Index: palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex	(revision 1165)
+++ palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex	(revision 1226)
@@ -65,11 +65,14 @@
       \texttt{ksh}-syntax) which can be used to compile and run programs, including 
       the handling of input/output files.
-      \vspace{4mm}
+      \vspace{3mm}
       \item<2-> The \texttt{mrun}-command has a number of options to control the 
       program execution\\
+         \vspace{2mm}
          \quad \footnotesize \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\
+         \vspace{2mm}
          \normalsize All options including a short description can be displayed by entering\\
+         \vspace{2mm}
          \quad \footnotesize \texttt{mrun ?}
-      \vspace{4mm}
+      \vspace{3mm}
       \item<3-> \normalsize The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} 
    \end{itemize}
@@ -184,6 +187,6 @@
             \draw<7-> [-] (yellow3.east) -- (yellow4.west);
             
-            \node [dummy, right=0.1cm of yellow4] (dummy1) {};
-            \node [dummy, right=2.055cm of green] (dummy2) {};
+            \node [dummy, right=0.06cm of yellow4] (dummy1) {};
+            \node [dummy, below=0.38cm of dummy1] (dummy2) {};
             
             \draw<9-> [-] (yellow4.east) -- (dummy1.center);
@@ -240,5 +243,5 @@
 \begin{frame}
    \tikzstyle{green} = [rectangle, draw, fill=green!20, 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{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\scriptsize, minimum height=0.6cm]
    \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
    
@@ -248,10 +251,11 @@
       \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/};}
+         \begin{tikzpicture}[auto, node distance=0] 
+            \uncover<2->{\node [yellow] (yellow1) {MONITORING/ };}
 
             \uncover<2->{\node [dummy, right=0.2cm of yellow1] (dummy2) {};}
@@ -264,5 +268,5 @@
             \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};}
                       	                     
-	         \uncover<2-3>{\node [green, left=5.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
+	         \uncover<2-3>{\node [green, left=4.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}
 	         
             \draw<2-3> [-] (green.east) -- (dummy1.center);
@@ -277,6 +281,6 @@
             \draw<2-> [-] (yellow4.west) -- (yellow5.east);
 	        
-	      \end{tikzpicture}
-	   \end{center}
+	\end{tikzpicture}
+     \end{center}
 	   
 	   \item<3-> Delete the temporary working directory\\
@@ -348,11 +352,15 @@
    \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}
    \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
-   \ \\
+   \vspace{1mm}
    \onslide<2-> Using the call\\
+   \vspace{1mm}
    \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\
+   \vspace{1mm}
    the input file will be expected under\\
+   \vspace{1mm}
    \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\
-   \ \\
+   \vspace{1mm}
    \onslide<3-> 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 
@@ -364,4 +372,5 @@
    this at the beginning of the configuration file and be used in the file 
    connection statements:\\
+   \vspace{1mm}
    \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}\\
@@ -379,19 +388,27 @@
    have to be activated by giving their activation string in the 
    \texttt{mrun}-option \texttt{-r}:\\
+   \vspace{1mm}
    \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\
    \ \\
    \onslide<2-> The permanent file 
+   \vspace{1mm}
    \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} 
+   \vspace{1mm}
    will only be copied to the local file PARIN by using the call:\\
+   \vspace{1mm}
    \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\
    \ \\
    \onslide<3-> \textbf{Example for an output file:}\\
    The file connection statement\\
-   \quad \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF out:loc pr\# 
-   \~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}\\
+   \vspace{1mm}
+   \quad \texttt{DATA\underline{ }1D\underline{ }PR\_NETCDF out:loc pr\# \textbackslash} \\
+   ~~~~~~\texttt{\~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}s\\
+   \vspace{1mm}
    \onslide<4-> will copy (after program execution) the local file 
    \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file 
+   \vspace{1mm}
    \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc} if
    \texttt{mrun} is called with the options\\
+   \vspace{1mm}
    \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...}
    
@@ -458,75 +475,76 @@
 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
-#
-DATA_1D_PR_NETCDF    out:loc:tr   pr#:prf   $base_data/$fname/OUTPUT  _pr     nc
-DATA_1D_SP_NETCDF    out:loc:tr   sp#:spf   $base_data/$fname/OUTPUT  _sp     nc
-DATA_1D_TS_NETCDF    out:loc:tr   ts#:tsf   $base_data/$fname/OUTPUT  _ts     nc
-DATA_1D_PTS_NETCDF   out:loc:tr   pts#:ptsf $base_data/$fname/OUTPUT  _pts    nc
-DATA_2D_XY_NETCDF    out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy     nc
-DATA_2D_XY_AV_NETCDF out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy_av  nc
-DATA_2D_XZ_NETCDF    out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz     nc
-DATA_2D_XZ_AV_NETCDF out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz_av  nc
-DATA_2D_YZ_NETCDF    out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz     nc
-DATA_2D_YZ_AV_NETCDF out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz_av  nc
-DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d     nc
-DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av  nc
-DATA_MASK_01_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01     nc
-DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01_av  nc
-DATA_MASK_02_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02     nc
-DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02_av  nc
-DATA_MASK_03_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03     nc
-DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03_av  nc
-DATA_MASK_04_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04     nc
-DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04_av  nc
-DATA_MASK_05_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05     nc
-DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05_av  nc
-DATA_MASK_06_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06     nc
-DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06_av  nc
-DATA_MASK_07_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07     nc
-DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07_av  nc
-DATA_MASK_08_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08     nc
-DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08_av  nc
-DATA_MASK_09_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09     nc
-DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09_av  nc
-DATA_MASK_10_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10     nc
-DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10_av  nc
-DATA_MASK_11_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11     nc
-DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11_av  nc
-DATA_MASK_12_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12     nc
-DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12_av  nc
-DATA_MASK_13_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13     nc
-DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13_av  nc
-DATA_MASK_14_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14     nc
-DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14_av  nc
-DATA_MASK_15_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15     nc
-DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15_av  nc
-DATA_MASK_16_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16     nc
-DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16_av  nc
-DATA_MASK_17_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17     nc
-DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17_av  nc
-DATA_MASK_18_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18     nc
-DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18_av  nc
-DATA_MASK_19_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19     nc
-DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19_av  nc
-DATA_MASK_20_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20     nc
-DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20_av  nc
-DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
-DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr 
-#
-DVRP_LOG          out:loc:tr   dv#       $base_data/$fname/MONITORING  _dvrp_log
-DVRP_LOG          out:loc:tra  dvf       $base_data/$fname/MONITORING  _dvrp_log
-PARTICLE_INFO     out:loc:tr   pt#       $base_data/$fname/MONITORING  _prt_info
-PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
-PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
       \end{lstlisting}
    \end{columns}
+% CPU_MEASURES      out:loc:tr   d3#     $base_data/$fname/MONITORING  _cpu
+% CPU_MEASURES      out:loc:tra  d3f     $base_data/$fname/MONITORING  _cpu
+% #
+% DATA_1D_PR_NETCDF    out:loc:tr   pr#:prf   $base_data/$fname/OUTPUT  _pr     nc
+% DATA_1D_SP_NETCDF    out:loc:tr   sp#:spf   $base_data/$fname/OUTPUT  _sp     nc
+% DATA_1D_TS_NETCDF    out:loc:tr   ts#:tsf   $base_data/$fname/OUTPUT  _ts     nc
+% DATA_1D_PTS_NETCDF   out:loc:tr   pts#:ptsf $base_data/$fname/OUTPUT  _pts    nc
+% DATA_2D_XY_NETCDF    out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy     nc
+% DATA_2D_XY_AV_NETCDF out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy_av  nc
+% DATA_2D_XZ_NETCDF    out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz     nc
+% DATA_2D_XZ_AV_NETCDF out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz_av  nc
+% DATA_2D_YZ_NETCDF    out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz     nc
+% DATA_2D_YZ_AV_NETCDF out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz_av  nc
+% DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d     nc
+% DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av  nc
+% DATA_MASK_01_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01     nc
+% DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01_av  nc
+% DATA_MASK_02_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02     nc
+% DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02_av  nc
+% DATA_MASK_03_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03     nc
+% DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03_av  nc
+% DATA_MASK_04_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04     nc
+% DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04_av  nc
+% DATA_MASK_05_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05     nc
+% DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05_av  nc
+% DATA_MASK_06_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06     nc
+% DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06_av  nc
+% DATA_MASK_07_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07     nc
+% DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07_av  nc
+% DATA_MASK_08_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08     nc
+% DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08_av  nc
+% DATA_MASK_09_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09     nc
+% DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09_av  nc
+% DATA_MASK_10_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10     nc
+% DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10_av  nc
+% DATA_MASK_11_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11     nc
+% DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11_av  nc
+% DATA_MASK_12_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12     nc
+% DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12_av  nc
+% DATA_MASK_13_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13     nc
+% DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13_av  nc
+% DATA_MASK_14_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14     nc
+% DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14_av  nc
+% DATA_MASK_15_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15     nc
+% DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15_av  nc
+% DATA_MASK_16_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16     nc
+% DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16_av  nc
+% DATA_MASK_17_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17     nc
+% DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17_av  nc
+% DATA_MASK_18_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18     nc
+% DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18_av  nc
+% DATA_MASK_19_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19     nc
+% DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19_av  nc
+% DATA_MASK_20_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20     nc
+% DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20_av  nc
+% DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
+% DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr 
+% #
+% DVRP_LOG          out:loc:tr   dv#       $base_data/$fname/MONITORING  _dvrp_log
+% DVRP_LOG          out:loc:tra  dvf       $base_data/$fname/MONITORING  _dvrp_log
+% PARTICLE_INFO     out:loc:tr   pt#       $base_data/$fname/MONITORING  _prt_info
+% PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
+% PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
+
 \end{frame}
 
 % Folie 12
 \begin{frame}
-   \frametitle{Additional Features of \texttt{mrun}}
+   \frametitle{Additional Features of \texttt{mrun} (I)}
+   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=1.15\textwidth, font=\Tiny]
    \begin{itemize}
       \footnotesize
@@ -535,12 +553,52 @@
       \item<3-> Values have to be set in the \texttt{mrun} configuration file \texttt{.mrun.config}:
    \end{itemize}
-   \onslide<4->\hspace{-1cm}\includegraphics[scale=0.3]{mrun_figures/add_feat1.png}
+   \onslide<4->{\hspace{-0.95cm}\begin{tikzpicture}[auto]
+         \node[yellow]{\texttt{\%sgi\_feature \hspace{0.53cm} ice2 \hspace{2.71cm} lcsgih parallel}\\
+                       \texttt{\%modules \hspace{0.87cm}  intel.compiler/11.1.072:mpt:phdf5/1.8.5-mpt-intel-11.1:pnetcdf/4.1.1-mpt-intel-11.1 \quad\quad lcsgih parallel}\\
+                       \texttt{\%login\_init\_cmd \hspace{0.25cm} .:/usr/share/modules/init/bash  \quad\quad lcsgih parallel}\\
+                       \texttt{\#\%remote\_username \hspace{0.07cm} <replace by your HLRN username> \quad\quad lcsgih parallel}\\
+                       \texttt{\%compiler\_name \hspace{0.35cm} ifort \hspace{2.61cm} lcsgih parallel}\\
+                       \texttt{\%compiler\_name\_ser~ ifort \hspace{2.61cm} lcsgih parallel}\\
+                       \texttt{\%cpp\_options \hspace{0.53cm} -DMPI\_REAL=MPI\_DOUBLE\_PRECISION:-DMPI\_2REAL=MPI\_2DOUBLE\_PRECISION:-D\_\_netcdf:-D\_\_netcdf4:-D\_\_mpi2 \quad lcsgih parallel}\\
+                       \texttt{\%netcdf\_inc \hspace{0.62cm} -I:/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/include:-I:/sw/dataformats/phdf5/hdf5-1.8.5-mpt-intel-11.1/in}\\ %clude    lcsgih parallel}\\
+                       \texttt{\%netcdf\_lib \hspace{0.62cm} -L/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/lib:-lnetcdf:-lnetcdff:-L/sw/dataformats/phdf5/hdf5-1.8.5-mpt-}\\ %intel-11.1/lib:-lhdf5:-lhdf5\_hl:-lz      lcsgih parallel}\\
+                       \texttt{\%mopts \hspace{1.06cm} -j:4 \hspace{2.71cm} lcsgih parallel}\\
+                       \texttt{\%fopts \hspace{1.06cm} -fpe0:-O3:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:}\\ %-convert:little\_endian:-diag-disable:8290,8291  lcsgih parallel}\\
+                       \texttt{\%lopts \hspace{1.06cm} -fpe0:-O3:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-}\\ %Vaxlib:-lmpi:-limf:-lm           lcsgih parallel}\\
+                       \texttt{\%memory \hspace{0.97cm} 1500 \hspace{2.71cm} lcsgih parallel}\\
+                       \texttt{\#\%tmp\_data\_catalog~  /gfs2/work/<replace by your HLRN username>/palm\_restart\_data \quad\quad lcsgih parallel}\\
+                       \texttt{\#\%tmp\_user\_catalog~  /gfs2/tmp/<replace by your HLRN username> \hspace{2.03cm} lcsgih parallel}};
+   \end{tikzpicture}}
+%  \onslide<4->\hspace{-1cm}\includegraphics[scale=0.3]{mrun_figures/add_feat1.png}
+%    \begin{itemize}
+%       \footnotesize
+%       \item<5-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands).
+%       These commands can also be defined in the \texttt{mrun} configuration file:
+%       \onslide<6-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png}
+%       \item<7-> Automatic generation of restart jobs.
+%    \end{itemize}
+\end{frame}
+
+\begin{frame}
+   \frametitle{Additional Features of \texttt{mrun} (II)}
+   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.75\textwidth, font=\Tiny]
+
    \begin{itemize}
       \footnotesize
-      \item<5-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands).
+      \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<6-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png}
-      \item<7-> Automatic generation of restart jobs.
+      \begin{center}
+         \onslide<2->{\begin{tikzpicture}
+            \node[yellow]{~\texttt{IC:echo ``PALM will soon start to execute in \textbackslash\$PWD'' > /home/h/niksiraa/mrun\_messages}\\
+                          ~\texttt{EC:ls -al}\\
+                          \vspace{0.5mm}
+                          ~\texttt{OC:tar -cf DEBUG.tar DEBUG\_*}};
+         \end{tikzpicture}}
+      \end{center}
+
+%      \onslide<2-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png}
+      \item<3-> Automatic generation of restart jobs.
    \end{itemize}
+
 \end{frame}
 
@@ -595,4 +653,5 @@
    \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]
@@ -624,5 +683,5 @@
     \node [green, below=0.2cm of second] (third) {
        \textbf{if job is running, you may follow its progress by watching the job protocol:} \\ 
-       \texttt{cd \~/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
+       \texttt{cd \~{}/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
     };
 }
@@ -636,9 +695,9 @@
     \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}
+       \texttt{cd \~{}/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}
     };
 }
 \uncover<7->{
-    \node [dummy, left=0.5cm of fifth] (dummy) {
+    \node [dummy, left=0.001mm of fifth] (dummy) {
        transfer results by \texttt{scp} \\
        \ \\
@@ -647,7 +706,7 @@
 }
 \uncover<8->{
-    \node [yellow, left=3.5cm of fifth] (sixth) {
+    \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\underline{ }queue \\ ls -al \\ cd ~/palm/current\underline{ }version/JOBS/example \\ ls -al *}
+       \texttt{cd \~{}/job\_queue \\ ls -al \\ cd \~{}/palm/current\_version/JOBS/example \\ ls -al *}
     };
 }
