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Mark Adams

Mark Adams (Full-time)
Phone: +1 510 486 5412
Fax: +1 510 486 6900

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 Applied Numerical Algorithms 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 numerical simulations, in particular, multigrid equation solvers and unstructured finite element simulation systems in solid mechanics.

I work as a devloper of the structured grid automatic mesh refinement (AMR) framework Chombo from Lawrence Berkeley National Laboratory, supporting multigrid solvers, particle methods and the PETSc solver interface. I also work as a developer in the PETSc numerical library - developing its algebraic multigrid (AMG) framework and methods. I work with computational physicists at Princeton Plasma Physics Laboratory (PPPL) on kinetic and MHD methods for simulating magnetically confined fusion plasmas.

I have developed parallelizing finite element code Athena , built on the serial finite element code FEAP . Athena uses my solver Olympus, an unstructured multigrid equation solver for large scale (106-109 degrees of freedom) finite element problems, which was the focus of my dissertion. I use the PETSc - numerical libraries, from Argonne National Laboratory (ANL), to provide high performance, cross platform, support for iterative solvers for discretized partial differential equations and ParMetis, from the University of Minnesota for parallel mesh partitioning. These components make up my parallel finite element code Olympus, which is used by the Berkeley Orthopaedic Biomechanics Laboratory  and Columbia Biomedical Engineering  bone mechanics group. Olympus was used to win a Gordon Bell Prize in 2004.



  • A low memory, highly concurrent multigrid algorithm, (bibtex entry)
  • Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics, (bibtex entry)
  • Scaling to 150K cores: recent algorithm and performance engineering developments enabling XGC1 to run at scale, Journal of Physics: Confernce 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. Computional Mechanics (2007) (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 catagory, 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, Jed Brown, Matt Knepley, Ravi Samtaney, "Segmental Refinement: A Multigrid Technique for Data Locality", Submitted to SISC, June 30, 2014,


    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,