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Changeset 954 for palm/trunk/TUTORIAL


Ignore:
Timestamp:
Jul 20, 2012 7:44:19 AM (12 years ago)
Author:
maronga
Message:

added/updated tutorial presentations

Location:
palm/trunk/TUTORIAL/SOURCE
Files:
77 added
5 edited

Legend:

Unmodified
Added
Removed

  • palm/trunk/TUTORIAL/SOURCE/exercise_cbl.tex

    r949 r954  
    5656\end{frame}
    5757
    58 \section{Exercise 1: Convection Between Plates}
    59 \subsection{Exercise 1: Convective Between Plates}
     58\section{Exercise}
     59\subsection{Exercise}
    6060
    6161% Folie 2
    … …  
    207207\end{frame}
    208208
    209 
    210 
     209% Folie 8
     210\section{Results}
     211\subsection{Results}
     212
     213\begin{frame}
     214   \frametitle{$xy$-cross sections (instantaneous)}
     215   \begin{center}
     216      \includegraphics[width=0.42\textwidth]{exercise_cbl_figures/xy_w_100.eps}
     217      \includegraphics[width=0.42\textwidth]{exercise_cbl_figures/xy_w_500.eps}\\
     218      \includegraphics[width=0.42\textwidth]{exercise_cbl_figures/xy_w_750.eps}
     219   \end{center}
     220\end{frame}
     221
     222% Folie 9
     223\begin{frame}
     224   \frametitle{$xz$-cross sections ($\unit[900]{s}$ average)}
     225   \begin{center}
     226      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y250m.eps}
     227      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y500m.eps}\\
     228      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y750m.eps}
     229      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y1000m.eps}
     230   \end{center}
     231\end{frame}
     232
     233% Folie 10
     234\begin{frame}
     235   \frametitle{Vertical profiles (I)}
     236   \begin{center}
     237      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_pt.eps}
     238      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_wpt.eps}
     239   \end{center}
     240\end{frame}
     241
     242% Folie 11
     243\begin{frame}
     244   \frametitle{LES?}
     245   \begin{center}
     246      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_wpt2.eps}
     247      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_wpt_resolved.eps}
     248   \end{center}
     249\end{frame}
     250
     251% Folie 12
     252\begin{frame}
     253   \frametitle{Time series (I)}
     254   \begin{center}
     255      \includegraphics[width=1.0\textwidth]{exercise_cbl_figures/ts.eps}
     256   \end{center}
     257\end{frame}
     258
     259% Folie 13
     260\begin{frame}
     261   \frametitle{Time series (II)}
     262   \begin{center}
     263      \includegraphics[width=1.0\textwidth]{exercise_cbl_figures/ts2.eps}
     264   \end{center}
     265\end{frame}
    211266\end{document}

  • palm/trunk/TUTORIAL/SOURCE/particle_model.tex

    r945 r954  
    412412            \node[text width=6em] at (2.8,-2.1) {\scriptsize Calculation of particle trajectories begins (default value: 0.0)};
    413413     
    414      
    415      
    416      
    417414            \onslide<3->
    418415            \draw[->, ultra thick, color=red] (5,0.5) -- (5,-0.5);
    … …  
    420417            \node at (3.75,0.3) {\scriptsize \texttt{dt\underline{ }prel}};
    421418            \draw[<->, thick, color=blue] (2.5,0.6) -- (4.95,0.6);
    422      
    423      
    424419     
    425420            \onslide<4->
    … …  
    867862   \small
    868863   \vspace{1mm}
    869    The position of a particle is found by integrating $ \dfrac{dX_{\text{particle}}}{dt} = \vec{V}_{\text{particle}}$\\
     864   The position of a particle is found by integrating $ \dfrac{d \vec{X}_{\text{particle}}}{dt} = \vec{V}_{\text{particle}}$\\
    870865   \vspace{2mm}
    871866   \onslide<2->Transferring the LES concept ...
    … …  
    982977   Assumption: subgrid scale turbulence locally isotropic\\
    983978   \vspace{6mm}
    984    $dV_{\text{sub}_i} = - \dfrac{3 f_s C_0}{4} \dfrac{V_{\text{sub}_i}}{e_s} dt + \dfrac{1}{3} \left( \dfrac{\partial e_s}{\partial x_i} + \dfrac{3}{2 e_s} \dfrac{d e_s}{dt} V_{\text{sub}_i}\right) dt + \sqrt{f_s C_0 \varepsilon}\, d\xi_i$\\
     979   $dV_{\text{sub}_i} = - \dfrac{3 f_s C_0 \varepsilon}{4} \dfrac{V_{\text{sub}_i}}{e_s} dt + \dfrac{1}{3} \left( \dfrac{\partial e_s}{\partial x_i} + \dfrac{3}{2 e_s} \dfrac{d e_s}{dt} V_{\text{sub}_i}\right) dt + \sqrt{f_s C_0 \varepsilon}\, d\xi_i$\\
    985980   \vspace{2mm}
    986981   $f_s = \dfrac{\langle 2 e_s / 3 \rangle}{\langle 2 e_s / 3 \rangle + \langle \left( \sigma^2_{\text{res}U} + \sigma^2_{\text{res}V} + \sigma^2_{\text{res}W} \right) /3 \rangle}$\\
    … …  
    12661261      \node (0) at (0,0) {};
    12671262      \node[draw, right=0.0cm of 0] {In case of cloud droplets: calculate the liquid water content};
    1268       \uncover<2->{\node[draw, right=0.0cm of 0, yshift=-0.6cm] {user defined setting of particle attributes (subroutine user\underline{ }particle\underline{ }attributes)};}
     1263      \uncover<2->{\node[draw, right=0.0cm of 0, yshift=-0.6cm] {user defined setting of particle attributes (subroutine \texttt{user\underline{ }particle\underline{ }attributes})};}
    12691264      \uncover<3->{\node[draw, right=0.0cm of 0, yshift=-1.2cm] {if necessary, add actual positions to the particle tails};}
    12701265      \uncover<4->{\node[draw, right=0.0cm of 0, yshift=-1.8cm] {write particle statistics on file \texttt{PARTICLE\underline{ }INFOS} (ASCII format)};  }   
    … …  
    13501345   \includegraphics[scale=0.5]{particle_model_figures/footprint3_2.png}
    13511346   \begin{itemize}
    1352       \item particles are released every 2min over a period of 30min at z=70m in the total model domain ($\rightarrow$ 7 * 106 particles)
     1347      \item particles are released every 2min over a period of 30min at z=70m in the total model domain ($\rightarrow$ 7 * $10^6$ particles)
    13531348      \item particles are measured at z=72.5m, 77.5m, 100.0m
    13541349   \end{itemize}

  • palm/trunk/TUTORIAL/SOURCE/program_control.tex

    r945 r954  
    11% $Id$
    22\input{header_tmp.tex}
    3 %\input{header_lectures.tex}
     3%\input{header_LECTURE.tex}
    44
    55\usepackage[utf8]{inputenc}
    … …  
    290290      errors have occurred!}}
    291291   \par\bigskip
    292    \includegraphics[width=1.6\textwidth]{program_control_figures/run_control_file.png}
     292   \includegraphics[width=\textwidth]{program_control_figures/run_control_file.png}
    293293   \normalsize
    294294\end{frame}

  • palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex

    r945 r954  
    4242    \end{beamercolorbox}
    4343  }
     44
    4445%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}}
    4546
    … …  
    6465      \texttt{ksh}-syntax) which can be used to compile and run programs, including
    6566      the handling of input/output files.
     67      \vspace{4mm}
    6668      \item<2-> The \texttt{mrun}-command has a number of options to control the
    6769      program execution\\
    68          \quad \footnotesize \texttt{mrun -d example\_cbl -h lcsgih -K parallel -X8 -T2 ...}\\
     70         \quad \footnotesize \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\
    6971         \normalsize All options including a short description can be displayed by entering\\
    7072         \quad \footnotesize \texttt{mrun ?}
     73      \vspace{4mm}
    7174      \item<3-> \normalsize The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config}
    7275   \end{itemize}
    … …  
    7578% Folie 3
    7679\begin{frame}
    77    \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\scriptsize]
    78    \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth,
    79    font=\scriptsize]
    80    \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\scriptsize]
    81    \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\scriptsize]
    82    \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\scriptsize]
     80   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\tiny]
     81   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, font=\tiny]
     82   \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\tiny]
     83   \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\tiny]
     84   \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\tiny]
    8385   \tikzstyle{line} = [draw, -]
    8486   \tikzstyle{alert} = [rectangle, draw, text width=0.77\textwidth, font=\scriptsize]
    … …  
    8688   \scriptsize
    8789   \frametitle{Carrying Out Runs Using \texttt{mrun}}
    88    Carrying out a program run typically needs two steps:\\
    89    1. compilation\\
    90    \quad \texttt{f90  ...  file1.f90 file2.f90 ...}\\
    91    \onslide<2-> 2. execution\\
    92    \quad \texttt{a.out}\\
     90   \textbf{Carrying out a program run typically needs two steps:}\\
    9391   \vspace{1mm}
    94    \onslide<3->Besides, a program needs input data and creates output data:\\
     92   \quad 1. compilation\\
     93   \qquad \texttt{f90  ...  file1.f90 file2.f90 ...}\\
     94   \vspace{1mm}
     95   \onslide<2->\quad 2. execution\\
     96   \qquad \texttt{a.out}\\
     97   \vspace{3mm}
     98   \onslide<3->\textbf{Besides, a program needs input data and creates output data:}\\
    9599   
    96100   \onslide<4->\begin{tikzpicture}[auto, node distance=0]
    … …  
    98102      \node [dummy, right=0.1cm of first] (second) {};
    99103     
    100       \node [yellow, above=0.5cm of second] (third) {\textbf{parameter for steering}};
    101       \node [yellow, below=0.5cm of third] (fourth) {\textbf{control output}};
     104      \node [yellow, above=0.4cm of second] (third) {\textbf{parameter for steering}};
     105      \node [yellow, below=0.4cm of third] (fourth) {\textbf{control output}};
    102106      \node [yellow, below=0.3cm of fourth] (fifth) {\textbf{output for analysis}};
    103107     
    … …  
    113117         \texttt{OPEN (11, FILE='PARIN', FORM='FORMATTED')}};}
    114118      \uncover<5->{\node [white, right=0.25cm of fourth] (tenth) {
    115          \texttt{OPEN (15, FILE='RUN\_CONTROL', FORM='FORMATTED')}};}
     119         \texttt{OPEN (15, FILE='RUN\underline{ }CONTROL', FORM='FORMATTED')}};}
    116120      \uncover<5->{\node [white, right=0.25cm of fifth] (eleventh) {
    117          \texttt{OPEN (40, FILE=‘DATA\_1D\_PR\_NETCDF', FORM='FORMATTED')}};}
     121         \texttt{OPEN (40, FILE=‘DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF', FORM='FORMATTED')}};}
    118122   \end{tikzpicture}
    119123   
    120    \vspace{1mm}
     124   \vspace{3mm}
    121125   \scriptsize
    122    \onslide<6->\textcolor{red}{Problems: The user has to copy or rename output files, if
     126   \onslide<6->\textcolor{red}{\textbf{Problems:} The user has to copy or rename output files, if
    123127   he/she wants to run the program more than once and if he concurrently wants to keep
    124    the files from the former run(s).
     128   the files from the former run(s).\\
    125129   If he/she is using different input parameter files for steering, these files also have
    126130   to be copied into the working directory before the program is executed.}\\
    127    \ \\
     131   \vspace{1mm}
    128132   \begin{tikzpicture}[auto, node distance=0]
    129       \uncover<7->{\node [alert] (alert) {\textcolor{red}{It is therefore very desirable
    130       to automate these tasks!}};}
     133      \uncover<7->{\node [alert] (alert) {\textcolor{red}{\textbf{It is therefore very desirable to automate these tasks!}}};}
    131134   \end{tikzpicture}
    132135\end{frame}
    … …  
    140143   
    141144   \frametitle{\texttt{mrun}: Principal Mode of Operation (I)}
    142    \texttt{mrun} runs a program (in our case the PALM model) by carrying out the
    143    following principle tasks in a sequential order:\\
    144    \scriptsize
     145   \scriptsize \texttt{mrun} \textbf{runs a program (in our case the PALM model) by carrying out the following principle tasks in a sequential order:}\\
     146   \vspace{1mm}
    145147   \begin{enumerate}
    146148      \item<2-> Create a temporary working directory and change into this directory:\\
    … …  
    149151      \ \\
    150152      The path of \texttt{<tempdir>} is given in the configuration file
    151       \texttt{.mrun.config} by the environment variable \texttt{tmp\_user\_catalog}, e.g.:\\
    152            \quad \texttt{\%tmp\_user\_catalog  /tmp \hspace{30mm} <hi>  parallel}\\
     153      \texttt{.mrun.config} by the environment variable \texttt{tmp\underline{ }user\underline{ }catalog}, e.g.:\\
     154           \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /tmp \hspace{30mm} <hi>  parallel}\\
    153155           \ \\
    154156           \onslide<3-> On SGI-ICE: \\
    155            \quad \texttt{\%tmp\_user\_catalog  /gfs2/work/<username>
    156            \hspace{5mm} <hi>  lcsgih parallel}
     157           \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /gfs2/work/<username>
     158           \hspace{5mm} lcsgih parallel}
    157159           \begin{center}
    158160              \begin{tikzpicture}[auto, node distance=0]
    … …  
    160162         \end{tikzpicture}
    161163           \end{center}
     164           \vspace{2mm}
    162165           \item<5-> Copy the input files from a directory of the user into this working directory:\\
    163            \scriptsize
    164            \onslide<6->\hspace{-15mm} \texttt{cp <user\_input\_file1>
    165            /tmp/<username>.<randomnumber>/<temporary\_input\_file1>}\\
    166       \hspace{-15mm} \texttt{cp <user\_input\_file2>
    167       /tmp/<username>.<randomnumber>/<temporary\_input\_file2>}
     166           \vspace{1mm}
     167           \onslide<6-> \tiny \quad \texttt{cp <user\underline{ }input\underline{ }file1>
     168           /tmp/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file1>}\\
     169      \quad \texttt{cp <user\underline{ }input\underline{ }file2>
     170      /tmp/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file2>}\\
     171      \vspace{2mm}
     172      \scriptsize
    168173      \begin{center}
    169174              \begin{tikzpicture}[auto, node distance=0]
    … …  
    172177       
    173178            \uncover<7->{\node [yellowsmall, above=0.1cm of green] (yellow2) {JOBS/};}
    174             \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\_version/};}
    175             \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\_cbl/};}
     179            \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\underline{ }version/};}
     180            \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
    176181            \uncover<7->{\node [yellowsmall, right=0.2cm of yellow3] (yellow4) {INPUT/};}
    177182           
    … …  
    208213      \begin{center}
    209214              \begin{tikzpicture}[auto, node distance=0]
    210                  \uncover<2->{\node [yellow] (yellow) {current\_version/};}
     215                 \uncover<2->{\node [yellow] (yellow) {current\underline{ }version/};}
    211216                 \uncover<1->{\node [dummy, right=0.0cm of yellow] (dummy1) {};}
    212                  \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\_DEPOSITORY\_\textit{parallel}/};}
     217                 \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\underline{ }DEPOSITORY\underline{ }\textit{parallel}/};}
    213218                 \uncover<1->{\node [dummy, right=0.2cm of green1] (dummy2) {};}
    214219            \uncover<3->{\node [green, below=0.5cm of dummy1] (green2) {/tmp/$<$username$>$.$<$randomnumber$>$};}
    … …  
    240245   
    241246   \frametitle{\texttt{mrun}: Principal Mode of Operation (III)}
    242 
     247   \footnotesize
    243248        \begin{enumerate}
    244249      \setcounter{enumi}{5}
    245250           \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\
    246        \scriptsize \hspace{-16mm} \texttt{cp /tmp/<username>.<randomnumber>/<temporary\_output\_file1> <user\_output\_file1>}\\
    247       \hspace{-16mm} \texttt{cp /tmp/<username>.<randomnumber>/<temporary\_output\_file2> <user\_output\_file2>}\\
    248      
     251       \tiny \quad \texttt{cp /tmp/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\
     252      \quad \texttt{cp /tmp/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\
     253      \footnotesize
    249254      \begin{center}
    250255              \begin{tikzpicture}[auto, node distance=0]
    … …  
    256261           
    257262            \uncover<2->{\node [yellow, left=0.2cm of dummy3] (yellow2) {OUTPUT/};}
    258             \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\_cbl/};}
     263            \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
    259264            \uncover<2->{\node [yellow, left=0.2cm of yellow3] (yellow4) {JOBS/};}
    260             \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\_version/};}
     265            \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};}
    261266                                             
    262267                 \uncover<2-3>{\node [green, left=5.0cm of dummy1] (green) {/tmp/$<$username$>$.$<$randomnumber$>$};}
    … …  
    278283           \item<3-> Delete the temporary working directory\\
    279284      \quad \texttt{rm -rf /tmp/<username>.<randomnumber>}\\
     285      \vspace{2mm}
    280286      \onslide<5->\textcolor{red}{Question: How does \texttt{mrun} know which files have to be copied and where from or where to they have to be copied?}
    281287
    … …  
    293299   \frametitle{Steering File Copy by the Configuration File (I)}
    294300   \scriptsize
    295    \textbf{Copying of files is controlled by so called \textit{file connection statements}. They connect local files in the temporary working directory with permanent files residing in the directory of the user.}\\
     301   \textbf{Copying of files is controlled by so called} \textit{file connection statements}. \textbf{They connect local files in the temporary working directory with permanent files residing in the directory of the user.}\\
    296302   \vspace{1mm}
    297303   Principle example of a file connection statement (for the PALM parameter file):
    … …  
    305311         \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
    306312         \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
    307               \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\_version/JOB/INPUT}};}
    308               \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\_p3d}};}
     313              \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
     314              \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
    309315              \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
    310316                   
    … …  
    330336   
    331337   \onslide<8->The full name of the permanent file results from the directory name, the suffix and the value of \texttt{mrun}-Option \texttt{-d}, which defines the so-called \textbf{base name} of all files handled by \texttt{mrun}:\\
    332    \quad \texttt{mrun -d \textcolor{blue}{example\_cbl} ...}\\
     338   \quad \texttt{mrun -d \textcolor{blue}{example\underline{ }cbl} ...}\\
    333339   gives the filename\\
    334    \quad \texttt{\~{}/palm/current\_version/JOB/INPUT/\textcolor{blue}{example\_cbl}\_p3d}\\
    335    \quad \texttt{( ... /\textcolor{blue}{example\_cbl}\_p3d\textcolor{red}{.nc} )}
     340   \quad \texttt{\~{}/palm/current\underline{ }version/JOB/INPUT/\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d}\\
     341   \quad \texttt{( ... /\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d\textcolor{red}{.nc} )}
    336342   
    337343\end{frame}
    … …  
    342348   \scriptsize
    343349   \onslide<1-> The \textbf{base name} can additionally be a part of the directory name
    344    by using \texttt{\$fname} in the directory column of the file connection statement:\\
    345    \quad \texttt{PARIN in d3\# \~{}/palm/current\_version/JOBS/\$fname/INPUT \_p3d}\\
     350   by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\
     351   \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
    346352   \ \\
    347353   \onslide<2-> Using the call\\
    348    \quad \texttt{mrun -d abcde ...}\\
     354   \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\
    349355   the input file will be expected under\\
    350    \quad \texttt{\~{}/palm/current\_version/JOBS/abcde/INPUT/abcde\_p3d }\\
     356   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\
    351357   \ \\
    352358   \onslide<3-> In this way, all files handled by the \texttt{mrun}-call are stored in
    353    the same subdirectory (abcde/) and will have the same string (\texttt{abcde}) as
    354    part of their names, so they can be easily identified as ''belonging'' to the model
     359   the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as
     360   part of their names, so they can be easily identified as \grqq belonging\grqq\, to the model
    355361   run initiated by that \texttt{mrun} call.\\
    356362   \ \\
    357363   \onslide<4-> Instead of always writing the full path name (i.e.
    358    \texttt{\~{}/palm/current\_version/JOBS}), an environment variable can be declared for
     364   \texttt{\~{}/palm/current\underline{ }version/JOBS}), an environment variable can be declared for
    359365   this at the beginning of the configuration file and be used in the file
    360366   connection statements:\\
    361    \quad \texttt{\%base\_data  \~{}/palm/current\_version/JOBS}\\
    362    \quad \texttt{PARIN in d3\#  \$base\_data/\$fname/INPUT \_p3d}\\
     367   \quad \texttt{\%base\underline{ }data  \~{}/palm/current\underline{ }version/JOBS}\\
     368   \quad \texttt{PARIN in d3\#  \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
    363369   \ \\
    364370   \onslide<5-> This easily allows to change the directories for all input/output files
    365    by just changing the value of \texttt{base\_data}.
     371   by just changing the value of \texttt{base\underline{ }data}.
    366372   
    367373\end{frame}
    … …  
    374380   have to be activated by giving their activation string in the
    375381   \texttt{mrun}-option \texttt{-r}:\\
    376    \quad \texttt{PARIN in d3\# \~{}/palm/current\_version/JOBS/\$fname/INPUT \_p3d}\\
     382   \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\
    377383   \ \\
    378384   \onslide<2-> The permanent file
    379    \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/INPUT/example\_cbl\_p3d}
     385   \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d}
    380386   will only be copied to the local file PARIN by using the call:\\
    381    \quad \texttt{mrun -d example\_cbl -r ''d3\#'' ...}\\
     387   \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\
    382388   \ \\
    383389   \onslide<3-> \textbf{Example for an output file:}\\
    384390   The file connection statement\\
    385    \quad \texttt{DATA\_1D\_PR\_NETCDF out:loc pr\#
    386    \~{}/palm/current\_version/JOBS/\$fname/OUTPUT \_pr nc}\\
     391   \quad \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF out:loc pr\#
     392   \~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}\\
    387393   \onslide<4-> will copy (after program execution) the local file
    388    \texttt{DATA\_1D\_PR\_NETCDF} to the permanent file
    389    \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/OUTPUT/example\_cbl\_pr.nc} if
     394   \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file
     395   \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc} if
    390396   \texttt{mrun} is called with the options\\
    391    \quad \texttt{mrun -d example\_cbl -r ''d3\# pr\#'' ...}
     397   \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...}
    392398   
    393399\end{frame}
    … …  
    401407   Instead, new, so-called file cycles are created.\\
    402408   If an output file, e.g.\\
    403    \quad \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/MONITORING/example\_cbl\_rc}\\
     409   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc}\\
    404410   \ \\
    405411   has been created from a first call of \texttt{mrun} and if the same \texttt{mrun}
    406412   call is submitted again, the second call will not replace the file
    407    \texttt{example\_cbl\_rc}, but will create a new file with name:\\
    408    \quad \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/MONITORING/example\_cbl\_rc.1}\\
     413   \texttt{example\underline{ }cbl\underline{ }rc}, but will create a new file with name:\\
     414   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc.1}\\
    409415   \ \\
    410416   \onslide<2->In case of netCDF-files, the file cycle number is inserted before
    411417   the netCDF-suffix .nc, e.g.\\
    412    \quad \texttt{example\_cbl\_pr.1.nc}\\
     418   \quad \texttt{example\underline{ }cbl\underline{ }pr.1.nc}\\
    413419   \ \\
    414420   \onslide<3->The implemented file cycle mechanism does not allow to use
    415421   any other dots "'."'  in the path or filename:\\
    416    \quad \texttt{\~{}/palm/version\_3.6/JOBS/example.sbl/MONITORING/example.sbl\_rc}
     422   \quad \texttt{\~{}/palm/version\underline{ }3.6/JOBS/example.sbl/MONITORING/example.sbl\underline{ }rc}
    417423\end{frame}
    418424
    … …  
    430436PARIN                    in:job        d3f      $base_data/$fname/INPUT    _p3df
    431437TOPOGRAPHY_DATA          in:locopt     d3#:d3f  $base_data/$fname/INPUT    _topo
    432 BININ                    in:loc:flpe   d3f:rec  $base_data/$fname/RESTART  _d3d
     438BININ                    in:loc:flpe   d3f      $base_data/$fname/RESTART  _d3d
    433439PARTICLE_RESTART_DATA_IN in:loc:flpe   prtf     $base_data/$fname/RESTART  _rprt
    434440DATA_1D_PR_NETCDF        in:locopt     prf      $base_data/$fname/OUTPUT   _pr     nc
    … …  
    468474DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d     nc
    469475DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av  nc
    470 DATA_PRT_NETCDF      out:loc:pe   prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
     476DATA_MASK_01_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01     nc
     477DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01_av  nc
     478DATA_MASK_02_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02     nc
     479DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02_av  nc
     480DATA_MASK_03_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03     nc
     481DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03_av  nc
     482DATA_MASK_04_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04     nc
     483DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04_av  nc
     484DATA_MASK_05_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05     nc
     485DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05_av  nc
     486DATA_MASK_06_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06     nc
     487DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06_av  nc
     488DATA_MASK_07_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07     nc
     489DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07_av  nc
     490DATA_MASK_08_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08     nc
     491DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08_av  nc
     492DATA_MASK_09_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09     nc
     493DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09_av  nc
     494DATA_MASK_10_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10     nc
     495DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10_av  nc
     496DATA_MASK_11_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11     nc
     497DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11_av  nc
     498DATA_MASK_12_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12     nc
     499DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12_av  nc
     500DATA_MASK_13_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13     nc
     501DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13_av  nc
     502DATA_MASK_14_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14     nc
     503DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14_av  nc
     504DATA_MASK_15_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15     nc
     505DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15_av  nc
     506DATA_MASK_16_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16     nc
     507DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16_av  nc
     508DATA_MASK_17_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17     nc
     509DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17_av  nc
     510DATA_MASK_18_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18     nc
     511DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18_av  nc
     512DATA_MASK_19_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19     nc
     513DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19_av  nc
     514DATA_MASK_20_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20     nc
     515DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20_av  nc
    471516DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
    472 DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr
     517DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr 
    473518#
    474519DVRP_LOG          out:loc:tr   dv#       $base_data/$fname/MONITORING  _dvrp_log
    … …  
    504549\begin{frame}
    505550   \frametitle{PALM \textit{Interactive} Example Run Using \texttt{mrun}: Tracing the Run by the User}
    506    \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
    507    \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.42\textwidth, font=\scriptsize, minimum height=0.6cm]
    508    \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
    509    \tikzstyle{notes} = [rectangle, text width=0.46\textwidth, font=\scriptsize, minimum height=0.6cm]
    510    \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
     551   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
     552   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
     553   \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.55\textwidth, font=\tiny, minimum height=0.6cm]
     554   \tikzstyle{notes} = [rectangle, text width=0.26\textwidth, font=\tiny, minimum height=0.6cm]
     555   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny, minimum height=0.6cm]
    511556   \vspace{-1.0cm}
    512557   \begin{center}
    513558           \begin{tikzpicture}[auto, node distance=0]
    514          \uncover<1->{\node [yellow] (box1) {start run on local machine:\\
    515                                             \texttt{mrun -d example\_cbl -h lcmuk ...}};}
    516          \uncover<1->{\node [dummy, right=0.2cm of box1] (dummy1) {};}
    517          \uncover<2->{\node [notes, above=0.2cm of dummy1] (notes1) {temporary working directory is created,\\all required files are copied there};}
    518          \uncover<3->{\node [green, right=0.2cm of dummy1] (box2) {follow runs messages on terminal};}
    519          \uncover<4->{\node [green, below=0.2cm of box2] (box3) {
    520          as soon as message
     559         \uncover<1->{\node [yellow] (box1) {\textbf{start run on local machine:}\\
     560                                            \texttt{mrun -d example\underline{ }cbl -h lcmuk ...}};}
     561         \uncover<1->{\node [dummy, right=1.4cm of box1] (dummy1) {};}
     562         \uncover<2->{\node [notes, above=-0.3cm of dummy1] (notes1) {temporary working directory is created, all required files are copied there};}
     563         \uncover<3->{\node [green, right=1.4cm of dummy1] (box2) {\textbf{follow run messages on terminal}};}
     564         \uncover<4->{\node [green, below=0.5cm of box2] (box3) {
     565         \textbf{as soon as message}
    521566         
    522          \texttt{*** execution starts in directory\\ \quad ''<tempdir>''}
    523 
    524          you can change to this directory (in a new terminal) and watch the progess of timesteps
     567         \texttt{*** execution starts in directory\\ \quad \dq <tempdir>\dq\, }\\
     568         \ \\
     569         \textbf{you can change to this directory (in a new terminal) and watch the progess of timesteps}
    525570
    526571         \texttt{cd <tempdir>}\\
    527          \texttt{tail -f RUN\_CONTROL}
    528 
     572         \texttt{tail -f RUN\underline{ }CONTROL}\\
     573         \ \\
    529574         However, this might be difficult in case of short run times, because the run may have finished before you have entered the commands!
    530575         };}
    531          \uncover<1->{\node [dummy, left=0.2cm of box3] (dummy2) {};}
    532          \uncover<5->{\node [notes, below=1.7cm of dummy2] (notes2) {results are copied from temporary \\ working directory to the user‘s permanent directory};}
    533          \uncover<6->{\node [yellow_big, left=0.2cm of dummy2] (box4) {
    534          check, if the output files have sucessfully been transferred to the permanent directory:\\
    535          \texttt{cd \~{}/palm/current\_version/JOBS/\\ \quad example\_cbl/MONITORING}\\
     576         \coordinate[below=0.3cm of box3] (A);
     577         \uncover<1->{\node [dummy, left=0.3cm of box3] (dummy2) {};}
     578         \uncover<5->{\node [notes, below=0.0cm of A, text width=0.35\textwidth] (notes2) {results are copied from temporary working directory to the user‘s permanent directory};}
     579         \uncover<6->{\node [yellow_big, left=2.5cm of A] (box4) {
     580         \textbf{check, if the output files have sucessfully been transferred to the permanent directory:}\\
     581         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING}\\
    536582         \texttt{ls -al}\\
    537          \texttt{cd \~{}/palm/current\_version/JOBS/\\ \quad example\_cbl/OUTPUT}\\
     583         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT}\\
    538584         \texttt{ls -al}
    539585};}
    540          \draw<2-> [->] (box1.east) -- (box2.west);   
    541          \draw<4-> [->] (box2.south) -- (box3.north);   
    542          \draw<5-> [->] (box3.west) -- (box4.east);   
     586         \draw<2-> [->,color=blue] (box1.east) -- (box2.west);   
     587         \draw<4-> [->,color=blue] (box2.south) -- (box3.north); 
     588         \draw<5-> [-,color=blue] (box3.south) -- (A); 
     589         \draw<5-> [->,color=blue] (A) -- (box4.east);   
    543590           \end{tikzpicture}
    544591        \end{center}
    … …  
    554601\tikzstyle{line} = [draw, -latex']
    555602\begin{itemize}
    556    \item Reminder: Running batch jobs requires a directory \texttt{~/job\_queue} for the job protocol files on the local \underline{and} remote host.
     603   \item Reminder: Running batch jobs requires a directory \texttt{~/job\underline{ }queue} for the job protocol files on the local \underline{and} remote host.
    557604\end{itemize}
    558605\begin{tikzpicture}[auto, node distance=0]
    559606    \node [yellow] (first) {
    560607       \textbf{start job on local machine:}\\
    561        \texttt{mrun -d example\_cbl -h lcsgih ...}
     608       \texttt{mrun -d example\underline{ }cbl -h lcsgih ...}
    562609    };
    563610\uncover<2->{
    … …  
    578625    \node [green, below=0.2cm of second] (third) {
    579626       \textbf{if job is running, you may follow its progress by watching the job protocol:} \\
    580        \texttt{cd ~/job\_queue \\ tail lcmuk\_example\_cbl}
     627       \texttt{cd ~/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
    581628    };
    582629}
    583630\uncover<5->{
    584631    \node [green, below=0.2cm of third] (fourth) {
    585        \textbf{when job is running, change to directory \texttt{<tmp\_usr\_catalog>} and try to find there the latest directory \texttt{<HLRN-username>.<randomnumber>} \\ change to this directory and execute}\\
    586        \texttt{tail -f RUN\_CONTROL}
     632       \textbf{when job is running, change to directory \texttt{<tmp\underline{ }usr\underline{ }catalog>} and try to find there the latest directory \texttt{<HLRN-username>.<randomnumber>} \\ change to this directory and execute}\\
     633       \texttt{tail -f RUN\underline{ }CONTROL}
    587634    };
    588635}
    … …  
    590637    \node [green, below=0.2cm of fourth] (fifth) {
    591638       \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\
    592        \texttt{cd ~/job\_queue \\ cat last\_job\_transfer\_protocol}
     639       \texttt{cd ~/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}
    593640    };
    594641}
    … …  
    603650    \node [yellow, left=3.5cm of fifth] (sixth) {
    604651       \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\
    605        \texttt{cd ~/job\_queue \\ ls -al \\ cd ~/palm/current\_version/JOBS/example \\ ls -al *}
     652       \texttt{cd ~/job\underline{ }queue \\ ls -al \\ cd ~/palm/current\underline{ }version/JOBS/example \\ ls -al *}
    606653    };
    607654}
    608655\uncover<9->{
    609656     \node [alert, below=0.5cm of first.south east] (alert) {
    610         \textcolor{red}{Attention: Commands for submitting jobs and the behaviour of job protocol files are depending on the qeueuing system! Manual adjustments may be required in the mrun and subjob script!}
     657        \textcolor{red}{Attention: Commands for submitting jobs and the behaviour of job protocol files are depending on the queueing system! Manual adjustments may be required in the mrun and subjob script!}
    611658     };
    612659}
    … …  
    649696         \uncover<3->{\node [yellow_small] (box1) {\$HOME/};}
    650697         \uncover<3->{\node [yellow_small, right=0.2cm of box1] (box2) {palm/};}
    651          \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\_version/};}
     698         \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\underline{ }version/};}
    652699         \uncover<3->{\node [green_small, right=0.4cm of box3] (box4) {trunk/};}
    653700         
    … …  
    661708         \uncover<5->{\node [notes, below=0.1cm of box3] (notes3) {\texttt{.mrun.config}};}
    662709         
    663          \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\_FOR\_RUN\_$<$run\_identifier$>$};}
     710         \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\underline{ }FOR\underline{ }RUN\underline{ }$<$run\underline{ }identifier$>$};}
    664711         
    665712         \uncover<1->{\node [dummy, left=1.5cm of box7] (dummy2) {};}
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