source: palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex @ 1799

% $Id: runs_with_mrun.tex 1526 2015-01-22 12:47:21Z gronemeier $
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\institute{Institute of Meteorology and Climatology, Leibniz UniversitÀt Hannover}
\selectlanguage{english}
\date{last update: \today}
\event{PALM Seminar}
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\title[Carrying out runs using mrun]{Carrying out runs using \texttt{mrun}}
\author{PALM group}

\begin{document}

% Folie 1
\begin{frame}
\titlepage
\end{frame}

\section{Carrying out runs using mrun}
\subsection{Carrying out runs using mrun}

% Folie 2
\begin{frame}
   \frametitle{What is \texttt{mrun}?}
   \footnotesize
   \begin{itemize}
      \item<1-> \texttt{mrun} (\textbf{m}odel \textbf{run}) is a shell script (using 
      \texttt{bash}/\texttt{ksh}-syntax) which can be used to compile and run programs, including 
      the handling of input/output files.
      \vspace{3mm}
      \item<2-> The \texttt{mrun}-command has a number of options to control the 
      program execution\\
         \vspace{3mm}
         \quad \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\
         \vspace{3mm}
         All options including a short description can be displayed by entering\\
         \vspace{3mm}
         \quad \texttt{mrun ?}
      \vspace{4mm}
      \item<3-> The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} 
   \end{itemize}
\end{frame}

% Folie 3
\begin{frame}
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\tiny]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, font=\tiny]
   \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\tiny]
   \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\tiny]
   \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\tiny]
   \tikzstyle{line} = [draw, -]
   \tikzstyle{alert} = [rectangle, draw, text width=0.77\textwidth, font=\scriptsize]
 
   \scriptsize
   \frametitle{Carrying Out Runs Using \texttt{mrun}}
   \textbf{Carrying out a program run typically needs two steps:}\\
   \vspace{1mm}
   \quad 1. compilation\\
   \qquad \texttt{f95  ...  file1.f90 file2.f90 ...}\\
   \vspace{1mm}
   \onslide<2->\quad 2. execution\\
   \qquad \texttt{a.out}\\
   \vspace{3mm}
   \onslide<3->\textbf{Besides, a program needs input data and creates output data:}\\
   
   \onslide<4->\begin{tikzpicture}[auto, node distance=0]
      \node [green] (first) {\textbf{a.out/} };
      \node [dummy, right=0.1cm of first] (second) {};
      
      \node [yellow, above=0.4cm of second] (third) {\textbf{parameter for steering}};
      \node [yellow, below=0.4cm of third] (fourth) {\textbf{control output}};
      \node [yellow, below=0.3cm of fourth] (fifth) {\textbf{output for analysis}};
      
      \node [info, above=-0.1cm of third] (sixth) {input file};
      \node [info, above=-0.1cm of fourth] (seventh) {output file 1};
      \node [info, above=-0.1cm of fifth] (eight) {output file 2};

      \draw [->] (third.west) -- (first.north);
      \draw [->] (first.east) -- (fourth.west);
      \draw [->] (first.south) -- (fifth.west);
      
      \uncover<5->{\node [white, right=0.25cm of third] (ninth) {
         \texttt{OPEN (11, FILE='PARIN', FORM='FORMATTED')}};}
      \uncover<5->{\node [white, right=0.25cm of fourth] (tenth) {
         \texttt{OPEN (15, FILE='RUN\underline{ }CONTROL', FORM='FORMATTED')}};}
      \uncover<5->{\node [white, right=0.25cm of fifth] (eleventh) {
         \texttt{OPEN (40, FILE=‘DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF', FORM='FORMATTED')}};}
   \end{tikzpicture}
   
   \vspace{3mm}
   \scriptsize
   \onslide<6->\textcolor{red}{\textbf{Problems:} The user has to copy or rename output files, if 
   he/she wants to run the program more than once and if he concurrently wants to keep 
   the files from the former run(s). If he/she is using different input parameter files for steering, these files also have 
   to be copied into the working directory before the program is executed.}\\
   \vspace{1mm}
   \begin{tikzpicture}[auto, node distance=0] 
      \uncover<7->{\node [alert] (alert) {\textcolor{red}{\textbf{It is therefore very desirable to automate these tasks!}}};}
   \end{tikzpicture}
\end{frame}

% Folie 4
\begin{frame}
   \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.10\textwidth, font=\scriptsize]
   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny]
   \scriptsize
   \frametitle{\texttt{mrun}: Principal Mode of Operation (I)}
   \texttt{mrun} \textbf{runs a program (in our case the PALM model) by carrying out the following principle tasks in a sequential order:}\\
   \begin{enumerate}
      \tiny
      \item<2-> Create a temporary working directory and change into this directory:\\
      \vspace{1.5mm}
      \scriptsize \quad \texttt{mkdir <tmpdir>/<username>.<randomnumber>}\\
      \quad \texttt{cd <tmpdir>/<username>.<randomnumber>}\\
      \tiny \ \\
      The path of \texttt{<tmpdir>} is given in the configuration file 
      \texttt{.mrun.config} by the environment variable \texttt{tmp\underline{ }user\underline{ }catalog}, e.g.:\\
      \vspace{1.5mm}
           \scriptsize \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /tmp \hspace{30mm} <hi>  parallel}\\
           \tiny \ \\
           \onslide<3-> On Cray-XC30: \\
      \vspace{1.5mm}
           \scriptsize \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /gfs1/work/<username> 
           \hspace{5mm} lcsgih parallel}
      \vspace{1mm}
           \begin{center}
              \begin{tikzpicture}[auto, node distance=0] 
            \uncover<4->{\node [green] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
         \end{tikzpicture}
           \end{center}
           \vspace{2mm}
           \item<5-> \fontsize{7}{1} Copy the input files from a directory of the user into this working directory:\\
           \vspace{1mm}
           \onslide<6-> \tiny \quad \texttt{cp <user\underline{ }input\underline{ }file1> 
           /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file1>}\\
      \quad \texttt{cp <user\underline{ }input\underline{ }file2> 
      /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file2>}\\
      \vspace{2mm}
      \scriptsize
      \begin{center}
              \begin{tikzpicture}[auto, node distance=0] 
              
            \uncover<8->{\node [green] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
       
            \uncover<7->{\node [yellowsmall, above=0.1cm of green] (yellow2) {JOBS/};}
            \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\underline{ }version/};}
            \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
            \uncover<7->{\node [yellowsmall, right=0.2cm of yellow3] (yellow4) {INPUT/};}
            
            \draw<7-> [-] (yellow1.east) -- (yellow2.west);
            \draw<7-> [-] (yellow2.east) -- (yellow3.west);
            \draw<7-> [-] (yellow3.east) -- (yellow4.west);
            
            \node [dummy, right=0.06cm of yellow4] (dummy1) {};
            \node [dummy, below=0.38cm of dummy1] (dummy2) {};
            
            \draw<9-> [-] (yellow4.east) -- (dummy1.center);
            \draw<9-> [-] (dummy1.center) -- (dummy2.center);
            \draw<9-> [->] (dummy2.center) -- (green.east);
            
         \end{tikzpicture}
           \end{center}
      
        \end{enumerate}

\end{frame}

% Folie 5
\begin{frame}
   \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm]
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   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
   
   \frametitle{\texttt{mrun}: Principal Mode of Operation (II)}

        \begin{enumerate}
      \setcounter{enumi}{2}
           \item<1-> Copy the pre-compiled routines to the temporary working directory:\\
      
      \begin{center}
              \begin{tikzpicture}[auto, node distance=0] 
                 \uncover<2->{\node [yellow] (yellow) {current\underline{ }version/};}
                 \uncover<1->{\node [dummy, right=0.0cm of yellow] (dummy1) {};}
                 \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\underline{ }DEPOSITORY\underline{ }\textit{parallel}/};}
                 \uncover<1->{\node [dummy, right=0.2cm of green1] (dummy2) {};}
            \uncover<3->{\node [green, below=0.5cm of dummy1] (green2) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
             \uncover<1->{\node [dummy, below=0.5cm of dummy2] (dummy3) {};}
             \uncover<4->{\node [dummy, right=0.0cm of dummy3] (text) {Makefile\\
                 *.f90\\
                 *.o\\
                 ...\\ \ \\};}
             
             \draw<2-> [-] (yellow.east) -- (green1.west);
             \draw<4-> [-] (green1.east) -- (dummy2.center);
             \draw<4-> [-] (dummy2.center) -- (dummy3.center);
             \draw<4-> [->] (dummy3.center) -- (green2.east);
              \end{tikzpicture}
           \end{center}
           
           \item<5-> Compile the main program and use pre-compiled object files:\\
     \quad \texttt{f95 palm.f90 *.o ...   ( make Makefile)}
      \item<6-> Execute the program:\\
     \quad \texttt{a.out}
   \end{enumerate}
\end{frame}

% Folie 6
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   \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm]
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   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
   
   \frametitle{\texttt{mrun}: Principal Mode of Operation (III)}
   \footnotesize 
        \begin{enumerate}
      \setcounter{enumi}{5}
           \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\
       \vspace{1mm}
       \tiny \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\
      \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\
      \footnotesize 
      \begin{center}
         \begin{tikzpicture}[auto, node distance=0] 
            \uncover<2->{\node [yellow] (yellow1) {MONITORING/ };}

            \uncover<2->{\node [dummy, right=0.2cm of yellow1] (dummy2) {};}
            \uncover<2->{\node [dummy, above=0.2cm of dummy2] (dummy1) {};}
            \uncover<2->{\node [dummy, below=0.2cm of dummy2] (dummy3) {};}
            
            \uncover<2->{\node [yellow, left=0.2cm of dummy3] (yellow2) {OUTPUT/};}
            \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
            \uncover<2->{\node [yellow, left=0.2cm of yellow3] (yellow4) {JOBS/};}
            \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};}
                                             
                 \uncover<2-3>{\node [green, left=4.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
                 
            \draw<2-3> [-] (green.east) -- (dummy1.center);
            \draw<2-3> [-] (dummy2.center) -- (dummy1.center);
            \draw<2-3> [-] (dummy3.center) -- (dummy1.center);
            
            \draw<2-3> [->] (dummy2.center) -- (yellow1.east);
            \draw<2-3> [->] (dummy3.center) -- (yellow2.east);
            
            \draw<2-> [-] (yellow2.west) -- (yellow3.east);
            \draw<2-> [-] (yellow3.west) -- (yellow4.east);
            \draw<2-> [-] (yellow4.west) -- (yellow5.east);
                
        \end{tikzpicture}
     \end{center}
           
           \item<3-> Delete the temporary working directory\\
      \quad \texttt{rm -rf /<tmpdir>/<username>.<randomnumber>}\\
      \vspace{2mm}
      \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?}

   \end{enumerate}
\end{frame}

% Folie 7
\begin{frame}
   \tikzstyle{small} = [rectangle, text width=0.08\textwidth, font=\scriptsize]
   \tikzstyle{large} = [rectangle, text width=0.45\textwidth, font=\scriptsize]
   \tikzstyle{box} = [rectangle, draw, text width=0.2\textwidth, font=\scriptsize]
   \tikzstyle{boxbig} = [rectangle, draw, text width=0.4\textwidth, font=\scriptsize]
   \tikzstyle{dummy} = [rectangle, text width=0.0\textwidth, font=\scriptsize, minimum height=0.5cm]
   
   \frametitle{Steering File Copy by the Configuration File (I)}
   \scriptsize
   \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.}\\
   \vspace{3mm}
   Principle example of a file connection statement (for the PALM parameter file):
   \vspace{-3mm}
   \begin{center}
           \begin{tikzpicture}[auto, node distance=0] 
         \uncover<1->{\node [small] (part1) {\texttt{PARIN}};}
         \uncover<1->{\node [dummy, left=-0.2cm of part1] (dummy1) {};}
         \uncover<1->{\node [dummy, below=1.25cm of dummy1] (dummy3) {};}
         \uncover<1->{\node [small, right=0.0cm of part1] (part2) {\quad \texttt{in}};}
         \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
         \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
              \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
              \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
              \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
                    
         \uncover<2->{\node [boxbig, below=1.25cm of dummy2] (box1) {local filename in the working directory (must correspond to the filename in the \texttt{OPEN} statement of the program)};}
              \draw<2-> [->] (dummy3.north) -- (dummy1.south);
              
              \uncover<3->{\node [box, below=0.7cm of part2] (box2) {file attributes};}
              \draw<3-> [->] (box2.north) -- (part2.south);
              
              \uncover<4->{\node [box, below=0.2cm of part3] (box3) {activating string};}
              \draw<4-> [->] (box3.north) -- (part3.south);
                      
              \uncover<5->{\node [box, below=0.2cm of part4] (box4) {directory in which the permanent user file resides};}
              \draw<5-> [->] (box4.north) -- (part4.south);
              
         \uncover<6->{\node [box, below=0.2cm of part5] (box5) {suffix of the permanent filename};}
              \draw<6-> [->] (box5.north) -- (part5.south);
              
         \uncover<7->{\node [box, below=1.0cm of part6] (box6) {additional suffix for netCDF files};}
              \draw<7-> [->] (box6.north) -- (part6.south);    
           \end{tikzpicture}
        \end{center}
   
\end{frame}


% Folie 8
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   \tikzstyle{small} = [rectangle, text width=0.08\textwidth, font=\scriptsize]
   \tikzstyle{large} = [rectangle, text width=0.45\textwidth, font=\scriptsize]
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   \tikzstyle{boxbig} = [rectangle, draw, text width=0.4\textwidth, font=\scriptsize]
   \tikzstyle{dummy} = [rectangle, text width=0.0\textwidth, font=\scriptsize, minimum height=0.5cm]
   
   \frametitle{Steering File Copy by the Configuration File (II)}
   \scriptsize
   \begin{center}
           \begin{tikzpicture}[auto, node distance=0] 
         \uncover<1->{\node [small] (part1) {\texttt{PARIN}};}
         \uncover<1->{\node [dummy, left=-0.2cm of part1] (dummy1) {};}
         \uncover<1->{\node [dummy, below=1.25cm of dummy1] (dummy3) {};}
         \uncover<1->{\node [small, right=0.0cm of part1] (part2) {\quad \texttt{in}};}
         \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
         \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
              \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
              \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
              \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
                    
         \uncover<1->{\node [boxbig, below=1.25cm of dummy2] (box1) {local filename in the working directory (must correspond to the filename in the \texttt{OPEN} statement of the program)};}
              \draw<1-> [->] (dummy3.north) -- (dummy1.south);
              
              \uncover<1->{\node [box, below=0.7cm of part2] (box2) {file attributes};}
              \draw<1-> [->] (box2.north) -- (part2.south);
              
              \uncover<1->{\node [box, below=0.2cm of part3] (box3) {activating string};}
              \draw<1-> [->] (box3.north) -- (part3.south);
                      
              \uncover<1->{\node [box, below=0.2cm of part4] (box4) {directory in which the permanent user file resides};}
              \draw<1-> [->] (box4.north) -- (part4.south);
              
         \uncover<1->{\node [box, below=0.2cm of part5] (box5) {suffix of the permanent filename};}
              \draw<1-> [->] (box5.north) -- (part5.south);
              
         \uncover<1->{\node [box, below=1.0cm of part6] (box6) {additional suffix for netCDF files};}
              \draw<1-> [->] (box6.north) -- (part6.south);    
           \end{tikzpicture}
        \end{center}
   \vspace{3mm}
   \onslide<2->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}:\\
   \footnotesize \quad \texttt{mrun -d \textcolor{blue}{example\underline{ }cbl} ...}\\
   \vspace{1mm}
   \scriptsize gives the filename\\
   \vspace{1mm}
   \footnotesize \quad \texttt{\~{}/palm/current\underline{ }version/JOB/INPUT/\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d}\\
   \quad \texttt{( ... /\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d\textcolor{red}{.nc} )}
   
\end{frame}


% Folie 9
\begin{frame}
   \frametitle{Steering File Copy by the Configuration File (III)}
   \tiny
   \onslide<1-> The \textbf{base name} can additionally be a part of the directory name 
   by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\
   \vspace{1mm}
   \scriptsize\quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
   \vspace{4mm}
   \onslide<2-> \tiny Using the call\\
   \vspace{1mm}
   \scriptsize \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\
   \vspace{1mm}
   \tiny the input file will be expected under\\
   \vspace{1mm}
   \scriptsize \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\
   \vspace{4mm}
   \onslide<3-> \tiny In this way, all files handled by the \texttt{mrun}-call are stored in 
   the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as 
   part of their names, so they can be easily identified as \grqq belonging\grqq\, to the model 
   run initiated by that \texttt{mrun} call.\\
   \ \\
   \onslide<4-> Instead of always writing the full path name (i.e. 
   \texttt{\~{}/palm/current\underline{ }version/JOBS}), an environment variable can be declared for 
   this at the beginning of the configuration file and be used in the file 
   connection statements:\\
   \vspace{1mm}
   \scriptsize \quad \texttt{\%base\underline{ }data  \~{}/palm/current\underline{ }version/JOBS}\\
   \quad \texttt{PARIN in d3\#  \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
   \ \\
   \onslide<5-> \tiny This easily allows to change the directories for all input/output files 
   by just changing the value of \texttt{base\underline{ }data}.
   
\end{frame}

% Folie 10
\begin{frame}
   \frametitle{Steering File Copy by the Configuration File (IV)}
   \tiny
   \onslide<1-> File connection statements which shall be carried out, 
   have to be activated by giving their activation string in the 
   \texttt{mrun}-option \texttt{-r}:\\
   \vspace{1mm}
   \scriptsize \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\
   \ \\
   \onslide<2-> \tiny The permanent file\\
   \vspace{1mm}
   \scriptsize \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} \\
   \vspace{2mm}
   \tiny will only be copied to the local file PARIN by using the call:\\
   \vspace{1mm}
   \scriptsize \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\
   \ \\
   \onslide<3-> \tiny \textbf{Example for an output file:}\\
   The file connection statement\\
   \vspace{1mm}
   \scriptsize \quad \texttt{DATA\underline{ }1D\underline{ }PR\_NETCDF out:loc pr\# } \\
   ~~~~~~\texttt{\~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}s\\
   \vspace{2mm}
   \onslide<4-> \tiny will copy (after program execution) the local file \\
   \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file \\
   \vspace{1mm}
   \scriptsize \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc}\\
   \vspace{1mm}
   \tiny if \texttt{mrun} is called with the options\\
   \vspace{1mm}
   \scriptsize \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...}
   
\end{frame}

% Folie 11
\begin{frame}
   \frametitle{Steering File Copy by the Configuration File (V)}
   \scriptsize 
   \onslide<1-> \texttt{mrun} never replaces/overwrites existing files!\\
   \ \\
   \tiny Instead, new, so-called file cycles are created.\\
   If an output file, e.g.\\
   \vspace{1mm}
   \scriptsize \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc}\\
   \ \\
   \ \\
   \tiny has been created from a first call of \texttt{mrun} and if the same \texttt{mrun} 
   call is submitted again, the second call will not replace the file 
   \texttt{example\underline{ }cbl\underline{ }rc}, but will create a new file with name:\\
   \vspace{1mm}
   \scriptsize \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc.1}\\
   \ \\
   \ \\
   \onslide<2-> \tiny In case of netCDF-files, the file cycle number is inserted before 
   the netCDF-suffix .nc, e.g.\\
   \vspace{1mm}
   \scriptsize \quad \texttt{example\underline{ }cbl\underline{ }pr.1.nc}\\
   \ \\
   \ \\
   \onslide<3-> \tiny The implemented file cycle mechanism does not allow to use 
   any other dots "'."'  in the path or filename:\\
   \vspace{1mm}
   \scriptsize \quad \texttt{\~{}/palm/version\underline{ }3.6/JOBS/example.sbl/MONITORING/example.sbl\underline{ }rc}\\
\end{frame}

% Folie 12
\begin{frame}[fragile]
   \frametitle{\normalsize File Connection Statements From the Default \texttt{.mrun.config} file}
   \begin{columns}
      \column{1.1\textwidth}
      \tiny
      \begin{lstlisting}
#----------------------------------------------------------------------------
# List of input-files
#----------------------------------------------------------------------------
PARIN                    in:job        d3#      $base_data/$fname/INPUT    _p3d
PARIN                    in:job        d3f      $base_data/$fname/INPUT    _p3df
TOPOGRAPHY_DATA          in:locopt     d3#:d3f  $base_data/$fname/INPUT    _topo
NUDGING_DATA             in:locopt     d3#:d3f  $base_data/$fname/INPUT    _nudge
LSF_DATA                 in:locopt     d3#:d3f  $base_data/$fname/INPUT    _lsf
BININ                    in:loc:flpe   d3f      $base_data/$fname/RESTART  _d3d
PARTICLE_RESTART_DATA_IN in:loc:flpe   prtf     $base_data/$fname/RESTART  _rprt
DATA_1D_PR_NETCDF        in:locopt     prf      $base_data/$fname/OUTPUT   _pr     nc
DATA_1D_SP_NETCDF        in:locopt     spf      $base_data/$fname/OUTPUT   _sp     nc
DATA_1D_TS_NETCDF        in:locopt     tsf      $base_data/$fname/OUTPUT   _ts     nc
DATA_1D_PTS_NETCDF       in:locopt     ptsf     $base_data/$fname/OUTPUT   _pts    nc
DATA_2D_XY_NETCDF        in:locopt     xyf      $base_data/$fname/OUTPUT   _xy     nc
DATA_2D_XY_AV_NETCDF     in:locopt     xyf      $base_data/$fname/OUTPUT   _xy_av  nc
DATA_2D_XZ_NETCDF        in:locopt     xzf      $base_data/$fname/OUTPUT   _xz     nc
DATA_2D_YZ_NETCDF        in:locopt     yzf      $base_data/$fname/OUTPUT   _yz     nc
DATA_3D_NETCDF           in:locopt     3df      $base_data/$fname/OUTPUT   _3d     nc
DATA_PRT_NETCDF          in:locopt:pe  prtf     $base_data/$fname/OUTPUT   _prt
#
#----------------------------------------------------------------------------
# List of output-files
#----------------------------------------------------------------------------
BINOUT                    out:loc:flpe restart   $base_data/$fname/RESTART  _d3d
PARTICLE_RESTART_DATA_OUT out:loc:flpe prt#:prtf $base_data/$fname/RESTART  _rprt
#
RUN_CONTROL       out:loc:tr   d3#     $base_data/$fname/MONITORING  _rc
RUN_CONTROL       out:loc:tra  d3f     $base_data/$fname/MONITORING  _rc
HEADER            out:loc:tr   d3#     $base_data/$fname/MONITORING  _header
HEADER            out:loc:tra  d3f     $base_data/$fname/MONITORING  _header
CPU_MEASURES      out:loc:tr   d3#     $base_data/$fname/MONITORING  _cpu
CPU_MEASURES      out:loc:tra  d3f     $base_data/$fname/MONITORING  _cpu
      \end{lstlisting}
   \end{columns}


\end{frame}

% Folie 13
\begin{frame}[fragile]
   \frametitle{Additional Features of \texttt{mrun} (I)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.975\textwidth, font=\Tiny]
   \begin{itemize}
      \footnotesize
      \item<1-> Generating batch jobs on local \textbf{and} remote host.
      \item<2-> Setting of unix environment variables for job and model control (e.g. for determining compiler options, etc.).
      \item<3-> Values have to be set in the \texttt{mrun} configuration file \texttt{.mrun.config}:
   \end{itemize}
   \onslide<4->
   \begin{center}
      \begin{tikzpicture}
        \node [yellow]{\begin{lstlisting}
%tmp_user_catalog    /gfs1/work/<replace by your HLRN-III username>     lccrayh parallel
%tmp_data_catalog    /gfs1/work/<replace by your HLRN-III username>     lccrayh parallel
%compiler_name       ftn                                                lccrayh parallel
%compiler_name_ser   ftn                                                lccrayh parallel
%cpp_options         -e:Z:-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:...
%mopts               -j:4                                               lccrayh parallel
%fopts               -em:-O3:-hnoomp:-hfp3:-hdynamic                    lccrayh parallel
%lopts               -em:-O3:-hnoomp:-hfp3:-hdynamic:-dynamic           lccrayh parallel
%remote_username     <replace by your HLRN-III username>                lccrayh parallel
%memory              2300                                               lccrayh parallel
%modules             fftw:cray-hdf5-parallel:cray-netcdf-hdf5parallel   lccrayh parallel
\end{lstlisting}};
      \end{tikzpicture}
   \end{center}
\end{frame}

% Folie 14
\begin{frame}[fragile]
   \frametitle{Additional Features of \texttt{mrun} (II)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.9\textwidth, font=\Tiny]

   \begin{itemize}
      \footnotesize
      \item<1-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands).
      These commands can also be defined in the \texttt{mrun} configuration file:
      \onslide<2->
      \begin{center}
         \begin{tikzpicture}
            \node [yellow]{\begin{lstlisting}
IC:echo ``PALM will soon start to execute in \$PWD'' > /home/h/niksiraa/mrun_messages
EC:ls -al
OC:tar -cf DEBUG.tar DEBUG_*
\end{lstlisting}};
         \end{tikzpicture}
      \end{center}
      \item<3-> Automatic generation of restart jobs.
   \end{itemize}


\end{frame}

% Folie 15
\begin{frame}[fragile]
   \frametitle{PALM \textit{Interactive} Example Run Using \texttt{mrun}: Tracing the Run by the User}
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
   \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.55\textwidth, font=\tiny, minimum height=0.6cm]
   \tikzstyle{notes} = [rectangle, text width=0.26\textwidth, font=\tiny, minimum height=0.6cm]
   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny, minimum height=0.6cm]
      \tikzstyle{green_term} = [rectangle, draw, fill=green!30, text width=0.83\textwidth, font=\Tiny,scale=0.6]
   \vspace{-1.0cm}
   \begin{center}
           \begin{tikzpicture}[auto, node distance=0] 
         \uncover<1->{\node [yellow] (box1) {\textbf{start run on local machine:}\\
                                            \texttt{mrun -d example\underline{ }cbl -h lcmuknb ...}};}
         \uncover<1->{\node [dummy, right=1.4cm of box1] (dummy1) {};}
         \uncover<2->{\node [notes, above=-0.3cm of dummy1] (notes1) {temporary working directory is created, all required files are copied there};}
         \uncover<3->{\node [green, right=1.4cm of dummy1] (box2) {\textbf{follow run messages on terminal}};}
         \uncover<4->{\node [green, below=0.5cm of box2] (box3) {
         \textbf{as soon as message}
         
         \texttt{*** execution starts in directory\\ \quad \dq <tmpdir>\dq\, }\\
         \ \\
         \textbf{you can change to this directory (in a new terminal) and watch the progess of timesteps}

         \texttt{cd <tmpdir>}\\
         \texttt{tail -f RUN\underline{ }CONTROL}\\
         \ \\
         However, this might be difficult in case of short run times, because the run may have finished before you have entered the commands!
         };}
         \coordinate[below=0.3cm of box3] (A);
         \uncover<1->{\node [dummy, left=0.3cm of box3] (dummy2) {};}
         \uncover<6->{\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};}
         \uncover<7->{\node [yellow_big, left=2.5cm of A] (box4) {
         \textbf{check, if the output files have sucessfully been transferred to the permanent directory:}\\
         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING}\\
         \texttt{ls -al}\\
         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT}\\
         \texttt{ls -al}
};}
         \draw<2-> [->,color=blue] (box1.east) -- (box2.west);    
         \draw<4-> [->,color=blue] (box2.south) -- (box3.north);  
         \draw<6-> [-,color=blue] (box3.south) -- (A);  
         \draw<6-> [->,color=blue] (A) -- (box4.east);  
         \onslide<5->\node [green_term, left=1.2cm of box3] (terminal) {\begin{lstlisting}  
  *** running on: laptop laptop

      ... reading environment parameters from ENVPAR      --- finished
      ... reading NAMELIST parameters from PARIN      --- finished
      ... creating virtual PE grids + MPI derived data types      --- finished
      ... checking parameters      --- finished
      ... allocating arrays      --- finished
      ... initializing with constant profiles      --- finished
      ... initializing statistics, boundary conditions, etc.      --- finished
      ... creating initial disturbances      --- finished
      ... calling pressure solver      --- finished
      --- leaving init_3d_model
      --- start with time-stepping

      [XXXXXXXXXXXXXXXXXXXXXXXXXXXX________________________________]  53.3 left
\end{lstlisting}
         };
         \uncover<5->{\node [notes, above=0.0cm of terminal, text width=0.55\textwidth] (notes_terminal) {Starting from version 3.10 (r 1402), some progress messages and a progress bar for estimating the time required to finish the simulation is output on the terminal};}
         %\draw<5-> [->,color=blue] (box3.west) -- (terminal.east); 
         \onslide<1-> 
           \end{tikzpicture}
        \end{center}
\end{frame}

% Folie 16
\begin{frame}
   \frametitle{PALM \textit{Batch} Example Run (on HLRN, remote) Using \texttt{mrun}: Tracing the Run by the User}
\tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, font=\Tiny]
\tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.4\textwidth, font=\Tiny]
\tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.4\textwidth, font=\Tiny]
\tikzstyle{dummy} = [text width=0.2\textwidth, font=\Tiny]
\tikzstyle{alert} = [rectangle, draw, text width=0.5\textwidth, font=\scriptsize]
\tikzstyle{line} = [draw, -latex']
\begin{itemize}
   \item \small Reminder: Running batch jobs requires a directory \texttt{~/job\underline{ }queue} for the job protocol files on the local \underline{and} remote host.
\end{itemize}
\begin{tikzpicture}[auto, node distance=0]
    \node [yellow] (first) {
       \textbf{start job on local machine:}\\
       \texttt{mrun -d example\underline{ }cbl -h lccrayh ...}
    };
\uncover<2->{
    \node [dummy, right=0.5cm of first] (dummy) {
       transfer of job by \texttt{scp} \\
       \ \\
       \ \\
       submit of job by executing the \texttt{msub} command via \texttt{ssh}
    };
}
\uncover<3->{
    \node [green, right=3.5cm of first] (second) {
       \textbf{follow job execution on remote host, by} \\
       \texttt{showq} (better: \texttt{showq | grep hzkurs})
    };
}
\uncover<4->{
    \node [green, below=0.2cm of second] (third) {
       \textbf{if job is running, you may follow its progress by watching the job protocol (does not work on HLRN-III system!):} \\ 
       \texttt{cd \~{}/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
    };
}
\uncover<5->{
    \node [green, below=0.2cm of third] (fourth) {
       \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}\\
       \texttt{tail -f RUN\underline{ }CONTROL}
    };
}
\uncover<6->{
    \node [green, below=0.2cm of fourth] (fifth) {
       \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\
       \texttt{cd \~{}/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}
    };
}
\uncover<7->{
    \node [dummy, left=0.001mm of fifth] (dummy) {
       transfer results by \texttt{scp} \\
       \ \\
       \ \\
    };
}
\uncover<8->{
    \node [yellow2, left=2.5cm of fifth] (sixth) {
       \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\
       \texttt{cd \~{}/job\_queue \\ ls -al \\ cd \~{}/palm/current\_version/JOBS/example \\ ls -al *}
    };
}
\uncover<9->{
     \node [alert, below=0.5cm of first.south east] (alert) {
        \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 \textbf{mrun} and \textbf{subjob} script!}
     };
}
    \path<2-> [line] (first) -- (second);
    \path<4-> [line] (second) -- (third);
    \path<5-> [line] (third) -- (fourth);
    \path<6-> [line] (fourth) -- (fifth);
    \path<7-> [line] (fifth) -- (sixth);
\end{tikzpicture}
\end{frame}



% Folie 17
\begin{frame}
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
   \tikzstyle{green_small} = [rectangle, draw, fill=green!20, text width=0.12\textwidth, font=\scriptsize, minimum height=0.6cm]
   \tikzstyle{yellow_small} = [rectangle, draw, fill=yellow!20, text width=0.1\textwidth, font=\scriptsize, minimum height=0.6cm]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, font=\scriptsize, minimum height=0.6cm]
   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
   \tikzstyle{notes} = [rectangle, text width=0.15\textwidth, font=\scriptsize, minimum height=0.6cm]
   
   \frametitle{PALM Runs Using \texttt{mrun}: Further Details}
   \begin{itemize}
      \footnotesize
      \item<2-> For every (initial) run, \texttt{mrun} creates a source directory which contains copies of
      \begin{itemize}
         \footnotesize
         \item<4-> those source code files to be translated (always the main program, \texttt{palm.f90}, plus user interface files)
         \item<4-> the Makefile
         \item<5-> the configuration file
         \item<6-> the mrun script
      \end{itemize}
   \end{itemize}
   
   \vspace{-0.8cm}
   \begin{center}
           \begin{tikzpicture}[auto, node distance=0] 
           
         \uncover<3->{\node [yellow_small] (box1) {\$HOME/};}
         \uncover<3->{\node [yellow_small, right=0.2cm of box1] (box2) {palm/};}
         \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\underline{ }version/};}
         \uncover<3->{\node [green_small, right=0.4cm of box3] (box4) {trunk/};}
         
         \uncover<1->{\node [dummy, right=1.0cm of box4] (dummy1) {};}
         
         \uncover<3->{\node [green_small, above=-0.2cm of dummy1] (box5) {SCRIPTS};}
         \uncover<3->{\node [green_small, below=-0.2cm of dummy1] (box6) {SOURCE};}
         
         \uncover<6->{\node [notes, right=0.1cm of box5] (notes1) {\texttt{mrun}};}
         \uncover<4->{\node [notes, right=0.1cm of box6] (notes2) {\texttt{Makefile \\ palm.f90}};}
         \uncover<5->{\node [notes, below=0.1cm of box3] (notes3) {\texttt{.mrun.config}};}
          
         \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\underline{ }FOR\underline{ }RUN\underline{ }$<$run\underline{ }identifier$>$};}
         
         \uncover<1->{\node [dummy, left=1.5cm of box7] (dummy2) {};}
         \uncover<1->{\node [dummy, right=2.0cm of box5] (dummy3) {};}
         \uncover<1->{\node [dummy, right=1.8cm of box6] (dummy4) {};}
         \uncover<1->{\node [dummy, below=0.2cm of dummy4] (dummy5) {};}
         \draw<3-> [-] (box1.east) -- (box2.west);  
         \draw<3-> [-] (box2.east) -- (box3.west);  
         \draw<3-> [-] (box3.east) -- (box4.west);  
         \draw<3-> [-] (box4.east) -- (box5.west);  
         \draw<3-> [-] (box4.east) -- (box6.west);     
         \draw<3-> [-] (box3.east) -- (box7.west);    
         \draw<6-> [-] ([xshift=-0.8cm]notes1.east) -- (dummy3.center);    
         \draw<4-> [-] ([xshift=-0.4cm]notes2.east) -- (dummy4.center); 
         \draw<4-> [-] (dummy4.center) -- ([yshift=0.1cm]dummy5.center); 
         \draw<4-> [->] ([yshift=0.1cm]dummy5.center) -- ([yshift=0.1cm]box7.east); 
         \draw<6-> [-] (dummy3.center) -- ([xshift=0.2cm, yshift=-0.1cm]dummy5.center); 
         \draw<6-> [->] ([xshift=0.2cm, yshift=-0.1cm]dummy5.center) -- ([yshift=-0.1cm]box7.east);
         \draw<5-> [-] ([yshift=0.3cm]dummy2.center) -- (dummy2.center);    
         \draw<5-> [->] (dummy2.center) -- (box7.west);    
           \end{tikzpicture}
        \end{center}
   
   \begin{itemize}
      \footnotesize
      \item<7-> These files are used in the run/job. They are also used by restart jobs, which guarantees, that all jobs in a job chain are using the same information. Please never modify these directories, unless you exactly know, what you are doing.
   \end{itemize}
\end{frame}


% Folie 17
\begin{frame}
 \footnotesize \texttt{mrun}
   \frametitle{PALM Runs Using \texttt{mrun}: most important \texttt{mrun} options}
   \begin{itemize}
      \footnotesize
      \item<2-> \texttt{-d example\_cbl}
      \begin{itemize}
         \item[] \tiny run identifier, basefile/directory name of all data files of this run
      \end{itemize}
      \item<3-> \texttt{-h} host identifier
      \begin{itemize}
         \item[] \tiny host on which the run shall be performed (reminder: this is not the UNIX hostname):\\ \texttt{lcmuknb, lcmuk, lccrayh...}
      \end{itemize}
      \item<4-> \texttt{-K parallel}
      \begin{itemize}
         \item[] \tiny run in parallel on several processor cores
      \end{itemize}
      \item<5-> \texttt{-X 4}
      \begin{itemize}
         \item[] \tiny number of processors to be used
      \end{itemize}
      \item<6-> \texttt{-T 4}
      \begin{itemize}
         \item[] \tiny number of tasks to be started on one node of the computer
      \end{itemize}
      \item<7-> \texttt{-t 100}
      \begin{itemize}
         \item[] \tiny CPU time allowed to be used for the batch jobs
      \end{itemize}
      \item<8-> \texttt{-b}
      \begin{itemize}
         \item[] \tiny run in batch mode
      \end{itemize}
      \item<9-> \texttt{-q mpp1q}
      \begin{itemize}
         \item[] \tiny batch job queue
      \end{itemize}
      \item<10-> \texttt{-r \dq ...\dq}
      \begin{itemize}
         \item[] \tiny activation strings
      \end{itemize}
   \end{itemize}   
\end{frame}
\end{document}