xref: /libCEED/doc/papers/joss/paper.bib (revision bcb2dfae4c301ddfdddf58806f08f6e7d17f4ea5)
1@article{Brown:2010,
2  Author = {{Brown}, J.},
3  Journal = {Journal of Scientific Computing},
4  Volume = 45,
5  Month = oct,
6  Title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in 3D},
7  Year = 2010,
8  doi = {10.1007/s10915-010-9396-8},
9}
10
11@misc{C99-lang,
12  title={ISO/IEC 9899: 1999 Programming Languages-C},
13  author={{International Standards Organisation}},
14  year={1999},
15  publisher={American National Standards Institute, New York}
16}
17
18@article{CEED-ECP-paper,
19  author  = {Kolev, Tzanio and
20             Fischer, Paul and
21             Min, Misun and
22             Dongarra, Jack and
23             Brown, Jed and
24             Dobrev, Veselin and
25             Warburton, Tim and
26             Tomov, Stanimire and
27             Shephard, Mark S. and
28             Abdelfattah, Ahmad and
29             Barra, Valeria and
30             Beams, Natalie and
31             Camier, Jean-Sylvain and
32             Chalmers, Noel and
33             Dudouit, Yohann and
34             Karakus, Ali and
35             Karlin, Ian and
36             Kerkemeier, Stefan and
37             Lan, Yu-Hsiang and
38             Medina, David and
39             Merzari, Elia and
40             Obabko, Aleksandr and
41             Pazner, Will and
42             Rathnayake, Thilina and
43             Smith, Cameron W. and
44             Spies, Lukas and
45             Swirydowicz, Kasia and
46             Thompson, Jeremy and
47             Tomboulides, Ananias and
48             Tomov, Vladimir},
49  title   = {Efficient Exascale Discretizations: High-Order Finite Element Methods},
50  journal = {International Journal of High Performance Computing Applications},
51  year    = {2021},
52  doi     = {10.1177/10943420211020803}
53}
54
55@misc{CEEDMS25,
56  author       = {Brown, Jed and
57                  Abdelfattah, Ahmad and
58                  Barra, Valeria and
59                  Dobrev, Veselin and
60                  Dudouit, Yohann and
61                  Fischer, Paul and
62                  Kolev, Tzanio and
63                  Medina, David and
64                  Min, Misun and
65                  Ratnayaka, Thilina and
66                  Smith, Cameron and
67                  Thompson, Jeremy and
68                  Tomov, Stanimire and
69                  Tomov, Vladimir and
70                  Warburton, Tim},
71  title        = {{CEED ECP Milestone Report: Public release of CEED
72                   2.0}},
73  year         = 2019,
74  publisher    = {Zenodo},
75  doi          = {10.5281/zenodo.2641316}
76}
77
78@misc{CEEDMS34,
79  author       = {Kolev, Tzanio and
80                  Fischer, Paul and
81                  Abdelfattah, Ahmad and
82                  Ananthan, Shreyas and
83                  Barra, Valeria and
84                  Beams, Natalie and
85                  Bleile, Ryan and
86                  Brown, Jed and
87                  Carson, Robert and
88                  Camier, Jean-Sylvain and
89                  Churchfield, Matthew and
90                  Dobrev, Veselin and
91                  Dongarra, Jack and
92                  Dudouit, Yohann and
93                  Karakus, Ali and
94                  Kerkemeier, Stefan and
95                  Lan, YuHsiang and
96                  Medina, David and
97                  Merzari, Elia and
98                  Min, Misun and
99                  Parker, Scott and
100                  Ratnayaka, Thilina and
101                  Smith, Cameron and
102                  Sprague, Michael and
103                  Stitt, Thomas and
104                  Thompson, Jeremy and
105                  Tomboulides, Ananias and
106                  Tomov, Stanimire and
107                  Tomov, Vladimir and
108                  Vargas, Arturo and
109                  Warburton, Tim and
110                  Weiss, Kenneth},
111  title        = {{CEED ECP Milestone Report: Improve performance and
112                   capabilities of CEED-enabled ECP applications on
113                   Summit/Sierra}},
114  year         = 2020,
115  publisher    = {Zenodo},
116  doi          = {10.5281/zenodo.3860804}
117}
118
119@misc{CEEDwebsite,
120  title = "CEED",
121  url = "https://ceed.exascaleproject.org/",
122  year = "2021"
123}
124
125@misc{CUDAwebsite,
126  title = "CUDA",
127  url = "https://developer.nvidia.com/about-cuda",
128  year = "2021"
129}
130
131@article{Fischer2020scalability,
132  title={Scalability of high-performance PDE solvers},
133  author={Paul Fischer and Misun Min and Thilina Rathnayake and Som Dutta and Tzanio Kolev and Veselin Dobrev and Jean-Sylvain Camier and Martin Kronbichler and Tim Warburton and Kasia Świrydowicz and Jed Brown},
134  journal={The International Journal of High Performance Computing Applications},
135  year={2020},
136  doi = "10.1177/1094342020915762"
137}
138
139@book{Fortran77-lang,
140  title={Standard {X3}. 9-1978, Programming Language {Fortran} (revision of {ANSI X2}. 9-1966)},
141  author={ANSI},
142  journal={New York: ANSI},
143  year={1978}
144}
145
146@misc{HIPwebsite,
147  title = "HIP",
148  url = "https://rocmdocs.amd.com/en/latest/Programming_Guides/HIP-GUIDE.html",
149  year = "2021"
150}
151
152@article{Julia-lang,
153  title={Julia: A fresh approach to numerical computing},
154  author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B},
155  journal={SIAM {R}eview},
156  volume={59},
157  number={1},
158  pages={65--98},
159  year={2017},
160  publisher={SIAM},
161  doi={10.1137/141000671}
162}
163
164@misc{libceed-user-manual,
165  author       = {Abdelfattah, Ahmad and
166                  Barra, Valeria and
167                  Beams, Natalie and
168                  Brown, Jed and
169                  Camier, Jean-Sylvain and
170                  Dobrev, Veselin and
171                  Dudouit, Yohann and
172                  Ghaffari, Leila and
173                  Kolev, Tzanio and
174                  Medina, David and
175                  Pazner, Will and
176                  Rathnayake, Thilina and
177                  Thompson, Jeremy L and
178                  Tomov, Stanimire},
179  title        = {libCEED User Manual},
180  month        = mar,
181  year         = 2021,
182  publisher    = {Zenodo},
183  version      = {0.8},
184  doi          = {10.5281/zenodo.4895340}
185}
186
187@InProceedings{libceed-paper-proc-scipy-2020,
188  author    = {Valeria Barra and Jed Brown and Jeremy Thompson and Yohann Dudouit},
189  title     = {{H}igh-performance operator evaluations with ease of use: lib{C}{E}{E}{D}'s {P}ython interface},
190  booktitle = {{P}roceedings of the 19th {P}ython in {S}cience {C}onference},
191  pages     = {85 - 90},
192  year      = {2020},
193  editor    = {{M}eghann {A}garwal and {C}hris {C}alloway and {D}illon {N}iederhut and {D}avid {S}hupe},
194  doi       = {10.25080/Majora-342d178e-00c}
195}
196
197@misc{LIBXSMM,
198  title = "{LIBXSMM development site}",
199  url = "http://github.com/hfp/libxsmm",
200  year = "2021"
201}
202
203@misc{MAGMAwebsite,
204  title = "{MAGMA development site}",
205  url = "https://bitbucket.org/icl/magma",
206  year = "2021"
207}
208
209@misc{MFEMlibrary,
210  title = "{MFEM}: {Modular Finite Element Methods Library}",
211  url = "https://mfem.org/",
212  year = "2021",
213  doi = "10.11578/dc.20171025.1248"
214}
215
216@article{mfem-paper,
217  title   = {{MFEM}: A Modular Finite Element Library},
218  author  = {R. Anderson and J. Andrej and A. Barker and J. Bramwell and J.-S. Camier and
219             J. Cerveny V. Dobrev and Y. Dudouit and A. Fisher and Tz. Kolev and W. Pazner and
220             M. Stowell and V. Tomov and I. Akkerman and J. Dahm and D. Medina and S. Zampini},
221  journal = {Computers \& Mathematics with Applications},
222  doi     = {10.1016/j.camwa.2020.06.009},
223  year    = {2020}
224}
225
226@misc{Nekwebsite,
227  title = "Nek5000",
228  url = "https://nek5000.mcs.anl.gov/",
229  year = "2021"
230}
231
232@inproceedings{Numba,
233author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
234title = {Numba: A LLVM-Based Python JIT Compiler},
235year = {2015},
236isbn = {9781450340052},
237publisher = {Association for Computing Machinery},
238address = {New York, NY, USA},
239doi = {10.1145/2833157.2833162},
240abstract = {Dynamic, interpreted languages, like Python, are attractive for domain-experts and scientists experimenting with new ideas. However, the performance of the interpreter is often a barrier when scaling to larger data sets. This paper presents a just-in-time compiler for Python that focuses in scientific and array-oriented computing. Starting with the simple syntax of Python, Numba compiles a subset of the language into efficient machine code that is comparable in performance to a traditional compiled language. In addition, we share our experience in building a JIT compiler using LLVM[1].},
241booktitle = {Proceedings of the Second Workshop on the LLVM Compiler Infrastructure in HPC},
242articleno = {7},
243numpages = {6},
244keywords = {compiler, LLVM, Python},
245location = {Austin, Texas},
246series = {LLVM '15}
247}
248
249@Article{NumPy,
250 title         = {Array programming with {NumPy}},
251 author        = {Charles R. Harris and K. Jarrod Millman and St{'{e}}fan J.
252                 van der Walt and Ralf Gommers and Pauli Virtanen and David
253                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
254                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
255                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
256                 Brett and Allan Haldane and Jaime Fern{'{a}}ndez del
257                 R{'{\i}}o and Mark Wiebe and Pearu Peterson and Pierre
258                 G{'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
259                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
260                 Travis E. Oliphant},
261 year          = {2020},
262 month         = sep,
263 journal       = {Nature},
264 volume        = {585},
265 number        = {7825},
266 pages         = {357--362},
267 doi           = {10.1038/s41586-020-2649-2},
268 publisher     = {Springer Science and Business Media {LLC}}
269}
270
271@misc{NVRTCwebsite,
272  title = "NVRTC",
273  url = "https://docs.nvidia.com/cuda/nvrtc/index.html",
274  year = "2021"
275}
276
277@misc{OCCAwebsite,
278  title = "{OCCA} development site",
279  url = "http://github.com/libocca/occa",
280  year = "2021"
281}
282
283@article{Orszag:1980,
284  title = "Spectral methods for problems in complex geometries",
285  journal = "Journal of Computational Physics",
286  volume = "37",
287  pages = "70 - 92",
288  year = "1980",
289  doi = "10.1016/0021-9991(80)90005-4",
290  author = "Steven A Orszag"
291}
292
293@TechReport{PETScUserManual,
294  author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune
295            and Kris Buschelman and Lisandro Dalcin and Alp Dener and Victor Eijkhout and William~D. Gropp
296            and Dmitry Karpeyev and Dinesh Kaushik and Matthew~G. Knepley and Dave~A. May and Lois Curfman McInnes
297            and Richard Tran Mills and Todd Munson and Karl Rupp and Patrick Sanan
298            and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang},
299  title  = {{PETS}c Users Manual},
300  institution = {Argonne National Laboratory},
301  year   = 2021,
302  number = {ANL-95/11 - Revision 3.15}
303}
304
305@misc{Python-lang,
306  title = "Python",
307  url = "https://www.python.org/",
308  year = "2021",
309}
310
311@misc{Rust-lang,
312  title = "Rust",
313  url = "https://www.rust-lang.org/",
314  year = "2021",
315}
316
317@misc{python-cffi,
318  title = "C Foreign Function Interface for {Python}",
319  url = "https://cffi.readthedocs.io",
320  year = "2021",
321}
322
323@article{straka1993numerical,
324  title={Numerical solutions of a non-linear density current: A benchmark solution and comparisons},
325  author={Straka, Jerry M and Wilhelmson, Robert B and Wicker, Louis J and Anderson, John R and Droegemeier, Kelvin K},
326  journal={International Journal for Numerical Methods in Fluids},
327  volume={17},
328  number={1},
329  pages={1--22},
330  year={1993},
331  publisher={Wiley Online Library},
332  doi={10.1002/fld.1650170103}
333}
334
335@book{deville2002highorder,
336  title={High-order methods for incompressible fluid flow},
337  author={Deville, Michel O and Fischer, Paul F and Mund, Ernest H},
338  year={2002},
339  publisher={Cambridge University Press},
340  isbn={0-521-45309-7}
341}
342
343@article{gropp2014using,
344  title={Using {MPI}: Portable Parallel Programming with the Message-Passing Interface},
345  author={Gropp, William and Lusk, Ewing and Skjellum, Anthony},
346  year={2014},
347  publisher={The MIT Press},
348  isbn={9780262527392}
349}
350
351@article{libMeshPaper,
352  author = {Benjamin S. Kirk and John W. Peterson and Roy H. Stogner and Graham F. Carey},
353  title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening Simulations}},
354  journal = {Engineering with Computers},
355  volume = 22,
356  number = {3--4},
357  pages = {237--254},
358  year = 2006,
359  doi = {10.1007/s00366-006-0049-3}
360}
361@book{LoggMardalWells2012,
362  title  = {Automated Solution of Differential Equations by the Finite Element Method: The {FEniCS} book},
363  author = {Anders Logg and Kent-Andre Mardal and Garth N. Wells and others},
364  editor = {Anders Logg and Kent-Andre Mardal and Garth N. Wells},
365  volume = {84},
366  year = {2012},
367  publisher = {Springer},
368  doi = {10.1007/978-3-642-23099-8},
369  isbn = {978-3-642-23098-1}
370}
371
372@article{dealII92,
373  title     = {The \texttt{deal.II} Library, Version 9.2},
374  author    = {Daniel Arndt and Wolfgang Bangerth and Bruno Blais and
375               Thomas C. Clevenger and Marc Fehling and Alexander V. Grayver and
376               Timo Heister and Luca Heltai and Martin Kronbichler and Matthias Maier and
377               Peter Munch and Jean-Paul Pelteret and Reza Rastak and
378               Ignacio Thomas and Bruno Turcksin and Zhuoran Wang and David Wells},
379  journal   = {Journal of Numerical Mathematics},
380  publisher = {De Gruyter},
381  year      = {2020},
382  volume    = {28},
383  number    = {3},
384  pages     = {131-146},
385  DOI       = {10.1515/jnma-2020-0043},
386  url       = {https://dealii.org/deal92-preprint.pdf}
387}
388
389@misc{kruppcomparison,
390  title="{CPU-GPU-MIC} Comparision Charts",
391  author={Karl Rupp},
392  url={https://github.com/karlrupp/cpu-gpu-mic-comparison},
393  year={2020}
394}
395
396@article{williams2009roofline,
397  title={Roofline: an insightful visual performance model for multicore architectures},
398  author={Williams, Samuel and Waterman, Andrew and Patterson, David},
399  journal={Communications of the ACM},
400  volume={52},
401  number={4},
402  pages={65--76},
403  year={2009},
404  publisher={ACM},
405  doi={10.1145/1498765.1498785}
406}
407
408@article{babuska1994hpfem,
409  title={The $p$ and $h-p$ versions of the finite element method, basic principles and properties},
410  author={Babu{\v{s}}ka, Ivo and Suri, Manil},
411  journal={SIAM Review},
412  volume={36},
413  number={4},
414  pages={578--632},
415  year={1994},
416  publisher={SIAM},
417  doi={10.1137/1036141}
418}
419
420@article{lottes2005hms,
421  title={Hybrid Multigrid/{Schwarz} Algorithms for the Spectral Element Method},
422  author={Lottes, J.W. and Fischer, P.F.},
423  journal={Journal of Scientific Computing},
424  volume={24},
425  number={1},
426  pages={45--78},
427  year={2005},
428  publisher={Springer},
429  doi={10.1007/s10915-004-4787-3}
430}
431
432@article{zhang2021petscsf,
433  title={The {PetscSF} Scalable Communication Layer},
434  author={Zhang, Junchao and Brown, Jed and Balay, Satish and Faibussowitsch, Jacob and Knepley, Matthew and Marin, Oana and Mills, Richard Tran and Munson, Todd and Smith, Barry F and Zampini, Stefano},
435  journal={IEEE Transactions on Parallel and Distributed Systems},
436  archivePrefix={arXiv},
437  eprint={2102.13018},
438  year={2021},
439  doi={10.1109/TPDS.2021.3084070}
440}
441