gearshifft_references.bib

@book{van1992computational,
  title={Computational frameworks for the fast Fourier transform},
  author={Van Loan, Charles},
  volume={10},
  year={1992},
  publisher={Siam}
}

@article{preibisch2014efficient,
  title={Efficient Bayesian-based multiview deconvolution},
  author={Preibisch, Stephan and Amat, Fernando and Stamataki, Evangelia and Sarov, Mihail and Singer, Robert H and Myers, Eugene and Tomancak, Pavel},
  journal={nature methods},
  volume={11},
  number={6},
  pages={645--648},
  year={2014},
  publisher={Nature Publishing Group}
}


@article{schmid2015real,
  title={Real-time multi-view deconvolution},
  author={Schmid, Benjamin and Huisken, Jan},
  journal={Bioinformatics},
  volume={31},
  number={20},
  pages={3398--3400},
  year={2015},
  publisher={Oxford Univ Press}
}

@article{maronga2015parallelized,
  title={The Parallelized Large-Eddy Simulation Model ({PALM}) version 4.0 for atmospheric and oceanic flows: model formulation, recent developments, and future perspectives},
  author={Maronga, Bj{\"o}rn and Gryschka, Micha and Heinze, Rieke and Hoffmann, Fabian and Kanani-S{\"u}hring, Farah and Keck, Marius and Ketelsen, K and Letzel, MO and S{\"u}hring, Matthias and Raasch, Siegfried},
  journal={Geoscientific Model Development Discussions 8 (2015), Nr. 2, S. 1539-1637},
  year={2015},
  publisher={G{\"o}ttingen: Copernicus}
}


@article{katoh2002mafft,
  title={{MAFFT}: a novel method for rapid multiple sequence alignment based on fast Fourier transform},
  author={Katoh, Kazutaka and Misawa, Kazuharu and Kuma, Kei-ichi and Miyata, Takashi},
  journal={Nucleic acids research},
  volume={30},
  number={14},
  pages={3059--3066},
  year={2002},
  publisher={Oxford Univ Press}
}

@article{dlstudy,
  author    = {Soheil Bahrampour and
               Naveen Ramakrishnan and
               Lukas Schott and
               Mohak Shah},
  title     = {Comparative Study of Caffe, Neon, Theano, and Torch for Deep Learning},
  journal   = {CoRR},
  volume    = {abs/1511.06435},
  year      = {2015},
  url       = {http://arxiv.org/abs/1511.06435},
  timestamp = {Tue, 01 Dec 2015 19:22:34 +0100},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/corr/BahrampourRSS15},
  bibsource = {dblp computer science bibliography, http://dblp.org}
}

@article{huisken2004optical,
  title={Optical sectioning deep inside live embryos by selective plane illumination microscopy},
  author={Huisken, Jan and Swoger, Jim and Del Bene, Filippo and Wittbrodt, Joachim and Stelzer, Ernst HK},
  journal={Science},
  volume={305},
  number={5686},
  pages={1007--1009},
  year={2004},
  publisher={American Association for the Advancement of Science}
}

@article{hurd2010fourier,
  title={A Fourier transform method for spread option pricing},
  author={Hurd, Thomas R and Zhou, Zhuowei},
  journal={SIAM Journal on Financial Mathematics},
  volume={1},
  number={1},
  pages={142--157},
  year={2010},
  publisher={SIAM}
}

@inproceedings{dempster2002spread,
  title={Spread option valuation and the fast Fourier transform},
  author={Dempster, Michael Alan Howarth and Hong, SS George},
  booktitle={Mathematical Finance--Bachelier Congress 2000},
  pages={203--220},
  year={2002},
  organization={Springer}
}


@article{du2012cuda,
  title={From {CUDA} to {OpenCL}: Towards a performance-portable solution for multi-platform GPU programming},
  author={Du, Peng and Weber, Rick and Luszczek, Piotr and Tomov, Stanimire and Peterson, Gregory and Dongarra, Jack},
  journal={Parallel Computing},
  volume={38},
  number={8},
  pages={391--407},
  year={2012},
  publisher={Elsevier}
}

@Manual{nvidia2010cufft,
  title={{CUFFT} library},
  author={NVIDIA},
  year={2010},
  publisher={Version},
  url={https://developer.nvidia.com/cufft}
}

@Online{clfft,
  author={{AMD}},
  title={{clFFT}},
  note={A software library containing FFT functions written in OpenCL},
  url = {https://github.com/clMathLibraries/clFFT},
  year = {2016}
}

@Online{steinbach_gtc2015,
  author={Peter Steinbach},
  title={Streaming FFTs on Large 3D Microscope Images},
  note={Presentation at GTC 2015, San Jose (CA, USA), March 20, 2015},
  url = {https://idisk.mpi-cbg.de/~steinbac/gtc2015},
  year = {2015}
}


@Manual{fftw_manual,
  title = 	 {FFTW User Manual},
  OPTkey = 	 {},
  OPTauthor = 	 {},
  OPTorganization = {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTyear = 	 {},
  note = 	 {November 29, 2016},
  OPTannote = 	 {},
  url = {http://www.fftw.org/fftw3_doc/index.html#Top}
}

@Article{FFTW05,
  author  = {Frigo, Matteo and Johnson, Steven G.},
  title   = {The Design and Implementation of {FFTW3}},
  journal = {Proceedings of the IEEE},
  year    = {2005},
  volume  = {93},
  number  = {2},
  pages   = {216--231},
  note    = {Special issue on "Program Generation, Optimization, and Platform Adaptation"}
}

@misc{intel2007intel,
  title={Intel math kernel library},
  author={Intel, MKL},
  year={2007},
  publisher={ed}
}

@inproceedings{shoc2010,
  title={The scalable heterogeneous computing (SHOC) benchmark suite},
  author={Danalis, Anthony and Marin, Gabriel and McCurdy, Collin and Meredith, Jeremy S and Roth, Philip C and Spafford, Kyle and Tipparaju, Vinod and Vetter, Jeffrey S},
  booktitle={Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units},
  pages={63--74},
  year={2010},
  organization={ACM}
}

@inproceedings{eleftheriou2005performance,
  title={Performance measurements of the 3d {FFT} on the Blue {Gene/L} supercomputer},
  author={Eleftheriou, Maria and Fitch, Blake and Rayshubskiy, Aleksandr and Ward, TJ Christopher and Germain, Robert},
  booktitle={European Conference on Parallel Processing},
  pages={795--803},
  year={2005},
  organization={Springer}
}

@article{dongarra2013hpc,
  title={{HPC} Challenge: Design, History, and Implementation Highlights},
  author={Dongarra, Jack and Luszczek, Piotr},
  journal={Contemporary High Performance Computing: From Petascale Toward Exascale},
  year={2013},
  publisher={Taylor and Francis, CRC Computational Science Series, Boca Raton, FL}
}

@article{park2015fast,
  title={Fast Fourier transform benchmark on X86 Xeon system for multimedia data processing},
  author={Park, Young-Soo and Park, Koo-Rack and Kim, Jin-Mook and Jeong, Hwa-Young},
  journal={Multimedia Tools and Applications},
  pages={1--16},
  year={2015},
  publisher={Springer}
}

@inproceedings{fialka2006fft,
  title={{FFT} and convolution performance in image filtering on GPU},
  author={Fialka, Ondirej and Cadik, Martin},
  booktitle={Tenth International Conference on Information Visualisation (IV'06)},
  pages={609--614},
  year={2006},
  organization={IEEE}
}

@TechReport{meuer2011top500,
  title={Top500 supercomputing sites},
  author={Meuer, Hans and Strohmaier, Erich and Dongarra, Jack and Simon, Horst},
  institution =  {top500.org},
  year={2011},
  publisher={Technical report},
  url={https://www.top500.org/lists/2016/11/}
}

@online{gearshifft_github,
  title = 	 {gearshifft: Benchmark Suite for Heterogeneous FFT Implementations},
  year = 	 {2016},
  url = {https://github.com/mpicbg-scicomp/gearshifft}
}

@online{taurus,
title = {Taurus},
author = {{\relax Zentrum für Informationsdienste und Hochleistungsrechnen, TU Dresden}},
url = {https://doc.zih.tu-dresden.de/hpc-wiki/bin/view/Compendium/SystemTaurus}
}

@online{hypnos,
title = {Hypnos},
author = {Abteilung IT-Infrastruktur, Helmholtz-Zentrum Dresden-Rossendorf},
url = {http://www.hzdr.de/db/Cms?pOid=12231&pNid=852}
}

@article{cooley1965algorithm,
  title={An algorithm for the machine calculation of complex Fourier series},
  author={Cooley, James W. and Tukey, John W.},
  journal={Mathematics of computation},
  volume={19},
  number={90},
  pages={297--301},
  year={1965},
  publisher={JSTOR}
}

@Book{gauss,
  author = 	 {Gauss, Carl Friedrich},
  title = 	 {Theoria interpolationis methodo nova tractata},
  publisher = 	 {König\-liche Gesellschaft der Wissenschaften, Göttingen},
  year = 	 {1866},
  pages = {265--327},
  OPTkey = 	 {},
  volume = 	 {3}
}

@ARTICLE{bluestein,
author={L. Bluestein},
journal={IEEE Transactions on Audio and Electroacoustics},
title={A linear filtering approach to the computation of discrete Fourier transform},
year={1970},
volume={18},
number={4},
pages={451-455},
keywords={Band pass filters;Chirp;Discrete Fourier transforms;Discrete transforms;Filtering;Frequency;Laboratories;Maximum likelihood detection;Nonlinear filters;Transversal filters},
doi={10.1109/TAU.1970.1162132},
ISSN={0018-9278},
month={Dec},}

@inproceedings{dftgpu,
 author = {Govindaraju, Naga K. and Lloyd, Brandon and Dotsenko, Yuri and Smith, Burton and Manferdelli, John},
 title = {High Performance Discrete Fourier Transforms on Graphics Processors},
 booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing},
 series = {SC '08},
 year = {2008},
 isbn = {978-1-4244-2835-9},
 location = {Austin, Texas},
 pages = {2:1--2:12},
 articleno = {2},
 numpages = {12},
 url = {http://dl.acm.org/citation.cfm?id=1413370.1413373},
 acmid = {1413373},
 publisher = {IEEE Press},
 address = {Piscataway, NJ, USA},
}

@article{williams2009roofline,
  title={Roofline: an insightful visual performance model for multicore architectures},
  author={Williams, Samuel and Waterman, Andrew and Patterson, David},
  journal={Communications of the ACM},
  volume={52},
  number={4},
  pages={65--76},
  year={2009},
  publisher={ACM}
}

@article{Akin:15,
author = {Berkin Akin and Franz Franchetti and James C. Hoe},
title = {{FFT}s with Near-Optimal Memory Access Through Block Data Layouts: Algorithm, Architecture and Design Automation},
journal = {Journal of Signal Processing Systems},
year = {2015}
}

@misc{cpp14std,
   Key = {{ISO 14882:2014}},
   publisher = {{ISO, Geneva, Switzerland}},
   type = {{Norm}},
   title = {{Information technology — Programming languages — C++}},
   number = {{ISO 14882}},
   year = {{2014}},
}

@misc{boost,
  title={Libraries},
  author={Boost, C++},
  year={2016},
  url={http://www.boost.org/}
}

@book{stroustrup1994design,
  title={The design and evolution of C++},
  author={Stroustrup, Bjarne},
  year={1994},
  publisher={Pearson Education India}
}

@inproceedings{stockham1966high,
  title={High-speed convolution and correlation},
  author={Stockham Jr, Thomas G},
  booktitle={Proceedings of the April 26-28, 1966, Spring joint computer conference},
  pages={229--233},
  year={1966},
  organization={ACM}
}

@inproceedings{bachmann,
 author = {Bachmann, Philipp},
 title = {Static and Metaprogramming Patterns and Static Frameworks: A Catalog. An Application},
 booktitle = {Proceedings of the 2006 Conference on Pattern Languages of Programs},
 series = {PLoP '06},
 year = {2006},
 isbn = {978-1-60558-372-3},
 location = {Portland, Oregon, USA},
 pages = {17:1--17:33},
 articleno = {17},
 numpages = {33},
 url = {http://doi.acm.org/10.1145/1415472.1415492},
 doi = {10.1145/1415472.1415492},
 acmid = {1415492},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {design pattern, generative programming, generic programming, metaprogramming, portability, software product lines, static polymorphism, template, template specialization},
}