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 Kaps-Rentrop-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 Runge-Kutta 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 Runge--Kutta methods for stiff ODEs}, 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-Newton 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 Schwarz 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 Schwarz 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 Schwarz 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 Schwarz 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 = {Schwarz 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 Schwarz 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 PDEs}, 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 Newton--Krylov--Schwarz 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 Cholesky 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, 592 title = {A {N}ewton basis {GMRES} implementation}, 593 author = {Bai, Zhaojun and Hu, Dan and Reichel, Lothar}, 594 journal = {IMA Journal of Numerical Analysis}, 595 volume = {14}, 596 number = {4}, 597 pages = {563--581}, 598 year = {1994}, 599 publisher = {Oxford University Press} 600} 601 602@article{sidje1997alternatives, 603 title = {Alternatives for parallel Krylov subspace basis computation}, 604 author = {Sidje, Roger B}, 605 journal = {Numerical linear algebra with applications}, 606 volume = {4}, 607 number = {4}, 608 pages = {305--331}, 609 year = {1997}, 610 publisher = {Wiley Online Library} 611} 612 613@inproceedings{mohiyuddin2009minimizing, 614 title = {Minimizing communication in sparse matrix solvers}, 615 author = {Mohiyuddin, Marghoob and Hoemmen, Mark and Demmel, James and Yelick, Katherine}, 616 booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis}, 617 pages = {1--12}, 618 year = {2009} 619} 620 621@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 engineering}, 675 volume = {50}, 676 number = {7}, 677 pages = {1523--1544}, 678 year = {2001}, 679 publisher = {Wiley Online Library} 680} 681 682@article{lottes2023optimal, 683 title = {Optimal polynomial smoothers for multigrid {V}-cycles}, 684 author = {Lottes, James}, 685 journal = {Numerical Linear Algebra with Applications}, 686 volume = {30}, 687 number = {6}, 688 pages = {e2518}, 689 year = {2023}, 690 publisher = {Wiley Online Library} 691} 692 693@article{phillips2022optimal, 694 title = {Optimal {C}hebyshev Smoothers and One-sided {V}-cycles}, 695 author = {Phillips, Malachi and Fischer, Paul}, 696 journal = {arXiv preprint arXiv:2210.03179}, 697 year = {2022} 698} 699 700@incollection{toint1981towards, 701 title = {Towards an efficient sparsity exploiting {N}ewton method for minimization}, 702 author = {Toint, Philippe}, 703 booktitle = {Sparse matrices and their uses}, 704 pages = {57--88}, 705 year = {1981}, 706 publisher = {Academic press} 707} 708 709@article{cools2019numerically, 710 title = {Numerically stable recurrence relations for the communication hiding pipelined conjugate gradient method}, 711 author = {Cools, Siegfried and Cornelis, Jeffrey and Vanroose, Wim}, 712 journal = {IEEE Transactions on Parallel and Distributed Systems}, 713 volume = {30}, 714 number = {11}, 715 pages = {2507--2522}, 716 year = {2019}, 717 publisher = {IEEE} 718} 719 720@article{cornelis2018communication, 721 title = {The communication-hiding conjugate gradient method with deep pipelines}, 722 author = {Cornelis, Jeffrey and Cools, Siegfried and Vanroose, Wim}, 723 journal = {arXiv preprint arXiv:1801.04728}, 724 year = {2018} 725} 726 727@article{d1993conjugate, 728 title = {Conjugate gradient algorithms with reduced synchronization overhead on distributed memory multiprocessors}, 729 author = {D’Azevedo, EF and Eijkhout, VL and Romine, CH}, 730 journal = {Computer Science Technical Report CS-93-185, University of Tennessee, Knoxville}, 731 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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 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 Maxwell-Bloch 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 Newton and hybrid Schwarz 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 Lagrangian 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 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 and G. 2224 Székely}, 2225 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 2226 a Schur 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 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 Brigham and Women'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 Bayesian 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 Fokker-Plank-Landau}, 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. Zhang}, 2572 booktitle = {Proceedings of SciDAC 2010 Conference}, 2573 year = {2010}, 2574 url = {http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf}, 2575 petsc_uses = {KSP} 2576} 2577 2578@InProceedings{ facets-fec2010, 2579 title = {Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using 2580 the {FACETS} Framework}, 2581 author = {J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina 2582 and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. 2583 McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang}, 2584 booktitle = {Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, 2585 Republic of Korea}, 2586 year = {2010}, 2587 petsc_uses = {KSP} 2588} 2589 2590@InProceedings{ facets-epdp2010, 2591 title = {{FACETS}: A Framework for Parallel Coupling of Fusion Components}, 2592 author = {J. Cary and A. Hakim and M. Miah and S. Kruger and A. 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Wang}, 2726 note = {American Physical Society 45th Annual Meeting Division of Plasma Physics, 2727 Albuquerque, New Mexico, October 2003}, 2728 year = {2003}, 2729 petsc_uses = {KSP} 2730} 2731 2732@TechReport{ tang2001, 2733 author = {X. Z. Tang and G. Y. Fu and S. C. Jardin and L. L. Lowe and W. Park and H. 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May and Matthew G. Knepley and Andreas Fichtner}, 2818 journal = {Geophysical Journal International}, 2819 volume = {216}, 2820 number = {3}, 2821 pages = {1675--1692}, 2822 doi = {10.1093/gji/ggy469}, 2823 year = {2019}, 2824 petsc_uses = {KSP} 2825} 2826 2827@Article{ haplaknepleyafanasievboehmdrielkrischerfichtner2020, 2828 title = {Fully Parallel Mesh {I/O} using {PETSc} {DMPlex} with an Application to Waveform 2829 Modeling}, 2830 author = {Vaclav Hapla and Matthew G. 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Roman and Enrique S. 3474 Quintana-Ort\'{\i}}, 3475 title = {Large scale simulation of wave propagation in soils interacting with structures 3476 using {FEM} and {SBFEM}}, 3477 journal = {Journal of Computational Acoustics}, 3478 volume = {19}, 3479 number = {1}, 3480 pages = {75--93}, 3481 year = {2011}, 3482 doi = {10.1142/S0218396X11004316}, 3483 petsc_uses = {KSP} 3484} 3485 3486@Misc{ bsa2010, 3487 author = {J. Brown and B. Smith and A. Ahmadia}, 3488 title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow}, 3489 note = {submitted to SIAM Journal on Scientific Computing}, 3490 year = {2012}, 3491 petsc_uses = {KSP} 3492} 3493 3494@Article{ kellerkatz2016, 3495 title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere}, 3496 author = {Tobias Keller and Richard F. 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Knepley}, 3795 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3796 Deformation}, 3797 booktitle = {Eos Transactions of the AGU}, 3798 organization = {American Geophysical Union}, 3799 volume = {89}, 3800 number = {53}, 3801 note = {Fall Meeting Supplemental, Abstract T41A-1925}, 3802 year = {2007}, 3803 petsc_uses = {KSP} 3804} 3805 3806@InProceedings{ aagaardknepleywilliams07, 3807 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3808 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3809 Deformation}, 3810 booktitle = {Eos Transactions of the AGU}, 3811 organization = {American Geophysical Union}, 3812 volume = {88}, 3813 number = {52}, 3814 note = {Fall Meeting Supplemental, Abstract T21B-1798}, 3815 year = {2007}, 3816 petsc_uses = {KSP} 3817} 3818 3819@InProceedings{ aagaardknepleywilliams05, 3820 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3821 title = {Development of software for studying earthquakes across multiple spatial and 3822 temporal scales by coupling quasi-static and dynamic simulations}, 3823 booktitle = {Eos Transactions of the AGU}, 3824 organization = {American Geophysical Union}, 3825 volume = {86}, 3826 number = {52}, 3827 note = {Fall Meeting Supplemental, Abstract S53A-1072}, 3828 year = {2005}, 3829 petsc_uses = {KSP} 3830} 3831 3832@InProceedings{ williamsgablehagermeadeaagaardknepley08, 3833 author = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and 3834 Brad Aagaard and Matthew G. Knepley}, 3835 title = {Modeling of Multiple Earthquake Cycles in Southern California Using the {SCEC} 3836 Community Fault Model}, 3837 booktitle = {Proceedings of Geosciences '08}, 3838 address = {Wellington, NZ}, 3839 month = nov, 3840 year = {2008}, 3841 petsc_uses = {KSP} 3842} 3843 3844@TechReport{ zhang07, 3845 title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for 3846 Tsunamis}, 3847 author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi}, 3848 type = {Preprint}, 3849 number = {ANL/MCS-P1459-0907}, 3850 institution = {ANL}, 3851 month = sep, 3852 year = {2007}, 3853 petsc_uses = {KSP} 3854} 3855 3856@Article{ katz08b, 3857 author = {Richard F. Katz}, 3858 title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic 3859 focusing at mid-ocean ridges}, 3860 journal = {J. Petrology}, 3861 year = {2008}, 3862 volume = {49}, 3863 pages = {2099--2121}, 3864 doi = {10.1093/petrology/egn058}, 3865 petsc_uses = {KSP} 3866} 3867 3868@Article{ hgrhkjvv2008, 3869 title = {On preconditioning for a parallel solution of the Richards equation}, 3870 author = {Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy 3871 Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena}, 3872 journal = {Computers and Geosciences}, 3873 volume = {34}, 3874 pages = {1958--1963}, 3875 year = {2008}, 3876 petsc_uses = {KSP} 3877} 3878 3879@Article{ maymoresi2008, 3880 title = {Preconditioned iterative methods for {Stokes} flow problems arising in 3881 computational geodynamics}, 3882 journal = {Physics of the Earth and Planetary Interiors}, 3883 volume = {171}, 3884 number = {1-4}, 3885 pages = {33--47}, 3886 year = {2008}, 3887 note = {{R}ecent Advances in Computational Geodynamics: Theory, Numerics and 3888 Applications}, 3889 issn = {0031-9201}, 3890 doi = {10.1016/j.pepi.2008.07.036}, 3891 author = {Dave A. May and Louis Moresi}, 3892 keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}, 3893 petsc_uses = {KSP} 3894} 3895 3896@Article{ kausmuhlhausmay2010, 3897 title = {A stabilization algorithm for geodynamic numerical simulations with a free 3898 surface}, 3899 author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May}, 3900 journal = {Physics of the Earth and Planetary Interiors}, 3901 volume = {181}, 3902 number = {1}, 3903 pages = {12--20}, 3904 year = {2010}, 3905 petsc_uses = {KSP} 3906} 3907 3908@Article{ duretzmaygeryatackley2011, 3909 title = {Discretization errors and free surface stabilization in the finite difference and 3910 marker-in-cell method for applied geodynamics: A numerical study}, 3911 author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley}, 3912 journal = {Geochemistry, Geophysics, Geosystems}, 3913 volume = {12}, 3914 number = {7}, 3915 year = {2011}, 3916 petsc_uses = {KSP} 3917} 3918 3919@Article{ furuichimaytackley2011, 3920 title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a 3921 {Schur} complement approach with mixed precision arithmetic}, 3922 author = {Mikito Furuichi and Dave A May and Paul J Tackley}, 3923 journal = {Journal of Computational Physics}, 3924 volume = {230}, 3925 number = {24}, 3926 pages = {8835--8851}, 3927 year = {2011}, 3928 petsc_uses = {KSP} 3929} 3930 3931@Article{ kellermaykaus2013, 3932 title = {Numerical modelling of magma dynamics coupled to tectonic deformation of 3933 lithosphere and crust}, 3934 author = {Tobias Keller and Dave A May and Boris JP Kaus}, 3935 journal = {Geophysical Journal International}, 3936 volume = {195}, 3937 number = {3}, 3938 pages = {1406--1442}, 3939 year = {2013}, 3940 petsc_uses = {KSP} 3941} 3942 3943@Article{ schellartfreemanstegmanmoresimay2007, 3944 title = {Evolution and diversity of subduction zones controlled by slab width}, 3945 author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A 3946 May}, 3947 journal = {Nature}, 3948 volume = {446}, 3949 number = {7133}, 3950 pages = {308--311}, 3951 year = {2007}, 3952 petsc_uses = {KSP} 3953} 3954 3955@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012, 3956 title = {A comparison of numerical surface topography calculations in geodynamic 3957 modelling: an evaluation of the sticky air method}, 3958 author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter 3959 and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley}, 3960 journal = {Geophysical Journal International}, 3961 volume = {189}, 3962 number = {1}, 3963 pages = {38--54}, 3964 year = {2012}, 3965 petsc_uses = {KSP} 3966} 3967 3968@Article{ stegmanfreemanschellartmoresimay2006, 3969 title = {Influence of trench width on subduction hinge retreat rates in 3-D models of slab 3970 rollback}, 3971 author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A 3972 May}, 3973 journal = {Geochemistry, Geophysics, Geosystems}, 3974 volume = {7}, 3975 number = {3}, 3976 year = {2006}, 3977 petsc_uses = {KSP} 3978} 3979 3980@InProceedings{ may2014ptatin, 3981 title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics}, 3982 author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}}, 3983 booktitle = {Proceedings of {SC14}: The {International Conference for High Performance 3984 Computing, Networking, Storage and Analysis}}, 3985 organization = {ACM}, 3986 pages = {274--284}, 3987 year = {2014}, 3988 doi = {10.1109/SC.2014.28}, 3989 petsc_uses = {KSP} 3990} 3991 3992@Article{ maybrownpourhiet2015, 3993 title = {A scalable, matrix-free multigrid preconditioner for finite element 3994 discretizations of heterogeneous {Stokes} flow}, 3995 author = {David A May and Jed Brown and Laetitia {Le Pourhiet}}, 3996 journal = {Computer Methods in Applied Mechanics and Engineering}, 3997 volume = {290}, 3998 pages = {496--523}, 3999 year = {2015}, 4000 doi = {10.1016/j.cma.2015.03.014}, 4001 petsc_uses = {KSP} 4002} 4003 4004@Article{ duretzmayyamato2016, 4005 title = {A free surface capturing discretization for the staggered grid finite difference 4006 scheme}, 4007 author = {Thibault Duretz and Dave A May and Philippe Yamato}, 4008 journal = {Geophysical Journal International}, 4009 volume = {204}, 4010 number = {3}, 4011 pages = {1518--1530}, 4012 year = {2016}, 4013 petsc_uses = {KSP} 4014} 4015 4016@Article{ rhebergenwellskatzwathen2014, 4017 author = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen}, 4018 title = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics}, 4019 journal = {SIAM J. Sci. Comput.}, 4020 volume = {36}, 4021 pages = {A1960--A1977}, 4022 year = {2014}, 4023 petsc_uses = {KSP} 4024} 4025 4026@Article{ katz08a, 4027 author = {R.F. Katz and M.G. Worster}, 4028 title = {Simulation of directional solidification, thermochemical convection, and chimney 4029 formation in a {H}ele-{S}haw cell}, 4030 journal = {J. Comp. Phys.}, 4031 volume = {227}, 4032 pages = {9823-9840}, 4033 year = {2008}, 4034 doi = {10.1016/j.jcp.2008.06.039}, 4035 petsc_uses = {KSP} 4036} 4037 4038@Article{ aabg2007, 4039 author = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas}, 4040 title = {Full waveform inversion for seismic velocity and anelastic losses in 4041 heterogeneous structures}, 4042 journal = {Bulletin of Seismological Society of America}, 4043 year = {2007}, 4044 volume = {97}, 4045 pages = {1990--2008}, 4046 petsc_uses = {KSP} 4047} 4048 4049@Article{ katz2006, 4050 author = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman}, 4051 title = {The dynamics of melt and shear localization in partially molten aggregates}, 4052 journal = {Nature}, 4053 year = {2006}, 4054 volume = {442}, 4055 pages = {676--679}, 4056 month = aug, 4057 day = {10}, 4058 url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}, 4059 petsc_uses = {KSP} 4060} 4061 4062@InProceedings{ mqrs2003, 4063 author = {Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl}, 4064 year = {2003}, 4065 title = {Parallel Preconditioning for Sedimentary Basin Simulations}, 4066 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 4067 Sozopol, Bulgaria, June 4-8, 2003}, 4068 petsc_uses = {KSP} 4069} 4070 4071@InProceedings{ lichtner1, 4072 author = {Chuan Lu and Peter C. Lichtner}, 4073 year = {2005}, 4074 title = {{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in 4075 Geologic Media}, 4076 booktitle = {Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL}, 4077 lab = {LANL}, 4078 petsc_uses = {KSP} 4079} 4080 4081@Article{ hammondlichtnermills2014, 4082 title = {Evaluating the Performance of Parallel Subsurface Simulators: An Illustrative 4083 Example with {PFLOTRAN}}, 4084 author = {Glenn E. Hammond and Peter C. Lichtner and Richard Tran Mills}, 4085 journal = {Water Resources Research}, 4086 volume = {50}, 4087 number = {1}, 4088 pages = {208--228}, 4089 doi = {10.1002/2012WR013483}, 4090 year = {2014}, 4091 petsc_uses = {KSP} 4092} 4093 4094@Article{ smw2003, 4095 author = {R. Scheichl and R. Masson and J. Wendebourg}, 4096 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 4097 journal = {Computational Geosciences}, 4098 year = {2003}, 4099 volume = {7}, 4100 pages = {295--318}, 4101 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 4102 petsc_uses = {KSP} 4103} 4104 4105@Article{ kees-miller-03, 4106 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 4107 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 4108 journal = {Computational Geosciences}, 4109 year = {2003}, 4110 volume = {7}, 4111 pages = {91--114}, 4112 petsc_uses = {KSP} 4113} 4114 4115@Article{ bk2003, 4116 author = {JN Buur and T Kuehnel}, 4117 title = {Improving depth imaging by automated model updating}, 4118 journal = {The Leading Edge}, 4119 year = {2003}, 4120 volume = {22}, 4121 pages = {310-318}, 4122 petsc_uses = {KSP} 4123} 4124 4125@Article{ frederickbuffett2016, 4126 title = {Submarine groundwater discharge as a possible formation mechanism for 4127 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 4128 author = {Jennifer M. Frederick and Bruce A. Buffett}, 4129 journal = {Journal of Geophysical Research: Solid Earth}, 4130 volume = {121}, 4131 number = {3}, 4132 pages = {1383--1404}, 4133 issn = {2169-9356}, 4134 doi = {10.1002/2015JB012627}, 4135 year = {2016}, 4136 petsc_uses = {KSP} 4137} 4138 4139% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4140% LiteralHTML:<font color="#FF0000"> 4141% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 4142% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 4143% LiteralHTML:variety of these simulations.</p> 4144% LiteralHTML:</font> 4145% LiteralHTML: 4146@InProceedings{ appelbe1, 4147 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4148 year = {2003}, 4149 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 4150 computational methodology}, 4151 page = {781}, 4152 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 4153 Proceedings}, 4154 publisher = {Springer-Verlag}, 4155 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 4156 petsc_uses = {KSP} 4157} 4158 4159% LiteralHTML:<a name="katz"> 4160@InProceedings{ gd1, 4161 author = {Guillaume Dumont and Michel Kern}, 4162 title = {Parallelization of a 3D Seismic Migration Code with PETSc}, 4163 year = {1999}, 4164 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 4165 Computing}, 4166 petsc_uses = {KSP} 4167} 4168 4169% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 4170% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 4171% LiteralHTML:<font color="#FF0000"> 4172% LiteralHTML: Figures from the work of Richard Katz 4173@PhDThesis{ katzthesis, 4174 author = {R.F. Katz}, 4175 title = {The deep roots of volcanoes: models of magma dynamics with applications to 4176 subduction zones}, 4177 school = {Columbia University}, 4178 year = {2005}, 4179 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 4180 petsc_uses = {KSP} 4181} 4182 4183@InCollection{ knepleykatzsmith06, 4184 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 4185 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 4186 USA}, 4187 title = {Developing a Geodynamics Simulator with {PETSc}}, 4188 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 4189 series = {Lecture Notes in Computational Science and Engineering}, 4190 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 4191 publisher = {Springer Berlin Heidelberg}, 4192 isbn = {978-3-540-31619-0}, 4193 keyword = {Mathematics and Statistics}, 4194 pages = {413-438}, 4195 volume = {51}, 4196 doi = {10.1007/3-540-31619-1_12}, 4197 year = {2006}, 4198 petsc_uses = {KSP} 4199} 4200 4201@Article{ katz04, 4202 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 4203 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 4204 the global mid-ocean ridge system}, 4205 journal = {Geophys.\ Res.\ Letts.}, 4206 year = {2004}, 4207 volume = {31}, 4208 pages = {L15605}, 4209 petsc_uses = {KSP} 4210} 4211 4212@Article{ katz07, 4213 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 4214 Ethan Coon}, 4215 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 4216 Toolkit for Scientific Computation}}, 4217 journal = {Phys. Earth Planet. In.}, 4218 volume = {163}, 4219 pages = {52--68}, 4220 year = {2007}, 4221 petsc_uses = {KSP} 4222} 4223 4224@Article{ williams2006development, 4225 title = {{Development of a package for modeling stress in the lithosphere}}, 4226 author = {Williams, CA}, 4227 journal = {Eos Trans. AGU}, 4228 volume = {87}, 4229 pages = {36}, 4230 year = {2006}, 4231 petsc_uses = {KSP} 4232} 4233 4234@Article{ goverswortel05, 4235 author = {R. Govers and M.J.R. Wortel}, 4236 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 4237 journal = {Earth and Planetary Science Letters}, 4238 volume = {236/1-2}, 4239 pages = {505-523}, 4240 year = {2005}, 4241 petsc_uses = {KSP} 4242} 4243 4244@InProceedings{ snark2, 4245 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4246 year = {2002}, 4247 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 4248 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 4249 petsc_uses = {KSP} 4250} 4251 4252@Article{ snark1, 4253 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 4254 Tan and Feng Wang}, 4255 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 4256 journal = {Submitted to Pure and Applied Geosciences}, 4257 petsc_uses = {KSP} 4258} 4259 4260@InProceedings{ earthquake2003, 4261 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 4262 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 4263 Tiankai Tu}, 4264 year = {2003}, 4265 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 4266 booktitle = {Proceedings of SC2003}, 4267 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 4268 petsc_uses = {KSP} 4269} 4270 4271@InProceedings{ stefano12, 4272 author = {Michele De Stefano}, 4273 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 4274 booktitle = {PIERS Proceedings}, 4275 month = aug, 4276 address = {Moscow, RUSSIA}, 4277 pages = {491--495}, 4278 year = {2012}, 4279 petsc_uses = {KSP} 4280} 4281 4282%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 4283 4284% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4285% LiteralHTML: <center><img alt="" 4286% LiteralHTML: src="images/ocean.jpg"></center></p> 4287@Article{ khatiwala07, 4288 author = {Khatiwala, S.}, 4289 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 4290 journal = {Glob. Biogeochem. Cycles}, 4291 volume = {21}, 4292 doi = {10.1029/2007GB002923}, 4293 year = {2007}, 4294 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 4295} 4296 4297@Article{ dks2004, 4298 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 4299 journal = {Ocean Modelling}, 4300 year = {2004}, 4301 volume = {6(2)}, 4302 pages = {125-150}, 4303 title = {A finite-element Ocean Model: Principles and Evaluation}, 4304 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}, 4305 petsc_uses = {KSP} 4306} 4307 4308@Article{ danilov1, 4309 author = {S. Danilov and G. Kivman and J. Schroter}, 4310 year = {2004}, 4311 title = {Evaluation of an eddy-permitting finite-element ocean model in the North 4312 Atlantic}, 4313 journal = {Ocean Modelling}, 4314 petsc_uses = {KSP} 4315} 4316 4317@Article{ nerger1, 4318 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 4319 year = {2004}, 4320 title = {Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to 4321 a Finite Element Model of the North Atlantic}, 4322 journal = {Journal of marine systems}, 4323 petsc_uses = {KSP} 4324} 4325 4326@Conference{ rakowsky2003self, 4327 title = {{A self-adaptive finite element model of the atmosphere}}, 4328 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 4329 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 4330 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 4331 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 4332 pages = {279}, 4333 isbn = {981238376X}, 4334 year = {2003}, 4335 organization = {World Scientific Pub Co}, 4336 petsc_uses = {KSP} 4337} 4338 4339@Article{ lauter3, 4340 author = {M. Lauter}, 4341 year = {2004}, 4342 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4343 AtmosphArenmodell}, 4344 journal = {Berichte zur Polar- und Meeresforschung}, 4345 petsc_uses = {KSP} 4346} 4347 4348@Article{ lauter2, 4349 author = {M. Lauter and D. Handorf and K. Dethloff}, 4350 year = {2004}, 4351 title = {Unsteady analytical solutions of the spherical shallow water equations}, 4352 journal = {Journal of computational physics}, 4353 petsc_uses = {KSP} 4354} 4355 4356@PhDThesis{ lauter1, 4357 author = {M. Lauter}, 4358 year = {2004}, 4359 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4360 AtmosphArenmodell}, 4361 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 4362 petsc_uses = {KSP} 4363} 4364 4365@Article{ frickenhaus1, 4366 author = {S. Frickenhaus and W. Hiller and M. Best}, 4367 year = {2005}, 4368 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 4369 parallel numerical atmosphere and ocean models}, 4370 journal = {Ocean Modelling}, 4371 volume = {10}, 4372 pages = {185--191}, 4373 petsc_uses = {KSP} 4374} 4375 4376@Article{ 0266-5611-24-3-034015, 4377 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 4378 title = {A Newton-CG method for large-scale three-dimensional elastic full-waveform 4379 seismic inversion}, 4380 journal = {Inverse Problems}, 4381 volume = {24}, 4382 number = {3}, 4383 pages = {034015 (26pp)}, 4384 url = {http://stacks.iop.org/0266-5611/24/034015}, 4385 year = {2008}, 4386 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 4387 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 4388 iterations with inner conjugate gradient linear iterations, globalized by an 4389 Armijo backtracking line search, solved on a sequence of finer grids and higher 4390 frequencies to remain in the vicinity of the global optimum, inexactly terminated 4391 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 4392 variation operator to capture sharp interfaces, finely discretized by finite 4393 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 4394 implemented in matrix-free fashion with adjoint-based computation of reduced 4395 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 4396 waveform storage, and partitioned spatially across processors to parallelize the 4397 solutions of the forward and adjoint wave equations and the evaluation of 4398 gradient-like information. Several numerical examples demonstrate the grid 4399 independence of linear and nonlinear iterations, the effectiveness of the 4400 preconditioner, the ability to solve inverse problems with up to 17 million 4401 inversion parameters on up to 2048 processors, the effectiveness of multiscale 4402 continuation in keeping iterates in the basin of attraction of the global minimum, 4403 and the ability to fit the observational data while reconstructing the model with 4404 reasonable resolution and capturing sharp interfaces.}, 4405 petsc_uses = {KSP} 4406} 4407 4408% LiteralHTML: 4409% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 4410% LiteralHTML: 4411% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4412% LiteralHTML:<font color="#FF0000"> 4413% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 4414% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 4415% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 4416% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 4417% LiteralHTML:for a variety of these simulations.</p> 4418% LiteralHTML:</font> 4419% LiteralHTML: 4420@Article{ mills2009modeling, 4421 title = {Modeling subsurface reactive flows using leadership-class computing}, 4422 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4423 Mahinthakumar, G.K. and Smith, B.F.}, 4424 journal = {Journal of Physics: Conference Series}, 4425 volume = {180}, 4426 pages = {012062}, 4427 year = {2009}, 4428 publisher = {IOP Publishing}, 4429 petsc_uses = {KSP} 4430} 4431 4432@Conference{ mills2007simulating, 4433 title = {{Simulating subsurface flow and transport on ultrascale computers using 4434 PFLOTRAN}}, 4435 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 4436 booktitle = {Journal of Physics: Conference Series}, 4437 volume = {78}, 4438 pages = {012051}, 4439 year = {2007}, 4440 organization = {IOP Publishing}, 4441 petsc_uses = {KSP} 4442} 4443 4444@InProceedings{ mills2009, 4445 title = {Modeling subsurface reactive flows using leadership-class computing}, 4446 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4447 Mahinthakmuar, G. and Smith, B.}, 4448 booktitle = {Journal of Physics: Conference Series}, 4449 volume = {180}, 4450 pages = {102062}, 4451 year = {2009}, 4452 organization = {IOP Publishing}, 4453 petsc_uses = {KSP} 4454} 4455 4456@Article{ guo2013parallel, 4457 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 4458 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 4459 }, 4460 journal = {Advances in Water Resources }, 4461 volume = {53}, 4462 number = {0}, 4463 pages = {101 - 108}, 4464 year = {2013}, 4465 note = {}, 4466 issn = {0309-1708}, 4467 doi = {10.1016/j.advwatres.2012.10.010}, 4468 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 4469 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 4470 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 4471 preconditioner}, 4472 petsc_uses = {KSP} 4473} 4474 4475@Unpublished{ stomp, 4476 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 4477 url = {http://stomp.pnl.gov/}, 4478 petsc_uses = {KSP} 4479} 4480 4481@InProceedings{ htfc2003, 4482 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 4483 title = {Methods and Experiences For Parallelizing Flood Models}, 4484 year = {2003}, 4485 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 4486 European PVM/MPI User's Group Meeting}, 4487 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 4488 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 4489 petsc_uses = {KSP} 4490} 4491 4492@InProceedings{ hulchy-tran-astalos-fmsip, 4493 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 4494 D.Froehlich}, 4495 title = {Flood Modeling System and Its Parallelization}, 4496 year = {2002}, 4497 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 4498 Engineering}, 4499 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 4500 petsc_uses = {KSP} 4501} 4502 4503@InProceedings{ gy1, 4504 author = {J. P. Gwo and G. T. Yeh}, 4505 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 4506 Transport at Watershed Scale}, 4507 year = {2004}, 4508 booktitle = {The International Conference on Computational Methods}, 4509 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 4510 petsc_uses = {KSP} 4511} 4512 4513@Conference{ cheng2009efficient, 4514 title = {{An efficient parallel method for large-scale groundwater flow equation based on 4515 PETSc}}, 4516 author = {Cheng, T. and Ji, X. and Wang, Q.}, 4517 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 4518 Conference on}, 4519 pages = {190--193}, 4520 organization = {IEEE}, 4521 petsc_uses = {KSP} 4522} 4523 4524@Unpublished{ sfrsm, 4525 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 4526 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 4527 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 4528 its linear solves}, 4529 petsc_uses = {KSP} 4530} 4531 4532% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4533@InProceedings{ bart_omar:sc05, 4534 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 4535 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 4536 title = {Dynamic data driven inversion for terascale simulations: real-time 4537 indentification of airborne contaminants}, 4538 booktitle = {Proceedings of SC2005}, 4539 organization = {IEEE/ACM}, 4540 address = {Seattle, WA}, 4541 year = {2005}, 4542 month = nov, 4543 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 4544 lab = {SNL}, 4545 petsc_uses = {KSP} 4546} 4547 4548@InProceedings{ anton-krassimir-lscc, 4549 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 4550 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 4551 Simulations}, 4552 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 4553 volume = {2907}, 4554 year = {2003}, 4555 publisher = {Springer-Verlag}, 4556 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 4557 petsc_uses = {KSP} 4558} 4559 4560@InProceedings{ aa2001, 4561 author = {Anton Antonov}, 4562 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 4563 year = {2001}, 4564 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 4565 Sozopol, Bulgaria}, 4566 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 4567 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 4568 petsc_uses = {KSP} 4569} 4570 4571% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4572@Article{ grassley-simmons-kercher-00, 4573 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 4574 year = {2000}, 4575 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 4576 reactive transport models}, 4577 journal = {Applied Geochemistry}, 4578 volume = {17}, 4579 pages = {699--708}, 4580 lab = {LLNL} 4581} 4582 4583@Article{ glassey-nitao-03, 4584 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 4585 and Carl I. Steefel and James R. Kercher}, 4586 year = {2003}, 4587 title = {The impact of climate change on vadose zone pore waters and its implication for 4588 long-term monitoring}, 4589 journal = {Computers and Geosciences}, 4590 volume = {29}, 4591 pages = {399-411}, 4592 lab = {LLNL}, 4593 petsc_uses = {KSP} 4594} 4595 4596@Article{ steefel-depaolo-lichtner-05, 4597 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 4598 year = {2005}, 4599 title = {Reactive transport modeling: An essential tool and a new research approach for 4600 the Earth sciences}, 4601 journal = {Earth and Planetary Science Letters}, 4602 lab = {LLNL,LANL}, 4603 petsc_uses = {KSP} 4604} 4605 4606% LiteralHTML:<a name="scalinglarge"> 4607% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4608% LiteralHTML: <center><img alt="" 4609% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 4610% LiteralHTML:<font color="#FF0000"> 4611% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 4612@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 4613 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 4614 Strategies for Large-Scale Numerical Simulations}, 4615 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 4616 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 4617 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 4618 Large-Scale Systems (scalA)}, 4619 pages = {65-72}, 4620 doi = {10.1109/ScalA.2018.00012}, 4621 month = nov, 4622 year = {2018}, 4623 petsc_uses = {KSP} 4624} 4625 4626@Article{ km2004, 4627 author = {A. Keese and H. G. Matthies}, 4628 journal = {Computers and Structures}, 4629 year = {2005}, 4630 volume = {83}, 4631 pages = {1033--1047}, 4632 title = {Hierarchical parallelisation for the solution of stochastic finite element 4633 equations}, 4634 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}, 4635 petsc_uses = {KSP} 4636} 4637 4638@Unpublished{ hvl2002, 4639 title = {Numerical Modeling of NAPL Source Zone Treatment}, 4640 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 4641 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 4642 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 4643 year = {2002}, 4644 lab = {LANL}, 4645 petsc_uses = {KSP} 4646} 4647 4648@PhDThesis{ hammond2003, 4649 author = {Glenn E. Hammond}, 4650 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 4651 Transport on Supercomputers}, 4652 school = {University of Illinois at Urbana-Champaign}, 4653 year = {2003}, 4654 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 4655 petsc_uses = {KSP} 4656} 4657 4658@Unpublished{ uk, 4659 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 4660 Scale Environmental Flows and Transport Processes}, 4661 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 4662 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 4663 buildings and in Green Bay. Used PETSc for its linear solvers}, 4664 year = {1999}, 4665 petsc_uses = {KSP} 4666} 4667 4668@InProceedings{ hammond2002, 4669 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 4670 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 4671 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 4672 year = {2002}, 4673 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 4674 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 4675 Resources, Delft, The Netherlands.}, 4676 lab = {LANL}, 4677 petsc_uses = {KSP} 4678} 4679 4680@TechReport{ steefel1, 4681 author = {C. I. Steefel}, 4682 title = {Software for modeling multicomponent, multidimensional reactive transport}, 4683 year = {2001}, 4684 institution = {Lawrence Livermore National Laboratory}, 4685 number = {UCRL-MA-143182}, 4686 lab = {LLNL}, 4687 petsc_uses = {KSP} 4688} 4689 4690@Article{ steefel2, 4691 author = {C. I. Steefel and A. C. Lasaga}, 4692 title = {A coupled model for transport of multiple chemical-species and kinetic 4693 precipitation dissolution reactions with application to reactive flow in 4694 single-phase hydrothermal systems}, 4695 journal = {Americal Journal of Science}, 4696 year = {1994}, 4697 pages = {529-592}, 4698 volume = {294}, 4699 number = {5}, 4700 petsc_uses = {KSP} 4701} 4702 4703@TechReport{ steefel3, 4704 author = {C. I. Steefel and S. B. Yabusaki}, 4705 title = {OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: 4706 User's manual and programmer's guide}, 4707 year = {1996}, 4708 institution = {Pacific Northwest National Laboratory}, 4709 number = {PNNL-11166}, 4710 lab = {PNNL}, 4711 petsc_uses = {KSP} 4712} 4713 4714@Article{ 2005hvl, 4715 author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner}, 4716 title = {Application of {J}acobian-free {N}ewton-{K}rylov with physics-based 4717 preconditioning to biogeochemical transport}, 4718 journal = {Advances in Water Resources}, 4719 year = {2005}, 4720 pages = {359--376}, 4721 volume = {28}, 4722 url = { 4723 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}, 4724 lab = {LANL}, 4725 petsc_uses = {KSP} 4726} 4727 4728@Article{ wang-zabar-05, 4729 author = {J Wang and N Zabaras}, 4730 journal = {Int. J. Heat and Mass Transfer}, 4731 title = {A Markov random field model of contamination source identification in porous 4732 media flow}, 4733 year = {2005}, 4734 petsc_uses = {KSP} 4735} 4736 4737@InBook{ kp1, 4738 author = {Jong G. Kim and Hyoung W. Park}, 4739 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 4740 Media}, 4741 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 4742 title = {Lecture Notes in Computer Science}, 4743 publisher = {Springer-Verlag}, 4744 volume = {3044}, 4745 year = {2004}, 4746 petsc_uses = {KSP} 4747} 4748 4749@Article{ 2001agusm...h32a06k, 4750 author = {{Kim}, J.~G. and {Kim}, J.}, 4751 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 4752 journal = {AGU Spring Meeting Abstracts}, 4753 year = {2001}, 4754 pages = {32-+}, 4755 petsc_uses = {KSP} 4756} 4757 4758@Article{ lzb2005, 4759 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 4760 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 4761 journal = {Journal of Hydraulic Engineering}, 4762 year = {2005}, 4763 volume = {131}, 4764 number = {4}, 4765 pages = {247--258}, 4766 petsc_uses = {KSP} 4767} 4768 4769@Article{ rao2005, 4770 author = {Prasada Rao}, 4771 title = {A parallel RMA2 model for simulating large-scale free surface flows}, 4772 journal = {Environmental Modelling and Software}, 4773 year = {2005}, 4774 pages = {47--53}, 4775 petsc_uses = {KSP} 4776} 4777 4778@InProceedings{ pr1, 4779 author = {Prasada Rao}, 4780 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 4781 Hydrodynamic Flows}, 4782 year = {2003}, 4783 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 4784 Conference}, 4785 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 4786 petsc_uses = {KSP} 4787} 4788 4789@InProceedings{ lichtner2004, 4790 author = {Peter C. Lichtner and Andrew Wolfsberg}, 4791 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 4792 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 4793 Challenge Supercomputing Problem}, 4794 year = {2004}, 4795 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 4796 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 4797 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 4798 lab = {LANL}, 4799 petsc_uses = {KSP} 4800} 4801 4802% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4803@Article{ aba01:petsc-app, 4804 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 4805 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 4806 journal = {Int. J. High Performance Computing Applications}, 4807 year = {2001}, 4808 volume = {15}, 4809 number = {1}, 4810 pages = {13--21}, 4811 petsc_uses = {KSP} 4812} 4813 4814@PhDThesis{ tjb200, 4815 author = {Thomas James Byer}, 4816 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 4817 Facilities}, 4818 school = {Stanford}, 4819 year = {2000}, 4820 petsc_uses = {KSP} 4821} 4822 4823@InProceedings{ puchyr2006, 4824 author = {Peter J. Puchyr}, 4825 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 4826 Win32 Cluster}, 4827 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 4828 note = {Paper number CIPC2006-207}, 4829 year = {2006}, 4830 petsc_uses = {KSP} 4831} 4832 4833@InProceedings{ texas98, 4834 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 4835 and G. A. Pope}, 4836 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 4837 Simulation}, 4838 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 4839 Symposium}, 4840 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 4841 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 4842 year = {1998}, 4843 petsc_uses = {KSP} 4844} 4845 4846% LiteralHTML: 4847% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 4848% LiteralHTML: 4849@Article{ farrellmitchellscottwechsung2021, 4850 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 4851 stationary incompressible {Navier-Stokes} equations}, 4852 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 4853 Wechsung}, 4854 journal = {The SMAI journal of computational mathematics}, 4855 volume = {7}, 4856 pages = {75--96}, 4857 year = {2021}, 4858 petsc_uses = {KSP} 4859} 4860 4861@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 4862 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 4863 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 4864 P MacLachlan and Ray S Tuminaro}, 4865 journal = {SIAM Journal on Scientific Computing}, 4866 number = {0}, 4867 pages = {S70--S91}, 4868 year = {2021}, 4869 petsc_uses = {KSP} 4870} 4871 4872@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 4873 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 4874 hyperelasticity}, 4875 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 4876 Oyar\'ua and Ricardo Ruiz-Baier}, 4877 journal = {Computer Methods in Applied Mechanics and Engineering}, 4878 volume = {374}, 4879 pages = {113562}, 4880 issn = {0045-7825}, 4881 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 4882 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 4883 year = {2021}, 4884 petsc_uses = {KSP} 4885} 4886 4887@Article{ farrellmitchellwechsung2018, 4888 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 4889 {Navier-Stokes} equations at high {Reynolds} number}, 4890 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 4891 journal = {SIAM Journal on Scientific Computing}, 4892 volume = {41}, 4893 number = {5}, 4894 eprint = {1810.03315}, 4895 pages = {A3073-A3096}, 4896 year = {2019}, 4897 petsc_uses = {KSP} 4898} 4899 4900@Article{ hevuikklaij2017, 4901 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 4902 discretized by a finite volume method}, 4903 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 4904 journal = {Journal of Numerical Mathematics}, 4905 volume = {25}, 4906 number = {2}, 4907 pages = {89--105}, 4908 year = {2017}, 4909 petsc_uses = {KSP} 4910} 4911 4912@InProceedings{ zou2015newton, 4913 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 4914 appearance/disappearance}, 4915 author = {Zou, L and Zhao, H and Zhang, H}, 4916 booktitle = {ANS 2015 Annual Meeting, June}, 4917 volume = {7}, 4918 number = {11}, 4919 year = {2015}, 4920 petsc_uses = {KSP} 4921} 4922 4923@Article{ guermond2009nonlinear, 4924 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 4925 Fourier/finite element technique and an interior penalty method}, 4926 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 4927 journal = {Journal of computational physics}, 4928 volume = {228}, 4929 number = {8}, 4930 pages = {2739--2757}, 4931 year = {2009}, 4932 publisher = {Elsevier}, 4933 petsc_uses = {KSP} 4934} 4935 4936@Article{ erzincanlisahin2015, 4937 title = {The numerical simulation of the wing kinematics effects on near wake topology and 4938 aerodynamic performance in hovering Drosophila flight}, 4939 author = {Belkis Erzincanli and Mehmet Sahin}, 4940 journal = {Computers \& Fluids}, 4941 volume = {122}, 4942 pages = {90--110}, 4943 year = {2015}, 4944 publisher = {Elsevier}, 4945 petsc_uses = {KSP} 4946} 4947 4948@Article{ ekensahin2015, 4949 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 4950 structure interaction problems}, 4951 author = {Ali Eken and Mehmet Sahin}, 4952 journal = {International Journal for Numerical Methods in Fluids}, 4953 year = {2015}, 4954 publisher = {Wiley Online Library}, 4955 petsc_uses = {KSP} 4956} 4957 4958@Article{ hwangsucai2015, 4959 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 4960 for transonic full potential equation}, 4961 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 4962 journal = {Computers \& Fluids}, 4963 volume = {110}, 4964 number = {30}, 4965 pages = {96--107}, 4966 year = {2015}, 4967 doi = {10.1016/j.compfluid.2014.04.005}, 4968 petsc_uses = {KSP} 4969} 4970 4971@Article{ yanghwangcai2016, 4972 title = {Nonlinear Preconditioning Techniques for Full-Space Lagrange--Newton Solution of 4973 PDE-Constrained Optimization Problems}, 4974 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 4975 journal = {SIAM Journal on Scientific Computing}, 4976 volume = {38}, 4977 number = {5}, 4978 pages = {A2756--A2778}, 4979 year = {2016}, 4980 petsc_uses = {KSP} 4981} 4982 4983@Article{ khanaidun2011, 4984 author = {Irfan Khan and Cyrus K. Aidun}, 4985 title = {Direct numerical simulation of saturated deformable porous media using parallel 4986 hybrid Lattice-Boltzmann and finite element method}, 4987 journal = {Int. J. Numer. Meth. Eng.}, 4988 volume = {86}, 4989 pages = {1379--1395}, 4990 year = {2011}, 4991 petsc_uses = {KSP} 4992} 4993 4994@Article{ khanaidun2014, 4995 author = {Irfan Khan and Cyrus K. Aidun}, 4996 title = {Modeling the deformation of saturate porous media using direct numerical 4997 simulation}, 4998 journal = {Int. J. Multiphase Flow}, 4999 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 5000 year = {2014}, 5001 petsc_uses = {KSP} 5002} 5003 5004@Article{ mofidi2014simulations, 5005 author = {A. Mofidi and P. M. Carrica}, 5006 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 5007 and Propeller}, 5008 journal = {Computers and Fluids}, 5009 pages = {191--203}, 5010 year = {2014}, 5011 petsc_uses = {KSP} 5012} 5013 5014@Article{ paik2014fluidstructure, 5015 author = {K. Paik and P. M. Carrica}, 5016 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 5017 Surface in a Rolling Tank}, 5018 journal = {Ocean Engineering}, 5019 pages = {201--212}, 5020 year = {2014}, 5021 petsc_uses = {KSP} 5022} 5023 5024@Article{ castro2013bubble, 5025 author = {A. M. Castro and P. M. Carrica}, 5026 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 5027 evaluation and numerical issues}, 5028 journal = {International Journal of Multiphase Flow 57}, 5029 pages = {131--150}, 5030 year = {2013}, 5031 petsc_uses = {KSP} 5032} 5033 5034@Article{ carrica2013turn, 5035 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 5036 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 5037 Dynamic Overset Grids}, 5038 journal = {Journal of Marine Science and Technology}, 5039 pages = {166--181}, 5040 year = {2013}, 5041 petsc_uses = {KSP} 5042} 5043 5044@Article{ castro2013eulerian, 5045 author = {A. M. Castro and P. M. Carrica}, 5046 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 5047 {Athena} {R}/V,}, 5048 journal = {International Shipbuilding Progress}, 5049 pages = {403--433}, 5050 year = {2013}, 5051 petsc_uses = {KSP} 5052} 5053 5054@Article{ chase2013overset, 5055 author = {N. Chase and T. Michael and P. M. Carrica}, 5056 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 5057 {Maneuvering} {Conditions}}, 5058 journal = {International Shipbuilding Progress}, 5059 pages = {171--205}, 5060 year = {2013}, 5061 petsc_uses = {KSP} 5062} 5063 5064@Article{ sadathosseini2013wu, 5065 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 5066 Stern}, 5067 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 5068 Free Surge Conditions in Short and Long Head Waves}, 5069 journal = {Ocean Engineering}, 5070 volume = {59}, 5071 pages = {240--273}, 5072 year = {2013}, 5073 petsc_uses = {KSP} 5074} 5075 5076@Article{ chase2013cfd, 5077 author = {N. Chase and P. M. Carrica}, 5078 title = {CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a 5079 Submarine}, 5080 journal = {Ocean Engineering}, 5081 pages = {68--80}, 5082 year = {2013}, 5083 petsc_uses = {KSP} 5084} 5085 5086@Article{ carrica2012cfd, 5087 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 5088 title = {CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 5089 of Moving Rudders and Rotating Propellers}, 5090 journal = {Computers and Fluids 53}, 5091 pages = {117--132}, 5092 year = {2012}, 5093 petsc_uses = {KSP} 5094} 5095 5096@Article{ sakamoto2012urans, 5097 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5098 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 5099 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 5100 publisher = {Journal of Marine Science and Technology}, 5101 pages = {422--445}, 5102 year = {2012}, 5103 petsc_uses = {KSP} 5104} 5105 5106@Article{ sakamoto2012uransb, 5107 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5108 title = {URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 5109 Analysis and Validation of Local Flow Characteristics}, 5110 journal = {Journal of Marine Science and Technology}, 5111 pages = {446--468}, 5112 year = {2012}, 5113 petsc_uses = {KSP} 5114} 5115 5116@Article{ li2012dynamic, 5117 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 5118 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 5119 journal = {Renewable Energy}, 5120 pages = {285--298}, 5121 year = {2012}, 5122 petsc_uses = {KSP} 5123} 5124 5125@Article{ huang2012a, 5126 author = {J. Huang and P. M. Carrica and F. Stern}, 5127 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 5128 journal = {International Journal for Numerical Methods in Fluids}, 5129 pages = {160--180}, 5130 year = {2012}, 5131 petsc_uses = {KSP} 5132} 5133 5134@Article{ huang2012b, 5135 author = {J. Huang and P. M. Carrica and F. Stern}, 5136 title = {A geometry-based level set method for curvilinear overset grids with application 5137 to ship hydrodynamics}, 5138 journal = {International Journal for Numerical Methods in Fluids}, 5139 pages = {494--521}, 5140 year = {2012}, 5141 petsc_uses = {KSP} 5142} 5143 5144@Article{ carrica2011computations, 5145 author = {P. M. Carrica and H. Fu and F. Stern}, 5146 title = {Computations of self-propulsion free to sink and trim and of motions in head 5147 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 5148 journal = {Applied Ocean Research}, 5149 pages = {309--320}, 5150 year = {2011}, 5151 petsc_uses = {KSP} 5152} 5153 5154@Article{ bhushan2011scalability, 5155 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 5156 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 5157 Using {CFDShip}-Iowa}, 5158 journal = {International Journal of High Performance Computing Applications}, 5159 pages = {466--487}, 5160 year = {2011}, 5161 petsc_uses = {KSP} 5162} 5163 5164@Article{ castro2011full, 5165 author = {A. M. Castro and P. M. Carrica and F. Stern}, 5166 title = {Full scale self-propulsion computations using discretized propeller for the 5167 {KRISO} container ship {KCS}}, 5168 journal = {Computers and Fluids}, 5169 pages = {35--47}, 5170 year = {2011}, 5171 petsc_uses = {KSP} 5172} 5173 5174@Article{ kandasamy2011multifidelity, 5175 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5176 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5177 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran 5178 for Low Wake}, 5179 journal = {Journal of Marine Science and Technology}, 5180 pages = {143--156}, 5181 year = {2011}, 5182 petsc_uses = {KSP} 5183} 5184 5185@Article{ kandasamy2011cfd, 5186 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5187 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5188 title = {CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran}, 5189 journal = {Journal of Marine Science and Technology}, 5190 pages = {157--167}, 5191 year = {2011}, 5192 petsc_uses = {KSP} 5193} 5194 5195@Article{ sadathosseini2011cfd, 5196 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 5197 and S. Yamamura and A. Mastuda}, 5198 title = {CFD System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 5199 Periodic Motion and Broaching}, 5200 journal = {Ocean Engineering}, 5201 pages = {88--110}, 5202 year = {2011}, 5203 petsc_uses = {KSP} 5204} 5205 5206@Article{ mosaviraad2010development, 5207 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 5208 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 5209 with Comparison to Regular Wave and Transient Wave Group Procedures Using 5210 {URANS}}, 5211 journal = {Ocean Engineering}, 5212 pages = {653--666}, 5213 year = {2010}, 5214 petsc_uses = {KSP} 5215} 5216 5217@Article{ carrica2010largescale, 5218 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5219 Stern}, 5220 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5221 Heave Problems for a Surface Combatant}, 5222 journal = {Computers and Fluids}, 5223 pages = {1095--1111}, 5224 year = {2010}, 5225 petsc_uses = {KSP} 5226} 5227 5228@Article{ carrica2010selfpropulsion, 5229 author = {P. M. Carrica and A. M. Castro and F. Stern}, 5230 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 5231 with Dynamic Overset Grids}, 5232 journal = {Journal of Marine Science and Technology}, 5233 pages = {316--330}, 5234 year = {2010}, 5235 petsc_uses = {KSP} 5236} 5237 5238@Article{ ismail2010evaluation, 5239 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 5240 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 5241 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 5242 journal = {International Journal of Numerical Methods in Fluids}, 5243 pages = {850--886}, 5244 year = {2010}, 5245 petsc_uses = {KSP} 5246} 5247 5248@Article{ kandasamy2010integral, 5249 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 5250 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 5251 journal = {Journal of Fluids Engineering}, 5252 pages = {101103}, 5253 year = {2010}, 5254 petsc_uses = {KSP} 5255} 5256 5257@Article{ kirk:2014de, 5258 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 5259 title = {{Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) 5260 stabilized finite element flow solver}}, 5261 journal = {Computers {\&} Fluids}, 5262 year = {2014}, 5263 volume = {92}, 5264 number = {0}, 5265 pages = {281--292}, 5266 month = mar, 5267 petsc_uses = {KSP} 5268} 5269 5270@Article{ carracciuolo20111382, 5271 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 5272 in high performance computing environment}, 5273 journal = {Journal of Non-Newtonian Fluid Mechanics }, 5274 volume = {166}, 5275 number = {23--24}, 5276 pages = {1382--1395}, 5277 year = {2011}, 5278 issn = {0377-0257}, 5279 doi = {10.1016/j.jnnfm.2011.08.014}, 5280 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 5281 Maffettone and A. Murli}, 5282 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 5283 method, High performance computing}, 5284 petsc_uses = {KSP} 5285} 5286 5287@Article{ bungartzgatzhammerliebmehlneckel11, 5288 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 5289 Miriam and Neckel, Tobias}, 5290 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 5291 journal = {Computational Mechanics}, 5292 volume = {48}, 5293 number = {3}, 5294 pages = {365-376}, 5295 year = {2011}, 5296 issn = {0178-7675}, 5297 doi = {10.1007/s00466-011-0626-1}, 5298 publisher = {Springer-Verlag}, 5299 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 5300 Thermohydraulics; Two-phase flow}, 5301 language = {English}, 5302 petsc_uses = {KSP} 5303} 5304 5305@Article{ bpr:cfl, 5306 author = {H.~M. B{\"u}cker and B. Pollul and A. Rasch}, 5307 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 5308 Equations}}, 5309 journal = {International Journal for Numerical Methods in Fluids}, 5310 year = {2009}, 5311 volume = {59}, 5312 number = {1}, 5313 pages = {1--18}, 5314 doi = {10.1002/fld.1798}, 5315 petsc_uses = {KSP} 5316} 5317 5318@InBook{ bonfiglioli_campobasso_carpentieri_2010, 5319 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 5320 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 5321 preconditioned newton-krylov solver}, 5322 publisher = {Curran Associates}, 5323 year = {2010}, 5324 url = {http://www.proceedings.com/05932.html}, 5325 petsc_uses = {KSP} 5326} 5327 5328@Article{ bonfiglioli_rans_2005, 5329 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 5330 Bernardo}, 5331 title = {RANS simulations of a junction flow}, 5332 journal = {International Journal of Computational Fluid Dynamics}, 5333 volume = {19}, 5334 number = {2}, 5335 pages = {179-189}, 5336 year = {2005}, 5337 doi = {10.1080/10618560410001729126}, 5338 petsc_uses = {KSP} 5339} 5340 5341@InCollection{ bonfiglioli__carpentieri_rans_2008, 5342 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 5343 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 5344 Italy}, 5345 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 5346 Equations Using Fluctuation Splitting Schemes}, 5347 booktitle = {Numerical Mathematics and Advanced Applications}, 5348 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 5349 publisher = {Springer Berlin Heidelberg}, 5350 isbn = {978-3-540-69777-0}, 5351 pages = {151-158}, 5352 doi = {10.1007/978-3-540-69777-0_17}, 5353 year = {2008}, 5354 petsc_uses = {KSP} 5355} 5356 5357@InCollection{ bonfiglioli__carpentieri_ens_2007, 5358 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 5359 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 5360 Italy}, 5361 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 5362 Problems on Unstructured Grids}, 5363 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 5364 series = {Lecture Notes in Computer Science}, 5365 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 5366 publisher = {Springer Berlin / Heidelberg}, 5367 isbn = {978-3-540-75754-2}, 5368 pages = {676-685}, 5369 volume = {4699}, 5370 doi = {10.1007/978-3-540-75755-9_83}, 5371 year = {2007}, 5372 petsc_uses = {KSP} 5373} 5374 5375@Article{ terrelscottknepleykirby08, 5376 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 5377 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 5378 journal = {BIT}, 5379 volume = {48}, 5380 number = {2}, 5381 year = {2008}, 5382 petsc_uses = {KSP} 5383} 5384 5385@Article{ martamadermartinsweidealonso07, 5386 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 5387 J. Alonso}, 5388 title = {A methodology for the development of discrete adjoint solvers using automatic 5389 differentiation tools}, 5390 journal = {Computational Fluid Dyanmics}, 5391 volume = {21}, 5392 pages = {307--327}, 5393 year = {2007}, 5394 petsc_uses = {KSP} 5395} 5396 5397@TechReport{ avb2008, 5398 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 5399 title = {Variational Space-time (Dis)continuous {G}alerkin Method for Linear Free Surface 5400 Waves}, 5401 year = {2008}, 5402 institution = {University of Twente, the Netherlands}, 5403 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 5404 petsc_uses = {KSP} 5405} 5406 5407@InProceedings{ bdsm2005, 5408 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal}, 5409 title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids}, 5410 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit}, 5411 year = {2005}, 5412 url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}, 5413 petsc_uses = {KSP} 5414} 5415 5416@InProceedings{ ms2006, 5417 author = {S. Muller and Y. Stiriba}, 5418 title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR 5419 STEADY COMPRESSIBLE FLOWS}, 5420 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006}, 5421 year = {2006}, 5422 url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}, 5423 petsc_uses = {KSP} 5424} 5425 5426@Article{ araujoteixeiracunhagroth08, 5427 author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth}, 5428 title = {Parallel three-dimensional simulation of the injection molding process}, 5429 journal = {International Journal for Numerical Methods in Fluids}, 5430 year = {2008}, 5431 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 5432 petsc_uses = {KSP} 5433} 5434 5435@PhDThesis{ a2008, 5436 author = {A. Cubero}, 5437 title = {a parallel coupled algorithm for collocated grids and its application to Large 5438 Eddy Simulation of a turbulent wake}, 5439 school = {University of Zaragoza (Spain)}, 5440 year = {2008}, 5441 petsc_uses = {KSP} 5442} 5443 5444@Article{ afa2007, 5445 author = {A. Cubero and N. Fueyo}, 5446 title = {A Compact Momentum Interpolation Method for unsteady flows and relaxation}, 5447 journal = {Numerical Heat Transfer, part B-Fundamentals}, 5448 volume = {56}, 5449 number = {6}, 5450 pages = {507--529}, 5451 year = {2007}, 5452 url = {http://www.informaworld.com/smpp/content~content=a782025305~db=all~order=page}, 5453 petsc_uses = {KSP} 5454} 5455 5456@TechReport{ af2007, 5457 title = {Preconditioning based on a partially implicit implementation of Momentum 5458 Interpolation for coupled solvers}, 5459 institution = {Fluid Mechanics Group of the University of Zaragoza (Spain)}, 5460 year = {2007}, 5461 author = {A. Cubero and N. Fueyo}, 5462 petsc_uses = {KSP} 5463} 5464 5465@InCollection{ dwight2004, 5466 author = {Richard Dwight}, 5467 title = {Robust Mesh Deformation using the Linear Elasticity Equations}, 5468 booktitle = {Computational Fluid Dynamics 2006}, 5469 editor = {H. Deconinck and E. Dick}, 5470 publisher = {Springer}, 5471 year = {2006}, 5472 url = {http://www.maths.man.ac.uk/\~{ 5473 }rdwight/pub/rdwight-ICCFD4-LinElastDeformation-2006.pdf}, 5474 petsc_uses = {KSP} 5475} 5476 5477@InProceedings{ dwight2006, 5478 author = {Richard Dwight and Joel Brezillon}, 5479 title = {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based 5480 Optimization}, 5481 booktitle = {Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. 5482 AIAA-2006-0690}, 5483 year = {2006}, 5484 url = {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-AIAAReno-ApproxAdjoint.pdf}, 5485 petsc_uses = {KSP} 5486} 5487 5488@PhDThesis{ dwight2006a, 5489 author = {Richard Dwight}, 5490 title = {Efficiency Improvements of {RANS}-Based Analysis and Optimization using Implicit 5491 and Adjoint Methods on Unstructured Grids}, 5492 school = {School of Mathematics, University of Manchester}, 5493 year = {2006}, 5494 url = {http://www.maths.man.ac.uk/\~{ 5495 }rdwight/pub/rdwight-PhDThesis-ImplicitAndAdjoint.pdf}, 5496 petsc_uses = {KSP} 5497} 5498 5499@InProceedings{ lhdfrh, 5500 author = {M. Lauter and D. Handorf and K. Dethloff and S. Frickenhaus and N. Rakowsky and 5501 W. Hiller}, 5502 title = {An adaptive Lagrange-Galerkin shallow-water model on the sphere}, 5503 booktitle = {Workshop Proceedings Current Development in Shallow Water Models on the Sphere 5504 March, 10-14, 2003, Munich University of Technology, German}, 5505 year = {2003}, 5506 petsc_uses = {KSP} 5507} 5508 5509@InProceedings{ brios-ying-2002, 5510 author = {George Biros and Lexing Ying and Denis Zorin}, 5511 title = {The Embedded Boundary Integral Method (EBI) for the Incompressible 5512 {Navier-Stokes} equations}, 5513 booktitle = {IABEM 2002, International Association for Boundary Element Methods, UT Austin}, 5514 year = {2002}, 5515 petsc_uses = {KSP} 5516} 5517 5518@InProceedings{ mohsen-straatman-ins, 5519 author = {S.A. Mohsen Karimian and Anthony G. Straatman}, 5520 title = {Benchmarking of a {3D}, unstructured, finite volume code for incompressible 5521 {Navier-Stokes} equation on a cluster of distributed-memory computers}, 5522 booktitle = {Proceedings of the 19th International Symposium on High Performance Computing 5523 Systems and Applications}, 5524 pages = {11--16}, 5525 year = {2005}, 5526 url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046}, 5527 petsc_uses = {KSP} 5528} 5529 5530@TechReport{ bonglioli-icnmfd98, 5531 title = {Multidimensional Residual Distribution Schemes for the Pseudo-Compressible 5532 {Euler} and {Navier-Stokes} equations on Unstructured Meshes}, 5533 institution = {Universita della Basilicata via della Tecnica 3}, 5534 year = {1996}, 5535 author = {A. Bonglioli}, 5536 url = {http://www.unibas.it/utenti/bonfiglioli/icnmfd98.ps.gz}, 5537 petsc_uses = {KSP} 5538} 5539 5540@Article{ deng-piquet-ctf, 5541 author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"}, 5542 title = {A new fully coupled method for computing turbulent flows}, 5543 journal = {Computers and Fluids}, 5544 volume = {30}, 5545 pages = {445--472}, 5546 year = {2001}, 5547 petsc_uses = {KSP} 5548} 5549 5550@InProceedings{ knepleysarinsameh99b, 5551 title = {Multilevel Preconditioning for Parallel {CFD}}, 5552 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 5553 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 5554 Problems In Industrial Applications}, 5555 address = {Minneapolis, MN}, 5556 year = {1999}, 5557 petsc_uses = {KSP} 5558} 5559 5560@InProceedings{ garbey1, 5561 author = {M. Garbey and B. Hadri and W. Shyy.}, 5562 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 5563 Problems on the Grid}, 5564 booktitle = {Aerospace Sciences Meeting and Exhibit}, 5565 note = {Paper No. 2005-1386}, 5566 year = {2005}, 5567 petsc_uses = {KSP} 5568} 5569 5570@Article{ carrica2007unsteady, 5571 title = {An unsteady single-phase level set method for viscous free surface flows}, 5572 author = {Carrica, PM and Wilson, RV and Stern, F.}, 5573 journal = {International Journal for Numerical Methods in Fluids}, 5574 volume = {53}, 5575 number = {2}, 5576 pages = {229--256}, 5577 year = {2007}, 5578 publisher = {Chichester; New York: Wiley, c1981-}, 5579 petsc_uses = {KSP} 5580} 5581 5582@Article{ pctw2004, 5583 author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber}, 5584 title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of 5585 Spillways}, 5586 journal = {Journal of Hydraulic Research}, 5587 note = {accepted for publication}, 5588 year = {2004}, 5589 petsc_uses = {KSP} 5590} 5591 5592@Article{ wcs2004, 5593 author = {R. V. Wilson and P. M. Carrica and F. Stern}, 5594 title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface 5595 Combatant}, 5596 journal = {Computers and Fluids}, 5597 note = {in press}, 5598 year = {2004}, 5599 petsc_uses = {KSP} 5600} 5601 5602@Article{ cws2005, 5603 author = {P. M. Carrica and R. V. Wilson and F. Stern}, 5604 title = {Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem}, 5605 journal = {Computers and Fluids}, 5606 note = {accepted for publication}, 5607 year = {2005}, 5608 petsc_uses = {KSP} 5609} 5610 5611@Article{ chndss2010, 5612 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5613 Stern}, 5614 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5615 Heave Problems for a Surface Combatant}, 5616 journal = {Computers and Fluids}, 5617 year = {2010}, 5618 volume = {39}, 5619 number = {7}, 5620 pages = {1095--1111}, 5621 petsc_uses = {KSP} 5622} 5623 5624@InProceedings{ chnkss2008, 5625 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5626 Stern}, 5627 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 5628 Grids}, 5629 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 5630 year = {2008}, 5631 petsc_uses = {KSP} 5632} 5633 5634@MastersThesis{ mtj, 5635 author = {M. T. Jozkowski}, 5636 title = {Application of Algebraic Multigrid Methods to the Solution of Stratified Flows 5637 About Submerged Bodies}, 5638 school = {The Pennsylvania State University}, 5639 year = {2005}, 5640 petsc_uses = {KSP} 5641} 5642 5643@Article{ pp, 5644 author = {E. G. Paterson and L. J. Peltier}, 5645 title = {Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and 5646 Wakes}, 5647 journal = {ASME Journal of Fluids Engineering}, 5648 note = {In press}, 5649 year = {2005}, 5650 petsc_uses = {KSP} 5651} 5652 5653@Article{ eps, 5654 author = {B. A. Edge and E. G. Paterson and G. Settles}, 5655 title = {Computational Study of the Wake and Contaminant Transport of a Walking Human}, 5656 journal = {ASME Journal of Fluids Engineering}, 5657 note = {In press}, 5658 year = {2005}, 5659 petsc_uses = {KSP} 5660} 5661 5662@InProceedings{ rp, 5663 author = {B. Racine and E. G. 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Peltier}, 5682 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 5683 refinement grids and detached-eddy simulation}, 5684 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 5685 year = {2004}, 5686 petsc_uses = {KSP} 5687} 5688 5689@InProceedings{ mzwp, 5690 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 5691 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 5692 booktitle = {25th Symposium on Naval Hydrodynamics}, 5693 year = {2004}, 5694 petsc_uses = {KSP} 5695} 5696 5697@InProceedings{ ppph, 5698 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 5699 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 5700 booktitle = {25th Symposium on Naval Hydrodynamics}, 5701 year = {2004}, 5702 petsc_uses = {KSP} 5703} 5704 5705@InProceedings{ ppd, 5706 author = {E. G. Paterson and L. J. 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Baker}, 5732 title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control 5733 Surfaces}, 5734 booktitle = {42nd AIAA Aerospace Sciences Meeting}, 5735 year = {2004}, 5736 petsc_uses = {KSP} 5737} 5738 5739@InProceedings{ gid1, 5740 author = {G. Frank and J. D'Elia}, 5741 title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model}, 5742 year = {2004}, 5743 booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD}, 5744 url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf}, 5745 petsc_uses = {KSP} 5746} 5747 5748@InBook{ b1, 5749 author = {A.Bonfiglioli}, 5750 chapter = {On the use of the PETSc library for unstructured {CFD} applications}, 5751 year = {2001}, 5752 title = {Science and Supercomputing at CINECA}, 5753 pages = {397--400}, 5754 petsc_uses = {KSP} 5755} 5756 5757@InProceedings{ b2004, 5758 author = {L. A. Barba}, 5759 title = {Computing high-Reynolds number vortical flows: a highly accurate method with a 5760 fully meshless formulation}, 5761 year = {2004}, 5762 booktitle = {International Conference on Parallel CFD, Grand Canary, May 2004}, 5763 note = {Submitted}, 5764 petsc_uses = {KSP} 5765} 5766 5767@InProceedings{ bl2004, 5768 author = {L. A. Barba and A. Leonard}, 5769 title = {Computation of Viscous Vortices with Fully Meshless Method}, 5770 year = {2004}, 5771 booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004}, 5772 note = {Submitted}, 5773 petsc_uses = {KSP} 5774} 5775 5776@Article{ vws1, 5777 author = {B. G. M. Van Wachem and J. C. Schouten}, 5778 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 5779 Velocity}, 5780 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 5781 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 5782 Netherlands}, 5783 journal = {AIChE}, 5784 volumne = {48}, 5785 number = {12}, 5786 month = dec, 5787 year = {2002}, 5788 petsc_uses = {KSP} 5789} 5790 5791@TechReport{ lbam1, 5792 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 5793 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 5794 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 5795 di Bari Italy}, 5796 year = {2002}, 5797 number = {25/02}, 5798 petsc_uses = {KSP} 5799} 5800 5801@Article{ kees_miller_02, 5802 author = {C. E. Kees and C. T. Miller}, 5803 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 5804 journal = {Advances in Water Resources}, 5805 year = {2002}, 5806 volume = {25}, 5807 number = {2}, 5808 pages = {159-177.}, 5809 petsc_uses = {KSP} 5810} 5811 5812@InProceedings{ lepotmeersessers2001, 5813 author = {I. Lepot and F. Meers and J.A. Essers}, 5814 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 5815 Unstructured Meshes}, 5816 year = {2001}, 5817 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 5818 url = {http://www.ulg.ac.be/aerodyn}, 5819 petsc_uses = {KSP} 5820} 5821 5822@InProceedings{ knepley98, 5823 author = {Matthew Knepley and Denis Vanderstraeten}, 5824 title = {Parallel Building Blocks for Finite Element Simulations: Application to 5825 Solid-Liquid Mixture Flows}, 5826 booktitle = {Proceedings of Parallel CFD'97}, 5827 publisher = {Elsevier}, 5828 pages = {281--287}, 5829 year = {1998}, 5830 petsc_uses = {KSP} 5831} 5832 5833@InProceedings{ pcfd97, 5834 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. 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High Performance Computing Applications}, 5860 year = {2000}, 5861 volume = {14}, 5862 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 5863 pages = {102-136}, 5864 petsc_uses = {KSP} 5865} 5866 5867@InProceedings{ agkks-sc99, 5868 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 5869 Smith}, 5870 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 5871 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 5872 editor = {}, 5873 publisher = {}, 5874 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 5875 year = {1999}, 5876 note = {Winner of Gordon Bell Special Prize at SC 99}, 5877 petsc_uses = {KSP} 5878} 5879 5880@Article{ gkks01, 5881 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 5882 title = {High Performance Parallel Implicit {CFD}}, 5883 journal = {Journal of Parallel Computing}, 5884 year = {2001}, 5885 volume = {27}, 5886 pages = {337-362}, 5887 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 5888 petsc_uses = {KSP} 5889} 5890 5891@Article{ cristea-sofonea-02, 5892 author = {Artur Cristea and Victor Sofonea}, 5893 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 5894 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 5895 Sciences, Information Sciences}, 5896 volume = {3}, 5897 number = {3}, 5898 year = {2002}, 5899 petsc_uses = {KSP} 5900} 5901 5902@Article{ cristea2, 5903 author = {Artur Cristea and Victor Sofonea}, 5904 title = {Two component lattice Boltzmann model with flux limiter techniques}, 5905 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 5906 Sciences, Information Sciences}, 5907 volume = {4}, 5908 number = {1}, 5909 year = {2003}, 5910 pages = {59--64}, 5911 petsc_uses = {KSP} 5912} 5913 5914@Article{ cristea1, 5915 author = {Artur Cristea and Victor Sofonea}, 5916 title = {Two component lattice Boltzmann model with flux limiters}, 5917 journal = {Central European Journal of Physics}, 5918 volume = {2}, 5919 number = {2}, 5920 year = {2004}, 5921 pages = {382--396}, 5922 petsc_uses = {KSP} 5923} 5924 5925@Article{ sofnea-lamura1, 5926 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 5927 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 5928 systems}, 5929 journal = {Physical Review E}, 5930 volume = {70}, 5931 number = {4}, 5932 year = {2004}, 5933 pages = {046702-1 / 046702-9}, 5934 petsc_uses = {KSP} 5935} 5936 5937@InProceedings{ gkks01b, 5938 author = {W. 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Smith}, 5952 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 5953 Code}, 5954 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 5955 (HiPC '2000)}, 5956 editor = {}, 5957 location = {Bangalore, India}, 5958 year = {2000}, 5959 pages = {395--404}, 5960 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 5961 petsc_uses = {KSP} 5962} 5963 5964@InProceedings{ gkks-sc00, 5965 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 5966 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 5967 booktitle = {Proceedings of SC2000}, 5968 editor = {}, 5969 publisher = {IEEE Computer Society}, 5970 year = {2000}, 5971 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 5972 petsc_uses = {KSP} 5973} 5974 5975@InProceedings{ knepleysamehsarin99, 5976 author = {Matthew Knepley and Ahmed H. 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Smith}, 6012 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 6013 Incompressible Flows on Unstructured Grids}, 6014 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6015 Methods}, 6016 editors = {C.-H. {Lai et al.}}, 6017 publisher = {Domain Decomposition Press, Bergen}, 6018 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 6019 year = {1999}, 6020 petsc_uses = {KSP} 6021} 6022 6023@InCollection{ kks97_cfd, 6024 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 6025 title = {Perspectives for {CFD} on Petaflops Systems}, 6026 booktitle = {CFD Review 1998}, 6027 editor = {M. Hafez and K. Oshima}, 6028 publisher = {World Scientific, Singapore}, 6029 pages = {1079--1096}, 6030 note = {}, 6031 year = {1998}, 6032 petsc_uses = {KSP} 6033} 6034 6035@Article{ hm99, 6036 author = {P. D. Hovland and L. C. McInnes}, 6037 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 6038 {PETSc}}, 6039 year = {2000}, 6040 journal = {Parallel Computing}, 6041 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 6042 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 6043 petsc_uses = {KSP} 6044} 6045 6046@InProceedings{ cruzbarbaknepley08, 6047 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 6048 title = {Fast Multipole Method for particle interactions: an open source parallel library 6049 component}, 6050 booktitle = {Proceedings of ParCFD2008}, 6051 year = {2008}, 6052 editor = {Tromeur-Dervout et. al.}, 6053 publisher = {Elsevier}, 6054 petsc_uses = {KSP} 6055} 6056 6057@Article{ hwangcai05, 6058 author = {F.-N. Hwang and X.-C. 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Keyes}, 6194 title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods}, 6195 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6196 editor = {John A. DeSanto}, 6197 year = {1998}, 6198 publisher = {SIAM}, 6199 address = {Philadelphia}, 6200 pages = {623--625}, 6201 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6202 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6203 petsc_uses = {KSP} 6204} 6205 6206@InProceedings{ mska98, 6207 author = {L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi}, 6208 title = {Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the 6209 Parallel Computation of {H}elmholtz Problems}, 6210 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6211 editor = {J. Mandel et al.}, 6212 publisher = {AMS}, 6213 pages = {349--357}, 6214 year = {1998}, 6215 petsc_uses = {KSP} 6216} 6217 6218@InProceedings{ ccew98, 6219 author = {X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund}, 6220 title = {Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation}, 6221 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6222 editor = {J. Mandel et al.}, 6223 publisher = {AMS}, 6224 pages = {437-445}, 6225 year = {1998}, 6226 petsc_uses = {KSP} 6227} 6228 6229@InProceedings{ ra98a, 6230 author = {R. Susan-Resiga and H. M. Atassi}, 6231 title = {Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic 6232 Problems}, 6233 booktitle = {Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference}, 6234 publisher = {AIAA}, 6235 pages = {86-96}, 6236 note = {AIAA paper 98-2218}, 6237 year = {1998}, 6238 petsc_uses = {KSP} 6239} 6240 6241@InProceedings{ ar98c, 6242 author = {H. M. Atassi and R. Susan-Resiga}, 6243 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: 6244 General Formulation}, 6245 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6246 publisher = {ASME}, 6247 note = {NCA-25}, 6248 pages = {375-379}, 6249 year = {1998}, 6250 petsc_uses = {KSP} 6251} 6252 6253@InProceedings{ ra98b, 6254 author = {R. Susan-Resiga and H. M. Atassi}, 6255 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: 6256 Numerical Implementation and Applications}, 6257 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6258 publisher = {ASME}, 6259 note = {NCA-25}, 6260 pages = {381 -388}, 6261 year = {1998}, 6262 petsc_uses = {KSP} 6263} 6264 6265@InProceedings{ cai-dd10-98, 6266 author = {Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. 6267 Widlund}, 6268 title = {Overlapping {S}chwarz methods for solving {H}elmholtz's Equation}, 6269 booktitle = {Domain Decomposition Methods 10}, 6270 editors = {Jan Mandel and Charbel Farhat and Xiao-Chuan Cai}, 6271 series = {Contemporary Mathematics}, 6272 volume = {218}, 6273 publisher = {American Mathematical Society}, 6274 address = {Providence, Rhode Island}, 6275 year = {1998}, 6276 pages = {437--445}, 6277 petsc_uses = {KSP} 6278} 6279 6280@InProceedings{ alghamdi2011petclaw, 6281 title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython}, 6282 booktitle = {Proceedings of SpringSim 2011}, 6283 publisher = {ACM}, 6284 author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and 6285 Kyle T. Mandli and Lisandro Dalcin}, 6286 year = {2011}, 6287 petsc_uses = {KSP} 6288} 6289 6290@Article{ pyclaw2012, 6291 author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and 6292 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 6293 Emmett}, 6294 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 6295 journal = {SIAM Journal on Scientific Computing}, 6296 volume = {34}, 6297 number = {4}, 6298 pages = {C210--C231}, 6299 note = {\url{http://arxiv.org/abs/1111.6583}}, 6300 year = {2012}, 6301 petsc_uses = {KSP} 6302} 6303 6304% LiteralHTML: 6305% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 6306% LiteralHTML: 6307@Article{ sojkahorakhaplacermak2018, 6308 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 6309 decomposition method}, 6310 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 6311 journal = {Applied Mathematics and Computation}, 6312 volume = {319}, 6313 pages = {586--597}, 6314 year = {2018}, 6315 petsc_uses = {KSP} 6316} 6317 6318@Article{ chencai2014, 6319 title = {A parallel two-level domain decomposition based one-shot method for shape 6320 optimization problems}, 6321 author = {Rongliang Chen and Xiao‐Chuan Cai}, 6322 journal = {International Journal for Numerical Methods in Engineering}, 6323 volume = {99}, 6324 number = {13}, 6325 year = {2014}, 6326 doi = {10.1002/nme.4711}, 6327 petsc_uses = {KSP} 6328} 6329 6330@PhDThesis{ prudencio2005, 6331 author = {Ernesto Prudencio}, 6332 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 6333 for Optimization Problems Constrained by Partial Differential Equations}, 6334 school = {University of Colorado, Boulder}, 6335 year = {2005}, 6336 petsc_uses = {KSP} 6337} 6338 6339@Article{ prudenciocai2007, 6340 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 6341 for {PDE}-constrained optimization}, 6342 author = {Ernesto Prudencio and X. C. Cai}, 6343 journal = {SIAM J. Sci. Comp.}, 6344 volume = {29}, 6345 number = {3}, 6346 pages = {964--985}, 6347 year = {2007}, 6348 petsc_uses = {KSP} 6349} 6350 6351@Article{ prudenciobyrdcai2006, 6352 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6353 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 6354 {PDE}-constrained Optimization Problems}, 6355 journal = {SIAM J. Sci. Comp.}, 6356 volume = {27}, 6357 pages = {1305--1328}, 6358 year = {2006}, 6359 petsc_uses = {KSP} 6360} 6361 6362@InProceedings{ prudenciobyrdcai2004, 6363 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 6364 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6365 booktitle = {VECPAR 2004}, 6366 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 6367 publisher = {Springer}, 6368 pages = {569--582}, 6369 year = {2004}, 6370 petsc_uses = {KSP} 6371} 6372 6373@Article{ belhamadia-fortin-pcp, 6374 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 6375 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 6376 journal = {Journal of Computational Physics}, 6377 volume = {201}, 6378 pages = {753-770}, 6379 year = {2004}, 6380 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 6381 petsc_uses = {KSP} 6382} 6383 6384@Article{ biros00, 6385 author = {George Biros and Omar Ghattas}, 6386 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 6387 journal = {SIAG-Opt Views and News}, 6388 volume = {11}, 6389 number = {2}, 6390 year = {2000}, 6391 month = aug, 6392 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 6393 petsc_uses = {KSP} 6394} 6395 6396@Article{ bmm01, 6397 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 6398 journal = {ACM Transactions on Mathematical Software}, 6399 title = {A case study in the performance and scalability of optimization algorithms}, 6400 year = {2001}, 6401 volume = {27}, 6402 number = {3}, 6403 pages = {361--376}, 6404 petsc_uses = {KSP} 6405} 6406 6407@InProceedings{ oghattas1999, 6408 author = {George Biros and Omar Ghattas}, 6409 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 6410 incompressible flows}, 6411 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 6412 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 6413 year = {1999}, 6414 petsc_uses = {KSP} 6415} 6416 6417@InProceedings{ hkms00, 6418 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 6419 PDE-constrained Optimization}, 6420 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 6421 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 6422 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 6423 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 6424 Hasco\"{e}t and Uwe Naumann}, 6425 publisher = {Springer}, 6426 year = {2002}, 6427 petsc_uses = {KSP} 6428} 6429 6430% old version: replace with biros2005pln1 6431@TechReport{ bg011, 6432 author = {George Biros and Omar Ghattas}, 6433 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 6434 Part I: The Krylov-Schur Solver}, 6435 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6436 year = {2001}, 6437 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 6438 petsc_uses = {KSP} 6439} 6440 6441% old version: replace with biros2005pln2 6442@TechReport{ bg012, 6443 author = {George Biros and Omar Ghattas}, 6444 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 6445 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 6446 Optimal Control of Steady Viscous Flows}, 6447 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6448 year = {2001}, 6449 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 6450 petsc_uses = {KSP} 6451} 6452 6453% LiteralHTML: 6454% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 6455% LiteralHTML: 6456@InProceedings{ ly2003, 6457 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 6458 title = {A New Parallel Kernel-independent Fast Multipole Method}, 6459 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 6460 year = {2003}, 6461 note = {Winner of the Best Student Paper at SC2003}, 6462 petsc_uses = {KSP} 6463} 6464 6465@Article{ yokotabarbaknepley10, 6466 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 6467 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 6468 journal = {Computer Methods in Applied Mechanics and Engineering}, 6469 volume = {199}, 6470 number = {25-28}, 6471 pages = {1793--1804}, 6472 url = {http://arxiv.org/abs/0909.5413v1}, 6473 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 6474 year = {2010}, 6475 petsc_uses = {KSP} 6476} 6477 6478@Article{ cruzknepleybarba10, 6479 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 6480 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 6481 journal = {International Journal of Numerical Methods in Engineering}, 6482 volume = {85}, 6483 number = {4}, 6484 pages = {403--428}, 6485 url = {http://arxiv.org/abs/0905.2637}, 6486 note = {\url{http://arxiv.org/abs/0905.2637}}, 6487 year = {2010}, 6488 petsc_uses = {KSP} 6489} 6490 6491% LiteralHTML: 6492% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 6493% LiteralHTML: 6494@Article{ buchanpainumplebysmedleystevenson2012, 6495 title = {A sub-grid scale finite element agglomeration multigrid method with application 6496 to the Boltzmann transport equation}, 6497 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 6498 journal = {International Journal for Numerical Methods in Engineering}, 6499 volume = {92}, 6500 number = {3}, 6501 pages = {318--342}, 6502 year = {2012}, 6503 publisher = {Wiley Online Library}, 6504 petsc_uses = {KSP} 6505} 6506 6507@Article{ magoulesahamedsuzuki2015, 6508 title = {Green computing on graphics processing units}, 6509 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 6510 journal = {Concurrency and Computation: Practice and Experience}, 6511 year = {2015}, 6512 publisher = {Wiley Online Library}, 6513 petsc_uses = {KSP} 6514} 6515 6516@InProceedings{ yanrhodes11, 6517 author = {Yan, Baoqiang and Rhodes, Philip J.}, 6518 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 6519 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 6520 series = {ICPP '11}, 6521 pages = {355--364}, 6522 year = {2011}, 6523 isbn = {978-0-7695-4510-3}, 6524 numpages = {10}, 6525 doi = {10.1109/ICPP.2011.70}, 6526 acmid = {2066965}, 6527 publisher = {IEEE Computer Society}, 6528 address = {Washington, DC, USA}, 6529 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 6530 petsc_uses = {KSP} 6531} 6532 6533@Article{ hakansson2013mdstochasticliouville, 6534 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 6535 Stulz, Eugen}, 6536 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 6537 equation study}, 6538 journal = {Phys. Chem. Chem. Phys.}, 6539 year = {2013}, 6540 volume = {15}, 6541 issue = {26}, 6542 pages = {10930-10941}, 6543 publisher = {The Royal Society of Chemistry}, 6544 doi = {10.1039/C3CP50788B}, 6545 petsc_uses = {KSP} 6546} 6547 6548@Article{ hakansson2011stochasticliouville, 6549 author = {Hakansson, Par and Nair, Prasanth B.}, 6550 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 6551 form}, 6552 journal = {Phys. Chem. Chem. Phys.}, 6553 year = {2011}, 6554 volume = {13}, 6555 issue = {20}, 6556 pages = {9578-9589}, 6557 publisher = {The Royal Society of Chemistry}, 6558 doi = {10.1039/C1CP20400A}, 6559 petsc_uses = {KSP} 6560} 6561 6562@InProceedings{ wang:lee:scidac2011, 6563 author = {Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman 6564 McInnes and Todd Munson and Barry Smith}, 6565 title = {A Differential Variational Inequality Approach for the Simulation of 6566 Heterogeneous Materials}, 6567 booktitle = {Proceedings of SciDAC 2011 Conference}, 6568 year = {2011}, 6569 petsc_uses = {KSP} 6570} 6571 6572@Article{ bourdinlarsenrichardson2011, 6573 author = {Blaise Bourdin and Christopher Larsen and Casey Richardson}, 6574 title = {A time-discrete model for dynamic fracture based on crack regularization}, 6575 journal = {International Journal of Fracture}, 6576 volume = {168}, 6577 issue = {2}, 6578 pages = {133--143}, 6579 doi = {10.1007/s10704-010-9562-x}, 6580 year = {2011}, 6581 petsc_uses = {KSP} 6582} 6583 6584@Article{ bourdinfrancfortmarigo2008, 6585 author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo}, 6586 title = {The Variational Approach to Fracture}, 6587 journal = {J. Elasticity}, 6588 volume = {91}, 6589 issue = {1}, 6590 pages = {1--148}, 6591 doi = {10.1007/s10659-007-9107-3}, 6592 year = {2008}, 6593 petsc_uses = {KSP} 6594} 6595 6596@Article{ lahtinen2008spectrum, 6597 title = {Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model}, 6598 author = {Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, 6599 J.K.}, 6600 journal = {Annals of Physics}, 6601 volume = {323}, 6602 number = {9}, 6603 pages = {2286--2310}, 6604 year = {2008}, 6605 publisher = {Elsevier}, 6606 petsc_uses = {KSP} 6607} 6608 6609@InProceedings{ roark2004discriminative, 6610 title = {Discriminative language modeling with conditional random fields and the 6611 perceptron algorithm}, 6612 author = {Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.}, 6613 booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational 6614 Linguistics}, 6615 pages = {47}, 6616 year = {2004}, 6617 organization = {Association for Computational Linguistics}, 6618 petsc_uses = {KSP} 6619} 6620 6621@Article{ roark2007discriminative, 6622 title = {Discriminative n-gram language modeling}, 6623 author = {Roark, B. and Saraclar, M. and Collins, M.}, 6624 journal = {Computer Speech \& Language}, 6625 volume = {21}, 6626 number = {2}, 6627 pages = {373--392}, 6628 year = {2007}, 6629 publisher = {Elsevier}, 6630 petsc_uses = {KSP} 6631} 6632 6633@Conference{ garcia2011parallel, 6634 title = {{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D 6635 nanodevice simulators}}, 6636 author = {Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and 6637 Aldegunde, M.}, 6638 booktitle = {Electron Devices (CDE), 2011 Spanish Conference on}, 6639 pages = {1--4}, 6640 organization = {IEEE}, 6641 petsc_uses = {KSP} 6642} 6643 6644@Conference{ wesley2006parallel, 6645 title = {{A parallel artificial neural network implementation}}, 6646 author = {Wesley-Smith, I.}, 6647 booktitle = {Proceedings of The National Conference On Undergraduate Research (NCUR)}, 6648 year = {2006}, 6649 petsc_uses = {KSP} 6650} 6651 6652@Article{ hcsw1, 6653 author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu}, 6654 title = {Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional 6655 Poisson-Boltzmann equation in numerical simulation of colloidal particle 6656 interactions}, 6657 journal = {Computer Physics Communications}, 6658 volumne = {181}, 6659 year = {2010}, 6660 pages = {1529--1537}, 6661 petsc_uses = {KSP} 6662} 6663 6664@Article{ hh1, 6665 author = {C.-Y. Huang and F.-N. Hwang}, 6666 title = {Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for 6667 bifurcation analysis of incompressible sudden expansion flows}, 6668 journal = {Applied Numerical Mathematics}, 6669 volume = {60}, 6670 year = {2010}, 6671 pages = {738--751}, 6672 petsc_uses = {KSP} 6673} 6674 6675@Article{ hwhw1, 6676 author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. Wang}, 6677 title = {A parallel additive Schwarz preconditioned Jacobi-Davidson algorithm for 6678 polynomial eigenvalue problems in quantum dot simulation}, 6679 journal = {Journal of Computational Physics}, 6680 volume = {229}, 6681 year = {2010}, 6682 pages = {2932--2947}, 6683 petsc_uses = {KSP} 6684} 6685 6686@Article{ wei2011parallel, 6687 title = {{A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with 6688 Application in Quantum Dot Simulation}}, 6689 author = {Wei, Z.H. and Hwang, F.N. and Huang, T.M. and Wang, W.}, 6690 journal = {Domain Decomposition Methods in Science and Engineering XIX}, 6691 pages = {157--164}, 6692 year = {2011}, 6693 publisher = {Springer}, 6694 petsc_uses = {KSP} 6695} 6696 6697@Article{ flores2007sequential, 6698 title = {{Sequential and parallel resolution of the two-group transient neutron diffusion 6699 equation using second-degree iterative methods}}, 6700 author = {Flores-S{\'a}nchez, O. and Vidal, V. and Garc{\'\i}a, V. and Flores-S{\'a}nchez, P.}, 6701 journal = {High Performance Computing for Computational Science-VECPAR 2006}, 6702 pages = {426--438}, 6703 year = {2007}, 6704 publisher = {Springer}, 6705 petsc_uses = {KSP} 6706} 6707 6708@InProceedings{ gordonbell09, 6709 author = {Dinesh Kaushik and Michael Smith and Allan Wollaber and Barry Smith and Andrew 6710 Siegel and Won Sik Yang}, 6711 title = {Enabling High Fidelity Neutron Transport Simulations on Petascale Architectures}, 6712 booktitle = {ACM/IEEE Proceedings of SC2009: High Performance Networking and Computing}, 6713 note = {{SC'09 Gordon Bell} Prize Finalist}, 6714 year = {2009}, 6715 petsc_uses = {KSP} 6716} 6717 6718@Article{ knepleykarpeevdavidovitseisenberggillespie10, 6719 author = {Matthew G. Knepley and Dmitry A. Karpeev and Seth Davidovits and Robert~S. 6720 Eisenberg and Dirk Gillespie}, 6721 title = {An Efficient Algorithm for Classical Density Functional Theory in Three 6722 Dimensions: Ionic Solutions}, 6723 journal = {Journal of Physical Chemistry}, 6724 volume = {132}, 6725 number = {12}, 6726 pages = {124101--124111}, 6727 url = {http://arxiv.org/abs/0910.1531}, 6728 year = {2010}, 6729 petsc_uses = {KSP} 6730} 6731 6732@Article{ knepleykarpeeveisenberggillespie09, 6733 author = {{Knepley}, M.~G. and {Karpeev}, D.~A. and {Eisenberg}, R.~S. and {Gillespie}, 6734 D.}, 6735 title = {{Energetics of Calcium Selectivity: A Three-Dimensional Classical Density 6736 Functional Theory Approach}}, 6737 journal = {Biophysical Journal}, 6738 month = feb, 6739 volume = {96}, 6740 pages = {661}, 6741 doi = {10.1016/j.bpj.2008.12.3494}, 6742 year = {2009}, 6743 petsc_uses = {KSP} 6744} 6745 6746@Article{ scx2008, 6747 author = {SUWITO AND XIAO-CHUAN CAI AND YUNPING XI}, 6748 title = {PARALLEL FINITE ELEMENT METHOD FOR COUPLED CHLORIDE MOISTURE DIFFUSION IN 6749 CONCRETE}, 6750 journal = {INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING}, 6751 volume = {3}, 6752 number = {4}, 6753 year = {2006}, 6754 url = {http://www.math.ualberta.ca/ijnam/Volume-3-2006/No-4-06/2006-04-06.pdf}, 6755 petsc_uses = {KSP} 6756} 6757 6758@TechReport{ kdgs2008, 6759 year = {2008}, 6760 school = {Centro Internacional de Methodos Numericos en Ingenieria, Argentina}, 6761 title = {High Performance Simulations of Electrokinetic Flow and Transport in Microfluidic 6762 Chips}, 6763 author = {Pablo A. Klera and Lisandro D. Dalcin and Fabio A. Guarnieria and Mario A. 6764 Stortia}, 6765 url = {http://www.cimec.org.ar/ojs/index.php/cmm/article/view/1383}, 6766 petsc_uses = {KSP} 6767} 6768 6769@Article{ springerlink:10.1007/s10915-011-9551-x, 6770 author = {Schauer, Marco and Roman, Jose and Quintana-Ortí, Enrique and Langer, Sabine}, 6771 affiliation = {Institut für Angewandte Mechanik, Technische Universität Carolo-Wilhelmina zu 6772 Braunschweig, Spielmannstraße 11, 38106 Braunschweig, Germany}, 6773 title = {Parallel Computation of 3-D Soil-Structure Interaction in Time Domain with a 6774 Coupled FEM/SBFEM Approach}, 6775 journal = {Journal of Scientific Computing}, 6776 publisher = {Springer Netherlands}, 6777 issn = {0885-7474}, 6778 keyword = {Mathematics and Statistics}, 6779 pages = {1-22}, 6780 doi = {10.1007/s10915-011-9551-x}, 6781 petsc_uses = {KSP} 6782} 6783 6784@TechReport{ jj2007, 6785 author = {Boris Jeremic and Guanzhou Jie}, 6786 title = {Parallel Finite Element Computations for Soil-Foundation-Structure Interaction 6787 Problems Report}, 6788 institution = {UCD CompGeoMech 02--2007}, 6789 year = {2007}, 6790 url = {http://sokocalo.engr.ucdavis.edu/~jeremic/wwwpublications/CV-R23.pdf}, 6791 petsc_uses = {KSP} 6792} 6793 6794@Unpublished{ kuiper08, 6795 title = {Fast 3D frequency-dependent Radiative Transfer for Magneto-Hydrodynamics}, 6796 author = {Rolf Kuiper}, 6797 institution = {Max-Planck-Institute for Astronomy}, 6798 url = {http://www.mpia.de/~kuiper/MAKEMAKE.html}, 6799 year = {2008}, 6800 petsc_uses = {KSP} 6801} 6802 6803@Article{ williamson2012multidimensional, 6804 title = {Multidimensional multiphysics simulation of nuclear fuel behavior}, 6805 author = {Williamson, R.L. and Hales, J.D. and Novascone, S.R. and Tonks, M.R. and Gaston, 6806 D.R. and Permann, C.J. and Andrs, D. and Martineau, R.C.}, 6807 journal = {Journal of Nuclear Materials}, 6808 volume = {423}, 6809 number = {1}, 6810 pages = {149--163}, 6811 year = {2012}, 6812 publisher = {Elsevier}, 6813 petsc_uses = {KSP} 6814} 6815 6816@InProceedings{ kucukboyaci2015cobra, 6817 title = {COBRA-TF parallelization and application to PWR reactor core subchannel DNB 6818 analysis}, 6819 author = {Kucukboyaci, Vefa and Sung, Yixing and Salko, Robert}, 6820 booktitle = {Joint International Conference on Mathematics and Computation, Supercomputing in 6821 Nuclear Applications and the Monte Carlo Method}, 6822 pages = {1--18}, 6823 year = {2015}, 6824 petsc_uses = {KSP} 6825} 6826 6827@Article{ hales2012solving, 6828 title = {Solving Nonlinear Solid Mechanics Problems with the {J}acobian-{F}ree {N}ewton 6829 {K}rylov Method}, 6830 author = {Hales, J.D. and Novascone, S.R. and Williamson, R.L. and Gaston, D.R. and Tonks, 6831 M.R.}, 6832 journal = {Computer Modeling in Engineering \& Sciences(CMES)}, 6833 volume = {84}, 6834 number = {2}, 6835 pages = {123--153}, 6836 year = {2012}, 6837 publisher = {Tech Science Press}, 6838 petsc_uses = {KSP} 6839} 6840 6841@InProceedings{ srksyp2008, 6842 author = {M. A. Smith and C. Rabiti and D. Kaushik and B. Smith and W. S. Yang and G. 6843 Palmiotti}, 6844 title = {Fast reactor core simulations using the {UNIC} code}, 6845 booktitle = {Proceedings of the International Conference on the Physics of Reactors, Nuclear 6846 Power: A Sustainable Resource}, 6847 year = {2008}, 6848 petsc_uses = {KSP} 6849} 6850 6851@InProceedings{ psrlkssl2007, 6852 author = {G. Palmiotti and M. A. Smith and C. Rabiti and M. Leclere and D. Kaushik and A. 6853 Siegel and B. Smith and E. E. Lewis}, 6854 title = {{UNIC}: Ultimate Neutronic Investigation Code}, 6855 booktitle = {Joint International Topical Meeting on Mathematics and Computation and 6856 Supercomputing in Nuclear Applications}, 6857 year = {2007}, 6858 petsc_uses = {KSP} 6859} 6860 6861@InProceedings{ sprkssl2007, 6862 author = {M. A. Smith and G. Palmiotti and C. Rabiti and D. Kaushik and A. Siegel and B. 6863 Smith and E. E. Lewis}, 6864 title = {{PNFE} Component of the {UNIC} Code}, 6865 booktitle = {Joint International Topical Meeting on Mathematics and Computation and 6866 Supercomputing in Nuclear Applications}, 6867 year = {2007}, 6868 petsc_uses = {KSP} 6869} 6870 6871@InProceedings{ dc-oop-03, 6872 author = {H. Digonnet and T. Coupez}, 6873 title = {Object-oriented programming for fast-and-easy development of parallel 6874 applications in forming processes simulation}, 6875 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 6876 Mechanics}, 6877 year = {2003}, 6878 petsc_uses = {KSP} 6879} 6880 6881@InProceedings{ dc-cfm-03, 6882 author = {H. Digonnet and T. Coupez}, 6883 title = {Calcul parallele en mise en forme des materiaux}, 6884 booktitle = {XVIeme Congres Francais de Mecanique}, 6885 year = {2003}, 6886 petsc_uses = {KSP} 6887} 6888 6889@InProceedings{ dsc-pcsev-04, 6890 author = {H. Digonnet and L. Silva and T. Coupez}, 6891 title = {Parallel computation for solving efficiently viscoelastic fluid flow problems}, 6892 booktitle = {Proceedings of ECCOMAS 2004}, 6893 year = {2004}, 6894 petsc_uses = {KSP} 6895} 6896 6897@InProceedings{ dsc-pca3fs-04, 6898 author = {H. Digonnet and L. Silva and T. Coupez}, 6899 title = {Parallel computation applied to 3D FE simulation of polymer injection molding}, 6900 booktitle = {Proceedings of WCCM VI}, 6901 year = {2004}, 6902 petsc_uses = {KSP} 6903} 6904 6905@InProceedings{ dbcs-cpaac-05, 6906 author = {H. Digonnet and O. Basset and T. Coupez and L. Silva}, 6907 title = {Calcul parallele appliqu aux coulements de fluides complexe}, 6908 booktitle = {Proceedings of Eme Congres Francais de Mecanique}, 6909 year = {2005}, 6910 petsc_uses = {KSP} 6911} 6912 6913@Article{ sz2010, 6914 author = {B. Smith and H. 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Balkema Publishers}, 7463 address = {Rotterdam, Netherlands}, 7464 month = jun, 7465 optpages = {}, 7466 petsc_uses = {KSP} 7467} 7468 7469% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7470@TechReport{ defordheld1, 7471 author = {JF DeFord and BL Held}, 7472 title = {RF3P-A New Parallel Driven Frequency Electromagnetic Solver}, 7473 year = {2002}, 7474 institution = {Simulation Technology and Applied Research}, 7475 url = {http://www.staarinc.com/support/papers/aces2002.pdf}, 7476 note = {Discusses their parallel commercial solver that uses PETSc}, 7477 petsc_uses = {KSP} 7478} 7479 7480@PhDThesis{ sande2003, 7481 author = {Hans Vande Sande}, 7482 title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic 7483 Quasi-Static Electromagnetic Systems}, 7484 school = {Katholieke Universiteit Leuven, Belgium}, 7485 year = {2003}, 7486 petsc_uses = {KSP} 7487} 7488 7489@Article{ sdchh2004, 7490 author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 7491 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 7492 Tolerance}, 7493 journal = {IEEE Transactions on Magnetics}, 7494 year = {2004}, 7495 volume = {40}, 7496 pages = {1306--1309}, 7497 petsc_uses = {KSP} 7498} 7499 7500@Article{ holst-lindblom-etal:2004, 7501 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 7502 Scheel and Lawrence E. Kidder}, 7503 title = {Optimal constraint projection for hyperbolic evolution systems, }, 7504 journal = {Phys. Rev. D}, 7505 year = {2004}, 7506 volume = {70}, 7507 pages = {084017}, 7508 petsc_uses = {KSP} 7509} 7510 7511@Article{ marm2005, 7512 author = {Matthew Anderson and Richard A. Matzner}, 7513 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 7514 journal = {Foundations of Physics}, 7515 volume = {35}, 7516 pages = {1572--9516}, 7517 year = {2005}, 7518 petsc_uses = {KSP} 7519} 7520 7521@Article{ cook-pfeiffer:2004, 7522 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 7523 title = {Excision boundary conditions for black hole initial data}, 7524 journal = {Phys. Rev. D}, 7525 volume = {70}, 7526 pages = {104016--24}, 7527 year = {2004}, 7528 petsc_uses = {KSP} 7529} 7530 7531@Article{ pfeiffer-kidder-etal:2005, 7532 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 7533 Shoemaker}, 7534 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 7535 journal = {Phys. Rev. D}, 7536 year = {2005}, 7537 volume = {71}, 7538 pages = {024020}, 7539 petsc_uses = {KSP} 7540} 7541 7542@Article{ pfeiffer-kidder-etal:2003, 7543 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 7544 Saul A.}, 7545 title = {A multidomain spectral method for solving elliptic equations}, 7546 journal = {CPC}, 7547 year = {2003}, 7548 volume = {152}, 7549 pages = {253--273}, 7550 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 7551 For a related online version, see arXiv:gr-qc/0202096}, 7552 petsc_uses = {KSP} 7553} 7554 7555@Article{ pfeiffer-cook-teukolsky:2002, 7556 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 7557 title = {Comparing initial-data sets for binary black hole}, 7558 journal = {PRD}, 7559 year = {2002}, 7560 volume = {66}, 7561 pages = {024047}, 7562 note = {for a related online version, seearXiv:gr-qc/0203085}, 7563 petsc_uses = {KSP} 7564} 7565 7566@PhDThesis{ pfeiffer:2003, 7567 author = {Pfeiffer, Harald P.}, 7568 title = {Initial Data for Black Hole Evolutions}, 7569 school = {Cornell University}, 7570 year = {2003}, 7571 petsc_uses = {KSP} 7572} 7573 7574@TechReport{ h1, 7575 author = {Erik Schnetter}, 7576 title = {A fast apparent horizon algorithm}, 7577 year = {2002}, 7578 number = {Arxiv preprint gr-qc/0206003}, 7579 url = {http://arxiv.org/pdf/gr-qc/0206003}, 7580 petsc_uses = {KSP} 7581} 7582 7583@Article{ h2, 7584 author = {Erik Schnetter}, 7585 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 7586 year = {2003}, 7587 journal = {Class. Quantum Grav.}, 7588 pages = {4719-4737}, 7589 volume = {20}, 7590 url = {http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf}, 7591 petsc_uses = {KSP} 7592} 7593 7594@Article{ adams-03a, 7595 author = {Adams, M.~F.}, 7596 journal = {Numerical Linear Algebra with Applications}, 7597 number = {2-3}, 7598 pages = {141-153}, 7599 title = {Algebraic multigrid methods for constrained linear systems with applications to 7600 contact problems in solid mechanics}, 7601 volume = {11}, 7602 year = {2004}, 7603 petsc_uses = {KSP} 7604} 7605 7606@Article{ vandesande1, 7607 author = {H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer}, 7608 journal = {IEEE TRANSACTIONS ON MAGNETICS}, 7609 year = {2003}, 7610 volume = {39}, 7611 pages = {1709--1712}, 7612 title = {Solving Nonlinear Magnetic Problems Using {N}ewton Trust Region Methods}, 7613 petsc_uses = {KSP} 7614} 7615 7616@InProceedings{ vbde1, 7617 author = {Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith}, 7618 year = {2002}, 7619 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 7620 Uintah PSE}, 7621 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 7622 2002}, 7623 pages = {49-55}, 7624 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 7625 note = {Extended abstract}, 7626 petsc_uses = {KSP} 7627} 7628 7629@Unpublished{ ep1, 7630 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 7631 author = {Bradley R. Eccleston and Todd S. Palmer}, 7632 institution = {Department of Nuclear Engineering, Oregon State University}, 7633 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 7634 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 7635 Parallel Simulations}, 7636 year = {1999}, 7637 petsc_uses = {KSP} 7638} 7639 7640@InProceedings{ teo2007scalable, 7641 title = {A scalable modular convex solver for regularized risk minimization}, 7642 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 7643 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 7644 discovery and data mining}, 7645 pages = {727--736}, 7646 year = {2007}, 7647 organization = {ACM}, 7648 petsc_uses = {KSP} 7649} 7650 7651@InProceedings{ rm02, 7652 author = {Robert Malouf}, 7653 year = {2002}, 7654 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 7655 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 7656 (CoNLL-2002)}, 7657 pages = {49-55}, 7658 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 7659 petsc_uses = {KSP} 7660} 7661 7662@Unpublished{ hrv02, 7663 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 7664 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7665 note = {Submitted to CMMSE}, 7666 petsc_uses = {KSP} 7667} 7668 7669@Article{ tmh2001, 7670 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 7671 journal = {Journal of Economic Dynamics and Control}, 7672 year = {2002}, 7673 volume = {26}, 7674 pages = {1499-1515}, 7675 title = {Solving finite difference schemes arising in trivariate option pricing}, 7676 petsc_uses = {KSP} 7677} 7678 7679@InProceedings{ a2, 7680 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 7681 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 7682 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 7683 Methods}, 7684 editor = {C.-H. Lai et al.}, 7685 publisher = {Domain Decomposition Press, Bergen}, 7686 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 7687 year = {1999}, 7688 petsc_uses = {KSP} 7689} 7690 7691@Unpublished{ mmmdcmaa-web-page, 7692 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 7693 {A}coustics {W}eb Page}, 7694 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 7695 author = {David E. Keyes}, 7696 institution = {Old Dominion University}, 7697 petsc_uses = {KSP} 7698} 7699 7700@Conference{ liu2010parallelization, 7701 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 7702 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 7703 booktitle = {International Symposium on Parallel and Distributed Processing with 7704 Applications}, 7705 pages = {528--535}, 7706 year = {2010}, 7707 organization = {IEEE}, 7708 petsc_uses = {KSP} 7709} 7710 7711@Unpublished{ oil-reservoir-sim-web-page, 7712 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 7713 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 7714 institution = {University of Texas at Austin and Argonne National Laboratory}, 7715 key = {University of Texas at Austin and Argonne National Laboratory}, 7716 petsc_uses = {KSP} 7717} 7718 7719@Article{ tmh2001b, 7720 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 7721 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 7722 year = {2001}, 7723 volume = {37}, 7724 pages = {143--146}, 7725 title = {Adapting EMAP3D to parallel processing}, 7726 petsc_uses = {KSP} 7727} 7728 7729@Article{ harbury98, 7730 author = {HK Harbury and W Porod}, 7731 journal = {VLSI Design}, 7732 year = {1998}, 7733 volume = {6}, 7734 pages = {47--51}, 7735 title = {Parallel computation for electronic waves in quantum corrals}, 7736 petsc_uses = {KSP} 7737} 7738 7739@Article{ bludszuwei98, 7740 author = {Mark Bludszuweit}, 7741 journal = {Journal of Lightwave Technology}, 7742 year = {1998}, 7743 volume = {16}, 7744 number = {7}, 7745 pages = {1336--42}, 7746 title = {Mixed Finite Element Beam Propagation Method}, 7747 petsc_uses = {KSP} 7748} 7749 7750@Article{ s1, 7751 author = {J. L. Friedman and N. Stergioulas}, 7752 journal = {Astrophysics Journal}, 7753 year = {1998}, 7754 volume = {492}, 7755 number = {301}, 7756 pages = {}, 7757 title = {}, 7758 petsc_uses = {KSP} 7759} 7760 7761@Article{ s1a, 7762 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 7763 journal = {Astrophysics Journal}, 7764 year = {1999}, 7765 volume = {510}, 7766 number = {854}, 7767 pages = {}, 7768 title = {}, 7769 petsc_uses = {KSP} 7770} 7771 7772@PhDThesis{ s2, 7773 author = {N. Stergioulas}, 7774 title = {Ph. D. thesis}, 7775 year = {1996}, 7776 institution = {University of Wisconsin-Milwaukee}, 7777 petsc_uses = {KSP} 7778} 7779 7780@InProceedings{ coral1, 7781 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7782 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 7783 Parallel Computing Environment}, 7784 booktitle = {Proceedings of the Miami TEAM Workshop}, 7785 location = {Florida International University, Department of Electrical Engineering and 7786 Computing Science}, 7787 month = nov, 7788 year = {1993}, 7789 petsc_uses = {KSP} 7790} 7791 7792@InProceedings{ coral2, 7793 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7794 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 7795 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 7796 month = dec, 7797 year = {1994}, 7798 petsc_uses = {KSP} 7799} 7800 7801@InProceedings{ coral3, 7802 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7803 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 7804 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 7805 location = {Florida International University, Department of Electrical Engineering and 7806 Computing Science}, 7807 year = {1995}, 7808 petsc_uses = {KSP} 7809} 7810 7811@InProceedings{ mijalkovic, 7812 author = {Slobodan Mijalkovi\'{c}}, 7813 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 7814 Process Simulation}, 7815 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 7816 Gent, Belgium, September 27--30, 1999.}, 7817 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 7818 optvolume = {14}, 7819 optseries = {Lecture Notes in Computational Science and Engineering}, 7820 year = {2000}, 7821 publisher = {Springer}, 7822 address = {Berlin}, 7823 optpages = {179--184}, 7824 petsc_uses = {KSP} 7825} 7826 7827@Article{ bludszuwei98a, 7828 author = {Mark Bludszuweit}, 7829 journal = {Journal of Lightwave Technology}, 7830 year = {1998}, 7831 volume = {16}, 7832 number = {7}, 7833 pages = {1336--42}, 7834 title = {Mixed Finite Element Beam Propagation Method}, 7835 petsc_uses = {KSP} 7836} 7837 7838@Article{ gilli-pauletto-1998, 7839 author = {Manfred Gilli and Giorgio Pauletto}, 7840 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 7841 journal = {Computational Economics}, 7842 year = {2000}, 7843 volume = {16}, 7844 pages = {173--186}, 7845 petsc_uses = {KSP} 7846} 7847 7848% LiteralHTML: 7849% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 7850% LiteralHTML: 7851@Article{ collierdalcincalo2013, 7852 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 7853 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 7854 journal = {arxiv}, 7855 year = {2013}, 7856 number = {1305.4452}, 7857 note = {\url{http://arxiv.org/abs/1305.4452}}, 7858 petsc_uses = {KSP} 7859} 7860 7861@Article{ collierdalcinvignalcortescalo2016, 7862 title = {PetIGA: A framework for high-performance isogeometric analysis}, 7863 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 7864 Victor M. Calo}, 7865 journal = {Computer Methods in Applied Mechanics and Engineering}, 7866 year = {2016}, 7867 petsc_uses = {KSP} 7868} 7869 7870@Misc{ petiga-web-page, 7871 author = {N. Collier and L. Dalcin and V.M. Calo}, 7872 title = {{PetIGA} {W}eb page}, 7873 url = {https://bitbucket.org/dalcinl/petiga/}, 7874 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 7875 year = {2014}, 7876 petsc_uses = {KSP} 7877} 7878 7879@Article{ logg07, 7880 author = {Logg, Anders}, 7881 title = {Automating the Finite Element Method}, 7882 journal = {Archives of Computational Methods in Engineering}, 7883 volume = {14}, 7884 number = {2}, 7885 pages = {93-138}, 7886 year = {2007}, 7887 doi = {10.1007/s11831-007-9003-9}, 7888 publisher = {Kluwer Academic Publishers}, 7889 issn = {1134-3060}, 7890 language = {English}, 7891 petsc_uses = {KSP} 7892} 7893 7894@Article{ jezequelcouturierdenis12, 7895 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 7896 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 7897 versus the PETSc library}, 7898 journal = {The Journal of Supercomputing}, 7899 volume = {59}, 7900 number = {3}, 7901 pages = {1517-1532}, 7902 year = {2012}, 7903 issn = {0920-8542}, 7904 doi = {10.1007/s11227-011-0563-y}, 7905 publisher = {Springer US}, 7906 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 7907 Sparse linear solver}, 7908 language = {English}, 7909 petsc_uses = {KSP} 7910} 7911 7912@Unpublished{ feap-web-page, 7913 title = {FEAP: A Finite Element Analysis Program}, 7914 url = {http://www.ce.berkeley.edu/projects/feap/}, 7915 author = {FEAP Team}, 7916 note = {Uses PETSc linear solvers - iterative and direct}, 7917 petsc_uses = {KSP} 7918} 7919 7920@Unpublished{ parpre-web-page, 7921 title = {{ParPre} {W}eb {P}age}, 7922 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 7923 institution = {University of Tennessee}, 7924 author = {Victor Eijkhout}, 7925 note = {This is no longer supported. A set of preconditioners built on PETSc}, 7926 petsc_uses = {KSP} 7927} 7928 7929@Unpublished{ pism, 7930 title = {{PISM}: a Parallel Ice Sheet Model}, 7931 author = {{PISM Team}}, 7932 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 7933 Sheet Model). The thickness, temperature, velocity and age of the ice are all 7934 simulated, as is the deformation of the earth underneath the ice. New techniques 7935 for fast ice dynamics, earth deformation, and verification have are included.}, 7936 note = {\url{http://www.pism-docs.org/}}, 7937 petsc_uses = {KSP} 7938} 7939 7940@Unpublished{ oofem, 7941 title = {OOFEM - an object oriented finite element package}, 7942 author = {Borek Patzak}, 7943 url = {http://www.oofem.org}, 7944 petsc_uses = {KSP} 7945} 7946 7947@Unpublished{ dks2openfvm, 7948 title = {OpenFVM - a finite volume based general purpose CFD solver}, 7949 author = {Open source development}, 7950 url = {http://openfvm.sourceforge.net/}, 7951 petsc_uses = {KSP} 7952} 7953 7954@Unpublished{ sundar-2008w, 7955 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 7956 octree meshes}, 7957 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 7958 institution = {University of Pennsylvania}, 7959 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 7960 petsc_uses = {KSP} 7961} 7962 7963@Unpublished{ khatiwala07-software, 7964 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 7965 author = {Khatiwala, S.}, 7966 institution = {Columbia University}, 7967 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 7968 petsc_uses = {KSP} 7969} 7970 7971@InBook{ jiaolima99, 7972 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 7973 chapter = {{SIFFEA}:Scalable Integrated Framework for Finite Element Analysis}, 7974 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 7975 title = {Lecture Notes in Computer Science}, 7976 publisher = {Springer-Verlag}, 7977 volume = {1732}, 7978 year = {1999}, 7979 petsc_uses = {KSP} 7980} 7981 7982@Article{ crow1, 7983 author = {C. S. Crow IV}, 7984 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 7985 journal = {Hopkins Undergraduate Research Journal}, 7986 year = {2003}, 7987 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 7988 petsc_uses = {KSP} 7989} 7990 7991@Unpublished{ petsc-python, 7992 title = {PETSc for Python}, 7993 author = {L. Dalcin}, 7994 url = {https://petsc.org/main/petsc4py}, 7995 note = {Provides Python bindings for PETSc}, 7996} 7997 7998@Unpublished{ cfdship, 7999 title = {{CFDShip-Iowa}}, 8000 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 8001 institution = {University of Iowa}, 8002 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 8003 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 8004 structured grids, designed for ship applications}, 8005 petsc_uses = {KSP} 8006} 8007 8008@Unpublished{ bvw, 8009 title = {Multiflow}, 8010 author = {Berend van Wachem}, 8011 institution = {Mechanical Engineering - Chalmers University of Technology}, 8012 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 8013 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 8014 flows.}, 8015 petsc_uses = {KSP} 8016} 8017 8018@Unpublished{ dks2, 8019 title = {FENA - A Finite Element Model for the North Atlantic}, 8020 author = {Jens Schroeter}, 8021 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 8022 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 8023 petsc_uses = {KSP} 8024} 8025 8026@TechReport{ piwonski2010idea, 8027 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 8028 and Simulation in {3-D}}, 8029 author = {Piwonski, J. and Slawig, T.}, 8030 year = {2010}, 8031 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8032 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 8033 petsc_uses = {KSP} 8034} 8035 8036@Unpublished{ metos3d-web, 8037 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 8038 author = {Piwonski, J. and Slawig, T.}, 8039 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8040 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 8041 petsc_uses = {KSP} 8042} 8043 8044@Unpublished{ magpar, 8045 author = {W. Scholz}, 8046 title = {Magpar: Parallel Micromagnetics Code}, 8047 institution = {Vienna University of Technology}, 8048 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 8049 petsc_uses = {KSP} 8050} 8051 8052@Misc{ libmesh:sourceforge, 8053 author = {}, 8054 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 8055 equations on serial and parallel platforms}, 8056 note = {[Online]}, 8057 url = {http://libmesh.github.io}, 8058 petsc_uses = {KSP} 8059} 8060 8061@Misc{ moose-web-page, 8062 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 8063 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 8064 Gaston and John Peterson and Jason Miller}, 8065 institution = {Idaho National Laboratory}, 8066 howpublished = {\url{http://mooseframework.org}}, 8067 petsc_uses = {KSP} 8068} 8069 8070@Article{ gaston2009moose, 8071 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 8072 equations}, 8073 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 8074 journal = {Nuclear Engineering and Design}, 8075 volume = {239}, 8076 number = {10}, 8077 pages = {1768--1778}, 8078 year = {2009}, 8079 publisher = {Elsevier}, 8080 petsc_uses = {KSP} 8081} 8082 8083@Article{ tonks2012object, 8084 title = {An object-oriented finite element framework for multiphysics phase field 8085 simulations}, 8086 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 8087 journal = {Computational Materials Science}, 8088 volume = {51}, 8089 number = {1}, 8090 pages = {20--29}, 8091 year = {2012}, 8092 publisher = {Elsevier}, 8093 petsc_uses = {KSP} 8094} 8095 8096@Misc{ pylithmanual, 8097 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 8098 Strand and Charles Williams}, 8099 title = {{PyLith} User Manual Version 2.0.0}, 8100 year = {2014}, 8101 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 8102 petsc_uses = {KSP} 8103} 8104 8105@Misc{ pylith-web-page, 8106 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 8107 title = {{PyLith}}, 8108 year = {2012}, 8109 url = {http://geodynamics.org/resources/pylith/}, 8110 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 8111 petsc_uses = {KSP} 8112} 8113 8114@Misc{ galemanual, 8115 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 8116 title = {Gale User Manual Version 2.0.0}, 8117 year = {2011}, 8118 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 8119 petsc_uses = {KSP} 8120} 8121 8122@Unpublished{ underworld, 8123 author = {Louis Moresi}, 8124 title = {{UnderWorld}: A Geodynamics Modelling Code}, 8125 institution = {Monash University}, 8126 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 8127 petsc_uses = {KSP} 8128} 8129 8130@Article{ moresi2007computational, 8131 title = {Computational approaches to studying non-linear dynamics of the crust and 8132 mantle}, 8133 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 8134 M{\"u}hlhaus, H.B.}, 8135 journal = {Physics of the Earth and Planetary Interiors}, 8136 volume = {163}, 8137 number = {1-4}, 8138 pages = {69--82}, 8139 year = {2007}, 8140 publisher = {Elsevier}, 8141 petsc_uses = {KSP} 8142} 8143 8144@Article{ pitt2009chaste, 8145 title = {Chaste: a test-driven approach to software development for biological modelling}, 8146 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 8147 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 8148 and Walter, A. and others}, 8149 journal = {Computer Physics Communications}, 8150 volume = {180}, 8151 number = {12}, 8152 pages = {2452--2471}, 8153 year = {2009}, 8154 publisher = {Elsevier}, 8155 petsc_uses = {KSP} 8156} 8157 8158@Misc{ fenicsproject, 8159 title = {{The FEniCS project}}, 8160 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 8161 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 8162 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 8163 url = {http://fenicsproject.org}, 8164 year = {2011}, 8165 petsc_uses = {KSP} 8166} 8167 8168@Unpublished{ snark, 8169 title = {Snark: A suite of software for geoscientific applications and a philosophy of 8170 scientific software development}, 8171 institution = {Victorian Partnership for Advanced Computing}, 8172 url = {http://vpac.org/Snark}, 8173 petsc_uses = {KSP} 8174} 8175 8176@Misc{ imoose:sourceforge, 8177 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 8178 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 8179 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 8180 note = {[Online]}, 8181 url = {http://imoose.sourceforge.net}, 8182 petsc_uses = {KSP} 8183} 8184 8185@Unpublished{ fossi, 8186 author = {Stephan Frickenhaus}, 8187 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 8188 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 8189 codes}, 8190 institution = {AWI-Bremerhaven, Germanny}, 8191 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 8192 petsc_uses = {KSP} 8193} 8194 8195@Unpublished{ fun3dweb, 8196 author = {Dinesh Kaushik}, 8197 title = {PETSC-FUN3D Benchmark Page}, 8198 institution = {ODU/ANL}, 8199 url = {http://www.mcs.anl.gov/petsc-fun3d}, 8200 note = {CFD Benchmark of some solvers in PETSc}, 8201 petsc_uses = {KSP} 8202} 8203 8204@Unpublished{ scirun, 8205 author = {SCIRun Development Team}, 8206 title = {SCIRun}, 8207 institution = {University of Utah}, 8208 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 8209 note = {SCIRun now uses PETSc linear solvers}, 8210 petsc_uses = {KSP} 8211} 8212 8213@Misc{ prometheus, 8214 author = {Mark F. Adams}, 8215 title = {Prometheus - A scalable unstructured finite element solver}, 8216 institution = {Berkeley}, 8217 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 8218 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 8219 petsc_uses = {KSP} 8220} 8221 8222@Unpublished{ illuminator, 8223 author = {Adam C. Powell, IV}, 8224 title = {Illuminator Distributed Visualization Library}, 8225 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 8226 petsc_uses = {KSP} 8227} 8228 8229@Unpublished{ rheoplast, 8230 title = {RheoPlast Phase Field Multi-Physics Code}, 8231 author = {Adam Powell and David Dussault and Bo Zhou}, 8232 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 8233 petsc_uses = {KSP} 8234} 8235 8236@Misc{ tao-web-page, 8237 title = {{Toolkit for Advanced Optimization ({TAO})} {W}eb Page}, 8238 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8239 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 8240 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8241 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 8242 petsc_uses = {KSP} 8243} 8244 8245@TechReport{ tao-user-ref, 8246 title = {{Toolkit for Advanced Optimization ({TAO}) users manual}}, 8247 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8248 and Steve Benson and Lois Curfman McInnes}, 8249 institution = {Argonne National Laboratory}, 8250 year = {2019}, 8251 number = {ANL/MCS-TM-322 - Rev 3.12}, 8252 petsc_uses = {KSP} 8253} 8254 8255% url = "http://www.mcs.anl.gov/tao", 8256@Unpublished{ mefpp-web-page, 8257 title = {{MEF++} {W}eb {P}age}, 8258 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 8259 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 8260 author = {Eric Chamberland}, 8261 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 8262 multiphysics}, 8263 petsc_uses = {KSP} 8264} 8265 8266@Unpublished{ tipetsc-titanium, 8267 title = {Ti-PETSc - an interface to PETSc from Titanium}, 8268 institution = {Berkeley}, 8269 author = {He, Yun and Liblit, Bun and Lin, Chang}, 8270 url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=9f7959be13337c735d52e5c0b0994bdea6d75a96}, 8271 year = {1999}, 8272 petsc_uses = {KSP}, 8273} 8274 8275@Unpublished{ ptatin-web-page, 8276 title = {ptatin3d}, 8277 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 8278 url = {https://bitbucket.org/jedbrown/ptatin3d}, 8279 year = {2018}, 8280 petsc_uses = {KSP} 8281} 8282 8283@Misc{ multiphase-web-page, 8284 author = {Q. Zou}, 8285 title = {Multiphase flow with {PETSc}}, 8286 institution = {LANL}, 8287 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 8288 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 8289 lab = {LANL}, 8290 petsc_uses = {KSP} 8291} 8292 8293@Misc{ electromag-web-page, 8294 title = {{EMSolve Web} page}, 8295 institution = {LLNL}, 8296 howpublished = {http://www.llnl.gov/casc/emsolve}, 8297 url = {http://www.Llnl.gov/casc/emsolve}, 8298 author = {Daniel {White et al.}}, 8299 lab = {LLNL}, 8300 petsc_uses = {KSP} 8301} 8302 8303@Unpublished{ fe-software-web-page, 8304 institution = {Kuleuven}, 8305 title = {Finite element software}, 8306 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 8307 petsc_uses = {KSP} 8308} 8309 8310@Misc{ petsc-web-page, 8311 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8312 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 8313 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8314 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8315 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 8316 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 8317 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 8318 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 8319 Zhang}, 8320 title = {{PETS}c {W}eb page}, 8321 url = {https://petsc.org/}, 8322 howpublished = {\url{https://petsc.org/}}, 8323 year = {2023} 8324} 8325 8326@Unpublished{ petsc-debian-package, 8327 author = {Adam C. Powell, IV}, 8328 title = {Debian package for PETSc}, 8329 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 8330 petsc_uses = {KSP} 8331} 8332 8333@Unpublished{ cactus, 8334 title = {Cactus Website}, 8335 url = {http://www.cactuscode.org/}, 8336 note = {Provides two interface to the PETSc solvers}, 8337 petsc_uses = {KSP} 8338} 8339 8340@Unpublished{ petsc-fem, 8341 author = {Mario Storti and Norberto Nigro}, 8342 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 8343 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 8344 url = {http://www.cimec.org.ar/petscfem}, 8345 petsc_uses = {KSP} 8346} 8347 8348@Misc{ fidap, 8349 title = {FIDAP 8.5}, 8350 howpublished = {\url{http://www.fluent.com}}, 8351 url = {http://www.fluent.com}, 8352 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 8353 solves.}, 8354 key = {FIDAP 8.5}, 8355 petsc_uses = {KSP} 8356} 8357 8358@Unpublished{ slepc, 8359 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8360 Vicente Hern\'andez and Vicent Vidal}, 8361 title = {{SLEPc} Website}, 8362 url = {http://slepc.upv.es/}, 8363 note = {Scalable Library for Eigenvalue Problem Computations}, 8364 petsc_uses = {KSP} 8365} 8366 8367@TechReport{ slepc-users-manual, 8368 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8369 Vicente Hern\'andez and Vicent Vidal}, 8370 title = {{SLEPc} Users Manual}, 8371 number = {DISC-II/24/02}, 8372 url = {http://slepc.upv.es/}, 8373 note = {Scalable Library for Eigenvalue Problem Computations}, 8374 petsc_uses = {KSP} 8375} 8376 8377@Misc{ deal.ii, 8378 title = {deal.II}, 8379 howpublished = {\url{http://www.dealii.org}}, 8380 url = {http://www.dealii.org}, 8381 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 8382 It allows PETSc linear algebra and solvers to be used underneath.}, 8383 key = {deal.II 5.0}, 8384 petsc_uses = {KSP} 8385} 8386 8387@Article{ bangerth2007deal, 8388 title = {{deal.II---A general-purpose object-oriented finite element library}}, 8389 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 8390 journal = {ACM Transactions on Mathematical Software (TOMS)}, 8391 volume = {33}, 8392 number = {4}, 8393 pages = {24--es}, 8394 issn = {0098-3500}, 8395 year = {2007}, 8396 publisher = {ACM}, 8397 petsc_uses = {KSP} 8398} 8399 8400@Misc{ globalarrays, 8401 author = {Jarek {Nieplocha et al.}}, 8402 title = {Global Arrays}, 8403 institution = {Pacific Northwest National Laboratories}, 8404 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 8405 url = {http://www.emsl.pnl.gov/docs/global}, 8406 note = {Global arrays can use PETSc linear solvers}, 8407 lab = {PNNL}, 8408 petsc_uses = {KSP} 8409} 8410 8411% LiteralHTML: 8412% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 8413% LiteralHTML: 8414@Article{ petsccommunity2022, 8415 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 8416 Community}, 8417 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 8418 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 8419 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 8420 and Hong Zhang and Junchao Zhang}, 8421 journal = {Computing in Science and Engineering}, 8422 volume = {24}, 8423 number = {03}, 8424 pages = {6--15}, 8425 issn = {1558-366X}, 8426 doi = {10.1109/MCSE.2022.3169974}, 8427 publisher = {IEEE Computer Society}, 8428 address = {Los Alamitos, CA, USA}, 8429 month = may, 8430 year = {2022}, 8431 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 8432 petsc_uses = {KSP} 8433} 8434 8435@Article{ brownknepleysmith14, 8436 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 8437 title = {Run-time extensibility and librarization of simulation software}, 8438 journal = {IEEE Computing in Science and Engineering}, 8439 month = jan, 8440 volume = {17}, 8441 number = {1}, 8442 pages = {38--45}, 8443 doi = {10.1109/MCSE.2014.95}, 8444 year = {2015}, 8445 petsc_uses = {KSP} 8446} 8447 8448@TechReport{ ass2012, 8449 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 8450 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 8451 institution = {Argonne National Laboratory}, 8452 type = {Preprint}, 8453 year = {2012}, 8454 number = {ANL/MCS-P2011-0112}, 8455 petsc_uses = {KSP} 8456} 8457 8458@TechReport{ clearyknepley99, 8459 author = {Andrew Cleary and Matthew G. Knepley}, 8460 title = {Solvers as Operators}, 8461 institution = {Lawrence Livermore National Laboratory}, 8462 type = {Technical Report}, 8463 number = {UCRL-ID-135342}, 8464 year = {1999}, 8465 petsc_uses = {KSP} 8466} 8467 8468@TechReport{ smcabbkz2012, 8469 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 8470 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 8471 title = {{PETSc's} software strategy for the design space of composable extreme-scale 8472 solvers}, 8473 institution = {Argonne National Laboratory}, 8474 type = {Preprint}, 8475 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 8476 year = {2012}, 8477 number = {ANL/MCS-P2059-0312}, 8478 petsc_uses = {KSP} 8479} 8480 8481@InProceedings{ mhwpmhs2009, 8482 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 8483 and G. E. Hammond and B. Smith}, 8484 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 8485 Toolkit {MPI} at Scale}, 8486 booktitle = {Cray Users Group Conference}, 8487 year = {2009}, 8488 petsc_uses = {KSP} 8489} 8490 8491@InProceedings{ msmhls2010, 8492 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 8493 Lichtner and B. F. Smith}, 8494 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 8495 {BlueGene} Architectures}, 8496 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 8497 year = {2010}, 8498 petsc_uses = {KSP} 8499} 8500 8501@InCollection{ msk2013, 8502 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 8503 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 8504 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8505 series = {Lecture Notes in Earth System Sciences}, 8506 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8507 Yaolin Shi}, 8508 doi = {10.1007/978-3-642-16405-7_7}, 8509 publisher = {Springer Berlin Heidelberg}, 8510 pages = {131--140}, 8511 year = {2013}, 8512 isbn = {978-3-642-16404-0}, 8513 petsc_uses = {KSP} 8514} 8515 8516@InCollection{ knepleyyuen13, 8517 author = {Matthew G. Knepley and David A. Yuen}, 8518 title = {Why Scientists and Engineers need {GPU}s today}, 8519 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8520 series = {Lecture Notes in Earth System Sciences}, 8521 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8522 Yaolin Shi}, 8523 doi = {10.1007/978-3-642-16405-7_1}, 8524 publisher = {Springer Berlin Heidelberg}, 8525 pages = {131--140}, 8526 year = {2013}, 8527 isbn = {978-3-642-16404-0}, 8528 petsc_uses = {KSP} 8529} 8530 8531@InCollection{ karpeevknepleybrune13, 8532 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 8533 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 8534 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8535 series = {Lecture Notes in Earth System Sciences}, 8536 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8537 Yaolin Shi}, 8538 doi = {10.1007/978-3-642-16405-7_30}, 8539 publisher = {Springer Berlin Heidelberg}, 8540 pages = {487--501}, 8541 year = {2013}, 8542 isbn = {978-3-642-16404-0}, 8543 petsc_uses = {KSP} 8544} 8545 8546@InCollection{ zhengetal13, 8547 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 8548 Variable Viscosity}, 8549 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8550 Zhang and Yaolin Shi}, 8551 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8552 series = {Lecture Notes in Earth System Sciences}, 8553 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8554 Yaolin Shi}, 8555 doi = {10.1007/978-3-642-16405-7_21}, 8556 publisher = {Springer Berlin Heidelberg}, 8557 pages = {321--333}, 8558 year = {2013}, 8559 isbn = {978-3-642-16404-0}, 8560 petsc_uses = {KSP} 8561} 8562 8563@Article{ zhengetal13b, 8564 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 8565 strongly variable viscosity based on {M}atlab and {CUDA}}, 8566 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8567 Zhang and Yaolin Shi}, 8568 journal = {IJHPCA}, 8569 volume = {28}, 8570 number = {1}, 8571 pages = {50--60}, 8572 doi = {10.1177/1094342013478640}, 8573 year = {2013}, 8574 petsc_uses = {KSP} 8575} 8576 8577@InBook{ s2011, 8578 author = {B. Smith}, 8579 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 8580 title = {Encyclopedia of Parallel Computing}, 8581 bookeditor = {D. Padua}, 8582 publisher = {Springer}, 8583 year = {2011}, 8584 petsc_uses = {KSP} 8585} 8586 8587@Article{ acostamejia06, 8588 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 8589 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 8590 journal = {Lecturas Matem\'aticas}, 8591 volume = {27}, 8592 year = {2006}, 8593 pages = {213--224}, 8594 petsc_uses = {KSP} 8595} 8596 8597@InProceedings{ quenettemoresisunterappelbe07, 8598 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 8599 title = {Explaining StGermain: An aspect oriented environment for building extensible 8600 computational mechanics modeling software}, 8601 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 8602 publisher = {IEEE}, 8603 pages = {1--8}, 8604 yerar = {2007}, 8605 petsc_uses = {KSP} 8606} 8607 8608@Article{ dfm1, 8609 title = {Vectorized sparse matrix multiply for compressed row storage format}, 8610 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 8611 journal = {Lecture Notes in Computer Science}, 8612 year = {2005}, 8613 pages = {99--106}, 8614 volume = {3514}, 8615 lab = {ORNL}, 8616 petsc_uses = {KSP} 8617} 8618 8619@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 8620 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 8621 Vandewalle and Stefaan Poedts}, 8622 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 8623 Scientific Computing Software}, 8624 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 8625 year = {2005}, 8626 note = {Lecture Notes in Computer Science}, 8627 volume = {3514}, 8628 publisher = {Springer-Verlag GmbH}, 8629 petsc_uses = {KSP} 8630} 8631 8632@InProceedings{ dalcin-paz-storti, 8633 author = {L. Dalcin and R. Paz and M. Storti}, 8634 title = {Desarrollo de Aplicaciones Paralelas en Python}, 8635 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 8636 Bariloche, Argentina}, 8637 year = {2004}, 8638 petsc_uses = {KSP} 8639} 8640 8641@Article{ mpi-python, 8642 author = {L. Dalcin and R. Paz and M. Storti}, 8643 title = {MPI for Python}, 8644 journal = {Journal of Parallel and Distributed Computing}, 8645 year = {2005}, 8646 petsc_uses = {KSP} 8647} 8648 8649@Unpublished{ hrv02a, 8650 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 8651 author = {V. Hernandex and J. E. Roman and V. Vidal}, 8652 note = {Submited to VecPar 2002}, 8653 year = {2002}, 8654 petsc_uses = {KSP} 8655} 8656 8657@Article{ knyazev2007block, 8658 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 8659 {PETSc}}, 8660 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 8661 journal = {SIAM Journal on Scientific Computing}, 8662 volume = {29}, 8663 pages = {2224-2239}, 8664 doi = {10.1137/060661624}, 8665 year = {2007}, 8666 petsc_uses = {KSP} 8667} 8668 8669@MastersThesis{ aarrestad-master, 8670 author = {Asbjorn Hoiland Aarrestad}, 8671 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 8672 school = {University of Bergen}, 8673 month = aug, 8674 year = {2003}, 8675 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 8676 note = {Implemented Runge-Kutta methods using PETSc}, 8677 petsc_uses = {KSP} 8678} 8679 8680@PhDThesis{ kaushik-phd, 8681 author = {D. K. Kaushik}, 8682 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 8683 Differential Equations on Unstructured Grids}, 8684 school = {Old Dominion University}, 8685 month = dec, 8686 year = {2002}, 8687 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 8688 petsc_uses = {KSP} 8689} 8690 8691@TechReport{ rb1, 8692 author = {Rickard Bergstrom}, 8693 title = {Object Oriented Implementation of a General Finite Element Code}, 8694 number = {2002-13}, 8695 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 8696 year = {2002}, 8697 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 8698 note = {Discribes a finite element software package that uses PETSc for its solvers}, 8699 petsc_uses = {KSP} 8700} 8701 8702@InProceedings{ dbl1, 8703 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 8704 title = {A Parallel General Purpose Finite Element System}, 8705 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 8706 publisher = {SIAM}, 8707 year = {1999}, 8708 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 8709 note = {Describes software that uses PETSc for its parallel linear solves}, 8710 petsc_uses = {KSP} 8711} 8712 8713@Article{ p1, 8714 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 8715 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 8716 and B. Smith}, 8717 journal = {Parallel Computing}, 8718 year = {2002}, 8719 pages = {1811--1831}, 8720 volume = {28 (12)}, 8721 petsc_uses = {KSP} 8722} 8723 8724@Article{ automatic-ad, 8725 author = {Paul Hovland and Boyana Norris and Barry Smith}, 8726 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 8727 year = {2005}, 8728 journal = {Future Generation Computer Systems}, 8729 volume = {21}, 8730 number = {8}, 8731 pages = {1426--1438}, 8732 petsc_uses = {KSP} 8733} 8734 8735@TechReport{ remote-math, 8736 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 8737 Smith}, 8738 title = {Remote Access to Mathematical Software}, 8739 number = {ANL/MCS-P889-0601}, 8740 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8741 month = jun, 8742 year = {2001}, 8743 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 8744 petsc_uses = {KSP} 8745} 8746 8747@InProceedings{ gropp98, 8748 author = {William D. Gropp}, 8749 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 8750 publisher = {SIAM}, 8751 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8752 Scientific and Engineering Computing}, 8753 year = {1999}, 8754 pages = {21-29}, 8755 petsc_uses = {KSP} 8756} 8757 8758@InProceedings{ knepleysarin99, 8759 author = {Matthew Knepley and Vivek Sarin}, 8760 title = {Algorithm Development for Large Scale Computing}, 8761 publisher = {SIAM}, 8762 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8763 Scientific and Engineering Computing}, 8764 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}}, 8765 year = {1999}, 8766 petsc_uses = {KSP} 8767} 8768 8769@InBook{ bgms00, 8770 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8771 chapter = {Software for the Scalable Solution of {PDEs}}, 8772 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 8773 title = {CRPC Handbook of Parallel Computing}, 8774 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 8775 and A. White}, 8776 publisher = {Morgan Kaufmann Publishers}, 8777 year = {2002}, 8778 petsc_uses = {KSP} 8779} 8780 8781@InProceedings{ hovland_norris_smith98, 8782 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 8783 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 8784 Computations}, 8785 publisher = {SIAM}, 8786 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8787 Scientific and Engineering Computing}, 8788 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 8789 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 8790 year = {1999}, 8791 pages = {129-137}, 8792 petsc_uses = {KSP} 8793} 8794 8795@InProceedings{ efficient, 8796 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 8797 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 8798 Libraries}, 8799 booktitle = {Modern Software Tools in Scientific Computing}, 8800 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 8801 publisher = {Birkhauser Press}, 8802 pages = {163--202}, 8803 year = {1997}, 8804 petsc_uses = {KSP} 8805} 8806 8807% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 8808@TechReport{ petsc-user-ref, 8809 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8810 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 8811 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8812 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8813 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 8814 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 8815 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 8816 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 8817 Zhang}, 8818 title = {{PETSc/TAO} Users Manual}, 8819 institution = {Argonne National Laboratory}, 8820 number = {ANL-21/39 - Revision 3.20}, 8821 doi = {10.2172/2205494}, 8822 year = {2023} 8823} 8824 8825% url = {https://petsc.org/release} 8826@TechReport{ petsc-developers, 8827 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 8828 title = {{PETS}c Developers Guide}, 8829 institution = {Argonne National Laboratory}, 8830 number = {ANL-18/18}, 8831 year = {2018}, 8832 url = {https://petsc.org/release/developers}, 8833 petsc_uses = {KSP} 8834} 8835 8836@Unpublished{ alice-memory-snooper, 8837 author = {Ibrahima Ba and Barry~F. Smith}, 8838 title = {The {ALICE} Memory Snooper}, 8839 year = {1999}, 8840 petsc_uses = {KSP} 8841} 8842 8843@TechReport{ petsc-user-ref-polish, 8844 author = {Marcin Bojko and Piotr Krzyzanowski}, 8845 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 8846 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 8847 year = {1998}, 8848 note = {An introduction to PETSc in Polish}, 8849 petsc_uses = {KSP} 8850} 8851 8852@InProceedings{ abghmn00, 8853 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 8854 High-Performance Scientific Computing}, 8855 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 8856 Norris}, 8857 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 8858 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 8859 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 8860 Hasco\"{e}t and Uwe Naumann}, 8861 publisher = {Springer}, 8862 year = {2002}, 8863 petsc_uses = {KSP} 8864} 8865 8866@Unpublished{ petsc-mpi-paper, 8867 author = {Lois Curfman McInnes and Barry F. Smith}, 8868 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 8869 Libraries}, 8870 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 8871 month = jun, 8872 year = {1995}, 8873 petsc_uses = {KSP} 8874} 8875 8876@InProceedings{ miss-paper, 8877 author = {William D. Gropp and Barry F. Smith}, 8878 title = {Scalable, Extensible, and Portable Numerical Libraries}, 8879 publisher = {IEEE}, 8880 year = {1994}, 8881 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 8882 address = {Mississippi State University}, 8883 pages = {87--93}, 8884 keyword = {numerical libraries, scientific computing, parallel computing}, 8885 petsc_uses = {KSP} 8886} 8887 8888@InProceedings{ snes-paper, 8889 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 8890 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 8891 Minimization Problems}, 8892 publisher = {IEEE}, 8893 year = {1995}, 8894 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 8895 address = {Mississippi State University}, 8896 pages = {60-67}, 8897 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 8898 petsc_uses = {KSP} 8899} 8900 8901@Article{ dsneutral, 8902 author = {Barry F. Smith and William D. Gropp}, 8903 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 8904 Sparse Linear Systems}, 8905 journal = {Scientific Programming}, 8906 volume = {5}, 8907 pages = {329--336}, 8908 key = {GroppSmith96 ! KSP design}, 8909 year = {1996}, 8910 petsc_uses = {KSP} 8911} 8912 8913@InProceedings{ bgms98, 8914 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 8915 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 8916 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8917 Scientific and Engineering Computing}, 8918 publisher = {SIAM}, 8919 pages = {58-67}, 8920 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 8921 year = {1998}, 8922 petsc_uses = {KSP} 8923} 8924 8925@Article{ hkm98, 8926 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 8927 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 8928 {PDE} Computation}, 8929 journal = {Advances in Engineering Software}, 8930 volume = {29}, 8931 pages = {415-424}, 8932 year = {1998}, 8933 petsc_uses = {KSP} 8934} 8935 8936@TechReport{ pdpta99, 8937 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 8938 Smith}, 8939 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 8940 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 8941 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 8942 Vegas, Nevada}, 8943 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8944 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 8945 number = {ANL/MCS-P751-0599}, 8946 year = {1999}, 8947 petsc_uses = {KSP} 8948} 8949 8950@InProceedings{ bbh:com, 8951 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 8952 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 8953 Computing}}, 8954 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 8955 Euro-Par Conference, Munich, Germany, August/September 2000}, 8956 year = {2000}, 8957 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 8958 volume = {1900}, 8959 series = {Lecture Notes in Computer Science}, 8960 pages = {86--94}, 8961 address = {Berlin}, 8962 publisher = {Springer}, 8963 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 8964 petsc_uses = {KSP} 8965} 8966 8967@InProceedings{ overture00, 8968 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8969 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 8970 Components}, 8971 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 8972 booktitle = {Proceedings of the International Federation for Information Processing Working 8973 Conference on Software Architectures for Scientific Computing, Kluwer}, 8974 year = {2000}, 8975 pages = {57--68}, 8976 petsc_uses = {KSP} 8977} 8978 8979@TechReport{ smith97, 8980 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 8981 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 8982 number = {ANL/MCS-P701}, 8983 author = {Barry F. Smith}, 8984 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8985 petsc_uses = {KSP} 8986} 8987 8988@Article{ smith98, 8989 author = {Barry Smith}, 8990 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 8991 journal = {SIGNUM Newsletter}, 8992 year = {1998}, 8993 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 8994 petsc_uses = {KSP} 8995} 8996 8997@TechReport{ ad-petsc-tm, 8998 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 8999 {PETSc}}, 9000 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 9001 year = {1997}, 9002 type = {Technical Memorandum}, 9003 institution = {ANL}, 9004 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 9005 number = {ANL/MCS-TM-233}, 9006 petsc_uses = {KSP} 9007} 9008 9009% LiteralHTML: 9010% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 9011% LiteralHTML: 9012@PhDThesis{ klotzthesis2019, 9013 author = {Thomas S. Klotz}, 9014 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 9015 Biology}, 9016 school = {Rice University}, 9017 year = {2019}, 9018 petsc_uses = {KSP} 9019} 9020 9021@Article{ klotzbardhanknepley2018, 9022 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 9023 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 9024 journal = {arXiv e-prints}, 9025 eprint = {1708.06028}, 9026 archiveprefix = {arXiv}, 9027 primaryclass = {math.na}, 9028 year = {2018}, 9029 note = {\url{http://arxiv.org/abs/1708.06028}}, 9030 petsc_uses = {KSP} 9031} 9032 9033@Misc{ brown2016, 9034 title = {Threading Tradeoffs in Domain Decomposition}, 9035 author = {Jed Brown}, 9036 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 9037 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 9038 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 9039 year = {2016}, 9040 petsc_uses = {KSP} 9041} 9042 9043@Article{ changnakshatralaknepleyjohnsson2017, 9044 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 9045 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 9046 Johnsson}, 9047 journal = {Concurency: Practice and Experience}, 9048 volume = {30}, 9049 number = {11}, 9050 eprint = {1705.03625}, 9051 doi = {10.1002/cpe.4401}, 9052 year = {2017}, 9053 petsc_uses = {KSP} 9054} 9055 9056@Article{ changfabienknepleymills2018, 9057 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 9058 spectrum analysis}, 9059 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 9060 journal = {SIAM Journal on Scientific Computing}, 9061 volume = {40}, 9062 number = {6}, 9063 pages = {C779--C802}, 9064 eprint = {1802.07832}, 9065 doi = {10.1137/18M1172260}, 9066 year = {2018}, 9067 petsc_uses = {KSP} 9068} 9069 9070@Article{ joshaghanichangnakshatralaknepley2019, 9071 title = {Composable solvers for the four-field double porosity/permeability model}, 9072 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 9073 Knepley}, 9074 journal = {Journal of Computational Physics}, 9075 volume = {386}, 9076 pages = {428--466}, 9077 doi = {10.1016/j.jcp.2019.02.020}, 9078 year = {2019}, 9079 petsc_uses = {KSP} 9080} 9081 9082@InProceedings{ barralknepleylangepiggottgorman2016, 9083 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 9084 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 9085 and Gerard J. Gorman}, 9086 booktitle = {25th International Meshing Roundtable}, 9087 editor = {Steve Owen and Hang Si}, 9088 month = sep, 9089 address = {Washington, DC}, 9090 pages = {1--5}, 9091 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 9092 year = {2016}, 9093 petsc_uses = {KSP} 9094} 9095 9096@Article{ adamsbrownknepleysamtaney2016, 9097 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 9098 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 9099 journal = {SIAM Journal on Scientific Computing}, 9100 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 9101 epub = {http://arxiv.org/abs/1406.7808}, 9102 volume = {8}, 9103 number = {4}, 9104 pages = {C426--C440}, 9105 doi = {10.1137/140975127}, 9106 year = {2016}, 9107 petsc_uses = {KSP} 9108} 9109 9110@InProceedings{ maysananruppknepleysmith2016, 9111 title = {Extreme-Scale Multigrid Components within {PETSc}}, 9112 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 9113 Smith}, 9114 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 9115 series = {PASC '16}, 9116 isbn = {978-1-4503-4126-4}, 9117 location = {Lausanne, Switzerland}, 9118 pages = {5:1--5:12}, 9119 articleno = {5}, 9120 numpages = {12}, 9121 doi = {10.1145/2929908.2929913}, 9122 acmid = {2929913}, 9123 publisher = {ACM}, 9124 address = {New York, NY, USA}, 9125 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 9126 preconditioning}, 9127 year = {2016}, 9128 petsc_uses = {KSP} 9129} 9130 9131@Article{ liu2015field, 9132 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 9133 author = {Lulu Liu and David E Keyes}, 9134 journal = {SIAM Journal on Scientific Computing}, 9135 volume = {37}, 9136 number = {3}, 9137 pages = {A1388--A1409}, 9138 year = {2015}, 9139 publisher = {SIAM}, 9140 petsc_uses = {KSP} 9141} 9142 9143@Article{ lujiaomissirlis2014, 9144 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 9145 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 9146 journal = {Numerical Linear Algebra with Applications}, 9147 volume = {21}, 9148 number = {2}, 9149 pages = {221--238}, 9150 year = {2014}, 9151 publisher = {Wiley Online Library}, 9152 petsc_uses = {KSP} 9153} 9154 9155@Article{ badiamartinprincipe2013, 9156 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 9157 solid mechanics}, 9158 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 9159 journal = {International Journal for Numerical Methods in Engineering}, 9160 volume = {96}, 9161 number = {4}, 9162 pages = {203--230}, 9163 year = {2013}, 9164 petsc_uses = {KSP} 9165} 9166 9167@Article{ morganknepleysananscott2016, 9168 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 9169 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 9170 journal = {Concurrency and Computation: Practice and Experience}, 9171 volume = {28}, 9172 pages = {4532--4542}, 9173 year = {2016}, 9174 url = {http://arxiv.org/abs/1602.04873}, 9175 doi = {10.1002/cpe.3820}, 9176 petsc_uses = {KSP} 9177} 9178 9179@Article{ morgansananknepleymills2020, 9180 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 9181 solvers}, 9182 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 9183 journal = {The International Journal of High Performance Computing Applications}, 9184 volume = {35}, 9185 issue = {1}, 9186 doi = {10.1177/1094342020966835}, 9187 url = {https://doi.org/10.1177/1094342020966835}, 9188 eprint = {https://doi.org/10.1177/1094342020966835}, 9189 year = {2020}, 9190 petsc_uses = {KSP} 9191} 9192 9193@Article{ msz2013, 9194 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 9195 author = {M. McCourt and B. F. Smith and H. Zhang}, 9196 journal = {SIAM Journal on Matrix Analysis and Applications}, 9197 year = {2015}, 9198 note = {To appear}, 9199 petsc_uses = {KSP} 9200} 9201 9202@Article{ bassi2014agglomeration, 9203 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 9204 free}, 9205 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 9206 journal = {Mathematical Models and Methods in Applied Sciences}, 9207 volume = {24}, 9208 number = {08}, 9209 pages = {1495--1539}, 9210 year = {2014}, 9211 publisher = {World Scientific}, 9212 petsc_uses = {KSP} 9213} 9214 9215@Article{ jhuranidemkowicz12, 9216 author = {{Jhurani}, C. and {Demkowicz}, L.}, 9217 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 9218 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 9219 journal = {Computer Methods in Applied Mechanics and Engineering}, 9220 volume = {213}, 9221 pages = {418-426}, 9222 year = {2012}, 9223 month = mar, 9224 doi = {10.1016/j.cma.2011.06.003}, 9225 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 9226 petsc_uses = {KSP} 9227} 9228 9229@Article{ yangcai11, 9230 author = {Yang, Haijian and Cai, Xiao-Chuan}, 9231 title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear 9232 Complementarity Problems}, 9233 journal = {J. Sci. Comput.}, 9234 issue_date = {May 2011}, 9235 volume = {47}, 9236 number = {2}, 9237 month = may, 9238 pages = {258--280}, 9239 year = {2011}, 9240 issn = {0885-7474}, 9241 numpages = {23}, 9242 doi = {10.1007/s10915-010-9436-4}, 9243 acmid = {1971246}, 9244 publisher = {Plenum Press}, 9245 address = {New York, NY, USA}, 9246 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 9247 preconditioners, Semismooth Newton, Two-level methods}, 9248 petsc_uses = {KSP} 9249} 9250 9251@Article{ rheinbach09, 9252 author = {Rheinbach, Oliver}, 9253 title = {Parallel Iterative Substructuring in Structural Mechanics}, 9254 journal = {Archives of Computational Methods in Engineering}, 9255 volume = {16}, 9256 number = {4}, 9257 pages = {425-463}, 9258 year = {2009}, 9259 issn = {1134-3060}, 9260 doi = {10.1007/s11831-009-9035-4}, 9261 publisher = {Springer Netherlands}, 9262 language = {English}, 9263 petsc_uses = {KSP} 9264} 9265 9266@Article{ knepleyterrel2013, 9267 author = {Matthew G. Knepley and Andy R. Terrel}, 9268 title = {Finite Element Integration on {GPUs}}, 9269 journal = {{ACM} Transactions on Mathematical Software}, 9270 volume = {39}, 9271 number = {2}, 9272 accepted = {17 April 2012}, 9273 year = {2013}, 9274 abstract = {We present a novel finite element integration method for low order elements on 9275 GPUs. We achieve more than 100GF for element integration on first order 9276 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 9277 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 9278 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 9279 url = {http://arxiv.org/abs/1103.0066}, 9280 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 9281 petsc_uses = {KSP} 9282} 9283 9284@Article{ knepleyruppterrel2016, 9285 title = {Finite Element Integration with Quadrature on the GPU}, 9286 journal = {ArXiv e-prints}, 9287 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 9288 version = {1}, 9289 date = {2016-07-14}, 9290 eprinttype = {arxiv}, 9291 eprintclass = {cs.MS}, 9292 eprint = {1607.04245v1}, 9293 petsc_uses = {KSP} 9294} 9295 9296@Article{ klawonnlanserrheinbach2014, 9297 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 9298 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 9299 journal = {SIAM Journal on Scientific Computing}, 9300 volume = {36}, 9301 number = {2}, 9302 pages = {A737--A765}, 9303 year = {2014}, 9304 petsc_uses = {KSP} 9305} 9306 9307@Article{ bruneknepleysmithtu15, 9308 title = {Composing Scalable Nonlinear Algebraic Solvers}, 9309 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 9310 journal = {SIAM Review}, 9311 volume = {57}, 9312 number = {4}, 9313 pages = {535--565}, 9314 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 9315 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 9316 doi = {10.1137/130936725}, 9317 year = {2015}, 9318 petsc_uses = {KSP} 9319} 9320 9321@Article{ mszm2014, 9322 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 9323 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9324 volume = {40}, 9325 pages = {17--31}, 9326 year = {2014}, 9327 journal = {Parallel Computing}, 9328 doi = {10.1016/j.parco.2013.10.001}, 9329 petsc_uses = {KSP} 9330} 9331 9332@TechReport{ mszm2012, 9333 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 9334 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9335 year = {2012}, 9336 number = {ANL/MCS-P2097-0512}, 9337 institution = {Argonne National Laboratory}, 9338 petsc_uses = {KSP} 9339} 9340 9341@InProceedings{ bkmms2012, 9342 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 9343 F. Smith}, 9344 title = {Composable linear solvers for multiphysics}, 9345 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 9346 Computing} ({ISPDC} 2012)}, 9347 year = {2012}, 9348 doi = {10.1109/ISPDC.2012.16}, 9349 publisher = {IEEE Computer Society}, 9350 pages = {55--62}, 9351 petsc_uses = {KSP} 9352} 9353 9354@Article{ bourdinbucuroudet2009, 9355 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 9356 title = {Optimal Partitions for Eigenvalues}, 9357 journal = {SIAM J. Sci. Comput.}, 9358 volume = {31}, 9359 number = {6}, 9360 pages = {4100--4114}, 9361 year = {2009}, 9362 petsc_uses = {KSP} 9363} 9364 9365@InBook{ kimnbourdin2007, 9366 author = {J.-H. Kimn and Blaise Bourdin}, 9367 title = {Numerical implementation of overlapping balancing domain decomposition methods on 9368 unstructured meshes}, 9369 editor = {O. B. Widlund and D. E. Keyes}, 9370 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 9371 series = {Lecture Notes in Computational Science and Engineering}, 9372 number = {55}, 9373 publisher = {Springer-Verlag}, 9374 pages = {309--315}, 9375 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 9376 year = {2007}, 9377 petsc_uses = {KSP} 9378} 9379 9380@Article{ bjm2005, 9381 author = {AH Baker and ER Jessup and T Manteuffel}, 9382 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 9383 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 9384 year = {2005}, 9385 petsc_uses = {KSP} 9386} 9387 9388@Unpublished{ sundar-2008a, 9389 author = {R.S. Sampath and G. Biros}, 9390 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 9391 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9392 petsc_uses = {KSP} 9393} 9394 9395@Article{ sundar-2008, 9396 author = {H. Sundar and R.S. Sampath and G. Biros}, 9397 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 9398 journal = {SIAM Journal on Scientific Computing}, 9399 year = {2008}, 9400 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9401 petsc_uses = {KSP} 9402} 9403 9404@InProceedings{ sundar-2007, 9405 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 9406 title = {Low-constant parallel algorithms for finite element simulations using linear 9407 octrees}, 9408 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 9409 year = {2007}, 9410 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9411 petsc_uses = {KSP} 9412} 9413 9414@InProceedings{ adams-98a, 9415 author = {Adams, Mark ~F.}, 9416 title = {A Parallel Maximal Independent Set Algorithm}, 9417 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 9418 year = {1998}, 9419 petsc_uses = {KSP} 9420} 9421 9422@Article{ akcelik2005ddd, 9423 title = {{Dynamic data-driven inversion for terascale simulations: real-time 9424 identification of airborne contaminants}}, 9425 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 9426 van Bloemen Waanders, B.}, 9427 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 9428 year = {2005}, 9429 publisher = {IEEE Computer Society Washington, DC, USA}, 9430 petsc_uses = {KSP} 9431} 9432 9433@InBook{ akcelik-2006, 9434 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 9435 Bloemen Waanders}, 9436 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 9437 title = {Frontiers of Parallel Computing}, 9438 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 9439 publisher = {SIAM}, 9440 year = {2006}, 9441 petsc_uses = {KSP} 9442} 9443 9444@Article{ dt, 9445 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 9446 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 9447 Convection Diffusion Equations}, 9448 journal = {The Journal of Supercomputing}, 9449 year = {2004}, 9450 pages = {235--253}, 9451 volume = {28}, 9452 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 9453 petsc_uses = {KSP} 9454} 9455 9456@PhDThesis{ hwang2004, 9457 author = {Feng-Nan Hwang}, 9458 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 9459 Computational Fluid Dynamics}, 9460 school = {University of Colorado at Boulder}, 9461 year = {2004}, 9462 petsc_uses = {KSP} 9463} 9464 9465@PhDThesis{ baker, 9466 author = {{A. H.} Baker}, 9467 title = {On improving the performance of the linear solver restarted {GMRES}}, 9468 school = {University of Colorado at Boulder}, 9469 year = {2003}, 9470 petsc_uses = {KSP} 9471} 9472 9473@TechReport{ klawonnrheinbach601, 9474 author = {Axel Klawonn and Oliver Rheinbach}, 9475 title = {A Parallel Implementation of Dual-Primal {FETI-DP} Methods for Three Dimensional 9476 Linear Elasticity Using a Transformation of Basis}, 9477 institution = {Universit\"at Duisburg-Essen}, 9478 year = {2005}, 9479 type = {Technical Report}, 9480 number = {SM-E-601}, 9481 petsc_uses = {KSP} 9482} 9483 9484@TechReport{ klawonnrheinbach609, 9485 author = {Axel Klawonn and Oliver Rheinbach}, 9486 title = {Inexact FETI-DP Methods}, 9487 institution = {Universit\"at Duisburg-Essen}, 9488 year = {2005}, 9489 type = {Technical Report}, 9490 number = {SM-E-609}, 9491 petsc_uses = {KSP} 9492} 9493 9494@TechReport{ klawonnrheinbach607, 9495 author = {Axel Klawonn and Oliver Rheinbach}, 9496 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 9497 institution = {Universit\"at Duisburg-Essen}, 9498 year = {2005}, 9499 type = {Technical Report}, 9500 number = {SM-E-607}, 9501 petsc_uses = {KSP} 9502} 9503 9504@Article{ kul-natraj-pbp, 9505 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 9506 title = {Performance of a parallel mixed finite element implementation for fourth order 9507 clamped anisotropic plate bending problems in distributed memory environments}, 9508 journal = {Applied Mathematics and Computation}, 9509 volume = {155}, 9510 year = {2004}, 9511 number = {3}, 9512 pages = {753--777}, 9513 petsc_uses = {KSP} 9514} 9515 9516@Article{ bramkamp2006uej, 9517 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 9518 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 9519 journal = {Computers \& Fluids}, 9520 volume = {35}, 9521 number = {10}, 9522 pages = {1063--1073}, 9523 doi = {10.1016/j.compfluid.2005.10.003}, 9524 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 9525 derivation of the analytic flux Jacobian can become quite complicated depending on 9526 the complexity of the numerical flux calculation. Practically, the derivation of 9527 the exact Jacobian by hand is an unrealistic option because of the enormous 9528 man-hour investment needed. In this work, automatic differentiation is used to 9529 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 9530 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 9531 approximated by first-order forward differences. For a two-dimensional airfoil 9532 under three different flight conditions (quasi-incompressible flow, compressible 9533 subsonic flow, and transonic flow), we show that the robustness and performance of 9534 the present finite volume scheme is significantly improved by using exact 9535 Jacobians.}, 9536 year = {2006}, 9537 petsc_uses = {KSP} 9538} 9539 9540@Article{ shahbazi1, 9541 author = {Khosro Shahbazi}, 9542 title = {An explicit expression for the penalty parameter of the interior penalty method}, 9543 journal = {Journal of Computational Physics}, 9544 volume = {205}, 9545 year = {2005}, 9546 pages = {401--407}, 9547 petsc_uses = {KSP} 9548} 9549 9550@TechReport{ kk, 9551 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 9552 author = {Hans-Peter Kersken and Uwe Kuster}, 9553 year = {1999}, 9554 institution = {University of Stuttgart}, 9555 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 9556 number = {310}, 9557 petsc_uses = {KSP} 9558} 9559 9560@Article{ miha-mija, 9561 author = {M. D. Mihajlovi and S. Mijalkovi}, 9562 title = {A component decomposition preconditioning for 3D stress analysis problems}, 9563 journal = {Numerical Linear Algebra with Applications}, 9564 volume = {9}, 9565 year = {2002}, 9566 pages = {567--583}, 9567 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 9568 petsc_uses = {KSP} 9569} 9570 9571@Article{ bjm, 9572 author = {M Benzi and W Joubert and G Mateescu}, 9573 journal = {Electronic Transactions on Numerical Analysis}, 9574 year = {1999}, 9575 volume = {8}, 9576 pages = {88--114}, 9577 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 9578 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}, 9579 petsc_uses = {KSP} 9580} 9581 9582@PhDThesis{ hyde, 9583 author = {EMK Hyde}, 9584 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 9585 school = {Caltech}, 9586 year = {2003}, 9587 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 9588 petsc_uses = {KSP} 9589} 9590 9591@Article{ km2003, 9592 author = {A. Keese and H. G. Matthies}, 9593 journal = {Proceedings in Applied Mathematics and Mechanics}, 9594 year = {2003}, 9595 volume = {2}, 9596 pages = {485--486}, 9597 title = {Parallel Solution of Stochastic PDEs}, 9598 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 9599 petsc_uses = {KSP} 9600} 9601 9602@Article{ whszss, 9603 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 9604 and Otmar Scherzer and H. Siegfried Stiehl}, 9605 journal = {Real Time Imaging}, 9606 year = {2001}, 9607 volume = {7}, 9608 pages = {31--45}, 9609 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 9610 approaches}, 9611 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 9612 petsc_uses = {KSP} 9613} 9614 9615@TechReport{ baker1, 9616 title = {An Efficient Block Variant of GMRES}, 9617 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 9618 year = {2003}, 9619 type = {Technical Report}, 9620 institution = {University of Colorado, Boulder}, 9621 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 9622 number = {CU-CS-957-03}, 9623 petsc_uses = {KSP} 9624} 9625 9626@InProceedings{ mc2003, 9627 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 9628 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 9629 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9630 Methods}, 9631 pages = {639--646}, 9632 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9633 note = {}, 9634 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9635 year = {2003}, 9636 petsc_uses = {KSP} 9637} 9638 9639@InProceedings{ kt2003, 9640 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 9641 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 9642 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9643 Methods}, 9644 pages = {615--622}, 9645 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9646 note = {}, 9647 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9648 year = {2003}, 9649 petsc_uses = {KSP} 9650} 9651 9652@InProceedings{ krw2003, 9653 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 9654 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 9655 3D}, 9656 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9657 Methods}, 9658 pages = {361--368}, 9659 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9660 note = {}, 9661 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9662 year = {2003}, 9663 petsc_uses = {KSP} 9664} 9665 9666@InProceedings{ hc2003, 9667 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 9668 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 9669 Nonlinear Preconditioning}, 9670 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9671 Methods}, 9672 pages = {201--208}, 9673 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9674 note = {}, 9675 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9676 year = {2003}, 9677 petsc_uses = {KSP} 9678} 9679 9680@InProceedings{ g2003, 9681 author = {P. Goldfeld}, 9682 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 9683 (Generalized) {Stokes} and Parallel Implementation}, 9684 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9685 Methods}, 9686 pages = {209--216}, 9687 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9688 publisher = {National Autonomous University of Mexico (UNAM)}, 9689 note = {}, 9690 url = {http://www.ddm.org/DD14}, 9691 year = {2003}, 9692 petsc_uses = {KSP} 9693} 9694 9695@InProceedings{ dhv2003, 9696 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 9697 title = {Toward scalable {FETI} algorithm for variational inequalities with applications to 9698 composites}, 9699 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9700 Methods}, 9701 pages = {395--401}, 9702 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9703 publisher = {National Autonomous University of Mexico (UNAM)}, 9704 note = {}, 9705 url = {http://www.ddm.org/DD14}, 9706 year = {2003}, 9707 petsc_uses = {KSP} 9708} 9709 9710@InProceedings{ dhsv2002, 9711 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9712 title = {Scalabilities of {FETI} for variational inequalities and contact shape 9713 optimization}, 9714 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9715 Methods}, 9716 pages = {359--367}, 9717 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9718 publisher = {CIMNE, Barcelona, Spain}, 9719 note = {}, 9720 url = {http://www.ddm.org/DD13}, 9721 year = {2002}, 9722 petsc_uses = {KSP} 9723} 9724 9725@InProceedings{ cky2002, 9726 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 9727 title = {A Nonlinear Additive {S}chwarz Preconditioned Inexact {N}ewton Method for Shocked 9728 Duct Flows}, 9729 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9730 Methods}, 9731 pages = {343--350}, 9732 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9733 publisher = {CIMNE, Barcelona, Spain}, 9734 note = {}, 9735 url = {http://www.ddm.org/DD13}, 9736 year = {2002}, 9737 petsc_uses = {KSP} 9738} 9739 9740@Conference{ li-etal:03, 9741 author = {Li, Z. and Lanteri S. and Saad, Y.}, 9742 title = {Multiplicative-additive preconditioning combination for general sparse linear 9743 systems}, 9744 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 9745 Matrix Problems in Scientific and Industrial Applications}, 9746 address = {Napa, California, USA}, 9747 date = {october 27-29}, 9748 year = {2003}, 9749 petsc_uses = {KSP} 9750} 9751 9752@Article{ bashir2008hessian, 9753 title = {Hessian-based model reduction for large-scale systems with initial-condition 9754 inputs}, 9755 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 9756 J.}, 9757 journal = {International journal for numerical methods in engineering}, 9758 volume = {73}, 9759 number = {6}, 9760 pages = {844--868}, 9761 year = {2008}, 9762 publisher = {Wiley Online Library}, 9763 petsc_uses = {KSP} 9764} 9765 9766@Article{ bashir2007hessian, 9767 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 9768 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 9769 K.}, 9770 journal = {Computational Science--ICCS 2007}, 9771 pages = {1010--1017}, 9772 year = {2007}, 9773 publisher = {Springer}, 9774 petsc_uses = {KSP} 9775} 9776 9777@Article{ akcelik2011fast, 9778 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 9779 inverse problems based on low-rank partial {H}essian approximations}, 9780 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 9781 Waanders, B. and Wilcox, L.}, 9782 journal = {SIAM Journal on Scientific Computing}, 9783 volume = {33}, 9784 number = {1}, 9785 year = {2011}, 9786 petsc_uses = {KSP} 9787} 9788 9789@InProceedings{ ff2003, 9790 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 9791 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 9792 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 9793 year = {2003}, 9794 petsc_uses = {KSP} 9795} 9796 9797@InProceedings{ d2b2004, 9798 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 9799 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 9800 Ordering Strategies}, 9801 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 9802 year = {2004}, 9803 petsc_uses = {KSP} 9804} 9805 9806@InProceedings{ d2v2005, 9807 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 9808 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 9809 Flow Equations}, 9810 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 9811 year = {2005}, 9812 petsc_uses = {KSP} 9813} 9814 9815@InProceedings{ dvs2006, 9816 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 9817 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 9818 Mixed Convection Equations}, 9819 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 9820 year = {2006}, 9821 petsc_uses = {KSP} 9822} 9823 9824@Article{ dsv2006, 9825 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 9826 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 9827 Flow Equations}, 9828 journal = {Computational Fluid Dynamics}, 9829 year = {2006}, 9830 volume = {15}, 9831 number = {1}, 9832 petsc_uses = {KSP} 9833} 9834 9835@Article{ lahaye03, 9836 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 9837 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 9838 journal = {J. Comput. Appl. Math.}, 9839 year = {2004}, 9840 pages = {267--275}, 9841 volume = {168}, 9842 petsc_uses = {KSP} 9843} 9844 9845@TechReport{ brmn, 9846 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 9847 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 9848 year = {2002}, 9849 type = {Technical Report}, 9850 institution = {ANL}, 9851 number = {ANL/MCS-P993-0902}, 9852 note = {To appear in Future Generation Computer Systems}, 9853 petsc_uses = {KSP} 9854} 9855 9856@InProceedings{ mnbr, 9857 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 9858 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 9859 Algorithms}, 9860 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 9861 Mechanics}, 9862 year = {2003}, 9863 petsc_uses = {KSP} 9864} 9865 9866@InProceedings{ bmnr, 9867 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 9868 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 9869 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 9870 Applications, Lecture notes in Computer Science 2677}, 9871 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 9872 pages = {828--839}, 9873 year = {2003}, 9874 petsc_uses = {KSP} 9875} 9876 9877@Article{ ph03, 9878 author = {M. Pernice and R. D. Hornung}, 9879 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 9880 journal = {Computing and Visualization in Science}, 9881 year = {2003}, 9882 lab = {LANL}, 9883 petsc_uses = {KSP} 9884} 9885 9886@Article{ adams-02, 9887 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 9888 journal = {J. Comp. Phys.}, 9889 number = {2}, 9890 pages = {593-610}, 9891 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 9892 volume = {188}, 9893 year = {2003}, 9894 petsc_uses = {KSP} 9895} 9896 9897@InProceedings{ adams2001distributed, 9898 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 9899 smoothers}, 9900 author = {Adams, M.F.}, 9901 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 9902 pages = {14--14}, 9903 year = {2001}, 9904 organization = {IEEE}, 9905 petsc_uses = {KSP} 9906} 9907 9908@PhDThesis{ els01, 9909 author = {Ulrich Elsner}, 9910 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 9911 algorithms}, 9912 school = {Technical University Chemnitz}, 9913 year = {2002}, 9914 publisher = {Logos Verlag, Berlin}, 9915 isbn = {3-89722-923-4}, 9916 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 9917 different graph partitioning algorithms}, 9918 petsc_uses = {KSP} 9919} 9920 9921@TechReport{ ckk02, 9922 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 9923 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 9924 year = {2002}, 9925 type = {Technical Report}, 9926 institution = {ODU}, 9927 url = {http://www.math.odu.edu/\~{ }keyes}, 9928 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 9929 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 9930 Methods}, 9931 petsc_uses = {KSP} 9932} 9933 9934@Article{ gpw2002, 9935 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 9936 Heterogeneous Problems in Linear Elasticity}, 9937 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 9938 year = {2003}, 9939 pages = {283--324}, 9940 volume = {95}, 9941 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 9942 journal = {Numerische Mathematik}, 9943 petsc_uses = {KSP} 9944} 9945 9946@Article{ dh1, 9947 title = {Scalability and FETI based algorithm for large discretized variational 9948 inequalities}, 9949 author = {Z Dostal and D Horak}, 9950 year = {2003}, 9951 pages = {347--357}, 9952 volume = {61}, 9953 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 9954 journal = {Mathematics and Computers in Simulation}, 9955 petsc_uses = {KSP} 9956} 9957 9958@InProceedings{ dhsv1, 9959 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9960 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 9961 title = {36 Scalabilities of {FETI} for Variational Inequalities and Contact Shape 9962 Optimization}, 9963 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9964 Methods}, 9965 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 9966 Kuznetsov}, 9967 petsc_uses = {KSP} 9968} 9969 9970@Article{ lahaye02, 9971 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 9972 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 9973 journal = {IEEEMAGN}, 9974 year = {2002}, 9975 volume = {38}, 9976 number = {2}, 9977 pages = {413-416}, 9978 petsc_uses = {KSP} 9979} 9980 9981@Article{ ckm01, 9982 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 9983 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 9984 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 9985 fluid dynamics}, 9986 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 9987 year = {2002}, 9988 volume = {40}, 9989 pages = {1463--1470}, 9990 petsc_uses = {KSP} 9991} 9992 9993@InProceedings{ cky01, 9994 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 9995 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 9996 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 9997 duct flow}, 9998 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9999 Methods}, 10000 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10001 Kuznetsov}, 10002 year = {2002}, 10003 petsc_uses = {KSP} 10004} 10005 10006@Article{ ck02, 10007 author = {X.-C. Cai and D. E. Keyes}, 10008 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 10009 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 10010 journal = {SIAM J. Sci. Comput.}, 10011 year = {2002}, 10012 pages = {183--200}, 10013 volume = {24}, 10014 petsc_uses = {KSP} 10015} 10016 10017@Article{ c04, 10018 author = {Feng-Nan Hwang and X.-C. Cai}, 10019 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 10020 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 10021 for incompressible {Navier-Stokes} equations}, 10022 journal = {Journal of Computational Physics}, 10023 year = {2005}, 10024 volume = {204}, 10025 pages = {666--691}, 10026 petsc_uses = {KSP} 10027} 10028 10029@Article{ hc06, 10030 author = {Feng-Nan Hwang and X.-C. Cai}, 10031 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 10032 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 10033 Algorithms}, 10034 journal = {Computer Methods in Applied Mechanics and Engineering}, 10035 year = {2006}, 10036 volume = {196}, 10037 pages = {1603--1611}, 10038 petsc_uses = {KSP} 10039} 10040 10041@InProceedings{ adams-01, 10042 author = {Mark F. Adams}, 10043 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 10044 Smoothers}, 10045 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 10046 address = {Denver, Colorado}, 10047 month = nov, 10048 year = {2001}, 10049 petsc_uses = {KSP} 10050} 10051 10052@Book{ 1dl, 10053 author = {Domenico Lahaye}, 10054 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 10055 Computations}, 10056 year = {2001}, 10057 publisher = {Katholieke Universiteit Leuven}, 10058 notes = {Thesis}, 10059 petsc_uses = {KSP} 10060} 10061 10062@Article{ adams-00, 10063 author = {Adams, M.~F.}, 10064 journal = {International Journal for Numerical Methods in Engineering}, 10065 number = {8}, 10066 pages = {1241-1262}, 10067 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 10068 Deformation Elasticity and Plasticity}, 10069 volume = {48}, 10070 year = {2000}, 10071 petsc_uses = {KSP} 10072} 10073 10074@Article{ adams2002evaluation, 10075 author = {Adams, M.~F.}, 10076 journal = {International Journal for Numerical Methods in Engineering}, 10077 number = {1}, 10078 pages = {519-534}, 10079 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 10080 Problems in Solid Mechanics}, 10081 volume = {55}, 10082 year = {2002}, 10083 petsc_uses = {KSP} 10084} 10085 10086@Article{ lahaye00, 10087 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 10088 title = {Algebraic Multigrid for Complex Symmetric Systems}, 10089 journal = {IEEEMAGN}, 10090 year = {2000}, 10091 volume = {36}, 10092 number = {4}, 10093 pages = {1535--1538}, 10094 petsc_uses = {KSP} 10095} 10096 10097@InProceedings{ adams-99c, 10098 author = {Mark F. Adams and J. Demmel}, 10099 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 10100 Finite Element Problems}, 10101 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 10102 address = {Portland, Oregon}, 10103 month = nov, 10104 year = {1999}, 10105 petsc_uses = {KSP} 10106} 10107 10108@Article{ chan95, 10109 author = {T. Chan and B. Smith and J. Zou}, 10110 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 10111 Grids}, 10112 journal = {Numer. Math.}, 10113 year = {1995}, 10114 volume = {73}, 10115 pages = {149--167}, 10116 petsc_uses = {KSP} 10117} 10118 10119@TechReport{ adams-csd-98-993, 10120 pages = {11}, 10121 year = {1998}, 10122 type = {Technical Report}, 10123 number = {CSD-98-993}, 10124 institution = {University of California, Berkeley}, 10125 title = {A Parallel Maximal Independent Set Algorithm}, 10126 bibdate = {March 11, 1998}, 10127 author = {Mark F. Adams and James Demmel}, 10128 abstract = {The parallel construction of maximal independent sets is a useful building block 10129 for many algorithms in the computational sciences, including graph coloring and 10130 multigrid coarse grid creation on unstructured meshes. We present an efficient 10131 asynchronous maximal independent set algorithm for use on parallel computers, for 10132 ``well partitioned'' graphs, that arise from finite element (FE) models. For 10133 appropriately partitioned bounded degree graphs, it is shown that the running time 10134 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 10135 improvement over the previous best P-RAM complexity for this class of graphs. We 10136 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 10137 model is indicative of the performance one can expect with practical partitions on 10138 graphs from FE problems.}, 10139 month = mar, 10140 petsc_uses = {KSP} 10141} 10142 10143@Article{ benzigolubliesen2005, 10144 title = {Numerical solution of saddle point problems}, 10145 author = {Michele Benzi and Gene H. Golub and J\"org Liesen}, 10146 volume = {14}, 10147 journal = {Acta Numerica}, 10148 pages = {1-–137}, 10149 doi = {10.1017/S0962492904000212}, 10150 year = {2005} 10151} 10152 10153@Article{ mardal2011preconditioning, 10154 title = {Preconditioning discretizations of systems of partial differential equations}, 10155 author = {Kent-Andre Mardal and Ragnar Winther}, 10156 journal = {Numerical Linear Algebra with Applications}, 10157 volume = {18}, 10158 number = {1}, 10159 pages = {1--40}, 10160 year = {2011} 10161} 10162 10163@TechReport{ k676, 10164 year = {1994}, 10165 type = {Technical Report}, 10166 number = {TR1994-676}, 10167 institution = {New York University}, 10168 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 10169 Term}, 10170 author = {Axel Klawonn}, 10171 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 10172 petsc_uses = {KSP} 10173} 10174 10175@Book{ ak1, 10176 author = {Axel Klawonn}, 10177 title = {Preconditioners for Indefinite Problems}, 10178 year = {1995}, 10179 publisher = {Westfalishen Wilhelms-Universitat Munster}, 10180 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 10181 notes = {Thesis}, 10182 petsc_uses = {KSP} 10183} 10184 10185@TechReport{ knepleykarpeev05, 10186 pages = {41}, 10187 year = {2005}, 10188 type = {Technical Report}, 10189 number = {ANL/MCS-P1295-1005}, 10190 institution = {Argonne National Laboratory}, 10191 title = {Flexible Representation of Computational Meshes}, 10192 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10193 abstract = {}, 10194 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 10195 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 10196 month = oct, 10197 petsc_uses = {DMPlex} 10198} 10199 10200@TechReport{ knepleykarpeev07a, 10201 pages = {14}, 10202 year = {2007}, 10203 type = {Technical Report}, 10204 number = {ANL/MCS-P1455-0907}, 10205 institution = {Argonne National Laboratory}, 10206 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10207 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10208 abstract = {}, 10209 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 10210 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 10211 month = feb, 10212 petsc_uses = {DMPlex} 10213} 10214 10215@Article{ knepleykarpeev09, 10216 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10217 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10218 journal = {Scientific Programming}, 10219 volume = {17}, 10220 number = {3}, 10221 pages = {215--230}, 10222 year = {2009}, 10223 doi = {10.3233/SPR-2009-0249}, 10224 url = {http://arxiv.org/abs/0908.4427}, 10225 note = {\url{http://arxiv.org/abs/0908.4427}}, 10226 petsc_uses = {DMPlex} 10227} 10228 10229@Article{ biezuner2012computing, 10230 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 10231 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 10232 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 10233 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 10234 Sublinear Supersolutions}, 10235 journal = {Journal of Scientific Computing}, 10236 publisher = {Springer Netherlands}, 10237 issn = {0885-7474}, 10238 keyword = {Mathematics and Statistics}, 10239 pages = {180--201}, 10240 volume = {52}, 10241 issue = {1}, 10242 year = {2012}, 10243 doi = {10.1007/s10915-011-9540-0}, 10244 petsc_uses = {KSP} 10245} 10246 10247% LiteralHTML: 10248% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 10249% LiteralHTML: 10250@Book{ knepley2017, 10251 title = {Computational Science I}, 10252 author = {Matthew G. Knepley}, 10253 url = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}, 10254 note = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}}, 10255 publisher = {PETSc}, 10256 year = {2017}, 10257 petsc_uses = {KSP} 10258} 10259 10260@Article{ verleyeuser, 10261 title = {{User friendly permeability predicting software for technical textiles}}, 10262 author = {Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and 10263 Roose, D.}, 10264 journal = {status: published}, 10265 issn = {1560-6074}, 10266 publisher = {Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}, 10267 petsc_uses = {KSP} 10268} 10269 10270@Book{ pacheco, 10271 author = {Peter Pacheco}, 10272 title = {Parallel Programming with MPI}, 10273 year = {1997}, 10274 publisher = {Morgan-Kaufmann}, 10275 note = {Devotes a couple of sections to PETSc}, 10276 petsc_uses = {KSP} 10277} 10278 10279@Book{ 1sbg, 10280 author = {Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp}, 10281 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 10282 Differential Equations}, 10283 year = {1996}, 10284 publisher = {Cambridge University Press}, 10285 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 10286 petsc_uses = {KSP} 10287} 10288 10289@Misc{ petsc-fem:homepage, 10290 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 10291 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 10292 G. Rodriguez and G. Filippini}, 10293 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 10294 petsc_uses = {KSP} 10295} 10296 10297@Misc{ petsc4py-web-page, 10298 author = {Lisandro Dalcin}, 10299 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 10300 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 10301 note = {http://code.google.com/p/petsc4py/}, 10302 petsc_uses = {KSP} 10303} 10304 10305@Article{ libmeshpaper06, 10306 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 10307 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 10308 Simulations}}, 10309 journal = {Engineering with Computers}, 10310 volume = {22}, 10311 number = {3--4}, 10312 pages = {237--254}, 10313 year = {2006}, 10314 doi = {10.1007/s00366-006-0049-3}, 10315 petsc_uses = {KSP} 10316} 10317 10318@Misc{ sisiphus:homepage, 10319 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 10320 High-Resolution, Unstructured Simulations}, 10321 author = {T. {Tautges et al.}}, 10322 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 10323 petsc_uses = {KSP} 10324} 10325 10326@Misc{ pflotran:homepage, 10327 title = {{PFLOTRAN} project}, 10328 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 10329 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 10330 howpublished = {\url{http://pflotran.org/}}, 10331 petsc_uses = {KSP} 10332} 10333 10334@Misc{ pism:homepage, 10335 title = {{PISM}: A Parallel Ice Sheet Model}, 10336 author = {E. {Bueler et al.}}, 10337 howpublished = {\url{http://pism-docs.org}}, 10338 petsc_uses = {KSP} 10339} 10340 10341@Misc{ dohp:homepage, 10342 title = {Dohp: Dual order $hp$-finite elements}, 10343 author = {J. Brown}, 10344 howpublished = {\url{http://dohp.org}}, 10345 petsc_uses = {KSP} 10346} 10347 10348@Article{ mccourtrognlienetal12, 10349 title = {Improving parallel scalability for edge plasma transport simulations with neutral 10350 gas species}, 10351 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 10352 journal = {Computational Science and Discovery}, 10353 year = {2012}, 10354 volume = {5}, 10355 number = {014012}, 10356 doi = {10.1088/1749-4699/5/1/014012}, 10357 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 10358 2011)}, 10359 petsc_uses = {KSP} 10360} 10361 10362@Misc{ petclaw-github, 10363 title = {Pet{C}law Software}, 10364 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 10365 year = {2011}, 10366 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 10367 petsc_uses = {KSP} 10368} 10369 10370@Misc{ pyclaw-web-page, 10371 author = {Kyle T. Mandli and David I. Ketcheson and others}, 10372 title = {{PyClaw} software}, 10373 howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}}, 10374 url = {http://clawpack.github.io/doc/pyclaw/}, 10375 year = {2012}, 10376 petsc_uses = {KSP} 10377} 10378 10379@Article{ ketcheson2011highorder, 10380 title = {High-order wave propagation algorithms for general hyperbolic systems}, 10381 author = {Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.}, 10382 year = {2011}, 10383 note = {submitted}, 10384 petsc_uses = {KSP} 10385} 10386 10387@Article{ biros2005pln1, 10388 title = {{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained 10389 optimization. Part I: The {Krylov-Schur} solver}}, 10390 author = {Biros, G. and Ghattas, O.}, 10391 journal = {SIAM Journal on Scientific Computing}, 10392 volume = {27}, 10393 number = {2}, 10394 pages = {687--713}, 10395 year = {2005}, 10396 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 10397 petsc_uses = {KSP} 10398} 10399 10400@Article{ biros2005pln2, 10401 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 10402 optimization. Part {II}: The {Lagrange Newton} solver, and its application to 10403 optimal control of steady viscous flows}, 10404 author = {Biros, G. and Ghattas, O.}, 10405 journal = {SIAM Journal on Scientific Computing}, 10406 volume = {27}, 10407 number = {2}, 10408 pages = {714--739}, 10409 year = {2005}, 10410 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 10411 petsc_uses = {KSP} 10412} 10413 10414@Misc{ issm:homepage, 10415 title = {{I}ce {S}heet {S}ystem {M}odel}, 10416 author = {Eric Larour and Mathieu Morlighem and Helene Seroussi}, 10417 year = {2010}, 10418 note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}, 10419 petsc_uses = {KSP} 10420} 10421 10422@Article{ morlighem2010spatial, 10423 title = {Spatial patterns of basal drag inferred using control methods from a 10424 full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est 10425 {A}ntarctica}, 10426 author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and 10427 Aubry, D.}, 10428 journal = {Geophysical Research Letters}, 10429 volume = {37}, 10430 number = {14}, 10431 pages = {L14502}, 10432 year = {2010}, 10433 publisher = {American Geophysical Union}, 10434 petsc_uses = {KSP} 10435} 10436 10437@Article{ jardin2012plasmas, 10438 title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics 10439 of tokamak plasmas}, 10440 author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 10441 journal = {Computational Science \& Discovery}, 10442 volume = {5}, 10443 number = {1}, 10444 url = {http://stacks.iop.org/1749-4699/5/014002}, 10445 year = {2012}, 10446 petsc_uses = {KSP} 10447} 10448 10449@Article{ cmz2016, 10450 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 10451 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 10452 journal = {Journal of Scientific Computing}, 10453 publisher = {Springer}, 10454 pages = {803--825}, 10455 volume = {68}, 10456 issue = {2}, 10457 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 10458 doi = {10.1007/s10915-015-0159-4}, 10459 year = {2016}, 10460 note = {Also preprint ANL/MCS-P3039-0912}, 10461 petsc_uses = {KSP} 10462} 10463 10464@Article{ knepleybrownruppsmith13, 10465 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 10466 title = {Achieving High Performance with Unified Residual Evaluation}, 10467 journal = {ArXiv e-prints}, 10468 eprint = {1309.1204}, 10469 archiveprefix = {arXiv}, 10470 primaryclass = {cs.MS}, 10471 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 10472 Engineering, Finance, and Science}, 10473 year = {2013}, 10474 month = sep, 10475 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 10476 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10477 petsc_uses = {KSP} 10478} 10479 10480@Book{ fenicsbook, 10481 title = {Automated Solution of Differential Equations by the Finite Element Method: The 10482 FEniCS Book}, 10483 series = {Lecture Notes in Computational Science and Engineering}, 10484 volume = {84}, 10485 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 10486 publisher = {Springer}, 10487 isbn = {978-3-642-23098-1}, 10488 year = {2012}, 10489 petsc_uses = {KSP} 10490} 10491 10492@Article{ demidovahnertruppgottschling12, 10493 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 10494 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 10495 journal = {ArXiv e-prints}, 10496 archiveprefix = {arXiv}, 10497 eprint = {1212.6326}, 10498 primaryclass = {cs.MS}, 10499 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 10500 Parallel, and Cluster Computing, Physics - Computational Physics}, 10501 year = {2012}, 10502 month = dec, 10503 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 10504 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10505 petsc_uses = {KSP} 10506} 10507 10508@InProceedings{ viennacl, 10509 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 10510 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 10511 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 10512 year = {2010}, 10513 pages = {51-56}, 10514 petsc_uses = {KSP} 10515} 10516 10517@Article{ knepleybrownmcinnessmithruppadams2015, 10518 title = {Exascale Computing without Threads}, 10519 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 10520 Karl Rupp and Mark Adams}, 10521 url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950}, 10522 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 10523 Scientific Software Architecture for Portability and Performance}, 10524 doi = {10.6084/m9.figshare.5824950.v1}, 10525 year = {2015}, 10526 petsc_uses = {KSP} 10527} 10528 10529@Article{ knepleybrownmcinnessmithruppadams2015b, 10530 title = {Overview of the {PETSc} Library}, 10531 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 10532 Karl Rupp and Mark Adams}, 10533 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 10534 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 10535 Scientific Software Architecture for Portability and Performance}, 10536 year = {2015}, 10537 petsc_uses = {KSP} 10538} 10539 10540@InBook{ balaybrownknepleymcinnessmith2015, 10541 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 10542 Smith}, 10543 bookeditor = {J. Carver}, 10544 title = {Software Engineering for Science}, 10545 chapter = {Providing Mixed Language and Legacy Support within a Library}, 10546 publisher = {Taylor \& Francis}, 10547 year = {2015}, 10548 petsc_uses = {KSP} 10549} 10550 10551@Article{ ruppbalaybrownknepleymcinnessmith2015, 10552 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 10553 Software}, 10554 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 10555 McInnes and Barry F. Smith}, 10556 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 10557 Productivity Challenges}, 10558 journal = {ArXiv e-prints}, 10559 archiveprefix = {arXiv}, 10560 eprint = {1510.01122}, 10561 year = {2015}, 10562 petsc_uses = {KSP} 10563} 10564 10565@InProceedings{ knepley2013accurately, 10566 title = {Accurately Citing Software and Algorithms Used in Publications}, 10567 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 10568 F.}, 10569 year = {2013}, 10570 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10571 (WSSSPE), held at SC13}, 10572 doi = {10.6084/m9.figshare.785731}, 10573 petsc_uses = {KSP} 10574} 10575 10576@InProceedings{ milleretal2013, 10577 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 10578 Strategies Developed for {FASTMath}}, 10579 author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and 10580 Barry Smith}, 10581 year = {2013}, 10582 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10583 (WSSSPE), held at SC13}, 10584 doi = {10.6084/m9.figshare.789055}, 10585 petsc_uses = {KSP} 10586} 10587 10588@TechReport{ dudsonetal2012, 10589 title = {Improved Nonlinear Solvers in {BOUT++}}, 10590 author = {Ben Dudson and Sean Farley and Lois Curfman McInnes}, 10591 institution = {Argonne National Laboratory}, 10592 number = {ANL/MCS-P3025-0812}, 10593 year = {2012}, 10594 petsc_uses = {KSP} 10595} 10596 10597@Misc{ brown13, 10598 author = {J. 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May}, 10905 journal = {SIAM Journal on Scientific Computing}, 10906 volume = {38}, 10907 number = {5}, 10908 pages = {C441-C470}, 10909 year = {2016}, 10910 doi = {10.1137/15M1049130}, 10911 petsc_uses = {KSP} 10912} 10913 10914@Article{ petscsf2022, 10915 author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and 10916 Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and 10917 Smith, Barry F. and Zampini, Stefano}, 10918 journal = {IEEE Transactions on Parallel and Distributed Systems}, 10919 title = {The {PetscSF} Scalable Communication Layer}, 10920 year = {2022}, 10921 volume = {33}, 10922 number = {4}, 10923 pages = {842-853}, 10924 doi = {10.1109/TPDS.2021.3084070} 10925} 10926 10927@Article{ brandt2000, 10928 title = {General highly accurate algebraic coarsening}, 10929 author = {Achi Brandt}, 10930 journal = {Electronic Transactions on Numerical Analysis}, 10931 volume = {10}, 10932 number = {9680}, 10933 pages = {1--20}, 10934 issn = {10689613}, 10935 year = {2000} 10936} 10937 10938@Article{ dalcinpazklercosimo2011, 10939 title = {Parallel distributed computing using Python}, 10940 author = {Lisandro D. 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Vignal and A.M.A. Cortes and Victor M. 10978 Calo}, 10979 journal = {Computer Methods in Applied Mechanics and Engineering}, 10980 volume = {308}, 10981 pages = {151 - 181}, 10982 issn = {0045-7825}, 10983 doi = {10.1016/j.cma.2016.05.011}, 10984 year = {2016} 10985} 10986 10987@Article{ collierpardodalcinpaszynskicalo2012, 10988 title = {The cost of continuity: A study of the performance of isogeometric finite 10989 elements using direct solvers}, 10990 author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M. 10991 Calo}, 10992 journal = {Computer Methods in Applied Mechanics and Engineering}, 10993 volume = {213-216}, 10994 pages = {353 - 361}, 10995 issn = {0045-7825}, 10996 doi = {10.1016/j.cma.2011.11.002}, 10997 year = {2012} 10998} 10999 11000@Article{ collierdalcinpardocalo2013, 11001 title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite 11002 Elements}, 11003 author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo}, 11004 journal = {SIAM Journal on Scientific Computing}, 11005 volume = {35}, 11006 number = {2}, 11007 pages = {A767-A784}, 11008 doi = {10.1137/120881038}, 11009 year = {2013} 11010} 11011 11012@Article{ dunning2017jump, 11013 title = {{JuMP}: a modeling language for mathematical optimization}, 11014 author = {Dunning, Iain and Huchette, Joey and Lubin, Miles}, 11015 journal = {SIAM Review}, 11016 volume = {59}, 11017 number = {2}, 11018 pages = {295--320}, 11019 year = {2017}, 11020 publisher = {SIAM} 11021} 11022 11023@InProceedings{ prudencioschulz2011, 11024 title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for 11025 Estimation, Simulation and Optimization}, 11026 author = {Ernesto E Prudencio and Karl W Schulz}, 11027 booktitle = {European Conference on Parallel Processing}, 11028 pages = {398--407}, 11029 year = {2011} 11030} 11031 11032@Misc{ rol-website, 11033 key = {ROL}, 11034 title = {{Rapid Optimization Library} Website}, 11035 howpublished = {\url{https://trilinos.org/packages/rol}}, 11036 year = {2018} 11037} 11038 11039@Article{ more1994line, 11040 title = {Line search algorithms with guaranteed sufficient decrease}, 11041 author = {Mor{\'e}, Jorge J and Thuente, David J}, 11042 journal = {ACM Transactions on Mathematical Software}, 11043 volume = {20}, 11044 number = {3}, 11045 pages = {286--307}, 11046 year = {1994}, 11047 publisher = {ACM} 11048} 11049 11050@Article{ griewank2000algorithm, 11051 title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or 11052 adjoint mode of computational differentiation}, 11053 author = {Griewank, Andreas and Walther, Andrea}, 11054 journal = {ACM Transactions on Mathematical Software}, 11055 volume = {26}, 11056 number = {1}, 11057 pages = {19--45}, 11058 year = {2000}, 11059 publisher = {ACM} 11060} 11061 11062@Article{ metcalf2011seven, 11063 title = {The seven ages of fortran}, 11064 author = {Metcalf, Michael}, 11065 journal = {Journal of Computer Science \& Technology}, 11066 volume = {11}, 11067 year = {2011} 11068} 11069 11070@Article{ giraldo_2013, 11071 title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified 11072 model of the atmosphere {(NUMA)}}, 11073 author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu}, 11074 journal = {SIAM Journal on Scientific Computing}, 11075 year = {2013}, 11076 number = {5}, 11077 pages = {B1162-B1194}, 11078 volume = {35}, 11079 doi = {10.1137/120876034} 11080} 11081 11082@Article{ constantinescu_tr2016b, 11083 author = {Constantinescu, E.M.}, 11084 title = {Estimating Global Errors in Time Stepping}, 11085 journal = {ArXiv e-prints}, 11086 archiveprefix = {arXiv}, 11087 eprint = {1503.05166}, 11088 primaryclass = {math.NA}, 11089 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70}, 11090 year = {2016}, 11091 month = mar, 11092 adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C}, 11093 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 11094} 11095 11096@Article{ pareschi_2005, 11097 title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems 11098 with Relaxation}, 11099 author = {L. Pareschi and G. Russo}, 11100 journal = {Journal of Scientific Computing}, 11101 year = {2005}, 11102 number = {1}, 11103 pages = {129--155}, 11104 volume = {25} 11105} 11106 11107@Article{ kennedy_2003, 11108 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 11109 author = {C.A. Kennedy and M.H. Carpenter}, 11110 journal = {Appl. Numer. Math.}, 11111 year = {2003}, 11112 number = {1-2}, 11113 pages = {139--181}, 11114 volume = {44}, 11115 doi = {10.1016/S0168-9274(02)00138-1}, 11116 publisher = {Elsevier Science Publishers B. V.} 11117} 11118 11119@Unpublished{ boscarino_tr2011, 11120 title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic 11121 equations in the diffusion limit}, 11122 author = {Boscarino, S. and Pareschi, L. and Russo, G.}, 11123 note = {Arxiv preprint arXiv:1110.4375}, 11124 year = {2011} 11125} 11126 11127@Article{ ascher_1997, 11128 title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential 11129 equations}, 11130 author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri}, 11131 journal = {Applied Numerical Mathematics}, 11132 year = {1997}, 11133 pages = {151--167}, 11134 volume = {25} 11135} 11136 11137@Book{ ascherpetzold1998, 11138 title = {Computer methods for ordinary differential equations and differential-algebraic 11139 equations}, 11140 author = {Uri M Ascher and Linda R Petzold}, 11141 volume = {61}, 11142 publisher = {SIAM}, 11143 year = {1998} 11144} 11145 11146@Article{ colomesbadia2016, 11147 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 11148 equations}, 11149 author = {Oriol Colom{\'e}s and Santiago Badia}, 11150 journal = {International Journal for Numerical Methods in Engineering}, 11151 volume = {105}, 11152 number = {5}, 11153 pages = {372--400}, 11154 year = {2016} 11155} 11156 11157@Article{ sandu_1997, 11158 title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry problems {II}: 11159 {R}osenbrock solvers}, 11160 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 11161 Potra}, 11162 journal = {Atmospheric Environment}, 11163 year = {1997}, 11164 number = {20}, 11165 pages = {3459--3472}, 11166 volume = {31}, 11167 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 11168 task is the integration of the stiff systems of ordinary differential equations 11169 describing the chemical transformations. It is therefore of interest to 11170 systematically search for stiff solvers which can be identified as close to 11171 optimal for atmospheric applications. In this paper we continue our investigation 11172 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 11173 and compare eight solvers on a set of seven box-models used in present day models. 11174 The focus is on Rosenbrock solvers. These turn out to be very well suited for our 11175 application when they are provided with highly efficient sparse matrix techniques 11176 to economize on the linear algebra. Two of the Rosenbrock solvers tested are from 11177 the literature, viz. and 4, and two are new and specially developed for air 11178 quality applications, viz. 3 and 3. } 11179} 11180 11181@Article{ rang_2005, 11182 title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic 11183 equations of index 1}, 11184 author = {Rang, J. and Angermann, L.}, 11185 journal = {BIT Numerical Mathematics}, 11186 year = {2005}, 11187 number = {4}, 11188 pages = {761--787}, 11189 volume = {45}, 11190 publisher = {Springer} 11191} 11192 11193@Article{ gottliebketchesonshu2009, 11194 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 11195 title = {{High order strong stability preserving time discretizations}}, 11196 journal = {Journal of Scientific Computing}, 11197 volume = {38}, 11198 number = {3}, 11199 pages = {251--289}, 11200 doi = {10.1007/s10915-008-9239-z}, 11201 year = {2009} 11202} 11203 11204@Article{ ketcheson_2008, 11205 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 11206 Low-Storage Implementations}, 11207 author = {D.I. Ketcheson}, 11208 journal = {SIAM Journal on Scientific Computing}, 11209 year = {2008}, 11210 number = {4}, 11211 pages = {2113--2136}, 11212 volume = {30}, 11213 doi = {10.1137/07070485X}, 11214 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 11215 RungeKutta methods}, 11216 publisher = {SIAM} 11217} 11218 11219@Article{ jansen_2000, 11220 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 11221 equations with a stabilized finite element method}, 11222 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 11223 journal = {Computer Methods in Applied Mechanics and Engineering}, 11224 year = {2000}, 11225 number = {3}, 11226 pages = {305--319}, 11227 volume = {190}, 11228 publisher = {Elsevier} 11229} 11230 11231@Article{ butcher_2007, 11232 title = {Error propagation of general linear methods for ordinary differential equations}, 11233 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 11234 journal = {Journal of Complexity}, 11235 year = {2007}, 11236 number = {4-6}, 11237 pages = {560--580}, 11238 volume = {23}, 11239 abstract = {We discuss error propagation for general linear methods for ordinary differential 11240 equations up to terms of order p+2, where p is the order of the method. These 11241 results are then applied to the estimation of local discretization errors for 11242 methods of order p and for the adjacent order p+1. The results of numerical 11243 experiments confirm the reliability of these estimates. This research has 11244 applications in the design of robust stepsize and order changing strategies for 11245 algorithms based on general linear methods.}, 11246 doi = {10.1016/j.jco.2007.01.009}, 11247 issn = {0885-064X} 11248} 11249 11250@Article{ constantinescu_a2010a, 11251 title = {Extrapolated implicit-explicit time stepping}, 11252 author = {E.M. Constantinescu and A. Sandu}, 11253 journal = {SIAM Journal on Scientific Computing}, 11254 year = {2010}, 11255 number = {6}, 11256 pages = {4452-4477}, 11257 volume = {31}, 11258 comment = {Preprint \# ANL/MCS-P1612-0409}, 11259 doi = {10.1137/080732833} 11260} 11261 11262@InProceedings{ devito2011liszt, 11263 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 11264 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 11265 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 11266 Aiken, Alex and Duraisamy, Karthik and others}, 11267 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 11268 Networking, Storage and Analysis}, 11269 pages = {9}, 11270 year = {2011}, 11271 organization = {ACM} 11272} 11273 11274@Article{ devito2011designing, 11275 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 11276 author = {DeVito, Zachary and Hanrahan, Pat}, 11277 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 11278 year = {2011} 11279} 11280 11281@Misc{ pgasintro, 11282 author = {Tim Stitt}, 11283 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 11284 Model}, 11285 note = {\url{http://cnx.org/content/m20649/latest/}} 11286} 11287 11288@InProceedings{ el2006upc, 11289 title = {UPC: unified parallel C}, 11290 author = {El-Ghazawi, Tarek and Smith, Lauren}, 11291 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 11292 pages = {27}, 11293 year = {2006}, 11294 organization = {ACM} 11295} 11296 11297@InProceedings{ numrich1998co, 11298 title = {Co-Array Fortran for parallel programming}, 11299 author = {Numrich, Robert W and Reid, John}, 11300 booktitle = {ACM Sigplan Fortran Forum}, 11301 volume = {17}, 11302 number = {2}, 11303 pages = {1--31}, 11304 year = {1998}, 11305 organization = {ACM} 11306} 11307 11308@Article{ aiken1997titanium, 11309 title = {Titanium: A high-performance Java dialect}, 11310 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 11311 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 11312 Geoff and Semenzato, Luigi and others}, 11313 year = {1997} 11314} 11315 11316@Article{ charles2005x10, 11317 title = {X10: an object-oriented approach to non-uniform cluster computing}, 11318 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 11319 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 11320 Sarkar, Vivek}, 11321 journal = {Acm Sigplan Notices}, 11322 volume = {40}, 11323 number = {10}, 11324 pages = {519--538}, 11325 year = {2005}, 11326 publisher = {ACM} 11327} 11328 11329@Article{ chamberlain2007parallel, 11330 title = {Parallel programmability and the chapel language}, 11331 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 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gannon1991object, 11392 title = {Object oriented parallelism: pC++ ideas and experiments}, 11393 author = {Gannon, Dennis and Lee, JK}, 11394 booktitle = {Proceedings of}, 11395 pages = {13--23}, 11396 year = {1991} 11397} 11398 11399@InProceedings{ lau1992object, 11400 title = {An object-oriented class library for scalable parallel heuristic search}, 11401 author = {Lau, Wing-cheong and Singh, Vineet}, 11402 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 11403 pages = {252--267}, 11404 year = {1992}, 11405 organization = {Springer} 11406} 11407 11408@Book{ chase1989amber, 11409 title = {The Amber system: Parallel programming on a network of multiprocessors}, 11410 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 11411 Littlefield, Richard}, 11412 volume = {23}, 11413 number = {5}, 11414 year = {1989}, 11415 publisher = {ACM} 11416} 11417 11418@InProceedings{ kaiser2009parallex, 11419 title = {Parallex an advanced parallel 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ICPPW'09. International Conference on}, 11422 pages = {394--401}, 11423 year = {2009}, 11424 organization = {IEEE} 11425} 11426 11427@TechReport{ ipm, 11428 author = {Barry F. Smith}, 11429 title = {A New Parallel Programming Model for Computer Simulation}, 11430 institution = {Argonne National Laboratory}, 11431 year = {2014}, 11432 number = {ANL/MCS-P5135-0414} 11433} 11434 11435@Article{ groppsnir, 11436 author = {William Gropp and Marc Snir}, 11437 title = {Programming for Exascale Computers}, 11438 journal = {Computing in Science and Engineering}, 11439 volume = {15}, 11440 number = {6}, 11441 issn = {1521-9615}, 11442 year = {2013}, 11443 pages = {27-35}, 11444 doi = {10.1109/MCSE.2013.96}, 11445 publisher = {IEEE Computer Society}, 11446 address = {Los Alamitos, CA} 11447} 11448 11449@Book{ mpi3, 11450 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 11451 author = {Message Passing Interface Forum}, 11452 year = {2012}, 11453 publisher = {High Performance Computing Center Stuttgart (HLRS)} 11454} 11455 11456@Book{ openmp4, 11457 title = {OpenMP Application Program Interface, Version 4.0}, 11458 year = {2013}, 11459 publisher = {OpenMP Architecture Review Board} 11460} 11461 11462@InProceedings{ hartono2009annotation, 11463 title = {Annotation-based empirical performance tuning using {Orio}}, 11464 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 11465 booktitle = {Parallel \& Distributed Processing, 2009. IPDPS 2009. IEEE International 11466 Symposium on}, 11467 pages = {1--11}, 11468 year = {2009}, 11469 organization = {IEEE} 11470} 11471 11472@Book{ toselli2005domain, 11473 title = {Domain Decomposition Methods: Algorithms and Theory}, 11474 author = {Toselli, Andrea and Widlund, Olof B}, 11475 volume = {34}, 11476 year = {2005}, 11477 publisher = {Springer} 11478} 11479 11480@InBook{ st2016, 11481 author = {Barry F. Smith and Xumin Tu}, 11482 chapter = {Domain Decomposition}, 11483 title = {Encyclopedia of Applied and Computational Mathematics}, 11484 bookeditor = {B. Engquist}, 11485 publisher = {Springer}, 11486 pages = {375--381}, 11487 year = {2016} 11488} 11489 11490@TechReport{ saws, 11491 author = {Matt Otten and Jed Brown and Barry F. Smith}, 11492 title = {Scientific Application Web Server {(SAWs)} Users Manual}, 11493 institution = {Argonne National Laboratory}, 11494 year = {2013} 11495} 11496 11497@Article{ smith1997domain, 11498 title = {Domain Decomposition Methods for Partial Differential Equations}, 11499 author = {Smith, B.F.}, 11500 journal = {ICASE LARC Interdisciplinary Series in Science and Engineering}, 11501 volume = {4}, 11502 pages = {225--244}, 11503 year = {1997}, 11504 publisher = {Citeseer} 11505} 11506 11507@Article{ spillane2011abstract, 11508 title = {Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems 11509 in the overlaps}, 11510 author = {Spillane, N and Dolean, V and Hauret, P and Nataf, F and Pechstein, C and 11511 Scheichl, R}, 11512 journal = {NuMa-Report}, 11513 volume = {7}, 11514 pages = {2007}, 11515 year = {2011} 11516} 11517 11518@InProceedings{ jolivet2013scalabledd, 11519 title = {Scalable domain decomposition preconditioners for heterogeneous elliptic 11520 problems}, 11521 author = {Jolivet, Pierre and Hecht, Fr{\'e}d{\'e}ric and Nataf, Fr{\'e}d{\'e}ric and 11522 Prud'homme, Christophe}, 11523 booktitle = {Proceedings of SC13: International Conference for High Performance Computing, 11524 Networking, Storage and Analysis}, 11525 pages = {80}, 11526 year = {2013}, 11527 organization = {ACM} 11528} 11529 11530@Book{ ks2000, 11531 author = {D. Kinderlehrer and G. Stampacchia}, 11532 publisher = {Society for Industrial Mathematics}, 11533 title = {An Introduction to Variational Inequalities and Their Applications}, 11534 year = {2000} 11535} 11536 11537@Article{ wan2000energy, 11538 title = {An energy-minimizing interpolation for robust multigrid methods}, 11539 author = {Wan, W.L. and Chan, T.F. and Smith, B. F.}, 11540 journal = {SIAM Journal on Scientific Computing}, 11541 volume = {21}, 11542 number = {4}, 11543 pages = {1632--1649}, 11544 year = {2000}, 11545 publisher = {Philadelphia, PA: SIAM, c1993-} 11546} 11547 11548@Article{ chansmith1994, 11549 title = {Domain decomposition and multigrid algorithms for elliptic problems on 11550 unstructured meshes}, 11551 author = {Chan, T.F. and Smith, B.F.}, 11552 journal = {Electronic Transactions on Numerical Analysis}, 11553 volume = {2}, 11554 pages = {171--182}, 11555 year = {1994} 11556} 11557 11558@TechReport{ proto-fsp, 11559 author = {Venkatramani Balaji and Barry Smith and Brian Van Straalen and Priya Vashishta 11560 and Michael Zarnstorff and Michael Zika}, 11561 title = {Report of the {Proto-FSP} {Assessment Panel for the FSP}}, 11562 institution = {Princeton Plasma Physics Laboratory}, 11563 year = {2010}, 11564 url = {http://www.pppl.gov/fsp/documents/Proto-FSPAssessmentReport.pdf} 11565} 11566 11567@Article{ hirvijoki2021, 11568 title = {Structure-preserving marker-particle discretizations of {Coulomb} collisions for 11569 particle-in-cell codes}, 11570 journal = {Plasma Phys. Control. Fusion}, 11571 author = {Eero Hirvijoki}, 11572 note = {in press}, 11573 doi = {10.1088/1361-6587/abe884}, 11574 year = {2021} 11575} 11576 11577@Article{ ipsen2001, 11578 author = {Ilse C. F. Ipsen}, 11579 journal = {SIAM J. Sci. Comput.}, 11580 pages = {1050--1051}, 11581 volume = {23}, 11582 publisher = {SIAM}, 11583 title = {A Note on Preconditioning Nonsymmetric Matrices}, 11584 year = {2001} 11585} 11586 11587% Random papers on solvers for GPUs 11588@InProceedings{ gpus-suck, 11589 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. }, 11590 title = { On the Limits of {GPU} Acceleration}, 11591 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism}, 11592 year = {2010}, 11593 publisher = {USENIX} 11594} 11595 11596@InProceedings{ 882364, 11597 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter}, 11598 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid}, 11599 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers}, 11600 year = {2003}, 11601 isbn = {1-58113-709-5}, 11602 pages = {917--924}, 11603 location = {San Diego, California}, 11604 doi = {10.1145/1201775.882364}, 11605 publisher = {ACM}, 11606 address = {New York, NY} 11607} 11608 11609@Conference{ feng2008multigrid, 11610 author = {Feng, Z. and Li, P.}, 11611 booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008}, 11612 date-added = {2010-08-19 15:57:06 -0500}, 11613 date-modified = {2010-08-19 15:57:06 -0500}, 11614 pages = {647--654}, 11615 title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms}, 11616 year = {2008} 11617} 11618 11619@Conference{ goodnight2003multigrid, 11620 author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.}, 11621 booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware}, 11622 date-added = {2010-08-19 15:45:20 -0500}, 11623 date-modified = {2010-08-19 15:45:20 -0500}, 11624 organization = {Eurographics Association}, 11625 pages = {102--111}, 11626 title = {A multigrid solver for boundary value problems using programmable graphics 11627 hardware}, 11628 year = {2003} 11629} 11630 11631@Article{ buatois2007concurrent, 11632 author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.}, 11633 date-added = {2010-08-19 15:45:02 -0500}, 11634 date-modified = {2010-08-19 15:45:02 -0500}, 11635 journal = {High Performance Computing and Communications}, 11636 pages = {358--371}, 11637 publisher = {Citeseer}, 11638 title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}}, 11639 year = {2007} 11640} 11641 11642@Article{ joldes2010real, 11643 author = {Joldes, G.R. and Wittek, A. and Miller, K.}, 11644 date-added = {2010-08-19 15:44:41 -0500}, 11645 date-modified = {2010-08-19 15:44:41 -0500}, 11646 journal = {Computer Methods in Applied Mechanics and Engineering}, 11647 publisher = {Elsevier}, 11648 title = {Real-time nonlinear finite element computations on {GPU}-application to 11649 neurosurgical simulation}, 11650 year = {2010} 11651} 11652 11653@Misc{ aharon2005gpu, 11654 author = {Aharon, S.}, 11655 date-added = {2010-08-19 15:44:32 -0500}, 11656 date-modified = {2010-08-19 15:44:32 -0500}, 11657 month = apr, 11658 note = {US Patent App. 11/115,642}, 11659 publisher = {Google Patents}, 11660 title = {{GPU}-based Finite Element}, 11661 year = {2005} 11662} 11663 11664@Article{ cevahir2009fast, 11665 author = {Cevahir, A. and Nukada, A. and Matsuoka, S.}, 11666 date-added = {2010-08-19 15:44:01 -0500}, 11667 date-modified = {2010-08-19 15:44:01 -0500}, 11668 journal = {Computational Science--ICCS 2009}, 11669 pages = {893--903}, 11670 publisher = {Springer}, 11671 title = {Fast conjugate gradients with multiple {GPU}s}, 11672 year = {2009} 11673} 11674 11675@Article{ maier1995symmetric, 11676 author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.}, 11677 date-added = {2010-08-19 15:43:57 -0500}, 11678 date-modified = {2010-08-19 15:43:57 -0500}, 11679 journal = {Computational Mechanics}, 11680 number = {1}, 11681 pages = {115--129}, 11682 publisher = {Springer}, 11683 title = {Symmetric {G}alerkin boundary element method in plasticity and gradient 11684 plasticity}, 11685 volume = {17}, 11686 year = {1995} 11687} 11688 11689@Article{ corrigan-running, 11690 author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.}, 11691 date-added = {2010-08-19 15:43:47 -0500}, 11692 date-modified = {2010-08-19 15:43:47 -0500}, 11693 journal = {International Journal for Numerical Methods in Fluids}, 11694 publisher = {John Wiley \& Sons}, 11695 title = {Running unstructured grid based CFD solvers on modern graphics hardware} 11696} 11697 11698@InProceedings{ volkov08, 11699 author = {Vasily Volkov and James W. Demmel}, 11700 title = {Benchmarking GPUs to tune dense linear algebra}, 11701 booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)}, 11702 note = {\url{http://mc.stanford.edu/cgi-bin/images/6/65/SC08_Volkov_GPU.pdf}}, 11703 year = {2008} 11704} 11705 11706@TechReport{ cray-mvmult, 11707 author = {Guy~E. Blelloch and Michael~A. Heroux and Marco Zagha}, 11708 title = {Segmented Operations for Sparse Matrix Computation on Vector Multiprocessors}, 11709 institution = {School of Computer Science, Carnegie Mellon University}, 11710 number = {CMU-CS-93-173}, 11711 month = aug, 11712 year = {1993} 11713} 11714 11715@Conference{ bell2009implementing, 11716 author = {Bell, N. and Garland, M.}, 11717 booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage 11718 and Analysis}, 11719 date-added = {2010-08-19 15:43:42 -0500}, 11720 date-modified = {2010-08-19 15:43:42 -0500}, 11721 organization = {ACM}, 11722 pages = {1--11}, 11723 title = {Implementing sparse matrix-vector multiplication on throughput-oriented 11724 processors}, 11725 year = {2009} 11726} 11727 11728@Article{ bell2008efficient, 11729 author = {Bell, N. and Garland, M.}, 11730 date-added = {2010-08-19 15:43:36 -0500}, 11731 date-modified = {2010-08-19 15:43:36 -0500}, 11732 journal = {{NVIDIA} Corporation, {NVIDIA} Technical Report NVR-2008-004}, 11733 title = {Efficient sparse matrix-vector multiplication on {CUDA}}, 11734 year = {2008} 11735} 11736 11737@Article{ cohen-fast, 11738 author = {Cohen, J. and Molemaker, M.J.}, 11739 date-added = {2010-08-19 15:43:34 -0500}, 11740 date-modified = {2010-08-19 15:43:34 -0500}, 11741 journal = {Parallel Computational Fluid Dynamics: Recent Advances and Future Directions}, 11742 pages = {414}, 11743 publisher = {DEStech Publications}, 11744 title = {A fast double precision CFD code using CUDA} 11745} 11746 11747@Article{ kazhdan2008streaming, 11748 author = {Kazhdan, M. and Hoppe, H.}, 11749 date-added = {2010-08-19 15:43:32 -0500}, 11750 date-modified = {2010-08-19 15:43:32 -0500}, 11751 journal = {ACM Transactions on Graphics (TOG)}, 11752 number = {3}, 11753 pages = {21}, 11754 publisher = {ACM}, 11755 title = {Streaming multigrid for gradient-domain operations on large images}, 11756 volume = {27}, 11757 year = {2008} 11758} 11759 11760@Article{ bonnet1998symmetric, 11761 author = {Bonnet, M. and Maier, G. and Polizzotto, C.}, 11762 date-added = {2010-08-19 15:43:18 -0500}, 11763 date-modified = {2010-08-19 15:43:18 -0500}, 11764 journal = {Appl. Mech. Rev}, 11765 pages = {669--704}, 11766 title = {Symmetric {G}alerkin boundary element method.}, 11767 volume = {51}, 11768 year = {1998} 11769} 11770 11771@Conference{ zamith2007gpu, 11772 author = {Zamith, M. and Clua, E. and Pagliosa, P. and Conci, A. and Montenegro, A. and 11773 Valente, L.}, 11774 booktitle = {Proceedings of the VI Brazilian Symposium on Computer Games and Digital 11775 Entertainment}, 11776 date-added = {2010-08-19 15:43:14 -0500}, 11777 date-modified = {2010-08-19 15:43:14 -0500}, 11778 pages = {37--43}, 11779 title = {The {GPU} used as a math co-processor in real time applications}, 11780 year = {2007} 11781} 11782 11783@Article{ baskaran2009optimizing, 11784 author = {Baskaran, M.M. and Bordawekar, R.}, 11785 date-added = {2010-08-19 15:42:56 -0500}, 11786 date-modified = {2010-08-19 15:42:56 -0500}, 11787 journal = {IBM Research Report RC24704, IBM}, 11788 title = {Optimizing sparse matrix-vector multiplication on {GPU}s}, 11789 year = {2009} 11790} 11791 11792@Misc{ szeliski2006locally, 11793 author = {Szeliski, R.}, 11794 date-added = {2010-08-19 15:42:45 -0500}, 11795 date-modified = {2010-08-19 15:42:45 -0500}, 11796 month = jul, 11797 note = {US Patent App. 11/459,724}, 11798 publisher = {Google Patents}, 11799 title = {Locally adapted hierarchical basis preconditioning}, 11800 year = {2006} 11801} 11802 11803@Article{ jung2006cholesky, 11804 author = {Jung, J.H. and O'Leary, D.P.}, 11805 date-added = {2010-08-19 15:42:34 -0500}, 11806 date-modified = {2010-08-19 15:42:34 -0500}, 11807 journal = {Scholarly Paper, University of Maryland}, 11808 publisher = {Citeseer}, 11809 title = {Cholesky decomposition and linear programming on a {GPU}}, 11810 year = {2006} 11811} 11812 11813@Conference{ filipovic2009gpu, 11814 author = {Filipovic, J. and Peterlik, I. and Fousek, J.}, 11815 booktitle = {SAAHPC: Symposium on Application Accelerators in HPC}, 11816 date-added = {2010-08-19 15:42:33 -0500}, 11817 date-modified = {2010-08-19 15:42:33 -0500}, 11818 title = {{GPU} Acceleration of Equations Assembly in Finite Elements Method-Preliminary 11819 Results}, 11820 year = {2009} 11821} 11822 11823@Article{ taylor2009modelling, 11824 author = {Taylor, ZA and Comas, O. and Cheng, M. and Passenger, J. and Hawkes, DJ and 11825 Atkinson, D. and Ourselin, S.}, 11826 date-added = {2010-08-19 15:42:23 -0500}, 11827 date-modified = {2010-08-19 15:42:23 -0500}, 11828 journal = {Medical Image Analysis}, 11829 number = {2}, 11830 pages = {234--244}, 11831 publisher = {Elsevier}, 11832 title = {On modelling of anisotropic viscoelasticity for soft tissue simulation: Numerical 11833 solution and {GPU} execution}, 11834 volume = {13}, 11835 year = {2009} 11836} 11837 11838@Conference{ owens2007survey, 11839 author = {Owens, J.D. and Luebke, D. and Govindaraju, N. and Harris, M. and Kr{\\"u}ger, J. 11840 and Lefohn, A.E. and Purcell, T.J.}, 11841 booktitle = {Computer Graphics Forum}, 11842 date-added = {2010-08-19 15:42:21 -0500}, 11843 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Markus}, 12658 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 12659 for {PDE} Based Applications}, 12660 year = {1994}, 12661 institution = {Department of Computer Sciences, Purdue University}, 12662 number = {CSD-TR-94-021} 12663} 12664 12665@Unpublished{ ilu-web-page, 12666 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 12667 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 12668 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 12669} 12670 12671@Unpublished{ doe2k-web-page, 12672 title = {{DOE2000 Initiative} {W}eb page}, 12673 note = {http://www.mcs.anl.gov/DOE2000}, 12674 key = {DOE2000 Initiative} 12675} 12676 12677@Misc{ pvode-web-page, 12678 title = {{PVODE} {W}eb Page}, 12679 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 12680 author = {A. {Hindmarsh et al.}} 12681} 12682 12683@Book{ szyperski97, 12684 author = {Clemens Szyperski}, 12685 title = {Component Software: Beyond Object-Oriented Programming}, 12686 publisher = {ACM Press}, 12687 address = {New York}, 12688 year = {1997} 12689} 12690 12691@Unpublished{ petsc:coloringuse, 12692 title = {Code for computing sparse {J}acobians}, 12693 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12694 institution = {Argonne National Laboratory} 12695} 12696 12697@Unpublished{ petsc:external, 12698 author = {B. F. {Smith et al.}}, 12699 title = {{External Software Used by PETSc}}, 12700 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12701 institution = {Argonne National Laboratory} 12702} 12703 12704@Unpublished{ petsc:use-by-external-packages, 12705 author = {B. F. {Smith et al.}}, 12706 title = {{Software Packages that Use or Interface to PETSc}}, 12707 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 12708 institution = {Argonne National Laboratory} 12709} 12710 12711@Unpublished{ petsc:prizes, 12712 author = {B. F. {Smith et al.}}, 12713 title = {{Prizes Won Using PETSc}}, 12714 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12715 institution = {Argonne National Laboratory} 12716} 12717 12718@Unpublished{ petsc:csgf, 12719 author = {B. F. {Smith et al.}}, 12720 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 12721 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12722 institution = {Argonne National Laboratory} 12723} 12724 12725@Unpublished{ flash-web-page, 12726 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 12727 {W}eb Page}, 12728 note = {http://www.asci.uchicago.edu}, 12729 author = {R. {Rosner et al.}}, 12730 institution = {University of Chicago} 12731} 12732 12733@Unpublished{ esi-web-page, 12734 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 12735 note = {http://z.ca.sandia.gov/esi}, 12736 author = {R. {Clay et al.}} 12737} 12738 12739@Unpublished{ infobus-web-page, 12740 title = {{I}nfo{B}us {W}eb Page}, 12741 note = {http://www.java.sun.com/beans/infobus}, 12742 key = {infobus} 12743} 12744 12745@Unpublished{ xray-web-page, 12746 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 12747 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 12748 note = {http://www.mcs.anl.gov/xray/}, 12749 institution = {Argonne National Laboratory} 12750} 12751 12752@InProceedings{ kohn98, 12753 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 12754 title = {Language Interoperability Mechanisms for High-Performance Scientific 12755 Applications}, 12756 publisher = {SIAM}, 12757 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12758 Scientific and Engineering Computing}, 12759 year = {1999}, 12760 pages = {30-39} 12761} 12762 12763@InProceedings{ kohn01, 12764 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 12765 title = {Divorcing Language Dependencies from a Scientific Software Library}, 12766 publisher = {SIAM}, 12767 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 12768 year = {2001} 12769} 12770 12771@InProceedings{ freitag_jones_plassmann98, 12772 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 12773 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 12774 publisher = {SIAM}, 12775 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12776 Scientific and Engineering Computing}, 12777 year = {1999}, 12778 pages = {215-224} 12779} 12780 12781@Book{ templates, 12782 author = {R. 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Browne}, 12802 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 12803 Techniques}, 12804 institution = {Department of Computer Science, University of Texas at Austin}, 12805 year = {1995} 12806} 12807 12808@Article{ parti, 12809 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 12810 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 12811 Memory Architectures}, 12812 journal = {Journal of Parallel and Distributed Computing}, 12813 year = {1994}, 12814 volume = {22}, 12815 pages = {462--478} 12816} 12817 12818@Article{ mparti, 12819 author = {G. Agrawal and A. Sussman and J. 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Ross}, 12843 publisher = {University of Toronto}, 12844 pages = {379--386}, 12845 year = {1994} 12846} 12847 12848@Article{ cs99, 12849 author = {X.-C. Cai and M. Sarkis}, 12850 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 12851 systems}, 12852 journal = {SIAM J. Scientific Computing}, 12853 year = {1999}, 12854 volume = {21}, 12855 pages = {792-797} 12856} 12857 12858@Article{ cai2003restricted, 12859 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 12860 positive definite linear systems}, 12861 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 12862 journal = {SIAM Journal on Numerical Analysis}, 12863 volume = {41}, 12864 issue = {1}, 12865 pages = {1209--1231}, 12866 year = {2003}, 12867 doi = {10.1137/S0036142901389621} 12868} 12869 12870@TechReport{ caisaad, 12871 author = {Xiao-Chuan Cai and Youcef Saad}, 12872 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 12873 institution = {Army High Performance Computing Research Center, University of Minnesota }, 12874 year = {1993}, 12875 number = {Preprint 93-027 }, 12876 note = {SIAM J. Sci. Comp. 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Merlin}, 12956 title = {Parallel versions of {S}tones strongly implicit algorithm}, 12957 journal = {Concurrency and Computation: Practice and Experience}, 12958 pages = {1049--1062}, 12959 volumne = {13}, 12960 year = {2001} 12961} 12962 12963@Article{ p4-paper, 12964 author = {Ralph Butler and Ewing Lusk}, 12965 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 12966 journal = {Journal of Parallel Computing}, 12967 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 12968 Division preprint P362-0493)}, 12969 year = {1993} 12970} 12971 12972@TechReport{ picl, 12973 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 12974 title = {{PICL}: A portable instrumented communications library}, 12975 institution = {Oak Ridge National Laboratory}, 12976 number = {TM-11130}, 12977 year = {1990}, 12978 key = {PICL} 12979} 12980 12981@TechReport{ upshot, 12982 author = {Virginia Herrarte and Ewing Lusk}, 12983 title = {Studying Parallel Program Behavior with {U}pshot}, 12984 institution = {Argonne National Laboratory}, 12985 number = {ANL-91/15}, 12986 month = aug, 12987 year = {1991}, 12988 key = {Upshot} 12989} 12990 12991@TechReport{ p4-manual, 12992 author = {Ralph Butler and Ewing Lusk}, 12993 title = {User's Guide to the p4 Parallel Programming System}, 12994 institution = {Argonne National Laboratory}, 12995 number = {ANL-92/17}, 12996 month = oct, 12997 year = {1992}, 12998 key = {p4-Manual} 12999} 13000 13001@InProceedings{ oldparti, 13002 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 13003 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 13004 booktitle = {Proceedings of Supercomputing '93}, 13005 pages = {578--587}, 13006 year = {1993} 13007} 13008 13009@Article{ parti2, 13010 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 13011 and J. Saltz}, 13012 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 13013 journal = {ACM SIGPLAN Notices}, 13014 year = {1995}, 13015 pages = {68-79}, 13016 volume = {30}, 13017 number = {8} 13018} 13019 13020@Article{ parti3, 13021 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 13022 title = {Run-Time Parallelization and Scheduling of Loops}, 13023 journal = {IEEE Trans. Computers}, 13024 year = {1991}, 13025 pages = {604-612}, 13026 volume = {40}, 13027 number = {5} 13028} 13029 13030@InProceedings{ disz-lusk:wamtrace, 13031 author = {Terrence Disz and Ewing Lusk}, 13032 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 13033 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13034 year = {1987}, 13035 pages = {46--53} 13036} 13037 13038@InProceedings{ gorlick-kesselman:gauge, 13039 author = {Michael Gorlick and Carl Kesselman}, 13040 title = {Timing {Prolog} programs without Clocks}, 13041 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13042 year = {1996}, 13043 publisher = {Birkhauser} 13044} 13045 13046@TechReport{ aztec, 13047 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 13048 title = {Aztec User's Guide Version 1.1}, 13049 institution = {Sandia National Laboratories}, 13050 month = oct, 13051 year = {1995}, 13052 number = {SAND95/1559} 13053} 13054 13055@TechReport{ aztec2, 13056 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 13057 title = {Official {Aztec} User's Guide Version 2.1}, 13058 institution = {Sandia National Laboratories}, 13059 year = {1999} 13060} 13061 13062@Book{ taylor-chandy:pcn, 13063 author = {Chandy, M. and Taylor, S.}, 13064 title = {An Introduction to Parallel Programming}, 13065 year = {1991}, 13066 publisher = {Jones and Bartlett} 13067} 13068 13069@Book{ foster-taylor:strand, 13070 title = {Strand: New Concepts in Parallel Programming}, 13071 author = {Ian Foster and Stephen Taylor}, 13072 publisher = {Prentice-Hall}, 13073 adress = { Englewood Cliffs, New Jersey}, 13074 year = {1990} 13075} 13076 13077@Article{ aurora, 13078 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 13079 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 13080 Carlsson and A. Ciepielewski and B. Hausman}, 13081 title = {The Aurora OR-Parallel Prolog System}, 13082 journal = {New Generation Computing}, 13083 volume = {7}, 13084 number = {3}, 13085 year = {1990}, 13086 pages = {243--271} 13087} 13088 13089@TechReport{ roo, 13090 author = {E. Lusk and W. McCune and J. Slaney}, 13091 title = {Roo---a Parallel Theorem Prover}, 13092 institution = {Argonne National Laboratory}, 13093 number = {MCS--TM--149}, 13094 year = {1991} 13095} 13096 13097@TechReport{ heath-etheridge:vppp, 13098 author = {M. T. Heath and J. A. Etheridge}, 13099 title = {Visualizing the Performance of Parallel Programs}, 13100 institution = {Oak Ridge National Laboratory}, 13101 number = {ORNL TM-11813}, 13102 year = {1991} 13103} 13104 13105@TechReport{ chem:vis, 13106 author = {Ewing L. Lusk}, 13107 title = {Performance Visualization for Parallel Programs}, 13108 institution = {Argonne National Laboratory}, 13109 number = {ANL/MCS--P287--0192}, 13110 year = {1991}, 13111 note = {(to appear in {\em Theoretica Chimica Acta})} 13112} 13113 13114@TechReport{ picltrace, 13115 author = {P.~H.~Worley}, 13116 title = {A new {PICL} trace file format}, 13117 institution = {Oak Ridge National Laboratory}, 13118 number = {ORNL TM-12125}, 13119 month = jun, 13120 year = {1992} 13121} 13122 13123@InProceedings{ hideo, 13124 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 13125 title = {Inference of Phylogenetic trees using maximum likelihood}, 13126 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 13127 year = {1992}, 13128 pages = {247--262} 13129} 13130 13131@InProceedings{ dw90, 13132 author = {M. Dryja and O. Widlund}, 13133 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 13134 Problems}, 13135 booktitle = {Third International Symposium on Domain Decomposition Methods}, 13136 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 13137 year = {1990}, 13138 pages = {3-21}, 13139 publisher = {SIAM}, 13140 address = {Philadelphia}, 13141 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 13142 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 13143 references, good introduction to the theory. No computations}, 13144 key = {DryjaWidlund90 !AS} 13145} 13146 13147@Unpublished{ rosing, 13148 author = {Matt Rosing and Joel Saltz}, 13149 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 13150 key = {LowLatency}, 13151 note = {manuscript, 1992} 13152} 13153 13154@TechReport{ jp:incomplete, 13155 author = {Mark T. Jones and Paul E. Plassmann}, 13156 title = {An Improved Incomplete {C}holesky Factorization}, 13157 institution = {Argonne National Laboratory}, 13158 address = {Argonne, IL}, 13159 type = {Preprint}, 13160 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 13161 number = {MCS-P206-0191}, 13162 year = {1991}, 13163 key = {jones} 13164} 13165 13166@InCollection{ jp:ima, 13167 author = {Mark Jones and Paul Plassmann}, 13168 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 13169 booktitle = {Graph Theory and Sparse Matrix Computation}, 13170 publisher = {Springer-Verlag}, 13171 series = {The IMA Volumes in Mathematics and Its Applications}, 13172 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 13173 volume = {56}, 13174 year = {1993}, 13175 pages = {229--245} 13176} 13177 13178@Article{ pw98, 13179 author = {M. Pernice and H. F. Walker}, 13180 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 13181 journal = {SIAM J. Sci. Stat. Comput.}, 13182 year = {1998}, 13183 volume = {19}, 13184 pages = {302--318} 13185} 13186 13187@TechReport{ ysmp83, 13188 key = {Eisenstat}, 13189 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13190 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13191 institution = {Department of Computer Science, Yale University}, 13192 number = {YALE/DCS/RR-265}, 13193 month = apr, 13194 year = {1983} 13195} 13196 13197@InBook{ ysmp84, 13198 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13199 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13200 title = {Elliptic Problem Solvers II}, 13201 publisher = {Academic Press}, 13202 pages = {45--52}, 13203 editors = {G. Birkhoff and A. Schoenstadt}, 13204 year = {1984} 13205} 13206 13207@TechReport{ sparsekit, 13208 key = {Saad}, 13209 author = {Youcef Saad}, 13210 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 13211 institution = {Center for Supercomputing Research and Development, University of Illinois at 13212 Urbana-Champaign}, 13213 number = {1029}, 13214 year = {1990} 13215} 13216 13217@TechReport{ pde-user-ref, 13218 author = {Barry F. Smith}, 13219 title = {Extensible {PDE} Solvers Package Users Manual}, 13220 institution = {Argonne National Laboratory}, 13221 month = sep, 13222 year = {1994}, 13223 number = {ANL-93/40}, 13224 key = {Smith94 ! PDE} 13225} 13226 13227@TechReport{ bs-user-ref, 13228 author = {Mark T. Jones and Paul E. Plassmann}, 13229 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 13230 of Sparse Linear Systems}, 13231 institution = {Argonne National Laboratory}, 13232 month = dec, 13233 year = {1995}, 13234 number = {ANL-95/48} 13235} 13236 13237@TechReport{ snes-user-ref, 13238 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 13239 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 13240 institution = {Argonne National Laboratory}, 13241 month = feb, 13242 year = {1995}, 13243 number = {ANL/MCS-TM-193}, 13244 key = {GroppMcInnesSmith95 ! SNES} 13245} 13246 13247@TechReport{ sles-user-ref, 13248 author = {William D. Gropp and Barry F. Smith}, 13249 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 13250 institution = {Argonne National Laboratory}, 13251 month = mar, 13252 year = {1993}, 13253 number = {ANL-93/8}, 13254 key = {GroppSmith93 ! SLES} 13255} 13256 13257@TechReport{ chameleon-user-ref, 13258 author = {William D. Gropp and Barry F. Smith}, 13259 title = {Chameleon Parallel programming tools Users Manual}, 13260 institution = {Argonne National Laboratory}, 13261 month = mar, 13262 year = {1993}, 13263 number = {ANL-93/23}, 13264 key = {GroppSmith93 ! Chameleon} 13265} 13266 13267@Article{ euclid2, 13268 author = {D. Hysom and A. Pothen}, 13269 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 13270 journal = {SIAM J. Sci. Comput.}, 13271 volume = {22}, 13272 number = {6}, 13273 pages = {2194--2215} 13274} 13275 13276@TechReport{ euclid1, 13277 author = {D. Hysom and A. Pothen}, 13278 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 13279 Solution of Sparse Linear Systems)}, 13280 institution = {Old Dominion University}, 13281 year = {2001} 13282} 13283 13284@TechReport{ ksp-user-ref, 13285 author = {William D. Gropp and Barry F. Smith}, 13286 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 13287 Methods}, 13288 institution = {Argonne National Laboratory}, 13289 month = aug, 13290 year = {1993}, 13291 number = {ANL-93/30}, 13292 key = {GroppSmith93 ! KSP} 13293} 13294 13295@TechReport{ mpi-chameleon, 13296 author = {William D. Gropp and Ewing Lusk}, 13297 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 13298 institution = {Argonne National Laboratory}, 13299 month = dec, 13300 year = {1992}, 13301 number = {ANL-92/47}, 13302 key = {GroppLusk92 ! MPI} 13303} 13304 13305@TechReport{ blockcomm-fortran, 13306 author = {William D. Gropp}, 13307 title = {Block{C}omm for {F}ortran}, 13308 institution = {Argonne National Laboratory}, 13309 month = may, 13310 year = {1993}, 13311 number = {ANL-93/00 (to appear)}, 13312 key = {Gropp93 ! BlockComm} 13313} 13314 13315@TechReport{ autodocument, 13316 author = {William D. Gropp}, 13317 title = {Automatic documentation of {C} programs}, 13318 institution = {Argonne National Laboratory}, 13319 month = may, 13320 year = {1993}, 13321 number = {ANL-93/00}, 13322 key = {Gropp93 ! Autodoc} 13323} 13324 13325@TechReport{ zipcode, 13326 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 13327 Manfred Morari}, 13328 title = {The {Z}ipcode message-passing system}, 13329 institution = {Lawrence Livermore National Laboratory}, 13330 month = sep, 13331 year = {1992}, 13332 number = {Unpublished}, 13333 key = {Skjellum92 ! Zipcode} 13334} 13335 13336@Article{ paragraph, 13337 author = {Michael T. Heath and Jennifer Etheridge Finger}, 13338 title = {Visualizing performance of parallel programs}, 13339 journal = {IEEE Software}, 13340 volume = {8}, 13341 number = {5}, 13342 month = sep, 13343 year = {1991}, 13344 pages = {29--39}, 13345 key = {Heath91 ! Paragraph} 13346} 13347 13348@Article{ gropp90, 13349 author = {William Gropp and Edward Smith}, 13350 title = {Computational Fluid Dynamics on Parallel Processors}, 13351 journal = {Computers and Fluids}, 13352 volume = {18}, 13353 year = {1990}, 13354 pages = {289--304}, 13355 key = {Gropp90 ! performance} 13356} 13357 13358@Article{ foster92, 13359 author = {Ian Foster and William Gropp and Rick Stevens}, 13360 title = {The parallel scalability of the spectral transform method}, 13361 journal = {Monthly Weather Review}, 13362 volume = {120}, 13363 year = {1992}, 13364 pages = {835--850}, 13365 key = {Foster92 ! performance} 13366} 13367 13368@InBook{ fgn, 13369 author = {R. Freund and G. H. Golub and N. Nachtigal}, 13370 title = {Iterative Solution of Linear Systems}, 13371 series = {Acta Numerica}, 13372 year = {1992}, 13373 publisher = {Cambridge University Press}, 13374 pages = {57--100} 13375} 13376 13377@TechReport{ nachtigal90, 13378 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 13379 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13380 institution = {Massachusetts Institute of Technology}, 13381 month = mar, 13382 year = {1990}, 13383 number = {90-2}, 13384 key = {Nachtigal | Krylov} 13385} 13386 13387@Article{ nachtigal1992fnm, 13388 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13389 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 13390 journal = {SIAM Journal on Matrix Analysis and Applications}, 13391 volume = {13}, 13392 pages = {778}, 13393 year = {1992}, 13394 publisher = {SIAM} 13395} 13396 13397@TechReport{ embree1999descriptive, 13398 title = {How descriptive are {GMRES} convergence bounds}, 13399 author = {Embree, M.}, 13400 year = {1999}, 13401 number = {08}, 13402 institution = {Oxford University Computing Laboratory} 13403} 13404 13405@Article{ vorst92, 13406 author = {H. van der Vorst}, 13407 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 13408 of nonsymmetric linear systems}, 13409 journal = {SIAM J. Sci. Stat. Comput.}, 13410 year = {1992}, 13411 volume = {13}, 13412 pages = {631--644} 13413} 13414 13415@Article{ eisenstat81, 13416 author = {S. Eisenstat}, 13417 title = {Efficient Implementation of a Class of {CG} Methods}, 13418 journal = {SIAM J. Sci. Stat. Comput.}, 13419 year = {1981}, 13420 volume = {2}, 13421 pages = {1--4} 13422} 13423 13424@Manual{ ibm-essl, 13425 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 13426 Reference}, 13427 organization = {IBM}, 13428 year = {1992}, 13429 key = {IBM-ESSL} 13430} 13431 13432@Manual{ ibm-eui, 13433 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 13434 Release 2.0}, 13435 organization = {IBM}, 13436 month = jun, 13437 year = {1994}, 13438 key = {IBM-EUI} 13439} 13440 13441@Manual{ ibm-euih, 13442 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 13443 organization = {IBM}, 13444 author = {Peter Hochschild}, 13445 year = {1993}, 13446 key = {IBM-EUIH} 13447} 13448 13449@TechReport{ mpi, 13450 title = {Document for a Standard Message-Passing Interface}, 13451 author = {Message Passing Interface Forum}, 13452 institution = {University of Tennessee}, 13453 number = {CS-93-214}, 13454 month = nov, 13455 year = {1993}, 13456 key = {MPI Standard} 13457} 13458 13459@Unpublished{ mpi-final-web, 13460 author = {Message Passing Interface Forum}, 13461 title = {{MPI}: A Message-Passing Interface Standard}, 13462 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 13463 year = {1994}, 13464 month = may 13465} 13466 13467@Book{ hockney-jesshope, 13468 author = {R. W. Hockney and C. R. Jesshope}, 13469 title = {Parallel Computers 2}, 13470 publisher = {Adam Hilger}, 13471 year = {1988} 13472} 13473 13474@Book{ cm-fortran, 13475 author = {{Thinking Machines Corporation}}, 13476 title = {Users Manual for CM-Fortran}, 13477 publisher = {Thinking Machines Corporation}, 13478 year = {1993} 13479} 13480 13481@TechReport{ chang93, 13482 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 13483 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 13484 institution = {Yale Department of Computer Science}, 13485 number = {YALEU/DCS/RR-994}, 13486 month = nov, 13487 year = {1993}, 13488 key = {BDD|diag} 13489} 13490 13491@InProceedings{ gropplevine93, 13492 author = {N. Galbreath and W. Gropp and D. Levine}, 13493 title = {Applications-Driven Parallel {I/O}}, 13494 booktitle = {Proceedings of Supercomputing '93}, 13495 year = {1993}, 13496 pages = {462--471} 13497} 13498 13499@Book{ siegle85, 13500 author = {H. J. Siegel}, 13501 title = {Interconnection Networks for Large Scale Parallel Processing}, 13502 publisher = {Lexington Books}, 13503 year = {1985}, 13504 key = {Network Comparison} 13505} 13506 13507@Article{ lawrie75, 13508 author = {D. H. Lawrie}, 13509 title = {Access and alignment of data in an array processor}, 13510 journal = {IEEE Transactions on Computers}, 13511 volume = {C-24}, 13512 number = {12}, 13513 month = dec, 13514 year = {1975}, 13515 pages = {1145--1155}, 13516 key = {Omega Network} 13517} 13518 13519@Book{ knuth1986, 13520 title = {The {\TeX}{Book}}, 13521 author = {Donald Ervin Knuth and Duane Bibby}, 13522 volume = {1993}, 13523 year = {1986}, 13524 publisher = {Addison-Wesley Reading, Massachusetts} 13525} 13526 13527@Book{ lamport86, 13528 author = {Leslie Lamport}, 13529 title = {{LaTeX}: A document preparation system}, 13530 publisher = {Addison-Wesley}, 13531 year = {1986}, 13532 key = {Latex Manual} 13533} 13534 13535@InProceedings{ gropp-lusk:unix-tools, 13536 author = {William Gropp and Ewing Lusk}, 13537 title = {Scalable {U}nix Tools on Parallel Processors}, 13538 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 13539 publisher = {IEEE}, 13540 pages = {56--62} 13541} 13542 13543@InProceedings{ jp:bell_prize, 13544 author = {Mark Jones and Paul Plassmann}, 13545 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 13546 Applications}, 13547 booktitle = {Proceedings of Supercomputing '92}, 13548 publisher = {IEEE Computer Society Press}, 13549 year = {1992}, 13550 pages = {551--560} 13551} 13552 13553@COMMENT{WEB, CWEB references (for doctext)} 13554@TechReport{ web, 13555 author = {Donald E. Knuth}, 13556 title = {The {\tt WEB} system of structured documentation}, 13557 institution = {Computer Science Department, Stanford University}, 13558 year = {1983}, 13559 number = {980}, 13560 month = sep 13561} 13562 13563@Article{ literatepgm, 13564 author = {Donald E. Knuth}, 13565 title = {Literate Programming}, 13566 journal = {Computer Journal}, 13567 year = {1984}, 13568 volume = {27}, 13569 number = {2}, 13570 pages = {91--111} 13571} 13572 13573@Unpublished{ cweb-code, 13574 author = {Silvio Levy and Donald E. Knuth}, 13575 title = {CWEB}, 13576 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 13577} 13578 13579@Article{ jp:scalable, 13580 author = {Mark Jones and Paul Plassmann}, 13581 title = {Scalable Iterative Solution of Sparse Linear Systems}, 13582 journal = {Parallel Computing}, 13583 volume = {20}, 13584 number = {5}, 13585 month = may, 13586 year = {1994}, 13587 pages = {753--773} 13588} 13589 13590@Article{ jp:pcolor, 13591 author = {Mark T. Jones and Paul E. Plassmann}, 13592 title = {A Parallel Graph Coloring Heuristic}, 13593 journal = {SIAM J. Sci. Comput.}, 13594 volume = {14}, 13595 number = {3}, 13596 pages = {654-669}, 13597 year = {1993} 13598} 13599 13600@TechReport{ block_solve, 13601 author = {Mark T. Jones and Paul E. Plassmann}, 13602 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 13603 Sparse Linear Systems}, 13604 institution = {Argonne National Laboratory}, 13605 year = {1992}, 13606 number = {ANL-92/46}, 13607 key = {JonesPlassmann92 ! block_solve} 13608} 13609 13610@InProceedings{ supercond, 13611 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 13612 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 13613 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 13614 Conference}, 13615 month = feb, 13616 year = {1994}, 13617 key = {McInnesPalumbo94 ! superconductivity } 13618} 13619 13620@Unpublished{ preosti:93, 13621 author = {Gianfranco Preosti}, 13622 title = { }, 13623 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 13624 year = {1993}, 13625 key = {preosti93 ! GL-tilt3d} 13626} 13627 13628@Unpublished{ more:93, 13629 author = {Jorge J. Mor\'{e}}, 13630 title = { }, 13631 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 13632 {A}rgonne {N}ational {L}aboratory}, 13633 year = {1993}, 13634 key = {more93 ! MINPACK-2} 13635} 13636 13637@Article{ brownsaad:90, 13638 author = {Peter N. Brown and Youcef Saad}, 13639 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 13640 journal = {SIAM J. Sci. Stat. Comput.}, 13641 year = {1990}, 13642 volume = {11}, 13643 pages = {450-481} 13644} 13645 13646@Book{ using-mpi, 13647 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 13648 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 13649 publisher = {MIT Press}, 13650 year = {1994} 13651} 13652 13653@Book{ using-mpi2, 13654 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 13655 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 13656 publisher = {MIT Press}, 13657 year = {1999} 13658} 13659 13660@Article{ hs:52, 13661 author = {Magnus R. Hestenes and Eduard Steifel}, 13662 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 13663 journal = {J. Research of the National Bureau of Standards}, 13664 year = {1952}, 13665 volume = {49}, 13666 pages = {409-436} 13667} 13668 13669@Article{ so:89, 13670 author = {Peter Sonneveld}, 13671 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 13672 journal = {SIAM J. Sci. Stat. Comput.}, 13673 year = {1989}, 13674 volume = {10}, 13675 pages = {36-52} 13676} 13677 13678@Article{ v:92, 13679 author = {{H. A.} {van der Vorst}}, 13680 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 13681 of nonsymmetric linear systems}, 13682 journal = {SIAM J. Sci. Stat. Comput.}, 13683 volume = {13}, 13684 year = {1992}, 13685 pages = {631-644} 13686} 13687 13688@Article{ f:93, 13689 author = {Roland W. Freund}, 13690 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 13691 Systems}, 13692 journal = {SIAM J. Sci. Stat. Comput.}, 13693 volume = {14}, 13694 year = {1993}, 13695 pages = {470-482} 13696} 13697 13698@Article{ ish:89, 13699 author = {S. Ishizuka}, 13700 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 13701 journal = {Combustion and Flame}, 13702 volume = {75}, 13703 year = {1989}, 13704 pages = {367-379} 13705} 13706 13707@Book{ williams89, 13708 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 13709 author = {F.A. Williams}, 13710 publisher = {Addison-Wesley}, 13711 year = {1989}, 13712 pages = {367-379} 13713} 13714 13715@Book{ ra75, 13716 author = {R. Aris}, 13717 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 13718 publisher = {Oxford}, 13719 year = {1975} 13720} 13721 13722@Book{ bebernes89, 13723 author = {J. Bebernes and D. Eberly}, 13724 title = {Mathematical Problems from Combustion Theory}, 13725 publisher = {Springer-Verlag}, 13726 series = {Applied Mathematical Sciences 83}, 13727 year = {1989} 13728} 13729 13730@InProceedings{ kikuchi89, 13731 author = {F. Kikuchi}, 13732 booktitle = { Computing Methods in Applied Sciences and Engineering}, 13733 editor = {R. Glowinski and J. L. Lions}, 13734 publisher = {Springer-Verlag}, 13735 series = {Lecture Notes in Mathematics}, 13736 title = {Finite element approximations to bifurcation problems of turning point type}, 13737 year = {1977} 13738} 13739 13740@Article{ rg85, 13741 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 13742 title = {Continuation-conjugate Gradient Methods fo the Least Squares Solution of 13743 Nonlinear Boundary Problems}, 13744 journal = {SIAM J. Sci. Stat. Comput.}, 13745 volume = {6}, 13746 year = {1985}, 13747 pages = {793-832} 13748} 13749 13750@InProceedings{ whitfield91, 13751 author = {D. Whitfield and L. Taylor}, 13752 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13753 Schemes}, 13754 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 13755 misc = {AIAA-91-1539}, 13756 pages = {134-145}, 13757 year = {1991} 13758} 13759 13760@InProceedings{ quinlan1, 13761 author = {M. Lemke and D. Quinlan}, 13762 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 13763 Architecture-Independent Development of Structured Grid Applications}, 13764 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 13765 publisher = {Springer Verlag}, 13766 year = {1992} 13767} 13768 13769@InProceedings{ quinlan2, 13770 author = {R. Parsons and D. Quinlan}, 13771 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 13772 Computations}, 13773 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 13774 year = {1994} 13775} 13776 13777% ***** Overview of functionality in Diffpack 13778@InBook{ dpoverview, 13779 author = {Bruaset, A. M. and Langtangen, H. P.}, 13780 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13781 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 13782 {Diffpack}}, 13783 publisher = {Birkh{\"{a}}user}, 13784 pages = {61--90}, 13785 year = {1997} 13786} 13787 13788% ***** Short overview of Diffpack 13789@InCollection{ dpoverview2, 13790 author = {Bruaset, A. M. and Langtangen, H. P.}, 13791 editor = {A. Sydow}, 13792 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 13793 and Applied Mathematics}, 13794 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 13795 pages = {553--558}, 13796 volume = {4}, 13797 year = {1997} 13798} 13799 13800% ***** Comprehensive documentation of Diffpack and 13801% associated numerical methods: 13802@Book{ dpbook, 13803 author = {H. P. Langtangen}, 13804 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 13805 Software. Part I}, 13806 series = {Lecture Notes in Computational Science and Engineering}, 13807 publisher = {Springer-Verlag}, 13808 year = {1998} 13809} 13810 13811% ***** Design issues of the linear solvers in Diffpack, serves also as a 13812% collection of examples on O-O in numerical computing 13813@Article{ ambhpl97a, 13814 author = {A. M. Bruaset and H. P. Langtangen }, 13815 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 13816 journal = {Transactions on Mathematical Software}, 13817 volume = {23 }, 13818 pages = {50--80}, 13819 year = {1997} 13820} 13821 13822@Misc{ dpurl, 13823 author = {{Diffpack Web page}}, 13824 howpublished = {\url{http://www.diffpack.com}} 13825} 13826 13827% ***** General intro to object-oriented numerics for "FORTRAN programmers" 13828@InCollection{ oonintro, 13829 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 13830 editor = {D{\ae}hlen, M. and Tveito, A.}, 13831 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13832 title = {Object-Oriented Numerics}, 13833 publisher = {Birkh{\"{a}}user}, 13834 year = {1997} 13835} 13836 13837% ***** Efficiency comparison: BLAS 1, Diffpack, C, 13838% and finite element applications (F77 vs Diffpack) 13839@InCollection{ dpefficiency, 13840 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 13841 H. P. and Miller, C. T.}, 13842 editor = {D{\ae}hlen, M. and Tveito, A.}, 13843 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13844 title = {On the Efficiency of {C++} in Scientific Computing}, 13845 publisher = {Birkh{\"{a}}user}, 13846 pages = {91--118}, 13847 year = {1997} 13848} 13849 13850% ***** Parallel concept in Diffpack: 13851@InCollection{ dpparallel, 13852 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 13853 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 13854 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 13855 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 13856 Simulators}, 13857 publisher = {Springer--Verlag}, 13858 series = {Lecture Notes in Computer Science}, 13859 pages = {161--168}, 13860 year = {1997} 13861} 13862 13863% ***** DD and ML methods in Diffpack: 13864@InCollection{ dpddml, 13865 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 13866 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 13867 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 13868 title = {Domain decomposition and multilevel methods in Diffpack}, 13869 year = {1997} 13870} 13871 13872@InProceedings{ bsca98, 13873 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 13874 Alexander}, 13875 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 13876 Optimization}, 13877 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 13878 Scientific and Engineering Computing}, 13879 editor = {Mike Henderson et al.}, 13880 pages = {165-173}, 13881 year = {1998} 13882} 13883 13884@Book{ scalapack-user-guide, 13885 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 13886 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 13887 Stanley and D. Walker and R. C. Whaley}, 13888 title = {Sca{LAPACK} Users' Guide}, 13889 publisher = {SIAM}, 13890 address = {Philadelphia, PA}, 13891 year = {1997} 13892} 13893 13894@InProceedings{ keyes99, 13895 author = {D. E. Keyes}, 13896 title = {How Scalable is Domain Decomposition in Practice?}, 13897 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 13898 Methods}, 13899 editor = {C.-H. Lai et al.}, 13900 publisher = {Domain Decomposition Press, Bergen}, 13901 note = {To appear}, 13902 year = {1999} 13903} 13904 13905@Article{ fun3d, 13906 author = {W. K. Anderson and D. L. Bonhaus}, 13907 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 13908 grids}, 13909 journal = {Computers and Fluids}, 13910 year = {1994}, 13911 volume = {23}, 13912 pages = {1--21} 13913} 13914 13915% ------------------------------------------------------------------------- 13916% ------------------------------------------------------------------------- 13917@Article{ torczon, 13918 author = {Dennis, Jr., J. E. and V.~Torczon}, 13919 title = {Direct Search Methods on Parallel Machines}, 13920 journal = {SIAM J. Optimization}, 13921 volume = {1}, 13922 pages = {448--474}, 13923 year = {1991}, 13924 key = {Torczon !PDS} 13925} 13926 13927@InProceedings{ wt91, 13928 author = {D. L. Whitfield and L. K. Taylor}, 13929 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13930 Schemes}, 13931 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 13932 misc = {AIAA-91-1539}, 13933 pages = {134-145}, 13934 year = {1991} 13935} 13936 13937@Article{ ew96, 13938 author = {S. C. Eisenstat and H. F. Walker}, 13939 title = {Choosing the forcing terms in an inexact {N}ewton method}, 13940 journal = {SIAM J. Scientific Computing}, 13941 volume = {17}, 13942 year = {1996}, 13943 pages = {16--32} 13944} 13945 13946@Book{ thi93, 13947 author = {{Thinking Machines Corporation}}, 13948 title = {Users Manual for CM-Fortran}, 13949 publisher = {Thinking Machines Corporation}, 13950 year = {1993} 13951} 13952 13953@Book{ mortonmayers94, 13954 author = {K. W. Morton and D. F. Mayers}, 13955 title = {Numerical Solution of Partial Differential Equations}, 13956 publisher = {Press Syndicate of the University of Cambridge}, 13957 year = {1994} 13958} 13959 13960@Book{ heath97, 13961 author = {Michael T. Heath}, 13962 title = {Scientific Computing: An Introductory Survey}, 13963 publisher = {McGraw Hill}, 13964 year = {1997} 13965} 13966 13967@Article{ captools96, 13968 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 13969 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 13970 Performance on the Parallelization of Structured Mesh Codes}, 13971 journal = {Parallel Computing}, 13972 volume = {22}, 13973 pages = {197-226}, 13974 year = {1996} 13975} 13976 13977@Unpublished{ nastran-web-page, 13978 author = {{MSC Software Corporation}}, 13979 title = {{NASTRAN} {W}eb page}, 13980 note = {See {\tt http://www.mechsolutions.com\-/products\-/nastran/}} 13981} 13982 13983@Book{ hpf, 13984 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 13985 Zosel}, 13986 title = {The High Performance Fotran Handbook}, 13987 publisher = {MIT Press}, 13988 year = {1994} 13989} 13990 13991@InProceedings{ keyes98, 13992 author = {D. E. Keyes}, 13993 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 13994 Architectures}, 13995 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 13996 editors = {M. D. Salas and W. K. Anderson}, 13997 ppublisher = {Elsevier}, 13998 year = {1998} 13999} 14000 14001@InProceedings{ pooma-atlas, 14002 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14003 J. V. W. Reynders and M. Tholburn}, 14004 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14005 Applications}, 14006 year = {1995}, 14007 month = dec, 14008 booktitle = {Supercomputing '95 Proceedings} 14009} 14010 14011% --------------------------------------------------------------------------------- 14012% New bib entries for CRPC paper 14013@Misc{ mgnet-web-page, 14014 author = {Craig C. Douglas}, 14015 title = {{MGNet Web page}}, 14016 note = {See {\tt http://\-www.mgnet.org}} 14017} 14018 14019@Misc{ dagh-web-page, 14020 author = {M. Parashar and J. C. Browne}, 14021 title = {{DAGH Web page}}, 14022 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14023} 14024 14025@Misc{ parasol-web-page, 14026 key = {PARASOL}, 14027 title = {{PARASOL Web page}}, 14028 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14029} 14030 14031@Misc{ pooma-web-page, 14032 author = {{POOMA Web page}}, 14033 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14034} 14035 14036@Misc{ mudpack-web-page, 14037 author = {John C. Adams}, 14038 title = {{MUDPACK Web page}}, 14039 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14040} 14041 14042@Misc{ pellpack-web-page, 14043 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14044 title = {{Parallel ELLPACK Web page}}, 14045 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14046} 14047 14048@InProceedings{ pellpack95, 14049 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14050 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14051 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14052 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14053 address = {Albuquerque, NM}, 14054 year = {1995} 14055} 14056 14057@Misc{ nhse-web-page, 14058 author = {{National High-Performance Software Exchange Web page}}, 14059 note = {See {\tt http://\-www.nhse.org}} 14060} 14061 14062@Misc{ doug-web-page, 14063 author = {Mark J. Hagger and Linda Stals}, 14064 title = {{DOUG Web Page}}, 14065 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14066} 14067 14068@TechReport{ doug97, 14069 author = {Mark J. Hagger}, 14070 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14071 institution = {Mathematical Sciences, University of Bath}, 14072 year = {1997}, 14073 number = {9706}, 14074 note = {Advances in Computational Mathematics (to appear)} 14075} 14076 14077@Misc{ ug-web-page, 14078 author = {{UG Web Page}}, 14079 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14080} 14081 14082@Article{ ug97, 14083 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14084 Rentz-Reichert and C. Wieners}, 14085 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14086 journal = {Computing and Visualization in Science}, 14087 year = {1997}, 14088 volume = {}, 14089 pages = {} 14090} 14091 14092@Misc{ vecfem-web-page, 14093 author = {Lutz Grosz}, 14094 title = {{VECFEM Web Page}}, 14095 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14096} 14097 14098@Misc{ atlas-web-page, 14099 author = {R. Clint {Whaley et al.}}, 14100 title = {{ATLAS Web Page}}, 14101 howpublished = {\url{http://math-atlas.sourceforge.net}} 14102} 14103 14104@Misc{ fenics-web-page, 14105 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14106 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14107 title = {{FEniCS Web Page}}, 14108 note = {\url{http://www.fenicsproject.org}}, 14109 year = {2005} 14110} 14111 14112@Misc{ matlab-web-page, 14113 author = {{The} {MathWorks}}, 14114 title = {{Matlab} {Web} page}, 14115 url = {http://www.mathworks.com} 14116} 14117 14118@Misc{ phipac-web-page, 14119 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14120 and D. Lam}, 14121 title = {{PHiPAC Web Page}}, 14122 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14123} 14124 14125@InProceedings{ kelp, 14126 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14127 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14128 booktitle = {Irregular '96}, 14129 year = {1996} 14130} 14131 14132@Unpublished{ kelp-web-page, 14133 author = {Scott Baden}, 14134 title = {{KeLP} {W}eb page}, 14135 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14136} 14137 14138@InProceedings{ hk99, 14139 author = {R. Hornung and S. Kohn}, 14140 title = {The Use of Object-Oriented Design Patterns in the {SAMRAI} Structured {AMR} 14141 Framework}, 14142 booktitle = {Proceedings of the SIAM Workshop on Object-Oriented Methods for Inter-Operable 14143 Scientific and Engineering Computing}, 14144 pages = {235-244}, 14145 year = {1999}, 14146 note = {See \url{http://www.llnl.gov/CASC/samrai}} 14147} 14148 14149@Unpublished{ samrai-web-page, 14150 title = {{SAMRAI} {W}eb Page}, 14151 author = {Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith}, 14152 note = {See {\tt http://www.llnl.gov/\-CASC/SAMRAI}} 14153} 14154 14155@Misc{ overture-web-page, 14156 author = {William Henshaw and Kyle Chand}, 14157 title = {{Overture} {W}eb page}, 14158 howpublished = {\url{http://www.llnl.gov/CASC/Overture}} 14159} 14160 14161@InProceedings{ overture99, 14162 author = {D.L. Brown and W.D. Henshaw and D.J. Quinlan}, 14163 title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations 14164 on Overlapping Grids}, 14165 publisher = {SIAM}, 14166 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14167 Scientific and Engineering Computing}, 14168 year = {1999}, 14169 pages = {215-224}, 14170 note = {See \url{http://www.llnl.gov/CASC/Overture}} 14171} 14172 14173@InProceedings{ diffpack, 14174 author = {A.M. Bruaset and H.P. Langtangen}, 14175 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations: 14176 {D}iffpack}, 14177 booktitle = {Numerical Methods and Software Tools in Industrial Mathematics}, 14178 year = {1997}, 14179 pages = {61--90}, 14180 publisher = {Birkhauser Press} 14181} 14182 14183@Article{ dongarra:1984:ila, 14184 author = {J. J. Dongarra and F. G. Gustavson and A. Karp}, 14185 title = {Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline 14186 Machine}, 14187 journal = {SIAM Review}, 14188 volume = {26}, 14189 number = {1}, 14190 pages = {91--112}, 14191 month = jan, 14192 year = {1984}, 14193 coden = {SIREAD}, 14194 issn = {0036-1445 (print), 1095-7200 (electronic)}, 14195 mrclass = {65F10 (65F30)}, 14196 mrnumber = {85c:65032}, 14197 bibdate = {Mon Jan 20 1997}, 14198 abstract = {The authors examine common implementations of linear algebra algorithms, such as 14199 matrix-vector multiplication, matrix-matrix multiplication and the solution of 14200 linear equations. The different versions are examined for efficiency on a computer 14201 architecture which uses vector processing and has pipelined instruction execution. 14202 By using the advanced architectural features of such machines, one can usually 14203 achieve maximum performance, and tremendous improvements in terms of execution 14204 speed can be seen over conventional computers.}, 14205 classification= {723; 921}, 14206 journalabr = {SIAM Rev}, 14207 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 14208 mathematical programming; vector pipeline machine} 14209} 14210 14211@Book{ qv99, 14212 author = {Alfio Quarteroni and Alberto Valli}, 14213 title = {Domain Decomposition Methods for Partial Differential Equations}, 14214 publisher = {Oxford Science Publications}, 14215 address = {Oxford}, 14216 year = {1999} 14217} 14218 14219@Book{ ksv97, 14220 editor = {David E. Keyes and Ahmed Sameh and V. Venkatakrishnan}, 14221 title = {Parallel Numerical Algorithms}, 14222 publisher = {Kluwer Academic Publishers}, 14223 address = {the Netherlands}, 14224 year = {1997} 14225} 14226 14227@Book{ hackbusch94, 14228 author = {Wolfgang Hackbusch}, 14229 title = {Iterative Solution of Large Sparse Systems of Equations}, 14230 publisher = {Springer-Verlag}, 14231 address = {New York}, 14232 year = {1994} 14233} 14234 14235@Article{ hackbusch1980fast, 14236 title = {Fast solution of elliptic control problems}, 14237 author = {Hackbusch, W.}, 14238 journal = {Journal of Optimization Theory and Applications}, 14239 volume = {31}, 14240 number = {4}, 14241 pages = {565--581}, 14242 year = {1980}, 14243 publisher = {Springer} 14244} 14245 14246@Book{ hackbusch1985multi, 14247 title = {{Multi-grid methods and applications}}, 14248 author = {Hackbusch, W.}, 14249 isbn = {3540127615}, 14250 issn = {0179-3632}, 14251 year = {1985}, 14252 publisher = {Springer Verlag} 14253} 14254 14255@Book{ axelsson94, 14256 author = {Owe Axelsson}, 14257 title = {Iterative Solution Methods}, 14258 publisher = {Cambridge University Press}, 14259 address = {Cambridge}, 14260 year = {1994} 14261} 14262 14263@Book{ saad96, 14264 author = {Yousef Saad}, 14265 title = {Iterative Methods for Sparse Linear Systems}, 14266 publisher = {PWS Publishing Company}, 14267 address = {Boston}, 14268 year = {1996} 14269} 14270 14271@Book{ saad2003, 14272 title = {Iterative Methods for Sparse Linear Systems}, 14273 author = {Saad, Yousef}, 14274 doi = {10.1016/S1570-579X(01)80025-2}, 14275 edition = {2nd}, 14276 publisher = {SIAM}, 14277 year = {2003} 14278} 14279 14280@Book{ vandervorst03, 14281 author = {Henk A. {van der Vorst}}, 14282 title = {Iterative Krylov Methods for Large Linear Systems}, 14283 publisher = {Cambridge Monographs on Applied ahd Computational Mathematics}, 14284 year = {2003} 14285} 14286 14287@Book{ koniges00, 14288 editor = {Alice E. Koniges}, 14289 title = {Industrial Strength Parallel Computing}, 14290 publisher = {Morgan Kaufmann Publishers}, 14291 address = {San Francisco}, 14292 year = {2000} 14293} 14294 14295@Misc{ fftw-web-page, 14296 key = {Fftw}, 14297 title = {{FFTW} {Web} page}, 14298 note = {\texttt{http://www.fftw.org/}}, 14299 annote = {fast FFT. Parallel versions with MPI and Cilk} 14300} 14301 14302@InProceedings{ frigojohnson93, 14303 author = {Matteo Frigo and Steven G. Johnson}, 14304 title = {The Design and Implementation of {FFTW3}}, 14305 booktitle = {Proceedings of the IEEE}, 14306 volume = {93}, 14307 number = {2}, 14308 pages = {216--231}, 14309 year = {2005} 14310} 14311 14312@Book{ kelley95, 14313 author = {C. T. Kelley}, 14314 title = {Iterative Methods for Linear and Nonlinear Equations}, 14315 year = {1995}, 14316 publisher = {SIAM}, 14317 address = {Philadelphia} 14318} 14319 14320@Unpublished{ spai-web-page, 14321 title = {{SPAI} {W}eb {P}age}, 14322 note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/}, 14323 author = {Steven Bernard and Marcus Grote}, 14324 institution = {NASA Ames Research Center and ETH Zurich} 14325} 14326 14327@Article{ gh97, 14328 author = {M. J. Grote and T. Huckle}, 14329 title = {Parallel Preconditioning with Sparse Approximate Inverses}, 14330 year = {1997}, 14331 journal = {SIAM J. of Scient. Comput.}, 14332 volume = {18}, 14333 pages = {838-853} 14334} 14335 14336@Article{ zhang96, 14337 author = {Wen Zhang}, 14338 title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the 14339 simulation of a sintering process}, 14340 year = {1996}, 14341 journal = {Appl. Numer. Math.}, 14342 volume = {20}, 14343 pages = {235-244} 14344} 14345 14346@Article{ zhang98, 14347 author = {Wen Zhang and Ian Gladwell}, 14348 title = {The sintering of two particles by surface and grain boundary diffusion - a 14349 three-dimensional numerical study}, 14350 journal = {Comp. Mater. Sci.}, 14351 year = {1998}, 14352 volume = {12} 14353} 14354 14355@InProceedings{ mollerschwartzbach01, 14356 author = {Anders M\o{}ller and Michael I. Schwartzbach}, 14357 title = {The Pointer Assertion Logic Engine}, 14358 booktitle = {ACM Proceedings of PLDI'01}, 14359 year = {2001} 14360} 14361 14362@InProceedings{ klarlandschwartzbach97, 14363 author = {Nils Klarland and Michael I. Schwartzbach}, 14364 title = {A Domain-Specific Languages for Regular Sets of Strings and Trees}, 14365 booktitle = {Proceedings of the Conference on Domain-Specific Languages}, 14366 publisher = {USENIX}, 14367 month = oct, 14368 year = {1997}, 14369 address = {Santa Barbara, CA} 14370} 14371 14372@InProceedings{ conselmarlet98, 14373 author = {C. Consel and R. Marlet}, 14374 title = {Architecturing software using a methodology for language development}, 14375 booktitle = {Proceedings of the 10th International Symposium on Programming Languages, 14376 Implementations, Logics and Programs}, 14377 year = {1998}, 14378 pages = {170-174}, 14379 month = sep, 14380 address = {Pisa, Italy} 14381} 14382 14383@Misc{ sundials:homepage, 14384 author = {C. {Woodward et al.}}, 14385 title = {{SUNDIALS {W}eb page}}, 14386 howpublished = {\url{https://computation.llnl.gov/casc/sundials/main.html}} 14387} 14388 14389@article{gardner2022sundials, 14390 title = {Enabling new flexibility in the {SUNDIALS} suite of nonlinear and differential/algebraic equation solvers}, 14391 author = {Gardner, David J and Reynolds, Daniel R and Woodward, Carol S and Balos, Cody J}, 14392 journal = {ACM Transactions on Mathematical Software (TOMS)}, 14393 publisher = {ACM}, 14394 year = {2022}, 14395 doi = {10.1145/3539801} 14396} 14397 14398@Misc{ sundials-user-ref, 14399 title = {{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 14400 note = {See \url{http://www.llnl.gov/CASC/sundials}}, 14401 author = {Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban 14402 and Dan Shumaker and Carol Woodward}, 14403 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 14404 number = {UCRL-JP-200037}, 14405 year = {2003} 14406} 14407 14408@Article{ sundials05, 14409 author = {A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 14410 and C. Woodward}, 14411 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 14412 journal = {ACM Transactions on Mathematical Software}, 14413 volume = {31}, 14414 number = {3}, 14415 pages = {363--396}, 14416 year = {2005} 14417} 14418 14419@InProceedings{ serban2005cvodes, 14420 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 14421 author = {Serban, Radu and Hindmarsh, Alan C}, 14422 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 14423 Dynamics and Control, Long Beach, CA}, 14424 year = {2005} 14425} 14426 14427@Article{ pvode99, 14428 author = {G. Byrne and A. Hindmarsh}, 14429 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 14430 journal = {Int. J. High Perf. Comput. Apps.}, 14431 volume = {13}, 14432 number = {4}, 14433 year = {1999}, 14434 pages = {354 -- 365} 14435} 14436 14437@Article{ cvode95, 14438 author = {S. Cohen and A. Hindmarsh}, 14439 title = {{CVODE}, A Stiff/Nonstiff {ODE} Solver in {C}}, 14440 journal = {Computers in Physics}, 14441 volume = {10}, 14442 number = {2}, 14443 year = {1996}, 14444 pages = {138 -- 143} 14445} 14446 14447@TechReport{ ifpack, 14448 title = {Robust Algebraic Preconditioners using {IFPACK} 3.0}, 14449 author = {Marzio Sala and Michael Heroux}, 14450 institution = {Sandia National Laboratories}, 14451 number = {SAND2005-0662}, 14452 year = {2005} 14453} 14454 14455@TechReport{ kinsol-user-ref, 14456 title = {User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel 14457 Computers}, 14458 author = {Allan Taylor and Alan Hindmarsh}, 14459 institution = {Center for Applied Scientific Computing, Lawrence Livermore National Laboratory}, 14460 number = {UCRL-ID-131185}, 14461 year = {1998} 14462} 14463 14464@Article{ fiardmanteuffelmccormick98, 14465 author = {J.-M. Fiard and T. Manteuffel and S. McCormick}, 14466 title = {First-order system least squares {(FOSLS)} for convection-diffusion problems: 14467 numerical results}, 14468 journal = {SIAM J. Sci. Comp.}, 14469 year = {1998}, 14470 volume = {19}, 14471 pages = {1958--1979} 14472} 14473 14474@InProceedings{ vuduc02, 14475 author = {Richard Vuduc and James W. Demmel and Katherine A. Yelick and Shoaib Kamil and 14476 Rajesh Nishtala and Benjamin Lee}, 14477 title = {Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply}, 14478 booktitle = {Proceedings of Supercomputing}, 14479 year = {2002}, 14480 month = nov, 14481 address = {Baltimore} 14482} 14483 14484@Article{ beckerbraackrannacher1999, 14485 title = {Numerical simulation of laminar flames at low Mach number by adaptive finite 14486 elements}, 14487 author = {Roland Becker and Malte Braack and Rolf Rannacher}, 14488 journal = {Combustion Theory and Modelling}, 14489 volume = {3}, 14490 pages = {503--534}, 14491 year = {1999} 14492} 14493 14494@Article{ beckerrannacher01, 14495 author = {R. Becker and R. Rannacher}, 14496 title = {An optimal control approach to a posteriori error estimation in finite element 14497 methods}, 14498 journal = {Acta Numerica}, 14499 year = {2001}, 14500 volume = {10}, 14501 pages = {1--102} 14502} 14503 14504@Article{ babuskamiller84a, 14505 author = {I. Babu$\check{s}$ka and A.D. Miller}, 14506 title = {The post-processing approach in the finite element method, {I}: Calculations of 14507 displacements, stresses, and other higher derivatives of the displacements}, 14508 journal = {Int. J. Numer. Meth. Eng.}, 14509 year = {1984}, 14510 volume = {20}, 14511 pages = {1085--1109} 14512} 14513 14514@Article{ babuskamiller84b, 14515 author = {I. Babu$\check{s}$ka and A.D. Miller}, 14516 title = {The post-processing approach in the finite element method, {II}: The calculation 14517 of stress intensity factors}, 14518 journal = {Int. J. Numer. Meth. Eng.}, 14519 year = {1984}, 14520 volume = {20}, 14521 pages = {1111--1129} 14522} 14523 14524@Article{ babuskamiller84c, 14525 author = {I. Babu$\check{s}$ka and A.D. Miller}, 14526 title = {The post-processing approach in the finite element method, {III}: A posteriori 14527 error estimation and adaptive mesh refinement}, 14528 journal = {Int. J. Numer. Meth. Eng.}, 14529 year = {1984}, 14530 volume = {20}, 14531 pages = {2311--2324} 14532} 14533 14534@Unpublished{ jtb-web-page, 14535 title = {{The Java Tree Builder}}, 14536 note = {See \url{http://www.cs.purdue.edu/jtb}}, 14537 author = {Jens Palsberg}, 14538 institution = {Purdue University} 14539} 14540 14541@Unpublished{ palsberg98, 14542 title = {Why Visitors?}, 14543 note = {See \url{http://www.cs.purdue.edu/jtb/whyvisitors}}, 14544 author = {Jens Palsberg}, 14545 institution = {Purdue University}, 14546 year = {1998} 14547} 14548 14549@Unpublished{ ply-web-page, 14550 title = {{PLY (Python Lex-Yacc)}}, 14551 note = {\url{http://systems.cs.chicago.edu/ply}}, 14552 author = {David Beazley}, 14553 institution = {University of Chicago} 14554} 14555 14556@Misc{ adic-web-page, 14557 title = {{ADIC Web page}}, 14558 note = {\url{http://www.mcs.anl.gov/autodiff}}, 14559 author = {Paul Hovland and Uwe Naumann and Boyana Norris}, 14560 institution = {Argonne National Laboratory} 14561} 14562 14563@Article{ naumann02, 14564 author = {Uwe Naumann}, 14565 title = {Optimal accumulation of {J}acobian matrices by elimination methods on the dual 14566 computational graph}, 14567 journal = {Mathematical Programming (to appear)}, 14568 note = {Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002}, 14569 year = {2003} 14570} 14571 14572@Article{ kaper1, 14573 author = {H. G. Kaper and T. J. Kaper}, 14574 title = {Asymptotic Analysis of Two Reduction Methods for Systems of Chemical Reactions}, 14575 journal = {Physica D}, 14576 year = {2002}, 14577 pages = {66--93}, 14578 volume = {165} 14579} 14580 14581@Misc{ veltisto-web-page, 14582 author = {George Biros}, 14583 title = {{Veltisto Web page}}, 14584 note = {\url{http://www.cs.nyu.edu/~biros/veltisto}} 14585} 14586 14587@Article{ karypiskumar98, 14588 author = {George Karypis and Vipin Kumar}, 14589 title = {A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix 14590 Ordering}, 14591 journal = {Journal of Parallel and Distributed Computing}, 14592 volume = {48}, 14593 pages = {71--85}, 14594 year = {1998} 14595} 14596 14597@TechReport{ karypiskumar97, 14598 author = {Karypis, George and Kumar, V.}, 14599 institution = {Department of Computer Science, University of Minnesota}, 14600 keywords = {graph partitioning; ParMetis}, 14601 note = {http://www.cs.umn.edu/~metis}, 14602 number = {97-060}, 14603 title = {{ParMETIS}: Parallel graph partitioning and sparse matrix ordering library}, 14604 year = {1997} 14605} 14606 14607@Misc{ parmetis-web-page, 14608 author = {George {Karypis et al.}}, 14609 title = {{ParMETIS Web page}}, 14610 note = {\url{http://www.cs.umn.edu/~karypis/metis/parmetis}}, 14611 year = {2005} 14612} 14613 14614@Misc{ sparskit-web-page, 14615 author = {Yousef {Saad et al.}}, 14616 title = {{SPARSKIT Web page}}, 14617 note = {\url{http://www.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html}} 14618} 14619 14620@Misc{ dscpack-web-page, 14621 author = {Padma Raghavan}, 14622 title = {{DSCPACK Web page}}, 14623 note = {\url{http://www.cse.psu.edu/~raghavan/Dscpack}} 14624} 14625 14626@Misc{ gaussian-web-page, 14627 author = {}, 14628 title = {{Gaussian Web page}}, 14629 note = {\url{http://gaussian.com}}, 14630 key = {{Gaussian} {Web} page} 14631} 14632 14633@Book{ lapack-user-guide, 14634 author = {E. 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Fishwick}, 15927 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 15928 to Interrelating Model Structures}, 15929 journal = {SCS Trans. on Simulation}, 15930 note = {Special Issue in Grand Challenges in Computer Simulation}, 15931 year = {2004} 15932} 15933 15934@Article{ fishwick03, 15935 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 15936 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 15937 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 15938 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 15939 year = {2003} 15940} 15941 15942@InProceedings{ kirner00, 15943 author = {T. G. Kirner and V. F. Martins}, 15944 title = {Development of an Information Visualization Tool Using Virtual Reality}, 15945 booktitle = {Proceedings of the 2000 ACM Symposium on Applied Computing}, 15946 year = {2000}, 15947 pages = {604--606} 15948} 15949 15950@InProceedings{ orso03, 15951 author = {A. Orso and J. Jones and M. J. Harrold}, 15952 title = {Visualization of Program-Execution Data for Deployed Software}, 15953 booktitle = {Proceedings of the 2003 ACM Symposium on Software Visualization}, 15954 year = {2003}, 15955 pages = {67--76} 15956} 15957 15958@Book{ tiller01, 15959 author = {M. Tiller}, 15960 title = {Introduction to Physical System Modeling with Modelica}, 15961 series = {Kluwer International Series inEngineering and Computer Science}, 15962 volume = {615}, 15963 publisher = {Kluwer}, 15964 year = {2001} 15965} 15966 15967@Article{ buck94, 15968 author = {J. Buck and S. Ha and E. Lee and D. Messerschmitt}, 15969 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 15970 journal = {Int. Journal of Computer Simulation}, 15971 volume = {4}, 15972 pages = {155--182}, 15973 year = {1994} 15974} 15975 15976@Article{ mu95, 15977 author = {M. Mu and J.R. Rice}, 15978 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 15979 journal = {Comp. Syst. Engr.}, 15980 volume = {6}, 15981 year = {1995}, 15982 pages = {87--95} 15983} 15984 15985@TechReport{ drashansky96, 15986 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 15987 author = {R. Drashansky and A. Joshi and J. R. Rice}, 15988 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 15989 year = {1996} 15990} 15991 15992@Article{ michopoulos05, 15993 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 15994 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 15995 journal = {Journal of Computing and Information Science in Engineering}, 15996 volume = {5}, 15997 issue = {3}, 15998 pages = {198--213}, 15999 year = {2005} 16000} 16001 16002@Article{ dubey09, 16003 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16004 Multiphysics Simulation Code}, 16005 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16006 Siegel and K. Weide}, 16007 journal = {Parallel Computing}, 16008 volume = {35}, 16009 issue = {10 -- 11}, 16010 pages = {512 -- 522}, 16011 year = {2009} 16012} 16013 16014@Book{ bottloring95, 16015 author = {Raoul Bott and Loring W. Tu}, 16016 title = {Differential Forms in Algebraic Topology}, 16017 publisher = {Springer}, 16018 year = {1995} 16019} 16020 16021@Book{ kobayashinomizu96, 16022 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16023 title = {Foundations of Differential Geometry}, 16024 publisher = {Wiley-Interscience}, 16025 year = {1996} 16026} 16027 16028@Article{ hornungkohn02, 16029 author = {Richard D. Hornung and Scott R. Kohn}, 16030 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16031 journal = {Concurrency and Computation: Practice and Experience}, 16032 volume = {14}, 16033 pages = {347--368}, 16034 year = {2002} 16035} 16036 16037@InProceedings{ concepts06, 16038 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16039 Gabriel Dos Reis and Andrew Lumsdaine}, 16040 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16041 booktitle = {Proceedings of OOPSLA 2006}, 16042 year = {2006}, 16043 pages = {???--???} 16044} 16045 16046@Book{ hatcher02, 16047 author = {Hatcher, Allen}, 16048 title = {Algebraic Topology}, 16049 publisher = {Cambridge University Press}, 16050 year = {2002} 16051} 16052 16053@Book{ gammahelmjohnsonvlissides95, 16054 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16055 development, offering timeless and elegant solutions to common problems in 16056 software design. It describes patterns for managing object creation, composing 16057 objects into larger structures, and coordinating control flow between objects. The 16058 book provides numerous examples where using composition rather than inheritance 16059 can improve the reusability and flexibility of code. Note, though, that it's not a 16060 tutorial but a catalog that you can use to find an object-oriented design pattern 16061 that's appropriate for the needs of your particular application--a selection for 16062 virtuoso programmers who appreciate (or require) consistent, well-engineered 16063 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16064 more valuable than ever! 16065 16066 Use the contents of the CD to create your own design documents and reusable 16067 components. The CD contains: 23 patterns you can cut and paste into your own 16068 design documents; sample code demonstrating pattern implementation; complete 16069 Design Patterns content in standard HTML format, with numerous hyperlinked 16070 cross-references; accessed through a standard web browser; Java-based dynamic 16071 search mechanism, enhancing online search capabilities; graphical user environment, 16072 allowing ease of navigation. 16073 16074 First published in 1995, this landmark work on object-oriented software design 16075 presents a catalog of simple and succinct solutions to common design problems. 16076 Created by four experienced designers, the 23 patterns contained herein have 16077 become an essential resource for anyone developing reusable object-oriented 16078 software. In response to reader demand, the complete text and pattern catalog are 16079 now available on CD-ROM. This electronic version of Design Patterns enables 16080 programmers to install the book directly onto a computer or network for use as an 16081 online reference for creating reusable object-oriented software. 16082 16083 The authors first describe what patterns are and how they can help you in the 16084 design process. They then systematically name, explain, evaluate, and catalog 16085 recurring designs in object-oriented systems. All patterns are compiled from 16086 real-world examples and include code that demonstrates how they may be implemented 16087 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16088 already own the book will want the CD to take advantage of its dynamic search 16089 mechanism and ready-to-install patterns.}}, 16090 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16091 citeulike-article-id={115158}, 16092 howpublished = {Hardcover}, 16093 isbn = {0201633612}, 16094 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16095 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16096 four gang gof java mathgamespatterns no-tag object object-orientation 16097 object-oriented of oo-patterns oop oriented pattern patterns programming se 16098 software software-development software-engineering software_design 16099 softwareengineering standard}, 16100 month = jan, 16101 publisher = {{Addison-Wesley Professional}}, 16102 title = {Design Patterns}, 16103 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16104 year = {1995} 16105} 16106 16107@InProceedings{ chaco95, 16108 author = {Bruce Hendrickson and Robert Leland}, 16109 title = {A multilevel algorithm for partitioning graphs}, 16110 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16111 (CDROM)}, 16112 year = {1995}, 16113 isbn = {0-89791-816-9}, 16114 pages = {28}, 16115 location = {San Diego, California, United States}, 16116 doi = {10.1145/224170.224228}, 16117 publisher = {ACM Press}, 16118 address = {New York} 16119} 16120 16121@Book{ aleksandrov98, 16122 author = {Aleksandrov, Pavel S.}, 16123 title = {Combinatorial Topology}, 16124 publisher = {Dover}, 16125 volume = {3}, 16126 year = {1998} 16127} 16128 16129@Book{ steenrod99, 16130 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16131 importance in modern physics--such as in gauge theory. This book, a succinct 16132 introduction to the subject by renown mathematician Norman Steenrod, was the first 16133 to present the subject systematically. 16134 16135 It begins with a general introduction to bundles, including such topics as 16136 differentiable manifolds and covering spaces. The author then provides brief 16137 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16138 using them to study further properties of fibre bundles. The result is a classic 16139 and timeless work of great utility that will appeal to serious mathematicians and 16140 theoretical physicists alike. }}, 16141 author = {Steenrod, Norman}, 16142 citeulike-article-id={712999}, 16143 howpublished = {Paperback}, 16144 isbn = {0691005486}, 16145 keywords = {fibre_bundles topology}, 16146 month = apr, 16147 publisher = {{Princeton University Press}}, 16148 title = {The Topology of Fibre Bundles. (PMS-14)}, 16149 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16150 year = {1999} 16151} 16152 16153@Book{ bredon97, 16154 author = {Bredon, Glen E.}, 16155 title = {Sheaf Theory}, 16156 publisher = {Springer}, 16157 pages = {524}, 16158 series = {Graduate Texts in Mathematics}, 16159 year = {1997} 16160} 16161 16162@TechReport{ tautgesmeyers04, 16163 title = {{MOAB}: A Mesh-Oriented Database}, 16164 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16165 Ernst}, 16166 institution = {Sandia National Laboratories}, 16167 number = {SAND2004-1592}, 16168 month = apr, 16169 year = {2004} 16170} 16171 16172@Article{ tautges04, 16173 author = {Timothy J. Tautges}, 16174 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16175 journal = {Engineering With Computers}, 16176 volume = {20}, 16177 pages = {286--293}, 16178 year = {2004} 16179} 16180 16181@InProceedings{ meyers02, 16182 author = {Ray Meyers et. al}, 16183 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16184 booktitle = {8th International conference on numerical grid generation in computational field 16185 simulations}, 16186 month = jun, 16187 year = {2002} 16188} 16189 16190@InProceedings{ seolshepard05, 16191 author = {E. S. Seol and Mark S. Shephard}, 16192 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16193 Analysis}, 16194 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16195 year = {2005} 16196} 16197 16198@Article{ beallwalshshephard04, 16199 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16200 title = {A comparison of techniques for geometry access related to mesh generation}, 16201 journal = {Engineering With Computers}, 16202 volume = {20}, 16203 number = {3}, 16204 pages = {210--221}, 16205 year = {2004} 16206} 16207 16208@Article{ careyandersoncarneskirk04, 16209 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16210 Kirk}, 16211 title = {Some aspects of adaptive grid technology related to boundary and interior 16212 layers}, 16213 journal = {Journal of Computational Applied Mathematics}, 16214 volume = {166}, 16215 number = {1}, 16216 pages = {55--86}, 16217 year = {2004} 16218} 16219 16220@PhDThesis{ gralthesis, 16221 author = {Guntram Berti}, 16222 title = {Generic Software Components for Scientific Computing}, 16223 school = {TU Cottbus}, 16224 year = {2000}, 16225 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16226} 16227 16228@Article{ whitehead1949, 16229 title = {Combinatorial homotopy. I}, 16230 author = {John HC Whitehead}, 16231 journal = {Bulletin of the American Mathematical Society}, 16232 volume = {55}, 16233 number = {3. P1}, 16234 pages = {213--245}, 16235 year = {1949}, 16236 publisher = {American Mathematical Society} 16237} 16238 16239@Article{ beylkincoifmanrokhlin91, 16240 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16241 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16242 journal = {Communications on Pure and Applied Mathematics}, 16243 volume = {44}, 16244 pages = {141--183}, 16245 year = {1991} 16246} 16247 16248@Book{ wesseling92, 16249 author = {Pieter Wesseling}, 16250 title = {An Introduction to Multigrid Methods}, 16251 publisher = {John Wiley and Sons}, 16252 year = {1992} 16253} 16254 16255@Book{ grakakos04, 16256 author = {Loukas Grakakos}, 16257 title = {Classical and Modern Fourier Analysis}, 16258 publisher = {Pearson Education}, 16259 address = {New Jersey}, 16260 year = {2004} 16261} 16262 16263@Misc{ hlib-web-page, 16264 key = {HLib}, 16265 title = {{HLib} {Web} page}, 16266 note = {{\texttt{http://www.hlib.org/}}}, 16267 annote = {Hierarchical matrices for fast integral transform} 16268} 16269 16270@Article{ hackbusch99, 16271 author = {Wolfgang Hackbusch}, 16272 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16273 Introduction to {$\mathcal H$}-matrices}, 16274 journal = {Computing}, 16275 volume = {62}, 16276 pages = {89--108}, 16277 year = {1999} 16278} 16279 16280@TechReport{ kay1999green, 16281 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16282 equations}, 16283 author = {Kay, D. and Loghin, D.}, 16284 year = {1999}, 16285 institution = {Oxford University Computing Laboratory}, 16286 number = {99/06} 16287} 16288 16289@Article{ bebendorf2003existence, 16290 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16291 elliptic operators with {$L^\infty$}-coefficients}, 16292 author = {Bebendorf, M. and Hackbusch, W.}, 16293 journal = {Numerische Mathematik}, 16294 volume = {95}, 16295 number = {1}, 16296 pages = {1--28}, 16297 year = {2003}, 16298 publisher = {Springer} 16299} 16300 16301@Article{ hackbusch2005direct, 16302 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16303 H$}-matrix approximation}, 16304 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16305 journal = {Computing and Visualization in Science}, 16306 volume = {8}, 16307 number = {3}, 16308 pages = {179--188}, 16309 year = {2005}, 16310 publisher = {Springer} 16311} 16312 16313@TechReport{ duphof2003, 16314 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16315 Logg and L. R. Scott}, 16316 title = {The {FE}ni{CS} project}, 16317 institution = {Chalmers Finite Element Center Preprint Series}, 16318 number = {2003--21}, 16319 year = {2003} 16320} 16321 16322@Article{ flame01, 16323 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16324 Geijn}, 16325 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16326 journal = {Transactions on Mathematical Software}, 16327 volume = {27}, 16328 number = {4}, 16329 year = {2001}, 16330 pages = {422--455} 16331} 16332 16333@Article{ puschel05, 16334 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16335 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16336 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16337 Nick Rizzolo}, 16338 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16339 journal = {Proceedings of the IEEE}, 16340 volume = {93}, 16341 number = {2}, 16342 year = {2005}, 16343 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16344} 16345 16346@Article{ kirbylogg06, 16347 author = {Robert C. Kirby and Anders Logg}, 16348 title = {A compiler for variational forms}, 16349 journal = {ACM Transactions on Mathematical Software}, 16350 volume = {32}, 16351 number = {3}, 16352 year = {2006}, 16353 issn = {0098-3500}, 16354 pages = {417--444}, 16355 doi = {10.1145/1163641.1163644}, 16356 publisher = {ACM Press}, 16357 address = {New York, NY} 16358} 16359 16360@Article{ kirbylogg07, 16361 author = {Robert C. Kirby and Anders Logg}, 16362 title = {Efficient compilation of a class of variational forms}, 16363 journal = {ACM Transactions on Mathematical Software}, 16364 volume = {33}, 16365 number = {3}, 16366 year = {2007}, 16367 issn = {0098-3500}, 16368 pages = {17}, 16369 doi = {10.1145/1268769.1268771}, 16370 publisher = {ACM Press}, 16371 address = {New York, NY} 16372} 16373 16374@Article{ bankdupont81, 16375 author = {Randolph Bank and Todd Dupont}, 16376 title = {An optimal order process for solving finite element equations}, 16377 journal = {Mathematics of Computation}, 16378 volume = {36}, 16379 pages = {35--51}, 16380 year = {1981} 16381} 16382 16383@TechReport{ adams00, 16384 author = {Mark F. Adams}, 16385 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16386 in solid mechanics}, 16387 institution = {UC Berkeley}, 16388 number = {CSD-00-1103}, 16389 year = {2000}, 16390 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16391} 16392 16393@Article{ bergengradlhuelsemannruede06, 16394 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16395 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16396 journal = {Computing in Science \& Engineering}, 16397 volume = {8}, 16398 number = {6}, 16399 pages = {56--62}, 16400 year = {2006} 16401} 16402 16403@MastersThesis{ brunethesis08, 16404 author = {Peter R. Brune}, 16405 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16406 school = {University of Chicago}, 16407 address = {Chicago, IL}, 16408 year = {2008}, 16409 month = feb 16410} 16411 16412@Article{ arnoldwinther02, 16413 author = {Douglas N. Arnold and Ragnar Winther}, 16414 title = {Mixed finite elements for elasticity}, 16415 journal = {Numerische Mathematik}, 16416 volume = {92}, 16417 number = {3}, 16418 month = sep, 16419 year = {2002}, 16420 pages = {401--419}, 16421 doi = {10.1007/s002110100348} 16422} 16423 16424@Article{ arnoldfalkwinther06, 16425 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16426 title = {Finite element exterior calculus, homological techniques, and applications}, 16427 journal = {Acta Numerica}, 16428 year = {2006}, 16429 volume = {15}, 16430 pages = {1--155}, 16431 publisher = {Cambridge University Press}, 16432 doi = {10.1017/S0962492906210018} 16433} 16434 16435@Article{ kirby04, 16436 author = {Robert C. Kirby}, 16437 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 16438 functions}, 16439 journal = {ACM Transactions on Mathematical Software}, 16440 volume = {30}, 16441 number = {4}, 16442 year = {2004}, 16443 issn = {0098-3500}, 16444 pages = {502--516}, 16445 doi = {10.1145/1039813.1039820}, 16446 publisher = {ACM Press}, 16447 address = {New York, NY} 16448} 16449 16450@Article{ kirby06, 16451 author = {Robert C. Kirby}, 16452 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16453 journal = {ACM Transactions on Mathematical Software}, 16454 volume = {32}, 16455 number = {2}, 16456 year = {2006}, 16457 issn = {0098-3500}, 16458 pages = {223--235}, 16459 doi = {10.1145/1141885.1141889}, 16460 publisher = {ACM Press}, 16461 address = {New York, NY} 16462} 16463 16464@Misc{ bluecrystal08, 16465 author = {{B}lue {C}rystal Cluster}, 16466 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16467 year = {2008}, 16468 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16469} 16470 16471@Article{ beylkin95, 16472 author = {Gregory Beylkin}, 16473 title = {On the Fast Fourier Transform of Functions With Singularities}, 16474 journal = {Applied and Computational Harmonic Analysis}, 16475 volume = {2}, 16476 pages = {363--381}, 16477 year = {1995} 16478} 16479 16480@InProceedings{ riehl08, 16481 author = {Jonathan Riehl}, 16482 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16483 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16484 Development (DSPD'08)}, 16485 address = {Nashville, TN}, 16486 year = {2008} 16487} 16488 16489@Article{ appel85, 16490 author = {Andrew W. Appel}, 16491 date-added = {2008-02-27 12:23:39 +0000}, 16492 date-modified = {2008-02-27 12:24:02 +0000}, 16493 doi = {10.1137/0906008}, 16494 journal = {SIAM Journal on Scientific and Statistical Computing}, 16495 keywords = {treecodes}, 16496 number = {1}, 16497 pages = {85-103}, 16498 publisher = {SIAM}, 16499 title = {An Efficient Program for Many-Body Simulation}, 16500 volume = {6}, 16501 year = {1985} 16502} 16503 16504@Article{ ewald21, 16505 author = {{Ewald}, P.~P.}, 16506 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 16507 journal = {Annalen der Physik}, 16508 year = {1921}, 16509 volume = {369}, 16510 pages = {253-287}, 16511 doi = {10.1002/andp.19213690304}, 16512 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 16513 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16514} 16515 16516@Article{ greengardrokhlin87, 16517 author = {L. Greengard and V. Rokhlin}, 16518 date-added = {2008-02-15 18:43:55 +0000}, 16519 date-modified = {2008-02-26 20:09:11 +0000}, 16520 doi = {10.1016/0021-9991(87)90140-9}, 16521 journal = {J. Comput.\ Phys.}, 16522 keywords = {FMM}, 16523 number = {2}, 16524 pages = {325--348}, 16525 title = {A Fast Algorithm for Particle Simulations}, 16526 url = {citeseer.ist.psu.edu/greengard87fast.html}, 16527 volume = {73}, 16528 year = {1987}, 16529 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 16530} 16531 16532@Article{ greengardrokhlin97, 16533 author = {L. Greengard and V. Rokhlin}, 16534 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 16535 Dimensions}, 16536 journal = {Acta Numerica}, 16537 volume = {6}, 16538 year = {1997}, 16539 pages = {229--269} 16540} 16541 16542@Article{ luchenghuangmccammon06, 16543 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon}, 16544 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 16545 systems}, 16546 journal = {PNAS}, 16547 doi = {10.1073/pnas.0605166103}, 16548 volume = {102}, 16549 number = {51}, 16550 year = {2006}, 16551 pages = {19314--19319} 16552} 16553 16554@Article{ schussnadlereisenberg01, 16555 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 16556 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 16557 from a molecular model}, 16558 journal = {Physical Review E}, 16559 volume = {64}, 16560 number = {3}, 16561 year = {2001} 16562} 16563 16564@Book{ hairerlubichwanner02, 16565 author = {E. Hairer and Ch. Lubich and G. Wanner}, 16566 title = {Geometric Numerical Integration}, 16567 publisher = {Springer-Verlag}, 16568 address = {Berlin Heidelberg}, 16569 year = {2002} 16570} 16571 16572@Article{ holstbakerwang00, 16573 author = {M. Holst and N. Baker and F. Wang}, 16574 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 16575 equation on massively parallel computers}, 16576 journal = {Journal of Computational Chemistry}, 16577 volume = {21}, 16578 year = {2000} 16579} 16580 16581@Book{ hockneyeastwood81, 16582 author = {R. Hockney and J. Eastwood}, 16583 title = {Computer simulation using particles}, 16584 publisher = {McGraw-Hill}, 16585 address = {New York}, 16586 year = {1981} 16587} 16588 16589@Article{ lutydavistironigunsteren94, 16590 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 16591 Gunsteren}, 16592 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 16593 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 16594 journal = {Molecular Simulation}, 16595 volume = {14}, 16596 number = {1}, 16597 year = {1994}, 16598 pages = {11--20} 16599} 16600 16601@Book{ briggshensonmccormick00, 16602 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 16603 title = {A Multigrid Tutorial (2nd ed.)}, 16604 year = {2000}, 16605 isbn = {0-89871-462-1}, 16606 publisher = {Society for Industrial and Applied Mathematics}, 16607 address = {Philadelphia, PA} 16608} 16609 16610@Article{ chartier2003spectral, 16611 title = {Spectral AMGe ($\rho$ AMGe)}, 16612 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 16613 McCormick, S and Ruge, J and Vassilevski, PS}, 16614 journal = {SIAM Journal on Scientific Computing}, 16615 volume = {25}, 16616 number = {1}, 16617 pages = {1--26}, 16618 year = {2003}, 16619 publisher = {SIAM} 16620} 16621 16622@Article{ galvis2010domain, 16623 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 16624 media}, 16625 author = {Galvis, Juan and Efendiev, Yalchin}, 16626 journal = {Multiscale Modeling \& Simulation}, 16627 volume = {8}, 16628 number = {4}, 16629 pages = {1461--1483}, 16630 year = {2010}, 16631 publisher = {SIAM} 16632} 16633 16634@Book{ brennerscott02, 16635 author = {Susanne~C. Brenner and L.~Ridgway Scott}, 16636 title = {The mathematical theory of finite element methods}, 16637 year = {2002}, 16638 isbn = {0-38795-451-1}, 16639 publisher = {Springer}, 16640 pages = {361} 16641} 16642 16643@Book{ trefethenbau97, 16644 author = {Lloyd N. Trefethen and David {Bau, III}}, 16645 title = {Numerical Linear Algebra}, 16646 publisher = {Society for Industrial and Applied Mathematics}, 16647 address = {Philadelphia, PA}, 16648 pages = {xii + 361}, 16649 year = {1997}, 16650 isbn = {0-89871-361-7}, 16651 isbn-13 = {978-0-89871-361-9}, 16652 lccn = {QA184 .T74 1997}, 16653 mrclass = {65-01 (65-02 65Fxx)}, 16654 mrnumber = {MR1444820 (98k:65002)}, 16655 mrreviewer = {Moody T. Chu}, 16656 bibdate = {Wed Jan 07 15:23:19 1998}, 16657 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16658} 16659 16660@Article{ liptonreagan2014, 16661 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16662 author = {Richard J Lipton and Kenneth W Regan}, 16663 pages = {206}, 16664 isbn = {978-0-26202-839-4}, 16665 year = {2014} 16666} 16667 16668@InProceedings{ rhea08, 16669 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16670 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16671 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16672 booktitle = {Proceedings of IEEE/ACM SC '08}, 16673 year = {2008} 16674} 16675 16676@Misc{ bursteddewilcox09, 16677 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16678 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16679 note = {in preparation} 16680} 16681 16682@Article{ skeeltezcanhardy02, 16683 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16684 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16685 journal = {J. Comp. Chem.}, 16686 volume = {23}, 16687 pages = {673--684}, 16688 year = {2002} 16689} 16690 16691@Article{ verschelde99, 16692 author = {Jan Verschelde}, 16693 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16694 homotopy continuation}, 16695 journal = {ACM Trans. Math. Softw.}, 16696 volume = {25}, 16697 number = {2}, 16698 issn = {0098-3500}, 16699 pages = {251--276}, 16700 doi = {10.1145/317275.317286}, 16701 publisher = {ACM}, 16702 address = {New York, NY}, 16703 year = {1999} 16704} 16705 16706@InProceedings{ sommeseverscheldewampler08, 16707 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16708 title = {Solving Polynomial Systems Equation by Equation}, 16709 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16710 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16711 pages = {133--152}, 16712 publisher = {Springer-Verlag}, 16713 year = {2008} 16714} 16715 16716@Article{ phanthientanner77, 16717 author = {N. Phan-Thien and R.~I. Tanner}, 16718 title = {A new constitutive equation derived from network theory}, 16719 journal = {J. Non-Newt. Fluid Mech.}, 16720 volume = {2}, 16721 pages = {353}, 16722 year = {1977} 16723} 16724 16725@Manual{ sage, 16726 key = {SAGE}, 16727 author = {W.\thinspace{}A. Stein and others}, 16728 organization = {The Sage~Development Team}, 16729 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16730 note = {{\tt http://www.sagemath.org}}, 16731 year = {2009} 16732} 16733 16734@Misc{ bateshauensteinsommesewampler06, 16735 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16736 Wampler}, 16737 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16738 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16739} 16740 16741@Article{ archer09, 16742 author = {A. J. Archer}, 16743 collaboration = {}, 16744 title = {Dynamical density functional theory for molecular and colloidal fluids: A 16745 microscopic approach to fluid mechanics}, 16746 publisher = {AIP}, 16747 year = {2009}, 16748 journal = {The Journal of Chemical Physics}, 16749 volume = {130}, 16750 number = {1}, 16751 eid = {014509}, 16752 numpages = {8}, 16753 pages = {014509}, 16754 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 16755 transition; statistical distributions; stochastic processes}, 16756 doi = {10.1063/1.3054633} 16757} 16758 16759@Article{ giesekus1966, 16760 author = {Hanswalter Giesekus}, 16761 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 16762 journal = {Rheologica Acta}, 16763 publisher = {Springer Berlin / Heidelberg}, 16764 volume = {5}, 16765 number = {1}, 16766 month = mar, 16767 year = {1966}, 16768 doi = {10.1007/BF01973575}, 16769 pages = {29-35} 16770} 16771 16772@Article{ baaijens98, 16773 author = {F.P. Baaijens}, 16774 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 16775 journal = {Journal of Non-Newtonian Fluid Mechanics}, 16776 volume = {79}, 16777 year = {1998}, 16778 pages = {361--385} 16779} 16780 16781@Book{ joseph90, 16782 author = {D.~D. Joseph}, 16783 title = {Fluid Dynamics of Viscoelastic Liquids}, 16784 publisher = {Springer}, 16785 address = {New York, NY}, 16786 year = {1990} 16787} 16788 16789@Article{ oldroyd50, 16790 author = {J.~G. Oldroyd}, 16791 title = {On the Formulation of Rheological Equations of State}, 16792 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 16793 Sciences}, 16794 volume = {200}, 16795 year = {1950}, 16796 pages = {523--541} 16797} 16798 16799@InProceedings{ bynasungroppthakur04, 16800 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 16801 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 16802 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 16803 year = {2004} 16804} 16805 16806@Book{ pozrikidis07, 16807 author = {C. Pozrikidis}, 16808 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 16809 publisher = {Kluwer (Springer)}, 16810 pages = {675}, 16811 year = {2001}, 16812 isbn = {0792373510} 16813} 16814 16815@Misc{ kritzkeyesfsp07, 16816 author = {A. Kritz and D. Keyes}, 16817 title = {{Fusion Simulation Project Workshop Report}}, 16818 month = jul, 16819 year = {2007}, 16820 note = {Available via 16821 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 16822} 16823 16824@Misc{ dahlburg02, 16825 author = {J. {Dahlburg (Chair)}}, 16826 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 16827 year = {2002}, 16828 note = {Available via 16829 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 16830} 16831 16832@Misc{ brown08, 16833 author = {D. {Brown (Chair)}}, 16834 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 16835 to the Future}}, 16836 year = {2008}, 16837 howpublished = {Office of Science, U.S. Department of Energy}, 16838 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 16839} 16840 16841@Misc{ crosscutting10, 16842 author = {D. Brown and P. {Messina (Chairs)}}, 16843 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 16844 Exascale}}, 16845 year = {2010}, 16846 howpublished = {Office of Science, U.S. Department of Energy}, 16847 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 16848} 16849 16850@Misc{ extreme-scale-solvers-workshop12, 16851 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 16852 L.C. McInnes and E. Ng and S. Wild}, 16853 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 16854 Architectures}, 16855 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 16856 note = {{Washington, DC}, March 8-9, 2012}, 16857 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 16858 year = {2012} 16859} 16860 16861@Misc{ monizrosner09, 16862 author = {{E. Moniz and R. Rosner}}, 16863 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 16864 and Simulation at the Extreme Scale}}, 16865 month = may, 16866 year = {2009}, 16867 note = {See 16868 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 16869} 16870 16871@Misc{ blanford08, 16872 author = {{R. Blandord (Chair)}}, 16873 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 16874 Computing at the Extreme Scale}}, 16875 month = dec, 16876 year = {2008}, 16877 note = {See 16878 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 16879} 16880 16881@Misc{ exascale07, 16882 author = {H. Simon and T. Zacharia and R. Stevens}, 16883 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 16884 year = {2007}, 16885 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 16886} 16887 16888@Misc{ ascrbreakthroughs08, 16889 author = {{Panel on Recent Significant Advancements in Computational Science}}, 16890 title = {Breakthroughs}, 16891 year = {2008}, 16892 note = {See 16893 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 16894} 16895 16896@Misc{ petsc-rd100-2009, 16897 author = {{R\&D Magazine}}, 16898 title = {{PETSc} {R}\&{D} 100 Award}, 16899 year = {2009}, 16900 note = {See 16901 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 16902} 16903 16904@Article{ compass-scidac08, 16905 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 16906 R. Ryne}, 16907 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 16908 Computational Science for Future Accelerators and Accelerator Technologies}, 16909 journal = {J. Phys.: Conf. Ser.}, 16910 volume = {125}, 16911 year = {2008}, 16912 pages = {012001}, 16913 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 16914} 16915 16916@Article{ compass-amundson-scidac08, 16917 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 16918 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 16919 Stoltz}, 16920 journal = {J. Phys.: Conf. Ser.}, 16921 volume = {125}, 16922 year = {2008} 16923} 16924 16925@InProceedings{ muszala09, 16926 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 16927 Simulations}, 16928 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 16929 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 16930 {(CBHPC 2009)}}, 16931 year = {2009} 16932} 16933 16934@Article{ gaston09, 16935 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 16936 Equations}, 16937 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 16938 journal = {Nuclear Engineering and Design}, 16939 volume = {239}, 16940 number = {10}, 16941 year = {2009}, 16942 pages = {1768 -- 1778} 16943} 16944 16945@Article{ gaston09b, 16946 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 16947 Engineering}, 16948 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 16949 and C. Permann and W. Taitano}, 16950 journal = {J. Phys.: Conf. Ser.}, 16951 volume = {180}, 16952 year = {2009}, 16953 pages = {012012} 16954} 16955 16956@Article{ newman09, 16957 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 16958 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 16959 author = {Chris Newman and Glen Hansen and Derek Gaston}, 16960 journal = {Journal of Nuclear Materials}, 16961 volume = {392}, 16962 issue = {1}, 16963 year = {2009}, 16964 pages = {6 -- 15} 16965} 16966 16967@Misc{ www:fenics, 16968 author = {{FE}ni{CS}}, 16969 title = {{FE}ni{CS} Project}, 16970 howpublished = {\url{http://www.fenics.org/}}, 16971 year = {2018} 16972} 16973 16974@InProceedings{ zwart08, 16975 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 16976 Systems}, 16977 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 16978 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 16979 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 16980 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 16981 booktitle = {Proceedings of ICCS 2008}, 16982 year = {2008} 16983} 16984 16985@Article{ klocknerwarburtonbridgehesthaven09, 16986 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 16987 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 16988 journal = {J. Comput. Phys.}, 16989 volume = {228}, 16990 number = {21}, 16991 year = {2009}, 16992 issn = {0021-9991}, 16993 pages = {7863--7882}, 16994 doi = {10.1016/j.jcp.2009.06.041}, 16995 publisher = {Academic Press Professional}, 16996 address = {San Diego, CA} 16997} 16998 16999@PhDThesis{ rankin99, 17000 author = {Rankin, W. T.}, 17001 keywords = {FMM, parallel FMM}, 17002 school = {Department of Electrical and Computer Engineering, Duke University}, 17003 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17004 year = {1999} 17005} 17006 17007@InProceedings{ warrensalmon93, 17008 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17009 and implemented. The algorithm computes the forces on an arbitrary distribution of 17010 bodies in a time which scales as N log N with the particle number. The accuracy of 17011 the force calculations is analytically bounded, and can be adjusted via a user 17012 defined parameter between a few percent relative accuracy, down to machine 17013 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17014 tree, we identify...}, 17015 address = {New York}, 17016 author = {Warren, Michael S. and Salmon, John K.}, 17017 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17018 citeulike-article-id={580952}, 17019 keywords = {oct-tree}, 17020 pages = {12--21}, 17021 publisher = {ACM}, 17022 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17023 year = {1993}, 17024 doi = {10.1145/169627.169640}, 17025 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17026} 17027 17028@Unpublished{ cruzwccm10, 17029 author = {Felipe A. Cruz}, 17030 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17031 note = {Presentation at WCCM 2010, Sydney Australia}, 17032 year = {2010} 17033} 17034 17035@Article{ mcguffee06, 17036 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17037 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17038 of salt, {pH}, point mutations, and protein concentration in simulations of 17039 1000-molecule systems}, 17040 journal = {Journal of the American Chemical Society}, 17041 volume = {128}, 17042 pages = {12098--12110}, 17043 year = {2006} 17044} 17045 17046@Article{ nilsencaihoylandlangtangen10, 17047 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17048 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17049 in Python}}, 17050 journal = {ArXiv e-prints}, 17051 archiveprefix = {arXiv}, 17052 eprint = {1002.0705}, 17053 primaryclass = {cs.DC}, 17054 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17055 - Programming Languages}, 17056 year = {2010}, 17057 month = feb, 17058 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17059 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17060} 17061 17062@Misc{ mcinnes:siam09:minisymposium, 17063 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17064 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17065 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17066 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17067 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17068 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17069 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17070 Austin).} 17071} 17072 17073@Misc{ mcinnes:fsp-summary:feb2011, 17074 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17075 title = {Solvers and Time Integration Breakout Summary}, 17076 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17077 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17078} 17079 17080@Misc{ dvi-materials:siamcse11, 17081 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17082 Materials}, 17083 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17084 Smith and L. Wang}, 17085 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17086 and Engineering, March 3, 2011} 17087} 17088 17089@Misc{ jamroz:cemm10, 17090 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17091 author = {B. Jamroz and S. Kruger and T. Austin}, 17092 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17093} 17094 17095@Misc{ kruger:feb4-2011, 17096 title = {personal communication}, 17097 author = {S. Kruger}, 17098 note = {February, 2011} 17099} 17100 17101@Article{ elman1996, 17102 author = {H.C. Elman}, 17103 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17104 viscosity}, 17105 journal = {SIAM J. Sci. Comput.}, 17106 volume = {20}, 17107 year = {1996}, 17108 pages = {1299--1316} 17109} 17110 17111@Article{ kayloghinwathen2002, 17112 author = {D. Kay and D. Loghin and A. Wathen}, 17113 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17114 journal = {SIAM J. Sci. Comput.}, 17115 volume = {24}, 17116 year = {2002}, 17117 pages = {237--256} 17118} 17119 17120@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17121 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17122 title = {Block preconditioners based on approximate commutators}, 17123 journal = {SIAM J. Sci. Comput.}, 17124 volume = {27}, 17125 number = {5}, 17126 year = {2006}, 17127 pages = {1651--1668} 17128} 17129 17130@Article{ braesssarazin1997, 17131 author = {Dietrich Braess and Regina Sarazin}, 17132 title = {An efficient smoother for the {Stokes} problem}, 17133 journal = {Applied Numerical Mathematics}, 17134 volume = {23}, 17135 number = {1}, 17136 year = {1997}, 17137 pages = {3--19}, 17138 doi = {10.1016/S0168-9274(96)00059-1} 17139} 17140 17141@Article{ wright2001large, 17142 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17143 author = {Wright, T.G. and Trefethen, L.N.}, 17144 journal = {SIAM Journal on Scientific Computing}, 17145 volume = {23}, 17146 pages = {591}, 17147 year = {2001} 17148} 17149 17150@Misc{ wright2002eigtool, 17151 title = {Eig{T}ool}, 17152 author = {Wright, T.G. and Trefethen, LN}, 17153 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17154 year = {2002} 17155} 17156 17157@Misc{ visit-web-site, 17158 key = {{VisIt}}, 17159 title = {{VisIt web site}}, 17160 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17161 url = {http://wci.llnl.gov/codes/visit/}, 17162 year = {2011} 17163} 17164 17165@Book{ trefethen1996, 17166 title = {Finite difference and spectral methods for ordinary and partial differential 17167 equations}, 17168 author = {Lloyd Nicholas Trefethen}, 17169 year = {1996}, 17170 publisher = {Cornell University-Department of Computer Science and Center for Applied 17171 Mathematics} 17172} 17173 17174@Book{ trefethen2005spectra, 17175 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17176 author = {Trefethen, L.N. and Embree, M.}, 17177 year = {2005}, 17178 publisher = {Princeton University Press} 17179} 17180 17181@Article{ gomez2010isogeometric, 17182 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17183 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17184 journal = {Computer Methods in Applied Mechanics and Engineering}, 17185 volume = {199}, 17186 number = {25-28}, 17187 pages = {1828--1840}, 17188 issn = {0045-7825}, 17189 year = {2010}, 17190 publisher = {Elsevier} 17191} 17192 17193@Article{ gomez2008isogeometric, 17194 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17195 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17196 journal = {Computer Methods in Applied Mechanics and Engineering}, 17197 volume = {197}, 17198 number = {49-50}, 17199 pages = {4333--4352}, 17200 year = {2008}, 17201 publisher = {Elsevier} 17202} 17203 17204@Misc{ fastmath:project, 17205 author = {Lori {Diachin (PI)}}, 17206 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17207 (FASTMath) Institute}}, 17208 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17209} 17210 17211@Misc{ exascale-software:proposal, 17212 author = {Peter {Beckman (PI)}}, 17213 title = {{Exascale Software Center}}, 17214 note = {proposal to DOE} 17215} 17216 17217@Misc{ imex:project, 17218 author = {Barry {Smith (PI)}}, 17219 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17220 Multimodel PDEs}}, 17221 note = {DOE ASCR applied math project} 17222} 17223 17224@Misc{ intel-mic:website, 17225 author = {Intel}, 17226 title = {{Many Integrated Core Architecture}}, 17227 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17228} 17229 17230@Article{ dudson:2009, 17231 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17232 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17233 journal = {Computer Physics Communications}, 17234 volume = {180}, 17235 pages = {1467}, 17236 year = {2009} 17237} 17238 17239@Article{ umansky:2009, 17240 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17241 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17242 journal = {Computer Physics Communications}, 17243 year = {2009}, 17244 volume = {180}, 17245 pages = {887-903} 17246} 17247 17248@Article{ xu:1998, 17249 author = {X.Q. Xu and R.H. Cohen}, 17250 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17251 journal = {Computer Physics Communications}, 17252 year = {1998}, 17253 volume = {36}, 17254 number = {1-2}, 17255 pages = {158} 17256} 17257 17258@Article{ tron:1999, 17259 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17260 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17261 journal = {SIAM Journal on Optimization}, 17262 volume = {9}, 17263 number = {4}, 17264 pages = {1100-1127}, 17265 year = {1999} 17266} 17267 17268@Article{ stubenamg, 17269 author = {K. St\"{u}ben}, 17270 title = {A review of algebraic multigrid}, 17271 journal = {J. Comput. Appl. Math.}, 17272 volume = {128}, 17273 number = {1-2}, 17274 year = {2001}, 17275 issn = {0377-0427}, 17276 pages = {281--309}, 17277 doi = {10.1016/S0377-0427(00)00516-1}, 17278 publisher = {Elsevier Science Publishers B. V.}, 17279 address = {Amsterdam, The Netherlands, The Netherlands} 17280} 17281 17282@Article{ feuchtermg, 17283 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17284 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17285 journal = {Computing and visualization in science}, 17286 publisher = {Springer}, 17287 volume = {6}, 17288 number = {1}, 17289 year = {2003}, 17290 pages = {1--13} 17291} 17292 17293@Article{ chowmgsmoothness, 17294 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17295 only attempts to interpolate in the directions of geometrical smoothness. These 17296 directions are determined by analyzing samples of algebraically smooth error, e. 17297 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17298 consistently nearby in value. In addition, these dierences may be used to dene 17299 interpolation weights. These new ideas may be incorporated into the algebraic 17300 multigrid method. Test results show that the new method can have much lower grid 17301 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17302 author = {Chow, Edmond}, 17303 citeulike-article-id={7675372}, 17304 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17305 journal = {American Journal of Mathematics}, 17306 keywords = {fem, multigrid}, 17307 pages = {197--215}, 17308 posted-at = {2010-08-17 23:29:51}, 17309 priority = {2}, 17310 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17311 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17312 volume = {65}, 17313 year = {2001} 17314} 17315 17316@Article{ jonesamge, 17317 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17318 elements) method based on element agglomeration. In the method, coarse grid 17319 elements are formed by agglomerating fine grid elements. Compatible interpolation 17320 operators are constructed which yield coarse grid basis functions with a minimal 17321 energy property. Heuristics based on interpolation quality measures are used to 17322 guide the agglomeration procedure. The performance of the resulting method is 17323 demonstrated in two-level numerical experiments.}}, 17324 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17325 citeulike-article-id={8598569}, 17326 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17327 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17328 journal = {SIAM Journal on Scientific Computing}, 17329 keywords = {amg, fem, multigrid}, 17330 number = {1}, 17331 pages = {109--133}, 17332 posted-at = {2011-01-13 18:05:55}, 17333 priority = {2}, 17334 publisher = {SIAM}, 17335 title = {{AMGE Based on Element Agglomeration}}, 17336 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17337 volume = {23}, 17338 year = {2001} 17339} 17340 17341@Article{ saad1993, 17342 author = {Saad, Youcef}, 17343 doi = {10.1137/0914028}, 17344 issn = {10648275}, 17345 journal = {SIAM Journal on Scientific Computing}, 17346 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17347 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17348 precondition-,preconditioned conju-,subject classi cations,variable 17349 preconditioners}, 17350 number = {2}, 17351 pages = {461--469}, 17352 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17353 volume = {14}, 17354 year = {1993} 17355} 17356 17357@Misc{ path:homepage, 17358 author = {S. Dirkse and M. Ferris and T. Munson}, 17359 title = {{{PATH} {W}eb page}}, 17360 howpublished = {\url{http://pages.cs.wisc.edu/~ferris/path.html}} 17361} 17362 17363@Article{ ketcheson2008, 17364 author = {David I Ketcheson}, 17365 title = {Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with 17366 Low-Storage Implementations}, 17367 volume = {30}, 17368 journal = {SIAM Journal on Scientific Computing}, 17369 year = {2008}, 17370 pages = {2113--2136} 17371} 17372 17373@Article{ elman2009boundary, 17374 title = {{Boundary conditions in approximate commutator preconditioners for the 17375 Navier-Stokes equations}}, 17376 author = {Elman, H.C. and Tuminaro, R.}, 17377 journal = {Electronic Transactions on Numerical Analysis}, 17378 volume = {35}, 17379 pages = {257--280}, 17380 year = {2009} 17381} 17382 17383@Article{ elman2008tcp, 17384 title = {{A taxonomy and comparison of parallel block multi-level preconditioners for the 17385 incompressible Navier-Stokes equations}}, 17386 author = {Elman, H.C. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, 17387 R.}, 17388 journal = {Journal of Computational Physics}, 17389 volume = {227}, 17390 number = {1}, 17391 pages = {1790--1808}, 17392 year = {2008}, 17393 publisher = {Academic Press}, 17394 url = {http://chess.cs.umd.edu/~elman/papers/tax.pdf} 17395} 17396 17397@Article{ arioli2013, 17398 title = {Generalized {G}olub--{K}ahan bidiagonalization and stopping criteria}, 17399 author = {Arioli, Mario}, 17400 journal = {SIAM Journal on Matrix Analysis and Applications}, 17401 volume = {34}, 17402 number = {2}, 17403 pages = {571--592}, 17404 year = {2013}, 17405 publisher = {SIAM} 17406} 17407 17408@Book{ wesseling2009, 17409 title = {Principles of computational fluid dynamics}, 17410 author = {Wesseling, Pieter}, 17411 volume = {29}, 17412 year = {2009}, 17413 publisher = {Springer Science \& Business Media} 17414} 17415 17416@Article{ silvester2001efficient, 17417 title = {{Efficient preconditioning of the linearized Navier-Stokes equations for 17418 incompressible flow}}, 17419 author = {Silvester, D. and Elman, H. and Kay, D. and Wathen, A.}, 17420 journal = {Journal of Computational and Applied Mathematics}, 17421 volume = {128}, 17422 number = {1-2}, 17423 pages = {261--279}, 17424 issn = {0377-0427}, 17425 year = {2001}, 17426 publisher = {Elsevier} 17427} 17428 17429@Article{ elman1999bfbt, 17430 title = {{Preconditioning for the steady-state Navier-Stokes equations with low 17431 viscosity}}, 17432 author = {Elman, H.C.}, 17433 journal = {SIAM Journal on Scientific Computing}, 17434 volume = {20}, 17435 number = {4}, 17436 pages = {1299--1316}, 17437 issn = {1064-8275}, 17438 year = {1999}, 17439 publisher = {Citeseer} 17440} 17441 17442@Article{ elman2006bpb, 17443 title = {{Block preconditioners based on approximate commutators}}, 17444 author = {Elman, H. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, R.}, 17445 journal = {SIAM Journal on Scientific Computing}, 17446 volume = {27}, 17447 number = {5}, 17448 pages = {1651--1668}, 17449 year = {2006}, 17450 publisher = {Philadelphia, PA: SIAM, c1993-} 17451} 17452 17453@Article{ olshanskii2006analysis, 17454 title = {{Analysis of a Stokes interface problem}}, 17455 author = {Olshanskii, M.A. and Reusken, A.}, 17456 journal = {Numerische Mathematik}, 17457 volume = {103}, 17458 number = {1}, 17459 pages = {129--149}, 17460 issn = {0029-599X}, 17461 year = {2006}, 17462 publisher = {Springer} 17463} 17464 17465@Article{ patankar1972cph, 17466 title = {{A calculation procedure for heat, mass and momentum transfer in 17467 three-dimensional parabolic flows}}, 17468 author = {Patankar, S.V. and Spalding, D.B.}, 17469 journal = {Int. J. Heat Mass Transfer}, 17470 volume = {15}, 17471 pages = {1787--1806}, 17472 year = {1972} 17473} 17474 17475@Article{ rannacher1992simple, 17476 title = {{Simple nonconforming quadrilateral Stokes element}}, 17477 author = {Rannacher, R. and Turek, S.}, 17478 journal = {Numerical Methods for Partial Differential Equations}, 17479 volume = {8}, 17480 number = {2}, 17481 pages = {97--111}, 17482 issn = {1098-2426}, 17483 year = {1992}, 17484 publisher = {Wiley Online Library} 17485} 17486 17487@Article{ rannacher2000finite, 17488 title = {Finite Element Methods for the Incompressible {N}avier-{S}tokes Equations}, 17489 author = {Rannacher, R.}, 17490 journal = {Fundamental Directions in Mathematical Fluid Mechanics}, 17491 pages = {191}, 17492 isbn = {3764364149}, 17493 year = {2000}, 17494 publisher = {Birkhauser} 17495} 17496 17497@Article{ vanka1986block, 17498 title = {{Block-implicit multigrid solution of Navier-Stokes equations in primitive 17499 variables}}, 17500 author = {Vanka, S.P.}, 17501 journal = {Journal of Computational Physics}, 17502 volume = {65}, 17503 number = {1}, 17504 pages = {138--158}, 17505 issn = {0021-9991}, 17506 year = {1986}, 17507 publisher = {Elsevier} 17508} 17509 17510@Article{ eisenstat1983variational, 17511 title = {Variational iterative methods for nonsymmetric systems of linear equations}, 17512 author = {Eisenstat, S.C. and Elman, H.C. and Schultz, M.H.}, 17513 journal = {SIAM Journal on Numerical Analysis}, 17514 volume = {20}, 17515 number = {2}, 17516 pages = {345--357}, 17517 year = {1983}, 17518 publisher = {JSTOR} 17519} 17520 17521@InProceedings{ burstedde2008scalable, 17522 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 17523 author = {Burstedde, C. and Ghattas, O. and Gurnis, M. and Stadler, G. and Tan, E. and Tu, 17524 T. and Wilcox, L.C. and Zhong, S.}, 17525 booktitle = {Proceedings of the 2008 ACM/IEEE conference on Supercomputing}, 17526 pages = {62}, 17527 year = {2008}, 17528 organization = {IEEE Press} 17529} 17530 17531@Article{ burstedde2009parallel, 17532 title = {Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes} 17533 flow problems}, 17534 author = {Burstedde, C. and Ghattas, O. and Stadler, G. and Tu, T. and Wilcox, L.C.}, 17535 journal = {Computer Methods in Applied Mechanics and Engineering}, 17536 volume = {198}, 17537 number = {21-26}, 17538 pages = {1691--1700}, 17539 year = {2009}, 17540 publisher = {Elsevier} 17541} 17542 17543@Article{ stadler2010dynamics, 17544 title = {The dynamics of plate tectonics and mantle flow: From local to global scales}, 17545 author = {Stadler, G. and Gurnis, M. and Burstedde, C. and Wilcox, L.C. and Alisic, L. and 17546 Ghattas, O.}, 17547 journal = {Science}, 17548 volume = {329}, 17549 number = {5995}, 17550 pages = {1033}, 17551 year = {2010}, 17552 publisher = {American Association for the Advancement of Science} 17553} 17554 17555@Article{ tackley2008modelling, 17556 title = {Modelling compressible mantle convection with large viscosity contrasts in a 17557 three-dimensional spherical shell using the yin-yang grid}, 17558 author = {Tackley, P.J.}, 17559 journal = {Physics of the Earth and Planetary Interiors}, 17560 volume = {171}, 17561 number = {1-4}, 17562 pages = {7--18}, 17563 year = {2008}, 17564 publisher = {Elsevier} 17565} 17566 17567@Article{ moresizhonggurnis96, 17568 author = {Louis N. Moresi and Shijie Zhong and Michael Gurnis}, 17569 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 17570 viscosity}, 17571 journal = {Physics of the Earth and Planetary Interiors}, 17572 volume = {97}, 17573 pages = {83-–94}, 17574 year = {1996} 17575} 17576 17577@Article{ moresisolomatov95, 17578 author = {Louis N. Moresi and V. S. Solomatov}, 17579 title = {Numerical investigation of {2D} convection with extremely large viscosity 17580 variations}, 17581 journal = {Physics of Fluids}, 17582 volume = {7}, 17583 number = {9}, 17584 pages = {2154-–2162}, 17585 year = {1995} 17586} 17587 17588@Article{ chenmolnar83, 17589 author = {W.-P. Chen and P. Molnar}, 17590 title = {Focal depths of intra-continental and intraplate earthquakes and their 17591 implications for the thermal and mechanical properties of the lithosphere}, 17592 journal = {Journal of Geophysical Research}, 17593 volume = {88}, 17594 pages = {4183–-4214}, 17595 year = {1983} 17596} 17597 17598@Article{ jackson02, 17599 author = {J. Jackson}, 17600 title = {Strength of the continental lithosphere: time to abandon the jelly sandwich?}, 17601 journal = {GSA Today}, 17602 volume = {12}, 17603 pages = {4–-10}, 17604 year = {2002} 17605} 17606 17607@Article{ burovwatts06, 17608 author = {E.B. Burov and A.B. Watts}, 17609 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 17610 brulee?}, 17611 journal = {GSA Today}, 17612 volume = {16}, 17613 pages = {4–-10}, 17614 year = {2006} 17615} 17616 17617@InProceedings{ yang:brent:2002, 17618 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 17619 Parallel Distributed Memory Architectures}, 17620 author = {Laurence T. Yang and Richard Brent}, 17621 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 17622 for Parallel Processing}, 17623 year = {2002}, 17624 publisher = {IEEE} 17625} 17626 17627@Article{ demmel2008communication, 17628 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 17629 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 17630 journal = {Arxiv preprint arXiv:0808.2664}, 17631 year = {2008} 17632} 17633 17634@Article{ demmel09, 17635 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 17636 title = {Communication-optimal Iterative Methods}, 17637 journal = {Journal of Physics: Conf. Series}, 17638 volume = {180}, 17639 year = {2009} 17640} 17641 17642@TechReport{ parms04, 17643 author = {Yousef Saad and Masha Sosonkina}, 17644 title = {{pARMS}: A package for the parallel iterative solution of general large sparse 17645 linear systems user's guide}, 17646 number = {UMSI2004-8}, 17647 institution = {Minnesota Supercomputer Institute, University of Minnesota}, 17648 year = {2004} 17649} 17650 17651@Article{ picard1890, 17652 author = {Emile Picard}, 17653 title = {M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la 17654 m\'ethode des approximations successives}, 17655 journal = {Journal De Math\'ematiques Pures et Appliqu\'ees}, 17656 volume = {4}, 17657 number = {6}, 17658 pages = {145--210}, 17659 year = {1890}, 17660 url = {http://math-doc.ujf-grenoble.fr/JMPA/PDF/JMPA_1890_4_6_A3_0.pdf} 17661} 17662 17663@Book{ rall1969, 17664 author = {Louis B. Rall}, 17665 title = {Computational solution of nonlinear operator equations}, 17666 publisher = {Krieger Pub Co.}, 17667 pages = {225}, 17668 year = {1969} 17669} 17670 17671@Article{ fletcherreeves1964, 17672 author = {R. Fletcher and C. M. Reeves}, 17673 title = {Function Minimization by Conjugate Gradients}, 17674 journal = {Computer Journal}, 17675 volume = {7}, 17676 pages = {149–-154}, 17677 year = {1964} 17678} 17679 17680@InBook{ mcinnesallanetal06, 17681 author = {Lois Curfman McInnes and Benjamin Allan and Robert Armstrong and Steven Benson 17682 and David Bernholdt and Tamara Dahlgren and Lori Diachin and Manojkumar Krishnan 17683 and James Kohl and Jay Larson and Sophia Lefantzi and Jarek Nieplocha and Boyana 17684 Norris and Steven Parker and Jaideep Ray and Shujia Zhou}, 17685 editor = {A.~M.~Bruaset and A.~Tveito}, 17686 title = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 17687 chapter = {Parallel {PDE}-Based Simulations Using the {Common Component Architecture}}, 17688 publisher = {Springer}, 17689 year = {2006}, 17690 number = {51}, 17691 series = {Lecture Notes in Computational Science and Engineering}, 17692 pages = {327--381}, 17693 doi = {10.1016/S0167-8191(02)00191-6} 17694} 17695 17696@Article{ cyrshadidtuminaro12, 17697 title = {Stabilization and scalable block preconditioning for the {Navier–Stokes} 17698 equations}, 17699 journal = {Journal of Computational Physics}, 17700 volume = {231}, 17701 number = {2}, 17702 pages = {345 - 363}, 17703 year = {2012}, 17704 issn = {0021-9991}, 17705 doi = {10.1016/j.jcp.2011.09.001}, 17706 author = {Eric C. Cyr and John N. Shadid and Raymond S. Tuminaro} 17707} 17708 17709@Article{ keyesmcinneswoodwardetal13, 17710 title = {Multiphysics Simulations: Challenges and Opportunities}, 17711 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17712 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17713 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17714 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17715 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17716 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17717 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17718 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17719 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17720 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17721 journal = {International Journal of High Performance Computing Applications}, 17722 month = feb, 17723 year = {2013}, 17724 volume = {27}, 17725 number = {1}, 17726 pages = {4--83}, 17727 doi = {10.1177/1094342012468181}, 17728 note = {Special issue}, 17729 abstract = {We consider multiphysics applications from algorithmic and architectural 17730 perspectives, where ``algorithmic'' includes both mathematical analysis and 17731 computational complexity and ``architectural'' includes both software and hardware 17732 environments. Many diverse multiphysics applications can be reduced, en route to 17733 their computational simulation, to a common algebraic coupling paradigm. 17734 Mathematical analysis of multiphysics coupling in this form is not always 17735 practical for realistic applications, but model problems representative of 17736 applications discussed herein can provide insight. A variety of software 17737 frameworks for multiphysics applications have been constructed and refined within 17738 disciplinary communities and executed on leading-edge computer systems. We examine 17739 several of these, expose some commonalities among them, and attempt to extrapolate 17740 best practices to future systems. From our study, we summarize challenges and 17741 forecast opportunities.} 17742} 17743 17744@Misc{ rosner10, 17745 author = {Robert {Rosner (Chair)}}, 17746 title = {{The Opportunities and Challenges of Exascale Computing}}, 17747 year = {2010}, 17748 howpublished = {Office of Science, U.S. Department of Energy}, 17749 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17750} 17751 17752@Misc{ kogge2008exascale, 17753 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 17754 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 17755 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 17756 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 17757 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 17758 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 17759 howpublished = {DARPA}, 17760 year = {2008}, 17761 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 17762} 17763 17764@Misc{ doegrandchallengeworkshops, 17765 key = {Office of Science, U.S. Department of Energy}, 17766 title = {{Scientific Grand Challenges Workshop Series}}, 17767 howpublished = {Office of Science, U.S. Department of Energy, see 17768 \url{http://extremecomputing.labworks.org/workshops.stm}} 17769} 17770 17771@Misc{ lawrence2011, 17772 key = {Lawrence}, 17773 title = {{Ernest Orlando Lawrence Award Winners}}, 17774 howpublished = {U.S. Department of Energy, {\footnotesize 17775 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 17776 year = {2011} 17777} 17778 17779@Article{ murphy2000npi, 17780 title = {{A note on preconditioning for indefinite linear systems}}, 17781 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 17782 journal = {SIAM Journal on Scientific Computing}, 17783 volume = {21}, 17784 number = {6}, 17785 pages = {1969--1972}, 17786 year = {2000}, 17787 publisher = {Philadelphia, PA: SIAM, c1993-} 17788} 17789 17790@Article{ elman2011bouyancy, 17791 title = {Fast iterative solvers for buoyancy driven flow problems}, 17792 journal = {Journal of Computational Physics}, 17793 volume = {230}, 17794 number = {10}, 17795 pages = {3900 - 3914}, 17796 year = {2011}, 17797 note = {}, 17798 issn = {0021-9991}, 17799 doi = {10.1016/j.jcp.2011.02.014}, 17800 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 17801 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 17802 Adaptivity, Preconditioning, Algebraic multigrid} 17803} 17804 17805@Article{ dongarrabeckman11, 17806 author = {J. Dongarra and P. Beckman and et al.}, 17807 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 17808 journal = {Int. J. High Perf. Comput. Applics.}, 17809 volume = {25}, 17810 year = {2011}, 17811 pages = {3--60} 17812} 17813 17814@Article{ mandel1999energy, 17815 title = {Energy optimization of algebraic multigrid bases}, 17816 author = {Mandel, J. and Brezina, M. and Van{\v{e}}k, P.}, 17817 journal = {Computing}, 17818 volume = {62}, 17819 number = {3}, 17820 pages = {205--228}, 17821 year = {1999}, 17822 publisher = {Springer} 17823} 17824 17825@Article{ vanek1996algebraic, 17826 title = {Algebraic multigrid by smoothed aggregation for second and fourth order elliptic 17827 problems}, 17828 author = {Van{\v{e}}k, P. and Mandel, J. and Brezina, M.}, 17829 journal = {Computing}, 17830 volume = {56}, 17831 number = {3}, 17832 pages = {179--196}, 17833 year = {1996}, 17834 publisher = {Springer} 17835} 17836 17837@Article{ vanek2001convergence, 17838 title = {Convergence of algebraic multigrid based on smoothed aggregation}, 17839 author = {Van{\v{e}}ek, P. and Brezina, M. and Mandel, J.}, 17840 journal = {Numerische Mathematik}, 17841 volume = {88}, 17842 number = {3}, 17843 pages = {559--579}, 17844 year = {2001}, 17845 publisher = {Springer} 17846} 17847 17848@Article{ brannick2007algebraic, 17849 title = {Algebraic multigrid methods based on compatible relaxation and energy 17850 minimization}, 17851 author = {Brannick, J. and Zikatanov, L.}, 17852 journal = {Domain decomposition methods in science and engineering XVI}, 17853 pages = {15--26}, 17854 year = {2007}, 17855 publisher = {Springer} 17856} 17857 17858@Article{ brannickfalgout2010, 17859 title = {{Compatible Relaxation and Coarsening in Algebraic Multigrid}}, 17860 author = {James J. Brannick and Robert D. Falgout}, 17861 journal = {SIAM Journal on Scientific Computing}, 17862 volume = {32}, 17863 number = {3}, 17864 pages = {1393--1416}, 17865 url = {http://epubs.siam.org/doi/10.1137/090772216}, 17866 doi = {10.1137/090772216}, 17867 issn = {1064-8275}, 17868 year = {2010} 17869} 17870 17871@Article{ xu2004energy, 17872 title = {On an energy minimizing basis for algebraic multigrid methods}, 17873 author = {Xu, J. and Zikatanov, L.}, 17874 journal = {Computing and Visualization in Science}, 17875 volume = {7}, 17876 number = {3}, 17877 pages = {121--127}, 17878 year = {2004}, 17879 publisher = {Springer} 17880} 17881 17882@Article{ dblp:journals/toms/bakerhlt09, 17883 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 17884 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 17885 journal = {ACM Trans. Math. Softw.}, 17886 volume = {36}, 17887 number = {3}, 17888 year = {2009}, 17889 doi = {10.1145/1527286.1527287}, 17890 bibsource = {DBLP, http://dblp.uni-trier.de} 17891} 17892 17893@Article{ dblp:journals/siamsc/yanggbllhn05, 17894 author = {Chao Yang and Weiguo Gao and Zhaojun Bai and Xiaoye S. Li and Lie-Quan Lee and 17895 Parry Husbands and Esmond G. Ng}, 17896 title = {An Algebraic Substructuring Method for Large-Scale Eigenvalue Calculation}, 17897 journal = {SIAM J. Scientific Computing}, 17898 volume = {27}, 17899 number = {3}, 17900 year = {2005}, 17901 pages = {873-892}, 17902 doi = {10.1137/040613767}, 17903 bibsource = {DBLP, http://dblp.uni-trier.de} 17904} 17905 17906@TechReport{ ml-guide, 17907 author = {M.W. Gee and C.M. Siefert and J.J. Hu and R.S. Tuminaro and M.G. Sala}, 17908 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 17909 institution = {Sandia National Laboratories}, 17910 year = {2006}, 17911 number = {SAND2006-2649} 17912} 17913 17914@Article{ brannick06, 17915 title = {An energy-based AMG coarsening strategy}, 17916 volume = {13}, 17917 doi = {10.1002/nla.480}, 17918 number = {2-3}, 17919 journal = {Numerical Linear Algebra with Applications}, 17920 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 17921 and Ruge, J}, 17922 year = {2006}, 17923 pages = {133--148} 17924} 17925 17926@Article{ olson10, 17927 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 17928 title = {A new perspective on strength measures in algebraic multigrid}, 17929 journal = {Numerical Linear Algebra with Applications}, 17930 volume = {17}, 17931 number = {4}, 17932 pages = {713--733}, 17933 year = {2010}, 17934 publisher = {John Wiley \& Sons, Ltd.}, 17935 issn = {1099-1506}, 17936 doi = {10.1002/nla.669} 17937} 17938 17939@Article{ olson11, 17940 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 17941 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 17942 Minimization}, 17943 journal = {SIAM J. Sci. Comput.}, 17944 issue_date = {April 2011}, 17945 volume = {33}, 17946 issue = {2}, 17947 month = apr, 17948 year = {2011}, 17949 issn = {1064-8275}, 17950 pages = {966--991}, 17951 numpages = {26}, 17952 doi = {10.1137/100803031}, 17953 acmid = {2078825}, 17954 publisher = {Society for Industrial and Applied Mathematics}, 17955 address = {Philadelphia, PA}, 17956 keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed 17957 aggregation} 17958} 17959 17960@Article{ dorit2011, 17961 author = {Dorit Ron and Ilya Safro and Achi Brandt}, 17962 title = {Relaxation-Based Coarsening and Multiscale Graph Organization}, 17963 journal = {Multiscale Modeling {\&} Simulation}, 17964 volume = {9}, 17965 number = {1}, 17966 year = {2011}, 17967 pages = {407-423}, 17968 doi = {10.1137/100791142} 17969} 17970 17971@Article{ chen2011algebraic, 17972 title = {Algebraic distance on graphs}, 17973 author = {Chen, Jie and Safro, Ilya}, 17974 journal = {SIAM Journal on Scientific Computing}, 17975 volume = {33}, 17976 number = {6}, 17977 pages = {3468--3490}, 17978 year = {2011}, 17979 publisher = {SIAM} 17980} 17981 17982@InProceedings{ adams04, 17983 author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.}, 17984 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 17985 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 17986 half a billion degrees of freedom}, 17987 note = {Gordon Bell Award}, 17988 year = {2004} 17989} 17990 17991@Article{ adams03a, 17992 author = {Adams, M.~F.}, 17993 journal = {Numerical Linear Algebra with Applications}, 17994 number = {2-3}, 17995 pages = {141-153}, 17996 title = {Algebraic multigrid methods for constrained linear systems with applications to 17997 contact problems in solid mechanics}, 17998 volume = {11}, 17999 year = {2004} 18000} 18001 18002@Article{ adams-10a, 18003 author = {M. ~F. 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A}, 23408 volume = {378}, 23409 number = {20190050}, 23410 doi = {10.1098/rsta.2019.0050}, 23411 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 23412 year = {2020} 23413} 23414 23415@Article{ schoberl1999, 23416 title = {Multigrid methods for a parameter dependent problem in primal variables}, 23417 author = {Joachim Sch{\"o}berl}, 23418 journal = {Numerische Mathematik}, 23419 volume = {84}, 23420 number = {1}, 23421 pages = {97--119}, 23422 year = {1999} 23423} 23424 23425@Article{ wuleexuzikatanov2008, 23426 title = {Convergence analysis on iterative methods for semidefinite systems}, 23427 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 23428 journal = {Journal of Computational Mathematics}, 23429 pages = {797--815}, 23430 year = {2008} 23431} 23432 23433@Article{ maierrannacher2016, 23434 title = {Duality-based adaptivity in finite element discretization of heterogeneous 23435 multiscale problems}, 23436 author = {Maier, Matthias and Rannacher, Rolf}, 23437 journal = {Journal of Numerical Mathematics}, 23438 volume = {24}, 23439 number = {3}, 23440 pages = {167--187}, 23441 year = {2016} 23442} 23443 23444@Article{ maierrannacher2018, 23445 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23446 multiscale problems}, 23447 author = {Maier, Matthias and Rannacher, Rolf}, 23448 journal = {Multiscale Modeling \& Simulation}, 23449 volume = {16}, 23450 number = {1}, 23451 pages = {412--428}, 23452 year = {2018} 23453} 23454 23455@Article{ margetismaierluskin2017, 23456 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23457 metamaterial sheet}, 23458 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23459 journal = {Studies in Applied Mathematics}, 23460 volume = {139}, 23461 number = {4}, 23462 pages = {599--625}, 23463 year = {2017} 23464} 23465 23466@Article{ maiermargetisluskin2017b, 23467 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23468 approximation and validation}, 23469 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23470 journal = {Journal of Computational Physics}, 23471 volume = {339}, 23472 pages = {126--145}, 23473 year = {2017} 23474} 23475 23476@Article{ maiermargetisluskin2018, 23477 title = {Generation of surface plasmon-polaritons by edge effects}, 23478 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23479 journal = {Communications in Mathematical Sciences}, 23480 volume = {16}, 23481 number = {1}, 23482 pages = {77--95}, 23483 url = {http://arxiv.org/abs/1702.00848}, 23484 year = {2018} 23485} 23486 23487@Article{ maiermattheakiskaxirasluskinmargetis2018, 23488 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23489 metamaterials}, 23490 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23491 Mitchell and Margetis, Dionisios}, 23492 journal = {Physical Review B}, 23493 volume = {97}, 23494 number = {3}, 23495 pages = {035307}, 23496 year = {2018} 23497} 23498 23499@Article{ maiermattheakiskaxirasluskinmargetis2019, 23500 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23501 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23502 Mitchell and Margetis, Dionisios}, 23503 journal = {Proceedings of the Royal Society A}, 23504 volume = {475}, 23505 number = {2230}, 23506 pages = {20190220}, 23507 year = {2019} 23508} 23509 23510@Article{ maiermargetisluskin2020, 23511 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23512 two scales}, 23513 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23514 journal = {Physical Review B}, 23515 volume = {102}, 23516 number = {7}, 23517 pages = {075308}, 23518 year = {2020} 23519} 23520 23521@Article{ margetismaierstauberlowluskin2020, 23522 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 23523 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 23524 Luskin, Mitchell}, 23525 journal = {Journal of Physics A: Mathematical and Theoretical}, 23526 volume = {53}, 23527 number = {5}, 23528 pages = {055201}, 23529 year = {2020} 23530} 23531 23532@Article{ maiermargetismellet2020, 23533 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 23534 structures}, 23535 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 23536 journal = {Journal of Computational and Applied Mathematics}, 23537 volume = {377}, 23538 pages = {112909}, 23539 year = {2020} 23540} 23541 23542@Article{ maierkronbichler2021, 23543 title = {Efficient parallel 3D computation of the compressible Euler equations with an 23544 invariant-domain preserving second-order finite-element scheme}, 23545 author = {Maier, Matthias and Kronbichler, Martin}, 23546 journal = {ACM Transactions on Parallel Computing}, 23547 volume = {8}, 23548 number = {3}, 23549 pages = {1--30}, 23550 year = {2021} 23551} 23552 23553@Article{ guermondmaierpopovtomas2021, 23554 title = {Second-order invariant domain preserving approximation of the compressible 23555 Navier--Stokes equations}, 23556 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 23557 journal = {Computer Methods in Applied Mechanics and Engineering}, 23558 volume = {375}, 23559 pages = {113608}, 23560 year = {2021} 23561} 23562 23563@Article{ liliptonmaier2021, 23564 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 23565 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 23566 eprint = {2009.12166}, 23567 archiveprefix = {arXiv}, 23568 primaryclass = {phys.optics}, 23569 year = {2021} 23570} 23571 23572@Article{ songmaierluskin2020, 23573 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 23574 gradient-index graphene waveguides}, 23575 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23576 journal = {Journal of Computational Physics}, 23577 volume = {423}, 23578 pages = {109871}, 23579 year = {2020} 23580} 23581 23582@Article{ songmaierluskin2019, 23583 title = {Adaptive finite element simulations of waveguide configurations involving 23584 parallel 2D material sheets}, 23585 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23586 journal = {Computer Methods in Applied Mechanics and Engineering}, 23587 volume = {351}, 23588 pages = {20--34}, 23589 year = {2019} 23590} 23591 23592% 23593% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23594% 23595% 23596@Unpublished{ rob1, 23597 author = {Rob Kunz}, 23598 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23599 State University}, 23600 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23601 sponsors = {U.S. Navy, NRC}, 23602 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23603 simulations, including lake warming by power plants}, 23604 dates = {Oct 3 and 4, 2002}, 23605 email = {rfk@wt.arl.psu.edu} 23606} 23607 23608@Unpublished{ au1, 23609 author = {Feng Wang and William Appelbe}, 23610 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23611 url = {http://www.vpac.org}, 23612 sponsors = { }, 23613 note = {Using PETSc for a Variety of Geophysical Simulations}, 23614 dates = {Nov 22, 2002} 23615} 23616 23617@Unpublished{ carl1, 23618 author = {Carl Sovinec}, 23619 institution = {Applied Physics, University of Wisconsin}, 23620 url = {http://nimrodteam.org}, 23621 sponsors = {DOE Office of Fusion Research}, 23622 note = {Investigating using PETSc for NIMROD}, 23623 dates = {Nov 21, 2002}, 23624 email = {sovinec@engr.wisc.edu} 23625} 23626 23627@Unpublished{ au1b, 23628 author = {Pablo Carrica and Robert Wilson}, 23629 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23630 url = {http://}, 23631 sponsors = {Office of Naval Research}, 23632 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23633 dates = {Sept, 2002}, 23634 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23635} 23636 23637% ------------------- TAO References ---------------------- 23638@Article{ benson:2001:csp, 23639 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 23640 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 23641 journal = {{ACM} Transactions on Mathematical Software}, 23642 volume = {27}, 23643 number = {3}, 23644 month = sep, 23645 year = {2001}, 23646 pages = {361--376} 23647} 23648 23649@TechReport{ tao-user-ref-2000, 23650 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 23651 title = {{TAO} Users Manual}, 23652 year = {2000}, 23653 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23654 number = {ANL/MCS-TM-242}, 23655 note = {See \url{http://www.mcs.anl.gov/tao}} 23656} 23657 23658% ------------------- Optimization References ---------------------- 23659@Book{ optguide93, 23660 title = {Optimization Software Guide}, 23661 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 23662 publisher = {SIAM Publications}, 23663 address = {Philadelphia}, 23664 year = {1993} 23665} 23666 23667@InProceedings{ more84, 23668 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 23669 Hillstrom}, 23670 title = {The {MINPACK} Project}, 23671 booktitle = {Sources and Development of Mathematical Software}, 23672 editor = {Wayne R. Cowell}, 23673 year = {1984}, 23674 pages = {88--111} 23675} 23676 23677@Article{ steihaug:83, 23678 author = {Trond Steihaug}, 23679 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 23680 journal = {SIAM J. Numer. Anal.}, 23681 volume = {20}, 23682 year = {1983}, 23683 pages = {626--637}, 23684 key = {steihaug92 ! trust_region} 23685} 23686 23687@TechReport{ minpack2test, 23688 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 23689 title = {The {MINPACK-2} Test Problem Collection}, 23690 institution = {Argonne National Laboratory}, 23691 year = {1991}, 23692 number = {ANL/MCS-TM-150}, 23693 key = {more91 ! MINPACK-2} 23694} 23695 23696@TechReport{ hohmann:94, 23697 author = {Andreas Hohmann}, 23698 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 23699 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 23700 year = {1994}, 23701 number = {SC-94-4}, 23702 key = {Hohmann94} 23703} 23704 23705@TechReport{ meza:94, 23706 author = {Juan C. Meza}, 23707 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 23708 institution = {Sandia National Laboratory}, 23709 year = {1994}, 23710 number = {SAND94-8225}, 23711 key = {Meza94} 23712} 23713 23714@Book{ dennis:83, 23715 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 23716 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 23717 publisher = {Prentice-Hall, Inc.}, 23718 address = {Englewood Cliffs, NJ}, 23719 year = {1983} 23720} 23721 23722@TechReport{ more:92, 23723 author = {Jorge J. Mor\'{e} and David Thuente}, 23724 title = {Line search algorithms with guaranteed sufficient decrease}, 23725 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23726 year = {1992}, 23727 number = {MCS-P330-1092} 23728} 23729 23730@Article{ more-toraldo, 23731 author = {Jorge J. Mor\'e and G. Toraldo}, 23732 journal = {SIOPT}, 23733 pages = {93--113}, 23734 title = {On the solution of large quadratic programming problems with bound constraints}, 23735 volume = {1}, 23736 year = {1991} 23737} 23738 23739@Article{ byrd:1995:lma, 23740 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 23741 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 23742 journal = {SIAM Journal on Scientific Computing}, 23743 volume = {16}, 23744 number = {5}, 23745 pages = {1190--1208}, 23746 month = sep, 23747 year = {1995}, 23748 coden = {SJOCE3}, 23749 issn = {1064-8275 (print), 1095-7197 (electronic)}, 23750 mrclass = {90C30 (65K05)}, 23751 mrnumber = {96e:90039}, 23752 mrreviewer = {Henry Wolkowicz}, 23753 bibdate = {Fri Dec 4 16:17:35 MST 1998} 23754} 23755 23756@Article{ lin_c3, 23757 author = {C.-J. Lin and J. J. Mor\'e}, 23758 title = {Newton's method for large bound-constrained optimization problems}, 23759 year = {1999}, 23760 journal = {SIOPT}, 23761 volume = {9(4)}, 23762 pages = {1100--1127}, 23763 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 23764} 23765 23766@TechReport{ dolan2, 23767 author = {E. Dolan and J. J. Mor\'{e}}, 23768 title = {Benchmarking Optimization Software with Performance Profiles}, 23769 year = {2001}, 23770 month = jan, 23771 number = {ANL/MCS-P861-1200}, 23772 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23773 address = {Argonne, IL}, 23774 url = {http://www.mcs.anl.gov/~more/cops/} 23775} 23776 23777@InProceedings{ owlqn, 23778 author = {Galen Andrew and Jianfeng Gao}, 23779 title = {Scalable training of L1-regularized log-linear models}, 23780 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 23781 pages = {33--40}, 23782 year = {2007} 23783} 23784 23785@Article{ bmrm, 23786 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 23787 title = {Bundle methods for regularized risk minimization}, 23788 year = {2010}, 23789 journal = {Journal of Machine Learning Research}, 23790 volume = {11}, 23791 pages = {311--365} 23792} 23793 23794% ------------------- Component Software References ---------------------- 23795@InProceedings{ cca99, 23796 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 23797 McInnes and S. Parker and B. Smolinski}, 23798 title = {Toward a Common Component Architecture for High-Performance Scientific 23799 Computing}, 23800 booktitle = {Proceedings of {High Performance Distributed Computing}}, 23801 pages = {115--124}, 23802 year = {1999}, 23803 note = {See \url{http://cca-forum.org}} 23804} 23805 23806@Book{ szyperski98, 23807 author = {Clemens Szyperski}, 23808 title = {Component Software: Beyond Object-Oriented Programming}, 23809 publisher = {ACM Press}, 23810 address = {New York}, 23811 year = {1998} 23812} 23813 23814@Article{ broy98, 23815 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 23816 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 23817 Stal and Clemens Szyperski}, 23818 title = {What Characterizes a (Software) Component?}, 23819 journal = {Software -- Concepts and Tools}, 23820 publisher = {Springer-Verlag}, 23821 year = {1998}, 23822 volume = {19}, 23823 pages = {49--56} 23824} 23825 23826@Article{ componentware:94, 23827 author = {Jon Udell}, 23828 title = {Componentware}, 23829 journal = {Byte}, 23830 volume = {may}, 23831 pages = {46--56}, 23832 year = {1994}, 23833 key = {Udell94 ! componentware} 23834} 23835 23836@Misc{ cca-web-page, 23837 author = {{Common Component Architecture Forum}}, 23838 note = {See \url{http://cca-forum.org}} 23839} 23840 23841% --------------- References for Tools Used by TAO Developers ----------------- 23842 23843% 23844% tohtml: Used to generate on-line TAO users manual and manual pages 23845% 23846@TechReport{ tohtml, 23847 author = {William Gropp}, 23848 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 23849 institution = {Argonne National Laboratory}, 23850 number = {ANL/MCS-TM-00}, 23851 month = jan, 23852 year = {1995}, 23853 key = {tohtml} 23854} 23855 23856% 23857% doctext: Used to generate tex version of TAO manual pages 23858% 23859@TechReport{ doctext, 23860 author = {William Gropp}, 23861 title = {Users Manual for doctext: Producing documentation from {C} source code}, 23862 institution = {Argonne National Laboratory}, 23863 number = {ANL/MCS-TM-00}, 23864 month = jan, 23865 year = {1995}, 23866 key = {doctext} 23867} 23868 23869% 23870% bfort: Used to generate TAO Fortran interface 23871% 23872@TechReport{ bfort, 23873 author = {William Gropp}, 23874 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 23875 institution = {Argonne National Laboratory}, 23876 number = {ANL/MCS-TM-208}, 23877 month = mar, 23878 year = {1995}, 23879 key = {doctext} 23880} 23881 23882% ------------------------- PETSc References ------------------------------ 23883@InProceedings{ petsc, 23884 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 23885 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 23886 Libraries}, 23887 booktitle = {Modern Software Tools in Scientific Computing}, 23888 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 23889 publisher = {Birkhauser Press}, 23890 pages = {163--202}, 23891 year = {1997} 23892} 23893 23894% ------------------------- Misc Other References ------------------------------ 23895@Misc{ indeps-web-page, 23896 title = {{InDEPS} {W}eb page}, 23897 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 23898 author = {et al. Robert Armstrong}, 23899 institution = {Sandia National Laboratory}, 23900 key = {{InDEPS} {W}eb page} 23901} 23902 23903@Misc{ pooma, 23904 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 23905 chitectures}, 23906 year = {1996}, 23907 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 23908 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 23909} 23910 23911@Misc{ isis++-web-page, 23912 title = {{ISIS++} {W}eb Page}, 23913 note = {See \url{http://ca.sandia.gov/isis}}, 23914 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 23915 institution = {Sandia National Laboratories} 23916} 23917 23918@Misc{ trilinos-web-page, 23919 title = {{Trilinos} {W}eb Page}, 23920 note = {See 23921 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 23922 author = {Mike Heroux et al.}, 23923 institution = {Sandia National Laboratories} 23924} 23925 23926@Misc{ alice-web-page, 23927 title = {{ALICE} {W}eb page}, 23928 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 23929 Argonne National Laboratory}, 23930 key = {{ALICE} {W}eb page} 23931} 23932 23933@Misc{ autodiff-webpage, 23934 author = {{Computational Differentiation Project}}, 23935 note = {See \url{http://www.mcs.anl.gov/autodiff}} 23936} 23937 23938@Misc{ coool-home-page, 23939 author = {Lydia Deng and Wences Gouveia and John Scales}, 23940 title = {{The CWP Object-Oriented Optimization Library}}, 23941 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 23942} 23943 23944@Misc{ rice-inversion-home-page, 23945 author = {Mark S. Gokenbach and William W. Symes}, 23946 title = {{The Hilbert Class Library}}, 23947 note = {See \url{http://www.trip.caam.rice.edu/}} 23948} 23949 23950@Misc{ opt++-home-page, 23951 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 23952 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 23953} 23954 23955@Article{ gockenbach:1999:ccl, 23956 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 23957 title = {C++ Classes for Linking Optimization with Complex Simulations}, 23958 journal = {{ACM} Transactions on Mathematical Software}, 23959 volume = {25}, 23960 number = {2}, 23961 month = jun, 23962 year = {1999}, 23963 pages = {191-212}, 23964 abstract = {The object-oriented programming paradigm can be used to overcome the 23965 incompatibilities between off-the-shelf optimization software and application 23966 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 23967 objects arising in optimization problems, such as vectors, linear operators, and 23968 so forth, as C++ classes, making it possible to write optimization code in a 23969 natural fashion, while allowing application software such as simulators to use the 23970 most convenient data structures and programming style. In spite of the poor 23971 reputation C++ has for runtime performance, the use of mixed-language programming 23972 allows performance equal to that achieved by standard Fortran packages, as 23973 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 23974 accepted = {April 1999}, 23975 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 23976} 23977 23978@Misc{ neos-guide, 23979 author = {{The Optimization Software Guide}}, 23980 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 23981} 23982 23983@Article{ boyd, 23984 title = {Distributed optimization and statistical learning via the alternating direction 23985 method of multipliers}, 23986 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 23987 Jonathan and others}, 23988 journal = {Foundations and Trends{\textregistered} in Machine learning}, 23989 volume = {3}, 23990 number = {1}, 23991 pages = {1-122}, 23992 year = {2011}, 23993 publisher = {Now Publishers, Inc.} 23994} 23995 23996@Misc{ :alertsys, 23997 title = {page{ALERT}}, 23998 organization = {Alert Systems, Inc}, 23999 address = {Madison, Wisconsin}, 24000 note = {http://www.alertsys.com/} 24001} 24002 24003@Manual{ :cmfortran, 24004 title = {{CM} {F}ortran Language Reference Manual}, 24005 organization = {Thinking Machines Corporation}, 24006 year = {1994}, 24007 address = {Cambridge, MA} 24008} 24009 24010@Manual{ :cmmd, 24011 title = {{CMMD} Reference Manual, Version 3.0}, 24012 organization = {Thinking Machines Corporation}, 24013 year = {1993}, 24014 address = {Cambridge, MA} 24015} 24016 24017@Manual{ :cmssl, 24018 title = {{CMSSL} for {CM} {F}ortran}, 24019 volume = {I}, 24020 organization = {Thinking Machines Corporation}, 24021 year = {1994}, 24022 address = {Cambridge, MA} 24023} 24024 24025@Misc{ :condor, 24026 author = {M. Livny}, 24027 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24028 howpublished = {www.cs.wisc.edu/condor} 24029} 24030 24031@Manual{ :connection, 24032 title = {Connection Machine {CM}--5 Technical Summary}, 24033 organization = {Thinking Machines Corporation}, 24034 year = {1993}, 24035 address = {Cambridge, MA} 24036} 24037 24038@Manual{ :cplex, 24039 title = {{CPLEX} Optimizer}, 24040 organization = {ILOG CPLEX Division}, 24041 address = {889 Alder Avenue, Incline Village, Nevada}, 24042 note = {http://www.cplex.com/} 24043} 24044 24045@Manual{ :cplextm, 24046 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24047 (Version 2.0)}, 24048 organization = {CPLEX Optimization Inc.}, 24049 year = {1992}, 24050 address = {Incline Village, Nevada} 24051} 24052 24053@Misc{ :fatcop, 24054 author = {M. C. Ferris}, 24055 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24056 Solver}, 24057 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24058} 24059 24060@Misc{ :metaneos, 24061 author = {S. J. Wright}, 24062 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24063 howpublished = {www-unix.mcs.anl.gov/metaneos} 24064} 24065 24066@InCollection{ gropp.more:optimization, 24067 author = {W. Gropp and J. J. Mor\'e}, 24068 title = {Optimization environments and the {NEOS} Server}, 24069 booktitle = {Approximation Theory and Optimization}, 24070 pages = {167--182}, 24071 publisher = {Cambridge University Press}, 24072 year = {1997}, 24073 editor = {M. D. Buhmann and A. Iserles} 24074} 24075 24076@Article{ czyzyk.mesnier.ea:neos, 24077 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24078 title = {The {NEOS} Server}, 24079 journal = {IEEE Journal on Computational Science and Engineering}, 24080 volume = {5}, 24081 year = {1998}, 24082 pages = {68--75} 24083} 24084 24085@Book{ :osl, 24086 title = {Handbook for {IBM OSL}}, 24087 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24088 year = {1994}, 24089 publisher = {Boyd and Fraser}, 24090 address = {Danvers, Massachusetts} 24091} 24092 24093@Manual{ :pro-matlab, 24094 title = {{PRO}--{MATLAB} User's Guide}, 24095 organization = {The MathWorks, Inc.}, 24096 year = {1989}, 24097 address = {21 Eliot Street, South Natick, MA 01760} 24098} 24099 24100@Misc{ :prostate, 24101 key = {Biomedical}, 24102 title = {Biomedical Business International Newsletter}, 24103 howpublished = {pp. 72--75}, 24104 year = {1996} 24105} 24106 24107@Misc{ :sipcase, 24108 key = {Natural}, 24109 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24110 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24111} 24112 24113@Book{ aarts.korst:simulated, 24114 author = {E. Aarts and J. 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Walter}, 24677 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 24678 journal = {Environmental and Resource Economics}, 24679 year = {1991}, 24680 volume = {1}, 24681 pages = {237--270} 24682} 24683 24684@PhDThesis{ bagley:behaviour, 24685 author = {J. D. Bagley}, 24686 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 24687 Algorithms}, 24688 year = {1967}, 24689 school = {University of Michigan} 24690} 24691 24692@Article{ bain.stewart:application, 24693 author = {R. S. Bain and W. E. Stewart}, 24694 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 24695 Algebraic Equation Systems}, 24696 journal = {Computers in Chemical Engineering}, 24697 year = {1991}, 24698 volume = {15}, 24699 pages = {203--208} 24700} 24701 24702@Article{ baker.lasdon:successive, 24703 author = {T. E. Baker and L. S. 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Whalley}, 24729 title = {A General Equilibrium Model for Tax Policy Evaluation}, 24730 publisher = {The University of Chicago Press}, 24731 year = {1985}, 24732 series = {National Bureau of Economic Research Monograph} 24733} 24734 24735@InProceedings{ balog.angelos.ea:dose, 24736 author = {J. Balog and L. Angelos and T. R. Mackie and P. Reckwerdt}, 24737 title = {Dose Computation for a One-Dimensional Multileaf Collimator}, 24738 booktitle = {Proceedings of the XII International Conference on the Use of Computers in 24739 Radiation Therapy, Salt Lake City}, 24740 year = {1997}, 24741 editor = {D. D. Leavitt and G. Starkshall}, 24742 publisher = {Medical Physics Publishing}, 24743 address = {St. Louis, Missouri}, 24744 pages = {323--326} 24745} 24746 24747@Article{ baraff:fast, 24748 author = {D. 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Model analysis and 26312 optimality conditions}, 26313 type = {Publication}, 26314 number = {CRT-94-56}, 26315 institution = {Centre de Recherche sur les Transports, Universit\'e de Montr\'eal}, 26316 address = {Montr\'eal, Canada}, 26317 year = {1994} 26318} 26319 26320@Article{ chen.harker:continuation, 26321 author = {B. Chen and P. T. Harker}, 26322 title = {A Continuation Method for Monotone Variational Inequalities}, 26323 journal = {Mathematical Programming}, 26324 volume = {69}, 26325 pages = {237--253}, 26326 year = {1995} 26327} 26328 26329@Article{ chen.harker:non-interior, 26330 author = {B. Chen and P. T. Harker}, 26331 title = {A Non-Interior-Point Continuation Method for Linear Complementarity Problems}, 26332 journal = {SIAM Journal on Matrix Analysis and Applications}, 26333 year = {1993}, 26334 volume = {14}, 26335 pages = {1168--1190} 26336} 26337 26338@Article{ chen.harker:smooth, 26339 author = {B. Chen and P. T. 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Cooper}, 26685 title = {A gradient method of optimizing external-beam radiotherapy treatment plans}, 26686 journal = {Radiology}, 26687 year = {1978}, 26688 volume = {128}, 26689 pages = {235--243} 26690} 26691 26692@Article{ cormack:problem, 26693 author = {A. M. Cormack}, 26694 title = {A problem in roatation therapy with x-rays}, 26695 journal = {International Journal of Radiation Oncology, Biology and Physics}, 26696 year = {1987}, 26697 volume = {13}, 26698 pages = {623--630} 26699} 26700 26701@Article{ cormack:problem*1, 26702 author = {A. M. Cormack}, 26703 title = {A problem in roatation therapy with x-rays2: dose distributions with an axis of 26704 symmetry}, 26705 journal = {International Journal of Radiation Oncology, Biology and Physics}, 26706 year = {1987}, 26707 volume = {13}, 26708 pages = {1921--1925} 26709} 26710 26711@Article{ cottle.dantzig:complementary, 26712 author = {R. W. Cottle and G. B. 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Mangasarian}, 28288 title = {Parallel Constraint Distribution}, 28289 journal = {SIAM Journal on Optimization}, 28290 year = {1991}, 28291 volume = {1}, 28292 pages = {487--500}, 28293 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28294 key = {18} 28295} 28296 28297@Article{ ferris.mangasarian:parallel*1, 28298 author = {M. C. Ferris and O. L. Mangasarian}, 28299 title = {Parallel Variable Distribution}, 28300 journal = {SIAM Journal on Optimization}, 28301 year = {1994}, 28302 volume = {4}, 28303 pages = {815--832}, 28304 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28305 key = {31} 28306} 28307 28308@Article{ ferris.meeraus.ea:computing, 28309 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28310 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28311 journal = {Optimization Methods and Software}, 28312 year = {1999}, 28313 volume = {10}, 28314 pages = {669--685}, 28315 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28316 key = {45} 28317} 28318 28319@Article{ ferris.mesnier.ea:neos, 28320 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28321 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28322 {I}nternet}, 28323 year = {2000}, 28324 journal = {{ACM} Transactions on Mathematical Software}, 28325 key = {54}, 28326 volume = {26}, 28327 pages = {1--18}, 28328 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28329 institution = {Computer Sciences Department, University of Wisconsin}, 28330 address = {Madison, Wisconsin}, 28331 number = {96-08}, 28332 type = {Mathematical Programming Technical Report}, 28333 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28334 Argonne National Laboratory}, 28335 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28336 1996} 28337} 28338 28339@InCollection{ ferris.meyer:models, 28340 author = {M. C. Ferris and R. R. Meyer}, 28341 title = {Models and Solution for On-Demand Data Delivery Problems}, 28342 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28343 key = {80}, 28344 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28345 Problems}, 28346 editor = {P. M. Pardalos}, 28347 series = {Nonconvex Optimization and its Applications}, 28348 volume = {42}, 28349 address = {Dordrect}, 28350 year = {2000}, 28351 pages = {175--188}, 28352 publisher = {Kluwer}, 28353 type = {Mathematical Programming Technical Report}, 28354 institution = {Computer Sciences Department, University of Wisconsin}, 28355 number = {99-04} 28356} 28357 28358@InProceedings{ ferris.munson.ea:homotopy, 28359 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28360 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28361 booktitle = {Numerical Analysis 1999}, 28362 key = {88}, 28363 year = {2000}, 28364 editor = {D. F. Griffiths and G. A. Watson}, 28365 series = {Research Notes in Mathematics}, 28366 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28367 address = {London}, 28368 pages = {143--167}, 28369 publisher = {Chapman and Hall}, 28370 institution = {Computer Sciences Department, University of Wisconsin}, 28371 number = {99-09}, 28372 type = {Mathematical Programming Technical Report} 28373} 28374 28375@TechReport{ ferris.munson.ea:practical, 28376 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28377 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28378 type = {Data Mining Institute Technical Report}, 28379 institution = {Computer Sciences Department, University of Wisconsin}, 28380 address = {Madison, Wisconsin}, 28381 year = {2000}, 28382 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28383 number = {00-03}, 28384 key = {92}, 28385 annote = {To appear in WSC 2000} 28386} 28387 28388@InCollection{ ferris.munson:case, 28389 author = {M. C. Ferris and T. S. Munson}, 28390 title = {Case Studies in Complementarity: Improving Model Formulation}, 28391 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28392 key = {73}, 28393 pages = {79--98}, 28394 publisher = {Springer Verlag}, 28395 year = {1999}, 28396 editor = {M. Th\'{e}ra and R. Tichatschke}, 28397 number = {477}, 28398 series = {Lecture Notes in Economics and Mathematical Systems}, 28399 address = {Berlin}, 28400 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28401 type = {Mathematical Programming Technical Report}, 28402 institution = {Computer Sciences Department, University of Wisconsin} 28403} 28404 28405@Article{ ferris.munson:complementarity, 28406 author = {M. C. Ferris and T. S. Munson}, 28407 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28408 year = {2000}, 28409 volume = {24}, 28410 pages = {165--188}, 28411 journal = {Journal of Economic Dynamics and Control}, 28412 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28413 key = {70}, 28414 type = {Mathematical Programming Technical Report}, 28415 institution = {Computer Sciences Department, University of Wisconsin}, 28416 address = {Madison, Wisconsin}, 28417 number = {98-12} 28418} 28419 28420@Misc{ ferris.munson:condor, 28421 author = {M. C. Ferris and T. S. Munson}, 28422 title = {Condor Modeling Language Interface}, 28423 organization = {Computer Sciences Department, University of Wisconsin}, 28424 address = {Madison, Wisconsin}, 28425 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28426} 28427 28428@Manual{ ferris.munson:gams, 28429 author = {M. C. Ferris and T. S. Munson}, 28430 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28431 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28432} 28433 28434@Article{ ferris.munson:interfaces, 28435 author = {M. C. Ferris and T. S. Munson}, 28436 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28437 journal = {Computational Optimization and Applications}, 28438 volume = {12}, 28439 pages = {207--227}, 28440 year = {1999}, 28441 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28442 key = {63}, 28443 institution = {Computer Sciences Department, University of Wisconsin}, 28444 address = {Madison, Wisconsin}, 28445 number = {97-12}, 28446 type = {Mathematical Programming Technical Report} 28447} 28448 28449@TechReport{ ferris.munson:interior, 28450 author = {M. C. Ferris and T. S. Munson}, 28451 title = {Interior Point Methods for Massive Support Vector Machines}, 28452 institution = {Computer Sciences Department, University of Wisconsin}, 28453 year = {2000}, 28454 key = {94}, 28455 type = {Data Mining Institute Technical Report}, 28456 number = {00-05}, 28457 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28458 address = {Madison, Wisconsin}, 28459 annote = {Submitted to SIOPT} 28460} 28461 28462@Article{ ferris.munson:linear, 28463 author = {M. C. Ferris and T. S. Munson}, 28464 title = {Linear Programming for Emergency Broadcast Systems}, 28465 year = {1999}, 28466 journal = {{SIAG/OPT} Newsletter}, 28467 volume = {10}, 28468 pages = {6--8}, 28469 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28470 key = {76}, 28471 type = {Mathematical Programming Technical Report}, 28472 institution = {Computer Sciences Department, University of Wisconsin}, 28473 address = {Madison, Wisconsin}, 28474 number = {98-20} 28475} 28476 28477@Article{ ferris.munson:modeling, 28478 author = {M. C. Ferris and T. S. Munson}, 28479 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28480 year = {2000}, 28481 journal = {Mathematical Programming}, 28482 volume = {88}, 28483 pages = {487--506}, 28484 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28485 key = {71}, 28486 type = {Mathematical Programming Technical Report}, 28487 institution = {Computer Sciences Department, University of Wisconsin}, 28488 address = {Madison, Wisconsin}, 28489 number = {98-13} 28490} 28491 28492@TechReport{ ferris.munson:preprocessing, 28493 author = {M. C. Ferris and T. S. Munson}, 28494 title = {Preprocessing Complementarity Problems}, 28495 type = {Mathematical Programming Technical Report}, 28496 institution = {Computer Sciences Department, University of Wisconsin}, 28497 address = {Madison, Wisconsin}, 28498 year = {1999}, 28499 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28500 number = {99-07}, 28501 key = {86}, 28502 annote = {Submitted to ICCP 99} 28503} 28504 28505@TechReport{ ferris.munson:semismooth, 28506 author = {M. C. Ferris and T. S. Munson}, 28507 title = {Semismooth Support Vector Machines}, 28508 institution = {Computer Sciences Department, University of Wisconsin}, 28509 year = {2000}, 28510 key = {97}, 28511 type = {Data Mining Institute Technical Report}, 28512 number = {00-09}, 28513 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28514 address = {Madison, Wisconsin}, 28515 annote = {Submitted to Math Prog B} 28516} 28517 28518@Article{ ferris.pang:engineering, 28519 author = {M. C. Ferris and J. S. Pang}, 28520 title = {Engineering and Economic Applications of Complementarity Problems}, 28521 year = {1997}, 28522 journal = {SIAM Review}, 28523 volume = {39}, 28524 pages = {669--713}, 28525 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28526 key = {46} 28527} 28528 28529@Article{ ferris.pang:nondegenerate, 28530 author = {M. C. Ferris and J. S. Pang}, 28531 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28532 journal = {SIAM Journal on Control and Optimization}, 28533 year = {1996}, 28534 volume = {34}, 28535 pages = {244--263}, 28536 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28537 key = {35} 28538} 28539 28540@Article{ ferris.philpott:affine, 28541 author = {M. C. Ferris and A. B. Philpott}, 28542 title = {On Affine Scaling and Semi--Infinite Programming}, 28543 journal = {Mathematical Programming}, 28544 year = {1992}, 28545 volume = {56}, 28546 pages = {361--364}, 28547 key = {15} 28548} 28549 28550@Article{ ferris.philpott:interior, 28551 author = {M. C. Ferris and A. B. Philpott}, 28552 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28553 journal = {Mathematical Programming}, 28554 year = {1989}, 28555 volume = {43}, 28556 pages = {257--276}, 28557 key = {04} 28558} 28559 28560@Article{ ferris.philpott:performance, 28561 author = {M. C. Ferris and A. B. Philpott}, 28562 title = {On the Performance of {K}armarkar's Algorithm}, 28563 journal = {Journal of the Operational Research Society}, 28564 year = {1988}, 28565 volume = {39}, 28566 pages = {257--270}, 28567 key = {03} 28568} 28569 28570@InCollection{ ferris.ralph:projected, 28571 author = {M. C. Ferris and D. Ralph}, 28572 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28573 Maps}, 28574 booktitle = {Recent Advances in Nonsmooth Optimization}, 28575 publisher = {World Scientific Publishers}, 28576 year = {1995}, 28577 pages = {57--87}, 28578 editor = {D. Du and L. Qi and R. Womersley}, 28579 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28580 key = {41} 28581} 28582 28583@Article{ ferris.ruszczynski:robust, 28584 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28585 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28586 year = {2000}, 28587 journal = {Networks}, 28588 volume = {35}, 28589 pages = {181--194}, 28590 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28591 key = {60} 28592} 28593 28594@InCollection{ ferris.rutherford:accessing, 28595 author = {M. C. Ferris and T. F. Rutherford}, 28596 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28597 booktitle = {Nonlinear Optimization and Applications}, 28598 key = {48}, 28599 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28600 editor = {G. Di Pillo and F. Giannessi}, 28601 year = {1996}, 28602 pages = {141--153}, 28603 publisher = {Plenum Press}, 28604 address = {New York} 28605} 28606 28607@InCollection{ ferris.shepard:optimizing, 28608 author = {M. C. Ferris and D. M. Shepard}, 28609 title = {Optimization of Gamma Knife Radiosurgery}, 28610 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28611 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28612 publisher = {AMS}, 28613 year = {2000}, 28614 optseries = {DIMACS}, 28615 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28616 key = {91}, 28617 type = {Data Mining Institute Technical Report}, 28618 institution = {Computer Sciences Department, University of Wisconsin}, 28619 address = {Madison, Wisconsin}, 28620 number = {00-01} 28621} 28622 28623@InCollection{ ferris.sinapiromsaran:formulating, 28624 author = {M. C. Ferris and K. Sinapiromsaran}, 28625 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28626 booktitle = {Optimization}, 28627 key = {77}, 28628 publisher = {Springer-Verlag}, 28629 year = {2000}, 28630 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28631 volume = {481}, 28632 series = {Lecture Notes in Economics and Mathematical Systems}, 28633 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28634 type = {Mathematical Programming Technical Report}, 28635 institution = {Computer Sciences Department, University of Wisconsin}, 28636 address = {Madison, Wisconsin}, 28637 number = {98-21} 28638} 28639 28640@Article{ ferris.tin-loi:limit, 28641 author = {M. C. Ferris and F. Tin-Loi}, 28642 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28643 Complementarity Constraints}, 28644 year = {2001}, 28645 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28646 key = {78}, 28647 journal = {International Journal of Mechanical Sciences}, 28648 pages = {209--224}, 28649 volume = {43}, 28650 type = {Mathematical Programming Technical Report}, 28651 institution = {Computer Sciences Department, University of Wisconsin}, 28652 address = {Madison, Wisconsin}, 28653 number = {99-01} 28654} 28655 28656@Article{ ferris.tin-loi:nonlinear, 28657 author = {M. C. Ferris and F. Tin-Loi}, 28658 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28659 Elastoplasticity}, 28660 year = {1998}, 28661 key = {64}, 28662 volume = {6}, 28663 pages = {857--870}, 28664 journal = {Structural Engineering and Mechanics} 28665} 28666 28667@Article{ ferris.tin-loi:solution, 28668 author = {M. C. Ferris and F. Tin-Loi}, 28669 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28670 and Complementarity Constraints}, 28671 year = {1999}, 28672 journal = {Computer Methods in Applied Mechanics and Engineering}, 28673 volume = {174}, 28674 pages = {107--120}, 28675 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 28676 key = {66} 28677} 28678 28679@Article{ ferris.vlach:scheduling, 28680 author = {M. C. Ferris and M. Vlach}, 28681 title = {Scheduling with Earliness and Tardiness Penalties}, 28682 journal = {Naval Research Logistics Quarterly}, 28683 year = {1992}, 28684 volume = {39}, 28685 pages = {229--245}, 28686 key = {13} 28687} 28688 28689@TechReport{ ferris.zavriev:linear, 28690 author = {M. C. Ferris and S. K Zavriev}, 28691 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 28692 institution = {Computer Sciences Department, University of Wisconsin}, 28693 year = {1996}, 28694 key = {56}, 28695 address = {Madison, Wisconsin}, 28696 type = {Mathematical Programming Technical Report}, 28697 number = {96--12}, 28698 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 28699} 28700 28701@Article{ ferris:finite, 28702 author = {M. C. Ferris}, 28703 title = {Finite Termination of the Proximal Point Algorithm}, 28704 journal = {Mathematical Programming}, 28705 year = {1991}, 28706 volume = {50}, 28707 pages = {359--366}, 28708 key = {06} 28709} 28710 28711@Article{ ferris:iterative, 28712 author = {M. C. Ferris}, 28713 title = {Iterative Linear Programming Solution of Convex Programs}, 28714 journal = {Journal of Optimization Theory and Applications}, 28715 year = {1990}, 28716 volume = {65}, 28717 pages = {53--65}, 28718 key = {07} 28719} 28720 28721@Article{ ferris:linear, 28722 author = {M. C. Ferris}, 28723 title = {The Linear Complementarity Problem}, 28724 journal = {Bulletin of the American Mathematical Society}, 28725 year = {1993}, 28726 volume = {28}, 28727 pages = {169--175}, 28728 key = {27} 28729} 28730 28731@MastersThesis{ ferris:linear*1, 28732 author = {M. C. Ferris}, 28733 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 28734 Solving a Class of Structural Optimization Problems}, 28735 year = {1985}, 28736 school = {University of Cambridge}, 28737 address = {England}, 28738 key = {01} 28739} 28740 28741@TechReport{ ferris:matlab, 28742 author = {M. C. Ferris}, 28743 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 28744 institution = {Computer Sciences Department, University of Wisconsin}, 28745 year = {1998}, 28746 address = {Madison, Wisconsin}, 28747 type = {Mathematical Programming Technical Report}, 28748 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 28749 number = {98-19}, 28750 key = {75} 28751} 28752 28753@Article{ ferris:parallel, 28754 author = {M. C. Ferris}, 28755 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 28756 journal = {Mathematics of Operations Research}, 28757 year = {1994}, 28758 volume = {19}, 28759 pages = {645--658}, 28760 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 28761 key = {20} 28762} 28763 28764@TechReport{ ferris:parallel*1, 28765 author = {M. C. Ferris}, 28766 title = {Parallel Solution of Extremely Large Knapsack Problems}, 28767 institution = {Computer Sciences Department, University of Wisconsin}, 28768 year = {1989}, 28769 address = {Madison, Wisconsin}, 28770 number = {842}, 28771 key = {09} 28772} 28773 28774@PhDThesis{ ferris:weak, 28775 author = {M. C. Ferris}, 28776 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 28777 year = {1988}, 28778 school = {University of Cambridge}, 28779 address = {England}, 28780 key = {02} 28781} 28782 28783@TechReport{ ferris:weak*1, 28784 author = {M. C. Ferris}, 28785 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 28786 institution = {Computer Sciences Department, University of Wisconsin}, 28787 year = {1988}, 28788 address = {Madison, Wisconsin}, 28789 number = {779}, 28790 key = {05} 28791} 28792 28793@Book{ fiacco.mccormick:nonlinear, 28794 author = {A. V. Fiacco and G. P. McCormick}, 28795 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 28796 year = {1968}, 28797 publisher = {John Wiley \& Sons}, 28798 address = {New York}, 28799 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 28800} 28801 28802@Book{ fiacco:introduction, 28803 author = {A. V. Fiacco}, 28804 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 28805 year = {1983}, 28806 publisher = {Academic Press}, 28807 address = {New York} 28808} 28809 28810@Article{ fiedler.ptak:matrices, 28811 author = {M. Fiedler and V. Pt\'{a}k}, 28812 title = {On matrices with nonpositive off-diagonal elements and positive principal 28813 minors}, 28814 journal = {Czechoslovak Mathematics Journal}, 28815 volume = {12}, 28816 pages = {382--400}, 28817 year = {1962} 28818} 28819 28820@Article{ fischer.kanzow:finite, 28821 author = {A. Fischer and C. Kanzow}, 28822 title = {On Finite Termination of an Iterative Method for Linear Complementarity 28823 Problems}, 28824 journal = {Mathematical Programming}, 28825 volume = {74}, 28826 pages = {279--292}, 28827 year = {1996} 28828} 28829 28830@TechReport{ fischer:constrained, 28831 author = {A. Fischer}, 28832 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 28833 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 28834 year = {1995}, 28835 type = {Technical Report}, 28836 number = {MATH-NM-10-1995}, 28837 address = {Dresden} 28838} 28839 28840@Article{ fischer:local, 28841 author = {A. Fischer}, 28842 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 28843 weak conditions}, 28844 journal = {Optimization Methods and Software}, 28845 year = {1995}, 28846 volume = {6}, 28847 pages = {83--107} 28848} 28849 28850@InCollection{ fischer:ncp-function, 28851 author = {A. Fischer}, 28852 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 28853 booktitle = {Recent Advances in Nonsmooth Optimization}, 28854 publisher = {World Scientific Publishers}, 28855 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 28856 year = {1995}, 28857 pages = {88--105} 28858} 28859 28860@Article{ fischer:newton-type, 28861 author = {A. Fischer}, 28862 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 28863 Problems}, 28864 journal = {Journal of Optimization Theory and Applications}, 28865 year = {1995}, 28866 volume = {86}, 28867 pages = {585--608} 28868} 28869 28870@Article{ fischer:solution, 28871 author = {A. Fischer}, 28872 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 28873 Functions}, 28874 year = {1997}, 28875 journal = {Mathematical Programming}, 28876 pages = {513--532} 28877} 28878 28879@Article{ fischer:special, 28880 author = {A. Fischer}, 28881 title = {A Special {N}ewton--Type Optimization Method}, 28882 journal = {Optimization}, 28883 year = {1992}, 28884 volume = {24}, 28885 pages = {269--284} 28886} 28887 28888@Article{ fisher:use, 28889 author = {R. A. Fisher}, 28890 title = {The Use of Multiple Measurements in Taxonomic Problems}, 28891 journal = {Annual Eugenics}, 28892 year = {1936}, 28893 volume = {7}, 28894 number = {Part II}, 28895 pages = {179--188} 28896} 28897 28898@Book{ fishman:principles, 28899 author = {G. Fishman}, 28900 title = {Principles of Discrete Event Simulation}, 28901 publisher = {Wiley}, 28902 address = {New York, NY}, 28903 year = {1978} 28904} 28905 28906@Article{ fitchard.aldridge.ea:registration, 28907 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 28908 title = {Registration of Synthetic Tomographic Projection Data Sets Using 28909 Cross-Correlation}, 28910 journal = {Physics in Medicine and Biology}, 28911 year = {1998}, 28912 volume = {43}, 28913 pages = {1645--1657} 28914} 28915 28916@Article{ fletcher.matthews:stable, 28917 author = {R. Fletcher and S. P. J. Matthews}, 28918 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 28919 journal = {Mathematical Programming}, 28920 year = {1984}, 28921 volume = {30}, 28922 pages = {267--284} 28923} 28924 28925@TechReport{ fletcher.maza:nonlinear, 28926 author = {R. Fletcher and E. Sainz de la Maza}, 28927 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 28928 Programming}, 28929 institution = {Department of Mathematical Sciences}, 28930 year = {1987}, 28931 address = {The University, Dundee, Scotland}, 28932 number = {NA/100}, 28933 type = {Numerical Analysis Report} 28934} 28935 28936@InCollection{ fletcher:class, 28937 author = {R. Fletcher}, 28938 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 28939 Properties}, 28940 booktitle = {Integer and Nonlinear Programming}, 28941 year = {1970}, 28942 editor = {J. Abadie}, 28943 publisher = {North--Holland}, 28944 address = {Amsterdam}, 28945 pages = {157--173} 28946} 28947 28948@Article{ fletcher:exact, 28949 author = {R. Fletcher}, 28950 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 28951 journal = {Mathematical Programming}, 28952 year = {1973}, 28953 volume = {5}, 28954 pages = {129--150} 28955} 28956 28957@Article{ fletcher:generalized, 28958 author = {R. Fletcher}, 28959 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 28960 Equations}, 28961 journal = {The Computer Journal}, 28962 year = {1968}, 28963 volume = {10}, 28964 pages = {392--399} 28965} 28966 28967@InProceedings{ fletcher:penalty, 28968 crossref = {bachem.grotschel.ea:mathematical}, 28969 author = {R. Fletcher}, 28970 title = {Penalty Functions}, 28971 pages = {87--114} 28972} 28973 28974@Book{ fletcher:practical, 28975 author = {R. Fletcher}, 28976 title = {Practical Methods of Optimization}, 28977 year = {1981}, 28978 publisher = {John Wiley \& Sons}, 28979 address = {Chichester}, 28980 volume = {1} 28981} 28982 28983@Book{ fletcher:practical*1, 28984 author = {R. Fletcher}, 28985 title = {Practical Methods of Optimization}, 28986 year = {1981}, 28987 publisher = {John Wiley \& Sons}, 28988 address = {Chichester}, 28989 volume = {2} 28990} 28991 28992@Book{ fletcher:practical*2, 28993 author = {R. Fletcher}, 28994 title = {Practical Methods of Optimization}, 28995 year = {1987}, 28996 publisher = {John Wiley \& Sons}, 28997 address = {New York}, 28998 edition = {second} 28999} 29000 29001@Unpublished{ fletcher:recent, 29002 author = {R. Fletcher}, 29003 title = {Recent Developments in Nonlinear Programming}, 29004 note = {Presentation at SOR 96, Braunchweig, Germany}, 29005 year = {1996} 29006} 29007 29008@InCollection{ fletcher:second, 29009 author = {R. Fletcher}, 29010 title = {Second Order Correction for Nondifferentiable Optimization}, 29011 booktitle = {Numerical Analysis}, 29012 year = {1982}, 29013 editor = {G. A. Watson}, 29014 publisher = {Springer-Verlag}, 29015 address = {Berlin}, 29016 pages = {85--114} 29017} 29018 29019@InCollection{ florian:mathematical, 29020 author = {M. Florian}, 29021 title = {Mathematical programming applications in national, regional, and urban planning}, 29022 editors = {M. Iri and K. Tanabe}, 29023 booktitle = {Mathematical Programming: Recent Developments and Applications}, 29024 publisher = {Kluwer Academic Publishers}, 29025 address = {Tokyo}, 29026 year = {1989} 29027} 29028 29029@Article{ florian:nonlinear, 29030 author = {M. Florian}, 29031 title = {Nonlinear Cost Network Models in Transportation Analysis}, 29032 journal = {Mathematical Programming Study}, 29033 year = {1986}, 29034 volume = {26}, 29035 pages = {167--196} 29036} 29037 29038@Article{ flynn:computer, 29039 author = {M.~J. 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Gill}, 29084 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 29085 institution = {Department of Mathematics, University of California}, 29086 year = {1996}, 29087 type = {Report NA}, 29088 number = {96-3}, 29089 address = {San Diego} 29090} 29091 29092@InCollection{ fortin.glowinski:decomposition-coordination, 29093 author = {M. Fortin and R. Glowinski}, 29094 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 29095 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 29096 Problems}, 29097 publisher = {North-Holland}, 29098 year = {1983}, 29099 editor = {M. Fortin and R. Glowinski}, 29100 address = {Amsterdam} 29101} 29102 29103@Misc{ foster.kesselman:globus, 29104 author = {I. Foster and C. Kesselman}, 29105 title = {The Globus Project}, 29106 howpublished = {www.globus.org} 29107} 29108 29109@Article{ foster.kesselman:globus*1, 29110 author = {I. Foster and C. 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Gao}, 29436 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 29437 Conditions}, 29438 type = {Manuscript}, 29439 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 29440 month = oct, 29441 year = {1994} 29442} 29443 29444@Article{ garcia-palomares.mangasarian:superlinearly, 29445 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 29446 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 29447 Optimization Problems}, 29448 journal = {Mathematical Programming}, 29449 year = {1976}, 29450 volume = {11}, 29451 pages = {1--13} 29452} 29453 29454@Article{ garcia-palomares.restuccia:global, 29455 author = {U. M. {Garcia--Palomares} and A. 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Zangwill}, 29481 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 29482 year = {1981}, 29483 publisher = {Prentice-Hall, Inc}, 29484 address = {Englewood Cliffs, New Jersey} 29485} 29486 29487@Book{ garey.johnson:computers, 29488 author = {M. R. Garey and D. S. Johnson}, 29489 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 29490 year = {1979}, 29491 publisher = {W.H. Freeman and Company}, 29492 address = {San Francisco} 29493} 29494 29495@Article{ garey.tarjan.ea:one-processor, 29496 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 29497 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 29498 journal = {Mathematics of Operations Research}, 29499 year = {1988}, 29500 volume = {13}, 29501 pages = {330--348} 29502} 29503 29504@Book{ garfinkel.nemhauser:integer, 29505 author = {R. S. Garfinkel and G. L. Nemhauser}, 29506 title = {Integer Programming}, 29507 year = {1972}, 29508 publisher = {John Wiley \& Sons}, 29509 address = {New York} 29510} 29511 29512@Book{ gass:linear, 29513 author = {S. Gass}, 29514 title = {Linear Programming Methods and Applications}, 29515 edition = {Fifth}, 29516 publisher = {Boyd and Fraser Publishing Company}, 29517 address = {Danvers, Massachusetts}, 29518 year = {1985} 29519} 29520 29521@InProceedings{ gay:combining, 29522 author = {D. M. Gay}, 29523 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 29524 booktitle = {Sparse Matrix Proceedings 1978}, 29525 editor = {I. S. Duff and G. W. Stewart}, 29526 year = {1978}, 29527 organization = {SIAM}, 29528 address = {Philadelphia, Pennsylvania}, 29529 pages = {313--334} 29530} 29531 29532@Article{ gay:electronic, 29533 author = {D. M. Gay}, 29534 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 29535 journal = {{COAL} Newsletter}, 29536 year = {1985}, 29537 volume = {13}, 29538 pages = {10--12} 29539} 29540 29541@TechReport{ gay:hooking, 29542 author = {D. M. Gay}, 29543 title = {Hooking Your Solver to {AMPL}}, 29544 year = {1997}, 29545 institution = {Bell Laboratories}, 29546 address = {Murray Hill, New Jersey}, 29547 note = {Revised 1994, 1997} 29548} 29549 29550@Article{ gay:variant, 29551 author = {D. Gay}, 29552 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 29553 Form}, 29554 journal = {Mathematical Programming}, 29555 year = {1987}, 29556 volume = {37}, 29557 pages = {81--90} 29558} 29559 29560@Article{ geiger.kanzow:resolution, 29561 author = {C. Geiger and C. Kanzow}, 29562 title = {On the Resolution of Monotone Complementarity Problems}, 29563 journal = {Computational Optimization and Applications}, 29564 volume = {5}, 29565 year = {1996}, 29566 pages = {155--173} 29567} 29568 29569@Book{ geist.beguelin.ea:pvm, 29570 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 29571 V. S. Sunderam}, 29572 title = {{PVM}: Parallel Virtual Machine}, 29573 publisher = {MIT Press}, 29574 address = {Cambridge, Massachusetts}, 29575 year = {1994} 29576} 29577 29578@Article{ gendron.crainic:parallel, 29579 author = {B. Gendron and T. G. Crainic}, 29580 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 29581 journal = {Operations Research}, 29582 year = {1994}, 29583 volume = {42}, 29584 pages = {1042--1060} 29585} 29586 29587@Article{ george:automatic, 29588 author = {A. George}, 29589 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 29590 journal = {SIAM Journal on Numerical Analysis}, 29591 vol = {17}, 29592 pages = {740--751}, 29593 year = {1980} 29594} 29595 29596@InProceedings{ georges-schleuter:asparagos, 29597 crossref = {schaeffer:third}, 29598 author = {M. Georges--Schleuter}, 29599 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 29600 pages = {416--421} 29601} 29602 29603@Article{ georgiou:comments, 29604 author = {G. M. Georgiou}, 29605 title = {Comments On Hidden Nodes in Neural Nets}, 29606 journal = {IEEE Transactions on Circuits and Systems}, 29607 year = {1991}, 29608 volume = {38}, 29609 pages = {1410} 29610} 29611 29612@TechReport{ gertz.linderoth.ea:object-oriented, 29613 author = {M. Gertz and J. Linderoth and S. Wright}, 29614 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 29615 institution = {MCS Division, Argonne National Laboratory}, 29616 year = {in preparation} 29617} 29618 29619@Article{ ghellinck.vial:polynomial, 29620 author = {G. de Ghellinck and J.--Ph. Vial}, 29621 title = {A Polynomial {N}ewton Method for Linear Programming}, 29622 journal = {Algorithmica}, 29623 year = {1986}, 29624 volume = {1}, 29625 pages = {425--453} 29626} 29627 29628@InCollection{ gilbert.ng:predicting, 29629 author = {J. R. Gilbert and E. Ng}, 29630 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 29631 year = {1993}, 29632 booktitle = {Graph Theory and Sparse Matrix Computation}, 29633 editor = {A. George and J. Gilbert and J. Liu}, 29634 publisher = {Springer-Verlag} 29635} 29636 29637@Article{ gilbert-lemarechal, 29638 author = {J. C. Gilbert and C. Lemarechal}, 29639 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 29640 journal = {Mathematical Programming}, 29641 year = {1989}, 29642 volume = {45}, 29643 pages = {407--434} 29644} 29645 29646@Article{ gill.murray.ea:computing, 29647 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29648 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 29649 journal = {SIAM Journal on Scientific and Statistical Computing}, 29650 year = {1983}, 29651 volume = {4}, 29652 pages = {310--321} 29653} 29654 29655@Article{ gill.murray.ea:maintaining, 29656 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29657 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 29658 year = {1987}, 29659 journal = {Linear Algebra and Its Applications}, 29660 volume = {88/89}, 29661 pages = {239--270} 29662} 29663 29664@Book{ gill.murray.ea:practical, 29665 author = {P. E. Gill and W. Murray and M. H. Wright}, 29666 title = {Practical Optimization}, 29667 year = {1981}, 29668 publisher = {Academic Press}, 29669 address = {London} 29670} 29671 29672@Article{ gill.murray.ea:practical*1, 29673 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29674 title = {A Practical Anti-Cycling Procedure for Linearly Constrained Optimization}, 29675 journal = {Mathematical Programming}, 29676 year = {1989}, 29677 volume = {45}, 29678 pages = {437--474} 29679} 29680 29681@Article{ gill.murray.ea:projected, 29682 author = {P. E. Gill and W. Murray and M. A. Saunders and J. A. Tomlin and M. H. Wright}, 29683 title = {On Projected {N}ewton Barrier Methods for Linear Programming and an Equivalence 29684 to {K}armarkar's Projective Method}, 29685 journal = {Mathematical Programming}, 29686 year = {1986}, 29687 volume = {36}, 29688 pages = {183--209} 29689} 29690 29691@Article{ gill.murray:newton-type, 29692 author = {P. E. Gill and W. 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Maguregui}, 32807 title = {A modified {N}ewton algorithm for functions over convex sets}, 32808 crossref = {mangasarian.meyer.ea:nonlinear*3}, 32809 pages = {461--473} 32810} 32811 32812@PhDThesis{ maguregui:regular, 32813 author = {J. Maguregui}, 32814 title = {Regular Multivalued Functions and Algorithmic Applications}, 32815 year = {1977}, 32816 address = {Madison, Wisconsin}, 32817 school = {Computer Sciences Department, University of Wisconsin} 32818} 32819 32820@Article{ mahey.oualibouch.ea:proximal, 32821 author = {P. Mahey and S. Oualibouch and D. T. Pham}, 32822 title = {Proximal Decomposition on the Graph of a Maximal Monotone Operator}, 32823 journal = {SIAM Journal on Optimization}, 32824 year = {1995}, 32825 volume = {5}, 32826 pages = {454--466} 32827} 32828 32829@Article{ mahey.pham:partial, 32830 author = {P. Mahey and D. T. Pham}, 32831 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 32832 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 32833 year = {1993}, 32834 volume = {27}, 32835 pages = {375--392} 32836} 32837 32838@InCollection{ maier.novati:shakedown, 32839 author = {G. Maier and G. Novati}, 32840 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 32841 geometric effects with reference to discrete structural models}, 32842 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 32843 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 32844 publisher = {Pineridge Press}, 32845 address = {Swansea}, 32846 year = {1990}, 32847 pages = {451--471} 32848} 32849 32850@Article{ maier:incremental, 32851 author = {G. Maier}, 32852 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 32853 Instabilizing Effects}, 32854 journal = {International Journal of Solids and Structures}, 32855 volume = {7}, 32856 year = {1971}, 32857 pages = {345--372} 32858} 32859 32860@InCollection{ maier:inverse, 32861 author = {G. Maier}, 32862 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 32863 booktitle = {Serie VIII}, 32864 publisher = {Academia Nazionale dei Lincei}, 32865 year = {1981}, 32866 volume = {LXX}, 32867 pages = {203--209} 32868} 32869 32870@Article{ maier:matrix, 32871 author = {G. Maier}, 32872 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 32873 yield planes}, 32874 journal = {Meccanica}, 32875 volume = {5}, 32876 year = {1970}, 32877 pages = {54--66} 32878} 32879 32880@Article{ maier:quadratic, 32881 author = {G. Maier}, 32882 title = {A quadratic programming approach for certain classes of nonlinear structural 32883 problems}, 32884 journal = {Meccanica}, 32885 volume = {3}, 32886 year = {1968}, 32887 pages = {121--130} 32888} 32889 32890@Book{ manber:introduction, 32891 author = {U. Manber}, 32892 title = {Introduction to Algorithms: {A} Creative Approach}, 32893 year = {1989}, 32894 publisher = {Addison-Wesley} 32895} 32896 32897@Article{ mangasarian.deleone:error, 32898 author = {O. L. Mangasarian and R. {De~Leone}}, 32899 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 32900 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 32901 journal = {Applied Mathematics and Optimization}, 32902 year = {1988}, 32903 volume = {17}, 32904 pages = {1--14} 32905} 32906 32907@Article{ mangasarian.deleone:parallel, 32908 author = {O. L. Mangasarian and R. {De~Leone}}, 32909 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 32910 Problems and Linear Programs}, 32911 journal = {Journal of Optimization Theory and Applications}, 32912 year = {1987}, 32913 volume = {54}, 32914 pages = {437--446} 32915} 32916 32917@Article{ mangasarian.fromovitz:fritz, 32918 author = {O. L. Mangasarian and S. Fromovitz}, 32919 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 32920 and inequality constraints}, 32921 journal = {Journal of Mathematical Analysis and its Applications}, 32922 year = {1967}, 32923 volume = {17}, 32924 pages = {37--47} 32925} 32926 32927@Article{ mangasarian.mclinden:simple, 32928 author = {O. L. Mangasarian and L. McLinden}, 32929 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 32930 Programs}, 32931 journal = {Mathematical Programming}, 32932 year = {1985}, 32933 volume = {32}, 32934 pages = {32--40} 32935} 32936 32937@Article{ mangasarian.meyer:nonlinear, 32938 author = {O. L. Mangasarian and R. R. Meyer}, 32939 title = {Nonlinear Perturbation of Linear Programs}, 32940 journal = {SIAM Journal on Control and Optimization}, 32941 year = {1979}, 32942 volume = {17}, 32943 pages = {745--752} 32944} 32945 32946@TechReport{ mangasarian.musicant:active, 32947 author = {O. L. Mangasarian and David R. Musicant}, 32948 title = {Active Set Support Vector Machine Classification}, 32949 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 32950 year = {2000}, 32951 number = {00-04}, 32952 address = {Madison, Wisconsin} 32953} 32954 32955@TechReport{ mangasarian.musicant:lagrangian, 32956 author = {O. L. Mangasarian and D. R. Musicant}, 32957 title = {Lagrangian Support Vector Machines}, 32958 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 32959 year = {2000}, 32960 number = {00-06}, 32961 address = {Madison, Wisconsin} 32962} 32963 32964@TechReport{ mangasarian.musicant:robust, 32965 author = {O. L. Mangasarian and David R. Musicant}, 32966 title = {Robust Linear and Support Vector Regression}, 32967 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 32968 year = {1999}, 32969 number = {99-09}, 32970 address = {Madison, Wisconsin} 32971} 32972 32973@Article{ mangasarian.musicant:successive, 32974 author = {O. L. Mangasarian and David R. Musicant}, 32975 title = {Successive Overrelaxation for Support Vector Machines}, 32976 journal = {IEEE Transactions on Neural Networks}, 32977 volume = {10}, 32978 year = {1999}, 32979 pages = {1032-1037} 32980} 32981 32982@Article{ mangasarian.pang:exact, 32983 author = {O. L. Mangasarian and J. S. Pang}, 32984 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 32985 Constraints}, 32986 journal = {Optimization}, 32987 year = {1997}, 32988 volume = {42}, 32989 pages = {1--8} 32990} 32991 32992@Article{ mangasarian.pang:extended, 32993 author = {O. L. Mangasarian and J. S. Pang}, 32994 title = {The Extended Linear Complementarity Problem}, 32995 journal = {SIAM Journal on Matrix Analysis and Applications}, 32996 year = {1994}, 32997 volume = {16} 32998} 32999 33000@Article{ mangasarian.ren:error, 33001 author = {O. L. Mangasarian and J. Ren}, 33002 title = {New error bounds for the nonlinear complementarity problem}, 33003 year = {1994}, 33004 volume = {1}, 33005 pages = {49--56}, 33006 journal = {Communications on Applied Nonlinear Analysis} 33007} 33008 33009@Article{ mangasarian.ren:improved, 33010 author = {O. L. Mangasarian and J. Ren}, 33011 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 33012 year = {1994}, 33013 volume = {66}, 33014 journal = {Mathematical Programming}, 33015 pages = {241--255} 33016} 33017 33018@InProceedings{ mangasarian.setiono.ea:pattern, 33019 crossref = {coleman.li:large-scale}, 33020 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 33021 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 33022 Diagnosis}, 33023 pages = {22--31} 33024} 33025 33026@Article{ mangasarian.shiau:error, 33027 author = {O. L. Mangasarian and T.--H. Shiau}, 33028 title = {Error Bounds for Monotone Linear Complementarity Problems}, 33029 journal = {Mathematical Programming}, 33030 year = {1986}, 33031 volume = {36}, 33032 pages = {81--89} 33033} 33034 33035@Article{ mangasarian.shiau:lipschitz, 33036 author = {O. L. Mangasarian and T.--H. Shiau}, 33037 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 33038 Complementarity Problems}, 33039 journal = {SIAM Journal on Control and Optimization}, 33040 year = {1987}, 33041 volume = {25}, 33042 pages = {583--595} 33043} 33044 33045@Article{ mangasarian.solodov:nonlinear, 33046 author = {O. L. Mangasarian and M. V. Solodov}, 33047 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 33048 journal = {Mathematical Programming}, 33049 year = {1993}, 33050 volume = {62}, 33051 pages = {277--298} 33052} 33053 33054@Article{ mangasarian.solodov:serial, 33055 author = {O. L. Mangasarian and M. V. Solodov}, 33056 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 33057 Minimization}, 33058 year = {1994}, 33059 journal = {Optimization Methods and Software}, 33060 volume = {4}, 33061 pages = {103--116} 33062} 33063 33064@Article{ mangasarian.street.ea:breast, 33065 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 33066 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 33067 journal = {Operations Research}, 33068 year = {1995}, 33069 volume = {43}, 33070 pages = {570--577} 33071} 33072 33073@Article{ mangasarian.wolberg:cancer, 33074 author = {O. L. Mangasarian and W. H. Wolberg}, 33075 title = {Cancer Diagnosis via Linear Programming}, 33076 journal = {SIAM News}, 33077 year = {1990}, 33078 volume = {23}, 33079 pages = {1 \& 18} 33080} 33081 33082@InCollection{ mangasarian:applications, 33083 author = {O. L. Mangasarian}, 33084 title = {Some Applications of Penalty Functions in Mathematical Programming}, 33085 booktitle = {Optimization and Related Fields}, 33086 year = {1986}, 33087 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 33088 publisher = {Springer-Verlag}, 33089 address = {Heidelberg}, 33090 pages = {307--329}, 33091 note = {Lecture Notes in Mathematics 1190} 33092} 33093 33094@Article{ mangasarian:characterization, 33095 author = {O. L. Mangasarian}, 33096 title = {Characterization of linear complementarity problems as linear programs}, 33097 journal = {Mathematical Programming Study}, 33098 year = {1978}, 33099 volume = {7}, 33100 pages = {74--87} 33101} 33102 33103@InProceedings{ mangasarian:condition, 33104 author = {O. L. Mangasarian}, 33105 title = {A condition number for linear inequalities and linear programs}, 33106 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 33107 1981}, 33108 year = {1981}, 33109 editor = {G. Bamberg and O. Opitz}, 33110 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 33111 address = {Konigstein}, 33112 pages = {3--15} 33113} 33114 33115@Article{ mangasarian:convergence, 33116 author = {O. L. Mangasarian}, 33117 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 33118 Symmetric Monotone Linear Complementarity Problem}, 33119 journal = {SIAM Journal on Optimization}, 33120 volume = {1}, 33121 pages = {114--122}, 33122 year = {1991} 33123} 33124 33125@Article{ mangasarian:equivalence, 33126 author = {O. L. Mangasarian}, 33127 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 33128 journal = {SIAM Journal on Applied Mathematics}, 33129 year = {1976}, 33130 volume = {31}, 33131 pages = {89--92} 33132} 33133 33134@Article{ mangasarian:error, 33135 author = {O. L. Mangasarian}, 33136 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 33137 journal = {ORSA Journal on Computing}, 33138 volume = {15}, 33139 pages = {187--192}, 33140 year = {1994} 33141} 33142 33143@Article{ mangasarian:error*1, 33144 author = {O. L. Mangasarian}, 33145 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 33146 journal = {Mathematical Programming}, 33147 year = {1990}, 33148 volume = {48}, 33149 pages = {437--445} 33150} 33151 33152@Article{ mangasarian:generalized, 33153 author = {O. L. Mangasarian}, 33154 title = {Generalized Linear Complementarity Problems as Linear Programs}, 33155 journal = {Methods of Operations Research}, 33156 year = {1979}, 33157 editor = {W. Oettli and F. Steffens}, 33158 volume = {31}, 33159 pages = {393--402} 33160} 33161 33162@InCollection{ mangasarian:generalized*1, 33163 author = {O. L. Mangasarian}, 33164 title = {Generalized Support Vector Machines}, 33165 year = {2000}, 33166 pages = {135-146}, 33167 booktitle = {Advances in Large Margin Classifiers}, 33168 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 33169 publisher = {MIT Press}, 33170 address = {Cambridge, MA} 33171} 33172 33173@Article{ mangasarian:global, 33174 author = {O. L. Mangasarian}, 33175 title = {Global error bounds for monotone affine variational inequality problems}, 33176 journal = {Linear Algebra and Its Applications}, 33177 year = {1992}, 33178 pages = {153--164} 33179} 33180 33181@InCollection{ mangasarian:least, 33182 author = {O. L. Mangasarian}, 33183 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 33184 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 33185 year = {1990}, 33186 publisher = {Oxford University Press}, 33187 address = {New York}, 33188 pages = {217--221} 33189} 33190 33191@Article{ mangasarian:least-norm, 33192 author = {O. L. Mangasarian}, 33193 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 33194 Problem}, 33195 journal = {Journal of Mathematical Analysis and Applications}, 33196 year = {1983}, 33197 volume = {92}, 33198 pages = {240--251} 33199} 33200 33201@Article{ mangasarian:linear, 33202 author = {O. L. Mangasarian}, 33203 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 33204 journal = {Mathematical Programming}, 33205 year = {1976}, 33206 volume = {10}, 33207 pages = {263--270} 33208} 33209 33210@Article{ mangasarian:linear*1, 33211 author = {O. L. Mangasarian}, 33212 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 33213 journal = {Operations Research}, 33214 year = {1965}, 33215 volume = {13}, 33216 pages = {444--452} 33217} 33218 33219@Article{ mangasarian:locally, 33220 author = {O. L. Mangasarian}, 33221 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 33222 Complementarity Problems}, 33223 journal = {Mathematical Programming}, 33224 year = {1980}, 33225 volume = {19}, 33226 pages = {200--212} 33227} 33228 33229@InCollection{ mangasarian:machine, 33230 author = {O. L. Mangasarian}, 33231 title = {Machine Learning via Polyhedral Concave Minimization}, 33232 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 33233 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 33234 pages = {175-188}, 33235 year = {1996}, 33236 address = {Heidelberg}, 33237 publisher = {Physica-Verlag A Springer-Verlag Company} 33238} 33239 33240@Article{ mangasarian:mathematical, 33241 author = {O. L. Mangasarian}, 33242 title = {Mathematical Programming in Neural Networks}, 33243 journal = {ORSA Journal on Computing}, 33244 volume = {5}, 33245 pages = {349--360}, 33246 year = {1993} 33247} 33248 33249@InProceedings{ mangasarian:mathematical*1, 33250 author = {O. L. Mangasarian}, 33251 title = {Mathematical Programming in Machine Learning}, 33252 booktitle = {Nonlinear Optimization and Applications}, 33253 editor = {G. Di Pillo and F. Giannessi}, 33254 publisher = {Plenum Publishing}, 33255 address = {New York}, 33256 pages = {283--295}, 33257 year = {1996} 33258} 33259 33260@Article{ mangasarian:mathematical*2, 33261 author = {O. L. Mangasarian}, 33262 title = {Mathematical Programming in Data Mining}, 33263 journal = {Data Mining and Knowledge Discovery}, 33264 volume = {1}, 33265 year = {1997}, 33266 pages = {183-201} 33267} 33268 33269@Article{ mangasarian:multi-surface, 33270 author = {O. L. Mangasarian}, 33271 title = {Multi-surface Method of Pattern Separation}, 33272 journal = {IEEE Transactions on Information Theory}, 33273 year = {1968}, 33274 volume = {IT-14}, 33275 pages = {801--807} 33276} 33277 33278@Book{ mangasarian:nonlinear, 33279 author = {O. L. Mangasarian}, 33280 title = {Nonlinear Programming}, 33281 year = {1969}, 33282 publisher = {McGraw--Hill}, 33283 address = {New York}, 33284 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 33285} 33286 33287@Article{ mangasarian:normal, 33288 author = {O. L. Mangasarian}, 33289 title = {Normal Solutions of Linear Programs}, 33290 journal = {Mathematical Programming Study}, 33291 year = {1984}, 33292 volume = {22}, 33293 pages = {206--216} 33294} 33295 33296@Article{ mangasarian:optimal, 33297 author = {O. L. Mangasarian}, 33298 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 33299 Linear Programs}, 33300 journal = {Journal of Optimization Theory and Applications}, 33301 year = {1981}, 33302 volume = {35}, 33303 pages = {123--128} 33304} 33305 33306@Article{ mangasarian:parallel, 33307 author = {O. L. Mangasarian}, 33308 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 33309 journal = {SIAM Journal on Control and Optimization}, 33310 volume = {33}, 33311 pages = {1916--1925}, 33312 year = {1995} 33313} 33314 33315@TechReport{ mangasarian:regularized, 33316 author = {O. L. Mangasarian}, 33317 title = {Regularized Linear Programs with Equilibrium Constraints}, 33318 institution = {Computer Sciences Department, University of Wisconsin}, 33319 year = {1997}, 33320 address = {Madison, Wisconsin}, 33321 type = {Mathematical Programming Technical Report}, 33322 number = {97--13}, 33323 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/97-13.ps} 33324} 33325 33326@Article{ mangasarian:simple, 33327 author = {O. L. Mangasarian}, 33328 title = {A Simple Characterization of Solution Sets of Convex Programs}, 33329 journal = {Operations Research Letters}, 33330 year = {1988}, 33331 volume = {7}, 33332 pages = {21--26} 33333} 33334 33335@Article{ mangasarian:solution, 33336 author = {O. L. Mangasarian}, 33337 title = {Solution of Symmetric Linear Complementarity Problems by Iterative Methods}, 33338 journal = {Journal of Optimization Theory and Applications}, 33339 year = {1977}, 33340 month = aug, 33341 volume = {22}, 33342 pages = {465--485} 33343} 33344 33345@Article{ mangasarian:stable, 33346 author = {O. L. Mangasarian}, 33347 title = {A Stable Theorem of the Alternative: An Extension of the {G}ordan Theorem}, 33348 journal = {Linear Algebra and Its Applications}, 33349 year = {1981}, 33350 volume = {41}, 33351 pages = {209--223} 33352} 33353 33354@Article{ mangasarian:sufficiency, 33355 author = {O. L. Mangasarian}, 33356 title = {Sufficiency of Exact Penalty Minimization}, 33357 journal = {SIAM Journal on Control and Optimization}, 33358 year = {1985}, 33359 month = jan, 33360 volume = {23}, 33361 pages = {30--37} 33362} 33363 33364@Article{ mangasarian:unconstrained, 33365 author = {O. L. 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Petri}, 35089 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35090 publisher = {Harvard University Press}, 35091 year = {1984} 35092} 35093 35094@InProceedings{ petrzykowski:application, 35095 author = {T. Petrzykowski}, 35096 title = {Application of the Steepest Ascent Method to Concave Programming}, 35097 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35098 year = {1962}, 35099 publisher = {North--Holland}, 35100 address = {Amsterdam}, 35101 pages = {185--189} 35102} 35103 35104@InProceedings{ pettey.leuze.ea:parallel, 35105 crossref = {grefenstette:genetic}, 35106 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35107 title = {A Parallel Genetic Algorithm}, 35108 pages = {155--161} 35109} 35110 35111@InProceedings{ pettey.leuze:theoretical, 35112 crossref = {schaeffer:third}, 35113 author = {C. C. Pettey and M. R. Leuze}, 35114 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35115 pages = {398--405} 35116} 35117 35118@Book{ pfeiffer.glocker:multibody, 35119 author = {F. Pfeiffer and C. Glocker}, 35120 title = {Multibody Dynamics with Unilateral Contact}, 35121 year = {1996}, 35122 publisher = {John Wiley \& Sons} 35123} 35124 35125@TechReport{ pierro.iusem:convergence, 35126 author = {A. R. de Pierro and A. N. Iusem}, 35127 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35128 Linear Complementarity Problems}, 35129 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35130 year = {1990}, 35131 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35132} 35133 35134@InCollection{ pillo.grippo.ea:class, 35135 author = {G. Di Pillo and L. Grippo and F. 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Bonnans}, 35322 title = {Infeasible path following algorithms for linear complementarity problems}, 35323 institution = {INRIA}, 35324 year = {1994}, 35325 month = dec, 35326 number = {RR--2445}, 35327 type = {Research Report} 35328} 35329 35330@Article{ potra.sheng:large-step, 35331 author = {F. A. Potra and R. Sheng}, 35332 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 35333 year = {1997}, 35334 journal = {SIAM Journal on Optimization}, 35335 volume = {7}, 35336 pages = {318--335} 35337} 35338 35339@Article{ potra:infeasible, 35340 author = {F. A. Potra}, 35341 title = {An infeasible interior-point predictor-corrector algorithm for linear 35342 programming}, 35343 journal = {SIAM Journal on Optimization}, 35344 year = {1996}, 35345 volume = {6}, 35346 pages = {19--32} 35347} 35348 35349@TechReport{ potra:onl, 35350 author = {F. A. 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Pruyne}, 35492 title = {Resource Management Services for Parallel Applications}, 35493 school = {University of Wisconsin--Madison}, 35494 year = {1996}, 35495 address = {Madison, Wisconsin} 35496} 35497 35498@Book{ pshenichny.danilin:numerical, 35499 author = {B. N. Pshenichny and Yu. M. Danilin}, 35500 title = {Numerical Methods in Extremal Problems}, 35501 year = {1978}, 35502 publisher = {MIR Publishers}, 35503 address = {Moscow} 35504} 35505 35506@TechReport{ qi.chen:globally, 35507 author = {L. Qi and X. Chen}, 35508 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 35509 institution = {School of Mathematics, University of New South Wales}, 35510 year = {1993}, 35511 annote = {revised}, 35512 address = {Sydney} 35513} 35514 35515@Article{ qi.jiang:semismooth, 35516 author = {L. Qi and H. 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Ralph}, 35540 booktitle = {Progress in Optimization}, 35541 pages = {121--146}, 35542 series = {Applied Optimization}, 35543 volume = {30}, 35544 publisher = {Kluwer Academic Publishers}, 35545 address = {Dordrecht} 35546} 35547 35548@Article{ qi.sun:nonsmooth, 35549 author = {L. Qi and J. Sun}, 35550 title = {A Nonsmooth Version of {N}ewton's Method}, 35551 journal = {Mathematical Programming}, 35552 year = {1993}, 35553 volume = {58}, 35554 pages = {353--368} 35555} 35556 35557@Article{ qi:convergence, 35558 author = {L. Qi}, 35559 title = {Convergence Analysis of Some Algorithms for Solving Nonsmooth Equations}, 35560 journal = {Mathematics of Operations Research}, 35561 year = {1993}, 35562 volume = {18}, 35563 pages = {227--244} 35564} 35565 35566@TechReport{ qi:regular, 35567 author = {L. 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Reich}, 35807 publisher = {Longman}, 35808 address = {Harlow, Essex, England}, 35809 pages = {240--248}, 35810 series = {Pitman Research Notes in Mathematics Series No. 244} 35811} 35812 35813@Article{ robinson:implicit-function, 35814 author = {S. M. Robinson}, 35815 title = {An Implicit--Function Theorem for a Class of Nonsmooth Functions}, 35816 journal = {Mathematics of Operations Research}, 35817 year = {1991}, 35818 volume = {16}, 35819 pages = {292--309} 35820} 35821 35822@Article{ robinson:local*1, 35823 author = {S. M. Robinson}, 35824 title = {Local Epi--Continuity and Local Optimization}, 35825 journal = {Mathematical Programming}, 35826 year = {1987}, 35827 volume = {37}, 35828 pages = {208--222} 35829} 35830 35831@Article{ robinson:local*2, 35832 author = {S. M. Robinson}, 35833 title = {Local Structure of Feasible Sets in Nonlinear Programming, {P}art~{II}: 35834 Nondegeneracy}, 35835 journal = {Mathematical Programming Study}, 35836 year = {1984}, 35837 volume = {22}, 35838 pages = {217--230} 35839} 35840 35841@Article{ robinson:local*3, 35842 author = {S. M. Robinson}, 35843 title = {Local Structure of Feasible Sets in Nonlinear Programming, {P}art~{III}: 35844 Stability and Sensitivity}, 35845 journal = {Mathematical Programming Study}, 35846 year = {1987}, 35847 volume = {30}, 35848 pages = {45--66} 35849} 35850 35851@Article{ robinson:mathematical, 35852 author = {S. M. Robinson}, 35853 title = {Mathematical Foundations of Nonsmooth Embedding Methods}, 35854 journal = {Mathematical Programming}, 35855 year = {1990}, 35856 volume = {48}, 35857 pages = {221--229} 35858} 35859 35860@Article{ robinson:newtons, 35861 author = {S. M. Robinson}, 35862 title = {{N}ewton's Method for a Class of Nonsmooth Functions}, 35863 journal = {Set Valued Analysis}, 35864 year = {1994}, 35865 volume = {2}, 35866 pages = {291--305} 35867} 35868 35869@Article{ robinson:nonsingularity, 35870 author = {S. M. Robinson}, 35871 title = {Nonsingularity and Symmetry for Linear Normal Maps}, 35872 journal = {Mathematical Programming}, 35873 year = {1993}, 35874 volume = {62}, 35875 pages = {415--425} 35876} 35877 35878@InCollection{ robinson:nonsmooth, 35879 author = {S. M. Robinson}, 35880 title = {Nonsmooth Continuation for Generalized Equations}, 35881 year = {1997}, 35882 pages = {282--291}, 35883 editors = {P. Gritzmann and R. Horst and E. Sachs and R. Tichatschke}, 35884 booktitle = {Recent Advances in Optimization}, 35885 series = {Lecture Notes in Economics and Mathematical Systems}, 35886 volume = {452}, 35887 publisher = {Springer-Verlag}, 35888 address = {Heidelberg} 35889} 35890 35891@Article{ robinson:normal, 35892 author = {S. M. Robinson}, 35893 title = {Normal Maps Induced by Linear Transformations}, 35894 journal = {Mathematics of Operations Research}, 35895 year = {1992}, 35896 volume = {17}, 35897 pages = {691--714} 35898} 35899 35900@Article{ robinson:normed, 35901 author = {S. M. Robinson}, 35902 title = {Normed Convex Processes}, 35903 journal = {Transactions of the American Mathematical Society}, 35904 year = {1972}, 35905 volume = {174}, 35906 pages = {127--140} 35907} 35908 35909@Article{ robinson:reduction, 35910 author = {S. M. Robinson}, 35911 title = {A reduction method for variational inequalities}, 35912 journal = {Mathematical Programming}, 35913 year = {1998}, 35914 volume = {80}, 35915 pages = {161--169} 35916} 35917 35918@Article{ robinson:regularity, 35919 author = {S. M. Robinson}, 35920 title = {Regularity and stability for convex multivalued functions}, 35921 journal = {Mathematics of Operations Research}, 35922 year = {1976}, 35923 volume = {1}, 35924 pages = {130--143} 35925} 35926 35927@Unpublished{ robinson:shadow, 35928 author = {S. M. Robinson}, 35929 title = {Shadow {JUNK} for biblio file}, 35930 year = {1800} 35931} 35932 35933@Article{ robinson:shadow*1, 35934 author = {S. M. Robinson}, 35935 title = {Shadow Prices for Measures of Effectiveness {I}: Linear Model}, 35936 journal = {Operations Research}, 35937 year = {1993}, 35938 volume = {41}, 35939 pages = {518--535} 35940} 35941 35942@Article{ robinson:shadow*2, 35943 author = {S. M. Robinson}, 35944 title = {Shadow Prices for Measures of Effectiveness {II}: General Model}, 35945 journal = {Operations Research}, 35946 year = {1993}, 35947 volume = {41}, 35948 pages = {536--548} 35949} 35950 35951@Unpublished{ robinson:stability, 35952 author = {S. M. Robinson}, 35953 title = {Stability {JUNK} for biblio file}, 35954 year = {1800} 35955} 35956 35957@Article{ robinson:stability*1, 35958 author = {S. M. Robinson}, 35959 title = {Stability theory for systems of inequalities, {P}art {I}: linear systems}, 35960 journal = {SIAM Journal on Numerical Analysis}, 35961 year = {1975}, 35962 volume = {12}, 35963 pages = {754--769} 35964} 35965 35966@Article{ robinson:stability*2, 35967 author = {S. M. Robinson}, 35968 title = {Stability theory for systems of inequalities, {P}art {II}: Differentiable 35969 Nonlinear Systems}, 35970 journal = {SIAM Journal on Numerical Analysis}, 35971 year = {1976}, 35972 volume = {13}, 35973 pages = {497--513} 35974} 35975 35976@Article{ robinson:strongly, 35977 author = {S. M. Robinson}, 35978 title = {Strongly Regular Generalized Equations}, 35979 journal = {Mathematics of Operations Research}, 35980 year = {1980}, 35981 volume = {5}, 35982 pages = {43--62} 35983} 35984 35985@Article{ rockafellar.wets:generalized, 35986 author = {R. T. Rockafellar and R. J.--B. Wets}, 35987 title = {Generalized Linear-Quadratic Problems of Deterministic and Stochastic Optimal 35988 Control in Discrete Time}, 35989 journal = {SIAM Journal on Control and Optimization}, 35990 year = {1990}, 35991 volume = {28}, 35992 pages = {810--822} 35993} 35994 35995@Article{ rockafellar.wets:lagrangian, 35996 author = {R. T. Rockafellar and R. J.--B. Wets}, 35997 title = {A {L}agrangian Finite Generation Technique for Solving Linear-Quadratic Problems 35998 in Stochastic Programming}, 35999 journal = {Mathematical Programming Study}, 36000 year = {1986}, 36001 volume = {28}, 36002 pages = {63--93} 36003} 36004 36005@InCollection{ rockafellar.wets:linear-quadratic, 36006 author = {R. T. Rockafellar and R. J.--B. Wets}, 36007 title = {Linear-Quadratic Programming Problems with Stochastic Penalties: the Finite 36008 Generation Algorithm}, 36009 booktitle = {Stochastic Optimization}, 36010 publisher = {Springer-Verlag}, 36011 year = {1987}, 36012 editor = {V. I. Arkin and A. Shiraer and R. J.--B. Wets}, 36013 series = {Lecture Notes in Control and Information Sciences, IIASA Series No. 81}, 36014 pages = {545--560}, 36015 address = {New York, Berlin} 36016} 36017 36018@Article{ rockafellar.wets:scenarios, 36019 author = {R. T. Rockafellar and R. J.--B. Wets}, 36020 title = {Scenarios and Policy Aggregation in Optimization under Uncertainty}, 36021 journal = {Mathematics of Operations Research}, 36022 year = {1991}, 36023 volume = {10}, 36024 pages = {119--147} 36025} 36026 36027@InProceedings{ rockafellar:applications, 36028 author = {R. T. Rockafellar}, 36029 title = {New Applications of Duality in Convex Programming}, 36030 booktitle = {Proceedings of the Fourth Conference on Probability}, 36031 year = {1971}, 36032 address = {Brasov, Romania} 36033} 36034 36035@Article{ rockafellar:augmented, 36036 author = {R. T. Rockafellar}, 36037 title = {Augmented {L}agrange Multiplier Functions and Duality in Nonconvex Programming}, 36038 journal = {SIAM Journal on Control and Optimization}, 36039 year = {1974}, 36040 volume = {12}, 36041 pages = {268--285} 36042} 36043 36044@Article{ rockafellar:augmented*1, 36045 author = {R. T. Rockafellar}, 36046 title = {Augmented {L}agrangians and Applications of the Proximal Point Algorithm in 36047 Convex Programming}, 36048 journal = {Mathematics of Operations Research}, 36049 year = {1976}, 36050 volume = {1}, 36051 pages = {97--116} 36052} 36053 36054@Article{ rockafellar:characterization, 36055 author = {R. T. Rockafellar}, 36056 title = {Characterization of the subdifferentials of convex functions}, 36057 journal = {Pacific Journal of Mathematics}, 36058 year = {1966}, 36059 volume = {17}, 36060 number = {3}, 36061 pages = {497--510} 36062} 36063 36064@Article{ rockafellar:computational, 36065 author = {R. T. Rockafellar}, 36066 title = {Computational Schemes for Large--Scale Problems in Extended Linear--Quadratic 36067 Programming}, 36068 journal = {Mathematical Programming}, 36069 year = {1990}, 36070 volume = {48}, 36071 pages = {447--474} 36072} 36073 36074@Book{ rockafellar:conjugate, 36075 author = {R. T. Rockafellar}, 36076 title = {Conjugate Duality and Optimization}, 36077 year = {1974}, 36078 publisher = {SIAM}, 36079 address = {Philadelphia, Pennsylvania}, 36080 volume = {16}, 36081 series = {Conference Board of the Mathematical Sciences} 36082} 36083 36084@Book{ rockafellar:convex, 36085 author = {R. T. Rockafellar}, 36086 title = {Convex Analysis}, 36087 year = {1970}, 36088 publisher = {Princeton University Press}, 36089 address = {Princeton, New Jersey} 36090} 36091 36092@Article{ rockafellar:first-, 36093 author = {R. T. Rockafellar}, 36094 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 36095 journal = {Transactions of the American Mathematical Society}, 36096 year = {1988}, 36097 volume = {307}, 36098 pages = {75--108} 36099} 36100 36101@InProceedings{ rockafellar:generalized, 36102 author = {R. T. Rockafellar}, 36103 title = {A Generalized Approach to Linear-Quadratic Programming}, 36104 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36105 Applications}, 36106 year = {1986}, 36107 pages = {58--66}, 36108 note = {(Xi'an, China)} 36109} 36110 36111@InProceedings{ rockafellar:generalized*1, 36112 crossref = {bachem.grotschel.ea:mathematical}, 36113 author = {R. T. Rockafellar}, 36114 title = {Generalized Subgradients in Mathematical Programming}, 36115 pages = {368--390} 36116} 36117 36118@InCollection{ rockafellar:large-scale, 36119 author = {R. T. Rockafellar}, 36120 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36121 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36122 chapter = {15}, 36123 year = {1991}, 36124 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 36125 publisher = {SIAM Publications}, 36126 pages = {247--261} 36127} 36128 36129@Article{ rockafellar:linear-quadratic, 36130 author = {R. T. Rockafellar}, 36131 title = {Linear-Quadratic Programming and Optimal Control}, 36132 journal = {SIAM Journal on Control and Optimization}, 36133 year = {1987}, 36134 volume = {25}, 36135 pages = {781--814} 36136} 36137 36138@Article{ rockafellar:maximality, 36139 author = {R. T. Rockafellar}, 36140 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 36141 journal = {Transactions of the American Mathematical Society}, 36142 year = {1970}, 36143 volume = {149}, 36144 pages = {75--88} 36145} 36146 36147@InCollection{ rockafellar:monotone, 36148 author = {R. T. Rockafellar}, 36149 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 36150 crossref = {mangasarian.meyer.ea:nonlinear*3}, 36151 pages = {1--26} 36152} 36153 36154@Article{ rockafellar:monotone*1, 36155 author = {R. T. Rockafellar}, 36156 title = {Monotone Operators and the Proximal Point Algorithm}, 36157 journal = {SIAM Journal on Control and Optimization}, 36158 year = {1976}, 36159 volume = {14}, 36160 pages = {877--898} 36161} 36162 36163@Article{ rockafellar:multiplier, 36164 author = {R. T. Rockafellar}, 36165 title = {The Multiplier Method of {H}estenes and {P}owell Applied to Convex Programming}, 36166 journal = {Journal of Optimization Theory and Applications}, 36167 year = {1973}, 36168 volume = {12}, 36169 pages = {555--562} 36170} 36171 36172@Article{ rockafellar:multistage, 36173 author = {R. T. Rockafellar}, 36174 title = {Multistage Convex Programming and Discrete-Time Optimal Control}, 36175 journal = {Control and Cybernetics}, 36176 year = {1988}, 36177 volume = {17}, 36178 number = {2-3}, 36179 pages = {225--245} 36180} 36181 36182@Book{ rockafellar:network, 36183 author = {R. T. Rockafellar}, 36184 title = {Network Flows and Monotropic Optimization}, 36185 publisher = {John Wiley}, 36186 year = {1984}, 36187 address = {New York} 36188} 36189 36190@Article{ rodrigues:mixed, 36191 author = {H. C. Rodrigues}, 36192 title = {A mixed variational formulation for shape optimization of solids with contact 36193 conditions}, 36194 journal = {Structural Optimization}, 36195 volume = {6}, 36196 year = {1993}, 36197 pages = {19--28} 36198} 36199 36200@Book{ rodrigues:obstacle, 36201 author = {J. F. Rodrigues}, 36202 title = {Obstacle Problems in Mathematical Physics}, 36203 publisher = {Elsevier Publishing Company}, 36204 address = {Amsterdam}, 36205 year = {1987} 36206} 36207 36208@Book{ roos.terlaky.ea:theory, 36209 author = {C. Roos and T. Terlaky and J.--Ph. Vial}, 36210 title = {Theory and Algorithms for Linear Optimization: An Interior-Point Approach}, 36211 publisher = {John Wiley \& Sons}, 36212 year = {1997}, 36213 address = {Chichester} 36214} 36215 36216@TechReport{ rosa:decomposition, 36217 author = {C. H. Rosa}, 36218 title = {A Decomposition Technique for Equilibrium Programming under Uncertainty}, 36219 institution = {IIASA}, 36220 year = {1996}, 36221 number = {WP-96-013}, 36222 address = {A-2361 Laxenburg, Austria} 36223} 36224 36225@Article{ rosen.lane.ea:treatment, 36226 author = {I. Rosen and R. Lane and S. Morrill and J. Belli}, 36227 title = {Treatment Plan Optimization Using Linear Programming}, 36228 journal = {Medical Physics}, 36229 year = {1990}, 36230 volume = {18}, 36231 number = {2}, 36232 pages = {141--152} 36233} 36234 36235@TechReport{ rosenblatt:perceptron-a, 36236 author = {F. 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Rosenbrock}, 36265 title = {Automatic Method for Finding the Greatest or Least Value of a Function}, 36266 journal = {Computer Journal}, 36267 year = {1960}, 36268 volume = {3}, 36269 pages = {175--184} 36270} 36271 36272@Article{ roy.mukhopadhyay:pattern, 36273 author = {A. Roy and S. Mukhopadhyay}, 36274 title = {Pattern Classification Using Linear Programming}, 36275 journal = {ORSA Journal on Computing}, 36276 year = {1990}, 36277 volume = {3}, 36278 pages = {66--80} 36279} 36280 36281@Book{ rubinstein:monte, 36282 author = {R. Rubinstein}, 36283 title = {Monte Carlo Optimization, Simulation, and Sensitivity Analysis of Queueing 36284 Networks}, 36285 publisher = {Wiley}, 36286 address = {New York, NY}, 36287 year = {1986} 36288} 36289 36290@Article{ ruchala.olivera.ea:comparison, 36291 author = {K. J. Ruchala and G. H. Olivera and T. R. Mackie}, 36292 title = {A Comparison of Maximum-Likelihood and Iterative Filtered Backprojection 36293 Reconstruction Algorithms for Megavoltage {CT} on a Tomotherapy System}, 36294 journal = {Physics in Medicine and Biology, forthcoming}, 36295 year = {1999} 36296} 36297 36298@Book{ rudin:principles, 36299 author = {W. Rudin}, 36300 title = {Principles of Mathematical Analysis}, 36301 year = {1976}, 36302 publisher = {McGraw--Hill}, 36303 address = {Tokyo, Japan}, 36304 edition = {Third} 36305} 36306 36307@Book{ rudin:real, 36308 author = {W. Rudin}, 36309 title = {Real and Complex Analysis}, 36310 year = {1974}, 36311 publisher = {McGraw--Hill}, 36312 address = {Tokyo, Japan}, 36313 edition = {Second} 36314} 36315 36316@InProceedings{ rumelhart.hinton.ea:learning, 36317 author = {D. E. Rumelhart and G. E. Hinton and R. J. Williams}, 36318 title = {Learning Internal Representations by Error Propagation}, 36319 booktitle = {Parallel Distributed Processing}, 36320 year = {1986}, 36321 editor = {D. E. Rumelhart and J. L. McClelland}, 36322 publisher = {MIT Press}, 36323 address = {Cambridge, Massachusetts}, 36324 pages = {318--362} 36325} 36326 36327@Book{ rumelhart.mcclelland:parallel, 36328 author = {D. E. Rumelhart and J. L. McClelland}, 36329 title = {Parallel Distributed Processing}, 36330 year = {1986}, 36331 publisher = {MIT Press}, 36332 address = {Cambridge, Massachusetts} 36333} 36334 36335@InCollection{ ruszczynski:regularized, 36336 author = {A. Ruszczynski}, 36337 title = {On the Regularized Decomposition for Stochastic Programming Problems}, 36338 year = {1995}, 36339 booktitle = {Stochastic Programming: Numerical Techniques and Engineering Applications}, 36340 editor = {K. Marti and P. 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Waterloo}, 38835 year = {2021} 38836} 38837 38838@Article{ brookshughes1982, 38839 title = {Streamline upwind/{Petrov-Galerkin} formulations for convection dominated flows 38840 with particular emphasis on the incompressible {Navier-Stokes} equations}, 38841 author = {Alexander N Brooks and Thomas JR Hughes}, 38842 journal = {Computer methods in applied mechanics and engineering}, 38843 volume = {32}, 38844 number = {1-3}, 38845 pages = {199--259}, 38846 year = {1982}, 38847 publisher = {Elsevier} 38848} 38849 38850@InProceedings{ suhisaac2020, 38851 title = {Evaluation of a minimally synchronous algorithm for 2: 1 octree balance}, 38852 author = {Hansol Suh and Tobin Isaac}, 38853 booktitle = {SC20: International Conference for High Performance Computing, Networking, 38854 Storage and Analysis}, 38855 pages = {1--12}, 38856 year = {2020}, 38857 organization = {IEEE} 38858} 38859 38860@Misc{ alauzet2010, 38861 title = {Metric-Based Anisotropic Mesh Adaptation}, 38862 author = {Fr\'{e}d\'{e}ric Alauzet}, 38863 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 38864 year = {2010} 38865} 38866 38867@Article{ chan1994qmrcgs, 38868 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 38869 systems}, 38870 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 38871 and Tong, Charles H}, 38872 journal = {SIAM Journal on Scientific Computing}, 38873 volume = {15}, 38874 number = {2}, 38875 pages = {338--347}, 38876 year = {1994}, 38877 publisher = {SIAM} 38878} 38879 38880@Article{ ghai2019comparison, 38881 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 38882 nonsymmetric linear systems}, 38883 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 38884 journal = {Numerical Linear Algebra with Applications}, 38885 volume = {26}, 38886 number = {1}, 38887 pages = {e2215}, 38888 year = {2019}, 38889 publisher = {Wiley Online Library} 38890} 38891 38892@Article{ mishrasalacknepley2022, 38893 title = {On the order of accuracy for finite difference approximations of partial 38894 differential equations using stencil composition}, 38895 author = {Abhishek Mishra and David Salac and Matthew G. Knepley}, 38896 journal = {International Journal on Numerical Methods in Engineering}, 38897 note = {Submitted}, 38898 year = {2022} 38899} 38900 38901@Article{ nathawaniknepley2022, 38902 title = {Droplet formation simulation using mixed finite elements}, 38903 author = {Darsh K. Nathawani and Matthew G. Knepley}, 38904 journal = {Physics of Fluids}, 38905 volume = {34}, 38906 pages = {064105}, 38907 doi = {10.1063/5.0089752}, 38908 year = {2022} 38909} 38910 38911@InProceedings{ nathawaniknepley2022b, 38912 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 38913 author = {Darsh K. Nathawani and Matthew G. Knepley}, 38914 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 38915 (ICCFD11)}, 38916 editor = {Christoph Brehm and Shishir Pandya}, 38917 number = {4103}, 38918 year = {2022} 38919} 38920 38921@Article{ nathawaniknepley2023, 38922 title = {One-dimensional model to simulate shear-induced droplet formation}, 38923 author = {Darsh K. Nathawani and Matthew G. Knepley}, 38924 journal = {International Journal of Multiphase Flow}, 38925 note = {Submitted}, 38926 year = {2023} 38927} 38928 38929@InProceedings{ georgalisnathawaniknepleypatra2023, 38930 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 38931 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. Knepley and Abani 38932 Patra}, 38933 booktitle = {AIAA SciTech 2024}, 38934 note = {Accepted}, 38935 year = {2023} 38936} 38937 38938@Article{ brownbarrabeamsghaffariknepleymosesshakeristengelthompsonzhang2022, 38939 title = {Performance Portable Solid Mechanics via Matrix-Free $p$-Multigrid}, 38940 author = {Jed Brown and Valeria Barra and Natalie Beams and Leila Ghaffari and Matthew 38941 Knepley and William Moses and Rezgar Shakeri and Karen Stengel and Jeremy L. 38942 Thompson and Junchao Zhang}, 38943 doi = {10.48550/ARXIV.2204.01722}, 38944 url = {https://arxiv.org/abs/2204.01722}, 38945 publisher = {arXiv}, 38946 note = {Submitted}, 38947 year = {2022} 38948} 38949 38950@InCollection{ mayknepley2023, 38951 title = {Numerical Modeling of Subduction}, 38952 author = {Dave A. May and Matthew G. Knepley}, 38953 booktitle = {Dynamics of Plate Tectonics and Mantle Convection}, 38954 editor = {João C. Duarte}, 38955 pages = {539-571}, 38956 isbn = {978-0-323-85733-8}, 38957 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 38958 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 38959 year = {2023} 38960} 38961 38962@Article{ adamsknepley2023, 38963 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 38964 plasmas in {PETSc}}, 38965 author = {Mark F. Adams and Matthew G. Knepley}, 38966 url = {https://arxiv.org/abs/2302.10242}, 38967 note = {In preparation}, 38968 year = {2023}, 38969 petsc_uses = {DMPlex} 38970} 38971 38972@Article{ finnknepleypusztayadams2023, 38973 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 38974 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. Adams}, 38975 url = {https://arxiv.org/abs/2303.12620}, 38976 journal = {Communications in Applied Mathematics and Computational Science}, 38977 note = {Accepted}, 38978 year = {2023} 38979} 38980 38981@Article{ eggersdupont1994, 38982 title = {Drop formation in a one-dimensional approximation of the {Navier--Stokes} 38983 equation}, 38984 author = {Jens Eggers and Todd F. Dupont}, 38985 journal = {Journal of fluid mechanics}, 38986 volume = {262}, 38987 pages = {205--221}, 38988 year = {1994}, 38989 publisher = {Cambridge University Press} 38990} 38991 38992@PhDThesis{ pusztaythesis2023, 38993 title = {A Particle Basis Vlasov-Poisson-Landau Solver for Plasma Simulation in PETSc}, 38994 author = {Joseph V. Pusztay}, 38995 type = {{PhD} thesis}, 38996 school = {University at Buffalo, Department of Computer Science and Engineering}, 38997 address = {Buffalo, NY}, 38998 month = may, 38999 year = {2022} 39000} 39001 39002@PhDThesis{ finnthesis2023, 39003 title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau 39004 System}, 39005 author = {Daniel S. Finn}, 39006 type = {{PhD} thesis}, 39007 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 39008 Engineering}, 39009 address = {Buffalo, NY}, 39010 month = may, 39011 year = {2023} 39012} 39013 39014@PhDThesis{ nathawanithesis2023, 39015 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 39016 author = {Darsh Kiritbhai Nathawani}, 39017 type = {{PhD} thesis}, 39018 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 39019 Engineering}, 39020 address = {Buffalo, NY}, 39021 month = may, 39022 year = {2023} 39023} 39024 39025@article{MckayEriksonKozdon2019, 39026 title = {A computational method for earthquake cycles within anisotropic media}, 39027 author = {Maricela Best Mckay and Brittany A Erickson and Jeremy E Kozdon}, 39028 journal = {Geophysical Journal International}, 39029 volume = {219}, 39030 number = {2}, 39031 pages = {816--833}, 39032 year = {2019}, 39033} 39034 39035article{EricksonOReillyNordstrom2019, 39036 title = {Accuracy of stable, high-order finite difference methods for hyperbolic systems with non-smooth wave speeds}, 39037 author = {Brittany A Erickson and Ossian O’Reilly and Jan Nordstr{\"o}m}, 39038 journal = {Journal of Scientific Computing}, 39039 volume = {81}, 39040 pages = {2356--2387}, 39041 year = {2019}, 39042} 39043 39044@article{KozdonEricksonWilcox2021, 39045 title = {Hybridized summation-by-parts finite difference methods}, 39046 author = {Jeremy E Kozdon and Brittany A Erickson and Lucas C Wilcox}, 39047 journal = {Journal of Scientific Computing}, 39048 volume = {87}, 39049 number = {3}, 39050 pages = {85}, 39051 year = {2021}, 39052} 39053 39054@article{SEAS2022, 39055 title = {Community-driven code comparisons for three-dimensional dynamic modeling of sequences of earthquakes and aseismic slip}, 39056 author = {Junle Jiang and Brittany A Erickson and Val{\`e}re R Lambert and Jean-Paul Ampuero and Ryosuke Ando and Sylvain D Barbot and Camilla Cattania and Luca Dal Zilio and Benchun Duan and Eric M Dunham and Alice-Agnes Gabriel and Nadia Lapusta and Duo Li and Meng Li and Dunyu Liu and Yajing Liu and So Ozawa and Casper Pranger and Ylona van Dinther}, 39057 journal = {Journal of Geophysical Research: Solid Earth}, 39058 volume = {127}, 39059 number = {3}, 39060 pages = {e2021JB023519}, 39061 year = {2022}, 39062} 39063 39064@article{EricksonKozdonHarvey2022, 39065 title = {A non-stiff summation-by-parts finite difference method for the scalar wave equation in second order form: Characteristic boundary conditions and nonlinear interfaces}, 39066 author = {Brittany A Erickson and Jeremy E Kozdon and Tobias Harvey}, 39067 journal = {Journal of Scientific Computing}, 39068 volume = {93}, 39069 number = {1}, 39070 pages = {17}, 39071 year = {2022}, 39072} 39073 39074@article{RuckerEriksonKarlstromLeeGopalakrishnan2022, 39075 title = {A Computational Framework for Time-Dependent Deformation in Viscoelastic Magmatic Systems}, 39076 author = {Cody Rucker and Brittany A Erickson and Leif Karlstrom and Brian Lee and Jay Gopalakrishnan}, 39077 journal = {Journal of Geophysical Research: Solid Earth}, 39078 volume = {127}, 39079 number = {9}, 39080 pages = {e2022JB024506}, 39081 year = {2022}, 39082} 39083 39084@article{HarveyEriksonKozdon2023, 39085 title = {A High-order Accurate Summation-by-Parts Finite Difference Method for Fully-dynamic Earthquake Sequence Simulations within Sedimentary Basins}, 39086 author = {Tobias W Harvey and Brittany A Erickson and Jeremy E Kozdon}, 39087 journal = {Journal of Geophysical Research: Solid Earth}, 39088 pages = {e2022JB025357}, 39089 year = {2023}, 39090} 39091 39092@article{SEAS2023, 39093 title = {Incorporating full elastodynamic effects and dipping fault geometries in community code verification exercises for simulations of earthquake sequences and aseismic slip {(SEAS)}}, 39094 author = {Brittany A Erickson and Junle Jiang and Val{\`e}re Lambert and Sylvain D Barbot and Mohamed Abdelmeguid and Martin Almquist and Jean-Paul Ampuero and Ryosuke Ando and Camilla Cattania and Alexandre Chen and Luca Dal Zilio and Shuai Deng and Eric M. Dunham and Ahmed E. Elbanna and Alice‐Agnes Gabriel and Tobias W. Harvey and Yihe Huang and Yoshihiro Kaneko and Jeremy E. Kozdon and Nadia Lapusta and Duo Li and Meng Li and Chao Liang and Yajing Liu and So Ozawa and Andrea Perez‐Silva and Casper Pranger and Paul Segall and Yudong Sun and Prithvi Thakur and Carsten Uphoff and Ylona van Dinther and Yuyun Yang}, 39095 journal = {Bulletin of the Seismological Society of America}, 39096 volume = {113}, 39097 number = {2}, 39098 pages = {499--523}, 39099 year = {2023}, 39100} 39101
