| 1 | % $Id: program_control.tex 1515 2015-01-02 11:35:51Z gronemeier $ |
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| 2 | \input{header_tmp.tex} |
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| 3 | %\input{header_LECTURE.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 | \usepackage{subfigure} |
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| 9 | \usepackage{units} |
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| 10 | \usepackage{multimedia} |
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| 11 | \usepackage{hyperref} |
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| 12 | \newcommand{\event}[1]{\newcommand{\eventname}{#1}} |
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| 13 | \usepackage{xmpmulti} |
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| 14 | \usepackage{tikz} |
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| 15 | \usetikzlibrary{shapes,arrows,positioning,decorations.pathreplacing} |
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| 16 | \def\Tiny{\fontsize{4pt}{4pt}\selectfont} |
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| 17 | \def\Tinytwo{\fontsize{3pt}{3pt}\selectfont} |
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| 18 | |
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| 19 | %---------- neue Pakete |
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| 20 | \usepackage{amsmath} |
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| 21 | \usepackage{amssymb} |
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| 22 | \usepackage{multicol} |
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| 23 | \usepackage{pdfcomment} |
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| 24 | \usepackage{listings} |
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| 25 | \lstset{showspaces=false,language=fortran,basicstyle= |
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| 26 | \ttfamily,showstringspaces=false, captionpos=b,aboveskip=0pt,belowskip=0pt} |
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| 27 | |
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| 28 | \institute{Institute of Meteorology and Climatology, Leibniz UniversitÀt Hannover} |
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| 29 | \selectlanguage{english} |
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| 30 | \date{last update: \today} |
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| 31 | \event{PALM Seminar} |
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| 32 | \setbeamertemplate{navigation symbols}{} |
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| 33 | |
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| 34 | \setbeamertemplate{footline} |
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| 35 | {% |
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| 36 | \begin{beamercolorbox}[rightskip=-0.1cm]& |
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| 37 | {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}} |
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| 38 | \end{beamercolorbox} |
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| 39 | \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,% |
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| 40 | leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}% |
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| 41 | {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}% |
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| 42 | \end{beamercolorbox}% |
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| 43 | % \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}% |
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| 44 | % \end{beamercolorbox} |
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| 45 | }%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.eps}} |
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| 46 | |
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| 47 | \title[Program Control by Physical Parameters]{Program Control by Physical Parameters} |
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| 48 | \author{PALM group} |
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| 49 | |
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| 50 | % Notes: |
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| 51 | % jede subsection bekommt einen punkt im menu (vertikal ausgerichtet. |
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| 52 | % jeder frame in einer subsection bekommt einen punkt (horizontal ausgerichtet) |
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| 53 | \begin{document} |
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| 54 | % Folie 1 |
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| 55 | \begin{frame} |
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| 56 | \titlepage |
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| 57 | \end{frame} |
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| 58 | |
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| 59 | \section{Program Control by Physical Parameters} |
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| 60 | \subsection{Program Control by Physical Parameters} |
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| 61 | |
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| 62 | % Folie 2 |
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| 63 | \begin{frame} |
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| 64 | \frametitle{Steering of PALM and Interpreting the Output} |
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| 65 | \begin{itemize} |
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| 66 | \item<1->{This section section describes how to steer the model and how to interpret the model output (\textbf{it does not explain, how to start and control model runs}).} |
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| 67 | \item<2->{It gives a general overview of the input and output files and explaines the contents of the most important files in some detail.} |
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| 68 | \end{itemize} |
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| 69 | \end{frame} |
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| 70 | |
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| 71 | % Folie 3 |
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| 72 | \begin{frame} |
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| 73 | \frametitle{PALM Input/Output Overview (I)} |
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| 74 | \tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small] |
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| 75 | \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny] |
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| 76 | \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny] |
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| 77 | \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny] |
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| 78 | \tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny] |
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| 79 | \tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny] |
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| 80 | \tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny] |
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| 81 | \tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny] |
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| 82 | \tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny] |
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| 83 | |
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| 84 | \tikzstyle{line} = [draw, -latex'] |
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| 85 | |
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| 86 | \begin{tikzpicture} [auto] |
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| 87 | \node[start] (palm) {\textbf{PALM}}; |
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| 88 | |
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| 89 | \uncover<2->{\node[yellow1] (parameterfile) [above left=1.5cm of palm] {parameter file \\ for steering};} |
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| 90 | \uncover<6->{\node[red] (restartdata1) [above right=1.8cm of palm] {restart data};} |
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| 91 | \uncover<5->{\node[red] (restartdata2) [below=4.5cm of restartdata1] {restart data};} |
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| 92 | |
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| 93 | \uncover<4->{ |
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| 94 | \node[orange1] (timeseries) [below left=4.4cm of palm] {time series}; |
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| 95 | \node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged}; |
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| 96 | \node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged}; |
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| 97 | |
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| 98 | \path<4->[line] (palm) -- (timeseries); |
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| 99 | \path<4->[line] (palm) -- (2dsectionstime); |
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| 100 | \path<4->[line] (palm) -- (3ddatatime); |
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| 101 | |
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| 102 | \node[orange1] (1dmean) [above=0.2cm of timeseries] {1D mean \\ profiles}; |
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| 103 | \node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections}; |
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| 104 | \node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data};} |
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| 105 | |
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| 106 | \path<4->[line] (palm) -- (1dmean); |
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| 107 | \path<4->[line] (palm) -- (2dsections); |
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| 108 | \path<4->[line] (palm) -- (3ddata); |
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| 109 | |
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| 110 | \uncover<3->{\node[yellow2] (headerfile) [above=0.5cm of 2dsections]{header file};} |
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| 111 | \uncover<3->{\node[yellow1] (runcontrol) [right=0.5cm of headerfile]{run control output\\ (parameter settings + \\ timestep informations)};} |
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| 112 | \uncover<3->{\node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements};} |
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| 113 | |
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| 114 | \node (program) [right=2.8cm of palm] {program}; |
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| 115 | \uncover<2->{\node (steeringdata) [right=0.45cm of restartdata1] {steering data};} |
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| 116 | \uncover<3->{\node (run) [right=2.7cm of runcontrol] {run informations};} |
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| 117 | \uncover<4->{\node (analysis) [right=3.8cm of 3ddata] {analysis data};} |
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| 118 | |
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| 119 | \uncover<7->{ |
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| 120 | \node[yellow3] (yellow) [below=0.5 of timeseries] {}; |
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| 121 | \node (ascii) [right=0.1cm of yellow] {ASCII}; |
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| 122 | \node[orange3] (orange) [right=0.4cm of ascii] {}; |
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| 123 | \node (netcdf) [right=0.1cm of orange] {netCDF}; |
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| 124 | \node[red2] (red) [right=0.4cm of netcdf] {}; |
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| 125 | \node (binary) [right=0.1cm of red] {binary};} |
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| 126 | |
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| 127 | \path<2->[line] (parameterfile) -- (palm); |
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| 128 | \path<3->[line] (palm) -- (cpumeasure); |
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| 129 | \path<3->[line] (palm) -- (headerfile); |
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| 130 | \path<3->[line] (palm) -- (runcontrol); |
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| 131 | \path<5->[line] (palm) -- (restartdata2); |
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| 132 | \path<6->[line] (restartdata1) -- (palm); |
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| 133 | \path<6->[line,dashed] (restartdata2) -- (restartdata1); |
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| 134 | \end{tikzpicture} |
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| 135 | \end{frame} |
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| 136 | |
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| 137 | % Folie 4 |
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| 138 | \begin{frame} |
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| 139 | \frametitle{PALM Input/Output Overview (II)} |
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| 140 | \tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small] |
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| 141 | \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny] |
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| 142 | \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny] |
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| 143 | \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny] |
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| 144 | \tikzstyle{yellow4} = [rectangle, draw, fill=yellow!100, text width=1.8cm, font=\Tiny] |
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| 145 | \tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny] |
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| 146 | \tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny] |
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| 147 | \tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny] |
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| 148 | \tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny] |
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| 149 | \tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny] |
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| 150 | |
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| 151 | \tikzstyle{line} = [draw, -] |
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| 152 | |
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| 153 | \begin{tikzpicture} [auto] |
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| 154 | \node[start] (palm) {\textbf{PALM}}; |
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| 155 | |
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| 156 | \node[yellow1] (parameterfile) [above left=1cm of palm] {parameter file \\ for steering}; |
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| 157 | \node[red] (restartdata1) [above right=1.3cm of palm] {restart data}; |
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| 158 | \node[red] (restartdata2) [below=2.5cm of restartdata1] {restart data}; |
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| 159 | |
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| 160 | \node[yellow1] (runcontrol) [below=0.4cm of palm]{run control output\\ (parameter settings + \\ timestep informations)}; |
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| 161 | \node[yellow2] (headerfile) [left=0.5cm of runcontrol]{header file}; |
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| 162 | \node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements}; |
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| 163 | |
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| 164 | \node[orange1] (1dmean) [below=0.3cm of cpumeasure] {1D mean \\ profiles}; |
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| 165 | \node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections}; |
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| 166 | \node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data}; |
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| 167 | |
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| 168 | \node[orange1] (timeseries) [below=0.2cm of 1dmean] {time series}; |
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| 169 | \node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged}; |
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| 170 | \node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged}; |
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| 171 | |
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| 172 | \node (program) [right=2.8cm of palm] {program}; |
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| 173 | \node (steeringdata) [right=0.8cm of restartdata1] {steering data}; |
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| 174 | \node (run) [right=2.5cm of runcontrol] {run informations}; |
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| 175 | \node (analysis) [right=3.6cm of 3ddata] {analysis data}; |
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| 176 | |
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| 177 | \node[yellow3] (yellow) [below=0.3 of timeseries] {}; |
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| 178 | \node (ascii) [right=0.1cm of yellow] {ASCII}; |
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| 179 | \node[orange3] (orange) [right=0.4cm of ascii] {}; |
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| 180 | \node (netcdf) [right=0.1cm of orange] {netCDF}; |
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| 181 | \node[red2] (red) [right=0.4cm of netcdf] {}; |
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| 182 | \node (binary) [right=0.1cm of red] {binary}; |
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| 183 | |
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| 184 | %--------- neue Ordner |
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| 185 | \uncover<2->{ |
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| 186 | \node[yellow4] (currentversion) [above=0.6cm of parameterfile] {current\_version/}; |
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| 187 | \node[yellow4] (jobs) [right=0.3cm of currentversion] {JOBS/}; |
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| 188 | \node[yellow4] (runidentifier) [right=0.4cm of jobs] {\textless run\_identifier \textgreater/}; |
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| 189 | \node[yellow4] (input) [above right=1cm of runidentifier] {INPUT/}; |
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| 190 | \node[yellow4] (monitoring) [below=0.1cm of input] {MONITORING/}; |
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| 191 | \node[yellow4] (output) [below=0.1cm of monitoring] {OUTPUT/}; |
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| 192 | \node[yellow4] (restart) [below=0.1cm of output] {RESTART\_DATA/};} |
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| 193 | |
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| 194 | \uncover<3->{\node[yellow4] (input2) [below=0.1cm of parameterfile] {INPUT/};} |
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| 195 | \uncover<4->{\node[yellow4] (monitoring2) [above=0.6cm of headerfile] {MONITORING/};} |
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| 196 | \uncover<6->{\node[yellow4] (restart2) [below=0.1cm of restartdata1] {RESTART\_DATA/};} |
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| 197 | \uncover<7->{\node[yellow4] (tmpdata) [below=0.1cm of restart2] {/tmp\_data\_catalog/};} |
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| 198 | \uncover<5->{\node[yellow4] (output2) [below=0.5cm of restartdata2] {OUTPUT/};} |
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| 199 | |
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| 200 | \path[line]<2-> (currentversion) -- (jobs); |
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| 201 | \path[line]<2-> (jobs) -- (runidentifier); |
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| 202 | \path[line]<2-> (runidentifier.east) -- (input.west); |
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| 203 | \path[line]<2-> (runidentifier.east) -- (monitoring.west); |
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| 204 | \path[line]<2-> (runidentifier.east) -- (output.west); |
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| 205 | \path[line]<2-> (runidentifier.east) -- (restart.west); |
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| 206 | |
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| 207 | \draw<4->[decorate,decoration={brace,raise=6pt,amplitude=9pt},thick] |
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| 208 | (-4.5,-0.95)--(-1,-0.95) ; |
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| 209 | \draw<5->[decorate,decoration={brace,mirror,raise=5pt,amplitude=6pt},thick] |
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| 210 | (0.45,-3)--(0.45,-1.9) ; |
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| 211 | \end{tikzpicture} |
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| 212 | \end{frame} |
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| 213 | |
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| 214 | % Folie 5 |
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| 215 | \begin{frame} |
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| 216 | \frametitle{The Parameter File} |
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| 217 | \tikzstyle{box} = [rectangle, draw, text width=0.9\textwidth, font=\tiny] |
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| 218 | \tikzstyle{line} = [draw, thick, -latex'] |
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| 219 | \footnotesize |
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| 220 | \begin{itemize} |
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| 221 | \item<1->{Physical and numerical features of a PALM run (e.g. initial and boundary conditions, numerical methods) |
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| 222 | are controlled by a so called \textbf{parameter file} which uses FORTRAN-NAMELIST syntax.} |
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| 223 | \item<2->{General structure of a FORTRAN-NAMELIST file} |
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| 224 | \end{itemize} |
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| 225 | \begin{tikzpicture}[auto] |
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| 226 | \uncover<3->{ |
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| 227 | \node[box](firstbox){ \begin{tabbing} |
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| 228 | \quad \&abcd \quad \=no\_of\_eggs = 100, litres\_of\_milk = 50.0, \= \\ |
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| 229 | \>kilos\_of\_butter = 20.0, \> / \end{tabbing}}; |
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| 230 | \node[font=\tiny] (leading_blank) at (-5,0.8) {\textbf{leading blank}}; |
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| 231 | \node[font=\tiny] (namelist) at (-2,0.8) {\textbf{NAMELIST group}}; |
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| 232 | \node[font=\tiny] (terminating) at (3,0.8) {\textbf{terminating character}}; |
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| 233 | \path[line] (-5,0.7) -- (-4.8,0); |
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| 234 | \path[line] (-2,0.7) -- (-4,0); |
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| 235 | \path[line] (3,0.7) -- (0.2,-0.3);} |
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| 236 | \end{tikzpicture} |
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| 237 | \begin{itemize} |
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| 238 | \item<4->{This file can be read from a FORTRAN program in the following way:} |
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| 239 | \end{itemize} |
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| 240 | \begin{tikzpicture}[auto, node distance=0] |
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| 241 | \uncover<4->{ |
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| 242 | \node[box](secondbox){ \begin{tabbing} |
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| 243 | INTEGER :: \=no\_of\_eggs = 30 \\ |
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| 244 | REAL :: \> litres\_of\_milk = 0.0, kilos\_of\_butter, kilos\_of\_cream = 33.0 \\ |
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| 245 | \\ |
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| 246 | NAMELIST /abcd/ \quad no\_of\_eggs, litres\_of\_milk, kilos\_of\_butter, kilos\_of\_cream \\ |
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| 247 | \\ |
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| 248 | OPEN ( 1, FILE='Filename' ) \\ |
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| 249 | \\ |
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| 250 | READ ( 1, abcd ) \end{tabbing}};} |
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| 251 | \end{tikzpicture} |
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| 252 | \normalsize |
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| 253 | \end{frame} |
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| 254 | |
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| 255 | % Folie 6 |
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| 256 | \begin{frame} |
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| 257 | \frametitle{An Example of PALM - NAMELIST Input} |
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| 258 | \tikzstyle{box} = [rectangle, draw, text width=\textwidth, font=\tiny] |
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| 259 | \begin{tikzpicture}[auto, node distance=0] |
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| 260 | \node[box](box){ \begin{tabbing} |
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| 261 | \&inipar \=nx = 39, ny = 39, nz = 40, \\ |
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| 262 | \>dx = 50.0, dy = 50.0, dz = 50.0, \\ |
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| 263 | \\ |
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| 264 | \>initializing\_actions = 'set\_constant\_profiles', \\ |
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| 265 | \>ug\_surface = 0.0, vg\_surface = 0.0, \\ |
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| 266 | \\ |
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| 267 | \>pt\_vertical\_gradient \qquad = 0.0, 1.0, \\ |
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| 268 | \>pt\_vertical\_gradient\_level = 0.0, 800.0, \\ |
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| 269 | \\ |
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| 270 | \>surface\_heatflux = 0.1, bc\_pt\_b ='neumann', / \\ |
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| 271 | \\ |
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| 272 | \\ |
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| 273 | \&d3par \>end\_time = 3600.0, \\ |
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| 274 | \\ |
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| 275 | \>dt\_dopr = 900.0, averaging\_interval\_pr = 600.0, \\ |
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| 276 | \>data\_output\_pr = 'pt', 'u', 'v', / \\ \end{tabbing}}; |
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| 277 | \end{tikzpicture} |
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| 278 | \footnotesize |
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| 279 | \vspace{-3mm} |
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| 280 | \begin{itemize} |
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| 281 | \item<2->{There are two NAMELIST groups ({\tt \&inipar} and {\tt \&d3par}).} |
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| 282 | \item<3->{Assignments to parameters in {\tt\&inipar} are ignored within restart runs \\ |
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| 283 | (exception: {\tt initializing\_actions} = {\tt'read\_restart\_data'} is obligatory for restart runs).} |
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| 284 | \item<4->{Values of {\tt \&d3par} parameters can be changed for restart runs.} |
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| 285 | \end{itemize} |
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| 286 | \end{frame} |
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| 287 | |
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| 288 | % Folie 7 |
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| 289 | \begin{frame}[fragile] |
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| 290 | \tikzstyle{green} = [rectangle, draw, fill=green!30, text width=2.1\textwidth, font=\Tinytwo] |
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| 291 | \frametitle{The Run Control File} |
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| 292 | \scriptsize |
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| 293 | \begin{itemize} |
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| 294 | \item<1->{For initial runs, the parameter settings and many additional informations about the run (header informations) are printed at the beginning of this file.} |
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| 295 | \item<2->{The parameter settings are followed by values of specific model variables for certain timesteps (one line for each timestep, the output intervall can be |
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| 296 | controlled by run parameter {\tt dt\_run\_control}).} |
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| 297 | \end{itemize} |
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| 298 | \onslide<3->{\textbf{Contents of this timestep output should be carefully checked after each run, because it allows a first control, if the model had run correctly, or if any |
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| 299 | errors have occurred!}} |
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| 300 | \par\bigskip |
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| 301 | \begin{tikzpicture}[scale=0.51, every node/.style={scale=0.51}] |
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| 302 | \node [green]{\begin{lstlisting} |
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| 303 | ****************************** ------------------------------------------ |
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| 304 | * PALM 3.10 Rev: 1443 * atmosphere - 3D - run without 1D - prerun |
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| 305 | ****************************** ------------------------------------------ |
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| 306 | |
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| 307 | Date: 30-07-14 Run: example_cbl |
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| 308 | Time: 14:41:23 Run-No.: 00 |
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| 309 | Run on host: lccrayh |
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| 310 | Number of PEs: 8 Processor grid (x,y): ( 2, 4) calculated |
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| 311 | ------------------------------------------------------------------------------ |
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| 312 | . |
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| 313 | . |
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| 314 | . |
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| 315 | Run-control output: |
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| 316 | ------------------ |
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| 317 | |
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| 318 | RUN ITER. HH:MM:SS.SS DT(E) UMAX VMAX WMAX U* W* THETA* Z_I ENERG. DISTENERG DIVOLD DIVNEW UMAX(KJI) VMAX(KJI) WMAX(KJI) ADVECX ADVECY MGCYC |
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| 319 | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| 320 | 0 0 00:00:00.00 20.0000A -0.2192D -0.2169D -0.1214 0.000 1.38 0.000E+00 800. 0.106E-02 0.000E+00 0.000E+00 0.000E+00 11 32 5 5 37 29 4 26 0 0.000 0.000 0 |
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| 321 | 0 1 00:00:20.00 20.0000A -0.2192 -0.2169 -0.1214 0.001 0.69 -0.124E+03 100. 0.105E-02 0.948E-03 0.491E-05 0.355E-15 11 32 5 5 37 29 4 26 0 0.000 0.000 0 |
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| 322 | 0 2 00:00:40.00 20.0000D -0.2151 -0.2176 -0.1209 0.001 0.69 -0.125E+03 100. 0.104E-02 0.940E-03 0.802E-05 0.359E-15 11 32 5 5 37 29 4 26 0 0.000 0.000 0 |
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| 323 | . |
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| 324 | . |
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| 325 | |
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| 326 | \end{lstlisting} |
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| 327 | }; |
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| 328 | \end{tikzpicture} |
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| 329 | \end{frame} |
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| 330 | |
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| 331 | % Folie 8 |
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| 332 | \begin{frame}[fragile] |
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| 333 | \tikzstyle{green} = [rectangle, draw, fill=green!30, text width=0.9\textwidth, font=\Tiny] |
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| 334 | \frametitle{The Header File} |
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| 335 | \scriptsize |
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| 336 | \begin{itemize} |
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| 337 | \item{The header file contains nearly the same informations as the header of the run control file of the initial run.} |
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| 338 | \item<2->{It is generated for \textbf{every} run (initial run as well as restart runs).} |
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| 339 | \item<3->{It is created at the beginning \textbf{and} at the end of a run (overwrites the file created at beginning).} |
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| 340 | \item<4->{Only at the end, cpu time information is included!} |
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| 341 | \end{itemize} |
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| 342 | \begin{center} |
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| 343 | \begin{tikzpicture}[scale=1, every node/.style={scale=1}] |
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| 344 | \node [green]{\begin{lstlisting} |
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| 345 | . |
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| 346 | . |
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| 347 | . |
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| 348 | Run time and time step information: |
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| 349 | ---------------------------------- |
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| 350 | |
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| 351 | Timestep: variable maximum value: 20.000 s CFL-factor: 0.90 |
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| 352 | Start time: 0.000 s |
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| 353 | End time: 3600.000 s |
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| 354 | |
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| 355 | Time reached: 3601.930 s |
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| 356 | CPU-time used: 4.391 s per timestep: 0.017 s |
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| 357 | per second of simulated time: 0.001 s |
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| 358 | |
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| 359 | |
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| 360 | Computational grid and domain size: |
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| 361 | ---------------------------------- |
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| 362 | |
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| 363 | Grid length: dx = 50.000 m dy = 50.000 m dz = 50.000 m |
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| 364 | . |
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| 365 | . |
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| 366 | . |
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| 367 | \end{lstlisting} |
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| 368 | }; |
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| 369 | \end{tikzpicture} |
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| 370 | \end{center} |
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| 371 | \normalsize |
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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}[fragile] |
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| 376 | \tikzstyle{green} = [rectangle, draw, fill=green!30, text width=1.4\textwidth, font=\Tiny] |
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| 377 | \frametitle{CPU Measurements File} |
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| 378 | \begin{columns}[c] |
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| 379 | \column{0.42\textwidth} |
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| 380 | \scriptsize |
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| 381 | \begin{itemize} |
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| 382 | \item{Contains informations about the CPU requirements of single parts of the program.} |
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| 383 | \item<2->{It should be inspected regularly in order to find out, if the code is still well optimized (e.g. load balance).} |
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| 384 | \item<3->{Prognostic-equations and pressure solver ({\tt pres}) should be the main consumer.} |
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| 385 | \item<4->{For larger grids ($1024^3$ points), {\tt pres} may need up to 50\% of the total time or more.} |
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| 386 | \item<5->{Time needed for communication (sum of {\tt exchange\_horiz}({\tt \_2d}) and {\tt mpi\_alltoall}) should not exceed about 10-15\% of the total time.} |
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| 387 | \end{itemize} |
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| 388 | \normalsize |
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| 389 | \column{0.58\textwidth} |
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| 390 | \vspace{-5mm} |
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| 391 | \begin{tikzpicture}[scale=0.75, every node/.style={scale=0.75}] |
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| 392 | \node [green]{\begin{lstlisting} |
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| 393 | PALM 3.10 Rev: 1443 run: example_cbl.00 host: lccrayh 30-07-14 14:41:23 |
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| 394 | ----------- |
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| 395 | |
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| 396 | CPU measures for 8 PEs ( 2(x) * 4(y) tasks * 1 threads): |
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| 397 | |
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| 398 | gridpoints (x/y/z): 40 * 40 * 40 |
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| 399 | nr of timesteps: 253 |
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| 400 | cpu time per grid point and timestep: 0.27546 * 10**-6 s |
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| 401 | ---------------------------------------------------------------------- |
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| 402 | |
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| 403 | place: mean counts min max rms |
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| 404 | sec. % sec. sec. sec. |
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| 405 | ------------------------------------------------------------------------------ |
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| 406 | total 4.460 100.00 1 4.460 4.460 0.001 |
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| 407 | all progn.equations 2.943 65.98 759 2.905 2.982 0.028 |
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| 408 | pres 0.611 13.70 760 0.611 0.611 0.000 |
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| 409 | diffusivities 0.338 7.59 759 0.338 0.339 0.001 |
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| 410 | exchange-horiz-progn 0.146 3.28 759 0.108 0.185 0.028 |
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| 411 | calculate_timestep 0.118 2.64 253 0.070 0.125 0.018 |
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| 412 | flow_statistics 0.103 2.31 254 0.102 0.104 0.001 |
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| 413 | prandtl_fluxes 0.062 1.40 759 0.062 0.063 0.000 |
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| 414 | initialisation 0.062 1.39 1 0.061 0.061 0.001 |
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| 415 | data_output_2d 0.028 0.62 10 0.021 0.028 0.002 |
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| 416 | sum_up_3d_data 0.004 0.10 146 0.004 0.005 0.000 |
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| 417 | disturb_field 0.004 0.08 10 0.003 0.007 0.001 |
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| 418 | run_control 0.003 0.07 254 0.000 0.000 0.008 |
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| 419 | last actions 0.003 0.07 1 0.003 0.003 0.000 |
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| 420 | data_output_tseries 0.003 0.06 253 0.000 0.000 0.007 |
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| 421 | data_output_profiles 0.001 0.02 4 0.000 0.000 0.002 |
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| 422 | swap_timelevel 0.000 0.01 759 0.000 0.000 0.000 |
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| 423 | user_actions 0.000 0.01 759 0.000 0.000 0.000 |
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| 424 | average_3d_data 0.000 0.00 2 0.000 0.000 0.000 |
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| 425 | |
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| 426 | special measures: |
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| 427 | ------------------------------------------------------------------------------- |
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| 428 | timesteps 4.391 98.45 253 4.391 4.391 0.000 |
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| 429 | poisfft 0.441 9.90 760 0.440 0.443 0.001 |
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| 430 | exchange_horiz 0.233 5.22 6866 0.193 0.275 0.029 |
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| 431 | fft_y 0.122 2.73 760 0.121 0.122 0.000 |
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| 432 | fft_x 0.121 2.71 760 0.121 0.121 0.000 |
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| 433 | transpo invers 0.084 1.89 760 0.084 0.085 0.000 |
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| 434 | transpo forward 0.077 1.72 760 0.075 0.078 0.001 |
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| 435 | mpi_alltoall 0.063 1.42 4560 0.060 0.065 0.002 |
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| 436 | divergence 0.043 0.97 1520 0.043 0.044 0.000 |
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| 437 | tridia 0.036 0.81 760 0.036 0.036 0.000 |
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| 438 | exchange_horiz_2d 0.021 0.47 3795 0.019 0.022 0.001 |
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| 439 | \end{lstlisting} |
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| 440 | }; |
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| 441 | \end{tikzpicture} |
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| 442 | \end{columns} |
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| 443 | \end{frame} |
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| 444 | |
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| 445 | % Folie 10 |
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| 446 | \begin{frame} |
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| 447 | \frametitle{Other Files} |
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| 448 | \small |
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| 449 | \begin{itemize} |
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| 450 | \item<1->{Data output files (1D profiles and timeseries, 2D cross sections, 3D volume data) are by default in \textbf{netCDF} format which is suitable to be processed by |
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| 451 | public domain graphics software like \textbf{ncview}, \textbf{ferret}, \textbf{ncl} (used by PALM group), \textbf{IDL}, etc. \\ |
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| 452 | \par\bigskip |
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| 453 | For a first look, {\tt ncview} is a convenient tool.} |
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| 454 | \item<2->{{\tt ncdump} can be used to display the netCDF file contents in ASCII format ({\tt ncdump -c} displays only header informations).} |
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| 455 | \item<3->{The simple viewer for netCDF-data - {\tt ncview} - as well as ncl graphic software is available on the notebooks and on the IMUK-cluster.} |
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| 456 | \end{itemize} |
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| 457 | \end{frame} |
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| 458 | |
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| 459 | % Folie 11 |
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| 460 | \begin{frame} |
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| 461 | \frametitle{Steering by Unix Environment Variables} |
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| 462 | \scriptsize |
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| 463 | Most features of PALM are controlled by the parameter file but a few are exclusively controlled by unix environment variables. The most important one is {\tt write\_binary}. \\ |
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| 464 | \par\bigskip |
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| 465 | Setting \\ |
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| 466 | \par\medskip |
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| 467 | {\centering \texttt{ write\_binary = true} \\ |
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| 468 | \par\medskip |
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| 469 | within the shell causes PALM to write binary data for restart runs at the end of a run.} |
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| 470 | \par\bigskip |
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| 471 | \uncover<2->{Setting of these environment variables is automatically done by {\tt mrun}. It generates a local file (named {\tt ENVPAR}) in FORTRAN-NAMELIST-format, which is then |
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| 472 | read by PALM. This file includes the following variables:} \\ |
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| 473 | \par\bigskip |
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| 474 | \tiny |
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| 475 | \uncover<3->{ |
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| 476 | \begin{tabular}{|p{3cm}|p{4cm}|p{3cm}|} \hline |
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| 477 | \textbf{Variable} & \textbf{Meaning} & \textbf{Value set by {\tt mrun}-option} \\ |
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| 478 | \hline |
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| 479 | {\tt host} & host identifier that mrun is using for the host on which the job is running & {\tt -h} \\ |
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| 480 | {\tt maximum\_cpu\_time\_allowed} & cpu time allowed for the job & {\tt -t} \\ |
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| 481 | {\tt run\_identifier} & identification string for the run & {\tt -d} \\ |
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| 482 | {\tt tasks\_per\_node} & number of MPI tasks to be started on each node & {\tt -T} \\ |
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| 483 | {\tt write\_binary} & switch for writing binary data to be used for restart runs & {\tt -r} (+setting in configuration file {\tt .mrun.config)} \\ |
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| 484 | \hline |
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| 485 | \end{tabular}} |
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| 486 | \normalsize |
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| 487 | \end{frame} |
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| 488 | |
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| 489 | % Folie 12 |
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| 490 | \begin{frame} |
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| 491 | \frametitle{PALM / netCDF Documentation} |
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| 492 | \begin{itemize} |
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| 493 | \item<1->{A detailed description of how to use PALM and a complete list of steering parameters and their meaning can be found on the PALM-server: \\ |
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| 494 | \par\bigskip |
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| 495 | \textbf{http://palm.muk.uni-hannover.de/wiki/doc/toc}} |
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| 496 | \par\bigskip |
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| 497 | \item<2->{General information about the netCDF data format can be found under \\ |
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| 498 | \par\bigskip |
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| 499 | \textbf{http://www.unidata.ucar.edu/software/netcdf/}} |
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| 500 | \end{itemize} |
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| 501 | \end{frame} |
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| 502 | |
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| 503 | \end{document} |
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