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fastmethods.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Tingyu Wang at 2017-01-27 18:22:25 -0500
%% Saved with string encoding Unicode (UTF-8)
@article{white1996rotating,
Author = {White, Christopher A and Head-Gordon, Martin},
Date-Added = {2017-01-27 23:21:51 +0000},
Date-Modified = {2017-01-27 23:21:51 +0000},
Journal = {The Journal of Chemical Physics},
Number = {12},
Pages = {5061--5067},
Publisher = {AIP},
Title = {Rotating around the quartic angular momentum barrier in fast multipole method calculations},
Volume = {105},
Year = {1996}}
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Date-Added = {2017-01-27 23:12:29 +0000},
Date-Modified = {2017-01-27 23:12:29 +0000}}
@article{Milthorpe2014-pgas,
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Date-Added = {2016-09-29 00:21:50 +0000},
Date-Modified = {2016-09-29 00:22:49 +0000},
Doi = {10.1002/cpe.3039},
Journal = {Concurrency and Computation: Practice and Experience},
Number = {3},
Pages = {712--727},
Publisher = {Wiley Online Library},
Title = {{PGAS-FMM}: Implementing a distributed fast multipole method using the {X10} programming language},
Volume = {26},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1002/cpe.3039}}
@inproceedings{TauraETal2012-task,
Author = {Taura, Kenjiro and Yokota, Rio and Maruyama, Naoya},
Booktitle = {Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (ScalA)},
Date-Added = {2016-09-28 23:53:37 +0000},
Date-Modified = {2016-09-28 23:56:46 +0000},
Month = {November},
Title = {A task parallelism meets fast multipole methods},
Year = {2012}}
@inproceedings{PericasETal-SC14,
Author = {Pericas, Miquel and Taura, Kenjiro and Matsuoka, Satoshi},
Booktitle = {Proceedings of the 28th ACM International Conference on Supercomputing, ICS'14},
Date-Added = {2016-09-28 23:38:55 +0000},
Date-Modified = {2016-09-29 00:15:51 +0000},
Doi = {10.1145/2597652.2597674},
Note = {21\% acceptance rate},
Organization = {ACM},
Pages = {353--362},
Title = {Scalable analysis of multicore data reuse and sharing},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1145/2597652.2597674}}
@inproceedings{LangeFortin2014,
Author = {Lange, Benoit and Fortin, Pierre},
Booktitle = {European Conference on Parallel Processing},
Date-Added = {2016-09-28 23:34:43 +0000},
Date-Modified = {2016-09-28 23:35:06 +0000},
Organization = {Springer},
Pages = {716--727},
Title = {Parallel dual tree traversal on multi-core and many-core architectures for astrophysical N-body simulations},
Year = {2014}}
@article{HitoshiNarume2015,
Author = {Hitoshi Ukawa and Tetsu Narumi},
Date-Added = {2016-09-28 23:30:43 +0000},
Date-Modified = {2016-09-28 23:30:59 +0000},
Doi = {10.1587/transinf.2014RCL0002},
Journal = {IEICE Transactions on Information and Systems},
Number = {2},
Pages = {309-312},
Title = {Acceleration of the Fast Multipole Method on {FPGA} Devices},
Volume = {E98.D},
Year = {2015},
Bdsk-Url-1 = {http://dx.doi.org/10.1587/transinf.2014RCL0002}}
@inproceedings{YokotaEDal2012scaling,
Address = {Singapore},
Author = {Yokota, Rio and Barba, Lorena and Narumi, Tetsu and Yasuoka, Kenji},
Booktitle = {Proceedings of the ATIP/A* CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way?},
Date-Added = {2016-09-28 22:48:14 +0000},
Date-Modified = {2016-09-28 23:02:49 +0000},
Month = {7--10 May},
Organization = {A* STAR Computational Resource Centre},
Publisher = {ACM SIGHPC},
Title = {Scaling fast multipole methods up to 4000 {GPUs}},
Year = {2012}}
@misc{PavlovETal-PRACEwhitepaper,
Author = {Pavlov, Valentin and Andonov, Nikola and Kremenliev, Georgi},
Date-Added = {2016-09-28 19:56:23 +0000},
Date-Modified = {2016-09-28 23:01:36 +0000},
Howpublished = {PRACE White Paper},
Note = {\url{http://www.prace-ri.eu/IMG/pdf/wp145.pdf}. Year unknown},
Title = {Porting and Verification of {ExaFMM} Library in {MIC} Architecture},
Url = {http://www.prace-ri.eu/IMG/pdf/wp145.pdf},
Bdsk-Url-1 = {http://www.prace-ri.eu/IMG/pdf/wp145.pdf}}
@article{OhnoYokotaETal2014-petascale,
Author = {Ohno, Yousuke and Yokota, Rio and Koyama, Hiroshi and Morimoto, Gentaro and Hasegawa, Aki and Masumoto, Gen and Okimoto, Noriaki and Hirano, Yoshinori and Ibeid, Huda and Narumi, Tetsu and others},
Date-Added = {2016-09-05 02:30:44 +0000},
Date-Modified = {2016-09-05 02:31:47 +0000},
Doi = {10.1016/j.cpc.2014.06.004},
Journal = {Comput. Phys. Comm.},
Number = {10},
Pages = {2575--2585},
Publisher = {Elsevier},
Title = {Petascale molecular dynamics simulation using the fast multipole method on K computer},
Volume = {185},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2014.06.004}}
@article{Yokota2013-dualtree,
Author = {Yokota, R},
Date-Added = {2016-09-05 02:17:33 +0000},
Date-Modified = {2016-09-05 02:22:36 +0000},
Doi = {10.1260/1748-3018.7.3.301},
Journal = {Journal of Algorithms \& Computational Technology},
Note = {Preprint \href{http://arxiv.org/abs/arXiv:1209.3516v3}{http://arxiv.org/abs/arXiv:1209.3516v3}},
Number = {3},
Pages = {301--324},
Publisher = {Multi Science Publishing},
Title = {An {FMM} based on dual tree traversal for many-core architectures},
Volume = {7},
Year = {2013},
Bdsk-Url-1 = {http://dx.doi.org/10.1260/1748-3018.7.3.301}}
@misc{BarbaYokota2012-figshare,
Author = {Lorena A. Barba and Rio Yokota},
Date-Added = {2016-09-04 23:48:13 +0000},
Date-Modified = {2016-09-05 00:01:19 +0000},
Doi = {10.6084/m9.figshare.92166.v1},
Howpublished = {Poster on \textbf{Figshare}, under CC-BY license, \href{https://dx.doi.org/10.6084/m9.figshare.92166.v1}{https://dx.doi.org/10.6084/m9.figshare.92166.v1}},
Keywords = {figshare},
Month = {5},
Title = {{ExaFMM: An open source library for Fast Multipole Methods aimed towards Exascale systems}},
Year = {2012},
Bdsk-Url-1 = {10.6084/m9.figshare.92166.v1}}
@article{Bebendorf2005,
Author = {M. Bebendorf},
Date-Added = {2014-03-26 19:52:59 +0000},
Date-Modified = {2014-03-26 19:54:04 +0000},
Journal = {Computing},
Pages = {225-247},
Title = {Hierarchical {LU} Decomposition-based preconditioners for {BEM}},
Volume = {74},
Year = {2005}}
@article{BebendorfRjasanow2003,
Author = {M. Bebendorf and S. Rjasanow},
Date-Added = {2014-03-26 18:10:15 +0000},
Date-Modified = {2014-06-06 16:26:55 +0000},
Journal = {Computing},
Number = {1},
Pages = {1-24},
Title = {Adaptive Low-Rank Approximation of Collocation Matrices},
Volume = {70},
Year = {2003}}
@article{Bebendorf2000,
Author = {M. Bebendorf},
Date-Added = {2014-03-26 18:09:07 +0000},
Date-Modified = {2014-03-26 18:10:09 +0000},
Journal = {Numer.\ Math.},
Number = {4},
Pages = {565-589},
Title = {Approximation of boundary element matrices},
Volume = {86},
Year = {2000}}
@article{fuEtAl98,
Author = {Fu, Y. and Klimkowski, K. J. and Rodin, G. J. and Berger, E. and Browne, J. C. and Singer, J. K. and Van De Geijn, R. A. and Vemangati, K. S},
Date-Added = {2013-07-29 14:12:45 +0000},
Date-Modified = {2013-07-29 14:14:48 +0000},
Journal = {Int.\ J. Num.\ Meth.\ Engineering},
Pages = {1215-1229},
Title = {A Fast Solution Method for Three-Dimensional Many-Particle Problems of Linear Elasticity},
Year = {1998}}
@article{Tornberg2008,
Author = {Tornberg, A.-K. and Greengard, L.},
Date-Added = {2013-05-30 15:57:33 +0000},
Date-Modified = {2013-05-30 15:57:33 +0000},
Journal = {Journal of Computational Physics},
Keywords = {FMM; Stokes; hot},
Pages = {1613--1619},
Title = {A Fast Multipole Method for the Three-dimensional Stokes Equations},
Volume = {227},
Year = {2008},
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@article{DarbasETal2012,
Author = {Darbas, Marion and Darrigrand, Eric and Lafranche, Yvon},
Date-Added = {2013-04-10 12:55:25 +0000},
Date-Modified = {2013-04-10 13:06:48 +0000},
Journal = {J. Comput.\ Phys.},
Pages = {289--316},
Publisher = {Elsevier},
Title = {Combining analytic preconditioner and Fast Multipole Method for the {3-D Helmholtz} equation},
Volume = {236},
Year = {2012}}
@article{GimbutasGreengard2012,
Author = {Gimbutas, Zydrunas and Greengard, Leslie},
Date-Added = {2013-04-10 12:51:18 +0000},
Date-Modified = {2013-04-10 12:53:43 +0000},
Journal = {J. Comput.\ Phys.},
Note = {preprint on \href{http://arxiv.org/abs/1104.5293}{http://arxiv.org/abs/1104.5293}},
Number = {1},
Pages = {22--32},
Publisher = {Elsevier},
Title = {Fast multi-particle scattering: a hybrid solver for the {Maxwell} equations in microstructured materials},
Volume = {232},
Year = {2012},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0021999112004184},
Bdsk-Url-2 = {http://arxiv.org/pdf/1104.5293.pdf}}
@article{ZhangETal2013,
Author = {Zhang, Bo and Lu, Benzhuo and Cheng, Xiaolin and Huang, Jingfang and Pitsianis, Nikos P and Sun, Xiaobai and McCammon, J Andrew},
Date-Added = {2013-04-10 12:32:34 +0000},
Date-Modified = {2013-04-10 12:40:37 +0000},
Journal = {Commun.\ Comput.\ Phys.},
Number = {1},
Pages = {107--128},
Title = {Mathematical and Numerical Aspects of the Adaptive Fast Multipole {Poisson-Boltzmann} Solver},
Volume = {13},
Year = {2013},
Bdsk-Url-1 = {http://www.global-sci.com/issue/contents/13/issue1.html},
Bdsk-Url-2 = {http://lsec.cc.ac.cn/~lubz/Publication/2012CiCP-BoZhang.pdf}}
@article{HoGreengard2012,
Author = {Ho, Kenneth L and Greengard, Leslie},
Date-Added = {2013-04-10 12:07:52 +0000},
Date-Modified = {2013-04-10 12:29:07 +0000},
Journal = {SIAM J. Sci.\ Comput.},
Number = {5},
Pages = {A2507--A2532},
Publisher = {SIAM},
Title = {A fast direct solver for structured linear systems by recursive skeletonization},
Volume = {34},
Year = {2012}}
@inproceedings{ChandramowlishwaranETal20120-SPAA,
Address = {Pittsburgh, PA},
Author = {Aparna Chandramowlishwaran and Jee Whan Choi and Kamesh Madduri and Richard Vuduc},
Booktitle = {Proc.~ACM Symposium on Parallel Algorithms and Architectures (SPAA)},
Date-Added = {2013-04-09 23:19:14 +0000},
Date-Modified = {2013-04-09 23:19:44 +0000},
Month = {June},
Title = {Brief Announcement: Towards a Communication Optimal Fast Multipole Method and its Implications at Exascale},
Year = {2012}}
@article{WinkelETal2012,
Author = {Winkel, Mathias and Speck, Robert and H{\"u}bner, Helge and Arnold, Lukas and Krause, Rolf and Gibbon, Paul},
Date-Added = {2013-04-09 22:52:50 +0000},
Date-Modified = {2013-04-09 22:52:50 +0000},
Doi = {10.1016/j.cpc.2011.12.013},
Journal = {Comput.\ Phys.\ Comm.},
Pages = {880--889},
Title = {A massively parallel, multi-disciplinary {Barnes-Hut} tree code for extreme-scale {$N$}-body simulations},
Volume = {183},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2011.12.013}}
@article{VuducCzechowski2011,
Author = {Vuduc, Richard and Czechowski, Kent},
Date-Added = {2013-04-07 22:47:05 +0000},
Date-Modified = {2013-04-07 22:47:54 +0000},
Journal = {Micro, IEEE},
Number = {4},
Pages = {74--78},
Publisher = {IEEE},
Title = {What GPU computing means for high-end systems},
Volume = {31},
Year = {2011},
Bdsk-Url-1 = {http://www.vuduc.com/pubs/vuduc2011-gpu-ieee-micro.pdf},
Bdsk-Url-2 = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5967004}}
@inproceedings{ChandramowlishwaranETal2012-IPDPS,
Author = {Chandramowlishwaran, Aparna and Vuduc, Richard W},
Booktitle = {Parallel and Distributed Processing Symposium Workshops \& PhD Forum (IPDPSW), 2012 IEEE 26th International},
Date-Added = {2013-04-07 22:44:02 +0000},
Date-Modified = {2013-04-07 22:45:48 +0000},
Organization = {IEEE},
Pages = {2462--2465},
Title = {Communication-Optimal Parallel {$N$}-body Solvers},
Year = {2012},
Bdsk-Url-1 = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6270869},
Bdsk-Url-2 = {http://www.cc.gatech.edu/grads/a/aparna/pubs/papers/chandramowlishwaran2012-ipdps-poster.pdf}}
@misc{ChandramowlishwaranETal2012brief,
Author = {Chandramowlishwaran, A. and Choi, Jee Whan and Madduri, Kamesh and Vuduc, Richard},
Date-Added = {2013-04-07 22:41:04 +0000},
Date-Modified = {2013-04-07 22:46:50 +0000},
Howpublished = {Author website preprint},
Title = {Brief Announcement: Towards a Communication Optimal Fast Multipole Method and its Implications at Exascale},
Year = {2012},
Bdsk-Url-1 = {http://www.cc.gatech.edu/grads/a/aparna/pubs/papers/chandramowlishwaran2012-spaa.pdf}}
@article{Chailletetal2011,
Author = {Chaillat, S. and Semblat, J.F and Bonnet, M.},
Date-Added = {2013-03-18 14:13:14 +0000},
Date-Modified = {2013-03-18 14:15:35 +0000},
Journal = {Comm, Comput. Phys.},
Keywords = {FMM, BEM, preconditioning},
Number = {2},
Pages = {594-609},
Title = {A Preconditioned 3-D Multi-Region Fast Multipole Solver for Seismic Wave Propagation in Complex Geometries},
Volume = {11},
Year = {2011}}
@book{greengard1987,
Author = {Greengard, L},
Date-Added = {2013-03-17 21:08:25 +0000},
Date-Modified = {2013-03-17 21:08:25 +0000},
Publisher = {The MIT Press},
Title = {The rapid evaluation of potential fields in particle systems},
Year = {1987}}
@article{LiJohnstonKrasny2009,
Author = {Li, P. and Johnston, H. and Krasny, R.},
Date-Added = {2013-01-25 01:43:50 +0000},
Date-Modified = {2013-01-25 01:44:22 +0000},
Journal = {J. Comput.\ Phys.},
Keywords = {yukawa, expansions},
Pages = {3858-3868},
Title = {A {Cartesian} treecode for screened {Coulomb} interactions},
Volume = {228},
Year = {2009}}
@misc{YokotaBarba-share92425,
Author = {Yokota, R. and Barba, L.~A.},
Date-Added = {2012-08-13 10:49:50 +0000},
Date-Modified = {2012-08-13 10:49:50 +0000},
Doi = {10.6084/m9.figshare.92425},
Howpublished = {Figure on \textbf{figshare}, used under CC-BY license, \href{http://dx.doi.org/10.6084/m9.figshare.92425}{http://dx.doi.org/10.6084/m9.figshare.92425}},
Keywords = {figshare},
Month = {July 18},
Title = {Weak scaling of parallel {FMM vs. FFT} up to 4096 processes},
Urldate = {23:46, Aug 04, 2012 (GMT)},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.6084/m9.figshare.92425}}
@article{GibbonETal2010,
Author = {Gibbon, P. and Speck, R. and Karmakar, A. and Arnold, L. and Frings, W. and Berberich, B. and Reiter, D. and Ma{\v s} andek, M.},
Date-Added = {2012-06-09 16:07:32 -0400},
Date-Modified = {2012-06-09 16:07:32 -0400},
Doi = {10.1109/TPS.2010.2055165},
Issn = {0093-3813},
Journal = {Plasma Science, IEEE Transactions on},
Keywords = {algorithm;edge plasma simulations;heating;high-intensity lasers;ion acceleration simulations;magnetoinductive models;mesh-free plasma simulation;multidimensional electrostatic plasma problems;nanostructured target dynamics;parallel tree codes;plasma modeling;tokamaks;Tokamak devices;plasma kinetic theory;plasma light propagation;plasma simulation;plasma transport processes;plasma-wall interactions;tree codes;},
Month = {sept.},
Number = {9},
Pages = {2367--2376},
Title = {Progress in Mesh-Free Plasma Simulation With Parallel Tree Codes},
Volume = {38},
Year = {2010},
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Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPS.2010.2055165}}
@article{ChristliebETal2006,
Author = {Christlieb, A.J. and Krasny, R. and Verboncoeur, J.P. and Emhoff, J.W. and Boyd, I.D.},
Date-Added = {2012-06-09 15:40:39 -0400},
Date-Modified = {2012-06-09 15:40:39 -0400},
Journal = {Plasma Science, IEEE Transactions on},
Number = {2},
Pages = {149--165},
Publisher = {IEEE},
Title = {Grid-free plasma simulation techniques},
Volume = {34},
Year = {2006},
Bdsk-Url-1 = {http://www.math.lsa.umich.edu/~krasny/paper_ieee_2006.pdf}}
@article{DuanKrasny2001,
Author = {Z.-H. Duan and R. Krasny},
Date-Added = {2012-05-23 19:15:45 +0000},
Date-Modified = {2013-01-25 01:42:27 +0000},
Journal = {J. Comp.\ Chem.},
Number = {2},
Pages = {184--195},
Title = {An Adaptive Treecode for Computing Nonbonded Potential Energy in Classical Molecular Systems},
Volume = {22},
Year = {2001}}
@inproceedings{MakinoETal2000,
Author = {Makino, J. and Fukushige, T. and Koga, M.},
Booktitle = {Proceedings of the 2000 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-12-02 19:34:37 -0500},
Date-Modified = {2011-12-02 19:34:37 -0500},
Keywords = {Gordon Bell},
Pages = {1-18},
Title = {A 1.349 {Tflops} Simulation of Black Holes in a Galactic Center on {GRAPE-6}},
Year = {2000}}
@inproceedings{HamadaNitadori2010,
Author = {Hamada, T. and Nitadori, K.},
Booktitle = {High Performance Computing, Networking, Storage and Analysis (SC), 2010 International Conference for},
Date-Added = {2011-12-02 19:17:19 -0500},
Date-Modified = {2011-12-02 19:18:48 -0500},
Doi = {10.1109/SC.2010.1},
Keywords = {astrophysical N-body simulation, treecode},
Month = {Nov.},
Pages = {1--9},
Title = {190 {TFlops} Astrophysical {$N$}-body Simulation on a Cluster of {GPUs}},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1109/SC.2010.1}}
@article{YokotaETal2011a,
Author = {Yokota, Rio and Bardhan, Jaydeep P. and Knepley, Matthew G. and Barba, L.~A. and Hamada, Tsuyoshi},
Date-Added = {2011-10-10 18:21:47 -0400},
Date-Modified = {2011-10-10 18:21:47 -0400},
Doi = {10.1016/j.cpc.2011.02.013},
Journal = {Comput.\ Phys.\ Comm.},
Keywords = {GPU, FMM, BEM, biomolecular physics},
Number = {6},
Pages = {1271--1283},
Title = {Biomolecular electrostatics using a fast multipole {BEM on up to 512 GPUs} and a billion unknowns},
Volume = {182},
Year = {2011},
Bdsk-Url-1 = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TJ5-529CNR2-4&_user=121739&_coverDate=03%2F03%2F2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C000010018&_version=1&_urlVersion=0&_userid=121739&md5=4970a74d6e0b14e267d527e2bf37a20d&searchtype=a},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.cpc.2011.02.013}}
@article{YokotaBarba2012a,
Author = {Yokota, R. and Barba, L.~A.},
Date-Added = {2011-09-14 21:07:45 -0400},
Date-Modified = {2012-06-16 18:42:40 -0400},
Doi = {10.1109/MCSE.2012.1},
Journal = {Computing in Science \& Engineering},
Month = {May/June},
Number = {3},
Pages = {30--39},
Title = {Hierarchical {$N$}-body simulations with auto-tuning for heterogeneous systems},
Volume = {14},
Year = {2012},
Bdsk-Url-1 = {http://www.computer.org/portal/web/csdl/doi/10.1109/MCSE.2012.1},
Bdsk-Url-2 = {http://dx.doi.org/10.1109/MCSE.2012.1}}
@unpublished{YokotaBarba2011b,
Author = {Yokota, R. and Barba, L.~A.},
Date-Added = {2011-09-14 20:31:40 -0400},
Date-Modified = {2011-09-14 20:43:45 -0400},
Note = {Submitted to \emph{Int.\ J.\ High-perf.\ Comput.\ Applic.}},
Title = {Parameter tuning of a hybrid treecode-{FMM on GPUs}},
Year = {2011}}
@article{YokotaBarba2011a,
Author = {Yokota, R. and Barba, L.~A.},
Date-Added = {2011-09-14 20:07:10 -0400},
Date-Modified = {2013-09-16 16:32:29 +0000},
Journal = {Int.\ J.\ High-perf.\ Comput.\ Applic.},
Note = {Published online 24 Jan.\ 2012 \href{http://doi.org/fzgqgm}{doi:10.1177/1094342011429952} preprint on \href{http://arxiv.org/abs/1106.2176}{http://arxiv.org/abs/1106.2176}},
Title = {A tuned and scalable fast multipole method as a preeminent algorithm for exascale systems},
Year = {2012}}
@article{Dubinski1996,
Author = {Dubinski, J.},
Date-Added = {2011-08-09 23:43:44 +0000},
Date-Modified = {2011-08-09 23:43:44 +0000},
Journal = {New Astronomy},
Keywords = {Treecode; ORB; parallel},
Pages = {133-147},
Title = {A Parallel Tree Code},
Volume = {1},
Year = {1996},
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@phdthesis{Salmon1990,
Author = {Salmon, J. K.},
Date-Added = {2011-08-09 23:40:54 +0000},
Date-Modified = {2011-08-09 23:41:17 +0000},
School = {California Institute of Technology},
Title = {Parallel Hierarchical N-body Methods},
Year = {1990}}
@article{WilliamsETal2008,
Author = {Williams, S. and Waterman, A. and Patterson, D.},
Date-Added = {2011-08-09 18:48:08 +0000},
Date-Modified = {2011-08-09 18:50:16 +0000},
Journal = {Communications of the ACM},
Number = {4},
Pages = {65-76},
Title = {Roofline: an insightful visual performance model for multicore architectures},
Volume = {52},
Year = {2008}}
@article{HamadaIitaka2007,
Author = {Hamada, T. and Iitaka, T.},
Date-Added = {2011-08-05 13:07:11 +0000},
Date-Modified = {2011-08-05 13:08:05 +0000},
Journal = {arXiv:astro-ph/0703100v1},
Title = {The Chamomile Scheme: An Optimized Algorithm for {N}-body Simulations on Programmable Graphics Processing Units},
Year = {2007},
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@inproceedings{NarumiETal2006,
Address = {Tampa, Florida},
Author = {Narumi, T. and Ohno, Y. and Okimoto, N. and Koishi, T. and Suenaga, A. and Futatsugi, N. and Yanai, R. and Himeno, R. and Fujikawa, S. and Taiji, M. and Ikei, M.},
Booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 14:12:38 +0000},
Date-Modified = {2011-12-02 19:41:12 -0500},
Keywords = {Gordon Bell},
Pages = {1--16},
Title = {A 55 {TFlops} Simulation of Amyloid-Forming Peptides from Yeast Prion {Sup35} with the Special-Purpose Computer System {MDGRAPE-3}},
Year = {2006}}
@inproceedings{MakinoETal2003,
Author = {Makino, J. and Kokubo, E. and Fukushige, T.},
Booktitle = {Proceedings of the 2003 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 14:10:24 +0000},
Date-Modified = {2011-12-02 19:39:53 -0500},
Keywords = {Gordon Bell},
Pages = {1--11},
Title = {Performance Evaluation and Tuning of {GRAPE-6} --Towards 40 "Real" {Tflops}},
Year = {2003}}
@inproceedings{MakinoETal2002,
Author = {Makino, J. and Kokubo, E. and Fukushige, T. and Daisaka, H.},
Booktitle = {Proceedings of the 2002 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 14:07:31 +0000},
Date-Modified = {2011-12-02 19:39:12 -0500},
Keywords = {Gordon Bell},
Pages = {1--14},
Title = {A 29.5 {Tflops} Simulation of Planetesimals in {Uranus-Neptune} Region on {GRAPE-6}},
Year = {2002}}
@inproceedings{MakinoFukushige2001,
Author = {Makino, J. and Fukushige, T.},
Booktitle = {Proceedings of the 2001 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 14:04:14 +0000},
Date-Modified = {2011-12-02 19:37:18 -0500},
Title = {A 11.55 {Tflops} Simulation of Black Holes in a Galactic Center on {GRAPE}-6},
Year = {2001}}
@inproceedings{NarumiETal2000,
Author = {Narumi, T. and Susukita, R. and Koishi, T. and Yasuoka, K. and Furusawa, H. and Kawai, A. and Ebisuzaki, T.},
Booktitle = {Proceedings of the 2000 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 13:57:49 +0000},
Date-Modified = {2011-12-02 19:35:32 -0500},
Title = {1.34 {Tflops} Molecular Dynamics Simulation for {NaCl} with a Special-purpose Computer: {MDM}},
Year = {2000},
Bdsk-Url-1 = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1592767&tag=1}}
@inproceedings{NarumiETal2001,
Author = {Narumi, T. and Kawai, A. and Koishi, T.},
Booktitle = {Proceedings of the 2001 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 13:55:40 +0000},
Date-Modified = {2011-08-04 13:55:51 +0000},
Keywords = {Gordon Bell},
Pages = {1-17},
Title = {An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM},
Year = {2001},
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@inproceedings{WarrenETal1998,
Author = {Warren, M. S. and Germann, T. C. and Lomdahl, P. S. and Beazley, D. M. and Salmon, J. K.},
Booktitle = {Proceedings of the 1998 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 13:44:49 +0000},
Date-Modified = {2011-12-02 19:32:29 -0500},
Pages = {1-10},
Title = {Avalon: An {Alpha/Linux} Cluster Achieves 10 {Gflops} for \$150k},
Year = {1998}}
@inproceedings{FukushigeMakino1996,
Author = {Fukushige, T. and Makino, J.},
Booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE conference on Supercomputing},
Date-Added = {2011-08-04 13:41:06 +0000},
Date-Modified = {2011-08-04 13:42:44 +0000},
Title = {{N}-body simulation of galaxy formation on {GRAPE}-4 special-purpose computer},
Year = {1996}}
@article{DarveETal2011,
Author = {Darve, E. and Cecka, C. and Takahashi, T.},
Date-Added = {2011-08-01 02:34:09 +0000},
Date-Modified = {2011-08-01 02:36:14 +0000},
Journal = {Computes Rendus Mecanique},
Pages = {185-193},
Title = {The Fast Multipole Method on Parallel Clusters, Multicore Processors, and Graphics Processing Units},
Volume = {339},
Year = {2011}}
@article{Wang2004,
Author = {Wang, Q. X.},
Date-Added = {2011-07-31 19:16:30 +0000},
Date-Modified = {2011-07-31 19:16:30 +0000},
Journal = {Journal of Computational Physics},
Keywords = {Treecode; variable p; real spherical harmonics; binary-tree; hot},
Number = {1},
Pages = {192-210},
Title = {Variable Order Revised Binary Treecode},
Volume = {200},
Year = {2004},
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@article{YokotaETal2012a,
Author = {Yokota, Rio and Barba, L.~A. and Narumi, T. and Yasuoka, K.},
Date-Added = {2011-07-25 11:56:06 -0400},
Date-Modified = {2016-09-05 02:33:50 +0000},
Journal = {Comput.\ Phys.\ Comm.},
Note = {Preprint on \href{http://arxiv.org/abs/1106.5273}{arXiv:1106.5273}},
Number = {3},
Pages = {445--455},
Title = {Petascale turbulence simulation using a highly parallel fast multipole method},
Volume = {184},
Year = {2012},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0010465512002974}}
@article{WarrenSalmon1995,
Author = {Warren, M. S. and Salmon, J. K.},
Date-Added = {2011-07-31 17:11:22 +0000},
Date-Modified = {2011-07-31 17:12:50 +0000},
Journal = {Computer Physics Communications},
Pages = {266-290},
Title = {A portable parallel particle program},
Volume = {87},
Year = {1995}}
@article{LuETal2010,
Author = {Benzhuo Lu and Xiaolin Cheng and Jingfang Huang and J. Andrew McCammon},
Date-Added = {2011-07-23 16:17:35 -0400},
Date-Modified = {2011-07-23 16:18:07 -0400},
Doi = {DOI: 10.1016/j.cpc.2010.02.015},
Issn = {0010-4655},
Journal = {Comput.\ Phys.\ Comm.},
Number = {6},
Pages = {1150--1160},
Title = {AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems},
Url = {http://www.sciencedirect.com/science/article/pii/S0010465510000548},
Volume = {181},
Year = {2010},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0010465510000548},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.cpc.2010.02.015}}
@incollection{YokotaBarba2010,
Author = {Yokota, Rio and Barba, L.~A.},
Booktitle = {{GPU Computing Gems Emerald Edition}},
Chapter = {9},
Date-Added = {2011-06-27 21:12:05 -0400},
Date-Modified = {2012-06-17 15:39:25 -0400},
Editor = {Wen-Mei Hwu},
Isbn = {978-0-12-384988-5},
Note = {Preprint on \href{http://arxiv.org/abs/1010.1482}{arXiv:1010.1482}},
Pages = {113--132},
Publisher = {Elsevier/ Morgan Kaufman},
Title = {Treecode and fast multipole method for {$N$}-body simulation with {CUDA}},
Year = {2011},
Bdsk-Url-1 = {http://www.elsevierdirect.com/ISBN/9780123849885/GPU-Computing-Gems-Emerald-Edition}}
@article{SundarETal2008,
Author = {Sundar, H. and Sampath, R. S. and Biros, G.},
Date-Added = {2011-04-28 18:53:38 -0400},
Date-Modified = {2011-04-28 18:54:20 -0400},
Journal = {SIAM J. Sci.\ Comput.},
Keywords = {FMM; parallel; partitioning},
Number = {5},
Pages = {2675--2708},
Title = {Bottom-up Construction and 2:1 Balance Refinement of Linear Octrees in Parallel},
Volume = {30},
Year = {2008}}
@article{Dehnen2002,
Author = {Dehnen, W.},
Date-Added = {2011-04-28 18:13:48 -0400},
Date-Modified = {2011-04-28 18:17:01 -0400},
Journal = {J. Comput.\ Phys.},
Keywords = {FMM; Treecode; cartesian; hot},
Number = {1},
Pages = {27--42},
Title = {A Hierarchical {$\mathcal{O}(N)$} Force Calculation Algorithm},
Volume = {179},
Year = {2002},
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@article{HamadaETal2009b,
Affiliation = {Nagasaki University Faculty of Engineering, Department of Computer and Information Sciences Bunkyo-machi 852-8521 Nagasaki Japan},
Author = {Hamada, Tsuyoshi and Nitadori, Keigo and Benkrid, Khaled and Ohno, Yousuke and Morimoto, Gentaro and Masada, Tomonari and Shibata, Yuichiro and Oguri, Kiyoshi and Taiji, Makoto},
Date-Added = {2011-04-28 16:54:03 -0400},
Date-Modified = {2011-04-28 18:49:12 -0400},
Issn = {1865-2034},
Journal = {Computer Science Research and Development},
Keywords = {treecode},
Number = {1--2},
Pages = {21--31},
Publisher = {Springer Berlin / Heidelberg},
Title = {A novel multiple-walk parallel algorithm for the {Barnes--Hut treecode on GPUs}---towards cost-effective, high-performance {$N$}-body simulation},
Url = {http://dx.doi.org/10.1007/s00450-009-0089-1},
Volume = {24},
Year = {2009},
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Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00450-009-0089-1}}
@inproceedings{WarrenSalmonETal1997,
Author = {Warren, M.S. and Salmon, J.K. and Becker, D.J. and Goda, M.P. and Sterling, T. and Winckelmans, W.},
Booktitle = {Supercomputing, ACM/IEEE 1997 Conference},
Date-Added = {2011-03-17 15:53:37 +0000},
Date-Modified = {2011-03-17 16:02:01 +0000},
Doi = {10.1109/SC.1997.10057},
Keywords = {Gordon Bell winner, treecodes},
Pages = {61},
Title = {{Pentium Pro inside: I. A treecode at 430 Gigaflops on ASCI Red, II. Price/performance of \$50/Mflop on Loki and Hyglac}},
Year = {1997},
Bdsk-Url-1 = {http://dx.doi.org/10.1109/SC.1997.10057}}
@inproceedings{RahimianETal2010,
Acmid = {1884648},
Author = {Rahimian, A. and Lashuk, I. and Veerapaneni, S. and Chandramowlishwaran, A. and Malhotra, D. and Moon, L. and Sampath, R. and Shringarpure, A. and Vetter, J. and Vuduc, R. and Zorin, D. and Biros, G.},
Booktitle = {Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis},
Date-Added = {2011-02-09 13:56:00 -0500},
Date-Modified = {2011-08-09 23:59:32 +0000},
Doi = {http://dx.doi.org/10.1109/SC.2010.42},
Isbn = {978-1-4244-7559-9},
Numpages = {11},
Pages = {1--11},
Publisher = {IEEE Computer Society},
Series = {SC '10},
Title = {Petascale Direct Numerical Simulation of Blood Flow on 200K Cores and Heterogeneous Architectures},
Url = {http://dx.doi.org/10.1109/SC.2010.42},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1109/SC.2010.42}}
@article{CruzKnepleyBarba2010,
Author = {Cruz, F. A. and Knepley, M. G. and Barba, L.~A.},
Date-Added = {2011-02-04 19:01:07 -0500},
Date-Modified = {2011-02-04 19:07:56 -0500},
Doi = {10.1002/nme.2972},
Journal = {Int.\ J. Num.\ Meth.\ Engineering},
Keywords = {FMM, Barbagroup papers},
Number = {4},
Pages = {403--428},
Read = {1},
Title = {{PetFMM}\,----A dynamically load-balancing parallel fast multipole library},
Volume = {85},
Year = {2010},
Bdsk-Url-1 = {http://onlinelibrary.wiley.com/doi/10.1002/nme.2972/abstract},
Bdsk-Url-2 = {http://dx.doi.org/10.1002/nme.2972}}
@article{FannETal2004,
Acmid = {1014636},
Address = {Riverton, NJ, USA},
Author = {Fann, G. and Beylkin, G. and Harrison, R. J. and Jordan, K. E.},
Date-Added = {2011-02-04 18:54:27 -0500},
Date-Modified = {2011-02-04 18:55:08 -0500},
Doi = {http://dx.doi.org/10.1147/rd.482.0161},
Issn = {0018-8646},
Issue = {2},
Journal = {IBM J. Res. Dev.},
Month = {March},
Numpages = {11},
Pages = {161--171},
Publisher = {IBM Corp.},
Title = {Singular operators in multiwavelet bases},
Url = {http://dx.doi.org/10.1147/rd.482.0161},
Volume = {48},
Year = {2004},
Bdsk-Url-1 = {http://dx.doi.org/10.1147/rd.482.0161}}
@inproceedings{WarrenSalmon1992,
Acmid = {148090},
Address = {Los Alamitos, CA, USA},
Author = {Warren, M. S. and Salmon, J. K.},
Booktitle = {Proceedings of the 1992 ACM/IEEE Conference on Supercomputing},
Date-Added = {2011-02-02 13:44:27 -0500},
Date-Modified = {2012-08-13 11:15:23 +0000},
Isbn = {0-8186-2630-5},
Keywords = {Gordon Bell winner, treecodes, ORB},
Location = {Minneapolis, Minnesota, United States},
Numpages = {7},
Pages = {570--576},
Publisher = {IEEE Computer Society Press},
Title = {Astrophysical {$N$}-body simulations using hierarchical tree data structures},
Url = {http://portal.acm.org/citation.cfm?id=147877.148090},
Year = {1992},
Bdsk-Url-1 = {http://portal.acm.org/citation.cfm?id=147877.148090}}
@article{ChengETal2006a,
Author = {Hongwei Cheng and Jingfang Huang and Terry Jo Leiterman},
Date-Added = {2010-12-03 21:33:08 -0500},
Date-Modified = {2010-12-03 21:34:05 -0500},
Doi = {DOI: 10.1016/j.jcp.2005.06.006},
Issn = {0021-9991},
Journal = {J. Comput.\ Phys.},
Keywords = {modified Helmholtz equation},
Number = {2},
Pages = {616--637},
Title = {An adaptive fast solver for the modified {Helmholtz} equation in two dimensions},
Url = {http://www.sciencedirect.com/science/article/B6WHY-4GSJRFH-2/2/32e8f4a63803035aef1b5f0f23df8b0a},
Volume = {211},
Year = {2006},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WHY-4GSJRFH-2/2/32e8f4a63803035aef1b5f0f23df8b0a},
Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2005.06.006}}
@article{Greengard1998b,
Author = {Greengard, L. and Huang, J. and Wandzura, S.},
Date-Added = {2010-11-08 17:06:10 -0500},
Date-Modified = {2010-11-08 17:06:10 -0500},
Journal = {IEEE Computational Science and Engineering},
Keywords = {FMM; Helmholtz; low-frequency},
Number = {3},
Pages = {32-38},
Title = {Acclelerating Fast Multipole Methods for the Helmholtz Equation at Low Frequencies},
Volume = {5},
Year = {1998},
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@techreport{GreengardRokhlin1988,
Author = {Greengard, L. and Rokhlin, V.},
Date-Added = {2010-11-08 17:04:05 -0500},
Date-Modified = {2010-11-09 10:22:20 -0500},
Institution = {Yale University},
Keywords = {FMM; Laplace},
Number = {RR-602},
Title = {On the Efficient Implementation of the Fast Multipole Algorithm},
Type = {Research Report},
Year = {1988},
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@article{GimbutasRokhlin2002,
Author = {Zydrunas Gimbutas and Vladimir Rokhlin},
Date-Added = {2010-11-08 14:25:46 -0500},
Date-Modified = {2011-02-04 19:08:52 -0500},
Doi = {10.1137/S1064827500381148},
Journal = {SIAM J. Sci.\ Comput.},
Keywords = {FMM; arbitrary kernels; potential theory},
Number = {3},
Pages = {796--817},
Publisher = {SIAM},
Title = {A Generalized Fast Multipole Method for Nonoscillatory Kernels},
Url = {http://link.aip.org/link/?SCE/24/796/1},
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Bdsk-Url-1 = {http://link.aip.org/link/?SCE/24/796/1},
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Date-Added = {2010-11-08 13:41:10 -0500},
Date-Modified = {2011-10-13 17:19:04 -0400},
Doi = {10.2140/camcos.2011.6.79},
Journal = {Comm.\ Applied Math.\ Comput.\ Science},
Keywords = {FMM,},
Month = {October},
Number = {1},
Pages = {79--122},
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Volume = {6},
Year = {2011},
Bdsk-Url-1 = {http://mrl.nyu.edu/~dzorin/papers/langston2008fsa.pdf},
Bdsk-Url-2 = {http://msp.berkeley.edu/camcos/2011/6-1/p04.xhtml},
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Booktitle = {IEEE International Symposium on Parallel Distributed Processing (IPDPS)},
Date-Added = {2010-11-06 19:53:24 -0400},
Date-Modified = {2011-02-04 19:09:39 -0500},
Doi = {10.1109/IPDPS.2010.5470415},
Issn = {1530-2075},
Keywords = {GPU;Nehalem;OpenMP parallelization;algorithmic tuning;data structure transformations;double-precision performance;FMM, low-level tuning;multicore architectures;numerical approximation;single-node performance optimization;multiprocessing systems;optimisation;},
Month = {April},
Organization = {IEEE},
Pages = {1--12},
Title = {Optimizing and tuning the fast multipole method for state-of-the-art multicore architectures},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1109/IPDPS.2010.5470415}}
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Address = {Berkeley, CA, USA},
Author = {Vuduc, Richard and Chandramowlishwaran, Aparna and Choi, Jee and Guney, Murat and Shringarpure, Aashay},
Booktitle = {Proceedings of the 2nd USENIX conference on Hot topics in parallelism},
Date-Added = {2010-11-02 18:09:05 -0400},
Date-Modified = {2010-11-02 18:09:18 -0400},
Location = {Berkeley, CA},
Numpages = {1},
Pages = {13--13},
Publisher = {USENIX Association},
Series = {HotPar'10},
Title = {On the limits of GPU acceleration},
Url = {http://portal.acm.org/citation.cfm?id=1863086.1863099},
Year = {2010},
Bdsk-Url-1 = {http://portal.acm.org/citation.cfm?id=1863086.1863099}}
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