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@Misc{ semver-webpage, 20 author = {{Semantic Versioning 2.0.0}}, 21 note = {\url{https://semver.org}} 22} 23 24@article{veldhuizen1984d, 25 title = {{D}-stability and {K}aps-{R}entrop-methods}, 26 author = {Veldhuizen, M van}, 27 journal = {Computing}, 28 volume = {32}, 29 number = {3}, 30 pages = {229--237}, 31 year = {1984}, 32 publisher = {Springer} 33} 34 35@article{shampine1982implementation, 36 title = {Implementation of {R}osenbrock methods}, 37 author = {Shampine, Lawrence F}, 38 journal = {ACM Transactions on Mathematical Software (TOMS)}, 39 volume = {8}, 40 number = {2}, 41 pages = {93--113}, 42 year = {1982}, 43 publisher = {ACM New York, NY, USA} 44} 45 46@book{wanner1996solving, 47 title = {Solving ordinary differential equations {II}}, 48 author = {Wanner, Gerhard and Hairer, Ernst}, 49 volume = {375}, 50 year = {1996}, 51 publisher = {Springer Berlin Heidelberg New York} 52} 53 54@article{kaps1979generalized, 55 title = {Generalized {R}unge--{K}utta methods of order four with stepsize control for stiff ordinary differential equations}, 56 author = {Kaps, Peter and Rentrop, Peter}, 57 journal = {Numerische Mathematik}, 58 volume = {33}, 59 pages = {55--68}, 60 year = {1979}, 61 publisher = {Springer} 62} 63 64@book{butcher2016numerical, 65 title = {Numerical methods for ordinary differential equations}, 66 author = {Butcher, John Charles}, 67 year = {2016}, 68 publisher = {John Wiley \& Sons} 69} 70 71@article{chung1993, 72 author = {Chung, J. and Hulbert, G. M.}, 73 title = {A Time Integration Algorithm for Structural Dynamics With Improved Numerical Dissipation: The Generalized-alpha Method}, 74 journal = {Journal of Applied Mechanics}, 75 volume = {60}, 76 number = {2}, 77 pages = {371-375}, 78 year = {1993}, 79 month = {06}, 80 issn = {0021-8936}, 81 doi = {10.1115/1.2900803}, 82 url = {https://doi.org/10.1115/1.2900803}, 83 eprint = {https://asmedigitalcollection.asme.org/appliedmechanics/article-pdf/60/2/371/5463014/371\_1.pdf}, 84} 85 86@article{hosea1996analysis, 87 title = {Analysis and implementation of {TR-BDF2}}, 88 author = {Hosea, ME and Shampine, LF}, 89 journal = {Applied Numerical Mathematics}, 90 volume = {20}, 91 number = {1-2}, 92 pages = {21--37}, 93 year = {1996}, 94 publisher = {Elsevier} 95} 96 97@article{kennedy2019diagonally, 98 title = {Diagonally implicit {R}unge--{K}utta methods for stiff {ODE}s}, 99 author = {Kennedy, Christopher A and Carpenter, Mark H}, 100 journal = {Applied Numerical Mathematics}, 101 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= {A Highly Parallel Multilevel {N}ewton--{K}rylov--{S}chwarz Method with Subspace-Based Coarsening and 370 Partition-Based Balancing for the Multigroup Neutron Transport Equation on Three-Dimensional Unstructured Meshes}, 371 author = {Kong, Fande and Wang, Yaqi and Gaston, Derek R and Permann, Cody J and Slaughter, Andrew E and Lindsay, 372 Alexander D and DeHart, Mark D and Martineau, Richard C}, 373 journal = {SIAM Journal on Scientific Computing}, 374 volume = {42}, 375 number = {5}, 376 pages = {C193--C220}, 377 year = {2020}, 378 publisher = {SIAM} 379} 380 381@article{ipsen2001note, 382 title = {A note on preconditioning nonsymmetric matrices}, 383 author = {Ipsen, Ilse CF}, 384 journal = {SIAM Journal on Scientific Computing}, 385 volume = {23}, 386 number = {3}, 387 pages = {1050--1051}, 388 year = {2001}, 389 publisher = {SIAM} 390} 391 392@article{murphy2000note, 393 title = {A note on preconditioning for indefinite linear systems}, 394 author = {Murphy, Malcolm F and 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Fernandez-de-Castro and Xiao Shen and Jianhua Xue and Yuming Zhou and S. 1380 Sharma}, 1381 title = {Writer Flux Closure and Transition Degradation Mechanism in Perpendicular 1382 Recording.}, 1383 journal = {IEEE Trans. Magn. Volume}, 1384 volume = {43}, 1385 pages = {2175-2177}, 1386 doi = {10.1109/TMAG.2007.893122}, 1387 petsc_uses = {KSP} 1388} 1389 1390@Article{ sb2006, 1391 author = {W. Scholz and S. Batra}, 1392 title = {Effect of write current waveform on magnetization and head field dynamics of 1393 perpendicular recording heads}, 1394 journal = {IEEE Trans. Magn.}, 1395 volume = {42}, 1396 year = {2006}, 1397 pages = {2264--2266}, 1398 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/ieee/scholz_2006_42_2264.pdf}, 1399 petsc_uses = {KSP} 1400} 1401 1402@Article{ bsr2006, 1403 author = {S. Batra and W. Scholz and T. Roscamp}, 1404 title = {Effect of thermal fluctuation field on the noise performance of a perpendicular 1405 recording system}, 1406 journal = {J. Appl. Phys.}, 1407 volume = {99}, 1408 year = {2006}, 1409 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 1410 petsc_uses = {KSP} 1411} 1412 1413@InProceedings{ japios2006, 1414 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 1415 Subramanian}, 1416 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 1417 in systems with cubic and uniaxial anisotropy.}, 1418 booktitle = {Intermag 2006 Conference}, 1419 petsc_uses = {KSP} 1420} 1421 1422@Article{ kbmb2006, 1423 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 1424 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 1425 Perpendicular Recording Heads}, 1426 journal = {IEEE Trans. Magn.}, 1427 volume = {42}, 1428 year = {2006}, 1429 pages = {2428--2430}, 1430 doi = {10.1109/TMAG.2006.879430}, 1431 petsc_uses = {KSP} 1432} 1433 1434@Article{ cclcw2006, 1435 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 1436 title = {Control of Domain Wall Motion in Permalloy Ring}, 1437 journal = {IEEE Trans. Magn.}, 1438 volume = {42}, 1439 year = {2006}, 1440 pages = {2960--2962}, 1441 doi = {10.1109/TMAG.2006.878414}, 1442 petsc_uses = {KSP} 1443} 1444 1445@Article{ bfmfzczg2007, 1446 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 1447 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 1448 title = {Micromagnetic modelling of ferromagnetic cones}, 1449 journal = {J. Magn. Magn. Mater.}, 1450 volume = {312}, 1451 year = {2007}, 1452 pages = {234-238}, 1453 url = {http://eprints.soton.ac.uk/45900/}, 1454 petsc_uses = {KSP} 1455} 1456 1457@PhDThesis{ rb2005, 1458 author = {Richard Boardman}, 1459 title = {Computer simulation studies of magnetic nanostructures}, 1460 school = {Computational Engineering and Design Group, School of Engineering Sciences, 1461 University of Southampton, United Kingdom}, 1462 year = {2005}, 1463 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 1464 petsc_uses = {KSP} 1465} 1466 1467@InProceedings{ cwwy2006, 1468 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 1469 title = {MPI Performance Analysis Tools on Blue Gene/L}, 1470 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 1471 year = {2006}, 1472 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 1473 petsc_uses = {KSP} 1474} 1475 1476@InProceedings{ ch2006, 1477 author = {I.-H. Chung and J.K. Hollingsworth}, 1478 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 1479 Programs}, 1480 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 1481 pages = {45--56}, 1482 doi = {10.1109/HPDC.2006.1652135}, 1483 petsc_uses = {KSP} 1484} 1485 1486@Article{ lkpl2005, 1487 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1488 title = {Multibit {MRAM} using a pair of memory cells}, 1489 journal = {IEEE Trans. Magn.}, 1490 volume = {41}, 1491 year = {2005}, 1492 pages = {2670-2672}, 1493 doi = {10.1109/TMAG.2005.855288}, 1494 petsc_uses = {KSP} 1495} 1496 1497@Article{ gscn2005, 1498 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 1499 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 1500 journal = {Phys. Rev. B}, 1501 volume = {71}, 1502 year = {2005}, 1503 doi = {10.1103/PhysRevB.71.144407}, 1504 petsc_uses = {KSP} 1505} 1506 1507@PhDThesis{ mda, 1508 author = {Massimiliano d'Aquino}, 1509 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 1510 school = { Universita di Napoli Federico II.}, 1511 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 1512 petsc_uses = {KSP} 1513} 1514 1515@TechReport{ ssdfssf2003, 1516 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 1517 Stehno and J. Fidler}, 1518 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 1519 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 1520 petsc_uses = {KSP} 1521} 1522 1523@InProceedings{ sb2006a, 1524 author = {W. Scholz and S. Batra}, 1525 title = {Effect of write current waveform on magnetization and head field dynamics of 1526 perpendicular recording heads}, 1527 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 1528 petsc_uses = {KSP} 1529} 1530 1531@Article{ scholz-batra1, 1532 author = {W. Scholz and S. Batra}, 1533 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 1534 Recording}, 1535 journal = {IEEE Trans. Magn.}, 1536 note = {submitted}, 1537 year = {2005}, 1538 petsc_uses = {KSP} 1539} 1540 1541@Article{ scholz-batra2, 1542 author = {W. Scholz and S. Batra}, 1543 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 1544 journal = {IEEE Trans. Magn.}, 1545 volume = {41}, 1546 year = {2005}, 1547 pages = {702-706}, 1548 petsc_uses = {KSP} 1549} 1550 1551@Article{ daquino-scholz1, 1552 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1553 title = {Micromagnetic Analysis of Fast Precessional Switching}, 1554 journal = {J. Magn. Magn. Mater.}, 1555 volume = {290-291}, 1556 year = {2005}, 1557 pages = {510-513}, 1558 petsc_uses = {KSP} 1559} 1560 1561@Article{ aq-scholz-fid, 1562 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1563 title = {Numerical and analytical study of fast precessional switching}, 1564 journal = {J. Appl. Phys.}, 1565 volume = {95}, 1566 year = {2004}, 1567 pages = {7055-7057}, 1568 petsc_uses = {KSP} 1569} 1570 1571@InProceedings{ gar-tabik-gar, 1572 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 1573 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 1574 Scatterers}, 1575 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 1576 (PDP'04)}, 1577 year = {2004}, 1578 pages = {80--}, 1579 petsc_uses = {KSP} 1580} 1581 1582@InProceedings{ aq-scholz-mia, 1583 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 1584 title = {Analysis of fast precessional switching in magnetic thin films}, 1585 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 1586 year = {2004}, 1587 pages = {257-260}, 1588 petsc_uses = {KSP} 1589} 1590 1591@Article{ scholz-fid-seus, 1592 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 1593 Dittrich and V. Tsiantos}, 1594 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 1595 Axes}, 1596 journal = {J. Magn. Magn. Mater.}, 1597 year = {2004}, 1598 pages = {1524-1525}, 1599 petsc_uses = {KSP} 1600} 1601 1602@Article{ boardman-zimmerman, 1603 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 1604 Peter de Groot}, 1605 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 1606 journal = {Journal of Applied Physics}, 1607 year = {2005}, 1608 petsc_uses = {KSP} 1609} 1610 1611@Article{ lim-kim-park, 1612 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1613 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 1614 journal = {IEEE Trans. Magn.}, 1615 note = {submitted}, 1616 petsc_uses = {KSP} 1617} 1618 1619@Article{ scholz-suess2, 1620 author = {W. Scholz and D. Suess and T. Schrefl and J. Fidler}, 1621 title = {Micromagnetic simulation of magnetization reversal in small particles with 1622 surface anisotropy}, 1623 journal = {J. Appl. Phys.}, 1624 volume = {95}, 1625 year = {2004}, 1626 pages = {6807-6809}, 1627 petsc_uses = {KSP} 1628} 1629 1630@Article{ scholz-schrefl1, 1631 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 1632 Tsiantos}, 1633 title = {Micromagnetic simulation of the pinning and depinning process in permanent 1634 magnets}, 1635 journal = {IEEE Trans. Magn.}, 1636 volume = {39}, 1637 year = {2003}, 1638 pages = {2920-2922}, 1639 petsc_uses = {KSP} 1640} 1641 1642@Article{ scholz-guslienko, 1643 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 1644 W. Chantrell and J. Fidler}, 1645 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 1646 nanodots}, 1647 journal = {J. Magn. Magn. Mater.}, 1648 volume = {266}, 1649 year = {2003}, 1650 pages = {155-163}, 1651 petsc_uses = {KSP} 1652} 1653 1654@Article{ scholz1, 1655 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 1656 Forster and V. Tsiantos}, 1657 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1658 journal = {Comp. Mat. Sci}, 1659 year = {2003}, 1660 pages = {366--383}, 1661 volume = {28}, 1662 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 1663 petsc_uses = {KSP} 1664} 1665 1666@PhDThesis{ scholz2, 1667 author = {W. Scholz}, 1668 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1669 school = {Vienna University of Technology, Vienna, Austria}, 1670 year = {2003}, 1671 petsc_uses = {KSP} 1672} 1673 1674@Article{ scholz3, 1675 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 1676 Forster and J. Fidler}, 1677 title = {Implementation of a high performance parallel finite element micromagnetics 1678 package}, 1679 journal = {J. Magn. Magn. Mater.}, 1680 year = {2004}, 1681 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 1682 petsc_uses = {KSP} 1683} 1684 1685% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1686@InBook{ zhanggladwell1, 1687 author = {W. Zhang and I. Gladwell}, 1688 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 1689 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 1690 year = {2000}, 1691 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 1692 Physics, vol. 552}, 1693 publisher = {Springer}, 1694 pages = {4190-}, 1695 petsc_uses = {KSP} 1696} 1697 1698@Article{ wolf1, 1699 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 1700 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 1701 thin films}, 1702 journal = {Phil. Mag. A}, 1703 year = {2003}, 1704 lab = {ANL}, 1705 petsc_uses = {KSP} 1706} 1707 1708@Article{ wolf2, 1709 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 1710 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 1711 grain-boundary properties}, 1712 journal = {Computational Materials Science}, 1713 year = {2001}, 1714 volume = {23}, 1715 pages = {15--32}, 1716 lab = {ANL}, 1717 petsc_uses = {KSP} 1718} 1719 1720@Article{ wolf3, 1721 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 1722 title = {Role of grain rotation in grain growth by mesoscale simulation}, 1723 journal = {Phil. Mag. A}, 1724 year = {2002}, 1725 volume = {82}, 1726 pages = {1271--1297}, 1727 lab = {ANL}, 1728 petsc_uses = {KSP} 1729} 1730 1731% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1732@Article{ saut, 1733 author = { Olivier Saut}, 1734 title = {Bidimensional Study of the {M}axwell-{B}loch Model in a Nonlinear Crystal}, 1735 journal = {SIAM Journal on Scientific Computing}, 1736 year = {2004}, 1737 note = {submitted}, 1738 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 1739 petsc_uses = {KSP} 1740} 1741 1742% LiteralHTML: 1743% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 1744% LiteralHTML: 1745@InBook{ khanallorenziayachepennec2016, 1746 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 1747 of Brain Deformation in {Alzheimer's} Disease}, 1748 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 1749 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 1750 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 1751 Miller}, 1752 pages = {167--176}, 1753 isbn = {978-3-319-28329-6}, 1754 doi = {10.1007/978-3-319-28329-6_15}, 1755 publisher = {Springer International Publishing}, 1756 year = {2016}, 1757 petsc_uses = {KSP} 1758} 1759 1760@Article{ ataseven, 1761 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 1762 title = {Parallel implementation of the accelerated {BEM} approach for {EMSI} of the human 1763 brain}, 1764 journal = {Medical and Biological Engineering and Computing}, 1765 month = feb, 1766 year = {2008}, 1767 doi = {10.1007/s11517-008-0316-0}, 1768 petsc_uses = {KSP} 1769} 1770 1771@Article{ dennis-eberhart-03, 1772 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 1773 pages = {832-840}, 1774 volume = {125}, 1775 number = {6}, 1776 title = {Finite-element simulation of cooling of realistic {3-D} human head and neck}, 1777 journal = {J Biomech Eng}, 1778 year = {2003}, 1779 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 1780 petsc_uses = {KSP} 1781} 1782 1783@Conference{ gu7174parallel, 1784 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 1785 frequency-domain small animal optical tomography}}, 1786 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 1787 booktitle = {Proc. of SPIE Vol}, 1788 volume = {7174}, 1789 number = {717406}, 1790 pages = {1}, 1791 petsc_uses = {KSP} 1792} 1793 1794@Article{ barchanski2005using, 1795 title = {{Using domain decomposition techniques for the calculation of low-frequency 1796 electric current densities in high-resolution 3D human anatomy models}}, 1797 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 1798 T.}, 1799 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 1800 and Electronic Engineering}, 1801 volume = {24}, 1802 number = {2}, 1803 pages = {458--467}, 1804 issn = {0332-1649}, 1805 year = {2005}, 1806 publisher = {Emerald Group Publishing Limited}, 1807 petsc_uses = {KSP} 1808} 1809 1810@Article{ motrescurienen05, 1811 author = {V. C. Motrescu and U. van Rienen}, 1812 pages = {227--231}, 1813 volume = {3}, 1814 title = {Computation of currents induced by {ELF} electric fields in anisotropic human 1815 tissues using the Finite Integration Technique}, 1816 journal = {Advances in Radio Science}, 1817 year = {2005}, 1818 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 1819 petsc_uses = {KSP} 1820} 1821 1822@Article{ motrescurienen04, 1823 author = {V. C. Motrescu and U. van Rienen}, 1824 pages = {309--313}, 1825 volume = {2}, 1826 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 1827 Integration Technique (FIT)}, 1828 journal = {Advances in Radio Science}, 1829 year = {2004}, 1830 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 1831 petsc_uses = {KSP} 1832} 1833 1834@InProceedings{ dbl2, 1835 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 1836 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 1837 booktitle = {ECCOMAS2000}, 1838 year = {2000}, 1839 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 1840 petsc_uses = {KSP} 1841} 1842 1843@Unpublished{ cell, 1844 title = {Parallel Simulation Engines for Whole-Cell Models}, 1845 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 1846 Weber}, 1847 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 1848 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 1849 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 1850 year = {2001}, 1851 petsc_uses = {KSP} 1852} 1853 1854@Article{ barker2010two, 1855 title = {Two-level {N}ewton and hybrid {S}chwarz preconditioners for fluid-structure 1856 interaction}, 1857 author = {Barker, A.T. and Cai, X.C.}, 1858 journal = {SIAM Journal on Scientific Computing}, 1859 volume = {32}, 1860 number = {4}, 1861 pages = {2395--2417}, 1862 year = {2010}, 1863 publisher = {Society for Industrial and Applied Mathematics}, 1864 petsc_uses = {KSP} 1865} 1866 1867@Article{ barker2010scalable, 1868 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 1869 with application to blood flow modeling}, 1870 author = {Barker, A.T. and Cai, X.C.}, 1871 journal = {Journal of Computational Physics}, 1872 volume = {229}, 1873 number = {3}, 1874 pages = {642--659}, 1875 year = {2010}, 1876 publisher = {Elsevier}, 1877 petsc_uses = {KSP} 1878} 1879 1880@Article{ barker2009nks, 1881 title = {{NKS} for fully coupled fluid-structure interaction with application}, 1882 author = {Barker, A.T. and Cai, X.C.}, 1883 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 1884 pages = {275--282}, 1885 year = {2009}, 1886 publisher = {Springer}, 1887 petsc_uses = {KSP} 1888} 1889 1890@Article{ mirams2013, 1891 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 1892 and Yi Cui and Gary R Mirams}, 1893 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 1894 to predict {QT} interval changes in the rabbit ventricular wedge}, 1895 journal = {Journal of pharmacological and toxicological methods}, 1896 volume = {68}, 1897 number = {1}, 1898 pages = {88--96}, 1899 year = {2013}, 1900 doi = {10.1016/j.vascn.2013.04.004}, 1901 petsc_uses = {KSP} 1902} 1903 1904% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1905% LiteralHTML: <center><img alt="" 1906% LiteralHTML: src="images/spine0l.jpg"></center></p> 1907% LiteralHTML: <center><img alt="" 1908% LiteralHTML: src="images/vertebra.jpg"></center></p> 1909% LiteralHTML:<font color="#FF0000"> 1910% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 1911% LiteralHTML:Understanding bone mechanical properties and how they may lead to 1912% LiteralHTML:fractures is thus an important medical research activity. PETSc and 1913% LiteralHTML:Prometheus have been used for extremely large scale finite element 1914% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 1915% LiteralHTML:team of doctors and computational scientists. This computation was 1916% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 1917% LiteralHTML:with over 4000 processors.</p> 1918% LiteralHTML: </font> 1919@Article{ arbenz2008scalable, 1920 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 1921 analysis of human bone structures}, 1922 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 1923 journal = {International Journal for Numerical Methods in Engineering}, 1924 volume = {73}, 1925 number = {7}, 1926 pages = {927--947}, 1927 year = {2008}, 1928 publisher = {Wiley Online Library}, 1929 petsc_uses = {KSP} 1930} 1931 1932@InProceedings{ adams-04, 1933 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1934 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 1935 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 1936 half a billion degrees of freedom}, 1937 note = {Gordon Bell Award}, 1938 year = {2004}, 1939 petsc_uses = {KSP} 1940} 1941 1942@InProceedings{ adams-03b, 1943 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1944 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 1945 Whole Bone Micro-Mechanics on the {IBM SP}}, 1946 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 1947 year = {2003}, 1948 petsc_uses = {KSP} 1949} 1950 1951@InProceedings{ oghattas2002, 1952 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 1953 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 1954 booktitle = {Procceedings of SC2002}, 1955 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 1956 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 1957 by time-dependent PDEs, and scalability results for an inverse wave propagation 1958 problem of determining the material field of an acoustic medium. Using the 1959 algorithm, they solved a synthetic inverse wave propagation problem though a 1960 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 1961 processors.}, 1962 year = {2002}, 1963 petsc_uses = {KSP} 1964} 1965 1966% LiteralHTML: <a name="biology:cardiology"> 1967% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1968% LiteralHTML: <center><img alt="" 1969% LiteralHTML: src="images/heart.jpg"> 1970% LiteralHTML: <img alt="" 1971% LiteralHTML: src="images/pump.jpg"></center></p> 1972% LiteralHTML: 1973% LiteralHTML:<font color="#FF0000"> 1974% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 1975% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 1976% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 1977% LiteralHTML: through the heart. PETSc has been used by several research groups to 1978% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 1979% LiteralHTML: fully understand the developments of arrhthmias.</p> 1980% LiteralHTML:</font> 1981@InProceedings{ oghattas2000, 1982 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 1983 Walkington}, 1984 title = {A Parallel Dynamic-Mesh {L}agrangian Method for Simulation of Flows with Dynamic 1985 Interfaces}, 1986 booktitle = {Procceedings of SC2000}, 1987 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 1988 note = {Blood flow modeling at the microscale including effects on individual blood 1989 cells, for designing heart assist pumps, etc.}, 1990 year = {2000}, 1991 petsc_uses = {KSP} 1992} 1993 1994@InBook{ cfps2006, 1995 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 1996 editor = {A. Quarteroni et al.}, 1997 title = {Complex Systems in Biomedicine}, 1998 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 1999 publisher = {Springer-Verlag}, 2000 pages = {187--241}, 2001 year = {2006}, 2002 petsc_uses = {KSP} 2003} 2004 2005@InProceedings{ cfpst2007, 2006 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 2007 title = {Determining recovery times from transmembrane action potentials and unipolar 2008 electrograms in normal heart tissue}, 2009 booktitle = {FIMH07}, 2010 publisher = {Springer-Verlag}, 2011 volume = {4466}, 2012 pages = {139--149}, 2013 year = {2007}, 2014 petsc_uses = {KSP} 2015} 2016 2017@Article{ seemann2010framework, 2018 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 2019 Equations Using PETSc}}, 2020 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 2021 D{\\"o}ssel, O.}, 2022 journal = {Progress in Industrial Mathematics at ECMI 2008}, 2023 pages = {363--369}, 2024 year = {2010}, 2025 publisher = {Springer}, 2026 petsc_uses = {KSP} 2027} 2028 2029@InProceedings{ pft2005, 2030 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 2031 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 2032 Intramural Heterogeneity}, 2033 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 2034 pages = {267--277}, 2035 editors = {A. Frangi et al.}, 2036 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 2037 year = {2005}, 2038 petsc_uses = {KSP} 2039} 2040 2041@Article{ bgcp2005, 2042 author = {Boyce E. Griffith and Charles S. Peskin}, 2043 title = {On the order of accuracy of the immersed boundary method: Higher order 2044 convergence rates for sufficiently smooth problems}, 2045 journal = {Journal of Computational Physics}, 2046 year = {2005}, 2047 volume = {208}, 2048 pages = {75--105}, 2049 petsc_uses = {KSP} 2050} 2051 2052@Article{ griffith2007adaptive, 2053 title = {An adaptive, formally second order accurate version of the immersed boundary 2054 method}, 2055 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 2056 journal = {Journal of Computational Physics}, 2057 volume = {223}, 2058 number = {1}, 2059 pages = {10--49}, 2060 year = {2007}, 2061 publisher = {Elsevier}, 2062 petsc_uses = {KSP} 2063} 2064 2065@PhDThesis{ griffith05, 2066 author = {Boyce Griffith}, 2067 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 2068 parallel version of the immersed boundary method}, 2069 school = {New York University}, 2070 year = {2005}, 2071 petsc_uses = {KSP} 2072} 2073 2074@PhDThesis{ murillo, 2075 author = {Maria S. Murillo}, 2076 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 2077 Differential Equations with an Application in Computational Biology}, 2078 school = {University of Colorado at Boulder}, 2079 year = {2002}, 2080 petsc_uses = {KSP} 2081} 2082 2083@Article{ spv2004, 2084 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 2085 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 2086 journal = {IEEE Trans. Biomed. Eng}, 2087 year = {2004}, 2088 volume = {51}, 2089 pages = {1960--1968}, 2090 petsc_uses = {KSP} 2091} 2092 2093@Article{ vphl2003, 2094 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 2095 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 2096 journal = {J. Electrocardiol.}, 2097 year = {2003}, 2098 volume = {36}, 2099 pages = {69--74}, 2100 petsc_uses = {KSP} 2101} 2102 2103@InProceedings{ spbv2003, 2104 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and E.J. Vigmond}, 2105 title = {Preconditioning Techniques for the Bidomain Equations}, 2106 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2107 Methods}, 2108 pages = {571--580}, 2109 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2110 note = {}, 2111 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2112 year = {2003}, 2113 petsc_uses = {KSP} 2114} 2115 2116@Article{ franz-pavir-04, 2117 author = {P. Colli Franzone and L.~F. Pavarino}, 2118 title = {A parallel solver for reaction-diffusion systems in computational 2119 electrocardiology}, 2120 journal = {Mathematical Models and Methods in Applied Sciences}, 2121 year = {2004}, 2122 volume = {14}, 2123 number = {6}, 2124 pages = {883--912}, 2125 petsc_uses = {KSP} 2126} 2127 2128@Article{ franz-pavir-05, 2129 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2130 title = {Simulating patterns of excitation, repolarization and action potential 2131 durationwith cardiac Bidomain and Monodomain models}, 2132 journal = {Mathematical Biosciences}, 2133 year = {2005}, 2134 volume = {197}, 2135 number = {1}, 2136 pages = {35--66}, 2137 petsc_uses = {KSP} 2138} 2139 2140@Article{ franz-pavir-06, 2141 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2142 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 2143 the dispersion of cardiac repolarization and action potential duration: a 2144 simulation study}, 2145 journal = {Mathematical Biosciences}, 2146 year = {2006}, 2147 volume = {204}, 2148 number = {1}, 2149 pages = {132--165}, 2150 petsc_uses = {KSP} 2151} 2152 2153@InProceedings{ colli-franz-sim, 2154 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 2155 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 2156 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 2157 Mediterranean Conference on Medical and Biological Engineering}, 2158 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 2159 year = {2004}, 2160 petsc_uses = {KSP} 2161} 2162 2163@InProceedings{ pf2003, 2164 author = {Luca F. Pavarino and Piero Colli Franzone}, 2165 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 2166 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2167 Methods}, 2168 pages = {669--776}, 2169 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2170 note = {}, 2171 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2172 year = {2003}, 2173 petsc_uses = {KSP} 2174} 2175 2176@Article{ maria-is04, 2177 author = {Maria Murillo and Xiao-Chuan Cai}, 2178 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 2179 activity of the heart}, 2180 journal = {Numerical Linear Algebra with Applications}, 2181 year = {2004}, 2182 volume = {11}, 2183 pages = {261 - 277}, 2184 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 2185 petsc_uses = {KSP} 2186} 2187 2188@Article{ murli2007monitoring, 2189 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 2190 Imaging in a Grid computing PSE}}, 2191 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 2192 and Lapegna, M.}, 2193 journal = {Grid-Based Problem Solving Environments}, 2194 pages = {421--432}, 2195 year = {2007}, 2196 publisher = {Springer}, 2197 petsc_uses = {KSP} 2198} 2199 2200@Article{ carracciuolo:2006:tpc, 2201 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 2202 title = {Towards a parallel component for imaging in {PETSc} programming environment: a case 2203 study in {3-D} echocardiography}, 2204 journal = {Parallel Comput.}, 2205 volume = {32}, 2206 issue = {1}, 2207 month = jan, 2208 year = {2006}, 2209 issn = {0167-8191}, 2210 pages = {67--83}, 2211 numpages = {17}, 2212 doi = {10.1016/j.parco.2005.09.001}, 2213 acmid = {1141218}, 2214 publisher = {Elsevier Science Publishers B. V.}, 2215 address = {Amsterdam, The Netherlands, The Netherlands}, 2216 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 2217 component}, 2218 petsc_uses = {KSP} 2219} 2220 2221@Article{ damore2011integration, 2222 title = {Integration of emerging computer technologies for an efficient image sequences 2223 analysis}, 2224 journal = {Integrated Computer-Aided Engineering }, 2225 volume = {18}, 2226 number = {4}, 2227 pages = {365 - 378}, 2228 year = {2011}, 2229 note = {}, 2230 issn = {1875-8835}, 2231 doi = {10.3233/ICA-2011-0382}, 2232 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 2233 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 2234 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 2235 petsc_uses = {KSP} 2236} 2237 2238@InProceedings{ eth_biwi_00721, 2239 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and G. 2240 Székely}, 2241 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 2242 a {S}chur Complement Preconditioner}, 2243 booktitle = {Euro-Par 2009 Parallel Processing}, 2244 year = {2009}, 2245 month = aug, 2246 pages = {747-759}, 2247 volume = {5704}, 2248 editor = {H. Sips and D. Epema and H.-X. Lin}, 2249 series = {Lecture Notes in Computer Science}, 2250 publisher = {Springer}, 2251 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 2252 parallel Krylov solver}, 2253 petsc_uses = {KSP} 2254} 2255 2256% LiteralHTML: <a name="biology:imagingandsurgery"> 2257% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 2258% LiteralHTML: <center><img alt="" 2259% LiteralHTML: src="images/brain.jpg"></center> 2260@Article{ ganser2004deformable, 2261 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 2262 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 2263 journal = {Medical Image Analysis}, 2264 volume = {8}, 2265 number = {1}, 2266 pages = {3--22}, 2267 year = {2004}, 2268 publisher = {Elsevier}, 2269 petsc_uses = {KSP} 2270} 2271 2272@Unpublished{ taccsurgery, 2273 title = {{TACC} supercomputer performs laser cancer surgery on canine}, 2274 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 2275 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 2276 Austin performed laser surgery on a dog in Houston without the intervention of a 2277 surgeon. The treatment was developed collaboratively by computational experts from 2278 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 2279 leading technologists from the M.D. Anderson Cancer Center in Houston, and 2280 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 2281 state-of-the-art thermal imaging technology, and advanced computational methods, 2282 dynamic, data-driven treatments are being pursued as a minimally invasive 2283 alternative to the standard treatment of cancer.}, 2284 petsc_uses = {KSP} 2285} 2286 2287@Article{ ffhbresso2008, 2288 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 2289 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 2290 Tinsley Oden}, 2291 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 2292 journal = {Engineering with Computers}, 2293 note = {Special issue on Computational Bioengineering}, 2294 year = {2008}, 2295 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 2296 petsc_uses = {KSP} 2297} 2298 2299@TechReport{ dobbhbbbdeffghkkps2008, 2300 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 2301 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 2302 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 2303 and S. Prudhomme and R. J. Stafford}, 2304 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 2305 Cancer}, 2306 year = {2008}, 2307 institution = {University of Texas at Austin}, 2308 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 2309 petsc_uses = {KSP} 2310} 2311 2312@Article{ ogdb2004, 2313 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 2314 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 2315 journal = {Physics in Medicine and Biology}, 2316 year = {2004}, 2317 volume = {49}, 2318 pages = {2955--2947}, 2319 petsc_uses = {KSP} 2320} 2321 2322@InProceedings{ majumdar11, 2323 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 2324 Baldridge and P. Krysl}, 2325 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 2326 booktitle = {ICCS 2005}, 2327 pages = {672--679}, 2328 editor = {V.S. Sunderam et al.}, 2329 year = {2005}, 2330 petsc_uses = {KSP} 2331} 2332 2333@Conference{ sermesant-etal:03, 2334 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 2335 Ayache, H.}, 2336 title = {A parallel implementation of non-rigid registration using a volumetric 2337 biomechanical model}, 2338 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 2339 address = {Philadelphia, PA, USA}, 2340 publisher = {Springer-Verlag}, 2341 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2342 series = {Lecture Notes in Computer Science}, 2343 volume = {2717}, 2344 pages = {398-407}, 2345 date = {june 23-24}, 2346 year = {2003}, 2347 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 2348 petsc_uses = {KSP} 2349} 2350 2351@Conference{ sermesant-etal:04, 2352 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 2353 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 2354 title = {A Novel Nonrigid Registration Algorithm And Applications}, 2355 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 2356 address = {Philadelphia, PA, USA}, 2357 publisher = {Springer-Verlag}, 2358 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2359 series = {Lecture Notes in Computer Science}, 2360 volume = {2208}, 2361 pages = {923}, 2362 year = {2003}, 2363 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 2364 petsc_uses = {KSP} 2365} 2366 2367@Article{ warfield-haker-talos-05, 2368 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 2369 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 2370 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 2371 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 2372 title = {Capturing intraoperative deformations: research experience at {B}righam and {W}omen's 2373 hospital}, 2374 journal = {Medical Image Analysis}, 2375 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 2376 year = {2005}, 2377 petsc_uses = {KSP} 2378} 2379 2380@Article{ brain3, 2381 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 2382 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 2383 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 2384 Deformation during Image Guided Neurosurgery}, 2385 journal = {Computing and Visualization in Science}, 2386 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 2387 year = {2002}, 2388 petsc_uses = {KSP} 2389} 2390 2391@Article{ brain2, 2392 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 2393 Kikinis and Simon K. Warfield}, 2394 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 2395 Element Biomechanical Model}, 2396 journal = {IEEE Transactions on Medical Imaging}, 2397 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 2398 year = {2001}, 2399 petsc_uses = {KSP} 2400} 2401 2402@InProceedings{ brain1, 2403 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 2404 Ferenc A. Jolesz and Ron Kikinis}, 2405 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 2406 Guided Neurosurgery}, 2407 booktitle = {Proceedings of SC2000}, 2408 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 2409 year = {2000}, 2410 petsc_uses = {KSP} 2411} 2412 2413@Article{ vanne06, 2414 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 2415 M. Lassas and M. Kalke}, 2416 title = {Parallelized {B}ayesian inversion for three-dimensional dental {X}-ray imaging}, 2417 journal = {IEEE Transactions on Medical Imaging}, 2418 volume = {25}, 2419 number = {2}, 2420 month = feb, 2421 year = {2006}, 2422 pages = {218--228}, 2423 petsc_uses = {KSP} 2424} 2425 2426@InProceedings{ knepleybardhan2015, 2427 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 2428 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 2429 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 2430 Exposition}, 2431 volume = {9}, 2432 pages = {V009T12A04}, 2433 doi = {10.1115/IMECE2015-53579}, 2434 year = {2015}, 2435 petsc_uses = {KSP} 2436} 2437 2438@InProceedings{ bardhanknepley2015, 2439 title = {Multiscale models and approximation algorithms for protein electrostatics}, 2440 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 2441 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 2442 volume = {61}, 2443 pages = {163--174}, 2444 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 2445 doi = {10.2495/BEM380131}, 2446 publisher = {WIT Press}, 2447 year = {2015}, 2448 petsc_uses = {KSP} 2449} 2450 2451% LiteralHTML: 2452% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 2453% LiteralHTML: 2454@InProceedings{ adamsbrennanknepleywang2022, 2455 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 2456 quench plasmas}, 2457 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 2458 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 2459 (IPDPS '22)}, 2460 doi = {10.1109/IPDPS53621.2022.00020}, 2461 year = {2022}, 2462 petsc_uses = {DMPlex} 2463} 2464 2465@Misc{ adamsknepleybrennan2021, 2466 title = {Runaway Electron Generation with High-Performance, Structure Preserving 2467 Discretization of {F}okker--{P}lank--{L}andau}, 2468 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 2469 year = {2021}, 2470 petsc_uses = {KSP} 2471} 2472 2473@Article{ adamshirvijokiknepleybrownisaacmills2017, 2474 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 2475 Architectures}, 2476 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 2477 Isaac and Richard Mills}, 2478 journal = {SIAM Journal on Scientific Computing}, 2479 volume = {39}, 2480 number = {6}, 2481 pages = {C452--C465}, 2482 doi = {10.1137/17M1118828}, 2483 eprint = {1702.08880}, 2484 year = {2017}, 2485 petsc_uses = {KSP} 2486} 2487 2488@Article{ pusztayknepleyadams2022, 2489 title = {Conservative Projection Between {FEM} and Particle Bases}, 2490 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 2491 journal = {SIAM Journal on Scientific Computing}, 2492 volume = {44}, 2493 number = {4}, 2494 pages = {C310--C319}, 2495 doi = {10.1137/21M145407}, 2496 year = {2022} 2497} 2498 2499@Article{ hirvijoki2017, 2500 author = {Eero Hirvijoki and Mark F. Adams}, 2501 title = {Conservative discretization of the {Landau} collision integral}, 2502 journal = {Physics of Plasmas}, 2503 volume = {24}, 2504 number = {3}, 2505 pages = {032121}, 2506 doi = {10.1063/1.4979122}, 2507 year = {2017}, 2508 petsc_uses = {KSP} 2509} 2510 2511@Article{ mollenadamsknepleyhagerchang2021, 2512 title = {Implementation of higher-order velocity mapping between marker particles and grid 2513 in the particle-in-cell code {XGC}}, 2514 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 2515 S. Chang}, 2516 journal = {Journal of Plasma Physics}, 2517 volume = {87}, 2518 number = {2}, 2519 pages = {905870229}, 2520 eprint = {2012.11764}, 2521 doi = {10.1017/S0022377821000441}, 2522 year = {2021}, 2523 petsc_uses = {KSP} 2524} 2525 2526@Article{ lsmh2014, 2527 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 2528 title = {Comparison of particle trajectories and collision operators for collisional 2529 transport in nonaxisymmetric plasmas}, 2530 journal = { Physics of Plasmas}, 2531 volume = {21}, 2532 year = {2014}, 2533 petsc_uses = {KSP} 2534} 2535 2536@Article{ lpcep2014, 2537 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 2538 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 2539 pedestal}, 2540 journal = {Plasma Physics and Controlled Fusion}, 2541 volume = {56}, 2542 year = {2014}, 2543 petsc_uses = {KSP} 2544} 2545 2546@Article{ facets-scidac08, 2547 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 2548 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 2549 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 2550 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 2551 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 2552 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 2553 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 2554 Stotler and A. Pigarov}, 2555 journal = {J. Phys.: Conf. Ser.}, 2556 volume = {125}, 2557 year = {2008}, 2558 pages = {012040}, 2559 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 2560 petsc_uses = {KSP} 2561} 2562 2563@Article{ facets-scidac09, 2564 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 2565 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 2566 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 2567 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 2568 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 2569 and T. 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Zhang}, 2588 booktitle = {Proceedings of SciDAC 2010 Conference}, 2589 year = {2010}, 2590 url = {http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf}, 2591 petsc_uses = {KSP} 2592} 2593 2594@InProceedings{ facets-fec2010, 2595 title = {Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using 2596 the {FACETS} Framework}, 2597 author = {J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina 2598 and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. 2599 McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang}, 2600 booktitle = {Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, 2601 Republic of Korea}, 2602 year = {2010}, 2603 petsc_uses = {KSP} 2604} 2605 2606@InProceedings{ facets-epdp2010, 2607 title = {{FACETS}: A Framework for Parallel Coupling of Fusion Components}, 2608 author = {J. Cary and A. Hakim and M. Miah and S. Kruger and A. 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Maurini}, 3589 title = {Secondary Thermal Cracks in {EGS}: a Variational Approach}, 3590 booktitle = {Proceedings of the 34th Annual Meeting of the Geothermal Resources Council}, 3591 url = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}, 3592 note = {\url{https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}}, 3593 address = {Sacramento, CA}, 3594 year = {2010}, 3595 petsc_uses = {KSP} 3596} 3597 3598@Article{ chen2007full, 3599 title = {Full {3D} tomography for the crustal structure of the {Los Angeles} region}, 3600 author = {Chen, P. and Zhao, L. and Jordan, T.H.}, 3601 journal = {Bulletin of the Seismological Society of America}, 3602 volume = {97}, 3603 number = {4}, 3604 pages = {1094}, 3605 year = {2007}, 3606 publisher = {Seismol Soc America}, 3607 petsc_uses = {KSP} 3608} 3609 3610@Article{ brown2010ens, 3611 author = {Brown, Jed}, 3612 affiliation = {Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, 3613 Zürich, Switzerland}, 3614 title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}}, 3615 journal = {Journal of Scientific Computing}, 3616 publisher = {Springer Netherlands}, 3617 issn = {0885-7474}, 3618 keyword = {Mathematics and Statistics}, 3619 pages = {48-63}, 3620 volume = {45}, 3621 issue = {1}, 3622 doi = {10.1007/s10915-010-9396-8}, 3623 year = {2010}, 3624 petsc_uses = {KSP} 3625} 3626 3627@PhDThesis{ brown2011, 3628 title = {Computational methods for ice flow simulation}, 3629 author = {Jed Brown}, 3630 school = {ETH Z{\"u}rich}, 3631 year = {2011}, 3632 petsc_uses = {KSP} 3633} 3634 3635@Article{ brown2013tmeice, 3636 title = {Achieving textbook multigrid efficiency for hydrostatic ice flow}, 3637 author = {Jed Brown and Barry F. Smith and Aron Ahmadia}, 3638 journal = {SIAM Journal on Scientific Computing}, 3639 volume = {35}, 3640 number = {2}, 3641 year = {2013}, 3642 pages = {359--375}, 3643 doi = {10.1137/110834512}, 3644 note = {Also preprint ANL/MCS-P743-1298}, 3645 petsc_uses = {KSP} 3646} 3647 3648@InProceedings{ brown2013quasinewton, 3649 author = {Jed Brown and Peter Brune}, 3650 title = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type 3651 methods}, 3652 year = {2013}, 3653 booktitle = {International Conference on Mathematics and Computational Methods Applied to 3654 Nuclear Science and Engineering}, 3655 pages = {2554--2565}, 3656 petsc_uses = {KSP} 3657} 3658 3659@Misc{ spiegelman-siampp10, 3660 title = {Block Preconditioners and Advanced Software for Multiphysics Problems in Solid 3661 Earth Geodynamics}, 3662 author = {Marc Spiegelman}, 3663 note = {presentation at the 2010 SIAM Conference on Parallel Processing for Scientific 3664 Computing}, 3665 year = {2010}, 3666 petsc_uses = {KSP} 3667} 3668 3669@Article{ schauer2011a, 3670 author = {Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. 3671 Quintana-Ort\'{\i}}, 3672 title = {Large scale simulation of wave propagation in soils interacting with structures 3673 using {FEM} and {SBFEM}}, 3674 journal = {Journal of Computational Acoustics}, 3675 volume = {19}, 3676 number = {1}, 3677 pages = {75--93}, 3678 year = {2011}, 3679 doi = {10.1142/S0218396X11004316}, 3680 petsc_uses = {KSP} 3681} 3682 3683@Misc{ bsa2010, 3684 author = {J. Brown and B. Smith and A. Ahmadia}, 3685 title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow}, 3686 note = {submitted to SIAM Journal on Scientific Computing}, 3687 year = {2012}, 3688 petsc_uses = {KSP} 3689} 3690 3691@Article{ kellerkatz2016, 3692 title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere}, 3693 author = {Tobias Keller and Richard F. 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Weatherley}, 3717 title = {Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges}, 3718 journal = {Earth\ Planet.\ Sci.\ Lett.}, 3719 year = {2012}, 3720 doi = {10.1016/j.epsl.2012.04.042}, 3721 volume = {335-336}, 3722 pages = {226-237}, 3723 petsc_uses = {KSP} 3724} 3725 3726@Article{ katz10b, 3727 author = {R.F. Katz}, 3728 title = {Porosity-driven convection and asymmetry beneath mid-ocean ridges}, 3729 journal = {Geochem.\ Geophys.\ Geosys.}, 3730 volume = {10}, 3731 number = {Q0AC07}, 3732 year = {2010}, 3733 doi = {10.1029/2010GC003282}, 3734 petsc_uses = {KSP} 3735} 3736 3737@Article{ england10, 3738 author = {P.C. England and R.F. Katz}, 3739 title = {Melting above the anhydrous solidus controls the location of volcanic arcs}, 3740 journal = {Nature}, 3741 year = {2010}, 3742 volume = {467}, 3743 pages = {700--703}, 3744 doi = {10.1038/nature09417}, 3745 petsc_uses = {KSP} 3746} 3747 3748@Article{ weatherley10, 3749 author = {S. Weatherley and R.F. 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Worster}, 3761 title = {The stability of ice-sheet grounding lines}, 3762 journal = {Proc.~Roy.~Soc.~A}, 3763 year = {2010}, 3764 volume = {466}, 3765 pages = {1597--1620}, 3766 doi = {10.1098/rspa.2009.0434}, 3767 url = {http://www.earth.ox.ac.uk/~richardk/publications/Katz_Worster_PRSA10.pdf}, 3768 petsc_uses = {KSP} 3769} 3770 3771@Article{ kyrkesmith2013stress, 3772 title = {Stress balances of ice streams in a vertically integrated, higher-order 3773 formulation}, 3774 author = {Kyrke-Smith, T.M. and Katz, R.F. and Fowler, A.C.}, 3775 journal = {Journal of Glaciology}, 3776 volume = {59}, 3777 number = {215}, 3778 pages = {449--466}, 3779 year = {2013}, 3780 doi = {10.3189/2013JoG12J140}, 3781 petsc_uses = {KSP} 3782} 3783 3784@Article{ takei2013anisotropy1, 3785 author = {Takei Y. and R.F. Katz}, 3786 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. 3787 Governing equations and linearised analysis}}, 3788 journal = {J.\ Fluid\ Mech.}, 3789 year = {2013}, 3790 volume = {734}, 3791 pages = {424-455}, 3792 doi = {10.1017/jfm.2013.482}, 3793 petsc_uses = {KSP} 3794} 3795 3796@Article{ katz2013anisotropy2, 3797 author = {Katz R.F. and Y. Takei}, 3798 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. 3799 Numerical solutions of the full equations}}, 3800 journal = {J.\ Fluid\ Mech.}, 3801 year = {2013}, 3802 volume = {734}, 3803 pages = {456-485}, 3804 doi = {10.1017/jfm.2013.483}, 3805 petsc_uses = {KSP} 3806} 3807 3808@Article{ kyrke-smith2014subglacial, 3809 author = {Kyrke-Smith, T.M. and R.F. Katz and A.C. Fowler}, 3810 title = {Subglacial hydrology and the formation of ice streams}, 3811 journal = {Proc.\ Roy.\ Soc.\ A}, 3812 year = {2014}, 3813 volume = {470}, 3814 number = {2161}, 3815 doi = {10.1098/rspa.2013.0494}, 3816 petsc_uses = {KSP} 3817} 3818 3819@Article{ spiegelmanwilsonvankeken2013, 3820 author = {{Spiegelman}, M.~W. and {Wilson}, C.~R. and {Van Keken}, P.~E. }, 3821 title = {{TerraFERMA: The Transparent Finite Element Rapid Model Assembler for 3822 multi-physics problems in the solid Earth sciences}}, 3823 journal = {AGU Fall Meeting Abstracts}, 3824 keywords = {0560 COMPUTATIONAL GEOPHYSICS Numerical solutions, 1902 INFORMATICS Community 3825 modeling frameworks, 1906 INFORMATICS Computational models, algorithms}, 3826 year = {2013}, 3827 month = dec, 3828 pages = {A2208}, 3829 adsurl = {http://adsabs.harvard.edu/abs/2013AGUFMDI31A2208S}, 3830 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 3831 petsc_uses = {KSP} 3832} 3833 3834@Article{ bueler2009shallow, 3835 title = {{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled 3836 ice sheet model}}, 3837 author = {Ed Bueler and Jed Brown}, 3838 journal = {Journal of Geophysical Research-Earth Surface}, 3839 volume = {114}, 3840 number = {F3}, 3841 pages = {F03008}, 3842 year = {2009}, 3843 publisher = {American Geophysical Union}, 3844 petsc_uses = {KSP} 3845} 3846 3847@Article{ bueler2007est, 3848 title = {{Exact solutions to the thermomechanically coupled shallow ice approximation: 3849 effective tools for verification}}, 3850 author = {Ed Bueler and Jed Brown and Craig Lingle}, 3851 journal = {J. Glaciol}, 3852 volume = {53}, 3853 pages = {499--516}, 3854 year = {2007}, 3855 petsc_uses = {KSP} 3856} 3857 3858@Article{ bueler2007fcv, 3859 title = {{Fast computation of a viscoelastic deformable Earth model for ice-sheet 3860 simulations}}, 3861 author = {Ed Bueler and Craig S. Lingle and Jed Brown}, 3862 journal = {Ann. Glaciol}, 3863 volume = {46}, 3864 pages = {97--105}, 3865 year = {2007}, 3866 petsc_uses = {KSP} 3867} 3868 3869@Article{ bueler2005iso, 3870 author = {Ed Bueler and Craig S. Lingle and Jed A. Kallen-Brown and David N. Covey and 3871 Latrice N. Bowman}, 3872 title = {Exact solutions and numerical verification for isothermal ice sheets}, 3873 journal = {J. Glaciol.}, 3874 volume = {51}, 3875 number = {173}, 3876 pages = {291--306}, 3877 year = {2005}, 3878 petsc_uses = {KSP} 3879} 3880 3881@Article{ chao2008programming, 3882 title = {{Programming on Numerical Simulation of Tsunami with PETSc and FEPG}}, 3883 author = {Chao-fan, Z. and Yao-lin, S.}, 3884 journal = {Earthquake}, 3885 year = {2008}, 3886 petsc_uses = {KSP} 3887} 3888 3889@Article{ marti2014, 3890 author = {Marti, P. and Schaeffer, N. and Hollerbach, R. and Cébron, D. and Nore, C. and 3891 Luddens, F. and Guermond, J.-L. and Aubert, J. and Takehiro, S. and Sasaki, Y. and 3892 Hayashi, Y.-Y. and Simitev, R. and Busse, F. and Vantieghem, S. and Jackson, A.}, 3893 title = {Full sphere hydrodynamic and dynamo benchmarks}, 3894 journal = {Geophysical Journal International}, 3895 year = {2014}, 3896 doi = {10.1093/gji/ggt518}, 3897 url = {http://gji.oxfordjournals.org/content/early/2014/01/26/gji.ggt518.abstract}, 3898 petsc_uses = {KSP} 3899} 3900 3901@InProceedings{ ganfulukyangxueyang2013, 3902 author = {Gan, Lin and Fu, Haohuan and Luk, Wayne and Yang, Chao and Xue, Wei and Yang, 3903 Guangwen}, 3904 title = {Global Atmospheric Simulation on a Reconfigurable Platform}, 3905 booktitle = {Proceedings of the 2013 IEEE 21st Annual International Symposium on 3906 Field-Programmable Custom Computing Machines}, 3907 series = {FCCM '13}, 3908 pages = {230--}, 3909 year = {2013}, 3910 isbn = {978-0-7695-4969-9}, 3911 doi = {10.1109/FCCM.2013.26}, 3912 acmid = {2495688}, 3913 publisher = {IEEE Computer Society}, 3914 petsc_uses = {KSP} 3915} 3916 3917@InProceedings{ ganfuchaolukxuemencerhuangyang2014, 3918 author = {Lin Gan and Haohuan Fu and Chao Yang and Luk, W. and Wei Xue and Mencer, O. and 3919 Xiaomeng Huang and Guangwen Yang}, 3920 booktitle = {Field Programmable Logic and Applications (FPL), 2014 24th International 3921 Conference on}, 3922 title = {A highly-efficient and green data flow engine for solving {E}uler atmospheric 3923 equations}, 3924 year = {2014}, 3925 month = sep, 3926 pages = {1-6}, 3927 doi = {10.1109/FPL.2014.6927462}, 3928 petsc_uses = {KSP} 3929} 3930 3931%Aagaard, B., Williams, C., Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), EarthScope National Meeting, Austin, Texas, May 17–20. 3932%Aagaard, B., Williams, C., and Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), Southern California Earthquake Center Annual Meeting, Palm Springs, California, September 11–14. 3933%Aagaard, B., Williams, C., and Knepley, M. (2012). PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation (abstract), Seismological Society of America Annual Meeting, San Diego, California, April 17-19. 3934@Article{ aagaardknepleywilliams13, 3935 title = {A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element 3936 Models of Quasi-static and Dynamic Crustal Deformation}, 3937 author = {Brad T. Aagaard and Matthew G. Knepley and Charles A. Williams}, 3938 journal = {Journal of Geophysical Research: Solid Earth}, 3939 volume = {118}, 3940 number = {6}, 3941 pages = {3059--3079}, 3942 issn = {2169-9356}, 3943 doi = {10.1002/jgrb.50217}, 3944 keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics}, 3945 year = {2013}, 3946 petsc_uses = {KSP} 3947} 3948 3949@InProceedings{ aagaardknepleywilliams11, 3950 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3951 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3952 Deformation}, 3953 booktitle = {Eos Transactions of the AGU}, 3954 organization = {American Geophysical Union}, 3955 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 3956 year = {2011}, 3957 petsc_uses = {KSP} 3958} 3959 3960@InProceedings{ knepley10b, 3961 author = {Matthew G. {Knepley}}, 3962 title = {Acceleration of low order finite element computation with {GPUs} (Invited)}, 3963 booktitle = {Eos Transactions of the AGU}, 3964 organization = {American Geophysical Union}, 3965 note = {Fall Meeting Supplemental, Abstract IN44A-01}, 3966 year = {2010}, 3967 petsc_uses = {KSP} 3968} 3969 3970@InProceedings{ mayknepleygurnis09, 3971 author = {Dave A. May and Matthew G. Knepley and Michael Gurnis}, 3972 title = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}}, 3973 booktitle = {Eos Transactions of the AGU}, 3974 organization = {American Geophysical Union}, 3975 note = {Fall Meeting Supplemental, Abstract P31A-A1241}, 3976 year = {2009}, 3977 petsc_uses = {KSP} 3978} 3979 3980@InProceedings{ yuenknepleyerlebacherwright09, 3981 author = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright}, 3982 title = {The Coming Role of {GPU} in Computational Geodynamics}, 3983 booktitle = {Eos Transactions of the AGU}, 3984 organization = {American Geophysical Union}, 3985 note = {Fall Meeting Supplemental, Abstract DI22A-05}, 3986 year = {2009}, 3987 petsc_uses = {KSP} 3988} 3989 3990@InProceedings{ aagaardknepleywilliams08, 3991 author = {Brad Aagaard and Charles A. Williams and Matthew G. Knepley}, 3992 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3993 Deformation}, 3994 booktitle = {Eos Transactions of the AGU}, 3995 organization = {American Geophysical Union}, 3996 volume = {89}, 3997 number = {53}, 3998 note = {Fall Meeting Supplemental, Abstract T41A-1925}, 3999 year = {2007}, 4000 petsc_uses = {KSP} 4001} 4002 4003@InProceedings{ aagaardknepleywilliams07, 4004 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 4005 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 4006 Deformation}, 4007 booktitle = {Eos Transactions of the AGU}, 4008 organization = {American Geophysical Union}, 4009 volume = {88}, 4010 number = {52}, 4011 note = {Fall Meeting Supplemental, Abstract T21B-1798}, 4012 year = {2007}, 4013 petsc_uses = {KSP} 4014} 4015 4016@InProceedings{ aagaardknepleywilliams05, 4017 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 4018 title = {Development of software for studying earthquakes across multiple spatial and 4019 temporal scales by coupling quasi-static and dynamic simulations}, 4020 booktitle = {Eos Transactions of the AGU}, 4021 organization = {American Geophysical Union}, 4022 volume = {86}, 4023 number = {52}, 4024 note = {Fall Meeting Supplemental, Abstract S53A-1072}, 4025 year = {2005}, 4026 petsc_uses = {KSP} 4027} 4028 4029@InProceedings{ williamsgablehagermeadeaagaardknepley08, 4030 author = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and 4031 Brad Aagaard and Matthew G. Knepley}, 4032 title = {Modeling of Multiple Earthquake Cycles in {S}outhern {C}alifornia Using the {SCEC} 4033 Community Fault Model}, 4034 booktitle = {Proceedings of Geosciences '08}, 4035 address = {Wellington, NZ}, 4036 month = nov, 4037 year = {2008}, 4038 petsc_uses = {KSP} 4039} 4040 4041@TechReport{ zhang07, 4042 title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for 4043 Tsunamis}, 4044 author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi}, 4045 type = {Preprint}, 4046 number = {ANL/MCS-P1459-0907}, 4047 institution = {ANL}, 4048 month = sep, 4049 year = {2007}, 4050 petsc_uses = {KSP} 4051} 4052 4053@Article{ katz08b, 4054 author = {Richard F. Katz}, 4055 title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic 4056 focusing at mid-ocean ridges}, 4057 journal = {J. Petrology}, 4058 year = {2008}, 4059 volume = {49}, 4060 pages = {2099--2121}, 4061 doi = {10.1093/petrology/egn058}, 4062 petsc_uses = {KSP} 4063} 4064 4065@Article{ hgrhkjvv2008, 4066 title = {On preconditioning for a parallel solution of the {R}ichards equation}, 4067 author = {Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy 4068 Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena}, 4069 journal = {Computers and Geosciences}, 4070 volume = {34}, 4071 pages = {1958--1963}, 4072 year = {2008}, 4073 petsc_uses = {KSP} 4074} 4075 4076@Article{ maymoresi2008, 4077 title = {Preconditioned iterative methods for {Stokes} flow problems arising in 4078 computational geodynamics}, 4079 journal = {Physics of the Earth and Planetary Interiors}, 4080 volume = {171}, 4081 number = {1-4}, 4082 pages = {33--47}, 4083 year = {2008}, 4084 note = {{R}ecent Advances in Computational Geodynamics: Theory, Numerics and 4085 Applications}, 4086 issn = {0031-9201}, 4087 doi = {10.1016/j.pepi.2008.07.036}, 4088 author = {Dave A. May and Louis Moresi}, 4089 keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}, 4090 petsc_uses = {KSP} 4091} 4092 4093@Article{ kausmuhlhausmay2010, 4094 title = {A stabilization algorithm for geodynamic numerical simulations with a free 4095 surface}, 4096 author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May}, 4097 journal = {Physics of the Earth and Planetary Interiors}, 4098 volume = {181}, 4099 number = {1}, 4100 pages = {12--20}, 4101 year = {2010}, 4102 petsc_uses = {KSP} 4103} 4104 4105@Article{ duretzmaygeryatackley2011, 4106 title = {Discretization errors and free surface stabilization in the finite difference and 4107 marker-in-cell method for applied geodynamics: A numerical study}, 4108 author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley}, 4109 journal = {Geochemistry, Geophysics, Geosystems}, 4110 volume = {12}, 4111 number = {7}, 4112 year = {2011}, 4113 petsc_uses = {KSP} 4114} 4115 4116@Article{ furuichimaytackley2011, 4117 title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a 4118 {Schur} complement approach with mixed precision arithmetic}, 4119 author = {Mikito Furuichi and Dave A May and Paul J Tackley}, 4120 journal = {Journal of Computational Physics}, 4121 volume = {230}, 4122 number = {24}, 4123 pages = {8835--8851}, 4124 year = {2011}, 4125 petsc_uses = {KSP} 4126} 4127 4128@Article{ kellermaykaus2013, 4129 title = {Numerical modelling of magma dynamics coupled to tectonic deformation of 4130 lithosphere and crust}, 4131 author = {Tobias Keller and Dave A May and Boris JP Kaus}, 4132 journal = {Geophysical Journal International}, 4133 volume = {195}, 4134 number = {3}, 4135 pages = {1406--1442}, 4136 year = {2013}, 4137 petsc_uses = {KSP} 4138} 4139 4140@Article{ schellartfreemanstegmanmoresimay2007, 4141 title = {Evolution and diversity of subduction zones controlled by slab width}, 4142 author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A 4143 May}, 4144 journal = {Nature}, 4145 volume = {446}, 4146 number = {7133}, 4147 pages = {308--311}, 4148 year = {2007}, 4149 petsc_uses = {KSP} 4150} 4151 4152@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012, 4153 title = {A comparison of numerical surface topography calculations in geodynamic 4154 modelling: an evaluation of the sticky air method}, 4155 author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter 4156 and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley}, 4157 journal = {Geophysical Journal International}, 4158 volume = {189}, 4159 number = {1}, 4160 pages = {38--54}, 4161 year = {2012}, 4162 petsc_uses = {KSP} 4163} 4164 4165@Article{ stegmanfreemanschellartmoresimay2006, 4166 title = {Influence of trench width on subduction hinge retreat rates in {3-D} models of slab 4167 rollback}, 4168 author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A 4169 May}, 4170 journal = {Geochemistry, Geophysics, Geosystems}, 4171 volume = {7}, 4172 number = {3}, 4173 year = {2006}, 4174 petsc_uses = {KSP} 4175} 4176 4177@InProceedings{ may2014ptatin, 4178 title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics}, 4179 author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}}, 4180 booktitle = {Proceedings of {SC14}: The {International Conference for High Performance 4181 Computing, Networking, Storage and Analysis}}, 4182 organization = {ACM}, 4183 pages = {274--284}, 4184 year = {2014}, 4185 doi = {10.1109/SC.2014.28}, 4186 petsc_uses = {KSP} 4187} 4188 4189@Article{ maybrownpourhiet2015, 4190 title = {A scalable, matrix-free multigrid preconditioner for finite element 4191 discretizations of heterogeneous {Stokes} flow}, 4192 author = {David A May and Jed Brown and Laetitia {Le Pourhiet}}, 4193 journal = {Computer Methods in Applied Mechanics and Engineering}, 4194 volume = {290}, 4195 pages = {496--523}, 4196 year = {2015}, 4197 doi = {10.1016/j.cma.2015.03.014}, 4198 petsc_uses = {KSP} 4199} 4200 4201@Article{ duretzmayyamato2016, 4202 title = {A free surface capturing discretization for the staggered grid finite difference 4203 scheme}, 4204 author = {Thibault Duretz and Dave A May and Philippe Yamato}, 4205 journal = {Geophysical Journal International}, 4206 volume = {204}, 4207 number = {3}, 4208 pages = {1518--1530}, 4209 year = {2016}, 4210 petsc_uses = {KSP} 4211} 4212 4213@Article{ rhebergenwellskatzwathen2014, 4214 author = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen}, 4215 title = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics}, 4216 journal = {SIAM J. Sci. Comput.}, 4217 volume = {36}, 4218 pages = {A1960--A1977}, 4219 year = {2014}, 4220 petsc_uses = {KSP} 4221} 4222 4223@Article{ katz08a, 4224 author = {R.F. Katz and M.G. Worster}, 4225 title = {Simulation of directional solidification, thermochemical convection, and chimney 4226 formation in a {H}ele-{S}haw cell}, 4227 journal = {J. Comp. Phys.}, 4228 volume = {227}, 4229 pages = {9823-9840}, 4230 year = {2008}, 4231 doi = {10.1016/j.jcp.2008.06.039}, 4232 petsc_uses = {KSP} 4233} 4234 4235@Article{ aabg2007, 4236 author = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas}, 4237 title = {Full waveform inversion for seismic velocity and anelastic losses in 4238 heterogeneous structures}, 4239 journal = {Bulletin of Seismological Society of America}, 4240 year = {2007}, 4241 volume = {97}, 4242 pages = {1990--2008}, 4243 petsc_uses = {KSP} 4244} 4245 4246@Article{ katz2006, 4247 author = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman}, 4248 title = {The dynamics of melt and shear localization in partially molten aggregates}, 4249 journal = {Nature}, 4250 year = {2006}, 4251 volume = {442}, 4252 pages = {676--679}, 4253 month = aug, 4254 day = {10}, 4255 url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}, 4256 petsc_uses = {KSP} 4257} 4258 4259@InProceedings{ mqrs2003, 4260 author = {Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl}, 4261 year = {2003}, 4262 title = {Parallel Preconditioning for Sedimentary Basin Simulations}, 4263 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 4264 Sozopol, Bulgaria, June 4-8, 2003}, 4265 petsc_uses = {KSP} 4266} 4267 4268@InProceedings{ lichtner1, 4269 author = {Chuan Lu and Peter C. Lichtner}, 4270 year = {2005}, 4271 title = {{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in 4272 Geologic Media}, 4273 booktitle = {Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL}, 4274 lab = {LANL}, 4275 petsc_uses = {KSP} 4276} 4277 4278@Article{ hammondlichtnermills2014, 4279 title = {Evaluating the Performance of Parallel Subsurface Simulators: An Illustrative 4280 Example with {PFLOTRAN}}, 4281 author = {Glenn E. Hammond and Peter C. Lichtner and Richard Tran Mills}, 4282 journal = {Water Resources Research}, 4283 volume = {50}, 4284 number = {1}, 4285 pages = {208--228}, 4286 doi = {10.1002/2012WR013483}, 4287 year = {2014}, 4288 petsc_uses = {KSP} 4289} 4290 4291@Article{ smw2003, 4292 author = {R. Scheichl and R. Masson and J. Wendebourg}, 4293 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 4294 journal = {Computational Geosciences}, 4295 year = {2003}, 4296 volume = {7}, 4297 pages = {295--318}, 4298 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 4299 petsc_uses = {KSP} 4300} 4301 4302@Article{ kees-miller-03, 4303 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 4304 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 4305 journal = {Computational Geosciences}, 4306 year = {2003}, 4307 volume = {7}, 4308 pages = {91--114}, 4309 petsc_uses = {KSP} 4310} 4311 4312@Article{ bk2003, 4313 author = {JN Buur and T Kuehnel}, 4314 title = {Improving depth imaging by automated model updating}, 4315 journal = {The Leading Edge}, 4316 year = {2003}, 4317 volume = {22}, 4318 pages = {310-318}, 4319 petsc_uses = {KSP} 4320} 4321 4322@Article{ frederickbuffett2016, 4323 title = {Submarine groundwater discharge as a possible formation mechanism for 4324 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 4325 author = {Jennifer M. Frederick and Bruce A. Buffett}, 4326 journal = {Journal of Geophysical Research: Solid Earth}, 4327 volume = {121}, 4328 number = {3}, 4329 pages = {1383--1404}, 4330 issn = {2169-9356}, 4331 doi = {10.1002/2015JB012627}, 4332 year = {2016}, 4333 petsc_uses = {KSP} 4334} 4335 4336% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4337% LiteralHTML:<font color="#FF0000"> 4338% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 4339% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 4340% LiteralHTML:variety of these simulations.</p> 4341% LiteralHTML:</font> 4342% LiteralHTML: 4343@InProceedings{ appelbe1, 4344 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4345 year = {2003}, 4346 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 4347 computational methodology}, 4348 page = {781}, 4349 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 4350 Proceedings}, 4351 publisher = {Springer-Verlag}, 4352 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 4353 petsc_uses = {KSP} 4354} 4355 4356% LiteralHTML:<a name="katz"> 4357@InProceedings{ gd1, 4358 author = {Guillaume Dumont and Michel Kern}, 4359 title = {Parallelization of a {3D} Seismic Migration Code with {PETSc}}, 4360 year = {1999}, 4361 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 4362 Computing}, 4363 petsc_uses = {KSP} 4364} 4365 4366% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 4367% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 4368% LiteralHTML:<font color="#FF0000"> 4369% LiteralHTML: Figures from the work of Richard Katz 4370@PhDThesis{ katzthesis, 4371 author = {R.F. Katz}, 4372 title = {The deep roots of volcanoes: models of magma dynamics with applications to 4373 subduction zones}, 4374 school = {Columbia University}, 4375 year = {2005}, 4376 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 4377 petsc_uses = {KSP} 4378} 4379 4380@InCollection{ knepleykatzsmith06, 4381 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 4382 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 4383 USA}, 4384 title = {Developing a Geodynamics Simulator with {PETSc}}, 4385 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 4386 series = {Lecture Notes in Computational Science and Engineering}, 4387 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 4388 publisher = {Springer Berlin Heidelberg}, 4389 isbn = {978-3-540-31619-0}, 4390 keyword = {Mathematics and Statistics}, 4391 pages = {413-438}, 4392 volume = {51}, 4393 doi = {10.1007/3-540-31619-1_12}, 4394 year = {2006}, 4395 petsc_uses = {KSP} 4396} 4397 4398@Article{ katz04, 4399 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 4400 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 4401 the global mid-ocean ridge system}, 4402 journal = {Geophys.\ Res.\ Letts.}, 4403 year = {2004}, 4404 volume = {31}, 4405 pages = {L15605}, 4406 petsc_uses = {KSP} 4407} 4408 4409@Article{ katz07, 4410 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 4411 Ethan Coon}, 4412 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 4413 Toolkit for Scientific Computation}}, 4414 journal = {Phys. Earth Planet. In.}, 4415 volume = {163}, 4416 pages = {52--68}, 4417 year = {2007}, 4418 petsc_uses = {KSP} 4419} 4420 4421@Article{ williams2006development, 4422 title = {{Development of a package for modeling stress in the lithosphere}}, 4423 author = {Williams, CA}, 4424 journal = {Eos Trans. AGU}, 4425 volume = {87}, 4426 pages = {36}, 4427 year = {2006}, 4428 petsc_uses = {KSP} 4429} 4430 4431@Article{ goverswortel05, 4432 author = {R. Govers and M.J.R. Wortel}, 4433 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 4434 journal = {Earth and Planetary Science Letters}, 4435 volume = {236/1-2}, 4436 pages = {505-523}, 4437 year = {2005}, 4438 petsc_uses = {KSP} 4439} 4440 4441@InProceedings{ snark2, 4442 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4443 year = {2002}, 4444 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 4445 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 4446 petsc_uses = {KSP} 4447} 4448 4449@Article{ snark1, 4450 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 4451 Tan and Feng Wang}, 4452 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 4453 journal = {Submitted to Pure and Applied Geosciences}, 4454 petsc_uses = {KSP} 4455} 4456 4457@InProceedings{ earthquake2003, 4458 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 4459 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 4460 Tiankai Tu}, 4461 year = {2003}, 4462 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 4463 booktitle = {Proceedings of SC2003}, 4464 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 4465 petsc_uses = {KSP} 4466} 4467 4468@InProceedings{ stefano12, 4469 author = {Michele De Stefano}, 4470 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 4471 booktitle = {PIERS Proceedings}, 4472 month = aug, 4473 address = {Moscow, RUSSIA}, 4474 pages = {491--495}, 4475 year = {2012}, 4476 petsc_uses = {KSP} 4477} 4478 4479%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 4480 4481% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4482% LiteralHTML: <center><img alt="" 4483% LiteralHTML: src="images/ocean.jpg"></center></p> 4484@Article{ khatiwala07, 4485 author = {Khatiwala, S.}, 4486 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 4487 journal = {Glob. Biogeochem. Cycles}, 4488 volume = {21}, 4489 doi = {10.1029/2007GB002923}, 4490 year = {2007}, 4491 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 4492} 4493 4494@Article{ dks2004, 4495 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 4496 journal = {Ocean Modelling}, 4497 year = {2004}, 4498 volume = {6(2)}, 4499 pages = {125-150}, 4500 title = {A finite-element Ocean Model: Principles and Evaluation}, 4501 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}, 4502 petsc_uses = {KSP} 4503} 4504 4505@Article{ danilov1, 4506 author = {S. Danilov and G. Kivman and J. Schroter}, 4507 year = {2004}, 4508 title = {Evaluation of an eddy-permitting finite-element ocean model in the {N}orth 4509 {A}tlantic}, 4510 journal = {Ocean Modelling}, 4511 petsc_uses = {KSP} 4512} 4513 4514@Article{ nerger1, 4515 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 4516 year = {2004}, 4517 title = {Data Assimilation with the Ensemble {K}alman Filter and the {SEIK} Filter applied to 4518 a Finite Element Model of the {N}orth {A}tlantic}, 4519 journal = {Journal of marine systems}, 4520 petsc_uses = {KSP} 4521} 4522 4523@Conference{ rakowsky2003self, 4524 title = {{A self-adaptive finite element model of the atmosphere}}, 4525 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 4526 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 4527 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 4528 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 4529 pages = {279}, 4530 isbn = {981238376X}, 4531 year = {2003}, 4532 organization = {World Scientific Pub Co}, 4533 petsc_uses = {KSP} 4534} 4535 4536@Article{ lauter3, 4537 author = {M. Lauter}, 4538 year = {2004}, 4539 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4540 AtmosphArenmodell}, 4541 journal = {Berichte zur Polar- und Meeresforschung}, 4542 petsc_uses = {KSP} 4543} 4544 4545@Article{ lauter2, 4546 author = {M. Lauter and D. Handorf and K. Dethloff}, 4547 year = {2004}, 4548 title = {Unsteady analytical solutions of the spherical shallow water equations}, 4549 journal = {Journal of computational physics}, 4550 petsc_uses = {KSP} 4551} 4552 4553@PhDThesis{ lauter1, 4554 author = {M. Lauter}, 4555 year = {2004}, 4556 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4557 AtmosphArenmodell}, 4558 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 4559 petsc_uses = {KSP} 4560} 4561 4562@Article{ frickenhaus1, 4563 author = {S. Frickenhaus and W. Hiller and M. Best}, 4564 year = {2005}, 4565 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 4566 parallel numerical atmosphere and ocean models}, 4567 journal = {Ocean Modelling}, 4568 volume = {10}, 4569 pages = {185--191}, 4570 petsc_uses = {KSP} 4571} 4572 4573@Article{ 0266-5611-24-3-034015, 4574 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 4575 title = {A {N}ewton-{CG} method for large-scale three-dimensional elastic full-waveform 4576 seismic inversion}, 4577 journal = {Inverse Problems}, 4578 volume = {24}, 4579 number = {3}, 4580 pages = {034015 (26pp)}, 4581 url = {http://stacks.iop.org/0266-5611/24/034015}, 4582 year = {2008}, 4583 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 4584 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 4585 iterations with inner conjugate gradient linear iterations, globalized by an 4586 Armijo backtracking line search, solved on a sequence of finer grids and higher 4587 frequencies to remain in the vicinity of the global optimum, inexactly terminated 4588 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 4589 variation operator to capture sharp interfaces, finely discretized by finite 4590 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 4591 implemented in matrix-free fashion with adjoint-based computation of reduced 4592 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 4593 waveform storage, and partitioned spatially across processors to parallelize the 4594 solutions of the forward and adjoint wave equations and the evaluation of 4595 gradient-like information. Several numerical examples demonstrate the grid 4596 independence of linear and nonlinear iterations, the effectiveness of the 4597 preconditioner, the ability to solve inverse problems with up to 17 million 4598 inversion parameters on up to 2048 processors, the effectiveness of multiscale 4599 continuation in keeping iterates in the basin of attraction of the global minimum, 4600 and the ability to fit the observational data while reconstructing the model with 4601 reasonable resolution and capturing sharp interfaces.}, 4602 petsc_uses = {KSP} 4603} 4604 4605% LiteralHTML: 4606% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 4607% LiteralHTML: 4608% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4609% LiteralHTML:<font color="#FF0000"> 4610% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 4611% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 4612% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 4613% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 4614% LiteralHTML:for a variety of these simulations.</p> 4615% LiteralHTML:</font> 4616% LiteralHTML: 4617@Article{ mills2009modeling, 4618 title = {Modeling subsurface reactive flows using leadership-class computing}, 4619 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4620 Mahinthakumar, G.K. and Smith, B.F.}, 4621 journal = {Journal of Physics: Conference Series}, 4622 volume = {180}, 4623 pages = {012062}, 4624 year = {2009}, 4625 publisher = {IOP Publishing}, 4626 petsc_uses = {KSP} 4627} 4628 4629@Conference{ mills2007simulating, 4630 title = {{Simulating subsurface flow and transport on ultrascale computers using 4631 PFLOTRAN}}, 4632 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 4633 booktitle = {Journal of Physics: Conference Series}, 4634 volume = {78}, 4635 pages = {012051}, 4636 year = {2007}, 4637 organization = {IOP Publishing}, 4638 petsc_uses = {KSP} 4639} 4640 4641@InProceedings{ mills2009, 4642 title = {Modeling subsurface reactive flows using leadership-class computing}, 4643 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4644 Mahinthakmuar, G. and Smith, B.}, 4645 booktitle = {Journal of Physics: Conference Series}, 4646 volume = {180}, 4647 pages = {102062}, 4648 year = {2009}, 4649 organization = {IOP Publishing}, 4650 petsc_uses = {KSP} 4651} 4652 4653@Article{ guo2013parallel, 4654 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 4655 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 4656 }, 4657 journal = {Advances in Water Resources }, 4658 volume = {53}, 4659 number = {0}, 4660 pages = {101 - 108}, 4661 year = {2013}, 4662 note = {}, 4663 issn = {0309-1708}, 4664 doi = {10.1016/j.advwatres.2012.10.010}, 4665 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 4666 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 4667 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 4668 preconditioner}, 4669 petsc_uses = {KSP} 4670} 4671 4672@Unpublished{ stomp, 4673 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 4674 url = {http://stomp.pnl.gov/}, 4675 petsc_uses = {KSP} 4676} 4677 4678@InProceedings{ htfc2003, 4679 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 4680 title = {Methods and Experiences For Parallelizing Flood Models}, 4681 year = {2003}, 4682 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 4683 European PVM/MPI User's Group Meeting}, 4684 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 4685 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 4686 petsc_uses = {KSP} 4687} 4688 4689@InProceedings{ hulchy-tran-astalos-fmsip, 4690 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 4691 D.Froehlich}, 4692 title = {Flood Modeling System and Its Parallelization}, 4693 year = {2002}, 4694 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 4695 Engineering}, 4696 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 4697 petsc_uses = {KSP} 4698} 4699 4700@InProceedings{ gy1, 4701 author = {J. P. Gwo and G. T. Yeh}, 4702 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 4703 Transport at Watershed Scale}, 4704 year = {2004}, 4705 booktitle = {The International Conference on Computational Methods}, 4706 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 4707 petsc_uses = {KSP} 4708} 4709 4710@Conference{ cheng2009efficient, 4711 title = {{An efficient parallel method for large-scale groundwater flow equation based on 4712 PETSc}}, 4713 author = {Cheng, T. and Ji, X. and Wang, Q.}, 4714 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 4715 Conference on}, 4716 pages = {190--193}, 4717 organization = {IEEE}, 4718 petsc_uses = {KSP} 4719} 4720 4721@Unpublished{ sfrsm, 4722 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 4723 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 4724 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 4725 its linear solves}, 4726 petsc_uses = {KSP} 4727} 4728 4729% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4730@InProceedings{ bart_omar:sc05, 4731 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 4732 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 4733 title = {Dynamic data driven inversion for terascale simulations: real-time 4734 indentification of airborne contaminants}, 4735 booktitle = {Proceedings of SC2005}, 4736 organization = {IEEE/ACM}, 4737 address = {Seattle, WA}, 4738 year = {2005}, 4739 month = nov, 4740 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 4741 lab = {SNL}, 4742 petsc_uses = {KSP} 4743} 4744 4745@InProceedings{ anton-krassimir-lscc, 4746 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 4747 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 4748 Simulations}, 4749 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 4750 volume = {2907}, 4751 year = {2003}, 4752 publisher = {Springer-Verlag}, 4753 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 4754 petsc_uses = {KSP} 4755} 4756 4757@InProceedings{ aa2001, 4758 author = {Anton Antonov}, 4759 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 4760 year = {2001}, 4761 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 4762 Sozopol, Bulgaria}, 4763 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 4764 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 4765 petsc_uses = {KSP} 4766} 4767 4768% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4769@Article{ grassley-simmons-kercher-00, 4770 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 4771 year = {2000}, 4772 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 4773 reactive transport models}, 4774 journal = {Applied Geochemistry}, 4775 volume = {17}, 4776 pages = {699--708}, 4777 lab = {LLNL} 4778} 4779 4780@Article{ glassey-nitao-03, 4781 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 4782 and Carl I. Steefel and James R. Kercher}, 4783 year = {2003}, 4784 title = {The impact of climate change on vadose zone pore waters and its implication for 4785 long-term monitoring}, 4786 journal = {Computers and Geosciences}, 4787 volume = {29}, 4788 pages = {399-411}, 4789 lab = {LLNL}, 4790 petsc_uses = {KSP} 4791} 4792 4793@Article{ steefel-depaolo-lichtner-05, 4794 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 4795 year = {2005}, 4796 title = {Reactive transport modeling: An essential tool and a new research approach for 4797 the Earth sciences}, 4798 journal = {Earth and Planetary Science Letters}, 4799 lab = {LLNL,LANL}, 4800 petsc_uses = {KSP} 4801} 4802 4803% LiteralHTML:<a name="scalinglarge"> 4804% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4805% LiteralHTML: <center><img alt="" 4806% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 4807% LiteralHTML:<font color="#FF0000"> 4808% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 4809@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 4810 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 4811 Strategies for Large-Scale Numerical Simulations}, 4812 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 4813 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 4814 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 4815 Large-Scale Systems (scalA)}, 4816 pages = {65-72}, 4817 doi = {10.1109/ScalA.2018.00012}, 4818 month = nov, 4819 year = {2018}, 4820 petsc_uses = {KSP} 4821} 4822 4823@Article{ km2004, 4824 author = {A. Keese and H. G. Matthies}, 4825 journal = {Computers and Structures}, 4826 year = {2005}, 4827 volume = {83}, 4828 pages = {1033--1047}, 4829 title = {Hierarchical parallelisation for the solution of stochastic finite element 4830 equations}, 4831 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}, 4832 petsc_uses = {KSP} 4833} 4834 4835@Unpublished{ hvl2002, 4836 title = {Numerical Modeling of {NAPL} Source Zone Treatment}, 4837 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 4838 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 4839 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 4840 year = {2002}, 4841 lab = {LANL}, 4842 petsc_uses = {KSP} 4843} 4844 4845@PhDThesis{ hammond2003, 4846 author = {Glenn E. Hammond}, 4847 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 4848 Transport on Supercomputers}, 4849 school = {University of Illinois at Urbana-Champaign}, 4850 year = {2003}, 4851 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 4852 petsc_uses = {KSP} 4853} 4854 4855@Unpublished{ uk, 4856 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 4857 Scale Environmental Flows and Transport Processes}, 4858 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 4859 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 4860 buildings and in Green Bay. Used PETSc for its linear solvers}, 4861 year = {1999}, 4862 petsc_uses = {KSP} 4863} 4864 4865@InProceedings{ hammond2002, 4866 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 4867 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 4868 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 4869 year = {2002}, 4870 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 4871 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 4872 Resources, Delft, The Netherlands.}, 4873 lab = {LANL}, 4874 petsc_uses = {KSP} 4875} 4876 4877@TechReport{ steefel1, 4878 author = {C. I. Steefel}, 4879 title = {Software for modeling multicomponent, multidimensional reactive transport}, 4880 year = {2001}, 4881 institution = {Lawrence Livermore National Laboratory}, 4882 number = {UCRL-MA-143182}, 4883 lab = {LLNL}, 4884 petsc_uses = {KSP} 4885} 4886 4887@Article{ steefel2, 4888 author = {C. I. Steefel and A. C. Lasaga}, 4889 title = {A coupled model for transport of multiple chemical-species and kinetic 4890 precipitation dissolution reactions with application to reactive flow in 4891 single-phase hydrothermal systems}, 4892 journal = {Americal Journal of Science}, 4893 year = {1994}, 4894 pages = {529-592}, 4895 volume = {294}, 4896 number = {5}, 4897 petsc_uses = {KSP} 4898} 4899 4900@TechReport{ steefel3, 4901 author = {C. I. Steefel and S. B. Yabusaki}, 4902 title = {{OS3D/GIMRT}, Software for Multicomponent-Multidimensional reactive transport: 4903 User's manual and programmer's guide}, 4904 year = {1996}, 4905 institution = {Pacific Northwest National Laboratory}, 4906 number = {PNNL-11166}, 4907 lab = {PNNL}, 4908 petsc_uses = {KSP} 4909} 4910 4911@Article{ 2005hvl, 4912 author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner}, 4913 title = {Application of {J}acobian-free {N}ewton-{K}rylov with physics-based 4914 preconditioning to biogeochemical transport}, 4915 journal = {Advances in Water Resources}, 4916 year = {2005}, 4917 pages = {359--376}, 4918 volume = {28}, 4919 url = { 4920 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}, 4921 lab = {LANL}, 4922 petsc_uses = {KSP} 4923} 4924 4925@Article{ wang-zabar-05, 4926 author = {J Wang and N Zabaras}, 4927 journal = {Int. J. Heat and Mass Transfer}, 4928 title = {A Markov random field model of contamination source identification in porous 4929 media flow}, 4930 year = {2005}, 4931 petsc_uses = {KSP} 4932} 4933 4934@InBook{ kp1, 4935 author = {Jong G. Kim and Hyoung W. Park}, 4936 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 4937 Media}, 4938 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 4939 title = {Lecture Notes in Computer Science}, 4940 publisher = {Springer-Verlag}, 4941 volume = {3044}, 4942 year = {2004}, 4943 petsc_uses = {KSP} 4944} 4945 4946@Article{ 2001agusm...h32a06k, 4947 author = {{Kim}, J.~G. and {Kim}, J.}, 4948 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 4949 journal = {AGU Spring Meeting Abstracts}, 4950 year = {2001}, 4951 pages = {32-+}, 4952 petsc_uses = {KSP} 4953} 4954 4955@Article{ lzb2005, 4956 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 4957 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 4958 journal = {Journal of Hydraulic Engineering}, 4959 year = {2005}, 4960 volume = {131}, 4961 number = {4}, 4962 pages = {247--258}, 4963 petsc_uses = {KSP} 4964} 4965 4966@Article{ rao2005, 4967 author = {Prasada Rao}, 4968 title = {A parallel {RMA2} model for simulating large-scale free surface flows}, 4969 journal = {Environmental Modelling and Software}, 4970 year = {2005}, 4971 pages = {47--53}, 4972 petsc_uses = {KSP} 4973} 4974 4975@InProceedings{ pr1, 4976 author = {Prasada Rao}, 4977 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 4978 Hydrodynamic Flows}, 4979 year = {2003}, 4980 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 4981 Conference}, 4982 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 4983 petsc_uses = {KSP} 4984} 4985 4986@InProceedings{ lichtner2004, 4987 author = {Peter C. Lichtner and Andrew Wolfsberg}, 4988 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 4989 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 4990 Challenge Supercomputing Problem}, 4991 year = {2004}, 4992 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 4993 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 4994 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 4995 lab = {LANL}, 4996 petsc_uses = {KSP} 4997} 4998 4999% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 5000@Article{ aba01:petsc-app, 5001 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 5002 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 5003 journal = {Int. J. High Performance Computing Applications}, 5004 year = {2001}, 5005 volume = {15}, 5006 number = {1}, 5007 pages = {13--21}, 5008 petsc_uses = {KSP} 5009} 5010 5011@PhDThesis{ tjb200, 5012 author = {Thomas James Byer}, 5013 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 5014 Facilities}, 5015 school = {Stanford}, 5016 year = {2000}, 5017 petsc_uses = {KSP} 5018} 5019 5020@InProceedings{ puchyr2006, 5021 author = {Peter J. Puchyr}, 5022 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 5023 {Win32} Cluster}, 5024 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 5025 note = {Paper number CIPC2006-207}, 5026 year = {2006}, 5027 petsc_uses = {KSP} 5028} 5029 5030@InProceedings{ texas98, 5031 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 5032 and G. A. Pope}, 5033 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 5034 Simulation}, 5035 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 5036 Symposium}, 5037 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 5038 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 5039 year = {1998}, 5040 petsc_uses = {KSP} 5041} 5042 5043% LiteralHTML: 5044% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 5045% LiteralHTML: 5046@Article{ farrellmitchellscottwechsung2021, 5047 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 5048 stationary incompressible {Navier-Stokes} equations}, 5049 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 5050 Wechsung}, 5051 journal = {The SMAI journal of computational mathematics}, 5052 volume = {7}, 5053 pages = {75--96}, 5054 year = {2021}, 5055 petsc_uses = {KSP} 5056} 5057 5058@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 5059 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 5060 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 5061 P MacLachlan and Ray S Tuminaro}, 5062 journal = {SIAM Journal on Scientific Computing}, 5063 number = {0}, 5064 pages = {S70--S91}, 5065 year = {2021}, 5066 petsc_uses = {KSP} 5067} 5068 5069@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 5070 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 5071 hyperelasticity}, 5072 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 5073 Oyar\'ua and Ricardo Ruiz-Baier}, 5074 journal = {Computer Methods in Applied Mechanics and Engineering}, 5075 volume = {374}, 5076 pages = {113562}, 5077 issn = {0045-7825}, 5078 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 5079 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 5080 year = {2021}, 5081 petsc_uses = {KSP} 5082} 5083 5084@Article{ farrellmitchellwechsung2018, 5085 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 5086 {Navier-Stokes} equations at high {Reynolds} number}, 5087 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 5088 journal = {SIAM Journal on Scientific Computing}, 5089 volume = {41}, 5090 number = {5}, 5091 eprint = {1810.03315}, 5092 pages = {A3073-A3096}, 5093 year = {2019}, 5094 petsc_uses = {KSP} 5095} 5096 5097@Article{ hevuikklaij2017, 5098 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 5099 discretized by a finite volume method}, 5100 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 5101 journal = {Journal of Numerical Mathematics}, 5102 volume = {25}, 5103 number = {2}, 5104 pages = {89--105}, 5105 year = {2017}, 5106 petsc_uses = {KSP} 5107} 5108 5109@InProceedings{ zou2015newton, 5110 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 5111 appearance/disappearance}, 5112 author = {Zou, L and Zhao, H and Zhang, H}, 5113 booktitle = {ANS 2015 Annual Meeting, June}, 5114 volume = {7}, 5115 number = {11}, 5116 year = {2015}, 5117 petsc_uses = {KSP} 5118} 5119 5120@Article{ guermond2009nonlinear, 5121 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 5122 Fourier/finite element technique and an interior penalty method}, 5123 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 5124 journal = {Journal of computational physics}, 5125 volume = {228}, 5126 number = {8}, 5127 pages = {2739--2757}, 5128 year = {2009}, 5129 publisher = {Elsevier}, 5130 petsc_uses = {KSP} 5131} 5132 5133@Article{ erzincanlisahin2015, 5134 title = {The numerical simulation of the wing kinematics effects on near wake topology and 5135 aerodynamic performance in hovering {D}rosophila flight}, 5136 author = {Belkis Erzincanli and Mehmet Sahin}, 5137 journal = {Computers \& Fluids}, 5138 volume = {122}, 5139 pages = {90--110}, 5140 year = {2015}, 5141 publisher = {Elsevier}, 5142 petsc_uses = {KSP} 5143} 5144 5145@Article{ ekensahin2015, 5146 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 5147 structure interaction problems}, 5148 author = {Ali Eken and Mehmet Sahin}, 5149 journal = {International Journal for Numerical Methods in Fluids}, 5150 year = {2015}, 5151 publisher = {Wiley Online Library}, 5152 petsc_uses = {KSP} 5153} 5154 5155@Article{ hwangsucai2015, 5156 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 5157 for transonic full potential equation}, 5158 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 5159 journal = {Computers \& Fluids}, 5160 volume = {110}, 5161 number = {30}, 5162 pages = {96--107}, 5163 year = {2015}, 5164 doi = {10.1016/j.compfluid.2014.04.005}, 5165 petsc_uses = {KSP} 5166} 5167 5168@Article{ yanghwangcai2016, 5169 title = {Nonlinear Preconditioning Techniques for Full-Space {L}agrange--{N}ewton Solution of 5170 {PDE}-Constrained Optimization Problems}, 5171 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 5172 journal = {SIAM Journal on Scientific Computing}, 5173 volume = {38}, 5174 number = {5}, 5175 pages = {A2756--A2778}, 5176 year = {2016}, 5177 petsc_uses = {KSP} 5178} 5179 5180@Article{ khanaidun2011, 5181 author = {Irfan Khan and Cyrus K. Aidun}, 5182 title = {Direct numerical simulation of saturated deformable porous media using parallel 5183 hybrid Lattice-{B}oltzmann and finite element method}, 5184 journal = {Int. J. Numer. Meth. Eng.}, 5185 volume = {86}, 5186 pages = {1379--1395}, 5187 year = {2011}, 5188 petsc_uses = {KSP} 5189} 5190 5191@Article{ khanaidun2014, 5192 author = {Irfan Khan and Cyrus K. Aidun}, 5193 title = {Modeling the deformation of saturate porous media using direct numerical 5194 simulation}, 5195 journal = {Int. J. Multiphase Flow}, 5196 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 5197 year = {2014}, 5198 petsc_uses = {KSP} 5199} 5200 5201@Article{ mofidi2014simulations, 5202 author = {A. Mofidi and P. M. Carrica}, 5203 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 5204 and Propeller}, 5205 journal = {Computers and Fluids}, 5206 pages = {191--203}, 5207 year = {2014}, 5208 petsc_uses = {KSP} 5209} 5210 5211@Article{ paik2014fluidstructure, 5212 author = {K. Paik and P. M. Carrica}, 5213 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 5214 Surface in a Rolling Tank}, 5215 journal = {Ocean Engineering}, 5216 pages = {201--212}, 5217 year = {2014}, 5218 petsc_uses = {KSP} 5219} 5220 5221@Article{ castro2013bubble, 5222 author = {A. M. Castro and P. M. Carrica}, 5223 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 5224 evaluation and numerical issues}, 5225 journal = {International Journal of Multiphase Flow 57}, 5226 pages = {131--150}, 5227 year = {2013}, 5228 petsc_uses = {KSP} 5229} 5230 5231@Article{ carrica2013turn, 5232 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 5233 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 5234 Dynamic Overset Grids}, 5235 journal = {Journal of Marine Science and Technology}, 5236 pages = {166--181}, 5237 year = {2013}, 5238 petsc_uses = {KSP} 5239} 5240 5241@Article{ castro2013eulerian, 5242 author = {A. M. Castro and P. M. Carrica}, 5243 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 5244 {Athena} {R}/V,}, 5245 journal = {International Shipbuilding Progress}, 5246 pages = {403--433}, 5247 year = {2013}, 5248 petsc_uses = {KSP} 5249} 5250 5251@Article{ chase2013overset, 5252 author = {N. Chase and T. Michael and P. M. Carrica}, 5253 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 5254 {Maneuvering} {Conditions}}, 5255 journal = {International Shipbuilding Progress}, 5256 pages = {171--205}, 5257 year = {2013}, 5258 petsc_uses = {KSP} 5259} 5260 5261@Article{ sadathosseini2013wu, 5262 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 5263 Stern}, 5264 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 5265 Free Surge Conditions in Short and Long Head Waves}, 5266 journal = {Ocean Engineering}, 5267 volume = {59}, 5268 pages = {240--273}, 5269 year = {2013}, 5270 petsc_uses = {KSP} 5271} 5272 5273@Article{ chase2013cfd, 5274 author = {N. Chase and P. M. Carrica}, 5275 title = {{CFD} Simulations of a Submarine Propeller and Application to Self-Propulsion of a 5276 Submarine}, 5277 journal = {Ocean Engineering}, 5278 pages = {68--80}, 5279 year = {2013}, 5280 petsc_uses = {KSP} 5281} 5282 5283@Article{ carrica2012cfd, 5284 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 5285 title = {{CFD} Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 5286 of Moving Rudders and Rotating Propellers}, 5287 journal = {Computers and Fluids 53}, 5288 pages = {117--132}, 5289 year = {2012}, 5290 petsc_uses = {KSP} 5291} 5292 5293@Article{ sakamoto2012urans, 5294 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5295 title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 5296 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 5297 publisher = {Journal of Marine Science and Technology}, 5298 pages = {422--445}, 5299 year = {2012}, 5300 petsc_uses = {KSP} 5301} 5302 5303@Article{ sakamoto2012uransb, 5304 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5305 title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 5306 Analysis and Validation of Local Flow Characteristics}, 5307 journal = {Journal of Marine Science and Technology}, 5308 pages = {446--468}, 5309 year = {2012}, 5310 petsc_uses = {KSP} 5311} 5312 5313@Article{ li2012dynamic, 5314 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 5315 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 5316 journal = {Renewable Energy}, 5317 pages = {285--298}, 5318 year = {2012}, 5319 petsc_uses = {KSP} 5320} 5321 5322@Article{ huang2012a, 5323 author = {J. Huang and P. M. Carrica and F. Stern}, 5324 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 5325 journal = {International Journal for Numerical Methods in Fluids}, 5326 pages = {160--180}, 5327 year = {2012}, 5328 petsc_uses = {KSP} 5329} 5330 5331@Article{ huang2012b, 5332 author = {J. Huang and P. M. Carrica and F. Stern}, 5333 title = {A geometry-based level set method for curvilinear overset grids with application 5334 to ship hydrodynamics}, 5335 journal = {International Journal for Numerical Methods in Fluids}, 5336 pages = {494--521}, 5337 year = {2012}, 5338 petsc_uses = {KSP} 5339} 5340 5341@Article{ carrica2011computations, 5342 author = {P. M. Carrica and H. Fu and F. Stern}, 5343 title = {Computations of self-propulsion free to sink and trim and of motions in head 5344 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 5345 journal = {Applied Ocean Research}, 5346 pages = {309--320}, 5347 year = {2011}, 5348 petsc_uses = {KSP} 5349} 5350 5351@Article{ bhushan2011scalability, 5352 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 5353 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 5354 Using {CFDShip}-Iowa}, 5355 journal = {International Journal of High Performance Computing Applications}, 5356 pages = {466--487}, 5357 year = {2011}, 5358 petsc_uses = {KSP} 5359} 5360 5361@Article{ castro2011full, 5362 author = {A. M. Castro and P. M. Carrica and F. Stern}, 5363 title = {Full scale self-propulsion computations using discretized propeller for the 5364 {KRISO} container ship {KCS}}, 5365 journal = {Computers and Fluids}, 5366 pages = {35--47}, 5367 year = {2011}, 5368 petsc_uses = {KSP} 5369} 5370 5371@Article{ kandasamy2011multifidelity, 5372 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5373 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5374 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing {C}atamaran 5375 for Low Wake}, 5376 journal = {Journal of Marine Science and Technology}, 5377 pages = {143--156}, 5378 year = {2011}, 5379 petsc_uses = {KSP} 5380} 5381 5382@Article{ kandasamy2011cfd, 5383 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5384 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5385 title = {{CFD} Validation Studies for a High-speed Foil-assisted Semi-planing {C}atamaran}, 5386 journal = {Journal of Marine Science and Technology}, 5387 pages = {157--167}, 5388 year = {2011}, 5389 petsc_uses = {KSP} 5390} 5391 5392@Article{ sadathosseini2011cfd, 5393 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 5394 and S. Yamamura and A. Mastuda}, 5395 title = {{CFD} System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 5396 Periodic Motion and Broaching}, 5397 journal = {Ocean Engineering}, 5398 pages = {88--110}, 5399 year = {2011}, 5400 petsc_uses = {KSP} 5401} 5402 5403@Article{ mosaviraad2010development, 5404 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 5405 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 5406 with Comparison to Regular Wave and Transient Wave Group Procedures Using 5407 {URANS}}, 5408 journal = {Ocean Engineering}, 5409 pages = {653--666}, 5410 year = {2010}, 5411 petsc_uses = {KSP} 5412} 5413 5414@Article{ carrica2010largescale, 5415 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5416 Stern}, 5417 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5418 Heave Problems for a Surface Combatant}, 5419 journal = {Computers and Fluids}, 5420 pages = {1095--1111}, 5421 year = {2010}, 5422 petsc_uses = {KSP} 5423} 5424 5425@Article{ carrica2010selfpropulsion, 5426 author = {P. M. Carrica and A. M. Castro and F. Stern}, 5427 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 5428 with Dynamic Overset Grids}, 5429 journal = {Journal of Marine Science and Technology}, 5430 pages = {316--330}, 5431 year = {2010}, 5432 petsc_uses = {KSP} 5433} 5434 5435@Article{ ismail2010evaluation, 5436 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 5437 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 5438 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 5439 journal = {International Journal of Numerical Methods in Fluids}, 5440 pages = {850--886}, 5441 year = {2010}, 5442 petsc_uses = {KSP} 5443} 5444 5445@Article{ kandasamy2010integral, 5446 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 5447 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 5448 journal = {Journal of Fluids Engineering}, 5449 pages = {101103}, 5450 year = {2010}, 5451 petsc_uses = {KSP} 5452} 5453 5454@Article{ kirk:2014de, 5455 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 5456 title = {{Modeling hypersonic entry with the fully-implicit {N}avier--{S}tokes (FIN-S) 5457 stabilized finite element flow solver}}, 5458 journal = {Computers {\&} Fluids}, 5459 year = {2014}, 5460 volume = {92}, 5461 number = {0}, 5462 pages = {281--292}, 5463 month = mar, 5464 petsc_uses = {KSP} 5465} 5466 5467@Article{ carracciuolo20111382, 5468 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 5469 in high performance computing environment}, 5470 journal = {Journal of Non-Newtonian Fluid Mechanics }, 5471 volume = {166}, 5472 number = {23--24}, 5473 pages = {1382--1395}, 5474 year = {2011}, 5475 issn = {0377-0257}, 5476 doi = {10.1016/j.jnnfm.2011.08.014}, 5477 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 5478 Maffettone and A. Murli}, 5479 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 5480 method, High performance computing}, 5481 petsc_uses = {KSP} 5482} 5483 5484@Article{ bungartzgatzhammerliebmehlneckel11, 5485 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 5486 Miriam and Neckel, Tobias}, 5487 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 5488 journal = {Computational Mechanics}, 5489 volume = {48}, 5490 number = {3}, 5491 pages = {365-376}, 5492 year = {2011}, 5493 issn = {0178-7675}, 5494 doi = {10.1007/s00466-011-0626-1}, 5495 publisher = {Springer-Verlag}, 5496 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 5497 Thermohydraulics; Two-phase flow}, 5498 language = {English}, 5499 petsc_uses = {KSP} 5500} 5501 5502@Article{ bpr:cfl, 5503 author = {H.~M. B{\"u}cker and B. Pollul and A. Rasch}, 5504 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 5505 Equations}}, 5506 journal = {International Journal for Numerical Methods in Fluids}, 5507 year = {2009}, 5508 volume = {59}, 5509 number = {1}, 5510 pages = {1--18}, 5511 doi = {10.1002/fld.1798}, 5512 petsc_uses = {KSP} 5513} 5514 5515@InBook{ bonfiglioli_campobasso_carpentieri_2010, 5516 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 5517 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 5518 preconditioned newton-krylov solver}, 5519 publisher = {Curran Associates}, 5520 year = {2010}, 5521 url = {http://www.proceedings.com/05932.html}, 5522 petsc_uses = {KSP} 5523} 5524 5525@Article{ bonfiglioli_rans_2005, 5526 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 5527 Bernardo}, 5528 title = {RANS simulations of a junction flow}, 5529 journal = {International Journal of Computational Fluid Dynamics}, 5530 volume = {19}, 5531 number = {2}, 5532 pages = {179-189}, 5533 year = {2005}, 5534 doi = {10.1080/10618560410001729126}, 5535 petsc_uses = {KSP} 5536} 5537 5538@InCollection{ bonfiglioli__carpentieri_rans_2008, 5539 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 5540 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 5541 Italy}, 5542 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 5543 Equations Using Fluctuation Splitting Schemes}, 5544 booktitle = {Numerical Mathematics and Advanced Applications}, 5545 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 5546 publisher = {Springer Berlin Heidelberg}, 5547 isbn = {978-3-540-69777-0}, 5548 pages = {151-158}, 5549 doi = {10.1007/978-3-540-69777-0_17}, 5550 year = {2008}, 5551 petsc_uses = {KSP} 5552} 5553 5554@InCollection{ bonfiglioli__carpentieri_ens_2007, 5555 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 5556 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 5557 Italy}, 5558 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 5559 Problems on Unstructured Grids}, 5560 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 5561 series = {Lecture Notes in Computer Science}, 5562 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 5563 publisher = {Springer Berlin / Heidelberg}, 5564 isbn = {978-3-540-75754-2}, 5565 pages = {676-685}, 5566 volume = {4699}, 5567 doi = {10.1007/978-3-540-75755-9_83}, 5568 year = {2007}, 5569 petsc_uses = {KSP} 5570} 5571 5572@Article{ terrelscottknepleykirby08, 5573 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 5574 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 5575 journal = {BIT}, 5576 volume = {48}, 5577 number = {2}, 5578 year = {2008}, 5579 petsc_uses = {KSP} 5580} 5581 5582@Article{ martamadermartinsweidealonso07, 5583 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 5584 J. Alonso}, 5585 title = {A methodology for the development of discrete adjoint solvers using automatic 5586 differentiation tools}, 5587 journal = {Computational Fluid Dyanmics}, 5588 volume = {21}, 5589 pages = {307--327}, 5590 year = {2007}, 5591 petsc_uses = {KSP} 5592} 5593 5594@TechReport{ avb2008, 5595 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 5596 title = {Variational Space-time (Dis)continuous {G}alerkin Method for Linear Free Surface 5597 Waves}, 5598 year = {2008}, 5599 institution = {University of Twente, the Netherlands}, 5600 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 5601 petsc_uses = {KSP} 5602} 5603 5604@InProceedings{ bdsm2005, 5605 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. 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Groth}, 5625 title = {Parallel three-dimensional simulation of the injection molding process}, 5626 journal = {International Journal for Numerical Methods in Fluids}, 5627 year = {2008}, 5628 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 5629 petsc_uses = {KSP} 5630} 5631 5632@PhDThesis{ a2008, 5633 author = {A. Cubero}, 5634 title = {a parallel coupled algorithm for collocated grids and its application to Large 5635 Eddy Simulation of a turbulent wake}, 5636 school = {University of Zaragoza (Spain)}, 5637 year = {2008}, 5638 petsc_uses = {KSP} 5639} 5640 5641@Article{ afa2007, 5642 author = {A. Cubero and N. 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Straatman}, 5717 title = {Benchmarking of a {3D}, unstructured, finite volume code for incompressible 5718 {Navier-Stokes} equation on a cluster of distributed-memory computers}, 5719 booktitle = {Proceedings of the 19th International Symposium on High Performance Computing 5720 Systems and Applications}, 5721 pages = {11--16}, 5722 year = {2005}, 5723 url = { http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1430046}, 5724 petsc_uses = {KSP} 5725} 5726 5727@TechReport{ bonglioli-icnmfd98, 5728 title = {Multidimensional Residual Distribution Schemes for the Pseudo-Compressible 5729 {Euler} and {Navier-Stokes} equations on Unstructured Meshes}, 5730 institution = {Universita della Basilicata via della Tecnica 3}, 5731 year = {1996}, 5732 author = {A. Bonglioli}, 5733 url = {http://www.unibas.it/utenti/bonfiglioli/icnmfd98.ps.gz}, 5734 petsc_uses = {KSP} 5735} 5736 5737@Article{ deng-piquet-ctf, 5738 author = {G. B. Deng and J. Piquet and X. Vasseur and M. Visonneau"}, 5739 title = {A new fully coupled method for computing turbulent flows}, 5740 journal = {Computers and Fluids}, 5741 volume = {30}, 5742 pages = {445--472}, 5743 year = {2001}, 5744 petsc_uses = {KSP} 5745} 5746 5747@InProceedings{ knepleysarinsameh99b, 5748 title = {Multilevel Preconditioning for Parallel {CFD}}, 5749 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 5750 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 5751 Problems In Industrial Applications}, 5752 address = {Minneapolis, MN}, 5753 year = {1999}, 5754 petsc_uses = {KSP} 5755} 5756 5757@InProceedings{ garbey1, 5758 author = {M. Garbey and B. Hadri and W. Shyy.}, 5759 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 5760 Problems on the Grid}, 5761 booktitle = {Aerospace Sciences Meeting and Exhibit}, 5762 note = {Paper No. 2005-1386}, 5763 year = {2005}, 5764 petsc_uses = {KSP} 5765} 5766 5767@Article{ carrica2007unsteady, 5768 title = {An unsteady single-phase level set method for viscous free surface flows}, 5769 author = {Carrica, PM and Wilson, RV and Stern, F.}, 5770 journal = {International Journal for Numerical Methods in Fluids}, 5771 volume = {53}, 5772 number = {2}, 5773 pages = {229--256}, 5774 year = {2007}, 5775 publisher = {Chichester; New York: Wiley, c1981-}, 5776 petsc_uses = {KSP} 5777} 5778 5779@Article{ pctw2004, 5780 author = {M. S. Politano and P. M. Carrica and C. Turan and L. 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Smith and F. 5810 Stern}, 5811 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5812 Heave Problems for a Surface Combatant}, 5813 journal = {Computers and Fluids}, 5814 year = {2010}, 5815 volume = {39}, 5816 number = {7}, 5817 pages = {1095--1111}, 5818 petsc_uses = {KSP} 5819} 5820 5821@InProceedings{ chnkss2008, 5822 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5823 Stern}, 5824 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 5825 Grids}, 5826 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 5827 year = {2008}, 5828 petsc_uses = {KSP} 5829} 5830 5831@MastersThesis{ mtj, 5832 author = {M. T. 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Peltier}, 5879 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 5880 refinement grids and detached-eddy simulation}, 5881 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 5882 year = {2004}, 5883 petsc_uses = {KSP} 5884} 5885 5886@InProceedings{ mzwp, 5887 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 5888 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 5889 booktitle = {25th Symposium on Naval Hydrodynamics}, 5890 year = {2004}, 5891 petsc_uses = {KSP} 5892} 5893 5894@InProceedings{ ppph, 5895 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 5896 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 5897 booktitle = {25th Symposium on Naval Hydrodynamics}, 5898 year = {2004}, 5899 petsc_uses = {KSP} 5900} 5901 5902@InProceedings{ ppd, 5903 author = {E. G. Paterson and L. J. 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Schouten}, 5975 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 5976 Velocity}, 5977 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 5978 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 5979 Netherlands}, 5980 journal = {AIChE}, 5981 volumne = {48}, 5982 number = {12}, 5983 month = dec, 5984 year = {2002}, 5985 petsc_uses = {KSP} 5986} 5987 5988@TechReport{ lbam1, 5989 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 5990 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 5991 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 5992 di Bari Italy}, 5993 year = {2002}, 5994 number = {25/02}, 5995 petsc_uses = {KSP} 5996} 5997 5998@Article{ kees_miller_02, 5999 author = {C. E. Kees and C. T. Miller}, 6000 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 6001 journal = {Advances in Water Resources}, 6002 year = {2002}, 6003 volume = {25}, 6004 number = {2}, 6005 pages = {159-177.}, 6006 petsc_uses = {KSP} 6007} 6008 6009@InProceedings{ lepotmeersessers2001, 6010 author = {I. Lepot and F. Meers and J.A. Essers}, 6011 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 6012 Unstructured Meshes}, 6013 year = {2001}, 6014 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 6015 url = {http://www.ulg.ac.be/aerodyn}, 6016 petsc_uses = {KSP} 6017} 6018 6019@InProceedings{ knepley98, 6020 author = {Matthew Knepley and Denis Vanderstraeten}, 6021 title = {Parallel Building Blocks for Finite Element Simulations: Application to 6022 Solid-Liquid Mixture Flows}, 6023 booktitle = {Proceedings of Parallel CFD'97}, 6024 publisher = {Elsevier}, 6025 pages = {281--287}, 6026 year = {1998}, 6027 petsc_uses = {KSP} 6028} 6029 6030@InProceedings{ pcfd97, 6031 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 6032 title = {Parallel Implicit {PDE} Computations: Algorithms and Software}, 6033 publisher = {Elsevier}, 6034 year = {1998}, 6035 booktitle = {Proceedings of Parallel CFD'97}, 6036 pages = {333-344}, 6037 petsc_uses = {KSP} 6038} 6039 6040@InProceedings{ knepleysamehsari98, 6041 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 6042 title = {Parallel Simulation of Particulate Flows}, 6043 booktitle = {Solving Irregularly Structured Problems in Parallel}, 6044 editors = {A. Ferreira et al}, 6045 year = {1998}, 6046 series = {Lecture Notes in Computer Science}, 6047 volume = {1457}, 6048 pages = {226--237}, 6049 petsc_uses = {KSP} 6050} 6051 6052@Article{ gkmt98, 6053 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 6054 title = {Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel 6055 Implicit {CFD}}, 6056 journal = {Int. J. High Performance Computing Applications}, 6057 year = {2000}, 6058 volume = {14}, 6059 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 6060 pages = {102-136}, 6061 petsc_uses = {KSP} 6062} 6063 6064@InProceedings{ agkks-sc99, 6065 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 6066 Smith}, 6067 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 6068 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 6069 editor = {}, 6070 publisher = {}, 6071 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 6072 year = {1999}, 6073 note = {Winner of Gordon Bell Special Prize at SC 99}, 6074 petsc_uses = {KSP} 6075} 6076 6077@Article{ gkks01, 6078 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6079 title = {High Performance Parallel Implicit {CFD}}, 6080 journal = {Journal of Parallel Computing}, 6081 year = {2001}, 6082 volume = {27}, 6083 pages = {337-362}, 6084 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 6085 petsc_uses = {KSP} 6086} 6087 6088@Article{ cristea-sofonea-02, 6089 author = {Artur Cristea and Victor Sofonea}, 6090 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 6091 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 6092 Sciences, Information Sciences}, 6093 volume = {3}, 6094 number = {3}, 6095 year = {2002}, 6096 petsc_uses = {KSP} 6097} 6098 6099@Article{ cristea2, 6100 author = {Artur Cristea and Victor Sofonea}, 6101 title = {Two component lattice Boltzmann model with flux limiter techniques}, 6102 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 6103 Sciences, Information Sciences}, 6104 volume = {4}, 6105 number = {1}, 6106 year = {2003}, 6107 pages = {59--64}, 6108 petsc_uses = {KSP} 6109} 6110 6111@Article{ cristea1, 6112 author = {Artur Cristea and Victor Sofonea}, 6113 title = {Two component lattice Boltzmann model with flux limiters}, 6114 journal = {Central European Journal of Physics}, 6115 volume = {2}, 6116 number = {2}, 6117 year = {2004}, 6118 pages = {382--396}, 6119 petsc_uses = {KSP} 6120} 6121 6122@Article{ sofnea-lamura1, 6123 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 6124 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 6125 systems}, 6126 journal = {Physical Review E}, 6127 volume = {70}, 6128 number = {4}, 6129 year = {2004}, 6130 pages = {046702-1 / 046702-9}, 6131 petsc_uses = {KSP} 6132} 6133 6134@InProceedings{ gkks01b, 6135 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6136 title = {Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}}, 6137 booktitle = {Proceedings of the First MIT Conference on Computational Fluid and Solid 6138 Mechanics}, 6139 editor = {}, 6140 location = {Cambridge, MA}, 6141 year = {2001}, 6142 month = jun, 6143 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf}, 6144 petsc_uses = {KSP} 6145} 6146 6147@InProceedings{ gkks00, 6148 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6149 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 6150 Code}, 6151 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 6152 (HiPC '2000)}, 6153 editor = {}, 6154 location = {Bangalore, India}, 6155 year = {2000}, 6156 pages = {395--404}, 6157 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 6158 petsc_uses = {KSP} 6159} 6160 6161@InProceedings{ gkks-sc00, 6162 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6163 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 6164 booktitle = {Proceedings of SC2000}, 6165 editor = {}, 6166 publisher = {IEEE Computer Society}, 6167 year = {2000}, 6168 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 6169 petsc_uses = {KSP} 6170} 6171 6172@InProceedings{ knepleysamehsarin99, 6173 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 6174 title = {Design of Large Scale Parallel Simulations}, 6175 booktitle = {Proceedings of Parallel CFD'99}, 6176 editors = {A. {Ecer et al.}}, 6177 publisher = {Elsevier}, 6178 year = {1999}, 6179 petsc_uses = {KSP} 6180} 6181 6182@InProceedings{ gkks-pcfd99, 6183 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 6184 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 6185 booktitle = {Proceedings of Parallel CFD'99}, 6186 editors = {A. {Ecer et al.}}, 6187 publisher = {Elsevier}, 6188 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 6189 year = {1999}, 6190 petsc_uses = {KSP} 6191} 6192 6193@InProceedings{ kks97, 6194 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6195 title = {On the Interaction of Architecture and Algorithm in the Domain-Based 6196 Parallelization of an Unstructured Grid Incompressible Flow Code}, 6197 booktitle = {Proceedings of the 10th International Conference on Domain Decomposition 6198 Methods}, 6199 editor = {J. Mandel et al.}, 6200 pages = {311--319}, 6201 publisher = {Wiley}, 6202 note = {}, 6203 year = {1997}, 6204 petsc_uses = {KSP} 6205} 6206 6207@InProceedings{ kks99, 6208 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6209 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 6210 Incompressible Flows on Unstructured Grids}, 6211 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6212 Methods}, 6213 editors = {C.-H. {Lai et al.}}, 6214 publisher = {Domain Decomposition Press, Bergen}, 6215 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 6216 year = {1999}, 6217 petsc_uses = {KSP} 6218} 6219 6220@InCollection{ kks97_cfd, 6221 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 6222 title = {Perspectives for {CFD} on Petaflops Systems}, 6223 booktitle = {CFD Review 1998}, 6224 editor = {M. Hafez and K. Oshima}, 6225 publisher = {World Scientific, Singapore}, 6226 pages = {1079--1096}, 6227 note = {}, 6228 year = {1998}, 6229 petsc_uses = {KSP} 6230} 6231 6232@Article{ hm99, 6233 author = {P. D. Hovland and L. C. McInnes}, 6234 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 6235 {PETSc}}, 6236 year = {2000}, 6237 journal = {Parallel Computing}, 6238 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 6239 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 6240 petsc_uses = {KSP} 6241} 6242 6243@InProceedings{ cruzbarbaknepley08, 6244 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 6245 title = {Fast Multipole Method for particle interactions: an open source parallel library 6246 component}, 6247 booktitle = {Proceedings of ParCFD2008}, 6248 year = {2008}, 6249 editor = {Tromeur-Dervout et. al.}, 6250 publisher = {Elsevier}, 6251 petsc_uses = {KSP} 6252} 6253 6254@Article{ hwangcai05, 6255 author = {F.-N. Hwang and X.-C. Cai}, 6256 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 6257 for incompressible {Navier-Stokes} equations}, 6258 journal = {J. Comput. Phys.}, 6259 volume = {204}, 6260 year = {2005}, 6261 pages = {666--691}, 6262 petsc_uses = {KSP} 6263} 6264 6265@Article{ barbaleonard07, 6266 author = {Lorena A Barba and Anthony Leonard}, 6267 title = {Emergence and evolution of tripole vortices from net-circulation initial 6268 conditions}, 6269 journal = {Phys. Fluids}, 6270 volume = {19}, 6271 pages = {017101}, 6272 year = {2007}, 6273 doi = {10.1063/1.2409734}, 6274 petsc_uses = {KSP} 6275} 6276 6277@Article{ barba07, 6278 author = {Lorena A Barba}, 6279 title = {Non-shielded multipolar vortices at high Reynolds number}, 6280 journal = {Phys. Rev. E}, 6281 volume = {73}, 6282 pages = {065303}, 6283 year = {2006}, 6284 doi = {10.1103/PhysRevE.73.065303}, 6285 petsc_uses = {KSP} 6286} 6287 6288@Article{ schofield2010multi, 6289 title = {Multi-material incompressible flow simulation using the moment-of-fluid method}, 6290 author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and 6291 Lowrie, R.B. and Swartz, B.K.}, 6292 journal = {International Journal for Numerical Methods in Fluids}, 6293 volume = {63}, 6294 number = {8}, 6295 pages = {931--952}, 6296 year = {2010}, 6297 publisher = {Wiley Online Library}, 6298 petsc_uses = {KSP} 6299} 6300 6301% LiteralHTML: 6302% LiteralHTML: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3> 6303% LiteralHTML: 6304% LiteralHTML: article{DeGersem99, 6305% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, 6306% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, 6307% LiteralHTML: } 6308@Article{ nagler2014, 6309 title = {Sound transmission through a poroelastic layered panel}, 6310 author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff}, 6311 journal = {Computational Mechanics}, 6312 volume = {53}, 6313 number = {4}, 6314 pages = {549--560}, 6315 issn = {1432-0924}, 6316 doi = {10.1007/s00466-013-0916-x}, 6317 year = {2014}, 6318 petsc_uses = {KSP} 6319} 6320 6321@Article{ sheikh2013, 6322 author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.}, 6323 title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel 6324 deflation}, 6325 journal = {Numerical Linear Algebra with Applications}, 6326 volume = {20}, 6327 number = {4}, 6328 issn = {1099-1506}, 6329 doi = {10.1002/nla.1882}, 6330 pages = {645--662}, 6331 keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier 6332 analysis}, 6333 year = {2013}, 6334 petsc_uses = {KSP} 6335} 6336 6337@InProceedings{ silence, 6338 author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. 6339 Fuenmayor}, 6340 title = {A parallel computing approach for solving the Helmholtz equation in 3D domains: 6341 Application to the study of acoustic behaviour of silencers}, 6342 year = {2004}, 6343 booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering 6344 (ECCOMAS)}, 6345 petsc_uses = {KSP} 6346} 6347 6348@Article{ degersem99, 6349 author = {H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer}, 6350 title = {Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods 6351 to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations}, 6352 journal = {COMPEL}, 6353 year = {1999}, 6354 volume = {18}, 6355 number = {3}, 6356 pages = {298--310}, 6357 bibdate = {}, 6358 petsc_uses = {KSP} 6359} 6360 6361@InProceedings{ widlund-wave-98, 6362 author = {Olof B. Widlund}, 6363 title = {Schwarz Methods for {H}elmholtz's Equation}, 6364 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6365 editor = {John A. DeSanto}, 6366 year = {1998}, 6367 publisher = {SIAM}, 6368 pages = {620--622}, 6369 address = {Philadelphia}, 6370 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6371 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6372 petsc_uses = {KSP} 6373} 6374 6375@InProceedings{ toselli-wave-98, 6376 author = {Andrea Toselli}, 6377 title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media}, 6378 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6379 editor = {John A. DeSanto}, 6380 year = {1998}, 6381 publisher = {SIAM}, 6382 address = {Philadelphia}, 6383 pages = {540--542}, 6384 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6385 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6386 petsc_uses = {KSP} 6387} 6388 6389@InProceedings{ mcinnes-wave-98, 6390 author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes}, 6391 title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods}, 6392 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6393 editor = {John A. DeSanto}, 6394 year = {1998}, 6395 publisher = {SIAM}, 6396 address = {Philadelphia}, 6397 pages = {623--625}, 6398 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6399 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6400 petsc_uses = {KSP} 6401} 6402 6403@InProceedings{ mska98, 6404 author = {L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi}, 6405 title = {Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the 6406 Parallel Computation of {H}elmholtz Problems}, 6407 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6408 editor = {J. Mandel et al.}, 6409 publisher = {AMS}, 6410 pages = {349--357}, 6411 year = {1998}, 6412 petsc_uses = {KSP} 6413} 6414 6415@InProceedings{ ccew98, 6416 author = {X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund}, 6417 title = {Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation}, 6418 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6419 editor = {J. Mandel et al.}, 6420 publisher = {AMS}, 6421 pages = {437-445}, 6422 year = {1998}, 6423 petsc_uses = {KSP} 6424} 6425 6426@InProceedings{ ra98a, 6427 author = {R. Susan-Resiga and H. M. Atassi}, 6428 title = {Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic 6429 Problems}, 6430 booktitle = {Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference}, 6431 publisher = {AIAA}, 6432 pages = {86-96}, 6433 note = {AIAA paper 98-2218}, 6434 year = {1998}, 6435 petsc_uses = {KSP} 6436} 6437 6438@InProceedings{ ar98c, 6439 author = {H. M. Atassi and R. Susan-Resiga}, 6440 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: 6441 General Formulation}, 6442 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6443 publisher = {ASME}, 6444 note = {NCA-25}, 6445 pages = {375-379}, 6446 year = {1998}, 6447 petsc_uses = {KSP} 6448} 6449 6450@InProceedings{ ra98b, 6451 author = {R. Susan-Resiga and H. M. Atassi}, 6452 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: 6453 Numerical Implementation and Applications}, 6454 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6455 publisher = {ASME}, 6456 note = {NCA-25}, 6457 pages = {381 -388}, 6458 year = {1998}, 6459 petsc_uses = {KSP} 6460} 6461 6462@InProceedings{ cai-dd10-98, 6463 author = {Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. 6464 Widlund}, 6465 title = {Overlapping {S}chwarz methods for solving {H}elmholtz's Equation}, 6466 booktitle = {Domain Decomposition Methods 10}, 6467 editors = {Jan Mandel and Charbel Farhat and Xiao-Chuan Cai}, 6468 series = {Contemporary Mathematics}, 6469 volume = {218}, 6470 publisher = {American Mathematical Society}, 6471 address = {Providence, Rhode Island}, 6472 year = {1998}, 6473 pages = {437--445}, 6474 petsc_uses = {KSP} 6475} 6476 6477@InProceedings{ alghamdi2011petclaw, 6478 title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython}, 6479 booktitle = {Proceedings of SpringSim 2011}, 6480 publisher = {ACM}, 6481 author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and 6482 Kyle T. Mandli and Lisandro Dalcin}, 6483 year = {2011}, 6484 petsc_uses = {KSP} 6485} 6486 6487@Article{ pyclaw2012, 6488 author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and 6489 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 6490 Emmett}, 6491 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 6492 journal = {SIAM Journal on Scientific Computing}, 6493 volume = {34}, 6494 number = {4}, 6495 pages = {C210--C231}, 6496 note = {\url{http://arxiv.org/abs/1111.6583}}, 6497 year = {2012}, 6498 petsc_uses = {KSP} 6499} 6500 6501% LiteralHTML: 6502% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 6503% LiteralHTML: 6504@Article{ sojkahorakhaplacermak2018, 6505 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 6506 decomposition method}, 6507 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 6508 journal = {Applied Mathematics and Computation}, 6509 volume = {319}, 6510 pages = {586--597}, 6511 year = {2018}, 6512 petsc_uses = {KSP} 6513} 6514 6515@Article{ chencai2014, 6516 title = {A parallel two-level domain decomposition based one-shot method for shape 6517 optimization problems}, 6518 author = {Rongliang Chen and Xiao‐Chuan Cai}, 6519 journal = {International Journal for Numerical Methods in Engineering}, 6520 volume = {99}, 6521 number = {13}, 6522 year = {2014}, 6523 doi = {10.1002/nme.4711}, 6524 petsc_uses = {KSP} 6525} 6526 6527@PhDThesis{ prudencio2005, 6528 author = {Ernesto Prudencio}, 6529 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 6530 for Optimization Problems Constrained by Partial Differential Equations}, 6531 school = {University of Colorado, Boulder}, 6532 year = {2005}, 6533 petsc_uses = {KSP} 6534} 6535 6536@Article{ prudenciocai2007, 6537 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 6538 for {PDE}-constrained optimization}, 6539 author = {Ernesto Prudencio and X. C. Cai}, 6540 journal = {SIAM J. Sci. Comp.}, 6541 volume = {29}, 6542 number = {3}, 6543 pages = {964--985}, 6544 year = {2007}, 6545 petsc_uses = {KSP} 6546} 6547 6548@Article{ prudenciobyrdcai2006, 6549 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6550 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 6551 {PDE}-constrained Optimization Problems}, 6552 journal = {SIAM J. Sci. Comp.}, 6553 volume = {27}, 6554 pages = {1305--1328}, 6555 year = {2006}, 6556 petsc_uses = {KSP} 6557} 6558 6559@InProceedings{ prudenciobyrdcai2004, 6560 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 6561 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6562 booktitle = {VECPAR 2004}, 6563 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 6564 publisher = {Springer}, 6565 pages = {569--582}, 6566 year = {2004}, 6567 petsc_uses = {KSP} 6568} 6569 6570@Article{ belhamadia-fortin-pcp, 6571 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 6572 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 6573 journal = {Journal of Computational Physics}, 6574 volume = {201}, 6575 pages = {753-770}, 6576 year = {2004}, 6577 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 6578 petsc_uses = {KSP} 6579} 6580 6581@Article{ biros00, 6582 author = {George Biros and Omar Ghattas}, 6583 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 6584 journal = {SIAG-Opt Views and News}, 6585 volume = {11}, 6586 number = {2}, 6587 year = {2000}, 6588 month = aug, 6589 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 6590 petsc_uses = {KSP} 6591} 6592 6593@Article{ bmm01, 6594 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 6595 journal = {ACM Transactions on Mathematical Software}, 6596 title = {A case study in the performance and scalability of optimization algorithms}, 6597 year = {2001}, 6598 volume = {27}, 6599 number = {3}, 6600 pages = {361--376}, 6601 petsc_uses = {KSP} 6602} 6603 6604@InProceedings{ oghattas1999, 6605 author = {George Biros and Omar Ghattas}, 6606 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 6607 incompressible flows}, 6608 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 6609 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 6610 year = {1999}, 6611 petsc_uses = {KSP} 6612} 6613 6614@InProceedings{ hkms00, 6615 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 6616 PDE-constrained Optimization}, 6617 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 6618 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 6619 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 6620 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 6621 Hasco\"{e}t and Uwe Naumann}, 6622 publisher = {Springer}, 6623 year = {2002}, 6624 petsc_uses = {KSP} 6625} 6626 6627% old version: replace with biros2005pln1 6628@TechReport{ bg011, 6629 author = {George Biros and Omar Ghattas}, 6630 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 6631 Part I: The Krylov-Schur Solver}, 6632 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6633 year = {2001}, 6634 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 6635 petsc_uses = {KSP} 6636} 6637 6638% old version: replace with biros2005pln2 6639@TechReport{ bg012, 6640 author = {George Biros and Omar Ghattas}, 6641 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 6642 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 6643 Optimal Control of Steady Viscous Flows}, 6644 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6645 year = {2001}, 6646 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 6647 petsc_uses = {KSP} 6648} 6649 6650% LiteralHTML: 6651% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 6652% LiteralHTML: 6653@InProceedings{ ly2003, 6654 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 6655 title = {A New Parallel Kernel-independent Fast Multipole Method}, 6656 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 6657 year = {2003}, 6658 note = {Winner of the Best Student Paper at SC2003}, 6659 petsc_uses = {KSP} 6660} 6661 6662@Article{ yokotabarbaknepley10, 6663 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 6664 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 6665 journal = {Computer Methods in Applied Mechanics and Engineering}, 6666 volume = {199}, 6667 number = {25-28}, 6668 pages = {1793--1804}, 6669 url = {http://arxiv.org/abs/0909.5413v1}, 6670 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 6671 year = {2010}, 6672 petsc_uses = {KSP} 6673} 6674 6675@Article{ cruzknepleybarba10, 6676 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 6677 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 6678 journal = {International Journal of Numerical Methods in Engineering}, 6679 volume = {85}, 6680 number = {4}, 6681 pages = {403--428}, 6682 url = {http://arxiv.org/abs/0905.2637}, 6683 note = {\url{http://arxiv.org/abs/0905.2637}}, 6684 year = {2010}, 6685 petsc_uses = {KSP} 6686} 6687 6688% LiteralHTML: 6689% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 6690% LiteralHTML: 6691@Article{ buchanpainumplebysmedleystevenson2012, 6692 title = {A sub-grid scale finite element agglomeration multigrid method with application 6693 to the Boltzmann transport equation}, 6694 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 6695 journal = {International Journal for Numerical Methods in Engineering}, 6696 volume = {92}, 6697 number = {3}, 6698 pages = {318--342}, 6699 year = {2012}, 6700 publisher = {Wiley Online Library}, 6701 petsc_uses = {KSP} 6702} 6703 6704@Article{ magoulesahamedsuzuki2015, 6705 title = {Green computing on graphics processing units}, 6706 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 6707 journal = {Concurrency and Computation: Practice and Experience}, 6708 year = {2015}, 6709 publisher = {Wiley Online Library}, 6710 petsc_uses = {KSP} 6711} 6712 6713@InProceedings{ yanrhodes11, 6714 author = {Yan, Baoqiang and Rhodes, Philip J.}, 6715 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 6716 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 6717 series = {ICPP '11}, 6718 pages = {355--364}, 6719 year = {2011}, 6720 isbn = {978-0-7695-4510-3}, 6721 numpages = {10}, 6722 doi = {10.1109/ICPP.2011.70}, 6723 acmid = {2066965}, 6724 publisher = {IEEE Computer Society}, 6725 address = {Washington, DC, USA}, 6726 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 6727 petsc_uses = {KSP} 6728} 6729 6730@Article{ hakansson2013mdstochasticliouville, 6731 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 6732 Stulz, Eugen}, 6733 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 6734 equation study}, 6735 journal = {Phys. Chem. Chem. Phys.}, 6736 year = {2013}, 6737 volume = {15}, 6738 issue = {26}, 6739 pages = {10930-10941}, 6740 publisher = {The Royal Society of Chemistry}, 6741 doi = {10.1039/C3CP50788B}, 6742 petsc_uses = {KSP} 6743} 6744 6745@Article{ hakansson2011stochasticliouville, 6746 author = {Hakansson, Par and Nair, Prasanth B.}, 6747 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 6748 form}, 6749 journal = {Phys. Chem. Chem. Phys.}, 6750 year = {2011}, 6751 volume = {13}, 6752 issue = {20}, 6753 pages = {9578-9589}, 6754 publisher = {The Royal Society of Chemistry}, 6755 doi = {10.1039/C1CP20400A}, 6756 petsc_uses = {KSP} 6757} 6758 6759@InProceedings{ wang:lee:scidac2011, 6760 author = {Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman 6761 McInnes and Todd Munson and Barry Smith}, 6762 title = {A Differential Variational Inequality Approach for the Simulation of 6763 Heterogeneous Materials}, 6764 booktitle = {Proceedings of SciDAC 2011 Conference}, 6765 year = {2011}, 6766 petsc_uses = {KSP} 6767} 6768 6769@Article{ bourdinlarsenrichardson2011, 6770 author = {Blaise Bourdin and Christopher Larsen and Casey Richardson}, 6771 title = {A time-discrete model for dynamic fracture based on crack regularization}, 6772 journal = {International Journal of Fracture}, 6773 volume = {168}, 6774 issue = {2}, 6775 pages = {133--143}, 6776 doi = {10.1007/s10704-010-9562-x}, 6777 year = {2011}, 6778 petsc_uses = {KSP} 6779} 6780 6781@Article{ bourdinfrancfortmarigo2008, 6782 author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo}, 6783 title = {The Variational Approach to Fracture}, 6784 journal = {J. Elasticity}, 6785 volume = {91}, 6786 issue = {1}, 6787 pages = {1--148}, 6788 doi = {10.1007/s10659-007-9107-3}, 6789 year = {2008}, 6790 petsc_uses = {KSP} 6791} 6792 6793@Article{ lahtinen2008spectrum, 6794 title = {Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model}, 6795 author = {Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, 6796 J.K.}, 6797 journal = {Annals of Physics}, 6798 volume = {323}, 6799 number = {9}, 6800 pages = {2286--2310}, 6801 year = {2008}, 6802 publisher = {Elsevier}, 6803 petsc_uses = {KSP} 6804} 6805 6806@InProceedings{ roark2004discriminative, 6807 title = {Discriminative language modeling with conditional random fields and the 6808 perceptron algorithm}, 6809 author = {Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.}, 6810 booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational 6811 Linguistics}, 6812 pages = {47}, 6813 year = {2004}, 6814 organization = {Association for Computational Linguistics}, 6815 petsc_uses = {KSP} 6816} 6817 6818@Article{ roark2007discriminative, 6819 title = {Discriminative n-gram language modeling}, 6820 author = {Roark, B. and Saraclar, M. and Collins, M.}, 6821 journal = {Computer Speech \& Language}, 6822 volume = {21}, 6823 number = {2}, 6824 pages = {373--392}, 6825 year = {2007}, 6826 publisher = {Elsevier}, 6827 petsc_uses = {KSP} 6828} 6829 6830@Conference{ garcia2011parallel, 6831 title = {{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D 6832 nanodevice simulators}}, 6833 author = {Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and 6834 Aldegunde, M.}, 6835 booktitle = {Electron Devices (CDE), 2011 Spanish Conference on}, 6836 pages = {1--4}, 6837 organization = {IEEE}, 6838 petsc_uses = {KSP} 6839} 6840 6841@Conference{ wesley2006parallel, 6842 title = {{A parallel artificial neural network implementation}}, 6843 author = {Wesley-Smith, I.}, 6844 booktitle = {Proceedings of The National Conference On Undergraduate Research (NCUR)}, 6845 year = {2006}, 6846 petsc_uses = {KSP} 6847} 6848 6849@Article{ hcsw1, 6850 author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu}, 6851 title = {Parallel {N}ewton--{K}rylov--{S}chwarz algorithms for the three-dimensional 6852 {P}oisson--{B}oltzmann equation in numerical simulation of colloidal particle 6853 interactions}, 6854 journal = {Computer Physics Communications}, 6855 volumne = {181}, 6856 year = {2010}, 6857 pages = {1529--1537}, 6858 petsc_uses = {KSP} 6859} 6860 6861@Article{ hh1, 6862 author = {C.-Y. Huang and F.-N. Hwang}, 6863 title = {Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for 6864 bifurcation analysis of incompressible sudden expansion flows}, 6865 journal = {Applied Numerical Mathematics}, 6866 volume = {60}, 6867 year = {2010}, 6868 pages = {738--751}, 6869 petsc_uses = {KSP} 6870} 6871 6872@Article{ hwhw1, 6873 author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. 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Cooke}, 7359 title = {Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three 7360 Dimensions}, 7361 year = {2004}, 7362 booktitle = {40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit}, 7363 url = {http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282}, 7364 petsc_uses = {KSP} 7365} 7366 7367@InProceedings{ allard-gouranton-ipts2002, 7368 author = {Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin}, 7369 title = {Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster}, 7370 year = {2002}, 7371 booktitle = {Immersive Projection Technology Symposium}, 7372 url = {http://www-id.imag.fr/\~{ }allardj/files/ipts2002.pdf}, 7373 petsc_uses = {KSP} 7374} 7375 7376@Article{ icc, 7377 author = {D Ioan and G Ciuprina and C Ciobotaru}, 7378 title = {Hybrid and concurrent algorithms for nonlinear magnetic field problems}, 7379 journal = {IEEE Transactions on Magnetics}, 7380 year = {2000}, 7381 url = {http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/20/19005/00877735.pdf}, 7382 petsc_uses = {KSP} 7383} 7384 7385@InProceedings{ hs1, 7386 author = {Brian J. Henz and Dale R. Shires}, 7387 title = {Development and Performance Analysis of a Parallel Finite Element Application 7388 Implemented in an Object-Oriented Programming Framework}, 7389 year = {2003}, 7390 booktitle = {PDPTA 2003}, 7391 pages = {1286-1292}, 7392 note = {Resin Transfer Modeling}, 7393 petsc_uses = {KSP} 7394} 7395 7396@TechReport{ b2000, 7397 author = {Rickard Bergstrom}, 7398 title = {Least-Squares Finite Element Methods for Electromagnetic Applications}, 7399 year = {2000}, 7400 institution = {Chalmers}, 7401 number = {2000-05}, 7402 url = {http://www.phi.chalmers.se/pub/preprints/ps/phiprint-2000-05.ps}, 7403 petsc_uses = {KSP} 7404} 7405 7406@Article{ fs2004, 7407 author = {Petri Fast and Michael J. Shelley}, 7408 title = {A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele 7409 Shaw Flow}, 7410 journal = {Journal of Computational Physics}, 7411 year = {2004}, 7412 volume = {195}, 7413 url = {http://www.math.nyu.edu/faculty/shelley/papers/FS2004.pdf}, 7414 pages = {117-142}, 7415 petsc_uses = {KSP} 7416} 7417 7418@MastersThesis{ wallach, 7419 author = {Hanna Wallach}, 7420 title = {Efficient Training of Conditional Random Fields}, 7421 school = {University of Edinburgh}, 7422 year = {2002}, 7423 url = {http://scholar.google.com/url?sa=U&q=http://www.hcrc.ed.ac.uk/\~{ 7424 }osborne/msc-projects/wallach.ps.gz}, 7425 petsc_uses = {KSP} 7426} 7427 7428@Article{ something, 7429 author = {T Rylander and A Bondeson}, 7430 title = {Stability of explicit-implicit hybrid time-stepping schemes for Maxwells 7431 equations}, 7432 journal = {Journal of Computational Physics}, 7433 year = {2002}, 7434 volume = {179}, 7435 pages = {426-438}, 7436 petsc_uses = {KSP} 7437} 7438 7439@TechReport{ uf1, 7440 author = {Uwe Fabricius}, 7441 title = {Comparison of two implementations of {AMG}-preconditioned {CG} considering an 7442 electrostatic problem}, 7443 year = {2004}, 7444 institution = {Friedrich Alexander Universitat Erlangen Nurnberg Germany}, 7445 url = {http://www10.informatik.uni-erlangen.de/de/Publications/TechnicalReports/TechRep04-1.pdf}, 7446 number = {04-1}, 7447 petsc_uses = {KSP} 7448} 7449 7450@InBook{ sg1, 7451 author = {Natalia Seoane and A.J.Garca-Loureiro}, 7452 chapter = {Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity 7453 Equation}, 7454 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=h0xlulyhugck3y2gnt2l&referrer=parent&backto=issue,79,112;journal,212,1787;linkingpublicationresults,1:105633,1}, 7455 title = {Lecture Notes in Computer Science}, 7456 publisher = {Springer-Verlag}, 7457 volume = {3037}, 7458 year = {2004}, 7459 petsc_uses = {KSP} 7460} 7461 7462@Article{ nikyilmazgivisheikhipope10, 7463 author = {M. B. Nik and S. L. Yilmaz and P. Givi and M. R. H. Sheikhi and S. B. Pope}, 7464 title = {Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function}, 7465 journal = {AIAA Journal}, 7466 volume = {48}, 7467 number = {7}, 7468 pages = {1513--1522}, 7469 year = {2010}, 7470 petsc_uses = {KSP} 7471} 7472 7473@Article{ nikyilmazsheikhigivi10, 7474 author = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi}, 7475 title = {Grid Resolution Effects on VSFMDF/LES}, 7476 journal = {Flow, Turbulence and Combustion}, 7477 doi = {10.1007/s10494-010-9272-5}, 7478 year = {2010}, 7479 petsc_uses = {KSP} 7480} 7481 7482@Article{ idema2013towards, 7483 title = {Towards faster solution of large power flow problems}, 7484 author = {Idema, Reijer and Papaefthymiou, Georgios and Lahaye, Domenico and Vuik, Cornelis 7485 and van der Sluis, Lou}, 7486 journal = {Power Systems, IEEE Transactions on}, 7487 volume = {28}, 7488 number = {4}, 7489 pages = {4918--4925}, 7490 year = {2013}, 7491 publisher = {IEEE}, 7492 petsc_uses = {KSP} 7493} 7494 7495@Article{ 6026245, 7496 author = {Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.}, 7497 journal = {Power Systems, IEEE Transactions on}, 7498 title = {Scalable Newton-Krylov Solver for Very Large Power Flow Problems}, 7499 year = {2012}, 7500 month = feb, 7501 volume = {27}, 7502 number = {1}, 7503 pages = {390-396}, 7504 doi = {10.1109/TPWRS.2011.2165860}, 7505 issn = {0885-8950}, 7506 petsc_uses = {KSP} 7507} 7508 7509@Book{ idema2014computational, 7510 title = {Computational Methods in Power System Analysis}, 7511 author = {Idema, Reijer and Lahaye, Domenico JP}, 7512 year = {2014}, 7513 publisher = {Springer}, 7514 petsc_uses = {KSP} 7515} 7516 7517@PhDThesis{ abhyankar2011thesis, 7518 author = {Shrirang Abhyankar}, 7519 title = {Development of an implicitly coupled electromechanical and electromagnetic 7520 transients simulator for power systems}, 7521 school = {Illinois Institute of Technology}, 7522 year = {2011}, 7523 petsc_uses = {KSP} 7524} 7525 7526@InProceedings{ abhyankarhipcna11-1, 7527 author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck}, 7528 title = {Using {PETSc} to develop scalable applications for next-generation power grid}, 7529 year = {2011}, 7530 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 7531 Networking and Analytics for the Power Grid}, 7532 url = {http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf}, 7533 publisher = {ACM}, 7534 petsc_uses = {KSP} 7535} 7536 7537@InProceedings{ abhyankarhipcna11-2, 7538 author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang}, 7539 title = {Development of a parallel three-phase transient stability simulator for power 7540 systems}, 7541 year = {2011}, 7542 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 7543 Networking and Analytics for the Power Grid}, 7544 publisher = {ACM}, 7545 petsc_uses = {KSP} 7546} 7547 7548@InProceedings{ abhyankarpesgeneral2012, 7549 author = {Shrirang Abhyankar and A. Flueck}, 7550 title = {An implicitly-coupled solution approach for combined electromechanical and 7551 electromagnetic transients simulation}, 7552 year = {2012}, 7553 booktitle = {Proceedings of the IEEE PES General Meeting}, 7554 publisher = {IEEE}, 7555 petsc_uses = {KSP} 7556} 7557 7558@Article{ idemalahayevuiksluis2012, 7559 author = {Reijer Idema and Domenico Lahaye and Cornelis Vuik and Lou van der Sluis}, 7560 title = {Scalable Newton-Krylov solver for very large Power Flow problems}, 7561 journal = {IEEE Transactions on Power Systems}, 7562 year = {2012}, 7563 volume = {27}, 7564 pages = {390-396}, 7565 petsc_uses = {KSP} 7566} 7567 7568@Article{ korrestzavellasgalinas2013, 7569 author = {George N. Korres and Anastasios Tzavellas and Evangelos Galinas}, 7570 title = {A distributed implementation of multi-area power system state estimation on a 7571 cluster of computers }, 7572 journal = {Electric Power Systems Research }, 7573 volume = {102}, 7574 number = {0}, 7575 pages = {20 - 32}, 7576 year = {2013}, 7577 issn = {0378-7796}, 7578 doi = {10.1016/j.epsr.2013.04.002}, 7579 petsc_uses = {KSP} 7580} 7581 7582% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7583% LiteralHTML:<font color="#FF0000"> 7584% LiteralHTML: Material failure, for example, cracking of steel beams resulting 7585% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 7586% LiteralHTML: are important for prediction and prevention. PETSc has been used 7587% LiteralHTML: in a variety of studies of material failure.</p> 7588% LiteralHTML:</font> 7589% LiteralHTML: 7590@InProceedings{ gray2, 7591 author = {Yuan He and Joshua Gray and Richard Braatz and Richard Alkire}, 7592 title = {Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel}, 7593 year = {2004}, 7594 booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}, 7595 petsc_uses = {KSP} 7596} 7597 7598@InProceedings{ gray1, 7599 author = {J. Gray and C. Homescu and L. Petzold and Richard Alkire}, 7600 title = {Algorithms and Computing Architectures for Solving Differential-Algebraic 7601 Equation Systems Typically Encountered in Models of Corrosion Pit Initiation}, 7602 year = {2003}, 7603 booktitle = {Abstracts of the Electrochemical Society 204th meeting}, 7604 petsc_uses = {KSP} 7605} 7606 7607@InProceedings{ crack2, 7608 author = {Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. Wawrzynek}, 7609 title = {A multiscale modeling approach to crack initiation in metallic polycrystals}, 7610 booktitle = {44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials 7611 Conference}, 7612 url = {http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=TRD&recid=A0325099AH}, 7613 year = {2003}, 7614 petsc_uses = {KSP} 7615} 7616 7617@TechReport{ hdams1, 7618 author = {Gerd Heber and Andrew J. Dolgert and Maxirn Alt and Karen A. Mazurkiewicz and 7619 Lynd Stringer}, 7620 title = {Fracture Mechanics on the Intel Itanium Architecture}, 7621 year = {2001}, 7622 institution = {Intel Corporation}, 7623 url = {http://cedar.intel.com/media/pdf/scs/cptconitanium.pdf}, 7624 petsc_uses = {KSP} 7625} 7626 7627@InProceedings{ ihwi, 7628 author = {E. Iesulauro and G. Heber and P. A. Wawrzynek and A. R. Ingraffea}, 7629 title = {Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation}, 7630 booktitle = {International Conference ON Computational Engineering and Sciences}, 7631 year = {2002}, 7632 url = {http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf}, 7633 petsc_uses = {KSP} 7634} 7635 7636@InProceedings{ crack, 7637 author = {Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and 7638 Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris 7639 Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis 7640 and Paul A. Wawrzynek}, 7641 title = {Parallel FEM Simulation of Crack Propagation}, 7642 booktitle = {Proceedings of Irregular 2000}, 7643 url = {http://www.cs.cornell.edu/stodghil/papers/irregular00.ps}, 7644 year = {2000}, 7645 petsc_uses = {KSP} 7646} 7647 7648@InProceedings{ beaudoin98, 7649 author = {A. J. Beaudoin}, 7650 title = {Use of Polycrystal Plasticity Theory in Assessing Material Performance}, 7651 booktitle = {Simulation of materials processing: Theory, methods, and applications - 7652 Proceedings of the Sixth International Conference, NUMIFORM'98}, 7653 editor = {J. Hu\'etink and F. P. T. Baaijens}, 7654 optvolume = {}, 7655 optnumber = {}, 7656 optseries = {}, 7657 year = {1998}, 7658 optorganization={}, 7659 publisher = {A. A. Balkema Publishers}, 7660 address = {Rotterdam, Netherlands}, 7661 month = jun, 7662 optpages = {}, 7663 petsc_uses = {KSP} 7664} 7665 7666% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7667@TechReport{ defordheld1, 7668 author = {JF DeFord and BL Held}, 7669 title = {RF3P-A New Parallel Driven Frequency Electromagnetic Solver}, 7670 year = {2002}, 7671 institution = {Simulation Technology and Applied Research}, 7672 url = {http://www.staarinc.com/support/papers/aces2002.pdf}, 7673 note = {Discusses their parallel commercial solver that uses PETSc}, 7674 petsc_uses = {KSP} 7675} 7676 7677@PhDThesis{ sande2003, 7678 author = {Hans Vande Sande}, 7679 title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic 7680 Quasi-Static Electromagnetic Systems}, 7681 school = {Katholieke Universiteit Leuven, Belgium}, 7682 year = {2003}, 7683 petsc_uses = {KSP} 7684} 7685 7686@Article{ sdchh2004, 7687 author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 7688 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 7689 Tolerance}, 7690 journal = {IEEE Transactions on Magnetics}, 7691 year = {2004}, 7692 volume = {40}, 7693 pages = {1306--1309}, 7694 petsc_uses = {KSP} 7695} 7696 7697@Article{ holst-lindblom-etal:2004, 7698 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 7699 Scheel and Lawrence E. Kidder}, 7700 title = {Optimal constraint projection for hyperbolic evolution systems, }, 7701 journal = {Phys. Rev. D}, 7702 year = {2004}, 7703 volume = {70}, 7704 pages = {084017}, 7705 petsc_uses = {KSP} 7706} 7707 7708@Article{ marm2005, 7709 author = {Matthew Anderson and Richard A. Matzner}, 7710 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 7711 journal = {Foundations of Physics}, 7712 volume = {35}, 7713 pages = {1572--9516}, 7714 year = {2005}, 7715 petsc_uses = {KSP} 7716} 7717 7718@Article{ cook-pfeiffer:2004, 7719 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 7720 title = {Excision boundary conditions for black hole initial data}, 7721 journal = {Phys. Rev. D}, 7722 volume = {70}, 7723 pages = {104016--24}, 7724 year = {2004}, 7725 petsc_uses = {KSP} 7726} 7727 7728@Article{ pfeiffer-kidder-etal:2005, 7729 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 7730 Shoemaker}, 7731 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 7732 journal = {Phys. Rev. D}, 7733 year = {2005}, 7734 volume = {71}, 7735 pages = {024020}, 7736 petsc_uses = {KSP} 7737} 7738 7739@Article{ pfeiffer-kidder-etal:2003, 7740 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 7741 Saul A.}, 7742 title = {A multidomain spectral method for solving elliptic equations}, 7743 journal = {CPC}, 7744 year = {2003}, 7745 volume = {152}, 7746 pages = {253--273}, 7747 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 7748 For a related online version, see arXiv:gr-qc/0202096}, 7749 petsc_uses = {KSP} 7750} 7751 7752@Article{ pfeiffer-cook-teukolsky:2002, 7753 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 7754 title = {Comparing initial-data sets for binary black hole}, 7755 journal = {PRD}, 7756 year = {2002}, 7757 volume = {66}, 7758 pages = {024047}, 7759 note = {for a related online version, seearXiv:gr-qc/0203085}, 7760 petsc_uses = {KSP} 7761} 7762 7763@PhDThesis{ pfeiffer:2003, 7764 author = {Pfeiffer, Harald P.}, 7765 title = {Initial Data for Black Hole Evolutions}, 7766 school = {Cornell University}, 7767 year = {2003}, 7768 petsc_uses = {KSP} 7769} 7770 7771@TechReport{ h1, 7772 author = {Erik Schnetter}, 7773 title = {A fast apparent horizon algorithm}, 7774 year = {2002}, 7775 number = {Arxiv preprint gr-qc/0206003}, 7776 url = {http://arxiv.org/pdf/gr-qc/0206003}, 7777 petsc_uses = {KSP} 7778} 7779 7780@Article{ h2, 7781 author = {Erik Schnetter}, 7782 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 7783 year = {2003}, 7784 journal = {Class. Quantum Grav.}, 7785 pages = {4719-4737}, 7786 volume = {20}, 7787 url = {http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf}, 7788 petsc_uses = {KSP} 7789} 7790 7791@Article{ adams-03a, 7792 author = {Adams, M.~F.}, 7793 journal = {Numerical Linear Algebra with Applications}, 7794 number = {2-3}, 7795 pages = {141-153}, 7796 title = {Algebraic multigrid methods for constrained linear systems with applications to 7797 contact problems in solid mechanics}, 7798 volume = {11}, 7799 year = {2004}, 7800 petsc_uses = {KSP} 7801} 7802 7803@Article{ vandesande1, 7804 author = {H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer}, 7805 journal = {IEEE TRANSACTIONS ON MAGNETICS}, 7806 year = {2003}, 7807 volume = {39}, 7808 pages = {1709--1712}, 7809 title = {Solving Nonlinear Magnetic Problems Using {N}ewton Trust Region Methods}, 7810 petsc_uses = {KSP} 7811} 7812 7813@InProceedings{ vbde1, 7814 author = {Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith}, 7815 year = {2002}, 7816 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 7817 Uintah PSE}, 7818 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 7819 2002}, 7820 pages = {49-55}, 7821 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 7822 note = {Extended abstract}, 7823 petsc_uses = {KSP} 7824} 7825 7826@Unpublished{ ep1, 7827 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 7828 author = {Bradley R. Eccleston and Todd S. Palmer}, 7829 institution = {Department of Nuclear Engineering, Oregon State University}, 7830 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 7831 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 7832 Parallel Simulations}, 7833 year = {1999}, 7834 petsc_uses = {KSP} 7835} 7836 7837@InProceedings{ teo2007scalable, 7838 title = {A scalable modular convex solver for regularized risk minimization}, 7839 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 7840 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 7841 discovery and data mining}, 7842 pages = {727--736}, 7843 year = {2007}, 7844 organization = {ACM}, 7845 petsc_uses = {KSP} 7846} 7847 7848@InProceedings{ rm02, 7849 author = {Robert Malouf}, 7850 year = {2002}, 7851 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 7852 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 7853 (CoNLL-2002)}, 7854 pages = {49-55}, 7855 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 7856 petsc_uses = {KSP} 7857} 7858 7859@Unpublished{ hrv02, 7860 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 7861 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7862 note = {Submitted to CMMSE}, 7863 petsc_uses = {KSP} 7864} 7865 7866@Article{ tmh2001, 7867 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 7868 journal = {Journal of Economic Dynamics and Control}, 7869 year = {2002}, 7870 volume = {26}, 7871 pages = {1499-1515}, 7872 title = {Solving finite difference schemes arising in trivariate option pricing}, 7873 petsc_uses = {KSP} 7874} 7875 7876@InProceedings{ a2, 7877 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 7878 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 7879 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 7880 Methods}, 7881 editor = {C.-H. Lai et al.}, 7882 publisher = {Domain Decomposition Press, Bergen}, 7883 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 7884 year = {1999}, 7885 petsc_uses = {KSP} 7886} 7887 7888@Unpublished{ mmmdcmaa-web-page, 7889 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 7890 {A}coustics {W}eb Page}, 7891 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 7892 author = {David E. Keyes}, 7893 institution = {Old Dominion University}, 7894 petsc_uses = {KSP} 7895} 7896 7897@Conference{ liu2010parallelization, 7898 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 7899 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 7900 booktitle = {International Symposium on Parallel and Distributed Processing with 7901 Applications}, 7902 pages = {528--535}, 7903 year = {2010}, 7904 organization = {IEEE}, 7905 petsc_uses = {KSP} 7906} 7907 7908@Unpublished{ oil-reservoir-sim-web-page, 7909 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 7910 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 7911 institution = {University of Texas at Austin and Argonne National Laboratory}, 7912 key = {University of Texas at Austin and Argonne National Laboratory}, 7913 petsc_uses = {KSP} 7914} 7915 7916@Article{ tmh2001b, 7917 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 7918 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 7919 year = {2001}, 7920 volume = {37}, 7921 pages = {143--146}, 7922 title = {Adapting EMAP3D to parallel processing}, 7923 petsc_uses = {KSP} 7924} 7925 7926@Article{ harbury98, 7927 author = {HK Harbury and W Porod}, 7928 journal = {VLSI Design}, 7929 year = {1998}, 7930 volume = {6}, 7931 pages = {47--51}, 7932 title = {Parallel computation for electronic waves in quantum corrals}, 7933 petsc_uses = {KSP} 7934} 7935 7936@Article{ bludszuwei98, 7937 author = {Mark Bludszuweit}, 7938 journal = {Journal of Lightwave Technology}, 7939 year = {1998}, 7940 volume = {16}, 7941 number = {7}, 7942 pages = {1336--42}, 7943 title = {Mixed Finite Element Beam Propagation Method}, 7944 petsc_uses = {KSP} 7945} 7946 7947@Article{ s1, 7948 author = {J. L. Friedman and N. Stergioulas}, 7949 journal = {Astrophysics Journal}, 7950 year = {1998}, 7951 volume = {492}, 7952 number = {301}, 7953 pages = {}, 7954 title = {}, 7955 petsc_uses = {KSP} 7956} 7957 7958@Article{ s1a, 7959 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 7960 journal = {Astrophysics Journal}, 7961 year = {1999}, 7962 volume = {510}, 7963 number = {854}, 7964 pages = {}, 7965 title = {}, 7966 petsc_uses = {KSP} 7967} 7968 7969@PhDThesis{ s2, 7970 author = {N. Stergioulas}, 7971 title = {Ph. D. thesis}, 7972 year = {1996}, 7973 institution = {University of Wisconsin-Milwaukee}, 7974 petsc_uses = {KSP} 7975} 7976 7977@InProceedings{ coral1, 7978 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7979 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 7980 Parallel Computing Environment}, 7981 booktitle = {Proceedings of the Miami TEAM Workshop}, 7982 location = {Florida International University, Department of Electrical Engineering and 7983 Computing Science}, 7984 month = nov, 7985 year = {1993}, 7986 petsc_uses = {KSP} 7987} 7988 7989@InProceedings{ coral2, 7990 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7991 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 7992 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 7993 month = dec, 7994 year = {1994}, 7995 petsc_uses = {KSP} 7996} 7997 7998@InProceedings{ coral3, 7999 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 8000 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 8001 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 8002 location = {Florida International University, Department of Electrical Engineering and 8003 Computing Science}, 8004 year = {1995}, 8005 petsc_uses = {KSP} 8006} 8007 8008@InProceedings{ mijalkovic, 8009 author = {Slobodan Mijalkovi\'{c}}, 8010 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 8011 Process Simulation}, 8012 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 8013 Gent, Belgium, September 27--30, 1999.}, 8014 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 8015 optvolume = {14}, 8016 optseries = {Lecture Notes in Computational Science and Engineering}, 8017 year = {2000}, 8018 publisher = {Springer}, 8019 address = {Berlin}, 8020 optpages = {179--184}, 8021 petsc_uses = {KSP} 8022} 8023 8024@Article{ bludszuwei98a, 8025 author = {Mark Bludszuweit}, 8026 journal = {Journal of Lightwave Technology}, 8027 year = {1998}, 8028 volume = {16}, 8029 number = {7}, 8030 pages = {1336--42}, 8031 title = {Mixed Finite Element Beam Propagation Method}, 8032 petsc_uses = {KSP} 8033} 8034 8035@Article{ gilli-pauletto-1998, 8036 author = {Manfred Gilli and Giorgio Pauletto}, 8037 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 8038 journal = {Computational Economics}, 8039 year = {2000}, 8040 volume = {16}, 8041 pages = {173--186}, 8042 petsc_uses = {KSP} 8043} 8044 8045% LiteralHTML: 8046% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 8047% LiteralHTML: 8048@Article{ collierdalcincalo2013, 8049 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 8050 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 8051 journal = {arxiv}, 8052 year = {2013}, 8053 number = {1305.4452}, 8054 note = {\url{http://arxiv.org/abs/1305.4452}}, 8055 petsc_uses = {KSP} 8056} 8057 8058@Article{ collierdalcinvignalcortescalo2016, 8059 title = {PetIGA: A framework for high-performance isogeometric analysis}, 8060 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 8061 Victor M. Calo}, 8062 journal = {Computer Methods in Applied Mechanics and Engineering}, 8063 year = {2016}, 8064 petsc_uses = {KSP} 8065} 8066 8067@Misc{ petiga-web-page, 8068 author = {N. Collier and L. Dalcin and V.M. Calo}, 8069 title = {{PetIGA} {W}eb page}, 8070 url = {https://bitbucket.org/dalcinl/petiga/}, 8071 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 8072 year = {2014}, 8073 petsc_uses = {KSP} 8074} 8075 8076@Article{ logg07, 8077 author = {Logg, Anders}, 8078 title = {Automating the Finite Element Method}, 8079 journal = {Archives of Computational Methods in Engineering}, 8080 volume = {14}, 8081 number = {2}, 8082 pages = {93-138}, 8083 year = {2007}, 8084 doi = {10.1007/s11831-007-9003-9}, 8085 publisher = {Kluwer Academic Publishers}, 8086 issn = {1134-3060}, 8087 language = {English}, 8088 petsc_uses = {KSP} 8089} 8090 8091@Article{ jezequelcouturierdenis12, 8092 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 8093 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 8094 versus the PETSc library}, 8095 journal = {The Journal of Supercomputing}, 8096 volume = {59}, 8097 number = {3}, 8098 pages = {1517-1532}, 8099 year = {2012}, 8100 issn = {0920-8542}, 8101 doi = {10.1007/s11227-011-0563-y}, 8102 publisher = {Springer US}, 8103 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 8104 Sparse linear solver}, 8105 language = {English}, 8106 petsc_uses = {KSP} 8107} 8108 8109@Unpublished{ feap-web-page, 8110 title = {FEAP: A Finite Element Analysis Program}, 8111 url = {http://www.ce.berkeley.edu/projects/feap/}, 8112 author = {FEAP Team}, 8113 note = {Uses PETSc linear solvers - iterative and direct}, 8114 petsc_uses = {KSP} 8115} 8116 8117@Unpublished{ parpre-web-page, 8118 title = {{ParPre} {W}eb {P}age}, 8119 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 8120 institution = {University of Tennessee}, 8121 author = {Victor Eijkhout}, 8122 note = {This is no longer supported. A set of preconditioners built on PETSc}, 8123 petsc_uses = {KSP} 8124} 8125 8126@Unpublished{ pism, 8127 title = {{PISM}: a Parallel Ice Sheet Model}, 8128 author = {{PISM Team}}, 8129 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 8130 Sheet Model). The thickness, temperature, velocity and age of the ice are all 8131 simulated, as is the deformation of the earth underneath the ice. New techniques 8132 for fast ice dynamics, earth deformation, and verification have are included.}, 8133 note = {\url{http://www.pism-docs.org/}}, 8134 petsc_uses = {KSP} 8135} 8136 8137@Unpublished{ oofem, 8138 title = {OOFEM - an object oriented finite element package}, 8139 author = {Borek Patzak}, 8140 url = {http://www.oofem.org}, 8141 petsc_uses = {KSP} 8142} 8143 8144@Unpublished{ dks2openfvm, 8145 title = {OpenFVM - a finite volume based general purpose CFD solver}, 8146 author = {Open source development}, 8147 url = {http://openfvm.sourceforge.net/}, 8148 petsc_uses = {KSP} 8149} 8150 8151@Unpublished{ sundar-2008w, 8152 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 8153 octree meshes}, 8154 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8155 institution = {University of Pennsylvania}, 8156 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 8157 petsc_uses = {KSP} 8158} 8159 8160@Unpublished{ khatiwala07-software, 8161 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 8162 author = {Khatiwala, S.}, 8163 institution = {Columbia University}, 8164 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 8165 petsc_uses = {KSP} 8166} 8167 8168@InBook{ jiaolima99, 8169 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 8170 chapter = {{SIFFEA}:Scalable Integrated Framework for Finite Element Analysis}, 8171 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 8172 title = {Lecture Notes in Computer Science}, 8173 publisher = {Springer-Verlag}, 8174 volume = {1732}, 8175 year = {1999}, 8176 petsc_uses = {KSP} 8177} 8178 8179@Article{ crow1, 8180 author = {C. S. Crow IV}, 8181 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 8182 journal = {Hopkins Undergraduate Research Journal}, 8183 year = {2003}, 8184 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 8185 petsc_uses = {KSP} 8186} 8187 8188@Unpublished{ petsc-python, 8189 title = {PETSc for Python}, 8190 author = {L. Dalcin}, 8191 url = {https://petsc.org/main/petsc4py}, 8192 note = {Provides Python bindings for PETSc}, 8193} 8194 8195@Unpublished{ cfdship, 8196 title = {{CFDShip-Iowa}}, 8197 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 8198 institution = {University of Iowa}, 8199 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 8200 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 8201 structured grids, designed for ship applications}, 8202 petsc_uses = {KSP} 8203} 8204 8205@Unpublished{ bvw, 8206 title = {Multiflow}, 8207 author = {Berend van Wachem}, 8208 institution = {Mechanical Engineering - Chalmers University of Technology}, 8209 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 8210 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 8211 flows.}, 8212 petsc_uses = {KSP} 8213} 8214 8215@Unpublished{ dks2, 8216 title = {FENA - A Finite Element Model for the North Atlantic}, 8217 author = {Jens Schroeter}, 8218 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 8219 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 8220 petsc_uses = {KSP} 8221} 8222 8223@TechReport{ piwonski2010idea, 8224 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 8225 and Simulation in {3-D}}, 8226 author = {Piwonski, J. and Slawig, T.}, 8227 year = {2010}, 8228 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8229 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 8230 petsc_uses = {KSP} 8231} 8232 8233@Unpublished{ metos3d-web, 8234 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 8235 author = {Piwonski, J. and Slawig, T.}, 8236 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8237 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 8238 petsc_uses = {KSP} 8239} 8240 8241@Unpublished{ magpar, 8242 author = {W. Scholz}, 8243 title = {Magpar: Parallel Micromagnetics Code}, 8244 institution = {Vienna University of Technology}, 8245 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 8246 petsc_uses = {KSP} 8247} 8248 8249@Misc{ libmesh:sourceforge, 8250 author = {}, 8251 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 8252 equations on serial and parallel platforms}, 8253 note = {[Online]}, 8254 url = {http://libmesh.github.io}, 8255 petsc_uses = {KSP} 8256} 8257 8258@Misc{ moose-web-page, 8259 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 8260 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 8261 Gaston and John Peterson and Jason Miller}, 8262 institution = {Idaho National Laboratory}, 8263 howpublished = {\url{http://mooseframework.org}}, 8264 petsc_uses = {KSP} 8265} 8266 8267@Article{ gaston2009moose, 8268 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 8269 equations}, 8270 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 8271 journal = {Nuclear Engineering and Design}, 8272 volume = {239}, 8273 number = {10}, 8274 pages = {1768--1778}, 8275 year = {2009}, 8276 publisher = {Elsevier}, 8277 petsc_uses = {KSP} 8278} 8279 8280@Article{ tonks2012object, 8281 title = {An object-oriented finite element framework for multiphysics phase field 8282 simulations}, 8283 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 8284 journal = {Computational Materials Science}, 8285 volume = {51}, 8286 number = {1}, 8287 pages = {20--29}, 8288 year = {2012}, 8289 publisher = {Elsevier}, 8290 petsc_uses = {KSP} 8291} 8292 8293@Misc{ pylithmanual, 8294 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 8295 Strand and Charles Williams}, 8296 title = {{PyLith} User Manual Version 2.0.0}, 8297 year = {2014}, 8298 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 8299 petsc_uses = {KSP} 8300} 8301 8302@Misc{ pylith-web-page, 8303 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 8304 title = {{PyLith}}, 8305 year = {2012}, 8306 url = {http://geodynamics.org/resources/pylith/}, 8307 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 8308 petsc_uses = {KSP} 8309} 8310 8311@Misc{ galemanual, 8312 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 8313 title = {Gale User Manual Version 2.0.0}, 8314 year = {2011}, 8315 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 8316 petsc_uses = {KSP} 8317} 8318 8319@Unpublished{ underworld, 8320 author = {Louis Moresi}, 8321 title = {{UnderWorld}: A Geodynamics Modelling Code}, 8322 institution = {Monash University}, 8323 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 8324 petsc_uses = {KSP} 8325} 8326 8327@Article{ moresi2007computational, 8328 title = {Computational approaches to studying non-linear dynamics of the crust and 8329 mantle}, 8330 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 8331 M{\"u}hlhaus, H.B.}, 8332 journal = {Physics of the Earth and Planetary Interiors}, 8333 volume = {163}, 8334 number = {1-4}, 8335 pages = {69--82}, 8336 year = {2007}, 8337 publisher = {Elsevier}, 8338 petsc_uses = {KSP} 8339} 8340 8341@Article{ pitt2009chaste, 8342 title = {Chaste: a test-driven approach to software development for biological modelling}, 8343 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 8344 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 8345 and Walter, A. and others}, 8346 journal = {Computer Physics Communications}, 8347 volume = {180}, 8348 number = {12}, 8349 pages = {2452--2471}, 8350 year = {2009}, 8351 publisher = {Elsevier}, 8352 petsc_uses = {KSP} 8353} 8354 8355@Misc{ fenicsproject, 8356 title = {{The FEniCS project}}, 8357 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 8358 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 8359 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 8360 url = {http://fenicsproject.org}, 8361 year = {2011}, 8362 petsc_uses = {KSP} 8363} 8364 8365@Unpublished{ snark, 8366 title = {Snark: A suite of software for geoscientific applications and a philosophy of 8367 scientific software development}, 8368 institution = {Victorian Partnership for Advanced Computing}, 8369 url = {http://vpac.org/Snark}, 8370 petsc_uses = {KSP} 8371} 8372 8373@Misc{ imoose:sourceforge, 8374 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 8375 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 8376 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 8377 note = {[Online]}, 8378 url = {http://imoose.sourceforge.net}, 8379 petsc_uses = {KSP} 8380} 8381 8382@Unpublished{ fossi, 8383 author = {Stephan Frickenhaus}, 8384 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 8385 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 8386 codes}, 8387 institution = {AWI-Bremerhaven, Germanny}, 8388 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 8389 petsc_uses = {KSP} 8390} 8391 8392@Unpublished{ fun3dweb, 8393 author = {Dinesh Kaushik}, 8394 title = {PETSC-FUN3D Benchmark Page}, 8395 institution = {ODU/ANL}, 8396 url = {http://www.mcs.anl.gov/petsc-fun3d}, 8397 note = {CFD Benchmark of some solvers in PETSc}, 8398 petsc_uses = {KSP} 8399} 8400 8401@Unpublished{ scirun, 8402 author = {SCIRun Development Team}, 8403 title = {SCIRun}, 8404 institution = {University of Utah}, 8405 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 8406 note = {SCIRun now uses PETSc linear solvers}, 8407 petsc_uses = {KSP} 8408} 8409 8410@Misc{ prometheus, 8411 author = {Mark F. Adams}, 8412 title = {Prometheus - A scalable unstructured finite element solver}, 8413 institution = {Berkeley}, 8414 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 8415 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 8416 petsc_uses = {KSP} 8417} 8418 8419@Unpublished{ illuminator, 8420 author = {Adam C. Powell, IV}, 8421 title = {Illuminator Distributed Visualization Library}, 8422 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 8423 petsc_uses = {KSP} 8424} 8425 8426@Unpublished{ rheoplast, 8427 title = {RheoPlast Phase Field Multi-Physics Code}, 8428 author = {Adam Powell and David Dussault and Bo Zhou}, 8429 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 8430 petsc_uses = {KSP} 8431} 8432 8433@Misc{ tao-web-page, 8434 title = {{Toolkit for Advanced Optimization ({TAO})} {W}eb Page}, 8435 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8436 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 8437 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8438 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 8439 petsc_uses = {KSP} 8440} 8441 8442@TechReport{ tao-user-ref, 8443 title = {{Toolkit for Advanced Optimization ({TAO}) users manual}}, 8444 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8445 and Steve Benson and Lois Curfman McInnes}, 8446 institution = {Argonne National Laboratory}, 8447 year = {2019}, 8448 number = {ANL/MCS-TM-322 - Rev 3.12}, 8449 petsc_uses = {KSP} 8450} 8451 8452% url = "http://www.mcs.anl.gov/tao", 8453@Unpublished{ mefpp-web-page, 8454 title = {{MEF++} {W}eb {P}age}, 8455 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 8456 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 8457 author = {Eric Chamberland}, 8458 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 8459 multiphysics}, 8460 petsc_uses = {KSP} 8461} 8462 8463@Unpublished{ tipetsc-titanium, 8464 title = {Ti-PETSc - an interface to PETSc from Titanium}, 8465 institution = {Berkeley}, 8466 author = {He, Yun and Liblit, Bun and Lin, Chang}, 8467 url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=9f7959be13337c735d52e5c0b0994bdea6d75a96}, 8468 year = {1999}, 8469 petsc_uses = {KSP}, 8470} 8471 8472@Unpublished{ ptatin-web-page, 8473 title = {ptatin3d}, 8474 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 8475 url = {https://bitbucket.org/jedbrown/ptatin3d}, 8476 year = {2018}, 8477 petsc_uses = {KSP} 8478} 8479 8480@Misc{ multiphase-web-page, 8481 author = {Q. Zou}, 8482 title = {Multiphase flow with {PETSc}}, 8483 institution = {LANL}, 8484 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 8485 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 8486 lab = {LANL}, 8487 petsc_uses = {KSP} 8488} 8489 8490@Misc{ electromag-web-page, 8491 title = {{EMSolve Web} page}, 8492 institution = {LLNL}, 8493 howpublished = {http://www.llnl.gov/casc/emsolve}, 8494 url = {http://www.Llnl.gov/casc/emsolve}, 8495 author = {Daniel {White et al.}}, 8496 lab = {LLNL}, 8497 petsc_uses = {KSP} 8498} 8499 8500@Unpublished{ fe-software-web-page, 8501 institution = {Kuleuven}, 8502 title = {Finite element software}, 8503 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 8504 petsc_uses = {KSP} 8505} 8506 8507@Misc{ petsc-web-page, 8508 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8509 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 8510 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8511 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8512 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 8513 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 8514 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 8515 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 8516 Zhang}, 8517 title = {{PETS}c {W}eb page}, 8518 url = {https://petsc.org/}, 8519 howpublished = {\url{https://petsc.org/}}, 8520 year = {2024} 8521} 8522 8523@Unpublished{ petsc-debian-package, 8524 author = {Adam C. Powell, IV}, 8525 title = {Debian package for PETSc}, 8526 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 8527 petsc_uses = {KSP} 8528} 8529 8530@Unpublished{ cactus, 8531 title = {Cactus Website}, 8532 url = {http://www.cactuscode.org/}, 8533 note = {Provides two interface to the PETSc solvers}, 8534 petsc_uses = {KSP} 8535} 8536 8537@Unpublished{ petsc-fem, 8538 author = {Mario Storti and Norberto Nigro}, 8539 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 8540 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 8541 url = {http://www.cimec.org.ar/petscfem}, 8542 petsc_uses = {KSP} 8543} 8544 8545@Misc{ fidap, 8546 title = {FIDAP 8.5}, 8547 howpublished = {\url{http://www.fluent.com}}, 8548 url = {http://www.fluent.com}, 8549 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 8550 solves.}, 8551 key = {FIDAP 8.5}, 8552 petsc_uses = {KSP} 8553} 8554 8555@Unpublished{ slepc, 8556 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8557 Vicente Hern\'andez and Vicent Vidal}, 8558 title = {{SLEPc} Website}, 8559 url = {http://slepc.upv.es/}, 8560 note = {Scalable Library for Eigenvalue Problem Computations}, 8561 petsc_uses = {KSP} 8562} 8563 8564@TechReport{ slepc-users-manual, 8565 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8566 Vicente Hern\'andez and Vicent Vidal}, 8567 title = {{SLEPc} Users Manual}, 8568 number = {DISC-II/24/02}, 8569 url = {http://slepc.upv.es/}, 8570 note = {Scalable Library for Eigenvalue Problem Computations}, 8571 petsc_uses = {KSP} 8572} 8573 8574@Misc{ deal.ii, 8575 title = {deal.II}, 8576 howpublished = {\url{http://www.dealii.org}}, 8577 url = {http://www.dealii.org}, 8578 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 8579 It allows PETSc linear algebra and solvers to be used underneath.}, 8580 key = {deal.II 5.0}, 8581 petsc_uses = {KSP} 8582} 8583 8584@Article{ bangerth2007deal, 8585 title = {{deal.II---A general-purpose object-oriented finite element library}}, 8586 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 8587 journal = {ACM Transactions on Mathematical Software (TOMS)}, 8588 volume = {33}, 8589 number = {4}, 8590 pages = {24--es}, 8591 issn = {0098-3500}, 8592 year = {2007}, 8593 publisher = {ACM}, 8594 petsc_uses = {KSP} 8595} 8596 8597@Misc{ globalarrays, 8598 author = {Jarek {Nieplocha et al.}}, 8599 title = {Global Arrays}, 8600 institution = {Pacific Northwest National Laboratories}, 8601 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 8602 url = {http://www.emsl.pnl.gov/docs/global}, 8603 note = {Global arrays can use PETSc linear solvers}, 8604 lab = {PNNL}, 8605 petsc_uses = {KSP} 8606} 8607 8608% LiteralHTML: 8609% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 8610% LiteralHTML: 8611@Article{ petsccommunity2022, 8612 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 8613 Community}, 8614 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 8615 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 8616 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 8617 and Hong Zhang and Junchao Zhang}, 8618 journal = {Computing in Science and Engineering}, 8619 volume = {24}, 8620 number = {03}, 8621 pages = {6--15}, 8622 issn = {1558-366X}, 8623 doi = {10.1109/MCSE.2022.3169974}, 8624 publisher = {IEEE Computer Society}, 8625 address = {Los Alamitos, CA, USA}, 8626 month = may, 8627 year = {2022}, 8628 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 8629 petsc_uses = {KSP} 8630} 8631 8632@Article{ brownknepleysmith14, 8633 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 8634 title = {Run-time extensibility and librarization of simulation software}, 8635 journal = {IEEE Computing in Science and Engineering}, 8636 month = jan, 8637 volume = {17}, 8638 number = {1}, 8639 pages = {38--45}, 8640 doi = {10.1109/MCSE.2014.95}, 8641 year = {2015}, 8642 petsc_uses = {KSP} 8643} 8644 8645@TechReport{ ass2012, 8646 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 8647 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 8648 institution = {Argonne National Laboratory}, 8649 type = {Preprint}, 8650 year = {2012}, 8651 number = {ANL/MCS-P2011-0112}, 8652 petsc_uses = {KSP} 8653} 8654 8655@TechReport{ clearyknepley99, 8656 author = {Andrew Cleary and Matthew G. Knepley}, 8657 title = {Solvers as Operators}, 8658 institution = {Lawrence Livermore National Laboratory}, 8659 type = {Technical Report}, 8660 number = {UCRL-ID-135342}, 8661 year = {1999}, 8662 petsc_uses = {KSP} 8663} 8664 8665@TechReport{ smcabbkz2012, 8666 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 8667 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 8668 title = {{PETSc's} software strategy for the design space of composable extreme-scale 8669 solvers}, 8670 institution = {Argonne National Laboratory}, 8671 type = {Preprint}, 8672 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 8673 year = {2012}, 8674 number = {ANL/MCS-P2059-0312}, 8675 petsc_uses = {KSP} 8676} 8677 8678@InProceedings{ mhwpmhs2009, 8679 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 8680 and G. E. Hammond and B. Smith}, 8681 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 8682 Toolkit {MPI} at Scale}, 8683 booktitle = {Cray Users Group Conference}, 8684 year = {2009}, 8685 petsc_uses = {KSP} 8686} 8687 8688@InProceedings{ msmhls2010, 8689 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 8690 Lichtner and B. F. Smith}, 8691 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 8692 {BlueGene} Architectures}, 8693 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 8694 year = {2010}, 8695 petsc_uses = {KSP} 8696} 8697 8698@InCollection{ msk2013, 8699 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 8700 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 8701 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8702 series = {Lecture Notes in Earth System Sciences}, 8703 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8704 Yaolin Shi}, 8705 doi = {10.1007/978-3-642-16405-7_7}, 8706 publisher = {Springer Berlin Heidelberg}, 8707 pages = {131--140}, 8708 year = {2013}, 8709 isbn = {978-3-642-16404-0}, 8710 petsc_uses = {KSP} 8711} 8712 8713@InCollection{ knepleyyuen13, 8714 author = {Matthew G. Knepley and David A. Yuen}, 8715 title = {Why Scientists and Engineers need {GPU}s today}, 8716 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8717 series = {Lecture Notes in Earth System Sciences}, 8718 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8719 Yaolin Shi}, 8720 doi = {10.1007/978-3-642-16405-7_1}, 8721 publisher = {Springer Berlin Heidelberg}, 8722 pages = {131--140}, 8723 year = {2013}, 8724 isbn = {978-3-642-16404-0}, 8725 petsc_uses = {KSP} 8726} 8727 8728@InCollection{ karpeevknepleybrune13, 8729 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 8730 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 8731 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8732 series = {Lecture Notes in Earth System Sciences}, 8733 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8734 Yaolin Shi}, 8735 doi = {10.1007/978-3-642-16405-7_30}, 8736 publisher = {Springer Berlin Heidelberg}, 8737 pages = {487--501}, 8738 year = {2013}, 8739 isbn = {978-3-642-16404-0}, 8740 petsc_uses = {KSP} 8741} 8742 8743@InCollection{ zhengetal13, 8744 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 8745 Variable Viscosity}, 8746 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8747 Zhang and Yaolin Shi}, 8748 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8749 series = {Lecture Notes in Earth System Sciences}, 8750 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8751 Yaolin Shi}, 8752 doi = {10.1007/978-3-642-16405-7_21}, 8753 publisher = {Springer Berlin Heidelberg}, 8754 pages = {321--333}, 8755 year = {2013}, 8756 isbn = {978-3-642-16404-0}, 8757 petsc_uses = {KSP} 8758} 8759 8760@Article{ zhengetal13b, 8761 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 8762 strongly variable viscosity based on {M}atlab and {CUDA}}, 8763 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8764 Zhang and Yaolin Shi}, 8765 journal = {IJHPCA}, 8766 volume = {28}, 8767 number = {1}, 8768 pages = {50--60}, 8769 doi = {10.1177/1094342013478640}, 8770 year = {2013}, 8771 petsc_uses = {KSP} 8772} 8773 8774@InBook{ s2011, 8775 author = {B. Smith}, 8776 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 8777 title = {Encyclopedia of Parallel Computing}, 8778 bookeditor = {D. Padua}, 8779 publisher = {Springer}, 8780 year = {2011}, 8781 petsc_uses = {KSP} 8782} 8783 8784@Article{ acostamejia06, 8785 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 8786 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 8787 journal = {Lecturas Matem\'aticas}, 8788 volume = {27}, 8789 year = {2006}, 8790 pages = {213--224}, 8791 petsc_uses = {KSP} 8792} 8793 8794@InProceedings{ quenettemoresisunterappelbe07, 8795 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 8796 title = {Explaining StGermain: An aspect oriented environment for building extensible 8797 computational mechanics modeling software}, 8798 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 8799 publisher = {IEEE}, 8800 pages = {1--8}, 8801 yerar = {2007}, 8802 petsc_uses = {KSP} 8803} 8804 8805@Article{ dfm1, 8806 title = {Vectorized sparse matrix multiply for compressed row storage format}, 8807 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 8808 journal = {Lecture Notes in Computer Science}, 8809 year = {2005}, 8810 pages = {99--106}, 8811 volume = {3514}, 8812 lab = {ORNL}, 8813 petsc_uses = {KSP} 8814} 8815 8816@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 8817 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 8818 Vandewalle and Stefaan Poedts}, 8819 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 8820 Scientific Computing Software}, 8821 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 8822 year = {2005}, 8823 note = {Lecture Notes in Computer Science}, 8824 volume = {3514}, 8825 publisher = {Springer-Verlag GmbH}, 8826 petsc_uses = {KSP} 8827} 8828 8829@InProceedings{ dalcin-paz-storti, 8830 author = {L. Dalcin and R. Paz and M. Storti}, 8831 title = {Desarrollo de Aplicaciones Paralelas en Python}, 8832 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 8833 Bariloche, Argentina}, 8834 year = {2004}, 8835 petsc_uses = {KSP} 8836} 8837 8838@Article{ mpi-python, 8839 author = {L. Dalcin and R. Paz and M. Storti}, 8840 title = {MPI for Python}, 8841 journal = {Journal of Parallel and Distributed Computing}, 8842 year = {2005}, 8843 petsc_uses = {KSP} 8844} 8845 8846@Unpublished{ hrv02a, 8847 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 8848 author = {V. Hernandex and J. E. Roman and V. Vidal}, 8849 note = {Submited to VecPar 2002}, 8850 year = {2002}, 8851 petsc_uses = {KSP} 8852} 8853 8854@Article{ knyazev2007block, 8855 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 8856 {PETSc}}, 8857 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 8858 journal = {SIAM Journal on Scientific Computing}, 8859 volume = {29}, 8860 pages = {2224-2239}, 8861 doi = {10.1137/060661624}, 8862 year = {2007}, 8863 petsc_uses = {KSP} 8864} 8865 8866@MastersThesis{ aarrestad-master, 8867 author = {Asbjorn Hoiland Aarrestad}, 8868 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 8869 school = {University of Bergen}, 8870 month = aug, 8871 year = {2003}, 8872 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 8873 note = {Implemented Runge-Kutta methods using PETSc}, 8874 petsc_uses = {KSP} 8875} 8876 8877@PhDThesis{ kaushik-phd, 8878 author = {D. K. Kaushik}, 8879 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 8880 Differential Equations on Unstructured Grids}, 8881 school = {Old Dominion University}, 8882 month = dec, 8883 year = {2002}, 8884 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 8885 petsc_uses = {KSP} 8886} 8887 8888@TechReport{ rb1, 8889 author = {Rickard Bergstrom}, 8890 title = {Object Oriented Implementation of a General Finite Element Code}, 8891 number = {2002-13}, 8892 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 8893 year = {2002}, 8894 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 8895 note = {Discribes a finite element software package that uses PETSc for its solvers}, 8896 petsc_uses = {KSP} 8897} 8898 8899@InProceedings{ dbl1, 8900 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 8901 title = {A Parallel General Purpose Finite Element System}, 8902 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 8903 publisher = {SIAM}, 8904 year = {1999}, 8905 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 8906 note = {Describes software that uses PETSc for its parallel linear solves}, 8907 petsc_uses = {KSP} 8908} 8909 8910@Article{ p1, 8911 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 8912 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 8913 and B. Smith}, 8914 journal = {Parallel Computing}, 8915 year = {2002}, 8916 pages = {1811--1831}, 8917 volume = {28 (12)}, 8918 petsc_uses = {KSP} 8919} 8920 8921@Article{ automatic-ad, 8922 author = {Paul Hovland and Boyana Norris and Barry Smith}, 8923 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 8924 year = {2005}, 8925 journal = {Future Generation Computer Systems}, 8926 volume = {21}, 8927 number = {8}, 8928 pages = {1426--1438}, 8929 petsc_uses = {KSP} 8930} 8931 8932@TechReport{ remote-math, 8933 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 8934 Smith}, 8935 title = {Remote Access to Mathematical Software}, 8936 number = {ANL/MCS-P889-0601}, 8937 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8938 month = jun, 8939 year = {2001}, 8940 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 8941 petsc_uses = {KSP} 8942} 8943 8944@InProceedings{ gropp98, 8945 author = {William D. Gropp}, 8946 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 8947 publisher = {SIAM}, 8948 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8949 Scientific and Engineering Computing}, 8950 year = {1999}, 8951 pages = {21-29}, 8952 petsc_uses = {KSP} 8953} 8954 8955@InProceedings{ knepleysarin99, 8956 author = {Matthew Knepley and Vivek Sarin}, 8957 title = {Algorithm Development for Large Scale Computing}, 8958 publisher = {SIAM}, 8959 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8960 Scientific and Engineering Computing}, 8961 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}}, 8962 year = {1999}, 8963 petsc_uses = {KSP} 8964} 8965 8966@InBook{ bgms00, 8967 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8968 chapter = {Software for the Scalable Solution of {PDEs}}, 8969 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 8970 title = {CRPC Handbook of Parallel Computing}, 8971 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 8972 and A. White}, 8973 publisher = {Morgan Kaufmann Publishers}, 8974 year = {2002}, 8975 petsc_uses = {KSP} 8976} 8977 8978@InProceedings{ hovland_norris_smith98, 8979 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 8980 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 8981 Computations}, 8982 publisher = {SIAM}, 8983 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8984 Scientific and Engineering Computing}, 8985 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 8986 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 8987 year = {1999}, 8988 pages = {129-137}, 8989 petsc_uses = {KSP} 8990} 8991 8992@InProceedings{ efficient, 8993 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 8994 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 8995 Libraries}, 8996 booktitle = {Modern Software Tools in Scientific Computing}, 8997 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 8998 publisher = {Birkhauser Press}, 8999 pages = {163--202}, 9000 year = {1997}, 9001 petsc_uses = {KSP} 9002} 9003 9004% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 9005@TechReport{ petsc-user-ref, 9006 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 9007 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 9008 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 9009 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 9010 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 9011 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 9012 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 9013 and Barry~F. Smith and Hansol Suh and Stefano Zampini and Hong Zhang and Hong Zhang 9014 and Junchao Zhang}, 9015 title = {{PETSc/TAO} Users Manual}, 9016 institution = {Argonne National Laboratory}, 9017 number = {ANL-21/39 - Revision 3.22}, 9018 doi = {10.2172/2205494}, 9019 year = {2024} 9020} 9021 9022% url = {https://petsc.org/release} 9023@TechReport{ petsc-developers, 9024 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 9025 title = {{PETS}c Developers Guide}, 9026 institution = {Argonne National Laboratory}, 9027 number = {ANL-18/18}, 9028 year = {2018}, 9029 url = {https://petsc.org/release/developers}, 9030 petsc_uses = {KSP} 9031} 9032 9033@Unpublished{ alice-memory-snooper, 9034 author = {Ibrahima Ba and Barry~F. Smith}, 9035 title = {The {ALICE} Memory Snooper}, 9036 year = {1999}, 9037 petsc_uses = {KSP} 9038} 9039 9040@TechReport{ petsc-user-ref-polish, 9041 author = {Marcin Bojko and Piotr Krzyzanowski}, 9042 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 9043 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 9044 year = {1998}, 9045 note = {An introduction to PETSc in Polish}, 9046 petsc_uses = {KSP} 9047} 9048 9049@InProceedings{ abghmn00, 9050 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 9051 High-Performance Scientific Computing}, 9052 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 9053 Norris}, 9054 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 9055 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 9056 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 9057 Hasco\"{e}t and Uwe Naumann}, 9058 publisher = {Springer}, 9059 year = {2002}, 9060 petsc_uses = {KSP} 9061} 9062 9063@Unpublished{ petsc-mpi-paper, 9064 author = {Lois Curfman McInnes and Barry F. Smith}, 9065 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 9066 Libraries}, 9067 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 9068 month = jun, 9069 year = {1995}, 9070 petsc_uses = {KSP} 9071} 9072 9073@InProceedings{ miss-paper, 9074 author = {William D. Gropp and Barry F. Smith}, 9075 title = {Scalable, Extensible, and Portable Numerical Libraries}, 9076 publisher = {IEEE}, 9077 year = {1994}, 9078 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 9079 address = {Mississippi State University}, 9080 pages = {87--93}, 9081 keyword = {numerical libraries, scientific computing, parallel computing}, 9082 petsc_uses = {KSP} 9083} 9084 9085@InProceedings{ snes-paper, 9086 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 9087 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 9088 Minimization Problems}, 9089 publisher = {IEEE}, 9090 year = {1995}, 9091 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 9092 address = {Mississippi State University}, 9093 pages = {60-67}, 9094 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 9095 petsc_uses = {KSP} 9096} 9097 9098@Article{ dsneutral, 9099 author = {Barry F. Smith and William D. Gropp}, 9100 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 9101 Sparse Linear Systems}, 9102 journal = {Scientific Programming}, 9103 volume = {5}, 9104 pages = {329--336}, 9105 key = {GroppSmith96 ! KSP design}, 9106 year = {1996}, 9107 petsc_uses = {KSP} 9108} 9109 9110@InProceedings{ bgms98, 9111 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 9112 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 9113 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 9114 Scientific and Engineering Computing}, 9115 publisher = {SIAM}, 9116 pages = {58-67}, 9117 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 9118 year = {1998}, 9119 petsc_uses = {KSP} 9120} 9121 9122@Article{ hkm98, 9123 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 9124 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 9125 {PDE} Computation}, 9126 journal = {Advances in Engineering Software}, 9127 volume = {29}, 9128 pages = {415-424}, 9129 year = {1998}, 9130 petsc_uses = {KSP} 9131} 9132 9133@TechReport{ pdpta99, 9134 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 9135 Smith}, 9136 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 9137 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 9138 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 9139 Vegas, Nevada}, 9140 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 9141 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 9142 number = {ANL/MCS-P751-0599}, 9143 year = {1999}, 9144 petsc_uses = {KSP} 9145} 9146 9147@InProceedings{ bbh:com, 9148 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 9149 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 9150 Computing}}, 9151 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 9152 Euro-Par Conference, Munich, Germany, August/September 2000}, 9153 year = {2000}, 9154 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 9155 volume = {1900}, 9156 series = {Lecture Notes in Computer Science}, 9157 pages = {86--94}, 9158 address = {Berlin}, 9159 publisher = {Springer}, 9160 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 9161 petsc_uses = {KSP} 9162} 9163 9164@InProceedings{ overture00, 9165 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 9166 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 9167 Components}, 9168 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 9169 booktitle = {Proceedings of the International Federation for Information Processing Working 9170 Conference on Software Architectures for Scientific Computing, Kluwer}, 9171 year = {2000}, 9172 pages = {57--68}, 9173 petsc_uses = {KSP} 9174} 9175 9176@TechReport{ smith97, 9177 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 9178 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 9179 number = {ANL/MCS-P701}, 9180 author = {Barry F. Smith}, 9181 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 9182 petsc_uses = {KSP} 9183} 9184 9185@Article{ smith98, 9186 author = {Barry Smith}, 9187 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 9188 journal = {SIGNUM Newsletter}, 9189 year = {1998}, 9190 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 9191 petsc_uses = {KSP} 9192} 9193 9194@TechReport{ ad-petsc-tm, 9195 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 9196 {PETSc}}, 9197 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 9198 year = {1997}, 9199 type = {Technical Memorandum}, 9200 institution = {ANL}, 9201 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 9202 number = {ANL/MCS-TM-233}, 9203 petsc_uses = {KSP} 9204} 9205 9206% LiteralHTML: 9207% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 9208% LiteralHTML: 9209@PhDThesis{ klotzthesis2019, 9210 author = {Thomas S. Klotz}, 9211 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 9212 Biology}, 9213 school = {Rice University}, 9214 year = {2019}, 9215 petsc_uses = {KSP} 9216} 9217 9218@Article{ klotzbardhanknepley2018, 9219 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 9220 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 9221 journal = {arXiv e-prints}, 9222 eprint = {1708.06028}, 9223 archiveprefix = {arXiv}, 9224 primaryclass = {math.na}, 9225 year = {2018}, 9226 note = {\url{http://arxiv.org/abs/1708.06028}}, 9227 petsc_uses = {KSP} 9228} 9229 9230@Misc{ brown2016, 9231 title = {Threading Tradeoffs in Domain Decomposition}, 9232 author = {Jed Brown}, 9233 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 9234 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 9235 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 9236 year = {2016}, 9237 petsc_uses = {KSP} 9238} 9239 9240@Article{ changnakshatralaknepleyjohnsson2017, 9241 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 9242 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 9243 Johnsson}, 9244 journal = {Concurency: Practice and Experience}, 9245 volume = {30}, 9246 number = {11}, 9247 eprint = {1705.03625}, 9248 doi = {10.1002/cpe.4401}, 9249 year = {2017}, 9250 petsc_uses = {KSP} 9251} 9252 9253@Article{ changfabienknepleymills2018, 9254 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 9255 spectrum analysis}, 9256 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 9257 journal = {SIAM Journal on Scientific Computing}, 9258 volume = {40}, 9259 number = {6}, 9260 pages = {C779--C802}, 9261 eprint = {1802.07832}, 9262 doi = {10.1137/18M1172260}, 9263 year = {2018}, 9264 petsc_uses = {KSP} 9265} 9266 9267@Article{ joshaghanichangnakshatralaknepley2019, 9268 title = {Composable solvers for the four-field double porosity/permeability model}, 9269 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 9270 Knepley}, 9271 journal = {Journal of Computational Physics}, 9272 volume = {386}, 9273 pages = {428--466}, 9274 doi = {10.1016/j.jcp.2019.02.020}, 9275 year = {2019}, 9276 petsc_uses = {KSP} 9277} 9278 9279@InProceedings{ barralknepleylangepiggottgorman2016, 9280 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 9281 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 9282 and Gerard J. Gorman}, 9283 booktitle = {25th International Meshing Roundtable}, 9284 editor = {Steve Owen and Hang Si}, 9285 month = sep, 9286 address = {Washington, DC}, 9287 pages = {1--5}, 9288 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 9289 year = {2016}, 9290 petsc_uses = {KSP} 9291} 9292 9293@Article{ adamsbrownknepleysamtaney2016, 9294 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 9295 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 9296 journal = {SIAM Journal on Scientific Computing}, 9297 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 9298 epub = {http://arxiv.org/abs/1406.7808}, 9299 volume = {8}, 9300 number = {4}, 9301 pages = {C426--C440}, 9302 doi = {10.1137/140975127}, 9303 year = {2016}, 9304 petsc_uses = {KSP} 9305} 9306 9307@InProceedings{ maysananruppknepleysmith2016, 9308 title = {Extreme-Scale Multigrid Components within {PETSc}}, 9309 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 9310 Smith}, 9311 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 9312 series = {PASC '16}, 9313 isbn = {978-1-4503-4126-4}, 9314 location = {Lausanne, Switzerland}, 9315 pages = {5:1--5:12}, 9316 articleno = {5}, 9317 numpages = {12}, 9318 doi = {10.1145/2929908.2929913}, 9319 acmid = {2929913}, 9320 publisher = {ACM}, 9321 address = {New York, NY, USA}, 9322 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 9323 preconditioning}, 9324 year = {2016}, 9325 petsc_uses = {KSP} 9326} 9327 9328@Article{ liu2015field, 9329 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 9330 author = {Lulu Liu and David E Keyes}, 9331 journal = {SIAM Journal on Scientific Computing}, 9332 volume = {37}, 9333 number = {3}, 9334 pages = {A1388--A1409}, 9335 year = {2015}, 9336 publisher = {SIAM}, 9337 petsc_uses = {KSP} 9338} 9339 9340@Article{ lujiaomissirlis2014, 9341 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 9342 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 9343 journal = {Numerical Linear Algebra with Applications}, 9344 volume = {21}, 9345 number = {2}, 9346 pages = {221--238}, 9347 year = {2014}, 9348 publisher = {Wiley Online Library}, 9349 petsc_uses = {KSP} 9350} 9351 9352@Article{ badiamartinprincipe2013, 9353 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 9354 solid mechanics}, 9355 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 9356 journal = {International Journal for Numerical Methods in Engineering}, 9357 volume = {96}, 9358 number = {4}, 9359 pages = {203--230}, 9360 year = {2013}, 9361 petsc_uses = {KSP} 9362} 9363 9364@Article{ morganknepleysananscott2016, 9365 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 9366 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 9367 journal = {Concurrency and Computation: Practice and Experience}, 9368 volume = {28}, 9369 pages = {4532--4542}, 9370 year = {2016}, 9371 url = {http://arxiv.org/abs/1602.04873}, 9372 doi = {10.1002/cpe.3820}, 9373 petsc_uses = {KSP} 9374} 9375 9376@Article{ morgansananknepleymills2020, 9377 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 9378 solvers}, 9379 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 9380 journal = {The International Journal of High Performance Computing Applications}, 9381 volume = {35}, 9382 issue = {1}, 9383 doi = {10.1177/1094342020966835}, 9384 url = {https://doi.org/10.1177/1094342020966835}, 9385 eprint = {https://doi.org/10.1177/1094342020966835}, 9386 year = {2020}, 9387 petsc_uses = {KSP} 9388} 9389 9390@Article{ msz2013, 9391 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 9392 author = {M. McCourt and B. F. Smith and H. Zhang}, 9393 journal = {SIAM Journal on Matrix Analysis and Applications}, 9394 year = {2015}, 9395 note = {To appear}, 9396 petsc_uses = {KSP} 9397} 9398 9399@Article{ bassi2014agglomeration, 9400 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 9401 free}, 9402 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 9403 journal = {Mathematical Models and Methods in Applied Sciences}, 9404 volume = {24}, 9405 number = {08}, 9406 pages = {1495--1539}, 9407 year = {2014}, 9408 publisher = {World Scientific}, 9409 petsc_uses = {KSP} 9410} 9411 9412@Article{ jhuranidemkowicz12, 9413 author = {{Jhurani}, C. and {Demkowicz}, L.}, 9414 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 9415 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 9416 journal = {Computer Methods in Applied Mechanics and Engineering}, 9417 volume = {213}, 9418 pages = {418-426}, 9419 year = {2012}, 9420 month = mar, 9421 doi = {10.1016/j.cma.2011.06.003}, 9422 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 9423 petsc_uses = {KSP} 9424} 9425 9426@Article{ yangcai11, 9427 author = {Yang, Haijian and Cai, Xiao-Chuan}, 9428 title = {Parallel Two-Grid Semismooth {N}ewton--{K}rylov--{S}chwarz Method for Nonlinear 9429 Complementarity Problems}, 9430 journal = {J. Sci. Comput.}, 9431 issue_date = {May 2011}, 9432 volume = {47}, 9433 number = {2}, 9434 month = may, 9435 pages = {258--280}, 9436 year = {2011}, 9437 issn = {0885-7474}, 9438 numpages = {23}, 9439 doi = {10.1007/s10915-010-9436-4}, 9440 acmid = {1971246}, 9441 publisher = {Plenum Press}, 9442 address = {New York, NY, USA}, 9443 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 9444 preconditioners, Semismooth Newton, Two-level methods}, 9445 petsc_uses = {KSP} 9446} 9447 9448@Article{ rheinbach09, 9449 author = {Rheinbach, Oliver}, 9450 title = {Parallel Iterative Substructuring in Structural Mechanics}, 9451 journal = {Archives of Computational Methods in Engineering}, 9452 volume = {16}, 9453 number = {4}, 9454 pages = {425-463}, 9455 year = {2009}, 9456 issn = {1134-3060}, 9457 doi = {10.1007/s11831-009-9035-4}, 9458 publisher = {Springer Netherlands}, 9459 language = {English}, 9460 petsc_uses = {KSP} 9461} 9462 9463@Article{ knepleyterrel2013, 9464 author = {Matthew G. Knepley and Andy R. Terrel}, 9465 title = {Finite Element Integration on {GPUs}}, 9466 journal = {{ACM} Transactions on Mathematical Software}, 9467 volume = {39}, 9468 number = {2}, 9469 accepted = {17 April 2012}, 9470 year = {2013}, 9471 abstract = {We present a novel finite element integration method for low order elements on 9472 GPUs. We achieve more than 100GF for element integration on first order 9473 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 9474 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 9475 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 9476 url = {http://arxiv.org/abs/1103.0066}, 9477 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 9478 petsc_uses = {KSP} 9479} 9480 9481@Article{ knepleyruppterrel2016, 9482 title = {Finite Element Integration with Quadrature on the GPU}, 9483 journal = {ArXiv e-prints}, 9484 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 9485 version = {1}, 9486 date = {2016-07-14}, 9487 eprinttype = {arxiv}, 9488 eprintclass = {cs.MS}, 9489 eprint = {1607.04245v1}, 9490 petsc_uses = {KSP} 9491} 9492 9493@Article{ klawonnlanserrheinbach2014, 9494 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 9495 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 9496 journal = {SIAM Journal on Scientific Computing}, 9497 volume = {36}, 9498 number = {2}, 9499 pages = {A737--A765}, 9500 year = {2014}, 9501 petsc_uses = {KSP} 9502} 9503 9504@Article{ bruneknepleysmithtu15, 9505 title = {Composing Scalable Nonlinear Algebraic Solvers}, 9506 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 9507 journal = {SIAM Review}, 9508 volume = {57}, 9509 number = {4}, 9510 pages = {535--565}, 9511 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 9512 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 9513 doi = {10.1137/130936725}, 9514 year = {2015}, 9515 petsc_uses = {KSP} 9516} 9517 9518@Article{ mszm2014, 9519 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 9520 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9521 volume = {40}, 9522 pages = {17--31}, 9523 year = {2014}, 9524 journal = {Parallel Computing}, 9525 doi = {10.1016/j.parco.2013.10.001}, 9526 petsc_uses = {KSP} 9527} 9528 9529@TechReport{ mszm2012, 9530 title = {Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing}, 9531 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9532 year = {2012}, 9533 number = {ANL/MCS-P2097-0512}, 9534 institution = {Argonne National Laboratory}, 9535 petsc_uses = {KSP} 9536} 9537 9538@InProceedings{ bkmms2012, 9539 author = {Jed Brown and Matthew Knepley and David A. May and Lois C. McInnes and Barry 9540 F. Smith}, 9541 title = {Composable linear solvers for multiphysics}, 9542 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 9543 Computing} ({ISPDC} 2012)}, 9544 year = {2012}, 9545 doi = {10.1109/ISPDC.2012.16}, 9546 publisher = {IEEE Computer Society}, 9547 pages = {55--62}, 9548 petsc_uses = {KSP} 9549} 9550 9551@Article{ bourdinbucuroudet2009, 9552 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 9553 title = {Optimal Partitions for Eigenvalues}, 9554 journal = {SIAM J. Sci. Comput.}, 9555 volume = {31}, 9556 number = {6}, 9557 pages = {4100--4114}, 9558 year = {2009}, 9559 petsc_uses = {KSP} 9560} 9561 9562@InBook{ kimnbourdin2007, 9563 author = {J.-H. Kimn and Blaise Bourdin}, 9564 title = {Numerical implementation of overlapping balancing domain decomposition methods on 9565 unstructured meshes}, 9566 editor = {O. B. Widlund and D. E. Keyes}, 9567 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 9568 series = {Lecture Notes in Computational Science and Engineering}, 9569 number = {55}, 9570 publisher = {Springer-Verlag}, 9571 pages = {309--315}, 9572 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 9573 year = {2007}, 9574 petsc_uses = {KSP} 9575} 9576 9577@Article{ bjm2005, 9578 author = {AH Baker and ER Jessup and T Manteuffel}, 9579 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 9580 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 9581 year = {2005}, 9582 petsc_uses = {KSP} 9583} 9584 9585@Unpublished{ sundar-2008a, 9586 author = {R.S. Sampath and G. Biros}, 9587 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 9588 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9589 petsc_uses = {KSP} 9590} 9591 9592@Article{ sundar-2008, 9593 author = {H. Sundar and R.S. Sampath and G. Biros}, 9594 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 9595 journal = {SIAM Journal on Scientific Computing}, 9596 year = {2008}, 9597 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9598 petsc_uses = {KSP} 9599} 9600 9601@InProceedings{ sundar-2007, 9602 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 9603 title = {Low-constant parallel algorithms for finite element simulations using linear 9604 octrees}, 9605 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 9606 year = {2007}, 9607 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9608 petsc_uses = {KSP} 9609} 9610 9611@InProceedings{ adams-98a, 9612 author = {Adams, Mark ~F.}, 9613 title = {A Parallel Maximal Independent Set Algorithm}, 9614 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 9615 year = {1998}, 9616 petsc_uses = {KSP} 9617} 9618 9619@Article{ akcelik2005ddd, 9620 title = {{Dynamic data-driven inversion for terascale simulations: real-time 9621 identification of airborne contaminants}}, 9622 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 9623 van Bloemen Waanders, B.}, 9624 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 9625 year = {2005}, 9626 publisher = {IEEE Computer Society Washington, DC, USA}, 9627 petsc_uses = {KSP} 9628} 9629 9630@InBook{ akcelik-2006, 9631 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 9632 Bloemen Waanders}, 9633 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 9634 title = {Frontiers of Parallel Computing}, 9635 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 9636 publisher = {SIAM}, 9637 year = {2006}, 9638 petsc_uses = {KSP} 9639} 9640 9641@Article{ dt, 9642 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 9643 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 9644 Convection Diffusion Equations}, 9645 journal = {The Journal of Supercomputing}, 9646 year = {2004}, 9647 pages = {235--253}, 9648 volume = {28}, 9649 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 9650 petsc_uses = {KSP} 9651} 9652 9653@PhDThesis{ hwang2004, 9654 author = {Feng-Nan Hwang}, 9655 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 9656 Computational Fluid Dynamics}, 9657 school = {University of Colorado at Boulder}, 9658 year = {2004}, 9659 petsc_uses = {KSP} 9660} 9661 9662@PhDThesis{ baker, 9663 author = {{A. H.} Baker}, 9664 title = {On improving the performance of the linear solver restarted {GMRES}}, 9665 school = {University of Colorado at Boulder}, 9666 year = {2003}, 9667 petsc_uses = {KSP} 9668} 9669 9670@TechReport{ klawonnrheinbach601, 9671 author = {Axel Klawonn and Oliver Rheinbach}, 9672 title = {A Parallel Implementation of Dual-Primal {FETI-DP} Methods for Three Dimensional 9673 Linear Elasticity Using a Transformation of Basis}, 9674 institution = {Universit\"at Duisburg-Essen}, 9675 year = {2005}, 9676 type = {Technical Report}, 9677 number = {SM-E-601}, 9678 petsc_uses = {KSP} 9679} 9680 9681@TechReport{ klawonnrheinbach609, 9682 author = {Axel Klawonn and Oliver Rheinbach}, 9683 title = {Inexact FETI-DP Methods}, 9684 institution = {Universit\"at Duisburg-Essen}, 9685 year = {2005}, 9686 type = {Technical Report}, 9687 number = {SM-E-609}, 9688 petsc_uses = {KSP} 9689} 9690 9691@TechReport{ klawonnrheinbach607, 9692 author = {Axel Klawonn and Oliver Rheinbach}, 9693 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 9694 institution = {Universit\"at Duisburg-Essen}, 9695 year = {2005}, 9696 type = {Technical Report}, 9697 number = {SM-E-607}, 9698 petsc_uses = {KSP} 9699} 9700 9701@Article{ kul-natraj-pbp, 9702 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 9703 title = {Performance of a parallel mixed finite element implementation for fourth order 9704 clamped anisotropic plate bending problems in distributed memory environments}, 9705 journal = {Applied Mathematics and Computation}, 9706 volume = {155}, 9707 year = {2004}, 9708 number = {3}, 9709 pages = {753--777}, 9710 petsc_uses = {KSP} 9711} 9712 9713@Article{ bramkamp2006uej, 9714 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 9715 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 9716 journal = {Computers \& Fluids}, 9717 volume = {35}, 9718 number = {10}, 9719 pages = {1063--1073}, 9720 doi = {10.1016/j.compfluid.2005.10.003}, 9721 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 9722 derivation of the analytic flux Jacobian can become quite complicated depending on 9723 the complexity of the numerical flux calculation. Practically, the derivation of 9724 the exact Jacobian by hand is an unrealistic option because of the enormous 9725 man-hour investment needed. In this work, automatic differentiation is used to 9726 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 9727 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 9728 approximated by first-order forward differences. For a two-dimensional airfoil 9729 under three different flight conditions (quasi-incompressible flow, compressible 9730 subsonic flow, and transonic flow), we show that the robustness and performance of 9731 the present finite volume scheme is significantly improved by using exact 9732 Jacobians.}, 9733 year = {2006}, 9734 petsc_uses = {KSP} 9735} 9736 9737@Article{ shahbazi1, 9738 author = {Khosro Shahbazi}, 9739 title = {An explicit expression for the penalty parameter of the interior penalty method}, 9740 journal = {Journal of Computational Physics}, 9741 volume = {205}, 9742 year = {2005}, 9743 pages = {401--407}, 9744 petsc_uses = {KSP} 9745} 9746 9747@TechReport{ kk, 9748 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 9749 author = {Hans-Peter Kersken and Uwe Kuster}, 9750 year = {1999}, 9751 institution = {University of Stuttgart}, 9752 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 9753 number = {310}, 9754 petsc_uses = {KSP} 9755} 9756 9757@Article{ miha-mija, 9758 author = {M. D. Mihajlovi and S. Mijalkovi}, 9759 title = {A component decomposition preconditioning for 3D stress analysis problems}, 9760 journal = {Numerical Linear Algebra with Applications}, 9761 volume = {9}, 9762 year = {2002}, 9763 pages = {567--583}, 9764 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 9765 petsc_uses = {KSP} 9766} 9767 9768@Article{ bjm, 9769 author = {M Benzi and W Joubert and G Mateescu}, 9770 journal = {Electronic Transactions on Numerical Analysis}, 9771 year = {1999}, 9772 volume = {8}, 9773 pages = {88--114}, 9774 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 9775 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}, 9776 petsc_uses = {KSP} 9777} 9778 9779@PhDThesis{ hyde, 9780 author = {EMK Hyde}, 9781 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 9782 school = {Caltech}, 9783 year = {2003}, 9784 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 9785 petsc_uses = {KSP} 9786} 9787 9788@Article{ km2003, 9789 author = {A. Keese and H. G. Matthies}, 9790 journal = {Proceedings in Applied Mathematics and Mechanics}, 9791 year = {2003}, 9792 volume = {2}, 9793 pages = {485--486}, 9794 title = {Parallel Solution of Stochastic PDEs}, 9795 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 9796 petsc_uses = {KSP} 9797} 9798 9799@Article{ whszss, 9800 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 9801 and Otmar Scherzer and H. Siegfried Stiehl}, 9802 journal = {Real Time Imaging}, 9803 year = {2001}, 9804 volume = {7}, 9805 pages = {31--45}, 9806 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 9807 approaches}, 9808 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 9809 petsc_uses = {KSP} 9810} 9811 9812@TechReport{ baker1, 9813 title = {An Efficient Block Variant of GMRES}, 9814 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 9815 year = {2003}, 9816 type = {Technical Report}, 9817 institution = {University of Colorado, Boulder}, 9818 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 9819 number = {CU-CS-957-03}, 9820 petsc_uses = {KSP} 9821} 9822 9823@InProceedings{ mc2003, 9824 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 9825 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 9826 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9827 Methods}, 9828 pages = {639--646}, 9829 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9830 note = {}, 9831 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9832 year = {2003}, 9833 petsc_uses = {KSP} 9834} 9835 9836@InProceedings{ kt2003, 9837 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 9838 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 9839 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9840 Methods}, 9841 pages = {615--622}, 9842 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9843 note = {}, 9844 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9845 year = {2003}, 9846 petsc_uses = {KSP} 9847} 9848 9849@InProceedings{ krw2003, 9850 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 9851 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 9852 3D}, 9853 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9854 Methods}, 9855 pages = {361--368}, 9856 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9857 note = {}, 9858 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9859 year = {2003}, 9860 petsc_uses = {KSP} 9861} 9862 9863@InProceedings{ hc2003, 9864 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 9865 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 9866 Nonlinear Preconditioning}, 9867 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9868 Methods}, 9869 pages = {201--208}, 9870 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9871 note = {}, 9872 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9873 year = {2003}, 9874 petsc_uses = {KSP} 9875} 9876 9877@InProceedings{ g2003, 9878 author = {P. Goldfeld}, 9879 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 9880 (Generalized) {Stokes} and Parallel Implementation}, 9881 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9882 Methods}, 9883 pages = {209--216}, 9884 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9885 publisher = {National Autonomous University of Mexico (UNAM)}, 9886 note = {}, 9887 url = {http://www.ddm.org/DD14}, 9888 year = {2003}, 9889 petsc_uses = {KSP} 9890} 9891 9892@InProceedings{ dhv2003, 9893 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 9894 title = {Toward scalable {FETI} algorithm for variational inequalities with applications to 9895 composites}, 9896 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9897 Methods}, 9898 pages = {395--401}, 9899 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9900 publisher = {National Autonomous University of Mexico (UNAM)}, 9901 note = {}, 9902 url = {http://www.ddm.org/DD14}, 9903 year = {2003}, 9904 petsc_uses = {KSP} 9905} 9906 9907@InProceedings{ dhsv2002, 9908 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9909 title = {Scalabilities of {FETI} for variational inequalities and contact shape 9910 optimization}, 9911 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9912 Methods}, 9913 pages = {359--367}, 9914 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9915 publisher = {CIMNE, Barcelona, Spain}, 9916 note = {}, 9917 url = {http://www.ddm.org/DD13}, 9918 year = {2002}, 9919 petsc_uses = {KSP} 9920} 9921 9922@InProceedings{ cky2002, 9923 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 9924 title = {A Nonlinear Additive {S}chwarz Preconditioned Inexact {N}ewton Method for Shocked 9925 Duct Flows}, 9926 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9927 Methods}, 9928 pages = {343--350}, 9929 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9930 publisher = {CIMNE, Barcelona, Spain}, 9931 note = {}, 9932 url = {http://www.ddm.org/DD13}, 9933 year = {2002}, 9934 petsc_uses = {KSP} 9935} 9936 9937@Conference{ li-etal:03, 9938 author = {Li, Z. and Lanteri S. and Saad, Y.}, 9939 title = {Multiplicative-additive preconditioning combination for general sparse linear 9940 systems}, 9941 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 9942 Matrix Problems in Scientific and Industrial Applications}, 9943 address = {Napa, California, USA}, 9944 date = {october 27-29}, 9945 year = {2003}, 9946 petsc_uses = {KSP} 9947} 9948 9949@Article{ bashir2008hessian, 9950 title = {Hessian-based model reduction for large-scale systems with initial-condition 9951 inputs}, 9952 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 9953 J.}, 9954 journal = {International journal for numerical methods in engineering}, 9955 volume = {73}, 9956 number = {6}, 9957 pages = {844--868}, 9958 year = {2008}, 9959 publisher = {Wiley Online Library}, 9960 petsc_uses = {KSP} 9961} 9962 9963@Article{ bashir2007hessian, 9964 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 9965 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 9966 K.}, 9967 journal = {Computational Science--ICCS 2007}, 9968 pages = {1010--1017}, 9969 year = {2007}, 9970 publisher = {Springer}, 9971 petsc_uses = {KSP} 9972} 9973 9974@Article{ akcelik2011fast, 9975 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 9976 inverse problems based on low-rank partial {H}essian approximations}, 9977 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 9978 Waanders, B. and Wilcox, L.}, 9979 journal = {SIAM Journal on Scientific Computing}, 9980 volume = {33}, 9981 number = {1}, 9982 year = {2011}, 9983 petsc_uses = {KSP} 9984} 9985 9986@InProceedings{ ff2003, 9987 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 9988 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 9989 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 9990 year = {2003}, 9991 petsc_uses = {KSP} 9992} 9993 9994@InProceedings{ d2b2004, 9995 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 9996 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 9997 Ordering Strategies}, 9998 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 9999 year = {2004}, 10000 petsc_uses = {KSP} 10001} 10002 10003@InProceedings{ d2v2005, 10004 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 10005 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 10006 Flow Equations}, 10007 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 10008 year = {2005}, 10009 petsc_uses = {KSP} 10010} 10011 10012@InProceedings{ dvs2006, 10013 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 10014 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 10015 Mixed Convection Equations}, 10016 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 10017 year = {2006}, 10018 petsc_uses = {KSP} 10019} 10020 10021@Article{ dsv2006, 10022 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 10023 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 10024 Flow Equations}, 10025 journal = {Computational Fluid Dynamics}, 10026 year = {2006}, 10027 volume = {15}, 10028 number = {1}, 10029 petsc_uses = {KSP} 10030} 10031 10032@Article{ lahaye03, 10033 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 10034 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 10035 journal = {J. Comput. Appl. Math.}, 10036 year = {2004}, 10037 pages = {267--275}, 10038 volume = {168}, 10039 petsc_uses = {KSP} 10040} 10041 10042@TechReport{ brmn, 10043 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 10044 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 10045 year = {2002}, 10046 type = {Technical Report}, 10047 institution = {ANL}, 10048 number = {ANL/MCS-P993-0902}, 10049 note = {To appear in Future Generation Computer Systems}, 10050 petsc_uses = {KSP} 10051} 10052 10053@InProceedings{ mnbr, 10054 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 10055 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 10056 Algorithms}, 10057 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 10058 Mechanics}, 10059 year = {2003}, 10060 petsc_uses = {KSP} 10061} 10062 10063@InProceedings{ bmnr, 10064 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 10065 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 10066 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 10067 Applications, Lecture notes in Computer Science 2677}, 10068 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 10069 pages = {828--839}, 10070 year = {2003}, 10071 petsc_uses = {KSP} 10072} 10073 10074@Article{ ph03, 10075 author = {M. Pernice and R. D. Hornung}, 10076 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 10077 journal = {Computing and Visualization in Science}, 10078 year = {2003}, 10079 lab = {LANL}, 10080 petsc_uses = {KSP} 10081} 10082 10083@Article{ adams-02, 10084 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 10085 journal = {J. Comp. Phys.}, 10086 number = {2}, 10087 pages = {593-610}, 10088 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 10089 volume = {188}, 10090 year = {2003}, 10091 petsc_uses = {KSP} 10092} 10093 10094@InProceedings{ adams2001distributed, 10095 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 10096 smoothers}, 10097 author = {Adams, M.F.}, 10098 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 10099 pages = {14--14}, 10100 year = {2001}, 10101 organization = {IEEE}, 10102 petsc_uses = {KSP} 10103} 10104 10105@PhDThesis{ els01, 10106 author = {Ulrich Elsner}, 10107 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 10108 algorithms}, 10109 school = {Technical University Chemnitz}, 10110 year = {2002}, 10111 publisher = {Logos Verlag, Berlin}, 10112 isbn = {3-89722-923-4}, 10113 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 10114 different graph partitioning algorithms}, 10115 petsc_uses = {KSP} 10116} 10117 10118@TechReport{ ckk02, 10119 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 10120 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 10121 year = {2002}, 10122 type = {Technical Report}, 10123 institution = {ODU}, 10124 url = {http://www.math.odu.edu/\~{ }keyes}, 10125 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 10126 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 10127 Methods}, 10128 petsc_uses = {KSP} 10129} 10130 10131@Article{ gpw2002, 10132 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 10133 Heterogeneous Problems in Linear Elasticity}, 10134 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 10135 year = {2003}, 10136 pages = {283--324}, 10137 volume = {95}, 10138 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 10139 journal = {Numerische Mathematik}, 10140 petsc_uses = {KSP} 10141} 10142 10143@Article{ dh1, 10144 title = {Scalability and FETI based algorithm for large discretized variational 10145 inequalities}, 10146 author = {Z Dostal and D Horak}, 10147 year = {2003}, 10148 pages = {347--357}, 10149 volume = {61}, 10150 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 10151 journal = {Mathematics and Computers in Simulation}, 10152 petsc_uses = {KSP} 10153} 10154 10155@InProceedings{ dhsv1, 10156 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 10157 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 10158 title = {36 Scalabilities of {FETI} for Variational Inequalities and Contact Shape 10159 Optimization}, 10160 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 10161 Methods}, 10162 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10163 Kuznetsov}, 10164 petsc_uses = {KSP} 10165} 10166 10167@Article{ lahaye02, 10168 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 10169 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 10170 journal = {IEEEMAGN}, 10171 year = {2002}, 10172 volume = {38}, 10173 number = {2}, 10174 pages = {413-416}, 10175 petsc_uses = {KSP} 10176} 10177 10178@Article{ ckm01, 10179 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 10180 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 10181 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 10182 fluid dynamics}, 10183 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 10184 year = {2002}, 10185 volume = {40}, 10186 pages = {1463--1470}, 10187 petsc_uses = {KSP} 10188} 10189 10190@InProceedings{ cky01, 10191 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 10192 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 10193 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 10194 duct flow}, 10195 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 10196 Methods}, 10197 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10198 Kuznetsov}, 10199 year = {2002}, 10200 petsc_uses = {KSP} 10201} 10202 10203@Article{ ck02, 10204 author = {X.-C. Cai and D. E. Keyes}, 10205 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 10206 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 10207 journal = {SIAM J. Sci. Comput.}, 10208 year = {2002}, 10209 pages = {183--200}, 10210 volume = {24}, 10211 petsc_uses = {KSP} 10212} 10213 10214@Article{ c04, 10215 author = {Feng-Nan Hwang and X.-C. Cai}, 10216 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 10217 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 10218 for incompressible {Navier-Stokes} equations}, 10219 journal = {Journal of Computational Physics}, 10220 year = {2005}, 10221 volume = {204}, 10222 pages = {666--691}, 10223 petsc_uses = {KSP} 10224} 10225 10226@Article{ hc06, 10227 author = {Feng-Nan Hwang and X.-C. Cai}, 10228 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 10229 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 10230 Algorithms}, 10231 journal = {Computer Methods in Applied Mechanics and Engineering}, 10232 year = {2006}, 10233 volume = {196}, 10234 pages = {1603--1611}, 10235 petsc_uses = {KSP} 10236} 10237 10238@InProceedings{ adams-01, 10239 author = {Mark F. Adams}, 10240 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 10241 Smoothers}, 10242 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 10243 address = {Denver, Colorado}, 10244 month = nov, 10245 year = {2001}, 10246 petsc_uses = {KSP} 10247} 10248 10249@Book{ 1dl, 10250 author = {Domenico Lahaye}, 10251 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 10252 Computations}, 10253 year = {2001}, 10254 publisher = {Katholieke Universiteit Leuven}, 10255 notes = {Thesis}, 10256 petsc_uses = {KSP} 10257} 10258 10259@Article{ adams-00, 10260 author = {Adams, M.~F.}, 10261 journal = {International Journal for Numerical Methods in Engineering}, 10262 number = {8}, 10263 pages = {1241-1262}, 10264 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 10265 Deformation Elasticity and Plasticity}, 10266 volume = {48}, 10267 year = {2000}, 10268 petsc_uses = {KSP} 10269} 10270 10271@Article{ adams2002evaluation, 10272 author = {Adams, M.~F.}, 10273 journal = {International Journal for Numerical Methods in Engineering}, 10274 number = {1}, 10275 pages = {519-534}, 10276 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 10277 Problems in Solid Mechanics}, 10278 volume = {55}, 10279 year = {2002}, 10280 petsc_uses = {KSP} 10281} 10282 10283@Article{ lahaye00, 10284 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 10285 title = {Algebraic Multigrid for Complex Symmetric Systems}, 10286 journal = {IEEEMAGN}, 10287 year = {2000}, 10288 volume = {36}, 10289 number = {4}, 10290 pages = {1535--1538}, 10291 petsc_uses = {KSP} 10292} 10293 10294@InProceedings{ adams-99c, 10295 author = {Mark F. Adams and J. Demmel}, 10296 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 10297 Finite Element Problems}, 10298 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 10299 address = {Portland, Oregon}, 10300 month = nov, 10301 year = {1999}, 10302 petsc_uses = {KSP} 10303} 10304 10305@Article{ chan95, 10306 author = {T. Chan and B. Smith and J. Zou}, 10307 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 10308 Grids}, 10309 journal = {Numer. Math.}, 10310 year = {1995}, 10311 volume = {73}, 10312 pages = {149--167}, 10313 petsc_uses = {KSP} 10314} 10315 10316@TechReport{ adams-csd-98-993, 10317 pages = {11}, 10318 year = {1998}, 10319 type = {Technical Report}, 10320 number = {CSD-98-993}, 10321 institution = {University of California, Berkeley}, 10322 title = {A Parallel Maximal Independent Set Algorithm}, 10323 bibdate = {March 11, 1998}, 10324 author = {Mark F. Adams and James Demmel}, 10325 abstract = {The parallel construction of maximal independent sets is a useful building block 10326 for many algorithms in the computational sciences, including graph coloring and 10327 multigrid coarse grid creation on unstructured meshes. We present an efficient 10328 asynchronous maximal independent set algorithm for use on parallel computers, for 10329 ``well partitioned'' graphs, that arise from finite element (FE) models. For 10330 appropriately partitioned bounded degree graphs, it is shown that the running time 10331 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 10332 improvement over the previous best P-RAM complexity for this class of graphs. We 10333 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 10334 model is indicative of the performance one can expect with practical partitions on 10335 graphs from FE problems.}, 10336 month = mar, 10337 petsc_uses = {KSP} 10338} 10339 10340@Article{ benzigolubliesen2005, 10341 title = {Numerical solution of saddle point problems}, 10342 author = {Michele Benzi and Gene H. Golub and J\"org Liesen}, 10343 volume = {14}, 10344 journal = {Acta Numerica}, 10345 pages = {1-–137}, 10346 doi = {10.1017/S0962492904000212}, 10347 year = {2005} 10348} 10349 10350@Article{ mardal2011preconditioning, 10351 title = {Preconditioning discretizations of systems of partial differential equations}, 10352 author = {Kent-Andre Mardal and Ragnar Winther}, 10353 journal = {Numerical Linear Algebra with Applications}, 10354 volume = {18}, 10355 number = {1}, 10356 pages = {1--40}, 10357 year = {2011} 10358} 10359 10360@TechReport{ k676, 10361 year = {1994}, 10362 type = {Technical Report}, 10363 number = {TR1994-676}, 10364 institution = {New York University}, 10365 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 10366 Term}, 10367 author = {Axel Klawonn}, 10368 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 10369 petsc_uses = {KSP} 10370} 10371 10372@Book{ ak1, 10373 author = {Axel Klawonn}, 10374 title = {Preconditioners for Indefinite Problems}, 10375 year = {1995}, 10376 publisher = {Westfalishen Wilhelms-Universitat Munster}, 10377 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 10378 notes = {Thesis}, 10379 petsc_uses = {KSP} 10380} 10381 10382@TechReport{ knepleykarpeev05, 10383 pages = {41}, 10384 year = {2005}, 10385 type = {Technical Report}, 10386 number = {ANL/MCS-P1295-1005}, 10387 institution = {Argonne National Laboratory}, 10388 title = {Flexible Representation of Computational Meshes}, 10389 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10390 abstract = {}, 10391 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 10392 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 10393 month = oct, 10394 petsc_uses = {DMPlex} 10395} 10396 10397@TechReport{ knepleykarpeev07a, 10398 pages = {14}, 10399 year = {2007}, 10400 type = {Technical Report}, 10401 number = {ANL/MCS-P1455-0907}, 10402 institution = {Argonne National Laboratory}, 10403 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10404 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10405 abstract = {}, 10406 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 10407 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 10408 month = feb, 10409 petsc_uses = {DMPlex} 10410} 10411 10412@Article{ knepleykarpeev09, 10413 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10414 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10415 journal = {Scientific Programming}, 10416 volume = {17}, 10417 number = {3}, 10418 pages = {215--230}, 10419 year = {2009}, 10420 doi = {10.3233/SPR-2009-0249}, 10421 url = {http://arxiv.org/abs/0908.4427}, 10422 note = {\url{http://arxiv.org/abs/0908.4427}}, 10423 petsc_uses = {DMPlex} 10424} 10425 10426@Article{ biezuner2012computing, 10427 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 10428 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 10429 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 10430 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 10431 Sublinear Supersolutions}, 10432 journal = {Journal of Scientific Computing}, 10433 publisher = {Springer Netherlands}, 10434 issn = {0885-7474}, 10435 keyword = {Mathematics and Statistics}, 10436 pages = {180--201}, 10437 volume = {52}, 10438 issue = {1}, 10439 year = {2012}, 10440 doi = {10.1007/s10915-011-9540-0}, 10441 petsc_uses = {KSP} 10442} 10443 10444% LiteralHTML: 10445% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 10446% LiteralHTML: 10447@Book{ knepley2017, 10448 title = {Computational Science I}, 10449 author = {Matthew G. 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Smith and Petter Bj{\o}rstad and William D. Gropp}, 10478 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 10479 Differential Equations}, 10480 year = {1996}, 10481 publisher = {Cambridge University Press}, 10482 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 10483 petsc_uses = {KSP} 10484} 10485 10486@Misc{ petsc-fem:homepage, 10487 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 10488 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 10489 G. Rodriguez and G. Filippini}, 10490 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 10491 petsc_uses = {KSP} 10492} 10493 10494@Misc{ petsc4py-web-page, 10495 author = {Lisandro Dalcin}, 10496 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 10497 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 10498 note = {http://code.google.com/p/petsc4py/}, 10499 petsc_uses = {KSP} 10500} 10501 10502@Article{ libmeshpaper06, 10503 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 10504 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 10505 Simulations}}, 10506 journal = {Engineering with Computers}, 10507 volume = {22}, 10508 number = {3--4}, 10509 pages = {237--254}, 10510 year = {2006}, 10511 doi = {10.1007/s00366-006-0049-3}, 10512 petsc_uses = {KSP} 10513} 10514 10515@Misc{ sisiphus:homepage, 10516 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 10517 High-Resolution, Unstructured Simulations}, 10518 author = {T. {Tautges et al.}}, 10519 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 10520 petsc_uses = {KSP} 10521} 10522 10523@Misc{ pflotran:homepage, 10524 title = {{PFLOTRAN} project}, 10525 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 10526 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 10527 howpublished = {\url{http://pflotran.org/}}, 10528 petsc_uses = {KSP} 10529} 10530 10531@Misc{ pism:homepage, 10532 title = {{PISM}: A Parallel Ice Sheet Model}, 10533 author = {E. {Bueler et al.}}, 10534 howpublished = {\url{http://pism-docs.org}}, 10535 petsc_uses = {KSP} 10536} 10537 10538@Misc{ dohp:homepage, 10539 title = {Dohp: Dual order $hp$-finite elements}, 10540 author = {J. Brown}, 10541 howpublished = {\url{http://dohp.org}}, 10542 petsc_uses = {KSP} 10543} 10544 10545@Article{ mccourtrognlienetal12, 10546 title = {Improving parallel scalability for edge plasma transport simulations with neutral 10547 gas species}, 10548 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 10549 journal = {Computational Science and Discovery}, 10550 year = {2012}, 10551 volume = {5}, 10552 number = {014012}, 10553 doi = {10.1088/1749-4699/5/1/014012}, 10554 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 10555 2011)}, 10556 petsc_uses = {KSP} 10557} 10558 10559@Misc{ petclaw-github, 10560 title = {Pet{C}law Software}, 10561 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 10562 year = {2011}, 10563 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 10564 petsc_uses = {KSP} 10565} 10566 10567@Misc{ pyclaw-web-page, 10568 author = {Kyle T. Mandli and David I. 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Part I: The {Krylov-Schur} solver}}, 10587 author = {Biros, G. and Ghattas, O.}, 10588 journal = {SIAM Journal on Scientific Computing}, 10589 volume = {27}, 10590 number = {2}, 10591 pages = {687--713}, 10592 year = {2005}, 10593 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 10594 petsc_uses = {KSP} 10595} 10596 10597@Article{ biros2005pln2, 10598 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 10599 optimization. Part {II}: The {Lagrange Newton} solver, and its application to 10600 optimal control of steady viscous flows}, 10601 author = {Biros, G. and Ghattas, O.}, 10602 journal = {SIAM Journal on Scientific Computing}, 10603 volume = {27}, 10604 number = {2}, 10605 pages = {714--739}, 10606 year = {2005}, 10607 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 10608 petsc_uses = {KSP} 10609} 10610 10611@Misc{ issm:homepage, 10612 title = {{I}ce {S}heet {S}ystem {M}odel}, 10613 author = {Eric Larour and Mathieu Morlighem and Helene Seroussi}, 10614 year = {2010}, 10615 note = {\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}, 10616 petsc_uses = {KSP} 10617} 10618 10619@Article{ morlighem2010spatial, 10620 title = {Spatial patterns of basal drag inferred using control methods from a 10621 full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est 10622 {A}ntarctica}, 10623 author = {Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and 10624 Aubry, D.}, 10625 journal = {Geophysical Research Letters}, 10626 volume = {37}, 10627 number = {14}, 10628 pages = {L14502}, 10629 year = {2010}, 10630 publisher = {American Geophysical Union}, 10631 petsc_uses = {KSP} 10632} 10633 10634@Article{ jardin2012plasmas, 10635 title = {Multiple timescale calculations of sawteeth and other global macroscopic dynamics 10636 of tokamak plasmas}, 10637 author = {S. C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 10638 journal = {Computational Science \& Discovery}, 10639 volume = {5}, 10640 number = {1}, 10641 url = {http://stacks.iop.org/1749-4699/5/014002}, 10642 year = {2012}, 10643 petsc_uses = {KSP} 10644} 10645 10646@Article{ cmz2016, 10647 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 10648 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 10649 journal = {Journal of Scientific Computing}, 10650 publisher = {Springer}, 10651 pages = {803--825}, 10652 volume = {68}, 10653 issue = {2}, 10654 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 10655 doi = {10.1007/s10915-015-0159-4}, 10656 year = {2016}, 10657 note = {Also preprint ANL/MCS-P3039-0912}, 10658 petsc_uses = {KSP} 10659} 10660 10661@Article{ knepleybrownruppsmith13, 10662 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 10663 title = {Achieving High Performance with Unified Residual Evaluation}, 10664 journal = {ArXiv e-prints}, 10665 eprint = {1309.1204}, 10666 archiveprefix = {arXiv}, 10667 primaryclass = {cs.MS}, 10668 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 10669 Engineering, Finance, and Science}, 10670 year = {2013}, 10671 month = sep, 10672 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 10673 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10674 petsc_uses = {KSP} 10675} 10676 10677@Book{ fenicsbook, 10678 title = {Automated Solution of Differential Equations by the Finite Element Method: The 10679 FEniCS Book}, 10680 series = {Lecture Notes in Computational Science and Engineering}, 10681 volume = {84}, 10682 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 10683 publisher = {Springer}, 10684 isbn = {978-3-642-23098-1}, 10685 year = {2012}, 10686 petsc_uses = {KSP} 10687} 10688 10689@Article{ demidovahnertruppgottschling12, 10690 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 10691 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 10692 journal = {ArXiv e-prints}, 10693 archiveprefix = {arXiv}, 10694 eprint = {1212.6326}, 10695 primaryclass = {cs.MS}, 10696 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 10697 Parallel, and Cluster Computing, Physics - Computational Physics}, 10698 year = {2012}, 10699 month = dec, 10700 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 10701 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10702 petsc_uses = {KSP} 10703} 10704 10705@InProceedings{ viennacl, 10706 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 10707 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 10708 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 10709 year = {2010}, 10710 pages = {51-56}, 10711 petsc_uses = {KSP} 10712} 10713 10714@Article{ knepleybrownmcinnessmithruppadams2015, 10715 title = {Exascale Computing without Threads}, 10716 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 10717 Karl Rupp and Mark Adams}, 10718 url = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950}, 10719 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 10720 Scientific Software Architecture for Portability and Performance}, 10721 doi = {10.6084/m9.figshare.5824950.v1}, 10722 year = {2015}, 10723 petsc_uses = {KSP} 10724} 10725 10726@Article{ knepleybrownmcinnessmithruppadams2015b, 10727 title = {Overview of the {PETSc} Library}, 10728 author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 10729 Karl Rupp and Mark Adams}, 10730 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 10731 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 10732 Scientific Software Architecture for Portability and Performance}, 10733 year = {2015}, 10734 petsc_uses = {KSP} 10735} 10736 10737@InCollection{ balaybrownknepleymcinnessmith2015, 10738 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 10739 Smith}, 10740 title = {Providing Mixed Language and Legacy Support within a Library}, 10741 editor = {J. Carver}, 10742 booktitle = {Software Engineering for Science}, 10743 publisher = {Taylor \& Francis}, 10744 year = {2015}, 10745 petsc_uses = {KSP} 10746} 10747 10748@Article{ ruppbalaybrownknepleymcinnessmith2015, 10749 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 10750 Software}, 10751 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 10752 McInnes and Barry F. Smith}, 10753 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 10754 Productivity Challenges}, 10755 journal = {ArXiv e-prints}, 10756 archiveprefix = {arXiv}, 10757 eprint = {1510.01122}, 10758 year = {2015}, 10759 petsc_uses = {KSP} 10760} 10761 10762@InProceedings{ knepley2013accurately, 10763 title = {Accurately Citing Software and Algorithms Used in Publications}, 10764 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 10765 F.}, 10766 year = {2013}, 10767 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10768 (WSSSPE), held at SC13}, 10769 doi = {10.6084/m9.figshare.785731}, 10770 petsc_uses = {KSP} 10771} 10772 10773@InProceedings{ milleretal2013, 10774 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 10775 Strategies Developed for {FASTMath}}, 10776 author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and 10777 Barry Smith}, 10778 year = {2013}, 10779 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10780 (WSSSPE), held at SC13}, 10781 doi = {10.6084/m9.figshare.789055}, 10782 petsc_uses = {KSP} 10783} 10784 10785@TechReport{ dudsonetal2012, 10786 title = {Improved Nonlinear Solvers in {BOUT++}}, 10787 author = {Ben Dudson and Sean Farley and Lois Curfman McInnes}, 10788 institution = {Argonne National Laboratory}, 10789 number = {ANL/MCS-P3025-0812}, 10790 year = {2012}, 10791 petsc_uses = {KSP} 10792} 10793 10794@Misc{ brown13, 10795 author = {J. Brown}, 10796 title = {Scalable Repository Workflows}, 10797 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 10798 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 10799 year = {2013}, 10800 petsc_uses = {KSP} 10801} 10802 10803@Misc{ starforest11, 10804 title = {Star forests as a parallel communication model}, 10805 author = {Jed Brown}, 10806 url = {https://jedbrown.org/files/StarForest.pdf}, 10807 year = {2011}, 10808 petsc_uses = {KSP} 10809} 10810 10811@Misc{ brownknepleysmith13, 10812 author = {J. Brown and M. Knepley and B. Smith}, 10813 title = {Run-time Extensibility: Anything Less is Unsustainable}, 10814 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 10815 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 10816 year = {2013}, 10817 petsc_uses = {KSP} 10818} 10819 10820@Article{ jzhaoyliwkliu15, 10821 author = {J. Zhao and Y. Li and W.K. Liu}, 10822 title = {Predicting band structure of 3{D} mechanical metamaterials with complex geometry 10823 via {XFEM}}, 10824 journal = {Computational Mechanics}, 10825 year = {2015}, 10826 url = {http://link.springer.com/article/10.1007/s00466-015-1129-2}, 10827 petsc_uses = {KSP} 10828} 10829 10830@Article{ alisic14, 10831 author = {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen}, 10832 title = {Compaction around a rigid, circular inclusion in partially molten rock}, 10833 journal = {J. Geophys. Res.}, 10834 year = {2014}, 10835 volume = {119}, 10836 number = {7}, 10837 pages = {5903-5920}, 10838 doi = {10.1002/2013JB010906}, 10839 petsc_uses = {KSP} 10840} 10841 10842@Article{ rhebergen14, 10843 author = {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen}, 10844 title = {Analysis of block preconditioners for models of coupled magma mantle dynamics}, 10845 journal = {SIAM J. Sci. Comp.}, 10846 year = {2014}, 10847 volume = {36}, 10848 number = {4}, 10849 pages = {1960-1977}, 10850 doi = {10.1137/130946678}, 10851 petsc_uses = {KSP} 10852} 10853 10854@Article{ allwright14, 10855 author = {J. Allwright and R.F. Katz}, 10856 title = {Pipe Poiseuille flow of viscously anisotropic, partially molten rock}, 10857 journal = {Geophys. J. Int.}, 10858 year = {2014}, 10859 volume = {199}, 10860 number = {3}, 10861 pages = {1608--1624}, 10862 doi = {10.1093/gji/ggu345}, 10863 petsc_uses = {KSP} 10864} 10865 10866@Misc{ gropp10, 10867 author = {William D. Gropp}, 10868 title = {Update on libraries for {B}lue {W}aters}, 10869 address = {Bordeaux, France}, 10870 year = {2010}, 10871 url = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf}, 10872 petsc_uses = {KSP} 10873} 10874 10875@InProceedings{ mayknepley2017, 10876 title = {{DMSwarm}: Particles in {PETSc}}, 10877 author = {Dave A May and Matthew G Knepley}, 10878 booktitle = {EGU General Assembly Conference Abstracts}, 10879 volume = {19}, 10880 pages = {10133}, 10881 year = {2017}, 10882 petsc_uses = {KSP} 10883} 10884 10885@InProceedings{ adamsbrownknepley2013, 10886 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley}, 10887 title = {Low-communication techniques for extreme-scale multilevel solvers}, 10888 booktitle = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC}, 10889 organization = {DOE Office of Advanced Scientific Computing Research}, 10890 year = {2013}, 10891 petsc_uses = {KSP} 10892} 10893 10894@Article{ bhallagriffithknepleyadamsguy2017, 10895 title = {Scalable smoothing strategies for a geometric multigrid method for the immersed 10896 boundary equations}, 10897 author = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F. 10898 Adams and Robert D. Guy}, 10899 journal = {arXiv e-prints}, 10900 eprint = {1612.02208}, 10901 year = {2017}, 10902 note = {\url{http://arxiv.org/abs/1612.02208}}, 10903 petsc_uses = {KSP} 10904} 10905 10906@Article{ zampini2016pcbddc, 10907 title = {{PCBDDC}: a class of robust dual-primal methods in {PETSc}}, 10908 author = {Zampini, Stefano}, 10909 journal = {SIAM Journal on Scientific Computing}, 10910 volume = {38}, 10911 number = {5}, 10912 pages = {S282--S306}, 10913 year = {2016}, 10914 publisher = {SIAM}, 10915 petsc_uses = {KSP} 10916} 10917 10918@Article{ jolivetromanzampini2020, 10919 title = {{KSPHPDDM} and {PCHPDDM}: extending {PETSc} with advanced {Krylov} methods and 10920 robust multilevel overlapping {Schwarz} preconditioners}, 10921 author = {Pierre Jolivet and Jose Roman and Stefano Zampini}, 10922 journal = {Computers and Mathematics with Applications}, 10923 volume = {84}, 10924 pages = {277--295}, 10925 year = {2021} 10926} 10927 10928@Article{ zampinitu2017, 10929 title = {Multilevel {BDDC} deluxe algorithms with adaptive coarse spaces for flow in 10930 porous media}, 10931 author = {Stefano Zampini and Xuemin Tu}, 10932 journal = {SIAM Journal of Scientific Computing}, 10933 volume = {39}, 10934 number = {4}, 10935 pages = {A1389--A1415}, 10936 year = {2017} 10937} 10938 10939@Article{ ohwidlundzampinidohrmann2017, 10940 title = {{BDDC} algorithms with deluxe scaling and adaptive selection of primal 10941 constraints for {Raviart-Thomas} vector fields}, 10942 author = {D.-S. Oh and Olof B. Widlund and Stefano Zampini and Clark Dohrmann}, 10943 journal = {Mathematics of Computation}, 10944 volume = {87}, 10945 number = {310}, 10946 pages = {659--692}, 10947 year = {2017} 10948} 10949 10950@Article{ veigapavarinoscacchiwidlundzampini2016, 10951 title = {Adaptive selection of primal constraints for isogeometric {BDDC} deluxe 10952 preconditioners}, 10953 author = {L. Beirao Da Veiga and Luca F. Pavarino and S. Scacchi and Olof B. Widlund and 10954 Stefano Zampini}, 10955 journal = {SIAM Journal of Scientific Computing}, 10956 volume = {39}, 10957 number = {1}, 10958 pages = {A281--A302}, 10959 year = {2016} 10960} 10961 10962@Article{ pavarinoscacchiwidlundzampini2018, 10963 title = {Isogeometric {BDDC} deluxe preconditioners for linear elasticity for isogeometric 10964 analysis}, 10965 author = {Luca F. Pavarino and S. Scacchi and Olof B. Widlund and Stefano Zampini}, 10966 journal = {Mathematical Models and Methods in Applied Sciences}, 10967 volume = {28}, 10968 number = {7}, 10969 pages = {1337--1370}, 10970 year = {2018} 10971} 10972 10973@Article{ bergervergiatwaisman2017, 10974 title = {An overlapping Domain Decomposition preconditioning method for monolithic 10975 solution of shear bands}, 10976 author = {Luc Berger-Vergiat and Haim Waisman}, 10977 journal = {Computer Methods in Applied Mechanics and Engineering}, 10978 volume = {318}, 10979 pages = {33--60}, 10980 year = {2017}, 10981 petsc_uses = {KSP} 10982} 10983 10984@Article{ abhyankarmaldonadosmithzhang2020, 10985 title = {{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics 10986 Simulations}, 10987 author = {S. Abhyankar and G. Betrie and D.A. Maldonado and L.C. McInnes and B. Smith and 10988 H. Zhang}, 10989 journal = {ACM Transactions on Mathematical Software}, 10990 volume = {46}, 10991 number = {1}, 10992 year = {2020}, 10993 doi = {10.1145/3344587}, 10994 petsc_uses = {KSP} 10995} 10996 10997@InProceedings{ zhangellpack2018, 10998 author = {Hong Zhang and Richard T. Mills and Karl Rupp and Barry F. Smith}, 10999 title = {Vectorized Parallel Sparse Matrix-Vector Multiplication in {PETSc} Using 11000 {AVX-512}}, 11001 booktitle = {Proceedings of the 47th International Conference on Parallel Processing}, 11002 year = {2018}, 11003 petsc_uses = {KSP} 11004} 11005 11006@Misc{ petsc-user-meetings:website, 11007 title = {{PETSc User Meetings}}, 11008 key = {PETSc User Meetings}, 11009 howpublished = {\url{https://petsc.org/release/community/meetings/meeting}}, 11010 petsc_uses = {KSP} 11011} 11012 11013@Article{ flexible-bicgstab-chen16, 11014 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 11015 author = {J. Chen and L.C. McInnes and H. Zhang}, 11016 journal = {Journal of Scientific Computing}, 11017 volume = {68}, 11018 number = {2}, 11019 month = jul, 11020 year = {2016}, 11021 pages = {803--825}, 11022 doi = {10.1007/s10915-015-0159-4}, 11023 petsc_uses = {KSP} 11024} 11025 11026@Misc{ petsc-extensibility2016, 11027 author = {M. Knepley and D. A. May and J. Brown and B. Smith}, 11028 title = {{Extensibility in PETSc}}, 11029 note = {SIAM News, available via 11030 \url{https://sinews.siam.org/Details-Page/extensibility-in-petsc}}, 11031 year = {2016}, 11032 petsc_uses = {KSP} 11033} 11034 11035@Misc{ error-estimation-whitepaper2017, 11036 author = {E. Constantinescu and O. Marin and T. Munson and B. Smith and H. 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Hansen and 11082 Jung-Han Kimn}, 11083 booktitle = {IEEE 9th Annual Computing and Communication Workshop and Conference (CCWC 2019)}, 11084 note = {Best Paper in Track}, 11085 year = {2019}, 11086 petsc_uses = {KSP} 11087} 11088 11089@MastersThesis{ rinaldo-ceresoli18, 11090 author = {Stefano Guido Rinaldo and Andrea Ceresoli}, 11091 title = {Newton–Krylov–Schwarz Methods for Distributed Power Flow and Related 11092 Applications}, 11093 school = {Politecnico di Milano}, 11094 year = {2018}, 11095 month = apr, 11096 petsc_uses = {KSP} 11097} 11098 11099@Article{ sananschneppmay2016, 11100 title = {Pipelined, Flexible {K}rylov Subspace Methods}, 11101 author = {P. Sanan and S. M. Schnepp and D. A. May}, 11102 journal = {SIAM Journal on Scientific Computing}, 11103 volume = {38}, 11104 number = {5}, 11105 pages = {C441-C470}, 11106 year = {2016}, 11107 doi = {10.1137/15M1049130}, 11108 petsc_uses = {KSP} 11109} 11110 11111@Article{ petscsf2022, 11112 author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and 11113 Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and 11114 Smith, Barry F. and Zampini, Stefano}, 11115 journal = {IEEE Transactions on Parallel and Distributed Systems}, 11116 title = {The {PetscSF} Scalable Communication Layer}, 11117 year = {2022}, 11118 volume = {33}, 11119 number = {4}, 11120 pages = {842-853}, 11121 doi = {10.1109/TPDS.2021.3084070} 11122} 11123 11124@Article{ brandt2000, 11125 title = {General highly accurate algebraic coarsening}, 11126 author = {Achi Brandt}, 11127 journal = {Electronic Transactions on Numerical Analysis}, 11128 volume = {10}, 11129 number = {9680}, 11130 pages = {1--20}, 11131 issn = {10689613}, 11132 year = {2000} 11133} 11134 11135@Article{ dalcinpazklercosimo2011, 11136 title = {Parallel distributed computing using Python}, 11137 author = {Lisandro D. Dalcin and Rodrigo R. Paz and Pablo A. Kler and Alejandro Cosimo}, 11138 journal = {Advances in Water Resources}, 11139 volume = {34}, 11140 number = {9}, 11141 pages = {1124 - 1139}, 11142 note = {New Computational Methods and Software Tools}, 11143 issn = {0309-1708}, 11144 doi = {10.1016/j.advwatres.2011.04.013}, 11145 year = {2011} 11146} 11147 11148@Article{ behnelbradshawcitrodalcinseljebotnsmith2011, 11149 title = {Cython: The Best of Both Worlds}, 11150 author = {Behnel,Stefan and Bradshaw,Robert and Citro,Craig and Dalcin,Lisandro and 11151 Seljebotn,Dag Sverre and Smith,Kurt }, 11152 journal = {Computing in Science \& Engineering}, 11153 volume = {13}, 11154 number = {2}, 11155 pages = {31-39}, 11156 doi = {10.1109/MCSE.2010.118}, 11157 year = {2011} 11158} 11159 11160@Article{ dalcinpazstorti2005, 11161 title = {MPI for Python}, 11162 author = {Lisandro Dalcín and Rodrigo Paz and Mario Storti}, 11163 journal = {Journal of Parallel and Distributed Computing}, 11164 volume = {65}, 11165 number = {9}, 11166 pages = {1108 - 1115}, 11167 issn = {0743-7315}, 11168 doi = {10.1016/j.jpdc.2005.03.010}, 11169 year = {2005} 11170} 11171 11172@Article{ dalcincolliervignalcortescalo2016, 11173 title = {PetIGA: A framework for high-performance isogeometric analysis}, 11174 author = {Lisandro Dalcin and Nathan Collier and P. Vignal and A.M.A. Cortes and Victor M. 11175 Calo}, 11176 journal = {Computer Methods in Applied Mechanics and Engineering}, 11177 volume = {308}, 11178 pages = {151 - 181}, 11179 issn = {0045-7825}, 11180 doi = {10.1016/j.cma.2016.05.011}, 11181 year = {2016} 11182} 11183 11184@Article{ collierpardodalcinpaszynskicalo2012, 11185 title = {The cost of continuity: A study of the performance of isogeometric finite 11186 elements using direct solvers}, 11187 author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M. 11188 Calo}, 11189 journal = {Computer Methods in Applied Mechanics and Engineering}, 11190 volume = {213-216}, 11191 pages = {353 - 361}, 11192 issn = {0045-7825}, 11193 doi = {10.1016/j.cma.2011.11.002}, 11194 year = {2012} 11195} 11196 11197@Article{ collierdalcinpardocalo2013, 11198 title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite 11199 Elements}, 11200 author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo}, 11201 journal = {SIAM Journal on Scientific Computing}, 11202 volume = {35}, 11203 number = {2}, 11204 pages = {A767-A784}, 11205 doi = {10.1137/120881038}, 11206 year = {2013} 11207} 11208 11209@Article{ dunning2017jump, 11210 title = {{JuMP}: a modeling language for mathematical optimization}, 11211 author = {Dunning, Iain and Huchette, Joey and Lubin, Miles}, 11212 journal = {SIAM Review}, 11213 volume = {59}, 11214 number = {2}, 11215 pages = {295--320}, 11216 year = {2017}, 11217 publisher = {SIAM} 11218} 11219 11220@InProceedings{ prudencioschulz2011, 11221 title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for 11222 Estimation, Simulation and Optimization}, 11223 author = {Ernesto E Prudencio and Karl W Schulz}, 11224 booktitle = {European Conference on Parallel Processing}, 11225 pages = {398--407}, 11226 year = {2011} 11227} 11228 11229@Misc{ rol-website, 11230 key = {ROL}, 11231 title = {{Rapid Optimization Library} Website}, 11232 howpublished = {\url{https://trilinos.org/packages/rol}}, 11233 year = {2018} 11234} 11235 11236@Article{ more1994line, 11237 title = {Line search algorithms with guaranteed sufficient decrease}, 11238 author = {Mor{\'e}, Jorge J and Thuente, David J}, 11239 journal = {ACM Transactions on Mathematical Software}, 11240 volume = {20}, 11241 number = {3}, 11242 pages = {286--307}, 11243 year = {1994}, 11244 publisher = {ACM} 11245} 11246 11247@Article{ griewank2000algorithm, 11248 title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or 11249 adjoint mode of computational differentiation}, 11250 author = {Griewank, Andreas and Walther, Andrea}, 11251 journal = {ACM Transactions on Mathematical Software}, 11252 volume = {26}, 11253 number = {1}, 11254 pages = {19--45}, 11255 year = {2000}, 11256 publisher = {ACM} 11257} 11258 11259@Article{ metcalf2011seven, 11260 title = {The seven ages of fortran}, 11261 author = {Metcalf, Michael}, 11262 journal = {Journal of Computer Science \& Technology}, 11263 volume = {11}, 11264 year = {2011} 11265} 11266 11267@Article{ giraldo_2013, 11268 title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified 11269 model of the atmosphere {(NUMA)}}, 11270 author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu}, 11271 journal = {SIAM Journal on Scientific Computing}, 11272 year = {2013}, 11273 number = {5}, 11274 pages = {B1162-B1194}, 11275 volume = {35}, 11276 doi = {10.1137/120876034} 11277} 11278 11279@Article{ constantinescu_tr2016b, 11280 author = {Constantinescu, E.M.}, 11281 title = {Estimating Global Errors in Time Stepping}, 11282 journal = {ArXiv e-prints}, 11283 archiveprefix = {arXiv}, 11284 eprint = {1503.05166}, 11285 primaryclass = {math.NA}, 11286 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70}, 11287 year = {2016}, 11288 month = mar, 11289 adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C}, 11290 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 11291} 11292 11293@Article{ pareschi_2005, 11294 title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems 11295 with Relaxation}, 11296 author = {L. Pareschi and G. Russo}, 11297 journal = {Journal of Scientific Computing}, 11298 year = {2005}, 11299 number = {1}, 11300 pages = {129--155}, 11301 volume = {25} 11302} 11303 11304@Article{ kennedy_2003, 11305 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 11306 author = {C.A. Kennedy and M.H. Carpenter}, 11307 journal = {Appl. Numer. Math.}, 11308 year = {2003}, 11309 number = {1-2}, 11310 pages = {139--181}, 11311 volume = {44}, 11312 doi = {10.1016/S0168-9274(02)00138-1}, 11313 publisher = {Elsevier Science Publishers B. V.} 11314} 11315 11316@Unpublished{ boscarino_tr2011, 11317 title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic 11318 equations in the diffusion limit}, 11319 author = {Boscarino, S. and Pareschi, L. and Russo, G.}, 11320 note = {Arxiv preprint arXiv:1110.4375}, 11321 year = {2011} 11322} 11323 11324@Article{ ascher_1997, 11325 title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential 11326 equations}, 11327 author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri}, 11328 journal = {Applied Numerical Mathematics}, 11329 year = {1997}, 11330 pages = {151--167}, 11331 volume = {25} 11332} 11333 11334@Book{ ascherpetzold1998, 11335 title = {Computer methods for ordinary differential equations and differential-algebraic 11336 equations}, 11337 author = {Uri M Ascher and Linda R Petzold}, 11338 volume = {61}, 11339 publisher = {SIAM}, 11340 year = {1998} 11341} 11342 11343@Article{ colomesbadia2016, 11344 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 11345 equations}, 11346 author = {Oriol Colom{\'e}s and Santiago Badia}, 11347 journal = {International Journal for Numerical Methods in Engineering}, 11348 volume = {105}, 11349 number = {5}, 11350 pages = {372--400}, 11351 year = {2016} 11352} 11353 11354@Article{ sandu_1997, 11355 title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry problems {II}: 11356 {R}osenbrock solvers}, 11357 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 11358 Potra}, 11359 journal = {Atmospheric Environment}, 11360 year = {1997}, 11361 number = {20}, 11362 pages = {3459--3472}, 11363 volume = {31}, 11364 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 11365 task is the integration of the stiff systems of ordinary differential equations 11366 describing the chemical transformations. It is therefore of interest to 11367 systematically search for stiff solvers which can be identified as close to 11368 optimal for atmospheric applications. In this paper we continue our investigation 11369 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 11370 and compare eight solvers on a set of seven box-models used in present day models. 11371 The focus is on Rosenbrock solvers. These turn out to be very well suited for our 11372 application when they are provided with highly efficient sparse matrix techniques 11373 to economize on the linear algebra. Two of the Rosenbrock solvers tested are from 11374 the literature, viz. and 4, and two are new and specially developed for air 11375 quality applications, viz. 3 and 3. } 11376} 11377 11378@Article{ rang_2005, 11379 title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic 11380 equations of index 1}, 11381 author = {Rang, J. and Angermann, L.}, 11382 journal = {BIT Numerical Mathematics}, 11383 year = {2005}, 11384 number = {4}, 11385 pages = {761--787}, 11386 volume = {45}, 11387 publisher = {Springer}, 11388 doi = {10.1007/s10543-005-0035-y} 11389} 11390 11391@article{rang2015improved, 11392 title = {Improved traditional {R}osenbrock--{W}anner methods for stiff {ODE}s and {DAE}s}, 11393 author = {Rang, Joachim}, 11394 journal = {Journal of Computational and Applied Mathematics}, 11395 volume = {286}, 11396 pages = {128--144}, 11397 year = {2015}, 11398 publisher = {Elsevier}, 11399 doi = {10.1016/j.cam.2015.03.010} 11400} 11401 11402@Article{ gottliebketchesonshu2009, 11403 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 11404 title = {{High order strong stability preserving time discretizations}}, 11405 journal = {Journal of Scientific Computing}, 11406 volume = {38}, 11407 number = {3}, 11408 pages = {251--289}, 11409 doi = {10.1007/s10915-008-9239-z}, 11410 year = {2009} 11411} 11412 11413@Article{ ZhouGuoShu2001, 11414 title = {Numerical study on Landau damping}, 11415 author = {Tie Zhou and Yan Guo and Chi Wang Shu}, 11416 journal = {Physica D: Nonlinear Phenomena}, 11417 volume = {157}, 11418 issue = {4}, 11419 pages = {322-333}, 11420 doi = {10.1016/S0167-2789(01)00289-5}, 11421 issn = {01672789}, 11422 year = {2001} 11423} 11424 11425@Article{ ketcheson_2008, 11426 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 11427 Low-Storage Implementations}, 11428 author = {D.I. Ketcheson}, 11429 journal = {SIAM Journal on Scientific Computing}, 11430 year = {2008}, 11431 number = {4}, 11432 pages = {2113--2136}, 11433 volume = {30}, 11434 doi = {10.1137/07070485X}, 11435 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 11436 RungeKutta methods}, 11437 publisher = {SIAM} 11438} 11439 11440@Article{ jansen_2000, 11441 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 11442 equations with a stabilized finite element method}, 11443 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 11444 journal = {Computer Methods in Applied Mechanics and Engineering}, 11445 year = {2000}, 11446 number = {3}, 11447 pages = {305--319}, 11448 volume = {190}, 11449 publisher = {Elsevier} 11450} 11451 11452@Article{ butcher_2007, 11453 title = {Error propagation of general linear methods for ordinary differential equations}, 11454 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 11455 journal = {Journal of Complexity}, 11456 year = {2007}, 11457 number = {4-6}, 11458 pages = {560--580}, 11459 volume = {23}, 11460 abstract = {We discuss error propagation for general linear methods for ordinary differential 11461 equations up to terms of order p+2, where p is the order of the method. These 11462 results are then applied to the estimation of local discretization errors for 11463 methods of order p and for the adjacent order p+1. The results of numerical 11464 experiments confirm the reliability of these estimates. This research has 11465 applications in the design of robust stepsize and order changing strategies for 11466 algorithms based on general linear methods.}, 11467 doi = {10.1016/j.jco.2007.01.009}, 11468 issn = {0885-064X} 11469} 11470 11471@Article{ constantinescu_a2010a, 11472 title = {Extrapolated implicit-explicit time stepping}, 11473 author = {E.M. Constantinescu and A. Sandu}, 11474 journal = {SIAM Journal on Scientific Computing}, 11475 year = {2010}, 11476 number = {6}, 11477 pages = {4452-4477}, 11478 volume = {31}, 11479 comment = {Preprint \# ANL/MCS-P1612-0409}, 11480 doi = {10.1137/080732833} 11481} 11482 11483@InProceedings{ devito2011liszt, 11484 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 11485 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 11486 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 11487 Aiken, Alex and Duraisamy, Karthik and others}, 11488 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 11489 Networking, Storage and Analysis}, 11490 pages = {9}, 11491 year = {2011}, 11492 organization = {ACM} 11493} 11494 11495@Article{ devito2011designing, 11496 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 11497 author = {DeVito, Zachary and Hanrahan, Pat}, 11498 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 11499 year = {2011} 11500} 11501 11502@Misc{ pgasintro, 11503 author = {Tim Stitt}, 11504 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 11505 Model}, 11506 note = {\url{http://cnx.org/content/m20649/latest/}} 11507} 11508 11509@InProceedings{ el2006upc, 11510 title = {UPC: unified parallel C}, 11511 author = {El-Ghazawi, Tarek and Smith, Lauren}, 11512 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 11513 pages = {27}, 11514 year = {2006}, 11515 organization = {ACM} 11516} 11517 11518@InProceedings{ numrich1998co, 11519 title = {Co-Array Fortran for parallel programming}, 11520 author = {Numrich, Robert W and Reid, John}, 11521 booktitle = {ACM Sigplan Fortran Forum}, 11522 volume = {17}, 11523 number = {2}, 11524 pages = {1--31}, 11525 year = {1998}, 11526 organization = {ACM} 11527} 11528 11529@Article{ aiken1997titanium, 11530 title = {Titanium: A high-performance Java dialect}, 11531 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 11532 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 11533 Geoff and Semenzato, Luigi and others}, 11534 year = {1997} 11535} 11536 11537@Article{ charles2005x10, 11538 title = {X10: an object-oriented approach to non-uniform cluster computing}, 11539 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 11540 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 11541 Sarkar, Vivek}, 11542 journal = {Acm Sigplan Notices}, 11543 volume = {40}, 11544 number = {10}, 11545 pages = {519--538}, 11546 year = {2005}, 11547 publisher = {ACM} 11548} 11549 11550@Article{ chamberlain2007parallel, 11551 title = {Parallel programmability and the chapel language}, 11552 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 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{Morgan Kaufmann Publishers Inc.} 11581} 11582 11583@Book{ yonezawa1990abcl, 11584 title = {ABCL: an object-oriented concurrent system}, 11585 author = {Yonezawa, Akinori}, 11586 year = {1990}, 11587 publisher = {MIT press} 11588} 11589 11590@InProceedings{ dally1988object, 11591 title = {Object-oriented concurrent programming in CST}, 11592 author = {Dally, William J and Chien, Andrew A}, 11593 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 11594 applications: Architecture, software, computer systems, and general issues-Volume 11595 1}, 11596 pages = {434--439}, 11597 year = {1988}, 11598 organization = {ACM} 11599} 11600 11601@Article{ grimshaw1993easy, 11602 title = {Easy-to-use object-oriented parallel processing with Mentat}, 11603 author = {Grimshaw, Andrew S.}, 11604 journal = {Computer}, 11605 volume = {26}, 11606 number = {5}, 11607 pages = {39--51}, 11608 year = {1993}, 11609 publisher = {IEEE} 11610} 11611 11612@InProceedings{ gannon1991object, 11613 title = {Object oriented parallelism: pC++ ideas and experiments}, 11614 author = {Gannon, Dennis and Lee, JK}, 11615 booktitle = {Proceedings of}, 11616 pages = {13--23}, 11617 year = {1991} 11618} 11619 11620@InProceedings{ lau1992object, 11621 title = {An object-oriented class library for scalable parallel heuristic search}, 11622 author = {Lau, Wing-cheong and Singh, Vineet}, 11623 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 11624 pages = {252--267}, 11625 year = {1992}, 11626 organization = {Springer} 11627} 11628 11629@Book{ chase1989amber, 11630 title = {The Amber system: Parallel programming on a network of multiprocessors}, 11631 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 11632 Littlefield, Richard}, 11633 volume = {23}, 11634 number = {5}, 11635 year = {1989}, 11636 publisher = {ACM} 11637} 11638 11639@InProceedings{ kaiser2009parallex, 11640 title = {Parallex an advanced parallel 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Markus}, 12879 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 12880 for {PDE} Based Applications}, 12881 year = {1994}, 12882 institution = {Department of Computer Sciences, Purdue University}, 12883 number = {CSD-TR-94-021} 12884} 12885 12886@Unpublished{ ilu-web-page, 12887 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 12888 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 12889 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 12890} 12891 12892@Unpublished{ doe2k-web-page, 12893 title = {{DOE2000 Initiative} {W}eb page}, 12894 note = {http://www.mcs.anl.gov/DOE2000}, 12895 key = {DOE2000 Initiative} 12896} 12897 12898@Misc{ pvode-web-page, 12899 title = {{PVODE} {W}eb Page}, 12900 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 12901 author = {A. {Hindmarsh et al.}} 12902} 12903 12904@Book{ szyperski97, 12905 author = {Clemens Szyperski}, 12906 title = {Component Software: Beyond Object-Oriented Programming}, 12907 publisher = {ACM Press}, 12908 address = {New York}, 12909 year = {1997} 12910} 12911 12912@Unpublished{ petsc:coloringuse, 12913 title = {Code for computing sparse {J}acobians}, 12914 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12915 institution = {Argonne National Laboratory} 12916} 12917 12918@Unpublished{ petsc:external, 12919 author = {B. F. {Smith et al.}}, 12920 title = {{External Software Used by PETSc}}, 12921 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12922 institution = {Argonne National Laboratory} 12923} 12924 12925@Unpublished{ petsc:use-by-external-packages, 12926 author = {B. F. {Smith et al.}}, 12927 title = {{Software Packages that Use or Interface to PETSc}}, 12928 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 12929 institution = {Argonne National Laboratory} 12930} 12931 12932@Unpublished{ petsc:prizes, 12933 author = {B. F. {Smith et al.}}, 12934 title = {{Prizes Won Using PETSc}}, 12935 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12936 institution = {Argonne National Laboratory} 12937} 12938 12939@Unpublished{ petsc:csgf, 12940 author = {B. F. {Smith et al.}}, 12941 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 12942 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12943 institution = {Argonne National Laboratory} 12944} 12945 12946@Unpublished{ flash-web-page, 12947 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 12948 {W}eb Page}, 12949 note = {http://www.asci.uchicago.edu}, 12950 author = {R. {Rosner et al.}}, 12951 institution = {University of Chicago} 12952} 12953 12954@Unpublished{ esi-web-page, 12955 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 12956 note = {http://z.ca.sandia.gov/esi}, 12957 author = {R. {Clay et al.}} 12958} 12959 12960@Unpublished{ infobus-web-page, 12961 title = {{I}nfo{B}us {W}eb Page}, 12962 note = {http://www.java.sun.com/beans/infobus}, 12963 key = {infobus} 12964} 12965 12966@Unpublished{ xray-web-page, 12967 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 12968 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 12969 note = {http://www.mcs.anl.gov/xray/}, 12970 institution = {Argonne National Laboratory} 12971} 12972 12973@InProceedings{ kohn98, 12974 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 12975 title = {Language Interoperability Mechanisms for High-Performance Scientific 12976 Applications}, 12977 publisher = {SIAM}, 12978 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12979 Scientific and Engineering Computing}, 12980 year = {1999}, 12981 pages = {30-39} 12982} 12983 12984@InProceedings{ kohn01, 12985 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 12986 title = {Divorcing Language Dependencies from a Scientific Software Library}, 12987 publisher = {SIAM}, 12988 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 12989 year = {2001} 12990} 12991 12992@InProceedings{ freitag_jones_plassmann98, 12993 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 12994 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 12995 publisher = {SIAM}, 12996 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12997 Scientific and Engineering Computing}, 12998 year = {1999}, 12999 pages = {215-224} 13000} 13001 13002@Book{ templates, 13003 author = {R. Barrett and M. Berry and T. F. Chan and J. Demmel and J. Donato and J. 13004 Dongarra and V. Eijkhout and R. Pozo and C. Romine and H. Van der Vorst }, 13005 title = {Templates for the Solution of Linear Systems: Building Blocks for Iterative 13006 Methods}, 13007 publisher = {SIAM}, 13008 year = {1994}, 13009 address = {Philadelphia, PA} 13010} 13011 13012@InProceedings{ parasha2, 13013 author = {M. Parashar and J. C. Browne and C. Edwards and K. Klimkowski}, 13014 title = { A Common Data Management Infrastructure for Parallel Adaptive Algorithms for 13015 {PDE} Solutions}, 13016 booktitle = {SC97 Proceedings}, 13017 publisher = {IEEE Computer Society Press}, 13018 year = {1997} 13019} 13020 13021@TechReport{ parasha, 13022 author = {M. Parashar and J. C. Browne}, 13023 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 13024 Techniques}, 13025 institution = {Department of Computer Science, University of Texas at Austin}, 13026 year = {1995} 13027} 13028 13029@Article{ parti, 13030 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 13031 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 13032 Memory Architectures}, 13033 journal = {Journal of Parallel and Distributed Computing}, 13034 year = {1994}, 13035 volume = {22}, 13036 pages = {462--478} 13037} 13038 13039@Article{ mparti, 13040 author = {G. Agrawal and A. Sussman and J. Saltz}, 13041 title = {An Integrated Runtime and Compile-time Approach for Parallelizing Structured and 13042 Block Structured Applications}, 13043 journal = {IEEE Trans. on Parallel and Distributed Systems}, 13044 volume = {6}, 13045 number = {7}, 13046 year = {1995} 13047} 13048 13049@Article{ gropp-lusk-doss-skjellum, 13050 author = { William Gropp and Ewing Lusk and Nathan Doss and Anthony Skjellum}, 13051 title = {A high-performance, portable implementation of the {MPI} Message Passing 13052 Interface standard}, 13053 journal = {Parallel Computing}, 13054 year = {1996}, 13055 volume = {22}, 13056 pages = {789--828} 13057} 13058 13059@InProceedings{ lam, 13060 author = {Greg Burns and Raja Daoud and James Vaigl}, 13061 title = {{LAM}: An Open Cluster Environment for {MPI}}, 13062 booktitle = {Proceedings of Supercomputing Symposium '94}, 13063 editor = {John W. Ross}, 13064 publisher = {University of Toronto}, 13065 pages = {379--386}, 13066 year = {1994} 13067} 13068 13069@Article{ cs99, 13070 author = {X.-C. Cai and M. Sarkis}, 13071 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 13072 systems}, 13073 journal = {SIAM J. Scientific Computing}, 13074 year = {1999}, 13075 volume = {21}, 13076 pages = {792-797} 13077} 13078 13079@Article{ cai2003restricted, 13080 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 13081 positive definite linear systems}, 13082 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 13083 journal = {SIAM Journal on Numerical Analysis}, 13084 volume = {41}, 13085 issue = {1}, 13086 pages = {1209--1231}, 13087 year = {2003}, 13088 doi = {10.1137/S0036142901389621} 13089} 13090 13091@TechReport{ caisaad, 13092 author = {Xiao-Chuan Cai and Youcef Saad}, 13093 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 13094 institution = {Army High Performance Computing Research Center, University of Minnesota }, 13095 year = {1993}, 13096 number = {Preprint 93-027 }, 13097 note = {SIAM J. Sci. Comp. 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Supercomputing Applications}, 13134 volume = {8}, 13135 number = {3/4}, 13136 year = {1994}, 13137 key = {MPI Standard - final} 13138} 13139 13140@Unpublished{ npb-web-page, 13141 key = {NAS Parallel Benchmarks}, 13142 title = {{NAS} {P}arallel {B}enchmarks {W}eb page}, 13143 note = {http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html}, 13144 year = {1996}, 13145 month = dec 13146} 13147 13148@Book{ george81, 13149 title = {Computer Solution of Large Sparse Positive Definite Systems}, 13150 author = {Alan George and Joseph W. Liu}, 13151 publisher = {Prentice-Hall}, 13152 year = {1981}, 13153 key = {SparseDirect} 13154} 13155 13156@Book{ p4-book, 13157 title = {Portable Programs for Parallel Processors}, 13158 publisher = {Holt, Rinehart, {and} Winston}, 13159 year = {1987}, 13160 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 13161 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 13162 key = {P4Book} 13163} 13164 13165@Article{ stones, 13166 author = {H. L. Stone}, 13167 title = {Iterative solution of implicit approximations of multidimensional partial 13168 differential equations}, 13169 journal = {SIAM J. Numerical Analysis}, 13170 pages = {87--113}, 13171 volumne = {5}, 13172 year = {1968} 13173} 13174 13175@Article{ parallelstones, 13176 author = {J. S. Reeve and A. D. Scurr and J. H. Merlin}, 13177 title = {Parallel versions of {S}tones strongly implicit algorithm}, 13178 journal = {Concurrency and Computation: Practice and Experience}, 13179 pages = {1049--1062}, 13180 volumne = {13}, 13181 year = {2001} 13182} 13183 13184@Article{ p4-paper, 13185 author = {Ralph Butler and Ewing Lusk}, 13186 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 13187 journal = {Journal of Parallel Computing}, 13188 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 13189 Division preprint P362-0493)}, 13190 year = {1993} 13191} 13192 13193@TechReport{ picl, 13194 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 13195 title = {{PICL}: A portable instrumented communications library}, 13196 institution = {Oak Ridge National Laboratory}, 13197 number = {TM-11130}, 13198 year = {1990}, 13199 key = {PICL} 13200} 13201 13202@TechReport{ upshot, 13203 author = {Virginia Herrarte and Ewing Lusk}, 13204 title = {Studying Parallel Program Behavior with {U}pshot}, 13205 institution = {Argonne National Laboratory}, 13206 number = {ANL-91/15}, 13207 month = aug, 13208 year = {1991}, 13209 key = {Upshot} 13210} 13211 13212@TechReport{ p4-manual, 13213 author = {Ralph Butler and Ewing Lusk}, 13214 title = {User's Guide to the p4 Parallel Programming System}, 13215 institution = {Argonne National Laboratory}, 13216 number = {ANL-92/17}, 13217 month = oct, 13218 year = {1992}, 13219 key = {p4-Manual} 13220} 13221 13222@InProceedings{ oldparti, 13223 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 13224 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 13225 booktitle = {Proceedings of Supercomputing '93}, 13226 pages = {578--587}, 13227 year = {1993} 13228} 13229 13230@Article{ parti2, 13231 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 13232 and J. Saltz}, 13233 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 13234 journal = {ACM SIGPLAN Notices}, 13235 year = {1995}, 13236 pages = {68-79}, 13237 volume = {30}, 13238 number = {8} 13239} 13240 13241@Article{ parti3, 13242 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 13243 title = {Run-Time Parallelization and Scheduling of Loops}, 13244 journal = {IEEE Trans. Computers}, 13245 year = {1991}, 13246 pages = {604-612}, 13247 volume = {40}, 13248 number = {5} 13249} 13250 13251@InProceedings{ disz-lusk:wamtrace, 13252 author = {Terrence Disz and Ewing Lusk}, 13253 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 13254 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13255 year = {1987}, 13256 pages = {46--53} 13257} 13258 13259@InProceedings{ gorlick-kesselman:gauge, 13260 author = {Michael Gorlick and Carl Kesselman}, 13261 title = {Timing {Prolog} programs without Clocks}, 13262 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13263 year = {1996}, 13264 publisher = {Birkhauser} 13265} 13266 13267@TechReport{ aztec, 13268 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 13269 title = {Aztec User's Guide Version 1.1}, 13270 institution = {Sandia National Laboratories}, 13271 month = oct, 13272 year = {1995}, 13273 number = {SAND95/1559} 13274} 13275 13276@TechReport{ aztec2, 13277 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 13278 title = {Official {Aztec} User's Guide Version 2.1}, 13279 institution = {Sandia National Laboratories}, 13280 year = {1999} 13281} 13282 13283@Book{ taylor-chandy:pcn, 13284 author = {Chandy, M. and Taylor, S.}, 13285 title = {An Introduction to Parallel Programming}, 13286 year = {1991}, 13287 publisher = {Jones and Bartlett} 13288} 13289 13290@Book{ foster-taylor:strand, 13291 title = {Strand: New Concepts in Parallel Programming}, 13292 author = {Ian Foster and Stephen Taylor}, 13293 publisher = {Prentice-Hall}, 13294 adress = { Englewood Cliffs, New Jersey}, 13295 year = {1990} 13296} 13297 13298@Article{ aurora, 13299 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 13300 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 13301 Carlsson and A. Ciepielewski and B. Hausman}, 13302 title = {The Aurora OR-Parallel Prolog System}, 13303 journal = {New Generation Computing}, 13304 volume = {7}, 13305 number = {3}, 13306 year = {1990}, 13307 pages = {243--271} 13308} 13309 13310@TechReport{ roo, 13311 author = {E. Lusk and W. McCune and J. Slaney}, 13312 title = {Roo---a Parallel Theorem Prover}, 13313 institution = {Argonne National Laboratory}, 13314 number = {MCS--TM--149}, 13315 year = {1991} 13316} 13317 13318@TechReport{ heath-etheridge:vppp, 13319 author = {M. T. Heath and J. A. Etheridge}, 13320 title = {Visualizing the Performance of Parallel Programs}, 13321 institution = {Oak Ridge National Laboratory}, 13322 number = {ORNL TM-11813}, 13323 year = {1991} 13324} 13325 13326@TechReport{ chem:vis, 13327 author = {Ewing L. Lusk}, 13328 title = {Performance Visualization for Parallel Programs}, 13329 institution = {Argonne National Laboratory}, 13330 number = {ANL/MCS--P287--0192}, 13331 year = {1991}, 13332 note = {(to appear in {\em Theoretica Chimica Acta})} 13333} 13334 13335@TechReport{ picltrace, 13336 author = {P.~H.~Worley}, 13337 title = {A new {PICL} trace file format}, 13338 institution = {Oak Ridge National Laboratory}, 13339 number = {ORNL TM-12125}, 13340 month = jun, 13341 year = {1992} 13342} 13343 13344@InProceedings{ hideo, 13345 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 13346 title = {Inference of Phylogenetic trees using maximum likelihood}, 13347 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 13348 year = {1992}, 13349 pages = {247--262} 13350} 13351 13352@InProceedings{ dw90, 13353 author = {M. Dryja and O. Widlund}, 13354 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 13355 Problems}, 13356 booktitle = {Third International Symposium on Domain Decomposition Methods}, 13357 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 13358 year = {1990}, 13359 pages = {3-21}, 13360 publisher = {SIAM}, 13361 address = {Philadelphia}, 13362 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 13363 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 13364 references, good introduction to the theory. No computations}, 13365 key = {DryjaWidlund90 !AS} 13366} 13367 13368@Unpublished{ rosing, 13369 author = {Matt Rosing and Joel Saltz}, 13370 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 13371 key = {LowLatency}, 13372 note = {manuscript, 1992} 13373} 13374 13375@TechReport{ jp:incomplete, 13376 author = {Mark T. Jones and Paul E. Plassmann}, 13377 title = {An Improved Incomplete {C}holesky Factorization}, 13378 institution = {Argonne National Laboratory}, 13379 address = {Argonne, IL}, 13380 type = {Preprint}, 13381 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 13382 number = {MCS-P206-0191}, 13383 year = {1991}, 13384 key = {jones} 13385} 13386 13387@InCollection{ jp:ima, 13388 author = {Mark Jones and Paul Plassmann}, 13389 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 13390 booktitle = {Graph Theory and Sparse Matrix Computation}, 13391 publisher = {Springer-Verlag}, 13392 series = {The IMA Volumes in Mathematics and Its Applications}, 13393 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 13394 volume = {56}, 13395 year = {1993}, 13396 pages = {229--245} 13397} 13398 13399@Article{ pw98, 13400 author = {M. Pernice and H. F. Walker}, 13401 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 13402 journal = {SIAM J. Sci. Stat. Comput.}, 13403 year = {1998}, 13404 volume = {19}, 13405 pages = {302--318} 13406} 13407 13408@TechReport{ ysmp83, 13409 key = {Eisenstat}, 13410 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13411 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13412 institution = {Department of Computer Science, Yale University}, 13413 number = {YALE/DCS/RR-265}, 13414 month = apr, 13415 year = {1983} 13416} 13417 13418@InBook{ ysmp84, 13419 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13420 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13421 title = {Elliptic Problem Solvers II}, 13422 publisher = {Academic Press}, 13423 pages = {45--52}, 13424 editors = {G. Birkhoff and A. Schoenstadt}, 13425 year = {1984} 13426} 13427 13428@TechReport{ sparsekit, 13429 key = {Saad}, 13430 author = {Youcef Saad}, 13431 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 13432 institution = {Center for Supercomputing Research and Development, University of Illinois at 13433 Urbana-Champaign}, 13434 number = {1029}, 13435 year = {1990} 13436} 13437 13438@TechReport{ pde-user-ref, 13439 author = {Barry F. Smith}, 13440 title = {Extensible {PDE} Solvers Package Users Manual}, 13441 institution = {Argonne National Laboratory}, 13442 month = sep, 13443 year = {1994}, 13444 number = {ANL-93/40}, 13445 key = {Smith94 ! PDE} 13446} 13447 13448@TechReport{ bs-user-ref, 13449 author = {Mark T. Jones and Paul E. Plassmann}, 13450 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 13451 of Sparse Linear Systems}, 13452 institution = {Argonne National Laboratory}, 13453 month = dec, 13454 year = {1995}, 13455 number = {ANL-95/48} 13456} 13457 13458@TechReport{ snes-user-ref, 13459 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 13460 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 13461 institution = {Argonne National Laboratory}, 13462 month = feb, 13463 year = {1995}, 13464 number = {ANL/MCS-TM-193}, 13465 key = {GroppMcInnesSmith95 ! SNES} 13466} 13467 13468@TechReport{ sles-user-ref, 13469 author = {William D. Gropp and Barry F. Smith}, 13470 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 13471 institution = {Argonne National Laboratory}, 13472 month = mar, 13473 year = {1993}, 13474 number = {ANL-93/8}, 13475 key = {GroppSmith93 ! SLES} 13476} 13477 13478@TechReport{ chameleon-user-ref, 13479 author = {William D. Gropp and Barry F. Smith}, 13480 title = {Chameleon Parallel programming tools Users Manual}, 13481 institution = {Argonne National Laboratory}, 13482 month = mar, 13483 year = {1993}, 13484 number = {ANL-93/23}, 13485 key = {GroppSmith93 ! Chameleon} 13486} 13487 13488@Article{ euclid2, 13489 author = {D. Hysom and A. Pothen}, 13490 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 13491 journal = {SIAM J. Sci. Comput.}, 13492 volume = {22}, 13493 number = {6}, 13494 pages = {2194--2215} 13495} 13496 13497@TechReport{ euclid1, 13498 author = {D. Hysom and A. Pothen}, 13499 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 13500 Solution of Sparse Linear Systems)}, 13501 institution = {Old Dominion University}, 13502 year = {2001} 13503} 13504 13505@TechReport{ ksp-user-ref, 13506 author = {William D. Gropp and Barry F. Smith}, 13507 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 13508 Methods}, 13509 institution = {Argonne National Laboratory}, 13510 month = aug, 13511 year = {1993}, 13512 number = {ANL-93/30}, 13513 key = {GroppSmith93 ! KSP} 13514} 13515 13516@TechReport{ mpi-chameleon, 13517 author = {William D. Gropp and Ewing Lusk}, 13518 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 13519 institution = {Argonne National Laboratory}, 13520 month = dec, 13521 year = {1992}, 13522 number = {ANL-92/47}, 13523 key = {GroppLusk92 ! MPI} 13524} 13525 13526@TechReport{ blockcomm-fortran, 13527 author = {William D. Gropp}, 13528 title = {Block{C}omm for {F}ortran}, 13529 institution = {Argonne National Laboratory}, 13530 month = may, 13531 year = {1993}, 13532 number = {ANL-93/00 (to appear)}, 13533 key = {Gropp93 ! BlockComm} 13534} 13535 13536@TechReport{ autodocument, 13537 author = {William D. Gropp}, 13538 title = {Automatic documentation of {C} programs}, 13539 institution = {Argonne National Laboratory}, 13540 month = may, 13541 year = {1993}, 13542 number = {ANL-93/00}, 13543 key = {Gropp93 ! Autodoc} 13544} 13545 13546@TechReport{ zipcode, 13547 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 13548 Manfred Morari}, 13549 title = {The {Z}ipcode message-passing system}, 13550 institution = {Lawrence Livermore National Laboratory}, 13551 month = sep, 13552 year = {1992}, 13553 number = {Unpublished}, 13554 key = {Skjellum92 ! Zipcode} 13555} 13556 13557@Article{ paragraph, 13558 author = {Michael T. Heath and Jennifer Etheridge Finger}, 13559 title = {Visualizing performance of parallel programs}, 13560 journal = {IEEE Software}, 13561 volume = {8}, 13562 number = {5}, 13563 month = sep, 13564 year = {1991}, 13565 pages = {29--39}, 13566 key = {Heath91 ! Paragraph} 13567} 13568 13569@Article{ gropp90, 13570 author = {William Gropp and Edward Smith}, 13571 title = {Computational Fluid Dynamics on Parallel Processors}, 13572 journal = {Computers and Fluids}, 13573 volume = {18}, 13574 year = {1990}, 13575 pages = {289--304}, 13576 key = {Gropp90 ! performance} 13577} 13578 13579@Article{ foster92, 13580 author = {Ian Foster and William Gropp and Rick Stevens}, 13581 title = {The parallel scalability of the spectral transform method}, 13582 journal = {Monthly Weather Review}, 13583 volume = {120}, 13584 year = {1992}, 13585 pages = {835--850}, 13586 key = {Foster92 ! performance} 13587} 13588 13589@InBook{ fgn, 13590 author = {R. Freund and G. H. Golub and N. Nachtigal}, 13591 title = {Iterative Solution of Linear Systems}, 13592 series = {Acta Numerica}, 13593 year = {1992}, 13594 publisher = {Cambridge University Press}, 13595 pages = {57--100} 13596} 13597 13598@TechReport{ nachtigal90, 13599 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 13600 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13601 institution = {Massachusetts Institute of Technology}, 13602 month = mar, 13603 year = {1990}, 13604 number = {90-2}, 13605 key = {Nachtigal | Krylov} 13606} 13607 13608@Article{ nachtigal1992fnm, 13609 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13610 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 13611 journal = {SIAM Journal on Matrix Analysis and Applications}, 13612 volume = {13}, 13613 pages = {778}, 13614 year = {1992}, 13615 publisher = {SIAM} 13616} 13617 13618@TechReport{ embree1999descriptive, 13619 title = {How descriptive are {GMRES} convergence bounds}, 13620 author = {Embree, M.}, 13621 year = {1999}, 13622 number = {08}, 13623 institution = {Oxford University Computing Laboratory} 13624} 13625 13626@Article{ vorst92, 13627 author = {H. van der Vorst}, 13628 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 13629 of nonsymmetric linear systems}, 13630 journal = {SIAM J. Sci. Stat. Comput.}, 13631 year = {1992}, 13632 volume = {13}, 13633 pages = {631--644} 13634} 13635 13636@Article{ eisenstat81, 13637 author = {S. Eisenstat}, 13638 title = {Efficient Implementation of a Class of {CG} Methods}, 13639 journal = {SIAM J. Sci. Stat. Comput.}, 13640 year = {1981}, 13641 volume = {2}, 13642 pages = {1--4} 13643} 13644 13645@Manual{ ibm-essl, 13646 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 13647 Reference}, 13648 organization = {IBM}, 13649 year = {1992}, 13650 key = {IBM-ESSL} 13651} 13652 13653@Manual{ ibm-eui, 13654 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 13655 Release 2.0}, 13656 organization = {IBM}, 13657 month = jun, 13658 year = {1994}, 13659 key = {IBM-EUI} 13660} 13661 13662@Manual{ ibm-euih, 13663 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 13664 organization = {IBM}, 13665 author = {Peter Hochschild}, 13666 year = {1993}, 13667 key = {IBM-EUIH} 13668} 13669 13670@TechReport{ mpi, 13671 title = {Document for a Standard Message-Passing Interface}, 13672 author = {Message Passing Interface Forum}, 13673 institution = {University of Tennessee}, 13674 number = {CS-93-214}, 13675 month = nov, 13676 year = {1993}, 13677 key = {MPI Standard} 13678} 13679 13680@Unpublished{ mpi-final-web, 13681 author = {Message Passing Interface Forum}, 13682 title = {{MPI}: A Message-Passing Interface Standard}, 13683 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 13684 year = {1994}, 13685 month = may 13686} 13687 13688@Book{ hockney-jesshope, 13689 author = {R. W. Hockney and C. R. Jesshope}, 13690 title = {Parallel Computers 2}, 13691 publisher = {Adam Hilger}, 13692 year = {1988} 13693} 13694 13695@Book{ cm-fortran, 13696 author = {{Thinking Machines Corporation}}, 13697 title = {Users Manual for CM-Fortran}, 13698 publisher = {Thinking Machines Corporation}, 13699 year = {1993} 13700} 13701 13702@TechReport{ chang93, 13703 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 13704 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 13705 institution = {Yale Department of Computer Science}, 13706 number = {YALEU/DCS/RR-994}, 13707 month = nov, 13708 year = {1993}, 13709 key = {BDD|diag} 13710} 13711 13712@InProceedings{ gropplevine93, 13713 author = {N. Galbreath and W. Gropp and D. Levine}, 13714 title = {Applications-Driven Parallel {I/O}}, 13715 booktitle = {Proceedings of Supercomputing '93}, 13716 year = {1993}, 13717 pages = {462--471} 13718} 13719 13720@Book{ siegle85, 13721 author = {H. J. Siegel}, 13722 title = {Interconnection Networks for Large Scale Parallel Processing}, 13723 publisher = {Lexington Books}, 13724 year = {1985}, 13725 key = {Network Comparison} 13726} 13727 13728@Article{ lawrie75, 13729 author = {D. H. Lawrie}, 13730 title = {Access and alignment of data in an array processor}, 13731 journal = {IEEE Transactions on Computers}, 13732 volume = {C-24}, 13733 number = {12}, 13734 month = dec, 13735 year = {1975}, 13736 pages = {1145--1155}, 13737 key = {Omega Network} 13738} 13739 13740@Book{ knuth1986, 13741 title = {The {\TeX}{Book}}, 13742 author = {Donald Ervin Knuth and Duane Bibby}, 13743 volume = {1993}, 13744 year = {1986}, 13745 publisher = {Addison-Wesley Reading, Massachusetts} 13746} 13747 13748@Book{ lamport86, 13749 author = {Leslie Lamport}, 13750 title = {{LaTeX}: A document preparation system}, 13751 publisher = {Addison-Wesley}, 13752 year = {1986}, 13753 key = {Latex Manual} 13754} 13755 13756@InProceedings{ gropp-lusk:unix-tools, 13757 author = {William Gropp and Ewing Lusk}, 13758 title = {Scalable {U}nix Tools on Parallel Processors}, 13759 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 13760 publisher = {IEEE}, 13761 pages = {56--62} 13762} 13763 13764@InProceedings{ jp:bell_prize, 13765 author = {Mark Jones and Paul Plassmann}, 13766 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 13767 Applications}, 13768 booktitle = {Proceedings of Supercomputing '92}, 13769 publisher = {IEEE Computer Society Press}, 13770 year = {1992}, 13771 pages = {551--560} 13772} 13773 13774@COMMENT{WEB, CWEB references (for doctext)} 13775@TechReport{ web, 13776 author = {Donald E. Knuth}, 13777 title = {The {\tt WEB} system of structured documentation}, 13778 institution = {Computer Science Department, Stanford University}, 13779 year = {1983}, 13780 number = {980}, 13781 month = sep 13782} 13783 13784@Article{ literatepgm, 13785 author = {Donald E. Knuth}, 13786 title = {Literate Programming}, 13787 journal = {Computer Journal}, 13788 year = {1984}, 13789 volume = {27}, 13790 number = {2}, 13791 pages = {91--111} 13792} 13793 13794@Unpublished{ cweb-code, 13795 author = {Silvio Levy and Donald E. Knuth}, 13796 title = {CWEB}, 13797 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 13798} 13799 13800@Article{ jp:scalable, 13801 author = {Mark Jones and Paul Plassmann}, 13802 title = {Scalable Iterative Solution of Sparse Linear Systems}, 13803 journal = {Parallel Computing}, 13804 volume = {20}, 13805 number = {5}, 13806 month = may, 13807 year = {1994}, 13808 pages = {753--773} 13809} 13810 13811@Article{ jp:pcolor, 13812 author = {Mark T. Jones and Paul E. Plassmann}, 13813 title = {A Parallel Graph Coloring Heuristic}, 13814 journal = {SIAM J. Sci. Comput.}, 13815 volume = {14}, 13816 number = {3}, 13817 pages = {654-669}, 13818 year = {1993} 13819} 13820 13821@TechReport{ block_solve, 13822 author = {Mark T. Jones and Paul E. Plassmann}, 13823 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 13824 Sparse Linear Systems}, 13825 institution = {Argonne National Laboratory}, 13826 year = {1992}, 13827 number = {ANL-92/46}, 13828 key = {JonesPlassmann92 ! block_solve} 13829} 13830 13831@InProceedings{ supercond, 13832 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 13833 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 13834 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 13835 Conference}, 13836 month = feb, 13837 year = {1994}, 13838 key = {McInnesPalumbo94 ! superconductivity } 13839} 13840 13841@Unpublished{ preosti:93, 13842 author = {Gianfranco Preosti}, 13843 title = { }, 13844 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 13845 year = {1993}, 13846 key = {preosti93 ! GL-tilt3d} 13847} 13848 13849@Unpublished{ more:93, 13850 author = {Jorge J. Mor\'{e}}, 13851 title = { }, 13852 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 13853 {A}rgonne {N}ational {L}aboratory}, 13854 year = {1993}, 13855 key = {more93 ! MINPACK-2} 13856} 13857 13858@Article{ brownsaad:90, 13859 author = {Peter N. Brown and Youcef Saad}, 13860 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 13861 journal = {SIAM J. Sci. Stat. Comput.}, 13862 year = {1990}, 13863 volume = {11}, 13864 pages = {450-481} 13865} 13866 13867@Book{ using-mpi, 13868 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 13869 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 13870 publisher = {MIT Press}, 13871 year = {1994} 13872} 13873 13874@Book{ using-mpi2, 13875 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 13876 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 13877 publisher = {MIT Press}, 13878 year = {1999} 13879} 13880 13881@Article{ hs:52, 13882 author = {Magnus R. Hestenes and Eduard Steifel}, 13883 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 13884 journal = {J. Research of the National Bureau of Standards}, 13885 year = {1952}, 13886 volume = {49}, 13887 pages = {409-436} 13888} 13889 13890@Article{ so:89, 13891 author = {Peter Sonneveld}, 13892 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 13893 journal = {SIAM J. Sci. Stat. Comput.}, 13894 year = {1989}, 13895 volume = {10}, 13896 pages = {36-52} 13897} 13898 13899@Article{ v:92, 13900 author = {{H. A.} {van der Vorst}}, 13901 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 13902 of nonsymmetric linear systems}, 13903 journal = {SIAM J. Sci. Stat. Comput.}, 13904 volume = {13}, 13905 year = {1992}, 13906 pages = {631-644} 13907} 13908 13909@Article{ f:93, 13910 author = {Roland W. Freund}, 13911 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 13912 Systems}, 13913 journal = {SIAM J. Sci. Stat. Comput.}, 13914 volume = {14}, 13915 year = {1993}, 13916 pages = {470-482} 13917} 13918 13919@Article{ ish:89, 13920 author = {S. Ishizuka}, 13921 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 13922 journal = {Combustion and Flame}, 13923 volume = {75}, 13924 year = {1989}, 13925 pages = {367-379} 13926} 13927 13928@Book{ williams89, 13929 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 13930 author = {F.A. Williams}, 13931 publisher = {Addison-Wesley}, 13932 year = {1989}, 13933 pages = {367-379} 13934} 13935 13936@Book{ ra75, 13937 author = {R. Aris}, 13938 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 13939 publisher = {Oxford}, 13940 year = {1975} 13941} 13942 13943@Book{ bebernes89, 13944 author = {J. Bebernes and D. Eberly}, 13945 title = {Mathematical Problems from Combustion Theory}, 13946 publisher = {Springer-Verlag}, 13947 series = {Applied Mathematical Sciences 83}, 13948 year = {1989} 13949} 13950 13951@InProceedings{ kikuchi89, 13952 author = {F. Kikuchi}, 13953 booktitle = { Computing Methods in Applied Sciences and Engineering}, 13954 editor = {R. Glowinski and J. L. Lions}, 13955 publisher = {Springer-Verlag}, 13956 series = {Lecture Notes in Mathematics}, 13957 title = {Finite element approximations to bifurcation problems of turning point type}, 13958 year = {1977} 13959} 13960 13961@Article{ rg85, 13962 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 13963 title = {Continuation-conjugate Gradient Methods for the Least Squares Solution of 13964 Nonlinear Boundary Problems}, 13965 journal = {SIAM J. Sci. Stat. Comput.}, 13966 volume = {6}, 13967 year = {1985}, 13968 pages = {793-832} 13969} 13970 13971@InProceedings{ whitfield91, 13972 author = {D. Whitfield and L. Taylor}, 13973 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13974 Schemes}, 13975 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 13976 misc = {AIAA-91-1539}, 13977 pages = {134-145}, 13978 year = {1991} 13979} 13980 13981@InProceedings{ quinlan1, 13982 author = {M. Lemke and D. Quinlan}, 13983 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 13984 Architecture-Independent Development of Structured Grid Applications}, 13985 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 13986 publisher = {Springer Verlag}, 13987 year = {1992} 13988} 13989 13990@InProceedings{ quinlan2, 13991 author = {R. Parsons and D. Quinlan}, 13992 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 13993 Computations}, 13994 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 13995 year = {1994} 13996} 13997 13998% ***** Overview of functionality in Diffpack 13999@InBook{ dpoverview, 14000 author = {Bruaset, A. M. and Langtangen, H. P.}, 14001 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14002 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 14003 {Diffpack}}, 14004 publisher = {Birkh{\"{a}}user}, 14005 pages = {61--90}, 14006 year = {1997} 14007} 14008 14009% ***** Short overview of Diffpack 14010@InCollection{ dpoverview2, 14011 author = {Bruaset, A. M. and Langtangen, H. P.}, 14012 editor = {A. Sydow}, 14013 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 14014 and Applied Mathematics}, 14015 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 14016 pages = {553--558}, 14017 volume = {4}, 14018 year = {1997} 14019} 14020 14021% ***** Comprehensive documentation of Diffpack and 14022% associated numerical methods: 14023@Book{ dpbook, 14024 author = {H. P. Langtangen}, 14025 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 14026 Software. Part I}, 14027 series = {Lecture Notes in Computational Science and Engineering}, 14028 publisher = {Springer-Verlag}, 14029 year = {1998} 14030} 14031 14032% ***** Design issues of the linear solvers in Diffpack, serves also as a 14033% collection of examples on O-O in numerical computing 14034@Article{ ambhpl97a, 14035 author = {A. M. Bruaset and H. P. Langtangen }, 14036 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 14037 journal = {Transactions on Mathematical Software}, 14038 volume = {23 }, 14039 pages = {50--80}, 14040 year = {1997} 14041} 14042 14043@Misc{ dpurl, 14044 author = {{Diffpack Web page}}, 14045 howpublished = {\url{http://www.diffpack.com}} 14046} 14047 14048% ***** General intro to object-oriented numerics for "FORTRAN programmers" 14049@InCollection{ oonintro, 14050 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 14051 editor = {D{\ae}hlen, M. and Tveito, A.}, 14052 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14053 title = {Object-Oriented Numerics}, 14054 publisher = {Birkh{\"{a}}user}, 14055 year = {1997} 14056} 14057 14058% ***** Efficiency comparison: BLAS 1, Diffpack, C, 14059% and finite element applications (F77 vs Diffpack) 14060@InCollection{ dpefficiency, 14061 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 14062 H. P. and Miller, C. T.}, 14063 editor = {D{\ae}hlen, M. and Tveito, A.}, 14064 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14065 title = {On the Efficiency of {C++} in Scientific Computing}, 14066 publisher = {Birkh{\"{a}}user}, 14067 pages = {91--118}, 14068 year = {1997} 14069} 14070 14071% ***** Parallel concept in Diffpack: 14072@InCollection{ dpparallel, 14073 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 14074 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 14075 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 14076 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 14077 Simulators}, 14078 publisher = {Springer--Verlag}, 14079 series = {Lecture Notes in Computer Science}, 14080 pages = {161--168}, 14081 year = {1997} 14082} 14083 14084% ***** DD and ML methods in Diffpack: 14085@InCollection{ dpddml, 14086 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 14087 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 14088 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 14089 title = {Domain decomposition and multilevel methods in Diffpack}, 14090 year = {1997} 14091} 14092 14093@InProceedings{ bsca98, 14094 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 14095 Alexander}, 14096 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 14097 Optimization}, 14098 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14099 Scientific and Engineering Computing}, 14100 editor = {Mike Henderson et al.}, 14101 pages = {165-173}, 14102 year = {1998} 14103} 14104 14105@Book{ scalapack-user-guide, 14106 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 14107 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 14108 Stanley and D. Walker and R. C. Whaley}, 14109 title = {Sca{LAPACK} Users' Guide}, 14110 publisher = {SIAM}, 14111 address = {Philadelphia, PA}, 14112 year = {1997} 14113} 14114 14115@InProceedings{ keyes99, 14116 author = {D. E. Keyes}, 14117 title = {How Scalable is Domain Decomposition in Practice?}, 14118 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 14119 Methods}, 14120 editor = {C.-H. Lai et al.}, 14121 publisher = {Domain Decomposition Press, Bergen}, 14122 note = {To appear}, 14123 year = {1999} 14124} 14125 14126@Article{ fun3d, 14127 author = {W. K. Anderson and D. L. Bonhaus}, 14128 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 14129 grids}, 14130 journal = {Computers and Fluids}, 14131 year = {1994}, 14132 volume = {23}, 14133 pages = {1--21} 14134} 14135 14136% ------------------------------------------------------------------------- 14137% ------------------------------------------------------------------------- 14138@Article{ torczon, 14139 author = {Dennis, Jr., J. E. and V.~Torczon}, 14140 title = {Direct Search Methods on Parallel Machines}, 14141 journal = {SIAM J. Optimization}, 14142 volume = {1}, 14143 pages = {448--474}, 14144 year = {1991}, 14145 key = {Torczon !PDS} 14146} 14147 14148@InProceedings{ wt91, 14149 author = {D. L. Whitfield and L. K. Taylor}, 14150 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 14151 Schemes}, 14152 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 14153 misc = {AIAA-91-1539}, 14154 pages = {134-145}, 14155 year = {1991} 14156} 14157 14158@Article{ ew96, 14159 author = {S. C. Eisenstat and H. F. Walker}, 14160 title = {Choosing the forcing terms in an inexact {N}ewton method}, 14161 journal = {SIAM J. Scientific Computing}, 14162 volume = {17}, 14163 year = {1996}, 14164 pages = {16--32} 14165} 14166 14167@Book{ thi93, 14168 author = {{Thinking Machines Corporation}}, 14169 title = {Users Manual for CM-Fortran}, 14170 publisher = {Thinking Machines Corporation}, 14171 year = {1993} 14172} 14173 14174@Book{ mortonmayers94, 14175 author = {K. W. Morton and D. F. Mayers}, 14176 title = {Numerical Solution of Partial Differential Equations}, 14177 publisher = {Press Syndicate of the University of Cambridge}, 14178 year = {1994} 14179} 14180 14181@Book{ heath97, 14182 author = {Michael T. Heath}, 14183 title = {Scientific Computing: An Introductory Survey}, 14184 publisher = {McGraw Hill}, 14185 year = {1997} 14186} 14187 14188@Article{ captools96, 14189 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 14190 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 14191 Performance on the Parallelization of Structured Mesh Codes}, 14192 journal = {Parallel Computing}, 14193 volume = {22}, 14194 pages = {197-226}, 14195 year = {1996} 14196} 14197 14198@Misc{ nastran-web-page, 14199 author = {{MSC Software Corporation}}, 14200 title = {{NASTRAN} {W}eb page}, 14201 howpublished = {\url{http://www.mechsolutions.com/products/nastran/}}, 14202 year = {2024} 14203} 14204 14205@Book{ hpf, 14206 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 14207 Zosel}, 14208 title = {The High Performance Fotran Handbook}, 14209 publisher = {MIT Press}, 14210 year = {1994} 14211} 14212 14213@InProceedings{ keyes98, 14214 author = {D. E. Keyes}, 14215 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 14216 Architectures}, 14217 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 14218 editors = {M. D. Salas and W. K. Anderson}, 14219 ppublisher = {Elsevier}, 14220 year = {1998} 14221} 14222 14223@InProceedings{ pooma-atlas, 14224 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14225 J. V. W. Reynders and M. Tholburn}, 14226 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14227 Applications}, 14228 year = {1995}, 14229 month = dec, 14230 booktitle = {Supercomputing '95 Proceedings} 14231} 14232 14233% --------------------------------------------------------------------------------- 14234% New bib entries for CRPC paper 14235@Misc{ mgnet-web-page, 14236 author = {Craig C. Douglas}, 14237 title = {{MGNet Web page}}, 14238 note = {See {\tt http://\-www.mgnet.org}} 14239} 14240 14241@Misc{ dagh-web-page, 14242 author = {M. Parashar and J. C. Browne}, 14243 title = {{DAGH Web page}}, 14244 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14245} 14246 14247@Misc{ parasol-web-page, 14248 key = {PARASOL}, 14249 title = {{PARASOL Web page}}, 14250 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14251} 14252 14253@Misc{ pooma-web-page, 14254 author = {{POOMA Web page}}, 14255 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14256} 14257 14258@Misc{ mudpack-web-page, 14259 author = {John C. Adams}, 14260 title = {{MUDPACK Web page}}, 14261 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14262} 14263 14264@Misc{ pellpack-web-page, 14265 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14266 title = {{Parallel ELLPACK Web page}}, 14267 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14268} 14269 14270@InProceedings{ pellpack95, 14271 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14272 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14273 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14274 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14275 address = {Albuquerque, NM}, 14276 year = {1995} 14277} 14278 14279@Misc{ nhse-web-page, 14280 author = {{National High-Performance Software Exchange Web page}}, 14281 note = {See {\tt http://\-www.nhse.org}} 14282} 14283 14284@Misc{ doug-web-page, 14285 author = {Mark J. Hagger and Linda Stals}, 14286 title = {{DOUG Web Page}}, 14287 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14288} 14289 14290@TechReport{ doug97, 14291 author = {Mark J. Hagger}, 14292 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14293 institution = {Mathematical Sciences, University of Bath}, 14294 year = {1997}, 14295 number = {9706}, 14296 note = {Advances in Computational Mathematics (to appear)} 14297} 14298 14299@Misc{ ug-web-page, 14300 author = {{UG Web Page}}, 14301 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14302} 14303 14304@Article{ ug97, 14305 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14306 Rentz-Reichert and C. Wieners}, 14307 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14308 journal = {Computing and Visualization in Science}, 14309 year = {1997}, 14310 volume = {}, 14311 pages = {} 14312} 14313 14314@Misc{ vecfem-web-page, 14315 author = {Lutz Grosz}, 14316 title = {{VECFEM Web Page}}, 14317 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14318} 14319 14320@Misc{ atlas-web-page, 14321 author = {R. Clint {Whaley et al.}}, 14322 title = {{ATLAS Web Page}}, 14323 howpublished = {\url{http://math-atlas.sourceforge.net}} 14324} 14325 14326@Misc{ fenics-web-page, 14327 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14328 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14329 title = {{FEniCS Web Page}}, 14330 note = {\url{http://www.fenicsproject.org}}, 14331 year = {2005} 14332} 14333 14334@Misc{ matlab-web-page, 14335 author = {{The} {MathWorks}}, 14336 title = {{Matlab} {Web} page}, 14337 url = {http://www.mathworks.com} 14338} 14339 14340@Misc{ phipac-web-page, 14341 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14342 and D. Lam}, 14343 title = {{PHiPAC Web Page}}, 14344 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14345} 14346 14347@InProceedings{ kelp, 14348 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14349 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14350 booktitle = {Irregular '96}, 14351 year = {1996} 14352} 14353 14354@Unpublished{ kelp-web-page, 14355 author = {Scott Baden}, 14356 title = {{KeLP} {W}eb page}, 14357 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14358} 14359 14360@InProceedings{ hk99, 14361 author = {R. Hornung and S. 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The different versions are examined for efficiency on a computer 14423 architecture which uses vector processing and has pipelined instruction execution. 14424 By using the advanced architectural features of such machines, one can usually 14425 achieve maximum performance, and tremendous improvements in terms of execution 14426 speed can be seen over conventional computers.}, 14427 classification= {723; 921}, 14428 journalabr = {SIAM Rev}, 14429 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 14430 mathematical programming; vector pipeline machine} 14431} 14432 14433@Book{ qv99, 14434 author = {Alfio Quarteroni and Alberto Valli}, 14435 title = {Domain Decomposition Methods for Partial Differential Equations}, 14436 publisher = {Oxford Science Publications}, 14437 address = {Oxford}, 14438 year = {1999} 14439} 14440 14441@Book{ ksv97, 14442 editor = {David E. Keyes and Ahmed Sameh and V. 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Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 14632 and C. Woodward}, 14633 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 14634 journal = {ACM Transactions on Mathematical Software}, 14635 volume = {31}, 14636 number = {3}, 14637 pages = {363--396}, 14638 year = {2005} 14639} 14640 14641@InProceedings{ serban2005cvodes, 14642 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 14643 author = {Serban, Radu and Hindmarsh, Alan C}, 14644 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 14645 Dynamics and Control, Long Beach, CA}, 14646 year = {2005} 14647} 14648 14649@Article{ pvode99, 14650 author = {G. Byrne and A. Hindmarsh}, 14651 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 14652 journal = {Int. J. High Perf. Comput. 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Softw.}, 15711 volume = {31}, 15712 year = {2005}, 15713 pages = {326--350} 15714} 15715 15716@Unpublished{ compass:homepage, 15717 author = {Panagiotis {Spentzouris (PI)}}, 15718 title = {Community Petascale Project for Accelerator Science and Simulation (ComPASS)}, 15719 note = {SciDAC2 project, see \url{https://compass.fnal.gov/}} 15720} 15721 15722@Unpublished{ cmsnf:homepage, 15723 author = {{Todd Allen, Director}}, 15724 title = {{Center for Materials Science of Nuclear Fuel}}, 15725 note = {Energy Frontier Research Center, see 15726 \url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}} 15727} 15728 15729@Unpublished{ dvi-materials:project, 15730 author = {{L.~C.} {McInnes (PI)}}, 15731 title = {Large-Scale Differential Variational Inequalities for Heterogeneous Materials}, 15732 note = {{SciDAC}-e project}, 15733 year = {2011} 15734} 15735 15736@Misc{ scidac:homepage, 15737 author = {{DOE Office of Science}}, 15738 title = {{Scientific Discovery through Advanced Computing}}, 15739 year = {2007}, 15740 howpublished = {\url{http://www.scidac.gov}} 15741} 15742 15743@Misc{ corba, 15744 author = {{Object Management Group}}, 15745 year = {2007}, 15746 title = {{Common Object Request Broker Architecture (CORBA)}}, 15747 howpublished = {\url{http://www.corba.org}} 15748} 15749 15750@Article{ uedge, 15751 author = {T.~D. Rognlien and D.~D. Ryutov and N. Mattor and G.~D. Porter}, 15752 title = {Two-Dimensional Electric Fields and Drifts near the Magnetic Separatrix in 15753 Divertor Tokamak}, 15754 journal = {J. Plasma Physics}, 15755 year = {1999}, 15756 volume = {6}, 15757 pages = {1851}, 15758 note = {also see user manual at http://www.mfescience.org, then UEDGE link} 15759} 15760 15761@Article{ bout, 15762 author = {X.~Q. Xu and R.~H. Cohen and T.~D. Rognlien and J.~R. Myra}, 15763 title = {Low-to-High Confinement Transition Simulations in Divertor Geometry}, 15764 journal = {J. Plasma Physics}, 15765 year = {2000}, 15766 volume = {7}, 15767 pages = {1951}, 15768 note = {} 15769} 15770 15771@Article{ bout++, 15772 author = {B. Dudson and M. Umansky and X.~Q. Xu and P. B. Snyder and H. R. Wilson}, 15773 title = {{BOUT++}: A Framework for Parallel Plasma Fluid Simulations}, 15774 journal = {Computer Physics Communications}, 15775 year = {2009}, 15776 volume = {180}, 15777 issue = {9}, 15778 pages = {1467 -- 1480}, 15779 note = {} 15780} 15781 15782@Article{ tempest, 15783 author = {Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and M.R. Dorr and J.A. Hittinger 15784 and G. Kerbel and W.M. Nevins and T. Rognlien}, 15785 title = {Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST}, 15786 journal = {Bull. Am. Phys. Soc. }, 15787 year = {2005}, 15788 volume = {50}, 15789 number = {86}, 15790 pages = {CP1}, 15791 note = {} 15792} 15793 15794@Article{ ccahpc, 15795 author = {David E. Bernholdt and Benjamin A. Allan and Robert Armstrong and Felipe Bertrand 15796 and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif 15797 and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James 15798 A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia 15799 Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek 15800 Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende 15801 and Theresa L. Windus and Shujia Zhou}, 15802 title = {A Component Architecture for High-Performance Scientific Computing}, 15803 journal = {Intl. J. High-Perf. Computing Appl.}, 15804 volume = {20}, 15805 pages = {163--202}, 15806 year = {2006}, 15807 note = {ACTS Collection special issue} 15808} 15809 15810@Misc{ cca-forum:homepage, 15811 author = {{Common Component Architecture Forum}}, 15812 note = {\url{http://www.cca-forum.org}}, 15813 year = {2010} 15814} 15815 15816@Misc{ petsc:driven-cavity-example, 15817 title = {{PETSc Driven Cavity Example Code}}, 15818 author = {B. F. {Smith et al.}}, 15819 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 15820} 15821 15822@Misc{ petsc-dm:webpage, 15823 author = {B. F. {Smith et al.}}, 15824 title = {{PETSc DM Webpage}}, 15825 howpublished = {\url{https://petsc.org/release/manualpages/DM/}}, 15826 year = {2018} 15827} 15828 15829@Misc{ unic-ref, 15830 author = {Giuseppe Palmiotti}, 15831 title = {{UNIC} Neutronics Software}, 15832 note = {Nuclear Engineering Division, Argonne National Laboratory} 15833} 15834 15835% ----------------------------------------------------------------------- 15836% Model coupling refs 15837@Book{ greve-blatter, 15838 author = {Ralf Greve and Heinz Blatter}, 15839 title = {Dynamics of Ice Sheets and Glaciers}, 15840 series = {Advances in Geophysical and Environmental Mechanics and Mathematics}, 15841 publisher = {Springer}, 15842 year = {2009} 15843} 15844 15845@Misc{ doe-isicles, 15846 key = {ISICLES}, 15847 title = {Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}}, 15848 howpublished = {\url{http://www.csm.ornl.gov/ISICLES/index.html}} 15849} 15850 15851@Article{ safta2011tchem, 15852 title = {TChem-a software toolkit for the analysis of complex kinetic models}, 15853 author = {Safta, Cosmin and Najm, Habib N and Knio, Omar}, 15854 journal = {Sandia Report, SAND2011-3282}, 15855 year = {2011} 15856} 15857 15858@Misc{ chemkin-website, 15859 key = {chemkin}, 15860 title = {ANSYS Chemkin-Pro Website}, 15861 howpublished = {\url{http://www.ansys.com/products/fluids/ansys-chemkin-pro}}, 15862 year = {2017} 15863} 15864 15865@Misc{ mct-website, 15866 key = {MCT}, 15867 title = {{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite}, 15868 howpublished = {\url{http://www.mcs.anl.gov/mct}} 15869} 15870 15871@Article{ larson:05, 15872 author = {Jay Larson and Robert Jacob and Everest Ong}, 15873 title = {{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building 15874 Multi-Physics Parallel Coupled Models}, 15875 journal = {Int. 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Dongarra and C. J. K. Tan}, 15937 series = {Lecture Notes in Computer Science}, 15938 volume = {2073}, 15939 publisher = {Springer-Verlag} 15940} 15941 15942@InProceedings{ lefantzi03, 15943 author = {S. Lefantzi and J. Ray}, 15944 year = {2003}, 15945 title = {A Component-based Scientific Toolkit for Reacting Flows}, 15946 booktitle = {Proc. Second MIT Conference on Computational Fluid and Solid Mechanics}, 15947 volume = {2}, 15948 publisher = {Elsevier} 15949} 15950 15951@Article{ boville98, 15952 author = {B. A. Boville and P. R. Gent}, 15953 title = {The {NCAR} Climate System Model, Version One}, 15954 journal = {Journal of Climate}, 15955 volume = {11}, 15956 year = {1998}, 15957 pages = {1115--1130} 15958} 15959 15960@Misc{ paraschivoiu99, 15961 author = {M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes}, 15962 title = {Multi-domain multi-model formulation for compressible flows: Conservative 15963 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 15964 note = {AIAA Paper 99-0784}, 15965 year = {1999} 15966} 15967 15968@Article{ peszynska, 15969 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 15970 title = {Mortar upscaling for multiphysics flow in porous media}, 15971 journal = {Computational Geosciences} 15972} 15973 15974@TechReport{ wheeler00, 15975 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 15976 title = {A distributed computing portal for coupling multi-physics and multiple domains in 15977 porous media}, 15978 institution = {University of Texas at Austin}, 15979 number = {TICAM 00-03}, 15980 year = {2000} 15981} 15982 15983@TechReport{ peszynska00, 15984 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 15985 title = {Multiphysics Coupling of Codes}, 15986 institution = {University of Texas at Austin}, 15987 number = {TICAM 00-02}, 15988 year = {2000} 15989} 15990 15991@Article{ joshaghanijoodatnakshatrala2019, 15992 title = {A stabilized mixed discontinuous Galerkin formulation for double 15993 porosity/permeability model}, 15994 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 15995 journal = {Computer Methods in Applied Mechanics and Engineering}, 15996 volume = {352}, 15997 pages = {508--560}, 15998 year = {2019} 15999} 16000 16001@InProceedings{ cai99, 16002 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 16003 title = {An explicit multi-model compressible flow formulation based on the full potential 16004 equation and the {Euler} equations on {3D} unstructured meshes}, 16005 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 16006 Methods}, 16007 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 16008 year = {1999} 16009} 16010 16011@Article{ he05, 16012 author = {Yun He and Chris H. Q. Ding}, 16013 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 16014 Architectures}, 16015 year = {2005}, 16016 volume = {19}, 16017 pages = {329--240}, 16018 number = {3}, 16019 journal = {Int. Journal of High Performance Computing Applications} 16020} 16021 16022@InProceedings{ uiuc-rocket-center02, 16023 author = {W. A. Dick and M. T. Heath}, 16024 title = {Whole System Simulation of Solid Propellant Rockets}, 16025 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 16026 month = jul, 16027 year = {2002} 16028} 16029 16030@InProceedings{ toth04, 16031 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 16032 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 16033 Oehmke}, 16034 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 16035 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 16036 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 16037 Sun-Earth Connection}, 16038 year = {2004}, 16039 publisher = {Elsevier}, 16040 pages = {383--397} 16041} 16042 16043@Misc{ csdrm:web, 16044 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 16045 Shepherd}, 16046 title = {{Center for Simulation of Dynamic Response of Materials}}, 16047 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 16048} 16049 16050@Misc{ csar:web, 16051 author = {M. {Heath (Director)}}, 16052 title = {{Center for Simulation of Advanced Rockets}}, 16053 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 16054} 16055 16056@Misc{ csafe:web, 16057 author = {D. {Pershing (Director)}}, 16058 title = {{Center for Simulation of Accidental Fires and Explosions}}, 16059 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 16060} 16061 16062@Misc{ cits:web, 16063 author = {P. {Moin (Director)}}, 16064 title = {{Center for Integrated Turbulence Simulations}}, 16065 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 16066} 16067 16068@Misc{ flash:web, 16069 author = {D. {Lamb (Director)}}, 16070 title = {{Center for Integrated Turbulence Simulations}}, 16071 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 16072} 16073 16074@TechReport{ utah-csafe03, 16075 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 16076 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 16077 Problems, Part 1: Algorithm Development}, 16078 institution = {University of Utah, Center for the Simulation of Accidental Fires and 16079 Explosions}, 16080 year = {2003} 16081} 16082 16083@InBook{ shepherd07, 16084 author = {M. Shepherd and E. Seol and B. FrantzDale}, 16085 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 16086 year = {2007}, 16087 booktitle = {CRC Handbook of Dynamic System Modeling}, 16088 publisher = {Wiley}, 16089 pages = {1--41}, 16090 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 16091} 16092 16093@InProceedings{ cactus02, 16094 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 16095 Radke and Edward Seidel and John Shalf}, 16096 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 16097 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 16098 year = {2002}, 16099 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 16100} 16101 16102@Misc{ cactus:homepage, 16103 author = {G. {Allen et al.}}, 16104 title = {{Cactus Web page}}, 16105 howpublished = {\url{http://cactuscode.org}} 16106} 16107 16108@Misc{ open-grid-forum:web, 16109 key = {{Open Grid Forum}}, 16110 title = {{Open Grid Forum}}, 16111 note = {See \url{http://www.ogf.org}} 16112} 16113 16114@Misc{ nox:web, 16115 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 16116 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 16117 note = {See \url{http://software.sandia.gov/nox}} 16118} 16119 16120@Misc{ chombo:web, 16121 author = {P. {Colella (PI)}}, 16122 title = {{Chombo}}, 16123 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 16124} 16125 16126@Article{ lanzkron96, 16127 author = {P. J. Lanzkron and D. J. Rose and J. T. Wilkes}, 16128 title = {An Analysis of Approximate Nonlinear Elimination}, 16129 journal = {SIAM J. Sci. Comput.}, 16130 volume = {17}, 16131 year = {1996}, 16132 pages = {538--559} 16133} 16134 16135@Article{ jiang95, 16136 author = {J. Jiang and P. Forsyth}, 16137 title = {Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} 16138 Equations}, 16139 journal = {Computers and Fluids}, 16140 volume = {24}, 16141 pages = {753--770}, 16142 year = {1995} 16143} 16144 16145@Article{ young90, 16146 author = {D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant}, 16147 title = {Global Convergence of Inexact {Newton} Methods for Transonic Flow}, 16148 journal = {Int. J. Numer. Methods Fluids}, 16149 volume = {11}, 16150 pages = {1075--1095}, 16151 year = {1990} 16152} 16153 16154@Article{ fishwick04, 16155 author = {Paul A. Fishwick}, 16156 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 16157 to Interrelating Model Structures}, 16158 journal = {SCS Trans. on Simulation}, 16159 note = {Special Issue in Grand Challenges in Computer Simulation}, 16160 year = {2004} 16161} 16162 16163@Article{ fishwick03, 16164 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 16165 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 16166 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 16167 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 16168 year = {2003} 16169} 16170 16171@InProceedings{ kirner00, 16172 author = {T. G. Kirner and V. F. 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Messerschmitt}, 16198 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 16199 journal = {Int. Journal of Computer Simulation}, 16200 volume = {4}, 16201 pages = {155--182}, 16202 year = {1994} 16203} 16204 16205@Article{ mu95, 16206 author = {M. Mu and J.R. Rice}, 16207 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 16208 journal = {Comp. Syst. Engr.}, 16209 volume = {6}, 16210 year = {1995}, 16211 pages = {87--95} 16212} 16213 16214@TechReport{ drashansky96, 16215 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 16216 author = {R. Drashansky and A. Joshi and J. R. Rice}, 16217 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 16218 year = {1996} 16219} 16220 16221@Article{ michopoulos05, 16222 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 16223 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 16224 journal = {Journal of Computing and Information Science in Engineering}, 16225 volume = {5}, 16226 issue = {3}, 16227 pages = {198--213}, 16228 year = {2005} 16229} 16230 16231@Article{ dubey09, 16232 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16233 Multiphysics Simulation Code}, 16234 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16235 Siegel and K. Weide}, 16236 journal = {Parallel Computing}, 16237 volume = {35}, 16238 issue = {10 -- 11}, 16239 pages = {512 -- 522}, 16240 year = {2009} 16241} 16242 16243@Book{ bottloring95, 16244 author = {Raoul Bott and Loring W. Tu}, 16245 title = {Differential Forms in Algebraic Topology}, 16246 publisher = {Springer}, 16247 year = {1995} 16248} 16249 16250@Book{ kobayashinomizu96, 16251 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16252 title = {Foundations of Differential Geometry}, 16253 publisher = {Wiley-Interscience}, 16254 year = {1996} 16255} 16256 16257@Article{ hornungkohn02, 16258 author = {Richard D. Hornung and Scott R. Kohn}, 16259 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16260 journal = {Concurrency and Computation: Practice and Experience}, 16261 volume = {14}, 16262 pages = {347--368}, 16263 year = {2002} 16264} 16265 16266@InProceedings{ concepts06, 16267 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16268 Gabriel Dos Reis and Andrew Lumsdaine}, 16269 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16270 booktitle = {Proceedings of OOPSLA 2006}, 16271 year = {2006}, 16272 pages = {???--???} 16273} 16274 16275@Book{ hatcher02, 16276 author = {Hatcher, Allen}, 16277 title = {Algebraic Topology}, 16278 publisher = {Cambridge University Press}, 16279 year = {2002} 16280} 16281 16282@Book{ gammahelmjohnsonvlissides95, 16283 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16284 development, offering timeless and elegant solutions to common problems in 16285 software design. It describes patterns for managing object creation, composing 16286 objects into larger structures, and coordinating control flow between objects. The 16287 book provides numerous examples where using composition rather than inheritance 16288 can improve the reusability and flexibility of code. Note, though, that it's not a 16289 tutorial but a catalog that you can use to find an object-oriented design pattern 16290 that's appropriate for the needs of your particular application--a selection for 16291 virtuoso programmers who appreciate (or require) consistent, well-engineered 16292 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16293 more valuable than ever! 16294 16295 Use the contents of the CD to create your own design documents and reusable 16296 components. The CD contains: 23 patterns you can cut and paste into your own 16297 design documents; sample code demonstrating pattern implementation; complete 16298 Design Patterns content in standard HTML format, with numerous hyperlinked 16299 cross-references; accessed through a standard web browser; Java-based dynamic 16300 search mechanism, enhancing online search capabilities; graphical user environment, 16301 allowing ease of navigation. 16302 16303 First published in 1995, this landmark work on object-oriented software design 16304 presents a catalog of simple and succinct solutions to common design problems. 16305 Created by four experienced designers, the 23 patterns contained herein have 16306 become an essential resource for anyone developing reusable object-oriented 16307 software. In response to reader demand, the complete text and pattern catalog are 16308 now available on CD-ROM. This electronic version of Design Patterns enables 16309 programmers to install the book directly onto a computer or network for use as an 16310 online reference for creating reusable object-oriented software. 16311 16312 The authors first describe what patterns are and how they can help you in the 16313 design process. They then systematically name, explain, evaluate, and catalog 16314 recurring designs in object-oriented systems. All patterns are compiled from 16315 real-world examples and include code that demonstrates how they may be implemented 16316 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16317 already own the book will want the CD to take advantage of its dynamic search 16318 mechanism and ready-to-install patterns.}}, 16319 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16320 citeulike-article-id={115158}, 16321 howpublished = {Hardcover}, 16322 isbn = {0201633612}, 16323 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16324 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16325 four gang gof java mathgamespatterns no-tag object object-orientation 16326 object-oriented of oo-patterns oop oriented pattern patterns programming se 16327 software software-development software-engineering software_design 16328 softwareengineering standard}, 16329 month = jan, 16330 publisher = {{Addison-Wesley Professional}}, 16331 title = {Design Patterns}, 16332 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16333 year = {1995} 16334} 16335 16336@InProceedings{ chaco95, 16337 author = {Bruce Hendrickson and Robert Leland}, 16338 title = {A multilevel algorithm for partitioning graphs}, 16339 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16340 (CDROM)}, 16341 year = {1995}, 16342 isbn = {0-89791-816-9}, 16343 pages = {28}, 16344 location = {San Diego, California, United States}, 16345 doi = {10.1145/224170.224228}, 16346 publisher = {ACM Press}, 16347 address = {New York} 16348} 16349 16350@Book{ aleksandrov98, 16351 author = {Aleksandrov, Pavel S.}, 16352 title = {Combinatorial Topology}, 16353 publisher = {Dover}, 16354 volume = {3}, 16355 year = {1998} 16356} 16357 16358@Book{ steenrod99, 16359 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16360 importance in modern physics--such as in gauge theory. This book, a succinct 16361 introduction to the subject by renown mathematician Norman Steenrod, was the first 16362 to present the subject systematically. 16363 16364 It begins with a general introduction to bundles, including such topics as 16365 differentiable manifolds and covering spaces. The author then provides brief 16366 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16367 using them to study further properties of fibre bundles. The result is a classic 16368 and timeless work of great utility that will appeal to serious mathematicians and 16369 theoretical physicists alike. }}, 16370 author = {Steenrod, Norman}, 16371 citeulike-article-id={712999}, 16372 howpublished = {Paperback}, 16373 isbn = {0691005486}, 16374 keywords = {fibre_bundles topology}, 16375 month = apr, 16376 publisher = {{Princeton University Press}}, 16377 title = {The Topology of Fibre Bundles. (PMS-14)}, 16378 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16379 year = {1999} 16380} 16381 16382@Book{ bredon97, 16383 author = {Bredon, Glen E.}, 16384 title = {Sheaf Theory}, 16385 publisher = {Springer}, 16386 pages = {524}, 16387 series = {Graduate Texts in Mathematics}, 16388 year = {1997} 16389} 16390 16391@TechReport{ tautgesmeyers04, 16392 title = {{MOAB}: A Mesh-Oriented Database}, 16393 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16394 Ernst}, 16395 institution = {Sandia National Laboratories}, 16396 number = {SAND2004-1592}, 16397 month = apr, 16398 year = {2004} 16399} 16400 16401@Article{ tautges04, 16402 author = {Timothy J. Tautges}, 16403 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16404 journal = {Engineering With Computers}, 16405 volume = {20}, 16406 pages = {286--293}, 16407 year = {2004} 16408} 16409 16410@InProceedings{ meyers02, 16411 author = {Ray Meyers et. al}, 16412 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16413 booktitle = {8th International conference on numerical grid generation in computational field 16414 simulations}, 16415 month = jun, 16416 year = {2002} 16417} 16418 16419@InProceedings{ seolshepard05, 16420 author = {E. S. Seol and Mark S. Shephard}, 16421 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16422 Analysis}, 16423 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16424 year = {2005} 16425} 16426 16427@Article{ lishephardbeall2005, 16428 title = {3D anisotropic mesh adaptation by mesh modification}, 16429 author = {Xiangrong Li and Mark S Shephard and Mark W Beall}, 16430 journal = {Computer methods in applied mechanics and engineering}, 16431 volume = {194}, 16432 number = {48-49}, 16433 pages = {4915--4950}, 16434 year = {2005}, 16435} 16436 16437@Article{ lushephardtendulkarbeall2014, 16438 title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry}, 16439 author = {Qiukai Lu and Mark S Shephard and Saurabh Tendulkar and Mark W Beall}, 16440 journal = {Engineering with Computers}, 16441 volume = {30}, 16442 pages = {271--286}, 16443 year = {2014}, 16444} 16445 16446@Article{ beallwalshshephard04, 16447 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16448 title = {A comparison of techniques for geometry access related to mesh generation}, 16449 journal = {Engineering With Computers}, 16450 volume = {20}, 16451 number = {3}, 16452 pages = {210--221}, 16453 year = {2004} 16454} 16455 16456@Article{ careyandersoncarneskirk04, 16457 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16458 Kirk}, 16459 title = {Some aspects of adaptive grid technology related to boundary and interior 16460 layers}, 16461 journal = {Journal of Computational Applied Mathematics}, 16462 volume = {166}, 16463 number = {1}, 16464 pages = {55--86}, 16465 year = {2004} 16466} 16467 16468@PhDThesis{ gralthesis, 16469 author = {Guntram Berti}, 16470 title = {Generic Software Components for Scientific Computing}, 16471 school = {TU Cottbus}, 16472 year = {2000}, 16473 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16474} 16475 16476@Article{ whitehead1949, 16477 title = {Combinatorial homotopy. I}, 16478 author = {John HC Whitehead}, 16479 journal = {Bulletin of the American Mathematical Society}, 16480 volume = {55}, 16481 number = {3. P1}, 16482 pages = {213--245}, 16483 year = {1949}, 16484 publisher = {American Mathematical Society} 16485} 16486 16487@Article{ beylkincoifmanrokhlin91, 16488 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16489 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16490 journal = {Communications on Pure and Applied Mathematics}, 16491 volume = {44}, 16492 pages = {141--183}, 16493 year = {1991} 16494} 16495 16496@Book{ wesseling92, 16497 author = {Pieter Wesseling}, 16498 title = {An Introduction to Multigrid Methods}, 16499 publisher = {John Wiley and Sons}, 16500 year = {1992} 16501} 16502 16503@Book{ grakakos04, 16504 author = {Loukas Grakakos}, 16505 title = {Classical and Modern Fourier Analysis}, 16506 publisher = {Pearson Education}, 16507 address = {New Jersey}, 16508 year = {2004} 16509} 16510 16511@Misc{ hlib-web-page, 16512 key = {HLib}, 16513 title = {{HLib} {Web} page}, 16514 note = {{\texttt{http://www.hlib.org/}}}, 16515 annote = {Hierarchical matrices for fast integral transform} 16516} 16517 16518@Article{ hackbusch99, 16519 author = {Wolfgang Hackbusch}, 16520 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16521 Introduction to {$\mathcal H$}-matrices}, 16522 journal = {Computing}, 16523 volume = {62}, 16524 pages = {89--108}, 16525 year = {1999} 16526} 16527 16528@TechReport{ kay1999green, 16529 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16530 equations}, 16531 author = {Kay, D. and Loghin, D.}, 16532 year = {1999}, 16533 institution = {Oxford University Computing Laboratory}, 16534 number = {99/06} 16535} 16536 16537@Article{ bebendorf2003existence, 16538 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16539 elliptic operators with {$L^\infty$}-coefficients}, 16540 author = {Bebendorf, M. and Hackbusch, W.}, 16541 journal = {Numerische Mathematik}, 16542 volume = {95}, 16543 number = {1}, 16544 pages = {1--28}, 16545 year = {2003}, 16546 publisher = {Springer} 16547} 16548 16549@Article{ hackbusch2005direct, 16550 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16551 H$}-matrix approximation}, 16552 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16553 journal = {Computing and Visualization in Science}, 16554 volume = {8}, 16555 number = {3}, 16556 pages = {179--188}, 16557 year = {2005}, 16558 publisher = {Springer} 16559} 16560 16561@TechReport{ duphof2003, 16562 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16563 Logg and L. R. Scott}, 16564 title = {The {FE}ni{CS} project}, 16565 institution = {Chalmers Finite Element Center Preprint Series}, 16566 number = {2003--21}, 16567 year = {2003} 16568} 16569 16570@Article{ flame01, 16571 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16572 Geijn}, 16573 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16574 journal = {Transactions on Mathematical Software}, 16575 volume = {27}, 16576 number = {4}, 16577 year = {2001}, 16578 pages = {422--455} 16579} 16580 16581@Article{ puschel05, 16582 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16583 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16584 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16585 Nick Rizzolo}, 16586 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16587 journal = {Proceedings of the IEEE}, 16588 volume = {93}, 16589 number = {2}, 16590 year = {2005}, 16591 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16592} 16593 16594@Article{ kirbylogg06, 16595 author = {Robert C. Kirby and Anders Logg}, 16596 title = {A compiler for variational forms}, 16597 journal = {ACM Transactions on Mathematical Software}, 16598 volume = {32}, 16599 number = {3}, 16600 year = {2006}, 16601 issn = {0098-3500}, 16602 pages = {417--444}, 16603 doi = {10.1145/1163641.1163644}, 16604 publisher = {ACM Press}, 16605 address = {New York, NY} 16606} 16607 16608@Article{ kirbylogg07, 16609 author = {Robert C. Kirby and Anders Logg}, 16610 title = {Efficient compilation of a class of variational forms}, 16611 journal = {ACM Transactions on Mathematical Software}, 16612 volume = {33}, 16613 number = {3}, 16614 year = {2007}, 16615 issn = {0098-3500}, 16616 pages = {17}, 16617 doi = {10.1145/1268769.1268771}, 16618 publisher = {ACM Press}, 16619 address = {New York, NY} 16620} 16621 16622@Article{ bankdupont81, 16623 author = {Randolph Bank and Todd Dupont}, 16624 title = {An optimal order process for solving finite element equations}, 16625 journal = {Mathematics of Computation}, 16626 volume = {36}, 16627 pages = {35--51}, 16628 year = {1981} 16629} 16630 16631@TechReport{ adams00, 16632 author = {Mark F. Adams}, 16633 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16634 in solid mechanics}, 16635 institution = {UC Berkeley}, 16636 number = {CSD-00-1103}, 16637 year = {2000}, 16638 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16639} 16640 16641@Article{ bergengradlhuelsemannruede06, 16642 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16643 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16644 journal = {Computing in Science \& Engineering}, 16645 volume = {8}, 16646 number = {6}, 16647 pages = {56--62}, 16648 year = {2006} 16649} 16650 16651@MastersThesis{ brunethesis08, 16652 author = {Peter R. Brune}, 16653 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16654 school = {University of Chicago}, 16655 address = {Chicago, IL}, 16656 year = {2008}, 16657 month = feb 16658} 16659 16660@Article{ arnoldwinther02, 16661 author = {Douglas N. Arnold and Ragnar Winther}, 16662 title = {Mixed finite elements for elasticity}, 16663 journal = {Numerische Mathematik}, 16664 volume = {92}, 16665 number = {3}, 16666 month = sep, 16667 year = {2002}, 16668 pages = {401--419}, 16669 doi = {10.1007/s002110100348} 16670} 16671 16672@Article{ arnoldfalkwinther06, 16673 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16674 title = {Finite element exterior calculus, homological techniques, and applications}, 16675 journal = {Acta Numerica}, 16676 year = {2006}, 16677 volume = {15}, 16678 pages = {1--155}, 16679 publisher = {Cambridge University Press}, 16680 doi = {10.1017/S0962492906210018} 16681} 16682 16683@Article{ kirby04, 16684 author = {Robert C. Kirby}, 16685 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 16686 functions}, 16687 journal = {ACM Transactions on Mathematical Software}, 16688 volume = {30}, 16689 number = {4}, 16690 year = {2004}, 16691 issn = {0098-3500}, 16692 pages = {502--516}, 16693 doi = {10.1145/1039813.1039820}, 16694 publisher = {ACM Press}, 16695 address = {New York, NY} 16696} 16697 16698@Article{ kirby06, 16699 author = {Robert C. Kirby}, 16700 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16701 journal = {ACM Transactions on Mathematical Software}, 16702 volume = {32}, 16703 number = {2}, 16704 year = {2006}, 16705 issn = {0098-3500}, 16706 pages = {223--235}, 16707 doi = {10.1145/1141885.1141889}, 16708 publisher = {ACM Press}, 16709 address = {New York, NY} 16710} 16711 16712@Misc{ bluecrystal08, 16713 author = {{B}lue {C}rystal Cluster}, 16714 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16715 year = {2008}, 16716 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16717} 16718 16719@Article{ beylkin95, 16720 author = {Gregory Beylkin}, 16721 title = {On the Fast Fourier Transform of Functions With Singularities}, 16722 journal = {Applied and Computational Harmonic Analysis}, 16723 volume = {2}, 16724 pages = {363--381}, 16725 year = {1995} 16726} 16727 16728@InProceedings{ riehl08, 16729 author = {Jonathan Riehl}, 16730 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16731 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16732 Development (DSPD'08)}, 16733 address = {Nashville, TN}, 16734 year = {2008} 16735} 16736 16737@Article{ appel85, 16738 author = {Andrew W. Appel}, 16739 date-added = {2008-02-27 12:23:39 +0000}, 16740 date-modified = {2008-02-27 12:24:02 +0000}, 16741 doi = {10.1137/0906008}, 16742 journal = {SIAM Journal on Scientific and Statistical Computing}, 16743 keywords = {treecodes}, 16744 number = {1}, 16745 pages = {85-103}, 16746 publisher = {SIAM}, 16747 title = {An Efficient Program for Many-Body Simulation}, 16748 volume = {6}, 16749 year = {1985} 16750} 16751 16752@Article{ ewald21, 16753 author = {{Ewald}, P.~P.}, 16754 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 16755 journal = {Annalen der Physik}, 16756 year = {1921}, 16757 volume = {369}, 16758 pages = {253-287}, 16759 doi = {10.1002/andp.19213690304}, 16760 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 16761 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16762} 16763 16764@Article{ greengardrokhlin87, 16765 author = {L. Greengard and V. Rokhlin}, 16766 date-added = {2008-02-15 18:43:55 +0000}, 16767 date-modified = {2008-02-26 20:09:11 +0000}, 16768 doi = {10.1016/0021-9991(87)90140-9}, 16769 journal = {J. Comput.\ Phys.}, 16770 keywords = {FMM}, 16771 number = {2}, 16772 pages = {325--348}, 16773 title = {A Fast Algorithm for Particle Simulations}, 16774 url = {citeseer.ist.psu.edu/greengard87fast.html}, 16775 volume = {73}, 16776 year = {1987}, 16777 bdsk-url-1 = {citeseer.ist.psu.edu/greengard87fast.html} 16778} 16779 16780@Article{ greengardrokhlin97, 16781 author = {L. Greengard and V. Rokhlin}, 16782 title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three 16783 Dimensions}, 16784 journal = {Acta Numerica}, 16785 volume = {6}, 16786 year = {1997}, 16787 pages = {229--269} 16788} 16789 16790@Article{ luchenghuangmccammon06, 16791 author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. 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Wang}, 16822 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 16823 equation on massively parallel computers}, 16824 journal = {Journal of Computational Chemistry}, 16825 volume = {21}, 16826 year = {2000} 16827} 16828 16829@Book{ hockneyeastwood81, 16830 author = {R. Hockney and J. Eastwood}, 16831 title = {Computer simulation using particles}, 16832 publisher = {McGraw-Hill}, 16833 address = {New York}, 16834 year = {1981} 16835} 16836 16837@Article{ lutydavistironigunsteren94, 16838 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van 16839 Gunsteren}, 16840 title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for 16841 Calculating Electrostatic Interactions in Periodic Molecular Systems}, 16842 journal = {Molecular Simulation}, 16843 volume = {14}, 16844 number = {1}, 16845 year = {1994}, 16846 pages = {11--20} 16847} 16848 16849@Book{ briggshensonmccormick00, 16850 author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.}, 16851 title = {A Multigrid Tutorial (2nd ed.)}, 16852 year = {2000}, 16853 isbn = {0-89871-462-1}, 16854 publisher = {Society for Industrial and Applied Mathematics}, 16855 address = {Philadelphia, PA} 16856} 16857 16858@Article{ chartier2003spectral, 16859 title = {Spectral AMGe ($\rho$ AMGe)}, 16860 author = {Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and 16861 McCormick, S and Ruge, J and Vassilevski, PS}, 16862 journal = {SIAM Journal on Scientific Computing}, 16863 volume = {25}, 16864 number = {1}, 16865 pages = {1--26}, 16866 year = {2003}, 16867 publisher = {SIAM} 16868} 16869 16870@Article{ galvis2010domain, 16871 title = {Domain decomposition preconditioners for multiscale flows in high-contrast 16872 media}, 16873 author = {Galvis, Juan and Efendiev, Yalchin}, 16874 journal = {Multiscale Modeling \& Simulation}, 16875 volume = {8}, 16876 number = {4}, 16877 pages = {1461--1483}, 16878 year = {2010}, 16879 publisher = {SIAM} 16880} 16881 16882@Book{ brennerscott02, 16883 author = {Susanne~C. 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Chu}, 16904 bibdate = {Wed Jan 07 15:23:19 1998}, 16905 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16906} 16907 16908@Article{ liptonreagan2014, 16909 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16910 author = {Richard J Lipton and Kenneth W Regan}, 16911 pages = {206}, 16912 isbn = {978-0-26202-839-4}, 16913 year = {2014} 16914} 16915 16916@InProceedings{ rhea08, 16917 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16918 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16919 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16920 booktitle = {Proceedings of IEEE/ACM SC '08}, 16921 year = {2008} 16922} 16923 16924@Misc{ bursteddewilcox09, 16925 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16926 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16927 note = {in preparation} 16928} 16929 16930@Article{ skeeltezcanhardy02, 16931 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16932 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16933 journal = {J. Comp. Chem.}, 16934 volume = {23}, 16935 pages = {673--684}, 16936 year = {2002} 16937} 16938 16939@Article{ verschelde99, 16940 author = {Jan Verschelde}, 16941 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16942 homotopy continuation}, 16943 journal = {ACM Trans. Math. Softw.}, 16944 volume = {25}, 16945 number = {2}, 16946 issn = {0098-3500}, 16947 pages = {251--276}, 16948 doi = {10.1145/317275.317286}, 16949 publisher = {ACM}, 16950 address = {New York, NY}, 16951 year = {1999} 16952} 16953 16954@InProceedings{ sommeseverscheldewampler08, 16955 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16956 title = {Solving Polynomial Systems Equation by Equation}, 16957 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16958 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16959 pages = {133--152}, 16960 publisher = {Springer-Verlag}, 16961 year = {2008} 16962} 16963 16964@Article{ phanthientanner77, 16965 author = {N. Phan-Thien and R.~I. Tanner}, 16966 title = {A new constitutive equation derived from network theory}, 16967 journal = {J. Non-Newt. Fluid Mech.}, 16968 volume = {2}, 16969 pages = {353}, 16970 year = {1977} 16971} 16972 16973@Manual{ sage, 16974 key = {SAGE}, 16975 author = {W.\thinspace{}A. Stein and others}, 16976 organization = {The Sage~Development Team}, 16977 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16978 note = {{\tt http://www.sagemath.org}}, 16979 year = {2009} 16980} 16981 16982@Misc{ bateshauensteinsommesewampler06, 16983 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16984 Wampler}, 16985 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16986 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16987} 16988 16989@Article{ archer09, 16990 author = {A. J. Archer}, 16991 collaboration = {}, 16992 title = {Dynamical density functional theory for molecular and colloidal fluids: A 16993 microscopic approach to fluid mechanics}, 16994 publisher = {AIP}, 16995 year = {2009}, 16996 journal = {The Journal of Chemical Physics}, 16997 volume = {130}, 16998 number = {1}, 16999 eid = {014509}, 17000 numpages = {8}, 17001 pages = {014509}, 17002 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 17003 transition; statistical distributions; stochastic processes}, 17004 doi = {10.1063/1.3054633} 17005} 17006 17007@Article{ giesekus1966, 17008 author = {Hanswalter Giesekus}, 17009 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 17010 journal = {Rheologica Acta}, 17011 publisher = {Springer Berlin / Heidelberg}, 17012 volume = {5}, 17013 number = {1}, 17014 month = mar, 17015 year = {1966}, 17016 doi = {10.1007/BF01973575}, 17017 pages = {29-35} 17018} 17019 17020@Article{ baaijens98, 17021 author = {F.P. Baaijens}, 17022 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 17023 journal = {Journal of Non-Newtonian Fluid Mechanics}, 17024 volume = {79}, 17025 year = {1998}, 17026 pages = {361--385} 17027} 17028 17029@Book{ joseph90, 17030 author = {D.~D. Joseph}, 17031 title = {Fluid Dynamics of Viscoelastic Liquids}, 17032 publisher = {Springer}, 17033 address = {New York, NY}, 17034 year = {1990} 17035} 17036 17037@Article{ oldroyd50, 17038 author = {J.~G. Oldroyd}, 17039 title = {On the Formulation of Rheological Equations of State}, 17040 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 17041 Sciences}, 17042 volume = {200}, 17043 year = {1950}, 17044 pages = {523--541} 17045} 17046 17047@InProceedings{ bynasungroppthakur04, 17048 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 17049 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 17050 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 17051 year = {2004} 17052} 17053 17054@Book{ pozrikidis07, 17055 author = {C. Pozrikidis}, 17056 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 17057 publisher = {Kluwer (Springer)}, 17058 pages = {675}, 17059 year = {2001}, 17060 isbn = {0792373510} 17061} 17062 17063@Misc{ kritzkeyesfsp07, 17064 author = {A. Kritz and D. Keyes}, 17065 title = {{Fusion Simulation Project Workshop Report}}, 17066 month = jul, 17067 year = {2007}, 17068 note = {Available via 17069 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 17070} 17071 17072@Misc{ dahlburg02, 17073 author = {J. {Dahlburg (Chair)}}, 17074 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 17075 year = {2002}, 17076 note = {Available via 17077 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 17078} 17079 17080@Misc{ brown08, 17081 author = {D. {Brown (Chair)}}, 17082 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 17083 to the Future}}, 17084 year = {2008}, 17085 howpublished = {Office of Science, U.S. Department of Energy}, 17086 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 17087} 17088 17089@Misc{ crosscutting10, 17090 author = {D. Brown and P. {Messina (Chairs)}}, 17091 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 17092 Exascale}}, 17093 year = {2010}, 17094 howpublished = {Office of Science, U.S. Department of Energy}, 17095 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 17096} 17097 17098@Misc{ extreme-scale-solvers-workshop12, 17099 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 17100 L.C. McInnes and E. Ng and S. Wild}, 17101 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 17102 Architectures}, 17103 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 17104 note = {{Washington, DC}, March 8-9, 2012}, 17105 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 17106 year = {2012} 17107} 17108 17109@Misc{ monizrosner09, 17110 author = {{E. Moniz and R. Rosner}}, 17111 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 17112 and Simulation at the Extreme Scale}}, 17113 month = may, 17114 year = {2009}, 17115 note = {See 17116 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 17117} 17118 17119@Misc{ blanford08, 17120 author = {{R. Blandord (Chair)}}, 17121 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 17122 Computing at the Extreme Scale}}, 17123 month = dec, 17124 year = {2008}, 17125 note = {See 17126 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 17127} 17128 17129@Misc{ exascale07, 17130 author = {H. Simon and T. Zacharia and R. Stevens}, 17131 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 17132 year = {2007}, 17133 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 17134} 17135 17136@Misc{ ascrbreakthroughs08, 17137 author = {{Panel on Recent Significant Advancements in Computational Science}}, 17138 title = {Breakthroughs}, 17139 year = {2008}, 17140 note = {See 17141 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 17142} 17143 17144@Misc{ petsc-rd100-2009, 17145 author = {{R\&D Magazine}}, 17146 title = {{PETSc} {R}\&{D} 100 Award}, 17147 year = {2009}, 17148 note = {See 17149 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 17150} 17151 17152@Article{ compass-scidac08, 17153 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 17154 R. Ryne}, 17155 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 17156 Computational Science for Future Accelerators and Accelerator Technologies}, 17157 journal = {J. Phys.: Conf. Ser.}, 17158 volume = {125}, 17159 year = {2008}, 17160 pages = {012001}, 17161 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 17162} 17163 17164@Article{ compass-amundson-scidac08, 17165 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 17166 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 17167 Stoltz}, 17168 journal = {J. Phys.: Conf. Ser.}, 17169 volume = {125}, 17170 year = {2008} 17171} 17172 17173@InProceedings{ muszala09, 17174 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 17175 Simulations}, 17176 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 17177 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 17178 {(CBHPC 2009)}}, 17179 year = {2009} 17180} 17181 17182@Article{ gaston09, 17183 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 17184 Equations}, 17185 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 17186 journal = {Nuclear Engineering and Design}, 17187 volume = {239}, 17188 number = {10}, 17189 year = {2009}, 17190 pages = {1768 -- 1778} 17191} 17192 17193@Article{ gaston09b, 17194 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 17195 Engineering}, 17196 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 17197 and C. Permann and W. Taitano}, 17198 journal = {J. Phys.: Conf. Ser.}, 17199 volume = {180}, 17200 year = {2009}, 17201 pages = {012012} 17202} 17203 17204@Article{ newman09, 17205 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 17206 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 17207 author = {Chris Newman and Glen Hansen and Derek Gaston}, 17208 journal = {Journal of Nuclear Materials}, 17209 volume = {392}, 17210 issue = {1}, 17211 year = {2009}, 17212 pages = {6 -- 15} 17213} 17214 17215@Misc{ www:fenics, 17216 author = {{FE}ni{CS}}, 17217 title = {{FE}ni{CS} Project}, 17218 howpublished = {\url{http://www.fenics.org/}}, 17219 year = {2018} 17220} 17221 17222@InProceedings{ zwart08, 17223 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 17224 Systems}, 17225 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 17226 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 17227 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 17228 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 17229 booktitle = {Proceedings of ICCS 2008}, 17230 year = {2008} 17231} 17232 17233@Article{ klocknerwarburtonbridgehesthaven09, 17234 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 17235 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 17236 journal = {J. Comput. Phys.}, 17237 volume = {228}, 17238 number = {21}, 17239 year = {2009}, 17240 issn = {0021-9991}, 17241 pages = {7863--7882}, 17242 doi = {10.1016/j.jcp.2009.06.041}, 17243 publisher = {Academic Press Professional}, 17244 address = {San Diego, CA} 17245} 17246 17247@PhDThesis{ rankin99, 17248 author = {Rankin, W. T.}, 17249 keywords = {FMM, parallel FMM}, 17250 school = {Department of Electrical and Computer Engineering, Duke University}, 17251 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17252 year = {1999} 17253} 17254 17255@InProceedings{ warrensalmon93, 17256 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17257 and implemented. The algorithm computes the forces on an arbitrary distribution of 17258 bodies in a time which scales as N log N with the particle number. The accuracy of 17259 the force calculations is analytically bounded, and can be adjusted via a user 17260 defined parameter between a few percent relative accuracy, down to machine 17261 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17262 tree, we identify...}, 17263 address = {New York}, 17264 author = {Warren, Michael S. and Salmon, John K.}, 17265 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17266 citeulike-article-id={580952}, 17267 keywords = {oct-tree}, 17268 pages = {12--21}, 17269 publisher = {ACM}, 17270 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17271 year = {1993}, 17272 doi = {10.1145/169627.169640}, 17273 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17274} 17275 17276@Unpublished{ cruzwccm10, 17277 author = {Felipe A. Cruz}, 17278 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17279 note = {Presentation at WCCM 2010, Sydney Australia}, 17280 year = {2010} 17281} 17282 17283@Article{ mcguffee06, 17284 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17285 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17286 of salt, {pH}, point mutations, and protein concentration in simulations of 17287 1000-molecule systems}, 17288 journal = {Journal of the American Chemical Society}, 17289 volume = {128}, 17290 pages = {12098--12110}, 17291 year = {2006} 17292} 17293 17294@Article{ nilsencaihoylandlangtangen10, 17295 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17296 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17297 in Python}}, 17298 journal = {ArXiv e-prints}, 17299 archiveprefix = {arXiv}, 17300 eprint = {1002.0705}, 17301 primaryclass = {cs.DC}, 17302 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17303 - Programming Languages}, 17304 year = {2010}, 17305 month = feb, 17306 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17307 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17308} 17309 17310@Misc{ mcinnes:siam09:minisymposium, 17311 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17312 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17313 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17314 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17315 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17316 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17317 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17318 Austin).} 17319} 17320 17321@Misc{ mcinnes:fsp-summary:feb2011, 17322 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17323 title = {Solvers and Time Integration Breakout Summary}, 17324 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17325 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17326} 17327 17328@Misc{ dvi-materials:siamcse11, 17329 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17330 Materials}, 17331 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17332 Smith and L. Wang}, 17333 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17334 and Engineering, March 3, 2011} 17335} 17336 17337@Misc{ jamroz:cemm10, 17338 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17339 author = {B. Jamroz and S. Kruger and T. Austin}, 17340 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17341} 17342 17343@Misc{ kruger:feb4-2011, 17344 title = {personal communication}, 17345 author = {S. Kruger}, 17346 note = {February, 2011} 17347} 17348 17349@Article{ elman1996, 17350 author = {H.C. Elman}, 17351 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17352 viscosity}, 17353 journal = {SIAM J. Sci. Comput.}, 17354 volume = {20}, 17355 year = {1996}, 17356 pages = {1299--1316} 17357} 17358 17359@Article{ kayloghinwathen2002, 17360 author = {D. Kay and D. Loghin and A. Wathen}, 17361 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17362 journal = {SIAM J. Sci. Comput.}, 17363 volume = {24}, 17364 year = {2002}, 17365 pages = {237--256} 17366} 17367 17368@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17369 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17370 title = {Block preconditioners based on approximate commutators}, 17371 journal = {SIAM J. Sci. Comput.}, 17372 volume = {27}, 17373 number = {5}, 17374 year = {2006}, 17375 pages = {1651--1668} 17376} 17377 17378@Article{ braesssarazin1997, 17379 author = {Dietrich Braess and Regina Sarazin}, 17380 title = {An efficient smoother for the {Stokes} problem}, 17381 journal = {Applied Numerical Mathematics}, 17382 volume = {23}, 17383 number = {1}, 17384 year = {1997}, 17385 pages = {3--19}, 17386 doi = {10.1016/S0168-9274(96)00059-1} 17387} 17388 17389@Article{ wright2001large, 17390 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17391 author = {Wright, T.G. and Trefethen, L.N.}, 17392 journal = {SIAM Journal on Scientific Computing}, 17393 volume = {23}, 17394 pages = {591}, 17395 year = {2001} 17396} 17397 17398@Misc{ wright2002eigtool, 17399 title = {Eig{T}ool}, 17400 author = {Wright, T.G. and Trefethen, LN}, 17401 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17402 year = {2002} 17403} 17404 17405@Misc{ visit-web-site, 17406 key = {{VisIt}}, 17407 title = {{VisIt web site}}, 17408 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17409 url = {http://wci.llnl.gov/codes/visit/}, 17410 year = {2011} 17411} 17412 17413@Book{ trefethen1996, 17414 title = {Finite difference and spectral methods for ordinary and partial differential 17415 equations}, 17416 author = {Lloyd Nicholas Trefethen}, 17417 year = {1996}, 17418 publisher = {Cornell University-Department of Computer Science and Center for Applied 17419 Mathematics} 17420} 17421 17422@Book{ trefethen2005spectra, 17423 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17424 author = {Trefethen, L.N. and Embree, M.}, 17425 year = {2005}, 17426 publisher = {Princeton University Press} 17427} 17428 17429@Article{ gomez2010isogeometric, 17430 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17431 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17432 journal = {Computer Methods in Applied Mechanics and Engineering}, 17433 volume = {199}, 17434 number = {25-28}, 17435 pages = {1828--1840}, 17436 issn = {0045-7825}, 17437 year = {2010}, 17438 publisher = {Elsevier} 17439} 17440 17441@Article{ gomez2008isogeometric, 17442 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17443 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17444 journal = {Computer Methods in Applied Mechanics and Engineering}, 17445 volume = {197}, 17446 number = {49-50}, 17447 pages = {4333--4352}, 17448 year = {2008}, 17449 publisher = {Elsevier} 17450} 17451 17452@Misc{ fastmath:project, 17453 author = {Lori {Diachin (PI)}}, 17454 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17455 (FASTMath) Institute}}, 17456 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17457} 17458 17459@Misc{ exascale-software:proposal, 17460 author = {Peter {Beckman (PI)}}, 17461 title = {{Exascale Software Center}}, 17462 note = {proposal to DOE} 17463} 17464 17465@Misc{ imex:project, 17466 author = {Barry {Smith (PI)}}, 17467 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17468 Multimodel PDEs}}, 17469 note = {DOE ASCR applied math project} 17470} 17471 17472@Misc{ intel-mic:website, 17473 author = {Intel}, 17474 title = {{Many Integrated Core Architecture}}, 17475 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17476} 17477 17478@Article{ dudson:2009, 17479 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17480 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17481 journal = {Computer Physics Communications}, 17482 volume = {180}, 17483 pages = {1467}, 17484 year = {2009} 17485} 17486 17487@Article{ umansky:2009, 17488 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17489 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17490 journal = {Computer Physics Communications}, 17491 year = {2009}, 17492 volume = {180}, 17493 pages = {887-903} 17494} 17495 17496@Article{ xu:1998, 17497 author = {X.Q. Xu and R.H. Cohen}, 17498 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17499 journal = {Computer Physics Communications}, 17500 year = {1998}, 17501 volume = {36}, 17502 number = {1-2}, 17503 pages = {158} 17504} 17505 17506@Article{ tron:1999, 17507 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17508 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17509 journal = {SIAM Journal on Optimization}, 17510 volume = {9}, 17511 number = {4}, 17512 pages = {1100-1127}, 17513 year = {1999} 17514} 17515 17516@Article{ stubenamg, 17517 author = {K. St\"{u}ben}, 17518 title = {A review of algebraic multigrid}, 17519 journal = {J. Comput. Appl. Math.}, 17520 volume = {128}, 17521 number = {1-2}, 17522 year = {2001}, 17523 issn = {0377-0427}, 17524 pages = {281--309}, 17525 doi = {10.1016/S0377-0427(00)00516-1}, 17526 publisher = {Elsevier Science Publishers B. V.}, 17527 address = {Amsterdam, The Netherlands, The Netherlands} 17528} 17529 17530@Article{ feuchtermg, 17531 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17532 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17533 journal = {Computing and visualization in science}, 17534 publisher = {Springer}, 17535 volume = {6}, 17536 number = {1}, 17537 year = {2003}, 17538 pages = {1--13} 17539} 17540 17541@Article{ chowmgsmoothness, 17542 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17543 only attempts to interpolate in the directions of geometrical smoothness. These 17544 directions are determined by analyzing samples of algebraically smooth error, e. 17545 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17546 consistently nearby in value. In addition, these dierences may be used to dene 17547 interpolation weights. These new ideas may be incorporated into the algebraic 17548 multigrid method. Test results show that the new method can have much lower grid 17549 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17550 author = {Chow, Edmond}, 17551 citeulike-article-id={7675372}, 17552 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17553 journal = {American Journal of Mathematics}, 17554 keywords = {fem, multigrid}, 17555 pages = {197--215}, 17556 posted-at = {2010-08-17 23:29:51}, 17557 priority = {2}, 17558 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17559 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17560 volume = {65}, 17561 year = {2001} 17562} 17563 17564@Article{ jonesamge, 17565 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17566 elements) method based on element agglomeration. In the method, coarse grid 17567 elements are formed by agglomerating fine grid elements. Compatible interpolation 17568 operators are constructed which yield coarse grid basis functions with a minimal 17569 energy property. Heuristics based on interpolation quality measures are used to 17570 guide the agglomeration procedure. The performance of the resulting method is 17571 demonstrated in two-level numerical experiments.}}, 17572 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17573 citeulike-article-id={8598569}, 17574 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17575 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17576 journal = {SIAM Journal on Scientific Computing}, 17577 keywords = {amg, fem, multigrid}, 17578 number = {1}, 17579 pages = {109--133}, 17580 posted-at = {2011-01-13 18:05:55}, 17581 priority = {2}, 17582 publisher = {SIAM}, 17583 title = {{AMGE Based on Element Agglomeration}}, 17584 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17585 volume = {23}, 17586 year = {2001} 17587} 17588 17589@Article{ saad1993, 17590 author = {Saad, Youcef}, 17591 doi = {10.1137/0914028}, 17592 issn = {10648275}, 17593 journal = {SIAM Journal on Scientific Computing}, 17594 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17595 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17596 precondition-,preconditioned conju-,subject classi cations,variable 17597 preconditioners}, 17598 number = {2}, 17599 pages = {461--469}, 17600 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17601 volume = {14}, 17602 year = {1993} 17603} 17604 17605@Misc{ path:homepage, 17606 author = {S. Dirkse and M. Ferris and T. 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Moresi and Shijie Zhong and Michael Gurnis}, 17817 title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying 17818 viscosity}, 17819 journal = {Physics of the Earth and Planetary Interiors}, 17820 volume = {97}, 17821 pages = {83-–94}, 17822 year = {1996} 17823} 17824 17825@Article{ moresisolomatov95, 17826 author = {Louis N. Moresi and V. S. Solomatov}, 17827 title = {Numerical investigation of {2D} convection with extremely large viscosity 17828 variations}, 17829 journal = {Physics of Fluids}, 17830 volume = {7}, 17831 number = {9}, 17832 pages = {2154-–2162}, 17833 year = {1995} 17834} 17835 17836@Article{ chenmolnar83, 17837 author = {W.-P. Chen and P. 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Watts}, 17857 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 17858 brulee?}, 17859 journal = {GSA Today}, 17860 volume = {16}, 17861 pages = {4–-10}, 17862 year = {2006} 17863} 17864 17865@InProceedings{ yang:brent:2002, 17866 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 17867 Parallel Distributed Memory Architectures}, 17868 author = {Laurence T. Yang and Richard Brent}, 17869 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 17870 for Parallel Processing}, 17871 year = {2002}, 17872 publisher = {IEEE} 17873} 17874 17875@Article{ demmel2008communication, 17876 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 17877 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 17878 journal = {Arxiv preprint arXiv:0808.2664}, 17879 year = {2008} 17880} 17881 17882@Article{ demmel09, 17883 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 17884 title = {Communication-optimal Iterative Methods}, 17885 journal = {Journal of Physics: Conf. 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Rall}, 17913 title = {Computational solution of nonlinear operator equations}, 17914 publisher = {Krieger Pub Co.}, 17915 pages = {225}, 17916 year = {1969} 17917} 17918 17919@Article{ fletcherreeves1964, 17920 author = {R. Fletcher and C. M. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 17955} 17956 17957@Article{ keyesmcinneswoodwardetal13, 17958 title = {Multiphysics Simulations: Challenges and Opportunities}, 17959 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17960 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17961 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17962 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17963 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17964 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17965 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17966 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17967 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17968 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17969 journal = {International Journal of High Performance Computing Applications}, 17970 month = feb, 17971 year = {2013}, 17972 volume = {27}, 17973 number = {1}, 17974 pages = {4--83}, 17975 doi = {10.1177/1094342012468181}, 17976 note = {Special issue}, 17977 abstract = {We consider multiphysics applications from algorithmic and architectural 17978 perspectives, where ``algorithmic'' includes both mathematical analysis and 17979 computational complexity and ``architectural'' includes both software and hardware 17980 environments. Many diverse multiphysics applications can be reduced, en route to 17981 their computational simulation, to a common algebraic coupling paradigm. 17982 Mathematical analysis of multiphysics coupling in this form is not always 17983 practical for realistic applications, but model problems representative of 17984 applications discussed herein can provide insight. A variety of software 17985 frameworks for multiphysics applications have been constructed and refined within 17986 disciplinary communities and executed on leading-edge computer systems. We examine 17987 several of these, expose some commonalities among them, and attempt to extrapolate 17988 best practices to future systems. From our study, we summarize challenges and 17989 forecast opportunities.} 17990} 17991 17992@Misc{ rosner10, 17993 author = {Robert {Rosner (Chair)}}, 17994 title = {{The Opportunities and Challenges of Exascale Computing}}, 17995 year = {2010}, 17996 howpublished = {Office of Science, U.S. Department of Energy}, 17997 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17998} 17999 18000@Misc{ kogge2008exascale, 18001 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 18002 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 18003 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 18004 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 18005 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 18006 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 18007 howpublished = {DARPA}, 18008 year = {2008}, 18009 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 18010} 18011 18012@Misc{ doegrandchallengeworkshops, 18013 key = {Office of Science, U.S. Department of Energy}, 18014 title = {{Scientific Grand Challenges Workshop Series}}, 18015 howpublished = {Office of Science, U.S. Department of Energy, see 18016 \url{http://extremecomputing.labworks.org/workshops.stm}} 18017} 18018 18019@Misc{ lawrence2011, 18020 key = {Lawrence}, 18021 title = {{Ernest Orlando Lawrence Award Winners}}, 18022 howpublished = {U.S. Department of Energy, {\footnotesize 18023 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 18024 year = {2011} 18025} 18026 18027@Article{ murphy2000npi, 18028 title = {{A note on preconditioning for indefinite linear systems}}, 18029 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 18030 journal = {SIAM Journal on Scientific Computing}, 18031 volume = {21}, 18032 number = {6}, 18033 pages = {1969--1972}, 18034 year = {2000}, 18035 publisher = {Philadelphia, PA: SIAM, c1993-} 18036} 18037 18038@Article{ elman2011bouyancy, 18039 title = {Fast iterative solvers for buoyancy driven flow problems}, 18040 journal = {Journal of Computational Physics}, 18041 volume = {230}, 18042 number = {10}, 18043 pages = {3900 - 3914}, 18044 year = {2011}, 18045 note = {}, 18046 issn = {0021-9991}, 18047 doi = {10.1016/j.jcp.2011.02.014}, 18048 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 18049 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 18050 Adaptivity, Preconditioning, Algebraic multigrid} 18051} 18052 18053@Article{ dongarrabeckman11, 18054 author = {J. Dongarra and P. Beckman and et al.}, 18055 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 18056 journal = {Int. J. High Perf. Comput. 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Brannick and Robert D. Falgout}, 18109 journal = {SIAM Journal on Scientific Computing}, 18110 volume = {32}, 18111 number = {3}, 18112 pages = {1393--1416}, 18113 url = {http://epubs.siam.org/doi/10.1137/090772216}, 18114 doi = {10.1137/090772216}, 18115 issn = {1064-8275}, 18116 year = {2010} 18117} 18118 18119@Article{ xu2004energy, 18120 title = {On an energy minimizing basis for algebraic multigrid methods}, 18121 author = {Xu, J. and Zikatanov, L.}, 18122 journal = {Computing and Visualization in Science}, 18123 volume = {7}, 18124 number = {3}, 18125 pages = {121--127}, 18126 year = {2004}, 18127 publisher = {Springer} 18128} 18129 18130@Article{ dblp:journals/toms/bakerhlt09, 18131 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 18132 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 18133 journal = {ACM Trans. Math. 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Sala}, 18156 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 18157 institution = {Sandia National Laboratories}, 18158 year = {2006}, 18159 number = {SAND2006-2649} 18160} 18161 18162@Article{ brannick06, 18163 title = {An energy-based AMG coarsening strategy}, 18164 volume = {13}, 18165 doi = {10.1002/nla.480}, 18166 number = {2-3}, 18167 journal = {Numerical Linear Algebra with Applications}, 18168 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 18169 and Ruge, J}, 18170 year = {2006}, 18171 pages = {133--148} 18172} 18173 18174@Article{ olson10, 18175 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 18176 title = {A new perspective on strength measures in algebraic multigrid}, 18177 journal = {Numerical Linear Algebra with Applications}, 18178 volume = {17}, 18179 number = {4}, 18180 pages = {713--733}, 18181 year = {2010}, 18182 publisher = {John Wiley \& Sons, Ltd.}, 18183 issn = {1099-1506}, 18184 doi = {10.1002/nla.669} 18185} 18186 18187@Article{ olson11, 18188 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 18189 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 18190 Minimization}, 18191 journal = {SIAM J. Sci. Comput.}, 18192 issue_date = {April 2011}, 18193 volume = {33}, 18194 issue = {2}, 18195 month = apr, 18196 year = {2011}, 18197 issn = {1064-8275}, 18198 pages = {966--991}, 18199 numpages = {26}, 18200 doi = {10.1137/100803031}, 18201 acmid = {2078825}, 18202 publisher = {Society for Industrial and Applied Mathematics}, 18203 address = {Philadelphia, PA}, 18204 keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed 18205 aggregation} 18206} 18207 18208@Article{ dorit2011, 18209 author = {Dorit Ron and Ilya Safro and Achi Brandt}, 18210 title = {Relaxation-Based Coarsening and Multiscale Graph Organization}, 18211 journal = {Multiscale Modeling {\&} Simulation}, 18212 volume = {9}, 18213 number = {1}, 18214 year = {2011}, 18215 pages = {407-423}, 18216 doi = {10.1137/100791142} 18217} 18218 18219@Article{ chen2011algebraic, 18220 title = {Algebraic distance on graphs}, 18221 author = {Chen, Jie and Safro, Ilya}, 18222 journal = {SIAM Journal on Scientific Computing}, 18223 volume = {33}, 18224 number = {6}, 18225 pages = {3468--3490}, 18226 year = {2011}, 18227 publisher = {SIAM} 18228} 18229 18230@InProceedings{ adams04, 18231 author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.}, 18232 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 18233 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 18234 half a billion degrees of freedom}, 18235 note = {Gordon Bell Award}, 18236 year = {2004} 18237} 18238 18239@Article{ adams03a, 18240 author = {Adams, M.~F.}, 18241 journal = {Numerical Linear Algebra with Applications}, 18242 number = {2-3}, 18243 pages = {141-153}, 18244 title = {Algebraic multigrid methods for constrained linear systems with applications to 18245 contact problems in solid mechanics}, 18246 volume = {11}, 18247 year = {2004} 18248} 18249 18250@Article{ adams-10a, 18251 author = {M. ~F. 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Schwab and J. {\v S}ukys}, 18294 keywords = {Conservation laws, Euler, MHD, Uncertainty quantification, Multi-level Monte 18295 Carlo, Parallelization} 18296} 18297 18298@Article{ barth2011mlmcfe, 18299 author = {Barth, Andrea and Schwab, Christoph and Zollinger, Nathaniel}, 18300 affiliation = {ETH Zentrum, Seminar für Angewandte Mathematik, Rämistrasse 101, 8092 Zurich, 18301 Switzerland}, 18302 title = {Multi-Level {M}onte {C}arlo Finite Element method for elliptic {PDE}s with 18303 stochastic coefficients}, 18304 journal = {Numerische Mathematik}, 18305 publisher = {Springer Berlin / Heidelberg}, 18306 issn = {0029-599X}, 18307 keyword = {Mathematics and Statistics}, 18308 pages = {123-161}, 18309 volume = {119}, 18310 issue = {1}, 18311 doi = {10.1007/s00211-011-0377-0}, 18312 year = {2011} 18313} 18314 18315@Article{ nguyen2011hybridizable, 18316 title = {Hybridizable discontinuous {G}alerkin methods}, 18317 author = {Nguyen, N.C. and Peraire, J. and Cockburn, B.}, 18318 journal = {Spectral and High Order Methods for Partial Differential Equations}, 18319 pages = {63--84}, 18320 year = {2011}, 18321 publisher = {Springer} 18322} 18323 18324@Misc{ snyder-scidac3:proposal, 18325 author = {Philip {Snyder (PI)}}, 18326 title = {{Plasma Edge Advanced Computation (PEAC) Center}}, 18327 note = {proposal to DOE SciDAC3}, 18328 month = oct, 18329 year = {2011} 18330} 18331 18332@Misc{ wirth-scidac3:proposal, 18333 author = {Brian {Wirth (PI)}}, 18334 title = {{Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier 18335 through Leadership Class Computing}}, 18336 note = {proposal to DOE SciDAC3}, 18337 month = oct, 18338 year = {2011} 18339} 18340 18341@Misc{ cary-scidac3:proposal, 18342 author = {John {Cary (PI)}}, 18343 title = {{Integrated Multiscale Modeling for Plasma Analysis and Control of Tokamak 18344 Stability (IMMPACTS)}}, 18345 note = {proposal to DOE SciDAC3}, 18346 month = oct, 18347 year = {2011} 18348} 18349 18350@Misc{ vashista-scidac3:proposal, 18351 author = {Priya {Vashista (PI)}}, 18352 title = {{Design of Damage-Tolerance Material Interfaces for Extreme 18353 Stress-Temperature-Corrosion Environments: Algorithms and Methods for 18354 Multi-Petaflops Simulations}}, 18355 note = {proposal to DOE SciDAC3}, 18356 month = mar, 18357 year = {2012} 18358} 18359 18360@Article{ elemental2012, 18361 author = {Jack Poulson and Bryan Marker and Jeff R. 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P.}, 18571 eprint = {arXiv:1002.0705v1}, 18572 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 18573 parallelization of scientific codes by a function-centric approach in 18574 Python.pdf:pdf}, 18575 journal = {Computational Science \& Discovery}, 18576 keywords = {parallel,programming,python,software}, 18577 mendeley-tags = {parallel,programming,python,software}, 18578 pages = {015003}, 18579 publisher = {IOP Publishing}, 18580 title = {{Simplifying the parallelization of scientific codes by a function-centric 18581 approach in Python}}, 18582 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 18583 volume = {3}, 18584 year = {2010} 18585} 18586 18587@Book{ langtangen09, 18588 author = {Hans Petter Langtangen}, 18589 title = {Python Scripting for Computational Science}, 18590 publisher = {Springer}, 18591 series = {Texts in Computational Science and Engineering}, 18592 pages = {784}, 18593 isbn = {3540739157}, 18594 year = {2009} 18595} 18596 18597@Book{ numpyguide, 18598 author = {Travis E. Oliphant}, 18599 title = {Guide to {N}umpy}, 18600 publisher = {Trelgol}, 18601 year = {2008} 18602} 18603 18604@Misc{ pycuda, 18605 author = {Andreas Kl\"ockner}, 18606 title = {{PyCUDA}}, 18607 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 18608 year = {2011} 18609} 18610 18611@Misc{ pyopencl, 18612 author = {Andreas Kl\"ockner}, 18613 title = {{PyOpenCL}}, 18614 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 18615 year = {2011} 18616} 18617 18618@Article{ klockner2012, 18619 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 18620 Paul Ivanov and Ahmed Fasih}, 18621 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 18622 generation}, 18623 journal = {Parallel Computing}, 18624 volume = {38}, 18625 number = {3}, 18626 pages = {157--174}, 18627 year = {2012}, 18628 issn = {0167-8191}, 18629 doi = {10.1016/j.parco.2011.09.001} 18630} 18631 18632%%%%%% Matt Stuff %%%%%% 18633@Article{ morrabozdagknepleyrassvesselinov, 18634 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 18635 author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and 18636 Velimir Vesselinov}, 18637 journal = {Eos}, 18638 volume = {102}, 18639 doi = {10.1029/2021EO159258}, 18640 month = {Jun}, 18641 year = {2021} 18642} 18643 18644@Misc{ knepley:icerm-workshop:2012, 18645 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 18646 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 18647 Models for Large-scale Simulations}, 18648 note = {Workshop sponsored by the Institute for Computational and Experimental Research 18649 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 18650 \url{http://icerm.brown.edu/tw12-1-exascale}}, 18651 year = {2012} 18652} 18653 18654@TechReport{ kirbyknepleyscott04, 18655 author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott}, 18656 title = {Optimal Evaluation of Finite Element Matrices}, 18657 type = {Technical Report}, 18658 number = {TR-2004-04}, 18659 institution = {University of Chicago}, 18660 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}, 18661 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}}, 18662 pages = {14}, 18663 month = may, 18664 year = {2004} 18665} 18666 18667@TechReport{ kirbyknepleyscott10, 18668 author = {Robert C. Kirby and Matthew G. Knepley and L. 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Ridgway Scott}, 18693 title = {Exponential grids in high-dimensional space}, 18694 type = {Technical Report}, 18695 number = {TR-2011-07}, 18696 institution = {University of Chicago}, 18697 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}, 18698 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}}, 18699 month = dec, 18700 year = {2011} 18701} 18702 18703@TechReport{ zheng11, 18704 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 18705 Zhang and Yaolin Shi}, 18706 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 18707 strongly variable viscosity based on {Matlab} and {CUDA}}, 18708 type = {Research Report}, 18709 number = {UMSI 2011/33}, 18710 institution = {University of Minnesota Supercomputing Institute}, 18711 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 18712 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 18713 month = mar, 18714 year = {2011} 18715} 18716 18717@InProceedings{ zheng2010, 18718 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai 18719 Zhang and Yaolin Shi}, 18720 title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients}, 18721 booktitle = {Eos Transactions of the AGU}, 18722 organization = {American Geophysical Union}, 18723 note = {Fall Meeting Supplemental, Abstract IN41A-1350}, 18724 year = {2010} 18725} 18726 18727@InCollection{ terrelkirbyknepleyscott12, 18728 author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott 18729 and Garth N. Wells}, 18730 title = {Finite elements for incompressible fluids}, 18731 editors = {A. Logg and K.A. Mardal and G. N. 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Terrel}, 18755 title = {Discrete optimization of finite element matrix evaluation}, 18756 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18757 booktitle = {Automated solutions of differential equations by the finite element method}, 18758 series = {Lecture Notes in Computational Science and Engineering}, 18759 volume = {84}, 18760 pages = {385--397}, 18761 publisher = {Springer-Verlag}, 18762 year = {2012} 18763} 18764 18765@InCollection{ kirby12, 18766 author = {Robert C. Kirby}, 18767 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 18768 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18769 booktitle = {Automated solutions of differential equations by the finite element method}, 18770 series = {Lecture Notes in Computational Science and Engineering}, 18771 volume = {84}, 18772 publisher = {Springer-Verlag}, 18773 year = {2012} 18774} 18775 18776@Article{ brownconveryhotesknepleypetropolous1993, 18777 author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and 18778 Labros Petropolous}, 18779 title = {Closed strings with low harmonics and kinks}, 18780 journal = {Physical Review D}, 18781 volume = {48}, 18782 number = {6}, 18783 year = {1993} 18784} 18785 18786@Article{ minimax1996, 18787 title = {MiniMax: What has been learned thus far}, 18788 author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and 18789 Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and 18790 C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. 18791 Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 18792 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. 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Knepley}, 18846 title = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a 18847 Hydration-Shell {Poisson}-{Boltzmann} Model}, 18848 journal = {Biophysical Journal}, 18849 volume = {110}, 18850 number = {3}, 18851 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 18852 doi = {10.1016/j.bpj.2015.11.1766}, 18853 year = {2017} 18854} 18855 18856@Article{ tabrizirahimigoossensknepleybardhan2018, 18857 title = {Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer 18858 Interface Condition (SLIC) Continuum Dielectric Model}, 18859 author = {Amirhossein Molavi Tabrizi and Ali Mehdizadeh Rahimi and Spencer Goossens and 18860 Matthew G. Knepley and Jaydeep P. Bardhan}, 18861 journal = {International Journal of Quantum Chemistry}, 18862 note = {Accepted}, 18863 year = {2018} 18864} 18865 18866@Article{ knepley2010, 18867 author = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. 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geometries}, 23615 author = {Nicolas Barral and Fr{\'e}d{\'e}ric Alauzet and Adrien Loseille}, 23616 booktitle = {53rd AIAA Aerospace Sciences Meeting}, 23617 pages = {2039}, 23618 year = {2015} 23619} 23620 23621@Article{ barralolivieralauzet2017, 23622 title = {Time-accurate anisotropic mesh adaptation for three-dimensional time-dependent 23623 problems with body-fitted moving geometries}, 23624 author = {Nicolas Barral and G{\'e}raldine Olivier and Fr{\'e}d{\'e}ric Alauzet}, 23625 journal = {Journal of Computational Physics}, 23626 volume = {331}, 23627 pages = {157--187}, 23628 year = {2017} 23629} 23630 23631@Article{ ibanezbarralkrakosloseillemichalpark2017, 23632 title = {First Benchmark of the Unstructured Grid Adaptation Working Group}, 23633 author = {Daniel Ibanez and Nicolas Barral and Joshua Krakos and Adrien Loseille and Todd 23634 Michal and Mike Park}, 23635 journal = {Procedia engineering}, 23636 volume = {203}, 23637 pages = {154--166}, 23638 year = {2017} 23639} 23640 23641@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 23642 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 23643 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 23644 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 23645 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 23646 pages = {1103}, 23647 year = {2018} 23648} 23649 23650@InProceedings{ barralangeloudiskramergormanpiggott2018, 23651 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 23652 modelling}, 23653 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 23654 and Matthew D Piggott}, 23655 booktitle = {EGU General Assembly Conference Abstracts}, 23656 volume = {20}, 23657 pages = {19168}, 23658 year = {2018} 23659} 23660 23661@Article{ principe2009, 23662 title = {{Mathematical models for thermally coupled low speed flows}}, 23663 author = {Javier Principe and Ramon Codina}, 23664 journal = {Advances in Theoretical and Applied Mechanics}, 23665 volume = {2}, 23666 number = {1-4}, 23667 pages = {93--112}, 23668 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 23669 year = {2009} 23670} 23671 23672@Book{ vandervorst2003, 23673 title = {Iterative {K}rylov Methods for Large Linear Systems}, 23674 author = {van der Vorst, H.}, 23675 isbn = {9780521818285}, 23676 publisher = {Cambridge University Press}, 23677 year = {2003} 23678} 23679 23680@Book{ peres2006, 23681 author = {Asher Peres}, 23682 title = {Quantum theory: concepts and methods}, 23683 volume = {57}, 23684 publisher = {Springer Science \& Business Media}, 23685 year = {2006} 23686} 23687 23688@Book{ kuttler2012, 23689 title = {Linear algebra: theory and applications}, 23690 author = {Kenneth Kuttler}, 23691 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 23692 year = {2012} 23693} 23694 23695@Book{ elman_silvester_wathen_2014, 23696 place = {Oxford}, 23697 title = {Finite elements and fast iterative solvers: with applications in incompressible 23698 fluid dynamics}, 23699 publisher = {Oxford University Press}, 23700 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 23701 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 23702 year = {2014} 23703} 23704 23705@Article{ alametal2007, 23706 title = {An evaluation of the ORNL Cray XT3}, 23707 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 23708 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 23709 journal = {International Journal of High Performance Computing Applications}, 23710 volume = {22}, 23711 number = {1}, 23712 pages = {52--80}, 23713 doi = {10.1177/1094342007085019}, 23714 year = {2007} 23715} 23716 23717@Article{ plazacarey2000, 23718 title = {Local refinement of simplicial grids based on the skeleton}, 23719 author = {Plaza, A. and Carey, Graham F.}, 23720 journal = {Applied Numerical Mathematics}, 23721 doi = {10.1016/S0168-9274(99)00022-7}, 23722 issn = {01689274}, 23723 volume = {32}, 23724 number = {2}, 23725 pages = {195--218}, 23726 year = {2000} 23727} 23728 23729@Article{ carsonstrakos2020, 23730 title = {On the cost of iterative computations}, 23731 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 23732 journal = {Phil. Trans. R. Soc. A}, 23733 volume = {378}, 23734 number = {20190050}, 23735 doi = {10.1098/rsta.2019.0050}, 23736 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 23737 year = {2020} 23738} 23739 23740@Article{ schoberl1999, 23741 title = {Multigrid methods for a parameter dependent problem in primal variables}, 23742 author = {Joachim Sch{\"o}berl}, 23743 journal = {Numerische Mathematik}, 23744 volume = {84}, 23745 number = {1}, 23746 pages = {97--119}, 23747 year = {1999} 23748} 23749 23750@Article{ wuleexuzikatanov2008, 23751 title = {Convergence analysis on iterative methods for semidefinite systems}, 23752 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 23753 journal = {Journal of Computational Mathematics}, 23754 pages = {797--815}, 23755 year = {2008} 23756} 23757 23758@Article{ maierrannacher2016, 23759 title = {Duality-based adaptivity in finite element discretization of heterogeneous 23760 multiscale problems}, 23761 author = {Maier, Matthias and Rannacher, Rolf}, 23762 journal = {Journal of Numerical Mathematics}, 23763 volume = {24}, 23764 number = {3}, 23765 pages = {167--187}, 23766 year = {2016} 23767} 23768 23769@Article{ maierrannacher2018, 23770 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23771 multiscale problems}, 23772 author = {Maier, Matthias and Rannacher, Rolf}, 23773 journal = {Multiscale Modeling \& Simulation}, 23774 volume = {16}, 23775 number = {1}, 23776 pages = {412--428}, 23777 year = {2018} 23778} 23779 23780@Article{ margetismaierluskin2017, 23781 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23782 metamaterial sheet}, 23783 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23784 journal = {Studies in Applied Mathematics}, 23785 volume = {139}, 23786 number = {4}, 23787 pages = {599--625}, 23788 year = {2017} 23789} 23790 23791@Article{ maiermargetisluskin2017b, 23792 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23793 approximation and validation}, 23794 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23795 journal = {Journal of Computational Physics}, 23796 volume = {339}, 23797 pages = {126--145}, 23798 year = {2017} 23799} 23800 23801@Article{ maiermargetisluskin2018, 23802 title = {Generation of surface plasmon-polaritons by edge effects}, 23803 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23804 journal = {Communications in Mathematical Sciences}, 23805 volume = {16}, 23806 number = {1}, 23807 pages = {77--95}, 23808 url = {http://arxiv.org/abs/1702.00848}, 23809 year = {2018} 23810} 23811 23812@Article{ maiermattheakiskaxirasluskinmargetis2018, 23813 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23814 metamaterials}, 23815 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23816 Mitchell and Margetis, Dionisios}, 23817 journal = {Physical Review B}, 23818 volume = {97}, 23819 number = {3}, 23820 pages = {035307}, 23821 year = {2018} 23822} 23823 23824@Article{ maiermattheakiskaxirasluskinmargetis2019, 23825 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23826 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23827 Mitchell and Margetis, Dionisios}, 23828 journal = {Proceedings of the Royal Society A}, 23829 volume = {475}, 23830 number = {2230}, 23831 pages = {20190220}, 23832 year = {2019} 23833} 23834 23835@Article{ maiermargetisluskin2020, 23836 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23837 two scales}, 23838 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23839 journal = {Physical Review B}, 23840 volume = {102}, 23841 number = {7}, 23842 pages = {075308}, 23843 year = {2020} 23844} 23845 23846@Article{ margetismaierstauberlowluskin2020, 23847 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 23848 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 23849 Luskin, Mitchell}, 23850 journal = {Journal of Physics A: Mathematical and Theoretical}, 23851 volume = {53}, 23852 number = {5}, 23853 pages = {055201}, 23854 year = {2020} 23855} 23856 23857@Article{ maiermargetismellet2020, 23858 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 23859 structures}, 23860 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 23861 journal = {Journal of Computational and Applied Mathematics}, 23862 volume = {377}, 23863 pages = {112909}, 23864 year = {2020} 23865} 23866 23867@Article{ maierkronbichler2021, 23868 title = {Efficient parallel 3D computation of the compressible Euler equations with an 23869 invariant-domain preserving second-order finite-element scheme}, 23870 author = {Maier, Matthias and Kronbichler, Martin}, 23871 journal = {ACM Transactions on Parallel Computing}, 23872 volume = {8}, 23873 number = {3}, 23874 pages = {1--30}, 23875 year = {2021} 23876} 23877 23878@Article{ guermondmaierpopovtomas2021, 23879 title = {Second-order invariant domain preserving approximation of the compressible 23880 Navier--Stokes equations}, 23881 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 23882 journal = {Computer Methods in Applied Mechanics and Engineering}, 23883 volume = {375}, 23884 pages = {113608}, 23885 year = {2021} 23886} 23887 23888@Article{ liliptonmaier2021, 23889 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 23890 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 23891 eprint = {2009.12166}, 23892 archiveprefix = {arXiv}, 23893 primaryclass = {phys.optics}, 23894 year = {2021} 23895} 23896 23897@Article{ songmaierluskin2020, 23898 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 23899 gradient-index graphene waveguides}, 23900 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23901 journal = {Journal of Computational Physics}, 23902 volume = {423}, 23903 pages = {109871}, 23904 year = {2020} 23905} 23906 23907@Article{ songmaierluskin2019, 23908 title = {Adaptive finite element simulations of waveguide configurations involving 23909 parallel 2D material sheets}, 23910 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23911 journal = {Computer Methods in Applied Mechanics and Engineering}, 23912 volume = {351}, 23913 pages = {20--34}, 23914 year = {2019} 23915} 23916 23917% 23918% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23919% 23920% 23921@Unpublished{ rob1, 23922 author = {Rob Kunz}, 23923 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23924 State University}, 23925 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23926 sponsors = {U.S. Navy, NRC}, 23927 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23928 simulations, including lake warming by power plants}, 23929 dates = {Oct 3 and 4, 2002}, 23930 email = {rfk@wt.arl.psu.edu} 23931} 23932 23933@Unpublished{ au1, 23934 author = {Feng Wang and William Appelbe}, 23935 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23936 url = {http://www.vpac.org}, 23937 sponsors = { }, 23938 note = {Using PETSc for a Variety of Geophysical Simulations}, 23939 dates = {Nov 22, 2002} 23940} 23941 23942@Unpublished{ carl1, 23943 author = {Carl Sovinec}, 23944 institution = {Applied Physics, University of Wisconsin}, 23945 url = {http://nimrodteam.org}, 23946 sponsors = {DOE Office of Fusion Research}, 23947 note = {Investigating using PETSc for NIMROD}, 23948 dates = {Nov 21, 2002}, 23949 email = {sovinec@engr.wisc.edu} 23950} 23951 23952@Unpublished{ au1b, 23953 author = {Pablo Carrica and Robert Wilson}, 23954 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23955 url = {http://}, 23956 sponsors = {Office of Naval Research}, 23957 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23958 dates = {Sept, 2002}, 23959 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23960} 23961 23962% ------------------- TAO References ---------------------- 23963@Article{ benson:2001:csp, 23964 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 23965 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 23966 journal = {{ACM} Transactions on Mathematical Software}, 23967 volume = {27}, 23968 number = {3}, 23969 month = sep, 23970 year = {2001}, 23971 pages = {361--376} 23972} 23973 23974@TechReport{ tao-user-ref-2000, 23975 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 23976 title = {{TAO} Users Manual}, 23977 year = {2000}, 23978 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23979 number = {ANL/MCS-TM-242}, 23980 note = {See \url{http://www.mcs.anl.gov/tao}} 23981} 23982 23983% ------------------- Optimization References ---------------------- 23984@Book{ optguide93, 23985 title = {Optimization Software Guide}, 23986 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 23987 publisher = {SIAM Publications}, 23988 address = {Philadelphia}, 23989 year = {1993} 23990} 23991 23992@InProceedings{ more84, 23993 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 23994 Hillstrom}, 23995 title = {The {MINPACK} Project}, 23996 booktitle = {Sources and Development of Mathematical Software}, 23997 editor = {Wayne R. Cowell}, 23998 year = {1984}, 23999 pages = {88--111} 24000} 24001 24002@Article{ steihaug:83, 24003 author = {Trond Steihaug}, 24004 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 24005 journal = {SIAM J. Numer. Anal.}, 24006 volume = {20}, 24007 year = {1983}, 24008 pages = {626--637}, 24009 key = {steihaug92 ! trust_region} 24010} 24011 24012@TechReport{ minpack2test, 24013 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 24014 title = {The {MINPACK-2} Test Problem Collection}, 24015 institution = {Argonne National Laboratory}, 24016 year = {1991}, 24017 number = {ANL/MCS-TM-150}, 24018 key = {more91 ! MINPACK-2} 24019} 24020 24021@TechReport{ hohmann:94, 24022 author = {Andreas Hohmann}, 24023 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 24024 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 24025 year = {1994}, 24026 number = {SC-94-4}, 24027 key = {Hohmann94} 24028} 24029 24030@TechReport{ meza:94, 24031 author = {Juan C. Meza}, 24032 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 24033 institution = {Sandia National Laboratory}, 24034 year = {1994}, 24035 number = {SAND94-8225}, 24036 key = {Meza94} 24037} 24038 24039@Book{ dennis:83, 24040 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 24041 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 24042 publisher = {Prentice-Hall, Inc.}, 24043 address = {Englewood Cliffs, NJ}, 24044 year = {1983} 24045} 24046 24047@TechReport{ more:92, 24048 author = {Jorge J. Mor\'{e} and David Thuente}, 24049 title = {Line search algorithms with guaranteed sufficient decrease}, 24050 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24051 year = {1992}, 24052 number = {MCS-P330-1092} 24053} 24054 24055@Article{ more-toraldo, 24056 author = {Jorge J. Mor\'e and G. Toraldo}, 24057 journal = {SIOPT}, 24058 pages = {93--113}, 24059 title = {On the solution of large quadratic programming problems with bound constraints}, 24060 volume = {1}, 24061 year = {1991} 24062} 24063 24064@Article{ byrd:1995:lma, 24065 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 24066 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 24067 journal = {SIAM Journal on Scientific Computing}, 24068 volume = {16}, 24069 number = {5}, 24070 pages = {1190--1208}, 24071 month = sep, 24072 year = {1995}, 24073 coden = {SJOCE3}, 24074 issn = {1064-8275 (print), 1095-7197 (electronic)}, 24075 mrclass = {90C30 (65K05)}, 24076 mrnumber = {96e:90039}, 24077 mrreviewer = {Henry Wolkowicz}, 24078 bibdate = {Fri Dec 4 16:17:35 MST 1998} 24079} 24080 24081@Article{ lin_c3, 24082 author = {C.-J. Lin and J. J. Mor\'e}, 24083 title = {Newton's method for large bound-constrained optimization problems}, 24084 year = {1999}, 24085 journal = {SIOPT}, 24086 volume = {9(4)}, 24087 pages = {1100--1127}, 24088 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 24089} 24090 24091@TechReport{ dolan2, 24092 author = {E. Dolan and J. J. Mor\'{e}}, 24093 title = {Benchmarking Optimization Software with Performance Profiles}, 24094 year = {2001}, 24095 month = jan, 24096 number = {ANL/MCS-P861-1200}, 24097 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24098 address = {Argonne, IL}, 24099 url = {http://www.mcs.anl.gov/~more/cops/} 24100} 24101 24102@InProceedings{ owlqn, 24103 author = {Galen Andrew and Jianfeng Gao}, 24104 title = {Scalable training of L1-regularized log-linear models}, 24105 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 24106 pages = {33--40}, 24107 year = {2007} 24108} 24109 24110@Article{ bmrm, 24111 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 24112 title = {Bundle methods for regularized risk minimization}, 24113 year = {2010}, 24114 journal = {Journal of Machine Learning Research}, 24115 volume = {11}, 24116 pages = {311--365} 24117} 24118 24119% ------------------- Component Software References ---------------------- 24120@InProceedings{ cca99, 24121 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 24122 McInnes and S. Parker and B. Smolinski}, 24123 title = {Toward a Common Component Architecture for High-Performance Scientific 24124 Computing}, 24125 booktitle = {Proceedings of {High Performance Distributed Computing}}, 24126 pages = {115--124}, 24127 year = {1999}, 24128 note = {See \url{http://cca-forum.org}} 24129} 24130 24131@Book{ szyperski98, 24132 author = {Clemens Szyperski}, 24133 title = {Component Software: Beyond Object-Oriented Programming}, 24134 publisher = {ACM Press}, 24135 address = {New York}, 24136 year = {1998} 24137} 24138 24139@Article{ broy98, 24140 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 24141 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 24142 Stal and Clemens Szyperski}, 24143 title = {What Characterizes a (Software) Component?}, 24144 journal = {Software -- Concepts and Tools}, 24145 publisher = {Springer-Verlag}, 24146 year = {1998}, 24147 volume = {19}, 24148 pages = {49--56} 24149} 24150 24151@Article{ componentware:94, 24152 author = {Jon Udell}, 24153 title = {Componentware}, 24154 journal = {Byte}, 24155 volume = {may}, 24156 pages = {46--56}, 24157 year = {1994}, 24158 key = {Udell94 ! componentware} 24159} 24160 24161@Misc{ cca-web-page, 24162 author = {{Common Component Architecture Forum}}, 24163 note = {See \url{http://cca-forum.org}} 24164} 24165 24166% --------------- References for Tools Used by TAO Developers ----------------- 24167 24168% 24169% tohtml: Used to generate on-line TAO users manual and manual pages 24170% 24171@TechReport{ tohtml, 24172 author = {William Gropp}, 24173 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 24174 institution = {Argonne National Laboratory}, 24175 number = {ANL/MCS-TM-00}, 24176 month = jan, 24177 year = {1995}, 24178 key = {tohtml} 24179} 24180 24181% 24182% doctext: Used to generate tex version of TAO manual pages 24183% 24184@TechReport{ doctext, 24185 author = {William Gropp}, 24186 title = {Users Manual for doctext: Producing documentation from {C} source code}, 24187 institution = {Argonne National Laboratory}, 24188 number = {ANL/MCS-TM-00}, 24189 month = jan, 24190 year = {1995}, 24191 key = {doctext} 24192} 24193 24194% 24195% bfort: Used to generate TAO Fortran interface 24196% 24197@TechReport{ bfort, 24198 author = {William Gropp}, 24199 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 24200 institution = {Argonne National Laboratory}, 24201 number = {ANL/MCS-TM-208}, 24202 month = mar, 24203 year = {1995}, 24204 key = {doctext} 24205} 24206 24207% ------------------------- PETSc References ------------------------------ 24208@InProceedings{ petsc, 24209 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 24210 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 24211 Libraries}, 24212 booktitle = {Modern Software Tools in Scientific Computing}, 24213 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 24214 publisher = {Birkhauser Press}, 24215 pages = {163--202}, 24216 year = {1997} 24217} 24218 24219% ------------------------- Misc Other References ------------------------------ 24220@Misc{ indeps-web-page, 24221 title = {{InDEPS} {W}eb page}, 24222 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 24223 author = {et al. Robert Armstrong}, 24224 institution = {Sandia National Laboratory}, 24225 key = {{InDEPS} {W}eb page} 24226} 24227 24228@Misc{ pooma, 24229 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 24230 chitectures}, 24231 year = {1996}, 24232 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 24233 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 24234} 24235 24236@Misc{ isis++-web-page, 24237 title = {{ISIS++} {W}eb Page}, 24238 note = {See \url{http://ca.sandia.gov/isis}}, 24239 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 24240 institution = {Sandia National Laboratories} 24241} 24242 24243@Misc{ trilinos-web-page, 24244 title = {{Trilinos} {W}eb Page}, 24245 note = {See 24246 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 24247 author = {Mike Heroux et al.}, 24248 institution = {Sandia National Laboratories} 24249} 24250 24251@Misc{ alice-web-page, 24252 title = {{ALICE} {W}eb page}, 24253 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 24254 Argonne National Laboratory}, 24255 key = {{ALICE} {W}eb page} 24256} 24257 24258@Misc{ autodiff-webpage, 24259 author = {{Computational Differentiation Project}}, 24260 note = {See \url{http://www.mcs.anl.gov/autodiff}} 24261} 24262 24263@Misc{ coool-home-page, 24264 author = {Lydia Deng and Wences Gouveia and John Scales}, 24265 title = {{The CWP Object-Oriented Optimization Library}}, 24266 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 24267} 24268 24269@Misc{ rice-inversion-home-page, 24270 author = {Mark S. Gokenbach and William W. Symes}, 24271 title = {{The Hilbert Class Library}}, 24272 note = {See \url{http://www.trip.caam.rice.edu/}} 24273} 24274 24275@Misc{ opt++-home-page, 24276 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 24277 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 24278} 24279 24280@Article{ gockenbach:1999:ccl, 24281 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 24282 title = {C++ Classes for Linking Optimization with Complex Simulations}, 24283 journal = {{ACM} Transactions on Mathematical Software}, 24284 volume = {25}, 24285 number = {2}, 24286 month = jun, 24287 year = {1999}, 24288 pages = {191-212}, 24289 abstract = {The object-oriented programming paradigm can be used to overcome the 24290 incompatibilities between off-the-shelf optimization software and application 24291 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 24292 objects arising in optimization problems, such as vectors, linear operators, and 24293 so forth, as C++ classes, making it possible to write optimization code in a 24294 natural fashion, while allowing application software such as simulators to use the 24295 most convenient data structures and programming style. In spite of the poor 24296 reputation C++ has for runtime performance, the use of mixed-language programming 24297 allows performance equal to that achieved by standard Fortran packages, as 24298 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 24299 accepted = {April 1999}, 24300 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 24301} 24302 24303@Misc{ neos-guide, 24304 author = {{The Optimization Software Guide}}, 24305 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 24306} 24307 24308@Article{ boyd, 24309 title = {Distributed optimization and statistical learning via the alternating direction 24310 method of multipliers}, 24311 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 24312 Jonathan and others}, 24313 journal = {Foundations and Trends{\textregistered} in Machine learning}, 24314 volume = {3}, 24315 number = {1}, 24316 pages = {1-122}, 24317 year = {2011}, 24318 publisher = {Now Publishers, Inc.} 24319} 24320 24321@Misc{ :alertsys, 24322 title = {page{ALERT}}, 24323 organization = {Alert Systems, Inc}, 24324 address = {Madison, Wisconsin}, 24325 note = {http://www.alertsys.com/} 24326} 24327 24328@Manual{ :cmfortran, 24329 title = {{CM} {F}ortran Language Reference Manual}, 24330 organization = {Thinking Machines Corporation}, 24331 year = {1994}, 24332 address = {Cambridge, MA} 24333} 24334 24335@Manual{ :cmmd, 24336 title = {{CMMD} Reference Manual, Version 3.0}, 24337 organization = {Thinking Machines Corporation}, 24338 year = {1993}, 24339 address = {Cambridge, MA} 24340} 24341 24342@Manual{ :cmssl, 24343 title = {{CMSSL} for {CM} {F}ortran}, 24344 volume = {I}, 24345 organization = {Thinking Machines Corporation}, 24346 year = {1994}, 24347 address = {Cambridge, MA} 24348} 24349 24350@Misc{ :condor, 24351 author = {M. Livny}, 24352 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24353 howpublished = {www.cs.wisc.edu/condor} 24354} 24355 24356@Manual{ :connection, 24357 title = {Connection Machine {CM}--5 Technical Summary}, 24358 organization = {Thinking Machines Corporation}, 24359 year = {1993}, 24360 address = {Cambridge, MA} 24361} 24362 24363@Manual{ :cplex, 24364 title = {{CPLEX} Optimizer}, 24365 organization = {ILOG CPLEX Division}, 24366 address = {889 Alder Avenue, Incline Village, Nevada}, 24367 note = {http://www.cplex.com/} 24368} 24369 24370@Manual{ :cplextm, 24371 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24372 (Version 2.0)}, 24373 organization = {CPLEX Optimization Inc.}, 24374 year = {1992}, 24375 address = {Incline Village, Nevada} 24376} 24377 24378@Misc{ :fatcop, 24379 author = {M. C. Ferris}, 24380 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24381 Solver}, 24382 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24383} 24384 24385@Misc{ :metaneos, 24386 author = {S. J. Wright}, 24387 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24388 howpublished = {www-unix.mcs.anl.gov/metaneos} 24389} 24390 24391@InCollection{ gropp.more:optimization, 24392 author = {W. Gropp and J. J. Mor\'e}, 24393 title = {Optimization environments and the {NEOS} Server}, 24394 booktitle = {Approximation Theory and Optimization}, 24395 pages = {167--182}, 24396 publisher = {Cambridge University Press}, 24397 year = {1997}, 24398 editor = {M. D. Buhmann and A. Iserles} 24399} 24400 24401@Article{ czyzyk.mesnier.ea:neos, 24402 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24403 title = {The {NEOS} Server}, 24404 journal = {IEEE Journal on Computational Science and Engineering}, 24405 volume = {5}, 24406 year = {1998}, 24407 pages = {68--75} 24408} 24409 24410@Book{ :osl, 24411 title = {Handbook for {IBM OSL}}, 24412 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24413 year = {1994}, 24414 publisher = {Boyd and Fraser}, 24415 address = {Danvers, Massachusetts} 24416} 24417 24418@Manual{ :pro-matlab, 24419 title = {{PRO}--{MATLAB} User's Guide}, 24420 organization = {The MathWorks, Inc.}, 24421 year = {1989}, 24422 address = {21 Eliot Street, South Natick, MA 01760} 24423} 24424 24425@Misc{ :prostate, 24426 key = {Biomedical}, 24427 title = {Biomedical Business International Newsletter}, 24428 howpublished = {pp. 72--75}, 24429 year = {1996} 24430} 24431 24432@Misc{ :sipcase, 24433 key = {Natural}, 24434 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24435 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24436} 24437 24438@Book{ aarts.korst:simulated, 24439 author = {E. Aarts and J. Korst}, 24440 title = {Simulated Annealing and Boltzman Machines}, 24441 year = {1990}, 24442 publisher = {John Wiley \& Sons}, 24443 address = {Chichester} 24444} 24445 24446@TechReport{ aarts.laarhoven.ea:local-search-based, 24447 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 24448 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 24449 institution = {Centre for Quantitative Methods}, 24450 year = {1991}, 24451 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 24452 number = {106}, 24453 type = {CQM-Not} 24454} 24455 24456@Article{ aashtiani.magnanti:equilibria, 24457 author = {H. Z. Aashtiani and T. L. Magnanti}, 24458 title = {Equilibria on a congested transportation network}, 24459 journal = {SIAM Journal on Algebraic and Discrete Methods}, 24460 volume = {2}, 24461 year = {1981}, 24462 pages = {213--226} 24463} 24464 24465@Article{ ablow.brigham:analog, 24466 author = {C. M. Ablow and G. Brigham}, 24467 title = {An Analog Solution of Programming Problems}, 24468 journal = {Operations Research}, 24469 year = {1955}, 24470 volume = {3}, 24471 pages = {388--394} 24472} 24473 24474@Article{ achuthan.grabowski.ea:optimal, 24475 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 24476 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 24477 journal = {Opsearch}, 24478 year = {1981}, 24479 volume = {18}, 24480 pages = {117--138} 24481} 24482 24483@Book{ adelman.robinson:income, 24484 author = {I. Adelman and S. Robinson}, 24485 title = {Income Distribution Policy in Developing Countries}, 24486 publisher = {Stanford University Press}, 24487 year = {1978}, 24488 address = {Stanford, California} 24489} 24490 24491@Article{ adler.resende.ea:implementation, 24492 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 24493 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 24494 journal = {Mathematical Programming}, 24495 year = {1989}, 24496 volume = {44}, 24497 pages = {297--336} 24498} 24499 24500@TechReport{ aeberhard.coomans.ea:comparison, 24501 author = {S. Aeberhard and D. Coomans and O. de Vel}, 24502 title = {Comparison of Classifiers in High Dimensional Settings}, 24503 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 24504 University of North Queensland}, 24505 year = {1992}, 24506 number = {92-02}, 24507 type = {Technical Report} 24508} 24509 24510@Article{ aganagic.cottle:constructive, 24511 author = {M. Aganagi\'{c} and R. W. Cottle}, 24512 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 24513 Minors}, 24514 journal = {Mathematical Programming}, 24515 year = {1987}, 24516 volume = {37}, 24517 pages = {223--231} 24518} 24519 24520@TechReport{ aganagic:iterative, 24521 author = {M. Aganagi\'{c}}, 24522 title = {Iterative Methods for the Linear Complementarity Problem}, 24523 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 24524 University}, 24525 year = {1978}, 24526 type = {SOL}, 24527 number = {78-10}, 24528 address = {Stanford, California} 24529} 24530 24531@Book{ ahlfors:complex, 24532 author = {L. V. Ahlfors}, 24533 title = {Complex Analysis}, 24534 publisher = {McGraw--Hill Book Company}, 24535 address = {New York}, 24536 series = {International Series in Pure and Applied Mathematics}, 24537 edition = {Second}, 24538 year = {1966} 24539} 24540 24541@Article{ ahn:solution, 24542 author = {B--H. Ahn}, 24543 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 24544 journal = {Journal of Optimization Theory and Applications}, 24545 year = {1981}, 24546 volume = {33}, 24547 pages = {175--185} 24548} 24549 24550@Article{ al-fahed.stavroulakis.ea:hard, 24551 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24552 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 24553 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 24554 volume = {71}, 24555 year = {1991}, 24556 pages = {257--265} 24557} 24558 24559@Article{ al-fahed.stavroulakis.ea:linear, 24560 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24561 title = {A linear complementarity approach to the frictionless gripper}, 24562 journal = {International Journal of Robotic Research}, 24563 volume = {11}, 24564 year = {1992}, 24565 pages = {112--122} 24566} 24567 24568@Article{ al-khayyal.falk:jointly, 24569 author = {F. A. Al--Khayyal and J. E. Falk}, 24570 title = {Jointly Constrained Biconvex Programming}, 24571 journal = {Mathematics of Operations Research}, 24572 year = {1983}, 24573 volume = {8}, 24574 pages = {273--286} 24575} 24576 24577@Article{ al-khayyal.kyparisis:finite, 24578 author = {F. A. Al--Khayyal and J. Kyparisis}, 24579 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 24580 Inequalities}, 24581 journal = {Journal of Optimization Theory and Applications}, 24582 year = {1991}, 24583 volume = {70}, 24584 pages = {319--332} 24585} 24586 24587@PhDThesis{ al-khayyal:biconvex, 24588 author = {F. A. Al--Khayyal}, 24589 title = {Biconvex Programming and Biconcave Minimization}, 24590 year = {1977}, 24591 school = {The George Washington University} 24592} 24593 24594@Article{ alart.curnier:mixed, 24595 author = {P. Alart and A. Curnier}, 24596 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 24597 solution methods}, 24598 journal = {Computer Methods in Applied Mechanics and Engineering}, 24599 volume = {92}, 24600 year = {1991}, 24601 pages = {353--375} 24602} 24603 24604@Misc{ alexander.kellog.ea:piecewise, 24605 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 24606 title = {Piecewise smooth continuation}, 24607 howpublished = {Manuscript}, 24608 year = {1979} 24609} 24610 24611@InCollection{ alexander.li.ea:piecewise, 24612 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 24613 title = {Piecewise smooth homotopies}, 24614 booktitle = {Homotopy Methods and Global Convergence}, 24615 pages = {1--14}, 24616 publisher = {Plenum Press}, 24617 year = {1983}, 24618 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 24619 address = {New York} 24620} 24621 24622@InCollection{ alexander:topological, 24623 author = {J.~C. Alexander}, 24624 title = {The topological theory of an embedding method}, 24625 booktitle = {Continuation Methods}, 24626 pages = {37--68}, 24627 publisher = {Academic Press}, 24628 year = {1978}, 24629 editor = {H. Wacker}, 24630 address = {New York} 24631} 24632 24633@Book{ allen:probability, 24634 author = {A. O. Allen}, 24635 title = {Probability, Statistics and Queueing Theory}, 24636 publisher = {Academic Press}, 24637 year = {1990}, 24638 address = {London}, 24639 edition = {Second} 24640} 24641 24642@Book{ allgower.georg:numerical, 24643 author = {E. L. Allgower and K. Georg}, 24644 title = {Numerical Continuation Methods, An Introduction}, 24645 publisher = {Springer-Verlag}, 24646 year = {1990}, 24647 address = {Berlin} 24648} 24649 24650@InProceedings{ allgower.georg:predictor-corrector, 24651 crossref = {bachem.grotschel.ea:mathematical}, 24652 author = {E. L. Allgower and K. Georg}, 24653 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 24654 Zero Points of Nonlinear Mappings}, 24655 pages = {15--56} 24656} 24657 24658@Article{ aluffi-pentini.parisi.ea:algorithm, 24659 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 24660 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 24661 Algorithm}, 24662 journal = {ACM Transactions on Mathematical Software}, 24663 year = {1988}, 24664 volume = {14}, 24665 pages = {366--380} 24666} 24667 24668@Article{ anandalingam.friesz:hierarchical, 24669 author = {G. Anandalingam and T. L. Friesz}, 24670 title = {Hierarchical Optimization: An Introduction}, 24671 journal = {Annals of Operations Research}, 24672 year = {1992}, 24673 volume = {34}, 24674 pages = {1--11} 24675} 24676 24677@Article{ anandalingam.white:solution, 24678 author = {G. Anandalingam and D. J. White}, 24679 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 24680 Functions}, 24681 journal = {IEEE Transactions on Automatic Control}, 24682 year = {1990}, 24683 volume = {35}, 24684 number = {10}, 24685 pages = {1170--1173} 24686} 24687 24688@Article{ andersen.andersen:presolving, 24689 author = {E. Andersen and K. Andersen}, 24690 title = {Presolving in Linear Programming}, 24691 year = {1995}, 24692 journal = {Mathematical Programming}, 24693 volume = {71}, 24694 pages = {221--245} 24695} 24696 24697@InProceedings{ andersen.ye:homogeneous, 24698 author = {E. Andersen and Y. Ye}, 24699 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 24700 Equality Constraints}, 24701 crossref = {ferris.pang:complementarity}, 24702 pages = {1--11} 24703} 24704 24705@Book{ anderson.bai.ea:lapack, 24706 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 24707 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 24708 Sorensen}, 24709 title = {{LAPACK} User's Guide}, 24710 publisher = {SIAM}, 24711 year = {1995}, 24712 address = {Philadelphia, Pennsylvania}, 24713 edition = {Second} 24714} 24715 24716@Article{ anderson.ferris:direct, 24717 author = {E. J. Anderson and M. C. Ferris}, 24718 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 24719 year = {2001}, 24720 journal = {SIAM Journal on Optimization, forthcoming}, 24721 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 24722 key = {55} 24723} 24724 24725@InProceedings{ anderson.ferris:genetic, 24726 author = {E. J. Anderson and M. C. Ferris}, 24727 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 24728 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 24729 Waterloo, Ontario, Canada, May 28--30}, 24730 publisher = {University of Waterloo Press}, 24731 key = {14}, 24732 year = {1990} 24733} 24734 24735@Article{ anderson.ferris:genetic*1, 24736 author = {E. J. Anderson and M. C. Ferris}, 24737 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 24738 Problem}, 24739 journal = {ORSA Journal on Computing}, 24740 year = {1994}, 24741 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 24742 volume = {6}, 24743 pages = {161--173}, 24744 key = {22} 24745} 24746 24747@InProceedings{ anderson.ferris:parallel, 24748 author = {E. J. Anderson and M. C. Ferris}, 24749 title = {Parallel Genetic Algorithms in Optimization}, 24750 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 24751 Computing, Chicago, Illinois, December 11-13}, 24752 year = {1989}, 24753 key = {12} 24754} 24755 24756@Unpublished{ anderson.lewis:primal, 24757 author = {E. J. Anderson and A. S. Lewis}, 24758 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24759 note = {In preparation} 24760} 24761 24762@Book{ anderson.nash:linear, 24763 author = {E. J. Anderson and P. Nash}, 24764 title = {Linear Programming in Infinite--Dimensional Spaces}, 24765 year = {1987}, 24766 publisher = {John Wiley \& Sons}, 24767 address = {Chichester} 24768} 24769 24770@InProceedings{ anderson:primal, 24771 author = {E. J. Anderson}, 24772 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24773 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 24774 Programming, Cambridge, September 1984}, 24775 year = {1985}, 24776 editor = {E. J. Anderson and A. B. Philpott}, 24777 publisher = {Springer-Verlag}, 24778 address = {Berlin} 24779} 24780 24781@Article{ andradottir:method, 24782 author = {S. Andrad\'{o}ttir}, 24783 title = {A Method of Discrete Stochastic Optimization}, 24784 journal = {Management Science}, 24785 year = {1995}, 24786 volume = {41}, 24787 pages = {1946--1961} 24788} 24789 24790@Article{ andradottir:global, 24791 author = {S. Andrad\'{o}ttir}, 24792 title = {A Global Search Method for Discrete Stochastic Optimization}, 24793 journal = {SIAM Journal on Optimization}, 24794 year = {1996}, 24795 volume = {6}, 24796 pages = {513--530} 24797} 24798 24799@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 24800 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 24801 title = {An infeasible--interior--point predictor--corrector algorithm for the 24802 {P}$_x$--geometric {LCP}}, 24803 institution = {Department of Mathematics, The University of Iowa}, 24804 address = {Iowa City, Iowa}, 24805 year = {1994}, 24806 number = {62}, 24807 type = {Reports on Computational Mathematics} 24808} 24809 24810@TechReport{ anitescu.potra:formulating, 24811 author = {M. Anitescu and F. A. Potra}, 24812 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 24813 Linear Complementarity Problems}, 24814 institution = {Department of Mathematics, The University of Iowa}, 24815 year = {1996}, 24816 type = {Report}, 24817 number = {93}, 24818 address = {Iowa City, Iowa} 24819} 24820 24821@Article{ anstreicher.lee.ea:crashing, 24822 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 24823 title = {Crashing a Maximum-Weight Complementarity Basis}, 24824 journal = {Mathematical Programming}, 24825 year = {1992}, 24826 volume = {54}, 24827 pages = {281--294} 24828} 24829 24830@Article{ anstreicher:combined, 24831 author = {K. M. Anstreicher}, 24832 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 24833 programming}, 24834 journal = {Mathematical Programming}, 24835 year = {1991}, 24836 volume = {52}, 24837 pages = {429--440} 24838} 24839 24840@Article{ anstreicher:combined*1, 24841 author = {K. M. Anstreicher}, 24842 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 24843 journal = {Mathematical Programming}, 24844 year = {1989}, 24845 volume = {43}, 24846 pages = {209--223} 24847} 24848 24849@InCollection{ arbenz.gander.ea:remote, 24850 author = {P. Arbenz and W. Gander and M. Oettli}, 24851 title = {The Remote Computational System}, 24852 booktitle = {High-Performance Computation and Networks}, 24853 publisher = {Springer-Verlag}, 24854 year = {1996}, 24855 volume = {1067}, 24856 series = {Lecture Notes in Computer Science}, 24857 pages = {662--667} 24858} 24859 24860@InCollection{ arcus:comsoal, 24861 author = {A. L. Arcus}, 24862 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 24863 booktitle = {Readings in Production and Operations Management}, 24864 year = {1966}, 24865 editor = {E. S. Buffa}, 24866 publisher = {John Wiley \& Sons}, 24867 address = {New York} 24868} 24869 24870@TechReport{ arioli.chan.ea:computing, 24871 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 24872 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 24873 Optimization Calculations}, 24874 institution = {CERFACS}, 24875 year = {1993}, 24876 number = {TR/PA/93/34} 24877} 24878 24879@Article{ armijo:minimization, 24880 author = {L. Armijo}, 24881 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 24882 Derivatives}, 24883 journal = {Pacific Journal of Mathematics}, 24884 year = {1966}, 24885 volume = {16}, 24886 pages = {1--3} 24887} 24888 24889@Article{ arrow.debreu:existence, 24890 author = {K. Arrow and G. Debreu}, 24891 title = {Existence of Equilibrium for a Competitive Economy}, 24892 journal = {Econometrica}, 24893 year = {1954}, 24894 volume = {22}, 24895 pages = {265--290} 24896} 24897 24898@InCollection{ arrow.solow:gradient, 24899 author = {K. J. Arrow and R. M. Solow}, 24900 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 24901 booktitle = {Studies in Linear and Nonlinear Programming}, 24902 year = {1958}, 24903 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 24904 publisher = {Stanford University Press}, 24905 address = {Stanford, California}, 24906 pages = {166--176} 24907} 24908 24909@Book{ aubin.ekeland:nonlinear, 24910 author = {J.-P. Aubin and I. Ekeland}, 24911 title = {Applied nonlinear analysis}, 24912 publisher = {John Wiley \& Sons}, 24913 address = {New York}, 24914 year = {1984} 24915} 24916 24917@Article{ auchmuty:variational, 24918 author = {G. Auchmuty}, 24919 title = {Variational Principles for Variational Inequalities}, 24920 journal = {Numerical Functional Analysis and Optimization}, 24921 year = {1989}, 24922 volume = {10}, 24923 pages = {863--874} 24924} 24925 24926@Book{ auerbach.kotlikoff:dynamic, 24927 author = {A. J. Auerbach and L. J. Kotlikoff}, 24928 title = {Dynamic Fiscal Policy}, 24929 publisher = {Cambridge University Press}, 24930 address = {Cambridge, England}, 24931 year = {1987} 24932} 24933 24934@InProceedings{ ault.deutsch.ea:interpolating, 24935 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 24936 title = {Interpolating Subspaces in Approximation Theory}, 24937 booktitle = {Approximation Theory}, 24938 year = {1970}, 24939 editor = {A. Talbot}, 24940 publisher = {Academic Press}, 24941 address = {London} 24942} 24943 24944@Article{ auslender.crouzeix:global, 24945 author = {A. A. Auslender and J.--P. Crouzeix}, 24946 title = {Global Regularity Theorems}, 24947 journal = {Mathematics of Operations Research}, 24948 year = {1988}, 24949 volume = {13}, 24950 pages = {243--253} 24951} 24952 24953@Article{ auslender.haddou:interior-proximal, 24954 author = {A. Auslender and M. Haddou}, 24955 title = {An interior-proximal method for convex linearly constrained problems and its 24956 extension to variational inequalities}, 24957 year = {1995}, 24958 journal = {Mathematical Programming}, 24959 pages = {77--100}, 24960 volume = {71} 24961} 24962 24963@Article{ auslender:convergence, 24964 author = {A. Auslender}, 24965 title = {Convergence of stationary sequences for variational inequalities with maximal 24966 monotone operators}, 24967 journal = {Applied Mathematics and Optimization}, 24968 volume = {28}, 24969 year = {1993}, 24970 pages = {161--172} 24971} 24972 24973@Book{ auslender:optimization, 24974 author = {A. Auslender}, 24975 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 24976 year = {1976}, 24977 publisher = {Masson}, 24978 address = {Paris} 24979} 24980 24981@TechReport{ averick.carter.ea:minpack-2, 24982 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 24983 title = {The {MINPACK-2} Test Problem Collection}, 24984 institution = {Argonne National Laboratory}, 24985 year = {1992}, 24986 address = {Argonne, Illinois}, 24987 number = {MCS-P153-0692} 24988} 24989 24990@TechReport{ axline.billups.ea:guidelines, 24991 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 24992 title = {Guidelines for Software Security ({U})}, 24993 institution = {SNL}, 24994 year = {1989}, 24995 month = oct, 24996 address = {Albuquerque, New Mexico}, 24997 number = {SAND88-2955} 24998} 24999 25000@Article{ ayres.walter:greenhouse, 25001 author = {R. U. Ayres and J. Walter}, 25002 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 25003 journal = {Environmental and Resource Economics}, 25004 year = {1991}, 25005 volume = {1}, 25006 pages = {237--270} 25007} 25008 25009@PhDThesis{ bagley:behaviour, 25010 author = {J. D. Bagley}, 25011 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 25012 Algorithms}, 25013 year = {1967}, 25014 school = {University of Michigan} 25015} 25016 25017@Article{ bain.stewart:application, 25018 author = {R. S. Bain and W. E. Stewart}, 25019 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 25020 Algebraic Equation Systems}, 25021 journal = {Computers in Chemical Engineering}, 25022 year = {1991}, 25023 volume = {15}, 25024 pages = {203--208} 25025} 25026 25027@Article{ baker.lasdon:successive, 25028 author = {T. E. Baker and L. S. 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Bertsekas}, 25472 title = {Nonlinear Programming}, 25473 publisher = {Athena Scientific}, 25474 year = {1995}, 25475 address = {Belmont, Massachusetts} 25476} 25477 25478@Article{ bertsekas:projected, 25479 author = {Dimitri P. Bertsekas}, 25480 title = {Projected {N}ewton Methods for Optimization Problems with Simple Constraints}, 25481 journal = {SIAM Journal on Control and Optimization}, 25482 year = {1982}, 25483 volume = {20}, 25484 pages = {221--246} 25485} 25486 25487@Article{ billups.dirkse.ea:comparison, 25488 author = {S. C. Billups and S. P. Dirkse and M. C. Ferris}, 25489 title = {A Comparison of Large Scale Mixed Complementarity Problem Solvers}, 25490 journal = {Computational Optimization and Applications}, 25491 year = {1997}, 25492 pages = {3--25}, 25493 volume = {7}, 25494 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps}, 25495 key = {51} 25496} 25497 25498@Article{ billups.ferris:convergence, 25499 author = {S. C. Billups and M. C. Ferris}, 25500 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 25501 Starting Points}, 25502 journal = {SIAM Journal on Optimization}, 25503 year = {1996}, 25504 volume = {6}, 25505 pages = {316--325}, 25506 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 25507 key = {34} 25508} 25509 25510@TechReport{ billups.ferris:convergence*1, 25511 author = {S. C. Billups and M. C. Ferris}, 25512 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 25513 Points}, 25514 institution = {Computer Sciences Department, University of Wisconsin}, 25515 year = {1993}, 25516 address = {Madison, Wisconsin}, 25517 number = {1180}, 25518 note = {Revised version in SIAM Journal on Optimization.} 25519} 25520 25521@Article{ billups.ferris:qpcomp, 25522 author = {S. C. Billups and M. C. Ferris}, 25523 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 25524 year = {1997}, 25525 journal = {Mathematical Programming}, 25526 pages = {533--562}, 25527 volume = {76}, 25528 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 25529 key = {47} 25530} 25531 25532@Article{ billups.ferris:solutions, 25533 author = {S. C. Billups and M. C. Ferris}, 25534 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 25535 journal = {Mathematics of Operations Research}, 25536 volume = {24}, 25537 pages = {219--236}, 25538 year = {1999}, 25539 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 25540 key = {42}, 25541 institution = {Computer Sciences Department, University of Wisconsin}, 25542 address = {Madison, Wisconsin}, 25543 type = {Mathematical Programming Technical Report}, 25544 number = {94--15} 25545} 25546 25547@TechReport{ billups.murata.ea:users, 25548 author = {S. C. Billups and K. K. 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Model analysis and 26637 optimality conditions}, 26638 type = {Publication}, 26639 number = {CRT-94-56}, 26640 institution = {Centre de Recherche sur les Transports, Universit\'e de Montr\'eal}, 26641 address = {Montr\'eal, Canada}, 26642 year = {1994} 26643} 26644 26645@Article{ chen.harker:continuation, 26646 author = {B. Chen and P. T. Harker}, 26647 title = {A Continuation Method for Monotone Variational Inequalities}, 26648 journal = {Mathematical Programming}, 26649 volume = {69}, 26650 pages = {237--253}, 26651 year = {1995} 26652} 26653 26654@Article{ chen.harker:non-interior, 26655 author = {B. Chen and P. T. Harker}, 26656 title = {A Non-Interior-Point Continuation Method for Linear Complementarity Problems}, 26657 journal = {SIAM Journal on Matrix Analysis and Applications}, 26658 year = {1993}, 26659 volume = {14}, 26660 pages = {1168--1190} 26661} 26662 26663@Article{ chen.harker:smooth, 26664 author = {B. Chen and P. T. 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Mangasarian}, 28563 title = {Breast Cancer Diagnosis via Linear Programming}, 28564 key = {50}, 28565 journal = {{IEEE} Computational Science and Engineering}, 28566 year = {1995}, 28567 volume = {2}, 28568 pages = {70--71} 28569} 28570 28571@Article{ ferris.mangasarian:error, 28572 author = {M. C. Ferris and O. L. Mangasarian}, 28573 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 28574 Inequalities}, 28575 journal = {Annals of Operations Research}, 28576 year = {1993}, 28577 volume = {47}, 28578 pages = {293--305}, 28579 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 28580 key = {24} 28581} 28582 28583@Article{ ferris.mangasarian:finite, 28584 author = {M. C. Ferris and O. L. Mangasarian}, 28585 title = {Finite Perturbation of Convex Programs}, 28586 journal = {Applied Mathematics and Optimization}, 28587 year = {1991}, 28588 volume = {23}, 28589 pages = {263--273}, 28590 key = {08} 28591} 28592 28593@Book{ ferris.mangasarian:linear, 28594 author = {M. C. Ferris and O. L. Mangasarian}, 28595 title = {Linear Programming via {MATLAB}}, 28596 publisher = {in preparation}, 28597 year = {1995}, 28598 address = {Madison, Wisconsin} 28599} 28600 28601@Article{ ferris.mangasarian:minimum, 28602 author = {M. C. Ferris and O. L. Mangasarian}, 28603 title = {Minimum Principle Sufficiency}, 28604 journal = {Mathematical Programming}, 28605 year = {1992}, 28606 volume = {57}, 28607 pages = {1--14}, 28608 key = {11} 28609} 28610 28611@Article{ ferris.mangasarian:parallel, 28612 author = {M. C. Ferris and O. L. Mangasarian}, 28613 title = {Parallel Constraint Distribution}, 28614 journal = {SIAM Journal on Optimization}, 28615 year = {1991}, 28616 volume = {1}, 28617 pages = {487--500}, 28618 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28619 key = {18} 28620} 28621 28622@Article{ ferris.mangasarian:parallel*1, 28623 author = {M. C. Ferris and O. L. Mangasarian}, 28624 title = {Parallel Variable Distribution}, 28625 journal = {SIAM Journal on Optimization}, 28626 year = {1994}, 28627 volume = {4}, 28628 pages = {815--832}, 28629 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28630 key = {31} 28631} 28632 28633@Article{ ferris.meeraus.ea:computing, 28634 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28635 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28636 journal = {Optimization Methods and Software}, 28637 year = {1999}, 28638 volume = {10}, 28639 pages = {669--685}, 28640 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28641 key = {45} 28642} 28643 28644@Article{ ferris.mesnier.ea:neos, 28645 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28646 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28647 {I}nternet}, 28648 year = {2000}, 28649 journal = {{ACM} Transactions on Mathematical Software}, 28650 key = {54}, 28651 volume = {26}, 28652 pages = {1--18}, 28653 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28654 institution = {Computer Sciences Department, University of Wisconsin}, 28655 address = {Madison, Wisconsin}, 28656 number = {96-08}, 28657 type = {Mathematical Programming Technical Report}, 28658 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28659 Argonne National Laboratory}, 28660 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28661 1996} 28662} 28663 28664@InCollection{ ferris.meyer:models, 28665 author = {M. C. Ferris and R. R. Meyer}, 28666 title = {Models and Solution for On-Demand Data Delivery Problems}, 28667 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28668 key = {80}, 28669 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28670 Problems}, 28671 editor = {P. M. Pardalos}, 28672 series = {Nonconvex Optimization and its Applications}, 28673 volume = {42}, 28674 address = {Dordrect}, 28675 year = {2000}, 28676 pages = {175--188}, 28677 publisher = {Kluwer}, 28678 type = {Mathematical Programming Technical Report}, 28679 institution = {Computer Sciences Department, University of Wisconsin}, 28680 number = {99-04} 28681} 28682 28683@InProceedings{ ferris.munson.ea:homotopy, 28684 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28685 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28686 booktitle = {Numerical Analysis 1999}, 28687 key = {88}, 28688 year = {2000}, 28689 editor = {D. F. Griffiths and G. A. Watson}, 28690 series = {Research Notes in Mathematics}, 28691 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28692 address = {London}, 28693 pages = {143--167}, 28694 publisher = {Chapman and Hall}, 28695 institution = {Computer Sciences Department, University of Wisconsin}, 28696 number = {99-09}, 28697 type = {Mathematical Programming Technical Report} 28698} 28699 28700@TechReport{ ferris.munson.ea:practical, 28701 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28702 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28703 type = {Data Mining Institute Technical Report}, 28704 institution = {Computer Sciences Department, University of Wisconsin}, 28705 address = {Madison, Wisconsin}, 28706 year = {2000}, 28707 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28708 number = {00-03}, 28709 key = {92}, 28710 annote = {To appear in WSC 2000} 28711} 28712 28713@InCollection{ ferris.munson:case, 28714 author = {M. C. Ferris and T. S. Munson}, 28715 title = {Case Studies in Complementarity: Improving Model Formulation}, 28716 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28717 key = {73}, 28718 pages = {79--98}, 28719 publisher = {Springer Verlag}, 28720 year = {1999}, 28721 editor = {M. Th\'{e}ra and R. Tichatschke}, 28722 number = {477}, 28723 series = {Lecture Notes in Economics and Mathematical Systems}, 28724 address = {Berlin}, 28725 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28726 type = {Mathematical Programming Technical Report}, 28727 institution = {Computer Sciences Department, University of Wisconsin} 28728} 28729 28730@Article{ ferris.munson:complementarity, 28731 author = {M. C. Ferris and T. S. Munson}, 28732 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28733 year = {2000}, 28734 volume = {24}, 28735 pages = {165--188}, 28736 journal = {Journal of Economic Dynamics and Control}, 28737 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28738 key = {70}, 28739 type = {Mathematical Programming Technical Report}, 28740 institution = {Computer Sciences Department, University of Wisconsin}, 28741 address = {Madison, Wisconsin}, 28742 number = {98-12} 28743} 28744 28745@Misc{ ferris.munson:condor, 28746 author = {M. C. Ferris and T. S. Munson}, 28747 title = {Condor Modeling Language Interface}, 28748 organization = {Computer Sciences Department, University of Wisconsin}, 28749 address = {Madison, Wisconsin}, 28750 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28751} 28752 28753@Manual{ ferris.munson:gams, 28754 author = {M. C. Ferris and T. S. Munson}, 28755 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28756 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28757} 28758 28759@Article{ ferris.munson:interfaces, 28760 author = {M. C. Ferris and T. S. Munson}, 28761 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28762 journal = {Computational Optimization and Applications}, 28763 volume = {12}, 28764 pages = {207--227}, 28765 year = {1999}, 28766 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28767 key = {63}, 28768 institution = {Computer Sciences Department, University of Wisconsin}, 28769 address = {Madison, Wisconsin}, 28770 number = {97-12}, 28771 type = {Mathematical Programming Technical Report} 28772} 28773 28774@TechReport{ ferris.munson:interior, 28775 author = {M. C. Ferris and T. S. Munson}, 28776 title = {Interior Point Methods for Massive Support Vector Machines}, 28777 institution = {Computer Sciences Department, University of Wisconsin}, 28778 year = {2000}, 28779 key = {94}, 28780 type = {Data Mining Institute Technical Report}, 28781 number = {00-05}, 28782 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28783 address = {Madison, Wisconsin}, 28784 annote = {Submitted to SIOPT} 28785} 28786 28787@Article{ ferris.munson:linear, 28788 author = {M. C. Ferris and T. S. Munson}, 28789 title = {Linear Programming for Emergency Broadcast Systems}, 28790 year = {1999}, 28791 journal = {{SIAG/OPT} Newsletter}, 28792 volume = {10}, 28793 pages = {6--8}, 28794 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28795 key = {76}, 28796 type = {Mathematical Programming Technical Report}, 28797 institution = {Computer Sciences Department, University of Wisconsin}, 28798 address = {Madison, Wisconsin}, 28799 number = {98-20} 28800} 28801 28802@Article{ ferris.munson:modeling, 28803 author = {M. C. Ferris and T. S. Munson}, 28804 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28805 year = {2000}, 28806 journal = {Mathematical Programming}, 28807 volume = {88}, 28808 pages = {487--506}, 28809 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28810 key = {71}, 28811 type = {Mathematical Programming Technical Report}, 28812 institution = {Computer Sciences Department, University of Wisconsin}, 28813 address = {Madison, Wisconsin}, 28814 number = {98-13} 28815} 28816 28817@TechReport{ ferris.munson:preprocessing, 28818 author = {M. C. Ferris and T. S. Munson}, 28819 title = {Preprocessing Complementarity Problems}, 28820 type = {Mathematical Programming Technical Report}, 28821 institution = {Computer Sciences Department, University of Wisconsin}, 28822 address = {Madison, Wisconsin}, 28823 year = {1999}, 28824 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28825 number = {99-07}, 28826 key = {86}, 28827 annote = {Submitted to ICCP 99} 28828} 28829 28830@TechReport{ ferris.munson:semismooth, 28831 author = {M. C. Ferris and T. S. Munson}, 28832 title = {Semismooth Support Vector Machines}, 28833 institution = {Computer Sciences Department, University of Wisconsin}, 28834 year = {2000}, 28835 key = {97}, 28836 type = {Data Mining Institute Technical Report}, 28837 number = {00-09}, 28838 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28839 address = {Madison, Wisconsin}, 28840 annote = {Submitted to Math Prog B} 28841} 28842 28843@Article{ ferris.pang:engineering, 28844 author = {M. C. Ferris and J. S. Pang}, 28845 title = {Engineering and Economic Applications of Complementarity Problems}, 28846 year = {1997}, 28847 journal = {SIAM Review}, 28848 volume = {39}, 28849 pages = {669--713}, 28850 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28851 key = {46} 28852} 28853 28854@Article{ ferris.pang:nondegenerate, 28855 author = {M. C. Ferris and J. S. Pang}, 28856 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28857 journal = {SIAM Journal on Control and Optimization}, 28858 year = {1996}, 28859 volume = {34}, 28860 pages = {244--263}, 28861 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28862 key = {35} 28863} 28864 28865@Article{ ferris.philpott:affine, 28866 author = {M. C. Ferris and A. B. Philpott}, 28867 title = {On Affine Scaling and Semi--Infinite Programming}, 28868 journal = {Mathematical Programming}, 28869 year = {1992}, 28870 volume = {56}, 28871 pages = {361--364}, 28872 key = {15} 28873} 28874 28875@Article{ ferris.philpott:interior, 28876 author = {M. C. Ferris and A. B. Philpott}, 28877 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28878 journal = {Mathematical Programming}, 28879 year = {1989}, 28880 volume = {43}, 28881 pages = {257--276}, 28882 key = {04} 28883} 28884 28885@Article{ ferris.philpott:performance, 28886 author = {M. C. Ferris and A. B. Philpott}, 28887 title = {On the Performance of {K}armarkar's Algorithm}, 28888 journal = {Journal of the Operational Research Society}, 28889 year = {1988}, 28890 volume = {39}, 28891 pages = {257--270}, 28892 key = {03} 28893} 28894 28895@InCollection{ ferris.ralph:projected, 28896 author = {M. C. Ferris and D. Ralph}, 28897 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28898 Maps}, 28899 booktitle = {Recent Advances in Nonsmooth Optimization}, 28900 publisher = {World Scientific Publishers}, 28901 year = {1995}, 28902 pages = {57--87}, 28903 editor = {D. Du and L. Qi and R. Womersley}, 28904 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28905 key = {41} 28906} 28907 28908@Article{ ferris.ruszczynski:robust, 28909 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28910 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28911 year = {2000}, 28912 journal = {Networks}, 28913 volume = {35}, 28914 pages = {181--194}, 28915 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28916 key = {60} 28917} 28918 28919@InCollection{ ferris.rutherford:accessing, 28920 author = {M. C. Ferris and T. F. Rutherford}, 28921 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28922 booktitle = {Nonlinear Optimization and Applications}, 28923 key = {48}, 28924 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28925 editor = {G. Di Pillo and F. Giannessi}, 28926 year = {1996}, 28927 pages = {141--153}, 28928 publisher = {Plenum Press}, 28929 address = {New York} 28930} 28931 28932@InCollection{ ferris.shepard:optimizing, 28933 author = {M. C. Ferris and D. M. Shepard}, 28934 title = {Optimization of Gamma Knife Radiosurgery}, 28935 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28936 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28937 publisher = {AMS}, 28938 year = {2000}, 28939 optseries = {DIMACS}, 28940 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28941 key = {91}, 28942 type = {Data Mining Institute Technical Report}, 28943 institution = {Computer Sciences Department, University of Wisconsin}, 28944 address = {Madison, Wisconsin}, 28945 number = {00-01} 28946} 28947 28948@InCollection{ ferris.sinapiromsaran:formulating, 28949 author = {M. C. Ferris and K. Sinapiromsaran}, 28950 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28951 booktitle = {Optimization}, 28952 key = {77}, 28953 publisher = {Springer-Verlag}, 28954 year = {2000}, 28955 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28956 volume = {481}, 28957 series = {Lecture Notes in Economics and Mathematical Systems}, 28958 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28959 type = {Mathematical Programming Technical Report}, 28960 institution = {Computer Sciences Department, University of Wisconsin}, 28961 address = {Madison, Wisconsin}, 28962 number = {98-21} 28963} 28964 28965@Article{ ferris.tin-loi:limit, 28966 author = {M. C. Ferris and F. Tin-Loi}, 28967 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28968 Complementarity Constraints}, 28969 year = {2001}, 28970 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28971 key = {78}, 28972 journal = {International Journal of Mechanical Sciences}, 28973 pages = {209--224}, 28974 volume = {43}, 28975 type = {Mathematical Programming Technical Report}, 28976 institution = {Computer Sciences Department, University of Wisconsin}, 28977 address = {Madison, Wisconsin}, 28978 number = {99-01} 28979} 28980 28981@Article{ ferris.tin-loi:nonlinear, 28982 author = {M. C. Ferris and F. Tin-Loi}, 28983 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28984 Elastoplasticity}, 28985 year = {1998}, 28986 key = {64}, 28987 volume = {6}, 28988 pages = {857--870}, 28989 journal = {Structural Engineering and Mechanics} 28990} 28991 28992@Article{ ferris.tin-loi:solution, 28993 author = {M. C. Ferris and F. Tin-Loi}, 28994 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28995 and Complementarity Constraints}, 28996 year = {1999}, 28997 journal = {Computer Methods in Applied Mechanics and Engineering}, 28998 volume = {174}, 28999 pages = {107--120}, 29000 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 29001 key = {66} 29002} 29003 29004@Article{ ferris.vlach:scheduling, 29005 author = {M. C. Ferris and M. Vlach}, 29006 title = {Scheduling with Earliness and Tardiness Penalties}, 29007 journal = {Naval Research Logistics Quarterly}, 29008 year = {1992}, 29009 volume = {39}, 29010 pages = {229--245}, 29011 key = {13} 29012} 29013 29014@TechReport{ ferris.zavriev:linear, 29015 author = {M. C. Ferris and S. K Zavriev}, 29016 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 29017 institution = {Computer Sciences Department, University of Wisconsin}, 29018 year = {1996}, 29019 key = {56}, 29020 address = {Madison, Wisconsin}, 29021 type = {Mathematical Programming Technical Report}, 29022 number = {96--12}, 29023 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 29024} 29025 29026@Article{ ferris:finite, 29027 author = {M. C. Ferris}, 29028 title = {Finite Termination of the Proximal Point Algorithm}, 29029 journal = {Mathematical Programming}, 29030 year = {1991}, 29031 volume = {50}, 29032 pages = {359--366}, 29033 key = {06} 29034} 29035 29036@Article{ ferris:iterative, 29037 author = {M. C. Ferris}, 29038 title = {Iterative Linear Programming Solution of Convex Programs}, 29039 journal = {Journal of Optimization Theory and Applications}, 29040 year = {1990}, 29041 volume = {65}, 29042 pages = {53--65}, 29043 key = {07} 29044} 29045 29046@Article{ ferris:linear, 29047 author = {M. C. Ferris}, 29048 title = {The Linear Complementarity Problem}, 29049 journal = {Bulletin of the American Mathematical Society}, 29050 year = {1993}, 29051 volume = {28}, 29052 pages = {169--175}, 29053 key = {27} 29054} 29055 29056@MastersThesis{ ferris:linear*1, 29057 author = {M. C. Ferris}, 29058 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 29059 Solving a Class of Structural Optimization Problems}, 29060 year = {1985}, 29061 school = {University of Cambridge}, 29062 address = {England}, 29063 key = {01} 29064} 29065 29066@TechReport{ ferris:matlab, 29067 author = {M. C. Ferris}, 29068 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 29069 institution = {Computer Sciences Department, University of Wisconsin}, 29070 year = {1998}, 29071 address = {Madison, Wisconsin}, 29072 type = {Mathematical Programming Technical Report}, 29073 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 29074 number = {98-19}, 29075 key = {75} 29076} 29077 29078@Article{ ferris:parallel, 29079 author = {M. C. Ferris}, 29080 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 29081 journal = {Mathematics of Operations Research}, 29082 year = {1994}, 29083 volume = {19}, 29084 pages = {645--658}, 29085 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 29086 key = {20} 29087} 29088 29089@TechReport{ ferris:parallel*1, 29090 author = {M. C. Ferris}, 29091 title = {Parallel Solution of Extremely Large Knapsack Problems}, 29092 institution = {Computer Sciences Department, University of Wisconsin}, 29093 year = {1989}, 29094 address = {Madison, Wisconsin}, 29095 number = {842}, 29096 key = {09} 29097} 29098 29099@PhDThesis{ ferris:weak, 29100 author = {M. C. Ferris}, 29101 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29102 year = {1988}, 29103 school = {University of Cambridge}, 29104 address = {England}, 29105 key = {02} 29106} 29107 29108@TechReport{ ferris:weak*1, 29109 author = {M. C. Ferris}, 29110 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29111 institution = {Computer Sciences Department, University of Wisconsin}, 29112 year = {1988}, 29113 address = {Madison, Wisconsin}, 29114 number = {779}, 29115 key = {05} 29116} 29117 29118@Book{ fiacco.mccormick:nonlinear, 29119 author = {A. V. Fiacco and G. P. McCormick}, 29120 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 29121 year = {1968}, 29122 publisher = {John Wiley \& Sons}, 29123 address = {New York}, 29124 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 29125} 29126 29127@Book{ fiacco:introduction, 29128 author = {A. V. Fiacco}, 29129 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 29130 year = {1983}, 29131 publisher = {Academic Press}, 29132 address = {New York} 29133} 29134 29135@Article{ fiedler.ptak:matrices, 29136 author = {M. Fiedler and V. Pt\'{a}k}, 29137 title = {On matrices with nonpositive off-diagonal elements and positive principal 29138 minors}, 29139 journal = {Czechoslovak Mathematics Journal}, 29140 volume = {12}, 29141 pages = {382--400}, 29142 year = {1962} 29143} 29144 29145@Article{ fischer.kanzow:finite, 29146 author = {A. Fischer and C. Kanzow}, 29147 title = {On Finite Termination of an Iterative Method for Linear Complementarity 29148 Problems}, 29149 journal = {Mathematical Programming}, 29150 volume = {74}, 29151 pages = {279--292}, 29152 year = {1996} 29153} 29154 29155@TechReport{ fischer:constrained, 29156 author = {A. Fischer}, 29157 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 29158 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 29159 year = {1995}, 29160 type = {Technical Report}, 29161 number = {MATH-NM-10-1995}, 29162 address = {Dresden} 29163} 29164 29165@Article{ fischer:local, 29166 author = {A. Fischer}, 29167 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 29168 weak conditions}, 29169 journal = {Optimization Methods and Software}, 29170 year = {1995}, 29171 volume = {6}, 29172 pages = {83--107} 29173} 29174 29175@InCollection{ fischer:ncp-function, 29176 author = {A. Fischer}, 29177 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 29178 booktitle = {Recent Advances in Nonsmooth Optimization}, 29179 publisher = {World Scientific Publishers}, 29180 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 29181 year = {1995}, 29182 pages = {88--105} 29183} 29184 29185@Article{ fischer:newton-type, 29186 author = {A. Fischer}, 29187 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 29188 Problems}, 29189 journal = {Journal of Optimization Theory and Applications}, 29190 year = {1995}, 29191 volume = {86}, 29192 pages = {585--608} 29193} 29194 29195@Article{ fischer:solution, 29196 author = {A. Fischer}, 29197 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 29198 Functions}, 29199 year = {1997}, 29200 journal = {Mathematical Programming}, 29201 pages = {513--532} 29202} 29203 29204@Article{ fischer:special, 29205 author = {A. Fischer}, 29206 title = {A Special {N}ewton--Type Optimization Method}, 29207 journal = {Optimization}, 29208 year = {1992}, 29209 volume = {24}, 29210 pages = {269--284} 29211} 29212 29213@Article{ fisher:use, 29214 author = {R. A. Fisher}, 29215 title = {The Use of Multiple Measurements in Taxonomic Problems}, 29216 journal = {Annual Eugenics}, 29217 year = {1936}, 29218 volume = {7}, 29219 number = {Part II}, 29220 pages = {179--188} 29221} 29222 29223@Book{ fishman:principles, 29224 author = {G. Fishman}, 29225 title = {Principles of Discrete Event Simulation}, 29226 publisher = {Wiley}, 29227 address = {New York, NY}, 29228 year = {1978} 29229} 29230 29231@Article{ fitchard.aldridge.ea:registration, 29232 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 29233 title = {Registration of Synthetic Tomographic Projection Data Sets Using 29234 Cross-Correlation}, 29235 journal = {Physics in Medicine and Biology}, 29236 year = {1998}, 29237 volume = {43}, 29238 pages = {1645--1657} 29239} 29240 29241@Article{ fletcher.matthews:stable, 29242 author = {R. Fletcher and S. P. J. Matthews}, 29243 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 29244 journal = {Mathematical Programming}, 29245 year = {1984}, 29246 volume = {30}, 29247 pages = {267--284} 29248} 29249 29250@TechReport{ fletcher.maza:nonlinear, 29251 author = {R. Fletcher and E. Sainz de la Maza}, 29252 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 29253 Programming}, 29254 institution = {Department of Mathematical Sciences}, 29255 year = {1987}, 29256 address = {The University, Dundee, Scotland}, 29257 number = {NA/100}, 29258 type = {Numerical Analysis Report} 29259} 29260 29261@InCollection{ fletcher:class, 29262 author = {R. Fletcher}, 29263 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 29264 Properties}, 29265 booktitle = {Integer and Nonlinear Programming}, 29266 year = {1970}, 29267 editor = {J. Abadie}, 29268 publisher = {North--Holland}, 29269 address = {Amsterdam}, 29270 pages = {157--173} 29271} 29272 29273@Article{ fletcher:exact, 29274 author = {R. Fletcher}, 29275 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 29276 journal = {Mathematical Programming}, 29277 year = {1973}, 29278 volume = {5}, 29279 pages = {129--150} 29280} 29281 29282@Article{ fletcher:generalized, 29283 author = {R. Fletcher}, 29284 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 29285 Equations}, 29286 journal = {The Computer Journal}, 29287 year = {1968}, 29288 volume = {10}, 29289 pages = {392--399} 29290} 29291 29292@InProceedings{ fletcher:penalty, 29293 crossref = {bachem.grotschel.ea:mathematical}, 29294 author = {R. Fletcher}, 29295 title = {Penalty Functions}, 29296 pages = {87--114} 29297} 29298 29299@Book{ fletcher:practical, 29300 author = {R. 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Gill}, 29409 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 29410 institution = {Department of Mathematics, University of California}, 29411 year = {1996}, 29412 type = {Report NA}, 29413 number = {96-3}, 29414 address = {San Diego} 29415} 29416 29417@InCollection{ fortin.glowinski:decomposition-coordination, 29418 author = {M. Fortin and R. Glowinski}, 29419 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 29420 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 29421 Problems}, 29422 publisher = {North-Holland}, 29423 year = {1983}, 29424 editor = {M. Fortin and R. Glowinski}, 29425 address = {Amsterdam} 29426} 29427 29428@Misc{ foster.kesselman:globus, 29429 author = {I. Foster and C. Kesselman}, 29430 title = {The Globus Project}, 29431 howpublished = {www.globus.org} 29432} 29433 29434@Article{ foster.kesselman:globus*1, 29435 author = {I. Foster and C. 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Gao}, 29761 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 29762 Conditions}, 29763 type = {Manuscript}, 29764 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 29765 month = oct, 29766 year = {1994} 29767} 29768 29769@Article{ garcia-palomares.mangasarian:superlinearly, 29770 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 29771 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 29772 Optimization Problems}, 29773 journal = {Mathematical Programming}, 29774 year = {1976}, 29775 volume = {11}, 29776 pages = {1--13} 29777} 29778 29779@Article{ garcia-palomares.restuccia:global, 29780 author = {U. M. {Garcia--Palomares} and A. 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Zangwill}, 29806 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 29807 year = {1981}, 29808 publisher = {Prentice-Hall, Inc}, 29809 address = {Englewood Cliffs, New Jersey} 29810} 29811 29812@Book{ garey.johnson:computers, 29813 author = {M. R. Garey and D. S. Johnson}, 29814 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 29815 year = {1979}, 29816 publisher = {W.H. Freeman and Company}, 29817 address = {San Francisco} 29818} 29819 29820@Article{ garey.tarjan.ea:one-processor, 29821 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 29822 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 29823 journal = {Mathematics of Operations Research}, 29824 year = {1988}, 29825 volume = {13}, 29826 pages = {330--348} 29827} 29828 29829@Book{ garfinkel.nemhauser:integer, 29830 author = {R. S. Garfinkel and G. L. Nemhauser}, 29831 title = {Integer Programming}, 29832 year = {1972}, 29833 publisher = {John Wiley \& Sons}, 29834 address = {New York} 29835} 29836 29837@Book{ gass:linear, 29838 author = {S. Gass}, 29839 title = {Linear Programming Methods and Applications}, 29840 edition = {Fifth}, 29841 publisher = {Boyd and Fraser Publishing Company}, 29842 address = {Danvers, Massachusetts}, 29843 year = {1985} 29844} 29845 29846@InProceedings{ gay:combining, 29847 author = {D. M. Gay}, 29848 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 29849 booktitle = {Sparse Matrix Proceedings 1978}, 29850 editor = {I. S. Duff and G. W. Stewart}, 29851 year = {1978}, 29852 organization = {SIAM}, 29853 address = {Philadelphia, Pennsylvania}, 29854 pages = {313--334} 29855} 29856 29857@Article{ gay:electronic, 29858 author = {D. M. Gay}, 29859 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 29860 journal = {{COAL} Newsletter}, 29861 year = {1985}, 29862 volume = {13}, 29863 pages = {10--12} 29864} 29865 29866@TechReport{ gay:hooking, 29867 author = {D. M. Gay}, 29868 title = {Hooking Your Solver to {AMPL}}, 29869 year = {1997}, 29870 institution = {Bell Laboratories}, 29871 address = {Murray Hill, New Jersey}, 29872 note = {Revised 1994, 1997} 29873} 29874 29875@Article{ gay:variant, 29876 author = {D. Gay}, 29877 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 29878 Form}, 29879 journal = {Mathematical Programming}, 29880 year = {1987}, 29881 volume = {37}, 29882 pages = {81--90} 29883} 29884 29885@Article{ geiger.kanzow:resolution, 29886 author = {C. Geiger and C. Kanzow}, 29887 title = {On the Resolution of Monotone Complementarity Problems}, 29888 journal = {Computational Optimization and Applications}, 29889 volume = {5}, 29890 year = {1996}, 29891 pages = {155--173} 29892} 29893 29894@Book{ geist.beguelin.ea:pvm, 29895 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 29896 V. S. Sunderam}, 29897 title = {{PVM}: Parallel Virtual Machine}, 29898 publisher = {MIT Press}, 29899 address = {Cambridge, Massachusetts}, 29900 year = {1994} 29901} 29902 29903@Article{ gendron.crainic:parallel, 29904 author = {B. Gendron and T. G. Crainic}, 29905 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 29906 journal = {Operations Research}, 29907 year = {1994}, 29908 volume = {42}, 29909 pages = {1042--1060} 29910} 29911 29912@Article{ george:automatic, 29913 author = {A. George}, 29914 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 29915 journal = {SIAM Journal on Numerical Analysis}, 29916 vol = {17}, 29917 pages = {740--751}, 29918 year = {1980} 29919} 29920 29921@InProceedings{ georges-schleuter:asparagos, 29922 crossref = {schaeffer:third}, 29923 author = {M. Georges--Schleuter}, 29924 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 29925 pages = {416--421} 29926} 29927 29928@Article{ georgiou:comments, 29929 author = {G. M. Georgiou}, 29930 title = {Comments On Hidden Nodes in Neural Nets}, 29931 journal = {IEEE Transactions on Circuits and Systems}, 29932 year = {1991}, 29933 volume = {38}, 29934 pages = {1410} 29935} 29936 29937@TechReport{ gertz.linderoth.ea:object-oriented, 29938 author = {M. Gertz and J. Linderoth and S. Wright}, 29939 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 29940 institution = {MCS Division, Argonne National Laboratory}, 29941 year = {in preparation} 29942} 29943 29944@Article{ ghellinck.vial:polynomial, 29945 author = {G. de Ghellinck and J.--Ph. Vial}, 29946 title = {A Polynomial {N}ewton Method for Linear Programming}, 29947 journal = {Algorithmica}, 29948 year = {1986}, 29949 volume = {1}, 29950 pages = {425--453} 29951} 29952 29953@InCollection{ gilbert.ng:predicting, 29954 author = {J. R. Gilbert and E. Ng}, 29955 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 29956 year = {1993}, 29957 booktitle = {Graph Theory and Sparse Matrix Computation}, 29958 editor = {A. George and J. Gilbert and J. Liu}, 29959 publisher = {Springer-Verlag} 29960} 29961 29962@Article{ gilbert-lemarechal, 29963 author = {J. C. Gilbert and C. Lemarechal}, 29964 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 29965 journal = {Mathematical Programming}, 29966 year = {1989}, 29967 volume = {45}, 29968 pages = {407--434} 29969} 29970 29971@Article{ gill.murray.ea:computing, 29972 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29973 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 29974 journal = {SIAM Journal on Scientific and Statistical Computing}, 29975 year = {1983}, 29976 volume = {4}, 29977 pages = {310--321} 29978} 29979 29980@Article{ gill.murray.ea:maintaining, 29981 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29982 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 29983 year = {1987}, 29984 journal = {Linear Algebra and Its Applications}, 29985 volume = {88/89}, 29986 pages = {239--270} 29987} 29988 29989@Book{ gill.murray.ea:practical, 29990 author = {P. E. Gill and W. Murray and M. H. 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Maier}, 33177 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 33178 Instabilizing Effects}, 33179 journal = {International Journal of Solids and Structures}, 33180 volume = {7}, 33181 year = {1971}, 33182 pages = {345--372} 33183} 33184 33185@InCollection{ maier:inverse, 33186 author = {G. Maier}, 33187 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 33188 booktitle = {Serie VIII}, 33189 publisher = {Academia Nazionale dei Lincei}, 33190 year = {1981}, 33191 volume = {LXX}, 33192 pages = {203--209} 33193} 33194 33195@Article{ maier:matrix, 33196 author = {G. Maier}, 33197 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 33198 yield planes}, 33199 journal = {Meccanica}, 33200 volume = {5}, 33201 year = {1970}, 33202 pages = {54--66} 33203} 33204 33205@Article{ maier:quadratic, 33206 author = {G. Maier}, 33207 title = {A quadratic programming approach for certain classes of nonlinear structural 33208 problems}, 33209 journal = {Meccanica}, 33210 volume = {3}, 33211 year = {1968}, 33212 pages = {121--130} 33213} 33214 33215@Book{ manber:introduction, 33216 author = {U. Manber}, 33217 title = {Introduction to Algorithms: {A} Creative Approach}, 33218 year = {1989}, 33219 publisher = {Addison-Wesley} 33220} 33221 33222@Article{ mangasarian.deleone:error, 33223 author = {O. L. Mangasarian and R. {De~Leone}}, 33224 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 33225 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 33226 journal = {Applied Mathematics and Optimization}, 33227 year = {1988}, 33228 volume = {17}, 33229 pages = {1--14} 33230} 33231 33232@Article{ mangasarian.deleone:parallel, 33233 author = {O. L. Mangasarian and R. {De~Leone}}, 33234 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 33235 Problems and Linear Programs}, 33236 journal = {Journal of Optimization Theory and Applications}, 33237 year = {1987}, 33238 volume = {54}, 33239 pages = {437--446} 33240} 33241 33242@Article{ mangasarian.fromovitz:fritz, 33243 author = {O. L. Mangasarian and S. Fromovitz}, 33244 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 33245 and inequality constraints}, 33246 journal = {Journal of Mathematical Analysis and its Applications}, 33247 year = {1967}, 33248 volume = {17}, 33249 pages = {37--47} 33250} 33251 33252@Article{ mangasarian.mclinden:simple, 33253 author = {O. L. Mangasarian and L. McLinden}, 33254 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 33255 Programs}, 33256 journal = {Mathematical Programming}, 33257 year = {1985}, 33258 volume = {32}, 33259 pages = {32--40} 33260} 33261 33262@Article{ mangasarian.meyer:nonlinear, 33263 author = {O. L. Mangasarian and R. R. Meyer}, 33264 title = {Nonlinear Perturbation of Linear Programs}, 33265 journal = {SIAM Journal on Control and Optimization}, 33266 year = {1979}, 33267 volume = {17}, 33268 pages = {745--752} 33269} 33270 33271@TechReport{ mangasarian.musicant:active, 33272 author = {O. L. Mangasarian and David R. Musicant}, 33273 title = {Active Set Support Vector Machine Classification}, 33274 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33275 year = {2000}, 33276 number = {00-04}, 33277 address = {Madison, Wisconsin} 33278} 33279 33280@TechReport{ mangasarian.musicant:lagrangian, 33281 author = {O. L. Mangasarian and D. R. Musicant}, 33282 title = {Lagrangian Support Vector Machines}, 33283 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33284 year = {2000}, 33285 number = {00-06}, 33286 address = {Madison, Wisconsin} 33287} 33288 33289@TechReport{ mangasarian.musicant:robust, 33290 author = {O. L. Mangasarian and David R. Musicant}, 33291 title = {Robust Linear and Support Vector Regression}, 33292 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33293 year = {1999}, 33294 number = {99-09}, 33295 address = {Madison, Wisconsin} 33296} 33297 33298@Article{ mangasarian.musicant:successive, 33299 author = {O. L. Mangasarian and David R. Musicant}, 33300 title = {Successive Overrelaxation for Support Vector Machines}, 33301 journal = {IEEE Transactions on Neural Networks}, 33302 volume = {10}, 33303 year = {1999}, 33304 pages = {1032-1037} 33305} 33306 33307@Article{ mangasarian.pang:exact, 33308 author = {O. L. Mangasarian and J. S. Pang}, 33309 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 33310 Constraints}, 33311 journal = {Optimization}, 33312 year = {1997}, 33313 volume = {42}, 33314 pages = {1--8} 33315} 33316 33317@Article{ mangasarian.pang:extended, 33318 author = {O. L. Mangasarian and J. S. Pang}, 33319 title = {The Extended Linear Complementarity Problem}, 33320 journal = {SIAM Journal on Matrix Analysis and Applications}, 33321 year = {1994}, 33322 volume = {16} 33323} 33324 33325@Article{ mangasarian.ren:error, 33326 author = {O. L. Mangasarian and J. Ren}, 33327 title = {New error bounds for the nonlinear complementarity problem}, 33328 year = {1994}, 33329 volume = {1}, 33330 pages = {49--56}, 33331 journal = {Communications on Applied Nonlinear Analysis} 33332} 33333 33334@Article{ mangasarian.ren:improved, 33335 author = {O. L. Mangasarian and J. Ren}, 33336 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 33337 year = {1994}, 33338 volume = {66}, 33339 journal = {Mathematical Programming}, 33340 pages = {241--255} 33341} 33342 33343@InProceedings{ mangasarian.setiono.ea:pattern, 33344 crossref = {coleman.li:large-scale}, 33345 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 33346 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 33347 Diagnosis}, 33348 pages = {22--31} 33349} 33350 33351@Article{ mangasarian.shiau:error, 33352 author = {O. L. Mangasarian and T.--H. Shiau}, 33353 title = {Error Bounds for Monotone Linear Complementarity Problems}, 33354 journal = {Mathematical Programming}, 33355 year = {1986}, 33356 volume = {36}, 33357 pages = {81--89} 33358} 33359 33360@Article{ mangasarian.shiau:lipschitz, 33361 author = {O. L. Mangasarian and T.--H. Shiau}, 33362 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 33363 Complementarity Problems}, 33364 journal = {SIAM Journal on Control and Optimization}, 33365 year = {1987}, 33366 volume = {25}, 33367 pages = {583--595} 33368} 33369 33370@Article{ mangasarian.solodov:nonlinear, 33371 author = {O. L. Mangasarian and M. V. Solodov}, 33372 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 33373 journal = {Mathematical Programming}, 33374 year = {1993}, 33375 volume = {62}, 33376 pages = {277--298} 33377} 33378 33379@Article{ mangasarian.solodov:serial, 33380 author = {O. L. Mangasarian and M. V. Solodov}, 33381 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 33382 Minimization}, 33383 year = {1994}, 33384 journal = {Optimization Methods and Software}, 33385 volume = {4}, 33386 pages = {103--116} 33387} 33388 33389@Article{ mangasarian.street.ea:breast, 33390 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 33391 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 33392 journal = {Operations Research}, 33393 year = {1995}, 33394 volume = {43}, 33395 pages = {570--577} 33396} 33397 33398@Article{ mangasarian.wolberg:cancer, 33399 author = {O. L. Mangasarian and W. H. Wolberg}, 33400 title = {Cancer Diagnosis via Linear Programming}, 33401 journal = {SIAM News}, 33402 year = {1990}, 33403 volume = {23}, 33404 pages = {1 \& 18} 33405} 33406 33407@InCollection{ mangasarian:applications, 33408 author = {O. L. Mangasarian}, 33409 title = {Some Applications of Penalty Functions in Mathematical Programming}, 33410 booktitle = {Optimization and Related Fields}, 33411 year = {1986}, 33412 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 33413 publisher = {Springer-Verlag}, 33414 address = {Heidelberg}, 33415 pages = {307--329}, 33416 note = {Lecture Notes in Mathematics 1190} 33417} 33418 33419@Article{ mangasarian:characterization, 33420 author = {O. L. Mangasarian}, 33421 title = {Characterization of linear complementarity problems as linear programs}, 33422 journal = {Mathematical Programming Study}, 33423 year = {1978}, 33424 volume = {7}, 33425 pages = {74--87} 33426} 33427 33428@InProceedings{ mangasarian:condition, 33429 author = {O. L. Mangasarian}, 33430 title = {A condition number for linear inequalities and linear programs}, 33431 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 33432 1981}, 33433 year = {1981}, 33434 editor = {G. Bamberg and O. Opitz}, 33435 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 33436 address = {Konigstein}, 33437 pages = {3--15} 33438} 33439 33440@Article{ mangasarian:convergence, 33441 author = {O. L. Mangasarian}, 33442 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 33443 Symmetric Monotone Linear Complementarity Problem}, 33444 journal = {SIAM Journal on Optimization}, 33445 volume = {1}, 33446 pages = {114--122}, 33447 year = {1991} 33448} 33449 33450@Article{ mangasarian:equivalence, 33451 author = {O. L. Mangasarian}, 33452 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 33453 journal = {SIAM Journal on Applied Mathematics}, 33454 year = {1976}, 33455 volume = {31}, 33456 pages = {89--92} 33457} 33458 33459@Article{ mangasarian:error, 33460 author = {O. L. Mangasarian}, 33461 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 33462 journal = {ORSA Journal on Computing}, 33463 volume = {15}, 33464 pages = {187--192}, 33465 year = {1994} 33466} 33467 33468@Article{ mangasarian:error*1, 33469 author = {O. L. Mangasarian}, 33470 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 33471 journal = {Mathematical Programming}, 33472 year = {1990}, 33473 volume = {48}, 33474 pages = {437--445} 33475} 33476 33477@Article{ mangasarian:generalized, 33478 author = {O. L. Mangasarian}, 33479 title = {Generalized Linear Complementarity Problems as Linear Programs}, 33480 journal = {Methods of Operations Research}, 33481 year = {1979}, 33482 editor = {W. Oettli and F. Steffens}, 33483 volume = {31}, 33484 pages = {393--402} 33485} 33486 33487@InCollection{ mangasarian:generalized*1, 33488 author = {O. L. Mangasarian}, 33489 title = {Generalized Support Vector Machines}, 33490 year = {2000}, 33491 pages = {135-146}, 33492 booktitle = {Advances in Large Margin Classifiers}, 33493 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 33494 publisher = {MIT Press}, 33495 address = {Cambridge, MA} 33496} 33497 33498@Article{ mangasarian:global, 33499 author = {O. L. Mangasarian}, 33500 title = {Global error bounds for monotone affine variational inequality problems}, 33501 journal = {Linear Algebra and Its Applications}, 33502 year = {1992}, 33503 pages = {153--164} 33504} 33505 33506@InCollection{ mangasarian:least, 33507 author = {O. L. Mangasarian}, 33508 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 33509 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 33510 year = {1990}, 33511 publisher = {Oxford University Press}, 33512 address = {New York}, 33513 pages = {217--221} 33514} 33515 33516@Article{ mangasarian:least-norm, 33517 author = {O. L. Mangasarian}, 33518 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 33519 Problem}, 33520 journal = {Journal of Mathematical Analysis and Applications}, 33521 year = {1983}, 33522 volume = {92}, 33523 pages = {240--251} 33524} 33525 33526@Article{ mangasarian:linear, 33527 author = {O. L. Mangasarian}, 33528 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 33529 journal = {Mathematical Programming}, 33530 year = {1976}, 33531 volume = {10}, 33532 pages = {263--270} 33533} 33534 33535@Article{ mangasarian:linear*1, 33536 author = {O. L. Mangasarian}, 33537 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 33538 journal = {Operations Research}, 33539 year = {1965}, 33540 volume = {13}, 33541 pages = {444--452} 33542} 33543 33544@Article{ mangasarian:locally, 33545 author = {O. L. Mangasarian}, 33546 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 33547 Complementarity Problems}, 33548 journal = {Mathematical Programming}, 33549 year = {1980}, 33550 volume = {19}, 33551 pages = {200--212} 33552} 33553 33554@InCollection{ mangasarian:machine, 33555 author = {O. L. Mangasarian}, 33556 title = {Machine Learning via Polyhedral Concave Minimization}, 33557 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 33558 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 33559 pages = {175-188}, 33560 year = {1996}, 33561 address = {Heidelberg}, 33562 publisher = {Physica-Verlag A Springer-Verlag Company} 33563} 33564 33565@Article{ mangasarian:mathematical, 33566 author = {O. L. Mangasarian}, 33567 title = {Mathematical Programming in Neural Networks}, 33568 journal = {ORSA Journal on Computing}, 33569 volume = {5}, 33570 pages = {349--360}, 33571 year = {1993} 33572} 33573 33574@InProceedings{ mangasarian:mathematical*1, 33575 author = {O. L. Mangasarian}, 33576 title = {Mathematical Programming in Machine Learning}, 33577 booktitle = {Nonlinear Optimization and Applications}, 33578 editor = {G. Di Pillo and F. Giannessi}, 33579 publisher = {Plenum Publishing}, 33580 address = {New York}, 33581 pages = {283--295}, 33582 year = {1996} 33583} 33584 33585@Article{ mangasarian:mathematical*2, 33586 author = {O. L. Mangasarian}, 33587 title = {Mathematical Programming in Data Mining}, 33588 journal = {Data Mining and Knowledge Discovery}, 33589 volume = {1}, 33590 year = {1997}, 33591 pages = {183-201} 33592} 33593 33594@Article{ mangasarian:multi-surface, 33595 author = {O. L. Mangasarian}, 33596 title = {Multi-surface Method of Pattern Separation}, 33597 journal = {IEEE Transactions on Information Theory}, 33598 year = {1968}, 33599 volume = {IT-14}, 33600 pages = {801--807} 33601} 33602 33603@Book{ mangasarian:nonlinear, 33604 author = {O. L. Mangasarian}, 33605 title = {Nonlinear Programming}, 33606 year = {1969}, 33607 publisher = {McGraw--Hill}, 33608 address = {New York}, 33609 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 33610} 33611 33612@Article{ mangasarian:normal, 33613 author = {O. L. Mangasarian}, 33614 title = {Normal Solutions of Linear Programs}, 33615 journal = {Mathematical Programming Study}, 33616 year = {1984}, 33617 volume = {22}, 33618 pages = {206--216} 33619} 33620 33621@Article{ mangasarian:optimal, 33622 author = {O. L. Mangasarian}, 33623 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 33624 Linear Programs}, 33625 journal = {Journal of Optimization Theory and Applications}, 33626 year = {1981}, 33627 volume = {35}, 33628 pages = {123--128} 33629} 33630 33631@Article{ mangasarian:parallel, 33632 author = {O. L. Mangasarian}, 33633 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 33634 journal = {SIAM Journal on Control and Optimization}, 33635 volume = {33}, 33636 pages = {1916--1925}, 33637 year = {1995} 33638} 33639 33640@TechReport{ mangasarian:regularized, 33641 author = {O. L. 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Petri}, 35414 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35415 publisher = {Harvard University Press}, 35416 year = {1984} 35417} 35418 35419@InProceedings{ petrzykowski:application, 35420 author = {T. Petrzykowski}, 35421 title = {Application of the Steepest Ascent Method to Concave Programming}, 35422 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35423 year = {1962}, 35424 publisher = {North--Holland}, 35425 address = {Amsterdam}, 35426 pages = {185--189} 35427} 35428 35429@InProceedings{ pettey.leuze.ea:parallel, 35430 crossref = {grefenstette:genetic}, 35431 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35432 title = {A Parallel Genetic Algorithm}, 35433 pages = {155--161} 35434} 35435 35436@InProceedings{ pettey.leuze:theoretical, 35437 crossref = {schaeffer:third}, 35438 author = {C. C. Pettey and M. R. Leuze}, 35439 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35440 pages = {398--405} 35441} 35442 35443@Book{ pfeiffer.glocker:multibody, 35444 author = {F. Pfeiffer and C. Glocker}, 35445 title = {Multibody Dynamics with Unilateral Contact}, 35446 year = {1996}, 35447 publisher = {John Wiley \& Sons} 35448} 35449 35450@TechReport{ pierro.iusem:convergence, 35451 author = {A. R. de Pierro and A. N. Iusem}, 35452 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35453 Linear Complementarity Problems}, 35454 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35455 year = {1990}, 35456 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35457} 35458 35459@InCollection{ pillo.grippo.ea:class, 35460 author = {G. Di Pillo and L. Grippo and F. 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Grippo}, 35481 title = {A New Class of Augmented {L}agrangians in Nonlinear Programming}, 35482 journal = {SIAM Journal on Control and Optimization}, 35483 year = {1979}, 35484 volume = {17}, 35485 pages = {618--628} 35486} 35487 35488@Article{ pillo.grippo:continuously, 35489 author = {G. Di Pillo and L. Grippo}, 35490 title = {A Continuously Differentiable Exact Penalty Function for Nonlinear Programming 35491 Problems with Inequality Constraints}, 35492 journal = {SIAM Journal on Control and Optimization}, 35493 year = {1985}, 35494 volume = {23}, 35495 pages = {72--84} 35496} 35497 35498@Article{ pillo.grippo:exact, 35499 author = {G. Di Pillo and L. Grippo}, 35500 title = {An Exact Penalty Method with Global Convergence Properties for Nonlinear 35501 Programming Problems}, 35502 journal = {Mathematical Programming}, 35503 year = {1986}, 35504 volume = {36}, 35505 pages = {1--18} 35506} 35507 35508@InProceedings{ plambeck.fu.ea:throughput, 35509 author = {E. L. 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Computational Mathematics and Mathematical Physics}, 35588 year = {1973}, 35589 volume = {13}, 35590 pages = {42--58} 35591} 35592 35593@Article{ polyak:conjugate, 35594 author = {B. T. Polyak}, 35595 title = {The conjugate gradient method in extremal problems}, 35596 journal = {USSR Computational Mathematics and Mathematical Physics}, 35597 year = {1969}, 35598 volume = {9}, 35599 pages = {94--112}, 35600 note = {Translated from Russian} 35601} 35602 35603@Book{ polyak:introduction, 35604 author = {B. T. Polyak}, 35605 title = {Introduction to Optimization}, 35606 year = {1987}, 35607 publisher = {Optimization Software, Inc.}, 35608 address = {Publications Division, New York} 35609} 35610 35611@Unpublished{ polyak:methods, 35612 author = {R. A. Polyak}, 35613 title = {On the Methods of Centers}, 35614 year = {1988}, 35615 note = {Unpublished manuscript} 35616} 35617 35618@Unpublished{ polyak:sharp, 35619 author = {B. T. Polyak}, 35620 title = {Sharp Minima}, 35621 year = {1979}, 35622 note = {A Talk given at the {IIASA} Workshop on Generalized {L}agrangians and their 35623 Applications, {IIASA}, Laxenburg, Austria} 35624} 35625 35626@InProceedings{ polyak:smooth, 35627 author = {R. A. Polyak}, 35628 title = {Smooth Optimization Methods for Solving Nonlinear Extremal and Equilibrium 35629 Problems with Constraints}, 35630 booktitle = {Abstracts of the Papers of the 11th International Symposium on Mathematical 35631 Programming}, 35632 year = {1982}, 35633 address = {Bonn} 35634} 35635 35636@Article{ polychronopoulos.tsitsiklis:analysis, 35637 author = {G. H. Polychronopoulos and J. N. Tsitsiklis}, 35638 title = {Stochastic Shortest Path Problems with Recourse}, 35639 journal = {Networks}, 35640 year = {1996}, 35641 volume = {27}, 35642 pages = {133--143} 35643} 35644 35645@TechReport{ potra.bonnans:infeasible, 35646 author = {F. A. Potra and J. F. Bonnans}, 35647 title = {Infeasible path following algorithms for linear complementarity problems}, 35648 institution = {INRIA}, 35649 year = {1994}, 35650 month = dec, 35651 number = {RR--2445}, 35652 type = {Research Report} 35653} 35654 35655@Article{ potra.sheng:large-step, 35656 author = {F. A. Potra and R. Sheng}, 35657 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 35658 year = {1997}, 35659 journal = {SIAM Journal on Optimization}, 35660 volume = {7}, 35661 pages = {318--335} 35662} 35663 35664@Article{ potra:infeasible, 35665 author = {F. A. Potra}, 35666 title = {An infeasible interior-point predictor-corrector algorithm for linear 35667 programming}, 35668 journal = {SIAM Journal on Optimization}, 35669 year = {1996}, 35670 volume = {6}, 35671 pages = {19--32} 35672} 35673 35674@TechReport{ potra:onl, 35675 author = {F. A. Potra}, 35676 title = {An ${O}(n{L})$ infeasible--interior--point algorithm for {LCP} with quadratic 35677 convergence.}, 35678 institution = {Department of Mathematics, The University of Iowa}, 35679 address = {Iowa City, Iowa}, 35680 year = {1994}, 35681 number = {50}, 35682 type = {Reports on Computational Mathematics} 35683} 35684 35685@TechReport{ potra:predictor-corrector, 35686 author = {F. A. Potra}, 35687 title = {On a predictor-corrector method for solving linear programs from infeasible 35688 starting points}, 35689 institution = {Department of Mathematics, University of Iowa}, 35690 address = {Iowa City, Iowa}, 35691 year = {1992}, 35692 number = {34}, 35693 type = {Reports on Computational Mathematics} 35694} 35695 35696@TechReport{ potra:quadratically, 35697 author = {F. A. Potra}, 35698 title = {A quadratically convergent infeasible interior-point algorithm for linear 35699 programming}, 35700 institution = {Department of Mathematics, University of Iowa}, 35701 year = {1992}, 35702 number = {28}, 35703 address = {Iowa City, Iowa}, 35704 month = jul 35705} 35706 35707@InCollection{ powell:convergence, 35708 author = {M. J. D. Powell}, 35709 title = {The Convergence of Variable Metric Methods for Nonlinearly Constrained 35710 Optimization Calculations}, 35711 crossref = {mangasarian.meyer.ea:nonlinear*3}, 35712 pages = {27--63} 35713} 35714 35715@InProceedings{ powell:direct, 35716 author = {M. J. D. 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Pruyne}, 35817 title = {Resource Management Services for Parallel Applications}, 35818 school = {University of Wisconsin--Madison}, 35819 year = {1996}, 35820 address = {Madison, Wisconsin} 35821} 35822 35823@Book{ pshenichny.danilin:numerical, 35824 author = {B. N. Pshenichny and Yu. M. Danilin}, 35825 title = {Numerical Methods in Extremal Problems}, 35826 year = {1978}, 35827 publisher = {MIR Publishers}, 35828 address = {Moscow} 35829} 35830 35831@TechReport{ qi.chen:globally, 35832 author = {L. Qi and X. Chen}, 35833 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 35834 institution = {School of Mathematics, University of New South Wales}, 35835 year = {1993}, 35836 annote = {revised}, 35837 address = {Sydney} 35838} 35839 35840@Article{ qi.jiang:semismooth, 35841 author = {L. Qi and H. Jiang}, 35842 title = {Semismooth {K}arush--{K}uhn--{T}ucker Equations and Convergence Analysis of 35843 {N}ewton Methods and Quasi--{N}ewton Methods for Solving these Equations}, 35844 journal = {Mathematics of Operations Research}, 35845 volume = {22}, 35846 pages = {301--325}, 35847 year = {1997} 35848} 35849 35850@TechReport{ qi.peng:unconstrained, 35851 author = {H. -D. Qi and J. -M. Peng}, 35852 title = {A New Unconstrained Optimization Approach for Nonlinear Complementarity 35853 Problems}, 35854 institution = {State Key Laboratory of Scientific and Engineering Computing, Academic Sinica}, 35855 year = {1996}, 35856 type = {Technical Report}, 35857 address = {Beijing} 35858} 35859 35860@InCollection{ qi.sun:survey, 35861 author = {L. Qi and D. Sun}, 35862 title = {A Survey of Some Nonsmooth Equations and Smoothing {N}ewton Methods}, 35863 year = {1999}, 35864 editor = {A. Eberhard and B. Glover and R. Hill and D. Ralph}, 35865 booktitle = {Progress in Optimization}, 35866 pages = {121--146}, 35867 series = {Applied Optimization}, 35868 volume = {30}, 35869 publisher = {Kluwer Academic Publishers}, 35870 address = {Dordrecht} 35871} 35872 35873@Article{ qi.sun:nonsmooth, 35874 author = {L. Qi and J. Sun}, 35875 title = {A Nonsmooth Version of {N}ewton's Method}, 35876 journal = {Mathematical Programming}, 35877 year = {1993}, 35878 volume = {58}, 35879 pages = {353--368} 35880} 35881 35882@Article{ qi:convergence, 35883 author = {L. Qi}, 35884 title = {Convergence Analysis of Some Algorithms for Solving Nonsmooth Equations}, 35885 journal = {Mathematics of Operations Research}, 35886 year = {1993}, 35887 volume = {18}, 35888 pages = {227--244} 35889} 35890 35891@TechReport{ qi:regular, 35892 author = {L. 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Robinson}, 36187 title = {{N}ewton's Method for a Class of Nonsmooth Functions}, 36188 journal = {Set Valued Analysis}, 36189 year = {1994}, 36190 volume = {2}, 36191 pages = {291--305} 36192} 36193 36194@Article{ robinson:nonsingularity, 36195 author = {S. M. Robinson}, 36196 title = {Nonsingularity and Symmetry for Linear Normal Maps}, 36197 journal = {Mathematical Programming}, 36198 year = {1993}, 36199 volume = {62}, 36200 pages = {415--425} 36201} 36202 36203@InCollection{ robinson:nonsmooth, 36204 author = {S. M. Robinson}, 36205 title = {Nonsmooth Continuation for Generalized Equations}, 36206 year = {1997}, 36207 pages = {282--291}, 36208 editors = {P. Gritzmann and R. Horst and E. Sachs and R. 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Rockafellar}, 36401 title = {Conjugate Duality and Optimization}, 36402 year = {1974}, 36403 publisher = {SIAM}, 36404 address = {Philadelphia, Pennsylvania}, 36405 volume = {16}, 36406 series = {Conference Board of the Mathematical Sciences} 36407} 36408 36409@Book{ rockafellar:convex, 36410 author = {R. T. Rockafellar}, 36411 title = {Convex Analysis}, 36412 year = {1970}, 36413 publisher = {Princeton University Press}, 36414 address = {Princeton, New Jersey} 36415} 36416 36417@Article{ rockafellar:first-, 36418 author = {R. T. Rockafellar}, 36419 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 36420 journal = {Transactions of the American Mathematical Society}, 36421 year = {1988}, 36422 volume = {307}, 36423 pages = {75--108} 36424} 36425 36426@InProceedings{ rockafellar:generalized, 36427 author = {R. T. Rockafellar}, 36428 title = {A Generalized Approach to Linear-Quadratic Programming}, 36429 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36430 Applications}, 36431 year = {1986}, 36432 pages = {58--66}, 36433 note = {(Xi'an, China)} 36434} 36435 36436@InProceedings{ rockafellar:generalized*1, 36437 crossref = {bachem.grotschel.ea:mathematical}, 36438 author = {R. T. Rockafellar}, 36439 title = {Generalized Subgradients in Mathematical Programming}, 36440 pages = {368--390} 36441} 36442 36443@InCollection{ rockafellar:large-scale, 36444 author = {R. T. Rockafellar}, 36445 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36446 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36447 chapter = {15}, 36448 year = {1991}, 36449 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 36450 publisher = {SIAM Publications}, 36451 pages = {247--261} 36452} 36453 36454@Article{ rockafellar:linear-quadratic, 36455 author = {R. T. Rockafellar}, 36456 title = {Linear-Quadratic Programming and Optimal Control}, 36457 journal = {SIAM Journal on Control and Optimization}, 36458 year = {1987}, 36459 volume = {25}, 36460 pages = {781--814} 36461} 36462 36463@Article{ rockafellar:maximality, 36464 author = {R. T. Rockafellar}, 36465 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 36466 journal = {Transactions of the American Mathematical Society}, 36467 year = {1970}, 36468 volume = {149}, 36469 pages = {75--88} 36470} 36471 36472@InCollection{ rockafellar:monotone, 36473 author = {R. T. Rockafellar}, 36474 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 36475 crossref = {mangasarian.meyer.ea:nonlinear*3}, 36476 pages = {1--26} 36477} 36478 36479@Article{ rockafellar:monotone*1, 36480 author = {R. T. Rockafellar}, 36481 title = {Monotone Operators and the Proximal Point Algorithm}, 36482 journal = {SIAM Journal on Control and Optimization}, 36483 year = {1976}, 36484 volume = {14}, 36485 pages = {877--898} 36486} 36487 36488@Article{ rockafellar:multiplier, 36489 author = {R. T. Rockafellar}, 36490 title = {The Multiplier Method of {H}estenes and {P}owell Applied to Convex Programming}, 36491 journal = {Journal of Optimization Theory and Applications}, 36492 year = {1973}, 36493 volume = {12}, 36494 pages = {555--562} 36495} 36496 36497@Article{ rockafellar:multistage, 36498 author = {R. T. Rockafellar}, 36499 title = {Multistage Convex Programming and Discrete-Time Optimal Control}, 36500 journal = {Control and Cybernetics}, 36501 year = {1988}, 36502 volume = {17}, 36503 number = {2-3}, 36504 pages = {225--245} 36505} 36506 36507@Book{ rockafellar:network, 36508 author = {R. T. Rockafellar}, 36509 title = {Network Flows and Monotropic Optimization}, 36510 publisher = {John Wiley}, 36511 year = {1984}, 36512 address = {New York} 36513} 36514 36515@Article{ rodrigues:mixed, 36516 author = {H. C. Rodrigues}, 36517 title = {A mixed variational formulation for shape optimization of solids with contact 36518 conditions}, 36519 journal = {Structural Optimization}, 36520 volume = {6}, 36521 year = {1993}, 36522 pages = {19--28} 36523} 36524 36525@Book{ rodrigues:obstacle, 36526 author = {J. F. Rodrigues}, 36527 title = {Obstacle Problems in Mathematical Physics}, 36528 publisher = {Elsevier Publishing Company}, 36529 address = {Amsterdam}, 36530 year = {1987} 36531} 36532 36533@Book{ roos.terlaky.ea:theory, 36534 author = {C. Roos and T. Terlaky and J.--Ph. 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Knepley}, 39220 journal = {SIAM Journal on Scientific Computing}, 39221 volume = {47}, 39222 number = {2}, 39223 doi = {10.1137/23M1596478}, 39224 year = {2025} 39225} 39226 39227@Article{ nathawaniknepley2022, 39228 title = {Droplet formation simulation using mixed finite elements}, 39229 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39230 journal = {Physics of Fluids}, 39231 volume = {34}, 39232 pages = {064105}, 39233 doi = {10.1063/5.0089752}, 39234 year = {2022} 39235} 39236 39237@InProceedings{ nathawaniknepley2022b, 39238 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 39239 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39240 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 39241 (ICCFD11)}, 39242 editor = {Christoph Brehm and Shishir Pandya}, 39243 number = {4103}, 39244 year = {2022} 39245} 39246 39247@Article{ nathawaniknepley2023, 39248 title = {A one-dimensional mathematical model for shear-induced droplet formation in co-flowing fluids}, 39249 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39250 journal = {Theoretical and Computational Fluid Dynamics}, 39251 url = {https://rdcu.be/dFtlR}, 39252 doi = {10.1007/s00162-024-00690-5}, 39253 year = {2024} 39254} 39255 39256@InProceedings{ georgalisnathawaniknepleypatra2023, 39257 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 39258 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. Knepley and Abani 39259 Patra}, 39260 booktitle = {AIAA SciTech 2024}, 39261 note = {Accepted}, 39262 year = {2023} 39263} 39264 39265@Article{ brownbarrabeamsghaffariknepleymosesshakeristengelthompsonzhang2022, 39266 title = {Performance Portable Solid Mechanics via Matrix-Free $p$-Multigrid}, 39267 author = {Jed Brown and Valeria Barra and Natalie Beams and Leila Ghaffari and Matthew 39268 Knepley and William Moses and Rezgar Shakeri and Karen Stengel and Jeremy L. 39269 Thompson and Junchao Zhang}, 39270 doi = {10.48550/ARXIV.2204.01722}, 39271 url = {https://arxiv.org/abs/2204.01722}, 39272 publisher = {arXiv}, 39273 note = {Submitted}, 39274 year = {2022} 39275} 39276 39277@InCollection{ mayknepley2023, 39278 title = {Numerical Modeling of Subduction}, 39279 author = {Dave A. May and Matthew G. Knepley}, 39280 booktitle = {Dynamics of Plate Tectonics and Mantle Convection}, 39281 editor = {João C. Duarte}, 39282 pages = {539-571}, 39283 isbn = {978-0-323-85733-8}, 39284 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 39285 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 39286 year = {2023} 39287} 39288 39289@Article{ adamswangmersonhucksknepley2024, 39290 title = {A performance portable, fully implicit {Landau} collision operator with batched linear solvers}, 39291 author = {Mark F. Adams and Peng Wang and Jacob Merson and Kevin Hucks and Matthew G. Knepley}, 39292 journal = {SIAM Journal on Scientific Computing}, 39293 volume = {47}, 39294 number = {2}, 39295 pages = {B360-B381}, 39296 doi = {10.1137/24M1640252}, 39297 url = {https://arxiv.org/abs/2209.03228}, 39298 year = {2025}, 39299 petsc_uses = {DMPlex} 39300} 39301 39302@Article{ adamsknepley2023, 39303 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 39304 plasmas in {PETSc}}, 39305 author = {Mark F. Adams and Matthew G. Knepley}, 39306 url = {https://arxiv.org/abs/2302.10242}, 39307 note = {In preparation}, 39308 year = {2023}, 39309 petsc_uses = {DMPlex} 39310} 39311 39312@Article{ finnknepleypusztayadams2023, 39313 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 39314 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. Adams}, 39315 url = {https://arxiv.org/abs/2303.12620}, 39316 journal = {Communications in Applied Mathematics and Computational Science}, 39317 volume = {18}, 39318 number = {1}, 39319 pages = {135--152}, 39320 doi = {10.2140/camcos.2023.18.135}, 39321 year = {2023}, 39322 petsc_uses = {DMPlex} 39323} 39324 39325@Article{ adamsfinnknepleypusztay2025, 39326 title = {A projection method for particle resampling}, 39327 author = {Mark F. Adams and Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay}, 39328 url = {https://arxiv.org/abs/2501.13681}, 39329 journal = {Computer Physics Communications}, 39330 note = {Submitted}, 39331 year = {2025}, 39332 petsc_uses = {DMPlex} 39333} 39334 39335@Article{ finnpusztayknepleyadams2025, 39336 title = {Entropy Monotonicity using {Discrete Gradients} in the {Vlasov-Poisson-Landau} System}, 39337 author = {Daniel S. Finn and Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 39338 journal = {Journal of Computational Physics}, 39339 note = {Submitted}, 39340 year = {2025} 39341} 39342 39343@Article{ hamhaplaknepleymitchellsagiyama2024, 39344 title = {Efficient N-to-M Checkpointing Algorithm for Finite Element Simulations}, 39345 author = {David A. Ham and Vaclav Hapla and Matthew G. 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