I received my Ph.D. in Civil Engineering, from U.C. Berkeley in 1998 and am a former student and postdoc with Jim Demmel in the Computer Science Division, at U.C. Berkeley. I work in the Scalable Solvers Group at Lawrence Berkeley National Laboratory, and as an adjunct research scientist in the Applied Physics and Applied Mathematics Department at Columbia University.
My research interests are in large scale simulations, extreme-scale multigrid equation solvers, adaptive mesh methods, and particle in cell methods for plasma physics applications.
I work as a developer in the PETSc numerical library - developing its algebraic multigrid (AMG) framework the advance Structure Preserving, Adaptive Discretizations for Extreme-scale Solver (SPADES) infrastructure in PETSc. I work with computational physicists at Princeton Plasma Physics Laboratory (PPPL) on kinetic and fluid models for magnetically confined fusion plasmas.
- A fast low-to-high confinement mode bifurcation dynamics in the boundary-plasma gyrokinetic code XGC1, Physics of Plasmas, 2018 (bibtex entry)
- Landau Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures, SISC, 2017 (bibtex entry).
- Conservative discretization of the Landau Collision Integral, Physics of Plasmas, 2017 (bibtex entry).
- Segmental Refinement: A Multigrid Technique for Data Locality, SISC, 2016 (bibtex entry).
- Trabecular Plates and Rods Determine Elastic Modulus and Yield Strength of Human Trabecular Bone. Bone, 2013.
- Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics, JCP, 2010 (bibtex entry).
- Scaling to 150K cores: recent algorithm and performance engineering developments enabling XGC1 to run at scale, Journal of Physics: Conference series 2009 (bibtex entry).
- High-Resolution Peripheral Quantitative Computed Tomography Can Assess Microstructural and Mechanical Properties of Human Distal Tibial Bone, Journal of Bone and Mineral Research, 2009 (bibtex entry).
- The micromechanics of cortical shell removal in the human vertebral body, Comp. Meth. Appl. Mech. Engrg. 196, pp 3025-3032. 2007 (bibtex entry).
- Performance of particle in cell methods on highly concurrent computational architectures. Journal of Physics: Conference Series(2007) (bibtex entry)
- Algebraic multigrid techniques for strongly indefinite linear systems from direct frequency response analysis in solid mechanics. Computational Mechanics (2007) (bibtex entry)
- Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics. Numerical Linear Algebra with Applications (2004) (bibtex entry).
- Cortical and trabecular load sharing in the human vertebral body, Journal of Bone and Mineral Research 21(2): 307-314 Feb 2006 (bibtex entry).
- Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom. Gordon Bell Award paper, Supercomputing 2004 (bibtex entry).
- Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics. Numerical Linear Algebra with Applications (bibtex entry).
- Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP. Proceedings Supercomputing '03 (bibtex entry).
- Parallel Multigrid Smoothing: Polynomial versus Gauss-Seidel, J. Comp. Phys. (bibtex entry).
- Evaluation of Three Unstructured Multigrid Methods on 3D Finite Element Problems in Solid Mechanics. (long version) (bibtex entry).
- A Distributed Memory Unstructured Gauss-Seidel Algorithm for Multigrid Smoothers. Proceedings Supercomputing '01 (bibtex entry).
- Parallel Multigrid Solvers for 3D Unstructured Finite Element Problems in Large Deformation Elasticity and Plasticity, International Journal for Numerical Methods in Engineering (bibtex entry).
- Parallel Multigrid Solver Algorithms and Implementations for 3D Unstructured Finite Element Problems, Proceedings Supercomputing '99, (bibtex entry).
- Multigrid equation solvers for large scale nonlinear finite element simulations, Ph.D. dissertation (bibtex entry).
- A Parallel Maximal Independent Set Algorithm, 5th Copper Mountain Conference on Iterative Methods, (bibtex entry).
- Gordon Bell Award, Special category, SuperComputing 2004, November 6-12, Pittsburgh PA.
- Carl Benz Award for the best industrial application in Mannheim SuParCup '99 at Mannheim Supercomputer '99 Conference, June 10-12, 1999.
- First prize in student paper competition at the 5th Copper Mountain Conference on Iterative Methods, March 30 - April 3,1998.
Mark Adams, Stephen Cornford, Daniel Martin, Peter McCorquodale, "Composite matrix construction for structured grid adaptive mesh refinement", Computer Physics Communications, November 2019, 244:35-39, doi: https://doi.org/10.1016/j.cpc.2019.07.006
- Download File: AdamsCornfordMartinMcCorquodale.pdf (pdf: 1.2 MB)
MF Adams, E Hirvijoki, MG Knepley, J Brown, T Isaac, R Mills, "Landau Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures", SIAM J. Sci. Comput., 2017, 39:C452--C465, doi: 10.1137/17M1118828
R Hager, J Lang, CS Chang, S Ku, Y Chen, SE Parker, MF Adams, "Verification of long wavelength electromagnetic modes with a gyrokinetic-fluid hybrid model in the XGC code", Physics of Plasmas, 2017, 24, doi: 10.1063/1.4983320
E Hirvijoki, MF Adams, "Conservative discretization of the Landau collision integral", Physics of Plasmas, 2017, 24, doi: 10.1063/1.4979122
Mark Adams, Jed Brown, Matt Knepley, Ravi Samtaney, "Segmental Refinement: A Multigrid Technique for Data Locality", SIAM J. Sci. Comput., 2016, 38:4,
David Trebotich, Mark F. Adams, Sergi Molins, Carl I. Steefel, Chaopeng Shen, "High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration", Computing in Science and Engineering, December 2014, 16:22-31, doi: 10.1109/MCSE.2014.77
- Download File: CISE-16-06-Trebotichappeared.pdf (pdf: 2.7 MB)
Mark Adams, Samuel Williams, HPGMG BoF - Introduction, HPGMG BoF, Supercomputing, November 2016,
- Download File: SC16-HPGMG-BoF-Intro.pdf (pdf: 1020 KB)
Samuel Williams, Mark Adams, Brian Van Straalen, Performance Portability in Hybrid and Heterogeneous Multigrid Solvers, Copper Moutain, March 2016,
- Download File: CU16SWWilliams.pptx (pptx: 1 MB)
Mark Adams, Samuel Williams, Jed Brown, HPGMG, Birds of a Feather (BoF), Supercomputing, November 2014,
- Download File: SC14HPGMGBoF.pdf (pdf: 1.9 MB)
M. Adams, P. Colella, D. T. Graves, J.N. Johnson, N.D. Keen, T. J. Ligocki. D. F. Martin. P.W. McCorquodale, D. Modiano. P.O. Schwartz, T.D. Sternberg, B. Van Straalen, "Chombo Software Package for AMR Applications - Design Document", Lawrence Berkeley National Laboratory Technical Report LBNL-6616E, January 9, 2015,
- Download File: chomboDesign.pdf (pdf: 994 KB)
Mark F. Adams, Jed Brown, John Shalf, Brian Van Straalen, Erich Strohmaier, Samuel Williams, "HPGMG 1.0: A Benchmark for Ranking High Performance Computing Systems", LBNL Technical Report, 2014, LBNL 6630E,
- Download File: hpgmg.pdf (pdf: 183 KB)