1 | % $Id: program_control.tex 973 2012-08-07 16:03:47Z boeske $ |
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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 | \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,decorations.pathreplacing} |
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17 | \def\Tiny{\fontsize{4pt}{4pt}\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 | |
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25 | \institute{Institut fÌr Meteorologie und Klimatologie, Leibniz UniversitÀt Hannover} |
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26 | \date{last update: \today} |
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27 | \event{PALM Seminar} |
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28 | \setbeamertemplate{navigation symbols}{} |
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29 | |
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30 | \setbeamertemplate{footline} |
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31 | {% |
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32 | \begin{beamercolorbox}[rightskip=-0.1cm]& |
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33 | {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}} |
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34 | \end{beamercolorbox} |
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35 | \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,% |
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36 | leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}% |
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37 | {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}% |
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38 | \end{beamercolorbox}% |
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39 | % \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}% |
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40 | % \end{beamercolorbox} |
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41 | }%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.eps}} |
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42 | |
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43 | \title[Program Control by Physical Parameters]{Program Control by Physical Parameters} |
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44 | \author{Siegfried Raasch} |
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45 | |
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46 | % Notes: |
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47 | % jede subsection bekommt einen punkt im menu (vertikal ausgerichtet. |
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48 | % jeder frame in einer subsection bekommt einen punkt (horizontal ausgerichtet) |
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49 | \begin{document} |
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50 | % Folie 1 |
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51 | \begin{frame} |
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52 | \titlepage |
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53 | \end{frame} |
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54 | |
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55 | % Folie 2 |
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56 | \begin{frame} |
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57 | \frametitle{Steering of PALM and Interpreting the Output} |
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58 | \begin{itemize} |
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59 | \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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60 | \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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61 | \end{itemize} |
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62 | \end{frame} |
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63 | |
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64 | % Folie 3 |
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65 | \begin{frame} |
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66 | \frametitle{PALM Input/Output Overview (I)} |
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67 | \tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small] |
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68 | \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny] |
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69 | \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny] |
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70 | \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny] |
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71 | \tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny] |
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72 | \tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny] |
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73 | \tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny] |
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74 | \tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny] |
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75 | \tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny] |
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76 | |
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77 | \tikzstyle{line} = [draw, -latex'] |
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78 | |
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79 | \begin{tikzpicture} [auto] |
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80 | \node[start] (palm) {\textbf{PALM}}; |
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81 | |
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82 | \uncover<2->{\node[yellow1] (parameterfile) [above left=1.5cm of palm] {parameter file \\ for steering};} |
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83 | \uncover<6->{\node[red] (restartdata1) [above right=1.8cm of palm] {restart data};} |
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84 | \uncover<5->{\node[red] (restartdata2) [below=4.5cm of restartdata1] {restart data};} |
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85 | |
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86 | \uncover<4->{ |
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87 | \node[orange1] (timeseries) [below left=4.4cm of palm] {time series}; |
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88 | \node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged}; |
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89 | \node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged}; |
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90 | |
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91 | \path<4->[line] (palm) -- (timeseries); |
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92 | \path<4->[line] (palm) -- (2dsectionstime); |
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93 | \path<4->[line] (palm) -- (3ddatatime); |
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94 | |
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95 | \node[orange1] (1dmean) [above=0.2cm of timeseries] {1D mean \\ profiles}; |
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96 | \node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections}; |
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97 | \node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data};} |
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98 | |
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99 | \path<4->[line] (palm) -- (1dmean); |
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100 | \path<4->[line] (palm) -- (2dsections); |
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101 | \path<4->[line] (palm) -- (3ddata); |
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102 | |
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103 | \uncover<3->{\node[yellow2] (headerfile) [above=0.5cm of 2dsections]{header file};} |
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104 | \uncover<3->{\node[yellow1] (runcontrol) [right=0.5cm of headerfile]{run control output\\ (parameter settings + \\ timestep informations)};} |
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105 | \uncover<3->{\node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements};} |
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106 | |
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107 | \node (program) [right=2.8cm of palm] {program}; |
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108 | \uncover<2->{\node (steeringdata) [right=0.45cm of restartdata1] {steering data};} |
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109 | \uncover<3->{\node (run) [right=2.7cm of runcontrol] {run informations};} |
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110 | \uncover<4->{\node (analysis) [right=3.8cm of 3ddata] {analysis data};} |
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111 | |
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112 | \uncover<7->{ |
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113 | \node[yellow3] (yellow) [below=0.5 of timeseries] {}; |
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114 | \node (ascii) [right=0.1cm of yellow] {ASCII}; |
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115 | \node[orange3] (orange) [right=0.4cm of ascii] {}; |
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116 | \node (netcdf) [right=0.1cm of orange] {netCDF}; |
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117 | \node[red2] (red) [right=0.4cm of netcdf] {}; |
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118 | \node (binary) [right=0.1cm of red] {binary};} |
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119 | |
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120 | \path<2->[line] (parameterfile) -- (palm); |
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121 | \path<3->[line] (palm) -- (cpumeasure); |
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122 | \path<3->[line] (palm) -- (headerfile); |
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123 | \path<3->[line] (palm) -- (runcontrol); |
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124 | \path<5->[line] (palm) -- (restartdata2); |
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125 | \path<6->[line] (restartdata1) -- (palm); |
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126 | \path<6->[line,dashed] (restartdata2) -- (restartdata1); |
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127 | \end{tikzpicture} |
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128 | \end{frame} |
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129 | |
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130 | % Folie 4 |
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131 | \begin{frame} |
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132 | \frametitle{PALM Input/Output Overview (II)} |
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133 | \tikzstyle{start} = [ellipse, draw, fill=green!20, font=\small] |
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134 | \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\Tiny] |
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135 | \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\Tiny] |
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136 | \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!20, text width=0.03\textwidth, font=\Tiny] |
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137 | \tikzstyle{yellow4} = [rectangle, draw, fill=yellow!100, text width=1.8cm, font=\Tiny] |
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138 | \tikzstyle{red} = [rectangle, draw, fill=red!100, text width=0.1\textwidth, font=\Tiny] |
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139 | \tikzstyle{red2} = [rectangle, draw, fill=red!100, text width=0.03\textwidth, font=\Tiny] |
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140 | \tikzstyle{orange1} = [rectangle, draw, fill=orange!50, text width=0.1\textwidth, font=\Tiny] |
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141 | \tikzstyle{orange2} = [rectangle, draw, fill=orange!50, text width=0.11\textwidth, font=\Tiny] |
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142 | \tikzstyle{orange3} = [rectangle, draw, fill=orange!50, text width=0.03\textwidth, font=\Tiny] |
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143 | |
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144 | \tikzstyle{line} = [draw, -] |
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145 | |
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146 | \begin{tikzpicture} [auto] |
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147 | \node[start] (palm) {\textbf{PALM}}; |
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148 | |
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149 | \node[yellow1] (parameterfile) [above left=1cm of palm] {parameter file \\ for steering}; |
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150 | \node[red] (restartdata1) [above right=1.3cm of palm] {restart data}; |
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151 | \node[red] (restartdata2) [below=2.5cm of restartdata1] {restart data}; |
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152 | |
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153 | \node[yellow1] (runcontrol) [below=0.4cm of palm]{run control output\\ (parameter settings + \\ timestep informations)}; |
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154 | \node[yellow2] (headerfile) [left=0.5cm of runcontrol]{header file}; |
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155 | \node[yellow2] (cpumeasure) [left=0.5cm of headerfile]{cpu\\ measurements}; |
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156 | |
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157 | \node[orange1] (1dmean) [below=0.3cm of cpumeasure] {1D mean \\ profiles}; |
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158 | \node[orange1] (2dsections) [right=0.5cm of 1dmean] {2D sections}; |
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159 | \node[orange1] (3ddata) [right=0.5cm of 2dsections] {3D data}; |
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160 | |
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161 | \node[orange1] (timeseries) [below=0.2cm of 1dmean] {time series}; |
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162 | \node[orange2] (2dsectionstime) [right=0.5cm of timeseries] {2D sections \\ time averaged}; |
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163 | \node[orange2] (3ddatatime) [right=0.39cm of 2dsectionstime] {3D data \\ time averaged}; |
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164 | |
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165 | \node (program) [right=2.8cm of palm] {program}; |
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166 | \node (steeringdata) [right=0.8cm of restartdata1] {steering data}; |
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167 | \node (run) [right=2.5cm of runcontrol] {run informations}; |
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168 | \node (analysis) [right=3.6cm of 3ddata] {analysis data}; |
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169 | |
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170 | \node[yellow3] (yellow) [below=0.3 of timeseries] {}; |
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171 | \node (ascii) [right=0.1cm of yellow] {ASCII}; |
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172 | \node[orange3] (orange) [right=0.4cm of ascii] {}; |
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173 | \node (netcdf) [right=0.1cm of orange] {netCDF}; |
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174 | \node[red2] (red) [right=0.4cm of netcdf] {}; |
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175 | \node (binary) [right=0.1cm of red] {binary}; |
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176 | |
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177 | %--------- neue Ordner |
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178 | \uncover<2->{ |
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179 | \node[yellow4] (currentversion) [above=0.6cm of parameterfile] {current\_version/}; |
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180 | \node[yellow4] (jobs) [right=0.3cm of currentversion] {JOBS/}; |
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181 | \node[yellow4] (runidentifier) [right=0.4cm of jobs] {\textless run\_identifier \textgreater/}; |
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182 | \node[yellow4] (input) [above right=1cm of runidentifier] {INPUT/}; |
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183 | \node[yellow4] (monitoring) [below=0.1cm of input] {MONITORING/}; |
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184 | \node[yellow4] (output) [below=0.1cm of monitoring] {OUTPUT/}; |
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185 | \node[yellow4] (restart) [below=0.1cm of output] {RESTART\_DATA/};} |
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186 | |
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187 | \uncover<3->{\node[yellow4] (input2) [below=0.1cm of parameterfile] {INPUT/};} |
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188 | \uncover<4->{\node[yellow4] (monitoring2) [above=0.6cm of headerfile] {MONITORING/};} |
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189 | \uncover<6->{\node[yellow4] (restart2) [below=0.1cm of restartdata1] {RESTART\_DATA/};} |
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190 | \uncover<7->{\node[yellow4] (tmpdata) [below=0.1cm of restart2] {/tmp\_data\_catalog/};} |
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191 | \uncover<5->{\node[yellow4] (output2) [below=0.5cm of restartdata2] {OUTPUT/};} |
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192 | |
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193 | \path[line]<2-> (currentversion) -- (jobs); |
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194 | \path[line]<2-> (jobs) -- (runidentifier); |
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195 | \path[line]<2-> (runidentifier.east) -- (input.west); |
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196 | \path[line]<2-> (runidentifier.east) -- (monitoring.west); |
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197 | \path[line]<2-> (runidentifier.east) -- (output.west); |
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198 | \path[line]<2-> (runidentifier.east) -- (restart.west); |
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199 | |
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200 | \draw<4->[decorate,decoration={brace,raise=6pt,amplitude=9pt},thick] |
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201 | (-4.5,-0.95)--(-1,-0.95) ; |
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202 | \draw<5->[decorate,decoration={brace,mirror,raise=5pt,amplitude=6pt},thick] |
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203 | (0.45,-3)--(0.45,-1.9) ; |
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204 | \end{tikzpicture} |
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205 | \end{frame} |
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206 | |
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207 | % Folie 5 |
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208 | \begin{frame} |
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209 | \frametitle{The Parameter File} |
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210 | \tikzstyle{box} = [rectangle, draw, text width=0.9\textwidth, font=\tiny] |
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211 | \tikzstyle{line} = [draw, thick, -latex'] |
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212 | \footnotesize |
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213 | \begin{itemize} |
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214 | \item<1->{Physical and numerical features of a PALM run (e.g. initial and boundary conditions, numerical methods) |
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215 | are controlled by a so called \textbf{parameter file} which uses FORTRAN-NAMELIST syntax.} |
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216 | \item<2->{General structure of a FORTRAN-NAMELIST file} |
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217 | \end{itemize} |
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218 | \begin{tikzpicture}[auto] |
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219 | \uncover<3->{ |
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220 | \node[box](firstbox){ \begin{tabbing} |
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221 | \quad \&abcd \quad \=no\_of\_eggs = 100, litres\_of\_milk = 50.0, \= \\ |
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222 | \>kilos\_of\_butter = 20.0, \> / \end{tabbing}}; |
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223 | \node[font=\tiny] (leading_blank) at (-5,0.8) {\textbf{leading blank}}; |
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224 | \node[font=\tiny] (namelist) at (-2,0.8) {\textbf{NAMELIST group}}; |
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225 | \node[font=\tiny] (terminating) at (3,0.8) {\textbf{terminating character}}; |
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226 | \path[line] (-5,0.7) -- (-4.8,0); |
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227 | \path[line] (-2,0.7) -- (-4,0); |
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228 | \path[line] (3,0.7) -- (0.2,-0.3);} |
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229 | \end{tikzpicture} |
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230 | \begin{itemize} |
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231 | \item<4->{This file can be read from a FORTRAN program in the following way:} |
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232 | \end{itemize} |
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233 | \begin{tikzpicture}[auto, node distance=0] |
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234 | \uncover<4->{ |
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235 | \node[box](secondbox){ \begin{tabbing} |
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236 | INTEGER :: \=no\_of\_eggs = 30 \\ |
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237 | REAL :: \> litres\_of\_milk = 0.0, kilos\_of\_butter, kilos\_of\_cream = 33.0 \\ |
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238 | \\ |
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239 | NAMELIST /abcd/ \quad no\_of\_eggs, litres\_of\_milk, kilos\_of\_butter, kilos\_of\_cream \\ |
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240 | \\ |
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241 | OPEN ( 1, FILE='Filename' ) \\ |
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242 | \\ |
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243 | READ ( 1, abcd ) \end{tabbing}};} |
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244 | \end{tikzpicture} |
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245 | \normalsize |
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246 | \end{frame} |
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247 | |
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248 | % Folie 6 |
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249 | \begin{frame} |
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250 | \frametitle{An Example of PALM - NAMELIST Input} |
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251 | \tikzstyle{box} = [rectangle, draw, text width=\textwidth, font=\tiny] |
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252 | \begin{tikzpicture}[auto, node distance=0] |
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253 | \node[box](box){ \begin{tabbing} |
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254 | \&inipar \=nx = 39, ny = 39, nz = 40, \\ |
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255 | \>dx = 50.0, dy = 50.0, dz = 50.0, \\ |
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256 | \\ |
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257 | \>initializing\_actions = 'set\_constant\_profiles', \\ |
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258 | \>ug\_surface = 0.0, vg\_surface = 0.0, \\ |
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259 | \\ |
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260 | \>pt\_vertical\_gradient \qquad = 0.0, 1.0, \\ |
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261 | \>pt\_vertical\_gradient\_level = 0.0, 800.0, \\ |
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262 | \\ |
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263 | \>surface\_heatflux = 0.1, bc\_pt\_b ='neumann', / \\ |
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264 | \\ |
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265 | \\ |
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266 | \&d3par \>end\_time = 3600.0, \\ |
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267 | \\ |
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268 | \>dt\_dopr = 900.0, averaging\_interval\_pr = 600.0, \\ |
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269 | \>data\_output\_pr = 'pt', 'u', 'v', / \\ \end{tabbing}}; |
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270 | \end{tikzpicture} |
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271 | \footnotesize |
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272 | \begin{itemize} |
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273 | \item<2->{There are two NAMELIST groups ({\tt \&inipar} and {\tt \&d3par}).} |
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274 | \item<3->{Assignments to parameters in {\tt\&inipar} are ignored within restart runs \\ |
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275 | (exception: {\tt initializing\_actions} = {\tt'read\_restart\_data'} is obligatory for restart runs).} |
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276 | \item<4->{Values of {\tt \&d3par} parameters can be changed for restart runs.} |
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277 | \end{itemize} |
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278 | \end{frame} |
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279 | |
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280 | % Folie 7 |
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281 | \begin{frame} |
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282 | \frametitle{The Run Control File} |
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283 | \scriptsize |
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284 | \begin{itemize} |
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285 | \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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286 | \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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287 | controlled by run parameter {\tt dt\_run\_control}).} |
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288 | \end{itemize} |
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289 | \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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290 | errors have occurred!}} |
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291 | \par\bigskip |
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292 | \includegraphics[width=1.08\textwidth]{program_control_figures/run_control_file.png} |
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293 | \normalsize |
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294 | \end{frame} |
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295 | |
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296 | % Folie 8 |
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297 | \begin{frame} |
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298 | \frametitle{The Header File} |
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299 | \scriptsize |
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300 | \begin{itemize} |
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301 | \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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302 | \item<2->{It is generated for \textbf{every} run (initial run as well as restart runs).} |
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303 | \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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304 | \item<4->{Only at the end, cpu time information is included!} |
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305 | \end{itemize} |
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306 | \begin{center} |
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307 | \includegraphics[width=0.9\textwidth]{program_control_figures/header_file.png} |
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308 | \end{center} |
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309 | \normalsize |
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310 | \end{frame} |
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311 | |
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312 | % Folie 9 |
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313 | \begin{frame} |
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314 | \frametitle{CPU Measurements File} |
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315 | \begin{columns}[c] |
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316 | \column{0.42\textwidth} |
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317 | \scriptsize |
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318 | \begin{itemize} |
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319 | \item{Contains informations about the CPU requirements of single parts of the program.} |
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320 | \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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321 | \item<3->{Prognostic-equations and pressure solver ({\tt pres}) should be the main consumer.} |
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322 | \item<4->{For larger grids ($400^3$ points), {\tt pres} may need up to 50\% of the total time.} |
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323 | \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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324 | \end{itemize} |
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325 | \normalsize |
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326 | \column{0.58\textwidth} |
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327 | \includegraphics[width=1.1\textwidth]{program_control_figures/cpu_measurements_file.png} |
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328 | \end{columns} |
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329 | \end{frame} |
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330 | |
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331 | % Folie 10 |
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332 | \begin{frame} |
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333 | \frametitle{Other Files} |
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334 | \small |
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335 | \begin{itemize} |
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336 | \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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337 | public domain graphics software like \textbf{ncview}, \textbf{ferret}, \textbf{ncl} (used by PALM group), \textbf{IDL}, etc. \\ |
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338 | \par\bigskip |
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339 | For a first look, {\tt ncview} is a convenient tool.} |
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340 | \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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341 | \item<3->{The simple viewer for netCDF-data - {\tt ncview} - as well as ncl graphic software is available on the IMUK-cluster.} |
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342 | \end{itemize} |
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343 | \end{frame} |
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344 | |
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345 | % Folie 11 |
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346 | \begin{frame} |
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347 | \frametitle{Steering by Unix Environment Variables} |
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348 | \scriptsize |
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349 | 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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350 | \par\bigskip |
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351 | Setting \\ |
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352 | \par\medskip |
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353 | {\centering \texttt{ write\_binary = true} \\ |
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354 | \par\medskip |
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355 | within the shell causes PALM to write binary data for restart runs at the end of a run.} |
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356 | \par\bigskip |
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357 | \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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358 | read by PALM. This file includes the following variables:} \\ |
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359 | \par\bigskip |
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360 | \tiny |
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361 | \uncover<3->{ |
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362 | \begin{tabular}{|p{3cm}|p{4cm}|p{3cm}|} \hline |
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363 | \textbf{Variable} & \textbf{Meaning} & \textbf{Value set by {\tt mrun}-option} \\ |
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364 | \hline |
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365 | {\tt host} & host identifier that mrun is using for the host on which the job is running & {\tt -h} \\ |
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366 | {\tt maximum\_cpu\_time\_allowed} & cpu time allowed for the job & {\tt -t} \\ |
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367 | {\tt run\_identifier} & identification string for the run & {\tt -d} \\ |
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368 | {\tt tasks\_per\_node} & number of MPI tasks to be started on each node & {\tt -T} \\ |
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369 | {\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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370 | \hline |
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371 | \end{tabular}} |
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372 | \normalsize |
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373 | \end{frame} |
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374 | |
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375 | % Folie 12 |
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376 | \begin{frame} |
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377 | \frametitle{PALM / netCDF Documentation} |
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378 | \begin{itemize} |
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379 | \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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380 | \par\bigskip |
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381 | \textbf{http://palm.muk.uni-hannover.de/wiki/doc/toc}} |
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382 | \par\bigskip |
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383 | \item<2->{General information about the netCDF data format can be found under \\ |
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384 | \par\bigskip |
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385 | \textbf{http://www.unidata.ucar.edu/software/netcdf/}} |
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386 | \end{itemize} |
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387 | \end{frame} |
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388 | |
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389 | \end{document} |
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