20120220-TACC.tex

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\title[PETSc]{The Portable Extensible Toolkit for Scientific computing}
\subtitle{This talk: \url{http://59A2.org/files/20120220-TACC.pdf}}

\author{Jed Brown}


% - 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{TACC 2012-02-20}


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\subject{Talks}



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

\section{Introduction}
\input{slides/PETSc/Timeline.tex}
\input{slides/PETSc/About.tex}
\input{slides/PETSc/RoleOfPETSc.tex}
\input{slides/PETSc/Installation.tex}
\begin{frame}{Compiling an example}
\begin{itemize}
  \item \shell{hg clone \\
  {\footnotesize http://petsc.cs.iit.edu/petsc/tutorials/TACC12}}
  \item \shell{cd TACC12}
  \item \shell{hg update \Rbasic}
  \item \shell{make}
  \item \shell{./pbratu -help | less}
\end{itemize}
\end{frame}

\section{Programming model}
\input{slides/PETSc/PETScPyramid.tex}
\input{slides/SNES/FlowControl.tex}
\input{slides/MPICollective.tex}
\input{slides/PETSc/OptionsDatabase.tex}

\section[Core/Algorithms]{Core PETSc Components and Algorithms Primer}
\input{slides/pbratu.tex}

\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}

\subsection{Profiling}
\input{slides/PETSc/Integration/Profiling.tex}
\input{slides/ReadingLogSummary.tex}
\input{slides/CommunicationCosts.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{Time integration}
\input{slides/PETSc/TSARKIMEX.tex}
\input{slides/PETSc/TSMethods.tex}
\input{slides/PETSc/TSUsage.tex}
\subsection{Variational inequalities}
\input{slides/PETSc/SNESVI.tex}
\input{slides/PETSc/SNESNew.tex}

\section*{Conclusions}
\begin{frame}{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 \url{petsc-{users,dev,maint}@mcs.anl.gov}
      \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}

\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, July 31 -- August 5 \\
    \url{http://www.ipd.anl.gov/anlpubs/2012/01/72183.pdf}
  \end{itemize}
\end{frame}

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