%
% 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{more1994line,
title={Line search algorithms with guaranteed sufficient decrease},
author={Mor{\'e}, Jorge J and Thuente, David J},
journal={ACM Transactions on Mathematical Software},
volume={20},
number={3},
pages={286--307},
year={1994},
publisher={ACM}
}
@article{griewank2000algorithm,
title={Algorithm 799: revolve: an implementation of checkpointing for the reverse or adjoint mode of computational differentiation},
author={Griewank, Andreas and Walther, Andrea},
journal={ACM Transactions on Mathematical Software},
volume={26},
number={1},
pages={19--45},
year={2000},
publisher={ACM}
}
@article{metcalf2011seven,
title={The seven ages of fortran},
author={Metcalf, Michael},
journal={Journal of Computer Science \& Technology},
volume={11},
year={2011}
}
@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{Constantinescu_TR2016b,
author = {Constantinescu, E.M.},
title = {Estimating Global Errors in Time Stepping},
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1503.05166},
primaryClass = "math.NA",
keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70},
year = 2016,
month = mar,
adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@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@Unpublished{Boscarino_TR2011,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},
}
@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},
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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",
}
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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",
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}
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author = "G. A. Geist and J. A. Kohl and P. M. Papadopoulos",
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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}
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AUTHOR= "Valeria Simoncini and Daniel B. Szyld",
TITLE= " Theory of Inexact Krylov Subspace Methods and Applications to Scientific Computing",
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institution = "Department of Mathematics, Temple University",
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year = 1994,
institution = "Department of Computer Sciences, Purdue University",
number = "CSD-TR-94-021"
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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},
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author = "A. {Hindmarsh et al.}",
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@BOOK{szyperski97,
AUTHOR = "Clemens Szyperski",
TITLE = "Component Software: Beyond Object-Oriented Programming",
PUBLISHER = "ACM Press",
address = "New York",
YEAR = 1997
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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",
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@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"
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author = {B. F. {Smith et al.}},
title = "{External Software Used by PETSc}",
note = "\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}",
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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}",
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author = {B. F. {Smith et al.}},
title = "{Prizes Won Using PETSc}",
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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}",
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}
@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",
}
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AUTHOR= "Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski",
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PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
Inter-operable Scientific and Engineering Computing",
year = 1999,
pages = "30-39"
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AUTHOR= "Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens",
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PUBLISHER= "SIAM",
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AUTHOR= "Lori Freitag and Mark Jones and Paul Plassmann",
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PUBLISHER= "SIAM",
BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
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year = 1999,
pages = "215-224",
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publisher = "IEEE Computer Society Press",
year = {1997}
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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"
}
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author = {R. Das and M. Uysal and J. Saltz and Y. S. Hwang},
title = {Communication Optimizations for Irregular
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journal = {Journal of Parallel and Distributed Computing},
year = {1994},
volume = {22},
pages = {462--478}
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Parallelizing Structured and Block Structured Applications},
journal = {IEEE Trans. on Parallel and Distributed Systems},
volume = {6},
number = {7},
year = "1995"
}
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author = { William Gropp and Ewing Lusk and Nathan Doss and Anthony
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title = {A high-performance, portable implementation of the {MPI}
Message Passing Interface standard},
journal = {Parallel Computing},
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author = "Greg Burns and Raja Daoud and James Vaigl",
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author = "X.-C. Cai and M. Sarkis",
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year = "1999",
volume = "21",
pages = "792-797"
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@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)"
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@BOOK{ruminations,
AUTHOR="Andrew Koenig and Barbara Moo",
TITLE="Ruminations on C++",
YEAR="1996",
PUBLISHER="Addison-Wesley"
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TITLE="{MPI}: The Complete Reference",
YEAR="1995",
PUBLISHER="MIT Press"
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month = Aug
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author = {William Gropp and {et. al.}},
title = {{MPICH} {W}eb page},
key = "MPICH",
url = {http://www.mpich.org},
howpublished = {\url{http://www.mpich.org}},
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@Article{ MPI-final,
Title = "{MPI}: A Message-Passing Interface Standard",
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key = "NAS Parallel Benchmarks",
title = "{NAS} {P}arallel {B}enchmarks {W}eb page",
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month = Dec
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TITLE = "Computer Solution of Large Sparse Positive Definite Systems",
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KEY = "SparseDirect"
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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"
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author = "H. L. Stone",
title = "Iterative solution of implicit approximations of multidimensional partial differential equations",
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title = "Monitors, Messages, and Clusters: {T}he p4 Parallel
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Year = 1993
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@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",
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Year= "1991",
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@TechReport( p4-manual,
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Title= "User's Guide to the p4 Parallel Programming System",
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Year= "1992",
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YEAR = "1993"
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Author = "S. S. Mukherjee and S. D. Sharma and
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Title = "Efficient Support for Irregular Applications on
Distributed Memory Machines",
journal = "ACM SIGPLAN Notices",
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pages = "68-79",
volume = "30",
number = "8"
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Author = "J. Saltz and R. Mirchandaney and K. Crowley",
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journal = "IEEE Trans. Computers",
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pages = "604-612",
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Logic Programs",
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YEAR = "1987",
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publisher = "Birkhauser"
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@TechReport( aztec,
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Institution = "Sandia National Laboratories",
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@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",
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@Book{taylor-chandy:pcn,
Author = "Chandy, M. and Taylor, S.",
Title = "An Introduction to Parallel Programming",
Year = 1991,
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@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",
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NUMBER = 3,
YEAR = 1990,
PAGES = "243--271"
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@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})"
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@Techreport{picltrace,
Author = "P.~H.~Worley",
Title = "A new {PICL} trace file format",
Institution = "Oak Ridge National Laboratory",
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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"
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@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
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Key= "DryjaWidlund90 !AS")
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Author= "Matt Rosing and Joel Saltz",
Title= "Low Latency Messages on Distributed Memory Multiprocessors",
Key= "LowLatency",
Note= "manuscript, 1992")
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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"
}
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AUTHOR = "M. Pernice and H. F. Walker",
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year = 1998,
volume = 19,
pages = "302--318"
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@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"
}
@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{Knuth1986,
title = {The {\TeX}{Book}},
author = {Donald Ervin Knuth and Duane Bibby},
volume = {1993},
year = {1986},
publisher = {Addison-Wesley Reading, Massachusetts}
}
@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,
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title = "Hybrid {K}rylov Methods for Nonlinear Systems of Equations",
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year = 1990,
volume = 11,
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}
@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
}
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author="Magnus R. Hestenes and Eduard Steifel",
title="Methods of Conjugate Gradients for Solving Linear Systems",
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volume=49,
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@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"}
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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",
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volume=14,
year=1993,
pages="470-482"}
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author="S. Ishizuka",
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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",
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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,
}
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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} {Web} page},
title = {Matlab},
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/}",
}
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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}"
}
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Author = "A.M. Bruaset and H.P. Langtangen",
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Year = 1997,
pages = "61--90",
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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.",
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
}
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EDITOR = "David E. Keyes and Ahmed Sameh and V. Venkatakrishnan",
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YEAR = 1997
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AUTHOR = "Wolfgang Hackbusch",
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pages={565--581},
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author="Yousef Saad",
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title = "Iterative Krylov Methods for Large Linear Systems",
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EDITOR = "Alice E. Koniges",
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address = "San Francisco",
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@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}
}
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author = {Matteo Frigo and Steven G. Johnson},
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AUTHOR="C. T. Kelley",
TITLE="Iterative Methods for Linear and Nonlinear Equations",
YEAR="1995",
PUBLISHER="SIAM",
address="Philadelphia"
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AUTHOR="Jorge Nocedal and Stephen J. Wright",
TITLE="Numerical Optimization",
YEAR="1999",
PUBLISHER="Springer-Verlag",
address="New York"
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Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael Stal
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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"
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AUTHOR = "Nils Klarland and Michael I. Schwartzbach",
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YEAR = "1997",
ADDRESS = "Santa Barbara, CA",
}
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AUTHOR = "C. Consel and R. Marlet",
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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
}
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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",
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year = 2005
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title={{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}},
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booktitle={Proceedings of the 5th International Conference on Multibody Systems, Nonlinear Dynamics and Control, Long Beach, CA},
year={2005}
}
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number = 4,
year = 1999,
pages = "354 -- 365"
}
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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"
}
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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",
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year = 1998,
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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",
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YEAR = "2002",
MONTH = "November",
ADDRESS = "Baltimore"
}
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}
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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
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journal = "Int. J. Numer. Meth. Eng.",
year = "1984",
volume = "20",
pages = {1085--1109}
}
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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"
}
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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{ 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}
}
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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}}
}
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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}
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author = "Manish {Parashar et al.}",
title = "{GrACE Web Page}",
howpublished = "\url{http://www.caip.rutgers.edu/~parashar/TASSL/Projects/GrACE}",
}
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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},
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% -----------------------------------------------------------------------
% Model coupling refs
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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.
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@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"
}
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title = {Preconditioning for the steady-state {Navier-Stokes} equations for low viscosity},
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volume = {20},
year = {1996},
pages = {1299--1316}
}
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author = {D. Kay and D. Loghin and A. Wathen},
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journal = {SIAM J. Sci. Comput.},
volume = {24},
year = {2002},
pages = {237--256}
}
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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,
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year = {1997},
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@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},
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pages={1828--1840},
issn={0045-7825},
year={2010},
publisher={Elsevier}
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@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.},
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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}}
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@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},
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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}},
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year = 2009,
volume = {180},
pages = {887-903},
}
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author = {X.Q. Xu and R.H. Cohen},
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title={Newton's Method for Large Bound-constrained Optimization Problems},
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number = {1-2},
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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}
}
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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}
}
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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}"
}
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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}
}
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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}
}
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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}
}
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issn={0377-0427},
year={2001},
publisher={Elsevier}
}
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title={{Preconditioning for the steady-state Navier-Stokes equations with low viscosity}},
author={Elman, H.C.},
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volume={20},
number={4},
pages={1299--1316},
issn={1064-8275},
year={1999},
publisher={Citeseer}
}
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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-}
}
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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},
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year={2008},
organization={IEEE Press}
}
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number = "UMSI2004-8",
Institution = "Minnesota Supercomputer Institute, University of Minnesota",
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)
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author = {Emile Picard},
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@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},
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number = {51},
series = {Lecture Notes in Computational Science and Engineering},
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@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}
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@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}"
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@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
}
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title={{A note on preconditioning for indefinite linear systems}},
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pages={1969--1972},
year={2000},
publisher={Philadelphia, PA: SIAM, c1993-}
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%%%%%% Matt Stuff %%%%%%
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booktitle = {Automated solutions of differential equations by the finite element method},
series = {Lecture Notes in Computational Science and Engineering},
volume = {84},
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},
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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},
pages = {104108},
note = {Selected for the March 15, 2009 issue of Virtual Journal of Biological Physics Research, \url{http://dx.doi.org/10.1063/1.3081148}},
year = {2008}
}
@article{BardhanKnepley2017,
author = {Jaydeep P. Bardhan and Matthew G. Knepley},
title = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a Hydration-Shell {Poisson}-{Boltzmann} Model},
journal = {Biophysical Journal},
volume = {110},
number = {3},
note = {Fall Meeting Supplemental, Abstract DI14A-08},
doi = {10.1016/j.bpj.2015.11.1766},
note = {poster at Biophysical Society Fall Meeting},
year = {2017}
}
@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},
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},
volume = {3},
number = {1},
pages = {1--22},
doi = {10.1515/mlbmb-2015-0001},
url = {http://dx.doi.org/10.1515/mlbmb-2015-0001},
note = {\url{http://dx.doi.org/10.1515/mlbmb-2015-0001}},
year = {2015}
}
@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},
pages = {131103},
url = {http://scitation.aip.org/content/aip/journal/jcp/141/13/10.1063/1.4897324},
note = {\url{http://dx.doi.org/10.1063/1.4897324}},
year = {2014}
}
@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},
pages = {1215--1221},
month = {July},
url = {http://piers.org/piersproceedings/piers2015PragueProc.php?start=250},
year = {2015}
}
@article{TabriziKnepleyBardhan2016,
title = {Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute-solvent interface},
author = {Amirhossein Molavi Tabrizi and Matthew G. Knepley and Jaydeep P. Bardhan},
journal = {Molecular Physics},
volume = {114},
number = {16-17},
pages = {2558--2567},
doi = {10.1080/00268976.2016.1198503},
url = {http://www.tandfonline.com/doi/full/10.1080/00268976.2016.1198503},
year = {2016}
}
% http://tex.stackexchange.com/questions/155532/biblatex-and-pubmed-pubmed-central-ids
@article{TabriziGoossensRahimiKnepleyBardhan2017,
title = {Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface Condition},
author = {Amirhossein Molavi Tabrizi and Spencer Goossens and Ali Mehdizadeh Rahimi and Matthew G. Knepley and Jaydeep P. Bardhan},
journal = {Journal of Chemical Physics},
volume = {146},
number = {9},
pages = {094103},
url = {http://scitation.aip.org/content/aip/journal/jcp/146/9/10.1063/1.4977037},
eprint = {https://arxiv.org/abs/1611.02150},
doi = {10.1063/1.4977037},
note = {PMCID: PMC5336475},
year = {2017}
}
@article{TabriziGoossensCooperKnepleyBardhan2017,
title = {Extending the Solvation-Layer Interface Condition {(SLIC)} Continum Electrostatic Model to Linearized {Poisson}-{Boltzmann} Solvent},
author = {Amirhossein Molavi Tabrizi and Spencer Goossens and Christopher D. Cooper and Matthew G. Knepley and Jaydeep P. Bardhan},
journal = {Journal of Chemical Theory and Computation},
year = {2017}
}
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