271} 13268} 13269 13270@TechReport{ roo, 13271 author = {E. Lusk and W. McCune and J. Slaney}, 13272 title = {Roo---a Parallel Theorem Prover}, 13273 institution = {Argonne National Laboratory}, 13274 number = {MCS--TM--149}, 13275 year = {1991} 13276} 13277 13278@TechReport{ heath-etheridge:vppp, 13279 author = {M. T. Heath and J. A. Etheridge}, 13280 title = {Visualizing the Performance of Parallel Programs}, 13281 institution = {Oak Ridge National Laboratory}, 13282 number = {ORNL TM-11813}, 13283 year = {1991} 13284} 13285 13286@TechReport{ chem:vis, 13287 author = {Ewing L. Lusk}, 13288 title = {Performance Visualization for Parallel Programs}, 13289 institution = {Argonne National Laboratory}, 13290 number = {ANL/MCS--P287--0192}, 13291 year = {1991}, 13292 note = {(to appear in {\em Theoretica Chimica Acta})} 13293} 13294 13295@TechReport{ picltrace, 13296 author = {P.~H.~Worley}, 13297 title = {A new {PICL} trace file format}, 13298 institution = {Oak Ridge National Laboratory}, 13299 number = {ORNL TM-12125}, 13300 month = jun, 13301 year = {1992} 13302} 13303 13304@InProceedings{ hideo, 13305 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 13306 title = {Inference of Phylogenetic trees using maximum likelihood}, 13307 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 13308 year = {1992}, 13309 pages = {247--262} 13310} 13311 13312@InProceedings{ dw90, 13313 author = {M. Dryja and O. Widlund}, 13314 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 13315 Problems}, 13316 booktitle = {Third International Symposium on Domain Decomposition Methods}, 13317 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 13318 year = {1990}, 13319 pages = {3-21}, 13320 publisher = {SIAM}, 13321 address = {Philadelphia}, 13322 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 13323 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 13324 references, good introduction to the theory. No computations}, 13325 key = {DryjaWidlund90 !AS} 13326} 13327 13328@Unpublished{ rosing, 13329 author = {Matt Rosing and Joel Saltz}, 13330 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 13331 key = {LowLatency}, 13332 note = {manuscript, 1992} 13333} 13334 13335@TechReport{ jp:incomplete, 13336 author = {Mark T. Jones and Paul E. Plassmann}, 13337 title = {An Improved Incomplete {C}holesky Factorization}, 13338 institution = {Argonne National Laboratory}, 13339 address = {Argonne, IL}, 13340 type = {Preprint}, 13341 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 13342 number = {MCS-P206-0191}, 13343 year = {1991}, 13344 key = {jones} 13345} 13346 13347@InCollection{ jp:ima, 13348 author = {Mark Jones and Paul Plassmann}, 13349 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 13350 booktitle = {Graph Theory and Sparse Matrix Computation}, 13351 publisher = {Springer-Verlag}, 13352 series = {The IMA Volumes in Mathematics and Its Applications}, 13353 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 13354 volume = {56}, 13355 year = {1993}, 13356 pages = {229--245} 13357} 13358 13359@Article{ pw98, 13360 author = {M. Pernice and H. F. Walker}, 13361 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 13362 journal = {SIAM J. Sci. Stat. Comput.}, 13363 year = {1998}, 13364 volume = {19}, 13365 pages = {302--318} 13366} 13367 13368@TechReport{ ysmp83, 13369 key = {Eisenstat}, 13370 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13371 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13372 institution = {Department of Computer Science, Yale University}, 13373 number = {YALE/DCS/RR-265}, 13374 month = apr, 13375 year = {1983} 13376} 13377 13378@InBook{ ysmp84, 13379 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13380 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13381 title = {Elliptic Problem Solvers II}, 13382 publisher = {Academic Press}, 13383 pages = {45--52}, 13384 editors = {G. Birkhoff and A. Schoenstadt}, 13385 year = {1984} 13386} 13387 13388@TechReport{ sparsekit, 13389 key = {Saad}, 13390 author = {Youcef Saad}, 13391 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 13392 institution = {Center for Supercomputing Research and Development, University of Illinois at 13393 Urbana-Champaign}, 13394 number = {1029}, 13395 year = {1990} 13396} 13397 13398@TechReport{ pde-user-ref, 13399 author = {Barry F. Smith}, 13400 title = {Extensible {PDE} Solvers Package Users Manual}, 13401 institution = {Argonne National Laboratory}, 13402 month = sep, 13403 year = {1994}, 13404 number = {ANL-93/40}, 13405 key = {Smith94 ! PDE} 13406} 13407 13408@TechReport{ bs-user-ref, 13409 author = {Mark T. Jones and Paul E. Plassmann}, 13410 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 13411 of Sparse Linear Systems}, 13412 institution = {Argonne National Laboratory}, 13413 month = dec, 13414 year = {1995}, 13415 number = {ANL-95/48} 13416} 13417 13418@TechReport{ snes-user-ref, 13419 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 13420 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 13421 institution = {Argonne National Laboratory}, 13422 month = feb, 13423 year = {1995}, 13424 number = {ANL/MCS-TM-193}, 13425 key = {GroppMcInnesSmith95 ! SNES} 13426} 13427 13428@TechReport{ sles-user-ref, 13429 author = {William D. Gropp and Barry F. Smith}, 13430 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 13431 institution = {Argonne National Laboratory}, 13432 month = mar, 13433 year = {1993}, 13434 number = {ANL-93/8}, 13435 key = {GroppSmith93 ! 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Smith}, 13467 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 13468 Methods}, 13469 institution = {Argonne National Laboratory}, 13470 month = aug, 13471 year = {1993}, 13472 number = {ANL-93/30}, 13473 key = {GroppSmith93 ! KSP} 13474} 13475 13476@TechReport{ mpi-chameleon, 13477 author = {William D. Gropp and Ewing Lusk}, 13478 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 13479 institution = {Argonne National Laboratory}, 13480 month = dec, 13481 year = {1992}, 13482 number = {ANL-92/47}, 13483 key = {GroppLusk92 ! MPI} 13484} 13485 13486@TechReport{ blockcomm-fortran, 13487 author = {William D. Gropp}, 13488 title = {Block{C}omm for {F}ortran}, 13489 institution = {Argonne National Laboratory}, 13490 month = may, 13491 year = {1993}, 13492 number = {ANL-93/00 (to appear)}, 13493 key = {Gropp93 ! BlockComm} 13494} 13495 13496@TechReport{ autodocument, 13497 author = {William D. Gropp}, 13498 title = {Automatic documentation of {C} programs}, 13499 institution = {Argonne National Laboratory}, 13500 month = may, 13501 year = {1993}, 13502 number = {ANL-93/00}, 13503 key = {Gropp93 ! Autodoc} 13504} 13505 13506@TechReport{ zipcode, 13507 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 13508 Manfred Morari}, 13509 title = {The {Z}ipcode message-passing system}, 13510 institution = {Lawrence Livermore National Laboratory}, 13511 month = sep, 13512 year = {1992}, 13513 number = {Unpublished}, 13514 key = {Skjellum92 ! Zipcode} 13515} 13516 13517@Article{ paragraph, 13518 author = {Michael T. Heath and Jennifer Etheridge Finger}, 13519 title = {Visualizing performance of parallel programs}, 13520 journal = {IEEE Software}, 13521 volume = {8}, 13522 number = {5}, 13523 month = sep, 13524 year = {1991}, 13525 pages = {29--39}, 13526 key = {Heath91 ! Paragraph} 13527} 13528 13529@Article{ gropp90, 13530 author = {William Gropp and Edward Smith}, 13531 title = {Computational Fluid Dynamics on Parallel Processors}, 13532 journal = {Computers and Fluids}, 13533 volume = {18}, 13534 year = {1990}, 13535 pages = {289--304}, 13536 key = {Gropp90 ! performance} 13537} 13538 13539@Article{ foster92, 13540 author = {Ian Foster and William Gropp and Rick Stevens}, 13541 title = {The parallel scalability of the spectral transform method}, 13542 journal = {Monthly Weather Review}, 13543 volume = {120}, 13544 year = {1992}, 13545 pages = {835--850}, 13546 key = {Foster92 ! performance} 13547} 13548 13549@InBook{ fgn, 13550 author = {R. Freund and G. H. Golub and N. Nachtigal}, 13551 title = {Iterative Solution of Linear Systems}, 13552 series = {Acta Numerica}, 13553 year = {1992}, 13554 publisher = {Cambridge University Press}, 13555 pages = {57--100} 13556} 13557 13558@TechReport{ nachtigal90, 13559 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 13560 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13561 institution = {Massachusetts Institute of Technology}, 13562 month = mar, 13563 year = {1990}, 13564 number = {90-2}, 13565 key = {Nachtigal | Krylov} 13566} 13567 13568@Article{ nachtigal1992fnm, 13569 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13570 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 13571 journal = {SIAM Journal on Matrix Analysis and Applications}, 13572 volume = {13}, 13573 pages = {778}, 13574 year = {1992}, 13575 publisher = {SIAM} 13576} 13577 13578@TechReport{ embree1999descriptive, 13579 title = {How descriptive are {GMRES} convergence bounds}, 13580 author = {Embree, M.}, 13581 year = {1999}, 13582 number = {08}, 13583 institution = {Oxford University Computing Laboratory} 13584} 13585 13586@Article{ vorst92, 13587 author = {H. van der Vorst}, 13588 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 13589 of nonsymmetric linear systems}, 13590 journal = {SIAM J. Sci. Stat. Comput.}, 13591 year = {1992}, 13592 volume = {13}, 13593 pages = {631--644} 13594} 13595 13596@Article{ eisenstat81, 13597 author = {S. Eisenstat}, 13598 title = {Efficient Implementation of a Class of {CG} Methods}, 13599 journal = {SIAM J. Sci. Stat. Comput.}, 13600 year = {1981}, 13601 volume = {2}, 13602 pages = {1--4} 13603} 13604 13605@Manual{ ibm-essl, 13606 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 13607 Reference}, 13608 organization = {IBM}, 13609 year = {1992}, 13610 key = {IBM-ESSL} 13611} 13612 13613@Manual{ ibm-eui, 13614 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 13615 Release 2.0}, 13616 organization = {IBM}, 13617 month = jun, 13618 year = {1994}, 13619 key = {IBM-EUI} 13620} 13621 13622@Manual{ ibm-euih, 13623 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 13624 organization = {IBM}, 13625 author = {Peter Hochschild}, 13626 year = {1993}, 13627 key = {IBM-EUIH} 13628} 13629 13630@TechReport{ mpi, 13631 title = {Document for a Standard Message-Passing Interface}, 13632 author = {Message Passing Interface Forum}, 13633 institution = {University of Tennessee}, 13634 number = {CS-93-214}, 13635 month = nov, 13636 year = {1993}, 13637 key = {MPI Standard} 13638} 13639 13640@Unpublished{ mpi-final-web, 13641 author = {Message Passing Interface Forum}, 13642 title = {{MPI}: A Message-Passing Interface Standard}, 13643 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 13644 year = {1994}, 13645 month = may 13646} 13647 13648@Book{ hockney-jesshope, 13649 author = {R. W. Hockney and C. R. Jesshope}, 13650 title = {Parallel Computers 2}, 13651 publisher = {Adam Hilger}, 13652 year = {1988} 13653} 13654 13655@Book{ cm-fortran, 13656 author = {{Thinking Machines Corporation}}, 13657 title = {Users Manual for CM-Fortran}, 13658 publisher = {Thinking Machines Corporation}, 13659 year = {1993} 13660} 13661 13662@TechReport{ chang93, 13663 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 13664 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 13665 institution = {Yale Department of Computer Science}, 13666 number = {YALEU/DCS/RR-994}, 13667 month = nov, 13668 year = {1993}, 13669 key = {BDD|diag} 13670} 13671 13672@InProceedings{ gropplevine93, 13673 author = {N. Galbreath and W. Gropp and D. Levine}, 13674 title = {Applications-Driven Parallel {I/O}}, 13675 booktitle = {Proceedings of Supercomputing '93}, 13676 year = {1993}, 13677 pages = {462--471} 13678} 13679 13680@Book{ siegle85, 13681 author = {H. J. Siegel}, 13682 title = {Interconnection Networks for Large Scale Parallel Processing}, 13683 publisher = {Lexington Books}, 13684 year = {1985}, 13685 key = {Network Comparison} 13686} 13687 13688@Article{ lawrie75, 13689 author = {D. H. Lawrie}, 13690 title = {Access and alignment of data in an array processor}, 13691 journal = {IEEE Transactions on Computers}, 13692 volume = {C-24}, 13693 number = {12}, 13694 month = dec, 13695 year = {1975}, 13696 pages = {1145--1155}, 13697 key = {Omega Network} 13698} 13699 13700@Book{ knuth1986, 13701 title = {The {\TeX}{Book}}, 13702 author = {Donald Ervin Knuth and Duane Bibby}, 13703 volume = {1993}, 13704 year = {1986}, 13705 publisher = {Addison-Wesley Reading, Massachusetts} 13706} 13707 13708@Book{ lamport86, 13709 author = {Leslie Lamport}, 13710 title = {{LaTeX}: A document preparation system}, 13711 publisher = {Addison-Wesley}, 13712 year = {1986}, 13713 key = {Latex Manual} 13714} 13715 13716@InProceedings{ gropp-lusk:unix-tools, 13717 author = {William Gropp and Ewing Lusk}, 13718 title = {Scalable {U}nix Tools on Parallel Processors}, 13719 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 13720 publisher = {IEEE}, 13721 pages = {56--62} 13722} 13723 13724@InProceedings{ jp:bell_prize, 13725 author = {Mark Jones and Paul Plassmann}, 13726 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 13727 Applications}, 13728 booktitle = {Proceedings of Supercomputing '92}, 13729 publisher = {IEEE Computer Society Press}, 13730 year = {1992}, 13731 pages = {551--560} 13732} 13733 13734@COMMENT{WEB, CWEB references (for doctext)} 13735@TechReport{ web, 13736 author = {Donald E. Knuth}, 13737 title = {The {\tt WEB} system of structured documentation}, 13738 institution = {Computer Science Department, Stanford University}, 13739 year = {1983}, 13740 number = {980}, 13741 month = sep 13742} 13743 13744@Article{ literatepgm, 13745 author = {Donald E. Knuth}, 13746 title = {Literate Programming}, 13747 journal = {Computer Journal}, 13748 year = {1984}, 13749 volume = {27}, 13750 number = {2}, 13751 pages = {91--111} 13752} 13753 13754@Unpublished{ cweb-code, 13755 author = {Silvio Levy and Donald E. Knuth}, 13756 title = {CWEB}, 13757 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 13758} 13759 13760@Article{ jp:scalable, 13761 author = {Mark Jones and Paul Plassmann}, 13762 title = {Scalable Iterative Solution of Sparse Linear Systems}, 13763 journal = {Parallel Computing}, 13764 volume = {20}, 13765 number = {5}, 13766 month = may, 13767 year = {1994}, 13768 pages = {753--773} 13769} 13770 13771@Article{ jp:pcolor, 13772 author = {Mark T. Jones and Paul E. Plassmann}, 13773 title = {A Parallel Graph Coloring Heuristic}, 13774 journal = {SIAM J. Sci. Comput.}, 13775 volume = {14}, 13776 number = {3}, 13777 pages = {654-669}, 13778 year = {1993} 13779} 13780 13781@TechReport{ block_solve, 13782 author = {Mark T. Jones and Paul E. Plassmann}, 13783 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 13784 Sparse Linear Systems}, 13785 institution = {Argonne National Laboratory}, 13786 year = {1992}, 13787 number = {ANL-92/46}, 13788 key = {JonesPlassmann92 ! block_solve} 13789} 13790 13791@InProceedings{ supercond, 13792 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 13793 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 13794 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 13795 Conference}, 13796 month = feb, 13797 year = {1994}, 13798 key = {McInnesPalumbo94 ! superconductivity } 13799} 13800 13801@Unpublished{ preosti:93, 13802 author = {Gianfranco Preosti}, 13803 title = { }, 13804 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 13805 year = {1993}, 13806 key = {preosti93 ! GL-tilt3d} 13807} 13808 13809@Unpublished{ more:93, 13810 author = {Jorge J. Mor\'{e}}, 13811 title = { }, 13812 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 13813 {A}rgonne {N}ational {L}aboratory}, 13814 year = {1993}, 13815 key = {more93 ! MINPACK-2} 13816} 13817 13818@Article{ brownsaad:90, 13819 author = {Peter N. Brown and Youcef Saad}, 13820 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 13821 journal = {SIAM J. Sci. Stat. Comput.}, 13822 year = {1990}, 13823 volume = {11}, 13824 pages = {450-481} 13825} 13826 13827@Book{ using-mpi, 13828 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 13829 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 13830 publisher = {MIT Press}, 13831 year = {1994} 13832} 13833 13834@Book{ using-mpi2, 13835 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 13836 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 13837 publisher = {MIT Press}, 13838 year = {1999} 13839} 13840 13841@Article{ hs:52, 13842 author = {Magnus R. Hestenes and Eduard Steifel}, 13843 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 13844 journal = {J. Research of the National Bureau of Standards}, 13845 year = {1952}, 13846 volume = {49}, 13847 pages = {409-436} 13848} 13849 13850@Article{ so:89, 13851 author = {Peter Sonneveld}, 13852 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 13853 journal = {SIAM J. Sci. Stat. Comput.}, 13854 year = {1989}, 13855 volume = {10}, 13856 pages = {36-52} 13857} 13858 13859@Article{ v:92, 13860 author = {{H. A.} {van der Vorst}}, 13861 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 13862 of nonsymmetric linear systems}, 13863 journal = {SIAM J. Sci. Stat. Comput.}, 13864 volume = {13}, 13865 year = {1992}, 13866 pages = {631-644} 13867} 13868 13869@Article{ f:93, 13870 author = {Roland W. Freund}, 13871 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 13872 Systems}, 13873 journal = {SIAM J. Sci. Stat. Comput.}, 13874 volume = {14}, 13875 year = {1993}, 13876 pages = {470-482} 13877} 13878 13879@Article{ ish:89, 13880 author = {S. Ishizuka}, 13881 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 13882 journal = {Combustion and Flame}, 13883 volume = {75}, 13884 year = {1989}, 13885 pages = {367-379} 13886} 13887 13888@Book{ williams89, 13889 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 13890 author = {F.A. Williams}, 13891 publisher = {Addison-Wesley}, 13892 year = {1989}, 13893 pages = {367-379} 13894} 13895 13896@Book{ ra75, 13897 author = {R. Aris}, 13898 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 13899 publisher = {Oxford}, 13900 year = {1975} 13901} 13902 13903@Book{ bebernes89, 13904 author = {J. Bebernes and D. Eberly}, 13905 title = {Mathematical Problems from Combustion Theory}, 13906 publisher = {Springer-Verlag}, 13907 series = {Applied Mathematical Sciences 83}, 13908 year = {1989} 13909} 13910 13911@InProceedings{ kikuchi89, 13912 author = {F. Kikuchi}, 13913 booktitle = { Computing Methods in Applied Sciences and Engineering}, 13914 editor = {R. Glowinski and J. L. Lions}, 13915 publisher = {Springer-Verlag}, 13916 series = {Lecture Notes in Mathematics}, 13917 title = {Finite element approximations to bifurcation problems of turning point type}, 13918 year = {1977} 13919} 13920 13921@Article{ rg85, 13922 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 13923 title = {Continuation-conjugate Gradient Methods for the Least Squares Solution of 13924 Nonlinear Boundary Problems}, 13925 journal = {SIAM J. Sci. Stat. Comput.}, 13926 volume = {6}, 13927 year = {1985}, 13928 pages = {793-832} 13929} 13930 13931@InProceedings{ whitfield91, 13932 author = {D. Whitfield and L. Taylor}, 13933 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13934 Schemes}, 13935 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 13936 misc = {AIAA-91-1539}, 13937 pages = {134-145}, 13938 year = {1991} 13939} 13940 13941@InProceedings{ quinlan1, 13942 author = {M. Lemke and D. Quinlan}, 13943 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 13944 Architecture-Independent Development of Structured Grid Applications}, 13945 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 13946 publisher = {Springer Verlag}, 13947 year = {1992} 13948} 13949 13950@InProceedings{ quinlan2, 13951 author = {R. Parsons and D. Quinlan}, 13952 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 13953 Computations}, 13954 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 13955 year = {1994} 13956} 13957 13958% ***** Overview of functionality in Diffpack 13959@InBook{ dpoverview, 13960 author = {Bruaset, A. M. and Langtangen, H. P.}, 13961 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13962 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 13963 {Diffpack}}, 13964 publisher = {Birkh{\"{a}}user}, 13965 pages = {61--90}, 13966 year = {1997} 13967} 13968 13969% ***** Short overview of Diffpack 13970@InCollection{ dpoverview2, 13971 author = {Bruaset, A. M. and Langtangen, H. P.}, 13972 editor = {A. Sydow}, 13973 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 13974 and Applied Mathematics}, 13975 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 13976 pages = {553--558}, 13977 volume = {4}, 13978 year = {1997} 13979} 13980 13981% ***** Comprehensive documentation of Diffpack and 13982% associated numerical methods: 13983@Book{ dpbook, 13984 author = {H. P. Langtangen}, 13985 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 13986 Software. Part I}, 13987 series = {Lecture Notes in Computational Science and Engineering}, 13988 publisher = {Springer-Verlag}, 13989 year = {1998} 13990} 13991 13992% ***** Design issues of the linear solvers in Diffpack, serves also as a 13993% collection of examples on O-O in numerical computing 13994@Article{ ambhpl97a, 13995 author = {A. M. Bruaset and H. P. Langtangen }, 13996 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 13997 journal = {Transactions on Mathematical Software}, 13998 volume = {23 }, 13999 pages = {50--80}, 14000 year = {1997} 14001} 14002 14003@Misc{ dpurl, 14004 author = {{Diffpack Web page}}, 14005 howpublished = {\url{http://www.diffpack.com}} 14006} 14007 14008% ***** General intro to object-oriented numerics for "FORTRAN programmers" 14009@InCollection{ oonintro, 14010 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 14011 editor = {D{\ae}hlen, M. and Tveito, A.}, 14012 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14013 title = {Object-Oriented Numerics}, 14014 publisher = {Birkh{\"{a}}user}, 14015 year = {1997} 14016} 14017 14018% ***** Efficiency comparison: BLAS 1, Diffpack, C, 14019% and finite element applications (F77 vs Diffpack) 14020@InCollection{ dpefficiency, 14021 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 14022 H. P. and Miller, C. T.}, 14023 editor = {D{\ae}hlen, M. and Tveito, A.}, 14024 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14025 title = {On the Efficiency of {C++} in Scientific Computing}, 14026 publisher = {Birkh{\"{a}}user}, 14027 pages = {91--118}, 14028 year = {1997} 14029} 14030 14031% ***** Parallel concept in Diffpack: 14032@InCollection{ dpparallel, 14033 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 14034 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 14035 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 14036 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 14037 Simulators}, 14038 publisher = {Springer--Verlag}, 14039 series = {Lecture Notes in Computer Science}, 14040 pages = {161--168}, 14041 year = {1997} 14042} 14043 14044% ***** DD and ML methods in Diffpack: 14045@InCollection{ dpddml, 14046 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 14047 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 14048 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 14049 title = {Domain decomposition and multilevel methods in Diffpack}, 14050 year = {1997} 14051} 14052 14053@InProceedings{ bsca98, 14054 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 14055 Alexander}, 14056 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 14057 Optimization}, 14058 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14059 Scientific and Engineering Computing}, 14060 editor = {Mike Henderson et al.}, 14061 pages = {165-173}, 14062 year = {1998} 14063} 14064 14065@Book{ scalapack-user-guide, 14066 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 14067 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 14068 Stanley and D. Walker and R. C. Whaley}, 14069 title = {Sca{LAPACK} Users' Guide}, 14070 publisher = {SIAM}, 14071 address = {Philadelphia, PA}, 14072 year = {1997} 14073} 14074 14075@InProceedings{ keyes99, 14076 author = {D. E. Keyes}, 14077 title = {How Scalable is Domain Decomposition in Practice?}, 14078 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 14079 Methods}, 14080 editor = {C.-H. Lai et al.}, 14081 publisher = {Domain Decomposition Press, Bergen}, 14082 note = {To appear}, 14083 year = {1999} 14084} 14085 14086@Article{ fun3d, 14087 author = {W. K. Anderson and D. L. Bonhaus}, 14088 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 14089 grids}, 14090 journal = {Computers and Fluids}, 14091 year = {1994}, 14092 volume = {23}, 14093 pages = {1--21} 14094} 14095 14096% ------------------------------------------------------------------------- 14097% ------------------------------------------------------------------------- 14098@Article{ torczon, 14099 author = {Dennis, Jr., J. E. and V.~Torczon}, 14100 title = {Direct Search Methods on Parallel Machines}, 14101 journal = {SIAM J. Optimization}, 14102 volume = {1}, 14103 pages = {448--474}, 14104 year = {1991}, 14105 key = {Torczon !PDS} 14106} 14107 14108@InProceedings{ wt91, 14109 author = {D. L. Whitfield and L. K. Taylor}, 14110 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 14111 Schemes}, 14112 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 14113 misc = {AIAA-91-1539}, 14114 pages = {134-145}, 14115 year = {1991} 14116} 14117 14118@Article{ ew96, 14119 author = {S. C. Eisenstat and H. F. Walker}, 14120 title = {Choosing the forcing terms in an inexact {N}ewton method}, 14121 journal = {SIAM J. Scientific Computing}, 14122 volume = {17}, 14123 year = {1996}, 14124 pages = {16--32} 14125} 14126 14127@Book{ thi93, 14128 author = {{Thinking Machines Corporation}}, 14129 title = {Users Manual for CM-Fortran}, 14130 publisher = {Thinking Machines Corporation}, 14131 year = {1993} 14132} 14133 14134@Book{ mortonmayers94, 14135 author = {K. W. Morton and D. F. Mayers}, 14136 title = {Numerical Solution of Partial Differential Equations}, 14137 publisher = {Press Syndicate of the University of Cambridge}, 14138 year = {1994} 14139} 14140 14141@Book{ heath97, 14142 author = {Michael T. Heath}, 14143 title = {Scientific Computing: An Introductory Survey}, 14144 publisher = {McGraw Hill}, 14145 year = {1997} 14146} 14147 14148@Article{ captools96, 14149 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 14150 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 14151 Performance on the Parallelization of Structured Mesh Codes}, 14152 journal = {Parallel Computing}, 14153 volume = {22}, 14154 pages = {197-226}, 14155 year = {1996} 14156} 14157 14158@Misc{ nastran-web-page, 14159 author = {{MSC Software Corporation}}, 14160 title = {{NASTRAN} {W}eb page}, 14161 howpublished = {\url{http://www.mechsolutions.com/products/nastran/}}, 14162 year = {2024} 14163} 14164 14165@Book{ hpf, 14166 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 14167 Zosel}, 14168 title = {The High Performance Fotran Handbook}, 14169 publisher = {MIT Press}, 14170 year = {1994} 14171} 14172 14173@InProceedings{ keyes98, 14174 author = {D. E. Keyes}, 14175 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 14176 Architectures}, 14177 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 14178 editors = {M. D. Salas and W. K. Anderson}, 14179 ppublisher = {Elsevier}, 14180 year = {1998} 14181} 14182 14183@InProceedings{ pooma-atlas, 14184 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14185 J. V. W. Reynders and M. Tholburn}, 14186 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14187 Applications}, 14188 year = {1995}, 14189 month = dec, 14190 booktitle = {Supercomputing '95 Proceedings} 14191} 14192 14193% --------------------------------------------------------------------------------- 14194% New bib entries for CRPC paper 14195@Misc{ mgnet-web-page, 14196 author = {Craig C. Douglas}, 14197 title = {{MGNet Web page}}, 14198 note = {See {\tt http://\-www.mgnet.org}} 14199} 14200 14201@Misc{ dagh-web-page, 14202 author = {M. Parashar and J. C. Browne}, 14203 title = {{DAGH Web page}}, 14204 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14205} 14206 14207@Misc{ parasol-web-page, 14208 key = {PARASOL}, 14209 title = {{PARASOL Web page}}, 14210 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14211} 14212 14213@Misc{ pooma-web-page, 14214 author = {{POOMA Web page}}, 14215 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14216} 14217 14218@Misc{ mudpack-web-page, 14219 author = {John C. Adams}, 14220 title = {{MUDPACK Web page}}, 14221 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14222} 14223 14224@Misc{ pellpack-web-page, 14225 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14226 title = {{Parallel ELLPACK Web page}}, 14227 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14228} 14229 14230@InProceedings{ pellpack95, 14231 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14232 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14233 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14234 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14235 address = {Albuquerque, NM}, 14236 year = {1995} 14237} 14238 14239@Misc{ nhse-web-page, 14240 author = {{National High-Performance Software Exchange Web page}}, 14241 note = {See {\tt http://\-www.nhse.org}} 14242} 14243 14244@Misc{ doug-web-page, 14245 author = {Mark J. Hagger and Linda Stals}, 14246 title = {{DOUG Web Page}}, 14247 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14248} 14249 14250@TechReport{ doug97, 14251 author = {Mark J. Hagger}, 14252 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14253 institution = {Mathematical Sciences, University of Bath}, 14254 year = {1997}, 14255 number = {9706}, 14256 note = {Advances in Computational Mathematics (to appear)} 14257} 14258 14259@Misc{ ug-web-page, 14260 author = {{UG Web Page}}, 14261 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14262} 14263 14264@Article{ ug97, 14265 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14266 Rentz-Reichert and C. Wieners}, 14267 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14268 journal = {Computing and Visualization in Science}, 14269 year = {1997}, 14270 volume = {}, 14271 pages = {} 14272} 14273 14274@Misc{ vecfem-web-page, 14275 author = {Lutz Grosz}, 14276 title = {{VECFEM Web Page}}, 14277 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14278} 14279 14280@Misc{ atlas-web-page, 14281 author = {R. Clint {Whaley et al.}}, 14282 title = {{ATLAS Web Page}}, 14283 howpublished = {\url{http://math-atlas.sourceforge.net}} 14284} 14285 14286@Misc{ fenics-web-page, 14287 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14288 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14289 title = {{FEniCS Web Page}}, 14290 note = {\url{http://www.fenicsproject.org}}, 14291 year = {2005} 14292} 14293 14294@Misc{ matlab-web-page, 14295 author = {{The} {MathWorks}}, 14296 title = {{Matlab} {Web} page}, 14297 url = {http://www.mathworks.com} 14298} 14299 14300@Misc{ phipac-web-page, 14301 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14302 and D. Lam}, 14303 title = {{PHiPAC Web Page}}, 14304 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14305} 14306 14307@InProceedings{ kelp, 14308 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14309 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14310 booktitle = {Irregular '96}, 14311 year = {1996} 14312} 14313 14314@Unpublished{ kelp-web-page, 14315 author = {Scott Baden}, 14316 title = {{KeLP} {W}eb page}, 14317 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14318} 14319 14320@InProceedings{ hk99, 14321 author = {R. Hornung and S. 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Softw.}, 15671 volume = {31}, 15672 year = {2005}, 15673 pages = {326--350} 15674} 15675 15676@Unpublished{ compass:homepage, 15677 author = {Panagiotis {Spentzouris (PI)}}, 15678 title = {Community Petascale Project for Accelerator Science and Simulation (ComPASS)}, 15679 note = {SciDAC2 project, see \url{https://compass.fnal.gov/}} 15680} 15681 15682@Unpublished{ cmsnf:homepage, 15683 author = {{Todd Allen, Director}}, 15684 title = {{Center for Materials Science of Nuclear Fuel}}, 15685 note = {Energy Frontier Research Center, see 15686 \url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}} 15687} 15688 15689@Unpublished{ dvi-materials:project, 15690 author = {{L.~C.} {McInnes (PI)}}, 15691 title = {Large-Scale Differential Variational Inequalities for Heterogeneous Materials}, 15692 note = {{SciDAC}-e project}, 15693 year = {2011} 15694} 15695 15696@Misc{ scidac:homepage, 15697 author = {{DOE Office of Science}}, 15698 title = {{Scientific Discovery through Advanced Computing}}, 15699 year = {2007}, 15700 howpublished = {\url{http://www.scidac.gov}} 15701} 15702 15703@Misc{ corba, 15704 author = {{Object Management Group}}, 15705 year = {2007}, 15706 title = {{Common Object Request Broker Architecture (CORBA)}}, 15707 howpublished = {\url{http://www.corba.org}} 15708} 15709 15710@Article{ uedge, 15711 author = {T.~D. 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Wilson}, 15733 title = {{BOUT++}: A Framework for Parallel Plasma Fluid Simulations}, 15734 journal = {Computer Physics Communications}, 15735 year = {2009}, 15736 volume = {180}, 15737 issue = {9}, 15738 pages = {1467 -- 1480}, 15739 note = {} 15740} 15741 15742@Article{ tempest, 15743 author = {Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and M.R. Dorr and J.A. Hittinger 15744 and G. Kerbel and W.M. Nevins and T. Rognlien}, 15745 title = {Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST}, 15746 journal = {Bull. Am. Phys. Soc. }, 15747 year = {2005}, 15748 volume = {50}, 15749 number = {86}, 15750 pages = {CP1}, 15751 note = {} 15752} 15753 15754@Article{ ccahpc, 15755 author = {David E. Bernholdt and Benjamin A. Allan and Robert Armstrong and Felipe Bertrand 15756 and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif 15757 and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James 15758 A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia 15759 Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek 15760 Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende 15761 and Theresa L. Windus and Shujia Zhou}, 15762 title = {A Component Architecture for High-Performance Scientific Computing}, 15763 journal = {Intl. J. High-Perf. Computing Appl.}, 15764 volume = {20}, 15765 pages = {163--202}, 15766 year = {2006}, 15767 note = {ACTS Collection special issue} 15768} 15769 15770@Misc{ cca-forum:homepage, 15771 author = {{Common Component Architecture Forum}}, 15772 note = {\url{http://www.cca-forum.org}}, 15773 year = {2010} 15774} 15775 15776@Misc{ petsc:driven-cavity-example, 15777 title = {{PETSc Driven Cavity Example Code}}, 15778 author = {B. F. {Smith et al.}}, 15779 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 15780} 15781 15782@Misc{ petsc-dm:webpage, 15783 author = {B. F. {Smith et al.}}, 15784 title = {{PETSc DM Webpage}}, 15785 howpublished = {\url{https://petsc.org/release/manualpages/DM/}}, 15786 year = {2018} 15787} 15788 15789@Misc{ unic-ref, 15790 author = {Giuseppe Palmiotti}, 15791 title = {{UNIC} Neutronics Software}, 15792 note = {Nuclear Engineering Division, Argonne National Laboratory} 15793} 15794 15795% ----------------------------------------------------------------------- 15796% Model coupling refs 15797@Book{ greve-blatter, 15798 author = {Ralf Greve and Heinz Blatter}, 15799 title = {Dynamics of Ice Sheets and Glaciers}, 15800 series = {Advances in Geophysical and Environmental Mechanics and Mathematics}, 15801 publisher = {Springer}, 15802 year = {2009} 15803} 15804 15805@Misc{ doe-isicles, 15806 key = {ISICLES}, 15807 title = {Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}}, 15808 howpublished = {\url{http://www.csm.ornl.gov/ISICLES/index.html}} 15809} 15810 15811@Article{ safta2011tchem, 15812 title = {TChem-a software toolkit for the analysis of complex kinetic models}, 15813 author = {Safta, Cosmin and Najm, Habib N and Knio, Omar}, 15814 journal = {Sandia Report, SAND2011-3282}, 15815 year = {2011} 15816} 15817 15818@Misc{ chemkin-website, 15819 key = {chemkin}, 15820 title = {ANSYS Chemkin-Pro Website}, 15821 howpublished = {\url{http://www.ansys.com/products/fluids/ansys-chemkin-pro}}, 15822 year = {2017} 15823} 15824 15825@Misc{ mct-website, 15826 key = {MCT}, 15827 title = {{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite}, 15828 howpublished = {\url{http://www.mcs.anl.gov/mct}} 15829} 15830 15831@Article{ larson:05, 15832 author = {Jay Larson and Robert Jacob and Everest Ong}, 15833 title = {{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building 15834 Multi-Physics Parallel Coupled Models}, 15835 journal = {Int. 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Tan}, 15872 series = {Lecture Notes in Computer Science}, 15873 volume = {2073}, 15874 publisher = {Springer-Verlag} 15875} 15876 15877@Article{ chen2008new, 15878 title = {New generation of multi-scale {NWP} system {(GRAPES)}: General scientific 15879 design}, 15880 author = {Chen, DeHui and Xue, JiShan and Yang, XueSheng and Zhang, HongLiang and Shen, 15881 XueShun and Hu, JiangLin and Wang, Yu and Ji, LiRen and Chen, JiaBin}, 15882 journal = {Chinese Science Bulletin}, 15883 volume = {53}, 15884 number = {22}, 15885 pages = {3433--3445}, 15886 year = {2008}, 15887 publisher = {Springer} 15888} 15889 15890@InProceedings{ baum01, 15891 author = {J. Baum and H. Luo and E. Mestreau and D. Sharov and R. Loehner and D. Pelessone 15892 and C. Charman}, 15893 year = {2001}, 15894 title = {Recent Developments of a Coupled {CFD/CSD} Methodology}, 15895 booktitle = {Proc. International Conference on Computational Science (ICCS) 2001}, 15896 editors = {V. N. Alexandrow and J. J. Dongarra and C. J. K. Tan}, 15897 series = {Lecture Notes in Computer Science}, 15898 volume = {2073}, 15899 publisher = {Springer-Verlag} 15900} 15901 15902@InProceedings{ lefantzi03, 15903 author = {S. Lefantzi and J. Ray}, 15904 year = {2003}, 15905 title = {A Component-based Scientific Toolkit for Reacting Flows}, 15906 booktitle = {Proc. Second MIT Conference on Computational Fluid and Solid Mechanics}, 15907 volume = {2}, 15908 publisher = {Elsevier} 15909} 15910 15911@Article{ boville98, 15912 author = {B. A. Boville and P. R. Gent}, 15913 title = {The {NCAR} Climate System Model, Version One}, 15914 journal = {Journal of Climate}, 15915 volume = {11}, 15916 year = {1998}, 15917 pages = {1115--1130} 15918} 15919 15920@Misc{ paraschivoiu99, 15921 author = {M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes}, 15922 title = {Multi-domain multi-model formulation for compressible flows: Conservative 15923 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 15924 note = {AIAA Paper 99-0784}, 15925 year = {1999} 15926} 15927 15928@Article{ peszynska, 15929 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 15930 title = {Mortar upscaling for multiphysics flow in porous media}, 15931 journal = {Computational Geosciences} 15932} 15933 15934@TechReport{ wheeler00, 15935 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 15936 title = {A distributed computing portal for coupling multi-physics and multiple domains in 15937 porous media}, 15938 institution = {University of Texas at Austin}, 15939 number = {TICAM 00-03}, 15940 year = {2000} 15941} 15942 15943@TechReport{ peszynska00, 15944 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 15945 title = {Multiphysics Coupling of Codes}, 15946 institution = {University of Texas at Austin}, 15947 number = {TICAM 00-02}, 15948 year = {2000} 15949} 15950 15951@Article{ joshaghanijoodatnakshatrala2019, 15952 title = {A stabilized mixed discontinuous Galerkin formulation for double 15953 porosity/permeability model}, 15954 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 15955 journal = {Computer Methods in Applied Mechanics and Engineering}, 15956 volume = {352}, 15957 pages = {508--560}, 15958 year = {2019} 15959} 15960 15961@InProceedings{ cai99, 15962 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 15963 title = {An explicit multi-model compressible flow formulation based on the full potential 15964 equation and the {Euler} equations on {3D} unstructured meshes}, 15965 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 15966 Methods}, 15967 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 15968 year = {1999} 15969} 15970 15971@Article{ he05, 15972 author = {Yun He and Chris H. Q. Ding}, 15973 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 15974 Architectures}, 15975 year = {2005}, 15976 volume = {19}, 15977 pages = {329--240}, 15978 number = {3}, 15979 journal = {Int. Journal of High Performance Computing Applications} 15980} 15981 15982@InProceedings{ uiuc-rocket-center02, 15983 author = {W. A. Dick and M. T. Heath}, 15984 title = {Whole System Simulation of Solid Propellant Rockets}, 15985 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 15986 month = jul, 15987 year = {2002} 15988} 15989 15990@InProceedings{ toth04, 15991 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 15992 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 15993 Oehmke}, 15994 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 15995 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 15996 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 15997 Sun-Earth Connection}, 15998 year = {2004}, 15999 publisher = {Elsevier}, 16000 pages = {383--397} 16001} 16002 16003@Misc{ csdrm:web, 16004 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 16005 Shepherd}, 16006 title = {{Center for Simulation of Dynamic Response of Materials}}, 16007 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 16008} 16009 16010@Misc{ csar:web, 16011 author = {M. {Heath (Director)}}, 16012 title = {{Center for Simulation of Advanced Rockets}}, 16013 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 16014} 16015 16016@Misc{ csafe:web, 16017 author = {D. {Pershing (Director)}}, 16018 title = {{Center for Simulation of Accidental Fires and Explosions}}, 16019 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 16020} 16021 16022@Misc{ cits:web, 16023 author = {P. {Moin (Director)}}, 16024 title = {{Center for Integrated Turbulence Simulations}}, 16025 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 16026} 16027 16028@Misc{ flash:web, 16029 author = {D. {Lamb (Director)}}, 16030 title = {{Center for Integrated Turbulence Simulations}}, 16031 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 16032} 16033 16034@TechReport{ utah-csafe03, 16035 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 16036 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 16037 Problems, Part 1: Algorithm Development}, 16038 institution = {University of Utah, Center for the Simulation of Accidental Fires and 16039 Explosions}, 16040 year = {2003} 16041} 16042 16043@InBook{ shepherd07, 16044 author = {M. Shepherd and E. Seol and B. FrantzDale}, 16045 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 16046 year = {2007}, 16047 booktitle = {CRC Handbook of Dynamic System Modeling}, 16048 publisher = {Wiley}, 16049 pages = {1--41}, 16050 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 16051} 16052 16053@InProceedings{ cactus02, 16054 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 16055 Radke and Edward Seidel and John Shalf}, 16056 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 16057 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 16058 year = {2002}, 16059 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 16060} 16061 16062@Misc{ cactus:homepage, 16063 author = {G. {Allen et al.}}, 16064 title = {{Cactus Web page}}, 16065 howpublished = {\url{http://cactuscode.org}} 16066} 16067 16068@Misc{ open-grid-forum:web, 16069 key = {{Open Grid Forum}}, 16070 title = {{Open Grid Forum}}, 16071 note = {See \url{http://www.ogf.org}} 16072} 16073 16074@Misc{ nox:web, 16075 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 16076 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 16077 note = {See \url{http://software.sandia.gov/nox}} 16078} 16079 16080@Misc{ chombo:web, 16081 author = {P. {Colella (PI)}}, 16082 title = {{Chombo}}, 16083 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 16084} 16085 16086@Article{ lanzkron96, 16087 author = {P. J. Lanzkron and D. J. Rose and J. T. Wilkes}, 16088 title = {An Analysis of Approximate Nonlinear Elimination}, 16089 journal = {SIAM J. Sci. Comput.}, 16090 volume = {17}, 16091 year = {1996}, 16092 pages = {538--559} 16093} 16094 16095@Article{ jiang95, 16096 author = {J. Jiang and P. Forsyth}, 16097 title = {Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} 16098 Equations}, 16099 journal = {Computers and Fluids}, 16100 volume = {24}, 16101 pages = {753--770}, 16102 year = {1995} 16103} 16104 16105@Article{ young90, 16106 author = {D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant}, 16107 title = {Global Convergence of Inexact {Newton} Methods for Transonic Flow}, 16108 journal = {Int. J. Numer. Methods Fluids}, 16109 volume = {11}, 16110 pages = {1075--1095}, 16111 year = {1990} 16112} 16113 16114@Article{ fishwick04, 16115 author = {Paul A. Fishwick}, 16116 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 16117 to Interrelating Model Structures}, 16118 journal = {SCS Trans. on Simulation}, 16119 note = {Special Issue in Grand Challenges in Computer Simulation}, 16120 year = {2004} 16121} 16122 16123@Article{ fishwick03, 16124 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 16125 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 16126 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 16127 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 16128 year = {2003} 16129} 16130 16131@InProceedings{ kirner00, 16132 author = {T. G. Kirner and V. F. 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Messerschmitt}, 16158 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 16159 journal = {Int. Journal of Computer Simulation}, 16160 volume = {4}, 16161 pages = {155--182}, 16162 year = {1994} 16163} 16164 16165@Article{ mu95, 16166 author = {M. Mu and J.R. Rice}, 16167 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 16168 journal = {Comp. Syst. Engr.}, 16169 volume = {6}, 16170 year = {1995}, 16171 pages = {87--95} 16172} 16173 16174@TechReport{ drashansky96, 16175 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 16176 author = {R. Drashansky and A. Joshi and J. R. Rice}, 16177 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 16178 year = {1996} 16179} 16180 16181@Article{ michopoulos05, 16182 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 16183 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 16184 journal = {Journal of Computing and Information Science in Engineering}, 16185 volume = {5}, 16186 issue = {3}, 16187 pages = {198--213}, 16188 year = {2005} 16189} 16190 16191@Article{ dubey09, 16192 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16193 Multiphysics Simulation Code}, 16194 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16195 Siegel and K. Weide}, 16196 journal = {Parallel Computing}, 16197 volume = {35}, 16198 issue = {10 -- 11}, 16199 pages = {512 -- 522}, 16200 year = {2009} 16201} 16202 16203@Book{ bottloring95, 16204 author = {Raoul Bott and Loring W. Tu}, 16205 title = {Differential Forms in Algebraic Topology}, 16206 publisher = {Springer}, 16207 year = {1995} 16208} 16209 16210@Book{ kobayashinomizu96, 16211 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16212 title = {Foundations of Differential Geometry}, 16213 publisher = {Wiley-Interscience}, 16214 year = {1996} 16215} 16216 16217@Article{ hornungkohn02, 16218 author = {Richard D. Hornung and Scott R. Kohn}, 16219 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16220 journal = {Concurrency and Computation: Practice and Experience}, 16221 volume = {14}, 16222 pages = {347--368}, 16223 year = {2002} 16224} 16225 16226@InProceedings{ concepts06, 16227 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16228 Gabriel Dos Reis and Andrew Lumsdaine}, 16229 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16230 booktitle = {Proceedings of OOPSLA 2006}, 16231 year = {2006}, 16232 pages = {???--???} 16233} 16234 16235@Book{ hatcher02, 16236 author = {Hatcher, Allen}, 16237 title = {Algebraic Topology}, 16238 publisher = {Cambridge University Press}, 16239 year = {2002} 16240} 16241 16242@Book{ gammahelmjohnsonvlissides95, 16243 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16244 development, offering timeless and elegant solutions to common problems in 16245 software design. It describes patterns for managing object creation, composing 16246 objects into larger structures, and coordinating control flow between objects. The 16247 book provides numerous examples where using composition rather than inheritance 16248 can improve the reusability and flexibility of code. Note, though, that it's not a 16249 tutorial but a catalog that you can use to find an object-oriented design pattern 16250 that's appropriate for the needs of your particular application--a selection for 16251 virtuoso programmers who appreciate (or require) consistent, well-engineered 16252 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16253 more valuable than ever! 16254 16255 Use the contents of the CD to create your own design documents and reusable 16256 components. The CD contains: 23 patterns you can cut and paste into your own 16257 design documents; sample code demonstrating pattern implementation; complete 16258 Design Patterns content in standard HTML format, with numerous hyperlinked 16259 cross-references; accessed through a standard web browser; Java-based dynamic 16260 search mechanism, enhancing online search capabilities; graphical user environment, 16261 allowing ease of navigation. 16262 16263 First published in 1995, this landmark work on object-oriented software design 16264 presents a catalog of simple and succinct solutions to common design problems. 16265 Created by four experienced designers, the 23 patterns contained herein have 16266 become an essential resource for anyone developing reusable object-oriented 16267 software. In response to reader demand, the complete text and pattern catalog are 16268 now available on CD-ROM. This electronic version of Design Patterns enables 16269 programmers to install the book directly onto a computer or network for use as an 16270 online reference for creating reusable object-oriented software. 16271 16272 The authors first describe what patterns are and how they can help you in the 16273 design process. They then systematically name, explain, evaluate, and catalog 16274 recurring designs in object-oriented systems. All patterns are compiled from 16275 real-world examples and include code that demonstrates how they may be implemented 16276 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16277 already own the book will want the CD to take advantage of its dynamic search 16278 mechanism and ready-to-install patterns.}}, 16279 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16280 citeulike-article-id={115158}, 16281 howpublished = {Hardcover}, 16282 isbn = {0201633612}, 16283 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16284 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16285 four gang gof java mathgamespatterns no-tag object object-orientation 16286 object-oriented of oo-patterns oop oriented pattern patterns programming se 16287 software software-development software-engineering software_design 16288 softwareengineering standard}, 16289 month = jan, 16290 publisher = {{Addison-Wesley Professional}}, 16291 title = {Design Patterns}, 16292 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16293 year = {1995} 16294} 16295 16296@InProceedings{ chaco95, 16297 author = {Bruce Hendrickson and Robert Leland}, 16298 title = {A multilevel algorithm for partitioning graphs}, 16299 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16300 (CDROM)}, 16301 year = {1995}, 16302 isbn = {0-89791-816-9}, 16303 pages = {28}, 16304 location = {San Diego, California, United States}, 16305 doi = {10.1145/224170.224228}, 16306 publisher = {ACM Press}, 16307 address = {New York} 16308} 16309 16310@Book{ aleksandrov98, 16311 author = {Aleksandrov, Pavel S.}, 16312 title = {Combinatorial Topology}, 16313 publisher = {Dover}, 16314 volume = {3}, 16315 year = {1998} 16316} 16317 16318@Book{ steenrod99, 16319 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16320 importance in modern physics--such as in gauge theory. This book, a succinct 16321 introduction to the subject by renown mathematician Norman Steenrod, was the first 16322 to present the subject systematically. 16323 16324 It begins with a general introduction to bundles, including such topics as 16325 differentiable manifolds and covering spaces. The author then provides brief 16326 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16327 using them to study further properties of fibre bundles. The result is a classic 16328 and timeless work of great utility that will appeal to serious mathematicians and 16329 theoretical physicists alike. }}, 16330 author = {Steenrod, Norman}, 16331 citeulike-article-id={712999}, 16332 howpublished = {Paperback}, 16333 isbn = {0691005486}, 16334 keywords = {fibre_bundles topology}, 16335 month = apr, 16336 publisher = {{Princeton University Press}}, 16337 title = {The Topology of Fibre Bundles. (PMS-14)}, 16338 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16339 year = {1999} 16340} 16341 16342@Book{ bredon97, 16343 author = {Bredon, Glen E.}, 16344 title = {Sheaf Theory}, 16345 publisher = {Springer}, 16346 pages = {524}, 16347 series = {Graduate Texts in Mathematics}, 16348 year = {1997} 16349} 16350 16351@TechReport{ tautgesmeyers04, 16352 title = {{MOAB}: A Mesh-Oriented Database}, 16353 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16354 Ernst}, 16355 institution = {Sandia National Laboratories}, 16356 number = {SAND2004-1592}, 16357 month = apr, 16358 year = {2004} 16359} 16360 16361@Article{ tautges04, 16362 author = {Timothy J. Tautges}, 16363 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16364 journal = {Engineering With Computers}, 16365 volume = {20}, 16366 pages = {286--293}, 16367 year = {2004} 16368} 16369 16370@InProceedings{ meyers02, 16371 author = {Ray Meyers et. al}, 16372 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16373 booktitle = {8th International conference on numerical grid generation in computational field 16374 simulations}, 16375 month = jun, 16376 year = {2002} 16377} 16378 16379@InProceedings{ seolshepard05, 16380 author = {E. S. Seol and Mark S. Shephard}, 16381 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16382 Analysis}, 16383 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16384 year = {2005} 16385} 16386 16387@Article{ lishephardbeall2005, 16388 title = {3D anisotropic mesh adaptation by mesh modification}, 16389 author = {Xiangrong Li and Mark S Shephard and Mark W Beall}, 16390 journal = {Computer methods in applied mechanics and engineering}, 16391 volume = {194}, 16392 number = {48-49}, 16393 pages = {4915--4950}, 16394 year = {2005}, 16395} 16396 16397@Article{ lushephardtendulkarbeall2014, 16398 title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry}, 16399 author = {Qiukai Lu and Mark S Shephard and Saurabh Tendulkar and Mark W Beall}, 16400 journal = {Engineering with Computers}, 16401 volume = {30}, 16402 pages = {271--286}, 16403 year = {2014}, 16404} 16405 16406@Article{ beallwalshshephard04, 16407 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16408 title = {A comparison of techniques for geometry access related to mesh generation}, 16409 journal = {Engineering With Computers}, 16410 volume = {20}, 16411 number = {3}, 16412 pages = {210--221}, 16413 year = {2004} 16414} 16415 16416@Article{ careyandersoncarneskirk04, 16417 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16418 Kirk}, 16419 title = {Some aspects of adaptive grid technology related to boundary and interior 16420 layers}, 16421 journal = {Journal of Computational Applied Mathematics}, 16422 volume = {166}, 16423 number = {1}, 16424 pages = {55--86}, 16425 year = {2004} 16426} 16427 16428@PhDThesis{ gralthesis, 16429 author = {Guntram Berti}, 16430 title = {Generic Software Components for Scientific Computing}, 16431 school = {TU Cottbus}, 16432 year = {2000}, 16433 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16434} 16435 16436@Article{ whitehead1949, 16437 title = {Combinatorial homotopy. I}, 16438 author = {John HC Whitehead}, 16439 journal = {Bulletin of the American Mathematical Society}, 16440 volume = {55}, 16441 number = {3. P1}, 16442 pages = {213--245}, 16443 year = {1949}, 16444 publisher = {American Mathematical Society} 16445} 16446 16447@Article{ beylkincoifmanrokhlin91, 16448 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16449 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16450 journal = {Communications on Pure and Applied Mathematics}, 16451 volume = {44}, 16452 pages = {141--183}, 16453 year = {1991} 16454} 16455 16456@Book{ wesseling92, 16457 author = {Pieter Wesseling}, 16458 title = {An Introduction to Multigrid Methods}, 16459 publisher = {John Wiley and Sons}, 16460 year = {1992} 16461} 16462 16463@Book{ grakakos04, 16464 author = {Loukas Grakakos}, 16465 title = {Classical and Modern Fourier Analysis}, 16466 publisher = {Pearson Education}, 16467 address = {New Jersey}, 16468 year = {2004} 16469} 16470 16471@Misc{ hlib-web-page, 16472 key = {HLib}, 16473 title = {{HLib} {Web} page}, 16474 note = {{\texttt{http://www.hlib.org/}}}, 16475 annote = {Hierarchical matrices for fast integral transform} 16476} 16477 16478@Article{ hackbusch99, 16479 author = {Wolfgang Hackbusch}, 16480 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16481 Introduction to {$\mathcal H$}-matrices}, 16482 journal = {Computing}, 16483 volume = {62}, 16484 pages = {89--108}, 16485 year = {1999} 16486} 16487 16488@TechReport{ kay1999green, 16489 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16490 equations}, 16491 author = {Kay, D. and Loghin, D.}, 16492 year = {1999}, 16493 institution = {Oxford University Computing Laboratory}, 16494 number = {99/06} 16495} 16496 16497@Article{ bebendorf2003existence, 16498 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16499 elliptic operators with {$L^\infty$}-coefficients}, 16500 author = {Bebendorf, M. and Hackbusch, W.}, 16501 journal = {Numerische Mathematik}, 16502 volume = {95}, 16503 number = {1}, 16504 pages = {1--28}, 16505 year = {2003}, 16506 publisher = {Springer} 16507} 16508 16509@Article{ hackbusch2005direct, 16510 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16511 H$}-matrix approximation}, 16512 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16513 journal = {Computing and Visualization in Science}, 16514 volume = {8}, 16515 number = {3}, 16516 pages = {179--188}, 16517 year = {2005}, 16518 publisher = {Springer} 16519} 16520 16521@TechReport{ duphof2003, 16522 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16523 Logg and L. R. Scott}, 16524 title = {The {FE}ni{CS} project}, 16525 institution = {Chalmers Finite Element Center Preprint Series}, 16526 number = {2003--21}, 16527 year = {2003} 16528} 16529 16530@Article{ flame01, 16531 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16532 Geijn}, 16533 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16534 journal = {Transactions on Mathematical Software}, 16535 volume = {27}, 16536 number = {4}, 16537 year = {2001}, 16538 pages = {422--455} 16539} 16540 16541@Article{ puschel05, 16542 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16543 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16544 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16545 Nick Rizzolo}, 16546 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16547 journal = {Proceedings of the IEEE}, 16548 volume = {93}, 16549 number = {2}, 16550 year = {2005}, 16551 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16552} 16553 16554@Article{ kirbylogg06, 16555 author = {Robert C. Kirby and Anders Logg}, 16556 title = {A compiler for variational forms}, 16557 journal = {ACM Transactions on Mathematical Software}, 16558 volume = {32}, 16559 number = {3}, 16560 year = {2006}, 16561 issn = {0098-3500}, 16562 pages = {417--444}, 16563 doi = {10.1145/1163641.1163644}, 16564 publisher = {ACM Press}, 16565 address = {New York, NY} 16566} 16567 16568@Article{ kirbylogg07, 16569 author = {Robert C. Kirby and Anders Logg}, 16570 title = {Efficient compilation of a class of variational forms}, 16571 journal = {ACM Transactions on Mathematical Software}, 16572 volume = {33}, 16573 number = {3}, 16574 year = {2007}, 16575 issn = {0098-3500}, 16576 pages = {17}, 16577 doi = {10.1145/1268769.1268771}, 16578 publisher = {ACM Press}, 16579 address = {New York, NY} 16580} 16581 16582@Article{ bankdupont81, 16583 author = {Randolph Bank and Todd Dupont}, 16584 title = {An optimal order process for solving finite element equations}, 16585 journal = {Mathematics of Computation}, 16586 volume = {36}, 16587 pages = {35--51}, 16588 year = {1981} 16589} 16590 16591@TechReport{ adams00, 16592 author = {Mark F. Adams}, 16593 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16594 in solid mechanics}, 16595 institution = {UC Berkeley}, 16596 number = {CSD-00-1103}, 16597 year = {2000}, 16598 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16599} 16600 16601@Article{ bergengradlhuelsemannruede06, 16602 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16603 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16604 journal = {Computing in Science \& Engineering}, 16605 volume = {8}, 16606 number = {6}, 16607 pages = {56--62}, 16608 year = {2006} 16609} 16610 16611@MastersThesis{ brunethesis08, 16612 author = {Peter R. Brune}, 16613 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16614 school = {University of Chicago}, 16615 address = {Chicago, IL}, 16616 year = {2008}, 16617 month = feb 16618} 16619 16620@Article{ arnoldwinther02, 16621 author = {Douglas N. Arnold and Ragnar Winther}, 16622 title = {Mixed finite elements for elasticity}, 16623 journal = {Numerische Mathematik}, 16624 volume = {92}, 16625 number = {3}, 16626 month = sep, 16627 year = {2002}, 16628 pages = {401--419}, 16629 doi = {10.1007/s002110100348} 16630} 16631 16632@Article{ arnoldfalkwinther06, 16633 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16634 title = {Finite element exterior calculus, homological techniques, and applications}, 16635 journal = {Acta Numerica}, 16636 year = {2006}, 16637 volume = {15}, 16638 pages = {1--155}, 16639 publisher = {Cambridge University Press}, 16640 doi = {10.1017/S0962492906210018} 16641} 16642 16643@Article{ kirby04, 16644 author = {Robert C. Kirby}, 16645 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 16646 functions}, 16647 journal = {ACM Transactions on Mathematical Software}, 16648 volume = {30}, 16649 number = {4}, 16650 year = {2004}, 16651 issn = {0098-3500}, 16652 pages = {502--516}, 16653 doi = {10.1145/1039813.1039820}, 16654 publisher = {ACM Press}, 16655 address = {New York, NY} 16656} 16657 16658@Article{ kirby06, 16659 author = {Robert C. Kirby}, 16660 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16661 journal = {ACM Transactions on Mathematical Software}, 16662 volume = {32}, 16663 number = {2}, 16664 year = {2006}, 16665 issn = {0098-3500}, 16666 pages = {223--235}, 16667 doi = {10.1145/1141885.1141889}, 16668 publisher = {ACM Press}, 16669 address = {New York, NY} 16670} 16671 16672@Misc{ bluecrystal08, 16673 author = {{B}lue {C}rystal Cluster}, 16674 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16675 year = {2008}, 16676 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16677} 16678 16679@Article{ beylkin95, 16680 author = {Gregory Beylkin}, 16681 title = {On the Fast Fourier Transform of Functions With Singularities}, 16682 journal = {Applied and Computational Harmonic Analysis}, 16683 volume = {2}, 16684 pages = {363--381}, 16685 year = {1995} 16686} 16687 16688@InProceedings{ riehl08, 16689 author = {Jonathan Riehl}, 16690 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16691 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16692 Development (DSPD'08)}, 16693 address = {Nashville, TN}, 16694 year = {2008} 16695} 16696 16697@Article{ appel85, 16698 author = {Andrew W. Appel}, 16699 date-added = {2008-02-27 12:23:39 +0000}, 16700 date-modified = {2008-02-27 12:24:02 +0000}, 16701 doi = {10.1137/0906008}, 16702 journal = {SIAM Journal on Scientific and Statistical Computing}, 16703 keywords = {treecodes}, 16704 number = {1}, 16705 pages = {85-103}, 16706 publisher = {SIAM}, 16707 title = {An Efficient Program for Many-Body Simulation}, 16708 volume = {6}, 16709 year = {1985} 16710} 16711 16712@Article{ ewald21, 16713 author = {{Ewald}, P.~P.}, 16714 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 16715 journal = {Annalen der Physik}, 16716 year = {1921}, 16717 volume = {369}, 16718 pages = {253-287}, 16719 doi = {10.1002/andp.19213690304}, 16720 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 16721 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16722} 16723 16724@Article{ greengardrokhlin87, 16725 author = {L. Greengard and V. Rokhlin}, 16726 date-added = {2008-02-15 18:43:55 +0000}, 16727 date-modified = {2008-02-26 20:09:11 +0000}, 16728 doi = {10.1016/0021-9991(87)90140-9}, 16729 journal = {J. Comput.\ Phys.}, 16730 keywords = {FMM}, 16731 number = {2}, 16732 pages = {325--348}, 16733 title = {A Fast Algorithm for Particle Simulations}, 16734 url = {citeseer.ist.psu.edu/greengard87fast.html}, 16735 volume = {73}, 16736 year = {1987}, 16737 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 16738} 16739 16740@Article{ greengardrokhlin97, 16741 author = {L. Greengard and V. Rokhlin}, 16742 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 16743 Dimensions}, 16744 journal = {Acta Numerica}, 16745 volume = {6}, 16746 year = {1997}, 16747 pages = {229--269} 16748} 16749 16750@Article{ luchenghuangmccammon06, 16751 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 16752 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 16753 systems}, 16754 journal = {PNAS}, 16755 doi = {10.1073/pnas.0605166103}, 16756 volume = {102}, 16757 number = {51}, 16758 year = {2006}, 16759 pages = {19314--19319} 16760} 16761 16762@Article{ schussnadlereisenberg01, 16763 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 16764 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 16765 from a molecular model}, 16766 journal = {Physical Review E}, 16767 volume = {64}, 16768 number = {3}, 16769 year = {2001} 16770} 16771 16772@Book{ hairerlubichwanner02, 16773 author = {E. Hairer and Ch. Lubich and G. Wanner}, 16774 title = {Geometric Numerical Integration}, 16775 publisher = {Springer-Verlag}, 16776 address = {Berlin Heidelberg}, 16777 year = {2002} 16778} 16779 16780@Article{ holstbakerwang00, 16781 author = {M. Holst and N. Baker and F. Wang}, 16782 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 16783 equation on massively parallel computers}, 16784 journal = {Journal of Computational Chemistry}, 16785 volume = {21}, 16786 year = {2000} 16787} 16788 16789@Book{ hockneyeastwood81, 16790 author = {R. Hockney and J. Eastwood}, 16791 title = {Computer simulation using particles}, 16792 publisher = {McGraw-Hill}, 16793 address = {New York}, 16794 year = {1981} 16795} 16796 16797@Article{ lutydavistironigunsteren94, 16798 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 16799 Gunsteren}, 16800 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 16801 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 16802 journal = {Molecular Simulation}, 16803 volume = {14}, 16804 number = {1}, 16805 year = {1994}, 16806 pages = {11--20} 16807} 16808 16809@Book{ briggshensonmccormick00, 16810 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 16811 title = {A Multigrid Tutorial (2nd ed.)}, 16812 year = {2000}, 16813 isbn = {0-89871-462-1}, 16814 publisher = {Society for Industrial and Applied Mathematics}, 16815 address = {Philadelphia, PA} 16816} 16817 16818@Article{ chartier2003spectral, 16819 title = {Spectral AMGe ($\rho$ AMGe)}, 16820 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 16821 McCormick, S and Ruge, J and Vassilevski, PS}, 16822 journal = {SIAM Journal on Scientific Computing}, 16823 volume = {25}, 16824 number = {1}, 16825 pages = {1--26}, 16826 year = {2003}, 16827 publisher = {SIAM} 16828} 16829 16830@Article{ galvis2010domain, 16831 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 16832 media}, 16833 author = {Galvis, Juan and Efendiev, Yalchin}, 16834 journal = {Multiscale Modeling \& Simulation}, 16835 volume = {8}, 16836 number = {4}, 16837 pages = {1461--1483}, 16838 year = {2010}, 16839 publisher = {SIAM} 16840} 16841 16842@Book{ brennerscott02, 16843 author = {Susanne~C. Brenner and L.~Ridgway Scott}, 16844 title = {The mathematical theory of finite element methods}, 16845 year = {2002}, 16846 isbn = {0-38795-451-1}, 16847 publisher = {Springer}, 16848 pages = {361} 16849} 16850 16851@Book{ trefethenbau97, 16852 author = {Lloyd N. Trefethen and David {Bau, III}}, 16853 title = {Numerical Linear Algebra}, 16854 publisher = {Society for Industrial and Applied Mathematics}, 16855 address = {Philadelphia, PA}, 16856 pages = {xii + 361}, 16857 year = {1997}, 16858 isbn = {0-89871-361-7}, 16859 isbn-13 = {978-0-89871-361-9}, 16860 lccn = {QA184 .T74 1997}, 16861 mrclass = {65-01 (65-02 65Fxx)}, 16862 mrnumber = {MR1444820 (98k:65002)}, 16863 mrreviewer = {Moody T. Chu}, 16864 bibdate = {Wed Jan 07 15:23:19 1998}, 16865 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16866} 16867 16868@Article{ liptonreagan2014, 16869 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16870 author = {Richard J Lipton and Kenneth W Regan}, 16871 pages = {206}, 16872 isbn = {978-0-26202-839-4}, 16873 year = {2014} 16874} 16875 16876@InProceedings{ rhea08, 16877 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16878 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16879 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16880 booktitle = {Proceedings of IEEE/ACM SC '08}, 16881 year = {2008} 16882} 16883 16884@Misc{ bursteddewilcox09, 16885 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16886 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16887 note = {in preparation} 16888} 16889 16890@Article{ skeeltezcanhardy02, 16891 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16892 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16893 journal = {J. Comp. Chem.}, 16894 volume = {23}, 16895 pages = {673--684}, 16896 year = {2002} 16897} 16898 16899@Article{ verschelde99, 16900 author = {Jan Verschelde}, 16901 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16902 homotopy continuation}, 16903 journal = {ACM Trans. Math. Softw.}, 16904 volume = {25}, 16905 number = {2}, 16906 issn = {0098-3500}, 16907 pages = {251--276}, 16908 doi = {10.1145/317275.317286}, 16909 publisher = {ACM}, 16910 address = {New York, NY}, 16911 year = {1999} 16912} 16913 16914@InProceedings{ sommeseverscheldewampler08, 16915 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16916 title = {Solving Polynomial Systems Equation by Equation}, 16917 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16918 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16919 pages = {133--152}, 16920 publisher = {Springer-Verlag}, 16921 year = {2008} 16922} 16923 16924@Article{ phanthientanner77, 16925 author = {N. Phan-Thien and R.~I. Tanner}, 16926 title = {A new constitutive equation derived from network theory}, 16927 journal = {J. Non-Newt. Fluid Mech.}, 16928 volume = {2}, 16929 pages = {353}, 16930 year = {1977} 16931} 16932 16933@Manual{ sage, 16934 key = {SAGE}, 16935 author = {W.\thinspace{}A. Stein and others}, 16936 organization = {The Sage~Development Team}, 16937 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16938 note = {{\tt http://www.sagemath.org}}, 16939 year = {2009} 16940} 16941 16942@Misc{ bateshauensteinsommesewampler06, 16943 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16944 Wampler}, 16945 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16946 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16947} 16948 16949@Article{ archer09, 16950 author = {A. J. Archer}, 16951 collaboration = {}, 16952 title = {Dynamical density functional theory for molecular and colloidal fluids: A 16953 microscopic approach to fluid mechanics}, 16954 publisher = {AIP}, 16955 year = {2009}, 16956 journal = {The Journal of Chemical Physics}, 16957 volume = {130}, 16958 number = {1}, 16959 eid = {014509}, 16960 numpages = {8}, 16961 pages = {014509}, 16962 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 16963 transition; statistical distributions; stochastic processes}, 16964 doi = {10.1063/1.3054633} 16965} 16966 16967@Article{ giesekus1966, 16968 author = {Hanswalter Giesekus}, 16969 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 16970 journal = {Rheologica Acta}, 16971 publisher = {Springer Berlin / Heidelberg}, 16972 volume = {5}, 16973 number = {1}, 16974 month = mar, 16975 year = {1966}, 16976 doi = {10.1007/BF01973575}, 16977 pages = {29-35} 16978} 16979 16980@Article{ baaijens98, 16981 author = {F.P. Baaijens}, 16982 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 16983 journal = {Journal of Non-Newtonian Fluid Mechanics}, 16984 volume = {79}, 16985 year = {1998}, 16986 pages = {361--385} 16987} 16988 16989@Book{ joseph90, 16990 author = {D.~D. Joseph}, 16991 title = {Fluid Dynamics of Viscoelastic Liquids}, 16992 publisher = {Springer}, 16993 address = {New York, NY}, 16994 year = {1990} 16995} 16996 16997@Article{ oldroyd50, 16998 author = {J.~G. Oldroyd}, 16999 title = {On the Formulation of Rheological Equations of State}, 17000 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 17001 Sciences}, 17002 volume = {200}, 17003 year = {1950}, 17004 pages = {523--541} 17005} 17006 17007@InProceedings{ bynasungroppthakur04, 17008 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 17009 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 17010 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 17011 year = {2004} 17012} 17013 17014@Book{ pozrikidis07, 17015 author = {C. Pozrikidis}, 17016 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 17017 publisher = {Kluwer (Springer)}, 17018 pages = {675}, 17019 year = {2001}, 17020 isbn = {0792373510} 17021} 17022 17023@Misc{ kritzkeyesfsp07, 17024 author = {A. Kritz and D. Keyes}, 17025 title = {{Fusion Simulation Project Workshop Report}}, 17026 month = jul, 17027 year = {2007}, 17028 note = {Available via 17029 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 17030} 17031 17032@Misc{ dahlburg02, 17033 author = {J. {Dahlburg (Chair)}}, 17034 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 17035 year = {2002}, 17036 note = {Available via 17037 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 17038} 17039 17040@Misc{ brown08, 17041 author = {D. {Brown (Chair)}}, 17042 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 17043 to the Future}}, 17044 year = {2008}, 17045 howpublished = {Office of Science, U.S. Department of Energy}, 17046 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 17047} 17048 17049@Misc{ crosscutting10, 17050 author = {D. Brown and P. {Messina (Chairs)}}, 17051 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 17052 Exascale}}, 17053 year = {2010}, 17054 howpublished = {Office of Science, U.S. Department of Energy}, 17055 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 17056} 17057 17058@Misc{ extreme-scale-solvers-workshop12, 17059 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 17060 L.C. McInnes and E. Ng and S. Wild}, 17061 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 17062 Architectures}, 17063 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 17064 note = {{Washington, DC}, March 8-9, 2012}, 17065 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 17066 year = {2012} 17067} 17068 17069@Misc{ monizrosner09, 17070 author = {{E. Moniz and R. Rosner}}, 17071 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 17072 and Simulation at the Extreme Scale}}, 17073 month = may, 17074 year = {2009}, 17075 note = {See 17076 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 17077} 17078 17079@Misc{ blanford08, 17080 author = {{R. Blandord (Chair)}}, 17081 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 17082 Computing at the Extreme Scale}}, 17083 month = dec, 17084 year = {2008}, 17085 note = {See 17086 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 17087} 17088 17089@Misc{ exascale07, 17090 author = {H. Simon and T. Zacharia and R. Stevens}, 17091 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 17092 year = {2007}, 17093 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 17094} 17095 17096@Misc{ ascrbreakthroughs08, 17097 author = {{Panel on Recent Significant Advancements in Computational Science}}, 17098 title = {Breakthroughs}, 17099 year = {2008}, 17100 note = {See 17101 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 17102} 17103 17104@Misc{ petsc-rd100-2009, 17105 author = {{R\&D Magazine}}, 17106 title = {{PETSc} {R}\&{D} 100 Award}, 17107 year = {2009}, 17108 note = {See 17109 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 17110} 17111 17112@Article{ compass-scidac08, 17113 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 17114 R. Ryne}, 17115 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 17116 Computational Science for Future Accelerators and Accelerator Technologies}, 17117 journal = {J. Phys.: Conf. Ser.}, 17118 volume = {125}, 17119 year = {2008}, 17120 pages = {012001}, 17121 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 17122} 17123 17124@Article{ compass-amundson-scidac08, 17125 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 17126 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 17127 Stoltz}, 17128 journal = {J. Phys.: Conf. Ser.}, 17129 volume = {125}, 17130 year = {2008} 17131} 17132 17133@InProceedings{ muszala09, 17134 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 17135 Simulations}, 17136 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 17137 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 17138 {(CBHPC 2009)}}, 17139 year = {2009} 17140} 17141 17142@Article{ gaston09, 17143 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 17144 Equations}, 17145 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 17146 journal = {Nuclear Engineering and Design}, 17147 volume = {239}, 17148 number = {10}, 17149 year = {2009}, 17150 pages = {1768 -- 1778} 17151} 17152 17153@Article{ gaston09b, 17154 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 17155 Engineering}, 17156 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 17157 and C. Permann and W. Taitano}, 17158 journal = {J. Phys.: Conf. Ser.}, 17159 volume = {180}, 17160 year = {2009}, 17161 pages = {012012} 17162} 17163 17164@Article{ newman09, 17165 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 17166 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 17167 author = {Chris Newman and Glen Hansen and Derek Gaston}, 17168 journal = {Journal of Nuclear Materials}, 17169 volume = {392}, 17170 issue = {1}, 17171 year = {2009}, 17172 pages = {6 -- 15} 17173} 17174 17175@Misc{ www:fenics, 17176 author = {{FE}ni{CS}}, 17177 title = {{FE}ni{CS} Project}, 17178 howpublished = {\url{http://www.fenics.org/}}, 17179 year = {2018} 17180} 17181 17182@InProceedings{ zwart08, 17183 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 17184 Systems}, 17185 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 17186 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 17187 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 17188 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 17189 booktitle = {Proceedings of ICCS 2008}, 17190 year = {2008} 17191} 17192 17193@Article{ klocknerwarburtonbridgehesthaven09, 17194 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 17195 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 17196 journal = {J. Comput. Phys.}, 17197 volume = {228}, 17198 number = {21}, 17199 year = {2009}, 17200 issn = {0021-9991}, 17201 pages = {7863--7882}, 17202 doi = {10.1016/j.jcp.2009.06.041}, 17203 publisher = {Academic Press Professional}, 17204 address = {San Diego, CA} 17205} 17206 17207@PhDThesis{ rankin99, 17208 author = {Rankin, W. T.}, 17209 keywords = {FMM, parallel FMM}, 17210 school = {Department of Electrical and Computer Engineering, Duke University}, 17211 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17212 year = {1999} 17213} 17214 17215@InProceedings{ warrensalmon93, 17216 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17217 and implemented. The algorithm computes the forces on an arbitrary distribution of 17218 bodies in a time which scales as N log N with the particle number. The accuracy of 17219 the force calculations is analytically bounded, and can be adjusted via a user 17220 defined parameter between a few percent relative accuracy, down to machine 17221 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17222 tree, we identify...}, 17223 address = {New York}, 17224 author = {Warren, Michael S. and Salmon, John K.}, 17225 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17226 citeulike-article-id={580952}, 17227 keywords = {oct-tree}, 17228 pages = {12--21}, 17229 publisher = {ACM}, 17230 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17231 year = {1993}, 17232 doi = {10.1145/169627.169640}, 17233 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17234} 17235 17236@Unpublished{ cruzwccm10, 17237 author = {Felipe A. Cruz}, 17238 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17239 note = {Presentation at WCCM 2010, Sydney Australia}, 17240 year = {2010} 17241} 17242 17243@Article{ mcguffee06, 17244 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17245 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17246 of salt, {pH}, point mutations, and protein concentration in simulations of 17247 1000-molecule systems}, 17248 journal = {Journal of the American Chemical Society}, 17249 volume = {128}, 17250 pages = {12098--12110}, 17251 year = {2006} 17252} 17253 17254@Article{ nilsencaihoylandlangtangen10, 17255 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17256 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17257 in Python}}, 17258 journal = {ArXiv e-prints}, 17259 archiveprefix = {arXiv}, 17260 eprint = {1002.0705}, 17261 primaryclass = {cs.DC}, 17262 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17263 - Programming Languages}, 17264 year = {2010}, 17265 month = feb, 17266 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17267 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17268} 17269 17270@Misc{ mcinnes:siam09:minisymposium, 17271 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17272 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17273 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17274 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17275 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17276 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17277 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17278 Austin).} 17279} 17280 17281@Misc{ mcinnes:fsp-summary:feb2011, 17282 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17283 title = {Solvers and Time Integration Breakout Summary}, 17284 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17285 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17286} 17287 17288@Misc{ dvi-materials:siamcse11, 17289 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17290 Materials}, 17291 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17292 Smith and L. Wang}, 17293 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17294 and Engineering, March 3, 2011} 17295} 17296 17297@Misc{ jamroz:cemm10, 17298 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17299 author = {B. Jamroz and S. Kruger and T. Austin}, 17300 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17301} 17302 17303@Misc{ kruger:feb4-2011, 17304 title = {personal communication}, 17305 author = {S. Kruger}, 17306 note = {February, 2011} 17307} 17308 17309@Article{ elman1996, 17310 author = {H.C. Elman}, 17311 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17312 viscosity}, 17313 journal = {SIAM J. Sci. Comput.}, 17314 volume = {20}, 17315 year = {1996}, 17316 pages = {1299--1316} 17317} 17318 17319@Article{ kayloghinwathen2002, 17320 author = {D. Kay and D. Loghin and A. Wathen}, 17321 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17322 journal = {SIAM J. Sci. Comput.}, 17323 volume = {24}, 17324 year = {2002}, 17325 pages = {237--256} 17326} 17327 17328@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17329 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17330 title = {Block preconditioners based on approximate commutators}, 17331 journal = {SIAM J. Sci. Comput.}, 17332 volume = {27}, 17333 number = {5}, 17334 year = {2006}, 17335 pages = {1651--1668} 17336} 17337 17338@Article{ braesssarazin1997, 17339 author = {Dietrich Braess and Regina Sarazin}, 17340 title = {An efficient smoother for the {Stokes} problem}, 17341 journal = {Applied Numerical Mathematics}, 17342 volume = {23}, 17343 number = {1}, 17344 year = {1997}, 17345 pages = {3--19}, 17346 doi = {10.1016/S0168-9274(96)00059-1} 17347} 17348 17349@Article{ wright2001large, 17350 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17351 author = {Wright, T.G. and Trefethen, L.N.}, 17352 journal = {SIAM Journal on Scientific Computing}, 17353 volume = {23}, 17354 pages = {591}, 17355 year = {2001} 17356} 17357 17358@Misc{ wright2002eigtool, 17359 title = {Eig{T}ool}, 17360 author = {Wright, T.G. and Trefethen, LN}, 17361 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17362 year = {2002} 17363} 17364 17365@Misc{ visit-web-site, 17366 key = {{VisIt}}, 17367 title = {{VisIt web site}}, 17368 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17369 url = {http://wci.llnl.gov/codes/visit/}, 17370 year = {2011} 17371} 17372 17373@Book{ trefethen1996, 17374 title = {Finite difference and spectral methods for ordinary and partial differential 17375 equations}, 17376 author = {Lloyd Nicholas Trefethen}, 17377 year = {1996}, 17378 publisher = {Cornell University-Department of Computer Science and Center for Applied 17379 Mathematics} 17380} 17381 17382@Book{ trefethen2005spectra, 17383 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17384 author = {Trefethen, L.N. and Embree, M.}, 17385 year = {2005}, 17386 publisher = {Princeton University Press} 17387} 17388 17389@Article{ gomez2010isogeometric, 17390 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17391 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17392 journal = {Computer Methods in Applied Mechanics and Engineering}, 17393 volume = {199}, 17394 number = {25-28}, 17395 pages = {1828--1840}, 17396 issn = {0045-7825}, 17397 year = {2010}, 17398 publisher = {Elsevier} 17399} 17400 17401@Article{ gomez2008isogeometric, 17402 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17403 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17404 journal = {Computer Methods in Applied Mechanics and Engineering}, 17405 volume = {197}, 17406 number = {49-50}, 17407 pages = {4333--4352}, 17408 year = {2008}, 17409 publisher = {Elsevier} 17410} 17411 17412@Misc{ fastmath:project, 17413 author = {Lori {Diachin (PI)}}, 17414 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17415 (FASTMath) Institute}}, 17416 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17417} 17418 17419@Misc{ exascale-software:proposal, 17420 author = {Peter {Beckman (PI)}}, 17421 title = {{Exascale Software Center}}, 17422 note = {proposal to DOE} 17423} 17424 17425@Misc{ imex:project, 17426 author = {Barry {Smith (PI)}}, 17427 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17428 Multimodel PDEs}}, 17429 note = {DOE ASCR applied math project} 17430} 17431 17432@Misc{ intel-mic:website, 17433 author = {Intel}, 17434 title = {{Many Integrated Core Architecture}}, 17435 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17436} 17437 17438@Article{ dudson:2009, 17439 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17440 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17441 journal = {Computer Physics Communications}, 17442 volume = {180}, 17443 pages = {1467}, 17444 year = {2009} 17445} 17446 17447@Article{ umansky:2009, 17448 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17449 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17450 journal = {Computer Physics Communications}, 17451 year = {2009}, 17452 volume = {180}, 17453 pages = {887-903} 17454} 17455 17456@Article{ xu:1998, 17457 author = {X.Q. Xu and R.H. Cohen}, 17458 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17459 journal = {Computer Physics Communications}, 17460 year = {1998}, 17461 volume = {36}, 17462 number = {1-2}, 17463 pages = {158} 17464} 17465 17466@Article{ tron:1999, 17467 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17468 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17469 journal = {SIAM Journal on Optimization}, 17470 volume = {9}, 17471 number = {4}, 17472 pages = {1100-1127}, 17473 year = {1999} 17474} 17475 17476@Article{ stubenamg, 17477 author = {K. St\"{u}ben}, 17478 title = {A review of algebraic multigrid}, 17479 journal = {J. Comput. Appl. Math.}, 17480 volume = {128}, 17481 number = {1-2}, 17482 year = {2001}, 17483 issn = {0377-0427}, 17484 pages = {281--309}, 17485 doi = {10.1016/S0377-0427(00)00516-1}, 17486 publisher = {Elsevier Science Publishers B. V.}, 17487 address = {Amsterdam, The Netherlands, The Netherlands} 17488} 17489 17490@Article{ feuchtermg, 17491 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17492 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17493 journal = {Computing and visualization in science}, 17494 publisher = {Springer}, 17495 volume = {6}, 17496 number = {1}, 17497 year = {2003}, 17498 pages = {1--13} 17499} 17500 17501@Article{ chowmgsmoothness, 17502 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17503 only attempts to interpolate in the directions of geometrical smoothness. These 17504 directions are determined by analyzing samples of algebraically smooth error, e. 17505 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17506 consistently nearby in value. In addition, these dierences may be used to dene 17507 interpolation weights. These new ideas may be incorporated into the algebraic 17508 multigrid method. Test results show that the new method can have much lower grid 17509 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17510 author = {Chow, Edmond}, 17511 citeulike-article-id={7675372}, 17512 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17513 journal = {American Journal of Mathematics}, 17514 keywords = {fem, multigrid}, 17515 pages = {197--215}, 17516 posted-at = {2010-08-17 23:29:51}, 17517 priority = {2}, 17518 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17519 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17520 volume = {65}, 17521 year = {2001} 17522} 17523 17524@Article{ jonesamge, 17525 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17526 elements) method based on element agglomeration. In the method, coarse grid 17527 elements are formed by agglomerating fine grid elements. Compatible interpolation 17528 operators are constructed which yield coarse grid basis functions with a minimal 17529 energy property. Heuristics based on interpolation quality measures are used to 17530 guide the agglomeration procedure. The performance of the resulting method is 17531 demonstrated in two-level numerical experiments.}}, 17532 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17533 citeulike-article-id={8598569}, 17534 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17535 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17536 journal = {SIAM Journal on Scientific Computing}, 17537 keywords = {amg, fem, multigrid}, 17538 number = {1}, 17539 pages = {109--133}, 17540 posted-at = {2011-01-13 18:05:55}, 17541 priority = {2}, 17542 publisher = {SIAM}, 17543 title = {{AMGE Based on Element Agglomeration}}, 17544 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17545 volume = {23}, 17546 year = {2001} 17547} 17548 17549@Article{ saad1993, 17550 author = {Saad, Youcef}, 17551 doi = {10.1137/0914028}, 17552 issn = {10648275}, 17553 journal = {SIAM Journal on Scientific Computing}, 17554 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17555 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17556 precondition-,preconditioned conju-,subject classi cations,variable 17557 preconditioners}, 17558 number = {2}, 17559 pages = {461--469}, 17560 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17561 volume = {14}, 17562 year = {1993} 17563} 17564 17565@Misc{ path:homepage, 17566 author = {S. Dirkse and M. Ferris and T. 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Watts}, 17817 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 17818 brulee?}, 17819 journal = {GSA Today}, 17820 volume = {16}, 17821 pages = {4–-10}, 17822 year = {2006} 17823} 17824 17825@InProceedings{ yang:brent:2002, 17826 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 17827 Parallel Distributed Memory Architectures}, 17828 author = {Laurence T. Yang and Richard Brent}, 17829 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 17830 for Parallel Processing}, 17831 year = {2002}, 17832 publisher = {IEEE} 17833} 17834 17835@Article{ demmel2008communication, 17836 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 17837 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 17838 journal = {Arxiv preprint arXiv:0808.2664}, 17839 year = {2008} 17840} 17841 17842@Article{ demmel09, 17843 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 17844 title = {Communication-optimal Iterative Methods}, 17845 journal = {Journal of Physics: Conf. 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Rall}, 17873 title = {Computational solution of nonlinear operator equations}, 17874 publisher = {Krieger Pub Co.}, 17875 pages = {225}, 17876 year = {1969} 17877} 17878 17879@Article{ fletcherreeves1964, 17880 author = {R. Fletcher and C. M. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 17915} 17916 17917@Article{ keyesmcinneswoodwardetal13, 17918 title = {Multiphysics Simulations: Challenges and Opportunities}, 17919 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17920 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17921 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17922 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17923 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17924 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17925 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17926 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17927 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17928 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17929 journal = {International Journal of High Performance Computing Applications}, 17930 month = feb, 17931 year = {2013}, 17932 volume = {27}, 17933 number = {1}, 17934 pages = {4--83}, 17935 doi = {10.1177/1094342012468181}, 17936 note = {Special issue}, 17937 abstract = {We consider multiphysics applications from algorithmic and architectural 17938 perspectives, where ``algorithmic'' includes both mathematical analysis and 17939 computational complexity and ``architectural'' includes both software and hardware 17940 environments. Many diverse multiphysics applications can be reduced, en route to 17941 their computational simulation, to a common algebraic coupling paradigm. 17942 Mathematical analysis of multiphysics coupling in this form is not always 17943 practical for realistic applications, but model problems representative of 17944 applications discussed herein can provide insight. A variety of software 17945 frameworks for multiphysics applications have been constructed and refined within 17946 disciplinary communities and executed on leading-edge computer systems. We examine 17947 several of these, expose some commonalities among them, and attempt to extrapolate 17948 best practices to future systems. From our study, we summarize challenges and 17949 forecast opportunities.} 17950} 17951 17952@Misc{ rosner10, 17953 author = {Robert {Rosner (Chair)}}, 17954 title = {{The Opportunities and Challenges of Exascale Computing}}, 17955 year = {2010}, 17956 howpublished = {Office of Science, U.S. Department of Energy}, 17957 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17958} 17959 17960@Misc{ kogge2008exascale, 17961 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 17962 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 17963 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 17964 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 17965 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 17966 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 17967 howpublished = {DARPA}, 17968 year = {2008}, 17969 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 17970} 17971 17972@Misc{ doegrandchallengeworkshops, 17973 key = {Office of Science, U.S. Department of Energy}, 17974 title = {{Scientific Grand Challenges Workshop Series}}, 17975 howpublished = {Office of Science, U.S. Department of Energy, see 17976 \url{http://extremecomputing.labworks.org/workshops.stm}} 17977} 17978 17979@Misc{ lawrence2011, 17980 key = {Lawrence}, 17981 title = {{Ernest Orlando Lawrence Award Winners}}, 17982 howpublished = {U.S. Department of Energy, {\footnotesize 17983 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 17984 year = {2011} 17985} 17986 17987@Article{ murphy2000npi, 17988 title = {{A note on preconditioning for indefinite linear systems}}, 17989 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 17990 journal = {SIAM Journal on Scientific Computing}, 17991 volume = {21}, 17992 number = {6}, 17993 pages = {1969--1972}, 17994 year = {2000}, 17995 publisher = {Philadelphia, PA: SIAM, c1993-} 17996} 17997 17998@Article{ elman2011bouyancy, 17999 title = {Fast iterative solvers for buoyancy driven flow problems}, 18000 journal = {Journal of Computational Physics}, 18001 volume = {230}, 18002 number = {10}, 18003 pages = {3900 - 3914}, 18004 year = {2011}, 18005 note = {}, 18006 issn = {0021-9991}, 18007 doi = {10.1016/j.jcp.2011.02.014}, 18008 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 18009 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 18010 Adaptivity, Preconditioning, Algebraic multigrid} 18011} 18012 18013@Article{ dongarrabeckman11, 18014 author = {J. Dongarra and P. Beckman and et al.}, 18015 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 18016 journal = {Int. J. High Perf. Comput. 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Brannick and Robert D. Falgout}, 18069 journal = {SIAM Journal on Scientific Computing}, 18070 volume = {32}, 18071 number = {3}, 18072 pages = {1393--1416}, 18073 url = {http://epubs.siam.org/doi/10.1137/090772216}, 18074 doi = {10.1137/090772216}, 18075 issn = {1064-8275}, 18076 year = {2010} 18077} 18078 18079@Article{ xu2004energy, 18080 title = {On an energy minimizing basis for algebraic multigrid methods}, 18081 author = {Xu, J. and Zikatanov, L.}, 18082 journal = {Computing and Visualization in Science}, 18083 volume = {7}, 18084 number = {3}, 18085 pages = {121--127}, 18086 year = {2004}, 18087 publisher = {Springer} 18088} 18089 18090@Article{ dblp:journals/toms/bakerhlt09, 18091 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 18092 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 18093 journal = {ACM Trans. Math. 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Sala}, 18116 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 18117 institution = {Sandia National Laboratories}, 18118 year = {2006}, 18119 number = {SAND2006-2649} 18120} 18121 18122@Article{ brannick06, 18123 title = {An energy-based AMG coarsening strategy}, 18124 volume = {13}, 18125 doi = {10.1002/nla.480}, 18126 number = {2-3}, 18127 journal = {Numerical Linear Algebra with Applications}, 18128 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 18129 and Ruge, J}, 18130 year = {2006}, 18131 pages = {133--148} 18132} 18133 18134@Article{ olson10, 18135 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 18136 title = {A new perspective on strength measures in algebraic multigrid}, 18137 journal = {Numerical Linear Algebra with Applications}, 18138 volume = {17}, 18139 number = {4}, 18140 pages = {713--733}, 18141 year = {2010}, 18142 publisher = {John Wiley \& Sons, Ltd.}, 18143 issn = {1099-1506}, 18144 doi = {10.1002/nla.669} 18145} 18146 18147@Article{ olson11, 18148 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 18149 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 18150 Minimization}, 18151 journal = {SIAM J. Sci. 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P.}, 18531 eprint = {arXiv:1002.0705v1}, 18532 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 18533 parallelization of scientific codes by a function-centric approach in 18534 Python.pdf:pdf}, 18535 journal = {Computational Science \& Discovery}, 18536 keywords = {parallel,programming,python,software}, 18537 mendeley-tags = {parallel,programming,python,software}, 18538 pages = {015003}, 18539 publisher = {IOP Publishing}, 18540 title = {{Simplifying the parallelization of scientific codes by a function-centric 18541 approach in Python}}, 18542 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 18543 volume = {3}, 18544 year = {2010} 18545} 18546 18547@Book{ langtangen09, 18548 author = {Hans Petter Langtangen}, 18549 title = {Python Scripting for Computational Science}, 18550 publisher = {Springer}, 18551 series = {Texts in Computational Science and Engineering}, 18552 pages = {784}, 18553 isbn = {3540739157}, 18554 year = {2009} 18555} 18556 18557@Book{ numpyguide, 18558 author = {Travis E. Oliphant}, 18559 title = {Guide to {N}umpy}, 18560 publisher = {Trelgol}, 18561 year = {2008} 18562} 18563 18564@Misc{ pycuda, 18565 author = {Andreas Kl\"ockner}, 18566 title = {{PyCUDA}}, 18567 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 18568 year = {2011} 18569} 18570 18571@Misc{ pyopencl, 18572 author = {Andreas Kl\"ockner}, 18573 title = {{PyOpenCL}}, 18574 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 18575 year = {2011} 18576} 18577 18578@Article{ klockner2012, 18579 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 18580 Paul Ivanov and Ahmed Fasih}, 18581 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 18582 generation}, 18583 journal = {Parallel Computing}, 18584 volume = {38}, 18585 number = {3}, 18586 pages = {157--174}, 18587 year = {2012}, 18588 issn = {0167-8191}, 18589 doi = {10.1016/j.parco.2011.09.001} 18590} 18591 18592%%%%%% Matt Stuff %%%%%% 18593@Article{ morrabozdagknepleyrassvesselinov, 18594 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 18595 author = {Gabriele Morra and Ebru Bozdag and Matthew G. 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Yuen and Huai 18665 Zhang and Yaolin Shi}, 18666 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 18667 strongly variable viscosity based on {Matlab} and {CUDA}}, 18668 type = {Research Report}, 18669 number = {UMSI 2011/33}, 18670 institution = {University of Minnesota Supercomputing Institute}, 18671 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 18672 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 18673 month = mar, 18674 year = {2011} 18675} 18676 18677@InProceedings{ zheng2010, 18678 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai 18679 Zhang and Yaolin Shi}, 18680 title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients}, 18681 booktitle = {Eos Transactions of the AGU}, 18682 organization = {American Geophysical Union}, 18683 note = {Fall Meeting Supplemental, Abstract IN41A-1350}, 18684 year = {2010} 18685} 18686 18687@InCollection{ terrelkirbyknepleyscott12, 18688 author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott 18689 and Garth N. Wells}, 18690 title = {Finite elements for incompressible fluids}, 18691 editors = {A. Logg and K.A. Mardal and G. N. 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Terrel}, 18715 title = {Discrete optimization of finite element matrix evaluation}, 18716 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18717 booktitle = {Automated solutions of differential equations by the finite element method}, 18718 series = {Lecture Notes in Computational Science and Engineering}, 18719 volume = {84}, 18720 pages = {385--397}, 18721 publisher = {Springer-Verlag}, 18722 year = {2012} 18723} 18724 18725@InCollection{ kirby12, 18726 author = {Robert C. Kirby}, 18727 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 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 publisher = {Springer-Verlag}, 18733 year = {2012} 18734} 18735 18736@Article{ brownconveryhotesknepleypetropolous1993, 18737 author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and 18738 Labros Petropolous}, 18739 title = {Closed strings with low harmonics and kinks}, 18740 journal = {Physical Review D}, 18741 volume = {48}, 18742 number = {6}, 18743 year = {1993} 18744} 18745 18746@Article{ minimax1996, 18747 title = {MiniMax: What has been learned thus far}, 18748 author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and 18749 Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and 18750 C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. 18751 Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 18752 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. 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23574 23575@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 23576 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 23577 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 23578 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 23579 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 23580 pages = {1103}, 23581 year = {2018} 23582} 23583 23584@InProceedings{ barralangeloudiskramergormanpiggott2018, 23585 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 23586 modelling}, 23587 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 23588 and Matthew D Piggott}, 23589 booktitle = {EGU General Assembly Conference Abstracts}, 23590 volume = {20}, 23591 pages = {19168}, 23592 year = {2018} 23593} 23594 23595@Article{ principe2009, 23596 title = {{Mathematical models for thermally coupled low speed flows}}, 23597 author = {Javier Principe and Ramon Codina}, 23598 journal = {Advances in Theoretical and Applied Mechanics}, 23599 volume = {2}, 23600 number = {1-4}, 23601 pages = {93--112}, 23602 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 23603 year = {2009} 23604} 23605 23606@Book{ vandervorst2003, 23607 title = {Iterative {K}rylov Methods for Large Linear Systems}, 23608 author = {van der Vorst, H.}, 23609 isbn = {9780521818285}, 23610 publisher = {Cambridge University Press}, 23611 year = {2003} 23612} 23613 23614@Book{ peres2006, 23615 author = {Asher Peres}, 23616 title = {Quantum theory: concepts and methods}, 23617 volume = {57}, 23618 publisher = {Springer Science \& Business Media}, 23619 year = {2006} 23620} 23621 23622@Book{ kuttler2012, 23623 title = {Linear algebra: theory and applications}, 23624 author = {Kenneth Kuttler}, 23625 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 23626 year = {2012} 23627} 23628 23629@Book{ elman_silvester_wathen_2014, 23630 place = {Oxford}, 23631 title = {Finite elements and fast iterative solvers: with applications in incompressible 23632 fluid dynamics}, 23633 publisher = {Oxford University Press}, 23634 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 23635 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 23636 year = {2014} 23637} 23638 23639@Article{ alametal2007, 23640 title = {An evaluation of the ORNL Cray XT3}, 23641 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 23642 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 23643 journal = {International Journal of High Performance Computing Applications}, 23644 volume = {22}, 23645 number = {1}, 23646 pages = {52--80}, 23647 doi = {10.1177/1094342007085019}, 23648 year = {2007} 23649} 23650 23651@Article{ plazacarey2000, 23652 title = {Local refinement of simplicial grids based on the skeleton}, 23653 author = {Plaza, A. and Carey, Graham F.}, 23654 journal = {Applied Numerical Mathematics}, 23655 doi = {10.1016/S0168-9274(99)00022-7}, 23656 issn = {01689274}, 23657 volume = {32}, 23658 number = {2}, 23659 pages = {195--218}, 23660 year = {2000} 23661} 23662 23663@Article{ carsonstrakos2020, 23664 title = {On the cost of iterative computations}, 23665 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 23666 journal = {Phil. Trans. R. Soc. A}, 23667 volume = {378}, 23668 number = {20190050}, 23669 doi = {10.1098/rsta.2019.0050}, 23670 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 23671 year = {2020} 23672} 23673 23674@Article{ schoberl1999, 23675 title = {Multigrid methods for a parameter dependent problem in primal variables}, 23676 author = {Joachim Sch{\"o}berl}, 23677 journal = {Numerische Mathematik}, 23678 volume = {84}, 23679 number = {1}, 23680 pages = {97--119}, 23681 year = {1999} 23682} 23683 23684@Article{ wuleexuzikatanov2008, 23685 title = {Convergence analysis on iterative methods for semidefinite systems}, 23686 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 23687 journal = {Journal of Computational Mathematics}, 23688 pages = {797--815}, 23689 year = {2008} 23690} 23691 23692@Article{ maierrannacher2016, 23693 title = {Duality-based adaptivity in finite element discretization of heterogeneous 23694 multiscale problems}, 23695 author = {Maier, Matthias and Rannacher, Rolf}, 23696 journal = {Journal of Numerical Mathematics}, 23697 volume = {24}, 23698 number = {3}, 23699 pages = {167--187}, 23700 year = {2016} 23701} 23702 23703@Article{ maierrannacher2018, 23704 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23705 multiscale problems}, 23706 author = {Maier, Matthias and Rannacher, Rolf}, 23707 journal = {Multiscale Modeling \& Simulation}, 23708 volume = {16}, 23709 number = {1}, 23710 pages = {412--428}, 23711 year = {2018} 23712} 23713 23714@Article{ margetismaierluskin2017, 23715 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23716 metamaterial sheet}, 23717 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23718 journal = {Studies in Applied Mathematics}, 23719 volume = {139}, 23720 number = {4}, 23721 pages = {599--625}, 23722 year = {2017} 23723} 23724 23725@Article{ maiermargetisluskin2017b, 23726 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23727 approximation and validation}, 23728 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23729 journal = {Journal of Computational Physics}, 23730 volume = {339}, 23731 pages = {126--145}, 23732 year = {2017} 23733} 23734 23735@Article{ maiermargetisluskin2018, 23736 title = {Generation of surface plasmon-polaritons by edge effects}, 23737 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23738 journal = {Communications in Mathematical Sciences}, 23739 volume = {16}, 23740 number = {1}, 23741 pages = {77--95}, 23742 url = {http://arxiv.org/abs/1702.00848}, 23743 year = {2018} 23744} 23745 23746@Article{ maiermattheakiskaxirasluskinmargetis2018, 23747 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23748 metamaterials}, 23749 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23750 Mitchell and Margetis, Dionisios}, 23751 journal = {Physical Review B}, 23752 volume = {97}, 23753 number = {3}, 23754 pages = {035307}, 23755 year = {2018} 23756} 23757 23758@Article{ maiermattheakiskaxirasluskinmargetis2019, 23759 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23760 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23761 Mitchell and Margetis, Dionisios}, 23762 journal = {Proceedings of the Royal Society A}, 23763 volume = {475}, 23764 number = {2230}, 23765 pages = {20190220}, 23766 year = {2019} 23767} 23768 23769@Article{ maiermargetisluskin2020, 23770 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23771 two scales}, 23772 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23773 journal = {Physical Review B}, 23774 volume = {102}, 23775 number = {7}, 23776 pages = {075308}, 23777 year = {2020} 23778} 23779 23780@Article{ margetismaierstauberlowluskin2020, 23781 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 23782 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 23783 Luskin, Mitchell}, 23784 journal = {Journal of Physics A: Mathematical and Theoretical}, 23785 volume = {53}, 23786 number = {5}, 23787 pages = {055201}, 23788 year = {2020} 23789} 23790 23791@Article{ maiermargetismellet2020, 23792 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 23793 structures}, 23794 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 23795 journal = {Journal of Computational and Applied Mathematics}, 23796 volume = {377}, 23797 pages = {112909}, 23798 year = {2020} 23799} 23800 23801@Article{ maierkronbichler2021, 23802 title = {Efficient parallel 3D computation of the compressible Euler equations with an 23803 invariant-domain preserving second-order finite-element scheme}, 23804 author = {Maier, Matthias and Kronbichler, Martin}, 23805 journal = {ACM Transactions on Parallel Computing}, 23806 volume = {8}, 23807 number = {3}, 23808 pages = {1--30}, 23809 year = {2021} 23810} 23811 23812@Article{ guermondmaierpopovtomas2021, 23813 title = {Second-order invariant domain preserving approximation of the compressible 23814 Navier--Stokes equations}, 23815 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 23816 journal = {Computer Methods in Applied Mechanics and Engineering}, 23817 volume = {375}, 23818 pages = {113608}, 23819 year = {2021} 23820} 23821 23822@Article{ liliptonmaier2021, 23823 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 23824 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 23825 eprint = {2009.12166}, 23826 archiveprefix = {arXiv}, 23827 primaryclass = {phys.optics}, 23828 year = {2021} 23829} 23830 23831@Article{ songmaierluskin2020, 23832 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 23833 gradient-index graphene waveguides}, 23834 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23835 journal = {Journal of Computational Physics}, 23836 volume = {423}, 23837 pages = {109871}, 23838 year = {2020} 23839} 23840 23841@Article{ songmaierluskin2019, 23842 title = {Adaptive finite element simulations of waveguide configurations involving 23843 parallel 2D material sheets}, 23844 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23845 journal = {Computer Methods in Applied Mechanics and Engineering}, 23846 volume = {351}, 23847 pages = {20--34}, 23848 year = {2019} 23849} 23850 23851% 23852% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23853% 23854% 23855@Unpublished{ rob1, 23856 author = {Rob Kunz}, 23857 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23858 State University}, 23859 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23860 sponsors = {U.S. Navy, NRC}, 23861 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23862 simulations, including lake warming by power plants}, 23863 dates = {Oct 3 and 4, 2002}, 23864 email = {rfk@wt.arl.psu.edu} 23865} 23866 23867@Unpublished{ au1, 23868 author = {Feng Wang and William Appelbe}, 23869 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23870 url = {http://www.vpac.org}, 23871 sponsors = { }, 23872 note = {Using PETSc for a Variety of Geophysical Simulations}, 23873 dates = {Nov 22, 2002} 23874} 23875 23876@Unpublished{ carl1, 23877 author = {Carl Sovinec}, 23878 institution = {Applied Physics, University of Wisconsin}, 23879 url = {http://nimrodteam.org}, 23880 sponsors = {DOE Office of Fusion Research}, 23881 note = {Investigating using PETSc for NIMROD}, 23882 dates = {Nov 21, 2002}, 23883 email = {sovinec@engr.wisc.edu} 23884} 23885 23886@Unpublished{ au1b, 23887 author = {Pablo Carrica and Robert Wilson}, 23888 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23889 url = {http://}, 23890 sponsors = {Office of Naval Research}, 23891 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23892 dates = {Sept, 2002}, 23893 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23894} 23895 23896% ------------------- TAO References ---------------------- 23897@Article{ benson:2001:csp, 23898 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 23899 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 23900 journal = {{ACM} Transactions on Mathematical Software}, 23901 volume = {27}, 23902 number = {3}, 23903 month = sep, 23904 year = {2001}, 23905 pages = {361--376} 23906} 23907 23908@TechReport{ tao-user-ref-2000, 23909 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 23910 title = {{TAO} Users Manual}, 23911 year = {2000}, 23912 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23913 number = {ANL/MCS-TM-242}, 23914 note = {See \url{http://www.mcs.anl.gov/tao}} 23915} 23916 23917% ------------------- Optimization References ---------------------- 23918@Book{ optguide93, 23919 title = {Optimization Software Guide}, 23920 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 23921 publisher = {SIAM Publications}, 23922 address = {Philadelphia}, 23923 year = {1993} 23924} 23925 23926@InProceedings{ more84, 23927 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 23928 Hillstrom}, 23929 title = {The {MINPACK} Project}, 23930 booktitle = {Sources and Development of Mathematical Software}, 23931 editor = {Wayne R. Cowell}, 23932 year = {1984}, 23933 pages = {88--111} 23934} 23935 23936@Article{ steihaug:83, 23937 author = {Trond Steihaug}, 23938 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 23939 journal = {SIAM J. Numer. Anal.}, 23940 volume = {20}, 23941 year = {1983}, 23942 pages = {626--637}, 23943 key = {steihaug92 ! trust_region} 23944} 23945 23946@TechReport{ minpack2test, 23947 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 23948 title = {The {MINPACK-2} Test Problem Collection}, 23949 institution = {Argonne National Laboratory}, 23950 year = {1991}, 23951 number = {ANL/MCS-TM-150}, 23952 key = {more91 ! MINPACK-2} 23953} 23954 23955@TechReport{ hohmann:94, 23956 author = {Andreas Hohmann}, 23957 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 23958 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 23959 year = {1994}, 23960 number = {SC-94-4}, 23961 key = {Hohmann94} 23962} 23963 23964@TechReport{ meza:94, 23965 author = {Juan C. Meza}, 23966 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 23967 institution = {Sandia National Laboratory}, 23968 year = {1994}, 23969 number = {SAND94-8225}, 23970 key = {Meza94} 23971} 23972 23973@Book{ dennis:83, 23974 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 23975 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 23976 publisher = {Prentice-Hall, Inc.}, 23977 address = {Englewood Cliffs, NJ}, 23978 year = {1983} 23979} 23980 23981@TechReport{ more:92, 23982 author = {Jorge J. Mor\'{e} and David Thuente}, 23983 title = {Line search algorithms with guaranteed sufficient decrease}, 23984 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23985 year = {1992}, 23986 number = {MCS-P330-1092} 23987} 23988 23989@Article{ more-toraldo, 23990 author = {Jorge J. Mor\'e and G. Toraldo}, 23991 journal = {SIOPT}, 23992 pages = {93--113}, 23993 title = {On the solution of large quadratic programming problems with bound constraints}, 23994 volume = {1}, 23995 year = {1991} 23996} 23997 23998@Article{ byrd:1995:lma, 23999 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 24000 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 24001 journal = {SIAM Journal on Scientific Computing}, 24002 volume = {16}, 24003 number = {5}, 24004 pages = {1190--1208}, 24005 month = sep, 24006 year = {1995}, 24007 coden = {SJOCE3}, 24008 issn = {1064-8275 (print), 1095-7197 (electronic)}, 24009 mrclass = {90C30 (65K05)}, 24010 mrnumber = {96e:90039}, 24011 mrreviewer = {Henry Wolkowicz}, 24012 bibdate = {Fri Dec 4 16:17:35 MST 1998} 24013} 24014 24015@Article{ lin_c3, 24016 author = {C.-J. Lin and J. J. Mor\'e}, 24017 title = {Newton's method for large bound-constrained optimization problems}, 24018 year = {1999}, 24019 journal = {SIOPT}, 24020 volume = {9(4)}, 24021 pages = {1100--1127}, 24022 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 24023} 24024 24025@TechReport{ dolan2, 24026 author = {E. Dolan and J. J. Mor\'{e}}, 24027 title = {Benchmarking Optimization Software with Performance Profiles}, 24028 year = {2001}, 24029 month = jan, 24030 number = {ANL/MCS-P861-1200}, 24031 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24032 address = {Argonne, IL}, 24033 url = {http://www.mcs.anl.gov/~more/cops/} 24034} 24035 24036@InProceedings{ owlqn, 24037 author = {Galen Andrew and Jianfeng Gao}, 24038 title = {Scalable training of L1-regularized log-linear models}, 24039 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 24040 pages = {33--40}, 24041 year = {2007} 24042} 24043 24044@Article{ bmrm, 24045 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 24046 title = {Bundle methods for regularized risk minimization}, 24047 year = {2010}, 24048 journal = {Journal of Machine Learning Research}, 24049 volume = {11}, 24050 pages = {311--365} 24051} 24052 24053% ------------------- Component Software References ---------------------- 24054@InProceedings{ cca99, 24055 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 24056 McInnes and S. Parker and B. Smolinski}, 24057 title = {Toward a Common Component Architecture for High-Performance Scientific 24058 Computing}, 24059 booktitle = {Proceedings of {High Performance Distributed Computing}}, 24060 pages = {115--124}, 24061 year = {1999}, 24062 note = {See \url{http://cca-forum.org}} 24063} 24064 24065@Book{ szyperski98, 24066 author = {Clemens Szyperski}, 24067 title = {Component Software: Beyond Object-Oriented Programming}, 24068 publisher = {ACM Press}, 24069 address = {New York}, 24070 year = {1998} 24071} 24072 24073@Article{ broy98, 24074 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 24075 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 24076 Stal and Clemens Szyperski}, 24077 title = {What Characterizes a (Software) Component?}, 24078 journal = {Software -- Concepts and Tools}, 24079 publisher = {Springer-Verlag}, 24080 year = {1998}, 24081 volume = {19}, 24082 pages = {49--56} 24083} 24084 24085@Article{ componentware:94, 24086 author = {Jon Udell}, 24087 title = {Componentware}, 24088 journal = {Byte}, 24089 volume = {may}, 24090 pages = {46--56}, 24091 year = {1994}, 24092 key = {Udell94 ! componentware} 24093} 24094 24095@Misc{ cca-web-page, 24096 author = {{Common Component Architecture Forum}}, 24097 note = {See \url{http://cca-forum.org}} 24098} 24099 24100% --------------- References for Tools Used by TAO Developers ----------------- 24101 24102% 24103% tohtml: Used to generate on-line TAO users manual and manual pages 24104% 24105@TechReport{ tohtml, 24106 author = {William Gropp}, 24107 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 24108 institution = {Argonne National Laboratory}, 24109 number = {ANL/MCS-TM-00}, 24110 month = jan, 24111 year = {1995}, 24112 key = {tohtml} 24113} 24114 24115% 24116% doctext: Used to generate tex version of TAO manual pages 24117% 24118@TechReport{ doctext, 24119 author = {William Gropp}, 24120 title = {Users Manual for doctext: Producing documentation from {C} source code}, 24121 institution = {Argonne National Laboratory}, 24122 number = {ANL/MCS-TM-00}, 24123 month = jan, 24124 year = {1995}, 24125 key = {doctext} 24126} 24127 24128% 24129% bfort: Used to generate TAO Fortran interface 24130% 24131@TechReport{ bfort, 24132 author = {William Gropp}, 24133 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 24134 institution = {Argonne National Laboratory}, 24135 number = {ANL/MCS-TM-208}, 24136 month = mar, 24137 year = {1995}, 24138 key = {doctext} 24139} 24140 24141% ------------------------- PETSc References ------------------------------ 24142@InProceedings{ petsc, 24143 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 24144 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 24145 Libraries}, 24146 booktitle = {Modern Software Tools in Scientific Computing}, 24147 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 24148 publisher = {Birkhauser Press}, 24149 pages = {163--202}, 24150 year = {1997} 24151} 24152 24153% ------------------------- Misc Other References ------------------------------ 24154@Misc{ indeps-web-page, 24155 title = {{InDEPS} {W}eb page}, 24156 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 24157 author = {et al. Robert Armstrong}, 24158 institution = {Sandia National Laboratory}, 24159 key = {{InDEPS} {W}eb page} 24160} 24161 24162@Misc{ pooma, 24163 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 24164 chitectures}, 24165 year = {1996}, 24166 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 24167 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 24168} 24169 24170@Misc{ isis++-web-page, 24171 title = {{ISIS++} {W}eb Page}, 24172 note = {See \url{http://ca.sandia.gov/isis}}, 24173 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 24174 institution = {Sandia National Laboratories} 24175} 24176 24177@Misc{ trilinos-web-page, 24178 title = {{Trilinos} {W}eb Page}, 24179 note = {See 24180 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 24181 author = {Mike Heroux et al.}, 24182 institution = {Sandia National Laboratories} 24183} 24184 24185@Misc{ alice-web-page, 24186 title = {{ALICE} {W}eb page}, 24187 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 24188 Argonne National Laboratory}, 24189 key = {{ALICE} {W}eb page} 24190} 24191 24192@Misc{ autodiff-webpage, 24193 author = {{Computational Differentiation Project}}, 24194 note = {See \url{http://www.mcs.anl.gov/autodiff}} 24195} 24196 24197@Misc{ coool-home-page, 24198 author = {Lydia Deng and Wences Gouveia and John Scales}, 24199 title = {{The CWP Object-Oriented Optimization Library}}, 24200 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 24201} 24202 24203@Misc{ rice-inversion-home-page, 24204 author = {Mark S. Gokenbach and William W. Symes}, 24205 title = {{The Hilbert Class Library}}, 24206 note = {See \url{http://www.trip.caam.rice.edu/}} 24207} 24208 24209@Misc{ opt++-home-page, 24210 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 24211 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 24212} 24213 24214@Article{ gockenbach:1999:ccl, 24215 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 24216 title = {C++ Classes for Linking Optimization with Complex Simulations}, 24217 journal = {{ACM} Transactions on Mathematical Software}, 24218 volume = {25}, 24219 number = {2}, 24220 month = jun, 24221 year = {1999}, 24222 pages = {191-212}, 24223 abstract = {The object-oriented programming paradigm can be used to overcome the 24224 incompatibilities between off-the-shelf optimization software and application 24225 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 24226 objects arising in optimization problems, such as vectors, linear operators, and 24227 so forth, as C++ classes, making it possible to write optimization code in a 24228 natural fashion, while allowing application software such as simulators to use the 24229 most convenient data structures and programming style. In spite of the poor 24230 reputation C++ has for runtime performance, the use of mixed-language programming 24231 allows performance equal to that achieved by standard Fortran packages, as 24232 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 24233 accepted = {April 1999}, 24234 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 24235} 24236 24237@Misc{ neos-guide, 24238 author = {{The Optimization Software Guide}}, 24239 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 24240} 24241 24242@Article{ boyd, 24243 title = {Distributed optimization and statistical learning via the alternating direction 24244 method of multipliers}, 24245 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 24246 Jonathan and others}, 24247 journal = {Foundations and Trends{\textregistered} in Machine learning}, 24248 volume = {3}, 24249 number = {1}, 24250 pages = {1-122}, 24251 year = {2011}, 24252 publisher = {Now Publishers, Inc.} 24253} 24254 24255@Misc{ :alertsys, 24256 title = {page{ALERT}}, 24257 organization = {Alert Systems, Inc}, 24258 address = {Madison, Wisconsin}, 24259 note = {http://www.alertsys.com/} 24260} 24261 24262@Manual{ :cmfortran, 24263 title = {{CM} {F}ortran Language Reference Manual}, 24264 organization = {Thinking Machines Corporation}, 24265 year = {1994}, 24266 address = {Cambridge, MA} 24267} 24268 24269@Manual{ :cmmd, 24270 title = {{CMMD} Reference Manual, Version 3.0}, 24271 organization = {Thinking Machines Corporation}, 24272 year = {1993}, 24273 address = {Cambridge, MA} 24274} 24275 24276@Manual{ :cmssl, 24277 title = {{CMSSL} for {CM} {F}ortran}, 24278 volume = {I}, 24279 organization = {Thinking Machines Corporation}, 24280 year = {1994}, 24281 address = {Cambridge, MA} 24282} 24283 24284@Misc{ :condor, 24285 author = {M. Livny}, 24286 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24287 howpublished = {www.cs.wisc.edu/condor} 24288} 24289 24290@Manual{ :connection, 24291 title = {Connection Machine {CM}--5 Technical Summary}, 24292 organization = {Thinking Machines Corporation}, 24293 year = {1993}, 24294 address = {Cambridge, MA} 24295} 24296 24297@Manual{ :cplex, 24298 title = {{CPLEX} Optimizer}, 24299 organization = {ILOG CPLEX Division}, 24300 address = {889 Alder Avenue, Incline Village, Nevada}, 24301 note = {http://www.cplex.com/} 24302} 24303 24304@Manual{ :cplextm, 24305 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24306 (Version 2.0)}, 24307 organization = {CPLEX Optimization Inc.}, 24308 year = {1992}, 24309 address = {Incline Village, Nevada} 24310} 24311 24312@Misc{ :fatcop, 24313 author = {M. C. Ferris}, 24314 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24315 Solver}, 24316 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24317} 24318 24319@Misc{ :metaneos, 24320 author = {S. J. Wright}, 24321 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24322 howpublished = {www-unix.mcs.anl.gov/metaneos} 24323} 24324 24325@InCollection{ gropp.more:optimization, 24326 author = {W. Gropp and J. J. Mor\'e}, 24327 title = {Optimization environments and the {NEOS} Server}, 24328 booktitle = {Approximation Theory and Optimization}, 24329 pages = {167--182}, 24330 publisher = {Cambridge University Press}, 24331 year = {1997}, 24332 editor = {M. D. Buhmann and A. Iserles} 24333} 24334 24335@Article{ czyzyk.mesnier.ea:neos, 24336 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24337 title = {The {NEOS} Server}, 24338 journal = {IEEE Journal on Computational Science and Engineering}, 24339 volume = {5}, 24340 year = {1998}, 24341 pages = {68--75} 24342} 24343 24344@Book{ :osl, 24345 title = {Handbook for {IBM OSL}}, 24346 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24347 year = {1994}, 24348 publisher = {Boyd and Fraser}, 24349 address = {Danvers, Massachusetts} 24350} 24351 24352@Manual{ :pro-matlab, 24353 title = {{PRO}--{MATLAB} User's Guide}, 24354 organization = {The MathWorks, Inc.}, 24355 year = {1989}, 24356 address = {21 Eliot Street, South Natick, MA 01760} 24357} 24358 24359@Misc{ :prostate, 24360 key = {Biomedical}, 24361 title = {Biomedical Business International Newsletter}, 24362 howpublished = {pp. 72--75}, 24363 year = {1996} 24364} 24365 24366@Misc{ :sipcase, 24367 key = {Natural}, 24368 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24369 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24370} 24371 24372@Book{ aarts.korst:simulated, 24373 author = {E. Aarts and J. Korst}, 24374 title = {Simulated Annealing and Boltzman Machines}, 24375 year = {1990}, 24376 publisher = {John Wiley \& Sons}, 24377 address = {Chichester} 24378} 24379 24380@TechReport{ aarts.laarhoven.ea:local-search-based, 24381 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 24382 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 24383 institution = {Centre for Quantitative Methods}, 24384 year = {1991}, 24385 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 24386 number = {106}, 24387 type = {CQM-Not} 24388} 24389 24390@Article{ aashtiani.magnanti:equilibria, 24391 author = {H. Z. Aashtiani and T. L. Magnanti}, 24392 title = {Equilibria on a congested transportation network}, 24393 journal = {SIAM Journal on Algebraic and Discrete Methods}, 24394 volume = {2}, 24395 year = {1981}, 24396 pages = {213--226} 24397} 24398 24399@Article{ ablow.brigham:analog, 24400 author = {C. M. Ablow and G. Brigham}, 24401 title = {An Analog Solution of Programming Problems}, 24402 journal = {Operations Research}, 24403 year = {1955}, 24404 volume = {3}, 24405 pages = {388--394} 24406} 24407 24408@Article{ achuthan.grabowski.ea:optimal, 24409 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 24410 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 24411 journal = {Opsearch}, 24412 year = {1981}, 24413 volume = {18}, 24414 pages = {117--138} 24415} 24416 24417@Book{ adelman.robinson:income, 24418 author = {I. Adelman and S. Robinson}, 24419 title = {Income Distribution Policy in Developing Countries}, 24420 publisher = {Stanford University Press}, 24421 year = {1978}, 24422 address = {Stanford, California} 24423} 24424 24425@Article{ adler.resende.ea:implementation, 24426 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 24427 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 24428 journal = {Mathematical Programming}, 24429 year = {1989}, 24430 volume = {44}, 24431 pages = {297--336} 24432} 24433 24434@TechReport{ aeberhard.coomans.ea:comparison, 24435 author = {S. Aeberhard and D. Coomans and O. de Vel}, 24436 title = {Comparison of Classifiers in High Dimensional Settings}, 24437 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 24438 University of North Queensland}, 24439 year = {1992}, 24440 number = {92-02}, 24441 type = {Technical Report} 24442} 24443 24444@Article{ aganagic.cottle:constructive, 24445 author = {M. Aganagi\'{c} and R. W. Cottle}, 24446 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 24447 Minors}, 24448 journal = {Mathematical Programming}, 24449 year = {1987}, 24450 volume = {37}, 24451 pages = {223--231} 24452} 24453 24454@TechReport{ aganagic:iterative, 24455 author = {M. Aganagi\'{c}}, 24456 title = {Iterative Methods for the Linear Complementarity Problem}, 24457 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 24458 University}, 24459 year = {1978}, 24460 type = {SOL}, 24461 number = {78-10}, 24462 address = {Stanford, California} 24463} 24464 24465@Book{ ahlfors:complex, 24466 author = {L. V. Ahlfors}, 24467 title = {Complex Analysis}, 24468 publisher = {McGraw--Hill Book Company}, 24469 address = {New York}, 24470 series = {International Series in Pure and Applied Mathematics}, 24471 edition = {Second}, 24472 year = {1966} 24473} 24474 24475@Article{ ahn:solution, 24476 author = {B--H. Ahn}, 24477 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 24478 journal = {Journal of Optimization Theory and Applications}, 24479 year = {1981}, 24480 volume = {33}, 24481 pages = {175--185} 24482} 24483 24484@Article{ al-fahed.stavroulakis.ea:hard, 24485 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24486 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 24487 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 24488 volume = {71}, 24489 year = {1991}, 24490 pages = {257--265} 24491} 24492 24493@Article{ al-fahed.stavroulakis.ea:linear, 24494 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24495 title = {A linear complementarity approach to the frictionless gripper}, 24496 journal = {International Journal of Robotic Research}, 24497 volume = {11}, 24498 year = {1992}, 24499 pages = {112--122} 24500} 24501 24502@Article{ al-khayyal.falk:jointly, 24503 author = {F. A. Al--Khayyal and J. E. Falk}, 24504 title = {Jointly Constrained Biconvex Programming}, 24505 journal = {Mathematics of Operations Research}, 24506 year = {1983}, 24507 volume = {8}, 24508 pages = {273--286} 24509} 24510 24511@Article{ al-khayyal.kyparisis:finite, 24512 author = {F. A. Al--Khayyal and J. Kyparisis}, 24513 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 24514 Inequalities}, 24515 journal = {Journal of Optimization Theory and Applications}, 24516 year = {1991}, 24517 volume = {70}, 24518 pages = {319--332} 24519} 24520 24521@PhDThesis{ al-khayyal:biconvex, 24522 author = {F. A. Al--Khayyal}, 24523 title = {Biconvex Programming and Biconcave Minimization}, 24524 year = {1977}, 24525 school = {The George Washington University} 24526} 24527 24528@Article{ alart.curnier:mixed, 24529 author = {P. Alart and A. Curnier}, 24530 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 24531 solution methods}, 24532 journal = {Computer Methods in Applied Mechanics and Engineering}, 24533 volume = {92}, 24534 year = {1991}, 24535 pages = {353--375} 24536} 24537 24538@Misc{ alexander.kellog.ea:piecewise, 24539 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 24540 title = {Piecewise smooth continuation}, 24541 howpublished = {Manuscript}, 24542 year = {1979} 24543} 24544 24545@InCollection{ alexander.li.ea:piecewise, 24546 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 24547 title = {Piecewise smooth homotopies}, 24548 booktitle = {Homotopy Methods and Global Convergence}, 24549 pages = {1--14}, 24550 publisher = {Plenum Press}, 24551 year = {1983}, 24552 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 24553 address = {New York} 24554} 24555 24556@InCollection{ alexander:topological, 24557 author = {J.~C. Alexander}, 24558 title = {The topological theory of an embedding method}, 24559 booktitle = {Continuation Methods}, 24560 pages = {37--68}, 24561 publisher = {Academic Press}, 24562 year = {1978}, 24563 editor = {H. Wacker}, 24564 address = {New York} 24565} 24566 24567@Book{ allen:probability, 24568 author = {A. O. Allen}, 24569 title = {Probability, Statistics and Queueing Theory}, 24570 publisher = {Academic Press}, 24571 year = {1990}, 24572 address = {London}, 24573 edition = {Second} 24574} 24575 24576@Book{ allgower.georg:numerical, 24577 author = {E. L. Allgower and K. Georg}, 24578 title = {Numerical Continuation Methods, An Introduction}, 24579 publisher = {Springer-Verlag}, 24580 year = {1990}, 24581 address = {Berlin} 24582} 24583 24584@InProceedings{ allgower.georg:predictor-corrector, 24585 crossref = {bachem.grotschel.ea:mathematical}, 24586 author = {E. L. Allgower and K. Georg}, 24587 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 24588 Zero Points of Nonlinear Mappings}, 24589 pages = {15--56} 24590} 24591 24592@Article{ aluffi-pentini.parisi.ea:algorithm, 24593 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 24594 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 24595 Algorithm}, 24596 journal = {ACM Transactions on Mathematical Software}, 24597 year = {1988}, 24598 volume = {14}, 24599 pages = {366--380} 24600} 24601 24602@Article{ anandalingam.friesz:hierarchical, 24603 author = {G. Anandalingam and T. L. Friesz}, 24604 title = {Hierarchical Optimization: An Introduction}, 24605 journal = {Annals of Operations Research}, 24606 year = {1992}, 24607 volume = {34}, 24608 pages = {1--11} 24609} 24610 24611@Article{ anandalingam.white:solution, 24612 author = {G. Anandalingam and D. J. White}, 24613 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 24614 Functions}, 24615 journal = {IEEE Transactions on Automatic Control}, 24616 year = {1990}, 24617 volume = {35}, 24618 number = {10}, 24619 pages = {1170--1173} 24620} 24621 24622@Article{ andersen.andersen:presolving, 24623 author = {E. Andersen and K. Andersen}, 24624 title = {Presolving in Linear Programming}, 24625 year = {1995}, 24626 journal = {Mathematical Programming}, 24627 volume = {71}, 24628 pages = {221--245} 24629} 24630 24631@InProceedings{ andersen.ye:homogeneous, 24632 author = {E. Andersen and Y. Ye}, 24633 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 24634 Equality Constraints}, 24635 crossref = {ferris.pang:complementarity}, 24636 pages = {1--11} 24637} 24638 24639@Book{ anderson.bai.ea:lapack, 24640 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 24641 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 24642 Sorensen}, 24643 title = {{LAPACK} User's Guide}, 24644 publisher = {SIAM}, 24645 year = {1995}, 24646 address = {Philadelphia, Pennsylvania}, 24647 edition = {Second} 24648} 24649 24650@Article{ anderson.ferris:direct, 24651 author = {E. J. Anderson and M. C. Ferris}, 24652 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 24653 year = {2001}, 24654 journal = {SIAM Journal on Optimization, forthcoming}, 24655 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 24656 key = {55} 24657} 24658 24659@InProceedings{ anderson.ferris:genetic, 24660 author = {E. J. Anderson and M. C. Ferris}, 24661 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 24662 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 24663 Waterloo, Ontario, Canada, May 28--30}, 24664 publisher = {University of Waterloo Press}, 24665 key = {14}, 24666 year = {1990} 24667} 24668 24669@Article{ anderson.ferris:genetic*1, 24670 author = {E. J. Anderson and M. C. Ferris}, 24671 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 24672 Problem}, 24673 journal = {ORSA Journal on Computing}, 24674 year = {1994}, 24675 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 24676 volume = {6}, 24677 pages = {161--173}, 24678 key = {22} 24679} 24680 24681@InProceedings{ anderson.ferris:parallel, 24682 author = {E. J. Anderson and M. C. Ferris}, 24683 title = {Parallel Genetic Algorithms in Optimization}, 24684 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 24685 Computing, Chicago, Illinois, December 11-13}, 24686 year = {1989}, 24687 key = {12} 24688} 24689 24690@Unpublished{ anderson.lewis:primal, 24691 author = {E. J. Anderson and A. S. Lewis}, 24692 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24693 note = {In preparation} 24694} 24695 24696@Book{ anderson.nash:linear, 24697 author = {E. J. Anderson and P. Nash}, 24698 title = {Linear Programming in Infinite--Dimensional Spaces}, 24699 year = {1987}, 24700 publisher = {John Wiley \& Sons}, 24701 address = {Chichester} 24702} 24703 24704@InProceedings{ anderson:primal, 24705 author = {E. J. Anderson}, 24706 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24707 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 24708 Programming, Cambridge, September 1984}, 24709 year = {1985}, 24710 editor = {E. J. Anderson and A. B. Philpott}, 24711 publisher = {Springer-Verlag}, 24712 address = {Berlin} 24713} 24714 24715@Article{ andradottir:method, 24716 author = {S. Andrad\'{o}ttir}, 24717 title = {A Method of Discrete Stochastic Optimization}, 24718 journal = {Management Science}, 24719 year = {1995}, 24720 volume = {41}, 24721 pages = {1946--1961} 24722} 24723 24724@Article{ andradottir:global, 24725 author = {S. Andrad\'{o}ttir}, 24726 title = {A Global Search Method for Discrete Stochastic Optimization}, 24727 journal = {SIAM Journal on Optimization}, 24728 year = {1996}, 24729 volume = {6}, 24730 pages = {513--530} 24731} 24732 24733@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 24734 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 24735 title = {An infeasible--interior--point predictor--corrector algorithm for the 24736 {P}$_x$--geometric {LCP}}, 24737 institution = {Department of Mathematics, The University of Iowa}, 24738 address = {Iowa City, Iowa}, 24739 year = {1994}, 24740 number = {62}, 24741 type = {Reports on Computational Mathematics} 24742} 24743 24744@TechReport{ anitescu.potra:formulating, 24745 author = {M. Anitescu and F. A. Potra}, 24746 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 24747 Linear Complementarity Problems}, 24748 institution = {Department of Mathematics, The University of Iowa}, 24749 year = {1996}, 24750 type = {Report}, 24751 number = {93}, 24752 address = {Iowa City, Iowa} 24753} 24754 24755@Article{ anstreicher.lee.ea:crashing, 24756 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 24757 title = {Crashing a Maximum-Weight Complementarity Basis}, 24758 journal = {Mathematical Programming}, 24759 year = {1992}, 24760 volume = {54}, 24761 pages = {281--294} 24762} 24763 24764@Article{ anstreicher:combined, 24765 author = {K. M. Anstreicher}, 24766 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 24767 programming}, 24768 journal = {Mathematical Programming}, 24769 year = {1991}, 24770 volume = {52}, 24771 pages = {429--440} 24772} 24773 24774@Article{ anstreicher:combined*1, 24775 author = {K. M. Anstreicher}, 24776 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 24777 journal = {Mathematical Programming}, 24778 year = {1989}, 24779 volume = {43}, 24780 pages = {209--223} 24781} 24782 24783@InCollection{ arbenz.gander.ea:remote, 24784 author = {P. Arbenz and W. Gander and M. Oettli}, 24785 title = {The Remote Computational System}, 24786 booktitle = {High-Performance Computation and Networks}, 24787 publisher = {Springer-Verlag}, 24788 year = {1996}, 24789 volume = {1067}, 24790 series = {Lecture Notes in Computer Science}, 24791 pages = {662--667} 24792} 24793 24794@InCollection{ arcus:comsoal, 24795 author = {A. L. Arcus}, 24796 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 24797 booktitle = {Readings in Production and Operations Management}, 24798 year = {1966}, 24799 editor = {E. S. Buffa}, 24800 publisher = {John Wiley \& Sons}, 24801 address = {New York} 24802} 24803 24804@TechReport{ arioli.chan.ea:computing, 24805 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 24806 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 24807 Optimization Calculations}, 24808 institution = {CERFACS}, 24809 year = {1993}, 24810 number = {TR/PA/93/34} 24811} 24812 24813@Article{ armijo:minimization, 24814 author = {L. Armijo}, 24815 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 24816 Derivatives}, 24817 journal = {Pacific Journal of Mathematics}, 24818 year = {1966}, 24819 volume = {16}, 24820 pages = {1--3} 24821} 24822 24823@Article{ arrow.debreu:existence, 24824 author = {K. Arrow and G. Debreu}, 24825 title = {Existence of Equilibrium for a Competitive Economy}, 24826 journal = {Econometrica}, 24827 year = {1954}, 24828 volume = {22}, 24829 pages = {265--290} 24830} 24831 24832@InCollection{ arrow.solow:gradient, 24833 author = {K. J. Arrow and R. M. Solow}, 24834 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 24835 booktitle = {Studies in Linear and Nonlinear Programming}, 24836 year = {1958}, 24837 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 24838 publisher = {Stanford University Press}, 24839 address = {Stanford, California}, 24840 pages = {166--176} 24841} 24842 24843@Book{ aubin.ekeland:nonlinear, 24844 author = {J.-P. Aubin and I. Ekeland}, 24845 title = {Applied nonlinear analysis}, 24846 publisher = {John Wiley \& Sons}, 24847 address = {New York}, 24848 year = {1984} 24849} 24850 24851@Article{ auchmuty:variational, 24852 author = {G. Auchmuty}, 24853 title = {Variational Principles for Variational Inequalities}, 24854 journal = {Numerical Functional Analysis and Optimization}, 24855 year = {1989}, 24856 volume = {10}, 24857 pages = {863--874} 24858} 24859 24860@Book{ auerbach.kotlikoff:dynamic, 24861 author = {A. J. Auerbach and L. J. Kotlikoff}, 24862 title = {Dynamic Fiscal Policy}, 24863 publisher = {Cambridge University Press}, 24864 address = {Cambridge, England}, 24865 year = {1987} 24866} 24867 24868@InProceedings{ ault.deutsch.ea:interpolating, 24869 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 24870 title = {Interpolating Subspaces in Approximation Theory}, 24871 booktitle = {Approximation Theory}, 24872 year = {1970}, 24873 editor = {A. Talbot}, 24874 publisher = {Academic Press}, 24875 address = {London} 24876} 24877 24878@Article{ auslender.crouzeix:global, 24879 author = {A. A. Auslender and J.--P. Crouzeix}, 24880 title = {Global Regularity Theorems}, 24881 journal = {Mathematics of Operations Research}, 24882 year = {1988}, 24883 volume = {13}, 24884 pages = {243--253} 24885} 24886 24887@Article{ auslender.haddou:interior-proximal, 24888 author = {A. Auslender and M. Haddou}, 24889 title = {An interior-proximal method for convex linearly constrained problems and its 24890 extension to variational inequalities}, 24891 year = {1995}, 24892 journal = {Mathematical Programming}, 24893 pages = {77--100}, 24894 volume = {71} 24895} 24896 24897@Article{ auslender:convergence, 24898 author = {A. Auslender}, 24899 title = {Convergence of stationary sequences for variational inequalities with maximal 24900 monotone operators}, 24901 journal = {Applied Mathematics and Optimization}, 24902 volume = {28}, 24903 year = {1993}, 24904 pages = {161--172} 24905} 24906 24907@Book{ auslender:optimization, 24908 author = {A. Auslender}, 24909 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 24910 year = {1976}, 24911 publisher = {Masson}, 24912 address = {Paris} 24913} 24914 24915@TechReport{ averick.carter.ea:minpack-2, 24916 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 24917 title = {The {MINPACK-2} Test Problem Collection}, 24918 institution = {Argonne National Laboratory}, 24919 year = {1992}, 24920 address = {Argonne, Illinois}, 24921 number = {MCS-P153-0692} 24922} 24923 24924@TechReport{ axline.billups.ea:guidelines, 24925 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 24926 title = {Guidelines for Software Security ({U})}, 24927 institution = {SNL}, 24928 year = {1989}, 24929 month = oct, 24930 address = {Albuquerque, New Mexico}, 24931 number = {SAND88-2955} 24932} 24933 24934@Article{ ayres.walter:greenhouse, 24935 author = {R. U. Ayres and J. Walter}, 24936 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 24937 journal = {Environmental and Resource Economics}, 24938 year = {1991}, 24939 volume = {1}, 24940 pages = {237--270} 24941} 24942 24943@PhDThesis{ bagley:behaviour, 24944 author = {J. D. Bagley}, 24945 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 24946 Algorithms}, 24947 year = {1967}, 24948 school = {University of Michigan} 24949} 24950 24951@Article{ bain.stewart:application, 24952 author = {R. S. Bain and W. E. Stewart}, 24953 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 24954 Algebraic Equation Systems}, 24955 journal = {Computers in Chemical Engineering}, 24956 year = {1991}, 24957 volume = {15}, 24958 pages = {203--208} 24959} 24960 24961@Article{ baker.lasdon:successive, 24962 author = {T. E. Baker and L. S. 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Bertsekas}, 25406 title = {Nonlinear Programming}, 25407 publisher = {Athena Scientific}, 25408 year = {1995}, 25409 address = {Belmont, Massachusetts} 25410} 25411 25412@Article{ bertsekas:projected, 25413 author = {Dimitri P. Bertsekas}, 25414 title = {Projected {N}ewton Methods for Optimization Problems with Simple Constraints}, 25415 journal = {SIAM Journal on Control and Optimization}, 25416 year = {1982}, 25417 volume = {20}, 25418 pages = {221--246} 25419} 25420 25421@Article{ billups.dirkse.ea:comparison, 25422 author = {S. C. Billups and S. P. Dirkse and M. C. Ferris}, 25423 title = {A Comparison of Large Scale Mixed Complementarity Problem Solvers}, 25424 journal = {Computational Optimization and Applications}, 25425 year = {1997}, 25426 pages = {3--25}, 25427 volume = {7}, 25428 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps}, 25429 key = {51} 25430} 25431 25432@Article{ billups.ferris:convergence, 25433 author = {S. C. Billups and M. C. Ferris}, 25434 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 25435 Starting Points}, 25436 journal = {SIAM Journal on Optimization}, 25437 year = {1996}, 25438 volume = {6}, 25439 pages = {316--325}, 25440 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 25441 key = {34} 25442} 25443 25444@TechReport{ billups.ferris:convergence*1, 25445 author = {S. C. Billups and M. C. Ferris}, 25446 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 25447 Points}, 25448 institution = {Computer Sciences Department, University of Wisconsin}, 25449 year = {1993}, 25450 address = {Madison, Wisconsin}, 25451 number = {1180}, 25452 note = {Revised version in SIAM Journal on Optimization.} 25453} 25454 25455@Article{ billups.ferris:qpcomp, 25456 author = {S. C. Billups and M. C. Ferris}, 25457 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 25458 year = {1997}, 25459 journal = {Mathematical Programming}, 25460 pages = {533--562}, 25461 volume = {76}, 25462 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 25463 key = {47} 25464} 25465 25466@Article{ billups.ferris:solutions, 25467 author = {S. C. Billups and M. C. Ferris}, 25468 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 25469 journal = {Mathematics of Operations Research}, 25470 volume = {24}, 25471 pages = {219--236}, 25472 year = {1999}, 25473 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 25474 key = {42}, 25475 institution = {Computer Sciences Department, University of Wisconsin}, 25476 address = {Madison, Wisconsin}, 25477 type = {Mathematical Programming Technical Report}, 25478 number = {94--15} 25479} 25480 25481@TechReport{ billups.murata.ea:users, 25482 author = {S. C. Billups and K. K. 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Billups}, 25503 title = {Algorithms for Complementarity Problems and Generalized Equations}, 25504 school = {University of Wisconsin--Madison}, 25505 year = {1995}, 25506 address = {Madison, Wisconsin}, 25507 month = aug 25508} 25509 25510@MastersThesis{ billups:augmented, 25511 author = {S. C. Billups}, 25512 title = {An Augmented Jacobian Matrix Algorithm for Tracking Homotopy Zero Curves}, 25513 school = {Virginia Tech}, 25514 year = {1985}, 25515 address = {Blacksburg, Virginia} 25516} 25517 25518@TechReport{ billups:homotopy, 25519 author = {S. C. Billups}, 25520 title = {A Homotopy Based Algorithm for Mixed Complementarity Problems}, 25521 institution = {Department of Mathematics, University of Colorado}, 25522 year = {1998}, 25523 address = {Denver, Colorado} 25524} 25525 25526@Article{ billups:improving, 25527 author = {S. C. 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Model analysis and 26571 optimality conditions}, 26572 type = {Publication}, 26573 number = {CRT-94-56}, 26574 institution = {Centre de Recherche sur les Transports, Universit\'e de Montr\'eal}, 26575 address = {Montr\'eal, Canada}, 26576 year = {1994} 26577} 26578 26579@Article{ chen.harker:continuation, 26580 author = {B. Chen and P. T. Harker}, 26581 title = {A Continuation Method for Monotone Variational Inequalities}, 26582 journal = {Mathematical Programming}, 26583 volume = {69}, 26584 pages = {237--253}, 26585 year = {1995} 26586} 26587 26588@Article{ chen.harker:non-interior, 26589 author = {B. Chen and P. T. Harker}, 26590 title = {A Non-Interior-Point Continuation Method for Linear Complementarity Problems}, 26591 journal = {SIAM Journal on Matrix Analysis and Applications}, 26592 year = {1993}, 26593 volume = {14}, 26594 pages = {1168--1190} 26595} 26596 26597@Article{ chen.harker:smooth, 26598 author = {B. Chen and P. T. 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Mangasarian}, 28497 title = {Breast Cancer Diagnosis via Linear Programming}, 28498 key = {50}, 28499 journal = {{IEEE} Computational Science and Engineering}, 28500 year = {1995}, 28501 volume = {2}, 28502 pages = {70--71} 28503} 28504 28505@Article{ ferris.mangasarian:error, 28506 author = {M. C. Ferris and O. L. Mangasarian}, 28507 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 28508 Inequalities}, 28509 journal = {Annals of Operations Research}, 28510 year = {1993}, 28511 volume = {47}, 28512 pages = {293--305}, 28513 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 28514 key = {24} 28515} 28516 28517@Article{ ferris.mangasarian:finite, 28518 author = {M. C. Ferris and O. L. Mangasarian}, 28519 title = {Finite Perturbation of Convex Programs}, 28520 journal = {Applied Mathematics and Optimization}, 28521 year = {1991}, 28522 volume = {23}, 28523 pages = {263--273}, 28524 key = {08} 28525} 28526 28527@Book{ ferris.mangasarian:linear, 28528 author = {M. C. Ferris and O. L. Mangasarian}, 28529 title = {Linear Programming via {MATLAB}}, 28530 publisher = {in preparation}, 28531 year = {1995}, 28532 address = {Madison, Wisconsin} 28533} 28534 28535@Article{ ferris.mangasarian:minimum, 28536 author = {M. C. Ferris and O. L. Mangasarian}, 28537 title = {Minimum Principle Sufficiency}, 28538 journal = {Mathematical Programming}, 28539 year = {1992}, 28540 volume = {57}, 28541 pages = {1--14}, 28542 key = {11} 28543} 28544 28545@Article{ ferris.mangasarian:parallel, 28546 author = {M. C. Ferris and O. L. Mangasarian}, 28547 title = {Parallel Constraint Distribution}, 28548 journal = {SIAM Journal on Optimization}, 28549 year = {1991}, 28550 volume = {1}, 28551 pages = {487--500}, 28552 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28553 key = {18} 28554} 28555 28556@Article{ ferris.mangasarian:parallel*1, 28557 author = {M. C. Ferris and O. L. Mangasarian}, 28558 title = {Parallel Variable Distribution}, 28559 journal = {SIAM Journal on Optimization}, 28560 year = {1994}, 28561 volume = {4}, 28562 pages = {815--832}, 28563 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28564 key = {31} 28565} 28566 28567@Article{ ferris.meeraus.ea:computing, 28568 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28569 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28570 journal = {Optimization Methods and Software}, 28571 year = {1999}, 28572 volume = {10}, 28573 pages = {669--685}, 28574 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28575 key = {45} 28576} 28577 28578@Article{ ferris.mesnier.ea:neos, 28579 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28580 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28581 {I}nternet}, 28582 year = {2000}, 28583 journal = {{ACM} Transactions on Mathematical Software}, 28584 key = {54}, 28585 volume = {26}, 28586 pages = {1--18}, 28587 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28588 institution = {Computer Sciences Department, University of Wisconsin}, 28589 address = {Madison, Wisconsin}, 28590 number = {96-08}, 28591 type = {Mathematical Programming Technical Report}, 28592 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28593 Argonne National Laboratory}, 28594 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28595 1996} 28596} 28597 28598@InCollection{ ferris.meyer:models, 28599 author = {M. C. Ferris and R. R. Meyer}, 28600 title = {Models and Solution for On-Demand Data Delivery Problems}, 28601 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28602 key = {80}, 28603 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28604 Problems}, 28605 editor = {P. M. Pardalos}, 28606 series = {Nonconvex Optimization and its Applications}, 28607 volume = {42}, 28608 address = {Dordrect}, 28609 year = {2000}, 28610 pages = {175--188}, 28611 publisher = {Kluwer}, 28612 type = {Mathematical Programming Technical Report}, 28613 institution = {Computer Sciences Department, University of Wisconsin}, 28614 number = {99-04} 28615} 28616 28617@InProceedings{ ferris.munson.ea:homotopy, 28618 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28619 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28620 booktitle = {Numerical Analysis 1999}, 28621 key = {88}, 28622 year = {2000}, 28623 editor = {D. F. Griffiths and G. A. Watson}, 28624 series = {Research Notes in Mathematics}, 28625 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28626 address = {London}, 28627 pages = {143--167}, 28628 publisher = {Chapman and Hall}, 28629 institution = {Computer Sciences Department, University of Wisconsin}, 28630 number = {99-09}, 28631 type = {Mathematical Programming Technical Report} 28632} 28633 28634@TechReport{ ferris.munson.ea:practical, 28635 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28636 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28637 type = {Data Mining Institute Technical Report}, 28638 institution = {Computer Sciences Department, University of Wisconsin}, 28639 address = {Madison, Wisconsin}, 28640 year = {2000}, 28641 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28642 number = {00-03}, 28643 key = {92}, 28644 annote = {To appear in WSC 2000} 28645} 28646 28647@InCollection{ ferris.munson:case, 28648 author = {M. C. Ferris and T. S. Munson}, 28649 title = {Case Studies in Complementarity: Improving Model Formulation}, 28650 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28651 key = {73}, 28652 pages = {79--98}, 28653 publisher = {Springer Verlag}, 28654 year = {1999}, 28655 editor = {M. Th\'{e}ra and R. Tichatschke}, 28656 number = {477}, 28657 series = {Lecture Notes in Economics and Mathematical Systems}, 28658 address = {Berlin}, 28659 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28660 type = {Mathematical Programming Technical Report}, 28661 institution = {Computer Sciences Department, University of Wisconsin} 28662} 28663 28664@Article{ ferris.munson:complementarity, 28665 author = {M. C. Ferris and T. S. Munson}, 28666 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28667 year = {2000}, 28668 volume = {24}, 28669 pages = {165--188}, 28670 journal = {Journal of Economic Dynamics and Control}, 28671 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28672 key = {70}, 28673 type = {Mathematical Programming Technical Report}, 28674 institution = {Computer Sciences Department, University of Wisconsin}, 28675 address = {Madison, Wisconsin}, 28676 number = {98-12} 28677} 28678 28679@Misc{ ferris.munson:condor, 28680 author = {M. C. Ferris and T. S. Munson}, 28681 title = {Condor Modeling Language Interface}, 28682 organization = {Computer Sciences Department, University of Wisconsin}, 28683 address = {Madison, Wisconsin}, 28684 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28685} 28686 28687@Manual{ ferris.munson:gams, 28688 author = {M. C. Ferris and T. S. Munson}, 28689 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28690 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28691} 28692 28693@Article{ ferris.munson:interfaces, 28694 author = {M. C. Ferris and T. S. Munson}, 28695 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28696 journal = {Computational Optimization and Applications}, 28697 volume = {12}, 28698 pages = {207--227}, 28699 year = {1999}, 28700 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28701 key = {63}, 28702 institution = {Computer Sciences Department, University of Wisconsin}, 28703 address = {Madison, Wisconsin}, 28704 number = {97-12}, 28705 type = {Mathematical Programming Technical Report} 28706} 28707 28708@TechReport{ ferris.munson:interior, 28709 author = {M. C. Ferris and T. S. Munson}, 28710 title = {Interior Point Methods for Massive Support Vector Machines}, 28711 institution = {Computer Sciences Department, University of Wisconsin}, 28712 year = {2000}, 28713 key = {94}, 28714 type = {Data Mining Institute Technical Report}, 28715 number = {00-05}, 28716 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28717 address = {Madison, Wisconsin}, 28718 annote = {Submitted to SIOPT} 28719} 28720 28721@Article{ ferris.munson:linear, 28722 author = {M. C. Ferris and T. S. Munson}, 28723 title = {Linear Programming for Emergency Broadcast Systems}, 28724 year = {1999}, 28725 journal = {{SIAG/OPT} Newsletter}, 28726 volume = {10}, 28727 pages = {6--8}, 28728 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28729 key = {76}, 28730 type = {Mathematical Programming Technical Report}, 28731 institution = {Computer Sciences Department, University of Wisconsin}, 28732 address = {Madison, Wisconsin}, 28733 number = {98-20} 28734} 28735 28736@Article{ ferris.munson:modeling, 28737 author = {M. C. Ferris and T. S. Munson}, 28738 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28739 year = {2000}, 28740 journal = {Mathematical Programming}, 28741 volume = {88}, 28742 pages = {487--506}, 28743 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28744 key = {71}, 28745 type = {Mathematical Programming Technical Report}, 28746 institution = {Computer Sciences Department, University of Wisconsin}, 28747 address = {Madison, Wisconsin}, 28748 number = {98-13} 28749} 28750 28751@TechReport{ ferris.munson:preprocessing, 28752 author = {M. C. Ferris and T. S. Munson}, 28753 title = {Preprocessing Complementarity Problems}, 28754 type = {Mathematical Programming Technical Report}, 28755 institution = {Computer Sciences Department, University of Wisconsin}, 28756 address = {Madison, Wisconsin}, 28757 year = {1999}, 28758 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28759 number = {99-07}, 28760 key = {86}, 28761 annote = {Submitted to ICCP 99} 28762} 28763 28764@TechReport{ ferris.munson:semismooth, 28765 author = {M. C. Ferris and T. S. Munson}, 28766 title = {Semismooth Support Vector Machines}, 28767 institution = {Computer Sciences Department, University of Wisconsin}, 28768 year = {2000}, 28769 key = {97}, 28770 type = {Data Mining Institute Technical Report}, 28771 number = {00-09}, 28772 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28773 address = {Madison, Wisconsin}, 28774 annote = {Submitted to Math Prog B} 28775} 28776 28777@Article{ ferris.pang:engineering, 28778 author = {M. C. Ferris and J. S. Pang}, 28779 title = {Engineering and Economic Applications of Complementarity Problems}, 28780 year = {1997}, 28781 journal = {SIAM Review}, 28782 volume = {39}, 28783 pages = {669--713}, 28784 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28785 key = {46} 28786} 28787 28788@Article{ ferris.pang:nondegenerate, 28789 author = {M. C. Ferris and J. S. Pang}, 28790 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28791 journal = {SIAM Journal on Control and Optimization}, 28792 year = {1996}, 28793 volume = {34}, 28794 pages = {244--263}, 28795 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28796 key = {35} 28797} 28798 28799@Article{ ferris.philpott:affine, 28800 author = {M. C. Ferris and A. B. Philpott}, 28801 title = {On Affine Scaling and Semi--Infinite Programming}, 28802 journal = {Mathematical Programming}, 28803 year = {1992}, 28804 volume = {56}, 28805 pages = {361--364}, 28806 key = {15} 28807} 28808 28809@Article{ ferris.philpott:interior, 28810 author = {M. C. Ferris and A. B. Philpott}, 28811 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28812 journal = {Mathematical Programming}, 28813 year = {1989}, 28814 volume = {43}, 28815 pages = {257--276}, 28816 key = {04} 28817} 28818 28819@Article{ ferris.philpott:performance, 28820 author = {M. C. Ferris and A. B. Philpott}, 28821 title = {On the Performance of {K}armarkar's Algorithm}, 28822 journal = {Journal of the Operational Research Society}, 28823 year = {1988}, 28824 volume = {39}, 28825 pages = {257--270}, 28826 key = {03} 28827} 28828 28829@InCollection{ ferris.ralph:projected, 28830 author = {M. C. Ferris and D. Ralph}, 28831 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28832 Maps}, 28833 booktitle = {Recent Advances in Nonsmooth Optimization}, 28834 publisher = {World Scientific Publishers}, 28835 year = {1995}, 28836 pages = {57--87}, 28837 editor = {D. Du and L. Qi and R. Womersley}, 28838 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28839 key = {41} 28840} 28841 28842@Article{ ferris.ruszczynski:robust, 28843 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28844 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28845 year = {2000}, 28846 journal = {Networks}, 28847 volume = {35}, 28848 pages = {181--194}, 28849 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28850 key = {60} 28851} 28852 28853@InCollection{ ferris.rutherford:accessing, 28854 author = {M. C. Ferris and T. F. Rutherford}, 28855 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28856 booktitle = {Nonlinear Optimization and Applications}, 28857 key = {48}, 28858 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28859 editor = {G. Di Pillo and F. Giannessi}, 28860 year = {1996}, 28861 pages = {141--153}, 28862 publisher = {Plenum Press}, 28863 address = {New York} 28864} 28865 28866@InCollection{ ferris.shepard:optimizing, 28867 author = {M. C. Ferris and D. M. Shepard}, 28868 title = {Optimization of Gamma Knife Radiosurgery}, 28869 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28870 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28871 publisher = {AMS}, 28872 year = {2000}, 28873 optseries = {DIMACS}, 28874 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28875 key = {91}, 28876 type = {Data Mining Institute Technical Report}, 28877 institution = {Computer Sciences Department, University of Wisconsin}, 28878 address = {Madison, Wisconsin}, 28879 number = {00-01} 28880} 28881 28882@InCollection{ ferris.sinapiromsaran:formulating, 28883 author = {M. C. Ferris and K. Sinapiromsaran}, 28884 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28885 booktitle = {Optimization}, 28886 key = {77}, 28887 publisher = {Springer-Verlag}, 28888 year = {2000}, 28889 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28890 volume = {481}, 28891 series = {Lecture Notes in Economics and Mathematical Systems}, 28892 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28893 type = {Mathematical Programming Technical Report}, 28894 institution = {Computer Sciences Department, University of Wisconsin}, 28895 address = {Madison, Wisconsin}, 28896 number = {98-21} 28897} 28898 28899@Article{ ferris.tin-loi:limit, 28900 author = {M. C. Ferris and F. Tin-Loi}, 28901 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28902 Complementarity Constraints}, 28903 year = {2001}, 28904 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28905 key = {78}, 28906 journal = {International Journal of Mechanical Sciences}, 28907 pages = {209--224}, 28908 volume = {43}, 28909 type = {Mathematical Programming Technical Report}, 28910 institution = {Computer Sciences Department, University of Wisconsin}, 28911 address = {Madison, Wisconsin}, 28912 number = {99-01} 28913} 28914 28915@Article{ ferris.tin-loi:nonlinear, 28916 author = {M. C. Ferris and F. Tin-Loi}, 28917 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28918 Elastoplasticity}, 28919 year = {1998}, 28920 key = {64}, 28921 volume = {6}, 28922 pages = {857--870}, 28923 journal = {Structural Engineering and Mechanics} 28924} 28925 28926@Article{ ferris.tin-loi:solution, 28927 author = {M. C. Ferris and F. Tin-Loi}, 28928 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28929 and Complementarity Constraints}, 28930 year = {1999}, 28931 journal = {Computer Methods in Applied Mechanics and Engineering}, 28932 volume = {174}, 28933 pages = {107--120}, 28934 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 28935 key = {66} 28936} 28937 28938@Article{ ferris.vlach:scheduling, 28939 author = {M. C. Ferris and M. Vlach}, 28940 title = {Scheduling with Earliness and Tardiness Penalties}, 28941 journal = {Naval Research Logistics Quarterly}, 28942 year = {1992}, 28943 volume = {39}, 28944 pages = {229--245}, 28945 key = {13} 28946} 28947 28948@TechReport{ ferris.zavriev:linear, 28949 author = {M. C. Ferris and S. K Zavriev}, 28950 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 28951 institution = {Computer Sciences Department, University of Wisconsin}, 28952 year = {1996}, 28953 key = {56}, 28954 address = {Madison, Wisconsin}, 28955 type = {Mathematical Programming Technical Report}, 28956 number = {96--12}, 28957 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 28958} 28959 28960@Article{ ferris:finite, 28961 author = {M. C. Ferris}, 28962 title = {Finite Termination of the Proximal Point Algorithm}, 28963 journal = {Mathematical Programming}, 28964 year = {1991}, 28965 volume = {50}, 28966 pages = {359--366}, 28967 key = {06} 28968} 28969 28970@Article{ ferris:iterative, 28971 author = {M. C. Ferris}, 28972 title = {Iterative Linear Programming Solution of Convex Programs}, 28973 journal = {Journal of Optimization Theory and Applications}, 28974 year = {1990}, 28975 volume = {65}, 28976 pages = {53--65}, 28977 key = {07} 28978} 28979 28980@Article{ ferris:linear, 28981 author = {M. C. Ferris}, 28982 title = {The Linear Complementarity Problem}, 28983 journal = {Bulletin of the American Mathematical Society}, 28984 year = {1993}, 28985 volume = {28}, 28986 pages = {169--175}, 28987 key = {27} 28988} 28989 28990@MastersThesis{ ferris:linear*1, 28991 author = {M. C. Ferris}, 28992 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 28993 Solving a Class of Structural Optimization Problems}, 28994 year = {1985}, 28995 school = {University of Cambridge}, 28996 address = {England}, 28997 key = {01} 28998} 28999 29000@TechReport{ ferris:matlab, 29001 author = {M. C. Ferris}, 29002 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 29003 institution = {Computer Sciences Department, University of Wisconsin}, 29004 year = {1998}, 29005 address = {Madison, Wisconsin}, 29006 type = {Mathematical Programming Technical Report}, 29007 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 29008 number = {98-19}, 29009 key = {75} 29010} 29011 29012@Article{ ferris:parallel, 29013 author = {M. C. Ferris}, 29014 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 29015 journal = {Mathematics of Operations Research}, 29016 year = {1994}, 29017 volume = {19}, 29018 pages = {645--658}, 29019 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 29020 key = {20} 29021} 29022 29023@TechReport{ ferris:parallel*1, 29024 author = {M. C. Ferris}, 29025 title = {Parallel Solution of Extremely Large Knapsack Problems}, 29026 institution = {Computer Sciences Department, University of Wisconsin}, 29027 year = {1989}, 29028 address = {Madison, Wisconsin}, 29029 number = {842}, 29030 key = {09} 29031} 29032 29033@PhDThesis{ ferris:weak, 29034 author = {M. C. Ferris}, 29035 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29036 year = {1988}, 29037 school = {University of Cambridge}, 29038 address = {England}, 29039 key = {02} 29040} 29041 29042@TechReport{ ferris:weak*1, 29043 author = {M. C. Ferris}, 29044 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29045 institution = {Computer Sciences Department, University of Wisconsin}, 29046 year = {1988}, 29047 address = {Madison, Wisconsin}, 29048 number = {779}, 29049 key = {05} 29050} 29051 29052@Book{ fiacco.mccormick:nonlinear, 29053 author = {A. V. Fiacco and G. P. McCormick}, 29054 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 29055 year = {1968}, 29056 publisher = {John Wiley \& Sons}, 29057 address = {New York}, 29058 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 29059} 29060 29061@Book{ fiacco:introduction, 29062 author = {A. V. Fiacco}, 29063 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 29064 year = {1983}, 29065 publisher = {Academic Press}, 29066 address = {New York} 29067} 29068 29069@Article{ fiedler.ptak:matrices, 29070 author = {M. Fiedler and V. Pt\'{a}k}, 29071 title = {On matrices with nonpositive off-diagonal elements and positive principal 29072 minors}, 29073 journal = {Czechoslovak Mathematics Journal}, 29074 volume = {12}, 29075 pages = {382--400}, 29076 year = {1962} 29077} 29078 29079@Article{ fischer.kanzow:finite, 29080 author = {A. Fischer and C. Kanzow}, 29081 title = {On Finite Termination of an Iterative Method for Linear Complementarity 29082 Problems}, 29083 journal = {Mathematical Programming}, 29084 volume = {74}, 29085 pages = {279--292}, 29086 year = {1996} 29087} 29088 29089@TechReport{ fischer:constrained, 29090 author = {A. Fischer}, 29091 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 29092 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 29093 year = {1995}, 29094 type = {Technical Report}, 29095 number = {MATH-NM-10-1995}, 29096 address = {Dresden} 29097} 29098 29099@Article{ fischer:local, 29100 author = {A. Fischer}, 29101 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 29102 weak conditions}, 29103 journal = {Optimization Methods and Software}, 29104 year = {1995}, 29105 volume = {6}, 29106 pages = {83--107} 29107} 29108 29109@InCollection{ fischer:ncp-function, 29110 author = {A. Fischer}, 29111 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 29112 booktitle = {Recent Advances in Nonsmooth Optimization}, 29113 publisher = {World Scientific Publishers}, 29114 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 29115 year = {1995}, 29116 pages = {88--105} 29117} 29118 29119@Article{ fischer:newton-type, 29120 author = {A. Fischer}, 29121 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 29122 Problems}, 29123 journal = {Journal of Optimization Theory and Applications}, 29124 year = {1995}, 29125 volume = {86}, 29126 pages = {585--608} 29127} 29128 29129@Article{ fischer:solution, 29130 author = {A. Fischer}, 29131 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 29132 Functions}, 29133 year = {1997}, 29134 journal = {Mathematical Programming}, 29135 pages = {513--532} 29136} 29137 29138@Article{ fischer:special, 29139 author = {A. Fischer}, 29140 title = {A Special {N}ewton--Type Optimization Method}, 29141 journal = {Optimization}, 29142 year = {1992}, 29143 volume = {24}, 29144 pages = {269--284} 29145} 29146 29147@Article{ fisher:use, 29148 author = {R. A. Fisher}, 29149 title = {The Use of Multiple Measurements in Taxonomic Problems}, 29150 journal = {Annual Eugenics}, 29151 year = {1936}, 29152 volume = {7}, 29153 number = {Part II}, 29154 pages = {179--188} 29155} 29156 29157@Book{ fishman:principles, 29158 author = {G. Fishman}, 29159 title = {Principles of Discrete Event Simulation}, 29160 publisher = {Wiley}, 29161 address = {New York, NY}, 29162 year = {1978} 29163} 29164 29165@Article{ fitchard.aldridge.ea:registration, 29166 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 29167 title = {Registration of Synthetic Tomographic Projection Data Sets Using 29168 Cross-Correlation}, 29169 journal = {Physics in Medicine and Biology}, 29170 year = {1998}, 29171 volume = {43}, 29172 pages = {1645--1657} 29173} 29174 29175@Article{ fletcher.matthews:stable, 29176 author = {R. Fletcher and S. P. J. Matthews}, 29177 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 29178 journal = {Mathematical Programming}, 29179 year = {1984}, 29180 volume = {30}, 29181 pages = {267--284} 29182} 29183 29184@TechReport{ fletcher.maza:nonlinear, 29185 author = {R. Fletcher and E. Sainz de la Maza}, 29186 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 29187 Programming}, 29188 institution = {Department of Mathematical Sciences}, 29189 year = {1987}, 29190 address = {The University, Dundee, Scotland}, 29191 number = {NA/100}, 29192 type = {Numerical Analysis Report} 29193} 29194 29195@InCollection{ fletcher:class, 29196 author = {R. Fletcher}, 29197 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 29198 Properties}, 29199 booktitle = {Integer and Nonlinear Programming}, 29200 year = {1970}, 29201 editor = {J. Abadie}, 29202 publisher = {North--Holland}, 29203 address = {Amsterdam}, 29204 pages = {157--173} 29205} 29206 29207@Article{ fletcher:exact, 29208 author = {R. Fletcher}, 29209 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 29210 journal = {Mathematical Programming}, 29211 year = {1973}, 29212 volume = {5}, 29213 pages = {129--150} 29214} 29215 29216@Article{ fletcher:generalized, 29217 author = {R. Fletcher}, 29218 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 29219 Equations}, 29220 journal = {The Computer Journal}, 29221 year = {1968}, 29222 volume = {10}, 29223 pages = {392--399} 29224} 29225 29226@InProceedings{ fletcher:penalty, 29227 crossref = {bachem.grotschel.ea:mathematical}, 29228 author = {R. Fletcher}, 29229 title = {Penalty Functions}, 29230 pages = {87--114} 29231} 29232 29233@Book{ fletcher:practical, 29234 author = {R. Fletcher}, 29235 title = {Practical Methods of Optimization}, 29236 year = {1981}, 29237 publisher = {John Wiley \& Sons}, 29238 address = {Chichester}, 29239 volume = {1} 29240} 29241 29242@Book{ fletcher:practical*1, 29243 author = {R. Fletcher}, 29244 title = {Practical Methods of Optimization}, 29245 year = {1981}, 29246 publisher = {John Wiley \& Sons}, 29247 address = {Chichester}, 29248 volume = {2} 29249} 29250 29251@Book{ fletcher:practical*2, 29252 author = {R. Fletcher}, 29253 title = {Practical Methods of Optimization}, 29254 year = {1987}, 29255 publisher = {John Wiley \& Sons}, 29256 address = {New York}, 29257 edition = {second} 29258} 29259 29260@Unpublished{ fletcher:recent, 29261 author = {R. Fletcher}, 29262 title = {Recent Developments in Nonlinear Programming}, 29263 note = {Presentation at SOR 96, Braunchweig, Germany}, 29264 year = {1996} 29265} 29266 29267@InCollection{ fletcher:second, 29268 author = {R. Fletcher}, 29269 title = {Second Order Correction for Nondifferentiable Optimization}, 29270 booktitle = {Numerical Analysis}, 29271 year = {1982}, 29272 editor = {G. A. Watson}, 29273 publisher = {Springer-Verlag}, 29274 address = {Berlin}, 29275 pages = {85--114} 29276} 29277 29278@InCollection{ florian:mathematical, 29279 author = {M. Florian}, 29280 title = {Mathematical programming applications in national, regional, and urban planning}, 29281 editors = {M. Iri and K. Tanabe}, 29282 booktitle = {Mathematical Programming: Recent Developments and Applications}, 29283 publisher = {Kluwer Academic Publishers}, 29284 address = {Tokyo}, 29285 year = {1989} 29286} 29287 29288@Article{ florian:nonlinear, 29289 author = {M. Florian}, 29290 title = {Nonlinear Cost Network Models in Transportation Analysis}, 29291 journal = {Mathematical Programming Study}, 29292 year = {1986}, 29293 volume = {26}, 29294 pages = {167--196} 29295} 29296 29297@Article{ flynn:computer, 29298 author = {M.~J. 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Tomlin}, 29324 title = {Updating Triangular Factors of the Basis to Maintain Sparsity in the Product Form 29325 Simplex Method}, 29326 journal = {Mathematical Programming}, 29327 year = {1972}, 29328 volume = {2}, 29329 pages = {263--278} 29330} 29331 29332@TechReport{ forsgren.gill.ea:computing, 29333 author = {A. Forsgren and P. E. Gill and W. Murray}, 29334 title = {Computing Modified {N}ewton Directions using a Partial {C}holesky Factorization}, 29335 institution = {Department of Mathematics, Royal Institute of Technology}, 29336 year = {1993}, 29337 number = {TRITA-MAT-1993-9}, 29338 address = {Stockholm, Sweden} 29339} 29340 29341@TechReport{ forsgren.gill:primal-dual, 29342 author = {A. Forsgren and P. E. Gill}, 29343 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 29344 institution = {Department of Mathematics, University of California}, 29345 year = {1996}, 29346 type = {Report NA}, 29347 number = {96-3}, 29348 address = {San Diego} 29349} 29350 29351@InCollection{ fortin.glowinski:decomposition-coordination, 29352 author = {M. Fortin and R. Glowinski}, 29353 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 29354 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 29355 Problems}, 29356 publisher = {North-Holland}, 29357 year = {1983}, 29358 editor = {M. Fortin and R. Glowinski}, 29359 address = {Amsterdam} 29360} 29361 29362@Misc{ foster.kesselman:globus, 29363 author = {I. Foster and C. Kesselman}, 29364 title = {The Globus Project}, 29365 howpublished = {www.globus.org} 29366} 29367 29368@Article{ foster.kesselman:globus*1, 29369 author = {I. Foster and C. 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Gabriel}, 29625 title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and 29626 Extensions}, 29627 school = {The Johns Hopkins University}, 29628 year = {1992}, 29629 address = {Baltimore, Maryland} 29630} 29631 29632@Article{ gafni.bertsekas:two-metric, 29633 author = {E. M. Gafni and D. P. Bertsekas}, 29634 title = {Two-Metric Projection Methods for Constrained Optimization}, 29635 journal = {SIAM Journal on Control and Optimization}, 29636 year = {1984}, 29637 volume = {22}, 29638 pages = {936--964} 29639} 29640 29641@InProceedings{ gaivoronski:convergence, 29642 author = {A. A. Gaivoronski}, 29643 title = {Convergence of Parallel Backpropagation for Neural Networks}, 29644 booktitle = {SIAM Journal on Optimization}, 29645 year = {1994}, 29646 note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993, 29647 submitted} 29648} 29649 29650@Misc{ gaivoronski:private, 29651 author = {A. A. 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Gao}, 29695 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 29696 Conditions}, 29697 type = {Manuscript}, 29698 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 29699 month = oct, 29700 year = {1994} 29701} 29702 29703@Article{ garcia-palomares.mangasarian:superlinearly, 29704 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 29705 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 29706 Optimization Problems}, 29707 journal = {Mathematical Programming}, 29708 year = {1976}, 29709 volume = {11}, 29710 pages = {1--13} 29711} 29712 29713@Article{ garcia-palomares.restuccia:global, 29714 author = {U. M. {Garcia--Palomares} and A. Restuccia}, 29715 title = {A Global Quadratic Algorithm for Solving a System of Mixed Equations}, 29716 journal = {Mathematical Programming}, 29717 year = {1981}, 29718 volume = {21}, 29719 pages = {290--300} 29720} 29721 29722@InProceedings{ garcia-palomares:superlinearly, 29723 author = {U. M. {Garcia--Palomares}}, 29724 title = {Superlinearly Convergent Algorithms for Linearly Constrained Optimization}, 29725 crossref = {mangasarian.meyer.ea:nonlinear*2}, 29726 pages = {101--119} 29727} 29728 29729@Article{ garcia.gould:theorem, 29730 author = {C. B. Garcia and F. J. Gould}, 29731 title = {A Theorem on Homotopy Paths}, 29732 journal = {Mathematics of Operations Research}, 29733 year = {1978}, 29734 volume = {3}, 29735 pages = {282--289} 29736} 29737 29738@Book{ garcia.zangwill:pathways, 29739 author = {C. B. Garcia and W. I. Zangwill}, 29740 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 29741 year = {1981}, 29742 publisher = {Prentice-Hall, Inc}, 29743 address = {Englewood Cliffs, New Jersey} 29744} 29745 29746@Book{ garey.johnson:computers, 29747 author = {M. R. Garey and D. S. Johnson}, 29748 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 29749 year = {1979}, 29750 publisher = {W.H. Freeman and Company}, 29751 address = {San Francisco} 29752} 29753 29754@Article{ garey.tarjan.ea:one-processor, 29755 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 29756 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 29757 journal = {Mathematics of Operations Research}, 29758 year = {1988}, 29759 volume = {13}, 29760 pages = {330--348} 29761} 29762 29763@Book{ garfinkel.nemhauser:integer, 29764 author = {R. S. Garfinkel and G. L. Nemhauser}, 29765 title = {Integer Programming}, 29766 year = {1972}, 29767 publisher = {John Wiley \& Sons}, 29768 address = {New York} 29769} 29770 29771@Book{ gass:linear, 29772 author = {S. Gass}, 29773 title = {Linear Programming Methods and Applications}, 29774 edition = {Fifth}, 29775 publisher = {Boyd and Fraser Publishing Company}, 29776 address = {Danvers, Massachusetts}, 29777 year = {1985} 29778} 29779 29780@InProceedings{ gay:combining, 29781 author = {D. M. Gay}, 29782 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 29783 booktitle = {Sparse Matrix Proceedings 1978}, 29784 editor = {I. S. Duff and G. W. Stewart}, 29785 year = {1978}, 29786 organization = {SIAM}, 29787 address = {Philadelphia, Pennsylvania}, 29788 pages = {313--334} 29789} 29790 29791@Article{ gay:electronic, 29792 author = {D. M. Gay}, 29793 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 29794 journal = {{COAL} Newsletter}, 29795 year = {1985}, 29796 volume = {13}, 29797 pages = {10--12} 29798} 29799 29800@TechReport{ gay:hooking, 29801 author = {D. M. Gay}, 29802 title = {Hooking Your Solver to {AMPL}}, 29803 year = {1997}, 29804 institution = {Bell Laboratories}, 29805 address = {Murray Hill, New Jersey}, 29806 note = {Revised 1994, 1997} 29807} 29808 29809@Article{ gay:variant, 29810 author = {D. Gay}, 29811 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 29812 Form}, 29813 journal = {Mathematical Programming}, 29814 year = {1987}, 29815 volume = {37}, 29816 pages = {81--90} 29817} 29818 29819@Article{ geiger.kanzow:resolution, 29820 author = {C. Geiger and C. Kanzow}, 29821 title = {On the Resolution of Monotone Complementarity Problems}, 29822 journal = {Computational Optimization and Applications}, 29823 volume = {5}, 29824 year = {1996}, 29825 pages = {155--173} 29826} 29827 29828@Book{ geist.beguelin.ea:pvm, 29829 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 29830 V. S. Sunderam}, 29831 title = {{PVM}: Parallel Virtual Machine}, 29832 publisher = {MIT Press}, 29833 address = {Cambridge, Massachusetts}, 29834 year = {1994} 29835} 29836 29837@Article{ gendron.crainic:parallel, 29838 author = {B. Gendron and T. G. Crainic}, 29839 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 29840 journal = {Operations Research}, 29841 year = {1994}, 29842 volume = {42}, 29843 pages = {1042--1060} 29844} 29845 29846@Article{ george:automatic, 29847 author = {A. George}, 29848 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 29849 journal = {SIAM Journal on Numerical Analysis}, 29850 vol = {17}, 29851 pages = {740--751}, 29852 year = {1980} 29853} 29854 29855@InProceedings{ georges-schleuter:asparagos, 29856 crossref = {schaeffer:third}, 29857 author = {M. Georges--Schleuter}, 29858 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 29859 pages = {416--421} 29860} 29861 29862@Article{ georgiou:comments, 29863 author = {G. M. Georgiou}, 29864 title = {Comments On Hidden Nodes in Neural Nets}, 29865 journal = {IEEE Transactions on Circuits and Systems}, 29866 year = {1991}, 29867 volume = {38}, 29868 pages = {1410} 29869} 29870 29871@TechReport{ gertz.linderoth.ea:object-oriented, 29872 author = {M. Gertz and J. Linderoth and S. Wright}, 29873 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 29874 institution = {MCS Division, Argonne National Laboratory}, 29875 year = {in preparation} 29876} 29877 29878@Article{ ghellinck.vial:polynomial, 29879 author = {G. de Ghellinck and J.--Ph. Vial}, 29880 title = {A Polynomial {N}ewton Method for Linear Programming}, 29881 journal = {Algorithmica}, 29882 year = {1986}, 29883 volume = {1}, 29884 pages = {425--453} 29885} 29886 29887@InCollection{ gilbert.ng:predicting, 29888 author = {J. R. Gilbert and E. Ng}, 29889 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 29890 year = {1993}, 29891 booktitle = {Graph Theory and Sparse Matrix Computation}, 29892 editor = {A. George and J. Gilbert and J. Liu}, 29893 publisher = {Springer-Verlag} 29894} 29895 29896@Article{ gilbert-lemarechal, 29897 author = {J. C. Gilbert and C. Lemarechal}, 29898 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 29899 journal = {Mathematical Programming}, 29900 year = {1989}, 29901 volume = {45}, 29902 pages = {407--434} 29903} 29904 29905@Article{ gill.murray.ea:computing, 29906 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29907 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 29908 journal = {SIAM Journal on Scientific and Statistical Computing}, 29909 year = {1983}, 29910 volume = {4}, 29911 pages = {310--321} 29912} 29913 29914@Article{ gill.murray.ea:maintaining, 29915 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29916 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 29917 year = {1987}, 29918 journal = {Linear Algebra and Its Applications}, 29919 volume = {88/89}, 29920 pages = {239--270} 29921} 29922 29923@Book{ gill.murray.ea:practical, 29924 author = {P. E. Gill and W. Murray and M. H. 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Luo}, 32953 title = {Convergence Analysis of Primal--Dual Interior--Point Algorithms for Convex 32954 Quadratic Programs}, 32955 institution = {Communications Research Laboratory, McMaster University}, 32956 year = {1992}, 32957 address = {Hamilton, Ontario} 32958} 32959 32960@Article{ lustig.marsten.ea:computational, 32961 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 32962 title = {Computational Experience with a Primal-Dual Interior Point Method for Linear 32963 Programming}, 32964 journal = {Linear Algebra and Its Applications}, 32965 year = {1991}, 32966 volume = {152}, 32967 pages = {191--222} 32968} 32969 32970@Article{ lustig.marsten.ea:implementing, 32971 author = {I. J. Lustig and R. E. Marsten and D. F. 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Pham}, 33090 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 33091 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 33092 year = {1993}, 33093 volume = {27}, 33094 pages = {375--392} 33095} 33096 33097@InCollection{ maier.novati:shakedown, 33098 author = {G. Maier and G. Novati}, 33099 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 33100 geometric effects with reference to discrete structural models}, 33101 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 33102 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 33103 publisher = {Pineridge Press}, 33104 address = {Swansea}, 33105 year = {1990}, 33106 pages = {451--471} 33107} 33108 33109@Article{ maier:incremental, 33110 author = {G. Maier}, 33111 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 33112 Instabilizing Effects}, 33113 journal = {International Journal of Solids and Structures}, 33114 volume = {7}, 33115 year = {1971}, 33116 pages = {345--372} 33117} 33118 33119@InCollection{ maier:inverse, 33120 author = {G. Maier}, 33121 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 33122 booktitle = {Serie VIII}, 33123 publisher = {Academia Nazionale dei Lincei}, 33124 year = {1981}, 33125 volume = {LXX}, 33126 pages = {203--209} 33127} 33128 33129@Article{ maier:matrix, 33130 author = {G. Maier}, 33131 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 33132 yield planes}, 33133 journal = {Meccanica}, 33134 volume = {5}, 33135 year = {1970}, 33136 pages = {54--66} 33137} 33138 33139@Article{ maier:quadratic, 33140 author = {G. Maier}, 33141 title = {A quadratic programming approach for certain classes of nonlinear structural 33142 problems}, 33143 journal = {Meccanica}, 33144 volume = {3}, 33145 year = {1968}, 33146 pages = {121--130} 33147} 33148 33149@Book{ manber:introduction, 33150 author = {U. Manber}, 33151 title = {Introduction to Algorithms: {A} Creative Approach}, 33152 year = {1989}, 33153 publisher = {Addison-Wesley} 33154} 33155 33156@Article{ mangasarian.deleone:error, 33157 author = {O. L. Mangasarian and R. {De~Leone}}, 33158 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 33159 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 33160 journal = {Applied Mathematics and Optimization}, 33161 year = {1988}, 33162 volume = {17}, 33163 pages = {1--14} 33164} 33165 33166@Article{ mangasarian.deleone:parallel, 33167 author = {O. L. Mangasarian and R. {De~Leone}}, 33168 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 33169 Problems and Linear Programs}, 33170 journal = {Journal of Optimization Theory and Applications}, 33171 year = {1987}, 33172 volume = {54}, 33173 pages = {437--446} 33174} 33175 33176@Article{ mangasarian.fromovitz:fritz, 33177 author = {O. L. Mangasarian and S. Fromovitz}, 33178 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 33179 and inequality constraints}, 33180 journal = {Journal of Mathematical Analysis and its Applications}, 33181 year = {1967}, 33182 volume = {17}, 33183 pages = {37--47} 33184} 33185 33186@Article{ mangasarian.mclinden:simple, 33187 author = {O. L. Mangasarian and L. McLinden}, 33188 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 33189 Programs}, 33190 journal = {Mathematical Programming}, 33191 year = {1985}, 33192 volume = {32}, 33193 pages = {32--40} 33194} 33195 33196@Article{ mangasarian.meyer:nonlinear, 33197 author = {O. L. Mangasarian and R. R. Meyer}, 33198 title = {Nonlinear Perturbation of Linear Programs}, 33199 journal = {SIAM Journal on Control and Optimization}, 33200 year = {1979}, 33201 volume = {17}, 33202 pages = {745--752} 33203} 33204 33205@TechReport{ mangasarian.musicant:active, 33206 author = {O. L. Mangasarian and David R. Musicant}, 33207 title = {Active Set Support Vector Machine Classification}, 33208 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33209 year = {2000}, 33210 number = {00-04}, 33211 address = {Madison, Wisconsin} 33212} 33213 33214@TechReport{ mangasarian.musicant:lagrangian, 33215 author = {O. L. Mangasarian and D. R. Musicant}, 33216 title = {Lagrangian Support Vector Machines}, 33217 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33218 year = {2000}, 33219 number = {00-06}, 33220 address = {Madison, Wisconsin} 33221} 33222 33223@TechReport{ mangasarian.musicant:robust, 33224 author = {O. L. Mangasarian and David R. Musicant}, 33225 title = {Robust Linear and Support Vector Regression}, 33226 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33227 year = {1999}, 33228 number = {99-09}, 33229 address = {Madison, Wisconsin} 33230} 33231 33232@Article{ mangasarian.musicant:successive, 33233 author = {O. L. Mangasarian and David R. Musicant}, 33234 title = {Successive Overrelaxation for Support Vector Machines}, 33235 journal = {IEEE Transactions on Neural Networks}, 33236 volume = {10}, 33237 year = {1999}, 33238 pages = {1032-1037} 33239} 33240 33241@Article{ mangasarian.pang:exact, 33242 author = {O. L. Mangasarian and J. S. Pang}, 33243 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 33244 Constraints}, 33245 journal = {Optimization}, 33246 year = {1997}, 33247 volume = {42}, 33248 pages = {1--8} 33249} 33250 33251@Article{ mangasarian.pang:extended, 33252 author = {O. L. Mangasarian and J. S. Pang}, 33253 title = {The Extended Linear Complementarity Problem}, 33254 journal = {SIAM Journal on Matrix Analysis and Applications}, 33255 year = {1994}, 33256 volume = {16} 33257} 33258 33259@Article{ mangasarian.ren:error, 33260 author = {O. L. Mangasarian and J. Ren}, 33261 title = {New error bounds for the nonlinear complementarity problem}, 33262 year = {1994}, 33263 volume = {1}, 33264 pages = {49--56}, 33265 journal = {Communications on Applied Nonlinear Analysis} 33266} 33267 33268@Article{ mangasarian.ren:improved, 33269 author = {O. L. Mangasarian and J. Ren}, 33270 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 33271 year = {1994}, 33272 volume = {66}, 33273 journal = {Mathematical Programming}, 33274 pages = {241--255} 33275} 33276 33277@InProceedings{ mangasarian.setiono.ea:pattern, 33278 crossref = {coleman.li:large-scale}, 33279 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 33280 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 33281 Diagnosis}, 33282 pages = {22--31} 33283} 33284 33285@Article{ mangasarian.shiau:error, 33286 author = {O. L. Mangasarian and T.--H. Shiau}, 33287 title = {Error Bounds for Monotone Linear Complementarity Problems}, 33288 journal = {Mathematical Programming}, 33289 year = {1986}, 33290 volume = {36}, 33291 pages = {81--89} 33292} 33293 33294@Article{ mangasarian.shiau:lipschitz, 33295 author = {O. L. Mangasarian and T.--H. Shiau}, 33296 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 33297 Complementarity Problems}, 33298 journal = {SIAM Journal on Control and Optimization}, 33299 year = {1987}, 33300 volume = {25}, 33301 pages = {583--595} 33302} 33303 33304@Article{ mangasarian.solodov:nonlinear, 33305 author = {O. L. Mangasarian and M. V. Solodov}, 33306 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 33307 journal = {Mathematical Programming}, 33308 year = {1993}, 33309 volume = {62}, 33310 pages = {277--298} 33311} 33312 33313@Article{ mangasarian.solodov:serial, 33314 author = {O. L. Mangasarian and M. V. Solodov}, 33315 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 33316 Minimization}, 33317 year = {1994}, 33318 journal = {Optimization Methods and Software}, 33319 volume = {4}, 33320 pages = {103--116} 33321} 33322 33323@Article{ mangasarian.street.ea:breast, 33324 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 33325 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 33326 journal = {Operations Research}, 33327 year = {1995}, 33328 volume = {43}, 33329 pages = {570--577} 33330} 33331 33332@Article{ mangasarian.wolberg:cancer, 33333 author = {O. L. Mangasarian and W. H. Wolberg}, 33334 title = {Cancer Diagnosis via Linear Programming}, 33335 journal = {SIAM News}, 33336 year = {1990}, 33337 volume = {23}, 33338 pages = {1 \& 18} 33339} 33340 33341@InCollection{ mangasarian:applications, 33342 author = {O. L. Mangasarian}, 33343 title = {Some Applications of Penalty Functions in Mathematical Programming}, 33344 booktitle = {Optimization and Related Fields}, 33345 year = {1986}, 33346 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 33347 publisher = {Springer-Verlag}, 33348 address = {Heidelberg}, 33349 pages = {307--329}, 33350 note = {Lecture Notes in Mathematics 1190} 33351} 33352 33353@Article{ mangasarian:characterization, 33354 author = {O. L. Mangasarian}, 33355 title = {Characterization of linear complementarity problems as linear programs}, 33356 journal = {Mathematical Programming Study}, 33357 year = {1978}, 33358 volume = {7}, 33359 pages = {74--87} 33360} 33361 33362@InProceedings{ mangasarian:condition, 33363 author = {O. L. Mangasarian}, 33364 title = {A condition number for linear inequalities and linear programs}, 33365 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 33366 1981}, 33367 year = {1981}, 33368 editor = {G. Bamberg and O. Opitz}, 33369 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 33370 address = {Konigstein}, 33371 pages = {3--15} 33372} 33373 33374@Article{ mangasarian:convergence, 33375 author = {O. L. Mangasarian}, 33376 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 33377 Symmetric Monotone Linear Complementarity Problem}, 33378 journal = {SIAM Journal on Optimization}, 33379 volume = {1}, 33380 pages = {114--122}, 33381 year = {1991} 33382} 33383 33384@Article{ mangasarian:equivalence, 33385 author = {O. L. Mangasarian}, 33386 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 33387 journal = {SIAM Journal on Applied Mathematics}, 33388 year = {1976}, 33389 volume = {31}, 33390 pages = {89--92} 33391} 33392 33393@Article{ mangasarian:error, 33394 author = {O. L. Mangasarian}, 33395 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 33396 journal = {ORSA Journal on Computing}, 33397 volume = {15}, 33398 pages = {187--192}, 33399 year = {1994} 33400} 33401 33402@Article{ mangasarian:error*1, 33403 author = {O. L. Mangasarian}, 33404 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 33405 journal = {Mathematical Programming}, 33406 year = {1990}, 33407 volume = {48}, 33408 pages = {437--445} 33409} 33410 33411@Article{ mangasarian:generalized, 33412 author = {O. L. Mangasarian}, 33413 title = {Generalized Linear Complementarity Problems as Linear Programs}, 33414 journal = {Methods of Operations Research}, 33415 year = {1979}, 33416 editor = {W. Oettli and F. Steffens}, 33417 volume = {31}, 33418 pages = {393--402} 33419} 33420 33421@InCollection{ mangasarian:generalized*1, 33422 author = {O. L. Mangasarian}, 33423 title = {Generalized Support Vector Machines}, 33424 year = {2000}, 33425 pages = {135-146}, 33426 booktitle = {Advances in Large Margin Classifiers}, 33427 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 33428 publisher = {MIT Press}, 33429 address = {Cambridge, MA} 33430} 33431 33432@Article{ mangasarian:global, 33433 author = {O. L. Mangasarian}, 33434 title = {Global error bounds for monotone affine variational inequality problems}, 33435 journal = {Linear Algebra and Its Applications}, 33436 year = {1992}, 33437 pages = {153--164} 33438} 33439 33440@InCollection{ mangasarian:least, 33441 author = {O. L. Mangasarian}, 33442 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 33443 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 33444 year = {1990}, 33445 publisher = {Oxford University Press}, 33446 address = {New York}, 33447 pages = {217--221} 33448} 33449 33450@Article{ mangasarian:least-norm, 33451 author = {O. L. Mangasarian}, 33452 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 33453 Problem}, 33454 journal = {Journal of Mathematical Analysis and Applications}, 33455 year = {1983}, 33456 volume = {92}, 33457 pages = {240--251} 33458} 33459 33460@Article{ mangasarian:linear, 33461 author = {O. L. Mangasarian}, 33462 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 33463 journal = {Mathematical Programming}, 33464 year = {1976}, 33465 volume = {10}, 33466 pages = {263--270} 33467} 33468 33469@Article{ mangasarian:linear*1, 33470 author = {O. L. Mangasarian}, 33471 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 33472 journal = {Operations Research}, 33473 year = {1965}, 33474 volume = {13}, 33475 pages = {444--452} 33476} 33477 33478@Article{ mangasarian:locally, 33479 author = {O. L. Mangasarian}, 33480 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 33481 Complementarity Problems}, 33482 journal = {Mathematical Programming}, 33483 year = {1980}, 33484 volume = {19}, 33485 pages = {200--212} 33486} 33487 33488@InCollection{ mangasarian:machine, 33489 author = {O. L. Mangasarian}, 33490 title = {Machine Learning via Polyhedral Concave Minimization}, 33491 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 33492 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 33493 pages = {175-188}, 33494 year = {1996}, 33495 address = {Heidelberg}, 33496 publisher = {Physica-Verlag A Springer-Verlag Company} 33497} 33498 33499@Article{ mangasarian:mathematical, 33500 author = {O. L. Mangasarian}, 33501 title = {Mathematical Programming in Neural Networks}, 33502 journal = {ORSA Journal on Computing}, 33503 volume = {5}, 33504 pages = {349--360}, 33505 year = {1993} 33506} 33507 33508@InProceedings{ mangasarian:mathematical*1, 33509 author = {O. L. Mangasarian}, 33510 title = {Mathematical Programming in Machine Learning}, 33511 booktitle = {Nonlinear Optimization and Applications}, 33512 editor = {G. Di Pillo and F. Giannessi}, 33513 publisher = {Plenum Publishing}, 33514 address = {New York}, 33515 pages = {283--295}, 33516 year = {1996} 33517} 33518 33519@Article{ mangasarian:mathematical*2, 33520 author = {O. L. Mangasarian}, 33521 title = {Mathematical Programming in Data Mining}, 33522 journal = {Data Mining and Knowledge Discovery}, 33523 volume = {1}, 33524 year = {1997}, 33525 pages = {183-201} 33526} 33527 33528@Article{ mangasarian:multi-surface, 33529 author = {O. L. Mangasarian}, 33530 title = {Multi-surface Method of Pattern Separation}, 33531 journal = {IEEE Transactions on Information Theory}, 33532 year = {1968}, 33533 volume = {IT-14}, 33534 pages = {801--807} 33535} 33536 33537@Book{ mangasarian:nonlinear, 33538 author = {O. L. Mangasarian}, 33539 title = {Nonlinear Programming}, 33540 year = {1969}, 33541 publisher = {McGraw--Hill}, 33542 address = {New York}, 33543 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 33544} 33545 33546@Article{ mangasarian:normal, 33547 author = {O. L. Mangasarian}, 33548 title = {Normal Solutions of Linear Programs}, 33549 journal = {Mathematical Programming Study}, 33550 year = {1984}, 33551 volume = {22}, 33552 pages = {206--216} 33553} 33554 33555@Article{ mangasarian:optimal, 33556 author = {O. L. Mangasarian}, 33557 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 33558 Linear Programs}, 33559 journal = {Journal of Optimization Theory and Applications}, 33560 year = {1981}, 33561 volume = {35}, 33562 pages = {123--128} 33563} 33564 33565@Article{ mangasarian:parallel, 33566 author = {O. L. Mangasarian}, 33567 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 33568 journal = {SIAM Journal on Control and Optimization}, 33569 volume = {33}, 33570 pages = {1916--1925}, 33571 year = {1995} 33572} 33573 33574@TechReport{ mangasarian:regularized, 33575 author = {O. L. 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Petri}, 35348 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35349 publisher = {Harvard University Press}, 35350 year = {1984} 35351} 35352 35353@InProceedings{ petrzykowski:application, 35354 author = {T. Petrzykowski}, 35355 title = {Application of the Steepest Ascent Method to Concave Programming}, 35356 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35357 year = {1962}, 35358 publisher = {North--Holland}, 35359 address = {Amsterdam}, 35360 pages = {185--189} 35361} 35362 35363@InProceedings{ pettey.leuze.ea:parallel, 35364 crossref = {grefenstette:genetic}, 35365 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35366 title = {A Parallel Genetic Algorithm}, 35367 pages = {155--161} 35368} 35369 35370@InProceedings{ pettey.leuze:theoretical, 35371 crossref = {schaeffer:third}, 35372 author = {C. C. Pettey and M. R. Leuze}, 35373 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35374 pages = {398--405} 35375} 35376 35377@Book{ pfeiffer.glocker:multibody, 35378 author = {F. Pfeiffer and C. Glocker}, 35379 title = {Multibody Dynamics with Unilateral Contact}, 35380 year = {1996}, 35381 publisher = {John Wiley \& Sons} 35382} 35383 35384@TechReport{ pierro.iusem:convergence, 35385 author = {A. R. de Pierro and A. N. Iusem}, 35386 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35387 Linear Complementarity Problems}, 35388 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35389 year = {1990}, 35390 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35391} 35392 35393@InCollection{ pillo.grippo.ea:class, 35394 author = {G. Di Pillo and L. Grippo and F. 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Polyak}, 35554 title = {Sharp Minima}, 35555 year = {1979}, 35556 note = {A Talk given at the {IIASA} Workshop on Generalized {L}agrangians and their 35557 Applications, {IIASA}, Laxenburg, Austria} 35558} 35559 35560@InProceedings{ polyak:smooth, 35561 author = {R. A. Polyak}, 35562 title = {Smooth Optimization Methods for Solving Nonlinear Extremal and Equilibrium 35563 Problems with Constraints}, 35564 booktitle = {Abstracts of the Papers of the 11th International Symposium on Mathematical 35565 Programming}, 35566 year = {1982}, 35567 address = {Bonn} 35568} 35569 35570@Article{ polychronopoulos.tsitsiklis:analysis, 35571 author = {G. H. Polychronopoulos and J. N. Tsitsiklis}, 35572 title = {Stochastic Shortest Path Problems with Recourse}, 35573 journal = {Networks}, 35574 year = {1996}, 35575 volume = {27}, 35576 pages = {133--143} 35577} 35578 35579@TechReport{ potra.bonnans:infeasible, 35580 author = {F. A. Potra and J. F. Bonnans}, 35581 title = {Infeasible path following algorithms for linear complementarity problems}, 35582 institution = {INRIA}, 35583 year = {1994}, 35584 month = dec, 35585 number = {RR--2445}, 35586 type = {Research Report} 35587} 35588 35589@Article{ potra.sheng:large-step, 35590 author = {F. A. Potra and R. Sheng}, 35591 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 35592 year = {1997}, 35593 journal = {SIAM Journal on Optimization}, 35594 volume = {7}, 35595 pages = {318--335} 35596} 35597 35598@Article{ potra:infeasible, 35599 author = {F. A. Potra}, 35600 title = {An infeasible interior-point predictor-corrector algorithm for linear 35601 programming}, 35602 journal = {SIAM Journal on Optimization}, 35603 year = {1996}, 35604 volume = {6}, 35605 pages = {19--32} 35606} 35607 35608@TechReport{ potra:onl, 35609 author = {F. A. Potra}, 35610 title = {An ${O}(n{L})$ infeasible--interior--point algorithm for {LCP} with quadratic 35611 convergence.}, 35612 institution = {Department of Mathematics, The University of Iowa}, 35613 address = {Iowa City, Iowa}, 35614 year = {1994}, 35615 number = {50}, 35616 type = {Reports on Computational Mathematics} 35617} 35618 35619@TechReport{ potra:predictor-corrector, 35620 author = {F. A. Potra}, 35621 title = {On a predictor-corrector method for solving linear programs from infeasible 35622 starting points}, 35623 institution = {Department of Mathematics, University of Iowa}, 35624 address = {Iowa City, Iowa}, 35625 year = {1992}, 35626 number = {34}, 35627 type = {Reports on Computational Mathematics} 35628} 35629 35630@TechReport{ potra:quadratically, 35631 author = {F. A. Potra}, 35632 title = {A quadratically convergent infeasible interior-point algorithm for linear 35633 programming}, 35634 institution = {Department of Mathematics, University of Iowa}, 35635 year = {1992}, 35636 number = {28}, 35637 address = {Iowa City, Iowa}, 35638 month = jul 35639} 35640 35641@InCollection{ powell:convergence, 35642 author = {M. J. D. Powell}, 35643 title = {The Convergence of Variable Metric Methods for Nonlinearly Constrained 35644 Optimization Calculations}, 35645 crossref = {mangasarian.meyer.ea:nonlinear*3}, 35646 pages = {27--63} 35647} 35648 35649@InProceedings{ powell:direct, 35650 author = {M. J. D. 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Teukolsky and William T. 35723 Vetterling}, 35724 title = {Numerical Recipes : the Art of Scientific Computing}, 35725 publisher = {Cambridge University Press}, 35726 year = {1988} 35727} 35728 35729@Article{ pruyne.livny:interfacing, 35730 author = {J. Pruyne and M. Livny}, 35731 title = {Interfacing {C}ondor and {PVM} to Harness the Cycles of Workstation Clusters}, 35732 journal = {Journal on Future Generations of Computer Systems}, 35733 volume = {12}, 35734 year = {1996}, 35735 pages = {67--85} 35736} 35737 35738@InCollection{ pruyne.livny:parallel, 35739 author = {J. Pruyne and M. Livny}, 35740 title = {Parallel Processing on Dynamic Resources using {CARMI}}, 35741 booktitle = {Job Scheduling Strategies for Parallel Processing}, 35742 publisher = {Springer-Verlag}, 35743 year = {1995}, 35744 editor = {D. G. Feitelson and L. Rudolph}, 35745 volume = {949}, 35746 series = {Lecture Notes in Computer Science} 35747} 35748 35749@PhDThesis{ pruyne:resource, 35750 author = {J. C. Pruyne}, 35751 title = {Resource Management Services for Parallel Applications}, 35752 school = {University of Wisconsin--Madison}, 35753 year = {1996}, 35754 address = {Madison, Wisconsin} 35755} 35756 35757@Book{ pshenichny.danilin:numerical, 35758 author = {B. N. Pshenichny and Yu. M. Danilin}, 35759 title = {Numerical Methods in Extremal Problems}, 35760 year = {1978}, 35761 publisher = {MIR Publishers}, 35762 address = {Moscow} 35763} 35764 35765@TechReport{ qi.chen:globally, 35766 author = {L. Qi and X. Chen}, 35767 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 35768 institution = {School of Mathematics, University of New South Wales}, 35769 year = {1993}, 35770 annote = {revised}, 35771 address = {Sydney} 35772} 35773 35774@Article{ qi.jiang:semismooth, 35775 author = {L. Qi and H. Jiang}, 35776 title = {Semismooth {K}arush--{K}uhn--{T}ucker Equations and Convergence Analysis of 35777 {N}ewton Methods and Quasi--{N}ewton Methods for Solving these Equations}, 35778 journal = {Mathematics of Operations Research}, 35779 volume = {22}, 35780 pages = {301--325}, 35781 year = {1997} 35782} 35783 35784@TechReport{ qi.peng:unconstrained, 35785 author = {H. -D. Qi and J. -M. Peng}, 35786 title = {A New Unconstrained Optimization Approach for Nonlinear Complementarity 35787 Problems}, 35788 institution = {State Key Laboratory of Scientific and Engineering Computing, Academic Sinica}, 35789 year = {1996}, 35790 type = {Technical Report}, 35791 address = {Beijing} 35792} 35793 35794@InCollection{ qi.sun:survey, 35795 author = {L. Qi and D. Sun}, 35796 title = {A Survey of Some Nonsmooth Equations and Smoothing {N}ewton Methods}, 35797 year = {1999}, 35798 editor = {A. Eberhard and B. Glover and R. Hill and D. Ralph}, 35799 booktitle = {Progress in Optimization}, 35800 pages = {121--146}, 35801 series = {Applied Optimization}, 35802 volume = {30}, 35803 publisher = {Kluwer Academic Publishers}, 35804 address = {Dordrecht} 35805} 35806 35807@Article{ qi.sun:nonsmooth, 35808 author = {L. Qi and J. Sun}, 35809 title = {A Nonsmooth Version of {N}ewton's Method}, 35810 journal = {Mathematical Programming}, 35811 year = {1993}, 35812 volume = {58}, 35813 pages = {353--368} 35814} 35815 35816@Article{ qi:convergence, 35817 author = {L. Qi}, 35818 title = {Convergence Analysis of Some Algorithms for Solving Nonsmooth Equations}, 35819 journal = {Mathematics of Operations Research}, 35820 year = {1993}, 35821 volume = {18}, 35822 pages = {227--244} 35823} 35824 35825@TechReport{ qi:regular, 35826 author = {L. 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Rockafellar}, 36335 title = {Conjugate Duality and Optimization}, 36336 year = {1974}, 36337 publisher = {SIAM}, 36338 address = {Philadelphia, Pennsylvania}, 36339 volume = {16}, 36340 series = {Conference Board of the Mathematical Sciences} 36341} 36342 36343@Book{ rockafellar:convex, 36344 author = {R. T. Rockafellar}, 36345 title = {Convex Analysis}, 36346 year = {1970}, 36347 publisher = {Princeton University Press}, 36348 address = {Princeton, New Jersey} 36349} 36350 36351@Article{ rockafellar:first-, 36352 author = {R. T. Rockafellar}, 36353 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 36354 journal = {Transactions of the American Mathematical Society}, 36355 year = {1988}, 36356 volume = {307}, 36357 pages = {75--108} 36358} 36359 36360@InProceedings{ rockafellar:generalized, 36361 author = {R. T. Rockafellar}, 36362 title = {A Generalized Approach to Linear-Quadratic Programming}, 36363 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36364 Applications}, 36365 year = {1986}, 36366 pages = {58--66}, 36367 note = {(Xi'an, China)} 36368} 36369 36370@InProceedings{ rockafellar:generalized*1, 36371 crossref = {bachem.grotschel.ea:mathematical}, 36372 author = {R. T. Rockafellar}, 36373 title = {Generalized Subgradients in Mathematical Programming}, 36374 pages = {368--390} 36375} 36376 36377@InCollection{ rockafellar:large-scale, 36378 author = {R. T. Rockafellar}, 36379 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36380 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36381 chapter = {15}, 36382 year = {1991}, 36383 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 36384 publisher = {SIAM Publications}, 36385 pages = {247--261} 36386} 36387 36388@Article{ rockafellar:linear-quadratic, 36389 author = {R. T. Rockafellar}, 36390 title = {Linear-Quadratic Programming and Optimal Control}, 36391 journal = {SIAM Journal on Control and Optimization}, 36392 year = {1987}, 36393 volume = {25}, 36394 pages = {781--814} 36395} 36396 36397@Article{ rockafellar:maximality, 36398 author = {R. T. Rockafellar}, 36399 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 36400 journal = {Transactions of the American Mathematical Society}, 36401 year = {1970}, 36402 volume = {149}, 36403 pages = {75--88} 36404} 36405 36406@InCollection{ rockafellar:monotone, 36407 author = {R. T. Rockafellar}, 36408 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 36409 crossref = {mangasarian.meyer.ea:nonlinear*3}, 36410 pages = {1--26} 36411} 36412 36413@Article{ rockafellar:monotone*1, 36414 author = {R. T. Rockafellar}, 36415 title = {Monotone Operators and the Proximal Point Algorithm}, 36416 journal = {SIAM Journal on Control and Optimization}, 36417 year = {1976}, 36418 volume = {14}, 36419 pages = {877--898} 36420} 36421 36422@Article{ rockafellar:multiplier, 36423 author = {R. T. Rockafellar}, 36424 title = {The Multiplier Method of {H}estenes and {P}owell Applied to Convex Programming}, 36425 journal = {Journal of Optimization Theory and Applications}, 36426 year = {1973}, 36427 volume = {12}, 36428 pages = {555--562} 36429} 36430 36431@Article{ rockafellar:multistage, 36432 author = {R. T. Rockafellar}, 36433 title = {Multistage Convex Programming and Discrete-Time Optimal Control}, 36434 journal = {Control and Cybernetics}, 36435 year = {1988}, 36436 volume = {17}, 36437 number = {2-3}, 36438 pages = {225--245} 36439} 36440 36441@Book{ rockafellar:network, 36442 author = {R. T. Rockafellar}, 36443 title = {Network Flows and Monotropic Optimization}, 36444 publisher = {John Wiley}, 36445 year = {1984}, 36446 address = {New York} 36447} 36448 36449@Article{ rodrigues:mixed, 36450 author = {H. C. Rodrigues}, 36451 title = {A mixed variational formulation for shape optimization of solids with contact 36452 conditions}, 36453 journal = {Structural Optimization}, 36454 volume = {6}, 36455 year = {1993}, 36456 pages = {19--28} 36457} 36458 36459@Book{ rodrigues:obstacle, 36460 author = {J. F. Rodrigues}, 36461 title = {Obstacle Problems in Mathematical Physics}, 36462 publisher = {Elsevier Publishing Company}, 36463 address = {Amsterdam}, 36464 year = {1987} 36465} 36466 36467@Book{ roos.terlaky.ea:theory, 36468 author = {C. Roos and T. Terlaky and J.--Ph. 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Knepley}, 39173 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 39174 (ICCFD11)}, 39175 editor = {Christoph Brehm and Shishir Pandya}, 39176 number = {4103}, 39177 year = {2022} 39178} 39179 39180@Article{ nathawaniknepley2023, 39181 title = {One-dimensional model to simulate shear-induced droplet formation}, 39182 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39183 journal = {International Journal of Multiphase Flow}, 39184 note = {Submitted}, 39185 year = {2023} 39186} 39187 39188@InProceedings{ georgalisnathawaniknepleypatra2023, 39189 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 39190 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. 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Dunham and Ahmed E. Elbanna and Alice‐Agnes Gabriel and Tobias W. Harvey and Yihe Huang and Yoshihiro Kaneko and Jeremy E. Kozdon and Nadia Lapusta and Duo Li and Meng Li and Chao Liang and Yajing Liu and So Ozawa and Andrea Perez‐Silva and Casper Pranger and Paul Segall and Yudong Sun and Prithvi Thakur and Carsten Uphoff and Ylona van Dinther and Yuyun Yang}, 39357 journal = {Bulletin of the Seismological Society of America}, 39358 volume = {113}, 39359 number = {2}, 39360 pages = {499--523}, 39361 year = {2023}, 39362} 39363
