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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, magnetohydrodynamics solvers for fusion plasmas (Tokamaks), structure preserving discretization methods for magnetized plasmas, 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 and support for kinetic discretization methods, and I added a Fokker-Planck in Landau form collision operator in the DMPlex framework in PETSc. I work with computational physicists at Princeton Plasma Physics Laboratory (PPPL) on kinetic and fluid codes for fusion energy sciences.
Selected Papers:
- A performance portable, fully implicit Landau collision operator with batched linear solvers, M. Adams, P. Wang, J. Merson, K. Huck, M. Knepley, Accepted to SIAM Journal on Scientific Computing
- 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
M. Adams, P. Wang, J. Merson, K. Huck, M. Knepley, "A performance portable, fully implicit Landau collision operator with batched linear solvers", SIAM Journal on Scientific Computing, January 1, 2025,
- Download File: 3f390d41-6a05-4c32-8f76-3059b1c8c71a.pdf (pdf: 3.3 MB)
Modern accelerators use hierarchical parallel programming models that enable massive multithreading within a processing element (PE), with multiple PEs per device driven by traditional processes. Batching is a technique for exposing PE-level parallelism in algorithms that have traditionally run on MPI processes or multiple threads within a single process. Opportunities for batching arise in, for example, kinetic discretizations of magnetized plasmas where collisions are advanced in velocity space at each spatial point independently.
This paper builds on previous work on a high-performance, fully nonlinear, Landau collision operator by batching the linear solver, as well as batching the spatial point problems and adding new support for multiple grids for multiscale, multi-species problems. An anisotropic relaxation verification test that agrees well with previous published results and analytical models is presented. The performance results from NVIDIA A100 and AMD MI250X nodes are presented with hardware utilization analysis for each architecture. The entire implicit Landau operator time advance is implemented in Kokkos for performance portability, running entirely on the device and is available in the PETSc numerical library.
Daniel Finn, Matthew Knepley, Joseph Pusztay and Mark Adams, "A Numerical Study of Landau Damping with PETSc-PIC", CAMCoS, March 1, 2023, doi: 10.2140/camcos.2023.18.135
- Download File: Finn2023-LD.pdf (pdf: 2.7 MB)
Mark Adams, Satish Balay, Oana Marin, Lois Curfman McInnes, Richard Tran Mills, Todd Munson, Hong Zhang, Junchao Zhang, Jed Brown, Victor Eijkhout, Jacob Faibussowitsch, Matthew Knepley, Fande Kong, Scott Kruger, Patrick Sanan, Barry F. Smith, Hong Zhang, "The PETSc Community as Infrastructure", May 1, 2022, 24, doi: 10.1109/MCSE.2022.3169974
- Download File: PetscInfrusturcure.pdf (pdf: 1.3 MB)
The communities that develop and support open-source scientific software packages are crucial to the utility and success of such packages. Moreover, they form an important part of the human infrastructure that enables scientific progress. This article discusses aspects of the Portable Extensible Toolkit for Scientific Computation community, its organization, and technical approaches that enable community members to help each other efficiently and effectively.
J. V. Pusztay, M. G. Knepley, and M. F. Adams, "Conservative Projection Between FEM and Particle Bases", SIAM Journal on Scientific Computing, January 1, 2022, doi: https://doi.org/10.1137/21M145407
- Download File: ffce2dc7-07bf-41ec-b97c-7971797b7cc5.pdf (pdf: 782 KB)
R. Mills, M.F. Adams, S. Balay, J. Brown, A. Dener, M. Knepley, S. Kruger, H. Morgan, T. Munson, K. Rupp, B. Smith, S. Zampini, H. Zhang, J. Zhang, Junchao, "Toward performance-portable PETSc for GPU-based exascale systems", Parallel Computing, December 1, 2021, 108, doi: 10.1016/j.parco.2021.102831
The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization. The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. A blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.
N.B. Bonnheim, M.F. Adams, T. Wu, T.M. Keaveny, "The Role of Vertebral Porosity and Implant Loading Mode on Bone-Tissue Stress in the Human Vertebral Body Following Lumbar Total Disc Arthroplasty", Spine, October 1, 2021, 1022-E1030, doi: 10.1097/BRS.0000000000004023
Sajid Ali, Ming Du, Mark F. Adams, Barry Smith, and Chris Jacobsen, "A comparison of distributed memory algorithms for x-ray wave propagation in inhomogeneous media", Optics Express, January 1, 2020, 28:29590-2961, doi: https://doi.org/10.1364/OE.400240
- Download File: Comparison-of-distributed-memory-algorithms-for-X-ray-wave-propagation-in-inhomogeneous-media.pdf (pdf: 2.8 MB)
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: 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)
M. F. Adams, R. Samtaney and A. Brandt, "Toward Textbook Multigrid Efficiency for Fully Implicit Resistive Magnetohydrodynamics", Journal of Computational Physics, January 1, 2010, 229:6208–19, doi: 10.1016/j.jcp.2010.04.024
- Download File: 1f786f96-59ff-4f46-a5b9-f1ced7d09937.pdf (pdf: 6 MB)
Conference Papers
M.F. Adams, D.P. Brennan, M.G. Knepley, P. Wang, "Landau collision operator in the CUDA programming model applied to thermal quench plasmas", 2022 IEEE International Parallel and Distributed Processing Symposium (IPDPS), July 15, 2022, doi: 10.1109/IPDPS53621.2022.00020
- Download File: d9e4ee12-a919-480f-bafe-db3c81602b4d.pdf (pdf: 1.6 MB)
M. F. Adams, H. H. Bayraktar, T. M. Keaveny and P. Papadopoulos, "Ultrascalable Implicit Finite Element Analyses in Solid Mechanics with Over Half a Billion Degrees of Freedom", ACM/IEEE Proceedings of SC2004, November 1, 2004, 34, doi: https://doi.org/10.1109/SC.2004.62
Gordon Bell Award, Special category, SuperComputing 2004
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
A. P. S. Bhalla, B. E. Griffith, M. G. Knepley, M. F. Adams, and R. D. Guy, "Scalable smoothing strategies for a geometric multigrid method for the immersed boundary equations", December 1, 2016, doi: https://doi.org/10.48550/arXiv.1612.02208
- Download File: arXiv_1612.02208v1-math.NA-7-Dec-2016.pdf (pdf: 770 KB)
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)
