1% 2% This file is formatted by: 3% bibtool petsc.bib -- expand.macros=on -- print.line.length=100 -- pass.comments=on 4% 5% If the reference uses PETSc, include a field listing components used, e.g. 6% petsc_uses = {KSP, SNES, TS, TAO}, 7% 8% For journal names, write out the full name, do not define abbreviations 9% 10% There are some additional historical comments below which may be of interest, 11% particularly in terms of notes about particularly impactful publications using PETSc. 12% 13 14% LiteralHTML: 15% LiteralHTML: <H2><center>Research and Publications that make use of PETSc</center></H2> 16% LiteralHTML: 17% LiteralHTML: <a name="nano"><H3><center>Nano-simulations</center></H3> 18% LiteralHTML: 19@article{veldhuizen1984d, 20 title = {{D}-stability and {K}aps-{R}entrop-methods}, 21 author = {Veldhuizen, M van}, 22 journal = {Computing}, 23 volume = {32}, 24 number = {3}, 25 pages = {229--237}, 26 year = {1984}, 27 publisher = {Springer} 28} 29 30@article{shampine1982implementation, 31 title = {Implementation of {R}osenbrock methods}, 32 author = {Shampine, Lawrence F}, 33 journal = {ACM Transactions on Mathematical Software (TOMS)}, 34 volume = {8}, 35 number = {2}, 36 pages = {93--113}, 37 year = {1982}, 38 publisher = {ACM New York, NY, USA} 39} 40 41@book{wanner1996solving, 42 title = {Solving ordinary differential equations {II}}, 43 author = {Wanner, Gerhard and Hairer, Ernst}, 44 volume = {375}, 45 year = {1996}, 46 publisher = {Springer Berlin Heidelberg New York} 47} 48 49@article{kaps1979generalized, 50 title = {Generalized {R}unge--{K}utta methods of order four with stepsize control for stiff ordinary differential equations}, 51 author = {Kaps, Peter and Rentrop, Peter}, 52 journal = {Numerische Mathematik}, 53 volume = {33}, 54 pages = {55--68}, 55 year = {1979}, 56 publisher = {Springer} 57} 58 59@book{butcher2016numerical, 60 title = {Numerical methods for ordinary differential equations}, 61 author = {Butcher, John Charles}, 62 year = {2016}, 63 publisher = {John Wiley \& Sons} 64} 65 66@article{chung1993, 67 author = {Chung, J. and Hulbert, G. M.}, 68 title = {A Time Integration Algorithm for Structural Dynamics With Improved Numerical Dissipation: The Generalized-alpha Method}, 69 journal = {Journal of Applied Mechanics}, 70 volume = {60}, 71 number = {2}, 72 pages = {371-375}, 73 year = {1993}, 74 month = {06}, 75 issn = {0021-8936}, 76 doi = {10.1115/1.2900803}, 77 url = {https://doi.org/10.1115/1.2900803}, 78 eprint = {https://asmedigitalcollection.asme.org/appliedmechanics/article-pdf/60/2/371/5463014/371\_1.pdf}, 79} 80 81@article{hosea1996analysis, 82 title = {Analysis and implementation of {TR-BDF2}}, 83 author = {Hosea, ME and Shampine, LF}, 84 journal = {Applied Numerical Mathematics}, 85 volume = {20}, 86 number = {1-2}, 87 pages = {21--37}, 88 year = {1996}, 89 publisher = {Elsevier} 90} 91 92@article{kennedy2019diagonally, 93 title = {Diagonally implicit {R}unge--{K}utta methods for stiff {ODE}s}, 94 author = {Kennedy, Christopher A and Carpenter, Mark H}, 95 journal = {Applied Numerical Mathematics}, 96 volume = {146}, 97 pages = {221--244}, 98 year = {2019}, 99 publisher = {Elsevier} 100} 101 102@inproceedings{xu2017adaptive, 103 title = {Adaptive relaxed {ADMM}: Convergence theory and practical implementation}, 104 author = {Xu, Zheng and Figueiredo, Mario AT and Yuan, Xiaoming and Studer, Christoph and Goldstein, Tom}, 105 booktitle = {Proceedings of the IEEE conference on computer vision and pattern recognition}, 106 pages = {7389--7398}, 107 year = {2017} 108} 109 110@article{hindmarsh1996time, 111 title = {Time-step limits for stable solutions of the ice-sheet equation}, 112 author = {Hindmarsh, Richard CA and Payne, Antony J}, 113 journal = {Annals of Glaciology}, 114 volume = {23}, 115 pages = {74--85}, 116 year = {1996}, 117 publisher = {Cambridge University Press} 118} 119 120@article{benson2006flexible, 121 title = {Flexible complementarity solvers for large-scale applications}, 122 author = {Benson, Steven J and Munson, Todd S}, 123 journal = {Optimization Methods and Software}, 124 volume = {21}, 125 number = {1}, 126 pages = {155--168}, 127 year = {2006}, 128 publisher ={Taylor \& Francis} 129} 130 131@article{byrd1994representations, 132 title = {Representations of quasi-{N}ewton matrices and their use in limited memory methods}, 133 author = {Byrd, Richard H and Nocedal, Jorge and Schnabel, Robert B}, 134 journal = {Mathematical Programming}, 135 volume = {63}, 136 number = {1-3}, 137 pages = {129--156}, 138 year = {1994}, 139 publisher = {Springer} 140} 141 142@article{gilbert1989some, 143 title = {Some numerical experiments with variable-storage quasi-{N}ewton algorithms}, 144 author = {Gilbert, Jean Charles and Lemar{\'e}chal, Claude}, 145 journal = {Mathematical programming}, 146 volume = {45}, 147 number = {1-3}, 148 pages = {407--435}, 149 year = {1989}, 150 publisher = {Springer} 151} 152 153@inproceedings{dener2019accelerating, 154 title = {Accelerating limited-memory quasi-{N}ewton convergence for large-scale optimization}, 155 author = {Dener, Alp and Munson, Todd}, 156 booktitle = {Computational Science--ICCS 2019: 19th International Conference, Faro, Portugal, June 12--14, 2019, Proceedings, Part III 19}, 157 pages = {495--507}, 158 year = {2019}, 159 organization = {Springer} 160} 161 162@article{park2021linear, 163 title = {Linear and nonlinear solvers for simulating multiphase flow within large-scale engineered subsurface systems}, 164 author = {Park, Heeho D and Hammond, Glenn E and Valocchi, Albert J and LaForce, Tara}, 165 journal = {Advances in Water Resources}, 166 volume = {156}, 167 pages = {104029}, 168 year = {2021}, 169 publisher = {Elsevier} 170} 171 172@inproceedings{va1981design, 173 title = {Design of optimally smoothing multi-stage schemes for the {E}uler equations}, 174 author = {Van Leer, Bram and Tai, Chang-Hsien and Powell, Kenneth}, 175 booktitle = {9th Computational Fluid Dynamics Conference}, 176 pages = {1933}, 177 year = {1981} 178} 179 180@article{pierce1997preconditioned, 181 title = {Preconditioned multigrid methods for compressible flow calculations on stretched meshes}, 182 author = {Pierce, Niles A and Giles, Michael B}, 183 journal = {Journal of Computational Physics}, 184 volume = {136}, 185 number = {2}, 186 pages = {425--445}, 187 year = {1997}, 188 publisher = {Elsevier} 189} 190 191@article{kong2016highly, 192 title = {A highly scalable multilevel {S}chwarz method with boundary geometry preserving coarse spaces for {3D} elasticity problems on domains with complex geometry}, 193 author = {Kong, Fande and Cai, Xiao-Chuan}, 194 journal = {SIAM Journal on Scientific Computing}, 195 volume = {38}, 196 number = {2}, 197 pages = {C73--C95}, 198 year = {2016}, 199 publisher = {SIAM} 200} 201 202@inproceedings{gutierrez2017accommodating, 203 title = {Accommodating thread-level heterogeneity in coupled parallel applications}, 204 author = {Guti{\'e}rrez, Samuel K and Davis, Kei and Arnold, Dorian C and Baker, Randal S and Robey, Robert W and McCormick, Patrick and 205 Holladay, Daniel and Dahl, Jon A and Zerr, R Joe and Weik, Florian and others}, 206 booktitle = {2017 {IEEE} International Parallel and Distributed Processing Symposium ({IPDPS})}, 207 pages = {469--478}, 208 year = {2017}, 209 organization = {IEEE} 210} 211 212@article{heroux2011bi, 213 title = {Bi-modal MPI and MPI+ threads computing on scalable multicore systems}, 214 author = {Heroux, Michael A and Brightwell, R and Wolf, Michael M}, 215 journal = {IJHPCA (Submitted)}, 216 year = {2011} 217} 218 219@inproceedings{bozdaug2005parallel, 220 title = {A parallel distance-2 graph coloring algorithm for distributed memory computers}, 221 author = {Bozda{\u{g}}, Doruk and Catalyurek, Umit and Gebremedhin, Assefaw H and Manne, Fredrik and Boman, Erik G and {\"O}zg{\"u}ner, F{\"u}sun}, 222 booktitle = {International conference on high performance computing and communications}, 223 pages = {796--806}, 224 year = {2005}, 225 organization = {Springer} 226} 227 228@article{dohrmann2009overlapping, 229 title = {An overlapping {S}chwarz algorithm for almost incompressible elasticity}, 230 author = {Dohrmann, Clark R and Widlund, Olof B}, 231 journal = {SIAM journal on numerical analysis}, 232 volume = {47}, 233 number = {4}, 234 pages = {2897--2923}, 235 year = {2009}, 236 publisher = {SIAM} 237} 238 239@article{dohrmann2008domain, 240 title = {Domain decomposition for less regular subdomains: Overlapping {S}chwarz in two dimensions}, 241 author = {Dohrmann, Clark R and Klawonn, Axel and Widlund, Olof B}, 242 journal = {SIAM journal on numerical analysis}, 243 volume = {46}, 244 number = {4}, 245 pages = {2153--2168}, 246 year = {2008}, 247 publisher = {SIAM} 248} 249 250@incollection{dohrmann2008family, 251 title = {A family of energy minimizing coarse spaces for overlapping {S}chwarz preconditioners}, 252 author = {Dohrmann, Clark R and Klawonn, Axel and Widlund, Olof B}, 253 booktitle = {Domain decomposition methods in science and engineering XVII}, 254 pages = {247--254}, 255 year = {2008}, 256 publisher = {Springer} 257} 258 259@book{dohrmann2008extending, 260 title = {Extending theory for domain decomposition algorithms to irregular subdomains}, 261 author = {Dohrmann, Clark R and Klawonn, Axel and Widlund, Olof B}, 262 year = {2008}, 263 publisher = {Springer} 264} 265 266@article{dryja1994schwarz, 267 title = {{S}chwarz analysis of iterative substructuring algorithms for elliptic problems in three dimensions}, 268 author = {Dryja, Maksymilian and Smith, Barry F and Widlund, Olof B}, 269 journal = {SIAM journal on numerical analysis}, 270 volume = {31}, 271 number = {6}, 272 pages = {1662--1694}, 273 year = {1994}, 274 publisher = {SIAM} 275} 276 277@book{smith1990domain, 278 title = {Domain decomposition algorithms for the partial differential equations of linear elasticity}, 279 author = {Smith, Barry F}, 280 year = {1990}, 281 publisher = {New York University} 282} 283 284@article{bramble1989construction, 285 title = {The construction of preconditioners for elliptic problems by substructuring. {IV}}, 286 author = {Bramble, James H and Pasciak, Joseph E and Schatz, Alfred H}, 287 journal = {Mathematics of Computation}, 288 volume = {53}, 289 number = {187}, 290 pages = {1--24}, 291 year = {1989} 292} 293 294@article{kaczmarz1937angenaherte, 295 title = {Angenaherte auflosung von systemen linearer gleichungen}, 296 author = {Kaczmarz, Stefan}, 297 journal = {Bull. Int. Acad. Pol. Sic. Let., Cl. Sci. Math. Nat.}, 298 pages = {355--357}, 299 year = {1937} 300} 301 302@article{nataf2022recent, 303 title = {Recent advances in domain decomposition methods for large-scale saddle point problems}, 304 author = {Nataf, Fr{\'e}d{\'e}ric and Tournier, Pierre-Henri}, 305 journal = {Comptes Rendus. M{\'e}canique}, 306 volume = {350}, 307 number = {S1}, 308 pages = {1--15}, 309 year = {2022} 310} 311 312@article{al2022robustpd, 313 title = {A robust algebraic multilevel domain decomposition preconditioner for sparse symmetric positive definite matrices}, 314 author = {Al Daas, Hussam and Jolivet, Pierre}, 315 journal = {SIAM Journal on Scientific Computing}, 316 volume = {44}, 317 number = {4}, 318 pages = {A2582--A2598}, 319 year = {2022}, 320 publisher = {SIAM} 321} 322 323@article{al2022robust, 324 title = {A robust algebraic domain decomposition preconditioner for sparse normal equations}, 325 author = {Al Daas, Hussam and Jolivet, Pierre and Scott, Jennifer A}, 326 journal = {SIAM Journal on Scientific Computing}, 327 volume = {44}, 328 number = {3}, 329 pages = {A1047--A1068}, 330 year = {2022}, 331 publisher = {SIAM} 332} 333 334@article{al2021multilevel, 335 title = {A multilevel {S}chwarz preconditioner based on a hierarchy of robust coarse spaces}, 336 author = {Al Daas, Hussam and Grigori, Laura and Jolivet, Pierre and Tournier, Pierre-Henri}, 337 journal = {SIAM Journal on Scientific Computing}, 338 volume = {43}, 339 number = {3}, 340 pages = {A1907--A1928}, 341 year = {2021}, 342 publisher = {SIAM} 343} 344 345@book{dolean2015introduction, 346 title = {An introduction to domain decomposition methods: algorithms, theory, and parallel implementation}, 347 author = {Dolean, Victorita and Jolivet, Pierre and Nataf, Fr{\'e}d{\'e}ric}, 348 year = {2015}, 349 publisher = {SIAM} 350} 351 352@article{spillane2011robust, 353 title = {A robust two-level domain decomposition preconditioner for systems of {PDE}s}, 354 author = {Spillane, Nicole and Dolean, Victorita and Hauret, Patrice and Nataf, Fr{\'e}d{\'e}ric and Pechstein, Clemens and Scheichl, Robert}, 355 journal = {Comptes Rendus Mathematique}, 356 volume = {349}, 357 number = {23-24}, 358 pages = {1255--1259}, 359 year = {2011}, 360 publisher = {Elsevier} 361} 362 363@article{kong2020highly, 364 title = {A Highly Parallel Multilevel {N}ewton--{K}rylov--{S}chwarz Method with Subspace-Based Coarsening and 365 Partition-Based Balancing for the Multigroup Neutron Transport Equation on Three-Dimensional Unstructured Meshes}, 366 author = {Kong, Fande and Wang, Yaqi and Gaston, Derek R and Permann, Cody J and Slaughter, Andrew E and Lindsay, 367 Alexander D and DeHart, Mark D and Martineau, Richard C}, 368 journal = {SIAM Journal on Scientific Computing}, 369 volume = {42}, 370 number = {5}, 371 pages = {C193--C220}, 372 year = {2020}, 373 publisher = {SIAM} 374} 375 376@article{ipsen2001note, 377 title = {A note on preconditioning nonsymmetric matrices}, 378 author = {Ipsen, Ilse CF}, 379 journal = {SIAM Journal on Scientific Computing}, 380 volume = {23}, 381 number = {3}, 382 pages = {1050--1051}, 383 year = {2001}, 384 publisher = {SIAM} 385} 386 387@article{murphy2000note, 388 title = {A note on preconditioning for indefinite linear systems}, 389 author = {Murphy, Malcolm F and Golub, Gene H and Wathen, Andrew J}, 390 journal = {SIAM Journal on Scientific Computing}, 391 volume = {21}, 392 number = {6}, 393 pages = {1969--1972}, 394 year = {2000}, 395 publisher = {SIAM} 396} 397 398@article{oliphant1961implicit, 399 title = {An implicit, numerical method for solving two-dimensional time-dependent diffusion problems}, 400 author = {Oliphant, Thomas A}, 401 journal = {Quarterly of Applied mathematics}, 402 volume = {19}, 403 number = {3}, 404 pages = {221--229}, 405 year = {1961} 406} 407 408@article{dupont1968approximate, 409 title = {An approximate factorization procedure for solving self-adjoint elliptic difference equations}, 410 author = {Dupont, Todd and Kendall, Richard P and Rachford, Jr, HH}, 411 journal = {SIAM Journal on Numerical Analysis}, 412 volume = {5}, 413 number = {3}, 414 pages = {559--573}, 415 year = {1968}, 416 publisher = {SIAM} 417} 418 419@inproceedings{manteuffel1979shifted, 420 title = {Shifted incomplete {C}holesky factorization}, 421 author = {Manteuffel, Thomas A}, 422 booktitle = {Sparse Matrix Proceedings 1978}, 423 pages = {41--61}, 424 year = {1979}, 425 organization = {SIAM, Philadelphia, PA} 426} 427 428@incollection{chan1997approximate, 429 title = {Approximate and incomplete factorizations}, 430 author = {Chan, Tony F and Van Der Vorst, Henk A}, 431 booktitle = {Parallel numerical algorithms}, 432 pages = {167--202}, 433 year = {1997}, 434 publisher = {Springer} 435} 436 437@article{mandel2008multispace, 438 title = {Multispace and multilevel {BDDC}}, 439 author = {Mandel, Jan and Soused{\'\i}k, Bed{\v{r}}ich and Dohrmann, Clark R}, 440 journal = {Computing}, 441 volume = {83}, 442 number = {2-3}, 443 pages = {55--85}, 444 year = {2008}, 445 publisher = {Springer} 446} 447 448@article{klawonn2006dual, 449 title = {Dual-primal {FETI} methods for linear elasticity}, 450 author = {Klawonn, Axel and Widlund, Olof B}, 451 journal = {Communications on Pure and Applied Mathematics: A Journal Issued by the Courant Institute of Mathematical Sciences}, 452 volume = {59}, 453 number = {11}, 454 pages = {1523--1572}, 455 year = {2006}, 456 publisher = {Wiley Online Library} 457} 458 459@article{dohrmann2007approximate, 460 title = {An approximate {BDDC} preconditioner}, 461 author = {Dohrmann, Clark R}, 462 journal = {Numerical Linear Algebra with Applications}, 463 volume = {14}, 464 number = {2}, 465 pages = {149--168}, 466 year = {2007}, 467 publisher = {Wiley Online Library} 468} 469 470@book{dryja1987additive, 471 title = {An additive variant of the {S}chwarz alternating method for the case of many subregions}, 472 author = {Dryja, Maksymilian and Widlund, Olof}, 473 year = {1987}, 474 publisher = {Ultracomputer Research Laboratory, Univ., Courant Inst. of Mathematical~…} 475} 476 477@article{couturier2016tsirm, 478 title = {{TSIRM}: A two-stage iteration with least-squares residual minimization algorithm to solve large sparse linear and nonlinear systems}, 479 author = {Couturier, Rapha{\"e}l and Khodja, Lilia Ziane and Guyeux, Christophe}, 480 journal = {Journal of Computational Science}, 481 volume = {17}, 482 pages = {535--546}, 483 year = {2016}, 484 publisher = {Elsevier} 485} 486 487@article{chan1998transpose, 488 title = {Transpose-free formulations of Lanczos-type methods for nonsymmetric linear systems}, 489 author = {Chan, Tony F and De Pillis, Lisette and Van Der Vorst, Henk}, 490 journal = {Numerical Algorithms}, 491 volume = {17}, 492 pages = {51--66}, 493 year = {1998}, 494 publisher = {Springer} 495} 496 497@article{catabriga2006performance, 498 title = {Performance of {LCD} iterative method in the finite element and finite difference solution of convection--diffusion equations}, 499 author = {Catabriga, L and Valli, AMP and Melotti, BZ and Pessoa, LM and Coutinho, ALGA}, 500 journal = {Communications in numerical methods in engineering}, 501 volume = {22}, 502 number = {6}, 503 pages = {643--656}, 504 year = {2006}, 505 publisher = {Wiley Online Library} 506} 507 508@article{catabriga2004evaluating, 509 title = {Evaluating the {LCD} algorithm for solving linear systems of equations arising from implicit {SUPG} formulation of compressible flows}, 510 author = {Catabriga, Lucia and Coutinho, Alvaro LGA and Franca, Leopoldo P}, 511 journal = {International Journal for Numerical Methods in Engineering}, 512 volume = {60}, 513 number = {9}, 514 pages = {1513--1534}, 515 year = {2004}, 516 publisher = {Wiley Online Library} 517} 518 519@article{dai2004study, 520 title = {Study on semi-conjugate direction methods for non-symmetric systems}, 521 author = {Dai, Yu-Hong and Yuan, Jinyun}, 522 journal = {International journal for numerical methods in engineering}, 523 volume = {60}, 524 number = {8}, 525 pages = {1383--1399}, 526 year = {2004}, 527 publisher = {Wiley Online Library} 528} 529 530@article{yuan2004semi, 531 title = {Semi-conjugate direction methods for real positive definite systems}, 532 author = {Yuan, JY and Golub, Gene H and Plemmons, Robert J and Cecilio, WAG}, 533 journal = {BIT Numerical Mathematics}, 534 volume = {44}, 535 pages = {189--207}, 536 year = {2004}, 537 publisher = {Springer} 538} 539 540@article{ji2017breakdown, 541 title = {A breakdown-free block conjugate gradient method}, 542 author = {Ji, Hao and Li, Yaohang}, 543 journal = {BIT Numerical Mathematics}, 544 volume = {57}, 545 pages = {379--403}, 546 year = {2017}, 547 publisher = {Springer} 548} 549 550@inproceedings{jolivet2016block, 551 title = {Block iterative methods and recycling for improved scalability of linear solvers}, 552 author = {Jolivet, Pierre and Tournier, Pierre-Henri}, 553 booktitle = {SC'16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis}, 554 pages = {190--203}, 555 year = {2016}, 556 organization = {IEEE} 557} 558 559@article{calandra2013modified, 560 title = {A modified block flexible {GMRES} method with deflation at each iteration for the solution of non-{H}ermitian linear systems with multiple right-hand sides}, 561 author = {Calandra, Henri and Gratton, Serge and Lago, Rafael and Vasseur, Xavier and Carvalho, Luiz Mariano}, 562 journal = {SIAM Journal on Scientific Computing}, 563 volume = {35}, 564 number = {5}, 565 pages = {S345--S367}, 566 year = {2013}, 567 publisher = {SIAM} 568} 569 570@article{o1980block, 571 title = {The block conjugate gradient algorithm and related methods}, 572 author = {O'Leary, Dianne P}, 573 journal = {Linear algebra and its applications}, 574 volume = {29}, 575 pages = {293--322}, 576 year = {1980}, 577 publisher = {Elsevier} 578} 579 580@article{erhel1996restarted, 581 title = {Restarted {GMRES} preconditioned by deflation}, 582 author = {Erhel, Jocelyne and Burrage, Kevin and Pohl, Bert}, 583 journal = {Journal of computational and applied mathematics}, 584 volume = {69}, 585 number = {2}, 586 pages = {303--318}, 587 year = {1996}, 588 publisher = {Elsevier} 589} 590 591@article{bai1994newton, 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621@article{demmel2012communication, 622 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 623 author = {Demmel, James and Grigori, Laura and Hoemmen, Mark and Langou, Julien}, 624 journal = {SIAM Journal on Scientific Computing}, 625 volume = {34}, 626 number = {1}, 627 pages = {A206--A239}, 628 year = {2012}, 629 publisher = {SIAM} 630} 631 632@article{philippe2012generation, 633 title = {On the generation of {K}rylov subspace bases}, 634 author = {Philippe, Bernard and Reichel, Lothar}, 635 journal = {Applied Numerical Mathematics}, 636 volume = {62}, 637 number = {9}, 638 pages = {1171--1186}, 639 year = {2012}, 640 publisher = {Elsevier} 641} 642 643@article{wakam2013memory, 644 title = {Memory efficient hybrid algebraic solvers for linear systems arising from compressible flows}, 645 author = {Wakam, D{\'e}sir{\'e} Nuentsa and Pacull, Fran{\c{c}}ois}, 646 journal = {Computers \& Fluids}, 647 volume = {80}, 648 pages = {158--167}, 649 year = {2013}, 650 publisher = {Elsevier} 651} 652 653@misc{wakam2011parallelism, 654 title = {Parallelism and robustness in {GMRES} with the {N}ewton basis and the deflated restarting}, 655 author = {Wakam, D{\'e}sir{\'e} Nuentsa and Erhel, Jocelyne}, 656 year = {2011}, 657 url = {https://hal.inria.fr/inria-00638247/en} 658} 659 660@article{tu2015feti, 661 title = {A {FETI-DP} type domain decomposition algorithm for three-dimensional incompressible {S}tokes equations}, 662 author = {Tu, Xuemin and Li, Jing}, 663 journal = {SIAM Journal on Numerical Analysis}, 664 volume = {53}, 665 number = {2}, 666 pages = {720--742}, 667 year = {2015}, 668 publisher = {SIAM} 669} 670 671@article{farhat2001feti, 672 title = {{FETI-DP}: a dual--primal unified {FETI} method—part {I}: A faster alternative to the two-level {FETI} method}, 673 author = {Farhat, Charbel and Lesoinne, Michel and LeTallec, Patrick and Pierson, Kendall and Rixen, Daniel}, 674 journal = {International journal for numerical methods in 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Appl. Phys.}, 1391 volume = {99}, 1392 year = {2006}, 1393 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 1394 petsc_uses = {KSP} 1395} 1396 1397@InProceedings{ japios2006, 1398 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 1399 Subramanian}, 1400 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 1401 in systems with cubic and uniaxial anisotropy.}, 1402 booktitle = {Intermag 2006 Conference}, 1403 petsc_uses = {KSP} 1404} 1405 1406@Article{ kbmb2006, 1407 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 1408 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 1409 Perpendicular Recording Heads}, 1410 journal = {IEEE Trans. Magn.}, 1411 volume = {42}, 1412 year = {2006}, 1413 pages = {2428--2430}, 1414 doi = {10.1109/TMAG.2006.879430}, 1415 petsc_uses = {KSP} 1416} 1417 1418@Article{ cclcw2006, 1419 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 1420 title = {Control of Domain Wall Motion in Permalloy Ring}, 1421 journal = {IEEE Trans. Magn.}, 1422 volume = {42}, 1423 year = {2006}, 1424 pages = {2960--2962}, 1425 doi = {10.1109/TMAG.2006.878414}, 1426 petsc_uses = {KSP} 1427} 1428 1429@Article{ bfmfzczg2007, 1430 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 1431 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 1432 title = {Micromagnetic modelling of ferromagnetic cones}, 1433 journal = {J. Magn. Magn. Mater.}, 1434 volume = {312}, 1435 year = {2007}, 1436 pages = {234-238}, 1437 url = {http://eprints.soton.ac.uk/45900/}, 1438 petsc_uses = {KSP} 1439} 1440 1441@PhDThesis{ rb2005, 1442 author = {Richard Boardman}, 1443 title = {Computer simulation studies of magnetic nanostructures}, 1444 school = {Computational Engineering and Design Group, School of Engineering Sciences, 1445 University of Southampton, United Kingdom}, 1446 year = {2005}, 1447 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 1448 petsc_uses = {KSP} 1449} 1450 1451@InProceedings{ cwwy2006, 1452 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 1453 title = {MPI Performance Analysis Tools on Blue Gene/L}, 1454 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 1455 year = {2006}, 1456 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 1457 petsc_uses = {KSP} 1458} 1459 1460@InProceedings{ ch2006, 1461 author = {I.-H. Chung and J.K. Hollingsworth}, 1462 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 1463 Programs}, 1464 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 1465 pages = {45--56}, 1466 doi = {10.1109/HPDC.2006.1652135}, 1467 petsc_uses = {KSP} 1468} 1469 1470@Article{ lkpl2005, 1471 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1472 title = {Multibit {MRAM} using a pair of memory cells}, 1473 journal = {IEEE Trans. Magn.}, 1474 volume = {41}, 1475 year = {2005}, 1476 pages = {2670-2672}, 1477 doi = {10.1109/TMAG.2005.855288}, 1478 petsc_uses = {KSP} 1479} 1480 1481@Article{ gscn2005, 1482 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 1483 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 1484 journal = {Phys. Rev. B}, 1485 volume = {71}, 1486 year = {2005}, 1487 doi = {10.1103/PhysRevB.71.144407}, 1488 petsc_uses = {KSP} 1489} 1490 1491@PhDThesis{ mda, 1492 author = {Massimiliano d'Aquino}, 1493 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 1494 school = { Universita di Napoli Federico II.}, 1495 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 1496 petsc_uses = {KSP} 1497} 1498 1499@TechReport{ ssdfssf2003, 1500 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 1501 Stehno and J. Fidler}, 1502 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 1503 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 1504 petsc_uses = {KSP} 1505} 1506 1507@InProceedings{ sb2006a, 1508 author = {W. Scholz and S. Batra}, 1509 title = {Effect of write current waveform on magnetization and head field dynamics of 1510 perpendicular recording heads}, 1511 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 1512 petsc_uses = {KSP} 1513} 1514 1515@Article{ scholz-batra1, 1516 author = {W. Scholz and S. Batra}, 1517 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 1518 Recording}, 1519 journal = {IEEE Trans. Magn.}, 1520 note = {submitted}, 1521 year = {2005}, 1522 petsc_uses = {KSP} 1523} 1524 1525@Article{ scholz-batra2, 1526 author = {W. Scholz and S. Batra}, 1527 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 1528 journal = {IEEE Trans. Magn.}, 1529 volume = {41}, 1530 year = {2005}, 1531 pages = {702-706}, 1532 petsc_uses = {KSP} 1533} 1534 1535@Article{ daquino-scholz1, 1536 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1537 title = {Micromagnetic Analysis of Fast Precessional Switching}, 1538 journal = {J. Magn. Magn. Mater.}, 1539 volume = {290-291}, 1540 year = {2005}, 1541 pages = {510-513}, 1542 petsc_uses = {KSP} 1543} 1544 1545@Article{ aq-scholz-fid, 1546 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1547 title = {Numerical and analytical study of fast precessional switching}, 1548 journal = {J. Appl. Phys.}, 1549 volume = {95}, 1550 year = {2004}, 1551 pages = {7055-7057}, 1552 petsc_uses = {KSP} 1553} 1554 1555@InProceedings{ gar-tabik-gar, 1556 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 1557 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 1558 Scatterers}, 1559 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 1560 (PDP'04)}, 1561 year = {2004}, 1562 pages = {80--}, 1563 petsc_uses = {KSP} 1564} 1565 1566@InProceedings{ aq-scholz-mia, 1567 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 1568 title = {Analysis of fast precessional switching in magnetic thin films}, 1569 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 1570 year = {2004}, 1571 pages = {257-260}, 1572 petsc_uses = {KSP} 1573} 1574 1575@Article{ scholz-fid-seus, 1576 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 1577 Dittrich and V. Tsiantos}, 1578 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 1579 Axes}, 1580 journal = {J. Magn. Magn. Mater.}, 1581 year = {2004}, 1582 pages = {1524-1525}, 1583 petsc_uses = {KSP} 1584} 1585 1586@Article{ boardman-zimmerman, 1587 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 1588 Peter de Groot}, 1589 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 1590 journal = {Journal of Applied Physics}, 1591 year = {2005}, 1592 petsc_uses = {KSP} 1593} 1594 1595@Article{ lim-kim-park, 1596 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1597 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 1598 journal = {IEEE Trans. Magn.}, 1599 note = {submitted}, 1600 petsc_uses = {KSP} 1601} 1602 1603@Article{ scholz-suess2, 1604 author = {W. Scholz and D. Suess and T. Schrefl and J. Fidler}, 1605 title = {Micromagnetic simulation of magnetization reversal in small particles with 1606 surface anisotropy}, 1607 journal = {J. Appl. Phys.}, 1608 volume = {95}, 1609 year = {2004}, 1610 pages = {6807-6809}, 1611 petsc_uses = {KSP} 1612} 1613 1614@Article{ scholz-schrefl1, 1615 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 1616 Tsiantos}, 1617 title = {Micromagnetic simulation of the pinning and depinning process in permanent 1618 magnets}, 1619 journal = {IEEE Trans. Magn.}, 1620 volume = {39}, 1621 year = {2003}, 1622 pages = {2920-2922}, 1623 petsc_uses = {KSP} 1624} 1625 1626@Article{ scholz-guslienko, 1627 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 1628 W. Chantrell and J. Fidler}, 1629 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 1630 nanodots}, 1631 journal = {J. Magn. Magn. Mater.}, 1632 volume = {266}, 1633 year = {2003}, 1634 pages = {155-163}, 1635 petsc_uses = {KSP} 1636} 1637 1638@Article{ scholz1, 1639 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 1640 Forster and V. Tsiantos}, 1641 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1642 journal = {Comp. Mat. Sci}, 1643 year = {2003}, 1644 pages = {366--383}, 1645 volume = {28}, 1646 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 1647 petsc_uses = {KSP} 1648} 1649 1650@PhDThesis{ scholz2, 1651 author = {W. Scholz}, 1652 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1653 school = {Vienna University of Technology, Vienna, Austria}, 1654 year = {2003}, 1655 petsc_uses = {KSP} 1656} 1657 1658@Article{ scholz3, 1659 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 1660 Forster and J. Fidler}, 1661 title = {Implementation of a high performance parallel finite element micromagnetics 1662 package}, 1663 journal = {J. Magn. Magn. Mater.}, 1664 year = {2004}, 1665 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 1666 petsc_uses = {KSP} 1667} 1668 1669% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1670@InBook{ zhanggladwell1, 1671 author = {W. Zhang and I. Gladwell}, 1672 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 1673 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 1674 year = {2000}, 1675 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 1676 Physics, vol. 552}, 1677 publisher = {Springer}, 1678 pages = {4190-}, 1679 petsc_uses = {KSP} 1680} 1681 1682@Article{ wolf1, 1683 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 1684 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 1685 thin films}, 1686 journal = {Phil. Mag. A}, 1687 year = {2003}, 1688 lab = {ANL}, 1689 petsc_uses = {KSP} 1690} 1691 1692@Article{ wolf2, 1693 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 1694 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 1695 grain-boundary properties}, 1696 journal = {Computational Materials Science}, 1697 year = {2001}, 1698 volume = {23}, 1699 pages = {15--32}, 1700 lab = {ANL}, 1701 petsc_uses = {KSP} 1702} 1703 1704@Article{ wolf3, 1705 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 1706 title = {Role of grain rotation in grain growth by mesoscale simulation}, 1707 journal = {Phil. Mag. A}, 1708 year = {2002}, 1709 volume = {82}, 1710 pages = {1271--1297}, 1711 lab = {ANL}, 1712 petsc_uses = {KSP} 1713} 1714 1715% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1716@Article{ saut, 1717 author = { Olivier Saut}, 1718 title = {Bidimensional Study of the {M}axwell-{B}loch Model in a Nonlinear Crystal}, 1719 journal = {SIAM Journal on Scientific Computing}, 1720 year = {2004}, 1721 note = {submitted}, 1722 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 1723 petsc_uses = {KSP} 1724} 1725 1726% LiteralHTML: 1727% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 1728% LiteralHTML: 1729@InBook{ khanallorenziayachepennec2016, 1730 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 1731 of Brain Deformation in {Alzheimer's} Disease}, 1732 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 1733 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 1734 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 1735 Miller}, 1736 pages = {167--176}, 1737 isbn = {978-3-319-28329-6}, 1738 doi = {10.1007/978-3-319-28329-6_15}, 1739 publisher = {Springer International Publishing}, 1740 year = {2016}, 1741 petsc_uses = {KSP} 1742} 1743 1744@Article{ ataseven, 1745 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 1746 title = {Parallel implementation of the accelerated {BEM} approach for {EMSI} of the human 1747 brain}, 1748 journal = {Medical and Biological Engineering and Computing}, 1749 month = feb, 1750 year = {2008}, 1751 doi = {10.1007/s11517-008-0316-0}, 1752 petsc_uses = {KSP} 1753} 1754 1755@Article{ dennis-eberhart-03, 1756 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 1757 pages = {832-840}, 1758 volume = {125}, 1759 number = {6}, 1760 title = {Finite-element simulation of cooling of realistic {3-D} human head and neck}, 1761 journal = {J Biomech Eng}, 1762 year = {2003}, 1763 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 1764 petsc_uses = {KSP} 1765} 1766 1767@Conference{ gu7174parallel, 1768 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 1769 frequency-domain small animal optical tomography}}, 1770 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 1771 booktitle = {Proc. of SPIE Vol}, 1772 volume = {7174}, 1773 number = {717406}, 1774 pages = {1}, 1775 petsc_uses = {KSP} 1776} 1777 1778@Article{ barchanski2005using, 1779 title = {{Using domain decomposition techniques for the calculation of low-frequency 1780 electric current densities in high-resolution 3D human anatomy models}}, 1781 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 1782 T.}, 1783 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 1784 and Electronic Engineering}, 1785 volume = {24}, 1786 number = {2}, 1787 pages = {458--467}, 1788 issn = {0332-1649}, 1789 year = {2005}, 1790 publisher = {Emerald Group Publishing Limited}, 1791 petsc_uses = {KSP} 1792} 1793 1794@Article{ motrescurienen05, 1795 author = {V. C. Motrescu and U. van Rienen}, 1796 pages = {227--231}, 1797 volume = {3}, 1798 title = {Computation of currents induced by {ELF} electric fields in anisotropic human 1799 tissues using the Finite Integration Technique}, 1800 journal = {Advances in Radio Science}, 1801 year = {2005}, 1802 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 1803 petsc_uses = {KSP} 1804} 1805 1806@Article{ motrescurienen04, 1807 author = {V. C. Motrescu and U. van Rienen}, 1808 pages = {309--313}, 1809 volume = {2}, 1810 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 1811 Integration Technique (FIT)}, 1812 journal = {Advances in Radio Science}, 1813 year = {2004}, 1814 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 1815 petsc_uses = {KSP} 1816} 1817 1818@InProceedings{ dbl2, 1819 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 1820 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 1821 booktitle = {ECCOMAS2000}, 1822 year = {2000}, 1823 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 1824 petsc_uses = {KSP} 1825} 1826 1827@Unpublished{ cell, 1828 title = {Parallel Simulation Engines for Whole-Cell Models}, 1829 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 1830 Weber}, 1831 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 1832 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 1833 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 1834 year = {2001}, 1835 petsc_uses = {KSP} 1836} 1837 1838@Article{ barker2010two, 1839 title = {Two-level {N}ewton and hybrid {S}chwarz preconditioners for fluid-structure 1840 interaction}, 1841 author = {Barker, A.T. and Cai, X.C.}, 1842 journal = {SIAM Journal on Scientific Computing}, 1843 volume = {32}, 1844 number = {4}, 1845 pages = {2395--2417}, 1846 year = {2010}, 1847 publisher = {Society for Industrial and Applied Mathematics}, 1848 petsc_uses = {KSP} 1849} 1850 1851@Article{ barker2010scalable, 1852 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 1853 with application to blood flow modeling}, 1854 author = {Barker, A.T. and Cai, X.C.}, 1855 journal = {Journal of Computational Physics}, 1856 volume = {229}, 1857 number = {3}, 1858 pages = {642--659}, 1859 year = {2010}, 1860 publisher = {Elsevier}, 1861 petsc_uses = {KSP} 1862} 1863 1864@Article{ barker2009nks, 1865 title = {{NKS} for fully coupled fluid-structure interaction with application}, 1866 author = {Barker, A.T. and Cai, X.C.}, 1867 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 1868 pages = {275--282}, 1869 year = {2009}, 1870 publisher = {Springer}, 1871 petsc_uses = {KSP} 1872} 1873 1874@Article{ mirams2013, 1875 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 1876 and Yi Cui and Gary R Mirams}, 1877 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 1878 to predict {QT} interval changes in the rabbit ventricular wedge}, 1879 journal = {Journal of pharmacological and toxicological methods}, 1880 volume = {68}, 1881 number = {1}, 1882 pages = {88--96}, 1883 year = {2013}, 1884 doi = {10.1016/j.vascn.2013.04.004}, 1885 petsc_uses = {KSP} 1886} 1887 1888% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1889% LiteralHTML: <center><img alt="" 1890% LiteralHTML: src="images/spine0l.jpg"></center></p> 1891% LiteralHTML: <center><img alt="" 1892% LiteralHTML: src="images/vertebra.jpg"></center></p> 1893% LiteralHTML:<font color="#FF0000"> 1894% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 1895% LiteralHTML:Understanding bone mechanical properties and how they may lead to 1896% LiteralHTML:fractures is thus an important medical research activity. PETSc and 1897% LiteralHTML:Prometheus have been used for extremely large scale finite element 1898% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 1899% LiteralHTML:team of doctors and computational scientists. This computation was 1900% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 1901% LiteralHTML:with over 4000 processors.</p> 1902% LiteralHTML: </font> 1903@Article{ arbenz2008scalable, 1904 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 1905 analysis of human bone structures}, 1906 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 1907 journal = {International Journal for Numerical Methods in Engineering}, 1908 volume = {73}, 1909 number = {7}, 1910 pages = {927--947}, 1911 year = {2008}, 1912 publisher = {Wiley Online Library}, 1913 petsc_uses = {KSP} 1914} 1915 1916@InProceedings{ adams-04, 1917 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1918 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 1919 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 1920 half a billion degrees of freedom}, 1921 note = {Gordon Bell Award}, 1922 year = {2004}, 1923 petsc_uses = {KSP} 1924} 1925 1926@InProceedings{ adams-03b, 1927 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1928 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 1929 Whole Bone Micro-Mechanics on the {IBM SP}}, 1930 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 1931 year = {2003}, 1932 petsc_uses = {KSP} 1933} 1934 1935@InProceedings{ oghattas2002, 1936 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 1937 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 1938 booktitle = {Procceedings of SC2002}, 1939 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 1940 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 1941 by time-dependent PDEs, and scalability results for an inverse wave propagation 1942 problem of determining the material field of an acoustic medium. Using the 1943 algorithm, they solved a synthetic inverse wave propagation problem though a 1944 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 1945 processors.}, 1946 year = {2002}, 1947 petsc_uses = {KSP} 1948} 1949 1950% LiteralHTML: <a name="biology:cardiology"> 1951% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1952% LiteralHTML: <center><img alt="" 1953% LiteralHTML: src="images/heart.jpg"> 1954% LiteralHTML: <img alt="" 1955% LiteralHTML: src="images/pump.jpg"></center></p> 1956% LiteralHTML: 1957% LiteralHTML:<font color="#FF0000"> 1958% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 1959% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 1960% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 1961% LiteralHTML: through the heart. PETSc has been used by several research groups to 1962% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 1963% LiteralHTML: fully understand the developments of arrhthmias.</p> 1964% LiteralHTML:</font> 1965@InProceedings{ oghattas2000, 1966 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 1967 Walkington}, 1968 title = {A Parallel Dynamic-Mesh {L}agrangian Method for Simulation of Flows with Dynamic 1969 Interfaces}, 1970 booktitle = {Procceedings of SC2000}, 1971 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 1972 note = {Blood flow modeling at the microscale including effects on individual blood 1973 cells, for designing heart assist pumps, etc.}, 1974 year = {2000}, 1975 petsc_uses = {KSP} 1976} 1977 1978@InBook{ cfps2006, 1979 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 1980 editor = {A. Quarteroni et al.}, 1981 title = {Complex Systems in Biomedicine}, 1982 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 1983 publisher = {Springer-Verlag}, 1984 pages = {187--241}, 1985 year = {2006}, 1986 petsc_uses = {KSP} 1987} 1988 1989@InProceedings{ cfpst2007, 1990 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 1991 title = {Determining recovery times from transmembrane action potentials and unipolar 1992 electrograms in normal heart tissue}, 1993 booktitle = {FIMH07}, 1994 publisher = {Springer-Verlag}, 1995 volume = {4466}, 1996 pages = {139--149}, 1997 year = {2007}, 1998 petsc_uses = {KSP} 1999} 2000 2001@Article{ seemann2010framework, 2002 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 2003 Equations Using PETSc}}, 2004 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 2005 D{\\"o}ssel, O.}, 2006 journal = {Progress in Industrial Mathematics at ECMI 2008}, 2007 pages = {363--369}, 2008 year = {2010}, 2009 publisher = {Springer}, 2010 petsc_uses = {KSP} 2011} 2012 2013@InProceedings{ pft2005, 2014 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 2015 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 2016 Intramural Heterogeneity}, 2017 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 2018 pages = {267--277}, 2019 editors = {A. Frangi et al.}, 2020 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 2021 year = {2005}, 2022 petsc_uses = {KSP} 2023} 2024 2025@Article{ bgcp2005, 2026 author = {Boyce E. Griffith and Charles S. Peskin}, 2027 title = {On the order of accuracy of the immersed boundary method: Higher order 2028 convergence rates for sufficiently smooth problems}, 2029 journal = {Journal of Computational Physics}, 2030 year = {2005}, 2031 volume = {208}, 2032 pages = {75--105}, 2033 petsc_uses = {KSP} 2034} 2035 2036@Article{ griffith2007adaptive, 2037 title = {An adaptive, formally second order accurate version of the immersed boundary 2038 method}, 2039 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 2040 journal = {Journal of Computational Physics}, 2041 volume = {223}, 2042 number = {1}, 2043 pages = {10--49}, 2044 year = {2007}, 2045 publisher = {Elsevier}, 2046 petsc_uses = {KSP} 2047} 2048 2049@PhDThesis{ griffith05, 2050 author = {Boyce Griffith}, 2051 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 2052 parallel version of the immersed boundary method}, 2053 school = {New York University}, 2054 year = {2005}, 2055 petsc_uses = {KSP} 2056} 2057 2058@PhDThesis{ murillo, 2059 author = {Maria S. Murillo}, 2060 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 2061 Differential Equations with an Application in Computational Biology}, 2062 school = {University of Colorado at Boulder}, 2063 year = {2002}, 2064 petsc_uses = {KSP} 2065} 2066 2067@Article{ spv2004, 2068 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 2069 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 2070 journal = {IEEE Trans. Biomed. Eng}, 2071 year = {2004}, 2072 volume = {51}, 2073 pages = {1960--1968}, 2074 petsc_uses = {KSP} 2075} 2076 2077@Article{ vphl2003, 2078 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 2079 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 2080 journal = {J. Electrocardiol.}, 2081 year = {2003}, 2082 volume = {36}, 2083 pages = {69--74}, 2084 petsc_uses = {KSP} 2085} 2086 2087@InProceedings{ spbv2003, 2088 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and E.J. Vigmond}, 2089 title = {Preconditioning Techniques for the Bidomain Equations}, 2090 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2091 Methods}, 2092 pages = {571--580}, 2093 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2094 note = {}, 2095 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2096 year = {2003}, 2097 petsc_uses = {KSP} 2098} 2099 2100@Article{ franz-pavir-04, 2101 author = {P. Colli Franzone and L.~F. Pavarino}, 2102 title = {A parallel solver for reaction-diffusion systems in computational 2103 electrocardiology}, 2104 journal = {Mathematical Models and Methods in Applied Sciences}, 2105 year = {2004}, 2106 volume = {14}, 2107 number = {6}, 2108 pages = {883--912}, 2109 petsc_uses = {KSP} 2110} 2111 2112@Article{ franz-pavir-05, 2113 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2114 title = {Simulating patterns of excitation, repolarization and action potential 2115 durationwith cardiac Bidomain and Monodomain models}, 2116 journal = {Mathematical Biosciences}, 2117 year = {2005}, 2118 volume = {197}, 2119 number = {1}, 2120 pages = {35--66}, 2121 petsc_uses = {KSP} 2122} 2123 2124@Article{ franz-pavir-06, 2125 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2126 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 2127 the dispersion of cardiac repolarization and action potential duration: a 2128 simulation study}, 2129 journal = {Mathematical Biosciences}, 2130 year = {2006}, 2131 volume = {204}, 2132 number = {1}, 2133 pages = {132--165}, 2134 petsc_uses = {KSP} 2135} 2136 2137@InProceedings{ colli-franz-sim, 2138 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 2139 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 2140 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 2141 Mediterranean Conference on Medical and Biological Engineering}, 2142 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 2143 year = {2004}, 2144 petsc_uses = {KSP} 2145} 2146 2147@InProceedings{ pf2003, 2148 author = {Luca F. Pavarino and Piero Colli Franzone}, 2149 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 2150 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2151 Methods}, 2152 pages = {669--776}, 2153 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2154 note = {}, 2155 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2156 year = {2003}, 2157 petsc_uses = {KSP} 2158} 2159 2160@Article{ maria-is04, 2161 author = {Maria Murillo and Xiao-Chuan Cai}, 2162 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 2163 activity of the heart}, 2164 journal = {Numerical Linear Algebra with Applications}, 2165 year = {2004}, 2166 volume = {11}, 2167 pages = {261 - 277}, 2168 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 2169 petsc_uses = {KSP} 2170} 2171 2172@Article{ murli2007monitoring, 2173 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 2174 Imaging in a Grid computing PSE}}, 2175 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 2176 and Lapegna, M.}, 2177 journal = {Grid-Based Problem Solving Environments}, 2178 pages = {421--432}, 2179 year = {2007}, 2180 publisher = {Springer}, 2181 petsc_uses = {KSP} 2182} 2183 2184@Article{ carracciuolo:2006:tpc, 2185 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 2186 title = {Towards a parallel component for imaging in {PETSc} programming environment: a case 2187 study in {3-D} echocardiography}, 2188 journal = {Parallel Comput.}, 2189 volume = {32}, 2190 issue = {1}, 2191 month = jan, 2192 year = {2006}, 2193 issn = {0167-8191}, 2194 pages = {67--83}, 2195 numpages = {17}, 2196 doi = {10.1016/j.parco.2005.09.001}, 2197 acmid = {1141218}, 2198 publisher = {Elsevier Science Publishers B. V.}, 2199 address = {Amsterdam, The Netherlands, The Netherlands}, 2200 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 2201 component}, 2202 petsc_uses = {KSP} 2203} 2204 2205@Article{ damore2011integration, 2206 title = {Integration of emerging computer technologies for an efficient image sequences 2207 analysis}, 2208 journal = {Integrated Computer-Aided Engineering }, 2209 volume = {18}, 2210 number = {4}, 2211 pages = {365 - 378}, 2212 year = {2011}, 2213 note = {}, 2214 issn = {1875-8835}, 2215 doi = {10.3233/ICA-2011-0382}, 2216 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 2217 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 2218 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 2219 petsc_uses = {KSP} 2220} 2221 2222@InProceedings{ eth_biwi_00721, 2223 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and G. 2224 Székely}, 2225 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 2226 a {S}chur Complement Preconditioner}, 2227 booktitle = {Euro-Par 2009 Parallel Processing}, 2228 year = {2009}, 2229 month = aug, 2230 pages = {747-759}, 2231 volume = {5704}, 2232 editor = {H. Sips and D. Epema and H.-X. Lin}, 2233 series = {Lecture Notes in Computer Science}, 2234 publisher = {Springer}, 2235 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 2236 parallel Krylov solver}, 2237 petsc_uses = {KSP} 2238} 2239 2240% LiteralHTML: <a name="biology:imagingandsurgery"> 2241% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 2242% LiteralHTML: <center><img alt="" 2243% LiteralHTML: src="images/brain.jpg"></center> 2244@Article{ ganser2004deformable, 2245 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 2246 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 2247 journal = {Medical Image Analysis}, 2248 volume = {8}, 2249 number = {1}, 2250 pages = {3--22}, 2251 year = {2004}, 2252 publisher = {Elsevier}, 2253 petsc_uses = {KSP} 2254} 2255 2256@Unpublished{ taccsurgery, 2257 title = {{TACC} supercomputer performs laser cancer surgery on canine}, 2258 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 2259 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 2260 Austin performed laser surgery on a dog in Houston without the intervention of a 2261 surgeon. The treatment was developed collaboratively by computational experts from 2262 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 2263 leading technologists from the M.D. Anderson Cancer Center in Houston, and 2264 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 2265 state-of-the-art thermal imaging technology, and advanced computational methods, 2266 dynamic, data-driven treatments are being pursued as a minimally invasive 2267 alternative to the standard treatment of cancer.}, 2268 petsc_uses = {KSP} 2269} 2270 2271@Article{ ffhbresso2008, 2272 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 2273 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 2274 Tinsley Oden}, 2275 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 2276 journal = {Engineering with Computers}, 2277 note = {Special issue on Computational Bioengineering}, 2278 year = {2008}, 2279 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 2280 petsc_uses = {KSP} 2281} 2282 2283@TechReport{ dobbhbbbdeffghkkps2008, 2284 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 2285 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 2286 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 2287 and S. Prudhomme and R. J. Stafford}, 2288 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 2289 Cancer}, 2290 year = {2008}, 2291 institution = {University of Texas at Austin}, 2292 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 2293 petsc_uses = {KSP} 2294} 2295 2296@Article{ ogdb2004, 2297 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 2298 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 2299 journal = {Physics in Medicine and Biology}, 2300 year = {2004}, 2301 volume = {49}, 2302 pages = {2955--2947}, 2303 petsc_uses = {KSP} 2304} 2305 2306@InProceedings{ majumdar11, 2307 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 2308 Baldridge and P. Krysl}, 2309 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 2310 booktitle = {ICCS 2005}, 2311 pages = {672--679}, 2312 editor = {V.S. Sunderam et al.}, 2313 year = {2005}, 2314 petsc_uses = {KSP} 2315} 2316 2317@Conference{ sermesant-etal:03, 2318 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 2319 Ayache, H.}, 2320 title = {A parallel implementation of non-rigid registration using a volumetric 2321 biomechanical model}, 2322 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 2323 address = {Philadelphia, PA, USA}, 2324 publisher = {Springer-Verlag}, 2325 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2326 series = {Lecture Notes in Computer Science}, 2327 volume = {2717}, 2328 pages = {398-407}, 2329 date = {june 23-24}, 2330 year = {2003}, 2331 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 2332 petsc_uses = {KSP} 2333} 2334 2335@Conference{ sermesant-etal:04, 2336 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 2337 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 2338 title = {A Novel Nonrigid Registration Algorithm And Applications}, 2339 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 2340 address = {Philadelphia, PA, USA}, 2341 publisher = {Springer-Verlag}, 2342 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2343 series = {Lecture Notes in Computer Science}, 2344 volume = {2208}, 2345 pages = {923}, 2346 year = {2003}, 2347 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 2348 petsc_uses = {KSP} 2349} 2350 2351@Article{ warfield-haker-talos-05, 2352 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 2353 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 2354 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 2355 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 2356 title = {Capturing intraoperative deformations: research experience at {B}righam and {W}omen's 2357 hospital}, 2358 journal = {Medical Image Analysis}, 2359 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 2360 year = {2005}, 2361 petsc_uses = {KSP} 2362} 2363 2364@Article{ brain3, 2365 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 2366 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 2367 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 2368 Deformation during Image Guided Neurosurgery}, 2369 journal = {Computing and Visualization in Science}, 2370 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 2371 year = {2002}, 2372 petsc_uses = {KSP} 2373} 2374 2375@Article{ brain2, 2376 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 2377 Kikinis and Simon K. Warfield}, 2378 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 2379 Element Biomechanical Model}, 2380 journal = {IEEE Transactions on Medical Imaging}, 2381 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 2382 year = {2001}, 2383 petsc_uses = {KSP} 2384} 2385 2386@InProceedings{ brain1, 2387 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 2388 Ferenc A. Jolesz and Ron Kikinis}, 2389 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 2390 Guided Neurosurgery}, 2391 booktitle = {Proceedings of SC2000}, 2392 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 2393 year = {2000}, 2394 petsc_uses = {KSP} 2395} 2396 2397@Article{ vanne06, 2398 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 2399 M. Lassas and M. Kalke}, 2400 title = {Parallelized {B}ayesian inversion for three-dimensional dental {X}-ray imaging}, 2401 journal = {IEEE Transactions on Medical Imaging}, 2402 volume = {25}, 2403 number = {2}, 2404 month = feb, 2405 year = {2006}, 2406 pages = {218--228}, 2407 petsc_uses = {KSP} 2408} 2409 2410@InProceedings{ knepleybardhan2015, 2411 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 2412 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 2413 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 2414 Exposition}, 2415 volume = {9}, 2416 pages = {V009T12A04}, 2417 doi = {10.1115/IMECE2015-53579}, 2418 year = {2015}, 2419 petsc_uses = {KSP} 2420} 2421 2422@InProceedings{ bardhanknepley2015, 2423 title = {Multiscale models and approximation algorithms for protein electrostatics}, 2424 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 2425 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 2426 volume = {61}, 2427 pages = {163--174}, 2428 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 2429 doi = {10.2495/BEM380131}, 2430 publisher = {WIT Press}, 2431 year = {2015}, 2432 petsc_uses = {KSP} 2433} 2434 2435% LiteralHTML: 2436% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 2437% LiteralHTML: 2438@InProceedings{ adamsbrennanknepleywang2022, 2439 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 2440 quench plasmas}, 2441 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 2442 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 2443 (IPDPS '22)}, 2444 doi = {10.1109/IPDPS53621.2022.00020}, 2445 year = {2022}, 2446 petsc_uses = {DMPlex} 2447} 2448 2449@Misc{ adamsknepleybrennan2021, 2450 title = {Runaway Electron Generation with High-Performance, Structure Preserving 2451 Discretization of {F}okker--{P}lank--{L}andau}, 2452 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 2453 year = {2021}, 2454 petsc_uses = {KSP} 2455} 2456 2457@Article{ adamshirvijokiknepleybrownisaacmills2017, 2458 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 2459 Architectures}, 2460 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 2461 Isaac and Richard Mills}, 2462 journal = {SIAM Journal on Scientific Computing}, 2463 volume = {39}, 2464 number = {6}, 2465 pages = {C452--C465}, 2466 doi = {10.1137/17M1118828}, 2467 eprint = {1702.08880}, 2468 year = {2017}, 2469 petsc_uses = {KSP} 2470} 2471 2472@Article{ pusztayknepleyadams2022, 2473 title = {Conservative Projection Between {FEM} and Particle Bases}, 2474 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 2475 journal = {SIAM Journal on Scientific Computing}, 2476 volume = {44}, 2477 number = {4}, 2478 pages = {C310--C319}, 2479 doi = {10.1137/21M145407}, 2480 year = {2022} 2481} 2482 2483@Article{ hirvijoki2017, 2484 author = {Eero Hirvijoki and Mark F. Adams}, 2485 title = {Conservative discretization of the {Landau} collision integral}, 2486 journal = {Physics of Plasmas}, 2487 volume = {24}, 2488 number = {3}, 2489 pages = {032121}, 2490 doi = {10.1063/1.4979122}, 2491 year = {2017}, 2492 petsc_uses = {KSP} 2493} 2494 2495@Article{ mollenadamsknepleyhagerchang2021, 2496 title = {Implementation of higher-order velocity mapping between marker particles and grid 2497 in the particle-in-cell code {XGC}}, 2498 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 2499 S. Chang}, 2500 journal = {Journal of Plasma Physics}, 2501 volume = {87}, 2502 number = {2}, 2503 pages = {905870229}, 2504 eprint = {2012.11764}, 2505 doi = {10.1017/S0022377821000441}, 2506 year = {2021}, 2507 petsc_uses = {KSP} 2508} 2509 2510@Article{ lsmh2014, 2511 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 2512 title = {Comparison of particle trajectories and collision operators for collisional 2513 transport in nonaxisymmetric plasmas}, 2514 journal = { Physics of Plasmas}, 2515 volume = {21}, 2516 year = {2014}, 2517 petsc_uses = {KSP} 2518} 2519 2520@Article{ lpcep2014, 2521 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 2522 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 2523 pedestal}, 2524 journal = {Plasma Physics and Controlled Fusion}, 2525 volume = {56}, 2526 year = {2014}, 2527 petsc_uses = {KSP} 2528} 2529 2530@Article{ facets-scidac08, 2531 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 2532 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 2533 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 2534 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 2535 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 2536 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 2537 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 2538 Stotler and A. Pigarov}, 2539 journal = {J. Phys.: Conf. Ser.}, 2540 volume = {125}, 2541 year = {2008}, 2542 pages = {012040}, 2543 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 2544 petsc_uses = {KSP} 2545} 2546 2547@Article{ facets-scidac09, 2548 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 2549 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 2550 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 2551 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 2552 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 2553 and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar 2554 and A. Pigarov and H. Zhang}, 2555 journal = {J. Phys.: Conf. Ser.}, 2556 volume = {180}, 2557 year = {2009}, 2558 pages = {012056}, 2559 url = {http://iopscience.iop.org/1742-6596/180/1/012056}, 2560 petsc_uses = {KSP} 2561} 2562 2563@InProceedings{ facets-scidac10, 2564 title = {Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the 2565 {FACETS} Code}, 2566 author = {A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. 2567 Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. 2568 Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. 2569 Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. 2570 Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. 2571 Pigarov and H. 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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Castillo}, 2752 title = {Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear 2753 Coastal Ocean Model}, 2754 journal = {Journal of Marine Science and Engineering}, 2755 volume = {7}, 2756 number = {6}, 2757 article-number= {185}, 2758 url = {https://www.mdpi.com/2077-1312/7/6/185}, 2759 issn = {2077-1312}, 2760 doi = {10.3390/jmse7060185}, 2761 year = {2019}, 2762 petsc_uses = {KSP} 2763} 2764 2765@Article{ furuichimat2015, 2766 title = {Implicit solution of the material transport in Stokes flow simulation: Toward 2767 thermal convection simulation surrounded by free surface}, 2768 author = {Mikito Furuichi and Dave A May}, 2769 journal = {Computer Physics Communications}, 2770 volume = {192}, 2771 pages = {1--11}, 2772 year = {2015}, 2773 petsc_uses = {KSP} 2774} 2775 2776@Article{ sharplesmoresivelicjadamecmay2016, 2777 title = {Simulating faults and plate boundaries with a transversely isotropic plasticity 2778 model}, 2779 author = {Wendy Sharples and Louis N Moresi and Mirko Velic and Margarete A Jadamec and 2780 Dave A May}, 2781 journal = {Physics of the Earth and Planetary Interiors}, 2782 volume = {252}, 2783 pages = {77--90}, 2784 year = {2016}, 2785 petsc_uses = {KSP} 2786} 2787 2788@Article{ spiegelmanmaywilson2016, 2789 title = {On the solvability of incompressible {S}tokes with viscoplastic rheologies in 2790 geodynamics}, 2791 author = {Marc Spiegelman and Dave A May and Cian R Wilson}, 2792 journal = {Geochemistry, Geophysics, Geosystems}, 2793 volume = {17}, 2794 number = {6}, 2795 pages = {2213--2238}, 2796 year = {2016}, 2797 petsc_uses = {KSP} 2798} 2799 2800@Article{ buiteretal2016, 2801 title = {Benchmarking numerical models of brittle thrust wedges}, 2802 author = {Susanne JH Buiter and Guido Schreurs and Markus Albertz and Taras V Gerya and 2803 Boris Kaus and Walter Landry and Laetitia {Le Pourhiet} and Yury Mishin and David 2804 L Egholm and Michele Cooke and Bertrand Maillot and Cedric Thieulot and Tony Crook 2805 and Dave May and Pauline Souloumiac and Christopher Beaumont}, 2806 journal = {Journal of structural geology}, 2807 volume = {92}, 2808 pages = {140--177}, 2809 year = {2016}, 2810 petsc_uses = {KSP} 2811} 2812 2813@Article{ afanasievboehmdrielkrischerrietmannmayknepleyfichtner2019, 2814 title = {Modular and flexible spectral-element waveform modelling in two and three 2815 dimensions}, 2816 author = {Michael Afanasiev and Christian Boehm and Martin van Driel and Lion Krischer and 2817 Max Rietmann and Dave A. 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. Knepley and Michael Afanasiev and Christian Boehm and 2831 Martin van Driel and Lion Krischer and Andreas Fichtner}, 2832 journal = {SIAM Journal on Scientific Computing}, 2833 volume = {43}, 2834 number = {2}, 2835 pages = {C127--C153}, 2836 eprint = {http://arxiv.org/abs/2004.08729}, 2837 doi = {10.1137/20M1332748}, 2838 year = {2021}, 2839 petsc_uses = {KSP} 2840} 2841 2842@Article{ parsani2021, 2843 title = {High-order accurate entropy-stable discontinuous collocated {G}alerkin methods with 2844 the summation-by-parts property for compressible {CFD} frameworks: Scalable {SSDC} 2845 algorithms and flow solver}, 2846 author = {Matteo Parsani and Radouan Boukharfane and Irving Reyna Nolasco and David C. {Del 2847 Rey Fernández} and Stefano Zampini and Bilel Hadri and Lisandro Dalcin}, 2848 journal = {Journal of Computational Physics}, 2849 volume = {424}, 2850 pages = {109844}, 2851 issn = {0021-9991}, 2852 doi = {https://doi.org/10.1016/j.jcp.2020.109844}, 2853 url = {http://www.sciencedirect.com/science/article/pii/S0021999120306185}, 2854 year = {2021}, 2855 petsc_uses = {KSP} 2856} 2857 2858@Article{ ambartsumyanbouakaramthanhghattaskeyesstadlerturkiyyahzampini2020, 2859 title = {Hierarchical matrix approximations of {Hessians} arising in inverse problems 2860 governed by {PDEs}}, 2861 author = {I. 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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 and Michael Gurnis}, 3775 title = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}}, 3776 booktitle = {Eos Transactions of the AGU}, 3777 organization = {American Geophysical Union}, 3778 note = {Fall Meeting Supplemental, Abstract P31A-A1241}, 3779 year = {2009}, 3780 petsc_uses = {KSP} 3781} 3782 3783@InProceedings{ yuenknepleyerlebacherwright09, 3784 author = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright}, 3785 title = {The Coming Role of {GPU} in Computational Geodynamics}, 3786 booktitle = {Eos Transactions of the AGU}, 3787 organization = {American Geophysical Union}, 3788 note = {Fall Meeting Supplemental, Abstract DI22A-05}, 3789 year = {2009}, 3790 petsc_uses = {KSP} 3791} 3792 3793@InProceedings{ aagaardknepleywilliams08, 3794 author = {Brad Aagaard and Charles A. Williams and Matthew G. 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 {S}outhern {C}alifornia 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 {R}ichards 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 {N}orth 4312 {A}tlantic}, 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 {K}alman Filter and the {SEIK} Filter applied to 4321 a Finite Element Model of the {N}orth {A}tlantic}, 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 {N}ewton-{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 {D}rosophila 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 {L}agrange--{N}ewton 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-{B}oltzmann 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 {C}atamaran 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 {C}atamaran}, 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 {N}avier--{S}tokes (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. Sameh and Vivek Sarin}, 5977 title = {Design of Large Scale Parallel Simulations}, 5978 booktitle = {Proceedings of Parallel CFD'99}, 5979 editors = {A. {Ecer et al.}}, 5980 publisher = {Elsevier}, 5981 year = {1999}, 5982 petsc_uses = {KSP} 5983} 5984 5985@InProceedings{ gkks-pcfd99, 5986 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 5987 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 5988 booktitle = {Proceedings of Parallel CFD'99}, 5989 editors = {A. {Ecer et al.}}, 5990 publisher = {Elsevier}, 5991 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 5992 year = {1999}, 5993 petsc_uses = {KSP} 5994} 5995 5996@InProceedings{ kks97, 5997 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 5998 title = {On the Interaction of Architecture and Algorithm in the Domain-Based 5999 Parallelization of an Unstructured Grid Incompressible Flow Code}, 6000 booktitle = {Proceedings of the 10th International Conference on Domain Decomposition 6001 Methods}, 6002 editor = {J. Mandel et al.}, 6003 pages = {311--319}, 6004 publisher = {Wiley}, 6005 note = {}, 6006 year = {1997}, 6007 petsc_uses = {KSP} 6008} 6009 6010@InProceedings{ kks99, 6011 author = {D. K. Kaushik and D. E. Keyes and B. F. 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. Cai}, 6059 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 6060 for incompressible {Navier-Stokes} equations}, 6061 journal = {J. Comput. Phys.}, 6062 volume = {204}, 6063 year = {2005}, 6064 pages = {666--691}, 6065 petsc_uses = {KSP} 6066} 6067 6068@Article{ barbaleonard07, 6069 author = {Lorena A Barba and Anthony Leonard}, 6070 title = {Emergence and evolution of tripole vortices from net-circulation initial 6071 conditions}, 6072 journal = {Phys. Fluids}, 6073 volume = {19}, 6074 pages = {017101}, 6075 year = {2007}, 6076 doi = {10.1063/1.2409734}, 6077 petsc_uses = {KSP} 6078} 6079 6080@Article{ barba07, 6081 author = {Lorena A Barba}, 6082 title = {Non-shielded multipolar vortices at high Reynolds number}, 6083 journal = {Phys. Rev. E}, 6084 volume = {73}, 6085 pages = {065303}, 6086 year = {2006}, 6087 doi = {10.1103/PhysRevE.73.065303}, 6088 petsc_uses = {KSP} 6089} 6090 6091@Article{ schofield2010multi, 6092 title = {Multi-material incompressible flow simulation using the moment-of-fluid method}, 6093 author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and 6094 Lowrie, R.B. and Swartz, B.K.}, 6095 journal = {International Journal for Numerical Methods in Fluids}, 6096 volume = {63}, 6097 number = {8}, 6098 pages = {931--952}, 6099 year = {2010}, 6100 publisher = {Wiley Online Library}, 6101 petsc_uses = {KSP} 6102} 6103 6104% LiteralHTML: 6105% LiteralHTML: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3> 6106% LiteralHTML: 6107% LiteralHTML: article{DeGersem99, 6108% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, 6109% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, 6110% LiteralHTML: } 6111@Article{ nagler2014, 6112 title = {Sound transmission through a poroelastic layered panel}, 6113 author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff}, 6114 journal = {Computational Mechanics}, 6115 volume = {53}, 6116 number = {4}, 6117 pages = {549--560}, 6118 issn = {1432-0924}, 6119 doi = {10.1007/s00466-013-0916-x}, 6120 year = {2014}, 6121 petsc_uses = {KSP} 6122} 6123 6124@Article{ sheikh2013, 6125 author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.}, 6126 title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel 6127 deflation}, 6128 journal = {Numerical Linear Algebra with Applications}, 6129 volume = {20}, 6130 number = {4}, 6131 issn = {1099-1506}, 6132 doi = {10.1002/nla.1882}, 6133 pages = {645--662}, 6134 keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier 6135 analysis}, 6136 year = {2013}, 6137 petsc_uses = {KSP} 6138} 6139 6140@InProceedings{ silence, 6141 author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. 6142 Fuenmayor}, 6143 title = {A parallel computing approach for solving the Helmholtz equation in 3D domains: 6144 Application to the study of acoustic behaviour of silencers}, 6145 year = {2004}, 6146 booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering 6147 (ECCOMAS)}, 6148 petsc_uses = {KSP} 6149} 6150 6151@Article{ degersem99, 6152 author = {H. 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DeSanto}, 6169 year = {1998}, 6170 publisher = {SIAM}, 6171 pages = {620--622}, 6172 address = {Philadelphia}, 6173 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6174 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6175 petsc_uses = {KSP} 6176} 6177 6178@InProceedings{ toselli-wave-98, 6179 author = {Andrea Toselli}, 6180 title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media}, 6181 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6182 editor = {John A. DeSanto}, 6183 year = {1998}, 6184 publisher = {SIAM}, 6185 address = {Philadelphia}, 6186 pages = {540--542}, 6187 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6188 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6189 petsc_uses = {KSP} 6190} 6191 6192@InProceedings{ mcinnes-wave-98, 6193 author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. 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 {N}ewton--{K}rylov--{S}chwarz algorithms for the three-dimensional 6655 {P}oisson--{B}oltzmann 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. 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Korres and Anastasios Tzavellas and Evangelos Galinas}, 7373 title = {A distributed implementation of multi-area power system state estimation on a 7374 cluster of computers }, 7375 journal = {Electric Power Systems Research }, 7376 volume = {102}, 7377 number = {0}, 7378 pages = {20 - 32}, 7379 year = {2013}, 7380 issn = {0378-7796}, 7381 doi = {10.1016/j.epsr.2013.04.002}, 7382 petsc_uses = {KSP} 7383} 7384 7385% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7386% LiteralHTML:<font color="#FF0000"> 7387% LiteralHTML: Material failure, for example, cracking of steel beams resulting 7388% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 7389% LiteralHTML: are important for prediction and prevention. PETSc has been used 7390% LiteralHTML: in a variety of studies of material failure.</p> 7391% LiteralHTML:</font> 7392% LiteralHTML: 7393@InProceedings{ gray2, 7394 author = {Yuan He and Joshua Gray and Richard Braatz and Richard Alkire}, 7395 title = {Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel}, 7396 year = {2004}, 7397 booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}, 7398 petsc_uses = {KSP} 7399} 7400 7401@InProceedings{ gray1, 7402 author = {J. Gray and C. Homescu and L. Petzold and Richard Alkire}, 7403 title = {Algorithms and Computing Architectures for Solving Differential-Algebraic 7404 Equation Systems Typically Encountered in Models of Corrosion Pit Initiation}, 7405 year = {2003}, 7406 booktitle = {Abstracts of the Electrochemical Society 204th meeting}, 7407 petsc_uses = {KSP} 7408} 7409 7410@InProceedings{ crack2, 7411 author = {Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. Wawrzynek}, 7412 title = {A multiscale modeling approach to crack initiation in metallic polycrystals}, 7413 booktitle = {44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials 7414 Conference}, 7415 url = {http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=TRD&recid=A0325099AH}, 7416 year = {2003}, 7417 petsc_uses = {KSP} 7418} 7419 7420@TechReport{ hdams1, 7421 author = {Gerd Heber and Andrew J. Dolgert and Maxirn Alt and Karen A. Mazurkiewicz and 7422 Lynd Stringer}, 7423 title = {Fracture Mechanics on the Intel Itanium Architecture}, 7424 year = {2001}, 7425 institution = {Intel Corporation}, 7426 url = {http://cedar.intel.com/media/pdf/scs/cptconitanium.pdf}, 7427 petsc_uses = {KSP} 7428} 7429 7430@InProceedings{ ihwi, 7431 author = {E. Iesulauro and G. Heber and P. A. Wawrzynek and A. R. Ingraffea}, 7432 title = {Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation}, 7433 booktitle = {International Conference ON Computational Engineering and Sciences}, 7434 year = {2002}, 7435 url = {http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf}, 7436 petsc_uses = {KSP} 7437} 7438 7439@InProceedings{ crack, 7440 author = {Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and 7441 Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris 7442 Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis 7443 and Paul A. Wawrzynek}, 7444 title = {Parallel FEM Simulation of Crack Propagation}, 7445 booktitle = {Proceedings of Irregular 2000}, 7446 url = {http://www.cs.cornell.edu/stodghil/papers/irregular00.ps}, 7447 year = {2000}, 7448 petsc_uses = {KSP} 7449} 7450 7451@InProceedings{ beaudoin98, 7452 author = {A. J. Beaudoin}, 7453 title = {Use of Polycrystal Plasticity Theory in Assessing Material Performance}, 7454 booktitle = {Simulation of materials processing: Theory, methods, and applications - 7455 Proceedings of the Sixth International Conference, NUMIFORM'98}, 7456 editor = {J. Hu\'etink and F. P. T. Baaijens}, 7457 optvolume = {}, 7458 optnumber = {}, 7459 optseries = {}, 7460 year = {1998}, 7461 optorganization={}, 7462 publisher = {A. A. 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 {N}ewton--{K}rylov--{S}chwarz 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. 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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}, 11332 journal = {International Journal of High Performance Computing Applications}, 11333 volume = {21}, 11334 number = {3}, 11335 pages = {291--312}, 11336 year = {2007}, 11337 publisher = {SAGE Publications} 11338} 11339 11340@InProceedings{ charmppoopsla93, 11341 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 11342 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 11343 editor = {Paepcke, A.}, 11344 fulleditor = {Paepcke, Andreas}, 11345 pages = {91--108}, 11346 month = sep, 11347 year = {1993}, 11348 booktitle = {{Proceedings of OOPSLA'93}}, 11349 publisher = {{ACM Press}} 11350} 11351 11352@InProceedings{ hewitt1973universal, 11353 title = {A universal modular actor formalism for artificial intelligence}, 11354 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 11355 booktitle = {Proceedings of the 3rd international joint conference on Artificial 11356 intelligence}, 11357 pages = {235--245}, 11358 year = {1973}, 11359 organization = {Morgan Kaufmann Publishers Inc.} 11360} 11361 11362@Book{ yonezawa1990abcl, 11363 title = {ABCL: an object-oriented concurrent system}, 11364 author = {Yonezawa, Akinori}, 11365 year = {1990}, 11366 publisher = {MIT press} 11367} 11368 11369@InProceedings{ dally1988object, 11370 title = {Object-oriented concurrent programming in CST}, 11371 author = {Dally, William J and Chien, Andrew A}, 11372 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 11373 applications: Architecture, software, computer systems, and general issues-Volume 11374 1}, 11375 pages = {434--439}, 11376 year = {1988}, 11377 organization = {ACM} 11378} 11379 11380@Article{ grimshaw1993easy, 11381 title = {Easy-to-use object-oriented parallel processing with Mentat}, 11382 author = {Grimshaw, Andrew S.}, 11383 journal = {Computer}, 11384 volume = {26}, 11385 number = {5}, 11386 pages = {39--51}, 11387 year = {1993}, 11388 publisher = {IEEE} 11389} 11390 11391@InProceedings{ 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 execution model for scaling-impaired applications}, 11420 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 11421 booktitle = {Parallel Processing Workshops, 2009. 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. 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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. 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Liu}, 12930 publisher = {Prentice-Hall}, 12931 year = {1981}, 12932 key = {SparseDirect} 12933} 12934 12935@Book{ p4-book, 12936 title = {Portable Programs for Parallel Processors}, 12937 publisher = {Holt, Rinehart, {and} Winston}, 12938 year = {1987}, 12939 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 12940 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 12941 key = {P4Book} 12942} 12943 12944@Article{ stones, 12945 author = {H. L. Stone}, 12946 title = {Iterative solution of implicit approximations of multidimensional partial 12947 differential equations}, 12948 journal = {SIAM J. Numerical Analysis}, 12949 pages = {87--113}, 12950 volumne = {5}, 12951 year = {1968} 12952} 12953 12954@Article{ parallelstones, 12955 author = {J. S. Reeve and A. D. Scurr and J. H. 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 for 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@Misc{ nastran-web-page, 13978 author = {{MSC Software Corporation}}, 13979 title = {{NASTRAN} {W}eb page}, 13980 howpublished = {\url{http://www.mechsolutions.com/products/nastran/}}, 13981 year = {2024} 13982} 13983 13984@Book{ hpf, 13985 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 13986 Zosel}, 13987 title = {The High Performance Fotran Handbook}, 13988 publisher = {MIT Press}, 13989 year = {1994} 13990} 13991 13992@InProceedings{ keyes98, 13993 author = {D. E. Keyes}, 13994 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 13995 Architectures}, 13996 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 13997 editors = {M. D. Salas and W. K. Anderson}, 13998 ppublisher = {Elsevier}, 13999 year = {1998} 14000} 14001 14002@InProceedings{ pooma-atlas, 14003 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14004 J. V. W. Reynders and M. Tholburn}, 14005 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14006 Applications}, 14007 year = {1995}, 14008 month = dec, 14009 booktitle = {Supercomputing '95 Proceedings} 14010} 14011 14012% --------------------------------------------------------------------------------- 14013% New bib entries for CRPC paper 14014@Misc{ mgnet-web-page, 14015 author = {Craig C. Douglas}, 14016 title = {{MGNet Web page}}, 14017 note = {See {\tt http://\-www.mgnet.org}} 14018} 14019 14020@Misc{ dagh-web-page, 14021 author = {M. Parashar and J. C. Browne}, 14022 title = {{DAGH Web page}}, 14023 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14024} 14025 14026@Misc{ parasol-web-page, 14027 key = {PARASOL}, 14028 title = {{PARASOL Web page}}, 14029 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14030} 14031 14032@Misc{ pooma-web-page, 14033 author = {{POOMA Web page}}, 14034 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14035} 14036 14037@Misc{ mudpack-web-page, 14038 author = {John C. Adams}, 14039 title = {{MUDPACK Web page}}, 14040 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14041} 14042 14043@Misc{ pellpack-web-page, 14044 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14045 title = {{Parallel ELLPACK Web page}}, 14046 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14047} 14048 14049@InProceedings{ pellpack95, 14050 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14051 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14052 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14053 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14054 address = {Albuquerque, NM}, 14055 year = {1995} 14056} 14057 14058@Misc{ nhse-web-page, 14059 author = {{National High-Performance Software Exchange Web page}}, 14060 note = {See {\tt http://\-www.nhse.org}} 14061} 14062 14063@Misc{ doug-web-page, 14064 author = {Mark J. Hagger and Linda Stals}, 14065 title = {{DOUG Web Page}}, 14066 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14067} 14068 14069@TechReport{ doug97, 14070 author = {Mark J. Hagger}, 14071 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14072 institution = {Mathematical Sciences, University of Bath}, 14073 year = {1997}, 14074 number = {9706}, 14075 note = {Advances in Computational Mathematics (to appear)} 14076} 14077 14078@Misc{ ug-web-page, 14079 author = {{UG Web Page}}, 14080 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14081} 14082 14083@Article{ ug97, 14084 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14085 Rentz-Reichert and C. Wieners}, 14086 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14087 journal = {Computing and Visualization in Science}, 14088 year = {1997}, 14089 volume = {}, 14090 pages = {} 14091} 14092 14093@Misc{ vecfem-web-page, 14094 author = {Lutz Grosz}, 14095 title = {{VECFEM Web Page}}, 14096 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14097} 14098 14099@Misc{ atlas-web-page, 14100 author = {R. Clint {Whaley et al.}}, 14101 title = {{ATLAS Web Page}}, 14102 howpublished = {\url{http://math-atlas.sourceforge.net}} 14103} 14104 14105@Misc{ fenics-web-page, 14106 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14107 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14108 title = {{FEniCS Web Page}}, 14109 note = {\url{http://www.fenicsproject.org}}, 14110 year = {2005} 14111} 14112 14113@Misc{ matlab-web-page, 14114 author = {{The} {MathWorks}}, 14115 title = {{Matlab} {Web} page}, 14116 url = {http://www.mathworks.com} 14117} 14118 14119@Misc{ phipac-web-page, 14120 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14121 and D. Lam}, 14122 title = {{PHiPAC Web Page}}, 14123 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14124} 14125 14126@InProceedings{ kelp, 14127 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14128 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14129 booktitle = {Irregular '96}, 14130 year = {1996} 14131} 14132 14133@Unpublished{ kelp-web-page, 14134 author = {Scott Baden}, 14135 title = {{KeLP} {W}eb page}, 14136 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14137} 14138 14139@InProceedings{ hk99, 14140 author = {R. Hornung and S. Kohn}, 14141 title = {The Use of Object-Oriented Design Patterns in the {SAMRAI} Structured {AMR} 14142 Framework}, 14143 booktitle = {Proceedings of the SIAM Workshop on Object-Oriented Methods for Inter-Operable 14144 Scientific and Engineering Computing}, 14145 pages = {235-244}, 14146 year = {1999}, 14147 note = {See \url{http://www.llnl.gov/CASC/samrai}} 14148} 14149 14150@Unpublished{ samrai-web-page, 14151 title = {{SAMRAI} {W}eb Page}, 14152 author = {Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith}, 14153 note = {See {\tt http://www.llnl.gov/\-CASC/SAMRAI}} 14154} 14155 14156@Misc{ overture-web-page, 14157 author = {William Henshaw and Kyle Chand}, 14158 title = {{Overture} {W}eb page}, 14159 howpublished = {\url{http://www.llnl.gov/CASC/Overture}} 14160} 14161 14162@InProceedings{ overture99, 14163 author = {D.L. Brown and W.D. Henshaw and D.J. Quinlan}, 14164 title = {Overture: An Object-Oriented Framework for Solving Partial Differential Equations 14165 on Overlapping Grids}, 14166 publisher = {SIAM}, 14167 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14168 Scientific and Engineering Computing}, 14169 year = {1999}, 14170 pages = {215-224}, 14171 note = {See \url{http://www.llnl.gov/CASC/Overture}} 14172} 14173 14174@InProceedings{ diffpack, 14175 author = {A.M. Bruaset and H.P. Langtangen}, 14176 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations: 14177 {D}iffpack}, 14178 booktitle = {Numerical Methods and Software Tools in Industrial Mathematics}, 14179 year = {1997}, 14180 pages = {61--90}, 14181 publisher = {Birkhauser Press} 14182} 14183 14184@Article{ dongarra:1984:ila, 14185 author = {J. J. Dongarra and F. G. Gustavson and A. Karp}, 14186 title = {Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline 14187 Machine}, 14188 journal = {SIAM Review}, 14189 volume = {26}, 14190 number = {1}, 14191 pages = {91--112}, 14192 month = jan, 14193 year = {1984}, 14194 coden = {SIREAD}, 14195 issn = {0036-1445 (print), 1095-7200 (electronic)}, 14196 mrclass = {65F10 (65F30)}, 14197 mrnumber = {85c:65032}, 14198 bibdate = {Mon Jan 20 1997}, 14199 abstract = {The authors examine common implementations of linear algebra algorithms, such as 14200 matrix-vector multiplication, matrix-matrix multiplication and the solution of 14201 linear equations. The different versions are examined for efficiency on a computer 14202 architecture which uses vector processing and has pipelined instruction execution. 14203 By using the advanced architectural features of such machines, one can usually 14204 achieve maximum performance, and tremendous improvements in terms of execution 14205 speed can be seen over conventional computers.}, 14206 classification= {723; 921}, 14207 journalabr = {SIAM Rev}, 14208 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 14209 mathematical programming; vector pipeline machine} 14210} 14211 14212@Book{ qv99, 14213 author = {Alfio Quarteroni and Alberto Valli}, 14214 title = {Domain Decomposition Methods for Partial Differential Equations}, 14215 publisher = {Oxford Science Publications}, 14216 address = {Oxford}, 14217 year = {1999} 14218} 14219 14220@Book{ ksv97, 14221 editor = {David E. Keyes and Ahmed Sameh and V. Venkatakrishnan}, 14222 title = {Parallel Numerical Algorithms}, 14223 publisher = {Kluwer Academic Publishers}, 14224 address = {the Netherlands}, 14225 year = {1997} 14226} 14227 14228@Book{ hackbusch94, 14229 author = {Wolfgang Hackbusch}, 14230 title = {Iterative Solution of Large Sparse Systems of Equations}, 14231 publisher = {Springer-Verlag}, 14232 address = {New York}, 14233 year = {1994} 14234} 14235 14236@Article{ hackbusch1980fast, 14237 title = {Fast solution of elliptic control problems}, 14238 author = {Hackbusch, W.}, 14239 journal = {Journal of Optimization Theory and Applications}, 14240 volume = {31}, 14241 number = {4}, 14242 pages = {565--581}, 14243 year = {1980}, 14244 publisher = {Springer} 14245} 14246 14247@Book{ hackbusch1985multi, 14248 title = {{Multi-grid methods and applications}}, 14249 author = {Hackbusch, W.}, 14250 isbn = {3540127615}, 14251 issn = {0179-3632}, 14252 year = {1985}, 14253 publisher = {Springer Verlag} 14254} 14255 14256@Book{ axelsson94, 14257 author = {Owe Axelsson}, 14258 title = {Iterative Solution Methods}, 14259 publisher = {Cambridge University Press}, 14260 address = {Cambridge}, 14261 year = {1994} 14262} 14263 14264@Book{ saad96, 14265 author = {Yousef Saad}, 14266 title = {Iterative Methods for Sparse Linear Systems}, 14267 publisher = {PWS Publishing Company}, 14268 address = {Boston}, 14269 year = {1996} 14270} 14271 14272@Book{ saad2003, 14273 title = {Iterative Methods for Sparse Linear Systems}, 14274 author = {Saad, Yousef}, 14275 doi = {10.1016/S1570-579X(01)80025-2}, 14276 edition = {2nd}, 14277 publisher = {SIAM}, 14278 year = {2003} 14279} 14280 14281@Book{ vandervorst03, 14282 author = {Henk A. {van der Vorst}}, 14283 title = {Iterative Krylov Methods for Large Linear Systems}, 14284 publisher = {Cambridge Monographs on Applied ahd Computational Mathematics}, 14285 year = {2003} 14286} 14287 14288@Book{ koniges00, 14289 editor = {Alice E. Koniges}, 14290 title = {Industrial Strength Parallel Computing}, 14291 publisher = {Morgan Kaufmann Publishers}, 14292 address = {San Francisco}, 14293 year = {2000} 14294} 14295 14296@Misc{ fftw-web-page, 14297 key = {Fftw}, 14298 title = {{FFTW} {Web} page}, 14299 note = {\texttt{http://www.fftw.org/}}, 14300 annote = {fast FFT. Parallel versions with MPI and Cilk} 14301} 14302 14303@InProceedings{ frigojohnson93, 14304 author = {Matteo Frigo and Steven G. Johnson}, 14305 title = {The Design and Implementation of {FFTW3}}, 14306 booktitle = {Proceedings of the IEEE}, 14307 volume = {93}, 14308 number = {2}, 14309 pages = {216--231}, 14310 year = {2005} 14311} 14312 14313@Book{ kelley95, 14314 author = {C. T. Kelley}, 14315 title = {Iterative Methods for Linear and Nonlinear Equations}, 14316 year = {1995}, 14317 publisher = {SIAM}, 14318 address = {Philadelphia} 14319} 14320 14321@Unpublished{ spai-web-page, 14322 title = {{SPAI} {W}eb {P}age}, 14323 note = {http://www.sam.math.ethz.ch/\~{ }grote/spai/}, 14324 author = {Steven Bernard and Marcus Grote}, 14325 institution = {NASA Ames Research Center and ETH Zurich} 14326} 14327 14328@Article{ gh97, 14329 author = {M. J. Grote and T. Huckle}, 14330 title = {Parallel Preconditioning with Sparse Approximate Inverses}, 14331 year = {1997}, 14332 journal = {SIAM J. of Scient. Comput.}, 14333 volume = {18}, 14334 pages = {838-853} 14335} 14336 14337@Article{ zhang96, 14338 author = {Wen Zhang}, 14339 title = {Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the 14340 simulation of a sintering process}, 14341 year = {1996}, 14342 journal = {Appl. Numer. 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Schwartzbach}, 14365 title = {A Domain-Specific Languages for Regular Sets of Strings and Trees}, 14366 booktitle = {Proceedings of the Conference on Domain-Specific Languages}, 14367 publisher = {USENIX}, 14368 month = oct, 14369 year = {1997}, 14370 address = {Santa Barbara, CA} 14371} 14372 14373@InProceedings{ conselmarlet98, 14374 author = {C. Consel and R. 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Dongarra and C. J. K. Tan}, 15716 series = {Lecture Notes in Computer Science}, 15717 volume = {2073}, 15718 publisher = {Springer-Verlag} 15719} 15720 15721@InProceedings{ lefantzi03, 15722 author = {S. Lefantzi and J. Ray}, 15723 year = {2003}, 15724 title = {A Component-based Scientific Toolkit for Reacting Flows}, 15725 booktitle = {Proc. Second MIT Conference on Computational Fluid and Solid Mechanics}, 15726 volume = {2}, 15727 publisher = {Elsevier} 15728} 15729 15730@Article{ boville98, 15731 author = {B. A. Boville and P. R. Gent}, 15732 title = {The {NCAR} Climate System Model, Version One}, 15733 journal = {Journal of Climate}, 15734 volume = {11}, 15735 year = {1998}, 15736 pages = {1115--1130} 15737} 15738 15739@Misc{ paraschivoiu99, 15740 author = {M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes}, 15741 title = {Multi-domain multi-model formulation for compressible flows: Conservative 15742 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 15743 note = {AIAA Paper 99-0784}, 15744 year = {1999} 15745} 15746 15747@Article{ peszynska, 15748 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 15749 title = {Mortar upscaling for multiphysics flow in porous media}, 15750 journal = {Computational Geosciences} 15751} 15752 15753@TechReport{ wheeler00, 15754 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 15755 title = {A distributed computing portal for coupling multi-physics and multiple domains in 15756 porous media}, 15757 institution = {University of Texas at Austin}, 15758 number = {TICAM 00-03}, 15759 year = {2000} 15760} 15761 15762@TechReport{ peszynska00, 15763 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 15764 title = {Multiphysics Coupling of Codes}, 15765 institution = {University of Texas at Austin}, 15766 number = {TICAM 00-02}, 15767 year = {2000} 15768} 15769 15770@Article{ joshaghanijoodatnakshatrala2019, 15771 title = {A stabilized mixed discontinuous Galerkin formulation for double 15772 porosity/permeability model}, 15773 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 15774 journal = {Computer Methods in Applied Mechanics and Engineering}, 15775 volume = {352}, 15776 pages = {508--560}, 15777 year = {2019} 15778} 15779 15780@InProceedings{ cai99, 15781 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 15782 title = {An explicit multi-model compressible flow formulation based on the full potential 15783 equation and the {Euler} equations on {3D} unstructured meshes}, 15784 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 15785 Methods}, 15786 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 15787 year = {1999} 15788} 15789 15790@Article{ he05, 15791 author = {Yun He and Chris H. Q. Ding}, 15792 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 15793 Architectures}, 15794 year = {2005}, 15795 volume = {19}, 15796 pages = {329--240}, 15797 number = {3}, 15798 journal = {Int. Journal of High Performance Computing Applications} 15799} 15800 15801@InProceedings{ uiuc-rocket-center02, 15802 author = {W. A. Dick and M. T. Heath}, 15803 title = {Whole System Simulation of Solid Propellant Rockets}, 15804 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 15805 month = jul, 15806 year = {2002} 15807} 15808 15809@InProceedings{ toth04, 15810 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 15811 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 15812 Oehmke}, 15813 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 15814 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 15815 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 15816 Sun-Earth Connection}, 15817 year = {2004}, 15818 publisher = {Elsevier}, 15819 pages = {383--397} 15820} 15821 15822@Misc{ csdrm:web, 15823 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 15824 Shepherd}, 15825 title = {{Center for Simulation of Dynamic Response of Materials}}, 15826 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 15827} 15828 15829@Misc{ csar:web, 15830 author = {M. {Heath (Director)}}, 15831 title = {{Center for Simulation of Advanced Rockets}}, 15832 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 15833} 15834 15835@Misc{ csafe:web, 15836 author = {D. {Pershing (Director)}}, 15837 title = {{Center for Simulation of Accidental Fires and Explosions}}, 15838 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 15839} 15840 15841@Misc{ cits:web, 15842 author = {P. {Moin (Director)}}, 15843 title = {{Center for Integrated Turbulence Simulations}}, 15844 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 15845} 15846 15847@Misc{ flash:web, 15848 author = {D. {Lamb (Director)}}, 15849 title = {{Center for Integrated Turbulence Simulations}}, 15850 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 15851} 15852 15853@TechReport{ utah-csafe03, 15854 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 15855 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 15856 Problems, Part 1: Algorithm Development}, 15857 institution = {University of Utah, Center for the Simulation of Accidental Fires and 15858 Explosions}, 15859 year = {2003} 15860} 15861 15862@InBook{ shepherd07, 15863 author = {M. Shepherd and E. Seol and B. FrantzDale}, 15864 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 15865 year = {2007}, 15866 booktitle = {CRC Handbook of Dynamic System Modeling}, 15867 publisher = {Wiley}, 15868 pages = {1--41}, 15869 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 15870} 15871 15872@InProceedings{ cactus02, 15873 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 15874 Radke and Edward Seidel and John Shalf}, 15875 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 15876 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 15877 year = {2002}, 15878 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 15879} 15880 15881@Misc{ cactus:homepage, 15882 author = {G. {Allen et al.}}, 15883 title = {{Cactus Web page}}, 15884 howpublished = {\url{http://cactuscode.org}} 15885} 15886 15887@Misc{ open-grid-forum:web, 15888 key = {{Open Grid Forum}}, 15889 title = {{Open Grid Forum}}, 15890 note = {See \url{http://www.ogf.org}} 15891} 15892 15893@Misc{ nox:web, 15894 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 15895 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 15896 note = {See \url{http://software.sandia.gov/nox}} 15897} 15898 15899@Misc{ chombo:web, 15900 author = {P. {Colella (PI)}}, 15901 title = {{Chombo}}, 15902 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 15903} 15904 15905@Article{ lanzkron96, 15906 author = {P. J. Lanzkron and D. J. Rose and J. T. Wilkes}, 15907 title = {An Analysis of Approximate Nonlinear Elimination}, 15908 journal = {SIAM J. Sci. Comput.}, 15909 volume = {17}, 15910 year = {1996}, 15911 pages = {538--559} 15912} 15913 15914@Article{ jiang95, 15915 author = {J. Jiang and P. Forsyth}, 15916 title = {Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} 15917 Equations}, 15918 journal = {Computers and Fluids}, 15919 volume = {24}, 15920 pages = {753--770}, 15921 year = {1995} 15922} 15923 15924@Article{ young90, 15925 author = {D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant}, 15926 title = {Global Convergence of Inexact {Newton} Methods for Transonic Flow}, 15927 journal = {Int. J. Numer. Methods Fluids}, 15928 volume = {11}, 15929 pages = {1075--1095}, 15930 year = {1990} 15931} 15932 15933@Article{ fishwick04, 15934 author = {Paul A. Fishwick}, 15935 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 15936 to Interrelating Model Structures}, 15937 journal = {SCS Trans. on Simulation}, 15938 note = {Special Issue in Grand Challenges in Computer Simulation}, 15939 year = {2004} 15940} 15941 15942@Article{ fishwick03, 15943 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 15944 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 15945 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 15946 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 15947 year = {2003} 15948} 15949 15950@InProceedings{ kirner00, 15951 author = {T. G. Kirner and V. F. Martins}, 15952 title = {Development of an Information Visualization Tool Using Virtual Reality}, 15953 booktitle = {Proceedings of the 2000 ACM Symposium on Applied Computing}, 15954 year = {2000}, 15955 pages = {604--606} 15956} 15957 15958@InProceedings{ orso03, 15959 author = {A. Orso and J. Jones and M. J. Harrold}, 15960 title = {Visualization of Program-Execution Data for Deployed Software}, 15961 booktitle = {Proceedings of the 2003 ACM Symposium on Software Visualization}, 15962 year = {2003}, 15963 pages = {67--76} 15964} 15965 15966@Book{ tiller01, 15967 author = {M. Tiller}, 15968 title = {Introduction to Physical System Modeling with Modelica}, 15969 series = {Kluwer International Series inEngineering and Computer Science}, 15970 volume = {615}, 15971 publisher = {Kluwer}, 15972 year = {2001} 15973} 15974 15975@Article{ buck94, 15976 author = {J. Buck and S. Ha and E. Lee and D. Messerschmitt}, 15977 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 15978 journal = {Int. Journal of Computer Simulation}, 15979 volume = {4}, 15980 pages = {155--182}, 15981 year = {1994} 15982} 15983 15984@Article{ mu95, 15985 author = {M. Mu and J.R. Rice}, 15986 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 15987 journal = {Comp. Syst. Engr.}, 15988 volume = {6}, 15989 year = {1995}, 15990 pages = {87--95} 15991} 15992 15993@TechReport{ drashansky96, 15994 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 15995 author = {R. Drashansky and A. Joshi and J. R. Rice}, 15996 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 15997 year = {1996} 15998} 15999 16000@Article{ michopoulos05, 16001 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 16002 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 16003 journal = {Journal of Computing and Information Science in Engineering}, 16004 volume = {5}, 16005 issue = {3}, 16006 pages = {198--213}, 16007 year = {2005} 16008} 16009 16010@Article{ dubey09, 16011 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16012 Multiphysics Simulation Code}, 16013 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16014 Siegel and K. Weide}, 16015 journal = {Parallel Computing}, 16016 volume = {35}, 16017 issue = {10 -- 11}, 16018 pages = {512 -- 522}, 16019 year = {2009} 16020} 16021 16022@Book{ bottloring95, 16023 author = {Raoul Bott and Loring W. Tu}, 16024 title = {Differential Forms in Algebraic Topology}, 16025 publisher = {Springer}, 16026 year = {1995} 16027} 16028 16029@Book{ kobayashinomizu96, 16030 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16031 title = {Foundations of Differential Geometry}, 16032 publisher = {Wiley-Interscience}, 16033 year = {1996} 16034} 16035 16036@Article{ hornungkohn02, 16037 author = {Richard D. Hornung and Scott R. Kohn}, 16038 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16039 journal = {Concurrency and Computation: Practice and Experience}, 16040 volume = {14}, 16041 pages = {347--368}, 16042 year = {2002} 16043} 16044 16045@InProceedings{ concepts06, 16046 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16047 Gabriel Dos Reis and Andrew Lumsdaine}, 16048 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16049 booktitle = {Proceedings of OOPSLA 2006}, 16050 year = {2006}, 16051 pages = {???--???} 16052} 16053 16054@Book{ hatcher02, 16055 author = {Hatcher, Allen}, 16056 title = {Algebraic Topology}, 16057 publisher = {Cambridge University Press}, 16058 year = {2002} 16059} 16060 16061@Book{ gammahelmjohnsonvlissides95, 16062 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16063 development, offering timeless and elegant solutions to common problems in 16064 software design. It describes patterns for managing object creation, composing 16065 objects into larger structures, and coordinating control flow between objects. The 16066 book provides numerous examples where using composition rather than inheritance 16067 can improve the reusability and flexibility of code. Note, though, that it's not a 16068 tutorial but a catalog that you can use to find an object-oriented design pattern 16069 that's appropriate for the needs of your particular application--a selection for 16070 virtuoso programmers who appreciate (or require) consistent, well-engineered 16071 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16072 more valuable than ever! 16073 16074 Use the contents of the CD to create your own design documents and reusable 16075 components. The CD contains: 23 patterns you can cut and paste into your own 16076 design documents; sample code demonstrating pattern implementation; complete 16077 Design Patterns content in standard HTML format, with numerous hyperlinked 16078 cross-references; accessed through a standard web browser; Java-based dynamic 16079 search mechanism, enhancing online search capabilities; graphical user environment, 16080 allowing ease of navigation. 16081 16082 First published in 1995, this landmark work on object-oriented software design 16083 presents a catalog of simple and succinct solutions to common design problems. 16084 Created by four experienced designers, the 23 patterns contained herein have 16085 become an essential resource for anyone developing reusable object-oriented 16086 software. In response to reader demand, the complete text and pattern catalog are 16087 now available on CD-ROM. This electronic version of Design Patterns enables 16088 programmers to install the book directly onto a computer or network for use as an 16089 online reference for creating reusable object-oriented software. 16090 16091 The authors first describe what patterns are and how they can help you in the 16092 design process. They then systematically name, explain, evaluate, and catalog 16093 recurring designs in object-oriented systems. All patterns are compiled from 16094 real-world examples and include code that demonstrates how they may be implemented 16095 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16096 already own the book will want the CD to take advantage of its dynamic search 16097 mechanism and ready-to-install patterns.}}, 16098 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16099 citeulike-article-id={115158}, 16100 howpublished = {Hardcover}, 16101 isbn = {0201633612}, 16102 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16103 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16104 four gang gof java mathgamespatterns no-tag object object-orientation 16105 object-oriented of oo-patterns oop oriented pattern patterns programming se 16106 software software-development software-engineering software_design 16107 softwareengineering standard}, 16108 month = jan, 16109 publisher = {{Addison-Wesley Professional}}, 16110 title = {Design Patterns}, 16111 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16112 year = {1995} 16113} 16114 16115@InProceedings{ chaco95, 16116 author = {Bruce Hendrickson and Robert Leland}, 16117 title = {A multilevel algorithm for partitioning graphs}, 16118 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16119 (CDROM)}, 16120 year = {1995}, 16121 isbn = {0-89791-816-9}, 16122 pages = {28}, 16123 location = {San Diego, California, United States}, 16124 doi = {10.1145/224170.224228}, 16125 publisher = {ACM Press}, 16126 address = {New York} 16127} 16128 16129@Book{ aleksandrov98, 16130 author = {Aleksandrov, Pavel S.}, 16131 title = {Combinatorial Topology}, 16132 publisher = {Dover}, 16133 volume = {3}, 16134 year = {1998} 16135} 16136 16137@Book{ steenrod99, 16138 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16139 importance in modern physics--such as in gauge theory. This book, a succinct 16140 introduction to the subject by renown mathematician Norman Steenrod, was the first 16141 to present the subject systematically. 16142 16143 It begins with a general introduction to bundles, including such topics as 16144 differentiable manifolds and covering spaces. The author then provides brief 16145 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16146 using them to study further properties of fibre bundles. The result is a classic 16147 and timeless work of great utility that will appeal to serious mathematicians and 16148 theoretical physicists alike. }}, 16149 author = {Steenrod, Norman}, 16150 citeulike-article-id={712999}, 16151 howpublished = {Paperback}, 16152 isbn = {0691005486}, 16153 keywords = {fibre_bundles topology}, 16154 month = apr, 16155 publisher = {{Princeton University Press}}, 16156 title = {The Topology of Fibre Bundles. (PMS-14)}, 16157 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16158 year = {1999} 16159} 16160 16161@Book{ bredon97, 16162 author = {Bredon, Glen E.}, 16163 title = {Sheaf Theory}, 16164 publisher = {Springer}, 16165 pages = {524}, 16166 series = {Graduate Texts in Mathematics}, 16167 year = {1997} 16168} 16169 16170@TechReport{ tautgesmeyers04, 16171 title = {{MOAB}: A Mesh-Oriented Database}, 16172 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16173 Ernst}, 16174 institution = {Sandia National Laboratories}, 16175 number = {SAND2004-1592}, 16176 month = apr, 16177 year = {2004} 16178} 16179 16180@Article{ tautges04, 16181 author = {Timothy J. Tautges}, 16182 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16183 journal = {Engineering With Computers}, 16184 volume = {20}, 16185 pages = {286--293}, 16186 year = {2004} 16187} 16188 16189@InProceedings{ meyers02, 16190 author = {Ray Meyers et. al}, 16191 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16192 booktitle = {8th International conference on numerical grid generation in computational field 16193 simulations}, 16194 month = jun, 16195 year = {2002} 16196} 16197 16198@InProceedings{ seolshepard05, 16199 author = {E. S. Seol and Mark S. Shephard}, 16200 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16201 Analysis}, 16202 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16203 year = {2005} 16204} 16205 16206@Article{ lishephardbeall2005, 16207 title = {3D anisotropic mesh adaptation by mesh modification}, 16208 author = {Xiangrong Li and Mark S Shephard and Mark W Beall}, 16209 journal = {Computer methods in applied mechanics and engineering}, 16210 volume = {194}, 16211 number = {48-49}, 16212 pages = {4915--4950}, 16213 year = {2005}, 16214} 16215 16216@Article{ lushephardtendulkarbeall2014, 16217 title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry}, 16218 author = {Qiukai Lu and Mark S Shephard and Saurabh Tendulkar and Mark W Beall}, 16219 journal = {Engineering with Computers}, 16220 volume = {30}, 16221 pages = {271--286}, 16222 year = {2014}, 16223} 16224 16225@Article{ beallwalshshephard04, 16226 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16227 title = {A comparison of techniques for geometry access related to mesh generation}, 16228 journal = {Engineering With Computers}, 16229 volume = {20}, 16230 number = {3}, 16231 pages = {210--221}, 16232 year = {2004} 16233} 16234 16235@Article{ careyandersoncarneskirk04, 16236 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16237 Kirk}, 16238 title = {Some aspects of adaptive grid technology related to boundary and interior 16239 layers}, 16240 journal = {Journal of Computational Applied Mathematics}, 16241 volume = {166}, 16242 number = {1}, 16243 pages = {55--86}, 16244 year = {2004} 16245} 16246 16247@PhDThesis{ gralthesis, 16248 author = {Guntram Berti}, 16249 title = {Generic Software Components for Scientific Computing}, 16250 school = {TU Cottbus}, 16251 year = {2000}, 16252 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16253} 16254 16255@Article{ whitehead1949, 16256 title = {Combinatorial homotopy. I}, 16257 author = {John HC Whitehead}, 16258 journal = {Bulletin of the American Mathematical Society}, 16259 volume = {55}, 16260 number = {3. P1}, 16261 pages = {213--245}, 16262 year = {1949}, 16263 publisher = {American Mathematical Society} 16264} 16265 16266@Article{ beylkincoifmanrokhlin91, 16267 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16268 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16269 journal = {Communications on Pure and Applied Mathematics}, 16270 volume = {44}, 16271 pages = {141--183}, 16272 year = {1991} 16273} 16274 16275@Book{ wesseling92, 16276 author = {Pieter Wesseling}, 16277 title = {An Introduction to Multigrid Methods}, 16278 publisher = {John Wiley and Sons}, 16279 year = {1992} 16280} 16281 16282@Book{ grakakos04, 16283 author = {Loukas Grakakos}, 16284 title = {Classical and Modern Fourier Analysis}, 16285 publisher = {Pearson Education}, 16286 address = {New Jersey}, 16287 year = {2004} 16288} 16289 16290@Misc{ hlib-web-page, 16291 key = {HLib}, 16292 title = {{HLib} {Web} page}, 16293 note = {{\texttt{http://www.hlib.org/}}}, 16294 annote = {Hierarchical matrices for fast integral transform} 16295} 16296 16297@Article{ hackbusch99, 16298 author = {Wolfgang Hackbusch}, 16299 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16300 Introduction to {$\mathcal H$}-matrices}, 16301 journal = {Computing}, 16302 volume = {62}, 16303 pages = {89--108}, 16304 year = {1999} 16305} 16306 16307@TechReport{ kay1999green, 16308 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16309 equations}, 16310 author = {Kay, D. and Loghin, D.}, 16311 year = {1999}, 16312 institution = {Oxford University Computing Laboratory}, 16313 number = {99/06} 16314} 16315 16316@Article{ bebendorf2003existence, 16317 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16318 elliptic operators with {$L^\infty$}-coefficients}, 16319 author = {Bebendorf, M. and Hackbusch, W.}, 16320 journal = {Numerische Mathematik}, 16321 volume = {95}, 16322 number = {1}, 16323 pages = {1--28}, 16324 year = {2003}, 16325 publisher = {Springer} 16326} 16327 16328@Article{ hackbusch2005direct, 16329 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16330 H$}-matrix approximation}, 16331 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16332 journal = {Computing and Visualization in Science}, 16333 volume = {8}, 16334 number = {3}, 16335 pages = {179--188}, 16336 year = {2005}, 16337 publisher = {Springer} 16338} 16339 16340@TechReport{ duphof2003, 16341 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16342 Logg and L. R. Scott}, 16343 title = {The {FE}ni{CS} project}, 16344 institution = {Chalmers Finite Element Center Preprint Series}, 16345 number = {2003--21}, 16346 year = {2003} 16347} 16348 16349@Article{ flame01, 16350 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16351 Geijn}, 16352 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16353 journal = {Transactions on Mathematical Software}, 16354 volume = {27}, 16355 number = {4}, 16356 year = {2001}, 16357 pages = {422--455} 16358} 16359 16360@Article{ puschel05, 16361 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16362 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16363 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16364 Nick Rizzolo}, 16365 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16366 journal = {Proceedings of the IEEE}, 16367 volume = {93}, 16368 number = {2}, 16369 year = {2005}, 16370 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16371} 16372 16373@Article{ kirbylogg06, 16374 author = {Robert C. Kirby and Anders Logg}, 16375 title = {A compiler for variational forms}, 16376 journal = {ACM Transactions on Mathematical Software}, 16377 volume = {32}, 16378 number = {3}, 16379 year = {2006}, 16380 issn = {0098-3500}, 16381 pages = {417--444}, 16382 doi = {10.1145/1163641.1163644}, 16383 publisher = {ACM Press}, 16384 address = {New York, NY} 16385} 16386 16387@Article{ kirbylogg07, 16388 author = {Robert C. Kirby and Anders Logg}, 16389 title = {Efficient compilation of a class of variational forms}, 16390 journal = {ACM Transactions on Mathematical Software}, 16391 volume = {33}, 16392 number = {3}, 16393 year = {2007}, 16394 issn = {0098-3500}, 16395 pages = {17}, 16396 doi = {10.1145/1268769.1268771}, 16397 publisher = {ACM Press}, 16398 address = {New York, NY} 16399} 16400 16401@Article{ bankdupont81, 16402 author = {Randolph Bank and Todd Dupont}, 16403 title = {An optimal order process for solving finite element equations}, 16404 journal = {Mathematics of Computation}, 16405 volume = {36}, 16406 pages = {35--51}, 16407 year = {1981} 16408} 16409 16410@TechReport{ adams00, 16411 author = {Mark F. Adams}, 16412 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16413 in solid mechanics}, 16414 institution = {UC Berkeley}, 16415 number = {CSD-00-1103}, 16416 year = {2000}, 16417 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16418} 16419 16420@Article{ bergengradlhuelsemannruede06, 16421 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16422 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16423 journal = {Computing in Science \& Engineering}, 16424 volume = {8}, 16425 number = {6}, 16426 pages = {56--62}, 16427 year = {2006} 16428} 16429 16430@MastersThesis{ brunethesis08, 16431 author = {Peter R. Brune}, 16432 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16433 school = {University of Chicago}, 16434 address = {Chicago, IL}, 16435 year = {2008}, 16436 month = feb 16437} 16438 16439@Article{ arnoldwinther02, 16440 author = {Douglas N. Arnold and Ragnar Winther}, 16441 title = {Mixed finite elements for elasticity}, 16442 journal = {Numerische Mathematik}, 16443 volume = {92}, 16444 number = {3}, 16445 month = sep, 16446 year = {2002}, 16447 pages = {401--419}, 16448 doi = {10.1007/s002110100348} 16449} 16450 16451@Article{ arnoldfalkwinther06, 16452 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16453 title = {Finite element exterior calculus, homological techniques, and applications}, 16454 journal = {Acta Numerica}, 16455 year = {2006}, 16456 volume = {15}, 16457 pages = {1--155}, 16458 publisher = {Cambridge University Press}, 16459 doi = {10.1017/S0962492906210018} 16460} 16461 16462@Article{ kirby04, 16463 author = {Robert C. 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Kirby}, 16479 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16480 journal = {ACM Transactions on Mathematical Software}, 16481 volume = {32}, 16482 number = {2}, 16483 year = {2006}, 16484 issn = {0098-3500}, 16485 pages = {223--235}, 16486 doi = {10.1145/1141885.1141889}, 16487 publisher = {ACM Press}, 16488 address = {New York, NY} 16489} 16490 16491@Misc{ bluecrystal08, 16492 author = {{B}lue {C}rystal Cluster}, 16493 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16494 year = {2008}, 16495 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16496} 16497 16498@Article{ beylkin95, 16499 author = {Gregory Beylkin}, 16500 title = {On the Fast Fourier Transform of Functions With Singularities}, 16501 journal = {Applied and Computational Harmonic Analysis}, 16502 volume = {2}, 16503 pages = {363--381}, 16504 year = {1995} 16505} 16506 16507@InProceedings{ riehl08, 16508 author = {Jonathan Riehl}, 16509 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16510 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16511 Development (DSPD'08)}, 16512 address = {Nashville, TN}, 16513 year = {2008} 16514} 16515 16516@Article{ appel85, 16517 author = {Andrew W. 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Chu}, 16683 bibdate = {Wed Jan 07 15:23:19 1998}, 16684 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16685} 16686 16687@Article{ liptonreagan2014, 16688 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16689 author = {Richard J Lipton and Kenneth W Regan}, 16690 pages = {206}, 16691 isbn = {978-0-26202-839-4}, 16692 year = {2014} 16693} 16694 16695@InProceedings{ rhea08, 16696 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16697 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16698 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16699 booktitle = {Proceedings of IEEE/ACM SC '08}, 16700 year = {2008} 16701} 16702 16703@Misc{ bursteddewilcox09, 16704 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16705 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16706 note = {in preparation} 16707} 16708 16709@Article{ skeeltezcanhardy02, 16710 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16711 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16712 journal = {J. Comp. Chem.}, 16713 volume = {23}, 16714 pages = {673--684}, 16715 year = {2002} 16716} 16717 16718@Article{ verschelde99, 16719 author = {Jan Verschelde}, 16720 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16721 homotopy continuation}, 16722 journal = {ACM Trans. Math. Softw.}, 16723 volume = {25}, 16724 number = {2}, 16725 issn = {0098-3500}, 16726 pages = {251--276}, 16727 doi = {10.1145/317275.317286}, 16728 publisher = {ACM}, 16729 address = {New York, NY}, 16730 year = {1999} 16731} 16732 16733@InProceedings{ sommeseverscheldewampler08, 16734 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16735 title = {Solving Polynomial Systems Equation by Equation}, 16736 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16737 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16738 pages = {133--152}, 16739 publisher = {Springer-Verlag}, 16740 year = {2008} 16741} 16742 16743@Article{ phanthientanner77, 16744 author = {N. Phan-Thien and R.~I. Tanner}, 16745 title = {A new constitutive equation derived from network theory}, 16746 journal = {J. Non-Newt. Fluid Mech.}, 16747 volume = {2}, 16748 pages = {353}, 16749 year = {1977} 16750} 16751 16752@Manual{ sage, 16753 key = {SAGE}, 16754 author = {W.\thinspace{}A. Stein and others}, 16755 organization = {The Sage~Development Team}, 16756 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16757 note = {{\tt http://www.sagemath.org}}, 16758 year = {2009} 16759} 16760 16761@Misc{ bateshauensteinsommesewampler06, 16762 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16763 Wampler}, 16764 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16765 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16766} 16767 16768@Article{ archer09, 16769 author = {A. J. 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Keyes}, 16844 title = {{Fusion Simulation Project Workshop Report}}, 16845 month = jul, 16846 year = {2007}, 16847 note = {Available via 16848 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 16849} 16850 16851@Misc{ dahlburg02, 16852 author = {J. {Dahlburg (Chair)}}, 16853 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 16854 year = {2002}, 16855 note = {Available via 16856 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 16857} 16858 16859@Misc{ brown08, 16860 author = {D. {Brown (Chair)}}, 16861 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 16862 to the Future}}, 16863 year = {2008}, 16864 howpublished = {Office of Science, U.S. Department of Energy}, 16865 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 16866} 16867 16868@Misc{ crosscutting10, 16869 author = {D. Brown and P. {Messina (Chairs)}}, 16870 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 16871 Exascale}}, 16872 year = {2010}, 16873 howpublished = {Office of Science, U.S. Department of Energy}, 16874 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 16875} 16876 16877@Misc{ extreme-scale-solvers-workshop12, 16878 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 16879 L.C. McInnes and E. Ng and S. Wild}, 16880 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 16881 Architectures}, 16882 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 16883 note = {{Washington, DC}, March 8-9, 2012}, 16884 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 16885 year = {2012} 16886} 16887 16888@Misc{ monizrosner09, 16889 author = {{E. Moniz and R. Rosner}}, 16890 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 16891 and Simulation at the Extreme Scale}}, 16892 month = may, 16893 year = {2009}, 16894 note = {See 16895 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 16896} 16897 16898@Misc{ blanford08, 16899 author = {{R. Blandord (Chair)}}, 16900 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 16901 Computing at the Extreme Scale}}, 16902 month = dec, 16903 year = {2008}, 16904 note = {See 16905 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 16906} 16907 16908@Misc{ exascale07, 16909 author = {H. Simon and T. Zacharia and R. Stevens}, 16910 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 16911 year = {2007}, 16912 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 16913} 16914 16915@Misc{ ascrbreakthroughs08, 16916 author = {{Panel on Recent Significant Advancements in Computational Science}}, 16917 title = {Breakthroughs}, 16918 year = {2008}, 16919 note = {See 16920 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 16921} 16922 16923@Misc{ petsc-rd100-2009, 16924 author = {{R\&D Magazine}}, 16925 title = {{PETSc} {R}\&{D} 100 Award}, 16926 year = {2009}, 16927 note = {See 16928 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 16929} 16930 16931@Article{ compass-scidac08, 16932 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 16933 R. Ryne}, 16934 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 16935 Computational Science for Future Accelerators and Accelerator Technologies}, 16936 journal = {J. Phys.: Conf. Ser.}, 16937 volume = {125}, 16938 year = {2008}, 16939 pages = {012001}, 16940 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 16941} 16942 16943@Article{ compass-amundson-scidac08, 16944 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 16945 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 16946 Stoltz}, 16947 journal = {J. Phys.: Conf. Ser.}, 16948 volume = {125}, 16949 year = {2008} 16950} 16951 16952@InProceedings{ muszala09, 16953 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 16954 Simulations}, 16955 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 16956 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 16957 {(CBHPC 2009)}}, 16958 year = {2009} 16959} 16960 16961@Article{ gaston09, 16962 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 16963 Equations}, 16964 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 16965 journal = {Nuclear Engineering and Design}, 16966 volume = {239}, 16967 number = {10}, 16968 year = {2009}, 16969 pages = {1768 -- 1778} 16970} 16971 16972@Article{ gaston09b, 16973 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 16974 Engineering}, 16975 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 16976 and C. Permann and W. Taitano}, 16977 journal = {J. Phys.: Conf. Ser.}, 16978 volume = {180}, 16979 year = {2009}, 16980 pages = {012012} 16981} 16982 16983@Article{ newman09, 16984 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 16985 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 16986 author = {Chris Newman and Glen Hansen and Derek Gaston}, 16987 journal = {Journal of Nuclear Materials}, 16988 volume = {392}, 16989 issue = {1}, 16990 year = {2009}, 16991 pages = {6 -- 15} 16992} 16993 16994@Misc{ www:fenics, 16995 author = {{FE}ni{CS}}, 16996 title = {{FE}ni{CS} Project}, 16997 howpublished = {\url{http://www.fenics.org/}}, 16998 year = {2018} 16999} 17000 17001@InProceedings{ zwart08, 17002 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 17003 Systems}, 17004 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 17005 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 17006 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 17007 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 17008 booktitle = {Proceedings of ICCS 2008}, 17009 year = {2008} 17010} 17011 17012@Article{ klocknerwarburtonbridgehesthaven09, 17013 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 17014 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 17015 journal = {J. Comput. Phys.}, 17016 volume = {228}, 17017 number = {21}, 17018 year = {2009}, 17019 issn = {0021-9991}, 17020 pages = {7863--7882}, 17021 doi = {10.1016/j.jcp.2009.06.041}, 17022 publisher = {Academic Press Professional}, 17023 address = {San Diego, CA} 17024} 17025 17026@PhDThesis{ rankin99, 17027 author = {Rankin, W. T.}, 17028 keywords = {FMM, parallel FMM}, 17029 school = {Department of Electrical and Computer Engineering, Duke University}, 17030 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17031 year = {1999} 17032} 17033 17034@InProceedings{ warrensalmon93, 17035 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17036 and implemented. The algorithm computes the forces on an arbitrary distribution of 17037 bodies in a time which scales as N log N with the particle number. The accuracy of 17038 the force calculations is analytically bounded, and can be adjusted via a user 17039 defined parameter between a few percent relative accuracy, down to machine 17040 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17041 tree, we identify...}, 17042 address = {New York}, 17043 author = {Warren, Michael S. and Salmon, John K.}, 17044 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17045 citeulike-article-id={580952}, 17046 keywords = {oct-tree}, 17047 pages = {12--21}, 17048 publisher = {ACM}, 17049 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17050 year = {1993}, 17051 doi = {10.1145/169627.169640}, 17052 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17053} 17054 17055@Unpublished{ cruzwccm10, 17056 author = {Felipe A. Cruz}, 17057 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17058 note = {Presentation at WCCM 2010, Sydney Australia}, 17059 year = {2010} 17060} 17061 17062@Article{ mcguffee06, 17063 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17064 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17065 of salt, {pH}, point mutations, and protein concentration in simulations of 17066 1000-molecule systems}, 17067 journal = {Journal of the American Chemical Society}, 17068 volume = {128}, 17069 pages = {12098--12110}, 17070 year = {2006} 17071} 17072 17073@Article{ nilsencaihoylandlangtangen10, 17074 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17075 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17076 in Python}}, 17077 journal = {ArXiv e-prints}, 17078 archiveprefix = {arXiv}, 17079 eprint = {1002.0705}, 17080 primaryclass = {cs.DC}, 17081 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17082 - Programming Languages}, 17083 year = {2010}, 17084 month = feb, 17085 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17086 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17087} 17088 17089@Misc{ mcinnes:siam09:minisymposium, 17090 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17091 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17092 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17093 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17094 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17095 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17096 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17097 Austin).} 17098} 17099 17100@Misc{ mcinnes:fsp-summary:feb2011, 17101 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17102 title = {Solvers and Time Integration Breakout Summary}, 17103 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17104 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17105} 17106 17107@Misc{ dvi-materials:siamcse11, 17108 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17109 Materials}, 17110 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17111 Smith and L. Wang}, 17112 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17113 and Engineering, March 3, 2011} 17114} 17115 17116@Misc{ jamroz:cemm10, 17117 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17118 author = {B. Jamroz and S. Kruger and T. Austin}, 17119 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17120} 17121 17122@Misc{ kruger:feb4-2011, 17123 title = {personal communication}, 17124 author = {S. Kruger}, 17125 note = {February, 2011} 17126} 17127 17128@Article{ elman1996, 17129 author = {H.C. Elman}, 17130 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17131 viscosity}, 17132 journal = {SIAM J. Sci. Comput.}, 17133 volume = {20}, 17134 year = {1996}, 17135 pages = {1299--1316} 17136} 17137 17138@Article{ kayloghinwathen2002, 17139 author = {D. Kay and D. Loghin and A. Wathen}, 17140 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17141 journal = {SIAM J. Sci. Comput.}, 17142 volume = {24}, 17143 year = {2002}, 17144 pages = {237--256} 17145} 17146 17147@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17148 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17149 title = {Block preconditioners based on approximate commutators}, 17150 journal = {SIAM J. Sci. Comput.}, 17151 volume = {27}, 17152 number = {5}, 17153 year = {2006}, 17154 pages = {1651--1668} 17155} 17156 17157@Article{ braesssarazin1997, 17158 author = {Dietrich Braess and Regina Sarazin}, 17159 title = {An efficient smoother for the {Stokes} problem}, 17160 journal = {Applied Numerical Mathematics}, 17161 volume = {23}, 17162 number = {1}, 17163 year = {1997}, 17164 pages = {3--19}, 17165 doi = {10.1016/S0168-9274(96)00059-1} 17166} 17167 17168@Article{ wright2001large, 17169 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17170 author = {Wright, T.G. and Trefethen, L.N.}, 17171 journal = {SIAM Journal on Scientific Computing}, 17172 volume = {23}, 17173 pages = {591}, 17174 year = {2001} 17175} 17176 17177@Misc{ wright2002eigtool, 17178 title = {Eig{T}ool}, 17179 author = {Wright, T.G. and Trefethen, LN}, 17180 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17181 year = {2002} 17182} 17183 17184@Misc{ visit-web-site, 17185 key = {{VisIt}}, 17186 title = {{VisIt web site}}, 17187 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17188 url = {http://wci.llnl.gov/codes/visit/}, 17189 year = {2011} 17190} 17191 17192@Book{ trefethen1996, 17193 title = {Finite difference and spectral methods for ordinary and partial differential 17194 equations}, 17195 author = {Lloyd Nicholas Trefethen}, 17196 year = {1996}, 17197 publisher = {Cornell University-Department of Computer Science and Center for Applied 17198 Mathematics} 17199} 17200 17201@Book{ trefethen2005spectra, 17202 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17203 author = {Trefethen, L.N. and Embree, M.}, 17204 year = {2005}, 17205 publisher = {Princeton University Press} 17206} 17207 17208@Article{ gomez2010isogeometric, 17209 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17210 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17211 journal = {Computer Methods in Applied Mechanics and Engineering}, 17212 volume = {199}, 17213 number = {25-28}, 17214 pages = {1828--1840}, 17215 issn = {0045-7825}, 17216 year = {2010}, 17217 publisher = {Elsevier} 17218} 17219 17220@Article{ gomez2008isogeometric, 17221 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17222 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17223 journal = {Computer Methods in Applied Mechanics and Engineering}, 17224 volume = {197}, 17225 number = {49-50}, 17226 pages = {4333--4352}, 17227 year = {2008}, 17228 publisher = {Elsevier} 17229} 17230 17231@Misc{ fastmath:project, 17232 author = {Lori {Diachin (PI)}}, 17233 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17234 (FASTMath) Institute}}, 17235 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17236} 17237 17238@Misc{ exascale-software:proposal, 17239 author = {Peter {Beckman (PI)}}, 17240 title = {{Exascale Software Center}}, 17241 note = {proposal to DOE} 17242} 17243 17244@Misc{ imex:project, 17245 author = {Barry {Smith (PI)}}, 17246 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17247 Multimodel PDEs}}, 17248 note = {DOE ASCR applied math project} 17249} 17250 17251@Misc{ intel-mic:website, 17252 author = {Intel}, 17253 title = {{Many Integrated Core Architecture}}, 17254 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17255} 17256 17257@Article{ dudson:2009, 17258 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17259 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17260 journal = {Computer Physics Communications}, 17261 volume = {180}, 17262 pages = {1467}, 17263 year = {2009} 17264} 17265 17266@Article{ umansky:2009, 17267 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17268 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17269 journal = {Computer Physics Communications}, 17270 year = {2009}, 17271 volume = {180}, 17272 pages = {887-903} 17273} 17274 17275@Article{ xu:1998, 17276 author = {X.Q. Xu and R.H. Cohen}, 17277 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17278 journal = {Computer Physics Communications}, 17279 year = {1998}, 17280 volume = {36}, 17281 number = {1-2}, 17282 pages = {158} 17283} 17284 17285@Article{ tron:1999, 17286 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17287 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17288 journal = {SIAM Journal on Optimization}, 17289 volume = {9}, 17290 number = {4}, 17291 pages = {1100-1127}, 17292 year = {1999} 17293} 17294 17295@Article{ stubenamg, 17296 author = {K. St\"{u}ben}, 17297 title = {A review of algebraic multigrid}, 17298 journal = {J. Comput. Appl. Math.}, 17299 volume = {128}, 17300 number = {1-2}, 17301 year = {2001}, 17302 issn = {0377-0427}, 17303 pages = {281--309}, 17304 doi = {10.1016/S0377-0427(00)00516-1}, 17305 publisher = {Elsevier Science Publishers B. V.}, 17306 address = {Amsterdam, The Netherlands, The Netherlands} 17307} 17308 17309@Article{ feuchtermg, 17310 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17311 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17312 journal = {Computing and visualization in science}, 17313 publisher = {Springer}, 17314 volume = {6}, 17315 number = {1}, 17316 year = {2003}, 17317 pages = {1--13} 17318} 17319 17320@Article{ chowmgsmoothness, 17321 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17322 only attempts to interpolate in the directions of geometrical smoothness. These 17323 directions are determined by analyzing samples of algebraically smooth error, e. 17324 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17325 consistently nearby in value. In addition, these dierences may be used to dene 17326 interpolation weights. These new ideas may be incorporated into the algebraic 17327 multigrid method. Test results show that the new method can have much lower grid 17328 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17329 author = {Chow, Edmond}, 17330 citeulike-article-id={7675372}, 17331 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17332 journal = {American Journal of Mathematics}, 17333 keywords = {fem, multigrid}, 17334 pages = {197--215}, 17335 posted-at = {2010-08-17 23:29:51}, 17336 priority = {2}, 17337 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17338 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17339 volume = {65}, 17340 year = {2001} 17341} 17342 17343@Article{ jonesamge, 17344 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17345 elements) method based on element agglomeration. In the method, coarse grid 17346 elements are formed by agglomerating fine grid elements. Compatible interpolation 17347 operators are constructed which yield coarse grid basis functions with a minimal 17348 energy property. Heuristics based on interpolation quality measures are used to 17349 guide the agglomeration procedure. The performance of the resulting method is 17350 demonstrated in two-level numerical experiments.}}, 17351 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17352 citeulike-article-id={8598569}, 17353 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17354 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17355 journal = {SIAM Journal on Scientific Computing}, 17356 keywords = {amg, fem, multigrid}, 17357 number = {1}, 17358 pages = {109--133}, 17359 posted-at = {2011-01-13 18:05:55}, 17360 priority = {2}, 17361 publisher = {SIAM}, 17362 title = {{AMGE Based on Element Agglomeration}}, 17363 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17364 volume = {23}, 17365 year = {2001} 17366} 17367 17368@Article{ saad1993, 17369 author = {Saad, Youcef}, 17370 doi = {10.1137/0914028}, 17371 issn = {10648275}, 17372 journal = {SIAM Journal on Scientific Computing}, 17373 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17374 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17375 precondition-,preconditioned conju-,subject classi cations,variable 17376 preconditioners}, 17377 number = {2}, 17378 pages = {461--469}, 17379 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17380 volume = {14}, 17381 year = {1993} 17382} 17383 17384@Misc{ path:homepage, 17385 author = {S. Dirkse and M. Ferris and T. Munson}, 17386 title = {{{PATH} {W}eb page}}, 17387 howpublished = {\url{http://pages.cs.wisc.edu/~ferris/path.html}} 17388} 17389 17390@Article{ ketcheson2008, 17391 author = {David I Ketcheson}, 17392 title = {Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with 17393 Low-Storage Implementations}, 17394 volume = {30}, 17395 journal = {SIAM Journal on Scientific Computing}, 17396 year = {2008}, 17397 pages = {2113--2136} 17398} 17399 17400@Article{ elman2009boundary, 17401 title = {{Boundary conditions in approximate commutator preconditioners for the 17402 Navier-Stokes equations}}, 17403 author = {Elman, H.C. and Tuminaro, R.}, 17404 journal = {Electronic Transactions on Numerical Analysis}, 17405 volume = {35}, 17406 pages = {257--280}, 17407 year = {2009} 17408} 17409 17410@Article{ elman2008tcp, 17411 title = {{A taxonomy and comparison of parallel block multi-level preconditioners for the 17412 incompressible Navier-Stokes equations}}, 17413 author = {Elman, H.C. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, 17414 R.}, 17415 journal = {Journal of Computational Physics}, 17416 volume = {227}, 17417 number = {1}, 17418 pages = {1790--1808}, 17419 year = {2008}, 17420 publisher = {Academic Press}, 17421 url = {http://chess.cs.umd.edu/~elman/papers/tax.pdf} 17422} 17423 17424@Article{ arioli2013, 17425 title = {Generalized {G}olub--{K}ahan bidiagonalization and stopping criteria}, 17426 author = {Arioli, Mario}, 17427 journal = {SIAM Journal on Matrix Analysis and Applications}, 17428 volume = {34}, 17429 number = {2}, 17430 pages = {571--592}, 17431 year = {2013}, 17432 publisher = {SIAM} 17433} 17434 17435@Book{ wesseling2009, 17436 title = {Principles of computational fluid dynamics}, 17437 author = {Wesseling, Pieter}, 17438 volume = {29}, 17439 year = {2009}, 17440 publisher = {Springer Science \& Business Media} 17441} 17442 17443@Article{ silvester2001efficient, 17444 title = {{Efficient preconditioning of the linearized Navier-Stokes equations for 17445 incompressible flow}}, 17446 author = {Silvester, D. and Elman, H. and Kay, D. and Wathen, A.}, 17447 journal = {Journal of Computational and Applied Mathematics}, 17448 volume = {128}, 17449 number = {1-2}, 17450 pages = {261--279}, 17451 issn = {0377-0427}, 17452 year = {2001}, 17453 publisher = {Elsevier} 17454} 17455 17456@Article{ elman1999bfbt, 17457 title = {{Preconditioning for the steady-state Navier-Stokes equations with low 17458 viscosity}}, 17459 author = {Elman, H.C.}, 17460 journal = {SIAM Journal on Scientific Computing}, 17461 volume = {20}, 17462 number = {4}, 17463 pages = {1299--1316}, 17464 issn = {1064-8275}, 17465 year = {1999}, 17466 publisher = {Citeseer} 17467} 17468 17469@Article{ elman2006bpb, 17470 title = {{Block preconditioners based on approximate commutators}}, 17471 author = {Elman, H. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, R.}, 17472 journal = {SIAM Journal on Scientific Computing}, 17473 volume = {27}, 17474 number = {5}, 17475 pages = {1651--1668}, 17476 year = {2006}, 17477 publisher = {Philadelphia, PA: SIAM, c1993-} 17478} 17479 17480@Article{ olshanskii2006analysis, 17481 title = {{Analysis of a Stokes interface problem}}, 17482 author = {Olshanskii, M.A. and Reusken, A.}, 17483 journal = {Numerische Mathematik}, 17484 volume = {103}, 17485 number = {1}, 17486 pages = {129--149}, 17487 issn = {0029-599X}, 17488 year = {2006}, 17489 publisher = {Springer} 17490} 17491 17492@Article{ patankar1972cph, 17493 title = {{A calculation procedure for heat, mass and momentum transfer in 17494 three-dimensional parabolic flows}}, 17495 author = {Patankar, S.V. and Spalding, D.B.}, 17496 journal = {Int. J. Heat Mass Transfer}, 17497 volume = {15}, 17498 pages = {1787--1806}, 17499 year = {1972} 17500} 17501 17502@Article{ rannacher1992simple, 17503 title = {{Simple nonconforming quadrilateral Stokes element}}, 17504 author = {Rannacher, R. and Turek, S.}, 17505 journal = {Numerical Methods for Partial Differential Equations}, 17506 volume = {8}, 17507 number = {2}, 17508 pages = {97--111}, 17509 issn = {1098-2426}, 17510 year = {1992}, 17511 publisher = {Wiley Online Library} 17512} 17513 17514@Article{ rannacher2000finite, 17515 title = {Finite Element Methods for the Incompressible {N}avier-{S}tokes Equations}, 17516 author = {Rannacher, R.}, 17517 journal = {Fundamental Directions in Mathematical Fluid Mechanics}, 17518 pages = {191}, 17519 isbn = {3764364149}, 17520 year = {2000}, 17521 publisher = {Birkhauser} 17522} 17523 17524@Article{ vanka1986block, 17525 title = {{Block-implicit multigrid solution of Navier-Stokes equations in primitive 17526 variables}}, 17527 author = {Vanka, S.P.}, 17528 journal = {Journal of Computational Physics}, 17529 volume = {65}, 17530 number = {1}, 17531 pages = {138--158}, 17532 issn = {0021-9991}, 17533 year = {1986}, 17534 publisher = {Elsevier} 17535} 17536 17537@Article{ eisenstat1983variational, 17538 title = {Variational iterative methods for nonsymmetric systems of linear equations}, 17539 author = {Eisenstat, S.C. and Elman, H.C. and Schultz, M.H.}, 17540 journal = {SIAM Journal on Numerical Analysis}, 17541 volume = {20}, 17542 number = {2}, 17543 pages = {345--357}, 17544 year = {1983}, 17545 publisher = {JSTOR} 17546} 17547 17548@InProceedings{ burstedde2008scalable, 17549 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 17550 author = {Burstedde, C. and Ghattas, O. and Gurnis, M. and Stadler, G. and Tan, E. and Tu, 17551 T. and Wilcox, L.C. and Zhong, S.}, 17552 booktitle = {Proceedings of the 2008 ACM/IEEE conference on Supercomputing}, 17553 pages = {62}, 17554 year = {2008}, 17555 organization = {IEEE Press} 17556} 17557 17558@Article{ burstedde2009parallel, 17559 title = {Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes} 17560 flow problems}, 17561 author = {Burstedde, C. and Ghattas, O. and Stadler, G. and Tu, T. and Wilcox, L.C.}, 17562 journal = {Computer Methods in Applied Mechanics and Engineering}, 17563 volume = {198}, 17564 number = {21-26}, 17565 pages = {1691--1700}, 17566 year = {2009}, 17567 publisher = {Elsevier} 17568} 17569 17570@Article{ stadler2010dynamics, 17571 title = {The dynamics of plate tectonics and mantle flow: From local to global scales}, 17572 author = {Stadler, G. and Gurnis, M. and Burstedde, C. and Wilcox, L.C. and Alisic, L. and 17573 Ghattas, O.}, 17574 journal = {Science}, 17575 volume = {329}, 17576 number = {5995}, 17577 pages = {1033}, 17578 year = {2010}, 17579 publisher = {American Association for the Advancement of Science} 17580} 17581 17582@Article{ tackley2008modelling, 17583 title = {Modelling compressible mantle convection with large viscosity contrasts in a 17584 three-dimensional spherical shell using the yin-yang grid}, 17585 author = {Tackley, P.J.}, 17586 journal = {Physics of the Earth and Planetary Interiors}, 17587 volume = {171}, 17588 number = {1-4}, 17589 pages = {7--18}, 17590 year = {2008}, 17591 publisher = {Elsevier} 17592} 17593 17594@Article{ moresizhonggurnis96, 17595 author = {Louis N. Moresi and Shijie Zhong and Michael Gurnis}, 17596 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 17597 viscosity}, 17598 journal = {Physics of the Earth and Planetary Interiors}, 17599 volume = {97}, 17600 pages = {83-–94}, 17601 year = {1996} 17602} 17603 17604@Article{ moresisolomatov95, 17605 author = {Louis N. Moresi and V. S. Solomatov}, 17606 title = {Numerical investigation of {2D} convection with extremely large viscosity 17607 variations}, 17608 journal = {Physics of Fluids}, 17609 volume = {7}, 17610 number = {9}, 17611 pages = {2154-–2162}, 17612 year = {1995} 17613} 17614 17615@Article{ chenmolnar83, 17616 author = {W.-P. Chen and P. Molnar}, 17617 title = {Focal depths of intra-continental and intraplate earthquakes and their 17618 implications for the thermal and mechanical properties of the lithosphere}, 17619 journal = {Journal of Geophysical Research}, 17620 volume = {88}, 17621 pages = {4183–-4214}, 17622 year = {1983} 17623} 17624 17625@Article{ jackson02, 17626 author = {J. Jackson}, 17627 title = {Strength of the continental lithosphere: time to abandon the jelly sandwich?}, 17628 journal = {GSA Today}, 17629 volume = {12}, 17630 pages = {4–-10}, 17631 year = {2002} 17632} 17633 17634@Article{ burovwatts06, 17635 author = {E.B. Burov and A.B. Watts}, 17636 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 17637 brulee?}, 17638 journal = {GSA Today}, 17639 volume = {16}, 17640 pages = {4–-10}, 17641 year = {2006} 17642} 17643 17644@InProceedings{ yang:brent:2002, 17645 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 17646 Parallel Distributed Memory Architectures}, 17647 author = {Laurence T. Yang and Richard Brent}, 17648 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 17649 for Parallel Processing}, 17650 year = {2002}, 17651 publisher = {IEEE} 17652} 17653 17654@Article{ demmel2008communication, 17655 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 17656 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 17657 journal = {Arxiv preprint arXiv:0808.2664}, 17658 year = {2008} 17659} 17660 17661@Article{ demmel09, 17662 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 17663 title = {Communication-optimal Iterative Methods}, 17664 journal = {Journal of Physics: Conf. Series}, 17665 volume = {180}, 17666 year = {2009} 17667} 17668 17669@TechReport{ parms04, 17670 author = {Yousef Saad and Masha Sosonkina}, 17671 title = {{pARMS}: A package for the parallel iterative solution of general large sparse 17672 linear systems user's guide}, 17673 number = {UMSI2004-8}, 17674 institution = {Minnesota Supercomputer Institute, University of Minnesota}, 17675 year = {2004} 17676} 17677 17678@Article{ picard1890, 17679 author = {Emile Picard}, 17680 title = {M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la 17681 m\'ethode des approximations successives}, 17682 journal = {Journal De Math\'ematiques Pures et Appliqu\'ees}, 17683 volume = {4}, 17684 number = {6}, 17685 pages = {145--210}, 17686 year = {1890}, 17687 url = {http://math-doc.ujf-grenoble.fr/JMPA/PDF/JMPA_1890_4_6_A3_0.pdf} 17688} 17689 17690@Book{ rall1969, 17691 author = {Louis B. Rall}, 17692 title = {Computational solution of nonlinear operator equations}, 17693 publisher = {Krieger Pub Co.}, 17694 pages = {225}, 17695 year = {1969} 17696} 17697 17698@Article{ fletcherreeves1964, 17699 author = {R. Fletcher and C. M. Reeves}, 17700 title = {Function Minimization by Conjugate Gradients}, 17701 journal = {Computer Journal}, 17702 volume = {7}, 17703 pages = {149–-154}, 17704 year = {1964} 17705} 17706 17707@InBook{ mcinnesallanetal06, 17708 author = {Lois Curfman McInnes and Benjamin Allan and Robert Armstrong and Steven Benson 17709 and David Bernholdt and Tamara Dahlgren and Lori Diachin and Manojkumar Krishnan 17710 and James Kohl and Jay Larson and Sophia Lefantzi and Jarek Nieplocha and Boyana 17711 Norris and Steven Parker and Jaideep Ray and Shujia Zhou}, 17712 editor = {A.~M.~Bruaset and A.~Tveito}, 17713 title = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 17714 chapter = {Parallel {PDE}-Based Simulations Using the {Common Component Architecture}}, 17715 publisher = {Springer}, 17716 year = {2006}, 17717 number = {51}, 17718 series = {Lecture Notes in Computational Science and Engineering}, 17719 pages = {327--381}, 17720 doi = {10.1016/S0167-8191(02)00191-6} 17721} 17722 17723@Article{ cyrshadidtuminaro12, 17724 title = {Stabilization and scalable block preconditioning for the {Navier–Stokes} 17725 equations}, 17726 journal = {Journal of Computational Physics}, 17727 volume = {231}, 17728 number = {2}, 17729 pages = {345 - 363}, 17730 year = {2012}, 17731 issn = {0021-9991}, 17732 doi = {10.1016/j.jcp.2011.09.001}, 17733 author = {Eric C. Cyr and John N. Shadid and Raymond S. Tuminaro} 17734} 17735 17736@Article{ keyesmcinneswoodwardetal13, 17737 title = {Multiphysics Simulations: Challenges and Opportunities}, 17738 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17739 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17740 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17741 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17742 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17743 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17744 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17745 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17746 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17747 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17748 journal = {International Journal of High Performance Computing Applications}, 17749 month = feb, 17750 year = {2013}, 17751 volume = {27}, 17752 number = {1}, 17753 pages = {4--83}, 17754 doi = {10.1177/1094342012468181}, 17755 note = {Special issue}, 17756 abstract = {We consider multiphysics applications from algorithmic and architectural 17757 perspectives, where ``algorithmic'' includes both mathematical analysis and 17758 computational complexity and ``architectural'' includes both software and hardware 17759 environments. Many diverse multiphysics applications can be reduced, en route to 17760 their computational simulation, to a common algebraic coupling paradigm. 17761 Mathematical analysis of multiphysics coupling in this form is not always 17762 practical for realistic applications, but model problems representative of 17763 applications discussed herein can provide insight. A variety of software 17764 frameworks for multiphysics applications have been constructed and refined within 17765 disciplinary communities and executed on leading-edge computer systems. We examine 17766 several of these, expose some commonalities among them, and attempt to extrapolate 17767 best practices to future systems. From our study, we summarize challenges and 17768 forecast opportunities.} 17769} 17770 17771@Misc{ rosner10, 17772 author = {Robert {Rosner (Chair)}}, 17773 title = {{The Opportunities and Challenges of Exascale Computing}}, 17774 year = {2010}, 17775 howpublished = {Office of Science, U.S. Department of Energy}, 17776 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17777} 17778 17779@Misc{ kogge2008exascale, 17780 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 17781 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 17782 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 17783 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 17784 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 17785 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 17786 howpublished = {DARPA}, 17787 year = {2008}, 17788 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 17789} 17790 17791@Misc{ doegrandchallengeworkshops, 17792 key = {Office of Science, U.S. Department of Energy}, 17793 title = {{Scientific Grand Challenges Workshop Series}}, 17794 howpublished = {Office of Science, U.S. Department of Energy, see 17795 \url{http://extremecomputing.labworks.org/workshops.stm}} 17796} 17797 17798@Misc{ lawrence2011, 17799 key = {Lawrence}, 17800 title = {{Ernest Orlando Lawrence Award Winners}}, 17801 howpublished = {U.S. Department of Energy, {\footnotesize 17802 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 17803 year = {2011} 17804} 17805 17806@Article{ murphy2000npi, 17807 title = {{A note on preconditioning for indefinite linear systems}}, 17808 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 17809 journal = {SIAM Journal on Scientific Computing}, 17810 volume = {21}, 17811 number = {6}, 17812 pages = {1969--1972}, 17813 year = {2000}, 17814 publisher = {Philadelphia, PA: SIAM, c1993-} 17815} 17816 17817@Article{ elman2011bouyancy, 17818 title = {Fast iterative solvers for buoyancy driven flow problems}, 17819 journal = {Journal of Computational Physics}, 17820 volume = {230}, 17821 number = {10}, 17822 pages = {3900 - 3914}, 17823 year = {2011}, 17824 note = {}, 17825 issn = {0021-9991}, 17826 doi = {10.1016/j.jcp.2011.02.014}, 17827 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 17828 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 17829 Adaptivity, Preconditioning, Algebraic multigrid} 17830} 17831 17832@Article{ dongarrabeckman11, 17833 author = {J. Dongarra and P. Beckman and et al.}, 17834 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 17835 journal = {Int. J. High Perf. Comput. Applics.}, 17836 volume = {25}, 17837 year = {2011}, 17838 pages = {3--60} 17839} 17840 17841@Article{ mandel1999energy, 17842 title = {Energy optimization of algebraic multigrid bases}, 17843 author = {Mandel, J. and Brezina, M. and Van{\v{e}}k, P.}, 17844 journal = {Computing}, 17845 volume = {62}, 17846 number = {3}, 17847 pages = {205--228}, 17848 year = {1999}, 17849 publisher = {Springer} 17850} 17851 17852@Article{ vanek1996algebraic, 17853 title = {Algebraic multigrid by smoothed aggregation for second and fourth order elliptic 17854 problems}, 17855 author = {Van{\v{e}}k, P. and Mandel, J. and Brezina, M.}, 17856 journal = {Computing}, 17857 volume = {56}, 17858 number = {3}, 17859 pages = {179--196}, 17860 year = {1996}, 17861 publisher = {Springer} 17862} 17863 17864@Article{ vanek2001convergence, 17865 title = {Convergence of algebraic multigrid based on smoothed aggregation}, 17866 author = {Van{\v{e}}ek, P. and Brezina, M. and Mandel, J.}, 17867 journal = {Numerische Mathematik}, 17868 volume = {88}, 17869 number = {3}, 17870 pages = {559--579}, 17871 year = {2001}, 17872 publisher = {Springer} 17873} 17874 17875@Article{ brannick2007algebraic, 17876 title = {Algebraic multigrid methods based on compatible relaxation and energy 17877 minimization}, 17878 author = {Brannick, J. and Zikatanov, L.}, 17879 journal = {Domain decomposition methods in science and engineering XVI}, 17880 pages = {15--26}, 17881 year = {2007}, 17882 publisher = {Springer} 17883} 17884 17885@Article{ brannickfalgout2010, 17886 title = {{Compatible Relaxation and Coarsening in Algebraic Multigrid}}, 17887 author = {James J. Brannick and Robert D. Falgout}, 17888 journal = {SIAM Journal on Scientific Computing}, 17889 volume = {32}, 17890 number = {3}, 17891 pages = {1393--1416}, 17892 url = {http://epubs.siam.org/doi/10.1137/090772216}, 17893 doi = {10.1137/090772216}, 17894 issn = {1064-8275}, 17895 year = {2010} 17896} 17897 17898@Article{ xu2004energy, 17899 title = {On an energy minimizing basis for algebraic multigrid methods}, 17900 author = {Xu, J. and Zikatanov, L.}, 17901 journal = {Computing and Visualization in Science}, 17902 volume = {7}, 17903 number = {3}, 17904 pages = {121--127}, 17905 year = {2004}, 17906 publisher = {Springer} 17907} 17908 17909@Article{ dblp:journals/toms/bakerhlt09, 17910 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 17911 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 17912 journal = {ACM Trans. Math. Softw.}, 17913 volume = {36}, 17914 number = {3}, 17915 year = {2009}, 17916 doi = {10.1145/1527286.1527287}, 17917 bibsource = {DBLP, http://dblp.uni-trier.de} 17918} 17919 17920@Article{ dblp:journals/siamsc/yanggbllhn05, 17921 author = {Chao Yang and Weiguo Gao and Zhaojun Bai and Xiaoye S. Li and Lie-Quan Lee and 17922 Parry Husbands and Esmond G. Ng}, 17923 title = {An Algebraic Substructuring Method for Large-Scale Eigenvalue Calculation}, 17924 journal = {SIAM J. Scientific Computing}, 17925 volume = {27}, 17926 number = {3}, 17927 year = {2005}, 17928 pages = {873-892}, 17929 doi = {10.1137/040613767}, 17930 bibsource = {DBLP, http://dblp.uni-trier.de} 17931} 17932 17933@TechReport{ ml-guide, 17934 author = {M.W. Gee and C.M. Siefert and J.J. Hu and R.S. Tuminaro and M.G. Sala}, 17935 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 17936 institution = {Sandia National Laboratories}, 17937 year = {2006}, 17938 number = {SAND2006-2649} 17939} 17940 17941@Article{ brannick06, 17942 title = {An energy-based AMG coarsening strategy}, 17943 volume = {13}, 17944 doi = {10.1002/nla.480}, 17945 number = {2-3}, 17946 journal = {Numerical Linear Algebra with Applications}, 17947 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 17948 and Ruge, J}, 17949 year = {2006}, 17950 pages = {133--148} 17951} 17952 17953@Article{ olson10, 17954 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 17955 title = {A new perspective on strength measures in algebraic multigrid}, 17956 journal = {Numerical Linear Algebra with Applications}, 17957 volume = {17}, 17958 number = {4}, 17959 pages = {713--733}, 17960 year = {2010}, 17961 publisher = {John Wiley \& Sons, Ltd.}, 17962 issn = {1099-1506}, 17963 doi = {10.1002/nla.669} 17964} 17965 17966@Article{ olson11, 17967 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 17968 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 17969 Minimization}, 17970 journal = {SIAM J. Sci. Comput.}, 17971 issue_date = {April 2011}, 17972 volume = {33}, 17973 issue = {2}, 17974 month = apr, 17975 year = {2011}, 17976 issn = {1064-8275}, 17977 pages = {966--991}, 17978 numpages = {26}, 17979 doi = {10.1137/100803031}, 17980 acmid = {2078825}, 17981 publisher = {Society for Industrial and Applied Mathematics}, 17982 address = {Philadelphia, PA}, 17983 keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed 17984 aggregation} 17985} 17986 17987@Article{ dorit2011, 17988 author = {Dorit Ron and Ilya Safro and Achi Brandt}, 17989 title = {Relaxation-Based Coarsening and Multiscale Graph Organization}, 17990 journal = {Multiscale Modeling {\&} Simulation}, 17991 volume = {9}, 17992 number = {1}, 17993 year = {2011}, 17994 pages = {407-423}, 17995 doi = {10.1137/100791142} 17996} 17997 17998@Article{ chen2011algebraic, 17999 title = {Algebraic distance on graphs}, 18000 author = {Chen, Jie and Safro, Ilya}, 18001 journal = {SIAM Journal on Scientific Computing}, 18002 volume = {33}, 18003 number = {6}, 18004 pages = {3468--3490}, 18005 year = {2011}, 18006 publisher = {SIAM} 18007} 18008 18009@InProceedings{ adams04, 18010 author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.}, 18011 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 18012 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 18013 half a billion degrees of freedom}, 18014 note = {Gordon Bell Award}, 18015 year = {2004} 18016} 18017 18018@Article{ adams03a, 18019 author = {Adams, M.~F.}, 18020 journal = {Numerical Linear Algebra with Applications}, 18021 number = {2-3}, 18022 pages = {141-153}, 18023 title = {Algebraic multigrid methods for constrained linear systems with applications to 18024 contact problems in solid mechanics}, 18025 volume = {11}, 18026 year = {2004} 18027} 18028 18029@Article{ adams-10a, 18030 author = {M. ~F. Adams and Ravi Samtaney and Achi Brandt}, 18031 doi = {10.1016/j.jcp.2010.04.024}, 18032 issn = {0021-9991}, 18033 journal = {Journal of Computational Physics}, 18034 keywords = {Implicit magnetohydrodynamics}, 18035 number = {18}, 18036 pages = {6208 - 6219}, 18037 title = {Toward textbook multigrid efficiency for fully implicit resistive 18038 magnetohydrodynamics}, 18039 volume = {229}, 18040 year = {2010} 18041} 18042 18043@InProceedings{ adams98, 18044 address = {Copper Mountain, CO}, 18045 author = {Adams, M.~F.}, 18046 booktitle = {Proceedings 5th Copper Mountain Conference on Iterative Methods}, 18047 title = {A Parallel Maximal Independent Set Algorithm}, 18048 year = {1998} 18049} 18050 18051@InProceedings{ madaypatera89, 18052 author = {Y. Maday and A. T. Patera}, 18053 title = {Spectral element methods for the {Navier-Stokes} equations}, 18054 editor = {A. K. Noor and J. T. Oden}, 18055 booktitle = {State-of-the-Art Surveys in Computational Mechanics}, 18056 pages = {71-–143}, 18057 publisher = {ASME}, 18058 address = {New York, NY}, 18059 year = {1989} 18060} 18061 18062@Article{ mishra2012mlmcfvm, 18063 title = {Multi-level {M}onte {C}arlo finite volume methods for nonlinear systems of 18064 conservation laws in multi-dimensions}, 18065 journal = {Journal of Computational Physics}, 18066 volume = {231}, 18067 number = {8}, 18068 pages = {3365--3388}, 18069 year = {2012}, 18070 issn = {0021-9991}, 18071 doi = {10.1016/j.jcp.2012.01.011}, 18072 author = {S. Mishra and Ch. Schwab and J. {\v S}ukys}, 18073 keywords = {Conservation laws, Euler, MHD, Uncertainty quantification, Multi-level Monte 18074 Carlo, Parallelization} 18075} 18076 18077@Article{ barth2011mlmcfe, 18078 author = {Barth, Andrea and Schwab, Christoph and Zollinger, Nathaniel}, 18079 affiliation = {ETH Zentrum, Seminar für Angewandte Mathematik, Rämistrasse 101, 8092 Zurich, 18080 Switzerland}, 18081 title = {Multi-Level {M}onte {C}arlo Finite Element method for elliptic {PDE}s with 18082 stochastic coefficients}, 18083 journal = {Numerische Mathematik}, 18084 publisher = {Springer Berlin / Heidelberg}, 18085 issn = {0029-599X}, 18086 keyword = {Mathematics and Statistics}, 18087 pages = {123-161}, 18088 volume = {119}, 18089 issue = {1}, 18090 doi = {10.1007/s00211-011-0377-0}, 18091 year = {2011} 18092} 18093 18094@Article{ nguyen2011hybridizable, 18095 title = {Hybridizable discontinuous {G}alerkin methods}, 18096 author = {Nguyen, N.C. and Peraire, J. and Cockburn, B.}, 18097 journal = {Spectral and High Order Methods for Partial Differential Equations}, 18098 pages = {63--84}, 18099 year = {2011}, 18100 publisher = {Springer} 18101} 18102 18103@Misc{ snyder-scidac3:proposal, 18104 author = {Philip {Snyder (PI)}}, 18105 title = {{Plasma Edge Advanced Computation (PEAC) Center}}, 18106 note = {proposal to DOE SciDAC3}, 18107 month = oct, 18108 year = {2011} 18109} 18110 18111@Misc{ wirth-scidac3:proposal, 18112 author = {Brian {Wirth (PI)}}, 18113 title = {{Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier 18114 through Leadership Class Computing}}, 18115 note = {proposal to DOE SciDAC3}, 18116 month = oct, 18117 year = {2011} 18118} 18119 18120@Misc{ cary-scidac3:proposal, 18121 author = {John {Cary (PI)}}, 18122 title = {{Integrated Multiscale Modeling for Plasma Analysis and Control of Tokamak 18123 Stability (IMMPACTS)}}, 18124 note = {proposal to DOE SciDAC3}, 18125 month = oct, 18126 year = {2011} 18127} 18128 18129@Misc{ vashista-scidac3:proposal, 18130 author = {Priya {Vashista (PI)}}, 18131 title = {{Design of Damage-Tolerance Material Interfaces for Extreme 18132 Stress-Temperature-Corrosion Environments: Algorithms and Methods for 18133 Multi-Petaflops Simulations}}, 18134 note = {proposal to DOE SciDAC3}, 18135 month = mar, 18136 year = {2012} 18137} 18138 18139@Article{ elemental2012, 18140 author = {Jack Poulson and Bryan Marker and Jeff R. Hammond and Nichols A. Romero and 18141 Robert {v}an~{d}e~{G}eijn}, 18142 title = {Elemental: A New Framework for Distributed Memory Dense Matrix Computations}, 18143 journal = {{ACM} Transactions on Mathematical Software}, 18144 volume = {39}, 18145 number = {2}, 18146 year = {2013} 18147} 18148 18149@Misc{ elemental-web-page, 18150 author = {Jack Poulson}, 18151 title = {Elemental: Distributed memory dense linear algebra}, 18152 howpublished = {\url{http://libelemental.org}}, 18153 url = {http://libelemental.org/}, 18154 year = {2015} 18155} 18156 18157@Book{ scalesreport, 18158 title = {A Science-based Case for Large-scale Simulation}, 18159 editor = {D. E. Keyes}, 18160 publisher = {U.S. Department of Energy}, 18161 year = {2004}, 18162 url = {http://www.pnl.gov/scales} 18163} 18164 18165@InProceedings{ cilk95, 18166 address = {Santa Barbara, California}, 18167 author = {Robert D. Blumofe and Christopher F. Joerg and Bradley C. Kuszmaul and Charles E. 18168 Leiserson and Keith H. Randall and Yuli Zhou}, 18169 booktitle = {Proceedings of the Fifth ACM SIGPLAN Symposium on Principles and Practice of 18170 Parallel Programming (PPoPP)}, 18171 day = {19--21}, 18172 month = jul, 18173 pages = {207--216}, 18174 title = {{Cilk}: An Efficient Multithreaded Runtime System}, 18175 year = {1995} 18176} 18177 18178@Misc{ valgrind-web-page, 18179 author = {Julian Seward}, 18180 title = {Valgrind}, 18181 url = {http://valgrind.org/}, 18182 howpublished = {\url{http://valgrind.org/}}, 18183 year = {2012} 18184} 18185 18186@Article{ blas79, 18187 author = {C.~L. Lawson and R.~J. Hanson and D. Kincaid and F.~T. Krogh}, 18188 title = {Basic linear algebra subprograms for Fortran usage}, 18189 journal = {ACM Transactions on Mathematical Software}, 18190 volume = {5}, 18191 pages = {308--323}, 18192 year = {1979} 18193} 18194 18195@TechReport{ lapack90, 18196 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. 18197 Du~Croz and A. Greenbaum and S. Hammarling and A. McKenney and D. Sorensen}, 18198 title = {{LAPACK}: A portable linear algebra library for high-performance computers}, 18199 institution = {Computer Science Dept., University of Tennessee}, 18200 number = {CS-90-105}, 18201 month = may, 18202 year = {1990} 18203} 18204 18205@TechReport{ nvidiafermi, 18206 author = {NVIDIA}, 18207 title = {{NVIDIA}'s Next Generation {CUDA} Compute Architecture: {F}ermi}, 18208 institution = {NVIDIA}, 18209 year = {2009} 18210} 18211 18212@Misc{ intelmic, 18213 author = {Many Core Group, Cambridge University}, 18214 title = {Intel Many Integrated Core Architecture}, 18215 howpublished = {\url{http://www.many-core.group.cam.ac.uk/ukgpucc2/talks/Elgar.pdf}}, 18216 month = dec, 18217 year = {2010} 18218} 18219 18220@Article{ abusufahkucklawrie81, 18221 author = {W. Abu-Sufah and D.~J. Kuck and D.~H. Lawrie}, 18222 title = {On the Performance Enhancement of Paging Systems Through Program Analysis and 18223 Transformations}, 18224 journal = {IEEE Trans. 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Bangerth and R. Hartmann and G. Kanschat}, 18287 title = {{deal.II} -- a General Purpose Object Oriented Finite Element Library}, 18288 journal = {ACM Trans. Math. Softw.}, 18289 year = {2007}, 18290 volume = {33}, 18291 number = {4}, 18292 pages = {24/1--24/27} 18293} 18294 18295@Misc{ dealii-web-page, 18296 author = {W. Bangerth and R. Hartmann and G. Kanschat}, 18297 title = {{deal.II}}, 18298 howpublished = {\url{http://www.dealii.org/}}, 18299 url = {http://www.dealii.org/}, 18300 year = {2012} 18301} 18302 18303@InBook{ siek2012, 18304 title = {The C++0x ``Concepts'' Effort}, 18305 author = {Jeremy G. Siek}, 18306 editor = {Jeremy Gibbons}, 18307 booktitle = {Generic and Indexed Programming: International Spring School, SSGIP 2010, Oxford, 18308 UK, March 22-26, 2010, Revised Lectures}, 18309 pages = {175--216}, 18310 isbn = {978-3-642-32202-0}, 18311 doi = {10.1007/978-3-642-32202-0_4}, 18312 url = {http://arxiv.org/abs/1201.0027}, 18313 note = {\url{http://arxiv.org/abs/1201.0027}}, 18314 publisher = {Springer Berlin Heidelberg}, 18315 year = {2012} 18316} 18317 18318@Misc{ sharpclaw, 18319 note = {\url{http://numerics.kaust.edu.sa/sharpclaw}}, 18320 author = {Ketcheson, D. I. and Parsani, M.}, 18321 keywords = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic 18322 PDEs,sharpclaw,software}, 18323 mendeley-tags = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic 18324 PDEs,sharpclaw,software}, 18325 title = {{SharpClaw software}}, 18326 year = {2011} 18327} 18328 18329@Book{ leveque2002, 18330 title = {Finite volume methods for hyperbolic problems}, 18331 author = {Randall J LeVeque}, 18332 volume = {31}, 18333 year = {2002} 18334} 18335 18336@Misc{ clawpack45, 18337 note = {\url{http://www.clawpack.org}}, 18338 author = {LeVeque, R. J. and Berger, M. J.}, 18339 keywords = {clawpack,finite volumes,hyperbolic PDEs,software}, 18340 mendeley-tags = {clawpack,finite volumes,hyperbolic PDEs,software}, 18341 title = {{Clawpack Software version 4.5}}, 18342 url = {www.clawpack.org}, 18343 year = {2011} 18344} 18345 18346@Article{ nilsen2010, 18347 archiveprefix = {arXiv}, 18348 arxivid = {arXiv:1002.0705v1}, 18349 author = {Nilsen, J.K. and Cai, X. and H{\o}yland, Bj{\o} rn and Langtangen, H. P.}, 18350 eprint = {arXiv:1002.0705v1}, 18351 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 18352 parallelization of scientific codes by a function-centric approach in 18353 Python.pdf:pdf}, 18354 journal = {Computational Science \& Discovery}, 18355 keywords = {parallel,programming,python,software}, 18356 mendeley-tags = {parallel,programming,python,software}, 18357 pages = {015003}, 18358 publisher = {IOP Publishing}, 18359 title = {{Simplifying the parallelization of scientific codes by a function-centric 18360 approach in Python}}, 18361 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 18362 volume = {3}, 18363 year = {2010} 18364} 18365 18366@Book{ langtangen09, 18367 author = {Hans Petter Langtangen}, 18368 title = {Python Scripting for Computational Science}, 18369 publisher = {Springer}, 18370 series = {Texts in Computational Science and Engineering}, 18371 pages = {784}, 18372 isbn = {3540739157}, 18373 year = {2009} 18374} 18375 18376@Book{ numpyguide, 18377 author = {Travis E. Oliphant}, 18378 title = {Guide to {N}umpy}, 18379 publisher = {Trelgol}, 18380 year = {2008} 18381} 18382 18383@Misc{ pycuda, 18384 author = {Andreas Kl\"ockner}, 18385 title = {{PyCUDA}}, 18386 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 18387 year = {2011} 18388} 18389 18390@Misc{ pyopencl, 18391 author = {Andreas Kl\"ockner}, 18392 title = {{PyOpenCL}}, 18393 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 18394 year = {2011} 18395} 18396 18397@Article{ klockner2012, 18398 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 18399 Paul Ivanov and Ahmed Fasih}, 18400 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 18401 generation}, 18402 journal = {Parallel Computing}, 18403 volume = {38}, 18404 number = {3}, 18405 pages = {157--174}, 18406 year = {2012}, 18407 issn = {0167-8191}, 18408 doi = {10.1016/j.parco.2011.09.001} 18409} 18410 18411%%%%%% Matt Stuff %%%%%% 18412@Article{ morrabozdagknepleyrassvesselinov, 18413 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 18414 author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and 18415 Velimir Vesselinov}, 18416 journal = {Eos}, 18417 volume = {102}, 18418 doi = {10.1029/2021EO159258}, 18419 month = {Jun}, 18420 year = {2021} 18421} 18422 18423@Misc{ knepley:icerm-workshop:2012, 18424 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 18425 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 18426 Models for Large-scale Simulations}, 18427 note = {Workshop sponsored by the Institute for Computational and Experimental Research 18428 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 18429 \url{http://icerm.brown.edu/tw12-1-exascale}}, 18430 year = {2012} 18431} 18432 18433@TechReport{ kirbyknepleyscott04, 18434 author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott}, 18435 title = {Optimal Evaluation of Finite Element Matrices}, 18436 type = {Technical Report}, 18437 number = {TR-2004-04}, 18438 institution = {University of Chicago}, 18439 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}, 18440 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}}, 18441 pages = {14}, 18442 month = may, 18443 year = {2004} 18444} 18445 18446@TechReport{ kirbyknepleyscott10, 18447 author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott}, 18448 title = {Languages and Compilers for Variational Forms}, 18449 type = {Technical Report}, 18450 number = {TR-2010-09}, 18451 institution = {University of Chicago}, 18452 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09}, 18453 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09}}, 18454 month = oct, 18455 year = {2010} 18456} 18457 18458@TechReport{ kirbyknepleyscott10b, 18459 author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott}, 18460 title = {Evaluation of the Action of Finite Element Operators}, 18461 type = {Technical Report}, 18462 number = {TR-2010-08}, 18463 institution = {University of Chicago}, 18464 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}, 18465 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}}, 18466 month = oct, 18467 year = {2010} 18468} 18469 18470@TechReport{ bruneknepleyscott11, 18471 author = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott}, 18472 title = {Exponential grids in high-dimensional space}, 18473 type = {Technical Report}, 18474 number = {TR-2011-07}, 18475 institution = {University of Chicago}, 18476 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}, 18477 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}}, 18478 month = dec, 18479 year = {2011} 18480} 18481 18482@TechReport{ zheng11, 18483 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 18484 Zhang and Yaolin Shi}, 18485 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 18486 strongly variable viscosity based on {Matlab} and {CUDA}}, 18487 type = {Research Report}, 18488 number = {UMSI 2011/33}, 18489 institution = {University of Minnesota Supercomputing Institute}, 18490 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 18491 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 18492 month = mar, 18493 year = {2011} 18494} 18495 18496@InProceedings{ zheng2010, 18497 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai 18498 Zhang and Yaolin Shi}, 18499 title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients}, 18500 booktitle = {Eos Transactions of the AGU}, 18501 organization = {American Geophysical Union}, 18502 note = {Fall Meeting Supplemental, Abstract IN41A-1350}, 18503 year = {2010} 18504} 18505 18506@InCollection{ terrelkirbyknepleyscott12, 18507 author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott 18508 and Garth N. Wells}, 18509 title = {Finite elements for incompressible fluids}, 18510 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18511 booktitle = {Automated solutions of differential equations by the finite element method}, 18512 series = {Lecture Notes in Computational Science and Engineering}, 18513 volume = {84}, 18514 pages = {163--169}, 18515 publisher = {Springer-Verlag}, 18516 year = {2012} 18517} 18518 18519@InCollection{ mardalhaga12, 18520 author = {Kent-Andre Mardal and Joachim Berdal Haga}, 18521 title = {Block preconditioning of systems of PDEs}, 18522 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18523 booktitle = {Automated solutions of differential equations by the finite element method}, 18524 series = {Lecture Notes in Computational Science and Engineering}, 18525 volume = {84}, 18526 pages = {643--655}, 18527 publisher = {Springer-Verlag}, 18528 year = {2012} 18529} 18530 18531@InCollection{ kirbyknepleyloggscottterrel12, 18532 author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott and 18533 Andy R. Terrel}, 18534 title = {Discrete optimization of finite element matrix evaluation}, 18535 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18536 booktitle = {Automated solutions of differential equations by the finite element method}, 18537 series = {Lecture Notes in Computational Science and Engineering}, 18538 volume = {84}, 18539 pages = {385--397}, 18540 publisher = {Springer-Verlag}, 18541 year = {2012} 18542} 18543 18544@InCollection{ kirby12, 18545 author = {Robert C. Kirby}, 18546 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 18547 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18548 booktitle = {Automated solutions of differential equations by the finite element method}, 18549 series = {Lecture Notes in Computational Science and Engineering}, 18550 volume = {84}, 18551 publisher = {Springer-Verlag}, 18552 year = {2012} 18553} 18554 18555@Article{ brownconveryhotesknepleypetropolous1993, 18556 author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and 18557 Labros Petropolous}, 18558 title = {Closed strings with low harmonics and kinks}, 18559 journal = {Physical Review D}, 18560 volume = {48}, 18561 number = {6}, 18562 year = {1993} 18563} 18564 18565@Article{ minimax1996, 18566 title = {MiniMax: What has been learned thus far}, 18567 author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and 18568 Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and 18569 C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. 18570 Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 18571 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. 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Ridgway Scott}, 18600 title = {Optimizing the evaluation of finite element matrices}, 18601 journal = {SIAM Journal on Scientific Computing}, 18602 volume = {27}, 18603 number = {3}, 18604 pages = {741--758}, 18605 year = {2005} 18606} 18607 18608@Article{ bardhanknepleyanitescu2008, 18609 author = {Jaydeep P. Bardhan and Matthew G. Knepley and Mihai Anitescu}, 18610 title = {Bounding the Electrostatic Free Energies Associated with Linear Continuum Models 18611 of Molecular Solvation}, 18612 journal = {Journal of Chemical Physics}, 18613 volume = {130}, 18614 number = {10}, 18615 pages = {104108}, 18616 note = {Selected for the March 15, 2009 issue of Virtual Journal of Biological Physics 18617 Research}, 18618 doi = {10.1063/1.3081148}, 18619 year = {2008} 18620} 18621 18622%Poster at Biophysical Society Fall Meeting 18623@Article{ bardhanknepley2017, 18624 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 18625 title = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a 18626 Hydration-Shell {Poisson}-{Boltzmann} Model}, 18627 journal = {Biophysical Journal}, 18628 volume = {110}, 18629 number = {3}, 18630 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 18631 doi = {10.1016/j.bpj.2015.11.1766}, 18632 year = {2017} 18633} 18634 18635@Article{ tabrizirahimigoossensknepleybardhan2018, 18636 title = {Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer 18637 Interface Condition (SLIC) Continuum Dielectric Model}, 18638 author = {Amirhossein Molavi Tabrizi and Ali Mehdizadeh Rahimi and Spencer Goossens and 18639 Matthew G. Knepley and Jaydeep P. Bardhan}, 18640 journal = {International Journal of Quantum Chemistry}, 18641 note = {Accepted}, 18642 year = {2018} 18643} 18644 18645@Article{ knepley2010, 18646 author = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. J. and Donoho, D. 18647 and Fomel, S. and Friedlander, M. P. and Gerstein, M. and Mitchell, I. and 18648 Ouellette, L. L. and Bramble, N. W. and Brown, P. O. and Carey, V. and DeNardis, 18649 L. and Gentleman, R. and {Gezelter, J}, D. and Goodman, A. and Moore, J. E. and 18650 Pasquale, F. A. and Rolnick, J. and Seringhaus, M. and Subramanian, R.}, 18651 title = {{Reproducible Research: addressing the need for data and code sharing in 18652 computational science}}, 18653 journal = {Computing in Science and Engineering}, 18654 volume = {12}, 18655 number = {5}, 18656 pages = {8--13}, 18657 url = {http://www.bepress.com/cgi/viewcontent.cgi?article=1034\&amp;context=sagmb}, 18658 year = {2010} 18659} 18660 18661@Article{ ketchesonahmadiaknepley2011, 18662 title = {Conference Review: High Performance Computing and Hybrid Programming Concepts for 18663 Hyperbolic PDE Codes}, 18664 author = {David I. Ketcheson and Aron Ahmadia and Matthew G. Knepley}, 18665 journal = {SIAM News}, 18666 volume = {44}, 18667 number = {7}, 18668 month = sep, 18669 note = {\url{http://www.siam.org/pdf/news/1912.pdf}}, 18670 year = {2011} 18671} 18672 18673@Article{ yokotabardhanknepleybarbahamada2011, 18674 author = {Rio Yokota and Jaydeep P. Bardhan and Matthew G. Knepley and L.A. Barba and 18675 Tsuyoshi Hamada}, 18676 title = {Biomolecular electrostatics using a fast multipole {BEM} on up to 512 {GPU}s and 18677 a billion unknowns}, 18678 journal = {Computer Physics Communications}, 18679 volume = {182}, 18680 number = {6}, 18681 pages = {1272--1283}, 18682 year = {2011}, 18683 issn = {0010-4655}, 18684 doi = {10.1016/j.cpc.2011.02.013}, 18685 url = {http://arxiv.org/abs/1007.4591} 18686} 18687 18688@Article{ bardhanknepley2011, 18689 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 18690 title = {Mathematical Analysis of the {BIBEE} Approximation for Molecular Solvation: Exact 18691 Results for Spherical Inclusions}, 18692 journal = {Journal of Chemical Physics}, 18693 volume = {135}, 18694 number = {12}, 18695 pages = {124107--124117}, 18696 url = {http://arxiv.org/abs/1109.0651}, 18697 note = {\url{http://arxiv.org/abs/1109.0651}}, 18698 year = {2011} 18699} 18700 18701@Article{ bruneknepleyscott2013, 18702 author = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott}, 18703 title = {Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and 18704 Graded Meshes}, 18705 journal = {SIAM Journal on Scientific Computing}, 18706 url = {http://arxiv.org/abs/1104.0261}, 18707 note = {\url{http://arxiv.org/abs/1104.0261}}, 18708 volume = {35}, 18709 number = {1}, 18710 pages = {A173--A191}, 18711 year = {2013} 18712} 18713 18714@Article{ bardhanknepley2012a, 18715 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 18716 title = {Computational science and re-discovery: open-source implementations of 18717 ellipsoidal harmonics for problems in potential theory}, 18718 journal = {Computational Science \& Discovery}, 18719 volume = {5}, 18720 pages = {014006}, 18721 note = {\url{http://arxiv.org/abs/1204.0267}}, 18722 doi = {10.1088/1749-4699/5/1/014006}, 18723 year = {2012} 18724} 18725 18726@Article{ kreienkampetal2013, 18727 author = {Amy Kreienkamp and Lucy Y. Liu and Mona S. Minkara and Matthew G. Knepley and 18728 Jaydeep P. Bardhan and Mala L. Radhakrishnan}, 18729 title = {Analysis of fast boundary-integral approximations for modeling electrostatic 18730 contributions of molecular binding}, 18731 journal = {Molecular Based Mathematical Biology}, 18732 volume = {1}, 18733 pages = {124--150}, 18734 doi = {10.2478/mlbmb-2013-0007}, 18735 issn = {2299-3266}, 18736 month = jun, 18737 note = {\url{http://www.degruyter.com/view/j/mlbmb.2012.1.issue/mlbmb-2013-0007/mlbmb-2013-0007.xml}}, 18738 year = {2013} 18739} 18740 18741@Article{ bardhanknepleybrune2015, 18742 author = {Jaydeep P. Bardhan and Matthew G. Knepley and Peter R. Brune}, 18743 title = {Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of 18744 Boundary-Integral Operators}, 18745 journal = {Molecular Based Mathematical Biology}, 18746 volume = {3}, 18747 number = {1}, 18748 pages = {1--22}, 18749 doi = {10.1515/mlbmb-2015-0001}, 18750 year = {2015} 18751} 18752 18753@Article{ bardhanknepley14, 18754 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 18755 title = {Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary 18756 Conditions}, 18757 journal = {Journal of Chemical Physics}, 18758 volume = {141}, 18759 number = {13}, 18760 pages = {131103}, 18761 doi = {10.1063/1.4897324}, 18762 year = {2014} 18763} 18764 18765@InProceedings{ bardhantejaniwieckowskiramaswamyknepley2015, 18766 title = {A Nonlinear Boundary Condition for Continuum Models of Biomolecular 18767 Electrostatics}, 18768 author = {Jaydeep P. Bardhan and D. A. Tejani and N. S. Wieckowski and A. Ramaswamy and 18769 Matthew G. Knepley}, 18770 booktitle = {Proceedings of PIERS}, 18771 pages = {1215--1221}, 18772 month = jul, 18773 url = {http://piers.org/piersproceedings/piers2015PragueProc.php?start=250}, 18774 year = {2015} 18775} 18776 18777@Article{ tabriziknepleybardhan2016, 18778 title = {Generalising the mean spherical approximation as a multiscale, nonlinear boundary 18779 condition at the solute-solvent interface}, 18780 author = {Amirhossein Molavi Tabrizi and Matthew G. Knepley and Jaydeep P. Bardhan}, 18781 journal = {Molecular Physics}, 18782 volume = {114}, 18783 number = {16-17}, 18784 pages = {2558--2567}, 18785 doi = {10.1080/00268976.2016.1198503}, 18786 year = {2016} 18787} 18788 18789% http://tex.stackexchange.com/questions/155532/biblatex-and-pubmed-pubmed-central-ids 18790@Article{ tabrizigoossensrahimiknepleybardhan2017, 18791 title = {Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and 18792 Mixtures Using a Solvation-Layer Interface Condition}, 18793 author = {Amirhossein Molavi Tabrizi and Spencer Goossens and Ali Mehdizadeh Rahimi and 18794 Matthew G. Knepley and Jaydeep P. Bardhan}, 18795 journal = {Journal of Chemical Physics}, 18796 volume = {146}, 18797 number = {9}, 18798 pages = {094103}, 18799 url = {http://scitation.aip.org/content/aip/journal/jcp/146/9/10.1063/1.4977037}, 18800 eprint = {https://arxiv.org/abs/1611.02150}, 18801 doi = {10.1063/1.4977037}, 18802 note = {PMCID: PMC5336475}, 18803 year = {2017} 18804} 18805 18806@Article{ tabrizigoossenscooperknepleybardhan2017, 18807 title = {Extending the Solvation-Layer Interface Condition {(SLIC)} Continum Electrostatic 18808 Model to Linearized {Poisson}-{Boltzmann} Solvent}, 18809 author = {Amirhossein Molavi Tabrizi and Spencer Goossens and Christopher D. Cooper and 18810 Matthew G. Knepley and Jaydeep P. Bardhan}, 18811 number = {6}, 18812 pages = {2897--2914}, 18813 journal = {Journal of Chemical Theory and Computation}, 18814 year = {2017} 18815} 18816 18817@InProceedings{ mcclanahan2011, 18818 author = {McClanahan, C and Czechowski, Kent and Battaglino, Casey and Iyer, K and Yeung, P 18819 K and Vuduc, Richard}, 18820 booktitle = {Proc. ACM/IEEE Conf. 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Matthias and Rannacher, Rolf}, 23506 journal = {Journal of Numerical Mathematics}, 23507 volume = {24}, 23508 number = {3}, 23509 pages = {167--187}, 23510 year = {2016} 23511} 23512 23513@Article{ maierrannacher2018, 23514 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23515 multiscale problems}, 23516 author = {Maier, Matthias and Rannacher, Rolf}, 23517 journal = {Multiscale Modeling \& Simulation}, 23518 volume = {16}, 23519 number = {1}, 23520 pages = {412--428}, 23521 year = {2018} 23522} 23523 23524@Article{ margetismaierluskin2017, 23525 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23526 metamaterial sheet}, 23527 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23528 journal = {Studies in Applied Mathematics}, 23529 volume = {139}, 23530 number = {4}, 23531 pages = {599--625}, 23532 year = {2017} 23533} 23534 23535@Article{ maiermargetisluskin2017b, 23536 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23537 approximation and validation}, 23538 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23539 journal = {Journal of Computational Physics}, 23540 volume = {339}, 23541 pages = {126--145}, 23542 year = {2017} 23543} 23544 23545@Article{ maiermargetisluskin2018, 23546 title = {Generation of surface plasmon-polaritons by edge effects}, 23547 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23548 journal = {Communications in Mathematical Sciences}, 23549 volume = {16}, 23550 number = {1}, 23551 pages = {77--95}, 23552 url = {http://arxiv.org/abs/1702.00848}, 23553 year = {2018} 23554} 23555 23556@Article{ maiermattheakiskaxirasluskinmargetis2018, 23557 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23558 metamaterials}, 23559 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23560 Mitchell and Margetis, Dionisios}, 23561 journal = {Physical Review B}, 23562 volume = {97}, 23563 number = {3}, 23564 pages = {035307}, 23565 year = {2018} 23566} 23567 23568@Article{ maiermattheakiskaxirasluskinmargetis2019, 23569 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23570 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23571 Mitchell and Margetis, Dionisios}, 23572 journal = {Proceedings of the Royal Society A}, 23573 volume = {475}, 23574 number = {2230}, 23575 pages = {20190220}, 23576 year = {2019} 23577} 23578 23579@Article{ maiermargetisluskin2020, 23580 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23581 two scales}, 23582 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23583 journal = {Physical Review B}, 23584 volume = {102}, 23585 number = {7}, 23586 pages = {075308}, 23587 year = {2020} 23588} 23589 23590@Article{ 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eigenvalue problems for coupled Helmholtz equations modeling 23643 gradient-index graphene waveguides}, 23644 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23645 journal = {Journal of Computational Physics}, 23646 volume = {423}, 23647 pages = {109871}, 23648 year = {2020} 23649} 23650 23651@Article{ songmaierluskin2019, 23652 title = {Adaptive finite element simulations of waveguide configurations involving 23653 parallel 2D material sheets}, 23654 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23655 journal = {Computer Methods in Applied Mechanics and Engineering}, 23656 volume = {351}, 23657 pages = {20--34}, 23658 year = {2019} 23659} 23660 23661% 23662% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23663% 23664% 23665@Unpublished{ rob1, 23666 author = {Rob Kunz}, 23667 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23668 State University}, 23669 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23670 sponsors = {U.S. Navy, NRC}, 23671 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23672 simulations, including lake warming by power plants}, 23673 dates = {Oct 3 and 4, 2002}, 23674 email = {rfk@wt.arl.psu.edu} 23675} 23676 23677@Unpublished{ au1, 23678 author = {Feng Wang and William Appelbe}, 23679 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23680 url = {http://www.vpac.org}, 23681 sponsors = { }, 23682 note = {Using PETSc for a Variety of Geophysical Simulations}, 23683 dates = {Nov 22, 2002} 23684} 23685 23686@Unpublished{ carl1, 23687 author = {Carl Sovinec}, 23688 institution = {Applied Physics, University of Wisconsin}, 23689 url = {http://nimrodteam.org}, 23690 sponsors = {DOE Office of Fusion Research}, 23691 note = {Investigating using PETSc for NIMROD}, 23692 dates = {Nov 21, 2002}, 23693 email = {sovinec@engr.wisc.edu} 23694} 23695 23696@Unpublished{ au1b, 23697 author = {Pablo Carrica and Robert Wilson}, 23698 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23699 url = {http://}, 23700 sponsors = {Office of Naval Research}, 23701 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23702 dates = {Sept, 2002}, 23703 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23704} 23705 23706% ------------------- TAO References ---------------------- 23707@Article{ benson:2001:csp, 23708 author = {Steven J. 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Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 23810 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 23811 journal = {SIAM Journal on Scientific Computing}, 23812 volume = {16}, 23813 number = {5}, 23814 pages = {1190--1208}, 23815 month = sep, 23816 year = {1995}, 23817 coden = {SJOCE3}, 23818 issn = {1064-8275 (print), 1095-7197 (electronic)}, 23819 mrclass = {90C30 (65K05)}, 23820 mrnumber = {96e:90039}, 23821 mrreviewer = {Henry Wolkowicz}, 23822 bibdate = {Fri Dec 4 16:17:35 MST 1998} 23823} 23824 23825@Article{ lin_c3, 23826 author = {C.-J. Lin and J. J. Mor\'e}, 23827 title = {Newton's method for large bound-constrained optimization problems}, 23828 year = {1999}, 23829 journal = {SIOPT}, 23830 volume = {9(4)}, 23831 pages = {1100--1127}, 23832 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 23833} 23834 23835@TechReport{ dolan2, 23836 author = {E. Dolan and J. J. Mor\'{e}}, 23837 title = {Benchmarking Optimization Software with Performance Profiles}, 23838 year = {2001}, 23839 month = jan, 23840 number = {ANL/MCS-P861-1200}, 23841 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23842 address = {Argonne, IL}, 23843 url = {http://www.mcs.anl.gov/~more/cops/} 23844} 23845 23846@InProceedings{ owlqn, 23847 author = {Galen Andrew and Jianfeng Gao}, 23848 title = {Scalable training of L1-regularized log-linear models}, 23849 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 23850 pages = {33--40}, 23851 year = {2007} 23852} 23853 23854@Article{ bmrm, 23855 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 23856 title = {Bundle methods for regularized risk minimization}, 23857 year = {2010}, 23858 journal = {Journal of Machine Learning Research}, 23859 volume = {11}, 23860 pages = {311--365} 23861} 23862 23863% ------------------- Component Software References ---------------------- 23864@InProceedings{ cca99, 23865 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 23866 McInnes and S. Parker and B. Smolinski}, 23867 title = {Toward a Common Component Architecture for High-Performance Scientific 23868 Computing}, 23869 booktitle = {Proceedings of {High Performance Distributed Computing}}, 23870 pages = {115--124}, 23871 year = {1999}, 23872 note = {See \url{http://cca-forum.org}} 23873} 23874 23875@Book{ szyperski98, 23876 author = {Clemens Szyperski}, 23877 title = {Component Software: Beyond Object-Oriented Programming}, 23878 publisher = {ACM Press}, 23879 address = {New York}, 23880 year = {1998} 23881} 23882 23883@Article{ broy98, 23884 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 23885 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 23886 Stal and Clemens Szyperski}, 23887 title = {What Characterizes a (Software) Component?}, 23888 journal = {Software -- Concepts and Tools}, 23889 publisher = {Springer-Verlag}, 23890 year = {1998}, 23891 volume = {19}, 23892 pages = {49--56} 23893} 23894 23895@Article{ componentware:94, 23896 author = {Jon Udell}, 23897 title = {Componentware}, 23898 journal = {Byte}, 23899 volume = {may}, 23900 pages = {46--56}, 23901 year = {1994}, 23902 key = {Udell94 ! componentware} 23903} 23904 23905@Misc{ cca-web-page, 23906 author = {{Common Component Architecture Forum}}, 23907 note = {See \url{http://cca-forum.org}} 23908} 23909 23910% --------------- References for Tools Used by TAO Developers ----------------- 23911 23912% 23913% tohtml: Used to generate on-line TAO users manual and manual pages 23914% 23915@TechReport{ tohtml, 23916 author = {William Gropp}, 23917 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 23918 institution = {Argonne National Laboratory}, 23919 number = {ANL/MCS-TM-00}, 23920 month = jan, 23921 year = {1995}, 23922 key = {tohtml} 23923} 23924 23925% 23926% doctext: Used to generate tex version of TAO manual pages 23927% 23928@TechReport{ doctext, 23929 author = {William Gropp}, 23930 title = {Users Manual for doctext: Producing documentation from {C} source code}, 23931 institution = {Argonne National Laboratory}, 23932 number = {ANL/MCS-TM-00}, 23933 month = jan, 23934 year = {1995}, 23935 key = {doctext} 23936} 23937 23938% 23939% bfort: Used to generate TAO Fortran interface 23940% 23941@TechReport{ bfort, 23942 author = {William Gropp}, 23943 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 23944 institution = {Argonne National Laboratory}, 23945 number = {ANL/MCS-TM-208}, 23946 month = mar, 23947 year = {1995}, 23948 key = {doctext} 23949} 23950 23951% ------------------------- PETSc References ------------------------------ 23952@InProceedings{ petsc, 23953 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 23954 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 23955 Libraries}, 23956 booktitle = {Modern Software Tools in Scientific Computing}, 23957 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 23958 publisher = {Birkhauser Press}, 23959 pages = {163--202}, 23960 year = {1997} 23961} 23962 23963% ------------------------- Misc Other References ------------------------------ 23964@Misc{ indeps-web-page, 23965 title = {{InDEPS} {W}eb page}, 23966 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 23967 author = {et al. Robert Armstrong}, 23968 institution = {Sandia National Laboratory}, 23969 key = {{InDEPS} {W}eb page} 23970} 23971 23972@Misc{ pooma, 23973 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 23974 chitectures}, 23975 year = {1996}, 23976 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 23977 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 23978} 23979 23980@Misc{ isis++-web-page, 23981 title = {{ISIS++} {W}eb Page}, 23982 note = {See \url{http://ca.sandia.gov/isis}}, 23983 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 23984 institution = {Sandia National Laboratories} 23985} 23986 23987@Misc{ trilinos-web-page, 23988 title = {{Trilinos} {W}eb Page}, 23989 note = {See 23990 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 23991 author = {Mike Heroux et al.}, 23992 institution = {Sandia National Laboratories} 23993} 23994 23995@Misc{ alice-web-page, 23996 title = {{ALICE} {W}eb page}, 23997 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 23998 Argonne National Laboratory}, 23999 key = {{ALICE} {W}eb page} 24000} 24001 24002@Misc{ autodiff-webpage, 24003 author = {{Computational Differentiation Project}}, 24004 note = {See \url{http://www.mcs.anl.gov/autodiff}} 24005} 24006 24007@Misc{ coool-home-page, 24008 author = {Lydia Deng and Wences Gouveia and John Scales}, 24009 title = {{The CWP Object-Oriented Optimization Library}}, 24010 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 24011} 24012 24013@Misc{ rice-inversion-home-page, 24014 author = {Mark S. Gokenbach and William W. Symes}, 24015 title = {{The Hilbert Class Library}}, 24016 note = {See \url{http://www.trip.caam.rice.edu/}} 24017} 24018 24019@Misc{ opt++-home-page, 24020 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 24021 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 24022} 24023 24024@Article{ gockenbach:1999:ccl, 24025 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 24026 title = {C++ Classes for Linking Optimization with Complex Simulations}, 24027 journal = {{ACM} Transactions on Mathematical Software}, 24028 volume = {25}, 24029 number = {2}, 24030 month = jun, 24031 year = {1999}, 24032 pages = {191-212}, 24033 abstract = {The object-oriented programming paradigm can be used to overcome the 24034 incompatibilities between off-the-shelf optimization software and application 24035 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 24036 objects arising in optimization problems, such as vectors, linear operators, and 24037 so forth, as C++ classes, making it possible to write optimization code in a 24038 natural fashion, while allowing application software such as simulators to use the 24039 most convenient data structures and programming style. In spite of the poor 24040 reputation C++ has for runtime performance, the use of mixed-language programming 24041 allows performance equal to that achieved by standard Fortran packages, as 24042 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 24043 accepted = {April 1999}, 24044 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 24045} 24046 24047@Misc{ neos-guide, 24048 author = {{The Optimization Software Guide}}, 24049 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 24050} 24051 24052@Article{ boyd, 24053 title = {Distributed optimization and statistical learning via the alternating direction 24054 method of multipliers}, 24055 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 24056 Jonathan and others}, 24057 journal = {Foundations and Trends{\textregistered} in Machine learning}, 24058 volume = {3}, 24059 number = {1}, 24060 pages = {1-122}, 24061 year = {2011}, 24062 publisher = {Now Publishers, Inc.} 24063} 24064 24065@Misc{ :alertsys, 24066 title = {page{ALERT}}, 24067 organization = {Alert Systems, Inc}, 24068 address = {Madison, Wisconsin}, 24069 note = {http://www.alertsys.com/} 24070} 24071 24072@Manual{ :cmfortran, 24073 title = {{CM} {F}ortran Language Reference Manual}, 24074 organization = {Thinking Machines Corporation}, 24075 year = {1994}, 24076 address = {Cambridge, MA} 24077} 24078 24079@Manual{ :cmmd, 24080 title = {{CMMD} Reference Manual, Version 3.0}, 24081 organization = {Thinking Machines Corporation}, 24082 year = {1993}, 24083 address = {Cambridge, MA} 24084} 24085 24086@Manual{ :cmssl, 24087 title = {{CMSSL} for {CM} {F}ortran}, 24088 volume = {I}, 24089 organization = {Thinking Machines Corporation}, 24090 year = {1994}, 24091 address = {Cambridge, MA} 24092} 24093 24094@Misc{ :condor, 24095 author = {M. Livny}, 24096 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24097 howpublished = {www.cs.wisc.edu/condor} 24098} 24099 24100@Manual{ :connection, 24101 title = {Connection Machine {CM}--5 Technical Summary}, 24102 organization = {Thinking Machines Corporation}, 24103 year = {1993}, 24104 address = {Cambridge, MA} 24105} 24106 24107@Manual{ :cplex, 24108 title = {{CPLEX} Optimizer}, 24109 organization = {ILOG CPLEX Division}, 24110 address = {889 Alder Avenue, Incline Village, Nevada}, 24111 note = {http://www.cplex.com/} 24112} 24113 24114@Manual{ :cplextm, 24115 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24116 (Version 2.0)}, 24117 organization = {CPLEX Optimization Inc.}, 24118 year = {1992}, 24119 address = {Incline Village, Nevada} 24120} 24121 24122@Misc{ :fatcop, 24123 author = {M. C. Ferris}, 24124 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24125 Solver}, 24126 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24127} 24128 24129@Misc{ :metaneos, 24130 author = {S. J. Wright}, 24131 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24132 howpublished = {www-unix.mcs.anl.gov/metaneos} 24133} 24134 24135@InCollection{ gropp.more:optimization, 24136 author = {W. Gropp and J. J. Mor\'e}, 24137 title = {Optimization environments and the {NEOS} Server}, 24138 booktitle = {Approximation Theory and Optimization}, 24139 pages = {167--182}, 24140 publisher = {Cambridge University Press}, 24141 year = {1997}, 24142 editor = {M. D. Buhmann and A. Iserles} 24143} 24144 24145@Article{ czyzyk.mesnier.ea:neos, 24146 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24147 title = {The {NEOS} Server}, 24148 journal = {IEEE Journal on Computational Science and Engineering}, 24149 volume = {5}, 24150 year = {1998}, 24151 pages = {68--75} 24152} 24153 24154@Book{ :osl, 24155 title = {Handbook for {IBM OSL}}, 24156 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24157 year = {1994}, 24158 publisher = {Boyd and Fraser}, 24159 address = {Danvers, Massachusetts} 24160} 24161 24162@Manual{ :pro-matlab, 24163 title = {{PRO}--{MATLAB} User's Guide}, 24164 organization = {The MathWorks, Inc.}, 24165 year = {1989}, 24166 address = {21 Eliot Street, South Natick, MA 01760} 24167} 24168 24169@Misc{ :prostate, 24170 key = {Biomedical}, 24171 title = {Biomedical Business International Newsletter}, 24172 howpublished = {pp. 72--75}, 24173 year = {1996} 24174} 24175 24176@Misc{ :sipcase, 24177 key = {Natural}, 24178 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24179 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24180} 24181 24182@Book{ aarts.korst:simulated, 24183 author = {E. Aarts and J. Korst}, 24184 title = {Simulated Annealing and Boltzman Machines}, 24185 year = {1990}, 24186 publisher = {John Wiley \& Sons}, 24187 address = {Chichester} 24188} 24189 24190@TechReport{ aarts.laarhoven.ea:local-search-based, 24191 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 24192 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 24193 institution = {Centre for Quantitative Methods}, 24194 year = {1991}, 24195 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 24196 number = {106}, 24197 type = {CQM-Not} 24198} 24199 24200@Article{ aashtiani.magnanti:equilibria, 24201 author = {H. Z. Aashtiani and T. L. Magnanti}, 24202 title = {Equilibria on a congested transportation network}, 24203 journal = {SIAM Journal on Algebraic and Discrete Methods}, 24204 volume = {2}, 24205 year = {1981}, 24206 pages = {213--226} 24207} 24208 24209@Article{ ablow.brigham:analog, 24210 author = {C. M. Ablow and G. Brigham}, 24211 title = {An Analog Solution of Programming Problems}, 24212 journal = {Operations Research}, 24213 year = {1955}, 24214 volume = {3}, 24215 pages = {388--394} 24216} 24217 24218@Article{ achuthan.grabowski.ea:optimal, 24219 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 24220 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 24221 journal = {Opsearch}, 24222 year = {1981}, 24223 volume = {18}, 24224 pages = {117--138} 24225} 24226 24227@Book{ adelman.robinson:income, 24228 author = {I. Adelman and S. Robinson}, 24229 title = {Income Distribution Policy in Developing Countries}, 24230 publisher = {Stanford University Press}, 24231 year = {1978}, 24232 address = {Stanford, California} 24233} 24234 24235@Article{ adler.resende.ea:implementation, 24236 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 24237 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 24238 journal = {Mathematical Programming}, 24239 year = {1989}, 24240 volume = {44}, 24241 pages = {297--336} 24242} 24243 24244@TechReport{ aeberhard.coomans.ea:comparison, 24245 author = {S. Aeberhard and D. Coomans and O. de Vel}, 24246 title = {Comparison of Classifiers in High Dimensional Settings}, 24247 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 24248 University of North Queensland}, 24249 year = {1992}, 24250 number = {92-02}, 24251 type = {Technical Report} 24252} 24253 24254@Article{ aganagic.cottle:constructive, 24255 author = {M. Aganagi\'{c} and R. W. Cottle}, 24256 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 24257 Minors}, 24258 journal = {Mathematical Programming}, 24259 year = {1987}, 24260 volume = {37}, 24261 pages = {223--231} 24262} 24263 24264@TechReport{ aganagic:iterative, 24265 author = {M. Aganagi\'{c}}, 24266 title = {Iterative Methods for the Linear Complementarity Problem}, 24267 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 24268 University}, 24269 year = {1978}, 24270 type = {SOL}, 24271 number = {78-10}, 24272 address = {Stanford, California} 24273} 24274 24275@Book{ ahlfors:complex, 24276 author = {L. V. Ahlfors}, 24277 title = {Complex Analysis}, 24278 publisher = {McGraw--Hill Book Company}, 24279 address = {New York}, 24280 series = {International Series in Pure and Applied Mathematics}, 24281 edition = {Second}, 24282 year = {1966} 24283} 24284 24285@Article{ ahn:solution, 24286 author = {B--H. Ahn}, 24287 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 24288 journal = {Journal of Optimization Theory and Applications}, 24289 year = {1981}, 24290 volume = {33}, 24291 pages = {175--185} 24292} 24293 24294@Article{ al-fahed.stavroulakis.ea:hard, 24295 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24296 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 24297 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 24298 volume = {71}, 24299 year = {1991}, 24300 pages = {257--265} 24301} 24302 24303@Article{ al-fahed.stavroulakis.ea:linear, 24304 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24305 title = {A linear complementarity approach to the frictionless gripper}, 24306 journal = {International Journal of Robotic Research}, 24307 volume = {11}, 24308 year = {1992}, 24309 pages = {112--122} 24310} 24311 24312@Article{ al-khayyal.falk:jointly, 24313 author = {F. A. Al--Khayyal and J. E. Falk}, 24314 title = {Jointly Constrained Biconvex Programming}, 24315 journal = {Mathematics of Operations Research}, 24316 year = {1983}, 24317 volume = {8}, 24318 pages = {273--286} 24319} 24320 24321@Article{ al-khayyal.kyparisis:finite, 24322 author = {F. A. Al--Khayyal and J. Kyparisis}, 24323 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 24324 Inequalities}, 24325 journal = {Journal of Optimization Theory and Applications}, 24326 year = {1991}, 24327 volume = {70}, 24328 pages = {319--332} 24329} 24330 24331@PhDThesis{ al-khayyal:biconvex, 24332 author = {F. A. Al--Khayyal}, 24333 title = {Biconvex Programming and Biconcave Minimization}, 24334 year = {1977}, 24335 school = {The George Washington University} 24336} 24337 24338@Article{ alart.curnier:mixed, 24339 author = {P. Alart and A. Curnier}, 24340 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 24341 solution methods}, 24342 journal = {Computer Methods in Applied Mechanics and Engineering}, 24343 volume = {92}, 24344 year = {1991}, 24345 pages = {353--375} 24346} 24347 24348@Misc{ alexander.kellog.ea:piecewise, 24349 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 24350 title = {Piecewise smooth continuation}, 24351 howpublished = {Manuscript}, 24352 year = {1979} 24353} 24354 24355@InCollection{ alexander.li.ea:piecewise, 24356 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 24357 title = {Piecewise smooth homotopies}, 24358 booktitle = {Homotopy Methods and Global Convergence}, 24359 pages = {1--14}, 24360 publisher = {Plenum Press}, 24361 year = {1983}, 24362 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 24363 address = {New York} 24364} 24365 24366@InCollection{ alexander:topological, 24367 author = {J.~C. Alexander}, 24368 title = {The topological theory of an embedding method}, 24369 booktitle = {Continuation Methods}, 24370 pages = {37--68}, 24371 publisher = {Academic Press}, 24372 year = {1978}, 24373 editor = {H. Wacker}, 24374 address = {New York} 24375} 24376 24377@Book{ allen:probability, 24378 author = {A. O. Allen}, 24379 title = {Probability, Statistics and Queueing Theory}, 24380 publisher = {Academic Press}, 24381 year = {1990}, 24382 address = {London}, 24383 edition = {Second} 24384} 24385 24386@Book{ allgower.georg:numerical, 24387 author = {E. L. Allgower and K. Georg}, 24388 title = {Numerical Continuation Methods, An Introduction}, 24389 publisher = {Springer-Verlag}, 24390 year = {1990}, 24391 address = {Berlin} 24392} 24393 24394@InProceedings{ allgower.georg:predictor-corrector, 24395 crossref = {bachem.grotschel.ea:mathematical}, 24396 author = {E. L. Allgower and K. Georg}, 24397 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 24398 Zero Points of Nonlinear Mappings}, 24399 pages = {15--56} 24400} 24401 24402@Article{ aluffi-pentini.parisi.ea:algorithm, 24403 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 24404 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 24405 Algorithm}, 24406 journal = {ACM Transactions on Mathematical Software}, 24407 year = {1988}, 24408 volume = {14}, 24409 pages = {366--380} 24410} 24411 24412@Article{ anandalingam.friesz:hierarchical, 24413 author = {G. Anandalingam and T. L. Friesz}, 24414 title = {Hierarchical Optimization: An Introduction}, 24415 journal = {Annals of Operations Research}, 24416 year = {1992}, 24417 volume = {34}, 24418 pages = {1--11} 24419} 24420 24421@Article{ anandalingam.white:solution, 24422 author = {G. Anandalingam and D. J. White}, 24423 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 24424 Functions}, 24425 journal = {IEEE Transactions on Automatic Control}, 24426 year = {1990}, 24427 volume = {35}, 24428 number = {10}, 24429 pages = {1170--1173} 24430} 24431 24432@Article{ andersen.andersen:presolving, 24433 author = {E. Andersen and K. Andersen}, 24434 title = {Presolving in Linear Programming}, 24435 year = {1995}, 24436 journal = {Mathematical Programming}, 24437 volume = {71}, 24438 pages = {221--245} 24439} 24440 24441@InProceedings{ andersen.ye:homogeneous, 24442 author = {E. Andersen and Y. Ye}, 24443 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 24444 Equality Constraints}, 24445 crossref = {ferris.pang:complementarity}, 24446 pages = {1--11} 24447} 24448 24449@Book{ anderson.bai.ea:lapack, 24450 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 24451 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 24452 Sorensen}, 24453 title = {{LAPACK} User's Guide}, 24454 publisher = {SIAM}, 24455 year = {1995}, 24456 address = {Philadelphia, Pennsylvania}, 24457 edition = {Second} 24458} 24459 24460@Article{ anderson.ferris:direct, 24461 author = {E. J. Anderson and M. C. Ferris}, 24462 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 24463 year = {2001}, 24464 journal = {SIAM Journal on Optimization, forthcoming}, 24465 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 24466 key = {55} 24467} 24468 24469@InProceedings{ anderson.ferris:genetic, 24470 author = {E. J. Anderson and M. C. Ferris}, 24471 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 24472 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 24473 Waterloo, Ontario, Canada, May 28--30}, 24474 publisher = {University of Waterloo Press}, 24475 key = {14}, 24476 year = {1990} 24477} 24478 24479@Article{ anderson.ferris:genetic*1, 24480 author = {E. J. Anderson and M. C. Ferris}, 24481 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 24482 Problem}, 24483 journal = {ORSA Journal on Computing}, 24484 year = {1994}, 24485 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 24486 volume = {6}, 24487 pages = {161--173}, 24488 key = {22} 24489} 24490 24491@InProceedings{ anderson.ferris:parallel, 24492 author = {E. J. Anderson and M. C. Ferris}, 24493 title = {Parallel Genetic Algorithms in Optimization}, 24494 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 24495 Computing, Chicago, Illinois, December 11-13}, 24496 year = {1989}, 24497 key = {12} 24498} 24499 24500@Unpublished{ anderson.lewis:primal, 24501 author = {E. J. Anderson and A. S. Lewis}, 24502 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24503 note = {In preparation} 24504} 24505 24506@Book{ anderson.nash:linear, 24507 author = {E. J. Anderson and P. Nash}, 24508 title = {Linear Programming in Infinite--Dimensional Spaces}, 24509 year = {1987}, 24510 publisher = {John Wiley \& Sons}, 24511 address = {Chichester} 24512} 24513 24514@InProceedings{ anderson:primal, 24515 author = {E. J. Anderson}, 24516 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24517 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 24518 Programming, Cambridge, September 1984}, 24519 year = {1985}, 24520 editor = {E. J. Anderson and A. B. Philpott}, 24521 publisher = {Springer-Verlag}, 24522 address = {Berlin} 24523} 24524 24525@Article{ andradottir:method, 24526 author = {S. Andrad\'{o}ttir}, 24527 title = {A Method of Discrete Stochastic Optimization}, 24528 journal = {Management Science}, 24529 year = {1995}, 24530 volume = {41}, 24531 pages = {1946--1961} 24532} 24533 24534@Article{ andradottir:global, 24535 author = {S. Andrad\'{o}ttir}, 24536 title = {A Global Search Method for Discrete Stochastic Optimization}, 24537 journal = {SIAM Journal on Optimization}, 24538 year = {1996}, 24539 volume = {6}, 24540 pages = {513--530} 24541} 24542 24543@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 24544 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 24545 title = {An infeasible--interior--point predictor--corrector algorithm for the 24546 {P}$_x$--geometric {LCP}}, 24547 institution = {Department of Mathematics, The University of Iowa}, 24548 address = {Iowa City, Iowa}, 24549 year = {1994}, 24550 number = {62}, 24551 type = {Reports on Computational Mathematics} 24552} 24553 24554@TechReport{ anitescu.potra:formulating, 24555 author = {M. Anitescu and F. A. Potra}, 24556 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 24557 Linear Complementarity Problems}, 24558 institution = {Department of Mathematics, The University of Iowa}, 24559 year = {1996}, 24560 type = {Report}, 24561 number = {93}, 24562 address = {Iowa City, Iowa} 24563} 24564 24565@Article{ anstreicher.lee.ea:crashing, 24566 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 24567 title = {Crashing a Maximum-Weight Complementarity Basis}, 24568 journal = {Mathematical Programming}, 24569 year = {1992}, 24570 volume = {54}, 24571 pages = {281--294} 24572} 24573 24574@Article{ anstreicher:combined, 24575 author = {K. M. Anstreicher}, 24576 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 24577 programming}, 24578 journal = {Mathematical Programming}, 24579 year = {1991}, 24580 volume = {52}, 24581 pages = {429--440} 24582} 24583 24584@Article{ anstreicher:combined*1, 24585 author = {K. M. 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Bertsekas}, 25216 title = {Nonlinear Programming}, 25217 publisher = {Athena Scientific}, 25218 year = {1995}, 25219 address = {Belmont, Massachusetts} 25220} 25221 25222@Article{ bertsekas:projected, 25223 author = {Dimitri P. Bertsekas}, 25224 title = {Projected {N}ewton Methods for Optimization Problems with Simple Constraints}, 25225 journal = {SIAM Journal on Control and Optimization}, 25226 year = {1982}, 25227 volume = {20}, 25228 pages = {221--246} 25229} 25230 25231@Article{ billups.dirkse.ea:comparison, 25232 author = {S. C. Billups and S. P. Dirkse and M. C. Ferris}, 25233 title = {A Comparison of Large Scale Mixed Complementarity Problem Solvers}, 25234 journal = {Computational Optimization and Applications}, 25235 year = {1997}, 25236 pages = {3--25}, 25237 volume = {7}, 25238 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps}, 25239 key = {51} 25240} 25241 25242@Article{ billups.ferris:convergence, 25243 author = {S. C. Billups and M. C. Ferris}, 25244 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 25245 Starting Points}, 25246 journal = {SIAM Journal on Optimization}, 25247 year = {1996}, 25248 volume = {6}, 25249 pages = {316--325}, 25250 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 25251 key = {34} 25252} 25253 25254@TechReport{ billups.ferris:convergence*1, 25255 author = {S. C. Billups and M. C. Ferris}, 25256 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 25257 Points}, 25258 institution = {Computer Sciences Department, University of Wisconsin}, 25259 year = {1993}, 25260 address = {Madison, Wisconsin}, 25261 number = {1180}, 25262 note = {Revised version in SIAM Journal on Optimization.} 25263} 25264 25265@Article{ billups.ferris:qpcomp, 25266 author = {S. C. Billups and M. C. 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Kanzow}, 28080 title = {Regularity Properties of a Semismooth Reformulation of Variational Inequalities}, 28081 journal = {SIAM Journal on Optimization}, 28082 year = {1998}, 28083 volume = {8}, 28084 pages = {850--869} 28085} 28086 28087@Article{ facchinei.fischer.ea:semismooth, 28088 title = {A Semismooth {N}ewton Method for Variational Inequalities: {T}he Case of Box 28089 Constraints}, 28090 author = {Facchinei, Francisco and Fischer, Andreas and Kanzow, Christian}, 28091 journal = {Complementarity and Variational Problems: State of the Art}, 28092 volume = {92}, 28093 pages = {76}, 28094 year = {1997} 28095} 28096 28097@TechReport{ facchinei.fischer.ea:simply, 28098 author = {F. Facchinei and A. Fischer and C. Kanzow and J. -M. Peng}, 28099 title = {A Simply Constrained Optimization Reformulation of {KKT} Systems Arising from 28100 Variational Inequalities}, 28101 institution = {University of Hamburg}, 28102 year = {1996} 28103} 28104 28105@Article{ facchinei.jiang.ea:smoothing, 28106 author = {F. Facchinei and H. Jiang and L. Qi}, 28107 title = {A Smoothing Method for Mathematical Programs with Equilibrium Constraints}, 28108 year = {1999}, 28109 journal = {Mathematical Programming}, 28110 volume = {85}, 28111 pages = {107--134} 28112} 28113 28114@Article{ facchinei.kanzow:nonsmooth, 28115 author = {F. Facchinei and C. Kanzow}, 28116 title = {A Nonsmooth Inexact {N}ewton Method for the solution of Large-Scale Nonlinear 28117 Complementarity Problems}, 28118 year = {1997}, 28119 journal = {Mathematical Programming}, 28120 volume = {76}, 28121 pages = {493--512} 28122} 28123 28124@Article{ facchinei.kanzow:unconstrained, 28125 author = {F. Facchinei and C. Kanzow}, 28126 title = {On Unconstrained and Constrained Stationary Points of the {I}mplicit 28127 {L}agrangian}, 28128 year = {1997}, 28129 journal = {Journal of Optimization Theory and Applications}, 28130 volume = {92}, 28131 pages = {99--115} 28132} 28133 28134@TechReport{ facchinei.pang:total, 28135 author = {F. Facchinei and J. S. Pang}, 28136 title = {Total stability of variational inequalities}, 28137 institution = {Universit\'a di Roma ``La Sapienza'', Dipartimento di Informatica e Sistemistica}, 28138 year = {1988}, 28139 type = {Manuscript}, 28140 address = {Roma, Italy} 28141} 28142 28143@Article{ facchinei.soares:merit, 28144 author = {F. Facchinei and J. Soares}, 28145 title = {A New Merit Function for Nonlinear Complementarity Problems and a Related 28146 Algorithm}, 28147 journal = {SIAM Journal on Optimization}, 28148 year = {1997}, 28149 volume = {7}, 28150 pages = {225--247} 28151} 28152 28153@InCollection{ facchinei.soares:testing, 28154 author = {F. Facchinei and J. Soares}, 28155 title = {Testing a new class of algorithms for nonlinear complementarity problems}, 28156 booktitle = {Variational Inequalities and Network Equilibrium Problems}, 28157 publisher = {Plenum Press}, 28158 address = {New York}, 28159 editor = {F. Giannessi and A. Maugeri}, 28160 year = {1995}, 28161 pages = {69--83} 28162} 28163 28164@InProceedings{ fahlman.lebiere:cascade-correlation, 28165 author = {S. E. Fahlman and C. Lebiere}, 28166 title = {The cascade-correlation learning architecture}, 28167 booktitle = {Advances in Neural Information Processing Systems II {(Denver 1989)}}, 28168 year = {1990}, 28169 editor = {D. S. Touretzky}, 28170 publisher = {Morgan Kaufmann}, 28171 address = {San Mateo, California}, 28172 pages = {524--532} 28173} 28174 28175@InProceedings{ fang.geiser.ea:software, 28176 author = {G. Fang and B. Geiser and T. R. Mackie}, 28177 title = {Software system for {UW}/{GE} tomotherapy prototype}, 28178 booktitle = {Proceedings of the XII International Conference on the Use of Computers in 28179 Radiation Therapy, Salt Lake City}, 28180 year = {1997}, 28181 editor = {D. D. Leavitt and G. Starkshall}, 28182 publisher = {Medical Physics Publishing}, 28183 address = {St. Louis, Missouri}, 28184 pages = {332--334} 28185} 28186 28187@Book{ fang.puthenpura:linear, 28188 author = {S.--C. Fang and S. Puthenpura}, 28189 title = {Linear Optimization and Extensions}, 28190 year = {1993}, 28191 publisher = {Prentice-Hall, Inc}, 28192 address = {Englewood Cliffs, New Jersey} 28193} 28194 28195@Article{ fayard.plateau:algorithm, 28196 author = {D. Fayard and G. Plateau}, 28197 title = {An Algorithm for the Solution of the 0--1 Knapsack Problem}, 28198 journal = {Computing}, 28199 year = {1982}, 28200 volume = {28}, 28201 pages = {269--287} 28202} 28203 28204@Book{ feller:introduction, 28205 author = {W. Feller}, 28206 title = {An Introduction to Probability Theory and its Applications}, 28207 publisher = {John Wiley \& Sons}, 28208 year = {1968}, 28209 address = {New York} 28210} 28211 28212@Article{ ferris.fourer.ea:expressing, 28213 author = {M. C. Ferris and R. Fourer and D. M. Gay}, 28214 title = {Expressing Complementarity Problems and Communicating them to Solvers}, 28215 journal = {SIAM Journal on Optimization}, 28216 volume = {9}, 28217 pages = {991--1009}, 28218 year = {1999}, 28219 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-02.ps}, 28220 key = {65}, 28221 institution = {Computer Sciences Department, University of Wisconsin}, 28222 address = {Madison, Wisconsin}, 28223 number = {98-02}, 28224 type = {Mathematical Programming Technical Report} 28225} 28226 28227@TechReport{ ferris.horn:nlp2mcp, 28228 author = {M. C. Ferris and J. D. Horn}, 28229 title = {{NLP2MCP}: Automatic conversion of nonlinear programs into mixed complementarity 28230 problems}, 28231 year = {1998}, 28232 institution = {Computer Sciences Department, University of Wisconsin}, 28233 note = {In preparation} 28234} 28235 28236@Article{ ferris.horn:partitioning, 28237 author = {M. C. Ferris and J. D. Horn}, 28238 title = {Partitioning Mathematical Programs for Parallel Solution}, 28239 year = {1998}, 28240 volume = {80}, 28241 pages = {35--62}, 28242 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/tr1232.ps}, 28243 journal = {Mathematical Programming}, 28244 key = {40} 28245} 28246 28247@Article{ ferris.kanzow.ea:feasible, 28248 author = {M. C. Ferris and C. Kanzow and T. S. Munson}, 28249 title = {Feasible Descent Algorithms for Mixed Complementarity Problems}, 28250 year = {1999}, 28251 journal = {Mathematical Programming}, 28252 volume = {86}, 28253 pages = {475--497}, 28254 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-04.ps}, 28255 key = {67} 28256} 28257 28258@InCollection{ ferris.kanzow:complementarity, 28259 author = {M. C. Ferris and C. Kanzow}, 28260 title = {Complementarity and Related Problems: {A} Survey}, 28261 booktitle = {Handbook of Applied Optimization, forthcoming}, 28262 key = {74}, 28263 publisher = {Oxford University Press}, 28264 year = {2000}, 28265 editor = {P. M. Pardalos and M. G. C. Resende}, 28266 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-17.ps}, 28267 institution = {Computer Sciences Department, University of Wisconsin}, 28268 address = {Madison, Wisconsin}, 28269 number = {98-17}, 28270 type = {Mathematical Programming Technical Report} 28271} 28272 28273@Article{ ferris.lucidi.ea:nonmonotone, 28274 author = {M. C. Ferris and S. Lucidi and M. Roma}, 28275 title = {Nonmonotone Curvilinear Stabilization Techniques for Unconstrained Optimization}, 28276 journal = {Computational Optimization and Applications}, 28277 volume = {6}, 28278 pages = {117--136}, 28279 year = {1996}, 28280 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/94-16.ps}, 28281 key = {43} 28282} 28283 28284@TechReport{ ferris.lucidi:globally, 28285 author = {M. C. Ferris and S. Lucidi}, 28286 title = {Globally Convergent Methods for Nonlinear Equations}, 28287 institution = {Computer Sciences Department, University of Wisconsin}, 28288 year = {1991}, 28289 address = {Madison, Wisconsin}, 28290 number = {1030}, 28291 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1991/tr1030.ps}, 28292 key = {21} 28293} 28294 28295@Article{ ferris.lucidi:nonmonotone, 28296 author = {M. C. Ferris and S. Lucidi}, 28297 title = {Nonmonotone Stabilization Methods for Nonlinear Equations}, 28298 journal = {Journal of Optimization Theory and Applications}, 28299 year = {1994}, 28300 volume = {81}, 28301 pages = {53--71}, 28302 key = {30} 28303} 28304 28305@Article{ ferris.mangasarian:breast, 28306 author = {M. C. Ferris and O. L. Mangasarian}, 28307 title = {Breast Cancer Diagnosis via Linear Programming}, 28308 key = {50}, 28309 journal = {{IEEE} Computational Science and Engineering}, 28310 year = {1995}, 28311 volume = {2}, 28312 pages = {70--71} 28313} 28314 28315@Article{ ferris.mangasarian:error, 28316 author = {M. C. Ferris and O. L. Mangasarian}, 28317 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 28318 Inequalities}, 28319 journal = {Annals of Operations Research}, 28320 year = {1993}, 28321 volume = {47}, 28322 pages = {293--305}, 28323 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 28324 key = {24} 28325} 28326 28327@Article{ ferris.mangasarian:finite, 28328 author = {M. C. Ferris and O. L. Mangasarian}, 28329 title = {Finite Perturbation of Convex Programs}, 28330 journal = {Applied Mathematics and Optimization}, 28331 year = {1991}, 28332 volume = {23}, 28333 pages = {263--273}, 28334 key = {08} 28335} 28336 28337@Book{ ferris.mangasarian:linear, 28338 author = {M. C. Ferris and O. L. Mangasarian}, 28339 title = {Linear Programming via {MATLAB}}, 28340 publisher = {in preparation}, 28341 year = {1995}, 28342 address = {Madison, Wisconsin} 28343} 28344 28345@Article{ ferris.mangasarian:minimum, 28346 author = {M. C. Ferris and O. L. Mangasarian}, 28347 title = {Minimum Principle Sufficiency}, 28348 journal = {Mathematical Programming}, 28349 year = {1992}, 28350 volume = {57}, 28351 pages = {1--14}, 28352 key = {11} 28353} 28354 28355@Article{ ferris.mangasarian:parallel, 28356 author = {M. C. Ferris and O. L. Mangasarian}, 28357 title = {Parallel Constraint Distribution}, 28358 journal = {SIAM Journal on Optimization}, 28359 year = {1991}, 28360 volume = {1}, 28361 pages = {487--500}, 28362 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28363 key = {18} 28364} 28365 28366@Article{ ferris.mangasarian:parallel*1, 28367 author = {M. C. Ferris and O. L. Mangasarian}, 28368 title = {Parallel Variable Distribution}, 28369 journal = {SIAM Journal on Optimization}, 28370 year = {1994}, 28371 volume = {4}, 28372 pages = {815--832}, 28373 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28374 key = {31} 28375} 28376 28377@Article{ ferris.meeraus.ea:computing, 28378 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28379 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28380 journal = {Optimization Methods and Software}, 28381 year = {1999}, 28382 volume = {10}, 28383 pages = {669--685}, 28384 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28385 key = {45} 28386} 28387 28388@Article{ ferris.mesnier.ea:neos, 28389 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28390 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28391 {I}nternet}, 28392 year = {2000}, 28393 journal = {{ACM} Transactions on Mathematical Software}, 28394 key = {54}, 28395 volume = {26}, 28396 pages = {1--18}, 28397 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28398 institution = {Computer Sciences Department, University of Wisconsin}, 28399 address = {Madison, Wisconsin}, 28400 number = {96-08}, 28401 type = {Mathematical Programming Technical Report}, 28402 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28403 Argonne National Laboratory}, 28404 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28405 1996} 28406} 28407 28408@InCollection{ ferris.meyer:models, 28409 author = {M. C. Ferris and R. R. Meyer}, 28410 title = {Models and Solution for On-Demand Data Delivery Problems}, 28411 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28412 key = {80}, 28413 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28414 Problems}, 28415 editor = {P. M. Pardalos}, 28416 series = {Nonconvex Optimization and its Applications}, 28417 volume = {42}, 28418 address = {Dordrect}, 28419 year = {2000}, 28420 pages = {175--188}, 28421 publisher = {Kluwer}, 28422 type = {Mathematical Programming Technical Report}, 28423 institution = {Computer Sciences Department, University of Wisconsin}, 28424 number = {99-04} 28425} 28426 28427@InProceedings{ ferris.munson.ea:homotopy, 28428 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28429 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28430 booktitle = {Numerical Analysis 1999}, 28431 key = {88}, 28432 year = {2000}, 28433 editor = {D. F. Griffiths and G. A. Watson}, 28434 series = {Research Notes in Mathematics}, 28435 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28436 address = {London}, 28437 pages = {143--167}, 28438 publisher = {Chapman and Hall}, 28439 institution = {Computer Sciences Department, University of Wisconsin}, 28440 number = {99-09}, 28441 type = {Mathematical Programming Technical Report} 28442} 28443 28444@TechReport{ ferris.munson.ea:practical, 28445 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28446 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28447 type = {Data Mining Institute Technical Report}, 28448 institution = {Computer Sciences Department, University of Wisconsin}, 28449 address = {Madison, Wisconsin}, 28450 year = {2000}, 28451 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28452 number = {00-03}, 28453 key = {92}, 28454 annote = {To appear in WSC 2000} 28455} 28456 28457@InCollection{ ferris.munson:case, 28458 author = {M. C. Ferris and T. S. Munson}, 28459 title = {Case Studies in Complementarity: Improving Model Formulation}, 28460 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28461 key = {73}, 28462 pages = {79--98}, 28463 publisher = {Springer Verlag}, 28464 year = {1999}, 28465 editor = {M. Th\'{e}ra and R. Tichatschke}, 28466 number = {477}, 28467 series = {Lecture Notes in Economics and Mathematical Systems}, 28468 address = {Berlin}, 28469 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28470 type = {Mathematical Programming Technical Report}, 28471 institution = {Computer Sciences Department, University of Wisconsin} 28472} 28473 28474@Article{ ferris.munson:complementarity, 28475 author = {M. C. Ferris and T. S. Munson}, 28476 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28477 year = {2000}, 28478 volume = {24}, 28479 pages = {165--188}, 28480 journal = {Journal of Economic Dynamics and Control}, 28481 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28482 key = {70}, 28483 type = {Mathematical Programming Technical Report}, 28484 institution = {Computer Sciences Department, University of Wisconsin}, 28485 address = {Madison, Wisconsin}, 28486 number = {98-12} 28487} 28488 28489@Misc{ ferris.munson:condor, 28490 author = {M. C. Ferris and T. S. Munson}, 28491 title = {Condor Modeling Language Interface}, 28492 organization = {Computer Sciences Department, University of Wisconsin}, 28493 address = {Madison, Wisconsin}, 28494 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28495} 28496 28497@Manual{ ferris.munson:gams, 28498 author = {M. C. Ferris and T. S. Munson}, 28499 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28500 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28501} 28502 28503@Article{ ferris.munson:interfaces, 28504 author = {M. C. Ferris and T. S. Munson}, 28505 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28506 journal = {Computational Optimization and Applications}, 28507 volume = {12}, 28508 pages = {207--227}, 28509 year = {1999}, 28510 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28511 key = {63}, 28512 institution = {Computer Sciences Department, University of Wisconsin}, 28513 address = {Madison, Wisconsin}, 28514 number = {97-12}, 28515 type = {Mathematical Programming Technical Report} 28516} 28517 28518@TechReport{ ferris.munson:interior, 28519 author = {M. C. Ferris and T. S. Munson}, 28520 title = {Interior Point Methods for Massive Support Vector Machines}, 28521 institution = {Computer Sciences Department, University of Wisconsin}, 28522 year = {2000}, 28523 key = {94}, 28524 type = {Data Mining Institute Technical Report}, 28525 number = {00-05}, 28526 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28527 address = {Madison, Wisconsin}, 28528 annote = {Submitted to SIOPT} 28529} 28530 28531@Article{ ferris.munson:linear, 28532 author = {M. C. Ferris and T. S. Munson}, 28533 title = {Linear Programming for Emergency Broadcast Systems}, 28534 year = {1999}, 28535 journal = {{SIAG/OPT} Newsletter}, 28536 volume = {10}, 28537 pages = {6--8}, 28538 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28539 key = {76}, 28540 type = {Mathematical Programming Technical Report}, 28541 institution = {Computer Sciences Department, University of Wisconsin}, 28542 address = {Madison, Wisconsin}, 28543 number = {98-20} 28544} 28545 28546@Article{ ferris.munson:modeling, 28547 author = {M. C. Ferris and T. S. Munson}, 28548 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28549 year = {2000}, 28550 journal = {Mathematical Programming}, 28551 volume = {88}, 28552 pages = {487--506}, 28553 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28554 key = {71}, 28555 type = {Mathematical Programming Technical Report}, 28556 institution = {Computer Sciences Department, University of Wisconsin}, 28557 address = {Madison, Wisconsin}, 28558 number = {98-13} 28559} 28560 28561@TechReport{ ferris.munson:preprocessing, 28562 author = {M. C. Ferris and T. S. Munson}, 28563 title = {Preprocessing Complementarity Problems}, 28564 type = {Mathematical Programming Technical Report}, 28565 institution = {Computer Sciences Department, University of Wisconsin}, 28566 address = {Madison, Wisconsin}, 28567 year = {1999}, 28568 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28569 number = {99-07}, 28570 key = {86}, 28571 annote = {Submitted to ICCP 99} 28572} 28573 28574@TechReport{ ferris.munson:semismooth, 28575 author = {M. C. Ferris and T. S. Munson}, 28576 title = {Semismooth Support Vector Machines}, 28577 institution = {Computer Sciences Department, University of Wisconsin}, 28578 year = {2000}, 28579 key = {97}, 28580 type = {Data Mining Institute Technical Report}, 28581 number = {00-09}, 28582 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28583 address = {Madison, Wisconsin}, 28584 annote = {Submitted to Math Prog B} 28585} 28586 28587@Article{ ferris.pang:engineering, 28588 author = {M. C. Ferris and J. S. Pang}, 28589 title = {Engineering and Economic Applications of Complementarity Problems}, 28590 year = {1997}, 28591 journal = {SIAM Review}, 28592 volume = {39}, 28593 pages = {669--713}, 28594 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28595 key = {46} 28596} 28597 28598@Article{ ferris.pang:nondegenerate, 28599 author = {M. C. Ferris and J. S. Pang}, 28600 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28601 journal = {SIAM Journal on Control and Optimization}, 28602 year = {1996}, 28603 volume = {34}, 28604 pages = {244--263}, 28605 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28606 key = {35} 28607} 28608 28609@Article{ ferris.philpott:affine, 28610 author = {M. C. Ferris and A. B. Philpott}, 28611 title = {On Affine Scaling and Semi--Infinite Programming}, 28612 journal = {Mathematical Programming}, 28613 year = {1992}, 28614 volume = {56}, 28615 pages = {361--364}, 28616 key = {15} 28617} 28618 28619@Article{ ferris.philpott:interior, 28620 author = {M. C. Ferris and A. B. Philpott}, 28621 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28622 journal = {Mathematical Programming}, 28623 year = {1989}, 28624 volume = {43}, 28625 pages = {257--276}, 28626 key = {04} 28627} 28628 28629@Article{ ferris.philpott:performance, 28630 author = {M. C. Ferris and A. B. Philpott}, 28631 title = {On the Performance of {K}armarkar's Algorithm}, 28632 journal = {Journal of the Operational Research Society}, 28633 year = {1988}, 28634 volume = {39}, 28635 pages = {257--270}, 28636 key = {03} 28637} 28638 28639@InCollection{ ferris.ralph:projected, 28640 author = {M. C. Ferris and D. Ralph}, 28641 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28642 Maps}, 28643 booktitle = {Recent Advances in Nonsmooth Optimization}, 28644 publisher = {World Scientific Publishers}, 28645 year = {1995}, 28646 pages = {57--87}, 28647 editor = {D. Du and L. Qi and R. Womersley}, 28648 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28649 key = {41} 28650} 28651 28652@Article{ ferris.ruszczynski:robust, 28653 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28654 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28655 year = {2000}, 28656 journal = {Networks}, 28657 volume = {35}, 28658 pages = {181--194}, 28659 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28660 key = {60} 28661} 28662 28663@InCollection{ ferris.rutherford:accessing, 28664 author = {M. C. Ferris and T. F. Rutherford}, 28665 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28666 booktitle = {Nonlinear Optimization and Applications}, 28667 key = {48}, 28668 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28669 editor = {G. Di Pillo and F. Giannessi}, 28670 year = {1996}, 28671 pages = {141--153}, 28672 publisher = {Plenum Press}, 28673 address = {New York} 28674} 28675 28676@InCollection{ ferris.shepard:optimizing, 28677 author = {M. C. Ferris and D. M. Shepard}, 28678 title = {Optimization of Gamma Knife Radiosurgery}, 28679 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28680 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28681 publisher = {AMS}, 28682 year = {2000}, 28683 optseries = {DIMACS}, 28684 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28685 key = {91}, 28686 type = {Data Mining Institute Technical Report}, 28687 institution = {Computer Sciences Department, University of Wisconsin}, 28688 address = {Madison, Wisconsin}, 28689 number = {00-01} 28690} 28691 28692@InCollection{ ferris.sinapiromsaran:formulating, 28693 author = {M. C. Ferris and K. Sinapiromsaran}, 28694 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28695 booktitle = {Optimization}, 28696 key = {77}, 28697 publisher = {Springer-Verlag}, 28698 year = {2000}, 28699 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28700 volume = {481}, 28701 series = {Lecture Notes in Economics and Mathematical Systems}, 28702 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28703 type = {Mathematical Programming Technical Report}, 28704 institution = {Computer Sciences Department, University of Wisconsin}, 28705 address = {Madison, Wisconsin}, 28706 number = {98-21} 28707} 28708 28709@Article{ ferris.tin-loi:limit, 28710 author = {M. C. Ferris and F. Tin-Loi}, 28711 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28712 Complementarity Constraints}, 28713 year = {2001}, 28714 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28715 key = {78}, 28716 journal = {International Journal of Mechanical Sciences}, 28717 pages = {209--224}, 28718 volume = {43}, 28719 type = {Mathematical Programming Technical Report}, 28720 institution = {Computer Sciences Department, University of Wisconsin}, 28721 address = {Madison, Wisconsin}, 28722 number = {99-01} 28723} 28724 28725@Article{ ferris.tin-loi:nonlinear, 28726 author = {M. C. Ferris and F. Tin-Loi}, 28727 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28728 Elastoplasticity}, 28729 year = {1998}, 28730 key = {64}, 28731 volume = {6}, 28732 pages = {857--870}, 28733 journal = {Structural Engineering and Mechanics} 28734} 28735 28736@Article{ ferris.tin-loi:solution, 28737 author = {M. C. Ferris and F. Tin-Loi}, 28738 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28739 and Complementarity Constraints}, 28740 year = {1999}, 28741 journal = {Computer Methods in Applied Mechanics and Engineering}, 28742 volume = {174}, 28743 pages = {107--120}, 28744 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 28745 key = {66} 28746} 28747 28748@Article{ ferris.vlach:scheduling, 28749 author = {M. C. Ferris and M. Vlach}, 28750 title = {Scheduling with Earliness and Tardiness Penalties}, 28751 journal = {Naval Research Logistics Quarterly}, 28752 year = {1992}, 28753 volume = {39}, 28754 pages = {229--245}, 28755 key = {13} 28756} 28757 28758@TechReport{ ferris.zavriev:linear, 28759 author = {M. C. Ferris and S. K Zavriev}, 28760 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 28761 institution = {Computer Sciences Department, University of Wisconsin}, 28762 year = {1996}, 28763 key = {56}, 28764 address = {Madison, Wisconsin}, 28765 type = {Mathematical Programming Technical Report}, 28766 number = {96--12}, 28767 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 28768} 28769 28770@Article{ ferris:finite, 28771 author = {M. C. Ferris}, 28772 title = {Finite Termination of the Proximal Point Algorithm}, 28773 journal = {Mathematical Programming}, 28774 year = {1991}, 28775 volume = {50}, 28776 pages = {359--366}, 28777 key = {06} 28778} 28779 28780@Article{ ferris:iterative, 28781 author = {M. C. 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Petri}, 35158 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35159 publisher = {Harvard University Press}, 35160 year = {1984} 35161} 35162 35163@InProceedings{ petrzykowski:application, 35164 author = {T. Petrzykowski}, 35165 title = {Application of the Steepest Ascent Method to Concave Programming}, 35166 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35167 year = {1962}, 35168 publisher = {North--Holland}, 35169 address = {Amsterdam}, 35170 pages = {185--189} 35171} 35172 35173@InProceedings{ pettey.leuze.ea:parallel, 35174 crossref = {grefenstette:genetic}, 35175 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35176 title = {A Parallel Genetic Algorithm}, 35177 pages = {155--161} 35178} 35179 35180@InProceedings{ pettey.leuze:theoretical, 35181 crossref = {schaeffer:third}, 35182 author = {C. C. Pettey and M. R. Leuze}, 35183 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35184 pages = {398--405} 35185} 35186 35187@Book{ pfeiffer.glocker:multibody, 35188 author = {F. Pfeiffer and C. Glocker}, 35189 title = {Multibody Dynamics with Unilateral Contact}, 35190 year = {1996}, 35191 publisher = {John Wiley \& Sons} 35192} 35193 35194@TechReport{ pierro.iusem:convergence, 35195 author = {A. R. de Pierro and A. N. Iusem}, 35196 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35197 Linear Complementarity Problems}, 35198 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35199 year = {1990}, 35200 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35201} 35202 35203@InCollection{ pillo.grippo.ea:class, 35204 author = {G. Di Pillo and L. Grippo and F. 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Rockafellar}, 36172 title = {A Generalized Approach to Linear-Quadratic Programming}, 36173 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36174 Applications}, 36175 year = {1986}, 36176 pages = {58--66}, 36177 note = {(Xi'an, China)} 36178} 36179 36180@InProceedings{ rockafellar:generalized*1, 36181 crossref = {bachem.grotschel.ea:mathematical}, 36182 author = {R. T. Rockafellar}, 36183 title = {Generalized Subgradients in Mathematical Programming}, 36184 pages = {368--390} 36185} 36186 36187@InCollection{ rockafellar:large-scale, 36188 author = {R. T. Rockafellar}, 36189 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36190 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36191 chapter = {15}, 36192 year = {1991}, 36193 editor = {S. Gomez and J. P. Hennart and R. A. 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Rockafellar}, 36253 title = {Network Flows and Monotropic Optimization}, 36254 publisher = {John Wiley}, 36255 year = {1984}, 36256 address = {New York} 36257} 36258 36259@Article{ rodrigues:mixed, 36260 author = {H. C. Rodrigues}, 36261 title = {A mixed variational formulation for shape optimization of solids with contact 36262 conditions}, 36263 journal = {Structural Optimization}, 36264 volume = {6}, 36265 year = {1993}, 36266 pages = {19--28} 36267} 36268 36269@Book{ rodrigues:obstacle, 36270 author = {J. F. Rodrigues}, 36271 title = {Obstacle Problems in Mathematical Physics}, 36272 publisher = {Elsevier Publishing Company}, 36273 address = {Amsterdam}, 36274 year = {1987} 36275} 36276 36277@Book{ roos.terlaky.ea:theory, 36278 author = {C. Roos and T. Terlaky and J.--Ph. 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Adams}, 39044 url = {https://arxiv.org/abs/2303.12620}, 39045 journal = {Communications in Applied Mathematics and Computational Science}, 39046 volume = {18}, 39047 number = {1}, 39048 pages = {135--152}, 39049 doi = {10.2140/camcos.2023.18.135}, 39050 year = {2023} 39051} 39052 39053@Article{ eggersdupont1994, 39054 title = {Drop formation in a one-dimensional approximation of the {Navier--Stokes} 39055 equation}, 39056 author = {Jens Eggers and Todd F. Dupont}, 39057 journal = {Journal of fluid mechanics}, 39058 volume = {262}, 39059 pages = {205--221}, 39060 year = {1994}, 39061 publisher = {Cambridge University Press} 39062} 39063 39064@PhDThesis{ pusztaythesis2023, 39065 title = {A Particle Basis Vlasov-Poisson-Landau Solver for Plasma Simulation in PETSc}, 39066 author = {Joseph V. Pusztay}, 39067 type = {{PhD} thesis}, 39068 school = {University at Buffalo, Department of Computer Science and Engineering}, 39069 address = {Buffalo, NY}, 39070 month = may, 39071 year = {2022} 39072} 39073 39074@PhDThesis{ finnthesis2023, 39075 title = {Structure-Preserving Particle-In-Cell Methods for the Vlasov-Poisson-Landau 39076 System}, 39077 author = {Daniel S. Finn}, 39078 type = {{PhD} thesis}, 39079 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 39080 Engineering}, 39081 address = {Buffalo, NY}, 39082 month = may, 39083 year = {2023} 39084} 39085 39086@PhDThesis{ nathawanithesis2023, 39087 title = {Droplet Formation: One-dimensional Mathematical Model and Computations}, 39088 author = {Darsh Kiritbhai Nathawani}, 39089 type = {{PhD} thesis}, 39090 school = {University at Buffalo, Program in Computational and Data-Enabled Science and 39091 Engineering}, 39092 address = {Buffalo, NY}, 39093 month = may, 39094 year = {2023} 39095} 39096 39097@article{MckayEriksonKozdon2019, 39098 title = {A computational method for earthquake cycles within anisotropic media}, 39099 author = {Maricela Best Mckay and Brittany A Erickson and Jeremy E Kozdon}, 39100 journal = {Geophysical Journal International}, 39101 volume = {219}, 39102 number = {2}, 39103 pages = {816--833}, 39104 year = {2019}, 39105} 39106 39107article{EricksonOReillyNordstrom2019, 39108 title = {Accuracy of stable, high-order finite difference methods for hyperbolic systems with non-smooth wave speeds}, 39109 author = {Brittany A Erickson and Ossian O’Reilly and Jan Nordstr{\"o}m}, 39110 journal = {Journal of Scientific Computing}, 39111 volume = {81}, 39112 pages = {2356--2387}, 39113 year = {2019}, 39114} 39115 39116@article{KozdonEricksonWilcox2021, 39117 title = {Hybridized summation-by-parts finite difference methods}, 39118 author = {Jeremy E Kozdon and Brittany A Erickson and Lucas C Wilcox}, 39119 journal = {Journal of Scientific Computing}, 39120 volume = {87}, 39121 number = {3}, 39122 pages = {85}, 39123 year = {2021}, 39124} 39125 39126@article{SEAS2022, 39127 title = {Community-driven code comparisons for three-dimensional dynamic modeling of sequences of earthquakes and aseismic slip}, 39128 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}, 39129 journal = {Journal of Geophysical Research: Solid Earth}, 39130 volume = {127}, 39131 number = {3}, 39132 pages = {e2021JB023519}, 39133 year = {2022}, 39134} 39135 39136@article{EricksonKozdonHarvey2022, 39137 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}, 39138 author = {Brittany A Erickson and Jeremy E Kozdon and Tobias Harvey}, 39139 journal = {Journal of Scientific Computing}, 39140 volume = {93}, 39141 number = {1}, 39142 pages = {17}, 39143 year = {2022}, 39144} 39145 39146@article{RuckerEriksonKarlstromLeeGopalakrishnan2022, 39147 title = {A Computational Framework for Time-Dependent Deformation in Viscoelastic Magmatic Systems}, 39148 author = {Cody Rucker and Brittany A Erickson and Leif Karlstrom and Brian Lee and Jay Gopalakrishnan}, 39149 journal = {Journal of Geophysical Research: Solid Earth}, 39150 volume = {127}, 39151 number = {9}, 39152 pages = {e2022JB024506}, 39153 year = {2022}, 39154} 39155 39156@article{HarveyEriksonKozdon2023, 39157 title = {A High-order Accurate Summation-by-Parts Finite Difference Method for Fully-dynamic Earthquake Sequence Simulations within Sedimentary Basins}, 39158 author = {Tobias W Harvey and Brittany A Erickson and Jeremy E Kozdon}, 39159 journal = {Journal of Geophysical Research: Solid Earth}, 39160 pages = {e2022JB025357}, 39161 year = {2023}, 39162} 39163 39164@article{SEAS2023, 39165 title = {Incorporating full elastodynamic effects and dipping fault geometries in community code verification exercises for simulations of earthquake sequences and aseismic slip {(SEAS)}}, 39166 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}, 39167 journal = {Bulletin of the Seismological Society of America}, 39168 volume = {113}, 39169 number = {2}, 39170 pages = {499--523}, 39171 year = {2023}, 39172} 39173
