[945] | 1 | % $Id: runs_with_mrun.tex 1165 2013-05-24 12:33:14Z raasch $ |
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| 2 | \input{header_tmp.tex} |
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| 3 | %\input{../header_lectures.tex} |
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| 4 | |
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| 5 | \usepackage[utf8]{inputenc} |
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| 6 | \usepackage{ngerman} |
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| 7 | \usepackage{pgf} |
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| 8 | \usetheme{Dresden} |
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| 9 | \usepackage{subfigure} |
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| 10 | \usepackage{units} |
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| 11 | \usepackage{multimedia} |
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| 12 | \usepackage{hyperref} |
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| 13 | \newcommand{\event}[1]{\newcommand{\eventname}{#1}} |
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| 14 | \usepackage{xmpmulti} |
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| 15 | \usepackage{tikz} |
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| 16 | \usetikzlibrary{shapes,arrows,positioning} |
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| 17 | \def\Tiny{\fontsize{4pt}{4pt}\selectfont} |
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| 18 | \usepackage{amsmath} |
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| 19 | \usepackage{amssymb} |
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| 20 | \usepackage{multicol} |
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| 21 | \usepackage{pdfcomment} |
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| 22 | \usepackage{graphicx} |
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| 23 | \usepackage{listings} |
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| 24 | \lstset{showspaces=false,language=fortran,basicstyle= |
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| 25 | \ttfamily,showstringspaces=false,captionpos=b} |
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| 26 | |
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| 27 | \institute{Institut fÌr Meteorologie und Klimatologie, Leibniz UniversitÀt Hannover} |
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| 28 | \date{last update: \today} |
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| 29 | \event{PALM Seminar} |
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| 30 | \setbeamertemplate{navigation symbols}{} |
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| 31 | |
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| 32 | \setbeamertemplate{footline} |
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| 33 | { |
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| 34 | \begin{beamercolorbox}[rightskip=-0.1cm]& |
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| 35 | {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}} |
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| 36 | \end{beamercolorbox} |
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| 37 | \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex, |
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| 38 | leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot} |
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| 39 | {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber} |
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| 40 | \end{beamercolorbox} |
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| 41 | \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot} |
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| 42 | \end{beamercolorbox} |
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| 43 | } |
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[954] | 44 | |
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[945] | 45 | %\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}} |
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| 46 | |
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| 47 | \title[Carrying out runs using mrun]{Carrying out runs using \texttt{mrun}} |
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| 48 | \author{Siegfried Raasch} |
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| 49 | |
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| 50 | \begin{document} |
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| 51 | |
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| 52 | % Folie 1 |
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| 53 | \begin{frame} |
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| 54 | \titlepage |
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| 55 | \end{frame} |
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| 56 | |
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| 57 | \section{Carrying out runs using mrun} |
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| 58 | \subsection{Carrying out runs using mrun} |
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| 59 | |
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| 60 | % Folie 2 |
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| 61 | \begin{frame} |
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| 62 | \frametitle{What is \texttt{mrun}?} |
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| 63 | \begin{itemize} |
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| 64 | \item<1-> \texttt{mrun} (\textbf{m}odel \textbf{run}) is a shell script (using |
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| 65 | \texttt{ksh}-syntax) which can be used to compile and run programs, including |
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| 66 | the handling of input/output files. |
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[954] | 67 | \vspace{4mm} |
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[945] | 68 | \item<2-> The \texttt{mrun}-command has a number of options to control the |
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| 69 | program execution\\ |
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[954] | 70 | \quad \footnotesize \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\ |
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[945] | 71 | \normalsize All options including a short description can be displayed by entering\\ |
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| 72 | \quad \footnotesize \texttt{mrun ?} |
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[954] | 73 | \vspace{4mm} |
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[945] | 74 | \item<3-> \normalsize The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} |
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| 75 | \end{itemize} |
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| 76 | \end{frame} |
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| 77 | |
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| 78 | % Folie 3 |
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| 79 | \begin{frame} |
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[954] | 80 | \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\tiny] |
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| 81 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, font=\tiny] |
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| 82 | \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\tiny] |
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| 83 | \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\tiny] |
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| 84 | \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\tiny] |
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[945] | 85 | \tikzstyle{line} = [draw, -] |
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| 86 | \tikzstyle{alert} = [rectangle, draw, text width=0.77\textwidth, font=\scriptsize] |
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| 87 | |
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| 88 | \scriptsize |
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| 89 | \frametitle{Carrying Out Runs Using \texttt{mrun}} |
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[954] | 90 | \textbf{Carrying out a program run typically needs two steps:}\\ |
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[945] | 91 | \vspace{1mm} |
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[954] | 92 | \quad 1. compilation\\ |
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| 93 | \qquad \texttt{f90 ... file1.f90 file2.f90 ...}\\ |
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| 94 | \vspace{1mm} |
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| 95 | \onslide<2->\quad 2. execution\\ |
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| 96 | \qquad \texttt{a.out}\\ |
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| 97 | \vspace{3mm} |
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| 98 | \onslide<3->\textbf{Besides, a program needs input data and creates output data:}\\ |
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[945] | 99 | |
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| 100 | \onslide<4->\begin{tikzpicture}[auto, node distance=0] |
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| 101 | \node [green] (first) {\textbf{a.out/} }; |
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| 102 | \node [dummy, right=0.1cm of first] (second) {}; |
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| 103 | |
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[954] | 104 | \node [yellow, above=0.4cm of second] (third) {\textbf{parameter for steering}}; |
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| 105 | \node [yellow, below=0.4cm of third] (fourth) {\textbf{control output}}; |
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[945] | 106 | \node [yellow, below=0.3cm of fourth] (fifth) {\textbf{output for analysis}}; |
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| 107 | |
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| 108 | \node [info, above=-0.1cm of third] (sixth) {input file}; |
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| 109 | \node [info, above=-0.1cm of fourth] (seventh) {output file 1}; |
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| 110 | \node [info, above=-0.1cm of fifth] (eight) {output file 2}; |
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| 111 | |
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| 112 | \draw [->] (third.west) -- (first.north); |
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| 113 | \draw [->] (first.east) -- (fourth.west); |
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| 114 | \draw [->] (first.south) -- (fifth.west); |
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| 115 | |
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| 116 | \uncover<5->{\node [white, right=0.25cm of third] (ninth) { |
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| 117 | \texttt{OPEN (11, FILE='PARIN', FORM='FORMATTED')}};} |
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| 118 | \uncover<5->{\node [white, right=0.25cm of fourth] (tenth) { |
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[954] | 119 | \texttt{OPEN (15, FILE='RUN\underline{ }CONTROL', FORM='FORMATTED')}};} |
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[945] | 120 | \uncover<5->{\node [white, right=0.25cm of fifth] (eleventh) { |
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[954] | 121 | \texttt{OPEN (40, FILE=âDATA\underline{ }1D\underline{ }PR\underline{ }NETCDF', FORM='FORMATTED')}};} |
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[945] | 122 | \end{tikzpicture} |
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| 123 | |
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[954] | 124 | \vspace{3mm} |
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[945] | 125 | \scriptsize |
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[954] | 126 | \onslide<6->\textcolor{red}{\textbf{Problems:} The user has to copy or rename output files, if |
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[945] | 127 | he/she wants to run the program more than once and if he concurrently wants to keep |
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[973] | 128 | the files from the former run(s). If he/she is using different input parameter files for steering, these files also have |
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[945] | 129 | to be copied into the working directory before the program is executed.}\\ |
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[954] | 130 | \vspace{1mm} |
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[945] | 131 | \begin{tikzpicture}[auto, node distance=0] |
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[954] | 132 | \uncover<7->{\node [alert] (alert) {\textcolor{red}{\textbf{It is therefore very desirable to automate these tasks!}}};} |
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[945] | 133 | \end{tikzpicture} |
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| 134 | \end{frame} |
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| 135 | |
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| 136 | % Folie 4 |
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| 137 | \begin{frame} |
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[1165] | 138 | \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize] |
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[945] | 139 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize] |
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| 140 | \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.10\textwidth, font=\scriptsize] |
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| 141 | \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny] |
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| 142 | |
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| 143 | \frametitle{\texttt{mrun}: Principal Mode of Operation (I)} |
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[954] | 144 | \scriptsize \texttt{mrun} \textbf{runs a program (in our case the PALM model) by carrying out the following principle tasks in a sequential order:}\\ |
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| 145 | \vspace{1mm} |
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[945] | 146 | \begin{enumerate} |
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| 147 | \item<2-> Create a temporary working directory and change into this directory:\\ |
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[1165] | 148 | \quad \texttt{mkdir <tmpdir>/<username>.<randomnumber>}\\ |
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| 149 | \quad \texttt{cd <tmpdir>/<username>.<randomnumber>}\\ |
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[945] | 150 | \ \\ |
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[1165] | 151 | The path of \texttt{<tmpdir>} is given in the configuration file |
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[954] | 152 | \texttt{.mrun.config} by the environment variable \texttt{tmp\underline{ }user\underline{ }catalog}, e.g.:\\ |
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| 153 | \quad \texttt{\%tmp\underline{ }user\underline{ }catalog /tmp \hspace{30mm} <hi> parallel}\\ |
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[945] | 154 | \ \\ |
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| 155 | \onslide<3-> On SGI-ICE: \\ |
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[954] | 156 | \quad \texttt{\%tmp\underline{ }user\underline{ }catalog /gfs2/work/<username> |
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| 157 | \hspace{5mm} lcsgih parallel} |
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[945] | 158 | \begin{center} |
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| 159 | \begin{tikzpicture}[auto, node distance=0] |
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[1165] | 160 | \uncover<4->{\node [green] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};} |
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[945] | 161 | \end{tikzpicture} |
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| 162 | \end{center} |
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[954] | 163 | \vspace{2mm} |
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[945] | 164 | \item<5-> Copy the input files from a directory of the user into this working directory:\\ |
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[954] | 165 | \vspace{1mm} |
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| 166 | \onslide<6-> \tiny \quad \texttt{cp <user\underline{ }input\underline{ }file1> |
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[1165] | 167 | /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file1>}\\ |
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[954] | 168 | \quad \texttt{cp <user\underline{ }input\underline{ }file2> |
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[1165] | 169 | /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file2>}\\ |
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[954] | 170 | \vspace{2mm} |
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| 171 | \scriptsize |
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[945] | 172 | \begin{center} |
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| 173 | \begin{tikzpicture}[auto, node distance=0] |
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| 174 | |
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[1165] | 175 | \uncover<8->{\node [green] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};} |
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[945] | 176 | |
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| 177 | \uncover<7->{\node [yellowsmall, above=0.1cm of green] (yellow2) {JOBS/};} |
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[954] | 178 | \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\underline{ }version/};} |
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| 179 | \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};} |
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[945] | 180 | \uncover<7->{\node [yellowsmall, right=0.2cm of yellow3] (yellow4) {INPUT/};} |
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| 181 | |
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| 182 | \draw<7-> [-] (yellow1.east) -- (yellow2.west); |
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| 183 | \draw<7-> [-] (yellow2.east) -- (yellow3.west); |
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| 184 | \draw<7-> [-] (yellow3.east) -- (yellow4.west); |
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| 185 | |
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| 186 | \node [dummy, right=0.1cm of yellow4] (dummy1) {}; |
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| 187 | \node [dummy, right=2.055cm of green] (dummy2) {}; |
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| 188 | |
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| 189 | \draw<9-> [-] (yellow4.east) -- (dummy1.center); |
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| 190 | \draw<9-> [-] (dummy1.center) -- (dummy2.center); |
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| 191 | \draw<9-> [->] (dummy2.center) -- (green.east); |
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| 192 | |
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| 193 | \end{tikzpicture} |
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| 194 | \end{center} |
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| 195 | |
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| 196 | \end{enumerate} |
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| 197 | |
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| 198 | \end{frame} |
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| 199 | |
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| 200 | % Folie 5 |
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| 201 | \begin{frame} |
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[1165] | 202 | \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm] |
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[945] | 203 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm] |
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| 204 | \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm] |
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| 205 | |
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| 206 | \frametitle{\texttt{mrun}: Principal Mode of Operation (II)} |
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| 207 | |
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| 208 | \begin{enumerate} |
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| 209 | \setcounter{enumi}{2} |
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| 210 | \item<1-> Copy the pre-compiled routines to the temporary working directory:\\ |
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| 211 | |
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| 212 | \begin{center} |
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| 213 | \begin{tikzpicture}[auto, node distance=0] |
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[954] | 214 | \uncover<2->{\node [yellow] (yellow) {current\underline{ }version/};} |
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[945] | 215 | \uncover<1->{\node [dummy, right=0.0cm of yellow] (dummy1) {};} |
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[954] | 216 | \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\underline{ }DEPOSITORY\underline{ }\textit{parallel}/};} |
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[945] | 217 | \uncover<1->{\node [dummy, right=0.2cm of green1] (dummy2) {};} |
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[1165] | 218 | \uncover<3->{\node [green, below=0.5cm of dummy1] (green2) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};} |
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[945] | 219 | \uncover<1->{\node [dummy, below=0.5cm of dummy2] (dummy3) {};} |
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| 220 | \uncover<4->{\node [dummy, right=0.0cm of dummy3] (text) {Makefile\\ |
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| 221 | *.f90\\ |
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| 222 | *.o\\ |
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| 223 | ...\\ \ \\};} |
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| 224 | |
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| 225 | \draw<2-> [-] (yellow.east) -- (green1.west); |
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| 226 | \draw<4-> [-] (green1.east) -- (dummy2.center); |
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| 227 | \draw<4-> [-] (dummy2.center) -- (dummy3.center); |
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| 228 | \draw<4-> [->] (dummy3.center) -- (green2.east); |
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| 229 | \end{tikzpicture} |
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| 230 | \end{center} |
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| 231 | |
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| 232 | \item<5-> Compile the main program and use pre-compiled object files:\\ |
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| 233 | \quad \texttt{f90 palm.f90 *.o ... ( make Makefile)} |
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| 234 | \item<6-> Execute the program:\\ |
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| 235 | \quad \texttt{a.out} |
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| 236 | \end{enumerate} |
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| 237 | \end{frame} |
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| 238 | |
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| 239 | % Folie 6 |
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| 240 | \begin{frame} |
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[1165] | 241 | \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm] |
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[945] | 242 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm] |
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| 243 | \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm] |
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| 244 | |
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| 245 | \frametitle{\texttt{mrun}: Principal Mode of Operation (III)} |
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[954] | 246 | \footnotesize |
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[945] | 247 | \begin{enumerate} |
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| 248 | \setcounter{enumi}{5} |
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| 249 | \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\ |
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[1165] | 250 | \tiny \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\ |
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| 251 | \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\ |
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[954] | 252 | \footnotesize |
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[945] | 253 | \begin{center} |
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| 254 | \begin{tikzpicture}[auto, node distance=0] |
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| 255 | \uncover<2->{\node [yellow] (yellow1) {MONITORING/};} |
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| 256 | |
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| 257 | \uncover<2->{\node [dummy, right=0.2cm of yellow1] (dummy2) {};} |
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| 258 | \uncover<2->{\node [dummy, above=0.2cm of dummy2] (dummy1) {};} |
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| 259 | \uncover<2->{\node [dummy, below=0.2cm of dummy2] (dummy3) {};} |
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| 260 | |
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| 261 | \uncover<2->{\node [yellow, left=0.2cm of dummy3] (yellow2) {OUTPUT/};} |
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[954] | 262 | \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};} |
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[945] | 263 | \uncover<2->{\node [yellow, left=0.2cm of yellow3] (yellow4) {JOBS/};} |
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[954] | 264 | \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};} |
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[945] | 265 | |
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[1165] | 266 | \uncover<2-3>{\node [green, left=5.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};} |
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[945] | 267 | |
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| 268 | \draw<2-3> [-] (green.east) -- (dummy1.center); |
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| 269 | \draw<2-3> [-] (dummy2.center) -- (dummy1.center); |
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| 270 | \draw<2-3> [-] (dummy3.center) -- (dummy1.center); |
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| 271 | |
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| 272 | \draw<2-3> [->] (dummy2.center) -- (yellow1.east); |
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| 273 | \draw<2-3> [->] (dummy3.center) -- (yellow2.east); |
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| 274 | |
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| 275 | \draw<2-> [-] (yellow2.west) -- (yellow3.east); |
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| 276 | \draw<2-> [-] (yellow3.west) -- (yellow4.east); |
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| 277 | \draw<2-> [-] (yellow4.west) -- (yellow5.east); |
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| 278 | |
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| 279 | \end{tikzpicture} |
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| 280 | \end{center} |
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| 281 | |
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| 282 | \item<3-> Delete the temporary working directory\\ |
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[1165] | 283 | \quad \texttt{rm -rf /<tmpdir>/<username>.<randomnumber>}\\ |
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[954] | 284 | \vspace{2mm} |
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[945] | 285 | \onslide<5->\textcolor{red}{Question: How does \texttt{mrun} know which files have to be copied and where from or where to they have to be copied?} |
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| 286 | |
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| 287 | \end{enumerate} |
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| 288 | \end{frame} |
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| 289 | |
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| 290 | % Folie 7 |
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| 291 | \begin{frame} |
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| 292 | \tikzstyle{small} = [rectangle, text width=0.08\textwidth, font=\scriptsize] |
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| 293 | \tikzstyle{large} = [rectangle, text width=0.45\textwidth, font=\scriptsize] |
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| 294 | \tikzstyle{box} = [rectangle, draw, text width=0.2\textwidth, font=\scriptsize] |
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| 295 | \tikzstyle{boxbig} = [rectangle, draw, text width=0.4\textwidth, font=\scriptsize] |
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| 296 | \tikzstyle{dummy} = [rectangle, text width=0.0\textwidth, font=\scriptsize, minimum height=0.5cm] |
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| 297 | |
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| 298 | \frametitle{Steering File Copy by the Configuration File (I)} |
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| 299 | \scriptsize |
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[954] | 300 | \textbf{Copying of files is controlled by so called} \textit{file connection statements}. \textbf{They connect local files in the temporary working directory with permanent files residing in the directory of the user.}\\ |
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[945] | 301 | \vspace{1mm} |
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| 302 | Principle example of a file connection statement (for the PALM parameter file): |
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| 303 | \vspace{-3mm} |
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| 304 | \begin{center} |
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| 305 | \begin{tikzpicture}[auto, node distance=0] |
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| 306 | \uncover<1->{\node [small] (part1) {\texttt{PARIN}};} |
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| 307 | \uncover<1->{\node [dummy, left=-0.2cm of part1] (dummy1) {};} |
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| 308 | \uncover<1->{\node [dummy, below=1.25cm of dummy1] (dummy3) {};} |
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| 309 | \uncover<1->{\node [small, right=0.0cm of part1] (part2) {\quad \texttt{in}};} |
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| 310 | \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};} |
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| 311 | \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};} |
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[954] | 312 | \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};} |
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| 313 | \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};} |
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[945] | 314 | \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};} |
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| 315 | |
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| 316 | \uncover<2->{\node [boxbig, below=1.25cm of dummy2] (box1) {local filename in the working directory (must correspond to the filename in the \texttt{OPEN} statement of the program)};} |
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| 317 | \draw<2-> [->] (dummy3.north) -- (dummy1.south); |
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| 318 | |
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| 319 | \uncover<3->{\node [box, below=0.7cm of part2] (box2) {file attributes};} |
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| 320 | \draw<3-> [->] (box2.north) -- (part2.south); |
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| 321 | |
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| 322 | \uncover<4->{\node [box, below=0.2cm of part3] (box3) {activating string};} |
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| 323 | \draw<4-> [->] (box3.north) -- (part3.south); |
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| 324 | |
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| 325 | \uncover<5->{\node [box, below=0.2cm of part4] (box4) {directory in which the permanent user file resides};} |
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| 326 | \draw<5-> [->] (box4.north) -- (part4.south); |
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| 327 | |
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| 328 | \uncover<6->{\node [box, below=0.2cm of part5] (box5) {suffix of the permanent filename};} |
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| 329 | \draw<6-> [->] (box5.north) -- (part5.south); |
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| 330 | |
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| 331 | \uncover<7->{\node [box, below=1.0cm of part6] (box6) {additional suffix for netCDF files};} |
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| 332 | \draw<7-> [->] (box6.north) -- (part6.south); |
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| 333 | \end{tikzpicture} |
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| 334 | \end{center} |
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| 335 | |
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| 336 | \onslide<8->The full name of the permanent file results from the directory name, the suffix and the value of \texttt{mrun}-Option \texttt{-d}, which defines the so-called \textbf{base name} of all files handled by \texttt{mrun}:\\ |
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[954] | 337 | \quad \texttt{mrun -d \textcolor{blue}{example\underline{ }cbl} ...}\\ |
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[945] | 338 | gives the filename\\ |
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[954] | 339 | \quad \texttt{\~{}/palm/current\underline{ }version/JOB/INPUT/\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d}\\ |
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| 340 | \quad \texttt{( ... /\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d\textcolor{red}{.nc} )} |
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[945] | 341 | |
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| 342 | \end{frame} |
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| 343 | |
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| 344 | % Folie 8 |
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| 345 | \begin{frame} |
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| 346 | \frametitle{Steering File Copy by the Configuration File (II)} |
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| 347 | \scriptsize |
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| 348 | \onslide<1-> The \textbf{base name} can additionally be a part of the directory name |
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[954] | 349 | by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\ |
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| 350 | \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\ |
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[945] | 351 | \ \\ |
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| 352 | \onslide<2-> Using the call\\ |
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[954] | 353 | \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\ |
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[945] | 354 | the input file will be expected under\\ |
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[954] | 355 | \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\ |
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[945] | 356 | \ \\ |
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| 357 | \onslide<3-> In this way, all files handled by the \texttt{mrun}-call are stored in |
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[954] | 358 | the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as |
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| 359 | part of their names, so they can be easily identified as \grqq belonging\grqq\, to the model |
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[945] | 360 | run initiated by that \texttt{mrun} call.\\ |
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| 361 | \ \\ |
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| 362 | \onslide<4-> Instead of always writing the full path name (i.e. |
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[954] | 363 | \texttt{\~{}/palm/current\underline{ }version/JOBS}), an environment variable can be declared for |
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[945] | 364 | this at the beginning of the configuration file and be used in the file |
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| 365 | connection statements:\\ |
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[954] | 366 | \quad \texttt{\%base\underline{ }data \~{}/palm/current\underline{ }version/JOBS}\\ |
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| 367 | \quad \texttt{PARIN in d3\# \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\ |
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[945] | 368 | \ \\ |
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| 369 | \onslide<5-> This easily allows to change the directories for all input/output files |
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[954] | 370 | by just changing the value of \texttt{base\underline{ }data}. |
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[945] | 371 | |
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| 372 | \end{frame} |
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| 373 | |
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| 374 | % Folie 9 |
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| 375 | \begin{frame} |
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| 376 | \frametitle{Steering File Copy by the Configuration File (III)} |
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| 377 | \scriptsize |
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| 378 | \onslide<1-> File connection statements which shall be carried out, |
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| 379 | have to be activated by giving their activation string in the |
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| 380 | \texttt{mrun}-option \texttt{-r}:\\ |
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[954] | 381 | \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\ |
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[945] | 382 | \ \\ |
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| 383 | \onslide<2-> The permanent file |
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[954] | 384 | \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} |
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[945] | 385 | will only be copied to the local file PARIN by using the call:\\ |
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[954] | 386 | \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\ |
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[945] | 387 | \ \\ |
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| 388 | \onslide<3-> \textbf{Example for an output file:}\\ |
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| 389 | The file connection statement\\ |
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[954] | 390 | \quad \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF out:loc pr\# |
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| 391 | \~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}\\ |
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[945] | 392 | \onslide<4-> will copy (after program execution) the local file |
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[954] | 393 | \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file |
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| 394 | \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc} if |
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[945] | 395 | \texttt{mrun} is called with the options\\ |
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[954] | 396 | \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...} |
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[945] | 397 | |
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| 398 | \end{frame} |
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| 399 | |
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| 400 | % Folie 10 |
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| 401 | \begin{frame} |
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| 402 | \frametitle{Steering File Copy by the Configuration File (IV)} |
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| 403 | \scriptsize |
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| 404 | \onslide<1-> \texttt{mrun} never replaces/overwrites existing files!\\ |
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| 405 | \ \\ |
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| 406 | Instead, new, so-called file cycles are created.\\ |
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| 407 | If an output file, e.g.\\ |
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[954] | 408 | \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc}\\ |
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[945] | 409 | \ \\ |
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| 410 | has been created from a first call of \texttt{mrun} and if the same \texttt{mrun} |
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| 411 | call is submitted again, the second call will not replace the file |
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[954] | 412 | \texttt{example\underline{ }cbl\underline{ }rc}, but will create a new file with name:\\ |
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| 413 | \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc.1}\\ |
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[945] | 414 | \ \\ |
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| 415 | \onslide<2->In case of netCDF-files, the file cycle number is inserted before |
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| 416 | the netCDF-suffix .nc, e.g.\\ |
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[954] | 417 | \quad \texttt{example\underline{ }cbl\underline{ }pr.1.nc}\\ |
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[945] | 418 | \ \\ |
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| 419 | \onslide<3->The implemented file cycle mechanism does not allow to use |
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| 420 | any other dots "'."' in the path or filename:\\ |
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[954] | 421 | \quad \texttt{\~{}/palm/version\underline{ }3.6/JOBS/example.sbl/MONITORING/example.sbl\underline{ }rc} |
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[945] | 422 | \end{frame} |
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| 423 | |
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| 424 | % Folie 11 |
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| 425 | \begin{frame}[fragile] |
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| 426 | \frametitle{\normalsize File Connection Statements From the Default \texttt{.mrun.config} file} |
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| 427 | \begin{columns} |
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| 428 | \column{1.1\textwidth} |
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| 429 | \tiny |
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| 430 | \begin{lstlisting} |
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| 431 | #---------------------------------------------------------------------------- |
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| 432 | # List of input-files |
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| 433 | #---------------------------------------------------------------------------- |
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| 434 | PARIN in:job d3# $base_data/$fname/INPUT _p3d |
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| 435 | PARIN in:job d3f $base_data/$fname/INPUT _p3df |
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| 436 | TOPOGRAPHY_DATA in:locopt d3#:d3f $base_data/$fname/INPUT _topo |
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[954] | 437 | BININ in:loc:flpe d3f $base_data/$fname/RESTART _d3d |
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[945] | 438 | PARTICLE_RESTART_DATA_IN in:loc:flpe prtf $base_data/$fname/RESTART _rprt |
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| 439 | DATA_1D_PR_NETCDF in:locopt prf $base_data/$fname/OUTPUT _pr nc |
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| 440 | DATA_1D_SP_NETCDF in:locopt spf $base_data/$fname/OUTPUT _sp nc |
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| 441 | DATA_1D_TS_NETCDF in:locopt tsf $base_data/$fname/OUTPUT _ts nc |
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| 442 | DATA_1D_PTS_NETCDF in:locopt ptsf $base_data/$fname/OUTPUT _pts nc |
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| 443 | DATA_2D_XY_NETCDF in:locopt xyf $base_data/$fname/OUTPUT _xy nc |
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| 444 | DATA_2D_XY_AV_NETCDF in:locopt xyf $base_data/$fname/OUTPUT _xy_av nc |
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| 445 | DATA_2D_XZ_NETCDF in:locopt xzf $base_data/$fname/OUTPUT _xz nc |
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| 446 | DATA_2D_YZ_NETCDF in:locopt yzf $base_data/$fname/OUTPUT _yz nc |
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| 447 | DATA_3D_NETCDF in:locopt 3df $base_data/$fname/OUTPUT _3d nc |
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| 448 | DATA_PRT_NETCDF in:locopt:pe prtf $base_data/$fname/OUTPUT _prt |
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| 449 | # |
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| 450 | #---------------------------------------------------------------------------- |
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| 451 | # List of output-files |
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| 452 | #---------------------------------------------------------------------------- |
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| 453 | BINOUT out:loc:flpe restart $base_data/$fname/RESTART _d3d |
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| 454 | PARTICLE_RESTART_DATA_OUT out:loc:flpe prt#:prtf $base_data/$fname/RESTART _rprt |
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| 455 | # |
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| 456 | RUN_CONTROL out:loc:tr d3# $base_data/$fname/MONITORING _rc |
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| 457 | RUN_CONTROL out:loc:tra d3f $base_data/$fname/MONITORING _rc |
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| 458 | HEADER out:loc:tr d3# $base_data/$fname/MONITORING _header |
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| 459 | HEADER out:loc:tra d3f $base_data/$fname/MONITORING _header |
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| 460 | CPU_MEASURES out:loc:tr d3# $base_data/$fname/MONITORING _cpu |
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| 461 | CPU_MEASURES out:loc:tra d3f $base_data/$fname/MONITORING _cpu |
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| 462 | # |
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| 463 | DATA_1D_PR_NETCDF out:loc:tr pr#:prf $base_data/$fname/OUTPUT _pr nc |
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| 464 | DATA_1D_SP_NETCDF out:loc:tr sp#:spf $base_data/$fname/OUTPUT _sp nc |
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| 465 | DATA_1D_TS_NETCDF out:loc:tr ts#:tsf $base_data/$fname/OUTPUT _ts nc |
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| 466 | DATA_1D_PTS_NETCDF out:loc:tr pts#:ptsf $base_data/$fname/OUTPUT _pts nc |
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| 467 | DATA_2D_XY_NETCDF out:loc:tr xy#:xyf $base_data/$fname/OUTPUT _xy nc |
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| 468 | DATA_2D_XY_AV_NETCDF out:loc:tr xy#:xyf $base_data/$fname/OUTPUT _xy_av nc |
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| 469 | DATA_2D_XZ_NETCDF out:loc:tr xz#:xzf $base_data/$fname/OUTPUT _xz nc |
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| 470 | DATA_2D_XZ_AV_NETCDF out:loc:tr xz#:xzf $base_data/$fname/OUTPUT _xz_av nc |
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| 471 | DATA_2D_YZ_NETCDF out:loc:tr yz#:yzf $base_data/$fname/OUTPUT _yz nc |
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| 472 | DATA_2D_YZ_AV_NETCDF out:loc:tr yz#:yzf $base_data/$fname/OUTPUT _yz_av nc |
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| 473 | DATA_3D_NETCDF out:loc:tr 3d#:3df $base_data/$fname/OUTPUT _3d nc |
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| 474 | DATA_3D_AV_NETCDF out:loc:tr 3d#:3df $base_data/$fname/OUTPUT _3d_av nc |
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[954] | 475 | DATA_MASK_01_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m01 nc |
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| 476 | DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m01_av nc |
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| 477 | DATA_MASK_02_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m02 nc |
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| 478 | DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m02_av nc |
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| 479 | DATA_MASK_03_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m03 nc |
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| 480 | DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m03_av nc |
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| 481 | DATA_MASK_04_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m04 nc |
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| 482 | DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m04_av nc |
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| 483 | DATA_MASK_05_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m05 nc |
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| 484 | DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m05_av nc |
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| 485 | DATA_MASK_06_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m06 nc |
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| 486 | DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m06_av nc |
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| 487 | DATA_MASK_07_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m07 nc |
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| 488 | DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m07_av nc |
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| 489 | DATA_MASK_08_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m08 nc |
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| 490 | DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m08_av nc |
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| 491 | DATA_MASK_09_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m09 nc |
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| 492 | DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m09_av nc |
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| 493 | DATA_MASK_10_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m10 nc |
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| 494 | DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m10_av nc |
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| 495 | DATA_MASK_11_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m11 nc |
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| 496 | DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m11_av nc |
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| 497 | DATA_MASK_12_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m12 nc |
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| 498 | DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m12_av nc |
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| 499 | DATA_MASK_13_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m13 nc |
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| 500 | DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m13_av nc |
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| 501 | DATA_MASK_14_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m14 nc |
---|
| 502 | DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m14_av nc |
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| 503 | DATA_MASK_15_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m15 nc |
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| 504 | DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m15_av nc |
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| 505 | DATA_MASK_16_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m16 nc |
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| 506 | DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m16_av nc |
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| 507 | DATA_MASK_17_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m17 nc |
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| 508 | DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m17_av nc |
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| 509 | DATA_MASK_18_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m18 nc |
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| 510 | DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m18_av nc |
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| 511 | DATA_MASK_19_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m19 nc |
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| 512 | DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m19_av nc |
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| 513 | DATA_MASK_20_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m20 nc |
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| 514 | DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m20_av nc |
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[945] | 515 | DATA_PRT_NETCDF out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT _prt nc |
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[954] | 516 | DATA_DVR out:loc:trpe dvr $base_data/$fname/OUTPUT _dvr |
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[945] | 517 | # |
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| 518 | DVRP_LOG out:loc:tr dv# $base_data/$fname/MONITORING _dvrp_log |
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| 519 | DVRP_LOG out:loc:tra dvf $base_data/$fname/MONITORING _dvrp_log |
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| 520 | PARTICLE_INFO out:loc:tr pt# $base_data/$fname/MONITORING _prt_info |
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| 521 | PARTICLE_INFO out:loc:tra ptf $base_data/$fname/MONITORING _prt_info |
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| 522 | PARTICLE_DATA out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT _prt_dat |
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| 523 | |
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| 524 | \end{lstlisting} |
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| 525 | \end{columns} |
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| 526 | \end{frame} |
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| 527 | |
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| 528 | % Folie 12 |
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| 529 | \begin{frame} |
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| 530 | \frametitle{Additional Features of \texttt{mrun}} |
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| 531 | \begin{itemize} |
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| 532 | \footnotesize |
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| 533 | \item<1-> Generating batch jobs on local \textbf{and} remote host. |
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| 534 | \item<2-> Setting of unix environment variables for job and model control (e.g. for determining compiler options, etc.). |
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| 535 | \item<3-> Values have to be set in the \texttt{mrun} configuration file \texttt{.mrun.config}: |
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| 536 | \end{itemize} |
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| 537 | \onslide<4->\hspace{-1cm}\includegraphics[scale=0.3]{mrun_figures/add_feat1.png} |
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| 538 | \begin{itemize} |
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| 539 | \footnotesize |
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| 540 | \item<5-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands). |
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| 541 | These commands can also be defined in the \texttt{mrun} configuration file: |
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| 542 | \onslide<6-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png} |
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| 543 | \item<7-> Automatic generation of restart jobs. |
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| 544 | \end{itemize} |
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| 545 | \end{frame} |
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| 546 | |
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| 547 | % Folie 13 |
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| 548 | \begin{frame} |
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| 549 | \frametitle{PALM \textit{Interactive} Example Run Using \texttt{mrun}: Tracing the Run by the User} |
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[954] | 550 | \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm] |
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| 551 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm] |
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| 552 | \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.55\textwidth, font=\tiny, minimum height=0.6cm] |
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| 553 | \tikzstyle{notes} = [rectangle, text width=0.26\textwidth, font=\tiny, minimum height=0.6cm] |
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| 554 | \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny, minimum height=0.6cm] |
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[945] | 555 | \vspace{-1.0cm} |
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| 556 | \begin{center} |
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| 557 | \begin{tikzpicture}[auto, node distance=0] |
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[954] | 558 | \uncover<1->{\node [yellow] (box1) {\textbf{start run on local machine:}\\ |
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| 559 | \texttt{mrun -d example\underline{ }cbl -h lcmuk ...}};} |
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| 560 | \uncover<1->{\node [dummy, right=1.4cm of box1] (dummy1) {};} |
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| 561 | \uncover<2->{\node [notes, above=-0.3cm of dummy1] (notes1) {temporary working directory is created, all required files are copied there};} |
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| 562 | \uncover<3->{\node [green, right=1.4cm of dummy1] (box2) {\textbf{follow run messages on terminal}};} |
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| 563 | \uncover<4->{\node [green, below=0.5cm of box2] (box3) { |
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| 564 | \textbf{as soon as message} |
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[945] | 565 | |
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[1165] | 566 | \texttt{*** execution starts in directory\\ \quad \dq <tmpdir>\dq\, }\\ |
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[954] | 567 | \ \\ |
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| 568 | \textbf{you can change to this directory (in a new terminal) and watch the progess of timesteps} |
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[945] | 569 | |
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[1165] | 570 | \texttt{cd <tmpdir>}\\ |
---|
[954] | 571 | \texttt{tail -f RUN\underline{ }CONTROL}\\ |
---|
| 572 | \ \\ |
---|
[945] | 573 | However, this might be difficult in case of short run times, because the run may have finished before you have entered the commands! |
---|
| 574 | };} |
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[954] | 575 | \coordinate[below=0.3cm of box3] (A); |
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| 576 | \uncover<1->{\node [dummy, left=0.3cm of box3] (dummy2) {};} |
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| 577 | \uncover<5->{\node [notes, below=0.0cm of A, text width=0.35\textwidth] (notes2) {results are copied from temporary working directory to the userâs permanent directory};} |
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| 578 | \uncover<6->{\node [yellow_big, left=2.5cm of A] (box4) { |
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| 579 | \textbf{check, if the output files have sucessfully been transferred to the permanent directory:}\\ |
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| 580 | \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING}\\ |
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[945] | 581 | \texttt{ls -al}\\ |
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[954] | 582 | \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT}\\ |
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[945] | 583 | \texttt{ls -al} |
---|
| 584 | };} |
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[954] | 585 | \draw<2-> [->,color=blue] (box1.east) -- (box2.west); |
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| 586 | \draw<4-> [->,color=blue] (box2.south) -- (box3.north); |
---|
| 587 | \draw<5-> [-,color=blue] (box3.south) -- (A); |
---|
| 588 | \draw<5-> [->,color=blue] (A) -- (box4.east); |
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[945] | 589 | \end{tikzpicture} |
---|
| 590 | \end{center} |
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| 591 | \end{frame} |
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| 592 | |
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| 593 | % Folie 14 |
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| 594 | \begin{frame} |
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| 595 | \frametitle{PALM \textit{Batch} Example Run (on HLRN, remote) Using \texttt{mrun}: Tracing the Run by the User} |
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| 596 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, font=\Tiny] |
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| 597 | \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.4\textwidth, font=\Tiny] |
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| 598 | \tikzstyle{dummy} = [text width=0.2\textwidth, font=\Tiny] |
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| 599 | \tikzstyle{alert} = [rectangle, draw, text width=0.5\textwidth, font=\scriptsize] |
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| 600 | \tikzstyle{line} = [draw, -latex'] |
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| 601 | \begin{itemize} |
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[954] | 602 | \item Reminder: Running batch jobs requires a directory \texttt{~/job\underline{ }queue} for the job protocol files on the local \underline{and} remote host. |
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[945] | 603 | \end{itemize} |
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| 604 | \begin{tikzpicture}[auto, node distance=0] |
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| 605 | \node [yellow] (first) { |
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| 606 | \textbf{start job on local machine:}\\ |
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[954] | 607 | \texttt{mrun -d example\underline{ }cbl -h lcsgih ...} |
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[945] | 608 | }; |
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| 609 | \uncover<2->{ |
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| 610 | \node [dummy, right=0.5cm of first] (dummy) { |
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| 611 | transfer of job by \texttt{scp} \\ |
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| 612 | \ \\ |
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| 613 | \ \\ |
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| 614 | submit of job by executing the \texttt{msub} command via \texttt{ssh} |
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| 615 | }; |
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| 616 | } |
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| 617 | \uncover<3->{ |
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| 618 | \node [green, right=3.5cm of first] (second) { |
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| 619 | \textbf{follow job execution on remote host, by} \\ |
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| 620 | \texttt{showq} (better: \texttt{showq | grep hzkurs}) |
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| 621 | }; |
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| 622 | } |
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| 623 | \uncover<4->{ |
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| 624 | \node [green, below=0.2cm of second] (third) { |
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| 625 | \textbf{if job is running, you may follow its progress by watching the job protocol:} \\ |
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[964] | 626 | \texttt{cd \~/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl} |
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[945] | 627 | }; |
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| 628 | } |
---|
| 629 | \uncover<5->{ |
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| 630 | \node [green, below=0.2cm of third] (fourth) { |
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[954] | 631 | \textbf{when job is running, change to directory \texttt{<tmp\underline{ }usr\underline{ }catalog>} and try to find there the latest directory \texttt{<HLRN-username>.<randomnumber>} \\ change to this directory and execute}\\ |
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| 632 | \texttt{tail -f RUN\underline{ }CONTROL} |
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[945] | 633 | }; |
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| 634 | } |
---|
| 635 | \uncover<6->{ |
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| 636 | \node [green, below=0.2cm of fourth] (fifth) { |
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| 637 | \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\ |
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[964] | 638 | \texttt{cd \~/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol} |
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[945] | 639 | }; |
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| 640 | } |
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| 641 | \uncover<7->{ |
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| 642 | \node [dummy, left=0.5cm of fifth] (dummy) { |
---|
| 643 | transfer results by \texttt{scp} \\ |
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| 644 | \ \\ |
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| 645 | \ \\ |
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| 646 | }; |
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| 647 | } |
---|
| 648 | \uncover<8->{ |
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| 649 | \node [yellow, left=3.5cm of fifth] (sixth) { |
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| 650 | \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\ |
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[964] | 651 | \texttt{cd \~/job\underline{ }queue \\ ls -al \\ cd ~/palm/current\underline{ }version/JOBS/example \\ ls -al *} |
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[945] | 652 | }; |
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| 653 | } |
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| 654 | \uncover<9->{ |
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| 655 | \node [alert, below=0.5cm of first.south east] (alert) { |
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[954] | 656 | \textcolor{red}{Attention: Commands for submitting jobs and the behaviour of job protocol files are depending on the queueing system! Manual adjustments may be required in the mrun and subjob script!} |
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[945] | 657 | }; |
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| 658 | } |
---|
| 659 | \path<2-> [line] (first) -- (second); |
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| 660 | \path<4-> [line] (second) -- (third); |
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| 661 | \path<5-> [line] (third) -- (fourth); |
---|
| 662 | \path<6-> [line] (fourth) -- (fifth); |
---|
| 663 | \path<7-> [line] (fifth) -- (sixth); |
---|
| 664 | \end{tikzpicture} |
---|
| 665 | \end{frame} |
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| 666 | |
---|
| 667 | |
---|
| 668 | |
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| 669 | % Folie 15 |
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| 670 | \begin{frame} |
---|
| 671 | \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm] |
---|
| 672 | \tikzstyle{green_small} = [rectangle, draw, fill=green!20, text width=0.12\textwidth, font=\scriptsize, minimum height=0.6cm] |
---|
| 673 | \tikzstyle{yellow_small} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\scriptsize, minimum height=0.6cm] |
---|
| 674 | \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm] |
---|
| 675 | \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm] |
---|
| 676 | \tikzstyle{notes} = [rectangle, text width=0.15\textwidth, font=\scriptsize, minimum height=0.6cm] |
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| 677 | |
---|
| 678 | \frametitle{PALM Runs Using \texttt{mrun}: Further Details} |
---|
| 679 | \begin{itemize} |
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| 680 | \footnotesize |
---|
| 681 | \item<2-> For every (initial) run, \texttt{mrun} creates a source directory which contains copies of |
---|
| 682 | \begin{itemize} |
---|
| 683 | \footnotesize |
---|
| 684 | \item<4-> those source code files to be translated (always the main program, \texttt{palm.f90}, plus user interface files) |
---|
| 685 | \item<4-> the Makefile |
---|
| 686 | \item<5-> the configuration file |
---|
| 687 | \item<6-> the mrun script |
---|
| 688 | \end{itemize} |
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| 689 | \end{itemize} |
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| 690 | |
---|
| 691 | \vspace{-0.8cm} |
---|
| 692 | \begin{center} |
---|
| 693 | \begin{tikzpicture}[auto, node distance=0] |
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| 694 | |
---|
| 695 | \uncover<3->{\node [yellow_small] (box1) {\$HOME/};} |
---|
| 696 | \uncover<3->{\node [yellow_small, right=0.2cm of box1] (box2) {palm/};} |
---|
[954] | 697 | \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\underline{ }version/};} |
---|
[945] | 698 | \uncover<3->{\node [green_small, right=0.4cm of box3] (box4) {trunk/};} |
---|
| 699 | |
---|
| 700 | \uncover<1->{\node [dummy, right=1.0cm of box4] (dummy1) {};} |
---|
| 701 | |
---|
| 702 | \uncover<3->{\node [green_small, above=-0.2cm of dummy1] (box5) {SCRIPTS};} |
---|
| 703 | \uncover<3->{\node [green_small, below=-0.2cm of dummy1] (box6) {SOURCE};} |
---|
| 704 | |
---|
| 705 | \uncover<6->{\node [notes, right=0.1cm of box5] (notes1) {\texttt{mrun}};} |
---|
| 706 | \uncover<4->{\node [notes, right=0.1cm of box6] (notes2) {\texttt{Makefile \\ palm.f90}};} |
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| 707 | \uncover<5->{\node [notes, below=0.1cm of box3] (notes3) {\texttt{.mrun.config}};} |
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| 708 | |
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[954] | 709 | \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\underline{ }FOR\underline{ }RUN\underline{ }$<$run\underline{ }identifier$>$};} |
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[945] | 710 | |
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| 711 | \uncover<1->{\node [dummy, left=1.5cm of box7] (dummy2) {};} |
---|
| 712 | \uncover<1->{\node [dummy, right=2.0cm of box5] (dummy3) {};} |
---|
| 713 | \uncover<1->{\node [dummy, right=1.8cm of box6] (dummy4) {};} |
---|
| 714 | \uncover<1->{\node [dummy, below=0.2cm of dummy4] (dummy5) {};} |
---|
| 715 | \draw<3-> [-] (box1.east) -- (box2.west); |
---|
| 716 | \draw<3-> [-] (box2.east) -- (box3.west); |
---|
| 717 | \draw<3-> [-] (box3.east) -- (box4.west); |
---|
| 718 | \draw<3-> [-] (box4.east) -- (box5.west); |
---|
| 719 | \draw<3-> [-] (box4.east) -- (box6.west); |
---|
| 720 | \draw<3-> [-] (box3.east) -- (box7.west); |
---|
| 721 | \draw<6-> [-] ([xshift=-0.8cm]notes1.east) -- (dummy3.center); |
---|
| 722 | \draw<4-> [-] ([xshift=-0.4cm]notes2.east) -- (dummy4.center); |
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| 723 | \draw<4-> [-] (dummy4.center) -- ([yshift=0.1cm]dummy5.center); |
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| 724 | \draw<4-> [->] ([yshift=0.1cm]dummy5.center) -- ([yshift=0.1cm]box7.east); |
---|
| 725 | \draw<6-> [-] (dummy3.center) -- ([xshift=0.2cm, yshift=-0.1cm]dummy5.center); |
---|
| 726 | \draw<6-> [->] ([xshift=0.2cm, yshift=-0.1cm]dummy5.center) -- ([yshift=-0.1cm]box7.east); |
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| 727 | \draw<5-> [-] ([yshift=0.3cm]dummy2.center) -- (dummy2.center); |
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| 728 | \draw<5-> [->] (dummy2.center) -- (box7.west); |
---|
| 729 | \end{tikzpicture} |
---|
| 730 | \end{center} |
---|
| 731 | |
---|
| 732 | \begin{itemize} |
---|
| 733 | \footnotesize |
---|
| 734 | \item<7-> These files are used in the run/job. They are also used by restart jobs, which guarantees, that all jobs in a job chain are using the same information. Please never modify these directories, unless you exactly know, what you are doing. |
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| 735 | \end{itemize} |
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| 736 | \end{frame} |
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| 737 | |
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| 738 | \end{document} |
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