%
% Papers that we reference, BUT NOT any paper that uses PETSc or is about PETSc
% those belong in petscapp.bib
%
% DO NOT DEFINE ANY ABREVIATIONS TO USE IN ENTRIES BELOW: Always write out the names of journels etc
@Article{Giraldo_2013,
Title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified model of the atmosphere {(NUMA)}},
Author = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu},
Journal = {SIAM Journal on Scientific Computing},
Year = {2013},
Number = {5},
Pages = {B1162-B1194},
Volume = {35},
Doi = {10.1137/120876034}
}
@Article{Pareschi_2005,
Title = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems with Relaxation},
Author = {L. Pareschi and G. Russo},
Journal = {Journal of Scientific Computing},
Year = {2005},
Number = {1},
Pages = {129--155},
Volume = {25}
}
@Article{Kennedy_2003,
Title = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations},
Author = {C.A. Kennedy and M.H. Carpenter},
Journal = {Appl. Numer. Math.},
Year = {2003},
Number = {1-2},
Pages = {139--181},
Volume = {44},
Doi = {10.1016/S0168-9274(02)00138-1},
Publisher = {Elsevier Science Publishers B. V.}
}
@Unpublished{Boscarino_TR2011,
Title = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic equations in the diffusion limit},
Author = {Boscarino, S. and Pareschi, L. and Russo, G.},
Note = {Arxiv preprint arXiv:1110.4375},
Year = {2011}
}
@Article{Ascher_1997,
Title = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential equations},
Author = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri},
Journal = {Applied Numerical Mathematics},
Year = {1997},
Pages = {151--167},
Volume = {25}
}
@Article{Sandu_1997,
Title = {Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: {R}osenbrock solvers},
Author = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. Potra},
Journal = {Atmospheric Environment},
Year = {1997},
Number = {20},
Pages = {3459--3472},
Volume = {31},
Abstract = {In the numerical simulation of atmospheric transport-chemistry processes, a major task is the integration of the stiff systems of ordinary differential equations describing the chemical transformations. It is therefore of interest to systematically search for stiff solvers which can be identified as close to optimal for atmospheric applications. In this paper we continue our investigation from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) and compare eight solvers on a set of seven box-models used in present day models. The focus is on Rosenbrock solvers. These turn out to be very well suited for our application when they are provided with highly efficient sparse matrix techniques to economize on the linear algebra. Two of the Rosenbrock solvers tested are from the literature, viz. and 4, and two are new and specially developed for air quality applications, viz. 3 and 3. }
}
@Article{Rang_2005,
Title = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic equations of index 1},
Author = {Rang, J. and Angermann, L.},
Journal = {BIT Numerical Mathematics},
Year = {2005},
Number = {4},
Pages = {761--787},
Volume = {45},
Publisher = {Springer}
}
@Article{Ketcheson_2008,
Title = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with Low-Storage Implementations},
Author = {D.I. Ketcheson},
Journal = {SIAM Journal on Scientific Computing},
Year = {2008},
Number = {4},
Pages = {2113--2136},
Volume = {30},
Doi = {10.1137/07070485X},
Keywords = {method of lines, strong stability-preserving, monotonicity, low-storage, RungeKutta methods},
Publisher = {SIAM}
}
@Article{Jansen_2000,
Title = {A generalized-$\alpha$ method for integrating the filtered {N}avier--{S}tokes equations with a stabilized finite element method},
Author = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.},
Journal = {Computer Methods in Applied Mechanics and Engineering},
Year = {2000},
Number = {3},
Pages = {305--319},
Volume = {190},
Publisher = {Elsevier}
}
@Article{Butcher_2007,
Title = {Error propagation of general linear methods for ordinary differential equations},
Author = {J.C. Butcher and Z. Jackiewicz and W.M. Wright},
Journal = {Journal of Complexity},
Year = {2007},
Number = {4-6},
Pages = {560--580},
Volume = {23},
Abstract = {We discuss error propagation for general linear methods for ordinary differential equations up to terms of order p+2, where p is the order of the method. These results are then applied to the estimation of local discretization errors for methods of order p and for the adjacent order p+1. The results of numerical experiments confirm the reliability of these estimates. This research has applications in the design of robust stepsize and order changing strategies for algorithms based on general linear methods.},
Doi = {10.1016/j.jco.2007.01.009},
ISSN = {0885-064X}
}
@Article{Constantinescu_A2010a,
Title = {Extrapolated implicit-explicit time stepping},
Author = {E.M. Constantinescu and A. Sandu},
Journal = {SIAM Journal on Scientific Computing},
Year = {2010},
Number = {6},
Pages = {4452-4477},
Volume = {31},
Comment = {Preprint \# ANL/MCS-P1612-0409},
Doi = {10.1137/080732833}
}
@inproceedings{devito2011liszt,
title={Liszt: a domain specific language for building portable mesh-based PDE solvers},
author={DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and Aiken, Alex and Duraisamy, Karthik and others},
booktitle={Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis},
pages={9},
year={2011},
organization={ACM}
}
@article{devito2011designing,
title={Designing the Language Liszt for Building Portable Mesh-based PDE Solvers},
author={DeVito, Zachary and Hanrahan, Pat},
journal={Scientific Discovery through Advanced Computing Program (SciDAC)},
year={2011}
}
@Misc{PGASintro,
author = {Tim Stitt},
title = {An Introduction to the Partitioned Global Address Space (PGAS) Programming Model},
note = {\url{http://cnx.org/content/m20649/latest/}}
}
@inproceedings{el2006upc,
title={UPC: unified parallel C},
author={El-Ghazawi, Tarek and Smith, Lauren},
booktitle={Proceedings of the 2006 ACM/IEEE conference on Supercomputing},
pages={27},
year={2006},
organization={ACM}
}
@inproceedings{numrich1998co,
title={Co-Array Fortran for parallel programming},
author={Numrich, Robert W and Reid, John},
booktitle={ACM Sigplan Fortran Forum},
volume={17},
number={2},
pages={1--31},
year={1998},
organization={ACM}
}
@article{aiken1997titanium,
title={Titanium: A high-performance Java dialect},
author={Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, Geoff and Semenzato, Luigi and others},
year={1997}
}
@article{charles2005x10,
title={X10: an object-oriented approach to non-uniform cluster computing},
author={Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and Sarkar, Vivek},
journal={Acm Sigplan Notices},
volume={40},
number={10},
pages={519--538},
year={2005},
publisher={ACM}
}
@article{chamberlain2007parallel,
title={Parallel programmability and the chapel language},
author={Chamberlain, Bradford L and Callahan, David and Zima, Hans P},
journal={International Journal of High Performance Computing Applications},
volume={21},
number={3},
pages={291--312},
year={2007},
publisher={SAGE Publications}
}
@inproceedings{CharmppOOPSLA93,
author = "{Kal\'{e}}, L.V. and Krishnan, S.",
title = "{CHARM++: A Portable Concurrent Object Oriented System
Based on C++}",
editor = "Paepcke, A.",
fulleditor = "Paepcke, Andreas",
pages = "91--108",
Month = "September",
Year = "1993",
booktitle = "{Proceedings of OOPSLA'93}",
publisher = "{ACM Press}",
}
@inproceedings{hewitt1973universal,
title={A universal modular actor formalism for artificial intelligence},
author={Hewitt, Carl and Bishop, Peter and Steiger, Richard},
booktitle={Proceedings of the 3rd international joint conference on Artificial intelligence},
pages={235--245},
year={1973},
organization={Morgan Kaufmann Publishers Inc.}
}
@book{yonezawa1990abcl,
title={ABCL: an object-oriented concurrent system},
author={Yonezawa, Akinori},
year={1990},
publisher={MIT press}
}
@inproceedings{dally1988object,
title={Object-oriented concurrent programming in CST},
author={Dally, William J and Chien, Andrew A},
booktitle={Proceedings of the third conference on Hypercube concurrent computers and applications: Architecture, software, computer systems, and general issues-Volume 1},
pages={434--439},
year={1988},
organization={ACM}
}
@article{grimshaw1993easy,
title={Easy-to-use object-oriented parallel processing with Mentat},
author={Grimshaw, Andrew S.},
journal={Computer},
volume={26},
number={5},
pages={39--51},
year={1993},
publisher={IEEE}
}
@inproceedings{gannon1991object,
title={Object oriented parallelism: pC++ ideas and experiments},
author={Gannon, Dennis and Lee, JK},
booktitle={Proceedings of},
pages={13--23},
year={1991}
}
@inproceedings{lau1992object,
title={An object-oriented class library for scalable parallel heuristic search},
author={Lau, Wing-cheong and Singh, Vineet},
booktitle={ECOOP’92 European Conference on Object-Oriented Programming},
pages={252--267},
year={1992},
organization={Springer}
}
@book{chase1989amber,
title={The Amber system: Parallel programming on a network of multiprocessors},
author={Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and Littlefield, Richard},
volume={23},
number={5},
year={1989},
publisher={ACM}
}
@inproceedings{kaiser2009parallex,
title={Parallex an advanced parallel execution model for scaling-impaired applications},
author={Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas},
booktitle={Parallel Processing Workshops, 2009. ICPPW'09. International Conference on},
pages={394--401},
year={2009},
organization={IEEE}
}
@TechReport{ipm,
Author = "Barry F. Smith",
Title = "A New Parallel Programming Model for Computer Simulation",
Institution = "Argonne National Laboratory",
Year = 2014,
Number = {ANL/MCS-P5135-0414}
}
@article{groppsnir,
author = {William Gropp and Marc Snir},
title = {Programming for Exascale Computers},
journal ={Computing in Science and Engineering},
volume = {15},
number = {6},
issn = {1521-9615},
year = {2013},
pages = {27-35},
doi = {http://doi.ieeecomputersociety.org/10.1109/MCSE.2013.96},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA},
}
# https://fs.hlrs.de/projects/par/mpi/mpi30/
@book{mpi3,
title="MPI: A Message-Passing Interface Standard, Version 3.0",
author={Message Passing Interface Forum},
year={2012},
publisher={High Performance Computing Center Stuttgart (HLRS)}
}
@book{openmp4,
title="OpenMP Application Program Interface, Version 4.0",
year={2013},
publisher={OpenMP Architecture Review Board}
}
@inproceedings{hartono2009annotation,
title={Annotation-based empirical performance tuning using {Orio}},
author={Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy},
booktitle={Parallel \& Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on},
pages={1--11},
year={2009},
organization={IEEE}
}
@book{toselli2005domain,
title="Domain Decomposition Methods: Algorithms and Theory",
author={Toselli, Andrea and Widlund, Olof B},
volume={34},
year={2005},
publisher={Springer}
}
@inbook{st2013,
author = "B. F. Smith and X. Tu",
chapter = "Domain Decomposition",
title = "Encyclopedia of Applied and Computational Mathematics",
bookeditor = "B. Engquist",
publisher = "Springer",
year = "2013"
}
@TechReport{ saws,
Author = "Matt Otten and Jed Brown and Barry F. Smith",
Title = "Scientific Application Web Server {(SAWs)} Users Manual",
Institution = "Argonne National Laboratory",
Year = 2013
}
@article{smith1997domain,
title={Domain Decomposition Methods for Partial Differential Equations},
author={Smith, B.F.},
journal={ICASE LARC Interdisciplinary Series in Science and Engineering},
volume={4},
pages={225--244},
year={1997},
publisher={Citeseer}
}
@article{spillane2011abstract,
title={Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems in the overlaps},
author={Spillane, N and Dolean, V and Hauret, P and Nataf, F and Pechstein, C and Scheichl, R},
journal={NuMa-Report},
volume={7},
pages={2007},
year={2011}
}
@inproceedings{jolivet2013scalabledd,
title={Scalable domain decomposition preconditioners for heterogeneous elliptic problems},
author={Jolivet, Pierre and Hecht, Fr{\'e}d{\'e}ric and Nataf, Fr{\'e}d{\'e}ric and Prud'homme, Christophe},
booktitle={Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis},
pages={80},
year={2013},
organization={ACM}
}
@book{KS2000,
Author = {D. Kinderlehrer and G. Stampacchia},
Publisher = {Society for Industrial Mathematics},
Title = {An Introduction to Variational Inequalities and Their Applications},
Year = {2000}
}
@article{wan2000energy,
title={An energy-minimizing interpolation for robust multigrid methods},
author={Wan, W.L. and Chan, T.F. and Smith, B. F.},
journal={SIAM Journal on Scientific Computing},
volume={21},
number={4},
pages={1632--1649},
year={2000},
publisher={Philadelphia, PA: SIAM, c1993-}
}
@article{chansmith1994,
title={Domain decomposition and multigrid algorithms for elliptic problems on unstructured meshes},
author={Chan, T.F. and Smith, B.F.},
journal={Electronic Transactions on Numerical Analysis},
volume={2},
pages={171--182},
year={1994}
}
@TechReport( proto-fsp,
Author = "Venkatramani Balaji and Barry Smith and Brian Van Straalen and Priya Vashishta and Michael Zarnstorff and Michael Zika",
Title = "Report of the {Proto-FSP} {Assessment Panel for the FSP}",
Institution = "Princeton Plasma Physics Laboratory",
Year = 2010,
url = {http://www.pppl.gov/fsp/documents/Proto-FSPAssessmentReport.pdf}
)
@article{ipsen2001,
Author = {Ilse C. F. Ipsen},
Journal = {SIAM J. Sci. Comput.},
Pages = {1050--1051},
Volume = 23,
Publisher = {SIAM},
Title = {A Note on Preconditioning Nonsymmetric Matrices},
Year = {2001}}
% Random papers on solvers for GPUs
@inproceedings{gpus-suck,
author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. },
title = { On the Limits of {GPU} Acceleration},
booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism},
year = {2010},
publisher = {USENIX}
}
@inproceedings{882364,
author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter},
title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid},
booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers},
year = {2003},
isbn = {1-58113-709-5},
pages = {917--924},
location = {San Diego, California},
doi = {http://doi.acm.org/10.1145/1201775.882364},
publisher = {ACM},
address = {New York, NY},
}
@conference{feng2008multigrid,
Author = {Feng, Z. and Li, P.},
Booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008},
Date-Added = {2010-08-19 15:57:06 -0500},
Date-Modified = {2010-08-19 15:57:06 -0500},
Pages = {647--654},
Title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms},
Year = {2008}}
@conference{goodnight2003multigrid,
Author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.},
Booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware},
Date-Added = {2010-08-19 15:45:20 -0500},
Date-Modified = {2010-08-19 15:45:20 -0500},
Organization = {Eurographics Association},
Pages = {102--111},
Title = {A multigrid solver for boundary value problems using programmable graphics hardware},
Year = {2003}}
@article{buatois2007concurrent,
Author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.},
Date-Added = {2010-08-19 15:45:02 -0500},
Date-Modified = {2010-08-19 15:45:02 -0500},
Journal = {High Performance Computing and Communications},
Pages = {358--371},
Publisher = {Citeseer},
Title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}},
Year = {2007}}
@article{joldes2010real,
Author = {Joldes, G.R. and Wittek, A. and Miller, K.},
Date-Added = {2010-08-19 15:44:41 -0500},
Date-Modified = {2010-08-19 15:44:41 -0500},
Journal = {Computer Methods in Applied Mechanics and Engineering},
Publisher = {Elsevier},
Title = {Real-time nonlinear finite element computations on {GPU}-application to neurosurgical simulation},
Year = {2010}}
@misc{aharon2005gpu,
Author = {Aharon, S.},
Date-Added = {2010-08-19 15:44:32 -0500},
Date-Modified = {2010-08-19 15:44:32 -0500},
Month = apr # {~27},
Note = {US Patent App. 11/115,642},
Publisher = {Google Patents},
Title = {{GPU}-based Finite Element},
Year = {2005}}
@article{cevahir2009fast,
Author = {Cevahir, A. and Nukada, A. and Matsuoka, S.},
Date-Added = {2010-08-19 15:44:01 -0500},
Date-Modified = {2010-08-19 15:44:01 -0500},
Journal = {Computational Science--ICCS 2009},
Pages = {893--903},
Publisher = {Springer},
Title = {Fast conjugate gradients with multiple {GPU}s},
Year = {2009}}
@article{maier1995symmetric,
Author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.},
Date-Added = {2010-08-19 15:43:57 -0500},
Date-Modified = {2010-08-19 15:43:57 -0500},
Journal = {Computational Mechanics},
Number = {1},
Pages = {115--129},
Publisher = {Springer},
Title = {Symmetric {G}alerkin boundary element method in plasticity and gradient plasticity},
Volume = {17},
Year = {1995}}
@article{corrigan-running,
Author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.},
Date-Added = {2010-08-19 15:43:47 -0500},
Date-Modified = {2010-08-19 15:43:47 -0500},
Journal = {International Journal for Numerical Methods in Fluids},
Publisher = {John Wiley \& Sons},
Title = {Running unstructured grid based CFD solvers on modern graphics hardware}}
@inproceedings{Volkov08,
author = {Vasily Volkov and James W. Demmel},
title = {Benchmarking GPUs to tune dense linear algebra},
booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)},
note = {\url{http://mc.stanford.edu/cgi-bin/images/6/65/SC08_Volkov_GPU.pdf}},
year = {2008}
}
@techreport{cray-mvmult,
author = "Guy~E. Blelloch and Michael~A. Heroux and Marco Zagha",
title = "Segmented Operations for Sparse Matrix Computation
on Vector Multiprocessors",
institution = "School of Computer Science, Carnegie Mellon University",
number = "CMU-CS-93-173",
month = aug,
year = 1993}
@conference{bell2009implementing,
Author = {Bell, N. and Garland, M.},
Booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis},
Date-Added = {2010-08-19 15:43:42 -0500},
Date-Modified = {2010-08-19 15:43:42 -0500},
Organization = {ACM},
Pages = {1--11},
Title = {Implementing sparse matrix-vector multiplication on throughput-oriented processors},
Year = {2009}}
@article{bell2008efficient,
Author = {Bell, N. and Garland, M.},
Date-Added = {2010-08-19 15:43:36 -0500},
Date-Modified = {2010-08-19 15:43:36 -0500},
Journal = {{NVIDIA} Corporation, {NVIDIA} Technical Report NVR-2008-004},
Title = {Efficient sparse matrix-vector multiplication on {CUDA}},
Year = {2008}}
@article{cohen-fast,
Author = {Cohen, J. and Molemaker, M.J.},
Date-Added = {2010-08-19 15:43:34 -0500},
Date-Modified = {2010-08-19 15:43:34 -0500},
Journal = {Parallel Computational Fluid Dynamics: Recent Advances and Future Directions},
Pages = {414},
Publisher = {DEStech Publications},
Title = {A fast double precision CFD code using CUDA}}
@article{kazhdan2008streaming,
Author = {Kazhdan, M. and Hoppe, H.},
Date-Added = {2010-08-19 15:43:32 -0500},
Date-Modified = {2010-08-19 15:43:32 -0500},
Journal = {ACM Transactions on Graphics (TOG)},
Number = {3},
Pages = {21},
Publisher = {ACM},
Title = {Streaming multigrid for gradient-domain operations on large images},
Volume = {27},
Year = {2008}}
@article{bonnet1998symmetric,
Author = {Bonnet, M. and Maier, G. and Polizzotto, C.},
Date-Added = {2010-08-19 15:43:18 -0500},
Date-Modified = {2010-08-19 15:43:18 -0500},
Journal = {Appl. Mech. Rev},
Pages = {669--704},
Title = {Symmetric {G}alerkin boundary element method.},
Volume = {51},
Year = {1998}}
@conference{zamith2007gpu,
Author = {Zamith, M. and Clua, E. and Pagliosa, P. and Conci, A. and Montenegro, A. and Valente, L.},
Booktitle = {Proceedings of the VI Brazilian Symposium on Computer Games and Digital Entertainment},
Date-Added = {2010-08-19 15:43:14 -0500},
Date-Modified = {2010-08-19 15:43:14 -0500},
Pages = {37--43},
Title = {The {GPU} used as a math co-processor in real time applications},
Year = {2007}}
@article{baskaran2009optimizing,
Author = {Baskaran, M.M. and Bordawekar, R.},
Date-Added = {2010-08-19 15:42:56 -0500},
Date-Modified = {2010-08-19 15:42:56 -0500},
Journal = {IBM Research Report RC24704, IBM},
Title = {Optimizing sparse matrix-vector multiplication on {GPU}s},
Year = {2009}}
@misc{szeliski2006locally,
Author = {Szeliski, R.},
Date-Added = {2010-08-19 15:42:45 -0500},
Date-Modified = {2010-08-19 15:42:45 -0500},
Month = jul # {~25},
Note = {US Patent App. 11/459,724},
Publisher = {Google Patents},
Title = {Locally adapted hierarchical basis preconditioning},
Year = {2006}}
@article{jung2006cholesky,
Author = {Jung, J.H. and O'Leary, D.P.},
Date-Added = {2010-08-19 15:42:34 -0500},
Date-Modified = {2010-08-19 15:42:34 -0500},
Journal = {Scholarly Paper, University of Maryland},
Publisher = {Citeseer},
Title = {Cholesky decomposition and linear programming on a {GPU}},
Year = {2006}}
@conference{filipovic2009gpu,
Author = {Filipovic, J. and Peterlik, I. and Fousek, J.},
Booktitle = {SAAHPC: Symposium on Application Accelerators in HPC},
Date-Added = {2010-08-19 15:42:33 -0500},
Date-Modified = {2010-08-19 15:42:33 -0500},
Title = {{GPU} Acceleration of Equations Assembly in Finite Elements Method-Preliminary Results},
Year = {2009}}
@article{taylor2009modelling,
Author = {Taylor, ZA and Comas, O. and Cheng, M. and Passenger, J. and Hawkes, DJ and Atkinson, D. and Ourselin, S.},
Date-Added = {2010-08-19 15:42:23 -0500},
Date-Modified = {2010-08-19 15:42:23 -0500},
Journal = {Medical Image Analysis},
Number = {2},
Pages = {234--244},
Publisher = {Elsevier},
Title = {On modelling of anisotropic viscoelasticity for soft tissue simulation: Numerical solution and {GPU} execution},
Volume = {13},
Year = {2009}}
@conference{owens2007survey,
Author = {Owens, J.D. and Luebke, D. and Govindaraju, N. and Harris, M. and Kr{\\"u}ger, J. and Lefohn, A.E. and Purcell, T.J.},
Booktitle = {Computer Graphics Forum},
Date-Added = {2010-08-19 15:42:21 -0500},
Date-Modified = {2010-08-19 15:42:21 -0500},
Number = {1},
Organization = {John Wiley \& Sons},
Pages = {80--113},
Title = {A survey of general-purpose computation on graphics hardware},
Volume = {26},
Year = {2007}}
@article{strzodka2005scientific,
Author = {Strzodka, R. and Doggett, M. and Kolb, A.},
Date-Added = {2010-08-19 15:42:18 -0500},
Date-Modified = {2010-08-19 15:42:18 -0500},
Journal = {Simulation Modelling Practice and Theory},
Number = {8},
Pages = {667--680},
Publisher = {Elsevier},
Title = {Scientific computation for simulations on programmable graphics hardware},
Volume = {13},
Year = {2005}}
@conference{rumpf2001using,
Author = {Rumpf, M. and Strzodka, R.},
Booktitle = {Proc. of IASTED Visualization, Imaging and Image Processing Conference (VIIP-01)},
Date-Added = {2010-08-19 15:42:15 -0500},
Date-Modified = {2010-08-19 15:42:15 -0500},
Organization = {Citeseer},
Pages = {193--202},
Title = {Using graphics cards for quantized FEM computations},
Year = {2001}}
@article{sirtori1992galerkin,
Author = {Sirtori, S. and Maier, G. and Novati, G. and Miccoli, S.},
Date-Added = {2010-08-19 15:42:14 -0500},
Date-Modified = {2010-08-19 15:42:14 -0500},
Journal = {International Journal for Numerical Methods in Engineering},
Number = {2},
Pages = {255--282},
Publisher = {John Wiley \& Sons},
Title = {A {G}alerkin symmetric boundary-element method in elasticity: formulation and implementation},
Volume = {35},
Year = {1992}}
@article{tejada2005large,
Author = {Tejada, E. and Ertl, T.},
Date-Added = {2010-08-19 15:42:09 -0500},
Date-Modified = {2010-08-19 15:42:09 -0500},
Journal = {Simulation Modelling Practice and Theory},
Number = {8},
Pages = {703--715},
Publisher = {Elsevier},
Title = {Large steps in {GPU}-based deformable bodies simulation},
Volume = {13},
Year = {2005}}
@article{goddeke2008using,
Author = {Goddeke, D. and Strzodka, R. and Mohd-Yusof, J. and McCormick, P. and Wobker, H. and Becker, C. and Turek, S.},
Date-Added = {2010-08-19 15:42:06 -0500},
Date-Modified = {2010-08-19 15:42:06 -0500},
Journal = {International Journal of Computational Science and Engineering},
Number = {1},
Pages = {36--55},
Publisher = {Inderscience},
Title = {Using {GPU}s to improve multigrid solver performance on a cluster},
Volume = {4},
Year = {2008}}
@article{garland2008parallel,
Author = {Garland, M. and Le Grand, S. and Nickolls, J. and Anderson, J. and Hardwick, J. and Morton, S. and Phillips, E. and Zhang, Y. and Volkov, V.},
Date-Added = {2010-08-19 15:41:51 -0500},
Date-Modified = {2010-08-19 15:41:51 -0500},
Journal = {IEEE Micro},
Number = {4},
Pages = {13--27},
Title = {Parallel computing experiences with CUDA},
Volume = {28},
Year = {2008}}
@article{wong1985method,
Author = {Wong, SH and Ciric, IR},
Date-Added = {2010-08-19 15:41:48 -0500},
Date-Modified = {2010-08-19 15:41:48 -0500},
Journal = {COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering},
Publisher = {MCB UP Ltd},
Title = {Method of conformal transformation for the finite-element solution of axisymmetric exterior-field problems},
Volume = {4},
Year = {1985}}
@article{turek-feast,
Author = {Turek, S. and G{\\"o}ddeke, D. and Becker, C. and Buijssen, S.H.M. and Wobker, H.},
Date-Added = {2010-08-19 15:41:47 -0500},
Date-Modified = {2010-08-19 15:41:47 -0500},
Journal = {Concurrency and Computation: Practice and Experience},
Publisher = {John Wiley \& Sons},
Title = {FEAST-realization of hardware-oriented numerics for HPC simulations with finite elements}}
@article{abedi2006space,
Author = {Abedi, R. and Petracovici, B. and Haber, R.B.},
Date-Added = {2010-08-19 15:41:46 -0500},
Date-Modified = {2010-08-19 15:41:46 -0500},
Journal = {Computer Methods in Applied Mechanics and Engineering},
Number = {25-28},
Pages = {3247--3273},
Publisher = {Elsevier},
Title = {A space-time discontinuous {G}alerkin method for linearized elastodynamics with element-wise momentum balance},
Volume = {195},
Year = {2006}}
@conference{georgii2005interactive,
Author = {Georgii, J. and Westermann, R.},
Booktitle = {Proceedings of VMV},
Date-Added = {2010-08-19 15:41:36 -0500},
Date-Modified = {2010-08-19 15:41:36 -0500},
Title = {Interactive simulation and rendering of heterogeneous deformable bodies},
Year = {2005}}
@article{mosegaard2005gpu,
Author = {Mosegaard, J. and others},
Date-Added = {2010-08-19 15:41:35 -0500},
Date-Modified = {2010-08-19 15:41:35 -0500},
Publisher = {IEEE Computer Society},
Title = {{GPU} accelerated surgical simulators for complex morphology},
Year = {2005}}
@article{meyer2007particle,
Author = {Meyer, M. and Nelson, B. and Kirby, R. and Whitaker, R.},
Date-Added = {2010-08-19 15:41:33 -0500},
Date-Modified = {2010-08-19 15:41:33 -0500},
Journal = {IEEE Transactions on Visualization and Computer Graphics},
Pages = {1015--1026},
Publisher = {Published by the IEEE Computer Society},
Title = {Particle systems for efficient and accurate high-order finite element visualization},
Year = {2007}}
@conference{rumpf2001nonlinear,
Author = {Rumpf, M. and Strzodka, R.},
Booktitle = {Data Visualization 2001: proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization in Ascona, Switzerland, May 28-30, 2001},
Date-Added = {2010-08-19 15:41:29 -0500},
Date-Modified = {2010-08-19 15:41:29 -0500},
Organization = {Springer Verlag Wien},
Pages = {75},
Title = {Nonlinear diffusion in graphics hardware},
Year = {2001}}
@article{georgii2005interactive,
Author = {Georgii, J. and Echtler, F. and Westermann, R.},
Date-Added = {2010-08-19 15:41:28 -0500},
Date-Modified = {2010-08-19 15:41:28 -0500},
Journal = {Simulation and Visualisation},
Pages = {247--258},
Publisher = {Citeseer},
Title = {Interactive simulation of deformable bodies on {GPU}s},
Volume = {2005},
Year = {2005}}
@article{harish2007accelerating,
Author = {Harish, P. and Narayanan, P.},
Date-Added = {2010-08-19 15:41:27 -0500},
Date-Modified = {2010-08-19 15:41:27 -0500},
Journal = {High Performance Computing--HiPC 2007},
Pages = {197--208},
Publisher = {Springer},
Title = {Accelerating large graph algorithms on the {GPU} using CUDA},
Year = {2007}}
@article{keunings1995parallel,
Author = {Keunings, R.},
Date-Added = {2010-08-19 15:41:19 -0500},
Date-Modified = {2010-08-19 15:41:19 -0500},
Journal = {Computers and Chemical Engineering},
Number = {6},
Pages = {647--670},
Publisher = {Oxford; New York: Pergamon Press, 1977-},
Title = {Parallel finite element algorithms applied to computational rheology},
Volume = {19},
Year = {1995}}
@conference{taylor2007real,
Author = {Taylor, Z.A. and Cheng, M. and Ourselin, S.},
Booktitle = {Proceedings of the 10th international conference on Medical image computing and computer-assisted intervention-Volume Part I},
Date-Added = {2010-08-19 15:41:17 -0500},
Date-Modified = {2010-08-19 15:41:17 -0500},
Organization = {Springer-Verlag},
Pages = {701--708},
Title = {Real-time nonlinear finite element analysis for surgical simulation using graphics processing units},
Year = {2007}}
@article{liu2000finite,
Author = {Liu, R. and Li, DY},
Date-Added = {2010-08-19 15:41:16 -0500},
Date-Modified = {2010-08-19 15:41:16 -0500},
Journal = {Materials Science and Engineering A},
Number = {1-2},
Pages = {169--175},
Publisher = {Elsevier},
Title = {A finite element model study on wear resistance of pseudoelastic {TiNi} alloy},
Volume = {277},
Year = {2000}}
@conference{kakadiaris1994active,
Author = {Kakadiaris, I.A. and Metaxas, D. and Bajcsy, R.},
Booktitle = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
Date-Added = {2010-08-19 15:41:15 -0500},
Date-Modified = {2010-08-19 15:41:15 -0500},
Organization = {Citeseer},
Pages = {980--980},
Title = {Active part-decomposition, shape, and motion estimation of articulated objects: A physics-based approach},
Year = {1994}}
@conference{de2004gpu,
Author = {De Pascale, M. and De Pascale, G. and Prattichizzo, D. and Barbagli, F.},
Booktitle = {Proceedings of Eurohaptics},
Date-Added = {2010-08-19 15:41:14 -0500},
Date-Modified = {2010-08-19 15:41:14 -0500},
Organization = {Citeseer},
Pages = {44--51},
Title = {A {GPU}-friendly method for haptic and graphic rendering of deformable objects},
Volume = {2004},
Year = {2004}}
@book{taflove1995computational,
Author = {Taflove, A. and Hagness, S.C.},
Date-Added = {2010-08-19 15:41:14 -0500},
Date-Modified = {2010-08-19 15:41:14 -0500},
Publisher = {Artech House Norwood, MA},
Title = {Computational electrodynamics},
Year = {1995}}
@conference{galoppo2005lu,
Author = {Galoppo, N. and Govindaraju, N.K. and Henson, M. and Manocha, D.},
Booktitle = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing},
Date-Added = {2010-08-19 15:41:13 -0500},
Date-Modified = {2010-08-19 15:41:13 -0500},
Organization = {IEEE Computer Society},
Pages = {3},
Title = {{LU-GPU}: Efficient algorithms for solving dense linear systems on graphics hardware},
Year = {2005}}
@conference{ryoo2008optimization,
Author = {Ryoo, S. and Rodrigues, C.I. and Baghsorkhi, S.S. and Stone, S.S. and Kirk, D.B. and Hwu, W.W.},
Booktitle = {Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming},
Date-Added = {2010-08-19 15:41:12 -0500},
Date-Modified = {2010-08-19 15:41:12 -0500},
Organization = {ACM},
Pages = {73--82},
Title = {Optimization principles and application performance evaluation of a multithreaded {GPU} using CUDA},
Year = {2008}}
@conference{micikevicius20093d,
Author = {Micikevicius, P.},
Booktitle = {Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units},
Date-Added = {2010-08-19 15:41:11 -0500},
Date-Modified = {2010-08-19 15:41:11 -0500},
Organization = {ACM},
Pages = {79--84},
Title = {3D finite difference computation on {GPU}s using {CUDA}},
Year = {2009}}
@conference{zhou2004pixel,
Author = {Zhou, Y. and Garland, M. and Haber, R.},
Booktitle = {IEEE Visualization, 2004},
Date-Added = {2010-08-19 15:41:03 -0500},
Date-Modified = {2010-08-19 15:41:03 -0500},
Pages = {425--432},
Title = {Pixel-exact rendering of spacetime finite element solutions},
Year = {2004}}
@article{komatitsch2009porting,
Author = {Komatitsch, D. and Mich{\'e}a, D. and Erlebacher, G.},
Date-Added = {2010-08-19 15:41:01 -0500},
Date-Modified = {2010-08-19 15:41:01 -0500},
Journal = {Journal of Parallel and Distributed Computing},
Number = {5},
Pages = {451--460},
Publisher = {Elsevier},
Title = {Porting a high-order finite-element earthquake modeling application to NVIDIA graphics cards using CUDA},
Volume = {69},
Year = {2009}}
@article{komatitsch1998spectral,
Author = {Komatitsch, D. and Vilotte, J.P.},
Date-Added = {2010-08-19 15:40:59 -0500},
Date-Modified = {2010-08-19 15:40:59 -0500},
Journal = {Bulletin of the Seismological Society of America},
Number = {2},
Pages = {368--392},
Publisher = {[El Cerrito, Calif., etc., Seismological Society of America, etc.]},
Title = {The spectral element method: {A}n efficient tool to simulate the seismic response of 2D and 3D geological structures},
Volume = {88},
Year = {1998}}
@article{wu2005improved,
Author = {Wu, W. and Heng, P.A.},
Date-Added = {2010-08-19 15:40:59 -0500},
Date-Modified = {2010-08-19 15:40:59 -0500},
Journal = {The Visual Computer},
Number = {8},
Pages = {707--716},
Publisher = {Springer},
Title = {An improved scheme of an interactive finite element model for 3D soft-tissue cutting and deformation},
Volume = {21},
Year = {2005}}
@article{taylor2008high,
Author = {Taylor, Z.A. and Cheng, M. and Ourselin, S.},
Date-Added = {2010-08-19 15:40:57 -0500},
Date-Modified = {2010-08-19 15:40:57 -0500},
Journal = {IEEE transactions on medical imaging},
Number = {5},
Pages = {650},
Title = {High-speed nonlinear finite element analysis for surgical simulation using graphics processing units.},
Volume = {27},
Year = {2008}}
@conference{bolz2003sparse,
Author = {Bolz, J. and Farmer, I. and Grinspun, E. and Schr{\\"o}oder, P.},
Booktitle = {ACM SIGGRAPH 2003 Papers},
Date-Added = {2010-08-19 15:40:55 -0500},
Date-Modified = {2010-08-19 15:40:55 -0500},
Organization = {ACM},
Pages = {924},
Title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid},
Year = {2003}}
@article{wu2004hybrid,
Author = {Wu, W. and Heng, P.A.},
Date-Added = {2010-08-19 15:40:54 -0500},
Date-Modified = {2010-08-19 15:40:54 -0500},
Journal = {Computer Animation and Virtual Worlds},
Number = {3-4},
Pages = {219--227},
Publisher = {John Wiley \& Sons},
Title = {A hybrid condensed finite element model with {GPU} acceleration for interactive 3D soft tissue cutting},
Volume = {15},
Year = {2004}}
% ----------------------------------------------------------------------------------------------------------------
@TechReport{davis97,
author = "T. Davis",
title = "The {U}niversity of {F}lorida Sparse Matrix Collection",
institution = "University of Florida",
year = 1997
}
@article{davis2011,
Author = {Davis, T. A. and Hu, Y.},
title = {The {U}niversity of {F}lorida sparse matrix collection},
Journal = {ACM Transactions on Mathematical Software},
Volume = {38},
Issue = {1},
Year = {2011},
Pages = {1--25}
}
@TechReport{streams,
author = "J. D. McCalpin",
title = "{STREAM}: Sustainable memory bandwidth in high performance computers",
institution = "University of Virginia",
note = "http://www.cs.virginia.edu/stream",
year = 1995
}
@article{AReusken_1988b,
author = "A. Reusken",
title = "Convergence of the multigrid full approximation scheme for
a class of elliptic mildly nonlinear boundary value
problems",
journal = "Numer. Math.",
volume = "52",
year = "1988",
pages = "251--277",
}
@article{AReusken_1988c,
author = "A. Reusken",
title = "Convergence of the multigrid full approximation scheme
including the {V}--cycle",
journal = "Numer. Math.",
volume = "53",
year = "1988",
pages = "663--686",
}
@unpublished{mgnet,
title = {Multigrid Net; http://www.mgnet.org/},
author = {Craig Douglas},
note = {Contains enormous bibliography on multigrid publications},
year = 2009
}
@unpublished{copper,
title = {Fourteenth Copper Mountain Conference on Multigrid Methods},
author = {},
note = {Held bi-annually},
year = 2009
}
@BOOK{wessling1992,
AUTHOR="Pieter Wesseling",
TITLE="An Introduction to Multigrid Methods",
YEAR="2004",
PUBLISHER="R. T. Edwards"
}
@BOOK{bhm2000,
AUTHOR="William L. Briggs and Van Emden Henson and Steve F. McCormick",
TITLE="A Multigrid Tutorial",
YEAR="2000",
PUBLISHER="SIAM",
}
@book{trottenberg2001multigrid,
title={{Multigrid}},
author={Trottenberg, U. and Oosterlee, C.W. and Sch{\"u}ller, A.},
isbn={012701070X},
year={2001},
publisher={Academic Press}
}
@TechReport{brandt1984,
author = "Achi Brandt",
title = "Multigrid Techniques: 1984 Guide with Applications for Fluid Dynamics",
institution = "Gesellschaft fur Mathematik und Dataenverarbeitung",
number = "GMD-Studien Nr. 85",
year = 1984
}
@article{yavneh1998coarse,
title={Coarse-Grid Correction for Nonelliptic and Singular Perturbation Problems},
author={Yavneh, I.},
journal={SIAM Journal on Scientific Computing},
volume={19},
number={5},
pages={1682--1699},
year={1998},
publisher={Society for Industrial and Applied Mathematics}
}
@article{wan2003phase,
title={A Phase Error Analysis of Multigrid Methods for Hyperbolic Equations},
author={Wan, WL and Chan, T.F.},
journal={SIAM Journal on Scientific Computing},
volume={25},
pages={857},
year={2003}
}
@ARTICLE{imex,
AUTHOR = "Uri M. Ascher and Steven J. Ruuth and Brian T. R. Wetton",
TITLE = "Implicit-Explicit Methods for Time-Dependent Partial Differential Equations",
JOURNAL = "SIAM Journel on Numerical Analysis",
VOLUME = "32",
NUMBER = 3,
PAGES = "797--823",
YEAR = "1995"
}
@ARTICLE{ow1,
AUTHOR = "T. Washio and C. W. Oosterlee",
TITLE = "Krylov Subspace Acceleration for Nonlinear Multigrid Schemes with Application to Recirculating Flow",
JOURNAL = "SIAM Journal on Scientific Computing",
VOLUME = "21",
PAGES = "1670--1690",
YEAR = "2000"
}
@ARTICLE{vm1,
AUTHOR = "V. A. Mousseau",
TITLE = "Implicitly Balanced Solution of the Two-Phase Flow Equations Coupled to Nonlinear Heat Conduction",
JOURNAL = "Journal Of Computational Physics",
VOLUME = "200",
PAGES = "104--132",
YEAR = "2004"
}
@ARTICLE{vm2,
AUTHOR = "V. A. Mousseau",
TITLE = "A Fully Implicit Hybrid Solution Method for a Two-Phase Thermal-Hydraulic Model",
JOURNAL = "Journal Of Heat Transfer",
VOLUME = "127",
PAGES = "531--539",
YEAR = "2005"
}
@Misc{salome1,
author = "Laurent Dada and Daniel Caruge",
title = "The {SALOME} Open Source {CAE} Platform Application to Reactor Physics Simulation",
year = 2005,
url = "http://conferences.esa.int/05c26/Seminar-2005-09-28-SALOME.pdf",
Note = "Presentation at an ESA/ESTEC conference"
}
@INPROCEEDINGS{downar1,
AUTHOR = "D. A. Barber and W. Wang and R. M. Miller and T. J. Downar and H. G. Joe and V. A. Mousseau and D. E. Ebert",
TITLE = "Application of a generalized interface module to the coupling of {PARCS} with both {RELAP5} and {TRAC-M}",
BOOKTITLE = "Proceedings of 1999 annual meeting of the American Nuclear Society",
YEAR = "1999"
}
@ARTICLE{lopez1,
AUTHOR = "A. P. Lopez and J. B. Sandova",
TITLE = "A methodology for the coupling of {RAMONA-3B} neutron kinetics and {TRAC-BF1} thermal-hydraulics",
JOURNAL = "Annals of Nuclear Energy",
VOLUME = "32(6)",
PAGES = "621--634",
YEAR = "2005"
}
@INPROCEEDINGS{OG-1996,
AUTHOR = "C. R. E. de Oliveira and A. J. H. Goddard",
TITLE = "{EVENT}: A Multidimensional Finite Element-Spherical Harmonics Radiation Transport Code",
BOOKTITLE = "Proceedings of the OECD International Seminar on 3D Deterministic Radiation Transport Codes",
EDITOR = "",
PUBLISHER = "",
PAGES = "",
NOTE = "Paris, France",
MONTH = "December 01--02,",
YEAR = "1996"
}
@ARTICLE{WO-2000,
AUTHOR = "P. Warner and C. R. E. de Oliveira",
TITLE = "Verification and Validation of the 3D Finite Element Transport Theory
Code {EVENT} for Shielding Applications",
JOURNAL = "J. Nucl. Sci. and Tech.",
VOLUME = "Supplement 1",
PAGES = "466--470",
YEAR = "2000"
}
@unpublished{GNEP-WEB,
AUTHOR = "{U.S. Department of Energy}",
TITLE = "Global Nuclear Energy Partnership ({GNEP})",
NOTE = "\url{ http://www.gnep.energy.gov}",
YEAR = "2007"
}
@Book{LEWIS-MILLER-1984,
AUTHOR = "E. E. Lewis and W. F. Miller, Jr.",
TITLE = "Computational Methods of Neutron Transport",
ADDRESS = "",
PUBLISHER = "Wiley",
YEAR = "1984"
}
@Article{couple1,
author = "J. M. Cook and D. Okrent and D. Satkus and R. B. Lazarus and M. B. Wells",
title = "{AX-1}, A COMPUTING PROGRAM FOR COUPLED NEUTRONICS-HYDRODYNAMICS CALCULATIONS ON THE {IBM-704}",
journal = "Nuclear Sci. and Eng.",
year = 1959,
pages = "113--115",
volume = "2(1)"
}
@inproceedings{weber1,
AUTHOR = "D. P. Weber and S. S. Chen and C. Y. Wang and T. Y. C. Wei and S. Jansson",
TITLE = "Coupled {CFD/CSM} vibration design methodology for generation {IV} long-life fuel and component design",
BOOKTITLE = "4th International Conference on Supercomputing in Nuclear Applications",
YEAR = "2000"
}
@Misc{gnep:report,
author = "Phillip Finck and David Keyes and Rick Stevens",
title = "{Report on the {DOE} Joint {NE/SC} Workshop Simulation and Modeling for Advanced Nuclear Energy Systems}",
year = 2006
}
@Misc{subsurface-workshop-ref,
author = "D. {Zachman (Chair)}",
title = "{Computational Subsurface Sciences Workshop}",
note = "January 9--12, 2007, Bethesda, MD, see \url{http://subsurface2007.labworks.org/}",
}
@Misc{fusion:report,
title = "{Report of the Fusion Energy Sciences Advisory Committee Burning Plasma Strategy Panel}",
author = "{Fusion Energy Sciences Advisory Committee}",
year = 2002,
note = "see \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/Austinfinal.pdf}"
}
@Misc{hecrtf:report,
title = "{Report of the High End Computing Revitalization Task Force (HECRTF)}",
key = "HECRTF",
year = 2004,
howpublished = "see \url{http://www.ostp.gov/nstc/html/HECRTF-FINAL_051004.pdf}"
}
@Misc{doesc20years,
title = "{Facilities for the Future of Science: A Twenty-Year Outlook}",
key = "Office of Science, U.S. Department of Energy",
year = 2003,
howpublished = "Office of Science, U.S. Department of Energy,
see \url{http://www.sc.doe.gov/Scientific_User_Facilities/History/20-Year-Outlook-screen.pdf}"
}
@phdthesis{karpeev-thesis,
author = "D. A. Karpeyev",
title = "Geometric Integrators for Hamiltonian PDEs",
school = "Old Dominion University",
year = "2002",
}
@incollection{fjp:ima,
AUTHOR= "Lori Freitag and Mark Jones and Paul Plassmann",
title = "The Scalability of Mesh Improvement Algorithms",
booktitle = "Algorithms for Parallel Processing",
publisher = "Springer-Verlag",
volume = "105",
series = "The IMA Volumes in Mathematics and Its Applications",
editor = "Michael T.\ Heath and Abhiram Ranade and Robert S.\ Schreiber",
year = "1998",
pages = "185--212"
}
@inproceedings{poet,
AUTHOR = "Rob Armstrong and Alex Cheung",
TITLE = "{POET} ({P}arallel {O}bject-Oriented {E}nvironment and {T}oolkit)
and Frameworks for Scientific Distributed Computing",
BOOKTITLE = "Proceedings of {HICSS97}",
YEAR = "1997",
}
@Misc{ pseware-web-page,
author = "",
title = "{PSEware} {Web} page",
note = "\url{http://www.extreme.indiana.edu/pseware}, Indiana University",
key = "{PSEware} {Web} page",
}
@Misc{ babel-web-page,
author = "Tom Epperly and Tamara Dahlgren and Gary Kumfert",
title = "{Babel} {Web} page",
note = "\url{http://www.llnl.gov/CASC/components/babel.html}",
}
@Misc{ infospheres-web-page,
author = "K.~M. {Chandy et al.}",
title = "{Infospheres} {W}eb page",
note = "\url{http://www.infospheres.caltech.edu}",
key = "{Infospheres} {Web} page",
}
@misc{ hammond,
author = "Glenn Hammond",
title = "{Sandia National Laboratory}, {C}omputations on {R}eactive {F}low, private communication"
}
@misc{ ornl,
author = "Oak Ridge National Laboratory",
title = "Private communication via petsc-maint email support"
}
@Unpublished{ cumulvs-web-page,
author = "",
title = "{Cumulvs} {W}eb page",
note = "http://www.epm.ornl.gov/cs/cumulvs.html",
key = "{Cumulvs} {W}eb page",
}
@Article{nonlinearGMRES,
author = "T. Washio and C. W. Oosterlee",
title = "Krylov Subspace Acceleration for Nonlinear Multigrid Schemes",
journal = "ETNA",
year = 1997,
pages = "271--290",
volume = "6"
}
@Article{pcice,
author = "Richard C. Martineau and Ray A. Berry",
title = "The pressure-corrected ICE finite element method for compressible flows on unstructured meshes",
journal = "Journal of Computational Physics",
year = 2004,
pages = "659--685",
volume = "198(2)"
}
@Article{cumulvs97,
author = "G. A. Geist and J. A. Kohl and P. M. Papadopoulos",
title = "{CUMULVS}: Providing Fault-Tolerance, Visualization,
and Steering of Parallel Applications",
journal = "International Journal of Supercomputing Applications",
year = 1997
}
@techreport{daly2012interagency,
author={John Daly and Bill Harrod and Thuc Hoang and Lucy Nowell and Bob Adolf and Shekhar Borkar and Nathan DeBardeleben and Mootaz Elnozahy and Mike Heroux and David Rogers and Rob Ross and Vivek Sarkar and Martin Schulz and Marc Snir and Paul Woodward},
title={Inter-Agency Workshop on HPC Resilience at Extreme Scale},
year=2012,
publisher={US Department of Defense}
}
@Article{karpeev1,
author = "A. L. Islas and D. A. Karpeev and C. M. Schober",
title = {Geometric Integrators for the Nonlinear Schr\"odinger Equation},
journal = "J. Comp. Phys.",
year = 2001,
pages = "116--148",
volume = 173
}
@InProceedings{scirun97,
author = "S. G. Parker and D. W. Weinstein and C. R. Johnson",
title = "The {SCIRun} Computational Steering System",
booktitle = "Modern Software Tools in Scientific Computing",
editor = "E. Arge and A. M. Bruaset and H. P. Langtangen",
publisher = "Birkhauser Press",
year = 1997,
}
@techreport{ szyld,
AUTHOR= "Valeria Simoncini and Daniel B. Szyld",
TITLE= " Theory of Inexact Krylov Subspace Methods and Applications to Scientific Computing",
year = "2002",
institution = "Department of Mathematics, Temple University",
number = "02-4-12"
}
@techreport{ pdelab,
AUTHOR= "S. Weerawarana and E. N. Houstis and J. R. Rice and A. C. Catlin and
C. Crabill and C. C. Chui and S. Markus",
TITLE= "{PDELab}: An Object-Oriented Framework for Building Problem Solving
Environments for {PDE} Based Applications",
year = 1994,
institution = "Department of Computer Sciences, Purdue University",
number = "CSD-TR-94-021"
}
@Unpublished{ilu-web-page,
author = "Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi",
title = "{I}nter-{L}anguage {U}nification Reference Manual",
note = "ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation",
}
@Unpublished{doe2k-web-page,
title = "{DOE2000 Initiative} {W}eb page",
note = "http://www.mcs.anl.gov/DOE2000",
key = "DOE2000 Initiative",
}
@Misc{pvode-web-page,
title = "{PVODE} {W}eb Page",
note = "\url{http://www.llnl.gov/CASC/PVODE},
Lawrence Livermore National Laboratory",
author = "A. {Hindmarsh et al.}",
}
@BOOK{szyperski97,
AUTHOR = "Clemens Szyperski",
TITLE = "Component Software: Beyond Object-Oriented Programming",
PUBLISHER = "ACM Press",
address = "New York",
YEAR = 1997
}
@Unpublished{isis++-web-page,
title = "{ISIS++} {W}eb Page",
note = "http://ca.sandia.gov/isis",
author = "Robert L. Clay and Kyran Mish and Alan B. Williams",
Institution = "Sandia National Laboratories",
}
@Unpublished{petsc:coloringuse,
title = "Code for computing sparse {J}acobians",
note = "\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}",
Institution = "Argonne National Laboratory"
}
@Unpublished{petsc:external,
author = {B. F. {Smith et al.}},
title = "{External Software Used by PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}",
Institution = "Argonne National Laboratory"
}
@Unpublished{petsc:use-by-external-packages,
author = {B. F. {Smith et al.}},
title = "{Software Packages that Use or Interface to PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}",
Institution = "Argonne National Laboratory"
}
@Unpublished{petsc:prizes,
author = {B. F. {Smith et al.}},
title = "{Prizes Won Using PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}",
Institution = "Argonne National Laboratory"
}
@Unpublished{petsc:csgf,
author = {B. F. {Smith et al.}},
title = "{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}",
Institution = "Argonne National Laboratory"
}
@Unpublished{flash-web-page,
title = "{U}niversity of {C}hicago {C}enter on {A}strophysical
{T}hermonuclear {F}lashes {W}eb Page",
note = "http://www.asci.uchicago.edu",
author = "R. {Rosner et al.}",
Institution = "University of Chicago",
}
@Unpublished{esi-web-page,
title = "{E}quation {S}olver {I}nterface {F}orum {W}eb Page",
note = "http://z.ca.sandia.gov/esi",
author = "R. {Clay et al.}",
}
@Unpublished{infobus-web-page,
title = "{I}nfo{B}us {W}eb Page",
note = "http://www.java.sun.com/beans/infobus",
key = "infobus"
}
@Unpublished{xray-web-page,
title = "{S}upercomputer {S}olution of {M}assive
{C}rystallographic and {M}icrotomographic {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)",
note = "http://www.mcs.anl.gov/xray/",
Institution = "Argonne National Laboratory",
}
@INPROCEEDINGS{ kohn98,
AUTHOR= "Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski",
TITLE= "Language Interoperability Mechanisms for High-Performance Scientific Applications",
PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
year = 1999,
pages = "30-39"
}
@INPROCEEDINGS{ kohn01,
AUTHOR= "Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens",
TITLE= "Divorcing Language Dependencies from a Scientific Software Library",
PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the Tenth SIAM Conference on Parallel Processing",
year = 2001,
}
@INPROCEEDINGS{ freitag_jones_plassmann98,
AUTHOR= "Lori Freitag and Mark Jones and Paul Plassmann",
TITLE= "Component Integration for Unstructured Mesh Algorithms and Software",
PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
year = 1999,
pages = "215-224",
}
@BOOK{templates,
AUTHOR = {R. Barrett and M. Berry and T. F. Chan and J. Demmel and J. Donato and J. Dongarra and V. Eijkhout
and R. Pozo and C. Romine and H. Van der Vorst },
TITLE = {Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods},
PUBLISHER = {SIAM},
YEAR = {1994},
ADDRESS = {Philadelphia, PA}
}
@InProceedings{parasha2,
author = {M. Parashar and J. C. Browne and C. Edwards and K. Klimkowski},
title = { A Common Data Management Infrastructure for Parallel Adaptive
Algorithms for {PDE} Solutions},
booktitle = {SC97 Proceedings},
publisher = "IEEE Computer Society Press",
year = {1997}
}
@TECHREPORT{parasha,
AUTHOR="M. Parashar and J. C. Browne",
TITLE="{DAGH}: A Data-Management Infrastructure for Parallel
Adaptive Mesh Refinement Techniques",
INSTITUTION="Department of Computer Science, University of
Texas at Austin",
YEAR="1995"
}
@Article{parti,
author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang},
title = {Communication Optimizations for Irregular
Scientific Computations on Distributed Memory Architectures},
journal = {Journal of Parallel and Distributed Computing},
year = {1994},
volume = {22},
pages = {462--478}
}
@Article{mparti,
author = {G. Agrawal and A. Sussman and J. Saltz},
title = {An Integrated Runtime and Compile-time Approach for
Parallelizing Structured and Block Structured Applications},
journal = {IEEE Trans. on Parallel and Distributed Systems},
volume = {6},
number = {7},
year = "1995"
}
@Article{gropp-lusk-doss-skjellum,
author = { William Gropp and Ewing Lusk and Nathan Doss and Anthony
Skjellum},
title = {A high-performance, portable implementation of the {MPI}
Message Passing Interface standard},
journal = {Parallel Computing},
year = 1996,
volume = 22,
pages = {789--828}
}
@InProceedings{lam,
author = "Greg Burns and Raja Daoud and James Vaigl",
title = "{LAM}: An Open Cluster Environment for {MPI}",
booktitle = "Proceedings of Supercomputing Symposium '94",
editor = "John W. Ross",
publisher = "University of Toronto",
pages = "379--386",
year = 1994,
}
@Article{cs99,
author = "X.-C. Cai and M. Sarkis",
title = "A restricted additive {S}chwarz preconditioner for general sparse linear systems",
journal = "SIAM J. Scientific Computing",
year = "1999",
volume = "21",
pages = "792-797"
}
@TechReport( cs97a,
AUTHOR = "X.-C. Cai and M. Sarkis",
TITLE = "A restricted additive {S}chwarz preconditioner for general sparse linear systems ",
YEAR = 1997,
Institution = "Computer Science Department,
University of Colorado-Boulder",
Number = "CU-CS 843-97",
Note= "(accepted by SIAM J. of Scientific Computing)"
)
@article{cai2003restricted,
title={Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric positive definite linear systems},
author={Cai, X.C. and Dryja, M. and Sarkis, M.},
journal={SIAM Journal on Numerical Analysis},
volume=41,
issue=1,
pages={1209--1231},
year=2003,
doi={10.1137/S0036142901389621}
}
@TECHREPORT{caisaad,
AUTHOR="Xiao-Chuan Cai and Youcef Saad",
TITLE="Overlapping domain decomposition algorithms for
general sparse matrices",
INSTITUTION="Army High Performance Computing
Research Center, University of Minnesota ",
YEAR="1993",
NUMBER="Preprint 93-027 ",
NOTE= "SIAM J. Sci. Comp. (submitted)"
}
@BOOK{ruminations,
AUTHOR="Andrew Koenig and Barbara Moo",
TITLE="Ruminations on C++",
YEAR="1996",
PUBLISHER="Addison-Wesley"
}
@BOOK{mpi-complete,
AUTHOR="Marc Snir and Steve Otto and Steven Huss-Lederman and David
Walker and Jack Dongarra",
TITLE="{MPI}: The Complete Reference",
YEAR="1995",
PUBLISHER="MIT Press"
}
@Unpublished{ tcl-tk-web-page,
title = "{Tcl/Tk} {W}orld {W}ide {W}eb page",
note = "http://www.sunlabs.com/research/tcl/",
year = 1996,
month = Aug
}
@misc{mpich-web-page,
author = {William Gropp and {et. al.}},
title = {{MPICH} {W}eb page},
key = "MPICH",
url = {http://www.mpich.org},
howpublished = {\url{http://www.mpich.org}},
}
@Article{ MPI-final,
Title = "{MPI}: A Message-Passing Interface Standard",
Journal = "International J. Supercomputing Applications",
Volume = 8,
Number = "3/4",
Year = 1994,
Key = "MPI Standard - final"
}
@Unpublished{ npb-web-page,
key = "NAS Parallel Benchmarks",
title = "{NAS} {P}arallel {B}enchmarks {W}eb page",
note = "http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html",
year = 1996,
month = Dec
}
@book{ george81,
TITLE = "Computer Solution of Large Sparse Positive Definite Systems",
AUTHOR= "Alan George and Joseph W. Liu",
PUBLISHER = "Prentice-Hall",
YEAR = 1981,
KEY = "SparseDirect"
}
@book{ p4-book,
TITLE = "Portable Programs for Parallel Processors",
PUBLISHER = "Holt, Rinehart, {and} Winston",
YEAR = 1987,
AUTHOR = "James Boyle and Ralph Butler and Terrence Disz and
Barnett Glickfeld and Ewing Lusk and Ross Overbeek and
James Patterson and Rick Stevens",
KEY = "P4Book"
}
@Article{stones,
author = "H. L. Stone",
title = "Iterative solution of implicit approximations of multidimensional partial differential equations",
journal = "SIAM J. Numerical Analysis",
pages = "87--113",
volumne = 5,
Year = 1968
}
@Article{parallelstones,
author = "J. S. Reeve and A. D. Scurr and J. H. Merlin",
title = "Parallel versions of {S}tones strongly implicit algorithm",
journal = "Concurrency and Computation: Practice and Experience",
pages = "1049--1062",
volumne = 13,
Year = 2001
}
@Article{p4-paper,
author = "Ralph Butler and Ewing Lusk",
title = "Monitors, Messages, and Clusters: {T}he p4 Parallel
Programming System",
journal = "Journal of Parallel Computing",
note = "To appear (Also Argonne National Laboratory Mathematics and
Computer Science Division preprint P362-0493)",
Year = 1993
}
@TechReport(picl,
Author= "G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and
Patrick~H.~Worley",
Title= "{PICL}: A portable instrumented communications library",
Institution= "Oak Ridge National Laboratory",
Number= "TM-11130",
Year= "1990",
Key= "PICL")
@TechReport( upshot,
Author= "Virginia Herrarte and Ewing Lusk",
Title= "Studying Parallel Program Behavior with {U}pshot",
Institution= "Argonne National Laboratory",
Number= "ANL-91/15",
Month= AUG,
Year= "1991",
Key= "Upshot" )
@TechReport( p4-manual,
Author= "Ralph Butler and Ewing Lusk",
Title= "User's Guide to the p4 Parallel Programming System",
Institution= "Argonne National Laboratory",
Number= "ANL-92/17",
Month= Oct,
Year= "1992",
Key= "p4-Manual" )
@inproceedings{oldparti,
Author = "Gagan Agrawal and Alan Sussman and Joel Saltz",
Title = "Compiler and Runtime Support for Unstructured and Block
Structured Problems",
BOOKTITLE = "Proceedings of Supercomputing '93",
pages = "578--587",
YEAR = "1993"
}
@article{parti2,
Author = "S. S. Mukherjee and S. D. Sharma and
M. DF. Hill and J. R. Larus and A. Rogers and J. Saltz",
Title = "Efficient Support for Irregular Applications on
Distributed Memory Machines",
journal = "ACM SIGPLAN Notices",
YEAR = "1995",
pages = "68-79",
volume = "30",
number = "8"
}
@article{parti3,
Author = "J. Saltz and R. Mirchandaney and K. Crowley",
Title = "Run-Time Parallelization and Scheduling of Loops",
journal = "IEEE Trans. Computers",
YEAR = "1991",
pages = "604-612",
volume = "40",
number = "5"
}
@inproceedings{disz-lusk:wamtrace,
AUTHOR = "Terrence Disz and Ewing Lusk",
TITLE = "A Graphical Tool for Observing the Behavior of Parallel
Logic Programs",
BOOKTITLE = "Proceedings of the 1987 Symposium on Logic Programming",
YEAR = "1987",
PAGES = "46--53"
}
@inproceedings{gorlick-kesselman:gauge,
AUTHOR = "Michael Gorlick and Carl Kesselman",
TITLE = "Timing {Prolog} programs without Clocks",
BOOKTITLE = "Proceedings of the 1987 Symposium on Logic Programming",
YEAR = "1996",
publisher = "Birkhauser"
}
@TechReport( aztec,
Author = "Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro",
Title = "Aztec User's Guide Version 1.1",
Institution = "Sandia National Laboratories",
Month = Oct,
Year = 1995,
Number = "SAND95/1559"
)
@TechReport( aztec2,
Author = "Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid",
Title = "Official {Aztec} User's Guide Version 2.1",
Institution = "Sandia National Laboratories",
Year = 1999,
)
@Book{taylor-chandy:pcn,
Author = "Chandy, M. and Taylor, S.",
Title = "An Introduction to Parallel Programming",
Year = 1991,
Publisher = "Jones and Bartlett"}
@Book{foster-taylor:strand,
Title = "Strand: New Concepts in Parallel Programming",
Author = "Ian Foster and Stephen Taylor",
Publisher = "Prentice-Hall",
Adress = " Englewood Cliffs, New Jersey",
Year = 1990}
@article{aurora,
AUTHOR = "E. Lusk and R. Butler and T. Disz and R. Olson and
R. Overbeek and R. Stevens and D.H.D. Warren and
A. Calderwood and P. Szeredi and S. Haridi and
P. Brand and M. Carlsson and A. Ciepielewski and
B. Hausman",
TITLE = "The Aurora OR-Parallel Prolog System",
JOURNAL = "New Generation Computing",
VOLUME = 7,
NUMBER = 3,
YEAR = 1990,
PAGES = "243--271"
}
@Techreport{roo,
Author = "E. Lusk and W. McCune and J. Slaney",
Title = "Roo---a Parallel Theorem Prover",
Institution = "Argonne National Laboratory",
Number = "MCS--TM--149",
Year = 1991}
@Techreport{heath-etheridge:vppp,
Author = "M. T. Heath and J. A. Etheridge",
Title = "Visualizing the Performance of Parallel Programs",
Institution = "Oak Ridge National Laboratory",
Number = "ORNL TM-11813",
Year = 1991}
@Techreport{chem:vis,
Author = "Ewing L. Lusk",
Title = "Performance Visualization for Parallel Programs",
Institution = "Argonne National Laboratory",
Number = "ANL/MCS--P287--0192",
Year = 1991,
Note = "(to appear in {\em Theoretica Chimica Acta})"
}
@Techreport{picltrace,
Author = "P.~H.~Worley",
Title = "A new {PICL} trace file format",
Institution = "Oak Ridge National Laboratory",
Number = "ORNL TM-12125",
Month = JUN,
Year = 1992}
@inproceedings{hideo,
AUTHOR = "Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda
and Ross Overbeek",
TITLE = "Inference of Phylogenetic trees using maximum likelihood",
BOOKTITLE = "Proceedings of the First Intel Delta Applications
Workshop",
YEAR = "1992",
PAGES = "247--262"
}
@InProceedings(DW90,
Author= "M. Dryja and O. Widlund",
Title= "Towards a Unified Theory of Domain Decomposition Algorithms
for Elliptic Problems",
Booktitle= "Third International Symposium on Domain Decomposition
Methods",
Editor= "T. F. Chan and R. Glowinski
and J. P\'eriaux and O. B. Widlund",
Year= "1990",
Pages= "3-21",
Publisher= "SIAM",
Address= "Philadelphia",
Annote= "Additive {S}chwarz. Surveys recent (1989) results; some
comments on 3-d and how many approaches may be cast in
the form of additive {S}chwarz-subspace form. 58
references, good introduction to the theory. No
computations",
Key= "DryjaWidlund90 !AS")
@UnPublished(rosing,
Author= "Matt Rosing and Joel Saltz",
Title= "Low Latency Messages on Distributed Memory Multiprocessors",
Key= "LowLatency",
Note= "manuscript, 1992")
@techreport{jp:incomplete,
AUTHOR = "Mark T. Jones and Paul E. Plassmann",
TITLE = "An Improved Incomplete {C}holesky Factorization",
INSTITUTION = "Argonne National Laboratory",
ADDRESS = "Argonne, IL",
TYPE = "Preprint",
NOTE = "(to appear in {\em ACM Trans. on Mathematical Software, 1995})",
NUMBER = "MCS-P206-0191",
YEAR = "1991",
KEY = "jones" }
@incollection{jp:ima,
AUTHOR = "Mark Jones and Paul Plassmann",
title = "The Efficient Parallel Iterative Solution
of Large Sparse Linear Systems",
booktitle = "Graph Theory and Sparse Matrix Computation",
publisher = "Springer-Verlag",
series = "The IMA Volumes in Mathematics and Its Applications",
editor = "Alan George and John Gilbert and Joseph W.H.~Liu",
volume = "56",
year = "1993",
pages="229--245"
}
@Article{ pw98,
AUTHOR = "M. Pernice and H. F. Walker",
TITLE = "{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems",
journal = "SIAM J. Sci. Stat. Comput.",
year = 1998,
volume = 19,
pages = "302--318"
}
@TechReport( ysmp83,
KEY = "Eisenstat",
AUTHOR = "S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and
A.~H.~Sherman",
TITLE = "The (New) {Y}ale {S}parse {M}atrix {P}ackage",
INSTITUTION= "Department of Computer Science, Yale University",
NUMBER = "YALE/DCS/RR-265",
MONTH = APR,
YEAR = "1983"
)
@inbook( ysmp84,
AUTHOR = "S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and
A.~H.~Sherman",
chapterTITLE = "The (New) {Y}ale {S}parse {M}atrix {P}ackage",
title = "Elliptic Problem Solvers II",
publisher = "Academic Press",
pages = "45--52",
editors = "G. Birkhoff and A. Schoenstadt",
YEAR = "1984"
)
@TechReport{ sparsekit,
KEY = "Saad",
AUTHOR = "Youcef Saad",
TITLE = "{SPARSKIT}, a basic tool kit for sparse matrix computations",
INSTITUTION= "Center for Supercomputing Research and Development,
University of Illinois at Urbana-Chanpaign",
NUMBER = "1029",
YEAR = 1990
}
@TechReport( pde-user-ref,
Author = "Barry F. Smith",
Title = "Extensible {PDE} Solvers Package Users Manual",
Institution = "Argonne National Laboratory",
Month = SEP,
Year = 1994,
Number = "ANL-93/40",
Key = "Smith94 ! PDE"
)
@TechReport( bs-user-ref,
Author = "Mark T. Jones and Paul E. Plassmann",
Title = "{BlockSolve95} Users Manual: Scalable Library Software for
the Parallel Solution of Sparse Linear Systems",
Institution = "Argonne National Laboratory",
Month = DEC,
Year = 1995,
Number = "ANL-95/48"
)
@TechReport( snes-user-ref,
Author = "William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
Title = "Using the {S}calable {N}onlinear {E}quations {S}olvers Package",
Institution = "Argonne National Laboratory",
Month = Feb,
Year = 1995,
Number = "ANL/MCS-TM-193",
Key = "GroppMcInnesSmith95 ! SNES"
)
@TechReport( sles-user-ref,
Author = "William D. Gropp and Barry F. Smith",
Title = "{S}implified {L}inear {E}quation {S}olvers Users Manual",
Institution = "Argonne National Laboratory",
Month = MAR,
Year = 1993,
Number = "ANL-93/8",
Key = "GroppSmith93 ! SLES"
)
@TechReport( chameleon-user-ref,
Author = "William D. Gropp and Barry F. Smith",
Title = "Chameleon Parallel programming tools Users Manual",
Institution = "Argonne National Laboratory",
Month = MAR,
Year = 1993,
Number = "ANL-93/23",
Key = "GroppSmith93 ! Chameleon"
)
@Article( euclid2,
Author = "D. Hysom and A. Pothen",
Title = "A Scalable Parallel Algorithm For Incomplete Factor Preconditioning",
Journal = "SIAM J. Sci. Comput.",
Volume = 22,
Number = 6,
Pages = "2194--2215"
)
@TechReport( euclid1,
Author = "D. Hysom and A. Pothen",
Title = "Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel Solution of Sparse Linear Systems)",
Institution = "Old Dominion University",
Year = "2001"
)
@TechReport( ksp-user-ref,
Author = "William D. Gropp and Barry F. Smith",
Title = "Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space Methods",
Institution = "Argonne National Laboratory",
Month = AUG,
Year = 1993,
Number = "ANL-93/30",
Key = "GroppSmith93 ! KSP"
)
@TechReport( mpi-chameleon,
Author = "William D. Gropp and Ewing Lusk",
Title = "A Test Implementation of the {MPI} Draft Message-Passing
Standard",
Institution = "Argonne National Laboratory",
Month = DEC,
Year = 1992,
Number = "ANL-92/47",
Key = "GroppLusk92 ! MPI"
)
@TechReport( blockcomm-fortran,
Author = "William D. Gropp",
Title = "Block{C}omm for {F}ortran",
Institution = "Argonne National Laboratory",
Month = MAY,
Year = 1993,
Number = "ANL-93/00 (to appear)",
Key = "Gropp93 ! BlockComm"
)
@TechReport( autodocument,
Author = "William D. Gropp",
Title = "Automatic documentation of {C} programs",
Institution = "Argonne National Laboratory",
Month = MAY,
Year = 1993,
Number = "ANL-93/00",
Key = "Gropp93 ! Autodoc"
)
@TechReport( zipcode,
Author = "Anthony Skjellum and Steven G. Smith and Charles H Still and
Alvin P. Leung and Manfred Morari",
Title = "The {Z}ipcode message-passing system",
Institution = "Lawrence Livermore National Laboratory",
Month = SEP,
Year = 1992,
Number = "Unpublished",
Key = "Skjellum92 ! Zipcode" )
@Article( paragraph,
Author = "Michael T. Heath and Jennifer Etheridge Finger",
Title = "Visualizing performance of parallel programs",
Journal = "IEEE Software",
Volume = 8,
Number = 5,
Month = SEP,
Year = 1991,
Pages = "29--39",
Key = "Heath91 ! Paragraph" )
@article( gropp90,
Author = "William Gropp and Edward Smith",
Title = "Computational Fluid Dynamics on Parallel Processors",
Journal = "Computers and Fluids",
Volume = 18,
Year = 1990,
Pages = "289--304",
Key = "Gropp90 ! performance" )
@article( foster92,
Author = "Ian Foster and William Gropp and Rick Stevens",
Title = "The parallel scalability of the spectral transform method",
Journal = "Monthly Weather Review",
Volume = 120,
Year = 1992,
Pages = "835--850",
Key = "Foster92 ! performance" )
@INBOOK{fgn,
AUTHOR="R. Freund and G. H. Golub and N. Nachtigal",
TITLE="Iterative Solution of Linear Systems",
SERIES="Acta Numerica",
YEAR="1992",
PUBLISHER="Cambridge University Press",
PAGES="57--100"
}
@TechReport( nachtigal90,
Author = "No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen",
Title = "How Fast are Nonsymmetric Matrix Iterations?",
Institution = "Massachusetts Institute of Technology",
Month = MAR,
Year = 1990,
Number = "90-2",
Key = "Nachtigal | Krylov"
)
@article{nachtigal1992fnm,
title={How Fast are Nonsymmetric Matrix Iterations?},
author={Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.},
journal={SIAM Journal on Matrix Analysis and Applications},
volume={13},
pages={778},
year={1992},
publisher={SIAM}
}
@techreport{embree1999descriptive,
title={How descriptive are {GMRES} convergence bounds},
author={Embree, M.},
year={1999},
number={08},
institution={Oxford University Computing Laboratory}
}
@Article{ vorst92,
author = "H. van der Vorst",
title = "Bi-{CGSTAB}: A fast and smoothly converging varient of
{Bi-CG} for the solution of nonsymmetric linear systems",
journal = "SIAM J. Sci. Stat. Comput.",
year = 1992,
volume = 13,
pages = "631--644"
}
@Article{ eisenstat81,
author = "S. Eisenstat",
title = "Efficient Implementation of a Class of {CG} Methods",
journal = "SIAM J. Sci. Stat. Comput.",
year = 1981,
volume = 2,
pages = "1--4"
}
n
@Manual( ibm-essl,
Title = "{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2:
Guide and Reference",
Organization = "IBM",
Year = 1992,
Key = "IBM-ESSL"
)
@Manual( IBM-EUI,
Title = "{IBM} {AIX} Parallel Environment Parallel Programming Subroutine
Reference Release 2.0",
Organization = "IBM",
Month = JUN,
Year = 1994,
Key = "IBM-EUI"
)
@Manual( IBM-EUIH,
Title = "Using {EUIH}: An Experimental {EUI} Implementation",
Organization = "IBM",
Author = "Peter Hochschild",
Year = 1993,
Key = "IBM-EUIH"
)
@TechReport{ MPI,
Title = "Document for a Standard Message-Passing Interface",
Author = "Message Passing Interface Forum",
Institution = "University of Tennessee",
Number = "CS-93-214",
Month = NOV,
Year = 1993,
Key = "MPI Standard"
}
@Unpublished{ mpi-final-web,
author = "Message Passing Interface Forum",
title = "{MPI}: A Message-Passing Interface Standard",
note = "http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html",
year = 1994,
month = MAY
}
@Book{hockney-jesshope,
author = "R. W. Hockney and C. R. Jesshope",
title = "Parallel Computers 2",
publisher = "Adam Hilger",
year = "1988"
}
@Book{cm-fortran,
author = "{Thinking Machines Corporation}",
title = "Users Manual for CM-Fortran",
publisher = "Thinking Machines Corporation",
year = 1993
}
@TechReport{ Chang93,
Title = "Experiments and Bounds on Block Diagonal Preconditioning",
Author = "Mark Yan-Ming Chang and Martin H. Schultz",
Institution = "Yale Department of Computer Science",
Number = "YALEU/DCS/RR-994",
Month = NOV,
Year = 1993,
Key = "BDD|diag" }
@inproceedings{gropplevine93,
AUTHOR = "N. Galbreath and W. Gropp and D. Levine",
TITLE = "Applications-Driven Parallel {I/O}",
BOOKTITLE = "Proceedings of Supercomputing '93",
YEAR = "1993",
PAGES = "462--471"
}
@book{ Siegle85,
AUTHOR = "H. J. Siegel",
TITLE = "Interconnection Networks for Large Scale Parallel Processing",
PUBLISHER = "Lexington Books",
YEAR = 1985,
KEY = "Network Comparison"
}
@article{ Lawrie75,
AUTHOR = "D. H. Lawrie",
TITLE = "Access and alignment of data in an array processor",
JOURNAL = "IEEE Transactions on Computers",
VOLUME = "C-24",
NUMBER = 12,
MONTH = DEC,
YEAR = 1975,
PAGES = "1145--1155",
KEY = "Omega Network"
}
@book{ Lamport86,
AUTHOR = "Leslie Lamport",
TITLE = "{LaTeX}: A document preparation system",
PUBLISHER = "Addison-Wesley",
YEAR = 1986,
KEY = "Latex Manual"
}
@TechReport( tohtml,
Author= "William Gropp",
Title= "Users Manual for tohtml: Producing true hypertext
documents from {LaTeX}",
Institution= "Argonne National Laboratory",
Number= "ANL/MCS-TM-00",
Month= JAN,
Year= "1995",
Key= "tohtml" )
@TechReport( doctext,
Author= "William Gropp",
Title= "Users Manual for doctext:
Producing documentation from {C} source code",
Institution= "Argonne National Laboratory",
Number= "ANL/MCS-TM-00",
Month= JAN,
Year= "1995",
Key= "doctext" )
@TechReport( bfort,
Author= "William Gropp",
Title= "Users Manual for bfort:
Producing {F}ortran interfaces to {C} source code",
Institution= "Argonne National Laboratory",
Number= "ANL/MCS-TM-208",
Month= MAR,
Year= "1995",
Key= "doctext" )
@InProceedings{ gropp-lusk:unix-tools,
Author= "William Gropp and Ewing Lusk",
Title= "Scalable {U}nix Tools on Parallel Processors",
Booktitle= "Proceedings of the 1994 Scalable High Performanc Computing
Conference",
Publisher= "IEEE",
Pages = "56--62"
}
@inproceedings{jp:bell_prize,
AUTHOR = "Mark Jones and Paul Plassmann",
TITLE = "Solution of Large, Sparse Systems of Linear Equations
in Massively Parallel Applications",
booktitle = "Proceedings of Supercomputing '92",
publisher = "IEEE Computer Society Press",
YEAR = "1992",
Pages = "551--560"
}
@comment{WEB, CWEB references (for doctext)}
@TechReport{ web,
author = "Donald E. Knuth",
title = "The {\tt WEB} system of structured documentation",
institution = "Computer Science Department, Stanford University",
year = 1983,
number = 980,
month = SEP
}
@Article{ literatepgm,
author = "Donald E. Knuth",
title = "Literate Programming",
journal = "Computer Journal",
year = 1984,
volume = 27,
number = 2,
pages = "91--111"
}
@Unpublished{ cweb-code,
author = "Silvio Levy and Donald E. Knuth",
title = "CWEB",
note = "CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb"
}
@Article( componentware:94,
AUTHOR = "Jon Udell",
TITLE = "Componentware",
JOURNAL = "Byte",
VOLUME = "May",
PAGES = "46-56",
YEAR = 1994,
KEY = "Udell94 ! componentware"
)
@article{jp:scalable,
AUTHOR = "Mark Jones and Paul Plassmann",
TITLE = "Scalable Iterative Solution of Sparse Linear Systems",
Journal = "Parallel Computing",
Volume = "20",
Number = "5",
Month = "May",
YEAR = "1994",
Pages = "753--773"
}
@article{jp:pcolor,
AUTHOR = "Mark T. Jones and Paul E. Plassmann",
Title = "A Parallel Graph Coloring Heuristic",
journal = "SIAM J. Sci. Comput.",
Volume = "14",
Number = "3",
Pages = "654-669",
Year = "1993",
}
@TechReport( block_solve,
AUTHOR = "Mark T. Jones and Paul E. Plassmann",
TITLE = "{B}lock{S}olve v1.1: Scalable Library Software for
the Parallel Solution of Sparse Linear Systems",
INSTITUTION = "Argonne National Laboratory",
YEAR = 1992,
NUMBER = "ANL-92/46",
KEY = "JonesPlassmann92 ! block_solve"
)
@book{ optguide93,
TITLE = "Optimization Software Guide",
AUTHOR = "Jorge J. Mor\'{e} and Stephen J. Wright",
PUBLISHER = "SIAM Publications",
ADDRESS = "Philadelphia",
YEAR = 1993,
}
@inproceedings{ more84,
AUTHOR = "Jorge J. Mor\'{e} and Danny C. Sorenson and
Burton S. Garbow and Kenneth E. Hillstrom",
TITLE = "The {MINPACK} Project",
BOOKTITLE = "Sources and Development of Mathematical Software",
EDITOR = "Wayne R. Cowell",
YEAR = 1984,
PAGES = "88-111"
}
@inproceedings{ supercond,
AUTHOR = "Lois Curfman Mc{I}nnes and Mario Palumbo",
TITLE = "Parallel Solution of the Anisotropic
{G}inzburg-{L}andau Model",
BOOKTITLE = "Proceedings of the Toward Teraflop Computing and New
Grand Challenge Applications Conference",
MONTH = Feb,
YEAR = "1994",
KEY = "McInnesPalumbo94 ! superconductivity "
}
@Article( steihaug:83,
AUTHOR = "Trond Steihaug",
TITLE = "The Conjugate Gradient Method and Trust Regions in
Large Scale Optimization",
JOURNAL = "SIAM J. Numer. Anal.",
VOLUME = 20,
YEAR = 1983,
PAGES = "626-637",
KEY = "steihaug92 ! trust_region"
)
@Unpublished( preosti:93,
AUTHOR = "Gianfranco Preosti",
TITLE = " ",
NOTE = "Unpublished information, {P}hysics {D}epartment,
{P}urdue {U}niversity",
YEAR = 1993,
KEY = "preosti93 ! GL-tilt3d"
)
@Unpublished( more:93,
AUTHOR = "Jorge J. Mor\'{e}",
TITLE = " ",
NOTE = "Unpublished information, {M}athematics and
{C}omputer {S}cience {D}ivision,
{A}rgonne {N}ational {L}aboratory",
YEAR = 1993,
KEY = "more93 ! MINPACK-2"
)
@TechReport( minpack2test,
AUTHOR = "Brett M. Averick and Richard G. Carter and
Jorge J. Mor\'{e}",
TITLE = "The {MINPACK-2} Test Problem Collection",
INSTITUTION = "Argonne National Laboratory",
YEAR = 1991,
NUMBER = "ANL/MCS-TM-150",
KEY = "more91 ! MINPACK-2"
)
@TechReport{ hohmann:94,
AUTHOR = "Andreas Hohmann",
TITLE = "Object Oriented Design of Multilevel {N}ewton and
Continuation Methods",
INSTITUTION = "Konrad-Zuse-Zentrum fur Informationstechnik Berlin",
YEAR = 1994,
NUMBER = "SC-94-4",
KEY = "Hohmann94"
}
@TechReport{ meza:94,
AUTHOR = "Juan C. Meza",
TITLE = "{OPT}++: An Object-Oriented Class Library for
Nonlinear Optimization",
INSTITUTION = "Sandia National Laboratory",
YEAR = 1994,
NUMBER = "SAND94-8225",
KEY = "Meza94"
}
@book{dennis:83,
AUTHOR = "Dennis, Jr., J. E. and Robert B. Schnabel",
TITLE = "Numerical Methods for Unconstrained Optimization and
Nonlinear Equations",
PUBLISHER = "Prentice-Hall",
ADDRESS = "Englewood Cliffs, NJ",
YEAR = 1983}
}
@TechReport{ more:92,
AUTHOR = "Jorge J. Mor\'{e} and David Thuente",
TITLE = "Line search algorithms with guaranteed sufficient decrease",
INSTITUTION = "Mathematics and Computer Science Division, Argonne National Laboratory",
YEAR = 1992,
NUMBER = "MCS-P330-1092",
}
@Article{ brownsaad:90,
author = "Peter N. Brown and Youcef Saad",
title = "Hybrid {K}rylov Methods for Nonlinear Systems of Equations",
journal = "SIAM J. Sci. Stat. Comput.",
year = 1990,
volume = 11,
pages = "450-481"
}
@Book{using-mpi,
author = "William Gropp and Ewing Lusk and Anthony Skjellum",
title = "Using MPI: Portable Parallel Programming with the Message
Passing Interface",
publisher = "MIT Press",
year = 1994
}
@Book{using-mpi2,
author = "William Gropp and Ewing Lusk and Rajeev Thakur",
title = "Using MPI 2: Advanced Features of the Message Passing Interface",
publisher = "MIT Press",
year = 1999
}
@article{hs:52,
author="Magnus R. Hestenes and Eduard Steifel",
title="Methods of Conjugate Gradients for Solving Linear Systems",
journal="J. Research of the National Bureau of Standards",
year=1952,
volume=49,
pages="409-436"}
@article{ss:86,
author="Youcef Saad and Martin H. Schultz",
title="{GMRES}: A Generalized Minimal Residual Algorithm
for Solving Nonsymmetric Linear Systems",
journal = "SIAM J. Sci. Stat. Comput.",
year=1986,
volume=7,
pages="856-869"}
@article{so:89,
author="Peter Sonneveld",
title="{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear
Systems",
journal = "SIAM J. Sci. Stat. Comput.",
year=1989,
volume=10,
pages="36-52"}
@article{v:92,
author="{H. A.} {van der Vorst}",
title="{B}i{CGSTAB}: A fast and smoothly converging variant
of {B}i{CG} for the solution of nonsymmetric linear
systems",
journal = "SIAM J. Sci. Stat. Comput.",
volume=13,
year=1992,
pages="631-644"}
@article{f:93,
author="Roland W. Freund",
title="A Transpose-Free Quasi-Minimal Residual Algorithm for
Non-{H}ermitian Linear Systems",
journal = "SIAM J. Sci. Stat. Comput.",
volume=14,
year=1993,
pages="470-482"}
@article{ish:89,
author="S. Ishizuka",
title="An Experimental Study on Extinction and
Stablity of Tubular Flames",
journal="Combustion and Flame",
volume=75,
year=1989,
pages="367-379"}
@book{williams89,
TITLE = "Combustion Theory, The
Fundamental Theory of Chemically Reacting Flow Systems",
AUTHOR= "F.A. Williams",
PUBLISHER = "Addison-Wesley",
YEAR = 1989,
pages = "367-379"}
@book{RA75,
author = {R. Aris},
title = {The Mathematical Theory of Diffusion and
Reaction in Permeable Catalysts},
publisher = {Oxford},
year = {1975}
}
@book{Bebernes89,
author = {J. Bebernes and D. Eberly},
title = {Mathematical Problems from Combustion Theory},
publisher = {Springer-Verlag},
series = {Applied Mathematical Sciences 83},
year = {1989}
}
@inproceedings{Kikuchi89,
author = {F. Kikuchi},
booktitle = { Computing Methods in Applied Sciences and Engineering},
editor = {R. Glowinski and J. L. Lions},
publisher = {Springer-Verlag},
series = {Lecture Notes in Mathematics},
title = {Finite element approximations to bifurcation
problems of turning point type},
year = {1977}
}
@article{RG85,
author="R. Glowinski and H.B. Keller and L. Reinhart",
title="Continuation-conjugate Gradient Methods fo the Least Squares
Solution of Nonlinear Boundary Problems",
journal = "SIAM J. Sci. Stat. Comput.",
volume=6,
year=1985,
pages="793-832"}
@InProceedings{whitfield91,
author = "D. Whitfield and L. Taylor",
title = "Discretized {N}ewton-Relaxation Solution of High
Resolution Flux-Difference Split Schemes",
booktitle = "Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference",
misc = "AIAA-91-1539",
pages = "134-145",
year = 1991,
}
@INPROCEEDINGS{Quinlan1,
AUTHOR= "M. Lemke and D. Quinlan",
TITLE= "P++, a {C}++ Virtual Shared Grids Based Programming
Environment for Architecture-Independent Development of
Structured Grid Applications",
BOOKTITLE= "CONPAR/VAPP V, Lecture Notes in Computer Science",
PUBLISHER= "Springer Verlag",
YEAR= "1992"
}
@INPROCEEDINGS{Quinlan2,
AUTHOR= "R. Parsons and D. Quinlan",
TITLE= "A++/{P}++ Array Classes for Architecture Independent Finite
Difference Computations",
BOOKTITLE= "Proceedings of the Second Annual Object-Oriented Numerics
Conference",
YEAR= "1994"
}
% ***** Overview of functionality in Diffpack
@inbook{DPoverview,
author = "Bruaset, A. M. and Langtangen, H. P.",
booktitle = "Mathematical Models and Software Tools in Industrial
Mathematics",
title = "A Comprehensive Set of Tools for Solving Partial Differential
Equations; {Diffpack}",
publisher = "Birkh{\"{a}}user",
pages = "61--90",
year = 1997}
% ***** Short overview of Diffpack
@incollection{DPoverview2,
author = "Bruaset, A. M. and Langtangen, H. P.",
editor = "A. Sydow",
booktitle = "Proceedings of the 15th IMACS World Congress
on Scientific Computation, Modelling and Applied Mathematics",
title = "Diffpack: A Software Environment for Rapid Prototyping of
{PDE} Solvers",
pages = "553--558",
volume = 4,
year = 1997}
% ***** Comprehensive documentation of Diffpack and
% associated numerical methods:
@Book{DPbook,
author = "H. P. Langtangen",
title = "Numerical Solution of Partial Differential Equations;
Models, Algorithms and Software. Part I",
series = "Lecture Notes in Computational Science and Engineering",
publisher = "Springer-Verlag",
year = "1998"
}
% ***** Design issues of the linear solvers in Diffpack, serves also as a
% collection of examples on O-O in numerical computing
@article{AmbHpl97a,
author = "A. M. Bruaset and H. P. Langtangen ",
title = "Object-Oriented Design of Preconditioned Iterative
Methods in {Diffpack}",
journal = "Transactions on Mathematical Software",
volume = {23 },
pages = "50--80",
year = {1997}
}
@misc{DPURL,
author = "{Diffpack Web page}",
howpublished = "\url{http://www.diffpack.com}"
}
% ***** General intro to object-oriented numerics for "FORTRAN programmers"
@incollection{OONintro,
author = "Arge, E. and Bruaset, A. M. and H. P. Langtangen",
editor = "D{\ae}hlen, M. and Tveito, A.",
booktitle = "Mathematical Models and Software Tools in Industrial Mathematics",
title = "Object-Oriented Numerics",
publisher = "Birkh{\"{a}}user",
year = 1997}
% ***** Efficiency comparison: BLAS 1, Diffpack, C,
% and finite element applications (F77 vs Diffpack)
@incollection{DPefficiency,
author = "Arge, E. and Bruaset, A. M. and Calvin, P. B. and
Kanney, J. F. and Langtangen, H. P. and Miller, C. T.",
editor = "D{\ae}hlen, M. and Tveito, A.",
booktitle = "Mathematical Models and Software Tools in Industrial
Mathematics",
title = "On the Efficiency of {C++} in Scientific Computing",
publisher = "Birkh{\"{a}}user",
pages = "91--118",
year = 1997}
% ***** Parallel concept in Diffpack:
@incollection{DPparallel,
author = "A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito",
editor = "Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn",
booktitle = "Scientific Computing in Object-Oriented Parallel Environments",
title = "Numerical Solution of {PDE}s on Parallel Computers Utilizing
Sequential Simulators",
publisher = "Springer--Verlag",
series = "Lecture Notes in Computer Science",
pages = "161--168",
year = 1997}
% ***** DD and ML methods in Diffpack:
@incollection{DPDDML,
author = "A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch",
editor = "P. Bj{\o}rstad and M. Espedal and D. Keyes",
booktitle = "Proceedings of the 9th Conference on Domain
Decomposition",
title = "Domain decomposition and multilevel methods in Diffpack",
year = 1997}
@inproceedings{bsca98,
author= "David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David Alexander",
title= "Design and Implementation of an Object Oriented C++ Library for Nonlinear Optimization",
booktitle= "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
editor= "Mike Henderson et al.",
pages= "165-173",
year= "1998"
}
@BOOK{scalapack-user-guide,
AUTHOR = "L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and
J. Demmel and I. Dhillon and J. Dongarra and S. Hammarling and
G. Henry and A. Petitet and K. Stanley and D. Walker and R. C. Whaley",
TITLE = "Sca{LAPACK} Users' Guide",
PUBLISHER = "SIAM",
ADDRESS = "Philadelphia, PA",
YEAR = 1997
}
@INPROCEEDINGS{KEYES99,
AUTHOR = "D. E. Keyes",
TITLE = "How Scalable is Domain Decomposition in Practice?",
BOOKTITLE = "Proceedings of the 11th International Conference on
Domain Decomposition Methods",
EDITOR = "C.-H. Lai et al.",
PUBLISHER = "Domain Decomposition Press, Bergen",
NOTE = "To appear",
YEAR = "1999" }
@article{fun3d,
author="W. K. Anderson and D. L. Bonhaus",
title="An implicit upwind algorithm for computing turbulent flows on unstructured grids",
journal="Computers and Fluids",
year=1994,
volume=23,
pages="1--21"
}
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
@Article(torczon,
Author= "Dennis, Jr., J. E. and V.~Torczon",
Title= "Direct Search Methods on Parallel Machines",
Journal= "SIAM J. Optimization",
Volume= 1,
Pages= "448--474",
Year= 1991,
Key= "Torczon !PDS")
@InProceedings{WT91,
author = "D. L. Whitfield and L. K. Taylor",
title = "Discretized {N}ewton-Relaxation Solution of High
Resolution Flux-Difference Split Schemes",
booktitle = "Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference",
misc = "AIAA-91-1539",
pages = "134-145",
year = 1991,
}
@article{EW96,
author="S. C. Eisenstat and H. F. Walker",
title="Choosing the forcing terms in an inexact {N}ewton method",
journal="SIAM J. Scientific Computing",
volume=17,
year=1996,
pages="16--32"
}
@Book{thi93,
author = "{Thinking Machines Corporation}",
title = "Users Manual for CM-Fortran",
publisher = "Thinking Machines Corporation",
year = 1993
}
@Book{mortonmayers94,
author = "K. W. Morton and D. F. Mayers",
title = "Numerical Solution of Partial Differential Equations",
publisher = "Press Syndicate of the University of Cambridge",
year = 1994
}
@Book{heath97,
author = "Michael T. Heath",
title = "Scientific Computing: An Introductory Survey",
publisher = "McGraw Hill",
year = 1997
}
@Article{captools96,
author = "C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett",
title = "Computer Aided Parallelization Tools ({CAPTools}) - Conceptual
Overview and Performance on the Parallelization of Structured Mesh Codes",
journal = "Parallel Computing",
volume = 22,
pages = "197-226",
year = 1996
}
@Unpublished{ nastran-web-page,
Author = "{MSC Software Corporation}",
title = "{NASTRAN} {W}eb page",
note = "See {\tt http://www.mechsolutions.com\-/products\-/nastran/}"
}
@Book{hpf,
author = "C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. Zosel",
title = "The High Performance Fotran Handbook",
publisher = "MIT Press",
year = "1994"
}
@inproceedings{keyes98,
AUTHOR = "D. E. Keyes",
TITLE = "Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed Architectures",
BOOKTITLE = "Proceedings of the Workshop on Computational Aerosciences for the 21st Century",
EDITORS = "M. D. Salas and W. K. Anderson",
PPUBLISHER = "Elsevier",
YEAR = "1998"
}
@inproceedings{cca99,
AUTHOR = "R. Armstrong and D. Gannon and A. Geist and K. Keahey and
S. Kohn and L. C. McInnes and S. Parker and B. Smolinski",
TITLE = "Toward a Common Component Architecture for High-Performance
Scientific Computing",
BOOKTITLE = "Proceedings of {High Performance Distributed Computing}",
pages = "115--124",
YEAR = "1999",
}
@inproceedings{pooma-atlas,
author = "S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and
M. Srikant and J. V. W. Reynders and M. Tholburn",
title = "{POOMA}: A High-Performance Distributed Simulation Environment for
Scientific Applications",
year = 1995,
month = "December",
Booktitle = "Supercomputing '95 Proceedings",
}
% ---------------------------------------------------------------------------------
% New bib entries for CRPC paper
@misc {
mgnet-web-page,
author = "Craig C. Douglas",
title = "{MGNet Web page}",
note = "See {\tt http://\-www.mgnet.org}"
}
@misc {
dagh-web-page,
author = "M. Parashar and J. C. Browne",
title = "{DAGH Web page}",
note = "\url{http://www.caip.rutgers.edu/~parashar/DAGH}"
}
@misc {
parasol-web-page,
key = "PARASOL",
title = "{PARASOL Web page}",
note = "See {\tt http://\-www.genias.de/\-projects/\-parasol}"
}
@misc {
pooma-web-page,
author = "{POOMA Web page}",
note = "See {\tt http://\-www.acl.lanl.gov/pooma}"
}
@misc {
mudpack-web-page,
author = "John C. Adams",
title = "{MUDPACK Web page}",
note = "See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}"
}
@misc {
pellpack-web-page,
author = "Elias Houstis and John Rice and Apostolos Hadjidimos",
title = "{Parallel ELLPACK Web page}",
note = "See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}"
}
@inproceedings{pellpack95,
AUTHOR = "E. N. Houstis and S. B. Kim and S. Markus and P. Wu and
N. E. Houstis and A.C. Catlin and S. Weerawarana and T.S. Papatheodorou",
TITLE = "Parallel {ELLPACK} Elliptic {PDE} Solvers",
BOOKTITLE = "Proceedings of INTEL Supercomputer User's Group Conference",
ADDRESS = "Albuquerque, NM",
YEAR = "1995",
}
@misc {
nhse-web-page,
author = "{National High-Performance Software Exchange Web page}",
note = "See {\tt http://\-www.nhse.org}"
}
@misc {
doug-web-page,
author = "Mark J. Hagger and Linda Stals",
title = "{DOUG Web Page}",
note = "See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}"
}
@TECHREPORT{doug97,
AUTHOR="Mark J. Hagger",
TITLE="Automatic Domain Decomposition on Unstructured Grids {(DOUG)}",
INSTITUTION="Mathematical Sciences, University of Bath",
YEAR="1997",
NUMBER="9706",
NOTE= "Advances in Computational Mathematics (to appear)"
}
@misc {
ug-web-page,
author = "{UG Web Page}",
note = "See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}"
}
@Article{ug97,
author = "P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and
H. Rentz-Reichert and C. Wieners",
title = "{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations",
journal = "Computing and Visualization in Science",
year = "1997",
volume = "",
pages = ""
}
@misc {
vecfem-web-page,
author = "Lutz Grosz",
title = "{VECFEM Web Page}",
note = "See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}"
}
@misc{atlas-web-page,
author = {R. Clint {Whaley et al.}},
title = {{ATLAS Web Page}},
howpublished = {\url{http://math-atlas.sourceforge.net}}
}
@misc {fenics-web-page,
author = "Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott",
title = "{FEniCS Web Page}",
note = "\url{http://www.fenicsproject.org}",
year = "2005"
}
@misc{matlab-web-page,
author = {{The} {MathWorks}},
title = {Matlab},
note = {\url{http://www.mathworks.com}}
}
@misc {
phipac-web-page,
author = "J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and
J. Demmel and C. Chin and D. Lam",
title = "{PHiPAC Web Page}",
note = "See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}"
}
@inproceedings{kelp,
Author = "Stephan J. Fink and Scott B. Baden and Scott R. Kohn",
title = "Flexible Communication Mechanisms for Dynamic Structured Applications",
BOOKTITLE = "Irregular '96",
YEAR = "1996"
}
@Unpublished{ kelp-web-page,
author = "Scott Baden",
title = "{KeLP} {W}eb page",
note = "See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}",
}
@inproceedings {
hk99,
author = "R. Hornung and S. Kohn",
title = "The Use of Object-Oriented Design Patterns in the {SAMRAI}
Structured {AMR} Framework",
booktitle = "Proceedings of the SIAM Workshop on Object-Oriented Methods
for Inter-Operable Scientific and Engineering Computing",
pages = "235-244",
year = 1999,
note = "See \url{http://www.llnl.gov/CASC/samrai}"
}
@Unpublished{samrai-web-page,
title = "{SAMRAI} {W}eb Page",
author = "Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith",
note = "See {\tt http://www.llnl.gov/\-CASC/SAMRAI}",
}
@Misc{overture-web-page,
author = "William Henshaw and Kyle Chand",
title = "{Overture} {W}eb page",
howpublished = "\url{http://www.llnl.gov/CASC/Overture}"
}
@INPROCEEDINGS{ overture99,
AUTHOR= "D.L. Brown and W.D. Henshaw and D.J. Quinlan",
TITLE= "Overture: An Object-Oriented Framework for Solving Partial Differential Equations
on Overlapping Grids",
PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
year = 1999,
pages = "215-224",
note = "See \url{http://www.llnl.gov/CASC/Overture}"
}
@inProceedings{diffpack,
Author = "A.M. Bruaset and H.P. Langtangen",
Title = "A Comprehensive Set of Tools for Solving Partial
Differential Equations: {D}iffpack",
BOOKTITLE = "Numerical Methods and Software Tools in Industrial Mathematics",
Year = 1997,
pages = "61--90",
Publisher = "Birkhauser Press"}
@Article{Dongarra:1984:ILA,
author = "J. J. Dongarra and F. G. Gustavson and A. Karp",
title = "Implementing Linear Algebra Algorithms for Dense
Matrices on a Vector Pipeline Machine",
journal = "SIAM Review",
volume = "26",
number = "1",
pages = "91--112",
month = jan,
year = "1984",
coden = "SIREAD",
ISSN = "0036-1445 (print), 1095-7200 (electronic)",
mrclass = "65F10 (65F30)",
mrnumber = "85c:65032",
bibdate = "Mon Jan 20 1997",
abstract = "The authors examine common implementations of linear
algebra algorithms, such as matrix-vector
multiplication, matrix-matrix multiplication and the
solution of linear equations. The different versions
are examined for efficiency on a computer architecture
which uses vector processing and has pipelined
instruction execution. By using the advanced
architectural features of such machines, one can
usually achieve maximum performance, and tremendous
improvements in terms of execution speed can be seen
over conventional computers.",
acknowledgement = ack-nhfb,
classification = "723; 921",
journalabr = "SIAM Rev",
keywords = "computer programming --- Algorithms; dense matrices;
linear algebra algorithms; mathematical programming;
vector pipeline machine",
}
@BOOK{qv99,
AUTHOR = "Alfio Quarteroni and Alberto Valli",
TITLE = "Domain Decomposition Methods for Partial Differential Equations",
PUBLISHER = "Oxford Science Publications",
address = "Oxford",
YEAR = 1999
}
@BOOK{ksv97,
EDITOR = "David E. Keyes and Ahmed Sameh and V. Venkatakrishnan",
TITLE = "Parallel Numerical Algorithms",
PUBLISHER = "Kluwer Academic Publishers",
address = "the Netherlands",
YEAR = 1997
}
@BOOK{hackbusch94,
AUTHOR = "Wolfgang Hackbusch",
TITLE = "Iterative Solution of Large Sparse Systems of Equations",
PUBLISHER = "Springer-Verlag",
address = "New York",
YEAR = 1994
}
@article{hackbusch1980fast,
title={Fast solution of elliptic control problems},
author={Hackbusch, W.},
journal={Journal of Optimization Theory and Applications},
volume={31},
number={4},
pages={565--581},
year={1980},
publisher={Springer}
}
@book{hackbusch1985multi,
title={{Multi-grid methods and applications}},
author={Hackbusch, W.},
isbn={3540127615},
issn={0179-3632},
year={1985},
publisher={Springer Verlag}
}
@BOOK{axelsson94,
AUTHOR = "Owe Axelsson",
TITLE = "Iterative Solution Methods",
PUBLISHER = "Cambridge University Press",
address = "Cambridge",
YEAR = 1994
}
@BOOK{saad96,
AUTHOR = "Yousef Saad",
TITLE = "Iterative Methods for Sparse Linear Systems",
PUBLISHER = "PWS Publishing Company",
address = "Boston",
YEAR = 1996
}
@book(saad2003,
author="Yousef Saad",
title={Iterative Methods for Sparse Linear Systems, 2nd edition},
Publisher="SIAM", address="Philadelpha, PA",
year="2003"
)
@book{vandervorst03,
author = "Henk A. {van der Vorst}",
title = "Iterative Krylov Methods for Large Linear Systems",
publisher = "Cambridge Monographs on Applied ahd Computational Mathematics",
year = 2003
}
@BOOK{koniges00,
EDITOR = "Alice E. Koniges",
TITLE = "Industrial Strength Parallel Computing",
PUBLISHER = "Morgan Kaufmann Publishers",
address = "San Francisco",
YEAR = 2000
}
@Misc{fftw-web-page,
key = {Fftw},
title = {{FFTW} {Web} page},
note = {\texttt{http://www.fftw.org/}},
annote = {fast FFT. Parallel versions with MPI and Cilk}
}
@inproceedings{FrigoJohnson93,
author = {Matteo Frigo and Steven G. Johnson},
title = {The Design and Implementation of {FFTW3}},
booktitle = {Proceedings of the IEEE},
volume = {93},
number = {2},
pages = {216--231},
year = {2005}
}
@BOOK{Kelley95,
AUTHOR="C. T. Kelley",
TITLE="Iterative Methods for Linear and Nonlinear Equations",
YEAR="1995",
PUBLISHER="SIAM",
address="Philadelphia"
}
@BOOK{NW99,
AUTHOR="Jorge Nocedal and Stephen J. Wright",
TITLE="Numerical Optimization",
YEAR="1999",
PUBLISHER="Springer-Verlag",
address="New York"
}
@book{szyperski98,
AUTHOR = "Clemens Szyperski",
TITLE = "Component Software: Beyond Object-Oriented Programming",
PUBLISHER = "ACM Press",
address = "New York",
YEAR = 1998
}
@article{broy98,
Author = "Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and
Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael Stal
and Clemens Szyperski",
Title = "What Characterizes a (Software) Component?" ,
Journal = "Software -- Concepts and Tools",
Publisher = "Springer-Verlag",
Year= 1998,
volume = 19,
pages = "49-56"
}
@Unpublished{spai-web-page,
title = "{SPAI} {W}eb {P}age",
note = "http://www.sam.math.ethz.ch/\~{ }grote/spai/",
author = "Steven Bernard and Marcus Grote",
institution = "NASA Ames Research Center and ETH Zurich"
}
@article( gh97,
Author = "M. J. Grote and T. Huckle",
Title = "Parallel Preconditioning with Sparse Approximate Inverses",
Year = 1997,
Journal = "SIAM J. of Scient. Comput.",
Volume = 18,
pages = "838-853"
)
@article( zhang96,
Author = "Wen Zhang",
Title = "Using {MOL} to Solve a high order nonlinear {PDE} with a moving
boundary in the simulation of a sintering process",
Year = 1996,
Journal = "Appl. Numer. Math.",
Volume = 20,
pages = "235-244",
)
@article( zhang98,
Author = "Wen Zhang and Ian Gladwell",
Title = "The sintering of two particles by surface and grain boundary
diffusion - a three-dimensional numerical study",
Journal = "Comp. Mater. Sci.",
year = 1998,
volume = 12
)
@inproceedings{MollerSchwartzbach01,
AUTHOR = "Anders M\o{}ller and Michael I. Schwartzbach",
TITLE = "The Pointer Assertion Logic Engine",
BOOKTITLE = "ACM Proceedings of PLDI'01",
YEAR = "2001",
}
@inproceedings{KlarlandSchwartzbach97,
AUTHOR = "Nils Klarland and Michael I. Schwartzbach",
TITLE = "A Domain-Specific Languages for Regular Sets of Strings and Trees",
BOOKTITLE = "Proceedings of the Conference on Domain-Specific Languages",
PUBLISHER = "USENIX",
MONTH = "October",
YEAR = "1997",
ADDRESS = "Santa Barbara, CA",
}
@inproceedings{ConselMarlet98,
AUTHOR = "C. Consel and R. Marlet",
TITLE = "Architecturing software using a methodology for language development",
BOOKTITLE = "Proceedings of the 10th International Symposium on Programming Languages, Implementations, Logics and Programs",
YEAR = "1998",
PAGES = "170-174",
MONTH = "September",
ADDRESS = "Pisa, Italy",
}
@misc{sundials:homepage,
author = "C. {Woodward et al.}",
title = "{SUNDIALS {W}eb page}",
howpublished = "\url{https://computation.llnl.gov/casc/sundials/main.html}"
}
@misc{sundials-user-ref,
title = "{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers",
note = "See \url{http://www.llnl.gov/CASC/sundials}",
author = "Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban and Dan Shumaker and Carol Woodward",
institution = "Center for Applied Scientific Computing, Lawrence Livermore National Laboratory",
number = "UCRL-JP-200037",
year = 2003
}
@article{sundials05,
author = "A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker and C. Woodward",
title = "{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers",
journal = "ACM Transactions on Mathematical Software",
volume = 31,
number = 3,
pages = "363--396",
year = 2005
}
@article{pvode99,
author = "G. Byrne and A. Hindmarsh",
title = "{PVODE}, An {ODE} Solver for Parallel Computers",
journal = "Int. J. High Perf. Comput. Apps.",
volume = 13,
number = 4,
year = 1999,
pages = "354 -- 365"
}
@article{cvode95,
author = "S. Cohen and A. Hindmarsh",
title = "{CVODE}, A Stiff/Nonstiff {ODE} Solver in {C}",
journal = "Computers in Physics",
volume = 10,
number = 2,
year = 1996,
pages = "138 -- 143"
}
@techreport{ifpack,
title = "Robust Algebraic Preconditioners using {IFPACK} 3.0",
author = "Marzio Sala and Michael Heroux",
institution = "Sandia National Laboratories",
number = "SAND2005-0662",
year = "2005"
}
@techreport{kinsol-user-ref,
title = "User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel Computers",
author = "Allan Taylor and Alan Hindmarsh",
institution = "Center for Applied Scientific Computing, Lawrence Livermore National Laboratory",
number = "UCRL-ID-131185",
year = 1998
}
@article{FiardManteuffelMcCormick98,
author = "J.-M. Fiard and T. Manteuffel and S. McCormick",
title = "First-order system least squares {(FOSLS)} for convection-diffusion problems: numerical results",
journal = "SIAM J. Sci. Comp.",
year = 1998,
volume = 19,
pages = {1958--1979}
}
@inproceedings{Vuduc02,
AUTHOR = "Richard Vuduc and James W. Demmel and Katherine A. Yelick and Shoaib Kamil and Rajesh Nishtala and Benjamin Lee",
TITLE = "Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply",
BOOKTITLE = "Proceedings of Supercomputing",
YEAR = "2002",
MONTH = "November",
ADDRESS = "Baltimore"
}
@article{BeckerRannacher01,
author = "R. Becker and R. Rannacher",
title = "An optimal control approach to a posteriori error estimation in finite element methods",
journal = "Acta Numerica",
year = "2001",
volume = "10",
pages = {1--102}
}
@article{BabuskaMiller84a,
author = "I. Babu$\check{s}$ka and A.D. Miller",
title = "The post-processing approach in the finite element method, {I}: Calculations of displacements, stresses, and
other higher derivatives of the displacements",
journal = "Int. J. Numer. Meth. Eng.",
year = "1984",
volume = "20",
pages = {1085--1109}
}
@article{BabuskaMiller84b,
author = "I. Babu$\check{s}$ka and A.D. Miller",
title = "The post-processing approach in the finite element method, {II}: The calculation of stress intensity
factors",
journal = "Int. J. Numer. Meth. Eng.",
year = "1984",
volume = "20",
pages = {1111--1129}
}
@article{BabuskaMiller84c,
author = "I. Babu$\check{s}$ka and A.D. Miller",
title = "The post-processing approach in the finite element method, {III}: A posteriori error estimation and adaptive
mesh refinement",
journal = "Int. J. Numer. Meth. Eng.",
year = "1984",
volume = "20",
pages = {2311--2324}
}
@unpublished{jtb-web-page,
title = "{The Java Tree Builder}",
note = "See \url{http://www.cs.purdue.edu/jtb}",
author = "Jens Palsberg",
institution = "Purdue University"
}
@unpublished{Palsberg98,
title = "Why Visitors?",
note = "See \url{http://www.cs.purdue.edu/jtb/whyvisitors}",
author = "Jens Palsberg",
institution = "Purdue University",
year = "1998"
}
@unpublished{ply-web-page,
title = "{PLY (Python Lex-Yacc)}",
note = "\url{http://systems.cs.chicago.edu/ply}",
author = "David Beazley",
institution = "University of Chicago"
}
@misc{adic-web-page,
title = "{ADIC Web page}",
note = "\url{http://www.mcs.anl.gov/autodiff}",
author = "Paul Hovland and Uwe Naumann and Boyana Norris",
institution = "Argonne National Laboratory"
}
@article{Naumann02,
author = "Uwe Naumann",
title = "Optimal accumulation of {J}acobian matrices by elimination methods on the dual computational graph",
journal = "Mathematical Programming (to appear)",
note = "Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002",
year = "2003"
}
@article{kaper1,
author = "H. G. Kaper and T. J. Kaper",
title = "Asymptotic Analysis of Two Reduction Methods for Systems of Chemical Reactions",
journal = "Physica D",
year = "2002",
pages = "66--93",
volume = "165"
}
@Misc{ matlab-web-page,
author = "",
title = "{Matlab Web page}",
howpublished = "\url{http://www.mathworks.com}",
key = "{Matlab} {Web} page"
}
@misc{ veltisto-web-page,
author = "George Biros",
title = "{Veltisto Web page}",
note = "\url{http://www.cs.nyu.edu/~biros/veltisto}",
}
@article{KarypisKumar98,
author = "George Karypis and Vipin Kumar",
title = "A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering",
journal = "Journal of Parallel and Distributed Computing",
volume = "48",
pages = "71--85",
year = "1998"
}
@techreport{KarypisKumar97,
Author = {Karypis, George and Kumar, V.},
Institution = {Department of Computer Science, University of Minnesota},
Keywords = {graph partitioning; ParMetis},
Note = {http://www.cs.umn.edu/~metis},
Number = {97-060},
Title = {{ParMETIS}: Parallel graph partitioning and sparse matrix ordering library},
Year = {1997}
}
@misc{ parmetis-web-page,
author = "George {Karypis et al.}",
title = "{ParMETIS Web page}",
note = "\url{http://www.cs.umn.edu/~karypis/metis/parmetis}",
year = "2005"
}
@misc{ sparskit-web-page,
author = "Yousef {Saad et al.}",
title = "{SPARSKIT Web page}",
note = "\url{http://www.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html}",
}
@misc{ dscpack-web-page,
author = "Padma Raghavan",
title = "{DSCPACK Web page}",
note = "\url{http://www.cse.psu.edu/~raghavan/Dscpack}"
}
@Misc{ gaussian-web-page,
author = "",
title = "{Gaussian Web page}",
note = "\url{http://gaussian.com}",
key = "{Gaussian} {Web} page",
}
@Book{lapack-user-guide,
author = "E. Anderson and Z. Bai and C. Bischof and S. Blackford and J. Demmel and
J. Dongarra and J. Du Cris and A. Greenbaum and S. Hammarling and
A. McKenney and D. Sorensen",
title = "LAPACK Users' Guide, Third Edition",
publisher = "SIAM",
year = "1999"
}
@Manual{ nwchem4.1,
author = {High Performance Computational Chemistry Group},
title = {{NWChem}, A Computational Chemistry Package for Parallel
Computers, Version 4.1},
year = 2002,
organization = {Pacific Northwest National Laboratory},
address = {Richland, Washington 99325-0999 USA},
note = {See \url{http://www.emsl.pnl.gov/pub/docs/nwchem/}},
}
@TechReport{tchem,
title={{TC}hem: {A} Software Toolkit for the Analysis of Complex Kinetic Models},
author={Cosmin Safta and Habib Najm and Omar Knio},
institution = {Sandia National Laboratories},
number = {SAND2011-3282},
year=2011,
}
@Misc{ scidac-web-page,
author = "",
title = "{{SciDAC Initiative Web page}}",
note = "\url{http://www.osti.gov/scidac}",
key = "{SciDAC Initiative Web page}"
}
@Misc{cmrs:homepage,
author = {Amitava {Bhattacharjee (PI)}},
title = {{Center for Magnetic Reconnection Studies}},
howpublished = {\url{http://www.physics.uiowa.edu/cmrs}}
}
@Misc{tops:homepage,
author = {David {Keyes (PI)}},
title = {{Towards Optimal Petascale Simulations (TOPS) Center}},
howpublished = {\url{http://scalablesolvers.org}}
}
@Misc{tstt:homepage,
author = {David Brown and Jim Glimm and Lori Freitag},
title = {{Terascale Simulation Tools and Technology (TSTT) Center}},
howpublished = {\url{http://www.tstt-scidac.org}},
year = {2005}
}
@Misc{petsc:applications,
author = {B. F. {Smith et al.}},
title = {{Scientific Applications Using {PETSc}}},
howpublished = {\url{http://www.mcs.anl.gov/petsc/publications}}
}
@Misc{petsc:users,
author = {B. F. {Smith et al.}},
title = {{PETSc User Statistics}},
howpublished = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/usage.html}}
}
@Misc{cemm:homepage,
author = {Steve {Jardin (PI)}},
title = {{Center for Extended MHD Modeling}},
howpublished = {\url{http://w3.pppl.gov/CEMM}}
}
@Misc{m3d:homepage,
author = {Steve {Jardin et al.}},
title = {{M3D Web page}},
howpublished = {\url{http://w3.pppl.gov/m3d}}
}
@Misc{nimrod:homepage,
author = {Carl R. {Sovinec et al.}},
title = {{NIMROD Web page}},
howpublished = {http://nimrodteam.org}
}
@misc{grace-web-page,
author = "Manish {Parashar et al.}",
title = "{GrACE Web Page}",
howpublished = "\url{http://www.caip.rutgers.edu/~parashar/TASSL/Projects/GrACE}",
}
@misc{accel1,
title = "Advanced Computing for 21st Century Accelerator Science and Technology Web page",
howpublished = "\url{http://scidac.nersc.gov/accelerator/}",
author = "K. Ko and R. Ryne (PIs)"
}
@unpublished{KatzSpiegelman03,
author = "Richard F. Katz and Marc Spiegelman",
title = "A semi-{L}agrangian {C}rank-{N}icholson algorithm for the numerical solution of advection-diffusion problems",
note = "Columbia University, in preparation",
}
@misc{acts:homepage,
author = "",
title = "{Advanced CompuTational Software (ACTS) Web page}",
howpublished = "\url{http://acts.nersc.gov}",
key = "{Advanced CompuTational Software (ACTS) Web page}",
}
@article{superlu99,
author = {James W. Demmel and Stanley C. Eisenstat and John R. Gilbert and Xiaoye S. Li and Joseph W. H. Liu},
title = {A supernodal approach to sparse partial pivoting},
journal = {SIAM J. Matrix Analysis and Applications},
year = {1999},
volume = {20},
number = {3},
pages = {720-755}
}
@misc{superlu:homepage,
author = "J. Demmel and J. Gilbert and X. Li",
title = "{SuperLU Web page}",
howpublished = "http://crd.lbl.gov/\~xiaoye/SuperLU"
}
@inproceedings{ccf98,
author= "E. Chow and A. Cleary and R. Falgout",
title= "Design of the hypre Preconditioner Library",
booktitle = "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
publisher = "SIAM",
year= 1999,
}
@TechReport{hypre-users-manual,
author = "R. Falgout",
title = "{hypre} Users Manual",
number = "Revision 2.0.0",
institution = "Lawrence Livermore National Laboratory",
year = 2006
}
@misc{hypre:homepage,
author = "R. Falgout",
title = "{hypre Web page}",
howpublished = "\url{http://www.llnl.gov/CASC/hypre}"
}
@InProceedings{trilinos:gpu,
author = {C.G. Baker and M.A. Heroux. and H.C. Edwards and A.B. Williams},
title = {A Light-weight API for Portable Multicore Programming},
booktitle = {18th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)},
pages = {601--606},
publisher = {IEEE},
year = {2010}
}
@misc{trilinos:homepage,
author = "M. {Heroux et al.}",
title = "{Trilinos Web page}",
howpublished = "{\tt http://trilinos.sandia.gov/}"
}
@article{trilinos:overview,
author = {Michael A. Heroux and Roscoe A. Bartlett and Vicki E. Howle and Robert J. Hoekstra and Jonathan J. Hu and Tamara G. Kolda and Richard B. Lehoucq and Kevin R. Long
and Roger P. Pawlowski and Eric T. Phipps and Andrew G. Salinger and Heidi K. Thornquist and Ray S. Tuminaro and James M. Willenbring and Alan Williams and Kendall S. Stanley},
title = {An overview of the {T}rilinos project},
journal = {ACM Trans. Math. Softw.},
volume = {31},
number = {3},
year = {2005},
issn = {0098-3500},
pages = {397--423},
doi = {http://doi.acm.org/10.1145/1089014.1089021},
publisher = {ACM Press}
}
@misc{rythmos:homepage,
author = "T. Coffey and R. Bartlett",
title = "Rythmos: Transient Integration of Differential Equations",
howpublished = "\url{http://trilinos.sandia.gov/packages/rythmos}"
}
@misc{triangle:homepage,
author = "J. {Shewchuk}",
title = "{Triangle: A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator}",
howpublished = "\url{http://www-2.cs.cmu.edu/~quake/triangle.html}",
year = "2005"
}
@misc{tetgen:homepage,
author = "Hang {Si}",
title = "{TetGen: A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator}",
howpublished = "\url{http://tetgen.berlios.de}",
year = "2005"
}
@misc{thrust,
author = "N. Bell and J. Hoberock",
title = {The {T}hrust Library},
howpublished = "{\tt http://code.google.com/p/thrust/}",
year = "2010"
}
@misc{cusp,
author = "N. Bell and M. Garland",
title = {The {C}usp Library},
howpublished = "{\tt http://code.google.com/p/cusp-library/}",
year = "2010"
}
@misc{CIG:homepage,
author = "M. {Gurnis et al.}",
title = "{Computational Infrastructure for Geodynamics}",
howpublished = "\url{http://www.geodynamics.org}"
}
@article{MaltsevSelkov00,
author = "R. Overbeek and N. Larsen and G. Pusch and M. D'Souza and E. Selkov Jr. and N. Kyrpides and M. Fonstein and N. Maltsev and E. Selkov",
title = "{WIT}: {I}ntegrated system for high-throughput genome sequence analysis and metabolic reconstruction",
journal = "Nucleic Acids Res.",
year = "2000",
month = "January",
pages = "123-125",
volume = "28",
number = "1",
}
@article{more:coloring,
author = "Thomas F. Coleman and Jorge J. More",
title = "Estimation of Sparse {J}acobian Matrices and Graph Coloring Problems",
journal = "SIAM Journal on Numerical Analysis",
year = "1983",
month = "Feb.",
pages = "187--209",
volume = "20",
number = "1",
}
@article{SelkovMaltsev97,
author = "E. Selkov and N. Maltsev and G.J. Olsen and R. Overbeek and W. B. Whitman",
title = "A reconstruction of the metabolism of Methanococcus jannaschii from sequence data",
journal = "Gene",
year = "1997",
pages = "GC11-GC26",
volume = "197",
number = "1-2",
}
@unpublished{rocketcenter,
title = "Center for Simulation of Advanced Rockets",
note = "http://www.csar.uiuc.edu",
institution = "University of Illinois at Urbana-Champaign"
}
@unpublished{Kirby03,
title = "A posteriori error estimates for the mixed hybrid finite element method",
note = "\url{http://www.ices.utexas.edu/~clint/nsf/apostmfem.ps}",
author = "Ricahrd Kirby",
institution = "University of Chicago"
}
@article{BarthLarson00,
author = "T. J. Barth and M. G. Larson",
title = "{\em A posteriori} Error Estimation for Discontiuous {G}alerkin Approximations of Hyperbolic Systems",
journal = "LNCS",
year = "2000",
volume = "11",
publisher = "Spinger-Verlag",
}
@Article{xu1,
author = "J. Xu",
title = "Iterative Methods by Space Decomposition and Subspace Correction",
journal = "SIAM Review",
volume = "34",
pages = "581--613",
year = 1992
}
@Article{Brandt77,
author = "Achi Brandt",
title = "Multi-Level Adaptive Solutions to Boundary-Value Problems",
journal = "Mathematics of Computation",
month = "April",
year = "1977",
pages = "333--390",
volume = "31",
number = "138",
note = "doi:10.2307/2006422"
}
@article{brandt1979multigrid,
title={{Multigrid solutions to elliptic flow problems}},
author={Brandt, A. and Dinar, N.},
journal={Numerical Methods for Partial Differential Equations},
pages={53--147},
year={1979}
}
@incollection{brandt1979singular,
title={Multi-Level Adaptive Techniques(MLAT) for singular-perturbation problems},
author={Achi Brandt},
booktitle={Numerical Analysis of Singular Perturbation Problems},
editor={Hemker, Pieter W. and Miller, John J.H.},
pages={53--142},
year={1979},
publisher={Academic Press}
}
@Article{amge1,
author = "M. Brezina and A. J. Cleary and R. D. Falgout and V. E. Henson and J. E. Jones and T. A. Manteuffel and
S. F. McCormick and J. W. Ruge",
title = "Algebraic Multigrid Based on Element Interpolation (AMGe)",
journal = "SIAM J. Scientific Computing",
volume = "22",
pages = "1570--1592",
year = 2000
}
@BOOK{bramble1,
AUTHOR = "J. H. Bramble",
TITLE = "Multigrid Methods",
PUBLISHER = "Longman Scientific and Technical",
address = "Essex, England",
YEAR = 1993
}
@BOOK{arpack98,
AUTHOR = "R. B. Lehoucq and D. C. Sorensen and C. Yang",
TITLE = "ARPACK, Users' Guide",
PUBLISHER = "SIAM",
YEAR = 1998
}
@Article{bbder96,
author = "R. Barrett and M. Berry and J. Dongarra and V. Eijkhout and C. Romine",
title = "Algorithmic bombardment for the iterative solution of linear systems: A polyIterative approach",
journal = "J. of Computational and Applied Mathematics",
year = "1996",
volume = "74",
pages = "91--110"
}
@Article{egks94,
author = "A. Ern and V. Giovangigli and D. E. Keyes and M. D. Smooke",
title = "Towards polyalgorithmic linear system solvers for nonlinear elliptic problems,",
journal = "SIAM J. Scientific Computing",
year = "1994",
volume = "15",
number = "3",
pages = "681--703"
}
@Article{dftb02,
author = "P. Zapol and M. Sternberg and L.A. Curtiss and Th. Frauenheim and D.M. Gruen",
title = "Tight-binding molecular-dynamics simulation of impurities in ultrananocrystalline diamond grain boundaries,",
journal = "Phys. Rev",
year = "2002",
volume = "B65",
pages = "045403"
}
@INBOOK{lsa,
AUTHOR="R. Bramley and D. Gannon and T. Stuckey and J. Villacis and
J. Balasubramanian and E. Akman and F. Berg and S. Diwan and M. Govindaraju",
TITLE="The linear system analyzer",
SERIES="enabling technologies for computational science",
YEAR="2002",
PUBLISHER="Kluwer",
LOCATION="Dordrecht"
}
@Article{kk97,
author = "C.T. Kelley and D.E. Keyes",
title = "Convergence analysis of pseudo-transient continuation",
journal = "SIAM J. Numerical Analysis",
year = "1998",
volume = "35",
pages = "508--523"
}
@Article{swtm01,
author = "R. Shepard and A. F. Wagner and J. L. Tilson and M. Minkoff",
journal = "Journal of Computational Physics",
year = "2001",
volume = "172",
number = "2",
pages = "472--514",
title = "The Subspace Projected Approximate Matrix {(SPAM)} Modification of the {D}avidson Method"
}
@techreport{ zhou03,
author = "Y. Zhou",
title = "Eigenvalue Computation from the Optimization Perspective: On {Jacobi-Davidson,
IIGD, RQI and Newton} Updates",
institution = "Argonne National Laboratory",
number = "ANL/MCS-P1074-0803",
note = "Submitted to Numerical Linear Algebra with Applications",
year = 2003
}
@Unpublished{ mtwm03,
author = "G. G. Maisuradze and D. L. Thompson and A. F. Wagner and M. Minkoff",
title = "Interpolating moving least squares methods for fitting
potential energy surfaces: Detailed analysis of one-dimensional applications",
note = "to appear in the Journal of Chemical Physics",
year = 2003
}
@article{SinghJosephHeslaGlowinskiPan00,
author = "P. Singh and D. D. Joseph and T. Hesla and R. Glowinski and T.-W. Pan",
title = "A distributed {L}agrange multiplier/fictitious domain model for viscoelastic particulate flows",
journal = "J. Non-Newtonian Fluid Mech.",
volume = "91",
pages = "165--188",
year = "2000"
}
@book{Joseph02,
author = "Daniel D. Joseph",
title = "Interrogations of Direct Numerical Simulations of Sloid-Liquid Flows",
publisher = "Springer-Verlag",
month = "March",
year = "2002",
note = "\url{http://www.efluids.com/efluids/books/joseph.htm}"
}
@Misc{triangle-web-page,
author = "Jonathan R. Shewchuk",
title = "{Triangle Web} page",
note = "\url{http://www-2.cs.cmu.edu/~quake/triangle.html}"
}
@incollection{shewchuk96,
author = {Jonathan R. Shewchuk},
title = {Triangle: {E}ngineering a {2D} Quality Mesh Generator and {D}elaunay Triangulator},
booktitle = {Applied Computational Geometry: Towards Geometric Engineering},
editor = {Ming C. Lin and Dinesh Manocha},
series = {Lecture Notes in Computer Science},
volume = 1148,
publisher = {Springer-Verlag},
pages = {203--222},
month = may,
year = 1996,
note = {From the First ACM Workshop on Applied Computational Geometry}
}
@article{leaf1,
author = "Transient Dynamics of Pinning of Domain Walls",
title = "G. K. Leaf and S. Obukhov and S. Scheidl and V. M. Vinokur",
journal = "J. Magnetism and Magnetic Materials",
volume = "241",
pages = "118--123",
year = "2002"
}
@article{leaf2,
author = "D. O. Gunter and H. G. Kaper and G. K. Leaf",
title = "Implicit Integration of the Time-Dependent {Ginzburg-Landau} Equations of Superconductivity",
journal = "SIAM J. Sci. Comp.",
volume = "23",
pages = "1944--1959",
year = "2002"
}
@article{leaf3,
author = " J. S. Jiang and H. G. Kaper and G. K. Leaf",
title = "Hysteresis in Layered Spring Magnets",
journal = " Discreet and Continuous Dynamical Systems, Series B",
volume = "1",
pages = "219--232",
year = "2001"
}
@article{leaf4,
author = "J. S. Jiang and S. D. Bader and H. G. Kaper and G. K. Leaf",
title = "Rotational Hysteresis of Exchange-Spring Magnets",
journal = "J. Phys. D Appl. Phys.",
volume = "35",
pages = "2339--2343",
year = "2002"
}
@article{leaf5,
author = "M. Grimsditch and G. K. Leaf and H. G. Kaper and D. A. Karpeev and R. E. Camley",
title = "Normal Modes of Spin Excitation in Magnetic Nanoparticles",
journal = "Submitted to Phys. Rev. B.",
note = "Submitted",
year = "2003"
}
@article{GraySumpterNoidBarnes01,
author = "S. K. Gray and B. G. Sumpter and D. W. Noid and M. d. Barnes",
title = "Quantum Mechanical Model of Localized Electrons on the Surface of Polymer Nanospheres",
journal = "Chem. Phys. Lett.",
volume = "333",
pages = "308--313",
year = "2001"
}
@InProceedings{petsc-efficient,
author = {Satish Balay and William~D. Gropp and Lois Curfman
McInnes and Barry F. Smith},
title = {Efficient Management of Parallelism in Object
Oriented Numerical Software Libraries},
booktitle = {Modern Software Tools in Scientific Computing},
editor = {E. Arge and A.~M. Bruaset and H.~P. Langtangen},
pages = {163--202},
publisher = {Birkh{\"{a}}user Press},
year = {1997}
}
@article{MUMPS01,
author = {P.~R. Amestoy and I.~S. Duff and J.-Y. L'Excellent and J. Koster},
title = {A fully asynchronous multifrontal solver using distributed dynamic scheduling},
journal = {SIAM Journal on Matrix Analysis and Applications},
volume = {23},
number = {1},
pages = {15--41},
year = {2001}
}
@article{Zoltan06,
author = {Karen D. Devine and Erik G. Boman and Robert T. Heaphy and \"Umit V. \c{C}ataly\"urek and Robert H. Bisseling},
title = {Parallel Hypergraph Partitioning for Irregular Problems},
journal = {SIAM Parallel Processing for Scientific Computing},
month = {February},
year = {2006}
}
@article{lidemmel03,
AUTHOR = {Xiaoye S. Li and James W. Demmel},
TITLE = {{SuperLU\_DIST}: A Scalable Distributed-Memory Sparse Direct
Solver for Unsymmetric Linear Systems},
JOURNAL = {ACM Trans. Mathematical Software},
YEAR = 2003,
MONTH = {June},
VOLUME = {29},
NUMBER = {2},
PAGES = {110--140}
}
@TechReport{SuperLU,
author = "James W. Demmel and John R. Gilbert and Xiaoye S. Li",
title = "{SuperLU} Users' Guide",
number = "LBNL-44289",
institution = "Lawrence Berkeley National Laboratory",
year = 2003,
url = "http://crd.lbl.gov/\~xiaoye/SuperLU/"
}
@techreport{Trilinos-Overview03,
title = "{An Overview of {T}rilinos}",
author = "Michael Heroux and Roscoe Bartlett and Vicki Howle Robert Hoekstra and Jonathan Hu and Tamara Kolda and Richard Lehoucq and Kevin Long and Roger Pawlowski and Eric Phipps and Andrew Salinger and Heidi Thornquist and Ray Tuminaro and James Willenbring and Alan Williams",
institution = "Sandia National Laboratories",
number = "SAND2003-2927",
year = 2003}
@techreport{Trilinos-Users-Guide,
title = "{Trilinos} Users Guide",
author = "Michael A. Heroux and James M. Willenbring",
institution = "Sandia National Laboratories",
number = "SAND2003-2952",
url = "http://trilinos.sandia.gov/",
year = 2003}
@article{PILUT01,
author = {David Hysom and Alex Pothen},
title = {A scalable parallel algorithm for incomplete factor preconditioning},
journal = {SIAM Journal on Scientific Computing},
volume = {22},
pages = {2194--2215},
year = {2001}
}
@techreport{BoomerAMG00,
author = {V.~E. Henson and U.~M. Yang},
title = {{BoomerAMG}: A parallel algebraic multigrid solver and preconditioner},
institution = {Lawrence Livermore National Laboratory},
number = {UCRL-JC-133948},
year = {2000}
}
@incollection{baker2012scaling,
title={Scaling algebraic multigrid solvers: {O}n the road to exascale},
author={Baker, Allison H. and Falgout, Robert D. and Gamblin, Todd and Kolev, Tzanio V. and Schulz, Martin and Yang, Ulrike Meier},
booktitle={Competence in High Performance Computing 2010},
pages={215--226},
year={2012},
publisher={Springer}
}
@article{knollkeyes:04,
author = "D. A. Knoll and D. E. Keyes",
year = 2004,
title = "Jacobian-free {Newton-Krylov} Methods: A Survey of Approaches and Applications",
journal = "J. Comp. Phys.",
volume = 193,
pages = "357-397"
}
@article{chacon02,
author = "L. Chacon and D. A. Knoll and J. M. Finn",
title = "An Implicit Nonlinear Reduced Resistive {MHD} Solver",
journal = "J. Comput. Phys",
volume = 188,
year = 2002,
pages = "15--36"
}
@article{mousseau03,
author = "V. A. Mousseau and D. A. Knoll",
title = "New Physics-based Preconditioning of Implicit Methods for
Non-Equilibrium Radiation Diffusion",
journal = "J. Comput. Physics",
year = 2003
}
@article{mousseau00,
author = "V. A. Mousseau and D. A. Knoll and W. J. Rider",
title = "Physics-based Preconditioning and the {Newton-Krylov} Method
for Non-Equilibrium Radiation Diffusion",
journal = "J. Comput. Physics",
year = 2000,
pages = "743--765",
volume = 160
}
@unpublished{facets:homepage,
author = "John {Cary (PI)}",
title = "{Framework Application for Core-Edge Transport Simulations (FACETS)}",
note = "Proto-FSP project, see \url{http://www.facetsproject.org}"
}
@unpublished{cpes:homepage,
author = "{C.S.} {Chang (PI)}",
title = "{Center for Plasma Edge Simulation (CPES)}",
note = "Proto-FSP project, see \url{http://www.cims.nyu.edu/cpes}"
}
@misc{epsi:homepage,
author = "{C.S.} {Chang (PI)}",
title = "{Center for Edge Physics Simulation (EPSI)}",
note = "\url{http://epsi.pppl.gov}"
}
@unpublished{groundwater-scidac2:web,
author = "Peter {Lichtner (PI)}",
title = "Modeling Multiscale-Multiphase-Multicomponent Subsurface Reactive Flows
Using Advanced Computing",
howpublished = "http://www.scidac.gov/groundwater/gwflow.html"
}
@misc{pflotran:web,
author = "Peter {Lichtner (PI)}",
title = "{Modeling Multiscale-Multiphase-Multicomponent Subsurface Reactive Flows
Using Advanced Computing}",
note = "\url{http://ees.lanl.gov/pflotran/}"
}
@Misc{accel-scidac2-solicitation,
author = {{DOE Office of Science}},
title = {{Program Announcement LAB 07-09, SciDAC: Accelerator Science and Simulation}},
year = 2006,
note = {\url{http://www.science.doe.gov/grants/LAB07_09.html}}
}
@ARTICLE{Nieter04,
author = "C. Nieter and J. R. Cary",
title = "{VORPAL}: A Versatile Plasma Simulation Code",
journal = "J. Comp. Phys.",
year = "2004",
volume = "196",
pages = "448"
}
@Article{Synergia06,
author = "J. Amundson and P. Spentzouris and J. Qiang and R. Ryne",
title = "Synergia: An accelerator modeling tool with {3-D} space charge",
journal = "J. Comp. Phys.",
year = 2006,
volume = "211",
pages = "229-248"
}
@unpublished{stoltz07,
author = "P. H. Stoltz",
title = "Maps of {RF} cavities generated from electromagnetic simulations",
year = 2007,
note = "to appear in Proceedings of the 2007 Particle Accelerator
Conference (PAC07), Albuquerque, NM, 2007"
}
@Misc{iter:homepage,
key = "{International Thermonuclear Experimental Reactor (ITER) homepage}",
year = 2007,
title = "{International Thermonuclear Experimental Reactor (ITER) homepage}",
howpublished = {\url{http://www.iter.org}}
}
@misc{epp2010,
author = {{Committee on Elementary Particle Physics in the 21st Century, National Research Council}},
title = {Revealing the Hidden Nature of Space and Time: Charting the Course for Elementary
Particle Physics},
year = {2006},
howpublished = {The National Academies Press, ISBN: 0309101948}
}
@misc{post-fsp-report,
author= "D.~E.~Post and D.~B.~Batchelor and R.~B.~Bramley and J.~R.~Cary and R.~H.~Cohen and P.~Colella and S.~C.~Jardin",
title= "{Report of Fusion Simulation Project Steering Committee}",
month= "August",
year = 2004,
note = "Available via \url{http://w3.pppl.gov/usjapanim/FSPReport.pdf}"
}
@misc{fsp:workshop2011,
key = "{Fusion Simulation Project (FSP) Planning Workshop}",
title = "{Fusion Simulation Project (FSP) Planning Workshop}",
month = "February",
year = 2011,
note = "\url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}"
}
@BOOK{hazeltine-meiss-book,
AUTHOR="R.~D.~Hazeltine and J.~D.~Meiss",
TITLE="Plasma Confinement",
YEAR="1991",
PUBLISHER="Addison-Wesley, Redwood City, CA",
}
@article{falgout05a,
author = "R. D. Falgout and J. E. Jones and U. M. Yang",
title = "Conceptual Interfaces in hypre",
journal = "Future Generation Computer Systems",
note = "Special issue on PDE software",
volume = 22,
year = 2005,
pages = "239--251"
}
@article{falgout05b,
author = "R. D. Falgout and J. E. Jones and U. M. Yang",
title = "Pursuing Scalability for hypre's Conceptual Interfaces",
journal = "ACM Trans. Math. Softw.",
volume = 31,
year = 2005,
pages = "326--350"
}
@unpublished{compass:homepage,
author = {Panagiotis {Spentzouris (PI)}},
title = {Community Petascale Project for Accelerator Science and Simulation (ComPASS)},
note = {SciDAC2 project, see \url{https://compass.fnal.gov/}}
}
@unpublished{cmsnf:homepage,
author = {{Todd Allen, Director}},
title = {{Center for Materials Science of Nuclear Fuel}},
note = {Energy Frontier Research Center, see
\url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}}
}
@unpublished{dvi-materials:project,
author = {{L.~C.} {McInnes (PI)}},
title = {Large-Scale Differential Variational Inequalities for Heterogeneous Materials},
note = {{SciDAC}-e project},
year = 2011
}
@Misc{scidac:homepage,
author = {{DOE Office of Science}},
title = {{Scientific Discovery through Advanced Computing}},
year = 2007,
howpublished = {\url{http://www.scidac.gov}}
}
@misc{corba,
author = "{Object Management Group}",
year = 2007,
title="{Common Object Request Broker Architecture (CORBA)}",
howpublished="\url{http://www.corba.org}"
}
@Article{ uedge,
author = "T.~D. Rognlien and D.~D. Ryutov and N. Mattor and G.~D. Porter",
title = "Two-Dimensional Electric Fields and Drifts near the Magnetic Separatrix in Divertor Tokamak",
journal = "J. Plasma Physics",
year = "1999",
volume = "6",
pages = "1851",
note = "also see user manual at http://www.mfescience.org, then UEDGE link"
}
@Article{ bout,
author = "X.~Q. Xu and R.~H. Cohen and T.~D. Rognlien and J.~R. Myra",
title = "Low-to-High Confinement Transition Simulations in
Divertor Geometry",
journal = "J. Plasma Physics",
year = "2000",
volume = "7",
pages = "1951",
note = ""
}
@Article{ bout++,
author = "B. Dudson and M. Umansky and X.~Q. Xu and P. B. Snyder and H. R. Wilson",
title = "{BOUT++}: A Framework for Parallel Plasma Fluid Simulations",
journal = "Computer Physics Communications",
year = "2009",
volume = "180",
issue = "9",
pages = "1467 -- 1480",
note = ""
}
@Article{ tempest,
author = "Z. Xiong and X.Q. Xu and B.I. Cohen and R. Cohen and
M.R. Dorr and J.A. Hittinger and G. Kerbel and W.M. Nevins and
T. Rognlien",
title = "Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST",
journal = "Bull. Am. Phys. Soc. ",
year = "2005",
volume = "50",
number = "86",
pages = "CP1",
note = ""
}
@Article{ccahpc,
author = {David E. Bernholdt and Benjamin A. Allan and Robert
Armstrong and Felipe Bertrand and Kenneth Chiu and
Tamara L. Dahlgren and Kostadin Damevski and Wael
R. Elwasif and Thomas G. W. Epperly and Madhusudhan
Govindaraju and Daniel S. Katz and James A. Kohl and
Manoj Krishnan and Gary Kumfert and J. Walter Larson
and Sophia Lefantzi and Michael J. Lewis and Allen
D. Malony and Lois C. McInnes and Jarek Nieplocha
and Boyana Norris and Steven G. Parker and Jaideep
Ray and Sameer Shende and Theresa L. Windus and
Shujia Zhou},
title = {A Component Architecture for High-Performance Scientific
Computing},
journal = {Intl. J. High-Perf. Computing Appl.},
volume = 20,
pages = {163--202},
year = 2006,
note = {ACTS Collection special issue},
}
@misc{cca-forum:homepage,
author = "{Common Component Architecture Forum}",
note = "\url{http://www.cca-forum.org}",
year = 2010
}
@misc{petsc:driven-cavity-example,
title = {{PETSc Driven Cavity Example Code}},
author = {B. F. {Smith et al.}},
howpublished = {\url{http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex19.c.html}}
}
@misc{unic-ref,
author = "Giuseppe Palmiotti",
title = "{UNIC} Neutronics Software",
note = "Nuclear Engineering Division, Argonne National Laboratory"
}
% -----------------------------------------------------------------------
% Model coupling refs
http://csdrm.caltech.edu/
@book{greve-blatter,
author = "Ralf Greve and Heinz Blatter",
title = "Dynamics of Ice Sheets and Glaciers",
series = "Advances in Geophysical and Environmental Mechanics and Mathematics",
publisher = "Springer",
year = 2009
}
@Misc{doe-isicles,
key = {ISICLES},
title ="Ice {S}heet {I}nitiative for {CL}-imate {E}xtreme{S}",
howpublished="\url{http://www.csm.ornl.gov/ISICLES/index.html}"
}
@Misc{mct-website,
key = {MCT},
title ="{M}odel {C}oupling {T}oolkit ({MCT}) {W}eb {S}ite",
howpublished="\url{http://www.mcs.anl.gov/mct}"
}
@article{larson:05,
author="Jay Larson and Robert Jacob and Everest Ong",
title="{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for
Building Multi-Physics Parallel Coupled Models",
journal="Int. J. High Perf. Comp. App.",
year=2005,
pages="277--292"
}
@article{dennis2012computational,
title={Computational performance of ultra-high-resolution capability in the Community Earth System Model},
author={Dennis, John M and Vertenstein, Mariana and Worley, Patrick H and Mirin, Arthur A and Craig, Anthony P and Jacob, Robert and Mickelson, Sheri},
journal={International Journal of High Performance Computing Applications},
volume={26},
number={1},
pages={5--16},
year={2012},
publisher={SAGE Publications}
}
@inproceedings{bettge01,
author = "T. Bettge and A. Craig and R. James and V. Wayland and G. Strand",
year = 2001,
title = "The {DOE} Parallel Climate Model {(PCM)}: The Computational Highway
and Backroads",
booktitle = "Proc. International Conference on Computational Science (ICCS) 2001",
editors = "V. N. Alexandrow and J. J. Dongarra and C. J. K. Tan",
pages = "148 -- 156",
series = "Lecture Notes in Computer Science",
volume = 2073,
publisher = "Springer-Verlag",
}
@inproceedings{jacob01,
author = "R. Jacob and C. Schafer and I. Foster and M. Tobis and J. Anderson",
year = 2001,
title = "Computational Design and Performance of the {Gast} Ocean Atmosphere Model",
booktitle = "Proc. International Conference on Computational Science (ICCS) 2001",
editors = "V. N. Alexandrow and J. J. Dongarra and C. J. K. Tan",
series = "Lecture Notes in Computer Science",
volume = 2073,
publisher = "Springer-Verlag",
}
@article{chen2008new,
title={New generation of multi-scale {NWP} system {(GRAPES)}: General scientific design},
author={Chen, DeHui and Xue, JiShan and Yang, XueSheng and Zhang, HongLiang and Shen, XueShun and Hu, JiangLin and Wang, Yu and Ji, LiRen and Chen, JiaBin},
journal={Chinese Science Bulletin},
volume={53},
number={22},
pages={3433--3445},
year={2008},
publisher={Springer}
}
@inproceedings{baum01,
author = "J. Baum and H. Luo and E. Mestreau and D. Sharov and R. Loehner and D. Pelessone and C. Charman",
year = 2001,
title = "Recent Developments of a Coupled {CFD/CSD} Methodology",
booktitle = "Proc. International Conference on Computational Science (ICCS) 2001",
editors = "V. N. Alexandrow and J. J. Dongarra and C. J. K. Tan",
series = "Lecture Notes in Computer Science",
volume = 2073,
publisher = "Springer-Verlag",
}
@inproceedings{lefantzi03,
author = "S. Lefantzi and J. Ray",
year = 2003,
title = "A Component-based Scientific Toolkit for Reacting Flows",
booktitle = "Proc. Second MIT Conference on Computational Fluid and Solid Mechanics",
volume = 2,
publisher = "Elsevier"
}
@article{boville98,
author = "B. A. Boville and P. R. Gent",
title = "The {NCAR} Climate System Model, Version One",
journal = "Journal of Climate",
volume = 11,
year = 1998,
pages = "1115--1130"
}
@misc{paraschivoiu99,
author = "M. Paraschivoiu and X.-C. Cai and M. Sarkis and D. P. Young and D. Keyes",
title = "Multi-domain multi-model formulation for compressible flows: Conservative interface
coupling and parallel implicit solvers for {3D} unstructured meshes",
note = "AIAA Paper 99-0784",
year = 1999
}
@article{peszynska,
author = "M. Peszynska and M. F. Wheeler and I. Yotov",
title = "Mortar upscaling for multiphysics flow in porous media",
journal = "Computational Geosciences"
}
@techreport{wheeler00,
author = "M. F. Wheeler and J. Wheeler and M. Peszynska",
title = "A distributed computing portal for coupling multi-physics and multiple domains
in porous media",
institution = "University of Texas at Austin",
number = "TICAM 00-03",
year = 2000,
}
@techreport{peszynska00,
author = "M. Peszynska and Q. Lu and M. F. Wheeler",
title = "Multiphysics Coupling of Codes",
institution = "University of Texas at Austin",
number = "TICAM 00-02",
year = 2000,
}
@inproceedings{cai99,
author = "X.-C. Cai and M. Paraschivoiu and M. Sarkis",
title = "An explicit multi-model compressible flow formulation based on the full potential
equation and the {Euler} equations on {3D} unstructured meshes",
booktitle = "Proceedings of the 11th International Conference on Domain Decomposition Methods",
editor = "C-H. Lai and P. Bjorstad and M. Cross and O. Widlund",
year = 1999
}
@article{he05,
author = "Yun He and Chris H. Q. Ding",
title = "Coupling Multi-Component Models with {MPH} on Distributed Memory Computer Architectures",
year = 2005,
volume = 19,
pages = "329--240",
number = 3,
journal = "Int. Journal of High Performance Computing Applications"
}
@inproceedings{uiuc-rocket-center02,
author = "W. A. Dick and M. T. Heath",
title = "Whole System Simulation of Solid Propellant Rockets",
booktitle = "Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345",
month = "July",
year = 2002,
}
@inproceedings{toth04,
AUTHOR = "G. Toth and O. Volberg and A. J. Ridley and T. I Gombosi and D. DeZeeuw and
K. W. Hansen and D. R. Chesney and Q. F. Stout and K. G. Powell and K. Kane and
R. Oehmke",
TITLE = "A Physics-Based Software Framework for Sun-Earth Connection Modeling",
editor = "A. T. Y. Lui and Y. Kamide and G. Consolini",
booktitle = "Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference
on the Sun-Earth Connection",
YEAR="2004",
PUBLISHER="Elsevier",
PAGES="383--397"
}
@Misc{csdrm:web,
author = "M. Aivazis and B. Goddard and D. Meiron and M. Ortiz and J. Pool and J. Shepherd",
title ="{Center for Simulation of Dynamic Response of Materials}",
note = "California Institute of Technology, see \url{http://csdrm.caltech.edu}"
}
@Misc{csar:web,
author = "M. {Heath (Director)}",
title ="{Center for Simulation of Advanced Rockets}",
note = "University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}"
}
@Misc{csafe:web,
author = "D. {Pershing (Director)}",
title ="{Center for Simulation of Accidental Fires and Explosions}",
note = "University of Utah, see \url{http://www.csafe.utah.edu}"
}
@Misc{cits:web,
author = "P. {Moin (Director)}",
title ="{Center for Integrated Turbulence Simulations}",
note = "Stanford University, see \url{http://www.stanford.edu/group/cits}"
}
@Misc{flash:web,
author = "D. {Lamb (Director)}",
title ="{Center for Integrated Turbulence Simulations}",
note = "University of Chicago, see \url{http://flash.uchicago.edu}"
}
@techreport{utah-csafe03,
author = "J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry",
title = "An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction
Problems, Part 1: Algorithm Development",
institution = "University of Utah, Center for the Simulation of Accidental Fires and Explosions",
year = 2003
}
@inbook{shepherd07,
author = "M. Shepherd and E. Seol and B. FrantzDale",
title = "Toward a Multi-Model Hierarchy to Support Multiscale Simulations",
year = 2007,
booktitle = "CRC Handbook of Dynamic System Modeling",
publisher = "Wiley",
pages = "1--41",
note = "also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute",
}
@INPROCEEDINGS{cactus02,
author = {Tom Goodale and Gabrielle Allen and Gerd Lanfermann and Joan Masso and Thomas Radke
and Edward Seidel and John Shalf},
title = {The {Cactus} Framework and Toolkit: Design and Applications},
booktitle = {VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science},
year = {2002},
url = {http://www.cactuscode.org/Papers/VecPar_2002.pdf}
}
@misc{cactus:homepage,
author = "G. {Allen et al.}",
title = "{Cactus Web page}",
howpublished = "\url{http://cactuscode.org}"
}
@Misc{open-grid-forum:web,
key = "{Open Grid Forum}",
title = "{Open Grid Forum}",
note = "See \url{http://www.ogf.org}"
}
@Misc{nox:web,
author = "Tamara Kolda and Roger {Pawlowski et al.}",
title = "Nonlinear Object-Oriented Solutions {(NOX)}",
note = "See \url{http://software.sandia.gov/nox}"
}
@Misc{chombo:web,
author = "P. {Colella (PI)}",
title = "{Chombo}",
note = "See \url{http://seesar.lbl.gov/anag/chombo}"
}
@article{lanzkron96,
author = "P. J. Kanzkron and D. J. Rose and J. T. Wilkes",
title = "An Analysis of Approximate Nonlinear Elimination",
journal = "SIAM J. Sci. Comput.",
volume = 17,
year = 1996,
pages = "538--559"
}
@article{jiang95,
author = "J. Jiang and P. Forsyth",
title = "Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} Equations",
journal = "Computers and Fluids",
volume = "24",
pages = "753--770",
year = "1995"
}
@article{young90,
author = "D. Young and R. Melbin and M. Bieterman and F. Johnson and S. Samant",
title = "Global Convergence of Inexact {Newton} Methods for Transonic Flow",
journal = "Int. J. Numer. Methods Fluids",
volume = "11",
pages = "1075--1095",
year = "1990"
}
@article{fishwick04,
author = "Paul A. Fishwick",
title = "Toward an Integrated Multimodeling Interface: A Human-Computer
Interface Approach to Interrelating Model Structures",
journal = "SCS Trans. on Simulation",
note = "Special Issue in Grand Challenges in Computer Simulation",
year = 2004,
}
@article{fishwick03,
author = "Paul Fishwick and Jinho Lee and Minho Park and Jyunju Shim",
title = "{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation",
booktitle = "Proceedings of the 2003 Winter Simulation Conference",
editor = "S. Chick and P. J. Sanchez and D. Ferrin and D. J. Morrice",
year = 2003,
}
@inproceedings{kirner00,
author = "T. G. Kirner and V. F. Martins",
title = "Development of an Information Visualization Tool Using Virtual Reality",
booktitle = "Proceedings of the 2000 ACM Symposium on Applied Computing",
year = 2000,
pages = "604--606"
}
@inproceedings{orso03,
author = "A. Orso and J. Jones and M. J. Harrold",
title = "Visualization of Program-Execution Data for Deployed Software",
booktitle = "Proceedings of the 2003 ACM Symposium on Software Visualization",
year = 2003,
pages = "67--76"
}
@book{tiller01,
author = "M. Tiller",
title = "Introduction to Physical System Modeling with Modelica",
series = "Kluwer International Series inEngineering and Computer Science",
volume = 615,
publisher = "Kluwer",
year = 2001
}
@article{buck94,
author = "J. Buck and S. Ha and E. Lee and D. Messerschmitt",
title = "Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems",
journal = "Int. Journal of Computer Simulation",
volume = 4,
pages = "155--182",
year = 1994
}
@article{mu95,
author = "M. Mu and J.R. Rice",
title = "Modeling with collaborating {PDE} solvers - Theory and practice",
journal = "Comp. Syst. Engr.",
volume = 6,
year = 1995,
pages = "87--95"
}
@techreport{drashansky96,
title = "Multidisciplinary Problem Solving using Agents in a Cluster Environment",
author = "R. Drashansky and A. Joshi and J. R. Rice",
institution = "Emory Universtity, Department of Mathematics and Computer Science",
year = 1996
}
@article{michopoulos05,
title = "Survey on Modeling and Simulation of Multiphysics Systems",
author = "John G. Michopoulos and Charbel Farhat and Jacob Fish",
journal = "Journal of Computing and Information Science in Engineering",
volume = 5,
issue = 3,
pages = "198--213",
year = 2005
}
@article{dubey09,
title = "Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel Multiphysics Simulation Code",
author = "A. Dubey and K. Antypass and M. Ganapathy and L. Reid and D. Sheeler and A. Siegel and K. Weide",
journal = "Parallel Computing",
volume = 35,
issue = "10 -- 11",
pages = "512 -- 522",
year = 2009
}
@Book{BottLoring95,
AUTHOR = "Raoul Bott and Loring W. Tu",
TITLE = "Differential Forms in Algebraic Topology",
PUBLISHER = "Springer",
YEAR = "1995"
}
@Book{KobayashiNomizu96,
AUTHOR = "Shoshichi Kobayashi and Katsumi Nomizu",
TITLE = "Foundations of Differential Geometry",
PUBLISHER = "Wiley-Interscience",
YEAR = "1996"
}
@Article{HornungKohn02,
author = {Richard D. Hornung and Scott R. Kohn},
title = {Managing Application Complexity in the SAMRAI Object-Oriented Framework},
journal = {Concurrency and Computation: Practice and Experience},
volume = 14,
pages = {347--368},
year = 2002,
}
@inproceedings{concepts06,
author = "Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and Gabriel Dos Reis and Andrew Lumsdaine",
title = "Concepts: Linguistic Support for Generic Programming in C++",
booktitle = "Proceedings of OOPSLA 2006",
year = 2006,
pages = "???--???"
}
@BOOK{Hatcher02,
AUTHOR = {Hatcher, Allen},
TITLE = {Algebraic Topology},
PUBLISHER = {Cambridge University Press},
YEAR = 2002
}
@book{GammaHelmJohnsonVlissides95,
abstract = {{Design Patterns is a modern classic in the literature of object-oriented development, offering timeless and elegant solutions to common problems in software design. It describes patterns for managing object creation, composing objects into larger structures, and coordinating control flow between objects. The book provides numerous examples where using composition rather than inheritance can improve the reusability and flexibility of code. Note, though, that it's not a tutorial but a catalog that you can use to find an object-oriented design pattern that's appropriate for the needs of your particular application--a selection for virtuoso programmers who appreciate (or require) consistent, well-engineered object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is more valuable than ever!
Use the contents of the CD to create your own design documents and reusable components. The CD contains: 23 patterns you can cut and paste into your own design documents; sample code demonstrating pattern implementation; complete Design Patterns content in standard HTML format, with numerous hyperlinked cross-references; accessed through a standard web browser; Java-based dynamic search mechanism, enhancing online seach capabilities; graphical user environment, allowing ease of navigation.
First published in 1995, this landmark work on object-oriented software design presents a catalog of simple and succinct solutions to common design problems. Created by four experienced designers, the 23 patterns contained herein have become an essential resource for anyone developing reusable object-oriented software. In response to reader demand, the complete text and pattern catalog are now available on CD-ROM. This electronic version of Design Patterns enables programmers to install the book directly onto a computer or network for use as an online reference for creating reusable object-oriented software.
The authors first describe what patterns are and how they can help you in the design process. They then systematically name, explain, evaluate, and catalog recurring designs in object-oriented systems. All patterns are compiled from real-world examples and include code that demonstrates how they may be implemented in object-oriented programming languages such as C++ and Smalltalk. Readers who already own the book will want the CD to take advantage of its dynamic search mechanism and ready-to-install patterns.}},
author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John},
citeulike-article-id = {115158},
howpublished = {Hardcover},
isbn = {0201633612},
keywords = {1995 algorithms architecture book books computer computing design design-pattern design-patterns design_patterns designpatterns development diplom entwurfsmuster four gang gof java mathgamespatterns no-tag object object-orientation object-oriented of oo-patterns oop oriented pattern patterns programming se software software-development software-engineering software_design softwareengineering standard},
month = {January},
publisher = {{Addison-Wesley Professional}},
title = {Design Patterns},
url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612},
year = {1995}
}
@inproceedings{Chaco95,
author = {Bruce Hendrickson and Robert Leland},
title = {A multilevel algorithm for partitioning graphs},
booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing (CDROM)},
year = {1995},
isbn = {0-89791-816-9},
pages = {28},
location = {San Diego, California, United States},
doi = {http://doi.acm.org/10.1145/224170.224228},
publisher = {ACM Press},
address = {New York},
}
@BOOK{Aleksandrov98,
AUTHOR = {Aleksandrov, Pavel S.},
TITLE = {Combinatorial Topology},
PUBLISHER = {Dover},
VOLUME = 3,
YEAR = 1998
}
@book{Steenrod99,
abstract = {{
Fibre bundles, now an integral part of differential geometry, are also of great importance in modern physics--such as in gauge theory. This book, a succinct introduction to the subject by renown mathematician Norman Steenrod, was the first to present the subject systematically.
It begins with a general introduction to bundles, including such topics as differentiable manifolds and covering spaces. The author then provides brief surveys of advanced topics, such as homotopy theory and cohomology theory, before using them to study further properties of fibre bundles. The result is a classic and timeless work of great utility that will appeal to serious mathematicians and theoretical physicists alike.
}},
author = {Steenrod, Norman},
citeulike-article-id = {712999},
howpublished = {Paperback},
isbn = {0691005486},
keywords = {fibre_bundles topology},
month = {April},
publisher = {{Princeton University Press}},
title = {The Topology of Fibre Bundles. (PMS-14)},
url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486},
year = {1999}
}
@BOOK{Bredon97,
AUTHOR = {Bredon, Glen E.},
TITLE = {Sheaf Theory},
PUBLISHER = {Springer},
PAGES = {524},
SERIES = {Graduate Texts in Mathematics},
YEAR = 1997
}
@techreport{TautgesMeyers04,
title = "{MOAB}: A Mesh-Oriented Database",
author = "Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey Ernst",
institution = "Sandia National Laboratories",
number = "SAND2004-1592",
month = "April",
year = "2004"
}
@article{Tautges04,
author = {Timothy J. Tautges},
title = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation},
journal = {Engineering With Computers},
volume = {20},
pages = {286--293},
year = {2004}
}
@inproceedings{Meyers02,
author = {Ray Meyers et. al},
title = {{SNL} Implementation of the {TSTT} Mesh Interface},
booktitle = {8th International conference on numerical grid generation in computational field simulations},
month = {June},
year = {2002}
}
@inproceedings{SeolShepard05,
author = {E. S. Seol and Mark S. Shephard},
title = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive Analysis},
booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics},
year = {2005},
}
@article{BeallWalshShephard04,
author = {Mark W. Beall and Joe Walsh and Mark S. Shephard},
title = {A comparison of techniques for geometry access related to mesh generation},
journal = {Engineering With Computers},
volume = {20},
number = {3},
pages = {210--221},
year = {2004}
}
@article{CareyAndersonCarnesKirk04,
author = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. Kirk},
title = {Some aspects of adaptive grid technology related to boundary and interior layers},
journal = {Journal of Computational Applied Mathematics},
volume = {166},
number = {1},
pages = {55--86},
year = {2004}
}
@PHDTHESIS{GrALThesis,
author = "Guntram Berti",
title = "Generic Software Components for Scientific Computing",
school = "TU Cottbus",
year = "2000",
note = "\url{http://www.math.tu-cottbus.de/~berti/diss}"
}
@article{BeylkinCoifmanRokhlin91,
author = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin},
title = {Fast Wavelet Transforms and Numerical Algorithms {I}},
journal = {Communications on Pure and Applied Mathematics},
volume = {44},
pages = {141--183},
year = {1991}
}
@book{Wesseling92,
author = {Pieter Wesseling},
title = {An Introduction to Multigrid Methods},
publisher = {John Wiley and Sons},
year = {1992},
}
@book{Grakakos04,
author = {Loukas Grakakos},
title = {Classical and Modern Fourier Analysis},
publisher = {Pearson Education},
address = {New Jersey},
year = {2004},
}
@Misc{hlib-web-page,
key = {HLib},
title = {{HLib} {Web} page},
note = {{\texttt{http://www.hlib.org/}}},
annote = {Hierarchical matrices for fast integral transform}
}
@article{Hackbusch99,
author = {Wolfgang Hackbusch},
title = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: Introduction to {$\mathcal H$}-matrices},
journal = {Computing},
volume = {62},
pages = {89--108},
year = {1999}
}
@techreport{kay1999green,
title={A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes equations},
author={Kay, D. and Loghin, D.},
year={1999},
institution={Oxford University Computing Laboratory},
number={99/06}
}
@article{bebendorf2003existence,
title={Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of elliptic operators with {$L^\infty$}-coefficients},
author={Bebendorf, M. and Hackbusch, W.},
journal={Numerische Mathematik},
volume={95},
number={1},
pages={1--28},
year={2003},
publisher={Springer}
}
@article{hackbusch2005direct,
title={Direct {S}chur complement method by domain decomposition based on {$\mathcal H$}-matrix approximation},
author={Hackbusch, W. and Khoromskij, B.N. and Kriemann, R.},
journal={Computing and Visualization in Science},
volume={8},
number={3},
pages={179--188},
year={2005},
publisher={Springer}
}
@techreport{DupHof2003,
author = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. Logg and L. R. Scott},
title = {The {FE}ni{CS} project},
institution = {Chalmers Finite Element Center Preprint Series},
number = {2003--21},
year = {2003}
}
@article{FLAME01,
author = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de Geijn},
title = {{FLAME}: Formal Linear Algebra Methods Environment},
journal = {Transactions on Mathematical Software},
volume = {27},
number = {4},
year = {2001},
pages = {422--455}
}
@article{Puschel05,
author = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and
David Padua and Manuela Veloso and Bryan W. Singer and Jianxin Xiong and
Franz Franchetti and Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen
and Robert W. Johnson and Nick Rizzolo},
title = {{SPIRAL}: Code Generation for {DSP} Transforms},
journal = {Proceedings of the IEEE},
volume = {93},
number = {2},
year = {2005},
note = {special issue on "Program Generation, Optimization, and Adaptation"}
}
@article{KirbyLogg06,
author = {Robert C. Kirby and Anders Logg},
title = {A compiler for variational forms},
journal = {ACM Transactions on Mathematical Software},
volume = {32},
number = {3},
year = {2006},
issn = {0098-3500},
pages = {417--444},
doi = {http://doi.acm.org/10.1145/1163641.1163644},
publisher = {ACM Press},
address = {New York, NY},
}
@article{KirbyLogg07,
author = {Robert C. Kirby and Anders Logg},
title = {Efficient compilation of a class of variational forms},
journal = {ACM Transactions on Mathematical Software},
volume = {33},
number = {3},
year = {2007},
issn = {0098-3500},
pages = {17},
doi = {http://doi.acm.org/10.1145/1268769.1268771},
publisher = {ACM Press},
address = {New York, NY},
}
@article{BankDupont81,
author = {Randolph Bank and Todd Dupont},
title = {An optimal order process for solving finite element equations},
journal = {Mathematics of Computation},
volume = {36},
pages = {35--51},
year = {1981}
}
@techreport{Adams00,
author = {Mark F. Adams},
title = {Evaluation of three unstructured multigrid methods on 3D finite element problems in solid mechanics},
institution = {UC Berkeley},
number = {CSD-00-1103},
year = {2000},
url = {citeseer.ist.psu.edu/article/adams00evaluation.html}
}
@article{BergenGradlHuelsemannRuede06,
author = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude},
title = {A Massively Parallel Multigrid Method for Finite Elements},
journal = {Computing in Science \& Engineering},
volume = {8},
number = {6},
pages = {56--62},
year = {2006}
}
@MastersThesis{BruneThesis08,
author = {Peter Brune},
title = {Enabling Unstructured Multigrid Under the Sieve Framework},
school = {University of Chicago},
address = {Chicago, IL},
year = {2008},
month = {February}
}
@article{ArnoldWinther02,
author = {Douglas N. Arnold and Ragnar Winther},
title = {Mixed finite elements for elasticity},
journal = {Numerische Mathematik},
volume = {92},
number = {3},
month = {September},
year = {2002},
pages = {401--419},
note = {DOI:10.1007/s002110100348}
}
@article{ArnoldFalkWinther06,
author = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther},
title = {Finite element exterior calculus, homological techniques, and applications},
journal = {Acta Numerica},
year = {2006},
volume = {15},
pages = {1--155},
publisher = {Cambridge University Press},
note = {doi:10.1017/S0962492906210018}
}
@article{Kirby04,
author = {Robert C. Kirby},
title = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis functions},
journal = {ACM Transactions on Mathematical Software},
volume = {30},
number = {4},
year = {2004},
issn = {0098-3500},
pages = {502--516},
doi = {http://doi.acm.org/10.1145/1039813.1039820},
publisher = {ACM Press},
address = {New York, NY},
}
@article{Kirby06,
author = {Robert C. Kirby},
title = {Optimizing {FIAT} with level 3 {BLAS}},
journal = {ACM Transactions on Mathematical Software},
volume = {32},
number = {2},
year = {2006},
issn = {0098-3500},
pages = {223--235},
doi = {http://doi.acm.org/10.1145/1141885.1141889},
publisher = {ACM Press},
address = {New York, NY},
}
@misc{BlueCrystal08,
author = {{B}lue {C}rystal Cluster},
title = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}},
year = {2008},
note = {\url{http://www.acrc.bris.ac.uk/acrc/hpc.htm}}
}
@article{Beylkin95,
author = {Gregory Beylkin},
title = {On the Fast Fourier Transform of Functions With Singularities},
journal = {Applied and Computational Harmonic Analysis},
volume = {2},
pages = {363--381},
year = {1995}
}
@inproceedings{Riehl08,
author = {Jonathan Riehl},
title = {Implementing the MyFEM Embedded Domain-specific Language},
booktitle = {Proceedings of the Second International Workshop on Domain-specific Program Development (DSPD'08)},
address = {Nashville, TN},
year = {2008},
}
@article{Appel85,
Author = {Andrew W. Appel},
Date-Added = {2008-02-27 12:23:39 +0000},
Date-Modified = {2008-02-27 12:24:02 +0000},
Doi = {10.1137/0906008},
Journal = {SIAM Journal on Scientific and Statistical Computing},
Keywords = {treecodes},
Number = {1},
Pages = {85-103},
Publisher = {SIAM},
Title = {An Efficient Program for Many-Body Simulation},
Url = {http://link.aip.org/link/?SCE/6/85/1},
Volume = {6},
Year = {1985},
Bdsk-Url-1 = {http://link.aip.org/link/?SCE/6/85/1},
Bdsk-Url-2 = {http://dx.doi.org/10.1137/0906008}
}
@ARTICLE{Ewald21,
author = {{Ewald}, P.~P.},
title = "{Die Berechnung optischer und elektrostatischer Gitterpotentiale}",
journal = {Annalen der Physik},
year = 1921,
volume = 369,
pages = {253-287},
doi = {10.1002/andp.19213690304},
adsurl = {http://adsabs.harvard.edu/abs/1921AnP...369..253E},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@article{GreengardRokhlin87,
Author = {L. Greengard and V. Rokhlin},
Date-Added = {2008-02-15 18:43:55 +0000},
Date-Modified = {2008-02-26 20:09:11 +0000},
Doi = {http://dx.doi.org/10.1016/0021-9991(87)90140-9},
Journal = {J. Comput.\ Phys.},
Keywords = {FMM},
Number = {2},
Pages = {325--348},
Title = {A Fast Algorithm for Particle Simulations},
Url = {citeseer.ist.psu.edu/greengard87fast.html},
Volume = {73},
Year = {1987},
Bdsk-Url-1 = {citeseer.ist.psu.edu/greengard87fast.html}
}
@article{GreengardRokhlin97,
author = {L. Greengard and V. Rokhlin},
title = {A New Version of the Fast Multipole Method for the Laplace Equation in Three Dimensions},
journal = {Acta Numerica},
volume = {6},
year = {1997},
pages = {229--269}
}
@article{LuChengHuangMcCammon06,
author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon},
title = {Order {N} algorithm for computation of electrostatic interactions in biomolecular systems},
journal = {PNAS},
doi = {http://dx.doi.org/10.1073/pnas.0605166103},
volume = {102},
number = {51},
year = {2006},
pages = {19314--19319}
}
@article{SchussNadlerEisenberg01,
author = {Zev Schuss and Boaz Nadler and Robert S. Eisenberg},
title = {Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel from a molecular model},
journal = {Physical Review E},
volume = {64},
number = {3},
year = {2001}
}
@book{HairerLubichWanner02,
author = {E. Hairer and Ch. Lubich and G. Wanner},
title = {Geometric Numerical Integration},
publisher = {Springer-Verlag},
address = {Berlin Heidelberg},
year = {2002}
}
@article{HolstBakerWang00,
author = {M. Holst and N. Baker and F. Wang},
title = {The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann equation on massively parallel computers},
journal = {Journal of Computational Chemistry},
volume = {21},
year = {2000}
}
@book{HockneyEastwood81,
author = {R. Hockney and J. Eastwood},
title = {Computer simulation using particles},
publisher = {McGraw-Hill},
address = {New York},
year = {1981}
}
@article{LutyDavisTironiGunsteren94,
author = {Brock A. Luty and Malcolm E. Davis and Ilario G. Tironi and Wilfred F. Van Gunsteren},
title = {A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems},
journal = {Molecular Simulation},
volume = {14},
number = {1},
year = {1994},
pages = {11--20}
}
@book{BriggsHensonMcCormick00,
author = {Briggs,, William L. and Henson,, Van Emden and McCormick,, Steve F.},
title = "A Multigrid Tutorial (2nd ed.)",
year = {2000},
isbn = {0-89871-462-1},
publisher = {Society for Industrial and Applied Mathematics},
address = {Philadelphia, PA}
}
@article{chartier2003spectral,
title={Spectral AMGe ($\rho$ AMGe)},
author={Chartier, Tim and Falgout, RD and Henson, VE and Jones, J and Manteuffel, T and McCormick, S and Ruge, J and Vassilevski, PS},
journal={SIAM Journal on Scientific Computing},
volume={25},
number={1},
pages={1--26},
year={2003},
publisher={SIAM}
}
@article{galvis2010domain,
title={Domain decomposition preconditioners for multiscale flows in high-contrast media},
author={Galvis, Juan and Efendiev, Yalchin},
journal={Multiscale Modeling \& Simulation},
volume={8},
number={4},
pages={1461--1483},
year={2010},
publisher={SIAM}
}
@book{BrennerScott02,
author = {Susanne~C. Brenner and L.~Ridgway Scott},
title = {The mathematical theory of finite element methods},
year = {2002},
isbn = {0-38795-451-1},
publisher = {Springer},
pages = {361}
}
@Book{TrefethenBau97,
editor = "Lloyd N. Trefethen and David {Bau, III}",
title = "Numerical Linear Algebra",
publisher = "Society for Industrial and Applied Mathematics",
address = "Philadelphia, PA",
pages = "xii + 361",
year = "1997",
ISBN = "0-89871-361-7",
ISBN-13 = "978-0-89871-361-9",
LCCN = "QA184 .T74 1997",
MRclass = "65-01 (65-02 65Fxx)",
MRnumber = "MR1444820 (98k:65002)",
MRreviewer = "Moody T. Chu",
bibdate = "Wed Jan 07 15:23:19 1998",
bibsource = "ftp://ftp.math.utah.edu/pub/bibnet/authors/t/trefethen-lloyd-n.bib",
acknowledgement = ack-nhfb
}
@inproceedings{Rhea08,
author = {Carsten Burstedde and Omar Ghattas and Michael Gurnis and Georg Stadler and Eh Tan and T.~Tu and Lucas~C. Wilcox and Shijie Zhong},
title = {Scalable adaptive mantle convection simulation on petascale supercomputers},
booktitle = {Proceedings of IEEE/ACM SC '08},
year = {2008}
}
@misc{BursteddeWilcox09,
author = {Carsten Burstedde and Lucas~C. Wilcox},
title = {The p4est library: A parallel scalable forest of adaptive octrees},
note = {in preparation}
}
@article{SkeelTezcanHardy02,
author = {R. D. Skeel and I. Tezcan and D. J. Hardy},
title = {Multiple Grid Methods for Classical Molecular Dynamics},
journal = {J. Comp. Chem.},
volume = {23},
pages = {673--684},
year = {2002}
}
@article{Verschelde99,
author = {Jan Verschelde},
title = {Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by homotopy continuation},
journal = {ACM Trans. Math. Softw.},
volume = {25},
number = {2},
issn = {0098-3500},
pages = {251--276},
doi = {http://doi.acm.org/10.1145/317275.317286},
publisher = {ACM},
address = {New York, NY},
year = {1999}
}
@inproceedings{SommeseVerscheldeWampler08,
author = {Andrew J. Sommese and Jan Verschelde and Charles W. Wampler},
title = {Solving Polynomial Systems Equation by Equation},
booktitle = {IMA Volume 146: Algorithms in Algebraic Geometry},
editor = {Alicia Dickenstein and Frank-Olaf Schreyer and Andrew J. Sommese},
pages = {133--152},
publisher = {Springer-Verlag},
year = {2008}
}
@article{PhanThienTanner77,
author = {N. Phan-Thien and R.~I. Tanner},
title = {A new constitutive equation derived from network theory},
journal = {J. Non-Newt. Fluid Mech.},
volume = {2},
pages = {353},
year = {1977}
}
@manual{sage,
Key = {SAGE},
Author = {W.\thinspace{}A. Stein and others},
Organization = {The Sage~Development Team},
Title = {{S}age {M}athematics {S}oftware ({V}ersion 3.3)},
note= {{\tt http://www.sagemath.org}},
Year = 2009
}
@Misc{BatesHauensteinSommeseWampler06,
author = {Daniel J. Bates and Jonathan D. Hauenstein and Andrew J. Sommese and Charles W. Wampler},
title = {{B}ertini: {S}oftware for {N}umerical {A}lgebraic {G}eometry},
howpublished = {Available at http://www.nd.edu/$\sim$sommese/bertini}
}
@article{Archer09,
author = {A. J. Archer},
collaboration = {},
title = {Dynamical density functional theory for molecular and colloidal fluids: A microscopic approach to fluid mechanics},
publisher = {AIP},
year = {2009},
journal = {The Journal of Chemical Physics},
volume = {130},
number = {1},
eid = {014509},
numpages = {8},
pages = {014509},
keywords = {colloids; continuum mechanics; density functional theory; free energy; glass transition; statistical distributions; stochastic processes},
url = {http://link.aip.org/link/?JCP/130/014509/1},
doi = {10.1063/1.3054633}
}
@article{Giesekus1966,
author = {Hanswalter Giesekus},
title = {Die Elastizit\"at von Fl\"ussigkeiten},
journal = {Rheologica Acta},
publisher = {Springer Berlin / Heidelberg},
volume = {5},
number = {1},
month = {March},
year = {1966},
doi = {10.1007/BF01973575},
pages = {29-35}
}
@article{Baaijens98,
author = {F.P. Baaijens},
title = {Mixed finite element methods for viscoelastic flow analysis: a review},
journal = {Journal of Non-Newtonian Fluid Mechanics},
volume = {79},
year = {1998},
pages = {361--385}
}
@book{Joseph90,
author = {D.~D. Joseph},
title = {Fluid Dynamics of Viscoelastic Liquids},
publisher = {Springer},
address = {New York, NY},
year = {1990}
}
@article{Oldroyd50,
author = {J.~G. Oldroyd},
title = {On the Formulation of Rheological Equations of State},
journal = {Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences},
volume = {200},
year = {1950},
pages = {523--541}
}
@inproceedings{BynaSunGroppThakur04,
author = {S. Byna and X.-H. Sun and W. Gropp and R. Thakur},
title = {Predicting Memory-Access Cost Based on Data-Access Patterns},
booktitle = {Proceedings of IEEE International Conference on Cluster Computing, San Diego},
year = {2004}
}
@book{Pozrikidis07,
author = {C. Pozrikidis},
title = {Fluid Dynamics: Theory, Computation, and Numerical Simulation},
publisher = {Kluwer (Springer)},
pages = {675},
year = {2001},
isbn = {0792373510}
}
@misc{KritzKeyesFSP07,
author= "A. Kritz and D. Keyes",
title= "{Fusion Simulation Project Workshop Report}",
month= "July",
year = 2007,
note = "Available via \url{http://www.sc.doe.gov/ofes/More_HTML/FESAC/FESAC07/FSP_report_070702d.pdf}"
}
@misc{Dahlburg02,
author= "J. {Dahlburg (Chair)}",
title= "{Final Report of the FESAC ISOFS SubCommittee}",
year = 2002,
note = "Available via \url{http://www.ofes.fusion.doe.gov/More_HTML/FESAC/FESAC11-02/Dahlburg.pdf}"
}
@misc{Brown08,
author= "D. {Brown (Chair)}",
title= "{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View to the Future}",
year = 2008,
howpublished = "Office of Science, U.S. Department of Energy",
url = "http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Brown_report_may_08.pdf"
}
@misc{Crosscutting10,
author= "D. Brown and P. {Messina (Chairs)}",
title= "{Scientific Grand Challenges: Crosscutting Technologies for Computing at the Exascale}",
year = 2010,
howpublished = "Office of Science, U.S. Department of Energy",
url = "http://extremecomputing.labworks.org/SumReps/Crosscutting-SumRep-PNNL_20168.pdf"
}
@misc{extreme-scale-solvers-workshop12,
author= "J. Ang and K. Evans and A. Geist and M. Heroux and P. Hovland and O. Marques and L.C. McInnes and E. Ng and S. Wild",
title = "Report on the Workshop on Extreme-Scale Solvers: Transitions to Future Architectures",
howpublished = "Office of Advanced Scientific Computing Research, U.S. Department of Energy",
note = "{Washington, DC}, March 8-9, 2012",
url = "http://science.energy.gov/~/media/ascr/pdf/program-documents/docs/reportExtremeScaleSolvers2012.pdf",
year = 2012
}
@misc{MonizRosner09,
author= "{E. Moniz and R. Rosner}",
title= "{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling and Simulation at the Extreme Scale}",
month= "May",
year = 2009,
note = "See \url{http://extremecomputing.labworks.org/crosscut/references/nuclearenergy10exascael.pdf}"
}
@misc{Blanford08,
author= "{R. Blandord (Chair)}",
title= "{Workshop on Challenges for Understanding the Quantum Universe and the Role of Computing at the Extreme Scale}",
month= "Dec",
year = 2008,
note = "See \url{http://extremecomputing.labworks.org/crosscut/references/HEPreport10exascale.pdf}"
}
@misc{Exascale07,
author= "H. Simon and T. Zacharia and R. Stevens",
title= "{Modeling and Simulation at the Exascale for Energy and the Environment}",
year = 2007,
note = "See \url{http://www.sc.doe.gov/ascr/ProgramDocuments/Docs/TownHall.pdf}"
}
@misc{ASCRBreakthroughs08,
author = "{Panel on Recent Significant Advancements in Computational Science}",
title = "Breakthroughs",
year = 2008,
note = "See \url{http://www.er.doe.gov/ASCR/ProgramDocuments/Docs/Breakthroughs_2008.pdf}"
}
@misc{petsc-RD100-2009,
author = "{R\&D Magazine}",
title = "{PETSc} {R}\&{D} 100 Award",
year = 2009,
note = "See \url{http://www.rdmag.com/Awards/RD-100-Awards/2009/07/PETSc-Release-3-0-Expands-Capabilities}"
}
@article{compass-scidac08,
author = "P. Spentzouris and J. Cary and L. C. McInnes and W. Mori and C. Ng and E. Ng and R. Ryne",
title = "Community Petascale Project for Accelerator Science and Simulation:
Advancing Computational Science for Future Accelerators and Accelerator Technologies",
journal = "J. Phys.: Conf. Ser.",
volume = 125,
year = 2008,
pages = 012001,
url = "http://iopscience.iop.org/1742-6596/125/1/012001"
}
@article{compass-amundson-scidac08,
title = "Multiscale, Multiphysics Beam Dynamics Framework Design and Applications",
author = "J. Amundson and D. Dechow and L. McInnes and B. Norris and P. Spentzouris and P. Stoltz",
journal = "J. Phys.: Conf. Ser.",
volume = 125,
year = 2008,
}
@inproceedings{muszala09,
title = "Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator Simulations",
author = "S. Muszala and J. Amundson and L. C. McInnes and B. Norris",
booktitle = "Proceedings of the 2009 Workshop on Component-Based High Performance Computing {(CBHPC 2009)}",
year = 2009
}
@article{gaston09,
title = "{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear Equations",
author = "Derek Gaston and Chris Newman and Glen Hansen and Damien Lebrun-Grandie",
journal = "Nuclear Engineering and Design",
volume = 239,
number = 10,
year = 2009,
pages = "1768 -- 1778"
}
@article{gaston09b,
title = "Parallel Multiphysics Algorithms and Software for Computational Nuclear Engineering",
author = "D. Gaston and G. Hansen and S. Kadioglu and D. Knoll and C. Newman and H. Park and C. Permann and W. Taitano",
journal = "J. Phys.: Conf. Ser.",
volume = 180,
year = 2009,
pages = 012012
}
@article{newman09,
title = "Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen Diffusion in {UO$_2$} Nuclear Fuel Rods",
author = "Chris Newman and Glen Hansen and Derek Gaston",
journal = "Journal of Nuclear Materials",
volume = 392,
issue = 1,
year = 2009,
pages = "6 -- 15"
}
@misc{www:fenics,
author = {{FE}ni{CS}},
title = {{FE}ni{CS} Project},
howpublished = {\url{http://www.fenics.org/}}},
year = {2010},
}
@inproceedings{zwart08,
title = "A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems",
author = "S. Zwart and S. McMillan and B. Nuallain and D. Heggie and J. Lombarsi and P. Hut and
S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. Gaburov and
E. Glebbeek and D. Groen and S. Harfst and R. Izzard and J. Juric and S. Justham and
P. Teuben and J. van Bever and O. Yaron and M. Zemp",
booktitle = "Proceedings of ICCS 2008",
year = 2008,
}
@article{KlocknerWarburtonBridgeHesthaven09,
author = {Kl\"{o}ckner, A. and Warburton, T. and Bridge, J. and Hesthaven, J. S.},
title = {Nodal discontinuous {G}alerkin methods on graphics processors},
journal = {J. Comput. Phys.},
volume = {228},
number = {21},
year = {2009},
issn = {0021-9991},
pages = {7863--7882},
doi = {http://dx.doi.org/10.1016/j.jcp.2009.06.041},
publisher = {Academic Press Professional},
address = {San Diego, CA},
}
@phdthesis{Rankin99,
Author = {Rankin, W. T.},
Keywords = {FMM, parallel FMM},
School = {Department of Electrical and Computer Engineering, Duke University},
Title = {Efficient parallel implementations of multipole-based {$N$}-body algorithms},
Year = {1999}
}
@inproceedings{WarrenSalmon93,
Abstract = {We report on an efficient adaptive N-body method which we have recently designed and implemented. The algorithm computes the forces on an arbitrary distribution of bodies in a time which scales as N log N with the particle number. The accuracy of the force calculations is analytically bounded, and can be adjusted via a user defined parameter between a few percent relative accuracy, down to machine arithmetic accuracy. Instead of using pointers to indicate the topology of the tree, we identify...},
Address = {New York},
Author = {Warren, Michael S. and Salmon, John K.},
Booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing},
Citeulike-Article-Id = {580952},
Keywords = {oct-tree},
Pages = {12--21},
Publisher = {ACM},
Title = {A parallel hashed Oct-Tree {N}-body algorithm},
Year = {1993},
url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.50.100}
}
@unpublished{CruzWCCM10,
author = {Felipe A. Cruz},
title = {Heterogeneous extension of the PetFMM a Fast Multipole Library},
note = {Presentation at WCCM 2010, Sydney Australia},
year = {2010}
}
@article{McGuffee06,
author = {S.~R. {McGuffee} and A.~H. Elcock},
title = {Atomistically detailed simulations of concentrated protein solutions: the effects of salt, {pH}, point mutations, and protein concentration in simulations of 1000-molecule systems},
journal = {Journal of the American Chemical Society},
volume = {128},
pages = {12098--12110},
year = {2006}
}
@ARTICLE{NilsenCaiHoylandLangtangen10,
author = {{Nilsen}, J.~K. and {Cai}, X. and {Hoyland}, B. and {Petter Langtangen}, H.},
title = "{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach in Python}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1002.0705},
primaryClass = "cs.DC",
keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Programming Languages},
year = 2010,
month = feb,
adsurl = {http://adsabs.harvard.edu/abs/2010arXiv1002.0705N},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@misc{mcinnes:siam09:minisymposium,
title = "Implicit Nonlinear Solvers in Multimodel Simulations",
author = "L. C. McInnes and C. {Woodward (co-organizers)}",
note = "invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, Denver, CO,
speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at Austin)."
}
@misc{mcinnes:fsp-summary:feb2011,
author = "Lois Curfman McInnes and Luis Chacon and John Shadid",
title = "Solvers and Time Integration Breakout Summary",
note = "FSP Planning Workshop, General Atomics, Feb 8-11, 2011,
see \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}"
}
@misc{dvi-materials:siamcse11,
title = "Progress in Large-Scale Differential Variational Inequalities for Heterogeneous Materials",
author = "M. Anitescu and A. El-Azab and J. Lee and L. C. McInnes and T. Munson and B. F. Smith and L. Wang",
note = "minisymposium presentation at the 2011 SIAM Conference on Computational Science and Engineering, March 3, 2011",
}
@misc{jamroz:cemm10,
title = "{JFNK} within the semi-implicit scheme in {NIMROD}",
author = "B. Jamroz and S. Kruger and T. Austin",
note = "presentation, CEMM Meeting, Chicago, IL, Nov 7, 2010",
}
@misc{kruger:feb4-2011,
title = "personal communication",
author = "S. Kruger",
note = "February, 2011"
}
@article{Elman1996,
author = {H.C. Elman},
title = {Preconditioning for the steady-state {Navier-Stokes} equations for low viscosity},
journal = {SIAM J. Sci. Comput.},
volume = {20},
year = {1996},
pages = {1299--1316}
}
@article{KayLoghinWathen2002,
author = {D. Kay and D. Loghin and A. Wathen},
title = {A preconditioning for the steady-state {Navier-Stokes} equations},
journal = {SIAM J. Sci. Comput.},
volume = {24},
year = {2002},
pages = {237--256}
}
@article{ElmanHowleShadidShuttleworthTuminaro2006,
author = {H.C. Elman and V.E. Howle and J. Shadid and R. Shuttleworth and R. Tuminaro},
title = {Block preconditioners based on approximate commutators},
journal = {SIAM J. Sci. Comput.},
volume = {27},
number = {5},
year = {2006},
pages = {1651--1668}
}
@article{BraessSarazin1997,
author = {D. Braess and R. Sarazin},
title = {An efficient smoother for the {Stokes} problem},
journal = {Applied Numerical Mathematics},
volume = {23},
year = {1997},
pages = {3--19},
doi = {10.1016/S0168-9274(96)00059-1}
}
@article{wright2001large,
title={Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}},
author={Wright, T.G. and Trefethen, L.N.},
journal={SIAM Journal on Scientific Computing},
volume={23},
pages={591},
year={2001}
}
@misc{wright2002eigtool,
title={Eig{T}ool},
author={Wright, T.G. and Trefethen, LN},
howpublished={Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}},
year={2002}
}
@misc{visit-web-site,
key={{VisIt}},
title={{VisIt web site}},
howpublished={\url{http://wci.llnl.gov/codes/visit/}},
url={http://wci.llnl.gov/codes/visit/},
year=2011
}
@book{trefethen2005spectra,
title={Spectra and pseudospectra: the behavior of nonnormal matrices and operators},
author={Trefethen, L.N. and Embree, M.},
year={2005},
publisher={Princeton University Press}
}
@article{gomez2010isogeometric,
title={Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations},
author={Gomez, H. and Hughes, T.J.R. and Nogueira, X. and Calo, V.M.},
journal={Computer Methods in Applied Mechanics and Engineering},
volume={199},
number={25-28},
pages={1828--1840},
issn={0045-7825},
year={2010},
publisher={Elsevier}
}
@article{gomez2008isogeometric,
title={Isogeometric analysis of the {C}ahn-{H}illiard phase-field model},
author={G{\'o}mez, H. and Calo, V.M. and Bazilevs, Y. and Hughes, T.J.R.},
journal={Computer Methods in Applied Mechanics and Engineering},
volume={197},
number={49-50},
pages={4333--4352},
year={2008},
publisher={Elsevier}
}
@Misc{fastmath:project,
author = {Lori {Diachin (PI)}},
title = {{SciDAC-3 Frameworks, Algorithms, and Scalable Technologies for Mathematics (FASTMath) Institute}},
howpublished = {\url{http://www.fastmath-scidac.org/}}
}
@Misc{exascale-software:proposal,
author = {Peter {Beckman (PI)}},
title = {{Exascale Software Center}},
note = {proposal to DOE}
}
@Misc{imex:project,
author = {Barry {Smith (PI)}},
title = {{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent Multimodel PDEs}},
note = {DOE ASCR applied math project}
}
@Misc{intel-mic:website,
author = {Intel},
title = {{Many Integrated Core Architecture}},
note = {\url{http://www.intel.com/technology/architecture-silicon/mic}}
}
@Article{dudson:2009,
author = {B.D. Dudson and M.V. Umansky and X.Q. Xu and P.B. Snyder and
H.R. Wilson},
title = {{{BOUT++:}} a framework for parallel plasma fluid simulations},
journal = {Computer Physics Communications},
volume = 180,
pages = 1467,
year = 2009}
@Article{umansky:2009,
author = {M.V. Umansky and X.Q. Xu and B. Dudson and L.L. LoDestro
and J.R. Myra},
title = {{Status and verification of edge plasma turbulence code BOUT}},
journal = CPP,
year = 2009,
volume = {180},
pages = {887-903},
}
@Article{xu:1998,
author = {X.Q. Xu and R.H. Cohen},
title = {{Scrape-Off Layer Turbulence Theory and Simulations}},
journal = CPP,
year = 1998,
volume = 36,
number = {1-2},
pages = 158,
}
@article{tron:1999,
title={Newton's Method for Large Bound-constrained Optimization Problems},
author={Chih-Jen Lin and Jorge Mor\'{e}},
journal={SIAM Journal on Optimization},
volume={9},
number={4},
pages={1100-1127},
year={1999}
}
@article{StubenAMG,
author = {K. St\"{u}ben},
title = {A review of algebraic multigrid},
journal = {J. Comput. Appl. Math.},
volume = {128},
number = {1-2},
year = {2001},
issn = {0377-0427},
pages = {281--309},
doi = {http://dx.doi.org/10.1016/S0377-0427(00)00516-1},
publisher = {Elsevier Science Publishers B. V.},
address = {Amsterdam, The Netherlands, The Netherlands},
}
@article{FeuchterMG,
author = "D. Feuchter and I. Heppner and S. Sauter and G. Wittum",
title = "Bridging the gap between geometric and algebraic multigrid methods",
journal = "Computing and visualization in science",
publisher = "Springer",
volume = "6",
number = "1",
year = "2003",
pages = "1--13",
}
@article{ChowMGSmoothness,
abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that only attempts to interpolate in the directions of geometrical smoothness. These directions are determined by analyzing samples of algebraically smooth error, e. Neighboring grid points i and j are called smoothly coupled if e i and e j are consistently nearby in value. In addition, these dierences may be used to dene interpolation weights. These new ideas may be incorporated into the algebraic multigrid method. Test results show that the new method can have much lower grid and operator complexities compared to AMG, leading to lower solve timings. 1 },
author = {Chow, Edmond},
citeulike-article-id = {7675372},
citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
journal = {American Journal of Mathematics},
keywords = {fem, multigrid},
pages = {197--215},
posted-at = {2010-08-17 23:29:51},
priority = {2},
title = {An Unstructured Multigrid Method Based on Geometric Smoothness},
url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
volume = {65},
year = {2001}
}
@article{JonesAMGe,
abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite elements) method based on element agglomeration. In the method, coarse grid elements are formed by agglomerating fine grid elements. Compatible interpolation operators are constructed which yield coarse grid basis functions with a minimal energy property. Heuristics based on interpolation quality measures are used to guide the agglomeration procedure. The performance of the resulting method is demonstrated in two-level numerical experiments.}},
author = {Jones, Jim E. and Vassilevski, Panayot S.},
citeulike-article-id = {8598569},
citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
citeulike-linkout-1 = {http://link.aip.org/link/?SCE/23/109},
journal = {SIAM Journal on Scientific Computing},
keywords = {amg, fem, multigrid},
number = {1},
pages = {109--133},
posted-at = {2011-01-13 18:05:55},
priority = {2},
publisher = {SIAM},
title = {{AMGE Based on Element Agglomeration}},
url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
volume = {23},
year = {2001}
}
@article{Saad1993,
author = {Saad, Youcef},
doi = {10.1137/0914028},
issn = {10648275},
journal = {SIAM Journal on Scientific Computing},
keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of precondition-,preconditioned conju-,subject classi cations,variable preconditioners},
number = {2},
pages = {461--469},
title = {{A flexible inner-outer preconditioned GMRES algorithm}},
url = {http://dx.doi.org/10.1137/0914028},
volume = {14},
year = {1993}
}
@misc{path:homepage,
author = "S. Dirkse and M. Ferris and T. Munson",
title = "{{PATH} {W}eb page}",
howpublished = "\url{http://pages.cs.wisc.edu/~ferris/path.html}"
}
@article{Ketcheson2008,
author = {David I Ketcheson},
title = {Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with Low-Storage Implementations},
volume = {30},
journal = {SIAM Journal on Scientific Computing},
year = {2008},
pages = {2113--2136}
}
@article{elman2009boundary,
title={{Boundary conditions in approximate commutator preconditioners for the Navier-Stokes equations}},
author={Elman, H.C. and Tuminaro, R.},
journal={Electronic Transactions on Numerical Analysis},
volume={35},
pages={257--280},
year={2009}
}
@article{elman2008tcp,
title={{A taxonomy and comparison of parallel block multi-level preconditioners for the incompressible Navier-Stokes equations}},
author={Elman, H.C. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, R.},
journal={Journal of Computational Physics},
volume={227},
number={1},
pages={1790--1808},
year={2008},
publisher={Academic Press}
}
@article{silvester2001efficient,
title={{Efficient preconditioning of the linearized Navier-Stokes equations for incompressible flow}},
author={Silvester, D. and Elman, H. and Kay, D. and Wathen, A.},
journal={Journal of Computational and Applied Mathematics},
volume={128},
number={1-2},
pages={261--279},
issn={0377-0427},
year={2001},
publisher={Elsevier}
}
}
@article{elman1999bfbt,
title={{Preconditioning for the steady-state Navier-Stokes equations with low viscosity}},
author={Elman, H.C.},
journal={SIAM Journal on Scientific Computing},
volume={20},
number={4},
pages={1299--1316},
issn={1064-8275},
year={1999},
publisher={Citeseer}
}
@article{elman2006bpb,
title={{Block preconditioners based on approximate commutators}},
author={Elman, H. and Howle, V.E. and Shadid, J. and Shuttleworth, R. and Tuminaro, R.},
journal={SIAM Journal on Scientific Computing},
volume={27},
number={5},
pages={1651--1668},
year={2006},
publisher={Philadelphia, PA: SIAM, c1993-}
}
@article{olshanskii2006analysis,
title={{Analysis of a Stokes interface problem}},
author={Olshanskii, M.A. and Reusken, A.},
journal={Numerische Mathematik},
volume={103},
number={1},
pages={129--149},
issn={0029-599X},
year={2006},
publisher={Springer}
}
@article{patankar1972cph,
title={{A calculation procedure for heat, mass and momentum transfer in three-dimensional parabolic flows}},
author={Patankar, S.V. and Spalding, D.B.},
journal={Int. J. Heat Mass Transfer},
volume={15},
pages={1787--1806},
year={1972}
}
@article{rannacher1992simple,
title={{Simple nonconforming quadrilateral Stokes element}},
author={Rannacher, R. and Turek, S.},
journal={Numerical Methods for Partial Differential Equations},
volume={8},
number={2},
pages={97--111},
issn={1098-2426},
year={1992},
publisher={Wiley Online Library}
}
@article{rannacher2000finite,
title={Finite Element Methods for the Incompressible {N}avier-{S}tokes Equations},
author={Rannacher, R.},
journal={Fundamental Directions in Mathematical Fluid Mechanics},
pages={191},
isbn={3764364149},
year={2000},
publisher={Birkhauser}
}
@article{vanka1986block,
title={{Block-implicit multigrid solution of Navier-Stokes equations in primitive variables}},
author={Vanka, S.P.},
journal={Journal of Computational Physics},
volume={65},
number={1},
pages={138--158},
issn={0021-9991},
year={1986},
publisher={Elsevier}
}
@article{eisenstat1983variational,
title={Variational iterative methods for nonsymmetric systems of linear equations},
author={Eisenstat, S.C. and Elman, H.C. and Schultz, M.H.},
journal={SIAM Journal on Numerical Analysis},
volume={20},
number={2},
pages={345--357},
year={1983},
publisher={JSTOR}
}
@inproceedings{burstedde2008scalable,
title={Scalable adaptive mantle convection simulation on petascale supercomputers},
author={Burstedde, C. and Ghattas, O. and Gurnis, M. and Stadler, G. and Tan, E. and Tu, T. and Wilcox, L.C. and Zhong, S.},
booktitle={Proceedings of the 2008 ACM/IEEE conference on Supercomputing},
pages={62},
year={2008},
organization={IEEE Press}
}
@article{burstedde2009parallel,
title={Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes} flow problems},
author={Burstedde, C. and Ghattas, O. and Stadler, G. and Tu, T. and Wilcox, L.C.},
journal={Computer Methods in Applied Mechanics and Engineering},
volume={198},
number={21-26},
pages={1691--1700},
year={2009},
publisher={Elsevier}
}
@article{stadler2010dynamics,
title={The dynamics of plate tectonics and mantle flow: From local to global scales},
author={Stadler, G. and Gurnis, M. and Burstedde, C. and Wilcox, L.C. and Alisic, L. and Ghattas, O.},
journal={Science},
volume={329},
number={5995},
pages={1033},
year={2010},
publisher={American Association for the Advancement of Science}
}
@article{tackley2008modelling,
title={Modelling compressible mantle convection with large viscosity contrasts in a three-dimensional spherical shell using the yin-yang grid},
author={Tackley, P.J.},
journal={Physics of the Earth and Planetary Interiors},
volume={171},
number={1-4},
pages={7--18},
year={2008},
publisher={Elsevier}
}
@article{MoresiZhongGurnis96,
author = {Louis N. Moresi and Shijie Zhong and Michael Gurnis},
title = {The accuracy of finite element solutions of {S}tokes' flow with strongly varying viscosity},
journal = {Physics of the Earth and Planetary Interiors},
volume = {97},
pages = {83-–94},
year = {1996}
}
@article{MoresiSolomatov95,
author = {Louis N. Moresi and V. S. Solomatov},
title = {Numerical investigation of {2D} convection with extremely large viscosity variations},
journal = {Physics of Fluids},
volume = {7},
number = {9},
pages = {2154-–2162},
year = {1995}
}
@article{ChenMolnar83,
author = {W.-P. Chen and P. Molnar},
title = {Focal depths of intra-continental and intraplate earthquakes and their implications for the thermal and mechanical properties of the lithosphere},
journal = {Journal of Geophysical Research},
volume = {88},
pages = {4183–-4214},
year = {1983}
}
@article{Jackson02,
author = {J. Jackson},
title = {Strength of the continental lithosphere: time to abandon the jelly sandwich?},
journal = {GSA Today},
volume = {12},
pages = {4–-10},
year = {2002}
}
@article{BurovWatts06,
author = {E.B. Burov and A.B. Watts},
title = {The long-term strength of continental lithosphere: jelly sandwich or creme brulee?},
journal = {GSA Today},
volume = {16},
pages = {4–-10},
year = {2006}
}
@inproceedings{Yang:Brent:2002,
title = "The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems
on Parallel Distributed Memory Architectures",
author = "Laurence T. Yang and Richard Brent",
booktitle = "Proceedings of the Fifth International Conference on Algorithms and Architectures for Parallel Processing",
year = 2002,
publisher = "IEEE"
}
@article{demmel2008communication,
title={Communication-optimal parallel and sequential {QR} and {LU} factorizations},
author={Demmel, J. and Grigori, L. and Hoemmen, M. and Langou, J.},
journal={Arxiv preprint arXiv:0808.2664},
year={2008}
}
@article{demmel09,
author = "J. Demmel and M. Hoemmen and M. Mohiyuddin and K Yelick",
title = "Communication-optimal Iterative Methods",
journal = "Journal of Physics: Conf. Series",
volume = 180,
year = 2009
}
@TechReport( parms04,
Author = "Yousef Saad and Masha Sosonkina",
Title = "{pARMS}: A package for the parallel iterative solution of general large sparse linear systems user's guide",
number = "UMSI2004-8",
Institution = "Minnesota Supercomputer Institute, University of Minnesota",
Year = 2004,
)
@article{Picard1890,
author = {Emile Picard},
title = {M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la m\'ethode des approximations successives},
journal = {Journal De Math\'ematiques Pures et Appliqu\'ees},
volume = {4},
number = {6},
pages = {145--210},
year = {1890},
url = {\url{http://math-doc.ujf-grenoble.fr/JMPA/PDF/JMPA_1890_4_6_A3_0.pdf}}
}
@book{Rall1969,
author = {Louis B. Rall},
title = {Computational solution of nonlinear operator equations},
publisher = {Krieger Pub Co.},
pages = {225},
year = {1969}
}
@article{FletcherReeves1964,
author = {R. Fletcher and C. M. Reeves},
title = {Function Minimization by Conjugate Gradients},
journal = {Computer Journal},
volume = {7},
pages = {149–-154},
year = {1964}
}
@InBook{McInnesAllanEtAl06,
author = {Lois Curfman McInnes and Benjamin Allan and Robert Armstrong and Steven Benson and
David Bernholdt and Tamara Dahlgren and Lori Diachin and Manojkumar Krishnan and
James Kohl and Jay Larson and Sophia Lefantzi and Jarek Nieplocha and Boyana Norris and
Steven Parker and Jaideep Ray and Shujia Zhou},
editor = {A.~M.~Bruaset and A.~Tveito},
title = {Numerical Solution of Partial Differential Equations on Parallel Computers},
chapter = {Parallel {PDE}-Based Simulations Using the {Common Component
Architecture}},
publisher = {Springer},
year = {2006},
number = {51},
series = {Lecture Notes in Computational Science and Engineering},
pages = {327--381},
URL = {http://dx.doi.org/10.1016/S0167-8191(02)00191-6}
}
@article{CyrShadidTuminaro12,
title = "Stabilization and scalable block preconditioning for the {Navier–Stokes} equations",
journal = "Journal of Computational Physics",
volume = "231",
number = "2",
pages = "345 - 363",
year = "2012",
issn = "0021-9991",
doi = "10.1016/j.jcp.2011.09.001",
url = "http://www.sciencedirect.com/science/article/pii/S0021999111005195",
author = "Eric C. Cyr and John N. Shadid and Raymond S. Tuminaro",
}
@article{KeyesMcInnesWoodwardEtAl13,
title = {Multiphysics Simulations: Challenges and Opportunities},
author = {David E. Keyes and Lois Curfman McInnes and Carol Woodward and
William Gropp and Eric Myra and Michael Pernice and
John Bell and Jed Brown and Alain Clo and Jeffrey Connors and
Emil Constantinescu and Don Estep and Kate Evans and Charbel Farhat and
Ammar Hakim and Glenn Hammond and Glen Hansen and Judith Hill and
Tobin Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and
Efthimios Kaxiras and Alice Koniges and Kihwan Lee and Aaron Lott and
Qiming Lu and John Magerlein and Reed Maxwell and Michael McCourt and
Miriam Mehl and Roger Pawlowski and Amanda Peters Randles and Daniel Reynolds and
Beatrice Rivi\`{e}re and Ulrich R\"{u}de and Tim Scheibe and John Shadid and
Brendan Sheehan and Mark Shephard and Andrew Siegel and
Barry Smith and Xianzhu Tang and Cian Wilson and Barbara Wohlmuth},
journal = {International Journal of High Performance Computing Applications},
month = {Feb},
year = {2013},
volume = {27},
number = {1},
pages = {4--83},
doi = {10.1177/1094342012468181},
note = {Special issue},
abstract = {We consider multiphysics applications from algorithmic and
architectural perspectives, where ``algorithmic'' includes both
mathematical analysis and computational complexity and
``architectural'' includes both software and hardware environments.
Many diverse multiphysics applications can be reduced, en route to
their computational simulation, to a common algebraic coupling
paradigm. Mathematical analysis of multiphysics coupling in this form
is not always practical for realistic applications, but model problems
representative of applications discussed herein can provide insight.
A variety of software frameworks for multiphysics applications have
been constructed and refined within disciplinary communities and
executed on leading-edge computer systems. We examine several of
these, expose some commonalities among them, and attempt to
extrapolate best practices to future systems. From our study, we
summarize challenges and forecast opportunities.}
}
@misc{Rosner10,
author= "Robert {Rosner (Chair)}",
title = "{The Opportunities and Challenges of Exascale Computing}",
year = 2010,
howpublished = "Office of Science, U.S. Department of Energy",
url = {http://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf}
}
@misc{kogge2008exascale,
title={ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems},
author={Peter Kogge and Keren Bergman and Shekhar Borkar and Dan Campbell and Willian Carlson and William Dally and Monty Denneau and Paul Franzon and William Harrod and Kerry Hill and Jon Hiller and Sherman Karp and Stephen Keckler and Dean Klein and Robert Lucas and Mark Richards and Al Scarpelly and Steven Scott and Allan Snavely and Themas Sterling and R. Stanley Williams and Katherine Yelick},
howpublished={DARPA},
year=2008,
url={http://www.cse.nd.edu/Reports/2008/TR-2008-13.pdf}
}
@Misc{DOEGrandChallengeWorkshops,
key = {Office of Science, U.S. Department of Energy},
title = "{Scientific Grand Challenges Workshop Series}",
howpublished = "Office of Science, U.S. Department of Energy, see
\url{http://extremecomputing.labworks.org/workshops.stm}"
}
@Misc{Lawrence2011,
key = {Lawrence},
title = "{Ernest Orlando Lawrence Award Winners}",
howpublished = "U.S. Department of Energy, {\footnotesize \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}",
year = 2011
}
@article{murphy2000npi,
title={{A note on preconditioning for indefinite linear systems}},
author={Murphy, M.F. and Golub, G.H. and Wathen, A.J.},
journal={SIAM Journal on Scientific Computing},
volume={21},
number={6},
pages={1969--1972},
year={2000},
publisher={Philadelphia, PA: SIAM, c1993-}
}
@article{elman2011bouyancy,
title = "Fast iterative solvers for buoyancy driven flow problems",
journal = "Journal of Computational Physics",
volume = "230",
number = "10",
pages = "3900 - 3914",
year = "2011",
note = "",
issn = "0021-9991",
doi = "DOI: 10.1016/j.jcp.2011.02.014",
url = "http://dx.doi.org/10.1016/j.jcp.2011.02.014",
author = "Howard Elman and Milan Mihajlovic and David Silvester",
keywords = "Navier-Stokes",
keywords = "Boussinesq",
keywords = "Finite element approximation",
keywords = "Time stepping",
keywords = "Adaptivity",
keywords = "Preconditioning",
keywords = "Algebraic multigrid"
}
@ARTICLE{DongarraBeckman11,
AUTHOR={J. Dongarra and P. Beckman and et al.},
TITLE={The {I}nternational {E}xascale {S}oftware {P}roject {R}oadmap},
JOURNAL={Int. J. High Perf. Comput. Applics.},
VOLUME={25},
YEAR={2011},
PAGES={3--60}
}
@article{mandel1999energy,
title={Energy optimization of algebraic multigrid bases},
author={Mandel, J. and Brezina, M. and Van{\v{e}}k, P.},
journal={Computing},
volume={62},
number={3},
pages={205--228},
year={1999},
publisher={Springer}
}
@article{vanek1996algebraic,
title={Algebraic multigrid by smoothed aggregation for second and fourth order elliptic problems},
author={Van{\v{e}}k, P. and Mandel, J. and Brezina, M.},
journal={Computing},
volume={56},
number={3},
pages={179--196},
year={1996},
publisher={Springer}
}
@article{vanek2001convergence,
title={Convergence of algebraic multigrid based on smoothed aggregation},
author={Van{\v{e}}ek, P. and Brezina, M. and Mandel, J.},
journal={Numerische Mathematik},
volume={88},
number={3},
pages={559--579},
year={2001},
publisher={Springer}
}
@article{brannick2007algebraic,
title={Algebraic multigrid methods based on compatible relaxation and energy minimization},
author={Brannick, J. and Zikatanov, L.},
journal={Domain decomposition methods in science and engineering XVI},
pages={15--26},
year={2007},
publisher={Springer}
}
@article{xu2004energy,
title={On an energy minimizing basis for algebraic multigrid methods},
author={Xu, J. and Zikatanov, L.},
journal={Computing and Visualization in Science},
volume={7},
number={3},
pages={121--127},
year={2004},
publisher={Springer}
}
@article{DBLP:journals/toms/BakerHLT09,
author = {C. G. Baker and
Ulrich Hetmaniuk and
Richard B. Lehoucq and
Heidi Thornquist},
title = {Anasazi software for the numerical solution of large-scale
eigenvalue problems},
journal = {ACM Trans. Math. Softw.},
volume = {36},
number = {3},
year = {2009},
ee = {http://doi.acm.org/10.1145/1527286.1527287},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@article{DBLP:journals/siamsc/YangGBLLHN05,
author = {Chao Yang and
Weiguo Gao and
Zhaojun Bai and
Xiaoye S. Li and
Lie-Quan Lee and
Parry Husbands and
Esmond G. Ng},
title = {An Algebraic Substructuring Method for Large-Scale Eigenvalue
Calculation},
journal = {SIAM J. Scientific Computing},
volume = {27},
number = {3},
year = {2005},
pages = {873-892},
ee = {http://dx.doi.org/10.1137/040613767},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@TechReport{ml-guide,
author = {M.W. Gee and C.M. Siefert and J.J. Hu and R.S. Tuminaro and M.G. Sala},
title = {{ML} 5.0 Smoothed Aggregation User's Guide},
institution = {Sandia National Laboratories},
year = {2006},
number = {SAND2006-2649},
}
@article{Brannick06,
title={An energy-based AMG coarsening strategy},
volume={13},
url={http://doi.wiley.com/10.1002/nla.480},
number={2-3},
journal={Numerical Linear Algebra with Applications},
author={Brannick, J and Brezina, M and MacLachlan, S and Manteuffel, T and McCormick, S and Ruge, J},
year={2006},
pages={133--148}
}
@article{Olson10,
author = {Olson, Luke N. and Schroder, Jacob and Tuminaro, Raymond S.},
title = {A new perspective on strength measures in algebraic multigrid},
journal = {Numerical Linear Algebra with Applications},
volume = {17},
number = {4},
pages = {713--733},
year = {2010},
publisher = {John Wiley \& Sons, Ltd.},
issn = {1099-1506},
url = {http://dx.doi.org/10.1002/nla.669},
doi = {10.1002/nla.669},
pdf = {./files/2010_OlScTu_evosoc.pdf}
}
@article{Olson11,
author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.},
title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy Minimization},
journal = {SIAM J. Sci. Comput.},
issue_date = {April 2011},
volume = {33},
issue = {2},
month = apr,
year = {2011},
issn = {1064-8275},
pages = {966--991},
numpages = {26},
url = {http://dx.doi.org/10.1137/100803031},
doi = {http://dx.doi.org/10.1137/100803031},
acmid = {2078825},
publisher = {Society for Industrial and Applied Mathematics},
address = {Philadelphia, PA},
keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed aggregation},
}
@article{Dorit2011,
author = {Dorit Ron and
Ilya Safro and
Achi Brandt},
title = {Relaxation-Based Coarsening and Multiscale Graph Organization},
journal = {Multiscale Modeling {\&} Simulation},
volume = {9},
number = {1},
year = {2011},
pages = {407-423},
ee = {http://dx.doi.org/10.1137/100791142}
}
@article{chen2011algebraic,
title={Algebraic distance on graphs},
author={Chen, Jie and Safro, Ilya},
journal={SIAM Journal on Scientific Computing},
volume={33},
number={6},
pages={3468--3490},
year={2011},
publisher={SIAM}
}
@inproceedings{Adams04,
Author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.},
Booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing},
Title = {Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom},
Note = {Gordon Bell Award},
Year = {2004}
}
@article{Adams03a,
Author = {Adams, M.~F.},
Journal = {Numerical Linear Algebra with Applications},
Number = {2-3},
Pages = {141-153},
Title = {Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics},
Volume = {11},
Year = {2004}
}
@article{Adams-10a,
Author = {M. ~F. Adams and Ravi Samtaney and Achi Brandt},
Doi = {DOI: 10.1016/j.jcp.2010.04.024},
Issn = {0021-9991},
Journal = {Journal of Computational Physics},
Keywords = {Implicit magnetohydrodynamics},
Number = {18},
Pages = {6208 - 6219},
Title = {Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics},
Url = {http://www.sciencedirect.com/science/article/B6WHY-4YY8N52-2/2/4a06d49560a7f24a4da5bb25d0c75d62},
Volume = {229},
Year = {2010},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WHY-4YY8N52-2/2/4a06d49560a7f24a4da5bb25d0c75d62},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2010.04.024}
}
@inproceedings{Adams98,
Address = {Copper Mountain, CO},
Author = {Adams, M.~F.},
Booktitle = {Proceedings 5th Copper Mountain Conference on Iterative Methods},
Title = {A Parallel Maximal Independent Set Algorithm},
Year = 1998
}
@inproceedings{MadayPatera89,
author = {Y. Maday and A. T. Patera},
title = {Spectral element methods for the {Navier-Stokes} equations},
editor = {A. K. Noor and J. T. Oden},
booktitle = {State-of-the-Art Surveys in Computational Mechanics},
pages = {71-–143},
publisher = {ASME},
address = {New York, NY},
year = {1989}
}
@article{mishra2012mlmcfvm,
title = "Multi-level {M}onte {C}arlo finite volume methods for nonlinear systems of conservation laws in multi-dimensions",
journal = "Journal of Computational Physics",
volume = 231,
number = 8,
pages = "3365--3388",
year = 2012,
issn = "0021-9991",
doi = "10.1016/j.jcp.2012.01.011",
author = "S. Mishra and Ch. Schwab and J. {\v S}ukys",
keywords = "Conservation laws",
keywords = "Euler",
keywords = "MHD",
keywords = "Uncertainty quantification",
keywords = "Multi-level Monte Carlo",
keywords = "Parallelization"
}
@article{barth2011mlmcfe,
author = {Barth, Andrea and Schwab, Christoph and Zollinger, Nathaniel},
affiliation = {ETH Zentrum, Seminar für Angewandte Mathematik, Rämistrasse 101, 8092 Zurich, Switzerland},
title = {Multi-Level {M}onte {C}arlo Finite Element method for elliptic {PDE}s with stochastic coefficients},
journal = {Numerische Mathematik},
publisher = {Springer Berlin / Heidelberg},
issn = {0029-599X},
keyword = {Mathematics and Statistics},
pages = {123-161},
volume = {119},
issue = {1},
url = {http://dx.doi.org/10.1007/s00211-011-0377-0},
note = {10.1007/s00211-011-0377-0},
year = {2011}
}
@article{nguyen2011hybridizable,
title={Hybridizable discontinuous {G}alerkin methods},
author={Nguyen, N.C. and Peraire, J. and Cockburn, B.},
journal={Spectral and High Order Methods for Partial Differential Equations},
pages={63--84},
year={2011},
publisher={Springer}
}
@Misc{snyder-scidac3:proposal,
author = {Philip {Snyder (PI)}},
title = {{Plasma Edge Advanced Computation (PEAC) Center}},
note = {proposal to DOE SciDAC3},
month = {Oct},
year = 2011
}
@Misc{wirth-scidac3:proposal,
author = {Brian {Wirth (PI)}},
title = {{Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier through Leadership Class Computing}},
note = {proposal to DOE SciDAC3},
month = {Oct},
year = 2011
}
@Misc{cary-scidac3:proposal,
author = {John {Cary (PI)}},
title = {{Integrated Multiscale Modeling for Plasma Analysis and Control of Tokamak Stability (IMMPACTS)}},
note = {proposal to DOE SciDAC3},
month = {Oct},
year = 2011
}
@Misc{vashista-scidac3:proposal,
author = {Priya {Vashista (PI)}},
title = {{Design of Damage-Tolerance Material Interfaces for Extreme Stress-Temperature-Corrosion Environments: Algorithms and Methods for Multi-Petaflops Simulations}},
note = {proposal to DOE SciDAC3},
month = {March},
year = 2012
}
@Article{Elemental2012,
author = {Jack Poulson and Bryan Marker and Jeff R. Hammond and Nichols A. Romero and Robert {v}an~{d}e~{G}eijn},
title = {Elemental: A New Framework for Distributed Memory Dense Matrix Computations},
journal = {{ACM} Transactions on Mathematical Software},
volume = {39},
number = {2},
year = {2013}
}
@misc{elemental-web-page,
author = {Jack Poulson},
title = {Elemental: Distributed memory dense linear algebra},
howpublished = {\url{http://libelemental.org}},
url = {http://libelemental.org/},
year = {2015}
}
@book{ScalesReport,
title = {A Science-based Case for Large-scale Simulation},
editor = {D. E. Keyes},
publisher = {U.S. Department of Energy},
year = {2004},
url = {http://www.pnl.gov/scales}
}
@InProceedings{Cilk95,
address = {Santa Barbara, California},
author = {Robert D. Blumofe and Christopher F. Joerg and Bradley C. Kuszmaul and Charles E. Leiserson and Keith H. Randall and Yuli Zhou},
booktitle = {Proceedings of the Fifth ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP)},
day = {19--21},
month = jul,
pages = {207--216},
title = {{Cilk}: An Efficient Multithreaded Runtime System},
year = {1995}
}
@misc{valgrind-web-page,
author = {Julian Seward, et.al.},
title = {Valgrind},
url = {http://valgrind.org/},
hoepublished = {\url{http://valgrind.org/}},
year = {2012}
}
@article{BLAS79,
author = {C.~L. Lawson and R.~J. Hanson and D. Kincaid and F.~T. Krogh},
title = {Basic linear algebra subprograms for Fortran usage},
journal = {ACM Transactions on Mathematical Software},
volume = {5},
pages = {308--323},
year = {1979}
}
@techreport{LAPACK90,
author = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du~Croz and A. Greenbaum and S. Hammarling and A. McKenney and D. Sorensen},
title = {{LAPACK}: A portable linear algebra library for high-performance computers},
institution = {Computer Science Dept., University of Tennessee},
number = {CS-90-105},
month = {May},
year = {1990}
}
@techreport{NvidiaFermi,
author = {NVIDIA},
title = {{NVIDIA}'s Next Generation {CUDA} Compute Architecture: {F}ermi},
institution = {NVIDIA},
year = {2009}
}
@misc{IntelMIC,
author = {Many Core Group, Cambridge University},
title = {Intel Many Integrated Core Architecture},
howpublished = {\url{http://www.many-core.group.cam.ac.uk/ukgpucc2/talks/Elgar.pdf}},
month = {December},
year = {2010}
}
@article{AbuSufahKuckLawrie81,
author = {W. Abu-Sufah and D.~J. Kuck and D.~H. Lawrie},
title = {On the Performance Enhancement of Paging Systems Through Program Analysis and Transformations},
journal = {IEEE Trans. Comput.},
volume = {30},
number = {5},
pages = {341--356},
year = {1981}
}
@inproceedings{GuoBikshandiFraguelaGarzaranPadua08,
author = {Guo, Jia and Bikshandi, Ganesh and Fraguela, Basilio B. and Garzaran, Maria J. and Padua, David},
title = {Programming with tiles},
booktitle = {Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming},
series = {PPoPP '08},
year = {2008},
isbn = {978-1-59593-795-7},
location = {Salt Lake City, UT},
pages = {111--122},
numpages = {12},
url = {http://doi.acm.org/10.1145/1345206.1345225},
doi = {10.1145/1345206.1345225},
acmid = {1345225},
publisher = {ACM},
address = {New York, NY},
}
@article{Strout04,
Journal = {International Journal of High Performance Computing Applications},
Year = {2004},
Title = {Sparse Tiling for Stationary Iterative Methods},
Month = {February},
Publisher = {Sage Publications},
Pages = {95-114},
Volume = {18},
Number = {1},
Author = {Michelle Mills Strout and Larry Carter and Jeanne Ferrante and Barbara Kreaseck}
}
@misc{OpenCLStandard,
author = {Khronos Group},
title = {{OpenCL} 1.2 Specification},
howpublished = {\url{http://www.khronos.org/registry/cl/specs/opencl-1.2.pdf}},
url = {http://www.khronos.org/registry/cl/specs/opencl-1.2.pdf},
year = {2011}
}
@misc{STLGuide,
author = {SGI},
title = {Standard Template Library Programmer's Guide},
howpublished = {\url{http://www.sgi.com/tech/stl/}},
url = {http://www.sgi.com/tech/stl/},
year = {2011}
}
@book{Stepanov09,
author = {Alexander Stepanov and Paul McJones},
title = {Elements of Programming},
publisher = {Addison-Wesley},
isbn = {978-0-321-63537-2},
year = {2009}
}
@Article{BangerthHartmannKanschat2007,
author = {W. Bangerth and R. Hartmann and G. Kanschat},
title = {{deal.II} -- a General Purpose Object Oriented Finite Element Library},
journal = {ACM Trans. Math. Softw.},
year = 2007,
volume = 33,
number = 4,
pages = {24/1--24/27}
}
@misc{dealii-web-page,
author = {W. Bangerth and R. Hartmann and G. Kanschat},
title = {{deal.II}},
howpublished = {\url{http://www.dealii.org/}},
url = {http://www.dealii.org/},
year = {2012}
}
@article{Siek2012,
author = {Jeremy G. Siek},
title = {The C++0x "Concepts" Effort},
journal = {arXiv},
year = {2012},
url = {http://arxiv.org/abs/1201.0027},
note = {\url{http://arxiv.org/abs/1201.0027}}
}
@misc{sharpclaw,
note = {\url{http://numerics.kaust.edu.sa/sharpclaw}},
author = {Ketcheson, D. I. and Parsani, M.},
keywords = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic PDEs,sharpclaw,software},
mendeley-tags = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic PDEs,sharpclaw,software},
title = {{SharpClaw software}},
year = {2011}
}
@misc{clawpack45,
note = {\url{http://www.clawpack.org}},
author = {LeVeque, R. J. and Berger, M. J.},
keywords = {clawpack,finite volumes,hyperbolic PDEs,software},
mendeley-tags = {clawpack,finite volumes,hyperbolic PDEs,software},
title = {{Clawpack Software version 4.5}},
url = {www.clawpack.org},
year = {2011}
}
@article{Nilsen2010,
archivePrefix = {arXiv},
arxivId = {arXiv:1002.0705v1},
author = {Nilsen, J.K. and Cai, X. and H{\o}yland, Bj{\o} rn and Langtangen, H. P.},
eprint = {arXiv:1002.0705v1},
file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the parallelization of scientific codes by a function-centric approach in Python.pdf:pdf},
journal = {Computational Science \& Discovery},
keywords = {parallel,programming,python,software},
mendeley-tags = {parallel,programming,python,software},
pages = {015003},
publisher = {IOP Publishing},
title = {{Simplifying the parallelization of scientific codes by a function-centric approach in Python}},
url = {http://iopscience.iop.org/1749-4699/3/1/015003},
volume = {3},
year = {2010}
}
@book{Langtangen09,
author = {Hans Petter Langtangen},
title = {Python Scripting for Computational Science},
publisher = {Springer},
series = {Texts in Computational Science and Engineering},
pages = {784},
isbn = {3540739157},
year = {2009}
}
@book{NumpyGuide,
author = {Travis E. Oliphant},
title = {Guide to Numpy},
publisher = {Trelgol},
year = {2008}
}
@misc{PyCUDA,
author = {Andreas Kl\"ockner},
title = {{PyCUDA}},
howpublished = {\url{http://mathema.tician.de/software/pycuda}},
year = {2011}
}
@misc{PyOpenCL,
author = {Andreas Kl\"ockner},
title = {{PyOpenCL}},
howpublished = {\url{http://mathema.tician.de/software/pyopencl}},
year = {2011}
}
@article{Klockner2012,
author = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and Paul Ivanov and Ahmed Fasih},
title = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code generation},
journal = {Parallel Computing},
volume = {38},
number = {3},
pages = {157--174},
year = {2012},
issn = {0167-8191},
doi = {10.1016/j.parco.2011.09.001},
url = {http://www.sciencedirect.com/science/article/pii/S0167819111001281}
}
%%%%%% Matt Stuff %%%%%%
@misc{knepley:icerm-workshop:2012,
author = {David Keyes and Matthew Knepley and Katherine Yelick},
title = {Synchronization-reducing and Communication-reducing Algorithms and Programming Models for Large-scale Simulations},
note = {Workshop sponsored by the Institute for Computational and Experimental Research in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, \url{http://icerm.brown.edu/tw12-1-exascale}},
year = {2012}
}
@techreport{KirbyKnepleyScott04,
author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
title = {Optimal Evaluation of Finite Element Matrices},
type = {Technical Report},
number = {TR-2004-04},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}},
pages = {14},
month = {May},
year = {2004}
}
@techreport{KirbyKnepleyScott10,
author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
title = {Languages and Compilers for Variational Forms},
type = {Technical Report},
number = {TR-2010-09},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09}},
month = {October},
year = {2010}
}
@techreport{KirbyKnepleyScott10b,
author = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
title = {Evaluation of the Action of Finite Element Operators},
type = {Technical Report},
number = {TR-2010-08},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}},
month = {October},
year = {2010}
}
@techreport{BruneKnepleyScott11,
author = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott},
title = {Exponential grids in high-dimensional space},
type = {Technical Report},
number = {TR-2011-07},
institution = {University of Chicago},
url = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07},
note = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}},
month = {December},
year = {2011}
}
@techreport{Zheng11,
author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
title = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with strongly variable viscosity based on {Matlab} and {CUDA}},
type = {Research Report},
number = {UMSI 2011/33},
institution = {University of Minnesota Supercomputing Institute},
url = {http://static.msi.umn.edu/rreports/2011/33.pdf},
note = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}},
month = {March},
year = {2011}
}
@inproceedings{Zheng2010,
author = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai Zhang and Yaolin Shi},
title = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients},
booktitle = {Eos Transactions of the AGU},
organization = {American Geophysical Union},
note = {Fall Meeting Supplemental, Abstract IN41A-1350},
year = {2010}
}
@incollection{TerrelKirbyKnepleyScott12,
author = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott and Garth N. Wells},
title = {Finite elements for incompressible fluids},
editors = {A. Logg and K.A. Mardal and G. N. Wells},
booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
pages = {163--169},
publisher = {Springer-Verlag},
year = {2012}
}
@incollection{KirbyKnepleyLoggScottTerrel12,
author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott and Andy R. Terrel},
title = {Discrete optimization of finite element matrix evaluation},
editors = {A. Logg and K.A. Mardal and G. N. Wells},
booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
pages = {385--397},
publisher = {Springer-Verlag},
year = {2012}
}
@article{BrownConveryHotesKnepleyPetropolous1993,
author = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and Labros Petropolous},
title = {Closed strings with low harmonics and kinks},
journal = {Physical Review D},
volume = {48},
number = {6},
year = {1993}
}
@article{Minimax1996,
title = {MiniMax: What has been learned thus far},
author = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. Pruneau},
journal = {Nuovo Cimento},
volume = {19},
number = {1},
pages = {1045--1049},
year = {1996}
}
@article{Minimax1997,
author = {Minimax Collaboration},
title = {Analysis of Charged Particle/Photon Correlations in Hadronic Multiparticle Production},
journal = {Physical Review D},
volume = {55},
number = {9},
year = {1997}
}
@article{Minimax2000,
author = {Minimax Collaboration},
title = {Search for disoriented chiral condensate at the {Fermilab} {Tevatron}},
journal = {Physical Review D},
volume = {61},
number = {3},
year = {2000}
}
@article{KirbyKnepleyLoggScott05,
author = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott},
title = {Optimizing the evaluation of finite element matrices},
journal = {SIAM Journal on Scientific Computing},
volume = {27},
number = {3},
pages = {741--758},
year = {2005}
}
@article{BardhanKnepleyAnitescu2008,
author = {Jaydeep P. Bardhan and Matthew G. Knepley and Mihai Anitescu},
title = {Bounding the Electrostatic Free Energies Associated with Linear Continuum Models of Molecular Solvation},
journal = {Journal of Chemical Physics},
volume = {130},
number = {10},
note = {Selected for the March 15, 2009 issue of Virtual Journal of Biological Physics Research},
year = {2008}
}
@article{Knepley2010,
author = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. J. and Donoho, D. and Fomel, S. and Friedlander, M. P. and Gerstein, M. and Mitchell, I. and Ouellette, L. L. and Bramble, N. W. and Brown, P. O. and Carey, V. and DeNardis, L. and Gentleman, R. and {Gezelter, J}, D. and Goodman, A. and Moore, J. E. and Pasquale, F. A. and Rolnick, J. and Seringhaus, M. and Subramanian, R.},
title = {{Reproducible Research: addressing the need for data and code sharing in computational science}},
journal = {Computing in Science and Engineering},
volume = {12},
number = {5},
pages = {8--13},
url = {http://www.bepress.com/cgi/viewcontent.cgi?article=1034\&context=sagmb},
note = {\url{http://www.bepress.com/cgi/viewcontent.cgi?article=1034}},
year = {2010}
}
@article{KetchesonAhmadiaKnepley2011,
title = {Conference Review: High Performance Computing and Hybrid Programming Concepts for Hyperbolic PDE Codes},
author = {David I. Ketcheson and Aron Ahmadia and Matthew G. Knepley},
journal = {SIAM News},
volume = {44},
number = {7},
month = {September},
note = {\url{http://www.siam.org/pdf/news/1912.pdf}},
year = {2011}
}
@article{YokotaBardhanKnepleyBarbaHamada2011,
author = {Rio Yokota and Jaydeep P. Bardhan and Matthew G. Knepley and L.A. Barba and Tsuyoshi Hamada},
title = {Biomolecular electrostatics using a fast multipole {BEM} on up to 512 {GPU}s and a billion unknowns},
journal = {Computer Physics Communications},
volume = {182},
number = {6},
pages = {1272--1283},
year = {2011},
issn = {0010-4655},
doi = {10.1016/j.cpc.2011.02.013},
note = {\url{http://arxiv.org/abs/1007.4591}},
url = {http://www.sciencedirect.com/science/article/pii/S0010465511000750}
}
@article{BardhanKnepley2011,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Mathematical Analysis of the {BIBEE} Approximation for Molecular Solvation: Exact Results for Spherical Inclusions},
journal = {Journal of Chemical Physics},
volume = {135},
number = {12},
pages = {124107--124117},
url = {http://arxiv.org/abs/1109.0651},
note = {\url{http://arxiv.org/abs/1109.0651}},
year = {2011}
}
@article{BruneKnepleyScott2013,
author = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott},
title = {Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and Graded Meshes},
journal = {SIAM Journal on Scientific Computing},
url = {http://arxiv.org/abs/1104.0261},
note = {\url{http://arxiv.org/abs/1104.0261}},
volume = {35},
number = {1},
pages = {A173--A191},
year = {2013}
}
@article{BardhanKnepley2012a,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory},
journal = {Computational Science \& Discovery},
volume = {5},
pages = {014006},
url = {http://iopscience.iop.org/1749-4699/5/1/014006/},
note = {\url{http://arxiv.org/abs/1204.0267}},
doi = {doi:10.1088/1749-4699/5/1/014006},
year = {2012}
}
@article{KreienkampEtAl2013,
author = {Amy Kreienkamp and Lucy Y. Liu and Mona S. Minkara and Matthew G. Knepley and Jaydeep P. Bardhan and Mala L. Radhakrishnan},
title = {Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding},
journal = {Molecular Based Mathematical Biology},
volume = {1},
pages = {124--150},
doi = {10.2478/mlbmb-2013-0007},
issn = {2299-3266},
month = {June},
note = {\url{http://www.degruyter.com/view/j/mlbmb.2012.1.issue/mlbmb-2013-0007/mlbmb-2013-0007.xml}},
year = {2013}
}
@article{BardhanKnepleyBrune2015,
author = {Jaydeep P. Bardhan and Matthew G. Knepley and Peter R. Brune},
title = {Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators},
journal = {Molecular Based Mathematical Biology},
doi = {10.1515/mlbmb-2015-0001},
year = {2015}
}
@inproceedings{BardhanTejaniWieckowskiRamaswamyKnepley2015,
title = {A Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics},
author = {Jaydeep P. Bardhan and D. A. Tejani and N. S. Wieckowski and A. Ramaswamy and Matthew G. Knepley},
booktitle = {Proceedings of PIERS},
month = {July},
year = {2015}
}
@inproceedings{McClanahan2011,
author = {McClanahan, C and Czechowski, Kent and Battaglino, Casey and Iyer, K and Yeung, P K and Vuduc, Richard},
booktitle = {Proc. ACM/IEEE Conf. Supercomputing (SC)},
title = {{Prospects for scalable 3D FFTs on heterogeneous exascale systems}},
url = {http://mcclanahoochie.com/blog/wp-content/uploads/2011/01/fft-sc11.pdf},
year = {2011}
}
@techreport{Ghysels_Ashby_Meerbergen_Vanroose_2012,
Author = {Ghysels, P. and Ashby, T.J. and Meerbergen, K. and Vanroose, W.},
Institution = {Intel Exascience Lab},
Address= {Leuven, Belgium},
Number = {04.2012.1},
Type = {Tech. report},
Title = {Hiding global communication latency in the {GMRES} algorithm on massively parallel machines},
url = {http://twna.ua.ac.be/sites/twna.ua.ac.be/files/latency_gmres.pdf},
Year = {2012}}
}
@article{GhyselsVanroose2014,
author = {P. Ghysels and W. Vanroose},
title = {Hiding Global Synchronization Latency in the Preconditioned Conjugate Gradient Algorithm},
journal = {Parallel Computing},
volume = {40},
number = {7},
pages = {224--238},
note = {7th Workshop on Parallel Matrix Algorithms and Applications},
doi = {http://dx.doi.org/10.1016/j.parco.2013.06.001},
url = {http://www.sciencedirect.com/science/article/pii/S0167819113000719},
year = {2014}
}
@inproceedings{StrzodkaGoddeke06,
author = {R. Strzodka and D. G\"oddeke},
title = {Pipelined Mixed Precision Algorithms on {FPGA}s for Fast and Accurate PDE Solvers from Low Precision Components},
booktitle = {Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines},
note = {FCCM ’06},
pages = {259--270},
year = {2006},
organization = {IEEE Computer Society}
}
@incollection{JacquesNicolasVollaire12,
author = {T. Jacques and L. Nicolas and C. Vollaire},
title = {Electromagnetic Scattering with the Boundary Integral Method on MIMD Systems},
editors = {P. Sloot, M. Bubak, A. Hoekstra, and B. Hertzberger},
booktitle = {High-Performance Computing and Networking},
series = {Lecture Notes in Computer Science},
volume = {1593},
pages = {1025--1031},
publisher = {Springer},
year = {1999}
}
@inproceedings{HoeflerLumsdaineRehm07,
author = {T. Hoefler and A. Lumsdaine and W. Rehm},
title = {{Implementation and Performance Analysis of Non-Blocking Collective Operations for MPI}},
booktitle = {Proceedings of the 2007 International Conference on High Performance Computing, Networking, Storage and Analysis, SC07},
location = {Reno, NV},
publisher = {IEEE Computer Society/ACM},
source = {http://www.unixer.de/~htor/publications/},
month = {Nov.},
year = {2007}
}
@inproceedings{HoeflerSiebretLumsdaine10,
author = {T. Hoefler and C. Siebert and A. Lumsdaine},
title = {{Scalable Communication Protocols for Dynamic Sparse Data Exchange}},
booktitle = {Proceedings of the 2010 ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP'10)},
month = {Jan.},
location = {Bangalore, India},
publisher = {ACM},
isbn = {978-1-60558-708-0},
source = {http://www.unixer.de/~htor/publications/},
pages = {159--168},
year = {2010},
}
@article{RuppWeinbubJungelGrasser15,
author = {K. Rupp and J. Weinbub and A. J\"ungel and T. Grasser},
title = {Pipelined Iterative Solvers for Graphics Processing Units},
journal = {SIAM Journal on Scientific Computing},
note = {to appear},
year = {2015}
}
@article{Bai_Hu_Reichel_1994,
title={A {Newton} basis {GMRES} implementation},
volume={14},
url={},
number={},
journal={IMA Journal of Numerical Analysis},
author={Z. Bai and D. Hu and L. Reichel},
year={1994},
pages={563--581}
}
@article{Chronopoulos_Gear_1989,
title={{S-step} iterative methods for symmetric linear systems},
volume={25},
url={},
number={},
journal={Journal of Computational and Applied Mathematics},
author={A. T. Chronopoulos and C. W. Gear},
year={1989},
pages={153--168}
}
@article{Chronopoulos_1996,
title={Parallel Iterative {S-step} Methods for Unsymmetric Linear Systems},
author={A. T. Chronopoulos and C. D. Swanson},
journal={Parallel Computing},
volume={22},
number={5},
year={1996},
pages={623--641}
}
@article{Chronopoulos_2010,
author={A. T. Chronopoulos and A. Kucherov},
title={Block {S-step} {Krylov} Iterative Methods},
journal={Numerical Linear Algebra with Applications},
volume={17},
number={1},
pages={3--15},
year={2010}
}
@article{Sturler_Vorst_1995,
title={Reducing the effect of global communication in {GMRES(m)} and
{CG} on parallel distributed memory computers},
volume={18},
url={},
number={},
journal={Applied Numerical Mathematics},
author={E. De Sturler and H. A. van der Vorst},
year={1995},
pages={441--459}
}
@article{Joubert_Carey_1992,
title={Parallelizable restarted iterative methods for nonsymmetric linear systems.
part I: Theory},
volume={44},
url={},
number={},
journal={International journal of computer mathematics},
author={W. D. Joubert and G. F. Carey},
year={1992},
pages={243--267}
}
@article{Elman_SaadSaylor_1986,
title={A hybrid {Chebyshev} {Krylov}-subspace algorithm for solving nonsymmetric systems of linear equations},
volume={7},
url={},
number={3},
journal={SIAM Journal on Scientific and Statistical Computing},
author={Howard Elman and Y. Saad and P. E. Saylor},
year={1986},
pages={840--855}
}
@ARTICLE{Golub95innerand,
author = {Eldar Giladi and Gene H. Golub and Joseph B. Keller},
title = {Inner and outer iterations for the {Chebyshev} algorithm},
journal = {SIAM J. Numer. Anal},
year = {1995},
volume = {35},
pages = {300--319}
}
@article{Golub_Varga_1961,
title={{Chebyshev} semi-iterative methods, successive overrelaxation iterative methods, and
second-order {Richardson} iterative methods, parts {I} and {II}},
volume={3},
url={},
number={},
journal={Numer. Math.},
author={Gene Golub and R.S. Varga},
year={1961},
pages={147--168}
}
@article{El_maliki_Guenette_Fortin_2011,
title={An efficient hierarchical preconditioner for quadratic discretizations of finite element problems},
volume={18},
doi={10.1002/nla.757},
number={5},
journal={Numerical Linear Algebra with Applications},
author={A. {El maliki} and R. Guenette and M. Fortin},
year={2011},
pages={789-803}
}
@article{adavani2008multigrid,
title={Multigrid Algorithms for Inverse Problems with Linear Parabolic {PDE} Constraints},
author={Adavani, S.S. and Biros, G.},
journal={SIAM Journal on Scientific Computing},
volume={31},
number={1},
pages={369--397},
year={2008},
publisher={Society for Industrial and Applied Mathematics}
}
@article{horton1995space,
title={A space-time multigrid method for parabolic {PDE}s},
author={Horton, G. and Vandewalle, S.},
journal={SIAM Journal on Scientific Computing},
volume={16},
number={4},
pages={848--864},
year={1995}
}
@article{lewis2005model,
title={Model problems for the multigrid optimization of systems governed by differential equations},
author={Lewis, R.M. and Nash, S.G.},
journal={SIAM Journal on Scientific Computing},
volume={26},
number={6},
pages={1811--1837},
year={2005},
publisher={Philadelphia, PA: SIAM, c1993-}
}
@article{nash2000mgopt,
title={A multigrid approach to discretized optimization problems},
author={Nash, S.G.},
journal={Optimization Methods and Software},
volume={14},
number={1-2},
pages={99--116},
year={2000},
publisher={Taylor \& Francis}
}
@article{borzi2009multigrid,
title={Multigrid Methods for {PDE} Optimization},
author={Borz{\`i}, A. and Schulz, V.},
journal={SIAM Review},
volume={51},
pages={361},
year={2009}
}
@article{borzi2005multigrid,
title={A multigrid scheme for elliptic constrained optimal control problems},
author={Borz{\`i}, A. and Kunisch, K.},
journal={Computational Optimization and Applications},
volume={31},
number={3},
pages={309--333},
year={2005},
publisher={Springer}
}
@article{borzi2003multigrid,
title={Multigrid methods for parabolic distributed optimal control problems},
author={Borz{\`i}, A.},
journal={Journal of Computational and Applied Mathematics},
volume={157},
number={2},
pages={365--382},
year={2003},
publisher={Elsevier}
}
@article{ito2002receding,
title={Receding horizon optimal control for infinite dimensional systems},
author={Ito, K. and Kunisch, K.},
journal={ESAIM: Control, Optimisation and Calculus of Variations},
volume={8},
number={1},
pages={741--760},
year={2002},
publisher={Cambridge University Press}
}
@article{schulz1998solving,
title={Solving discretized optimization problems by partially reduced {SQP} methods},
author={Schulz, V.H.},
journal={Computing and Visualization in Science},
volume={1},
number={2},
pages={83--96},
year={1998},
publisher={Springer}
}
@article{hazra2005aerodynamic,
title={Aerodynamic shape optimization using simultaneous pseudo-timestepping},
author={Hazra, S.B. and Schulz, V. and Brezillon, J. and Gauger, N.R.},
journal={Journal of Computational Physics},
volume={204},
number={1},
pages={46--64},
year={2005},
publisher={Elsevier}
}
@article{mandel1985multilevel,
title={On multilevel iterative methods for integral equations of the second kind and related problems},
author={Mandel, J.},
journal={Numerische Mathematik},
volume={46},
number={1},
pages={147--157},
year={1985},
publisher={Springer}
}
@article{king1992multilevel,
title={Multilevel algorithms for ill-posed problems},
author={King, J.T.},
journal={Numerische Mathematik},
volume={61},
number={1},
pages={311--334},
year={1992},
publisher={Springer}
}
@article{kaltenbacher2001regularizing,
title={On the regularizing properties of a full multigrid method for ill-posed problems},
author={Kaltenbacher, B.},
journal={Inverse Problems},
volume={17},
pages={767},
year={2001},
publisher={IOP Publishing}
}
@article{kaltenbacher2002multi,
title={A multi-grid method with a priori and a posteriori level choice for the regularization of nonlinear ill-posed problems},
author={Kaltenbacher, B. and Schicho, J.},
journal={Numerische Mathematik},
volume={93},
number={1},
pages={77--107},
year={2002},
publisher={Springer}
}
@article{burger2006regularizing,
title={Regularizing {N}ewton-{K}aczmarz Methods for Nonlinear Ill-Posed Problems},
author={Burger, M. and Kaltenbacher, B.},
journal={SIAM Journal on Numerical Analysis},
volume={44},
pages={153},
year={2006}
}
@article{draganescu2008optimal,
title={Optimal order multilevel preconditioners for regularized ill-posed problems},
author={Draganescu, A. and Dupont, T.F.},
journal={Mathematics of Computation},
volume={77},
number={264},
pages={2001--2038},
year={2008},
publisher={Washington, DC: National Academy of Sciences-National Research Council,[1960?-}
}
@article{bastian1998additive,
title={Additive and multiplicative multi-grid---a comparison},
author={Bastian, P. and Wittum, G. and Hackbusch, W.},
journal={Computing},
volume={60},
number={4},
pages={345--364},
year={1998},
publisher={Springer}
}
@article{fournier2001multiplicative,
title={Multiplicative and additive parallel multigrid algorithms for the acceleration of compressible flow computations on unstructured meshes},
author={Fournier, L. and Lanteri, S.},
journal={Applied Numerical Mathematics},
volume={36},
number={4},
pages={401--426},
year={2001},
publisher={Elsevier}
}
@article{chow2006survey,
title={A survey of parallelization techniques for multigrid solvers},
author={Chow, E. and Falgout, R.D. and Hu, J.J. and Tuminaro, R.S. and Yang, U.M.},
journal={Parallel Processing for Scientific Computing, MA Heroux, P. Raghavan, and HD Simon, eds},
volume={20},
pages={179--201},
year={2006}
}
@inbook{brandt2001multiscale,
title={Multiscale scientific computation: {R}eview 2001},
author={Brandt, A.},
booktitle={Multiscale and Multiresolution Methods: Theory and Applications},
editors={Barth, T.J. and Chan, T.F. and Haimes, R.},
series={Lecture Notes in Computational Science and Engineering},
year={2001},
volume={20},
pages={3--96},
publisher={Springer Verlag}
}
@incollection{brandt2003multigrid,
title={Multigrid solvers and multilevel optimization strategies},
author={Brandt, A. and Ron, D.},
booktitle={Multilevel Optimization and VLSICAD},
editors={J. Cong and J.R. Shinnerl},
pages={1--69},
publisher={Kluwer Academic Publishers},
year={2003}
}
@inbook{brandt2009principles,
title={Principles of systematic upscaling},
author={Brandt, A.},
booktitle={Bridging the Scales in Science and Engineering},
editors={J. Fish},
publisher={Oxford University Press},
pages={193--215},
year={2009}
}
@article{livne2004coarsening,
title={Coarsening by compatible relaxation},
author={Livne, O.E.},
journal={Numerical Linear Algebra with Applications},
volume={11},
number={2-3},
pages={205--227},
year={2004},
publisher={Wiley Online Library}
}
@inproceedings{brandt1986stochastic,
title={Multi-Level Approaches to Discrete-State and Stochastic Problems},
author={Brandt, A. and Ron, D. and Amit, D.J.},
booktitle={Multigrid methods II: proceedings of the 2nd European Conference on Multigrid Methods, held at Cologne, October 1-4, 1985},
volume={1228},
pages={65--98},
year={1986},
organization={Springer}
}
@article{halko2011finding,
author = {Nathan Halko and
Per-Gunnar Martinsson and
Joel A. Tropp},
title = {Finding Structure with Randomness: Probabilistic Algorithms
for Constructing Approximate Matrix Decompositions},
journal = {SIAM Review},
volume = {53},
number = {2},
year = {2011},
pages = {217-288},
doi = {10.1137/090771806}
}
@inproceedings{MHDY09,
Author = {Mohiyuddin, M. and Hoemmen, M. and Demmel, J. and Yelick, K.},
Booktitle = {Proceedings of SC09},
Organization = {ACM},
Title = {Minimizing communication in sparse matrix solvers},
doi = {10.1145/1654059.1654096},
Year = {2009}
}
@inproceedings{vanRosendale83,
title={Minimizing inner product data dependencies in conjugate gradient iteration},
booktitle={Proceedings of the IEEE International Conference on Parallel Processing},
author={J. van Rosendale},
year={1983},
publisher = "IEEE Computer Society",
}
@phdthesis{Vuduc95,
title={Quantitative performance modeling of scientific computations and creating locality in numerical algorithms},
author={R. Vuduc},
journal={Massachusetts Institute of Technology},
school={Massachusetts Institute of Technology},
year={1995}
}
@article{simoncini2003flexible,
title={Flexible inner-outer {Krylov} subspace methods},
author={Simoncini, V. and Szyld, D.B.},
journal={SIAM Journal on Numerical Analysis},
pages={2219--2239},
year={2003},
publisher={JSTOR}
}
@article{parks2006recycling,
title={Recycling {K}rylov Subspaces for Sequences of Linear Systems},
author={Parks, M.L. and de Sturler, E. and Mackey, G. and Johnson, D.D. and Maiti, S.},
journal={SIAM Journal on Scientific Computing},
volume={28},
number={5},
pages={1651--1674},
year={2006},
publisher={Society for Industrial and Applied Mathematics}
}
@article{freund2003model,
title={Model reduction methods based on Krylov subspaces},
author={Freund, R.W.},
journal={Acta Numerica},
volume={12},
number={1},
pages={267--319},
year={2003},
publisher={Cambridge Univ Press}
}
@inbook{gutknecht2006block,
title={Block {K}rylov space methods for linear systems with multiple right-hand sides: an introduction},
booktitle={Modern Mathematical Models, Methods and Algorithms for Real World Systems},
author={Gutknecht, M.H.},
editors={Siddiqi A.H. and Duff I.S. and Christensen O.},
publisher={Anamaya Publishers},
location={New Delhi},
pages = {420-447},
year={2006}
}
@article{moulton1998black,
title={The black box multigrid numerical homogenization algorithm},
author={Moulton, J.D. and Dendy, J.E. and Hyman, J.M. and others},
journal={Journal of Computational Physics},
volume={142},
number={1},
pages={80--108},
year={1998},
publisher={Elsevier}
}
@article{neuss2001homogenization,
title={Homogenization and multigrid},
author={Neuss, N. and J{\"a}ger, W. and Wittum, G.},
journal={Computing},
volume={66},
number={1},
pages={1--26},
year={2001},
publisher={Springer}
}
@article{bai2002krylov,
title={Krylov subspace techniques for reduced-order modeling of large-scale dynamical systems},
author={Bai, Z.},
journal={Applied Numerical Mathematics},
volume={43},
number={1},
pages={9--44},
year={2002},
publisher={Elsevier}
}
@inproceedings{dong2003piecewise,
title={Piecewise polynomial nonlinear model reduction},
author={Dong, N. and Roychowdhury, J.},
booktitle={Design Automation Conference, 2003. Proceedings},
pages={484--489},
year={2003},
organization={IEEE}
}
@article{bond2009stable,
title={Stable reduced models for nonlinear descriptor systems through piecewise-linear approximation and projection},
author={Bond, B.N. and Daniel, L.},
journal={IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems},
volume={28},
number={10},
pages={1467--1480},
year={2009},
publisher={IEEE}
}
@article{xin2000front,
title={Front Propagation in Heterogeneous Media},
author={Xin, J.},
journal={SIAM Review},
volume={42},
number={2},
pages={161--230},
year={2000},
publisher={Society for Industrial and Applied Mathematics}
}
@article{owhadi2011localized,
title={Localized Bases for Finite-Dimensional Homogenization Approximations with Nonseparated Scales and High Contrast},
author={Owhadi, H. and Zhang, L.},
journal={Multiscale Modeling and Simulation},
volume={9},
pages={1373},
year={2011}
}
@article{berlyand2010flux,
title={Flux norm approach to finite dimensional homogenization approximations with non-separated scales and high contrast},
author={Berlyand, L. and Owhadi, H.},
journal={Archive for rational mechanics and analysis},
volume={198},
number={2},
pages={677--721},
year={2010},
publisher={Springer}
}
@article{babuska2011optimal,
title={Optimal Local Approximation Spaces for Generalized Finite Element Methods with Application to Multiscale Problems},
author={Babuska, I. and Lipton, R.},
journal={Multiscale Modeling \& Simulation},
volume={9},
pages={373},
year={2011}
}
@article{boettinger2002phase,
title={Phase-Field Simulation of Solidification},
author={Boettinger, W.J. and Warren, J.A. and Beckermann, C. and Karma, A.},
journal={Annual review of materials research},
volume={32},
number={1},
pages={163--194},
year={2002},
publisher={Annual Reviews}
}
@article{karma1998quantitative,
title={Quantitative phase-field modeling of dendritic growth in two and three dimensions},
author={Karma, A. and Rappel, W.J.},
journal={Physical Review E},
volume={57},
number={4},
pages={4323},
year={1998},
publisher={APS}
}
@article{chen2002phase,
title={Phase-field models for microstructure evolution},
author={Chen, L.Q.},
journal={Annual review of materials research},
volume={32},
number={1},
pages={113--140},
year={2002},
publisher={Annual Reviews}
}
@article{galbally2010reductionuq,
title={Non-linear model reduction for uncertainty quantification in large-scale inverse problems},
author={Galbally, D. and Fidkowski, K. and Willcox, K. and Ghattas, O.},
journal={International journal for numerical methods in engineering},
volume={81},
number={12},
pages={1581--1608},
year={2010},
publisher={Wiley Online Library}
}
@article{griebel1995abstract,
title={On the abstract theory of additive and multiplicative {Schwarz} algorithms},
author={Griebel, M. and Oswald, P.},
journal={Numerische Mathematik},
volume={70},
number={2},
pages={163--180},
year={1995},
publisher={Springer}
}
@inproceedings{voutchkov2006multiobjective,
title={Multiobjective optimization using surrogates},
author={Voutchkov, I. and Keane, A.J.},
booktitle={Adaptive Computing in Design and Manufacture},
pages={167--175},
year={2006},
publisher={The MC Escher Company}
}
@article{leary2001constraint,
title={A constraint mapping approach to the structural optimization of an expensive model using surrogates},
author={Leary, S.J. and Bhaskar, A. and Keane, A.J.},
journal={Optimization and Engineering},
volume={2},
number={4},
pages={385--398},
year={2001},
publisher={Springer}
}
@inproceedings{legresley2000airfoil,
title={Airfoil design optimization using reduced order models based on proper orthogonal decomposition},
author={LeGresley, P.A. and Alonso, J.J.},
booktitle={Fluids 2000 Conference and Exhibit, Denver, CO},
year={2000}
}
@book{myers2009response,
title={Response surface methodology: process and product optimization using designed experiments},
author={Myers, R.H. and Montgomery, D.C. and Anderson-Cook, C.M.},
volume={705},
year={2009},
publisher={John Wiley \& Sons}
}
@article{carlberg2012gnat,
title={The {GNAT} method for nonlinear model reduction: effective implementation and application to computational fluid dynamics and turbulent flows},
author = {Kevin Carlberg and Charbel Farhat and Julien Cortial and David Amsallem},
journal={arXiv},
volume={1207.1349},
year = 2012
}
@article{biros2008multilevel,
title={A multilevel algorithm for inverse problems with elliptic {PDE} constraints},
author={Biros, G. and Dogan, G.},
journal={Inverse Problems},
volume={24},
pages={034010},
year={2008},
publisher={IOP Publishing}
}
@article{rees2010optimal,
title={Optimal Solvers for {PDE}-Constrained Optimization},
author={Rees, T. and Dollar, H.S. and Wathen, A.J.},
journal={SIAM Journal on Scientific Computing},
volume={32},
pages={271},
year={2010}
}
@article{rees2010block,
title={Block-triangular preconditioners for {PDE}-constrained optimization},
author={Rees, T. and Stoll, M.},
journal={Numerical Linear Algebra with Applications},
volume={17},
number={6},
pages={977--996},
year={2010},
publisher={Wiley Online Library}
}
@article{rees2011preconditioning,
title={Preconditioning Iterative Methods for the Optimal Control of the {S}tokes Equations},
author={Rees, T. and Wathen, A.J.},
journal={SIAM Journal on Scientific Computing},
volume={33},
number={5},
pages={2903--2926},
year={2011},
publisher={Society for Industrial and Applied Mathematics}
}
@article{vogel2007fbicg,
title={Flexible {BiCG} and flexible {Bi-CGSTAB} for nonsymmetric linear systems},
author={Vogel,J.A.},
journal={Applied Mathematics and Computation},
volume={188},
number={1},
pages={226–-233},
year={2007},
publisher={Elsevier}
}
@article{ZhengEtAl12,
title = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with strongly variable viscosity based on {M}atlab and {CUDA}},
author = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
journal = {IJHPCA},
year = {2012},
note = {submitted}
}
@UnPublished(LeeHammond2010,
Author= "B. Lee and G.E. Hammond",
Title= "Parallel Performance of Preconditioned {Krylov} Solvers for the {Richards} Equation",
Key= "multigrid",
Note= "manuscript, 2010")
@article{vandeneshop2004inexact,
title={Inexact {Krylov} Subspace Methods for Linear Systems},
author={Jasper {van den} Eshof and Gerard L. G. Sleijpen},
journal={SIAM Journal on Matrix Analysis and Applications},
volume={26},
number={1},
pages={125--153},
year={2004},
}
@article{fbicg.fbcgs,
title={Flexible {BiCG} and flexible {Bi-CGSTAB} for nonsymmetric linear systems},
author={Judith A. Vogel},
journal={Applied Mathematics and Computation},
volume={188},
number={1},
pages={226--233},
year={2007},
}
@article{simoncini2003inexact,
title={Theory of Inexact {Krylov} Subspace Methods and Applications to Scientific Computing},
author={Valeria Simoncini and Daniel B. Szyld},
journal={SIAM Journal on Scientific Computing},
volume={25},
number={2},
pages={454--477},
year={2003},
}
@article{fqmr,
title={{FQMR}: A Flexible {Quasi-Minimal Residual} Method with Inexact Preconditioning},
author={Daniel B. Szyld and Judith A. Vogel},
journal={SIAM Journal on Scientific Computing},
volume={23},
number={2},
pages={363--380},
year={2001},
}
@article{ipcg,
title={Inexact Preconditioned {Conjugate Gradient} Method with Inner-Outer Iteration},
author={Gene H. Golub and Qiang Ye},
journal={SIAM Journal on Scientific Computing},
volume={21},
number={4},
pages={1305--1320},
year={1999},
}
@article{idr.Sonneveld,
title={{IDR}(s): A Family of Simple and Fast Algorithms for Solving Large Nonsymmetric Systems of Linear Equations},
author={Peter Sonneveld and Martin B. van Gijzen},
journal={SIAM Journal on Scientific Computing},
volume={31},
number={2},
pages={1035--1062},
year={2008},
}
@article{flexibleCG,
title={Flexible {Conjugate Gradients}},
author={Yvan Notay},
journal={SIAM Journal on Scientific Computing},
volume={22},
number={4},
pages={1444--1460},
year={2000},
}
@article{generalizedCG,
title={A Black Box Generalized {Conjugate Gradient} Solver with Inner Iterations and Variable-Step Preconditioning},
author={O. Axelsson and P. S. Vassilevski},
journal={SIAM Journal on Matrix Analysis and Applications},
volume={12},
number={4},
pages={625--644},
year={1991},
}
@article{bicg,
title={{Conjugate Gradient} methods for indefinite systems},
author={R. Fletcher},
journal={Lecture Notes in Mathematics},
volume={506},
pages={73--89},
year={1976},
}
@article{idr.bcgs,
title={{Bi-CGSTAB} as an induced dimension reduction method},
author={Gerard L.G. Sleijpen and Peter Sonneveld and Martin B. van Gijzen},
journal={Applied Numerical Mathematics},
volume={60},
pages={1100--1114},
year={2010},
}
@article{idr.bcgsl,
title={Exploiting {BiCGstab($\ell$)} strategies to induce dimension reduction},
author={Gerard L.G. Sleijpen and Martin B. van Gijzen},
journal={SIAM J. Sci. Comput.},
volume={32},
number={5},
pages={2687--2709},
year={2010},
}
@article{idr.min.sync,
title={Minimizing synchronization in {IDR(s)}},
author={T.P. Collignon and M.B. van Gijzen},
journal={Numerical Linear Algebra with Applications},
volume={18},
number={5},
pages={805--825},
year={2011},
}
@techreport{flexible.idr,
title={Flexible and Multi-Shift Induced Dimension Reduction Algorithms for solving Large Sparse Linear Systems},
author={Martin B. van Gijzen and Gerard L.G. Sleijpen and Jens-Peter M. Zemke},
institution={Delft University of Technology},
number={11-06},
year={2011},
}
@article{vanGenuchten1980,
title="A Closed-form Equation for Predicting the Hydraulic Conductivity of Unsaturated Soils",
author={M. Th. van Genuchten},
journal={Soil Science Society of America Journal},
volume={44},
pages={892--898},
year={1980},
}
@article{gmresr94,
title={{GMRESR}: a family of nested {GMRES} methods},
author={H. A. Van der Vorst and C. Vuik},
journal={Numerical Linear Algebra with Applications},
volume={1},
number={4},
pages={369--386},
year={1994},
}
@article{Knepley10,
author = {Matthew G. Knepley},
title = {Removing the Barrier to Scalability in Parallel FMM},
journal = {CoRR},
volume = {abs/1008.2410},
note = {\url{http://arxiv.org/abs/1008.2410}},
year = {2010}
}
@article{Teng1998,
author = {Shang-Hua Teng},
title = {Provably Good Partitioning and Load Balancing Algorithms for Parallel Adaptive N-Body Simulation},
journal = {SIAM J. Sci. Comput.},
volume = {19},
number = {2},
month = mar,
pages = {635--656},
year = {1998},
issn = {1064-8275},
numpages = {22},
url = {http://dx.doi.org/10.1137/S1064827595288942},
doi = {10.1137/S1064827595288942},
acmid = {289842},
issue_date = {March 1998},
publisher = {Society for Industrial and Applied Mathematics},
address = {Philadelphia, PA},
keywords = {N-body simulation, adaptive computing, hierarchical methods, load balancing, parallel processing, partitioning, scientific computing, the fast multipole method, tree-codes},
}
@inproceedings{SkinnerKramer05,
author = {David Skinner and William Kramer},
title = {Understanding the causes of performance variability in HPC workloads},
booktitle = {Workload Characterization Symposium, 2005. Proceedings of the IEEE International},
organization = {IEEE},
pages = {137--149},
year = {2005}
}
@article{Notay_2000,
author = {Yvan Notay},
title = {Flexible {Conjugate Gradients}},
journal = {SIAM Journal on Scientific Computing},
volume = {22},
number = {4},
year = {2000},
pages = {1444--1460}
}
@article{pawlowski2006globalization,
title={Globalization techniques for {N}ewton-{K}rylov methods and applications to the fully coupled solution of the {N}avier-{S}tokes equations},
author={Pawlowski, Roger P and Shadid, John N and Simonis, Joseph P and Walker, Homer F},
journal={SIAM Review},
volume={48},
number={4},
pages={700--721},
year={2006},
publisher={SIAM}
}
@article{brown1985experiments,
title={Experiments with quasi-{N}ewton methods in solving stiff {ODE} systems},
author={Brown, P.N. and Hindmarsh, A.C. and Walker, H.F.},
journal={SIAM Journal on Scientific and Statistical Computing},
volume={6},
number={2},
pages={297--313},
year={1985},
publisher={SIAM}
}
@article{bicgsl_1993,
author = {GERARD L.G. SLEIJPEN and DIEDERIK R. FOKKEMA},
title = {{BiCGSTAB(l)} for Linear Equations involving Unsymmetric Matrices with Complex Spectrum},
journal = {Electronic Transactions on Numerical Analysis},
volume = {1},
year = {1993},
pages = {11--32}
}
@book{brandt2011revised,
title={Multigrid Techniques: 1984 Guide with Applications to Fluid Dynamics, Revised Edition},
author={Achi Brandt and Oren Livne},
year=2011,
publisher={SIAM}
}
@article{axelsson1990algebraic,
title={Algebraic multilevel preconditioning methods, {II}},
author={Axelsson, O. and Vassilevski, P.S.},
journal={SIAM Journal on Numerical Analysis},
volume={27},
number={6},
pages={1569--1590},
year={1990},
publisher={SIAM}
}
@article{zulehner2002analysis,
title={Analysis of iterative methods for saddle point problems: a unified approach},
author={Zulehner, W.},
journal={Mathematics of computation},
volume={71},
number={238},
pages={479--506},
year={2002}
}
@article{Pralet2010,
author={L. Giraud and A. Haidar and S. Pralet},
title={Using multiple levels of parallelism to enhance the performance of domain decomposition solvers},
journal={Parallel Computing},
volume={36},
number={5-6},
pages={285--296},
year={2010}
}
@book{BrennerScottFEM,
title = {The Mathematical Theory of Finite Element Methods},
author = {Susanne C. Brenner and L. Ridgway Scott},
edition = {3rd Edition},
series = {Texts in Applied Mathematics},
year = {2008},
publisher = {Springer-Verlag}
}
@book{ortega1987iterative,
title = {Iterative solution of nonlinear equations in several variables},
author = {Ortega, James M and Rheinboldt, Werner C},
volume = {30},
publisher = {Society for Industrial and Applied Mathematics},
year = {1987}
}
@inbook{RheinboldtCh6,
author = {Werner C. Rheinboldt},
title = {6. Combinations of Processes},
booktitle = {Methods for Solving Systems of Nonlinear Equations},
chapter = {6},
pages = {59--74},
doi = {10.1137/1.9781611970012.ch6},
URL = {http://epubs.siam.org/doi/abs/10.1137/1.9781611970012.ch6},
eprint = {http://epubs.siam.org/doi/pdf/10.1137/1.9781611970012.ch6},
year = {1998}
}
@article{AllgowerBohmerPotraRheinboldt86,
author = {E. Allgower and K. B\"ohmer and F. Potra and W.~C. Rheinboldt},
title = {A Mesh-Independence Principle for Operator Equations and Their Discretizations},
journal = {SIAM Journal on Numerical Analysis},
volume = {23},
number = {1},
pages = {160-169},
year = {1986},
doi = {10.1137/0723011},
URL = {http://epubs.siam.org/doi/abs/10.1137/0723011},
eprint = {http://epubs.siam.org/doi/pdf/10.1137/0723011}
}
@article{Rheinboldt76,
author = {Werner C. Rheinboldt},
title = {On measures of ill-conditioning for nonlinear equations},
journal = {Mathematics of Computation},
volume = {30},
number = {133},
pages = {104--111},
year = {1976}
}
@article{Little61,
author = {John D. C. Little},
title = {A Proof for the Queuing Formula: {$L = \lambda W$}},
journal = {Operations Research},
volume = {9},
number = {3},
pages = {383--387},
note = {\url{http://www.jstor.org/stable/167570}},
year = {1961}
}
@misc{Top500,
author = {{TOP500 Supercomputer Sites}},
url = {http://www.top500.org},
year = {2013}
}
@misc{HasseDiagram,
author = {Wikipedia},
title = {Hasse Diagram},
url = {http://en.wikipedia.org/wiki/Hasse_diagram},
note = {\url{http://en.wikipedia.org/wiki/Hasse_diagram}},
year = {2015}
}
@misc{Groupoid,
author = {Wikipedia},
title = {Groupoid},
url = {https://en.wikipedia.org/wiki/Groupoid},
note = {\url{http://en.wikipedia.org/wiki/Groupoid}},
year = {2015}
}
@misc{CWcomplex,
author = {Wikipedia},
title = {CW complex},
url = {http://en.wikipedia.org/wiki/CW_complex},
note = {\url{http://en.wikipedia.org/wiki/CW_complex}},
year = {2015}
}
@article{korelc2002multilanguage,
title={Multi-language and multi-environment generation of nonlinear finite element codes},
author={Korelc, J.},
journal={Engineering with Computers},
volume={18},
number={4},
pages={312--327},
year={2002},
publisher={Springer}
}
@techreport{taylor2011feap,
title={{FEAP}: A Finite Element Analysis Program},
subtitle={Version 8.3 User Manual},
author={R. L. Taylor},
year=2011,
institution={University of California, Berkeley}
}
@article{BergerAftosmisMurman2005,
title={Analysis of slope limiters on irregular grids},
author={Berger, Marsha and Aftosmis, Michael J and Murman, Scott M},
journal={AIAA paper},
volume={490},
pages={2005},
year={2005}
}
@inproceedings{FerreiraBridgesBrightwell08,
author = {Kurt B. Ferreira and Patrick Bridges and Ron Brightwell},
title = {Characterizing Application Sensitivity to OS Interference Using Kernel-level Noise Injection},
booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing},
series = {SC '08},
year = {2008},
isbn = {978-1-4244-2835-9},
location = {Austin, Texas},
pages = {19:1--19:12},
articleno = {19},
numpages = {12},
url = {http://dl.acm.org/citation.cfm?id=1413370.1413390},
acmid = {1413390},
publisher = {IEEE Press},
address = {Piscataway, NJ},
}
@article{BardhanKnepley14,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions},
journal = {Journal of Chemical Physics},
volume = {141},
number = {13},
eid = {131103},
url = {http://scitation.aip.org/content/aip/journal/jcp/141/13/10.1063/1.4897324},
doi = {http://dx.doi.org/10.1063/1.4897324},
year = {2014}
}
@article{Banach22,
author = {Stefan Banach},
title = {Sur les op\'erations dans les ensembles abstraits et leur application aux \'equations int\'egrales},
journal = {Fund. Math.},
volume = {3},
pages = {133--181},
year = {1922}
}
@article{BangerthBursteddeHeisterKronbichler2012,
author = {Wolfgang Bangerth and Carsten Burstedde and Timo Heister and Martin Kronbichler},
title = {Algorithms and Data Structures for Massively Parallel Generic Adaptive Finite Element Codes},
journal = {ACM Trans. Math. Softw.},
issue_date = {December 2011},
volume = {38},
number = {2},
month = jan,
year = {2012},
issn = {0098-3500},
pages = {14:1--14:28},
articleno = {14},
numpages = {28},
url = {http://doi.acm.org/10.1145/2049673.2049678},
doi = {10.1145/2049673.2049678},
acmid = {2049678},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {Adaptive mesh refinement, object-orientation, parallel algorithms, software design},
}
@article{EisenstatWalker1994,
author = {Stanley Eisenstat and Homer Walker},
title = {Globally Convergent Inexact {N}ewton Methods},
journal = {SIAM Journal on Optimization},
volume = {4},
number = {2},
pages = {393--422},
year = {1994},
doi = {10.1137/0804022},
url = {http://dx.doi.org/10.1137/0804022},
eprint = {http://dx.doi.org/10.1137/0804022}
}
@book{BlumCuckerShubSmale98,
title = {Complexity and Real Computation},
author = {Lenore Blum and Felipe Cucker and Michael Shub and Steve Smale},
year = {1998},
publisher = {Springer}
}
@article{CaiLi2011,
author = {Cai, X.-C. and Li, X.},
title = {Inexact {N}ewton Methods with Restricted Additive {S}chwarz Based Nonlinear Elimination for Problems with High Local Nonlinearity},
journal = {SIAM Journal on Scientific Computing},
volume = {33},
number = {2},
pages = {746-762},
year = {2011},
doi = {10.1137/080736272},
URL = {http://epubs.siam.org/doi/abs/10.1137/080736272},
eprint = {http://epubs.siam.org/doi/pdf/10.1137/080736272}
}
@article{Cai2009,
author = {X.-C. Cai},
title = { Nonlinear overlapping domain decomposition methods},
journal = {Lecture Notes in Computational Science},
volume = {70},
pages = {217-224},
year = {2009}
}
@article{LanzkronRoseWilkes1996,
title={An analysis of approximate nonlinear elimination},
author={Lanzkron, Paul J and Rose, Donald J and Wilkes, James T},
journal={SIAM Journal on Scientific Computing},
volume={17},
number={2},
pages={538--559},
year={1996},
publisher={SIAM}
}
@misc{SimplifiedBSD,
author = {{University of California, Berkeley}},
title = {Simplified {Berkeley} Software Distribution License},
note = {see \url{http://en.wikipedia.org/wiki/BSD_licenses#2-clause_license_.28.22Simplified_BSD_License.22_or_.22FreeBSD_License.22.29}},
}
@book{ChaconStraub14,
author = {Scott Chacon and Ben Straub},
title = {Pro Git},
publisher = {Apress},
year = {2014},
pages = {456},
note = {Available online at \url{http://git-scm.com/book/}}
}
@misc{Bitbucket,
author = {Atlassian},
title = {Bitbucket},
note = {Platform available from \url{http://bitbucket.org}}
}
@misc{GitWorkflows,
author = {GitWorkflows},
note = {Available at \url{https://www.kernel.org/pub/software/scm/git/docs/gitworkflows.html}}
}
@misc{FigShare,
author = {FigShare},
note = {Available at \url{http://palgrave.figshare.com/}}
}
@misc{SoftwareProductivityWorkshopReport14,
author = {H. Johansen and L. C. McInnes and D. Bernholdt and J. Carver and M. Heroux and
R. Hornung and P. Jones and B. Lucas and A. Siegel and T. Ndousse-Fetter},
title = {Software Productivity for Extreme-Scale Science},
note = {Report on DOE Workshop, January 13-14, 2014},
url = {http://www.orau.gov/swproductivity2014/SoftwareProductivityWorkshopReport2014.pdf},
year = 2014
}
@misc{SoftwareProductivityWhitepaper13,
author = {H. Johansen and D. Bernholdt and B. Collins and M. Heroux and R. Jacob and
P. Jones and L. C. McInnes and J. D. Moulton and T. Ndousse-Fetter and
D. Post and W. Tang},
title = {Extreme-Scale Scientific Application Software Productivity: Harnessing the Full Capability of Extreme-Scale Computing},
note = {whitepaper submitted to DOE, available via \url{http://www.orau.gov/swproductivity2014/reference.htm}},
year = 2013
}
@Misc{IDEAS:project,
author = {Michael Heroux and Lois Curfman McInnes and J. David {Moulton (PIs)}},
title = {{Interoperable Design of Extreme-Scale Application Software (IDEAS)}},
howpublished = "\url{http://ideas-productivity.org}",
year = 2015
}
@techreport{KeyesMcInnesWoodwardEtAl2012,
author = {D. E. Keyes and L. C. McInnes and C. Woodward and E. Constantinescu and D. Estep and B. Sheehan},
title = {First Steps Toward a Multiphysics Exemplars and Benchmarks Suite},
institution = {Argonne National Laboratory},
number = {ANL/MCS-TM-330},
month = {Oct},
year = 2012
}
@Misc{ sawsFS-web-page,
author = "Surtai Han and Barry Smith and Hong Zhang",
title = "{{SAWs Tutorial: Fieldsplit Preconditioner}}",
note = "\url{https://www.youtube.com/watch?v=-w0fPhmZT3c}",
year = 2015
}
@Misc{ sawsHK-web-page,
author = "Surtai Han and Barry Smith and Hong Zhang",
title = "{{SAWs Tutorial: Hierarchical Krylov Method}}",
note = "\url{https://www.youtube.com/watch?v=hWbqppTrcOw}",
year = 2015
}
@Misc{ sawsNestK-web-page,
author = "Surtai Han and Barry Smith and Hong Zhang",
title = "{{SAWs Tutorial: Nested Krylov Method}}",
note = "\url{https://www.youtube.com/watch?v=kqPXZxMOJmA}",
year = 2015
}
@misc{m2acs:project,
author = "M. {Anitescu et al.}",
title = "{Multifaceted Mathematics for Complex Energy Systems (M2ACS) {W}eb page}",
howpublished = "\url{http://www.mcs.anl.gov/MACS}",
year = 2015
}
@misc{hssmn13,
author = {P. Hovland and B. Smith and M. Snir and L. C. McInnes and B. Norris},
title = {Exposing and Expanding Compiler Technologies to Improve Software Productivity in Developing Mathematical Libraries and Simulation Codes},
note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}},
year = 2013
}
@misc{atpesc:website,
author = "P. {Messina et al.}",
title = "{Argonne Training Program for Extreme-Scale Computing}",
howpublished = "\url{http://extremecomputingtraining.anl.gov}",
year = 2015
}
@article{BarraultMadayNguyenPatera2004,
author = "Maxime Barrault and Yvon Maday and Ngoc Cuong Nguyen and Anthony T. Patera",
title = "An empirical interpolation method: application to efficient reduced-basis discretization of partial differential equations",
journal = "Comptes Rendus Mathematique",
volume = "339",
number = "9",
pages = "667--672",
year = "2004",
issn = "1631-073X",
doi = "http://dx.doi.org/10.1016/j.crma.2004.08.006",
url = "http://www.sciencedirect.com/science/article/pii/S1631073X04004248"
}
@article{SimonGogotsi08,
title = {Materials for electrochemical capacitors},
author = {Patrice Simon and Yury Gogotsi},
journal = {Nature Materials},
volume = {7},
number = {11},
pages = {845--854},
year = {2008},
doi = {http://dx.doi.org/10.1038/nmat2297}
}
@article{VladSinghRollandMelinteAjayanGohy14,
title = {Hybrid supercapacitor-battery materials for fast electrochemical charge storage},
author = {A. Vlad and N. Singh and J. Rolland and S. Melinte and P. M. Ajayan and J.-F. Gohy},
journal = {Scientific Reports},
volume = {4},
year = {2014},
doi = {http://dx.doi.org/10.1038/srep04315}
}
@article{LiChengShashurinKeidar12,
title = {Review of Electrochemical Capacitors Based on Carbon Nanotubes and Graphene},
author = {J. Li and X. Cheng and A. Shashurin and M. Keidar},
journal = {Graphene},
volume = {1},
number = {1},
pages = {1--13},
year = {2012},
doi = {10.4236/graphene.2012.11001}
}
@article{Miller07,
title = {A Brief History of Supercapacitors},
author = {John R. Miller},
journal = {Battery and Energy Storage Technology},
pages = {61--78},
year = {2007}
}
@book{Deshpande14,
title = {Ultracapacitors: Future of Energy Storage},
author = {R. P. Deshpande},
publisher = {McGraw Hill Education},
isbn = {978-9339214050},
pages = {452},
year = {2014}
}
@article{HoJowBoggs10,
title = {Historical introduction to capacitor technology},
author = {J. Ho and T.R. Jow and S. Boggs},
journal = {IEEE Electrical Insulation Magazine},
month = {January},
volume = {26},
number = {1},
pages = {20--25},
year = {2010},
doi = {10.1109/MEI.2010.5383924},
issn = {0883-7554}
}
@article{Gillespie14,
title = {A review of steric interactions of ions: Why some theories succeed and others fail to acount for ion size},
author = {Dirk Gillespie},
journal = {Microfluidics and Nanofluidics},
note = {in press},
year = {2014}
}
@article{GillespieValiskoBoda05,
author = {Dirk Gillespie and Monica Valisk\'{o} and Dezs\H{o} Boda},
title = {Density functional theory of the electrical double layer: the RFD functional},
journal = {J. Phys.: Condens. Matter},
volume = {17},
pages = {6609--6626},
year = {2005}
}
@article{ValiskoBodaGillespie07,
author = {Monica Valisk\'{o} and Dezs\H{o} Boda and Dirk Gillespie},
title = {Selective adsorption of ions with different diameter and valence at highly-charged interfaces},
journal = {J. Phys. Chem. C},
volume = {111},
pages = {15575--15585},
year = {2007}
}
@article{Gillespie08,
author = {Dirk Gillespie},
title = {Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study},
journal = {Biophys. J.},
volume = {94},
pages = {1169--1184},
year = {2008}
}
@article{LiWuWang15,
title = {Osmotic Pressure and Packaging Structure of Caged DNA},
author = {Zhidong Li and Jianzhong Wu and Zhen-Gang Wang},
journal = {Biophysical Journal},
volume = {94},
number = {3},
pages = {737--746},
doi = {10.1529/biophysj.107.112508},
url = {http://www.cell.com/biophysj/abstract/S0006-3495(08)70675-1},
year = {2015}
}
@article{Gillespie12,
title = {High energy conversion efficiency in nanofluidic channels},
author = {Dirk Gillespie},
journal = {Nano Letters},
volume = {12},
pages = {1410--1416},
year = {2012}
}
@article{Dieterich79,
title = {Modeling of rock friction: 1. Experimental results and constitutive equations},
author = {James H. Dieterich},
journal = {Journal of Geophysical Research: Solid Earth},
volume = {84},
number = {B5},
pages = {2161--2168},
year = {1979},
publisher = {Wiley Online Library}
}
@article{BodaKovacsGillespieKristof14,
title = {Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst--Planck equation},
author = {Dezs{\H{o}} Boda and R{\'o}bert Kov{\'a}cs and Dirk Gillespie and Tam{\'a}s Krist{\'o}f},
journal = {Journal of Molecular Liquids},
volume = {189},
pages = {100--112},
year = {2014},
publisher = {Elsevier}
}
@article{Brandt05,
title={Multiscale solvers and systematic upscaling in computational physics},
author={Brandt, A},
journal={Computer Physics Communications},
volume={169},
number={1},
pages={438--441},
year={2005},
publisher={Elsevier}
}
@article{Rosenfeld89,
title={Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing},
author={Yaakov Rosenfeld},
journal={Physical review letters},
volume={63},
number={9},
pages={980},
year={1989},
publisher={APS}
}
@article{SchindlerMitchellMcCabeCummingsLeVan13,
title={Adsorption of Chain Molecules in Slit-Shaped Pores: Development of a SAFT-FMT-DFT Approach},
author={Bryan J Schindler and Lucas A Mitchell and Clare McCabe and Peter T Cummings and M Douglas LeVan},
journal={The Journal of Physical Chemistry C},
volume={117},
number={41},
pages={21337--21350},
year={2013},
publisher={ACS Publications}
}
@misc{TRAMONTO,
author = {Laura Frink and et. al.},
title = {TRAMONTO 3.0 web site},
url = {https://software.sandia.gov/DFTfluids/tramonto3_0.html},
year = {2014}
}
@incollection{ZhongYuenMoresiKnepley15,
author = {Shijie Zhong and David A. Yuen and Louis N. Moresi and Matthew G. Knepley},
title = {Numerical Methods for Mantle Convection},
booktitle = {Treatise on Geophysics},
publisher = {Elsevier},
volume = {7},
editor = {Gerald Schubert},
edition = {Second Edition},
year = {2015},
}
@article{Richarson1911,
author = {Lewis Fry Richardson},
title = {The approximate arithmetical solution by finite differences of physical problems including differential equations, with an application to the stresses in a masonry dam},
journal = {Philosophical Transactions of the Royal Society A},
volume = {210},
number = {459--470},
pages = {307--357},
doi = {doi:10.1098/rsta.1911.0009},
year = {1911},
}
@article{Kirkwood34,
author = {John G. Kirkwood},
title = {Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions},
journal = {The Journal of Chemical Physics},
volume = {2},
number = {7},
year = {1934}
}
@techreport{schoof1994exodus,
title = {{EXODUS II}: a finite element data model},
author = {Larry A Schoof and Victor R Yarberry},
institution = {Sandia National Laboratories},
number = {SAND92-2137},
address = {Albuquerque, NM},
year = {1994}
}
@misc{poirier1998cgns,
author = {Diane Poirier and Steven R Allmaras and Douglas R McCarthy and Matthew F Smith and Fancis Y Enomoto},
title = {The CGNS system},
note = {AIAA Paper 98-3007},
year = {1998}
}
@article{geuzaine2009gmsh,
title = {Gmsh: A 3-D finite element mesh generator with built-in pre-and post-processing facilities},
author = {Christophe Geuzaine and Jean-Fran{\c{c}}ois Remacle},
journal = {International Journal for Numerical Methods in Engineering},
volume = {79},
number = {11},
pages = {1309--1331},
year = {2009},
publisher = {Wiley Online Library}
}
@article{Si2015,
title = {TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator},
author = {Hang Si},
journal = {ACM Trans. on Mathematical Software},
volume = {41},
number = {2},
month = {February},
doi = {10.1145/2629697},
year = {2015},
}
@article{Bjorck1994,
title = {Numerics of Gram-Schmidt orthogonalization},
author = {{\AA}ke Bj{\"o}rck},
journal = {Linear Algebra and Its Applications},
volume = {197},
pages = {297--316},
year = {1994},
publisher = {Elsevier}
}
@phdthesis{Yood05,
author = {Charles Nelson Yood},
title = {Argonne National Laboratory and the Emergence of Computer and Computational Science, 1946--1992},
school = {The Pennsylvania State University},
month = {August},
year = {2005},
}