# Mark Adams

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.

## Research Interests:

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.

## Selected Papers:

*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).

## Awards:

- 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.

## Journal Articles

### 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)

## Presentation/Talks

### 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)

## Reports

### 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)