20141031-PETSc.tex

%\documentclass[handout]{beamer}
\documentclass{beamer}

\mode<presentation>
{
%\usetheme{Singapore}
%\usetheme{Warsaw}
\usetheme{Malmoe}
\useinnertheme{circles}
\useoutertheme{infolines}
% \useinnertheme{rounded}

\setbeamercovered{transparent}
}

\usepackage[english]{babel}
\usepackage[latin1]{inputenc}
\usepackage{bm,textpos,alltt,listings,multirow,ulem,minted}
\usepackage{JedMacros}

% font definitions, try \usepackage{ae} instead of the following
% three lines if you don't like this look
\usepackage{mathptmx}
\usepackage[scaled=.90]{helvet}
\usepackage{courier}
\usepackage[T1]{fontenc}
\usepackage{tikz}
\usetikzlibrary[shapes.arrows,arrows,shapes.misc,chains]


\makeatletter
\def\sectionintoc{}
\def\beamer@sectionintoc#1#2#3#4#5{%
\ifnum\c@tocdepth>0%
\ifnum#4=\beamer@showpartnumber%
{
  \beamer@saveanother%
  \gdef\beamer@todo{}%
  \beamer@slideinframe=#1\relax%
  \expandafter\only\beamer@tocsections{\gdef\beamer@todo{%
      \beamer@tempcount=#5\relax%
      \advance\beamer@tempcount by\beamer@sectionadjust%
      \edef\inserttocsectionnumber{\the\beamer@tempcount}%
      \def\inserttocsection{\hyperlink{Navigation#3}{#2}}%
      \beamer@tocifnothide{\ifnum\c@section=#1\beamer@toc@cs\else\beamer@toc@os\fi}%
      {
        \ifbeamer@pausesections\pause\fi%
        \ifx\beamer@toc@ooss\beamer@hidetext
          \vskip.2em
        \else
          \vskip.2em
        \fi
        {%
          \hbox{\vbox{%
              \def\beamer@breakhere{\\}%
              \beamer@tocact{\ifnum\c@section=#1\beamer@toc@cs\else\beamer@toc@os\fi}    {section in toc}}}%
         \par%
        }%
      }%
    }
  }%
  \beamer@restoreanother%
  }
  \beamer@todo%
  \fi\fi%
}
\makeatother


% \usepackage{pgfpages}
% \pgfpagesuselayout{4 on 1}[letterpaper,landscape,border shrink=5mm]

% Macros for the p-Bratu revision numbers
\def\Rbasic{0}
\def\Rrlap{1}
\def\Rrbratu{2}
\def\Rrpbratu{3}
\def\Rassemblebratu{4}
\def\Rassemblepicard{5}
\def\Rmyprealloc{6}
\def\Rnewtoncrash{7}
\def\Rnewtonbug{8}
\def\Rnewtonfix{9}

\title[PETSc]{Intro to Parallel Algebraic Solvers using PETSc}

\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]{Argonne National Laboratory \& CU Boulder}

\date{UC Merced 2014-10-31}


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



% If you have a file called "university-logo-filename.xxx", where xxx
% is a graphic format that can be processed by latex or pdflatex,
% resp., then you can add a logo as follows:

% \pgfdeclareimage[height=0.5cm]{university-logo}{university-logo-filename}
% \logo{\pgfuseimage{university-logo}}



% Delete this, if you do not want the table of contents to pop up at
% the beginning of each subsection:
\AtBeginSubsection[]
{
 \begin{frame}<beamer>
 \frametitle{Outline}
 \tableofcontents[currentsection,currentsubsection]
 \end{frame}
}

\AtBeginSection[]{
\begin{frame}<beamer>
  \frametitle{Outline}
  \tableofcontents[currentsection]
\end{frame}
}

% If you wish to uncover everything in a step-wise fashion, uncomment
% the following command:

%\beamerdefaultoverlayspecification{<+->}

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

\begin{frame}
  \titlepage
\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/About.tex}
\input{slides/PETSc/RoleOfPETSc.tex}
\input{slides/PETSc/BetterthanPETSc.tex}
\input{slides/BillGroppAdvice.tex}

\input{slides/PETSc/Composition.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}
\input{slides/MG/HPGMGFE.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/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/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}