Publications

BHM+21

Jed Brown, Yunhui He, Scott MacLachlan, Matt Menickelly, and Stefan M Wild. Tuning multigrid methods with robust optimization. SIAM Journal on Scientific Computing, 43:A109–A138, 2021. arXiv:2001.00887, doi:10.1137/19M1308669.

FMR+20

Paul Fischer, Misun Min, Thilina Rathnayake, Som Dutta, Tzanio Kolev, Veselin Dobrev, Jean-Sylvain Camier, Martin Kronbichler, Tim Warburton, Kasia Świrydowicz, and Jed Brown. Scalability of high-performance PDE solvers. International Journal of High Performance Computing Applications, 34:562–586, 2020. arXiv:2004.06722, doi:10.1177/1094342020915762.

BHM19

Jed Brown, Yunhui He, and Scott MacLachlan. Local Fourier analysis of BDDC-like algorithms. SIAM Journal on Scientific Computing, 41:S346–S369, 2019. doi:10.1137/18M1191373.

AHK+17

Mark F Adams, Eero Hirvijoki, Matthew G Knepley, Jed Brown, Tobin Isaac, and Richard Mills. Landau collision integral solver with adaptive mesh refinement on emerging architectures. SIAM Journal on Scientific Computing, 39(6):C452–C465, 2017. arXiv:1702.08880, doi:10.1137/17M1118828.

ABKS16

Mark F. Adams, Jed Brown, Matthew G. Knepley, and Ravi Samtaney. Segmental refinement: a multigrid technique for data locality. SIAM Journal on Scientific Computing, 38(4):C426–C440, 2016. arXiv:1406.7808, doi:10.1137/140975127.

GCB15

Debojyoti Ghosh, Emil M. Constantinescu, and Jed Brown. Efficient implementation of nonlinear compact schemes on massively parallel platforms. SIAM Journal on Scientific Computing, 37(3):C354–C383, 2015. Also preprint ANL/MCS-P5121-0414. doi:10.1137/140989261.

MBP15

David A. May, Jed Brown, and Laetitia Le Pourhiet. A scalable, matrix-free multigrid preconditioner for finite element discretizations of heterogeneous Stokes flow. Computer Methods in Applied Mechanics and Engineering, 290(0):496–523, 2015. doi:10.1016/j.cma.2015.03.014.

BKS15

Jed Brown, Matthew G. Knepley, and Barry F. Smith. Run-time extensibility and librarization of simulation software. IEEE Computing in Science and Engineering, 17(1):38–45, 2015. doi:10.1109/MCSE.2014.95.

BSA13

Jed Brown, Barry F. Smith, and Aron Ahmadia. Achieving textbook multigrid efficiency for hydrostatic ice flow. SIAM Journal on Scientific Computing, 35(2):359–375, 2013. Also preprint ANL/MCS-P743-1298. doi:10.1137/110834512.

KMW+13

David E. Keyes, Lois Curfman McInnes, Carol Woodward, William Gropp, Eric Myra, Michael Pernice, John Bell, Jed Brown, Alain Clo, Jeffrey Connors, Emil Constantinescu, Don Estep, Kate Evans, Charbel Farhat, Ammar Hakim, Glenn Hammond, Glen Hansen, Judith Hill, Tobin Isaac, Xiangmin Jiao, Kirk Jordan, Dinesh Kaushik, Efthimios Kaxiras, Alice Koniges, Kihwan Lee, Aaron Lott, Qiming Lu, John Magerlein, Reed Maxwell, Michael McCourt, Miriam Mehl, Roger Pawlowski, Amanda Peters Randles, Daniel Reynolds, Beatrice Rivière, Ulrich Rüde, Tim Scheibe, John Shadid, Brendan Sheehan, Mark Shephard, Andrew Siegel, Barry Smith, Xianzhu Tang, Cian Wilson, and Barbara Wohlmuth. Multiphysics simulations: challenges and opportunities. International Journal of High Performance Computing Applications, 27(1):4–83, Feb 2013. Special issue. doi:10.1177/1094342012468181.

MAB+13

Tareq M. Malas, Aron J. Ahmadia, Jed Brown, John A. Gunnels, and David E. Keyes. Optimizing the performance of streaming numerical kernels on the IBM BlueGene/P PowerPC 450 processor. International Journal of High Performance Computing Applications, 27(2):193–209, 2013. doi:10.1177/1094342012444795.

BBEM12

Rodney Biezuner, Jed Brown, Grey Ercole, and Eder Martins. Computing the first eigenpair of the $p$-Laplacian via inverse iteration of sublinear supersolutions. Journal of Scientific Computing, 52:180–201, 2012. doi:10.1007/s10915-011-9540-0.

Bro10

Jed Brown. Efficient nonlinear solvers for nodal high-order finite elements in 3D. Journal of Scientific Computing, 45:48–63, 2010. doi:10.1007/s10915-010-9396-8.

AFT+10

Jason M. Amundson, Mark Fahnestock, Martin Truffer, Jed Brown, Martin P. Lüthi, and Roman J. Motyka. Ice mélange dynamics and implications for terminus stability, Jakobshavn Isbræ, Greenland. J. Geophys. Res, 115:F01005, 2010. doi:10.1029/2009JF001405.

BB09

E. Bueler and J. Brown. Shallow shelf approximation as a “sliding law” in a thermomechanically coupled ice sheet model. Journal of Geophysical Research-Earth Surface, 114(F3):F03008, 2009. arXiv:0810.3449, doi:10.1029/2008JF001179.

BBL07

E. Bueler, J. Brown, and C. Lingle. Exact solutions to the thermomechanically coupled shallow ice approximation: effective tools for verification. J. Glaciol, 53:499–516, 2007. doi:10.3189/002214307783258396.

BLB07

E. Bueler, C.S. Lingle, and J. Brown. Fast computation of a viscoelastic deformable Earth model for ice-sheet simulations. Ann. Glaciol, 46:97–105, 2007. doi:10.3189/172756407782871567.

BLKB+05

E. Bueler, C. S. Lingle, J. A. Kallen-Brown, D. N. Covey, and L. N. Bowman. Exact solutions and numerical verification for isothermal ice sheets. J. Glaciol., 51(173):291–306, 2005. doi:10.3189/172756505781829449.

BBTD20

Valeria Barra, Jed Brown, Jeremy Thompson, and Yohann Dudouit. High-performance operator evaluations with ease of use: libCEED's Python interface. In Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, editors, Proceedings of the 19th Python in Science Conference, 85 – 90. 2020. doi:10.25080/Majora-342d178e-00c.

KonoligeB18

Tristan Konolige* and Jed Brown. A parallel solver for graph Laplacians. In Proceedings of the Platform for Advanced Scientific Computing (PASC). 2018. Best Paper Award. arXiv:1705.06266, doi:10.1145/3218176.3218227.

DuplyakinBC18

Dmitry Duplyakin*, Jed Brown, and Donna Calhoun. Evaluating active learning with cost and memory awareness. In 2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 214–223. IEEE, 2018. Acceptance Rate 24.4%. doi:10.1109/IPDPS.2018.00031.

DuplyakinBR16

Dmitry Duplyakin*, Jed Brown, and Robert Ricci. Active learning in performance analysis. In Proceedings of the IEEE Cluster Conference. September 2016. Acceptance Rate 24.1%. URL: http://www.flux.utah.edu/paper/duplyakin-cluster16, doi:10.1109/CLUSTER.2016.63.

MBP14

Dave A. May, Jed Brown, and Laetitia Le Pourhiet. pTatin3D: High-performance methods for long-term lithospheric dynamics. In Proceedings of SC14: International Conference for High Performance Computing, Networking, Storage and Analysis. ACM, 2014. Acceptance Rate 21%. doi:10.1109/SC.2014.28.

KBMS13

Matthew G. Knepley, Jed Brown, Lois Curfman McInnes, and Barry F. Smith. Accurately citing software and algorithms used in publications. In Workshop towards Sustainable Software for Science: Practice and Experiences (WSSSPE). 2013. doi:10.6084/m9.figshare.785731.

JB13

Barry F. Smith Jed Brown, Matthew G. Knepley. Run-time extensibility: anything less is unsustainable. In Workshop towards Sustainable Software for Science: Practice and Experiences (WSSSPE). 2013. doi:10.6084/m9.figshare.791571.

BB13

Jed Brown and Peter Brune. Low-rank quasi-Newton updates for robust Jacobian lagging in Newton-type methods. In International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering, 2554–2565. 2013.

BKM+12

J. Brown, M. G. Knepley, D. A. May, L. C. McInnes, and B. F. Smith. Composable linear solvers for multiphysics. In Proceeedings of the 11th International Symposium on Parallel and Distributed Computing (ISPDC 2012), 55–62. IEEE Computer Society, 2012. doi:10.1109/ISPDC.2012.16.

BSB+09

K. Burckhardt, D. Szczerba, J. Brown, K. Muralidhar, and and G. Székely. Fast implicit simulation of oscillatory flow in human abdominal bifurcation using a schur complement preconditioner. In H. Sips, D. Epema, and and H.-X. Lin, editors, Euro-Par 2009 Parallel Processing, volume 5704 of Lecture Notes in Computer Science, 747–759. Springer, August 2009. doi:10.1007/978-3-642-03869-3_70.

ABC+18

Shrirang Abhyankar, Jed Brown, Emil M. Constantinescu, Debojyoti Ghosh, Barry F. Smith, and Hong Zhang. PETSc/TS: A modern scalable ODE/DAE solver library. 2018. arXiv:1806.01437.

KB20

Tristan Konolige and Jed Brown. Multigrid for bundle adjustment. 2020. arXiv:2007.01941.

TAB+19

Stanimire Tomov, Ahmad Abdelfattah, Valeria Barra, Natalie Beams, Jed Brown, Jean-Sylvain Camier, Veselin Dobrev, Jack Dongarra, Yohann Dudouit, Paul Fischer, Ali Karakus, Stefan Kerkemeier, Tzanio Kolev, YuHsiang Lan, Elia Merzari, Misun Min, Aleks Obabko, Scott Parker, Thilina Ratnayaka, Jeremy Thompson, Ananias Tomboulides, Vladimir Tomov, and Tim Warburton. CEED ECP Milestone Report: Performance tuning of CEED software and 1st and 2nd wave apps. October 2019. doi:10.5281/zenodo.3477618.

SBB+19

Mark Shephard, Valeria Barra, Jed Brown, Jean-Sylvain Camier, Yohan Dudouit, Paul Fischer, Tzanio Kolev, David Medina, Misun Min, Cameron Smith, Morteza H. Siboni, Jeremy Thompson, and Tim Warburton. CEED ECP Milestone Report: Improved Support for Parallel Adaptive Simulation in CEED. July 2019. doi:10.5281/zenodo.3336420.

BAB+19

Jed Brown, Ahmad Abdelfattah, Valeria Barra, Veselin Dobrev, Yohann Dudouit, Paul Fischer, Tzanio Kolev, David Medina, Misun Min, Thilina Ratnayaka, Cameron Smith, Jeremy Thompson, Stanimire Tomov, Vladimir Tomov, and Tim Warburton. CEED ECP Milestone Report: Public release of CEED 2.0. March 2019. doi:10.5281/zenodo.2641316.

CFK+19

Jean-Sylvain Camier, Paul Fischer, Ali Karakus, Stefan Kerkemeier, Tzanio Kolev, Yu-Hsiang Lan, David Medina, Elia Merzari, Misun Min, Aleks Obabko, Thilina Ratnayaka, Dillon Shaver, Ananias Tomboulides, Vladimir Tomov, and Tim Warburton. CEED ECP Milestone Report: Engage second wave ECP/CEED applications. March 2019. doi:10.5281/zenodo.2542359.

BBB+19a

Lorena Barba, Juanjo Bazán, Jed Brown, Roman V Guimera, Melissa Gymrek, Alex Hanna, Lindsey J Heagy, Kathryn D Huff, Daniel S Katz, Christopher R Madan, and et al. Giving software its due through community-driven review and publication. Apr 2019. URL: osf.io/f4vx6, doi:10.31219/osf.io/f4vx6.

BBB+19b

Lorena A. Barba, Lecia J. Barker, Douglas S. Blank, Jed Brown, Allen B. Downey, Timothy George, Lindsey J. Heagy, Kyle T. Mandli, Jason K. Moore, David Lippert, Kyle E. Niemeyer, Ryan R. Watkins, Richard H. West, Elizabeth Wickes, Carol Willing, and Michael Zingale. Teaching and Learning with Jupyter. GitHub, 2019. URL: https://jupyter4edu.github.io/jupyter-edu-book/.

BBB+18

Katherine Barnhart, Thorsten Becker, Mark Behn, Jed Brown, Eunseo Choi, Catherine Cooper, Juliane Dannberg, Nicole Gasparini, Rene Gassmoeller, Lorraine Hwang, Boris Kaus, Louise Kellogg, Luc Lavier, Eric Mittelstaedt, Louis Moresi, Adina Pusok, Greg Tucker, Phaedra Upton, and Pedro Va. CTSP: coupling of tectonic and surface processes. Technical Report, University of Colorado, 2018.

WAB18

Samuel Williams, Mark F. Adams, and Jed Brown. High-performance geometric multigrid: An HPC performance benchmark. SIAM News, 2018. URL: https://sinews.siam.org/Details-Page/the-high-performance-geometric-multigrid-an-hpc-performance-benchmark.

TBMB+18

Stanimire Tomov, Pedro Bello-Maldonado, Jed Brown, Jean-Sylvain Camier, Veselin Dobrev, Jack Dongarr, Paul Fischer, Azzam Haidar, Tzanio Kolev, Elia Merzari, Misun Min, Aleks Obabko, Scott Parker, Thilina Ratnayaka, Jeremy Thompson, Ahmad Abdelfattah, Vladimir Tomov, and Tim Warburton. CEED ECP Milestone Report: Performance tuning of CEED software and first wave apps. September 2018. doi:10.5281/zenodo.2542350.

BDD+18

Jed Brown, Veselin Dobrev, Som Dutta, Paul Fischer, Kazem Kamran, Tzanio Kolev, David Medina, Misun' Min, Thilina Ratnayaka, Mark Shephard, Cameron Smith, and Jeremy Thompson. CEED ECP Milestone Report: Propose high-order mesh/data format. June 2018. doi:10.5281/zenodo.2542346.

BAC+18

Jed Brown, Ahmad Abdelfata, Jean-Sylvain Camier, Veselin Dobrev, Jack Dongarra, Paul Fischer, Aaron Fisher, Yohann Dudouit, Azzam Haidar, Kazem Kamran, Tzanio Kalev, Misun Min, Thilina Ratnayaka, Mark Shephard, Cameron Smith, Stanimire Tomov, Vladimir Tomov, and Tim Warburton. CEED ECP Milestone Report: Public release of CEED 1.0. March 2018. doi:10.5281/zenodo.2542343.

BCD+17

Jed Brown, Jean-Sylvain Camier, Veselin Dobrev, Paul Fischer, Tzanio Kolev, Thilina' Ratnayaka, Mark Shephard, Jeremy Thompson, and Vladimir Tomov. Ceed ecp milestone report: initial ceed api. December 2017. doi:10.5281/zenodo.2542340.

MBD+17

Misun Min, Jed Brown, Veselin Dobrev, Paul Fischer, Tzanio Kolev, David Medina, Elia Merzari, Aleks Obabko, Scott Parker, Ron Rahaman, Stanimire Tomov, Vladimir Tomov, and Tim Warburton. CEED ECP Milestone Report: Initial Integration of CEED Software in ECP Applications. October 2017. doi:10.5281/zenodo.2542338.

DDB+17

Veselin Dobrev, Jack Dongarra, Jed Brown, Paul Fischer, Azzam Haidar, Ian Karlin, Tzanio Kolev, Misun Min, Tim Moon, Thilina Ratnayaka, Stanimire Tomov, and Vladimir Tomov. CEED ECP Milestone Report: Identify initial kernels, bake-off problems (benchmarks) and miniapps. July 2017. doi:10.5281/zenodo.2542333.

Bro16

Jed Brown. Higher standards on the control of numerical accuracy. 2016. Whitepaper accepted to the DOE Advancing X-cutting Ideas for Computational Climate Science (AXICCS).

KMBS16

M. Knepley, D. A. May, J. Brown, and B. Smith. Extensibility in PETSc. SIAM News, 2016. URL: https://sinews.siam.org/Details-Page/extensibility-in-petsc.

KBM+15a

Matthew G. Knepley, Jed Brown, Lois Curfman McInnes, Barry Smith, Karl Rupp, and Mark Adams. Exascale computing without threads. 2015. Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance.

KBM+15b

Matthew G. Knepley, Jed Brown, Lois Curfman McInnes, Barry Smith, Karl Rupp, and Mark Adams. Overview of the PETSc library. 2015. Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance.

BBK+15

Satish Balay, Jed Brown, Matthew G. Knepley, Lois McInnes, and Barry Smith. Software Engineering for Science, chapter Providing Mixed Language and Legacy Support within a Library. Taylor & Francis, 2015.

RBB+15

Karl Rupp, Satish Balay, Jed Brown, Matthew G. Knepley, Lois Curfman McInnes, and Barry F. Smith. On the evolution of user support topics in computational science and engineering software. ArXiv e-prints, 2015. Whitepaper for Computational Science & Engineering Software Sustainability and Productivity Challenges. arXiv:1510.01122.

GCB14

Debojyoti Ghosh, Emil M. Constantinescu, and Jed Brown. Scalable nonlinear compact schemes. Technical Report ANL/MCS-TM-340, Argonne National Laboratory, 2014.

ABK+13

Jennifer Arrigo, Jed Brown, Louise Kellogg, Lorraine Hwang, Scott Peckham, and David Tarboton. EarthCube modeling workshop results. Technical Report, Computational Infrastructure for Geodynamics, 2013. URL: http://geodynamics.org/cig/community/workshops/Earthcube13/ExecSummary.

Bro13a

Jed Brown. Vectorization, communication aggregation, and reuse in stochastic and temporal dimensions. In Exascale Mathematics Workshop, Aug 21–22, Washington, DC. DOE Office of Advanced Scientific Computing Research, 2013.

ABK13

Mark F. Adams, Jed Brown, and Matthew G. Knepley. Low-communication techniques for extreme-scale multilevel solvers. In Exascale Mathematics Workshop, Aug 21–22, Washington, DC. DOE Office of Advanced Scientific Computing Research, 2013.

KnepleyBrownRuppSmith13

M. G. Knepley, J. Brown, K. Rupp, and B. F. Smith. Achieving high performance with unified residual evaluation. ArXiv e-prints, September 2013. arXiv:1309.1204.

Bro13b

J. Brown. Scalable repository workflows. 2013. Whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale Science, available via http://www.orau.gov/swproductivity2014/papers.htm.

Bro12

Jed Brown. User-defined non-blocking collectives must make progress. IEEE Technical Committee on Scalable Computing, 2012. URL: https://www.ieeetcsc.org/activities/blog/user_defined_nonblocking_collectives_must_make_progress.

ABS12

Mark Adams, Jed Brown, and Barry F. Smith. Exascale programming models must vigorously enable libraries. In DOE Exascale Research Conference. 2012.

SMC+12

Barry Smith, Lois Curfman McInnes, Emil Constantinescu, Mark Adams, Satish Balay, Jed Brown, Matthew Knepley, and Hong Zhang. PETSc's software strategy for the design space of composable extreme-scale solvers. Preprint ANL/MCS-P2059-0312, Argonne National Laboratory, 2012. DOE Exascale Research Conference, April 16-18, 2012, Portland, OR.

ABF+12

Mihai Anitescu, Jed Brown, Paul Fischer, Sven Leyffer, Lois Curfman McInnes, Todd Munson, and Barry F. Smith. Exascale co-design opportunities: Multilevel approaches for hierarchical models, architectures, algorithms, and software. In DOE Exascale Research Conference. 2012.

SBB+12

L. Ridgway Scott, Jed Brown, George W. Bergantz, Dan Cooley, Clint Dawson, Maarten de Hoop, Donald Estep, Natasha Flyer, Efi Foufoula-Georgiou, Michael Ghil, Matthew Knepley, Randall J. LeVeque, Lek-Heng Lim, Serge Prudhomme, Adrian Sandu, Frederik J. Simons, Philip B. Stark, Michael Stein, Seth Stein, Toshiro Tanimoto, Daniel Tartakovsky, Jonathan Weare, Robert Weiss, Grady B. Wright, and Dave Yuen. Fostering interactions between the geosciences and mathematics, statistics, and computer science. Technical Report 2012-02, University of Chicago, 2012.

BAA+19

Satish Balay, Shrirang Abhyankar, Mark F. Adams, Jed Brown, Peter Brune, Kris Buschelman, Lisandro Dalcin, Alp Dener, Victor Eijkhout, William D. Gropp, Dinesh Kaushik, Matthew G. Knepley, Dave A. May, Lois Curfman McInnes, Richard Tran Mills, Todd Munson, Karl Rupp, Patrick Sanan, Barry F. Smith, Stefano Zampini, Hong Zhang, and Hong Zhang. PETSc users manual: revision 3.12. Technical Report ANL-95/11 - Rev 3.12, Argonne National Laboratory, 2019. URL: https://mcs.anl.gov/petsc.

ABS+14

M. F. Adams, J. Brown, J. Shalf, B. Van Straalen, E. Strohmaier, and S. Williams. HPGMG 1.0: a benchmark for ranking high performance computing systems. Technical Report LBNL-6630E, LBNL, Berkeley, 2014. doi:10.2172/1131029.

CPH+15

Eric C Cyr, Eric Phipps, Michael A Heroux, Jed Brown, Ethan T Coon, Mark Hoemmen, Robert C Kirby, Tzanio V Kolev, James C Sutherland, and Christian R Trott. Algorithms and abstractions for assembly in PDE codes: workshop report. Technical Report SAND2015-1379, Sandia National Laboratory, 2015.