Index: palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex	(revision 949)
+++ palm/trunk/TUTORIAL/SOURCE/restarts_with_mrun.tex	(revision 973)
@@ -93,27 +93,40 @@
 
 
-% Folie 4 (Zu voll)?
+% Folie 4 
 \begin{frame}
    \frametitle{Carrying Out Restart Runs With \texttt{mrun}}
    \scriptsize
-
-   Concerning \texttt{mrun}, the first thing required to enable restart runs is to use the additional activating string \grqq \texttt{restart}\grqq\, in the \texttt{mrun}-call for the \underline{initial run}:\\
-   \quad \texttt{mrun -d test ... -r ''d3\# restart''}\\
-   This will have the following effects:
-   \vspace{2mm}
-   \begin{itemize}
-      \item<2-> At the end of the run, all necessary variables will bei written as binary data to the local file \texttt{BINOUT}. This is caused by an entry in the configuration file\\
-      \quad \texttt{\%write\underline{ }binary true restart}\\
-      which sets the environment variable \texttt{write\underline{ }binary}, which is in turn read by PALM from the local file \texttt{ENVPAR} created by \texttt{mrun}.
-      \item<3-> This binary file will be permanently stored in case that an appropriate file connection statement exists\\
-      \begin{columns}
-         \column{1.05\textwidth}
-         \texttt{BINOUT  out:loc:flpe restart \~{}/palm/current\underline{ }version/JOBS/\$fname/RESTART  \underline{ }d3d}
-      \end{columns}
-      \item<4-> If, during the run, PALM detects that the simulation cannot be finished due to limited job time, it tells \texttt{mrun} (by creating a local file named \texttt{CONTINUE\underline{ }RUN}) that a restart job has to be started. \texttt{mrun} will then automatically start such a job by submitting the command\\
-      \quad \texttt{mrun -d test ... -r ''d3f restart''}\\
-      on the \textbf{local host}. Options of this command are nearly the same as of the initial run, but every sharp symbol (\grqq\#\grqq) in the activating strings is replaced by an \grqq f\grqq.
-   \end{itemize}
-   \onslide<5->\textcolor{red}{\textbf{This effects the activation of file connections for the restart job!}}
+   \begin{columns}[T]
+      \begin{column}{1.0\textwidth}
+         Concerning \texttt{mrun}, the first thing required to enable restart runs is to use the additional activating string \grqq \texttt{restart}\grqq\, in the \texttt{mrun}-call for the \underline{initial run}:\\
+         \vspace{1mm}
+         \quad \texttt{mrun -d test ... -r \dq d3\# restart\dq}\\
+         \ \\
+         This will have the following effects:
+         \vspace{1mm}
+         \tiny
+         \begin{itemize}
+            \item<2-> At the end of the run, all necessary variables will bei written as binary data to the local file \texttt{BINOUT}. This is caused by an entry in the configuration file\\
+            \vspace{1mm}
+            \quad \texttt{\%write\underline{ }binary true restart}\\
+            \vspace{1mm}
+            which sets the environment variable \texttt{write\underline{ }binary}, which is in turn read by PALM from the local file \texttt{ENVPAR} created by \texttt{mrun}.
+            \vspace{3mm}
+            \item<3-> This binary file will be permanently stored in case that an appropriate file connection statement exists\\
+            \vspace{1mm}
+            \quad \texttt{BINOUT  out:loc:flpe restart \~{}/palm/current\underline{ }version/JOBS/\$fname/RESTART  \underline{ }d3d}
+            \vspace{3mm}
+            \item<4-> If, during the run, PALM detects that the simulation cannot be finished due to limited job time, it tells \texttt{mrun} (by creating a local file named \texttt{CONTINUE\underline{ }RUN}) that a restart job has to be started. \texttt{mrun} will then automatically start such a job by submitting the command\\
+            \vspace{1mm}
+            \quad \texttt{mrun -d test ... -r \dq d3f restart\dq}\\
+            \vspace{1mm}
+            on the \textbf{local host}. Options of this command are nearly the same as of the initial run, but every sharp symbol (\grqq\#\grqq) in the activating strings is replaced by an \grqq f\grqq.
+         \end{itemize}
+         \scriptsize
+         \vspace{2mm}
+         \onslide<5->\textcolor{red}{\textbf{This effects the activation of file connections for the restart job!}}
+      \end{column}
+   \end{columns}
+
 \end{frame}
 
@@ -131,12 +144,14 @@
    \begin{itemize}
       \item<2-> For the restart job, the model receives a different parameter file than for the initial job (e.g. \texttt{example\underline{ }cbl\underline{ }p3d\textcolor{blue}{f}} instead of \texttt{example\underline{ }cbl\underline{ }p3d}).\\
-   \vspace{2mm}
+   \vspace{4mm}
    The parameter file for the restart job is nearly the same as for the initial run, but it must contain the parameter setting\\
+   \vspace{1mm}
    \quad \texttt{initializing\underline{ }actions = 'read\underline{ }restart\underline{ }data'}\\
+   \vspace{1mm}
    in the \texttt{\&inipar}-NAMELIST-group. All other \texttt{\&inipar}-parameter-settings are ignored!\\
-   \vspace{2mm}
+   \vspace{4mm}
    \texttt{\&d3par}-parameter values can freely be changed compared with the parameter file for the initial run.\\
    \vspace{4mm}
-   \item<3-> Input binary data file (\texttt{BININ}) is necessary (and available) only for restart jobs
+   \item<3-> Input binary data file (\texttt{BININ}) is necessary (and available) only for\\ restart jobs
    \end{itemize}
 \end{frame}
@@ -167,5 +182,5 @@
 
 
-% Folie 7 (Zu voll?)
+% Folie 7
 \begin{frame}
    \frametitle{Handling of Large Binary Data Files}
@@ -173,11 +188,14 @@
    \begin{columns}
       \column{1.1\textwidth}
+      \vspace{-1mm}
       \begin{itemize}
          \item<1-> Typically, the binary restart files are very large, so that they cannot be stored in the user's home-directory because of limited file quotas. Also, hard disks where \texttt{/home} is stored are typically very slow, so that the copy process needs very long time.
+         \vspace{1mm}
          \item<2-> Using the file attribute \texttt{fl} (abbreviation for german \grqq Fortsetzungslauf\grqq) in the output file connection statement causes \texttt{mrun} to copy the local file to a special directory, which can be defined in the configuration file by the environment variable \texttt{tmp\underline{ }data\underline{ }catalog}. The permanent file described in the connection statement is also created, but it is \textbf{empty}.
+         \vspace{1mm}
          \item<3-> At the end of the job, the second last cycle of the respective file with attribute \texttt{fl} is automatically deleted by \texttt{mrun} from the \texttt{tmp\underline{ }data\underline{ }catalog} in order to spare disc space. This can be prevented by setting the \texttt{mrun}-option \grqq\texttt{-k}\grqq (keep data from previous run).
       \end{itemize}
    \end{columns}
-   \ \\
+   \vspace{2mm}
       \onslide<4-> \textbf{Example:}\\
       \tiny \quad \texttt{\%base\underline{ }data\hspace{4.5em}\~{}/palm/current\underline{ }version/JOBS}\\
@@ -189,6 +207,6 @@
       \tiny \quad \texttt{/gfs2/work/niksiraa/palm\underline{ }restart\underline{ }data/example\underline{ }cbl\underline{ }d3d}\\
       \tiny \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example/RESTART/example\underline{ }cbl\underline{ }d3d \# empty file (directory)}\\
-   \vspace{1mm}
-   \onslide<6-> \scriptsize \textcolor{red}{Concerning input files, \texttt{mrun} always determines the current cycle number to be \underline{used from the contents of the directory defined by the file connection statement!}}
+   \vspace{2mm}
+   \onslide<6-> \scriptsize \textcolor{red}{Concerning input files, \texttt{mrun} always determines the current cycle number to be \underline{used from the contents of the directory defined by the file connection}\\ \underline{statement!}}
 
 \end{frame}
@@ -222,13 +240,18 @@
       \begin{itemize}
          \item<1-> By default, PALM checks after every timestep, if enough time remains from the job cpu limit to carry out the next timestep:\\
-         \quad \grqq\texttt{total job time}\grqq\, - \grqq\texttt{time already consumed}\grqq\, $\leftarrow$ \texttt{termination\underline{ }time\underline{ }needed}\\
-(as given by \texttt{mrun}-option \texttt{-t} ...) \hspace{5mm}  (as given by parameter in \texttt{\&d3par}-NAMELIST)
+         \vspace{1mm}
+         (\quad \grqq\texttt{total job time}\grqq\, - \grqq\texttt{time already consumed}\grqq\,) \texttt{<=} \texttt{termination\underline{ }time\underline{ }needed}\\
+         (as given by \texttt{mrun}-option \texttt{-t} ...) \hspace{5mm}  (as given by parameter in \texttt{\&d3par}-NAMELIST)\\
+         \vspace{3mm}
          \item<2-> \texttt{termination\underline{ }time\underline{ }needed} has to include the cpu time needed before running PALM (e.g. for compilation, copying of input data, etc.; default value: 300 s)!\\
          \ \\
          \onslide<3-> \textbf{Warning:}\\
-         \quad \quad \grqq\texttt{total job time}\grqq\, $\leftarrow$ \texttt{termination\underline{ }time\underline{ }needed},\\
+         \vspace{1mm}
+         \quad \quad \grqq\texttt{total job time}\grqq\, \texttt{<=} \texttt{termination\underline{ }time\underline{ }needed},\\
          \quad forces a restart after the first timestep!
-         \item<4-> \texttt{\&d3par}-parameters \texttt{restart\underline{ }time} and \texttt{dt\underline{ }restart} can be used to set restart time(s) manually.
-         \item<5-> In case of manually setting the restart time, the default checking (see above) is still active and a restart will be automatically forced if the job reaches its cpu limit, even if the manually set restart time has not been reached!
+         \vspace{3mm}
+         \item<4-> \texttt{\&d3par}-parameters \texttt{restart\underline{ }time} and \texttt{dt\underline{ }restart} can be used to set restart time(s) manually.\\
+         \vspace{3mm}
+         \item<5-> In case of manually setting the restart time, the default checking (see above) is still active and a restart will be automatically forced if the job reaches its cpu limit, even if the manually set restart time has not been reached!\\
       \end{itemize} 
    \end{columns}
@@ -243,9 +266,10 @@
          \item<1-> After a job has finished (\texttt{end\underline{ }time} has been reached), the user can submit a restart job manually (provided that restart data have been saved) by entering:\\
          \vspace{2mm}
-         \quad \texttt{mrun ... -r ''d3f ...'' ...}\\
+         \quad \texttt{mrun ... -r \dq d3f ...\dq\, ...}\\
          or\\
-	      \quad \texttt{mrun ... -r ''d3f restart ...'' ...}\\
+	      \quad \texttt{mrun ... -r \dq d3f restart ...\dq\, ...}\\
 	      \ \\
          \item<2-> Remember to increase the value of \texttt{end\underline{ }time} in the parameter file before submitting the job.
+         \vspace{2mm}
          \item<3-> If a manually started restart job shall continue a run of a former job chain which is somewhere in the middle of this chain, all binary files with respective higher cycle numbers have to be deleted or removed from their respective directories.
    \end{itemize} 
