20130802-ATPESC.tex

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\title[PETSc]{The Portable Extensible Toolkit for Scientific computing}

\author{Barry Smith}


% - Use the \inst command only if there are several affiliations.
% - Keep it simple, no one is interested in your street address.
\institute[ANL]{Mathematics and Computer Science Division, Argonne National Laboratory}

\date{ATPESC 2013-08-02}


% This is only inserted into the PDF information catalog. Can be left
% out.
\subject{Talks}



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\begin{document}
\lstset{language=C}

\begin{frame}
\titlepage
Thanks to Jed Brown and Matt Knepley for the slides
\end{frame}

\begin{frame}
\frametitle{Outline}
\tableofcontents
% You might wish to add the option [pausesections]
\end{frame}
\input{slides/PETSc/RequestsNotSpecific.tex}

\section{Introduction}
\input{slides/PETSc/Timeline.tex}
\input{slides/PETSc/Commits.tex}
\input{slides/PETSc/About.tex}
\input{slides/PETSc/RoleOfPETSc.tex}
\input{slides/PETSc/BetterthanPETSc.tex}
\input{slides/BillGroppAdvice.tex}

\input{slides/PETSc/PETScPyramid.tex}

\section{Objects - Building Blocks of the Code}
\input{slides/MPICommunicator.tex}
\input{slides/PETSc/OptionsDatabase.tex}

\section[Core/Algorithms]{Core PETSc Components and Algorithms Primer}
\subsection{Time integration}
\input{slides/PETSc/TSARKIMEX.tex}
\input{slides/SNES/FlowControl.tex}
\input{slides/PETSc/TSMethods.tex}
\input{slides/PETSc/TSUsage.tex}

\subsection{Nonlinear solvers: SNES}
\input{slides/SNES/SNESNewton.tex}
\input{slides/SNES/Callbacks.tex}
\input{slides/SNES/Function.tex}
\input{slides/SNES/Jacobian.tex}


\subsection{Linear Algebra background/theory}
\input{slides/MatrixDefinition.tex}
\input{slides/MatricesImportant.tex}
\input{slides/MatrixNoEntries.tex}
\input{slides/GMRES.tex}

\subsection{Structured grid distribution: DMDA}
\input{slides/DM/DMDA.tex}
\input{slides/DA/GhostValues.tex}
\input{slides/DA/GlobalNumberings.tex}
\input{slides/DA/LocalNumbering.tex}
\input{slides/DA/Vectors.tex}
\input{slides/DA/UpdatingGhosts.tex}
\input{slides/DA/Stencils.tex}
\input{slides/DA/CreatingDA2d.tex}
\input{slides/DA/WorkingWithLocal.tex}
\input{slides/DA/LocalFunction.tex}
\input{slides/DA/BratuResidual.tex}
\input{slides/DM/OtherDMs.tex}

\subsection{Profiling}
\input{slides/PETSc/Integration/Profiling.tex}
\input{slides/ReadingLogSummary.tex}
\input{slides/CommunicationCosts.tex}

\subsection{Matrix Redux}
\input{slides/PETSc/Integration/MatrixRedux.tex}
\input{slides/PETSc/Integration/MatrixCreation.tex}
\input{slides/PETSc/Integration/MatrixPolymorphism.tex}
\input{slides/PETSc/Integration/MatrixAssembly.tex}
\input{slides/PETSc/Integration/MisguidedMatrixAssembly.tex}
\input{slides/PETSc/Integration/EfficientMatrixAssembly.tex}
\input{slides/PETSc/Integration/WhyArePETScMatricesThatWay.tex}

\section*{Preliminary Conclusions}
\begin{frame}{Preliminary Conclusions}
  \begin{block}{PETSc can help you}
    \begin{itemize}
    \item solve algebraic and DAE problems in your application area
    \item rapidly develop efficient parallel code, can start from examples
    \item develop new solution methods and data structures
    \item debug and analyze performance
    \item advice on software design, solution algorithms, and performance
      \begin{itemize}
        \item Public questions: \url{petsc-users@mcs.anl.gov}, archived
        \item Private questions: \url{petsc-maint@mcs.anl.gov}, not archived
      \end{itemize}
    \end{itemize}
  \end{block}
  \begin{block}{You can help PETSc}
    \begin{itemize}
    \item report bugs and inconsistencies, or if you think there is a better way
    \item tell us if the documentation is inconsistent or unclear
    \item consider developing new algebraic methods as plugins, contribute if your idea works
    \end{itemize}
  \end{block}
\end{frame}


\part{Integration and Efficiency}
\section{Application Integration}
\input{slides/PETSc/Integration/ApplicationIntegration.tex}
\input{slides/ApplicationIntegration.tex}
\input{slides/PETSc/Integration/Stages.tex}
\input{slides/PETSc/Integration/Initialization.tex}
\input{slides/PETSc/MatrixMemoryPreallocation.tex}
\input{slides/PETSc/Integration/LinearSolvers.tex}
\input{slides/PETSc/Integration/NonlinearSolvers.tex}

\section{Performance and Scalability}
\input{slides/JFNKBottlenecks.tex}
\input{slides/ScalabilityDefinition.tex}
\input{slides/ScalabilityWarning.tex}
\subsection{Memory hierarchy}
\input{slides/CPUArchitecture.tex}
\input{slides/HardwareCapability.tex}
\input{slides/OlikerSpMVOptimization.tex}
\input{slides/SpMVPerformanceModel.tex}
\input{slides/StreamTriad-XT5-BGP.tex}
\input{slides/OptimizingSpMV.tex}
\input{slides/ACaseForUnassembledMatrices.tex}
\input{slides/OptimizingSpMVUnassembled.tex}
\input{slides/HardwareArithmeticIntensity.tex}

%\input{slides/MultigridAdvice.tex}


\part{Special topics}
\section{Representative examples and algorithms}
\subsection{Hydrostatic Ice}
\input{slides/ToyHydrostaticIce.tex}
\subsection{Driven cavity}
\input{slides/SNES/DrivenCavity.tex}
\input{slides/DrivenCavityRun.tex}

\section{Hard problems}
\input{slides/FieldSplit.tex}
\input{slides/CoupledMultiphysics.tex}
%\input{slides/Anisotropy.tex}
\input{slides/SIPreconditioning.tex}

\section{Recent developments in PETSc}
\subsection{Improved multiphysics support}
\input{slides/MultiphysicsExamples.tex}
\input{slides/MonolithicOrSplit.tex}
\input{slides/PETSc/Coupling.tex}
\input{slides/PETSc/LocalSpaces.tex}
\input{slides/SNES/MultiphysicsAssemblyResiduals.tex}
\input{slides/SNES/MultiphysicsAssemblyJacobians.tex}
\input{slides/PETSc/MatGetLocalSubMatrix.tex}
\subsection{Variational inequalities}
\input{slides/PETSc/SNESVI.tex}


\begin{frame}{References}
  \begin{itemize}
  \item Knoll and Keyes, \emph{Jacobian-free Newton-Krylov methods: a survey of approaches and applications}, JCP, 2004.
  \item Elman et. al., \emph{A Taxonomy and Comparison of Parallel Block Multi-Level Preconditioners for the Incompressible Navier-Stokes Equations}, JCP, 2008.
  \item Wan, Chan, and Smith, \emph{An Energy-minimizing Interpolation for Robust Multigrid Methods}, SIAM J. Sci. Comp, 2000.
  \item Gropp, Kaushik, Keyes, Smith, \emph{Performance Modeling and Tuning of an Unstructured Mesh CFD Application}, Supercomputing, 2000.
  \item Gropp, \emph{Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why}, OO methods for interoperable scientific and engineering computing, 1999.
  \item ICiS Multiphysics workshop report:  IJHPCA 27(1), Feb 2013, http://dx.doi.org/10.1177/1094342012468181 
  \end{itemize}
\end{frame}

\end{document}