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[svn:einsteintoolkit] Workshop_Summer_2013/ (Rev. 17)
by sbrandt＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: sbrandt Date: 2013/07/26 08:27 AM Added: /tutorial/global/ ProcessHorizontal.jpg, preamble.tex Log: Needed to compile tutorial slides Directory Changes: Directory: /svn:mime-type/ ========================== + image/jpeg File Changes: Directory: /tutorial/global/ ============================ File [added]: ProcessHorizontal.jpg Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: tutorial/global/ProcessHorizontal.jpg ___________________________________________________________________ File [added]: preamble.tex Delta lines: +78 -0 =================================================================== --- tutorial/global/preamble.tex (rev 0) +++ tutorial/global/preamble.tex 2013-07-26 13:27:46 UTC (rev 17) @@ -0,0 +1,78 @@ +\documentclass{beamer} + +\usepackage[utf8]{inputenc} +%\usepackage{beamerthemesplit} +\usepackage{url} +\usepackage{tikz} +\usepackage{alltt} +\usepackage{listings} +\usepackage{marvosym} +\usepackage{color} +\usepackage[multidot]{grffile} +\usepackage{multirow} +\usepackage{array} +\usepackage{setspace} +\usepackage{hyperref} +\usepackage{verbatim} +\usepackage{fancyvrb} +%\hypersetup{colorlinks=true, linkcolor=blue, anchorcolor=blue, +%citecolor=blue, filecolor=blue, menucolor=blue, pagecolor=blue, +%urlcolor=blue} +\lstset{keywordstyle=\bfseries\color{brown}, + stringstyle=\ttfamily, + commentstyle=\color{blue}\textit, + showstringspaces=false} + +\useoutertheme{} +\usetheme{Madrid} +\graphicspath{{pics/}{global/} +{pics/I/}{pics/A1/}{pics/A2/}{pics/A3/}{pics/A4/}{pics/A5/}{pics/A6/} +} + +\logo{\includegraphics[height=1cm]{ProcessHorizontal}} + +\institute{Center for Computation and Technology\\Louisiana State University, Baton Rouge, LA} + +\setbeamertemplate{navigation symbols}{} + +%\title{CSC 7700: Scientific Computing} +\title{} + +% We want to use the infolines outer theme because it does not use a lot of +% space, but it also tries to print an institution and the slide +% numbers (which we might not want to show). Therefore, we here redefine the +% footline ourselfes - mostly a copy & paste from +% /usr/share/texmf/tex/latex/beamer/themes/outer/beamerouterthemeinfolines.sty +\defbeamertemplate*{footline}{infolines theme without institution and slide numbers} +{ + \leavevmode% + \hbox{% + \begin{beamercolorbox}[wd=.25\paperwidth,ht=2.25ex,dp=1ex,center]{author in head/foot}% + \usebeamerfont{author in head/foot}\insertshortauthor + \end{beamercolorbox}% + \begin{beamercolorbox}[wd=.5\paperwidth,ht=2.25ex,dp=1ex,center]{title in head/foot}% + \usebeamerfont{title in head/foot}\insertshorttitle + \end{beamercolorbox}% + \begin{beamercolorbox}[wd=.25\paperwidth,ht=2.25ex,dp=1ex,center]{date in head/foot}% + \usebeamerfont{date in head/foot}\insertshortdate{} + \end{beamercolorbox}}% + \vskip0pt% +} + +% Some useful commands +\newcommand{\abspic}[4] + {\vspace{ #2\paperheight}\hspace{ #3\paperwidth}\includegraphics[height=#4\paperheight]{#1}\\ + \vspace{-#2\paperheight}\vspace{-#4\paperheight}\vspace{-0.0038\paperheight}} + +\newcommand{\picw}[4]{{ + \usebackgroundtemplate{ + \color{black}\vrule width\paperwidth height\paperheight\hspace{-\paperwidth}\hspace{-0.01\paperwidth} + \hspace{#4\paperwidth}\includegraphics[width=#3\paperwidth, height=\paperheight]{#1}}\logo{} + \frame[plain]{\frametitle{#2}} +}} +\newcommand{\pic}[2]{\picw{#1}{#2}{}{0}} + +\newcommand{\question}[1]{\frame{\frametitle{#1} + \begin{centering}\Huge #1\\\end{centering} +}} +

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[svn:einsteintoolkit] Workshop_Summer_2013/tutorial/ (Rev. 16)
by sbrandt＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: sbrandt Date: 2013/07/26 08:26 AM Added: /tutorial/ Cac.tex, Makefile Log: added slides File Changes: Directory: /tutorial/ ===================== File [added]: Cac.tex Delta lines: +181 -0 =================================================================== --- tutorial/Cac.tex (rev 0) +++ tutorial/Cac.tex 2013-07-26 13:26:13 UTC (rev 16) @@ -0,0 +1,181 @@ +\include{global/preamble} + +%\usecolortheme[RGB={200,200,200}]{structure} + +\subtitle[Module C]{{\large CGWAS Workshop 2013}\\*[0.3em]} +\author[Dr. Steven R. Brandt]{Dr. Steven R. Brandt} +\date{July 2013} +%\usecolortheme[RGB={160,45,140}]{structure} +\usecolortheme[RGB={80,45,200}]{structure} + +\begin{document} + +\frame{\titlepage} + +\section*{Outline} +\frame{\tableofcontents} + +\section{Goals} +\frame{\frametitle{}\begin{centering}\LARGE\insertsectionhead\\\end{centering}} + +\frame[containsverbatim]{ \frametitle{Goals} + \begin{itemize} + \item building + \item running + \item synchronizing + \item remote building + \item remote submitting + \end{itemize} +} + +\section{Building} +\frame{\frametitle{}\begin{centering}\LARGE\insertsectionhead\\\end{centering}} + +\frame[containsverbatim]{ \frametitle{Building} +\begin{itemize} +\item To build cactus on your virtual machine, type + +\begin{verbatim} +cgwas@cgwas:~$ cd Cactus +cgaws@cgwas:~/Cactus$ ./simfactory/bin/sim build +Building sim +Cactus - version: 4.2.0 +Building configuration sim +... +\end{verbatim} + +\item Afterwards, you will have a file in the exe directory + +\begin{verbatim} +$ ls ./exe +cactus_sim sim +\end{verbatim} +\end{itemize} + +} + +\section{Running} +\frame{\frametitle{}\begin{centering}\LARGE\insertsectionhead\\\end{centering}} + +\frame[containsverbatim]{ \frametitle{Running} +To run Cactus, simply call the binary and give it a parameter +file as an argument. You can use the WaveDemo.par file as a +simple test. +\begin{verbatim} +cgwas@cwas:~/Cactus$ ./exe/cactus_sim ./arrangements/Einstein +InitialData/IDLinearWaves/par/WaveDemo.par +-------------------------------------------------------------------------------- + + 10 + 1 0101 ************************ + 01 1010 10 The Cactus Code V4.0 + 1010 1101 011 www.cactuscode.org + 1001 100101 ************************ + 00010101 + 100011 (c) Copyright The Authors + 0100 GNU Licensed. No Warranty + 0101 +\end{verbatim} +... +} + +\frame[containsverbatim]{ \frametitle{Running} +Alternatively, you can invoke Cactus using MPI (Message +Passing Interface) +\begin{verbatim} +cgwas@cwas:~/Cactus$ mpirun -np 2 ./exe/cactus_sim ./arrangem +ents/Einstein InitialData/IDLinearWaves/par/WaveDemo.par +... +------------------------------------------------- + it | | ADMANALYSIS::grr | + | t | minimum | maximum | +------------------------------------------------- + 0 | 0.000 | 0.99485833 | 1.00514167 | +INFO (ADM): 1+log slicing +INFO (ADM): curved space diffusion = 0 for efficiency + 10 | 1.667 | 0.99737048 | 1.00295396 | +-------------------------------------------------------------------------------- +Done. +\end{verbatim} +} + +\frame[containsverbatim]{ \frametitle{Running} +Running with Simfactory is a bit more complicated. Simfactory +allows you to manage your simulations and keep track of what +you've done. + +Steps: +\begin{itemize} +\item Create a simulation. The simulation should have a configuration name and + a parameter file. +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim create \ + --configuration sim --parfile WaveDemo.par s1 +\end{verbatim} +\item The next step is to submit a simulation (or run it). When running, specify +the simulation you wish to use, and the number of procs. +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim run \ + --procs 1 s1 +\end{verbatim} +\end{itemize} +} + +\frame[containsverbatim]{ \frametitle{Running} +\begin{itemize} +\item Your simulation will be stored in the ~/simulations directory. +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ls ~/simulations +CACHE s1 +\end{verbatim} +\item If you attempt to run the simulation twice, the second time you will see an error. Simfactory doesn't let you overwrite your simulations. +\item Visualize: +\begin{verbatim} +cgwas@cgwas:~/Cactus$ gnuplot +gnuplot> plot "/home/cgwas/simluations/s1/output-0001/Wa +veDemo/grr_x_[5][5].xg" using 1:2 with linespoints +\end{verbatim} +\end{itemize} +} + +\section{Running Remotely} +\frame{\frametitle{}\begin{centering}\LARGE\insertsectionhead\\\end{centering}} + +\frame[containsverbatim]{ \frametitle{Running Remotely} +\begin{itemize} +\item Configure zwicky in simfactory/etc/defs.local.ini +by adding the following: +\begin{verbatim} +[zwicky] +user = sxs-39 +basedir = /home/@USER@/simulations +\end{verbatim} +\item Copy local changes to the remote machine using the +synchronize command: +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim sync \ + zwicky.cacr.caltech.edu +\end{verbatim} +\end{itemize} +} + +\frame[containsverbatim]{ \frametitle{Running Remotely} +\begin{itemize} +\item Submit the job on the remote machine (after creating +an appropriately named simulation): +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim submit \ + --procs 12 \ + --remotemachine zwicky.cacr.caltech.edu \ + s2 +\end{verbatim} +\item Monitor the simulations: +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim list-simulations \ + --remotemachine zwicky.cacr.caltech.edu + s1 [ACTIVE (FINISHED), restart 0001, job id -1] +\end{verbatim} +\end{itemize} +} + +\end{document} File [added]: Makefile Delta lines: +6 -0 =================================================================== --- tutorial/Makefile (rev 0) +++ tutorial/Makefile 2013-07-26 13:26:13 UTC (rev 16) @@ -0,0 +1,6 @@ +Cac.pdf : Cac.tex + pdflatex Cac + pdflatex Cac + +clean: + rm -fr Cac.aux Cac.bbl Cac.nav Cac.ind Cac.log Cac.out Cac.toc Cac.ent Cac.pdf Cac.blg

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[svn:einsteintoolkit] Workshop_Summer_2013/et_intro_details/ (Rev. 15)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 08:04 AM Modified: /et_intro_details/ et_intro_details.tex Log: add wavetoy example File Changes: Directory: /et_intro_details/ ============================= File [modified]: et_intro_details.tex Delta lines: +684 -7 =================================================================== --- et_intro_details/et_intro_details.tex 2013-07-26 13:04:35 UTC (rev 14) +++ et_intro_details/et_intro_details.tex 2013-07-26 13:04:44 UTC (rev 15) @@ -153,7 +153,9 @@ \begin{itemize} \item $\sim 100$ thorns used for simulation -\item Thorns come from a variety of sources: \texttt{git}, \texttt{svn}, \texttt{cvs}, \texttt{darcs}, \ldots +\item Thorns come from a variety of sources: core Cactus thorns, ET thorns, + AEIthorns, LSUThorn, Carpet, github.com, bitbucket.org +\item Thorns come in a variety of formats: \texttt{git}, \texttt{svn}, \texttt{cvs}, \texttt{darcs}, \ldots \item Multiple access levels: publicly available, password required \item Multiple thorns per repository? Separate documentation? Example files? \item Specific code version, release date @@ -175,15 +177,16 @@ \end{frame} \begin{frame}[containsverbatim] \frametitle{GetComponents -- how?} -\scriptsize\begin{alltt} -!CRL_VERSION = 1.0 +\scriptsize% +\begin{alltt} +!CRL\_VERSION = 1.0 !DEFINE ROOT = Cactus !DEFINE ARR = $ROOT/arrangements !TARGET = $ROOT !TYPE = svn -!AUTH_URL = https://svn.cactuscode.org/flesh/trunk +!AUTH\_URL = https://svn.cactuscode.org/flesh/trunk !CHECKOUT = Cactus !NAME = . @@ -201,20 +204,694 @@ The Simulation Factory: \begin{columns} \column{0.25\textwidth} - \includegraphics[width=\textwidth]{pics/factory.png} + \includegraphics[width=\textwidth]{factory.png} \column{0.75\textwidth} \begin{itemize} \item Command-line tools for setting up Cactus distribution and managing simulations on a variety of supercomputers, - including most of the TeraGrid machines. + including most of the \texttt{XSEDE} machines. \end{itemize} \end{columns} \begin{itemize} \item Captures the best practices of experienced users, ensuring repeatable and well-documented scientific results. \item Developed by Erik Schnetter and Michael Thomas. - \item Included in Cactus-OS distro: {\tt Cactus/simfactory}. + \item Included in virtual machine: {\tt Cactus/simfactory}. \item For more, see: {\tt http://simfactory.org} \end{itemize} + More on \texttt{Simfactory} in the hands-on session. \end{frame} + +\begin{frame} \frametitle{Example: solving scalar wave equation} + For a given source function $S(x,y,t)$ find a scalar wave + field $\varphi(x,y,t)$ inside the domain $\mathcal{D}$ + with a boundary condition: + \begin{columns}[t] + \column{.3\textwidth} + \begin{figure}[!htp] + \begin{center} + \begin{tikzpicture}[rotate=5,scale=1.2] + \filldraw[fill=green!60!white, draw=green!50!black, thick] + (-1,-1) rectangle (1,1); + \draw (0,0) node {{\large $\mathcal{D}$}}; + \draw (1.4,0.2) node {$\partial\mathcal{D}$}; + \draw[->,thick,color=red] (1.1,0.2) -- (1,0.2); + \end{tikzpicture} + \end{center} + \end{figure} + + \column{.6\textwidth} + \begin{itemize} + \item inside $\mathcal{D}$: + \begin{equation*} + \frac{\partial^2\varphi}{\partial t^2} = c^2\Delta\varphi + S + \end{equation*} + \item on the boundary $\partial\mathcal{D}$: + \begin{equation*} + \varphi_{|\partial\mathcal{D}} = 0 + \end{equation*} + \end{itemize} + \end{columns} +\end{frame} + +\frame{ \frametitle{WaveToy Thorn: Discretization} + Discretization: \\ + approximating continuous function $\varphi(x,y,t)$ + with a grid function $\varphi^{(n)}_{i,j}$: + \begin{columns}[t] + \column{.2\textwidth} + \begin{figure}[!htp] + \begin{center} + \begin{tikzpicture}[scale=1.1] + \draw (-1,0) -- (1,0); + \draw (-1,1) -- (1,1); + \draw (-1,-1) -- (1,-1); + \scope[fill=green!50!blue, draw=black] + \filldraw (0,0) circle (0.07cm); + \filldraw (1,0) circle (0.07cm); + \filldraw (-1,0) circle (0.07cm); + \filldraw (0,1) circle (0.07cm); + \filldraw (1,1) circle (0.07cm); + \filldraw (-1,1) circle (0.07cm); + \filldraw (0,-1) circle (0.07cm); + \filldraw (1,-1) circle (0.07cm); + \filldraw (-1,-1) circle (0.07cm); + \endscope + \scope[xshift=0.45cm,yshift=0.25cm] + \draw (0,0) node {{\tiny $\varphi^{(n)}_{i}$}}; + \draw (1,0) node {{\tiny $\varphi^{(n)}_{i+1}$}}; + \draw (-1,0) node {{\tiny $\varphi^{(n)}_{i}$}}; + \draw (0,1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; + \draw (1,1) node {{\tiny $\varphi^{(n+1)}_{i+1}$}}; + \draw (-1,1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; + \draw (0,-1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; + \draw (1,-1) node {{\tiny $\varphi^{(n+1)}_{i+1}$}}; + \draw (-1,-1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; + \endscope + \end{tikzpicture} + \end{center} + \end{figure} + + \column{.8\textwidth} + \begin{gather*} + \\ + \frac{\partial^2\varphi}{\partial t^2} = + c^2 (\partial_x^2\varphi + \partial_y^2\varphi) + + S \\ + \Downarrow (c\equiv1)\\ + \begin{aligned} + %\text{\makebox[0pt][l]{\framebox{\parbox{4cm}{Semi-descretization for Method of Lines}}}} + \frac{\partial \phi_{i,j}}{\partial t} = & \psi_{i,j} \\ + \frac{\partial \psi_{i,j}}{\partial t} = & + \frac{\varphi_{i+1,j} - 2\varphi_{i,j}+\varphi_{i-1,j}} + {2\Delta x^2} + \\ + & \frac{\varphi_{i,j+1} - 2\varphi_{i,j}+\varphi_{i,j-1}} + {2\Delta y^2} + S_{i,j} + \end{aligned} + \end{gather*} + \end{columns} +} + +\frame{ \frametitle{WaveToyMoL Thorn} + Thorn structure: + + \begin{columns}[t] + \column{.4\textwidth} + \begin{exampleblock}{interface.ccl} + \begin{itemize} + \item grid function {\color{blue}phi[3]}: + \end{itemize} + \begin{figure}[!htp] + \begin{center} + \begin{tikzpicture} + \scope[fill=white!90!green, draw=black] + \filldraw (-1.5,-1) -- (0.5,-1) -- (1.5,-0.2) -- (-0.5,-0.2) -- cycle; + \filldraw (-1.5,-0.4) -- (0.5,-0.4) -- (1.5,0.4) -- (-0.5,0.4) -- cycle; + \filldraw (-1.5,0.2) -- (0.5,0.2) -- (1.5,1) -- (-0.5,1) -- cycle; + \endscope + \scope[fill=green!50!blue, draw=black, dashed, very thin] + \draw (-0.6,0) -- (0.6,0); + \draw (0,-0.6) -- (0,0.6); + \draw (-0.35,-0.3) -- (0.35,0.3); + \filldraw (0,0) circle (0.07cm); + \filldraw (0.6,0) circle (0.07cm); + \filldraw (0,0.6) circle (0.07cm); + \filldraw (-0.6,0) circle (0.07cm); + \filldraw (0,-0.6) circle (0.07cm); + \filldraw (-0.35,-0.3) circle (0.07cm); + \filldraw (0.35,0.3) circle (0.07cm); + \endscope + \scope[left=2pt,yshift=0.2cm] + \draw (-1.5,-1) node {\color{blue}phi\_p\_p}; + \draw (-1.5,-0.4) node {\color{blue}phi\_p}; + \draw (-1.5, 0.2) node {\color{blue}phi}; + \endscope + \scope[xshift=0.6cm,yshift=0.2cm] + \draw (-1.5,-1) node {{\tiny $\varphi^{(n-2)}$}}; + \draw (-1.5,-0.4) node {{\tiny $\varphi^{(n-1)}$}}; + \draw (-1.5, 0.2) node {{\tiny $\varphi^{(n)}$}}; + \endscope + %\includegraphics[height=0.3\textheight]{time_levels} + \end{tikzpicture} + \end{center} + \end{figure} + \begin{itemize} + \item {\small Boundary\_SelectVarForBC} + \end{itemize} + \end{exampleblock} + + \column{.4\textwidth} + \begin{exampleblock}{param.ccl} + \begin{itemize} + \item Parameters of initial Gaussian pulse: + amplitude {\color{brown}$A$}, + radius {\color{brown}$R$}, + width {\color{brown}$\sigma$} + \end{itemize} + \end{exampleblock} + + \begin{exampleblock}{schedule.ccl} + \begin{itemize} + \item WaveToy\_InitialData + \item WaveToy\_Evolution + \item WaveToy\_Boundaries + \end{itemize} + \end{exampleblock} + \end{columns} +} + +% \frame{ \frametitle{WaveToy Thorn} +% \begin{itemize} +% \item Choose initial values $\Phi_{i,j,k,0}$; +% \item Loop: +% \begin{itemize} +% \item Calculate field at current time based on discretized wave equation +% \item On boundary points, where derivatives may not be present, apply chosen +% boundary conditions +% \end{itemize} +% \end{itemize} +% } + +\frame{ \frametitle{WaveToy Thorn: Algorithm Illustration} + \begin{columns}[t] + \column{.7\textwidth} + \begin{figure}[!htp] + \begin{center} + \begin{tikzpicture} + + %\draw[->] (0,0) -- (1,1); + % Step 1: axes and grid + \draw[->,very thin] (-.6,-.4) -- (6,-.4); + \draw[->,very thin] (-.4,-.6) -- (-.4,3); + \draw[left=2pt] (-.4,2.5) node {$t$}; + \draw[above=2pt] (5.8,-0.4) node {$x$}; + + \uncover<1>{ + \draw[xstep=.6cm,ystep=.4cm,gray,dashed] + (0,0) grid(5.4cm,2.6cm); + }% + + % Step 2: splitting between two processors + \uncover<2->{ + \draw (0,2.8) -- (.6,3.2) -- (2.4,3.2) -- (3,2.8); + \draw[above=1pt] (1.4,3.2) node {\emph{PROC0}}; + + \draw[xshift=2.4cm] (0,2.8) -- (.6,3.2) -- (2.4,3.2) -- (3,2.8); + \draw[above=1pt] (3.8,3.2) node {\emph{PROC1}}; + }% + \uncover<2-4>{ + \draw[xstep=.6cm,ystep=.4cm,gray,dashed] + (0,0) grid (3.0cm,2.6cm); + \draw[xstep=.6cm,ystep=.4cm,gray,dashed,xshift=0.05cm,yshift=0.05cm] + (2.4,0) grid (5.4cm,2.6cm); + }% + + % Step 3: memory "allocations" + \uncover<3>{ + \draw[color=blue] (1.5,-0.6) node {\tiny x, phi, phi\_p, phi\_p\_p}; + \draw[color=blue] (4.2,-0.6) node {\tiny x, phi, phi\_p, phi\_p\_p}; + }% + + % Step 4: CoordBase / CartGrid3D + \uncover<4->{ + \foreach \x in {0.0,0.6,1.2,1.8,2.4,3.0,3.6,4.2,4.8,5.4} + \draw (\x cm,-0.4cm) node[anchor=south] {{\tiny $\x$}}; + \draw[very thick,color=brown,xstep=0.6cm,ystep=1cm,yshift=-0.4cm] + (0cm,-1pt) grid (3.0cm,1pt); + \draw[color=blue] (1.5,-0.6) node {\small x}; + + \draw[very thick,color=brown,xstep=0.6cm,ystep=1cm,xshift=2.45cm,yshift=-0.35cm] + (0cm,-1pt) grid (3.0cm,1pt); + \draw[color=blue] (4.2,-0.6) node {\small x}; + } + \uncover<4-5>{ + \draw[color=blue] (1.5,-1.0) node {\tiny phi, phi\_p, phi\_p\_p}; + \draw[color=blue] (4.2,-1.0) node {\tiny phi, phi\_p, phi\_p\_p}; + }% + + % Step 5: Time + \uncover<5->{ + \draw[xstep=.6cm,ystep=.4cm,gray,dashed] + (0,0) grid (3.0cm,2.6cm); + \draw[xstep=.6cm,ystep=.4cm,gray,dashed,xshift=0.05cm,yshift=0.05cm] + (2.4,0) grid (5.4cm,2.6cm); + }% + \uncover<5>{ + \scope[color=red,thick,fill=white] + \draw (-0.5,0.4) -- (0.0,0.4); + \draw (-0.5,0.8) -- (0.0,0.8); + \draw[->] (-0.1,1.2) -- (-0.1,0.8); + \draw[<-] (-0.1,0.4) -- (-0.1,0.0); + \endscope + \draw (0,0.6) node[anchor=west,fill=white] {$\Delta t = \lambda\Delta x_{\min}$}; + } + + % Step 6: Initial data routines + \uncover<6>{ + \scope[very thick,color=green,xstep=0.6cm,ystep=1cm] + \draw[xshift=0cm,yshift=0cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.05cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=0.4cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.45cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=0.8cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.85cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \endscope + \scope[color=blue] + \draw (-0.5,0.4) node[anchor=east] {\small phi\_p}; + \draw (-0.5,0.8) node[anchor=east] {\small phi}; + \draw (-0.5,0.0) node[anchor=east] {\small phi\_p\_p}; + \endscope + } + + % Step 7: Layers rotation + \uncover<7->{ + \scope[very thick,color=green,xstep=0.6cm,ystep=1cm] + \draw[xshift=0cm,yshift=0cm,color=gray] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.05cm,color=gray] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=0.4cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.45cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=0.8cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.85cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=1.2cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=1.25cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \endscope + }% + \uncover<7>{ + %\draw[thick,color=red,->] (-0.5,-0.1) arc (-25:25:1.1cm); + \draw[thick,color=red,->] (-1.8, 0.0) arc (205:155:1.5cm); + } + \uncover<7-11>{ + \scope[color=blue] + \draw (-0.5,0.4) node[anchor=east] {\small phi\_p\_p}; + \draw (-0.5,0.8) node[anchor=east] {\small phi\_p}; + \draw (-0.5,1.2) node[anchor=east] {\small phi}; + \endscope + } + + % Step 8: Evaluation of RHS + \uncover<8>{ + \scope[draw=red,thick,fill=green] + \draw (0.0,0.8) -- (1.2,0.8); + \draw[->] (0.6,0.8) -- (0.6,1.1); + \filldraw (0.6,1.2) circle (0.1cm); + \filldraw (0.6,0.4) circle (0.1cm); + \filldraw (0.0,0.8) circle (0.1cm); + \filldraw (0.6,0.8) circle (0.1cm); + \filldraw (1.2,0.8) circle (0.1cm); + + % second processor: + \scope[xshift=0.05cm,yshift=0.05cm] + \fill (3.0,0.8) circle (0.05cm); + \fill (3.6,0.8) circle (0.05cm); + \scope[xshift=3.6cm] + \draw (0.0,0.8) -- (1.2,0.8); + \draw[->] (0.6,0.8) -- (0.6,1.1); + \filldraw (0.6,1.2) circle (0.1cm); + \filldraw (0.6,0.4) circle (0.1cm); + \filldraw (0.0,0.8) circle (0.1cm); + \filldraw (0.6,0.8) circle (0.1cm); + \filldraw (1.2,0.8) circle (0.1cm); + \endscope + \endscope + \endscope + }% + + % Step 9: Ghost zones + \uncover<9>{ + \scope[very thick,color=green,xstep=0.6cm,ystep=1cm] + \draw[xshift=0.6cm,yshift=1.2cm] (0cm,-1pt) grid (1.8cm,1pt); + \draw[xshift=3.05cm,yshift=1.25cm] (0cm,-1pt) grid (1.8cm,1pt); + \draw[->,color=red] (2.4,1.1) -- (2.4,1.3); + \draw[->,color=red] (3.05,1.3) -- (3.05,1.1); + \endscope + }% + + % Step 10: Boundary conditions + \uncover<10>{ + \scope[very thick,color=green,xstep=0.6cm,ystep=1cm] + \draw[xshift=0.6cm,yshift=1.2cm] (0cm,-1pt) grid (2.4cm,1pt); + \draw[xshift=2.45cm,yshift=1.25cm] (0cm,-1pt) grid (2.4cm,1pt); + \draw[->,color=red] (-0.4,1.2) -- (0.0,1.2); + \draw[->,color=red] (5.85,1.25) -- (5.45,1.25); + \endscope + }% + + % Step 11: Output data + \uncover<11->{ + \scope[very thick,color=green,xstep=0.6cm,ystep=1cm] + \draw[xshift=0cm,yshift=1.2cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=1.25cm] (0cm,-1pt) grid (3.0cm,1pt); + \endscope + } + + % Step 12: Advance to the next time level + \uncover<12>{ + \draw[thick,color=red,->] (-1.8, 0.4) arc (205:155:1.5cm); + \scope[very thick,color=green,xstep=0.6cm,ystep=1.4cm] + \draw[xshift=0cm,yshift=1.6cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=1.65cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=1.2cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=1.25cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=0.4cm,color=gray] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.45cm,color=gray] (0cm,-1pt) grid (3.0cm,1pt); + \endscope + \scope[color=blue] + \draw (-0.5,0.8) node[anchor=east] {\small phi\_p\_p}; + \draw (-0.5,1.2) node[anchor=east] {\small phi\_p}; + \draw (-0.5,1.6) node[anchor=east] {\small phi}; + \endscope + } + + \end{tikzpicture} + \end{center} + \end{figure} + + + \column{.3\textwidth} + \begin{figure}[!htp] + \begin{center} + \vspace{-1cm} + \begin{tikzpicture} + \draw (0,7) node + [anchor=north,right,text width=3cm,rounded corners,fill=green!20,draw=blue!50!black] %,inner sep=1ex] + (begin) + {\begin{footnotesize} + \begin{itemize} + \item[] \hspace{-0.5cm} {\color<2>{blue}Grid structure} + \item[] \hspace{-0.5cm} {\color<3>{blue}GF allocation} + \end{itemize} + \end{footnotesize}}; + + \draw (0,5.3) node + [anchor=north,right,text width=3cm,rounded corners,fill=green!20,draw=blue!50!black] %,inner sep=1ex] + (init) + {\begin{footnotesize} + \begin{itemize} + \item[] \hspace{-0.5cm} {\color<4>{blue}Set up coords} + \item[] \hspace{-0.5cm} {\color<5>{blue}Compute $\Delta t$} + \item[] \hspace{-0.5cm} {\color<6>{blue}Initial data} + \end{itemize} + \end{footnotesize} }; + + \draw[->,thick,draw=blue!50!black] (0,2.15) -- (-0.3,2.15) -- (-0.3,3.8) -- (-0.05,3.8); + + \draw (0,3) node + [anchor=north,right,text width=3cm,rounded corners,fill=green!20,draw=blue!50!black] %,inner sep=1ex] + (evol) + {\begin{footnotesize} + \begin{itemize} + \item[]\hspace{-0.5cm} {\color<7,12>{blue}Rotate timelevels} + \item[]\hspace{-0.5cm} {\color<8>{blue}Evolve GF}, {\color<9>{blue}sync} + \item[]\hspace{-0.5cm} {\color<10>{blue}Apply BCs} + \item[]\hspace{-0.5cm} {\color<11>{blue}Output data} + \end{itemize} + \end{footnotesize} }; + + \scope[color=blue!50!black,thick] + \draw[->,shorten >=2pt] (begin.south) -- (init.north); + \draw[->,shorten >=2pt] (init.south) -- (evol.north); + \endscope + \end{tikzpicture} + \end{center} + \end{figure} + \end{columns} +} + +%\frame[containsverbatim]{ \frametitle{WaveToy Thorn} +% Implemented in \verb|CactusWave/WaveToy|: +% \begin{itemize} +% \item \href{http://www.cct.lsu.edu/~bentivegna/WaveToy/interface.ccl}{interface.ccl} +% \item \href{http://www.cct.lsu.edu/~bentivegna/WaveToy/schedule.ccl}{schedule.ccl} +% \item \href{http://www.cct.lsu.edu/~bentivegna/WaveToy/param.ccl}{param.ccl} +% \item \href{http://www.cct.lsu.edu/~bentivegna/WaveToy/src}{src/ directory} +% \end{itemize} +%} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn} + Directory structure: + \begin{alltt} +WaveToy/ +|-- COPYRIGHT +|-- README +|-- configuration.ccl +|-- doc +| `-- documentation.tex +|-- interface.ccl +|-- schedule.ccl +|-- param.ccl +`-- src + |-- WaveToy.c + `-- make.code.defn +\end{alltt} +} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn} + Directory structure: + \begin{alltt} +WaveToy/ +|-- COPYRIGHT +|-- README +|-- configuration.ccl +|-- doc +| `-- documentation.tex +\textcolor{blue}{|-- interface.ccl +|-- schedule.ccl +|-- param.ccl} +`-- src + |-- WaveToy.c + `-- make.code.defn +\end{alltt} +} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn} + \begin{itemize} + \item \verb|interface.ccl|: + \tiny\begin{verbatim} + IMPLEMENTS: wavetoy_simple + INHERITS: grid + + PUBLIC: + + CCTK_REAL scalarevolve TYPE=gf TIMELEVELS=3 + { + phi + } "The evolved scalar field" + + CCTK_INT FUNCTION Boundary_SelectVarForBC( \ + CCTK_POINTER_TO_CONST IN GH, CCTK_INT IN faces, \ + CCTK_INT IN boundary_width, CCTK_INT IN table_handle, \ + CCTK_STRING IN var_name, CCTK_STRING IN bc_name) + + REQUIRES FUNCTION Boundary_SelectVarForBC\end{verbatim} + \end{itemize} +} +\frame[containsverbatim]{ \frametitle{WaveToy Thorn cont.} + \begin{itemize} + \item \verb|schedule.ccl|: + \tiny\begin{verbatim} + STORAGE: scalarevolve[3] + + SCHEDULE WaveToy_InitialData AT CCTK_INITIAL + { + LANG: C + } "Initial data for 3D wave equation" + + SCHEDULE WaveToy_Evolution AT CCTK_EVOL + { + LANG: C + SYNC: scalarevolve + } "Evolution of 3D wave equation" + + SCHEDULE WaveToy_Boundaries AT CCTK_EVOL AFTER WaveToy_Evolution + { + LANG: C + } "Select boundary conditions for the evolved scalar" + + SCHEDULE GROUP ApplyBCs as WaveToy_ApplyBCs AT CCTK_EVOL AFTER WaveToy_Boundaries + { + } "Apply boundary conditions"\end{verbatim} + \end{itemize} +} +\frame[containsverbatim]{ \frametitle{WaveToy Thorn cont.} + \begin{itemize} + \item \verb|param.ccl|: + \tiny\begin{verbatim} + CCTK_REAL amplitude "The amplitude of the waves" + { + *:* :: "Anything" + } 1.0 + + CCTK_REAL radius "The radius of the gaussian wave" + { + 0:* :: "Positive" + } 0.0 + + CCTK_REAL sigma "The sigma for the gaussian wave" + { + 0:* :: "Positive" + } 0.1\end{verbatim} + \end{itemize} +} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn cont.} + Directory structure: + \begin{alltt} +WaveToy/ +|-- COPYRIGHT +|-- README +|-- configuration.ccl +|-- doc +| `-- documentation.tex +|-- interface.ccl +|-- schedule.ccl +|-- param.ccl +`-- src +\textcolor{blue}{ |-- WaveToy.c + `-- make.code.defn} +\end{alltt} +} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn cont.} + \begin{itemize} + \item \verb|WaveToy.c|: + \tiny\begin{alltt} +void WaveToy\_Evolution(\textcolor{BurntOrange}{CCTK\_ARGUMENTS}) \{ + \textcolor{BurntOrange}{DECLARE\_CCTK\_ARGUMENTS;} + + CCTK\_REAL dt2,dx2i,dy2i,dz2i; + + dt2 = CCTK\_DELTA\_TIME*CCTK\_DELTA\_SPACE(2); + dx2i = 1.0/(CCTK\_DELTA\_SPACE(0)*CCTK\_DELTA\_SPACE(0)); + dy2i = 1.0/(CCTK\_DELTA\_SPACE(1)*CCTK\_DELTA\_SPACE(1)); + dz2i = 1.0/(CCTK\_DELTA\_SPACE(2)*CCTK\_DELTA\_SPACE(2)); + + /* Do the evolution */ + \textcolor{Green}{for (int k=1; k<cctk\_lsh[2]-1; k++) \{ + for (int j=1; j<cctk\_lsh[1]-1; j++) \{ + for (int i=1; i<cctk\_lsh[0]-1; i++) \{} + \textcolor{blue}{phi[CCTK\_GFINDEX3D(cctkGH,i,j,k)] = 2*(1 - (dt2)*(dx2i + dy2i + dz2i)) * + phi\_p[CCTK\_GFINDEX3D(cctkGH,i,j,k)] - phi\_p\_p[CCTK\_GFINDEX3D(cctkGH,i,j,k)] + + (dt2) * + ( ( phi\_p[CCTK\_GFINDEX3D(cctkGH,i+1,j ,k )] + +phi\_p[CCTK\_GFINDEX3D(cctkGH,i-1,j ,k )] )*dx2i + +( phi\_p[CCTK\_GFINDEX3D(cctkGH,i ,j+1,k )] + +phi\_p[CCTK\_GFINDEX3D(cctkGH,i ,j-1,k )] )*dy2i + +( phi\_p[CCTK\_GFINDEX3D(cctkGH,i ,j ,k+1)] + +phi\_p[CCTK\_GFINDEX3D(cctkGH,i ,j, k-1)] )*dz2i);} + \textcolor{Green}{\} + \} + \}} +\} +\end{alltt} + \end{itemize} +} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn cont.} + \begin{itemize} + \item \verb|WaveToy.c cont.|: + \tiny\begin{alltt} +void WaveToy\_InitialData(\textcolor{BurntOrange}{CCTK\_ARGUMENTS}) \{ + \textcolor{BurntOrange}{DECLARE\_CCTK\_ARGUMENTS; + DECLARE\_CCTK\_PARAMETERS;} + + \textcolor{Green}{for(int k=0; k<cctk\_lsh[2]; k++) \{ + for(int j=0; j<cctk\_lsh[1]; j++) \{ + for(int i=0; i<cctk\_lsh[0]; i++) \{} + int vindex = CCTK\_GFINDEX3D(cctkGH,i,j,k); + CCTK\_REAL dt = CCTK\_DELTA\_TIME; + CCTK\_REAL X = x[vindex]; + CCTK\_REAL Y = y[vindex]; + CCTK\_REAL Z = z[vindex]; + CCTK\_REAL R = sqrt(X*X + Y*Y + Z*Z); + + \textcolor{blue}{phi[vindex] = amplitude*exp( - SQ( (R - radius) / sigma ) );} + + if (R == 0.0) \{ + phi\_p[vindex] = amplitude*(1.0 - 2.0*dt*dt/sigma)*exp(-dt*dt/sigma); + \} else \{ + phi\_p[vindex] = amplitude/2.0*(R-dt)/R* + exp( - SQ( (R - radius - dt)/ sigma ) ) + + amplitude/2.0*(R+dt)/R* + exp( - SQ( (R - radius + dt)/ sigma ) ); + \textcolor{Green}{\} + \} + \}} + \} +\} +\end{alltt} + \end{itemize} +} + +\frame[containsverbatim]{ \frametitle{WaveToy Thorn cont.} + \begin{itemize} + \item \verb|WaveToy.c|: + \tiny\begin{alltt} +void WaveToy\_Boundaries(\textcolor{BurntOrange}{CCTK\_ARGUMENTS}) \{ + \textcolor{BurntOrange}{DECLARE\_CCTK\_ARGUMENTS;} + + /* Uses all default arguments, so invalid table handle -1 can be passed */ + if (\textcolor{blue}{Boundary\_SelectVarForBC (cctkGH, CCTK\_ALL\_FACES, 1, -1, + "wavetoy\_simple::phi", "scalar")} < 0) \{ + CCTK\_WARN (0, "WaveToy\_Boundaries: Error selecting boundary condition"); + \} +\} +\end{alltt} + \item \verb|make.config.defn|: + \tiny\begin{verbatim} +SRCS = WaveToy.c +\end{verbatim} + \end{itemize} +} + + +\frame[containsverbatim]{ \frametitle{Parameter file} + \begin{itemize} + \item Example parameter file: + \tiny\begin{verbatim} +Cactus::cctk_run_title = "Simple WaveToy" + +ActiveThorns = "Time Boundary Carpet CarpetLib CartGrid3D CoordBase IOUtil + CarpetIOBasic CarpetIOASCII CarpetIOHDF5 SymBase WaveToy" + +Cactus::cctk_itlast = 10000 +Time::dtfac = 0.5 + +IO::out_dir = $parfile +IOBasic::outInfo_every = 1 +IOASCII::out1D_every = 10 +IOASCII::out1D_vars = "wavetoy_simple::phi" + +IOHdf5::out_every = 100 +IOHdf5::out_vars = "wavetoy_simple::phi" +\end{verbatim} + \end{itemize} +} + +\frame{\frametitle{Exercise: compute wave energy} +\begin{itemize} +\item compute energy density $\rho_E = \phi^2 \, \mathrm{d}x \, \mathrm{d}y \, \mathrm{d}z$ +\item compute integral as '\texttt{sum}' reduction of \texttt{IOScalar::out\_reductions} during output +\end{itemize} +} + \end{document}

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[svn:einsteintoolkit] Workshop_Summer_2013/pics/ (Rev. 14)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 08:04 AM Added: /pics/ factory.png Log: add missing image for simfactory File Changes: Directory: /pics/ ================= File [added]: factory.png Delta lines: <Unavailable>

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[svn:einsteintoolkit] Workshop_Summer_2013/cactuswriting/ (Rev. 13)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 01:31 AM Added: /cactuswriting/ cactuswriting.tex, config.png, config.tiff, interface1.png, interface1.tiff, interface2.png, interface2.tiff, interface3.png, interface3.tiff, make.png, make.tiff, param1.png, param1.tiff, param2.png, param2.tiff, schedule1.png, schedule1.tiff, schedule2.png, schedule2.tiff, schedule3.png, schedule3.tiff, srccode.png, srccode.tiff, srccode2.png, srccode2.tiff, thornlist.png, thornlist.tiff Log: add old cactuswriting intro File Changes: Directory: /cactuswriting/ ========================== File [added]: cactuswriting.tex Delta lines: <Unavailable> File [added]: config.png Delta lines: <Unavailable> File [added]: config.tiff Delta lines: <Unavailable> File [added]: interface1.png Delta lines: <Unavailable> File [added]: interface1.tiff Delta lines: <Unavailable> File [added]: interface2.png Delta lines: <Unavailable> File [added]: interface2.tiff Delta lines: <Unavailable> File [added]: interface3.png Delta lines: <Unavailable> File [added]: interface3.tiff Delta lines: <Unavailable> File [added]: make.png Delta lines: <Unavailable> File [added]: make.tiff Delta lines: <Unavailable> File [added]: param1.png Delta lines: <Unavailable> File [added]: param1.tiff Delta lines: <Unavailable> File [added]: param2.png Delta lines: <Unavailable> File [added]: param2.tiff Delta lines: <Unavailable> File [added]: schedule1.png Delta lines: <Unavailable> File [added]: schedule1.tiff Delta lines: <Unavailable> File [added]: schedule2.png Delta lines: <Unavailable> File [added]: schedule2.tiff Delta lines: <Unavailable> File [added]: schedule3.png Delta lines: <Unavailable> File [added]: schedule3.tiff Delta lines: <Unavailable> File [added]: srccode.png Delta lines: <Unavailable> File [added]: srccode.tiff Delta lines: <Unavailable> File [added]: srccode2.png Delta lines: <Unavailable> File [added]: srccode2.tiff Delta lines: <Unavailable> File [added]: thornlist.png Delta lines: <Unavailable> File [added]: thornlist.tiff Delta lines: <Unavailable>

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[svn:einsteintoolkit] Workshop_Summer_2013/handson_viz/ (Rev. 12)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 01:31 AM Added: /handson_viz/ Makefile, add_isosurface.png, add_pseudocolor.png, add_reflection.png, annotation_menu.png, change_colour_scheme.png, difference_black_colorscheme.png, disable_x_axis.png, fast_tov.par, final_plot_snapshot.png, handson_viz.pdf, handson_viz.tex, initial_plot_snapshot.png, isocontour_options.png, movie_frame_options.png, open_file.png, pseudocolour_options.png, psi4.volume.session, psi4_expression.png, psi4r_final.png, reflection_options.png, render_frames_menu.png, rendering_options.png, rho.final.session, volume_rendering_options.png, volume_transfer_options.png Log: add handson visualization exercise from last time File Changes: Directory: /handson_viz/ ======================== File [added]: Makefile Delta lines: <Unavailable> File [added]: add_isosurface.png Delta lines: <Unavailable> File [added]: add_pseudocolor.png Delta lines: <Unavailable> File [added]: add_reflection.png Delta lines: <Unavailable> File [added]: annotation_menu.png Delta lines: <Unavailable> File [added]: change_colour_scheme.png Delta lines: <Unavailable> File [added]: difference_black_colorscheme.png Delta lines: <Unavailable> File [added]: disable_x_axis.png Delta lines: <Unavailable> File [added]: fast_tov.par Delta lines: <Unavailable> File [added]: final_plot_snapshot.png Delta lines: <Unavailable> File [added]: handson_viz.pdf Delta lines: <Unavailable> File [added]: handson_viz.tex Delta lines: <Unavailable> File [added]: initial_plot_snapshot.png Delta lines: <Unavailable> File [added]: isocontour_options.png Delta lines: <Unavailable> File [added]: movie_frame_options.png Delta lines: <Unavailable> File [added]: open_file.png Delta lines: <Unavailable> File [added]: pseudocolour_options.png Delta lines: <Unavailable> File [added]: psi4.volume.session Delta lines: <Unavailable> File [added]: psi4_expression.png Delta lines: <Unavailable> File [added]: psi4r_final.png Delta lines: <Unavailable> File [added]: reflection_options.png Delta lines: <Unavailable> File [added]: render_frames_menu.png Delta lines: <Unavailable> File [added]: rendering_options.png Delta lines: <Unavailable> File [added]: rho.final.session Delta lines: <Unavailable> File [added]: volume_rendering_options.png Delta lines: <Unavailable> File [added]: volume_transfer_options.png Delta lines: <Unavailable>

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[svn:einsteintoolkit] Workshop_Summer_2013/et_intro_details/ (Rev. 11)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 01:31 AM Added: /et_intro_details/ Makefile, et_intro_details.tex Log: add current state of detailed et intro File Changes: Directory: /et_intro_details/ ============================= File [added]: Makefile Delta lines: +10 -0 =================================================================== --- et_intro_details/Makefile (rev 0) +++ et_intro_details/Makefile 2013-07-26 06:31:31 UTC (rev 11) @@ -0,0 +1,10 @@ +all: et_intro_details.pdf + +%.pdf: %.tex + pdflatex $* + +clean: + /bin/bash -exec "rm -f et_intro_details.{aux,log,nav,out,snm,pdf,toc} *~" + +.PHONY: all clean + File [added]: et_intro_details.tex Delta lines: +220 -0 =================================================================== --- et_intro_details/et_intro_details.tex (rev 0) +++ et_intro_details/et_intro_details.tex 2013-07-26 06:31:31 UTC (rev 11) @@ -0,0 +1,220 @@ +\input{../preamble.tex} +\usepackage{ragged2e} +\usepackage{amsmath} +\usepackage{listings} +\usepackage{scrextend} +\newcommand{\Heaviside}{\operatorname{\Theta}} + +\title[ET details]{Introduction to the Einstein Toolkit -- Details} +\author{Roland Haas\\ +\scriptsize TAPIR, Caltech} +\date{July 26\textsuperscript{th} 2013} + +%\usecolortheme[RGB={200,200,200}]{structure} +\usecolortheme[RGB={132,186,75}]{structure} +\definecolor{cactusgreen}{RGB}{132,186,75} +\newcommand{\red}[1]{\textcolor{cactusgreen}{#1}} +\newcommand{\black}[1]{\textcolor{black}{#1}} + +\begin{document} + +\begin{frame} +\titlepage +\end{frame} + +\begin{frame} +\frametitle{Einstein Toolkit main components} +Toolkit is based on three core components +\begin{labeling}{Simulation Factory} +\item[\red{Cactus}] provides the numerical framework and defines interfaces for +codes from different authors to interact with each other +\item[\red{GetComponents}] downloads modules the make up a simulation code +\item[\red{Simulation Factory}] unified user interface to start and manage +simulations on a variety of machines -- from laptops to supercomputers +\end{labeling} +\end{frame} + +\begin{frame} +\frametitle{What is Cactus?} +Cactus is +\begin{itemize} +\item<1-> a framework for developing portable, modular applications +\item<2-> focusing, although not exclusively, on high-performance simulation +codes +he other modules +\item<3-> separate concerns: designed to allow experts in different fields to develop modules based +upon their experience and to use modules developed by experts in +other fields with minimal knowledge of the internals or operation of +the other modules +\item<4-> mature $\ge12$ years of development +\end{itemize} +\end{frame} + +\frame { \frametitle{Cactus Goals} + \begin{itemize} + \item<1-> Portable + \begin{itemize} + \item Different development machines + \item Different production machines + \end{itemize} + \item<2-> Modular + \begin{itemize} + \item Standard interfaces for module interaction for easier + code interaction, writing and debugging + \item Interchangeable modules with same functionality + \end{itemize} + \item<3-> Easy to use + \begin{itemize} + \item Good documentation + \item Try to let users program the way they are used to + \item Support all major (HPC) programming languages + \end {itemize} + \end{itemize} } + +\begin{frame} +\frametitle{Flesh} + \begin{itemize} + \item The \textbf{flesh} is the central component of Cactus. It interfaces + with modular components called \textbf{thorns}. The flesh provides: + \begin{columns}[t] + \column{.6\textwidth} + \begin{itemize} + \item Variables \& Data Types + \item Parameters + \item Functions for: + \begin{itemize} + \item Parallelisation + \item Input/Output + \item Coordinates + \item Reduction + \item Interpolation + \item Information + \end{itemize} + \item Staggering + \begin{itemize} + \item Indexing + \item Ghostzones + \end{itemize} + \end{itemize} + + \column{.3\textwidth} + \begin{center} + \begin{figure}[h] + \includegraphics[width=40mm]{cactusflesh} + \end{figure} + \end{center} + \end{columns} + \end{itemize} +\end{frame} + +\begin{frame} \frametitle{Thorns} + \begin{itemize} + \item Some thorns provide additional functionality, while others serve as applications. + \item Thorns are grouped into \textbf{arrangements} which supply some common functionality. + \item Example thorns: + \\ \vspace{12pt} + \small + \begin{tabular}{ll} + \textit{EinsteinInitialData} & initial data \\ + \ \textbf{TwoPunctures} & initial data for binary black holes\\ + \ \textbf{TOVSolver} & initial data for single spherical star\\ + \textit{Carpet} & adaptive mesh refinement driver\\ + \ \textbf{Carpet} & simulation driver, adaptive mesh refinement\\ + \ \textbf{CarpetIOHDF5} & 1d, 2d, 3d output to HDF5\\ + \textit{EinsteinAnalysis} & extract data from simulation\\ + \ \textbf{WeylScal4} & computes gravitational wave content\\ + \ \textbf{Multipole} & decompose into spherical harmonic modes\\ + \end{tabular} + \end{itemize} +\end{frame} + +\begin{frame}[containsverbatim] \frametitle{Directory structure} + + \begin{alltt} +Cactus +|-- doc +| |-- UsersGuide.pdf +| `-- ReferenceManual.pdf +|-- configs +| |-- sim +| `-- sim-debug +|-- src +|-- repos +|-- simfactory +`-- arrangements + |-- EinsteinInitialData + | `-- TwoPunctures + `-- Carpet + `-- CarpetIOHDF5 +\end{alltt} +\end{frame} + +\begin{frame} \frametitle{GetComponents -- why?} + +\begin{itemize} +\item $\sim 100$ thorns used for simulation +\item Thorns come from a variety of sources: \texttt{git}, \texttt{svn}, \texttt{cvs}, \texttt{darcs}, \ldots +\item Multiple access levels: publicly available, password required +\item Multiple thorns per repository? Separate documentation? Example files? +\item Specific code version, release date +\end{itemize} + +\end{frame} + +\begin{frame} \frametitle{GetComponents -- what?} + +\begin{itemize} +\item (parallised) download of modules from source code repositories +\item access to sub-parts of repositories +\item assemble directory structure +\item simplify update of modules +\item show local changes in all thorns +\item operates on \texttt{thornlist} describing collection of thorns +\end{itemize} + +\end{frame} + +\begin{frame}[containsverbatim] \frametitle{GetComponents -- how?} +\scriptsize\begin{alltt} +!CRL_VERSION = 1.0 + +!DEFINE ROOT = Cactus +!DEFINE ARR = $ROOT/arrangements + +!TARGET = $ROOT +!TYPE = svn +!AUTH_URL = https://svn.cactuscode.org/flesh/trunk +!CHECKOUT = Cactus +!NAME = . + +!TARGET = $ARR +!TYPE = git +!AUTH_URL = carpetgit@carpetcode.org:carpet +!URL = git://carpetcode.org/carpet +!CHECKOUT = Carpet/doc +Carpet/Carpet +Carpet/CarpetIOHDF5 +\end{alltt} +\end{frame} + +\begin{frame} \frametitle{Simulation Factory} + The Simulation Factory: + \begin{columns} + \column{0.25\textwidth} + \includegraphics[width=\textwidth]{pics/factory.png} + \column{0.75\textwidth} + \begin{itemize} + \item Command-line tools for setting up Cactus distribution + and managing simulations on a variety of supercomputers, + including most of the TeraGrid machines. + \end{itemize} + \end{columns} + \begin{itemize} + \item Captures the best practices of experienced users, ensuring + repeatable and well-documented scientific results. + \item Developed by Erik Schnetter and Michael Thomas. + \item Included in Cactus-OS distro: {\tt Cactus/simfactory}. + \item For more, see: {\tt http://simfactory.org} + \end{itemize} +\end{frame} +\end{document}

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[svn:einsteintoolkit] Workshop_Summer_2013/cactus_intro/ (Rev. 10)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 01:31 AM Removed: /cactus_intro/ cactus_intro.tex, recompile Log: remove unused cactus_intro File Changes: Directory: /cactus_intro/ ========================= File [removed]: cactus_intro.tex Delta lines: +0 -374 =================================================================== --- cactus_intro/cactus_intro.tex 2013-07-26 06:14:59 UTC (rev 9) +++ cactus_intro/cactus_intro.tex 2013-07-26 06:31:27 UTC (rev 10) @@ -1,374 +0,0 @@ -\input{../preamble} -\usepackage{ragged2e} -\usecolortheme[RGB={200,200,200}]{structure} - -\begin{document} - - \frame { \frametitle{What is Cactus?} - Cactus is - \begin{itemize}[<+->] - \item \textcolor{black}{a \hyperlink{framework}{framework} for developing portable, modular applications} - \item \textcolor{black}{focusing, although not exclusively, on high-performance - simulation codes} - \item \textcolor{black}{designed to allow experts in different fields to develop - modules based upon their experience and to use modules - developed by experts in other fields with minimal knowledge - of the internals or operation of the other modules} - \end{itemize} } - - \frame { \frametitle{Cactus Goals} - \begin{itemize} - \item<1-> Portable - \begin{itemize} - \item Different development machines - \item Different production machines - \end{itemize} - \item<2-> Modular - \begin{itemize} - \item Standard interfaces for module interaction for easier - code interaction, writing and debugging - \item Interchangeable modules with same functionality - \end{itemize} - \item<3-> Easy to use - \begin{itemize} - \item Good documentation - \item Try to let users program the way they are used to - \item Support all major (HPC) programming languages - \end {itemize} - \end{itemize} } - - \frame { \frametitle{Philosophy} - \begin{center} - \begin{figure}[h] - \includegraphics[width=30mm]{Opensource} - \end{figure} - \end{center} - \begin{itemize}[<+->] - \item Open code base to encourage community contributions - \item Strict quality control for base framework - \item Development always driven by real user requirements - \item Support and develop for a wide range of application domains - \end{itemize} } - - \frame { \frametitle{What is Cactus for?} - Assume: - \begin{itemize} - \item Computational problem - \item Too large for single machine - \begin{itemize} - \item<2-> \only<5->{\textcolor{cactusgreen}}{OpenMP} - \item<2-> \only<5->{\textcolor{cactusgreen}}{MPI} - \end{itemize} - \item Distributed development - \begin{itemize} - \item<3-> \only<5->{\textcolor{cactusgreen}}{Modularize Problem} - \item<3-> \only<5->{\textcolor{cactusgreen}}{Versioning system(s)} - \end{itemize} - \item Multiple programming languages - \begin{itemize} - \item<4-> \only<5->{\textcolor{cactusgreen}}{Modularize Problem} - \item<4-> \only<5->{\textcolor{cactusgreen}}{Interfaces for inter-language communication} - \end{itemize} - \end{itemize} - } - -\frame{\frametitle{Modularization Motivation} -Simulations are complex, may contain several models at once.\\ -Example: Long Gamma Ray Burst: - \begin{columns}[t] - \column{.4\textwidth} - \begin{center} - \includegraphics[width=0.9\textwidth]{supernova_model} - \end{center} - \column{.5\textwidth} - \begin{itemize} - \item General Relativity (black hole) - \item Relativistic Hydrodynamics (star) - \item Microphysics, equation of state (shock wave) - \item Neutrino radiation (cooling, heating) - \item Magnetic Fields (Jet formation) - \item Photon radiation (afterglow) - \end{itemize} - - \end{columns} -} - -\frame{\frametitle{Modularization Motivation} - Added Problems: - \begin{itemize} - \item Example: Einstein Toolkit (not untypical) - \item Code 12+ years old - \item Grad students leave after 3 productive years - \item Most original authors not available anymore - \item Developers distributed over many places in several continents - \item Most physicists are not good programmers - \end{itemize} -} - -\frame{\frametitle{Component Architecture} - \begin{itemize} - \item Split program into independent components (as much as possible) - \item \textit{Framework} provides glue between these - \item Components are developed independently by small groups - \item End user assembles all code: no central control, no authorative version - \item Framework itself does no real work - \item Components don't interact directly with each other - \end{itemize} -} - -\frame { \frametitle{Cactus History} - \begin{itemize} - \item Direct descendant of many years of code development in Ed Seidel's group of - researchers at NCSA - \item 1995, Paul Walker, Joan Masso, Ed Seidel, and John Shalf: Cactus~1.0 - \item Originally for numerical relativity - \item Over the years generalized for use by scientists in other domains - \end{itemize} -} - -\frame { \frametitle{Current Users and Developers} - \centering - \includegraphics[height=7cm]{groups_map}\\ -} - -\frame { \frametitle{Covers} - \hspace{0cm}\includegraphics[height=3.5cm]{covers/ACMCommunications} - \hspace{1cm}\includegraphics[height=3.5cm]{covers/FutureTechPhysCosm} - \hspace{1cm}\includegraphics[height=3.5cm]{covers/Gravity}\\\vspace{-1.5cm} - \hspace{1cm}\includegraphics[height=3.5cm]{covers/max-planck-research2} - \hspace{1cm}\includegraphics[height=3.5cm]{covers/nsffy2006budgetcover} - \hspace{1cm}\includegraphics[height=3.5cm]{covers/mmcover}\\\vspace{-1.5cm} - \hspace{2cm}\includegraphics[height=3.5cm]{covers/visprocessingtensor} - \hspace{1.5cm}\includegraphics[height=3.5cm]{covers/PetascaleComputingBook} - \hspace{1cm}\includegraphics[height=3.5cm]{covers/NR689} -} - -\frame { \frametitle{Cactus Funding} - \begin{itemize} - \item Organizations: - \begin{itemize} - \item Max-Planck-Gesellschaft - \item Center for Computation \& Technology at LSU - \item National Center for Supercomputing Applications - \item Lawrence Berkeley National Laboratory - \item Washington University - \item University of TÃ¼bingen - \end{itemize} - \item Grants: - \begin{itemize} - \item NSF (PHY-9979985, 0540374, 0653303, 0701491, 0701566, - PIF-0904015, 0903973, 0903782) - \item Europ. Commission (HPRN-CT-2000-00137, IST-2001-32133) - \item DFN-Verein (TK 6-2-AN 200) - \item DFG (TiKSL) - \item ONR (COMI) - \item DOE/BOR (OE DE-FG02-04ER46136, BOR DOE/LEQSF) - \end{itemize} - \end{itemize} -} - -% Copied from web site -\begin{frame} \frametitle{Cactus Awards} - \begin{tabular}{ll} - IEEE SCALE09 Challenge Winner & 2009\\ - IEEE Sidney Fernback Award & 2006\\ - High-Performance Bandwidth Challenge & SC2002\\ - High-Performance Computing Challenge & SC2002\\ - Gordon Bell Prize for Supercomputing & SC2001\\ - HPC ``Most Stellar'' Challenge Award & SC1998\\ - Heinz Billing Prize for Scientific Computing & 1998 - \end{tabular} -\end{frame} - -\begin{frame} \frametitle{The Flesh} - \begin{itemize} - \item The \textbf{flesh} is the central component of Cactus. It interfaces - with modular components called \textbf{thorns}. The flesh provides: - \begin{columns}[t] - \column{.6\textwidth} - \begin{itemize} - \item Variables \& Data Types - \item Parameters - \item Functions for: - \begin{itemize} - \item Parallelisation - \item Input/Output - \item Coordinates - \item Reduction - \item Interpolation - \item Information - \end{itemize} - \item Staggering - \begin{itemize} - \item Indexing - \item Ghostzones - \end{itemize} - \end{itemize} - - \column{.3\textwidth} - \begin{center} - \begin{figure}[h] - \includegraphics[width=40mm]{cactusflesh} - \end{figure} - \end{center} - \end{columns} - \end{itemize} - \end{frame} - -\begin{frame} \frametitle{Thorns} - \begin{itemize} - \item Some thorns provide additional functionality, while others serve as applications. - \item Thorns are grouped into \textbf{arrangements} which supply some common functionality. - \item Example thorns: - \\ \vspace{12pt} - \small - \begin{tabular}{ll} - \textit{CactusIO} & input and output operations\\ - \ \textbf{CactusIOJpeg} & JPEG image data compression and writing operations\\ - \textit{CactusConnect} & networking\\ - \ \textbf{HTTPD} & starts the HTTP daemon for remote connections\\ - \textit{PUGH} & unigrid driver + tools; reductions and interpolations\\ - \ \textbf{PUGH} & unigrid driver handles grid scalars, arrays and functions\\ - \end{tabular} - \end{itemize} -\end{frame} - - -% Should put more here. -\begin{frame} \frametitle{Application Toolkits} - \begin{columns}[t] - \column{.5\textwidth} - \begin{center} - \begin{figure} - \includegraphics[width=0.4\textwidth]{einstein} - \end{figure} - \end{center} - - \justifying The \textbf{Cactus Computational Toolkit} is a collection of - arrangements that provides general computational infrastructure. - - \column{.5\textwidth} - \justifying The \textbf{Einstein Toolkit} is a collection of arrangements for - computational relativity. The toolkit includes a vacuum spacetime solver - (McLachlan), a relativistic hydrodynamics solver, along with thorns for initial - data, analysis and computational infrastructure. - \begin{center} - \begin{figure} - \includegraphics[width=20mm]{cactuslogo} - \end{figure} - \end{center} - \end{columns} -\end{frame} - -\frame { \frametitle{Typical list of component tasks} - \abspic{puzzle}{0.0}{0.6}{0.4} - \begin{itemize} - \item Evolution systems - \item Boundary conditions - \item Initial conditions - \item Time stepping method - \item Finite Difference methods - \item Simulation grid (distributed arrays) - \item I/O (more on next slide) - \item Simulation domain specification - \item Termination condition - \item Twitter client - \end{itemize} -} - -\frame { \frametitle{I/O Capabilities} - Usual I/O and checkpointing in different formats: - \begin{columns}[t] - \column{.6\textwidth} - \begin{itemize} - \item Screen output - \item ASCII file output - \item HDF5 file in-/output - \item Online Jpeg rendering - \item Online VisIt visualization - \end{itemize} - - \column{.3\textwidth} - \begin{center} - \begin{figure}[h] - \includegraphics[width=40mm]{viz} - \end{figure} - \end{center} - \end{columns} -} - -\frame { \frametitle{More Capabilities: Grids, Boundaries, Symmetries} - \begin{columns}[t] - \column{.5\textwidth} - \begin{itemize} - \item Grids - \begin{itemize} - \item Only structured meshes (at the moment) - \item Unigrid (PUGH) - \item Adaptive Mesh Refinement (Carpet) - \end{itemize} - \item Boundaries / Symmetries - \begin{itemize} - \item Periodic - \item Static - \item Mirror symmetries - \item Rotational symmetries - \item Problemspecific boundaries - \end{itemize} - \end{itemize} - - - \column{.4\textwidth} - \begin{center} - \begin{figure}[h] - \includegraphics[width=45mm]{amr} - \end{figure} - \end{center} - \end{columns} -} - -\frame { \frametitle{The Cactus Computational Toolkit} - \begin{columns}[t] - \column{.3\textwidth} - \begin{center} - \begin{figure} - \includegraphics[height=40mm]{potcact} - \end{figure} - \end{center} - - - \column{.6\textwidth} - Core modules (thorns) providing many basic utilities: - \begin{itemize} - \item I/O methods - \item Boundary conditions - \item Parallel unigrid driver - \item Reduction and Interpolation operators - \item Interface to external elliptic solvers - \item Web-based interaction and monitoring interface - \item Simple example thorns (wavetoy) - \end{itemize} - \end{columns} -} - -\frame { \frametitle{Many arrangements with many modules...} - \begin{tabular}{ll} - CactusBase& Basic utility and interface thorns\\ - CactusBench& Benchmark utility thorns\\ - CactusConnect& Network utility thorns\\ - CactusElliptic& Elliptic solvers / interface thorns\\ - CactusExamples& Example thorns\\ - CactusExternal& External library interface thorns\\ - CactusIO& General I/O thorns\\ - CactusNumerical& General numerical methods\\ - CactusPUGH& Cactus Unigrid Driver thorn\\ - CactusPUGHIO& I/O thorns specifix for PUGH driver\\ - CactusTest& Thorns for Cactus testing\\ - CactusUtils& Misc. utility thorns\\ - CactusWave& Wave example thorns\\ - \end{tabular} -} - - -\end{document} - File [removed]: recompile Delta lines: +0 -14 =================================================================== --- cactus_intro/recompile 2013-07-26 06:14:59 UTC (rev 9) +++ cactus_intro/recompile 2013-07-26 06:31:27 UTC (rev 10) @@ -1,14 +0,0 @@ -#!/bin/bash - -function pdf { - NAME=$1 - pdflatex $NAME.tex - pgrep -f "xpdf -remote 127.0.0.1 $NAME.pdf" 2>&1 > /dev/null - if [ $? == 0 ]; then - xpdf -remote 127.0.0.1 -reload -raise - else - xpdf -remote 127.0.0.1 $NAME.pdf & - fi -} - -pdf cactus_intro

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[svn:einsteintoolkit] Workshop_Summer_2013/handson_analysis/ (Rev. 9)
by knarf＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: knarf Date: 2013/07/26 01:15 AM Modified: /handson_analysis/ handson_analysis.tex Log: update date File Changes: Directory: /handson_analysis/ ============================= File [modified]: handson_analysis.tex Delta lines: +1 -1 =================================================================== --- handson_analysis/handson_analysis.tex 2013-07-26 06:10:25 UTC (rev 8) +++ handson_analysis/handson_analysis.tex 2013-07-26 06:14:59 UTC (rev 9) @@ -7,7 +7,7 @@ \subtitle[Analysis hands-on]{{\large Einstein Toolkit Workshop}\\*[0.3em]Hands-on exercise: tracking stars} \author{Roland Haas} -\date{Apr 01 2012} +\date{Jul 26 2013} \usecolortheme[RGB={200,200,200}]{structure}

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[svn:einsteintoolkit] Workshop_Summer_2013/et_intro/ (Rev. 8)
by knarf＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: knarf Date: 2013/07/26 01:10 AM Modified: /et_intro/ slides.tex Log: Cactus -> ET File Changes: Directory: /et_intro/ ===================== File [modified]: slides.tex Delta lines: +1 -1 =================================================================== --- et_intro/slides.tex 2013-07-23 19:15:09 UTC (rev 7) +++ et_intro/slides.tex 2013-07-26 06:10:25 UTC (rev 8) @@ -251,7 +251,7 @@ (meaningful initial conditions, numerical stability,\\ accuracy/resolution, have patience, have curiosity,\\ develop a ``gut feeling'' for what is right ...) - \item Cactus Toolkit \textbf{cannot} give that, \textbf{however}: + \item Einstein Toolkit \textbf{cannot} give that, \textbf{however}: \item Open codes that are easy to use allow to concentrate on these things! \end{itemize} \end{itemize}

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