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 G. 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. Zhang}, 11037 title = {End-to-end error estimation and control}, 11038 note = {whitepaper for 2017 ASCR Applied Mathematics PI Meeting}, 11039 doi = {10.6084/m9.figshare.5339866}, 11040 year = {2017}, 11041 petsc_uses = {KSP} 11042} 11043 11044@Misc{ petsc-user-support15, 11045 title = {On the Evolution of User Support Topics in Computational Science and Engineering 11046 Software}, 11047 author = {K. Rupp and S. Balay and J. Brown and M. Knepley and L. C. McInnes and B. Smith}, 11048 note = {Workshop on CSE Software Sustainability and Productivity (CSESSP) Challenges, Oct 11049 15-16, 2015}, 11050 year = {2015}, 11051 petsc_uses = {KSP} 11052} 11053 11054@InBook{ petsc-mixed-language-support2016, 11055 title = {Numerical Library Support for High-Performance Mixed Language Applications and 11056 Legacy Code}, 11057 author = {S. Balay and J. Brown and M. Knepley and L.C. McInnes and B. Smith}, 11058 booktitle = {Software Engineering for Science}, 11059 editors = {J. 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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{ ketcheson_2008, 11414 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 11415 Low-Storage Implementations}, 11416 author = {D.I. Ketcheson}, 11417 journal = {SIAM Journal on Scientific Computing}, 11418 year = {2008}, 11419 number = {4}, 11420 pages = {2113--2136}, 11421 volume = {30}, 11422 doi = {10.1137/07070485X}, 11423 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 11424 RungeKutta methods}, 11425 publisher = {SIAM} 11426} 11427 11428@Article{ jansen_2000, 11429 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 11430 equations with a stabilized finite element method}, 11431 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 11432 journal = {Computer Methods in Applied Mechanics and Engineering}, 11433 year = {2000}, 11434 number = {3}, 11435 pages = {305--319}, 11436 volume = {190}, 11437 publisher = {Elsevier} 11438} 11439 11440@Article{ butcher_2007, 11441 title = {Error propagation of general linear methods for ordinary differential equations}, 11442 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 11443 journal = {Journal of Complexity}, 11444 year = {2007}, 11445 number = {4-6}, 11446 pages = {560--580}, 11447 volume = {23}, 11448 abstract = {We discuss error propagation for general linear methods for ordinary differential 11449 equations up to terms of order p+2, where p is the order of the method. These 11450 results are then applied to the estimation of local discretization errors for 11451 methods of order p and for the adjacent order p+1. The results of numerical 11452 experiments confirm the reliability of these estimates. This research has 11453 applications in the design of robust stepsize and order changing strategies for 11454 algorithms based on general linear methods.}, 11455 doi = {10.1016/j.jco.2007.01.009}, 11456 issn = {0885-064X} 11457} 11458 11459@Article{ constantinescu_a2010a, 11460 title = {Extrapolated implicit-explicit time stepping}, 11461 author = {E.M. Constantinescu and A. Sandu}, 11462 journal = {SIAM Journal on Scientific Computing}, 11463 year = {2010}, 11464 number = {6}, 11465 pages = {4452-4477}, 11466 volume = {31}, 11467 comment = {Preprint \# ANL/MCS-P1612-0409}, 11468 doi = {10.1137/080732833} 11469} 11470 11471@InProceedings{ devito2011liszt, 11472 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 11473 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 11474 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 11475 Aiken, Alex and Duraisamy, Karthik and others}, 11476 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 11477 Networking, Storage and Analysis}, 11478 pages = {9}, 11479 year = {2011}, 11480 organization = {ACM} 11481} 11482 11483@Article{ devito2011designing, 11484 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 11485 author = {DeVito, Zachary and Hanrahan, Pat}, 11486 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 11487 year = {2011} 11488} 11489 11490@Misc{ pgasintro, 11491 author = {Tim Stitt}, 11492 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 11493 Model}, 11494 note = {\url{http://cnx.org/content/m20649/latest/}} 11495} 11496 11497@InProceedings{ el2006upc, 11498 title = {UPC: unified parallel C}, 11499 author = {El-Ghazawi, Tarek and Smith, Lauren}, 11500 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 11501 pages = {27}, 11502 year = {2006}, 11503 organization = {ACM} 11504} 11505 11506@InProceedings{ numrich1998co, 11507 title = {Co-Array Fortran for parallel programming}, 11508 author = {Numrich, Robert W and Reid, John}, 11509 booktitle = {ACM Sigplan Fortran Forum}, 11510 volume = {17}, 11511 number = {2}, 11512 pages = {1--31}, 11513 year = {1998}, 11514 organization = {ACM} 11515} 11516 11517@Article{ aiken1997titanium, 11518 title = {Titanium: A high-performance Java dialect}, 11519 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 11520 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 11521 Geoff and Semenzato, Luigi and others}, 11522 year = {1997} 11523} 11524 11525@Article{ charles2005x10, 11526 title = {X10: an object-oriented approach to non-uniform cluster computing}, 11527 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 11528 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 11529 Sarkar, Vivek}, 11530 journal = {Acm Sigplan Notices}, 11531 volume = {40}, 11532 number = {10}, 11533 pages = {519--538}, 11534 year = {2005}, 11535 publisher = {ACM} 11536} 11537 11538@Article{ chamberlain2007parallel, 11539 title = {Parallel programmability and the chapel language}, 11540 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 11541 journal = {International Journal of High Performance Computing Applications}, 11542 volume = {21}, 11543 number = {3}, 11544 pages = {291--312}, 11545 year = {2007}, 11546 publisher = {SAGE Publications} 11547} 11548 11549@InProceedings{ charmppoopsla93, 11550 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 11551 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 11552 editor = {Paepcke, A.}, 11553 fulleditor = {Paepcke, Andreas}, 11554 pages = {91--108}, 11555 month = sep, 11556 year = {1993}, 11557 booktitle = {{Proceedings of OOPSLA'93}}, 11558 publisher = {{ACM Press}} 11559} 11560 11561@InProceedings{ hewitt1973universal, 11562 title = {A universal modular actor formalism for artificial intelligence}, 11563 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 11564 booktitle = {Proceedings of the 3rd international joint conference on Artificial 11565 intelligence}, 11566 pages = {235--245}, 11567 year = {1973}, 11568 organization = {Morgan Kaufmann Publishers Inc.} 11569} 11570 11571@Book{ yonezawa1990abcl, 11572 title = {ABCL: an object-oriented concurrent system}, 11573 author = {Yonezawa, Akinori}, 11574 year = {1990}, 11575 publisher = {MIT press} 11576} 11577 11578@InProceedings{ dally1988object, 11579 title = {Object-oriented concurrent programming in CST}, 11580 author = {Dally, William J and Chien, Andrew A}, 11581 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 11582 applications: Architecture, software, computer systems, and general issues-Volume 11583 1}, 11584 pages = {434--439}, 11585 year = {1988}, 11586 organization = {ACM} 11587} 11588 11589@Article{ grimshaw1993easy, 11590 title = {Easy-to-use object-oriented parallel processing with Mentat}, 11591 author = {Grimshaw, Andrew S.}, 11592 journal = {Computer}, 11593 volume = {26}, 11594 number = {5}, 11595 pages = {39--51}, 11596 year = {1993}, 11597 publisher = {IEEE} 11598} 11599 11600@InProceedings{ gannon1991object, 11601 title = {Object oriented parallelism: pC++ ideas and experiments}, 11602 author = {Gannon, Dennis and Lee, JK}, 11603 booktitle = {Proceedings of}, 11604 pages = {13--23}, 11605 year = {1991} 11606} 11607 11608@InProceedings{ lau1992object, 11609 title = {An object-oriented class library for scalable parallel heuristic search}, 11610 author = {Lau, Wing-cheong and Singh, Vineet}, 11611 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 11612 pages = {252--267}, 11613 year = {1992}, 11614 organization = {Springer} 11615} 11616 11617@Book{ chase1989amber, 11618 title = {The Amber system: Parallel programming on a network of multiprocessors}, 11619 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 11620 Littlefield, Richard}, 11621 volume = {23}, 11622 number = {5}, 11623 year = {1989}, 11624 publisher = {ACM} 11625} 11626 11627@InProceedings{ kaiser2009parallex, 11628 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 11629 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 11630 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 11631 pages = {394--401}, 11632 year = {2009}, 11633 organization = {IEEE} 11634} 11635 11636@TechReport{ ipm, 11637 author = {Barry F. Smith}, 11638 title = {A New Parallel Programming Model for Computer Simulation}, 11639 institution = {Argonne National Laboratory}, 11640 year = {2014}, 11641 number = {ANL/MCS-P5135-0414} 11642} 11643 11644@Article{ groppsnir, 11645 author = {William Gropp and Marc Snir}, 11646 title = {Programming for Exascale Computers}, 11647 journal = {Computing in Science and Engineering}, 11648 volume = {15}, 11649 number = {6}, 11650 issn = {1521-9615}, 11651 year = {2013}, 11652 pages = {27-35}, 11653 doi = {10.1109/MCSE.2013.96}, 11654 publisher = {IEEE Computer Society}, 11655 address = {Los Alamitos, CA} 11656} 11657 11658@Book{ mpi3, 11659 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 11660 author = {Message Passing Interface Forum}, 11661 year = {2012}, 11662 publisher = {High Performance Computing Center Stuttgart (HLRS)} 11663} 11664 11665@Book{ openmp4, 11666 title = {OpenMP Application Program Interface, Version 4.0}, 11667 year = {2013}, 11668 publisher = {OpenMP Architecture Review Board} 11669} 11670 11671@InProceedings{ hartono2009annotation, 11672 title = {Annotation-based empirical performance tuning using {Orio}}, 11673 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 11674 booktitle = {Parallel \& Distributed Processing, 2009. 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Markus}, 12867 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 12868 for {PDE} Based Applications}, 12869 year = {1994}, 12870 institution = {Department of Computer Sciences, Purdue University}, 12871 number = {CSD-TR-94-021} 12872} 12873 12874@Unpublished{ ilu-web-page, 12875 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 12876 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 12877 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 12878} 12879 12880@Unpublished{ doe2k-web-page, 12881 title = {{DOE2000 Initiative} {W}eb page}, 12882 note = {http://www.mcs.anl.gov/DOE2000}, 12883 key = {DOE2000 Initiative} 12884} 12885 12886@Misc{ pvode-web-page, 12887 title = {{PVODE} {W}eb Page}, 12888 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 12889 author = {A. {Hindmarsh et al.}} 12890} 12891 12892@Book{ szyperski97, 12893 author = {Clemens Szyperski}, 12894 title = {Component Software: Beyond Object-Oriented Programming}, 12895 publisher = {ACM Press}, 12896 address = {New York}, 12897 year = {1997} 12898} 12899 12900@Unpublished{ petsc:coloringuse, 12901 title = {Code for computing sparse {J}acobians}, 12902 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12903 institution = {Argonne National Laboratory} 12904} 12905 12906@Unpublished{ petsc:external, 12907 author = {B. F. {Smith et al.}}, 12908 title = {{External Software Used by PETSc}}, 12909 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12910 institution = {Argonne National Laboratory} 12911} 12912 12913@Unpublished{ petsc:use-by-external-packages, 12914 author = {B. F. {Smith et al.}}, 12915 title = {{Software Packages that Use or Interface to PETSc}}, 12916 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 12917 institution = {Argonne National Laboratory} 12918} 12919 12920@Unpublished{ petsc:prizes, 12921 author = {B. F. {Smith et al.}}, 12922 title = {{Prizes Won Using PETSc}}, 12923 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12924 institution = {Argonne National Laboratory} 12925} 12926 12927@Unpublished{ petsc:csgf, 12928 author = {B. F. {Smith et al.}}, 12929 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 12930 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12931 institution = {Argonne National Laboratory} 12932} 12933 12934@Unpublished{ flash-web-page, 12935 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 12936 {W}eb Page}, 12937 note = {http://www.asci.uchicago.edu}, 12938 author = {R. {Rosner et al.}}, 12939 institution = {University of Chicago} 12940} 12941 12942@Unpublished{ esi-web-page, 12943 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 12944 note = {http://z.ca.sandia.gov/esi}, 12945 author = {R. {Clay et al.}} 12946} 12947 12948@Unpublished{ infobus-web-page, 12949 title = {{I}nfo{B}us {W}eb Page}, 12950 note = {http://www.java.sun.com/beans/infobus}, 12951 key = {infobus} 12952} 12953 12954@Unpublished{ xray-web-page, 12955 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 12956 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 12957 note = {http://www.mcs.anl.gov/xray/}, 12958 institution = {Argonne National Laboratory} 12959} 12960 12961@InProceedings{ kohn98, 12962 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 12963 title = {Language Interoperability Mechanisms for High-Performance Scientific 12964 Applications}, 12965 publisher = {SIAM}, 12966 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12967 Scientific and Engineering Computing}, 12968 year = {1999}, 12969 pages = {30-39} 12970} 12971 12972@InProceedings{ kohn01, 12973 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 12974 title = {Divorcing Language Dependencies from a Scientific Software Library}, 12975 publisher = {SIAM}, 12976 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 12977 year = {2001} 12978} 12979 12980@InProceedings{ freitag_jones_plassmann98, 12981 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 12982 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 12983 publisher = {SIAM}, 12984 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12985 Scientific and Engineering Computing}, 12986 year = {1999}, 12987 pages = {215-224} 12988} 12989 12990@Book{ templates, 12991 author = {R. Barrett and M. Berry and T. F. Chan and J. Demmel and J. Donato and J. 12992 Dongarra and V. Eijkhout and R. Pozo and C. Romine and H. Van der Vorst }, 12993 title = {Templates for the Solution of Linear Systems: Building Blocks for Iterative 12994 Methods}, 12995 publisher = {SIAM}, 12996 year = {1994}, 12997 address = {Philadelphia, PA} 12998} 12999 13000@InProceedings{ parasha2, 13001 author = {M. Parashar and J. C. Browne and C. Edwards and K. Klimkowski}, 13002 title = { A Common Data Management Infrastructure for Parallel Adaptive Algorithms for 13003 {PDE} Solutions}, 13004 booktitle = {SC97 Proceedings}, 13005 publisher = {IEEE Computer Society Press}, 13006 year = {1997} 13007} 13008 13009@TechReport{ parasha, 13010 author = {M. Parashar and J. C. Browne}, 13011 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 13012 Techniques}, 13013 institution = {Department of Computer Science, University of Texas at Austin}, 13014 year = {1995} 13015} 13016 13017@Article{ parti, 13018 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 13019 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 13020 Memory Architectures}, 13021 journal = {Journal of Parallel and Distributed Computing}, 13022 year = {1994}, 13023 volume = {22}, 13024 pages = {462--478} 13025} 13026 13027@Article{ mparti, 13028 author = {G. Agrawal and A. Sussman and J. 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Ross}, 13052 publisher = {University of Toronto}, 13053 pages = {379--386}, 13054 year = {1994} 13055} 13056 13057@Article{ cs99, 13058 author = {X.-C. Cai and M. Sarkis}, 13059 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 13060 systems}, 13061 journal = {SIAM J. Scientific Computing}, 13062 year = {1999}, 13063 volume = {21}, 13064 pages = {792-797} 13065} 13066 13067@Article{ cai2003restricted, 13068 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 13069 positive definite linear systems}, 13070 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 13071 journal = {SIAM Journal on Numerical Analysis}, 13072 volume = {41}, 13073 issue = {1}, 13074 pages = {1209--1231}, 13075 year = {2003}, 13076 doi = {10.1137/S0036142901389621} 13077} 13078 13079@TechReport{ caisaad, 13080 author = {Xiao-Chuan Cai and Youcef Saad}, 13081 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 13082 institution = {Army High Performance Computing Research Center, University of Minnesota }, 13083 year = {1993}, 13084 number = {Preprint 93-027 }, 13085 note = {SIAM J. Sci. Comp. 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Supercomputing Applications}, 13122 volume = {8}, 13123 number = {3/4}, 13124 year = {1994}, 13125 key = {MPI Standard - final} 13126} 13127 13128@Unpublished{ npb-web-page, 13129 key = {NAS Parallel Benchmarks}, 13130 title = {{NAS} {P}arallel {B}enchmarks {W}eb page}, 13131 note = {http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html}, 13132 year = {1996}, 13133 month = dec 13134} 13135 13136@Book{ george81, 13137 title = {Computer Solution of Large Sparse Positive Definite Systems}, 13138 author = {Alan George and Joseph W. Liu}, 13139 publisher = {Prentice-Hall}, 13140 year = {1981}, 13141 key = {SparseDirect} 13142} 13143 13144@Book{ p4-book, 13145 title = {Portable Programs for Parallel Processors}, 13146 publisher = {Holt, Rinehart, {and} Winston}, 13147 year = {1987}, 13148 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 13149 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 13150 key = {P4Book} 13151} 13152 13153@Article{ stones, 13154 author = {H. L. Stone}, 13155 title = {Iterative solution of implicit approximations of multidimensional partial 13156 differential equations}, 13157 journal = {SIAM J. Numerical Analysis}, 13158 pages = {87--113}, 13159 volumne = {5}, 13160 year = {1968} 13161} 13162 13163@Article{ parallelstones, 13164 author = {J. S. Reeve and A. D. Scurr and J. H. Merlin}, 13165 title = {Parallel versions of {S}tones strongly implicit algorithm}, 13166 journal = {Concurrency and Computation: Practice and Experience}, 13167 pages = {1049--1062}, 13168 volumne = {13}, 13169 year = {2001} 13170} 13171 13172@Article{ p4-paper, 13173 author = {Ralph Butler and Ewing Lusk}, 13174 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 13175 journal = {Journal of Parallel Computing}, 13176 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 13177 Division preprint P362-0493)}, 13178 year = {1993} 13179} 13180 13181@TechReport{ picl, 13182 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 13183 title = {{PICL}: A portable instrumented communications library}, 13184 institution = {Oak Ridge National Laboratory}, 13185 number = {TM-11130}, 13186 year = {1990}, 13187 key = {PICL} 13188} 13189 13190@TechReport{ upshot, 13191 author = {Virginia Herrarte and Ewing Lusk}, 13192 title = {Studying Parallel Program Behavior with {U}pshot}, 13193 institution = {Argonne National Laboratory}, 13194 number = {ANL-91/15}, 13195 month = aug, 13196 year = {1991}, 13197 key = {Upshot} 13198} 13199 13200@TechReport{ p4-manual, 13201 author = {Ralph Butler and Ewing Lusk}, 13202 title = {User's Guide to the p4 Parallel Programming System}, 13203 institution = {Argonne National Laboratory}, 13204 number = {ANL-92/17}, 13205 month = oct, 13206 year = {1992}, 13207 key = {p4-Manual} 13208} 13209 13210@InProceedings{ oldparti, 13211 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 13212 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 13213 booktitle = {Proceedings of Supercomputing '93}, 13214 pages = {578--587}, 13215 year = {1993} 13216} 13217 13218@Article{ parti2, 13219 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 13220 and J. Saltz}, 13221 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 13222 journal = {ACM SIGPLAN Notices}, 13223 year = {1995}, 13224 pages = {68-79}, 13225 volume = {30}, 13226 number = {8} 13227} 13228 13229@Article{ parti3, 13230 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 13231 title = {Run-Time Parallelization and Scheduling of Loops}, 13232 journal = {IEEE Trans. Computers}, 13233 year = {1991}, 13234 pages = {604-612}, 13235 volume = {40}, 13236 number = {5} 13237} 13238 13239@InProceedings{ disz-lusk:wamtrace, 13240 author = {Terrence Disz and Ewing Lusk}, 13241 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 13242 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13243 year = {1987}, 13244 pages = {46--53} 13245} 13246 13247@InProceedings{ gorlick-kesselman:gauge, 13248 author = {Michael Gorlick and Carl Kesselman}, 13249 title = {Timing {Prolog} programs without Clocks}, 13250 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13251 year = {1996}, 13252 publisher = {Birkhauser} 13253} 13254 13255@TechReport{ aztec, 13256 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 13257 title = {Aztec User's Guide Version 1.1}, 13258 institution = {Sandia National Laboratories}, 13259 month = oct, 13260 year = {1995}, 13261 number = {SAND95/1559} 13262} 13263 13264@TechReport{ aztec2, 13265 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 13266 title = {Official {Aztec} User's Guide Version 2.1}, 13267 institution = {Sandia National Laboratories}, 13268 year = {1999} 13269} 13270 13271@Book{ taylor-chandy:pcn, 13272 author = {Chandy, M. and Taylor, S.}, 13273 title = {An Introduction to Parallel Programming}, 13274 year = {1991}, 13275 publisher = {Jones and Bartlett} 13276} 13277 13278@Book{ foster-taylor:strand, 13279 title = {Strand: New Concepts in Parallel Programming}, 13280 author = {Ian Foster and Stephen Taylor}, 13281 publisher = {Prentice-Hall}, 13282 adress = { Englewood Cliffs, New Jersey}, 13283 year = {1990} 13284} 13285 13286@Article{ aurora, 13287 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 13288 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 13289 Carlsson and A. Ciepielewski and B. Hausman}, 13290 title = {The Aurora OR-Parallel Prolog System}, 13291 journal = {New Generation Computing}, 13292 volume = {7}, 13293 number = {3}, 13294 year = {1990}, 13295 pages = {243--271} 13296} 13297 13298@TechReport{ roo, 13299 author = {E. Lusk and W. McCune and J. Slaney}, 13300 title = {Roo---a Parallel Theorem Prover}, 13301 institution = {Argonne National Laboratory}, 13302 number = {MCS--TM--149}, 13303 year = {1991} 13304} 13305 13306@TechReport{ heath-etheridge:vppp, 13307 author = {M. T. Heath and J. A. Etheridge}, 13308 title = {Visualizing the Performance of Parallel Programs}, 13309 institution = {Oak Ridge National Laboratory}, 13310 number = {ORNL TM-11813}, 13311 year = {1991} 13312} 13313 13314@TechReport{ chem:vis, 13315 author = {Ewing L. Lusk}, 13316 title = {Performance Visualization for Parallel Programs}, 13317 institution = {Argonne National Laboratory}, 13318 number = {ANL/MCS--P287--0192}, 13319 year = {1991}, 13320 note = {(to appear in {\em Theoretica Chimica Acta})} 13321} 13322 13323@TechReport{ picltrace, 13324 author = {P.~H.~Worley}, 13325 title = {A new {PICL} trace file format}, 13326 institution = {Oak Ridge National Laboratory}, 13327 number = {ORNL TM-12125}, 13328 month = jun, 13329 year = {1992} 13330} 13331 13332@InProceedings{ hideo, 13333 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 13334 title = {Inference of Phylogenetic trees using maximum likelihood}, 13335 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 13336 year = {1992}, 13337 pages = {247--262} 13338} 13339 13340@InProceedings{ dw90, 13341 author = {M. Dryja and O. Widlund}, 13342 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 13343 Problems}, 13344 booktitle = {Third International Symposium on Domain Decomposition Methods}, 13345 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 13346 year = {1990}, 13347 pages = {3-21}, 13348 publisher = {SIAM}, 13349 address = {Philadelphia}, 13350 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 13351 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 13352 references, good introduction to the theory. No computations}, 13353 key = {DryjaWidlund90 !AS} 13354} 13355 13356@Unpublished{ rosing, 13357 author = {Matt Rosing and Joel Saltz}, 13358 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 13359 key = {LowLatency}, 13360 note = {manuscript, 1992} 13361} 13362 13363@TechReport{ jp:incomplete, 13364 author = {Mark T. Jones and Paul E. Plassmann}, 13365 title = {An Improved Incomplete {C}holesky Factorization}, 13366 institution = {Argonne National Laboratory}, 13367 address = {Argonne, IL}, 13368 type = {Preprint}, 13369 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 13370 number = {MCS-P206-0191}, 13371 year = {1991}, 13372 key = {jones} 13373} 13374 13375@InCollection{ jp:ima, 13376 author = {Mark Jones and Paul Plassmann}, 13377 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 13378 booktitle = {Graph Theory and Sparse Matrix Computation}, 13379 publisher = {Springer-Verlag}, 13380 series = {The IMA Volumes in Mathematics and Its Applications}, 13381 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 13382 volume = {56}, 13383 year = {1993}, 13384 pages = {229--245} 13385} 13386 13387@Article{ pw98, 13388 author = {M. Pernice and H. F. Walker}, 13389 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 13390 journal = {SIAM J. Sci. Stat. Comput.}, 13391 year = {1998}, 13392 volume = {19}, 13393 pages = {302--318} 13394} 13395 13396@TechReport{ ysmp83, 13397 key = {Eisenstat}, 13398 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13399 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13400 institution = {Department of Computer Science, Yale University}, 13401 number = {YALE/DCS/RR-265}, 13402 month = apr, 13403 year = {1983} 13404} 13405 13406@InBook{ ysmp84, 13407 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13408 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13409 title = {Elliptic Problem Solvers II}, 13410 publisher = {Academic Press}, 13411 pages = {45--52}, 13412 editors = {G. Birkhoff and A. Schoenstadt}, 13413 year = {1984} 13414} 13415 13416@TechReport{ sparsekit, 13417 key = {Saad}, 13418 author = {Youcef Saad}, 13419 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 13420 institution = {Center for Supercomputing Research and Development, University of Illinois at 13421 Urbana-Champaign}, 13422 number = {1029}, 13423 year = {1990} 13424} 13425 13426@TechReport{ pde-user-ref, 13427 author = {Barry F. Smith}, 13428 title = {Extensible {PDE} Solvers Package Users Manual}, 13429 institution = {Argonne National Laboratory}, 13430 month = sep, 13431 year = {1994}, 13432 number = {ANL-93/40}, 13433 key = {Smith94 ! PDE} 13434} 13435 13436@TechReport{ bs-user-ref, 13437 author = {Mark T. Jones and Paul E. Plassmann}, 13438 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 13439 of Sparse Linear Systems}, 13440 institution = {Argonne National Laboratory}, 13441 month = dec, 13442 year = {1995}, 13443 number = {ANL-95/48} 13444} 13445 13446@TechReport{ snes-user-ref, 13447 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 13448 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 13449 institution = {Argonne National Laboratory}, 13450 month = feb, 13451 year = {1995}, 13452 number = {ANL/MCS-TM-193}, 13453 key = {GroppMcInnesSmith95 ! SNES} 13454} 13455 13456@TechReport{ sles-user-ref, 13457 author = {William D. Gropp and Barry F. Smith}, 13458 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 13459 institution = {Argonne National Laboratory}, 13460 month = mar, 13461 year = {1993}, 13462 number = {ANL-93/8}, 13463 key = {GroppSmith93 ! SLES} 13464} 13465 13466@TechReport{ chameleon-user-ref, 13467 author = {William D. Gropp and Barry F. Smith}, 13468 title = {Chameleon Parallel programming tools Users Manual}, 13469 institution = {Argonne National Laboratory}, 13470 month = mar, 13471 year = {1993}, 13472 number = {ANL-93/23}, 13473 key = {GroppSmith93 ! Chameleon} 13474} 13475 13476@Article{ euclid2, 13477 author = {D. Hysom and A. Pothen}, 13478 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 13479 journal = {SIAM J. Sci. Comput.}, 13480 volume = {22}, 13481 number = {6}, 13482 pages = {2194--2215} 13483} 13484 13485@TechReport{ euclid1, 13486 author = {D. Hysom and A. Pothen}, 13487 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 13488 Solution of Sparse Linear Systems)}, 13489 institution = {Old Dominion University}, 13490 year = {2001} 13491} 13492 13493@TechReport{ ksp-user-ref, 13494 author = {William D. Gropp and Barry F. Smith}, 13495 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 13496 Methods}, 13497 institution = {Argonne National Laboratory}, 13498 month = aug, 13499 year = {1993}, 13500 number = {ANL-93/30}, 13501 key = {GroppSmith93 ! KSP} 13502} 13503 13504@TechReport{ mpi-chameleon, 13505 author = {William D. Gropp and Ewing Lusk}, 13506 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 13507 institution = {Argonne National Laboratory}, 13508 month = dec, 13509 year = {1992}, 13510 number = {ANL-92/47}, 13511 key = {GroppLusk92 ! MPI} 13512} 13513 13514@TechReport{ blockcomm-fortran, 13515 author = {William D. Gropp}, 13516 title = {Block{C}omm for {F}ortran}, 13517 institution = {Argonne National Laboratory}, 13518 month = may, 13519 year = {1993}, 13520 number = {ANL-93/00 (to appear)}, 13521 key = {Gropp93 ! BlockComm} 13522} 13523 13524@TechReport{ autodocument, 13525 author = {William D. Gropp}, 13526 title = {Automatic documentation of {C} programs}, 13527 institution = {Argonne National Laboratory}, 13528 month = may, 13529 year = {1993}, 13530 number = {ANL-93/00}, 13531 key = {Gropp93 ! Autodoc} 13532} 13533 13534@TechReport{ zipcode, 13535 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 13536 Manfred Morari}, 13537 title = {The {Z}ipcode message-passing system}, 13538 institution = {Lawrence Livermore National Laboratory}, 13539 month = sep, 13540 year = {1992}, 13541 number = {Unpublished}, 13542 key = {Skjellum92 ! Zipcode} 13543} 13544 13545@Article{ paragraph, 13546 author = {Michael T. Heath and Jennifer Etheridge Finger}, 13547 title = {Visualizing performance of parallel programs}, 13548 journal = {IEEE Software}, 13549 volume = {8}, 13550 number = {5}, 13551 month = sep, 13552 year = {1991}, 13553 pages = {29--39}, 13554 key = {Heath91 ! Paragraph} 13555} 13556 13557@Article{ gropp90, 13558 author = {William Gropp and Edward Smith}, 13559 title = {Computational Fluid Dynamics on Parallel Processors}, 13560 journal = {Computers and Fluids}, 13561 volume = {18}, 13562 year = {1990}, 13563 pages = {289--304}, 13564 key = {Gropp90 ! performance} 13565} 13566 13567@Article{ foster92, 13568 author = {Ian Foster and William Gropp and Rick Stevens}, 13569 title = {The parallel scalability of the spectral transform method}, 13570 journal = {Monthly Weather Review}, 13571 volume = {120}, 13572 year = {1992}, 13573 pages = {835--850}, 13574 key = {Foster92 ! performance} 13575} 13576 13577@InBook{ fgn, 13578 author = {R. Freund and G. H. Golub and N. Nachtigal}, 13579 title = {Iterative Solution of Linear Systems}, 13580 series = {Acta Numerica}, 13581 year = {1992}, 13582 publisher = {Cambridge University Press}, 13583 pages = {57--100} 13584} 13585 13586@TechReport{ nachtigal90, 13587 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 13588 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13589 institution = {Massachusetts Institute of Technology}, 13590 month = mar, 13591 year = {1990}, 13592 number = {90-2}, 13593 key = {Nachtigal | Krylov} 13594} 13595 13596@Article{ nachtigal1992fnm, 13597 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13598 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 13599 journal = {SIAM Journal on Matrix Analysis and Applications}, 13600 volume = {13}, 13601 pages = {778}, 13602 year = {1992}, 13603 publisher = {SIAM} 13604} 13605 13606@TechReport{ embree1999descriptive, 13607 title = {How descriptive are {GMRES} convergence bounds}, 13608 author = {Embree, M.}, 13609 year = {1999}, 13610 number = {08}, 13611 institution = {Oxford University Computing Laboratory} 13612} 13613 13614@Article{ vorst92, 13615 author = {H. van der Vorst}, 13616 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 13617 of nonsymmetric linear systems}, 13618 journal = {SIAM J. Sci. Stat. Comput.}, 13619 year = {1992}, 13620 volume = {13}, 13621 pages = {631--644} 13622} 13623 13624@Article{ eisenstat81, 13625 author = {S. Eisenstat}, 13626 title = {Efficient Implementation of a Class of {CG} Methods}, 13627 journal = {SIAM J. Sci. Stat. Comput.}, 13628 year = {1981}, 13629 volume = {2}, 13630 pages = {1--4} 13631} 13632 13633@Manual{ ibm-essl, 13634 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 13635 Reference}, 13636 organization = {IBM}, 13637 year = {1992}, 13638 key = {IBM-ESSL} 13639} 13640 13641@Manual{ ibm-eui, 13642 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 13643 Release 2.0}, 13644 organization = {IBM}, 13645 month = jun, 13646 year = {1994}, 13647 key = {IBM-EUI} 13648} 13649 13650@Manual{ ibm-euih, 13651 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 13652 organization = {IBM}, 13653 author = {Peter Hochschild}, 13654 year = {1993}, 13655 key = {IBM-EUIH} 13656} 13657 13658@TechReport{ mpi, 13659 title = {Document for a Standard Message-Passing Interface}, 13660 author = {Message Passing Interface Forum}, 13661 institution = {University of Tennessee}, 13662 number = {CS-93-214}, 13663 month = nov, 13664 year = {1993}, 13665 key = {MPI Standard} 13666} 13667 13668@Unpublished{ mpi-final-web, 13669 author = {Message Passing Interface Forum}, 13670 title = {{MPI}: A Message-Passing Interface Standard}, 13671 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 13672 year = {1994}, 13673 month = may 13674} 13675 13676@Book{ hockney-jesshope, 13677 author = {R. W. Hockney and C. R. Jesshope}, 13678 title = {Parallel Computers 2}, 13679 publisher = {Adam Hilger}, 13680 year = {1988} 13681} 13682 13683@Book{ cm-fortran, 13684 author = {{Thinking Machines Corporation}}, 13685 title = {Users Manual for CM-Fortran}, 13686 publisher = {Thinking Machines Corporation}, 13687 year = {1993} 13688} 13689 13690@TechReport{ chang93, 13691 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 13692 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 13693 institution = {Yale Department of Computer Science}, 13694 number = {YALEU/DCS/RR-994}, 13695 month = nov, 13696 year = {1993}, 13697 key = {BDD|diag} 13698} 13699 13700@InProceedings{ gropplevine93, 13701 author = {N. Galbreath and W. Gropp and D. Levine}, 13702 title = {Applications-Driven Parallel {I/O}}, 13703 booktitle = {Proceedings of Supercomputing '93}, 13704 year = {1993}, 13705 pages = {462--471} 13706} 13707 13708@Book{ siegle85, 13709 author = {H. J. Siegel}, 13710 title = {Interconnection Networks for Large Scale Parallel Processing}, 13711 publisher = {Lexington Books}, 13712 year = {1985}, 13713 key = {Network Comparison} 13714} 13715 13716@Article{ lawrie75, 13717 author = {D. H. Lawrie}, 13718 title = {Access and alignment of data in an array processor}, 13719 journal = {IEEE Transactions on Computers}, 13720 volume = {C-24}, 13721 number = {12}, 13722 month = dec, 13723 year = {1975}, 13724 pages = {1145--1155}, 13725 key = {Omega Network} 13726} 13727 13728@Book{ knuth1986, 13729 title = {The {\TeX}{Book}}, 13730 author = {Donald Ervin Knuth and Duane Bibby}, 13731 volume = {1993}, 13732 year = {1986}, 13733 publisher = {Addison-Wesley Reading, Massachusetts} 13734} 13735 13736@Book{ lamport86, 13737 author = {Leslie Lamport}, 13738 title = {{LaTeX}: A document preparation system}, 13739 publisher = {Addison-Wesley}, 13740 year = {1986}, 13741 key = {Latex Manual} 13742} 13743 13744@InProceedings{ gropp-lusk:unix-tools, 13745 author = {William Gropp and Ewing Lusk}, 13746 title = {Scalable {U}nix Tools on Parallel Processors}, 13747 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 13748 publisher = {IEEE}, 13749 pages = {56--62} 13750} 13751 13752@InProceedings{ jp:bell_prize, 13753 author = {Mark Jones and Paul Plassmann}, 13754 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 13755 Applications}, 13756 booktitle = {Proceedings of Supercomputing '92}, 13757 publisher = {IEEE Computer Society Press}, 13758 year = {1992}, 13759 pages = {551--560} 13760} 13761 13762@COMMENT{WEB, CWEB references (for doctext)} 13763@TechReport{ web, 13764 author = {Donald E. Knuth}, 13765 title = {The {\tt WEB} system of structured documentation}, 13766 institution = {Computer Science Department, Stanford University}, 13767 year = {1983}, 13768 number = {980}, 13769 month = sep 13770} 13771 13772@Article{ literatepgm, 13773 author = {Donald E. Knuth}, 13774 title = {Literate Programming}, 13775 journal = {Computer Journal}, 13776 year = {1984}, 13777 volume = {27}, 13778 number = {2}, 13779 pages = {91--111} 13780} 13781 13782@Unpublished{ cweb-code, 13783 author = {Silvio Levy and Donald E. Knuth}, 13784 title = {CWEB}, 13785 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 13786} 13787 13788@Article{ jp:scalable, 13789 author = {Mark Jones and Paul Plassmann}, 13790 title = {Scalable Iterative Solution of Sparse Linear Systems}, 13791 journal = {Parallel Computing}, 13792 volume = {20}, 13793 number = {5}, 13794 month = may, 13795 year = {1994}, 13796 pages = {753--773} 13797} 13798 13799@Article{ jp:pcolor, 13800 author = {Mark T. Jones and Paul E. Plassmann}, 13801 title = {A Parallel Graph Coloring Heuristic}, 13802 journal = {SIAM J. Sci. Comput.}, 13803 volume = {14}, 13804 number = {3}, 13805 pages = {654-669}, 13806 year = {1993} 13807} 13808 13809@TechReport{ block_solve, 13810 author = {Mark T. Jones and Paul E. Plassmann}, 13811 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 13812 Sparse Linear Systems}, 13813 institution = {Argonne National Laboratory}, 13814 year = {1992}, 13815 number = {ANL-92/46}, 13816 key = {JonesPlassmann92 ! block_solve} 13817} 13818 13819@InProceedings{ supercond, 13820 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 13821 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 13822 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 13823 Conference}, 13824 month = feb, 13825 year = {1994}, 13826 key = {McInnesPalumbo94 ! superconductivity } 13827} 13828 13829@Unpublished{ preosti:93, 13830 author = {Gianfranco Preosti}, 13831 title = { }, 13832 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 13833 year = {1993}, 13834 key = {preosti93 ! GL-tilt3d} 13835} 13836 13837@Unpublished{ more:93, 13838 author = {Jorge J. Mor\'{e}}, 13839 title = { }, 13840 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 13841 {A}rgonne {N}ational {L}aboratory}, 13842 year = {1993}, 13843 key = {more93 ! MINPACK-2} 13844} 13845 13846@Article{ brownsaad:90, 13847 author = {Peter N. Brown and Youcef Saad}, 13848 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 13849 journal = {SIAM J. Sci. Stat. Comput.}, 13850 year = {1990}, 13851 volume = {11}, 13852 pages = {450-481} 13853} 13854 13855@Book{ using-mpi, 13856 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 13857 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 13858 publisher = {MIT Press}, 13859 year = {1994} 13860} 13861 13862@Book{ using-mpi2, 13863 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 13864 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 13865 publisher = {MIT Press}, 13866 year = {1999} 13867} 13868 13869@Article{ hs:52, 13870 author = {Magnus R. Hestenes and Eduard Steifel}, 13871 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 13872 journal = {J. Research of the National Bureau of Standards}, 13873 year = {1952}, 13874 volume = {49}, 13875 pages = {409-436} 13876} 13877 13878@Article{ so:89, 13879 author = {Peter Sonneveld}, 13880 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 13881 journal = {SIAM J. Sci. Stat. Comput.}, 13882 year = {1989}, 13883 volume = {10}, 13884 pages = {36-52} 13885} 13886 13887@Article{ v:92, 13888 author = {{H. A.} {van der Vorst}}, 13889 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 13890 of nonsymmetric linear systems}, 13891 journal = {SIAM J. Sci. Stat. Comput.}, 13892 volume = {13}, 13893 year = {1992}, 13894 pages = {631-644} 13895} 13896 13897@Article{ f:93, 13898 author = {Roland W. Freund}, 13899 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 13900 Systems}, 13901 journal = {SIAM J. Sci. Stat. Comput.}, 13902 volume = {14}, 13903 year = {1993}, 13904 pages = {470-482} 13905} 13906 13907@Article{ ish:89, 13908 author = {S. Ishizuka}, 13909 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 13910 journal = {Combustion and Flame}, 13911 volume = {75}, 13912 year = {1989}, 13913 pages = {367-379} 13914} 13915 13916@Book{ williams89, 13917 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 13918 author = {F.A. Williams}, 13919 publisher = {Addison-Wesley}, 13920 year = {1989}, 13921 pages = {367-379} 13922} 13923 13924@Book{ ra75, 13925 author = {R. Aris}, 13926 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 13927 publisher = {Oxford}, 13928 year = {1975} 13929} 13930 13931@Book{ bebernes89, 13932 author = {J. Bebernes and D. Eberly}, 13933 title = {Mathematical Problems from Combustion Theory}, 13934 publisher = {Springer-Verlag}, 13935 series = {Applied Mathematical Sciences 83}, 13936 year = {1989} 13937} 13938 13939@InProceedings{ kikuchi89, 13940 author = {F. Kikuchi}, 13941 booktitle = { Computing Methods in Applied Sciences and Engineering}, 13942 editor = {R. Glowinski and J. L. Lions}, 13943 publisher = {Springer-Verlag}, 13944 series = {Lecture Notes in Mathematics}, 13945 title = {Finite element approximations to bifurcation problems of turning point type}, 13946 year = {1977} 13947} 13948 13949@Article{ rg85, 13950 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 13951 title = {Continuation-conjugate Gradient Methods for the Least Squares Solution of 13952 Nonlinear Boundary Problems}, 13953 journal = {SIAM J. Sci. Stat. Comput.}, 13954 volume = {6}, 13955 year = {1985}, 13956 pages = {793-832} 13957} 13958 13959@InProceedings{ whitfield91, 13960 author = {D. Whitfield and L. Taylor}, 13961 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13962 Schemes}, 13963 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 13964 misc = {AIAA-91-1539}, 13965 pages = {134-145}, 13966 year = {1991} 13967} 13968 13969@InProceedings{ quinlan1, 13970 author = {M. Lemke and D. Quinlan}, 13971 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 13972 Architecture-Independent Development of Structured Grid Applications}, 13973 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 13974 publisher = {Springer Verlag}, 13975 year = {1992} 13976} 13977 13978@InProceedings{ quinlan2, 13979 author = {R. Parsons and D. Quinlan}, 13980 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 13981 Computations}, 13982 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 13983 year = {1994} 13984} 13985 13986% ***** Overview of functionality in Diffpack 13987@InBook{ dpoverview, 13988 author = {Bruaset, A. M. and Langtangen, H. P.}, 13989 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13990 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 13991 {Diffpack}}, 13992 publisher = {Birkh{\"{a}}user}, 13993 pages = {61--90}, 13994 year = {1997} 13995} 13996 13997% ***** Short overview of Diffpack 13998@InCollection{ dpoverview2, 13999 author = {Bruaset, A. M. and Langtangen, H. P.}, 14000 editor = {A. Sydow}, 14001 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 14002 and Applied Mathematics}, 14003 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 14004 pages = {553--558}, 14005 volume = {4}, 14006 year = {1997} 14007} 14008 14009% ***** Comprehensive documentation of Diffpack and 14010% associated numerical methods: 14011@Book{ dpbook, 14012 author = {H. P. Langtangen}, 14013 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 14014 Software. Part I}, 14015 series = {Lecture Notes in Computational Science and Engineering}, 14016 publisher = {Springer-Verlag}, 14017 year = {1998} 14018} 14019 14020% ***** Design issues of the linear solvers in Diffpack, serves also as a 14021% collection of examples on O-O in numerical computing 14022@Article{ ambhpl97a, 14023 author = {A. M. Bruaset and H. P. Langtangen }, 14024 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 14025 journal = {Transactions on Mathematical Software}, 14026 volume = {23 }, 14027 pages = {50--80}, 14028 year = {1997} 14029} 14030 14031@Misc{ dpurl, 14032 author = {{Diffpack Web page}}, 14033 howpublished = {\url{http://www.diffpack.com}} 14034} 14035 14036% ***** General intro to object-oriented numerics for "FORTRAN programmers" 14037@InCollection{ oonintro, 14038 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 14039 editor = {D{\ae}hlen, M. and Tveito, A.}, 14040 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14041 title = {Object-Oriented Numerics}, 14042 publisher = {Birkh{\"{a}}user}, 14043 year = {1997} 14044} 14045 14046% ***** Efficiency comparison: BLAS 1, Diffpack, C, 14047% and finite element applications (F77 vs Diffpack) 14048@InCollection{ dpefficiency, 14049 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 14050 H. P. and Miller, C. T.}, 14051 editor = {D{\ae}hlen, M. and Tveito, A.}, 14052 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14053 title = {On the Efficiency of {C++} in Scientific Computing}, 14054 publisher = {Birkh{\"{a}}user}, 14055 pages = {91--118}, 14056 year = {1997} 14057} 14058 14059% ***** Parallel concept in Diffpack: 14060@InCollection{ dpparallel, 14061 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 14062 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 14063 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 14064 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 14065 Simulators}, 14066 publisher = {Springer--Verlag}, 14067 series = {Lecture Notes in Computer Science}, 14068 pages = {161--168}, 14069 year = {1997} 14070} 14071 14072% ***** DD and ML methods in Diffpack: 14073@InCollection{ dpddml, 14074 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 14075 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 14076 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 14077 title = {Domain decomposition and multilevel methods in Diffpack}, 14078 year = {1997} 14079} 14080 14081@InProceedings{ bsca98, 14082 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 14083 Alexander}, 14084 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 14085 Optimization}, 14086 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14087 Scientific and Engineering Computing}, 14088 editor = {Mike Henderson et al.}, 14089 pages = {165-173}, 14090 year = {1998} 14091} 14092 14093@Book{ scalapack-user-guide, 14094 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 14095 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 14096 Stanley and D. Walker and R. C. Whaley}, 14097 title = {Sca{LAPACK} Users' Guide}, 14098 publisher = {SIAM}, 14099 address = {Philadelphia, PA}, 14100 year = {1997} 14101} 14102 14103@InProceedings{ keyes99, 14104 author = {D. E. Keyes}, 14105 title = {How Scalable is Domain Decomposition in Practice?}, 14106 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 14107 Methods}, 14108 editor = {C.-H. Lai et al.}, 14109 publisher = {Domain Decomposition Press, Bergen}, 14110 note = {To appear}, 14111 year = {1999} 14112} 14113 14114@Article{ fun3d, 14115 author = {W. K. Anderson and D. L. Bonhaus}, 14116 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 14117 grids}, 14118 journal = {Computers and Fluids}, 14119 year = {1994}, 14120 volume = {23}, 14121 pages = {1--21} 14122} 14123 14124% ------------------------------------------------------------------------- 14125% ------------------------------------------------------------------------- 14126@Article{ torczon, 14127 author = {Dennis, Jr., J. E. and V.~Torczon}, 14128 title = {Direct Search Methods on Parallel Machines}, 14129 journal = {SIAM J. Optimization}, 14130 volume = {1}, 14131 pages = {448--474}, 14132 year = {1991}, 14133 key = {Torczon !PDS} 14134} 14135 14136@InProceedings{ wt91, 14137 author = {D. L. Whitfield and L. K. Taylor}, 14138 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 14139 Schemes}, 14140 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 14141 misc = {AIAA-91-1539}, 14142 pages = {134-145}, 14143 year = {1991} 14144} 14145 14146@Article{ ew96, 14147 author = {S. C. Eisenstat and H. F. Walker}, 14148 title = {Choosing the forcing terms in an inexact {N}ewton method}, 14149 journal = {SIAM J. Scientific Computing}, 14150 volume = {17}, 14151 year = {1996}, 14152 pages = {16--32} 14153} 14154 14155@Book{ thi93, 14156 author = {{Thinking Machines Corporation}}, 14157 title = {Users Manual for CM-Fortran}, 14158 publisher = {Thinking Machines Corporation}, 14159 year = {1993} 14160} 14161 14162@Book{ mortonmayers94, 14163 author = {K. W. Morton and D. F. Mayers}, 14164 title = {Numerical Solution of Partial Differential Equations}, 14165 publisher = {Press Syndicate of the University of Cambridge}, 14166 year = {1994} 14167} 14168 14169@Book{ heath97, 14170 author = {Michael T. Heath}, 14171 title = {Scientific Computing: An Introductory Survey}, 14172 publisher = {McGraw Hill}, 14173 year = {1997} 14174} 14175 14176@Article{ captools96, 14177 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 14178 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 14179 Performance on the Parallelization of Structured Mesh Codes}, 14180 journal = {Parallel Computing}, 14181 volume = {22}, 14182 pages = {197-226}, 14183 year = {1996} 14184} 14185 14186@Misc{ nastran-web-page, 14187 author = {{MSC Software Corporation}}, 14188 title = {{NASTRAN} {W}eb page}, 14189 howpublished = {\url{http://www.mechsolutions.com/products/nastran/}}, 14190 year = {2024} 14191} 14192 14193@Book{ hpf, 14194 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 14195 Zosel}, 14196 title = {The High Performance Fotran Handbook}, 14197 publisher = {MIT Press}, 14198 year = {1994} 14199} 14200 14201@InProceedings{ keyes98, 14202 author = {D. E. Keyes}, 14203 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 14204 Architectures}, 14205 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 14206 editors = {M. D. Salas and W. K. Anderson}, 14207 ppublisher = {Elsevier}, 14208 year = {1998} 14209} 14210 14211@InProceedings{ pooma-atlas, 14212 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14213 J. V. W. Reynders and M. Tholburn}, 14214 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14215 Applications}, 14216 year = {1995}, 14217 month = dec, 14218 booktitle = {Supercomputing '95 Proceedings} 14219} 14220 14221% --------------------------------------------------------------------------------- 14222% New bib entries for CRPC paper 14223@Misc{ mgnet-web-page, 14224 author = {Craig C. Douglas}, 14225 title = {{MGNet Web page}}, 14226 note = {See {\tt http://\-www.mgnet.org}} 14227} 14228 14229@Misc{ dagh-web-page, 14230 author = {M. Parashar and J. C. Browne}, 14231 title = {{DAGH Web page}}, 14232 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14233} 14234 14235@Misc{ parasol-web-page, 14236 key = {PARASOL}, 14237 title = {{PARASOL Web page}}, 14238 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14239} 14240 14241@Misc{ pooma-web-page, 14242 author = {{POOMA Web page}}, 14243 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14244} 14245 14246@Misc{ mudpack-web-page, 14247 author = {John C. Adams}, 14248 title = {{MUDPACK Web page}}, 14249 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14250} 14251 14252@Misc{ pellpack-web-page, 14253 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14254 title = {{Parallel ELLPACK Web page}}, 14255 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14256} 14257 14258@InProceedings{ pellpack95, 14259 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14260 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14261 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14262 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14263 address = {Albuquerque, NM}, 14264 year = {1995} 14265} 14266 14267@Misc{ nhse-web-page, 14268 author = {{National High-Performance Software Exchange Web page}}, 14269 note = {See {\tt http://\-www.nhse.org}} 14270} 14271 14272@Misc{ doug-web-page, 14273 author = {Mark J. Hagger and Linda Stals}, 14274 title = {{DOUG Web Page}}, 14275 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14276} 14277 14278@TechReport{ doug97, 14279 author = {Mark J. Hagger}, 14280 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14281 institution = {Mathematical Sciences, University of Bath}, 14282 year = {1997}, 14283 number = {9706}, 14284 note = {Advances in Computational Mathematics (to appear)} 14285} 14286 14287@Misc{ ug-web-page, 14288 author = {{UG Web Page}}, 14289 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14290} 14291 14292@Article{ ug97, 14293 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14294 Rentz-Reichert and C. Wieners}, 14295 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14296 journal = {Computing and Visualization in Science}, 14297 year = {1997}, 14298 volume = {}, 14299 pages = {} 14300} 14301 14302@Misc{ vecfem-web-page, 14303 author = {Lutz Grosz}, 14304 title = {{VECFEM Web Page}}, 14305 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14306} 14307 14308@Misc{ atlas-web-page, 14309 author = {R. Clint {Whaley et al.}}, 14310 title = {{ATLAS Web Page}}, 14311 howpublished = {\url{http://math-atlas.sourceforge.net}} 14312} 14313 14314@Misc{ fenics-web-page, 14315 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14316 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14317 title = {{FEniCS Web Page}}, 14318 note = {\url{http://www.fenicsproject.org}}, 14319 year = {2005} 14320} 14321 14322@Misc{ matlab-web-page, 14323 author = {{The} {MathWorks}}, 14324 title = {{Matlab} {Web} page}, 14325 url = {http://www.mathworks.com} 14326} 14327 14328@Misc{ phipac-web-page, 14329 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14330 and D. Lam}, 14331 title = {{PHiPAC Web Page}}, 14332 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14333} 14334 14335@InProceedings{ kelp, 14336 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14337 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14338 booktitle = {Irregular '96}, 14339 year = {1996} 14340} 14341 14342@Unpublished{ kelp-web-page, 14343 author = {Scott Baden}, 14344 title = {{KeLP} {W}eb page}, 14345 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14346} 14347 14348@InProceedings{ hk99, 14349 author = {R. Hornung and S. 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Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker 14620 and C. Woodward}, 14621 title = {{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers}, 14622 journal = {ACM Transactions on Mathematical Software}, 14623 volume = {31}, 14624 number = {3}, 14625 pages = {363--396}, 14626 year = {2005} 14627} 14628 14629@InProceedings{ serban2005cvodes, 14630 title = {{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}}, 14631 author = {Serban, Radu and Hindmarsh, Alan C}, 14632 booktitle = {Proceedings of the 5th International Conference on Multibody Systems, Nonlinear 14633 Dynamics and Control, Long Beach, CA}, 14634 year = {2005} 14635} 14636 14637@Article{ pvode99, 14638 author = {G. Byrne and A. Hindmarsh}, 14639 title = {{PVODE}, An {ODE} Solver for Parallel Computers}, 14640 journal = {Int. J. High Perf. Comput. 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Softw.}, 15699 volume = {31}, 15700 year = {2005}, 15701 pages = {326--350} 15702} 15703 15704@Unpublished{ compass:homepage, 15705 author = {Panagiotis {Spentzouris (PI)}}, 15706 title = {Community Petascale Project for Accelerator Science and Simulation (ComPASS)}, 15707 note = {SciDAC2 project, see \url{https://compass.fnal.gov/}} 15708} 15709 15710@Unpublished{ cmsnf:homepage, 15711 author = {{Todd Allen, Director}}, 15712 title = {{Center for Materials Science of Nuclear Fuel}}, 15713 note = {Energy Frontier Research Center, see 15714 \url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}} 15715} 15716 15717@Unpublished{ dvi-materials:project, 15718 author = {{L.~C.} {McInnes (PI)}}, 15719 title = {Large-Scale Differential Variational Inequalities for Heterogeneous Materials}, 15720 note = {{SciDAC}-e project}, 15721 year = {2011} 15722} 15723 15724@Misc{ scidac:homepage, 15725 author = {{DOE Office of Science}}, 15726 title = {{Scientific Discovery through Advanced Computing}}, 15727 year = {2007}, 15728 howpublished = {\url{http://www.scidac.gov}} 15729} 15730 15731@Misc{ corba, 15732 author = {{Object Management Group}}, 15733 year = {2007}, 15734 title = {{Common Object Request Broker Architecture (CORBA)}}, 15735 howpublished = {\url{http://www.corba.org}} 15736} 15737 15738@Article{ uedge, 15739 author = {T.~D. 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Wilson}, 15761 title = {{BOUT++}: A Framework for Parallel Plasma Fluid Simulations}, 15762 journal = {Computer Physics Communications}, 15763 year = {2009}, 15764 volume = {180}, 15765 issue = {9}, 15766 pages = {1467 -- 1480}, 15767 note = {} 15768} 15769 15770@Article{ tempest, 15771 author = {Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and M.R. Dorr and J.A. Hittinger 15772 and G. Kerbel and W.M. Nevins and T. Rognlien}, 15773 title = {Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST}, 15774 journal = {Bull. Am. Phys. Soc. }, 15775 year = {2005}, 15776 volume = {50}, 15777 number = {86}, 15778 pages = {CP1}, 15779 note = {} 15780} 15781 15782@Article{ ccahpc, 15783 author = {David E. Bernholdt and Benjamin A. Allan and Robert Armstrong and Felipe Bertrand 15784 and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif 15785 and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James 15786 A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia 15787 Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek 15788 Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende 15789 and Theresa L. Windus and Shujia Zhou}, 15790 title = {A Component Architecture for High-Performance Scientific Computing}, 15791 journal = {Intl. J. High-Perf. Computing Appl.}, 15792 volume = {20}, 15793 pages = {163--202}, 15794 year = {2006}, 15795 note = {ACTS Collection special issue} 15796} 15797 15798@Misc{ cca-forum:homepage, 15799 author = {{Common Component Architecture Forum}}, 15800 note = {\url{http://www.cca-forum.org}}, 15801 year = {2010} 15802} 15803 15804@Misc{ petsc:driven-cavity-example, 15805 title = {{PETSc Driven Cavity Example Code}}, 15806 author = {B. F. {Smith et al.}}, 15807 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 15808} 15809 15810@Misc{ petsc-dm:webpage, 15811 author = {B. F. {Smith et al.}}, 15812 title = {{PETSc DM Webpage}}, 15813 howpublished = {\url{https://petsc.org/release/manualpages/DM/}}, 15814 year = {2018} 15815} 15816 15817@Misc{ unic-ref, 15818 author = {Giuseppe Palmiotti}, 15819 title = {{UNIC} Neutronics Software}, 15820 note = {Nuclear Engineering Division, Argonne National Laboratory} 15821} 15822 15823% ----------------------------------------------------------------------- 15824% Model coupling refs 15825@Book{ greve-blatter, 15826 author = {Ralf Greve and Heinz Blatter}, 15827 title = {Dynamics of Ice Sheets and Glaciers}, 15828 series = {Advances in Geophysical and Environmental Mechanics and Mathematics}, 15829 publisher = {Springer}, 15830 year = {2009} 15831} 15832 15833@Misc{ doe-isicles, 15834 key = {ISICLES}, 15835 title = {Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}}, 15836 howpublished = {\url{http://www.csm.ornl.gov/ISICLES/index.html}} 15837} 15838 15839@Article{ safta2011tchem, 15840 title = {TChem-a software toolkit for the analysis of complex kinetic models}, 15841 author = {Safta, Cosmin and Najm, Habib N and Knio, Omar}, 15842 journal = {Sandia Report, SAND2011-3282}, 15843 year = {2011} 15844} 15845 15846@Misc{ chemkin-website, 15847 key = {chemkin}, 15848 title = {ANSYS Chemkin-Pro Website}, 15849 howpublished = {\url{http://www.ansys.com/products/fluids/ansys-chemkin-pro}}, 15850 year = {2017} 15851} 15852 15853@Misc{ mct-website, 15854 key = {MCT}, 15855 title = {{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite}, 15856 howpublished = {\url{http://www.mcs.anl.gov/mct}} 15857} 15858 15859@Article{ larson:05, 15860 author = {Jay Larson and Robert Jacob and Everest Ong}, 15861 title = {{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building 15862 Multi-Physics Parallel Coupled Models}, 15863 journal = {Int. 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Alexandrow and J. J. Dongarra and C. J. K. Tan}, 15888 pages = {148 -- 156}, 15889 series = {Lecture Notes in Computer Science}, 15890 volume = {2073}, 15891 publisher = {Springer-Verlag} 15892} 15893 15894@InProceedings{ jacob01, 15895 author = {R. Jacob and C. Schafer and I. Foster and M. Tobis and J. Anderson}, 15896 year = {2001}, 15897 title = {Computational Design and Performance of the {Gast} Ocean Atmosphere Model}, 15898 booktitle = {Proc. International Conference on Computational Science (ICCS) 2001}, 15899 editors = {V. N. Alexandrow and J. J. Dongarra and C. J. K. Tan}, 15900 series = {Lecture Notes in Computer Science}, 15901 volume = {2073}, 15902 publisher = {Springer-Verlag} 15903} 15904 15905@Article{ chen2008new, 15906 title = {New generation of multi-scale {NWP} system {(GRAPES)}: General scientific 15907 design}, 15908 author = {Chen, DeHui and Xue, JiShan and Yang, XueSheng and Zhang, HongLiang and Shen, 15909 XueShun and Hu, JiangLin and Wang, Yu and Ji, LiRen and Chen, JiaBin}, 15910 journal = {Chinese Science Bulletin}, 15911 volume = {53}, 15912 number = {22}, 15913 pages = {3433--3445}, 15914 year = {2008}, 15915 publisher = {Springer} 15916} 15917 15918@InProceedings{ baum01, 15919 author = {J. Baum and H. Luo and E. Mestreau and D. Sharov and R. Loehner and D. Pelessone 15920 and C. Charman}, 15921 year = {2001}, 15922 title = {Recent Developments of a Coupled {CFD/CSD} Methodology}, 15923 booktitle = {Proc. International Conference on Computational Science (ICCS) 2001}, 15924 editors = {V. N. Alexandrow and J. J. Dongarra and C. J. K. Tan}, 15925 series = {Lecture Notes in Computer Science}, 15926 volume = {2073}, 15927 publisher = {Springer-Verlag} 15928} 15929 15930@InProceedings{ lefantzi03, 15931 author = {S. Lefantzi and J. Ray}, 15932 year = {2003}, 15933 title = {A Component-based Scientific Toolkit for Reacting Flows}, 15934 booktitle = {Proc. Second MIT Conference on Computational Fluid and Solid Mechanics}, 15935 volume = {2}, 15936 publisher = {Elsevier} 15937} 15938 15939@Article{ boville98, 15940 author = {B. A. Boville and P. R. Gent}, 15941 title = {The {NCAR} Climate System Model, Version One}, 15942 journal = {Journal of Climate}, 15943 volume = {11}, 15944 year = {1998}, 15945 pages = {1115--1130} 15946} 15947 15948@Misc{ paraschivoiu99, 15949 author = {M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes}, 15950 title = {Multi-domain multi-model formulation for compressible flows: Conservative 15951 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 15952 note = {AIAA Paper 99-0784}, 15953 year = {1999} 15954} 15955 15956@Article{ peszynska, 15957 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 15958 title = {Mortar upscaling for multiphysics flow in porous media}, 15959 journal = {Computational Geosciences} 15960} 15961 15962@TechReport{ wheeler00, 15963 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 15964 title = {A distributed computing portal for coupling multi-physics and multiple domains in 15965 porous media}, 15966 institution = {University of Texas at Austin}, 15967 number = {TICAM 00-03}, 15968 year = {2000} 15969} 15970 15971@TechReport{ peszynska00, 15972 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 15973 title = {Multiphysics Coupling of Codes}, 15974 institution = {University of Texas at Austin}, 15975 number = {TICAM 00-02}, 15976 year = {2000} 15977} 15978 15979@Article{ joshaghanijoodatnakshatrala2019, 15980 title = {A stabilized mixed discontinuous Galerkin formulation for double 15981 porosity/permeability model}, 15982 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 15983 journal = {Computer Methods in Applied Mechanics and Engineering}, 15984 volume = {352}, 15985 pages = {508--560}, 15986 year = {2019} 15987} 15988 15989@InProceedings{ cai99, 15990 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 15991 title = {An explicit multi-model compressible flow formulation based on the full potential 15992 equation and the {Euler} equations on {3D} unstructured meshes}, 15993 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 15994 Methods}, 15995 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 15996 year = {1999} 15997} 15998 15999@Article{ he05, 16000 author = {Yun He and Chris H. Q. Ding}, 16001 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 16002 Architectures}, 16003 year = {2005}, 16004 volume = {19}, 16005 pages = {329--240}, 16006 number = {3}, 16007 journal = {Int. Journal of High Performance Computing Applications} 16008} 16009 16010@InProceedings{ uiuc-rocket-center02, 16011 author = {W. A. Dick and M. T. Heath}, 16012 title = {Whole System Simulation of Solid Propellant Rockets}, 16013 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 16014 month = jul, 16015 year = {2002} 16016} 16017 16018@InProceedings{ toth04, 16019 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 16020 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 16021 Oehmke}, 16022 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 16023 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 16024 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 16025 Sun-Earth Connection}, 16026 year = {2004}, 16027 publisher = {Elsevier}, 16028 pages = {383--397} 16029} 16030 16031@Misc{ csdrm:web, 16032 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 16033 Shepherd}, 16034 title = {{Center for Simulation of Dynamic Response of Materials}}, 16035 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 16036} 16037 16038@Misc{ csar:web, 16039 author = {M. {Heath (Director)}}, 16040 title = {{Center for Simulation of Advanced Rockets}}, 16041 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 16042} 16043 16044@Misc{ csafe:web, 16045 author = {D. {Pershing (Director)}}, 16046 title = {{Center for Simulation of Accidental Fires and Explosions}}, 16047 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 16048} 16049 16050@Misc{ cits:web, 16051 author = {P. {Moin (Director)}}, 16052 title = {{Center for Integrated Turbulence Simulations}}, 16053 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 16054} 16055 16056@Misc{ flash:web, 16057 author = {D. {Lamb (Director)}}, 16058 title = {{Center for Integrated Turbulence Simulations}}, 16059 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 16060} 16061 16062@TechReport{ utah-csafe03, 16063 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 16064 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 16065 Problems, Part 1: Algorithm Development}, 16066 institution = {University of Utah, Center for the Simulation of Accidental Fires and 16067 Explosions}, 16068 year = {2003} 16069} 16070 16071@InBook{ shepherd07, 16072 author = {M. Shepherd and E. Seol and B. FrantzDale}, 16073 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 16074 year = {2007}, 16075 booktitle = {CRC Handbook of Dynamic System Modeling}, 16076 publisher = {Wiley}, 16077 pages = {1--41}, 16078 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 16079} 16080 16081@InProceedings{ cactus02, 16082 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 16083 Radke and Edward Seidel and John Shalf}, 16084 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 16085 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 16086 year = {2002}, 16087 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 16088} 16089 16090@Misc{ cactus:homepage, 16091 author = {G. {Allen et al.}}, 16092 title = {{Cactus Web page}}, 16093 howpublished = {\url{http://cactuscode.org}} 16094} 16095 16096@Misc{ open-grid-forum:web, 16097 key = {{Open Grid Forum}}, 16098 title = {{Open Grid Forum}}, 16099 note = {See \url{http://www.ogf.org}} 16100} 16101 16102@Misc{ nox:web, 16103 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 16104 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 16105 note = {See \url{http://software.sandia.gov/nox}} 16106} 16107 16108@Misc{ chombo:web, 16109 author = {P. {Colella (PI)}}, 16110 title = {{Chombo}}, 16111 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 16112} 16113 16114@Article{ lanzkron96, 16115 author = {P. J. Lanzkron and D. J. Rose and J. T. Wilkes}, 16116 title = {An Analysis of Approximate Nonlinear Elimination}, 16117 journal = {SIAM J. Sci. Comput.}, 16118 volume = {17}, 16119 year = {1996}, 16120 pages = {538--559} 16121} 16122 16123@Article{ jiang95, 16124 author = {J. Jiang and P. Forsyth}, 16125 title = {Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} 16126 Equations}, 16127 journal = {Computers and Fluids}, 16128 volume = {24}, 16129 pages = {753--770}, 16130 year = {1995} 16131} 16132 16133@Article{ young90, 16134 author = {D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant}, 16135 title = {Global Convergence of Inexact {Newton} Methods for Transonic Flow}, 16136 journal = {Int. J. Numer. Methods Fluids}, 16137 volume = {11}, 16138 pages = {1075--1095}, 16139 year = {1990} 16140} 16141 16142@Article{ fishwick04, 16143 author = {Paul A. Fishwick}, 16144 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 16145 to Interrelating Model Structures}, 16146 journal = {SCS Trans. on Simulation}, 16147 note = {Special Issue in Grand Challenges in Computer Simulation}, 16148 year = {2004} 16149} 16150 16151@Article{ fishwick03, 16152 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 16153 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 16154 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 16155 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 16156 year = {2003} 16157} 16158 16159@InProceedings{ kirner00, 16160 author = {T. G. Kirner and V. F. Martins}, 16161 title = {Development of an Information Visualization Tool Using Virtual Reality}, 16162 booktitle = {Proceedings of the 2000 ACM Symposium on Applied Computing}, 16163 year = {2000}, 16164 pages = {604--606} 16165} 16166 16167@InProceedings{ orso03, 16168 author = {A. Orso and J. Jones and M. J. Harrold}, 16169 title = {Visualization of Program-Execution Data for Deployed Software}, 16170 booktitle = {Proceedings of the 2003 ACM Symposium on Software Visualization}, 16171 year = {2003}, 16172 pages = {67--76} 16173} 16174 16175@Book{ tiller01, 16176 author = {M. Tiller}, 16177 title = {Introduction to Physical System Modeling with Modelica}, 16178 series = {Kluwer International Series inEngineering and Computer Science}, 16179 volume = {615}, 16180 publisher = {Kluwer}, 16181 year = {2001} 16182} 16183 16184@Article{ buck94, 16185 author = {J. Buck and S. Ha and E. Lee and D. Messerschmitt}, 16186 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 16187 journal = {Int. Journal of Computer Simulation}, 16188 volume = {4}, 16189 pages = {155--182}, 16190 year = {1994} 16191} 16192 16193@Article{ mu95, 16194 author = {M. Mu and J.R. Rice}, 16195 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 16196 journal = {Comp. Syst. Engr.}, 16197 volume = {6}, 16198 year = {1995}, 16199 pages = {87--95} 16200} 16201 16202@TechReport{ drashansky96, 16203 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 16204 author = {R. Drashansky and A. Joshi and J. R. Rice}, 16205 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 16206 year = {1996} 16207} 16208 16209@Article{ michopoulos05, 16210 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 16211 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 16212 journal = {Journal of Computing and Information Science in Engineering}, 16213 volume = {5}, 16214 issue = {3}, 16215 pages = {198--213}, 16216 year = {2005} 16217} 16218 16219@Article{ dubey09, 16220 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16221 Multiphysics Simulation Code}, 16222 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16223 Siegel and K. Weide}, 16224 journal = {Parallel Computing}, 16225 volume = {35}, 16226 issue = {10 -- 11}, 16227 pages = {512 -- 522}, 16228 year = {2009} 16229} 16230 16231@Book{ bottloring95, 16232 author = {Raoul Bott and Loring W. Tu}, 16233 title = {Differential Forms in Algebraic Topology}, 16234 publisher = {Springer}, 16235 year = {1995} 16236} 16237 16238@Book{ kobayashinomizu96, 16239 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16240 title = {Foundations of Differential Geometry}, 16241 publisher = {Wiley-Interscience}, 16242 year = {1996} 16243} 16244 16245@Article{ hornungkohn02, 16246 author = {Richard D. Hornung and Scott R. Kohn}, 16247 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16248 journal = {Concurrency and Computation: Practice and Experience}, 16249 volume = {14}, 16250 pages = {347--368}, 16251 year = {2002} 16252} 16253 16254@InProceedings{ concepts06, 16255 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16256 Gabriel Dos Reis and Andrew Lumsdaine}, 16257 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16258 booktitle = {Proceedings of OOPSLA 2006}, 16259 year = {2006}, 16260 pages = {???--???} 16261} 16262 16263@Book{ hatcher02, 16264 author = {Hatcher, Allen}, 16265 title = {Algebraic Topology}, 16266 publisher = {Cambridge University Press}, 16267 year = {2002} 16268} 16269 16270@Book{ gammahelmjohnsonvlissides95, 16271 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16272 development, offering timeless and elegant solutions to common problems in 16273 software design. It describes patterns for managing object creation, composing 16274 objects into larger structures, and coordinating control flow between objects. The 16275 book provides numerous examples where using composition rather than inheritance 16276 can improve the reusability and flexibility of code. Note, though, that it's not a 16277 tutorial but a catalog that you can use to find an object-oriented design pattern 16278 that's appropriate for the needs of your particular application--a selection for 16279 virtuoso programmers who appreciate (or require) consistent, well-engineered 16280 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16281 more valuable than ever! 16282 16283 Use the contents of the CD to create your own design documents and reusable 16284 components. The CD contains: 23 patterns you can cut and paste into your own 16285 design documents; sample code demonstrating pattern implementation; complete 16286 Design Patterns content in standard HTML format, with numerous hyperlinked 16287 cross-references; accessed through a standard web browser; Java-based dynamic 16288 search mechanism, enhancing online search capabilities; graphical user environment, 16289 allowing ease of navigation. 16290 16291 First published in 1995, this landmark work on object-oriented software design 16292 presents a catalog of simple and succinct solutions to common design problems. 16293 Created by four experienced designers, the 23 patterns contained herein have 16294 become an essential resource for anyone developing reusable object-oriented 16295 software. In response to reader demand, the complete text and pattern catalog are 16296 now available on CD-ROM. This electronic version of Design Patterns enables 16297 programmers to install the book directly onto a computer or network for use as an 16298 online reference for creating reusable object-oriented software. 16299 16300 The authors first describe what patterns are and how they can help you in the 16301 design process. They then systematically name, explain, evaluate, and catalog 16302 recurring designs in object-oriented systems. All patterns are compiled from 16303 real-world examples and include code that demonstrates how they may be implemented 16304 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16305 already own the book will want the CD to take advantage of its dynamic search 16306 mechanism and ready-to-install patterns.}}, 16307 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16308 citeulike-article-id={115158}, 16309 howpublished = {Hardcover}, 16310 isbn = {0201633612}, 16311 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16312 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16313 four gang gof java mathgamespatterns no-tag object object-orientation 16314 object-oriented of oo-patterns oop oriented pattern patterns programming se 16315 software software-development software-engineering software_design 16316 softwareengineering standard}, 16317 month = jan, 16318 publisher = {{Addison-Wesley Professional}}, 16319 title = {Design Patterns}, 16320 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16321 year = {1995} 16322} 16323 16324@InProceedings{ chaco95, 16325 author = {Bruce Hendrickson and Robert Leland}, 16326 title = {A multilevel algorithm for partitioning graphs}, 16327 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16328 (CDROM)}, 16329 year = {1995}, 16330 isbn = {0-89791-816-9}, 16331 pages = {28}, 16332 location = {San Diego, California, United States}, 16333 doi = {10.1145/224170.224228}, 16334 publisher = {ACM Press}, 16335 address = {New York} 16336} 16337 16338@Book{ aleksandrov98, 16339 author = {Aleksandrov, Pavel S.}, 16340 title = {Combinatorial Topology}, 16341 publisher = {Dover}, 16342 volume = {3}, 16343 year = {1998} 16344} 16345 16346@Book{ steenrod99, 16347 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16348 importance in modern physics--such as in gauge theory. This book, a succinct 16349 introduction to the subject by renown mathematician Norman Steenrod, was the first 16350 to present the subject systematically. 16351 16352 It begins with a general introduction to bundles, including such topics as 16353 differentiable manifolds and covering spaces. The author then provides brief 16354 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16355 using them to study further properties of fibre bundles. The result is a classic 16356 and timeless work of great utility that will appeal to serious mathematicians and 16357 theoretical physicists alike. }}, 16358 author = {Steenrod, Norman}, 16359 citeulike-article-id={712999}, 16360 howpublished = {Paperback}, 16361 isbn = {0691005486}, 16362 keywords = {fibre_bundles topology}, 16363 month = apr, 16364 publisher = {{Princeton University Press}}, 16365 title = {The Topology of Fibre Bundles. (PMS-14)}, 16366 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16367 year = {1999} 16368} 16369 16370@Book{ bredon97, 16371 author = {Bredon, Glen E.}, 16372 title = {Sheaf Theory}, 16373 publisher = {Springer}, 16374 pages = {524}, 16375 series = {Graduate Texts in Mathematics}, 16376 year = {1997} 16377} 16378 16379@TechReport{ tautgesmeyers04, 16380 title = {{MOAB}: A Mesh-Oriented Database}, 16381 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16382 Ernst}, 16383 institution = {Sandia National Laboratories}, 16384 number = {SAND2004-1592}, 16385 month = apr, 16386 year = {2004} 16387} 16388 16389@Article{ tautges04, 16390 author = {Timothy J. Tautges}, 16391 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16392 journal = {Engineering With Computers}, 16393 volume = {20}, 16394 pages = {286--293}, 16395 year = {2004} 16396} 16397 16398@InProceedings{ meyers02, 16399 author = {Ray Meyers et. al}, 16400 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16401 booktitle = {8th International conference on numerical grid generation in computational field 16402 simulations}, 16403 month = jun, 16404 year = {2002} 16405} 16406 16407@InProceedings{ seolshepard05, 16408 author = {E. S. Seol and Mark S. Shephard}, 16409 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16410 Analysis}, 16411 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16412 year = {2005} 16413} 16414 16415@Article{ lishephardbeall2005, 16416 title = {3D anisotropic mesh adaptation by mesh modification}, 16417 author = {Xiangrong Li and Mark S Shephard and Mark W Beall}, 16418 journal = {Computer methods in applied mechanics and engineering}, 16419 volume = {194}, 16420 number = {48-49}, 16421 pages = {4915--4950}, 16422 year = {2005}, 16423} 16424 16425@Article{ lushephardtendulkarbeall2014, 16426 title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry}, 16427 author = {Qiukai Lu and Mark S Shephard and Saurabh Tendulkar and Mark W Beall}, 16428 journal = {Engineering with Computers}, 16429 volume = {30}, 16430 pages = {271--286}, 16431 year = {2014}, 16432} 16433 16434@Article{ beallwalshshephard04, 16435 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16436 title = {A comparison of techniques for geometry access related to mesh generation}, 16437 journal = {Engineering With Computers}, 16438 volume = {20}, 16439 number = {3}, 16440 pages = {210--221}, 16441 year = {2004} 16442} 16443 16444@Article{ careyandersoncarneskirk04, 16445 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16446 Kirk}, 16447 title = {Some aspects of adaptive grid technology related to boundary and interior 16448 layers}, 16449 journal = {Journal of Computational Applied Mathematics}, 16450 volume = {166}, 16451 number = {1}, 16452 pages = {55--86}, 16453 year = {2004} 16454} 16455 16456@PhDThesis{ gralthesis, 16457 author = {Guntram Berti}, 16458 title = {Generic Software Components for Scientific Computing}, 16459 school = {TU Cottbus}, 16460 year = {2000}, 16461 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16462} 16463 16464@Article{ whitehead1949, 16465 title = {Combinatorial homotopy. I}, 16466 author = {John HC Whitehead}, 16467 journal = {Bulletin of the American Mathematical Society}, 16468 volume = {55}, 16469 number = {3. P1}, 16470 pages = {213--245}, 16471 year = {1949}, 16472 publisher = {American Mathematical Society} 16473} 16474 16475@Article{ beylkincoifmanrokhlin91, 16476 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16477 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16478 journal = {Communications on Pure and Applied Mathematics}, 16479 volume = {44}, 16480 pages = {141--183}, 16481 year = {1991} 16482} 16483 16484@Book{ wesseling92, 16485 author = {Pieter Wesseling}, 16486 title = {An Introduction to Multigrid Methods}, 16487 publisher = {John Wiley and Sons}, 16488 year = {1992} 16489} 16490 16491@Book{ grakakos04, 16492 author = {Loukas Grakakos}, 16493 title = {Classical and Modern Fourier Analysis}, 16494 publisher = {Pearson Education}, 16495 address = {New Jersey}, 16496 year = {2004} 16497} 16498 16499@Misc{ hlib-web-page, 16500 key = {HLib}, 16501 title = {{HLib} {Web} page}, 16502 note = {{\texttt{http://www.hlib.org/}}}, 16503 annote = {Hierarchical matrices for fast integral transform} 16504} 16505 16506@Article{ hackbusch99, 16507 author = {Wolfgang Hackbusch}, 16508 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16509 Introduction to {$\mathcal H$}-matrices}, 16510 journal = {Computing}, 16511 volume = {62}, 16512 pages = {89--108}, 16513 year = {1999} 16514} 16515 16516@TechReport{ kay1999green, 16517 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16518 equations}, 16519 author = {Kay, D. and Loghin, D.}, 16520 year = {1999}, 16521 institution = {Oxford University Computing Laboratory}, 16522 number = {99/06} 16523} 16524 16525@Article{ bebendorf2003existence, 16526 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16527 elliptic operators with {$L^\infty$}-coefficients}, 16528 author = {Bebendorf, M. and Hackbusch, W.}, 16529 journal = {Numerische Mathematik}, 16530 volume = {95}, 16531 number = {1}, 16532 pages = {1--28}, 16533 year = {2003}, 16534 publisher = {Springer} 16535} 16536 16537@Article{ hackbusch2005direct, 16538 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16539 H$}-matrix approximation}, 16540 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16541 journal = {Computing and Visualization in Science}, 16542 volume = {8}, 16543 number = {3}, 16544 pages = {179--188}, 16545 year = {2005}, 16546 publisher = {Springer} 16547} 16548 16549@TechReport{ duphof2003, 16550 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16551 Logg and L. R. Scott}, 16552 title = {The {FE}ni{CS} project}, 16553 institution = {Chalmers Finite Element Center Preprint Series}, 16554 number = {2003--21}, 16555 year = {2003} 16556} 16557 16558@Article{ flame01, 16559 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16560 Geijn}, 16561 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16562 journal = {Transactions on Mathematical Software}, 16563 volume = {27}, 16564 number = {4}, 16565 year = {2001}, 16566 pages = {422--455} 16567} 16568 16569@Article{ puschel05, 16570 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16571 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16572 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16573 Nick Rizzolo}, 16574 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16575 journal = {Proceedings of the IEEE}, 16576 volume = {93}, 16577 number = {2}, 16578 year = {2005}, 16579 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16580} 16581 16582@Article{ kirbylogg06, 16583 author = {Robert C. Kirby and Anders Logg}, 16584 title = {A compiler for variational forms}, 16585 journal = {ACM Transactions on Mathematical Software}, 16586 volume = {32}, 16587 number = {3}, 16588 year = {2006}, 16589 issn = {0098-3500}, 16590 pages = {417--444}, 16591 doi = {10.1145/1163641.1163644}, 16592 publisher = {ACM Press}, 16593 address = {New York, NY} 16594} 16595 16596@Article{ kirbylogg07, 16597 author = {Robert C. Kirby and Anders Logg}, 16598 title = {Efficient compilation of a class of variational forms}, 16599 journal = {ACM Transactions on Mathematical Software}, 16600 volume = {33}, 16601 number = {3}, 16602 year = {2007}, 16603 issn = {0098-3500}, 16604 pages = {17}, 16605 doi = {10.1145/1268769.1268771}, 16606 publisher = {ACM Press}, 16607 address = {New York, NY} 16608} 16609 16610@Article{ bankdupont81, 16611 author = {Randolph Bank and Todd Dupont}, 16612 title = {An optimal order process for solving finite element equations}, 16613 journal = {Mathematics of Computation}, 16614 volume = {36}, 16615 pages = {35--51}, 16616 year = {1981} 16617} 16618 16619@TechReport{ adams00, 16620 author = {Mark F. Adams}, 16621 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16622 in solid mechanics}, 16623 institution = {UC Berkeley}, 16624 number = {CSD-00-1103}, 16625 year = {2000}, 16626 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16627} 16628 16629@Article{ bergengradlhuelsemannruede06, 16630 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16631 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16632 journal = {Computing in Science \& Engineering}, 16633 volume = {8}, 16634 number = {6}, 16635 pages = {56--62}, 16636 year = {2006} 16637} 16638 16639@MastersThesis{ brunethesis08, 16640 author = {Peter R. Brune}, 16641 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16642 school = {University of Chicago}, 16643 address = {Chicago, IL}, 16644 year = {2008}, 16645 month = feb 16646} 16647 16648@Article{ arnoldwinther02, 16649 author = {Douglas N. Arnold and Ragnar Winther}, 16650 title = {Mixed finite elements for elasticity}, 16651 journal = {Numerische Mathematik}, 16652 volume = {92}, 16653 number = {3}, 16654 month = sep, 16655 year = {2002}, 16656 pages = {401--419}, 16657 doi = {10.1007/s002110100348} 16658} 16659 16660@Article{ arnoldfalkwinther06, 16661 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16662 title = {Finite element exterior calculus, homological techniques, and applications}, 16663 journal = {Acta Numerica}, 16664 year = {2006}, 16665 volume = {15}, 16666 pages = {1--155}, 16667 publisher = {Cambridge University Press}, 16668 doi = {10.1017/S0962492906210018} 16669} 16670 16671@Article{ kirby04, 16672 author = {Robert C. Kirby}, 16673 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 16674 functions}, 16675 journal = {ACM Transactions on Mathematical Software}, 16676 volume = {30}, 16677 number = {4}, 16678 year = {2004}, 16679 issn = {0098-3500}, 16680 pages = {502--516}, 16681 doi = {10.1145/1039813.1039820}, 16682 publisher = {ACM Press}, 16683 address = {New York, NY} 16684} 16685 16686@Article{ kirby06, 16687 author = {Robert C. Kirby}, 16688 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16689 journal = {ACM Transactions on Mathematical Software}, 16690 volume = {32}, 16691 number = {2}, 16692 year = {2006}, 16693 issn = {0098-3500}, 16694 pages = {223--235}, 16695 doi = {10.1145/1141885.1141889}, 16696 publisher = {ACM Press}, 16697 address = {New York, NY} 16698} 16699 16700@Misc{ bluecrystal08, 16701 author = {{B}lue {C}rystal Cluster}, 16702 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16703 year = {2008}, 16704 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16705} 16706 16707@Article{ beylkin95, 16708 author = {Gregory Beylkin}, 16709 title = {On the Fast Fourier Transform of Functions With Singularities}, 16710 journal = {Applied and Computational Harmonic Analysis}, 16711 volume = {2}, 16712 pages = {363--381}, 16713 year = {1995} 16714} 16715 16716@InProceedings{ riehl08, 16717 author = {Jonathan Riehl}, 16718 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16719 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16720 Development (DSPD'08)}, 16721 address = {Nashville, TN}, 16722 year = {2008} 16723} 16724 16725@Article{ appel85, 16726 author = {Andrew W. Appel}, 16727 date-added = {2008-02-27 12:23:39 +0000}, 16728 date-modified = {2008-02-27 12:24:02 +0000}, 16729 doi = {10.1137/0906008}, 16730 journal = {SIAM Journal on Scientific and Statistical Computing}, 16731 keywords = {treecodes}, 16732 number = {1}, 16733 pages = {85-103}, 16734 publisher = {SIAM}, 16735 title = {An Efficient Program for Many-Body Simulation}, 16736 volume = {6}, 16737 year = {1985} 16738} 16739 16740@Article{ ewald21, 16741 author = {{Ewald}, P.~P.}, 16742 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 16743 journal = {Annalen der Physik}, 16744 year = {1921}, 16745 volume = {369}, 16746 pages = {253-287}, 16747 doi = {10.1002/andp.19213690304}, 16748 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 16749 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16750} 16751 16752@Article{ greengardrokhlin87, 16753 author = {L. Greengard and V. 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Wang}, 16810 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 16811 equation on massively parallel computers}, 16812 journal = {Journal of Computational Chemistry}, 16813 volume = {21}, 16814 year = {2000} 16815} 16816 16817@Book{ hockneyeastwood81, 16818 author = {R. Hockney and J. Eastwood}, 16819 title = {Computer simulation using particles}, 16820 publisher = {McGraw-Hill}, 16821 address = {New York}, 16822 year = {1981} 16823} 16824 16825@Article{ lutydavistironigunsteren94, 16826 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. 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Chu}, 16892 bibdate = {Wed Jan 07 15:23:19 1998}, 16893 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16894} 16895 16896@Article{ liptonreagan2014, 16897 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16898 author = {Richard J Lipton and Kenneth W Regan}, 16899 pages = {206}, 16900 isbn = {978-0-26202-839-4}, 16901 year = {2014} 16902} 16903 16904@InProceedings{ rhea08, 16905 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16906 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16907 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16908 booktitle = {Proceedings of IEEE/ACM SC '08}, 16909 year = {2008} 16910} 16911 16912@Misc{ bursteddewilcox09, 16913 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16914 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16915 note = {in preparation} 16916} 16917 16918@Article{ skeeltezcanhardy02, 16919 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16920 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16921 journal = {J. Comp. Chem.}, 16922 volume = {23}, 16923 pages = {673--684}, 16924 year = {2002} 16925} 16926 16927@Article{ verschelde99, 16928 author = {Jan Verschelde}, 16929 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16930 homotopy continuation}, 16931 journal = {ACM Trans. Math. Softw.}, 16932 volume = {25}, 16933 number = {2}, 16934 issn = {0098-3500}, 16935 pages = {251--276}, 16936 doi = {10.1145/317275.317286}, 16937 publisher = {ACM}, 16938 address = {New York, NY}, 16939 year = {1999} 16940} 16941 16942@InProceedings{ sommeseverscheldewampler08, 16943 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16944 title = {Solving Polynomial Systems Equation by Equation}, 16945 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16946 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16947 pages = {133--152}, 16948 publisher = {Springer-Verlag}, 16949 year = {2008} 16950} 16951 16952@Article{ phanthientanner77, 16953 author = {N. Phan-Thien and R.~I. Tanner}, 16954 title = {A new constitutive equation derived from network theory}, 16955 journal = {J. Non-Newt. Fluid Mech.}, 16956 volume = {2}, 16957 pages = {353}, 16958 year = {1977} 16959} 16960 16961@Manual{ sage, 16962 key = {SAGE}, 16963 author = {W.\thinspace{}A. Stein and others}, 16964 organization = {The Sage~Development Team}, 16965 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16966 note = {{\tt http://www.sagemath.org}}, 16967 year = {2009} 16968} 16969 16970@Misc{ bateshauensteinsommesewampler06, 16971 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16972 Wampler}, 16973 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16974 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16975} 16976 16977@Article{ archer09, 16978 author = {A. J. Archer}, 16979 collaboration = {}, 16980 title = {Dynamical density functional theory for molecular and colloidal fluids: A 16981 microscopic approach to fluid mechanics}, 16982 publisher = {AIP}, 16983 year = {2009}, 16984 journal = {The Journal of Chemical Physics}, 16985 volume = {130}, 16986 number = {1}, 16987 eid = {014509}, 16988 numpages = {8}, 16989 pages = {014509}, 16990 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 16991 transition; statistical distributions; stochastic processes}, 16992 doi = {10.1063/1.3054633} 16993} 16994 16995@Article{ giesekus1966, 16996 author = {Hanswalter Giesekus}, 16997 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 16998 journal = {Rheologica Acta}, 16999 publisher = {Springer Berlin / Heidelberg}, 17000 volume = {5}, 17001 number = {1}, 17002 month = mar, 17003 year = {1966}, 17004 doi = {10.1007/BF01973575}, 17005 pages = {29-35} 17006} 17007 17008@Article{ baaijens98, 17009 author = {F.P. Baaijens}, 17010 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 17011 journal = {Journal of Non-Newtonian Fluid Mechanics}, 17012 volume = {79}, 17013 year = {1998}, 17014 pages = {361--385} 17015} 17016 17017@Book{ joseph90, 17018 author = {D.~D. Joseph}, 17019 title = {Fluid Dynamics of Viscoelastic Liquids}, 17020 publisher = {Springer}, 17021 address = {New York, NY}, 17022 year = {1990} 17023} 17024 17025@Article{ oldroyd50, 17026 author = {J.~G. Oldroyd}, 17027 title = {On the Formulation of Rheological Equations of State}, 17028 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 17029 Sciences}, 17030 volume = {200}, 17031 year = {1950}, 17032 pages = {523--541} 17033} 17034 17035@InProceedings{ bynasungroppthakur04, 17036 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 17037 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 17038 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 17039 year = {2004} 17040} 17041 17042@Book{ pozrikidis07, 17043 author = {C. Pozrikidis}, 17044 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 17045 publisher = {Kluwer (Springer)}, 17046 pages = {675}, 17047 year = {2001}, 17048 isbn = {0792373510} 17049} 17050 17051@Misc{ kritzkeyesfsp07, 17052 author = {A. Kritz and D. Keyes}, 17053 title = {{Fusion Simulation Project Workshop Report}}, 17054 month = jul, 17055 year = {2007}, 17056 note = {Available via 17057 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 17058} 17059 17060@Misc{ dahlburg02, 17061 author = {J. {Dahlburg (Chair)}}, 17062 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 17063 year = {2002}, 17064 note = {Available via 17065 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 17066} 17067 17068@Misc{ brown08, 17069 author = {D. {Brown (Chair)}}, 17070 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 17071 to the Future}}, 17072 year = {2008}, 17073 howpublished = {Office of Science, U.S. Department of Energy}, 17074 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 17075} 17076 17077@Misc{ crosscutting10, 17078 author = {D. Brown and P. {Messina (Chairs)}}, 17079 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 17080 Exascale}}, 17081 year = {2010}, 17082 howpublished = {Office of Science, U.S. Department of Energy}, 17083 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 17084} 17085 17086@Misc{ extreme-scale-solvers-workshop12, 17087 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 17088 L.C. McInnes and E. Ng and S. Wild}, 17089 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 17090 Architectures}, 17091 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 17092 note = {{Washington, DC}, March 8-9, 2012}, 17093 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 17094 year = {2012} 17095} 17096 17097@Misc{ monizrosner09, 17098 author = {{E. Moniz and R. Rosner}}, 17099 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 17100 and Simulation at the Extreme Scale}}, 17101 month = may, 17102 year = {2009}, 17103 note = {See 17104 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 17105} 17106 17107@Misc{ blanford08, 17108 author = {{R. Blandord (Chair)}}, 17109 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 17110 Computing at the Extreme Scale}}, 17111 month = dec, 17112 year = {2008}, 17113 note = {See 17114 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 17115} 17116 17117@Misc{ exascale07, 17118 author = {H. Simon and T. Zacharia and R. Stevens}, 17119 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 17120 year = {2007}, 17121 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 17122} 17123 17124@Misc{ ascrbreakthroughs08, 17125 author = {{Panel on Recent Significant Advancements in Computational Science}}, 17126 title = {Breakthroughs}, 17127 year = {2008}, 17128 note = {See 17129 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 17130} 17131 17132@Misc{ petsc-rd100-2009, 17133 author = {{R\&D Magazine}}, 17134 title = {{PETSc} {R}\&{D} 100 Award}, 17135 year = {2009}, 17136 note = {See 17137 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 17138} 17139 17140@Article{ compass-scidac08, 17141 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 17142 R. Ryne}, 17143 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 17144 Computational Science for Future Accelerators and Accelerator Technologies}, 17145 journal = {J. Phys.: Conf. Ser.}, 17146 volume = {125}, 17147 year = {2008}, 17148 pages = {012001}, 17149 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 17150} 17151 17152@Article{ compass-amundson-scidac08, 17153 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 17154 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 17155 Stoltz}, 17156 journal = {J. Phys.: Conf. Ser.}, 17157 volume = {125}, 17158 year = {2008} 17159} 17160 17161@InProceedings{ muszala09, 17162 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 17163 Simulations}, 17164 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 17165 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 17166 {(CBHPC 2009)}}, 17167 year = {2009} 17168} 17169 17170@Article{ gaston09, 17171 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 17172 Equations}, 17173 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 17174 journal = {Nuclear Engineering and Design}, 17175 volume = {239}, 17176 number = {10}, 17177 year = {2009}, 17178 pages = {1768 -- 1778} 17179} 17180 17181@Article{ gaston09b, 17182 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 17183 Engineering}, 17184 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 17185 and C. Permann and W. Taitano}, 17186 journal = {J. Phys.: Conf. Ser.}, 17187 volume = {180}, 17188 year = {2009}, 17189 pages = {012012} 17190} 17191 17192@Article{ newman09, 17193 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 17194 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 17195 author = {Chris Newman and Glen Hansen and Derek Gaston}, 17196 journal = {Journal of Nuclear Materials}, 17197 volume = {392}, 17198 issue = {1}, 17199 year = {2009}, 17200 pages = {6 -- 15} 17201} 17202 17203@Misc{ www:fenics, 17204 author = {{FE}ni{CS}}, 17205 title = {{FE}ni{CS} Project}, 17206 howpublished = {\url{http://www.fenics.org/}}, 17207 year = {2018} 17208} 17209 17210@InProceedings{ zwart08, 17211 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 17212 Systems}, 17213 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 17214 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 17215 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 17216 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 17217 booktitle = {Proceedings of ICCS 2008}, 17218 year = {2008} 17219} 17220 17221@Article{ klocknerwarburtonbridgehesthaven09, 17222 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 17223 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 17224 journal = {J. Comput. Phys.}, 17225 volume = {228}, 17226 number = {21}, 17227 year = {2009}, 17228 issn = {0021-9991}, 17229 pages = {7863--7882}, 17230 doi = {10.1016/j.jcp.2009.06.041}, 17231 publisher = {Academic Press Professional}, 17232 address = {San Diego, CA} 17233} 17234 17235@PhDThesis{ rankin99, 17236 author = {Rankin, W. T.}, 17237 keywords = {FMM, parallel FMM}, 17238 school = {Department of Electrical and Computer Engineering, Duke University}, 17239 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17240 year = {1999} 17241} 17242 17243@InProceedings{ warrensalmon93, 17244 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17245 and implemented. The algorithm computes the forces on an arbitrary distribution of 17246 bodies in a time which scales as N log N with the particle number. The accuracy of 17247 the force calculations is analytically bounded, and can be adjusted via a user 17248 defined parameter between a few percent relative accuracy, down to machine 17249 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17250 tree, we identify...}, 17251 address = {New York}, 17252 author = {Warren, Michael S. and Salmon, John K.}, 17253 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17254 citeulike-article-id={580952}, 17255 keywords = {oct-tree}, 17256 pages = {12--21}, 17257 publisher = {ACM}, 17258 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17259 year = {1993}, 17260 doi = {10.1145/169627.169640}, 17261 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17262} 17263 17264@Unpublished{ cruzwccm10, 17265 author = {Felipe A. Cruz}, 17266 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17267 note = {Presentation at WCCM 2010, Sydney Australia}, 17268 year = {2010} 17269} 17270 17271@Article{ mcguffee06, 17272 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17273 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17274 of salt, {pH}, point mutations, and protein concentration in simulations of 17275 1000-molecule systems}, 17276 journal = {Journal of the American Chemical Society}, 17277 volume = {128}, 17278 pages = {12098--12110}, 17279 year = {2006} 17280} 17281 17282@Article{ nilsencaihoylandlangtangen10, 17283 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17284 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17285 in Python}}, 17286 journal = {ArXiv e-prints}, 17287 archiveprefix = {arXiv}, 17288 eprint = {1002.0705}, 17289 primaryclass = {cs.DC}, 17290 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17291 - Programming Languages}, 17292 year = {2010}, 17293 month = feb, 17294 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17295 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17296} 17297 17298@Misc{ mcinnes:siam09:minisymposium, 17299 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17300 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17301 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17302 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17303 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17304 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17305 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17306 Austin).} 17307} 17308 17309@Misc{ mcinnes:fsp-summary:feb2011, 17310 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17311 title = {Solvers and Time Integration Breakout Summary}, 17312 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17313 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17314} 17315 17316@Misc{ dvi-materials:siamcse11, 17317 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17318 Materials}, 17319 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17320 Smith and L. Wang}, 17321 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17322 and Engineering, March 3, 2011} 17323} 17324 17325@Misc{ jamroz:cemm10, 17326 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17327 author = {B. Jamroz and S. Kruger and T. Austin}, 17328 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17329} 17330 17331@Misc{ kruger:feb4-2011, 17332 title = {personal communication}, 17333 author = {S. Kruger}, 17334 note = {February, 2011} 17335} 17336 17337@Article{ elman1996, 17338 author = {H.C. Elman}, 17339 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17340 viscosity}, 17341 journal = {SIAM J. Sci. Comput.}, 17342 volume = {20}, 17343 year = {1996}, 17344 pages = {1299--1316} 17345} 17346 17347@Article{ kayloghinwathen2002, 17348 author = {D. Kay and D. Loghin and A. Wathen}, 17349 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17350 journal = {SIAM J. Sci. Comput.}, 17351 volume = {24}, 17352 year = {2002}, 17353 pages = {237--256} 17354} 17355 17356@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17357 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17358 title = {Block preconditioners based on approximate commutators}, 17359 journal = {SIAM J. Sci. Comput.}, 17360 volume = {27}, 17361 number = {5}, 17362 year = {2006}, 17363 pages = {1651--1668} 17364} 17365 17366@Article{ braesssarazin1997, 17367 author = {Dietrich Braess and Regina Sarazin}, 17368 title = {An efficient smoother for the {Stokes} problem}, 17369 journal = {Applied Numerical Mathematics}, 17370 volume = {23}, 17371 number = {1}, 17372 year = {1997}, 17373 pages = {3--19}, 17374 doi = {10.1016/S0168-9274(96)00059-1} 17375} 17376 17377@Article{ wright2001large, 17378 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17379 author = {Wright, T.G. and Trefethen, L.N.}, 17380 journal = {SIAM Journal on Scientific Computing}, 17381 volume = {23}, 17382 pages = {591}, 17383 year = {2001} 17384} 17385 17386@Misc{ wright2002eigtool, 17387 title = {Eig{T}ool}, 17388 author = {Wright, T.G. and Trefethen, LN}, 17389 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17390 year = {2002} 17391} 17392 17393@Misc{ visit-web-site, 17394 key = {{VisIt}}, 17395 title = {{VisIt web site}}, 17396 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17397 url = {http://wci.llnl.gov/codes/visit/}, 17398 year = {2011} 17399} 17400 17401@Book{ trefethen1996, 17402 title = {Finite difference and spectral methods for ordinary and partial differential 17403 equations}, 17404 author = {Lloyd Nicholas Trefethen}, 17405 year = {1996}, 17406 publisher = {Cornell University-Department of Computer Science and Center for Applied 17407 Mathematics} 17408} 17409 17410@Book{ trefethen2005spectra, 17411 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17412 author = {Trefethen, L.N. and Embree, M.}, 17413 year = {2005}, 17414 publisher = {Princeton University Press} 17415} 17416 17417@Article{ gomez2010isogeometric, 17418 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17419 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17420 journal = {Computer Methods in Applied Mechanics and Engineering}, 17421 volume = {199}, 17422 number = {25-28}, 17423 pages = {1828--1840}, 17424 issn = {0045-7825}, 17425 year = {2010}, 17426 publisher = {Elsevier} 17427} 17428 17429@Article{ gomez2008isogeometric, 17430 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17431 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17432 journal = {Computer Methods in Applied Mechanics and Engineering}, 17433 volume = {197}, 17434 number = {49-50}, 17435 pages = {4333--4352}, 17436 year = {2008}, 17437 publisher = {Elsevier} 17438} 17439 17440@Misc{ fastmath:project, 17441 author = {Lori {Diachin (PI)}}, 17442 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17443 (FASTMath) Institute}}, 17444 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17445} 17446 17447@Misc{ exascale-software:proposal, 17448 author = {Peter {Beckman (PI)}}, 17449 title = {{Exascale Software Center}}, 17450 note = {proposal to DOE} 17451} 17452 17453@Misc{ imex:project, 17454 author = {Barry {Smith (PI)}}, 17455 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17456 Multimodel PDEs}}, 17457 note = {DOE ASCR applied math project} 17458} 17459 17460@Misc{ intel-mic:website, 17461 author = {Intel}, 17462 title = {{Many Integrated Core Architecture}}, 17463 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17464} 17465 17466@Article{ dudson:2009, 17467 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17468 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17469 journal = {Computer Physics Communications}, 17470 volume = {180}, 17471 pages = {1467}, 17472 year = {2009} 17473} 17474 17475@Article{ umansky:2009, 17476 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17477 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17478 journal = {Computer Physics Communications}, 17479 year = {2009}, 17480 volume = {180}, 17481 pages = {887-903} 17482} 17483 17484@Article{ xu:1998, 17485 author = {X.Q. Xu and R.H. Cohen}, 17486 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17487 journal = {Computer Physics Communications}, 17488 year = {1998}, 17489 volume = {36}, 17490 number = {1-2}, 17491 pages = {158} 17492} 17493 17494@Article{ tron:1999, 17495 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17496 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17497 journal = {SIAM Journal on Optimization}, 17498 volume = {9}, 17499 number = {4}, 17500 pages = {1100-1127}, 17501 year = {1999} 17502} 17503 17504@Article{ stubenamg, 17505 author = {K. St\"{u}ben}, 17506 title = {A review of algebraic multigrid}, 17507 journal = {J. Comput. Appl. Math.}, 17508 volume = {128}, 17509 number = {1-2}, 17510 year = {2001}, 17511 issn = {0377-0427}, 17512 pages = {281--309}, 17513 doi = {10.1016/S0377-0427(00)00516-1}, 17514 publisher = {Elsevier Science Publishers B. V.}, 17515 address = {Amsterdam, The Netherlands, The Netherlands} 17516} 17517 17518@Article{ feuchtermg, 17519 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17520 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17521 journal = {Computing and visualization in science}, 17522 publisher = {Springer}, 17523 volume = {6}, 17524 number = {1}, 17525 year = {2003}, 17526 pages = {1--13} 17527} 17528 17529@Article{ chowmgsmoothness, 17530 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17531 only attempts to interpolate in the directions of geometrical smoothness. These 17532 directions are determined by analyzing samples of algebraically smooth error, e. 17533 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17534 consistently nearby in value. In addition, these dierences may be used to dene 17535 interpolation weights. These new ideas may be incorporated into the algebraic 17536 multigrid method. Test results show that the new method can have much lower grid 17537 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17538 author = {Chow, Edmond}, 17539 citeulike-article-id={7675372}, 17540 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17541 journal = {American Journal of Mathematics}, 17542 keywords = {fem, multigrid}, 17543 pages = {197--215}, 17544 posted-at = {2010-08-17 23:29:51}, 17545 priority = {2}, 17546 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17547 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17548 volume = {65}, 17549 year = {2001} 17550} 17551 17552@Article{ jonesamge, 17553 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17554 elements) method based on element agglomeration. In the method, coarse grid 17555 elements are formed by agglomerating fine grid elements. Compatible interpolation 17556 operators are constructed which yield coarse grid basis functions with a minimal 17557 energy property. Heuristics based on interpolation quality measures are used to 17558 guide the agglomeration procedure. The performance of the resulting method is 17559 demonstrated in two-level numerical experiments.}}, 17560 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17561 citeulike-article-id={8598569}, 17562 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17563 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17564 journal = {SIAM Journal on Scientific Computing}, 17565 keywords = {amg, fem, multigrid}, 17566 number = {1}, 17567 pages = {109--133}, 17568 posted-at = {2011-01-13 18:05:55}, 17569 priority = {2}, 17570 publisher = {SIAM}, 17571 title = {{AMGE Based on Element Agglomeration}}, 17572 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17573 volume = {23}, 17574 year = {2001} 17575} 17576 17577@Article{ saad1993, 17578 author = {Saad, Youcef}, 17579 doi = {10.1137/0914028}, 17580 issn = {10648275}, 17581 journal = {SIAM Journal on Scientific Computing}, 17582 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17583 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17584 precondition-,preconditioned conju-,subject classi cations,variable 17585 preconditioners}, 17586 number = {2}, 17587 pages = {461--469}, 17588 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17589 volume = {14}, 17590 year = {1993} 17591} 17592 17593@Misc{ path:homepage, 17594 author = {S. Dirkse and M. Ferris and T. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 17943} 17944 17945@Article{ keyesmcinneswoodwardetal13, 17946 title = {Multiphysics Simulations: Challenges and Opportunities}, 17947 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17948 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17949 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17950 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17951 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17952 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17953 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17954 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17955 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17956 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17957 journal = {International Journal of High Performance Computing Applications}, 17958 month = feb, 17959 year = {2013}, 17960 volume = {27}, 17961 number = {1}, 17962 pages = {4--83}, 17963 doi = {10.1177/1094342012468181}, 17964 note = {Special issue}, 17965 abstract = {We consider multiphysics applications from algorithmic and architectural 17966 perspectives, where ``algorithmic'' includes both mathematical analysis and 17967 computational complexity and ``architectural'' includes both software and hardware 17968 environments. Many diverse multiphysics applications can be reduced, en route to 17969 their computational simulation, to a common algebraic coupling paradigm. 17970 Mathematical analysis of multiphysics coupling in this form is not always 17971 practical for realistic applications, but model problems representative of 17972 applications discussed herein can provide insight. A variety of software 17973 frameworks for multiphysics applications have been constructed and refined within 17974 disciplinary communities and executed on leading-edge computer systems. We examine 17975 several of these, expose some commonalities among them, and attempt to extrapolate 17976 best practices to future systems. From our study, we summarize challenges and 17977 forecast opportunities.} 17978} 17979 17980@Misc{ rosner10, 17981 author = {Robert {Rosner (Chair)}}, 17982 title = {{The Opportunities and Challenges of Exascale Computing}}, 17983 year = {2010}, 17984 howpublished = {Office of Science, U.S. Department of Energy}, 17985 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17986} 17987 17988@Misc{ kogge2008exascale, 17989 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 17990 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 17991 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 17992 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 17993 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 17994 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 17995 howpublished = {DARPA}, 17996 year = {2008}, 17997 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 17998} 17999 18000@Misc{ doegrandchallengeworkshops, 18001 key = {Office of Science, U.S. Department of Energy}, 18002 title = {{Scientific Grand Challenges Workshop Series}}, 18003 howpublished = {Office of Science, U.S. Department of Energy, see 18004 \url{http://extremecomputing.labworks.org/workshops.stm}} 18005} 18006 18007@Misc{ lawrence2011, 18008 key = {Lawrence}, 18009 title = {{Ernest Orlando Lawrence Award Winners}}, 18010 howpublished = {U.S. Department of Energy, {\footnotesize 18011 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 18012 year = {2011} 18013} 18014 18015@Article{ murphy2000npi, 18016 title = {{A note on preconditioning for indefinite linear systems}}, 18017 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 18018 journal = {SIAM Journal on Scientific Computing}, 18019 volume = {21}, 18020 number = {6}, 18021 pages = {1969--1972}, 18022 year = {2000}, 18023 publisher = {Philadelphia, PA: SIAM, c1993-} 18024} 18025 18026@Article{ elman2011bouyancy, 18027 title = {Fast iterative solvers for buoyancy driven flow problems}, 18028 journal = {Journal of Computational Physics}, 18029 volume = {230}, 18030 number = {10}, 18031 pages = {3900 - 3914}, 18032 year = {2011}, 18033 note = {}, 18034 issn = {0021-9991}, 18035 doi = {10.1016/j.jcp.2011.02.014}, 18036 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 18037 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 18038 Adaptivity, Preconditioning, Algebraic multigrid} 18039} 18040 18041@Article{ dongarrabeckman11, 18042 author = {J. Dongarra and P. Beckman and et al.}, 18043 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 18044 journal = {Int. J. High Perf. Comput. 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P.}, 18559 eprint = {arXiv:1002.0705v1}, 18560 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 18561 parallelization of scientific codes by a function-centric approach in 18562 Python.pdf:pdf}, 18563 journal = {Computational Science \& Discovery}, 18564 keywords = {parallel,programming,python,software}, 18565 mendeley-tags = {parallel,programming,python,software}, 18566 pages = {015003}, 18567 publisher = {IOP Publishing}, 18568 title = {{Simplifying the parallelization of scientific codes by a function-centric 18569 approach in Python}}, 18570 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 18571 volume = {3}, 18572 year = {2010} 18573} 18574 18575@Book{ langtangen09, 18576 author = {Hans Petter Langtangen}, 18577 title = {Python Scripting for Computational Science}, 18578 publisher = {Springer}, 18579 series = {Texts in Computational Science and Engineering}, 18580 pages = {784}, 18581 isbn = {3540739157}, 18582 year = {2009} 18583} 18584 18585@Book{ numpyguide, 18586 author = {Travis E. Oliphant}, 18587 title = {Guide to {N}umpy}, 18588 publisher = {Trelgol}, 18589 year = {2008} 18590} 18591 18592@Misc{ pycuda, 18593 author = {Andreas Kl\"ockner}, 18594 title = {{PyCUDA}}, 18595 howpublished = {\url{http://mathema.tician.de/software/pycuda}}, 18596 year = {2011} 18597} 18598 18599@Misc{ pyopencl, 18600 author = {Andreas Kl\"ockner}, 18601 title = {{PyOpenCL}}, 18602 howpublished = {\url{http://mathema.tician.de/software/pyopencl}}, 18603 year = {2011} 18604} 18605 18606@Article{ klockner2012, 18607 author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and 18608 Paul Ivanov and Ahmed Fasih}, 18609 title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code 18610 generation}, 18611 journal = {Parallel Computing}, 18612 volume = {38}, 18613 number = {3}, 18614 pages = {157--174}, 18615 year = {2012}, 18616 issn = {0167-8191}, 18617 doi = {10.1016/j.parco.2011.09.001} 18618} 18619 18620%%%%%% Matt Stuff %%%%%% 18621@Article{ morrabozdagknepleyrassvesselinov, 18622 title = {A Tectonic Shift in Analytics and Computing Is Coming}, 18623 author = {Gabriele Morra and Ebru Bozdag and Matthew G. Knepley and Ludovic R\"ass and 18624 Velimir Vesselinov}, 18625 journal = {Eos}, 18626 volume = {102}, 18627 doi = {10.1029/2021EO159258}, 18628 month = {Jun}, 18629 year = {2021} 18630} 18631 18632@Misc{ knepley:icerm-workshop:2012, 18633 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 18634 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 18635 Models for Large-scale Simulations}, 18636 note = {Workshop sponsored by the Institute for Computational and Experimental Research 18637 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 18638 \url{http://icerm.brown.edu/tw12-1-exascale}}, 18639 year = {2012} 18640} 18641 18642@TechReport{ kirbyknepleyscott04, 18643 author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott}, 18644 title = {Optimal Evaluation of Finite Element Matrices}, 18645 type = {Technical Report}, 18646 number = {TR-2004-04}, 18647 institution = {University of Chicago}, 18648 url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}, 18649 note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}}, 18650 pages = {14}, 18651 month = may, 18652 year = {2004} 18653} 18654 18655@TechReport{ kirbyknepleyscott10, 18656 author = {Robert C. Kirby and Matthew G. Knepley and L. 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Yuen and Huai 18693 Zhang and Yaolin Shi}, 18694 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 18695 strongly variable viscosity based on {Matlab} and {CUDA}}, 18696 type = {Research Report}, 18697 number = {UMSI 2011/33}, 18698 institution = {University of Minnesota Supercomputing Institute}, 18699 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 18700 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 18701 month = mar, 18702 year = {2011} 18703} 18704 18705@InProceedings{ zheng2010, 18706 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai 18707 Zhang and Yaolin Shi}, 18708 title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients}, 18709 booktitle = {Eos Transactions of the AGU}, 18710 organization = {American Geophysical Union}, 18711 note = {Fall Meeting Supplemental, Abstract IN41A-1350}, 18712 year = {2010} 18713} 18714 18715@InCollection{ terrelkirbyknepleyscott12, 18716 author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott 18717 and Garth N. Wells}, 18718 title = {Finite elements for incompressible fluids}, 18719 editors = {A. Logg and K.A. Mardal and G. N. 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Terrel}, 18743 title = {Discrete optimization of finite element matrix evaluation}, 18744 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18745 booktitle = {Automated solutions of differential equations by the finite element method}, 18746 series = {Lecture Notes in Computational Science and Engineering}, 18747 volume = {84}, 18748 pages = {385--397}, 18749 publisher = {Springer-Verlag}, 18750 year = {2012} 18751} 18752 18753@InCollection{ kirby12, 18754 author = {Robert C. Kirby}, 18755 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 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 publisher = {Springer-Verlag}, 18761 year = {2012} 18762} 18763 18764@Article{ brownconveryhotesknepleypetropolous1993, 18765 author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and 18766 Labros Petropolous}, 18767 title = {Closed strings with low harmonics and kinks}, 18768 journal = {Physical Review D}, 18769 volume = {48}, 18770 number = {6}, 18771 year = {1993} 18772} 18773 18774@Article{ minimax1996, 18775 title = {MiniMax: What has been learned thus far}, 18776 author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and 18777 Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and 18778 C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. 18779 Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 18780 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. 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23610 23611@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 23612 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 23613 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 23614 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 23615 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 23616 pages = {1103}, 23617 year = {2018} 23618} 23619 23620@InProceedings{ barralangeloudiskramergormanpiggott2018, 23621 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 23622 modelling}, 23623 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 23624 and Matthew D Piggott}, 23625 booktitle = {EGU General Assembly Conference Abstracts}, 23626 volume = {20}, 23627 pages = {19168}, 23628 year = {2018} 23629} 23630 23631@Article{ principe2009, 23632 title = {{Mathematical models for thermally coupled low speed flows}}, 23633 author = {Javier Principe and Ramon Codina}, 23634 journal = {Advances in Theoretical and Applied Mechanics}, 23635 volume = {2}, 23636 number = {1-4}, 23637 pages = {93--112}, 23638 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 23639 year = {2009} 23640} 23641 23642@Book{ vandervorst2003, 23643 title = {Iterative {K}rylov Methods for Large Linear Systems}, 23644 author = {van der Vorst, H.}, 23645 isbn = {9780521818285}, 23646 publisher = {Cambridge University Press}, 23647 year = {2003} 23648} 23649 23650@Book{ peres2006, 23651 author = {Asher Peres}, 23652 title = {Quantum theory: concepts and methods}, 23653 volume = {57}, 23654 publisher = {Springer Science \& Business Media}, 23655 year = {2006} 23656} 23657 23658@Book{ kuttler2012, 23659 title = {Linear algebra: theory and applications}, 23660 author = {Kenneth Kuttler}, 23661 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 23662 year = {2012} 23663} 23664 23665@Book{ elman_silvester_wathen_2014, 23666 place = {Oxford}, 23667 title = {Finite elements and fast iterative solvers: with applications in incompressible 23668 fluid dynamics}, 23669 publisher = {Oxford University Press}, 23670 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 23671 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 23672 year = {2014} 23673} 23674 23675@Article{ alametal2007, 23676 title = {An evaluation of the ORNL Cray XT3}, 23677 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 23678 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 23679 journal = {International Journal of High Performance Computing Applications}, 23680 volume = {22}, 23681 number = {1}, 23682 pages = {52--80}, 23683 doi = {10.1177/1094342007085019}, 23684 year = {2007} 23685} 23686 23687@Article{ plazacarey2000, 23688 title = {Local refinement of simplicial grids based on the skeleton}, 23689 author = {Plaza, A. and Carey, Graham F.}, 23690 journal = {Applied Numerical Mathematics}, 23691 doi = {10.1016/S0168-9274(99)00022-7}, 23692 issn = {01689274}, 23693 volume = {32}, 23694 number = {2}, 23695 pages = {195--218}, 23696 year = {2000} 23697} 23698 23699@Article{ carsonstrakos2020, 23700 title = {On the cost of iterative computations}, 23701 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 23702 journal = {Phil. Trans. R. Soc. A}, 23703 volume = {378}, 23704 number = {20190050}, 23705 doi = {10.1098/rsta.2019.0050}, 23706 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 23707 year = {2020} 23708} 23709 23710@Article{ schoberl1999, 23711 title = {Multigrid methods for a parameter dependent problem in primal variables}, 23712 author = {Joachim Sch{\"o}berl}, 23713 journal = {Numerische Mathematik}, 23714 volume = {84}, 23715 number = {1}, 23716 pages = {97--119}, 23717 year = {1999} 23718} 23719 23720@Article{ wuleexuzikatanov2008, 23721 title = {Convergence analysis on iterative methods for semidefinite systems}, 23722 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 23723 journal = {Journal of Computational Mathematics}, 23724 pages = {797--815}, 23725 year = {2008} 23726} 23727 23728@Article{ maierrannacher2016, 23729 title = {Duality-based adaptivity in finite element discretization of heterogeneous 23730 multiscale problems}, 23731 author = {Maier, Matthias and Rannacher, Rolf}, 23732 journal = {Journal of Numerical Mathematics}, 23733 volume = {24}, 23734 number = {3}, 23735 pages = {167--187}, 23736 year = {2016} 23737} 23738 23739@Article{ maierrannacher2018, 23740 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23741 multiscale problems}, 23742 author = {Maier, Matthias and Rannacher, Rolf}, 23743 journal = {Multiscale Modeling \& Simulation}, 23744 volume = {16}, 23745 number = {1}, 23746 pages = {412--428}, 23747 year = {2018} 23748} 23749 23750@Article{ margetismaierluskin2017, 23751 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23752 metamaterial sheet}, 23753 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23754 journal = {Studies in Applied Mathematics}, 23755 volume = {139}, 23756 number = {4}, 23757 pages = {599--625}, 23758 year = {2017} 23759} 23760 23761@Article{ maiermargetisluskin2017b, 23762 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23763 approximation and validation}, 23764 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23765 journal = {Journal of Computational Physics}, 23766 volume = {339}, 23767 pages = {126--145}, 23768 year = {2017} 23769} 23770 23771@Article{ maiermargetisluskin2018, 23772 title = {Generation of surface plasmon-polaritons by edge effects}, 23773 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23774 journal = {Communications in Mathematical Sciences}, 23775 volume = {16}, 23776 number = {1}, 23777 pages = {77--95}, 23778 url = {http://arxiv.org/abs/1702.00848}, 23779 year = {2018} 23780} 23781 23782@Article{ maiermattheakiskaxirasluskinmargetis2018, 23783 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23784 metamaterials}, 23785 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23786 Mitchell and Margetis, Dionisios}, 23787 journal = {Physical Review B}, 23788 volume = {97}, 23789 number = {3}, 23790 pages = {035307}, 23791 year = {2018} 23792} 23793 23794@Article{ maiermattheakiskaxirasluskinmargetis2019, 23795 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23796 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23797 Mitchell and Margetis, Dionisios}, 23798 journal = {Proceedings of the Royal Society A}, 23799 volume = {475}, 23800 number = {2230}, 23801 pages = {20190220}, 23802 year = {2019} 23803} 23804 23805@Article{ maiermargetisluskin2020, 23806 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23807 two scales}, 23808 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23809 journal = {Physical Review B}, 23810 volume = {102}, 23811 number = {7}, 23812 pages = {075308}, 23813 year = {2020} 23814} 23815 23816@Article{ margetismaierstauberlowluskin2020, 23817 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 23818 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 23819 Luskin, Mitchell}, 23820 journal = {Journal of Physics A: Mathematical and Theoretical}, 23821 volume = {53}, 23822 number = {5}, 23823 pages = {055201}, 23824 year = {2020} 23825} 23826 23827@Article{ maiermargetismellet2020, 23828 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 23829 structures}, 23830 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 23831 journal = {Journal of Computational and Applied Mathematics}, 23832 volume = {377}, 23833 pages = {112909}, 23834 year = {2020} 23835} 23836 23837@Article{ maierkronbichler2021, 23838 title = {Efficient parallel 3D computation of the compressible Euler equations with an 23839 invariant-domain preserving second-order finite-element scheme}, 23840 author = {Maier, Matthias and Kronbichler, Martin}, 23841 journal = {ACM Transactions on Parallel Computing}, 23842 volume = {8}, 23843 number = {3}, 23844 pages = {1--30}, 23845 year = {2021} 23846} 23847 23848@Article{ guermondmaierpopovtomas2021, 23849 title = {Second-order invariant domain preserving approximation of the compressible 23850 Navier--Stokes equations}, 23851 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 23852 journal = {Computer Methods in Applied Mechanics and Engineering}, 23853 volume = {375}, 23854 pages = {113608}, 23855 year = {2021} 23856} 23857 23858@Article{ liliptonmaier2021, 23859 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 23860 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 23861 eprint = {2009.12166}, 23862 archiveprefix = {arXiv}, 23863 primaryclass = {phys.optics}, 23864 year = {2021} 23865} 23866 23867@Article{ songmaierluskin2020, 23868 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 23869 gradient-index graphene waveguides}, 23870 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23871 journal = {Journal of Computational Physics}, 23872 volume = {423}, 23873 pages = {109871}, 23874 year = {2020} 23875} 23876 23877@Article{ songmaierluskin2019, 23878 title = {Adaptive finite element simulations of waveguide configurations involving 23879 parallel 2D material sheets}, 23880 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23881 journal = {Computer Methods in Applied Mechanics and Engineering}, 23882 volume = {351}, 23883 pages = {20--34}, 23884 year = {2019} 23885} 23886 23887% 23888% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23889% 23890% 23891@Unpublished{ rob1, 23892 author = {Rob Kunz}, 23893 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23894 State University}, 23895 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23896 sponsors = {U.S. Navy, NRC}, 23897 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23898 simulations, including lake warming by power plants}, 23899 dates = {Oct 3 and 4, 2002}, 23900 email = {rfk@wt.arl.psu.edu} 23901} 23902 23903@Unpublished{ au1, 23904 author = {Feng Wang and William Appelbe}, 23905 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23906 url = {http://www.vpac.org}, 23907 sponsors = { }, 23908 note = {Using PETSc for a Variety of Geophysical Simulations}, 23909 dates = {Nov 22, 2002} 23910} 23911 23912@Unpublished{ carl1, 23913 author = {Carl Sovinec}, 23914 institution = {Applied Physics, University of Wisconsin}, 23915 url = {http://nimrodteam.org}, 23916 sponsors = {DOE Office of Fusion Research}, 23917 note = {Investigating using PETSc for NIMROD}, 23918 dates = {Nov 21, 2002}, 23919 email = {sovinec@engr.wisc.edu} 23920} 23921 23922@Unpublished{ au1b, 23923 author = {Pablo Carrica and Robert Wilson}, 23924 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23925 url = {http://}, 23926 sponsors = {Office of Naval Research}, 23927 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23928 dates = {Sept, 2002}, 23929 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23930} 23931 23932% ------------------- TAO References ---------------------- 23933@Article{ benson:2001:csp, 23934 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 23935 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 23936 journal = {{ACM} Transactions on Mathematical Software}, 23937 volume = {27}, 23938 number = {3}, 23939 month = sep, 23940 year = {2001}, 23941 pages = {361--376} 23942} 23943 23944@TechReport{ tao-user-ref-2000, 23945 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 23946 title = {{TAO} Users Manual}, 23947 year = {2000}, 23948 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23949 number = {ANL/MCS-TM-242}, 23950 note = {See \url{http://www.mcs.anl.gov/tao}} 23951} 23952 23953% ------------------- Optimization References ---------------------- 23954@Book{ optguide93, 23955 title = {Optimization Software Guide}, 23956 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 23957 publisher = {SIAM Publications}, 23958 address = {Philadelphia}, 23959 year = {1993} 23960} 23961 23962@InProceedings{ more84, 23963 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 23964 Hillstrom}, 23965 title = {The {MINPACK} Project}, 23966 booktitle = {Sources and Development of Mathematical Software}, 23967 editor = {Wayne R. Cowell}, 23968 year = {1984}, 23969 pages = {88--111} 23970} 23971 23972@Article{ steihaug:83, 23973 author = {Trond Steihaug}, 23974 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 23975 journal = {SIAM J. Numer. Anal.}, 23976 volume = {20}, 23977 year = {1983}, 23978 pages = {626--637}, 23979 key = {steihaug92 ! trust_region} 23980} 23981 23982@TechReport{ minpack2test, 23983 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 23984 title = {The {MINPACK-2} Test Problem Collection}, 23985 institution = {Argonne National Laboratory}, 23986 year = {1991}, 23987 number = {ANL/MCS-TM-150}, 23988 key = {more91 ! MINPACK-2} 23989} 23990 23991@TechReport{ hohmann:94, 23992 author = {Andreas Hohmann}, 23993 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 23994 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 23995 year = {1994}, 23996 number = {SC-94-4}, 23997 key = {Hohmann94} 23998} 23999 24000@TechReport{ meza:94, 24001 author = {Juan C. Meza}, 24002 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 24003 institution = {Sandia National Laboratory}, 24004 year = {1994}, 24005 number = {SAND94-8225}, 24006 key = {Meza94} 24007} 24008 24009@Book{ dennis:83, 24010 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 24011 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 24012 publisher = {Prentice-Hall, Inc.}, 24013 address = {Englewood Cliffs, NJ}, 24014 year = {1983} 24015} 24016 24017@TechReport{ more:92, 24018 author = {Jorge J. Mor\'{e} and David Thuente}, 24019 title = {Line search algorithms with guaranteed sufficient decrease}, 24020 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24021 year = {1992}, 24022 number = {MCS-P330-1092} 24023} 24024 24025@Article{ more-toraldo, 24026 author = {Jorge J. Mor\'e and G. Toraldo}, 24027 journal = {SIOPT}, 24028 pages = {93--113}, 24029 title = {On the solution of large quadratic programming problems with bound constraints}, 24030 volume = {1}, 24031 year = {1991} 24032} 24033 24034@Article{ byrd:1995:lma, 24035 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 24036 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 24037 journal = {SIAM Journal on Scientific Computing}, 24038 volume = {16}, 24039 number = {5}, 24040 pages = {1190--1208}, 24041 month = sep, 24042 year = {1995}, 24043 coden = {SJOCE3}, 24044 issn = {1064-8275 (print), 1095-7197 (electronic)}, 24045 mrclass = {90C30 (65K05)}, 24046 mrnumber = {96e:90039}, 24047 mrreviewer = {Henry Wolkowicz}, 24048 bibdate = {Fri Dec 4 16:17:35 MST 1998} 24049} 24050 24051@Article{ lin_c3, 24052 author = {C.-J. Lin and J. J. Mor\'e}, 24053 title = {Newton's method for large bound-constrained optimization problems}, 24054 year = {1999}, 24055 journal = {SIOPT}, 24056 volume = {9(4)}, 24057 pages = {1100--1127}, 24058 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 24059} 24060 24061@TechReport{ dolan2, 24062 author = {E. Dolan and J. J. Mor\'{e}}, 24063 title = {Benchmarking Optimization Software with Performance Profiles}, 24064 year = {2001}, 24065 month = jan, 24066 number = {ANL/MCS-P861-1200}, 24067 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24068 address = {Argonne, IL}, 24069 url = {http://www.mcs.anl.gov/~more/cops/} 24070} 24071 24072@InProceedings{ owlqn, 24073 author = {Galen Andrew and Jianfeng Gao}, 24074 title = {Scalable training of L1-regularized log-linear models}, 24075 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 24076 pages = {33--40}, 24077 year = {2007} 24078} 24079 24080@Article{ bmrm, 24081 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 24082 title = {Bundle methods for regularized risk minimization}, 24083 year = {2010}, 24084 journal = {Journal of Machine Learning Research}, 24085 volume = {11}, 24086 pages = {311--365} 24087} 24088 24089% ------------------- Component Software References ---------------------- 24090@InProceedings{ cca99, 24091 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 24092 McInnes and S. Parker and B. Smolinski}, 24093 title = {Toward a Common Component Architecture for High-Performance Scientific 24094 Computing}, 24095 booktitle = {Proceedings of {High Performance Distributed Computing}}, 24096 pages = {115--124}, 24097 year = {1999}, 24098 note = {See \url{http://cca-forum.org}} 24099} 24100 24101@Book{ szyperski98, 24102 author = {Clemens Szyperski}, 24103 title = {Component Software: Beyond Object-Oriented Programming}, 24104 publisher = {ACM Press}, 24105 address = {New York}, 24106 year = {1998} 24107} 24108 24109@Article{ broy98, 24110 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 24111 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 24112 Stal and Clemens Szyperski}, 24113 title = {What Characterizes a (Software) Component?}, 24114 journal = {Software -- Concepts and Tools}, 24115 publisher = {Springer-Verlag}, 24116 year = {1998}, 24117 volume = {19}, 24118 pages = {49--56} 24119} 24120 24121@Article{ componentware:94, 24122 author = {Jon Udell}, 24123 title = {Componentware}, 24124 journal = {Byte}, 24125 volume = {may}, 24126 pages = {46--56}, 24127 year = {1994}, 24128 key = {Udell94 ! componentware} 24129} 24130 24131@Misc{ cca-web-page, 24132 author = {{Common Component Architecture Forum}}, 24133 note = {See \url{http://cca-forum.org}} 24134} 24135 24136% --------------- References for Tools Used by TAO Developers ----------------- 24137 24138% 24139% tohtml: Used to generate on-line TAO users manual and manual pages 24140% 24141@TechReport{ tohtml, 24142 author = {William Gropp}, 24143 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 24144 institution = {Argonne National Laboratory}, 24145 number = {ANL/MCS-TM-00}, 24146 month = jan, 24147 year = {1995}, 24148 key = {tohtml} 24149} 24150 24151% 24152% doctext: Used to generate tex version of TAO manual pages 24153% 24154@TechReport{ doctext, 24155 author = {William Gropp}, 24156 title = {Users Manual for doctext: Producing documentation from {C} source code}, 24157 institution = {Argonne National Laboratory}, 24158 number = {ANL/MCS-TM-00}, 24159 month = jan, 24160 year = {1995}, 24161 key = {doctext} 24162} 24163 24164% 24165% bfort: Used to generate TAO Fortran interface 24166% 24167@TechReport{ bfort, 24168 author = {William Gropp}, 24169 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 24170 institution = {Argonne National Laboratory}, 24171 number = {ANL/MCS-TM-208}, 24172 month = mar, 24173 year = {1995}, 24174 key = {doctext} 24175} 24176 24177% ------------------------- PETSc References ------------------------------ 24178@InProceedings{ petsc, 24179 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 24180 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 24181 Libraries}, 24182 booktitle = {Modern Software Tools in Scientific Computing}, 24183 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 24184 publisher = {Birkhauser Press}, 24185 pages = {163--202}, 24186 year = {1997} 24187} 24188 24189% ------------------------- Misc Other References ------------------------------ 24190@Misc{ indeps-web-page, 24191 title = {{InDEPS} {W}eb page}, 24192 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 24193 author = {et al. Robert Armstrong}, 24194 institution = {Sandia National Laboratory}, 24195 key = {{InDEPS} {W}eb page} 24196} 24197 24198@Misc{ pooma, 24199 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 24200 chitectures}, 24201 year = {1996}, 24202 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 24203 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 24204} 24205 24206@Misc{ isis++-web-page, 24207 title = {{ISIS++} {W}eb Page}, 24208 note = {See \url{http://ca.sandia.gov/isis}}, 24209 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 24210 institution = {Sandia National Laboratories} 24211} 24212 24213@Misc{ trilinos-web-page, 24214 title = {{Trilinos} {W}eb Page}, 24215 note = {See 24216 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 24217 author = {Mike Heroux et al.}, 24218 institution = {Sandia National Laboratories} 24219} 24220 24221@Misc{ alice-web-page, 24222 title = {{ALICE} {W}eb page}, 24223 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 24224 Argonne National Laboratory}, 24225 key = {{ALICE} {W}eb page} 24226} 24227 24228@Misc{ autodiff-webpage, 24229 author = {{Computational Differentiation Project}}, 24230 note = {See \url{http://www.mcs.anl.gov/autodiff}} 24231} 24232 24233@Misc{ coool-home-page, 24234 author = {Lydia Deng and Wences Gouveia and John Scales}, 24235 title = {{The CWP Object-Oriented Optimization Library}}, 24236 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 24237} 24238 24239@Misc{ rice-inversion-home-page, 24240 author = {Mark S. Gokenbach and William W. Symes}, 24241 title = {{The Hilbert Class Library}}, 24242 note = {See \url{http://www.trip.caam.rice.edu/}} 24243} 24244 24245@Misc{ opt++-home-page, 24246 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 24247 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 24248} 24249 24250@Article{ gockenbach:1999:ccl, 24251 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 24252 title = {C++ Classes for Linking Optimization with Complex Simulations}, 24253 journal = {{ACM} Transactions on Mathematical Software}, 24254 volume = {25}, 24255 number = {2}, 24256 month = jun, 24257 year = {1999}, 24258 pages = {191-212}, 24259 abstract = {The object-oriented programming paradigm can be used to overcome the 24260 incompatibilities between off-the-shelf optimization software and application 24261 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 24262 objects arising in optimization problems, such as vectors, linear operators, and 24263 so forth, as C++ classes, making it possible to write optimization code in a 24264 natural fashion, while allowing application software such as simulators to use the 24265 most convenient data structures and programming style. In spite of the poor 24266 reputation C++ has for runtime performance, the use of mixed-language programming 24267 allows performance equal to that achieved by standard Fortran packages, as 24268 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 24269 accepted = {April 1999}, 24270 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 24271} 24272 24273@Misc{ neos-guide, 24274 author = {{The Optimization Software Guide}}, 24275 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 24276} 24277 24278@Article{ boyd, 24279 title = {Distributed optimization and statistical learning via the alternating direction 24280 method of multipliers}, 24281 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 24282 Jonathan and others}, 24283 journal = {Foundations and Trends{\textregistered} in Machine learning}, 24284 volume = {3}, 24285 number = {1}, 24286 pages = {1-122}, 24287 year = {2011}, 24288 publisher = {Now Publishers, Inc.} 24289} 24290 24291@Misc{ :alertsys, 24292 title = {page{ALERT}}, 24293 organization = {Alert Systems, Inc}, 24294 address = {Madison, Wisconsin}, 24295 note = {http://www.alertsys.com/} 24296} 24297 24298@Manual{ :cmfortran, 24299 title = {{CM} {F}ortran Language Reference Manual}, 24300 organization = {Thinking Machines Corporation}, 24301 year = {1994}, 24302 address = {Cambridge, MA} 24303} 24304 24305@Manual{ :cmmd, 24306 title = {{CMMD} Reference Manual, Version 3.0}, 24307 organization = {Thinking Machines Corporation}, 24308 year = {1993}, 24309 address = {Cambridge, MA} 24310} 24311 24312@Manual{ :cmssl, 24313 title = {{CMSSL} for {CM} {F}ortran}, 24314 volume = {I}, 24315 organization = {Thinking Machines Corporation}, 24316 year = {1994}, 24317 address = {Cambridge, MA} 24318} 24319 24320@Misc{ :condor, 24321 author = {M. Livny}, 24322 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24323 howpublished = {www.cs.wisc.edu/condor} 24324} 24325 24326@Manual{ :connection, 24327 title = {Connection Machine {CM}--5 Technical Summary}, 24328 organization = {Thinking Machines Corporation}, 24329 year = {1993}, 24330 address = {Cambridge, MA} 24331} 24332 24333@Manual{ :cplex, 24334 title = {{CPLEX} Optimizer}, 24335 organization = {ILOG CPLEX Division}, 24336 address = {889 Alder Avenue, Incline Village, Nevada}, 24337 note = {http://www.cplex.com/} 24338} 24339 24340@Manual{ :cplextm, 24341 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24342 (Version 2.0)}, 24343 organization = {CPLEX Optimization Inc.}, 24344 year = {1992}, 24345 address = {Incline Village, Nevada} 24346} 24347 24348@Misc{ :fatcop, 24349 author = {M. C. Ferris}, 24350 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24351 Solver}, 24352 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24353} 24354 24355@Misc{ :metaneos, 24356 author = {S. J. Wright}, 24357 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24358 howpublished = {www-unix.mcs.anl.gov/metaneos} 24359} 24360 24361@InCollection{ gropp.more:optimization, 24362 author = {W. Gropp and J. J. Mor\'e}, 24363 title = {Optimization environments and the {NEOS} Server}, 24364 booktitle = {Approximation Theory and Optimization}, 24365 pages = {167--182}, 24366 publisher = {Cambridge University Press}, 24367 year = {1997}, 24368 editor = {M. D. Buhmann and A. Iserles} 24369} 24370 24371@Article{ czyzyk.mesnier.ea:neos, 24372 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24373 title = {The {NEOS} Server}, 24374 journal = {IEEE Journal on Computational Science and Engineering}, 24375 volume = {5}, 24376 year = {1998}, 24377 pages = {68--75} 24378} 24379 24380@Book{ :osl, 24381 title = {Handbook for {IBM OSL}}, 24382 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24383 year = {1994}, 24384 publisher = {Boyd and Fraser}, 24385 address = {Danvers, Massachusetts} 24386} 24387 24388@Manual{ :pro-matlab, 24389 title = {{PRO}--{MATLAB} User's Guide}, 24390 organization = {The MathWorks, Inc.}, 24391 year = {1989}, 24392 address = {21 Eliot Street, South Natick, MA 01760} 24393} 24394 24395@Misc{ :prostate, 24396 key = {Biomedical}, 24397 title = {Biomedical Business International Newsletter}, 24398 howpublished = {pp. 72--75}, 24399 year = {1996} 24400} 24401 24402@Misc{ :sipcase, 24403 key = {Natural}, 24404 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24405 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24406} 24407 24408@Book{ aarts.korst:simulated, 24409 author = {E. Aarts and J. Korst}, 24410 title = {Simulated Annealing and Boltzman Machines}, 24411 year = {1990}, 24412 publisher = {John Wiley \& Sons}, 24413 address = {Chichester} 24414} 24415 24416@TechReport{ aarts.laarhoven.ea:local-search-based, 24417 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 24418 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 24419 institution = {Centre for Quantitative Methods}, 24420 year = {1991}, 24421 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 24422 number = {106}, 24423 type = {CQM-Not} 24424} 24425 24426@Article{ aashtiani.magnanti:equilibria, 24427 author = {H. Z. Aashtiani and T. L. Magnanti}, 24428 title = {Equilibria on a congested transportation network}, 24429 journal = {SIAM Journal on Algebraic and Discrete Methods}, 24430 volume = {2}, 24431 year = {1981}, 24432 pages = {213--226} 24433} 24434 24435@Article{ ablow.brigham:analog, 24436 author = {C. M. Ablow and G. Brigham}, 24437 title = {An Analog Solution of Programming Problems}, 24438 journal = {Operations Research}, 24439 year = {1955}, 24440 volume = {3}, 24441 pages = {388--394} 24442} 24443 24444@Article{ achuthan.grabowski.ea:optimal, 24445 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 24446 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 24447 journal = {Opsearch}, 24448 year = {1981}, 24449 volume = {18}, 24450 pages = {117--138} 24451} 24452 24453@Book{ adelman.robinson:income, 24454 author = {I. Adelman and S. Robinson}, 24455 title = {Income Distribution Policy in Developing Countries}, 24456 publisher = {Stanford University Press}, 24457 year = {1978}, 24458 address = {Stanford, California} 24459} 24460 24461@Article{ adler.resende.ea:implementation, 24462 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 24463 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 24464 journal = {Mathematical Programming}, 24465 year = {1989}, 24466 volume = {44}, 24467 pages = {297--336} 24468} 24469 24470@TechReport{ aeberhard.coomans.ea:comparison, 24471 author = {S. Aeberhard and D. Coomans and O. de Vel}, 24472 title = {Comparison of Classifiers in High Dimensional Settings}, 24473 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 24474 University of North Queensland}, 24475 year = {1992}, 24476 number = {92-02}, 24477 type = {Technical Report} 24478} 24479 24480@Article{ aganagic.cottle:constructive, 24481 author = {M. Aganagi\'{c} and R. W. Cottle}, 24482 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 24483 Minors}, 24484 journal = {Mathematical Programming}, 24485 year = {1987}, 24486 volume = {37}, 24487 pages = {223--231} 24488} 24489 24490@TechReport{ aganagic:iterative, 24491 author = {M. Aganagi\'{c}}, 24492 title = {Iterative Methods for the Linear Complementarity Problem}, 24493 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 24494 University}, 24495 year = {1978}, 24496 type = {SOL}, 24497 number = {78-10}, 24498 address = {Stanford, California} 24499} 24500 24501@Book{ ahlfors:complex, 24502 author = {L. V. Ahlfors}, 24503 title = {Complex Analysis}, 24504 publisher = {McGraw--Hill Book Company}, 24505 address = {New York}, 24506 series = {International Series in Pure and Applied Mathematics}, 24507 edition = {Second}, 24508 year = {1966} 24509} 24510 24511@Article{ ahn:solution, 24512 author = {B--H. Ahn}, 24513 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 24514 journal = {Journal of Optimization Theory and Applications}, 24515 year = {1981}, 24516 volume = {33}, 24517 pages = {175--185} 24518} 24519 24520@Article{ al-fahed.stavroulakis.ea:hard, 24521 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24522 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 24523 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 24524 volume = {71}, 24525 year = {1991}, 24526 pages = {257--265} 24527} 24528 24529@Article{ al-fahed.stavroulakis.ea:linear, 24530 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24531 title = {A linear complementarity approach to the frictionless gripper}, 24532 journal = {International Journal of Robotic Research}, 24533 volume = {11}, 24534 year = {1992}, 24535 pages = {112--122} 24536} 24537 24538@Article{ al-khayyal.falk:jointly, 24539 author = {F. A. Al--Khayyal and J. E. Falk}, 24540 title = {Jointly Constrained Biconvex Programming}, 24541 journal = {Mathematics of Operations Research}, 24542 year = {1983}, 24543 volume = {8}, 24544 pages = {273--286} 24545} 24546 24547@Article{ al-khayyal.kyparisis:finite, 24548 author = {F. A. Al--Khayyal and J. Kyparisis}, 24549 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 24550 Inequalities}, 24551 journal = {Journal of Optimization Theory and Applications}, 24552 year = {1991}, 24553 volume = {70}, 24554 pages = {319--332} 24555} 24556 24557@PhDThesis{ al-khayyal:biconvex, 24558 author = {F. A. Al--Khayyal}, 24559 title = {Biconvex Programming and Biconcave Minimization}, 24560 year = {1977}, 24561 school = {The George Washington University} 24562} 24563 24564@Article{ alart.curnier:mixed, 24565 author = {P. Alart and A. Curnier}, 24566 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 24567 solution methods}, 24568 journal = {Computer Methods in Applied Mechanics and Engineering}, 24569 volume = {92}, 24570 year = {1991}, 24571 pages = {353--375} 24572} 24573 24574@Misc{ alexander.kellog.ea:piecewise, 24575 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 24576 title = {Piecewise smooth continuation}, 24577 howpublished = {Manuscript}, 24578 year = {1979} 24579} 24580 24581@InCollection{ alexander.li.ea:piecewise, 24582 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 24583 title = {Piecewise smooth homotopies}, 24584 booktitle = {Homotopy Methods and Global Convergence}, 24585 pages = {1--14}, 24586 publisher = {Plenum Press}, 24587 year = {1983}, 24588 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 24589 address = {New York} 24590} 24591 24592@InCollection{ alexander:topological, 24593 author = {J.~C. Alexander}, 24594 title = {The topological theory of an embedding method}, 24595 booktitle = {Continuation Methods}, 24596 pages = {37--68}, 24597 publisher = {Academic Press}, 24598 year = {1978}, 24599 editor = {H. Wacker}, 24600 address = {New York} 24601} 24602 24603@Book{ allen:probability, 24604 author = {A. O. Allen}, 24605 title = {Probability, Statistics and Queueing Theory}, 24606 publisher = {Academic Press}, 24607 year = {1990}, 24608 address = {London}, 24609 edition = {Second} 24610} 24611 24612@Book{ allgower.georg:numerical, 24613 author = {E. L. Allgower and K. Georg}, 24614 title = {Numerical Continuation Methods, An Introduction}, 24615 publisher = {Springer-Verlag}, 24616 year = {1990}, 24617 address = {Berlin} 24618} 24619 24620@InProceedings{ allgower.georg:predictor-corrector, 24621 crossref = {bachem.grotschel.ea:mathematical}, 24622 author = {E. L. Allgower and K. Georg}, 24623 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 24624 Zero Points of Nonlinear Mappings}, 24625 pages = {15--56} 24626} 24627 24628@Article{ aluffi-pentini.parisi.ea:algorithm, 24629 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 24630 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 24631 Algorithm}, 24632 journal = {ACM Transactions on Mathematical Software}, 24633 year = {1988}, 24634 volume = {14}, 24635 pages = {366--380} 24636} 24637 24638@Article{ anandalingam.friesz:hierarchical, 24639 author = {G. Anandalingam and T. L. Friesz}, 24640 title = {Hierarchical Optimization: An Introduction}, 24641 journal = {Annals of Operations Research}, 24642 year = {1992}, 24643 volume = {34}, 24644 pages = {1--11} 24645} 24646 24647@Article{ anandalingam.white:solution, 24648 author = {G. Anandalingam and D. J. White}, 24649 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 24650 Functions}, 24651 journal = {IEEE Transactions on Automatic Control}, 24652 year = {1990}, 24653 volume = {35}, 24654 number = {10}, 24655 pages = {1170--1173} 24656} 24657 24658@Article{ andersen.andersen:presolving, 24659 author = {E. Andersen and K. Andersen}, 24660 title = {Presolving in Linear Programming}, 24661 year = {1995}, 24662 journal = {Mathematical Programming}, 24663 volume = {71}, 24664 pages = {221--245} 24665} 24666 24667@InProceedings{ andersen.ye:homogeneous, 24668 author = {E. Andersen and Y. Ye}, 24669 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 24670 Equality Constraints}, 24671 crossref = {ferris.pang:complementarity}, 24672 pages = {1--11} 24673} 24674 24675@Book{ anderson.bai.ea:lapack, 24676 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 24677 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 24678 Sorensen}, 24679 title = {{LAPACK} User's Guide}, 24680 publisher = {SIAM}, 24681 year = {1995}, 24682 address = {Philadelphia, Pennsylvania}, 24683 edition = {Second} 24684} 24685 24686@Article{ anderson.ferris:direct, 24687 author = {E. J. Anderson and M. C. Ferris}, 24688 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 24689 year = {2001}, 24690 journal = {SIAM Journal on Optimization, forthcoming}, 24691 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 24692 key = {55} 24693} 24694 24695@InProceedings{ anderson.ferris:genetic, 24696 author = {E. J. Anderson and M. C. Ferris}, 24697 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 24698 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 24699 Waterloo, Ontario, Canada, May 28--30}, 24700 publisher = {University of Waterloo Press}, 24701 key = {14}, 24702 year = {1990} 24703} 24704 24705@Article{ anderson.ferris:genetic*1, 24706 author = {E. J. Anderson and M. C. Ferris}, 24707 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 24708 Problem}, 24709 journal = {ORSA Journal on Computing}, 24710 year = {1994}, 24711 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 24712 volume = {6}, 24713 pages = {161--173}, 24714 key = {22} 24715} 24716 24717@InProceedings{ anderson.ferris:parallel, 24718 author = {E. J. Anderson and M. C. Ferris}, 24719 title = {Parallel Genetic Algorithms in Optimization}, 24720 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 24721 Computing, Chicago, Illinois, December 11-13}, 24722 year = {1989}, 24723 key = {12} 24724} 24725 24726@Unpublished{ anderson.lewis:primal, 24727 author = {E. J. Anderson and A. S. Lewis}, 24728 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24729 note = {In preparation} 24730} 24731 24732@Book{ anderson.nash:linear, 24733 author = {E. J. Anderson and P. Nash}, 24734 title = {Linear Programming in Infinite--Dimensional Spaces}, 24735 year = {1987}, 24736 publisher = {John Wiley \& Sons}, 24737 address = {Chichester} 24738} 24739 24740@InProceedings{ anderson:primal, 24741 author = {E. J. Anderson}, 24742 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24743 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 24744 Programming, Cambridge, September 1984}, 24745 year = {1985}, 24746 editor = {E. J. Anderson and A. B. Philpott}, 24747 publisher = {Springer-Verlag}, 24748 address = {Berlin} 24749} 24750 24751@Article{ andradottir:method, 24752 author = {S. Andrad\'{o}ttir}, 24753 title = {A Method of Discrete Stochastic Optimization}, 24754 journal = {Management Science}, 24755 year = {1995}, 24756 volume = {41}, 24757 pages = {1946--1961} 24758} 24759 24760@Article{ andradottir:global, 24761 author = {S. Andrad\'{o}ttir}, 24762 title = {A Global Search Method for Discrete Stochastic Optimization}, 24763 journal = {SIAM Journal on Optimization}, 24764 year = {1996}, 24765 volume = {6}, 24766 pages = {513--530} 24767} 24768 24769@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 24770 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 24771 title = {An infeasible--interior--point predictor--corrector algorithm for the 24772 {P}$_x$--geometric {LCP}}, 24773 institution = {Department of Mathematics, The University of Iowa}, 24774 address = {Iowa City, Iowa}, 24775 year = {1994}, 24776 number = {62}, 24777 type = {Reports on Computational Mathematics} 24778} 24779 24780@TechReport{ anitescu.potra:formulating, 24781 author = {M. Anitescu and F. A. Potra}, 24782 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 24783 Linear Complementarity Problems}, 24784 institution = {Department of Mathematics, The University of Iowa}, 24785 year = {1996}, 24786 type = {Report}, 24787 number = {93}, 24788 address = {Iowa City, Iowa} 24789} 24790 24791@Article{ anstreicher.lee.ea:crashing, 24792 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 24793 title = {Crashing a Maximum-Weight Complementarity Basis}, 24794 journal = {Mathematical Programming}, 24795 year = {1992}, 24796 volume = {54}, 24797 pages = {281--294} 24798} 24799 24800@Article{ anstreicher:combined, 24801 author = {K. M. Anstreicher}, 24802 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 24803 programming}, 24804 journal = {Mathematical Programming}, 24805 year = {1991}, 24806 volume = {52}, 24807 pages = {429--440} 24808} 24809 24810@Article{ anstreicher:combined*1, 24811 author = {K. M. Anstreicher}, 24812 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 24813 journal = {Mathematical Programming}, 24814 year = {1989}, 24815 volume = {43}, 24816 pages = {209--223} 24817} 24818 24819@InCollection{ arbenz.gander.ea:remote, 24820 author = {P. Arbenz and W. Gander and M. Oettli}, 24821 title = {The Remote Computational System}, 24822 booktitle = {High-Performance Computation and Networks}, 24823 publisher = {Springer-Verlag}, 24824 year = {1996}, 24825 volume = {1067}, 24826 series = {Lecture Notes in Computer Science}, 24827 pages = {662--667} 24828} 24829 24830@InCollection{ arcus:comsoal, 24831 author = {A. L. Arcus}, 24832 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 24833 booktitle = {Readings in Production and Operations Management}, 24834 year = {1966}, 24835 editor = {E. S. Buffa}, 24836 publisher = {John Wiley \& Sons}, 24837 address = {New York} 24838} 24839 24840@TechReport{ arioli.chan.ea:computing, 24841 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 24842 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 24843 Optimization Calculations}, 24844 institution = {CERFACS}, 24845 year = {1993}, 24846 number = {TR/PA/93/34} 24847} 24848 24849@Article{ armijo:minimization, 24850 author = {L. Armijo}, 24851 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 24852 Derivatives}, 24853 journal = {Pacific Journal of Mathematics}, 24854 year = {1966}, 24855 volume = {16}, 24856 pages = {1--3} 24857} 24858 24859@Article{ arrow.debreu:existence, 24860 author = {K. Arrow and G. Debreu}, 24861 title = {Existence of Equilibrium for a Competitive Economy}, 24862 journal = {Econometrica}, 24863 year = {1954}, 24864 volume = {22}, 24865 pages = {265--290} 24866} 24867 24868@InCollection{ arrow.solow:gradient, 24869 author = {K. J. Arrow and R. M. Solow}, 24870 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 24871 booktitle = {Studies in Linear and Nonlinear Programming}, 24872 year = {1958}, 24873 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 24874 publisher = {Stanford University Press}, 24875 address = {Stanford, California}, 24876 pages = {166--176} 24877} 24878 24879@Book{ aubin.ekeland:nonlinear, 24880 author = {J.-P. Aubin and I. Ekeland}, 24881 title = {Applied nonlinear analysis}, 24882 publisher = {John Wiley \& Sons}, 24883 address = {New York}, 24884 year = {1984} 24885} 24886 24887@Article{ auchmuty:variational, 24888 author = {G. Auchmuty}, 24889 title = {Variational Principles for Variational Inequalities}, 24890 journal = {Numerical Functional Analysis and Optimization}, 24891 year = {1989}, 24892 volume = {10}, 24893 pages = {863--874} 24894} 24895 24896@Book{ auerbach.kotlikoff:dynamic, 24897 author = {A. J. Auerbach and L. J. Kotlikoff}, 24898 title = {Dynamic Fiscal Policy}, 24899 publisher = {Cambridge University Press}, 24900 address = {Cambridge, England}, 24901 year = {1987} 24902} 24903 24904@InProceedings{ ault.deutsch.ea:interpolating, 24905 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 24906 title = {Interpolating Subspaces in Approximation Theory}, 24907 booktitle = {Approximation Theory}, 24908 year = {1970}, 24909 editor = {A. Talbot}, 24910 publisher = {Academic Press}, 24911 address = {London} 24912} 24913 24914@Article{ auslender.crouzeix:global, 24915 author = {A. A. Auslender and J.--P. Crouzeix}, 24916 title = {Global Regularity Theorems}, 24917 journal = {Mathematics of Operations Research}, 24918 year = {1988}, 24919 volume = {13}, 24920 pages = {243--253} 24921} 24922 24923@Article{ auslender.haddou:interior-proximal, 24924 author = {A. Auslender and M. Haddou}, 24925 title = {An interior-proximal method for convex linearly constrained problems and its 24926 extension to variational inequalities}, 24927 year = {1995}, 24928 journal = {Mathematical Programming}, 24929 pages = {77--100}, 24930 volume = {71} 24931} 24932 24933@Article{ auslender:convergence, 24934 author = {A. Auslender}, 24935 title = {Convergence of stationary sequences for variational inequalities with maximal 24936 monotone operators}, 24937 journal = {Applied Mathematics and Optimization}, 24938 volume = {28}, 24939 year = {1993}, 24940 pages = {161--172} 24941} 24942 24943@Book{ auslender:optimization, 24944 author = {A. Auslender}, 24945 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 24946 year = {1976}, 24947 publisher = {Masson}, 24948 address = {Paris} 24949} 24950 24951@TechReport{ averick.carter.ea:minpack-2, 24952 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 24953 title = {The {MINPACK-2} Test Problem Collection}, 24954 institution = {Argonne National Laboratory}, 24955 year = {1992}, 24956 address = {Argonne, Illinois}, 24957 number = {MCS-P153-0692} 24958} 24959 24960@TechReport{ axline.billups.ea:guidelines, 24961 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 24962 title = {Guidelines for Software Security ({U})}, 24963 institution = {SNL}, 24964 year = {1989}, 24965 month = oct, 24966 address = {Albuquerque, New Mexico}, 24967 number = {SAND88-2955} 24968} 24969 24970@Article{ ayres.walter:greenhouse, 24971 author = {R. U. Ayres and J. Walter}, 24972 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 24973 journal = {Environmental and Resource Economics}, 24974 year = {1991}, 24975 volume = {1}, 24976 pages = {237--270} 24977} 24978 24979@PhDThesis{ bagley:behaviour, 24980 author = {J. D. Bagley}, 24981 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 24982 Algorithms}, 24983 year = {1967}, 24984 school = {University of Michigan} 24985} 24986 24987@Article{ bain.stewart:application, 24988 author = {R. S. Bain and W. E. Stewart}, 24989 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 24990 Algebraic Equation Systems}, 24991 journal = {Computers in Chemical Engineering}, 24992 year = {1991}, 24993 volume = {15}, 24994 pages = {203--208} 24995} 24996 24997@Article{ baker.lasdon:successive, 24998 author = {T. E. Baker and L. S. 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Ferris}, 25470 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 25471 Starting Points}, 25472 journal = {SIAM Journal on Optimization}, 25473 year = {1996}, 25474 volume = {6}, 25475 pages = {316--325}, 25476 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 25477 key = {34} 25478} 25479 25480@TechReport{ billups.ferris:convergence*1, 25481 author = {S. C. Billups and M. C. Ferris}, 25482 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 25483 Points}, 25484 institution = {Computer Sciences Department, University of Wisconsin}, 25485 year = {1993}, 25486 address = {Madison, Wisconsin}, 25487 number = {1180}, 25488 note = {Revised version in SIAM Journal on Optimization.} 25489} 25490 25491@Article{ billups.ferris:qpcomp, 25492 author = {S. C. Billups and M. C. Ferris}, 25493 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 25494 year = {1997}, 25495 journal = {Mathematical Programming}, 25496 pages = {533--562}, 25497 volume = {76}, 25498 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 25499 key = {47} 25500} 25501 25502@Article{ billups.ferris:solutions, 25503 author = {S. C. Billups and M. C. Ferris}, 25504 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 25505 journal = {Mathematics of Operations Research}, 25506 volume = {24}, 25507 pages = {219--236}, 25508 year = {1999}, 25509 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 25510 key = {42}, 25511 institution = {Computer Sciences Department, University of Wisconsin}, 25512 address = {Madison, Wisconsin}, 25513 type = {Mathematical Programming Technical Report}, 25514 number = {94--15} 25515} 25516 25517@TechReport{ billups.murata.ea:users, 25518 author = {S. C. Billups and K. K. 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Model analysis and 26607 optimality conditions}, 26608 type = {Publication}, 26609 number = {CRT-94-56}, 26610 institution = {Centre de Recherche sur les Transports, Universit\'e de Montr\'eal}, 26611 address = {Montr\'eal, Canada}, 26612 year = {1994} 26613} 26614 26615@Article{ chen.harker:continuation, 26616 author = {B. Chen and P. T. Harker}, 26617 title = {A Continuation Method for Monotone Variational Inequalities}, 26618 journal = {Mathematical Programming}, 26619 volume = {69}, 26620 pages = {237--253}, 26621 year = {1995} 26622} 26623 26624@Article{ chen.harker:non-interior, 26625 author = {B. Chen and P. T. Harker}, 26626 title = {A Non-Interior-Point Continuation Method for Linear Complementarity Problems}, 26627 journal = {SIAM Journal on Matrix Analysis and Applications}, 26628 year = {1993}, 26629 volume = {14}, 26630 pages = {1168--1190} 26631} 26632 26633@Article{ chen.harker:smooth, 26634 author = {B. Chen and P. T. 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Toint}, 26924 title = {Numerical Experiments with the {LANCELOT} Package (Release {A}) for Large-Scale 26925 Nonlinear Optimization}, 26926 journal = {Mathematical Programming}, 26927 year = {1996}, 26928 volume = {75}, 26929 pages = {73--110} 26930} 26931 26932@Book{ cgt, 26933 author = {A. R. Conn and N. I. M. Gould and Ph. L. Toint}, 26934 title = {Trust-Region Methods}, 26935 year = {2000}, 26936 publisher = {SIAM}, 26937 address = {Philadelphia, Pennsylvania} 26938} 26939 26940@InCollection{ conn.toint:algorithm, 26941 author = {A. R. Conn and Ph. L. Toint}, 26942 title = {An Algorithm using Quadratic Interpolation for Unconstrained Derivative Free 26943 Optimization}, 26944 booktitle = {Nonlinear Optimization and Applications}, 26945 editor = {G. Di Pillo and F. Giannessi}, 26946 year = {1996}, 26947 publisher = {Plenum Press}, 26948 address = {New York} 26949} 26950 26951@Article{ conry.seireg:mathematical, 26952 author = {T. F. Conry and A. 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Mangasarian}, 28533 title = {Breast Cancer Diagnosis via Linear Programming}, 28534 key = {50}, 28535 journal = {{IEEE} Computational Science and Engineering}, 28536 year = {1995}, 28537 volume = {2}, 28538 pages = {70--71} 28539} 28540 28541@Article{ ferris.mangasarian:error, 28542 author = {M. C. Ferris and O. L. Mangasarian}, 28543 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 28544 Inequalities}, 28545 journal = {Annals of Operations Research}, 28546 year = {1993}, 28547 volume = {47}, 28548 pages = {293--305}, 28549 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 28550 key = {24} 28551} 28552 28553@Article{ ferris.mangasarian:finite, 28554 author = {M. C. Ferris and O. L. Mangasarian}, 28555 title = {Finite Perturbation of Convex Programs}, 28556 journal = {Applied Mathematics and Optimization}, 28557 year = {1991}, 28558 volume = {23}, 28559 pages = {263--273}, 28560 key = {08} 28561} 28562 28563@Book{ ferris.mangasarian:linear, 28564 author = {M. C. Ferris and O. L. Mangasarian}, 28565 title = {Linear Programming via {MATLAB}}, 28566 publisher = {in preparation}, 28567 year = {1995}, 28568 address = {Madison, Wisconsin} 28569} 28570 28571@Article{ ferris.mangasarian:minimum, 28572 author = {M. C. Ferris and O. L. Mangasarian}, 28573 title = {Minimum Principle Sufficiency}, 28574 journal = {Mathematical Programming}, 28575 year = {1992}, 28576 volume = {57}, 28577 pages = {1--14}, 28578 key = {11} 28579} 28580 28581@Article{ ferris.mangasarian:parallel, 28582 author = {M. C. Ferris and O. L. Mangasarian}, 28583 title = {Parallel Constraint Distribution}, 28584 journal = {SIAM Journal on Optimization}, 28585 year = {1991}, 28586 volume = {1}, 28587 pages = {487--500}, 28588 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28589 key = {18} 28590} 28591 28592@Article{ ferris.mangasarian:parallel*1, 28593 author = {M. C. Ferris and O. L. Mangasarian}, 28594 title = {Parallel Variable Distribution}, 28595 journal = {SIAM Journal on Optimization}, 28596 year = {1994}, 28597 volume = {4}, 28598 pages = {815--832}, 28599 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28600 key = {31} 28601} 28602 28603@Article{ ferris.meeraus.ea:computing, 28604 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28605 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28606 journal = {Optimization Methods and Software}, 28607 year = {1999}, 28608 volume = {10}, 28609 pages = {669--685}, 28610 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28611 key = {45} 28612} 28613 28614@Article{ ferris.mesnier.ea:neos, 28615 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28616 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28617 {I}nternet}, 28618 year = {2000}, 28619 journal = {{ACM} Transactions on Mathematical Software}, 28620 key = {54}, 28621 volume = {26}, 28622 pages = {1--18}, 28623 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28624 institution = {Computer Sciences Department, University of Wisconsin}, 28625 address = {Madison, Wisconsin}, 28626 number = {96-08}, 28627 type = {Mathematical Programming Technical Report}, 28628 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28629 Argonne National Laboratory}, 28630 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28631 1996} 28632} 28633 28634@InCollection{ ferris.meyer:models, 28635 author = {M. C. Ferris and R. R. Meyer}, 28636 title = {Models and Solution for On-Demand Data Delivery Problems}, 28637 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28638 key = {80}, 28639 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28640 Problems}, 28641 editor = {P. M. Pardalos}, 28642 series = {Nonconvex Optimization and its Applications}, 28643 volume = {42}, 28644 address = {Dordrect}, 28645 year = {2000}, 28646 pages = {175--188}, 28647 publisher = {Kluwer}, 28648 type = {Mathematical Programming Technical Report}, 28649 institution = {Computer Sciences Department, University of Wisconsin}, 28650 number = {99-04} 28651} 28652 28653@InProceedings{ ferris.munson.ea:homotopy, 28654 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28655 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28656 booktitle = {Numerical Analysis 1999}, 28657 key = {88}, 28658 year = {2000}, 28659 editor = {D. F. Griffiths and G. A. Watson}, 28660 series = {Research Notes in Mathematics}, 28661 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28662 address = {London}, 28663 pages = {143--167}, 28664 publisher = {Chapman and Hall}, 28665 institution = {Computer Sciences Department, University of Wisconsin}, 28666 number = {99-09}, 28667 type = {Mathematical Programming Technical Report} 28668} 28669 28670@TechReport{ ferris.munson.ea:practical, 28671 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28672 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28673 type = {Data Mining Institute Technical Report}, 28674 institution = {Computer Sciences Department, University of Wisconsin}, 28675 address = {Madison, Wisconsin}, 28676 year = {2000}, 28677 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28678 number = {00-03}, 28679 key = {92}, 28680 annote = {To appear in WSC 2000} 28681} 28682 28683@InCollection{ ferris.munson:case, 28684 author = {M. C. Ferris and T. S. Munson}, 28685 title = {Case Studies in Complementarity: Improving Model Formulation}, 28686 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28687 key = {73}, 28688 pages = {79--98}, 28689 publisher = {Springer Verlag}, 28690 year = {1999}, 28691 editor = {M. Th\'{e}ra and R. Tichatschke}, 28692 number = {477}, 28693 series = {Lecture Notes in Economics and Mathematical Systems}, 28694 address = {Berlin}, 28695 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28696 type = {Mathematical Programming Technical Report}, 28697 institution = {Computer Sciences Department, University of Wisconsin} 28698} 28699 28700@Article{ ferris.munson:complementarity, 28701 author = {M. C. Ferris and T. S. Munson}, 28702 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28703 year = {2000}, 28704 volume = {24}, 28705 pages = {165--188}, 28706 journal = {Journal of Economic Dynamics and Control}, 28707 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28708 key = {70}, 28709 type = {Mathematical Programming Technical Report}, 28710 institution = {Computer Sciences Department, University of Wisconsin}, 28711 address = {Madison, Wisconsin}, 28712 number = {98-12} 28713} 28714 28715@Misc{ ferris.munson:condor, 28716 author = {M. C. Ferris and T. S. Munson}, 28717 title = {Condor Modeling Language Interface}, 28718 organization = {Computer Sciences Department, University of Wisconsin}, 28719 address = {Madison, Wisconsin}, 28720 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28721} 28722 28723@Manual{ ferris.munson:gams, 28724 author = {M. C. Ferris and T. S. Munson}, 28725 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28726 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28727} 28728 28729@Article{ ferris.munson:interfaces, 28730 author = {M. C. Ferris and T. S. Munson}, 28731 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28732 journal = {Computational Optimization and Applications}, 28733 volume = {12}, 28734 pages = {207--227}, 28735 year = {1999}, 28736 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28737 key = {63}, 28738 institution = {Computer Sciences Department, University of Wisconsin}, 28739 address = {Madison, Wisconsin}, 28740 number = {97-12}, 28741 type = {Mathematical Programming Technical Report} 28742} 28743 28744@TechReport{ ferris.munson:interior, 28745 author = {M. C. Ferris and T. S. Munson}, 28746 title = {Interior Point Methods for Massive Support Vector Machines}, 28747 institution = {Computer Sciences Department, University of Wisconsin}, 28748 year = {2000}, 28749 key = {94}, 28750 type = {Data Mining Institute Technical Report}, 28751 number = {00-05}, 28752 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28753 address = {Madison, Wisconsin}, 28754 annote = {Submitted to SIOPT} 28755} 28756 28757@Article{ ferris.munson:linear, 28758 author = {M. C. Ferris and T. S. Munson}, 28759 title = {Linear Programming for Emergency Broadcast Systems}, 28760 year = {1999}, 28761 journal = {{SIAG/OPT} Newsletter}, 28762 volume = {10}, 28763 pages = {6--8}, 28764 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28765 key = {76}, 28766 type = {Mathematical Programming Technical Report}, 28767 institution = {Computer Sciences Department, University of Wisconsin}, 28768 address = {Madison, Wisconsin}, 28769 number = {98-20} 28770} 28771 28772@Article{ ferris.munson:modeling, 28773 author = {M. C. Ferris and T. S. Munson}, 28774 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28775 year = {2000}, 28776 journal = {Mathematical Programming}, 28777 volume = {88}, 28778 pages = {487--506}, 28779 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28780 key = {71}, 28781 type = {Mathematical Programming Technical Report}, 28782 institution = {Computer Sciences Department, University of Wisconsin}, 28783 address = {Madison, Wisconsin}, 28784 number = {98-13} 28785} 28786 28787@TechReport{ ferris.munson:preprocessing, 28788 author = {M. C. Ferris and T. S. Munson}, 28789 title = {Preprocessing Complementarity Problems}, 28790 type = {Mathematical Programming Technical Report}, 28791 institution = {Computer Sciences Department, University of Wisconsin}, 28792 address = {Madison, Wisconsin}, 28793 year = {1999}, 28794 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28795 number = {99-07}, 28796 key = {86}, 28797 annote = {Submitted to ICCP 99} 28798} 28799 28800@TechReport{ ferris.munson:semismooth, 28801 author = {M. C. Ferris and T. S. Munson}, 28802 title = {Semismooth Support Vector Machines}, 28803 institution = {Computer Sciences Department, University of Wisconsin}, 28804 year = {2000}, 28805 key = {97}, 28806 type = {Data Mining Institute Technical Report}, 28807 number = {00-09}, 28808 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28809 address = {Madison, Wisconsin}, 28810 annote = {Submitted to Math Prog B} 28811} 28812 28813@Article{ ferris.pang:engineering, 28814 author = {M. C. Ferris and J. S. Pang}, 28815 title = {Engineering and Economic Applications of Complementarity Problems}, 28816 year = {1997}, 28817 journal = {SIAM Review}, 28818 volume = {39}, 28819 pages = {669--713}, 28820 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28821 key = {46} 28822} 28823 28824@Article{ ferris.pang:nondegenerate, 28825 author = {M. C. Ferris and J. S. Pang}, 28826 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28827 journal = {SIAM Journal on Control and Optimization}, 28828 year = {1996}, 28829 volume = {34}, 28830 pages = {244--263}, 28831 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28832 key = {35} 28833} 28834 28835@Article{ ferris.philpott:affine, 28836 author = {M. C. Ferris and A. B. Philpott}, 28837 title = {On Affine Scaling and Semi--Infinite Programming}, 28838 journal = {Mathematical Programming}, 28839 year = {1992}, 28840 volume = {56}, 28841 pages = {361--364}, 28842 key = {15} 28843} 28844 28845@Article{ ferris.philpott:interior, 28846 author = {M. C. Ferris and A. B. Philpott}, 28847 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28848 journal = {Mathematical Programming}, 28849 year = {1989}, 28850 volume = {43}, 28851 pages = {257--276}, 28852 key = {04} 28853} 28854 28855@Article{ ferris.philpott:performance, 28856 author = {M. C. Ferris and A. B. Philpott}, 28857 title = {On the Performance of {K}armarkar's Algorithm}, 28858 journal = {Journal of the Operational Research Society}, 28859 year = {1988}, 28860 volume = {39}, 28861 pages = {257--270}, 28862 key = {03} 28863} 28864 28865@InCollection{ ferris.ralph:projected, 28866 author = {M. C. Ferris and D. Ralph}, 28867 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28868 Maps}, 28869 booktitle = {Recent Advances in Nonsmooth Optimization}, 28870 publisher = {World Scientific Publishers}, 28871 year = {1995}, 28872 pages = {57--87}, 28873 editor = {D. Du and L. Qi and R. Womersley}, 28874 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28875 key = {41} 28876} 28877 28878@Article{ ferris.ruszczynski:robust, 28879 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28880 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28881 year = {2000}, 28882 journal = {Networks}, 28883 volume = {35}, 28884 pages = {181--194}, 28885 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28886 key = {60} 28887} 28888 28889@InCollection{ ferris.rutherford:accessing, 28890 author = {M. C. Ferris and T. F. Rutherford}, 28891 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28892 booktitle = {Nonlinear Optimization and Applications}, 28893 key = {48}, 28894 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28895 editor = {G. Di Pillo and F. Giannessi}, 28896 year = {1996}, 28897 pages = {141--153}, 28898 publisher = {Plenum Press}, 28899 address = {New York} 28900} 28901 28902@InCollection{ ferris.shepard:optimizing, 28903 author = {M. C. Ferris and D. M. Shepard}, 28904 title = {Optimization of Gamma Knife Radiosurgery}, 28905 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28906 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28907 publisher = {AMS}, 28908 year = {2000}, 28909 optseries = {DIMACS}, 28910 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28911 key = {91}, 28912 type = {Data Mining Institute Technical Report}, 28913 institution = {Computer Sciences Department, University of Wisconsin}, 28914 address = {Madison, Wisconsin}, 28915 number = {00-01} 28916} 28917 28918@InCollection{ ferris.sinapiromsaran:formulating, 28919 author = {M. C. Ferris and K. Sinapiromsaran}, 28920 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28921 booktitle = {Optimization}, 28922 key = {77}, 28923 publisher = {Springer-Verlag}, 28924 year = {2000}, 28925 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28926 volume = {481}, 28927 series = {Lecture Notes in Economics and Mathematical Systems}, 28928 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28929 type = {Mathematical Programming Technical Report}, 28930 institution = {Computer Sciences Department, University of Wisconsin}, 28931 address = {Madison, Wisconsin}, 28932 number = {98-21} 28933} 28934 28935@Article{ ferris.tin-loi:limit, 28936 author = {M. C. Ferris and F. Tin-Loi}, 28937 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28938 Complementarity Constraints}, 28939 year = {2001}, 28940 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28941 key = {78}, 28942 journal = {International Journal of Mechanical Sciences}, 28943 pages = {209--224}, 28944 volume = {43}, 28945 type = {Mathematical Programming Technical Report}, 28946 institution = {Computer Sciences Department, University of Wisconsin}, 28947 address = {Madison, Wisconsin}, 28948 number = {99-01} 28949} 28950 28951@Article{ ferris.tin-loi:nonlinear, 28952 author = {M. C. Ferris and F. Tin-Loi}, 28953 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28954 Elastoplasticity}, 28955 year = {1998}, 28956 key = {64}, 28957 volume = {6}, 28958 pages = {857--870}, 28959 journal = {Structural Engineering and Mechanics} 28960} 28961 28962@Article{ ferris.tin-loi:solution, 28963 author = {M. C. Ferris and F. Tin-Loi}, 28964 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28965 and Complementarity Constraints}, 28966 year = {1999}, 28967 journal = {Computer Methods in Applied Mechanics and Engineering}, 28968 volume = {174}, 28969 pages = {107--120}, 28970 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 28971 key = {66} 28972} 28973 28974@Article{ ferris.vlach:scheduling, 28975 author = {M. C. Ferris and M. Vlach}, 28976 title = {Scheduling with Earliness and Tardiness Penalties}, 28977 journal = {Naval Research Logistics Quarterly}, 28978 year = {1992}, 28979 volume = {39}, 28980 pages = {229--245}, 28981 key = {13} 28982} 28983 28984@TechReport{ ferris.zavriev:linear, 28985 author = {M. C. Ferris and S. K Zavriev}, 28986 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 28987 institution = {Computer Sciences Department, University of Wisconsin}, 28988 year = {1996}, 28989 key = {56}, 28990 address = {Madison, Wisconsin}, 28991 type = {Mathematical Programming Technical Report}, 28992 number = {96--12}, 28993 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 28994} 28995 28996@Article{ ferris:finite, 28997 author = {M. C. Ferris}, 28998 title = {Finite Termination of the Proximal Point Algorithm}, 28999 journal = {Mathematical Programming}, 29000 year = {1991}, 29001 volume = {50}, 29002 pages = {359--366}, 29003 key = {06} 29004} 29005 29006@Article{ ferris:iterative, 29007 author = {M. C. Ferris}, 29008 title = {Iterative Linear Programming Solution of Convex Programs}, 29009 journal = {Journal of Optimization Theory and Applications}, 29010 year = {1990}, 29011 volume = {65}, 29012 pages = {53--65}, 29013 key = {07} 29014} 29015 29016@Article{ ferris:linear, 29017 author = {M. C. Ferris}, 29018 title = {The Linear Complementarity Problem}, 29019 journal = {Bulletin of the American Mathematical Society}, 29020 year = {1993}, 29021 volume = {28}, 29022 pages = {169--175}, 29023 key = {27} 29024} 29025 29026@MastersThesis{ ferris:linear*1, 29027 author = {M. C. Ferris}, 29028 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 29029 Solving a Class of Structural Optimization Problems}, 29030 year = {1985}, 29031 school = {University of Cambridge}, 29032 address = {England}, 29033 key = {01} 29034} 29035 29036@TechReport{ ferris:matlab, 29037 author = {M. C. Ferris}, 29038 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 29039 institution = {Computer Sciences Department, University of Wisconsin}, 29040 year = {1998}, 29041 address = {Madison, Wisconsin}, 29042 type = {Mathematical Programming Technical Report}, 29043 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 29044 number = {98-19}, 29045 key = {75} 29046} 29047 29048@Article{ ferris:parallel, 29049 author = {M. C. Ferris}, 29050 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 29051 journal = {Mathematics of Operations Research}, 29052 year = {1994}, 29053 volume = {19}, 29054 pages = {645--658}, 29055 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 29056 key = {20} 29057} 29058 29059@TechReport{ ferris:parallel*1, 29060 author = {M. C. Ferris}, 29061 title = {Parallel Solution of Extremely Large Knapsack Problems}, 29062 institution = {Computer Sciences Department, University of Wisconsin}, 29063 year = {1989}, 29064 address = {Madison, Wisconsin}, 29065 number = {842}, 29066 key = {09} 29067} 29068 29069@PhDThesis{ ferris:weak, 29070 author = {M. C. Ferris}, 29071 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29072 year = {1988}, 29073 school = {University of Cambridge}, 29074 address = {England}, 29075 key = {02} 29076} 29077 29078@TechReport{ ferris:weak*1, 29079 author = {M. C. Ferris}, 29080 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29081 institution = {Computer Sciences Department, University of Wisconsin}, 29082 year = {1988}, 29083 address = {Madison, Wisconsin}, 29084 number = {779}, 29085 key = {05} 29086} 29087 29088@Book{ fiacco.mccormick:nonlinear, 29089 author = {A. V. Fiacco and G. P. McCormick}, 29090 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 29091 year = {1968}, 29092 publisher = {John Wiley \& Sons}, 29093 address = {New York}, 29094 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 29095} 29096 29097@Book{ fiacco:introduction, 29098 author = {A. V. Fiacco}, 29099 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 29100 year = {1983}, 29101 publisher = {Academic Press}, 29102 address = {New York} 29103} 29104 29105@Article{ fiedler.ptak:matrices, 29106 author = {M. Fiedler and V. Pt\'{a}k}, 29107 title = {On matrices with nonpositive off-diagonal elements and positive principal 29108 minors}, 29109 journal = {Czechoslovak Mathematics Journal}, 29110 volume = {12}, 29111 pages = {382--400}, 29112 year = {1962} 29113} 29114 29115@Article{ fischer.kanzow:finite, 29116 author = {A. Fischer and C. Kanzow}, 29117 title = {On Finite Termination of an Iterative Method for Linear Complementarity 29118 Problems}, 29119 journal = {Mathematical Programming}, 29120 volume = {74}, 29121 pages = {279--292}, 29122 year = {1996} 29123} 29124 29125@TechReport{ fischer:constrained, 29126 author = {A. Fischer}, 29127 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 29128 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 29129 year = {1995}, 29130 type = {Technical Report}, 29131 number = {MATH-NM-10-1995}, 29132 address = {Dresden} 29133} 29134 29135@Article{ fischer:local, 29136 author = {A. Fischer}, 29137 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 29138 weak conditions}, 29139 journal = {Optimization Methods and Software}, 29140 year = {1995}, 29141 volume = {6}, 29142 pages = {83--107} 29143} 29144 29145@InCollection{ fischer:ncp-function, 29146 author = {A. Fischer}, 29147 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 29148 booktitle = {Recent Advances in Nonsmooth Optimization}, 29149 publisher = {World Scientific Publishers}, 29150 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 29151 year = {1995}, 29152 pages = {88--105} 29153} 29154 29155@Article{ fischer:newton-type, 29156 author = {A. Fischer}, 29157 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 29158 Problems}, 29159 journal = {Journal of Optimization Theory and Applications}, 29160 year = {1995}, 29161 volume = {86}, 29162 pages = {585--608} 29163} 29164 29165@Article{ fischer:solution, 29166 author = {A. Fischer}, 29167 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 29168 Functions}, 29169 year = {1997}, 29170 journal = {Mathematical Programming}, 29171 pages = {513--532} 29172} 29173 29174@Article{ fischer:special, 29175 author = {A. Fischer}, 29176 title = {A Special {N}ewton--Type Optimization Method}, 29177 journal = {Optimization}, 29178 year = {1992}, 29179 volume = {24}, 29180 pages = {269--284} 29181} 29182 29183@Article{ fisher:use, 29184 author = {R. A. Fisher}, 29185 title = {The Use of Multiple Measurements in Taxonomic Problems}, 29186 journal = {Annual Eugenics}, 29187 year = {1936}, 29188 volume = {7}, 29189 number = {Part II}, 29190 pages = {179--188} 29191} 29192 29193@Book{ fishman:principles, 29194 author = {G. Fishman}, 29195 title = {Principles of Discrete Event Simulation}, 29196 publisher = {Wiley}, 29197 address = {New York, NY}, 29198 year = {1978} 29199} 29200 29201@Article{ fitchard.aldridge.ea:registration, 29202 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 29203 title = {Registration of Synthetic Tomographic Projection Data Sets Using 29204 Cross-Correlation}, 29205 journal = {Physics in Medicine and Biology}, 29206 year = {1998}, 29207 volume = {43}, 29208 pages = {1645--1657} 29209} 29210 29211@Article{ fletcher.matthews:stable, 29212 author = {R. Fletcher and S. P. J. Matthews}, 29213 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 29214 journal = {Mathematical Programming}, 29215 year = {1984}, 29216 volume = {30}, 29217 pages = {267--284} 29218} 29219 29220@TechReport{ fletcher.maza:nonlinear, 29221 author = {R. Fletcher and E. Sainz de la Maza}, 29222 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 29223 Programming}, 29224 institution = {Department of Mathematical Sciences}, 29225 year = {1987}, 29226 address = {The University, Dundee, Scotland}, 29227 number = {NA/100}, 29228 type = {Numerical Analysis Report} 29229} 29230 29231@InCollection{ fletcher:class, 29232 author = {R. Fletcher}, 29233 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 29234 Properties}, 29235 booktitle = {Integer and Nonlinear Programming}, 29236 year = {1970}, 29237 editor = {J. Abadie}, 29238 publisher = {North--Holland}, 29239 address = {Amsterdam}, 29240 pages = {157--173} 29241} 29242 29243@Article{ fletcher:exact, 29244 author = {R. Fletcher}, 29245 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 29246 journal = {Mathematical Programming}, 29247 year = {1973}, 29248 volume = {5}, 29249 pages = {129--150} 29250} 29251 29252@Article{ fletcher:generalized, 29253 author = {R. Fletcher}, 29254 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 29255 Equations}, 29256 journal = {The Computer Journal}, 29257 year = {1968}, 29258 volume = {10}, 29259 pages = {392--399} 29260} 29261 29262@InProceedings{ fletcher:penalty, 29263 crossref = {bachem.grotschel.ea:mathematical}, 29264 author = {R. Fletcher}, 29265 title = {Penalty Functions}, 29266 pages = {87--114} 29267} 29268 29269@Book{ fletcher:practical, 29270 author = {R. 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Gill}, 29379 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 29380 institution = {Department of Mathematics, University of California}, 29381 year = {1996}, 29382 type = {Report NA}, 29383 number = {96-3}, 29384 address = {San Diego} 29385} 29386 29387@InCollection{ fortin.glowinski:decomposition-coordination, 29388 author = {M. Fortin and R. Glowinski}, 29389 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 29390 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 29391 Problems}, 29392 publisher = {North-Holland}, 29393 year = {1983}, 29394 editor = {M. Fortin and R. Glowinski}, 29395 address = {Amsterdam} 29396} 29397 29398@Misc{ foster.kesselman:globus, 29399 author = {I. Foster and C. Kesselman}, 29400 title = {The Globus Project}, 29401 howpublished = {www.globus.org} 29402} 29403 29404@Article{ foster.kesselman:globus*1, 29405 author = {I. Foster and C. 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Gao}, 29731 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 29732 Conditions}, 29733 type = {Manuscript}, 29734 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 29735 month = oct, 29736 year = {1994} 29737} 29738 29739@Article{ garcia-palomares.mangasarian:superlinearly, 29740 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 29741 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 29742 Optimization Problems}, 29743 journal = {Mathematical Programming}, 29744 year = {1976}, 29745 volume = {11}, 29746 pages = {1--13} 29747} 29748 29749@Article{ garcia-palomares.restuccia:global, 29750 author = {U. M. {Garcia--Palomares} and A. 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Zangwill}, 29776 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 29777 year = {1981}, 29778 publisher = {Prentice-Hall, Inc}, 29779 address = {Englewood Cliffs, New Jersey} 29780} 29781 29782@Book{ garey.johnson:computers, 29783 author = {M. R. Garey and D. S. Johnson}, 29784 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 29785 year = {1979}, 29786 publisher = {W.H. Freeman and Company}, 29787 address = {San Francisco} 29788} 29789 29790@Article{ garey.tarjan.ea:one-processor, 29791 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 29792 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 29793 journal = {Mathematics of Operations Research}, 29794 year = {1988}, 29795 volume = {13}, 29796 pages = {330--348} 29797} 29798 29799@Book{ garfinkel.nemhauser:integer, 29800 author = {R. S. Garfinkel and G. L. Nemhauser}, 29801 title = {Integer Programming}, 29802 year = {1972}, 29803 publisher = {John Wiley \& Sons}, 29804 address = {New York} 29805} 29806 29807@Book{ gass:linear, 29808 author = {S. Gass}, 29809 title = {Linear Programming Methods and Applications}, 29810 edition = {Fifth}, 29811 publisher = {Boyd and Fraser Publishing Company}, 29812 address = {Danvers, Massachusetts}, 29813 year = {1985} 29814} 29815 29816@InProceedings{ gay:combining, 29817 author = {D. M. Gay}, 29818 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 29819 booktitle = {Sparse Matrix Proceedings 1978}, 29820 editor = {I. S. Duff and G. W. Stewart}, 29821 year = {1978}, 29822 organization = {SIAM}, 29823 address = {Philadelphia, Pennsylvania}, 29824 pages = {313--334} 29825} 29826 29827@Article{ gay:electronic, 29828 author = {D. M. Gay}, 29829 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 29830 journal = {{COAL} Newsletter}, 29831 year = {1985}, 29832 volume = {13}, 29833 pages = {10--12} 29834} 29835 29836@TechReport{ gay:hooking, 29837 author = {D. M. Gay}, 29838 title = {Hooking Your Solver to {AMPL}}, 29839 year = {1997}, 29840 institution = {Bell Laboratories}, 29841 address = {Murray Hill, New Jersey}, 29842 note = {Revised 1994, 1997} 29843} 29844 29845@Article{ gay:variant, 29846 author = {D. Gay}, 29847 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 29848 Form}, 29849 journal = {Mathematical Programming}, 29850 year = {1987}, 29851 volume = {37}, 29852 pages = {81--90} 29853} 29854 29855@Article{ geiger.kanzow:resolution, 29856 author = {C. Geiger and C. Kanzow}, 29857 title = {On the Resolution of Monotone Complementarity Problems}, 29858 journal = {Computational Optimization and Applications}, 29859 volume = {5}, 29860 year = {1996}, 29861 pages = {155--173} 29862} 29863 29864@Book{ geist.beguelin.ea:pvm, 29865 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 29866 V. S. Sunderam}, 29867 title = {{PVM}: Parallel Virtual Machine}, 29868 publisher = {MIT Press}, 29869 address = {Cambridge, Massachusetts}, 29870 year = {1994} 29871} 29872 29873@Article{ gendron.crainic:parallel, 29874 author = {B. Gendron and T. G. Crainic}, 29875 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 29876 journal = {Operations Research}, 29877 year = {1994}, 29878 volume = {42}, 29879 pages = {1042--1060} 29880} 29881 29882@Article{ george:automatic, 29883 author = {A. George}, 29884 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 29885 journal = {SIAM Journal on Numerical Analysis}, 29886 vol = {17}, 29887 pages = {740--751}, 29888 year = {1980} 29889} 29890 29891@InProceedings{ georges-schleuter:asparagos, 29892 crossref = {schaeffer:third}, 29893 author = {M. Georges--Schleuter}, 29894 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 29895 pages = {416--421} 29896} 29897 29898@Article{ georgiou:comments, 29899 author = {G. M. Georgiou}, 29900 title = {Comments On Hidden Nodes in Neural Nets}, 29901 journal = {IEEE Transactions on Circuits and Systems}, 29902 year = {1991}, 29903 volume = {38}, 29904 pages = {1410} 29905} 29906 29907@TechReport{ gertz.linderoth.ea:object-oriented, 29908 author = {M. Gertz and J. Linderoth and S. Wright}, 29909 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 29910 institution = {MCS Division, Argonne National Laboratory}, 29911 year = {in preparation} 29912} 29913 29914@Article{ ghellinck.vial:polynomial, 29915 author = {G. de Ghellinck and J.--Ph. Vial}, 29916 title = {A Polynomial {N}ewton Method for Linear Programming}, 29917 journal = {Algorithmica}, 29918 year = {1986}, 29919 volume = {1}, 29920 pages = {425--453} 29921} 29922 29923@InCollection{ gilbert.ng:predicting, 29924 author = {J. R. Gilbert and E. Ng}, 29925 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 29926 year = {1993}, 29927 booktitle = {Graph Theory and Sparse Matrix Computation}, 29928 editor = {A. George and J. Gilbert and J. Liu}, 29929 publisher = {Springer-Verlag} 29930} 29931 29932@Article{ gilbert-lemarechal, 29933 author = {J. C. Gilbert and C. Lemarechal}, 29934 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 29935 journal = {Mathematical Programming}, 29936 year = {1989}, 29937 volume = {45}, 29938 pages = {407--434} 29939} 29940 29941@Article{ gill.murray.ea:computing, 29942 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29943 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 29944 journal = {SIAM Journal on Scientific and Statistical Computing}, 29945 year = {1983}, 29946 volume = {4}, 29947 pages = {310--321} 29948} 29949 29950@Article{ gill.murray.ea:maintaining, 29951 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29952 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 29953 year = {1987}, 29954 journal = {Linear Algebra and Its Applications}, 29955 volume = {88/89}, 29956 pages = {239--270} 29957} 29958 29959@Book{ gill.murray.ea:practical, 29960 author = {P. E. Gill and W. Murray and M. H. 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Maguregui}, 33102 title = {A modified {N}ewton algorithm for functions over convex sets}, 33103 crossref = {mangasarian.meyer.ea:nonlinear*3}, 33104 pages = {461--473} 33105} 33106 33107@PhDThesis{ maguregui:regular, 33108 author = {J. Maguregui}, 33109 title = {Regular Multivalued Functions and Algorithmic Applications}, 33110 year = {1977}, 33111 address = {Madison, Wisconsin}, 33112 school = {Computer Sciences Department, University of Wisconsin} 33113} 33114 33115@Article{ mahey.oualibouch.ea:proximal, 33116 author = {P. Mahey and S. Oualibouch and D. T. Pham}, 33117 title = {Proximal Decomposition on the Graph of a Maximal Monotone Operator}, 33118 journal = {SIAM Journal on Optimization}, 33119 year = {1995}, 33120 volume = {5}, 33121 pages = {454--466} 33122} 33123 33124@Article{ mahey.pham:partial, 33125 author = {P. Mahey and D. T. Pham}, 33126 title = {Partial Regularization of the Sum of Two Maximal Monotone Operators}, 33127 journal = {{RAIRO} Mod\'{e}lisation et Analyse Num\'{e}rique}, 33128 year = {1993}, 33129 volume = {27}, 33130 pages = {375--392} 33131} 33132 33133@InCollection{ maier.novati:shakedown, 33134 author = {G. Maier and G. Novati}, 33135 title = {A shakedown and bounding theory allowing for nonlinear hardening and second order 33136 geometric effects with reference to discrete structural models}, 33137 editors = {J. A. K{\"{o}}nig and M. Kleiber}, 33138 booktitle = {Inelastic Solids and Structures, A. Sawczuk memorial volume}, 33139 publisher = {Pineridge Press}, 33140 address = {Swansea}, 33141 year = {1990}, 33142 pages = {451--471} 33143} 33144 33145@Article{ maier:incremental, 33146 author = {G. Maier}, 33147 title = {Incremental Plastic Analysis in the Presence of Large Displacement and Physical 33148 Instabilizing Effects}, 33149 journal = {International Journal of Solids and Structures}, 33150 volume = {7}, 33151 year = {1971}, 33152 pages = {345--372} 33153} 33154 33155@InCollection{ maier:inverse, 33156 author = {G. Maier}, 33157 title = {Inverse Problems in Engineering Plasticity: {A} Quadratic Programming Approach}, 33158 booktitle = {Serie VIII}, 33159 publisher = {Academia Nazionale dei Lincei}, 33160 year = {1981}, 33161 volume = {LXX}, 33162 pages = {203--209} 33163} 33164 33165@Article{ maier:matrix, 33166 author = {G. Maier}, 33167 title = {A matrix structural theory of piecewise linear elastoplasticity with interacting 33168 yield planes}, 33169 journal = {Meccanica}, 33170 volume = {5}, 33171 year = {1970}, 33172 pages = {54--66} 33173} 33174 33175@Article{ maier:quadratic, 33176 author = {G. Maier}, 33177 title = {A quadratic programming approach for certain classes of nonlinear structural 33178 problems}, 33179 journal = {Meccanica}, 33180 volume = {3}, 33181 year = {1968}, 33182 pages = {121--130} 33183} 33184 33185@Book{ manber:introduction, 33186 author = {U. Manber}, 33187 title = {Introduction to Algorithms: {A} Creative Approach}, 33188 year = {1989}, 33189 publisher = {Addison-Wesley} 33190} 33191 33192@Article{ mangasarian.deleone:error, 33193 author = {O. L. Mangasarian and R. {De~Leone}}, 33194 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 33195 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 33196 journal = {Applied Mathematics and Optimization}, 33197 year = {1988}, 33198 volume = {17}, 33199 pages = {1--14} 33200} 33201 33202@Article{ mangasarian.deleone:parallel, 33203 author = {O. L. Mangasarian and R. {De~Leone}}, 33204 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 33205 Problems and Linear Programs}, 33206 journal = {Journal of Optimization Theory and Applications}, 33207 year = {1987}, 33208 volume = {54}, 33209 pages = {437--446} 33210} 33211 33212@Article{ mangasarian.fromovitz:fritz, 33213 author = {O. L. Mangasarian and S. Fromovitz}, 33214 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 33215 and inequality constraints}, 33216 journal = {Journal of Mathematical Analysis and its Applications}, 33217 year = {1967}, 33218 volume = {17}, 33219 pages = {37--47} 33220} 33221 33222@Article{ mangasarian.mclinden:simple, 33223 author = {O. L. Mangasarian and L. McLinden}, 33224 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 33225 Programs}, 33226 journal = {Mathematical Programming}, 33227 year = {1985}, 33228 volume = {32}, 33229 pages = {32--40} 33230} 33231 33232@Article{ mangasarian.meyer:nonlinear, 33233 author = {O. L. Mangasarian and R. R. Meyer}, 33234 title = {Nonlinear Perturbation of Linear Programs}, 33235 journal = {SIAM Journal on Control and Optimization}, 33236 year = {1979}, 33237 volume = {17}, 33238 pages = {745--752} 33239} 33240 33241@TechReport{ mangasarian.musicant:active, 33242 author = {O. L. Mangasarian and David R. Musicant}, 33243 title = {Active Set Support Vector Machine Classification}, 33244 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33245 year = {2000}, 33246 number = {00-04}, 33247 address = {Madison, Wisconsin} 33248} 33249 33250@TechReport{ mangasarian.musicant:lagrangian, 33251 author = {O. L. Mangasarian and D. R. Musicant}, 33252 title = {Lagrangian Support Vector Machines}, 33253 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33254 year = {2000}, 33255 number = {00-06}, 33256 address = {Madison, Wisconsin} 33257} 33258 33259@TechReport{ mangasarian.musicant:robust, 33260 author = {O. L. Mangasarian and David R. Musicant}, 33261 title = {Robust Linear and Support Vector Regression}, 33262 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33263 year = {1999}, 33264 number = {99-09}, 33265 address = {Madison, Wisconsin} 33266} 33267 33268@Article{ mangasarian.musicant:successive, 33269 author = {O. L. Mangasarian and David R. Musicant}, 33270 title = {Successive Overrelaxation for Support Vector Machines}, 33271 journal = {IEEE Transactions on Neural Networks}, 33272 volume = {10}, 33273 year = {1999}, 33274 pages = {1032-1037} 33275} 33276 33277@Article{ mangasarian.pang:exact, 33278 author = {O. L. Mangasarian and J. S. Pang}, 33279 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 33280 Constraints}, 33281 journal = {Optimization}, 33282 year = {1997}, 33283 volume = {42}, 33284 pages = {1--8} 33285} 33286 33287@Article{ mangasarian.pang:extended, 33288 author = {O. L. Mangasarian and J. S. Pang}, 33289 title = {The Extended Linear Complementarity Problem}, 33290 journal = {SIAM Journal on Matrix Analysis and Applications}, 33291 year = {1994}, 33292 volume = {16} 33293} 33294 33295@Article{ mangasarian.ren:error, 33296 author = {O. L. Mangasarian and J. Ren}, 33297 title = {New error bounds for the nonlinear complementarity problem}, 33298 year = {1994}, 33299 volume = {1}, 33300 pages = {49--56}, 33301 journal = {Communications on Applied Nonlinear Analysis} 33302} 33303 33304@Article{ mangasarian.ren:improved, 33305 author = {O. L. Mangasarian and J. Ren}, 33306 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 33307 year = {1994}, 33308 volume = {66}, 33309 journal = {Mathematical Programming}, 33310 pages = {241--255} 33311} 33312 33313@InProceedings{ mangasarian.setiono.ea:pattern, 33314 crossref = {coleman.li:large-scale}, 33315 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 33316 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 33317 Diagnosis}, 33318 pages = {22--31} 33319} 33320 33321@Article{ mangasarian.shiau:error, 33322 author = {O. L. Mangasarian and T.--H. Shiau}, 33323 title = {Error Bounds for Monotone Linear Complementarity Problems}, 33324 journal = {Mathematical Programming}, 33325 year = {1986}, 33326 volume = {36}, 33327 pages = {81--89} 33328} 33329 33330@Article{ mangasarian.shiau:lipschitz, 33331 author = {O. L. Mangasarian and T.--H. Shiau}, 33332 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 33333 Complementarity Problems}, 33334 journal = {SIAM Journal on Control and Optimization}, 33335 year = {1987}, 33336 volume = {25}, 33337 pages = {583--595} 33338} 33339 33340@Article{ mangasarian.solodov:nonlinear, 33341 author = {O. L. Mangasarian and M. V. Solodov}, 33342 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 33343 journal = {Mathematical Programming}, 33344 year = {1993}, 33345 volume = {62}, 33346 pages = {277--298} 33347} 33348 33349@Article{ mangasarian.solodov:serial, 33350 author = {O. L. Mangasarian and M. V. Solodov}, 33351 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 33352 Minimization}, 33353 year = {1994}, 33354 journal = {Optimization Methods and Software}, 33355 volume = {4}, 33356 pages = {103--116} 33357} 33358 33359@Article{ mangasarian.street.ea:breast, 33360 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 33361 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 33362 journal = {Operations Research}, 33363 year = {1995}, 33364 volume = {43}, 33365 pages = {570--577} 33366} 33367 33368@Article{ mangasarian.wolberg:cancer, 33369 author = {O. L. Mangasarian and W. H. Wolberg}, 33370 title = {Cancer Diagnosis via Linear Programming}, 33371 journal = {SIAM News}, 33372 year = {1990}, 33373 volume = {23}, 33374 pages = {1 \& 18} 33375} 33376 33377@InCollection{ mangasarian:applications, 33378 author = {O. L. Mangasarian}, 33379 title = {Some Applications of Penalty Functions in Mathematical Programming}, 33380 booktitle = {Optimization and Related Fields}, 33381 year = {1986}, 33382 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 33383 publisher = {Springer-Verlag}, 33384 address = {Heidelberg}, 33385 pages = {307--329}, 33386 note = {Lecture Notes in Mathematics 1190} 33387} 33388 33389@Article{ mangasarian:characterization, 33390 author = {O. L. Mangasarian}, 33391 title = {Characterization of linear complementarity problems as linear programs}, 33392 journal = {Mathematical Programming Study}, 33393 year = {1978}, 33394 volume = {7}, 33395 pages = {74--87} 33396} 33397 33398@InProceedings{ mangasarian:condition, 33399 author = {O. L. Mangasarian}, 33400 title = {A condition number for linear inequalities and linear programs}, 33401 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 33402 1981}, 33403 year = {1981}, 33404 editor = {G. Bamberg and O. Opitz}, 33405 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 33406 address = {Konigstein}, 33407 pages = {3--15} 33408} 33409 33410@Article{ mangasarian:convergence, 33411 author = {O. L. Mangasarian}, 33412 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 33413 Symmetric Monotone Linear Complementarity Problem}, 33414 journal = {SIAM Journal on Optimization}, 33415 volume = {1}, 33416 pages = {114--122}, 33417 year = {1991} 33418} 33419 33420@Article{ mangasarian:equivalence, 33421 author = {O. L. Mangasarian}, 33422 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 33423 journal = {SIAM Journal on Applied Mathematics}, 33424 year = {1976}, 33425 volume = {31}, 33426 pages = {89--92} 33427} 33428 33429@Article{ mangasarian:error, 33430 author = {O. L. Mangasarian}, 33431 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 33432 journal = {ORSA Journal on Computing}, 33433 volume = {15}, 33434 pages = {187--192}, 33435 year = {1994} 33436} 33437 33438@Article{ mangasarian:error*1, 33439 author = {O. L. Mangasarian}, 33440 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 33441 journal = {Mathematical Programming}, 33442 year = {1990}, 33443 volume = {48}, 33444 pages = {437--445} 33445} 33446 33447@Article{ mangasarian:generalized, 33448 author = {O. L. Mangasarian}, 33449 title = {Generalized Linear Complementarity Problems as Linear Programs}, 33450 journal = {Methods of Operations Research}, 33451 year = {1979}, 33452 editor = {W. Oettli and F. Steffens}, 33453 volume = {31}, 33454 pages = {393--402} 33455} 33456 33457@InCollection{ mangasarian:generalized*1, 33458 author = {O. L. Mangasarian}, 33459 title = {Generalized Support Vector Machines}, 33460 year = {2000}, 33461 pages = {135-146}, 33462 booktitle = {Advances in Large Margin Classifiers}, 33463 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 33464 publisher = {MIT Press}, 33465 address = {Cambridge, MA} 33466} 33467 33468@Article{ mangasarian:global, 33469 author = {O. L. Mangasarian}, 33470 title = {Global error bounds for monotone affine variational inequality problems}, 33471 journal = {Linear Algebra and Its Applications}, 33472 year = {1992}, 33473 pages = {153--164} 33474} 33475 33476@InCollection{ mangasarian:least, 33477 author = {O. L. Mangasarian}, 33478 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 33479 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 33480 year = {1990}, 33481 publisher = {Oxford University Press}, 33482 address = {New York}, 33483 pages = {217--221} 33484} 33485 33486@Article{ mangasarian:least-norm, 33487 author = {O. L. Mangasarian}, 33488 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 33489 Problem}, 33490 journal = {Journal of Mathematical Analysis and Applications}, 33491 year = {1983}, 33492 volume = {92}, 33493 pages = {240--251} 33494} 33495 33496@Article{ mangasarian:linear, 33497 author = {O. L. Mangasarian}, 33498 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 33499 journal = {Mathematical Programming}, 33500 year = {1976}, 33501 volume = {10}, 33502 pages = {263--270} 33503} 33504 33505@Article{ mangasarian:linear*1, 33506 author = {O. L. Mangasarian}, 33507 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 33508 journal = {Operations Research}, 33509 year = {1965}, 33510 volume = {13}, 33511 pages = {444--452} 33512} 33513 33514@Article{ mangasarian:locally, 33515 author = {O. L. Mangasarian}, 33516 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 33517 Complementarity Problems}, 33518 journal = {Mathematical Programming}, 33519 year = {1980}, 33520 volume = {19}, 33521 pages = {200--212} 33522} 33523 33524@InCollection{ mangasarian:machine, 33525 author = {O. L. Mangasarian}, 33526 title = {Machine Learning via Polyhedral Concave Minimization}, 33527 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 33528 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 33529 pages = {175-188}, 33530 year = {1996}, 33531 address = {Heidelberg}, 33532 publisher = {Physica-Verlag A Springer-Verlag Company} 33533} 33534 33535@Article{ mangasarian:mathematical, 33536 author = {O. L. Mangasarian}, 33537 title = {Mathematical Programming in Neural Networks}, 33538 journal = {ORSA Journal on Computing}, 33539 volume = {5}, 33540 pages = {349--360}, 33541 year = {1993} 33542} 33543 33544@InProceedings{ mangasarian:mathematical*1, 33545 author = {O. L. Mangasarian}, 33546 title = {Mathematical Programming in Machine Learning}, 33547 booktitle = {Nonlinear Optimization and Applications}, 33548 editor = {G. Di Pillo and F. Giannessi}, 33549 publisher = {Plenum Publishing}, 33550 address = {New York}, 33551 pages = {283--295}, 33552 year = {1996} 33553} 33554 33555@Article{ mangasarian:mathematical*2, 33556 author = {O. L. Mangasarian}, 33557 title = {Mathematical Programming in Data Mining}, 33558 journal = {Data Mining and Knowledge Discovery}, 33559 volume = {1}, 33560 year = {1997}, 33561 pages = {183-201} 33562} 33563 33564@Article{ mangasarian:multi-surface, 33565 author = {O. L. Mangasarian}, 33566 title = {Multi-surface Method of Pattern Separation}, 33567 journal = {IEEE Transactions on Information Theory}, 33568 year = {1968}, 33569 volume = {IT-14}, 33570 pages = {801--807} 33571} 33572 33573@Book{ mangasarian:nonlinear, 33574 author = {O. L. Mangasarian}, 33575 title = {Nonlinear Programming}, 33576 year = {1969}, 33577 publisher = {McGraw--Hill}, 33578 address = {New York}, 33579 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 33580} 33581 33582@Article{ mangasarian:normal, 33583 author = {O. L. Mangasarian}, 33584 title = {Normal Solutions of Linear Programs}, 33585 journal = {Mathematical Programming Study}, 33586 year = {1984}, 33587 volume = {22}, 33588 pages = {206--216} 33589} 33590 33591@Article{ mangasarian:optimal, 33592 author = {O. L. Mangasarian}, 33593 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 33594 Linear Programs}, 33595 journal = {Journal of Optimization Theory and Applications}, 33596 year = {1981}, 33597 volume = {35}, 33598 pages = {123--128} 33599} 33600 33601@Article{ mangasarian:parallel, 33602 author = {O. L. Mangasarian}, 33603 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 33604 journal = {SIAM Journal on Control and Optimization}, 33605 volume = {33}, 33606 pages = {1916--1925}, 33607 year = {1995} 33608} 33609 33610@TechReport{ mangasarian:regularized, 33611 author = {O. L. 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Wang}, 35072 title = {Embedding Methods for Variational Inequality and Nonlinear Complementarity 35073 Problems}, 35074 institution = {Department of Mathematical Sciences, The Johns Hopkins University}, 35075 year = {1990}, 35076 address = {Baltimore, Maryland} 35077} 35078 35079@TechReport{ pang.yang:parallel, 35080 author = {J. S. Pang and J. M. Yang}, 35081 title = {Parallel {N}ewton Methods for the Nonlinear Complementarity Problem}, 35082 institution = {Department of Mathematical Sciences, The Johns Hopkins University}, 35083 year = {1987}, 35084 address = {Baltimore, Maryland}, 35085 type = {Manuscript} 35086} 35087 35088@Article{ pang.yu:linearized, 35089 author = {J. S. Pang and C. S. Yu}, 35090 title = {Linearized Simplicial Decomposition Methods for Computing Traffic Equilibria on 35091 Networks}, 35092 journal = {Networks}, 35093 volume = {14}, 35094 pages = {427--438}, 35095 year = {1984} 35096} 35097 35098@Article{ pang:b-differentiable, 35099 author = {J. S. 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Petri}, 35384 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35385 publisher = {Harvard University Press}, 35386 year = {1984} 35387} 35388 35389@InProceedings{ petrzykowski:application, 35390 author = {T. Petrzykowski}, 35391 title = {Application of the Steepest Ascent Method to Concave Programming}, 35392 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35393 year = {1962}, 35394 publisher = {North--Holland}, 35395 address = {Amsterdam}, 35396 pages = {185--189} 35397} 35398 35399@InProceedings{ pettey.leuze.ea:parallel, 35400 crossref = {grefenstette:genetic}, 35401 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35402 title = {A Parallel Genetic Algorithm}, 35403 pages = {155--161} 35404} 35405 35406@InProceedings{ pettey.leuze:theoretical, 35407 crossref = {schaeffer:third}, 35408 author = {C. C. Pettey and M. R. Leuze}, 35409 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35410 pages = {398--405} 35411} 35412 35413@Book{ pfeiffer.glocker:multibody, 35414 author = {F. Pfeiffer and C. Glocker}, 35415 title = {Multibody Dynamics with Unilateral Contact}, 35416 year = {1996}, 35417 publisher = {John Wiley \& Sons} 35418} 35419 35420@TechReport{ pierro.iusem:convergence, 35421 author = {A. R. de Pierro and A. N. Iusem}, 35422 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35423 Linear Complementarity Problems}, 35424 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35425 year = {1990}, 35426 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35427} 35428 35429@InCollection{ pillo.grippo.ea:class, 35430 author = {G. Di Pillo and L. Grippo and F. 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Polyak}, 35590 title = {Sharp Minima}, 35591 year = {1979}, 35592 note = {A Talk given at the {IIASA} Workshop on Generalized {L}agrangians and their 35593 Applications, {IIASA}, Laxenburg, Austria} 35594} 35595 35596@InProceedings{ polyak:smooth, 35597 author = {R. A. Polyak}, 35598 title = {Smooth Optimization Methods for Solving Nonlinear Extremal and Equilibrium 35599 Problems with Constraints}, 35600 booktitle = {Abstracts of the Papers of the 11th International Symposium on Mathematical 35601 Programming}, 35602 year = {1982}, 35603 address = {Bonn} 35604} 35605 35606@Article{ polychronopoulos.tsitsiklis:analysis, 35607 author = {G. H. Polychronopoulos and J. N. Tsitsiklis}, 35608 title = {Stochastic Shortest Path Problems with Recourse}, 35609 journal = {Networks}, 35610 year = {1996}, 35611 volume = {27}, 35612 pages = {133--143} 35613} 35614 35615@TechReport{ potra.bonnans:infeasible, 35616 author = {F. A. Potra and J. F. Bonnans}, 35617 title = {Infeasible path following algorithms for linear complementarity problems}, 35618 institution = {INRIA}, 35619 year = {1994}, 35620 month = dec, 35621 number = {RR--2445}, 35622 type = {Research Report} 35623} 35624 35625@Article{ potra.sheng:large-step, 35626 author = {F. A. Potra and R. Sheng}, 35627 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 35628 year = {1997}, 35629 journal = {SIAM Journal on Optimization}, 35630 volume = {7}, 35631 pages = {318--335} 35632} 35633 35634@Article{ potra:infeasible, 35635 author = {F. A. Potra}, 35636 title = {An infeasible interior-point predictor-corrector algorithm for linear 35637 programming}, 35638 journal = {SIAM Journal on Optimization}, 35639 year = {1996}, 35640 volume = {6}, 35641 pages = {19--32} 35642} 35643 35644@TechReport{ potra:onl, 35645 author = {F. A. Potra}, 35646 title = {An ${O}(n{L})$ infeasible--interior--point algorithm for {LCP} with quadratic 35647 convergence.}, 35648 institution = {Department of Mathematics, The University of Iowa}, 35649 address = {Iowa City, Iowa}, 35650 year = {1994}, 35651 number = {50}, 35652 type = {Reports on Computational Mathematics} 35653} 35654 35655@TechReport{ potra:predictor-corrector, 35656 author = {F. A. Potra}, 35657 title = {On a predictor-corrector method for solving linear programs from infeasible 35658 starting points}, 35659 institution = {Department of Mathematics, University of Iowa}, 35660 address = {Iowa City, Iowa}, 35661 year = {1992}, 35662 number = {34}, 35663 type = {Reports on Computational Mathematics} 35664} 35665 35666@TechReport{ potra:quadratically, 35667 author = {F. A. Potra}, 35668 title = {A quadratically convergent infeasible interior-point algorithm for linear 35669 programming}, 35670 institution = {Department of Mathematics, University of Iowa}, 35671 year = {1992}, 35672 number = {28}, 35673 address = {Iowa City, Iowa}, 35674 month = jul 35675} 35676 35677@InCollection{ powell:convergence, 35678 author = {M. J. D. Powell}, 35679 title = {The Convergence of Variable Metric Methods for Nonlinearly Constrained 35680 Optimization Calculations}, 35681 crossref = {mangasarian.meyer.ea:nonlinear*3}, 35682 pages = {27--63} 35683} 35684 35685@InProceedings{ powell:direct, 35686 author = {M. J. D. 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Pruyne}, 35787 title = {Resource Management Services for Parallel Applications}, 35788 school = {University of Wisconsin--Madison}, 35789 year = {1996}, 35790 address = {Madison, Wisconsin} 35791} 35792 35793@Book{ pshenichny.danilin:numerical, 35794 author = {B. N. Pshenichny and Yu. M. Danilin}, 35795 title = {Numerical Methods in Extremal Problems}, 35796 year = {1978}, 35797 publisher = {MIR Publishers}, 35798 address = {Moscow} 35799} 35800 35801@TechReport{ qi.chen:globally, 35802 author = {L. Qi and X. Chen}, 35803 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 35804 institution = {School of Mathematics, University of New South Wales}, 35805 year = {1993}, 35806 annote = {revised}, 35807 address = {Sydney} 35808} 35809 35810@Article{ qi.jiang:semismooth, 35811 author = {L. Qi and H. 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Ralph}, 35835 booktitle = {Progress in Optimization}, 35836 pages = {121--146}, 35837 series = {Applied Optimization}, 35838 volume = {30}, 35839 publisher = {Kluwer Academic Publishers}, 35840 address = {Dordrecht} 35841} 35842 35843@Article{ qi.sun:nonsmooth, 35844 author = {L. Qi and J. Sun}, 35845 title = {A Nonsmooth Version of {N}ewton's Method}, 35846 journal = {Mathematical Programming}, 35847 year = {1993}, 35848 volume = {58}, 35849 pages = {353--368} 35850} 35851 35852@Article{ qi:convergence, 35853 author = {L. Qi}, 35854 title = {Convergence Analysis of Some Algorithms for Solving Nonsmooth Equations}, 35855 journal = {Mathematics of Operations Research}, 35856 year = {1993}, 35857 volume = {18}, 35858 pages = {227--244} 35859} 35860 35861@TechReport{ qi:regular, 35862 author = {L. 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Rockafellar}, 36371 title = {Conjugate Duality and Optimization}, 36372 year = {1974}, 36373 publisher = {SIAM}, 36374 address = {Philadelphia, Pennsylvania}, 36375 volume = {16}, 36376 series = {Conference Board of the Mathematical Sciences} 36377} 36378 36379@Book{ rockafellar:convex, 36380 author = {R. T. Rockafellar}, 36381 title = {Convex Analysis}, 36382 year = {1970}, 36383 publisher = {Princeton University Press}, 36384 address = {Princeton, New Jersey} 36385} 36386 36387@Article{ rockafellar:first-, 36388 author = {R. T. Rockafellar}, 36389 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 36390 journal = {Transactions of the American Mathematical Society}, 36391 year = {1988}, 36392 volume = {307}, 36393 pages = {75--108} 36394} 36395 36396@InProceedings{ rockafellar:generalized, 36397 author = {R. T. Rockafellar}, 36398 title = {A Generalized Approach to Linear-Quadratic Programming}, 36399 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36400 Applications}, 36401 year = {1986}, 36402 pages = {58--66}, 36403 note = {(Xi'an, China)} 36404} 36405 36406@InProceedings{ rockafellar:generalized*1, 36407 crossref = {bachem.grotschel.ea:mathematical}, 36408 author = {R. T. Rockafellar}, 36409 title = {Generalized Subgradients in Mathematical Programming}, 36410 pages = {368--390} 36411} 36412 36413@InCollection{ rockafellar:large-scale, 36414 author = {R. T. Rockafellar}, 36415 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36416 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36417 chapter = {15}, 36418 year = {1991}, 36419 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 36420 publisher = {SIAM Publications}, 36421 pages = {247--261} 36422} 36423 36424@Article{ rockafellar:linear-quadratic, 36425 author = {R. T. Rockafellar}, 36426 title = {Linear-Quadratic Programming and Optimal Control}, 36427 journal = {SIAM Journal on Control and Optimization}, 36428 year = {1987}, 36429 volume = {25}, 36430 pages = {781--814} 36431} 36432 36433@Article{ rockafellar:maximality, 36434 author = {R. T. Rockafellar}, 36435 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 36436 journal = {Transactions of the American Mathematical Society}, 36437 year = {1970}, 36438 volume = {149}, 36439 pages = {75--88} 36440} 36441 36442@InCollection{ rockafellar:monotone, 36443 author = {R. T. Rockafellar}, 36444 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 36445 crossref = {mangasarian.meyer.ea:nonlinear*3}, 36446 pages = {1--26} 36447} 36448 36449@Article{ rockafellar:monotone*1, 36450 author = {R. T. 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Rockafellar}, 36479 title = {Network Flows and Monotropic Optimization}, 36480 publisher = {John Wiley}, 36481 year = {1984}, 36482 address = {New York} 36483} 36484 36485@Article{ rodrigues:mixed, 36486 author = {H. C. Rodrigues}, 36487 title = {A mixed variational formulation for shape optimization of solids with contact 36488 conditions}, 36489 journal = {Structural Optimization}, 36490 volume = {6}, 36491 year = {1993}, 36492 pages = {19--28} 36493} 36494 36495@Book{ rodrigues:obstacle, 36496 author = {J. F. Rodrigues}, 36497 title = {Obstacle Problems in Mathematical Physics}, 36498 publisher = {Elsevier Publishing Company}, 36499 address = {Amsterdam}, 36500 year = {1987} 36501} 36502 36503@Book{ roos.terlaky.ea:theory, 36504 author = {C. Roos and T. Terlaky and J.--Ph. Vial}, 36505 title = {Theory and Algorithms for Linear Optimization: An Interior-Point Approach}, 36506 publisher = {John Wiley \& Sons}, 36507 year = {1997}, 36508 address = {Chichester} 36509} 36510 36511@TechReport{ rosa:decomposition, 36512 author = {C. H. Rosa}, 36513 title = {A Decomposition Technique for Equilibrium Programming under Uncertainty}, 36514 institution = {IIASA}, 36515 year = {1996}, 36516 number = {WP-96-013}, 36517 address = {A-2361 Laxenburg, Austria} 36518} 36519 36520@Article{ rosen.lane.ea:treatment, 36521 author = {I. Rosen and R. Lane and S. Morrill and J. Belli}, 36522 title = {Treatment Plan Optimization Using Linear Programming}, 36523 journal = {Medical Physics}, 36524 year = {1990}, 36525 volume = {18}, 36526 number = {2}, 36527 pages = {141--152} 36528} 36529 36530@TechReport{ rosenblatt:perceptron-a, 36531 author = {F. 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