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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Appl. Phys.}, 1396 volume = {99}, 1397 year = {2006}, 1398 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf}, 1399 petsc_uses = {KSP} 1400} 1401 1402@InProceedings{ japios2006, 1403 author = {F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. 1404 Subramanian}, 1405 title = {Micromagnetic simulations of the dependence of domain wall width with grain size 1406 in systems with cubic and uniaxial anisotropy.}, 1407 booktitle = {Intermag 2006 Conference}, 1408 petsc_uses = {KSP} 1409} 1410 1411@Article{ kbmb2006, 1412 author = {A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain}, 1413 title = {A Micromagnetic Study of the Effect of Spatial Variations in Damping in 1414 Perpendicular Recording Heads}, 1415 journal = {IEEE Trans. Magn.}, 1416 volume = {42}, 1417 year = {2006}, 1418 pages = {2428--2430}, 1419 doi = {10.1109/TMAG.2006.879430}, 1420 petsc_uses = {KSP} 1421} 1422 1423@Article{ cclcw2006, 1424 author = {C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu}, 1425 title = {Control of Domain Wall Motion in Permalloy Ring}, 1426 journal = {IEEE Trans. Magn.}, 1427 volume = {42}, 1428 year = {2006}, 1429 pages = {2960--2962}, 1430 doi = {10.1109/TMAG.2006.878414}, 1431 petsc_uses = {KSP} 1432} 1433 1434@Article{ bfmfzczg2007, 1435 author = {Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and 1436 Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot}, 1437 title = {Micromagnetic modelling of ferromagnetic cones}, 1438 journal = {J. Magn. Magn. Mater.}, 1439 volume = {312}, 1440 year = {2007}, 1441 pages = {234-238}, 1442 url = {http://eprints.soton.ac.uk/45900/}, 1443 petsc_uses = {KSP} 1444} 1445 1446@PhDThesis{ rb2005, 1447 author = {Richard Boardman}, 1448 title = {Computer simulation studies of magnetic nanostructures}, 1449 school = {Computational Engineering and Design Group, School of Engineering Sciences, 1450 University of Southampton, United Kingdom}, 1451 year = {2005}, 1452 url = {http://www.soton.ac.uk/~rpb/thesis.pdf}, 1453 petsc_uses = {KSP} 1454} 1455 1456@InProceedings{ cwwy2006, 1457 author = {I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu}, 1458 title = {MPI Performance Analysis Tools on Blue Gene/L}, 1459 booktitle = {ACM/IEEE SC 2006 Conference (SC'06)}, 1460 year = {2006}, 1461 url = {http://sc06.supercomputing.org/schedule/pdf/pap159.pdf}, 1462 petsc_uses = {KSP} 1463} 1464 1465@InProceedings{ ch2006, 1466 author = {I.-H. Chung and J.K. Hollingsworth}, 1467 title = {A Case Study Using Automatic Performance Tuning for Large-Scale Scientific 1468 Programs}, 1469 booktitle = {High Performance Distributed Computing, 2006 15th IEEE International Symposium}, 1470 pages = {45--56}, 1471 doi = {10.1109/HPDC.2006.1652135}, 1472 petsc_uses = {KSP} 1473} 1474 1475@Article{ lkpl2005, 1476 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1477 title = {Multibit {MRAM} using a pair of memory cells}, 1478 journal = {IEEE Trans. Magn.}, 1479 volume = {41}, 1480 year = {2005}, 1481 pages = {2670-2672}, 1482 doi = {10.1109/TMAG.2005.855288}, 1483 petsc_uses = {KSP} 1484} 1485 1486@Article{ gscn2005, 1487 author = {K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad}, 1488 title = {Vortex state oscillations in soft magnetic cylindrical dots}, 1489 journal = {Phys. Rev. B}, 1490 volume = {71}, 1491 year = {2005}, 1492 doi = {10.1103/PhysRevB.71.144407}, 1493 petsc_uses = {KSP} 1494} 1495 1496@PhDThesis{ mda, 1497 author = {Massimiliano d'Aquino}, 1498 title = {Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles}, 1499 school = { Universita di Napoli Federico II.}, 1500 url = {http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf}, 1501 petsc_uses = {KSP} 1502} 1503 1504@TechReport{ ssdfssf2003, 1505 author = {T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. 1506 Stehno and J. Fidler}, 1507 title = {Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films}, 1508 url = {http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html}, 1509 petsc_uses = {KSP} 1510} 1511 1512@InProceedings{ sb2006a, 1513 author = {W. Scholz and S. Batra}, 1514 title = {Effect of write current waveform on magnetization and head field dynamics of 1515 perpendicular recording heads}, 1516 booktitle = {Intermag 2006 Conference, San Diego, CA, paper no. EF-03}, 1517 petsc_uses = {KSP} 1518} 1519 1520@Article{ scholz-batra1, 1521 author = {W. Scholz and S. Batra}, 1522 title = {Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular 1523 Recording}, 1524 journal = {IEEE Trans. Magn.}, 1525 note = {submitted}, 1526 year = {2005}, 1527 petsc_uses = {KSP} 1528} 1529 1530@Article{ scholz-batra2, 1531 author = {W. Scholz and S. Batra}, 1532 title = {Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording}, 1533 journal = {IEEE Trans. Magn.}, 1534 volume = {41}, 1535 year = {2005}, 1536 pages = {702-706}, 1537 petsc_uses = {KSP} 1538} 1539 1540@Article{ daquino-scholz1, 1541 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1542 title = {Micromagnetic Analysis of Fast Precessional Switching}, 1543 journal = {J. Magn. Magn. Mater.}, 1544 volume = {290-291}, 1545 year = {2005}, 1546 pages = {510-513}, 1547 petsc_uses = {KSP} 1548} 1549 1550@Article{ aq-scholz-fid, 1551 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler}, 1552 title = {Numerical and analytical study of fast precessional switching}, 1553 journal = {J. Appl. Phys.}, 1554 volume = {95}, 1555 year = {2004}, 1556 pages = {7055-7057}, 1557 petsc_uses = {KSP} 1558} 1559 1560@InProceedings{ gar-tabik-gar, 1561 author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones}, 1562 title = {Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and 1563 Scatterers}, 1564 booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing 1565 (PDP'04)}, 1566 year = {2004}, 1567 pages = {80--}, 1568 petsc_uses = {KSP} 1569} 1570 1571@InProceedings{ aq-scholz-mia, 1572 author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano}, 1573 title = {Analysis of fast precessional switching in magnetic thin films}, 1574 booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)}, 1575 year = {2004}, 1576 pages = {257-260}, 1577 petsc_uses = {KSP} 1578} 1579 1580@Article{ scholz-fid-seus, 1581 author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. 1582 Dittrich and V. Tsiantos}, 1583 title = {Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy 1584 Axes}, 1585 journal = {J. Magn. Magn. Mater.}, 1586 year = {2004}, 1587 pages = {1524-1525}, 1588 petsc_uses = {KSP} 1589} 1590 1591@Article{ boardman-zimmerman, 1592 author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and 1593 Peter de Groot}, 1594 title = {Micromagnetic simulation studies of ferromagnetic part-spheres}, 1595 journal = {Journal of Applied Physics}, 1596 year = {2005}, 1597 petsc_uses = {KSP} 1598} 1599 1600@Article{ lim-kim-park, 1601 author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee}, 1602 title = {High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell}, 1603 journal = {IEEE Trans. Magn.}, 1604 note = {submitted}, 1605 petsc_uses = {KSP} 1606} 1607 1608@Article{ scholz-suess2, 1609 author = {W. Scholz and D. Suess and T. Schrefl and J. Fidler}, 1610 title = {Micromagnetic simulation of magnetization reversal in small particles with 1611 surface anisotropy}, 1612 journal = {J. Appl. Phys.}, 1613 volume = {95}, 1614 year = {2004}, 1615 pages = {6807-6809}, 1616 petsc_uses = {KSP} 1617} 1618 1619@Article{ scholz-schrefl1, 1620 author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. 1621 Tsiantos}, 1622 title = {Micromagnetic simulation of the pinning and depinning process in permanent 1623 magnets}, 1624 journal = {IEEE Trans. Magn.}, 1625 volume = {39}, 1626 year = {2003}, 1627 pages = {2920-2922}, 1628 petsc_uses = {KSP} 1629} 1630 1631@Article{ scholz-guslienko, 1632 author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. 1633 W. Chantrell and J. Fidler}, 1634 title = {Transition from single-domain to vortex state in soft magnetic cylindrical 1635 nanodots}, 1636 journal = {J. Magn. Magn. Mater.}, 1637 volume = {266}, 1638 year = {2003}, 1639 pages = {155-163}, 1640 petsc_uses = {KSP} 1641} 1642 1643@Article{ scholz1, 1644 author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. 1645 Forster and V. Tsiantos}, 1646 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1647 journal = {Comp. Mat. Sci}, 1648 year = {2003}, 1649 pages = {366--383}, 1650 volume = {28}, 1651 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}, 1652 petsc_uses = {KSP} 1653} 1654 1655@PhDThesis{ scholz2, 1656 author = {W. Scholz}, 1657 title = {Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures}, 1658 school = {Vienna University of Technology, Vienna, Austria}, 1659 year = {2003}, 1660 petsc_uses = {KSP} 1661} 1662 1663@Article{ scholz3, 1664 author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. 1665 Forster and J. Fidler}, 1666 title = {Implementation of a high performance parallel finite element micromagnetics 1667 package}, 1668 journal = {J. Magn. Magn. Mater.}, 1669 year = {2004}, 1670 url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}, 1671 petsc_uses = {KSP} 1672} 1673 1674% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1675@InBook{ zhanggladwell1, 1676 author = {W. Zhang and I. Gladwell}, 1677 chapter = {Performance of MOL for Surface Motion Driven by a Laplacian of Curvature}, 1678 editor = {Z. Chen and R.E. Ewing and Z.-C. Shi}, 1679 year = {2000}, 1680 title = {Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in 1681 Physics, vol. 552}, 1682 publisher = {Springer}, 1683 pages = {4190-}, 1684 petsc_uses = {KSP} 1685} 1686 1687@Article{ wolf1, 1688 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov}, 1689 title = {Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline 1690 thin films}, 1691 journal = {Phil. Mag. A}, 1692 year = {2003}, 1693 lab = {ANL}, 1694 petsc_uses = {KSP} 1695} 1696 1697@Article{ wolf2, 1698 author = {A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter}, 1699 title = {Mesoscopic simulation of two dimensional grain growth with anisotropic 1700 grain-boundary properties}, 1701 journal = {Computational Materials Science}, 1702 year = {2001}, 1703 volume = {23}, 1704 pages = {15--32}, 1705 lab = {ANL}, 1706 petsc_uses = {KSP} 1707} 1708 1709@Article{ wolf3, 1710 author = {D. Moldovan and S. R. Phillpot and A. J. Haslan}, 1711 title = {Role of grain rotation in grain growth by mesoscale simulation}, 1712 journal = {Phil. Mag. A}, 1713 year = {2002}, 1714 volume = {82}, 1715 pages = {1271--1297}, 1716 lab = {ANL}, 1717 petsc_uses = {KSP} 1718} 1719 1720% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1721@Article{ saut, 1722 author = { Olivier Saut}, 1723 title = {Bidimensional Study of the {M}axwell-{B}loch Model in a Nonlinear Crystal}, 1724 journal = {SIAM Journal on Scientific Computing}, 1725 year = {2004}, 1726 note = {submitted}, 1727 url = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}, 1728 petsc_uses = {KSP} 1729} 1730 1731% LiteralHTML: 1732% LiteralHTML: <a name="biology"><H3><center>Biology -- Medical</center></H3> 1733% LiteralHTML: 1734@InBook{ khanallorenziayachepennec2016, 1735 title = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model 1736 of Brain Deformation in {Alzheimer's} Disease}, 1737 booktitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing}, 1738 author = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec}, 1739 editor = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol 1740 Miller}, 1741 pages = {167--176}, 1742 isbn = {978-3-319-28329-6}, 1743 doi = {10.1007/978-3-319-28329-6_15}, 1744 publisher = {Springer International Publishing}, 1745 year = {2016}, 1746 petsc_uses = {KSP} 1747} 1748 1749@Article{ ataseven, 1750 author = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er}, 1751 title = {Parallel implementation of the accelerated {BEM} approach for {EMSI} of the human 1752 brain}, 1753 journal = {Medical and Biological Engineering and Computing}, 1754 month = feb, 1755 year = {2008}, 1756 doi = {10.1007/s11517-008-0316-0}, 1757 petsc_uses = {KSP} 1758} 1759 1760@Article{ dennis-eberhart-03, 1761 author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons}, 1762 pages = {832-840}, 1763 volume = {125}, 1764 number = {6}, 1765 title = {Finite-element simulation of cooling of realistic {3-D} human head and neck}, 1766 journal = {J Biomech Eng}, 1767 year = {2003}, 1768 url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}, 1769 petsc_uses = {KSP} 1770} 1771 1772@Conference{ gu7174parallel, 1773 title = {{A parallel reduced-space sequential-quadratic programming algorithm for 1774 frequency-domain small animal optical tomography}}, 1775 author = {Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.}, 1776 booktitle = {Proc. of SPIE Vol}, 1777 volume = {7174}, 1778 number = {717406}, 1779 pages = {1}, 1780 petsc_uses = {KSP} 1781} 1782 1783@Article{ barchanski2005using, 1784 title = {{Using domain decomposition techniques for the calculation of low-frequency 1785 electric current densities in high-resolution 3D human anatomy models}}, 1786 author = {Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, 1787 T.}, 1788 journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical 1789 and Electronic Engineering}, 1790 volume = {24}, 1791 number = {2}, 1792 pages = {458--467}, 1793 issn = {0332-1649}, 1794 year = {2005}, 1795 publisher = {Emerald Group Publishing Limited}, 1796 petsc_uses = {KSP} 1797} 1798 1799@Article{ motrescurienen05, 1800 author = {V. C. Motrescu and U. van Rienen}, 1801 pages = {227--231}, 1802 volume = {3}, 1803 title = {Computation of currents induced by {ELF} electric fields in anisotropic human 1804 tissues using the Finite Integration Technique}, 1805 journal = {Advances in Radio Science}, 1806 year = {2005}, 1807 url = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}, 1808 petsc_uses = {KSP} 1809} 1810 1811@Article{ motrescurienen04, 1812 author = {V. C. Motrescu and U. van Rienen}, 1813 pages = {309--313}, 1814 volume = {2}, 1815 title = {Computation of electrostatic fields in anisotropic human tissues using the Finite 1816 Integration Technique (FIT)}, 1817 journal = {Advances in Radio Science}, 1818 year = {2004}, 1819 url = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}, 1820 petsc_uses = {KSP} 1821} 1822 1823@InProceedings{ dbl2, 1824 author = {Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo}, 1825 title = {Computational arterial flow modeling using a parallel {Navier-Stokes} solver}, 1826 booktitle = {ECCOMAS2000}, 1827 year = {2000}, 1828 url = {http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html}, 1829 petsc_uses = {KSP} 1830} 1831 1832@Unpublished{ cell, 1833 title = {Parallel Simulation Engines for Whole-Cell Models}, 1834 author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin 1835 Weber}, 1836 note = {Poster at Second International Conference on Systems Biology (ICSB) 2001}, 1837 url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf}, 1838 institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen}, 1839 year = {2001}, 1840 petsc_uses = {KSP} 1841} 1842 1843@Article{ barker2010two, 1844 title = {Two-level {N}ewton and hybrid {S}chwarz preconditioners for fluid-structure 1845 interaction}, 1846 author = {Barker, A.T. and Cai, X.C.}, 1847 journal = {SIAM Journal on Scientific Computing}, 1848 volume = {32}, 1849 number = {4}, 1850 pages = {2395--2417}, 1851 year = {2010}, 1852 publisher = {Society for Industrial and Applied Mathematics}, 1853 petsc_uses = {KSP} 1854} 1855 1856@Article{ barker2010scalable, 1857 title = {Scalable parallel methods for monolithic coupling in fluid-structure interaction 1858 with application to blood flow modeling}, 1859 author = {Barker, A.T. and Cai, X.C.}, 1860 journal = {Journal of Computational Physics}, 1861 volume = {229}, 1862 number = {3}, 1863 pages = {642--659}, 1864 year = {2010}, 1865 publisher = {Elsevier}, 1866 petsc_uses = {KSP} 1867} 1868 1869@Article{ barker2009nks, 1870 title = {{NKS} for fully coupled fluid-structure interaction with application}, 1871 author = {Barker, A.T. and Cai, X.C.}, 1872 journal = {Domain Decomposition Methods in Science and Engineering XVIII}, 1873 pages = {275--282}, 1874 year = {2009}, 1875 publisher = {Springer}, 1876 petsc_uses = {KSP} 1877} 1878 1879@Article{ mirams2013, 1880 author = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan 1881 and Yi Cui and Gary R Mirams}, 1882 title = {Evaluation of an in silico cardiac safety assay: using ion channel screening data 1883 to predict {QT} interval changes in the rabbit ventricular wedge}, 1884 journal = {Journal of pharmacological and toxicological methods}, 1885 volume = {68}, 1886 number = {1}, 1887 pages = {88--96}, 1888 year = {2013}, 1889 doi = {10.1016/j.vascn.2013.04.004}, 1890 petsc_uses = {KSP} 1891} 1892 1893% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1894% LiteralHTML: <center><img alt="" 1895% LiteralHTML: src="images/spine0l.jpg"></center></p> 1896% LiteralHTML: <center><img alt="" 1897% LiteralHTML: src="images/vertebra.jpg"></center></p> 1898% LiteralHTML:<font color="#FF0000"> 1899% LiteralHTML:Treating fractures of the hip and spine is a major medical cost. 1900% LiteralHTML:Understanding bone mechanical properties and how they may lead to 1901% LiteralHTML:fractures is thus an important medical research activity. PETSc and 1902% LiteralHTML:Prometheus have been used for extremely large scale finite element 1903% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a 1904% LiteralHTML:team of doctors and computational scientists. This computation was 1905% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably 1906% LiteralHTML:with over 4000 processors.</p> 1907% LiteralHTML: </font> 1908@Article{ arbenz2008scalable, 1909 title = {A scalable multi-level preconditioner for matrix-free $\mu$-finite element 1910 analysis of human bone structures}, 1911 author = {Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.}, 1912 journal = {International Journal for Numerical Methods in Engineering}, 1913 volume = {73}, 1914 number = {7}, 1915 pages = {927--947}, 1916 year = {2008}, 1917 publisher = {Wiley Online Library}, 1918 petsc_uses = {KSP} 1919} 1920 1921@InProceedings{ adams-04, 1922 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1923 booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing}, 1924 title = {Ultrascalable implicit finite element analyses in solid mechanics with over a 1925 half a billion degrees of freedom}, 1926 note = {Gordon Bell Award}, 1927 year = {2004}, 1928 petsc_uses = {KSP} 1929} 1930 1931@InProceedings{ adams-03b, 1932 author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.}, 1933 title = {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of 1934 Whole Bone Micro-Mechanics on the {IBM SP}}, 1935 booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing}, 1936 year = {2003}, 1937 petsc_uses = {KSP} 1938} 1939 1940@InProceedings{ oghattas2002, 1941 author = {Volkan Akcelik and George Biros and Omar Ghattas}, 1942 title = {Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation}, 1943 booktitle = {Procceedings of SC2002}, 1944 url = {http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf}, 1945 note = {Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed 1946 by time-dependent PDEs, and scalability results for an inverse wave propagation 1947 problem of determining the material field of an acoustic medium. Using the 1948 algorithm, they solved a synthetic inverse wave propagation problem though a 1949 pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 1950 processors.}, 1951 year = {2002}, 1952 petsc_uses = {KSP} 1953} 1954 1955% LiteralHTML: <a name="biology:cardiology"> 1956% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 1957% LiteralHTML: <center><img alt="" 1958% LiteralHTML: src="images/heart.jpg"> 1959% LiteralHTML: <img alt="" 1960% LiteralHTML: src="images/pump.jpg"></center></p> 1961% LiteralHTML: 1962% LiteralHTML:<font color="#FF0000"> 1963% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the 1964% LiteralHTML: heart; they are the cause of the majority of sudden cardiac 1965% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving 1966% LiteralHTML: through the heart. PETSc has been used by several research groups to 1967% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more 1968% LiteralHTML: fully understand the developments of arrhthmias.</p> 1969% LiteralHTML:</font> 1970@InProceedings{ oghattas2000, 1971 author = {J. Antaki and G. Belloch and O. Ghattas and I. Malcevic and G. Miller and N. 1972 Walkington}, 1973 title = {A Parallel Dynamic-Mesh {L}agrangian Method for Simulation of Flows with Dynamic 1974 Interfaces}, 1975 booktitle = {Procceedings of SC2000}, 1976 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf}, 1977 note = {Blood flow modeling at the microscale including effects on individual blood 1978 cells, for designing heart assist pumps, etc.}, 1979 year = {2000}, 1980 petsc_uses = {KSP} 1981} 1982 1983@InBook{ cfps2006, 1984 author = {P. Colli Franzone and L. F. Pavarino and G. Savare}, 1985 editor = {A. Quarteroni et al.}, 1986 title = {Complex Systems in Biomedicine}, 1987 chapter = {Computational Electrocardiology: mathematical and numerical modeling}, 1988 publisher = {Springer-Verlag}, 1989 pages = {187--241}, 1990 year = {2006}, 1991 petsc_uses = {KSP} 1992} 1993 1994@InProceedings{ cfpst2007, 1995 author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi}, 1996 title = {Determining recovery times from transmembrane action potentials and unipolar 1997 electrograms in normal heart tissue}, 1998 booktitle = {FIMH07}, 1999 publisher = {Springer-Verlag}, 2000 volume = {4466}, 2001 pages = {139--149}, 2002 year = {2007}, 2003 petsc_uses = {KSP} 2004} 2005 2006@Article{ seemann2010framework, 2007 title = {{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain 2008 Equations Using PETSc}}, 2009 author = {Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and 2010 D{\\"o}ssel, O.}, 2011 journal = {Progress in Industrial Mathematics at ECMI 2008}, 2012 pages = {363--369}, 2013 year = {2010}, 2014 publisher = {Springer}, 2015 petsc_uses = {KSP} 2016} 2017 2018@InProceedings{ pft2005, 2019 author = {Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi}, 2020 title = {Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with 2021 Intramural Heterogeneity}, 2022 booktitle = {Functional Imaging and modeling of the Heart (FIMH05)}, 2023 pages = {267--277}, 2024 editors = {A. Frangi et al.}, 2025 publisher = {Springer, Lecture Notes in Computer Science (LNCS), v. 3504}, 2026 year = {2005}, 2027 petsc_uses = {KSP} 2028} 2029 2030@Article{ bgcp2005, 2031 author = {Boyce E. Griffith and Charles S. Peskin}, 2032 title = {On the order of accuracy of the immersed boundary method: Higher order 2033 convergence rates for sufficiently smooth problems}, 2034 journal = {Journal of Computational Physics}, 2035 year = {2005}, 2036 volume = {208}, 2037 pages = {75--105}, 2038 petsc_uses = {KSP} 2039} 2040 2041@Article{ griffith2007adaptive, 2042 title = {An adaptive, formally second order accurate version of the immersed boundary 2043 method}, 2044 author = {Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.}, 2045 journal = {Journal of Computational Physics}, 2046 volume = {223}, 2047 number = {1}, 2048 pages = {10--49}, 2049 year = {2007}, 2050 publisher = {Elsevier}, 2051 petsc_uses = {KSP} 2052} 2053 2054@PhDThesis{ griffith05, 2055 author = {Boyce Griffith}, 2056 title = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and 2057 parallel version of the immersed boundary method}, 2058 school = {New York University}, 2059 year = {2005}, 2060 petsc_uses = {KSP} 2061} 2062 2063@PhDThesis{ murillo, 2064 author = {Maria S. Murillo}, 2065 title = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial 2066 Differential Equations with an Application in Computational Biology}, 2067 school = {University of Colorado at Boulder}, 2068 year = {2002}, 2069 petsc_uses = {KSP} 2070} 2071 2072@Article{ spv2004, 2073 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer}, 2074 title = {Parallel multigrid preconditioner for the cardiac bidomain model}, 2075 journal = {IEEE Trans. Biomed. Eng}, 2076 year = {2004}, 2077 volume = {51}, 2078 pages = {1960--1968}, 2079 petsc_uses = {KSP} 2080} 2081 2082@Article{ vphl2003, 2083 author = {E. J. Vigmond and M. Hughes and G. Plank, L.J. Leon}, 2084 title = { Computational Tools for Modeling Electrical Activity in Cardiac Tissue}, 2085 journal = {J. Electrocardiol.}, 2086 year = {2003}, 2087 volume = {36}, 2088 pages = {69--74}, 2089 petsc_uses = {KSP} 2090} 2091 2092@InProceedings{ spbv2003, 2093 author = {Rodrigo Weber Dos Santos and G. Plank and S. Bauer and E.J. Vigmond}, 2094 title = {Preconditioning Techniques for the Bidomain Equations}, 2095 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2096 Methods}, 2097 pages = {571--580}, 2098 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2099 note = {}, 2100 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2101 year = {2003}, 2102 petsc_uses = {KSP} 2103} 2104 2105@Article{ franz-pavir-04, 2106 author = {P. Colli Franzone and L.~F. Pavarino}, 2107 title = {A parallel solver for reaction-diffusion systems in computational 2108 electrocardiology}, 2109 journal = {Mathematical Models and Methods in Applied Sciences}, 2110 year = {2004}, 2111 volume = {14}, 2112 number = {6}, 2113 pages = {883--912}, 2114 petsc_uses = {KSP} 2115} 2116 2117@Article{ franz-pavir-05, 2118 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2119 title = {Simulating patterns of excitation, repolarization and action potential 2120 durationwith cardiac Bidomain and Monodomain models}, 2121 journal = {Mathematical Biosciences}, 2122 year = {2005}, 2123 volume = {197}, 2124 number = {1}, 2125 pages = {35--66}, 2126 petsc_uses = {KSP} 2127} 2128 2129@Article{ franz-pavir-06, 2130 author = {P. Colli Franzone and L.~F. Pavarino and B. Taccardi}, 2131 title = {Effects of transmural electrical heterogeneities and electrotonic interactions on 2132 the dispersion of cardiac repolarization and action potential duration: a 2133 simulation study}, 2134 journal = {Mathematical Biosciences}, 2135 year = {2006}, 2136 volume = {204}, 2137 number = {1}, 2138 pages = {132--165}, 2139 petsc_uses = {KSP} 2140} 2141 2142@InProceedings{ colli-franz-sim, 2143 author = {P. Colli-Franzone and L.F. Pavarino and B. Taccardi}, 2144 title = {MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS}, 2145 booktitle = {MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X 2146 Mediterranean Conference on Medical and Biological Engineering}, 2147 url = {http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf}, 2148 year = {2004}, 2149 petsc_uses = {KSP} 2150} 2151 2152@InProceedings{ pf2003, 2153 author = {Luca F. Pavarino and Piero Colli Franzone}, 2154 title = {Parallel Solution of Cardiac Reaction-Diffusion Models}, 2155 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 2156 Methods}, 2157 pages = {669--776}, 2158 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 2159 note = {}, 2160 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 2161 year = {2003}, 2162 petsc_uses = {KSP} 2163} 2164 2165@Article{ maria-is04, 2166 author = {Maria Murillo and Xiao-Chuan Cai}, 2167 title = {A fully implicit parallel algorithm for simulating the non-linear electrical 2168 activity of the heart}, 2169 journal = {Numerical Linear Algebra with Applications}, 2170 year = {2004}, 2171 volume = {11}, 2172 pages = {261 - 277}, 2173 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT}, 2174 petsc_uses = {KSP} 2175} 2176 2177@Article{ murli2007monitoring, 2178 title = {{Monitoring and Migration of a PETSc-based Parallel Application for Medical 2179 Imaging in a Grid computing PSE}}, 2180 author = {Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. 2181 and Lapegna, M.}, 2182 journal = {Grid-Based Problem Solving Environments}, 2183 pages = {421--432}, 2184 year = {2007}, 2185 publisher = {Springer}, 2186 petsc_uses = {KSP} 2187} 2188 2189@Article{ carracciuolo:2006:tpc, 2190 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.}, 2191 title = {Towards a parallel component for imaging in {PETSc} programming environment: a case 2192 study in {3-D} echocardiography}, 2193 journal = {Parallel Comput.}, 2194 volume = {32}, 2195 issue = {1}, 2196 month = jan, 2197 year = {2006}, 2198 issn = {0167-8191}, 2199 pages = {67--83}, 2200 numpages = {17}, 2201 doi = {10.1016/j.parco.2005.09.001}, 2202 acmid = {1141218}, 2203 publisher = {Elsevier Science Publishers B. V.}, 2204 address = {Amsterdam, The Netherlands, The Netherlands}, 2205 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel 2206 component}, 2207 petsc_uses = {KSP} 2208} 2209 2210@Article{ damore2011integration, 2211 title = {Integration of emerging computer technologies for an efficient image sequences 2212 analysis}, 2213 journal = {Integrated Computer-Aided Engineering }, 2214 volume = {18}, 2215 number = {4}, 2216 pages = {365 - 378}, 2217 year = {2011}, 2218 note = {}, 2219 issn = {1875-8835}, 2220 doi = {10.3233/ICA-2011-0382}, 2221 url = {http://iospress.metapress.com/content/KM614806M50TKVP7}, 2222 author = {L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli}, 2223 keywords = {Image sequence, pipe and filters, parallel computing, multicore processors}, 2224 petsc_uses = {KSP} 2225} 2226 2227@InProceedings{ eth_biwi_00721, 2228 author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and G. 2229 Székely}, 2230 title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using 2231 a {S}chur Complement Preconditioner}, 2232 booktitle = {Euro-Par 2009 Parallel Processing}, 2233 year = {2009}, 2234 month = aug, 2235 pages = {747-759}, 2236 volume = {5704}, 2237 editor = {H. Sips and D. Epema and H.-X. Lin}, 2238 series = {Lecture Notes in Computer Science}, 2239 publisher = {Springer}, 2240 keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, 2241 parallel Krylov solver}, 2242 petsc_uses = {KSP} 2243} 2244 2245% LiteralHTML: <a name="biology:imagingandsurgery"> 2246% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 2247% LiteralHTML: <center><img alt="" 2248% LiteralHTML: src="images/brain.jpg"></center> 2249@Article{ ganser2004deformable, 2250 title = {A deformable digital brain atlas system according to Talairach and Tournoux}, 2251 author = {Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.}, 2252 journal = {Medical Image Analysis}, 2253 volume = {8}, 2254 number = {1}, 2255 pages = {3--22}, 2256 year = {2004}, 2257 publisher = {Elsevier}, 2258 petsc_uses = {KSP} 2259} 2260 2261@Unpublished{ taccsurgery, 2262 title = {{TACC} supercomputer performs laser cancer surgery on canine}, 2263 url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}, 2264 note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in 2265 Austin performed laser surgery on a dog in Houston without the intervention of a 2266 surgeon. The treatment was developed collaboratively by computational experts from 2267 the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, 2268 leading technologists from the M.D. Anderson Cancer Center in Houston, and 2269 cyberinfrastructure specialists and systems from TACC. Using precise lasers, 2270 state-of-the-art thermal imaging technology, and advanced computational methods, 2271 dynamic, data-driven treatments are being pursued as a minimally invasive 2272 alternative to the standard treatment of cancer.}, 2273 petsc_uses = {KSP} 2274} 2275 2276@Article{ ffhbresso2008, 2277 author = {Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa 2278 Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. 2279 Tinsley Oden}, 2280 title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment}, 2281 journal = {Engineering with Computers}, 2282 note = {Special issue on Computational Bioengineering}, 2283 year = {2008}, 2284 url = {http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf}, 2285 petsc_uses = {KSP} 2286} 2287 2288@TechReport{ dobbhbbbdeffghkkps2008, 2289 author = {K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. 2290 Babu{\v{s}}ka and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. 2291 Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon 2292 and S. Prudhomme and R. J. Stafford}, 2293 title = {Computational Infrastructure for the Real-Time Patient-Specific Treatment of 2294 Cancer}, 2295 year = {2008}, 2296 institution = {University of Texas at Austin}, 2297 url = {http://www.tacc.utexas.edu/research/users/features/cancer.pdf}, 2298 petsc_uses = {KSP} 2299} 2300 2301@Article{ ogdb2004, 2302 author = {A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber}, 2303 title = {Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging}, 2304 journal = {Physics in Medicine and Biology}, 2305 year = {2004}, 2306 volume = {49}, 2307 pages = {2955--2947}, 2308 petsc_uses = {KSP} 2309} 2310 2311@InProceedings{ majumdar11, 2312 author = {A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. 2313 Baldridge and P. Krysl}, 2314 title = {A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery}, 2315 booktitle = {ICCS 2005}, 2316 pages = {672--679}, 2317 editor = {V.S. Sunderam et al.}, 2318 year = {2005}, 2319 petsc_uses = {KSP} 2320} 2321 2322@Conference{ sermesant-etal:03, 2323 author = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S. and Delingette, H. and 2324 Ayache, H.}, 2325 title = {A parallel implementation of non-rigid registration using a volumetric 2326 biomechanical model}, 2327 booktitle = {Second International Workshop on Biomedical Image Registration {WBIR'03}}, 2328 address = {Philadelphia, PA, USA}, 2329 publisher = {Springer-Verlag}, 2330 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2331 series = {Lecture Notes in Computer Science}, 2332 volume = {2717}, 2333 pages = {398-407}, 2334 date = {june 23-24}, 2335 year = {2003}, 2336 url = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}, 2337 petsc_uses = {KSP} 2338} 2339 2340@Conference{ sermesant-etal:04, 2341 author = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. 2342 Wolfson and M. Shenton and H. Handels and R. Kikinis}, 2343 title = {A Novel Nonrigid Registration Algorithm And Applications}, 2344 booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001}, 2345 address = {Philadelphia, PA, USA}, 2346 publisher = {Springer-Verlag}, 2347 editor = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.}, 2348 series = {Lecture Notes in Computer Science}, 2349 volume = {2208}, 2350 pages = {923}, 2351 year = {2003}, 2352 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}, 2353 petsc_uses = {KSP} 2354} 2355 2356@Article{ warfield-haker-talos-05, 2357 author = {Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper 2358 and Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. 2359 Zou and Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and 2360 Alexandra Golby and Peter M. Black and Ferenc A. Jolesz and Ron Kikinis}, 2361 title = {Capturing intraoperative deformations: research experience at {B}righam and {W}omen's 2362 hospital}, 2363 journal = {Medical Image Analysis}, 2364 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf}, 2365 year = {2005}, 2366 petsc_uses = {KSP} 2367} 2368 2369@Article{ brain3, 2370 author = {Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu 2371 Ferrant and Peter McL. Black and Ferenc A. Jolesz and Ron Kikinis}, 2372 title = {Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of 2373 Deformation during Image Guided Neurosurgery}, 2374 journal = {Computing and Visualization in Science}, 2375 url = {http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf}, 2376 year = {2002}, 2377 petsc_uses = {KSP} 2378} 2379 2380@Article{ brain2, 2381 author = {Matthieu Ferrant and Arya Nabavi and Benoit Macq and Ferenc A. Jolesz and Ron 2382 Kikinis and Simon K. Warfield}, 2383 title = {Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite 2384 Element Biomechanical Model}, 2385 journal = {IEEE Transactions on Medical Imaging}, 2386 url = {http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf}, 2387 year = {2001}, 2388 petsc_uses = {KSP} 2389} 2390 2391@InProceedings{ brain1, 2392 author = {Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and 2393 Ferenc A. Jolesz and Ron Kikinis}, 2394 title = {Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image 2395 Guided Neurosurgery}, 2396 booktitle = {Proceedings of SC2000}, 2397 url = {http://www.sc2000.org/techpapr/papers/pap.pap230.pdf}, 2398 year = {2000}, 2399 petsc_uses = {KSP} 2400} 2401 2402@Article{ vanne06, 2403 author = {V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and 2404 M. Lassas and M. Kalke}, 2405 title = {Parallelized {B}ayesian inversion for three-dimensional dental {X}-ray imaging}, 2406 journal = {IEEE Transactions on Medical Imaging}, 2407 volume = {25}, 2408 number = {2}, 2409 month = feb, 2410 year = {2006}, 2411 pages = {218--228}, 2412 petsc_uses = {KSP} 2413} 2414 2415@InProceedings{ knepleybardhan2015, 2416 title = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics}, 2417 author = {Matthew G. Knepley and Jaydeep P. Bardhan}, 2418 booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& 2419 Exposition}, 2420 volume = {9}, 2421 pages = {V009T12A04}, 2422 doi = {10.1115/IMECE2015-53579}, 2423 year = {2015}, 2424 petsc_uses = {KSP} 2425} 2426 2427@InProceedings{ bardhanknepley2015, 2428 title = {Multiscale models and approximation algorithms for protein electrostatics}, 2429 author = {Jaydeep P. Bardhan and Matthew G. Knepley}, 2430 booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII}, 2431 volume = {61}, 2432 pages = {163--174}, 2433 url = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf}, 2434 doi = {10.2495/BEM380131}, 2435 publisher = {WIT Press}, 2436 year = {2015}, 2437 petsc_uses = {KSP} 2438} 2439 2440% LiteralHTML: 2441% LiteralHTML: <a name="fusion"><H3><center>Fusion</center></H3> 2442% LiteralHTML: 2443@InProceedings{ adamsbrennanknepleywang2022, 2444 title = {{Landau} collision operator in the {CUDA} programming model applied to thermal 2445 quench plasmas}, 2446 author = {Mark. F. Adams and Dylan P. Brennan and Matthew G. Knepley and Peng Wang}, 2447 booktitle = {36th IEEE International Parallel \& Distributed Processing Symposium Conference 2448 (IPDPS '22)}, 2449 doi = {10.1109/IPDPS53621.2022.00020}, 2450 year = {2022}, 2451 petsc_uses = {DMPlex} 2452} 2453 2454@Misc{ adamsknepleybrennan2021, 2455 title = {Runaway Electron Generation with High-Performance, Structure Preserving 2456 Discretization of {F}okker--{P}lank--{L}andau}, 2457 author = {Mark F. Adams and Matthew G. Knepley and Dylan Brennan}, 2458 year = {2021}, 2459 petsc_uses = {KSP} 2460} 2461 2462@Article{ adamshirvijokiknepleybrownisaacmills2017, 2463 title = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging 2464 Architectures}, 2465 author = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin 2466 Isaac and Richard Mills}, 2467 journal = {SIAM Journal on Scientific Computing}, 2468 volume = {39}, 2469 number = {6}, 2470 pages = {C452--C465}, 2471 doi = {10.1137/17M1118828}, 2472 eprint = {1702.08880}, 2473 year = {2017}, 2474 petsc_uses = {KSP} 2475} 2476 2477@Article{ pusztayknepleyadams2022, 2478 title = {Conservative Projection Between {FEM} and Particle Bases}, 2479 author = {Joseph V. Pusztay and Matthew G. Knepley and Mark F. Adams}, 2480 journal = {SIAM Journal on Scientific Computing}, 2481 volume = {44}, 2482 number = {4}, 2483 pages = {C310--C319}, 2484 doi = {10.1137/21M145407}, 2485 year = {2022} 2486} 2487 2488@Article{ hirvijoki2017, 2489 author = {Eero Hirvijoki and Mark F. Adams}, 2490 title = {Conservative discretization of the {Landau} collision integral}, 2491 journal = {Physics of Plasmas}, 2492 volume = {24}, 2493 number = {3}, 2494 pages = {032121}, 2495 doi = {10.1063/1.4979122}, 2496 year = {2017}, 2497 petsc_uses = {KSP} 2498} 2499 2500@Article{ mollenadamsknepleyhagerchang2021, 2501 title = {Implementation of higher-order velocity mapping between marker particles and grid 2502 in the particle-in-cell code {XGC}}, 2503 author = {Albert Moll\'en and Mark F. Adams and Matthew G. Knepley and Robert Hager and C. 2504 S. Chang}, 2505 journal = {Journal of Plasma Physics}, 2506 volume = {87}, 2507 number = {2}, 2508 pages = {905870229}, 2509 eprint = {2012.11764}, 2510 doi = {10.1017/S0022377821000441}, 2511 year = {2021}, 2512 petsc_uses = {KSP} 2513} 2514 2515@Article{ lsmh2014, 2516 author = {M. Landreman and H. M. Smith and A. Mollen and P. Helander}, 2517 title = {Comparison of particle trajectories and collision operators for collisional 2518 transport in nonaxisymmetric plasmas}, 2519 journal = { Physics of Plasmas}, 2520 volume = {21}, 2521 year = {2014}, 2522 petsc_uses = {KSP} 2523} 2524 2525@Article{ lpcep2014, 2526 author = {M. Landreman and F. I Parra and P. J. Catto and D. Ernst and I. Pusztai}, 2527 title = {Radially global delta-f computation of neoclassical phenomena in a tokamak 2528 pedestal}, 2529 journal = {Plasma Physics and Controlled Fusion}, 2530 volume = {56}, 2531 year = {2014}, 2532 petsc_uses = {KSP} 2533} 2534 2535@Article{ facets-scidac08, 2536 title = {First Results from Core-Edge Parallel Composition in the {FACETS} Project}, 2537 author = {J. Cary and J. Candy and R. Cohen and S. Krasheninnikov and D. McCune and D. 2538 Estep and J. Larson and A. Malony and A. Pankin and P. Worley and J. Carlsson and 2539 A. Hakim and P. Hamill and S. Kruger and M. Miah and S. Muzsala and A. Pletzer and 2540 S. Shasharina and D. Wade-Stein and N. Wang and S. Balay and L. McInnes and H. 2541 Zhang and T. Casper and L. Diachin and T. Epperly and T. Rognlien and M. Fahey and 2542 J. Cobb and A. Morris and S. Shende and G. Hammett and K. Indireshkumar and D. 2543 Stotler and A. Pigarov}, 2544 journal = {J. Phys.: Conf. Ser.}, 2545 volume = {125}, 2546 year = {2008}, 2547 pages = {012040}, 2548 url = {http://www.iop.org/EJ/abstract/1742-6596/125/1/012040}, 2549 petsc_uses = {KSP} 2550} 2551 2552@Article{ facets-scidac09, 2553 title = {Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project}, 2554 author = {J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and D. Estep and 2555 S. Krasheninnikov and A. Malony and D. McCune and L. McInnes and A. Pankin and S. 2556 Balay and J. Carlsson and M. R. Fahey and R. Groebner and A. Hakim and S. Kruger 2557 and M. Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein 2558 and T. Rognlien and A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar 2559 and A. Pigarov and H. Zhang}, 2560 journal = {J. Phys.: Conf. Ser.}, 2561 volume = {180}, 2562 year = {2009}, 2563 pages = {012056}, 2564 url = {http://iopscience.iop.org/1742-6596/180/1/012056}, 2565 petsc_uses = {KSP} 2566} 2567 2568@InProceedings{ facets-scidac10, 2569 title = {Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the 2570 {FACETS} Code}, 2571 author = {A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. 2572 Estep and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. 2573 Pankin and S. Balay J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. 2574 Miah and A. Pletzer and S. Shasharina and S. Vadlamani and D. Wade-Stein and T. 2575 Rognlein and A. Morris and S. Shende and G. Hammett and K. Indareshkumar and A. 2576 Pigarov and H. Zhang}, 2577 booktitle = {Proceedings of SciDAC 2010 Conference}, 2578 year = {2010}, 2579 url = {http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf}, 2580 petsc_uses = {KSP} 2581} 2582 2583@InProceedings{ facets-fec2010, 2584 title = {Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using 2585 the {FACETS} Framework}, 2586 author = {J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina 2587 and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and D. 2588 McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang}, 2589 booktitle = {Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, 2590 Republic of Korea}, 2591 year = {2010}, 2592 petsc_uses = {KSP} 2593} 2594 2595@InProceedings{ facets-epdp2010, 2596 title = {{FACETS}: A Framework for Parallel Coupling of Fusion Components}, 2597 author = {J. Cary and A. Hakim and M. Miah and S. Kruger and A. 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Brubeck}, 3224 school = {Oxford University}, 3225 year = {2022} 3226} 3227 3228@Misc{ firedrakeproject, 3229 title = {{The {F}iredrake project}}, 3230 author = {David A Ham and Firedrake Team}, 3231 url = {http://firedrakeproject.org}, 3232 year = {2022}, 3233 petsc_uses = {KSP} 3234} 3235 3236@Article{ rathgeberhammitchelllangeluporinimcraeberceamarkallkelly2016, 3237 title = {Firedrake: automating the finite element method by composing abstractions}, 3238 author = {Florian Rathgeber and David A Ham and Lawrence Mitchell and Michael Lange and 3239 Fabio Luporini and Andrew TT McRae and Gheorghe-Teodor Bercea and Graham R Markall 3240 and Paul HJ Kelly}, 3241 journal = {ACM Transactions on Mathematical Software (TOMS)}, 3242 volume = {43}, 3243 number = {3}, 3244 pages = {24}, 3245 year = {2016}, 3246 petsc_uses = {KSP} 3247} 3248 3249@Article{ mitchellmuller2016, 3250 title = {High level implementation of geometric multigrid solvers for finite element 3251 problems: Applications in atmospheric modelling}, 3252 author = {Lawrence Mitchell and Eike Hermann M{\"u}ller}, 3253 journal = {Journal of Computational Physics}, 3254 volume = {327}, 3255 pages = {1--18}, 3256 year = {2016}, 3257 petsc_uses = {KSP} 3258} 3259 3260@Article{ mcraeberceamitchellhamcotter2016, 3261 title = {Automated generation and symbolic manipulation of tensor product finite 3262 elements}, 3263 author = {Andrew TT McRae and Gheorghe-Teodor Bercea and Lawrence Mitchell and David A Ham 3264 and Colin J Cotter}, 3265 journal = {SIAM Journal on Scientific Computing}, 3266 volume = {38}, 3267 number = {5}, 3268 pages = {S25--S47}, 3269 year = {2016}, 3270 petsc_uses = {KSP} 3271} 3272 3273@Article{ berceamcraehammitchellrathgebernardiluporinikelly2016, 3274 title = {A structure-exploiting numbering algorithm for finite elements on extruded 3275 meshes, and its performance evaluation in {Firedrake}}, 3276 author = {Gheorghe-Teodor Bercea and Andrew TT McRae and David A Ham and Lawrence Mitchell 3277 and Florian Rathgeber and L. Nardi and Fabio Luporini and Paul HJ Kelly}, 3278 journal = {Geoscientific Model Development}, 3279 volume = {9}, 3280 number = {10}, 3281 pages = {3803--3815}, 3282 doi = {10.5194/gmd-9-3803-2016}, 3283 year = {2016}, 3284 petsc_uses = {KSP} 3285} 3286 3287@InProceedings{ markallrathgebermitchellloriantbertollihamkelly2013, 3288 author = {Graham R. Markall and Florian Rathgeber and Lawrence Mitchell and Nicolas Loriant 3289 and Carlo Bertolli and David A. Ham and Paul HJ Kelly}, 3290 editor = {Julian Martin Kunkel and Thomas Ludwig and Hans Werner Meuer}, 3291 title = {Performance-Portable Finite Element Assembly Using {PyOP2} and {FEniCS}}, 3292 booktitle = {Proceedings of 28th International Supercomputing Conference, ISC 2013}, 3293 publisher = {Springer Berlin Heidelberg}, 3294 pages = {279--289}, 3295 isbn = {978-3-642-38750-0}, 3296 doi = {10.1007/978-3-642-38750-0_21}, 3297 year = {2013}, 3298 petsc_uses = {KSP} 3299} 3300 3301@Article{ kirbymitchell2017, 3302 title = {Solver composition across the {PDE}/linear algebra barrier}, 3303 author = {Robert C Kirby and Lawrence Mitchell}, 3304 journal = {arXiv preprint arXiv:1706.01346}, 3305 year = {2017}, 3306 petsc_uses = {KSP} 3307} 3308 3309@Article{ saibaba2012application, 3310 title = {Application of hierarchical matrices to linear inverse problems in 3311 geostatistics}, 3312 author = {Saibaba, Arvind Krishna and Ambikasaran, Sivaram and Yue Li, J and Kitanidis, 3313 Peter K and Darve, Eric F}, 3314 journal = {Oil and Gas Science and Technology-Revue de l'IFP-Institut Francais du Petrole}, 3315 volume = {67}, 3316 number = {5}, 3317 pages = {857}, 3318 year = {2012}, 3319 petsc_uses = {KSP} 3320} 3321 3322@Article{ collignonkausmayfernandez14, 3323 author = {Collignon, M. and Kaus, B. and May, D.A. and Fern\'andez, N.}, 3324 title = {Influences of surface processes on fold growth during {3-D} detachment folding}, 3325 journal = {Geochem Geophy Geosy}, 3326 year = {2014}, 3327 petsc_uses = {KSP} 3328} 3329 3330@Article{ fernandezkaus14, 3331 author = {Fern\'andez, N. and Kaus, B.}, 3332 title = {Fold interaction and wavelength selection in {3D} models of multilayer detachment 3333 folding}, 3334 journal = {Tectonophysics}, 3335 year = {2014}, 3336 petsc_uses = {KSP} 3337} 3338 3339@Article{ baumannkauspopov14, 3340 author = {Baumann, T. and Kaus, B. 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Snyder}, 3523 collaboration = {}, 3524 title = {Multiple-domain, simultaneous joint inversion of geophysical data with 3525 application to subsalt imaging}, 3526 publisher = {SEG}, 3527 year = {2011}, 3528 journal = {Geophysics}, 3529 volume = {76}, 3530 number = {3}, 3531 pages = {R69-R80}, 3532 keywords = {geophysical image processing; inverse problems; seismology}, 3533 doi = {10.1190/1.3554652}, 3534 petsc_uses = {KSP} 3535} 3536 3537@Article{ stefano:806, 3538 author = {Michele De Stefano}, 3539 collaboration = {}, 3540 title = {Simultaneous joint inversion for susceptibility and velocity}, 3541 publisher = {SEG}, 3542 year = {2011}, 3543 journal = {SEG Technical Program Expanded Abstracts}, 3544 volume = {30}, 3545 number = {1}, 3546 pages = {806-810}, 3547 keywords = {3D; imaging; inversion; magnetics; multiparameter}, 3548 doi = {10.1190/1.3628198}, 3549 petsc_uses = {KSP} 3550} 3551 3552@Article{ mayknepley2011, 3553 author = {Dave A. May and Matthew G. Knepley}, 3554 title = {Optimal, scalable forward models for computing gravity anomalies}, 3555 journal = {Geophysical Journal International}, 3556 volume = {187}, 3557 number = {1}, 3558 pages = {161--177}, 3559 url = {http://arxiv.org/abs/1107.5951}, 3560 note = {\url{http://arxiv.org/abs/1107.5951}}, 3561 year = {2011}, 3562 petsc_uses = {KSP} 3563} 3564 3565@InProceedings{ bourdinknepleymaurini2010, 3566 author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini}, 3567 title = {Numerical Simulation of Reservoir Stimulation - A Variational Approach}, 3568 booktitle = {Proceedings of the 37th Stanford Geothermal Workshop}, 3569 url = {https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}, 3570 note = {\url{https://es.stanford.edu/ERE/pdf/IGAstandard/SGW/2011/bourdin.pdf}}, 3571 address = {Stanford, CA}, 3572 year = {2010}, 3573 petsc_uses = {KSP} 3574} 3575 3576@InProceedings{ bourdinknepleymaurini2010b, 3577 author = {Blaise Bourdin and Matthew G. Knepley and C. Maurini}, 3578 title = {Secondary Thermal Cracks in {EGS}: a Variational Approach}, 3579 booktitle = {Proceedings of the 34th Annual Meeting of the Geothermal Resources Council}, 3580 url = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}, 3581 note = {\url{https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}}, 3582 address = {Sacramento, CA}, 3583 year = {2010}, 3584 petsc_uses = {KSP} 3585} 3586 3587@Article{ chen2007full, 3588 title = {Full {3D} tomography for the crustal structure of the {Los Angeles} region}, 3589 author = {Chen, P. and Zhao, L. and Jordan, T.H.}, 3590 journal = {Bulletin of the Seismological Society of America}, 3591 volume = {97}, 3592 number = {4}, 3593 pages = {1094}, 3594 year = {2007}, 3595 publisher = {Seismol Soc America}, 3596 petsc_uses = {KSP} 3597} 3598 3599@Article{ brown2010ens, 3600 author = {Brown, Jed}, 3601 affiliation = {Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, 3602 Zürich, Switzerland}, 3603 title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}}, 3604 journal = {Journal of Scientific Computing}, 3605 publisher = {Springer Netherlands}, 3606 issn = {0885-7474}, 3607 keyword = {Mathematics and Statistics}, 3608 pages = {48-63}, 3609 volume = {45}, 3610 issue = {1}, 3611 doi = {10.1007/s10915-010-9396-8}, 3612 year = {2010}, 3613 petsc_uses = {KSP} 3614} 3615 3616@PhDThesis{ brown2011, 3617 title = {Computational methods for ice flow simulation}, 3618 author = {Jed Brown}, 3619 school = {ETH Z{\"u}rich}, 3620 year = {2011}, 3621 petsc_uses = {KSP} 3622} 3623 3624@Article{ brown2013tmeice, 3625 title = {Achieving textbook multigrid efficiency for hydrostatic ice flow}, 3626 author = {Jed Brown and Barry F. Smith and Aron Ahmadia}, 3627 journal = {SIAM Journal on Scientific Computing}, 3628 volume = {35}, 3629 number = {2}, 3630 year = {2013}, 3631 pages = {359--375}, 3632 doi = {10.1137/110834512}, 3633 note = {Also preprint ANL/MCS-P743-1298}, 3634 petsc_uses = {KSP} 3635} 3636 3637@InProceedings{ brown2013quasinewton, 3638 author = {Jed Brown and Peter Brune}, 3639 title = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type 3640 methods}, 3641 year = {2013}, 3642 booktitle = {International Conference on Mathematics and Computational Methods Applied to 3643 Nuclear Science and Engineering}, 3644 pages = {2554--2565}, 3645 petsc_uses = {KSP} 3646} 3647 3648@Misc{ spiegelman-siampp10, 3649 title = {Block Preconditioners and Advanced Software for Multiphysics Problems in Solid 3650 Earth Geodynamics}, 3651 author = {Marc Spiegelman}, 3652 note = {presentation at the 2010 SIAM Conference on Parallel Processing for Scientific 3653 Computing}, 3654 year = {2010}, 3655 petsc_uses = {KSP} 3656} 3657 3658@Article{ schauer2011a, 3659 author = {Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. 3660 Quintana-Ort\'{\i}}, 3661 title = {Large scale simulation of wave propagation in soils interacting with structures 3662 using {FEM} and {SBFEM}}, 3663 journal = {Journal of Computational Acoustics}, 3664 volume = {19}, 3665 number = {1}, 3666 pages = {75--93}, 3667 year = {2011}, 3668 doi = {10.1142/S0218396X11004316}, 3669 petsc_uses = {KSP} 3670} 3671 3672@Misc{ bsa2010, 3673 author = {J. Brown and B. Smith and A. Ahmadia}, 3674 title = {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow}, 3675 note = {submitted to SIAM Journal on Scientific Computing}, 3676 year = {2012}, 3677 petsc_uses = {KSP} 3678} 3679 3680@Article{ kellerkatz2016, 3681 title = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere}, 3682 author = {Tobias Keller and Richard F. 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Weatherley}, 3706 title = {Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges}, 3707 journal = {Earth\ Planet.\ Sci.\ Lett.}, 3708 year = {2012}, 3709 doi = {10.1016/j.epsl.2012.04.042}, 3710 volume = {335-336}, 3711 pages = {226-237}, 3712 petsc_uses = {KSP} 3713} 3714 3715@Article{ katz10b, 3716 author = {R.F. Katz}, 3717 title = {Porosity-driven convection and asymmetry beneath mid-ocean ridges}, 3718 journal = {Geochem.\ Geophys.\ Geosys.}, 3719 volume = {10}, 3720 number = {Q0AC07}, 3721 year = {2010}, 3722 doi = {10.1029/2010GC003282}, 3723 petsc_uses = {KSP} 3724} 3725 3726@Article{ england10, 3727 author = {P.C. England and R.F. Katz}, 3728 title = {Melting above the anhydrous solidus controls the location of volcanic arcs}, 3729 journal = {Nature}, 3730 year = {2010}, 3731 volume = {467}, 3732 pages = {700--703}, 3733 doi = {10.1038/nature09417}, 3734 petsc_uses = {KSP} 3735} 3736 3737@Article{ weatherley10, 3738 author = {S. Weatherley and R.F. 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Katz}, 3775 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. 3776 Governing equations and linearised analysis}}, 3777 journal = {J.\ Fluid\ Mech.}, 3778 year = {2013}, 3779 volume = {734}, 3780 pages = {424-455}, 3781 doi = {10.1017/jfm.2013.482}, 3782 petsc_uses = {KSP} 3783} 3784 3785@Article{ katz2013anisotropy2, 3786 author = {Katz R.F. and Y. Takei}, 3787 title = {{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. 3788 Numerical solutions of the full equations}}, 3789 journal = {J.\ Fluid\ Mech.}, 3790 year = {2013}, 3791 volume = {734}, 3792 pages = {456-485}, 3793 doi = {10.1017/jfm.2013.483}, 3794 petsc_uses = {KSP} 3795} 3796 3797@Article{ kyrke-smith2014subglacial, 3798 author = {Kyrke-Smith, T.M. and R.F. Katz and A.C. Fowler}, 3799 title = {Subglacial hydrology and the formation of ice streams}, 3800 journal = {Proc.\ Roy.\ Soc.\ A}, 3801 year = {2014}, 3802 volume = {470}, 3803 number = {2161}, 3804 doi = {10.1098/rspa.2013.0494}, 3805 petsc_uses = {KSP} 3806} 3807 3808@Article{ spiegelmanwilsonvankeken2013, 3809 author = {{Spiegelman}, M.~W. and {Wilson}, C.~R. and {Van Keken}, P.~E. }, 3810 title = {{TerraFERMA: The Transparent Finite Element Rapid Model Assembler for 3811 multi-physics problems in the solid Earth sciences}}, 3812 journal = {AGU Fall Meeting Abstracts}, 3813 keywords = {0560 COMPUTATIONAL GEOPHYSICS Numerical solutions, 1902 INFORMATICS Community 3814 modeling frameworks, 1906 INFORMATICS Computational models, algorithms}, 3815 year = {2013}, 3816 month = dec, 3817 pages = {A2208}, 3818 adsurl = {http://adsabs.harvard.edu/abs/2013AGUFMDI31A2208S}, 3819 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 3820 petsc_uses = {KSP} 3821} 3822 3823@Article{ bueler2009shallow, 3824 title = {{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled 3825 ice sheet model}}, 3826 author = {Ed Bueler and Jed Brown}, 3827 journal = {Journal of Geophysical Research-Earth Surface}, 3828 volume = {114}, 3829 number = {F3}, 3830 pages = {F03008}, 3831 year = {2009}, 3832 publisher = {American Geophysical Union}, 3833 petsc_uses = {KSP} 3834} 3835 3836@Article{ bueler2007est, 3837 title = {{Exact solutions to the thermomechanically coupled shallow ice approximation: 3838 effective tools for verification}}, 3839 author = {Ed Bueler and Jed Brown and Craig Lingle}, 3840 journal = {J. 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Glaciol.}, 3863 volume = {51}, 3864 number = {173}, 3865 pages = {291--306}, 3866 year = {2005}, 3867 petsc_uses = {KSP} 3868} 3869 3870@Article{ chao2008programming, 3871 title = {{Programming on Numerical Simulation of Tsunami with PETSc and FEPG}}, 3872 author = {Chao-fan, Z. and Yao-lin, S.}, 3873 journal = {Earthquake}, 3874 year = {2008}, 3875 petsc_uses = {KSP} 3876} 3877 3878@Article{ marti2014, 3879 author = {Marti, P. and Schaeffer, N. and Hollerbach, R. and Cébron, D. and Nore, C. and 3880 Luddens, F. and Guermond, J.-L. and Aubert, J. and Takehiro, S. and Sasaki, Y. and 3881 Hayashi, Y.-Y. and Simitev, R. and Busse, F. and Vantieghem, S. and Jackson, A.}, 3882 title = {Full sphere hydrodynamic and dynamo benchmarks}, 3883 journal = {Geophysical Journal International}, 3884 year = {2014}, 3885 doi = {10.1093/gji/ggt518}, 3886 url = {http://gji.oxfordjournals.org/content/early/2014/01/26/gji.ggt518.abstract}, 3887 petsc_uses = {KSP} 3888} 3889 3890@InProceedings{ ganfulukyangxueyang2013, 3891 author = {Gan, Lin and Fu, Haohuan and Luk, Wayne and Yang, Chao and Xue, Wei and Yang, 3892 Guangwen}, 3893 title = {Global Atmospheric Simulation on a Reconfigurable Platform}, 3894 booktitle = {Proceedings of the 2013 IEEE 21st Annual International Symposium on 3895 Field-Programmable Custom Computing Machines}, 3896 series = {FCCM '13}, 3897 pages = {230--}, 3898 year = {2013}, 3899 isbn = {978-0-7695-4969-9}, 3900 doi = {10.1109/FCCM.2013.26}, 3901 acmid = {2495688}, 3902 publisher = {IEEE Computer Society}, 3903 petsc_uses = {KSP} 3904} 3905 3906@InProceedings{ ganfuchaolukxuemencerhuangyang2014, 3907 author = {Lin Gan and Haohuan Fu and Chao Yang and Luk, W. and Wei Xue and Mencer, O. and 3908 Xiaomeng Huang and Guangwen Yang}, 3909 booktitle = {Field Programmable Logic and Applications (FPL), 2014 24th International 3910 Conference on}, 3911 title = {A highly-efficient and green data flow engine for solving {E}uler atmospheric 3912 equations}, 3913 year = {2014}, 3914 month = sep, 3915 pages = {1-6}, 3916 doi = {10.1109/FPL.2014.6927462}, 3917 petsc_uses = {KSP} 3918} 3919 3920%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. 3921%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. 3922%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. 3923@Article{ aagaardknepleywilliams13, 3924 title = {A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element 3925 Models of Quasi-static and Dynamic Crustal Deformation}, 3926 author = {Brad T. Aagaard and Matthew G. Knepley and Charles A. Williams}, 3927 journal = {Journal of Geophysical Research: Solid Earth}, 3928 volume = {118}, 3929 number = {6}, 3930 pages = {3059--3079}, 3931 issn = {2169-9356}, 3932 doi = {10.1002/jgrb.50217}, 3933 keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics}, 3934 year = {2013}, 3935 petsc_uses = {KSP} 3936} 3937 3938@InProceedings{ aagaardknepleywilliams11, 3939 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3940 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3941 Deformation}, 3942 booktitle = {Eos Transactions of the AGU}, 3943 organization = {American Geophysical Union}, 3944 note = {Fall Meeting Supplemental, Abstract DI14A-08}, 3945 year = {2011}, 3946 petsc_uses = {KSP} 3947} 3948 3949@InProceedings{ knepley10b, 3950 author = {Matthew G. {Knepley}}, 3951 title = {Acceleration of low order finite element computation with {GPUs} (Invited)}, 3952 booktitle = {Eos Transactions of the AGU}, 3953 organization = {American Geophysical Union}, 3954 note = {Fall Meeting Supplemental, Abstract IN44A-01}, 3955 year = {2010}, 3956 petsc_uses = {KSP} 3957} 3958 3959@InProceedings{ mayknepleygurnis09, 3960 author = {Dave A. May and Matthew G. Knepley and Michael Gurnis}, 3961 title = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}}, 3962 booktitle = {Eos Transactions of the AGU}, 3963 organization = {American Geophysical Union}, 3964 note = {Fall Meeting Supplemental, Abstract P31A-A1241}, 3965 year = {2009}, 3966 petsc_uses = {KSP} 3967} 3968 3969@InProceedings{ yuenknepleyerlebacherwright09, 3970 author = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright}, 3971 title = {The Coming Role of {GPU} in Computational Geodynamics}, 3972 booktitle = {Eos Transactions of the AGU}, 3973 organization = {American Geophysical Union}, 3974 note = {Fall Meeting Supplemental, Abstract DI22A-05}, 3975 year = {2009}, 3976 petsc_uses = {KSP} 3977} 3978 3979@InProceedings{ aagaardknepleywilliams08, 3980 author = {Brad Aagaard and Charles A. Williams and Matthew G. Knepley}, 3981 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3982 Deformation}, 3983 booktitle = {Eos Transactions of the AGU}, 3984 organization = {American Geophysical Union}, 3985 volume = {89}, 3986 number = {53}, 3987 note = {Fall Meeting Supplemental, Abstract T41A-1925}, 3988 year = {2007}, 3989 petsc_uses = {KSP} 3990} 3991 3992@InProceedings{ aagaardknepleywilliams07, 3993 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 3994 title = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal 3995 Deformation}, 3996 booktitle = {Eos Transactions of the AGU}, 3997 organization = {American Geophysical Union}, 3998 volume = {88}, 3999 number = {52}, 4000 note = {Fall Meeting Supplemental, Abstract T21B-1798}, 4001 year = {2007}, 4002 petsc_uses = {KSP} 4003} 4004 4005@InProceedings{ aagaardknepleywilliams05, 4006 author = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley}, 4007 title = {Development of software for studying earthquakes across multiple spatial and 4008 temporal scales by coupling quasi-static and dynamic simulations}, 4009 booktitle = {Eos Transactions of the AGU}, 4010 organization = {American Geophysical Union}, 4011 volume = {86}, 4012 number = {52}, 4013 note = {Fall Meeting Supplemental, Abstract S53A-1072}, 4014 year = {2005}, 4015 petsc_uses = {KSP} 4016} 4017 4018@InProceedings{ williamsgablehagermeadeaagaardknepley08, 4019 author = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and 4020 Brad Aagaard and Matthew G. Knepley}, 4021 title = {Modeling of Multiple Earthquake Cycles in {S}outhern {C}alifornia Using the {SCEC} 4022 Community Fault Model}, 4023 booktitle = {Proceedings of Geosciences '08}, 4024 address = {Wellington, NZ}, 4025 month = nov, 4026 year = {2008}, 4027 petsc_uses = {KSP} 4028} 4029 4030@TechReport{ zhang07, 4031 title = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for 4032 Tsunamis}, 4033 author = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi}, 4034 type = {Preprint}, 4035 number = {ANL/MCS-P1459-0907}, 4036 institution = {ANL}, 4037 month = sep, 4038 year = {2007}, 4039 petsc_uses = {KSP} 4040} 4041 4042@Article{ katz08b, 4043 author = {Richard F. Katz}, 4044 title = {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic 4045 focusing at mid-ocean ridges}, 4046 journal = {J. Petrology}, 4047 year = {2008}, 4048 volume = {49}, 4049 pages = {2099--2121}, 4050 doi = {10.1093/petrology/egn058}, 4051 petsc_uses = {KSP} 4052} 4053 4054@Article{ hgrhkjvv2008, 4055 title = {On preconditioning for a parallel solution of the {R}ichards equation}, 4056 author = {Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy 4057 Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena}, 4058 journal = {Computers and Geosciences}, 4059 volume = {34}, 4060 pages = {1958--1963}, 4061 year = {2008}, 4062 petsc_uses = {KSP} 4063} 4064 4065@Article{ maymoresi2008, 4066 title = {Preconditioned iterative methods for {Stokes} flow problems arising in 4067 computational geodynamics}, 4068 journal = {Physics of the Earth and Planetary Interiors}, 4069 volume = {171}, 4070 number = {1-4}, 4071 pages = {33--47}, 4072 year = {2008}, 4073 note = {{R}ecent Advances in Computational Geodynamics: Theory, Numerics and 4074 Applications}, 4075 issn = {0031-9201}, 4076 doi = {10.1016/j.pepi.2008.07.036}, 4077 author = {Dave A. May and Louis Moresi}, 4078 keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}, 4079 petsc_uses = {KSP} 4080} 4081 4082@Article{ kausmuhlhausmay2010, 4083 title = {A stabilization algorithm for geodynamic numerical simulations with a free 4084 surface}, 4085 author = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May}, 4086 journal = {Physics of the Earth and Planetary Interiors}, 4087 volume = {181}, 4088 number = {1}, 4089 pages = {12--20}, 4090 year = {2010}, 4091 petsc_uses = {KSP} 4092} 4093 4094@Article{ duretzmaygeryatackley2011, 4095 title = {Discretization errors and free surface stabilization in the finite difference and 4096 marker-in-cell method for applied geodynamics: A numerical study}, 4097 author = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley}, 4098 journal = {Geochemistry, Geophysics, Geosystems}, 4099 volume = {12}, 4100 number = {7}, 4101 year = {2011}, 4102 petsc_uses = {KSP} 4103} 4104 4105@Article{ furuichimaytackley2011, 4106 title = {Development of a {Stokes} flow solver robust to large viscosity jumps using a 4107 {Schur} complement approach with mixed precision arithmetic}, 4108 author = {Mikito Furuichi and Dave A May and Paul J Tackley}, 4109 journal = {Journal of Computational Physics}, 4110 volume = {230}, 4111 number = {24}, 4112 pages = {8835--8851}, 4113 year = {2011}, 4114 petsc_uses = {KSP} 4115} 4116 4117@Article{ kellermaykaus2013, 4118 title = {Numerical modelling of magma dynamics coupled to tectonic deformation of 4119 lithosphere and crust}, 4120 author = {Tobias Keller and Dave A May and Boris JP Kaus}, 4121 journal = {Geophysical Journal International}, 4122 volume = {195}, 4123 number = {3}, 4124 pages = {1406--1442}, 4125 year = {2013}, 4126 petsc_uses = {KSP} 4127} 4128 4129@Article{ schellartfreemanstegmanmoresimay2007, 4130 title = {Evolution and diversity of subduction zones controlled by slab width}, 4131 author = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A 4132 May}, 4133 journal = {Nature}, 4134 volume = {446}, 4135 number = {7133}, 4136 pages = {308--311}, 4137 year = {2007}, 4138 petsc_uses = {KSP} 4139} 4140 4141@Article{ cramerischmelinggolabekduretzorendtbuitermaykausgeryatackley2012, 4142 title = {A comparison of numerical surface topography calculations in geodynamic 4143 modelling: an evaluation of the sticky air method}, 4144 author = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter 4145 and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley}, 4146 journal = {Geophysical Journal International}, 4147 volume = {189}, 4148 number = {1}, 4149 pages = {38--54}, 4150 year = {2012}, 4151 petsc_uses = {KSP} 4152} 4153 4154@Article{ stegmanfreemanschellartmoresimay2006, 4155 title = {Influence of trench width on subduction hinge retreat rates in {3-D} models of slab 4156 rollback}, 4157 author = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A 4158 May}, 4159 journal = {Geochemistry, Geophysics, Geosystems}, 4160 volume = {7}, 4161 number = {3}, 4162 year = {2006}, 4163 petsc_uses = {KSP} 4164} 4165 4166@InProceedings{ may2014ptatin, 4167 title = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics}, 4168 author = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}}, 4169 booktitle = {Proceedings of {SC14}: The {International Conference for High Performance 4170 Computing, Networking, Storage and Analysis}}, 4171 organization = {ACM}, 4172 pages = {274--284}, 4173 year = {2014}, 4174 doi = {10.1109/SC.2014.28}, 4175 petsc_uses = {KSP} 4176} 4177 4178@Article{ maybrownpourhiet2015, 4179 title = {A scalable, matrix-free multigrid preconditioner for finite element 4180 discretizations of heterogeneous {Stokes} flow}, 4181 author = {David A May and Jed Brown and Laetitia {Le Pourhiet}}, 4182 journal = {Computer Methods in Applied Mechanics and Engineering}, 4183 volume = {290}, 4184 pages = {496--523}, 4185 year = {2015}, 4186 doi = {10.1016/j.cma.2015.03.014}, 4187 petsc_uses = {KSP} 4188} 4189 4190@Article{ duretzmayyamato2016, 4191 title = {A free surface capturing discretization for the staggered grid finite difference 4192 scheme}, 4193 author = {Thibault Duretz and Dave A May and Philippe Yamato}, 4194 journal = {Geophysical Journal International}, 4195 volume = {204}, 4196 number = {3}, 4197 pages = {1518--1530}, 4198 year = {2016}, 4199 petsc_uses = {KSP} 4200} 4201 4202@Article{ rhebergenwellskatzwathen2014, 4203 author = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen}, 4204 title = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics}, 4205 journal = {SIAM J. Sci. Comput.}, 4206 volume = {36}, 4207 pages = {A1960--A1977}, 4208 year = {2014}, 4209 petsc_uses = {KSP} 4210} 4211 4212@Article{ katz08a, 4213 author = {R.F. Katz and M.G. Worster}, 4214 title = {Simulation of directional solidification, thermochemical convection, and chimney 4215 formation in a {H}ele-{S}haw cell}, 4216 journal = {J. Comp. Phys.}, 4217 volume = {227}, 4218 pages = {9823-9840}, 4219 year = {2008}, 4220 doi = {10.1016/j.jcp.2008.06.039}, 4221 petsc_uses = {KSP} 4222} 4223 4224@Article{ aabg2007, 4225 author = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas}, 4226 title = {Full waveform inversion for seismic velocity and anelastic losses in 4227 heterogeneous structures}, 4228 journal = {Bulletin of Seismological Society of America}, 4229 year = {2007}, 4230 volume = {97}, 4231 pages = {1990--2008}, 4232 petsc_uses = {KSP} 4233} 4234 4235@Article{ katz2006, 4236 author = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman}, 4237 title = {The dynamics of melt and shear localization in partially molten aggregates}, 4238 journal = {Nature}, 4239 year = {2006}, 4240 volume = {442}, 4241 pages = {676--679}, 4242 month = aug, 4243 day = {10}, 4244 url = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}, 4245 petsc_uses = {KSP} 4246} 4247 4248@InProceedings{ mqrs2003, 4249 author = {Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl}, 4250 year = {2003}, 4251 title = {Parallel Preconditioning for Sedimentary Basin Simulations}, 4252 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, 4253 Sozopol, Bulgaria, June 4-8, 2003}, 4254 petsc_uses = {KSP} 4255} 4256 4257@InProceedings{ lichtner1, 4258 author = {Chuan Lu and Peter C. Lichtner}, 4259 year = {2005}, 4260 title = {{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in 4261 Geologic Media}, 4262 booktitle = {Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL}, 4263 lab = {LANL}, 4264 petsc_uses = {KSP} 4265} 4266 4267@Article{ hammondlichtnermills2014, 4268 title = {Evaluating the Performance of Parallel Subsurface Simulators: An Illustrative 4269 Example with {PFLOTRAN}}, 4270 author = {Glenn E. Hammond and Peter C. Lichtner and Richard Tran Mills}, 4271 journal = {Water Resources Research}, 4272 volume = {50}, 4273 number = {1}, 4274 pages = {208--228}, 4275 doi = {10.1002/2012WR013483}, 4276 year = {2014}, 4277 petsc_uses = {KSP} 4278} 4279 4280@Article{ smw2003, 4281 author = {R. Scheichl and R. Masson and J. Wendebourg}, 4282 title = {Decoupling and Block Preconditioning for Sedimentary Basin Simulations}, 4283 journal = {Computational Geosciences}, 4284 year = {2003}, 4285 volume = {7}, 4286 pages = {295--318}, 4287 url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}, 4288 petsc_uses = {KSP} 4289} 4290 4291@Article{ kees-miller-03, 4292 author = {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley}, 4293 title = {Versatile multilevel Schwarz preconditioners for multiphase flow}, 4294 journal = {Computational Geosciences}, 4295 year = {2003}, 4296 volume = {7}, 4297 pages = {91--114}, 4298 petsc_uses = {KSP} 4299} 4300 4301@Article{ bk2003, 4302 author = {JN Buur and T Kuehnel}, 4303 title = {Improving depth imaging by automated model updating}, 4304 journal = {The Leading Edge}, 4305 year = {2003}, 4306 volume = {22}, 4307 pages = {310-318}, 4308 petsc_uses = {KSP} 4309} 4310 4311@Article{ frederickbuffett2016, 4312 title = {Submarine groundwater discharge as a possible formation mechanism for 4313 permafrost-associated gas hydrate on the circum-Arctic continental shelf}, 4314 author = {Jennifer M. Frederick and Bruce A. Buffett}, 4315 journal = {Journal of Geophysical Research: Solid Earth}, 4316 volume = {121}, 4317 number = {3}, 4318 pages = {1383--1404}, 4319 issn = {2169-9356}, 4320 doi = {10.1002/2015JB012627}, 4321 year = {2016}, 4322 petsc_uses = {KSP} 4323} 4324 4325% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4326% LiteralHTML:<font color="#FF0000"> 4327% LiteralHTML:Simulation of the earth's mantle and crust is valuable to 4328% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a 4329% LiteralHTML:variety of these simulations.</p> 4330% LiteralHTML:</font> 4331% LiteralHTML: 4332@InProceedings{ appelbe1, 4333 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4334 year = {2003}, 4335 title = {Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and 4336 computational methodology}, 4337 page = {781}, 4338 booktitle = {Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference 4339 Proceedings}, 4340 publisher = {Springer-Verlag}, 4341 url = {http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf}, 4342 petsc_uses = {KSP} 4343} 4344 4345% LiteralHTML:<a name="katz"> 4346@InProceedings{ gd1, 4347 author = {Guillaume Dumont and Michel Kern}, 4348 title = {Parallelization of a {3D} Seismic Migration Code with {PETSc}}, 4349 year = {1999}, 4350 booktitle = {Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific 4351 Computing}, 4352 petsc_uses = {KSP} 4353} 4354 4355% LiteralHTML: <center><img alt="" src="images/katz1.jpg"> <img alt="" src="images/katz3.jpg"> 4356% LiteralHTML: <img alt="" src="images/katz2.jpg"></center></p> 4357% LiteralHTML:<font color="#FF0000"> 4358% LiteralHTML: Figures from the work of Richard Katz 4359@PhDThesis{ katzthesis, 4360 author = {R.F. Katz}, 4361 title = {The deep roots of volcanoes: models of magma dynamics with applications to 4362 subduction zones}, 4363 school = {Columbia University}, 4364 year = {2005}, 4365 url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}, 4366 petsc_uses = {KSP} 4367} 4368 4369@InCollection{ knepleykatzsmith06, 4370 author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry}, 4371 affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL 4372 USA}, 4373 title = {Developing a Geodynamics Simulator with {PETSc}}, 4374 booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers}, 4375 series = {Lecture Notes in Computational Science and Engineering}, 4376 editor = {Bruaset, Are Magnus and Tveito, Aslak}, 4377 publisher = {Springer Berlin Heidelberg}, 4378 isbn = {978-3-540-31619-0}, 4379 keyword = {Mathematics and Statistics}, 4380 pages = {413-438}, 4381 volume = {51}, 4382 doi = {10.1007/3-540-31619-1_12}, 4383 year = {2006}, 4384 petsc_uses = {KSP} 4385} 4386 4387@Article{ katz04, 4388 author = {Richard F. Katz and Marc Spiegelman and S.M. Carbotte}, 4389 title = {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in 4390 the global mid-ocean ridge system}, 4391 journal = {Geophys.\ Res.\ Letts.}, 4392 year = {2004}, 4393 volume = {31}, 4394 pages = {L15605}, 4395 petsc_uses = {KSP} 4396} 4397 4398@Article{ katz07, 4399 author = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and 4400 Ethan Coon}, 4401 title = {Numerical simulation of geodynamic processes with the {Portable Extensible 4402 Toolkit for Scientific Computation}}, 4403 journal = {Phys. Earth Planet. In.}, 4404 volume = {163}, 4405 pages = {52--68}, 4406 year = {2007}, 4407 petsc_uses = {KSP} 4408} 4409 4410@Article{ williams2006development, 4411 title = {{Development of a package for modeling stress in the lithosphere}}, 4412 author = {Williams, CA}, 4413 journal = {Eos Trans. AGU}, 4414 volume = {87}, 4415 pages = {36}, 4416 year = {2006}, 4417 petsc_uses = {KSP} 4418} 4419 4420@Article{ goverswortel05, 4421 author = {R. Govers and M.J.R. Wortel}, 4422 title = {Lithosphere tearing at STEP faults: response to edges of subduction zones}, 4423 journal = {Earth and Planetary Science Letters}, 4424 volume = {236/1-2}, 4425 pages = {505-523}, 4426 year = {2005}, 4427 petsc_uses = {KSP} 4428} 4429 4430@InProceedings{ snark2, 4431 author = {B. Appelbe and D. May and S. Quenette and S. Tang and F. Wang and L. Moresi}, 4432 year = {2002}, 4433 title = {Towards Rapid Geoscience Model Development - The {Snark} Project}, 4434 booktitle = {Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop}, 4435 petsc_uses = {KSP} 4436} 4437 4438@Article{ snark1, 4439 author = {Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang 4440 Tan and Feng Wang}, 4441 title = {Snark - A Reusable Framwork for Geoscience Computational Models}, 4442 journal = {Submitted to Pure and Applied Geosciences}, 4443 petsc_uses = {KSP} 4444} 4445 4446@InProceedings{ earthquake2003, 4447 author = {Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and 4448 Antonio Fernandez and Omar Ghattas and Eui Joong Kim and David O'Hallaron and 4449 Tiankai Tu}, 4450 year = {2003}, 4451 title = {High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers}, 4452 booktitle = {Proceedings of SC2003}, 4453 note = {A winner of the Gordon Bell Prize for special achievement at SC2003}, 4454 petsc_uses = {KSP} 4455} 4456 4457@InProceedings{ stefano12, 4458 author = {Michele De Stefano}, 4459 title = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data}, 4460 booktitle = {PIERS Proceedings}, 4461 month = aug, 4462 address = {Moscow, RUSSIA}, 4463 pages = {491--495}, 4464 year = {2012}, 4465 petsc_uses = {KSP} 4466} 4467 4468%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY= 4469 4470% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4471% LiteralHTML: <center><img alt="" 4472% LiteralHTML: src="images/ocean.jpg"></center></p> 4473@Article{ khatiwala07, 4474 author = {Khatiwala, S.}, 4475 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 4476 journal = {Glob. Biogeochem. Cycles}, 4477 volume = {21}, 4478 doi = {10.1029/2007GB002923}, 4479 year = {2007}, 4480 url = { http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf} 4481} 4482 4483@Article{ dks2004, 4484 author = {Sergey Danilov, Gennady Kivman and Jens Schroeter}, 4485 journal = {Ocean Modelling}, 4486 year = {2004}, 4487 volume = {6(2)}, 4488 pages = {125-150}, 4489 title = {A finite-element Ocean Model: Principles and Evaluation}, 4490 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}, 4491 petsc_uses = {KSP} 4492} 4493 4494@Article{ danilov1, 4495 author = {S. Danilov and G. Kivman and J. Schroter}, 4496 year = {2004}, 4497 title = {Evaluation of an eddy-permitting finite-element ocean model in the {N}orth 4498 {A}tlantic}, 4499 journal = {Ocean Modelling}, 4500 petsc_uses = {KSP} 4501} 4502 4503@Article{ nerger1, 4504 author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter}, 4505 year = {2004}, 4506 title = {Data Assimilation with the Ensemble {K}alman Filter and the {SEIK} Filter applied to 4507 a Finite Element Model of the {N}orth {A}tlantic}, 4508 journal = {Journal of marine systems}, 4509 petsc_uses = {KSP} 4510} 4511 4512@Conference{ rakowsky2003self, 4513 title = {{A self-adaptive finite element model of the atmosphere}}, 4514 author = {Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, 4515 D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.}, 4516 booktitle = {Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of 4517 High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002}, 4518 pages = {279}, 4519 isbn = {981238376X}, 4520 year = {2003}, 4521 organization = {World Scientific Pub Co}, 4522 petsc_uses = {KSP} 4523} 4524 4525@Article{ lauter3, 4526 author = {M. Lauter}, 4527 year = {2004}, 4528 title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4529 AtmosphArenmodell}, 4530 journal = {Berichte zur Polar- und Meeresforschung}, 4531 petsc_uses = {KSP} 4532} 4533 4534@Article{ lauter2, 4535 author = {M. Lauter and D. Handorf and K. Dethloff}, 4536 year = {2004}, 4537 title = {Unsteady analytical solutions of the spherical shallow water equations}, 4538 journal = {Journal of computational physics}, 4539 petsc_uses = {KSP} 4540} 4541 4542@PhDThesis{ lauter1, 4543 author = {M. Lauter}, 4544 year = {2004}, 4545 title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven 4546 AtmosphArenmodell}, 4547 institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}, 4548 petsc_uses = {KSP} 4549} 4550 4551@Article{ frickenhaus1, 4552 author = {S. Frickenhaus and W. Hiller and M. Best}, 4553 year = {2005}, 4554 title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of 4555 parallel numerical atmosphere and ocean models}, 4556 journal = {Ocean Modelling}, 4557 volume = {10}, 4558 pages = {185--191}, 4559 petsc_uses = {KSP} 4560} 4561 4562@Article{ 0266-5611-24-3-034015, 4563 author = {I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak}, 4564 title = {A {N}ewton-{CG} method for large-scale three-dimensional elastic full-waveform 4565 seismic inversion}, 4566 journal = {Inverse Problems}, 4567 volume = {24}, 4568 number = {3}, 4569 pages = {034015 (26pp)}, 4570 url = {http://stacks.iop.org/0266-5611/24/034015}, 4571 year = {2008}, 4572 abstract = {We present a nonlinear optimization method for large-scale 3D elastic 4573 full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear 4574 iterations with inner conjugate gradient linear iterations, globalized by an 4575 Armijo backtracking line search, solved on a sequence of finer grids and higher 4576 frequencies to remain in the vicinity of the global optimum, inexactly terminated 4577 to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total 4578 variation operator to capture sharp interfaces, finely discretized by finite 4579 elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, 4580 implemented in matrix-free fashion with adjoint-based computation of reduced 4581 gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime 4582 waveform storage, and partitioned spatially across processors to parallelize the 4583 solutions of the forward and adjoint wave equations and the evaluation of 4584 gradient-like information. Several numerical examples demonstrate the grid 4585 independence of linear and nonlinear iterations, the effectiveness of the 4586 preconditioner, the ability to solve inverse problems with up to 17 million 4587 inversion parameters on up to 2048 processors, the effectiveness of multiscale 4588 continuation in keeping iterates in the basin of attraction of the global minimum, 4589 and the ability to fit the observational data while reconstructing the model with 4590 reasonable resolution and capturing sharp interfaces.}, 4591 petsc_uses = {KSP} 4592} 4593 4594% LiteralHTML: 4595% LiteralHTML: <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3> 4596% LiteralHTML: 4597% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4598% LiteralHTML:<font color="#FF0000"> 4599% LiteralHTML:Modeling surface flow of water is valuable for both flood control and 4600% LiteralHTML:agricultural and environmental reasons. For example, regenerating the 4601% LiteralHTML:Florida Everglades requires extensive understanding of the surface water 4602% LiteralHTML:characteristics over thousands of square miles. PETSc has been used 4603% LiteralHTML:for a variety of these simulations.</p> 4604% LiteralHTML:</font> 4605% LiteralHTML: 4606@Article{ mills2009modeling, 4607 title = {Modeling subsurface reactive flows using leadership-class computing}, 4608 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4609 Mahinthakumar, G.K. and Smith, B.F.}, 4610 journal = {Journal of Physics: Conference Series}, 4611 volume = {180}, 4612 pages = {012062}, 4613 year = {2009}, 4614 publisher = {IOP Publishing}, 4615 petsc_uses = {KSP} 4616} 4617 4618@Conference{ mills2007simulating, 4619 title = {{Simulating subsurface flow and transport on ultrascale computers using 4620 PFLOTRAN}}, 4621 author = {Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.}, 4622 booktitle = {Journal of Physics: Conference Series}, 4623 volume = {78}, 4624 pages = {012051}, 4625 year = {2007}, 4626 organization = {IOP Publishing}, 4627 petsc_uses = {KSP} 4628} 4629 4630@InProceedings{ mills2009, 4631 title = {Modeling subsurface reactive flows using leadership-class computing}, 4632 author = {Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and 4633 Mahinthakmuar, G. and Smith, B.}, 4634 booktitle = {Journal of Physics: Conference Series}, 4635 volume = {180}, 4636 pages = {102062}, 4637 year = {2009}, 4638 organization = {IOP Publishing}, 4639 petsc_uses = {KSP} 4640} 4641 4642@Article{ guo2013parallel, 4643 title = {A parallel, fully coupled, fully implicit solution to reactive transport in 4644 porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method 4645 }, 4646 journal = {Advances in Water Resources }, 4647 volume = {53}, 4648 number = {0}, 4649 pages = {101 - 108}, 4650 year = {2013}, 4651 note = {}, 4652 issn = {0309-1708}, 4653 doi = {10.1016/j.advwatres.2012.10.010}, 4654 author = {Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David 4655 Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita}, 4656 keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block 4657 preconditioner}, 4658 petsc_uses = {KSP} 4659} 4660 4661@Unpublished{ stomp, 4662 title = {STOMP (Subsurface Transport Over Multiple Phases) webpage}, 4663 url = {http://stomp.pnl.gov/}, 4664 petsc_uses = {KSP} 4665} 4666 4667@InProceedings{ htfc2003, 4668 author = {L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings}, 4669 title = {Methods and Experiences For Parallelizing Flood Models}, 4670 year = {2003}, 4671 booktitle = {Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th 4672 European PVM/MPI User's Group Meeting}, 4673 note = {Springer Lecture Notes in Computer Science, Volume 2840}, 4674 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1}, 4675 petsc_uses = {KSP} 4676} 4677 4678@InProceedings{ hulchy-tran-astalos-fmsip, 4679 author = {L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and 4680 D.Froehlich}, 4681 title = {Flood Modeling System and Its Parallelization}, 4682 year = {2002}, 4683 booktitle = {Proceedings of the International Conference on Parallel Computing in Electrical 4684 Engineering}, 4685 url = {http://portal.acm.org/citation.cfm?id=824476.825951}, 4686 petsc_uses = {KSP} 4687} 4688 4689@InProceedings{ gy1, 4690 author = {J. P. Gwo and G. T. Yeh}, 4691 title = {High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive 4692 Transport at Watershed Scale}, 4693 year = {2004}, 4694 booktitle = {The International Conference on Computational Methods}, 4695 url = {http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf}, 4696 petsc_uses = {KSP} 4697} 4698 4699@Conference{ cheng2009efficient, 4700 title = {{An efficient parallel method for large-scale groundwater flow equation based on 4701 PETSc}}, 4702 author = {Cheng, T. and Ji, X. and Wang, Q.}, 4703 booktitle = {Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth 4704 Conference on}, 4705 pages = {190--193}, 4706 organization = {IEEE}, 4707 petsc_uses = {KSP} 4708} 4709 4710@Unpublished{ sfrsm, 4711 title = {The South Florida Regional Simulation Model and Hydrologic Simulation Engine}, 4712 url = {http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf}, 4713 note = {Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for 4714 its linear solves}, 4715 petsc_uses = {KSP} 4716} 4717 4718% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4719@InProceedings{ bart_omar:sc05, 4720 author = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar 4721 Ghattas and Judith~C. Hill and Gart~G. van Bloemen Waanders}, 4722 title = {Dynamic data driven inversion for terascale simulations: real-time 4723 indentification of airborne contaminants}, 4724 booktitle = {Proceedings of SC2005}, 4725 organization = {IEEE/ACM}, 4726 address = {Seattle, WA}, 4727 year = {2005}, 4728 month = nov, 4729 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf}, 4730 lab = {SNL}, 4731 petsc_uses = {KSP} 4732} 4733 4734@InProceedings{ anton-krassimir-lscc, 4735 author = {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev}, 4736 title = {Comparison of Two Local Refinement Methods for Large Scale Air Pollution 4737 Simulations}, 4738 booktitle = {Large-Scale Scientific Computing: 4th International Conference, LSSC 2003}, 4739 volume = {2907}, 4740 year = {2003}, 4741 publisher = {Springer-Verlag}, 4742 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1}, 4743 petsc_uses = {KSP} 4744} 4745 4746@InProceedings{ aa2001, 4747 author = {Anton Antonov}, 4748 title = {Object-Oriented Framework for Large Scale Air Pollution Modeling}, 4749 year = {2001}, 4750 booktitle = {Large-Scale Scientific Computing : Third International Conference, LSSC 2001, 4751 Sozopol, Bulgaria}, 4752 note = {Springer Lecture Notes in Computer Science, Volume 2179}, 4753 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1}, 4754 petsc_uses = {KSP} 4755} 4756 4757% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4758@Article{ grassley-simmons-kercher-00, 4759 author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher}, 4760 year = {2000}, 4761 title = {Mineralogical heterogeneity in fractured, porous media and its representation in 4762 reactive transport models}, 4763 journal = {Applied Geochemistry}, 4764 volume = {17}, 4765 pages = {699--708}, 4766 lab = {LLNL} 4767} 4768 4769@Article{ glassey-nitao-03, 4770 author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson 4771 and Carl I. Steefel and James R. Kercher}, 4772 year = {2003}, 4773 title = {The impact of climate change on vadose zone pore waters and its implication for 4774 long-term monitoring}, 4775 journal = {Computers and Geosciences}, 4776 volume = {29}, 4777 pages = {399-411}, 4778 lab = {LLNL}, 4779 petsc_uses = {KSP} 4780} 4781 4782@Article{ steefel-depaolo-lichtner-05, 4783 author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner}, 4784 year = {2005}, 4785 title = {Reactive transport modeling: An essential tool and a new research approach for 4786 the Earth sciences}, 4787 journal = {Earth and Planetary Science Letters}, 4788 lab = {LLNL,LANL}, 4789 petsc_uses = {KSP} 4790} 4791 4792% LiteralHTML:<a name="scalinglarge"> 4793% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4794% LiteralHTML: <center><img alt="" 4795% LiteralHTML: src="images/scalinglarge.jpg"></center></p> 4796% LiteralHTML:<font color="#FF0000"> 4797% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL) 4798@InProceedings{ kongstognergastonpetersonpermannslaughtermartineau2018, 4799 title = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing 4800 Strategies for Large-Scale Numerical Simulations}, 4801 author = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody 4802 J. Permann and Andrew E. Slaughter and Richard C. Martineau}, 4803 booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for 4804 Large-Scale Systems (scalA)}, 4805 pages = {65-72}, 4806 doi = {10.1109/ScalA.2018.00012}, 4807 month = nov, 4808 year = {2018}, 4809 petsc_uses = {KSP} 4810} 4811 4812@Article{ km2004, 4813 author = {A. Keese and H. G. Matthies}, 4814 journal = {Computers and Structures}, 4815 year = {2005}, 4816 volume = {83}, 4817 pages = {1033--1047}, 4818 title = {Hierarchical parallelisation for the solution of stochastic finite element 4819 equations}, 4820 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}, 4821 petsc_uses = {KSP} 4822} 4823 4824@Unpublished{ hvl2002, 4825 title = {Numerical Modeling of {NAPL} Source Zone Treatment}, 4826 author = {Hammond, G.E., A.J. Valocchi and P.C. Lichtner}, 4827 note = {Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.}, 4828 url = {http://cee.uiuc.edu/transport/hammond/agu_2002.pdf}, 4829 year = {2002}, 4830 lab = {LANL}, 4831 petsc_uses = {KSP} 4832} 4833 4834@PhDThesis{ hammond2003, 4835 author = {Glenn E. Hammond}, 4836 title = {Innovative Methods for Solving Multicomponent Biogeochemical Groundwater 4837 Transport on Supercomputers}, 4838 school = {University of Illinois at Urbana-Champaign}, 4839 year = {2003}, 4840 url = {http://cee.uiuc.edu/transport/hammond/dissertation.pdf}, 4841 petsc_uses = {KSP} 4842} 4843 4844@Unpublished{ uk, 4845 title = {Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large 4846 Scale Environmental Flows and Transport Processes}, 4847 url = {http://es.epa.gov/ncer/progress/grants/96/high/tsang99.html}, 4848 note = {EPA funded work to simulate turbulent dispersion of toxic chemicals around 4849 buildings and in Green Bay. Used PETSc for its linear solvers}, 4850 year = {1999}, 4851 petsc_uses = {KSP} 4852} 4853 4854@InProceedings{ hammond2002, 4855 author = {Glenn E. Hammond and Albert J. Valocchi and Peter C. Lichtner}, 4856 title = {Modeling Multicomponent Reactive Transport on Parallel Computers Using 4857 {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners}, 4858 year = {2002}, 4859 url = {http://www.cee.uiuc.edu/transport/publications/hammond/CMWR_2002.pdf}, 4860 booktitle = {Proceedings of the XIV International Conference on Computational Methods in Water 4861 Resources, Delft, The Netherlands.}, 4862 lab = {LANL}, 4863 petsc_uses = {KSP} 4864} 4865 4866@TechReport{ steefel1, 4867 author = {C. I. Steefel}, 4868 title = {Software for modeling multicomponent, multidimensional reactive transport}, 4869 year = {2001}, 4870 institution = {Lawrence Livermore National Laboratory}, 4871 number = {UCRL-MA-143182}, 4872 lab = {LLNL}, 4873 petsc_uses = {KSP} 4874} 4875 4876@Article{ steefel2, 4877 author = {C. I. Steefel and A. C. Lasaga}, 4878 title = {A coupled model for transport of multiple chemical-species and kinetic 4879 precipitation dissolution reactions with application to reactive flow in 4880 single-phase hydrothermal systems}, 4881 journal = {Americal Journal of Science}, 4882 year = {1994}, 4883 pages = {529-592}, 4884 volume = {294}, 4885 number = {5}, 4886 petsc_uses = {KSP} 4887} 4888 4889@TechReport{ steefel3, 4890 author = {C. I. Steefel and S. B. Yabusaki}, 4891 title = {{OS3D/GIMRT}, Software for Multicomponent-Multidimensional reactive transport: 4892 User's manual and programmer's guide}, 4893 year = {1996}, 4894 institution = {Pacific Northwest National Laboratory}, 4895 number = {PNNL-11166}, 4896 lab = {PNNL}, 4897 petsc_uses = {KSP} 4898} 4899 4900@Article{ 2005hvl, 4901 author = {G. E. Hammond and A.J. Valocchi and P.C. Lichtner}, 4902 title = {Application of {J}acobian-free {N}ewton-{K}rylov with physics-based 4903 preconditioning to biogeochemical transport}, 4904 journal = {Advances in Water Resources}, 4905 year = {2005}, 4906 pages = {359--376}, 4907 volume = {28}, 4908 url = { 4909 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}, 4910 lab = {LANL}, 4911 petsc_uses = {KSP} 4912} 4913 4914@Article{ wang-zabar-05, 4915 author = {J Wang and N Zabaras}, 4916 journal = {Int. J. Heat and Mass Transfer}, 4917 title = {A Markov random field model of contamination source identification in porous 4918 media flow}, 4919 year = {2005}, 4920 petsc_uses = {KSP} 4921} 4922 4923@InBook{ kp1, 4924 author = {Jong G. Kim and Hyoung W. Park}, 4925 chapter = {Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous 4926 Media}, 4927 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=m5uc84pqrh1qrg8clyuh&referrer=parent&backto=issue,1,117;journal,206,1787;linkingpublicationresults,1:105633,1}, 4928 title = {Lecture Notes in Computer Science}, 4929 publisher = {Springer-Verlag}, 4930 volume = {3044}, 4931 year = {2004}, 4932 petsc_uses = {KSP} 4933} 4934 4935@Article{ 2001agusm...h32a06k, 4936 author = {{Kim}, J.~G. and {Kim}, J.}, 4937 title = {Parallel Implementation of Finite Element Groundwater Flow Model}, 4938 journal = {AGU Spring Meeting Abstracts}, 4939 year = {2001}, 4940 pages = {32-+}, 4941 petsc_uses = {KSP} 4942} 4943 4944@Article{ lzb2005, 4945 author = {A. M. Wasantha Lal and Randy Van Zee and Mark Belnap}, 4946 title = {CASE STUDY: A MODEL TO SIMULATE REGIONAL FLOW IN SOUTH FLORIDA}, 4947 journal = {Journal of Hydraulic Engineering}, 4948 year = {2005}, 4949 volume = {131}, 4950 number = {4}, 4951 pages = {247--258}, 4952 petsc_uses = {KSP} 4953} 4954 4955@Article{ rao2005, 4956 author = {Prasada Rao}, 4957 title = {A parallel {RMA2} model for simulating large-scale free surface flows}, 4958 journal = {Environmental Modelling and Software}, 4959 year = {2005}, 4960 pages = {47--53}, 4961 petsc_uses = {KSP} 4962} 4963 4964@InProceedings{ pr1, 4965 author = {Prasada Rao}, 4966 title = {An Efficient Scalable Finite Element Model for Simulating Large Scale 4967 Hydrodynamic Flows}, 4968 year = {2003}, 4969 booktitle = {Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics 4970 Conference}, 4971 url = {http://www.ce.washington.edu/em03/proceedings/papers/477.pdf}, 4972 petsc_uses = {KSP} 4973} 4974 4975@InProceedings{ lichtner2004, 4976 author = {Peter C. Lichtner and Andrew Wolfsberg}, 4977 title = {Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with 4978 Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand 4979 Challenge Supercomputing Problem}, 4980 year = {2004}, 4981 booktitle = {MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport 4982 Modeling of Inorganic Contaminants, Radionuclides and Nutrients}, 4983 note = {Also Los Alamos National Laboratory report: LA-UR-04-1826}, 4984 lab = {LANL}, 4985 petsc_uses = {KSP} 4986} 4987 4988% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 4989@Article{ aba01:petsc-app, 4990 author = {Jason Abate and Peng Wang and Kamy Sepehrnoori}, 4991 title = {Parallel Compositional Reservior Simulation on Clusters of {PC}s}, 4992 journal = {Int. J. High Performance Computing Applications}, 4993 year = {2001}, 4994 volume = {15}, 4995 number = {1}, 4996 pages = {13--21}, 4997 petsc_uses = {KSP} 4998} 4999 5000@PhDThesis{ tjb200, 5001 author = {Thomas James Byer}, 5002 title = {Preconditioned Newton Methods for Simulation of Reservoirs with Surface 5003 Facilities}, 5004 school = {Stanford}, 5005 year = {2000}, 5006 petsc_uses = {KSP} 5007} 5008 5009@InProceedings{ puchyr2006, 5010 author = {Peter J. Puchyr}, 5011 title = {Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a 5012 {Win32} Cluster}, 5013 booktitle = {Proceedings of the Canadian International Petroleum Conference}, 5014 note = {Paper number CIPC2006-207}, 5015 year = {2006}, 5016 petsc_uses = {KSP} 5017} 5018 5019@InProceedings{ texas98, 5020 author = {P. Wang and S. Balay and K. Seperhrnoori and J. Wheeler and J. Abate and B. Smith 5021 and G. A. Pope}, 5022 title = {A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir 5023 Simulation}, 5024 booktitle = {Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation 5025 Symposium}, 5026 note = {also available as Argonne preprint ANL/MCS-P743-1298}, 5027 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P743.pdf}, 5028 year = {1998}, 5029 petsc_uses = {KSP} 5030} 5031 5032% LiteralHTML: 5033% LiteralHTML: <a name="cfd"><H3><center>CFD</center></H3> 5034% LiteralHTML: 5035@Article{ farrellmitchellscottwechsung2021, 5036 title = {A {Reynolds-robust} preconditioner for the {Scott-Vogelius} discretization of the 5037 stationary incompressible {Navier-Stokes} equations}, 5038 author = {Patrick E Farrell and Lawrence Mitchell and L Ridgway Scott and Florian 5039 Wechsung}, 5040 journal = {The SMAI journal of computational mathematics}, 5041 volume = {7}, 5042 pages = {75--96}, 5043 year = {2021}, 5044 petsc_uses = {KSP} 5045} 5046 5047@Article{ adlerbensoncyrfarrellmaclachlantuminaro2021, 5048 title = {Monolithic Multigrid Methods for Magnetohydrodynamics}, 5049 author = {James H Adler and Thomas R Benson and Eric C Cyr and Patrick E Farrell and Scott 5050 P MacLachlan and Ray S Tuminaro}, 5051 journal = {SIAM Journal on Scientific Computing}, 5052 number = {0}, 5053 pages = {S70--S91}, 5054 year = {2021}, 5055 petsc_uses = {KSP} 5056} 5057 5058@Article{ farrellgaticalamichhaneoyarzuaruizbaier2021, 5059 title = {Mixed Kirchhoff stress–displacement–pressure formulations for incompressible 5060 hyperelasticity}, 5061 author = {Patrick E. Farrell and Luis F. Gatica and Bishnu P. Lamichhane and Ricardo 5062 Oyar\'ua and Ricardo Ruiz-Baier}, 5063 journal = {Computer Methods in Applied Mechanics and Engineering}, 5064 volume = {374}, 5065 pages = {113562}, 5066 issn = {0045-7825}, 5067 doi = {https://doi.org/10.1016/j.cma.2020.113562}, 5068 url = {https://www.sciencedirect.com/science/article/pii/S0045782520307477}, 5069 year = {2021}, 5070 petsc_uses = {KSP} 5071} 5072 5073@Article{ farrellmitchellwechsung2018, 5074 title = {An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible 5075 {Navier-Stokes} equations at high {Reynolds} number}, 5076 author = {Patrick E Farrell and Lawrence Mitchell and Florian Wechsung}, 5077 journal = {SIAM Journal on Scientific Computing}, 5078 volume = {41}, 5079 number = {5}, 5080 eprint = {1810.03315}, 5081 pages = {A3073-A3096}, 5082 year = {2019}, 5083 petsc_uses = {KSP} 5084} 5085 5086@Article{ hevuikklaij2017, 5087 title = {Block-preconditioners for the incompressible {Navier}--{Stokes} equations 5088 discretized by a finite volume method}, 5089 author = {Xin He and Cornelis Vuik and Christiaan Klaij}, 5090 journal = {Journal of Numerical Mathematics}, 5091 volume = {25}, 5092 number = {2}, 5093 pages = {89--105}, 5094 year = {2017}, 5095 petsc_uses = {KSP} 5096} 5097 5098@InProceedings{ zou2015newton, 5099 title = {Newton--Krylov methods in applications of two-phase flow problems with phase 5100 appearance/disappearance}, 5101 author = {Zou, L and Zhao, H and Zhang, H}, 5102 booktitle = {ANS 2015 Annual Meeting, June}, 5103 volume = {7}, 5104 number = {11}, 5105 year = {2015}, 5106 petsc_uses = {KSP} 5107} 5108 5109@Article{ guermond2009nonlinear, 5110 title = {Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a 5111 Fourier/finite element technique and an interior penalty method}, 5112 author = {Guermond, J-L and Laguerre, Raphael and L{\'e}orat, Jacques and Nore, Caroline}, 5113 journal = {Journal of computational physics}, 5114 volume = {228}, 5115 number = {8}, 5116 pages = {2739--2757}, 5117 year = {2009}, 5118 publisher = {Elsevier}, 5119 petsc_uses = {KSP} 5120} 5121 5122@Article{ erzincanlisahin2015, 5123 title = {The numerical simulation of the wing kinematics effects on near wake topology and 5124 aerodynamic performance in hovering {D}rosophila flight}, 5125 author = {Belkis Erzincanli and Mehmet Sahin}, 5126 journal = {Computers \& Fluids}, 5127 volume = {122}, 5128 pages = {90--110}, 5129 year = {2015}, 5130 publisher = {Elsevier}, 5131 petsc_uses = {KSP} 5132} 5133 5134@Article{ ekensahin2015, 5135 title = {A parallel monolithic algorithm for the numerical simulation of large-scale fluid 5136 structure interaction problems}, 5137 author = {Ali Eken and Mehmet Sahin}, 5138 journal = {International Journal for Numerical Methods in Fluids}, 5139 year = {2015}, 5140 publisher = {Wiley Online Library}, 5141 petsc_uses = {KSP} 5142} 5143 5144@Article{ hwangsucai2015, 5145 title = {A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method 5146 for transonic full potential equation}, 5147 author = {Feng-Nan Hwang and Yi-Cheng Su and Xiao-Chuan Cai}, 5148 journal = {Computers \& Fluids}, 5149 volume = {110}, 5150 number = {30}, 5151 pages = {96--107}, 5152 year = {2015}, 5153 doi = {10.1016/j.compfluid.2014.04.005}, 5154 petsc_uses = {KSP} 5155} 5156 5157@Article{ yanghwangcai2016, 5158 title = {Nonlinear Preconditioning Techniques for Full-Space {L}agrange--{N}ewton Solution of 5159 {PDE}-Constrained Optimization Problems}, 5160 author = {Haijian Yang and Feng-Nan Hwang and Xiao-Chuan Cai}, 5161 journal = {SIAM Journal on Scientific Computing}, 5162 volume = {38}, 5163 number = {5}, 5164 pages = {A2756--A2778}, 5165 year = {2016}, 5166 petsc_uses = {KSP} 5167} 5168 5169@Article{ khanaidun2011, 5170 author = {Irfan Khan and Cyrus K. Aidun}, 5171 title = {Direct numerical simulation of saturated deformable porous media using parallel 5172 hybrid Lattice-{B}oltzmann and finite element method}, 5173 journal = {Int. J. Numer. Meth. Eng.}, 5174 volume = {86}, 5175 pages = {1379--1395}, 5176 year = {2011}, 5177 petsc_uses = {KSP} 5178} 5179 5180@Article{ khanaidun2014, 5181 author = {Irfan Khan and Cyrus K. Aidun}, 5182 title = {Modeling the deformation of saturate porous media using direct numerical 5183 simulation}, 5184 journal = {Int. J. Multiphase Flow}, 5185 doi = {10.1016/j.ijmultiphaseflow.2014.12.003}, 5186 year = {2014}, 5187 petsc_uses = {KSP} 5188} 5189 5190@Article{ mofidi2014simulations, 5191 author = {A. Mofidi and P. M. Carrica}, 5192 title = {Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder 5193 and Propeller}, 5194 journal = {Computers and Fluids}, 5195 pages = {191--203}, 5196 year = {2014}, 5197 petsc_uses = {KSP} 5198} 5199 5200@Article{ paik2014fluidstructure, 5201 author = {K. Paik and P. M. Carrica}, 5202 title = {Fluid-Structure Interaction for an Elastic Structure Interacting with Free 5203 Surface in a Rolling Tank}, 5204 journal = {Ocean Engineering}, 5205 pages = {201--212}, 5206 year = {2014}, 5207 petsc_uses = {KSP} 5208} 5209 5210@Article{ castro2013bubble, 5211 author = {A. M. Castro and P. M. Carrica}, 5212 title = {Bubble size distribution prediction for large-scale ship flows: {Model} 5213 evaluation and numerical issues}, 5214 journal = {International Journal of Multiphase Flow 57}, 5215 pages = {131--150}, 5216 year = {2013}, 5217 petsc_uses = {KSP} 5218} 5219 5220@Article{ carrica2013turn, 5221 author = {P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern}, 5222 title = {Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with 5223 Dynamic Overset Grids}, 5224 journal = {Journal of Marine Science and Technology}, 5225 pages = {166--181}, 5226 year = {2013}, 5227 petsc_uses = {KSP} 5228} 5229 5230@Article{ castro2013eulerian, 5231 author = {A. M. Castro and P. M. Carrica}, 5232 title = {Eulerian polydispersed modeling of bubbly flows around ships with application to 5233 {Athena} {R}/V,}, 5234 journal = {International Shipbuilding Progress}, 5235 pages = {403--433}, 5236 year = {2013}, 5237 petsc_uses = {KSP} 5238} 5239 5240@Article{ chase2013overset, 5241 author = {N. Chase and T. Michael and P. M. Carrica}, 5242 title = {Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and 5243 {Maneuvering} {Conditions}}, 5244 journal = {International Shipbuilding Progress}, 5245 pages = {171--205}, 5246 year = {2013}, 5247 petsc_uses = {KSP} 5248} 5249 5250@Article{ sadathosseini2013wu, 5251 author = {H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. 5252 Stern}, 5253 title = {{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and 5254 Free Surge Conditions in Short and Long Head Waves}, 5255 journal = {Ocean Engineering}, 5256 volume = {59}, 5257 pages = {240--273}, 5258 year = {2013}, 5259 petsc_uses = {KSP} 5260} 5261 5262@Article{ chase2013cfd, 5263 author = {N. Chase and P. M. Carrica}, 5264 title = {{CFD} Simulations of a Submarine Propeller and Application to Self-Propulsion of a 5265 Submarine}, 5266 journal = {Ocean Engineering}, 5267 pages = {68--80}, 5268 year = {2013}, 5269 petsc_uses = {KSP} 5270} 5271 5272@Article{ carrica2012cfd, 5273 author = {P. M. Carrica and H. Sadat-Hosseini and F. Stern}, 5274 title = {{CFD} Analysis of Broaching for a Model Surface Combatant with Explicit Simulation 5275 of Moving Rudders and Rotating Propellers}, 5276 journal = {Computers and Fluids 53}, 5277 pages = {117--132}, 5278 year = {2012}, 5279 petsc_uses = {KSP} 5280} 5281 5282@Article{ sakamoto2012urans, 5283 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5284 title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: 5285 Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives}, 5286 publisher = {Journal of Marine Science and Technology}, 5287 pages = {422--445}, 5288 year = {2012}, 5289 petsc_uses = {KSP} 5290} 5291 5292@Article{ sakamoto2012uransb, 5293 author = {N. Sakamoto and P. M. Carrica and F. Stern}, 5294 title = {{URANS} Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: 5295 Analysis and Validation of Local Flow Characteristics}, 5296 journal = {Journal of Marine Science and Technology}, 5297 pages = {446--468}, 5298 year = {2012}, 5299 petsc_uses = {KSP} 5300} 5301 5302@Article{ li2012dynamic, 5303 author = {Y. Li and T. Xing and K. Paik and P. M. Carrica}, 5304 title = {Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics}, 5305 journal = {Renewable Energy}, 5306 pages = {285--298}, 5307 year = {2012}, 5308 petsc_uses = {KSP} 5309} 5310 5311@Article{ huang2012a, 5312 author = {J. Huang and P. M. Carrica and F. Stern}, 5313 title = {A Method to Compute Ship Exhaust Plumes with Waves and Wind}, 5314 journal = {International Journal for Numerical Methods in Fluids}, 5315 pages = {160--180}, 5316 year = {2012}, 5317 petsc_uses = {KSP} 5318} 5319 5320@Article{ huang2012b, 5321 author = {J. Huang and P. M. Carrica and F. Stern}, 5322 title = {A geometry-based level set method for curvilinear overset grids with application 5323 to ship hydrodynamics}, 5324 journal = {International Journal for Numerical Methods in Fluids}, 5325 pages = {494--521}, 5326 year = {2012}, 5327 petsc_uses = {KSP} 5328} 5329 5330@Article{ carrica2011computations, 5331 author = {P. M. Carrica and H. Fu and F. Stern}, 5332 title = {Computations of self-propulsion free to sink and trim and of motions in head 5333 waves of the {KRISO} {Container} {Ship} ({KCS}) model}, 5334 journal = {Applied Ocean Research}, 5335 pages = {309--320}, 5336 year = {2011}, 5337 petsc_uses = {KSP} 5338} 5339 5340@Article{ bhushan2011scalability, 5341 author = {S. Bhushan and P. M. Carrica and J. Yang and F. Stern}, 5342 title = {Scalability and Validation Study for Large Scale Surface Combatant Computations 5343 Using {CFDShip}-Iowa}, 5344 journal = {International Journal of High Performance Computing Applications}, 5345 pages = {466--487}, 5346 year = {2011}, 5347 petsc_uses = {KSP} 5348} 5349 5350@Article{ castro2011full, 5351 author = {A. M. Castro and P. M. Carrica and F. Stern}, 5352 title = {Full scale self-propulsion computations using discretized propeller for the 5353 {KRISO} container ship {KCS}}, 5354 journal = {Computers and Fluids}, 5355 pages = {35--47}, 5356 year = {2011}, 5357 petsc_uses = {KSP} 5358} 5359 5360@Article{ kandasamy2011multifidelity, 5361 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and 5362 D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal}, 5363 title = {Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing {C}atamaran 5364 for Low Wake}, 5365 journal = {Journal of Marine Science and Technology}, 5366 pages = {143--156}, 5367 year = {2011}, 5368 petsc_uses = {KSP} 5369} 5370 5371@Article{ kandasamy2011cfd, 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 = {{CFD} Validation Studies for a High-speed Foil-assisted Semi-planing {C}atamaran}, 5375 journal = {Journal of Marine Science and Technology}, 5376 pages = {157--167}, 5377 year = {2011}, 5378 petsc_uses = {KSP} 5379} 5380 5381@Article{ sadathosseini2011cfd, 5382 author = {H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto 5383 and S. Yamamura and A. Mastuda}, 5384 title = {{CFD} System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, 5385 Periodic Motion and Broaching}, 5386 journal = {Ocean Engineering}, 5387 pages = {88--110}, 5388 year = {2011}, 5389 petsc_uses = {KSP} 5390} 5391 5392@Article{ mosaviraad2010development, 5393 author = {M. Mosaviraad and P. M. Carrica and F. Stern}, 5394 title = {Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} 5395 with Comparison to Regular Wave and Transient Wave Group Procedures Using 5396 {URANS}}, 5397 journal = {Ocean Engineering}, 5398 pages = {653--666}, 5399 year = {2010}, 5400 petsc_uses = {KSP} 5401} 5402 5403@Article{ carrica2010largescale, 5404 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5405 Stern}, 5406 title = {Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5407 Heave Problems for a Surface Combatant}, 5408 journal = {Computers and Fluids}, 5409 pages = {1095--1111}, 5410 year = {2010}, 5411 petsc_uses = {KSP} 5412} 5413 5414@Article{ carrica2010selfpropulsion, 5415 author = {P. M. Carrica and A. M. Castro and F. Stern}, 5416 title = {Self-Propulsion Computations Using Speed Controller and Discretized Propeller 5417 with Dynamic Overset Grids}, 5418 journal = {Journal of Marine Science and Technology}, 5419 pages = {316--330}, 5420 year = {2010}, 5421 petsc_uses = {KSP} 5422} 5423 5424@Article{ ismail2010evaluation, 5425 author = {F. Ismail and P. M. Carrica and T. Xing and F. Stern}, 5426 title = {Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional 5427 Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker}, 5428 journal = {International Journal of Numerical Methods in Fluids}, 5429 pages = {850--886}, 5430 year = {2010}, 5431 petsc_uses = {KSP} 5432} 5433 5434@Article{ kandasamy2010integral, 5435 author = {M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern}, 5436 title = {Integral Force/Moment Waterjet Model for {CFD} Simulations}, 5437 journal = {Journal of Fluids Engineering}, 5438 pages = {101103}, 5439 year = {2010}, 5440 petsc_uses = {KSP} 5441} 5442 5443@Article{ kirk:2014de, 5444 author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A}, 5445 title = {{Modeling hypersonic entry with the fully-implicit {N}avier--{S}tokes (FIN-S) 5446 stabilized finite element flow solver}}, 5447 journal = {Computers {\&} Fluids}, 5448 year = {2014}, 5449 volume = {92}, 5450 number = {0}, 5451 pages = {281--292}, 5452 month = mar, 5453 petsc_uses = {KSP} 5454} 5455 5456@Article{ carracciuolo20111382, 5457 title = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows 5458 in high performance computing environment}, 5459 journal = {Journal of Non-Newtonian Fluid Mechanics }, 5460 volume = {166}, 5461 number = {23--24}, 5462 pages = {1382--1395}, 5463 year = {2011}, 5464 issn = {0377-0257}, 5465 doi = {10.1016/j.jnnfm.2011.08.014}, 5466 author = {L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. 5467 Maffettone and A. Murli}, 5468 keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element 5469 method, High performance computing}, 5470 petsc_uses = {KSP} 5471} 5472 5473@Article{ bungartzgatzhammerliebmehlneckel11, 5474 author = {Bungartz, Hans-Joachim and Gatzhammer, Bernhard and Lieb, Michael and Mehl, 5475 Miriam and Neckel, Tobias}, 5476 title = {Towards multi-phase flow simulations in the PDE framework Peano}, 5477 journal = {Computational Mechanics}, 5478 volume = {48}, 5479 number = {3}, 5480 pages = {365-376}, 5481 year = {2011}, 5482 issn = {0178-7675}, 5483 doi = {10.1007/s00466-011-0626-1}, 5484 publisher = {Springer-Verlag}, 5485 keywords = {PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; 5486 Thermohydraulics; Two-phase flow}, 5487 language = {English}, 5488 petsc_uses = {KSP} 5489} 5490 5491@Article{ bpr:cfl, 5492 author = {H.~M. 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Rasch}, 5493 title = {{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler 5494 Equations}}, 5495 journal = {International Journal for Numerical Methods in Fluids}, 5496 year = {2009}, 5497 volume = {59}, 5498 number = {1}, 5499 pages = {1--18}, 5500 doi = {10.1002/fld.1798}, 5501 petsc_uses = {KSP} 5502} 5503 5504@InBook{ bonfiglioli_campobasso_carpentieri_2010, 5505 author = {Bonfiglioli, A and Campobasso, M S and Carpentieri, B}, 5506 title = {Parallel unstructured three-dimensional turbulent flow analyses using efficiently 5507 preconditioned newton-krylov solver}, 5508 publisher = {Curran Associates}, 5509 year = {2010}, 5510 url = {http://www.proceedings.com/05932.html}, 5511 petsc_uses = {KSP} 5512} 5513 5514@Article{ bonfiglioli_rans_2005, 5515 author = {Paciorri, Renato and Bonfiglioli, Aldo and Di Mascio, Andrea and Favini, 5516 Bernardo}, 5517 title = {RANS simulations of a junction flow}, 5518 journal = {International Journal of Computational Fluid Dynamics}, 5519 volume = {19}, 5520 number = {2}, 5521 pages = {179-189}, 5522 year = {2005}, 5523 doi = {10.1080/10618560410001729126}, 5524 petsc_uses = {KSP} 5525} 5526 5527@InCollection{ bonfiglioli__carpentieri_rans_2008, 5528 author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.}, 5529 affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza 5530 Italy}, 5531 title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS 5532 Equations Using Fluctuation Splitting Schemes}, 5533 booktitle = {Numerical Mathematics and Advanced Applications}, 5534 editor = {Kunisch, Karl and Of, Günther and Steinbach, Olaf}, 5535 publisher = {Springer Berlin Heidelberg}, 5536 isbn = {978-3-540-69777-0}, 5537 pages = {151-158}, 5538 doi = {10.1007/978-3-540-69777-0_17}, 5539 year = {2008}, 5540 petsc_uses = {KSP} 5541} 5542 5543@InCollection{ bonfiglioli__carpentieri_ens_2007, 5544 author = {Bonfiglioli, Aldo and Carpentieri, Bruno and Sosonkina, Masha}, 5545 affiliation = {Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, 5546 Italy}, 5547 title = {EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} 5548 Problems on Unstructured Grids}, 5549 booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing}, 5550 series = {Lecture Notes in Computer Science}, 5551 editor = {Kågström, Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy}, 5552 publisher = {Springer Berlin / Heidelberg}, 5553 isbn = {978-3-540-75754-2}, 5554 pages = {676-685}, 5555 volume = {4699}, 5556 doi = {10.1007/978-3-540-75755-9_83}, 5557 year = {2007}, 5558 petsc_uses = {KSP} 5559} 5560 5561@Article{ terrelscottknepleykirby08, 5562 author = {Andy R. Terrel and L. Ridgway Scott and Matthew G. Knepley and Robert C. Kirby}, 5563 title = {Automated {FEM} Discretizations for the {Stokes} Equation}, 5564 journal = {BIT}, 5565 volume = {48}, 5566 number = {2}, 5567 year = {2008}, 5568 petsc_uses = {KSP} 5569} 5570 5571@Article{ martamadermartinsweidealonso07, 5572 author = {A. C. Marta and C. A. Mader and J. R. R. A. Martins and E. {Van der Weide} and J. 5573 J. Alonso}, 5574 title = {A methodology for the development of discrete adjoint solvers using automatic 5575 differentiation tools}, 5576 journal = {Computational Fluid Dyanmics}, 5577 volume = {21}, 5578 pages = {307--327}, 5579 year = {2007}, 5580 petsc_uses = {KSP} 5581} 5582 5583@TechReport{ avb2008, 5584 author = {V.R. Ambati and J.J.W. van der Vegt and O. Bokhove}, 5585 title = {Variational Space-time (Dis)continuous {G}alerkin Method for Linear Free Surface 5586 Waves}, 5587 year = {2008}, 5588 institution = {University of Twente, the Netherlands}, 5589 url = {http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf}, 5590 petsc_uses = {KSP} 5591} 5592 5593@InProceedings{ bdsm2005, 5594 author = {M. Bozkurttas and H. Dong and V. Seshadri and R. Mittal}, 5595 title = {Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids}, 5596 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit}, 5597 year = {2005}, 5598 url = {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}, 5599 petsc_uses = {KSP} 5600} 5601 5602@InProceedings{ ms2006, 5603 author = {S. Muller and Y. Stiriba}, 5604 title = {A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR 5605 STEADY COMPRESSIBLE FLOWS}, 5606 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006}, 5607 year = {2006}, 5608 url = {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}, 5609 petsc_uses = {KSP} 5610} 5611 5612@Article{ araujoteixeiracunhagroth08, 5613 author = {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth}, 5614 title = {Parallel three-dimensional simulation of the injection molding process}, 5615 journal = {International Journal for Numerical Methods in Fluids}, 5616 year = {2008}, 5617 url = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}, 5618 petsc_uses = {KSP} 5619} 5620 5621@PhDThesis{ a2008, 5622 author = {A. Cubero}, 5623 title = {a parallel coupled algorithm for collocated grids and its application to Large 5624 Eddy Simulation of a turbulent wake}, 5625 school = {University of Zaragoza (Spain)}, 5626 year = {2008}, 5627 petsc_uses = {KSP} 5628} 5629 5630@Article{ afa2007, 5631 author = {A. Cubero and N. 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Visonneau"}, 5728 title = {A new fully coupled method for computing turbulent flows}, 5729 journal = {Computers and Fluids}, 5730 volume = {30}, 5731 pages = {445--472}, 5732 year = {2001}, 5733 petsc_uses = {KSP} 5734} 5735 5736@InProceedings{ knepleysarinsameh99b, 5737 title = {Multilevel Preconditioning for Parallel {CFD}}, 5738 author = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh}, 5739 booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix 5740 Problems In Industrial Applications}, 5741 address = {Minneapolis, MN}, 5742 year = {1999}, 5743 petsc_uses = {KSP} 5744} 5745 5746@InProceedings{ garbey1, 5747 author = {M. Garbey and B. Hadri and W. Shyy.}, 5748 title = {Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer 5749 Problems on the Grid}, 5750 booktitle = {Aerospace Sciences Meeting and Exhibit}, 5751 note = {Paper No. 2005-1386}, 5752 year = {2005}, 5753 petsc_uses = {KSP} 5754} 5755 5756@Article{ carrica2007unsteady, 5757 title = {An unsteady single-phase level set method for viscous free surface flows}, 5758 author = {Carrica, PM and Wilson, RV and Stern, F.}, 5759 journal = {International Journal for Numerical Methods in Fluids}, 5760 volume = {53}, 5761 number = {2}, 5762 pages = {229--256}, 5763 year = {2007}, 5764 publisher = {Chichester; New York: Wiley, c1981-}, 5765 petsc_uses = {KSP} 5766} 5767 5768@Article{ pctw2004, 5769 author = {M. S. Politano and P. M. Carrica and C. Turan and L. Weber}, 5770 title = {A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of 5771 Spillways}, 5772 journal = {Journal of Hydraulic Research}, 5773 note = {accepted for publication}, 5774 year = {2004}, 5775 petsc_uses = {KSP} 5776} 5777 5778@Article{ wcs2004, 5779 author = {R. V. Wilson and P. M. Carrica and F. Stern}, 5780 title = {Unsteady RANS Method for Ship Motions with Application to Roll for a Surface 5781 Combatant}, 5782 journal = {Computers and Fluids}, 5783 note = {in press}, 5784 year = {2004}, 5785 petsc_uses = {KSP} 5786} 5787 5788@Article{ cws2005, 5789 author = {P. M. Carrica and R. V. Wilson and F. Stern}, 5790 title = {Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem}, 5791 journal = {Computers and Fluids}, 5792 note = {accepted for publication}, 5793 year = {2005}, 5794 petsc_uses = {KSP} 5795} 5796 5797@Article{ chndss2010, 5798 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5799 Stern}, 5800 title = { Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and 5801 Heave Problems for a Surface Combatant}, 5802 journal = {Computers and Fluids}, 5803 year = {2010}, 5804 volume = {39}, 5805 number = {7}, 5806 pages = {1095--1111}, 5807 petsc_uses = {KSP} 5808} 5809 5810@InProceedings{ chnkss2008, 5811 author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. 5812 Stern}, 5813 title = {Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear 5814 Grids}, 5815 booktitle = {Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea}, 5816 year = {2008}, 5817 petsc_uses = {KSP} 5818} 5819 5820@MastersThesis{ mtj, 5821 author = {M. T. 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Peltier}, 5868 title = {Localized turbulence simulation for naval hydrodynamics: issues in using overset 5869 refinement grids and detached-eddy simulation}, 5870 booktitle = {7th Overset Composite Grid and Solution Technology Symposium}, 5871 year = {2004}, 5872 petsc_uses = {KSP} 5873} 5874 5875@InProceedings{ mzwp, 5876 author = {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson}, 5877 title = {Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles}, 5878 booktitle = {25th Symposium on Naval Hydrodynamics}, 5879 year = {2004}, 5880 petsc_uses = {KSP} 5881} 5882 5883@InProceedings{ ppph, 5884 author = {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric}, 5885 title = {A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing}, 5886 booktitle = {25th Symposium on Naval Hydrodynamics}, 5887 year = {2004}, 5888 petsc_uses = {KSP} 5889} 5890 5891@InProceedings{ ppd, 5892 author = {E. G. Paterson and L. J. 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Baker}, 5918 title = {Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control 5919 Surfaces}, 5920 booktitle = {42nd AIAA Aerospace Sciences Meeting}, 5921 year = {2004}, 5922 petsc_uses = {KSP} 5923} 5924 5925@InProceedings{ gid1, 5926 author = {G. Frank and J. D'Elia}, 5927 title = {{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model}, 5928 year = {2004}, 5929 booktitle = {Proceedings of the 2nd Conference on Advances and Applications of GiD}, 5930 url = {http://www.gid.cimne.upc.es/2004/papers/p216.pdf}, 5931 petsc_uses = {KSP} 5932} 5933 5934@InBook{ b1, 5935 author = {A.Bonfiglioli}, 5936 chapter = {On the use of the PETSc library for unstructured {CFD} applications}, 5937 year = {2001}, 5938 title = {Science and Supercomputing at CINECA}, 5939 pages = {397--400}, 5940 petsc_uses = {KSP} 5941} 5942 5943@InProceedings{ b2004, 5944 author = {L. A. Barba}, 5945 title = {Computing high-Reynolds number vortical flows: a highly accurate method with a 5946 fully meshless formulation}, 5947 year = {2004}, 5948 booktitle = {International Conference on Parallel CFD, Grand Canary, May 2004}, 5949 note = {Submitted}, 5950 petsc_uses = {KSP} 5951} 5952 5953@InProceedings{ bl2004, 5954 author = {L. A. Barba and A. Leonard}, 5955 title = {Computation of Viscous Vortices with Fully Meshless Method}, 5956 year = {2004}, 5957 booktitle = {Proceedings of ICTAM meeting in Warsaw, August 2004}, 5958 note = {Submitted}, 5959 petsc_uses = {KSP} 5960} 5961 5962@Article{ vws1, 5963 author = {B. G. M. Van Wachem and J. C. Schouten}, 5964 title = {Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise 5965 Velocity}, 5966 institution = {Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering 5967 and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The 5968 Netherlands}, 5969 journal = {AIChE}, 5970 volumne = {48}, 5971 number = {12}, 5972 month = dec, 5973 year = {2002}, 5974 petsc_uses = {KSP} 5975} 5976 5977@TechReport{ lbam1, 5978 author = {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi}, 5979 title = {Precondizionatori paralleli per la fluidodinamica computazionale}, 5980 institution = {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico 5981 di Bari Italy}, 5982 year = {2002}, 5983 number = {25/02}, 5984 petsc_uses = {KSP} 5985} 5986 5987@Article{ kees_miller_02, 5988 author = {C. E. Kees and C. T. Miller}, 5989 title = {Higher Order Time Integration Methods for Two-Phase Flow}, 5990 journal = {Advances in Water Resources}, 5991 year = {2002}, 5992 volume = {25}, 5993 number = {2}, 5994 pages = {159-177.}, 5995 petsc_uses = {KSP} 5996} 5997 5998@InProceedings{ lepotmeersessers2001, 5999 author = {I. Lepot and F. Meers and J.A. Essers}, 6000 title = {Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D 6001 Unstructured Meshes}, 6002 year = {2001}, 6003 booktitle = {ECCOMAS Computational Fluid Dynamics Conference 2001}, 6004 url = {http://www.ulg.ac.be/aerodyn}, 6005 petsc_uses = {KSP} 6006} 6007 6008@InProceedings{ knepley98, 6009 author = {Matthew Knepley and Denis Vanderstraeten}, 6010 title = {Parallel Building Blocks for Finite Element Simulations: Application to 6011 Solid-Liquid Mixture Flows}, 6012 booktitle = {Proceedings of Parallel CFD'97}, 6013 publisher = {Elsevier}, 6014 pages = {281--287}, 6015 year = {1998}, 6016 petsc_uses = {KSP} 6017} 6018 6019@InProceedings{ pcfd97, 6020 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 6021 title = {Parallel Implicit {PDE} Computations: Algorithms and Software}, 6022 publisher = {Elsevier}, 6023 year = {1998}, 6024 booktitle = {Proceedings of Parallel CFD'97}, 6025 pages = {333-344}, 6026 petsc_uses = {KSP} 6027} 6028 6029@InProceedings{ knepleysamehsari98, 6030 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 6031 title = {Parallel Simulation of Particulate Flows}, 6032 booktitle = {Solving Irregularly Structured Problems in Parallel}, 6033 editors = {A. Ferreira et al}, 6034 year = {1998}, 6035 series = {Lecture Notes in Computer Science}, 6036 volume = {1457}, 6037 pages = {226--237}, 6038 petsc_uses = {KSP} 6039} 6040 6041@Article{ gkmt98, 6042 author = {William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri}, 6043 title = {Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel 6044 Implicit {CFD}}, 6045 journal = {Int. J. High Performance Computing Applications}, 6046 year = {2000}, 6047 volume = {14}, 6048 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z}, 6049 pages = {102-136}, 6050 petsc_uses = {KSP} 6051} 6052 6053@InProceedings{ agkks-sc99, 6054 author = {W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. 6055 Smith}, 6056 title = {Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application}, 6057 booktitle = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing}, 6058 editor = {}, 6059 publisher = {}, 6060 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z}, 6061 year = {1999}, 6062 note = {Winner of Gordon Bell Special Prize at SC 99}, 6063 petsc_uses = {KSP} 6064} 6065 6066@Article{ gkks01, 6067 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6068 title = {High Performance Parallel Implicit {CFD}}, 6069 journal = {Journal of Parallel Computing}, 6070 year = {2001}, 6071 volume = {27}, 6072 pages = {337-362}, 6073 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf}, 6074 petsc_uses = {KSP} 6075} 6076 6077@Article{ cristea-sofonea-02, 6078 author = {Artur Cristea and Victor Sofonea}, 6079 title = {Finite Difference lattice Boltzmann model for Liquid Vapour Systems}, 6080 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 6081 Sciences, Information Sciences}, 6082 volume = {3}, 6083 number = {3}, 6084 year = {2002}, 6085 petsc_uses = {KSP} 6086} 6087 6088@Article{ cristea2, 6089 author = {Artur Cristea and Victor Sofonea}, 6090 title = {Two component lattice Boltzmann model with flux limiter techniques}, 6091 journal = {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical 6092 Sciences, Information Sciences}, 6093 volume = {4}, 6094 number = {1}, 6095 year = {2003}, 6096 pages = {59--64}, 6097 petsc_uses = {KSP} 6098} 6099 6100@Article{ cristea1, 6101 author = {Artur Cristea and Victor Sofonea}, 6102 title = {Two component lattice Boltzmann model with flux limiters}, 6103 journal = {Central European Journal of Physics}, 6104 volume = {2}, 6105 number = {2}, 6106 year = {2004}, 6107 pages = {382--396}, 6108 petsc_uses = {KSP} 6109} 6110 6111@Article{ sofnea-lamura1, 6112 author = {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea}, 6113 title = {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor 6114 systems}, 6115 journal = {Physical Review E}, 6116 volume = {70}, 6117 number = {4}, 6118 year = {2004}, 6119 pages = {046702-1 / 046702-9}, 6120 petsc_uses = {KSP} 6121} 6122 6123@InProceedings{ gkks01b, 6124 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6125 title = {Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}}, 6126 booktitle = {Proceedings of the First MIT Conference on Computational Fluid and Solid 6127 Mechanics}, 6128 editor = {}, 6129 location = {Cambridge, MA}, 6130 year = {2001}, 6131 month = jun, 6132 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf}, 6133 petsc_uses = {KSP} 6134} 6135 6136@InProceedings{ gkks00, 6137 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6138 title = {Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} 6139 Code}, 6140 booktitle = {Proceedings of the 7th International Conference on High Performance Computing 6141 (HiPC '2000)}, 6142 editor = {}, 6143 location = {Bangalore, India}, 6144 year = {2000}, 6145 pages = {395--404}, 6146 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf}, 6147 petsc_uses = {KSP} 6148} 6149 6150@InProceedings{ gkks-sc00, 6151 author = {W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6152 title = {Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application}, 6153 booktitle = {Proceedings of SC2000}, 6154 editor = {}, 6155 publisher = {IEEE Computer Society}, 6156 year = {2000}, 6157 url = {http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf}, 6158 petsc_uses = {KSP} 6159} 6160 6161@InProceedings{ knepleysamehsarin99, 6162 author = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin}, 6163 title = {Design of Large Scale Parallel Simulations}, 6164 booktitle = {Proceedings of Parallel CFD'99}, 6165 editors = {A. {Ecer et al.}}, 6166 publisher = {Elsevier}, 6167 year = {1999}, 6168 petsc_uses = {KSP} 6169} 6170 6171@InProceedings{ gkks-pcfd99, 6172 author = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith}, 6173 title = {Towards Realistic Performance Bounds for Implicit {CFD} codes}, 6174 booktitle = {Proceedings of Parallel CFD'99}, 6175 editors = {A. {Ecer et al.}}, 6176 publisher = {Elsevier}, 6177 url = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf}, 6178 year = {1999}, 6179 petsc_uses = {KSP} 6180} 6181 6182@InProceedings{ kks97, 6183 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6184 title = {On the Interaction of Architecture and Algorithm in the Domain-Based 6185 Parallelization of an Unstructured Grid Incompressible Flow Code}, 6186 booktitle = {Proceedings of the 10th International Conference on Domain Decomposition 6187 Methods}, 6188 editor = {J. Mandel et al.}, 6189 pages = {311--319}, 6190 publisher = {Wiley}, 6191 note = {}, 6192 year = {1997}, 6193 petsc_uses = {KSP} 6194} 6195 6196@InProceedings{ kks99, 6197 author = {D. K. Kaushik and D. E. Keyes and B. F. Smith}, 6198 title = {{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and 6199 Incompressible Flows on Unstructured Grids}, 6200 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 6201 Methods}, 6202 editors = {C.-H. {Lai et al.}}, 6203 publisher = {Domain Decomposition Press, Bergen}, 6204 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z}, 6205 year = {1999}, 6206 petsc_uses = {KSP} 6207} 6208 6209@InCollection{ kks97_cfd, 6210 author = {D. E. Keyes and D. K. Kaushik and B. F. Smith}, 6211 title = {Perspectives for {CFD} on Petaflops Systems}, 6212 booktitle = {CFD Review 1998}, 6213 editor = {M. Hafez and K. Oshima}, 6214 publisher = {World Scientific, Singapore}, 6215 pages = {1079--1096}, 6216 note = {}, 6217 year = {1998}, 6218 petsc_uses = {KSP} 6219} 6220 6221@Article{ hm99, 6222 author = {P. D. Hovland and L. C. McInnes}, 6223 title = {Parallel Simulation of Compressible Flow Using Automatic Differentiation and 6224 {PETSc}}, 6225 year = {2000}, 6226 journal = {Parallel Computing}, 6227 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z}, 6228 note = {special issue of Parallel Computing on ``Parallel Computing in Aerospace''}, 6229 petsc_uses = {KSP} 6230} 6231 6232@InProceedings{ cruzbarbaknepley08, 6233 author = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley}, 6234 title = {Fast Multipole Method for particle interactions: an open source parallel library 6235 component}, 6236 booktitle = {Proceedings of ParCFD2008}, 6237 year = {2008}, 6238 editor = {Tromeur-Dervout et. al.}, 6239 publisher = {Elsevier}, 6240 petsc_uses = {KSP} 6241} 6242 6243@Article{ hwangcai05, 6244 author = {F.-N. Hwang and X.-C. Cai}, 6245 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 6246 for incompressible {Navier-Stokes} equations}, 6247 journal = {J. Comput. Phys.}, 6248 volume = {204}, 6249 year = {2005}, 6250 pages = {666--691}, 6251 petsc_uses = {KSP} 6252} 6253 6254@Article{ barbaleonard07, 6255 author = {Lorena A Barba and Anthony Leonard}, 6256 title = {Emergence and evolution of tripole vortices from net-circulation initial 6257 conditions}, 6258 journal = {Phys. Fluids}, 6259 volume = {19}, 6260 pages = {017101}, 6261 year = {2007}, 6262 doi = {10.1063/1.2409734}, 6263 petsc_uses = {KSP} 6264} 6265 6266@Article{ barba07, 6267 author = {Lorena A Barba}, 6268 title = {Non-shielded multipolar vortices at high Reynolds number}, 6269 journal = {Phys. Rev. E}, 6270 volume = {73}, 6271 pages = {065303}, 6272 year = {2006}, 6273 doi = {10.1103/PhysRevE.73.065303}, 6274 petsc_uses = {KSP} 6275} 6276 6277@Article{ schofield2010multi, 6278 title = {Multi-material incompressible flow simulation using the moment-of-fluid method}, 6279 author = {Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and 6280 Lowrie, R.B. and Swartz, B.K.}, 6281 journal = {International Journal for Numerical Methods in Fluids}, 6282 volume = {63}, 6283 number = {8}, 6284 pages = {931--952}, 6285 year = {2010}, 6286 publisher = {Wiley Online Library}, 6287 petsc_uses = {KSP} 6288} 6289 6290% LiteralHTML: 6291% LiteralHTML: <a name="wave"><H3><center>Wave propagation and the Helmholtz equation</center></H3> 6292% LiteralHTML: 6293% LiteralHTML: article{DeGersem99, 6294% LiteralHTML: author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du}, 6295% LiteralHTML: title = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids}, 6296% LiteralHTML: } 6297@Article{ nagler2014, 6298 title = {Sound transmission through a poroelastic layered panel}, 6299 author = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff}, 6300 journal = {Computational Mechanics}, 6301 volume = {53}, 6302 number = {4}, 6303 pages = {549--560}, 6304 issn = {1432-0924}, 6305 doi = {10.1007/s00466-013-0916-x}, 6306 year = {2014}, 6307 petsc_uses = {KSP} 6308} 6309 6310@Article{ sheikh2013, 6311 author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.}, 6312 title = {On the convergence of shifted {L}aplace preconditioner combined with multilevel 6313 deflation}, 6314 journal = {Numerical Linear Algebra with Applications}, 6315 volume = {20}, 6316 number = {4}, 6317 issn = {1099-1506}, 6318 doi = {10.1002/nla.1882}, 6319 pages = {645--662}, 6320 keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier 6321 analysis}, 6322 year = {2013}, 6323 petsc_uses = {KSP} 6324} 6325 6326@InProceedings{ silence, 6327 author = {J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. 6328 Fuenmayor}, 6329 title = {A parallel computing approach for solving the Helmholtz equation in 3D domains: 6330 Application to the study of acoustic behaviour of silencers}, 6331 year = {2004}, 6332 booktitle = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering 6333 (ECCOMAS)}, 6334 petsc_uses = {KSP} 6335} 6336 6337@Article{ degersem99, 6338 author = {H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer}, 6339 title = {Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods 6340 to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations}, 6341 journal = {COMPEL}, 6342 year = {1999}, 6343 volume = {18}, 6344 number = {3}, 6345 pages = {298--310}, 6346 bibdate = {}, 6347 petsc_uses = {KSP} 6348} 6349 6350@InProceedings{ widlund-wave-98, 6351 author = {Olof B. Widlund}, 6352 title = {Schwarz Methods for {H}elmholtz's Equation}, 6353 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6354 editor = {John A. DeSanto}, 6355 year = {1998}, 6356 publisher = {SIAM}, 6357 pages = {620--622}, 6358 address = {Philadelphia}, 6359 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6360 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6361 petsc_uses = {KSP} 6362} 6363 6364@InProceedings{ toselli-wave-98, 6365 author = {Andrea Toselli}, 6366 title = {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media}, 6367 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6368 editor = {John A. DeSanto}, 6369 year = {1998}, 6370 publisher = {SIAM}, 6371 address = {Philadelphia}, 6372 pages = {540--542}, 6373 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6374 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6375 petsc_uses = {KSP} 6376} 6377 6378@InProceedings{ mcinnes-wave-98, 6379 author = {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes}, 6380 title = {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods}, 6381 booktitle = {Mathematical and Numerical Aspects of Wave Propagation}, 6382 editor = {John A. DeSanto}, 6383 year = {1998}, 6384 publisher = {SIAM}, 6385 address = {Philadelphia}, 6386 pages = {623--625}, 6387 note = {Proceedings of the Fourth International Conference on Mathematical and Numerical 6388 Aspects of Wave Propagation, Golden, Colorado, June 1--5}, 6389 petsc_uses = {KSP} 6390} 6391 6392@InProceedings{ mska98, 6393 author = {L. C. McInnes and R. Susan-Resiga and D. E. Keyes and H. M. Atassi}, 6394 title = {Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the 6395 Parallel Computation of {H}elmholtz Problems}, 6396 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6397 editor = {J. Mandel et al.}, 6398 publisher = {AMS}, 6399 pages = {349--357}, 6400 year = {1998}, 6401 petsc_uses = {KSP} 6402} 6403 6404@InProceedings{ ccew98, 6405 author = {X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund}, 6406 title = {Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation}, 6407 booktitle = {Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods}, 6408 editor = {J. Mandel et al.}, 6409 publisher = {AMS}, 6410 pages = {437-445}, 6411 year = {1998}, 6412 petsc_uses = {KSP} 6413} 6414 6415@InProceedings{ ra98a, 6416 author = {R. Susan-Resiga and H. M. Atassi}, 6417 title = {Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic 6418 Problems}, 6419 booktitle = {Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference}, 6420 publisher = {AIAA}, 6421 pages = {86-96}, 6422 note = {AIAA paper 98-2218}, 6423 year = {1998}, 6424 petsc_uses = {KSP} 6425} 6426 6427@InProceedings{ ar98c, 6428 author = {H. M. Atassi and R. Susan-Resiga}, 6429 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: 6430 General Formulation}, 6431 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6432 publisher = {ASME}, 6433 note = {NCA-25}, 6434 pages = {375-379}, 6435 year = {1998}, 6436 petsc_uses = {KSP} 6437} 6438 6439@InProceedings{ ra98b, 6440 author = {R. Susan-Resiga and H. M. Atassi}, 6441 title = {Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: 6442 Numerical Implementation and Applications}, 6443 booktitle = {Proceedings of the ASME Noise Control and Acoustics Division}, 6444 publisher = {ASME}, 6445 note = {NCA-25}, 6446 pages = {381 -388}, 6447 year = {1998}, 6448 petsc_uses = {KSP} 6449} 6450 6451@InProceedings{ cai-dd10-98, 6452 author = {Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. 6453 Widlund}, 6454 title = {Overlapping {S}chwarz methods for solving {H}elmholtz's Equation}, 6455 booktitle = {Domain Decomposition Methods 10}, 6456 editors = {Jan Mandel and Charbel Farhat and Xiao-Chuan Cai}, 6457 series = {Contemporary Mathematics}, 6458 volume = {218}, 6459 publisher = {American Mathematical Society}, 6460 address = {Providence, Rhode Island}, 6461 year = {1998}, 6462 pages = {437--445}, 6463 petsc_uses = {KSP} 6464} 6465 6466@InProceedings{ alghamdi2011petclaw, 6467 title = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython}, 6468 booktitle = {Proceedings of SpringSim 2011}, 6469 publisher = {ACM}, 6470 author = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and 6471 Kyle T. Mandli and Lisandro Dalcin}, 6472 year = {2011}, 6473 petsc_uses = {KSP} 6474} 6475 6476@Article{ pyclaw2012, 6477 author = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and 6478 Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew 6479 Emmett}, 6480 title = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems}, 6481 journal = {SIAM Journal on Scientific Computing}, 6482 volume = {34}, 6483 number = {4}, 6484 pages = {C210--C231}, 6485 note = {\url{http://arxiv.org/abs/1111.6583}}, 6486 year = {2012}, 6487 petsc_uses = {KSP} 6488} 6489 6490% LiteralHTML: 6491% LiteralHTML: <a name="optimization"><H3><center>Optimization</center></H3> 6492% LiteralHTML: 6493@Article{ sojkahorakhaplacermak2018, 6494 title = {The impact of enabling multiple subdomains per MPI process in the TFETI domain 6495 decomposition method}, 6496 author = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k}, 6497 journal = {Applied Mathematics and Computation}, 6498 volume = {319}, 6499 pages = {586--597}, 6500 year = {2018}, 6501 petsc_uses = {KSP} 6502} 6503 6504@Article{ chencai2014, 6505 title = {A parallel two-level domain decomposition based one-shot method for shape 6506 optimization problems}, 6507 author = {Rongliang Chen and Xiao‐Chuan Cai}, 6508 journal = {International Journal for Numerical Methods in Engineering}, 6509 volume = {99}, 6510 number = {13}, 6511 year = {2014}, 6512 doi = {10.1002/nme.4711}, 6513 petsc_uses = {KSP} 6514} 6515 6516@PhDThesis{ prudencio2005, 6517 author = {Ernesto Prudencio}, 6518 title = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software 6519 for Optimization Problems Constrained by Partial Differential Equations}, 6520 school = {University of Colorado, Boulder}, 6521 year = {2005}, 6522 petsc_uses = {KSP} 6523} 6524 6525@Article{ prudenciocai2007, 6526 title = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing 6527 for {PDE}-constrained optimization}, 6528 author = {Ernesto Prudencio and X. C. Cai}, 6529 journal = {SIAM J. Sci. Comp.}, 6530 volume = {29}, 6531 number = {3}, 6532 pages = {964--985}, 6533 year = {2007}, 6534 petsc_uses = {KSP} 6535} 6536 6537@Article{ prudenciobyrdcai2006, 6538 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6539 title = {Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for 6540 {PDE}-constrained Optimization Problems}, 6541 journal = {SIAM J. Sci. Comp.}, 6542 volume = {27}, 6543 pages = {1305--1328}, 6544 year = {2006}, 6545 petsc_uses = {KSP} 6546} 6547 6548@InProceedings{ prudenciobyrdcai2004, 6549 title = {Domain decomposition methods for {PDE}-constrained optimization problems}, 6550 author = {Ernesto Prudencio and R. Byrd and X. C. Cai}, 6551 booktitle = {VECPAR 2004}, 6552 editor = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma}, 6553 publisher = {Springer}, 6554 pages = {569--582}, 6555 year = {2004}, 6556 petsc_uses = {KSP} 6557} 6558 6559@Article{ belhamadia-fortin-pcp, 6560 author = {Youssef Belhamadia and Andre Fortin and Eric Chamberland}, 6561 title = {Three-dimensional anisotropic mesh adaptation for phase change problems}, 6562 journal = {Journal of Computational Physics}, 6563 volume = {201}, 6564 pages = {753-770}, 6565 year = {2004}, 6566 url = {http://portal.acm.org/citation.cfm?id=1055817.1055834#references}, 6567 petsc_uses = {KSP} 6568} 6569 6570@Article{ biros00, 6571 author = {George Biros and Omar Ghattas}, 6572 title = {A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization}, 6573 journal = {SIAG-Opt Views and News}, 6574 volume = {11}, 6575 number = {2}, 6576 year = {2000}, 6577 month = aug, 6578 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf}, 6579 petsc_uses = {KSP} 6580} 6581 6582@Article{ bmm01, 6583 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 6584 journal = {ACM Transactions on Mathematical Software}, 6585 title = {A case study in the performance and scalability of optimization algorithms}, 6586 year = {2001}, 6587 volume = {27}, 6588 number = {3}, 6589 pages = {361--376}, 6590 petsc_uses = {KSP} 6591} 6592 6593@InProceedings{ oghattas1999, 6594 author = {George Biros and Omar Ghattas}, 6595 title = {Parallel preconditioners for {KKT} systems arising in optimal control of viscous 6596 incompressible flows}, 6597 booktitle = {Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999}, 6598 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf}, 6599 year = {1999}, 6600 petsc_uses = {KSP} 6601} 6602 6603@InProceedings{ hkms00, 6604 title = {Using Automatic Differentiation for Second-order Matrix-free Methods in 6605 PDE-constrained Optimization}, 6606 author = {P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono}, 6607 url = {http://www.icase.edu/\~{ }keyes/papers/ad2000.ps}, 6608 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 6609 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 6610 Hasco\"{e}t and Uwe Naumann}, 6611 publisher = {Springer}, 6612 year = {2002}, 6613 petsc_uses = {KSP} 6614} 6615 6616% old version: replace with biros2005pln1 6617@TechReport{ bg011, 6618 author = {George Biros and Omar Ghattas}, 6619 title = {Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. 6620 Part I: The Krylov-Schur Solver}, 6621 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6622 year = {2001}, 6623 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf}, 6624 petsc_uses = {KSP} 6625} 6626 6627% old version: replace with biros2005pln2 6628@TechReport{ bg012, 6629 author = {George Biros and Omar Ghattas}, 6630 title = {Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained 6631 Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to 6632 Optimal Control of Steady Viscous Flows}, 6633 institution = {Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University}, 6634 year = {2001}, 6635 url = {http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf}, 6636 petsc_uses = {KSP} 6637} 6638 6639% LiteralHTML: 6640% LiteralHTML: <a name="fastmethods"><H3><center>Fast Algorithms</center></H3> 6641% LiteralHTML: 6642@InProceedings{ ly2003, 6643 author = {Lexing Ying and G. Biros and D. Zorin and H. Langston}, 6644 title = {A New Parallel Kernel-independent Fast Multipole Method}, 6645 booktitle = {Proceedings of the ACM/IEEE conference on Supercomputing 2003}, 6646 year = {2003}, 6647 note = {Winner of the Best Student Paper at SC2003}, 6648 petsc_uses = {KSP} 6649} 6650 6651@Article{ yokotabarbaknepley10, 6652 author = {Rio Yokota and L A Barba and Matthew G Knepley}, 6653 title = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation}, 6654 journal = {Computer Methods in Applied Mechanics and Engineering}, 6655 volume = {199}, 6656 number = {25-28}, 6657 pages = {1793--1804}, 6658 url = {http://arxiv.org/abs/0909.5413v1}, 6659 note = {\url{http://arxiv.org/abs/0909.5413v1}}, 6660 year = {2010}, 6661 petsc_uses = {KSP} 6662} 6663 6664@Article{ cruzknepleybarba10, 6665 author = {Felipe A. Cruz and Matthew G Knepley and L A Barba}, 6666 title = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library}, 6667 journal = {International Journal of Numerical Methods in Engineering}, 6668 volume = {85}, 6669 number = {4}, 6670 pages = {403--428}, 6671 url = {http://arxiv.org/abs/0905.2637}, 6672 note = {\url{http://arxiv.org/abs/0905.2637}}, 6673 year = {2010}, 6674 petsc_uses = {KSP} 6675} 6676 6677% LiteralHTML: 6678% LiteralHTML: <a name="otherapps"><H3><center>Other Application Areas</center></H3> 6679% LiteralHTML: 6680@Article{ buchanpainumplebysmedleystevenson2012, 6681 title = {A sub-grid scale finite element agglomeration multigrid method with application 6682 to the Boltzmann transport equation}, 6683 author = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson}, 6684 journal = {International Journal for Numerical Methods in Engineering}, 6685 volume = {92}, 6686 number = {3}, 6687 pages = {318--342}, 6688 year = {2012}, 6689 publisher = {Wiley Online Library}, 6690 petsc_uses = {KSP} 6691} 6692 6693@Article{ magoulesahamedsuzuki2015, 6694 title = {Green computing on graphics processing units}, 6695 author = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki}, 6696 journal = {Concurrency and Computation: Practice and Experience}, 6697 year = {2015}, 6698 publisher = {Wiley Online Library}, 6699 petsc_uses = {KSP} 6700} 6701 6702@InProceedings{ yanrhodes11, 6703 author = {Yan, Baoqiang and Rhodes, Philip J.}, 6704 title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets}, 6705 booktitle = {Proceedings of the 2011 International Conference on Parallel Processing}, 6706 series = {ICPP '11}, 6707 pages = {355--364}, 6708 year = {2011}, 6709 isbn = {978-0-7695-4510-3}, 6710 numpages = {10}, 6711 doi = {10.1109/ICPP.2011.70}, 6712 acmid = {2066965}, 6713 publisher = {IEEE Computer Society}, 6714 address = {Washington, DC, USA}, 6715 keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning}, 6716 petsc_uses = {KSP} 6717} 6718 6719@Article{ hakansson2013mdstochasticliouville, 6720 author = {Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and 6721 Stulz, Eugen}, 6722 title = {Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville 6723 equation study}, 6724 journal = {Phys. Chem. Chem. Phys.}, 6725 year = {2013}, 6726 volume = {15}, 6727 issue = {26}, 6728 pages = {10930-10941}, 6729 publisher = {The Royal Society of Chemistry}, 6730 doi = {10.1039/C3CP50788B}, 6731 petsc_uses = {KSP} 6732} 6733 6734@Article{ hakansson2011stochasticliouville, 6735 author = {Hakansson, Par and Nair, Prasanth B.}, 6736 title = {Implicit numerical schemes for the stochastic Liouville equation in Langevin 6737 form}, 6738 journal = {Phys. Chem. Chem. Phys.}, 6739 year = {2011}, 6740 volume = {13}, 6741 issue = {20}, 6742 pages = {9578-9589}, 6743 publisher = {The Royal Society of Chemistry}, 6744 doi = {10.1039/C1CP20400A}, 6745 petsc_uses = {KSP} 6746} 6747 6748@InProceedings{ wang:lee:scidac2011, 6749 author = {Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman 6750 McInnes and Todd Munson and Barry Smith}, 6751 title = {A Differential Variational Inequality Approach for the Simulation of 6752 Heterogeneous Materials}, 6753 booktitle = {Proceedings of SciDAC 2011 Conference}, 6754 year = {2011}, 6755 petsc_uses = {KSP} 6756} 6757 6758@Article{ bourdinlarsenrichardson2011, 6759 author = {Blaise Bourdin and Christopher Larsen and Casey Richardson}, 6760 title = {A time-discrete model for dynamic fracture based on crack regularization}, 6761 journal = {International Journal of Fracture}, 6762 volume = {168}, 6763 issue = {2}, 6764 pages = {133--143}, 6765 doi = {10.1007/s10704-010-9562-x}, 6766 year = {2011}, 6767 petsc_uses = {KSP} 6768} 6769 6770@Article{ bourdinfrancfortmarigo2008, 6771 author = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo}, 6772 title = {The Variational Approach to Fracture}, 6773 journal = {J. Elasticity}, 6774 volume = {91}, 6775 issue = {1}, 6776 pages = {1--148}, 6777 doi = {10.1007/s10659-007-9107-3}, 6778 year = {2008}, 6779 petsc_uses = {KSP} 6780} 6781 6782@Article{ lahtinen2008spectrum, 6783 title = {Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model}, 6784 author = {Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, 6785 J.K.}, 6786 journal = {Annals of Physics}, 6787 volume = {323}, 6788 number = {9}, 6789 pages = {2286--2310}, 6790 year = {2008}, 6791 publisher = {Elsevier}, 6792 petsc_uses = {KSP} 6793} 6794 6795@InProceedings{ roark2004discriminative, 6796 title = {Discriminative language modeling with conditional random fields and the 6797 perceptron algorithm}, 6798 author = {Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.}, 6799 booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational 6800 Linguistics}, 6801 pages = {47}, 6802 year = {2004}, 6803 organization = {Association for Computational Linguistics}, 6804 petsc_uses = {KSP} 6805} 6806 6807@Article{ roark2007discriminative, 6808 title = {Discriminative n-gram language modeling}, 6809 author = {Roark, B. and Saraclar, M. and Collins, M.}, 6810 journal = {Computer Speech \& Language}, 6811 volume = {21}, 6812 number = {2}, 6813 pages = {373--392}, 6814 year = {2007}, 6815 publisher = {Elsevier}, 6816 petsc_uses = {KSP} 6817} 6818 6819@Conference{ garcia2011parallel, 6820 title = {{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D 6821 nanodevice simulators}}, 6822 author = {Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and 6823 Aldegunde, M.}, 6824 booktitle = {Electron Devices (CDE), 2011 Spanish Conference on}, 6825 pages = {1--4}, 6826 organization = {IEEE}, 6827 petsc_uses = {KSP} 6828} 6829 6830@Conference{ wesley2006parallel, 6831 title = {{A parallel artificial neural network implementation}}, 6832 author = {Wesley-Smith, I.}, 6833 booktitle = {Proceedings of The National Conference On Undergraduate Research (NCUR)}, 6834 year = {2006}, 6835 petsc_uses = {KSP} 6836} 6837 6838@Article{ hcsw1, 6839 author = {F.-N. Hwang and S.-R. Cai and Y.-L. Shao and J.-S. Wu}, 6840 title = {Parallel {N}ewton--{K}rylov--{S}chwarz algorithms for the three-dimensional 6841 {P}oisson--{B}oltzmann equation in numerical simulation of colloidal particle 6842 interactions}, 6843 journal = {Computer Physics Communications}, 6844 volumne = {181}, 6845 year = {2010}, 6846 pages = {1529--1537}, 6847 petsc_uses = {KSP} 6848} 6849 6850@Article{ hh1, 6851 author = {C.-Y. Huang and F.-N. Hwang}, 6852 title = {Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for 6853 bifurcation analysis of incompressible sudden expansion flows}, 6854 journal = {Applied Numerical Mathematics}, 6855 volume = {60}, 6856 year = {2010}, 6857 pages = {738--751}, 6858 petsc_uses = {KSP} 6859} 6860 6861@Article{ hwhw1, 6862 author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. 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Cooke}, 7348 title = {Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three 7349 Dimensions}, 7350 year = {2004}, 7351 booktitle = {40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit}, 7352 url = {http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282}, 7353 petsc_uses = {KSP} 7354} 7355 7356@InProceedings{ allard-gouranton-ipts2002, 7357 author = {Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin}, 7358 title = {Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster}, 7359 year = {2002}, 7360 booktitle = {Immersive Projection Technology Symposium}, 7361 url = {http://www-id.imag.fr/\~{ }allardj/files/ipts2002.pdf}, 7362 petsc_uses = {KSP} 7363} 7364 7365@Article{ icc, 7366 author = {D Ioan and G Ciuprina and C Ciobotaru}, 7367 title = {Hybrid and concurrent algorithms for nonlinear magnetic field problems}, 7368 journal = {IEEE Transactions on Magnetics}, 7369 year = {2000}, 7370 url = {http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/20/19005/00877735.pdf}, 7371 petsc_uses = {KSP} 7372} 7373 7374@InProceedings{ hs1, 7375 author = {Brian J. Henz and Dale R. Shires}, 7376 title = {Development and Performance Analysis of a Parallel Finite Element Application 7377 Implemented in an Object-Oriented Programming Framework}, 7378 year = {2003}, 7379 booktitle = {PDPTA 2003}, 7380 pages = {1286-1292}, 7381 note = {Resin Transfer Modeling}, 7382 petsc_uses = {KSP} 7383} 7384 7385@TechReport{ b2000, 7386 author = {Rickard Bergstrom}, 7387 title = {Least-Squares Finite Element Methods for Electromagnetic Applications}, 7388 year = {2000}, 7389 institution = {Chalmers}, 7390 number = {2000-05}, 7391 url = {http://www.phi.chalmers.se/pub/preprints/ps/phiprint-2000-05.ps}, 7392 petsc_uses = {KSP} 7393} 7394 7395@Article{ fs2004, 7396 author = {Petri Fast and Michael J. Shelley}, 7397 title = {A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele 7398 Shaw Flow}, 7399 journal = {Journal of Computational Physics}, 7400 year = {2004}, 7401 volume = {195}, 7402 url = {http://www.math.nyu.edu/faculty/shelley/papers/FS2004.pdf}, 7403 pages = {117-142}, 7404 petsc_uses = {KSP} 7405} 7406 7407@MastersThesis{ wallach, 7408 author = {Hanna Wallach}, 7409 title = {Efficient Training of Conditional Random Fields}, 7410 school = {University of Edinburgh}, 7411 year = {2002}, 7412 url = {http://scholar.google.com/url?sa=U&q=http://www.hcrc.ed.ac.uk/\~{ 7413 }osborne/msc-projects/wallach.ps.gz}, 7414 petsc_uses = {KSP} 7415} 7416 7417@Article{ something, 7418 author = {T Rylander and A Bondeson}, 7419 title = {Stability of explicit-implicit hybrid time-stepping schemes for Maxwells 7420 equations}, 7421 journal = {Journal of Computational Physics}, 7422 year = {2002}, 7423 volume = {179}, 7424 pages = {426-438}, 7425 petsc_uses = {KSP} 7426} 7427 7428@TechReport{ uf1, 7429 author = {Uwe Fabricius}, 7430 title = {Comparison of two implementations of {AMG}-preconditioned {CG} considering an 7431 electrostatic problem}, 7432 year = {2004}, 7433 institution = {Friedrich Alexander Universitat Erlangen Nurnberg Germany}, 7434 url = {http://www10.informatik.uni-erlangen.de/de/Publications/TechnicalReports/TechRep04-1.pdf}, 7435 number = {04-1}, 7436 petsc_uses = {KSP} 7437} 7438 7439@InBook{ sg1, 7440 author = {Natalia Seoane and A.J.Garca-Loureiro}, 7441 chapter = {Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity 7442 Equation}, 7443 url = {http://www.springerlink.com/app/home/contribution.asp?wasp=h0xlulyhugck3y2gnt2l&referrer=parent&backto=issue,79,112;journal,212,1787;linkingpublicationresults,1:105633,1}, 7444 title = {Lecture Notes in Computer Science}, 7445 publisher = {Springer-Verlag}, 7446 volume = {3037}, 7447 year = {2004}, 7448 petsc_uses = {KSP} 7449} 7450 7451@Article{ nikyilmazgivisheikhipope10, 7452 author = {M. B. Nik and S. L. Yilmaz and P. Givi and M. R. H. Sheikhi and S. B. Pope}, 7453 title = {Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function}, 7454 journal = {AIAA Journal}, 7455 volume = {48}, 7456 number = {7}, 7457 pages = {1513--1522}, 7458 year = {2010}, 7459 petsc_uses = {KSP} 7460} 7461 7462@Article{ nikyilmazsheikhigivi10, 7463 author = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi}, 7464 title = {Grid Resolution Effects on VSFMDF/LES}, 7465 journal = {Flow, Turbulence and Combustion}, 7466 doi = {10.1007/s10494-010-9272-5}, 7467 year = {2010}, 7468 petsc_uses = {KSP} 7469} 7470 7471@Article{ idema2013towards, 7472 title = {Towards faster solution of large power flow problems}, 7473 author = {Idema, Reijer and Papaefthymiou, Georgios and Lahaye, Domenico and Vuik, Cornelis 7474 and van der Sluis, Lou}, 7475 journal = {Power Systems, IEEE Transactions on}, 7476 volume = {28}, 7477 number = {4}, 7478 pages = {4918--4925}, 7479 year = {2013}, 7480 publisher = {IEEE}, 7481 petsc_uses = {KSP} 7482} 7483 7484@Article{ 6026245, 7485 author = {Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.}, 7486 journal = {Power Systems, IEEE Transactions on}, 7487 title = {Scalable Newton-Krylov Solver for Very Large Power Flow Problems}, 7488 year = {2012}, 7489 month = feb, 7490 volume = {27}, 7491 number = {1}, 7492 pages = {390-396}, 7493 doi = {10.1109/TPWRS.2011.2165860}, 7494 issn = {0885-8950}, 7495 petsc_uses = {KSP} 7496} 7497 7498@Book{ idema2014computational, 7499 title = {Computational Methods in Power System Analysis}, 7500 author = {Idema, Reijer and Lahaye, Domenico JP}, 7501 year = {2014}, 7502 publisher = {Springer}, 7503 petsc_uses = {KSP} 7504} 7505 7506@PhDThesis{ abhyankar2011thesis, 7507 author = {Shrirang Abhyankar}, 7508 title = {Development of an implicitly coupled electromechanical and electromagnetic 7509 transients simulator for power systems}, 7510 school = {Illinois Institute of Technology}, 7511 year = {2011}, 7512 petsc_uses = {KSP} 7513} 7514 7515@InProceedings{ abhyankarhipcna11-1, 7516 author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck}, 7517 title = {Using {PETSc} to develop scalable applications for next-generation power grid}, 7518 year = {2011}, 7519 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 7520 Networking and Analytics for the Power Grid}, 7521 url = {http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf}, 7522 publisher = {ACM}, 7523 petsc_uses = {KSP} 7524} 7525 7526@InProceedings{ abhyankarhipcna11-2, 7527 author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang}, 7528 title = {Development of a parallel three-phase transient stability simulator for power 7529 systems}, 7530 year = {2011}, 7531 booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, 7532 Networking and Analytics for the Power Grid}, 7533 publisher = {ACM}, 7534 petsc_uses = {KSP} 7535} 7536 7537@InProceedings{ abhyankarpesgeneral2012, 7538 author = {Shrirang Abhyankar and A. Flueck}, 7539 title = {An implicitly-coupled solution approach for combined electromechanical and 7540 electromagnetic transients simulation}, 7541 year = {2012}, 7542 booktitle = {Proceedings of the IEEE PES General Meeting}, 7543 publisher = {IEEE}, 7544 petsc_uses = {KSP} 7545} 7546 7547@Article{ idemalahayevuiksluis2012, 7548 author = {Reijer Idema and Domenico Lahaye and Cornelis Vuik and Lou van der Sluis}, 7549 title = {Scalable Newton-Krylov solver for very large Power Flow problems}, 7550 journal = {IEEE Transactions on Power Systems}, 7551 year = {2012}, 7552 volume = {27}, 7553 pages = {390-396}, 7554 petsc_uses = {KSP} 7555} 7556 7557@Article{ korrestzavellasgalinas2013, 7558 author = {George N. Korres and Anastasios Tzavellas and Evangelos Galinas}, 7559 title = {A distributed implementation of multi-area power system state estimation on a 7560 cluster of computers }, 7561 journal = {Electric Power Systems Research }, 7562 volume = {102}, 7563 number = {0}, 7564 pages = {20 - 32}, 7565 year = {2013}, 7566 issn = {0378-7796}, 7567 doi = {10.1016/j.epsr.2013.04.002}, 7568 petsc_uses = {KSP} 7569} 7570 7571% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7572% LiteralHTML:<font color="#FF0000"> 7573% LiteralHTML: Material failure, for example, cracking of steel beams resulting 7574% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations 7575% LiteralHTML: are important for prediction and prevention. PETSc has been used 7576% LiteralHTML: in a variety of studies of material failure.</p> 7577% LiteralHTML:</font> 7578% LiteralHTML: 7579@InProceedings{ gray2, 7580 author = {Yuan He and Joshua Gray and Richard Braatz and Richard Alkire}, 7581 title = {Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel}, 7582 year = {2004}, 7583 booktitle = {American Institute of Chemical Engineers 2004 Annual Meeting}, 7584 petsc_uses = {KSP} 7585} 7586 7587@InProceedings{ gray1, 7588 author = {J. Gray and C. Homescu and L. Petzold and Richard Alkire}, 7589 title = {Algorithms and Computing Architectures for Solving Differential-Algebraic 7590 Equation Systems Typically Encountered in Models of Corrosion Pit Initiation}, 7591 year = {2003}, 7592 booktitle = {Abstracts of the Electrochemical Society 204th meeting}, 7593 petsc_uses = {KSP} 7594} 7595 7596@InProceedings{ crack2, 7597 author = {Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. Wawrzynek}, 7598 title = {A multiscale modeling approach to crack initiation in metallic polycrystals}, 7599 booktitle = {44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials 7600 Conference}, 7601 url = {http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=TRD&recid=A0325099AH}, 7602 year = {2003}, 7603 petsc_uses = {KSP} 7604} 7605 7606@TechReport{ hdams1, 7607 author = {Gerd Heber and Andrew J. Dolgert and Maxirn Alt and Karen A. Mazurkiewicz and 7608 Lynd Stringer}, 7609 title = {Fracture Mechanics on the Intel Itanium Architecture}, 7610 year = {2001}, 7611 institution = {Intel Corporation}, 7612 url = {http://cedar.intel.com/media/pdf/scs/cptconitanium.pdf}, 7613 petsc_uses = {KSP} 7614} 7615 7616@InProceedings{ ihwi, 7617 author = {E. Iesulauro and G. Heber and P. A. Wawrzynek and A. R. Ingraffea}, 7618 title = {Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation}, 7619 booktitle = {International Conference ON Computational Engineering and Sciences}, 7620 year = {2002}, 7621 url = {http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf}, 7622 petsc_uses = {KSP} 7623} 7624 7625@InProceedings{ crack, 7626 author = {Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and 7627 Guang R. Gao and Gerd Heber and Antony R. Ingraffea and Roland Krause and Chris 7628 Myers and Demian Nave and Keshav Pingali and Paul Stodghill and Stephen Vavasis 7629 and Paul A. Wawrzynek}, 7630 title = {Parallel FEM Simulation of Crack Propagation}, 7631 booktitle = {Proceedings of Irregular 2000}, 7632 url = {http://www.cs.cornell.edu/stodghil/papers/irregular00.ps}, 7633 year = {2000}, 7634 petsc_uses = {KSP} 7635} 7636 7637@InProceedings{ beaudoin98, 7638 author = {A. J. Beaudoin}, 7639 title = {Use of Polycrystal Plasticity Theory in Assessing Material Performance}, 7640 booktitle = {Simulation of materials processing: Theory, methods, and applications - 7641 Proceedings of the Sixth International Conference, NUMIFORM'98}, 7642 editor = {J. Hu\'etink and F. P. T. Baaijens}, 7643 optvolume = {}, 7644 optnumber = {}, 7645 optseries = {}, 7646 year = {1998}, 7647 optorganization={}, 7648 publisher = {A. A. Balkema Publishers}, 7649 address = {Rotterdam, Netherlands}, 7650 month = jun, 7651 optpages = {}, 7652 petsc_uses = {KSP} 7653} 7654 7655% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td> 7656@TechReport{ defordheld1, 7657 author = {JF DeFord and BL Held}, 7658 title = {RF3P-A New Parallel Driven Frequency Electromagnetic Solver}, 7659 year = {2002}, 7660 institution = {Simulation Technology and Applied Research}, 7661 url = {http://www.staarinc.com/support/papers/aces2002.pdf}, 7662 note = {Discusses their parallel commercial solver that uses PETSc}, 7663 petsc_uses = {KSP} 7664} 7665 7666@PhDThesis{ sande2003, 7667 author = {Hans Vande Sande}, 7668 title = {Modelling and Finite Element Simulation of Non-Linear and Anisotropic 7669 Quasi-Static Electromagnetic Systems}, 7670 school = {Katholieke Universiteit Leuven, Belgium}, 7671 year = {2003}, 7672 petsc_uses = {KSP} 7673} 7674 7675@Article{ sdchh2004, 7676 author = {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer}, 7677 title = {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System 7678 Tolerance}, 7679 journal = {IEEE Transactions on Magnetics}, 7680 year = {2004}, 7681 volume = {40}, 7682 pages = {1306--1309}, 7683 petsc_uses = {KSP} 7684} 7685 7686@Article{ holst-lindblom-etal:2004, 7687 author = {Michael Holst and Lee Lindblom and Robert Owen and Harald P. Pfeiffer and Mark A. 7688 Scheel and Lawrence E. Kidder}, 7689 title = {Optimal constraint projection for hyperbolic evolution systems, }, 7690 journal = {Phys. Rev. D}, 7691 year = {2004}, 7692 volume = {70}, 7693 pages = {084017}, 7694 petsc_uses = {KSP} 7695} 7696 7697@Article{ marm2005, 7698 author = {Matthew Anderson and Richard A. Matzner}, 7699 title = {Extended Lifetime in Computational Evolution of Isolated Black Holes}, 7700 journal = {Foundations of Physics}, 7701 volume = {35}, 7702 pages = {1572--9516}, 7703 year = {2005}, 7704 petsc_uses = {KSP} 7705} 7706 7707@Article{ cook-pfeiffer:2004, 7708 author = {Cook, Gregory B. and Pfeiffer, Harald P.}, 7709 title = {Excision boundary conditions for black hole initial data}, 7710 journal = {Phys. Rev. D}, 7711 volume = {70}, 7712 pages = {104016--24}, 7713 year = {2004}, 7714 petsc_uses = {KSP} 7715} 7716 7717@Article{ pfeiffer-kidder-etal:2005, 7718 author = {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre 7719 Shoemaker}, 7720 title = {Initial data for {E}instein's equations with superposed gravitational waves}, 7721 journal = {Phys. Rev. D}, 7722 year = {2005}, 7723 volume = {71}, 7724 pages = {024020}, 7725 petsc_uses = {KSP} 7726} 7727 7728@Article{ pfeiffer-kidder-etal:2003, 7729 author = {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, 7730 Saul A.}, 7731 title = {A multidomain spectral method for solving elliptic equations}, 7732 journal = {CPC}, 7733 year = {2003}, 7734 volume = {152}, 7735 pages = {253--273}, 7736 note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. 7737 For a related online version, see arXiv:gr-qc/0202096}, 7738 petsc_uses = {KSP} 7739} 7740 7741@Article{ pfeiffer-cook-teukolsky:2002, 7742 author = {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.}, 7743 title = {Comparing initial-data sets for binary black hole}, 7744 journal = {PRD}, 7745 year = {2002}, 7746 volume = {66}, 7747 pages = {024047}, 7748 note = {for a related online version, seearXiv:gr-qc/0203085}, 7749 petsc_uses = {KSP} 7750} 7751 7752@PhDThesis{ pfeiffer:2003, 7753 author = {Pfeiffer, Harald P.}, 7754 title = {Initial Data for Black Hole Evolutions}, 7755 school = {Cornell University}, 7756 year = {2003}, 7757 petsc_uses = {KSP} 7758} 7759 7760@TechReport{ h1, 7761 author = {Erik Schnetter}, 7762 title = {A fast apparent horizon algorithm}, 7763 year = {2002}, 7764 number = {Arxiv preprint gr-qc/0206003}, 7765 url = {http://arxiv.org/pdf/gr-qc/0206003}, 7766 petsc_uses = {KSP} 7767} 7768 7769@Article{ h2, 7770 author = {Erik Schnetter}, 7771 title = {Finding apparent horizons and other 2-surfaces of constant expansion}, 7772 year = {2003}, 7773 journal = {Class. Quantum Grav.}, 7774 pages = {4719-4737}, 7775 volume = {20}, 7776 url = {http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf}, 7777 petsc_uses = {KSP} 7778} 7779 7780@Article{ adams-03a, 7781 author = {Adams, M.~F.}, 7782 journal = {Numerical Linear Algebra with Applications}, 7783 number = {2-3}, 7784 pages = {141-153}, 7785 title = {Algebraic multigrid methods for constrained linear systems with applications to 7786 contact problems in solid mechanics}, 7787 volume = {11}, 7788 year = {2004}, 7789 petsc_uses = {KSP} 7790} 7791 7792@Article{ vandesande1, 7793 author = {H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer}, 7794 journal = {IEEE TRANSACTIONS ON MAGNETICS}, 7795 year = {2003}, 7796 volume = {39}, 7797 pages = {1709--1712}, 7798 title = {Solving Nonlinear Magnetic Problems Using {N}ewton Trust Region Methods}, 7799 petsc_uses = {KSP} 7800} 7801 7802@InProceedings{ vbde1, 7803 author = {Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith}, 7804 year = {2002}, 7805 title = {Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the 7806 Uintah PSE}, 7807 booktitle = {In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 7808 2002}, 7809 pages = {49-55}, 7810 url = {http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf}, 7811 note = {Extended abstract}, 7812 petsc_uses = {KSP} 7813} 7814 7815@Unpublished{ ep1, 7816 title = {An Inherently-Parallel Method for Solving Discretized Diffusion Equations}, 7817 author = {Bradley R. Eccleston and Todd S. Palmer}, 7818 institution = {Department of Nuclear Engineering, Oregon State University}, 7819 url = {http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf}, 7820 note = {Funded under the ASCI Level III: Computational Transport Issues for Large-Scale 7821 Parallel Simulations}, 7822 year = {1999}, 7823 petsc_uses = {KSP} 7824} 7825 7826@InProceedings{ teo2007scalable, 7827 title = {A scalable modular convex solver for regularized risk minimization}, 7828 author = {Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.}, 7829 booktitle = {Proceedings of the 13th ACM SIGKDD international conference on Knowledge 7830 discovery and data mining}, 7831 pages = {727--736}, 7832 year = {2007}, 7833 organization = {ACM}, 7834 petsc_uses = {KSP} 7835} 7836 7837@InProceedings{ rm02, 7838 author = {Robert Malouf}, 7839 year = {2002}, 7840 title = {A comparison of algorithms for maximum entropy Parameter estimation}, 7841 booktitle = {In Proceedings of the Sixth Conference on Natural Language Learning 7842 (CoNLL-2002)}, 7843 pages = {49-55}, 7844 url = {http://bulba.sdsu.edu/malouf/papers/conll02.pdf}, 7845 petsc_uses = {KSP} 7846} 7847 7848@Unpublished{ hrv02, 7849 title = {Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}}, 7850 author = {V. Hernandex and J. E. Roman and V. Vidal}, 7851 note = {Submitted to CMMSE}, 7852 petsc_uses = {KSP} 7853} 7854 7855@Article{ tmh2001, 7856 author = {Manfred Gilli and Evis Kellezi and Giorgio Pauletto}, 7857 journal = {Journal of Economic Dynamics and Control}, 7858 year = {2002}, 7859 volume = {26}, 7860 pages = {1499-1515}, 7861 title = {Solving finite difference schemes arising in trivariate option pricing}, 7862 petsc_uses = {KSP} 7863} 7864 7865@InProceedings{ a2, 7866 author = {C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes}, 7867 title = {Comparison of three algorithms for nonlinear metal cutting problems}, 7868 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 7869 Methods}, 7870 editor = {C.-H. Lai et al.}, 7871 publisher = {Domain Decomposition Press, Bergen}, 7872 url = {http://www.ddm.org/DD11/Palansuriya.ps.gz}, 7873 year = {1999}, 7874 petsc_uses = {KSP} 7875} 7876 7877@Unpublished{ mmmdcmaa-web-page, 7878 title = {{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and 7879 {A}coustics {W}eb Page}, 7880 url = {http://www.cs.odu.edu/\~{ }keyes/nsf}, 7881 author = {David E. Keyes}, 7882 institution = {Old Dominion University}, 7883 petsc_uses = {KSP} 7884} 7885 7886@Conference{ liu2010parallelization, 7887 title = {{Parallelization of Thermal Recovery Simulation Based on PETSc}}, 7888 author = {Liu, L. and Xue, W. and Shu, J. and Ma, L.}, 7889 booktitle = {International Symposium on Parallel and Distributed Processing with 7890 Applications}, 7891 pages = {528--535}, 7892 year = {2010}, 7893 organization = {IEEE}, 7894 petsc_uses = {KSP} 7895} 7896 7897@Unpublished{ oil-reservoir-sim-web-page, 7898 title = {{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation}, 7899 url = {http://www.pe.utexas.edu/CPGE/new_generation}, 7900 institution = {University of Texas at Austin and Argonne National Laboratory}, 7901 key = {University of Texas at Austin and Argonne National Laboratory}, 7902 petsc_uses = {KSP} 7903} 7904 7905@Article{ tmh2001b, 7906 author = {V. Thiagarajan and K. Milfeld and KT. Milfeld}, 7907 journal = {IEEE TRANSACTIONS ON MAGNETICS }, 7908 year = {2001}, 7909 volume = {37}, 7910 pages = {143--146}, 7911 title = {Adapting EMAP3D to parallel processing}, 7912 petsc_uses = {KSP} 7913} 7914 7915@Article{ harbury98, 7916 author = {HK Harbury and W Porod}, 7917 journal = {VLSI Design}, 7918 year = {1998}, 7919 volume = {6}, 7920 pages = {47--51}, 7921 title = {Parallel computation for electronic waves in quantum corrals}, 7922 petsc_uses = {KSP} 7923} 7924 7925@Article{ bludszuwei98, 7926 author = {Mark Bludszuweit}, 7927 journal = {Journal of Lightwave Technology}, 7928 year = {1998}, 7929 volume = {16}, 7930 number = {7}, 7931 pages = {1336--42}, 7932 title = {Mixed Finite Element Beam Propagation Method}, 7933 petsc_uses = {KSP} 7934} 7935 7936@Article{ s1, 7937 author = {J. L. Friedman and N. Stergioulas}, 7938 journal = {Astrophysics Journal}, 7939 year = {1998}, 7940 volume = {492}, 7941 number = {301}, 7942 pages = {}, 7943 title = {}, 7944 petsc_uses = {KSP} 7945} 7946 7947@Article{ s1a, 7948 author = {S. M. Morsink and N. Stergioulas and S. Blattnig}, 7949 journal = {Astrophysics Journal}, 7950 year = {1999}, 7951 volume = {510}, 7952 number = {854}, 7953 pages = {}, 7954 title = {}, 7955 petsc_uses = {KSP} 7956} 7957 7958@PhDThesis{ s2, 7959 author = {N. Stergioulas}, 7960 title = {Ph. D. thesis}, 7961 year = {1996}, 7962 institution = {University of Wisconsin-Milwaukee}, 7963 petsc_uses = {KSP} 7964} 7965 7966@InProceedings{ coral1, 7967 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7968 title = {Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and 7969 Parallel Computing Environment}, 7970 booktitle = {Proceedings of the Miami TEAM Workshop}, 7971 location = {Florida International University, Department of Electrical Engineering and 7972 Computing Science}, 7973 month = nov, 7974 year = {1993}, 7975 petsc_uses = {KSP} 7976} 7977 7978@InProceedings{ coral2, 7979 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7980 title = {Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation}, 7981 booktitle = {Proceedings of Aix-les-Bains TEAM Workshop}, 7982 month = dec, 7983 year = {1994}, 7984 petsc_uses = {KSP} 7985} 7986 7987@InProceedings{ coral3, 7988 author = {L. Kettunen and K. Forsman and D. Levine and W. Gropp}, 7989 title = {Computational Electromagnetics and Parallel Dense Matrix Computations}, 7990 booktitle = {Proceedings of the SIAM Parallel Processing for Scientific Computing Conference}, 7991 location = {Florida International University, Department of Electrical Engineering and 7992 Computing Science}, 7993 year = {1995}, 7994 petsc_uses = {KSP} 7995} 7996 7997@InProceedings{ mijalkovic, 7998 author = {Slobodan Mijalkovi\'{c}}, 7999 title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor 8000 Process Simulation}, 8001 booktitle = {Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held 8002 Gent, Belgium, September 27--30, 1999.}, 8003 editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels}, 8004 optvolume = {14}, 8005 optseries = {Lecture Notes in Computational Science and Engineering}, 8006 year = {2000}, 8007 publisher = {Springer}, 8008 address = {Berlin}, 8009 optpages = {179--184}, 8010 petsc_uses = {KSP} 8011} 8012 8013@Article{ bludszuwei98a, 8014 author = {Mark Bludszuweit}, 8015 journal = {Journal of Lightwave Technology}, 8016 year = {1998}, 8017 volume = {16}, 8018 number = {7}, 8019 pages = {1336--42}, 8020 title = {Mixed Finite Element Beam Propagation Method}, 8021 petsc_uses = {KSP} 8022} 8023 8024@Article{ gilli-pauletto-1998, 8025 author = {Manfred Gilli and Giorgio Pauletto}, 8026 title = {Parallel {K}rylov Methods for Econometric Model Simulation}, 8027 journal = {Computational Economics}, 8028 year = {2000}, 8029 volume = {16}, 8030 pages = {173--186}, 8031 petsc_uses = {KSP} 8032} 8033 8034% LiteralHTML: 8035% LiteralHTML: <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3> 8036% LiteralHTML: 8037@Article{ collierdalcincalo2013, 8038 title = {{PetIGA}: High-Performance Isogeometric Analysis}, 8039 author = {Nathan Collier and Lisandro Dalcin and Victor M. Calo}, 8040 journal = {arxiv}, 8041 year = {2013}, 8042 number = {1305.4452}, 8043 note = {\url{http://arxiv.org/abs/1305.4452}}, 8044 petsc_uses = {KSP} 8045} 8046 8047@Article{ collierdalcinvignalcortescalo2016, 8048 title = {PetIGA: A framework for high-performance isogeometric analysis}, 8049 author = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and 8050 Victor M. Calo}, 8051 journal = {Computer Methods in Applied Mechanics and Engineering}, 8052 year = {2016}, 8053 petsc_uses = {KSP} 8054} 8055 8056@Misc{ petiga-web-page, 8057 author = {N. Collier and L. Dalcin and V.M. Calo}, 8058 title = {{PetIGA} {W}eb page}, 8059 url = {https://bitbucket.org/dalcinl/petiga/}, 8060 howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}}, 8061 year = {2014}, 8062 petsc_uses = {KSP} 8063} 8064 8065@Article{ logg07, 8066 author = {Logg, Anders}, 8067 title = {Automating the Finite Element Method}, 8068 journal = {Archives of Computational Methods in Engineering}, 8069 volume = {14}, 8070 number = {2}, 8071 pages = {93-138}, 8072 year = {2007}, 8073 doi = {10.1007/s11831-007-9003-9}, 8074 publisher = {Kluwer Academic Publishers}, 8075 issn = {1134-3060}, 8076 language = {English}, 8077 petsc_uses = {KSP} 8078} 8079 8080@Article{ jezequelcouturierdenis12, 8081 author = {Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe}, 8082 title = {Solving large sparse linear systems in a grid environment: the GREMLINS code 8083 versus the PETSc library}, 8084 journal = {The Journal of Supercomputing}, 8085 volume = {59}, 8086 number = {3}, 8087 pages = {1517-1532}, 8088 year = {2012}, 8089 issn = {0920-8542}, 8090 doi = {10.1007/s11227-011-0563-y}, 8091 publisher = {Springer US}, 8092 keywords = {Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; 8093 Sparse linear solver}, 8094 language = {English}, 8095 petsc_uses = {KSP} 8096} 8097 8098@Unpublished{ feap-web-page, 8099 title = {FEAP: A Finite Element Analysis Program}, 8100 url = {http://www.ce.berkeley.edu/projects/feap/}, 8101 author = {FEAP Team}, 8102 note = {Uses PETSc linear solvers - iterative and direct}, 8103 petsc_uses = {KSP} 8104} 8105 8106@Unpublished{ parpre-web-page, 8107 title = {{ParPre} {W}eb {P}age}, 8108 url = {http://www.cs.utk.edu/\~{ }eijkhout/parpre.html}, 8109 institution = {University of Tennessee}, 8110 author = {Victor Eijkhout}, 8111 note = {This is no longer supported. A set of preconditioners built on PETSc}, 8112 petsc_uses = {KSP} 8113} 8114 8115@Unpublished{ pism, 8116 title = {{PISM}: a Parallel Ice Sheet Model}, 8117 author = {{PISM Team}}, 8118 abstract = {We have developed a numerical model of ice sheets called PISM (a Parallel Ice 8119 Sheet Model). The thickness, temperature, velocity and age of the ice are all 8120 simulated, as is the deformation of the earth underneath the ice. New techniques 8121 for fast ice dynamics, earth deformation, and verification have are included.}, 8122 note = {\url{http://www.pism-docs.org/}}, 8123 petsc_uses = {KSP} 8124} 8125 8126@Unpublished{ oofem, 8127 title = {OOFEM - an object oriented finite element package}, 8128 author = {Borek Patzak}, 8129 url = {http://www.oofem.org}, 8130 petsc_uses = {KSP} 8131} 8132 8133@Unpublished{ dks2openfvm, 8134 title = {OpenFVM - a finite volume based general purpose CFD solver}, 8135 author = {Open source development}, 8136 url = {http://openfvm.sourceforge.net/}, 8137 petsc_uses = {KSP} 8138} 8139 8140@Unpublished{ sundar-2008w, 8141 title = {DENDRO: a parallel geometric multigrid library for trilinear finite elements on 8142 octree meshes}, 8143 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 8144 institution = {University of Pennsylvania}, 8145 url = {http://www.seas.upenn.edu/~csela/dendro/html/index.html}, 8146 petsc_uses = {KSP} 8147} 8148 8149@Unpublished{ khatiwala07-software, 8150 title = {A computational framework for simulation of biogeochemical tracers in the ocean}, 8151 author = {Khatiwala, S.}, 8152 institution = {Columbia University}, 8153 url = {http://www.ldeo.columbia.edu/\~{ }spk}, 8154 petsc_uses = {KSP} 8155} 8156 8157@InBook{ jiaolima99, 8158 author = {Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma}, 8159 chapter = {{SIFFEA}:Scalable Integrated Framework for Finite Element Analysis}, 8160 url = {http://portal.acm.org/citation.cfm?id=646895.709725}, 8161 title = {Lecture Notes in Computer Science}, 8162 publisher = {Springer-Verlag}, 8163 volume = {1732}, 8164 year = {1999}, 8165 petsc_uses = {KSP} 8166} 8167 8168@Article{ crow1, 8169 author = {C. S. Crow IV}, 8170 title = {DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations}, 8171 journal = {Hopkins Undergraduate Research Journal}, 8172 year = {2003}, 8173 url = {http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf}, 8174 petsc_uses = {KSP} 8175} 8176 8177@Unpublished{ petsc-python, 8178 title = {PETSc for Python}, 8179 author = {L. Dalcin}, 8180 url = {https://petsc.org/main/petsc4py}, 8181 note = {Provides Python bindings for PETSc}, 8182} 8183 8184@Unpublished{ cfdship, 8185 title = {{CFDShip-Iowa}}, 8186 author = {Pablo M. Carrica and Robert V. Wilson and Fred Stern}, 8187 institution = {University of Iowa}, 8188 url = {http://www.iihr.uiowa.edu/\~{ }cfdship/}, 8189 note = {CFDShip-Iowa is a multiblock free surface flow solver that uses overset 8190 structured grids, designed for ship applications}, 8191 petsc_uses = {KSP} 8192} 8193 8194@Unpublished{ bvw, 8195 title = {Multiflow}, 8196 author = {Berend van Wachem}, 8197 institution = {Mechanical Engineering - Chalmers University of Technology}, 8198 url = {http://www.tfd.chalmers.se/\~{ }berend/page3.html}, 8199 note = {MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase 8200 flows.}, 8201 petsc_uses = {KSP} 8202} 8203 8204@Unpublished{ dks2, 8205 title = {FENA - A Finite Element Model for the North Atlantic}, 8206 author = {Jens Schroeter}, 8207 institution = {Alfred-Wegener-Institute for Polar and Marine Research}, 8208 url = {http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html}, 8209 petsc_uses = {KSP} 8210} 8211 8212@TechReport{ piwonski2010idea, 8213 title = {The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization 8214 and Simulation in {3-D}}, 8215 author = {Piwonski, J. and Slawig, T.}, 8216 year = {2010}, 8217 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8218 url = {http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}, 8219 petsc_uses = {KSP} 8220} 8221 8222@Unpublished{ metos3d-web, 8223 title = {{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D}, 8224 author = {Piwonski, J. and Slawig, T.}, 8225 institution = {Christian-Albrechts-Universit\"at zu Kiel}, 8226 url = {http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}, 8227 petsc_uses = {KSP} 8228} 8229 8230@Unpublished{ magpar, 8231 author = {W. Scholz}, 8232 title = {Magpar: Parallel Micromagnetics Code}, 8233 institution = {Vienna University of Technology}, 8234 url = {http://magnet.atp.tuwien.ac.at/scholz/magpar/}, 8235 petsc_uses = {KSP} 8236} 8237 8238@Misc{ libmesh:sourceforge, 8239 author = {}, 8240 title = {{libMesh}:a C++ framework for the numerical simulation of partial differential 8241 equations on serial and parallel platforms}, 8242 note = {[Online]}, 8243 url = {http://libmesh.github.io}, 8244 petsc_uses = {KSP} 8245} 8246 8247@Misc{ moose-web-page, 8248 title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})}, 8249 author = {David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek 8250 Gaston and John Peterson and Jason Miller}, 8251 institution = {Idaho National Laboratory}, 8252 howpublished = {\url{http://mooseframework.org}}, 8253 petsc_uses = {KSP} 8254} 8255 8256@Article{ gaston2009moose, 8257 title = {MOOSE: {A} parallel computational framework for coupled systems of nonlinear 8258 equations}, 8259 author = {Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.}, 8260 journal = {Nuclear Engineering and Design}, 8261 volume = {239}, 8262 number = {10}, 8263 pages = {1768--1778}, 8264 year = {2009}, 8265 publisher = {Elsevier}, 8266 petsc_uses = {KSP} 8267} 8268 8269@Article{ tonks2012object, 8270 title = {An object-oriented finite element framework for multiphysics phase field 8271 simulations}, 8272 author = {Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.}, 8273 journal = {Computational Materials Science}, 8274 volume = {51}, 8275 number = {1}, 8276 pages = {20--29}, 8277 year = {2012}, 8278 publisher = {Elsevier}, 8279 petsc_uses = {KSP} 8280} 8281 8282@Misc{ pylithmanual, 8283 author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif 8284 Strand and Charles Williams}, 8285 title = {{PyLith} User Manual Version 2.0.0}, 8286 year = {2014}, 8287 url = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}, 8288 petsc_uses = {KSP} 8289} 8290 8291@Misc{ pylith-web-page, 8292 author = {Brad Aagaard and Matthew G. Knepley and Charles Williams}, 8293 title = {{PyLith}}, 8294 year = {2012}, 8295 url = {http://geodynamics.org/resources/pylith/}, 8296 howpublished = {\url{http://geodynamics.org/resources/pylith/}}, 8297 petsc_uses = {KSP} 8298} 8299 8300@Misc{ galemanual, 8301 author = {Walter Landry and Luke Hodkinson and Susan Kientz}, 8302 title = {Gale User Manual Version 2.0.0}, 8303 year = {2011}, 8304 url = {http://geodynamics.org/cig/software/gale/gale.pdf}, 8305 petsc_uses = {KSP} 8306} 8307 8308@Unpublished{ underworld, 8309 author = {Louis Moresi}, 8310 title = {{UnderWorld}: A Geodynamics Modelling Code}, 8311 institution = {Monash University}, 8312 url = {http://www.mcc.monash.edu/twiki/view/Codes}, 8313 petsc_uses = {KSP} 8314} 8315 8316@Article{ moresi2007computational, 8317 title = {Computational approaches to studying non-linear dynamics of the crust and 8318 mantle}, 8319 author = {Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and 8320 M{\"u}hlhaus, H.B.}, 8321 journal = {Physics of the Earth and Planetary Interiors}, 8322 volume = {163}, 8323 number = {1-4}, 8324 pages = {69--82}, 8325 year = {2007}, 8326 publisher = {Elsevier}, 8327 petsc_uses = {KSP} 8328} 8329 8330@Article{ pitt2009chaste, 8331 title = {Chaste: a test-driven approach to software development for biological modelling}, 8332 author = {Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and 8333 Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. 8334 and Walter, A. and others}, 8335 journal = {Computer Physics Communications}, 8336 volume = {180}, 8337 number = {12}, 8338 pages = {2452--2471}, 8339 year = {2009}, 8340 publisher = {Elsevier}, 8341 petsc_uses = {KSP} 8342} 8343 8344@Misc{ fenicsproject, 8345 title = {{The FEniCS project}}, 8346 author = {Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and 8347 Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.}, 8348 note = {A continually updated technical report. \url{http://fenicsproject.org}}, 8349 url = {http://fenicsproject.org}, 8350 year = {2011}, 8351 petsc_uses = {KSP} 8352} 8353 8354@Unpublished{ snark, 8355 title = {Snark: A suite of software for geoscientific applications and a philosophy of 8356 scientific software development}, 8357 institution = {Victorian Partnership for Advanced Computing}, 8358 url = {http://vpac.org/Snark}, 8359 petsc_uses = {KSP} 8360} 8361 8362@Misc{ imoose:sourceforge, 8363 author = {Guido Arians and Thomas Bauer and Christian Kaehler and Wolfgang Mai and 8364 Christoph Monzel and Dirk {van Riesen} and Christoph Schlensok}, 8365 title = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}}, 8366 note = {[Online]}, 8367 url = {http://imoose.sourceforge.net}, 8368 petsc_uses = {KSP} 8369} 8370 8371@Unpublished{ fossi, 8372 author = {Stephan Frickenhaus}, 8373 title = {FoSSI: Family of Simplified Solver Interfaces, offers scalable access to 8374 MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector 8375 codes}, 8376 institution = {AWI-Bremerhaven, Germanny}, 8377 url = {http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/}, 8378 petsc_uses = {KSP} 8379} 8380 8381@Unpublished{ fun3dweb, 8382 author = {Dinesh Kaushik}, 8383 title = {PETSC-FUN3D Benchmark Page}, 8384 institution = {ODU/ANL}, 8385 url = {http://www.mcs.anl.gov/petsc-fun3d}, 8386 note = {CFD Benchmark of some solvers in PETSc}, 8387 petsc_uses = {KSP} 8388} 8389 8390@Unpublished{ scirun, 8391 author = {SCIRun Development Team}, 8392 title = {SCIRun}, 8393 institution = {University of Utah}, 8394 url = {http://www.sci.utah.edu/stories/2001/jul_scirun120.html}, 8395 note = {SCIRun now uses PETSc linear solvers}, 8396 petsc_uses = {KSP} 8397} 8398 8399@Misc{ prometheus, 8400 author = {Mark F. Adams}, 8401 title = {Prometheus - A scalable unstructured finite element solver}, 8402 institution = {Berkeley}, 8403 howpublished = {\url{http://www.cs.berkeley.edu/~madams/prometheus}}, 8404 url = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}, 8405 petsc_uses = {KSP} 8406} 8407 8408@Unpublished{ illuminator, 8409 author = {Adam C. Powell, IV}, 8410 title = {Illuminator Distributed Visualization Library}, 8411 url = {http://lyre.mit.edu/\~{ }powell/Illuminator.html}, 8412 petsc_uses = {KSP} 8413} 8414 8415@Unpublished{ rheoplast, 8416 title = {RheoPlast Phase Field Multi-Physics Code}, 8417 author = {Adam Powell and David Dussault and Bo Zhou}, 8418 url = {http://lyre.mit.edu/\~{ }powell/rheoplast.html}, 8419 petsc_uses = {KSP} 8420} 8421 8422@Misc{ tao-web-page, 8423 title = {{Toolkit for Advanced Optimization ({TAO})} {W}eb Page}, 8424 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8425 and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}}, 8426 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8427 howpublished = {\url{http://www.mcs.anl.gov/tao}}, 8428 petsc_uses = {KSP} 8429} 8430 8431@TechReport{ tao-user-ref, 8432 title = {{Toolkit for Advanced Optimization ({TAO}) users manual}}, 8433 author = {Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild 8434 and Steve Benson and Lois Curfman McInnes}, 8435 institution = {Argonne National Laboratory}, 8436 year = {2019}, 8437 number = {ANL/MCS-TM-322 - Rev 3.12}, 8438 petsc_uses = {KSP} 8439} 8440 8441% url = "http://www.mcs.anl.gov/tao", 8442@Unpublished{ mefpp-web-page, 8443 title = {{MEF++} {W}eb {P}age}, 8444 url = {http://www.giref.ulaval.ca/ressources/projets/mefpp.html}, 8445 institution = {Groupe Interdisiplinaire de Recherche en Elements Finis}, 8446 author = {Eric Chamberland}, 8447 note = {A finite element code for fluid dynamics, solid mechanics, thermal and 8448 multiphysics}, 8449 petsc_uses = {KSP} 8450} 8451 8452@Unpublished{ tipetsc-titanium, 8453 title = {Ti-PETSc - an interface to PETSc from Titanium}, 8454 institution = {Berkeley}, 8455 author = {He, Yun and Liblit, Bun and Lin, Chang}, 8456 url = {https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=9f7959be13337c735d52e5c0b0994bdea6d75a96}, 8457 year = {1999}, 8458 petsc_uses = {KSP}, 8459} 8460 8461@Unpublished{ ptatin-web-page, 8462 title = {ptatin3d}, 8463 author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan}, 8464 url = {https://bitbucket.org/jedbrown/ptatin3d}, 8465 year = {2018}, 8466 petsc_uses = {KSP} 8467} 8468 8469@Misc{ multiphase-web-page, 8470 author = {Q. Zou}, 8471 title = {Multiphase flow with {PETSc}}, 8472 institution = {LANL}, 8473 howpublished = {\url{http://cnls-www.lanl.gov/~qzou}}, 8474 url = {http://cnls-www.lanl.gov/\~{ }qzou}, 8475 lab = {LANL}, 8476 petsc_uses = {KSP} 8477} 8478 8479@Misc{ electromag-web-page, 8480 title = {{EMSolve Web} page}, 8481 institution = {LLNL}, 8482 howpublished = {http://www.llnl.gov/casc/emsolve}, 8483 url = {http://www.Llnl.gov/casc/emsolve}, 8484 author = {Daniel {White et al.}}, 8485 lab = {LLNL}, 8486 petsc_uses = {KSP} 8487} 8488 8489@Unpublished{ fe-software-web-page, 8490 institution = {Kuleuven}, 8491 title = {Finite element software}, 8492 url = {http://www.esat.kuleuven.ac.be/elen/research/software-development}, 8493 petsc_uses = {KSP} 8494} 8495 8496@Misc{ petsc-web-page, 8497 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8498 Brown and Peter Brune and Kris Buschelman and Emil~M. Constantinescu and Lisandro 8499 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8500 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8501 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 8502 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 8503 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 8504 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 8505 Zhang}, 8506 title = {{PETS}c {W}eb page}, 8507 url = {https://petsc.org/}, 8508 howpublished = {\url{https://petsc.org/}}, 8509 year = {2024} 8510} 8511 8512@Unpublished{ petsc-debian-package, 8513 author = {Adam C. Powell, IV}, 8514 title = {Debian package for PETSc}, 8515 url = {http://lyre.mit.edu/\~{ }powell/petsc.html}, 8516 petsc_uses = {KSP} 8517} 8518 8519@Unpublished{ cactus, 8520 title = {Cactus Website}, 8521 url = {http://www.cactuscode.org/}, 8522 note = {Provides two interface to the PETSc solvers}, 8523 petsc_uses = {KSP} 8524} 8525 8526@Unpublished{ petsc-fem, 8527 author = {Mario Storti and Norberto Nigro}, 8528 title = {PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program}, 8529 institution = {Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)}, 8530 url = {http://www.cimec.org.ar/petscfem}, 8531 petsc_uses = {KSP} 8532} 8533 8534@Misc{ fidap, 8535 title = {FIDAP 8.5}, 8536 howpublished = {\url{http://www.fluent.com}}, 8537 url = {http://www.fluent.com}, 8538 note = {Fluent's commercial finite element fluid code uses PETSc for parallel linear 8539 solves.}, 8540 key = {FIDAP 8.5}, 8541 petsc_uses = {KSP} 8542} 8543 8544@Unpublished{ slepc, 8545 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8546 Vicente Hern\'andez and Vicent Vidal}, 8547 title = {{SLEPc} Website}, 8548 url = {http://slepc.upv.es/}, 8549 note = {Scalable Library for Eigenvalue Problem Computations}, 8550 petsc_uses = {KSP} 8551} 8552 8553@TechReport{ slepc-users-manual, 8554 author = {Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and Andr\'es Tom\'as and 8555 Vicente Hern\'andez and Vicent Vidal}, 8556 title = {{SLEPc} Users Manual}, 8557 number = {DISC-II/24/02}, 8558 url = {http://slepc.upv.es/}, 8559 note = {Scalable Library for Eigenvalue Problem Computations}, 8560 petsc_uses = {KSP} 8561} 8562 8563@Misc{ deal.ii, 8564 title = {deal.II}, 8565 howpublished = {\url{http://www.dealii.org}}, 8566 url = {http://www.dealii.org}, 8567 note = {deal.II is a C++ library targeting adaptive finite elements and error estimation. 8568 It allows PETSc linear algebra and solvers to be used underneath.}, 8569 key = {deal.II 5.0}, 8570 petsc_uses = {KSP} 8571} 8572 8573@Article{ bangerth2007deal, 8574 title = {{deal.II---A general-purpose object-oriented finite element library}}, 8575 author = {Bangerth, W. and Hartmann, R. and Kanschat, G.}, 8576 journal = {ACM Transactions on Mathematical Software (TOMS)}, 8577 volume = {33}, 8578 number = {4}, 8579 pages = {24--es}, 8580 issn = {0098-3500}, 8581 year = {2007}, 8582 publisher = {ACM}, 8583 petsc_uses = {KSP} 8584} 8585 8586@Misc{ globalarrays, 8587 author = {Jarek {Nieplocha et al.}}, 8588 title = {Global Arrays}, 8589 institution = {Pacific Northwest National Laboratories}, 8590 howpublished = {\url{http://www.emsl.pnl.gov/docs/global}}, 8591 url = {http://www.emsl.pnl.gov/docs/global}, 8592 note = {Global arrays can use PETSc linear solvers}, 8593 lab = {PNNL}, 8594 petsc_uses = {KSP} 8595} 8596 8597% LiteralHTML: 8598% LiteralHTML: <a name="software"><H3><center>Software Engineering</center></H3> 8599% LiteralHTML: 8600@Article{ petsccommunity2022, 8601 title = {The Community is the Infrastructure: A Short Discussion of the {PETSc} User 8602 Community}, 8603 author = {Mark Adams and Satish Balay and Jed Brown and Victor Eijkhout and Jacob 8604 Faibussowitsch and Fande Kong and Matthew Knepley and Scott Kruger and Oana Marin 8605 and Richard Mills and Todd Munson and Patrick Sanan and Barry Smith and Hong Zhang 8606 and Hong Zhang and Junchao Zhang}, 8607 journal = {Computing in Science and Engineering}, 8608 volume = {24}, 8609 number = {03}, 8610 pages = {6--15}, 8611 issn = {1558-366X}, 8612 doi = {10.1109/MCSE.2022.3169974}, 8613 publisher = {IEEE Computer Society}, 8614 address = {Los Alamitos, CA, USA}, 8615 month = may, 8616 year = {2022}, 8617 url = {https://figshare.com/articles/conference_contribution/The_Community_is_the_Infrastructure_A_Short_Discussion_of_the_PETSc_User_Community/16523043}, 8618 petsc_uses = {KSP} 8619} 8620 8621@Article{ brownknepleysmith14, 8622 author = {Jed Brown and Matthew G. Knepley and Barry Smith}, 8623 title = {Run-time extensibility and librarization of simulation software}, 8624 journal = {IEEE Computing in Science and Engineering}, 8625 month = jan, 8626 volume = {17}, 8627 number = {1}, 8628 pages = {38--45}, 8629 doi = {10.1109/MCSE.2014.95}, 8630 year = {2015}, 8631 petsc_uses = {KSP} 8632} 8633 8634@TechReport{ ass2012, 8635 author = {Shrirang Abhyankar and Barry Smith and Kerry Stevens}, 8636 title = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}}, 8637 institution = {Argonne National Laboratory}, 8638 type = {Preprint}, 8639 year = {2012}, 8640 number = {ANL/MCS-P2011-0112}, 8641 petsc_uses = {KSP} 8642} 8643 8644@TechReport{ clearyknepley99, 8645 author = {Andrew Cleary and Matthew G. Knepley}, 8646 title = {Solvers as Operators}, 8647 institution = {Lawrence Livermore National Laboratory}, 8648 type = {Technical Report}, 8649 number = {UCRL-ID-135342}, 8650 year = {1999}, 8651 petsc_uses = {KSP} 8652} 8653 8654@TechReport{ smcabbkz2012, 8655 author = {Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and 8656 Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang}, 8657 title = {{PETSc's} software strategy for the design space of composable extreme-scale 8658 solvers}, 8659 institution = {Argonne National Laboratory}, 8660 type = {Preprint}, 8661 note = {{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR}, 8662 year = {2012}, 8663 number = {ANL/MCS-P2059-0312}, 8664 petsc_uses = {KSP} 8665} 8666 8667@InProceedings{ mhwpmhs2009, 8668 author = {R. T. Mills and F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin 8669 and G. E. Hammond and B. Smith}, 8670 title = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing 8671 Toolkit {MPI} at Scale}, 8672 booktitle = {Cray Users Group Conference}, 8673 year = {2009}, 8674 petsc_uses = {KSP} 8675} 8676 8677@InProceedings{ msmhls2010, 8678 author = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. 8679 Lichtner and B. F. Smith}, 8680 title = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} 8681 {BlueGene} Architectures}, 8682 booktitle = {Proceedings of SciDAC 2010 Annual Meeting}, 8683 year = {2010}, 8684 petsc_uses = {KSP} 8685} 8686 8687@InCollection{ msk2013, 8688 author = {Victor Minden and Barry F. Smith and Matthew G. Knepley}, 8689 title = {Preliminary Implementation of {PETSc} Using {GPUs}}, 8690 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8691 series = {Lecture Notes in Earth System Sciences}, 8692 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8693 Yaolin Shi}, 8694 doi = {10.1007/978-3-642-16405-7_7}, 8695 publisher = {Springer Berlin Heidelberg}, 8696 pages = {131--140}, 8697 year = {2013}, 8698 isbn = {978-3-642-16404-0}, 8699 petsc_uses = {KSP} 8700} 8701 8702@InCollection{ knepleyyuen13, 8703 author = {Matthew G. Knepley and David A. Yuen}, 8704 title = {Why Scientists and Engineers need {GPU}s today}, 8705 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8706 series = {Lecture Notes in Earth System Sciences}, 8707 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8708 Yaolin Shi}, 8709 doi = {10.1007/978-3-642-16405-7_1}, 8710 publisher = {Springer Berlin Heidelberg}, 8711 pages = {131--140}, 8712 year = {2013}, 8713 isbn = {978-3-642-16404-0}, 8714 petsc_uses = {KSP} 8715} 8716 8717@InCollection{ karpeevknepleybrune13, 8718 author = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune}, 8719 title = {Accurate Evaluation of Local Averages on {GPGPUs}}, 8720 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8721 series = {Lecture Notes in Earth System Sciences}, 8722 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8723 Yaolin Shi}, 8724 doi = {10.1007/978-3-642-16405-7_30}, 8725 publisher = {Springer Berlin Heidelberg}, 8726 pages = {487--501}, 8727 year = {2013}, 8728 isbn = {978-3-642-16404-0}, 8729 petsc_uses = {KSP} 8730} 8731 8732@InCollection{ zhengetal13, 8733 title = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly 8734 Variable Viscosity}, 8735 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8736 Zhang and Yaolin Shi}, 8737 booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering}, 8738 series = {Lecture Notes in Earth System Sciences}, 8739 editor = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and 8740 Yaolin Shi}, 8741 doi = {10.1007/978-3-642-16405-7_21}, 8742 publisher = {Springer Berlin Heidelberg}, 8743 pages = {321--333}, 8744 year = {2013}, 8745 isbn = {978-3-642-16404-0}, 8746 petsc_uses = {KSP} 8747} 8748 8749@Article{ zhengetal13b, 8750 title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with 8751 strongly variable viscosity based on {M}atlab and {CUDA}}, 8752 author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai 8753 Zhang and Yaolin Shi}, 8754 journal = {IJHPCA}, 8755 volume = {28}, 8756 number = {1}, 8757 pages = {50--60}, 8758 doi = {10.1177/1094342013478640}, 8759 year = {2013}, 8760 petsc_uses = {KSP} 8761} 8762 8763@InBook{ s2011, 8764 author = {B. Smith}, 8765 chapter = {PETSc, the Portable, Extensible Toolkit for Scientific computing}, 8766 title = {Encyclopedia of Parallel Computing}, 8767 bookeditor = {D. Padua}, 8768 publisher = {Springer}, 8769 year = {2011}, 8770 petsc_uses = {KSP} 8771} 8772 8773@Article{ acostamejia06, 8774 author = {Carlos D. Acosta and Carlos E. Mej\'ia}, 8775 title = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc}, 8776 journal = {Lecturas Matem\'aticas}, 8777 volume = {27}, 8778 year = {2006}, 8779 pages = {213--224}, 8780 petsc_uses = {KSP} 8781} 8782 8783@InProceedings{ quenettemoresisunterappelbe07, 8784 author = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe}, 8785 title = {Explaining StGermain: An aspect oriented environment for building extensible 8786 computational mechanics modeling software}, 8787 booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007}, 8788 publisher = {IEEE}, 8789 pages = {1--8}, 8790 yerar = {2007}, 8791 petsc_uses = {KSP} 8792} 8793 8794@Article{ dfm1, 8795 title = {Vectorized sparse matrix multiply for compressed row storage format}, 8796 author = {E. F. D'Azevedo and M. R. Fahey and R. T. Mills}, 8797 journal = {Lecture Notes in Computer Science}, 8798 year = {2005}, 8799 pages = {99--106}, 8800 volume = {3514}, 8801 lab = {ORNL}, 8802 petsc_uses = {KSP} 8803} 8804 8805@InProceedings{ laniquintinokimpedeconinckvandewallepoedts05, 8806 author = {Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan 8807 Vandewalle and Stefaan Poedts}, 8808 title = {The COOLFluiD Framework: Design Solutions for High Performance Object Oriented 8809 Scientific Computing Software}, 8810 booktitle = {Computational Science ICCS 2005: 5th International Conference}, 8811 year = {2005}, 8812 note = {Lecture Notes in Computer Science}, 8813 volume = {3514}, 8814 publisher = {Springer-Verlag GmbH}, 8815 petsc_uses = {KSP} 8816} 8817 8818@InProceedings{ dalcin-paz-storti, 8819 author = {L. Dalcin and R. Paz and M. Storti}, 8820 title = {Desarrollo de Aplicaciones Paralelas en Python}, 8821 booktitle = {Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). 8822 Bariloche, Argentina}, 8823 year = {2004}, 8824 petsc_uses = {KSP} 8825} 8826 8827@Article{ mpi-python, 8828 author = {L. Dalcin and R. Paz and M. Storti}, 8829 title = {MPI for Python}, 8830 journal = {Journal of Parallel and Distributed Computing}, 8831 year = {2005}, 8832 petsc_uses = {KSP} 8833} 8834 8835@Unpublished{ hrv02a, 8836 title = {{SLEPc}: Scalable Library for Eigenvalue Problem Computations}, 8837 author = {V. Hernandex and J. E. Roman and V. Vidal}, 8838 note = {Submited to VecPar 2002}, 8839 year = {2002}, 8840 petsc_uses = {KSP} 8841} 8842 8843@Article{ knyazev2007block, 8844 title = {Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and 8845 {PETSc}}, 8846 author = {Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.}, 8847 journal = {SIAM Journal on Scientific Computing}, 8848 volume = {29}, 8849 pages = {2224-2239}, 8850 doi = {10.1137/060661624}, 8851 year = {2007}, 8852 petsc_uses = {KSP} 8853} 8854 8855@MastersThesis{ aarrestad-master, 8856 author = {Asbjorn Hoiland Aarrestad}, 8857 title = {Time Dependent Solution of the Schrodinger Equation for Parallel Computers}, 8858 school = {University of Bergen}, 8859 month = aug, 8860 year = {2003}, 8861 url = {http://www.parallab.uib.no/projects/molecul/matrix/}, 8862 note = {Implemented Runge-Kutta methods using PETSc}, 8863 petsc_uses = {KSP} 8864} 8865 8866@PhDThesis{ kaushik-phd, 8867 author = {D. K. Kaushik}, 8868 title = {Performance Modeling and Prediction for the Scalable Solution of Partial 8869 Differential Equations on Unstructured Grids}, 8870 school = {Old Dominion University}, 8871 month = dec, 8872 year = {2002}, 8873 url = {http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps}, 8874 petsc_uses = {KSP} 8875} 8876 8877@TechReport{ rb1, 8878 author = {Rickard Bergstrom}, 8879 title = {Object Oriented Implementation of a General Finite Element Code}, 8880 number = {2002-13}, 8881 institution = {Chalmers Finite Element Center, Chalmers University of Technology}, 8882 year = {2002}, 8883 url = {http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf}, 8884 note = {Discribes a finite element software package that uses PETSc for its solvers}, 8885 petsc_uses = {KSP} 8886} 8887 8888@InProceedings{ dbl1, 8889 author = {Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew}, 8890 title = {A Parallel General Purpose Finite Element System}, 8891 booktitle = {IX SIAM Conference on Parallel Processing for Scientific Computing}, 8892 publisher = {SIAM}, 8893 year = {1999}, 8894 url = {http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz}, 8895 note = {Describes software that uses PETSc for its parallel linear solves}, 8896 petsc_uses = {KSP} 8897} 8898 8899@Article{ p1, 8900 title = {Parallel Components for PDEs and Optimization: Some Issues and Experiences}, 8901 author = {B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes 8902 and B. Smith}, 8903 journal = {Parallel Computing}, 8904 year = {2002}, 8905 pages = {1811--1831}, 8906 volume = {28 (12)}, 8907 petsc_uses = {KSP} 8908} 8909 8910@Article{ automatic-ad, 8911 author = {Paul Hovland and Boyana Norris and Barry Smith}, 8912 title = {Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}}, 8913 year = {2005}, 8914 journal = {Future Generation Computer Systems}, 8915 volume = {21}, 8916 number = {8}, 8917 pages = {1426--1438}, 8918 petsc_uses = {KSP} 8919} 8920 8921@TechReport{ remote-math, 8922 author = {Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry 8923 Smith}, 8924 title = {Remote Access to Mathematical Software}, 8925 number = {ANL/MCS-P889-0601}, 8926 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 8927 month = jun, 8928 year = {2001}, 8929 url = {http://icm.mcs.kent.edu/research/iamc01proceedings.html}, 8930 petsc_uses = {KSP} 8931} 8932 8933@InProceedings{ gropp98, 8934 author = {William D. Gropp}, 8935 title = {Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, 8936 publisher = {SIAM}, 8937 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8938 Scientific and Engineering Computing}, 8939 year = {1999}, 8940 pages = {21-29}, 8941 petsc_uses = {KSP} 8942} 8943 8944@InProceedings{ knepleysarin99, 8945 author = {Matthew Knepley and Vivek Sarin}, 8946 title = {Algorithm Development for Large Scale Computing}, 8947 publisher = {SIAM}, 8948 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8949 Scientific and Engineering Computing}, 8950 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}}, 8951 year = {1999}, 8952 petsc_uses = {KSP} 8953} 8954 8955@InBook{ bgms00, 8956 author = {S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith}, 8957 chapter = {Software for the Scalable Solution of {PDEs}}, 8958 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z}, 8959 title = {CRPC Handbook of Parallel Computing}, 8960 editor = {J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon 8961 and A. White}, 8962 publisher = {Morgan Kaufmann Publishers}, 8963 year = {2002}, 8964 petsc_uses = {KSP} 8965} 8966 8967@InProceedings{ hovland_norris_smith98, 8968 author = {Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith}, 8969 title = {Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific 8970 Computations}, 8971 publisher = {SIAM}, 8972 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 8973 Scientific and Engineering Computing}, 8974 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z}, 8975 note = {also available as Argonne preprint ANL/MCS-P731-1098}, 8976 year = {1999}, 8977 pages = {129-137}, 8978 petsc_uses = {KSP} 8979} 8980 8981@InProceedings{ efficient, 8982 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 8983 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 8984 Libraries}, 8985 booktitle = {Modern Software Tools in Scientific Computing}, 8986 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 8987 publisher = {Birkhauser Press}, 8988 pages = {163--202}, 8989 year = {1997}, 8990 petsc_uses = {KSP} 8991} 8992 8993% url = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z" 8994@TechReport{ petsc-user-ref, 8995 author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Steven Benson and Jed 8996 Brown and Peter Brune and Kris Buschelman and Emil Constantinescu and Lisandro 8997 Dalcin and Alp Dener and Victor Eijkhout and Jacob Faibussowitsch and William~D. 8998 Gropp and V\'{a}clav Hapla and Tobin Isaac and Pierre Jolivet and Dmitry Karpeev 8999 and Dinesh Kaushik and Matthew~G. Knepley and Fande Kong and Scott Kruger and 9000 Dave~A. May and Lois Curfman McInnes and Richard Tran Mills and Lawrence Mitchell 9001 and Todd Munson and Jose~E. Roman and Karl Rupp and Patrick Sanan and Jason Sarich 9002 and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang and Junchao 9003 Zhang}, 9004 title = {{PETSc/TAO} Users Manual}, 9005 institution = {Argonne National Laboratory}, 9006 number = {ANL-21/39 - Revision 3.21}, 9007 doi = {10.2172/2205494}, 9008 year = {2024} 9009} 9010 9011% url = {https://petsc.org/release} 9012@TechReport{ petsc-developers, 9013 author = {Scott Kruger and Patrick Sanan and Barry~F. Smith}, 9014 title = {{PETS}c Developers Guide}, 9015 institution = {Argonne National Laboratory}, 9016 number = {ANL-18/18}, 9017 year = {2018}, 9018 url = {https://petsc.org/release/developers}, 9019 petsc_uses = {KSP} 9020} 9021 9022@Unpublished{ alice-memory-snooper, 9023 author = {Ibrahima Ba and Barry~F. Smith}, 9024 title = {The {ALICE} Memory Snooper}, 9025 year = {1999}, 9026 petsc_uses = {KSP} 9027} 9028 9029@TechReport{ petsc-user-ref-polish, 9030 author = {Marcin Bojko and Piotr Krzyzanowski}, 9031 title = {Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc}, 9032 institution = {Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski}, 9033 year = {1998}, 9034 note = {An introduction to PETSc in Polish}, 9035 petsc_uses = {KSP} 9036} 9037 9038@InProceedings{ abghmn00, 9039 title = {Integrating Automatic Differentiation with Object-Oriented Toolkits for 9040 High-Performance Scientific Computing}, 9041 author = {J. Abate and S. Benson and L. Grignon and P. Hovland and L. C. McInnes and B. 9042 Norris}, 9043 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z}, 9044 booktitle = {Automatic Differentiation of Algorithms: From Simulation to Optimization}, 9045 editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent 9046 Hasco\"{e}t and Uwe Naumann}, 9047 publisher = {Springer}, 9048 year = {2002}, 9049 petsc_uses = {KSP} 9050} 9051 9052@Unpublished{ petsc-mpi-paper, 9053 author = {Lois Curfman McInnes and Barry F. Smith}, 9054 title = {{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software 9055 Libraries}, 9056 note = {Proceedings of the MPI Developers Conference, Notre Dame, IN}, 9057 month = jun, 9058 year = {1995}, 9059 petsc_uses = {KSP} 9060} 9061 9062@InProceedings{ miss-paper, 9063 author = {William D. Gropp and Barry F. Smith}, 9064 title = {Scalable, Extensible, and Portable Numerical Libraries}, 9065 publisher = {IEEE}, 9066 year = {1994}, 9067 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 9068 address = {Mississippi State University}, 9069 pages = {87--93}, 9070 keyword = {numerical libraries, scientific computing, parallel computing}, 9071 petsc_uses = {KSP} 9072} 9073 9074@InProceedings{ snes-paper, 9075 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 9076 title = {Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained 9077 Minimization Problems}, 9078 publisher = {IEEE}, 9079 year = {1995}, 9080 booktitle = {Proceedings of the Scalable Parallel Libraries Conference}, 9081 address = {Mississippi State University}, 9082 pages = {60-67}, 9083 keyword = {nonlinear equations, optimization, superconductivity, parallel computing}, 9084 petsc_uses = {KSP} 9085} 9086 9087@Article{ dsneutral, 9088 author = {Barry F. Smith and William D. Gropp}, 9089 title = {The Design of Data-structure-neutral Libraries for the Iterative Solution of 9090 Sparse Linear Systems}, 9091 journal = {Scientific Programming}, 9092 volume = {5}, 9093 pages = {329--336}, 9094 key = {GroppSmith96 ! KSP design}, 9095 year = {1996}, 9096 petsc_uses = {KSP} 9097} 9098 9099@InProceedings{ bgms98, 9100 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 9101 title = {A Microkernel Design for Component-based Parallel Numerical Software Systems}, 9102 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 9103 Scientific and Engineering Computing}, 9104 publisher = {SIAM}, 9105 pages = {58-67}, 9106 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z}, 9107 year = {1998}, 9108 petsc_uses = {KSP} 9109} 9110 9111@Article{ hkm98, 9112 author = {M. E. Hayder and D. E. Keyes and P. Mehrotra}, 9113 title = {A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal 9114 {PDE} Computation}, 9115 journal = {Advances in Engineering Software}, 9116 volume = {29}, 9117 pages = {415-424}, 9118 year = {1998}, 9119 petsc_uses = {KSP} 9120} 9121 9122@TechReport{ pdpta99, 9123 author = {L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. 9124 Smith}, 9125 title = {Infrastructure and Interfaces for Large-Scale Numerical Software}, 9126 note = {to appear in the Proceedings of the 1999 International Conference on Parallel and 9127 Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las 9128 Vegas, Nevada}, 9129 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 9130 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z}, 9131 number = {ANL/MCS-P751-0599}, 9132 year = {1999}, 9133 petsc_uses = {KSP} 9134} 9135 9136@InProceedings{ bbh:com, 9137 author = {C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland}, 9138 title = {{On Combining Computational Differentiation and Toolkits for Parallel Scientific 9139 Computing}}, 9140 booktitle = {Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International 9141 Euro-Par Conference, Munich, Germany, August/September 2000}, 9142 year = {2000}, 9143 editor = {A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller}, 9144 volume = {1900}, 9145 series = {Lecture Notes in Computer Science}, 9146 pages = {86--94}, 9147 address = {Berlin}, 9148 publisher = {Springer}, 9149 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z}, 9150 petsc_uses = {KSP} 9151} 9152 9153@InProceedings{ overture00, 9154 author = {K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith}, 9155 title = { {PETSc and Overture}: Lessons Learned Developing an Interface between 9156 Components}, 9157 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z}, 9158 booktitle = {Proceedings of the International Federation for Information Processing Working 9159 Conference on Software Architectures for Scientific Computing, Kluwer}, 9160 year = {2000}, 9161 pages = {57--68}, 9162 petsc_uses = {KSP} 9163} 9164 9165@TechReport{ smith97, 9166 title = {An Interface for Efficient Vector Scatters and Gathers on Parallel Machines}, 9167 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z}, 9168 number = {ANL/MCS-P701}, 9169 author = {Barry F. Smith}, 9170 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 9171 petsc_uses = {KSP} 9172} 9173 9174@Article{ smith98, 9175 author = {Barry Smith}, 9176 title = {The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction}, 9177 journal = {SIGNUM Newsletter}, 9178 year = {1998}, 9179 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z}, 9180 petsc_uses = {KSP} 9181} 9182 9183@TechReport{ ad-petsc-tm, 9184 title = {Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of 9185 {PETSc}}, 9186 author = {Christian Bischof and Paul Hovland and Po-Ting Wu}, 9187 year = {1997}, 9188 type = {Technical Memorandum}, 9189 institution = {ANL}, 9190 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z}, 9191 number = {ANL/MCS-TM-233}, 9192 petsc_uses = {KSP} 9193} 9194 9195% LiteralHTML: 9196% LiteralHTML: <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3> 9197% LiteralHTML: 9198@PhDThesis{ klotzthesis2019, 9199 author = {Thomas S. Klotz}, 9200 title = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular 9201 Biology}, 9202 school = {Rice University}, 9203 year = {2019}, 9204 petsc_uses = {KSP} 9205} 9206 9207@Article{ klotzbardhanknepley2018, 9208 title = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling}, 9209 author = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley}, 9210 journal = {arXiv e-prints}, 9211 eprint = {1708.06028}, 9212 archiveprefix = {arXiv}, 9213 primaryclass = {math.na}, 9214 year = {2018}, 9215 note = {\url{http://arxiv.org/abs/1708.06028}}, 9216 petsc_uses = {KSP} 9217} 9218 9219@Misc{ brown2016, 9220 title = {Threading Tradeoffs in Domain Decomposition}, 9221 author = {Jed Brown}, 9222 note = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, 9223 \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}}, 9224 url = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}, 9225 year = {2016}, 9226 petsc_uses = {KSP} 9227} 9228 9229@Article{ changnakshatralaknepleyjohnsson2017, 9230 title = {A performance spectrum for parallel computational frameworks that solve {PDEs}}, 9231 author = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart 9232 Johnsson}, 9233 journal = {Concurency: Practice and Experience}, 9234 volume = {30}, 9235 number = {11}, 9236 eprint = {1705.03625}, 9237 doi = {10.1002/cpe.4401}, 9238 year = {2017}, 9239 petsc_uses = {KSP} 9240} 9241 9242@Article{ changfabienknepleymills2018, 9243 title = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} 9244 spectrum analysis}, 9245 author = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills}, 9246 journal = {SIAM Journal on Scientific Computing}, 9247 volume = {40}, 9248 number = {6}, 9249 pages = {C779--C802}, 9250 eprint = {1802.07832}, 9251 doi = {10.1137/18M1172260}, 9252 year = {2018}, 9253 petsc_uses = {KSP} 9254} 9255 9256@Article{ joshaghanichangnakshatralaknepley2019, 9257 title = {Composable solvers for the four-field double porosity/permeability model}, 9258 author = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. 9259 Knepley}, 9260 journal = {Journal of Computational Physics}, 9261 volume = {386}, 9262 pages = {428--466}, 9263 doi = {10.1016/j.jcp.2019.02.020}, 9264 year = {2019}, 9265 petsc_uses = {KSP} 9266} 9267 9268@InProceedings{ barralknepleylangepiggottgorman2016, 9269 title = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}}, 9270 author = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott 9271 and Gerard J. Gorman}, 9272 booktitle = {25th International Meshing Roundtable}, 9273 editor = {Steve Owen and Hang Si}, 9274 month = sep, 9275 address = {Washington, DC}, 9276 pages = {1--5}, 9277 url = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf}, 9278 year = {2016}, 9279 petsc_uses = {KSP} 9280} 9281 9282@Article{ adamsbrownknepleysamtaney2016, 9283 title = {Segmental Refinement: A Multigrid Technique for Data Locality}, 9284 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney}, 9285 journal = {SIAM Journal on Scientific Computing}, 9286 url = {http://epubs.siam.org/toc/sjoce3/38/4 }, 9287 epub = {http://arxiv.org/abs/1406.7808}, 9288 volume = {8}, 9289 number = {4}, 9290 pages = {C426--C440}, 9291 doi = {10.1137/140975127}, 9292 year = {2016}, 9293 petsc_uses = {KSP} 9294} 9295 9296@InProceedings{ maysananruppknepleysmith2016, 9297 title = {Extreme-Scale Multigrid Components within {PETSc}}, 9298 author = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. 9299 Smith}, 9300 booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}}, 9301 series = {PASC '16}, 9302 isbn = {978-1-4503-4126-4}, 9303 location = {Lausanne, Switzerland}, 9304 pages = {5:1--5:12}, 9305 articleno = {5}, 9306 numpages = {12}, 9307 doi = {10.1145/2929908.2929913}, 9308 acmid = {2929913}, 9309 publisher = {ACM}, 9310 address = {New York, NY, USA}, 9311 keywords = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, 9312 preconditioning}, 9313 year = {2016}, 9314 petsc_uses = {KSP} 9315} 9316 9317@Article{ liu2015field, 9318 title = {Field-Split Preconditioned Inexact Newton Algorithms}, 9319 author = {Lulu Liu and David E Keyes}, 9320 journal = {SIAM Journal on Scientific Computing}, 9321 volume = {37}, 9322 number = {3}, 9323 pages = {A1388--A1409}, 9324 year = {2015}, 9325 publisher = {SIAM}, 9326 petsc_uses = {KSP} 9327} 9328 9329@Article{ lujiaomissirlis2014, 9330 title = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers}, 9331 author = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis}, 9332 journal = {Numerical Linear Algebra with Applications}, 9333 volume = {21}, 9334 number = {2}, 9335 pages = {221--238}, 9336 year = {2014}, 9337 publisher = {Wiley Online Library}, 9338 petsc_uses = {KSP} 9339} 9340 9341@Article{ badiamartinprincipe2013, 9342 title = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and 9343 solid mechanics}, 9344 author = {Santiago Badia and Alberto F. Mart\'in and Javier Principe}, 9345 journal = {International Journal for Numerical Methods in Engineering}, 9346 volume = {96}, 9347 number = {4}, 9348 pages = {203--230}, 9349 year = {2013}, 9350 petsc_uses = {KSP} 9351} 9352 9353@Article{ morganknepleysananscott2016, 9354 title = {A Stochastic Performance Model for Pipelined {Krylov} Methods}, 9355 author = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott}, 9356 journal = {Concurrency and Computation: Practice and Experience}, 9357 volume = {28}, 9358 pages = {4532--4542}, 9359 year = {2016}, 9360 url = {http://arxiv.org/abs/1602.04873}, 9361 doi = {10.1002/cpe.3820}, 9362 petsc_uses = {KSP} 9363} 9364 9365@Article{ morgansananknepleymills2020, 9366 title = {Understanding performance variability in standard and pipelined parallel {Krylov} 9367 solvers}, 9368 author = {Hannah Morgan and Patrick Sanan and Matthew G. Knepley and Richard Tran Mills}, 9369 journal = {The International Journal of High Performance Computing Applications}, 9370 volume = {35}, 9371 issue = {1}, 9372 doi = {10.1177/1094342020966835}, 9373 url = {https://doi.org/10.1177/1094342020966835}, 9374 eprint = {https://doi.org/10.1177/1094342020966835}, 9375 year = {2020}, 9376 petsc_uses = {KSP} 9377} 9378 9379@Article{ msz2013, 9380 title = {Efficient Sparse Matrix-Matrix Products Using Colorings}, 9381 author = {M. McCourt and B. F. Smith and H. Zhang}, 9382 journal = {SIAM Journal on Matrix Analysis and Applications}, 9383 year = {2015}, 9384 note = {To appear}, 9385 petsc_uses = {KSP} 9386} 9387 9388@Article{ bassi2014agglomeration, 9389 title = {Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh 9390 free}, 9391 author = {Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro}, 9392 journal = {Mathematical Models and Methods in Applied Sciences}, 9393 volume = {24}, 9394 number = {08}, 9395 pages = {1495--1539}, 9396 year = {2014}, 9397 publisher = {World Scientific}, 9398 petsc_uses = {KSP} 9399} 9400 9401@Article{ jhuranidemkowicz12, 9402 author = {{Jhurani}, C. and {Demkowicz}, L.}, 9403 title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. 9404 Part II: Algorithms for the Moore-Penrose pseudoinverse}}, 9405 journal = {Computer Methods in Applied Mechanics and Engineering}, 9406 volume = {213}, 9407 pages = {418-426}, 9408 year = {2012}, 9409 month = mar, 9410 doi = {10.1016/j.cma.2011.06.003}, 9411 adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}, 9412 petsc_uses = {KSP} 9413} 9414 9415@Article{ yangcai11, 9416 author = {Yang, Haijian and Cai, Xiao-Chuan}, 9417 title = {Parallel Two-Grid Semismooth {N}ewton--{K}rylov--{S}chwarz Method for Nonlinear 9418 Complementarity Problems}, 9419 journal = {J. Sci. Comput.}, 9420 issue_date = {May 2011}, 9421 volume = {47}, 9422 number = {2}, 9423 month = may, 9424 pages = {258--280}, 9425 year = {2011}, 9426 issn = {0885-7474}, 9427 numpages = {23}, 9428 doi = {10.1007/s10915-010-9436-4}, 9429 acmid = {1971246}, 9430 publisher = {Plenum Press}, 9431 address = {New York, NY, USA}, 9432 keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz 9433 preconditioners, Semismooth Newton, Two-level methods}, 9434 petsc_uses = {KSP} 9435} 9436 9437@Article{ rheinbach09, 9438 author = {Rheinbach, Oliver}, 9439 title = {Parallel Iterative Substructuring in Structural Mechanics}, 9440 journal = {Archives of Computational Methods in Engineering}, 9441 volume = {16}, 9442 number = {4}, 9443 pages = {425-463}, 9444 year = {2009}, 9445 issn = {1134-3060}, 9446 doi = {10.1007/s11831-009-9035-4}, 9447 publisher = {Springer Netherlands}, 9448 language = {English}, 9449 petsc_uses = {KSP} 9450} 9451 9452@Article{ knepleyterrel2013, 9453 author = {Matthew G. Knepley and Andy R. Terrel}, 9454 title = {Finite Element Integration on {GPUs}}, 9455 journal = {{ACM} Transactions on Mathematical Software}, 9456 volume = {39}, 9457 number = {2}, 9458 accepted = {17 April 2012}, 9459 year = {2013}, 9460 abstract = {We present a novel finite element integration method for low order elements on 9461 GPUs. We achieve more than 100GF for element integration on first order 9462 discretizations of both the Laplacian and Elasticity operators on an NVIDIA 9463 GTX285, which has a nominal single precision peak flop rate of 1 TF/s and 9464 bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.}, 9465 url = {http://arxiv.org/abs/1103.0066}, 9466 note = {no. 10, \url{http://arxiv.org/abs/1103.0066}}, 9467 petsc_uses = {KSP} 9468} 9469 9470@Article{ knepleyruppterrel2016, 9471 title = {Finite Element Integration with Quadrature on the GPU}, 9472 journal = {ArXiv e-prints}, 9473 author = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel}, 9474 version = {1}, 9475 date = {2016-07-14}, 9476 eprinttype = {arxiv}, 9477 eprintclass = {cs.MS}, 9478 eprint = {1607.04245v1}, 9479 petsc_uses = {KSP} 9480} 9481 9482@Article{ klawonnlanserrheinbach2014, 9483 title = {Nonlinear {FETI-DP} and {BDDC} Methods}, 9484 author = {Axel Klawonn and Martin Lanser and Oliver Rheinbach}, 9485 journal = {SIAM Journal on Scientific Computing}, 9486 volume = {36}, 9487 number = {2}, 9488 pages = {A737--A765}, 9489 year = {2014}, 9490 petsc_uses = {KSP} 9491} 9492 9493@Article{ bruneknepleysmithtu15, 9494 title = {Composing Scalable Nonlinear Algebraic Solvers}, 9495 author = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu}, 9496 journal = {SIAM Review}, 9497 volume = {57}, 9498 number = {4}, 9499 pages = {535--565}, 9500 note = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}}, 9501 url = {http://www.mcs.anl.gov/papers/P2010-0112.pdf}, 9502 doi = {10.1137/130936725}, 9503 year = {2015}, 9504 petsc_uses = {KSP} 9505} 9506 9507@Article{ mszm2014, 9508 title = {Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing}, 9509 author = {Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills}, 9510 volume = {40}, 9511 pages = {17--31}, 9512 year = {2014}, 9513 journal = {Parallel Computing}, 9514 doi = {10.1016/j.parco.2013.10.001}, 9515 petsc_uses = {KSP} 9516} 9517 9518@TechReport{ mszm2012, 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 year = {2012}, 9522 number = {ANL/MCS-P2097-0512}, 9523 institution = {Argonne National Laboratory}, 9524 petsc_uses = {KSP} 9525} 9526 9527@InProceedings{ bkmms2012, 9528 author = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry 9529 F. Smith}, 9530 title = {Composable linear solvers for multiphysics}, 9531 booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed 9532 Computing} ({ISPDC} 2012)}, 9533 year = {2012}, 9534 doi = {10.1109/ISPDC.2012.16}, 9535 publisher = {IEEE Computer Society}, 9536 pages = {55--62}, 9537 petsc_uses = {KSP} 9538} 9539 9540@Article{ bourdinbucuroudet2009, 9541 author = {Blaise Bourdin and D. Bucur and E. Oudet}, 9542 title = {Optimal Partitions for Eigenvalues}, 9543 journal = {SIAM J. Sci. Comput.}, 9544 volume = {31}, 9545 number = {6}, 9546 pages = {4100--4114}, 9547 year = {2009}, 9548 petsc_uses = {KSP} 9549} 9550 9551@InBook{ kimnbourdin2007, 9552 author = {J.-H. Kimn and Blaise Bourdin}, 9553 title = {Numerical implementation of overlapping balancing domain decomposition methods on 9554 unstructured meshes}, 9555 editor = {O. B. Widlund and D. E. Keyes}, 9556 booktitle = {Domain Decomposition Methods in Science and Engineering XVI}, 9557 series = {Lecture Notes in Computational Science and Engineering}, 9558 number = {55}, 9559 publisher = {Springer-Verlag}, 9560 pages = {309--315}, 9561 url = {http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf}, 9562 year = {2007}, 9563 petsc_uses = {KSP} 9564} 9565 9566@Article{ bjm2005, 9567 author = {AH Baker and ER Jessup and T Manteuffel}, 9568 title = {A Technique for Accelerating the Convergence of Restarted GMRES}, 9569 journal = {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS}, 9570 year = {2005}, 9571 petsc_uses = {KSP} 9572} 9573 9574@Unpublished{ sundar-2008a, 9575 author = {R.S. Sampath and G. Biros}, 9576 title = {A parallel geometric multigrid method for finite elements on octree meshes}, 9577 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9578 petsc_uses = {KSP} 9579} 9580 9581@Article{ sundar-2008, 9582 author = {H. Sundar and R.S. Sampath and G. Biros}, 9583 title = {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel}, 9584 journal = {SIAM Journal on Scientific Computing}, 9585 year = {2008}, 9586 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9587 petsc_uses = {KSP} 9588} 9589 9590@InProceedings{ sundar-2007, 9591 author = {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros}, 9592 title = {Low-constant parallel algorithms for finite element simulations using linear 9593 octrees}, 9594 booktitle = {SC'07: ACM/IEEE Conference on Supercomputing}, 9595 year = {2007}, 9596 url = {http://www.seas.upenn.edu/\~{ }rahulss}, 9597 petsc_uses = {KSP} 9598} 9599 9600@InProceedings{ adams-98a, 9601 author = {Adams, Mark ~F.}, 9602 title = {A Parallel Maximal Independent Set Algorithm}, 9603 booktitle = {Proceedings 5th copper mountain conference on iterative methods}, 9604 year = {1998}, 9605 petsc_uses = {KSP} 9606} 9607 9608@Article{ akcelik2005ddd, 9609 title = {{Dynamic data-driven inversion for terascale simulations: real-time 9610 identification of airborne contaminants}}, 9611 author = {Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and 9612 van Bloemen Waanders, B.}, 9613 journal = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, 9614 year = {2005}, 9615 publisher = {IEEE Computer Society Washington, DC, USA}, 9616 petsc_uses = {KSP} 9617} 9618 9619@InBook{ akcelik-2006, 9620 author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van 9621 Bloemen Waanders}, 9622 bookeditor = {M. Heroux and P. Raghaven and H. Simon}, 9623 title = {Frontiers of Parallel Computing}, 9624 chapter = {Parallel algorithms for {PDE}-constrained optimization}, 9625 publisher = {SIAM}, 9626 year = {2006}, 9627 petsc_uses = {KSP} 9628} 9629 9630@Article{ dt, 9631 author = {Matthew F. Dixon and C. J. Kenneth Tan}, 9632 title = {Using Distributed Computers to Deterministically Approximate Higher Dimensional 9633 Convection Diffusion Equations}, 9634 journal = {The Journal of Supercomputing}, 9635 year = {2004}, 9636 pages = {235--253}, 9637 volume = {28}, 9638 url = {http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1}, 9639 petsc_uses = {KSP} 9640} 9641 9642@PhDThesis{ hwang2004, 9643 author = {Feng-Nan Hwang}, 9644 title = {Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in 9645 Computational Fluid Dynamics}, 9646 school = {University of Colorado at Boulder}, 9647 year = {2004}, 9648 petsc_uses = {KSP} 9649} 9650 9651@PhDThesis{ baker, 9652 author = {{A. H.} Baker}, 9653 title = {On improving the performance of the linear solver restarted {GMRES}}, 9654 school = {University of Colorado at Boulder}, 9655 year = {2003}, 9656 petsc_uses = {KSP} 9657} 9658 9659@TechReport{ klawonnrheinbach601, 9660 author = {Axel Klawonn and Oliver Rheinbach}, 9661 title = {A Parallel Implementation of Dual-Primal {FETI-DP} Methods for Three Dimensional 9662 Linear Elasticity Using a Transformation of Basis}, 9663 institution = {Universit\"at Duisburg-Essen}, 9664 year = {2005}, 9665 type = {Technical Report}, 9666 number = {SM-E-601}, 9667 petsc_uses = {KSP} 9668} 9669 9670@TechReport{ klawonnrheinbach609, 9671 author = {Axel Klawonn and Oliver Rheinbach}, 9672 title = {Inexact FETI-DP Methods}, 9673 institution = {Universit\"at Duisburg-Essen}, 9674 year = {2005}, 9675 type = {Technical Report}, 9676 number = {SM-E-609}, 9677 petsc_uses = {KSP} 9678} 9679 9680@TechReport{ klawonnrheinbach607, 9681 author = {Axel Klawonn and Oliver Rheinbach}, 9682 title = {Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems}, 9683 institution = {Universit\"at Duisburg-Essen}, 9684 year = {2005}, 9685 type = {Technical Report}, 9686 number = {SM-E-607}, 9687 petsc_uses = {KSP} 9688} 9689 9690@Article{ kul-natraj-pbp, 9691 author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung}, 9692 title = {Performance of a parallel mixed finite element implementation for fourth order 9693 clamped anisotropic plate bending problems in distributed memory environments}, 9694 journal = {Applied Mathematics and Computation}, 9695 volume = {155}, 9696 year = {2004}, 9697 number = {3}, 9698 pages = {753--777}, 9699 petsc_uses = {KSP} 9700} 9701 9702@Article{ bramkamp2006uej, 9703 author = {F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch}, 9704 title = {Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method}, 9705 journal = {Computers \& Fluids}, 9706 volume = {35}, 9707 number = {10}, 9708 pages = {1063--1073}, 9709 doi = {10.1016/j.compfluid.2005.10.003}, 9710 abstract = {In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the 9711 derivation of the analytic flux Jacobian can become quite complicated depending on 9712 the complexity of the numerical flux calculation. Practically, the derivation of 9713 the exact Jacobian by hand is an unrealistic option because of the enormous 9714 man-hour investment needed. In this work, automatic differentiation is used to 9715 evaluate the exact Jacobian of upwind schemes implemented in the flow solver 9716 QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically 9717 approximated by first-order forward differences. For a two-dimensional airfoil 9718 under three different flight conditions (quasi-incompressible flow, compressible 9719 subsonic flow, and transonic flow), we show that the robustness and performance of 9720 the present finite volume scheme is significantly improved by using exact 9721 Jacobians.}, 9722 year = {2006}, 9723 petsc_uses = {KSP} 9724} 9725 9726@Article{ shahbazi1, 9727 author = {Khosro Shahbazi}, 9728 title = {An explicit expression for the penalty parameter of the interior penalty method}, 9729 journal = {Journal of Computational Physics}, 9730 volume = {205}, 9731 year = {2005}, 9732 pages = {401--407}, 9733 petsc_uses = {KSP} 9734} 9735 9736@TechReport{ kk, 9737 title = {A Parallel Lanczos Algorithm for Eigensystem Calculation}, 9738 author = {Hans-Peter Kersken and Uwe Kuster}, 9739 year = {1999}, 9740 institution = {University of Stuttgart}, 9741 url = {http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf}, 9742 number = {310}, 9743 petsc_uses = {KSP} 9744} 9745 9746@Article{ miha-mija, 9747 author = {M. D. Mihajlovi and S. Mijalkovi}, 9748 title = {A component decomposition preconditioning for 3D stress analysis problems}, 9749 journal = {Numerical Linear Algebra with Applications}, 9750 volume = {9}, 9751 year = {2002}, 9752 pages = {567--583}, 9753 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}, 9754 petsc_uses = {KSP} 9755} 9756 9757@Article{ bjm, 9758 author = {M Benzi and W Joubert and G Mateescu}, 9759 journal = {Electronic Transactions on Numerical Analysis}, 9760 year = {1999}, 9761 volume = {8}, 9762 pages = {88--114}, 9763 title = {Numerical experiments with parallel orderings for {ILU} preconditioners}, 9764 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}, 9765 petsc_uses = {KSP} 9766} 9767 9768@PhDThesis{ hyde, 9769 author = {EMK Hyde}, 9770 title = {Fast, High-Order Methods for Scattering by Inhomogeneous Media}, 9771 school = {Caltech}, 9772 year = {2003}, 9773 url = {http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf}, 9774 petsc_uses = {KSP} 9775} 9776 9777@Article{ km2003, 9778 author = {A. Keese and H. G. Matthies}, 9779 journal = {Proceedings in Applied Mathematics and Mechanics}, 9780 year = {2003}, 9781 volume = {2}, 9782 pages = {485--486}, 9783 title = {Parallel Solution of Stochastic PDEs}, 9784 url = {http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT}, 9785 petsc_uses = {KSP} 9786} 9787 9788@Article{ whszss, 9789 author = {Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld 9790 and Otmar Scherzer and H. Siegfried Stiehl}, 9791 journal = {Real Time Imaging}, 9792 year = {2001}, 9793 volume = {7}, 9794 pages = {31--45}, 9795 title = {Fast parallel algorithms for a broad class of nonlinear variational diffusion 9796 approaches}, 9797 url = {http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz}, 9798 petsc_uses = {KSP} 9799} 9800 9801@TechReport{ baker1, 9802 title = {An Efficient Block Variant of GMRES}, 9803 author = {A. H. Baker and J. M. Dennis and E. R. Jessup}, 9804 year = {2003}, 9805 type = {Technical Report}, 9806 institution = {University of Colorado, Boulder}, 9807 url = {http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf}, 9808 number = {CU-CS-957-03}, 9809 petsc_uses = {KSP} 9810} 9811 9812@InProceedings{ mc2003, 9813 author = {Leszek Marcinkowski and Xiao-Chuan Cai}, 9814 title = {Parallel Performance of Some Two-Level {ASPIN} Algorithms}, 9815 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9816 Methods}, 9817 pages = {639--646}, 9818 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9819 note = {}, 9820 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9821 year = {2003}, 9822 petsc_uses = {KSP} 9823} 9824 9825@InProceedings{ kt2003, 9826 author = {Deepak V. Kulkarni and Daniel A. Tortorelli}, 9827 title = {A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems}, 9828 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9829 Methods}, 9830 pages = {615--622}, 9831 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9832 note = {}, 9833 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9834 year = {2003}, 9835 petsc_uses = {KSP} 9836} 9837 9838@InProceedings{ krw2003, 9839 author = {Axel Klawonn and Oliver Rheinbach and Olof B. Widlund}, 9840 title = {Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 9841 3D}, 9842 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9843 Methods}, 9844 pages = {361--368}, 9845 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9846 note = {}, 9847 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9848 year = {2003}, 9849 petsc_uses = {KSP} 9850} 9851 9852@InProceedings{ hc2003, 9853 author = {Feng-Nan Hwang and Xiao-Chuan Cai}, 9854 title = {Improving Robustness and Parallel Scalability of {Newton's} Method Through 9855 Nonlinear Preconditioning}, 9856 booktitle = {Proceedings of the 15th International Conference on Domain Decomposition 9857 Methods}, 9858 pages = {201--208}, 9859 publisher = {Springer, Lecture Notes in Computational Science and Engineering (LNCSE).}, 9860 note = {}, 9861 url = {http://www.ddm.org/DD15/proceedings-dd15.html}, 9862 year = {2003}, 9863 petsc_uses = {KSP} 9864} 9865 9866@InProceedings{ g2003, 9867 author = {P. Goldfeld}, 9868 title = {Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and 9869 (Generalized) {Stokes} and Parallel Implementation}, 9870 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9871 Methods}, 9872 pages = {209--216}, 9873 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9874 publisher = {National Autonomous University of Mexico (UNAM)}, 9875 note = {}, 9876 url = {http://www.ddm.org/DD14}, 9877 year = {2003}, 9878 petsc_uses = {KSP} 9879} 9880 9881@InProceedings{ dhv2003, 9882 author = {Zdenek Dostal and David Horak and Oldrich Vlach}, 9883 title = {Toward scalable {FETI} algorithm for variational inequalities with applications to 9884 composites}, 9885 booktitle = {Proceedings of the 14th International Conference on Domain Decomposition 9886 Methods}, 9887 pages = {395--401}, 9888 editor = {I. Herrera and D. Keyes and O. Widlund and R. Yates}, 9889 publisher = {National Autonomous University of Mexico (UNAM)}, 9890 note = {}, 9891 url = {http://www.ddm.org/DD14}, 9892 year = {2003}, 9893 petsc_uses = {KSP} 9894} 9895 9896@InProceedings{ dhsv2002, 9897 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 9898 title = {Scalabilities of {FETI} for variational inequalities and contact shape 9899 optimization}, 9900 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9901 Methods}, 9902 pages = {359--367}, 9903 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9904 publisher = {CIMNE, Barcelona, Spain}, 9905 note = {}, 9906 url = {http://www.ddm.org/DD13}, 9907 year = {2002}, 9908 petsc_uses = {KSP} 9909} 9910 9911@InProceedings{ cky2002, 9912 author = {Xiao-Chuan Cai and David E. Keyes and David P. Young}, 9913 title = {A Nonlinear Additive {S}chwarz Preconditioned Inexact {N}ewton Method for Shocked 9914 Duct Flows}, 9915 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 9916 Methods}, 9917 pages = {343--350}, 9918 editor = {N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov}, 9919 publisher = {CIMNE, Barcelona, Spain}, 9920 note = {}, 9921 url = {http://www.ddm.org/DD13}, 9922 year = {2002}, 9923 petsc_uses = {KSP} 9924} 9925 9926@Conference{ li-etal:03, 9927 author = {Li, Z. and Lanteri S. and Saad, Y.}, 9928 title = {Multiplicative-additive preconditioning combination for general sparse linear 9929 systems}, 9930 booktitle = {2003 International Conference on Preconditioning Techniques for Large Sparse 9931 Matrix Problems in Scientific and Industrial Applications}, 9932 address = {Napa, California, USA}, 9933 date = {october 27-29}, 9934 year = {2003}, 9935 petsc_uses = {KSP} 9936} 9937 9938@Article{ bashir2008hessian, 9939 title = {Hessian-based model reduction for large-scale systems with initial-condition 9940 inputs}, 9941 author = {Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, 9942 J.}, 9943 journal = {International journal for numerical methods in engineering}, 9944 volume = {73}, 9945 number = {6}, 9946 pages = {844--868}, 9947 year = {2008}, 9948 publisher = {Wiley Online Library}, 9949 petsc_uses = {KSP} 9950} 9951 9952@Article{ bashir2007hessian, 9953 title = {Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems}, 9954 author = {Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, 9955 K.}, 9956 journal = {Computational Science--ICCS 2007}, 9957 pages = {1010--1017}, 9958 year = {2007}, 9959 publisher = {Springer}, 9960 petsc_uses = {KSP} 9961} 9962 9963@Article{ akcelik2011fast, 9964 title = {Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear 9965 inverse problems based on low-rank partial {H}essian approximations}, 9966 author = {Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen 9967 Waanders, B. and Wilcox, L.}, 9968 journal = {SIAM Journal on Scientific Computing}, 9969 volume = {33}, 9970 number = {1}, 9971 year = {2011}, 9972 petsc_uses = {KSP} 9973} 9974 9975@InProceedings{ ff2003, 9976 author = {Abul K. M. Fahimuddin and Heike Fassbender}, 9977 title = {Model Reduction for Large Scale Applications in Microsystem Technology}, 9978 booktitle = {Proceedings of the 2004 SIAM Parallel Processing Conference}, 9979 year = {2003}, 9980 petsc_uses = {KSP} 9981} 9982 9983@InProceedings{ d2b2004, 9984 author = {Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost}, 9985 title = {Parallel Computation of a Fully Implicit Finite Volume Method Using Different 9986 Ordering Strategies}, 9987 booktitle = {Proceedings of AIAA Conference, Reno, Nevada}, 9988 year = {2004}, 9989 petsc_uses = {KSP} 9990} 9991 9992@InProceedings{ d2v2005, 9993 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 9994 title = {A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid 9995 Flow Equations}, 9996 booktitle = {The 13th Annual Conference on Computational Fluid Dynamics}, 9997 year = {2005}, 9998 petsc_uses = {KSP} 9999} 10000 10001@InProceedings{ dvs2006, 10002 author = {Masoud Darbandi and Soheyl Vakili and Gerry E. Schneider}, 10003 title = {The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit 10004 Mixed Convection Equations}, 10005 booktitle = { The 44th AIAA Aerospace Sciences Meeting and Exhibit}, 10006 year = {2006}, 10007 petsc_uses = {KSP} 10008} 10009 10010@Article{ dsv2006, 10011 author = {Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili}, 10012 title = {Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid 10013 Flow Equations}, 10014 journal = {Computational Fluid Dynamics}, 10015 year = {2006}, 10016 volume = {15}, 10017 number = {1}, 10018 petsc_uses = {KSP} 10019} 10020 10021@Article{ lahaye03, 10022 author = {Lahaye, D. and Vandewalle, S. and Hameyer, K.}, 10023 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 10024 journal = {J. Comput. Appl. Math.}, 10025 year = {2004}, 10026 pages = {267--275}, 10027 volume = {168}, 10028 petsc_uses = {KSP} 10029} 10030 10031@TechReport{ brmn, 10032 title = {Faster {PDE}-based Simulations Using Robust Composite Linear Solvers}, 10033 author = {S. Bhowmick and P. Raghavan and L. McInnes and B. Norris}, 10034 year = {2002}, 10035 type = {Technical Report}, 10036 institution = {ANL}, 10037 number = {ANL/MCS-P993-0902}, 10038 note = {To appear in Future Generation Computer Systems}, 10039 petsc_uses = {KSP} 10040} 10041 10042@InProceedings{ mnbr, 10043 author = {L. McInnes and B. Norris and S. Bhowmick and P. Raghavan}, 10044 title = {Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} 10045 Algorithms}, 10046 booktitle = {Proceedings of the Second MIT Conference on Computational Fluid and Solid 10047 Mechanics}, 10048 year = {2003}, 10049 petsc_uses = {KSP} 10050} 10051 10052@InProceedings{ bmnr, 10053 author = {S. Bhowmick and L. McInnes and B. Norris and P. Raghavan}, 10054 title = {The Role of Multi-Method Linear Solvers in {PDE}-based Simulations}, 10055 booktitle = {Proceedings of the 2003 International Conference on Computational Science and its 10056 Applications, Lecture notes in Computer Science 2677}, 10057 editor = {V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer}, 10058 pages = {828--839}, 10059 year = {2003}, 10060 petsc_uses = {KSP} 10061} 10062 10063@Article{ ph03, 10064 author = {M. Pernice and R. D. Hornung}, 10065 title = {Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids}, 10066 journal = {Computing and Visualization in Science}, 10067 year = {2003}, 10068 lab = {LANL}, 10069 petsc_uses = {KSP} 10070} 10071 10072@Article{ adams-02, 10073 author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S}, 10074 journal = {J. Comp. Phys.}, 10075 number = {2}, 10076 pages = {593-610}, 10077 title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel}, 10078 volume = {188}, 10079 year = {2003}, 10080 petsc_uses = {KSP} 10081} 10082 10083@InProceedings{ adams2001distributed, 10084 title = {A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid 10085 smoothers}, 10086 author = {Adams, M.F.}, 10087 booktitle = {Supercomputing, ACM/IEEE 2001 Conference}, 10088 pages = {14--14}, 10089 year = {2001}, 10090 organization = {IEEE}, 10091 petsc_uses = {KSP} 10092} 10093 10094@PhDThesis{ els01, 10095 author = {Ulrich Elsner}, 10096 title = {Static and Dynamic Graph Partitioning. A comparative study of existing 10097 algorithms}, 10098 school = {Technical University Chemnitz}, 10099 year = {2002}, 10100 publisher = {Logos Verlag, Berlin}, 10101 isbn = {3-89722-923-4}, 10102 annote = {Uses PETSc's high quality parallel algorithms to provide a framework to compare 10103 different graph partitioning algorithms}, 10104 petsc_uses = {KSP} 10105} 10106 10107@TechReport{ ckk02, 10108 title = {Pseudo-Transient Continuation and Differential-Algebraic Equations}, 10109 author = {Todd S. Coffey and C. T. Kelley and David E. Keyes}, 10110 year = {2002}, 10111 type = {Technical Report}, 10112 institution = {ODU}, 10113 url = {http://www.math.odu.edu/\~{ }keyes}, 10114 note = {Submitted to the special issue of the SIAM Journal of Scientific Computing 10115 dedicated to papers from the 2002 Copper Mountain Conference on Iterative 10116 Methods}, 10117 petsc_uses = {KSP} 10118} 10119 10120@Article{ gpw2002, 10121 title = {Balancing Neumann-Neumann Preconditioners for Mixed Approximations of 10122 Heterogeneous Problems in Linear Elasticity}, 10123 author = {Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund}, 10124 year = {2003}, 10125 pages = {283--324}, 10126 volume = {95}, 10127 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf}, 10128 journal = {Numerische Mathematik}, 10129 petsc_uses = {KSP} 10130} 10131 10132@Article{ dh1, 10133 title = {Scalability and FETI based algorithm for large discretized variational 10134 inequalities}, 10135 author = {Z Dostal and D Horak}, 10136 year = {2003}, 10137 pages = {347--357}, 10138 volume = {61}, 10139 url = {http://portal.acm.org/citation.cfm?id=770222.770239}, 10140 journal = {Mathematics and Computers in Simulation}, 10141 petsc_uses = {KSP} 10142} 10143 10144@InProceedings{ dhsv1, 10145 author = {Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak}, 10146 url = {http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf}, 10147 title = {36 Scalabilities of {FETI} for Variational Inequalities and Contact Shape 10148 Optimization}, 10149 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 10150 Methods}, 10151 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10152 Kuznetsov}, 10153 petsc_uses = {KSP} 10154} 10155 10156@Article{ lahaye02, 10157 author = {Domenico Lahaye and S. Vandewalle and K. Hameyer}, 10158 title = {An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems}, 10159 journal = {IEEEMAGN}, 10160 year = {2002}, 10161 volume = {38}, 10162 number = {2}, 10163 pages = {413-416}, 10164 petsc_uses = {KSP} 10165} 10166 10167@Article{ ckm01, 10168 author = {X.-C. Cai and D. E. Keyes and L. Marcinkowski}, 10169 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps}, 10170 title = {Nonlinear additive {Schwarz} preconditioners and applications in computational 10171 fluid dynamics}, 10172 journal = {International Journal of Numerical Methods in Fluid Mechanics}, 10173 year = {2002}, 10174 volume = {40}, 10175 pages = {1463--1470}, 10176 petsc_uses = {KSP} 10177} 10178 10179@InProceedings{ cky01, 10180 author = {X.-C. Cai and D. E. Keyes and D. P. Young}, 10181 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps}, 10182 title = {A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked 10183 duct flow}, 10184 booktitle = {Proceedings of the 13th International Conference on Domain Decomposition 10185 Methods}, 10186 editor = { N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. 10187 Kuznetsov}, 10188 year = {2002}, 10189 petsc_uses = {KSP} 10190} 10191 10192@Article{ ck02, 10193 author = {X.-C. Cai and D. E. Keyes}, 10194 url = {http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps}, 10195 title = {Nonlinearly preconditioned inexact {Newton} algorithms}, 10196 journal = {SIAM J. Sci. Comput.}, 10197 year = {2002}, 10198 pages = {183--200}, 10199 volume = {24}, 10200 petsc_uses = {KSP} 10201} 10202 10203@Article{ c04, 10204 author = {Feng-Nan Hwang and X.-C. Cai}, 10205 url = {http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf}, 10206 title = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm 10207 for incompressible {Navier-Stokes} equations}, 10208 journal = {Journal of Computational Physics}, 10209 year = {2005}, 10210 volume = {204}, 10211 pages = {666--691}, 10212 petsc_uses = {KSP} 10213} 10214 10215@Article{ hc06, 10216 author = {Feng-Nan Hwang and X.-C. Cai}, 10217 url = {http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf}, 10218 title = {A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} 10219 Algorithms}, 10220 journal = {Computer Methods in Applied Mechanics and Engineering}, 10221 year = {2006}, 10222 volume = {196}, 10223 pages = {1603--1611}, 10224 petsc_uses = {KSP} 10225} 10226 10227@InProceedings{ adams-01, 10228 author = {Mark F. Adams}, 10229 title = {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid 10230 Smoothers}, 10231 booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing}, 10232 address = {Denver, Colorado}, 10233 month = nov, 10234 year = {2001}, 10235 petsc_uses = {KSP} 10236} 10237 10238@Book{ 1dl, 10239 author = {Domenico Lahaye}, 10240 title = {Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field 10241 Computations}, 10242 year = {2001}, 10243 publisher = {Katholieke Universiteit Leuven}, 10244 notes = {Thesis}, 10245 petsc_uses = {KSP} 10246} 10247 10248@Article{ adams-00, 10249 author = {Adams, M.~F.}, 10250 journal = {International Journal for Numerical Methods in Engineering}, 10251 number = {8}, 10252 pages = {1241-1262}, 10253 title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large 10254 Deformation Elasticity and Plasticity}, 10255 volume = {48}, 10256 year = {2000}, 10257 petsc_uses = {KSP} 10258} 10259 10260@Article{ adams2002evaluation, 10261 author = {Adams, M.~F.}, 10262 journal = {International Journal for Numerical Methods in Engineering}, 10263 number = {1}, 10264 pages = {519-534}, 10265 title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element 10266 Problems in Solid Mechanics}, 10267 volume = {55}, 10268 year = {2002}, 10269 petsc_uses = {KSP} 10270} 10271 10272@Article{ lahaye00, 10273 author = {Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.}, 10274 title = {Algebraic Multigrid for Complex Symmetric Systems}, 10275 journal = {IEEEMAGN}, 10276 year = {2000}, 10277 volume = {36}, 10278 number = {4}, 10279 pages = {1535--1538}, 10280 petsc_uses = {KSP} 10281} 10282 10283@InProceedings{ adams-99c, 10284 author = {Mark F. Adams and J. Demmel}, 10285 title = {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured 10286 Finite Element Problems}, 10287 booktitle = {Proceedings of SC99: High Performance Networking and Computing}, 10288 address = {Portland, Oregon}, 10289 month = nov, 10290 year = {1999}, 10291 petsc_uses = {KSP} 10292} 10293 10294@Article{ chan95, 10295 author = {T. Chan and B. Smith and J. Zou}, 10296 title = {Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse 10297 Grids}, 10298 journal = {Numer. Math.}, 10299 year = {1995}, 10300 volume = {73}, 10301 pages = {149--167}, 10302 petsc_uses = {KSP} 10303} 10304 10305@TechReport{ adams-csd-98-993, 10306 pages = {11}, 10307 year = {1998}, 10308 type = {Technical Report}, 10309 number = {CSD-98-993}, 10310 institution = {University of California, Berkeley}, 10311 title = {A Parallel Maximal Independent Set Algorithm}, 10312 bibdate = {March 11, 1998}, 10313 author = {Mark F. Adams and James Demmel}, 10314 abstract = {The parallel construction of maximal independent sets is a useful building block 10315 for many algorithms in the computational sciences, including graph coloring and 10316 multigrid coarse grid creation on unstructured meshes. We present an efficient 10317 asynchronous maximal independent set algorithm for use on parallel computers, for 10318 ``well partitioned'' graphs, that arise from finite element (FE) models. For 10319 appropriately partitioned bounded degree graphs, it is shown that the running time 10320 of our algorithm under the P-RAM computational model is of $O(1)$, which is an 10321 improvement over the previous best P-RAM complexity for this class of graphs. We 10322 present numerical experiments on an IBM SP, that confirm our P-RAM complexity 10323 model is indicative of the performance one can expect with practical partitions on 10324 graphs from FE problems.}, 10325 month = mar, 10326 petsc_uses = {KSP} 10327} 10328 10329@Article{ benzigolubliesen2005, 10330 title = {Numerical solution of saddle point problems}, 10331 author = {Michele Benzi and Gene H. Golub and J\"org Liesen}, 10332 volume = {14}, 10333 journal = {Acta Numerica}, 10334 pages = {1-–137}, 10335 doi = {10.1017/S0962492904000212}, 10336 year = {2005} 10337} 10338 10339@Article{ mardal2011preconditioning, 10340 title = {Preconditioning discretizations of systems of partial differential equations}, 10341 author = {Kent-Andre Mardal and Ragnar Winther}, 10342 journal = {Numerical Linear Algebra with Applications}, 10343 volume = {18}, 10344 number = {1}, 10345 pages = {1--40}, 10346 year = {2011} 10347} 10348 10349@TechReport{ k676, 10350 year = {1994}, 10351 type = {Technical Report}, 10352 number = {TR1994-676}, 10353 institution = {New York University}, 10354 title = {An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty 10355 Term}, 10356 author = {Axel Klawonn}, 10357 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf}, 10358 petsc_uses = {KSP} 10359} 10360 10361@Book{ ak1, 10362 author = {Axel Klawonn}, 10363 title = {Preconditioners for Indefinite Problems}, 10364 year = {1995}, 10365 publisher = {Westfalishen Wilhelms-Universitat Munster}, 10366 url = {http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf}, 10367 notes = {Thesis}, 10368 petsc_uses = {KSP} 10369} 10370 10371@TechReport{ knepleykarpeev05, 10372 pages = {41}, 10373 year = {2005}, 10374 type = {Technical Report}, 10375 number = {ANL/MCS-P1295-1005}, 10376 institution = {Argonne National Laboratory}, 10377 title = {Flexible Representation of Computational Meshes}, 10378 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10379 abstract = {}, 10380 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}, 10381 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}}, 10382 month = oct, 10383 petsc_uses = {DMPlex} 10384} 10385 10386@TechReport{ knepleykarpeev07a, 10387 pages = {14}, 10388 year = {2007}, 10389 type = {Technical Report}, 10390 number = {ANL/MCS-P1455-0907}, 10391 institution = {Argonne National Laboratory}, 10392 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10393 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10394 abstract = {}, 10395 url = {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}, 10396 note = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}}, 10397 month = feb, 10398 petsc_uses = {DMPlex} 10399} 10400 10401@Article{ knepleykarpeev09, 10402 author = {Matthew G. Knepley and Dmitry A. Karpeev}, 10403 title = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution}, 10404 journal = {Scientific Programming}, 10405 volume = {17}, 10406 number = {3}, 10407 pages = {215--230}, 10408 year = {2009}, 10409 doi = {10.3233/SPR-2009-0249}, 10410 url = {http://arxiv.org/abs/0908.4427}, 10411 note = {\url{http://arxiv.org/abs/0908.4427}}, 10412 petsc_uses = {DMPlex} 10413} 10414 10415@Article{ biezuner2012computing, 10416 author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder}, 10417 affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. 10418 Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil}, 10419 title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of 10420 Sublinear Supersolutions}, 10421 journal = {Journal of Scientific Computing}, 10422 publisher = {Springer Netherlands}, 10423 issn = {0885-7474}, 10424 keyword = {Mathematics and Statistics}, 10425 pages = {180--201}, 10426 volume = {52}, 10427 issue = {1}, 10428 year = {2012}, 10429 doi = {10.1007/s10915-011-9540-0}, 10430 petsc_uses = {KSP} 10431} 10432 10433% LiteralHTML: 10434% LiteralHTML: <a name="books"><H3><center>Books</center></H3> 10435% LiteralHTML: 10436@Book{ knepley2017, 10437 title = {Computational Science I}, 10438 author = {Matthew G. 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Smith and Petter Bj{\o}rstad and William D. Gropp}, 10467 title = {Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial 10468 Differential Equations}, 10469 year = {1996}, 10470 publisher = {Cambridge University Press}, 10471 url = {http://www.mcs.anl.gov/~bsmith/ddbook.html}, 10472 petsc_uses = {KSP} 10473} 10474 10475@Misc{ petsc-fem:homepage, 10476 title = {{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program}, 10477 author = {M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and 10478 G. Rodriguez and G. Filippini}, 10479 howpublished = {\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}}, 10480 petsc_uses = {KSP} 10481} 10482 10483@Misc{ petsc4py-web-page, 10484 author = {Lisandro Dalcin}, 10485 title = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries}, 10486 howpublished = {\url{http://code.google.com/p/petsc4py/}}, 10487 note = {http://code.google.com/p/petsc4py/}, 10488 petsc_uses = {KSP} 10489} 10490 10491@Article{ libmeshpaper06, 10492 author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey}, 10493 title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening 10494 Simulations}}, 10495 journal = {Engineering with Computers}, 10496 volume = {22}, 10497 number = {3--4}, 10498 pages = {237--254}, 10499 year = {2006}, 10500 doi = {10.1007/s00366-006-0049-3}, 10501 petsc_uses = {KSP} 10502} 10503 10504@Misc{ sisiphus:homepage, 10505 title = {{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, 10506 High-Resolution, Unstructured Simulations}, 10507 author = {T. {Tautges et al.}}, 10508 howpublished = {\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}}, 10509 petsc_uses = {KSP} 10510} 10511 10512@Misc{ pflotran:homepage, 10513 title = {{PFLOTRAN} project}, 10514 author = {Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra 10515 and Jitendra Kumar and Peter Lichtner and Richard Mills}, 10516 howpublished = {\url{http://pflotran.org/}}, 10517 petsc_uses = {KSP} 10518} 10519 10520@Misc{ pism:homepage, 10521 title = {{PISM}: A Parallel Ice Sheet Model}, 10522 author = {E. {Bueler et al.}}, 10523 howpublished = {\url{http://pism-docs.org}}, 10524 petsc_uses = {KSP} 10525} 10526 10527@Misc{ dohp:homepage, 10528 title = {Dohp: Dual order $hp$-finite elements}, 10529 author = {J. Brown}, 10530 howpublished = {\url{http://dohp.org}}, 10531 petsc_uses = {KSP} 10532} 10533 10534@Article{ mccourtrognlienetal12, 10535 title = {Improving parallel scalability for edge plasma transport simulations with neutral 10536 gas species}, 10537 author = {M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang}, 10538 journal = {Computational Science and Discovery}, 10539 year = {2012}, 10540 volume = {5}, 10541 number = {014012}, 10542 doi = {10.1088/1749-4699/5/1/014012}, 10543 note = {Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 10544 2011)}, 10545 petsc_uses = {KSP} 10546} 10547 10548@Misc{ petclaw-github, 10549 title = {Pet{C}law Software}, 10550 author = {Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia}, 10551 year = {2011}, 10552 howpublished = {\url{https://github.com/pyclaw/pyclaw}}, 10553 petsc_uses = {KSP} 10554} 10555 10556@Misc{ pyclaw-web-page, 10557 author = {Kyle T. Mandli and David I. 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Part I: The {Krylov-Schur} solver}}, 10576 author = {Biros, G. and Ghattas, O.}, 10577 journal = {SIAM Journal on Scientific Computing}, 10578 volume = {27}, 10579 number = {2}, 10580 pages = {687--713}, 10581 year = {2005}, 10582 publisher = {Society for Industrial and Applied Mathematics Philadelphia, PA, USA}, 10583 petsc_uses = {KSP} 10584} 10585 10586@Article{ biros2005pln2, 10587 title = {Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained 10588 optimization. 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C. Jardin and N. Ferraro and J. Breslau and J. Chen}, 10627 journal = {Computational Science \& Discovery}, 10628 volume = {5}, 10629 number = {1}, 10630 url = {http://stacks.iop.org/1749-4699/5/014002}, 10631 year = {2012}, 10632 petsc_uses = {KSP} 10633} 10634 10635@Article{ cmz2016, 10636 title = {Analysis and Practical Use of Flexible {BiCGStab}}, 10637 author = {Jie Chen and Lois Curfman McInnes and Hong Zhang}, 10638 journal = {Journal of Scientific Computing}, 10639 publisher = {Springer}, 10640 pages = {803--825}, 10641 volume = {68}, 10642 issue = {2}, 10643 url = {http://link.springer.com/article/10.1007/s10915-015-0159-4}, 10644 doi = {10.1007/s10915-015-0159-4}, 10645 year = {2016}, 10646 note = {Also preprint ANL/MCS-P3039-0912}, 10647 petsc_uses = {KSP} 10648} 10649 10650@Article{ knepleybrownruppsmith13, 10651 author = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.}, 10652 title = {Achieving High Performance with Unified Residual Evaluation}, 10653 journal = {ArXiv e-prints}, 10654 eprint = {1309.1204}, 10655 archiveprefix = {arXiv}, 10656 primaryclass = {cs.MS}, 10657 keywords = {Computer Science - Mathematical Software, Computer Science - Computational 10658 Engineering, Finance, and Science}, 10659 year = {2013}, 10660 month = sep, 10661 adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K}, 10662 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10663 petsc_uses = {KSP} 10664} 10665 10666@Book{ fenicsbook, 10667 title = {Automated Solution of Differential Equations by the Finite Element Method: The 10668 FEniCS Book}, 10669 series = {Lecture Notes in Computational Science and Engineering}, 10670 volume = {84}, 10671 editor = {Anders Logg, Kent-Andre Mardal, Garth Wells}, 10672 publisher = {Springer}, 10673 isbn = {978-3-642-23098-1}, 10674 year = {2012}, 10675 petsc_uses = {KSP} 10676} 10677 10678@Article{ demidovahnertruppgottschling12, 10679 author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.}, 10680 title = {{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}}, 10681 journal = {ArXiv e-prints}, 10682 archiveprefix = {arXiv}, 10683 eprint = {1212.6326}, 10684 primaryclass = {cs.MS}, 10685 keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, 10686 Parallel, and Cluster Computing, Physics - Computational Physics}, 10687 year = {2012}, 10688 month = dec, 10689 adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D}, 10690 adsnote = {Provided by the SAO/NASA Astrophysics Data System}, 10691 petsc_uses = {KSP} 10692} 10693 10694@InProceedings{ viennacl, 10695 author = {Rupp, K. and Rudolf, F. and Weinbub, J.}, 10696 title = {{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}}, 10697 booktitle = {Intl.~Workshop on GPUs and Scientific Applications}, 10698 year = {2010}, 10699 pages = {51-56}, 10700 petsc_uses = {KSP} 10701} 10702 10703@Article{ knepleybrownmcinnessmithruppadams2015, 10704 title = {Exascale Computing without Threads}, 10705 author = {Matthew G. 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Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and 10718 Karl Rupp and Mark Adams}, 10719 url = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf}, 10720 note = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on 10721 Scientific Software Architecture for Portability and Performance}, 10722 year = {2015}, 10723 petsc_uses = {KSP} 10724} 10725 10726@InCollection{ balaybrownknepleymcinnessmith2015, 10727 author = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry 10728 Smith}, 10729 title = {Providing Mixed Language and Legacy Support within a Library}, 10730 editor = {J. Carver}, 10731 booktitle = {Software Engineering for Science}, 10732 publisher = {Taylor \& Francis}, 10733 year = {2015}, 10734 petsc_uses = {KSP} 10735} 10736 10737@Article{ ruppbalaybrownknepleymcinnessmith2015, 10738 title = {On The Evolution Of User Support Topics in Computational Science and Engineering 10739 Software}, 10740 author = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman 10741 McInnes and Barry F. Smith}, 10742 note = {Whitepaper for Computational Science \& Engineering Software Sustainability and 10743 Productivity Challenges}, 10744 journal = {ArXiv e-prints}, 10745 archiveprefix = {arXiv}, 10746 eprint = {1510.01122}, 10747 year = {2015}, 10748 petsc_uses = {KSP} 10749} 10750 10751@InProceedings{ knepley2013accurately, 10752 title = {Accurately Citing Software and Algorithms Used in Publications}, 10753 author = {Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry 10754 F.}, 10755 year = {2013}, 10756 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10757 (WSSSPE), held at SC13}, 10758 doi = {10.6084/m9.figshare.785731}, 10759 petsc_uses = {KSP} 10760} 10761 10762@InProceedings{ milleretal2013, 10763 title = {Package Management Practice Essential for Interoperability: Lessons Learned and 10764 Strategies Developed for {FASTMath}}, 10765 author = {Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and 10766 Barry Smith}, 10767 year = {2013}, 10768 booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences 10769 (WSSSPE), held at SC13}, 10770 doi = {10.6084/m9.figshare.789055}, 10771 petsc_uses = {KSP} 10772} 10773 10774@TechReport{ dudsonetal2012, 10775 title = {Improved Nonlinear Solvers in {BOUT++}}, 10776 author = {Ben Dudson and Sean Farley and Lois Curfman McInnes}, 10777 institution = {Argonne National Laboratory}, 10778 number = {ANL/MCS-P3025-0812}, 10779 year = {2012}, 10780 petsc_uses = {KSP} 10781} 10782 10783@Misc{ brown13, 10784 author = {J. Brown}, 10785 title = {Scalable Repository Workflows}, 10786 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 10787 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 10788 year = {2013}, 10789 petsc_uses = {KSP} 10790} 10791 10792@Misc{ starforest11, 10793 title = {Star forests as a parallel communication model}, 10794 author = {Jed Brown}, 10795 url = {https://jedbrown.org/files/StarForest.pdf}, 10796 year = {2011}, 10797 petsc_uses = {KSP} 10798} 10799 10800@Misc{ brownknepleysmith13, 10801 author = {J. Brown and M. Knepley and B. Smith}, 10802 title = {Run-time Extensibility: Anything Less is Unsustainable}, 10803 note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale 10804 Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}}, 10805 year = {2013}, 10806 petsc_uses = {KSP} 10807} 10808 10809@Article{ jzhaoyliwkliu15, 10810 author = {J. Zhao and Y. Li and W.K. Liu}, 10811 title = {Predicting band structure of 3{D} mechanical metamaterials with complex geometry 10812 via {XFEM}}, 10813 journal = {Computational Mechanics}, 10814 year = {2015}, 10815 url = {http://link.springer.com/article/10.1007/s00466-015-1129-2}, 10816 petsc_uses = {KSP} 10817} 10818 10819@Article{ alisic14, 10820 author = {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen}, 10821 title = {Compaction around a rigid, circular inclusion in partially molten rock}, 10822 journal = {J. Geophys. Res.}, 10823 year = {2014}, 10824 volume = {119}, 10825 number = {7}, 10826 pages = {5903-5920}, 10827 doi = {10.1002/2013JB010906}, 10828 petsc_uses = {KSP} 10829} 10830 10831@Article{ rhebergen14, 10832 author = {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen}, 10833 title = {Analysis of block preconditioners for models of coupled magma mantle dynamics}, 10834 journal = {SIAM J. Sci. 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Gropp}, 10857 title = {Update on libraries for {B}lue {W}aters}, 10858 address = {Bordeaux, France}, 10859 year = {2010}, 10860 url = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf}, 10861 petsc_uses = {KSP} 10862} 10863 10864@InProceedings{ mayknepley2017, 10865 title = {{DMSwarm}: Particles in {PETSc}}, 10866 author = {Dave A May and Matthew G Knepley}, 10867 booktitle = {EGU General Assembly Conference Abstracts}, 10868 volume = {19}, 10869 pages = {10133}, 10870 year = {2017}, 10871 petsc_uses = {KSP} 10872} 10873 10874@InProceedings{ adamsbrownknepley2013, 10875 author = {Mark F. Adams and Jed Brown and Matthew G. Knepley}, 10876 title = {Low-communication techniques for extreme-scale multilevel solvers}, 10877 booktitle = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC}, 10878 organization = {DOE Office of Advanced Scientific Computing Research}, 10879 year = {2013}, 10880 petsc_uses = {KSP} 10881} 10882 10883@Article{ bhallagriffithknepleyadamsguy2017, 10884 title = {Scalable smoothing strategies for a geometric multigrid method for the immersed 10885 boundary equations}, 10886 author = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F. 10887 Adams and Robert D. Guy}, 10888 journal = {arXiv e-prints}, 10889 eprint = {1612.02208}, 10890 year = {2017}, 10891 note = {\url{http://arxiv.org/abs/1612.02208}}, 10892 petsc_uses = {KSP} 10893} 10894 10895@Article{ zampini2016pcbddc, 10896 title = {{PCBDDC}: a class of robust dual-primal methods in {PETSc}}, 10897 author = {Zampini, Stefano}, 10898 journal = {SIAM Journal on Scientific Computing}, 10899 volume = {38}, 10900 number = {5}, 10901 pages = {S282--S306}, 10902 year = {2016}, 10903 publisher = {SIAM}, 10904 petsc_uses = {KSP} 10905} 10906 10907@Article{ jolivetromanzampini2020, 10908 title = {{KSPHPDDM} and {PCHPDDM}: extending {PETSc} with advanced {Krylov} methods and 10909 robust multilevel overlapping {Schwarz} preconditioners}, 10910 author = {Pierre Jolivet and Jose Roman and Stefano Zampini}, 10911 journal = {Computers and Mathematics with Applications}, 10912 volume = {84}, 10913 pages = {277--295}, 10914 year = {2020} 10915} 10916 10917@Article{ zampinitu2017, 10918 title = {Multilevel {BDDC} deluxe algorithms with adaptive coarse spaces for flow in 10919 porous media}, 10920 author = {Stefano Zampini and Xuemin Tu}, 10921 journal = {SIAM Journal of Scientific Computing}, 10922 volume = {39}, 10923 number = {4}, 10924 pages = {A1389--A1415}, 10925 year = {2017} 10926} 10927 10928@Article{ ohwidlundzampinidohrmann2017, 10929 title = {{BDDC} algorithms with deluxe scaling and adaptive selection of primal 10930 constraints for {Raviart-Thomas} vector fields}, 10931 author = {D.-S. Oh and Olof B. Widlund and Stefano Zampini and Clark Dohrmann}, 10932 journal = {Mathematics of Computation}, 10933 volume = {87}, 10934 number = {310}, 10935 pages = {659--692}, 10936 year = {2017} 10937} 10938 10939@Article{ veigapavarinoscacchiwidlundzampini2016, 10940 title = {Adaptive selection of primal constraints for isogeometric {BDDC} deluxe 10941 preconditioners}, 10942 author = {L. Beirao Da Veiga and Luca F. Pavarino and S. Scacchi and Olof B. Widlund and 10943 Stefano Zampini}, 10944 journal = {SIAM Journal of Scientific Computing}, 10945 volume = {39}, 10946 number = {1}, 10947 pages = {A281--A302}, 10948 year = {2016} 10949} 10950 10951@Article{ pavarinoscacchiwidlundzampini2018, 10952 title = {Isogeometric {BDDC} deluxe preconditioners for linear elasticity for isogeometric 10953 analysis}, 10954 author = {Luca F. Pavarino and S. Scacchi and Olof B. Widlund and Stefano Zampini}, 10955 journal = {Mathematical Models and Methods in Applied Sciences}, 10956 volume = {28}, 10957 number = {7}, 10958 pages = {1337--1370}, 10959 year = {2018} 10960} 10961 10962@Article{ bergervergiatwaisman2017, 10963 title = {An overlapping Domain Decomposition preconditioning method for monolithic 10964 solution of shear bands}, 10965 author = {Luc Berger-Vergiat and Haim Waisman}, 10966 journal = {Computer Methods in Applied Mechanics and Engineering}, 10967 volume = {318}, 10968 pages = {33--60}, 10969 year = {2017}, 10970 petsc_uses = {KSP} 10971} 10972 10973@Article{ abhyankarmaldonadosmithzhang2020, 10974 title = {{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics 10975 Simulations}, 10976 author = {S. Abhyankar and G. Betrie and D.A. Maldonado and L.C. McInnes and B. Smith and 10977 H. 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Hansen and 11071 Jung-Han Kimn}, 11072 booktitle = {IEEE 9th Annual Computing and Communication Workshop and Conference (CCWC 2019)}, 11073 note = {Best Paper in Track}, 11074 year = {2019}, 11075 petsc_uses = {KSP} 11076} 11077 11078@MastersThesis{ rinaldo-ceresoli18, 11079 author = {Stefano Guido Rinaldo and Andrea Ceresoli}, 11080 title = {Newton–Krylov–Schwarz Methods for Distributed Power Flow and Related 11081 Applications}, 11082 school = {Politecnico di Milano}, 11083 year = {2018}, 11084 month = apr, 11085 petsc_uses = {KSP} 11086} 11087 11088@Article{ sananschneppmay2016, 11089 title = {Pipelined, Flexible {K}rylov Subspace Methods}, 11090 author = {P. Sanan and S. M. Schnepp and D. A. May}, 11091 journal = {SIAM Journal on Scientific Computing}, 11092 volume = {38}, 11093 number = {5}, 11094 pages = {C441-C470}, 11095 year = {2016}, 11096 doi = {10.1137/15M1049130}, 11097 petsc_uses = {KSP} 11098} 11099 11100@Article{ petscsf2022, 11101 author = {Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and 11102 Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and 11103 Smith, Barry F. and Zampini, Stefano}, 11104 journal = {IEEE Transactions on Parallel and Distributed Systems}, 11105 title = {The {PetscSF} Scalable Communication Layer}, 11106 year = {2022}, 11107 volume = {33}, 11108 number = {4}, 11109 pages = {842-853}, 11110 doi = {10.1109/TPDS.2021.3084070} 11111} 11112 11113@Article{ brandt2000, 11114 title = {General highly accurate algebraic coarsening}, 11115 author = {Achi Brandt}, 11116 journal = {Electronic Transactions on Numerical Analysis}, 11117 volume = {10}, 11118 number = {9680}, 11119 pages = {1--20}, 11120 issn = {10689613}, 11121 year = {2000} 11122} 11123 11124@Article{ dalcinpazklercosimo2011, 11125 title = {Parallel distributed computing using Python}, 11126 author = {Lisandro D. Dalcin and Rodrigo R. Paz and Pablo A. Kler and Alejandro Cosimo}, 11127 journal = {Advances in Water Resources}, 11128 volume = {34}, 11129 number = {9}, 11130 pages = {1124 - 1139}, 11131 note = {New Computational Methods and Software Tools}, 11132 issn = {0309-1708}, 11133 doi = {10.1016/j.advwatres.2011.04.013}, 11134 year = {2011} 11135} 11136 11137@Article{ behnelbradshawcitrodalcinseljebotnsmith2011, 11138 title = {Cython: The Best of Both Worlds}, 11139 author = {Behnel,Stefan and Bradshaw,Robert and Citro,Craig and Dalcin,Lisandro and 11140 Seljebotn,Dag Sverre and Smith,Kurt }, 11141 journal = {Computing in Science \& Engineering}, 11142 volume = {13}, 11143 number = {2}, 11144 pages = {31-39}, 11145 doi = {10.1109/MCSE.2010.118}, 11146 year = {2011} 11147} 11148 11149@Article{ dalcinpazstorti2005, 11150 title = {MPI for Python}, 11151 author = {Lisandro Dalcín and Rodrigo Paz and Mario Storti}, 11152 journal = {Journal of Parallel and Distributed Computing}, 11153 volume = {65}, 11154 number = {9}, 11155 pages = {1108 - 1115}, 11156 issn = {0743-7315}, 11157 doi = {10.1016/j.jpdc.2005.03.010}, 11158 year = {2005} 11159} 11160 11161@Article{ dalcincolliervignalcortescalo2016, 11162 title = {PetIGA: A framework for high-performance isogeometric analysis}, 11163 author = {Lisandro Dalcin and Nathan Collier and P. Vignal and A.M.A. Cortes and Victor M. 11164 Calo}, 11165 journal = {Computer Methods in Applied Mechanics and Engineering}, 11166 volume = {308}, 11167 pages = {151 - 181}, 11168 issn = {0045-7825}, 11169 doi = {10.1016/j.cma.2016.05.011}, 11170 year = {2016} 11171} 11172 11173@Article{ collierpardodalcinpaszynskicalo2012, 11174 title = {The cost of continuity: A study of the performance of isogeometric finite 11175 elements using direct solvers}, 11176 author = {Nathan Collier and David Pardo and Lisandro Dalcin and Maciej Paszynski and V.M. 11177 Calo}, 11178 journal = {Computer Methods in Applied Mechanics and Engineering}, 11179 volume = {213-216}, 11180 pages = {353 - 361}, 11181 issn = {0045-7825}, 11182 doi = {10.1016/j.cma.2011.11.002}, 11183 year = {2012} 11184} 11185 11186@Article{ collierdalcinpardocalo2013, 11187 title = {The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite 11188 Elements}, 11189 author = {Nathan Collier and Lisandro Dalcin and David Pardo and Victor M. Calo}, 11190 journal = {SIAM Journal on Scientific Computing}, 11191 volume = {35}, 11192 number = {2}, 11193 pages = {A767-A784}, 11194 doi = {10.1137/120881038}, 11195 year = {2013} 11196} 11197 11198@Article{ dunning2017jump, 11199 title = {{JuMP}: a modeling language for mathematical optimization}, 11200 author = {Dunning, Iain and Huchette, Joey and Lubin, Miles}, 11201 journal = {SIAM Review}, 11202 volume = {59}, 11203 number = {2}, 11204 pages = {295--320}, 11205 year = {2017}, 11206 publisher = {SIAM} 11207} 11208 11209@InProceedings{ prudencioschulz2011, 11210 title = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for 11211 Estimation, Simulation and Optimization}, 11212 author = {Ernesto E Prudencio and Karl W Schulz}, 11213 booktitle = {European Conference on Parallel Processing}, 11214 pages = {398--407}, 11215 year = {2011} 11216} 11217 11218@Misc{ rol-website, 11219 key = {ROL}, 11220 title = {{Rapid Optimization Library} Website}, 11221 howpublished = {\url{https://trilinos.org/packages/rol}}, 11222 year = {2018} 11223} 11224 11225@Article{ more1994line, 11226 title = {Line search algorithms with guaranteed sufficient decrease}, 11227 author = {Mor{\'e}, Jorge J and Thuente, David J}, 11228 journal = {ACM Transactions on Mathematical Software}, 11229 volume = {20}, 11230 number = {3}, 11231 pages = {286--307}, 11232 year = {1994}, 11233 publisher = {ACM} 11234} 11235 11236@Article{ griewank2000algorithm, 11237 title = {Algorithm 799: revolve: an implementation of checkpointing for the reverse or 11238 adjoint mode of computational differentiation}, 11239 author = {Griewank, Andreas and Walther, Andrea}, 11240 journal = {ACM Transactions on Mathematical Software}, 11241 volume = {26}, 11242 number = {1}, 11243 pages = {19--45}, 11244 year = {2000}, 11245 publisher = {ACM} 11246} 11247 11248@Article{ metcalf2011seven, 11249 title = {The seven ages of fortran}, 11250 author = {Metcalf, Michael}, 11251 journal = {Journal of Computer Science \& Technology}, 11252 volume = {11}, 11253 year = {2011} 11254} 11255 11256@Article{ giraldo_2013, 11257 title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified 11258 model of the atmosphere {(NUMA)}}, 11259 author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu}, 11260 journal = {SIAM Journal on Scientific Computing}, 11261 year = {2013}, 11262 number = {5}, 11263 pages = {B1162-B1194}, 11264 volume = {35}, 11265 doi = {10.1137/120876034} 11266} 11267 11268@Article{ constantinescu_tr2016b, 11269 author = {Constantinescu, E.M.}, 11270 title = {Estimating Global Errors in Time Stepping}, 11271 journal = {ArXiv e-prints}, 11272 archiveprefix = {arXiv}, 11273 eprint = {1503.05166}, 11274 primaryclass = {math.NA}, 11275 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70}, 11276 year = {2016}, 11277 month = mar, 11278 adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C}, 11279 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 11280} 11281 11282@Article{ pareschi_2005, 11283 title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems 11284 with Relaxation}, 11285 author = {L. Pareschi and G. Russo}, 11286 journal = {Journal of Scientific Computing}, 11287 year = {2005}, 11288 number = {1}, 11289 pages = {129--155}, 11290 volume = {25} 11291} 11292 11293@Article{ kennedy_2003, 11294 title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations}, 11295 author = {C.A. Kennedy and M.H. Carpenter}, 11296 journal = {Appl. Numer. Math.}, 11297 year = {2003}, 11298 number = {1-2}, 11299 pages = {139--181}, 11300 volume = {44}, 11301 doi = {10.1016/S0168-9274(02)00138-1}, 11302 publisher = {Elsevier Science Publishers B. V.} 11303} 11304 11305@Unpublished{ boscarino_tr2011, 11306 title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic 11307 equations in the diffusion limit}, 11308 author = {Boscarino, S. and Pareschi, L. and Russo, G.}, 11309 note = {Arxiv preprint arXiv:1110.4375}, 11310 year = {2011} 11311} 11312 11313@Article{ ascher_1997, 11314 title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential 11315 equations}, 11316 author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri}, 11317 journal = {Applied Numerical Mathematics}, 11318 year = {1997}, 11319 pages = {151--167}, 11320 volume = {25} 11321} 11322 11323@Book{ ascherpetzold1998, 11324 title = {Computer methods for ordinary differential equations and differential-algebraic 11325 equations}, 11326 author = {Uri M Ascher and Linda R Petzold}, 11327 volume = {61}, 11328 publisher = {SIAM}, 11329 year = {1998} 11330} 11331 11332@Article{ colomesbadia2016, 11333 title = {Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} 11334 equations}, 11335 author = {Oriol Colom{\'e}s and Santiago Badia}, 11336 journal = {International Journal for Numerical Methods in Engineering}, 11337 volume = {105}, 11338 number = {5}, 11339 pages = {372--400}, 11340 year = {2016} 11341} 11342 11343@Article{ sandu_1997, 11344 title = {Benchmarking stiff {ODE} solvers for atmospheric chemistry problems {II}: 11345 {R}osenbrock solvers}, 11346 author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. 11347 Potra}, 11348 journal = {Atmospheric Environment}, 11349 year = {1997}, 11350 number = {20}, 11351 pages = {3459--3472}, 11352 volume = {31}, 11353 abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major 11354 task is the integration of the stiff systems of ordinary differential equations 11355 describing the chemical transformations. It is therefore of interest to 11356 systematically search for stiff solvers which can be identified as close to 11357 optimal for atmospheric applications. In this paper we continue our investigation 11358 from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) 11359 and compare eight solvers on a set of seven box-models used in present day models. 11360 The focus is on Rosenbrock solvers. These turn out to be very well suited for our 11361 application when they are provided with highly efficient sparse matrix techniques 11362 to economize on the linear algebra. Two of the Rosenbrock solvers tested are from 11363 the literature, viz. and 4, and two are new and specially developed for air 11364 quality applications, viz. 3 and 3. } 11365} 11366 11367@Article{ rang_2005, 11368 title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic 11369 equations of index 1}, 11370 author = {Rang, J. and Angermann, L.}, 11371 journal = {BIT Numerical Mathematics}, 11372 year = {2005}, 11373 number = {4}, 11374 pages = {761--787}, 11375 volume = {45}, 11376 publisher = {Springer} 11377} 11378 11379@Article{ gottliebketchesonshu2009, 11380 author = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu}, 11381 title = {{High order strong stability preserving time discretizations}}, 11382 journal = {Journal of Scientific Computing}, 11383 volume = {38}, 11384 number = {3}, 11385 pages = {251--289}, 11386 doi = {10.1007/s10915-008-9239-z}, 11387 year = {2009} 11388} 11389 11390@Article{ ketcheson_2008, 11391 title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with 11392 Low-Storage Implementations}, 11393 author = {D.I. Ketcheson}, 11394 journal = {SIAM Journal on Scientific Computing}, 11395 year = {2008}, 11396 number = {4}, 11397 pages = {2113--2136}, 11398 volume = {30}, 11399 doi = {10.1137/07070485X}, 11400 keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, 11401 RungeKutta methods}, 11402 publisher = {SIAM} 11403} 11404 11405@Article{ jansen_2000, 11406 title = {A generalized-alpha method for integrating the filtered {N}avier--{S}tokes 11407 equations with a stabilized finite element method}, 11408 author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.}, 11409 journal = {Computer Methods in Applied Mechanics and Engineering}, 11410 year = {2000}, 11411 number = {3}, 11412 pages = {305--319}, 11413 volume = {190}, 11414 publisher = {Elsevier} 11415} 11416 11417@Article{ butcher_2007, 11418 title = {Error propagation of general linear methods for ordinary differential equations}, 11419 author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright}, 11420 journal = {Journal of Complexity}, 11421 year = {2007}, 11422 number = {4-6}, 11423 pages = {560--580}, 11424 volume = {23}, 11425 abstract = {We discuss error propagation for general linear methods for ordinary differential 11426 equations up to terms of order p+2, where p is the order of the method. These 11427 results are then applied to the estimation of local discretization errors for 11428 methods of order p and for the adjacent order p+1. The results of numerical 11429 experiments confirm the reliability of these estimates. This research has 11430 applications in the design of robust stepsize and order changing strategies for 11431 algorithms based on general linear methods.}, 11432 doi = {10.1016/j.jco.2007.01.009}, 11433 issn = {0885-064X} 11434} 11435 11436@Article{ constantinescu_a2010a, 11437 title = {Extrapolated implicit-explicit time stepping}, 11438 author = {E.M. Constantinescu and A. Sandu}, 11439 journal = {SIAM Journal on Scientific Computing}, 11440 year = {2010}, 11441 number = {6}, 11442 pages = {4452-4477}, 11443 volume = {31}, 11444 comment = {Preprint \# ANL/MCS-P1612-0409}, 11445 doi = {10.1137/080732833} 11446} 11447 11448@InProceedings{ devito2011liszt, 11449 title = {Liszt: a domain specific language for building portable mesh-based PDE solvers}, 11450 author = {DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen 11451 and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and 11452 Aiken, Alex and Duraisamy, Karthik and others}, 11453 booktitle = {Proceedings of 2011 International Conference for High Performance Computing, 11454 Networking, Storage and Analysis}, 11455 pages = {9}, 11456 year = {2011}, 11457 organization = {ACM} 11458} 11459 11460@Article{ devito2011designing, 11461 title = {Designing the Language Liszt for Building Portable Mesh-based PDE Solvers}, 11462 author = {DeVito, Zachary and Hanrahan, Pat}, 11463 journal = {Scientific Discovery through Advanced Computing Program (SciDAC)}, 11464 year = {2011} 11465} 11466 11467@Misc{ pgasintro, 11468 author = {Tim Stitt}, 11469 title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming 11470 Model}, 11471 note = {\url{http://cnx.org/content/m20649/latest/}} 11472} 11473 11474@InProceedings{ el2006upc, 11475 title = {UPC: unified parallel C}, 11476 author = {El-Ghazawi, Tarek and Smith, Lauren}, 11477 booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, 11478 pages = {27}, 11479 year = {2006}, 11480 organization = {ACM} 11481} 11482 11483@InProceedings{ numrich1998co, 11484 title = {Co-Array Fortran for parallel programming}, 11485 author = {Numrich, Robert W and Reid, John}, 11486 booktitle = {ACM Sigplan Fortran Forum}, 11487 volume = {17}, 11488 number = {2}, 11489 pages = {1--31}, 11490 year = {1998}, 11491 organization = {ACM} 11492} 11493 11494@Article{ aiken1997titanium, 11495 title = {Titanium: A high-performance Java dialect}, 11496 author = {Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, 11497 Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, 11498 Geoff and Semenzato, Luigi and others}, 11499 year = {1997} 11500} 11501 11502@Article{ charles2005x10, 11503 title = {X10: an object-oriented approach to non-uniform cluster computing}, 11504 author = {Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, 11505 Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and 11506 Sarkar, Vivek}, 11507 journal = {Acm Sigplan Notices}, 11508 volume = {40}, 11509 number = {10}, 11510 pages = {519--538}, 11511 year = {2005}, 11512 publisher = {ACM} 11513} 11514 11515@Article{ chamberlain2007parallel, 11516 title = {Parallel programmability and the chapel language}, 11517 author = {Chamberlain, Bradford L and Callahan, David and Zima, Hans P}, 11518 journal = {International Journal of High Performance Computing Applications}, 11519 volume = {21}, 11520 number = {3}, 11521 pages = {291--312}, 11522 year = {2007}, 11523 publisher = {SAGE Publications} 11524} 11525 11526@InProceedings{ charmppoopsla93, 11527 author = {{Kal\'{e}}, L.V. and Krishnan, S.}, 11528 title = {{CHARM++: A Portable Concurrent Object Oriented System Based on C++}}, 11529 editor = {Paepcke, A.}, 11530 fulleditor = {Paepcke, Andreas}, 11531 pages = {91--108}, 11532 month = sep, 11533 year = {1993}, 11534 booktitle = {{Proceedings of OOPSLA'93}}, 11535 publisher = {{ACM Press}} 11536} 11537 11538@InProceedings{ hewitt1973universal, 11539 title = {A universal modular actor formalism for artificial intelligence}, 11540 author = {Hewitt, Carl and Bishop, Peter and Steiger, Richard}, 11541 booktitle = {Proceedings of the 3rd international joint conference on Artificial 11542 intelligence}, 11543 pages = {235--245}, 11544 year = {1973}, 11545 organization = {Morgan Kaufmann Publishers Inc.} 11546} 11547 11548@Book{ yonezawa1990abcl, 11549 title = {ABCL: an object-oriented concurrent system}, 11550 author = {Yonezawa, Akinori}, 11551 year = {1990}, 11552 publisher = {MIT press} 11553} 11554 11555@InProceedings{ dally1988object, 11556 title = {Object-oriented concurrent programming in CST}, 11557 author = {Dally, William J and Chien, Andrew A}, 11558 booktitle = {Proceedings of the third conference on Hypercube concurrent computers and 11559 applications: Architecture, software, computer systems, and general issues-Volume 11560 1}, 11561 pages = {434--439}, 11562 year = {1988}, 11563 organization = {ACM} 11564} 11565 11566@Article{ grimshaw1993easy, 11567 title = {Easy-to-use object-oriented parallel processing with Mentat}, 11568 author = {Grimshaw, Andrew S.}, 11569 journal = {Computer}, 11570 volume = {26}, 11571 number = {5}, 11572 pages = {39--51}, 11573 year = {1993}, 11574 publisher = {IEEE} 11575} 11576 11577@InProceedings{ gannon1991object, 11578 title = {Object oriented parallelism: pC++ ideas and experiments}, 11579 author = {Gannon, Dennis and Lee, JK}, 11580 booktitle = {Proceedings of}, 11581 pages = {13--23}, 11582 year = {1991} 11583} 11584 11585@InProceedings{ lau1992object, 11586 title = {An object-oriented class library for scalable parallel heuristic search}, 11587 author = {Lau, Wing-cheong and Singh, Vineet}, 11588 booktitle = {ECOOP’92 European Conference on Object-Oriented Programming}, 11589 pages = {252--267}, 11590 year = {1992}, 11591 organization = {Springer} 11592} 11593 11594@Book{ chase1989amber, 11595 title = {The Amber system: Parallel programming on a network of multiprocessors}, 11596 author = {Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and 11597 Littlefield, Richard}, 11598 volume = {23}, 11599 number = {5}, 11600 year = {1989}, 11601 publisher = {ACM} 11602} 11603 11604@InProceedings{ kaiser2009parallex, 11605 title = {Parallex an advanced parallel execution model for scaling-impaired applications}, 11606 author = {Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas}, 11607 booktitle = {Parallel Processing Workshops, 2009. ICPPW'09. International Conference on}, 11608 pages = {394--401}, 11609 year = {2009}, 11610 organization = {IEEE} 11611} 11612 11613@TechReport{ ipm, 11614 author = {Barry F. Smith}, 11615 title = {A New Parallel Programming Model for Computer Simulation}, 11616 institution = {Argonne National Laboratory}, 11617 year = {2014}, 11618 number = {ANL/MCS-P5135-0414} 11619} 11620 11621@Article{ groppsnir, 11622 author = {William Gropp and Marc Snir}, 11623 title = {Programming for Exascale Computers}, 11624 journal = {Computing in Science and Engineering}, 11625 volume = {15}, 11626 number = {6}, 11627 issn = {1521-9615}, 11628 year = {2013}, 11629 pages = {27-35}, 11630 doi = {10.1109/MCSE.2013.96}, 11631 publisher = {IEEE Computer Society}, 11632 address = {Los Alamitos, CA} 11633} 11634 11635@Book{ mpi3, 11636 title = {MPI: A Message-Passing Interface Standard, Version 3.0}, 11637 author = {Message Passing Interface Forum}, 11638 year = {2012}, 11639 publisher = {High Performance Computing Center Stuttgart (HLRS)} 11640} 11641 11642@Book{ openmp4, 11643 title = {OpenMP Application Program Interface, Version 4.0}, 11644 year = {2013}, 11645 publisher = {OpenMP Architecture Review Board} 11646} 11647 11648@InProceedings{ hartono2009annotation, 11649 title = {Annotation-based empirical performance tuning using {Orio}}, 11650 author = {Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy}, 11651 booktitle = {Parallel \& Distributed Processing, 2009. 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Comput.}, 11766 pages = {1050--1051}, 11767 volume = {23}, 11768 publisher = {SIAM}, 11769 title = {A Note on Preconditioning Nonsymmetric Matrices}, 11770 year = {2001} 11771} 11772 11773% Random papers on solvers for GPUs 11774@InProceedings{ gpus-suck, 11775 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. }, 11776 title = { On the Limits of {GPU} Acceleration}, 11777 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism}, 11778 year = {2010}, 11779 publisher = {USENIX} 11780} 11781 11782@InProceedings{ 882364, 11783 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter}, 11784 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid}, 11785 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers}, 11786 year = {2003}, 11787 isbn = {1-58113-709-5}, 11788 pages = {917--924}, 11789 location = {San Diego, California}, 11790 doi = {10.1145/1201775.882364}, 11791 publisher = {ACM}, 11792 address = {New York, NY} 11793} 11794 11795@Conference{ feng2008multigrid, 11796 author = {Feng, Z. and Li, P.}, 11797 booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. 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Markus}, 12844 title = {{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments 12845 for {PDE} Based Applications}, 12846 year = {1994}, 12847 institution = {Department of Computer Sciences, Purdue University}, 12848 number = {CSD-TR-94-021} 12849} 12850 12851@Unpublished{ ilu-web-page, 12852 author = {Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi}, 12853 title = {{I}nter-{L}anguage {U}nification Reference Manual}, 12854 note = {ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation} 12855} 12856 12857@Unpublished{ doe2k-web-page, 12858 title = {{DOE2000 Initiative} {W}eb page}, 12859 note = {http://www.mcs.anl.gov/DOE2000}, 12860 key = {DOE2000 Initiative} 12861} 12862 12863@Misc{ pvode-web-page, 12864 title = {{PVODE} {W}eb Page}, 12865 note = {\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory}, 12866 author = {A. {Hindmarsh et al.}} 12867} 12868 12869@Book{ szyperski97, 12870 author = {Clemens Szyperski}, 12871 title = {Component Software: Beyond Object-Oriented Programming}, 12872 publisher = {ACM Press}, 12873 address = {New York}, 12874 year = {1997} 12875} 12876 12877@Unpublished{ petsc:coloringuse, 12878 title = {Code for computing sparse {J}acobians}, 12879 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12880 institution = {Argonne National Laboratory} 12881} 12882 12883@Unpublished{ petsc:external, 12884 author = {B. F. {Smith et al.}}, 12885 title = {{External Software Used by PETSc}}, 12886 note = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}}, 12887 institution = {Argonne National Laboratory} 12888} 12889 12890@Unpublished{ petsc:use-by-external-packages, 12891 author = {B. F. {Smith et al.}}, 12892 title = {{Software Packages that Use or Interface to PETSc}}, 12893 note = {\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}}, 12894 institution = {Argonne National Laboratory} 12895} 12896 12897@Unpublished{ petsc:prizes, 12898 author = {B. F. {Smith et al.}}, 12899 title = {{Prizes Won Using PETSc}}, 12900 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12901 institution = {Argonne National Laboratory} 12902} 12903 12904@Unpublished{ petsc:csgf, 12905 author = {B. F. {Smith et al.}}, 12906 title = {{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}}, 12907 note = {\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}}, 12908 institution = {Argonne National Laboratory} 12909} 12910 12911@Unpublished{ flash-web-page, 12912 title = {{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes 12913 {W}eb Page}, 12914 note = {http://www.asci.uchicago.edu}, 12915 author = {R. {Rosner et al.}}, 12916 institution = {University of Chicago} 12917} 12918 12919@Unpublished{ esi-web-page, 12920 title = {{E}quation {S}olver {I}nterface {F}orum {W}eb Page}, 12921 note = {http://z.ca.sandia.gov/esi}, 12922 author = {R. {Clay et al.}} 12923} 12924 12925@Unpublished{ infobus-web-page, 12926 title = {{I}nfo{B}us {W}eb Page}, 12927 note = {http://www.java.sun.com/beans/infobus}, 12928 key = {infobus} 12929} 12930 12931@Unpublished{ xray-web-page, 12932 title = {{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic 12933 {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)}, 12934 note = {http://www.mcs.anl.gov/xray/}, 12935 institution = {Argonne National Laboratory} 12936} 12937 12938@InProceedings{ kohn98, 12939 author = {Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski}, 12940 title = {Language Interoperability Mechanisms for High-Performance Scientific 12941 Applications}, 12942 publisher = {SIAM}, 12943 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12944 Scientific and Engineering Computing}, 12945 year = {1999}, 12946 pages = {30-39} 12947} 12948 12949@InProceedings{ kohn01, 12950 author = {Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens}, 12951 title = {Divorcing Language Dependencies from a Scientific Software Library}, 12952 publisher = {SIAM}, 12953 booktitle = {Proceedings of the Tenth SIAM Conference on Parallel Processing}, 12954 year = {2001} 12955} 12956 12957@InProceedings{ freitag_jones_plassmann98, 12958 author = {Lori Freitag and Mark Jones and Paul Plassmann}, 12959 title = {Component Integration for Unstructured Mesh Algorithms and Software}, 12960 publisher = {SIAM}, 12961 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 12962 Scientific and Engineering Computing}, 12963 year = {1999}, 12964 pages = {215-224} 12965} 12966 12967@Book{ templates, 12968 author = {R. 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Browne}, 12988 title = {{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement 12989 Techniques}, 12990 institution = {Department of Computer Science, University of Texas at Austin}, 12991 year = {1995} 12992} 12993 12994@Article{ parti, 12995 author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang}, 12996 title = {Communication Optimizations for Irregular Scientific Computations on Distributed 12997 Memory Architectures}, 12998 journal = {Journal of Parallel and Distributed Computing}, 12999 year = {1994}, 13000 volume = {22}, 13001 pages = {462--478} 13002} 13003 13004@Article{ mparti, 13005 author = {G. Agrawal and A. Sussman and J. 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Ross}, 13029 publisher = {University of Toronto}, 13030 pages = {379--386}, 13031 year = {1994} 13032} 13033 13034@Article{ cs99, 13035 author = {X.-C. Cai and M. Sarkis}, 13036 title = {A restricted additive {S}chwarz preconditioner for general sparse linear 13037 systems}, 13038 journal = {SIAM J. Scientific Computing}, 13039 year = {1999}, 13040 volume = {21}, 13041 pages = {792-797} 13042} 13043 13044@Article{ cai2003restricted, 13045 title = {Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric 13046 positive definite linear systems}, 13047 author = {Cai, X.C. and Dryja, M. and Sarkis, M.}, 13048 journal = {SIAM Journal on Numerical Analysis}, 13049 volume = {41}, 13050 issue = {1}, 13051 pages = {1209--1231}, 13052 year = {2003}, 13053 doi = {10.1137/S0036142901389621} 13054} 13055 13056@TechReport{ caisaad, 13057 author = {Xiao-Chuan Cai and Youcef Saad}, 13058 title = {Overlapping domain decomposition algorithms for general sparse matrices}, 13059 institution = {Army High Performance Computing Research Center, University of Minnesota }, 13060 year = {1993}, 13061 number = {Preprint 93-027 }, 13062 note = {SIAM J. Sci. Comp. 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Liu}, 13116 publisher = {Prentice-Hall}, 13117 year = {1981}, 13118 key = {SparseDirect} 13119} 13120 13121@Book{ p4-book, 13122 title = {Portable Programs for Parallel Processors}, 13123 publisher = {Holt, Rinehart, {and} Winston}, 13124 year = {1987}, 13125 author = {James Boyle and Ralph Butler and Terrence Disz and Barnett Glickfeld and Ewing 13126 Lusk and Ross Overbeek and James Patterson and Rick Stevens}, 13127 key = {P4Book} 13128} 13129 13130@Article{ stones, 13131 author = {H. L. Stone}, 13132 title = {Iterative solution of implicit approximations of multidimensional partial 13133 differential equations}, 13134 journal = {SIAM J. Numerical Analysis}, 13135 pages = {87--113}, 13136 volumne = {5}, 13137 year = {1968} 13138} 13139 13140@Article{ parallelstones, 13141 author = {J. S. Reeve and A. D. Scurr and J. H. Merlin}, 13142 title = {Parallel versions of {S}tones strongly implicit algorithm}, 13143 journal = {Concurrency and Computation: Practice and Experience}, 13144 pages = {1049--1062}, 13145 volumne = {13}, 13146 year = {2001} 13147} 13148 13149@Article{ p4-paper, 13150 author = {Ralph Butler and Ewing Lusk}, 13151 title = {Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System}, 13152 journal = {Journal of Parallel Computing}, 13153 note = {To appear (Also Argonne National Laboratory Mathematics and Computer Science 13154 Division preprint P362-0493)}, 13155 year = {1993} 13156} 13157 13158@TechReport{ picl, 13159 author = {G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and Patrick~H.~Worley}, 13160 title = {{PICL}: A portable instrumented communications library}, 13161 institution = {Oak Ridge National Laboratory}, 13162 number = {TM-11130}, 13163 year = {1990}, 13164 key = {PICL} 13165} 13166 13167@TechReport{ upshot, 13168 author = {Virginia Herrarte and Ewing Lusk}, 13169 title = {Studying Parallel Program Behavior with {U}pshot}, 13170 institution = {Argonne National Laboratory}, 13171 number = {ANL-91/15}, 13172 month = aug, 13173 year = {1991}, 13174 key = {Upshot} 13175} 13176 13177@TechReport{ p4-manual, 13178 author = {Ralph Butler and Ewing Lusk}, 13179 title = {User's Guide to the p4 Parallel Programming System}, 13180 institution = {Argonne National Laboratory}, 13181 number = {ANL-92/17}, 13182 month = oct, 13183 year = {1992}, 13184 key = {p4-Manual} 13185} 13186 13187@InProceedings{ oldparti, 13188 author = {Gagan Agrawal and Alan Sussman and Joel Saltz}, 13189 title = {Compiler and Runtime Support for Unstructured and Block Structured Problems}, 13190 booktitle = {Proceedings of Supercomputing '93}, 13191 pages = {578--587}, 13192 year = {1993} 13193} 13194 13195@Article{ parti2, 13196 author = {S. S. Mukherjee and S. D. Sharma and M. DF. Hill and J. R. Larus and A. Rogers 13197 and J. Saltz}, 13198 title = {Efficient Support for Irregular Applications on Distributed Memory Machines}, 13199 journal = {ACM SIGPLAN Notices}, 13200 year = {1995}, 13201 pages = {68-79}, 13202 volume = {30}, 13203 number = {8} 13204} 13205 13206@Article{ parti3, 13207 author = {J. Saltz and R. Mirchandaney and K. Crowley}, 13208 title = {Run-Time Parallelization and Scheduling of Loops}, 13209 journal = {IEEE Trans. Computers}, 13210 year = {1991}, 13211 pages = {604-612}, 13212 volume = {40}, 13213 number = {5} 13214} 13215 13216@InProceedings{ disz-lusk:wamtrace, 13217 author = {Terrence Disz and Ewing Lusk}, 13218 title = {A Graphical Tool for Observing the Behavior of Parallel Logic Programs}, 13219 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13220 year = {1987}, 13221 pages = {46--53} 13222} 13223 13224@InProceedings{ gorlick-kesselman:gauge, 13225 author = {Michael Gorlick and Carl Kesselman}, 13226 title = {Timing {Prolog} programs without Clocks}, 13227 booktitle = {Proceedings of the 1987 Symposium on Logic Programming}, 13228 year = {1996}, 13229 publisher = {Birkhauser} 13230} 13231 13232@TechReport{ aztec, 13233 author = {Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro}, 13234 title = {Aztec User's Guide Version 1.1}, 13235 institution = {Sandia National Laboratories}, 13236 month = oct, 13237 year = {1995}, 13238 number = {SAND95/1559} 13239} 13240 13241@TechReport{ aztec2, 13242 author = {Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid}, 13243 title = {Official {Aztec} User's Guide Version 2.1}, 13244 institution = {Sandia National Laboratories}, 13245 year = {1999} 13246} 13247 13248@Book{ taylor-chandy:pcn, 13249 author = {Chandy, M. and Taylor, S.}, 13250 title = {An Introduction to Parallel Programming}, 13251 year = {1991}, 13252 publisher = {Jones and Bartlett} 13253} 13254 13255@Book{ foster-taylor:strand, 13256 title = {Strand: New Concepts in Parallel Programming}, 13257 author = {Ian Foster and Stephen Taylor}, 13258 publisher = {Prentice-Hall}, 13259 adress = { Englewood Cliffs, New Jersey}, 13260 year = {1990} 13261} 13262 13263@Article{ aurora, 13264 author = {E. Lusk and R. Butler and T. Disz and R. Olson and R. Overbeek and R. Stevens and 13265 D.H.D. Warren and A. Calderwood and P. Szeredi and S. Haridi and P. Brand and M. 13266 Carlsson and A. Ciepielewski and B. Hausman}, 13267 title = {The Aurora OR-Parallel Prolog System}, 13268 journal = {New Generation Computing}, 13269 volume = {7}, 13270 number = {3}, 13271 year = {1990}, 13272 pages = {243--271} 13273} 13274 13275@TechReport{ roo, 13276 author = {E. Lusk and W. McCune and J. Slaney}, 13277 title = {Roo---a Parallel Theorem Prover}, 13278 institution = {Argonne National Laboratory}, 13279 number = {MCS--TM--149}, 13280 year = {1991} 13281} 13282 13283@TechReport{ heath-etheridge:vppp, 13284 author = {M. T. Heath and J. A. Etheridge}, 13285 title = {Visualizing the Performance of Parallel Programs}, 13286 institution = {Oak Ridge National Laboratory}, 13287 number = {ORNL TM-11813}, 13288 year = {1991} 13289} 13290 13291@TechReport{ chem:vis, 13292 author = {Ewing L. Lusk}, 13293 title = {Performance Visualization for Parallel Programs}, 13294 institution = {Argonne National Laboratory}, 13295 number = {ANL/MCS--P287--0192}, 13296 year = {1991}, 13297 note = {(to appear in {\em Theoretica Chimica Acta})} 13298} 13299 13300@TechReport{ picltrace, 13301 author = {P.~H.~Worley}, 13302 title = {A new {PICL} trace file format}, 13303 institution = {Oak Ridge National Laboratory}, 13304 number = {ORNL TM-12125}, 13305 month = jun, 13306 year = {1992} 13307} 13308 13309@InProceedings{ hideo, 13310 author = {Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda and Ross Overbeek}, 13311 title = {Inference of Phylogenetic trees using maximum likelihood}, 13312 booktitle = {Proceedings of the First Intel Delta Applications Workshop}, 13313 year = {1992}, 13314 pages = {247--262} 13315} 13316 13317@InProceedings{ dw90, 13318 author = {M. Dryja and O. Widlund}, 13319 title = {Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic 13320 Problems}, 13321 booktitle = {Third International Symposium on Domain Decomposition Methods}, 13322 editor = {T. F. Chan and R. Glowinski and J. P\'eriaux and O. B. Widlund}, 13323 year = {1990}, 13324 pages = {3-21}, 13325 publisher = {SIAM}, 13326 address = {Philadelphia}, 13327 annote = {Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how 13328 many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 13329 references, good introduction to the theory. No computations}, 13330 key = {DryjaWidlund90 !AS} 13331} 13332 13333@Unpublished{ rosing, 13334 author = {Matt Rosing and Joel Saltz}, 13335 title = {Low Latency Messages on Distributed Memory Multiprocessors}, 13336 key = {LowLatency}, 13337 note = {manuscript, 1992} 13338} 13339 13340@TechReport{ jp:incomplete, 13341 author = {Mark T. Jones and Paul E. Plassmann}, 13342 title = {An Improved Incomplete {C}holesky Factorization}, 13343 institution = {Argonne National Laboratory}, 13344 address = {Argonne, IL}, 13345 type = {Preprint}, 13346 note = {(to appear in {\em ACM Trans. on Mathematical Software, 1995})}, 13347 number = {MCS-P206-0191}, 13348 year = {1991}, 13349 key = {jones} 13350} 13351 13352@InCollection{ jp:ima, 13353 author = {Mark Jones and Paul Plassmann}, 13354 title = {The Efficient Parallel Iterative Solution of Large Sparse Linear Systems}, 13355 booktitle = {Graph Theory and Sparse Matrix Computation}, 13356 publisher = {Springer-Verlag}, 13357 series = {The IMA Volumes in Mathematics and Its Applications}, 13358 editor = {Alan George and John Gilbert and Joseph W.H.~Liu}, 13359 volume = {56}, 13360 year = {1993}, 13361 pages = {229--245} 13362} 13363 13364@Article{ pw98, 13365 author = {M. Pernice and H. F. Walker}, 13366 title = {{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems}, 13367 journal = {SIAM J. Sci. Stat. Comput.}, 13368 year = {1998}, 13369 volume = {19}, 13370 pages = {302--318} 13371} 13372 13373@TechReport{ ysmp83, 13374 key = {Eisenstat}, 13375 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13376 title = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13377 institution = {Department of Computer Science, Yale University}, 13378 number = {YALE/DCS/RR-265}, 13379 month = apr, 13380 year = {1983} 13381} 13382 13383@InBook{ ysmp84, 13384 author = {S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and A.~H.~Sherman}, 13385 chaptertitle = {The (New) {Y}ale {S}parse {M}atrix {P}ackage}, 13386 title = {Elliptic Problem Solvers II}, 13387 publisher = {Academic Press}, 13388 pages = {45--52}, 13389 editors = {G. Birkhoff and A. Schoenstadt}, 13390 year = {1984} 13391} 13392 13393@TechReport{ sparsekit, 13394 key = {Saad}, 13395 author = {Youcef Saad}, 13396 title = {{SPARSKIT}, a basic tool kit for sparse matrix computations}, 13397 institution = {Center for Supercomputing Research and Development, University of Illinois at 13398 Urbana-Champaign}, 13399 number = {1029}, 13400 year = {1990} 13401} 13402 13403@TechReport{ pde-user-ref, 13404 author = {Barry F. Smith}, 13405 title = {Extensible {PDE} Solvers Package Users Manual}, 13406 institution = {Argonne National Laboratory}, 13407 month = sep, 13408 year = {1994}, 13409 number = {ANL-93/40}, 13410 key = {Smith94 ! PDE} 13411} 13412 13413@TechReport{ bs-user-ref, 13414 author = {Mark T. Jones and Paul E. Plassmann}, 13415 title = {{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution 13416 of Sparse Linear Systems}, 13417 institution = {Argonne National Laboratory}, 13418 month = dec, 13419 year = {1995}, 13420 number = {ANL-95/48} 13421} 13422 13423@TechReport{ snes-user-ref, 13424 author = {William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 13425 title = {Using the {S}calable {N}onlinear {E}quations {S}olvers Package}, 13426 institution = {Argonne National Laboratory}, 13427 month = feb, 13428 year = {1995}, 13429 number = {ANL/MCS-TM-193}, 13430 key = {GroppMcInnesSmith95 ! SNES} 13431} 13432 13433@TechReport{ sles-user-ref, 13434 author = {William D. Gropp and Barry F. Smith}, 13435 title = {{S}implified {L}inear {E}quation {S}olvers Users Manual}, 13436 institution = {Argonne National Laboratory}, 13437 month = mar, 13438 year = {1993}, 13439 number = {ANL-93/8}, 13440 key = {GroppSmith93 ! SLES} 13441} 13442 13443@TechReport{ chameleon-user-ref, 13444 author = {William D. Gropp and Barry F. Smith}, 13445 title = {Chameleon Parallel programming tools Users Manual}, 13446 institution = {Argonne National Laboratory}, 13447 month = mar, 13448 year = {1993}, 13449 number = {ANL-93/23}, 13450 key = {GroppSmith93 ! Chameleon} 13451} 13452 13453@Article{ euclid2, 13454 author = {D. Hysom and A. Pothen}, 13455 title = {A Scalable Parallel Algorithm For Incomplete Factor Preconditioning}, 13456 journal = {SIAM J. Sci. Comput.}, 13457 volume = {22}, 13458 number = {6}, 13459 pages = {2194--2215} 13460} 13461 13462@TechReport{ euclid1, 13463 author = {D. Hysom and A. Pothen}, 13464 title = {Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel 13465 Solution of Sparse Linear Systems)}, 13466 institution = {Old Dominion University}, 13467 year = {2001} 13468} 13469 13470@TechReport{ ksp-user-ref, 13471 author = {William D. Gropp and Barry F. Smith}, 13472 title = {Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space 13473 Methods}, 13474 institution = {Argonne National Laboratory}, 13475 month = aug, 13476 year = {1993}, 13477 number = {ANL-93/30}, 13478 key = {GroppSmith93 ! KSP} 13479} 13480 13481@TechReport{ mpi-chameleon, 13482 author = {William D. Gropp and Ewing Lusk}, 13483 title = {A Test Implementation of the {MPI} Draft Message-Passing Standard}, 13484 institution = {Argonne National Laboratory}, 13485 month = dec, 13486 year = {1992}, 13487 number = {ANL-92/47}, 13488 key = {GroppLusk92 ! MPI} 13489} 13490 13491@TechReport{ blockcomm-fortran, 13492 author = {William D. Gropp}, 13493 title = {Block{C}omm for {F}ortran}, 13494 institution = {Argonne National Laboratory}, 13495 month = may, 13496 year = {1993}, 13497 number = {ANL-93/00 (to appear)}, 13498 key = {Gropp93 ! BlockComm} 13499} 13500 13501@TechReport{ autodocument, 13502 author = {William D. Gropp}, 13503 title = {Automatic documentation of {C} programs}, 13504 institution = {Argonne National Laboratory}, 13505 month = may, 13506 year = {1993}, 13507 number = {ANL-93/00}, 13508 key = {Gropp93 ! Autodoc} 13509} 13510 13511@TechReport{ zipcode, 13512 author = {Anthony Skjellum and Steven G. Smith and Charles H Still and Alvin P. Leung and 13513 Manfred Morari}, 13514 title = {The {Z}ipcode message-passing system}, 13515 institution = {Lawrence Livermore National Laboratory}, 13516 month = sep, 13517 year = {1992}, 13518 number = {Unpublished}, 13519 key = {Skjellum92 ! Zipcode} 13520} 13521 13522@Article{ paragraph, 13523 author = {Michael T. Heath and Jennifer Etheridge Finger}, 13524 title = {Visualizing performance of parallel programs}, 13525 journal = {IEEE Software}, 13526 volume = {8}, 13527 number = {5}, 13528 month = sep, 13529 year = {1991}, 13530 pages = {29--39}, 13531 key = {Heath91 ! Paragraph} 13532} 13533 13534@Article{ gropp90, 13535 author = {William Gropp and Edward Smith}, 13536 title = {Computational Fluid Dynamics on Parallel Processors}, 13537 journal = {Computers and Fluids}, 13538 volume = {18}, 13539 year = {1990}, 13540 pages = {289--304}, 13541 key = {Gropp90 ! performance} 13542} 13543 13544@Article{ foster92, 13545 author = {Ian Foster and William Gropp and Rick Stevens}, 13546 title = {The parallel scalability of the spectral transform method}, 13547 journal = {Monthly Weather Review}, 13548 volume = {120}, 13549 year = {1992}, 13550 pages = {835--850}, 13551 key = {Foster92 ! performance} 13552} 13553 13554@InBook{ fgn, 13555 author = {R. Freund and G. H. Golub and N. Nachtigal}, 13556 title = {Iterative Solution of Linear Systems}, 13557 series = {Acta Numerica}, 13558 year = {1992}, 13559 publisher = {Cambridge University Press}, 13560 pages = {57--100} 13561} 13562 13563@TechReport{ nachtigal90, 13564 author = {No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen}, 13565 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13566 institution = {Massachusetts Institute of Technology}, 13567 month = mar, 13568 year = {1990}, 13569 number = {90-2}, 13570 key = {Nachtigal | Krylov} 13571} 13572 13573@Article{ nachtigal1992fnm, 13574 title = {How Fast are Nonsymmetric Matrix Iterations?}, 13575 author = {Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.}, 13576 journal = {SIAM Journal on Matrix Analysis and Applications}, 13577 volume = {13}, 13578 pages = {778}, 13579 year = {1992}, 13580 publisher = {SIAM} 13581} 13582 13583@TechReport{ embree1999descriptive, 13584 title = {How descriptive are {GMRES} convergence bounds}, 13585 author = {Embree, M.}, 13586 year = {1999}, 13587 number = {08}, 13588 institution = {Oxford University Computing Laboratory} 13589} 13590 13591@Article{ vorst92, 13592 author = {H. van der Vorst}, 13593 title = {Bi-{CGSTAB}: A fast and smoothly converging variant of {Bi-CG} for the solution 13594 of nonsymmetric linear systems}, 13595 journal = {SIAM J. Sci. Stat. Comput.}, 13596 year = {1992}, 13597 volume = {13}, 13598 pages = {631--644} 13599} 13600 13601@Article{ eisenstat81, 13602 author = {S. Eisenstat}, 13603 title = {Efficient Implementation of a Class of {CG} Methods}, 13604 journal = {SIAM J. Sci. Stat. Comput.}, 13605 year = {1981}, 13606 volume = {2}, 13607 pages = {1--4} 13608} 13609 13610@Manual{ ibm-essl, 13611 title = {{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and 13612 Reference}, 13613 organization = {IBM}, 13614 year = {1992}, 13615 key = {IBM-ESSL} 13616} 13617 13618@Manual{ ibm-eui, 13619 title = {{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference 13620 Release 2.0}, 13621 organization = {IBM}, 13622 month = jun, 13623 year = {1994}, 13624 key = {IBM-EUI} 13625} 13626 13627@Manual{ ibm-euih, 13628 title = {Using {EUIH}: An Experimental {EUI} Implementation}, 13629 organization = {IBM}, 13630 author = {Peter Hochschild}, 13631 year = {1993}, 13632 key = {IBM-EUIH} 13633} 13634 13635@TechReport{ mpi, 13636 title = {Document for a Standard Message-Passing Interface}, 13637 author = {Message Passing Interface Forum}, 13638 institution = {University of Tennessee}, 13639 number = {CS-93-214}, 13640 month = nov, 13641 year = {1993}, 13642 key = {MPI Standard} 13643} 13644 13645@Unpublished{ mpi-final-web, 13646 author = {Message Passing Interface Forum}, 13647 title = {{MPI}: A Message-Passing Interface Standard}, 13648 note = {http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html}, 13649 year = {1994}, 13650 month = may 13651} 13652 13653@Book{ hockney-jesshope, 13654 author = {R. W. Hockney and C. R. Jesshope}, 13655 title = {Parallel Computers 2}, 13656 publisher = {Adam Hilger}, 13657 year = {1988} 13658} 13659 13660@Book{ cm-fortran, 13661 author = {{Thinking Machines Corporation}}, 13662 title = {Users Manual for CM-Fortran}, 13663 publisher = {Thinking Machines Corporation}, 13664 year = {1993} 13665} 13666 13667@TechReport{ chang93, 13668 title = {Experiments and Bounds on Block Diagonal Preconditioning}, 13669 author = {Mark Yan-Ming Chang and Martin H. Schultz}, 13670 institution = {Yale Department of Computer Science}, 13671 number = {YALEU/DCS/RR-994}, 13672 month = nov, 13673 year = {1993}, 13674 key = {BDD|diag} 13675} 13676 13677@InProceedings{ gropplevine93, 13678 author = {N. Galbreath and W. Gropp and D. Levine}, 13679 title = {Applications-Driven Parallel {I/O}}, 13680 booktitle = {Proceedings of Supercomputing '93}, 13681 year = {1993}, 13682 pages = {462--471} 13683} 13684 13685@Book{ siegle85, 13686 author = {H. J. Siegel}, 13687 title = {Interconnection Networks for Large Scale Parallel Processing}, 13688 publisher = {Lexington Books}, 13689 year = {1985}, 13690 key = {Network Comparison} 13691} 13692 13693@Article{ lawrie75, 13694 author = {D. H. Lawrie}, 13695 title = {Access and alignment of data in an array processor}, 13696 journal = {IEEE Transactions on Computers}, 13697 volume = {C-24}, 13698 number = {12}, 13699 month = dec, 13700 year = {1975}, 13701 pages = {1145--1155}, 13702 key = {Omega Network} 13703} 13704 13705@Book{ knuth1986, 13706 title = {The {\TeX}{Book}}, 13707 author = {Donald Ervin Knuth and Duane Bibby}, 13708 volume = {1993}, 13709 year = {1986}, 13710 publisher = {Addison-Wesley Reading, Massachusetts} 13711} 13712 13713@Book{ lamport86, 13714 author = {Leslie Lamport}, 13715 title = {{LaTeX}: A document preparation system}, 13716 publisher = {Addison-Wesley}, 13717 year = {1986}, 13718 key = {Latex Manual} 13719} 13720 13721@InProceedings{ gropp-lusk:unix-tools, 13722 author = {William Gropp and Ewing Lusk}, 13723 title = {Scalable {U}nix Tools on Parallel Processors}, 13724 booktitle = {Proceedings of the 1994 Scalable High Performanc Computing Conference}, 13725 publisher = {IEEE}, 13726 pages = {56--62} 13727} 13728 13729@InProceedings{ jp:bell_prize, 13730 author = {Mark Jones and Paul Plassmann}, 13731 title = {Solution of Large, Sparse Systems of Linear Equations in Massively Parallel 13732 Applications}, 13733 booktitle = {Proceedings of Supercomputing '92}, 13734 publisher = {IEEE Computer Society Press}, 13735 year = {1992}, 13736 pages = {551--560} 13737} 13738 13739@COMMENT{WEB, CWEB references (for doctext)} 13740@TechReport{ web, 13741 author = {Donald E. Knuth}, 13742 title = {The {\tt WEB} system of structured documentation}, 13743 institution = {Computer Science Department, Stanford University}, 13744 year = {1983}, 13745 number = {980}, 13746 month = sep 13747} 13748 13749@Article{ literatepgm, 13750 author = {Donald E. Knuth}, 13751 title = {Literate Programming}, 13752 journal = {Computer Journal}, 13753 year = {1984}, 13754 volume = {27}, 13755 number = {2}, 13756 pages = {91--111} 13757} 13758 13759@Unpublished{ cweb-code, 13760 author = {Silvio Levy and Donald E. Knuth}, 13761 title = {CWEB}, 13762 note = {CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb} 13763} 13764 13765@Article{ jp:scalable, 13766 author = {Mark Jones and Paul Plassmann}, 13767 title = {Scalable Iterative Solution of Sparse Linear Systems}, 13768 journal = {Parallel Computing}, 13769 volume = {20}, 13770 number = {5}, 13771 month = may, 13772 year = {1994}, 13773 pages = {753--773} 13774} 13775 13776@Article{ jp:pcolor, 13777 author = {Mark T. Jones and Paul E. Plassmann}, 13778 title = {A Parallel Graph Coloring Heuristic}, 13779 journal = {SIAM J. Sci. Comput.}, 13780 volume = {14}, 13781 number = {3}, 13782 pages = {654-669}, 13783 year = {1993} 13784} 13785 13786@TechReport{ block_solve, 13787 author = {Mark T. Jones and Paul E. Plassmann}, 13788 title = {{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of 13789 Sparse Linear Systems}, 13790 institution = {Argonne National Laboratory}, 13791 year = {1992}, 13792 number = {ANL-92/46}, 13793 key = {JonesPlassmann92 ! block_solve} 13794} 13795 13796@InProceedings{ supercond, 13797 author = {Lois Curfman Mc{I}nnes and Mario Palumbo}, 13798 title = {Parallel Solution of the Anisotropic {G}inzburg-{L}andau Model}, 13799 booktitle = {Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications 13800 Conference}, 13801 month = feb, 13802 year = {1994}, 13803 key = {McInnesPalumbo94 ! superconductivity } 13804} 13805 13806@Unpublished{ preosti:93, 13807 author = {Gianfranco Preosti}, 13808 title = { }, 13809 note = {Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity}, 13810 year = {1993}, 13811 key = {preosti93 ! GL-tilt3d} 13812} 13813 13814@Unpublished{ more:93, 13815 author = {Jorge J. Mor\'{e}}, 13816 title = { }, 13817 note = {Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, 13818 {A}rgonne {N}ational {L}aboratory}, 13819 year = {1993}, 13820 key = {more93 ! MINPACK-2} 13821} 13822 13823@Article{ brownsaad:90, 13824 author = {Peter N. Brown and Youcef Saad}, 13825 title = {Hybrid {K}rylov Methods for Nonlinear Systems of Equations}, 13826 journal = {SIAM J. Sci. Stat. Comput.}, 13827 year = {1990}, 13828 volume = {11}, 13829 pages = {450-481} 13830} 13831 13832@Book{ using-mpi, 13833 author = {William Gropp and Ewing Lusk and Anthony Skjellum}, 13834 title = {Using MPI: Portable Parallel Programming with the Message Passing Interface}, 13835 publisher = {MIT Press}, 13836 year = {1994} 13837} 13838 13839@Book{ using-mpi2, 13840 author = {William Gropp and Ewing Lusk and Rajeev Thakur}, 13841 title = {Using MPI 2: Advanced Features of the Message Passing Interface}, 13842 publisher = {MIT Press}, 13843 year = {1999} 13844} 13845 13846@Article{ hs:52, 13847 author = {Magnus R. Hestenes and Eduard Steifel}, 13848 title = {Methods of Conjugate Gradients for Solving Linear Systems}, 13849 journal = {J. Research of the National Bureau of Standards}, 13850 year = {1952}, 13851 volume = {49}, 13852 pages = {409-436} 13853} 13854 13855@Article{ so:89, 13856 author = {Peter Sonneveld}, 13857 title = {{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems}, 13858 journal = {SIAM J. Sci. Stat. Comput.}, 13859 year = {1989}, 13860 volume = {10}, 13861 pages = {36-52} 13862} 13863 13864@Article{ v:92, 13865 author = {{H. A.} {van der Vorst}}, 13866 title = {{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution 13867 of nonsymmetric linear systems}, 13868 journal = {SIAM J. Sci. Stat. Comput.}, 13869 volume = {13}, 13870 year = {1992}, 13871 pages = {631-644} 13872} 13873 13874@Article{ f:93, 13875 author = {Roland W. Freund}, 13876 title = {A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear 13877 Systems}, 13878 journal = {SIAM J. Sci. Stat. Comput.}, 13879 volume = {14}, 13880 year = {1993}, 13881 pages = {470-482} 13882} 13883 13884@Article{ ish:89, 13885 author = {S. Ishizuka}, 13886 title = {An Experimental Study on Extinction and Stablity of Tubular Flames}, 13887 journal = {Combustion and Flame}, 13888 volume = {75}, 13889 year = {1989}, 13890 pages = {367-379} 13891} 13892 13893@Book{ williams89, 13894 title = {Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems}, 13895 author = {F.A. Williams}, 13896 publisher = {Addison-Wesley}, 13897 year = {1989}, 13898 pages = {367-379} 13899} 13900 13901@Book{ ra75, 13902 author = {R. Aris}, 13903 title = {The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts}, 13904 publisher = {Oxford}, 13905 year = {1975} 13906} 13907 13908@Book{ bebernes89, 13909 author = {J. Bebernes and D. Eberly}, 13910 title = {Mathematical Problems from Combustion Theory}, 13911 publisher = {Springer-Verlag}, 13912 series = {Applied Mathematical Sciences 83}, 13913 year = {1989} 13914} 13915 13916@InProceedings{ kikuchi89, 13917 author = {F. Kikuchi}, 13918 booktitle = { Computing Methods in Applied Sciences and Engineering}, 13919 editor = {R. Glowinski and J. L. Lions}, 13920 publisher = {Springer-Verlag}, 13921 series = {Lecture Notes in Mathematics}, 13922 title = {Finite element approximations to bifurcation problems of turning point type}, 13923 year = {1977} 13924} 13925 13926@Article{ rg85, 13927 author = {R. Glowinski and H.B. Keller and L. Reinhart}, 13928 title = {Continuation-conjugate Gradient Methods for the Least Squares Solution of 13929 Nonlinear Boundary Problems}, 13930 journal = {SIAM J. Sci. Stat. Comput.}, 13931 volume = {6}, 13932 year = {1985}, 13933 pages = {793-832} 13934} 13935 13936@InProceedings{ whitfield91, 13937 author = {D. Whitfield and L. Taylor}, 13938 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 13939 Schemes}, 13940 booktitle = {Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference}, 13941 misc = {AIAA-91-1539}, 13942 pages = {134-145}, 13943 year = {1991} 13944} 13945 13946@InProceedings{ quinlan1, 13947 author = {M. Lemke and D. Quinlan}, 13948 title = {P++, a {C}++ Virtual Shared Grids Based Programming Environment for 13949 Architecture-Independent Development of Structured Grid Applications}, 13950 booktitle = {CONPAR/VAPP V, Lecture Notes in Computer Science}, 13951 publisher = {Springer Verlag}, 13952 year = {1992} 13953} 13954 13955@InProceedings{ quinlan2, 13956 author = {R. Parsons and D. Quinlan}, 13957 title = {A++/{P}++ Array Classes for Architecture Independent Finite Difference 13958 Computations}, 13959 booktitle = {Proceedings of the Second Annual Object-Oriented Numerics Conference}, 13960 year = {1994} 13961} 13962 13963% ***** Overview of functionality in Diffpack 13964@InBook{ dpoverview, 13965 author = {Bruaset, A. M. and Langtangen, H. P.}, 13966 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 13967 title = {A Comprehensive Set of Tools for Solving Partial Differential Equations; 13968 {Diffpack}}, 13969 publisher = {Birkh{\"{a}}user}, 13970 pages = {61--90}, 13971 year = {1997} 13972} 13973 13974% ***** Short overview of Diffpack 13975@InCollection{ dpoverview2, 13976 author = {Bruaset, A. M. and Langtangen, H. P.}, 13977 editor = {A. Sydow}, 13978 booktitle = {Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling 13979 and Applied Mathematics}, 13980 title = {Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers}, 13981 pages = {553--558}, 13982 volume = {4}, 13983 year = {1997} 13984} 13985 13986% ***** Comprehensive documentation of Diffpack and 13987% associated numerical methods: 13988@Book{ dpbook, 13989 author = {H. P. Langtangen}, 13990 title = {Numerical Solution of Partial Differential Equations; Models, Algorithms and 13991 Software. Part I}, 13992 series = {Lecture Notes in Computational Science and Engineering}, 13993 publisher = {Springer-Verlag}, 13994 year = {1998} 13995} 13996 13997% ***** Design issues of the linear solvers in Diffpack, serves also as a 13998% collection of examples on O-O in numerical computing 13999@Article{ ambhpl97a, 14000 author = {A. M. Bruaset and H. P. Langtangen }, 14001 title = {Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}}, 14002 journal = {Transactions on Mathematical Software}, 14003 volume = {23 }, 14004 pages = {50--80}, 14005 year = {1997} 14006} 14007 14008@Misc{ dpurl, 14009 author = {{Diffpack Web page}}, 14010 howpublished = {\url{http://www.diffpack.com}} 14011} 14012 14013% ***** General intro to object-oriented numerics for "FORTRAN programmers" 14014@InCollection{ oonintro, 14015 author = {Arge, E. and Bruaset, A. M. and H. P. Langtangen}, 14016 editor = {D{\ae}hlen, M. and Tveito, A.}, 14017 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14018 title = {Object-Oriented Numerics}, 14019 publisher = {Birkh{\"{a}}user}, 14020 year = {1997} 14021} 14022 14023% ***** Efficiency comparison: BLAS 1, Diffpack, C, 14024% and finite element applications (F77 vs Diffpack) 14025@InCollection{ dpefficiency, 14026 author = {Arge, E. and Bruaset, A. M. and Calvin, P. B. and Kanney, J. F. and Langtangen, 14027 H. P. and Miller, C. T.}, 14028 editor = {D{\ae}hlen, M. and Tveito, A.}, 14029 booktitle = {Mathematical Models and Software Tools in Industrial Mathematics}, 14030 title = {On the Efficiency of {C++} in Scientific Computing}, 14031 publisher = {Birkh{\"{a}}user}, 14032 pages = {91--118}, 14033 year = {1997} 14034} 14035 14036% ***** Parallel concept in Diffpack: 14037@InCollection{ dpparallel, 14038 author = {A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito}, 14039 editor = {Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn}, 14040 booktitle = {Scientific Computing in Object-Oriented Parallel Environments}, 14041 title = {Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential 14042 Simulators}, 14043 publisher = {Springer--Verlag}, 14044 series = {Lecture Notes in Computer Science}, 14045 pages = {161--168}, 14046 year = {1997} 14047} 14048 14049% ***** DD and ML methods in Diffpack: 14050@InCollection{ dpddml, 14051 author = {A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch}, 14052 editor = {P. Bj{\o}rstad and M. Espedal and D. Keyes}, 14053 booktitle = {Proceedings of the 9th Conference on Domain Decomposition}, 14054 title = {Domain decomposition and multilevel methods in Diffpack}, 14055 year = {1997} 14056} 14057 14058@InProceedings{ bsca98, 14059 author = {David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David 14060 Alexander}, 14061 title = {Design and Implementation of an Object Oriented C++ Library for Nonlinear 14062 Optimization}, 14063 booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable 14064 Scientific and Engineering Computing}, 14065 editor = {Mike Henderson et al.}, 14066 pages = {165-173}, 14067 year = {1998} 14068} 14069 14070@Book{ scalapack-user-guide, 14071 author = {L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and J. Demmel and I. 14072 Dhillon and J. Dongarra and S. Hammarling and G. Henry and A. Petitet and K. 14073 Stanley and D. Walker and R. C. Whaley}, 14074 title = {Sca{LAPACK} Users' Guide}, 14075 publisher = {SIAM}, 14076 address = {Philadelphia, PA}, 14077 year = {1997} 14078} 14079 14080@InProceedings{ keyes99, 14081 author = {D. E. Keyes}, 14082 title = {How Scalable is Domain Decomposition in Practice?}, 14083 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 14084 Methods}, 14085 editor = {C.-H. Lai et al.}, 14086 publisher = {Domain Decomposition Press, Bergen}, 14087 note = {To appear}, 14088 year = {1999} 14089} 14090 14091@Article{ fun3d, 14092 author = {W. K. Anderson and D. L. Bonhaus}, 14093 title = {An implicit upwind algorithm for computing turbulent flows on unstructured 14094 grids}, 14095 journal = {Computers and Fluids}, 14096 year = {1994}, 14097 volume = {23}, 14098 pages = {1--21} 14099} 14100 14101% ------------------------------------------------------------------------- 14102% ------------------------------------------------------------------------- 14103@Article{ torczon, 14104 author = {Dennis, Jr., J. E. and V.~Torczon}, 14105 title = {Direct Search Methods on Parallel Machines}, 14106 journal = {SIAM J. Optimization}, 14107 volume = {1}, 14108 pages = {448--474}, 14109 year = {1991}, 14110 key = {Torczon !PDS} 14111} 14112 14113@InProceedings{ wt91, 14114 author = {D. L. Whitfield and L. K. Taylor}, 14115 title = {Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split 14116 Schemes}, 14117 booktitle = {Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference}, 14118 misc = {AIAA-91-1539}, 14119 pages = {134-145}, 14120 year = {1991} 14121} 14122 14123@Article{ ew96, 14124 author = {S. C. Eisenstat and H. F. Walker}, 14125 title = {Choosing the forcing terms in an inexact {N}ewton method}, 14126 journal = {SIAM J. Scientific Computing}, 14127 volume = {17}, 14128 year = {1996}, 14129 pages = {16--32} 14130} 14131 14132@Book{ thi93, 14133 author = {{Thinking Machines Corporation}}, 14134 title = {Users Manual for CM-Fortran}, 14135 publisher = {Thinking Machines Corporation}, 14136 year = {1993} 14137} 14138 14139@Book{ mortonmayers94, 14140 author = {K. W. Morton and D. F. Mayers}, 14141 title = {Numerical Solution of Partial Differential Equations}, 14142 publisher = {Press Syndicate of the University of Cambridge}, 14143 year = {1994} 14144} 14145 14146@Book{ heath97, 14147 author = {Michael T. Heath}, 14148 title = {Scientific Computing: An Introductory Survey}, 14149 publisher = {McGraw Hill}, 14150 year = {1997} 14151} 14152 14153@Article{ captools96, 14154 author = {C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett}, 14155 title = {Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and 14156 Performance on the Parallelization of Structured Mesh Codes}, 14157 journal = {Parallel Computing}, 14158 volume = {22}, 14159 pages = {197-226}, 14160 year = {1996} 14161} 14162 14163@Misc{ nastran-web-page, 14164 author = {{MSC Software Corporation}}, 14165 title = {{NASTRAN} {W}eb page}, 14166 howpublished = {\url{http://www.mechsolutions.com/products/nastran/}}, 14167 year = {2024} 14168} 14169 14170@Book{ hpf, 14171 author = {C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. 14172 Zosel}, 14173 title = {The High Performance Fotran Handbook}, 14174 publisher = {MIT Press}, 14175 year = {1994} 14176} 14177 14178@InProceedings{ keyes98, 14179 author = {D. E. Keyes}, 14180 title = {Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed 14181 Architectures}, 14182 booktitle = {Proceedings of the Workshop on Computational Aerosciences for the 21st Century}, 14183 editors = {M. D. Salas and W. K. Anderson}, 14184 ppublisher = {Elsevier}, 14185 year = {1998} 14186} 14187 14188@InProceedings{ pooma-atlas, 14189 author = {S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and M. Srikant and 14190 J. V. W. Reynders and M. Tholburn}, 14191 title = {{POOMA}: A High-Performance Distributed Simulation Environment for Scientific 14192 Applications}, 14193 year = {1995}, 14194 month = dec, 14195 booktitle = {Supercomputing '95 Proceedings} 14196} 14197 14198% --------------------------------------------------------------------------------- 14199% New bib entries for CRPC paper 14200@Misc{ mgnet-web-page, 14201 author = {Craig C. Douglas}, 14202 title = {{MGNet Web page}}, 14203 note = {See {\tt http://\-www.mgnet.org}} 14204} 14205 14206@Misc{ dagh-web-page, 14207 author = {M. Parashar and J. C. Browne}, 14208 title = {{DAGH Web page}}, 14209 note = {\url{http://www.caip.rutgers.edu/~parashar/DAGH}} 14210} 14211 14212@Misc{ parasol-web-page, 14213 key = {PARASOL}, 14214 title = {{PARASOL Web page}}, 14215 note = {See {\tt http://\-www.genias.de/\-projects/\-parasol}} 14216} 14217 14218@Misc{ pooma-web-page, 14219 author = {{POOMA Web page}}, 14220 note = {See {\tt http://\-www.acl.lanl.gov/pooma}} 14221} 14222 14223@Misc{ mudpack-web-page, 14224 author = {John C. Adams}, 14225 title = {{MUDPACK Web page}}, 14226 note = {See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}} 14227} 14228 14229@Misc{ pellpack-web-page, 14230 author = {Elias Houstis and John Rice and Apostolos Hadjidimos}, 14231 title = {{Parallel ELLPACK Web page}}, 14232 note = {See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}} 14233} 14234 14235@InProceedings{ pellpack95, 14236 author = {E. N. Houstis and S. B. Kim and S. Markus and P. Wu and N. E. Houstis and A.C. 14237 Catlin and S. Weerawarana and T.S. Papatheodorou}, 14238 title = {Parallel {ELLPACK} Elliptic {PDE} Solvers}, 14239 booktitle = {Proceedings of INTEL Supercomputer User's Group Conference}, 14240 address = {Albuquerque, NM}, 14241 year = {1995} 14242} 14243 14244@Misc{ nhse-web-page, 14245 author = {{National High-Performance Software Exchange Web page}}, 14246 note = {See {\tt http://\-www.nhse.org}} 14247} 14248 14249@Misc{ doug-web-page, 14250 author = {Mark J. Hagger and Linda Stals}, 14251 title = {{DOUG Web Page}}, 14252 note = {See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}} 14253} 14254 14255@TechReport{ doug97, 14256 author = {Mark J. Hagger}, 14257 title = {Automatic Domain Decomposition on Unstructured Grids {(DOUG)}}, 14258 institution = {Mathematical Sciences, University of Bath}, 14259 year = {1997}, 14260 number = {9706}, 14261 note = {Advances in Computational Mathematics (to appear)} 14262} 14263 14264@Misc{ ug-web-page, 14265 author = {{UG Web Page}}, 14266 note = {See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}} 14267} 14268 14269@Article{ ug97, 14270 author = {P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and H. 14271 Rentz-Reichert and C. Wieners}, 14272 title = {{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations}, 14273 journal = {Computing and Visualization in Science}, 14274 year = {1997}, 14275 volume = {}, 14276 pages = {} 14277} 14278 14279@Misc{ vecfem-web-page, 14280 author = {Lutz Grosz}, 14281 title = {{VECFEM Web Page}}, 14282 note = {See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}} 14283} 14284 14285@Misc{ atlas-web-page, 14286 author = {R. Clint {Whaley et al.}}, 14287 title = {{ATLAS Web Page}}, 14288 howpublished = {\url{http://math-atlas.sourceforge.net}} 14289} 14290 14291@Misc{ fenics-web-page, 14292 author = {Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. 14293 Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott}, 14294 title = {{FEniCS Web Page}}, 14295 note = {\url{http://www.fenicsproject.org}}, 14296 year = {2005} 14297} 14298 14299@Misc{ matlab-web-page, 14300 author = {{The} {MathWorks}}, 14301 title = {{Matlab} {Web} page}, 14302 url = {http://www.mathworks.com} 14303} 14304 14305@Misc{ phipac-web-page, 14306 author = {J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and J. Demmel and C. Chin 14307 and D. Lam}, 14308 title = {{PHiPAC Web Page}}, 14309 note = {See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}} 14310} 14311 14312@InProceedings{ kelp, 14313 author = {Stephan J. Fink and Scott B. Baden and Scott R. Kohn}, 14314 title = {Flexible Communication Mechanisms for Dynamic Structured Applications}, 14315 booktitle = {Irregular '96}, 14316 year = {1996} 14317} 14318 14319@Unpublished{ kelp-web-page, 14320 author = {Scott Baden}, 14321 title = {{KeLP} {W}eb page}, 14322 note = {See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}} 14323} 14324 14325@InProceedings{ hk99, 14326 author = {R. Hornung and S. 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The different versions are examined for efficiency on a computer 14388 architecture which uses vector processing and has pipelined instruction execution. 14389 By using the advanced architectural features of such machines, one can usually 14390 achieve maximum performance, and tremendous improvements in terms of execution 14391 speed can be seen over conventional computers.}, 14392 classification= {723; 921}, 14393 journalabr = {SIAM Rev}, 14394 keywords = {computer programming --- Algorithms; dense matrices; linear algebra algorithms; 14395 mathematical programming; vector pipeline machine} 14396} 14397 14398@Book{ qv99, 14399 author = {Alfio Quarteroni and Alberto Valli}, 14400 title = {Domain Decomposition Methods for Partial Differential Equations}, 14401 publisher = {Oxford Science Publications}, 14402 address = {Oxford}, 14403 year = {1999} 14404} 14405 14406@Book{ ksv97, 14407 editor = {David E. Keyes and Ahmed Sameh and V. 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Softw.}, 15676 volume = {31}, 15677 year = {2005}, 15678 pages = {326--350} 15679} 15680 15681@Unpublished{ compass:homepage, 15682 author = {Panagiotis {Spentzouris (PI)}}, 15683 title = {Community Petascale Project for Accelerator Science and Simulation (ComPASS)}, 15684 note = {SciDAC2 project, see \url{https://compass.fnal.gov/}} 15685} 15686 15687@Unpublished{ cmsnf:homepage, 15688 author = {{Todd Allen, Director}}, 15689 title = {{Center for Materials Science of Nuclear Fuel}}, 15690 note = {Energy Frontier Research Center, see 15691 \url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}} 15692} 15693 15694@Unpublished{ dvi-materials:project, 15695 author = {{L.~C.} {McInnes (PI)}}, 15696 title = {Large-Scale Differential Variational Inequalities for Heterogeneous Materials}, 15697 note = {{SciDAC}-e project}, 15698 year = {2011} 15699} 15700 15701@Misc{ scidac:homepage, 15702 author = {{DOE Office of Science}}, 15703 title = {{Scientific Discovery through Advanced Computing}}, 15704 year = {2007}, 15705 howpublished = {\url{http://www.scidac.gov}} 15706} 15707 15708@Misc{ corba, 15709 author = {{Object Management Group}}, 15710 year = {2007}, 15711 title = {{Common Object Request Broker Architecture (CORBA)}}, 15712 howpublished = {\url{http://www.corba.org}} 15713} 15714 15715@Article{ uedge, 15716 author = {T.~D. 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Wilson}, 15738 title = {{BOUT++}: A Framework for Parallel Plasma Fluid Simulations}, 15739 journal = {Computer Physics Communications}, 15740 year = {2009}, 15741 volume = {180}, 15742 issue = {9}, 15743 pages = {1467 -- 1480}, 15744 note = {} 15745} 15746 15747@Article{ tempest, 15748 author = {Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and M.R. Dorr and J.A. Hittinger 15749 and G. Kerbel and W.M. Nevins and T. Rognlien}, 15750 title = {Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST}, 15751 journal = {Bull. Am. Phys. Soc. }, 15752 year = {2005}, 15753 volume = {50}, 15754 number = {86}, 15755 pages = {CP1}, 15756 note = {} 15757} 15758 15759@Article{ ccahpc, 15760 author = {David E. Bernholdt and Benjamin A. Allan and Robert Armstrong and Felipe Bertrand 15761 and Kenneth Chiu and Tamara L. Dahlgren and Kostadin Damevski and Wael R. Elwasif 15762 and Thomas G. W. Epperly and Madhusudhan Govindaraju and Daniel S. Katz and James 15763 A. Kohl and Manoj Krishnan and Gary Kumfert and J. Walter Larson and Sophia 15764 Lefantzi and Michael J. Lewis and Allen D. Malony and Lois C. McInnes and Jarek 15765 Nieplocha and Boyana Norris and Steven G. Parker and Jaideep Ray and Sameer Shende 15766 and Theresa L. Windus and Shujia Zhou}, 15767 title = {A Component Architecture for High-Performance Scientific Computing}, 15768 journal = {Intl. J. High-Perf. Computing Appl.}, 15769 volume = {20}, 15770 pages = {163--202}, 15771 year = {2006}, 15772 note = {ACTS Collection special issue} 15773} 15774 15775@Misc{ cca-forum:homepage, 15776 author = {{Common Component Architecture Forum}}, 15777 note = {\url{http://www.cca-forum.org}}, 15778 year = {2010} 15779} 15780 15781@Misc{ petsc:driven-cavity-example, 15782 title = {{PETSc Driven Cavity Example Code}}, 15783 author = {B. F. {Smith et al.}}, 15784 howpublished = {\url{https://petsc.org/release/src/snes/tutorials/ex19.c.html}} 15785} 15786 15787@Misc{ petsc-dm:webpage, 15788 author = {B. F. {Smith et al.}}, 15789 title = {{PETSc DM Webpage}}, 15790 howpublished = {\url{https://petsc.org/release/manualpages/DM/}}, 15791 year = {2018} 15792} 15793 15794@Misc{ unic-ref, 15795 author = {Giuseppe Palmiotti}, 15796 title = {{UNIC} Neutronics Software}, 15797 note = {Nuclear Engineering Division, Argonne National Laboratory} 15798} 15799 15800% ----------------------------------------------------------------------- 15801% Model coupling refs 15802@Book{ greve-blatter, 15803 author = {Ralf Greve and Heinz Blatter}, 15804 title = {Dynamics of Ice Sheets and Glaciers}, 15805 series = {Advances in Geophysical and Environmental Mechanics and Mathematics}, 15806 publisher = {Springer}, 15807 year = {2009} 15808} 15809 15810@Misc{ doe-isicles, 15811 key = {ISICLES}, 15812 title = {Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}}, 15813 howpublished = {\url{http://www.csm.ornl.gov/ISICLES/index.html}} 15814} 15815 15816@Article{ safta2011tchem, 15817 title = {TChem-a software toolkit for the analysis of complex kinetic models}, 15818 author = {Safta, Cosmin and Najm, Habib N and Knio, Omar}, 15819 journal = {Sandia Report, SAND2011-3282}, 15820 year = {2011} 15821} 15822 15823@Misc{ chemkin-website, 15824 key = {chemkin}, 15825 title = {ANSYS Chemkin-Pro Website}, 15826 howpublished = {\url{http://www.ansys.com/products/fluids/ansys-chemkin-pro}}, 15827 year = {2017} 15828} 15829 15830@Misc{ mct-website, 15831 key = {MCT}, 15832 title = {{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite}, 15833 howpublished = {\url{http://www.mcs.anl.gov/mct}} 15834} 15835 15836@Article{ larson:05, 15837 author = {Jay Larson and Robert Jacob and Everest Ong}, 15838 title = {{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building 15839 Multi-Physics Parallel Coupled Models}, 15840 journal = {Int. 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Dongarra and C. J. K. Tan}, 15902 series = {Lecture Notes in Computer Science}, 15903 volume = {2073}, 15904 publisher = {Springer-Verlag} 15905} 15906 15907@InProceedings{ lefantzi03, 15908 author = {S. Lefantzi and J. Ray}, 15909 year = {2003}, 15910 title = {A Component-based Scientific Toolkit for Reacting Flows}, 15911 booktitle = {Proc. Second MIT Conference on Computational Fluid and Solid Mechanics}, 15912 volume = {2}, 15913 publisher = {Elsevier} 15914} 15915 15916@Article{ boville98, 15917 author = {B. A. Boville and P. R. Gent}, 15918 title = {The {NCAR} Climate System Model, Version One}, 15919 journal = {Journal of Climate}, 15920 volume = {11}, 15921 year = {1998}, 15922 pages = {1115--1130} 15923} 15924 15925@Misc{ paraschivoiu99, 15926 author = {M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes}, 15927 title = {Multi-domain multi-model formulation for compressible flows: Conservative 15928 interface coupling and parallel implicit solvers for {3D} unstructured meshes}, 15929 note = {AIAA Paper 99-0784}, 15930 year = {1999} 15931} 15932 15933@Article{ peszynska, 15934 author = {M. Peszynska and M. F. Wheeler and I. Yotov}, 15935 title = {Mortar upscaling for multiphysics flow in porous media}, 15936 journal = {Computational Geosciences} 15937} 15938 15939@TechReport{ wheeler00, 15940 author = {M. F. Wheeler and J. Wheeler and M. Peszynska}, 15941 title = {A distributed computing portal for coupling multi-physics and multiple domains in 15942 porous media}, 15943 institution = {University of Texas at Austin}, 15944 number = {TICAM 00-03}, 15945 year = {2000} 15946} 15947 15948@TechReport{ peszynska00, 15949 author = {M. Peszynska and Q. Lu and M. F. Wheeler}, 15950 title = {Multiphysics Coupling of Codes}, 15951 institution = {University of Texas at Austin}, 15952 number = {TICAM 00-02}, 15953 year = {2000} 15954} 15955 15956@Article{ joshaghanijoodatnakshatrala2019, 15957 title = {A stabilized mixed discontinuous Galerkin formulation for double 15958 porosity/permeability model}, 15959 author = {MS Joshaghani and SHS Joodat and KB Nakshatrala}, 15960 journal = {Computer Methods in Applied Mechanics and Engineering}, 15961 volume = {352}, 15962 pages = {508--560}, 15963 year = {2019} 15964} 15965 15966@InProceedings{ cai99, 15967 author = {X.-C. Cai and M. Paraschivoiu and M. Sarkis}, 15968 title = {An explicit multi-model compressible flow formulation based on the full potential 15969 equation and the {Euler} equations on {3D} unstructured meshes}, 15970 booktitle = {Proceedings of the 11th International Conference on Domain Decomposition 15971 Methods}, 15972 editor = {C-H. Lai and P. Bjorstad and M. Cross and O. Widlund}, 15973 year = {1999} 15974} 15975 15976@Article{ he05, 15977 author = {Yun He and Chris H. Q. Ding}, 15978 title = {Coupling Multi-Component Models with {MPH} on Distributed Memory Computer 15979 Architectures}, 15980 year = {2005}, 15981 volume = {19}, 15982 pages = {329--240}, 15983 number = {3}, 15984 journal = {Int. Journal of High Performance Computing Applications} 15985} 15986 15987@InProceedings{ uiuc-rocket-center02, 15988 author = {W. A. Dick and M. T. Heath}, 15989 title = {Whole System Simulation of Solid Propellant Rockets}, 15990 booktitle = {Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345}, 15991 month = jul, 15992 year = {2002} 15993} 15994 15995@InProceedings{ toth04, 15996 author = {G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and K. W. 15997 Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and R. 15998 Oehmke}, 15999 title = {A Physics-Based Software Framework for Sun-Earth Connection Modeling}, 16000 editor = {A. T. Y. Lui and Y. Kamide and G. Consolini}, 16001 booktitle = {Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the 16002 Sun-Earth Connection}, 16003 year = {2004}, 16004 publisher = {Elsevier}, 16005 pages = {383--397} 16006} 16007 16008@Misc{ csdrm:web, 16009 author = {M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. 16010 Shepherd}, 16011 title = {{Center for Simulation of Dynamic Response of Materials}}, 16012 note = {California Institute of Technology, see \url{http://csdrm.caltech.edu}} 16013} 16014 16015@Misc{ csar:web, 16016 author = {M. {Heath (Director)}}, 16017 title = {{Center for Simulation of Advanced Rockets}}, 16018 note = {University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}} 16019} 16020 16021@Misc{ csafe:web, 16022 author = {D. {Pershing (Director)}}, 16023 title = {{Center for Simulation of Accidental Fires and Explosions}}, 16024 note = {University of Utah, see \url{http://www.csafe.utah.edu}} 16025} 16026 16027@Misc{ cits:web, 16028 author = {P. {Moin (Director)}}, 16029 title = {{Center for Integrated Turbulence Simulations}}, 16030 note = {Stanford University, see \url{http://www.stanford.edu/group/cits}} 16031} 16032 16033@Misc{ flash:web, 16034 author = {D. {Lamb (Director)}}, 16035 title = {{Center for Integrated Turbulence Simulations}}, 16036 note = {University of Chicago, see \url{http://flash.uchicago.edu}} 16037} 16038 16039@TechReport{ utah-csafe03, 16040 author = {J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry}, 16041 title = {An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction 16042 Problems, Part 1: Algorithm Development}, 16043 institution = {University of Utah, Center for the Simulation of Accidental Fires and 16044 Explosions}, 16045 year = {2003} 16046} 16047 16048@InBook{ shepherd07, 16049 author = {M. Shepherd and E. Seol and B. FrantzDale}, 16050 title = {Toward a Multi-Model Hierarchy to Support Multiscale Simulations}, 16051 year = {2007}, 16052 booktitle = {CRC Handbook of Dynamic System Modeling}, 16053 publisher = {Wiley}, 16054 pages = {1--41}, 16055 note = {also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute} 16056} 16057 16058@InProceedings{ cactus02, 16059 author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas 16060 Radke and Edward Seidel and John Shalf}, 16061 title = {The {Cactus} Framework and Toolkit: Design and Applications}, 16062 booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science}, 16063 year = {2002}, 16064 url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf} 16065} 16066 16067@Misc{ cactus:homepage, 16068 author = {G. {Allen et al.}}, 16069 title = {{Cactus Web page}}, 16070 howpublished = {\url{http://cactuscode.org}} 16071} 16072 16073@Misc{ open-grid-forum:web, 16074 key = {{Open Grid Forum}}, 16075 title = {{Open Grid Forum}}, 16076 note = {See \url{http://www.ogf.org}} 16077} 16078 16079@Misc{ nox:web, 16080 author = {Tamara Kolda and Roger {Pawlowski et al.}}, 16081 title = {Nonlinear Object-Oriented Solutions {(NOX)}}, 16082 note = {See \url{http://software.sandia.gov/nox}} 16083} 16084 16085@Misc{ chombo:web, 16086 author = {P. {Colella (PI)}}, 16087 title = {{Chombo}}, 16088 note = {See \url{http://seesar.lbl.gov/anag/chombo}} 16089} 16090 16091@Article{ lanzkron96, 16092 author = {P. J. Lanzkron and D. J. Rose and J. T. Wilkes}, 16093 title = {An Analysis of Approximate Nonlinear Elimination}, 16094 journal = {SIAM J. Sci. Comput.}, 16095 volume = {17}, 16096 year = {1996}, 16097 pages = {538--559} 16098} 16099 16100@Article{ jiang95, 16101 author = {J. Jiang and P. Forsyth}, 16102 title = {Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} 16103 Equations}, 16104 journal = {Computers and Fluids}, 16105 volume = {24}, 16106 pages = {753--770}, 16107 year = {1995} 16108} 16109 16110@Article{ young90, 16111 author = {D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant}, 16112 title = {Global Convergence of Inexact {Newton} Methods for Transonic Flow}, 16113 journal = {Int. J. Numer. Methods Fluids}, 16114 volume = {11}, 16115 pages = {1075--1095}, 16116 year = {1990} 16117} 16118 16119@Article{ fishwick04, 16120 author = {Paul A. Fishwick}, 16121 title = {Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach 16122 to Interrelating Model Structures}, 16123 journal = {SCS Trans. on Simulation}, 16124 note = {Special Issue in Grand Challenges in Computer Simulation}, 16125 year = {2004} 16126} 16127 16128@Article{ fishwick03, 16129 author = {Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim}, 16130 title = {{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation}, 16131 booktitle = {Proceedings of the 2003 Winter Simulation Conference}, 16132 editor = {S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice}, 16133 year = {2003} 16134} 16135 16136@InProceedings{ kirner00, 16137 author = {T. G. Kirner and V. F. 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Messerschmitt}, 16163 title = {Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems}, 16164 journal = {Int. Journal of Computer Simulation}, 16165 volume = {4}, 16166 pages = {155--182}, 16167 year = {1994} 16168} 16169 16170@Article{ mu95, 16171 author = {M. Mu and J.R. Rice}, 16172 title = {Modeling with collaborating {PDE} solvers - Theory and practice}, 16173 journal = {Comp. Syst. Engr.}, 16174 volume = {6}, 16175 year = {1995}, 16176 pages = {87--95} 16177} 16178 16179@TechReport{ drashansky96, 16180 title = {Multidisciplinary Problem Solving using Agents in a Cluster Environment}, 16181 author = {R. Drashansky and A. Joshi and J. R. Rice}, 16182 institution = {Emory Universtity, Department of Mathematics and Computer Science}, 16183 year = {1996} 16184} 16185 16186@Article{ michopoulos05, 16187 title = {Survey on Modeling and Simulation of Multiphysics Systems}, 16188 author = {John G. Michopoulos and Charbel Farhat and Jacob Fish}, 16189 journal = {Journal of Computing and Information Science in Engineering}, 16190 volume = {5}, 16191 issue = {3}, 16192 pages = {198--213}, 16193 year = {2005} 16194} 16195 16196@Article{ dubey09, 16197 title = {Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel 16198 Multiphysics Simulation Code}, 16199 author = {A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. 16200 Siegel and K. Weide}, 16201 journal = {Parallel Computing}, 16202 volume = {35}, 16203 issue = {10 -- 11}, 16204 pages = {512 -- 522}, 16205 year = {2009} 16206} 16207 16208@Book{ bottloring95, 16209 author = {Raoul Bott and Loring W. Tu}, 16210 title = {Differential Forms in Algebraic Topology}, 16211 publisher = {Springer}, 16212 year = {1995} 16213} 16214 16215@Book{ kobayashinomizu96, 16216 author = {Shoshichi Kobayashi and Katsumi Nomizu}, 16217 title = {Foundations of Differential Geometry}, 16218 publisher = {Wiley-Interscience}, 16219 year = {1996} 16220} 16221 16222@Article{ hornungkohn02, 16223 author = {Richard D. Hornung and Scott R. Kohn}, 16224 title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework}, 16225 journal = {Concurrency and Computation: Practice and Experience}, 16226 volume = {14}, 16227 pages = {347--368}, 16228 year = {2002} 16229} 16230 16231@InProceedings{ concepts06, 16232 author = {Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and 16233 Gabriel Dos Reis and Andrew Lumsdaine}, 16234 title = {Concepts: Linguistic Support for Generic Programming in C++}, 16235 booktitle = {Proceedings of OOPSLA 2006}, 16236 year = {2006}, 16237 pages = {???--???} 16238} 16239 16240@Book{ hatcher02, 16241 author = {Hatcher, Allen}, 16242 title = {Algebraic Topology}, 16243 publisher = {Cambridge University Press}, 16244 year = {2002} 16245} 16246 16247@Book{ gammahelmjohnsonvlissides95, 16248 abstract = {{Design Patterns is a modern classic in the literature of object-oriented 16249 development, offering timeless and elegant solutions to common problems in 16250 software design. It describes patterns for managing object creation, composing 16251 objects into larger structures, and coordinating control flow between objects. The 16252 book provides numerous examples where using composition rather than inheritance 16253 can improve the reusability and flexibility of code. Note, though, that it's not a 16254 tutorial but a catalog that you can use to find an object-oriented design pattern 16255 that's appropriate for the needs of your particular application--a selection for 16256 virtuoso programmers who appreciate (or require) consistent, well-engineered 16257 object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is 16258 more valuable than ever! 16259 16260 Use the contents of the CD to create your own design documents and reusable 16261 components. The CD contains: 23 patterns you can cut and paste into your own 16262 design documents; sample code demonstrating pattern implementation; complete 16263 Design Patterns content in standard HTML format, with numerous hyperlinked 16264 cross-references; accessed through a standard web browser; Java-based dynamic 16265 search mechanism, enhancing online search capabilities; graphical user environment, 16266 allowing ease of navigation. 16267 16268 First published in 1995, this landmark work on object-oriented software design 16269 presents a catalog of simple and succinct solutions to common design problems. 16270 Created by four experienced designers, the 23 patterns contained herein have 16271 become an essential resource for anyone developing reusable object-oriented 16272 software. In response to reader demand, the complete text and pattern catalog are 16273 now available on CD-ROM. This electronic version of Design Patterns enables 16274 programmers to install the book directly onto a computer or network for use as an 16275 online reference for creating reusable object-oriented software. 16276 16277 The authors first describe what patterns are and how they can help you in the 16278 design process. They then systematically name, explain, evaluate, and catalog 16279 recurring designs in object-oriented systems. All patterns are compiled from 16280 real-world examples and include code that demonstrates how they may be implemented 16281 in object-oriented programming languages such as C++ and Smalltalk. Readers who 16282 already own the book will want the CD to take advantage of its dynamic search 16283 mechanism and ready-to-install patterns.}}, 16284 author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John}, 16285 citeulike-article-id={115158}, 16286 howpublished = {Hardcover}, 16287 isbn = {0201633612}, 16288 keywords = {1995 algorithms architecture book books computer computing design design-pattern 16289 design-patterns design_patterns designpatterns development diplom entwurfsmuster 16290 four gang gof java mathgamespatterns no-tag object object-orientation 16291 object-oriented of oo-patterns oop oriented pattern patterns programming se 16292 software software-development software-engineering software_design 16293 softwareengineering standard}, 16294 month = jan, 16295 publisher = {{Addison-Wesley Professional}}, 16296 title = {Design Patterns}, 16297 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612}, 16298 year = {1995} 16299} 16300 16301@InProceedings{ chaco95, 16302 author = {Bruce Hendrickson and Robert Leland}, 16303 title = {A multilevel algorithm for partitioning graphs}, 16304 booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing 16305 (CDROM)}, 16306 year = {1995}, 16307 isbn = {0-89791-816-9}, 16308 pages = {28}, 16309 location = {San Diego, California, United States}, 16310 doi = {10.1145/224170.224228}, 16311 publisher = {ACM Press}, 16312 address = {New York} 16313} 16314 16315@Book{ aleksandrov98, 16316 author = {Aleksandrov, Pavel S.}, 16317 title = {Combinatorial Topology}, 16318 publisher = {Dover}, 16319 volume = {3}, 16320 year = {1998} 16321} 16322 16323@Book{ steenrod99, 16324 abstract = {{ Fibre bundles, now an integral part of differential geometry, are also of great 16325 importance in modern physics--such as in gauge theory. This book, a succinct 16326 introduction to the subject by renown mathematician Norman Steenrod, was the first 16327 to present the subject systematically. 16328 16329 It begins with a general introduction to bundles, including such topics as 16330 differentiable manifolds and covering spaces. The author then provides brief 16331 surveys of advanced topics, such as homotopy theory and cohomology theory, before 16332 using them to study further properties of fibre bundles. The result is a classic 16333 and timeless work of great utility that will appeal to serious mathematicians and 16334 theoretical physicists alike. }}, 16335 author = {Steenrod, Norman}, 16336 citeulike-article-id={712999}, 16337 howpublished = {Paperback}, 16338 isbn = {0691005486}, 16339 keywords = {fibre_bundles topology}, 16340 month = apr, 16341 publisher = {{Princeton University Press}}, 16342 title = {The Topology of Fibre Bundles. (PMS-14)}, 16343 url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486}, 16344 year = {1999} 16345} 16346 16347@Book{ bredon97, 16348 author = {Bredon, Glen E.}, 16349 title = {Sheaf Theory}, 16350 publisher = {Springer}, 16351 pages = {524}, 16352 series = {Graduate Texts in Mathematics}, 16353 year = {1997} 16354} 16355 16356@TechReport{ tautgesmeyers04, 16357 title = {{MOAB}: A Mesh-Oriented Database}, 16358 author = {Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey 16359 Ernst}, 16360 institution = {Sandia National Laboratories}, 16361 number = {SAND2004-1592}, 16362 month = apr, 16363 year = {2004} 16364} 16365 16366@Article{ tautges04, 16367 author = {Timothy J. Tautges}, 16368 title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation}, 16369 journal = {Engineering With Computers}, 16370 volume = {20}, 16371 pages = {286--293}, 16372 year = {2004} 16373} 16374 16375@InProceedings{ meyers02, 16376 author = {Ray Meyers et. al}, 16377 title = {{SNL} Implementation of the {TSTT} Mesh Interface}, 16378 booktitle = {8th International conference on numerical grid generation in computational field 16379 simulations}, 16380 month = jun, 16381 year = {2002} 16382} 16383 16384@InProceedings{ seolshepard05, 16385 author = {E. S. Seol and Mark S. Shephard}, 16386 title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive 16387 Analysis}, 16388 booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics}, 16389 year = {2005} 16390} 16391 16392@Article{ lishephardbeall2005, 16393 title = {3D anisotropic mesh adaptation by mesh modification}, 16394 author = {Xiangrong Li and Mark S Shephard and Mark W Beall}, 16395 journal = {Computer methods in applied mechanics and engineering}, 16396 volume = {194}, 16397 number = {48-49}, 16398 pages = {4915--4950}, 16399 year = {2005}, 16400} 16401 16402@Article{ lushephardtendulkarbeall2014, 16403 title = {Parallel mesh adaptation for high-order finite element methods with curved element geometry}, 16404 author = {Qiukai Lu and Mark S Shephard and Saurabh Tendulkar and Mark W Beall}, 16405 journal = {Engineering with Computers}, 16406 volume = {30}, 16407 pages = {271--286}, 16408 year = {2014}, 16409} 16410 16411@Article{ beallwalshshephard04, 16412 author = {Mark W. Beall and Joe Walsh and Mark S. Shephard}, 16413 title = {A comparison of techniques for geometry access related to mesh generation}, 16414 journal = {Engineering With Computers}, 16415 volume = {20}, 16416 number = {3}, 16417 pages = {210--221}, 16418 year = {2004} 16419} 16420 16421@Article{ careyandersoncarneskirk04, 16422 author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. 16423 Kirk}, 16424 title = {Some aspects of adaptive grid technology related to boundary and interior 16425 layers}, 16426 journal = {Journal of Computational Applied Mathematics}, 16427 volume = {166}, 16428 number = {1}, 16429 pages = {55--86}, 16430 year = {2004} 16431} 16432 16433@PhDThesis{ gralthesis, 16434 author = {Guntram Berti}, 16435 title = {Generic Software Components for Scientific Computing}, 16436 school = {TU Cottbus}, 16437 year = {2000}, 16438 note = {\url{http://www.math.tu-cottbus.de/~berti/diss}} 16439} 16440 16441@Article{ whitehead1949, 16442 title = {Combinatorial homotopy. I}, 16443 author = {John HC Whitehead}, 16444 journal = {Bulletin of the American Mathematical Society}, 16445 volume = {55}, 16446 number = {3. P1}, 16447 pages = {213--245}, 16448 year = {1949}, 16449 publisher = {American Mathematical Society} 16450} 16451 16452@Article{ beylkincoifmanrokhlin91, 16453 author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin}, 16454 title = {Fast Wavelet Transforms and Numerical Algorithms {I}}, 16455 journal = {Communications on Pure and Applied Mathematics}, 16456 volume = {44}, 16457 pages = {141--183}, 16458 year = {1991} 16459} 16460 16461@Book{ wesseling92, 16462 author = {Pieter Wesseling}, 16463 title = {An Introduction to Multigrid Methods}, 16464 publisher = {John Wiley and Sons}, 16465 year = {1992} 16466} 16467 16468@Book{ grakakos04, 16469 author = {Loukas Grakakos}, 16470 title = {Classical and Modern Fourier Analysis}, 16471 publisher = {Pearson Education}, 16472 address = {New Jersey}, 16473 year = {2004} 16474} 16475 16476@Misc{ hlib-web-page, 16477 key = {HLib}, 16478 title = {{HLib} {Web} page}, 16479 note = {{\texttt{http://www.hlib.org/}}}, 16480 annote = {Hierarchical matrices for fast integral transform} 16481} 16482 16483@Article{ hackbusch99, 16484 author = {Wolfgang Hackbusch}, 16485 title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: 16486 Introduction to {$\mathcal H$}-matrices}, 16487 journal = {Computing}, 16488 volume = {62}, 16489 pages = {89--108}, 16490 year = {1999} 16491} 16492 16493@TechReport{ kay1999green, 16494 title = {A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes 16495 equations}, 16496 author = {Kay, D. and Loghin, D.}, 16497 year = {1999}, 16498 institution = {Oxford University Computing Laboratory}, 16499 number = {99/06} 16500} 16501 16502@Article{ bebendorf2003existence, 16503 title = {Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of 16504 elliptic operators with {$L^\infty$}-coefficients}, 16505 author = {Bebendorf, M. and Hackbusch, W.}, 16506 journal = {Numerische Mathematik}, 16507 volume = {95}, 16508 number = {1}, 16509 pages = {1--28}, 16510 year = {2003}, 16511 publisher = {Springer} 16512} 16513 16514@Article{ hackbusch2005direct, 16515 title = {Direct {S}chur complement method by domain decomposition based on {$\mathcal 16516 H$}-matrix approximation}, 16517 author = {Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.}, 16518 journal = {Computing and Visualization in Science}, 16519 volume = {8}, 16520 number = {3}, 16521 pages = {179--188}, 16522 year = {2005}, 16523 publisher = {Springer} 16524} 16525 16526@TechReport{ duphof2003, 16527 author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. 16528 Logg and L. R. Scott}, 16529 title = {The {FE}ni{CS} project}, 16530 institution = {Chalmers Finite Element Center Preprint Series}, 16531 number = {2003--21}, 16532 year = {2003} 16533} 16534 16535@Article{ flame01, 16536 author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de 16537 Geijn}, 16538 title = {{FLAME}: Formal Linear Algebra Methods Environment}, 16539 journal = {Transactions on Mathematical Software}, 16540 volume = {27}, 16541 number = {4}, 16542 year = {2001}, 16543 pages = {422--455} 16544} 16545 16546@Article{ puschel05, 16547 author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and David Padua 16548 and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and Franz Franchetti and 16549 Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen and Robert W. Johnson and 16550 Nick Rizzolo}, 16551 title = {{SPIRAL}: Code Generation for {DSP} Transforms}, 16552 journal = {Proceedings of the IEEE}, 16553 volume = {93}, 16554 number = {2}, 16555 year = {2005}, 16556 note = {special issue on "Program Generation, Optimization, and Adaptation"} 16557} 16558 16559@Article{ kirbylogg06, 16560 author = {Robert C. Kirby and Anders Logg}, 16561 title = {A compiler for variational forms}, 16562 journal = {ACM Transactions on Mathematical Software}, 16563 volume = {32}, 16564 number = {3}, 16565 year = {2006}, 16566 issn = {0098-3500}, 16567 pages = {417--444}, 16568 doi = {10.1145/1163641.1163644}, 16569 publisher = {ACM Press}, 16570 address = {New York, NY} 16571} 16572 16573@Article{ kirbylogg07, 16574 author = {Robert C. Kirby and Anders Logg}, 16575 title = {Efficient compilation of a class of variational forms}, 16576 journal = {ACM Transactions on Mathematical Software}, 16577 volume = {33}, 16578 number = {3}, 16579 year = {2007}, 16580 issn = {0098-3500}, 16581 pages = {17}, 16582 doi = {10.1145/1268769.1268771}, 16583 publisher = {ACM Press}, 16584 address = {New York, NY} 16585} 16586 16587@Article{ bankdupont81, 16588 author = {Randolph Bank and Todd Dupont}, 16589 title = {An optimal order process for solving finite element equations}, 16590 journal = {Mathematics of Computation}, 16591 volume = {36}, 16592 pages = {35--51}, 16593 year = {1981} 16594} 16595 16596@TechReport{ adams00, 16597 author = {Mark F. Adams}, 16598 title = {Evaluation of three unstructured multigrid methods on 3D finite element problems 16599 in solid mechanics}, 16600 institution = {UC Berkeley}, 16601 number = {CSD-00-1103}, 16602 year = {2000}, 16603 url = {citeseer.ist.psu.edu/article/adams00evaluation.html} 16604} 16605 16606@Article{ bergengradlhuelsemannruede06, 16607 author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude}, 16608 title = {A Massively Parallel Multigrid Method for Finite Elements}, 16609 journal = {Computing in Science \& Engineering}, 16610 volume = {8}, 16611 number = {6}, 16612 pages = {56--62}, 16613 year = {2006} 16614} 16615 16616@MastersThesis{ brunethesis08, 16617 author = {Peter R. Brune}, 16618 title = {Enabling Unstructured Multigrid Under the Sieve Framework}, 16619 school = {University of Chicago}, 16620 address = {Chicago, IL}, 16621 year = {2008}, 16622 month = feb 16623} 16624 16625@Article{ arnoldwinther02, 16626 author = {Douglas N. Arnold and Ragnar Winther}, 16627 title = {Mixed finite elements for elasticity}, 16628 journal = {Numerische Mathematik}, 16629 volume = {92}, 16630 number = {3}, 16631 month = sep, 16632 year = {2002}, 16633 pages = {401--419}, 16634 doi = {10.1007/s002110100348} 16635} 16636 16637@Article{ arnoldfalkwinther06, 16638 author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther}, 16639 title = {Finite element exterior calculus, homological techniques, and applications}, 16640 journal = {Acta Numerica}, 16641 year = {2006}, 16642 volume = {15}, 16643 pages = {1--155}, 16644 publisher = {Cambridge University Press}, 16645 doi = {10.1017/S0962492906210018} 16646} 16647 16648@Article{ kirby04, 16649 author = {Robert C. Kirby}, 16650 title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis 16651 functions}, 16652 journal = {ACM Transactions on Mathematical Software}, 16653 volume = {30}, 16654 number = {4}, 16655 year = {2004}, 16656 issn = {0098-3500}, 16657 pages = {502--516}, 16658 doi = {10.1145/1039813.1039820}, 16659 publisher = {ACM Press}, 16660 address = {New York, NY} 16661} 16662 16663@Article{ kirby06, 16664 author = {Robert C. Kirby}, 16665 title = {Optimizing {FIAT} with level 3 {BLAS}}, 16666 journal = {ACM Transactions on Mathematical Software}, 16667 volume = {32}, 16668 number = {2}, 16669 year = {2006}, 16670 issn = {0098-3500}, 16671 pages = {223--235}, 16672 doi = {10.1145/1141885.1141889}, 16673 publisher = {ACM Press}, 16674 address = {New York, NY} 16675} 16676 16677@Misc{ bluecrystal08, 16678 author = {{B}lue {C}rystal Cluster}, 16679 title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}}, 16680 year = {2008}, 16681 note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}} 16682} 16683 16684@Article{ beylkin95, 16685 author = {Gregory Beylkin}, 16686 title = {On the Fast Fourier Transform of Functions With Singularities}, 16687 journal = {Applied and Computational Harmonic Analysis}, 16688 volume = {2}, 16689 pages = {363--381}, 16690 year = {1995} 16691} 16692 16693@InProceedings{ riehl08, 16694 author = {Jonathan Riehl}, 16695 title = {Implementing the MyFEM Embedded Domain-specific Language}, 16696 booktitle = {Proceedings of the Second International Workshop on Domain-specific Program 16697 Development (DSPD'08)}, 16698 address = {Nashville, TN}, 16699 year = {2008} 16700} 16701 16702@Article{ appel85, 16703 author = {Andrew W. Appel}, 16704 date-added = {2008-02-27 12:23:39 +0000}, 16705 date-modified = {2008-02-27 12:24:02 +0000}, 16706 doi = {10.1137/0906008}, 16707 journal = {SIAM Journal on Scientific and Statistical Computing}, 16708 keywords = {treecodes}, 16709 number = {1}, 16710 pages = {85-103}, 16711 publisher = {SIAM}, 16712 title = {An Efficient Program for Many-Body Simulation}, 16713 volume = {6}, 16714 year = {1985} 16715} 16716 16717@Article{ ewald21, 16718 author = {{Ewald}, P.~P.}, 16719 title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, 16720 journal = {Annalen der Physik}, 16721 year = {1921}, 16722 volume = {369}, 16723 pages = {253-287}, 16724 doi = {10.1002/andp.19213690304}, 16725 adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E}, 16726 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 16727} 16728 16729@Article{ greengardrokhlin87, 16730 author = {L. Greengard and V. 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Andrew McCammon}, 16757 title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular 16758 systems}, 16759 journal = {PNAS}, 16760 doi = {10.1073/pnas.0605166103}, 16761 volume = {102}, 16762 number = {51}, 16763 year = {2006}, 16764 pages = {19314--19319} 16765} 16766 16767@Article{ schussnadlereisenberg01, 16768 author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg}, 16769 title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel 16770 from a molecular model}, 16771 journal = {Physical Review E}, 16772 volume = {64}, 16773 number = {3}, 16774 year = {2001} 16775} 16776 16777@Book{ hairerlubichwanner02, 16778 author = {E. Hairer and Ch. Lubich and G. Wanner}, 16779 title = {Geometric Numerical Integration}, 16780 publisher = {Springer-Verlag}, 16781 address = {Berlin Heidelberg}, 16782 year = {2002} 16783} 16784 16785@Article{ holstbakerwang00, 16786 author = {M. Holst and N. Baker and F. Wang}, 16787 title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann 16788 equation on massively parallel computers}, 16789 journal = {Journal of Computational Chemistry}, 16790 volume = {21}, 16791 year = {2000} 16792} 16793 16794@Book{ hockneyeastwood81, 16795 author = {R. Hockney and J. Eastwood}, 16796 title = {Computer simulation using particles}, 16797 publisher = {McGraw-Hill}, 16798 address = {New York}, 16799 year = {1981} 16800} 16801 16802@Article{ lutydavistironigunsteren94, 16803 author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. 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Chu}, 16869 bibdate = {Wed Jan 07 15:23:19 1998}, 16870 bibsource = {ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib} 16871} 16872 16873@Article{ liptonreagan2014, 16874 title = {Quantum Algorithms via Linear Algebra: A Primer}, 16875 author = {Richard J Lipton and Kenneth W Regan}, 16876 pages = {206}, 16877 isbn = {978-0-26202-839-4}, 16878 year = {2014} 16879} 16880 16881@InProceedings{ rhea08, 16882 author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh 16883 Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong}, 16884 title = {Scalable adaptive mantle convection simulation on petascale supercomputers}, 16885 booktitle = {Proceedings of IEEE/ACM SC '08}, 16886 year = {2008} 16887} 16888 16889@Misc{ bursteddewilcox09, 16890 author = {Carsten Burstedde and Lucas~C. Wilcox}, 16891 title = {The p4est library: A parallel scalable forest of adaptive octrees}, 16892 note = {in preparation} 16893} 16894 16895@Article{ skeeltezcanhardy02, 16896 author = {R. D. Skeel and I. Tezcan and D. J. Hardy}, 16897 title = {Multiple Grid Methods for Classical Molecular Dynamics}, 16898 journal = {J. Comp. Chem.}, 16899 volume = {23}, 16900 pages = {673--684}, 16901 year = {2002} 16902} 16903 16904@Article{ verschelde99, 16905 author = {Jan Verschelde}, 16906 title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by 16907 homotopy continuation}, 16908 journal = {ACM Trans. Math. Softw.}, 16909 volume = {25}, 16910 number = {2}, 16911 issn = {0098-3500}, 16912 pages = {251--276}, 16913 doi = {10.1145/317275.317286}, 16914 publisher = {ACM}, 16915 address = {New York, NY}, 16916 year = {1999} 16917} 16918 16919@InProceedings{ sommeseverscheldewampler08, 16920 author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler}, 16921 title = {Solving Polynomial Systems Equation by Equation}, 16922 booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry}, 16923 editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese}, 16924 pages = {133--152}, 16925 publisher = {Springer-Verlag}, 16926 year = {2008} 16927} 16928 16929@Article{ phanthientanner77, 16930 author = {N. Phan-Thien and R.~I. Tanner}, 16931 title = {A new constitutive equation derived from network theory}, 16932 journal = {J. Non-Newt. Fluid Mech.}, 16933 volume = {2}, 16934 pages = {353}, 16935 year = {1977} 16936} 16937 16938@Manual{ sage, 16939 key = {SAGE}, 16940 author = {W.\thinspace{}A. Stein and others}, 16941 organization = {The Sage~Development Team}, 16942 title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)}, 16943 note = {{\tt http://www.sagemath.org}}, 16944 year = {2009} 16945} 16946 16947@Misc{ bateshauensteinsommesewampler06, 16948 author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. 16949 Wampler}, 16950 title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry}, 16951 howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini} 16952} 16953 16954@Article{ archer09, 16955 author = {A. J. Archer}, 16956 collaboration = {}, 16957 title = {Dynamical density functional theory for molecular and colloidal fluids: A 16958 microscopic approach to fluid mechanics}, 16959 publisher = {AIP}, 16960 year = {2009}, 16961 journal = {The Journal of Chemical Physics}, 16962 volume = {130}, 16963 number = {1}, 16964 eid = {014509}, 16965 numpages = {8}, 16966 pages = {014509}, 16967 keywords = {colloids; continuum mechanics; density functional theory; free energy; glass 16968 transition; statistical distributions; stochastic processes}, 16969 doi = {10.1063/1.3054633} 16970} 16971 16972@Article{ giesekus1966, 16973 author = {Hanswalter Giesekus}, 16974 title = {Die Elastizit\"at von Fl\"ussigkeiten}, 16975 journal = {Rheologica Acta}, 16976 publisher = {Springer Berlin / Heidelberg}, 16977 volume = {5}, 16978 number = {1}, 16979 month = mar, 16980 year = {1966}, 16981 doi = {10.1007/BF01973575}, 16982 pages = {29-35} 16983} 16984 16985@Article{ baaijens98, 16986 author = {F.P. Baaijens}, 16987 title = {Mixed finite element methods for viscoelastic flow analysis: a review}, 16988 journal = {Journal of Non-Newtonian Fluid Mechanics}, 16989 volume = {79}, 16990 year = {1998}, 16991 pages = {361--385} 16992} 16993 16994@Book{ joseph90, 16995 author = {D.~D. Joseph}, 16996 title = {Fluid Dynamics of Viscoelastic Liquids}, 16997 publisher = {Springer}, 16998 address = {New York, NY}, 16999 year = {1990} 17000} 17001 17002@Article{ oldroyd50, 17003 author = {J.~G. Oldroyd}, 17004 title = {On the Formulation of Rheological Equations of State}, 17005 journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical 17006 Sciences}, 17007 volume = {200}, 17008 year = {1950}, 17009 pages = {523--541} 17010} 17011 17012@InProceedings{ bynasungroppthakur04, 17013 author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur}, 17014 title = {Predicting Memory-Access Cost Based on Data-Access Patterns}, 17015 booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego}, 17016 year = {2004} 17017} 17018 17019@Book{ pozrikidis07, 17020 author = {C. Pozrikidis}, 17021 title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation}, 17022 publisher = {Kluwer (Springer)}, 17023 pages = {675}, 17024 year = {2001}, 17025 isbn = {0792373510} 17026} 17027 17028@Misc{ kritzkeyesfsp07, 17029 author = {A. Kritz and D. Keyes}, 17030 title = {{Fusion Simulation Project Workshop Report}}, 17031 month = jul, 17032 year = {2007}, 17033 note = {Available via 17034 \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}} 17035} 17036 17037@Misc{ dahlburg02, 17038 author = {J. {Dahlburg (Chair)}}, 17039 title = {{Final Report of the FESAC ISOFS SubCommittee}}, 17040 year = {2002}, 17041 note = {Available via 17042 \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}} 17043} 17044 17045@Misc{ brown08, 17046 author = {D. {Brown (Chair)}}, 17047 title = {{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View 17048 to the Future}}, 17049 year = {2008}, 17050 howpublished = {Office of Science, U.S. Department of Energy}, 17051 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf} 17052} 17053 17054@Misc{ crosscutting10, 17055 author = {D. Brown and P. {Messina (Chairs)}}, 17056 title = {{Scientific Grand Challenges: Crosscutting Technologies for Computing at the 17057 Exascale}}, 17058 year = {2010}, 17059 howpublished = {Office of Science, U.S. Department of Energy}, 17060 url = {http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf} 17061} 17062 17063@Misc{ extreme-scale-solvers-workshop12, 17064 author = {J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and 17065 L.C. McInnes and E. Ng and S. Wild}, 17066 title = {Report on the Workshop on Extreme-Scale Solvers: Transitions to Future 17067 Architectures}, 17068 howpublished = {Office of Advanced Scientific Computing Research, U.S. Department of Energy}, 17069 note = {{Washington, DC}, March 8-9, 2012}, 17070 url = {http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf}, 17071 year = {2012} 17072} 17073 17074@Misc{ monizrosner09, 17075 author = {{E. Moniz and R. Rosner}}, 17076 title = {{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling 17077 and Simulation at the Extreme Scale}}, 17078 month = may, 17079 year = {2009}, 17080 note = {See 17081 \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}} 17082} 17083 17084@Misc{ blanford08, 17085 author = {{R. Blandord (Chair)}}, 17086 title = {{Workshop on Challenges for Understanding the Quantum Universe and the Role of 17087 Computing at the Extreme Scale}}, 17088 month = dec, 17089 year = {2008}, 17090 note = {See 17091 \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}} 17092} 17093 17094@Misc{ exascale07, 17095 author = {H. Simon and T. Zacharia and R. Stevens}, 17096 title = {{Modeling and Simulation at the Exascale for Energy and the Environment}}, 17097 year = {2007}, 17098 note = {See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}} 17099} 17100 17101@Misc{ ascrbreakthroughs08, 17102 author = {{Panel on Recent Significant Advancements in Computational Science}}, 17103 title = {Breakthroughs}, 17104 year = {2008}, 17105 note = {See 17106 \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}} 17107} 17108 17109@Misc{ petsc-rd100-2009, 17110 author = {{R\&D Magazine}}, 17111 title = {{PETSc} {R}\&{D} 100 Award}, 17112 year = {2009}, 17113 note = {See 17114 \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}} 17115} 17116 17117@Article{ compass-scidac08, 17118 author = {P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and 17119 R. Ryne}, 17120 title = {Community Petascale Project for Accelerator Science and Simulation: Advancing 17121 Computational Science for Future Accelerators and Accelerator Technologies}, 17122 journal = {J. Phys.: Conf. Ser.}, 17123 volume = {125}, 17124 year = {2008}, 17125 pages = {012001}, 17126 url = {http://iopscience.iop.org/1742-6596/125/1/012001} 17127} 17128 17129@Article{ compass-amundson-scidac08, 17130 title = {Multiscale, Multiphysics Beam Dynamics Framework Design and Applications}, 17131 author = {J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. 17132 Stoltz}, 17133 journal = {J. Phys.: Conf. Ser.}, 17134 volume = {125}, 17135 year = {2008} 17136} 17137 17138@InProceedings{ muszala09, 17139 title = {Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator 17140 Simulations}, 17141 author = {S. Muszala and J. Amundson and L. C. McInnes and B. Norris}, 17142 booktitle = {Proceedings of the 2009 Workshop on Component-Based High Performance Computing 17143 {(CBHPC 2009)}}, 17144 year = {2009} 17145} 17146 17147@Article{ gaston09, 17148 title = {{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear 17149 Equations}, 17150 author = {Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie}, 17151 journal = {Nuclear Engineering and Design}, 17152 volume = {239}, 17153 number = {10}, 17154 year = {2009}, 17155 pages = {1768 -- 1778} 17156} 17157 17158@Article{ gaston09b, 17159 title = {Parallel Multiphysics Algorithms and Software for Computational Nuclear 17160 Engineering}, 17161 author = {D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park 17162 and C. Permann and W. Taitano}, 17163 journal = {J. Phys.: Conf. Ser.}, 17164 volume = {180}, 17165 year = {2009}, 17166 pages = {012012} 17167} 17168 17169@Article{ newman09, 17170 title = {Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen 17171 Diffusion in {UO$_2$} Nuclear Fuel Rods}, 17172 author = {Chris Newman and Glen Hansen and Derek Gaston}, 17173 journal = {Journal of Nuclear Materials}, 17174 volume = {392}, 17175 issue = {1}, 17176 year = {2009}, 17177 pages = {6 -- 15} 17178} 17179 17180@Misc{ www:fenics, 17181 author = {{FE}ni{CS}}, 17182 title = {{FE}ni{CS} Project}, 17183 howpublished = {\url{http://www.fenics.org/}}, 17184 year = {2018} 17185} 17186 17187@InProceedings{ zwart08, 17188 title = {A Multiphysics and Multiscale Software Environment for Modeling Astrophysical 17189 Systems}, 17190 author = {S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut 17191 and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. 17192 Gaburov and E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and 17193 S. Justham and P. Teuben and J. van Bever and O. Yaron and M. Zemp}, 17194 booktitle = {Proceedings of ICCS 2008}, 17195 year = {2008} 17196} 17197 17198@Article{ klocknerwarburtonbridgehesthaven09, 17199 author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.}, 17200 title = {Nodal discontinuous {G}alerkin methods on graphics processors}, 17201 journal = {J. Comput. Phys.}, 17202 volume = {228}, 17203 number = {21}, 17204 year = {2009}, 17205 issn = {0021-9991}, 17206 pages = {7863--7882}, 17207 doi = {10.1016/j.jcp.2009.06.041}, 17208 publisher = {Academic Press Professional}, 17209 address = {San Diego, CA} 17210} 17211 17212@PhDThesis{ rankin99, 17213 author = {Rankin, W. T.}, 17214 keywords = {FMM, parallel FMM}, 17215 school = {Department of Electrical and Computer Engineering, Duke University}, 17216 title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms}, 17217 year = {1999} 17218} 17219 17220@InProceedings{ warrensalmon93, 17221 abstract = {We report on an efficient adaptive N-body method which we have recently designed 17222 and implemented. The algorithm computes the forces on an arbitrary distribution of 17223 bodies in a time which scales as N log N with the particle number. The accuracy of 17224 the force calculations is analytically bounded, and can be adjusted via a user 17225 defined parameter between a few percent relative accuracy, down to machine 17226 arithmetic accuracy. Instead of using pointers to indicate the topology of the 17227 tree, we identify...}, 17228 address = {New York}, 17229 author = {Warren, Michael S. and Salmon, John K.}, 17230 booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing}, 17231 citeulike-article-id={580952}, 17232 keywords = {oct-tree}, 17233 pages = {12--21}, 17234 publisher = {ACM}, 17235 title = {A parallel hashed Oct-Tree {N}-body algorithm}, 17236 year = {1993}, 17237 doi = {10.1145/169627.169640}, 17238 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100} 17239} 17240 17241@Unpublished{ cruzwccm10, 17242 author = {Felipe A. Cruz}, 17243 title = {Heterogeneous extension of the PetFMM a Fast Multipole Library}, 17244 note = {Presentation at WCCM 2010, Sydney Australia}, 17245 year = {2010} 17246} 17247 17248@Article{ mcguffee06, 17249 author = {S.~R. {McGuffee} and A.~H. Elcock}, 17250 title = {Atomistically detailed simulations of concentrated protein solutions: the effects 17251 of salt, {pH}, point mutations, and protein concentration in simulations of 17252 1000-molecule systems}, 17253 journal = {Journal of the American Chemical Society}, 17254 volume = {128}, 17255 pages = {12098--12110}, 17256 year = {2006} 17257} 17258 17259@Article{ nilsencaihoylandlangtangen10, 17260 author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.}, 17261 title = {{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach 17262 in Python}}, 17263 journal = {ArXiv e-prints}, 17264 archiveprefix = {arXiv}, 17265 eprint = {1002.0705}, 17266 primaryclass = {cs.DC}, 17267 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science 17268 - Programming Languages}, 17269 year = {2010}, 17270 month = feb, 17271 adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N}, 17272 adsnote = {Provided by the SAO/NASA Astrophysics Data System} 17273} 17274 17275@Misc{ mcinnes:siam09:minisymposium, 17276 title = {Implicit Nonlinear Solvers in Multimodel Simulations}, 17277 author = {L. C. McInnes and C. {Woodward (co-organizers)}}, 17278 note = {invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, 17279 Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. 17280 White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. 17281 of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll 17282 (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at 17283 Austin).} 17284} 17285 17286@Misc{ mcinnes:fsp-summary:feb2011, 17287 author = {Lois Curfman McInnes and Luis Chacon and John Shadid}, 17288 title = {Solvers and Time Integration Breakout Summary}, 17289 note = {FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see 17290 \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}} 17291} 17292 17293@Misc{ dvi-materials:siamcse11, 17294 title = {Progress in Large-Scale Differential Variational Inequalities for Heterogeneous 17295 Materials}, 17296 author = {M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. 17297 Smith and L. Wang}, 17298 note = {minisymposium presentation at the 2011 SIAM Conference on Computational Science 17299 and Engineering, March 3, 2011} 17300} 17301 17302@Misc{ jamroz:cemm10, 17303 title = {{JFNK} within the semi-implicit scheme in {NIMROD}}, 17304 author = {B. Jamroz and S. Kruger and T. Austin}, 17305 note = {presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010} 17306} 17307 17308@Misc{ kruger:feb4-2011, 17309 title = {personal communication}, 17310 author = {S. Kruger}, 17311 note = {February, 2011} 17312} 17313 17314@Article{ elman1996, 17315 author = {H.C. Elman}, 17316 title = {Preconditioning for the steady-state {Navier-Stokes} equations for low 17317 viscosity}, 17318 journal = {SIAM J. Sci. Comput.}, 17319 volume = {20}, 17320 year = {1996}, 17321 pages = {1299--1316} 17322} 17323 17324@Article{ kayloghinwathen2002, 17325 author = {D. Kay and D. Loghin and A. Wathen}, 17326 title = {A preconditioning for the steady-state {Navier-Stokes} equations}, 17327 journal = {SIAM J. Sci. Comput.}, 17328 volume = {24}, 17329 year = {2002}, 17330 pages = {237--256} 17331} 17332 17333@Article{ elmanhowleshadidshuttleworthtuminaro2006, 17334 author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro}, 17335 title = {Block preconditioners based on approximate commutators}, 17336 journal = {SIAM J. Sci. Comput.}, 17337 volume = {27}, 17338 number = {5}, 17339 year = {2006}, 17340 pages = {1651--1668} 17341} 17342 17343@Article{ braesssarazin1997, 17344 author = {Dietrich Braess and Regina Sarazin}, 17345 title = {An efficient smoother for the {Stokes} problem}, 17346 journal = {Applied Numerical Mathematics}, 17347 volume = {23}, 17348 number = {1}, 17349 year = {1997}, 17350 pages = {3--19}, 17351 doi = {10.1016/S0168-9274(96)00059-1} 17352} 17353 17354@Article{ wright2001large, 17355 title = {Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}}, 17356 author = {Wright, T.G. and Trefethen, L.N.}, 17357 journal = {SIAM Journal on Scientific Computing}, 17358 volume = {23}, 17359 pages = {591}, 17360 year = {2001} 17361} 17362 17363@Misc{ wright2002eigtool, 17364 title = {Eig{T}ool}, 17365 author = {Wright, T.G. and Trefethen, LN}, 17366 howpublished = {Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}}, 17367 year = {2002} 17368} 17369 17370@Misc{ visit-web-site, 17371 key = {{VisIt}}, 17372 title = {{VisIt web site}}, 17373 howpublished = {\url{http://wci.llnl.gov/codes/visit/}}, 17374 url = {http://wci.llnl.gov/codes/visit/}, 17375 year = {2011} 17376} 17377 17378@Book{ trefethen1996, 17379 title = {Finite difference and spectral methods for ordinary and partial differential 17380 equations}, 17381 author = {Lloyd Nicholas Trefethen}, 17382 year = {1996}, 17383 publisher = {Cornell University-Department of Computer Science and Center for Applied 17384 Mathematics} 17385} 17386 17387@Book{ trefethen2005spectra, 17388 title = {Spectra and pseudospectra: the behavior of nonnormal matrices and operators}, 17389 author = {Trefethen, L.N. and Embree, M.}, 17390 year = {2005}, 17391 publisher = {Princeton University Press} 17392} 17393 17394@Article{ gomez2010isogeometric, 17395 title = {Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations}, 17396 author = {Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.}, 17397 journal = {Computer Methods in Applied Mechanics and Engineering}, 17398 volume = {199}, 17399 number = {25-28}, 17400 pages = {1828--1840}, 17401 issn = {0045-7825}, 17402 year = {2010}, 17403 publisher = {Elsevier} 17404} 17405 17406@Article{ gomez2008isogeometric, 17407 title = {Isogeometric analysis of the {C}ahn-{H}illiard phase-field model}, 17408 author = {G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.}, 17409 journal = {Computer Methods in Applied Mechanics and Engineering}, 17410 volume = {197}, 17411 number = {49-50}, 17412 pages = {4333--4352}, 17413 year = {2008}, 17414 publisher = {Elsevier} 17415} 17416 17417@Misc{ fastmath:project, 17418 author = {Lori {Diachin (PI)}}, 17419 title = {{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics 17420 (FASTMath) Institute}}, 17421 howpublished = {\url{https://fastmath-scidac.llnl.gov}} 17422} 17423 17424@Misc{ exascale-software:proposal, 17425 author = {Peter {Beckman (PI)}}, 17426 title = {{Exascale Software Center}}, 17427 note = {proposal to DOE} 17428} 17429 17430@Misc{ imex:project, 17431 author = {Barry {Smith (PI)}}, 17432 title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent 17433 Multimodel PDEs}}, 17434 note = {DOE ASCR applied math project} 17435} 17436 17437@Misc{ intel-mic:website, 17438 author = {Intel}, 17439 title = {{Many Integrated Core Architecture}}, 17440 note = {\url{http://www.intel.com/technology/architecture-silicon/mic}} 17441} 17442 17443@Article{ dudson:2009, 17444 author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and H.R. Wilson}, 17445 title = {{{BOUT++:}} a framework for parallel plasma fluid simulations}, 17446 journal = {Computer Physics Communications}, 17447 volume = {180}, 17448 pages = {1467}, 17449 year = {2009} 17450} 17451 17452@Article{ umansky:2009, 17453 author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro and J.R. Myra}, 17454 title = {{Status and verification of edge plasma turbulence code BOUT}}, 17455 journal = {Computer Physics Communications}, 17456 year = {2009}, 17457 volume = {180}, 17458 pages = {887-903} 17459} 17460 17461@Article{ xu:1998, 17462 author = {X.Q. Xu and R.H. Cohen}, 17463 title = {{Scrape-Off Layer Turbulence Theory and Simulations}}, 17464 journal = {Computer Physics Communications}, 17465 year = {1998}, 17466 volume = {36}, 17467 number = {1-2}, 17468 pages = {158} 17469} 17470 17471@Article{ tron:1999, 17472 title = {Newton's Method for Large Bound-constrained Optimization Problems}, 17473 author = {Chih-Jen Lin and Jorge Mor\'{e}}, 17474 journal = {SIAM Journal on Optimization}, 17475 volume = {9}, 17476 number = {4}, 17477 pages = {1100-1127}, 17478 year = {1999} 17479} 17480 17481@Article{ stubenamg, 17482 author = {K. St\"{u}ben}, 17483 title = {A review of algebraic multigrid}, 17484 journal = {J. Comput. Appl. Math.}, 17485 volume = {128}, 17486 number = {1-2}, 17487 year = {2001}, 17488 issn = {0377-0427}, 17489 pages = {281--309}, 17490 doi = {10.1016/S0377-0427(00)00516-1}, 17491 publisher = {Elsevier Science Publishers B. V.}, 17492 address = {Amsterdam, The Netherlands, The Netherlands} 17493} 17494 17495@Article{ feuchtermg, 17496 author = {D. Feuchter and I. Heppner and S. Sauter and G. Wittum}, 17497 title = {Bridging the gap between geometric and algebraic multigrid methods}, 17498 journal = {Computing and visualization in science}, 17499 publisher = {Springer}, 17500 volume = {6}, 17501 number = {1}, 17502 year = {2003}, 17503 pages = {1--13} 17504} 17505 17506@Article{ chowmgsmoothness, 17507 abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that 17508 only attempts to interpolate in the directions of geometrical smoothness. These 17509 directions are determined by analyzing samples of algebraically smooth error, e. 17510 Neighboring grid points i and j are called smoothly coupled if e i and e j are 17511 consistently nearby in value. In addition, these dierences may be used to dene 17512 interpolation weights. These new ideas may be incorporated into the algebraic 17513 multigrid method. Test results show that the new method can have much lower grid 17514 and operator complexities compared to AMG, leading to lower solve timings. 1 }, 17515 author = {Chow, Edmond}, 17516 citeulike-article-id={7675372}, 17517 citeulike-linkout-0={http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17518 journal = {American Journal of Mathematics}, 17519 keywords = {fem, multigrid}, 17520 pages = {197--215}, 17521 posted-at = {2010-08-17 23:29:51}, 17522 priority = {2}, 17523 title = {An Unstructured Multigrid Method Based on Geometric Smoothness}, 17524 url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305}, 17525 volume = {65}, 17526 year = {2001} 17527} 17528 17529@Article{ jonesamge, 17530 abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite 17531 elements) method based on element agglomeration. In the method, coarse grid 17532 elements are formed by agglomerating fine grid elements. Compatible interpolation 17533 operators are constructed which yield coarse grid basis functions with a minimal 17534 energy property. Heuristics based on interpolation quality measures are used to 17535 guide the agglomeration procedure. The performance of the resulting method is 17536 demonstrated in two-level numerical experiments.}}, 17537 author = {Jones, Jim E. and Vassilevski, Panayot S.}, 17538 citeulike-article-id={8598569}, 17539 citeulike-linkout-0={http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17540 citeulike-linkout-1={http://link.aip.org/link/?SCE/23/109}, 17541 journal = {SIAM Journal on Scientific Computing}, 17542 keywords = {amg, fem, multigrid}, 17543 number = {1}, 17544 pages = {109--133}, 17545 posted-at = {2011-01-13 18:05:55}, 17546 priority = {2}, 17547 publisher = {SIAM}, 17548 title = {{AMGE Based on Element Agglomeration}}, 17549 url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes}, 17550 volume = {23}, 17551 year = {2001} 17552} 17553 17554@Article{ saad1993, 17555 author = {Saad, Youcef}, 17556 doi = {10.1137/0914028}, 17557 issn = {10648275}, 17558 journal = {SIAM Journal on Scientific Computing}, 17559 keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose 17560 iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of 17561 precondition-,preconditioned conju-,subject classi cations,variable 17562 preconditioners}, 17563 number = {2}, 17564 pages = {461--469}, 17565 title = {{A flexible inner-outer preconditioned GMRES algorithm}}, 17566 volume = {14}, 17567 year = {1993} 17568} 17569 17570@Misc{ path:homepage, 17571 author = {S. Dirkse and M. Ferris and T. 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Watts}, 17822 title = {The long-term strength of continental lithosphere: jelly sandwich or creme 17823 brulee?}, 17824 journal = {GSA Today}, 17825 volume = {16}, 17826 pages = {4–-10}, 17827 year = {2006} 17828} 17829 17830@InProceedings{ yang:brent:2002, 17831 title = {The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on 17832 Parallel Distributed Memory Architectures}, 17833 author = {Laurence T. Yang and Richard Brent}, 17834 booktitle = {Proceedings of the Fifth International Conference on Algorithms and Architectures 17835 for Parallel Processing}, 17836 year = {2002}, 17837 publisher = {IEEE} 17838} 17839 17840@Article{ demmel2008communication, 17841 title = {Communication-optimal parallel and sequential {QR} and {LU} factorizations}, 17842 author = {Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.}, 17843 journal = {Arxiv preprint arXiv:0808.2664}, 17844 year = {2008} 17845} 17846 17847@Article{ demmel09, 17848 author = {J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick}, 17849 title = {Communication-optimal Iterative Methods}, 17850 journal = {Journal of Physics: Conf. 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Cyr and John N. Shadid and Raymond S. Tuminaro} 17920} 17921 17922@Article{ keyesmcinneswoodwardetal13, 17923 title = {Multiphysics Simulations: Challenges and Opportunities}, 17924 author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and William Gropp and 17925 Eric Myra and Michael Pernice and John Bell and Jed Brown and Alain Clo and 17926 Jeffrey Connors and Emil Constantinescu and Don Estep and Kate Evans and Charbel 17927 Farhat and Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and Tobin 17928 Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and Efthimios Kaxiras 17929 and Alice Koniges and Kihwan Lee and Aaron Lott and Qiming Lu and John Magerlein 17930 and Reed Maxwell and Michael McCourt and Miriam Mehl and Roger Pawlowski and 17931 Amanda Peters Randles and Daniel Reynolds and B\'{e}atrice Rivi\`{e}re and Ulrich 17932 R\"{u}de and Tim Scheibe and John Shadid and Brendan Sheehan and Mark Shephard and 17933 Andrew Siegel and Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth}, 17934 journal = {International Journal of High Performance Computing Applications}, 17935 month = feb, 17936 year = {2013}, 17937 volume = {27}, 17938 number = {1}, 17939 pages = {4--83}, 17940 doi = {10.1177/1094342012468181}, 17941 note = {Special issue}, 17942 abstract = {We consider multiphysics applications from algorithmic and architectural 17943 perspectives, where ``algorithmic'' includes both mathematical analysis and 17944 computational complexity and ``architectural'' includes both software and hardware 17945 environments. Many diverse multiphysics applications can be reduced, en route to 17946 their computational simulation, to a common algebraic coupling paradigm. 17947 Mathematical analysis of multiphysics coupling in this form is not always 17948 practical for realistic applications, but model problems representative of 17949 applications discussed herein can provide insight. A variety of software 17950 frameworks for multiphysics applications have been constructed and refined within 17951 disciplinary communities and executed on leading-edge computer systems. We examine 17952 several of these, expose some commonalities among them, and attempt to extrapolate 17953 best practices to future systems. From our study, we summarize challenges and 17954 forecast opportunities.} 17955} 17956 17957@Misc{ rosner10, 17958 author = {Robert {Rosner (Chair)}}, 17959 title = {{The Opportunities and Challenges of Exascale Computing}}, 17960 year = {2010}, 17961 howpublished = {Office of Science, U.S. Department of Energy}, 17962 url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf} 17963} 17964 17965@Misc{ kogge2008exascale, 17966 title = {ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems}, 17967 author = {Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian 17968 Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod 17969 and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein 17970 and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan 17971 Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick}, 17972 howpublished = {DARPA}, 17973 year = {2008}, 17974 url = {http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf} 17975} 17976 17977@Misc{ doegrandchallengeworkshops, 17978 key = {Office of Science, U.S. Department of Energy}, 17979 title = {{Scientific Grand Challenges Workshop Series}}, 17980 howpublished = {Office of Science, U.S. Department of Energy, see 17981 \url{http://extremecomputing.labworks.org/workshops.stm}} 17982} 17983 17984@Misc{ lawrence2011, 17985 key = {Lawrence}, 17986 title = {{Ernest Orlando Lawrence Award Winners}}, 17987 howpublished = {U.S. Department of Energy, {\footnotesize 17988 \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}}, 17989 year = {2011} 17990} 17991 17992@Article{ murphy2000npi, 17993 title = {{A note on preconditioning for indefinite linear systems}}, 17994 author = {Murphy, M.F. and Golub, G.H. and Wathen, A.J.}, 17995 journal = {SIAM Journal on Scientific Computing}, 17996 volume = {21}, 17997 number = {6}, 17998 pages = {1969--1972}, 17999 year = {2000}, 18000 publisher = {Philadelphia, PA: SIAM, c1993-} 18001} 18002 18003@Article{ elman2011bouyancy, 18004 title = {Fast iterative solvers for buoyancy driven flow problems}, 18005 journal = {Journal of Computational Physics}, 18006 volume = {230}, 18007 number = {10}, 18008 pages = {3900 - 3914}, 18009 year = {2011}, 18010 note = {}, 18011 issn = {0021-9991}, 18012 doi = {10.1016/j.jcp.2011.02.014}, 18013 author = {Howard Elman and Milan Mihajlovic and David Silvester}, 18014 keywords = {Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, 18015 Adaptivity, Preconditioning, Algebraic multigrid} 18016} 18017 18018@Article{ dongarrabeckman11, 18019 author = {J. Dongarra and P. Beckman and et al.}, 18020 title = {The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap}, 18021 journal = {Int. J. High Perf. Comput. 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Brannick and Robert D. Falgout}, 18074 journal = {SIAM Journal on Scientific Computing}, 18075 volume = {32}, 18076 number = {3}, 18077 pages = {1393--1416}, 18078 url = {http://epubs.siam.org/doi/10.1137/090772216}, 18079 doi = {10.1137/090772216}, 18080 issn = {1064-8275}, 18081 year = {2010} 18082} 18083 18084@Article{ xu2004energy, 18085 title = {On an energy minimizing basis for algebraic multigrid methods}, 18086 author = {Xu, J. and Zikatanov, L.}, 18087 journal = {Computing and Visualization in Science}, 18088 volume = {7}, 18089 number = {3}, 18090 pages = {121--127}, 18091 year = {2004}, 18092 publisher = {Springer} 18093} 18094 18095@Article{ dblp:journals/toms/bakerhlt09, 18096 author = {C. G. Baker and Ulrich Hetmaniuk and Richard B. Lehoucq and Heidi Thornquist}, 18097 title = {Anasazi software for the numerical solution of large-scale eigenvalue problems}, 18098 journal = {ACM Trans. Math. 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Sala}, 18121 title = {{ML} 5.0 Smoothed Aggregation User's Guide}, 18122 institution = {Sandia National Laboratories}, 18123 year = {2006}, 18124 number = {SAND2006-2649} 18125} 18126 18127@Article{ brannick06, 18128 title = {An energy-based AMG coarsening strategy}, 18129 volume = {13}, 18130 doi = {10.1002/nla.480}, 18131 number = {2-3}, 18132 journal = {Numerical Linear Algebra with Applications}, 18133 author = {Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S 18134 and Ruge, J}, 18135 year = {2006}, 18136 pages = {133--148} 18137} 18138 18139@Article{ olson10, 18140 author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.}, 18141 title = {A new perspective on strength measures in algebraic multigrid}, 18142 journal = {Numerical Linear Algebra with Applications}, 18143 volume = {17}, 18144 number = {4}, 18145 pages = {713--733}, 18146 year = {2010}, 18147 publisher = {John Wiley \& Sons, Ltd.}, 18148 issn = {1099-1506}, 18149 doi = {10.1002/nla.669} 18150} 18151 18152@Article{ olson11, 18153 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.}, 18154 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy 18155 Minimization}, 18156 journal = {SIAM J. Sci. 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P.}, 18536 eprint = {arXiv:1002.0705v1}, 18537 file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the 18538 parallelization of scientific codes by a function-centric approach in 18539 Python.pdf:pdf}, 18540 journal = {Computational Science \& Discovery}, 18541 keywords = {parallel,programming,python,software}, 18542 mendeley-tags = {parallel,programming,python,software}, 18543 pages = {015003}, 18544 publisher = {IOP Publishing}, 18545 title = {{Simplifying the parallelization of scientific codes by a function-centric 18546 approach in Python}}, 18547 url = {http://iopscience.iop.org/1749-4699/3/1/015003}, 18548 volume = {3}, 18549 year = {2010} 18550} 18551 18552@Book{ langtangen09, 18553 author = {Hans Petter Langtangen}, 18554 title = {Python Scripting for Computational Science}, 18555 publisher = {Springer}, 18556 series = {Texts in Computational Science and Engineering}, 18557 pages = {784}, 18558 isbn = {3540739157}, 18559 year = {2009} 18560} 18561 18562@Book{ numpyguide, 18563 author = {Travis E. 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Knepley and Ludovic R\"ass and 18601 Velimir Vesselinov}, 18602 journal = {Eos}, 18603 volume = {102}, 18604 doi = {10.1029/2021EO159258}, 18605 month = {Jun}, 18606 year = {2021} 18607} 18608 18609@Misc{ knepley:icerm-workshop:2012, 18610 author = {David Keyes and Matthew Knepley and Katherine Yelick}, 18611 title = {Synchronization-reducing and Communication-reducing Algorithms and Programming 18612 Models for Large-scale Simulations}, 18613 note = {Workshop sponsored by the Institute for Computational and Experimental Research 18614 in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, 18615 \url{http://icerm.brown.edu/tw12-1-exascale}}, 18616 year = {2012} 18617} 18618 18619@TechReport{ kirbyknepleyscott04, 18620 author = {Robert C. Kirby and Matthew G. Knepley and L. 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Yuen and Huai 18670 Zhang and Yaolin Shi}, 18671 title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with 18672 strongly variable viscosity based on {Matlab} and {CUDA}}, 18673 type = {Research Report}, 18674 number = {UMSI 2011/33}, 18675 institution = {University of Minnesota Supercomputing Institute}, 18676 url = {http://static.msi.umn.edu/rreports/2011/33.pdf}, 18677 note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}}, 18678 month = mar, 18679 year = {2011} 18680} 18681 18682@InProceedings{ zheng2010, 18683 author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai 18684 Zhang and Yaolin Shi}, 18685 title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients}, 18686 booktitle = {Eos Transactions of the AGU}, 18687 organization = {American Geophysical Union}, 18688 note = {Fall Meeting Supplemental, Abstract IN41A-1350}, 18689 year = {2010} 18690} 18691 18692@InCollection{ terrelkirbyknepleyscott12, 18693 author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott 18694 and Garth N. Wells}, 18695 title = {Finite elements for incompressible fluids}, 18696 editors = {A. Logg and K.A. Mardal and G. N. 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Terrel}, 18720 title = {Discrete optimization of finite element matrix evaluation}, 18721 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18722 booktitle = {Automated solutions of differential equations by the finite element method}, 18723 series = {Lecture Notes in Computational Science and Engineering}, 18724 volume = {84}, 18725 pages = {385--397}, 18726 publisher = {Springer-Verlag}, 18727 year = {2012} 18728} 18729 18730@InCollection{ kirby12, 18731 author = {Robert C. Kirby}, 18732 title = {{FIAT}: Numerical Construction of Finite Element Basis Functions}, 18733 editors = {A. Logg and K.A. Mardal and G. N. Wells}, 18734 booktitle = {Automated solutions of differential equations by the finite element method}, 18735 series = {Lecture Notes in Computational Science and Engineering}, 18736 volume = {84}, 18737 publisher = {Springer-Verlag}, 18738 year = {2012} 18739} 18740 18741@Article{ brownconveryhotesknepleypetropolous1993, 18742 author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and 18743 Labros Petropolous}, 18744 title = {Closed strings with low harmonics and kinks}, 18745 journal = {Physical Review D}, 18746 volume = {48}, 18747 number = {6}, 18748 year = {1993} 18749} 18750 18751@Article{ minimax1996, 18752 title = {MiniMax: What has been learned thus far}, 18753 author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and 18754 Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and 18755 C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. 18756 Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and 18757 M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. 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23579 23580@InProceedings{ parkbarralibanezkamenetskiykrakosmichalloseille2018, 23581 title = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows}, 23582 author = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and 23583 Joshua A Krakos and Todd R Michal and Adrien Loseille}, 23584 booktitle = {2018 AIAA Aerospace Sciences Meeting}, 23585 pages = {1103}, 23586 year = {2018} 23587} 23588 23589@InProceedings{ barralangeloudiskramergormanpiggott2018, 23590 title = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics 23591 modelling}, 23592 author = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman 23593 and Matthew D Piggott}, 23594 booktitle = {EGU General Assembly Conference Abstracts}, 23595 volume = {20}, 23596 pages = {19168}, 23597 year = {2018} 23598} 23599 23600@Article{ principe2009, 23601 title = {{Mathematical models for thermally coupled low speed flows}}, 23602 author = {Javier Principe and Ramon Codina}, 23603 journal = {Advances in Theoretical and Applied Mechanics}, 23604 volume = {2}, 23605 number = {1-4}, 23606 pages = {93--112}, 23607 url = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf}, 23608 year = {2009} 23609} 23610 23611@Book{ vandervorst2003, 23612 title = {Iterative {K}rylov Methods for Large Linear Systems}, 23613 author = {van der Vorst, H.}, 23614 isbn = {9780521818285}, 23615 publisher = {Cambridge University Press}, 23616 year = {2003} 23617} 23618 23619@Book{ peres2006, 23620 author = {Asher Peres}, 23621 title = {Quantum theory: concepts and methods}, 23622 volume = {57}, 23623 publisher = {Springer Science \& Business Media}, 23624 year = {2006} 23625} 23626 23627@Book{ kuttler2012, 23628 title = {Linear algebra: theory and applications}, 23629 author = {Kenneth Kuttler}, 23630 url = {http://www.math.byu.edu/~klkuttle/Linearalgebra.pdf}, 23631 year = {2012} 23632} 23633 23634@Book{ elman_silvester_wathen_2014, 23635 place = {Oxford}, 23636 title = {Finite elements and fast iterative solvers: with applications in incompressible 23637 fluid dynamics}, 23638 publisher = {Oxford University Press}, 23639 author = {Elman, Howard C. and Silvester, David J. and Wathen, Andrew J.}, 23640 url = {https://global.oup.com/academic/product/finite-elements-and-fast-iterative-solvers-9780199678792?cc=us&lang=en&}, 23641 year = {2014} 23642} 23643 23644@Article{ alametal2007, 23645 title = {An evaluation of the ORNL Cray XT3}, 23646 author = {S. R. Alam and R. F. Barrett and M. R. Fahey and J. A. Kuehn and O. E. B. Messer 23647 and R. T. Mills and P. C. Roth and J. S. Vetter and P. H. Worley}, 23648 journal = {International Journal of High Performance Computing Applications}, 23649 volume = {22}, 23650 number = {1}, 23651 pages = {52--80}, 23652 doi = {10.1177/1094342007085019}, 23653 year = {2007} 23654} 23655 23656@Article{ plazacarey2000, 23657 title = {Local refinement of simplicial grids based on the skeleton}, 23658 author = {Plaza, A. and Carey, Graham F.}, 23659 journal = {Applied Numerical Mathematics}, 23660 doi = {10.1016/S0168-9274(99)00022-7}, 23661 issn = {01689274}, 23662 volume = {32}, 23663 number = {2}, 23664 pages = {195--218}, 23665 year = {2000} 23666} 23667 23668@Article{ carsonstrakos2020, 23669 title = {On the cost of iterative computations}, 23670 author = {Eric Carson and Zden\v{e}k Strako\v{s}}, 23671 journal = {Phil. Trans. R. Soc. A}, 23672 volume = {378}, 23673 number = {20190050}, 23674 doi = {10.1098/rsta.2019.0050}, 23675 url = {https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0050}, 23676 year = {2020} 23677} 23678 23679@Article{ schoberl1999, 23680 title = {Multigrid methods for a parameter dependent problem in primal variables}, 23681 author = {Joachim Sch{\"o}berl}, 23682 journal = {Numerische Mathematik}, 23683 volume = {84}, 23684 number = {1}, 23685 pages = {97--119}, 23686 year = {1999} 23687} 23688 23689@Article{ wuleexuzikatanov2008, 23690 title = {Convergence analysis on iterative methods for semidefinite systems}, 23691 author = {Jinbiao Wu and Young-Ju Lee and Jinchao Xu and Ludmil Zikatanov}, 23692 journal = {Journal of Computational Mathematics}, 23693 pages = {797--815}, 23694 year = {2008} 23695} 23696 23697@Article{ maierrannacher2016, 23698 title = {Duality-based adaptivity in finite element discretization of heterogeneous 23699 multiscale problems}, 23700 author = {Maier, Matthias and Rannacher, Rolf}, 23701 journal = {Journal of Numerical Mathematics}, 23702 volume = {24}, 23703 number = {3}, 23704 pages = {167--187}, 23705 year = {2016} 23706} 23707 23708@Article{ maierrannacher2018, 23709 title = {A duality-based optimization approach for model adaptivity in heterogeneous 23710 multiscale problems}, 23711 author = {Maier, Matthias and Rannacher, Rolf}, 23712 journal = {Multiscale Modeling \& Simulation}, 23713 volume = {16}, 23714 number = {1}, 23715 pages = {412--428}, 23716 year = {2018} 23717} 23718 23719@Article{ margetismaierluskin2017, 23720 title = {On the Wiener--Hopf method for surface plasmons: Diffraction from semiinfinite 23721 metamaterial sheet}, 23722 author = {Margetis, Dionisios and Maier, Matthias and Luskin, Mitchell}, 23723 journal = {Studies in Applied Mathematics}, 23724 volume = {139}, 23725 number = {4}, 23726 pages = {599--625}, 23727 year = {2017} 23728} 23729 23730@Article{ maiermargetisluskin2017b, 23731 title = {Dipole excitation of surface plasmon on a conducting sheet: Finite element 23732 approximation and validation}, 23733 author = {Maier, Matthias and Margetis, Dionisios and Luskin, Mitchell}, 23734 journal = {Journal of Computational Physics}, 23735 volume = {339}, 23736 pages = {126--145}, 23737 year = {2017} 23738} 23739 23740@Article{ maiermargetisluskin2018, 23741 title = {Generation of surface plasmon-polaritons by edge effects}, 23742 author = {Matthias Maier and Dionisios Margetis and Mitchell Luskin}, 23743 journal = {Communications in Mathematical Sciences}, 23744 volume = {16}, 23745 number = {1}, 23746 pages = {77--95}, 23747 url = {http://arxiv.org/abs/1702.00848}, 23748 year = {2018} 23749} 23750 23751@Article{ maiermattheakiskaxirasluskinmargetis2018, 23752 title = {Universal behavior of a dispersive Dirac cone in gradient-index plasmonic 23753 metamaterials}, 23754 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23755 Mitchell and Margetis, Dionisios}, 23756 journal = {Physical Review B}, 23757 volume = {97}, 23758 number = {3}, 23759 pages = {035307}, 23760 year = {2018} 23761} 23762 23763@Article{ maiermattheakiskaxirasluskinmargetis2019, 23764 title = {Homogenization of plasmonic crystals: seeking the epsilon-near-zero effect}, 23765 author = {Maier, Matthias and Mattheakis, Marios and Kaxiras, Efthimios and Luskin, 23766 Mitchell and Margetis, Dionisios}, 23767 journal = {Proceedings of the Royal Society A}, 23768 volume = {475}, 23769 number = {2230}, 23770 pages = {20190220}, 23771 year = {2019} 23772} 23773 23774@Article{ maiermargetisluskin2020, 23775 title = {Finite-size effects in wave transmission through plasmonic crystals: A tale of 23776 two scales}, 23777 author = {Maier, Matthias and Luskin, Mitchell and Margetis, Dionisios}, 23778 journal = {Physical Review B}, 23779 volume = {102}, 23780 number = {7}, 23781 pages = {075308}, 23782 year = {2020} 23783} 23784 23785@Article{ margetismaierstauberlowluskin2020, 23786 title = {Nonretarded edge plasmon-polaritons in anisotropic two-dimensional materials}, 23787 author = {Margetis, Dionisios and Maier, Matthias and Stauber, Tobias and Low, Tony and 23788 Luskin, Mitchell}, 23789 journal = {Journal of Physics A: Mathematical and Theoretical}, 23790 volume = {53}, 23791 number = {5}, 23792 pages = {055201}, 23793 year = {2020} 23794} 23795 23796@Article{ maiermargetismellet2020, 23797 title = {Homogenization of time-harmonic Maxwell’s equations in nonhomogeneous plasmonic 23798 structures}, 23799 author = {Maier, Matthias and Margetis, Dionisios and Mellet, Antoine}, 23800 journal = {Journal of Computational and Applied Mathematics}, 23801 volume = {377}, 23802 pages = {112909}, 23803 year = {2020} 23804} 23805 23806@Article{ maierkronbichler2021, 23807 title = {Efficient parallel 3D computation of the compressible Euler equations with an 23808 invariant-domain preserving second-order finite-element scheme}, 23809 author = {Maier, Matthias and Kronbichler, Martin}, 23810 journal = {ACM Transactions on Parallel Computing}, 23811 volume = {8}, 23812 number = {3}, 23813 pages = {1--30}, 23814 year = {2021} 23815} 23816 23817@Article{ guermondmaierpopovtomas2021, 23818 title = {Second-order invariant domain preserving approximation of the compressible 23819 Navier--Stokes equations}, 23820 author = {Guermond, Jean-Luc and Maier, Matthias and Popov, Bojan and Tomas, Ignacio}, 23821 journal = {Computer Methods in Applied Mechanics and Engineering}, 23822 volume = {375}, 23823 pages = {113608}, 23824 year = {2021} 23825} 23826 23827@Article{ liliptonmaier2021, 23828 title = {Lorentz Resonance in the Homogenization of Plasmonic Crystals}, 23829 author = {Li, Wei and Lipton, Robert and Maier, Matthias}, 23830 eprint = {2009.12166}, 23831 archiveprefix = {arXiv}, 23832 primaryclass = {phys.optics}, 23833 year = {2021} 23834} 23835 23836@Article{ songmaierluskin2020, 23837 title = {Nonlinear eigenvalue problems for coupled Helmholtz equations modeling 23838 gradient-index graphene waveguides}, 23839 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23840 journal = {Journal of Computational Physics}, 23841 volume = {423}, 23842 pages = {109871}, 23843 year = {2020} 23844} 23845 23846@Article{ songmaierluskin2019, 23847 title = {Adaptive finite element simulations of waveguide configurations involving 23848 parallel 2D material sheets}, 23849 author = {Song, Jung Heon and Maier, Matthias and Luskin, Mitchell}, 23850 journal = {Computer Methods in Applied Mechanics and Engineering}, 23851 volume = {351}, 23852 pages = {20--34}, 23853 year = {2019} 23854} 23855 23856% 23857% <a name="consults"></a><H3><center>Users Who have Visited ANL for Consulting on PETSc</center></H3> 23858% 23859% 23860@Unpublished{ rob1, 23861 author = {Rob Kunz}, 23862 institution = {Computational Mechanics Division, Applied Research Laboratory, The Pennsylvania 23863 State University}, 23864 url = {http://www.arl.psu.edu/areas/compmech/compmech.html}, 23865 sponsors = {U.S. Navy, NRC}, 23866 note = {Using the PETSc and hypre linear solvers to solve pressure equations in CFD 23867 simulations, including lake warming by power plants}, 23868 dates = {Oct 3 and 4, 2002}, 23869 email = {rfk@wt.arl.psu.edu} 23870} 23871 23872@Unpublished{ au1, 23873 author = {Feng Wang and William Appelbe}, 23874 institution = {VPAC, Victorian Partnership for Advanced Computing, Melbourne, Australia}, 23875 url = {http://www.vpac.org}, 23876 sponsors = { }, 23877 note = {Using PETSc for a Variety of Geophysical Simulations}, 23878 dates = {Nov 22, 2002} 23879} 23880 23881@Unpublished{ carl1, 23882 author = {Carl Sovinec}, 23883 institution = {Applied Physics, University of Wisconsin}, 23884 url = {http://nimrodteam.org}, 23885 sponsors = {DOE Office of Fusion Research}, 23886 note = {Investigating using PETSc for NIMROD}, 23887 dates = {Nov 21, 2002}, 23888 email = {sovinec@engr.wisc.edu} 23889} 23890 23891@Unpublished{ au1b, 23892 author = {Pablo Carrica and Robert Wilson}, 23893 institution = {INSTITUTE HYDRAULIC RESEARCH, University of Iowa}, 23894 url = {http://}, 23895 sponsors = {Office of Naval Research}, 23896 note = {Using PETSc for a hydrodynamics of ships and submarines}, 23897 dates = {Sept, 2002}, 23898 email = {pablo-carrica@uiowa.edu and robert-wilson@uiowa.edu} 23899} 23900 23901% ------------------- TAO References ---------------------- 23902@Article{ benson:2001:csp, 23903 author = {Steven J. Benson and Lois Curfman McInnes and Jorge J. More'}, 23904 title = {A Case Study in the Performance and Scalability of Optimization Algorithms}, 23905 journal = {{ACM} Transactions on Mathematical Software}, 23906 volume = {27}, 23907 number = {3}, 23908 month = sep, 23909 year = {2001}, 23910 pages = {361--376} 23911} 23912 23913@TechReport{ tao-user-ref-2000, 23914 author = {Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}}, 23915 title = {{TAO} Users Manual}, 23916 year = {2000}, 23917 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23918 number = {ANL/MCS-TM-242}, 23919 note = {See \url{http://www.mcs.anl.gov/tao}} 23920} 23921 23922% ------------------- Optimization References ---------------------- 23923@Book{ optguide93, 23924 title = {Optimization Software Guide}, 23925 author = {Jorge J. Mor\'{e} and Stephen J. Wright}, 23926 publisher = {SIAM Publications}, 23927 address = {Philadelphia}, 23928 year = {1993} 23929} 23930 23931@InProceedings{ more84, 23932 author = {Jorge J. Mor\'{e} and Danny C. Sorenson and Burton S. Garbow and Kenneth E. 23933 Hillstrom}, 23934 title = {The {MINPACK} Project}, 23935 booktitle = {Sources and Development of Mathematical Software}, 23936 editor = {Wayne R. Cowell}, 23937 year = {1984}, 23938 pages = {88--111} 23939} 23940 23941@Article{ steihaug:83, 23942 author = {Trond Steihaug}, 23943 title = {The Conjugate Gradient Method and Trust Regions in Large Scale Optimization}, 23944 journal = {SIAM J. Numer. Anal.}, 23945 volume = {20}, 23946 year = {1983}, 23947 pages = {626--637}, 23948 key = {steihaug92 ! trust_region} 23949} 23950 23951@TechReport{ minpack2test, 23952 author = {Brett M. Averick and Richard G. Carter and Jorge J. Mor\'{e}}, 23953 title = {The {MINPACK-2} Test Problem Collection}, 23954 institution = {Argonne National Laboratory}, 23955 year = {1991}, 23956 number = {ANL/MCS-TM-150}, 23957 key = {more91 ! MINPACK-2} 23958} 23959 23960@TechReport{ hohmann:94, 23961 author = {Andreas Hohmann}, 23962 title = {Object Oriented Design of Multilevel {N}ewton and Continuation Methods}, 23963 institution = {Konrad-Zuse-Zentrum fur Informationstechnik Berlin}, 23964 year = {1994}, 23965 number = {SC-94-4}, 23966 key = {Hohmann94} 23967} 23968 23969@TechReport{ meza:94, 23970 author = {Juan C. Meza}, 23971 title = {{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization}, 23972 institution = {Sandia National Laboratory}, 23973 year = {1994}, 23974 number = {SAND94-8225}, 23975 key = {Meza94} 23976} 23977 23978@Book{ dennis:83, 23979 author = {J. E. {Dennis Jr.} and Robert B. Schnabel}, 23980 title = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations}, 23981 publisher = {Prentice-Hall, Inc.}, 23982 address = {Englewood Cliffs, NJ}, 23983 year = {1983} 23984} 23985 23986@TechReport{ more:92, 23987 author = {Jorge J. Mor\'{e} and David Thuente}, 23988 title = {Line search algorithms with guaranteed sufficient decrease}, 23989 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 23990 year = {1992}, 23991 number = {MCS-P330-1092} 23992} 23993 23994@Article{ more-toraldo, 23995 author = {Jorge J. Mor\'e and G. Toraldo}, 23996 journal = {SIOPT}, 23997 pages = {93--113}, 23998 title = {On the solution of large quadratic programming problems with bound constraints}, 23999 volume = {1}, 24000 year = {1991} 24001} 24002 24003@Article{ byrd:1995:lma, 24004 author = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu}, 24005 title = {A Limited Memory Algorithm for Bound Constrained Optimization}, 24006 journal = {SIAM Journal on Scientific Computing}, 24007 volume = {16}, 24008 number = {5}, 24009 pages = {1190--1208}, 24010 month = sep, 24011 year = {1995}, 24012 coden = {SJOCE3}, 24013 issn = {1064-8275 (print), 1095-7197 (electronic)}, 24014 mrclass = {90C30 (65K05)}, 24015 mrnumber = {96e:90039}, 24016 mrreviewer = {Henry Wolkowicz}, 24017 bibdate = {Fri Dec 4 16:17:35 MST 1998} 24018} 24019 24020@Article{ lin_c3, 24021 author = {C.-J. Lin and J. J. Mor\'e}, 24022 title = {Newton's method for large bound-constrained optimization problems}, 24023 year = {1999}, 24024 journal = {SIOPT}, 24025 volume = {9(4)}, 24026 pages = {1100--1127}, 24027 url = {http://www.mcs.anl.gov/home/more/papers/nb.ps.gz} 24028} 24029 24030@TechReport{ dolan2, 24031 author = {E. Dolan and J. J. Mor\'{e}}, 24032 title = {Benchmarking Optimization Software with Performance Profiles}, 24033 year = {2001}, 24034 month = jan, 24035 number = {ANL/MCS-P861-1200}, 24036 institution = {Mathematics and Computer Science Division, Argonne National Laboratory}, 24037 address = {Argonne, IL}, 24038 url = {http://www.mcs.anl.gov/~more/cops/} 24039} 24040 24041@InProceedings{ owlqn, 24042 author = {Galen Andrew and Jianfeng Gao}, 24043 title = {Scalable training of L1-regularized log-linear models}, 24044 booktitle = {Proceedings of the 24th international conference on Machine learning (ICML)}, 24045 pages = {33--40}, 24046 year = {2007} 24047} 24048 24049@Article{ bmrm, 24050 author = {Choon Hue Teo and S.V.N. Vishwanathan and Alex J. Smola and Quoc V. Le}, 24051 title = {Bundle methods for regularized risk minimization}, 24052 year = {2010}, 24053 journal = {Journal of Machine Learning Research}, 24054 volume = {11}, 24055 pages = {311--365} 24056} 24057 24058% ------------------- Component Software References ---------------------- 24059@InProceedings{ cca99, 24060 author = {R. Armstrong and D. Gannon and A. Geist and K. Keahey and S. Kohn and L. C. 24061 McInnes and S. Parker and B. Smolinski}, 24062 title = {Toward a Common Component Architecture for High-Performance Scientific 24063 Computing}, 24064 booktitle = {Proceedings of {High Performance Distributed Computing}}, 24065 pages = {115--124}, 24066 year = {1999}, 24067 note = {See \url{http://cca-forum.org}} 24068} 24069 24070@Book{ szyperski98, 24071 author = {Clemens Szyperski}, 24072 title = {Component Software: Beyond Object-Oriented Programming}, 24073 publisher = {ACM Press}, 24074 address = {New York}, 24075 year = {1998} 24076} 24077 24078@Article{ broy98, 24079 author = {Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and 24080 Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael 24081 Stal and Clemens Szyperski}, 24082 title = {What Characterizes a (Software) Component?}, 24083 journal = {Software -- Concepts and Tools}, 24084 publisher = {Springer-Verlag}, 24085 year = {1998}, 24086 volume = {19}, 24087 pages = {49--56} 24088} 24089 24090@Article{ componentware:94, 24091 author = {Jon Udell}, 24092 title = {Componentware}, 24093 journal = {Byte}, 24094 volume = {may}, 24095 pages = {46--56}, 24096 year = {1994}, 24097 key = {Udell94 ! componentware} 24098} 24099 24100@Misc{ cca-web-page, 24101 author = {{Common Component Architecture Forum}}, 24102 note = {See \url{http://cca-forum.org}} 24103} 24104 24105% --------------- References for Tools Used by TAO Developers ----------------- 24106 24107% 24108% tohtml: Used to generate on-line TAO users manual and manual pages 24109% 24110@TechReport{ tohtml, 24111 author = {William Gropp}, 24112 title = {Users Manual for tohtml: Producing true hypertext documents from {LaTeX}}, 24113 institution = {Argonne National Laboratory}, 24114 number = {ANL/MCS-TM-00}, 24115 month = jan, 24116 year = {1995}, 24117 key = {tohtml} 24118} 24119 24120% 24121% doctext: Used to generate tex version of TAO manual pages 24122% 24123@TechReport{ doctext, 24124 author = {William Gropp}, 24125 title = {Users Manual for doctext: Producing documentation from {C} source code}, 24126 institution = {Argonne National Laboratory}, 24127 number = {ANL/MCS-TM-00}, 24128 month = jan, 24129 year = {1995}, 24130 key = {doctext} 24131} 24132 24133% 24134% bfort: Used to generate TAO Fortran interface 24135% 24136@TechReport{ bfort, 24137 author = {William Gropp}, 24138 title = {Users Manual for bfort: Producing {F}ortran interfaces to {C} source code}, 24139 institution = {Argonne National Laboratory}, 24140 number = {ANL/MCS-TM-208}, 24141 month = mar, 24142 year = {1995}, 24143 key = {doctext} 24144} 24145 24146% ------------------------- PETSc References ------------------------------ 24147@InProceedings{ petsc, 24148 author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith}, 24149 title = {Efficient Management of Parallelism in Object Oriented Numerical Software 24150 Libraries}, 24151 booktitle = {Modern Software Tools in Scientific Computing}, 24152 editor = {E. Arge and A. M. Bruaset and H. P. Langtangen}, 24153 publisher = {Birkhauser Press}, 24154 pages = {163--202}, 24155 year = {1997} 24156} 24157 24158% ------------------------- Misc Other References ------------------------------ 24159@Misc{ indeps-web-page, 24160 title = {{InDEPS} {W}eb page}, 24161 note = {http://z.ca.sandia.gov/\~{ }indeps/}, 24162 author = {et al. Robert Armstrong}, 24163 institution = {Sandia National Laboratory}, 24164 key = {{InDEPS} {W}eb page} 24165} 24166 24167@Misc{ pooma, 24168 title = {{POOMA}: {A} FrameWork for scientific computing applications on parallel ar 24169 chitectures}, 24170 year = {1996}, 24171 author = {J. V. W. Reynders and J. C. Cummings and P. J. Hinker and M. Tholburn a nd M. S. 24172 S. Banerjee and S. Karmesin and S. Atlas and K. Keahey and W. F. Humphr ey} 24173} 24174 24175@Misc{ isis++-web-page, 24176 title = {{ISIS++} {W}eb Page}, 24177 note = {See \url{http://ca.sandia.gov/isis}}, 24178 author = {Robert L. Clay and Kyran Mish and Alan B. Williams}, 24179 institution = {Sandia National Laboratories} 24180} 24181 24182@Misc{ trilinos-web-page, 24183 title = {{Trilinos} {W}eb Page}, 24184 note = {See 24185 \url{http://www.cs.sandia.gov/\~mheroux/Trilinos/doc/TrilinosIntroduction.htm}}, 24186 author = {Mike Heroux et al.}, 24187 institution = {Sandia National Laboratories} 24188} 24189 24190@Misc{ alice-web-page, 24191 title = {{ALICE} {W}eb page}, 24192 note = {http://www.mcs.anl.gov/\-alice, Mathematics and Computer Science Division, 24193 Argonne National Laboratory}, 24194 key = {{ALICE} {W}eb page} 24195} 24196 24197@Misc{ autodiff-webpage, 24198 author = {{Computational Differentiation Project}}, 24199 note = {See \url{http://www.mcs.anl.gov/autodiff}} 24200} 24201 24202@Misc{ coool-home-page, 24203 author = {Lydia Deng and Wences Gouveia and John Scales}, 24204 title = {{The CWP Object-Oriented Optimization Library}}, 24205 note = {See \url{http://www.cwp.mines.edu/cwpcodes/coool}} 24206} 24207 24208@Misc{ rice-inversion-home-page, 24209 author = {Mark S. Gokenbach and William W. Symes}, 24210 title = {{The Hilbert Class Library}}, 24211 note = {See \url{http://www.trip.caam.rice.edu/}} 24212} 24213 24214@Misc{ opt++-home-page, 24215 author = {{OPT++: An Object-Oriented Nonlinear Optimization Library}}, 24216 note = {See \url{http://csmr.ca.sandia.gov/projects/opt/opt++.html}} 24217} 24218 24219@Article{ gockenbach:1999:ccl, 24220 author = {Mark S. Gockenbach and Matthew J. Petro and William W. Symes}, 24221 title = {C++ Classes for Linking Optimization with Complex Simulations}, 24222 journal = {{ACM} Transactions on Mathematical Software}, 24223 volume = {25}, 24224 number = {2}, 24225 month = jun, 24226 year = {1999}, 24227 pages = {191-212}, 24228 abstract = {The object-oriented programming paradigm can be used to overcome the 24229 incompatibilities between off-the-shelf optimization software and application 24230 software. The Hilbert Class Library (HCL) defines the fundamental mathematical 24231 objects arising in optimization problems, such as vectors, linear operators, and 24232 so forth, as C++ classes, making it possible to write optimization code in a 24233 natural fashion, while allowing application software such as simulators to use the 24234 most convenient data structures and programming style. In spite of the poor 24235 reputation C++ has for runtime performance, the use of mixed-language programming 24236 allows performance equal to that achieved by standard Fortran packages, as 24237 comparisons with the popular code LBFGS and ARPACK demonstrate.}, 24238 accepted = {April 1999}, 24239 url = {http://www.acm.org/pubs/citations/journals/toms/1999-25-2/p191-gockenbach/} 24240} 24241 24242@Misc{ neos-guide, 24243 author = {{The Optimization Software Guide}}, 24244 note = {See \url{http://www.mcs.anl.gov/otc/Guide/}} 24245} 24246 24247@Article{ boyd, 24248 title = {Distributed optimization and statistical learning via the alternating direction 24249 method of multipliers}, 24250 author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, 24251 Jonathan and others}, 24252 journal = {Foundations and Trends{\textregistered} in Machine learning}, 24253 volume = {3}, 24254 number = {1}, 24255 pages = {1-122}, 24256 year = {2011}, 24257 publisher = {Now Publishers, Inc.} 24258} 24259 24260@Misc{ :alertsys, 24261 title = {page{ALERT}}, 24262 organization = {Alert Systems, Inc}, 24263 address = {Madison, Wisconsin}, 24264 note = {http://www.alertsys.com/} 24265} 24266 24267@Manual{ :cmfortran, 24268 title = {{CM} {F}ortran Language Reference Manual}, 24269 organization = {Thinking Machines Corporation}, 24270 year = {1994}, 24271 address = {Cambridge, MA} 24272} 24273 24274@Manual{ :cmmd, 24275 title = {{CMMD} Reference Manual, Version 3.0}, 24276 organization = {Thinking Machines Corporation}, 24277 year = {1993}, 24278 address = {Cambridge, MA} 24279} 24280 24281@Manual{ :cmssl, 24282 title = {{CMSSL} for {CM} {F}ortran}, 24283 volume = {I}, 24284 organization = {Thinking Machines Corporation}, 24285 year = {1994}, 24286 address = {Cambridge, MA} 24287} 24288 24289@Misc{ :condor, 24290 author = {M. Livny}, 24291 title = {{PI}, The {Condor} Project, High Throughput Computing}, 24292 howpublished = {www.cs.wisc.edu/condor} 24293} 24294 24295@Manual{ :connection, 24296 title = {Connection Machine {CM}--5 Technical Summary}, 24297 organization = {Thinking Machines Corporation}, 24298 year = {1993}, 24299 address = {Cambridge, MA} 24300} 24301 24302@Manual{ :cplex, 24303 title = {{CPLEX} Optimizer}, 24304 organization = {ILOG CPLEX Division}, 24305 address = {889 Alder Avenue, Incline Village, Nevada}, 24306 note = {http://www.cplex.com/} 24307} 24308 24309@Manual{ :cplextm, 24310 title = {Using the {CPLEX(TM)} Linear Optimizer and {CPLEX(TM)} Mixed Integer Optimizer 24311 (Version 2.0)}, 24312 organization = {CPLEX Optimization Inc.}, 24313 year = {1992}, 24314 address = {Incline Village, Nevada} 24315} 24316 24317@Misc{ :fatcop, 24318 author = {M. C. Ferris}, 24319 title = {{PI}, {FATCOP}: {A} Fault Tolerant {Condor} {PVM} Mixed Integer Programming 24320 Solver}, 24321 howpublished = {www.cs.wisc.edu/math-prog/fatcop} 24322} 24323 24324@Misc{ :metaneos, 24325 author = {S. J. Wright}, 24326 title = {{metaNEOS}: Metacomputing Environments for Optimization}, 24327 howpublished = {www-unix.mcs.anl.gov/metaneos} 24328} 24329 24330@InCollection{ gropp.more:optimization, 24331 author = {W. Gropp and J. J. Mor\'e}, 24332 title = {Optimization environments and the {NEOS} Server}, 24333 booktitle = {Approximation Theory and Optimization}, 24334 pages = {167--182}, 24335 publisher = {Cambridge University Press}, 24336 year = {1997}, 24337 editor = {M. D. Buhmann and A. Iserles} 24338} 24339 24340@Article{ czyzyk.mesnier.ea:neos, 24341 author = {J. Czyzyk and M. P. Mesnier and J. J. Mor\'e}, 24342 title = {The {NEOS} Server}, 24343 journal = {IEEE Journal on Computational Science and Engineering}, 24344 volume = {5}, 24345 year = {1998}, 24346 pages = {68--75} 24347} 24348 24349@Book{ :osl, 24350 title = {Handbook for {IBM OSL}}, 24351 author = {M. S. Hung and W. O. Rom and A. D. Warren}, 24352 year = {1994}, 24353 publisher = {Boyd and Fraser}, 24354 address = {Danvers, Massachusetts} 24355} 24356 24357@Manual{ :pro-matlab, 24358 title = {{PRO}--{MATLAB} User's Guide}, 24359 organization = {The MathWorks, Inc.}, 24360 year = {1989}, 24361 address = {21 Eliot Street, South Natick, MA 01760} 24362} 24363 24364@Misc{ :prostate, 24365 key = {Biomedical}, 24366 title = {Biomedical Business International Newsletter}, 24367 howpublished = {pp. 72--75}, 24368 year = {1996} 24369} 24370 24371@Misc{ :sipcase, 24372 key = {Natural}, 24373 title = {Natural Gas Planning: An Application of Stochastic Linear Programming}, 24374 howpublished = {http://www-fp.mcs.anl.gov/otc/Guide/CaseStudies/slp/index.html} 24375} 24376 24377@Book{ aarts.korst:simulated, 24378 author = {E. Aarts and J. Korst}, 24379 title = {Simulated Annealing and Boltzman Machines}, 24380 year = {1990}, 24381 publisher = {John Wiley \& Sons}, 24382 address = {Chichester} 24383} 24384 24385@TechReport{ aarts.laarhoven.ea:local-search-based, 24386 author = {E. H. L. Aarts and P. J. M. van Laarhoven and N. L. J. Ulder}, 24387 title = {Local-Search-Based Algorithms for Job Shop Scheduling}, 24388 institution = {Centre for Quantitative Methods}, 24389 year = {1991}, 24390 address = {Nederlandse Philips Bedrijven B.V., P.O. Box 218, NL-5600 MD Eindhoven}, 24391 number = {106}, 24392 type = {CQM-Not} 24393} 24394 24395@Article{ aashtiani.magnanti:equilibria, 24396 author = {H. Z. Aashtiani and T. L. Magnanti}, 24397 title = {Equilibria on a congested transportation network}, 24398 journal = {SIAM Journal on Algebraic and Discrete Methods}, 24399 volume = {2}, 24400 year = {1981}, 24401 pages = {213--226} 24402} 24403 24404@Article{ ablow.brigham:analog, 24405 author = {C. M. Ablow and G. Brigham}, 24406 title = {An Analog Solution of Programming Problems}, 24407 journal = {Operations Research}, 24408 year = {1955}, 24409 volume = {3}, 24410 pages = {388--394} 24411} 24412 24413@Article{ achuthan.grabowski.ea:optimal, 24414 author = {N. R. Achuthan and J. Grabowski and J. B. Sidney}, 24415 title = {Optimal Flow--Shop Scheduling with Earliness and Tardiness Penalties}, 24416 journal = {Opsearch}, 24417 year = {1981}, 24418 volume = {18}, 24419 pages = {117--138} 24420} 24421 24422@Book{ adelman.robinson:income, 24423 author = {I. Adelman and S. Robinson}, 24424 title = {Income Distribution Policy in Developing Countries}, 24425 publisher = {Stanford University Press}, 24426 year = {1978}, 24427 address = {Stanford, California} 24428} 24429 24430@Article{ adler.resende.ea:implementation, 24431 author = {I. Adler and M. G. C. Resende and G. Veiga and N. K. Karmarkar}, 24432 title = {An Implementation of {K}armarkar's Algorithm for Linear Programming}, 24433 journal = {Mathematical Programming}, 24434 year = {1989}, 24435 volume = {44}, 24436 pages = {297--336} 24437} 24438 24439@TechReport{ aeberhard.coomans.ea:comparison, 24440 author = {S. Aeberhard and D. Coomans and O. de Vel}, 24441 title = {Comparison of Classifiers in High Dimensional Settings}, 24442 institution = {Departments of Computer Science and of Mathematics and Statistics, James Cook 24443 University of North Queensland}, 24444 year = {1992}, 24445 number = {92-02}, 24446 type = {Technical Report} 24447} 24448 24449@Article{ aganagic.cottle:constructive, 24450 author = {M. Aganagi\'{c} and R. W. Cottle}, 24451 title = {A Constructive Characterization of ${Q}_0$ Matrices with Nonnegative Principal 24452 Minors}, 24453 journal = {Mathematical Programming}, 24454 year = {1987}, 24455 volume = {37}, 24456 pages = {223--231} 24457} 24458 24459@TechReport{ aganagic:iterative, 24460 author = {M. Aganagi\'{c}}, 24461 title = {Iterative Methods for the Linear Complementarity Problem}, 24462 institution = {Systems Optimization Laboratory, Department of Operations Research, Stanford 24463 University}, 24464 year = {1978}, 24465 type = {SOL}, 24466 number = {78-10}, 24467 address = {Stanford, California} 24468} 24469 24470@Book{ ahlfors:complex, 24471 author = {L. V. Ahlfors}, 24472 title = {Complex Analysis}, 24473 publisher = {McGraw--Hill Book Company}, 24474 address = {New York}, 24475 series = {International Series in Pure and Applied Mathematics}, 24476 edition = {Second}, 24477 year = {1966} 24478} 24479 24480@Article{ ahn:solution, 24481 author = {B--H. Ahn}, 24482 title = {Solution of Non--Symmetric Linear Complementarity Problems by Iterative Methods}, 24483 journal = {Journal of Optimization Theory and Applications}, 24484 year = {1981}, 24485 volume = {33}, 24486 pages = {175--185} 24487} 24488 24489@Article{ al-fahed.stavroulakis.ea:hard, 24490 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24491 title = {Hard and soft fingered robot grippers. The linear complementarity approach}, 24492 journal = {Zeitschrift f{\"{u}}r Angewandte Mathematik und Mechanik}, 24493 volume = {71}, 24494 year = {1991}, 24495 pages = {257--265} 24496} 24497 24498@Article{ al-fahed.stavroulakis.ea:linear, 24499 author = {A. M. Al-Fahed and G. E. Stavroulakis and P. D. Panagiotopoulos}, 24500 title = {A linear complementarity approach to the frictionless gripper}, 24501 journal = {International Journal of Robotic Research}, 24502 volume = {11}, 24503 year = {1992}, 24504 pages = {112--122} 24505} 24506 24507@Article{ al-khayyal.falk:jointly, 24508 author = {F. A. Al--Khayyal and J. E. Falk}, 24509 title = {Jointly Constrained Biconvex Programming}, 24510 journal = {Mathematics of Operations Research}, 24511 year = {1983}, 24512 volume = {8}, 24513 pages = {273--286} 24514} 24515 24516@Article{ al-khayyal.kyparisis:finite, 24517 author = {F. A. Al--Khayyal and J. Kyparisis}, 24518 title = {Finite Convergence of Algorithms for Nonlinear Programs and Variational 24519 Inequalities}, 24520 journal = {Journal of Optimization Theory and Applications}, 24521 year = {1991}, 24522 volume = {70}, 24523 pages = {319--332} 24524} 24525 24526@PhDThesis{ al-khayyal:biconvex, 24527 author = {F. A. Al--Khayyal}, 24528 title = {Biconvex Programming and Biconcave Minimization}, 24529 year = {1977}, 24530 school = {The George Washington University} 24531} 24532 24533@Article{ alart.curnier:mixed, 24534 author = {P. Alart and A. Curnier}, 24535 title = {A mixed formulation for frictional contact problems prone to {N}ewton like 24536 solution methods}, 24537 journal = {Computer Methods in Applied Mechanics and Engineering}, 24538 volume = {92}, 24539 year = {1991}, 24540 pages = {353--375} 24541} 24542 24543@Misc{ alexander.kellog.ea:piecewise, 24544 author = {J.~C. Alexander and R.~B. Kellog and T.-Y. Li and J~.A. Yorke}, 24545 title = {Piecewise smooth continuation}, 24546 howpublished = {Manuscript}, 24547 year = {1979} 24548} 24549 24550@InCollection{ alexander.li.ea:piecewise, 24551 author = {J.~C. Alexander and T.-Y. Li and J~.A. Yorke}, 24552 title = {Piecewise smooth homotopies}, 24553 booktitle = {Homotopy Methods and Global Convergence}, 24554 pages = {1--14}, 24555 publisher = {Plenum Press}, 24556 year = {1983}, 24557 editor = {B.~C. Eaves and F.~J. Gould and H.-O. Peitgen and M.~J. Todd}, 24558 address = {New York} 24559} 24560 24561@InCollection{ alexander:topological, 24562 author = {J.~C. Alexander}, 24563 title = {The topological theory of an embedding method}, 24564 booktitle = {Continuation Methods}, 24565 pages = {37--68}, 24566 publisher = {Academic Press}, 24567 year = {1978}, 24568 editor = {H. Wacker}, 24569 address = {New York} 24570} 24571 24572@Book{ allen:probability, 24573 author = {A. O. Allen}, 24574 title = {Probability, Statistics and Queueing Theory}, 24575 publisher = {Academic Press}, 24576 year = {1990}, 24577 address = {London}, 24578 edition = {Second} 24579} 24580 24581@Book{ allgower.georg:numerical, 24582 author = {E. L. Allgower and K. Georg}, 24583 title = {Numerical Continuation Methods, An Introduction}, 24584 publisher = {Springer-Verlag}, 24585 year = {1990}, 24586 address = {Berlin} 24587} 24588 24589@InProceedings{ allgower.georg:predictor-corrector, 24590 crossref = {bachem.grotschel.ea:mathematical}, 24591 author = {E. L. Allgower and K. Georg}, 24592 title = {Predictor--Corrector and Simplicial Methods for Approximating Fixed Points and 24593 Zero Points of Nonlinear Mappings}, 24594 pages = {15--56} 24595} 24596 24597@Article{ aluffi-pentini.parisi.ea:algorithm, 24598 author = {F. Aluffi-Pentini and V. Parisi and F. Zirilli}, 24599 title = {Algorithm 667: {SIGMA}- {A} Stochastic-Integration Global Minimization 24600 Algorithm}, 24601 journal = {ACM Transactions on Mathematical Software}, 24602 year = {1988}, 24603 volume = {14}, 24604 pages = {366--380} 24605} 24606 24607@Article{ anandalingam.friesz:hierarchical, 24608 author = {G. Anandalingam and T. L. Friesz}, 24609 title = {Hierarchical Optimization: An Introduction}, 24610 journal = {Annals of Operations Research}, 24611 year = {1992}, 24612 volume = {34}, 24613 pages = {1--11} 24614} 24615 24616@Article{ anandalingam.white:solution, 24617 author = {G. Anandalingam and D. J. White}, 24618 title = {A Solution Method for the Linear Static Stackelberg Problem Using Penalty 24619 Functions}, 24620 journal = {IEEE Transactions on Automatic Control}, 24621 year = {1990}, 24622 volume = {35}, 24623 number = {10}, 24624 pages = {1170--1173} 24625} 24626 24627@Article{ andersen.andersen:presolving, 24628 author = {E. Andersen and K. Andersen}, 24629 title = {Presolving in Linear Programming}, 24630 year = {1995}, 24631 journal = {Mathematical Programming}, 24632 volume = {71}, 24633 pages = {221--245} 24634} 24635 24636@InProceedings{ andersen.ye:homogeneous, 24637 author = {E. Andersen and Y. Ye}, 24638 title = {On a Homogeneous Algorithm for a Monotone Complementarity Problem with Nonlinear 24639 Equality Constraints}, 24640 crossref = {ferris.pang:complementarity}, 24641 pages = {1--11} 24642} 24643 24644@Book{ anderson.bai.ea:lapack, 24645 author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du 24646 Cros and A. Greenbaum and S. Hammarling and A. McKenney and S. Ostrouchov and D. 24647 Sorensen}, 24648 title = {{LAPACK} User's Guide}, 24649 publisher = {SIAM}, 24650 year = {1995}, 24651 address = {Philadelphia, Pennsylvania}, 24652 edition = {Second} 24653} 24654 24655@Article{ anderson.ferris:direct, 24656 author = {E. J. Anderson and M. C. Ferris}, 24657 title = {A Direct Search Algorithm for Optimization with Noisy Function Evaluations}, 24658 year = {2001}, 24659 journal = {SIAM Journal on Optimization, forthcoming}, 24660 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-11.ps}, 24661 key = {55} 24662} 24663 24664@InProceedings{ anderson.ferris:genetic, 24665 author = {E. J. Anderson and M. C. Ferris}, 24666 title = {A Genetic Algorithm for the Assembly Line Balancing Problem}, 24667 booktitle = {Proceedings of the Integer Programming / Combinatorial Optimization Conference, 24668 Waterloo, Ontario, Canada, May 28--30}, 24669 publisher = {University of Waterloo Press}, 24670 key = {14}, 24671 year = {1990} 24672} 24673 24674@Article{ anderson.ferris:genetic*1, 24675 author = {E. J. Anderson and M. C. Ferris}, 24676 title = {Genetic Algorithms for Combinatorial Optimization: The Assembly Line Balancing 24677 Problem}, 24678 journal = {ORSA Journal on Computing}, 24679 year = {1994}, 24680 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/93-ga.ps}, 24681 volume = {6}, 24682 pages = {161--173}, 24683 key = {22} 24684} 24685 24686@InProceedings{ anderson.ferris:parallel, 24687 author = {E. J. Anderson and M. C. Ferris}, 24688 title = {Parallel Genetic Algorithms in Optimization}, 24689 booktitle = {Proceedings of the Fourth SIAM conference on Parallel Processing for Scientific 24690 Computing, Chicago, Illinois, December 11-13}, 24691 year = {1989}, 24692 key = {12} 24693} 24694 24695@Unpublished{ anderson.lewis:primal, 24696 author = {E. J. Anderson and A. S. Lewis}, 24697 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24698 note = {In preparation} 24699} 24700 24701@Book{ anderson.nash:linear, 24702 author = {E. J. Anderson and P. Nash}, 24703 title = {Linear Programming in Infinite--Dimensional Spaces}, 24704 year = {1987}, 24705 publisher = {John Wiley \& Sons}, 24706 address = {Chichester} 24707} 24708 24709@InProceedings{ anderson:primal, 24710 author = {E. J. Anderson}, 24711 title = {A New Primal Algorithm for Semi-Infinite Linear Programming}, 24712 booktitle = {Proceedings of an International Symposium on Infinite Dimensional Linear 24713 Programming, Cambridge, September 1984}, 24714 year = {1985}, 24715 editor = {E. J. Anderson and A. B. Philpott}, 24716 publisher = {Springer-Verlag}, 24717 address = {Berlin} 24718} 24719 24720@Article{ andradottir:method, 24721 author = {S. Andrad\'{o}ttir}, 24722 title = {A Method of Discrete Stochastic Optimization}, 24723 journal = {Management Science}, 24724 year = {1995}, 24725 volume = {41}, 24726 pages = {1946--1961} 24727} 24728 24729@Article{ andradottir:global, 24730 author = {S. Andrad\'{o}ttir}, 24731 title = {A Global Search Method for Discrete Stochastic Optimization}, 24732 journal = {SIAM Journal on Optimization}, 24733 year = {1996}, 24734 volume = {6}, 24735 pages = {513--530} 24736} 24737 24738@TechReport{ anitescu.lesaja.ea:infeasible-interior-point, 24739 author = {M. Anitescu and G. Lesaja and F. A. Potra}, 24740 title = {An infeasible--interior--point predictor--corrector algorithm for the 24741 {P}$_x$--geometric {LCP}}, 24742 institution = {Department of Mathematics, The University of Iowa}, 24743 address = {Iowa City, Iowa}, 24744 year = {1994}, 24745 number = {62}, 24746 type = {Reports on Computational Mathematics} 24747} 24748 24749@TechReport{ anitescu.potra:formulating, 24750 author = {M. Anitescu and F. A. Potra}, 24751 title = {Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable 24752 Linear Complementarity Problems}, 24753 institution = {Department of Mathematics, The University of Iowa}, 24754 year = {1996}, 24755 type = {Report}, 24756 number = {93}, 24757 address = {Iowa City, Iowa} 24758} 24759 24760@Article{ anstreicher.lee.ea:crashing, 24761 author = {K. M. Anstreicher and J. Lee and T. F. Rutherford}, 24762 title = {Crashing a Maximum-Weight Complementarity Basis}, 24763 journal = {Mathematical Programming}, 24764 year = {1992}, 24765 volume = {54}, 24766 pages = {281--294} 24767} 24768 24769@Article{ anstreicher:combined, 24770 author = {K. M. Anstreicher}, 24771 title = {A combined phase {I}--phase {II} scaled potential algorithm for linear 24772 programming}, 24773 journal = {Mathematical Programming}, 24774 year = {1991}, 24775 volume = {52}, 24776 pages = {429--440} 24777} 24778 24779@Article{ anstreicher:combined*1, 24780 author = {K. M. Anstreicher}, 24781 title = {A combined phase {I}--phase {II} projective algorithm for linear programming}, 24782 journal = {Mathematical Programming}, 24783 year = {1989}, 24784 volume = {43}, 24785 pages = {209--223} 24786} 24787 24788@InCollection{ arbenz.gander.ea:remote, 24789 author = {P. Arbenz and W. Gander and M. Oettli}, 24790 title = {The Remote Computational System}, 24791 booktitle = {High-Performance Computation and Networks}, 24792 publisher = {Springer-Verlag}, 24793 year = {1996}, 24794 volume = {1067}, 24795 series = {Lecture Notes in Computer Science}, 24796 pages = {662--667} 24797} 24798 24799@InCollection{ arcus:comsoal, 24800 author = {A. L. Arcus}, 24801 title = {{COMSOAL}: {A} Computer Method of Sequencing Operations for Assembly Lines}, 24802 booktitle = {Readings in Production and Operations Management}, 24803 year = {1966}, 24804 editor = {E. S. Buffa}, 24805 publisher = {John Wiley \& Sons}, 24806 address = {New York} 24807} 24808 24809@TechReport{ arioli.chan.ea:computing, 24810 author = {M. Arioli and T. F. Chan and I. S. Duff and N. I. M. Gould and J. K. Reid}, 24811 title = {Computing a Search Direction for Large-Scale Linearly-Constrained Nonlinear 24812 Optimization Calculations}, 24813 institution = {CERFACS}, 24814 year = {1993}, 24815 number = {TR/PA/93/34} 24816} 24817 24818@Article{ armijo:minimization, 24819 author = {L. Armijo}, 24820 title = {Minimization of Functions having {L}ipschitz-continuous First Partial 24821 Derivatives}, 24822 journal = {Pacific Journal of Mathematics}, 24823 year = {1966}, 24824 volume = {16}, 24825 pages = {1--3} 24826} 24827 24828@Article{ arrow.debreu:existence, 24829 author = {K. Arrow and G. Debreu}, 24830 title = {Existence of Equilibrium for a Competitive Economy}, 24831 journal = {Econometrica}, 24832 year = {1954}, 24833 volume = {22}, 24834 pages = {265--290} 24835} 24836 24837@InCollection{ arrow.solow:gradient, 24838 author = {K. J. Arrow and R. M. Solow}, 24839 title = {Gradient Methods for Constrained Maxima with Weakened Assumptions}, 24840 booktitle = {Studies in Linear and Nonlinear Programming}, 24841 year = {1958}, 24842 editor = {K. J. Arrow and L. Hurwicz and H. Uzawa}, 24843 publisher = {Stanford University Press}, 24844 address = {Stanford, California}, 24845 pages = {166--176} 24846} 24847 24848@Book{ aubin.ekeland:nonlinear, 24849 author = {J.-P. Aubin and I. Ekeland}, 24850 title = {Applied nonlinear analysis}, 24851 publisher = {John Wiley \& Sons}, 24852 address = {New York}, 24853 year = {1984} 24854} 24855 24856@Article{ auchmuty:variational, 24857 author = {G. Auchmuty}, 24858 title = {Variational Principles for Variational Inequalities}, 24859 journal = {Numerical Functional Analysis and Optimization}, 24860 year = {1989}, 24861 volume = {10}, 24862 pages = {863--874} 24863} 24864 24865@Book{ auerbach.kotlikoff:dynamic, 24866 author = {A. J. Auerbach and L. J. Kotlikoff}, 24867 title = {Dynamic Fiscal Policy}, 24868 publisher = {Cambridge University Press}, 24869 address = {Cambridge, England}, 24870 year = {1987} 24871} 24872 24873@InProceedings{ ault.deutsch.ea:interpolating, 24874 author = {D. A. Ault and F. R. Deutsch and P. D. Morris and J. E. Olson}, 24875 title = {Interpolating Subspaces in Approximation Theory}, 24876 booktitle = {Approximation Theory}, 24877 year = {1970}, 24878 editor = {A. Talbot}, 24879 publisher = {Academic Press}, 24880 address = {London} 24881} 24882 24883@Article{ auslender.crouzeix:global, 24884 author = {A. A. Auslender and J.--P. Crouzeix}, 24885 title = {Global Regularity Theorems}, 24886 journal = {Mathematics of Operations Research}, 24887 year = {1988}, 24888 volume = {13}, 24889 pages = {243--253} 24890} 24891 24892@Article{ auslender.haddou:interior-proximal, 24893 author = {A. Auslender and M. Haddou}, 24894 title = {An interior-proximal method for convex linearly constrained problems and its 24895 extension to variational inequalities}, 24896 year = {1995}, 24897 journal = {Mathematical Programming}, 24898 pages = {77--100}, 24899 volume = {71} 24900} 24901 24902@Article{ auslender:convergence, 24903 author = {A. Auslender}, 24904 title = {Convergence of stationary sequences for variational inequalities with maximal 24905 monotone operators}, 24906 journal = {Applied Mathematics and Optimization}, 24907 volume = {28}, 24908 year = {1993}, 24909 pages = {161--172} 24910} 24911 24912@Book{ auslender:optimization, 24913 author = {A. Auslender}, 24914 title = {Optimization {M}\'{e}thodes Num\'{e}riques}, 24915 year = {1976}, 24916 publisher = {Masson}, 24917 address = {Paris} 24918} 24919 24920@TechReport{ averick.carter.ea:minpack-2, 24921 author = {B. M. Averick and R. G. Carter and J. J. Mor\'e and G. -L. Xue}, 24922 title = {The {MINPACK-2} Test Problem Collection}, 24923 institution = {Argonne National Laboratory}, 24924 year = {1992}, 24925 address = {Argonne, Illinois}, 24926 number = {MCS-P153-0692} 24927} 24928 24929@TechReport{ axline.billups.ea:guidelines, 24930 author = {R. A. Axline and S. C. Billups and M. F. Grady}, 24931 title = {Guidelines for Software Security ({U})}, 24932 institution = {SNL}, 24933 year = {1989}, 24934 month = oct, 24935 address = {Albuquerque, New Mexico}, 24936 number = {SAND88-2955} 24937} 24938 24939@Article{ ayres.walter:greenhouse, 24940 author = {R. U. Ayres and J. Walter}, 24941 title = {The Greenhouse Effect: Damages, Costs and Abatement}, 24942 journal = {Environmental and Resource Economics}, 24943 year = {1991}, 24944 volume = {1}, 24945 pages = {237--270} 24946} 24947 24948@PhDThesis{ bagley:behaviour, 24949 author = {J. D. Bagley}, 24950 title = {The Behaviour of Adaptive Systems which employ Genetic and Correlation 24951 Algorithms}, 24952 year = {1967}, 24953 school = {University of Michigan} 24954} 24955 24956@Article{ bain.stewart:application, 24957 author = {R. S. Bain and W. E. Stewart}, 24958 title = {Application of Robust Nonmonotonic Descent Criteria to the Solution of Nonlinear 24959 Algebraic Equation Systems}, 24960 journal = {Computers in Chemical Engineering}, 24961 year = {1991}, 24962 volume = {15}, 24963 pages = {203--208} 24964} 24965 24966@Article{ baker.lasdon:successive, 24967 author = {T. E. Baker and L. S. 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Bertsekas}, 25411 title = {Nonlinear Programming}, 25412 publisher = {Athena Scientific}, 25413 year = {1995}, 25414 address = {Belmont, Massachusetts} 25415} 25416 25417@Article{ bertsekas:projected, 25418 author = {Dimitri P. Bertsekas}, 25419 title = {Projected {N}ewton Methods for Optimization Problems with Simple Constraints}, 25420 journal = {SIAM Journal on Control and Optimization}, 25421 year = {1982}, 25422 volume = {20}, 25423 pages = {221--246} 25424} 25425 25426@Article{ billups.dirkse.ea:comparison, 25427 author = {S. C. Billups and S. P. Dirkse and M. C. Ferris}, 25428 title = {A Comparison of Large Scale Mixed Complementarity Problem Solvers}, 25429 journal = {Computational Optimization and Applications}, 25430 year = {1997}, 25431 pages = {3--25}, 25432 volume = {7}, 25433 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-16.ps}, 25434 key = {51} 25435} 25436 25437@Article{ billups.ferris:convergence, 25438 author = {S. C. Billups and M. C. Ferris}, 25439 title = {Convergence of an Infeasible Interior--Point Algorithm from Arbitrary Positive 25440 Starting Points}, 25441 journal = {SIAM Journal on Optimization}, 25442 year = {1996}, 25443 volume = {6}, 25444 pages = {316--325}, 25445 url = {ftp: //ftp.cs.wisc.edu/tech-reports/reports/1993/tr1180.ps}, 25446 key = {34} 25447} 25448 25449@TechReport{ billups.ferris:convergence*1, 25450 author = {S. C. Billups and M. C. Ferris}, 25451 title = {Convergence of Infeasible Interior--Point Algorithms from Arbitrary Starting 25452 Points}, 25453 institution = {Computer Sciences Department, University of Wisconsin}, 25454 year = {1993}, 25455 address = {Madison, Wisconsin}, 25456 number = {1180}, 25457 note = {Revised version in SIAM Journal on Optimization.} 25458} 25459 25460@Article{ billups.ferris:qpcomp, 25461 author = {S. C. Billups and M. C. Ferris}, 25462 title = {{QPCOMP}: {A} Quadratic Program Based Solver for Mixed Complementarity Problems}, 25463 year = {1997}, 25464 journal = {Mathematical Programming}, 25465 pages = {533--562}, 25466 volume = {76}, 25467 url = {ftp: //ftp.cs.wisc.edu/math-prog/tech-reports/95-09.ps}, 25468 key = {47} 25469} 25470 25471@Article{ billups.ferris:solutions, 25472 author = {S. C. Billups and M. C. Ferris}, 25473 title = {Solutions to Affine Generalized Equations Using Proximal Mappings}, 25474 journal = {Mathematics of Operations Research}, 25475 volume = {24}, 25476 pages = {219--236}, 25477 year = {1999}, 25478 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-15.ps}, 25479 key = {42}, 25480 institution = {Computer Sciences Department, University of Wisconsin}, 25481 address = {Madison, Wisconsin}, 25482 type = {Mathematical Programming Technical Report}, 25483 number = {94--15} 25484} 25485 25486@TechReport{ billups.murata.ea:users, 25487 author = {S. C. Billups and K. K. 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Billups}, 25508 title = {Algorithms for Complementarity Problems and Generalized Equations}, 25509 school = {University of Wisconsin--Madison}, 25510 year = {1995}, 25511 address = {Madison, Wisconsin}, 25512 month = aug 25513} 25514 25515@MastersThesis{ billups:augmented, 25516 author = {S. C. Billups}, 25517 title = {An Augmented Jacobian Matrix Algorithm for Tracking Homotopy Zero Curves}, 25518 school = {Virginia Tech}, 25519 year = {1985}, 25520 address = {Blacksburg, Virginia} 25521} 25522 25523@TechReport{ billups:homotopy, 25524 author = {S. C. Billups}, 25525 title = {A Homotopy Based Algorithm for Mixed Complementarity Problems}, 25526 institution = {Department of Mathematics, University of Colorado}, 25527 year = {1998}, 25528 address = {Denver, Colorado} 25529} 25530 25531@Article{ billups:improving, 25532 author = {S. C. 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Mangasarian}, 28502 title = {Breast Cancer Diagnosis via Linear Programming}, 28503 key = {50}, 28504 journal = {{IEEE} Computational Science and Engineering}, 28505 year = {1995}, 28506 volume = {2}, 28507 pages = {70--71} 28508} 28509 28510@Article{ ferris.mangasarian:error, 28511 author = {M. C. Ferris and O. L. Mangasarian}, 28512 title = {Error Bounds and Strong Upper Semicontinuity for Monotone Affine Variational 28513 Inequalities}, 28514 journal = {Annals of Operations Research}, 28515 year = {1993}, 28516 volume = {47}, 28517 pages = {293--305}, 28518 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1056a.ps}, 28519 key = {24} 28520} 28521 28522@Article{ ferris.mangasarian:finite, 28523 author = {M. C. Ferris and O. L. Mangasarian}, 28524 title = {Finite Perturbation of Convex Programs}, 28525 journal = {Applied Mathematics and Optimization}, 28526 year = {1991}, 28527 volume = {23}, 28528 pages = {263--273}, 28529 key = {08} 28530} 28531 28532@Book{ ferris.mangasarian:linear, 28533 author = {M. C. Ferris and O. L. Mangasarian}, 28534 title = {Linear Programming via {MATLAB}}, 28535 publisher = {in preparation}, 28536 year = {1995}, 28537 address = {Madison, Wisconsin} 28538} 28539 28540@Article{ ferris.mangasarian:minimum, 28541 author = {M. C. Ferris and O. L. Mangasarian}, 28542 title = {Minimum Principle Sufficiency}, 28543 journal = {Mathematical Programming}, 28544 year = {1992}, 28545 volume = {57}, 28546 pages = {1--14}, 28547 key = {11} 28548} 28549 28550@Article{ ferris.mangasarian:parallel, 28551 author = {M. C. Ferris and O. L. Mangasarian}, 28552 title = {Parallel Constraint Distribution}, 28553 journal = {SIAM Journal on Optimization}, 28554 year = {1991}, 28555 volume = {1}, 28556 pages = {487--500}, 28557 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1990/tr971a.ps}, 28558 key = {18} 28559} 28560 28561@Article{ ferris.mangasarian:parallel*1, 28562 author = {M. C. Ferris and O. L. Mangasarian}, 28563 title = {Parallel Variable Distribution}, 28564 journal = {SIAM Journal on Optimization}, 28565 year = {1994}, 28566 volume = {4}, 28567 pages = {815--832}, 28568 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1993/tr1175.ps}, 28569 key = {31} 28570} 28571 28572@Article{ ferris.meeraus.ea:computing, 28573 title = {Computing {W}ardropian Equilibrium in a Complementarity Framework}, 28574 author = {M. C. Ferris and A. Meeraus and T. F. Rutherford}, 28575 journal = {Optimization Methods and Software}, 28576 year = {1999}, 28577 volume = {10}, 28578 pages = {669--685}, 28579 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-03.ps}, 28580 key = {45} 28581} 28582 28583@Article{ ferris.mesnier.ea:neos, 28584 author = {M. C. Ferris and M. P. Mesnier and J. Mor\'{e}}, 28585 title = {{NEOS} and {C}ondor: Solving Nonlinear Optimization Problems over the 28586 {I}nternet}, 28587 year = {2000}, 28588 journal = {{ACM} Transactions on Mathematical Software}, 28589 key = {54}, 28590 volume = {26}, 28591 pages = {1--18}, 28592 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-08.ps}, 28593 institution = {Computer Sciences Department, University of Wisconsin}, 28594 address = {Madison, Wisconsin}, 28595 number = {96-08}, 28596 type = {Mathematical Programming Technical Report}, 28597 note = {Also available as ANL/MCS-P708-0398, Mathematics and Computer Science Division, 28598 Argonne National Laboratory}, 28599 annote = {Revised version of: The {NEOS} System for Complementarity Problems: {PATH}, 28600 1996} 28601} 28602 28603@InCollection{ ferris.meyer:models, 28604 author = {M. C. Ferris and R. R. Meyer}, 28605 title = {Models and Solution for On-Demand Data Delivery Problems}, 28606 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-04.ps}, 28607 key = {80}, 28608 booktitle = {Approximation and Complexity in Numerical Optimization: Continuous and Discrete 28609 Problems}, 28610 editor = {P. M. Pardalos}, 28611 series = {Nonconvex Optimization and its Applications}, 28612 volume = {42}, 28613 address = {Dordrect}, 28614 year = {2000}, 28615 pages = {175--188}, 28616 publisher = {Kluwer}, 28617 type = {Mathematical Programming Technical Report}, 28618 institution = {Computer Sciences Department, University of Wisconsin}, 28619 number = {99-04} 28620} 28621 28622@InProceedings{ ferris.munson.ea:homotopy, 28623 author = {M. C. Ferris and T. S. Munson and D. Ralph}, 28624 title = {A Homotopy Method for Mixed Complementarity Problems based on the {PATH} Solver}, 28625 booktitle = {Numerical Analysis 1999}, 28626 key = {88}, 28627 year = {2000}, 28628 editor = {D. F. Griffiths and G. A. Watson}, 28629 series = {Research Notes in Mathematics}, 28630 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-09.ps}, 28631 address = {London}, 28632 pages = {143--167}, 28633 publisher = {Chapman and Hall}, 28634 institution = {Computer Sciences Department, University of Wisconsin}, 28635 number = {99-09}, 28636 type = {Mathematical Programming Technical Report} 28637} 28638 28639@TechReport{ ferris.munson.ea:practical, 28640 author = {M. C. Ferris and T. S. Munson and K. Sinapiromsaran}, 28641 title = {A Practical Approach to Sample-Path Simulation Optimization}, 28642 type = {Data Mining Institute Technical Report}, 28643 institution = {Computer Sciences Department, University of Wisconsin}, 28644 address = {Madison, Wisconsin}, 28645 year = {2000}, 28646 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-03.ps}, 28647 number = {00-03}, 28648 key = {92}, 28649 annote = {To appear in WSC 2000} 28650} 28651 28652@InCollection{ ferris.munson:case, 28653 author = {M. C. Ferris and T. S. Munson}, 28654 title = {Case Studies in Complementarity: Improving Model Formulation}, 28655 booktitle = {Ill--Posed Variational Problems and Regularization Techniques}, 28656 key = {73}, 28657 pages = {79--98}, 28658 publisher = {Springer Verlag}, 28659 year = {1999}, 28660 editor = {M. Th\'{e}ra and R. Tichatschke}, 28661 number = {477}, 28662 series = {Lecture Notes in Economics and Mathematical Systems}, 28663 address = {Berlin}, 28664 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-16.ps}, 28665 type = {Mathematical Programming Technical Report}, 28666 institution = {Computer Sciences Department, University of Wisconsin} 28667} 28668 28669@Article{ ferris.munson:complementarity, 28670 author = {M. C. Ferris and T. S. Munson}, 28671 title = {Complementarity Problems in {GAMS} and the {PATH} Solver}, 28672 year = {2000}, 28673 volume = {24}, 28674 pages = {165--188}, 28675 journal = {Journal of Economic Dynamics and Control}, 28676 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-12.ps}, 28677 key = {70}, 28678 type = {Mathematical Programming Technical Report}, 28679 institution = {Computer Sciences Department, University of Wisconsin}, 28680 address = {Madison, Wisconsin}, 28681 number = {98-12} 28682} 28683 28684@Misc{ ferris.munson:condor, 28685 author = {M. C. Ferris and T. S. Munson}, 28686 title = {Condor Modeling Language Interface}, 28687 organization = {Computer Sciences Department, University of Wisconsin}, 28688 address = {Madison, Wisconsin}, 28689 note = {ftp://ftp.cs.wisc.edu/math-prog/condor} 28690} 28691 28692@Manual{ ferris.munson:gams, 28693 author = {M. C. Ferris and T. S. Munson}, 28694 title = {{GAMS}/{PATH} User Guide: Version 4.3}, 28695 organization = {Department of Computer Sciences, University of Wisconsin, Madison} 28696} 28697 28698@Article{ ferris.munson:interfaces, 28699 author = {M. C. Ferris and T. S. Munson}, 28700 title = {Interfaces to {PATH} 3.0: Design, Implementation and Usage}, 28701 journal = {Computational Optimization and Applications}, 28702 volume = {12}, 28703 pages = {207--227}, 28704 year = {1999}, 28705 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-12.ps}, 28706 key = {63}, 28707 institution = {Computer Sciences Department, University of Wisconsin}, 28708 address = {Madison, Wisconsin}, 28709 number = {97-12}, 28710 type = {Mathematical Programming Technical Report} 28711} 28712 28713@TechReport{ ferris.munson:interior, 28714 author = {M. C. Ferris and T. S. Munson}, 28715 title = {Interior Point Methods for Massive Support Vector Machines}, 28716 institution = {Computer Sciences Department, University of Wisconsin}, 28717 year = {2000}, 28718 key = {94}, 28719 type = {Data Mining Institute Technical Report}, 28720 number = {00-05}, 28721 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-05.ps}, 28722 address = {Madison, Wisconsin}, 28723 annote = {Submitted to SIOPT} 28724} 28725 28726@Article{ ferris.munson:linear, 28727 author = {M. C. Ferris and T. S. Munson}, 28728 title = {Linear Programming for Emergency Broadcast Systems}, 28729 year = {1999}, 28730 journal = {{SIAG/OPT} Newsletter}, 28731 volume = {10}, 28732 pages = {6--8}, 28733 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-20.ps}, 28734 key = {76}, 28735 type = {Mathematical Programming Technical Report}, 28736 institution = {Computer Sciences Department, University of Wisconsin}, 28737 address = {Madison, Wisconsin}, 28738 number = {98-20} 28739} 28740 28741@Article{ ferris.munson:modeling, 28742 author = {M. C. Ferris and T. S. Munson}, 28743 title = {Modeling Languages and {C}ondor: Metacomputing for Optimization}, 28744 year = {2000}, 28745 journal = {Mathematical Programming}, 28746 volume = {88}, 28747 pages = {487--506}, 28748 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-13.ps}, 28749 key = {71}, 28750 type = {Mathematical Programming Technical Report}, 28751 institution = {Computer Sciences Department, University of Wisconsin}, 28752 address = {Madison, Wisconsin}, 28753 number = {98-13} 28754} 28755 28756@TechReport{ ferris.munson:preprocessing, 28757 author = {M. C. Ferris and T. S. Munson}, 28758 title = {Preprocessing Complementarity Problems}, 28759 type = {Mathematical Programming Technical Report}, 28760 institution = {Computer Sciences Department, University of Wisconsin}, 28761 address = {Madison, Wisconsin}, 28762 year = {1999}, 28763 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-07.ps}, 28764 number = {99-07}, 28765 key = {86}, 28766 annote = {Submitted to ICCP 99} 28767} 28768 28769@TechReport{ ferris.munson:semismooth, 28770 author = {M. C. Ferris and T. S. Munson}, 28771 title = {Semismooth Support Vector Machines}, 28772 institution = {Computer Sciences Department, University of Wisconsin}, 28773 year = {2000}, 28774 key = {97}, 28775 type = {Data Mining Institute Technical Report}, 28776 number = {00-09}, 28777 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-09.ps}, 28778 address = {Madison, Wisconsin}, 28779 annote = {Submitted to Math Prog B} 28780} 28781 28782@Article{ ferris.pang:engineering, 28783 author = {M. C. Ferris and J. S. Pang}, 28784 title = {Engineering and Economic Applications of Complementarity Problems}, 28785 year = {1997}, 28786 journal = {SIAM Review}, 28787 volume = {39}, 28788 pages = {669--713}, 28789 url = {http: //www.siam.org/journals/sirev/39-4/28596.html}, 28790 key = {46} 28791} 28792 28793@Article{ ferris.pang:nondegenerate, 28794 author = {M. C. Ferris and J. S. Pang}, 28795 title = {Nondegenerate Solutions and Related Concepts in Affine Variational Inequalities}, 28796 journal = {SIAM Journal on Control and Optimization}, 28797 year = {1996}, 28798 volume = {34}, 28799 pages = {244--263}, 28800 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1994/tr1203.ps}, 28801 key = {35} 28802} 28803 28804@Article{ ferris.philpott:affine, 28805 author = {M. C. Ferris and A. B. Philpott}, 28806 title = {On Affine Scaling and Semi--Infinite Programming}, 28807 journal = {Mathematical Programming}, 28808 year = {1992}, 28809 volume = {56}, 28810 pages = {361--364}, 28811 key = {15} 28812} 28813 28814@Article{ ferris.philpott:interior, 28815 author = {M. C. Ferris and A. B. Philpott}, 28816 title = {An Interior Point Algorithm for Semi--Infinite Linear Programming}, 28817 journal = {Mathematical Programming}, 28818 year = {1989}, 28819 volume = {43}, 28820 pages = {257--276}, 28821 key = {04} 28822} 28823 28824@Article{ ferris.philpott:performance, 28825 author = {M. C. Ferris and A. B. Philpott}, 28826 title = {On the Performance of {K}armarkar's Algorithm}, 28827 journal = {Journal of the Operational Research Society}, 28828 year = {1988}, 28829 volume = {39}, 28830 pages = {257--270}, 28831 key = {03} 28832} 28833 28834@InCollection{ ferris.ralph:projected, 28835 author = {M. C. Ferris and D. Ralph}, 28836 title = {Projected Gradient Methods for Nonlinear Complementarity Problems via Normal 28837 Maps}, 28838 booktitle = {Recent Advances in Nonsmooth Optimization}, 28839 publisher = {World Scientific Publishers}, 28840 year = {1995}, 28841 pages = {57--87}, 28842 editor = {D. Du and L. Qi and R. Womersley}, 28843 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/94-08.ps}, 28844 key = {41} 28845} 28846 28847@Article{ ferris.ruszczynski:robust, 28848 author = {M. C. Ferris and A. Ruszczy{\'{n}}ski}, 28849 title = {Robust Path Choice and Vehicle Guidance in Networks with Failures}, 28850 year = {2000}, 28851 journal = {Networks}, 28852 volume = {35}, 28853 pages = {181--194}, 28854 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/97-04.ps}, 28855 key = {60} 28856} 28857 28858@InCollection{ ferris.rutherford:accessing, 28859 author = {M. C. Ferris and T. F. Rutherford}, 28860 title = {Accessing Realistic Complementarity Problems within {Matlab}}, 28861 booktitle = {Nonlinear Optimization and Applications}, 28862 key = {48}, 28863 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/95-10.ps}, 28864 editor = {G. Di Pillo and F. Giannessi}, 28865 year = {1996}, 28866 pages = {141--153}, 28867 publisher = {Plenum Press}, 28868 address = {New York} 28869} 28870 28871@InCollection{ ferris.shepard:optimizing, 28872 author = {M. C. Ferris and D. M. Shepard}, 28873 title = {Optimization of Gamma Knife Radiosurgery}, 28874 booktitle = {Discrete Mathematical Problems with Medical Applications, forthcoming}, 28875 editor = {D.-Z. Du and P. Pardolas and J. Wang}, 28876 publisher = {AMS}, 28877 year = {2000}, 28878 optseries = {DIMACS}, 28879 url = {ftp://ftp.cs.wisc.edu/pub/dmi/tech-reports/00-01.ps}, 28880 key = {91}, 28881 type = {Data Mining Institute Technical Report}, 28882 institution = {Computer Sciences Department, University of Wisconsin}, 28883 address = {Madison, Wisconsin}, 28884 number = {00-01} 28885} 28886 28887@InCollection{ ferris.sinapiromsaran:formulating, 28888 author = {M. C. Ferris and K. Sinapiromsaran}, 28889 title = {Formulating and Solving Nonlinear Programs as Mixed Complementarity Problems}, 28890 booktitle = {Optimization}, 28891 key = {77}, 28892 publisher = {Springer-Verlag}, 28893 year = {2000}, 28894 editor = {V.H. Nguyen and J. J. Strodiot and P. Tossings}, 28895 volume = {481}, 28896 series = {Lecture Notes in Economics and Mathematical Systems}, 28897 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-21.ps}, 28898 type = {Mathematical Programming Technical Report}, 28899 institution = {Computer Sciences Department, University of Wisconsin}, 28900 address = {Madison, Wisconsin}, 28901 number = {98-21} 28902} 28903 28904@Article{ ferris.tin-loi:limit, 28905 author = {M. C. Ferris and F. Tin-Loi}, 28906 title = {Limit Analysis of Frictional Block Assemblies as a Mathematical Program with 28907 Complementarity Constraints}, 28908 year = {2001}, 28909 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/99-01.ps}, 28910 key = {78}, 28911 journal = {International Journal of Mechanical Sciences}, 28912 pages = {209--224}, 28913 volume = {43}, 28914 type = {Mathematical Programming Technical Report}, 28915 institution = {Computer Sciences Department, University of Wisconsin}, 28916 address = {Madison, Wisconsin}, 28917 number = {99-01} 28918} 28919 28920@Article{ ferris.tin-loi:nonlinear, 28921 author = {M. C. Ferris and F. Tin-Loi}, 28922 title = {Nonlinear Programming Approach for a Class of Inverse Problems in 28923 Elastoplasticity}, 28924 year = {1998}, 28925 key = {64}, 28926 volume = {6}, 28927 pages = {857--870}, 28928 journal = {Structural Engineering and Mechanics} 28929} 28930 28931@Article{ ferris.tin-loi:solution, 28932 author = {M. C. Ferris and F. Tin-Loi}, 28933 title = {On the Solution of a Minimum Weight Elastoplastic Problem involving Displacement 28934 and Complementarity Constraints}, 28935 year = {1999}, 28936 journal = {Computer Methods in Applied Mechanics and Engineering}, 28937 volume = {174}, 28938 pages = {107--120}, 28939 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/minwt.ps}, 28940 key = {66} 28941} 28942 28943@Article{ ferris.vlach:scheduling, 28944 author = {M. C. Ferris and M. Vlach}, 28945 title = {Scheduling with Earliness and Tardiness Penalties}, 28946 journal = {Naval Research Logistics Quarterly}, 28947 year = {1992}, 28948 volume = {39}, 28949 pages = {229--245}, 28950 key = {13} 28951} 28952 28953@TechReport{ ferris.zavriev:linear, 28954 author = {M. C. Ferris and S. K Zavriev}, 28955 title = {The Linear Convergence of a Successive Linear Programming Algorithm}, 28956 institution = {Computer Sciences Department, University of Wisconsin}, 28957 year = {1996}, 28958 key = {56}, 28959 address = {Madison, Wisconsin}, 28960 type = {Mathematical Programming Technical Report}, 28961 number = {96--12}, 28962 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/96-12.ps} 28963} 28964 28965@Article{ ferris:finite, 28966 author = {M. C. Ferris}, 28967 title = {Finite Termination of the Proximal Point Algorithm}, 28968 journal = {Mathematical Programming}, 28969 year = {1991}, 28970 volume = {50}, 28971 pages = {359--366}, 28972 key = {06} 28973} 28974 28975@Article{ ferris:iterative, 28976 author = {M. C. Ferris}, 28977 title = {Iterative Linear Programming Solution of Convex Programs}, 28978 journal = {Journal of Optimization Theory and Applications}, 28979 year = {1990}, 28980 volume = {65}, 28981 pages = {53--65}, 28982 key = {07} 28983} 28984 28985@Article{ ferris:linear, 28986 author = {M. C. Ferris}, 28987 title = {The Linear Complementarity Problem}, 28988 journal = {Bulletin of the American Mathematical Society}, 28989 year = {1993}, 28990 volume = {28}, 28991 pages = {169--175}, 28992 key = {27} 28993} 28994 28995@MastersThesis{ ferris:linear*1, 28996 author = {M. C. Ferris}, 28997 title = {Linear Programming and Minimum Weight Design -- {A} Comparison of Methods for 28998 Solving a Class of Structural Optimization Problems}, 28999 year = {1985}, 29000 school = {University of Cambridge}, 29001 address = {England}, 29002 key = {01} 29003} 29004 29005@TechReport{ ferris:matlab, 29006 author = {M. C. Ferris}, 29007 title = {{MATLAB} and {GAMS}: Interfacing Optimization and Visualization Software}, 29008 institution = {Computer Sciences Department, University of Wisconsin}, 29009 year = {1998}, 29010 address = {Madison, Wisconsin}, 29011 type = {Mathematical Programming Technical Report}, 29012 url = {ftp://ftp.cs.wisc.edu/math-prog/tech-reports/98-19.ps}, 29013 number = {98-19}, 29014 key = {75} 29015} 29016 29017@Article{ ferris:parallel, 29018 author = {M. C. Ferris}, 29019 title = {Parallel Constraint Distribution for Convex Quadratic Programs}, 29020 journal = {Mathematics of Operations Research}, 29021 year = {1994}, 29022 volume = {19}, 29023 pages = {645--658}, 29024 url = {ftp://ftp.cs.wisc.edu/tech-reports/reports/1991/tr1009a.ps}, 29025 key = {20} 29026} 29027 29028@TechReport{ ferris:parallel*1, 29029 author = {M. C. Ferris}, 29030 title = {Parallel Solution of Extremely Large Knapsack Problems}, 29031 institution = {Computer Sciences Department, University of Wisconsin}, 29032 year = {1989}, 29033 address = {Madison, Wisconsin}, 29034 number = {842}, 29035 key = {09} 29036} 29037 29038@PhDThesis{ ferris:weak, 29039 author = {M. C. Ferris}, 29040 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29041 year = {1988}, 29042 school = {University of Cambridge}, 29043 address = {England}, 29044 key = {02} 29045} 29046 29047@TechReport{ ferris:weak*1, 29048 author = {M. C. Ferris}, 29049 title = {Weak Sharp Minima and Penalty Functions in Mathematical Programming}, 29050 institution = {Computer Sciences Department, University of Wisconsin}, 29051 year = {1988}, 29052 address = {Madison, Wisconsin}, 29053 number = {779}, 29054 key = {05} 29055} 29056 29057@Book{ fiacco.mccormick:nonlinear, 29058 author = {A. V. Fiacco and G. P. McCormick}, 29059 title = {Nonlinear Programming: Sequential Unconstrained Minimization Techniques}, 29060 year = {1968}, 29061 publisher = {John Wiley \& Sons}, 29062 address = {New York}, 29063 note = {SIAM Classics in Applied Mathematics 4, SIAM, Philadelphia, 1990} 29064} 29065 29066@Book{ fiacco:introduction, 29067 author = {A. V. Fiacco}, 29068 title = {Introduction to Sensitivity and Stability Analysis in Nonlinear Programming}, 29069 year = {1983}, 29070 publisher = {Academic Press}, 29071 address = {New York} 29072} 29073 29074@Article{ fiedler.ptak:matrices, 29075 author = {M. Fiedler and V. Pt\'{a}k}, 29076 title = {On matrices with nonpositive off-diagonal elements and positive principal 29077 minors}, 29078 journal = {Czechoslovak Mathematics Journal}, 29079 volume = {12}, 29080 pages = {382--400}, 29081 year = {1962} 29082} 29083 29084@Article{ fischer.kanzow:finite, 29085 author = {A. Fischer and C. Kanzow}, 29086 title = {On Finite Termination of an Iterative Method for Linear Complementarity 29087 Problems}, 29088 journal = {Mathematical Programming}, 29089 volume = {74}, 29090 pages = {279--292}, 29091 year = {1996} 29092} 29093 29094@TechReport{ fischer:constrained, 29095 author = {A. Fischer}, 29096 title = {A New Constrained Optimization Reformulation for Complementarity Problems}, 29097 institution = {Institute of Numerical Mathematics, Technical University of Dresden}, 29098 year = {1995}, 29099 type = {Technical Report}, 29100 number = {MATH-NM-10-1995}, 29101 address = {Dresden} 29102} 29103 29104@Article{ fischer:local, 29105 author = {A. Fischer}, 29106 title = {On the local superlinear convergence of a {N}ewton-type method for {LCP} under 29107 weak conditions}, 29108 journal = {Optimization Methods and Software}, 29109 year = {1995}, 29110 volume = {6}, 29111 pages = {83--107} 29112} 29113 29114@InCollection{ fischer:ncp-function, 29115 author = {A. Fischer}, 29116 title = {An {NCP}--Function and its Use for the Solution of Complementarity Problems}, 29117 booktitle = {Recent Advances in Nonsmooth Optimization}, 29118 publisher = {World Scientific Publishers}, 29119 editor = {D. Z. Du and L. Qi and R. S. Womersley}, 29120 year = {1995}, 29121 pages = {88--105} 29122} 29123 29124@Article{ fischer:newton-type, 29125 author = {A. Fischer}, 29126 title = {A {N}ewton-Type Method for Positive Semidefinite Linear Complementarity 29127 Problems}, 29128 journal = {Journal of Optimization Theory and Applications}, 29129 year = {1995}, 29130 volume = {86}, 29131 pages = {585--608} 29132} 29133 29134@Article{ fischer:solution, 29135 author = {A. Fischer}, 29136 title = {Solution of Monotone Complementarity Problems with Locally {L}ipschitzian 29137 Functions}, 29138 year = {1997}, 29139 journal = {Mathematical Programming}, 29140 pages = {513--532} 29141} 29142 29143@Article{ fischer:special, 29144 author = {A. Fischer}, 29145 title = {A Special {N}ewton--Type Optimization Method}, 29146 journal = {Optimization}, 29147 year = {1992}, 29148 volume = {24}, 29149 pages = {269--284} 29150} 29151 29152@Article{ fisher:use, 29153 author = {R. A. Fisher}, 29154 title = {The Use of Multiple Measurements in Taxonomic Problems}, 29155 journal = {Annual Eugenics}, 29156 year = {1936}, 29157 volume = {7}, 29158 number = {Part II}, 29159 pages = {179--188} 29160} 29161 29162@Book{ fishman:principles, 29163 author = {G. Fishman}, 29164 title = {Principles of Discrete Event Simulation}, 29165 publisher = {Wiley}, 29166 address = {New York, NY}, 29167 year = {1978} 29168} 29169 29170@Article{ fitchard.aldridge.ea:registration, 29171 author = {E. E. Fitchard and J. S. Aldridge and P. J. Reckwerdt and T. R. Mackie}, 29172 title = {Registration of Synthetic Tomographic Projection Data Sets Using 29173 Cross-Correlation}, 29174 journal = {Physics in Medicine and Biology}, 29175 year = {1998}, 29176 volume = {43}, 29177 pages = {1645--1657} 29178} 29179 29180@Article{ fletcher.matthews:stable, 29181 author = {R. Fletcher and S. P. J. Matthews}, 29182 title = {Stable Modifications of Explicit {LU} Factors for Simplex Updates}, 29183 journal = {Mathematical Programming}, 29184 year = {1984}, 29185 volume = {30}, 29186 pages = {267--284} 29187} 29188 29189@TechReport{ fletcher.maza:nonlinear, 29190 author = {R. Fletcher and E. Sainz de la Maza}, 29191 title = {Nonlinear Programming and Nonsmooth Optimization by Successive Linear 29192 Programming}, 29193 institution = {Department of Mathematical Sciences}, 29194 year = {1987}, 29195 address = {The University, Dundee, Scotland}, 29196 number = {NA/100}, 29197 type = {Numerical Analysis Report} 29198} 29199 29200@InCollection{ fletcher:class, 29201 author = {R. Fletcher}, 29202 title = {A Class of Methods for Nonlinear Programming with Termination and Convergence 29203 Properties}, 29204 booktitle = {Integer and Nonlinear Programming}, 29205 year = {1970}, 29206 editor = {J. Abadie}, 29207 publisher = {North--Holland}, 29208 address = {Amsterdam}, 29209 pages = {157--173} 29210} 29211 29212@Article{ fletcher:exact, 29213 author = {R. Fletcher}, 29214 title = {An Exact Penalty Function for Nonlinear Programming with Inequalities}, 29215 journal = {Mathematical Programming}, 29216 year = {1973}, 29217 volume = {5}, 29218 pages = {129--150} 29219} 29220 29221@Article{ fletcher:generalized, 29222 author = {R. Fletcher}, 29223 title = {Generalized Inverse Methods for the Best Least Squares Solution of Non--Linear 29224 Equations}, 29225 journal = {The Computer Journal}, 29226 year = {1968}, 29227 volume = {10}, 29228 pages = {392--399} 29229} 29230 29231@InProceedings{ fletcher:penalty, 29232 crossref = {bachem.grotschel.ea:mathematical}, 29233 author = {R. Fletcher}, 29234 title = {Penalty Functions}, 29235 pages = {87--114} 29236} 29237 29238@Book{ fletcher:practical, 29239 author = {R. 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Gill}, 29348 title = {Primal-Dual Interior Methods for Nonconvex Nonlinear Programming}, 29349 institution = {Department of Mathematics, University of California}, 29350 year = {1996}, 29351 type = {Report NA}, 29352 number = {96-3}, 29353 address = {San Diego} 29354} 29355 29356@InCollection{ fortin.glowinski:decomposition-coordination, 29357 author = {M. Fortin and R. Glowinski}, 29358 title = {On Decomposition-Coordination Methods Using an Augmented Lagrangian}, 29359 booktitle = {Augmented Lagrangian methods: Applications to the Solution of Boundary Value 29360 Problems}, 29361 publisher = {North-Holland}, 29362 year = {1983}, 29363 editor = {M. Fortin and R. Glowinski}, 29364 address = {Amsterdam} 29365} 29366 29367@Misc{ foster.kesselman:globus, 29368 author = {I. Foster and C. Kesselman}, 29369 title = {The Globus Project}, 29370 howpublished = {www.globus.org} 29371} 29372 29373@Article{ foster.kesselman:globus*1, 29374 author = {I. Foster and C. 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Gabriel}, 29630 title = {Algorithms for the Nonlinear Complementarity Problem: The {NE}/{SQP} Method and 29631 Extensions}, 29632 school = {The Johns Hopkins University}, 29633 year = {1992}, 29634 address = {Baltimore, Maryland} 29635} 29636 29637@Article{ gafni.bertsekas:two-metric, 29638 author = {E. M. Gafni and D. P. Bertsekas}, 29639 title = {Two-Metric Projection Methods for Constrained Optimization}, 29640 journal = {SIAM Journal on Control and Optimization}, 29641 year = {1984}, 29642 volume = {22}, 29643 pages = {936--964} 29644} 29645 29646@InProceedings{ gaivoronski:convergence, 29647 author = {A. A. Gaivoronski}, 29648 title = {Convergence of Parallel Backpropagation for Neural Networks}, 29649 booktitle = {SIAM Journal on Optimization}, 29650 year = {1994}, 29651 note = {Proceedings of Symposium on Parallel Optimization 3, Madison July 7-9, 1993, 29652 submitted} 29653} 29654 29655@Misc{ gaivoronski:private, 29656 author = {A. A. 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Gao}, 29700 title = {Nonlinear Complementarity Problems in Large Deformed Beam Subject to Unilateral 29701 Conditions}, 29702 type = {Manuscript}, 29703 institution = {Department of Mathematics, Virginia Polytechnic Institute and State University}, 29704 month = oct, 29705 year = {1994} 29706} 29707 29708@Article{ garcia-palomares.mangasarian:superlinearly, 29709 author = {U. M. {Garcia--Palomares} and O. L. Mangasarian}, 29710 title = {Superlinearly Convergent {Q}uasi--{N}ewton Algorithms for Nonlinearly Constrained 29711 Optimization Problems}, 29712 journal = {Mathematical Programming}, 29713 year = {1976}, 29714 volume = {11}, 29715 pages = {1--13} 29716} 29717 29718@Article{ garcia-palomares.restuccia:global, 29719 author = {U. M. {Garcia--Palomares} and A. 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Zangwill}, 29745 title = {Pathways to Solutions, Fixed Points, and Equilibria}, 29746 year = {1981}, 29747 publisher = {Prentice-Hall, Inc}, 29748 address = {Englewood Cliffs, New Jersey} 29749} 29750 29751@Book{ garey.johnson:computers, 29752 author = {M. R. Garey and D. S. Johnson}, 29753 title = {Computers and Intractability, {A} Guide to the Theory of {NP}--Completeness}, 29754 year = {1979}, 29755 publisher = {W.H. Freeman and Company}, 29756 address = {San Francisco} 29757} 29758 29759@Article{ garey.tarjan.ea:one-processor, 29760 author = {M. R. Garey and R. E. Tarjan and G. T. Wilfong}, 29761 title = {One--Processor Scheduling with Symmetric Earliness and Tardiness Penalties}, 29762 journal = {Mathematics of Operations Research}, 29763 year = {1988}, 29764 volume = {13}, 29765 pages = {330--348} 29766} 29767 29768@Book{ garfinkel.nemhauser:integer, 29769 author = {R. S. Garfinkel and G. L. Nemhauser}, 29770 title = {Integer Programming}, 29771 year = {1972}, 29772 publisher = {John Wiley \& Sons}, 29773 address = {New York} 29774} 29775 29776@Book{ gass:linear, 29777 author = {S. Gass}, 29778 title = {Linear Programming Methods and Applications}, 29779 edition = {Fifth}, 29780 publisher = {Boyd and Fraser Publishing Company}, 29781 address = {Danvers, Massachusetts}, 29782 year = {1985} 29783} 29784 29785@InProceedings{ gay:combining, 29786 author = {D. M. Gay}, 29787 title = {On Combining the Schemes of {R}eid and {S}aunders for Sparse {LP} Bases}, 29788 booktitle = {Sparse Matrix Proceedings 1978}, 29789 editor = {I. S. Duff and G. W. Stewart}, 29790 year = {1978}, 29791 organization = {SIAM}, 29792 address = {Philadelphia, Pennsylvania}, 29793 pages = {313--334} 29794} 29795 29796@Article{ gay:electronic, 29797 author = {D. M. Gay}, 29798 title = {Electronic Mail Distribution of Linear Programming Test Problems}, 29799 journal = {{COAL} Newsletter}, 29800 year = {1985}, 29801 volume = {13}, 29802 pages = {10--12} 29803} 29804 29805@TechReport{ gay:hooking, 29806 author = {D. M. Gay}, 29807 title = {Hooking Your Solver to {AMPL}}, 29808 year = {1997}, 29809 institution = {Bell Laboratories}, 29810 address = {Murray Hill, New Jersey}, 29811 note = {Revised 1994, 1997} 29812} 29813 29814@Article{ gay:variant, 29815 author = {D. Gay}, 29816 title = {A Variant of {K}armarkar's Linear Programming Algorithm for Problems in Standard 29817 Form}, 29818 journal = {Mathematical Programming}, 29819 year = {1987}, 29820 volume = {37}, 29821 pages = {81--90} 29822} 29823 29824@Article{ geiger.kanzow:resolution, 29825 author = {C. Geiger and C. Kanzow}, 29826 title = {On the Resolution of Monotone Complementarity Problems}, 29827 journal = {Computational Optimization and Applications}, 29828 volume = {5}, 29829 year = {1996}, 29830 pages = {155--173} 29831} 29832 29833@Book{ geist.beguelin.ea:pvm, 29834 author = {G. A. Geist and A. L. Beguelin and J. J. Dongarra and W. Jiang and R. Manchek and 29835 V. S. Sunderam}, 29836 title = {{PVM}: Parallel Virtual Machine}, 29837 publisher = {MIT Press}, 29838 address = {Cambridge, Massachusetts}, 29839 year = {1994} 29840} 29841 29842@Article{ gendron.crainic:parallel, 29843 author = {B. Gendron and T. G. Crainic}, 29844 title = {Parallel Branch-and-Bound Algorithms: Survey and Synthesis}, 29845 journal = {Operations Research}, 29846 year = {1994}, 29847 volume = {42}, 29848 pages = {1042--1060} 29849} 29850 29851@Article{ george:automatic, 29852 author = {A. George}, 29853 title = {An automatic one-way dissection algorithm for irregular finite-element problems}, 29854 journal = {SIAM Journal on Numerical Analysis}, 29855 vol = {17}, 29856 pages = {740--751}, 29857 year = {1980} 29858} 29859 29860@InProceedings{ georges-schleuter:asparagos, 29861 crossref = {schaeffer:third}, 29862 author = {M. Georges--Schleuter}, 29863 title = {Asparagos: An Asynchronous Parallel Genetic Algorithm}, 29864 pages = {416--421} 29865} 29866 29867@Article{ georgiou:comments, 29868 author = {G. M. Georgiou}, 29869 title = {Comments On Hidden Nodes in Neural Nets}, 29870 journal = {IEEE Transactions on Circuits and Systems}, 29871 year = {1991}, 29872 volume = {38}, 29873 pages = {1410} 29874} 29875 29876@TechReport{ gertz.linderoth.ea:object-oriented, 29877 author = {M. Gertz and J. Linderoth and S. Wright}, 29878 title = {Object-Oriented Software for Linear Complementarity and Quadratic Programming}, 29879 institution = {MCS Division, Argonne National Laboratory}, 29880 year = {in preparation} 29881} 29882 29883@Article{ ghellinck.vial:polynomial, 29884 author = {G. de Ghellinck and J.--Ph. Vial}, 29885 title = {A Polynomial {N}ewton Method for Linear Programming}, 29886 journal = {Algorithmica}, 29887 year = {1986}, 29888 volume = {1}, 29889 pages = {425--453} 29890} 29891 29892@InCollection{ gilbert.ng:predicting, 29893 author = {J. R. Gilbert and E. Ng}, 29894 title = {Predicting Structure in Nonsymmetric Sparse Matrix Factorizations}, 29895 year = {1993}, 29896 booktitle = {Graph Theory and Sparse Matrix Computation}, 29897 editor = {A. George and J. Gilbert and J. Liu}, 29898 publisher = {Springer-Verlag} 29899} 29900 29901@Article{ gilbert-lemarechal, 29902 author = {J. C. Gilbert and C. Lemarechal}, 29903 title = {Some Numerical Experiments with Variable-Storage Quasi-Newton Algorithms}, 29904 journal = {Mathematical Programming}, 29905 year = {1989}, 29906 volume = {45}, 29907 pages = {407--434} 29908} 29909 29910@Article{ gill.murray.ea:computing, 29911 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29912 title = {Computing Forward-Difference Intervals for Numerical Optimization}, 29913 journal = {SIAM Journal on Scientific and Statistical Computing}, 29914 year = {1983}, 29915 volume = {4}, 29916 pages = {310--321} 29917} 29918 29919@Article{ gill.murray.ea:maintaining, 29920 author = {P. E. Gill and W. Murray and M. A. Saunders and M. H. Wright}, 29921 title = {Maintaining {LU} Factors of a General Sparse Matrix}, 29922 year = {1987}, 29923 journal = {Linear Algebra and Its Applications}, 29924 volume = {88/89}, 29925 pages = {239--270} 29926} 29927 29928@Book{ gill.murray.ea:practical, 29929 author = {P. E. Gill and W. Murray and M. H. 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Luo}, 32958 title = {Convergence Analysis of Primal--Dual Interior--Point Algorithms for Convex 32959 Quadratic Programs}, 32960 institution = {Communications Research Laboratory, McMaster University}, 32961 year = {1992}, 32962 address = {Hamilton, Ontario} 32963} 32964 32965@Article{ lustig.marsten.ea:computational, 32966 author = {I. J. Lustig and R. E. Marsten and D. F. Shanno}, 32967 title = {Computational Experience with a Primal-Dual Interior Point Method for Linear 32968 Programming}, 32969 journal = {Linear Algebra and Its Applications}, 32970 year = {1991}, 32971 volume = {152}, 32972 pages = {191--222} 32973} 32974 32975@Article{ lustig.marsten.ea:implementing, 32976 author = {I. J. Lustig and R. E. Marsten and D. F. 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Maier}, 33146 title = {A quadratic programming approach for certain classes of nonlinear structural 33147 problems}, 33148 journal = {Meccanica}, 33149 volume = {3}, 33150 year = {1968}, 33151 pages = {121--130} 33152} 33153 33154@Book{ manber:introduction, 33155 author = {U. Manber}, 33156 title = {Introduction to Algorithms: {A} Creative Approach}, 33157 year = {1989}, 33158 publisher = {Addison-Wesley} 33159} 33160 33161@Article{ mangasarian.deleone:error, 33162 author = {O. L. Mangasarian and R. {De~Leone}}, 33163 title = {Error Bounds for Strongly Convex Programs and (Super)linearly Convergent 33164 Iterative Schemes for the Least 2--norm Solution of Linear Programs}, 33165 journal = {Applied Mathematics and Optimization}, 33166 year = {1988}, 33167 volume = {17}, 33168 pages = {1--14} 33169} 33170 33171@Article{ mangasarian.deleone:parallel, 33172 author = {O. L. Mangasarian and R. {De~Leone}}, 33173 title = {Parallel Successive Overrelaxation Methods for Symmetric Linear Complementarity 33174 Problems and Linear Programs}, 33175 journal = {Journal of Optimization Theory and Applications}, 33176 year = {1987}, 33177 volume = {54}, 33178 pages = {437--446} 33179} 33180 33181@Article{ mangasarian.fromovitz:fritz, 33182 author = {O. L. Mangasarian and S. Fromovitz}, 33183 title = {The {F}ritz {J}ohn necessary optimality conditions in the presence of equality 33184 and inequality constraints}, 33185 journal = {Journal of Mathematical Analysis and its Applications}, 33186 year = {1967}, 33187 volume = {17}, 33188 pages = {37--47} 33189} 33190 33191@Article{ mangasarian.mclinden:simple, 33192 author = {O. L. Mangasarian and L. McLinden}, 33193 title = {Simple Bounds for Solutions of Monotone Complementarity Problems and Convex 33194 Programs}, 33195 journal = {Mathematical Programming}, 33196 year = {1985}, 33197 volume = {32}, 33198 pages = {32--40} 33199} 33200 33201@Article{ mangasarian.meyer:nonlinear, 33202 author = {O. L. Mangasarian and R. R. Meyer}, 33203 title = {Nonlinear Perturbation of Linear Programs}, 33204 journal = {SIAM Journal on Control and Optimization}, 33205 year = {1979}, 33206 volume = {17}, 33207 pages = {745--752} 33208} 33209 33210@TechReport{ mangasarian.musicant:active, 33211 author = {O. L. Mangasarian and David R. Musicant}, 33212 title = {Active Set Support Vector Machine Classification}, 33213 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33214 year = {2000}, 33215 number = {00-04}, 33216 address = {Madison, Wisconsin} 33217} 33218 33219@TechReport{ mangasarian.musicant:lagrangian, 33220 author = {O. L. Mangasarian and D. R. Musicant}, 33221 title = {Lagrangian Support Vector Machines}, 33222 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33223 year = {2000}, 33224 number = {00-06}, 33225 address = {Madison, Wisconsin} 33226} 33227 33228@TechReport{ mangasarian.musicant:robust, 33229 author = {O. L. Mangasarian and David R. Musicant}, 33230 title = {Robust Linear and Support Vector Regression}, 33231 institution = {Data Mining Institute, Computer Sciences Department, University of Wisconsin}, 33232 year = {1999}, 33233 number = {99-09}, 33234 address = {Madison, Wisconsin} 33235} 33236 33237@Article{ mangasarian.musicant:successive, 33238 author = {O. L. Mangasarian and David R. Musicant}, 33239 title = {Successive Overrelaxation for Support Vector Machines}, 33240 journal = {IEEE Transactions on Neural Networks}, 33241 volume = {10}, 33242 year = {1999}, 33243 pages = {1032-1037} 33244} 33245 33246@Article{ mangasarian.pang:exact, 33247 author = {O. L. Mangasarian and J. S. Pang}, 33248 title = {Exact Penalty Functions for Mathematical Programs with Linear Complementarity 33249 Constraints}, 33250 journal = {Optimization}, 33251 year = {1997}, 33252 volume = {42}, 33253 pages = {1--8} 33254} 33255 33256@Article{ mangasarian.pang:extended, 33257 author = {O. L. Mangasarian and J. S. Pang}, 33258 title = {The Extended Linear Complementarity Problem}, 33259 journal = {SIAM Journal on Matrix Analysis and Applications}, 33260 year = {1994}, 33261 volume = {16} 33262} 33263 33264@Article{ mangasarian.ren:error, 33265 author = {O. L. Mangasarian and J. Ren}, 33266 title = {New error bounds for the nonlinear complementarity problem}, 33267 year = {1994}, 33268 volume = {1}, 33269 pages = {49--56}, 33270 journal = {Communications on Applied Nonlinear Analysis} 33271} 33272 33273@Article{ mangasarian.ren:improved, 33274 author = {O. L. Mangasarian and J. Ren}, 33275 title = {New Improved Error Bounds for the Linear Complementarity Problem}, 33276 year = {1994}, 33277 volume = {66}, 33278 journal = {Mathematical Programming}, 33279 pages = {241--255} 33280} 33281 33282@InProceedings{ mangasarian.setiono.ea:pattern, 33283 crossref = {coleman.li:large-scale}, 33284 author = {O. L. Mangasarian and R. Setiono and W. H. Wolberg}, 33285 title = {Pattern Recognition via Linear Programming: Theory and Application to Medical 33286 Diagnosis}, 33287 pages = {22--31} 33288} 33289 33290@Article{ mangasarian.shiau:error, 33291 author = {O. L. Mangasarian and T.--H. Shiau}, 33292 title = {Error Bounds for Monotone Linear Complementarity Problems}, 33293 journal = {Mathematical Programming}, 33294 year = {1986}, 33295 volume = {36}, 33296 pages = {81--89} 33297} 33298 33299@Article{ mangasarian.shiau:lipschitz, 33300 author = {O. L. Mangasarian and T.--H. Shiau}, 33301 title = {{L}ipschitz Continuity of Solutions of Linear Inequalities, Programs and 33302 Complementarity Problems}, 33303 journal = {SIAM Journal on Control and Optimization}, 33304 year = {1987}, 33305 volume = {25}, 33306 pages = {583--595} 33307} 33308 33309@Article{ mangasarian.solodov:nonlinear, 33310 author = {O. L. Mangasarian and M. V. Solodov}, 33311 title = {Nonlinear Complementarity as Unconstrained and Constrained Minimization}, 33312 journal = {Mathematical Programming}, 33313 year = {1993}, 33314 volume = {62}, 33315 pages = {277--298} 33316} 33317 33318@Article{ mangasarian.solodov:serial, 33319 author = {O. L. Mangasarian and M. V. Solodov}, 33320 title = {Serial and Parallel Backpropagation Convergence via Nonmonotone Perturbed 33321 Minimization}, 33322 year = {1994}, 33323 journal = {Optimization Methods and Software}, 33324 volume = {4}, 33325 pages = {103--116} 33326} 33327 33328@Article{ mangasarian.street.ea:breast, 33329 author = {O. L. Mangasarian and W. N. Street and W. H. Wolberg}, 33330 title = {Breast Cancer Diagnosis and Prognosis via Linear Programming}, 33331 journal = {Operations Research}, 33332 year = {1995}, 33333 volume = {43}, 33334 pages = {570--577} 33335} 33336 33337@Article{ mangasarian.wolberg:cancer, 33338 author = {O. L. Mangasarian and W. H. Wolberg}, 33339 title = {Cancer Diagnosis via Linear Programming}, 33340 journal = {SIAM News}, 33341 year = {1990}, 33342 volume = {23}, 33343 pages = {1 \& 18} 33344} 33345 33346@InCollection{ mangasarian:applications, 33347 author = {O. L. Mangasarian}, 33348 title = {Some Applications of Penalty Functions in Mathematical Programming}, 33349 booktitle = {Optimization and Related Fields}, 33350 year = {1986}, 33351 editor = {R. Conti and E. De~Giorgi and F. Giannessi}, 33352 publisher = {Springer-Verlag}, 33353 address = {Heidelberg}, 33354 pages = {307--329}, 33355 note = {Lecture Notes in Mathematics 1190} 33356} 33357 33358@Article{ mangasarian:characterization, 33359 author = {O. L. Mangasarian}, 33360 title = {Characterization of linear complementarity problems as linear programs}, 33361 journal = {Mathematical Programming Study}, 33362 year = {1978}, 33363 volume = {7}, 33364 pages = {74--87} 33365} 33366 33367@InProceedings{ mangasarian:condition, 33368 author = {O. L. Mangasarian}, 33369 title = {A condition number for linear inequalities and linear programs}, 33370 booktitle = {Proceedings of 6. Symposium uber Operations Research, Augsburg, 7-9 September 33371 1981}, 33372 year = {1981}, 33373 editor = {G. Bamberg and O. Opitz}, 33374 publisher = {Verlagsgruppe Athenaum/Hain/Scriptor/Hanstein}, 33375 address = {Konigstein}, 33376 pages = {3--15} 33377} 33378 33379@Article{ mangasarian:convergence, 33380 author = {O. L. Mangasarian}, 33381 title = {On the Convergence of Iterates of an Inexact Matrix Splitting Algorithm for the 33382 Symmetric Monotone Linear Complementarity Problem}, 33383 journal = {SIAM Journal on Optimization}, 33384 volume = {1}, 33385 pages = {114--122}, 33386 year = {1991} 33387} 33388 33389@Article{ mangasarian:equivalence, 33390 author = {O. L. Mangasarian}, 33391 title = {Equivalence of the Complementarity Problem to a System of Nonlinear Equations}, 33392 journal = {SIAM Journal on Applied Mathematics}, 33393 year = {1976}, 33394 volume = {31}, 33395 pages = {89--92} 33396} 33397 33398@Article{ mangasarian:error, 33399 author = {O. L. Mangasarian}, 33400 title = {Error Bounds for Inconsistent Linear Inequalities and Programs}, 33401 journal = {ORSA Journal on Computing}, 33402 volume = {15}, 33403 pages = {187--192}, 33404 year = {1994} 33405} 33406 33407@Article{ mangasarian:error*1, 33408 author = {O. L. Mangasarian}, 33409 title = {Error Bounds for Nondegenerate Monotone Linear Complementarity Problems}, 33410 journal = {Mathematical Programming}, 33411 year = {1990}, 33412 volume = {48}, 33413 pages = {437--445} 33414} 33415 33416@Article{ mangasarian:generalized, 33417 author = {O. L. Mangasarian}, 33418 title = {Generalized Linear Complementarity Problems as Linear Programs}, 33419 journal = {Methods of Operations Research}, 33420 year = {1979}, 33421 editor = {W. Oettli and F. Steffens}, 33422 volume = {31}, 33423 pages = {393--402} 33424} 33425 33426@InCollection{ mangasarian:generalized*1, 33427 author = {O. L. Mangasarian}, 33428 title = {Generalized Support Vector Machines}, 33429 year = {2000}, 33430 pages = {135-146}, 33431 booktitle = {Advances in Large Margin Classifiers}, 33432 editor = {A. Smola and P.~Bartlett and B.~Sch{\"o}lkopf and D.~Schuurmans}, 33433 publisher = {MIT Press}, 33434 address = {Cambridge, MA} 33435} 33436 33437@Article{ mangasarian:global, 33438 author = {O. L. Mangasarian}, 33439 title = {Global error bounds for monotone affine variational inequality problems}, 33440 journal = {Linear Algebra and Its Applications}, 33441 year = {1992}, 33442 pages = {153--164} 33443} 33444 33445@InCollection{ mangasarian:least, 33446 author = {O. L. Mangasarian}, 33447 title = {Least Norm Solution of Non--Monotone Complementarity Problems}, 33448 booktitle = {Functional Analysis, Optimization and Mathematical Economics}, 33449 year = {1990}, 33450 publisher = {Oxford University Press}, 33451 address = {New York}, 33452 pages = {217--221} 33453} 33454 33455@Article{ mangasarian:least-norm, 33456 author = {O. L. Mangasarian}, 33457 title = {Least--Norm Linear Programming Solution as an Unconstrained Minimization 33458 Problem}, 33459 journal = {Journal of Mathematical Analysis and Applications}, 33460 year = {1983}, 33461 volume = {92}, 33462 pages = {240--251} 33463} 33464 33465@Article{ mangasarian:linear, 33466 author = {O. L. Mangasarian}, 33467 title = {Linear Complementarity Problems Solvable by a Single Linear Program}, 33468 journal = {Mathematical Programming}, 33469 year = {1976}, 33470 volume = {10}, 33471 pages = {263--270} 33472} 33473 33474@Article{ mangasarian:linear*1, 33475 author = {O. L. Mangasarian}, 33476 title = {Linear and Nonlinear Separation of Patterns by Linear Programming}, 33477 journal = {Operations Research}, 33478 year = {1965}, 33479 volume = {13}, 33480 pages = {444--452} 33481} 33482 33483@Article{ mangasarian:locally, 33484 author = {O. L. Mangasarian}, 33485 title = {Locally Unique Solutions of Quadratic Programs, Linear and Nonlinear 33486 Complementarity Problems}, 33487 journal = {Mathematical Programming}, 33488 year = {1980}, 33489 volume = {19}, 33490 pages = {200--212} 33491} 33492 33493@InCollection{ mangasarian:machine, 33494 author = {O. L. Mangasarian}, 33495 title = {Machine Learning via Polyhedral Concave Minimization}, 33496 editor = {H. Fischer and B. Riedmueller and S. Schaeffler}, 33497 booktitle = {Applied Mathematics and Parallel Computing - Festschrift for Klaus Ritter}, 33498 pages = {175-188}, 33499 year = {1996}, 33500 address = {Heidelberg}, 33501 publisher = {Physica-Verlag A Springer-Verlag Company} 33502} 33503 33504@Article{ mangasarian:mathematical, 33505 author = {O. L. Mangasarian}, 33506 title = {Mathematical Programming in Neural Networks}, 33507 journal = {ORSA Journal on Computing}, 33508 volume = {5}, 33509 pages = {349--360}, 33510 year = {1993} 33511} 33512 33513@InProceedings{ mangasarian:mathematical*1, 33514 author = {O. L. Mangasarian}, 33515 title = {Mathematical Programming in Machine Learning}, 33516 booktitle = {Nonlinear Optimization and Applications}, 33517 editor = {G. Di Pillo and F. Giannessi}, 33518 publisher = {Plenum Publishing}, 33519 address = {New York}, 33520 pages = {283--295}, 33521 year = {1996} 33522} 33523 33524@Article{ mangasarian:mathematical*2, 33525 author = {O. L. Mangasarian}, 33526 title = {Mathematical Programming in Data Mining}, 33527 journal = {Data Mining and Knowledge Discovery}, 33528 volume = {1}, 33529 year = {1997}, 33530 pages = {183-201} 33531} 33532 33533@Article{ mangasarian:multi-surface, 33534 author = {O. L. Mangasarian}, 33535 title = {Multi-surface Method of Pattern Separation}, 33536 journal = {IEEE Transactions on Information Theory}, 33537 year = {1968}, 33538 volume = {IT-14}, 33539 pages = {801--807} 33540} 33541 33542@Book{ mangasarian:nonlinear, 33543 author = {O. L. Mangasarian}, 33544 title = {Nonlinear Programming}, 33545 year = {1969}, 33546 publisher = {McGraw--Hill}, 33547 address = {New York}, 33548 note = {SIAM Classics in Applied Mathematics 10, SIAM, Philadelphia, 1994} 33549} 33550 33551@Article{ mangasarian:normal, 33552 author = {O. L. Mangasarian}, 33553 title = {Normal Solutions of Linear Programs}, 33554 journal = {Mathematical Programming Study}, 33555 year = {1984}, 33556 volume = {22}, 33557 pages = {206--216} 33558} 33559 33560@Article{ mangasarian:optimal, 33561 author = {O. L. Mangasarian}, 33562 title = {Optimal Simplex Tableau Characterization of Unique and Bounded Solutions of 33563 Linear Programs}, 33564 journal = {Journal of Optimization Theory and Applications}, 33565 year = {1981}, 33566 volume = {35}, 33567 pages = {123--128} 33568} 33569 33570@Article{ mangasarian:parallel, 33571 author = {O. L. Mangasarian}, 33572 title = {Parallel Gradient Distribution in Unconstrained Optimization}, 33573 journal = {SIAM Journal on Control and Optimization}, 33574 volume = {33}, 33575 pages = {1916--1925}, 33576 year = {1995} 33577} 33578 33579@TechReport{ mangasarian:regularized, 33580 author = {O. L. 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Petri}, 35353 title = {Modelling {J}apanese--{A}merican Trade, {A} Study of Asymmetric Interdependence}, 35354 publisher = {Harvard University Press}, 35355 year = {1984} 35356} 35357 35358@InProceedings{ petrzykowski:application, 35359 author = {T. Petrzykowski}, 35360 title = {Application of the Steepest Ascent Method to Concave Programming}, 35361 booktitle = {Proceedings of the {IFIPS} Congress, Munich, 1962}, 35362 year = {1962}, 35363 publisher = {North--Holland}, 35364 address = {Amsterdam}, 35365 pages = {185--189} 35366} 35367 35368@InProceedings{ pettey.leuze.ea:parallel, 35369 crossref = {grefenstette:genetic}, 35370 author = {C. C. Pettey and M. R. Leuze and J. J. Grefenstette}, 35371 title = {A Parallel Genetic Algorithm}, 35372 pages = {155--161} 35373} 35374 35375@InProceedings{ pettey.leuze:theoretical, 35376 crossref = {schaeffer:third}, 35377 author = {C. C. Pettey and M. R. Leuze}, 35378 title = {A Theoretical Investigation of a Parallel Genetic Algorithm}, 35379 pages = {398--405} 35380} 35381 35382@Book{ pfeiffer.glocker:multibody, 35383 author = {F. Pfeiffer and C. Glocker}, 35384 title = {Multibody Dynamics with Unilateral Contact}, 35385 year = {1996}, 35386 publisher = {John Wiley \& Sons} 35387} 35388 35389@TechReport{ pierro.iusem:convergence, 35390 author = {A. R. de Pierro and A. N. Iusem}, 35391 title = {Convergence Properties of Iterative Methods for Symmetric Positive Semidefinite 35392 Linear Complementarity Problems}, 35393 institution = {Instituto de Matematica, Elasticita e Ciencia da Computacao}, 35394 year = {1990}, 35395 address = {Universidade Estadual de Campinas, CP 6065, Campinas, 13081, SP, Brazil} 35396} 35397 35398@InCollection{ pillo.grippo.ea:class, 35399 author = {G. Di Pillo and L. Grippo and F. 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Grippo}, 35420 title = {A New Class of Augmented {L}agrangians in Nonlinear Programming}, 35421 journal = {SIAM Journal on Control and Optimization}, 35422 year = {1979}, 35423 volume = {17}, 35424 pages = {618--628} 35425} 35426 35427@Article{ pillo.grippo:continuously, 35428 author = {G. Di Pillo and L. Grippo}, 35429 title = {A Continuously Differentiable Exact Penalty Function for Nonlinear Programming 35430 Problems with Inequality Constraints}, 35431 journal = {SIAM Journal on Control and Optimization}, 35432 year = {1985}, 35433 volume = {23}, 35434 pages = {72--84} 35435} 35436 35437@Article{ pillo.grippo:exact, 35438 author = {G. Di Pillo and L. Grippo}, 35439 title = {An Exact Penalty Method with Global Convergence Properties for Nonlinear 35440 Programming Problems}, 35441 journal = {Mathematical Programming}, 35442 year = {1986}, 35443 volume = {36}, 35444 pages = {1--18} 35445} 35446 35447@InProceedings{ plambeck.fu.ea:throughput, 35448 author = {E. L. 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Polyak}, 35559 title = {Sharp Minima}, 35560 year = {1979}, 35561 note = {A Talk given at the {IIASA} Workshop on Generalized {L}agrangians and their 35562 Applications, {IIASA}, Laxenburg, Austria} 35563} 35564 35565@InProceedings{ polyak:smooth, 35566 author = {R. A. Polyak}, 35567 title = {Smooth Optimization Methods for Solving Nonlinear Extremal and Equilibrium 35568 Problems with Constraints}, 35569 booktitle = {Abstracts of the Papers of the 11th International Symposium on Mathematical 35570 Programming}, 35571 year = {1982}, 35572 address = {Bonn} 35573} 35574 35575@Article{ polychronopoulos.tsitsiklis:analysis, 35576 author = {G. H. Polychronopoulos and J. N. Tsitsiklis}, 35577 title = {Stochastic Shortest Path Problems with Recourse}, 35578 journal = {Networks}, 35579 year = {1996}, 35580 volume = {27}, 35581 pages = {133--143} 35582} 35583 35584@TechReport{ potra.bonnans:infeasible, 35585 author = {F. A. Potra and J. F. Bonnans}, 35586 title = {Infeasible path following algorithms for linear complementarity problems}, 35587 institution = {INRIA}, 35588 year = {1994}, 35589 month = dec, 35590 number = {RR--2445}, 35591 type = {Research Report} 35592} 35593 35594@Article{ potra.sheng:large-step, 35595 author = {F. A. Potra and R. Sheng}, 35596 title = {A Large--Step Infeasible--Interior--Point Method for the ${P}_*$--Matrix {LCP}}, 35597 year = {1997}, 35598 journal = {SIAM Journal on Optimization}, 35599 volume = {7}, 35600 pages = {318--335} 35601} 35602 35603@Article{ potra:infeasible, 35604 author = {F. A. Potra}, 35605 title = {An infeasible interior-point predictor-corrector algorithm for linear 35606 programming}, 35607 journal = {SIAM Journal on Optimization}, 35608 year = {1996}, 35609 volume = {6}, 35610 pages = {19--32} 35611} 35612 35613@TechReport{ potra:onl, 35614 author = {F. A. Potra}, 35615 title = {An ${O}(n{L})$ infeasible--interior--point algorithm for {LCP} with quadratic 35616 convergence.}, 35617 institution = {Department of Mathematics, The University of Iowa}, 35618 address = {Iowa City, Iowa}, 35619 year = {1994}, 35620 number = {50}, 35621 type = {Reports on Computational Mathematics} 35622} 35623 35624@TechReport{ potra:predictor-corrector, 35625 author = {F. A. Potra}, 35626 title = {On a predictor-corrector method for solving linear programs from infeasible 35627 starting points}, 35628 institution = {Department of Mathematics, University of Iowa}, 35629 address = {Iowa City, Iowa}, 35630 year = {1992}, 35631 number = {34}, 35632 type = {Reports on Computational Mathematics} 35633} 35634 35635@TechReport{ potra:quadratically, 35636 author = {F. A. Potra}, 35637 title = {A quadratically convergent infeasible interior-point algorithm for linear 35638 programming}, 35639 institution = {Department of Mathematics, University of Iowa}, 35640 year = {1992}, 35641 number = {28}, 35642 address = {Iowa City, Iowa}, 35643 month = jul 35644} 35645 35646@InCollection{ powell:convergence, 35647 author = {M. J. D. Powell}, 35648 title = {The Convergence of Variable Metric Methods for Nonlinearly Constrained 35649 Optimization Calculations}, 35650 crossref = {mangasarian.meyer.ea:nonlinear*3}, 35651 pages = {27--63} 35652} 35653 35654@InProceedings{ powell:direct, 35655 author = {M. J. D. 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Teukolsky and William T. 35728 Vetterling}, 35729 title = {Numerical Recipes : the Art of Scientific Computing}, 35730 publisher = {Cambridge University Press}, 35731 year = {1988} 35732} 35733 35734@Article{ pruyne.livny:interfacing, 35735 author = {J. Pruyne and M. Livny}, 35736 title = {Interfacing {C}ondor and {PVM} to Harness the Cycles of Workstation Clusters}, 35737 journal = {Journal on Future Generations of Computer Systems}, 35738 volume = {12}, 35739 year = {1996}, 35740 pages = {67--85} 35741} 35742 35743@InCollection{ pruyne.livny:parallel, 35744 author = {J. Pruyne and M. Livny}, 35745 title = {Parallel Processing on Dynamic Resources using {CARMI}}, 35746 booktitle = {Job Scheduling Strategies for Parallel Processing}, 35747 publisher = {Springer-Verlag}, 35748 year = {1995}, 35749 editor = {D. G. Feitelson and L. Rudolph}, 35750 volume = {949}, 35751 series = {Lecture Notes in Computer Science} 35752} 35753 35754@PhDThesis{ pruyne:resource, 35755 author = {J. C. Pruyne}, 35756 title = {Resource Management Services for Parallel Applications}, 35757 school = {University of Wisconsin--Madison}, 35758 year = {1996}, 35759 address = {Madison, Wisconsin} 35760} 35761 35762@Book{ pshenichny.danilin:numerical, 35763 author = {B. N. Pshenichny and Yu. M. Danilin}, 35764 title = {Numerical Methods in Extremal Problems}, 35765 year = {1978}, 35766 publisher = {MIR Publishers}, 35767 address = {Moscow} 35768} 35769 35770@TechReport{ qi.chen:globally, 35771 author = {L. Qi and X. Chen}, 35772 title = {A Globally Convergent Successive Approximation Method for Nonsmooth Equations}, 35773 institution = {School of Mathematics, University of New South Wales}, 35774 year = {1993}, 35775 annote = {revised}, 35776 address = {Sydney} 35777} 35778 35779@Article{ qi.jiang:semismooth, 35780 author = {L. Qi and H. Jiang}, 35781 title = {Semismooth {K}arush--{K}uhn--{T}ucker Equations and Convergence Analysis of 35782 {N}ewton Methods and Quasi--{N}ewton Methods for Solving these Equations}, 35783 journal = {Mathematics of Operations Research}, 35784 volume = {22}, 35785 pages = {301--325}, 35786 year = {1997} 35787} 35788 35789@TechReport{ qi.peng:unconstrained, 35790 author = {H. -D. Qi and J. -M. Peng}, 35791 title = {A New Unconstrained Optimization Approach for Nonlinear Complementarity 35792 Problems}, 35793 institution = {State Key Laboratory of Scientific and Engineering Computing, Academic Sinica}, 35794 year = {1996}, 35795 type = {Technical Report}, 35796 address = {Beijing} 35797} 35798 35799@InCollection{ qi.sun:survey, 35800 author = {L. Qi and D. Sun}, 35801 title = {A Survey of Some Nonsmooth Equations and Smoothing {N}ewton Methods}, 35802 year = {1999}, 35803 editor = {A. Eberhard and B. Glover and R. Hill and D. Ralph}, 35804 booktitle = {Progress in Optimization}, 35805 pages = {121--146}, 35806 series = {Applied Optimization}, 35807 volume = {30}, 35808 publisher = {Kluwer Academic Publishers}, 35809 address = {Dordrecht} 35810} 35811 35812@Article{ qi.sun:nonsmooth, 35813 author = {L. Qi and J. Sun}, 35814 title = {A Nonsmooth Version of {N}ewton's Method}, 35815 journal = {Mathematical Programming}, 35816 year = {1993}, 35817 volume = {58}, 35818 pages = {353--368} 35819} 35820 35821@Article{ qi:convergence, 35822 author = {L. Qi}, 35823 title = {Convergence Analysis of Some Algorithms for Solving Nonsmooth Equations}, 35824 journal = {Mathematics of Operations Research}, 35825 year = {1993}, 35826 volume = {18}, 35827 pages = {227--244} 35828} 35829 35830@TechReport{ qi:regular, 35831 author = {L. 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Rockafellar}, 36340 title = {Conjugate Duality and Optimization}, 36341 year = {1974}, 36342 publisher = {SIAM}, 36343 address = {Philadelphia, Pennsylvania}, 36344 volume = {16}, 36345 series = {Conference Board of the Mathematical Sciences} 36346} 36347 36348@Book{ rockafellar:convex, 36349 author = {R. T. Rockafellar}, 36350 title = {Convex Analysis}, 36351 year = {1970}, 36352 publisher = {Princeton University Press}, 36353 address = {Princeton, New Jersey} 36354} 36355 36356@Article{ rockafellar:first-, 36357 author = {R. T. Rockafellar}, 36358 title = {First-- and Second--Order Epi--Differentiabilty in Nonlinear Programming}, 36359 journal = {Transactions of the American Mathematical Society}, 36360 year = {1988}, 36361 volume = {307}, 36362 pages = {75--108} 36363} 36364 36365@InProceedings{ rockafellar:generalized, 36366 author = {R. T. Rockafellar}, 36367 title = {A Generalized Approach to Linear-Quadratic Programming}, 36368 booktitle = {Proceedings of the International Conference on Numerical Optimization and 36369 Applications}, 36370 year = {1986}, 36371 pages = {58--66}, 36372 note = {(Xi'an, China)} 36373} 36374 36375@InProceedings{ rockafellar:generalized*1, 36376 crossref = {bachem.grotschel.ea:mathematical}, 36377 author = {R. T. Rockafellar}, 36378 title = {Generalized Subgradients in Mathematical Programming}, 36379 pages = {368--390} 36380} 36381 36382@InCollection{ rockafellar:large-scale, 36383 author = {R. T. Rockafellar}, 36384 title = {Large-Scale Extended Linear-Quadratic Programming and Multistage Optimization}, 36385 booktitle = {Advances in Numerical Partial Differential Equations and Optimization}, 36386 chapter = {15}, 36387 year = {1991}, 36388 editor = {S. Gomez and J. P. Hennart and R. A. Tapia}, 36389 publisher = {SIAM Publications}, 36390 pages = {247--261} 36391} 36392 36393@Article{ rockafellar:linear-quadratic, 36394 author = {R. T. Rockafellar}, 36395 title = {Linear-Quadratic Programming and Optimal Control}, 36396 journal = {SIAM Journal on Control and Optimization}, 36397 year = {1987}, 36398 volume = {25}, 36399 pages = {781--814} 36400} 36401 36402@Article{ rockafellar:maximality, 36403 author = {R. T. Rockafellar}, 36404 title = {On the Maximality of Sums of Nonlinear Monotone Operators}, 36405 journal = {Transactions of the American Mathematical Society}, 36406 year = {1970}, 36407 volume = {149}, 36408 pages = {75--88} 36409} 36410 36411@InCollection{ rockafellar:monotone, 36412 author = {R. T. Rockafellar}, 36413 title = {Monotone Operators and Augmented {L}agrangian Methods in Nonlinear Programming}, 36414 crossref = {mangasarian.meyer.ea:nonlinear*3}, 36415 pages = {1--26} 36416} 36417 36418@Article{ rockafellar:monotone*1, 36419 author = {R. T. Rockafellar}, 36420 title = {Monotone Operators and the Proximal Point Algorithm}, 36421 journal = {SIAM Journal on Control and Optimization}, 36422 year = {1976}, 36423 volume = {14}, 36424 pages = {877--898} 36425} 36426 36427@Article{ rockafellar:multiplier, 36428 author = {R. T. Rockafellar}, 36429 title = {The Multiplier Method of {H}estenes and {P}owell Applied to Convex Programming}, 36430 journal = {Journal of Optimization Theory and Applications}, 36431 year = {1973}, 36432 volume = {12}, 36433 pages = {555--562} 36434} 36435 36436@Article{ rockafellar:multistage, 36437 author = {R. T. Rockafellar}, 36438 title = {Multistage Convex Programming and Discrete-Time Optimal Control}, 36439 journal = {Control and Cybernetics}, 36440 year = {1988}, 36441 volume = {17}, 36442 number = {2-3}, 36443 pages = {225--245} 36444} 36445 36446@Book{ rockafellar:network, 36447 author = {R. T. Rockafellar}, 36448 title = {Network Flows and Monotropic Optimization}, 36449 publisher = {John Wiley}, 36450 year = {1984}, 36451 address = {New York} 36452} 36453 36454@Article{ rodrigues:mixed, 36455 author = {H. C. Rodrigues}, 36456 title = {A mixed variational formulation for shape optimization of solids with contact 36457 conditions}, 36458 journal = {Structural Optimization}, 36459 volume = {6}, 36460 year = {1993}, 36461 pages = {19--28} 36462} 36463 36464@Book{ rodrigues:obstacle, 36465 author = {J. F. Rodrigues}, 36466 title = {Obstacle Problems in Mathematical Physics}, 36467 publisher = {Elsevier Publishing Company}, 36468 address = {Amsterdam}, 36469 year = {1987} 36470} 36471 36472@Book{ roos.terlaky.ea:theory, 36473 author = {C. Roos and T. Terlaky and J.--Ph. 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{Fr\'{e}d\'{e}ric Alauzet}, 39127 howpublished = {\url{https://pages.saclay.inria.fr/frederic.alauzet/cours/cea2010_V3.pdf}}, 39128 year = {2010} 39129} 39130 39131@Article{ chan1994qmrcgs, 39132 title = {A quasi-minimal residual variant of the {Bi-CGSTAB} algorithm for nonsymmetric 39133 systems}, 39134 author = {Chan, Tony F and Gallopoulos, Efstratios and Simoncini, Valeria and Szeto, Tedd 39135 and Tong, Charles H}, 39136 journal = {SIAM Journal on Scientific Computing}, 39137 volume = {15}, 39138 number = {2}, 39139 pages = {338--347}, 39140 year = {1994}, 39141 publisher = {SIAM} 39142} 39143 39144@Article{ ghai2019comparison, 39145 title = {A comparison of preconditioned {K}rylov subspace methods for large-scale 39146 nonsymmetric linear systems}, 39147 author = {Ghai, Aditi and Lu, Cao and Jiao, Xiangmin}, 39148 journal = {Numerical Linear Algebra with Applications}, 39149 volume = {26}, 39150 number = {1}, 39151 pages = {e2215}, 39152 year = {2019}, 39153 publisher = {Wiley 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Knepley}, 39160 journal = {International Journal on Numerical Methods in Engineering}, 39161 note = {Submitted}, 39162 year = {2022} 39163} 39164 39165@Article{ nathawaniknepley2022, 39166 title = {Droplet formation simulation using mixed finite elements}, 39167 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39168 journal = {Physics of Fluids}, 39169 volume = {34}, 39170 pages = {064105}, 39171 doi = {10.1063/5.0089752}, 39172 year = {2022} 39173} 39174 39175@InProceedings{ nathawaniknepley2022b, 39176 title = {Simulating Paraffin Wax Droplets Using Mixed Finite Element Method}, 39177 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39178 booktitle = {Proceeedings of the International Conference on Computational Fluid Dynamics 11 39179 (ICCFD11)}, 39180 editor = {Christoph Brehm and Shishir Pandya}, 39181 number = {4103}, 39182 year = {2022} 39183} 39184 39185@Article{ nathawaniknepley2023, 39186 title = {One-dimensional model to simulate shear-induced droplet formation}, 39187 author = {Darsh K. Nathawani and Matthew G. Knepley}, 39188 journal = {International Journal of Multiphase Flow}, 39189 note = {Submitted}, 39190 year = {2023} 39191} 39192 39193@InProceedings{ georgalisnathawaniknepleypatra2023, 39194 title = {Uncertainty Quantification of Shear-induced Paraffin Droplet Pinch-off in Hybrid Rocket Motors}, 39195 author = {Georgios Georgalis and Darsh K. Nathawani and Matthew G. 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Duarte}, 39219 pages = {539-571}, 39220 isbn = {978-0-323-85733-8}, 39221 doi = {https://doi.org/10.1016/B978-0-323-85733-8.00020-2}, 39222 url = {https://www.sciencedirect.com/science/article/pii/B9780323857338000202}, 39223 year = {2023} 39224} 39225 39226@Article{ adamsknepley2023, 39227 title = {A bespoke multigrid approach for magnetohydrodynamics models of magnetized 39228 plasmas in {PETSc}}, 39229 author = {Mark F. Adams and Matthew G. Knepley}, 39230 url = {https://arxiv.org/abs/2302.10242}, 39231 note = {In preparation}, 39232 year = {2023}, 39233 petsc_uses = {DMPlex} 39234} 39235 39236@Article{ finnknepleypusztayadams2023, 39237 title = {A Numerical Study of {Landau} Damping with {PETSc-PIC}}, 39238 author = {Daniel S. Finn and Matthew G. Knepley and Joseph V. Pusztay and Mark F. 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